Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 65
Found at i:3876740 original size:31 final size:31
Alignment explanation
Indices: 3876694--3876772 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
3876684 AAAGTTACTC
* *
3876694 AGGGCCACGGGGCCTACCCAAGAAAGATCTT
1 AGGGCCACAGAGCCTACCCAAGAAAGATCTT
*
3876725 GGGGCCACAGAGCCTACCCAAGAAAGATCTT
1 AGGGCCACAGAGCCTACCCAAGAAAGATCTT
*
3876756 AGGGCCTCAGAGCCTAC
1 AGGGCCACAGAGCCTAC
3876773 TCAAAGGTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.29, C:0.30, G:0.28, T:0.13
Consensus pattern (31 bp):
AGGGCCACAGAGCCTACCCAAGAAAGATCTT
Found at i:3877971 original size:63 final size:63
Alignment explanation
Indices: 3877894--3878026 Score: 144
Period size: 63 Copynumber: 2.1 Consensus size: 63
3877884 AATGTGTATT
* * * *
3877894 GATGCACTCTTTAAAGAAG-AAACATCGAATGCAATTAGTGCATCGATGCATAAGG-AGTGCATC
1 GATGCACCCCTTAAA-AAGAAAACATCGAAGGCAATTAGTGCATCGATGCAT-AGGTAATGCATC
* ** * * *
3877957 GATGCACCCCTTAAAATGAAAACATCGAAGGTGATTGGTGTATCGATGCATGGGTAATGCATC
1 GATGCACCCCTTAAAAAGAAAACATCGAAGGCAATTAGTGCATCGATGCATAGGTAATGCATC
3878020 GATGCAC
1 GATGCAC
3878027 TGTAGAATGT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
62 4 0.07
63 54 0.93
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (63 bp):
GATGCACCCCTTAAAAAGAAAACATCGAAGGCAATTAGTGCATCGATGCATAGGTAATGCATC
Found at i:3881610 original size:15 final size:15
Alignment explanation
Indices: 3881592--3881620 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3881582 CGCTTCTTCC
3881592 CCCTTTTTCTCTTTT
1 CCCTTTTTCTCTTTT
3881607 CCCTTTTTCTCTTT
1 CCCTTTTTCTCTTT
3881621 GCAGCAGTCC
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:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (15 bp):
CCCTTTTTCTCTTTT
Found at i:3883688 original size:27 final size:27
Alignment explanation
Indices: 3883653--3883714 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
3883643 ATATTACTAT
3883653 AACCGAATTAACTGGTTAAGCCATCTA
1 AACCGAATTAACTGGTTAAGCCATCTA
*
3883680 AACTGAATTAACTGGTTAAGCCATCTA
1 AACCGAATTAACTGGTTAAGCCATCTA
3883707 AACCGAAT
1 AACCGAAT
3883715 ATATTGAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.26
Consensus pattern (27 bp):
AACCGAATTAACTGGTTAAGCCATCTA
Found at i:3885448 original size:2 final size:2
Alignment explanation
Indices: 3885441--3885469 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3885431 TCAATCTACA
3885441 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 A
3885470 ATTTACGAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3885589 original size:85 final size:86
Alignment explanation
Indices: 3885489--3885667 Score: 213
Period size: 85 Copynumber: 2.1 Consensus size: 86
3885479 ATACATTCAC
** * * *
3885489 GACACA-AGAATGTGTGTCAT-TTTTTTTAATGATGTGTGCTTCAATGACACGCAATGTA-AGTC
1 GACACACAGAATGTGTGTCATCTTCATTT-ATGACGGGGGCTTCAATGACACGCAATG-AGAGTC
* *
3885551 ATACATGCGTGTCATAAATTTAT
64 ATAAATGCGCGTCATAAATTTAT
** *
3885574 GACACACA-AATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACGTGCAATGAGTGTCAT
1 GACACACAGAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGAGAGTCAT
3885638 AAATGCGCGTCATAAATTTAT
66 AAATGCGCGTCATAAATTTAT
*
3885659 GACGCACAG
1 GACACACAG
3885668 TTACGCGTCA
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
84 1 0.01
85 72 0.91
86 6 0.08
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (86 bp):
GACACACAGAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGAGAGTCAT
AAATGCGCGTCATAAATTTAT
Found at i:3888271 original size:25 final size:23
Alignment explanation
Indices: 3888227--3888276 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3888217 CGGGACATAC
*
3888227 AGTGATCCTTCGGGATATTTCAT
1 AGTGATCCTTCGGGAAATTTCAT
*
3888250 AGTGGTCCTTCGGGACAAATTTCAT
1 AGTGATCCTTCGGG--AAATTTCAT
3888275 AG
1 AG
3888277 CCCCTAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 13 0.57
25 10 0.43
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (23 bp):
AGTGATCCTTCGGGAAATTTCAT
Found at i:3891857 original size:2 final size:2
Alignment explanation
Indices: 3891852--3891881 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3891842 TGTGTGTGTG
3891852 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3891882 GCTTTGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3895113 original size:16 final size:16
Alignment explanation
Indices: 3895092--3895123 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3895082 CAATTATGTC
3895092 AATTTAAACTATCAAT
1 AATTTAAACTATCAAT
3895108 AATTTAAACTATCAAT
1 AATTTAAACTATCAAT
3895124 GCATACAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTTAAACTATCAAT
Found at i:3900677 original size:14 final size:14
Alignment explanation
Indices: 3900658--3900696 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
3900648 AAAATAAATT
3900658 ACATTTTATGGAAA
1 ACATTTTATGGAAA
*
3900672 ACA-TTTACTTGAAA
1 ACATTTTA-TGGAAA
3900686 ACATTTTATGG
1 ACATTTTATGG
3900697 TGTTTGGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
13 4 0.19
14 13 0.62
15 4 0.19
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (14 bp):
ACATTTTATGGAAA
Found at i:3900812 original size:25 final size:25
Alignment explanation
Indices: 3900764--3900843 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
3900754 TTATTACAAA
3900764 TATTAAATAAAATAAATAATATTATT
1 TATTAAA-AAAATAAATAATATTATT
* * *
3900790 TATTAAAAAAGTTAATATTATTATT
1 TATTAAAAAAATAAATAATATTATT
* *
3900815 T-TTAAAATATTAGAATAAT-TTATT
1 TATTAAAAAAATA-AATAATATTATT
3900839 TATTA
1 TATTA
3900844 TTATTTAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
24 14 0.31
25 24 0.53
26 7 0.16
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (25 bp):
TATTAAAAAAATAAATAATATTATT
Found at i:3900858 original size:17 final size:17
Alignment explanation
Indices: 3900803--3900859 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
3900793 TAAAAAAGTT
3900803 AATATTATTATT-TTTAA
1 AATATTATTATTATTT-A
** *
3900820 AATATTAGAATAATTT-
1 AATATTATTATTATTTA
3900836 -AT-TTATTATTATTTA
1 AATATTATTATTATTTA
3900851 AATATTATT
1 AATATTATT
3900860 TCTATAATTC
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
14 9 0.30
15 2 0.07
16 2 0.07
17 14 0.47
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
AATATTATTATTATTTA
Found at i:3901615 original size:23 final size:23
Alignment explanation
Indices: 3901566--3901634 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
3901556 GTATCGTATT
* * * * *
3901566 ATATTTTAAAAAGAATTAATAAT
1 ATATTTTAAATATATTTATTAAA
3901589 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
*
3901612 ATATTATTAGAT-TATTTTATTAA
1 ATATT-TTAAATATA-TTTATTAA
3901635 TATTAAATAC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
23 25 0.66
24 13 0.34
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:3901851 original size:21 final size:21
Alignment explanation
Indices: 3901793--3901853 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
3901783 AGTATTTTAT
**
3901793 TATAATATTAAAAAATA-TAA
1 TATAATATTATTAAATATTAA
3901813 TATAATATTATTAGAATATTAA
1 TATAATATTATTA-AATATTAA
*
3901835 TA-AATATATTTTAAATATT
1 TATAATAT-TATTAAATATT
3901854 TTCATAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 11 0.31
21 15 0.43
22 9 0.26
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TATAATATTATTAAATATTAA
Found at i:3902046 original size:612 final size:606
Alignment explanation
Indices: 3900889--3902107 Score: 2158
Period size: 612 Copynumber: 2.0 Consensus size: 606
3900879 AATATTAATA
3900889 TTAGTACATTTTATTGAAATAAAAATGTTATAAATTATATTAATTATTTATTAAATTAATAGTAT
1 TTAGTACATTTTATTGAAATAAAAATGTTATAAATTATATTAATTATTTATTAAATTAATAGTAT
* *
3900954 CGTATTATATTTTAAAAAGAATTAATAATATATTATCTTTATTAAAATTCTATTATATTATTTTA
66 CGTATTATATTTTAAAAAGAATTAATAATATATTATATTTATTAAAATTCTATTAGATTATTTTA
3901019 TTAATATTAAATACATAAATAATATTATTCATTATTAATAATTTAATAATATTATTTCTATGAAA
131 TTAATATTAAATACATAAATAATATTATTCATTATTAATAATTTAATAATATTATTTCTATGAAA
3901084 ATTAATAAATAATATAAATTTTATTAATATTTTATTATATAATATTAAAATAAAAATATAATATC
196 ATTAATAAATAATATAAATTTTATTAATATTTTATTATATAATATTAAAATAAAAATATAATATC
3901149 TTATATTATTATAATATAATTGAGTATTTTATTATAATATTAAAAAAATAATATAATATTATTAG
261 TTATATTATTATAATATAATTGAGTATTTTATTATAATATTAAAAAAATAATATAATATTATTAG
*
3901214 AATATTAATAAATATATTTTAAATATTTTAATAATTAATATTTTGATTAAAATTATATTAAAATA
326 AATATTAATAAATATATTTTAAATATTTTAATAATTAATATTTTGATTAAAATGATATTAAAATA
* * *
3901279 TTTTATTAATTTTAAATTTATAAAATAAAATTGTTTTGAATATTTATTTTTTGAAGAGAAAAGTT
391 TTTTATTAATTTTAAATTTATAAAATAAAATTATTTTGAATATTTATTTTTTGAAGAAAAAAATT
*
3901344 CGGAAAATGACTTACGAAAAATTAGACTGTAAGTCATTTTCCAGAAAACACAAAGGAAATTCTGT
456 CGGAAAATGACTTACGAAAAATCAGACTGTAAGTCATTTTCCAGAAAACACAAAGGAAATTCTGT
* *
3901409 TGAGCAGGAAATATTTTAAGTTGACCAACTAGTTTTCCTCCGACCAAACACTGGAAAAT-GGAAA
521 TGAGCAGGAAATATTTTAAGTTGACCAACTAGTTTTCCTCCAACCAAACACTGAAAAATAGG-AA
3901473 AAACGTTTTCAAAAAAATGTTT
585 AAACGTTTTCAAAAAAATGTTT
*
3901495 TTAGTACATTTTATTGAAATAAAAATGTTATAAATTATATTTATTATTTATTACAA-TAATAGTA
1 TTAGTACATTTTATTGAAATAAAAATGTTATAAATTATATTAATTATTTATTA-AATTAATAGTA
3901559 TCGTATTATATTTTAAAAAGAATTAATAATATATTTTAAATATATTTATTAAAATAT-TATTAGA
65 TCGTATTATATTTTAAAAAGAATTAATAATATA---T---TATATTTATTAAAAT-TCTATTAGA
3901623 TTATTTTATTAATATTAAATACATAAATAATATTATTCATTATTAATAATTTAATAATATTATTT
123 TTATTTTATTAATATTAAATACATAAATAATATTATTCATTATTAATAATTTAATAATATTATTT
*
3901688 CTATGAAAATTAATAAATAATATAAATTTTATTAATATTTTATTATATAATATTAAACTAAAAAT
188 CTATGAAAATTAATAAATAATATAAATTTTATTAATATTTTATTATATAATATTAAAATAAAAAT
3901753 ATAATATCTTATATTATTATAATATAATTGAGTATTTTATTATAATATTAAAAAATATAATATAA
253 ATAATATCTTATATTATTATAATATAATTGAGTATTTTATTATAATATTAAAAAA-ATAATATAA
*
3901818 TATTATTAGAATATTAATAAATATATTTTAAATATTTTCATAATTAATATTTTGATTAAAATGAT
