Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_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: 5583615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 26
Found at i:770208 original size:22 final size:23
Alignment explanation
Indices: 770180--770227 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
770170 TTAATTTTTG
770180 TTTGGGTGCTA-TTTGTGTAAA-A
1 TTTGGGTGCTAGTTT-TGTAAATA
*
770202 TTTGGGTGTTAGTTTTGTAAATA
1 TTTGGGTGCTAGTTTTGTAAATA
770225 TTT
1 TTT
770228 ACAGAAGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.21, C:0.02, G:0.25, T:0.52
Consensus pattern (23 bp):
TTTGGGTGCTAGTTTTGTAAATA
Found at i:775221 original size:24 final size:24
Alignment explanation
Indices: 775191--775304 Score: 149
Period size: 24 Copynumber: 4.8 Consensus size: 24
775181 TCGATTTGAT
*
775191 TTCTGATCTAATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
*
775215 TTCTGATCTGATA-TCTAACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
775239 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
775263 TTCTGATATGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
775287 TTTTGATATGATACTTGA
1 TTCTGATCTGATACTTGA
775305 TGTGAATTAT
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.40
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:775317 original size:24 final size:23
Alignment explanation
Indices: 775235--775317 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
775225 ATATCTAACA
* *
775235 TGGATTCTGATCTGATACTTGACT
1 TGGATTATGATATGATACTTGA-T
* *
775259 TGGATTCTGATATGATACTTGACC
1 TGGATTATGATATGATACTTGA-T
*
775283 TGGATTTTGATATGATACTTGAT
1 TGGATTATGATATGATACTTGAT
*
775306 GTGAATTATGAT
1 -TGGATTATGAT
775318 TTGAGTTTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (23 bp):
TGGATTATGATATGATACTTGAT
Found at i:778971 original size:24 final size:24
Alignment explanation
Indices: 778845--778959 Score: 144
Period size: 24 Copynumber: 4.8 Consensus size: 24
778835 TTGATTTGAT
* *
778845 TTCTAATATAATACTTGACATT-GA
1 TTCTGATATGATACTTGAC-TTGGA
*
778869 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACTTGGA
*
778893 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATATGATACTTGACTTGGA
*
778917 TTCTGATATGATACTTGACCTGGA
1 TTCTGATATGATACTTGACTTGGA
*
778941 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
778960 GTGAATTATG
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
23 2 0.03
24 77 0.96
25 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (24 bp):
TTCTGATATGATACTTGACTTGGA
Found at i:778976 original size:24 final size:24
Alignment explanation
Indices: 778850--778976 Score: 121
Period size: 24 Copynumber: 5.3 Consensus size: 24
778840 TTGATTTCTA
* * * *
778850 ATATAATACTTGACATTGATTCTG
1 ATATGATACTTGACCTGGATTATG
* *
778874 ATATGATA-TCTGACATGGATTCTG
1 ATATGATACT-TGACCTGGATTATG
* * *
778898 ATCTGATACTTGACTTGGATTCTG
1 ATATGATACTTGACCTGGATTATG
*
778922 ATATGATACTTGACCTGGATTTTG
1 ATATGATACTTGACCTGGATTATG
* *
778946 ATATGATACTTGACGTGAATTATG
1 ATATGATACTTGACCTGGATTATG
*
778970 ATTTGAT
1 ATATGAT
778977 TTTTGATATA
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 88 0.98
25 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (24 bp):
ATATGATACTTGACCTGGATTATG
Found at i:779147 original size:2 final size:2
Alignment explanation
Indices: 779140--779198 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
779130 CTGATGGGGG
779140 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
779182 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
779199 GTTTTAAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:782871 original size:24 final size:24
Alignment explanation
Indices: 782844--782953 Score: 132
Period size: 24 Copynumber: 4.6 Consensus size: 24
782834 TTGATTTGAT
*
782844 TTCTGATCTAATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
*
782868 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
* *
782892 TTCTGATCTGATACTGGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
782916 TTCTGATCTGATGCTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
782940 TTTTGATATGATAC
1 TTCTGATCTGATAC
782954 ATGATGTGAA
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
23 1 0.01
24 72 0.97
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:782896 original size:12 final size:12
Alignment explanation
Indices: 782859--782897 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
782849 ATCTAATACT
782859 TGACATGGATTC
1 TGACATGGATTC
*
782871 TGATAT-GATATC
1 TGACATGGAT-TC
782883 TGACATGGATTC
1 TGACATGGATTC
782895 TGA
1 TGA
782898 TCTGATACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:797725 original size:19 final size:19
Alignment explanation
Indices: 797697--797745 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
797687 TTGTTATTTT
797697 AAAA-AAAAAAAAAAAAAA
1 AAAACAAAAAAAAAAAAAA
***
797715 AAAACAAAAAAAAGGCAAA
1 AAAACAAAAAAAAAAAAAA
797734 AAAACAAAAAAA
1 AAAACAAAAAAA
797746 GCCAAAAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.90, C:0.06, G:0.04, T:0.00
Consensus pattern (19 bp):
AAAACAAAAAAAAAAAAAA
Found at i:797741 original size:8 final size:8
Alignment explanation
Indices: 797697--797745 Score: 55
Period size: 8 Copynumber: 5.9 Consensus size: 8
797687 TTGTTATTTT
797697 AAAAAAA-
1 AAAAAAAC
*
797704 AAAAAAAA
1 AAAAAAAC
797712 AAAAAAAC
1 AAAAAAAC
797720 AAAAAAAAGGC
1 -AAAAAAA--C
797731 AAAAAAAC
1 AAAAAAAC
797739 AAAAAAA
1 AAAAAAA
797746 GCCAAAAAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
7 7 0.19
8 15 0.41
9 7 0.19
10 7 0.19
11 1 0.03
ACGTcount: A:0.90, C:0.06, G:0.04, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:797745 original size:1 final size:1
Alignment explanation
Indices: 797697--797727 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
797687 TTGTTATTTT
*
797697 AAAAAAAAAAAAAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
797728 GGCAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:797745 original size:11 final size:11
Alignment explanation
