Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009609.1 Hibiscus syriacus cultivar Beakdansim tig00116995_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: 1078827
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:613726 original size:14 final size:15
Alignment explanation
Indices: 613707--613743 Score: 67
Period size: 14 Copynumber: 2.5 Consensus size: 15
613697 TCCCGTGGCA
613707 TTTTCTTCGGGGAC-
1 TTTTCTTCGGGGACT
613721 TTTTCTTCGGGGACT
1 TTTTCTTCGGGGACT
613736 TTTTCTTC
1 TTTTCTTC
613744 TTCTTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (15 bp):
TTTTCTTCGGGGACT
Found at i:613731 original size:181 final size:180
Alignment explanation
Indices: 613422--613782 Score: 681
Period size: 181 Copynumber: 2.0 Consensus size: 180
613412 AAAACAATCA
613422 TCTTTCTTGATACAAATAATTTTTGTGTAACAATCAACTGCTATTTTACCACTCTCTTCCGGTAT
1 TCTTTCTTGATACAAATAATTTTTGTGTAACAATCAACTGCTATTTTACCACTCTCTTCCGGTAT
613487 CTGAAGTATTCTGGCATATTCCATTATACTCCCGTGGCATTTTCTTCGGGGACTTTTCTTCGGGG
66 CTGAAGTATTCTGGCATATTCCATTATACTCCCGTGGCATTTTCTTCGGGGACTTTTCTTCGGGG
613552 ACTTTTTCTTCTTC-TTTTCTTCTTCAGGGTTATATGAATTACAGAATGG
131 ACTTTTTCTTCTTCTTTTTCTTCTTCAGGGTTATATGAATTACAGAATGG
613601 TCTTTCTTGATACAAAT-ATTTTTGTGTAACAATCAACTGCTATTTTACCAACTCTCTTCCGGTA
1 TCTTTCTTGATACAAATAATTTTTGTGTAACAATCAACTGCTATTTTACC-ACTCTCTTCCGGTA
613665 TCTGAAGTAATTCTGGCATATTCCAGTTATACTCCCGTGGCATTTTCTTCGGGGACTTTTCTTCG
65 TCTGAAGT-ATTCTGGCATATTCCA-TTATACTCCCGTGGCATTTTCTTCGGGGACTTTTCTTCG
613730 GGGACTTTTTCTTCTTCTTTTTCTTCTTCAGGGTTATATGAATTACAGAATGG
128 GGGACTTTTTCTTCTTCTTTTTCTTCTTCAGGGTTATATGAATTACAGAATGG
613783 ATGTTCAACA
Statistics
Matches: 178, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
178 32 0.18
179 39 0.22
180 16 0.09
181 56 0.31
182 35 0.20
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (180 bp):
TCTTTCTTGATACAAATAATTTTTGTGTAACAATCAACTGCTATTTTACCACTCTCTTCCGGTAT
CTGAAGTATTCTGGCATATTCCATTATACTCCCGTGGCATTTTCTTCGGGGACTTTTCTTCGGGG
ACTTTTTCTTCTTCTTTTTCTTCTTCAGGGTTATATGAATTACAGAATGG
Found at i:613751 original size:12 final size:12
Alignment explanation
Indices: 613734--613758 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
613724 TCTTCGGGGA
613734 CTTTTTCTTCTT
1 CTTTTTCTTCTT
613746 CTTTTTCTTCTT
1 CTTTTTCTTCTT
613758 C
1 C
613759 AGGGTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:613967 original size:24 final size:24
Alignment explanation
Indices: 613933--613986 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
613923 CTGAAACATC
613933 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
613957 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
613981 ATCAAA
1 ATCAAA
613987 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:614750 original size:20 final size:20
Alignment explanation
Indices: 614725--614792 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
614715 AAAATTCAGT
*
614725 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
614745 GTTGCGATAGTCAGAATCTC
1 GTTGCGATAGTCAGAATCGC
*
614765 GTTGCGATAGTCATAATCGC
1 GTTGCGATAGTCAGAATCGC
*
614785 ATTGCGAT
1 GTTGCGAT
614793 TTACATATTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:614799 original size:20 final size:20
Alignment explanation
Indices: 614776--614831 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
614766 TTGCGATAGT
*
614776 CATAATCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
614796 CATATTCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
614816 CATATTCGCATTGCGA
1 CATATTCGCATTGCGA
614832 ATTCGGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (20 bp):
CATATTCGCATTGCGATTTA
Found at i:614852 original size:21 final size:21
Alignment explanation
Indices: 614828--614873 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
614818 TATTCGCATT
614828 GCGAATTCGGAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
* *
614849 GCGAATTTGGAAAATCGCAAT
1 GCGAATTCGGAAAATCGCAAC
614870 GCGA
1 GCGA
614874 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:616523 original size:29 final size:29
Alignment explanation
Indices: 616480--616562 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
616470 CTCACCTAAC
616480 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
616510 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
616539 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
616563 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:619941 original size:15 final size:15
Alignment explanation
Indices: 619921--619950 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
619911 CTTTCTCATA
619921 GTTATTGTTGGAATT
1 GTTATTGTTGGAATT
*
619936 GTTATTGTTGTAATT
1 GTTATTGTTGGAATT
619951 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
GTTATTGTTGGAATT
Found at i:621272 original size:29 final size:29
Alignment explanation
Indices: 621229--621311 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
621219 CTCACCTAAC
621229 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
621259 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
621288 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
621312 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:632636 original size:35 final size:35
Alignment explanation
Indices: 632590--632665 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
632580 AAAACAGTCC
* *
632590 TCAATTTCATTCTAAACACC-AATTTCCAAAGTAAT
1 TCAATTTCATTCTAAAC-CCTAAATTCCAAAATAAT
632625 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
632660 TCAATT
1 TCAATT
632666 AAATTCAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 2 0.05
35 36 0.95
ACGTcount: A:0.41, C:0.22, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
Found at i:633208 original size:130 final size:130
Alignment explanation
Indices: 633062--633309 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
633052 TATTTATATA
* **
633062 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
633127 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
*
633192 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCATGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
633257 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
633310 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:633340 original size:130 final size:129
Alignment explanation
Indices: 633076--633340 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
633066 ATTTGGTCCT
* ** *
633076 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
633141 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
633206 AAATTAAATAAAATTTAATAAATTAATCATTTAACCATGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
633271 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
633335 -A
128 CA
633336 AAATT
1 AAATT
633341 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:633666 original size:28 final size:27
Alignment explanation
Indices: 633635--633697 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
633625 AGTTAATACA
*
633635 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
633663 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
633691 ATATTTT
1 ATATTTT
633698 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:633798 original size:16 final size:18
Alignment explanation
Indices: 633777--633810 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
633767 ATTTCTTATT
633777 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
633793 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
633811 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:634352 original size:20 final size:20
Alignment explanation
Indices: 634327--634365 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
634317 TAGTAATTTT
634327 TAATAATAATTTAATAATTC
1 TAATAATAATTTAATAATTC
* *
634347 TAATAATTATTTTATAATT
1 TAATAATAATTTAATAATT
634366 TTTAAAAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATAATAATTTAATAATTC
Found at i:654526 original size:19 final size:20
Alignment explanation
Indices: 654502--654546 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
654492 TATTTCCATA
*
654502 AATTTAATAATCATTT-TAT
1 AATTTAATAAACATTTATAT
654521 AATTTAATAAACATTTATAT
1 AATTTAATAAACATTTATAT
654541 ATATTT
1 A-ATTT
654547 TTAAATGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.65
20 4 0.17
21 4 0.17
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTAATAAACATTTATAT
Found at i:654846 original size:29 final size:29
Alignment explanation
Indices: 654792--654847 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
654782 TTTATGGCAT
* * *
654792 GTTTTCTTTGTTTTTATTGAGCTTTTTAG
1 GTTTTATTTGTTATTATTGAGATTTTTAG
654821 GTTTTATTTGTTATTA-TGACGATTTTT
1 GTTTTATTTGTTATTATTGA-GATTTTT
654848 CCTGCTTCCG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.14, C:0.05, G:0.16, T:0.64
Consensus pattern (29 bp):
GTTTTATTTGTTATTATTGAGATTTTTAG
Found at i:661512 original size:16 final size:16
Alignment explanation
Indices: 661493--661530 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
661483 ATTGAATAAA
*
661493 AATTTTAATGAATTAT
1 AATTTTAACGAATTAT
*
661509 AATTTTAACGAATTGT
1 AATTTTAACGAATTAT
661525 AATTTT
1 AATTTT
661531 TTAAAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (16 bp):
AATTTTAACGAATTAT
