Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007860.1 Hibiscus syriacus cultivar Beakdansim tig00110223_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: 2941097
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 16
Found at i:601957 original size:13 final size:14
Alignment explanation
Indices: 601909--601967 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
601899 ATGCGAAATG
*
601909 AAAATCGCAACGAC
1 AAAATCGCAACGAA
601923 AAAATCGCAATGCGAAATA
1 AAAATCGCAA--CG--A-A
601942 AAAATCGCAACGAA
1 AAAATCGCAACGAA
601956 AAAATCGCAACG
1 AAAATCGCAACG
601968 CGAAACACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 23 0.59
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.53, C:0.22, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:602006 original size:19 final size:19
Alignment explanation
Indices: 601984--602075 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
601974 ACAAATTGCA
601984 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
602003 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
*
602017 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
*
602036 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
*
602050 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
602069 TTGCGAT
1 TTGCGAT
602076 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 7, Indels: 20
0.67 0.08 0.24
Matches are distributed among these distances:
14 15 0.27
15 6 0.11
16 4 0.07
17 4 0.07
18 6 0.11
19 21 0.38
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:602020 original size:14 final size:14
Alignment explanation
Indices: 602001--602059 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
601991 TTTCATTTCG
602001 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
602015 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
602032 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
602048 CGTTGCGATTTT
1 CGTTGCGATTTT
602060 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:602026 original size:33 final size:33
Alignment explanation
Indices: 601984--602075 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
601974 ACAAATTGCA
*
601984 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
602017 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
602050 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
602076 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:602114 original size:20 final size:20
Alignment explanation
Indices: 602060--602103 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
602050 TTGCGATTTT
602060 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
602079 CATTTCCGCATTGCGATAGT
1 CATTTCCGCATTGCGATAGC
602099 CATTT
1 CATTT
602104 TCGTGTTGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:602672 original size:18 final size:18
Alignment explanation
Indices: 602649--602696 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
602639 CGGGTCGATC
602649 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
602667 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
602685 AGGTGATGGCTC
1 AGGTGATGGCTC
602697 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:604064 original size:20 final size:20
Alignment explanation
Indices: 604016--604074 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
604006 AATAGTTTCT
* *
604016 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
604036 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
604056 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
604075 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:604364 original size:22 final size:22
Alignment explanation
Indices: 604337--604380 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
604327 GATGGAGATA
604337 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
604359 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
604381 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:604595 original size:20 final size:20
Alignment explanation
Indices: 604567--604660 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
604557 GATTATGTAT
* *
604567 TATCTCGTTGTGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
604587 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
** *
604607 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTAAG
* *
604628 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTAAG
604648 TATCGCGTTGCGA
1 TATCGCGTTGCGA
604661 TTTTCCAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.70
21 14 0.22
22 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:604632 original size:41 final size:41
Alignment explanation
Indices: 604587--604664 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
604577 TGAAAGTAAG
604587 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
*
604628 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTT
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTT
604665 CCAAATTCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (41 bp):
TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
Found at i:604661 original size:20 final size:20
Alignment explanation
Indices: 604585--604661 Score: 102
Period size: 20 Copynumber: 3.8 Consensus size: 20
604575 TGTGAAAGTA
*
604585 AGTATCGCGTTGCGAAAGTC
1 AGTATCGCGTTGCGATAGTC
*
604605 AGTATCGCGTTGCGATTTTGT-
1 AGTATCGCGTTGCGA--TAGTC
*
604626 ATTATCGCGTTGCGATAGTC
1 AGTATCGCGTTGCGATAGTC
604646 AGTATCGCGTTGCGAT
1 AGTATCGCGTTGCGAT
604662 TTTCCAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
19 3 0.06
20 30 0.61
21 14 0.29
22 2 0.04
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (20 bp):
AGTATCGCGTTGCGATAGTC
Found at i:604680 original size:41 final size:41
Alignment explanation
Indices: 604589--604724 Score: 141
Period size: 41 Copynumber: 3.3 Consensus size: 41
604579 AAAGTAAGTA
* * ** *
604589 TCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTT-GTATT
1 TCGCATTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT
*
604629 ATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT
1 -TCGCATTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT
** * *
604671 TCGCATTGCGATTTTCCA-AATTCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATAGT-CAGTA-TCGCGTTGCGATTTTCCAAAT
604713 TCGCATTGCGAT
1 TCGCATTGCGAT
604725 TTACTTATTC
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
41 47 0.57
42 36 0.43
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (41 bp):
TCGCATTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT
Found at i:604736 original size:20 final size:21
Alignment explanation
Indices: 604650--604743 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
604640 ATAGTCAGTA
*
604650 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
604671 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
604692 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
604713 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCAAAT
604733 TCGCATTGCGA
1 TCGCATTGCGA
604744 ATTGGGAAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
20 17 0.25
21 52 0.75
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:604758 original size:41 final size:42
Alignment explanation
Indices: 604650--604758 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 42
604640 ATAGTCAGTA
* * * * *
604650 TCGCGTTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGAATTGCCAAAATCGCATTGCGATTTTACAAAT
* * * **
604692 TCGCATTGCGATTTTCCAAATTCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGAATTGCCAAAATCGCATTGCGATTTTACAAAT
**
604733 TCGCATTGCGAATTGGGAAAATCGCA
1 TCGCATTGCGAATTGCCAAAATCGCA
604759 ACGCGAAATT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
41 27 0.47
42 31 0.53
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (42 bp):
TCGCATTGCGAATTGCCAAAATCGCATTGCGATTTTACAAAT
Found at i:604785 original size:21 final size:22
Alignment explanation
Indices: 604733--604785 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
604723 ATTTACTTAT
*
604733 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGAAAAA
**
604754 TCGCAACGCGAAATT-GAAAAA
1 TCGCATTGCGAAATTGGAAAAA
604775 TCGCATTGCGA
1 TCGCATTGCGA
604786 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGAAAAA
Found at i:606099 original size:37 final size:35
Alignment explanation
Indices: 606025--606099 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 35
606015 TTTTTATATT
* * *
606025 TTTAATTTTGTAAAAAATTGTATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATATATAAATATTATCAA
* *
606060 TTTAATTTTTTAAAGAAAATATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATATATAAATATTAT-CAA
606097 TTT
1 TTT
606100 GTAATATTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
35 13 0.39
36 15 0.45
37 5 0.15
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.48
Consensus pattern (35 bp):
TTTAATTTTGTAAAAAAATATATAAATATTATCAA
Found at i:613213 original size:7 final size:7
Alignment explanation
Indices: 613201--613225 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
613191 GTATTAAAGA
613201 AAAGGGG
1 AAAGGGG
613208 AAAGGGG
1 AAAGGGG
613215 AAAGGGG
1 AAAGGGG
613222 AAAG
1 AAAG
613226 TGAAAATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (7 bp):
AAAGGGG
Found at i:613927 original size:22 final size:21
Alignment explanation
Indices: 613897--613953 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
613887 CGATACTGAA
*
613897 ATAGAGTATCGGTACCATGGT
1 ATAGAGTATCGATACCATGGT
613918 ATAGAAGTATCGATACCATGGT
1 ATAG-AGTATCGATACCATGGT
* *
613940 A-GGGGTATCGATAC
1 ATAGAGTATCGATAC
613954 TATTGAACCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.31
21 5 0.16
22 17 0.53
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (21 bp):
ATAGAGTATCGATACCATGGT
