Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007909.1 Hibiscus syriacus cultivar Beakdansim tig00110303_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: 3382237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 17
Found at i:2942382 original size:124 final size:123
Alignment explanation
Indices: 2942163--2942386 Score: 324
Period size: 124 Copynumber: 1.8 Consensus size: 123
2942153 ATCAACATTT
* * * * * * *
2942163 CCAGAGAAAGTTCATAATAAGAAGAATTTATTTGAAGAGGAAGAAGAAGTTCACAATGAGAAGAG
1 CCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAAAGAAAGAAGAAGTTCACAATAAGAAGAA
* * *
2942228 CTTGTTCAACCTTTTGCATAATTCTATCACAGAAGCAGATATATTAGCATAAACCTTC
66 CTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAGATATATTAGCATAAACCTTC
2942286 CCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCA-AGATAAGAAG
1 CCAGAGAAAGTTCATAATAAGAAGAACTCATCTG-AAAAGAAAGAAGAAGTTCACA-ATAAGAAG
*
2942350 AACTTATTCAACCTTTTGAATGACTCTATCACAGAAG
64 AACTTATTCAACCTTTTGAATAACTCTATCACAGAAG
2942387 GAAATAGGTT
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
123 32 0.36
124 56 0.64
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (123 bp):
CCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAAAGAAAGAAGAAGTTCACAATAAGAAGAA
CTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAGATATATTAGCATAAACCTTC
Found at i:2942587 original size:5 final size:5
Alignment explanation
Indices: 2942572--2942601 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
2942562 GTAAACATCA
2942572 ATTTT -TTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A
2942602 AAATTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:2942614 original size:3 final size:3
Alignment explanation
Indices: 2942606--2942671 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
2942596 ATTTTAAAAT
** * * *
2942606 TTA TTA TTA TTA TTA AAA TTA TAA TTA TTT TTA TTA TTA TTA ATA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
2942655 TTA TTTA TTA ATA TTA T
1 TTA -TTA TTA TTA TTA T
2942672 AAAGCCCAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2942664 original size:17 final size:16
Alignment explanation
Indices: 2942594--2942668 Score: 57
Period size: 15 Copynumber: 4.8 Consensus size: 16
2942584 TTATTTTATT
* *
2942594 TTATT-TTAAAATTTA
1 TTATTATTAATATATA
* *
2942609 TTATTATTATTA-AAA
1 TTATTATTAATATATA
* * *
2942624 TTATAATT-ATTTTTA
1 TTATTATTAATATATA
2942639 TTATTATTAATATATA
1 TTATTATTAATATATA
2942655 TTATTTATTAATAT
1 TTA-TTATTAATAT
2942669 TATAAAGCCC
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
14 1 0.02
15 21 0.48
16 12 0.27
17 10 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATTATTAATATATA
Found at i:2947961 original size:2 final size:2
Alignment explanation
Indices: 2947889--2947950 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
2947879 CATTCCAGAT
2947889 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2947931 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
2947951 AACTCATATA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2957626 original size:22 final size:22
Alignment explanation
Indices: 2957601--2957686 Score: 93
Period size: 22 Copynumber: 3.9 Consensus size: 22
2957591 ACTAGAACCC
*
2957601 CAAGGGGGTATCGATTCCCCTA
1 CAAGGGGGAATCGATTCCCCTA
* *
2957623 CAAGGGGAAATCGGTTCCCCTTTA
1 CAAGGGGGAATCGATTCCCC--TA
* *
2957647 -AAGGGGGAATCGGTTCCCCTT
1 CAAGGGGGAATCGATTCCCCTA
*
2957668 CAAGGGGGTATCGATTCCC
1 CAAGGGGGAATCGATTCCC
2957687 TCTGCACTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
21 1 0.02
22 33 0.61
23 18 0.33
24 2 0.04
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.23
Consensus pattern (22 bp):
CAAGGGGGAATCGATTCCCCTA
Found at i:2963200 original size:109 final size:109
Alignment explanation
Indices: 2963029--2963364 Score: 353
Period size: 109 Copynumber: 3.1 Consensus size: 109
2963019 ACTTAAATAA
* * * * * * *
2963029 GGGGACTAAACAACAAATTTTCCAATAAACATATAATATACAAG-A-AAAAAATGGTAAATAACA
1 GGGGACTAAACAACAAATATCCCAAAAAAAATAT-ATA-ACATGCATGAAAAAGGGTAAATAACA
*
2963092 ATGGTGGTCCTCACAGTTGACCAACATGCAAAAACATGCTAAACTATG
64 AT-TTGGTCCTCACAG-TGACCAACATGCAAAAACATGCTAAACTATG
*
2963140 GGGGACTAAACAACAAATATCTCC-AAAACAA-ATATAACATGCATG-AAAAGGGTAAATAACAA
1 GGGGACTAAACAACAAATATC-CCAAAAAAAATATATAACATGCATGAAAAAGGGTAAATAACAA
* * * * *
2963202 CTTTAGTCATCACAGGTAACCAACATGCAAAAACACGCTAAACTATA
65 -TTTGGTCCTCACA-GTGACCAACATGCAAAAACATGCTAAACTATG
* * *
2963249 GGGGACTAAACAACAAATTTCCCAAAAAAAATATATAACTTGCATGAAAAAGGGTAAATAATAAT
1 GGGGACTAAACAACAAATATCCCAAAAAAAATATATAACATGCATGAAAAAGGGTAAATAACAA-
**
2963314 TTTGGTCCTTGCA-AGTGACCAACATATAAAAA-ATGCTAAACTATG
65 TTTGGTCC-T-CACAGTGACCAACATGCAAAAACATGCTAAACTATG
*
2963359 GTGGAC
1 GGGGAC
2963365 CTATGCGATA
Statistics
Matches: 188, Mismatches: 27, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
108 6 0.03
109 83 0.44
110 33 0.18
111 60 0.32
112 4 0.02
113 2 0.01
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (109 bp):
GGGGACTAAACAACAAATATCCCAAAAAAAATATATAACATGCATGAAAAAGGGTAAATAACAAT
TTGGTCCTCACAGTGACCAACATGCAAAAACATGCTAAACTATG
Found at i:2964338 original size:6 final size:6
Alignment explanation
Indices: 2964327--2964356 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2964317 ATATTAAAAT
*
2964327 TTTATA TTTATA TTTATA TTTAAA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA
2964357 ATTAGATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TTTATA
Found at i:2964344 original size:12 final size:12
Alignment explanation
Indices: 2964317--2964356 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2964307 AAAATTTAAA
*
2964317 ATATTAAAATTTT
1 ATATTTAAA-TTT
*
2964330 ATATTTATATTT
1 ATATTTAAATTT
2964342 ATATTTAAATTT
1 ATATTTAAATTT
2964354 ATA
1 ATA
2964357 ATTAGATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATATTTAAATTT
Found at i:2964757 original size:134 final size:134
Alignment explanation
Indices: 2964568--2965057 Score: 513
Period size: 133 Copynumber: 3.6 Consensus size: 134
2964558 ATCGAATCTG
* * * *
2964568 AAAAGGGG-TCTGCTTCGCTAC-TCTTCAGGGTAGATCATATCTGGAAATGTTGATTCATTCCAC
1 AAAAGGGGATCTACTCCGCTACTTCTTCAGGGTAGATCAGATCTGAAAATGTTGATTCATTCCAC
* * * * * *
2964631 TATTCTTCAGGGAAGATAT-AATTGAGGAAGATTTGTTCCACTGCTACTTCATGGAAGATCAAAT
66 TATTCTTCAGGGAAGAT-TGAATCGAGGTAGACTTGTTTCACTGCTTCTTCAGGGAAGATCAAAT
2964695 ATGGA
130 ATGGA
* * * * *
2964700 AAAAGGGGATATACTCCGCTGCTTCTTCAGGGTAGATTAGATCTGAAAATATTGATTCATTCCAT
1 AAAAGGGGATCTACTCCGCTACTTCTTCAGGGTAGATCAGATCTGAAAATGTTGATTCATTCCAC
* * * * * * *
2964765 TGTTCTTCATGGAATATTGAATCGATGTAGACTTGTTTCATTTCTTCTTCAGGGAAGTTCAAATA
66 TATTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTTCACTGCTTCTTCAGGGAAGATCAAATA
2964830 TGG-
131 TGGA
* * ** * * *
2964833 AAAAGGGGATCTACCCCACTACTTCTTCAGGGTAGATCTTATTTGGAAATGGTGATTCATTCCAC
1 AAAAGGGGATCTACTCCGCTACTTCTTCAGGGTAGATCAGATCTGAAAATGTTGATTCATTCCAC
* * * * * *
2964898 TGTTCTTCAAGGAATATTGAATCGAGGTAGACTTGTTTCAGTGCTTCTTCAGGGAGGATCAAATC
66 TATTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTTCACTGCTTCTTCAGGGAAGATCAAATA
2964963 TGGAAAA
131 TGG---A
* * * * * * *
2964970 AGAAAGGGGATCTTCTCCGCTTCTTTTTCAAGGTAAATCAGATCCGAAAACGTTGATTCATTCCA
1 A-AAAGGGGATCTACTCCGCTACTTCTTCAGGGTAGATCAGATCTGAAAATGTTGATTCATTCCA
2965035 C-AGTTCTTCAGGGAAGATTGAAT
65 CTA-TTCTTCAGGGAAGATTGAAT
2965058 GGAGTTCAAT
Statistics
Matches: 291, Mismatches: 58, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
132 8 0.03
133 124 0.43
134 90 0.31
137 1 0.00
138 68 0.23
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (134 bp):
AAAAGGGGATCTACTCCGCTACTTCTTCAGGGTAGATCAGATCTGAAAATGTTGATTCATTCCAC
TATTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTTCACTGCTTCTTCAGGGAAGATCAAATA
TGGA
Found at i:2966527 original size:644 final size:646
Alignment explanation
Indices: 2965286--2966556 Score: 1951
Period size: 644 Copynumber: 2.0 Consensus size: 646
2965276 TGGGACTTTG
* *
2965286 AATTGGTTACTTTTATATTGGGTCCCGACATCTTCAACCTTTCCCTTTAGAAAACTTGTAAGTAC
1 AATTGGTTACTTTTATATTGGATCCCGACATCTTCAACCTTTCCCTTTAGAAAACCTGTAAGTAC
* * * *
2965351 TCAATTACAACTATCATCATCATGCATTTTATGAATATCATGATCTTATTTATACTTAATATGTG
66 TCAATTACAACTATCATCATCATGCATTTCATGAATATCACGATCTTATTTATACCTAAAATGTG
* * * * * *
2965416 CGCAATTATGTAATTTTAGGGTATTTTCTTTTTCAAATGATAACTCTCTTTTGTCGACCCCTTGT
131 CGAAATGATGCAATTTTAGGGTATTTTCATTTTCAAATGAGAACTCTCTTTTGTCGAACCCTTGT
* *
2965481 AATTCAATCAAATCTTGGGAATAAAAATCACCAACAGTTCACCCTAACTAACAATCCTGATCAGT
196 AATTCAATCAAATCTTGGGAATAAAAATCACCAACAGTTCACCCCAACTAACAATCCTGATCAGA
2965546 CACTCTTTGGTTAGACATGACTTTGATTCTCTTTAATCTTGAACCCAGGCATTATTCATGACCAA
261 CACTCTTTGGTTAGACATGACTTTGATTCTCTTTAATCTTGAACCCAGGCATTATTCATGACCAA
* * *
2965611 CTACTTGATCAGCGATAAATATCTTGGATTATCCCAACTTGCTGAGCTTTTATATGTAGCCCAAG
326 CTACTTGATCAACGACAAATATATTGGATTATCCCAACTTGCTGAGCTTTTATATGTAGCCCAAG
* * * * *
2965676 GTTTTAATTTTCTATAACCCATCTTCATGTAAGCATCATGCTAAAACCATTTTCATCTTCGGAAC
391 GTTTTAATTTTCCATAACCCATCATCATGTAAACATCATGCTAAAACCATTTTCAGCTTCAGAAC
* *
2965741 ACTTACACTTTTCCAAAACTTTTTGTACAATAATACACACTGATCTCATATTTCCCAAGTTAATC
456 ACATACACTTTTCCAAAACCTTTTGTACAATAATACACACTGATCTCATATTTCCCAAGTTAATC
* *
2965806 TACATGTTTTTATCTTCAAATTAGGATGCTTGCAATATGGTTTTAATAAGAAAAATCACTCATAT
521 TACATGTTTTTATCTTCAAATTAGGATGCTTGCAACATGGTTTTAACAAGAAAAATCACTCATAT
2965871 TATTTATATAAATGTAAAGAGTTTTTTTGGGTAAATACATGGAAAAATATTAATTTAACTC
586 TATTTATATAAATGTAAAGAGTTTTTTTGGGTAAATACATGGAAAAATATTAATTTAACTC
* *
2965932 AATTGGTTACTTTTATATTGGATCTCGACATCTTCAACCTTT-CCTTTCGAAAAACCTGTAAGTA
1 AATTGGTTACTTTTATATTGGATCCCGACATCTTCAACCTTTCCCTTTAG-AAAACCTGTAAGTA
* * * *
2965996 CTCAATTGCATCTATCATCATCATGCATTTCATGAATGTCACGAT-TCTATTTATGCCTAAAATG
65 CTCAATTACAACTATCATCATCATGCATTTCATGAATATCACGATCT-TATTTATACCTAAAATG
*
2966060 TGTGAAATGATGCAATTTTAGGGTATTTTCATTTTCAAATGAGAACT-TACTTTTGTC-AACCCT
129 TGCGAAATGATGCAATTTTAGGGTATTTTCATTTTCAAATGAGAACTCT-CTTTTGTCGAACCCT
* ** * *
2966123 TGTAATTCAGTCAAATC-TGGGACATAAAAAT-ACCAGTAGTTCACCCCAGCTGACAATCCTGAT
193 TGTAATTCAATCAAATCTTGGGA-ATAAAAATCACCAACAGTTCACCCCAACTAACAATCCTGAT
* * * *
2966186 CAGAGACTCTTTGGTTTGACATGACTTTGATTCTCTTTATTCTTGAACCCATGCATTATTCATGA
257 CAGACACTCTTTGGTTAGACATGACTTTGATTCTCTTTAATCTTGAACCCAGGCATTATTCATGA
* *
2966251 CCAGCTACTTGATCAATGACAAATATATTGGATTATCCCAACTTGCTGAGCTTTTATATGTAGCC