Found at i:663901 original size:75 final size:75
Alignment explanation
Indices: 663749--663912 Score: 197
Period size: 75 Copynumber: 2.2 Consensus size: 75
663739 TCAACTATAA
* * * * ** * *
663749 TAACATAATAGGTAACGCCTATTTTATTTTACCGTTTACATTATTATTAATCTTTAAACAAATCG
1 TAACATAATATGTAGCGTCTATTTTATTTTACCATTTACATTATTAACAACCTTCAAACAAATCG
*
663814 GTAATTATTT
66 GTAATTAATT
**
663824 TAATGTAATATGTAGCGTCTATTTTATTTTACCATTTACATTATTAACAACCTTCAAAC-AATCC
1 TAACATAATATGTAGCGTCTATTTTATTTTACCATTTACATTATTAACAACCTTCAAACAAAT-C
663888 GGTAGA-TAATT
65 GGTA-ATTAATT
663899 TAACATAATATGTA
1 TAACATAATATGTA
663913 TCACTTAATA
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
74 3 0.04
75 70 0.95
76 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (75 bp):
TAACATAATATGTAGCGTCTATTTTATTTTACCATTTACATTATTAACAACCTTCAAACAAATCG
GTAATTAATT
Found at i:664134 original size:75 final size:73
Alignment explanation
Indices: 663939--664176 Score: 298
Period size: 75 Copynumber: 3.2 Consensus size: 73
663929 ATAACGCCTA
* *
663939 TTTAACAAAATATGTAGCGCCTATTTTATTTTACCGTTTATATTATTAGTAACTTTTAAATCAAA
1 TTTAACATAATATGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAAC-TTTAAA--AAA
* *
664004 CCGGTAGATAT
63 ACGGTAGGTAT
* *
664015 TTTAACGTAATATGTAGCGCCTATTTTATTTTACC-ATTACATTATTAGTAATCTTTAAAAAAAT
1 TTTAACATAATATGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAA-CTTTAAAAAAA-
664079 CGGTAGGTAT
64 CGGTAGGTAT
* * * * *
664089 TTTAATATAATAGGTAGCGTCTATTTTATTTTACCGTTTACATTATTAGCAACCTTAAAACAAAC
1 TTTAACATAATATGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACTTTAAAA-AAAC
*
664154 TGGTAGGTAG
65 -GGTAGGTAT
664164 TTTAACATAATAT
1 TTTAACATAATAT
664177 ATATCACTTA
Statistics
Matches: 141, Mismatches: 16, Indels: 11
0.84 0.10 0.07
Matches are distributed among these distances:
73 3 0.02
74 48 0.34
75 56 0.40
76 34 0.24
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (73 bp):
TTTAACATAATATGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACTTTAAAAAAACG
GTAGGTAT
Found at i:664764 original size:16 final size:16
Alignment explanation
Indices: 664740--664770 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
664730 TTCTAAATTT
*
664740 TTTTTGAGTTCAAGTC
1 TTTTCGAGTTCAAGTC
664756 TTTTCGAGTTCAAGT
1 TTTTCGAGTTCAAGT
664771 TTTAATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTTCGAGTTCAAGTC
Found at i:665219 original size:75 final size:75
Alignment explanation
Indices: 665129--665363 Score: 330
Period size: 75 Copynumber: 3.1 Consensus size: 75
665119 TATTTAACAA
* * * *
665129 AATACGTAGCACCTATTTTATTTTACCGTTTACATTATTAATAATATTTAAAAAAACCAGTAGAT
1 AATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAATATTTAAACAAACCAGTAGAT
665194 ATTTTAACGT
66 ATTTTAACGT
* * * *
665204 AATAGGTAGTGCCTATTTTATTTTACCGTTTACATTATCAGTAATCTTTAAACAAACCGGTAGAT
1 AATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAATATTTAAACAAACCAGTAGAT
665269 ATTTTAACGT
66 ATTTTAACGT
* *
665279 AATAGGTAACGCCTATTTTATTTTACCGTTTACATTATTAGTAA-ATTTCAAACAAA-CTGATAG
1 AATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAATATTT-AAACAAACCAG-TAG
* *
665342 ATAATTTAACAT
64 ATATTTTAACGT
665354 AATAGGTAGC
1 AATAGGTAGC
665364 ACTTATTTAA
Statistics
Matches: 142, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
74 5 0.04
75 137 0.96
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.39
Consensus pattern (75 bp):
AATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAATATTTAAACAAACCAGTAGAT
ATTTTAACGT
Found at i:665399 original size:248 final size:248
Alignment explanation
Indices: 665097--665551 Score: 637
Period size: 248 Copynumber: 1.8 Consensus size: 248
665087 AAAATAATTT
* * *
665097 ATTTAACGTAATAGGTAGTATCTATTTAACAAAATACGTAGCACCTATTTTATTTTACCGTTTAC
1 ATTTAACATAATAGGTAGCATCTATTTAACAAAATACGCAGCACCTATTTTATTTTACCGTTTAC
* * *
665162 ATTATTAATAATATTTAAAAAAACCAGT-AGATATTTTAACGTAATAGGTAGTGCCTATTTTATT
66 ATTATTAATAACATTTAAAAAAACCAGTAAG-TATTTTAACGTAATAGGTAGTACATATTTTATT
* * * * *
665226 TTACCGTTTACATTATCAGTAATC-TTTAAACAAACCGGTAGATATTTTAACGTAATAGGTAACG
130 TTACCATTTACATTATCAGTAA-CATTCAAACAAACCAGTAGATAATTTAACATAATAGGTAACG
665290 CCTATTTTATTTTACCGTTTACATTATTAGTAAATTTCAAACAAACTGATAGATA
194 CCTATTTTATTTTACCGTTTACATTATTAGTAAATTTCAAACAAACTGATAGATA
* * * *
665345 ATTTAACATAATAGGTAGCA-CTTATTTAATATAATATGCAGCGCCTATTTTATTTTACCGTTTA
1 ATTTAACATAATAGGTAGCATC-TATTTAACAAAATACGCAGCACCTATTTTATTTTACCGTTTA
* * * * *
665409 TATTATTAGTAACATTTAAACAAATCGGTAAGTATTTTAACGTAATAGGTAGTACATATTTTATT
65 CATTATTAATAACATTTAAAAAAACCAGTAAGTATTTTAACGTAATAGGTAGTACATATTTTATT
* * * * *
665474 TTACCATTTACATTATTAGTAACATTCAAACAAATCAGTAGGTAATTTAACATAATAGGTAGCGT
130 TTACCATTTACATTATCAGTAACATTCAAACAAACCAGTAGATAATTTAACATAATAGGTAACGC
665539 CTATTTTATTTTA
195 CTATTTTATTTTA
665552 ACCCGTTAAA
Statistics
Matches: 179, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
247 2 0.01
248 175 0.98
249 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (248 bp):
ATTTAACATAATAGGTAGCATCTATTTAACAAAATACGCAGCACCTATTTTATTTTACCGTTTAC
ATTATTAATAACATTTAAAAAAACCAGTAAGTATTTTAACGTAATAGGTAGTACATATTTTATTT
TACCATTTACATTATCAGTAACATTCAAACAAACCAGTAGATAATTTAACATAATAGGTAACGCC
TATTTTATTTTACCGTTTACATTATTAGTAAATTTCAAACAAACTGATAGATA
Found at i:665429 original size:173 final size:173
Alignment explanation
Indices: 665214--665536 Score: 492
Period size: 173 Copynumber: 1.9 Consensus size: 173
665204 AATAGGTAGT
665214 GCCTATTTTATTTTACCGTTTACATTATCAGTAATCTTTAAACAAACCGGT-AGATATTTTAACG
1 GCCTATTTTATTTTACCGTTTACATTATCAGTAATCTTTAAACAAACCGGTAAG-TATTTTAACG
* * * *
665278 TAATAGGTAACGCCTATTTTATTTTACCGTTTACATTATTAGTAA-ATTTCAAACAAA-CTGATA
65 TAATAGGTAACACATATTTTATTTTACCATTTACATTATTAGTAACA-TTCAAACAAATCAG-TA
665341 GATAATTTAACATAATAGGTAGCACTTATTTAATATAATATGCAGC
128 GATAATTTAACATAATAGGTAGCACTTATTTAATATAATATGCAGC
* * *
665387 GCCTATTTTATTTTACCGTTTATATTATTAGTAA-CATTTAAACAAATCGGTAAGTATTTTAACG
1 GCCTATTTTATTTTACCGTTTACATTATCAGTAATC-TTTAAACAAACCGGTAAGTATTTTAACG
** *
665451 TAATAGGTAGTACATATTTTATTTTACCATTTACATTATTAGTAACATTCAAACAAATCAGTAGG
65 TAATAGGTAACACATATTTTATTTTACCATTTACATTATTAGTAACATTCAAACAAATCAGTAGA
665516 TAATTTAACATAATAGGTAGC
130 TAATTTAACATAATAGGTAGC
665537 GTCTATTTTA
Statistics
Matches: 136, Mismatches: 10, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
172 1 0.01
173 130 0.96
174 5 0.04
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (173 bp):
GCCTATTTTATTTTACCGTTTACATTATCAGTAATCTTTAAACAAACCGGTAAGTATTTTAACGT
AATAGGTAACACATATTTTATTTTACCATTTACATTATTAGTAACATTCAAACAAATCAGTAGAT
AATTTAACATAATAGGTAGCACTTATTTAATATAATATGCAGC
Found at i:665448 original size:98 final size:98
Alignment explanation
Indices: 665288--665469 Score: 262
Period size: 98 Copynumber: 1.9 Consensus size: 98
665278 TAATAGGTAA
*
665288 CGCCTATTTTATTTTACCGTTTACATTATTAGTAAATTTCAAACAAACTGATAGATAATTTAACA
1 CGCCTATTTTATTTTACCGTTTACATTATTAGTAAATTTCAAACAAACGGATAGATAATTTAACA
*
665353 TAATAGGTAGCACTTATTTAATATAATATGCAG
66 TAATAGGTAGCACATATTTAATATAATATGCAG
* *
665386 CGCCTATTTTATTTTACCGTTTATATTATTAGTAACATTT-AAACAAATCGG-TA-AGTATTTTA
1 CGCCTATTTTATTTTACCGTTTACATTATTAGTAA-ATTTCAAACAAA-CGGATAGA-TAATTTA
* *
665448 ACGTAATAGGTAGTACATATTT
63 ACATAATAGGTAGCACATATTT
665470 TATTTTACCA
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
97 1 0.01
98 68 0.91
99 6 0.08
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.41
Consensus pattern (98 bp):
CGCCTATTTTATTTTACCGTTTACATTATTAGTAAATTTCAAACAAACGGATAGATAATTTAACA
TAATAGGTAGCACATATTTAATATAATATGCAG
Found at i:665469 original size:75 final size:74
Alignment explanation
Indices: 665389--665551 Score: 229
Period size: 75 Copynumber: 2.2 Consensus size: 74
665379 TATGCAGCGC
* * * * * *
665389 CTATTTTATTTTACCGTTTATATTATTAGTAACATTTAAACAAATCGGTAAGTATTTTAACGTAA
1 CTATTTTATTTTACCATTTACATTATTAGTAACATTCAAACAAATCAGTAAGTAATTTAACATAA
665454 TAGGTA-GT
66 TAGGTACGT
*
665462 ACATATTTTATTTTACCATTTACATTATTAGTAACATTCAAACAAATCAGTAGGTAATTTAACAT
1 -C-TATTTTATTTTACCATTTACATTATTAGTAACATTCAAACAAATCAGTAAGTAATTTAACAT
665527 AATAGGTAGCGT
64 AATAGGTA-CGT
665539 CTATTTTATTTTA
1 CTATTTTATTTTA
665552 ACCCGTTAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
74 1 0.01
75 75 0.95
76 1 0.01
77 2 0.03
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (74 bp):
CTATTTTATTTTACCATTTACATTATTAGTAACATTCAAACAAATCAGTAAGTAATTTAACATAA
TAGGTACGT
Found at i:665906 original size:37 final size:37
Alignment explanation
Indices: 665865--665967 Score: 163
Period size: 37 Copynumber: 2.8 Consensus size: 37
665855 AGATAGCGTT
*
665865 AGAGTTTTACTAGGATTTAAACTCCTAAAAATATGAC
1 AGAGTTTTACTAGGATTCAAACTCCTAAAAATATGAC
*
665902 AGAGTTTTACTAGGATTCAAACTCCTAAAAATATGAT
1 AGAGTTTTACTAGGATTCAAACTCCTAAAAATATGAC
*
665939 AGA-TTTCTACTATGATTCAAACTCCTAAA
1 AGAGTTT-TACTAGGATTCAAACTCCTAAA
665968 TGTAGGATCC
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
36 3 0.05
37 59 0.95
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.33
Consensus pattern (37 bp):
AGAGTTTTACTAGGATTCAAACTCCTAAAAATATGAC
Found at i:666438 original size:16 final size:16
Alignment explanation
Indices: 666417--666458 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
666407 ATTCCAACAG
666417 TATATTTATTATTATA
1 TATATTTATTATTATA
