Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 78
Found at i:5021269 original size:22 final size:21
Alignment explanation
Indices: 5021212--5021270 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 21
5021202 TATATACAAC
*
5021212 ATATACTATAATAATACACCAT
1 ATATACTATAAT-ATATACCAT
5021234 ATAT--TAT-ATAATATACCAT
1 ATATACTATAAT-ATATACCAT
5021253 ATACTACTATAATATATA
1 ATA-TACTATAATATATA
5021271 TTATACTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 14 0.44
20 4 0.12
22 12 0.38
23 2 0.06
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATACTATAATATATACCAT
Found at i:5021339 original size:2 final size:2
Alignment explanation
Indices: 5021332--5021428 Score: 187
Period size: 2 Copynumber: 49.0 Consensus size: 2
5021322 CACACTAACA
5021332 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
5021374 AT AT AT AT AT -T 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
5021415 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
5021429 TTAATATTAT
Statistics
Matches: 94, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 93 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5022177 original size:218 final size:218
Alignment explanation
Indices: 5021799--5022237 Score: 833
Period size: 218 Copynumber: 2.0 Consensus size: 218
5021789 TCCTTTGTTC
*
5021799 ATCTGTATATGACATTCTGTTGGTTCTAGGATATATGTGTCAAACAAGACTGTGGTTAAATGATG
1 ATCTGTATATGACATTCTGTTGGTTCTAGGATATATGTGTCAAACAAGACTGTGGTTAAAGGATG
* *
5021864 ATTCGTTTTTCATTCACTCACTTAGGATTATTCTTCAGGTAGGTTTTCCTCCTATATGTCTAATG
66 ATTCGGTTTTCATTCACTCACTTAGGATTATTCTTCAAGTAGGTTTTCCTCCTATATGTCTAATG
5021929 CTTTGGGACGTCGGAGTGATCCATCTTTGTATGTCGTTGCCTCAATTATTCACGCTCTTGCTCTT
131 CTTTGGGACGTCGGAGTGATCCATCTTTGTATGTCGTTGCCTCAATTATTCACGCTCTTGCTCTT
5021994 GCTCATCAGACTGTCACTGGTCG
196 GCTCATCAGACTGTCACTGGTCG
5022017 ATCTGTATATGACATTCTGTTGGTTCTAGGATATATGTGTCAAACAAGACTGTGGTTAAAGGATG
1 ATCTGTATATGACATTCTGTTGGTTCTAGGATATATGTGTCAAACAAGACTGTGGTTAAAGGATG
*
5022082 ATTTGGTTTTCATTCACTCACTTAGGATTATTCTTCAAGTAGGTTTTCCTCCTATATGTCTAATG
66 ATTCGGTTTTCATTCACTCACTTAGGATTATTCTTCAAGTAGGTTTTCCTCCTATATGTCTAATG
*
5022147 CTTTGGGACGTCGGAGTGATTCATCTTTGTATGTCGTTGCCTCAATTATTCACGCTCTTGCTCTT
131 CTTTGGGACGTCGGAGTGATCCATCTTTGTATGTCGTTGCCTCAATTATTCACGCTCTTGCTCTT
5022212 GCTCATCAGACTGTCACTGGTCG
196 GCTCATCAGACTGTCACTGGTCG
5022235 ATC
1 ATC
5022238 ACTGTTATAT
Statistics
Matches: 216, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
218 216 1.00
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (218 bp):
ATCTGTATATGACATTCTGTTGGTTCTAGGATATATGTGTCAAACAAGACTGTGGTTAAAGGATG
ATTCGGTTTTCATTCACTCACTTAGGATTATTCTTCAAGTAGGTTTTCCTCCTATATGTCTAATG
CTTTGGGACGTCGGAGTGATCCATCTTTGTATGTCGTTGCCTCAATTATTCACGCTCTTGCTCTT
GCTCATCAGACTGTCACTGGTCG
Found at i:5028639 original size:17 final size:17
Alignment explanation
Indices: 5028586--5028639 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
5028576 ATTCAAAAAC
* *
5028586 AATATATAAAATAATAA
1 AATATTTAAATTAATAA
* *
5028603 AATATTTAAAATAAAAAA
1 AATATTT-AAATTAATAA
*
5028621 AATATTTAAATTATTAA
1 AATATTTAAATTAATAA
5028638 AA
1 AA
5028640 ATTGTAGAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATATTTAAATTAATAA
Found at i:5028641 original size:18 final size:18
Alignment explanation
Indices: 5028580--5028630 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 18
5028570 CATACAATTC
* *
5028580 AAAAACAATATATAAAAT
1 AAAAAAAATATTTAAAAT
*
5028598 -AATAAAATATTTAAAAT
1 AAAAAAAATATTTAAAAT
5028615 AAAAAAAATATTTAAA
1 AAAAAAAATATTTAAA
5028631 TTATTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAAAAAATATTTAAAAT
Found at i:5029526 original size:60 final size:60
Alignment explanation
Indices: 5029404--5029516 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
5029394 CATAACTCTT
*
5029404 ATTCTAAATTAGTCCCTAAACTTTTAAACATTCCAATTTCATCCATAAACTATGACTATC
1 ATTCTAAATTACTCCCTAAACTTTTAAACATTCCAATTTCATCCATAAACTATGACTATC
* * *
5029464 ATTCTAAATTACT-CCTCAAACTTTTGAACATTTCATTTTCATCC-TCAAACTAT
1 ATTCTAAATTACTCCCT-AAACTTTTAAACATTCCAATTTCATCCAT-AAACTAT
5029517 TACCTTCATT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
59 4 0.09
60 43 0.91
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.39
Consensus pattern (60 bp):
ATTCTAAATTACTCCCTAAACTTTTAAACATTCCAATTTCATCCATAAACTATGACTATC
Found at i:5029878 original size:60 final size:60
Alignment explanation
Indices: 5029739--5029880 Score: 164
Period size: 60 Copynumber: 2.4 Consensus size: 60
5029729 GGGGACCAAT
** * * * * *
5029739 TTTAGAATGAGGGCCATAGTTTGGGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAA
1 TTTAGAATGAAAGTCATAGTTTGAGAATGAAATGAGAATATTCAAAAGTTTAAGGACTAA
*
5029799 TTTAGAATGAAAGTTATAGTTTGAGAATGAAAGTGA-AATATTCAAAAGTTTAAGGACTAA
1 TTTAGAATGAAAGTCATAGTTTGAGAATGAAA-TGAGAATATTCAAAAGTTTAAGGACTAA
5029859 TTTA-AATTGAGAA-TCATAGTTT
1 TTTAGAA-TGA-AAGTCATAGTTT
5029881 TGGGACATAT
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 2 0.03
60 64 0.91
61 4 0.06
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (60 bp):
TTTAGAATGAAAGTCATAGTTTGAGAATGAAATGAGAATATTCAAAAGTTTAAGGACTAA
Found at i:5030463 original size:2 final size:2
Alignment explanation
Indices: 5030456--5030510 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
5030446 TTTATTATTA
5030456 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
5030498 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
5030511 AGCCATAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5033619 original size:3 final size:3
Alignment explanation
Indices: 5033611--5033704 Score: 98
Period size: 3 Copynumber: 30.7 Consensus size: 3
5033601 ATGTTATTTA
* * * *
5033611 TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT AAT TAT AAT TAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
5033659 AAT TAT AAT AAT TAT TAT TAT TAT TAT ATAT TATT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT TAT TA
5033705 CAAAACCCAA
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
3 71 0.92
4 6 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:5039106 original size:15 final size:15
Alignment explanation
Indices: 5039086--5039117 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5039076 ATCAATACCT
5039086 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
5039101 TTTTGCATACATTCA
1 TTTTGCATACATGCA
5039116 TT
1 TT
5039118 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:5046438 original size:17 final size:15
Alignment explanation
Indices: 5046422--5046482 Score: 63
Period size: 15 Copynumber: 4.0 Consensus size: 15
5046412 ATGCTTAAAG
*
5046422 AGAAAAAGAAAAGAA
1 AGAAAAAGAAAAAAA
5046437 AG-AAAAGAAAAGAAA
1 AGAAAAAGAAAA-AAA
*
5046452 A-AAGAAGAAAAAAAA
1 AGAAAAAG-AAAAAAA
5046467 AGAAAAAAGAAAAAAA
1 AG-AAAAAGAAAAAAA
5046483 GGGGTCAAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.24
15 13 0.34
16 11 0.29
17 5 0.13
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AGAAAAAGAAAAAAA
Found at i:5046447 original size:20 final size:21
Alignment explanation
Indices: 5046422--5046483 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 21
5046412 ATGCTTAAAG
*
5046422 AGAAAAAGAAAAGA-AAGAAA
1 AGAAAAAGAAAAAAGAAGAAA
5046442 AG-AAAAGAAAAAAGAAGAAA
1 AGAAAAAGAAAAAAGAAGAAA
*
5046462 A-AAAAAGAAAAAAGAAAAAA
1 AGAAAAAGAAAAAAGAAGAAA
5046482 AG
1 AG
5046484 GGGTCAAGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
19 10 0.27
20 27 0.73
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
AGAAAAAGAAAAAAGAAGAAA
Found at i:5046450 original size:25 final size:24
Alignment explanation
Indices: 5046422--5046483 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 24
5046412 ATGCTTAAAG
5046422 AGAAAAAGAAAAGAAAGAAAAGAAA
1 AGAAAAAGAAAAGAAAGAAAA-AAA
* *
5046447 AGAAAAA-AGAAGAAA-AAAAAAG
1 AGAAAAAGAAAAGAAAGAAAAAAA
5046469 A-AAAAAGAAAA-AAAG
1 AGAAAAAGAAAAGAAAG
5046484 GGGTCAAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 8 0.25
22 6 0.19
23 4 0.12
24 7 0.22
25 7 0.22
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (24 bp):
AGAAAAAGAAAAGAAAGAAAAAAA
Found at i:5046479 original size:5 final size:5
Alignment explanation
Indices: 5046425--5046472 Score: 64
Period size: 5 Copynumber: 9.8 Consensus size: 5
5046415 CTTAAAGAGA
*
5046425 AAAAG AAAAG -AAAG AAAAG AAAAG AAAA- AAGAAG AAAAA AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG AAAAG AAAA
5046473 AAGAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 6 0.16
5 30 0.79
6 2 0.05
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:5046829 original size:16 final size:18
Alignment explanation
Indices: 5046810--5046855 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
5046800 CTATTTCAAG
5046810 TTCAATTTATTT-G-AAA
1 TTCAATTTATTTCGAAAA
5046826 TTCAATTTATTTTCGAAAA
1 TTCAATTTA-TTTCGAAAA
5046845 TTCAATTTATT
1 TTCAATTTATT
5046856 CTTCTATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.33
17 3 0.11
18 3 0.11
19 12 0.44
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (18 bp):
TTCAATTTATTTCGAAAA
Found at i:5047934 original size:93 final size:83
Alignment explanation
Indices: 5047514--5047912 Score: 672
Period size: 83 Copynumber: 4.7 Consensus size: 83
5047504 GAACAAATGC
5047514 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
5047579 CATTGAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
*
5047597 AATGTGCTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
5047662 CATTGAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
*
5047680 AATGTGCTCATAGCAACTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
5047745 CATTGAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
5047763 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT-G---G-----T
*
5047828 AAAAACCAATCATTAAATTTGAAAGATG
57 -AAAACCAATCATTGAATTTGAAAGATG
*
5047856 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
5047913 TGAAACCATA
Statistics
Matches: 300, Mismatches: 6, Indels: 20
0.92 0.02 0.06
Matches are distributed among these distances:
83 216 0.72
84 2 0.01
87 1 0.00
89 1 0.00
92 2 0.01
93 78 0.26
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (83 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
CATTGAATTTGAAAGATG
Found at i:5049043 original size:113 final size:112
Alignment explanation
Indices: 5048882--5049406 Score: 827
Period size: 113 Copynumber: 4.7 Consensus size: 112
5048872 GTCAGTTAGT
5048882 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
*
5048947 ACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAA
66 ACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTT-CCAGAGAAA
5048995 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
*
5049060 ACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAA
66 ACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTT-CCAGAGAAA
*
5049108 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAAAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
* *
5049173 ACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTCTCCAGAAAAA
66 ACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTT-TCCAGAGAAA
* *
5049221 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
* * * * * * * *
5049286 A-CTTTTCGCTCGAATTCATCCCTCGATAGATCAACTTTTCAGAGAGA
66 ACCTTTT-GCTCAAATCCATCACTTGATGGATCAGCTTTCCAGAGAAA
* * ** *
5049333 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCG
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
5049398 ACCTTTTGC
66 ACCTTTTGC
5049407 ATGACTCTAT
Statistics
Matches: 389, Mismatches: 20, Indels: 7
0.94 0.05 0.02
Matches are distributed among these distances:
112 77 0.20
113 311 0.80
114 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (112 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
ACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTCCAGAGAAA
Found at i:5049572 original size:117 final size:115
Alignment explanation
Indices: 5049364--5049598 Score: 272
Period size: 117 Copynumber: 2.0 Consensus size: 115
5049354 TCTGAAGAAA
* * * * * *
5049364 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTGCATGACTCTATCATAAAAGGAGA
1 GAAGAAGAAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGAATGACTCTATCACAAAAGGAAA
* * * **** *
5049429 TATATCATCATCAGCATTTCCAGAAAGAGTTCACAATGAGAAGAACTCATCT
66 GAGATCAACATCAGCACCAACAG-AA-AGTTCACAATGACAAGAACTCATCT
*
5049481 GAAGAAGAAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAA
1 GAAGAAGAAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGAATGACTCTATCACAAAAGGAAA
* * * * *
5049546 GAGGTCAACATCATCCCCAACGGAAAGTTCATAATGACAAGAACTCATCT
66 GAGATCAACATCAGCACCAACAGAAAGTTCACAATGACAAGAACTCATCT
5049596 GAA
1 GAA
5049599 AGAAAAAGAA
Statistics
Matches: 98, Mismatches: 20, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
115 26 0.27
116 2 0.02
117 70 0.71
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (115 bp):
GAAGAAGAAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGAATGACTCTATCACAAAAGGAAA
GAGATCAACATCAGCACCAACAGAAAGTTCACAATGACAAGAACTCATCT
Found at i:5049786 original size:3 final size:3
Alignment explanation
Indices: 5049780--5049827 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
5049770 AATAATAATA
* *
5049780 ATT ATT ATT ATT ATT ATT ATT ATT AAT ATAT ATT ATTT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT A-TT ATT ATT ATT
5049827 A
1 A
5049828 CAAAACCCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:5056997 original size:3 final size:3
Alignment explanation
Indices: 5056989--5057061 Score: 73
Period size: 3 Copynumber: 25.0 Consensus size: 3
5056979 TTTTACTTAA
*
5056989 ATT ATT ATT ATT ATT ATT ATT AAAT ATT ATT ATT A-T ATT A-T ATAT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT AT-T
* *
5057034 ATT A-T ATT ATT ATT A-A ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5057062 TACAAACCGG
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 7 0.12
3 48 0.80
4 5 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:5057019 original size:22 final size:22
Alignment explanation
Indices: 5056976--5057061 Score: 96
Period size: 22 Copynumber: 4.1 Consensus size: 22
5056966 CACCAATTTT
5056976 TTATT-TTACTTAAATTATTATTA
1 TTATTATTA-TTAAA-TATTATTA
5056999 TTATTATTATTAAATATTATTA
1 TTATTATTATTAAATATTATTA
5057021 TTA-TATTA-T--ATA-TATTA
1 TTATTATTATTAAATATTATTA
5057038 -TATTATTATTAAATAATTATTA
1 TTATTATTATTAAAT-ATTATTA
5057060 TT
1 TT
5057062 TACAAACCGG
Statistics
Matches: 55, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
16 2 0.04
17 10 0.18
18 4 0.07
20 3 0.05
21 6 0.11
22 16 0.29
23 11 0.20
24 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATTATTATTAAATATTATTA
Found at i:5057061 original size:25 final size:25
Alignment explanation
Indices: 5056976--5057061 Score: 83
Period size: 25 Copynumber: 3.4 Consensus size: 25
5056966 CACCAATTTT
5056976 TTATT-TTACTTAA-ATTATTATT-A
1 TTATTATTA-TTAATATTATTATTAA
5056999 TTATTATTATTAAATATTATTATTATA
1 TTATTATTATT-AATATTATTATTA-A
5057026 TTA-TATATATT-ATATTATTATTAAA
1 TTATTAT-TATTAATATTATTATT-AA
*
5057051 TAATTATTATT
1 TTATTATTATT
5057062 TACAAACCGG
Statistics
Matches: 54, Mismatches: 1, Indels: 14
0.78 0.01 0.20
Matches are distributed among these distances:
23 7 0.13
24 5 0.09
25 27 0.50
26 7 0.13
27 8 0.15
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (25 bp):
TTATTATTATTAATATTATTATTAA
Found at i:5060137 original size:23 final size:23
Alignment explanation
Indices: 5060111--5060154 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
5060101 ACATATTAGG
*
5060111 TAGCGTTTATATAATATAATAGT
1 TAGCGTTTATATAATAAAATAGT
5060134 TAGCGTTTATATAATAAAATA
1 TAGCGTTTATATAATAAAATA
5060155 AGTATTTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (23 bp):
TAGCGTTTATATAATAAAATAGT
Found at i:5066603 original size:114 final size:114
Alignment explanation
Indices: 5066403--5066622 Score: 379
Period size: 114 Copynumber: 1.9 Consensus size: 114
5066393 CATGTTCTCG
*
5066403 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTAATCTGGTTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTAATCTGGTTC
* * *
5066468 GGTATGAACCTCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTATGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCA
*
5066517 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTAATCTGGTTC
5066582 GGTA-GAAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
66 GGTATG-AACCCCAAAACCAATCATTAGAATTGAAAGATGAA
5066623 CTGCATGATC
Statistics
Matches: 100, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
113 1 0.01
114 99 0.99
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTAATCTGGTTC
GGTATGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCA
Found at i:5069094 original size:22 final size:22
Alignment explanation
Indices: 5069068--5069141 Score: 139
Period size: 22 Copynumber: 3.4 Consensus size: 22
5069058 TACACTCTTC
5069068 AAAGATGATAGATTCTCTTTTT
1 AAAGATGATAGATTCTCTTTTT
5069090 AAAGATGATAGATTCTCTTTTT
1 AAAGATGATAGATTCTCTTTTT
*
5069112 AAAGATGATAGATTCTCTTTTC
1 AAAGATGATAGATTCTCTTTTT
5069134 AAAGATGA
1 AAAGATGA
5069142 AAGCTTTATG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (22 bp):
AAAGATGATAGATTCTCTTTTT
Found at i:5069959 original size:166 final size:167
Alignment explanation
Indices: 5069656--5069982 Score: 514
Period size: 166 Copynumber: 2.0 Consensus size: 167
5069646 AAAATGAGCA
* *
5069656 TTATCTTCATATTGGGTCATGTTACCCAATCAACATGTTATTTCAAAAAAATAGAATGAGAAAAC
1 TTATCTTCAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATA-AATGAGAAAAC
* **
5069721 GATTTTCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
65 GATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
* *
5069786 TCTTAGTTTTTTTACTTAGTAAACTATTTCCAACAGCC
130 CCTTAGTTTTTTTACTTAATAAACTATTTCCAACAGCC
* * * **
5069824 TTATCTTGAGATTGGGGCATGTTACCCAATCAATATGTTATTT-TAAAAAAT-AATGAGAAAGTG
1 TTATCTTCAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAAATGAGAAAACG
5069887 ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
66 ATTTCCATAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
5069952 CCTTAGTTTTTTTACTTAATAAACTATTTCC
130 CCTTAGTTTTTTTACTTAATAAACTATTTCC
5069983 CACATCTGTA
Statistics
Matches: 146, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
165 37 0.25
166 63 0.43
167 7 0.05
168 39 0.27
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39
Consensus pattern (167 bp):
TTATCTTCAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAAATGAGAAAACG
ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
CTTAGTTTTTTTACTTAATAAACTATTTCCAACAGCC
Found at i:5070084 original size:76 final size:76
Alignment explanation
Indices: 5069985--5070847 Score: 1581
Period size: 76 Copynumber: 11.4 Consensus size: 76
5069975 CTATTTCCCA
*
5069985 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5070050 AGCCTTAGGGT
66 AGCCTTAGGGT
5070061 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5070126 AGCCTTAGGGT
66 AGCCTTAGGGT
5070137 CATCTGTAAGTCCTGCAGTGCATGATGTTT-CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5070201 AGCCTTAGGGT
66 AGCCTTAGGGT
*
5070212 CATCTGTAAGTCTTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5070277 AGCCTTAGGGT
66 AGCCTTAGGGT
*
5070288 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5070353 AGCCTTAGGGT
66 AGCCTTAGGGT
*
5070364 C-TCTGTAAGTCTTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5070427 AGCCTTAGGGT
66 AGCCTTAGGGT
5070438 CATCTGTAAGT-CTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5070502 AGCCCTTAGGGT
66 AG-CCTTAGGGT
*
5070514 CATCTGTAAGTCTTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5070579 AGCCTTAGGGT
66 AGCCTTAGGGT
*
5070590 CATCTGTAAGTCCTGCAGTGCATGATTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5070655 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
5070666 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5070731 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
5070742 CATATGTAAGTCCTGCAGTGCATGATGTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTGTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
5070807 AACCTTAGGGT
66 AGCCTTAGGGT
5070818 CATCTGTAAGTCCTGCAGTGCATGATGTTT
1 CATCTGTAAGTCCTGCAGTGCATGATGTTT
5070848 TTACGACCTC
Statistics
Matches: 762, Mismatches: 20, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
74 63 0.08
75 145 0.19
76 500 0.66
77 54 0.07
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:5071005 original size:3 final size:3
Alignment explanation
Indices: 5070997--5071078 Score: 73
Period size: 3 Copynumber: 28.0 Consensus size: 3
5070987 TTTTACTTAA
** *
5070997 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT AAAT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
* *
5071042 ATT A-T ATAT ATT A-T ATT ATT ATT A-A ATA ATT ATT ATT
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5071079 TACAAACCGA
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
2 7 0.11
3 53 0.82
4 5 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:5071057 original size:25 final size:22
Alignment explanation
Indices: 5070997--5071078 Score: 106
Period size: 21 Copynumber: 4.0 Consensus size: 22
5070987 TTTTACTTAA
5070997 ATTATTATTAAA-ATTATTATT
1 ATTATTATTAAATATTATTATT
5071018 ATTATTATTAAATATTATTATT
1 ATTATTATTAAATATTATTATT
5071040 A-TATTA-T--ATA-TATTA-T
1 ATTATTATTAAATATTATTATT
5071056 ATTATTATTAAATAATTATTATT
1 ATTATTATTAAAT-ATTATTATT
5071079 TACAAACCGA
Statistics
Matches: 53, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.04
17 10 0.19
18 4 0.08
20 3 0.06
21 18 0.34