Indices: 797698--797737 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
797688 TGTTATTTTA
*
797698 AAAAAAAAAAA
1 AAAAAAAAAAC
797709 AAAAAAAAAAC
1 AAAAAAAAAAC
**
797720 AAAAAAAAGGC
1 AAAAAAAAAAC
797731 AAAAAAA
1 AAAAAAA
797738 CAAAAAAAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.90, C:0.05, G:0.05, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:797746 original size:18 final size:19
Alignment explanation
Indices: 797697--797753 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 19
797687 TTGTTATTTT
797697 AAAAAAA-AAAAAAAA---
1 AAAAAAACAAAAAAAAGCC
*
797712 AAAAAAACAAAAAAAAGGC
1 AAAAAAACAAAAAAAAGCC
797731 AAAAAAAC-AAAAAAAGCC
1 AAAAAAACAAAAAAAAGCC
797749 AAAAA
1 AAAAA
797754 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
15 7 0.19
16 8 0.22
18 14 0.38
19 8 0.22
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAAAAAGCC
Found at i:797753 original size:19 final size:20
Alignment explanation
Indices: 797711--797753 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
797701 AAAAAAAAAA
*
797711 AAAAAAAACAAAAAAAAGGC
1 AAAAAAAACAAAAAAAAGCC
797731 -AAAAAAAC-AAAAAAAGCC
1 AAAAAAAACAAAAAAAAGCC
797749 AAAAA
1 AAAAA
797754 GCCAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.81, C:0.12, G:0.07, T:0.00
Consensus pattern (20 bp):
AAAAAAAACAAAAAAAAGCC
Found at i:812895 original size:24 final size:24
Alignment explanation
Indices: 812868--812961 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 24
812858 AAACGGAGAT
*
812868 ATCATAAATCAAAACAGAATTCAG
1 ATCATAAATCAGAACAGAATTCAG
* *
812892 ATCAGATATCAGAACAGAA-TCTAG
1 ATCATAAATCAGAACAGAATTC-AG
*
812916 ATTA-AAATCAGAACAGAATTCAG
1 ATCATAAATCAGAACAGAATTCAG
* * **
812939 TTAATTTATCAGAACAGAATTCA
1 ATCATAAATCAGAACAGAATTCA
812962 AGTCGGAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
23 19 0.33
24 39 0.67
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCATAAATCAGAACAGAATTCAG
Found at i:815829 original size:90 final size:90
Alignment explanation
Indices: 815673--815850 Score: 259
Period size: 90 Copynumber: 2.0 Consensus size: 90
815663 CCTAACACAC
* * * * *
815673 CCTTTTATTGCCAACTTACCCTAGTTATATTAGGGTTTTTATTATTTCAAATTAACTAAATCTAT
1 CCTTTTATTGCCAACTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAACTAAATATAT
* *
815738 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* *
815763 CCTTTTATAT-CCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATA
1 CCTTTTAT-TGCCAACTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAACTAAATATA
815827 TATTTAATTAATTGAAATTAAATA
65 TATTTAATTAATTGAAATTAAATA
815851 TTCGGGATTA
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 77 0.99
91 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.45
Consensus pattern (90 bp):
CCTTTTATTGCCAACTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAACTAAATATAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:822580 original size:90 final size:90
Alignment explanation
Indices: 822424--822601 Score: 268
Period size: 90 Copynumber: 2.0 Consensus size: 90
822414 CCTAACACAC
* * * * *
822424 CCTTTTATTGCCAAGTTACCCTAGTTATATTAGGGTTTTTATTATTTCAAATTAACTAAATCTAT
1 CCTTTTATTGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAACTAAATATAT
* *
822489 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
822514 CCTTTTATAT-CCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATA
1 CCTTTTAT-TGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAACTAAATATA
822578 TATTTAATTAATTGAAATTAAATA
65 TATTTAATTAATTGAAATTAAATA
822602 TTCGGGATTA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
90 78 0.99
91 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (90 bp):
CCTTTTATTGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAACTAAATATAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:825935 original size:24 final size:24
Alignment explanation
Indices: 825876--825943 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
825866 AAATGGAGAT
* * * *
825876 ATCAGAAATCAAAAAAAAATTCAG
1 ATCAGAAATCAGAACAGAATCCAG
*
825900 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATCCAG
825924 ATCAGAAATCAGAACAGAAT
1 ATCAGAAATCAGAACAGAAT
825944 TCAGTTAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.54, C:0.16, G:0.13, T:0.16
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATCCAG
Found at i:825947 original size:12 final size:12
Alignment explanation
Indices: 825893--825947 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
825883 ATCAAAAAAA
*
825893 AATTCAGATCAG
1 AATTCAGAACAG
825905 -ATATCAGAACAG
1 AAT-TCAGAACAG
* *
825917 AATCCAGATCAG
1 AATTCAGAACAG
*
825929 AAATCAGAACAG
1 AATTCAGAACAG
825941 AATTCAG
1 AATTCAG
825948 TTAATTTATC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
11 2 0.06
12 30 0.88
13 2 0.06
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.18
Consensus pattern (12 bp):
AATTCAGAACAG
Found at i:828669 original size:21 final size:23
Alignment explanation
Indices: 828638--828687 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
828628 CCACCTTCTA
*
828638 CAAATATTTACA-AACTAACACC
1 CAAATATTTACACAAATAACACC
*
828660 CAAAT-TTTACACAAATAGCACC
1 CAAATATTTACACAAATAACACC
828682 CAAATA
1 CAAATA
828688 GAAATTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.50, C:0.26, G:0.02, T:0.22
Consensus pattern (23 bp):
CAAATATTTACACAAATAACACC
Found at i:829498 original size:15 final size:15
Alignment explanation
Indices: 829462--829491 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
829452 ATAATTTTAA
829462 TAATATTATATTTTT
1 TAATATTATATTTTT
829477 TAATATTATATTTTT
1 TAATATTATATTTTT
829492 ATATATTGAA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATATTATATTTTT
Found at i:829519 original size:25 final size:25
Alignment explanation
Indices: 829503--829552 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
829493 TATATTGAAT
829503 TATATTATAATAATATATAATAATA
1 TATATTATAATAATATATAATAATA
* *
829528 TATTTTATAATAA-AT-TATTAATA
1 TATATTATAATAATATATAATAATA
829551 TA
1 TA