666433 TATATTTAATT-TTATA
1 TATATTT-ATTATTATA
666449 T-T-TTTATTAT
1 TATATTTATTAT
666459 CTATTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.12
14 4 0.17
15 1 0.04
16 13 0.54
17 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATTTATTATTATA
Found at i:666476 original size:23 final size:23
Alignment explanation
Indices: 666435--666493 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
666425 TTATTATATA
* *
666435 TATTTAATTTTATATTTTTATTAT
1 TATTT-ATTTTTTAGTTTTATTAT
*
666459 CTA-TTATTTTTTAGTTTTTTTAT
1 -TATTTATTTTTTAGTTTTATTAT
666482 TATTTATTTTTT
1 TATTTATTTTTT
666494 CGTCATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 2 0.07
23 24 0.80
24 2 0.07
25 2 0.07
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (23 bp):
TATTTATTTTTTAGTTTTATTAT
Found at i:666481 original size:16 final size:15
Alignment explanation
Indices: 666419--666493 Score: 53
Period size: 16 Copynumber: 4.8 Consensus size: 15
666409 TCCAACAGTA
* *
666419 TATTTATTATTATAT
1 TATTTATTTTTTTAT
* *
666434 ATATTTAATTTTATAT
1 -TATTTATTTTTTTAT
*
666450 T-TTTATTATCTATTAT
1 TATTTATT-T-TTTTAT
*
666466 TTTTTAGTTTTTTTAT
1 TATTTA-TTTTTTTAT
666482 TATTTATTTTTT
1 TATTTATTTTTT
666494 CGTCATTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
14 5 0.10
15 8 0.17
16 28 0.58
17 5 0.10
18 2 0.04
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.72
Consensus pattern (15 bp):
TATTTATTTTTTTAT
Found at i:666487 original size:7 final size:7
Alignment explanation
Indices: 666419--666489 Score: 51
Period size: 7 Copynumber: 10.1 Consensus size: 7
666409 TCCAACAGTA
666419 TATTTAT
1 TATTTAT
666426 TATTATAT
1 TATT-TAT
666434 ATATTTAAT
1 -TATTT-AT
666443 T-TTATAT
1 TATT-TAT
666450 T-TTTAT
1 TATTTAT
*
666456 TATCTAT
1 TATTTAT
*
666463 TATTTTT
1 TATTTAT
*
666470 TAGTT-T
1 TATTTAT
666476 T-TTTAT
1 TATTTAT
666482 TATTTAT
1 TATTTAT
666489 T
1 T
666490 TTTTCGTCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
5 2 0.04
6 8 0.15
7 30 0.58
8 6 0.12
9 6 0.12
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.70
Consensus pattern (7 bp):
TATTTAT
Found at i:666776 original size:21 final size:19
Alignment explanation
Indices: 666765--667080 Score: 245
Period size: 21 Copynumber: 15.3 Consensus size: 19
666755 TGCGATTTAT
* *
666765 TCCAAATTCGTTGAGATAG
1 TCCAAGTTCGTTGCGATAG
*
666784 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
666807 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
666826 TCCAAGTTCGCGTTGCGATAG
1 TCCAAGTT--CGTTGCGATAG
*
666847 TCTAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
666866 TCCAAGTTTGCGTTGCGATTTAT
1 TCCAAG-TT-CGTTGCGA--TAG
*
666889 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
666908 TCTAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
666931 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
666950 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
666973 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
666992 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
667015 TCCAAGTTCATTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
667034 TCGAAGTTCACGTTGTGATTTAG
1 TCCAAGTT--CGTTGCGA--TAG
* *
667057 TCCAAATTCGTTGCGATGG
1 TCCAAGTTCGTTGCGATAG
667076 TCCAA
1 TCCAA
667081 AATCGCAACG
Statistics
Matches: 241, Mismatches: 30, Indels: 52
0.75 0.09 0.16
Matches are distributed among these distances:
19 75 0.31
20 2 0.01
21 109 0.45
22 2 0.01
23 53 0.22
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:666797 original size:42 final size:42
Alignment explanation
Indices: 666738--667080 Score: 519
Period size: 42 Copynumber: 8.2 Consensus size: 42
666728 TTCCAAGTTC
* *
666738 ATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGAG
1 ATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCG
666780 ATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCG
1 ATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCG
* * *
666822 ATAGTCCAAGTTCGCGTTGCGA--TAGTCTAAGTTCGTTGCG
1 ATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCG
*
666862 ATAGTCCAAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCG
1 ATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCG
* *
666904 ATAGTCTAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCG
1 ATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCG
*
666946 ATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCG
1 ATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCG
* * *
666988 ATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCATTGCG
1 ATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCG
* * * *
667030 ATAGTCGAAGTTCACGTTGTGATTTAGTCCAAATTCGTTGCG
1 ATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCG
*
667072 ATGGTCCAA
1 ATAGTCCAA
667081 AATCGCAACG
Statistics
Matches: 277, Mismatches: 22, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
40 36 0.13
42 241 0.87
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.36
Consensus pattern (42 bp):
ATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCG
Found at i:667979 original size:21 final size:21
Alignment explanation
Indices: 667950--668020 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
667940 GATTTTGGAC
*
667950 AATCACAACGAATTTGGAATA
1 AATCGCAACGAATTTGGAATA
* *
667971 AATCGCAACACGAACTTGGACT-
1 AATCGC-A-ACGAATTTGGAATA
*
667993 -ATCGCAACGAATTTGTAATA
1 AATCGCAACGAATTTGGAATA
668013 AATCGCAA
1 AATCGCAA
668021 TGCGAACTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 10 0.25
20 1 0.03
21 17 0.43
22 1 0.03
23 11 0.28
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (21 bp):
AATCGCAACGAATTTGGAATA
Found at i:668003 original size:42 final size:42
Alignment explanation
Indices: 667944--668043 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
667934 CGTTGCGATT
* *
667944 TTGGACAATCACAACGAATTTGGAATAAATCGCAACACGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACACGAAC
* **
667986 TTGGACTATCGCAACGAATTTGTAATAAATCGCAATGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACACGAAC
*
668028 TTTGACTATCGCAACG
1 TTGGACTATCGCAACG
668044 CGAACTTGGA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACACGAAC
Found at i:668038 original size:21 final size:21
Alignment explanation
Indices: 668014--668068 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
668004 TTTGTAATAA
** *
668014 ATCGCAATGCGAACTTTGACT
1 ATCGCAACACGAACTTGGACT
*
668035 ATCGCAACGCGAACTTGGACT
1 ATCGCAACACGAACTTGGACT
*
668056 ATCGCAATACGAA
1 ATCGCAACACGAA
668069 TATGTAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAACACGAACTTGGACT
Found at i:668450 original size:22 final size:22
Alignment explanation
Indices: 668403--668462 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
668393 ATTTTTATTT
*
668403 ATTTTATATTTTCTTGACATTT
1 ATTTTATATTTTCTTGACATTC
**
668425 ATTTTATATTTTCTTGATGTTC
1 ATTTTATATTTTCTTGACATTC
*
668447 ATTTTATTACTTTCTT
1 ATTTTA-TATTTTCTT
668463 TCTTATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 25 0.76
23 8 0.24
ACGTcount: A:0.20, C:0.10, G:0.05, T:0.65
Consensus pattern (22 bp):
ATTTTATATTTTCTTGACATTC
Found at i:668454 original size:27 final size:22
Alignment explanation
Indices: 668399--668441 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
668389 TTTCATTTTT
668399 ATTTATTTTATATTTTCTTGAC
1 ATTTATTTTATATTTTCTTGAC
668421 ATTTATTTTATATTTTCTTGA
1 ATTTATTTTATATTTTCTTGA
668442 TGTTCATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.65
Consensus pattern (22 bp):
ATTTATTTTATATTTTCTTGAC
Found at i:668527 original size:24 final size:23
Alignment explanation
Indices: 668495--668542 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
668485 TATATAGATT
668495 TTTACTATTCTATCTATTTTTTTA
1 TTTACTATTCTATC-ATTTTTTTA
* * *
668519 TTTATTATTTTTTCATTTTTTTA
1 TTTACTATTCTATCATTTTTTTA
668542 T
1 T
668543 CTTCATGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTACTATTCTATCATTTTTTTA
Found at i:670345 original size:3 final size:3
Alignment explanation
Indices: 670337--670365 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
670327 ACTCTAGGAA
670337 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
670366 ACATGTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:671674 original size:2 final size:2
Alignment explanation
Indices: 671667--671692 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
671657 GTATTAACCC
671667 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
671693 CAACTCAAAA
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):
TA
Found at i:671782 original size:15 final size:15
Alignment explanation
Indices: 671762--671795 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
671752 CATTGTTTCT
671762 GAACCAAACATTTGA
1 GAACCAAACATTTGA
671777 GAACCAAACATTTGA
1 GAACCAAACATTTGA
671792 GAAC
1 GAAC
671796 ATGGAGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.18
Consensus pattern (15 bp):
GAACCAAACATTTGA
Found at i:672197 original size:18 final size:18
Alignment explanation
Indices: 672174--672220 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
672164 TGTTTCTGAC
* *
672174 GGAATTGAAATCTGTGAA
1 GGAATTGGAATCTGTCAA
*
672192 GGAATTGGAATTTGTCAA
1 GGAATTGGAATCTGTCAA
672210 -GAATTGGAATC
1 GGAATTGGAATC