Found at i:614000 original size:18 final size:18
Alignment explanation
Indices: 613963--614003 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
613953 CTATTGAACC
* *
613963 TGAAATTGTAAGATAGGT
1 TGAAATTGTAAGAGAAGT
*
613981 TGAAATTGTAATAGAAGT
1 TGAAATTGTAAGAGAAGT
613999 TGAAA
1 TGAAA
614004 ATAATAGTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (18 bp):
TGAAATTGTAAGAGAAGT
Found at i:614427 original size:46 final size:46
Alignment explanation
Indices: 614358--614817 Score: 582
Period size: 46 Copynumber: 10.0 Consensus size: 46
614348 AAATGAATGA
* *
614358 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGGTGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * * *
614404 ATAAATGAAAATACATAATGGTGCATTATTGGCATGAAAAGATGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* ** *
614450 ATAAATGAAAATGCATAATGGTGCATTATCATCATGAAATGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
614496 ATAAATGAAAATACATAACGGTGCATTATCGGCATGAAAGGATGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
614542 ATAAATGAAAATGCATAACGGTGCATTATCGGTATGAAATGATACC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
614588 ATAAATGAAAATGTATAATGGTGCATTATCAGCATGAAAGGATGAC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * **
614634 ATAAATGAAAATGTATAGCAGTGCATTATCAACATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* **
614680 ATAAATGAAAATGCATAACGGTGCATTATCAGCATGAAAGGATTTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
614726 ATAAATGAAAATGCATAACAGTGCATAATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * * *
614772 ATAAATGAAATTACATAATGGTGTATTAAT-GGCATAAAAGG-TGCC
1 ATAAATGAAAATGCATAACGGTGCATT-ATCGGCATGAAAGGATGCC
614817 A
1 A
614818 CTCATGGTAT
Statistics
Matches: 361, Mismatches: 52, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
45 5 0.01
46 354 0.98
47 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:619105 original size:41 final size:41
Alignment explanation
Indices: 619059--619138 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
619049 ATAGAATTAA
619059 CTATACTCAGTCTTAGAGTATTGGTACTACCTTTCTTTCAT
1 CTATACTCAGTCTTAGAGTATTGGTACTACCTTTCTTTCAT
619100 CTATACTCAGTCTTAGAGTATTGGTACTACCTTTCTTTC
1 CTATACTCAGTCTTAGAGTATTGGTACTACCTTTCTTTC
619139 TCATCTTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (41 bp):
CTATACTCAGTCTTAGAGTATTGGTACTACCTTTCTTTCAT
Found at i:620359 original size:54 final size:53
Alignment explanation
Indices: 620299--620530 Score: 257
Period size: 54 Copynumber: 4.3 Consensus size: 53
620289 ATTTCTAAAT
* * * *
620299 CGTTCCTTTATGATGGAGGAGTATAGCAAATTTCTAAGACCGATCAACCTCTAG
1 CGTTCCTTTGTTATGGAGGAGTAGAGCAAATTTCTAAGACCGA-CAAACTCTAG
* * * * * * *
620353 AGTTCCTTTGTTATGGACGAGTAGAGCAAATTTATAAGATCAAGCAAGCTCCAG
1 CGTTCCTTTGTTATGGAGGAGTAGAGCAAATTTCTAAGACCGA-CAAACTCTAG
* * * *
620407 CGTTTCTTTGTTATGGAGGAGTAGAGAAAATTTCTAAGACTGAGAAACTCTAG
1 CGTTCCTTTGTTATGGAGGAGTAGAGCAAATTTCTAAGACCGACAAACTCTAG
* * * * *
620460 CGTTCCTTTGTTATGAAGGAGTAGAGCAAATTTCGATGACCGAGTAAACTTTAG
1 CGTTCCTTTGTTATGGAGGAGTAGAGCAAATTTCTAAGACCGA-CAAACTCTAG
620514 CGTTCCTTTGTTATGGA
1 CGTTCCTTTGTTATGGA
620531 TGTGGACACT
Statistics
Matches: 146, Mismatches: 31, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
53 44 0.30
54 102 0.70
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (53 bp):
CGTTCCTTTGTTATGGAGGAGTAGAGCAAATTTCTAAGACCGACAAACTCTAG
Found at i:620516 original size:107 final size:108
Alignment explanation
Indices: 620299--620530 Score: 277
Period size: 107 Copynumber: 2.2 Consensus size: 108
620289 ATTTCTAAAT
* * * * *
620299 CGTTCCTTTATGATGGAGGAGTATAGCAAATTTCTAAGACCGATCAACCTCTAGAGTTCCTTTGT
1 CGTTCCTTTGTTATGGAGGAGTAGAGAAAATTTCTAAGACCGATCAAACTCTAGAGTTCCTTTGT
* * * *
620364 TATGGACGAGTAGAGCAAATTTATAAGATCAAGCAAGCTCCAG
66 TATGAACGAGTAGAGCAAATTTAGAAGACCAAGCAAACTCCAG
* * * *
620407 CGTTTCTTTGTTATGGAGGAGTAGAGAAAATTTCTAAGACTGA-GAAACTCTAGCGTTCCTTTGT
1 CGTTCCTTTGTTATGGAGGAGTAGAGAAAATTTCTAAGACCGATCAAACTCTAGAGTTCCTTTGT
* * * * * **
620471 TATGAAGGAGTAGAGCAAATTTCGATGACCGAGTAAACTTTAG
66 TATGAACGAGTAGAGCAAATTTAGAAGACCAAGCAAACTCCAG
620514 CGTTCCTTTGTTATGGA
1 CGTTCCTTTGTTATGGA
620531 TGTGGACACT
Statistics
Matches: 103, Mismatches: 21, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
107 66 0.64
108 37 0.36
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (108 bp):
CGTTCCTTTGTTATGGAGGAGTAGAGAAAATTTCTAAGACCGATCAAACTCTAGAGTTCCTTTGT
TATGAACGAGTAGAGCAAATTTAGAAGACCAAGCAAACTCCAG
Found at i:621734 original size:15 final size:14
Alignment explanation
Indices: 621716--621833 Score: 60
Period size: 15 Copynumber: 7.9 Consensus size: 14
621706 TTATTATACA
621716 TATTTTTTATATTTT
1 TATTTTTTAT-TTTT
621731 TA-TTTTTATCTTCTT
1 TATTTTTTAT-TT-TT
*
621746 TATTCTTTATTTTT
1 TATTTTTTATTTTT
*
621760 AATATTTTTATTTTT
1 TAT-TTTTTATTTTT
** *
621775 GGTTTATTATTATTAT
1 TATTTTTTATT-TT-T
*
621791 TATTATTATTATTATT
1 TATT-TT-TTATTTTT
*
621807 TATTTACTTATATTTT
1 TATTT-TTTAT-TTTT
*
621823 T-CTTTTTATTT
1 TATTTTTTATTT
621834 ATATGTGTGT
Statistics
Matches: 79, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
13 2 0.03
14 24 0.30
15 28 0.35
16 18 0.23
17 2 0.03
18 5 0.06
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (14 bp):
TATTTTTTATTTTT
Found at i:621736 original size:6 final size:6
Alignment explanation
Indices: 621720--621833 Score: 52
Period size: 6 Copynumber: 17.5 Consensus size: 6
621710 TATACATATT
621720 TTTTATA TTTTTA TTTTTA TCTTCTTTA TTCTTTA TTTTTAATA TTTTTA
1 TTTT-TA TTTTTA TTTTTA --TT-TTTA TT-TTTA -TTTT--TA TTTTTA
* * * * * *
621770 TTTTTGG TTTATTA TTATTA TTATTA TTATTA TTATTTA --TTTA CTTATA
1 TTTTT-A TTT-TTA TTTTTA TTTTTA TTTTTA TT-TTTA TTTTTA TTTTTA
*
621819 TTTTTC TTTTTA TTT
1 TTTTTA TTTTTA TTT
621834 ATATGTGTGT
Statistics
Matches: 87, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
4 4 0.05
6 46 0.53
7 21 0.24
8 10 0.11
9 6 0.07
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTTTA
Found at i:621769 original size:22 final size:21
Alignment explanation
Indices: 621719--621771 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
621709 TTATACATAT
* *
621719 TTTTTATATTTTTATTTTTATC
1 TTTTTAT-TCTTTATTTTTATA
621741 TTCTTTATTCTTTATTTTTAATA
1 TT-TTTATTCTTTATTTTT-ATA
621764 TTTTTATT
1 TTTTTATT
621772 TTTGGTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTATTCTTTATTTTTATA
Found at i:621786 original size:3 final size:3
Alignment explanation
Indices: 621778--621900 Score: 79
Period size: 3 Copynumber: 37.7 Consensus size: 3
621768 TATTTTTGGT
* *
621778 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTTA CTTA -TA TTT TTC
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA -TTA TTA TTA TTA
* * *
621825 TTT TTA TTTA TATG TGTG TGTA TATA TATA TATA CCTT- TTA TTA TTA
1 TTA TTA -TTA T-TA T-TA T-TA T-TA T-TA T-TA --TTA TTA TTA TTA
621872 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
621901 GTTGTTGTTG
Statistics
Matches: 104, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
2 4 0.04
3 67 0.64
4 31 0.30
5 1 0.01
6 1 0.01
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:621905 original size:3 final size:3
Alignment explanation
Indices: 621899--621927 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
621889 ATTATTATTA
621899 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
621928 TTTACCTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:621947 original size:2 final size:2
Alignment explanation
Indices: 621936--622057 Score: 157
Period size: 2 Copynumber: 64.0 Consensus size: 2
621926 TTTTTACCTA
* *
621936 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT -T TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
621976 TT TT AT -T TT AT -T AT -T AT -T 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
622014 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
622056 AT
1 AT
622058 CACCTCACAT
Statistics
Matches: 110, Mismatches: 4, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
1 6 0.05
2 104 0.95
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
AT
Found at i:622193 original size:16 final size:16
Alignment explanation
Indices: 622172--622204 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
622162 TGTTTTCTTT
622172 TTTATTATTGTTT-TTC
1 TTTATT-TTGTTTGTTC
622188 TTTATTTTGTTTGTTC
1 TTTATTTTGTTTGTTC
622204 T
1 T
622205 CATTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.76
Consensus pattern (16 bp):
TTTATTTTGTTTGTTC
Found at i:622244 original size:2 final size:2
Alignment explanation
Indices: 622237--622261 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
622227 CCTATTAATT
622237 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
622262 TTACATGTTC
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:622501 original size:37 final size:35
Alignment explanation
Indices: 622438--622506 Score: 93
Period size: 37 Copynumber: 1.9 Consensus size: 35
622428 CCACTGTTCT
622438 TTATTTTTAGTTTTGGTTATTAATTTTATTTTGCC
1 TTATTTTTAGTTTTGGTTATTAATTTTATTTTGCC
** *
622473 TTATTTTTAGCTTTATTTTTATTTATTTTATTTT
1 TTATTTTTAG-TTT-TGGTTATTAATTTTATTTT
622507 TTATTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 10 0.34
36 3 0.10
37 16 0.55
ACGTcount: A:0.17, C:0.04, G:0.07, T:0.71
Consensus pattern (35 bp):
TTATTTTTAGTTTTGGTTATTAATTTTATTTTGCC
Found at i:622504 original size:15 final size:15
Alignment explanation
Indices: 622484--622516 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
622474 TATTTTTAGC
622484 TTTA-TTTTTATTTAT
1 TTTATTTTTTATTT-T
622499 TTTATTTTTTATTTT
1 TTTATTTTTTATTTT
622514 TTT
1 TTT
622517 GTGTTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTATTTTTTATTTT
Found at i:625847 original size:25 final size:25
Alignment explanation
