Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008280.1 Hibiscus syriacus cultivar Beakdansim tig00110940_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: 3557051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 17
Found at i:729943 original size:17 final size:17
Alignment explanation
Indices: 729921--729959 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
729911 AGAATAGTTT
729921 AAAAAATAGTTTAT-TTA
1 AAAAAATA-TTTATATTA
*
729938 AAAAAATATTTTTATTA
1 AAAAAATATTTATATTA
729955 AAAAA
1 AAAAA
729960 TTAAAAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AAAAAATATTTATATTA
Found at i:734707 original size:2 final size:2
Alignment explanation
Indices: 734700--734731 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
734690 ATGTGAAATT
734700 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
734732 GTTAGATAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:735211 original size:2 final size:2
Alignment explanation
Indices: 735204--735239 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
735194 TATAAAATAG
735204 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
735240 TTCTTCATGT
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):
AT
Found at i:740825 original size:168 final size:168
Alignment explanation
Indices: 740547--740883 Score: 674
Period size: 168 Copynumber: 2.0 Consensus size: 168
740537 AACACGAAGA
740547 GAACACCGAGTGACAGAAGTATGATAGCAGCACAACTTACAGAGGTTACAACAATTCTAATTTTG
1 GAACACCGAGTGACAGAAGTATGATAGCAGCACAACTTACAGAGGTTACAACAATTCTAATTTTG
740612 GACCTATTGATTGAAACTACAAAAACAGACCACATTCAAGCTCACATGTGAAATGAATGTAGTAA
66 GACCTATTGATTGAAACTACAAAAACAGACCACATTCAAGCTCACATGTGAAATGAATGTAGTAA
740677 AAAAGCTGGTACAGAGAACAAACCAGACAACGTAGTAG
131 AAAAGCTGGTACAGAGAACAAACCAGACAACGTAGTAG
740715 GAACACCGAGTGACAGAAGTATGATAGCAGCACAACTTACAGAGGTTACAACAATTCTAATTTTG
1 GAACACCGAGTGACAGAAGTATGATAGCAGCACAACTTACAGAGGTTACAACAATTCTAATTTTG
740780 GACCTATTGATTGAAACTACAAAAACAGACCACATTCAAGCTCACATGTGAAATGAATGTAGTAA
66 GACCTATTGATTGAAACTACAAAAACAGACCACATTCAAGCTCACATGTGAAATGAATGTAGTAA
740845 AAAAGCTGGTACAGAGAACAAACCAGACAACGTAGTAG
131 AAAAGCTGGTACAGAGAACAAACCAGACAACGTAGTAG
740883 G
1 G
740884 TGAAACACAA
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
168 169 1.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.20
Consensus pattern (168 bp):
GAACACCGAGTGACAGAAGTATGATAGCAGCACAACTTACAGAGGTTACAACAATTCTAATTTTG
GACCTATTGATTGAAACTACAAAAACAGACCACATTCAAGCTCACATGTGAAATGAATGTAGTAA
AAAAGCTGGTACAGAGAACAAACCAGACAACGTAGTAG
Found at i:748513 original size:2 final size:2
Alignment explanation
Indices: 748506--748538 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
748496 TGGAAAGATA
748506 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
748539 CTAAACTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:749629 original size:37 final size:37
Alignment explanation
Indices: 749579--749657 Score: 158
Period size: 37 Copynumber: 2.1 Consensus size: 37
749569 TTGACTTATT
749579 TAAACCAATACTTTTGGAAGAACTACGGACAATATGA
1 TAAACCAATACTTTTGGAAGAACTACGGACAATATGA
749616 TAAACCAATACTTTTGGAAGAACTACGGACAATATGA
1 TAAACCAATACTTTTGGAAGAACTACGGACAATATGA
749653 TAAAC
1 TAAAC
749658 AAAATTTGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.24
Consensus pattern (37 bp):
TAAACCAATACTTTTGGAAGAACTACGGACAATATGA
Found at i:750844 original size:2 final size:2
Alignment explanation
Indices: 750837--750878 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
750827 CTTTAACTTA
750837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
750877 AT
1 AT
750879 TTGAAGAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:751573 original size:28 final size:28
Alignment explanation
Indices: 751527--751582 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
751517 CTGCGTTTAC
* * *
751527 ATTATATTGTGGAGTTAGTGCTTGAAAG
1 ATTATATCGTCGAGCTAGTGCTTGAAAG
*
751555 ATTATATCGTCGAGCTAGTGGTTGAAAG
1 ATTATATCGTCGAGCTAGTGCTTGAAAG
751583 CAACGACAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (28 bp):
ATTATATCGTCGAGCTAGTGCTTGAAAG
Found at i:752078 original size:34 final size:34
Alignment explanation
Indices: 752035--752099 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
752025 TCATGCTTCG
*
752035 ATCACCATTTGTGTTAATACCTGTGCCAAATTCA
1 ATCACCATTTGTGTTAATACCAGTGCCAAATTCA
752069 ATCACCATTTGTGTTAATACCAGTGCCAAAT
1 ATCACCATTTGTGTTAATACCAGTGCCAAAT
752100 GAAAGTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (34 bp):
ATCACCATTTGTGTTAATACCAGTGCCAAATTCA
Found at i:755951 original size:10 final size:10
Alignment explanation
Indices: 755936--755965 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
755926 AAGAGGAAAA
755936 GAAGAAAAGT
1 GAAGAAAAGT
755946 GAAGAAAAGT
1 GAAGAAAAGT
755956 GAAGAGAAAG
1 GAAGA-AAAG
755966 AAAGAAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.33, T:0.07
Consensus pattern (10 bp):
GAAGAAAAGT
Found at i:766199 original size:2 final size:2
Alignment explanation
Indices: 766194--766227 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
766184 TTTTACGTAA
766194 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
766228 TAATGAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:768109 original size:44 final size:44
Alignment explanation
Indices: 768044--768177 Score: 232
Period size: 44 Copynumber: 3.0 Consensus size: 44
768034 ATATTAGAGT
*
768044 AGTACGTAGAGTGGAATGTGTGGGTTGTATTATTTAAAGTGAAC
1 AGTACGTAGAGTGGTATGTGTGGGTTGTATTATTTAAAGTGAAC
*
768088 AGTACGTAGAGTGGTAGGTGTGGGTTGTATTATTTAAAGTGAAC
1 AGTACGTAGAGTGGTATGTGTGGGTTGTATTATTTAAAGTGAAC
* *
768132 AGTACGTAGAGTGGTATGTGTGGGTTGTATTATTGAAAGGGAAC
1 AGTACGTAGAGTGGTATGTGTGGGTTGTATTATTTAAAGTGAAC
768176 AG
1 AG
768178 AACCTAACTA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 85 1.00
ACGTcount: A:0.28, C:0.04, G:0.34, T:0.33
Consensus pattern (44 bp):
AGTACGTAGAGTGGTATGTGTGGGTTGTATTATTTAAAGTGAAC
Found at i:773624 original size:22 final size:23
Alignment explanation
Indices: 773590--773632 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
773580 ATATAATAAA
*
773590 TAATATTTTTTATTATAAAAACT
1 TAATATTTATTATTATAAAAACT
*
773613 TAATA-TTATTATTTTAAAAA
1 TAATATTTATTATTATAAAAA
773633 TATTAGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATATTTATTATTATAAAAACT
Found at i:773779 original size:20 final size:20
Alignment explanation
Indices: 773754--773805 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
773744 ACGCGATATC
*
773754 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGGTAAAAAG
*
773774 AAAATCGCAACGGTCAAAAG
1 AAAATCGCAACGGTAAAAAG
773794 AAAATCGCAACG
1 AAAATCGCAACG
773806 CGAGCTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.52, C:0.19, G:0.17, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGGTAAAAAG
Found at i:773865 original size:20 final size:20
Alignment explanation
Indices: 773840--773990 Score: 187
Period size: 20 Copynumber: 7.4 Consensus size: 20
773830 TTTAGAAGAA
773840 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
773860 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
* *
773880 AATCGCAATGCGATTTATAT
1 AATCGCAATGCGATTGATAG
*
773900 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGATAG
* *
773920 AGTCGCAACGCGATTTAGA-AG
1 AATCGCAATGCGA-TT-GATAG
* *
773941 AAAATCGCAATGCGACTGAGAG
1 --AATCGCAATGCGATTGATAG
*
773963 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGATAG
773983 AATCGCAA
1 AATCGCAA
773991 CGTTAAAAAT
Statistics
Matches: 113, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
20 91 0.81
21 6 0.05
22 5 0.04
23 11 0.10
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (20 bp):
AATCGCAATGCGATTGATAG
Found at i:774090 original size:6 final size:6
Alignment explanation
Indices: 774079--774132 Score: 78
Period size: 6 Copynumber: 9.5 Consensus size: 6
774069 GACACGTATT
*
774079 ACCACG ACCACG ACCACG ACCACG ACAACG ACCACG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
774125 ACC-CG ACC
1 ACCACG ACC
774133 CGTGACGAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
5 15 0.33
6 31 0.67
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:774844 original size:6 final size:6
Alignment explanation
Indices: 774823--774865 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
774813 TCTCGTCTCG
774823 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
774866 AATACGTGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:774955 original size:20 final size:20
Alignment explanation
Indices: 774932--775089 Score: 136
Period size: 20 Copynumber: 7.6 Consensus size: 20
774922 GAAACTAACG
*
774932 TTGCGATTTTCTAAATCGCG
1 TTGCGATTTTCTAAATCGCA
* * *
774952 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCA
*
774972 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TT-TTCTAAATCGCA
* * *
774995 TTGCGACTCTCTCAATCGCA
1 TTGCGATTTTCTAAATCGCA
* *
775015 TTGCGATTATATAAATCGCA
1 TTGCGATTTTCTAAATCGCA
* * *
775035 TTGCGATTCTATCAATCGCA
1 TTGCGATTTTCTAAATCGCA
*
775055 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TT-TTCTAAATCGCA
775078 TTGCGATTTTCT
1 TTGCGATTTTCT
775090 TTTGACCGTT
Statistics
Matches: 110, Mismatches: 22, Indels: 12
0.76 0.15 0.08
Matches are distributed among these distances:
20 75 0.68
21 3 0.03
22 4 0.04
23 28 0.25
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCTAAATCGCA
Found at i:774988 original size:43 final size:43
Alignment explanation
Indices: 774940--775085 Score: 217
Period size: 43 Copynumber: 3.5 Consensus size: 43
774930 CGTTGCGATT
*
774940 TTCTAAATCGCGTTGCGATTCTCTCAGTCGCATTGCGATTTTC
1 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTC
*
774983 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGA--TT-
1 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTC
* * * *
775023 ATATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTC
1 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTC
775066 TTCTAAATCGCGTTGCGATT
1 TTCTAAATCGCGTTGCGATT
775086 TTCTTTTGAC
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
40 33 0.37
41 2 0.02
42 2 0.02
43 53 0.59
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (43 bp):
TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTTTC
Found at i:775099 original size:20 final size:20
Alignment explanation
Indices: 775076--775127 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
775066 TTCTAAATCG
*
775076 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
775096 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
775116 CGTTGCGATTTT
1 CGTTGCGATTTT
775128 ATTGGTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:775105 original size:83 final size:83
Alignment explanation
Indices: 774930--775083 Score: 254
Period size: 83 Copynumber: 1.9 Consensus size: 83
774920 AAGAAACTAA
* * * * *
774930 CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCG
1 CGTTGCGATTATATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCG
774995 TTGCGACTCTCTCAATCG
66 TTGCGACTCTCTCAATCG
*
775013 CATTGCGATTATATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCG
1 CGTTGCGATTATATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCG
775078 TTGCGA
66 TTGCGA
775084 TTTTCTTTTG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 65 1.00
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (83 bp):
CGTTGCGATTATATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCG
TTGCGACTCTCTCAATCG
Found at i:775307 original size:21 final size:23
Alignment explanation
Indices: 775278--775323 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
775268 TATAAAAATA
*
775278 AAAAATATT-AT-ATTATATTTT
1 AAAAATATTAATAAATATATTTT
*
775299 AAAATTATTAATAAATATATTTT
1 AAAAATATTAATAAATATATTTT
775322 AA
1 AA
775324 GGAATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 2 0.10
23 11 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAAATATTAATAAATATATTTT
Found at i:775338 original size:23 final size:22
Alignment explanation
Indices: 775285--775339 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
775275 ATAAAAAATA
*
775285 TTATATTATATTTTAAAATTAT
1 TTATAATATATTTTAAAATTAT
*
775307 TAATAAATATATTTTAAGGAATT-T
1 TTAT-AATATATTTTAA--AATTAT
775331 TTATAATAT
1 TTATAATAT
775340 TATTAGACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 3 0.11
23 16 0.59
24 4 0.15
25 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
TTATAATATATTTTAAAATTAT
Found at i:775566 original size:23 final size:24
Alignment explanation
Indices: 775521--775579 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
775511 TATATTTTGT
775521 AATAATATTATTAAAAATATTAATA
1 AATAATATT-TTAAAAATATTAATA
* *
775546 AAT-ATATTTTAAATATGTTAATA
1 AATAATATTTTAAAAATATTAATA
*
775569 ATTAATATTTT
1 AATAATATTTT
775580 TATTAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.50
24 12 0.40
25 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
AATAATATTTTAAAAATATTAATA
Found at i:779775 original size:40 final size:40
Alignment explanation
Indices: 779719--779820 Score: 159
Period size: 40 Copynumber: 2.5 Consensus size: 40
779709 CCCCCAACAT
* *
779719 TTAGTTTGTTTGCAATATGGTCCCCGACGTTACACTGTCG
1 TTAGTATGTTTACAATATGGTCCCCGACGTTACACTGTCG
* *
779759 TTAGTATGTTTACAATATGATCCCTGACGTTACACTGTCG
1 TTAGTATGTTTACAATATGGTCCCCGACGTTACACTGTCG
*
779799 TTAGTACGTTTACAATATGGTC
1 TTAGTATGTTTACAATATGGTC
779821 ACTGAACTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (40 bp):
TTAGTATGTTTACAATATGGTCCCCGACGTTACACTGTCG
Found at i:779938 original size:20 final size:20
Alignment explanation
Indices: 779905--779954 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
779895 AAACCTCAAA
*
779905 TTCC-TTTTCAATCTCGAAT
1 TTCCTTTTTCGATCTCGAAT
779924 TTCCTTTTTCGATCTCGAAT
1 TTCCTTTTTCGATCTCGAAT
779944 TTCCTTTTTCG
1 TTCCTTTTTCG
779955 CTGATCTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.14, C:0.26, G:0.08, T:0.52
Consensus pattern (20 bp):
TTCCTTTTTCGATCTCGAAT
Found at i:784643 original size:18 final size:18
Alignment explanation
Indices: 784622--784660 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
784612 GGTCAACAGT
784622 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
784640 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
784658 GGT
1 GGT
784661 TGTGACTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.21, G:0.51, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:802341 original size:13 final size:13
Alignment explanation
Indices: 802323--802347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
802313 GATCAAAATA
802323 ATGATTATTAGAC
1 ATGATTATTAGAC
802336 ATGATTATTAGA
1 ATGATTATTAGA
802348 TGTGTAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (13 bp):
ATGATTATTAGAC
Found at i:812234 original size:37 final size:37
Alignment explanation
Indices: 812190--812307 Score: 90
Period size: 37 Copynumber: 3.2 Consensus size: 37
812180 ACGAGTATAA
812190 AATCAAAGTTTGATCTAAAATCAAGATTTAAGGCCAT
1 AATCAAAGTTTGATCTAAAATCAAGATTTAAGGCCAT
* * *
812227 AATCAAAGATATTGAAAGCGGTACAAA-CGAG-TATAA----A-
1 AATCAAAG-T-TTG--ATC--TA-AAATCAAGATTTAAGGCCAT
812264 -ATCAAAGTTTGATCTAAAATCAAGATTTAAGGCCAT
1 AATCAAAGTTTGATCTAAAATCAAGATTTAAGGCCAT
812300 AATCAAAG
1 AATCAAAG
812308 ATATTGAAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 30
0.62 0.06 0.31
Matches are distributed among these distances:
29 3 0.05
30 5 0.08
31 4 0.07
32 2 0.03
34 3 0.05
35 2 0.03
36 7 0.12
37 15 0.25
38 2 0.03
39 3 0.05
41 2 0.03
42 4 0.07
43 5 0.08
44 3 0.05
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.25
Consensus pattern (37 bp):
AATCAAAGTTTGATCTAAAATCAAGATTTAAGGCCAT
Found at i:812283 original size:73 final size:73
Alignment explanation
Indices: 812124--812351 Score: 339
Period size: 73 Copynumber: 3.0 Consensus size: 73
812114 AATGATATGA
* *
812124 ATCTAAAATCAAGATTTAAGGCAATAATCAAAGAAATTGAAAGTTCAGCGGTACAAACGAGTATA
1 ATCTAAAATCAAGATTTAAGGCCATAATCAAAGATATTG-AA----AGCGGTACAAACGAGTATA
812189 AAATCAAAGTTTG
61 AAATCAAAGTTTG
812202 ATCTAAAATCAAGATTTAAGGCCATAATCAAAGATATTGAAAGCGGTACAAACGAGTATAAAATC
1 ATCTAAAATCAAGATTTAAGGCCATAATCAAAGATATTGAAAGCGGTACAAACGAGTATAAAATC
812267 AAAGTTTG
66 AAAGTTTG
*
812275 ATCTAAAATCAAGATTTAAGGCCATAATCAAAGATATTGAAAGTTCAGTGGTATAAACGAGTATA
1 ATCTAAAATCAAGATTTAAGGCCATAATCAAAGATATTGAAAG--C---GGTACAAACGAGTATA
812340 AAATCAAAGTTT
61 AAATCAAAGTTT
812352 AATGCCATAG
Statistics
Matches: 142, Mismatches: 3, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
73 75 0.53
75 1 0.01
77 2 0.01
78 64 0.45
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.26
Consensus pattern (73 bp):
ATCTAAAATCAAGATTTAAGGCCATAATCAAAGATATTGAAAGCGGTACAAACGAGTATAAAATC
AAAGTTTG
Found at i:812374 original size:60 final size:60
Alignment explanation
Indices: 812278--812394 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
812268 AAGTTTGATC
*
812278 TAAAATCAAGATTTAAGGCCATAATCAAAGATATTGAAAGTTCAGTGGTATAAACGAGTA
1 TAAAATCAAGATTTAAGGCCATAATCAAAGAAATTGAAAGTTCAGTGGTATAAACGAGTA
* * ** * *
812338 TAAAATCAA-AGTTTAATGCCATAGTTGAAGAAATTGAAAGTTCGGTGGTGTAAACGA
1 TAAAATCAAGA-TTTAAGGCCATAATCAAAGAAATTGAAAGTTCAGTGGTATAAACGA
812395 ATCAGCGGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
59 1 0.02
60 48 0.98
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (60 bp):
TAAAATCAAGATTTAAGGCCATAATCAAAGAAATTGAAAGTTCAGTGGTATAAACGAGTA
Found at i:819006 original size:18 final size:18
Alignment explanation
Indices: 818976--819024 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
818966 TTTTTTTTCT
818976 CTCTTTTTCTTTCGAACAA
1 CTCTTTTT-TTTCGAACAA
**
818995 CTCTTTTTTTTCGAACTG
1 CTCTTTTTTTTCGAACAA
*
819013 CTGTTTTTTTTC
1 CTCTTTTTTTTC
819025 TTCTTTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 19 0.70
19 8 0.30
ACGTcount: A:0.12, C:0.22, G:0.08, T:0.57
Consensus pattern (18 bp):
CTCTTTTTTTTCGAACAA
Found at i:822065 original size:21 final size:21
Alignment explanation
Indices: 822039--822083 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
822029 GATTTCTGGG
* *
822039 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
822060 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
822081 CAA
1 CAA
822084 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:823003 original size:31 final size:31
Alignment explanation
Indices: 822965--823151 Score: 313
Period size: 31 Copynumber: 6.0 Consensus size: 31
822955 AGGGTCGAGG
*
822965 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
822996 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
823027 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
823058 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
823089 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * * *
823120 GATTACCTAGGTTATTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
823151 G
1 G
823152 GTCCTTCGGG
Statistics
Matches: 150, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
31 149 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:823657 original size:21 final size:21
Alignment explanation
Indices: 823632--823674 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
823622 AAAGAATATA
823632 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
823653 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
823674 T
1 T
823675 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:826926 original size:21 final size:21
Alignment explanation
Indices: 826900--826944 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
826890 GATTTCTGGG
* *
826900 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
826921 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
826942 CAA
1 CAA
826945 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:828012 original size:31 final size:31
Alignment explanation
Indices: 827826--827997 Score: 290
Period size: 31 Copynumber: 5.5 Consensus size: 31
827816 AGGGTCGAGG
827826 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
827857 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
827888 GTTTACCTATGTTCTTTGGGACATATAGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
827919 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
827950 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
827981 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