672221 CAATTCCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (18 bp):
GGAATTGGAATCTGTCAA
Found at i:672530 original size:19 final size:20
Alignment explanation
Indices: 672506--672556 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
672496 AAATGACCAA
* *
672506 CAAATTCGCAACGCGATCT-
1 CAAATTCGCAACACGAACTC
672525 CAAATTCGCAACACGAACTC
1 CAAATTCGCAACACGAACTC
*
672545 CAATTTCGCAAC
1 CAAATTCGCAAC
672557 CCAGTTTCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.35, C:0.33, G:0.12, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACACGAACTC
Found at i:672554 original size:20 final size:19
Alignment explanation
Indices: 672506--672661 Score: 73
Period size: 20 Copynumber: 7.9 Consensus size: 19
672496 AAATGACCAA
* *
672506 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACACGAACT
672525 CAAATTCGCAACACGAACT
1 CAAATTCGCAACACGAACT
* * **
672544 CCAATTTCGCAAC-CCAGTTT
1 -CAAATTCGCAACACGA-ACT
* * * *
672564 CCAATTTCGCAACGCAAATAT
1 -CAAATTCGCAACACGAA-CT
* *
672585 GTAAA-TCGCAACACAGAAGT
1 -CAAATTCGCAACAC-GAACT
*
672605 CAAATTCGCAACACGATAGT
1 CAAATTCGCAACACGA-ACT
* * *
672625 CAAATTCGCAATACAAAAGT
1 CAAATTCGCAACAC-GAACT
*
672645 CAAATTCGCAACGCGAA
1 CAAATTCGCAACACGAA
672662 TTTGTAAATC
Statistics
Matches: 108, Mismatches: 21, Indels: 16
0.74 0.14 0.11
Matches are distributed among these distances:
19 26 0.24
20 74 0.69
21 8 0.07
ACGTcount: A:0.39, C:0.28, G:0.13, T:0.20
Consensus pattern (19 bp):
CAAATTCGCAACACGAACT
Found at i:672613 original size:40 final size:39
Alignment explanation
Indices: 672569--672755 Score: 173
Period size: 40 Copynumber: 4.7 Consensus size: 39
672559 AGTTTCCAAT
*
672569 TTCGCAACGCAAATATGTAAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGC-AATA-GTAAATTCGCAACACAAAAGTCAAA
* * *
672609 TTCGCAACACGATAGTCAAATTCGCAATACAAAAGTCAAA
1 TTCGCAACGCAATAGT-AAATTCGCAACACAAAAGTCAAA
* ** * *
672649 TTCGCAACGCGAATTTGTAAA-TCGCAACTTATAAGTAAAA
1 TTCGCAACGC-AA-TAGTAAATTCGCAACACAAAAGTCAAA
* * *
672689 TTCGCAATGCGATAGCAAAATTCGCAACACAAAAGTCAAA
1 TTCGCAACGCAATAG-TAAATTCGCAACACAAAAGTCAAA
672729 TTCGCAACGCGAA-AGTCAAATTCGCAA
1 TTCGCAACGC-AATAGT-AAATTCGCAA
672756 TGCGAAACAC
Statistics
Matches: 116, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
38 4 0.03
39 10 0.09
40 94 0.81
41 5 0.04
42 3 0.03
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (39 bp):
TTCGCAACGCAATAGTAAATTCGCAACACAAAAGTCAAA
Found at i:672708 original size:20 final size:20
Alignment explanation
Indices: 672681--672762 Score: 94
Period size: 20 Copynumber: 4.1 Consensus size: 20
672671 CGCAACTTAT
* *
672681 AAGTAAAATTCGCAATGCGA
1 AAGTCAAATTCGCAACGCGA
* * *
672701 TAG-CAAAATTCGCAACACAA
1 AAGTC-AAATTCGCAACGCGA
672721 AAGTCAAATTCGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
*
672741 AAGTCAAATTCGCAATGCGA
1 AAGTCAAATTCGCAACGCGA
672761 AA
1 AA
672763 CACAATATTA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
20 50 0.98
21 1 0.02
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (20 bp):
AAGTCAAATTCGCAACGCGA
Found at i:672739 original size:80 final size:80
Alignment explanation
Indices: 672569--672741 Score: 249
Period size: 80 Copynumber: 2.2 Consensus size: 80
672559 AGTTTCCAAT
* *
672569 TTCGCAACGCAAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACACGATAGTCAAATTCGC
1 TTCGCAACGCGAATATGTAAATCGCAACACAGAAGTAAAATTCGCAACACGATAGTCAAATTCGC
*
672634 AATACAAAAGTCAAA
66 AACACAAAAGTCAAA
* ** * **
672649 TTCGCAACGCGAATTTGTAAATCGCAACTTATAAGTAAAATTCGCAATGCGATAG-CAAAATTCG
1 TTCGCAACGCGAATATGTAAATCGCAACACAGAAGTAAAATTCGCAACACGATAGTC-AAATTCG
672713 CAACACAAAAGTCAAA
65 CAACACAAAAGTCAAA
672729 TTCGCAACGCGAA
1 TTCGCAACGCGAA
672742 AGTCAAATTC
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
79 1 0.01
80 82 0.99
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (80 bp):
TTCGCAACGCGAATATGTAAATCGCAACACAGAAGTAAAATTCGCAACACGATAGTCAAATTCGC
AACACAAAAGTCAAA
Found at i:674127 original size:18 final size:18
Alignment explanation
Indices: 674104--674139 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
674094 ATTTATAGTA
674104 GAAATTCAAACTCAAATT
1 GAAATTCAAACTCAAATT
* *
674122 GAAATTTAAATTCAAATT
1 GAAATTCAAACTCAAATT
674140 CCAATTACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (18 bp):
GAAATTCAAACTCAAATT
Found at i:674551 original size:25 final size:25
Alignment explanation
Indices: 674523--674572 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
674513 CATTATTTTC
*
674523 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
674548 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
674573 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:674739 original size:54 final size:56
Alignment explanation
Indices: 674637--674745 Score: 177
Period size: 54 Copynumber: 2.0 Consensus size: 56
674627 ATGTTGAAGT
674637 TAAACTTTCGCAACGCGAAATAAGCATTGCGATAGTCAAATTCACAACGCGAAAGG
1 TAAACTTTCGCAACGCGAAATAAGCATTGCGATAGTCAAATTCACAACGCGAAAGG
* **
674693 TAAA-TTT-GCAATGCGAAATAAGCATTGCGATAGTCAAATTTGCAACGCGAAAG
1 TAAACTTTCGCAACGCGAAATAAGCATTGCGATAGTCAAATTCACAACGCGAAAG
674746 TCAAATTCGC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 43 0.86
55 3 0.06
56 4 0.08
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.22
Consensus pattern (56 bp):
TAAACTTTCGCAACGCGAAATAAGCATTGCGATAGTCAAATTCACAACGCGAAAGG
Found at i:677193 original size:3 final size:3
Alignment explanation
Indices: 677187--677220 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
677177 TCTTCGGGGA
677187 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
677221 AGGATTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:677432 original size:24 final size:24
Alignment explanation
Indices: 677395--677448 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
677385 CCATCACATC
*
677395 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
677419 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
677443 ATCAAA
1 ATCAAA
677449 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:677462 original size:24 final size:24
Alignment explanation
Indices: 677411--677462 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
677401 ATCTGAGTAT
* *
677411 TGACCAAGATCAAAGTCCGAGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* **
677435 TGACCAAGATCAAATTTTGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
677459 TGAC
1 TGAC
677463 TAGTACTCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:677595 original size:12 final size:12
Alignment explanation
Indices: 677569--677608 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
677559 GAAAAGGTTG
*
677569 TGGGTTTTGAGAT
1 TGGG-TTTGATAT
*
677582 TGTGTTTGATAT
1 TGGGTTTGATAT
677594 TGGGTTTGATAT
1 TGGGTTTGATAT
677606 TGG
1 TGG
677609 AAATGTGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 21 0.88
13 3 0.12
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (12 bp):
TGGGTTTGATAT
Found at i:678400 original size:18 final size:18
Alignment explanation
Indices: 678377--678442 Score: 69
Period size: 18 Copynumber: 3.5 Consensus size: 18
678367 AAAATATTTG
678377 TGTTGCGAAACTAAAATC
1 TGTTGCGAAACTAAAATC
* *
678395 TGTTGCGAAATTAAATTC
1 TGTTGCGAAACTAAAATC
* *
678413 GTGTTGCGAATTCGAAAATC
1 -TGTTGCGAA-ACTAAAATC
678433 TAGTTGCGAA
1 T-GTTGCGAA
678443 TTTGAAATTC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
18 16 0.41
19 10 0.26
20 13 0.33
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (18 bp):
TGTTGCGAAACTAAAATC
Found at i:678500 original size:20 final size:20
Alignment explanation
Indices: 678479--678577 Score: 90
Period size: 20 Copynumber: 5.0 Consensus size: 20
678469 TTCCGCGTTG
*
678479 CGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTTTGTGTTA
* * *
678499 CGAATTTGACTATCGCGTTA
1 CGAATTTGACTTTTGTGTTA
* *
678519 CGAATTTGACATCTGTGTTA
1 CGAATTTGACTTTTGTGTTA
* * **
678539 CGAATTTGACTATCGCATTA
1 CGAATTTGACTTTTGTGTTA
* *
678559 CAAATTTGACTTCTGTGTT
1 CGAATTTGACTTTTGTGTT
678578 GCGATTTACA
Statistics
Matches: 58, Mismatches: 21, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.41
Consensus pattern (20 bp):
CGAATTTGACTTTTGTGTTA
Found at i:678516 original size:40 final size:40
Alignment explanation
Indices: 678472--678606 Score: 166
Period size: 40 Copynumber: 3.4 Consensus size: 40
678462 TTTGAAATTC
* *
678472 CGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTAT
1 CGCGTTACGAATTTGACTTCTGTGTTGCGAATTTGACTAT
* *
678512 CGCGTTACGAATTTGACATCTGTGTTACGAATTTGACTAT
1 CGCGTTACGAATTTGACTTCTGTGTTGCGAATTTGACTAT
* * *
678552 CGCATTACAAATTTGACTTCTGTGTTGCG-ATTT-ACAGATT
1 CGCGTTACGAATTTGACTTCTGTGTTGCGAATTTGAC-TA-T
*
678592 CGCGTTGCGAATTTG
1 CGCGTTACGAATTTG
678607 TTGGTCATTT
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
38 2 0.02
39 5 0.06
40 74 0.91
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.39
Consensus pattern (40 bp):
CGCGTTACGAATTTGACTTCTGTGTTGCGAATTTGACTAT
Found at i:679231 original size:232 final size:229
Alignment explanation
Indices: 678769--679277 Score: 742
Period size: 232 Copynumber: 2.2 Consensus size: 229
678759 TTGGTCTACC
* *
678769 CGACCCGACCCTACCAAAATAAAGTTTCACCTGACCTGACCCGAAATAATAAAAAATTATTTTTA
1 CGACCCGACCCGACCAAAATAAAGTTTCACCTGACCCGACCCGAAATAATAAAAAATTATTTTTA