Indices: 625811--625879 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
625801 CACCACAGCT
* *
625811 CGTATAAA-TTGCACCGTAGTGCCA
1 CGTAGAAATTTGCACCGAAGTGCCA
* *
625835 CGTAGAATTTTGCACCGAAGTGCCG
1 CGTAGAAATTTGCACCGAAGTGCCA
625860 CGTAGAAATTTGTC-CCGAAG
1 CGTAGAAATTTG-CACCGAAG
625880 GACTGCATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
24 6 0.16
25 31 0.82
26 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (25 bp):
CGTAGAAATTTGCACCGAAGTGCCA
Found at i:630833 original size:25 final size:25
Alignment explanation
Indices: 630797--630880 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
630787 CACCACAGCT
* * *
630797 CGTATAAA-TTGCACCGTAGTGCCA
1 CGTAGAAATTTGCACCGAAGTACCA
* *
630821 CGTAGAATTTTGCACCGAAGTACCG
1 CGTAGAAATTTGCACCGAAGTACCA
*
630846 CGTAGAAATTTGTC-CCGAAGGACCA
1 CGTAGAAATTTG-CACCGAAGTACCA
*
630871 CATAGAAATT
1 CGTAGAAATT
630881 CCTTAAGAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
24 6 0.12
25 42 0.86
26 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (25 bp):
CGTAGAAATTTGCACCGAAGTACCA
Found at i:635973 original size:84 final size:84
Alignment explanation
Indices: 635687--637143 Score: 1585
Period size: 84 Copynumber: 17.3 Consensus size: 84
635677 AAAGAACCTT
* ** * * *
635687 CAACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCGTATCATTTGTAGCATAGTTTAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* *
635752 GGCGAGAAGGGCTATCTGC
66 GGAGAGAAGGGTTATCTGC
* * * * * * * *
635771 CAACAAAATACCTTCAAGTTTGATTACACTTAGCTCAAAGGCACATCCAATTTACAACATAACTT
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-C-ATTTGCAGCATAGCTC
* * **
635836 AAGGCGAGAAGTGTTATCTAT
64 AAGGAGAGAAGGGTTATCTGC
* * * * *
635857 CAAC-CAAGACCTTTGAGTTTGATTACACTCAGCTCAAAGACACATCATTTGTAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
*
635921 GGAGAAAAGGGTTATCTGC
66 GGAGAGAAGGGTTATCTGC
* * * * *
635940 CAACAAAAGACCTTCGCGTTCGATTACAATCAGCTCAAAGGCACATAATTTACAGGATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* **
636005 GGCA-AGAAGGGCTATCTAT
66 GG-AGAGAAGGGTTATCTGC
* *
636024 CAGCAAAAGACCTTCGAGTTCGATTACACTTAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* **
636089 GGCGAGAAGGACTATCTGC
66 GGAGAGAAGGGTTATCTGC
** * * * *
636108 CAACAAAAGACCTTTAAGTGCGATTACACTCAGCTTAAAGGCACATCCAATTTACAGCATAACTC
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-C-ATTTGCAGCATAGCTC
* *
636173 AAGGTGAGAAGGGTTATCTGT
64 AAGGAGAGAAGGGTTATCTGC
* * * * *
636194 TAAC-CAAGACCTTCGAG-TCCAGTTACACTCAGCTCAAATGCACATCATTTGTAGCATAGCTCA
1 CAACAAAAGACCTTCGAGTTCGA-TTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCA
* *
636257 A-GATGAGAAGTGTTATCTTC
65 AGGA-GAGAAGGGTTATCTGC
* * * ** *
636277 TAACAAAAGACCTTCGAGTTCGATTACAGTCATCTCAAAGGCGTATCATTTGCAGTATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* *
636342 -GACGAGAAGGGCTATCTAC
66 GGA-GAGAAGGGTTATCTGC
636361 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
*
636426 GGCA-AGAAGGGCTATCTGC
66 GG-AGAGAAGGGTTATCTGC
** * * *
636445 CAACAAAAGATGTTCCAGTTCAATTACACTCAGCTCAAAGGCACATCATTTGCATCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
*
636510 GGCGAGAAGGGCTT-TCTGC
66 GGAGAGAAGGG-TTATCTGC
* * * * *
636529 CAACAAAAGACCTTCGAGTTTGATTATACTCAGTTCAAATGCACATCATTTACAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
*
636594 GGTGAGAAGGGTTATCTGC
66 GGAGAGAAGGGTTATCTGC
* * * *
636613 CAACAAACA-ACCTTCAAGTTCAATTAGACTCAGCTCAAAGGCACATTATTTGCAGCATAGCTCA
1 CAACAAA-AGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCA
* **
636677 AGGCGAGAAGATTTATCTGC
65 AGGAGAGAAGGGTTATCTGC
* * * * *
636697 CAACAAAAGACCTTCGAGTTTGATTACACTCTGTTCAAAGGTACATCATTTGAAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * * * *
636762 GGCGAGAAGGGATGTTTTC
66 GGAGAGAAGGGTTATCTGC
* * *
636781 CAACAAAAGACCTTTGAGTTTGATTACACTCAGCTCAAAGGTACATCATTTGCAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
*
636846 GGTA-AGAAGGGCTATCTGC
66 GG-AGAGAAGGGTTATCTGC
* * *
636865 CAACAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATTATTTACAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * **
636930 -TACGATAAGGGTTATCTAT
66 GGA-GAGAAGGGTTATCTGC
* * * *
636949 CAACAAAAGACCTTCGAGTTCGATTACAATCAGCTCAAAGGCACATCAAACTTACAGCATAACTC
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTGCAGCATAGCTC
* *
637014 AAGGAGAGAAGGATTATCTGT
64 AAGGAGAGAAGGGTTATCTGC
* * * * * *
637035 CAGC-AAAGACCTTCGAGTTCGATCACATTCAGCTCAAAGGCATATCAAATTTACAACATAGCTC
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTGCAGCATAGCTC
*
637099 AAGGCA-AGAAGGGCTATCT-C
64 AAGG-AGAGAAGGGTTATCTGC
*
637119 TCAA-TAAAGACCTTCGAGTTCGATT
1 -CAACAAAAGACCTTCGAGTTCGATT
637144 CAATTTAGCT
Statistics
Matches: 1159, Mismatches: 187, Indels: 53
0.83 0.13 0.04
Matches are distributed among these distances:
82 2 0.00
83 66 0.06
84 825 0.71
85 165 0.14
86 100 0.09
87 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (84 bp):
CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
GGAGAGAAGGGTTATCTGC
Found at i:637759 original size:2 final size:2
Alignment explanation
Indices: 637752--637785 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
637742 CATATAAAAT
637752 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
637786 TTAATTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:638920 original size:7 final size:7
Alignment explanation
Indices: 638899--639020 Score: 77
Period size: 7 Copynumber: 16.7 Consensus size: 7
638889 TTATTATACA
638899 TATTTTT
1 TATTTTT
638906 TATATTTT
1 TAT-TTTT
638914 TA-TTTT
1 TATTTTT
638920 TATCTTCTT
1 TAT-TT-TT
*
638929 TATTCTT
1 TATTTTT
*
638936 TGTTTTT
1 TATTTTT
*
638943 AATATTTT
1 TAT-TTTT
638951 TATTTTT
1 TATTTTT
** *
638958 GGTTTAT
1 TATTTTT
638965 TATTTTT
1 TATTTTT
* *
638972 AATTATT
1 TATTTTT
*
638979 TATTATT
1 TATTTTT
638986 TATTATTT
1 TATT-TTT
*
638994 ATTTTATTT
1 -TATT-TTT
639003 TATTTTT
1 TATTTTT
639010 TA-TTTT
1 TATTTTT
639016 TATTT
1 TATTT
639021 ATATGTGTAT
Statistics
Matches: 89, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
6 12 0.13
7 45 0.51
8 20 0.22
9 12 0.13
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (7 bp):
TATTTTT
Found at i:639004 original size:24 final size:23
Alignment explanation
Indices: 638960--639020 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 23
638950 TTATTTTTGG
638960 TTTATTATTT-TTAATTATTTATTA
1 TTTATTATTTATT--TTATTTATTA
*
638984 TTTATTATTTATTTTATTTTATTT
1 TTTATTATTTATTTTA-TTTATTA
639008 TTTATT-TTTATTT
1 TTTATTATTTATTT
639021 ATATGTGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
23 10 0.29
24 22 0.65
25 2 0.06
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTATTATTTATTTTATTTATTA
Found at i:639021 original size:17 final size:17
Alignment explanation
Indices: 638964--639022 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
638954 TTTTGGTTTA
*
638964 TTATTT-TTAATTATTT
1 TTATTTATTATTTATTT
638980 ATTATTTATTATTTA-TT
1 -TTATTTATTATTTATTT
*
638997 TTATTTTATTTTTTATTT
1 TTA-TTTATTATTTATTT
639015 TTATTTAT
1 TTATTTAT
639023 ATGTGTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
16 3 0.08
17 23 0.62
18 11 0.30
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTTATTATTTATTT
Found at i:641817 original size:3 final size:3
Alignment explanation
Indices: 641809--641863 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
641799 GTAAATATGT
* * *
641809 TAA TAA TAA TTA TAA TAA TAA TGA TAA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
641857 T-A TAA TA
1 TAA TAA TA
641864 TTTTTAAAGC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:642169 original size:40 final size:41
Alignment explanation
Indices: 642118--642434 Score: 164
Period size: 40 Copynumber: 7.4 Consensus size: 41
642108 TACGGCTCCC
642118 ACGTGATGAGGA-GATCTGG-TCTAGGGATGACACAGTTCCT
1 ACGTGATGAGGACGA-CTGGATCTAGGGATGACACAGTTCCT
** *
642158 ACGTGATGAGGACGAAAGGCCATCATTAGGGATGATAACACGGTTCCT
1 ACGTGATGAGGACGACTGG--ATC--TAGGGATG---ACACAGTTCCT
* * * *
642206 ACGTGATGAGGACGACTGGTTATCTAAGGTTGACACGGCTCCT
1 ACGTGATGAGGACGACTGG--ATCTAGGGATGACACAGTTCCT
*
642249 ACGTGATGAGGA-GATCTGG-TCGAGGGATGACACAGTTCCT
1 ACGTGATGAGGACGA-CTGGATCTAGGGATGACACAGTTCCT
* * * * *
642289 ACTTGATGAGGATGACAGACCATCATTAGGGATGATAACACGATTCCT
1 ACGTGATGAGGACGACTG--GATC--TAGGGATGA-CACA-G-TTCCT
*** * * * * * *
642337 ATACGATGTGGATGGCTGATTATCTAGGG-TAACACAGTTCTT
1 ACGTGATGAGGACGACTG--GATCTAGGGATGACACAGTTCCT
* *
642379 ACGTGATGAGGAC-AGTTGG-TC-AGTGGATGACACGGTTCCT
1 ACGTGATGAGGACGA-CTGGATCTAG-GGATGACACAGTTCCT
642419 ACGTGATGAGGACGAC
1 ACGTGATGAGGACGAC
642435 ATGCCATCTT
Statistics
Matches: 211, Mismatches: 43, Indels: 46
0.70 0.14 0.15
Matches are distributed among these distances:
38 2 0.01
39 4 0.02
40 66 0.31
41 5 0.02
42 16 0.08
43 31 0.15
44 3 0.01
45 18 0.09
46 14 0.07
47 1 0.00
48 51 0.24
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (41 bp):
ACGTGATGAGGACGACTGGATCTAGGGATGACACAGTTCCT
Found at i:642256 original size:43 final size:42
Alignment explanation
Indices: 642064--642268 Score: 155
Period size: 43 Copynumber: 4.7 Consensus size: 42
642054 AAGGATGATA
* * *
642064 ACACGGTTCTTACGTGATGAGGATGGCTGATTATCTAAGGTTG
1 ACACGGTTCCTACGTGATGAGGA-GACTGGTTATCTAAGGTTG
* * * * *
642107 ATACGGCTCCCACGTGATGAGGAGATCTGG---TCTAGGGATG
1 ACACGGTTCCTACGTGATGAGGAGA-CTGGTTATCTAAGGTTG
* ** ** * *
642147 ACACAGTTCCTACGTGATGAGGACGAAAGGCCATCATTAGGGATGATA
1 ACACGGTTCCTACGTGATGAGGA-GACTGGTTATC--TAAGG-T--TG
642195 ACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAAGGTTG
1 ACACGGTTCCTACGTGATGAGGA-GACTGGTTATCTAAGGTTG
*
642238 ACACGGCTCCTACGTGATGAGGAGATCTGGT
1 ACACGGTTCCTACGTGATGAGGAGA-CTGGT
642269 CGAGGGATGA
Statistics
Matches: 127, Mismatches: 24, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
40 29 0.23