829553 ATTGATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 9 0.39
24 2 0.09
25 12 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TATATTATAATAATATATAATAATA
Found at i:829546 original size:15 final size:15
Alignment explanation
Indices: 829445--829540 Score: 58
Period size: 15 Copynumber: 6.5 Consensus size: 15
829435 TTTTAAAATA
*
829445 TATAAGAATA-ATTT
1 TATAATAATATATTT
*
829459 TAATAATATTATATTT
1 T-ATAATAATATATTT
* *
829475 TTTAATATTATATTT
1 TATAATAATATATTT
* *
829490 T-TATATATTGA-ATTA
1 TATA-ATAAT-ATATTT
* *
829505 TATTATAATA-A-TA
1 TATAATAATATATTT
829518 TATAATAATATATTT
1 TATAATAATATATTT
829533 TATAATAA
1 TATAATAA
829541 ATTATTAATA
Statistics
Matches: 67, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
13 11 0.16
14 6 0.09
15 43 0.64
16 7 0.10
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
TATAATAATATATTT
Found at i:830566 original size:24 final size:23
Alignment explanation
Indices: 830539--830609 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 23
830529 ATTATTTTAA
830539 TAAAATACTAATTATTATAATATT
1 TAAAATA-TAATTATTATAATATT
* *
830563 TAAAGTATAGTTATTAATAA-ATTT
1 TAAAATATAATTATT-ATAATA-TT
*
830587 TAATAATATAA-TATAATAATATT
1 TAA-AATATAATTATTATAATATT
830610 ATTTTAATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
23 14 0.37
24 19 0.50
25 5 0.13
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (23 bp):
TAAAATATAATTATTATAATATT
Found at i:830628 original size:11 final size:11
Alignment explanation
Indices: 830577--830630 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
830567 GTATAGTTAT
*
830577 TAATAA-ATTT
1 TAATAATATTA
830587 TAATAATATAATA
1 TAATAATAT--TA
830600 TAATAATATTA
1 TAATAATATTA
**
830611 TTTTAATATTA
1 TAATAATATTA
830622 TAATAATAT
1 TAATAATAT
830631 ATTCAATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
10 6 0.17
11 20 0.56
13 10 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TAATAATATTA
Found at i:833402 original size:26 final size:27
Alignment explanation
Indices: 833372--833422 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
833362 GTCTGAAGTG
*
833372 GTAG-TTTCTAGAAGGTCCAGTCAGTA
1 GTAGTTTTCTAGAAGATCCAGTCAGTA
*
833398 GTAGTTTTCTAGAAGATCTAGTCAG
1 GTAGTTTTCTAGAAGATCCAGTCAG
833423 AGCCTTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.33
Consensus pattern (27 bp):
GTAGTTTTCTAGAAGATCCAGTCAGTA
Found at i:833677 original size:24 final size:24
Alignment explanation
Indices: 833645--833702 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
833635 TATAAAGTTC
* *
833645 TTTCCTTTTT-TTTTCTTTTCAAGT
1 TTTCATTTTTATTTTATTTT-AAGT
833669 TTTCATTTTTATTTTATTTTAAGT
1 TTTCATTTTTATTTTATTTTAAGT
833693 TTT-ATTTTTA
1 TTTCATTTTTA
833703 AACATGTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 7 0.23
24 16 0.52
25 8 0.26
ACGTcount: A:0.16, C:0.09, G:0.03, T:0.72
Consensus pattern (24 bp):
TTTCATTTTTATTTTATTTTAAGT
Found at i:833703 original size:13 final size:13
Alignment explanation
Indices: 833655--833703 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
833645 TTTCCTTTTT
* *
833655 TTTTCTTTTCAAG
1 TTTTATTTTTAAG
833668 TTTTCATTTTT-A-
1 TTTT-ATTTTTAAG
833680 TTTTA-TTTTAAG
1 TTTTATTTTTAAG
833692 TTTTATTTTTAA
1 TTTTATTTTTAA
833704 ACATGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 4 0.13
11 2 0.07
12 9 0.30
13 11 0.37
14 4 0.13
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.69
Consensus pattern (13 bp):
TTTTATTTTTAAG
Found at i:839437 original size:12 final size:12
Alignment explanation
Indices: 839416--839448 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
839406 GCGGACGAGA
*
839416 TCATGTATCACG
1 TCATGCATCACG
839428 TCATGCATCACG
1 TCATGCATCACG
839440 TCATGCATC
1 TCATGCATC
839449 TGTCATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.30
Consensus pattern (12 bp):
TCATGCATCACG
Found at i:843857 original size:14 final size:14
Alignment explanation
Indices: 843838--843865 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
843828 AGAGAATAAA
843838 TCACGGAGTCAGCT
1 TCACGGAGTCAGCT
843852 TCACGGAGTCAGCT
1 TCACGGAGTCAGCT
843866 GCTGTTCTCC
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:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (14 bp):
TCACGGAGTCAGCT
Found at i:849590 original size:15 final size:15
Alignment explanation
Indices: 849561--849596 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
849551 TTTTCCATAG
*
849561 CATTCCCTTCCATTT
1 CATTCCCTTCAATTT
849576 CATTCCCTTCAATTT
1 CATTCCCTTCAATTT
849591 CATTCC
1 CATTCC
849597 ATTTGCTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.17, C:0.39, G:0.00, T:0.44
Consensus pattern (15 bp):
CATTCCCTTCAATTT
Found at i:853576 original size:25 final size:24
Alignment explanation
Indices: 853520--853608 Score: 63
Period size: 25 Copynumber: 3.5 Consensus size: 24
853510 TAAATTACGA
* **
853520 AAATAAAACAATTAATAATAAACTT
1 AAATAAAATAATTAA-AATAAAAAT
*
853545 AATTAAAATAATTAAAATAACAAAT
1 AAATAAAATAATTAAAATAA-AAAT
*
853570 AAATAAAA-ACAGTAAAAAAATAAAAAAT
1 AAATAAAATA-A-T--TAAAAT-AAAAAT
853598 AAATAAAATAA
1 AAATAAAATAA
853609 ACATACATTC
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
24 6 0.12
25 23 0.45
26 1 0.02
28 18 0.35
29 3 0.06
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.22
Consensus pattern (24 bp):
AAATAAAATAATTAAAATAAAAAT
Found at i:853594 original size:16 final size:16
Alignment explanation
Indices: 853549--853609 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 16
853539 AAACTTAATT
*
853549 AAAATAATTAAAATAA
1 AAAATAAATAAAATAA
*
853565 CAAATAAAT--AA-AA
1 AAAATAAATAAAATAA
* *
853578 ACAGTAAA-AAAATAA
1 AAAATAAATAAAATAA
853593 AAAATAAATAAAATAA
1 AAAATAAATAAAATAA
853609 A
1 A
853610 CATACATTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
13 7 0.21
14 4 0.12
15 8 0.24
16 15 0.44
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.18
Consensus pattern (16 bp):
AAAATAAATAAAATAA
Found at i:853721 original size:30 final size:30
Alignment explanation
Indices: 853681--853737 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