* *
678834 TTCAATAAAAACAATTACTTAGTTGGGAAAAAATTATATATAAAGGGGTATTATAGTAATTATTC
66 TTCAATAAAAACAATGACTTAATT-GGAAAAAATTATATATAAAGGGGTATTATAGTAATTATTC
* *
678899 CTAAATATATAAGGTAAAATTATATATATTTTGGGTCGGGTGGGGTCGGATATTTTTCACCCTAA
130 CTAAATATATAAGGTAAAATTATATATATTTT--GTCAGGTCGGGTCGGATATTTTTCACCCTAA
* *
678964 ACCCGAACTCTACCCGAATTTCACACTTAAAAAAAA-
193 ACCCGAACTCGACCCGAATATCACACTTAAAAAAAAT
*
679000 CTGACCCGACCCGACCAAAATAAAGTTTCACCTGACCCGTCCCGAAATAATAAAAAATTATTTTT
1 C-GACCCGACCCGACCAAAATAAAGTTTCACCTGACCCGACCCGAAATAATAAAAAATTATTTTT
* *
679065 ATTCAATAAAAACAGTGACTTAATT-GAAAACAAGTTATATATAGAGGGGTATTAGT-GTAATTA
65 ATTCAATAAAAACAATGACTTAATTGGAAAA-AA-TTATATATAAAGGGGTATTA-TAGTAATTA
*
679128 TTCCTAAATATATAAGGTAAAATTATATATA-TTT-TCAGGTCGGGTCGGGTATTTTTCACCCTA
127 TTCCTAAATATATAAGGTAAAATTATATATATTTTGTCAGGTCGGGTCGGATATTTTTCACCCTA
679191 AACCCGAACTCGACCCGATCCGAATATCACACTT-AAAAAAAT
192 AACCCGAACTCGA--C---CCGAATATCACACTTAAAAAAAAT
* *
679233 CGACCTGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAA
1 CGACCCGACCCGACCAAAATAAAGTTTCACCTGACCCGACCCGAA
679278 TATATGAATT
Statistics
Matches: 253, Mismatches: 15, Indels: 19
0.88 0.05 0.07
Matches are distributed among these distances:
228 38 0.15
230 6 0.02
231 6 0.02
232 187 0.74
233 16 0.06
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (229 bp):
CGACCCGACCCGACCAAAATAAAGTTTCACCTGACCCGACCCGAAATAATAAAAAATTATTTTTA
TTCAATAAAAACAATGACTTAATTGGAAAAAATTATATATAAAGGGGTATTATAGTAATTATTCC
TAAATATATAAGGTAAAATTATATATATTTTGTCAGGTCGGGTCGGATATTTTTCACCCTAAACC
CGAACTCGACCCGAATATCACACTTAAAAAAAAT
Found at i:679765 original size:4 final size:4
Alignment explanation
Indices: 679756--679842 Score: 54
Period size: 4 Copynumber: 20.8 Consensus size: 4
679746 ATGTTAGAGA
* * *
679756 AAAT AAAT AAAT AAAT AAAT ACTAAT AAAT CAAAAG AAAGA AAAT TAA-
1 AAAT AAAT AAAT AAAT AAAT A--AAT AAAT --AAAT AAA-T AAAT AAAT
*
679804 AATT AAA- AAA- AATAT AAAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AA-AT -AAAT AAAT AAAT AAAT AAAT AAA
679843 GAGAGACAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
3 6 0.09
4 47 0.70
5 5 0.07
6 9 0.13
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:679894 original size:12 final size:12
Alignment explanation
Indices: 679879--679931 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 12
679869 GAAAACTAAG
679879 ATAAAAAAATAA
1 ATAAAAAAATAA
679891 AT-AAAAAATAA
1 ATAAAAAAATAA
*
679902 A-AAAAAATAAAA
1 ATAAAAAA-ATAA
*
679914 ATAAAAATATTAA
1 ATAAAAA-AATAA
679927 ATAAA
1 ATAAA
679932 GCAAAGAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
11 15 0.44
12 6 0.18
13 12 0.35
14 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
ATAAAAAAATAA
Found at i:679896 original size:11 final size:10
Alignment explanation
Indices: 679881--679919 Score: 60
Period size: 11 Copynumber: 3.7 Consensus size: 10
679871 AAACTAAGAT
679881 AAAAAAATAA
1 AAAAAAATAA
679891 ATAAAAAATAA
1 A-AAAAAATAA
679902 AAAAAAATAA
1 AAAAAAATAA
679912 AAATAAAA
1 AAA-AAAA
679920 ATATTAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 13 0.48
11 14 0.52
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:679909 original size:17 final size:17
Alignment explanation
Indices: 679882--679931 Score: 66
Period size: 16 Copynumber: 2.8 Consensus size: 17
679872 AACTAAGATA
679882 AAAAAATAAATAAAAAAT
1 AAAAAATAAAT-AAAAAT
679900 AAAAAA-AAATAAAAAT
1 AAAAAATAAATAAAAAT
679916 AAAAATATTAAATAAA
1 AAAAA-A-TAAATAAA
679932 GCAAAGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 11 0.38
17 5 0.17
18 6 0.21
19 7 0.24
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAAAATAAATAAAAAT
Found at i:679913 original size:6 final size:6
Alignment explanation
Indices: 679883--679922 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
679873 ACTAAGATAA
*
679883 AAAAAT AAATA- AAAAAT -AAAA- AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
679923 TTAAATAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
5 12 0.41
6 17 0.59
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:679919 original size:22 final size:21
Alignment explanation
Indices: 679881--679922 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
679871 AAACTAAGAT
*
679881 AAAAAAATAAATAAAAAATAA
1 AAAAAAATAAAAAAAAAATAA
679902 AAAAAAATAAAAATAAAAATA
1 AAAAAAATAAAAA-AAAAATA
679923 TTAAATAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (21 bp):
AAAAAAATAAAAAAAAAATAA
Found at i:679965 original size:23 final size:23
Alignment explanation
Indices: 679938--680006 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
679928 TAAAGCAAAG
679938 AATATAAGATAACATAAAATAAA
1 AATATAAGATAACATAAAATAAA
* *
679961 AATAT-A-AT-A-A-GAAGT--A
1 AATATAAGATAACATAAAATAAA
679977 AATATAAGATAACATAAAATAAA
1 AATATAAGATAACATAAAATAAA
680000 AATATAA
1 AATATAA
680007 TAAGAAGTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
16 6 0.17
17 1 0.03
18 5 0.14
19 2 0.06
20 2 0.06
21 5 0.14
22 1 0.03
23 13 0.37
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (23 bp):
AATATAAGATAACATAAAATAAA
Found at i:679989 original size:39 final size:39
Alignment explanation
Indices: 679938--680020 Score: 166
Period size: 39 Copynumber: 2.1 Consensus size: 39
679928 TAAAGCAAAG
679938 AATATAAGATAACATAAAATAAAAATATAATAAGAAGTA
1 AATATAAGATAACATAAAATAAAAATATAATAAGAAGTA
679977 AATATAAGATAACATAAAATAAAAATATAATAAGAAGTA
1 AATATAAGATAACATAAAATAAAAATATAATAAGAAGTA
680016 AATAT
1 AATAT
680021 TATATATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.24
Consensus pattern (39 bp):
AATATAAGATAACATAAAATAAAAATATAATAAGAAGTA
Found at i:680144 original size:18 final size:18
Alignment explanation
Indices: 680096--680145 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 18
680086 ATTTATACAA
**
680096 AATAAATCAAAGAAAAAT
1 AATAAATCAAACTAAAAT
680114 AAT-AA--AAACTAAAAT
1 AATAAATCAAACTAAAAT
*
680129 AATAAATCAAATTAAAA
1 AATAAATCAAACTAAAA
680146 AGAAAACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
15 11 0.42
16 2 0.08
17 2 0.08
18 11 0.42
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (18 bp):
AATAAATCAAACTAAAAT
Found at i:682103 original size:84 final size:83
Alignment explanation
Indices: 681920--682387 Score: 409
Period size: 84 Copynumber: 5.7 Consensus size: 83
681910 CTTGCCTTGG
* * * * * * *
681920 GTTATGCTGTAAATGATGTGCCTTGGAACTAAACGTAGTCGAACTCGGAGGTCTTT-G-G-CAGA
1 GTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGAGACAGA
** *
681982 TAGTCCTTCTAGCCTTAA
66 TAACCCTTCTAGACTTAA
* * * * *
682000 GCTATGTTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGACAT
1 GTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-AGACAG
**
682065 ATAACCCTTCCCGACTTAA
65 ATAACCCTTCTAGACTTAA
*
682084 GTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGCCTTTTGGAGACAG
1 GTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGAGACAG
* *
682149 ATAACCCTTCTAGCCTTGA
65 ATAACCCTTCTAGACTTAA
* * * * * ** * *
682168 GTTATGCTGTAAATGATGTGCCCTCGAAGCTAAGTATAATTGAACTCG-AGG---TT-G-G-CA-
1 GTTATGCTGCAAATGATATGCCTTAG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGAGACAG
* *
682225 ACTAGCCCTTCTTGACTTAA
65 A-TAACCCTTCTAGACTTAA
* * *
682245 GATATACTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTAGAGACAG
1 GTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGAGACAG
* *
682310 ATAACCCTTCTAGCCTTGA
65 ATAACCCTTCTAGACTTAA
* * * * * * * *
682329 GTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
1 GTTATGCTGCAAATGATATGCCTTAG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
682388 CAGCTAGCCC
Statistics
Matches: 306, Mismatches: 65, Indels: 30
0.76 0.16 0.07
Matches are distributed among these distances:
76 17 0.06
77 39 0.13
78 1 0.00
79 1 0.00
80 48 0.16
81 3 0.01
82 1 0.00
83 2 0.01
84 148 0.48
85 46 0.15
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (83 bp):
GTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGAGACAGA
TAACCCTTCTAGACTTAA
Found at i:682263 original size:161 final size:161
Alignment explanation
Indices: 682077--682379 Score: 534
Period size: 161 Copynumber: 1.9 Consensus size: 161
682067 AACCCTTCCC
* * *
682077 GACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGCCTTTTG
1 GACTTAAGATATACTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGCCTTTTA
682142 GAGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTAAGTATAA
66 GAGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTAAGTATAA
*
682207 TTGAACTCGAGGTTGGCAACTAGCCCTTCTT
131 TCGAACTCGAGGTTGGCAACTAGCCCTTCTT
*
682238 GACTTAAGATATACTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTA
1 GACTTAAGATATACTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGCCTTTTA
* * *
682303 GAGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
66 GAGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTAAGTATAA
682368 TCGAACTCGAGG
131 TCGAACTCGAGG
682380 GTCTTTGGCA
Statistics
Matches: 134, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
161 134 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (161 bp):
GACTTAAGATATACTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGCCTTTTA
GAGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTAAGTATAA
TCGAACTCGAGGTTGGCAACTAGCCCTTCTT