41 2 0.02
42 3 0.02
43 52 0.41
45 6 0.05
46 4 0.03
48 31 0.24
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (42 bp):
ACACGGTTCCTACGTGATGAGGAGACTGGTTATCTAAGGTTG
Found at i:642290 original size:131 final size:130
Alignment explanation
Indices: 642047--642451 Score: 526
Period size: 131 Copynumber: 3.1 Consensus size: 130
642037 AAGAGTTCGA
* * *
642047 ATCATCTAAGGATGATAACACGGTTCTTACGTGATGAGGATGGCTGATTATCTAAGGTTGATACG
1 ATCAT-TAGGGATGATAACACGGTTCCTACGTGATGAGGATGGCTGATTATCTAAGGTTGACACG
* *
642112 GCTCCCACGTGATGAGGAGATCTGGTCTAGGGATGACACAGTTCCTACGTGATGAGGACGAAAGG
65 GCTCCTACGTGATGAGGAGATCTGGTC-AGGGATGACACAGTTCCTACGTGATGAGGACGACAGG
642177 CC
129 CC
* * *
642179 ATCATTAGGGATGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAAGGTTGACACGG
1 ATCATTAGGGATGATAACACGGTTCCTACGTGATGAGGATGGCTGATTATCTAAGGTTGACACGG
* * *
642244 CTCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACAGTTCCTACTTGATGAGGATGACAGAC
66 CTCCTACGTGATGAGGAGATCTGGTC-AGGGATGACACAGTTCCTACGTGATGAGGACGACAGGC
642309 C
130 C
* *** * * * *
642310 ATCATTAGGGATGATAACACGATTCCTATACGATGTGGATGGCTGATTATCT-AGGGTAACACAG
1 ATCATTAGGGATGATAACACGGTTCCTACGTGATGAGGATGGCTGATTATCTAAGGTTGACACGG
* * * * *
642374 TTCTTACGTGATGAGGACAGT-TGGTCAGTGGATGACACGGTTCCTACGTGATGAGGACGACATG
66 CTCCTACGTGATGAGGAGA-TCTGGTCAG-GGATGACACAGTTCCTACGTGATGAGGACGACAGG
642438 CC
129 CC
*
642440 ATCTTTAGGGAT
1 ATCATTAGGGAT
642452 AATGGTTTCA
Statistics
Matches: 239, Mismatches: 32, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
129 2 0.01
130 73 0.31
131 159 0.67
132 5 0.02
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (130 bp):
ATCATTAGGGATGATAACACGGTTCCTACGTGATGAGGATGGCTGATTATCTAAGGTTGACACGG
CTCCTACGTGATGAGGAGATCTGGTCAGGGATGACACAGTTCCTACGTGATGAGGACGACAGGCC
Found at i:642645 original size:70 final size:69
Alignment explanation
Indices: 642511--642651 Score: 187
Period size: 69 Copynumber: 2.0 Consensus size: 69
642501 TTCAAAAGAG
*
642511 ATAAAATTTATTTCAAGGGAAACGATCTCAAATATATTTTTTGTTTCATGGAAAACAATCTCAAA
1 ATAAAATTTATTTCAAGAGAAACGATCTCAAATATATTTTTTGTTTCATGGAAAACAATCTCAAA
642576 GAAA
66 GAAA
* * * * *
642580 ATAAGATTTGTTTCAAGAGAAAC-ATCTCAAAGTTTTTTTTGTTGTTTCAT-GAGAAACGATCTC
1 ATAAAATTTATTTCAAGAGAAACGATCTCAAA-TATATTTT-TTGTTTCATGGA-AAACAATCTC
642643 AAAGAAA
63 AAAGAAA
642650 AT
1 AT
642652 GGGATTTATT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
68 8 0.13
69 28 0.44
70 27 0.43
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (69 bp):
ATAAAATTTATTTCAAGAGAAACGATCTCAAATATATTTTTTGTTTCATGGAAAACAATCTCAAA
GAAA
Found at i:642658 original size:70 final size:69
Alignment explanation
Indices: 642511--642662 Score: 191
Period size: 70 Copynumber: 2.2 Consensus size: 69
642501 TTCAAAAGAG
* *
642511 ATAAAATTTATTTCAAGGGAAACGATCTCAAATATATTTTTTGTTTCATGGAAAACAATCTCAAA
1 ATAAGATTTATTTCAAGAGAAACGATCTCAAATATATTTTTTGTTTCATGGAAAACAATCTCAAA
642576 GAAA
66 GAAA
* * * *
642580 ATAAGATTTGTTTCAAGAGAAAC-ATCTCAAAGTTTTTTTTGTTGTTTCAT-GAGAAACGATCTC
1 ATAAGATTTATTTCAAGAGAAACGATCTCAAA-TATATTTT-TTGTTTCATGGA-AAACAATCTC
642643 AAAGAAA
63 AAAGAAA
**
642650 ATGGGATTTATTT
1 ATAAGATTTATTT
642663 GGTGTTTCAT
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
68 8 0.11
69 28 0.39
70 35 0.49
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (69 bp):
ATAAGATTTATTTCAAGAGAAACGATCTCAAATATATTTTTTGTTTCATGGAAAACAATCTCAAA
GAAA
Found at i:642714 original size:36 final size:36
Alignment explanation
Indices: 642665--642787 Score: 149
Period size: 36 Copynumber: 3.4 Consensus size: 36
642655 ATTTATTTGG
* * * *
642665 TGTTTCATA-AGAAACTGCCTCGAGGGAGACAAAATT
1 TGTTTCA-AGAGAAACTGTCTCAAGAGAGACAAAATA
* * *
642701 TGTTTCAAGAGAAACAGTCTCAAGCGAGACAAAAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATA
*
642737 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATA
*
642773 TGTTTCAAGGGAAAC
1 TGTTTCAAGAGAAAC
642788 AATCTCAAAG
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
35 1 0.01
36 75 0.99
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATA
Found at i:642794 original size:36 final size:36
Alignment explanation
Indices: 642690--642795 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
642680 TGCCTCGAGG
* * *
642690 GAGACAAAATTTGTTTCAAGAGAAACAGTCTCAAGC
1 GAGACAAAATATGTTTCAAGGGAAACAGTCTCAAGA
* *
642726 GAGACAAAAAATGTTTCAAGGGAAACTGTCTCAAGA
1 GAGACAAAATATGTTTCAAGGGAAACAGTCTCAAGA
*
642762 GAGACAAAATATGTTTCAAGGGAAACAATCTCAA
1 GAGACAAAATATGTTTCAAGGGAAACAGTCTCAA
642796 AGGTTTTGGA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.21
Consensus pattern (36 bp):
GAGACAAAATATGTTTCAAGGGAAACAGTCTCAAGA
Found at i:643128 original size:2 final size:2
Alignment explanation
Indices: 643121--643172 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
643111 GCATATGTAC
* *
643121 AT AT AT AT AC AT AT AT AT AT AT AT AC 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
643163 AT AT AT AT AT
1 AT AT AT AT AT
643173 GTGTGTGTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:647176 original size:65 final size:64
Alignment explanation
Indices: 646980--647187 Score: 194
Period size: 65 Copynumber: 3.2 Consensus size: 64
646970 TGCACTAAGA
* * * * * *
646980 GTGCATCGATGCATCAAGTGCATTCTAT-TTT-A-AAATAGCCAGAGTGCATCGATGCATTGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCCATAGTGCATCGATGCATGGTTG
* *
647042 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTTAGTACATC-AGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCATAGTGCATCGA-TGCATGGT-
647106 T-
63 TG
* ** * *
647107 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCCATAGTGCATCGATGCATGG-TT
647171 G
64 G
*
647172 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
647188 CTCTGAAAAG
Statistics
Matches: 119, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
62 26 0.22
63 3 0.03
64 25 0.21
65 61 0.51
66 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCATAGTGCATCGATGCATGGTTG
Found at i:647652 original size:2 final size:2
Alignment explanation
Indices: 647645--647669 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
647635 AATTGATTAA
647645 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 A
647670 GCTTAAGCTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:653719 original size:23 final size:21
Alignment explanation
Indices: 653676--653716 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
653666 GAGTTTATTT
*
653676 TCATTTTTTAATTTTGAAACA
1 TCATTTTTTAATTTTAAAACA
653697 TCATTTTTTATATTTTAAAA
1 TCATTTTTTA-ATTTTAAAA
653717 ACAATTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
TCATTTTTTAATTTTAAAACA
Found at i:657082 original size:21 final size:21
Alignment explanation
Indices: 657073--657154 Score: 123
Period size: 21 Copynumber: 3.9 Consensus size: 21
657063 GAAAAGATCG
657073 TTCATAAAGACGAGAAGACCA
1 TTCATAAAGACGAGAAGACCA
657094 TTCATAAAGACGAGAAGACCA
1 TTCATAAAGACGAGAAGACCA
*
657115 TTCATAAAGAC-ATGAAGACCC
1 TTCATAAAGACGA-GAAGACCA
657136 TTCATAAAGAC-ATGAAGAC
1 TTCATAAAGACGA-GAAGAC
657155 TACTTCGCAT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
20 1 0.02
21 58 0.98
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (21 bp):
TTCATAAAGACGAGAAGACCA
Found at i:657103 original size:42 final size:42
Alignment explanation
Indices: 657057--657146 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
657047 TAGTCATACC
* * *
657057 AAAGATGAAAAGATCGTTCATAAAGACGA-GAAGACCATTCAT
1 AAAGACGAAAAGACCATTCATAAAGAC-ATGAAGACCATTCAT
* *
657099 AAAGACGAGAAGACCATTCATAAAGACATGAAGACCCTTCAT
1 AAAGACGAAAAGACCATTCATAAAGACATGAAGACCATTCAT
657141 AAAGAC
1 AAAGAC
657147 ATGAAGACTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 1 0.02
42 41 0.98
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.17
Consensus pattern (42 bp):
AAAGACGAAAAGACCATTCATAAAGACATGAAGACCATTCAT
Found at i:660899 original size:125 final size:125
Alignment explanation
Indices: 660677--660924 Score: 372
Period size: 125 Copynumber: 2.0 Consensus size: 125
660667 AAGTTGTGAT
* *
660677 ATGTTAGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGGAGGCATGAA
1 ATGTTAGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGGAATGAA
* * *
660742 GAATGAGCCTTATAATTTGAGGTGATGGGGCATTTTGAAGGCTCGTACCAATATAAGACA
66 GAATGAGCCTTACAATCTGAGATGATGGGGCATTTTGAAGGCTCGTACCAATATAAGACA
* *
660802 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTTAGACCAAGAAGGAATTG-
1 ATGTTAGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGGAA-TGA
* * * * *
660866 AGAGTGATCCTTACAATCTGATATGTTGGGGCATTTTGAAGGCTCGTACCAGTATAAGA
65 AGAATGAGCCTTACAATCTGAGATGATGGGGCATTTTGAAGGCTCGTACCAATATAAGA
660925 TAATATTGCG
Statistics
Matches: 110, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
125 108 0.98
126 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (125 bp):
ATGTTAGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGGAATGAA
GAATGAGCCTTACAATCTGAGATGATGGGGCATTTTGAAGGCTCGTACCAATATAAGACA
Found at i:662232 original size:38 final size:38
Alignment explanation
Indices: 662127--662232 Score: 137
Period size: 37 Copynumber: 2.8 Consensus size: 38
662117 GGCAAAGTCA
* *
662127 ATCTTAAGCCTTCACCGAATATTAGTGAAG-CAACTCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCCAACTCC
*
662164 ATCTTAAGCCTTCACCGAAGAGTGGTGAAGCCAA-T-C
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCCAACTCC
*
662200 AGTCTTAAGCCTTTACCGAAAGAGTAGTGAAGC
1 A-TCTTAAGCCTTCACCG-AAGAGTAGTGAAGC
662233 AGATTTGTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
36 2 0.03
37 43 0.70
38 16 0.26
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (38 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCCAACTCC
Found at i:662665 original size:54 final size:54
Alignment explanation
Indices: 662606--663091 Score: 615