317 TATTATTAGAATATTAATAAATATATTTTAAATATTTTAATAATTAATATTTTGATTAAAATGAT
*
3901883 ATTAAAATATTTTATTAATTTTAAATTTATGAAATAAAATTATTTTGAATATTTATTTTTTGAAG
382 ATTAAAATATTTTATTAATTTTAAATTTATAAAATAAAATTATTTTGAATATTTATTTTTTGAAG
3901948 AAAAAAATTCGGAAAATGACTTACG-AAAATCAGACTGTAAGTCATTTTCCAGAAAACACAAAGG
447 AAAAAAATTCGGAAAATGACTTACGAAAAATCAGACTGTAAGTCATTTTCCAGAAAACACAAAGG
* *
3902012 AAATTCTGTTGAGCATGAAATATTTTAAGTTGACCAACTAGTTTTCTTCCAACCAAACACTGAAA
512 AAATTCTGTTGAGCAGGAAATATTTTAAGTTGACCAACTAGTTTTCCTCCAACCAAACACTGAAA
* * *
3902077 AATAGGGAAAACGTTTTCCAAAAATTGTTT
577 AATAGGAAAAACGTTTTCAAAAAAATGTTT
3902107 T
1 T
3902108 ATGTAAAACA
Statistics
Matches: 585, Mismatches: 18, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
606 93 0.16
607 2 0.00
609 1 0.00
612 328 0.56
613 161 0.28
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (606 bp):
TTAGTACATTTTATTGAAATAAAAATGTTATAAATTATATTAATTATTTATTAAATTAATAGTAT
CGTATTATATTTTAAAAAGAATTAATAATATATTATATTTATTAAAATTCTATTAGATTATTTTA
TTAATATTAAATACATAAATAATATTATTCATTATTAATAATTTAATAATATTATTTCTATGAAA
ATTAATAAATAATATAAATTTTATTAATATTTTATTATATAATATTAAAATAAAAATATAATATC
TTATATTATTATAATATAATTGAGTATTTTATTATAATATTAAAAAAATAATATAATATTATTAG
AATATTAATAAATATATTTTAAATATTTTAATAATTAATATTTTGATTAAAATGATATTAAAATA
TTTTATTAATTTTAAATTTATAAAATAAAATTATTTTGAATATTTATTTTTTGAAGAAAAAAATT
CGGAAAATGACTTACGAAAAATCAGACTGTAAGTCATTTTCCAGAAAACACAAAGGAAATTCTGT
TGAGCAGGAAATATTTTAAGTTGACCAACTAGTTTTCCTCCAACCAAACACTGAAAAATAGGAAA
AACGTTTTCAAAAAAATGTTT
Found at i:3906031 original size:27 final size:27
Alignment explanation
Indices: 3906001--3906064 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
3905991 TATTATTTAT
3906001 ATTATTATTATTATAATAATAATAATA
1 ATTATTATTATTATAATAATAATAATA
** * *
3906028 ATTATTATTATTATTTTATTATTAATA
1 ATTATTATTATTATAATAATAATAATA
*
3906055 AATATTATTA
1 ATTATTATTA
3906065 CAGGCCCAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
ATTATTATTATTATAATAATAATAATA
Found at i:3906064 original size:3 final size:3
Alignment explanation
Indices: 3905991--3906051 Score: 54
Period size: 3 Copynumber: 20.7 Consensus size: 3
3905981 TTCATTTGAA
* * * * *
3905991 TAT TAT T-T ATAT TAT TAT TAT TAT AAT AAT AAT AAT AAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3906036 TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TA
3906052 ATAAATATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 3 0.06
3 49 0.92
4 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:3907628 original size:112 final size:109
Alignment explanation
Indices: 3907449--3907652 Score: 259
Period size: 112 Copynumber: 1.8 Consensus size: 109
3907439 TATTTTAATC
* * * *
3907449 ATGTTTTAATATTTATTTATTTTTCAATATTAAGAAAGGGCAGTCTTAAAACAACTGGATGTCCA
1 ATGTTTTAATATTTATTTATTTTTCAATATAAAGAAAGAGCAGTCTTAAAACAACTAGAAGTCCA
3907514 TTTTCTAAATATTT-TAAATAAATAAATATCCTATTTTTTAAAAA
66 TTTTCT-AATATTTCTAAATAAATAAATATCCTATTTTTTAAAAA
* * ** *
3907558 ATGTTTTAATTATTTATTTATTTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAG
1 ATGTTTTAA-TATTTATTTA-TTTTTCAATAT-AAAG-AAAGAGCAGTCTTAAAACAACTAGAAG
*
3907623 T-CATTTTCTGATATTTCTAAATAAATAAAT
62 TCCATTTTCTAATATTTCTAAATAAATAAAT
3907653 TTATTTTTTA
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
109 9 0.11
110 10 0.12
111 16 0.20
112 24 0.30
113 21 0.26
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.43
Consensus pattern (109 bp):
ATGTTTTAATATTTATTTATTTTTCAATATAAAGAAAGAGCAGTCTTAAAACAACTAGAAGTCCA
TTTTCTAATATTTCTAAATAAATAAATATCCTATTTTTTAAAAA
Found at i:3908260 original size:33 final size:33
Alignment explanation
Indices: 3908184--3908267 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 33
3908174 TTCAAATTTT
* *
3908184 TTTATATATA-TACTTA--TTATTTTCATAGTA
1 TTTATATATATTATTTATTTTATTTGCATAGTA
3908214 TTTATATATATTATTTCATTTTATTTGCA-AGTA
1 TTTATATATATTATTT-ATTTTATTTGCATAGTA
*
3908247 TTT-TATTTCATTATTTATTTT
1 TTTATATAT-ATTATTTATTTT
3908268 TCTGTTAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
30 10 0.22
31 4 0.09
32 10 0.22
33 14 0.30
34 8 0.17
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.62
Consensus pattern (33 bp):
TTTATATATATTATTTATTTTATTTGCATAGTA
Found at i:3911564 original size:15 final size:15
Alignment explanation
Indices: 3911518--3911556 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
3911508 GATCAATACC
3911518 TTTTGCATAAATGCA
1 TTTTGCATAAATGCA
3911533 TTTTGCATAAATGCA
1 TTTTGCATAAATGCA
3911548 TTTTGCATA
1 TTTTGCATA
3911557 CATTCATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (15 bp):
TTTTGCATAAATGCA
Found at i:3915366 original size:8 final size:9
Alignment explanation
Indices: 3915339--3915369 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3915329 AAATGGCAAT
3915339 CATTCTTTA
1 CATTCTTTA
3915348 CATTCTTTA
1 CATTCTTTA
3915357 CATT-TTTA
1 CATTCTTTA
3915365 CATTC
1 CATTC
3915370 ATTATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (9 bp):
CATTCTTTA
Found at i:3918894 original size:10 final size:10
Alignment explanation
Indices: 3918879--3918920 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
3918869 TATGCTTGAA
3918879 GAAAAAAAAG
1 GAAAAAAAAG
3918889 GAAAAAAAAG
1 GAAAAAAAAG
3918899 AGAAAAAAGAA-
1 -GAAAAAA-AAG
3918910 GAAGAAAAAAG
1 GAA-AAAAAAG
3918921 AAGGGTCAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 15 0.54
11 11 0.39
12 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAG
Found at i:3918917 original size:22 final size:21
Alignment explanation
Indices: 3918878--3918921 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
3918868 TTATGCTTGA
3918878 AGAAAAAAAAGGAAAAAAAAG
1 AGAAAAAAAAGGAAAAAAAAG
3918899 AGAAAAAAGAA-GAAGAAAAAAG
1 AGAAAAAA-AAGGAA-AAAAAAG
3918921 A
1 A
3918922 AGGGTCAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AGAAAAAAAAGGAAAAAAAAG
Found at i:3920654 original size:113 final size:112
Alignment explanation
Indices: 3920442--3920734 Score: 426
Period size: 113 Copynumber: 2.6 Consensus size: 112
3920432 TAGCAAAGAT
*
3920442 TCAAATCCATCAC-AATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCCATCACTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
*
3920506 GAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
3920553 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCAC-TGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
3920618 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * ** * ** **
3920666 TTAAATTCATCACTCGGTGGATCAACAATGCCAGTTAGTGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACT-GATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
3920731 AGAA
65 AGAA
3920735 CTTGTTCAAC
Statistics
Matches: 163, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
111 13 0.08
112 1 0.01
113 149 0.91
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (112 bp):
TCAAATCCATCACTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:3920788 original size:86 final size:86
Alignment explanation
Indices: 3920643--3920820 Score: 329
Period size: 86 Copynumber: 2.1 Consensus size: 86
3920633 TTCATAATGA
*
3920643 GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAACAATGCCAGTTAGTGTT
1 GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAACAATGCCAGTTAGAGTT
3920708 CATAATGAGAAGAACTCATCT
66 CATAATGAGAAGAACTCATCT
*
3920729 GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAGCAATGCCAGTTAGAGTT
1 GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAACAATGCCAGTTAGAGTT
*
3920794 CATAATGGGAAGAACTCATCT
66 CATAATGAGAAGAACTCATCT
3920815 GAAGAA
1 GAAGAA
3920821 GGAAGAAGAA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 89 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (86 bp):
GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAACAATGCCAGTTAGAGTT
CATAATGAGAAGAACTCATCT
Found at i:3920846 original size:113 final size:113
Alignment explanation
Indices: 3920729--3920977 Score: 327
Period size: 113 Copynumber: 2.2 Consensus size: 113
3920719 GAACTCATCT
* * * * ** *
3920729 GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAGCAATGCCAGTTAGAGTT
1 GAAGAATTTGTTCAACATTTTGCTTAAATTCATCACTCGATGGATCAACAATGCCAGAGAAAGTT
* *
3920794 CATAATGGGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
66 CATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCATAATGA
* ** *
3920842 GAAGAATTTGTTCAACATTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTT
1 GAAGAATTTGTTCAACATTTTGCTTAAATTCATCACTCGATGGATCAACAATGCCAGAGAAAGTT
* **
3920907 CATAATGAGAAGAATTCATCTGAAGAAGAAAGAAGATGTTCATAATGA
66 CATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCATAATGA
* * *
3920955 GAAGAGTTTGTTCGACCTTTTGC
1 GAAGAATTTGTTCAACATTTTGC
3920978 ATGACTCTAT
Statistics
Matches: 117, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
113 117 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (113 bp):
GAAGAATTTGTTCAACATTTTGCTTAAATTCATCACTCGATGGATCAACAATGCCAGAGAAAGTT
CATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCATAATGA
Found at i:3920876 original size:199 final size:199
Alignment explanation
Indices: 3920530--3920933 Score: 574
Period size: 199 Copynumber: 2.0 Consensus size: 199
3920520 TTCATAATGA
* * ** *
3920530 GAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTT
1 GAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAGCAATGCCAGAGAAAGTT
* *
3920595 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACT
66 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACA
* ** **
3920660 TTTTGCTTAAATTCATCACTCGGTGGATCAACAATGCCAGTTAGTGTTCATAATGAGAAGAACTC
131 TTTTGCTTAAATTCATCACTCGATGGATCAACAATGCCAGAGAAAGTTCATAATGAGAAGAACTC
3920725 ATCT
196 ATCT
* * * * ** *
3920729 GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAGCAATGCCAGTTAGAGTT
1 GAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAGCAATGCCAGAGAAAGTT
* *
3920794 CATAATGGGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACA
66 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACA
* ** * *
3920859 TTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAATTC
131 TTTTGCTTAAATTCATCACTCGATGGATCAACAATGCCAGAGAAAGTTCATAATGAGAAGAACTC
3920924 ATCT
196 ATCT
3920928 GAAGAA
1 GAAGAA
3920934 GAAAGAAGAT
Statistics
Matches: 179, Mismatches: 26, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
199 179 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (199 bp):
GAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAGCAATGCCAGAGAAAGTT
CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACA
TTTTGCTTAAATTCATCACTCGATGGATCAACAATGCCAGAGAAAGTTCATAATGAGAAGAACTC
ATCT
Found at i:3921367 original size:36 final size:36
Alignment explanation
Indices: 3921318--3921394 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
3921308 TTCATTTGAA
*
3921318 TATTATTTATATTATTATAATAATAATAATAATTAT
1 TATTATTTATATTATTATAATAATAATAATAAATAT
** * *
3921354 TATTA-TTATTATTATTATTTTATTATTAATAAATAT
1 TATTATTTA-TATTATTATAATAATAATAATAAATAT
3921390 TATTA
1 TATTA
3921395 CAGGCCCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 3 0.09
36 32 0.91
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (36 bp):
TATTATTTATATTATTATAATAATAATAATAAATAT
Found at i:3921394 original size:3 final size:3
Alignment explanation
Indices: 3921318--3921381 Score: 60
Period size: 3 Copynumber: 21.7 Consensus size: 3
3921308 TTCATTTGAA
* * * * *
3921318 TAT TAT T-T ATAT TAT TAT AAT AAT AAT AAT AAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3921363 TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
3921382 ATAAATATTA
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 3 0.05
3 52 0.93
4 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:3924894 original size:3 final size:3
Alignment explanation
Indices: 3924880--3924936 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
3924870 GGGTCTTTTC
* * *
3924880 TAT TAT TTT TAT TAT TAT TAT TAT TTT TAT TAT TAT TTT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3924928 TAT TAT TAT
1 TAT TAT TAT
3924937 AAATTACATT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:3925228 original size:22 final size:22
Alignment explanation
Indices: 3925200--3925242 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3925190 ATCAACTCAG
3925200 CCGTTTGGCCTTCCAGCTCCAA
1 CCGTTTGGCCTTCCAGCTCCAA
3925222 CCGTTTGGCCTTCCAGCTCCA
1 CCGTTTGGCCTTCCAGCTCCA
3925243 GCCGCCAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.12, C:0.42, G:0.19, T:0.28
Consensus pattern (22 bp):
CCGTTTGGCCTTCCAGCTCCAA
Found at i:3938042 original size:12 final size:12
Alignment explanation
Indices: 3938005--3938059 Score: 67
Period size: 12 Copynumber: 4.6 Consensus size: 12
3937995 AAATGAATGA
*
3938005 AAAAAGAAGAAAG
1 AAAAA-AAGAGAG
* *
3938018 GAAAAAA-ACAG
1 AAAAAAAGAGAG
3938029 AAAAAAAGAGAG
1 AAAAAAAGAGAG
3938041 AAAAAAAGAGAG
1 AAAAAAAGAGAG
3938053 AAAAAAA
1 AAAAAAA
3938060 AGAAGAAGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 9 0.24
12 24 0.65
13 4 0.11
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAGAG
Found at i:3938066 original size:12 final size:12
Alignment explanation
Indices: 3938004--3938076 Score: 60
Period size: 12 Copynumber: 5.8 Consensus size: 12
3937994 AAAATGAATG
3938004 AAAAAAGAAGAA
1 AAAAAAGAAGAA
*
3938016 AGGAAAAA-AACAGA
1 A--AAAAAGAAGA-A
3938030 AAAAAAG-AGAGA
1 AAAAAAGAAGA-A
3938042 AAAAAAGAGAGAA
1 AAAAAAGA-AGAA
3938055 AAAAAAGAAGAA
1 AAAAAAGAAGAA
*
3938067 GGAAAAAGAA
1 -AAAAAAGAA
3938077 AAATAAATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
12 21 0.41
13 20 0.39
14 10 0.20
ACGTcount: A:0.77, C:0.01, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAGAA
Found at i:3938074 original size:26 final size:25
Alignment explanation
Indices: 3938004--3938075 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 25
3937994 AAAATGAATG
*
3938004 AAAAAAGAAGAAAGGAAAAAAACAGA
1 AAAAAAGAAG-AAGGAAAAAGACAGA
*
3938030 AAAAAAGAGAGAA--AAAAAGAGAGAA
1 AAAAAAGA-AGAAGGAAAAAGACAG-A
3938055 AAAAAAGAAGAAGGAAAAAGA
1 AAAAAAGAAGAAGGAAAAAGA
3938076 AAAATAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
24 12 0.30
25 9 0.22
26 17 0.43
27 2 0.05
ACGTcount: A:0.76, C:0.01, G:0.22, T:0.00
Consensus pattern (25 bp):
AAAAAAGAAGAAGGAAAAAGACAGA
Found at i:3939198 original size:47 final size:45
Alignment explanation
Indices: 3939146--3939393 Score: 164
Period size: 43 Copynumber: 5.4 Consensus size: 45
3939136 CCAGAATTCT
*
3939146 TCATCACGTACGAACCGTGTCATCTGCCCTTAGATGACCAGACCTCC
1 TCATCACGTAGGAACCGTGTCA-CT-CCCTTAGATGACCAGACCTCC
* * * * *
3939193 TCATCAGGTAGGAGCCGTGTCA--CCCTTAGATAATC-GGCCGTCC
1 TCATCACGTAGGAACCGTGTCACTCCCTTAGATGACCAGACC-TCC
* * * * * ** *
3939236 TCATCACGTATGAACCGAGTTATCACCTTTCCTAAAGATGGCCAGAATTCT
1 TCATCACGTAGGAACC--G-TGTCA-C-TCCCT-TAGATGACCAGACCTCC
* *
3939287 TCATCACGTATGAACCGTGTCATCTGCCCTTAGATGACCAAACCTCC
1 TCATCACGTAGGAACCGTGTCA-CT-CCCTTAGATGACCAGACCTCC
* * * * * *
3939334 TCATCAGGTAGGAGCCGTGTCA--CCCTTAGATAATCAGTCGTCC
1 TCATCACGTAGGAACCGTGTCACTCCCTTAGATGACCAGACCTCC
3939377 TCATCACGTAGGAACCG
1 TCATCACGTAGGAACCG
3939394 AGTTATCACC
Statistics
Matches: 152, Mismatches: 38, Indels: 26
0.70 0.18 0.12
Matches are distributed among these distances:
42 3 0.02
43 58 0.38
45 1 0.01
46 4 0.03
47 50 0.33
48 8 0.05
49 1 0.01
50 3 0.02
51 23 0.15
52 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (45 bp):
TCATCACGTAGGAACCGTGTCACTCCCTTAGATGACCAGACCTCC
Found at i:3939258 original size:141 final size:141
Alignment explanation
Indices: 3939080--3939451 Score: 645
Period size: 141 Copynumber: 2.6 Consensus size: 141
3939070 TCAACATTAG
*
3939080 GATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCTTTCCTAAAGATGGCCAGAATTC
1 GATAATCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCTTTCCTAAAGATGGCCAGAATTC
* *
3939145 TTCATCACGTACGAACCGTGTCATCTGCCCTTAGATGACCAGACCTCCTCATCAGGTAGGAGCCG
66 TTCATCACGTATGAACCGTGTCATCTGCCCTTAGATGACCAAACCTCCTCATCAGGTAGGAGCCG
3939210 TGTCACCCTTA
131 TGTCACCCTTA
* *
3939221 GATAATCGGCCGTCCTCATCACGTATGAACCGAGTTATCACCTTTCCTAAAGATGGCCAGAATTC
1 GATAATCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCTTTCCTAAAGATGGCCAGAATTC
3939286 TTCATCACGTATGAACCGTGTCATCTGCCCTTAGATGACCAAACCTCCTCATCAGGTAGGAGCCG
66 TTCATCACGTATGAACCGTGTCATCTGCCCTTAGATGACCAAACCTCCTCATCAGGTAGGAGCCG
3939351 TGTCACCCTTA
131 TGTCACCCTTA
* * *
3939362 GATAATCAGTCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGACTTC
1 GATAATCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCTTTCCTAAAGATGGCCAGAATTC
* * *
3939427 TTCATCGCGTATGAGCAGTGTCATC
66 TTCATCACGTATGAACCGTGTCATC
3939452 CCCAACAACA
Statistics
Matches: 218, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
141 218 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (141 bp):
GATAATCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCTTTCCTAAAGATGGCCAGAATTC
TTCATCACGTATGAACCGTGTCATCTGCCCTTAGATGACCAAACCTCCTCATCAGGTAGGAGCCG
TGTCACCCTTA
Found at i:3939604 original size:3 final size:3
Alignment explanation
Indices: 3939598--3939669 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
3939588 GGGTCTTTTC
*
3939598 TAT TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3939646 TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
3939670 AAATTACATT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3939962 original size:22 final size:22
Alignment explanation
Indices: 3939931--3939979 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
3939921 ATCATCAACT
*
3939931 CAGCCGTTTGGCCTTCCAGCTC
1 CAGCCATTTGGCCTTCCAGCTC
3939953 CAGCCATTTGGCCTTCCAGCTC
1 CAGCCATTTGGCCTTCCAGCTC
3939975 CAGCC
1 CAGCC
3939980 GCCAACCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.12, C:0.43, G:0.20, T:0.24
Consensus pattern (22 bp):
CAGCCATTTGGCCTTCCAGCTC
Found at i:3941209 original size:12 final size:13
Alignment explanation
Indices: 3941184--3941216 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3941174 GTTGTTTTTA
*
3941184 TTTATTTATTTAT
1 TTTATTTATATAT
3941197 TTTATTTA-ATAT
1 TTTATTTATATAT
3941209 TTTATTTA
1 TTTATTTA
3941217 GTATGAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTATTTATATAT
Found at i:3945836 original size:20 final size:19
Alignment explanation
Indices: 3945811--3945864 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
3945801 ACGAAATAAA
3945811 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
3945831 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
3945851 AATCGCAACGCGAT
1 AATCGCAACGCGAT
3945865 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:3945926 original size:21 final size:21
Alignment explanation
Indices: 3945811--3945926 Score: 67
Period size: 21 Copynumber: 5.6 Consensus size: 21
3945801 ACGAAATAAA
*
3945811 AATCGCAACGCGA-TCTCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
3945831 AATCGCAAATC-AGTTCCCAG
1 AATCGCAACGCGATTTTCCAG
* **
3945851 AATCGCAACGCGATTATGAAG
1 AATCGCAACGCGATTTTCCAG
* ** *
3945872 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
* **
3945892 AATTCGTATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
3945914 AATCGCAACGCGA
1 AATCGCAACGCGA
3945927 ATATGAAAAT
Statistics
Matches: 68, Mismatches: 24, Indels: 7
0.69 0.24 0.07
Matches are distributed among these distances:
19 1 0.01
20 25 0.37
21 40 0.59
22 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:3945939 original size:20 final size:20
Alignment explanation
Indices: 3945914--3946389 Score: 213
Period size: 20 Copynumber: 23.5 Consensus size: 20
3945904 GATTTTCCAG
* *