22 15 0.28
23 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTATTATTAAATATTATTATT
Found at i:5072411 original size:3 final size:3
Alignment explanation
Indices: 5072403--5072437 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5072393 ATATGTTTAC
5072403 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
5072438 TAACCATAAA
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:5072646 original size:20 final size:19
Alignment explanation
Indices: 5072621--5072662 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
5072611 TTATTTTATA
5072621 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
5072641 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
5072660 AAT
1 AAT
5072663 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:5074185 original size:23 final size:23
Alignment explanation
Indices: 5074159--5074202 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
5074149 ACATATTAGG
*
5074159 TAGCGCTTATATAATATAATAGT
1 TAGCGCTTATATAATAAAATAGT
5074182 TAGCGCTTATATAATAAAATA
1 TAGCGCTTATATAATAAAATA
5074203 AGTATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (23 bp):
TAGCGCTTATATAATAAAATAGT
Found at i:5074266 original size:87 final size:87
Alignment explanation
Indices: 5074119--5074280 Score: 261
Period size: 87 Copynumber: 1.9 Consensus size: 87
5074109 ATGTTATATC
* * * * *
5074119 ATTTAATCGGAAATATTATCAAGTACAATTACATATTAGGTAGCGCTTATATAATATAATAGTTA
1 ATTTAATCAGAAATATTATCAAGTAAAATAACATATTAGGTAGCACTTATATAATATAATAGGTA
*
5074184 GCGCTTATATAATAAAATAAGT
66 GCACTTATATAATAAAATAAGT
*
5074206 ATTTAATCAGAAATATTATCAAGTAAAATAACATATTAGGTAGCACTTATATAATGTAATAGGTA
1 ATTTAATCAGAAATATTATCAAGTAAAATAACATATTAGGTAGCACTTATATAATATAATAGGTA
5074271 GCACTTATAT
66 GCACTTATAT
5074281 TAACATATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 68 1.00
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.35
Consensus pattern (87 bp):
ATTTAATCAGAAATATTATCAAGTAAAATAACATATTAGGTAGCACTTATATAATATAATAGGTA
GCACTTATATAATAAAATAAGT
Found at i:5074729 original size:200 final size:198
Alignment explanation
Indices: 5074275--5074786 Score: 597
Period size: 200 Copynumber: 2.6 Consensus size: 198
5074265 TAGGTAGCAC
* * * ** * * *
5074275 TTATATTAACATATTTTCTAACT-AAATCGGTATATTTATACATGTAATATTGCAAAATTACCTA
1 TTATATTGACATATTTTCTCA-TAAAACCGGTATATTTATACCGGTTATATTGTAAATTTACCTA
* * * *
5074339 TTATATTATAATTATTAGTTTCGAA-GTTTTCGGGATCGATACAATTT--TAAATGTATCGACAC
65 TTACATTATAATTATTGGTTTC-AATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACAC
*
5074401 TTTATGCGTGCACCTCGTTGGGCATTCATTCTGAAAAAAAGTATTAACATAATCTTAAAAGTGTC
128 TTTATGCGTGCACCTCGTTGGGCATTCATTCTGAAAAAAAGTATGAACATAATCTTAAAAGTGTC
5074466 GATACA
193 GATACA
* * * * * * *
5074472 TTATGTAGACCTATTTTCTCATAAAACCGATATATTTCTACCGGGTACATTGTAAATTTACCTAT
1 TTATATTGACATATTTTCTCATAAAACCGGTATATTTATACCGGTTATATTGTAAATTTACCTAT
* *
5074537 TACATTGTAATTATCGGTTTCAATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
66 TACATTATAATTATTGGTTTCAATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
* * *
5074602 ATGCGTGCACC-CTGTTTGGCATTCATTCTTGACAAAATGTATCGACACA-AAT-TTAAAAAGTG
131 ATGCGTGCACCTC-GTTGGGCATTCATTC-TGAAAAAAAGTAT-GA-ACATAATCTT-AAAAGTG
*
5074664 TTGATACA
191 TCGATACA
* * * *
5074672 TTATATTGACATATTCTCTCATAAAAGCGGTATATTTATACCGGTTATATAGTAAATTTACCAAT
1 TTATATTGACATATTTTCTCATAAAACCGGTATATTTATACCGGTTATATTGTAAATTTACCTAT
* * * *
5074737 TACATTATAATTATTGTTTTCGATGTTTTTTGGATCGATAATTTTAATAA
66 TACATTATAATTATTGGTTTCAATGTTTTTGGGATCGATACTTTTAATAA
5074787 GAGAAAATAA
Statistics
Matches: 263, Mismatches: 43, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
196 6 0.02
197 82 0.31
198 43 0.16
199 13 0.05
200 116 0.44
201 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (198 bp):
TTATATTGACATATTTTCTCATAAAACCGGTATATTTATACCGGTTATATTGTAAATTTACCTAT
TACATTATAATTATTGGTTTCAATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
ATGCGTGCACCTCGTTGGGCATTCATTCTGAAAAAAAGTATGAACATAATCTTAAAAGTGTCGAT
ACA
Found at i:5074957 original size:21 final size:20
Alignment explanation
Indices: 5074931--5074984 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
5074921 AGTTTCCAGA
5074931 TTCGCAACGCGAACATCGACT
1 TTCGCAACGCGAACATCGA-T
*
5074952 TTCGCAACGCGAACTTCGAT
1 TTCGCAACGCGAACATCGAT
*
5074972 TATCGCAATGCGA
1 T-TCGCAACGCGA
5074985 TTTTCCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (20 bp):
TTCGCAACGCGAACATCGAT
Found at i:5075039 original size:42 final size:42
Alignment explanation
Indices: 5074980--5075235 Score: 249
Period size: 42 Copynumber: 6.1 Consensus size: 42
5074970 ATTATCGCAA
*
5074980 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
* *
5075020 TACGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
* * * *
5075062 TGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT--CGT
1 TGCGATTTATTCCAAGTT--CGTTGCGA--TAGTCCAAGTTCGCGT
** * *
5075104 T--GAGGTAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTT--CGTTGCGATAGTCCAAGTTCGCGT
* * * *
5075146 TGTGATTTATTCCAAGTTCGTTACGATAGTCGAAGTTCGCAT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
* *
5075188 TGCGATTTATTCCAAGTTCTTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
5075230 TGCGAT
1 TGCGAT
5075236 AGTCCAAAAT
Statistics
Matches: 184, Mismatches: 20, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
40 22 0.12
41 2 0.01
42 139 0.76
44 21 0.11
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (42 bp):
TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:5075077 original size:63 final size:63
Alignment explanation
Indices: 5074996--5075193 Score: 315
Period size: 63 Copynumber: 3.1 Consensus size: 63
5074986 TTTCCAAATT
* *
5074996 CGTTGCGATAGTCCAAGTTCGCGTTACGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
* *
5075059 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGAGGTAGTCCAAGTTCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
* * * *
5075122 CGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAGTTCGTTACGATAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
*
5075185 CATTGCGAT
1 CGTTGCGAT
5075194 TTATTCCAAG
Statistics
Matches: 124, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 124 1.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (63 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
Found at i:5075113 original size:105 final size:104
Alignment explanation
Indices: 5074974--5075243 Score: 327
Period size: 105 Copynumber: 2.6 Consensus size: 104
5074964 ACTTCGATTA
* * *
5074974 TCGCAATGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTACGATTTATTCCAAAT
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGA-TTAGTCCAAAT
*
5075037 T-CGTTGCGA-TAGTCCAAGTTCGCGTTGCGATAGTCGAAGT
65 TCCGTTGCGATTAGTCCAAGTT--CGTTACGATAGTCGAAGT
* * * * *
5075077 TCGCGTTGCGATTTATTCCAAATTCGTTGAGGTAGTCCAAGTTCGCGTTGCGA-TAGTCGAAGTT
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTAGTCCAAATT
* *
5075141 CGCGTTGTGATTTATTCCAAGTTCGTTACGATAGTCGAAGT
66 C-CGTTGCGA-TTAGTCCAAGTTCGTTACGATAGTCGAAGT
* * *
5075182 TCGCATTGCGATTTATTCCAAGTTCTTTGCGATAGTCGAAGTTCGCGTTGCGA-TAGTCCAAA
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTAGTCCAAA
5075244 ATCGCAACGA
Statistics
Matches: 142, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
103 17 0.12
104 2 0.01
105 113 0.80
107 10 0.07
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (104 bp):
TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTAGTCCAAATT
CCGTTGCGATTAGTCCAAGTTCGTTACGATAGTCGAAGT
Found at i:5075183 original size:19 final size:19
Alignment explanation
Indices: 5074994--5075239 Score: 123
Period size: 21 Copynumber: 11.8 Consensus size: 19
5074984 ATTTTCCAAA
*
5074994 TTCGTTGCGATAGTCCAAG
1 TTCGTTGCGATAGTCGAAG
* * * *
5075013 TTCGCGTTACGATTTATTCCAAA
1 TT--CGTTGCGA--TAGTCGAAG
*
5075036 TTCGTTGCGATAGTCCAAG
1 TTCGTTGCGATAGTCGAAG
5075055 TTCGCGTTGCGATAGTCGAAG
1 TT--CGTTGCGATAGTCGAAG
* * *
5075076 TTCGCGTTGCGATTTATTCCAAA
1 TT--CGTTGCGA--TAGTCGAAG
* * *
5075099 TTCGTTGAGGTAGTCCAAG
1 TTCGTTGCGATAGTCGAAG
5075118 TTCGCGTTGCGATAGTCGAAG
1 TT--CGTTGCGATAGTCGAAG
* * *
5075139 TTCGCGTTGTGATTTATTCCAAG
1 TT--CGTTGCGA--TAGTCGAAG
*
5075162 TTCGTTACGATAGTCGAAG
1 TTCGTTGCGATAGTCGAAG
* *
5075181 TTCGCATTGCGATTTATTCCAAG
1 TTCG--TTGCGA--TAGTCGAAG
*
5075204 TTCTTTGCGATAGTCGAAG
1 TTCGTTGCGATAGTCGAAG
5075223 TTCGCGTTGCGATAGTC
1 TT--CGTTGCGATAGTC
5075240 CAAAATCGCA
Statistics
Matches: 178, Mismatches: 31, Indels: 34
0.73 0.13 0.14
Matches are distributed among these distances:
19 40 0.22
21 102 0.57
23 36 0.20
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (19 bp):
TTCGTTGCGATAGTCGAAG
Found at i:5075248 original size:21 final size:21
Alignment explanation
Indices: 5075208--5075248 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5075198 TCCAAGTTCT
* **
5075208 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAAATCGCG
5075229 TTGCGATAGTCCAAAATCGC
1 TTGCGATAGTCCAAAATCGC
5075249 AACGACCGGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
TTGCGATAGTCCAAAATCGCG
Found at i:5076103 original size:21 final size:21
Alignment explanation
Indices: 5076079--5076271 Score: 157
Period size: 21 Copynumber: 9.3 Consensus size: 21
5076069 ACTAGTCGTT
*
5076079 GCGATTTTGGACTATCGCAAC
1 GCGAATTTGGACTATCGCAAC
* *
5076100 GCGAACTTCGACTATCGCAA-
1 GCGAATTTGGACTATCGCAAC
* * * *
5076120 -TGAATTTGTAATAAATCACAAC
1 GCGAATTTGGACT--ATCGCAAC
*
5076142 GCGAATTTGGACTATCACAA-
1 GCGAATTTGGACTATCGCAAC
*
5076162 -CGAATTTGGAATAAATCGCAAC
1 GCGAATTTGGACT--ATCGCAAC
* *
5076184 GCGAACTTGAACTATCGCAA-
1 GCGAATTTGGACTATCGCAAC
**
5076204 -CGAATTTGGAAAATCGCAAC
1 GCGAATTTGGACTATCGCAAC
5076224 GCGAACTTT-GACTATCGCAAC
1 GCGAA-TTTGGACTATCGCAAC
* *
5076245 GCGAACTTGGACTATCGCAAT
1 GCGAATTTGGACTATCGCAAC
5076266 GCGAAT
1 GCGAAT
5076272 ATGTAAATCG
Statistics
Matches: 134, Mismatches: 26, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
19 33 0.25
20 2 0.01
21 78 0.58
22 3 0.02
23 18 0.13
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (21 bp):
GCGAATTTGGACTATCGCAAC
Found at i:5076155 original size:42 final size:41
Alignment explanation
Indices: 5076092--5076245 Score: 211
Period size: 42 Copynumber: 3.7 Consensus size: 41
5076082 ATTTTGGACT
* *
5076092 ATCGCAACGCGAACTTCGACTATCGCAATGAATTTGTAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTG-AATAA
* * *
5076134 ATCACAACGCGAATTTGGACTATCACAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTT-GAATAA
* *
5076176 ATCGCAACGCGAACTTGAACTATCGCAACGAATTTGGA-AA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAATAA
*
5076216 ATCGCAACGCGAACTTTGACTATCGCAACG
1 ATCGCAACGCGAACTTGGACTATCGCAACG
5076246 CGAACTTGGA
Statistics
Matches: 99, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