Period size: 54 Copynumber: 9.0 Consensus size: 54
662596 AGTGAAGCAA
*
662606 AAGAAGATGTTCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCATTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTTTG
* *
662660 AAGAAGATGTCCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAAACCCGTTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTG
* * **
662714 AAGAAGATGTCCAAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
1 AAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTG
* * * * **
662768 AAGAAGATGTTCGAGTTCCATACTTCCTGAAAAAAGAGGGAGTGAACCCGTAAG
1 AAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTG
* * *
662822 AAGAAGATGTTCGAGTT-TCATACTTCCTGAAGAAAGAGGGAGCAAACCCATTTG
1 AAGAAGATGTTCGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTG
* * *
662876 AAGAAGATGTTCGAGTTCCATACTCCCT-AGAGAATGAGGGAGCGAACTCGTTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTTTG
* *
662930 AAGAAGATGTCCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGTGAACCCGTTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTTTG
* **
662984 AAGAAGAT-TTCCGAGTTCTATACTCCTTGAAGAAAGAGGGAGCGAACCCGTAAG
1 AAGAAGATGTT-CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTG
* * * * *
663038 AAGAAGATGTCCGAGTTCCATACTTCCT-AGAGAAAGAGAGAGCGAACACGTTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTTTG
663092 TTAAAAATTG
Statistics
Matches: 380, Mismatches: 44, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
53 3 0.01
54 374 0.98
55 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (54 bp):
AAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTG
Found at i:663166 original size:55 final size:55
Alignment explanation
Indices: 663083--663787 Score: 730
Period size: 55 Copynumber: 13.0 Consensus size: 55
663073 GAGAGAGCGA
* * * * *
663083 ACACGTTTGTTAAAAATTGTTTGAGTCTTATACTCTCTGAAGGAATAGGGAGCAG
1 ACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG
* *** * * * *
663138 ACACGATTGTCGAAGATAACTCGAGTCTTATACTCTCTGAAGGAATAGGAAACAA
1 ACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG
* * *
663193 ACACAATTGTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAGGGAGCAA
1 ACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG
* *
663248 ACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAACAG
1 ACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG
* * *
663303 ACACGATTGTTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAGAAG
1 ACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG
* * *
663358 ACATGATTGTTGAAGATTGTTCTAGTCTTATACTCTCTGAAGAAATAGGGAGTAG
1 ACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG
* * * *
663413 ATACGATTGCTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAGCAT
1 ACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG
* * * * *
663468 ACATGATTGTTAAAGATTGTTCGAGTATTATACTCTCTGAAGAAATAGTGAGCAT
1 ACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG
* * * * * *
663523 ATACAATTGTTGAAGATTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
1 ACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG
* * * * *
663578 ACATGTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
1 ACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG
* * * * * * *
663629 ACACGTTTGTTGAAGGTTGTTCAAGTCCTATACTCTCTGAAAAAATAGGGAACGG
1 ACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG
* * * * * *
663684 ACACGTTTATTGAAGA----ACGAGTCCTATACTCTCTGAATG-AATAGGGAACAA
1 ACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAA-GAAATAGGGAGCAG
* * * * * * *
663735 AC-CTG-TTTTATGAAGATTGTTTGAGTTTTATACTCCCTCAAGCAGTAGGGAGC
1 ACAC-GATTGT-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGC
663788 GAATCCGTTT
Statistics
Matches: 554, Mismatches: 84, Indels: 24
0.84 0.13 0.04
Matches are distributed among these distances:
50 4 0.01
51 84 0.15
52 2 0.00
54 3 0.01
55 461 0.83
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (55 bp):
ACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG
Found at i:664123 original size:2 final size:2
Alignment explanation
Indices: 664116--664148 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
664106 TAAATTATCG
664116 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
664149 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:664153 original size:2 final size:2
Alignment explanation
Indices: 664148--664194 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
664138 TATATATATA
664148 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
664190 TG TG T
1 TG TG T
664195 TAAGAGAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:673159 original size:3 final size:3
Alignment explanation
Indices: 673151--673228 Score: 115
Period size: 3 Copynumber: 26.7 Consensus size: 3
673141 GTAAATATGT
* *
673151 TAA TAA TAA TTA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
673199 TAA TAA TAA TAA T-A CAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
673229 TTTTTAAGCC
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
2 3 0.04
3 64 0.96
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:673377 original size:54 final size:55
Alignment explanation
Indices: 673261--673391 Score: 142
Period size: 54 Copynumber: 2.4 Consensus size: 55
673251 GGTGTTTACA
* * * *
673261 CATGGAAGAGTACAGCAAATTTCTAAAGATCAAGCAAGCTCTAGCATTCTTCTGT
1 CATGGAGGAGTAAAGCAAATTTCTAAAGACCAAGCAAGCTCTAGCACTCTTCTGT
* * * * *
673316 TACGGAGGAGTAGAGCACATTTCT-AAGACCGAGCAAGCTCTAGTGC-CTCTT-TGT
1 CATGGAGGAGTAAAGCAAATTTCTAAAGACCAAGCAAGCTCTA--GCACTCTTCTGT
673370 CATGGAGGAGTAAAGCAAATTT
1 CATGGAGGAGTAAAGCAAATTT
673392 TTAGTACTGA
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
54 37 0.60
55 23 0.37
56 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (55 bp):
CATGGAGGAGTAAAGCAAATTTCTAAAGACCAAGCAAGCTCTAGCACTCTTCTGT
Found at i:680452 original size:20 final size:20
Alignment explanation
Indices: 680427--680480 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
680417 ATACCAAGTG
*
680427 GGTATCGATACTATAAAGG-C
1 GGTATCGATACCAT-AAGGAC
680447 GGTATCGATACCATAAGGAC
1 GGTATCGATACCATAAGGAC
680467 GGTATCGATACCAT
1 GGTATCGATACCAT
680481 CTTTAAAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (20 bp):
GGTATCGATACCATAAGGAC
Found at i:686915 original size:22 final size:23
Alignment explanation
Indices: 686888--686930 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
686878 ATGTGATAAG
686888 TTATGTG-ATATGTGAAAATGAA
1 TTATGTGTATATGTGAAAATGAA
*
686910 TTATGTGTCTATGTGAAAATG
1 TTATGTGTATATGTGAAAATG
686931 TGAAATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.40
Consensus pattern (23 bp):
TTATGTGTATATGTGAAAATGAA
Found at i:689032 original size:20 final size:20
Alignment explanation
Indices: 688995--689033 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
688985 TTTAGGTTTG
*
688995 AGTATCGATATTGAATGAAT
1 AGTATCGATACTGAATGAAT
* *
689015 AGTATTGATACTGGATGAA
1 AGTATCGATACTGAATGAA
689034 CTAGGATGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.33
Consensus pattern (20 bp):
AGTATCGATACTGAATGAAT
Found at i:690897 original size:37 final size:37
Alignment explanation
Indices: 690856--690940 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 37
690846 GGATAAAGAT
*
690856 AAAAAGAAAATAGATAAATAAATGAGTAAAATATATAA
1 AAAAAGAAAATAGATAAATAAATAAGTAAAATA-ATAA
** * * *
690894 AAAATTAAAA-GGATATATATATAAGTAAAATAATAA
1 AAAAAGAAAATAGATAAATAAATAAGTAAAATAATAA
690930 AAAAAGAAAAT
1 AAAAAGAAAAT
690941 CAAAAGTAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
36 12 0.32
37 18 0.47
38 8 0.21
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.22
Consensus pattern (37 bp):
AAAAAGAAAATAGATAAATAAATAAGTAAAATAATAA
Found at i:691448 original size:37 final size:37
Alignment explanation
Indices: 691407--691508 Score: 138
Period size: 34 Copynumber: 2.8 Consensus size: 37
691397 GTGCTTGTGA
* * * *
691407 ATCCTATCTTTAAGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
691444 ATCCTATTTTTAGGAGTTTGAATCCTA--A-AATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
691478 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
691509 GACGAAAAGG
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
34 32 0.56
35 1 0.02
36 1 0.02
37 23 0.40
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:692442 original size:106 final size:106
Alignment explanation
Indices: 692258--693426 Score: 1743
Period size: 106 Copynumber: 11.0 Consensus size: 106
692248 GGATTGTTCC
* * * * * *
692258 GAGTCCAATATCCTCCG-TCGTGAAGTTTAAATTGGCTCTGGAATCGGGAAAATGTTTGTTGATA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * *
692322 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
692364 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
692429 ACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
692470 CAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
692535 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
692576 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
692641 CCAGCGCTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
692682 GAGTCCAATATCTTTCGATGTGAAGTTGAAATTGGCTCTGAAATT-GGAAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTGTTGACA
*
692746 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTCGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*** * * * *
692788 GAGTCCAATATCCTTTATTTTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTG-TGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
692852 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
692893 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTGTTGACA
*
692957 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
692999 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
693064 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