3945914 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* * **
3945934 AATCGCAACGTGAACATATA
1 AATCGCAACGCGAATACGTA
* * *
3945954 AATCACAACACGAGTATCCGTAA
1 AATCGCAACGCGA--ATACGT-A
*
3945977 AATCAG-AACGC-ATATCCGTA
1 AATC-GCAACGCGA-ATACGTA
3945997 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
3946018 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
* *
3946038 AATCACAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
*
3946058 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
*
3946078 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
3946098 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
* *
3946118 AATCGCAATGAC-AATATGTAA
1 AATCGCAACG-CGAATACGT-A
* *
3946139 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
3946159 AATCGCAACGCG-AT-CGATA
1 AATCGCAACGCGAATACG-TA
* *
3946178 ATTCGCAACGCGATATCCG-A
1 AATCGCAACGCGA-ATACGTA
* ** * * *
3946198 TATCGCAAATC-AGTTTC-CA
1 AATCGCAACGCGA-ATACGTA
* *
3946217 GATTCGCAACGCG-ATTC-TGA
1 -AATCGCAACGCGAATACGT-A
* ** * * **
3946237 CTATCGCATTGCGATTTCCCA
1 -AATCGCAACGCGAATACGTA
*** * * *
3946258 AATTCGCGTTGCGATTTTCCTA
1 AA-TCGCAACGCGA-ATACGTA
*
3946280 ATTCGCAACGCGAATACGTA
1 AATCGCAACGCGAATACGTA
*
3946300 AATCGCAACGCGATTACGTA
1 AATCGCAACGCGAATACGTA
*
3946320 AATCGCAACACGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
3946340 AATCGCAATGTGATTACGTA
1 AATCGCAACGCGAATACGTA
*
3946360 AATCGCAATGCGAAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
3946380 AATCGCAACG
1 AATCGCAACG
3946390 AGATTCAGAC
Statistics
Matches: 352, Mismatches: 78, Indels: 52
0.73 0.16 0.11
Matches are distributed among these distances:
18 2 0.01
19 25 0.07
20 239 0.68
21 65 0.18
22 12 0.03
23 9 0.03
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:3946072 original size:40 final size:41
Alignment explanation
Indices: 3945963--3946205 Score: 293
Period size: 40 Copynumber: 6.0 Consensus size: 41
3945953 AAATCACAAC
* * *
3945963 ACGAGTATCCGTAAAATCAG-AACGCATATCCGTAAATCGCA
1 ACGAGAATACGTAAAATC-GCAACGCGTATCCGTAAATCGCA
* *
3946004 ACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCACA
1 ACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCA
*
3946045 ACGAGAATACGT-AAATCGCAACGCGTATCTGTAAATCGCA
1 ACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCA
*
3946085 ACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATCGCA
1 ACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCA
* * *
3946125 ATGACAATATGTAAAATCGCAACGCGTATCCGTAAATCGCA
1 ACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCA
* * *
3946166 ACGCG-AT-CG-ATAATTCGCAACGCGATATCCG-ATATCGCA
1 ACGAGAATACGTA-AAATCGCAACGCG-TATCCGTAAATCGCA
3946205 A
1 A
3946206 ATCAGTTTCC
Statistics
Matches: 178, Mismatches: 20, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 21 0.12
40 82 0.46
41 74 0.42
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (41 bp):
ACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCA
Found at i:3946195 original size:81 final size:80
Alignment explanation
Indices: 3945972--3946205 Score: 287
Period size: 81 Copynumber: 2.9 Consensus size: 80
3945962 CACGAGTATC
* *
3945972 CGTAAAATCAG-AACGCATATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCG
1 CGTAAAATC-GCAACGCGTATCCGTAAATCGCAACG-CGATACGT-AAATCGCAACGCGTATCCG
* *
3946036 TAAATCACAACGAGAATA
63 TAAATCGCAACGACAATA
* * *
3946054 CGT-AAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTA
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCG-ATACGTAAATCGCAACGCGTATCCGTA
*
3946118 AATCGCAATGACAATA
65 AATCGCAACGACAATA
* *
3946134 TGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCGAT-CGATAATTCGCAACGCGATATCCG-
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCGATACG-TAAATCGCAACGCG-TATCCGT
*
3946197 ATATCGCAA
64 AAATCGCAA
3946206 ATCAGTTTCC
Statistics
Matches: 133, Mismatches: 14, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
79 2 0.02
80 58 0.44
81 70 0.53
82 3 0.02
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (80 bp):
CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCGATACGTAAATCGCAACGCGTATCCGTAA
ATCGCAACGACAATA
Found at i:3946269 original size:21 final size:21
Alignment explanation
Indices: 3946240--3946286 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3946230 ATTCTGACTA
3946240 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
3946261 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
3946282 TCGCA
1 TCGCA
3946287 ACGCGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:3947281 original size:24 final size:24
Alignment explanation
Indices: 3947249--3947302 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3947239 GTATTCGAAA
3947249 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
3947273 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
3947297 TTTGAT
1 TTTGAT
3947303 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:3949757 original size:20 final size:20
Alignment explanation
Indices: 3949732--3949819 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
3949722 CAACGCAGAA
3949732 ATCGCAACAC-GAATATGACT
1 ATCGCAACACGGAA-ATGACT
3949752 ATCGCAACACGGAAATGACT
1 ATCGCAACACGGAAATGACT
* *
3949772 ATCGCAATACGGAATTGACT
1 ATCGCAACACGGAAATGACT
* **
3949792 ATCTCAATGCGGAAATGACT
1 ATCGCAACACGGAAATGACT
3949812 ATCGCAAC
1 ATCGCAAC
3949820 GAGAGAATCG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 57 0.95
21 3 0.05
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACACGGAAATGACT
Found at i:3949880 original size:34 final size:33
Alignment explanation
Indices: 3949796--3949887 Score: 139
Period size: 33 Copynumber: 2.7 Consensus size: 33
3949786 TTGACTATCT
**
3949796 CAATGCGGAAATGACTATCGCAACGAGAGAATCG
1 CAATGC-GAAATGAAAATCGCAACGAGAGAATCG
*
3949830 CAATGCGAAATGAAAATCGCAACGAGTGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
3949863 CAATGCGAAAATGAAAATCGCAACG
1 CAATGCG-AAATGAAAATCGCAACG
3949888 CGAAATTAGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 31 0.57
34 23 0.43
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCG
Found at i:3949883 original size:20 final size:19
Alignment explanation
Indices: 3949825--3949893 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
3949815 GCAACGAGAG
3949825 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3949844 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
3949858 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
3949878 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
3949894 TAGTTTCGCG
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.07
19 12 0.29
20 11 0.27
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3949945 original size:34 final size:34
Alignment explanation
Indices: 3949902--3949997 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
3949892 ATTAGTTTCG
3949902 CGTTGTGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGTGATTTTCATTTTCGCATTGCGATTCACT
*
3949936 CGTTGTGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGTGATTTTCATTTTCGCATTGCGATTCACT
* ** * *
3949969 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGTGATTTTCATTTTCGCATTGCGAT
3949998 AGTATGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.53
34 26 0.47
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (34 bp):
CGTTGTGATTTTCATTTTCGCATTGCGATTCACT
Found at i:3950038 original size:21 final size:21
Alignment explanation
Indices: 3950012--3950059 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
3950002 TGTTTTGCAT
3950012 TCAACATAATGCAGATTGAAA
1 TCAACATAATGCAGATTGAAA
3950033 TCAACATAATGCAGATTGAAA
1 TCAACATAATGCAGATTGAAA
3950054 TCAACA
1 TCAACA
3950060 AATCAACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (21 bp):
TCAACATAATGCAGATTGAAA
Found at i:3951608 original size:42 final size:42
Alignment explanation
Indices: 3951529--3951621 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
3951519 CCTCTTCAAC
* * *
3951529 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
3951571 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
3951613 GATGACAGG
1 GATGACAGG
3951622 TGAGTCAGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:3952124 original size:20 final size:20
Alignment explanation
Indices: 3952101--3952169 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
3952091 GAAACTTAAA
3952101 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
3952121 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * **
3952141 ATCGCAATGTGAATTTGACT
1 ATCGCAACGCGAAAATGACT
3952161 ATCGCAACG
1 ATCGCAACG
3952170 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:3952224 original size:19 final size:19
Alignment explanation
Indices: 3952211--3952278 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
3952201 CGCGATTATA
3952211 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
3952230 GTTTCGCGTTGCGATTTT-
1 GTTTCGCGTTGCGATTTTG
3952248 G--T--CGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
3952263 GTTTCGCGTTGCGATT
1 GTTTCGCGTTGCGATT
3952279 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 12 0.27
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 28 0.64
ACGTcount: A:0.06, C:0.16, G:0.31, T:0.47
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:3952255 original size:14 final size:14
Alignment explanation
Indices: 3952236--3952294 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
3952226 TTTGGTTTCG
3952236 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
3952250 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
* *
3952267 CGCGTTGCGATTCTCT
1 --CGTTGCGATTTTGT
3952283 CGTTGCGATTTT
1 CGTTGCGATTTT
3952295 CATTTCTCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 23 0.62
15 1 0.03
16 1 0.03
17 1 0.03
19 11 0.30