40 30 0.30
41 2 0.02
42 66 0.67
43 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (41 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAATAA
Found at i:5076219 original size:19 final size:19
Alignment explanation
Indices: 5076143--5076224 Score: 67
Period size: 19 Copynumber: 4.1 Consensus size: 19
5076133 AATCACAACG
** *
5076143 CGAATTTGGACTATCACAA
1 CGAATTTGGAAAATCGCAA
5076162 CGAATTTGGAATAAATCGCAA
1 CGAATTTGG-A-AAATCGCAA
* *
5076183 CGCGAACTT-GAACTATCGCAA
1 --CGAATTTGGAA-AATCGCAA
5076204 CGAATTTGGAAAATCGCAA
1 CGAATTTGGAAAATCGCAA
5076223 CG
1 CG
5076225 CGAACTTTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
19 24 0.48
20 5 0.10
21 14 0.28
22 1 0.02
23 6 0.12
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (19 bp):
CGAATTTGGAAAATCGCAA
Found at i:5076270 original size:42 final size:40
Alignment explanation
Indices: 5076084--5076270 Score: 198
Period size: 42 Copynumber: 4.5 Consensus size: 40
5076074 TCGTTGCGAT
* * *
5076084 TTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGAA
1 TTTGGAATATCGCAACGCGAACTTTGACTATCGCAACGAA
* * *
5076124 TTTGTAATAAATCACAACGCGAA-TTTGGACTATCACAACGAA
1 TTTGGAAT--ATCGCAACGCGAACTTT-GACTATCGCAACGAA
5076166 TTTGGAATAAATCGCAACGCGAAC-TTGAACTATCGCAACGAA
1 TTTGGAAT--ATCGCAACGCGAACTTTG-ACTATCGCAACGAA
*
5076208 TTTGGAAAATCGCAACGCGAACTTTGACTATCGCAACGCGAA
1 TTTGGAATATCGCAACGCGAACTTTGACTATCGCAA--CGAA
* * *
5076250 CTTGGACTATCGCAATGCGAA
1 TTTGGAATATCGCAACGCGAA
5076271 TATGTAAATC
Statistics
Matches: 125, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
40 30 0.24
41 6 0.05
42 89 0.71
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (40 bp):
TTTGGAATATCGCAACGCGAACTTTGACTATCGCAACGAA
Found at i:5076309 original size:21 final size:21
Alignment explanation
Indices: 5076279--5076331 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
5076269 AATATGTAAA
*
5076279 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
5076300 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
5076321 TCGCGTTGCGA
1 TCGCATTGCGA
5076332 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:5079362 original size:19 final size:19
Alignment explanation
Indices: 5079338--5079385 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
5079328 TTACATTCAC
5079338 ATACAAAATTATAAATCAT
1 ATACAAAATTATAAATCAT
* *
5079357 ATACAAAATTATGAATCGT
1 ATACAAAATTATAAATCAT
5079376 ATACAAAATT
1 ATACAAAATT
5079386 TCCCCTACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:5081265 original size:20 final size:20
Alignment explanation
Indices: 5081235--5081272 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5081225 GCGGTGGTAT
5081235 CCTAGTTACATTGTTAATTTA
1 CCTAGTTACATTG-TAATTTA
5081256 CCTA-TTACATTGTAATT
1 CCTAGTTACATTGTAATT
5081273 ATCGGTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (20 bp):
CCTAGTTACATTGTAATTTA
Found at i:5081702 original size:200 final size:199
Alignment explanation
Indices: 5081239--5082120 Score: 1333
Period size: 200 Copynumber: 4.4 Consensus size: 199
5081229 TGGTATCCTA
** * * *
5081239 GTTACATTGTTAATTTACCTATTACATTGTAATTATCGGTTTTGATGTTTTTGGGATCGATACAT
1 GTTACATTGGAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGATAC-T
* * * *
5081304 TTT-A-AAATGTATCGACACTTTATGCATACACCCCCTTTGGCATTCATTCTGGAAAAAAAGTAT
65 TTTAATAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATTCTGGACAAAAAGTAT
*
5081367 CGACAAAAATTT-AAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCGGTATATTTC
130 CGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCGGTATATTTC
*
5081431 TACCA
195 TACCG
* *
5081436 GTTACATTGGAAATTTACCTATTACATTATAATTATCTATTTCGATGTTTTTGGGATCGCTACTT
1 GTTACATTGGAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGATACTT
* *
5081501 TTAATAAATGTATCGACACTTTATGCGTGCACCTCGGTTGGGCATTCATTCTGGACAAAAAGTAT
66 TTAATAAATGTATCGACACTTTATGCGTGCACC-CCGTTTGGCATTCATTCTGGACAAAAAGTAT
** * *
5081566 CGACAC-AATTTAAAAAGTGTCGATACATTATGTTTACCTGTTTTCTAATTAAACCGGTATATAT
130 CGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATT-AACCGGTATATTT
5081630 CTACCG
194 CTACCG
** *
5081636 GTTACATTGGGGATTTACGTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGATACTT
1 GTTACATTGGAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGATACTT
*
5081701 TTAATAAATGTATCGACACTTTATGAGTGCACCCCGTTTGGCATTCATTCTGGACAAAAAAGTAT
66 TTAATAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATTCTGGAC-AAAAAGTAT
* * **
5081766 CGACACAAATTTAAGAAGTGTCGATACATTATGTAGACCTGTTTTCTAATTAATTGGTATATTTC
130 CGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCGGTATATTTC
5081831 TACCG
195 TACCG
* * * *
5081836 GTTACATTAGAAAATTACCTATTACATTATAATTATATGTTTCGATATTTTTGGGATCGATACTT
1 GTTACATTGGAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGATACTT
* *
5081901 TTAATAAATGTATCGACACTTTATGCGTGCACCCCGTTTGACATTCATTCTGGACAAAACGTATC
66 TTAATAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATTCTGGACAAAAAGTATC
* * * * *
5081966 GACACAAATTTAAAAAGTATTGATACATTATGTAGACATATTTTCTAATTAACTGTTATATTTCT
131 GACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCGGTATATTTCT
5082031 ACCG
196 ACCG
* *
5082035 GTTACATTGGAAATTTACCTAGTACATTATAATTATTTGTTTCGATGTTTTT-GGATCGATACTT
1 GTTACATTGGAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGATACTT
5082099 TTAATAAATGTATCGACACTTT
66 TTAATAAATGTATCGACACTTT
5082121 TGTTTACCTA
Statistics
Matches: 623, Mismatches: 55, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
196 4 0.01
197 57 0.09
198 65 0.10
199 205 0.33
200 251 0.40
201 41 0.07
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (199 bp):
GTTACATTGGAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGATACTT
TTAATAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATTCTGGACAAAAAGTATC
GACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCGGTATATTTCT
ACCG
Found at i:5086073 original size:30 final size:30
Alignment explanation
Indices: 5086037--5086199 Score: 308
Period size: 30 Copynumber: 5.4 Consensus size: 30
5086027 TCCGAAGGAC
5086037 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5086067 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5086097 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
5086127 CTATCCAGAGGTCAAAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5086157 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
5086187 CTATCCATAGGTC
1 CTATCCAGAGGTC
5086200 CCGAAGAACC
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 130 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:5086216 original size:30 final size:30
Alignment explanation
Indices: 5086037--5086224 Score: 277
Period size: 30 Copynumber: 6.2 Consensus size: 30
5086027 TCCGAAGGAC
*
5086037 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAA
*
5086067 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAA
*
5086097 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAA
*
5086127 CTATCCAGAGGTCAAAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAA
*
5086157 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAA
* * * * *
5086187 CTATCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCACAAAGATCCTCGGT-AA
5086218 CTATCCA
1 CTATCCA
5086225 TATGTTCCTT
Statistics
Matches: 149, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 140 0.94
31 9 0.06
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGATCCTCGGTAA
Found at i:5086216 original size:90 final size:91
Alignment explanation
Indices: 5086037--5086224 Score: 306
Period size: 90 Copynumber: 2.1 Consensus size: 91
5086027 TCCGAAGGAC
*
5086037 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCAAAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
* * *
5086102 CAGAGGTCATAAAGATCCTCGGT-AA
66 CAGAGGTCACAAAGAACCTAGGTAAA
5086127 CTATCCAGAGGTCAAAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCAAAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
* * *
5086192 CATAGGTCCCGAAGAACCTAGGTAAA
66 CAGAGGTCACAAAGAACCTAGGTAAA
5086218 CTATCCA
1 CTATCCA
5086225 TATGTTCCTT
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
90 81 0.90
91 9 0.10
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (91 bp):
CTATCCAGAGGTCAAAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
CAGAGGTCACAAAGAACCTAGGTAAA
Found at i:5086223 original size:31 final size:31
Alignment explanation
Indices: 5086185--5086277 Score: 107
Period size: 31 Copynumber: 3.0 Consensus size: 31
5086175 GATCCTCGGT
* *
5086185 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
5086216 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* *
5086247 TACTATCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
5086278 GTTCTTTAAC
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 1 0.02
31 50 0.98
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:5088090 original size:3 final size:3
Alignment explanation
Indices: 5088082--5088106 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5088072 AATCCATCTA
5088082 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
5088107 TTTTATGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5090552 original size:59 final size:60
Alignment explanation
Indices: 5090459--5090616 Score: 300
Period size: 59 Copynumber: 2.6 Consensus size: 60
5090449 TTCCGAAGGA
5090459 CCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTAT
1 CCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTAT
5090519 CCAGAGGTCAT-AAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTAT
1 CCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTAT
*
5090578 CCAGAGGTCATAAAGATCCTCGGTAACTATCCATAGGTC
1 CCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTC
5090617 CCGAAGAACC
Statistics
Matches: 96, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
59 59 0.61
60 37 0.39
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (60 bp):
CCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTAT
Found at i:5090633 original size:30 final size:30
Alignment explanation
Indices: 5090459--5090616 Score: 300
Period size: 30 Copynumber: 5.3 Consensus size: 30
5090449 TTCCGAAGGA
5090459 CCAGAGGTCATAAAGATCCTCGGTAACTAT
1 CCAGAGGTCATAAAGATCCTCGGTAACTAT
5090489 CCAGAGGTCATAAAGATCCTCGGTAACTAT
1 CCAGAGGTCATAAAGATCCTCGGTAACTAT
5090519 CCAGAGGTCAT-AAGATCCTCGGTAACTAT
1 CCAGAGGTCATAAAGATCCTCGGTAACTAT
5090548 CCAGAGGTCATAAAGATCCTCGGTAACTAT
1 CCAGAGGTCATAAAGATCCTCGGTAACTAT
5090578 CCAGAGGTCATAAAGATCCTCGGTAACTAT
1 CCAGAGGTCATAAAGATCCTCGGTAACTAT
*
5090608 CCATAGGTC
1 CCAGAGGTC
5090617 CCGAAGAACC
Statistics
Matches: 126, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
29 29 0.23
30 97 0.77
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (30 bp):
CCAGAGGTCATAAAGATCCTCGGTAACTAT
Found at i:5090655 original size:30 final size:31