693105 GAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
693170 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
693211 GAGTACAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
693276 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
693317 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
693382 CCAGCAGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
693423 GAGT
1 GAGT
693427 GACACAATAT
Statistics
Matches: 969, Mismatches: 88, Indels: 12
0.91 0.08 0.01
Matches are distributed among these distances:
104 3 0.00
105 96 0.10
106 861 0.89
107 9 0.01
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:693324 original size:529 final size:530
Alignment explanation
Indices: 692259--693426 Score: 1874
Period size: 529 Copynumber: 2.2 Consensus size: 530
692249 GATTGTTCCG
* * * * * * * ** *
692259 AGTCCAATATCCTCCGTCGTGAAGTTTAAATTGGCTCTGGAATCGGGAAAATGTTTGTTGATAAC
1 AGTCCAATATCCTTCATTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
692324 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAG
66 CAGCAGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAG
*
692389 TTGAAATTGACTCCGAAATTGGGAAATTGTTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGACTCCGAAATTGGGAAATTGTTTATTGACAAACAGCGGTCCCTTCGTCGTGAAGTT
* *
692454 GAACTTGCGTTGTCTGCAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGA
196 GAACTTGCGTTGTCTGCAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGATCTAAAATTGAGA
* *
692519 AGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
261 AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
*
692584 TATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGCT
326 TATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGCT
* *
692649 CCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGATGTGAAGTTGAAAT
391 CCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTACAATATCATTCGATGTGAAGTTGAAAT
*
692714 TGGCTCTGAAATTGGAAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
456 TGGCTCTGAAATTGGAAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
* *
692779 CGTCGTCTGG
521 CATCGTCTGA
* *
692789 AGTCCAATATCCTTTATTTTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTG-TGACAAC
1 AGTCCAATATCCTTCATTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* * * * * *
692853 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCAGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAG
* * *
692918 TTGAAATTGGCTCTGAAATT-GGAAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 TTGAAATTGACTCCGAAATTGGGAAA-TTGTTTATTGACAAACAGCGGTCCCTTCGTCGTGAAGT
* * * * *
692982 TGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGGG
195 TGAACTTGCGTTGTCTGCAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGATCTAAAATTGAG
*
693047 AAATTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
260 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
693112 ATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
325 ATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGC
*
693177 TCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTACAATATCATTCGCTGTGAAGTTGAAA
390 TCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTACAATATCATTCGATGTGAAGTTGAAA
693242 TTGGCTCTGAAATTGGGAAA-TTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
455 TTGGCTCTGAAATT-GGAAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
*
693306 TGCATTGTCTGA
519 TGCATCGTCTGA
* * * *
693318 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTATTTGTTGACAAC
1 AGTCCAATATCCTTCATTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
693383 CAGCAGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
66 CAGCAGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
693427 GACACAATAT
Statistics
Matches: 584, Mismatches: 51, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
528 5 0.01
529 481 0.82
530 98 0.17
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (530 bp):
AGTCCAATATCCTTCATTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
CAGCAGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAG
TTGAAATTGACTCCGAAATTGGGAAATTGTTTATTGACAAACAGCGGTCCCTTCGTCGTGAAGTT
GAACTTGCGTTGTCTGCAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGATCTAAAATTGAGA
AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
TATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGCT
CCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTACAATATCATTCGATGTGAAGTTGAAAT
TGGCTCTGAAATTGGAAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CATCGTCTGA
Found at i:694886 original size:7 final size:7
Alignment explanation
Indices: 694854--694935 Score: 60
Period size: 7 Copynumber: 11.6 Consensus size: 7
694844 TTTTTGTCCC
694854 TTTTTC-
1 TTTTTCT
**
694860 TTTTTGA
1 TTTTTCT
*
694867 TTTTTGT
1 TTTTTCT
*
694874 TCTTTCT
1 TTTTTCT
694881 TTTTTCT
1 TTTTTCT
*
694888 TTTGT-T
1 TTTTTCT
*
694894 TTCTTCT
1 TTTTTCT
694901 TTTTTGCT
1 TTTTT-CT
694909 TCTTTTCT
1 T-TTTTCT
*
694917 TTTTTGTT
1 TTTTT-CT
694925 TTTTTCT
1 TTTTTCT
694932 TTTT
1 TTTT
694936 GTTATGATTG
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
6 9 0.15
7 35 0.58
8 12 0.20
9 4 0.07
ACGTcount: A:0.01, C:0.12, G:0.06, T:0.80
Consensus pattern (7 bp):
TTTTTCT
Found at i:694890 original size:20 final size:20
Alignment explanation
Indices: 694854--694938 Score: 73
Period size: 20 Copynumber: 4.0 Consensus size: 20
694844 TTTTTGTCCC
**
694854 TTTTTCTTTTTGATTTTTGT
1 TTTTTCTTTTTTCTTTTTGT
*
694874 TCTTTCTTTTTTC-TTTTGT
1 TTTTTCTTTTTTCTTTTTGT
*
694893 TTTCTTCTTTTTTGCTTCTTTTCT
1 TTT-TTCTTTTTT-C-T-TTTTGT
*
694917 TTTTTGTTTTTTTCTTTTTGT
1 TTTTT-CTTTTTTCTTTTTGT
694938 T
1 T
694939 ATGATTGAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
19 8 0.15
20 19 0.37
21 7 0.13
22 1 0.02
23 3 0.06
24 14 0.27
ACGTcount: A:0.01, C:0.12, G:0.07, T:0.80
Consensus pattern (20 bp):
TTTTTCTTTTTTCTTTTTGT
Found at i:694900 original size:24 final size:23
Alignment explanation
Indices: 694854--694938 Score: 66
Period size: 24 Copynumber: 3.6 Consensus size: 23
694844 TTTTTGTCCC
*
694854 TTTTTCTTTTTGATTTTTGTTCTTTCT
1 TTTTTC-TTTTG--TTTTCTTCTTT-T
694881 TTTTTCTTTTGTTTTCTTCTTTT
1 TTTTTCTTTTGTTTTCTTCTTTT
* * *
694904 TTGCTTCTTTTCTTTT-TTGTTTT
1 TT-TTTCTTTTGTTTTCTTCTTTT
*
694927 TTTCT-TTTTGTT
1 TTTTTCTTTTGTT
694939 ATGATTGAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 6 0.12
22 1 0.02
23 11 0.22
24 21 0.42
26 5 0.10
27 6 0.12
ACGTcount: A:0.01, C:0.12, G:0.07, T:0.80
Consensus pattern (23 bp):
TTTTTCTTTTGTTTTCTTCTTTT
Found at i:694919 original size:15 final size:15
Alignment explanation
Indices: 694877--694935 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
694867 TTTTTGTTCT
694877 TTCTTTT-TTCTTTTG
1 TTCTTTTCTT-TTTTG
694892 TT-TTCTTCTTTTTTG
1 TTCTT-TTCTTTTTTG
694907 CTTCTTTTCTTTTTTG
1 -TTCTTTTCTTTTTTG
*
694923 TTTTTTTCTTTTT
1 TTCTTTTCTTTTT
694936 GTTATGATTG
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.05
15 21 0.54
16 14 0.36
17 2 0.05
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (15 bp):
TTCTTTTCTTTTTTG
Found at i:694922 original size:31 final size:31
Alignment explanation
Indices: 694877--694935 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
694867 TTTTTGTTCT
694877 TTCTTTTTTCTTTTGTTTTCTTCTTTTTTGC
1 TTCTTTTTTCTTTTGTTTTCTTCTTTTTTGC
*
694908 TTCTTTTCTT-TTTTGTTTTTTTCTTTTT
1 TTCTTTT-TTCTTTTGTTTTCTTCTTTTT
694936 GTTATGATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (31 bp):
TTCTTTTTTCTTTTGTTTTCTTCTTTTTTGC
Found at i:698305 original size:16 final size:15
Alignment explanation
Indices: 698276--698304 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
698266 AATGATGAAA
698276 ACAAAATAAAAAAAG
1 ACAAAATAAAAAAAG
698291 ACAAAATAAAAAAA
1 ACAAAATAAAAAAA
698305 ATTAGTGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.07, G:0.03, T:0.07
Consensus pattern (15 bp):
ACAAAATAAAAAAAG
Found at i:699461 original size:16 final size:18
Alignment explanation
Indices: 699429--699463 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
699419 AATAAAGTAA
699429 ATATAAAATGAATAAAAT
1 ATATAAAATGAATAAAAT
699447 ATATAAAAT-AA-AAAAT
1 ATATAAAATGAATAAAAT
699463 A
1 A
699464 CAACAACACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 2 0.12
18 9 0.53
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
ATATAAAATGAATAAAAT
Found at i:699596 original size:19 final size:21
Alignment explanation
Indices: 699574--699655 Score: 63
Period size: 21 Copynumber: 4.2 Consensus size: 21
699564 TAGGATAAAG
699574 ATAAA-AAG-AAAATATATAA
1 ATAAATAAGTAAAATATATAA
*
699593 ATAAATGAGTAAAATATAT--
1 ATAAATAAGTAAAATATATAA
* *
699612 A-AAA-AAGTAAAAGCATATAT
1 ATAAATAAGTAAAA-TATATAA
*
699632 ATATATAAGTAAAATA-AT-A
1 ATAAATAAGTAAAATATATAA
699651 ATAAA
1 ATAAA
699656 AAAAATCAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
17 7 0.14
18 7 0.14
19 10 0.20
20 5 0.10
21 12 0.24
22 8 0.16
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.26
Consensus pattern (21 bp):
ATAAATAAGTAAAATATATAA
Found at i:701773 original size:40 final size:40
Alignment explanation
Indices: 701708--701818 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 40
701698 AAATGACCAA
* * ***
701708 CAAATTCGCAACGCGAT-CTCAAATTCGCAAC-CCAGTTT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
* *
701746 CCAATTTCGAAACGCGATAGTCAAATTCGCAACACAAAAGT
1 -CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
701787 CAAATTCGCAACGCGATAGTCAAATTCGCAAC
1 CAAATTCGCAACGCGATAGTCAAATTCGCAAC
701819 TGAATTTCAA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 15 0.25
40 43 0.70
41 3 0.05
ACGTcount: A:0.37, C:0.28, G:0.14, T:0.21
Consensus pattern (40 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