827998 AGAATCTATG
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 133 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:828518 original size:21 final size:21
Alignment explanation
Indices: 828493--828535 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
828483 AAAGAATATA
828493 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
828514 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
828535 T
1 T
828536 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:846586 original size:51 final size:51
Alignment explanation
Indices: 846510--846656 Score: 258
Period size: 51 Copynumber: 2.9 Consensus size: 51
846500 TACTCGTTCA
846510 ATCTAAACATGGAAAGCTCGTATCAACGTATTAAAGCATGGTATTAGCTCC
1 ATCTAAACATGGAAAGCTCGTATCAACGTATTAAAGCATGGTATTAGCTCC
*
846561 ATCTAAACATGGCAAGCTCGTATCAACGTATTAAAGCATGGTATTAGCTCC
1 ATCTAAACATGGAAAGCTCGTATCAACGTATTAAAGCATGGTATTAGCTCC
* * *
846612 ATCTAAACATGGAAAGCTCGCATCAGCGTATTAAAGCACGGTATT
1 ATCTAAACATGGAAAGCTCGTATCAACGTATTAAAGCATGGTATT
846657 CCCTCTAAAG
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 91 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (51 bp):
ATCTAAACATGGAAAGCTCGTATCAACGTATTAAAGCATGGTATTAGCTCC
Found at i:849042 original size:6 final size:6
Alignment explanation
Indices: 849033--849078 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
849023 CACACACAGA
*
849033 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGA GAGA
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGA
849079 TGAGAATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:850411 original size:17 final size:18
Alignment explanation
Indices: 850383--850419 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
850373 TAATTTTATT
*
850383 TATTTAAAATTATTTTAA
1 TATTTAAAATTATATTAA
850401 TATTT-AAATTATATTAA
1 TATTTAAAATTATATTAA
850418 TA
1 TA
850420 AAATCACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTTAAAATTATATTAA
Found at i:853661 original size:16 final size:16
Alignment explanation
Indices: 853640--853673 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
853630 TTACTATTCA
*
853640 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
853656 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
853672 CG
1 CG
853674 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:865018 original size:14 final size:13
Alignment explanation
Indices: 864976--865018 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
864966 TTACTTTATC
864976 AAAATAAGATTTTT
1 AAAATAAGA-TTTT
*
864990 AAAATATATATTTT
1 AAAATA-AGATTTT
865004 AATAATAAGATTTT
1 AA-AATAAGATTTT
865018 A
1 A
865019 CTCAAGGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (13 bp):
AAAATAAGATTTT
Found at i:865346 original size:21 final size:21
Alignment explanation
Indices: 865320--865363 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
865310 ATCCGAGTTA
865320 CCCGCTACACCCGCAATAGCG
1 CCCGCTACACCCGCAATAGCG
865341 CCCGCTACACCCGCAATAGCG
1 CCCGCTACACCCGCAATAGCG
865362 CC
1 CC
865364 AACGACAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.50, G:0.18, T:0.09
Consensus pattern (21 bp):
CCCGCTACACCCGCAATAGCG
Found at i:870001 original size:26 final size:25
Alignment explanation
Indices: 869950--870001 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
869940 GAGCAGCTCG
* * *
869950 AAAATATAATATATTAAGATTTTTA
1 AAAATATAATATATAAAGAATATTA
*
869975 AAAATATATATATATAAATAATATTA
1 AAAATATA-ATATATAAAGAATATTA
870001 A
1 A
870002 TATTTATGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
AAAATATAATATATAAAGAATATTA
Found at i:870521 original size:10 final size:10
Alignment explanation
Indices: 870499--870541 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
870489 TTCATCACAC
*
870499 CAAAACCTCT
1 CAAATCCTCT
*
870509 CAAATCCTTT
1 CAAATCCTCT
* *
870519 CAACTTCTCT
1 CAAATCCTCT
870529 CAAATCCTCT
1 CAAATCCTCT
870539 CAA
1 CAA
870542 CTTAAGGTAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (10 bp):
CAAATCCTCT
Found at i:870530 original size:20 final size:20
Alignment explanation
Indices: 870505--870544 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
870495 ACACCAAAAC
*
870505 CTCTCAAATCCTTTCAACTT
1 CTCTCAAATCCTCTCAACTT
870525 CTCTCAAATCCTCTCAACTT
1 CTCTCAAATCCTCTCAACTT
870545 AAGGTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (20 bp):
CTCTCAAATCCTCTCAACTT
Found at i:870572 original size:17 final size:18
Alignment explanation
Indices: 870550--870583 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
870540 AACTTAAGGT
870550 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
870567 ATATTTTATTAGTATTT
1 ATATTTTATTAGTATTT
870584 TATTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:870595 original size:11 final size:12
Alignment explanation
Indices: 870556--870620 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 12
870546 AGGTATATTT
*
870556 TATTATATTTAA
1 TATTTTATTTAA
*
870568 TATTTTA-TTAG
1 TATTTTATTTAA
870579 TATTTTATTTAA
1 TATTTTATTTAA
*
870591 TTTTTTAATTTTTTAAA
1 TATTTT-A---TTT-AA
870608 TATTTTATTTAA
1 TATTTTATTTAA
870620 T
1 T
870621 TAATTTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
11 10 0.24
12 17 0.40
13 4 0.10
16 4 0.10
17 7 0.17
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (12 bp):
TATTTTATTTAA
Found at i:872643 original size:13 final size:12
Alignment explanation
Indices: 872625--872679 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 12
872615 CATTTAATAC
872625 TTAATTTATTTTG
1 TTAATTT-TTTTG
*
872638 TTAATTTTGTTG
1 TTAATTTTTTTG
*
872650 -GAA--TTTTTG
1 TTAATTTTTTTG
872659 TTAATTTATTTTG
1 TTAATTT-TTTTG
872672 TTAATTTT
1 TTAATTTT
872680 GTTTATTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
9 5 0.15
10 2 0.06
11 2 0.06
12 6 0.18
13 19 0.56
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (12 bp):
TTAATTTTTTTG
Found at i:872727 original size:38 final size:33
Alignment explanation
Indices: 872673--872757 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 33
872663 TTTATTTTGT
872673 TAATTTTG-TTTATTACCATTTAATACCAGTTATTG
1 TAATTTTGTTTTATTACCATTTAATA-C--TTATTG
872708 TAATTTTGTTATTATTTACCATTTAATACTTATTG
1 TAATTTTGTT-TTA-TTACCATTTAATACTTATTG
* *
872743 TAAGTTTGTTGTATT
1 TAATTTTGTTTTATT
872758 TAAAATTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
33 2 0.04
34 2 0.04
35 23 0.51
36 1 0.02
37 4 0.09
38 13 0.29
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTTTATTACCATTTAATACTTATTG
Found at i:876558 original size:28 final size:29
Alignment explanation
Indices: 876500--876558 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 29
876490 CCTTTCTGCA
* * *
876500 AAGGGTGTTAGATCGGGAAATAAATATGG
1 AAGGGTGTTAGATAGGGAAATAAAGAGGG
* *
876529 AAGGGTG-TCGATAGGGGAATAAAGAGGG
1 AAGGGTGTTAGATAGGGAAATAAAGAGGG
876557 AA
1 AA
876559 AAATGTGATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.39, C:0.03, G:0.39, T:0.19
Consensus pattern (29 bp):
AAGGGTGTTAGATAGGGAAATAAAGAGGG
Found at i:880575 original size:45 final size:47
Alignment explanation
Indices: 880516--880607 Score: 161
Period size: 45 Copynumber: 2.0 Consensus size: 47
880506 TCAAATAAAT
880516 GCATGCGAACTAGATATCATGCGGTTAGG-TTTATTTTT-TGAATAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAA
*
880561 GCATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAA
880608 CAAAGCATGG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 28 0.64
46 9 0.20
47 7 0.16
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAA
Found at i:884308 original size:15 final size:16
Alignment explanation
Indices: 884279--884313 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
884269 GGGGCTAAGT
884279 CAGAGCAGACCCGAAG
1 CAGAGCAGACCCGAAG
884295 CAGAGCAG-CCCGAAG
1 CAGAGCAGACCCGAAG
884310 CAGA
1 CAGA
884314 ACAGTTGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.37, C:0.31, G:0.31, T:0.00
Consensus pattern (16 bp):
CAGAGCAGACCCGAAG
Found at i:896849 original size:10 final size:10
Alignment explanation
Indices: 896828--896865 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
896818 TGCTTGAAGA
896828 AGAAATAAATG
1 AGAAA-AAATG
896839 AGAAAAAATG
1 AGAAAAAATG
896849 AG-AAAAATG
1 AGAAAAAATG
896858 AGAAAAAA
1 AGAAAAAA
896866 GAAAAATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.35
10 12 0.46
11 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (10 bp):
AGAAAAAATG
Found at i:896863 original size:8 final size:9
Alignment explanation
Indices: 896834--896957 Score: 76
Period size: 8 Copynumber: 14.7 Consensus size: 9
896824 AAGAAGAAAT
896834 AAATGAGAAA
1 AAATGAG-AA
896844 AAATGAGAA
1 AAATGAGAA
896853 AAATGAGAA
1 AAATGAGAA
896862 AAA--AGAA
1 AAATGAGAA
896869 AAATGATGGAA
1 AAATGA--GAA
*
896880 AAA--ATAA
1 AAATGAGAA
896887 AAA-GA-AA
1 AAATGAGAA
896894 AAATG-GAA
1 AAATGAGAA
**
896902 AAGGGAAGAA
1 AAATG-AGAA
896912 AAA--ATGAA
1 AAATGA-GAA
896920 AAATGA-AA
1 AAATGAGAA
896928 AAA--AGAA
1 AAATGAGAA
896935 AAATGA-AA
1 AAATGAGAA
*
896943 AAAAGAGAA
1 AAATGAGAA
896952 AAATGA
1 AAATGA
896958 AAGAAAAAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 33
0.70 0.05 0.25
Matches are distributed among these distances:
6 1 0.01
7 23 0.25
8 25 0.27
9 24 0.26
10 13 0.14
11 6 0.07
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (9 bp):
AAATGAGAA
Found at i:896880 original size:18 final size:16
Alignment explanation
Indices: 896834--896957 Score: 101
Period size: 18 Copynumber: 7.4 Consensus size: 16
896824 AAGAAGAAAT
896834 AAATGAGAAAAAATGAGAA
1 AAATGAG-AAAAA--AGAA
896853 AAATGAGAAAAAAGAA
1 AAATGAGAAAAAAGAA
*
896869 AAATGATGGAAAAAATAA
1 AAATGA--GAAAAAAGAA
*
896887 AAA-GA-AAAAATGGAA
1 AAATGAGAAAAA-AGAA
**
896902 AAGGGAAGAAAAAATGAA
1 AAATG-AGAAAAAA-GAA
896920 AAATGA-AAAAAAGAA
1 AAATGAGAAAAAAGAA
*
896935 AAATGAAAAAAAGAGAA
1 AAATGAGAAAAA-AGAA
896952 AAATGA
1 AAATGA
896958 AAGAAAAAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
14 5 0.06
15 13 0.15
16 22 0.25
17 14 0.16
18 28 0.31
19 7 0.08
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (16 bp):
AAATGAGAAAAAAGAA
Found at i:896893 original size:40 final size:40
Alignment explanation