Alignment explanation
Indices: 5090602--5090693 Score: 89
Period size: 30 Copynumber: 3.0 Consensus size: 31
5090592 GATCCTCGGT
*
5090602 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATAGGTCCCGAAGAACATAGGTA
* **
5090633 AACTATCCATA-GTTCCTTAGAACATAGGTA
1 AACTATCCATAGGTCCCGAAGAACATAGGTA
* * * *
5090663 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATAGGTCCCGAAGA-ACATAGGTA
5090694 GTTCTTTGAC
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
30 25 0.51
31 24 0.49
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (31 bp):
AACTATCCATAGGTCCCGAAGAACATAGGTA
Found at i:5091036 original size:2 final size:2
Alignment explanation
Indices: 5091023--5091066 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
5091013 TACACAACTC
*
5091023 AT AT AA AT AT AT AT AT A- AT AT AT AT A- 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
5091063 AT AT
1 AT AT
5091067 GTAAATGTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5091045 original size:9 final size:9
Alignment explanation
Indices: 5091031--5091065 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
5091021 TCATATAAAT
5091031 ATATATATA
1 ATATATATA
5091040 ATATATATA
1 ATATATATA
5091049 ATATATAT-
1 ATATATATA
5091057 ATATATATA
1 ATATATATA
5091066 TGTAAATGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
ATATATATA
Found at i:5092142 original size:2 final size:2
Alignment explanation
Indices: 5092135--5092190 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
5092125 ATCCTTATCC
5092135 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
5092177 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
5092191 CATTTAATTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5093238 original size:15 final size:15
Alignment explanation
Indices: 5093197--5093246 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
5093187 GAAGAATCAA
*
5093197 TTGGTTGAGAAGGAGG
1 TTGGTTGAGAA-GAGC
5093213 TTGTCGTTGAGAAGAGC
1 TTG--GTTGAGAAGAGC
5093230 TTGGTTGAGAAGAGC
1 TTGGTTGAGAAGAGC
5093245 TT
1 TT
5093247 TGAGAAAGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 14 0.45
16 3 0.10
17 6 0.19
18 8 0.26
ACGTcount: A:0.24, C:0.06, G:0.40, T:0.30
Consensus pattern (15 bp):
TTGGTTGAGAAGAGC
Found at i:5094015 original size:201 final size:199
Alignment explanation
Indices: 5093535--5094502 Score: 1230
Period size: 201 Copynumber: 4.8 Consensus size: 199
5093525 CGTGAAATTT
* * *
5093535 AAAAAGGTATCGACACAAATTTAAAAAGTGTTGATACATTATGTTGATCGCT-TT-TCTAATTAA
1 AAAAA-GTATCGACACAAA-TTAAAAAGTGTCGATACATTATGTTGA-C-CTATTCTCTCATAAA
* * * *
5093598 ACTGGTATATTTATACCGATTACATTGTAAATTTACTTATTACATTATAATTATCGATTTCGATG
62 ACTGGTATATTTATACCGATTACATTGAAAAATTACATATTACATTATAATTATCGGTTTCGATG
* * * ** *
5093663 TTTTTGGGATCGATACTTTTTATAAATATATCGACACTTTGTGTGTGCACCTCGTTGGGCATTGA
127 TTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTATTTGGGCATTCA
5093728 TTCTGGAC
192 TTCTGGAC
* * * * ** * * *
5093736 AAAGAGTATTGACACAAAGTTAAAAAGTGTTGATACATTATATTGACCGCTTTTCTAATTAAACT
1 AAAAAGTATCGACACAAA-TTAAAAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAACT
* * * *
5093801 GGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGGTTTTGATGTTT
65 GGTATATTTATACCGATTACATTGAAAAATTACATATTACATTATAATTATCGGTTTCGATGTTT
* * * *
5093866 TTGGGATCGATACTTTTTTATAAATGTATTGGCACTTTATGTGTGCACCCT-TTTGGACATTCAT
130 TTGGGATCGATAC-TTTTTATAAATGTATCGACACTTTATGCGTGCA-CCTATTTGGGCATTCAT
5093930 TCTGGAC
193 TCTGGAC
* * * *
5093937 AAAAAGTATCGACACAAATTCCATAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAAAT
1 AAAAAGTATCGACACAAATT-AAAAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAACT
* * * * * *
5094002 GGTATATTTATACCGGTTAAATTGAAAAATTATATATTATATTATAATTATGGGTTTCGATATTT
65 GGTATATTTATACCGATTACATTGAAAAATTACATATTACATTATAATTATCGGTTTCGATGTTT
5094067 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATT
130 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTA-TTTGGGCATTCATT
5094132 CTGGAC
194 CTGGAC
* * *
5094138 AAAAAGTATCGACACAAACATAAAAAGTGTCGATACATTATGTTGACCTATTCTCACATAAAACC
1 AAAAAGTATCGACACAAA-TTAAAAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAACT
** *
5094203 GGTATATTTATATTGATTACATT-ACAAAATTACATATTACATTATAATTATGGGTTTCGATGTT
65 GGTATATTTATACCGATTACATTGA-AAAATTACATATTACATTATAATTATCGGTTTCGATGTT
* * *
5094267 TTTGGGAAT-AATACTTTTTATAAATGTACCGATACTTTATGCGTGCACCCCT-TTTGGGCATTC
129 TTTGGG-ATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCA--CCTATTTGGGCATTC
5094330 ATTCTGGAC
191 ATTCTGGAC
* * * * *
5094339 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACATATTCTCTCATAAAACC
1 AAAAAGTATCGACACAAATT-AAAAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAACT
* *
5094404 GGTATATTTATATCGATTACATTGAAAAATTACATATTACATTATAATTAT-GTGTTTCGAAGTT
65 GGTATATTTATACCGATTACATTGAAAAATTACATATTACATTATAATTATCG-GTTTCGATGTT
*
5094468 TTTGGGATCGATACTTTTTATAAATGCATCGACAC
129 TTTGGGATCGATACTTTTTATAAATGTATCGACAC
5094503 GTCTGTTTAC
Statistics
Matches: 680, Mismatches: 71, Indels: 32
0.87 0.09 0.04
Matches are distributed among these distances:
198 1 0.00
199 6 0.01
200 160 0.24
201 503 0.74
202 7 0.01
203 3 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (199 bp):
AAAAAGTATCGACACAAATTAAAAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAACTG
GTATATTTATACCGATTACATTGAAAAATTACATATTACATTATAATTATCGGTTTCGATGTTTT
TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTATTTGGGCATTCATTCT
GGAC
Found at i:5094974 original size:19 final size:19
Alignment explanation
Indices: 5094951--5094999 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
5094941 TTACATTCAC
*
5094951 ATACAAAATTATAATTCGTT
1 ATACAAAATTATAAATC-TT
5094971 -TACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
5094989 ATACAAAATTA
1 ATACAAAATTA
5095000 ACCCTACATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (19 bp):
ATACAAAATTATAAATCTT
Found at i:5096576 original size:18 final size:18
Alignment explanation
Indices: 5096553--5096591 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5096543 TCCTCCTCAT
* *
5096553 TTCCTCCATCTTTTCTTC
1 TTCCTCCATATTTTATTC
5096571 TTCCTCCATATTTTATTC
1 TTCCTCCATATTTTATTC
5096589 TTC
1 TTC
5096592 ATATTTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.33, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCCTCCATATTTTATTC
Found at i:5097032 original size:18 final size:18
Alignment explanation
Indices: 5097005--5097039 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5096995 CTTCCTTCTC
5097005 ATCTGCCTCCACTACCTA
1 ATCTGCCTCCACTACCTA
* *
5097023 ATCTGTCTCCTCTACCT
1 ATCTGCCTCCACTACCT
5097040 CCTTGCCAAT
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:0.17, C:0.43, G:0.06, T:0.34
Consensus pattern (18 bp):
ATCTGCCTCCACTACCTA
Found at i:5097303 original size:22 final size:22
Alignment explanation
Indices: 5097275--5097331 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
5097265 AACCTACATT
*
5097275 TATAATAAAAATTATCATTTTA
1 TATAATAAAAACTATCATTTTA
* *
5097297 TATAATAGCTATACTATCATTTTA
1 TATAATA--AAAACTATCATTTTA
5097321 TATAA-AAAAAC
1 TATAATAAAAAC
5097332 AAAAAACATT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
21 3 0.11
22 7 0.25
23 1 0.04
24 17 0.61
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (22 bp):
TATAATAAAAACTATCATTTTA
Found at i:5099619 original size:182 final size:182
Alignment explanation
Indices: 5099283--5099944 Score: 930
Period size: 182 Copynumber: 3.7 Consensus size: 182
5099273 GTTATTACGC
* *
5099283 ATACTTAT--TAAAGTATCGACACTTTCAACATATCCGGAAGCGATTTACCGGTTTTGTCATTTC
1 ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTC
* * *
5099346 GAGACCGGTTTTGTCATA----T--TT-TTATATTGTTATGGATTGATACATTTTTATAAAGTAT
66 GAGACCGATTTTATCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTTATAAAGTAT
* * *
5099404 CGATACTTTATAGGGGCTATTACTGCTTGTCTTTTAAATTCCAAAAGTGTCG
131 CGACACTTTATAGGCGCTATTACTGTTTGTCTTTTAAATTCCAAAAGTGTCG
* *
5099456 ATACTTATAATACAA-TATCGACACTTTCAACATATCTGGTAGCGTTTTACCGGTTTTGTCATTT
1 ATACTTATAATA-AAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTT
* *
5099520 TGAGACCGATTTTATCATATTTTTACTTGTTATATTGTTATGGATCGATGCATTTTTATAAAGTA
65 CGAGACCGATTTTATCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTTATAAAGTA
* * * *
5099585 TTGACACTTTATAGGCGTTATTACTGTTTGTCTTTTTAAATTCAAAAAGTGTCT
130 TCGACACTTTATAGGCGCTATTACTGTTTGTC-TTTTAAATTCCAAAAGTGTCG
* * * *
5099639 ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCACTTTACCAGTTTTTTCATTTT
1 ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTC
*
5099704 GAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTAT
66 GAGACCGATTTTATCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTTATAAAGTAT
*
5099769 CGACACTTTATAGGCGCTATTACTGTTTCTCTTTTAAATTCCAAAAGTGTCG
131 CGACACTTTATAGGCGCTATTACTGTTTGTCTTTTAAATTCCAAAAGTGTCG
* * * * *
5099821 ATGCTTATATTAAAGTATCGACACTTTCAACATATCTGGTAGTGCTTTACCGGTTTGGTCATTTC
1 ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTC
* * * * * *
5099886 GAGATCAATTTTGTCATATTTTTACATATTATATTGCTATGGATCGATACATTATTTAT
66 GAGACCGATTTTATCATATTTTTACTTGTTATATTGTTATGGATCGATACATT-TTTAT
5099945 TTGTATCGAC
Statistics
Matches: 434, Mismatches: 42, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
173 8 0.02
175 64 0.15
176 2 0.00
179 1 0.00
181 2 0.00
182 185 0.43
183 172 0.40
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (182 bp):
ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTC
GAGACCGATTTTATCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTTATAAAGTAT
CGACACTTTATAGGCGCTATTACTGTTTGTCTTTTAAATTCCAAAAGTGTCG
Found at i:5104604 original size:20 final size:21
Alignment explanation
Indices: 5104562--5104605 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5104552 ATCTAAGAAC
*
5104562 AAATAAAAAAGTTATGATGTT
1 AAATAAAAAAGATATGATGTT
*
5104583 AAATAAAATAGATATGAT-TT
1 AAATAAAAAAGATATGATGTT
5104603 AAA
1 AAA
5104606 GAAAGAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (21 bp):
AAATAAAAAAGATATGATGTT
Found at i:5106731 original size:28 final size:28
Alignment explanation
Indices: 5106688--5106742 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
5106678 GCTTCAACTT
5106688 ACTCATTTTTTGCATGTTTAGTCGGCAC
1 ACTCATTTTTTGCATGTTTAGTCGGCAC
5106716 ACTCATTTCTTT-CATGTTTAGTCGGCA
1 ACTCATTT-TTTGCATGTTTAGTCGGCA
5106743 AACTTAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.44
Consensus pattern (28 bp):
ACTCATTTTTTGCATGTTTAGTCGGCAC
Found at i:5107137 original size:28 final size:28
Alignment explanation
Indices: 5107097--5107155 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
5107087 TGTATCTTTC
*
5107097 CTTGCTAATATATTTGTTTTATTGTTTA
1 CTTGCTAATATATTTGTTTTATTGATTA
*
5107125 CTTGCTACTATATTTGTTTTATTGATTA