ACGTcount: A:0.07, C:0.19, G:0.27, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3952259 original size:33 final size:33
Alignment explanation
Indices: 3952217--3952341 Score: 164
Period size: 33 Copynumber: 3.8 Consensus size: 33
3952207 TATAGTTTCG
** * *
3952217 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
**
3952250 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
3952283 CGTTGCGATTTTCATTTCTCGTTTCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
3952316 CGTTGCGA--TTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
3952342 AGTCATTTTT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
31 16 0.19
33 68 0.81
ACGTcount: A:0.08, C:0.21, G:0.25, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:3952304 original size:19 final size:18
Alignment explanation
Indices: 3952280--3952364 Score: 63
Period size: 14 Copynumber: 4.8 Consensus size: 18
3952270 GTTGCGATTC
3952280 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGA-TTTCATT
*
3952299 TCTCGTTTCGA-TTC---
1 TCTCGTTGCGATTTCATT
3952313 TCTCGTTGCGA-TTCATT
1 TCTCGTTGCGATTTCATT
* *
3952330 TCGCGTTGCGATAGTCATTTT
1 TCTCGTTGCGAT-TTCA--TT
*
3952351 TCACGTTGCGATTT
1 TCTCGTTGCGATTT
3952365 TAAGTTTCGT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
14 13 0.25
17 13 0.25
19 13 0.25
20 1 0.02
21 13 0.25
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (18 bp):
TCTCGTTGCGATTTCATT
Found at i:3952318 original size:14 final size:14
Alignment explanation
Indices: 3952269--3952326 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
3952259 TTTGGTTTCG
3952269 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3952283 CGTTGCGATTTTCATTTCT
1 CGTTGCGA--TTC---TCT
*
3952302 CGTTTCGATTCTCT
1 CGTTGCGATTCTCT
3952316 CGTTGCGATTC
1 CGTTGCGATTC
3952327 ATTTCGCGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.57
16 3 0.08
17 3 0.08
19 10 0.27
ACGTcount: A:0.09, C:0.26, G:0.19, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3952575 original size:94 final size:94
Alignment explanation
Indices: 3952429--3952808 Score: 622
Period size: 94 Copynumber: 4.1 Consensus size: 94
3952419 ATGGATTGCA
* *
3952429 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
3952493 TTAGCAGAATTGGCAACAACCGAACAAAT
66 TTAGCAGAATTGGCAACAACCGAACAAAT
3952522 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
3952587 TTAGCAGAATTAG-AAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAA-CAACCGAACAAAT
*
3952616 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACATAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
3952681 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAACAACCGAACAAAT
*
3952710 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * * *
3952774 TTTAGCAGTATTGGCAGCAACTGAATAAAT
65 TTTAGCAGAATTGGCAACAACCGAACAAAT
3952804 TTACT
1 TTACT
3952809 AAGCAATCTA
Statistics
Matches: 271, Mismatches: 11, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
93 25 0.09
94 245 0.90
95 1 0.00
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAACAACCGAACAAAT
Found at i:3954529 original size:21 final size:20
Alignment explanation
Indices: 3954510--3954581 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
3954500 CGATTCTCTC
3954510 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
3954530 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
3954551 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
3954571 GTTGCGATTTT
1 GTTGCGATTTT
3954582 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:3955166 original size:20 final size:20
Alignment explanation
Indices: 3955141--3955354 Score: 225
Period size: 20 Copynumber: 10.6 Consensus size: 20
3955131 TTTTAAAAAT
3955141 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3955161 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
3955181 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * * *
3955202 CGCATTACGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
3955222 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* * *
3955242 CGCGTTGCAATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
3955262 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3955282 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
3955302 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
3955323 CGCATTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
3955344 CTCGTTGCGAT
1 CGCGTTGCGAT
3955355 AGTCAGAATC
Statistics
Matches: 156, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
20 104 0.67
21 52 0.33
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3955175 original size:40 final size:40
Alignment explanation
Indices: 3955138--3955415 Score: 240
Period size: 41 Copynumber: 6.9 Consensus size: 40
3955128 GCGTTTTAAA
3955138 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACG
1 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACG
* * * *
3955178 TATTGTCGTTGCGATTTACGGATACGCATTACGA-TTTACG
1 AATCG-CGTTGCGATTTACGGATACGCGTTGCGATTTTACG
* * * *
3955218 TATTCTCGTTGCGATTTACAGATACGCGTTGC-AATTTACG
1 -AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACG
* *
3955258 TATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACG
1 -AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACG
* * *
3955299 TATTGTCGTTGCGATTTACGGATACGCATTGCGATTTTACG
1 AATCG-CGTTGCGATTTACGGATACGCGTTGCGATTTTACG
* * * * ** *
3955340 GATACTCGTTGCGATAGT-CAGA-ATCGCGTTGCGATAGTAAG
1 AAT-CGCGTTGCGAT-TTACGGATA-CGCGTTGCGATTTTACG
* *** *
3955381 AATCGCGTTGCAATTTATATATTCGCGTTGCGATT
1 AATCGCGTTGCGATTTACGGATACGCGTTGCGATT
3955416 CTGGAAAATC
Statistics
Matches: 193, Mismatches: 35, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
39 2 0.01
40 93 0.48
41 97 0.50
42 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (40 bp):
AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACG
Found at i:3955188 original size:41 final size:41
Alignment explanation
Indices: 3955143--3955354 Score: 329
Period size: 41 Copynumber: 5.2 Consensus size: 41
3955133 TTAAAAATCG
*
3955143 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
3955184 CGTTGCGATTTACGGATACGCATTACGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
3955224 CGTTGCGATTTACAGATACGCGTTGC-AATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
3955264 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
3955305 CGTTGCGATTTACGGATACGCATTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
3955346 CGTTGCGAT
1 CGTTGCGAT
3955355 AGTCAGAATC
Statistics
Matches: 156, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 1 0.01
40 71 0.46
41 84 0.54
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:3955371 original size:20 final size:20
Alignment explanation
Indices: 3955346--3955391 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
3955336 TACGGATACT
*
3955346 CGTTGCGATAGTCAGAATCG
1 CGTTGCGATAGTAAGAATCG
3955366 CGTTGCGATAGTAAGAATCG
1 CGTTGCGATAGTAAGAATCG
3955386 CGTTGC
1 CGTTGC
3955392 AATTTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (20 bp):
CGTTGCGATAGTAAGAATCG
Found at i:3955476 original size:42 final size:42
Alignment explanation
Indices: 3955381--3955476 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
3955371 CGATAGTAAG
* *
3955381 AATCGCGTTGC-AATTTATATATTCGCGTTGCGATTCTGGAA
1 AATCGCGTTGCGAATTTATATATTCGCATTGCGATTCTGCAA
** * * *
3955422 AATCGCAATGCGAATTTGTACTA-TCGCATTGCGATTCTTCAT
1 AATCGCGTTGCGAATTTATA-TATTCGCATTGCGATTCTGCAA
3955464 AATCGCGTTGCGA
1 AATCGCGTTGCGA
3955477 TTCTGGGAAC
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 9 0.20
42 33 0.75
43 2 0.05
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (42 bp):
AATCGCGTTGCGAATTTATATATTCGCATTGCGATTCTGCAA
Found at i:3957815 original size:15 final size:16
Alignment explanation
Indices: 3957791--3957838 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 16
3957781 TTAATAAAAT
*
3957791 AAATTA-GAGTGATTA
1 AAATTATGAGTAATTA
3957806 AAA-TATGAGTAATTA
1 AAATTATGAGTAATTA
*
3957821 AAATTTTGAGTAATTA
1 AAATTATGAGTAATTA
3957837 AA
1 AA
3957839 TTGAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 14 0.48
16 13 0.45
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (16 bp):
AAATTATGAGTAATTA
Found at i:3957839 original size:15 final size:15
Alignment explanation
Indices: 3957790--3957840 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 15
3957780 GTTAATAAAA
*
3957790 TAAATTA-GAGTGAT
1 TAAATTATGAGTAAT
*
3957804 TAAAATATGAGTAAT
1 TAAATTATGAGTAAT
*
3957819 TAAAATTTTGAGTAAT
1 T-AAATTATGAGTAAT
3957835 TAAATT
1 TAAATT
3957841 GAAAATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
14 6 0.19
15 12 0.39
16 13 0.42
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (15 bp):
TAAATTATGAGTAAT
Found at i:3958897 original size:16 final size:16
Alignment explanation
Indices: 3958871--3958928 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
3958861 CTATTTAAGT
*
3958871 TTTTCGGTTTGGGTTAC
1 TTTT-GGTTTGGATTAC
*
3958888 TTTTGGTTTGTATTAC
1 TTTTGGTTTGGATTAC
* *
3958904 TTTTAGTTTGGATTGC
1 TTTTGGTTTGGATTAC
*
3958920 TTTCGGTTT
1 TTTTGGTTT
3958929 ATGTTACTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
16 30 0.88
17 4 0.12
ACGTcount: A:0.09, C:0.09, G:0.24, T:0.59
Consensus pattern (16 bp):
TTTTGGTTTGGATTAC
Found at i:3958928 original size:32 final size:32
Alignment explanation
Indices: 3958877--3958959 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 32
3958867 AAGTTTTTCG
* * * *
3958877 GTTTGGGTTACTTTTGGTTTGTATTACTTTTA
1 GTTTGGATTACTTTCGGTTTATATTACTTTAA
* *
3958909 GTTTGGATTGCTTTCGGTTTATGTTACTTTAA
1 GTTTGGATTACTTTCGGTTTATATTACTTTAA
* * *
3958941 GTTCGGGTTAATTTCGGTT
1 GTTTGGATTACTTTCGGTT
3958960 CGAGTTGATT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.13, C:0.08, G:0.24, T:0.54