Found at i:682298 original size:245 final size:247
Alignment explanation
Indices: 681899--682377 Score: 599
Period size: 245 Copynumber: 1.9 Consensus size: 247
681889 TTTTATTGAT
* * * * * * *
681899 AGATAGCCCTTCTTGCCTTGGGTTATGCTGTAAATGATGTGCCTTGGAACTAAACGTAGTCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAACTAAACATAATCGAAC
* * * **
681964 TCGGAGGTCTTTGGCAGATAGTCCTTCTAGCCTTAAGCTATGTTGCAAATGATATGCCTTAGAGC
66 TCGGAGG--TTTGGCAGATAGCCCTTCTAGACTTAAGATATACTGCAAATGATATGCCTTAGAGC
* * * *
682029 TGAGCGTAGTCGAACTCAAAGGTC-TTTGGTTGACATATAACCCTTCCCGACTTAAGTTATGCTG
129 TGAGCGTAGTCGAACTCAAAGGTCTTTTAG-AGACAGATAACCCTTCCAGACTTAAGTTATGCTG
* *
682093 CAAATGATATGCCTTAG-AGCTGAGCGTAGTCGAACTCGAAGGCCTTTTGGAGAC
193 CAAATGATATGCCCTAGAAGCTGAGCGTAATCGAACTCGAAGGCCTTTTGGAGAC
** *
682147 AGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTAAGTATAATTGAA
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAA-CTAAACATAATCGAA
*
682212 CTC-GAGG-TTGGCA-ACTAGCCCTTCTTGACTTAAGATATACTGCAAATGATATGCCTTAGAGC
65 CTCGGAGGTTTGGCAGA-TAGCCCTTCTAGACTTAAGATATACTGCAAATGATATGCCTTAGAGC
* * * * * *
682274 TGAGCGTAGTCGAACTCGAAGGTCTTTTAGAGACAGATAACCCTTCTAGCCTTGAGTTATGTTGT
129 TGAGCGTAGTCGAACTCAAAGGTCTTTTAGAGACAGATAACCCTTCCAGACTTAAGTTATGCTGC
* * *
682339 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGA
194 AAATGATATGCCCTAGAAGCTGAGCGTAATCGAACTCGA
682378 GGGTCTTTGG
Statistics
Matches: 196, Mismatches: 31, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
244 1 0.01
245 110 0.56
246 24 0.12
248 48 0.24
249 13 0.07
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (247 bp):
AGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAACTAAACATAATCGAAC
TCGGAGGTTTGGCAGATAGCCCTTCTAGACTTAAGATATACTGCAAATGATATGCCTTAGAGCTG
AGCGTAGTCGAACTCAAAGGTCTTTTAGAGACAGATAACCCTTCCAGACTTAAGTTATGCTGCAA
ATGATATGCCCTAGAAGCTGAGCGTAATCGAACTCGAAGGCCTTTTGGAGAC
Found at i:687786 original size:15 final size:16
Alignment explanation
Indices: 687766--687796 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
687756 TGCAAATTAT
687766 GAAAAC-AAAATAAAA
1 GAAAACAAAAATAAAA
687781 GAAAACAAAAATAAAA
1 GAAAACAAAAATAAAA
687797 AGGGTTAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.06
Consensus pattern (16 bp):
GAAAACAAAAATAAAA
Found at i:688826 original size:4 final size:4
Alignment explanation
Indices: 688817--688903 Score: 61
Period size: 4 Copynumber: 20.8 Consensus size: 4
688807 ATGTTAGAGA
*
688817 AAAT AAAT AAAT AAAT AAAT AAAT AAAT ACTAAT AAAT CAAAT GAAAGA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A--AAT AAAT -AAAT -AAA-T
** * *
688866 AAATT AAA- ATTT AAAA AAAT ATA- AAAT AAAT AAAT AAA
1 AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
688904 CAAAGAGAGA
Statistics
Matches: 65, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
3 3 0.05
4 45 0.69
5 13 0.20
6 4 0.06
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:688966 original size:15 final size:15
Alignment explanation
Indices: 688946--688988 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
688936 AAACTAAGAT
688946 AAAAAATAAATAATGAA
1 AAAAAATAAATAAT--A
688963 AAAAAATAAAATAAT-
1 AAAAAAT-AAATAATA
688978 AAAAAATAAAT
1 AAAAAATAAAT
688989 TTTTTAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.16
15 7 0.28
17 7 0.28
18 7 0.28
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (15 bp):
AAAAAATAAATAATA
Found at i:688968 original size:17 final size:17
Alignment explanation
Indices: 688946--688983 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
688936 AAACTAAGAT
688946 AAAAAAT-AAATAATGAA
1 AAAAAATAAAATAAT-AA
688963 AAAAAATAAAATAATAA
1 AAAAAATAAAATAATAA
688980 AAAA
1 AAAA
688984 TAAATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (17 bp):
AAAAAATAAAATAATAA
Found at i:690192 original size:190 final size:190
Alignment explanation
Indices: 689869--690254 Score: 700
Period size: 190 Copynumber: 2.0 Consensus size: 190
689859 TACCTTTGGT
*
689869 TTTGGTTGAAACAATTTCAGTTCCTTCTTGTTTTTATTGTTGATAAATGTGTTTCGATTGAAAGA
1 TTTGGTTGAAACAATTTCAGTTCCTTCTTGTTTTTATTATTGATAAATGTGTTTCGATTGAAAGA
689934 AATTTCTCTCTATTTTTCGCTTCCCCCTTCTTTACATATTGATTTTACACTTATTTATAGCAAAA
66 AATTTCTCTCTATTTTTCGCTTCCCCCTTCTTTACATATTGATTTTACACTTATTTATAGCAAAA
* * *
689999 ATGAAAGCCTATTCCGTGCGGTTTTAAATTTCTAATGAGATTAAAACCCTTTTCTTTGTC
131 ATGAAAGCATATTCCGTGCGGTTTTAAAGTTCTAATGAGATTAAAACCCTTTGCTTTGTC
690059 TTTGGTTGAAACAATTTCAGTTCCTTCTTGTTTTTATTATTGATAAATGTGTTTCGATTGAAAGA
1 TTTGGTTGAAACAATTTCAGTTCCTTCTTGTTTTTATTATTGATAAATGTGTTTCGATTGAAAGA
*
690124 AATTTCTCTCTATTTTTCGCTTCCCCCTTCTTTACATATTGATTTTATACTTATTTATAGCAAAA
66 AATTTCTCTCTATTTTTCGCTTCCCCCTTCTTTACATATTGATTTTACACTTATTTATAGCAAAA
* * *
690189 ATGAAAGTATATTCCGTGCGGTTTTAGAGTTCTAATGAGATTAAAACTCTTTGCTTTGTC
131 ATGAAAGCATATTCCGTGCGGTTTTAAAGTTCTAATGAGATTAAAACCCTTTGCTTTGTC
690249 TTTGGT
1 TTTGGT
690255 CTTCATGTGG
Statistics
Matches: 188, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
190 188 1.00
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (190 bp):
TTTGGTTGAAACAATTTCAGTTCCTTCTTGTTTTTATTATTGATAAATGTGTTTCGATTGAAAGA
AATTTCTCTCTATTTTTCGCTTCCCCCTTCTTTACATATTGATTTTACACTTATTTATAGCAAAA
ATGAAAGCATATTCCGTGCGGTTTTAAAGTTCTAATGAGATTAAAACCCTTTGCTTTGTC
Found at i:692633 original size:9 final size:9
Alignment explanation
Indices: 692619--692648 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
692609 GGACCGGCTG
692619 AAAACCGGA
1 AAAACCGGA
*
692628 AAAACCGGG
1 AAAACCGGA
692637 AAAACCGGA
1 AAAACCGGA
692646 AAA
1 AAA
692649 CCCGCCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.20, G:0.23, T:0.00
Consensus pattern (9 bp):
AAAACCGGA
Found at i:693779 original size:2 final size:2
Alignment explanation
Indices: 693772--693807 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
693762 CATATTTATT
693772 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
693808 AAAACTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:703121 original size:25 final size:24
Alignment explanation
Indices: 703077--703123 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
703067 ATTTTGTAAA
*
703077 AATATATATATTAATCTAAATTTT
1 AATATATAAATTAATCTAAATTTT
703101 AATATATAAAATTAAAT-TAAATT
1 AATATAT-AAATT-AATCTAAATT
703124 ACGATCCGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 10 0.50
26 3 0.15
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
AATATATAAATTAATCTAAATTTT
Found at i:704468 original size:2 final size:2
Alignment explanation
Indices: 704463--704509 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
704453 TTTTATATGC
704463 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
704505 AT AT A
1 AT AT A
704510 AGAAAATTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:705527 original size:20 final size:19
Alignment explanation
Indices: 705485--705527 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
705475 TTTTTAGATT
**
705485 TTTTTTTAGAATTTAAGGT
1 TTTTTTTAGAATTTAAGAA
*
705504 TTTTTTTAGAATTTTAATAA
1 TTTTTTTAGAA-TTTAAGAA
705524 TTTT
1 TTTT
705528 ATGGGTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (19 bp):
TTTTTTTAGAATTTAAGAA
Found at i:707540 original size:14 final size:14
Alignment explanation
Indices: 707515--707549 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
707505 TTGTTTCCAT
707515 AAAATCATTTTCCGG
1 AAAAT-ATTTTCCGG
*
707530 AAAATATTTTCCGT
1 AAAATATTTTCCGG
707544 AAAATA
1 AAAATA
707550 AATTATATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (14 bp):
AAAATATTTTCCGG
Found at i:707692 original size:23 final size:22
Alignment explanation
Indices: 707657--707711 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
707647 AAATATGAAA
707657 TATAAAAA-ATAATATTATTTAT
1 TATAAAAATATAATATTA-TTAT
*
707679 TATAAAAATTTAATATTATTAT
1 TATAAAAATATAATATTATTAT
*
707701 TTTAAAAATAT
1 TATAAAAATAT
707712 TAGAATAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATAAAAATATAATATTATTAT
Found at i:708423 original size:14 final size:14
Alignment explanation
Indices: 708389--708416 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
708379 AAGAAAATGA
708389 GGAAAACGTTTTAC
1 GGAAAACGTTTTAC
708403 GGAAAACGTTTTAC
1 GGAAAACGTTTTAC
708417 ATGAAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
GGAAAACGTTTTAC
Found at i:710077 original size:11 final size:11
Alignment explanation
Indices: 710061--710085 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
710051 ATCGTCGTAG
710061 ATTCCTCATTA
1 ATTCCTCATTA
710072 ATTCCTCATTA
1 ATTCCTCATTA
710083 ATT
1 ATT
710086 TCATCTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTCCTCATTA
Found at i:713807 original size:3 final size:3
Alignment explanation
Indices: 713799--713831 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
713789 TAATTATCTC
713799 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
713832 CATATCTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:715722 original size:17 final size:16
Alignment explanation
Indices: 715698--715732 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
715688 TTAATTATAT
*
715698 TTTTAAAAGTATTTAA
1 TTTTAAAAATATTTAA
*
715714 TTTTAAAAATATTTTA
1 TTTTAAAAATATTTAA
715730 TTT
1 TTT
715733 AATTATCGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TTTTAAAAATATTTAA