1 CTTGCTAATATATTTGTTTTATTGATTA
5107153 CTT
1 CTT
5107156 TTAAATATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.59
Consensus pattern (28 bp):
CTTGCTAATATATTTGTTTTATTGATTA
Found at i:5107327 original size:42 final size:42
Alignment explanation
Indices: 5107280--5107404 Score: 189
Period size: 42 Copynumber: 3.0 Consensus size: 42
5107270 CCGGTTAAAC
*
5107280 CTTCTAATAATCCGATTGGAAATTCTAATGATTCACCTAATA
1 CTTCTAATAATCCTATTGGAAATTCTAATGATTCACCTAATA
5107322 CTTCTAATAATCCTATTGGAAATT-TCAATGATTCACCTAATA
1 CTTCTAATAATCCTATTGGAAATTCT-AATGATTCACCTAATA
* ** *
5107364 CTTTTAATAATAATATTGGAAATTCCAATGATTCACCTAAT
1 CTTCTAATAATCCTATTGGAAATTCTAATGATTCACCTAAT
5107405 GATTCGATTG
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
41 1 0.01
42 75 0.99
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.38
Consensus pattern (42 bp):
CTTCTAATAATCCTATTGGAAATTCTAATGATTCACCTAATA
Found at i:5110458 original size:20 final size:20
Alignment explanation
Indices: 5110433--5110531 Score: 119
Period size: 20 Copynumber: 5.0 Consensus size: 20
5110423 ATTTAGAAAA
*
5110433 TCGCAACAAAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* ** *
5110453 TCGCAACGC-GTTTGCCAAAT
1 TCGCAACACAG-AAGTCAAAT
*
5110473 TCGCAACACTGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
5110493 TCGCAACACATAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
5110513 TCGCAACACAGAAGTCAAA
1 TCGCAACACAGAAGTCAAA
5110532 GCACGTTTAT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
19 1 0.02
20 63 0.97
21 1 0.02
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.18
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:5110488 original size:40 final size:39
Alignment explanation
Indices: 5110408--5110531 Score: 133
Period size: 40 Copynumber: 3.1 Consensus size: 39
5110398 CCCAGTTTCT
* *
5110408 AAATTCGCAACGCGAATTTAG-AAAATCGCAACAAAGAAGTC
1 AAATTCGCAACGCG--TTT-GCAAATTCGCAACACAGAAGTC
*
5110449 AAATTCGCAACGCGTTTGCCAAATTCGCAACACTGAAGTC
1 AAATTCGCAACGCGTTTG-CAAATTCGCAACACAGAAGTC
* * **
5110489 AAATTCGCAACACATAAGTCAAATTCGCAACACAGAAGTC
1 AAATTCGCAACGCGTTTG-CAAATTCGCAACACAGAAGTC
5110529 AAA
1 AAA
5110532 GCACGTTTAT
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
38 1 0.01
39 3 0.04
40 54 0.75
41 14 0.19
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.19
Consensus pattern (39 bp):
AAATTCGCAACGCGTTTGCAAATTCGCAACACAGAAGTC
Found at i:5110757 original size:20 final size:20
Alignment explanation
Indices: 5110710--5110777 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
5110700 GCAACCAAAG
* *
5110710 AAGTCAAATTCGCAACGCGT
1 AAGTCAAATTCGCAACACAT
** *
5110730 TTGCCAAATTCGCAACACAT
1 AAGTCAAATTCGCAACACAT
*
5110750 AAGTCAAATTCGCAACACAG
1 AAGTCAAATTCGCAACACAT
5110770 AAGTCAAA
1 AAGTCAAA
5110778 GCACGTTTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.19
Consensus pattern (20 bp):
AAGTCAAATTCGCAACACAT
Found at i:5110902 original size:246 final size:246
Alignment explanation
Indices: 5110488--5110951 Score: 928
Period size: 246 Copynumber: 1.9 Consensus size: 246
5110478 ACACTGAAGT
5110488 CAAATTCGCAACACATAAGTCAAATTCGCAACACAGAAGTCAAAGCACGTTTATTTTCGCAATAT
1 CAAATTCGCAACACATAAGTCAAATTCGCAACACAGAAGTCAAAGCACGTTTATTTTCGCAATAT
5110553 TAATTTCGCAACATAAATGTAAATAGTATTATCGCAAATCATAACCTAAAACCCTAAATCACAAC
66 TAATTTCGCAACATAAATGTAAATAGTATTATCGCAAATCATAACCTAAAACCCTAAATCACAAC
5110618 TCAGTCTCATCTCCATCTCTCACTCTCTACGGCGACATCCGTCCCCATCTCCGACGTAATCCGTC
131 TCAGTCTCATCTCCATCTCTCACTCTCTACGGCGACATCCGTCCCCATCTCCGACGTAATCCGTC
5110683 TATCTCCATCTCTCATAGCAACCAAAGAAGTCAAATTCGCAACGCGTTTGC
196 TATCTCCATCTCTCATAGCAACCAAAGAAGTCAAATTCGCAACGCGTTTGC
5110734 CAAATTCGCAACACATAAGTCAAATTCGCAACACAGAAGTCAAAGCACGTTTATTTTCGCAATAT
1 CAAATTCGCAACACATAAGTCAAATTCGCAACACAGAAGTCAAAGCACGTTTATTTTCGCAATAT
5110799 TAATTTCGCAACATAAATGTAAATAGTATTATCGCAAATCATAACCTAAAACCCTAAATCACAAC
66 TAATTTCGCAACATAAATGTAAATAGTATTATCGCAAATCATAACCTAAAACCCTAAATCACAAC
5110864 TCAGTCTCATCTCCATCTCTCACTCTCTACGGCGACATCCGTCCCCATCTCCGACGTAATCCGTC
131 TCAGTCTCATCTCCATCTCTCACTCTCTACGGCGACATCCGTCCCCATCTCCGACGTAATCCGTC
5110929 TATCTCCATCTCTCATAGCAACC
196 TATCTCCATCTCTCATAGCAACC
5110952 CTCACAACCA
Statistics
Matches: 218, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
246 218 1.00
ACGTcount: A:0.34, C:0.30, G:0.10, T:0.26
Consensus pattern (246 bp):
CAAATTCGCAACACATAAGTCAAATTCGCAACACAGAAGTCAAAGCACGTTTATTTTCGCAATAT
TAATTTCGCAACATAAATGTAAATAGTATTATCGCAAATCATAACCTAAAACCCTAAATCACAAC
TCAGTCTCATCTCCATCTCTCACTCTCTACGGCGACATCCGTCCCCATCTCCGACGTAATCCGTC
TATCTCCATCTCTCATAGCAACCAAAGAAGTCAAATTCGCAACGCGTTTGC
Found at i:5111338 original size:34 final size:34
Alignment explanation
Indices: 5111295--5111481 Score: 257
Period size: 34 Copynumber: 5.1 Consensus size: 34
5111285 ACGCGATTTC
5111295 ATTTTCGCGTTGCGATTTTCATTTTCGCGTTGCG
1 ATTTTCGCGTTGCGATTTTCATTTTCGCGTTGCG
5111329 ATTTTCGCGTTGCGATTTTCATTTTCGCGTTGCG
1 ATTTTCGCGTTGCGATTTTCATTTTCGCGTTGCG
5111363 ATTTTCGCGTTGCGATTTTCATTTTCGCGTTGCG
1 ATTTTCGCGTTGCGATTTTCATTTTCGCGTTGCG
5111397 ATTTTCATTTTCGCGTTGCGATTTTCATTTTCGCGTTGCG
1 ------ATTTTCGCGTTGCGATTTTCATTTTCGCGTTGCG
*
5111437 ATTTTCATTTTCGCGTTGCGATTTTCATTTTCGTGTTGCG
1 ------ATTTTCGCGTTGCGATTTTCATTTTCGCGTTGCG
5111477 ATTTT
1 ATTTT
5111482 AAGTTTCAGA
Statistics
Matches: 146, Mismatches: 1, Indels: 12
0.92 0.01 0.08
Matches are distributed among these distances:
34 73 0.50
40 73 0.50
ACGTcount: A:0.10, C:0.19, G:0.21, T:0.50
Consensus pattern (34 bp):
ATTTTCGCGTTGCGATTTTCATTTTCGCGTTGCG
Found at i:5111402 original size:14 final size:14
Alignment explanation
Indices: 5111315--5111382 Score: 82
Period size: 14 Copynumber: 4.4 Consensus size: 14
5111305 TGCGATTTTC
5111315 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
5111329 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
5111343 ATTTTCATTTTCGCGTTGCG
1 ------ATTTTCGCGTTGCG
5111363 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
5111377 ATTTTC
1 ATTTTC
5111383 ATTTTCGCGT
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
14 34 0.71
20 14 0.29
ACGTcount: A:0.09, C:0.21, G:0.24, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:5111488 original size:20 final size:20
Alignment explanation
Indices: 5111287--5111481 Score: 290
Period size: 20 Copynumber: 10.4 Consensus size: 20
5111277 AAATCGCAAC
5111287 GCGA-TTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
5111306 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
5111326 GCG------ATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
5111340 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
5111360 GCG------ATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
5111374 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
5111394 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
5111414 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
5111434 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
5111454 GCGATTTTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
5111474 GCGATTTT
1 GCGATTTT
5111482 AAGTTTCAGA
Statistics
Matches: 162, Mismatches: 1, Indels: 25
0.86 0.01 0.13
Matches are distributed among these distances:
14 28 0.17
19 4 0.02
20 130 0.80
ACGTcount: A:0.10, C:0.19, G:0.22, T:0.49
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:5113231 original size:63 final size:63
Alignment explanation
Indices: 5113154--5113273 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 63
5113144 AGGTCGGTAC
* * *
5113154 TTTACGTGAAGACAATGAG-GTATCTACGTGATGAGGTA-CGT-CTTTACGTGGTGAGGTGGATG
1 TTTACGCGAAGACAATG-GTGT-GCTACGTGATGAGGTATC-TACTTTACGTGATGAGGTGGATG
5113216 T
63 T
* *
5113217 TTTACGCGATGACAATGGTGTGCTACGTGGTGAGGTATCTACTTTACGTGATGAGGT
1 TTTACGCGAAGACAATGGTGTGCTACGTGATGAGGTATCTACTTTACGTGATGAGGT
5113274 AACCGCTCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
62 16 0.33
63 33 0.67
ACGTcount: A:0.23, C:0.12, G:0.33, T:0.33
Consensus pattern (63 bp):
TTTACGCGAAGACAATGGTGTGCTACGTGATGAGGTATCTACTTTACGTGATGAGGTGGATGT
Found at i:5113596 original size:21 final size:21
Alignment explanation
Indices: 5113572--5113665 Score: 102
Period size: 21 Copynumber: 4.5 Consensus size: 21
5113562 TGCACCTGTC
* *
5113572 ATCGTTCAAGATGCGCCTTCT
1 ATCGTTCAAGAGGCCCCTTCT
*
5113593 ATCGTTCAAGAGGCTCCTT-T
1 ATCGTTCAAGAGGCCCCTTCT
* *
5113613 CATCGTTCAAGAGGCCCCTCCC
1 -ATCGTTCAAGAGGCCCCTTCT
*
5113635 ACCGTTCAAGAGGCCCCTGTC-
1 ATCGTTCAAGAGGCCCCT-TCT
5113656 ATCGTTCAAG
1 ATCGTTCAAG
5113666 GGGTCCTTCC
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
20 1 0.02
21 60 0.97
22 1 0.02
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTTCT
Found at i:5113617 original size:42 final size:42
Alignment explanation
Indices: 5113566--5113688 Score: 156
Period size: 42 Copynumber: 2.9 Consensus size: 42
5113556 GACCGATGCA
* * * * * *
5113566 CCTGTCATCGTTCAAGATGCGCCTTCTATCGTTCAAGAGGCT
1 CCTGTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
*
5113608 CCTTTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
* * *
5113650 CCTGTCATCGTTCAAGGGGTCCTTCCCACCGTTCAAGAG
1 CCTGTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAG
5113689 CCCGATTCAC
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.19, C:0.34, G:0.21, T:0.26
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
Found at i:5113682 original size:21 final size:21
Alignment explanation
Indices: 5113595--5113688 Score: 98
Period size: 21 Copynumber: 4.5 Consensus size: 21
5113585 CGCCTTCTAT
* ** *
5113595 CGTTCAAGAGGCTCCTTTCAT
1 CGTTCAAGAGGCCCCTCCCAC
5113616 CGTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
** *
5113637 CGTTCAAGAGGCCCCTGTCAT
1 CGTTCAAGAGGCCCCTCCCAC
* * *
5113658 CGTTCAAGGGGTCCTTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
5113679 CGTTCAAGAG
1 CGTTCAAGAG
5113689 CCCGATTCAC
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.19, C:0.35, G:0.22, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCCAC
Found at i:5115163 original size:64 final size:64
Alignment explanation
Indices: 5115053--5115210 Score: 280
Period size: 64 Copynumber: 2.5 Consensus size: 64
5115043 TTAATTGAAT
5115053 TTTACATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
1 TTTA-ATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
* *
5115118 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAAGAATTATTTTTTGCTTG
1 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
*
5115182 TTTAATTGATTTGTAAAAGTTAATTTGTT
1 TTTAATTGATTTGTAAAAGTTGATTTGTT
5115211 GTTTATTCAA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 86 0.96
65 4 0.04
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.51
Consensus pattern (64 bp):
TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