853671 AACATAAAAT
*
853681 AAGGGCTAAATTAAAACAAATTAAAAATGC
1 AAGGGCTAAATTAAAACAAAATAAAAATGC
* * *
853711 AAGGGTTAAATTGAAATAAAATAAAAA
1 AAGGGCTAAATTAAAACAAAATAAAAA
853738 AAGTTTTAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (30 bp):
AAGGGCTAAATTAAAACAAAATAAAAATGC
Found at i:863676 original size:14 final size:14
Alignment explanation
Indices: 863657--863704 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
863647 ATAATGAATT
863657 CTAAACCTTAAACC
1 CTAAACCTTAAACC
*
863671 CTAAACCTTAAATC
1 CTAAACCTTAAACC
* *
863685 TTAAA-TTCTAAACC
1 CTAAACCT-TAAACC
863699 CTAAAC
1 CTAAAC
863705 TTGACAACAC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
13 1 0.04
14 26 0.96
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (14 bp):
CTAAACCTTAAACC
Found at i:863687 original size:21 final size:21
Alignment explanation
Indices: 863657--863704 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
863647 ATAATGAATT
863657 CTAAACCTTAAACCCTAAACC
1 CTAAACCTTAAACCCTAAACC
* * **
863678 TTAAATCTTAAATTCTAAACC
1 CTAAACCTTAAACCCTAAACC
863699 CTAAAC
1 CTAAAC
863705 TTGACAACAC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (21 bp):
CTAAACCTTAAACCCTAAACC
Found at i:867383 original size:29 final size:30
Alignment explanation
Indices: 867345--867409 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
867335 ATTATATATT
* *
867345 TTATACCACTGAACTTTTAATTTTG-TCAA
1 TTATAACACTGAACTTTGAATTTTGTTCAA
*
867374 TTATAACACTGAACTTTGATTTTTGTTTCAA
1 TTATAACACTGAACTTTGAATTTTG-TTCAA
867405 TTATA
1 TTATA
867410 CCATTAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 22 0.71
31 9 0.29
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.48
Consensus pattern (30 bp):
TTATAACACTGAACTTTGAATTTTGTTCAA
Found at i:871233 original size:25 final size:24
Alignment explanation
Indices: 871177--871271 Score: 68
Period size: 25 Copynumber: 3.8 Consensus size: 24
871167 TTAAATTACG
**
871177 AAATAAAACAATTAATAATAA-ACTT
1 AAATAAAA-AATTAA-AATAACAAAT
*
871202 AATTAAAATAATTAAAATAACAAAT
1 AAATAAAA-AATTAAAATAACAAAT
* * *
871227 AAATAAAAGCAGTAAAAAAACAACAT
1 AAATAAAA-AATTAAAATAACAA-AT
871253 AAAATAAAAAA-TAAAATAA
1 -AAATAAAAAATTAAAATAA
871272 ACATACATCC
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
24 5 0.09
25 40 0.71
26 3 0.05
27 8 0.14
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.21
Consensus pattern (24 bp):
AAATAAAAAATTAAAATAACAAAT
Found at i:871266 original size:12 final size:12
Alignment explanation
Indices: 871214--871272 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
871204 TTAAAATAAT
*
871214 TAAAATAACAAA
1 TAAAATAAAAAA
*
871226 T-AAATAAAAGCAG
1 TAAAATAAAA--AA
871239 TAAAA-AAACAACA
1 TAAAATAAA-AA-A
871252 TAAAATAAAAAA
1 TAAAATAAAAAA
871264 TAAAATAAA
1 TAAAATAAA
871273 CATACATCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
11 7 0.18
12 12 0.32
13 12 0.32
14 7 0.18
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.15
Consensus pattern (12 bp):
TAAAATAAAAAA
Found at i:875355 original size:29 final size:29
Alignment explanation
Indices: 875320--875386 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
875310 TCATTGTGAA
875320 GTTTAAATCCAACTTGTATAAGTTGTATT
1 GTTTAAATCCAACTTGTATAAGTTGTATT
875349 GTTTAAATCCAACTTGTATAAGTTGTATT
1 GTTTAAATCCAACTTGTATAAGTTGTATT
* *
875378 ATTTTAATC
1 GTTTAAATC
875387 TCGAGTGTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.46
Consensus pattern (29 bp):
GTTTAAATCCAACTTGTATAAGTTGTATT
Found at i:876412 original size:48 final size:48
Alignment explanation
Indices: 876312--876432 Score: 138
Period size: 48 Copynumber: 2.5 Consensus size: 48
876302 TTCTTTTTAT
* * * * * *
876312 TTAGAGTGCCCTCTCAGGTTTTCACTCTAACCGTTTTTTTATTTAGAT
1 TTAGAGCGCCCTTTCAGGTTTTCACTATAACAGTTTTTTTATTCAGAC
*
876360 TTAGAGCGTCCTTTCTA-GTTTTCACTATAACAGTTTTTTTACTTCA-AC
1 TTAGAGCGCCCTTTC-AGGTTTTCACTATAACAGTTTTTTTA-TTCAGAC
*
876408 TTAGAGTGCCCTTTCAGGTTTTCAC
1 TTAGAGCGCCCTTTCAGGTTTTCAC
876433 CCTAAGCAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
47 1 0.02
48 56 0.92
49 4 0.07
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (48 bp):
TTAGAGCGCCCTTTCAGGTTTTCACTATAACAGTTTTTTTATTCAGAC
Found at i:886544 original size:23 final size:24
Alignment explanation
Indices: 886528--886585 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
886518 AAAATATGAT
886528 AAAATAAAATGAAAAAA-ATAAATA
1 AAAAT-AAATGAAAAAATATAAATA
*
886552 AAAATAAATGAAAAAATATTAAATT
1 AAAATAAATGAAAAAATA-TAAATA
*
886577 AAAAGAAAT
1 AAAATAAAT
886586 ATTACAGAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 11 0.37
24 6 0.20
25 13 0.43
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (24 bp):
AAAATAAATGAAAAAATATAAATA
Found at i:886547 original size:14 final size:13
Alignment explanation
Indices: 886528--886586 Score: 52
Period size: 10 Copynumber: 4.5 Consensus size: 13
886518 AAAATATGAT
886528 AAAATAAAATGAAA
1 AAAAT-AAATGAAA
886542 AAAATAAAT---A
1 AAAATAAATGAAA
886552 AAAATAAATGAAA
1 AAAATAAATGAAA
*
886565 AAATATTAAATTAAA
1 AAA-A-TAAATGAAA
886580 AGAAATA
1 A-AAATA
886587 TTACAGAAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
10 10 0.26
13 8 0.21
14 8 0.21
15 10 0.26
16 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (13 bp):
AAAATAAATGAAA
Found at i:887995 original size:2 final size:2
Alignment explanation
Indices: 887976--888156 Score: 130
Period size: 2 Copynumber: 98.0 Consensus size: 2
887966 CAAATAAATA
* *
887976 AT AT AT A- AT AA AT A- AT AT AT AT A- AT -T A- AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* ** * *
888013 AT AC ACT GC AT A- AT AT ACT AT AT A- AT AA AC AT AT AT A- AT AT
1 AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
888054 A- AT AT AT AT AT AT AT AT AT -T AT AT AT A- AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
888091 AT AT A- AT A- AT AT AT AT -T AT AGT -T AT AT AGT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT
888130 -T 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