Found at i:717847 original size:65 final size:65
Alignment explanation
Indices: 717778--717939 Score: 204
Period size: 65 Copynumber: 2.5 Consensus size: 65
717768 AATTAAATTG
* * * *
717778 AACATCGAATGCATTTCATGCATCGATGCACTTA-CCATGCACCGATGCATTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTT-TG
717841 AA
65 -A
* * *
717843 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTTTGA
* *
717907 AACATCGAATGCACTTGATGCATCGTTGCACTC
1 AACATCGAATGCATTTGATGCATCGATGCACTC
717940 TTAGTGCACC
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
64 31 0.36
65 51 0.60
66 3 0.04
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTTTGA
Found at i:723717 original size:24 final size:23
Alignment explanation
Indices: 723672--723749 Score: 56
Period size: 24 Copynumber: 3.4 Consensus size: 23
723662 ACACTTAACA
*
723672 GTGCATCGATACATCCCTTTGAAT
1 GTGCATCGATACAT-CATTTGAAT
*
723696 GTGCATCGATTCATCATGTTG-A-
1 GTGCATCGATACATCAT-TTGAAT
* * *
723718 -TGCACCGATGCA-CACCTTGAAT
1 GTGCATCGATACATCA-TTTGAAT
723740 GTGCATCGAT
1 GTGCATCGAT
723750 GTACAGGGTC
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
20 5 0.12
21 11 0.26
23 11 0.26
24 16 0.37
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (23 bp):
GTGCATCGATACATCATTTGAAT
Found at i:725925 original size:2 final size:2
Alignment explanation
Indices: 725918--725943 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
725908 CAGCTAAAAC
725918 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
725944 ATCAATTGGC
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):
TA
Found at i:726507 original size:65 final size:65
Alignment explanation
Indices: 726437--726598 Score: 186
Period size: 65 Copynumber: 2.5 Consensus size: 65
726427 AATTAAATTG
* *
726437 AACATCGAATGCATTTCATGCATCGATGCACTTA-CCATGCACCGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTGAGGATATTT-TG
726500 AA
65 -A
* * * * ** *
726502 AACATCGAATGCATTTGATGCATCGTTTCAC-CAGTCATGCATCGATGCACTTTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTGAGGATATTTTGA
* *
726566 AATATCGAATGCACTTGATGCATCGATGCACTC
1 AACATCGAATGCATTTGATGCATCGATGCACTC
726599 TTAGTGCACC
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
64 29 0.36
65 49 0.60
66 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTGAGGATATTTTGA
Found at i:726596 original size:17 final size:19
Alignment explanation
Indices: 726569--726616 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
726559 ATTTTGAAAT
726569 ATCGAATGCACT-TGA-TGC
1 ATCG-ATGCACTCTGAGTGC
*
726587 ATCGATGCACTCTTAGTGC
1 ATCGATGCACTCTGAGTGC
*
726606 ACCGATGCACT
1 ATCGATGCACT
726617 AAGGGTCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 7 0.27
18 6 0.23
19 13 0.50
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (19 bp):
ATCGATGCACTCTGAGTGC
Found at i:727462 original size:35 final size:35
Alignment explanation
Indices: 727421--727498 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
727411 CACAATCACC
* ** **
727421 AATTACATTTTAAACCCCAAATTTTAAAATACTTT
1 AATTACATTCTAAAAACCAAATTCCAAAATACTTT
* *
727456 AATTACATTCTAAAAATCAAATTCCAAAGTACTTT
1 AATTACATTCTAAAAACCAAATTCCAAAATACTTT
727491 AATTACAT
1 AATTACAT
727499 GCCCAACCCC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.01, T:0.37
Consensus pattern (35 bp):
AATTACATTCTAAAAACCAAATTCCAAAATACTTT
Found at i:727837 original size:143 final size:146
Alignment explanation
Indices: 727673--727958 Score: 434
Period size: 148 Copynumber: 2.0 Consensus size: 146
727663 TACTCAATTC
727673 AGTTTATAAAAACAATTGACTCGAAATTTTTTCGAATTGAGTTTATAAAATTTAAATC-A-AATT
1 AGTTTATAAAAACAATTGACTCGAAATTTTTTCGAATTGAGTTTATAAAATTTAAATCAAGAATT
* * *
727736 GAATTGAATTTTCGAGTTTTTGTTCAAATTTAATTATAAATATTTATCATATTATAATATTATTT
66 GAATTGAATTTTCGAGTTTCTGTTCAAATTTAATTATAAATATTTATAATACTATAATATTATTT
*
727801 TATTCTAATTCAGTTT
131 GATTCTAATTCAGTTT
* * *
727817 AGTTTAT-AAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGA
1 AGTTTATAAAAACAATTGACTCGAAATTTTTTCGAATTGAGTTTATAAAATTTAAATCAA---GA
* * *
727881 ATTGAATTGAATTTTTGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATGCTATAATATTA
63 ATTGAATTGAATTTTCGAGTTTCTGTTCAAATTTAATTATAAATATTTATAATACTATAATATTA
727946 TTTGATTCTAATT
128 TTTGATTCTAATT
727959 TAAATAGTTT
Statistics
Matches: 127, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
143 47 0.37
144 8 0.06
148 72 0.57
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (146 bp):
AGTTTATAAAAACAATTGACTCGAAATTTTTTCGAATTGAGTTTATAAAATTTAAATCAAGAATT
GAATTGAATTTTCGAGTTTCTGTTCAAATTTAATTATAAATATTTATAATACTATAATATTATTT
GATTCTAATTCAGTTT
Found at i:728389 original size:21 final size:21
Alignment explanation
Indices: 728365--728415 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
728355 AAATTTAGCA
728365 TTTAGGGTTATATTTTGAGGG
1 TTTAGGGTTATATTTTGAGGG
728386 TTTAGGGTTATATTTTGAGGG
1 TTTAGGGTTATATTTTGAGGG
728407 TTTAGGGTT
1 TTTAGGGTT
728416 GATGCTTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (21 bp):
TTTAGGGTTATATTTTGAGGG
Found at i:728503 original size:35 final size:35
Alignment explanation
Indices: 728464--728544 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
728454 ATGTATTATG
*
728464 AATTTGGGGTTGGGCA-TGTAATTGAAATATTTTGA
1 AATTTGGGGTTGAG-AGTGTAATTGAAATATTTTGA
* * *
728499 AATTTGTGGTTTAGAGTGTAATTGAAGTATTTTGA
1 AATTTGGGGTTGAGAGTGTAATTGAAATATTTTGA
*
728534 AGTTTGGGGTT
1 AATTTGGGGTT
728545 TAAAAGGTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 1 0.03
35 38 0.97
ACGTcount: A:0.26, C:0.01, G:0.30, T:0.43
Consensus pattern (35 bp):
AATTTGGGGTTGAGAGTGTAATTGAAATATTTTGA
Found at i:728545 original size:35 final size:35
Alignment explanation
Indices: 728480--728546 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
728470 GGGTTGGGCA
*
728480 TGTAATTGAAATATTTTGAAATTTGTGGTTTAGAG
1 TGTAATTGAAATATTTTGAAATTTGGGGTTTAGAG
* *
728515 TGTAATTGAAGTATTTTGAAGTTTGGGGTTTA
1 TGTAATTGAAATATTTTGAAATTTGGGGTTTA
728547 AAAGGTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.46
Consensus pattern (35 bp):
TGTAATTGAAATATTTTGAAATTTGGGGTTTAGAG
Found at i:728555 original size:35 final size:35
Alignment explanation
Indices: 728480--728557 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
728470 GGGTTGGGCA
* *
728480 TGTAATTGAAATATTTTGAAATTTGTGGTTTAGAG
1 TGTAATTGAAATATTTTGAAATTTGGGGTTTAAAG
* *
728515 TGTAATTGAAGTATTTTGAAGTTTGGGGTTTAAAAG
1 TGTAATTGAAATATTTTGAAATTTGGGGTTT-AAAG
728551 -GTAATTG
1 TGTAATTG
728558 GTGATCGTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 35 0.92
36 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.44
Consensus pattern (35 bp):
TGTAATTGAAATATTTTGAAATTTGGGGTTTAAAG
Found at i:729700 original size:18 final size:20
Alignment explanation
Indices: 729665--729702 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
729655 CACGGAATGT
729665 AAGATTATCAGTGAGAATAA
1 AAGATTATCAGTGAGAATAA
729685 AAGATTATC-G-GAGAATAA
1 AAGATTATCAGTGAGAATAA
729703 GATTACTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 1 0.06
20 9 0.50
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (20 bp):
AAGATTATCAGTGAGAATAA
Found at i:730220 original size:17 final size:18
Alignment explanation
Indices: 730198--730235 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
730188 AAAAATCTAC
730198 TATTGGTAAT-AAAAAAT
1 TATTGGTAATAAAAAAAT
730215 TATTGGTAATAAAAAAAT
1 TATTGGTAATAAAAAAAT
730233 TAT
1 TAT
730236 ATAAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (18 bp):
TATTGGTAATAAAAAAAT
Found at i:735063 original size:12 final size:12
Alignment explanation
Indices: 735048--735103 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
735038 TGCACTGGCA
* *
735048 CCAGCGCCGGCT
1 CCAGCACCGGTT
*
735060 CCAGCGCCGGTT
1 CCAGCACCGGTT
735072 CCAGCACCGGTT
1 CCAGCACCGGTT
*
735084 CCAGCACCGGTA
1 CCAGCACCGGTT
735096 CCAGCACC
1 CCAGCACC
735104 AGCATCAGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.16, C:0.46, G:0.27, T:0.11
Consensus pattern (12 bp):
CCAGCACCGGTT
Found at i:740057 original size:43 final size:44
Alignment explanation
Indices: 740002--740090 Score: 126
Period size: 43 Copynumber: 2.0 Consensus size: 44
739992 TTATTTTTTG
*
740002 AATTAAAAATATTTCATTTATAGAGAGATGAATTTTTATTATCA
1 AATTAAAAATATTTCATTTATAGAAAGATGAATTTTTATTATCA
* * * *
740046 AATT-AAAATATTTTATTTATGGAAAGATTAATTTTTATTTTCA
1 AATTAAAAATATTTCATTTATAGAAAGATGAATTTTTATTATCA
740089 AA
1 AA
740091 AGATTGAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 36 0.90
44 4 0.10
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (44 bp):
AATTAAAAATATTTCATTTATAGAAAGATGAATTTTTATTATCA
Found at i:740647 original size:2 final size:2
Alignment explanation
Indices: 740640--740665 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
740630 TCTTTCAATA
740640 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
740666 GATGTATTGA
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:743024 original size:26 final size:26
Alignment explanation
Indices: 742987--743037 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
742977 ATTAAGTGAC
**
742987 AATAAAAAATATAATATTTTTTTAAT
1 AATAAAAAATATAATAGATTTTTAAT
*
743013 AATAAAAGATATAATAGATTTTTAA
1 AATAAAAAATATAATAGATTTTTAA