Found at i:5115399 original size:20 final size:20
Alignment explanation
Indices: 5115376--5115430 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
5115366 TCGCGTTGCA
*
5115376 AATTTGACTATCGCAATGCG
1 AATTTGACTTTCGCAATGCG
* **
5115396 AATTTGACTTTCACGTTGCG
1 AATTTGACTTTCGCAATGCG
5115416 AATTTGACTTTCGCA
1 AATTTGACTTTCGCA
5115431 TCAATCGCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (20 bp):
AATTTGACTTTCGCAATGCG
Found at i:5117944 original size:24 final size:24
Alignment explanation
Indices: 5117917--5117963 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
5117907 CAAAATCCAA
5117917 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
5117941 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
5117964 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:5117972 original size:24 final size:24
Alignment explanation
Indices: 5117921--5117972 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5117911 ATCCAAGTAT
** *
5117921 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
5117945 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
5117969 TGAC
1 TGAC
5117973 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:5118722 original size:16 final size:15
Alignment explanation
Indices: 5118700--5118736 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
5118690 GAAATCATTG
5118700 AAAAATTATATAAAA
1 AAAAATTATATAAAA
*
5118715 ATAAAATTATGTAAAA
1 A-AAAATTATATAAAA
5118731 AAAAAT
1 AAAAAT
5118737 AGAGATGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:5118917 original size:19 final size:19
Alignment explanation
Indices: 5118893--5119021 Score: 134
Period size: 19 Copynumber: 6.7 Consensus size: 19
5118883 AACTAAAACT
*
5118893 TGTTGCGAAATT-AAATTC
1 TGTTGCGAATTTGAAATTC
5118911 GTGTTGCGAATTTGAAATTC
1 -TGTTGCGAATTTGAAATTC
*
5118931 AGTTGCGAATTTGAAATTC
1 TGTTGCGAATTTGAAATTC
*
5118950 AGTTGCGAATTTGAAATTC
1 TGTTGCGAATTTGAAATTC
* * *
5118969 AGATGTGAATTTGAAATTC
1 TGTTGCGAATTTGAAATTC
** *
5118988 AATTGTGAATTTGAAATTC
1 TGTTGCGAATTTGAAATTC
*
5119007 AGTGTTACGAATTTG
1 --TGTTGCGAATTTG
5119022 GCAAACGCGT
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
19 82 0.85
20 6 0.06
21 9 0.09
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.39
Consensus pattern (19 bp):
TGTTGCGAATTTGAAATTC
Found at i:5118955 original size:38 final size:38
Alignment explanation
Indices: 5118894--5119009 Score: 162
Period size: 38 Copynumber: 3.1 Consensus size: 38
5118884 ACTAAAACTT
* *
5118894 GTTGCGAAATT-AAATTCGTGTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTCA
5118932 GTTGCGAATTTGAAATTCAGTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCAGTTGCGAATTTGAAATTCA
* * * *
5118970 GATGTGAATTTGAAATTCAATTGTGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCAGTTGCGAATTTGAAATTCA
5119008 GT
1 GT
5119010 GTTACGAATT
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
38 64 0.91
39 6 0.09
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.38
Consensus pattern (38 bp):
GTTGCGAATTTGAAATTCAGTTGCGAATTTGAAATTCA
Found at i:5119979 original size:60 final size:60
Alignment explanation
Indices: 5119852--5119979 Score: 132
Period size: 60 Copynumber: 2.1 Consensus size: 60
5119842 ATAGTTGGGT
* * * * * * * *
5119852 GACCGTTTTGTAACTTTTAATAGTCAAGCGACTCAATAAAACAATACCTTATAGTTGGAG
1 GACCATTTTGTAACTTGTAATAGTCAAGAGACTCAATAAAACAACACCCTATAATCGAAG
* * * *
5119912 AATCATTTTTTAACTTGTAATAGTC-AGAGACTTAATAAAACAACACCCTATAATCGAAGG
1 GACCATTTTGTAACTTGTAATAGTCAAGAGACTCAATAAAACAACACCCTATAATCGAA-G
5119972 GACCATTT
1 GACCATTT
5119980 ATGTTTCACC
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
59 26 0.49
60 27 0.51
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (60 bp):
GACCATTTTGTAACTTGTAATAGTCAAGAGACTCAATAAAACAACACCCTATAATCGAAG
Found at i:5124118 original size:15 final size:15
Alignment explanation
Indices: 5124090--5124138 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
5124080 TAATATTATC
5124090 ATTTTATAACAAATTG
1 ATTTTAT-ACAAATTG
**
5124106 ATTTTATACAAATCA
1 ATTTTATACAAATTG
*
5124121 ATTTTATTATAAATTG
1 ATTTTA-TACAAATTG
5124137 AT
1 AT
5124139 CATTCAACCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (15 bp):
ATTTTATACAAATTG
Found at i:5124686 original size:169 final size:169
Alignment explanation
Indices: 5124448--5124853 Score: 591
Period size: 169 Copynumber: 2.4 Consensus size: 169
5124438 CGTTTAAAAT
* * * *
5124448 CGCTATTTCACAATCACAATACCTGTAGTGACTGCAATAGCACTCGCTATTGTTATAATCACAAT
1 CGCTATTTCACAATCACAATACCCGTAGTGACTGCAATAGCACCCGCTATTGTTATAATCGCGAT
* *
5124513 AAAATGAAAATTTAAGTGGAGGGACATTGAGGAGCAGAGATTTAAATAATTG-TCCATTATCGGA
66 AAAATGAAAATTTAAGTGGAGGGACATTGAGGAGCAGAAATTTAAAT-AGTGATCCATTATCGGA
*** ** *
5124577 ATAGTGGTCGTTATGTAGTGGTAAAGGTGCCATTCC-AAAC
130 ATAGTGGTCGTTACACAACGGTAAAGGTGCC-GTCCGAAAC
* * * *
5124617 CGCTATTTCATAATCACAATACCCGTAGTGACTGCAATAGCACCCACTATTGCTATAATCGTGAT
1 CGCTATTTCACAATCACAATACCCGTAGTGACTGCAATAGCACCCGCTATTGTTATAATCGCGAT
* *
5124682 AAAATGGAAATTTAAGTGGAGGGACATTGAGGAGCAGAAATTTTAATAGTGATCCATTATCGGAA
66 AAAATGAAAATTTAAGTGGAGGGACATTGAGGAGCAGAAATTTAAATAGTGATCCATTATCGGAA
*
5124747 TAGTGGTCGTTACACAACGGTAAATGTGCCGTCCGAAAC
131 TAGTGGTCGTTACACAACGGTAAAGGTGCCGTCCGAAAC
* *
5124786 CGCTATTTCACAATCACAATACCCGTAGTGACTGCAATAACACCCGCTATTGTTGTAATCGCGAT
1 CGCTATTTCACAATCACAATACCCGTAGTGACTGCAATAGCACCCGCTATTGTTATAATCGCGAT
5124851 AAA
66 AAA
5124854 CACAATGAAA
Statistics
Matches: 210, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
168 6 0.03
169 204 0.97
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (169 bp):
CGCTATTTCACAATCACAATACCCGTAGTGACTGCAATAGCACCCGCTATTGTTATAATCGCGAT
AAAATGAAAATTTAAGTGGAGGGACATTGAGGAGCAGAAATTTAAATAGTGATCCATTATCGGAA
TAGTGGTCGTTACACAACGGTAAAGGTGCCGTCCGAAAC
Found at i:5129725 original size:30 final size:29
Alignment explanation
Indices: 5129641--5129750 Score: 103
Period size: 30 Copynumber: 3.7 Consensus size: 29
5129631 GTTATATCTC
* *
5129641 AAATAAGTGCCTAAAGTATTTTTTTGTCA
1 AAATAAATACCTAAAGTATTTTTTTGTCA
* *
5129670 AAATAAATACCTAAACTTATCTTTTTGGTCA
1 AAATAAATACCTAAA-GTAT-TTTTTTGTCA
** * *
5129701 AAATAGGTACTTAAAGTATTTTTTTAGTCT
1 AAATAAATACCTAAAGTATTTTTTT-GTCA
* *
5129731 AAATAACTACCTAATGTATT
1 AAATAAATACCTAAAGTATT
5129751 CAATATTTTC
Statistics
Matches: 64, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
29 18 0.28
30 25 0.39
31 21 0.33
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (29 bp):
AAATAAATACCTAAAGTATTTTTTTGTCA
Found at i:5129862 original size:29 final size:29
Alignment explanation
Indices: 5129830--5129899 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 29
5129820 TGAAAAAATT
5129830 AAATAATTTAGGTACCTATTTTGATCAAA
1 AAATAATTTAGGTACCTATTTTGATCAAA
* * * *
5129859 AAATAAGTTTAAGTGCTTATTTTGATTAAA
1 AAATAA-TTTAGGTACCTATTTTGATCAAA
5129889 AAATAATTTAG
1 AAATAATTTAG
5129900 ATACTTAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 10 0.29
30 25 0.71
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (29 bp):
AAATAATTTAGGTACCTATTTTGATCAAA
Found at i:5131197 original size:20 final size:20
Alignment explanation
Indices: 5131172--5131264 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
5131162 TTTTCCCAAT
5131172 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
5131192 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
*
5131212 TTCGCAATGCGAATAATTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
5131233 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
5131254 TCGCAATGCGA
1 TCGCAATGCGA
5131265 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 27 0.48
21 29 0.52
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:5131214 original size:41 final size:41
Alignment explanation
Indices: 5131169--5131264 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
5131159 CGATTTTCCC
5131169 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
5131210 AATTCGCAATGCGAATAATTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
5131251 AAATCGCAATGCGA
1 AATTCGCAATGCGA
5131265 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:5131218 original size:21 final size:20
Alignment explanation
Indices: 5131172--5131264 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
5131162 TTTTCCCAAT
*
5131172 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
5131192 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
**
5131212 TTCGCAATGCGAATAATTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
5131233 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
5131254 TCGCAATGCGA
1 TCGCAATGCGA
5131265 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 28 0.50
21 28 0.50
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:5131278 original size:20 final size:20
Alignment explanation
Indices: 5131253--5131387 Score: 137
Period size: 20 Copynumber: 6.7 Consensus size: 20
5131243 AATTGGGAAA
5131253 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
5131273 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * **
5131293 ATCGCAATGCGATAATAAAAA
1 ATCGCAATGCGATACT-GACT
* * *
5131314 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
5131334 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
5131354 TTCGCAATGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
5131374 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
5131388 TTTCAAAGCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
19 2 0.02
20 68 0.71
21 26 0.27
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:5131297 original size:61 final size:61
Alignment explanation
Indices: 5131250--5131381 Score: 192
Period size: 61 Copynumber: 2.2 Consensus size: 61
5131240 GCGAATTGGG
* * *
5131250 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAATGCGATAATAA
* * * *
5131311 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGACTTTCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAATGCGATAATAA
*
5131372 ATAATCGCAA
1 AAAATCGCAA
5131382 TGCGATTTTC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAATGCGATAATAA
Found at i:5131583 original size:22 final size:22
Alignment explanation
Indices: 5131555--5131598 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5131545 CACTCTCTCA
5131555 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
5131577 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
5131599 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:5131887 original size:20 final size:20
Alignment explanation
Indices: 5131862--5131899 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5131852 CGATTCTCTC
5131862 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
5131882 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
5131900 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:5133240 original size:18 final size:18