322 CCAACTACTTGATCAACGACAAATATATTGGATTATCCCAACTTGCTGAGCTTTTATATGTAGCC
* * * * *
2966316 CAAGTTTTTGATTTTCCGTAGCCCATCATCATGTAAACCTCATGCTAAAACCATTTTCAGCTTCA
387 CAAGGTTTTAATTTTCCATAACCCATCATCATGTAAACATCATGCTAAAACCATTTTCAGCTTCA
* * *
2966381 GAACGCATGCACTTTTCCAAAACCTTTTGTACAATAATACACACTGATCTCATGTTTCCCAAGTT
452 GAACACATACACTTTTCCAAAACCTTTTGTACAATAATACACACTGATCTCATATTTCCCAAGTT
* *
2966446 AATCTACATGTTTTTATCTTCAAATTAGGATGTTTGCAACATGGTTTTAACAAGAAAAATGACTC
517 AATCTACATGTTTTTATCTTCAAATTAGGATGCTTGCAACATGGTTTTAACAAGAAAAATCACTC
* * *
2966511 GTTTTATTTTTATAAATGTAAAGAGTTTTTTTGGGTAAATACATGG
582 ATATTATTTATATAAATGTAAAGAGTTTTTTTGGGTAAATACATGG
2966557 TAAACTTTTA
Statistics
Matches: 564, Mismatches: 57, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
644 371 0.66
645 37 0.07
646 156 0.28
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (646 bp):
AATTGGTTACTTTTATATTGGATCCCGACATCTTCAACCTTTCCCTTTAGAAAACCTGTAAGTAC
TCAATTACAACTATCATCATCATGCATTTCATGAATATCACGATCTTATTTATACCTAAAATGTG
CGAAATGATGCAATTTTAGGGTATTTTCATTTTCAAATGAGAACTCTCTTTTGTCGAACCCTTGT
AATTCAATCAAATCTTGGGAATAAAAATCACCAACAGTTCACCCCAACTAACAATCCTGATCAGA
CACTCTTTGGTTAGACATGACTTTGATTCTCTTTAATCTTGAACCCAGGCATTATTCATGACCAA
CTACTTGATCAACGACAAATATATTGGATTATCCCAACTTGCTGAGCTTTTATATGTAGCCCAAG
GTTTTAATTTTCCATAACCCATCATCATGTAAACATCATGCTAAAACCATTTTCAGCTTCAGAAC
ACATACACTTTTCCAAAACCTTTTGTACAATAATACACACTGATCTCATATTTCCCAAGTTAATC
TACATGTTTTTATCTTCAAATTAGGATGCTTGCAACATGGTTTTAACAAGAAAAATCACTCATAT
TATTTATATAAATGTAAAGAGTTTTTTTGGGTAAATACATGGAAAAATATTAATTTAACTC
Found at i:2967027 original size:14 final size:13
Alignment explanation
Indices: 2967005--2967038 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2966995 CTTTTATTTA
*
2967005 TTTTCTTTTCTTT
1 TTTTTTTTTCTTT
2967018 TTTATTTTTTCTTT
1 TTT-TTTTTTCTTT
2967032 TTTTTTT
1 TTTTTTT
2967039 ATTTTCCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTCTTT
Found at i:2967036 original size:18 final size:18
Alignment explanation
Indices: 2967005--2967053 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 18
2966995 CTTTTATTTA
2967005 TTTTCTTTTCTTTTTTATT
1 TTTTCTTTT-TTTTTTATT
2967024 TTTTCTTTTTTTTTTATT
1 TTTTCTTTTTTTTTTATT
*
2967042 TTCCTCTTTTTT
1 TT-TTCTTTTTT
2967054 CATTTTTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTCTTTTTTTTTTATT
Found at i:2967040 original size:35 final size:34
Alignment explanation
Indices: 2966996--2967062 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 34
2966986 TTGAAGCCCC
*
2966996 TTTTATTTATTTTCTTTTCTTTTTT-ATTTTTTCTT
1 TTTTATTTATTTTC--CTCTTTTTTCATTTTTTCTT
*
2967031 TTTTTTTTATTTTCCTCTTTTTTCATTTTTTC
1 TTTTATTTATTTTCCTCTTTTTTCATTTTTTC
2967063 CATTTTTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 8 0.28
34 8 0.28
35 13 0.45
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (34 bp):
TTTTATTTATTTTCCTCTTTTTTCATTTTTTCTT
Found at i:2967051 original size:17 final size:16
Alignment explanation
Indices: 2966995--2967053 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
2966985 CTTGAAGCCC
*
2966995 CTTTTATTTATTTTCT
1 CTTTTTTTTATTTTCT
*
2967011 TTTCTTTTTTATTTTTTCT
1 CTT-TTTTTTA--TTTTCT
*
2967030 TTTTTTTTTATTTTCCT
1 CTTTTTTTTATTTT-CT
2967047 CTTTTTT
1 CTTTTTT
2967054 CATTTTTTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 6 0.17
17 14 0.39
18 7 0.19
19 9 0.25
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (16 bp):
CTTTTTTTTATTTTCT
Found at i:2967061 original size:18 final size:16
Alignment explanation
Indices: 2967015--2967069 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 16
2967005 TTTTCTTTTC
2967015 TTTTTTATTTTTT-CT
1 TTTTTTATTTTTTCCT
*
2967030 TTTTTTTTTATTTTCCT
1 TTTTTTATT-TTTTCCT
2967047 CTTTTTTCATTTTTTCCAT
1 -TTTTTT-ATTTTTTCC-T
2967066 TTTT
1 TTTT
2967070 CTCATTTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 2 0.06
18 16 0.48
19 3 0.09
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTATTTTTTCCT
Found at i:2967069 original size:34 final size:33
Alignment explanation
Indices: 2967013--2967078 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
2967003 TATTTTCTTT
** * *
2967013 TCTTTTTTATTTTTTCTTTTTTTTTTATTTTCC
1 TCTTTTTTATTTTTTCCATTTTTCTCATTTTCC
2967046 TCTTTTTTCATTTTTTCCATTTTTCTCATTTTC
1 TCTTTTTT-ATTTTTTCCATTTTTCTCATTTTC
2967079 ATTTTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 8 0.29
34 20 0.71
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.76
Consensus pattern (33 bp):
TCTTTTTTATTTTTTCCATTTTTCTCATTTTCC
Found at i:2967077 original size:24 final size:24
Alignment explanation
Indices: 2966996--2967116 Score: 74
Period size: 24 Copynumber: 5.5 Consensus size: 24
2966986 TTGAAGCCCC
*
2966996 TTTTATTTATT-TTC-TTTTC-TT
1 TTTTATTTCTTCTTCATTTTCATT
2967017 TTTTA-TT-TT-TTC-TTTT--TT
1 TTTTATTTCTTCTTCATTTTCATT
*
2967035 TTTTATTTTCCTCTT--TTTTCATT
1 TTTTA-TTTCTTCTTCATTTTCATT
2967058 TTTTCCATTT-TTC-TCATTTTCA-T
1 TTTT--ATTTCTTCTTCATTTTCATT
2967081 TTTTATTTCTTCTTTCATTTTCA-T
1 TTTTATTTCTTC-TTCATTTTCATT
*
2967105 TTTTCTTTCTTC
1 TTTTATTTCTTC
2967117 AGGCGAAGTA
Statistics
Matches: 84, Mismatches: 3, Indels: 23
0.76 0.03 0.21
Matches are distributed among these distances:
18 7 0.08
19 9 0.11
20 4 0.05
21 14 0.17
22 6 0.07
23 13 0.15
24 30 0.36
25 1 0.01
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTATTTCTTCTTCATTTTCATT
Found at i:2967096 original size:18 final size:17
Alignment explanation
Indices: 2967075--2967113 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
2967065 TTTTTCTCAT
*
2967075 TTTCATTTTTATTTCTTC
1 TTTCATTTTCATTT-TTC
2967093 TTTCATTTTCATTTTTC
1 TTTCATTTTCATTTTTC
2967110 TTTC
1 TTTC
2967114 TTCAGGCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTCATTTTCATTTTTC
Found at i:2970638 original size:21 final size:20
Alignment explanation
Indices: 2970610--2970648 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2970600 CATTGCAGGA
* *
2970610 ATTTATGGCTTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
2970630 ATTTCATGGCCTCAACAAA
1 ATTT-ATGGCCTCAACAAA
2970649 GACCTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:2982211 original size:20 final size:20
Alignment explanation
Indices: 2982188--2982230 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2982178 AATCCACCAT
*
2982188 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGATTCTAA
* *
2982208 ATGCATCTATATGATTCTAA
1 ATGCAACTAAATGATTCTAA
2982228 ATG
1 ATG
2982231 GTCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGATTCTAA
Found at i:2991360 original size:16 final size:16
Alignment explanation
Indices: 2991339--2991388 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
2991329 TGCACTGATA
*
2991339 TACATGAGCTATGTGT
1 TACATGACCTATGTGT
*
2991355 TACATGTCATCCTAGGTGT
1 TACATG--A-CCTATGTGT
2991374 TACATGACCTATGTG
1 TACATGACCTATGTG
2991389 GATATATGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 13 0.46
17 1 0.04
18 1 0.04
19 13 0.46
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (16 bp):
TACATGACCTATGTGT
Found at i:2991576 original size:23 final size:23
Alignment explanation
Indices: 2991550--2991641 Score: 94
Period size: 23 Copynumber: 4.0 Consensus size: 23
2991540 TTTTACGTAA
*
2991550 TCCTTCGGGACAATTCTACGTGG
1 TCCTTCGGGACAATTCTATGTGG
* * **
2991573 TCCTTCGGGACATTTATATACGG
1 TCCTTCGGGACAATTCTATGTGG
* * *
2991596 TCCTTTGGGATAATACTATGTGG
1 TCCTTCGGGACAATTCTATGTGG
* *
2991619 TCCTTCGAGACATTTCTATGTGG
1 TCCTTCGGGACAATTCTATGTGG
2991642 CACTTCGATG
Statistics
Matches: 52, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.36
Consensus pattern (23 bp):
TCCTTCGGGACAATTCTATGTGG
Found at i:2997237 original size:108 final size:109
Alignment explanation
Indices: 2997104--2997391 Score: 400
Period size: 108 Copynumber: 2.7 Consensus size: 109
2997094 TAATATACAA
* * * *
2997104 GAAAAAAGGTAAATAACAATTTTGGTCCTTGCAGGTGACCAACATGCACAAACACGCTAAACTAT
1 GAAAAATGGTAAATAACAACTTTGGTCCTCGCAGGTGACCAACATGCAAAAACACGCTAAACTAT
2997169 GGGGGACTAAACAGCAAATATCCCAAA-AATATATAACATGCAT
66 GGGGGACTAAACAGCAAATATCCCAAAGAATATATAACATGCAT
* * *
2997212 GAAAAATGGTAAATAACAACCTTGGTCATCGCAGGTGACCAACATGCAAAAACATGCTAAACTAT
1 GAAAAATGGTAAATAACAACTTTGGTCCTCGCAGGTGACCAACATGCAAAAACACGCTAAACTAT
* * * *
2997277 -GGGGAGTAAATAGCAAATATCCCAAAGAATATATAGCATTCAT
66 GGGGGACTAAACAGCAAATATCCCAAAGAATATATAACATGCAT
* * * ** **
2997320 GAAAATTGGTAAATAACAACTTTGGTCCTCACAGATGATTAACATGCAAAAATGCGCTAAACTAT
1 GAAAAATGGTAAATAACAACTTTGGTCCTCGCAGGTGACCAACATGCAAAAACACGCTAAACTAT
2997385 GGGGGAC
66 GGGGGAC
2997392 CTATGCATGA
Statistics
Matches: 156, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
107 24 0.15
108 127 0.81
109 5 0.03
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (109 bp):
GAAAAATGGTAAATAACAACTTTGGTCCTCGCAGGTGACCAACATGCAAAAACACGCTAAACTAT
GGGGGACTAAACAGCAAATATCCCAAAGAATATATAACATGCAT
Found at i:2998326 original size:7 final size:6
Alignment explanation
Indices: 2998313--2998369 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
2998303 AATAATAATA
* * * *
2998313 AAAATT AAACATT AAAATT ATAATT ATAATTT AAAATT ATAATT ATAATT
1 AAAATT AAA-ATT AAAATT AAAATT A-AAATT AAAATT AAAATT AAAATT
*
2998363 ATAATT A
1 AAAATT A
2998370 GATAATAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
6 34 0.77
7 10 0.23
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (6 bp):
AAAATT
Found at i:2998335 original size:25 final size:24
Alignment explanation
Indices: 2998307--2998361 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
2998297 CAAAATAATA
2998307 ATAATAAAAATTAAACATTAAAATT
1 ATAATAAAAATTAAA-ATTAAAATT
* * *
2998332 ATAATTATAATTTAAAATTATAATT
1 ATAA-TAAAAATTAAAATTAAAATT
2998357 ATAAT
1 ATAAT
2998362 TATAATTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 16 0.62
26 9 0.35
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
ATAATAAAAATTAAAATTAAAATT
Found at i:2998346 original size:19 final size:19
Alignment explanation
Indices: 2998324--2998362 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2998314 AAATTAAACA
2998324 TTAAAATTATAATTATAAT
1 TTAAAATTATAATTATAAT
2998343 TTAAAATTATAATTATAAT
1 TTAAAATTATAATTATAAT
2998362 T
1 T
2998363 ATAATTAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAAAATTATAATTATAAT
Found at i:3006094 original size:18 final size:18