888157 TAAAAAAATA
Statistics
Matches: 143, Mismatches: 13, Indels: 46
0.71 0.06 0.23
Matches are distributed among these distances:
1 19 0.13
2 119 0.83
3 5 0.03
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:888006 original size:9 final size:8
Alignment explanation
Indices: 887968--888103 Score: 56
Period size: 9 Copynumber: 17.1 Consensus size: 8
887958 TAAATAAACA
887968 AATAA-AT
1 AATAATAT
887975 AAT-ATAT
1 AATAATAT
887982 AATAA-AT
1 AATAATAT
887989 AATATATAT
1 AATA-ATAT
887998 AATTAATAT
1 AA-TAATAT
* *
888007 ATTTATAT
1 AATAATAT
* * *
888015 -ACACT-G
1 AATAATAT
*
888021 CATAATAT
1 AATAATAT
*
888029 ACT-ATAT
1 AATAATAT
*
888036 AATAAACAT
1 AAT-AATAT
888045 ATATAATAT
1 A-ATAATAT
888054 AAT-ATAT
1 AATAATAT
888061 -AT-ATAT
1 AATAATAT
*
888067 ATATATTAT
1 A-ATAATAT
888076 ATATAATAAT
1 A-ATAAT-AT
888086 AATATATAT
1 AATA-ATAT
888095 AATAATAT
1 AATAATAT
888103 A
1 A
888104 TATTATAGTT
Statistics
Matches: 97, Mismatches: 17, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
6 7 0.07
7 28 0.29
8 17 0.18
9 36 0.37
10 9 0.09
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (8 bp):
AATAATAT
Found at i:888049 original size:15 final size:14
Alignment explanation
Indices: 888031--888161 Score: 75
Period size: 15 Copynumber: 8.9 Consensus size: 14
888021 CATAATATAC
888031 TATATAATAAACATA
1 TATATAATAAA-ATA
*
888046 TATA-ATATAATATA
1 TATATA-ATAAAATA
* *
888060 TATATATATATATTA
1 TATATA-ATAAAATA
888075 TATATAATAATAATA
1 TATATAATAA-AATA
*
888090 TATATAATAATATA
1 TATATAATAAAATA
* * *
888104 TATTATAGTTATATA
1 TA-TATAATAAAATA
* **
888119 GTATATATTATTATA
1 -TATATAATAAAATA
*
888134 TATATATATATATATA
1 TATATA-ATA-AAATA
*
888150 TATATATTAAAA
1 TATATAATAAAA
888162 AAATAAACCC
Statistics
Matches: 93, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
14 24 0.26
15 57 0.61
16 12 0.13
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.46
Consensus pattern (14 bp):
TATATAATAAAATA
Found at i:888103 original size:54 final size:55
Alignment explanation
Indices: 887972--888153 Score: 169
Period size: 57 Copynumber: 3.2 Consensus size: 55
887962 TAAACAAATA
* *
887972 AATAATATATAATAAATAATATATATAAT-TA-ATATATTTATA-TACACTGCATAAT
1 AATAATATATAATAAATAATATATATAATATATATATATATATATTATA-T--ATAAT
* *
888027 -ATACTATATAATAAACATATATAATATAATATATATATATATATATTATATATAAT
1 AATAATATATAATAAATA-ATAT-ATATAATATATATATATATATATTATATATAAT
*
888083 AATAATATAT-AT-AATAATATATATTATAGTTATATAGTATATATTATTATATATATAT
1 AATAATATATAATAAATAATATATATAATA--TATATA-TATATA-TATTATATATA-AT
888141 ATATATATATATA
1 A-ATA-ATATATA
888154 TATTAAAAAA
Statistics
Matches: 106, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
53 7 0.07
54 19 0.18
55 13 0.12
56 20 0.19
57 21 0.20
58 14 0.13
59 6 0.06
60 6 0.06
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (55 bp):
AATAATATATAATAAATAATATATATAATATATATATATATATATTATATATAAT
Found at i:890016 original size:41 final size:41
Alignment explanation
Indices: 889960--890083 Score: 187
Period size: 41 Copynumber: 3.0 Consensus size: 41
889950 ATAATTTTAA
* * *
889960 ACTATATTTATTCCTTTATTTTTA-ATTTATAAAATATATAT
1 ACTAGATTTATTCCTTTATTTTTATAATT-TAATATATATAT
*
890001 ACTAGATTCATTCCTTTATTTTTATAATTTAATATATATAT
1 ACTAGATTTATTCCTTTATTTTTATAATTTAATATATATAT
*
890042 ACTAGATTTATTCGTTTATTTTTATAATTTAATATATATAT
1 ACTAGATTTATTCCTTTATTTTTATAATTTAATATATATAT
890083 A
1 A
890084 TATATATATA
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
41 73 0.96
42 3 0.04
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.55
Consensus pattern (41 bp):
ACTAGATTTATTCCTTTATTTTTATAATTTAATATATATAT
Found at i:896901 original size:2 final size:2
Alignment explanation
Indices: 896894--896932 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
896884 CGAATAGATT
*
896894 TC TC TC TC TC TC TC TC TC TC TT 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 TC TC TC TC T
896933 GAAAGGATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:897033 original size:2 final size:2
Alignment explanation
Indices: 897026--897074 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
897016 GAAATAGATT
897026 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
897068 TC TC TC T
1 TC TC TC T
897075 GAAAGGATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:897054 original size:142 final size:142
Alignment explanation
Indices: 896894--897161 Score: 527
Period size: 142 Copynumber: 1.9 Consensus size: 142
896884 CGAATAGATT
*
896894 TCTCTCTCTCTCTCTCTCTCTTTCTCTCTCTCTCTCTCTGAAAGGATATAGATTTCTCCTGGATG
1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGAAAGGATATAGATTTCTCCTGGATG
896959 TCATTTAGTGACCATACTTCTTATATCTTGATATACTTCTTCCTCTGTACATTTCAGGAAATAGA
66 TCATTTAGTGACCATACTTCTTATATCTTGATATACTTCTTCCTCTGTACATTTCAGGAAATAGA
897024 TTTCTCTCTCTC
131 TTTCTCTCTCTC
897036 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGAAAGGATATAGATTTCTCCTGGATG
1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGAAAGGATATAGATTTCTCCTGGATG
897101 TCATTTAGTGACCATACTTCTTATATCTTGATATACTTCTTCCTCTGTACATTTCAGGAAA
66 TCATTTAGTGACCATACTTCTTATATCTTGATATACTTCTTCCTCTGTACATTTCAGGAAA
897162 GAAGGCCTCG
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 125 1.00
ACGTcount: A:0.19, C:0.28, G:0.10, T:0.44
Consensus pattern (142 bp):
TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGAAAGGATATAGATTTCTCCTGGATG
TCATTTAGTGACCATACTTCTTATATCTTGATATACTTCTTCCTCTGTACATTTCAGGAAATAGA
TTTCTCTCTCTC
Found at i:899181 original size:39 final size:39
Alignment explanation
Indices: 899138--899218 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
899128 AACTGATATT
*
899138 ATTGTTAATAAAATCAGGTAATTAGACATGTTTAGTTGG
1 ATTGTTAATAAAATCAGGTAATTAGACATGTTTAGTTCG
899177 ATTGTTAATAAAATCAGGTAATTAGACATGTTTAGTTCG
1 ATTGTTAATAAAATCAGGTAATTAGACATGTTTAGTTCG
899216 ATT
1 ATT
899219 ATGACAGATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.40
Consensus pattern (39 bp):
ATTGTTAATAAAATCAGGTAATTAGACATGTTTAGTTCG
Found at i:900172 original size:21 final size:21