Alignment explanation
Indices: 5133219--5133263 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
5133209 TCCACTTCGG
*
5133219 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
5133237 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
5133255 GAGCCATCA
1 GAGCCATCA
5133264 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:5133790 original size:19 final size:20
Alignment explanation
Indices: 5133736--5133802 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
5133726 TAGTTTACTT
* *
5133736 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
5133756 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
5133776 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
5133795 TCGCAACG
1 TCGCAACG
5133803 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:5133810 original size:14 final size:14
Alignment explanation
Indices: 5133791--5133848 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
5133781 ATGCGAAATG
5133791 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
5133805 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
5133821 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
5133837 AAAATCGCAACG
1 AAAATCGCAACG
5133849 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:5133833 original size:32 final size:33
Alignment explanation
Indices: 5133775--5133865 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
5133765 GGAAATGGCT
*
5133775 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
5133808 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
5133840 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
5133866 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:5133859 original size:19 final size:19
Alignment explanation
Indices: 5133736--5133870 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
5133726 TAGTTTACTT
* **
5133736 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
5133756 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
5133776 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5133795 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
5133809 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
5133827 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
5133841 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5133860 TCGCAATGCGA
1 TCGCAACGCGA
5133871 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:5133901 original size:14 final size:14
Alignment explanation
Indices: 5133882--5133939 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
5133872 TTGTGTTTCG
5133882 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
5133896 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
5133912 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
5133928 CGTTGCGATTTT
1 CGTTGCGATTTT
5133940 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:5133916 original size:32 final size:33
Alignment explanation
Indices: 5133877--5133955 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
5133867 GCGATTTGTG
5133877 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
5133909 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
5133942 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
5133956 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:5133954 original size:19 final size:19
Alignment explanation
Indices: 5133896--5134013 Score: 86
Period size: 20 Copynumber: 6.4 Consensus size: 19
5133886 GCGATTTTGT
5133896 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
5133914 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
5133928 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
5133947 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
5133967 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
* *
5133986 CGTTGCAATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
5134006 TGTTGCGA
1 CGTTGCGA
5134014 AAGTAAACTA
Statistics
Matches: 79, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.03
17 2 0.03
18 11 0.14
19 25 0.32
20 28 0.35
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:5135879 original size:14 final size:14
Alignment explanation
Indices: 5135860--5135895 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5135850 ATTGTTTAAT
5135860 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
5135874 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
5135888 TGATTTGT
1 TGATTTGT
5135896 TTAATTGATG
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:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:5136021 original size:14 final size:14
Alignment explanation
Indices: 5136002--5136073 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 14
5135992 CGAAATGGCT
5136002 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
*
5136016 ATCGCAATGCGAAATGAA
1 ATCGCAA--CGAGA--AA
5136034 ATCGCAATACGAAATGAAA
1 ATCGC-A-ACG--A-GAAA
5136053 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
5136067 ATCGCAA
1 ATCGCAA
5136074 TGCGATTTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 18
0.70 0.03 0.27
Matches are distributed among these distances:
14 18 0.38
15 1 0.02
16 4 0.09
17 3 0.06
18 10 0.21
19 8 0.17
20 2 0.04
21 1 0.02
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:5136034 original size:19 final size:19
Alignment explanation
Indices: 5136012--5136078 Score: 83
Period size: 18 Copynumber: 3.8 Consensus size: 19
5136002 ATCGCAACGA
5136012 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
5136031 G-AAATCGCAATACGAAAT
1 GAAAATCGCAATGCGAAAT
5136049 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
5136063 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
5136079 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
18 17 0.40
19 10 0.23
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:5136154 original size:20 final size:20
Alignment explanation
Indices: 5136104--5136154 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
5136094 GCGATATTCT
* *
5136104 CGTTGCGATAACCATTTTCG
1 CGTTGCGATAGCCATTTTCA
5136124 CGTTGCGATAGCCATTTTCA
1 CGTTGCGATAGCCATTTTCA
5136144 CGTTGCGATAG
1 CGTTGCGATAG
5136155 TCAAATGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCA
Found at i:5137267 original size:24 final size:23
Alignment explanation
Indices: 5137211--5137269 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
5137201 AGTCAGTATT
*
5137211 CGAAATTTGATCTTGGTCAATAC
1 CGAAATTTGATATTGGTCAATAC
* *
5137234 CCAGACTTTGATATTGGTCAATAC
1 CGA-AATTTGATATTGGTCAATAC
*
5137258 ACGAATTTTGAT
1 -CGAAATTTGAT
5137270 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 2 0.07
24 25 0.86
25 2 0.07
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (23 bp):
CGAAATTTGATATTGGTCAATAC
Found at i:5139803 original size:33 final size:33
Alignment explanation
Indices: 5139761--5139854 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
5139751 GGAAATTACT
*
5139761 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
5139794 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
5139827 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
5139855 CGAATTTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:5139817 original size:19 final size:19
Alignment explanation
Indices: 5139761--5139858 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
5139751 GGAAATTACT
5139761 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
5139780 ATCACAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
5139794 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
5139813 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
5139827 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
5139846 ATCGCAACGCGAA
1 ATCGCAATGCGAA
5139859 TTTAATTTCG
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 18 0.30
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 30 0.50
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:5139889 original size:20 final size:20
Alignment explanation
Indices: 5139864--5139916 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
5139854 GCGAATTTAA
*
5139864 TTTCGCGTTGTGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
5139884 TTTCGCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
*
5139903 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
5139917 AGTACTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.11, C:0.19, G:0.21, T:0.49
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:5140042 original size:14 final size:14
Alignment explanation
Indices: 5140023--5140059 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5140013 CATCAATTAA
5140023 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5140037 ACAAATCACCTTTT
1 ACAAATCAACTTTT
5140051 ACAAATCAA
1 ACAAATCAA
5140060 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5141503 original size:42 final size:42
Alignment explanation
Indices: 5141457--5141540 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
5141447 CGATGACAGT
* * *
5141457 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
5141499 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
5141541 CGAGTCGAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:5143585 original size:20 final size:19
Alignment explanation
Indices: 5143540--5143724 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
5143530 TCTTTTGGTT
*
5143540 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
5143559 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
5143579 GGAAATGACTATCGCAA--T
1 -GAAATGAAAATCGCAACGC
*
5143597 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
5143613 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
5143631 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
5143646 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
* *
5143666 GAAATTAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
5143685 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
5143704 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
5143723 GA
1 GA
5143725 TTTTGGTTTC
Statistics
Matches: 134, Mismatches: 19, Indels: 26
0.75 0.11 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 1 0.01
17 1 0.01
18 3 0.02
19 60 0.45
20 45 0.34
21 2 0.01
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:5143622 original size:33 final size:33
Alignment explanation
Indices: 5143565--5143663 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
5143555 ACGAGATAAT
**
5143565 GAGAATCGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
5143599 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
5143632 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
5143664 GCGAAATTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Done.