Found at i:701830 original size:19 final size:19
Alignment explanation
Indices: 701806--701875 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
701796 AACGCGATAG
701806 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
701825 TCAAATTTGCAACTGAATT
1 TCAAATTCGCAACTGAATT
* *
701844 TCAAGTTCGCAACGCGAATT
1 TCAAATTCGCAAC-TGAATT
*
701864 T-AATTTCGCAAC
1 TCAAATTCGCAAC
701876 AGGTTTTAGG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
19 39 0.87
20 6 0.13
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.31
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:701864 original size:20 final size:20
Alignment explanation
Indices: 701708--701875 Score: 116
Period size: 20 Copynumber: 8.6 Consensus size: 20
701698 AAATGACCAA
*
701708 CAAATTCGCAACGCG-ATCT
1 CAAATTCGCAACGCGAATTT
* *
701727 CAAATTCGCAAC-CCAGTTT
1 CAAATTCGCAACGCGAATTT
* * *
701746 CCAATTTCGAAACGCG-ATAGT
1 -CAAATTCGCAACGCGAAT-TT
* * **
701767 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGAATTT
*
701787 CAAATTCGCAACGCG-ATAGT
1 CAAATTCGCAACGCGAAT-TT
*
701807 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
* *
701826 CAAATTTGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
*
701845 CAAGTTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
701865 -AATTTCGCAAC
1 CAAATTCGCAAC
701876 AGGTTTTAGG
Statistics
Matches: 118, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
18 1 0.01
19 55 0.47
20 59 0.50
21 3 0.03
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:702809 original size:24 final size:24
Alignment explanation
Indices: 702782--702827 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
702772 TATTCGAAAT
702782 TTGATCTTGGTCAATACCCGGACA
1 TTGATCTTGGTCAATACCCGGACA
*
702806 TTGATCTTGGTCAATACTCGGA
1 TTGATCTTGGTCAATACCCGGA
702828 TTTTGATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (24 bp):
TTGATCTTGGTCAATACCCGGACA
Found at i:702833 original size:24 final size:24
Alignment explanation
Indices: 702781--702834 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
702771 GTATTCGAAA
702781 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
702805 ATTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
702829 TTTGAT
1 TTTGAT
702835 GATGTGATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:703026 original size:12 final size:12
Alignment explanation
Indices: 703009--703033 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
702999 ATATAACCCC
703009 GAAGAAGAAAAA
1 GAAGAAGAAAAA
703021 GAAGAAGAAAAA
1 GAAGAAGAAAAA
703033 G
1 G
703034 TCCTCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:704611 original size:18 final size:18
Alignment explanation
Indices: 704588--704623 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
704578 AAGCAAAAGG
*
704588 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
704606 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
704624 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:704990 original size:20 final size:20
Alignment explanation
Indices: 704930--704991 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
704920 TAAGCATTGT
*
704930 GATAGTCAAATTCGTAACGC
1 GATAGTCAAATTCGCAACGC
* * *
704950 AAAAGACAAATTCGCAACGC
1 GATAGTCAAATTCGCAACGC
704970 GATAGTCAAATTCGCAACGC
1 GATAGTCAAATTCGCAACGC
704990 GA
1 GA
704992 AATCGCAAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.18
Consensus pattern (20 bp):
GATAGTCAAATTCGCAACGC
Found at i:705176 original size:25 final size:25
Alignment explanation
Indices: 705148--705196 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
705138 ATATCAATTA
*
705148 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
705173 AACATTGTTATGGGTACATTATTT
1 AACATTGTTATGGGTACATTATTT
705197 AGAAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:705605 original size:18 final size:18
Alignment explanation
Indices: 705584--705620 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
705574 GTAATTGGAG
705584 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
705602 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
705620 T
1 T
705621 ATAAATTTCG
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:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:705627 original size:24 final size:24
Alignment explanation
Indices: 705576--705628 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
705566 TTTCATATGT
* * *
705576 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
705600 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
705624 AATTT
1 AATTT
705629 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:705975 original size:39 final size:39
Alignment explanation
Indices: 705932--706018 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
705922 TCCGATTCTC
*
705932 ATCAAAATCCAAAGCTCATATGGTGTCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
705971 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
706010 ATCAAAATC
1 ATCAAAATC
706019 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:706298 original size:20 final size:20
Alignment explanation
Indices: 706273--706310 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
706263 CAAACGTTTA
706273 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
706293 TTTCGCGTTGCGAATTTG
1 TTTCGCGTTGCGAATTTG
706311 TACCTTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.18, G:0.26, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:706449 original size:66 final size:60
Alignment explanation
Indices: 706369--706508 Score: 172
Period size: 66 Copynumber: 2.2 Consensus size: 60
706359 TTTTAGAAAC
* *
706369 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAACT----AAGC-AAAAAATAAATCTTATTTACAAATC-AATT
706434 A
60 A
* * **
706435 AACAAATCAACTTTTACAAATCAACTAATCAAAAAATAAATCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAACTAAGCAAAAAATAAATCTTATTTACAAATCAATTA
706495 AACAAATCAACTTT
1 AACAAATCAACTTT
706509 CAATATAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
60 19 0.28
61 21 0.31
62 3 0.04
66 25 0.37
ACGTcount: A:0.51, C:0.18, G:0.01, T:0.30
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAACTAAGCAAAAAATAAATCTTATTTACAAATCAATTA
Found at i:706459 original size:14 final size:14
Alignment explanation
Indices: 706419--706460 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
706409 ATAATTCTTA
*
706419 TTTACAAATCAAAT
1 TTTACAAATCAACT
**
706433 TAAACAAATCAACT
1 TTTACAAATCAACT
706447 TTTACAAATCAACT
1 TTTACAAATCAACT
706461 AATCAAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (14 bp):
TTTACAAATCAACT
Found at i:710143 original size:19 final size:20
Alignment explanation
Indices: 710121--710159 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
710111 AAATCGCAAA
710121 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
*
710140 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
710160 ACGAATTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.10, C:0.18, G:0.23, T:0.49
Consensus pattern (20 bp):
GCGATTTTCAGTTTCGCGTT
Found at i:710210 original size:13 final size:13
Alignment explanation
Indices: 710192--710223 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
710182 GGGTTTCTTC
710192 AACAAAAAGACAA
1 AACAAAAAGACAA
710205 AACAAAAAGACAA
1 AACAAAAAGACAA
710218 AACAAA
1 AACAAA
710224 GACAAATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.78, C:0.16, G:0.06, T:0.00
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:710226 original size:11 final size:12
Alignment explanation
Indices: 710196--710229 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
710186 TTCTTCAACA
710196 AAAAGACAAAAC
1 AAAAGACAAAAC
710208 AAAAAGACAAAAC
1 -AAAAGACAAAAC
710221 -AAAGACAAA
1 AAAAGACAAA
710230 TACTAACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
13 12 0.57
ACGTcount: A:0.76, C:0.15, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAGACAAAAC
Found at i:710462 original size:22 final size:22
Alignment explanation
Indices: 710436--710493 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
710426 GATGGAGATA
*
710436 GACGGATCTT-GTCGGAAATGGG
1 GACGGAT-TTCGTCAGAAATGGG
*
710458 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGTCAGAAATGGG
*
710480 GACGGATGTCGTCA
1 GACGGATTTCGTCA
710494 TAGAGAGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.22, C:0.16, G:0.40, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCAGAAATGGG
Found at i:710639 original size:20 final size:20
Alignment explanation
Indices: 710614--710738 Score: 148
Period size: 20 Copynumber: 6.2 Consensus size: 20
710604 GTGTAAAAAC
*
710614 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
*
710634 ATTTGACTATCGCATTGCGA
1 ATTTGACTATCGCGTTGCGA
*
710654 ATTTGACT-TCTGTGTTGCG-
1 ATTTGACTATC-GCGTTGCGA
* **
710673 ATTT-ACAAATTTTCGTTGCGA
1 ATTTGAC-TA-TCGCGTTGCGA
710694 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
710714 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
710734 ATTTG
1 ATTTG
710739 GAAAATCGCA
Statistics
Matches: 88, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
18 2 0.02
19 6 0.07
20 72 0.82
21 6 0.07
22 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:710755 original size:21 final size:21
Alignment explanation
Indices: 710731--710770 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
710721 TATCGCGTTG
710731 CGAATTTGGAAAATCGCAACA
1 CGAATTTGGAAAATCGCAACA
710752 CGAATTTGGAAAATCGCAA
1 CGAATTTGGAAAATCGCAA
710771 TGCAATTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (21 bp):
CGAATTTGGAAAATCGCAACA
Found at i:710832 original size:20 final size:20
Alignment explanation
Indices: 710787--710836 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
710777 TTACATATTC
710787 GCGTTGCGAAATTGGAAACT
1 GCGTTGCGAAATTGGAAACT