Consensus pattern (32 bp):
GTTTGGATTACTTTCGGTTTATATTACTTTAA
Found at i:3960262 original size:33 final size:33
Alignment explanation
Indices: 3960199--3960262 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
3960189 TTATTTTTAT
* **
3960199 TAATTAAATATATAAATTTAAAATTCATATACA
1 TAATTAAATATATAAAATTAAAATAAATATACA
*
3960232 TAATTAAATATCTAATAATT-AAATAAATATA
1 TAATTAAATATATAA-AATTAAAATAAATATA
3960263 AATTAAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 23 0.88
34 3 0.12
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (33 bp):
TAATTAAATATATAAAATTAAAATAAATATACA
Found at i:3960928 original size:19 final size:18
Alignment explanation
Indices: 3960904--3960940 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
3960894 ATTTTTGTAG
3960904 AAAAAAAAACAAATGAAAT
1 AAAAAAAAACAAAT-AAAT
3960923 AAAAAAAAACAAATAAAT
1 AAAAAAAAACAAATAAAT
3960941 CATAGTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.81, C:0.05, G:0.03, T:0.11
Consensus pattern (18 bp):
AAAAAAAAACAAATAAAT
Found at i:3961234 original size:15 final size:15
Alignment explanation
Indices: 3961214--3961251 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
3961204 TTCCAGAAAA
3961214 TGAATTACTGGAATT
1 TGAATTACTGGAATT
3961229 TGAATTACTGGAATT
1 TGAATTACTGGAATT
3961244 TGAATTAC
1 TGAATTAC
3961252 ATTTCTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.39
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:3961269 original size:20 final size:20
Alignment explanation
Indices: 3961244--3961303 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
3961234 TACTGGAATT
*
3961244 TGAATTACATTTCTGTAAAA
1 TGAATTACATTTCTGGAAAA
3961264 TGAATTACATTTCTGGAAAA
1 TGAATTACATTTCTGGAAAA
3961284 TGAATTACATTTCTGGAAAA
1 TGAATTACATTTCTGGAAAA
3961304 CATCTGGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (20 bp):
TGAATTACATTTCTGGAAAA
Found at i:3961525 original size:28 final size:27
Alignment explanation
Indices: 3961470--3961534 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
3961460 TTTACTAAAA
*
3961470 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAAAAATATTAT
3961498 TCATTATTAAATATATAAAAAA-ATTTAT
1 T-ATTATTAAATATATAAAAAATA-TTAT
3961526 TATATATTA
1 TAT-TATTA
3961535 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 3 0.09
28 24 0.73
29 6 0.18
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAATATTAT
Found at i:3961560 original size:31 final size:32
Alignment explanation
Indices: 3961470--3961567 Score: 84
Period size: 31 Copynumber: 3.2 Consensus size: 32
3961460 TTTACTAAAA
*
3961470 TATTATTGAAATATAT--AAATA-ATATTAT-T
1 TATTATT-AAATATATAAAAAAATATATTATAT
* *
3961499 CATTATTAAATATATAAAAAAATTTATTATA-
1 TATTATTAAATATATAAAAAAATATATTATAT
*
3961530 TATTATTAAA-ATA-AAAATATAATATCTTATAT
1 TATTATTAAATATATAAAA-A-AATATATTATAT
3961562 TATTAT
1 TATTAT
3961568 AATATAATTG
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
28 8 0.14
29 10 0.18
30 8 0.14
31 24 0.43
32 6 0.11
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (32 bp):
TATTATTAAATATATAAAAAAATATATTATAT
Found at i:3961612 original size:22 final size:23
Alignment explanation
Indices: 3961587--3961630 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3961577 GATTATTTTA
3961587 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
3961609 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
3961631 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:3961635 original size:22 final size:22
Alignment explanation
Indices: 3961591--3961647 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
3961581 ATTTTATATA
* *
3961591 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
3961612 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
3961634 ATATTTTAAATATT
1 ATATTATAAATATT
3961648 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:3961646 original size:52 final size:51
Alignment explanation
Indices: 3961527--3961647 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 51
3961517 AAAATTTATT
**
3961527 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATAATAA
3961578 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTTATATTATTAT-AATA-TAATAA
3961632 ATATATTTTAAATATT
1 ATATATTTTAAATATT
3961648 TTAATAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 20 0.33
53 7 0.12
54 22 0.37
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATAATAA
Found at i:3961887 original size:42 final size:42
Alignment explanation
Indices: 3961837--3961956 Score: 204
Period size: 42 Copynumber: 2.9 Consensus size: 42
3961827 ATGAATTACA
*
3961837 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* * *
3961879 TTTCGGAAAACGAATTACGTGAAATAAACACGTGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
3961921 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
3961957 TTCGAGGAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.18
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:3964022 original size:15 final size:15
Alignment explanation
Indices: 3964002--3964050 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
3963992 GACATTACCT
3964002 GCCCCGCATCCGCCC
1 GCCCCGCATCCGCCC
* *
3964017 GCCCCGCATCCACCT
1 GCCCCGCATCCGCCC
*
3964032 GCCCCACATCCGCCC
1 GCCCCGCATCCGCCC
3964047 GCCC
1 GCCC
3964051 AGCCAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.10, C:0.65, G:0.16, T:0.08
Consensus pattern (15 bp):
GCCCCGCATCCGCCC
Found at i:3966188 original size:16 final size:16
Alignment explanation
Indices: 3966164--3966194 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3966154 TTCTAATTTT
*
3966164 TTTTTGAGTTCAAGTC
1 TTTTCGAGTTCAAGTC
3966180 TTTTCGAGTTCAAGT
1 TTTTCGAGTTCAAGT
3966195 TTCAATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTTCGAGTTCAAGTC
Found at i:3966680 original size:2 final size:2
Alignment explanation
Indices: 3966673--3966706 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3966663 TAGATTGAGA
3966673 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
3966707 CTTGAGATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3968837 original size:18 final size:20
Alignment explanation
Indices: 3968814--3968852 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3968804 TATATCTATT
3968814 TTATTTA-AA-ATTAAAATA
1 TTATTTATAATATTAAAATA
*
3968832 TTATTTATAATATTATAATA
1 TTATTTATAATATTAAAATA
3968852 T
1 T
3968853 AATATCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATTTATAATATTAAAATA
Found at i:3968845 original size:12 final size:12
Alignment explanation
Indices: 3968828--3968888 Score: 61
Period size: 12 Copynumber: 5.0 Consensus size: 12
3968818 TTAAAATTAA
3968828 AATATTATTTAT
1 AATATTATTTAT
*
3968840 AATATTATAATAT
1 AATATTAT-TTAT
*
3968853 AATATCATTTAT
1 AATATTATTTAT
*
3968865 AA-ATATATTTAA
1 AATAT-TATTTAT
*
3968877 AATAATATTTAT
1 AATATTATTTAT
3968889 TCAAAGATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
11 2 0.05
12 26 0.67
13 11 0.28
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
AATATTATTTAT
Found at i:3968862 original size:25 final size:27
Alignment explanation
Indices: 3968828--3968884 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 27
3968818 TTAAAATTAA
* *
3968828 AATATTATTTAT-AATAT-TATAATAT
1 AATATCATTTATAAATATATATAAAAT
*
3968853 AATATCATTTATAAATATATTTAAAAT
1 AATATCATTTATAAATATATATAAAAT
3968880 AATAT
1 AATAT
3968885 TTATTCAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 11 0.41
26 5 0.19
27 11 0.41
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
AATATCATTTATAAATATATATAAAAT
Found at i:3975561 original size:43 final size:43
Alignment explanation
Indices: 3975506--3975909 Score: 352
Period size: 43 Copynumber: 9.5 Consensus size: 43
3975496 CAATAGGTCA
* * *
3975506 AGATCTATAGCGGCGTTTTTGGAACAAATGCCACAAAAGGTAA
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTAG
* * *
3975549 AAATCTATAGCGGTGTTTTTAGAACAAACAG-CGCAAAAGGTAG
1 AGATCTATAGCGGCGTTTTTGGAACAAAC-GCCGCAAAAGGTAG
* * ** * *
3975592 AGATCTATAGCGGCGTTTGTGGAACAAATGTTGCAATAGGTCG
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTAG
* * * * *
3975635 AGATCTATAGCGACATTTTTGGAACAAATGCTGCAAAAGGTCG
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTAG
* ** * * *
3975678 AGATGTATAGCGATGTTTTTAGAACAAACGCCGCAAATGGTTG
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTAG
* * * ** *
3975721 AGATATATAACGGCGTTTTTGGAACAAACACCATAAAAGGTTG
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTAG
* * * *
3975764 AGATATATAGCGGCATTTTTGAAACAAACGCCGCAAAA--TATC
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTA-G
* * * * *
3975806 AAATCTATAGCAGCGATTTTGGAA-AAACACCGCAAAAGGT-T
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTAG
* * *
3975847 AGATCTATAGCGGCATTTTCGGAACAAACGCCGCAAAAGGT-T
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTAG
* **
3975889 AGATATATAGCATCGTTTTTG
1 AGATCTATAGCGGCGTTTTTG
3975910 TATACAAATG
Statistics
Matches: 292, Mismatches: 63, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
41 32 0.11
42 51 0.17
43 208 0.71
44 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (43 bp):
AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTAG
Found at i:3977195 original size:11 final size:11
Alignment explanation
Indices: 3977163--3977199 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
3977153 ATTACCACGA
3977163 CGACCACGACC
1 CGACCACGACC
3977174 ACGACCACGACC
1 -CGACCACGACC
*
3977186 CGACCCCGACC
1 CGACCACGACC
3977197 CGA
1 CGA
3977200 GACGAGACGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.27, C:0.54, G:0.19, T:0.00
Consensus pattern (11 bp):
CGACCACGACC
Found at i:3977197 original size:6 final size:6
Alignment explanation
Indices: 3977162--3977196 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