Alignment explanation
Indices: 3006071--3006105 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3006061 CATTTCAAAA
3006071 TAGATATCAACTCTTCGC
1 TAGATATCAACTCTTCGC
**
3006089 TAGATATTTACTCTTCG
1 TAGATATCAACTCTTCG
3006106 TGTAAAGCTT
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:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (18 bp):
TAGATATCAACTCTTCGC
Found at i:3007524 original size:30 final size:30
Alignment explanation
Indices: 3007480--3007551 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
3007470 AAACATTTTT
*
3007480 TAATTTTTTAATAGTAGGAGACTTAACAAAG
1 TAATATTTT-ATAGTAGGAGACTTAACAAAG
* * *
3007511 TAATATTTTATAGTCGGGGATTTAACAAAG
1 TAATATTTTATAGTAGGAGACTTAACAAAG
*
3007541 TAATATCTTAT
1 TAATATTTTAT
3007552 TGTTGGGGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 28 0.78
31 8 0.22
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (30 bp):
TAATATTTTATAGTAGGAGACTTAACAAAG
Found at i:3007560 original size:30 final size:30
Alignment explanation
Indices: 3007502--3007560 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
3007492 AGTAGGAGAC
*
3007502 TTAACAAAGTAATATTTTATAGTCGGGGAT
1 TTAACAAAGTAATATCTTATAGTCGGGGAT
* *
3007532 TTAACAAAGTAATATCTTATTGTTGGGGA
1 TTAACAAAGTAATATCTTATAGTCGGGGA
3007561 CCATTTGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.37
Consensus pattern (30 bp):
TTAACAAAGTAATATCTTATAGTCGGGGAT
Found at i:3008663 original size:16 final size:17
Alignment explanation
Indices: 3008635--3008669 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3008625 TATTTTTATT
3008635 TTTCATGTTTTTGA-TA
1 TTTCATGTTTTTGAGTA
*
3008651 TTTCATTTTTTTGAGTA
1 TTTCATGTTTTTGAGTA
3008668 TT
1 TT
3008670 CTTTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.66
Consensus pattern (17 bp):
TTTCATGTTTTTGAGTA
Found at i:3010639 original size:38 final size:37
Alignment explanation
Indices: 3010565--3010640 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
3010555 GTTGGAAAAT
*
3010565 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* * *
3010602 ATTTATATAATTTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAA
3010640 A
1 A
3010641 AGTTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 8 0.24
38 21 0.64
39 4 0.12
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:3016846 original size:44 final size:44
Alignment explanation
Indices: 3016798--3016924 Score: 175
Period size: 44 Copynumber: 2.9 Consensus size: 44
3016788 TCTCTTATTG
* *
3016798 TTAATTACATTATGTTCGTTACTTTCCATGCATTTACTTCATCT
1 TTAATTACTTTATGTTCTTTACTTTCCATGCATTTACTTCATCT
* * **
3016842 TTAATTATTTTATGTTCTTTACTTTCCTTGCATTTACAACATCT
1 TTAATTACTTTATGTTCTTTACTTTCCATGCATTTACTTCATCT
*
3016886 TTAATTACTTTATGTTATTTACTTT-CATTGCATTTACTT
1 TTAATTACTTTATGTTCTTTACTTTCCA-TGCATTTACTT
3016925 TTATGCATTT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
43 1 0.01
44 70 0.99
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (44 bp):
TTAATTACTTTATGTTCTTTACTTTCCATGCATTTACTTCATCT
Found at i:3016933 original size:14 final size:14
Alignment explanation
Indices: 3016902--3016942 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3016892 ACTTTATGTT
*
3016902 ATTTACTTTCATTGC
1 ATTTACTTTTA-TGC
3016917 ATTTACTTTTATGC
1 ATTTACTTTTATGC
*
3016931 ATTTACTATTAT
1 ATTTACTTTTAT
3016943 TTTACTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (14 bp):
ATTTACTTTTATGC
Found at i:3017470 original size:79 final size:79
Alignment explanation
Indices: 3017339--3017490 Score: 268
Period size: 79 Copynumber: 1.9 Consensus size: 79
3017329 CAACACTCTT
* *
3017339 TGGATGATTACTTAAGCTACAGTAGCTAGAGTGAAATGCAACTTGACACCATTAGAGAAGTATTG
1 TGGATGATTACTTAAGCTACAGTAGATAGAGTGAAATGCAACTTAACACCATTAGAGAAGTATTG
3017404 CAAAATGAACACCG
66 CAAAATGAACACCG
* *
3017418 TGGATGATTACTTAAGCTACAGTAGATAGAGTGAGATGCAACTTAACACCATTAGAGAAGTATTT
1 TGGATGATTACTTAAGCTACAGTAGATAGAGTGAAATGCAACTTAACACCATTAGAGAAGTATTG
3017483 CAAAATGA
66 CAAAATGA
3017491 GTGAAGGAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (79 bp):
TGGATGATTACTTAAGCTACAGTAGATAGAGTGAAATGCAACTTAACACCATTAGAGAAGTATTG
CAAAATGAACACCG
Found at i:3018341 original size:22 final size:22
Alignment explanation
Indices: 3018313--3018359 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
3018303 TGTTTGGGTG
3018313 CATTAGAAATGCTTTAGTGCTA
1 CATTAGAAATGCTTTAGTGCTA
3018335 CATTAGAAATGCTTTAGTGCTA
1 CATTAGAAATGCTTTAGTGCTA
3018357 CAT
1 CAT
3018360 AATATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (22 bp):
CATTAGAAATGCTTTAGTGCTA
Found at i:3019442 original size:27 final size:27
Alignment explanation
Indices: 3019412--3019469 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
3019402 AGTCTCTTAG
3019412 AAGCTTGCTAGGTCTTTGAGTCCCGAT
1 AAGCTTGCTAGGTCTTTGAGTCCCGAT
* *
3019439 AAGCTTGCTAGTTCTTTGAGTCCCGCT
1 AAGCTTGCTAGGTCTTTGAGTCCCGAT
3019466 AAGC
1 AAGC
3019470 ATACTAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (27 bp):
AAGCTTGCTAGGTCTTTGAGTCCCGAT
Found at i:3019476 original size:27 final size:27
Alignment explanation
Indices: 3019419--3019485 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
3019409 TAGAAGCTTG
* * *
3019419 CTAGGTCTTTGAGTCCCGATAAGCTTG
1 CTAGTTCTTTGAGTCCCGATAAGCATA
*
3019446 CTAGTTCTTTGAGTCCCGCTAAGCATA
1 CTAGTTCTTTGAGTCCCGATAAGCATA
3019473 CTAGTT-TTTGAGT
1 CTAGTTCTTTGAGT
3019486 AGAGGATAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 7 0.19
27 29 0.81
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (27 bp):
CTAGTTCTTTGAGTCCCGATAAGCATA
Found at i:3028124 original size:13 final size:14
Alignment explanation
Indices: 3028100--3028129 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3028090 AGTTAACTAA
3028100 ATTATTTAAGTTAT
1 ATTATTTAAGTTAT
3028114 ATTATTT-AGTTAT
1 ATTATTTAAGTTAT
3028127 ATT
1 ATT
3028130 GTACATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (14 bp):
ATTATTTAAGTTAT
Found at i:3030420 original size:24 final size:27
Alignment explanation
Indices: 3030375--3030433 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 27
3030365 TAAGATTTAA
3030375 ATATTAATATATTCTTATTAAA-AAATAT
1 ATATTAATATATTC-TATTAAATAAA-AT
3030403 ATATTAATATA-TC-A-TAAATAAAAT
1 ATATTAATATATTCTATTAAATAAAAT
*
3030427 AAATTAA
1 ATATTAA
3030434 AATAATAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 12 0.41
25 4 0.14
27 2 0.07
28 11 0.38
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (27 bp):
ATATTAATATATTCTATTAAATAAAAT
Found at i:3030753 original size:23 final size:23
Alignment explanation
Indices: 3030722--3030768 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3030712 AATTTGTTTG
3030722 TATGATACGTTTTCATATGTCTT
1 TATGATACGTTTTCATATGTCTT
* * *
3030745 TATGGTACGTTTTCTTCTGTCTT
1 TATGATACGTTTTCATATGTCTT
3030768 T
1 T
3030769 TGGCATGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (23 bp):
TATGATACGTTTTCATATGTCTT
Found at i:3048072 original size:41 final size:40
Alignment explanation
Indices: 3048009--3048120 Score: 108
Period size: 41 Copynumber: 2.8 Consensus size: 40
3047999 AATTTTATTT
*
3048009 CTAAAAT-TTA-TAAATAAAAATATTAATTATT-TTCTAATA
1 CTAAAATATTATTAAATAAGAATATTAATTATTATT-T-ATA
*
3048048 CTAAAATATTATTAAATAAGAATATTATACTATTATTTATA
1 CTAAAATATTATTAAATAAGAATATTA-ATTATTATTTATA
* *
3048089 -TTAATTACTTATTAAATTAAGAATATT-ATTAT
1 CTAAAATA-TTATTAAA-TAAGAATATTAATTAT
3048121 AATATAAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
39 7 0.11
40 12 0.19
41 25 0.40
42 16 0.26
43 2 0.03
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (40 bp):
CTAAAATATTATTAAATAAGAATATTAATTATTATTTATA
Found at i:3048136 original size:15 final size:16
Alignment explanation
Indices: 3048116--3048145 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3048106 TAAGAATATT
3048116 ATTATAATA-TAAAAA
1 ATTATAATATTAAAAA
3048131 ATTATAATATTAAAA
1 ATTATAATATTAAAA
3048146 TGATACTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTATAATATTAAAAA
Found at i:3055589 original size:35 final size:35
Alignment explanation
Indices: 3055543--3055610 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 35
3055533 TTATTCTAGA
3055543 TTTAATATTGTGGTTTGAATCTTGAA-ATTTGACAT
1 TTTAATATTGTGGTTTGAATCTT-AATATTTGACAT
*
3055578 TTTAATATTGTGGTTTGAGTCTTAATATTTGAC
1 TTTAATATTGTGGTTTGAATCTTAATATTTGAC
3055611 TTTATTTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 2 0.06
35 29 0.94
ACGTcount: A:0.26, C:0.06, G:0.18, T:0.50
Consensus pattern (35 bp):
TTTAATATTGTGGTTTGAATCTTAATATTTGACAT
Found at i:3056296 original size:74 final size:75
Alignment explanation
Indices: 3056192--3056394 Score: 200
Period size: 74 Copynumber: 2.7 Consensus size: 75
3056182 ATAAAAAATC
* * * *
3056192 ATTAATAAAGTCAAATATTAATATTCAAACCACAATATTAAGTTTAGAACATTAAAATCCATAA-
1 ATTAA-AATGTCAAATCTTAAGATTCAAACCACAATATTAAGTTTAGAACAATAAAATCCATAAT
3056256 ACAAA-CAACAAT
65 A-AAATC-ACAAT
* * *
3056268 GTTAAAATGTC-AAT-TTCAAGATTCAAACCACAATATTCA-TTCTAGAATAATAAAATCCATAA
1 ATTAAAATGTCAAATCTT-AAGATTCAAACCACAATATTAAGTT-TAGAACAATAAAATCCATAA
*
3056330 TAAAATCATAAT
64 TAAAATCACAAT
* * * * * *
3056342 ATTAAAGTGTCAAATCTTAAGACTCGAACCATAATATTAAGTCTAGAAAAATA
1 ATTAAAATGTCAAATCTTAAGATTCAAACCACAATATTAAGTTTAGAACAATA
3056395 TTAAACCCAA
Statistics
Matches: 105, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
73 4 0.04
74 57 0.54
75 37 0.35
76 7 0.07
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.29
Consensus pattern (75 bp):
ATTAAAATGTCAAATCTTAAGATTCAAACCACAATATTAAGTTTAGAACAATAAAATCCATAATA
AAATCACAAT
Found at i:3056341 original size:11 final size:12
Alignment explanation
Indices: 3056314--3056342 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3056304 TCATTCTAGA
3056314 ATAATAAAATCC
1 ATAATAAAATCC
3056326 ATAATAAAAT-C
1 ATAATAAAATCC
3056337 ATAATA
1 ATAATA
3056343 TTAAAGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (12 bp):
ATAATAAAATCC
Found at i:3059163 original size:22 final size:23
Alignment explanation
Indices: 3059118--3059166 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
3059108 ATTCAGTAAT
** *
3059118 GAAAAAAATTTGAAAAGGGTAGA
1 GAAAAAAATTTGAAAAACGCAGA
3059141 GAAAAAAA-TTGAAAAACGCAGA
1 GAAAAAAATTTGAAAAACGCAGA
3059163 GAAA
1 GAAA
3059167 TTGAGAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.61, C:0.04, G:0.22, T:0.12