* **
710807 GGGTTGCGAAATTGGAATTT
1 GCGTTGCGAAATTGGAAACT
710827 GCGTTGCGAA
1 GCGTTGCGAA
710837 TTTGTTGGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.12, G:0.34, T:0.28
Consensus pattern (20 bp):
GCGTTGCGAAATTGGAAACT
Found at i:711306 original size:9 final size:10
Alignment explanation
Indices: 711274--711307 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
711264 ATTTGATTTT
*
711274 AAAATAAATA
1 AAAATAATTA
711284 AAAATAATTA
1 AAAATAATTA
711294 AAAAT-ATTA
1 AAAATAATTA
711303 AAAAT
1 AAAAT
711308 TAAATGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAATAATTA
Found at i:711976 original size:7 final size:7
Alignment explanation
Indices: 711964--711988 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
711954 TAATATAATT
711964 TTTTTAA
1 TTTTTAA
711971 TTTTTAA
1 TTTTTAA
711978 TTTTTAA
1 TTTTTAA
711985 TTTT
1 TTTT
711989 GGTATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTAA
Found at i:713379 original size:38 final size:37
Alignment explanation
Indices: 713266--713383 Score: 89
Period size: 38 Copynumber: 3.1 Consensus size: 37
713256 ATAAAAATAT
* *
713266 ATATATATTAAATT-ATTTATGTAAAAATTTTATCAAAA
1 ATATATATTAAATTAATTTA--TATAAATTTTATTAAAA
* * * * * * *
713304 AGATATAAATAATTTTATTAAAAGTAAA-TTTAATAAAA
1 ATATAT-ATTAAATTAATTTATA-TAAATTTTATTAAAA
713342 ATATATATTAAATTAATTGTATATAAATTTTATT-AAA
1 ATATATATTAAATTAATT-TATATAAATTTTATTAAAA
713379 ATATA
1 ATATA
713384 AAAATTAGAA
Statistics
Matches: 60, Mismatches: 15, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
37 21 0.35
38 26 0.43
39 9 0.15
40 4 0.07
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (37 bp):
ATATATATTAAATTAATTTATATAAATTTTATTAAAA
Found at i:714138 original size:18 final size:20
Alignment explanation
Indices: 714100--714138 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
714090 AATTTTGAGT
*
714100 TATTAAAAATAGATCATATA
1 TATTAAAAATAGATAATATA
714120 TATTAAAAA-A-ATAATATA
1 TATTAAAAATAGATAATATA
714138 T
1 T
714139 TTATTCACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 1 0.06
20 9 0.50
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (20 bp):
TATTAAAAATAGATAATATA
Found at i:716661 original size:14 final size:14
Alignment explanation
Indices: 716639--716674 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
716629 TTAGTGAAAC
* *
716639 AAATCAAATAAAAT
1 AAATAAAATAAAAG
716653 AAATAAAATAAAAG
1 AAATAAAATAAAAG
716667 AAATAAAA
1 AAATAAAA
716675 AGAAGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (14 bp):
AAATAAAATAAAAG
Found at i:716703 original size:20 final size:20
Alignment explanation
Indices: 716657--716695 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
716647 TAAAATAAAT
*
716657 AAAATAAAAGAAATAAAAAG
1 AAAAAAAAAGAAATAAAAAG
* *
716677 AAGAAAAAATAAATAAAAA
1 AAAAAAAAAGAAATAAAAA
716696 ACAAAAAACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (20 bp):
AAAAAAAAAGAAATAAAAAG
Found at i:716909 original size:10 final size:9
Alignment explanation
Indices: 716888--716927 Score: 62
Period size: 10 Copynumber: 4.2 Consensus size: 9
716878 AAATGTCCCG
716888 AAAATAAAA
1 AAAATAAAA
716897 AAAATACAAA
1 AAAATA-AAA
716907 AAAATAAAAA
1 AAAAT-AAAA
716917 AAAATAAAA
1 AAAATAAAA
716926 AA
1 AA
716928 CCAAATAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 12 0.41
10 16 0.55
11 1 0.03
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAATAAAA
Found at i:716988 original size:17 final size:18
Alignment explanation
Indices: 716956--716992 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
716946 CTAGGGAAAC
*
716956 AAATCAAATCAAATAAAA
1 AAATAAAATCAAATAAAA
716974 AAATAAAAT-AAATAAAA
1 AAATAAAATCAAATAAAA
716991 AA
1 AA
716993 GAAGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.16
Consensus pattern (18 bp):
AAATAAAATCAAATAAAA
Found at i:717018 original size:27 final size:26
Alignment explanation
Indices: 716971--717029 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
716961 AAATCAAATA
* *
716971 AAAAAATAAAATAAATAAAAAAGAAG
1 AAAAAATAAAATAAAAAAAAAACAAG
*
716997 AAAAAAT-AAATAAAAAACAAAAACACG
1 AAAAAATAAAAT-AAAAA-AAAAACAAG
717024 AAAAAA
1 AAAAAA
717030 AGGAAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 4 0.14
26 11 0.39
27 13 0.46
ACGTcount: A:0.81, C:0.05, G:0.05, T:0.08
Consensus pattern (26 bp):
AAAAAATAAAATAAAAAAAAAACAAG
Found at i:717019 original size:17 final size:16
Alignment explanation
Indices: 716961--717013 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
716951 GAAACAAATC
716961 AAATCAAATAAAAAAATA
1 AAAT-AAATAAAAAAA-A
716979 AAATAAATAAAAAAGAA
1 AAATAAATAAAAAA-AA
716996 GAAA-AAATAAATAAAAA
1 -AAATAAATAAA-AAAAA
717013 A
1 A
717014 CAAAAACACG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 1 0.03
17 20 0.62
18 11 0.34
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (16 bp):
AAATAAATAAAAAAAA
Found at i:717046 original size:2 final size:2
Alignment explanation
Indices: 717041--717071 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
717031 GGAAAAAATA
717041 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
717072 ACCGTTAGGT
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:718006 original size:20 final size:20
Alignment explanation
Indices: 717981--718018 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
717971 CAATTTATTC
717981 ATTGGTGCATCGATGCATGT
1 ATTGGTGCATCGATGCATGT
*
718001 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
718019 CCCTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGT
Found at i:718368 original size:2 final size:2
Alignment explanation
Indices: 718363--718389 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
718353 GAATAAAGTA
718363 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 A
718390 AACATTAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:718430 original size:9 final size:9
Alignment explanation
Indices: 718412--718487 Score: 54
Period size: 9 Copynumber: 8.8 Consensus size: 9
718402 AAAAAGATAG
718412 TAAA-AAAA
1 TAAATAAAA
718420 TAAATAAAA
1 TAAATAAAA
**
718429 TAAATAAGG
1 TAAATAAAA
718438 TAAATAAAA
1 TAAATAAAA
*
718447 -AAATATAA
1 TAAATAAAA
718455 T-AATAATAA
1 TAAATAA-AA
*
718464 TAACA-AAAT
1 TAA-ATAAAA
718473 TAAA-AAAA
1 TAAATAAAA
*
718481 TATATAA
1 TAAATAA
718488 TAAAAATATA
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
8 22 0.42
9 27 0.51
10 3 0.06
11 1 0.02
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (9 bp):
TAAATAAAA
Found at i:718457 original size:31 final size:31
Alignment explanation
Indices: 718412--718495 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 31
718402 AAAAAGATAG
**
718412 TAAAAAAATA-AATAA-AATAAATAAGGTAAA-
1 TAAAAAAATATAATAATAAT-AATAA-CAAAAT
718442 TAAAAAAATATAATAATAATAATAACAAAAT
1 TAAAAAAATATAATAATAATAATAACAAAAT
*
718473 TAAAAAAATAT-ATAATAAAAATA
1 TAAAAAAATATAATAATAATAATA
718496 TATATATATA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
30 24 0.50
31 21 0.44
32 3 0.06
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.24
Consensus pattern (31 bp):
TAAAAAAATATAATAATAATAATAACAAAAT
Found at i:721310 original size:9 final size:9
Alignment explanation
Indices: 721292--721323 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
721282 CCTTATTTTC
*
721292 TTTTCTTTT
1 TTTTCCTTT
721301 TTTTCCTTT
1 TTTTCCTTT
721310 TTTTCCTTT
1 TTTTCCTTT
721319 TTTTC
1 TTTTC
721324 AATTTAGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTCCTTT
Found at i:721380 original size:8 final size:8
Alignment explanation
Indices: 721367--721401 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
721357 ACGTTCTTTC
721367 TTTTTCTT
1 TTTTTCTT
721375 TTTTTCTT
1 TTTTTCTT
**
721383 TTTTGATT
1 TTTTTCTT
721391 TTTTTCTT
1 TTTTTCTT
721399 TTT
1 TTT
721402 CGACTTAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.03, C:0.09, G:0.03, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:731905 original size:15 final size:15
Alignment explanation
Indices: 731824--731870 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
731814 GAAACAAATC
*
731824 AAATAAAATTAAAAA
1 AAATAAAAATAAAAA
731839 AAATAAAAGA-AAAAA
1 AAATAAAA-ATAAAAA
*
731854 AAACAATAAATAAAAA
1 AAATAA-AAATAAAAA
731870 A
1 A
731871 CAAAAACATG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 19 0.70
16 8 0.30
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (15 bp):
AAATAAAAATAAAAA
Found at i:731967 original size:3 final size:3
Alignment explanation
Indices: 731961--732038 Score: 142
Period size: 3 Copynumber: 26.7 Consensus size: 3
731951 GGAGAGAGAA
731961 AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
732008 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
732039 ACCACCTACC
Statistics
Matches: 73, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.05
3 69 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:732262 original size:17 final size:17
Alignment explanation
Indices: 732218--732259 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
732208 TAAAATGAGT
732218 TAAAAACAATAATAAGA
1 TAAAAACAATAATAAGA
*
732235 TAAAAACAATATTAAG-
1 TAAAAACAATAATAAGA
732251 TAAAAACAA
1 TAAAAACAA
732260 ATAAAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.69, C:0.07, G:0.05, T:0.19
Consensus pattern (17 bp):
TAAAAACAATAATAAGA
Found at i:732343 original size:17 final size:18
Alignment explanation
Indices: 732323--732364 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
732313 AGAAATAGTA
732323 AAAAATAAA-AAATAAAT
1 AAAAATAAATAAATAAAT
*
732340 -AAAATAAATAAATATAT
1 AAAAATAAATAAATAAAT
*
732357 AATAATAA
1 AAAAATAA
732365 TCATAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 8 0.38
17 7 0.33
18 6 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAATAAATAAATAAAT
Done.