3977152 TATTACCACG
*
3977162 ACGACC ACGACC ACGACC ACGACC -CGACC CCGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
3977197 CGAGACGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:3977708 original size:6 final size:6
Alignment explanation
Indices: 3977697--3977793 Score: 194
Period size: 6 Copynumber: 16.2 Consensus size: 6
3977687 TCGTCTCGTC
3977697 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
3977745 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
3977793 T
1 T
3977794 AATACGTGTC
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 91 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:3977901 original size:19 final size:19
Alignment explanation
Indices: 3977877--3977942 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
3977867 TTAACTATCA
3977877 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
3977896 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
3977918 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
3977937 CAACGA
1 CAACGA
3977943 CAACTGTAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 19 0.53
20 2 0.06
21 2 0.06
22 13 0.36
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:3977919 original size:22 final size:22
Alignment explanation
Indices: 3977892--3977963 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
3977882 AATTTGGAAA
3977892 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
3977914 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
3977933 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
3977955 ATCGCAACG
1 ATCGCAACG
3977964 CGATTTTCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.33
20 2 0.05
21 2 0.05
22 22 0.56
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:3977927 original size:41 final size:41
Alignment explanation
Indices: 3977870--3977963 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
3977860 CTTTTTTTTA
*
3977870 ACTATCACAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
3977911 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
3977952 ACTATCGCAACG
1 ACTATCGCAACG
3977964 CGATTTTCAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
Found at i:3977995 original size:21 final size:21
Alignment explanation
Indices: 3977952--3977995 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3977942 ACAACTGTAG
** *
3977952 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
3977973 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
3977994 AC
1 AC
3977996 GCGAATTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:3979946 original size:22 final size:22
Alignment explanation
Indices: 3979921--3979981 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
3979911 CAAGCATTTG
3979921 TTTTCCTATTCGAAAGCTATTA
1 TTTTCCTATTCGAAAGCTATTA
* *
3979943 TTTTCATAATT-GAAAACTATTA
1 TTTTCCT-ATTCGAAAGCTATTA
* *
3979965 TTTTTCTATTCAAAAGC
1 TTTTCCTATTCGAAAGC
3979982 AGTAAAACAC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
21 3 0.10
22 25 0.81
23 3 0.10
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (22 bp):
TTTTCCTATTCGAAAGCTATTA
Found at i:3980003 original size:21 final size:21
Alignment explanation
Indices: 3979977--3980029 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
3979967 TTTCTATTCA
3979977 AAAGCAGTAAAACACTGCTCT
1 AAAGCAGTAAAACACTGCTCT
3979998 AAAGCAGTAAAACACTGCTCT
1 AAAGCAGTAAAACACTGCTCT
3980019 AAAGCAGTAAA
1 AAAGCAGTAAA
3980030 GCAGTAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (21 bp):
AAAGCAGTAAAACACTGCTCT
Found at i:3981511 original size:37 final size:37
Alignment explanation
Indices: 3981465--3981566 Score: 168
Period size: 37 Copynumber: 2.8 Consensus size: 37
3981455 TAGGTCACCA
3981465 GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
1 GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
* * *
3981502 GTCGATATGTCCCGAAGGACATAGGTAATCTGTAACT
1 GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
*
3981539 GTCCATATATCCCGAAGAACATAGGTAA
1 GTCCATATGTCCCGAAGAACATAGGTAA
3981567 CCCTCGACTC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (37 bp):
GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
Found at i:3982124 original size:7 final size:7
Alignment explanation
Indices: 3982106--3982140 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
3982096 ATAATTACTT
3982106 ATATCA-
1 ATATCAC
3982112 ATATCAC
1 ATATCAC
3982119 ATATCAC
1 ATATCAC
3982126 ATATCAC
1 ATATCAC
3982133 ATAT-AC
1 ATATCAC
3982139 AT
1 AT
3982141 GTAATTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 10 0.36
7 18 0.64
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (7 bp):
ATATCAC
Found at i:3983574 original size:83 final size:81
Alignment explanation
Indices: 3983380--3983605 Score: 233
Period size: 83 Copynumber: 2.8 Consensus size: 81
3983370 ATGTTACATG
** * * * *
3983380 ATGAACCCTATTA-AGGCATTTGTATAAAAATGCCACTAAAGTACTA-TTTATCGCGGCGTTTGT
1 ATGAACCCTATTACA--CATTTGTATAAAAACACCGCTAAAGTACTACTCTATCACGGCGTTTAT
* *
3983443 TGGAAAATGCCACTATGA
64 TGGAAAATACCACTATAA
** * * *
3983461 ACAAACCCTATTACATTATTTGTATTAAAACACCGCTAAAGTACTACTCTATTACGGCGTTTATT
1 ATGAACCCTATTACA-CATTTGTATAAAAACACCGCTAAAGTACTACTCTATCACGGCGTTTATT
3983526 GGAAAA-ACATCACTATAA
65 GGAAAATAC--CACTATAA
* **
3983544 ATGAACCCTATTACTACATTTATATAAAAACACCGCTAAAGTACTACTCTATCGTGGCGTTT
1 ATGAACCCTATTAC-ACATTTGTATAAAAACACCGCTAAAGTACTACTCTATCACGGCGTTT
3983606 GTTTAAGAAA
Statistics
Matches: 118, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
81 37 0.31
82 21 0.18
83 59 0.50
84 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.31
Consensus pattern (81 bp):
ATGAACCCTATTACACATTTGTATAAAAACACCGCTAAAGTACTACTCTATCACGGCGTTTATTG
GAAAATACCACTATAA
Found at i:3983947 original size:3 final size:3
Alignment explanation
Indices: 3983939--3983973 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3983929 TGTAAAAGTT
3983939 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3983974 GTAATACCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3993428 original size:117 final size:118
Alignment explanation
Indices: 3993130--3993462 Score: 285
Period size: 117 Copynumber: 2.8 Consensus size: 118
3993120 GCATTCCCTG
* * * * * *
3993130 TGGAAGGGTTCAAAATGAGAAGAACTCGTCCGAT-AAGGGATAAGAAGTTTC-TAATGAGAAGAA
1 TGGAAGTGTTCAAAATGAGAAGAACCCATCCAATGAA-GGAGAAGAAG-TTCATAATGAAAAGAA
* * *
3993193 CTTGTTCATAATTG--ACTCG--TCCATCACAAGAGGAGGTGGACCAACATTTCCAA
64 CTTGTTCA-ACTTGTTCCT-GATTCCATCACAAAAGGAGGTGGACCAACATTTCCAA
* * * * *
3993246 TGGAAGTGTTCATAATGAGAAGAGCTCGTCCAATGAAGGAGAAGAAGTTCCTAATGAAAAGAACT
1 TGGAAGTGTTCAAAATGAGAAGAACCCATCCAATGAAGGAGAAGAAGTTCATAATGAAAAGAACT
* * * *
3993311 TGTTCAACCTTGGTT-C-GATTCCATCACAAAAGGAGGTGGATCAATATTTCTAT
66 TGTTCAA-CTT-GTTCCTGATTCCATCACAAAAGGAGGTGGACCAACATTTCCAA
** *
3993364 TGGAGAGT-TT-AAAATGAGAAGAACCCATCTGATGACA-GAGACGAAGTTCATAATGAGAAA-A
1 TGGA-AGTGTTCAAAATGAGAAGAACCCATCCAATGA-AGGAGAAGAAGTTCATAATGA-AAAGA
* * *
3993425 ACTTGTTTAACTTTTTCCTGATTCCATCACATAAGGAG
63 ACTTGTTCAACTTGTTCCTGATTCCATCACAAAAGGAG
3993463 ATAGATCGAC
Statistics
Matches: 181, Mismatches: 23, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
115 6 0.03
116 65 0.36
117 67 0.37
118 40 0.22
119 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.26
Consensus pattern (118 bp):
TGGAAGTGTTCAAAATGAGAAGAACCCATCCAATGAAGGAGAAGAAGTTCATAATGAAAAGAACT
TGTTCAACTTGTTCCTGATTCCATCACAAAAGGAGGTGGACCAACATTTCCAA
Found at i:3996876 original size:18 final size:18
Alignment explanation
Indices: 3996853--3996887 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3996843 AGGGATTATC
3996853 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
* *
3996871 AGTGGTCCTTTGGGACA
1 AGTGGTCATTCGGGACA
3996888 AATTTTCAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:4006168 original size:113 final size:113
Alignment explanation
Indices: 4005965--4006190 Score: 407
Period size: 113 Copynumber: 2.0 Consensus size: 113
4005955 CGTCAATCTT
* *
4005965 CCTCTCGTATATGATTGAGTGCAAGAGTAGCAGTCTCTTCATGAGGAATGTGGTATTTTGGGACG
1 CCTCCCGTATATGATTGAGTGCAAGAGTAGCAGTCTCTTCATGAGGAATGTGGTATTGTGGGACG
* *
4006030 TTAGCATCAGTTTGCCTTTGAGAAAGTGGTTCCATAATTTCACTTGCG
66 TTAGCATCAGCTTGACTTTGAGAAAGTGGTTCCATAATTTCACTTGCG
*
4006078 CCTCCCGTATATGATTGAGTGCAAGAGTAGTAGTCTCTTCATGAGGAATGTGGTATTGTGGGACG
1 CCTCCCGTATATGATTGAGTGCAAGAGTAGCAGTCTCTTCATGAGGAATGTGGTATTGTGGGACG
4006143 TTAGCATCAGCTTGACTTTGAGAAAGTGGTTCCATAATTTCACTTGCG
66 TTAGCATCAGCTTGACTTTGAGAAAGTGGTTCCATAATTTCACTTGCG
4006191 GTTTTAGTGC
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 108 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (113 bp):
CCTCCCGTATATGATTGAGTGCAAGAGTAGCAGTCTCTTCATGAGGAATGTGGTATTGTGGGACG
TTAGCATCAGCTTGACTTTGAGAAAGTGGTTCCATAATTTCACTTGCG
Found at i:4016471 original size:11 final size:10
Alignment explanation
Indices: 4016455--4016503 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 10
4016445 TTAAAATAAA
4016455 TTTTTTATAGT
1 TTTTTTAT-GT
*
4016466 TTTTTTATTT
1 TTTTTTATGT
4016476 TTTTATGTATGT
1 TTTT-T-TATGT
4016488 TTATTTTATGT
1 TT-TTTTATGT
4016499 TTTTT
1 TTTTT
4016504 AGGGATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
10 8 0.24
11 16 0.48
12 7 0.21
13 2 0.06
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (10 bp):
TTTTTTATGT
Found at i:4016490 original size:18 final size:19
Alignment explanation
Indices: 4016455--4016494 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
4016445 TTAAAATAAA
* *
4016455 TTTTTTATAGTTTTTTTAT
1 TTTTTTATAGTATGTTTAT
4016474 TTTTTTAT-GTATGTTTAT
1 TTTTTTATAGTATGTTTAT
4016492 TTT
1 TTT
4016495 ATGTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (19 bp):
TTTTTTATAGTATGTTTAT
Found at i:4020709 original size:14 final size:15