Consensus pattern (23 bp):
GAAAAAAATTTGAAAAACGCAGA
Found at i:3062298 original size:82 final size:82
Alignment explanation
Indices: 3062194--3062348 Score: 186
Period size: 82 Copynumber: 1.9 Consensus size: 82
3062184 TATAGCAACG
* * * * * * *
3062194 TTTTTGGGAAAATGCCATTAAAAACACGTACTTTAGTGGTGTTTG-TGAAACAAACGCTGCTATA
1 TTTTTGAGAAAACGCCACTAAAAACACGTAATTTAGTGGCGTTTGAT-AAACAAAAGCCGCTATA
3062258 GACTGATATACGGTAGCA
65 GACTGATATACGGTAGCA
* * * *
3062276 TTTTTGAGAAAACGCCGCTAAAACCATGTAATTTAGTGGCGTTTGATACACAAAAGCCGCTATAG
1 TTTTTGAGAAAACGCCACTAAAAACACGTAATTTAGTGGCGTTTGATAAACAAAAGCCGCTATAG
*
3062341 ACTTATAT
66 ACTGATAT
3062349 GTAATGGCAT
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
82 59 0.98
83 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (82 bp):
TTTTTGAGAAAACGCCACTAAAAACACGTAATTTAGTGGCGTTTGATAAACAAAAGCCGCTATAG
ACTGATATACGGTAGCA
Found at i:3065424 original size:17 final size:17
Alignment explanation
Indices: 3065402--3065442 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
3065392 ACACGTCAAA
3065402 TTCTAGAGGAAAATTTG
1 TTCTAGAGGAAAATTTG
3065419 TTCTAGAGGAAAATTTG
1 TTCTAGAGGAAAATTTG
3065436 TTCTAGA
1 TTCTAGA
3065443 ATTGGTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (17 bp):
TTCTAGAGGAAAATTTG
Found at i:3066050 original size:20 final size:20
Alignment explanation
Indices: 3066012--3066051 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3066002 ACATATTACC
** *
3066012 CATAGGGTATTGATGCCCCT
1 CATAGGGTACCGATACCCCT
3066032 CATAGGGTACCGATACCCCT
1 CATAGGGTACCGATACCCCT
3066052 ATGCAAGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (20 bp):
CATAGGGTACCGATACCCCT
Found at i:3072179 original size:13 final size:13
Alignment explanation
Indices: 3072161--3072207 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
3072151 TACATTTTGA
3072161 TTTTCAAACATTG
1 TTTTCAAACATTG
*
3072174 TTTTCAAATATTG
1 TTTTCAAACATTG
*
3072187 TTTTCAAACATAG
1 TTTTCAAACATTG
3072200 TTTTCAAA
1 TTTTCAAA
3072208 GTTTGCCCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (13 bp):
TTTTCAAACATTG
Found at i:3072701 original size:29 final size:29
Alignment explanation
Indices: 3072669--3072724 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 29
3072659 TATTTGGATT
3072669 TGTTTAAATTTGTGTT-TTTGGAT-TTTAGA
1 TGTTTAAA-TTGT-TTGTTTGGATGTTTAGA
*
3072698 TGTTTCAATTGTTTGTTTGGATGTTTA
1 TGTTTAAATTGTTTGTTTGGATGTTTA
3072725 TTTTGGTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 2 0.08
28 11 0.46
29 11 0.46
ACGTcount: A:0.18, C:0.02, G:0.21, T:0.59
Consensus pattern (29 bp):
TGTTTAAATTGTTTGTTTGGATGTTTAGA
Found at i:3079538 original size:13 final size:13
Alignment explanation
Indices: 3079520--3079566 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
3079510 TACATTTTGA
3079520 TTTTCAAACATTG
1 TTTTCAAACATTG
*
3079533 TTTTCAAATATTG
1 TTTTCAAACATTG
**
3079546 TTTTCAAACATAC
1 TTTTCAAACATTG
3079559 TTTTCAAA
1 TTTTCAAA
3079567 GTTTGCCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.47
Consensus pattern (13 bp):
TTTTCAAACATTG
Found at i:3096877 original size:26 final size:26
Alignment explanation
Indices: 3096846--3096918 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
3096836 AACAATTAAA
3096846 TTTTAAAATACATTTTTCAAAAACAC
1 TTTTAAAATACATTTTTCAAAAACAC
** *
3096872 TTTTAAAAGTAC-TTTTTTTATAACAC
1 TTTTAAAA-TACATTTTTCAAAAACAC
* *
3096898 TTTTTAAAT-CAATTTTCAAAA
1 TTTTAAAATACATTTTTCAAAA
3096919 GTAATATCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
24 1 0.03
25 7 0.19
26 26 0.70
27 3 0.08
ACGTcount: A:0.41, C:0.12, G:0.01, T:0.45
Consensus pattern (26 bp):
TTTTAAAATACATTTTTCAAAAACAC
Found at i:3096969 original size:32 final size:32
Alignment explanation
Indices: 3096929--3096989 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
3096919 GTAATATCAA
3096929 TTACTTACACCAATGTAAATAAGTTGTAACCC
1 TTACTTACACCAATGTAAATAAGTTGTAACCC
*
3096961 TTACTTACACCAGTGTAAATAAGTTGTAA
1 TTACTTACACCAATGTAAATAAGTTGTAA
3096990 TTTAATTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (32 bp):
TTACTTACACCAATGTAAATAAGTTGTAACCC
Found at i:3097475 original size:71 final size:71
Alignment explanation
Indices: 3097398--3097536 Score: 215
Period size: 71 Copynumber: 2.0 Consensus size: 71
3097388 GATCAAAAAT
* * * *
3097398 TTCAAGCAAAGCATTGTTGTTCCTGCTACACAAAAACAAGGAGGAATAGTAAGCCATGATGAATC
1 TTCAAGCAAAGCATTATTGTTCCTGCTACACAAAAACAAGAAGAAATAGTAAGCCATAATGAATC
3097463 AAAGGA
66 AAAGGA
* * *
3097469 TTCAAGCAAAGCATTATTGTTCCTGCTATACAAACACAAGAAGAAATAGTAAGCCATAATGGATC
1 TTCAAGCAAAGCATTATTGTTCCTGCTACACAAAAACAAGAAGAAATAGTAAGCCATAATGAATC
3097534 AAA
66 AAA
3097537 TAGTTAAAGT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.22
Consensus pattern (71 bp):
TTCAAGCAAAGCATTATTGTTCCTGCTACACAAAAACAAGAAGAAATAGTAAGCCATAATGAATC
AAAGGA
Found at i:3100232 original size:31 final size:31
Alignment explanation
Indices: 3100196--3100255 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3100186 AACTTAAAAG
* *
3100196 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
3100227 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
3100256 AATACAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:3100765 original size:20 final size:20
Alignment explanation
Indices: 3100717--3100778 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
3100707 AACTTAAATC
*
3100717 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
3100737 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
3100755 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
3100774 AAAAT
1 AAAAT
3100779 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:3100835 original size:37 final size:40
Alignment explanation
Indices: 3100793--3100876 Score: 106
Period size: 39 Copynumber: 2.2 Consensus size: 40
3100783 TATCTATAAT
*
3100793 ATAATATTAAAAATTAATAT-T-TAAT-TTAT-TTAAAAAA
1 ATAATATT-AAAATTAATATCTATAATATAATATTAAAAAA
3100830 ATAATA-TAAAATTAATATCTATAATATAATATTAAAAAA
1 ATAATATTAAAATTAATATCTATAATATAATATTAAAAAA
*
3100869 TTAATATT
1 ATAATATT
3100877 TAATTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
35 11 0.28
36 2 0.05
37 10 0.25
38 3 0.08
39 13 0.32
40 1 0.03
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (40 bp):
ATAATATTAAAATTAATATCTATAATATAATATTAAAAAA
Found at i:3100875 original size:63 final size:63
Alignment explanation
Indices: 3100770--3100927 Score: 243
Period size: 63 Copynumber: 2.5 Consensus size: 63
3100760 AATTTATATG
3100770 ATATAAAATTAAATATCTATAATATAATATT-AAAAATTAATATTTAATTTATTTAAAAAAATA
1 ATATAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAAATA
*
3100833 ATATAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTA
1 ATATAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAAATA
* *
3100896 ATATTAAAACTAAAATC-A-AATATAATA-TAAAA
1 ATA-TAAAATTAATATCTATAATATAATATTAAAA
3100928 TTAAATATAA
Statistics
Matches: 90, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
61 5 0.06
62 29 0.32
63 45 0.50
64 11 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (63 bp):
ATATAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAAATA
Found at i:3100893 original size:24 final size:27
Alignment explanation
Indices: 3100837--3100901 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 27
3100827 AAAATAATAT
3100837 AAAATTAATATCTATAATATAATATTAA
1 AAAATTAATAT-TATAATATAATATTAA
*
3100865 AAAATTAATATT-TAAT-TTAT-TTAA
1 AAAATTAATATTATAATATAATATTAA
3100889 AAAATTAATATTA
1 AAAATTAATATTA
3100902 AAACTAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
24 16 0.46
25 3 0.09
26 4 0.11
27 1 0.03
28 11 0.31
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
AAAATTAATATTATAATATAATATTAA
Found at i:3104461 original size:26 final size:26
Alignment explanation
Indices: 3104431--3104485 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
3104421 AGTAGACAAT
3104431 GAGTGAGAGAGATAGAGACGTAGAGA
1 GAGTGAGAGAGATAGAGACGTAGAGA
3104457 GAGTGAGAGAGATAGAGACGTAGAGA
1 GAGTGAGAGAGATAGAGACGTAGAGA
3104483 GAG
1 GAG
3104486 AAAAAGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.42, C:0.04, G:0.44, T:0.11
Consensus pattern (26 bp):
GAGTGAGAGAGATAGAGACGTAGAGA
Found at i:3115672 original size:12 final size:12
Alignment explanation
Indices: 3115655--3115688 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
3115645 AAAGCAGAAG
3115655 TTACAAAAGGGT
1 TTACAAAAGGGT
3115667 TTACAAAAGGGT
1 TTACAAAAGGGT
3115679 TTACAAAAGG
1 TTACAAAAGG
3115689 TGTAGGGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.24
Consensus pattern (12 bp):
TTACAAAAGGGT
Found at i:3124548 original size:19 final size:19
Alignment explanation
Indices: 3124509--3124550 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3124499 AGATGGATGG
*
3124509 TTAGGATTATAGGATATCT
1 TTAGGATTATAGGATAACT
3124528 TTAGGATTATA-GACTAACT
1 TTAGGATTATAGGA-TAACT
3124547 TTAG
1 TTAG
3124551 TGTTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.40
Consensus pattern (19 bp):
TTAGGATTATAGGATAACT
Found at i:3129091 original size:22 final size:22
Alignment explanation
Indices: 3129066--3129113 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
3129056 AGATGTTATC
* * *
3129066 TTTATCTCCACTTAGGATGAGA
1 TTTATCTACACTGAGGATAAGA
*
3129088 TTTATCTATACTGAGGATAAGA
1 TTTATCTACACTGAGGATAAGA
3129110 TTTA
1 TTTA
3129114 GAATAATACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (22 bp):
TTTATCTACACTGAGGATAAGA
Found at i:3136686 original size:26 final size:26
Alignment explanation
Indices: 3136651--3136702 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
3136641 CTTATAAAAT
3136651 GATTTATCAGTA-TGCAGAAATAAAACA
1 GATTTATCAG-ACT-CAGAAATAAAACA
*
3136678 GATTT-TCAGACTCAGATATAAAACA
1 GATTTATCAGACTCAGAAATAAAACA
3136703 AAATACAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 13 0.57
26 5 0.22
27 5 0.22
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.27
Consensus pattern (26 bp):
GATTTATCAGACTCAGAAATAAAACA
Found at i:3137260 original size:24 final size:24
Alignment explanation
Indices: 3137233--3137344 Score: 93
Period size: 24 Copynumber: 4.7 Consensus size: 24
3137223 TATATCAAAA
3137233 ATCAAAACATAATTCAGGTC-AGAT
1 ATCAAAACATAATTCAGGTCAAG-T
* * *
3137257 ATCATAACATAATCCATGTCAAGT
1 ATCAAAACATAATTCAGGTCAAGT
* *
3137281 ATAAAAACAGAA-TCTAGGTCAAGT