Alignment explanation
Indices: 900143--900195 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
900133 ATTCTGACTA
900143 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
900164 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
900185 TCGCAATGCGA
1 TCGCATTGCGA
900196 ATACGTAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:900246 original size:21 final size:21
Alignment explanation
Indices: 900185--900291 Score: 114
Period size: 20 Copynumber: 5.3 Consensus size: 21
900175 TTTTCCTAAT
900185 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGTAAA
*
900205 CCGCAATGC-AATTACGTAAA
1 TCGCAATGCGAATTACGTAAA
* *
900225 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGTAAA
* *
900246 TCGCAATGCGATTTACAT-AA
1 TCGCAATGCGAATTACGTAAA
* * *
900266 TCGCATTACGATTTA-GTAAA
1 TCGCAATGCGAATTACGTAAA
900286 TCGCAA
1 TCGCAA
900292 CGAGATTCTA
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.04
20 46 0.64
21 23 0.32
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAATTACGTAAA
Found at i:900268 original size:41 final size:40
Alignment explanation
Indices: 900170--900270 Score: 105
Period size: 41 Copynumber: 2.5 Consensus size: 40
900160 AAATTCGCGT
* * *
900170 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAACCGCAA
1 TGCGATTTACATAA-TCGCAATGCGAATACGAAAACCGCAA
* * * *
900211 TGC-AATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTACAT-AATCGCAATGCGAA-TACGAAAACCGCAA
900252 TGCGATTTACATAATCGCA
1 TGCGATTTACATAATCGCA
900271 TTACGATTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
40 17 0.35
41 26 0.53
42 6 0.12
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (40 bp):
TGCGATTTACATAATCGCAATGCGAATACGAAAACCGCAA
Found at i:903575 original size:20 final size:19
Alignment explanation
Indices: 903547--903601 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
903537 TAATCATCTT
*
903547 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
903567 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
903586 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
903602 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:903611 original size:14 final size:14
Alignment explanation
Indices: 903592--903678 Score: 66
Period size: 14 Copynumber: 5.6 Consensus size: 14
903582 GCGAAATGAA
903592 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
903606 AATCGCAATGCGAAATG
1 AATCGCAA--CGAGA-G
903623 AAATCGCAACGAGAG
1 -AATCGCAACGAGAG
*
903638 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
903657 AATCGCAACGAGGG
1 AATCGCAACGAGAG
903671 AATCGCAA
1 AATCGCAA
903679 AGCGAATGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
14 25 0.42
15 2 0.03
16 10 0.17
17 3 0.05
18 9 0.15
19 10 0.17
ACGTcount: A:0.44, C:0.20, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:903632 original size:32 final size:33
Alignment explanation
Indices: 903574--903697 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
903564 GGAAATGACT
903574 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
903607 ATCGCAATGCGAAATG-AAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
903639 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
903672 ATCGCAAAGCG-AATG-AAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
903698 CGAATTAGTT
Statistics
Matches: 88, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
31 11 0.12
32 36 0.41
33 41 0.47
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:903678 original size:65 final size:64
Alignment explanation
Indices: 903574--903697 Score: 221
Period size: 65 Copynumber: 1.9 Consensus size: 64
903564 GGAAATGACT
*
903574 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAAGCG-AATGAAATCGCAACGAGAGA
*
903639 ATCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAAAGCGAATGAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAATGAAATCGCAACG
903698 CGAATTAGTT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 15 0.26
65 42 0.74
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (64 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAATGAAATCGCAACGAGAGA
Found at i:903730 original size:14 final size:14
Alignment explanation
Indices: 903706--903769 Score: 56
Period size: 14 Copynumber: 4.3 Consensus size: 14
903696 CGCGAATTAG
*
903706 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
*
903720 TTTGTCGTTGCGATTT
1 TTTCTCGTTGCGA--T
*
903736 CATTTCGCGTTGCGAT
1 --TTTCTCGTTGCGAT
*
903752 TCTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
903766 TTTC
1 TTTC
903770 ATTTCGCATT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
14 26 0.67
16 2 0.05
18 11 0.28
ACGTcount: A:0.08, C:0.22, G:0.23, T:0.47
Consensus pattern (14 bp):
TTTCTCGTTGCGAT
Found at i:903747 original size:32 final size:33
Alignment explanation
Indices: 903706--903784 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
903696 CGCGAATTAG
* *
903706 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
903738 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
903771 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
903785 AATCATTTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 25 0.58
33 18 0.42
ACGTcount: A:0.10, C:0.22, G:0.23, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:903917 original size:13 final size:14
Alignment explanation
Indices: 903888--903923 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
903878 CATCAATTAA
903888 ACAAATCATCTTTT
1 ACAAATCATCTTTT
903902 ACAAATCATC-TTT
1 ACAAATCATCTTTT
903915 ACAAATCAT
1 ACAAATCAT
903924 TAAACAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.42, C:0.22, G:0.00, T:0.36
Consensus pattern (14 bp):
ACAAATCATCTTTT
Found at i:905185 original size:20 final size:20
Alignment explanation
Indices: 905162--905255 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
905152 CGATAGTCAG
905162 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
905182 ATTCACATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
905202 AATTCGCATTGTGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* *