Indices: 896849--896972 Score: 112
Period size: 40 Copynumber: 3.0 Consensus size: 40
896839 AGAAAAAATG
896849 AGAAAAATGAGAAAAAAGAAAAATGATGGAAAAAATAAAA
1 AGAAAAATGAGAAAAAAGAAAAATGATGGAAAAAATAAAA
*
896889 AGAAAAAATG-GAAAAGGGAAGAAAAA--AT-GAAAAATGAAAAAA
1 AG-AAAAATGAGAAAA---AAGAAAAATGATGGAAAAA--ATAAAA
* * *
896931 AGAAAAATGAAAAAAAGAGAAAAATGAAAGAAAAAAATAAAA
1 AGAAAAATGAGAAAAA-AGAAAAATG-ATGGAAAAAATAAAA
896973 GGAGGGTTCA
Statistics
Matches: 67, Mismatches: 5, Indels: 22
0.71 0.05 0.23
Matches are distributed among these distances:
39 1 0.01
40 20 0.30
41 16 0.24
42 16 0.24
43 9 0.13
44 5 0.07
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (40 bp):
AGAAAAATGAGAAAAAAGAAAAATGATGGAAAAAATAAAA
Found at i:896903 original size:15 final size:15
Alignment explanation
Indices: 896840--896959 Score: 73
Period size: 15 Copynumber: 7.3 Consensus size: 15
896830 AAATAAATGA
896840 GAAAAAATGAGAAAAAT
1 GAAAAAAT--GAAAAAT
*
896857 GAGAAAAAAGAAAAATGAT
1 GA-AAAAATG-AAAA--AT
896876 GGAAAAAAT-AAAAA-
1 -GAAAAAATGAAAAAT
*
896890 GAAAAAATGGAAAAGGGAA
1 GAAAAAAT-GAAAA---AT
896909 GAAAAAATGAAAAAT
1 GAAAAAATGAAAAAT
*
896924 GAAAAAAAGAAAAAT
1 GAAAAAATGAAAAAT
*
896939 GAAAAAAAGAGAAAAAT
1 G-AAAAAA-TGAAAAAT
896956 GAAA
1 GAAA
896960 GAAAAAAATA
Statistics
Matches: 86, Mismatches: 4, Indels: 27
0.74 0.03 0.23
Matches are distributed among these distances:
13 8 0.09
15 21 0.24
16 10 0.12
17 19 0.22
18 11 0.13
19 15 0.17
20 2 0.02
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.08
Consensus pattern (15 bp):
GAAAAAATGAAAAAT
Found at i:896912 original size:50 final size:48
Alignment explanation
Indices: 896830--896954 Score: 137
Period size: 50 Copynumber: 2.5 Consensus size: 48
896820 CTTGAAGAAG
* *
896830 AAATAAATGAGAAAAAATGAGAAAAATGAGAAAAAA-GAAAAATGATGGAAA
1 AAATAAA-AAGAAAAAATGAGAAAAAGGAGAAAAAATGAAAAATGA---AAA
*
896881 AAATAAAAAGAAAAAATG-GAAAAGGGAAGAAAAAATGAAAAATGAAAA
1 AAATAAAAAGAAAAAATGAGAAAAAGG-AGAAAAAATGAAAAATGAAAA
* *
896929 AAAGAAAAATGAAAAAAAGAGAAAAA
1 AAATAAAAA-GAAAAAATGAGAAAAA
896955 TGAAAGAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
48 11 0.17
49 14 0.22
50 23 0.36
51 16 0.25
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (48 bp):
AAATAAAAAGAAAAAATGAGAAAAAGGAGAAAAAATGAAAAATGAAAA
Found at i:896915 original size:51 final size:49
Alignment explanation
Indices: 896830--896972 Score: 139
Period size: 51 Copynumber: 2.9 Consensus size: 49
896820 CTTGAAGAAG
* *
896830 AAATAAATGAGAAAAAATGAGAAAAATG-AG-AAAAAAGAAAAATGATGGAAA
1 AAATAAA-AAGAAAAAATGAGAAAAAGGAAGAAAAAAAGAAAAATGA---AAA
* *
896881 AAATAAAAAGAAAAAATG-GAAAAGGGAAGAAAAAATGAAAAATGAAAA
1 AAATAAAAAGAAAAAATGAGAAAAAGGAAGAAAAAAAGAAAAATGAAAA
* * * *
896929 AAAGAAAAATGAAAAAAAGAGAAAAATGAAAGAAAAAAATAAAA
1 AAATAAAAA-GAAAAAATGAGAAAAA-GGAAGAAAAAAAGAAAA
896973 GGAGGGTTCA
Statistics
Matches: 77, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
48 11 0.14
49 14 0.18
50 17 0.22
51 35 0.45
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.09
Consensus pattern (49 bp):
AAATAAAAAGAAAAAATGAGAAAAAGGAAGAAAAAAAGAAAAATGAAAA
Found at i:896928 original size:6 final size:7
Alignment explanation
Indices: 896911--896944 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
896901 AAAGGGAAGA
896911 AAAAATG
1 AAAAATG
896918 AAAAATG
1 AAAAATG
*
896925 AAAAAAAG
1 -AAAAATG
896933 AAAAATG
1 AAAAATG
896940 AAAAA
1 AAAAA
896945 AAGAGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (7 bp):
AAAAATG
Found at i:898393 original size:51 final size:51
Alignment explanation
Indices: 898328--898687 Score: 468
Period size: 51 Copynumber: 6.9 Consensus size: 51
898318 AAATTCGTTG
*
898328 GTTGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
898379 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
898430 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * *
898481 GTTGAAGATTGAATCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * * ** *
898532 ATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCTGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * * * * *
898583 GTTGAAGATTATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTT
1 GTTGAAG---ATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * * *
898638 GTTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACA
1 GTTGAAGATTG----AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
898688 CATTTTATGA
Statistics
Matches: 281, Mismatches: 20, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
51 201 0.72
52 3 0.01
54 2 0.01
55 75 0.27
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:898624 original size:55 final size:52
Alignment explanation
Indices: 898328--898737 Score: 435
Period size: 51 Copynumber: 7.8 Consensus size: 52
898318 AAATTCGTTG
* *
898328 GTTGAAGA-TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCAGTTT
* *
898379 GTTGAAGATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCAGTTT
* *
898430 GTTGAAGATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCAGTTT
*
898481 GTTGAAGATT-GAATCCTATACTCTCTGAAGGAATAGGGAGCGGA-CACGTTT
1 GTTGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCA-GTTT
* * *
898532 ATTGAAGA-TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCTGTTT
1 GTTGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCAGTTT
* * * *
898583 GTTGAAGATTATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGA-CACGTTT
1 GTTGAAG---ATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCA-GTTT
* * * * *
898638 GTTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACA-TTT
1 GTTGAAGA---TTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC-CAGTTT
* *
898693 -TATGAAGATTGTTCGAGTCTTGTACT-TCCTGAAGGAATAGGGAGC
1 GT-TGAAGA---TTCGAGTCCTATACTCT-CTGAAGGAATAGGGAGC
898738 AGGCTCGTCA
Statistics
Matches: 323, Mismatches: 20, Indels: 28
0.87 0.05 0.08
Matches are distributed among these distances:
50 2 0.01
51 195 0.60
52 3 0.01
54 4 0.01
55 117 0.36
57 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (52 bp):
GTTGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCAGTTT
Found at i:898943 original size:16 final size:15
Alignment explanation
Indices: 898922--898956 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
898912 GGGGCTAAGT
898922 CAGAGCATACCCGAAG
1 CAGAGCA-ACCCGAAG
*
898938 CAGAGCAGCCCGAAG
1 CAGAGCAACCCGAAG
898953 CAGA
1 CAGA
898957 ACAGTTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.37, C:0.31, G:0.29, T:0.03
Consensus pattern (15 bp):
CAGAGCAACCCGAAG
Found at i:907157 original size:9 final size:9
Alignment explanation
Indices: 907143--907187 Score: 60
Period size: 9 Copynumber: 5.2 Consensus size: 9
907133 ATGAAAACTG
907143 AAAAAGAGA
1 AAAAAGAGA
907152 AAAAAGAGA
1 AAAAAGAGA
907161 AAAAA-ATG-
1 AAAAAGA-GA
907169 AAAAAGAG-
1 AAAAAGAGA
907177 AAAAAGAGA
1 AAAAAGAGA
907186 AA
1 AA
907188 TGAAAAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 15 0.45
9 18 0.55
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (9 bp):
AAAAAGAGA
Found at i:907162 original size:17 final size:17
Alignment explanation
Indices: 907142--907187 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
907132 AATGAAAACT
907142 GAAAAAGAGAAAAAAGA
1 GAAAAAGAGAAAAAAGA
*
907159 GAAAAAAATG-AAAAAGA
1 GAAAAAGA-GAAAAAAGA
907176 GAAAAAGAGAAA
1 GAAAAAGAGAAA
907188 TGAAAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 1 0.04
17 23 0.92
18 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (17 bp):
GAAAAAGAGAAAAAAGA
Found at i:907170 original size:26 final size:25
Alignment explanation
Indices: 907136--907310 Score: 95
Period size: 23 Copynumber: 7.1 Consensus size: 25
907126 AGAAGAAATG
*
907136 AAAACTGAAAAAGAGAAAAAAGAGAA
1 AAAAATGAAAAAGAG-AAAAAGAGAA
907162 AAAAATGAAAAAGAGAAAAAGAGAA
1 AAAAATGAAAAAGAGAAAAAGAGAA
** *
907187 ATGAA--AAAAAGAG-AAATGA-AA
1 AAAAATGAAAAAGAGAAAAAGAGAA
* *
907208 AAAAATGAAGAAA-TG-AAAA-ATAA
1 AAAAATGAA-AAAGAGAAAAAGAGAA
*
907231 AAAAATAAAAAATGA-AAAAATGA-AA
1 AAAAATGAAAAA-GAGAAAAA-GAGAA
*
907256 ATGAAAATGAAAAAATGATGGAAAAGA-AA
1 A--AAAATG-AAAAA-GA-GAAAAAGAGAA
*
907285 AAAAATGATGAAA-AGAAAAAGA-AA
1 AAAAATGA-AAAAGAGAAAAAGAGAA
907309 AA
1 AA
907311 TGGAATAAAA
Statistics
Matches: 120, Mismatches: 14, Indels: 32
0.72 0.08 0.19
Matches are distributed among these distances:
21 5 0.04
22 9 0.08
23 24 0.20
24 18 0.15
25 17 0.14
26 16 0.13
27 14 0.12
28 8 0.07
29 5 0.04
30 4 0.03
ACGTcount: A:0.74, C:0.01, G:0.17, T:0.09
Consensus pattern (25 bp):
AAAAATGAAAAAGAGAAAAAGAGAA
Found at i:907195 original size:15 final size:16
Alignment explanation
Indices: 907159--907304 Score: 82
Period size: 15 Copynumber: 9.4 Consensus size: 16
907149 AGAAAAAAGA
*
907159 GAAAAAAATGA-AAAA
1 GAAAAAAATGAGAAAT
*
907174 GAGAAAAA-GAGAAAT
1 GAAAAAAATGAGAAAT
907189 GAAAAAAA-GAGAAAT
1 GAAAAAAATGAGAAAT
907204 GAAAAAAAATGAAGAAAT
1 G-AAAAAAATG-AGAAAT
*
907222 GAAAAATAA--AAAAAT
1 GAAAAA-AATGAGAAAT
907237 --AAAAAATGA-AAA-
1 GAAAAAAATGAGAAAT
*
907249 -AATGAAAATGA-AAAT
1 GAA-AAAAATGAGAAAT
*
907264 G-AAAAAATGATGGAAAA
1 GAAAAAAATGA--GAAAT
*
907281 GAAAAAAAATGATGAAAA
1 G-AAAAAAATGA-GAAAT
907299 GAAAAA
1 GAAAAA
907305 GAAAAATGGA
Statistics
Matches: 107, Mismatches: 8, Indels: 30
0.74 0.06 0.21
Matches are distributed among these distances:
12 2 0.02
13 8 0.07
14 20 0.19
15 31 0.29
16 7 0.07
17 15 0.14
18 15 0.14
19 9 0.08
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.10
Consensus pattern (16 bp):
GAAAAAAATGAGAAAT
Found at i:907223 original size:8 final size:8
Alignment explanation
Indices: 907131--907273 Score: 78
Period size: 8 Copynumber: 18.8 Consensus size: 8
907121 CTTGAAGAAG
907131 AAATG-AA
1 AAATGAAA
*
907138 AACTGAAA
1 AAATGAAA
907146 AAGA-GAAA
1 AA-ATGAAA
*
907154 AAAGAGAAAA
1 AAA-TG-AAA
907164 AAATG-AA
1 AAATGAAA
907171 AAA-GAGAA
1 AAATGA-AA
*
907179 AAA-G-AG
1 AAATGAAA
907185 AAATGAAA
1 AAATGAAA
* *
907193 AAAAG-AG
1 AAATGAAA
907200 AAATGAAAAA
1 AAATG--AAA
*
907210 AAATGAAG
1 AAATGAAA
907218 AAATG-AA
1 AAATGAAA
*
907225 AAATAAAA
1 AAATGAAA
907233 AAAT-AAA
1 AAATGAAA
907240 AAATGAAA
1 AAATGAAA
907248 AAATG--A
1 AAATGAAA
907254 AAATG--A
1 AAATGAAA
907260 AAATGAAA