1 ATCAAAACATAATTC-AGGTCAAGT
* * * * *
3137305 ATCAAATCAGAATCCAGGTTAGGT
1 ATCAAAACATAATTCAGGTCAAGT
*
3137329 ATCATAACATAATTCA
1 ATCAAAACATAATTCA
3137345 AATCAGAAAT
Statistics
Matches: 68, Mismatches: 17, Indels: 6
0.75 0.19 0.07
Matches are distributed among these distances:
23 1 0.01
24 64 0.94
25 3 0.04
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (24 bp):
ATCAAAACATAATTCAGGTCAAGT
Found at i:3144417 original size:35 final size:35
Alignment explanation
Indices: 3144377--3144476 Score: 105
Period size: 34 Copynumber: 2.9 Consensus size: 35
3144367 ATTCTAAATG
*
3144377 TTTACAGTTATAAGATGATTTTCAATTATCAGATA
1 TTTACAGATATAAGATGATTTTCAATTATCAGATA
* ** *
3144412 TTTACAGATATTAGATGA-TGACATTTATCAGATA
1 TTTACAGATATAAGATGATTTTCAATTATCAGATA
* * *
3144446 TTTATAGATATCAGATG-TTTTACAGTTATCA
1 TTTACAGATATAAGATGATTTT-CAATTATCA
3144477 TACACAGATT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
34 29 0.55
35 24 0.45
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (35 bp):
TTTACAGATATAAGATGATTTTCAATTATCAGATA
Found at i:3144456 original size:10 final size:11
Alignment explanation
Indices: 3144402--3144456 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 11
3144392 TGATTTTCAA
3144402 TTATCAGATAT
1 TTATCAGATAT
3144413 TTA-CAGATAT
1 TTATCAGATAT
* * *
3144423 TAGATGATGACAT
1 T-TATCA-GATAT
3144436 TTATCAGATAT
1 TTATCAGATAT
3144447 TTAT-AGATAT
1 TTATCAGATAT
3144457 CAGATGTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
10 14 0.40
11 12 0.34
12 4 0.11
13 5 0.14
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (11 bp):
TTATCAGATAT
Found at i:3150171 original size:28 final size:27
Alignment explanation
Indices: 3150134--3150187 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
3150124 TTTTTGTGGG
3150134 AGTATGA-TTTAGTTTTATATC-AATTTA
1 AGTATGATTTTA--TTTATATCGAATTTA
3150161 AGTATAGATTTTATTTATATCGAATTT
1 AGTAT-GATTTTATTTATATCGAATTT
3150188 TATATTTACG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 13 0.54
28 7 0.29
29 4 0.17
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.52
Consensus pattern (27 bp):
AGTATGATTTTATTTATATCGAATTTA
Found at i:3151315 original size:17 final size:17
Alignment explanation
Indices: 3151243--3151316 Score: 78
Period size: 17 Copynumber: 4.3 Consensus size: 17
3151233 TGTTTACAAT
*
3151243 TATCAGATGATTT-TCAGT
1 TATCAGAT-ATTTAT-AGA
*
3151261 TATCAGATATTTACAGA
1 TATCAGATATTTATAGA
* * *
3151278 TATAAGATAATTATAGT
1 TATCAGATATTTATAGA
3151295 TATCAGATATTTATAGA
1 TATCAGATATTTATAGA
3151312 TATCA
1 TATCA
3151317 AATTTTTTAC
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
17 38 0.83
18 8 0.17
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (17 bp):
TATCAGATATTTATAGA
Found at i:3152932 original size:22 final size:22
Alignment explanation
Indices: 3152891--3152976 Score: 95
Period size: 22 Copynumber: 3.9 Consensus size: 22
3152881 CCCCATAGGA
*
3152891 TACCGATACCCCTATGCAAAGAGG
1 TACCGATA--CCTATCCAAAGAGG
*
3152915 TATCGATACCTATCC-AA-AGG
1 TACCGATACCTATCCAAAGAGG
* *
3152935 TGCCGATACCCTATACAAAGAGG
1 TACCGATA-CCTATCCAAAGAGG
3152958 TACCGATACCTATCCAAAG
1 TACCGATACCTATCCAAAG
3152977 GTGCTGATAC
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
20 9 0.17
21 8 0.15
22 18 0.35
23 10 0.19
24 7 0.13
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (22 bp):
TACCGATACCTATCCAAAGAGG
Found at i:3152941 original size:20 final size:20
Alignment explanation
Indices: 3152918--3152987 Score: 86
Period size: 20 Copynumber: 3.4 Consensus size: 20
3152908 AAAGAGGTAT
3152918 CGATACCTATCCAAAGGTGC
1 CGATACCTATCCAAAGGTGC
* *
3152938 CGATACCCTATACAAAGAGGTAC
1 CGATA-CCTAT-CCAA-AGGTGC
3152961 CGATACCTATCCAAAGGTGC
1 CGATACCTATCCAAAGGTGC
*
3152981 TGATACC
1 CGATACC
3152988 CCTTATGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
20 16 0.38
21 8 0.19
22 8 0.19
23 10 0.24
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.20
Consensus pattern (20 bp):
CGATACCTATCCAAAGGTGC
Found at i:3152947 original size:43 final size:43
Alignment explanation
Indices: 3152893--3152988 Score: 156
Period size: 43 Copynumber: 2.2 Consensus size: 43
3152883 CCATAGGATA
* *
3152893 CCGATACCCCTATGCAAAGAGGTATCGATACCTATCCAAAGGTG
1 CCGATA-CCCTATACAAAGAGGTACCGATACCTATCCAAAGGTG
3152937 CCGATACCCTATACAAAGAGGTACCGATACCTATCCAAAGGTG
1 CCGATACCCTATACAAAGAGGTACCGATACCTATCCAAAGGTG
*
3152980 CTGATACCC
1 CCGATACCC
3152989 CTTATGTTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
43 43 0.88
44 6 0.12
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (43 bp):
CCGATACCCTATACAAAGAGGTACCGATACCTATCCAAAGGTG
Found at i:3165865 original size:18 final size:18
Alignment explanation
Indices: 3165842--3165890 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
3165832 CCTTTATATC
3165842 TAGAATAGGCACAAGTCT
1 TAGAATAGGCACAAGTCT
*
3165860 TAGAATATGCACAAGTCT
1 TAGAATAGGCACAAGTCT
*
3165878 TAGAATAGTCACA
1 TAGAATAGGCACA
3165891 CTTGTATAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.24
Consensus pattern (18 bp):
TAGAATAGGCACAAGTCT
Found at i:3168530 original size:15 final size:17
Alignment explanation
Indices: 3168510--3168541 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
3168500 TTAAGTATGA
3168510 TTTTGTT-A-TGTGTTG
1 TTTTGTTCACTGTGTTG
3168525 TTTTGTTCACTGTGTTG
1 TTTTGTTCACTGTGTTG
3168542 ACCTTTTGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.06, C:0.06, G:0.25, T:0.62
Consensus pattern (17 bp):
TTTTGTTCACTGTGTTG
Found at i:3179959 original size:16 final size:16
Alignment explanation
Indices: 3179914--3179961 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 16
3179904 TGCACTGTTC
* *
3179914 TACATGATCTATGTGT
1 TACATAATCTATGAGT
3179930 TACATTTCAATCTATGAGT
1 TACA--T-AATCTATGAGT
3179949 TACATAATCTATG
1 TACATAATCTATG
3179962 TGATTATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 1 0.04
19 13 0.48
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (16 bp):
TACATAATCTATGAGT
Found at i:3179975 original size:16 final size:15
Alignment explanation
Indices: 3179952--3179994 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
3179942 TATGAGTTAC
3179952 ATAA-TCTATGTGATT
1 ATAAGTCTATGTGA-T
*
3179967 ATATGTCTATGTGAT
1 ATAAGTCTATGTGAT
3179982 ATAAG-CTATGTGA
1 ATAAGTCTATGTGA
3179995 AATGGTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 8 0.32
15 8 0.32
16 9 0.36
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.42
Consensus pattern (15 bp):
ATAAGTCTATGTGAT
Found at i:3179992 original size:14 final size:15
Alignment explanation
Indices: 3179952--3179994 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
3179942 TATGAGTTAC
*
3179952 ATAATCTATGTGATT
1 ATAAGCTATGTGATT
*
3179967 ATATGTCTATGTGA-T
1 ATAAG-CTATGTGATT
3179982 ATAAGCTATGTGA
1 ATAAGCTATGTGA
3179995 AATGGTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.33
15 8 0.33
16 8 0.33
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.42
Consensus pattern (15 bp):
ATAAGCTATGTGATT
Found at i:3180100 original size:22 final size:23
Alignment explanation
Indices: 3180072--3180171 Score: 112
Period size: 23 Copynumber: 4.4 Consensus size: 23
3180062 AGTCGAGGGT
*
3180072 TCTACGTGGTCCTTCGGGATA-A
1 TCTACGTGGTCCTTCGGGACATA
* *
3180094 TCTACGTGGTCCTTCGAGACATT
1 TCTACGTGGTCCTTCGGGACATA
* **
3180117 TCTACGCGGTCCTTTAGGACATA
1 TCTACGTGGTCCTTCGGGACATA
* * *
3180140 TCTATGTGGTCCTTCTGGACATT
1 TCTACGTGGTCCTTCGGGACATA
3180163 TCTACGTGG
1 TCTACGTGG
3180172 CACTTCGATG
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
22 19 0.30
23 44 0.70
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGGGACATA
Found at i:3180153 original size:46 final size:45
Alignment explanation
Indices: 3180071--3180168 Score: 126
Period size: 46 Copynumber: 2.2 Consensus size: 45
3180061 GAGTCGAGGG
* * *
3180071 TTCTACGTGGTCCTTCGGGATAATCTACGTGGTCCTTC-GAGACAT
1 TTCTACGCGGTCCTTCAGGACAATCTACGTGGTCCTTCTG-GACAT
* *
3180116 TTCTACGCGGTCCTTTAGGACATATCTATGTGGTCCTTCTGGACAT
1 TTCTACGCGGTCCTTCAGGACA-ATCTACGTGGTCCTTCTGGACAT
3180162 TTCTACG
1 TTCTACG
3180169 TGGCACTTCG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 18 0.39
46 27 0.59
47 1 0.02
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.36
Consensus pattern (45 bp):
TTCTACGCGGTCCTTCAGGACAATCTACGTGGTCCTTCTGGACAT
Found at i:3180198 original size:24 final size:24
Alignment explanation
Indices: 3180162--3180207 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3180152 TTCTGGACAT
**
3180162 TTCTACGTGGCACTTCGATGTATA
1 TTCTACGCAGCACTTCGATGTATA
*
3180186 TTCTACGCAGCACTTCGGTGTA
1 TTCTACGCAGCACTTCGATGTA
3180208 ATTTATACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (24 bp):
TTCTACGCAGCACTTCGATGTATA
Found at i:3180332 original size:2 final size:2
Alignment explanation
Indices: 3180327--3180352 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3180317 ATAGTGCATG
3180327 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
3180353 GCATGTATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3186671 original size:15 final size:16
Alignment explanation
Indices: 3186630--3186695 Score: 55
Period size: 19 Copynumber: 4.1 Consensus size: 16
3186620 CTAGCATATG
3186630 TCTATGTGTTACATGA
1 TCTATGTGTTACATGA
* * *
3186646 ACTGT-TCTTAC-TGA
1 TCTATGTGTTACATGA
*
3186660 TCTATGTGTTACATTTCA
1 TCTATGTGTTACA--TGA
3186678 TCCTATGTGTTACATGA
1 T-CTATGTGTTACATGA
3186695 T
1 T
3186696 GTGAGAGCTA
Statistics
Matches: 37, Mismatches: 8, Indels: 9
0.69 0.15 0.17
Matches are distributed among these distances:
14 6 0.16
15 10 0.27
16 3 0.08
17 3 0.08
18 3 0.08
19 12 0.32
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (16 bp):
TCTATGTGTTACATGA
Found at i:3186789 original size:23 final size:22
Alignment explanation
Indices: 3186736--3186789 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
3186726 AGAGTCGAGG
*
3186736 TTCTACGCGGTCCTTCGAGACA
1 TTCTACGTGGTCCTTCGAGACA
* * *
3186758 ATCTACGTGGTCCTTCGGGATA
1 TTCTACGTGGTCCTTCGAGACA
3186780 TTTCTACGTG
1 -TTCTACGTG
3186790 TCATACCCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (22 bp):
TTCTACGTGGTCCTTCGAGACA
Found at i:3207057 original size:23 final size:23
Alignment explanation
Indices: 3207027--3207081 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