905223 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
905243 AATCGCGTTGCGA
1 ATTCGCATTGCGA
905256 ATTAGGAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 47 0.75
21 16 0.25
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:905211 original size:41 final size:41
Alignment explanation
Indices: 905162--905255 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
905152 CGATAGTCAG
* *
905162 ATTCGCATTGCGATTTACGTATTCACATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACCTA
* * * *
905203 ATTCGCATTGTGATTTACGTAATCGCGTTGCGATTTACGTA
1 ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACCTA
*
905244 A-TCGCGTTGCGA
1 ATTCGCATTGCGA
905256 ATTAGGAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 9 0.20
41 36 0.80
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (41 bp):
ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACCTA
Found at i:905269 original size:21 final size:20
Alignment explanation
Indices: 905217--905269 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
905207 GCATTGTGAT
* *
905217 TTACGTAATCGCGTTGCGAT
1 TTACGAAATCGCGTTGCGAA
*
905237 TTACGTAATCGCGTTGCGAA
1 TTACGAAATCGCGTTGCGAA
*
905257 TTAGGAAAATCGC
1 TTACG-AAATCGC
905270 AATGCGATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 23 0.79
21 6 0.21
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (20 bp):
TTACGAAATCGCGTTGCGAA
Found at i:905797 original size:2 final size:2
Alignment explanation
Indices: 905693--905782 Score: 103
Period size: 2 Copynumber: 45.0 Consensus size: 2
905683 AAACTATGTA
905693 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
* * * * *
905735 AA AT AT AT A- AT AT AT A- AG AT TT AT GT AT AT AGT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
905776 AGT AT AT
1 A-T AT AT
905783 TAAGTACATA
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
1 2 0.03
2 70 0.93
3 3 0.04
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:905918 original size:19 final size:20
Alignment explanation
Indices: 905896--905951 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
905886 ATTATATAAA
905896 ATATTAAAATATATAA-TTT
1 ATATTAAAATATATAAGTTT
*
905915 ATATTAATATAATATAAGTTT
1 ATATTAAAAT-ATATAAGTTT
*
905936 ATATATAAACTATATA
1 ATAT-TAAAATATATA
905952 TATAAACTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 9 0.29
20 6 0.19
21 12 0.39
22 4 0.13
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
ATATTAAAATATATAAGTTT
Found at i:905951 original size:13 final size:13
Alignment explanation
Indices: 905935--906049 Score: 104
Period size: 13 Copynumber: 8.2 Consensus size: 13
905925 AATATAAGTT
905935 TATATATAAACTA
1 TATATATAAACTA
905948 TATATATAAACTA
1 TATATATAAACTA
*
905961 TATAATTATTATAAGTTA
1 TAT-A-TA-TA-AA-CTA
*
905979 TATATATAAATTA
1 TATATATAAACTA
* *
905992 TGTTTATATTAACTA
1 --TATATATAAACTA
906007 TATATATAAACTA
1 TATATATAAACTA
*
906020 TGTATATAAACTA
1 TATATATAAACTA
906033 TATATGTATAAACTA
1 TATA--TATAAACTA
906048 TA
1 TA
906050 AAAAGTATAT
Statistics
Matches: 85, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
13 45 0.53
14 3 0.04
15 25 0.29
16 4 0.05
17 3 0.04
18 5 0.06
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:906021 original size:28 final size:29
Alignment explanation
Indices: 905932--906048 Score: 118
Period size: 28 Copynumber: 4.0 Consensus size: 29
905922 TATAATATAA
905932 GTTTATATATAAACTATATATATAAACTAT
1 GTTTATATAT-AACTATATATATAAACTAT
* * *
905962 ATAATTAT-TATAAGTTATATATATAAATTAT
1 GT--TTATATATAA-CTATATATATAAACTAT
905993 GTTTATAT-TAACTATATATATAAACTAT
1 GTTTATATATAACTATATATATAAACTAT
906021 G--TATATA-AACTATATATGTATAAACTAT
1 GTTTATATATAACTATATA--TATAAACTAT
906049 AAAAAGTATA
Statistics
Matches: 74, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
26 14 0.19
28 26 0.35
29 7 0.09
30 4 0.05
31 19 0.26
32 4 0.05
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (29 bp):
GTTTATATATAACTATATATATAAACTAT
Found at i:906134 original size:99 final size:100
Alignment explanation
Indices: 906018--906203 Score: 311
Period size: 99 Copynumber: 1.9 Consensus size: 100
906008 ATATATAAAC
906018 TATGTATATAAACTATATATGTATAAACTATAAAAAGTATATAGTTTATAAACTATAATTTATAT
1 TATGTATATAAACTATATATGTATAAACTATAAAAAGTATATAGTTTATAAACTATAATTTATAT
*
906083 TAATATAGTGTATA-TATATATGTATGTATGTATG
66 TAATATAGTATATAGTATATATGTATGTATGTATG
* * * * *
906117 TATGTATGTAAATTATATATGTATAAACTATATAAAGTATATAGTTTATAAATTATAGTTTATAT
1 TATGTATATAAACTATATATGTATAAACTATAAAAAGTATATAGTTTATAAACTATAATTTATAT
906182 TAATATAGTATATAGTATATAT
66 TAATATAGTATATAGTATATAT
906204 ATATATATAT
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
99 73 0.91
100 7 0.09
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.45
Consensus pattern (100 bp):
TATGTATATAAACTATATATGTATAAACTATAAAAAGTATATAGTTTATAAACTATAATTTATAT
TAATATAGTATATAGTATATATGTATGTATGTATG
Found at i:906208 original size:15 final size:15
Alignment explanation
Indices: 906130--906233 Score: 72
Period size: 15 Copynumber: 6.9 Consensus size: 15
906120 GTATGTAAAT
* * *
906130 TATATATGTATAAAC
1 TATATATATATATAG
*
906145 TATATAAAGTATATAG
1 TATATATA-TATATAG
* *
906161 TTTATAAAT-TATAG
1 TATATATATATATAG
*
906175 TTTATAT-TAATATAG
1 TATATATAT-ATATAG
906190 TATATAGTATATATA-
1 TATATA-TATATATAG
906205 TATATATATATTATA-
1 TATATATATA-TATAG
*
906220 TATACATATATATA
1 TATATATATATATA
906234 TGAACTATAT
Statistics
Matches: 75, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
13 1 0.01
14 19 0.25
15 36 0.48
16 18 0.24
17 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (15 bp):
TATATATATATATAG
Found at i:906234 original size:19 final size:19
Alignment explanation
Indices: 906190--906234 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
906180 ATTAATATAG
* *
906190 TATATAGTATATATATATA
1 TATATATTATATATACATA
906209 TATATATTATATATACATA
1 TATATATTATATATACATA
906228 TATATAT
1 TATATAT
906235 GAACTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
TATATATTATATATACATA
Found at i:906242 original size:19 final size:19