1 AAATGAAA
907268 AAATGA
1 AAATGA
907274 TGGAAAAGAA
Statistics
Matches: 108, Mismatches: 12, Indels: 31
0.72 0.08 0.21
Matches are distributed among these distances:
6 17 0.16
7 28 0.26
8 49 0.45
9 2 0.02
10 12 0.11
ACGTcount: A:0.73, C:0.01, G:0.16, T:0.10
Consensus pattern (8 bp):
AAATGAAA
Found at i:907243 original size:22 final size:23
Alignment explanation
Indices: 907160--907269 Score: 81
Period size: 22 Copynumber: 5.0 Consensus size: 23
907150 GAAAAAAGAG
907160 AAAAAAATG-AAAAA-GAGAAAA-
1 AAAAAAATGAAAAAATGA-AAAAT
* * * *
907181 AGAGAAATGAAAAAAAGAGAAAT
1 AAAAAAATGAAAAAATGAAAAAT
*
907204 GAAAAAAAATGAAGAAATGAAAAAT
1 --AAAAAAATGAAAAAATGAAAAAT
907229 AAAAAAAT-AAAAAATGAAAAA-
1 AAAAAAATGAAAAAATGAAAAAT
**
907250 ATGAAAATG--AAAATGAAAAA
1 AAAAAAATGAAAAAATGAAAAA
907270 ATGATGGAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
20 11 0.15
21 13 0.18
22 20 0.28
23 10 0.14
25 18 0.25
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (23 bp):
AAAAAAATGAAAAAATGAAAAAT
Found at i:907279 original size:18 final size:16
Alignment explanation
Indices: 907256--907304 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 16
907246 AAAAATGAAA
907256 ATGAAAATGAAAAAATG
1 ATGAAAA-GAAAAAATG
907273 ATGGAAAAGAAAAAAAATG
1 AT-GAAAAG--AAAAAATG
907292 ATGAAAAGAAAAA
1 ATGAAAAGAAAAA
907305 GAAAAATGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.17
17 3 0.10
18 11 0.38
19 10 0.34
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.12
Consensus pattern (16 bp):
ATGAAAAGAAAAAATG
Found at i:907287 original size:19 final size:18
Alignment explanation
Indices: 907265--907304 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
907255 AATGAAAATG
907265 AAAAAATGATGGAAAAGAA
1 AAAAAATGAT-GAAAAGAA
907284 AAAAAATGATGAAAAGAA
1 AAAAAATGATGAAAAGAA
907302 AAA
1 AAA
907305 GAAAAATGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.10
Consensus pattern (18 bp):
AAAAAATGATGAAAAGAA
Found at i:908715 original size:213 final size:213
Alignment explanation
Indices: 908348--908773 Score: 825
Period size: 213 Copynumber: 2.0 Consensus size: 213
908338 TCAGGGATAG
908348 TTGAAGATGGAAGATATGAAAGCATCAAGATGAGGATAACTAGTTTTGAAATCTTGAAAAGAATG
1 TTGAAGATGGAAGATATGAAAGCATCAAGATGAGGATAACTAGTTTTGAAATCTTGAAAAGAATG
*
908413 ACATTTAAACGACAATTGAGCCAAAGTAGATTCACATATCCAATGGCTTCCAGACAAGTTTTCAC
66 ACATTTAAACAACAATTGAGCCAAAGTAGATTCACATATCCAATGGCTTCCAGACAAGTTTTCAC
908478 GATGGAGATGGATTTTCAGAAATTTTCTCAAATTTTAAATTTTTGAGTATAATATTTTCAAGCAT
131 GATGGAGATGGATTTTCAGAAATTTTCTCAAATTTTAAATTTTTGAGTATAATATTTTCAAGCAT
908543 ATGTTCATGATTGATAAT
196 ATGTTCATGATTGATAAT
908561 TTGAAGATGGAAGATATGAAAGCATCAAGATGAGGATAACTAGTTTTGAAATCTTGAAAAGAATG
1 TTGAAGATGGAAGATATGAAAGCATCAAGATGAGGATAACTAGTTTTGAAATCTTGAAAAGAATG
*
908626 ACGTTTAAACAACAATTGAGCCAAAGTAGATTCACATATCCAATGGCTTCCAGACAAGTTTTCAC
66 ACATTTAAACAACAATTGAGCCAAAGTAGATTCACATATCCAATGGCTTCCAGACAAGTTTTCAC
908691 GATGGAGATGGATTTTCAGAAATTTTCTCAAATTTTAAATTTTTGAGTATAATATTTTCAAGCAT
131 GATGGAGATGGATTTTCAGAAATTTTCTCAAATTTTAAATTTTTGAGTATAATATTTTCAAGCAT
*
908756 ATGTTCATGGTTGATAAT
196 ATGTTCATGATTGATAAT
908774 GTTTGATTTT
Statistics
Matches: 210, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
213 210 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (213 bp):
TTGAAGATGGAAGATATGAAAGCATCAAGATGAGGATAACTAGTTTTGAAATCTTGAAAAGAATG
ACATTTAAACAACAATTGAGCCAAAGTAGATTCACATATCCAATGGCTTCCAGACAAGTTTTCAC
GATGGAGATGGATTTTCAGAAATTTTCTCAAATTTTAAATTTTTGAGTATAATATTTTCAAGCAT
ATGTTCATGATTGATAAT
Found at i:908925 original size:55 final size:55
Alignment explanation
Indices: 908858--909224 Score: 370
Period size: 55 Copynumber: 6.7 Consensus size: 55
908848 TTTATGAAGA
* * * * *
908858 TCGAGTCTTATACTCTCTG-GTAGAATAGGGAGCGGACTCGTTTGGTGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAT-GAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* * * *
908913 TCGAGT-TCTATACTCTCTG-GTAGAATAGGGAGCAGACTCGTTTGTTGAAGATTAT
1 TCGAGTCT-TATACTCCCTGAAT-GAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* * * * * *
908968 TCGAGT-TCTATACTCTCTG-GTAGAATAGAGAGCGGACCCATTT-TATGAAGATTGT
1 TCGAGTCT-TATACTCCCTGAAT-GAATAGGGAGCAGACACGTTTGT-TGAAGATTGT
* * * * *
909023 TTGAGTTTTATACTCCCTGAATGAATAGGGAGCGGACCCGTTTATTGAAGATTGAT
1 TCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATTG-T
* * *
909079 T-GAGTCTTATACTCCCTAAATGAATAGGGAGCAGACACGCTTGTTGAAGATTGA
1 TCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* * *
909133 TCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGCTAAAGATTGG
1 TCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* *
909188 TCGAGTCTTATACTCCCTGAAGGGATAGGGAGCAGAC
1 TCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGAC
909225 CCATCATTCG
Statistics
Matches: 278, Mismatches: 27, Indels: 14
0.87 0.08 0.04
Matches are distributed among these distances:
54 3 0.01
55 270 0.97
56 5 0.02
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (55 bp):
TCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
Found at i:909263 original size:110 final size:110
Alignment explanation
Indices: 909030--909251 Score: 277
Period size: 110 Copynumber: 2.0 Consensus size: 110
909020 TGTTTGAGTT
* * * * *
909030 TTATACTCCCTGAATGAATAGGGAGCGGACCCGTTTATTGAAGATTGATTGAGTCTTATACTCCC
1 TTATACTCCCTGAATGAATAGGGAGCAGACACGTTTACTAAAGATTGATCGAGTCTTATACTCCC
* ** *
909095 TAAATGAATAGGGAGCAGACACGCTTGTTGAAGATTGATCGAGTC
66 TAAAGGAATAGGGAGCAGACACGCTCATTGAAGATTGATCAAGTC
* *
909140 TTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGCTAAAGATTGGTCGAGTCTTATACTCCC
1 TTATACTCCCTGAATGAATAGGGAGCAGACACGTTTACTAAAGATTGATCGAGTCTTATACTCCC
* * **
909205 TGAAGGGATAGGGAGCAGAC-C-CATCATTCGAAGATTTTTCAAGTC
66 TAAAGGAATAGGGAGCAGACACGC-TCATT-GAAGATTGATCAAGTC
909250 TT
1 TT
909252 GCTTATCCTG
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
108 1 0.01
109 4 0.04
110 90 0.95
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (110 bp):
TTATACTCCCTGAATGAATAGGGAGCAGACACGTTTACTAAAGATTGATCGAGTCTTATACTCCC
TAAAGGAATAGGGAGCAGACACGCTCATTGAAGATTGATCAAGTC
Found at i:917388 original size:2 final size:2
Alignment explanation
Indices: 917383--917409 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
917373 AAATTTAATC
917383 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
917410 GCTATAGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:918865 original size:42 final size:42
Alignment explanation
Indices: 918806--918907 Score: 177
Period size: 42 Copynumber: 2.4 Consensus size: 42
918796 GGTTGGTTCG
918806 AGTCGGGTCGGGTTTTTAGTAAATAAAAAATAAATCAGATAT
1 AGTCGGGTCGGGTTTTTAGTAAATAAAAAATAAATCAGATAT
918848 AGTCGGGTCGGGTTTTTAGTAAATAAAAAATAAATCAGATAT
1 AGTCGGGTCGGGTTTTTAGTAAATAAAAAATAAATCAGATAT
* * *
918890 GGTTGGGTCGGATTTTTA
1 AGTCGGGTCGGGTTTTTA
918908 AGTTATGTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (42 bp):
AGTCGGGTCGGGTTTTTAGTAAATAAAAAATAAATCAGATAT
Found at i:925431 original size:84 final size:87
Alignment explanation
Indices: 925270--925438 Score: 263
Period size: 84 Copynumber: 2.0 Consensus size: 87
925260 ATTTGAACTC
* * * *
925270 AAACTGCTATATTTCTAATCACTTGGAATTTTCTTAATTTTTTTTTATCAGGAATGTTCCATCAC
1 AAACTGCCATATTTCTAATCACTTGGAATTTTCCTAATTTTTTATTATCAGGAATATTCCATCAC
*
925335 TGCAAGCTACATTCACCTTTTG
66 TGCAAGCAACATTCACCTTTTG
*
925357 AAACTGCCATATTTCTAATCACTTGGAA-TTTCCTAA-TTTTTATT-TCAGGTATATTCCATCAC
1 AAACTGCCATATTTCTAATCACTTGGAATTTTCCTAATTTTTTATTATCAGGAATATTCCATCAC
925419 TGCAAGCAACATTCACCTTT
66 TGCAAGCAACATTCACCTTT
925439 CCGCAATGCC
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
84 35 0.46
85 7 0.09
86 7 0.09
87 27 0.36
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.41
Consensus pattern (87 bp):
AAACTGCCATATTTCTAATCACTTGGAATTTTCCTAATTTTTTATTATCAGGAATATTCCATCAC
TGCAAGCAACATTCACCTTTTG
Found at i:928634 original size:17 final size:18
Alignment explanation
Indices: 928601--928634 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
928591 TCGTTATTAG
928601 TGAACCGGTTAGAACCGT
1 TGAACCGGTTAGAACCGT
*
928619 TGAACC-GTTCGAACCG
1 TGAACCGGTTAGAACCG
928635 GACCGGTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (18 bp):
TGAACCGGTTAGAACCGT
Found at i:934441 original size:22 final size:22
Alignment explanation
Indices: 934416--934462 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
934406 TAATTAAAGA
934416 TTAATATTATATCATTTTAATT
1 TTAATATTATATCATTTTAATT
* * * *
934438 TTAATTTTTTGTTATTTTAATT
1 TTAATATTATATCATTTTAATT
934460 TTA
1 TTA
934463 TAGATTCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (22 bp):
TTAATATTATATCATTTTAATT
Found at i:936893 original size:50 final size:50
Alignment explanation
Indices: 936805--936899 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 50
936795 TATATGTTGA
* * * * *
936805 TTTGGCGCCACGTGGGTATAGTGTGCCTCTTGCCCCGCGATATACAGTGT
1 TTTGGCGCCACGTGGGTATAGCGCGCCCCCTGACCCGCGATATACAGTGT
* *
936855 TTTGGCGCCACGTGGGTATAGCGCGCCCCCTGATCCGCGCTATAC
1 TTTGGCGCCACGTGGGTATAGCGCGCCCCCTGACCCGCGATATAC
936900 TTGGATATCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.14, C:0.31, G:0.29, T:0.26
Consensus pattern (50 bp):
TTTGGCGCCACGTGGGTATAGCGCGCCCCCTGACCCGCGATATACAGTGT
Found at i:937140 original size:17 final size:18
Alignment explanation
Indices: 937103--937143 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
937093 CTATTATGTA
*
937103 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
937121 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
937138 TTTACT
1 TTTACT
937144 AATATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:937399 original size:111 final size:111
Alignment explanation
Indices: 937230--937532 Score: 570
Period size: 111 Copynumber: 2.7 Consensus size: 111
937220 GCTGATACGA
937230 TAACATTTTAACGTTTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTA
1 TAACATTTTAA---TTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTA
937295 TTAGATTAAGAATTAAATATCTCGACACTTTGCTGATACAGTAACATTT
63 TTAGATTAAGAATTAAATATCTCGACACTTTGCTGATACAGTAACATTT
937344 TAACATTTTAATTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTA
1 TAACATTTTAATTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTA
937409 GATTAAGAATTAAATATCTCGACACTTTGCTGATACAGTAACATTT
66 GATTAAGAATTAAATATCTCGACACTTTGCTGATACAGTAACATTT
*
937455 TAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTA
1 TAACATTTTAATTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTA
937520 GATTAAGAATTAA
66 GATTAAGAATTAA
937533 TTTTTGTAAT
Statistics
Matches: 188, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
111 177 0.94
114 11 0.06
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (111 bp):
TAACATTTTAATTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTA
GATTAAGAATTAAATATCTCGACACTTTGCTGATACAGTAACATTT
Found at i:943464 original size:21 final size:20
Alignment explanation
Indices: 943438--943491 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
943428 TGATGAATTT
943438 ATAAAATTTAAAAAAATAAAA
1 ATAAAATTTAAAAAAA-AAAA
* **
943459 ATAAAATTTTAATTAAAAAA
1 ATAAAATTTAAAAAAAAAAA
*
943479 ATTAAATTTAAAA
1 ATAAAATTTAAAA
943492 TTTTTAGGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAAAATTTAAAAAAAAAAA
Found at i:943479 original size:26 final size:27
Alignment explanation
Indices: 943445--943495 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
943435 TTTATAAAAT
943445 TTAAAAAAA-TAAAAATAAAATTTTAA
1 TTAAAAAAATTAAAAATAAAATTTTAA
**
943471 TTAAAAAAATTAAATTTAAAATTTT
1 TTAAAAAAATTAAAAATAAAATTTT
943496 TAGGAAGCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
TTAAAAAAATTAAAAATAAAATTTTAA
Found at i:943493 original size:21 final size:22
Alignment explanation
Indices: 943438--943493 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
943428 TGATGAATTT
*
943438 ATAAAATTTAAAA-AAATAAAA
1 ATAAAATTTAAAATTAATAAAA
*
943459 ATAAAATTT-TAATTAA-AAAA
1 ATAAAATTTAAAATTAATAAAA
*
943479 ATTAAATTTAAAATT
1 ATAAAATTTAAAATT
943494 TTTAGGAAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
ATAAAATTTAAAATTAATAAAA
Found at i:944458 original size:2 final size:2
Alignment explanation
Indices: 944446--944495 Score: 75
Period size: 2 Copynumber: 25.0 Consensus size: 2
944436 CTTTTCATAC
*
944446 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
944487 AT AT GAT AT
1 AT AT -AT AT
944496 TCTACGTCTA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.93
3 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:945525 original size:61 final size:61
Alignment explanation
Indices: 945451--945706 Score: 248
Period size: 61 Copynumber: 4.2 Consensus size: 61
945441 AATGAGTTTA
** * * * * *
945451 GATTCTTCCCAATTAGGTCCTGAATGCATAATGTTGATCAGTAATTAGGTCTTGTAATTTT
1 GATTCTTTTCAATTAGGTCCTAAATGCATAATCTTGATTAGTAATTAGGCCTTGCAATTTT
* *
945512 GATTCTTTTCAATTAGGTCCTAAATGCATATTCTTGATTAGTAATCAGGCCTTGCAA-TTT
1 GATTCTTTTCAATTAGGTCCTAAATGCATAATCTTGATTAGTAATTAGGCCTTGCAATTTT
* * * * *
945572 GATTCTTTCCAATTAGGCCCTAAATGCATAATCTCGATTAGT-ATCTAGGCCCTACAATTTT
1 GATTCTTTTCAATTAGGTCCTAAATGCATAATCTTGATTAGTAAT-TAGGCCTTGCAATTTT
* * * * * * * ** *
945633 AATTC-TTTCAAATTAGGTCCTATATGCACAATTTTGATTAGCAACTAAGTTTTGTAATTTT
1 GATTCTTTTC-AATTAGGTCCTAAATGCATAATCTTGATTAGTAATTAGGCCTTGCAATTTT
*
945694 TATTCTTTTCAAT
1 GATTCTTTTCAAT
945707 CATGCCCTCA
Statistics
Matches: 158, Mismatches: 32, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
59 2 0.01
60 53 0.34
61 98 0.62
62 5 0.03
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (61 bp):
GATTCTTTTCAATTAGGTCCTAAATGCATAATCTTGATTAGTAATTAGGCCTTGCAATTTT
Found at i:945594 original size:60 final size:61
Alignment explanation
Indices: 945451--945673 Score: 261
Period size: 61 Copynumber: 3.7 Consensus size: 61
945441 AATGAGTTTA
* * * * * * *
945451 GATTCTTCCCAATTAGGTCCTGAATGCATAATGTTGATCAGTAATTAGGTCTTGTAATTTT
1 GATTCTTTCCAATTAGGTCCTAAATGCATAATCTTGATTAGTAATCAGGCCTTGCAATTTT
* *
945512 GATTCTTTTCAATTAGGTCCTAAATGCATATTCTTGATTAGTAATCAGGCCTTGCAA-TTT
1 GATTCTTTCCAATTAGGTCCTAAATGCATAATCTTGATTAGTAATCAGGCCTTGCAATTTT
* * * *
945572 GATTCTTTCCAATTAGGCCCTAAATGCATAATCTCGATTAGT-ATCTAGGCCCTACAATTTT
1 GATTCTTTCCAATTAGGTCCTAAATGCATAATCTTGATTAGTAATC-AGGCCTTGCAATTTT
* * * * *
945633 AATTCTTTCAAATTAGGTCCTATATGCACAATTTTGATTAG
1 GATTCTTTCCAATTAGGTCCTAAATGCATAATCTTGATTAG
945674 CAACTAAGTT
Statistics
Matches: 138, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
59 3 0.02
60 50 0.36
61 85 0.62
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (61 bp):
GATTCTTTCCAATTAGGTCCTAAATGCATAATCTTGATTAGTAATCAGGCCTTGCAATTTT
Found at i:945670 original size:121 final size:121
Alignment explanation
Indices: 945451--945673 Score: 281
Period size: 121 Copynumber: 1.8 Consensus size: 121
945441 AATGAGTTTA
* * * * * * ** *
945451 GATTCTTCCCAATTAGGTCCTGAATGCATAATGTTGATCAGTAATTAGGTCTTGTAATTTTGATT
1 GATTCTTCCCAATTAGGCCCTAAATGCATAATCTCGATCAGTAATTAGGCCCTACAATTTTAATT
*
945516 CTTTTCAATTAGGTCCTAAATGCATATTCTTGATTAGTAATCAGGCCTTGCAATTT
66 CTTTTCAATTAGGTCCTAAATGCAAATTCTTGATTAGTAATCAGGCCTTGCAATTT
* *
945572 GATTCTTTCCAATTAGGCCCTAAATGCATAATCTCGATTAGT-ATCTAGGCCCTACAATTTTAAT
1 GATTCTTCCCAATTAGGCCCTAAATGCATAATCTCGATCAGTAAT-TAGGCCCTACAATTTTAAT
*
945636 TC-TTTCAAATTAGGTCCTATATGCACAATT-TTGATTAG
65 TCTTTTC-AATTAGGTCCTAAATGCA-AATTCTTGATTAG
945674 CAACTAAGTT
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
120 6 0.07
121 77 0.90
122 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (121 bp):
GATTCTTCCCAATTAGGCCCTAAATGCATAATCTCGATCAGTAATTAGGCCCTACAATTTTAATT
CTTTTCAATTAGGTCCTAAATGCAAATTCTTGATTAGTAATCAGGCCTTGCAATTT
Found at i:946934 original size:51 final size:52
Alignment explanation
Indices: 946870--946969 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
946860 CGTGAGAAAT
*
946870 CACGGGTTGAGCA-GGATATGTTGTTCCATGTCCCAGGGTGAGCACAGAGAG
1 CACGGGTTGAGCAGGGAGATGTTGTTCCATGTCCCAGGGTGAGCACAGAGAG
* *
946921 CACGGGTTTAGCAGGGAGATGTTGTTGCATGTCCCAGGGTGAGCACAGA
1 CACGGGTTGAGCAGGGAGATGTTGTTCCATGTCCCAGGGTGAGCACAGA
946970 ACGCTGTATG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 12 0.27
52 33 0.73
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (52 bp):
CACGGGTTGAGCAGGGAGATGTTGTTCCATGTCCCAGGGTGAGCACAGAGAG
Found at i:950215 original size:31 final size:31
Alignment explanation
Indices: 950177--950330 Score: 265
Period size: 31 Copynumber: 5.0 Consensus size: 31
950167 GGGTCGAGGG
950177 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
950208 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
950239 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
950270 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* * *
950301 TTACCTAGGTTCTACGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
950331 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:952117 original size:14 final size:14
Alignment explanation
Indices: 952088--952145 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
952078 ATATCATTAC
952088 TATTATTAAA-ACAT
1 TATTATTAAATA-AT
952102 TATTATTAAATAAT
1 TATTATTAAATAAT
* *
952116 TA-AAGTTAAATTAT
1 TATTA-TTAAATAAT
*
952130 TATTATTAAATCAT
1 TATTATTAAATAAT
952144 TA
1 TA
952146 AATTTAATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
13 1 0.03
14 34 0.92
15 2 0.05
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (14 bp):
TATTATTAAATAAT
Found at i:952163 original size:31 final size:31
Alignment explanation
Indices: 952100--952367 Score: 215
Period size: 31 Copynumber: 9.0 Consensus size: 31
952090 TTATTAAAAC
* *
952100 ATTATTATTAAATAATTAAAGTTAA---ATT
1 ATTATTATTAAATCATTAAAGTTAACTCATA
* *
952128 ATTATTATTAAATCATTAAATTTAATTCAT-
1 ATTATTATTAAATCATTAAAGTTAACTCATA
952158 A--ATTATTAAATCATTAAAGTTAA-TCATTAA
1 ATTATTATTAAATCATTAAAGTTAACTCA-T-A
* * * * **
952188 ATT-TAACT-AATAATT--AG-TATCAAATA
1 ATTATTATTAAATCATTAAAGTTAACTCATA
*
952214 ATTA-AACTTAAATCATTAAAGTTAACT-ACTA
1 ATTATTA-TTAAATCATTAAAGTTAACTCA-TA
*
952245 ATTATTATTAAATCATTAAAGTTAAAT-ACTA
1 ATTATTATTAAATCATTAAAGTTAACTCA-TA
*
952276 ATTATTATTAAATCATTAAAGTTAACTAATA
1 ATTATTATTAAATCATTAAAGTTAACTCATA
* * *
952307 ATTATTATCAAATCATTAAAGTTAGCTAATA
1 ATTATTATTAAATCATTAAAGTTAACTCATA
* * *
952338 ATTAGTATCAAATCATTAAAGTTAAATCAT
1 ATTATTATTAAATCATTAAAGTTAACTCAT
952368 TAAAGTTAAC
Statistics
Matches: 200, Mismatches: 22, Indels: 33
0.78 0.09 0.13
Matches are distributed among these distances:
26 6 0.03
27 7 0.04
28 54 0.27
30 11 0.05
31 120 0.60
32 2 0.01
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (31 bp):
ATTATTATTAAATCATTAAAGTTAACTCATA
Found at i:952239 original size:45 final size:45
Alignment explanation
Indices: 952135--952406 Score: 236
Period size: 45 Copynumber: 6.1 Consensus size: 45
952125 ATTATTATTA
* * *
952135 TTAAATCATTAAATTTAATTCATAATTA-T-T-AAATCATTAAAG
1 TTAAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAG
* * *
952177 TT-AATCATTAAATTTAACTAATAATTAGTATCAAATAATTAAAC
1 TTAAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAG
* * *
952221 TTAAATCATTAAAGTTAACTACTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAG
* * * * * * *
952266 TTAAAT-ACT-AA-TTATTATTAAATCATTAAAGTTAACTAATAATTATTA-
1 TTAAATCATTAAAGTTA--ACT-AATAATT--AG-TATCAAATCATTA-AAG
* *
952314 TCAAATCATTAAAGTTAGCTAATAATTAGTATCAAATCATTAAAG
1 TTAAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAG
* * *
952359 TTAAATCATTAAAGTTAACTACTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAG
952404 TTA
1 TTA
952407 TCTATTAATT
Statistics
Matches: 181, Mismatches: 34, Indels: 27
0.75 0.14 0.11
Matches are distributed among these distances:
41 23 0.13
42 6 0.03
43 3 0.02
44 17 0.09
45 100 0.55
46 2 0.01
47 1 0.01
48 20 0.11
49 4 0.02
50 2 0.01
51 3 0.02
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.40
Consensus pattern (45 bp):
TTAAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAG
Found at i:952261 original size:76 final size:75
Alignment explanation
Indices: 952179--952478 Score: 297
Period size: 76 Copynumber: 4.1 Consensus size: 75
952169 CATTAAAGTT
* * * *
952179 AATCATTAAATTTAACTAATAATTAGTATCAAATAATTAAACTTAAATCATTAAAGTTAACTACT
1 AATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTTAAATCAATAAAGTTAACTA-T
952244 AATTATTATTA
65 AATTATTATTA
* * * *
952255 AATCATTAAAGTTAAATACTAATTATTATTAAATCATTAAAGTT-AA-C--------TAA-TA-A