3207017 GTTTGTTTAG
3207027 TTAT-TGTTCACGAACATGTTCG-T
1 TTATATGTTCAC-AA-ATGTTCGTT
*
3207050 TTA-ATGTTCGCAAATGTTCGTT
1 TTATATGTTCACAAATGTTCGTT
3207072 TTATATGTTC
1 TTATATGTTC
3207082 TTGAACGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 7 0.25
22 6 0.21
23 15 0.54
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.47
Consensus pattern (23 bp):
TTATATGTTCACAAATGTTCGTT
Found at i:3208607 original size:115 final size:116
Alignment explanation
Indices: 3208341--3208737 Score: 622
Period size: 115 Copynumber: 3.4 Consensus size: 116
3208331 TTCCTGAAAA
* * * **
3208341 ATACACCTACCTGCACA-CAGTAAGGACTTACCCTAAGCACAAAGCCGAGGAGCCTGC-AGTAAT
1 ATACACCCACCTACACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTGCGA-TAAT
*
3208404 AACTTCCCCATCCAGTCACT-CAATCACTACAATGTGTAGGTTCCCCAAAACC
65 AACTTCCCCATCCAGTCACTCCAATCACTACAA-GTGTAGGTTCCCCAGAACC
*
3208456 ATACACCCACCTACACACCAGTAAGGACTTACCCTGAGCACACAGCAAAGGAGCCTGCGATAATA
1 ATACACCCACCTACACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTGCGATAATA
3208521 ACTTCCCCATCCAGTCACTCCAATCACTACAA-TGTAGGTTCCCCAGAACC
66 ACTTCCCCATCCAGTCACTCCAATCACTACAAGTGTAGGTTCCCCAGAACC
* * *
3208571 ATACACCCACCTGCACACCAGTAAGGACTTATCCTGAGCACACAGCAAAGGAGCCTGCGATAATA
1 ATACACCCACCTACACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTGCGATAATA
*
3208636 ACTTCCCCTTCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAGAACC
66 ACTTCCCCATCCAGTCACTCCAATCACTACAA-GTGTAGGTTCCCCAGAACC
* *
3208688 ATACACCCACTTACACACCAGTAAGGACTTACCCTAAGCACACAACAAAG
1 ATACACCCACCTACACACCAGTAAGGACTTACCCTAAGCACACAGCAAAG
3208738 CCTGAAATAC
Statistics
Matches: 262, Mismatches: 15, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
115 126 0.48
116 60 0.23
117 76 0.29
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.18
Consensus pattern (116 bp):
ATACACCCACCTACACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTGCGATAATA
ACTTCCCCATCCAGTCACTCCAATCACTACAAGTGTAGGTTCCCCAGAACC
Found at i:3209826 original size:29 final size:29
Alignment explanation
Indices: 3209671--3209861 Score: 109
Period size: 29 Copynumber: 6.6 Consensus size: 29
3209661 AACATTTTTA
* * *
3209671 AATTACGAAAA-AACACCATTTTGAAATT
1 AATTACCAAAATAACACCATTTTCAAAAT
* *
3209699 AATTACCAAAATAGCAACATTTTCAAAAT
1 AATTACCAAAATAACACCATTTTCAAAAT
* * **
3209728 AATTACTAAAATATCACTC-TTTGAAAAAT
1 AATTACCAAAATAACAC-CATTTTCAAAAT
* * * ** * * *
3209757 -TTTACGAAATTGTCACCTTTTTTAAAAA
1 AATTACCAAAATAACACCATTTTCAAAAT
* *
3209785 AATTACAAAAATAACACCCTTTTCAAAAT
1 AATTACCAAAATAACACCATTTTCAAAAT
* ** * * *
3209814 AATTACCAGAATAGTACTATTTCCTAAAT
1 AATTACCAAAATAACACCATTTTCAAAAT
*
3209843 AATTACCCAAAATATCACC
1 AATTA-CCAAAATAACACC
3209862 CGTCAACGGT
Statistics
Matches: 121, Mismatches: 37, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
27 1 0.01
28 29 0.24
29 81 0.67
30 10 0.08
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (29 bp):
AATTACCAAAATAACACCATTTTCAAAAT
Found at i:3216012 original size:117 final size:115
Alignment explanation
Indices: 3215842--3216166 Score: 474
Period size: 117 Copynumber: 2.9 Consensus size: 115
3215832 TTTCCCAAAA
* * * **
3215842 CATACACCCACCTACACACCAGTAAGGACTTACCCTAAGCACAAAGCCGAGGAGCCTGCAGTAAT
1 CATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAGCAAAGGAGCCTGC-GTAAT
3215907 AACTTCCTCATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAGAAC
65 AACTTCC-CATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAGAAC
*
3215959 CATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAGCAAAGGAGCCTTCGATAAT
1 CATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAGCAAAGGAGCCTGCG-TAAT
* *
3216024 AAATTCCCATCTAGTCACTCCAATCA-TACAATGTGTAGGTTCCCCAGAAC
65 AACTTCCCATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAGAAC
3216074 CATACACCCACCTGCACACCA-TAAGGACTTACCCTGAGCACACAGCAAAGGA----GCG--AT-
1 CATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAGCAAAGGAGCCTGCGTAATA
3216131 -CTTCCCATCCAGTCACTCCAA-CACTACAATGTGTAG
66 ACTTCCCATCCAGTCACTCCAATCACTACAATGTGTAG
3216167 TCCCGAAATA
Statistics
Matches: 195, Mismatches: 11, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
104 2 0.01
105 31 0.16
107 2 0.01
110 2 0.01
114 31 0.16
115 45 0.23
116 19 0.10
117 63 0.32
ACGTcount: A:0.33, C:0.34, G:0.15, T:0.19
Consensus pattern (115 bp):
CATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAGCAAAGGAGCCTGCGTAATA
ACTTCCCATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAGAAC
Found at i:3217145 original size:29 final size:29
Alignment explanation
Indices: 3217107--3217175 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
3217097 ATTAACATTT
* * *
3217107 AAAAAAATTACGAAAATAGCACCATTTTG
1 AAAATAATTACCAAAATAGCACCATTTTC
* **
3217136 AAATTAATTACCAAAATAGCATTATTTTC
1 AAAATAATTACCAAAATAGCACCATTTTC
3217165 AAAATAATTAC
1 AAAATAATTAC
3217176 TACAATTCAC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAATAATTACCAAAATAGCACCATTTTC
Found at i:3221262 original size:21 final size:24
Alignment explanation
Indices: 3221229--3221272 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
3221219 TATAATTTTT
*
3221229 ATTTGATTTAT-AAT-ATATTCAA
1 ATTTGATTGATAAATAATATTCAA
3221251 ATTT-ATTGATAAATAATATTCA
1 ATTTGATTGATAAATAATATTCA
3221273 TTATTTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (24 bp):
ATTTGATTGATAAATAATATTCAA
Found at i:3221610 original size:16 final size:16
Alignment explanation
Indices: 3221591--3221673 Score: 55
Period size: 16 Copynumber: 5.3 Consensus size: 16
3221581 GACCTAAAAC
*
3221591 CAACCTGAATCGAAAG
1 CAACCTGAACCGAAAG
*
3221607 CAACCTGAACCGAAAT
1 CAACCTGAACCGAAAG
* * *
3221623 TAA-CTCGAACGGAAAA
1 CAACCT-GAACCGAAAG
* **
3221639 CAGCCCAAACCGAAA-
1 CAACCTGAACCGAAAG
*
3221654 -AACTTGAACCGAAAG
1 CAACCTGAACCGAAAG
3221669 CAACC
1 CAACC
3221674 CGAATTTAGT
Statistics
Matches: 48, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
14 10 0.21
15 2 0.04
16 35 0.73
17 1 0.02
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.10
Consensus pattern (16 bp):
CAACCTGAACCGAAAG
Found at i:3222432 original size:14 final size:16
Alignment explanation
Indices: 3222401--3222433 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3222391 GACCCAAAAT
3222401 GATCTGAATCGCACCC
1 GATCTGAATCGCACCC
3222417 GATCTGAAT-G-ACCC
1 GATCTGAATCGCACCC
3222431 GAT
1 GAT
3222434 TGTCACCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 1 0.06
16 9 0.53
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.21
Consensus pattern (16 bp):
GATCTGAATCGCACCC
Found at i:3223745 original size:2 final size:2
Alignment explanation
Indices: 3223711--3223736 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3223701 AAATACGAAA
3223711 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
3223737 GCATATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3223791 original size:2 final size:2
Alignment explanation
Indices: 3223784--3223808 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3223774 AAAGAGAAAA
3223784 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
3223809 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3223813 original size:2 final size:2
Alignment explanation
Indices: 3223808--3223833 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3223798 ACACACACAC
3223808 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
3223834 GATAATAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3224748 original size:16 final size:15
Alignment explanation
Indices: 3224722--3224751 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3224712 CATGTGTGAC
3224722 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
3224737 GGTCAGTCCCGGGAT
1 GGTCA-TCCCGGGAT
3224752 ACCGGCCGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.27, G:0.40, T:0.20
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:3224917 original size:4 final size:4
Alignment explanation
Indices: 3224910--3224960 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
3224900 AAACAGTAAT
* *
3224910 AATA AATA AAT- AATA AATGA GATA AA-A TAATA AATA GATA AATA AATA
1 AATA AATA AATA AATA AAT-A AATA AATA -AATA AATA AATA AATA AATA
3224958 AAT
1 AAT
3224961 TAAAAACATT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 4 0.10
4 31 0.79
5 4 0.10
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:3224948 original size:16 final size:16
Alignment explanation
Indices: 3224915--3224960 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 16
3224905 GTAATAATAA
3224915 ATAAATAATAAATGAG
1 ATAAATAATAAATGAG
3224931 ATAAAATAATAAAT-AG
1 AT-AAATAATAAATGAG
3224947 ATAAATAAATAAAT
1 ATAAAT-AATAAAT
3224961 TAAAAACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.14
16 13 0.46
17 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (16 bp):
ATAAATAATAAATGAG
Found at i:3225023 original size:34 final size:33
Alignment explanation
Indices: 3224976--3225272 Score: 215
Period size: 33 Copynumber: 8.5 Consensus size: 33
3224966 ACATTTTTTT
* *
3224976 AAACTATACAATATGTTTAAAAAAATAATTTTCA
1 AAACTATATAATATATTT-AAAAAATAATTTTCA
*
3225010 AAACCATATAATATATTTAAAAAATAATTTTCA
1 AAACTATATAATATATTTAAAAAATAATTTTCA
* *
3225043 AAA-TATATAATATATTTTAAAAACTAAATTTCA
1 AAACTATATAATATA-TTTAAAAAATAATTTTCA
* *
3225076 AAACTATATAATATATATATTTTAAAAACTAA-TTTCC
1 AAAC--TAT-ATA-ATATA-TTTAAAAAATAATTTTCA
* * * *
3225113 AAACTATTTATATATTTTTAGAAACTAATTTTCA
1 AAACTATATA-ATATATTTAAAAAATAATTTTCA
* ** *
3225147 AAACTATATAATATATGTTTTTCAAAAATGTTTTTTA
1 AAACTATATAATATA----TTTAAAAAATAATTTTCA
* *
3225184 AAACTATATTATATATATTTTAAAAA-AGTTTTCA
1 AAACTATA-TA-ATATATTTAAAAAATAATTTTCA
* * *
3225218 AAACAATATAATATGTATTTTCAAAAAT-GTTTTCAA
1 AAACTATATAATA--TA-TTTAAAAAATAATTTTC-A
3225254 AAACTATATATATATATTT
1 AAACTATATA-ATATATTT
3225273 TCAAATATTT
Statistics
Matches: 218, Mismatches: 26, Indels: 38
0.77 0.09 0.13
Matches are distributed among these distances:
32 13 0.06
33 54 0.25
34 52 0.24
35 27 0.12
36 13 0.06
37 34 0.16
38 20 0.09
39 5 0.02
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (33 bp):
AAACTATATAATATATTTAAAAAATAATTTTCA
Found at i:3225119 original size:37 final size:36
Alignment explanation
Indices: 3225015--3225270 Score: 202
Period size: 34 Copynumber: 7.3 Consensus size: 36
3225005 TTTCAAAACC
*
3225015 ATATA-ATATA-TTTAAAAAATAATTTTC-AAA--AT