Alignment explanation
Indices: 4020687--4020715 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4020677 ATAGTTAAAA
4020687 ATTTAAAAATAAATT
1 ATTTAAAAATAAATT
4020702 ATTT-AAAATAAATT
1 ATTTAAAAATAAATT
4020716 GTAAATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTAAAAATAAATT
Found at i:4021969 original size:2 final size:2
Alignment explanation
Indices: 4021962--4022053 Score: 175
Period size: 2 Copynumber: 46.0 Consensus size: 2
4021952 AAGAATCATC
4021962 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
*
4022004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4022046 AT AT AT AT
1 AT AT AT AT
4022054 GGATTATTAT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4028629 original size:117 final size:116
Alignment explanation
Indices: 4028355--4028725 Score: 328
Period size: 117 Copynumber: 3.2 Consensus size: 116
4028345 CTGTGGAAGG
* * * *
4028355 GTTCAAAATGAGAAGAATTCGTCTC-AT-AAGGGAGAA-AGAGTTTCTAATGAGAAGAACTTGTT
1 GTTCATAATGAGAAGAACTCATC-CAATGAA-GGAGAAGA-AGTTCCTAATGAGAAGAACTTGTT
* * * *
4028417 CAACCTTGACTC-A-TCCATCACA-AGAGGAGGTAGACCAACATTTCCGATGGAAGT
63 CAACCTTGATTCGATTCCATCACAGA-AGGAGGTAGATCAACATTT-CTATGG-AGA
* * * *
4028471 GTTCATAATAATAAGAGCTCATCCAATGAAGGAGAAGAAGTTCCTAATGAAAAGAACTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCCAATGAAGGAGAAGAAGTTCCTAATGAGAAGAACTTGTTCAA
* *
4028536 CCTTGGTTCGATTCCATCACAGAAGGAGGTGGATCAACATTTCTATTGGAGA
66 CCTTGATTCGATTCCATCACAGAAGGAGGTAGATCAACATTTCTA-TGGAGA
** * * * * *
4028588 GTTCATAATGAGAAGAACTCATCTGATGATGGAGACGAAGTTCATAATGAGAATAACTTGTTTAA
1 GTTCATAATGAGAAGAACTCATCCAATGAAGGAGAAGAAGTTCCTAATGAGAAGAACTTGTTCAA
* * * * *
4028653 CCTT-TTTCTTGATTCCACCACAGAAAGAGATAGATCAATATTT-TCA-GAGAAGA
66 CCTTGATTC--GATTCCATCACAGAAGGAGGTAGATCAACATTTCT-ATG-G-AGA
4028706 CGTTCATAATGAGAAGAACT
1 -GTTCATAATGAGAAGAACT
4028726 TGTTCAAACC
Statistics
Matches: 211, Mismatches: 31, Indels: 23
0.80 0.12 0.09
Matches are distributed among these distances:
115 1 0.00
116 61 0.29
117 68 0.32
118 61 0.29
119 20 0.09
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.27
Consensus pattern (116 bp):
GTTCATAATGAGAAGAACTCATCCAATGAAGGAGAAGAAGTTCCTAATGAGAAGAACTTGTTCAA
CCTTGATTCGATTCCATCACAGAAGGAGGTAGATCAACATTTCTATGGAGA
Found at i:4034750 original size:4 final size:4
Alignment explanation
Indices: 4034721--4034791 Score: 119
Period size: 4 Copynumber: 18.2 Consensus size: 4
4034711 GTGTGCGCGC
*
4034721 GCGT GCGC GCGT GCGT GCGT GC-- GCGT GCGT GCGT GCGT GCGT GCGT
1 GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT
4034767 GCGT GCGT GCGT GCGT GCGT GCGT G
1 GCGT GCGT GCGT GCGT GCGT GCGT G
4034792 TGAATAGGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
4 61 0.97
ACGTcount: A:0.00, C:0.27, G:0.51, T:0.23
Consensus pattern (4 bp):
GCGT
Found at i:4034851 original size:40 final size:40
Alignment explanation
Indices: 4034796--4034876 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
4034786 TGCGTGTGAA
4034796 TAGGAAAATTCTACAGCGCTCGATGAGCAATGATGAACAC
1 TAGGAAAATTCTACAGCGCTCGATGAGCAATGATGAACAC
4034836 TAGGAAAATTCTACAGCGCTCGATGAGCAATGATGAACAC
1 TAGGAAAATTCTACAGCGCTCGATGAGCAATGATGAACAC
4034876 T
1 T
4034877 GCTAACGACG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (40 bp):
TAGGAAAATTCTACAGCGCTCGATGAGCAATGATGAACAC
Found at i:4035542 original size:18 final size:19
Alignment explanation
Indices: 4035519--4035554 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4035509 TTTTTTAATT
4035519 GAAATTG-ATAATCAAATA
1 GAAATTGAATAATCAAATA
4035537 GAAATTGAATAATCAAAT
1 GAAATTGAATAATCAAAT
4035555 TGATTCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.28
Consensus pattern (19 bp):
GAAATTGAATAATCAAATA
Found at i:4035786 original size:111 final size:111
Alignment explanation
Indices: 4035588--4035966 Score: 634
Period size: 111 Copynumber: 3.4 Consensus size: 111
4035578 TTGATGTTGG
*
4035588 ATATAACAGGTAAAAATATGATAAAATCAGTTTCATTATGACAAAAACGGTAAAATTTACTTAAT
1 ATATAACAGGTAAAAATATGATAAAATCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAAT
* *
4035653 ATGTTGAAAGTATCTATATTTTTATAAAAAGGATCGATACTTTACA
66 ATGTTGAAAGTATCGATCTTTTTATAAAAAGGATCGATACTTTACA
4035699 ATATAACAGGTAAAAATATGATAAAATCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAAT
1 ATATAACAGGTAAAAATATGATAAAATCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAAT
4035764 ATGTTGAAAGTATCGATCTTTTTATAAAAAGGATCGATACTTTACA
66 ATGTTGAAAGTATCGATCTTTTTATAAAAAGGATCGATACTTTACA
* *
4035810 ATATAACATGTAAAAATATGATAAAACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAAT
1 ATATAACAGGTAAAAATATGATAAAATCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAAT
* * *
4035875 ATATTGAAAGTATCGATCATTTTATAAAAAAGATCGATACTTTACA
66 ATGTTGAAAGTATCGATCTTTTTATAAAAAGGATCGATACTTTACA
* * * *
4035921 ATATAATATGTATAAATATGACAAAA-CTAGTTTCATTATGACAAAA
1 ATATAACAGGTAAAAATATGATAAAATC-AGTTTCATTATGACAAAA
4035967 CCAGTTTTAT
Statistics
Matches: 256, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
110 1 0.00
111 255 1.00
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (111 bp):
ATATAACAGGTAAAAATATGATAAAATCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAAT
ATGTTGAAAGTATCGATCTTTTTATAAAAAGGATCGATACTTTACA
Found at i:4035962 original size:20 final size:20
Alignment explanation
Indices: 4035937--4035988 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
4035927 TATGTATAAA
*
4035937 TATGACAAAACTAGTTTCAT
1 TATGACAAAACCAGTTTCAT
*
4035957 TATGACAAAACCAGTTTTAT
1 TATGACAAAACCAGTTTCAT
*
4035977 TATGATAAAACC
1 TATGACAAAACC
4035989 GGTAAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (20 bp):
TATGACAAAACCAGTTTCAT
Found at i:4036593 original size:2 final size:2
Alignment explanation
Indices: 4036530--4036582 Score: 81
Period size: 2 Copynumber: 26.0 Consensus size: 2
4036520 ATATCTTTTA
4036530 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
4036572 AT AT CAT AT AT
1 AT AT -AT AT AT
4036583 TAACAATATA
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.02
2 43 0.90
3 4 0.08
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4037055 original size:27 final size:27
Alignment explanation
Indices: 4037026--4037078 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
4037016 TATTATTAAA
*
4037026 TTTTAGATAAAATATTATTTTGATATAT
1 TTTTAGATAAAATATCA-TTTGATATAT
**
4037054 TTTTTTATAAAATATCATTTGATAT
1 TTTTAGATAAAATATCATTTGATAT
4037079 TAAATGAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (27 bp):
TTTTAGATAAAATATCATTTGATATAT
Found at i:4038381 original size:10 final size:10
Alignment explanation
Indices: 4038366--4038424 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
4038356 CATTTAATAA
4038366 ATAAACGAAC
1 ATAAACGAAC
4038376 ATAAACGAAC
1 ATAAACGAAC
* * *
4038386 ACAAACAAAA
1 ATAAACGAAC
4038396 ATGAATACGAAC
1 AT-AA-ACGAAC
*
4038408 ATAAACGAAA
1 ATAAACGAAC
4038418 ATAAACG
1 ATAAACG
4038425 TTGGAGACCC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 30 0.75
11 4 0.10
12 6 0.15
ACGTcount: A:0.63, C:0.17, G:0.10, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:4039483 original size:10 final size:10
Alignment explanation
Indices: 4039468--4039518 Score: 57
Period size: 10 Copynumber: 4.7 Consensus size: 10
4039458 AACATAAATG
4039468 AACGAACATA
1 AACGAACATA
4039478 AACGAACATAA
1 AACGAACAT-A
4039489 CCGAACGAACATA
1 ---AACGAACATA
4039502 AACGAACATA
1 AACGAACATA
*
4039512 ATCGAAC
1 AACGAAC
4039519 GAAAATGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 25 0.69
11 1 0.03
13 1 0.03
14 9 0.25
ACGTcount: A:0.55, C:0.24, G:0.12, T:0.10
Consensus pattern (10 bp):
AACGAACATA
Found at i:4039519 original size:14 final size:13
Alignment explanation
Indices: 4039458--4039534 Score: 58
Period size: 14 Copynumber: 6.1 Consensus size: 13
4039448 GATTGTGTTA
4039458 AACATAAATGAACG
1 AACAT-AATGAACG
4039472 AACAT-A--AACG
1 AACATAATGAACG
*
4039482 AACATAACCGAACG
1 AACATAA-TGAACG
4039496 AACAT-A--AACG
1 AACATAATGAACG
4039506 AACATAATCGAACG
1 AACATAAT-GAACG
*
4039520 AAAATGAATGAACG
1 AACAT-AATGAACG
4039534 A
1 A
4039535 GACCTATGTT
Statistics
Matches: 53, Mismatches: 1, Indels: 18
0.74 0.01 0.25
Matches are distributed among these distances:
10 18 0.34
11 2 0.04
12 1 0.02
13 1 0.02
14 28 0.53
15 3 0.06
ACGTcount: A:0.56, C:0.18, G:0.14, T:0.12
Consensus pattern (13 bp):
AACATAATGAACG
Found at i:4039532 original size:24 final size:24
Alignment explanation
Indices: 4039458--4039521 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
4039448 GATTGTGTTA
4039458 AACATAAAT-GAACGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
4039482 AACATAACCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
4039506 AACATAATCGAACGAA
1 AACATAATCGAACGAA
4039522 AATGAATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 2 0.05
24 35 0.95
ACGTcount: A:0.56, C:0.20, G:0.12, T:0.11
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:4039967 original size:21 final size:21
Alignment explanation
Indices: 4039921--4039961 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4039911 TGATTTCAAC
* *
4039921 CATAATGGGTGCTATTGCGGT
1 CATAATGGATGCTATTACGGT
4039942 CATAATGGATGCTATTACGG
1 CATAATGGATGCTATTACGG
4039962 GTATAACGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (21 bp):
CATAATGGATGCTATTACGGT
Found at i:4039972 original size:21 final size:21
Alignment explanation
Indices: 4039921--4039972 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
4039911 TGATTTCAAC
* * *
4039921 CATAATGGGTGCTATTGCGGT
1 CATAACGGATGCTATTACGGT
*
4039942 CATAATGGATGCTATTACGGGT
1 CATAACGGATGCTATTAC-GGT
4039964 -ATAACGGAT
1 CATAACGGAT
4039973 ATATCAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (21 bp):
CATAACGGATGCTATTACGGT
Done.