1 AATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTTAAATCAATAAAGTTAACTATA
*
952308 -TTATTATCA
66 ATTATTATTA
* *
952317 AATCATTAAAGTTAGCTAATAATTAGTATCAAATCATTAAAGTTAAATCATTAAAGTTAACTACT
1 AATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTTAAATCAATAAAGTTAACTA-T
952382 AATTATTATTA
65 AATTATTATTA
* * * * *
952393 AATCATTAAAGTTATCTATTAATTATTATCAAATCATTAAAGTTAAAATTTAATAATGATTAA--
1 AATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTT-AAA-TCAATAAAG-TTAACT
*
952456 ATTATTATTATTA
63 ATAATTATTATTA
952469 AATCATTAAA
1 AATCATTAAA
952479 TTTTACCATT
Statistics
Matches: 186, Mismatches: 21, Indels: 34
0.77 0.09 0.14
Matches are distributed among these distances:
62 47 0.25
63 3 0.02
64 1 0.01
65 2 0.01
66 3 0.02
72 3 0.02
73 2 0.01
74 1 0.01
75 3 0.02
76 107 0.58
77 4 0.02
78 6 0.03
79 4 0.02
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (75 bp):
AATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTTAAATCAATAAAGTTAACTATA
ATTATTATTA
Found at i:952269 original size:14 final size:14
Alignment explanation
Indices: 952107--952376 Score: 101
Period size: 14 Copynumber: 18.3 Consensus size: 14
952097 AACATTATTA
*
952107 TTAAATAATTAAAG
1 TTAAATCATTAAAG
* *
952121 TTAAATTATTATTA-
1 TTAAATCATTA-AAG
*
952135 TTAAATCATTAAAT
1 TTAAATCATTAAAG
*
952149 TTAATTCA-TAATTA-
1 TTAAATCATTAA--AG
952163 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
952177 TT-AATCATTAAAT
1 TTAAATCATTAAAG
* *
952190 TTAACT-AATAATTAG
1 TTAAATCATTAA--AG
* *
952205 TATCAAATAATTAAAC
1 T-T-AAATCATTAAAG
952221 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
952235 TTAACTACTAATTATTA-
1 TTAA--A-TCATTA-AAG
952252 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
952266 TTAAATACTAATTATTA-
1 TTAAAT-C--ATTA-AAG
952283 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
952297 TTAACTAATAATTATTA-
1 TT-A--AATCATTA-AAG
*
952314 TCAAATCATTAAAG
1 TTAAATCATTAAAG
*
952328 TTAGCTAATAATT--AG
1 TTA---AATCATTAAAG
952343 TATCAAATCATTAAAG
1 T-T-AAATCATTAAAG
952359 TTAAATCATTAAAG
1 TTAAATCATTAAAG
952373 TTAA
1 TTAA
952377 CTACTAATTA
Statistics
Matches: 193, Mismatches: 29, Indels: 68
0.67 0.10 0.23
Matches are distributed among these distances:
13 24 0.12
14 100 0.52
15 15 0.08
16 10 0.05
17 37 0.19
18 7 0.04
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.40
Consensus pattern (14 bp):
TTAAATCATTAAAG
Found at i:952286 original size:17 final size:17
Alignment explanation
Indices: 952235--952288 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
952225 ATCATTAAAG
*
952235 TTAACTACTAATTATTA
1 TTAAATACTAATTATTA
*
952252 TTAAAT-C--ATTA-AA
1 TTAAATACTAATTATTA
952265 GTTAAATACTAATTATTA
1 -TTAAATACTAATTATTA
952283 TTAAAT
1 TTAAAT
952289 CATTAAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
13 1 0.03
14 10 0.34
15 1 0.03
16 1 0.03
17 15 0.52
18 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (17 bp):
TTAAATACTAATTATTA
Found at i:952363 original size:138 final size:138
Alignment explanation
Indices: 952179--952438 Score: 448
Period size: 138 Copynumber: 1.9 Consensus size: 138
952169 CATTAAAGTT
*
952179 AATCATTAAATTTAACTAATAATTAGTATCAAATAATTAAACTTAAATCATTAAAGTTAACTACT
1 AATCATTAAAGTTAACTAATAATTAGTATCAAATAATTAAACTTAAATCATTAAAGTTAACTACT
*
952244 AATTATTATTAAATCATTAAAGTTAAATACTAATTATTATTAAATCATTAAAGTTAACTAATAAT
66 AATTATTATTAAATCATTAAAGTTAAATACTAATTATTATCAAATCATTAAAGTTAACTAATAAT
952309 TATTATCA
131 TATTATCA
* * *
952317 AATCATTAAAGTTAGCTAATAATTAGTATCAAATCATTAAAGTTAAATCATTAAAGTTAACTACT
1 AATCATTAAAGTTAACTAATAATTAGTATCAAATAATTAAACTTAAATCATTAAAGTTAACTACT
** *
952382 AATTATTATTAAATCATTAAAGTTATCTATTAATTATTATCAAATCATTAAAGTTAA
66 AATTATTATTAAATCATTAAAGTTAAATACTAATTATTATCAAATCATTAAAGTTAA
952439 AATTTAATAA
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
138 114 1.00
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (138 bp):
AATCATTAAAGTTAACTAATAATTAGTATCAAATAATTAAACTTAAATCATTAAAGTTAACTACT
AATTATTATTAAATCATTAAAGTTAAATACTAATTATTATCAAATCATTAAAGTTAACTAATAAT
TATTATCA
Found at i:952394 original size:31 final size:31
Alignment explanation
Indices: 952359--952438 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
952349 ATCATTAAAG
952359 TTAAATCATTAAAGTTAACTACTAATTATTA
1 TTAAATCATTAAAGTTAACTACTAATTATTA
* *
952390 TTAAATCATTAAAGTTATCTATTAATTATTA
1 TTAAATCATTAAAGTTAACTACTAATTATTA
*
952421 TCAAATCATTAAAGTTAA
1 TTAAATCATTAAAGTTAA
952439 AATTTAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (31 bp):
TTAAATCATTAAAGTTAACTACTAATTATTA
Found at i:952478 original size:107 final size:107
Alignment explanation
Indices: 952179--952437 Score: 337
Period size: 107 Copynumber: 2.4 Consensus size: 107
952169 CATTAAAGTT
* * * * * * *
952179 AATCATTAAATTTAACTAATAATTAGTATCAAATAATTAAACTTA---AATCATTAAAGTTAACT
1 AATCATTAAAGTTAACTAATAATTATTATCAAATCATTAAAGTTAGCTAATAATT--AG-TATCA
* *
952241 ACTAATTATTATTAAATCATTAAAGTTAAATACTAATTATTATTA
63 AATCATTATTATTAAATCATTAAAGTTAAATACTAATTATTATTA
952286 AATCATTAAAGTTAACTAATAATTATTATCAAATCATTAAAGTTAGCTAATAATTAGTATCAAAT
1 AATCATTAAAGTTAACTAATAATTATTATCAAATCATTAAAGTTAGCTAATAATTAGTATCAAAT
* *
952351 CATTA-AAGTTAAATCATTAAAGTTAACTACTAATTATTATTA
66 CATTATTA-TTAAATCATTAAAGTTAAATACTAATTATTATTA
* *
952393 AATCATTAAAGTTATCTATTAATTATTATCAAATCATTAAAGTTA
1 AATCATTAAAGTTAACTAATAATTATTATCAAATCATTAAAGTTA
952438 AAATTTAATA
Statistics
Matches: 135, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
106 1 0.01
107 126 0.93
108 2 0.01
110 6 0.04
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (107 bp):
AATCATTAAAGTTAACTAATAATTATTATCAAATCATTAAAGTTAGCTAATAATTAGTATCAAAT
CATTATTATTAAATCATTAAAGTTAAATACTAATTATTATTA
Found at i:953705 original size:31 final size:31
Alignment explanation
Indices: 953670--953761 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
953660 CTCGGCAACT
* *
953670 GTCCATAGGTCCCGAAGAACACAGGTAAACA
1 GTCCATATGTCCCGAAGAACATAGGTAAACA
* ** * *
953701 GTCCATATGTTCCTTAGAACATAGGTATACT
1 GTCCATATGTCCCGAAGAACATAGGTAAACA
953732 GTCCATATGTCCCGAA-AGACATAGGTAAAC
1 GTCCATATGTCCCGAAGA-ACATAGGTAAAC
953762 CCTCGACTCT
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
30 1 0.02
31 48 0.98
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (31 bp):
GTCCATATGTCCCGAAGAACATAGGTAAACA
Found at i:958701 original size:27 final size:25
Alignment explanation
Indices: 958618--958702 Score: 77
Period size: 27 Copynumber: 3.4 Consensus size: 25
958608 CCAAGATAAA
958618 TTGAAGACGCCTAGAGATCCATCAAAG
1 TTGAAGACGCC-AGAG-TCCATCAAAG
* * * *
958645 CTGAAGAC-AC-GAGT-AATAAAAG
1 TTGAAGACGCCAGAGTCCATCAAAG
958667 TTGAAGACGCCGAGAGCTCCATCAAAG
1 TTGAAGACGCC-AGAG-TCCATCAAAG
958694 TTGAAGACG
1 TTGAAGACG
958703 TCGTGTAATC
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
22 13 0.29
23 2 0.04
24 3 0.07
25 3 0.07
26 2 0.04
27 22 0.49
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (25 bp):
TTGAAGACGCCAGAGTCCATCAAAG
Found at i:972698 original size:77 final size:77
Alignment explanation
Indices: 972548--972690 Score: 182
Period size: 77 Copynumber: 1.9 Consensus size: 77
972538 CTAGTGAGAT
* * * * *
972548 GAGACAATAAATTCTTTAAACAAGGTTAGGATTTTGAATCCTAACGTTTGCGTATGGAGCAAACT
1 GAGACAATAAATTCCTTAAACAAGGTCAGGAGTTTGAATCCTAACGTTTGCGAATGGAACAAACT
972613 GAATTGGAAGGG
66 GAATTGGAAGGG
* * *
972625 GAGACACTAAATTCCTTAAACAATGTCA-GAGGTTTGAAT-CTCGACGTTTGCGAATGGAACAAA
1 GAGACAATAAATTCCTTAAACAAGGTCAGGA-GTTTGAATCCT-AACGTTTGCGAATGGAACAAA
972688 CTG
64 CTG
972691 GGTTGGAATG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
76 4 0.07
77 52 0.93
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (77 bp):
GAGACAATAAATTCCTTAAACAAGGTCAGGAGTTTGAATCCTAACGTTTGCGAATGGAACAAACT
GAATTGGAAGGG
Found at i:977741 original size:16 final size:16
Alignment explanation
Indices: 977717--977750 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
977707 AAGAAAAAGG
* *
977717 AAATTTTATTTTAAAA
1 AAATATTATATTAAAA
977733 AAATATTATATTAAAA
1 AAATATTATATTAAAA
977749 AA
1 AA
977751 CAGGTATGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATATTATATTAAAA
Found at i:984458 original size:57 final size:57
Alignment explanation
Indices: 984384--984562 Score: 216
Period size: 57 Copynumber: 3.0 Consensus size: 57
984374 CTTACAAGCA
* *
984384 AGTAAAAGTGTAGATACTTTCAAGTGCCTTTGTAATTAACAAATCATGTGTTAGTAC
1 AGTAAAAGTGTATATACTTTCAAGTGCATTTGTAATTAACAAATCATGTGTTAGTAC
* *
984441 CGTAAAAGTGTATATACTTTCAAGTTTCAAGTGAAATTGTAATTAACAAATCATGTGTTAGTAC
1 AGTAAAAGTGTATATACTTTCAAG-TGC-A-T----TTGTAATTAACAAATCATGTGTTAGTAC
* * *
984505 AGTACAAGTGT-TGATACTTTCAAGTGAAATTGTAATTAACAAATCATGTGTTAGTAC
1 AGTAAAAGTGTAT-ATACTTTCAAGTGCATTTGTAATTAACAAATCATGTGTTAGTAC
984562 A
1 A
984563 TTACCTTCTA
Statistics
Matches: 105, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
57 51 0.49
58 2 0.02
60 1 0.01
62 1 0.01
63 2 0.02
64 48 0.46
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (57 bp):
AGTAAAAGTGTATATACTTTCAAGTGCATTTGTAATTAACAAATCATGTGTTAGTAC
Found at i:985083 original size:14 final size:15
Alignment explanation
Indices: 985055--985083 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
985045 AAAGTTTGGT
985055 AAATGTTTCTTTAAA
1 AAATGTTTCTTTAAA
985070 AAATGTTT-TTTAAA
1 AAATGTTTCTTTAAA
985084 GTTTGGTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (15 bp):
AAATGTTTCTTTAAA
Found at i:985085 original size:36 final size:35
Alignment explanation
Indices: 984993--985098 Score: 167
Period size: 35 Copynumber: 3.0 Consensus size: 35
984983 TGGCAACTAA
984993 CTTTAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
985028 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* * *
985063 CTTTAAAAAATGTTTTTTAAAGTTTGGTAGATGTTT
1 CTTT-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
985099 GTTGAAAATA
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 38 0.58
36 27 0.42
ACGTcount: A:0.30, C:0.05, G:0.18, T:0.47
Consensus pattern (35 bp):
CTTTAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:989672 original size:35 final size:36
Alignment explanation
Indices: 989607--989674 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
989597 TTTGAAAACA
* *