1 ATATATATATATTTTAAAAACTAA-TTTCAAAACTAT
3225047 ATATA-ATATATTTTAAAAACTAAATTTCAAAACTAT
1 ATATATATATATTTTAAAAACT-AATTTCAAAACTAT
*
3225083 ATAATATATATATTTTAAAAACTAATTTCCAAACTAT
1 AT-ATATATATATTTTAAAAACTAATTTCAAAACTAT
*
3225120 -T-TATATAT-TTTTAGAAACTAATTTTCAAAACTAT
1 ATATATATATATTTTAAAAACTAA-TTTCAAAACTAT
* ** *
3225154 ATA-ATATATGTTTTTCAAAAA-TGTTTTTTAAAACTAT
1 ATATATATAT-ATTTT-AAAAACT-AATTTCAAAACTAT
* *
3225191 AT-TATATATATTTTAAAAA--AGTTTTCAAAACAAT
1 ATATATATATATTTTAAAAACTA-ATTTCAAAACTAT
* **
3225225 ATA-ATATGTATTTTCAAAAA-TGTTTTCAAAAACTAT
1 ATATATATATATTTT-AAAAACTAATTTC-AAAACTAT
3225261 ATATATATAT
1 ATATATATAT
3225271 TTTCAAATAT
Statistics
Matches: 187, Mismatches: 16, Indels: 37
0.78 0.07 0.15
Matches are distributed among these distances:
32 10 0.05
33 25 0.13
34 46 0.25
35 22 0.12
36 19 0.10
37 45 0.24
38 20 0.11
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (36 bp):
ATATATATATATTTTAAAAACTAATTTCAAAACTAT
Found at i:3225132 original size:71 final size:70
Alignment explanation
Indices: 3224986--3225273 Score: 277
Period size: 71 Copynumber: 4.1 Consensus size: 70
3224976 AAACTATACA
* * * * * *
3224986 ATATGTTTAAAAAAATAATTTTCAAAACCATAT-A-ATATA-TTTAAAAAATAATTTTCAAAATA
1 ATATATTTTAAAAACTAATTTTCAAAACTATATAATATATATTTTTAAAAATAATTTTCAAACTA
*
3225048 TATA-
66 TTTAT
* *
3225052 ATATATTTTAAAAACTAAATTTCAAAACTATATAATATATATATTTTAAAAACTAATTTCCAAAC
1 ATATATTTTAAAAACTAATTTTCAAAACTATATAATATATAT-TTTTAAAAA-TAATTTTCAAAC
3225117 TATTTAT
64 TATTTAT
* * ** *
3225124 ATAT-TTTTAGAAACTAATTTTCAAAACTATATAATATATGTTTTTCAAAAATGTTTTTTAAAAC
1 ATATATTTTAAAAACTAATTTTCAAAACTATATAATATATATTTTT-AAAAAT-AATTTTCAAAC
3225188 TATATTAT
64 TAT-TTAT
* * * * *
3225196 ATATATTTTAAAAA--AGTTTTCAAAACAATATAATATGTATTTTCAAAAAT-GTTTTCAAAAAC
1 ATATATTTTAAAAACTAATTTTCAAAACTATATAATATATATTTTTAAAAATAATTTTC--AAAC
*
3225258 TATATAT
64 TATTTAT
3225265 ATATATTTT
1 ATATATTTT
3225274 CAAATATTTA
Statistics
Matches: 185, Mismatches: 25, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
66 28 0.15
67 1 0.01
68 9 0.05
69 12 0.06
70 26 0.14
71 89 0.48
72 12 0.06
73 8 0.04
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (70 bp):
ATATATTTTAAAAACTAATTTTCAAAACTATATAATATATATTTTTAAAAATAATTTTCAAACTA
TTTAT
Found at i:3225297 original size:70 final size:68
Alignment explanation
Indices: 3225037--3225339 Score: 201
Period size: 71 Copynumber: 4.3 Consensus size: 68
3225027 TAAAAAATAA
* * * * *
3225037 TTTTCAAAA-TATATA-ATATATTTTAAAAACTAAATTT-CAAAACTATATAATATATATATTTT
1 TTTTCAAAACTATATATATATATTTT-AAAA--AAGTTTAAAAAACAATATAATATGTAT-TTTC
*
3225099 AAAAACTA
62 AAAAA-TG
* * * ** *
3225107 ATTTCCAAACTATTTATATAT-TTTTAGAAACTAA-TTTTCAAAACTATATAATATATGT-TTTT
1 TTTTCAAAACTATATATATATATTTTA-AAA--AAGTTTAAAAAACAATAT-A-ATATGTATTTT
3225169 CAAAAATG
61 CAAAAATG
* **
3225177 TTTTTTAAAACTATATTATATATATTTTAAAAAAGTTTTCAAAACAATATAATATGTATTTTCAA
1 -TTTTCAAAACTATA-TATATATATTTTAAAAAAGTTTAAAAAACAATATAATATGTATTTTCAA
3225242 AAATG
64 AAATG
* * * * *
3225247 TTTTCAAAAACTATATATATATATTTTCAAATA-TTTAAAAAAAGCCATATATTATATAATTTTC
1 TTTTC-AAAACTATATATATATATTTTAAAAAAGTTT-AAAAAA-CAATATAATATGT-ATTTTC
3225311 -AAAATG
62 AAAAATG
*
3225317 ATTTC-AAACTATATAATATATAT
1 TTTTCAAAACTATAT-ATATATAT
3225340 AAATAAAAAA
Statistics
Matches: 197, Mismatches: 20, Indels: 33
0.79 0.08 0.13
Matches are distributed among these distances:
68 12 0.06
69 38 0.19
70 56 0.28
71 65 0.33
72 16 0.08
73 10 0.05
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.43
Consensus pattern (68 bp):
TTTTCAAAACTATATATATATATTTTAAAAAAGTTTAAAAAACAATATAATATGTATTTTCAAAA
ATG
Found at i:3227772 original size:24 final size:24
Alignment explanation
Indices: 3227745--3227822 Score: 113
Period size: 24 Copynumber: 3.3 Consensus size: 24
3227735 AGTGGAGCTG
* *
3227745 AAATTTATATTGAAATTCAAACTC
1 AAATTTAAATTTAAATTCAAACTC
*
3227769 AAA-TGAAATTTAAATTCAAACTC
1 AAATTTAAATTTAAATTCAAACTC
*
3227792 AAATTTAAATTTAAATTTAAACTC
1 AAATTTAAATTTAAATTCAAACTC
3227816 AAATTTA
1 AAATTTA
3227823 TAGTGGAGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 20 0.42
24 28 0.58
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37
Consensus pattern (24 bp):
AAATTTAAATTTAAATTCAAACTC
Found at i:3227777 original size:17 final size:17
Alignment explanation
Indices: 3227755--3227788 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3227745 AAATTTATAT
3227755 TGAAATTCAAACTCAAA
1 TGAAATTCAAACTCAAA
* *
3227772 TGAAATTTAAATTCAAA
1 TGAAATTCAAACTCAAA
3227789 CTCAAATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (17 bp):
TGAAATTCAAACTCAAA
Found at i:3227783 original size:6 final size:6
Alignment explanation
Indices: 3227774--3227822 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
3227764 AACTCAAATG
* * * * *
3227774 AAATTT AAATTC AAACTC AAATTT AAATTT AAATTT AAACTC AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
3227822 A
1 A
3227823 TAGTGGAGCC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (6 bp):
AAATTT
Found at i:3227821 original size:12 final size:12
Alignment explanation
Indices: 3227757--3227822 Score: 62
Period size: 12 Copynumber: 5.6 Consensus size: 12
3227747 ATTTATATTG
*
3227757 AAATTCAAACTC
1 AAATTTAAACTC
* * *
3227769 AAA-TGAAATTT
1 AAATTTAAACTC
*
3227780 AAATTCAAACTC
1 AAATTTAAACTC
* *
3227792 AAATTTAAATTT
1 AAATTTAAACTC
3227804 AAATTTAAACTC
1 AAATTTAAACTC
3227816 AAATTTA
1 AAATTTA
3227823 TAGTGGAGCC
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
11 8 0.19
12 34 0.81
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.35
Consensus pattern (12 bp):
AAATTTAAACTC
Found at i:3231167 original size:200 final size:198
Alignment explanation
Indices: 3230681--3231606 Score: 1261
Period size: 200 Copynumber: 4.7 Consensus size: 198
3230671 TTAAAAAACA
* * * * * *
3230681 TATCGATATAATTTTAAAAATTGTCGATACATTATGTTTACCTATTCTCTCATAAAATCGATATA
1 TATCGACACAATTTTAAAAAGTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGATATA
* * * * * *
3230746 TTTTTATCGGTTACATTGTTAATTAACCTATTACTGTATAATTATCGATTTTGAT-GTTTTGGAA
66 TTTTTAT-GGTTACATTGTAAATTTACCTATTACTTTATAATTATCG-TTTCGATATTTTTGGGA
* *
3230810 TCAATACTTATAAT-AATGTATCGACACTTTATGTGTGCACCTCATTGGGCATTCATTCTGGACA
129 TCAATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCATTGGGCATTCATTCTGGACA
*
3230874 AAATG
194 AAAAG
*
3230879 TATCGACACAATTTT-AAAAGTATCGATACAATATGTTTACCTATTCTCTCATTAAACCGATATA
1 TATCGACACAATTTTAAAAAGTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGATATA
* *
3230943 TTTTTACTGGTTACATTTTAAATTTACCTATTACTTTATAATTATTTGTTTCGATATTTTTGGGA
66 TTTTTA-TGGTTACATTGTAAATTTACCTATTACTTTATAATTA-TCGTTTCGATATTTTTGGGA
* * * * *
3231008 TCGATACTTATAATAAATGTATTGACACTTTATGCATGCACCTCGTTGGGCATTCATTCTGGACA
129 TCAATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCATTGGGCATTCATTCTGGACA
*
3231073 AAACG
194 AAAAG
* * *
3231078 TATAGGCACAATTTTAAAAAGTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGTTATA
1 TATCGACACAATTTTAAAAAGTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGATATA
* *
3231143 TTTTTACTAGTTACATTGTAAATTTACCTATTACTTTATAATTATCGGTTCGATA-TTTTGGGAT
66 TTTTTA-TGGTTACATTGTAAATTTACCTATTACTTTATAATTATCGTTTCGATATTTTTGGGAT
* * *
3231207 CAAAACTTACAATACATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAA
130 CAATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCATTGGGCATTCATTCTGGACAA
3231272 AAAG
195 AAAG
*
3231276 TATCGACACATTTTTAAAAAGTATCGATACATTATGTTTACCTATTCTCTCATTAAACC-ATTAT
1 TATCGACACAATTTTAAAAAGTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGA-TAT
* * * *
3231340 ATTTTTATCGATTACATTGTAAATTTACCTATTACTTTATAATTATCGGTTTTGATGTTTTTAGG
65 ATTTTTAT-GGTTACATTGTAAATTTACCTATTACTTTATAATTATC-GTTTCGATATTTTTGGG
* * * * * * *
3231405 ATCGATACTTGCAATAAATTTATCGACACTTTATGTGTGCACCTCATTGGGCATTAATTATGGGC
128 ATCAATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCATTGGGCATTCATTCTGGAC
3231470 AAAAAG
193 AAAAAG
* * * *
3231476 TATCGATACAATTTAAAAAAATGTCGATACATTATGTTTACCTATTCTCTCATTAAACC-AGTAT
1 TATCGACACAATTTTAAAAAGTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGA-TAT
* *
3231540 ATTTTTATCGGTTACATTTTAAATTTACCTATTACTTTATAATTATCGATTTCGATGTTTTTGGG
65 ATTTTTAT-GGTTACATTGTAAATTTACCTATTACTTTATAATTATCG-TTTCGATATTTTTGGG
3231605 AT
128 AT
3231607 ATACTTCAAG
Statistics
Matches: 652, Mismatches: 66, Indels: 18
0.89 0.09 0.02
Matches are distributed among these distances:
197 89 0.14
198 209 0.32
199 79 0.12
200 275 0.42
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (198 bp):
TATCGACACAATTTTAAAAAGTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGATATA
TTTTTATGGTTACATTGTAAATTTACCTATTACTTTATAATTATCGTTTCGATATTTTTGGGATC
AATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCATTGGGCATTCATTCTGGACAAA
AAG
Found at i:3231506 original size:398 final size:396
Alignment explanation
Indices: 3230681--3231606 Score: 1338
Period size: 398 Copynumber: 2.3 Consensus size: 396
3230671 TTAAAAAACA
* * * *
3230681 TATCGATATAATTTTAAAAATTGTCGATACATTATGTTTACCTATTCTCTCATAAAATCGATATA
1 TATCGATACAATTTTAAAAAATGTCGATACATTATGTTTACCTATTCTCTCATTAAACCG-TATA
* * * * * *
3230746 TTTTTATCGGTTACATTGTTAATTAACCTATTACTGTATAATTATCGATTTTGATGTTTTGGAAT
65 TTTTTATCGGTTACATTGTAAATTTACCTATTACTTTATAATTATCGATTTCGATATTTTGGGAT
* * *
3230811 CAATACTTATAATAATGTATCGACACTTTATGTGTGCACCTCATTGGGCATTCATTCTGGACAAA
130 CAAAACTTACAATAATGTATCGACACTTTATGCGTGCACCTCATTGGGCATTCATTCTGGACAAA
*
3230876 ATGTATCGACACAATTTTAAAAGTATCGATACAATATGTTTACCTATTCTCTCATTAAACCGATA
195 AAGTATCGACACAATTTTAAAAGTATCGATACAATATGTTTACCTATTCTCTCATTAAACCGATA
* * ** *
3230941 TATTTTTACTGGTTACATTTTAAATTTACCTATTACTTTATAATTATTTGTTTCGATATTTTTGG
260 TATTTTTACTGATTACATTGTAAATTTACCTATTACTTTATAATTATCGGTTTCGATATTTTTAG
* * * * *
3231006 GATCGATACTTATAATAAATGTATTGACACTTTATGCATGCACCTCGTTGGGCATTCATTCTGGA
325 GATCGATACTTACAATAAATGTATCGACACTTTATGCATGCACCTCATTGGGCATTAATTATGGA
*
3231071 CAAAACG
390 CAAAAAG
* ** * *
3231078 TATAGGCACAATTTTAAAAAGTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGTTATA
1 TATCGATACAATTTTAAAAAATGTCGATACATTATGTTTACCTATTCTCTCATTAAACCG-TATA
* *
3231143 TTTTTA-CTAGTTACATTGTAAATTTACCTATTACTTTATAATTATCG-GTTCGATATTTTGGGA
65 TTTTTATC-GGTTACATTGTAAATTTACCTATTACTTTATAATTATCGATTTCGATATTTTGGGA
*
3231206 TCAAAACTTACAATACATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACA
129 TCAAAACTTACAATA-ATGTATCGACACTTTATGCGTGCACCTCATTGGGCATTCATTCTGGACA
* *
3231271 AAAAGTATCGACACATTTTTAAAAAGTATCGATACATTATGTTTACCTATTCTCTCATTAAACC-
193 AAAAGTATCGACACAATTTT-AAAAGTATCGATACAATATGTTTACCTATTCTCTCATTAAACCG
* *
3231335 ATTATATTTTTA-TCGATTACATTGTAAATTTACCTATTACTTTATAATTATCGGTTTTGATGTT
257 A-TATATTTTTACT-GATTACATTGTAAATTTACCTATTACTTTATAATTATCGGTTTCGATATT
* * **
3231399 TTTAGGATCGATACTTGCAATAAATTTATCGACACTTTATGTGTGCACCTCATTGGGCATTAATT
320 TTTAGGATCGATACTTACAATAAATGTATCGACACTTTATGCATGCACCTCATTGGGCATTAATT
*
3231464 ATGGGCAAAAAG
385 ATGGACAAAAAG
*
3231476 TATCGATACAATTTAAAAAAATGTCGATACATTATGTTTACCTATTCTCTCATTAAACCAGTATA
1 TATCGATACAATTTTAAAAAATGTCGATACATTATGTTTACCTATTCTCTCATTAAACC-GTATA
* *
3231541 TTTTTATCGGTTACATTTTAAATTTACCTATTACTTTATAATTATCGATTTCGATGTTTTTGGGA
65 TTTTTATCGGTTACATTGTAAATTTACCTATTACTTTATAATTATCGATTTCGAT-ATTTTGGGA
3231606 T
129 T
3231607 ATACTTCAAG
Statistics
Matches: 468, Mismatches: 52, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
396 26 0.06
397 164 0.35
398 261 0.56
399 8 0.02
400 9 0.02
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (396 bp):
TATCGATACAATTTTAAAAAATGTCGATACATTATGTTTACCTATTCTCTCATTAAACCGTATAT
TTTTATCGGTTACATTGTAAATTTACCTATTACTTTATAATTATCGATTTCGATATTTTGGGATC
AAAACTTACAATAATGTATCGACACTTTATGCGTGCACCTCATTGGGCATTCATTCTGGACAAAA
AGTATCGACACAATTTTAAAAGTATCGATACAATATGTTTACCTATTCTCTCATTAAACCGATAT
ATTTTTACTGATTACATTGTAAATTTACCTATTACTTTATAATTATCGGTTTCGATATTTTTAGG
ATCGATACTTACAATAAATGTATCGACACTTTATGCATGCACCTCATTGGGCATTAATTATGGAC
AAAAAG
Found at i:3238375 original size:16 final size:16
Alignment explanation
Indices: 3238323--3238375 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
3238313 TATCATTTTC
3238323 TACCTATAATATTATA
1 TACCTATAATATTATA
* * *
3238339 TACAAGTATCCATATTTTA
1 TAC--CTAT-AATATTATA
3238358 TACCTATAATATTATA
1 TACCTATAATATTATA
3238374 TA
1 TA
3238376 ATCGGTCTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
16 12 0.43
17 3 0.11
18 3 0.11
19 10 0.36
ACGTcount: A:0.42, C:0.13, G:0.02, T:0.43
Consensus pattern (16 bp):
TACCTATAATATTATA
Found at i:3239300 original size:178 final size:178
Alignment explanation
Indices: 3238949--3239593 Score: 796
Period size: 178 Copynumber: 3.6 Consensus size: 178
3238939 TTATAGTATT
* * *
3238949 GATACATTT-AACATATCCGGTAACGTTTTACCGGTTTTGTCATAATGAAACCGGTTTTGTCAT-
1 GATAC-TTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATG-AACCGGTTTTGTCATA
* *
3239012 TTTTACCTGTTATAGTG-T-TGTATCGATATTTTTATAAAGTATCGATACTTTATAGGAGCTATT
64 TTTTACCT-TTATATTGTTATGTATCGATATTTTTATAAAGTATCGATACTTTATAGGTGCTATT
* * * *
3239075 ACT-TTTTTCTTTTTAATTCCAAAAGTGTCGATATTTATTTGAATGGAATC
128 ACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATC
* * * *
3239125 GATATTTTCAACATATCTGG-AGCTCTTTACCAGTTTTGTCATAATGAACCTGATTTTGTCATAT
1 GATACTTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAACC-GGTTTTGTCATAT
* **
3239189 TTTACCTTTATATTGTTATGTATCAATATATTTTTATAAAGTATTAATAC-TTATAGGTGCTATT
65 TTTACCTTTATATTGTTATGTATC--GATATTTTTATAAAGTATCGATACTTTATAGGTGCTATT
3239253 ACTGCTTTTCTTTTAAATTCC-AAAGTGTCGATACTTATTTAAATGGAATC
128 ACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATC
* *
3239303 GATACTTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATTATGAACCGGTTTTATCATATT
1 GATACTTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAACCGGTTTTGTCATATT
* * *
3239368 TTACTTTTTATATCGTTATGTATCGATATGTTTAT-AAGTATCGATACTTTATAGGTGCTATTAC
66 TTAC-CTTTATATTGTTATGTATCGATATTTTTATAAAGTATCGATACTTTATAGGTGCTATTAC
* * * *
3239432 TGCTTTTCTTTTAAATTCCAAAAGTTTCGATACTTATTTCATTAGAATC
130 TGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATC
* * *
3239481 G-TACTTTCAACATAT-TCGGTAGCGCTTTACCGGTTTTGTCATATTAAATCGGTTTT-TCATAT
1 GATACTTTCAACATATCT-GGTAGCGCTTTACCGGTTTTGTCATAATGAACCGGTTTTGTCATA-
* * *
3239543 TTTTACC-TGATATATATTATGTATTGATATATATTT-TAATAGTATCGATAC
64 TTTTACCTTTATAT-TGTTATGTATCGATAT-T-TTTATAA-AGTATCGATAC
3239594 GTACCGACAA
Statistics
Matches: 408, Mismatches: 42, Indels: 35
0.84 0.09 0.07
Matches are distributed among these distances:
174 4 0.01
175 47 0.12
176 52 0.13
177 106 0.26
178 108 0.26
179 91 0.22
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.45
Consensus pattern (178 bp):
GATACTTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAACCGGTTTTGTCATATT
TTACCTTTATATTGTTATGTATCGATATTTTTATAAAGTATCGATACTTTATAGGTGCTATTACT
GCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATC
Found at i:3239420 original size:17 final size:18
Alignment explanation
Indices: 3239387--3239420 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3239377 ATATCGTTAT
*
3239387 GTATCGATATGTTTATAA
1 GTATCGATATCTTTATAA
3239405 GTATCGATA-CTTTATA
1 GTATCGATATCTTTATA
3239421 GGTGCTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (18 bp):
GTATCGATATCTTTATAA
Found at i:3239488 original size:177 final size:177
Alignment explanation
Indices: 3238949--3239593 Score: 776
Period size: 177 Copynumber: 3.6 Consensus size: 177
3238939 TTATAGTATT
* * *
3238949 GATACATTT-AACATATCCGGTAACGTTTTACCGGTTTTGTCATAATGAAACCGGTTTTGTCAT-
1 GATAC-TTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATG-AACCGGTTTTGTCATA
* *
3239012 TTTTACCTGTTATA-GTGT-TGTATCGATATTTTTATAAAGTATCGATACTTTATAGGAGCTATT
64 TTTTA-CTTTTATATGT-TATGTATCGATATTTTTATAAAGTATCGATACTTTATAGGTGCTATT
* * * *
3239075 ACT-TTTTTCTTTTTAATTCCAAAAGTGTCGATATTTATTTGAATGGAATC
127 ACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATC
* * * *
3239125 GATATTTTCAACATATCTGG-AGCTCTTTACCAGTTTTGTCATAATGAACCTGATTTTGTCATAT
1 GATACTTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAACC-GGTTTTGTCATAT
* * **
3239189 TTTACCTTTATATTGTTATGTATCAATATATTTTTATAAAGTATTAATAC-TTATAGGTGCTATT
65 TTTACTTTTATA-TGTTATGTATC--GATATTTTTATAAAGTATCGATACTTTATAGGTGCTATT
3239253 ACTGCTTTTCTTTTAAATTCC-AAAGTGTCGATACTTATTTAAATGGAATC
127 ACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATC
* *
3239303 GATACTTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATTATGAACCGGTTTTATCATATT
1 GATACTTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAACCGGTTTTGTCATATT
*
3239368 TTACTTTTTATATCGTTATGTATCGATATGTTTAT-AAGTATCGATACTTTATAGGTGCTATTAC
66 TTAC-TTTTATAT-GTTATGTATCGATATTTTTATAAAGTATCGATACTTTATAGGTGCTATTAC
* * * *
3239432 TGCTTTTCTTTTAAATTCCAAAAGTTTCGATACTTATTTCATTAGAATC
129 TGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATC
* * *
3239481 G-TACTTTCAACATAT-TCGGTAGCGCTTTACCGGTTTTGTCATATTAAATCGGTTTT-TCATAT
1 GATACTTTCAACATATCT-GGTAGCGCTTTACCGGTTTTGTCATAATGAACCGGTTTTGTCATA-
** * *
3239543 TTTTACCTGATATATATTATGTATTGATATATATTT-TAATAGTATCGATAC
64 TTTTA-CTTTTATATGTTATGTATCGATAT-T-TTTATAA-AGTATCGATAC
3239594 GTACCGACAA
Statistics
Matches: 407, Mismatches: 41, Indels: 39
0.84 0.08 0.08
Matches are distributed among these distances:
174 4 0.01
175 41 0.10
176 49 0.12
177 113 0.28
178 110 0.27
179 90 0.22
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.45
Consensus pattern (177 bp):
GATACTTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAACCGGTTTTGTCATATT
TTACTTTTATATGTTATGTATCGATATTTTTATAAAGTATCGATACTTTATAGGTGCTATTACTG
CTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATC
Found at i:3241569 original size:2 final size:2
Alignment explanation
Indices: 3241564--3241592 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3241554 AATGATTTTG
3241564 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3241593 TGTGGTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3242016 original size:17 final size:18
Alignment explanation
Indices: 3241989--3242023 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
3241979 TGAAACTTTC
3241989 TCAAGAGTTTCAAAACTT
1 TCAAGAGTTTCAAAACTT
3242007 TCAA-AGTTTCAAAACTT
1 TCAAGAGTTTCAAAACTT
3242024 AGGGTTCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (18 bp):
TCAAGAGTTTCAAAACTT
Found at i:3250023 original size:53 final size:53
Alignment explanation
Indices: 3249950--3250052 Score: 170
Period size: 53 Copynumber: 1.9 Consensus size: 53
3249940 TTTGGCACTA
*
3249950 TGTGCACCCATGGTATTCATAATGAGTTTATGAATGACCATTTCGACACTATG
1 TGTGCACCCATGGAATTCATAATGAGTTTATGAATGACCATTTCGACACTATG
* * *
3250003 TGTGCATCCATGGAATTCATAATGAGTTTTTGAATTACCATTTCGACACT
1 TGTGCACCCATGGAATTCATAATGAGTTTATGAATGACCATTTCGACACT
3250053 TAGGTGCAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.36
Consensus pattern (53 bp):
TGTGCACCCATGGAATTCATAATGAGTTTATGAATGACCATTTCGACACTATG
Found at i:3251839 original size:20 final size:20
Alignment explanation
Indices: 3251816--3251861 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
3251806 AGAAGTTTCA
3251816 AAACTTTC-TCAATAGTTTTG
1 AAACTTTCATCAA-AGTTTTG
3251836 AAACTTTCATCAAAGTTTTG
1 AAACTTTCATCAAAGTTTTG
3251856 AAACTT
1 AAACTT
3251862 AGTTTCCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (20 bp):
AAACTTTCATCAAAGTTTTG
Found at i:3260157 original size:16 final size:17
Alignment explanation
Indices: 3260136--3260169 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3260126 TTGTTTTGGG
*
3260136 TTACTTTCGATTC-AGT
1 TTACTTTCAATTCGAGT
3260152 TTACTTTCAATTCGAGT
1 TTACTTTCAATTCGAGT
3260169 T
1 T
3260170 GATTTCGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.50
Consensus pattern (17 bp):
TTACTTTCAATTCGAGT
Found at i:3260192 original size:32 final size:31
Alignment explanation
Indices: 3260156--3260222 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
3260146 TTCAGTTTAC
* **
3260156 TTTCAATTCGAGTTGATTTCGGTTCAAATTAA
1 TTTCAATTCAAGTTGATTTC-AATCAAATTAA
* *
3260188 TTTCAGTTCAAGTTGTTTTCAATCAAATTAA
1 TTTCAATTCAAGTTGATTTCAATCAAATTAA
3260219 TTTC
1 TTTC
3260223 GATTTGAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.46
Consensus pattern (31 bp):
TTTCAATTCAAGTTGATTTCAATCAAATTAA
Found at i:3260207 original size:16 final size:16
Alignment explanation
Indices: 3260156--3260208 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
3260146 TTCAGTTTAC
* *
3260156 TTTCAATTCGAGTTGA
1 TTTCAGTTCAAGTTGA
* * *
3260172 TTTCGGTTCAAATTAA
1 TTTCAGTTCAAGTTGA
*
3260188 TTTCAGTTCAAGTTGT
1 TTTCAGTTCAAGTTGA
3260204 TTTCA
1 TTTCA
3260209 ATCAAATTAA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.47
Consensus pattern (16 bp):
TTTCAGTTCAAGTTGA
Done.