743038 AATTAATACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (26 bp):
AATAAAAAATATAATAGATTTTTAAT
Found at i:743869 original size:22 final size:24
Alignment explanation
Indices: 743834--743880 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
743824 ATATATATTT
743834 TAAATATTTTAATTA-TTTGATAA
1 TAAATATTTTAATTACTTTGATAA
*
743857 TAAATA-TTTAATTACTTTTATAA
1 TAAATATTTTAATTACTTTGATAA
743880 T
1 T
743881 TATTGGTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TAAATATTTTAATTACTTTGATAA
Found at i:745921 original size:2 final size:2
Alignment explanation
Indices: 745914--745944 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
745904 CTAGTTTTAT
745914 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
745945 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:745949 original size:2 final size:2
Alignment explanation
Indices: 745944--745996 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
745934 TCTCTCTCTC
745944 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
*
745986 TA TA CA TA TA T
1 TA TA TA TA TA T
745997 TGTAATTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:749910 original size:2 final size:2
Alignment explanation
Indices: 749903--749932 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
749893 CTTGTTTGTA
749903 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
749933 GTACGTGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:759638 original size:34 final size:35
Alignment explanation
Indices: 759594--759668 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 35
759584 GTTAATAAGA
*
759594 AATAGTTTATGGGCCCTGC-TTTAATTTAGTTTATT
1 AATA-TTTATGGGCCCTGCTTTTAATTTAGTATATT
759629 AATATTTATGGGCCCTGCTTTTAATTTAGTATATT
1 AATATTTATGGGCCCTGCTTTTAATTTAGTATATT
*
759664 GATAT
1 AATAT
759669 AGTTTTAACG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 14 0.38
35 23 0.62
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (35 bp):
AATATTTATGGGCCCTGCTTTTAATTTAGTATATT
Found at i:762818 original size:82 final size:82
Alignment explanation
Indices: 762710--762876 Score: 334
Period size: 82 Copynumber: 2.0 Consensus size: 82
762700 CAGGTATATC
762710 TGTTGATGATGTGTATTTTTCCTGTTTACATAAAATTTTGTGCGAGTTTTACAAATTGTCTTGTC
1 TGTTGATGATGTGTATTTTTCCTGTTTACATAAAATTTTGTGCGAGTTTTACAAATTGTCTTGTC
762775 TTTGTTTTTTATAGTCT
66 TTTGTTTTTTATAGTCT
762792 TGTTGATGATGTGTATTTTTCCTGTTTACATAAAATTTTGTGCGAGTTTTACAAATTGTCTTGTC
1 TGTTGATGATGTGTATTTTTCCTGTTTACATAAAATTTTGTGCGAGTTTTACAAATTGTCTTGTC
762857 TTTGTTTTTTATAGTCT
66 TTTGTTTTTTATAGTCT
762874 TGT
1 TGT
762877 AAGACACGTC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 85 1.00
ACGTcount: A:0.19, C:0.10, G:0.17, T:0.54
Consensus pattern (82 bp):
TGTTGATGATGTGTATTTTTCCTGTTTACATAAAATTTTGTGCGAGTTTTACAAATTGTCTTGTC
TTTGTTTTTTATAGTCT
Found at i:768306 original size:25 final size:26
Alignment explanation
Indices: 768278--768352 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
768268 CTCATTTGGC
768278 CCATGC-AATAGATT-AGGGTTTGAAT
1 CCATGCTAAT-GATTCAGGGTTTGAAT
* * *
768303 CCATTCTCATGTTTCAGGGTTTGAAT
1 CCATGCTAATGATTCAGGGTTTGAAT
* * *
768329 CCATTCTCATGTTTCAGGGTTTGA
1 CCATGCTAATGATTCAGGGTTTGA
768353 CTCTTGGCCT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 8 0.18
26 37 0.82
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (26 bp):
CCATGCTAATGATTCAGGGTTTGAAT
Found at i:768321 original size:26 final size:26
Alignment explanation
Indices: 768292--768352 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
768282 GCAATAGATT
768292 AGGGTTTGAATCCATTCTCATGTTTC
1 AGGGTTTGAATCCATTCTCATGTTTC
768318 AGGGTTTGAATCCATTCTCATGTTTC
1 AGGGTTTGAATCCATTCTCATGTTTC
768344 AGGGTTTGA
1 AGGGTTTGA
768353 CTCTTGGCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (26 bp):
AGGGTTTGAATCCATTCTCATGTTTC
Found at i:779723 original size:15 final size:15
Alignment explanation
Indices: 779703--779732 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
779693 AGAGTTTGTT
779703 CATATTGATGTATGG
1 CATATTGATGTATGG
779718 CATATTGATGTATGG
1 CATATTGATGTATGG
779733 GTATCATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.27, T:0.40
Consensus pattern (15 bp):
CATATTGATGTATGG
Found at i:780565 original size:65 final size:65
Alignment explanation
Indices: 780487--780614 Score: 220
Period size: 65 Copynumber: 2.0 Consensus size: 65
780477 ATCAGTCCTA
780487 AAGAAGTTCAAGAAGAACCAAACACAACAGAACTGAGAGCTCCTCCAGAATTCCTAAACCAACTG
1 AAGAAGTTCAAGAAGAACCAAACACAACAGAACTGAGAGCTCCTCCAGAATTCCTAAACCAACTG
* * * *
780552 AAGAAGTTCAAGAAGAACCAGACACACCAGAATTGAGAGCTCCTTCAGAATTCCTAAACCAAC
1 AAGAAGTTCAAGAAGAACCAAACACAACAGAACTGAGAGCTCCTCCAGAATTCCTAAACCAAC
780615 CTAGCGTTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.44, C:0.26, G:0.16, T:0.15
Consensus pattern (65 bp):
AAGAAGTTCAAGAAGAACCAAACACAACAGAACTGAGAGCTCCTCCAGAATTCCTAAACCAACTG
Found at i:787293 original size:26 final size:26
Alignment explanation
Indices: 787240--787293 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
787230 CAATCCCTAA
* *
787240 CCCTTGCGCATCCATTCCCAATTTCT
1 CCCTTGCGCATCCATTCCCAAATCCT
* *
787266 CCCTTGCTCGTCCATTCCCAAATCCT
1 CCCTTGCGCATCCATTCCCAAATCCT
787292 CC
1 CC
787294 TCTCCTTGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.15, C:0.46, G:0.07, T:0.31
Consensus pattern (26 bp):
CCCTTGCGCATCCATTCCCAAATCCT
Found at i:795211 original size:19 final size:20
Alignment explanation
Indices: 795176--795219 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
795166 ATAAAAAAAA
*
795176 TTAAAATAATAAAATTCCTT
1 TTAAAATAATAAAATTCATT
*
795196 TTAAAAT-ATTAAATTCATT
1 TTAAAATAATAAAATTCATT
795215 TTAAA
1 TTAAA
795220 TATGATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAAAATAATAAAATTCATT
Found at i:801339 original size:150 final size:149
Alignment explanation
Indices: 801094--801373 Score: 488
Period size: 150 Copynumber: 1.9 Consensus size: 149
801084 TGATCAGTTC
801094 AAAAATTGTGAGATGAATATGATAAACCACGTATGATATTTAACCAAAGAGTTCATTATAAGTAC
1 AAAAATTGTGAGATGAATATGATAAACCACGTATGATATTTAACCAAAGAGTTCATTATAAGTAC
801159 TCCATATTCTGTTGCTTGATTTTGCATGTCTAATTAGAAGTCCTAGACTTTGTCCCCGAGTGATA
66 TCCATATTCTGTTGCTTGATTTTGCATGTCTAATTAGAAGTCCTAGACTTTGTCCCCGAGTGATA
801224 CTAAACCTCCTGTGTATTA
131 CTAAACCTCCTGTGTATTA
* * *
801243 AAAAATTGTGAGATGAATATGATAAATCAGGTATGATATTTAACCAAAGTAGTTCATTGTAAGTA
1 AAAAATTGTGAGATGAATATGATAAACCACGTATGATATTTAACCAAAG-AGTTCATTATAAGTA
* * * *
801308 CTCCATATTCTGTTGCTTTATTTTTCCTGTCTAATTAGAAGTCCTAGACTTTGTCCCTGAGTGAT
65 CTCCATATTCTGTTGCTTGATTTTGCATGTCTAATTAGAAGTCCTAGACTTTGTCCCCGAGTGAT
801373 A
130 A
801374 TATTAAAAAA
Statistics
Matches: 123, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
149 47 0.38
150 76 0.62
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (149 bp):
AAAAATTGTGAGATGAATATGATAAACCACGTATGATATTTAACCAAAGAGTTCATTATAAGTAC
TCCATATTCTGTTGCTTGATTTTGCATGTCTAATTAGAAGTCCTAGACTTTGTCCCCGAGTGATA
CTAAACCTCCTGTGTATTA
Found at i:802229 original size:219 final size:218
Alignment explanation
Indices: 801824--802263 Score: 848
Period size: 217 Copynumber: 2.0 Consensus size: 218
801814 TAAAGTTGTC
801824 ATATCCCTTGATTTTGTGTTTTTATAGAGGTATGCATTGTACATAAAGTTAACTTCTCAAAACCC
1 ATATCCCTTGATTTTGTGTTTTTATAGAGGTATGCATTGTACATAAAGTTAACTTCTCAAAACCC
801889 CGCCTCAAGTTTGAGGGCTCAACTGTGTATGGGACGATGGAAAAAAAGTAGTTATGTATGGACTG
66 CGCCTCAAGTTTGAGGGCTCAACTGTGTATGGGACGATGGAAAAAAAGTAGTTA-GTATGGACTG
801954 TTGATGAGTCATCTGTATTGATGTACAATGGTGTGATTTCTTTCTCTTGGTTTTTTTTTTCTTTA
130 TTGATGAGTCATCTGTATTGATGTACAATGGTGTGATTTCTTTCTCTTGGTTTTTTTTTTCTTTA
802019 AAGTTTCTAAGATATACTTTAAGA
195 AAGTTTCTAAGATATACTTTAAGA
802043 ATATCCCTTGATTTTGTGTTTTTATAGAGGTATGCATTGTACATAAAGTTAACTTCTCAAAACCC
1 ATATCCCTTGATTTTGTGTTTTTATAGAGGTATGCATTGTACATAAAGTTAACTTCTCAAAACCC
802108 CGCCTCAAGTTTGAGGGCTCAACTGTGTATGGGGACGATGGAAAAAAAGTAGTTA-T-TGGACTG
66 CGCCTCAAGTTTGAGGGCTCAACTGTGTAT-GGGACGATGGAAAAAAAGTAGTTAGTATGGACTG
802171 TTGATGAGTCATCTGTATTGATGTACAATGGTGTGATTTCTTTCTCTTGGTTTTTTTTTTCTTTA
130 TTGATGAGTCATCTGTATTGATGTACAATGGTGTGATTTCTTTCTCTTGGTTTTTTTTTTCTTTA
802236 AAGTTTCTAAGATATACTTTAAGA
195 AAGTTTCTAAGATATACTTTAAGA
802260 ATAT
1 ATAT
802264 AGTCTTTGTG
Statistics
Matches: 220, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
217 100 0.45
218 1 0.00
219 95 0.43
220 24 0.11
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (218 bp):
ATATCCCTTGATTTTGTGTTTTTATAGAGGTATGCATTGTACATAAAGTTAACTTCTCAAAACCC
CGCCTCAAGTTTGAGGGCTCAACTGTGTATGGGACGATGGAAAAAAAGTAGTTAGTATGGACTGT
TGATGAGTCATCTGTATTGATGTACAATGGTGTGATTTCTTTCTCTTGGTTTTTTTTTTCTTTAA
AGTTTCTAAGATATACTTTAAGA
Found at i:805341 original size:34 final size:34
Alignment explanation
Indices: 805298--805400 Score: 152
Period size: 34 Copynumber: 3.0 Consensus size: 34
805288 GTTCAAGCTG
*
805298 TGAATGACAAAAAGAATAGAGTTATTATTTTTAT
1 TGAATGACAAAAAGAATAGAGTTATTATTTATAT
* *
805332 TGAATGACAAAAAGAATGGAGTTAATATTTATAT
1 TGAATGACAAAAAGAATAGAGTTATTATTTATAT
* * *
805366 TGGATGACAAAAAGAATAGAGTTGTTATCTATAT
1 TGAATGACAAAAAGAATAGAGTTATTATTTATAT
805400 T
1 T
805401 TCAATTACTC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 61 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (34 bp):
TGAATGACAAAAAGAATAGAGTTATTATTTATAT
Done.