989607 TTTTTGAAAGTTTGGTAAATGTTTCTTTGAAAAATG
1 TTTTTCAAAGTTTGGTAAATGTTTCGTTGAAAAATG
*
989643 TTTTTCAAAGTTTGGTAGATGTTT-GTTGAAAA
1 TTTTTCAAAGTTTGGTAAATGTTTCGTTGAAAA
989675 TAGGAATGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 7 0.24
36 22 0.76
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (36 bp):
TTTTTCAAAGTTTGGTAAATGTTTCGTTGAAAAATG
Found at i:992131 original size:262 final size:260
Alignment explanation
Indices: 991658--992251 Score: 875
Period size: 263 Copynumber: 2.3 Consensus size: 260
991648 TTTATTCATA
*
991658 TATTGAATAAAAATATTTTTTTATTA-TT----TCGGGTCGGATTTCTAATTCATACATTCGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGT
* * *
991718 CTGGTCAGGTGAAACATTATTTTGTCAGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGAGTCGA
66 CGGGTCGGGTGAAACATTATTTTGTCAGGTCAGGTCGGTTTTTTTAAGTGTGATATT---GTCGA
* * *
991783 GTCGAGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACTCGAAAATATATATAATTTTACCTTA
128 GTCGAGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCCAAAAAATATATAATTTTACCTTA
991848 TATATTTAGAAATAATTACAATAATACCCCTCTATATATAATT-TTTTTT-AATTAAGTCAATGT
193 TATATTTAGAAATAATTACAATAATACCCCTCTATATATAATTGTTTTTTCAATTAAGTCAATGT
991911 TTT
258 TTT
*
991914 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTTGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGT
* * *
991979 CGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAGGTCGGCTTTTTTTAAGTGTGATATT-T-GGG
66 CGGGTCGGGTGAAACATTATTTT-GTCAGGTCAGGTCGG-TTTTTTTAAGTGTGATATTGTCGAG
* * *
992042 TCGGGTCGGGTTCGGGTTTAGGGTGGAAAATACCCGACCCAACCCAAAAAATATATAATTTTACC
129 TCGAGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGA--C--CCCAAAAAATATATAATTTTACC
* *
992107 TTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTGTTTTTTCAATTAAGTCAT
190 TTATATATTTAGAAATAATTACAATAATACCCCTCTATATATAATTGTTTTTTCAATTAAGTCAA
992172 TGTTTT
255 TGTTTT
* *
992178 TATTGAATAAAAATA-TTTTTTATTATTTCGGGTCTGATCGGATTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGT
992242 CGGGTCGGGT
66 CGGGTCGGGT
992252 AGGGTGAAAA
Statistics
Matches: 306, Mismatches: 19, Indels: 19
0.89 0.06 0.06
Matches are distributed among these distances:
256 26 0.08
257 2 0.01
258 36 0.12
259 1 0.00
260 1 0.00
261 50 0.16
262 78 0.25
263 81 0.26
264 31 0.10
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (260 bp):
TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGT
CGGGTCGGGTGAAACATTATTTTGTCAGGTCAGGTCGGTTTTTTTAAGTGTGATATTGTCGAGTC
GAGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCCAAAAAATATATAATTTTACCTTATAT
ATTTAGAAATAATTACAATAATACCCCTCTATATATAATTGTTTTTTCAATTAAGTCAATGTTTT
Found at i:992315 original size:263 final size:256
Alignment explanation
Indices: 991658--992289 Score: 705
Period size: 262 Copynumber: 2.4 Consensus size: 256
991648 TTTATTCATA
* *
991658 TATTGAATAAAAATATTTTTTTATTATTTC--G--GG-TCGGATTTCTAATTCATACATTCGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGATCGGATTTCTAATTCATATATTTGGGT
* * * **** *
991718 CTGGTCA-GGTGAAACATTATTTT-GTCAGGTCGGGTCGG-TTTTTTTAAGTGTGATA-TTCGAG
66 CGGGT-AGGGTGAAACATTATTTTGGTCGGGTCAGG-CGGCTCGGATGAAGTGT-ATACTT-G-G
* * * * *
991779 TCGAGTCGAGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACTCGAAAATATATATAATTTTAC
126 -C---TCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCCAAAAAATATATAATTTTAC
991844 CTTATATATTTAGAAATAATTACAATAATACCCCTCTATATATAATTTTTTTTAATTAAGTCAAT
187 CTTATATATTTAGAAATAATTACAATAATACCCCTCTATATATAATTTTTTTTAATTAAGTCAAT
991909 GTTTT
252 GTTTT
*
991914 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTTGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGATCGGATTTCTAATTCATATATTTGGGT
* * **** * * *
991979 CGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAGGTCGGCTTTTTTTAAGTGTGATATTTGGGTC
66 CGGGTAGGGTGAAACATTATTTTGGTCGGGTCAGG-CGGCTCGGATGAAGTGT-ATACTTGGCTC
*
992044 GGGTCGGGTTCGGGTTTAGGGTGGAAAATACCCGACCCAACCCAAAAAATATATAATTTTACCTT
129 GGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGA--C--CCCAAAAAATATATAATTTTACCTT
* *
992109 ATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTGTTTTTTCAATTAAGTCATTG
190 ATATATTTAGAAATAATTACAATAATACCCCTCTATATATAATT-TTTTTT-AATTAAGTCAATG
992174 TTTT
253 TTTT
*
992178 TATTGAATAAAAATA-TTTTTTATTATTTCGGGTCTGATCGGATTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGATCGGATTTCTAATTCATATATT----T
*
992242 CGGGTCGGGTAGGGTGAAA-ATTATTTTGGTCGGGTC-GG-GTCTCGGATG
62 -GGGTCGGGTAGGGTGAAACATTATTTTGGTCGGGTCAGGCGGCTCGGATG
992290 GAGGTTCCCT
Statistics
Matches: 330, Mismatches: 26, Indels: 32
0.85 0.07 0.08
Matches are distributed among these distances:
256 30 0.09
258 35 0.11
260 3 0.01
261 44 0.13
262 79 0.24
263 66 0.20
264 37 0.11
266 2 0.01
267 17 0.05
268 17 0.05
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (256 bp):
TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGATCGGATTTCTAATTCATATATTTGGGT
CGGGTAGGGTGAAACATTATTTTGGTCGGGTCAGGCGGCTCGGATGAAGTGTATACTTGGCTCGG
GTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCCAAAAAATATATAATTTTACCTTATATAT
TTAGAAATAATTACAATAATACCCCTCTATATATAATTTTTTTTAATTAAGTCAATGTTTT
Found at i:992675 original size:18 final size:18
Alignment explanation
Indices: 992637--992684 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
992627 ATACGGAATT
*
992637 AGATTCCAATT-CTTGAC
1 AGATTCCAATTCCTTCAC
992654 AGATTCCAATTCCTTCAC
1 AGATTCCAATTCCTTCAC
*
992672 AGATTTCAATTCC
1 AGATTCCAATTCC
992685 CTCATAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.35
Consensus pattern (18 bp):
AGATTCCAATTCCTTCAC
Found at i:999624 original size:28 final size:27
Alignment explanation
Indices: 999592--999656 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
999582 TTATAAGGTA
999592 TATTTTATT-CTATTTAATATTTTGTTAG
1 TATTTTATTACTATTTAA-ATTTT-TTAG
* *
999620 TATTTTTTTAATTATTTAAATTTTTTAG
1 TATTTTATT-ACTATTTAAATTTTTTAG
999648 TATTTTATT
1 TATTTTATT
999657 TAATTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 20 0.62
29 5 0.16
30 7 0.22
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.68
Consensus pattern (27 bp):
TATTTTATTACTATTTAAATTTTTTAG
Found at i:999643 original size:29 final size:30
Alignment explanation
Indices: 999602--999674 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
999592 TATTTTATTC
999602 TATTTAATATTTTGTTAGTATTTT-TTTAAT
1 TATTTAATATTTT-TTAGTATTTTATTTAAT
999632 TATTTAA-ATTTTTTAGTATTTTATTTAAT
1 TATTTAATATTTTTTAGTATTTTATTTAAT
*
999661 TATTT-TTATTTTTT
1 TATTTAATATTTTTT
999675 TACAGTTATA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
28 10 0.25
29 23 0.57
30 7 0.17
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (30 bp):
TATTTAATATTTTTTAGTATTTTATTTAAT
Found at i:1005829 original size:24 final size:24
Alignment explanation
Indices: 1005802--1005884 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
1005792 ATTTCCGATT
*
1005802 TGAATTATGTTCTGACATATGATC
1 TGAATTATGTTCTGATATATGATC
* * *
1005826 TGAAATT-TGTTCT-ATTTCCTGACC
1 TG-AATTATGTTCTGATAT-ATGATC
*
1005850 TGGATTATGTTCTGATATATGATC
1 TGAATTATGTTCTGATATATGATC
1005874 TGAATTATGTT
1 TGAATTATGTT
1005885 TTGTTTTCTG
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
23 5 0.11
24 34 0.74
25 7 0.15
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (24 bp):
TGAATTATGTTCTGATATATGATC
Found at i:1006244 original size:159 final size:158
Alignment explanation
Indices: 1005955--1006384 Score: 720
Period size: 159 Copynumber: 2.7 Consensus size: 158
1005945 AAAGTATATA
* * *
1005955 TGCAGGTTCCTCGGCTTTATGCTCAGGGCCTTACTTGGTGTGTTGGTGAGTGTATGGTTCTGGGG
1 TGCAGGCTCCTCTGCTTTGTGCTCAGGGCCTTACTTGGTGTGTTGGTGAGTGTATGGTTCTGGGG
*
1006020 AACCTACACATTATGGTGTGTTCGGTTGGAGGGATTACTATGGTTTTTTATAAATGTTTTATGGG
66 AACCTACACATTATGGTGTGATCGGTTGGAGGGATTACTATGG-TTTTTATAAATGTTTTATGGG
*
1006085 AGGGTGTTGTTGGAGGAAGTTATCGTTAC
130 AGGGTGTTGTTGGAGGAAGTTACCGTTAC
1006114 TGCAGGCTCCTCTGCTTTGTGCTCAGGGCCTTACTTGGTGTGTTGGTGAGTGTATGGTTCTGGGG
1 TGCAGGCTCCTCTGCTTTGTGCTCAGGGCCTTACTTGGTGTGTTGGTGAGTGTATGGTTCTGGGG
1006179 AACCTACACATTATGGTGTGATCGGTTGGAGGGATTACTATGGCTTTTTATAAATGTTTTATGGG
66 AACCTACACATTATGGTGTGATCGGTTGGAGGGATTACTATGG-TTTTTATAAATGTTTTATGGG
*
1006244 AGGGTGTTGTTGGATGAAGTTACCGTTAC
130 AGGGTGTTGTTGGAGGAAGTTACCGTTAC
* * *
1006273 TGCAGACTCCTCTGTTTTGTGCTCAGGGCCTTACTTGGTGTGTTGGTG-GTGTATGGTTCTAGGG
1 TGCAGGCTCCTCTGCTTTGTGCTCAGGGCCTTACTTGGTGTGTTGGTGAGTGTATGGTTCTGGGG
* *
1006337 AACCTACACATTATGGTGTGTAT-GGTTAGAGGGATTAATATGGTTTTT
66 AACCTACACATTATGGTGTG-ATCGGTTGGAGGGATTACTATGGTTTTT
1006385 GAATAAAAAT
Statistics
Matches: 258, Mismatches: 12, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
157 5 0.02
158 53 0.21
159 200 0.78
ACGTcount: A:0.17, C:0.13, G:0.32, T:0.38
Consensus pattern (158 bp):
TGCAGGCTCCTCTGCTTTGTGCTCAGGGCCTTACTTGGTGTGTTGGTGAGTGTATGGTTCTGGGG
AACCTACACATTATGGTGTGATCGGTTGGAGGGATTACTATGGTTTTTATAAATGTTTTATGGGA
GGGTGTTGTTGGAGGAAGTTACCGTTAC
Found at i:1009553 original size:16 final size:16
Alignment explanation
Indices: 1009532--1009564 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1009522 TAATAAATAA
1009532 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1009548 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1009564 A
1 A
1009565 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1009655 original size:16 final size:16
Alignment explanation
Indices: 1009634--1009694 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
1009624 TAATAAATAA
1009634 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1009650 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1009666 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1009682 ACGAACATAAACG
1 ACGAACATAAACG
1009695 TTGGAGACCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1010444 original size:14 final size:14
Alignment explanation
Indices: 1010427--1010482 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1010417 AATGAACATA
*
1010427 AACGAACATAATCG
1 AACGAACATAACCG
1010441 AACGAACAT-A---
1 AACGAACATAACCG
*
1010451 AACGAACATAACCA
1 AACGAACATAACCG
1010465 AACGAACATAACCG
1 AACGAACATAACCG
1010479 AACG
1 AACG
1010483 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Done.