Alignment explanation
Indices: 906184--906236 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
906174 GTTTATATTA
*
906184 ATATAGTATATAGTATATATAT
1 ATATA-TATAT-G-ATATATAC
*
906206 ATATATATATTATATATAC
1 ATATATATATGATATATAC
906225 ATATATATATGA
1 ATATATATATGA
906237 ACTATATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 18 0.64
21 5 0.18
22 5 0.18
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (19 bp):
ATATATATATGATATATAC
Found at i:906242 original size:21 final size:19
Alignment explanation
Indices: 906184--906244 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 19
906174 GTTTATATTA
*
906184 ATATAGTATATAGTATATATAT
1 ATATA-TATATA--ATATATAC
*
906206 ATATATATATTATATATAC
1 ATATATATATAATATATAC
906225 ATATATATATGAACTATATA
1 ATATATATAT-AA-TATATA
906245 AAGTAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 17 0.50
20 1 0.03
21 11 0.32
22 5 0.15
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (19 bp):
ATATATATATAATATATAC
Found at i:906244 original size:2 final size:2
Alignment explanation
Indices: 906093--906234 Score: 69
Period size: 2 Copynumber: 70.5 Consensus size: 2
906083 TAATATAGTG
* * * * * * *
906093 TA TA TA TA TA TG TA TG TA TG TA TG TA TG TA TG TA AA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
906134 TA TG TA TA AA CTA TA TA AA GTA TA TA GTT TA TA AA T- TA TA GTT
1 TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA -TA
906177 TA TA T- TA -A TA TA GTA TA TA GTA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
*
906218 TA TA TA CA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
906235 GAACTATATA
Statistics
Matches: 101, Mismatches: 28, Indels: 22
0.67 0.19 0.15
Matches are distributed among these distances:
1 5 0.05
2 88 0.87
3 8 0.08
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.47
Consensus pattern (2 bp):
TA
Found at i:906268 original size:26 final size:25
Alignment explanation
Indices: 906239--906322 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 25
906229 ATATATGAAC
*
906239 TATATAAAGTAATAAAGTATATAATT
1 TATATAAA-TAATAAAATATATAATT
* * **
906265 TATA-AAA-AA-ACATTATGCATAAAC
1 TATATAAATAATAAAATAT--ATAATT
906289 TATATAAATTAATAAAATATATAATT
1 TATATAAA-TAATAAAATATATAATT
906315 TATATAAA
1 TATATAAA
906323 CCCTAAACCT
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
22 5 0.11
23 2 0.05
24 8 0.18
25 6 0.14
26 16 0.36
27 2 0.05
28 5 0.11
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (25 bp):
TATATAAATAATAAAATATATAATT
Found at i:906303 original size:17 final size:18
Alignment explanation
Indices: 906230--906352 Score: 64
Period size: 17 Copynumber: 6.8 Consensus size: 18
906220 TATACATATA
* *
906230 TATATGAACTATATAAAG
1 TATATAAACTATATAAAT
*
906248 TA-ATAAAGTATAT-AAT
1 TATATAAACTATATAAAT
906264 T-TATAAA--A-A-AACAT
1 TATATAAACTATATAA-AT
906278 TATGCATAAACTATATAAAT
1 TAT--ATAAACTATATAAAT
* *
906298 TA-ATAAAATATATAATT
1 TATATAAACTATATAAAT
*
906315 TATATAAACCCTAAACCTTAAAT
1 TATATAAA--CTATA---TAAAT
906338 TATATAAACTATATA
1 TATATAAACTATATA
906353 TGTATAGACA
Statistics
Matches: 80, Mismatches: 9, Indels: 32
0.66 0.07 0.26
Matches are distributed among these distances:
13 2 0.03
14 4 0.05
15 1 0.01
16 8 0.10
17 29 0.36
18 9 0.11
19 1 0.01
20 8 0.10
21 6 0.08
23 12 0.15
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (18 bp):
TATATAAACTATATAAAT
Found at i:906510 original size:16 final size:16
Alignment explanation
Indices: 906450--906513 Score: 56
Period size: 16 Copynumber: 3.7 Consensus size: 16
906440 AAACAATAGT
*
906450 TAATATATGTAACCTA
1 TAATATATGTAACTTA
*
906466 TAGTATATGTATACATGTA
1 TAATATATGTA-AC-T-TA
*
906485 AACTATATATGTAACTTA
1 TA--ATATATGTAACTTA
906503 TAATATATGTA
1 TAATATATGTA
906514 TGTATAAACT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
16 19 0.50
17 2 0.05
18 3 0.08
19 4 0.11
20 2 0.05
21 8 0.21
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (16 bp):
TAATATATGTAACTTA
Found at i:906522 original size:35 final size:36
Alignment explanation
Indices: 906452--906525 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
906442 ACAATAGTTA
* *
906452 ATATATGTAACCTATAGTATATGTATACATGTAAACT
1 ATATATGTAACCTATAATATATGTATA-ATATAAACT
* *
906489 ATATATGTAACTTATAATATATGTAT-GTATAAACT
1 ATATATGTAACCTATAATATATGTATAATATAAACT
906524 AT
1 AT
906526 GTATAGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 9 0.27
37 24 0.73
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (36 bp):
ATATATGTAACCTATAATATATGTATAATATAAACT
Found at i:906534 original size:20 final size:21
Alignment explanation
Indices: 906505--906584 Score: 90
Period size: 20 Copynumber: 3.7 Consensus size: 21
906495 GTAACTTATA
*
906505 ATATATGTATGTATAAACTAT
1 ATATATGTATATATAAACTAT
*
906526 GTATA-GTATATATAAACTAT
1 ATATATGTATATATAAACTAT
* *
906546 ATATATATATATATATTACATAT
1 ATATATGTATATATA-AAC-TAT
906569 AGTATATGTATATATA
1 A-TATATGTATATATA
906585 CAATCTATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
20 18 0.37
21 12 0.24
22 2 0.04
23 4 0.08
24 13 0.27
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (21 bp):
ATATATGTATATATAAACTAT
Found at i:906539 original size:2 final size:2
Alignment explanation
Indices: 906527--906584 Score: 55
Period size: 2 Copynumber: 28.0 Consensus size: 2
906517 ATAAACTATG
* *
906527 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA TA TA T- TA CA TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
906570 GTA TA TG TA TA TA TA
1 -TA TA TA TA TA TA TA
906585 CAATCTATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
1 1 0.02
2 40 0.87
3 5 0.11
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:906779 original size:36 final size:36
Alignment explanation
Indices: 906739--906871 Score: 154
Period size: 36 Copynumber: 3.9 Consensus size: 36
906729 TAATGATCTT
906739 AACTATAATTTATATTAATATAGTATATAGTTTATA
1 AACTATAATTTATATTAATATAGTATATAGTTTATA
*
906775 AACTATAATTTATATTAA-ATTAGTAGATAGTTTATA
1 AACTATAATTTATATTAATA-TAGTATATAGTTTATA
* * * *
906811 AGCTATAATTTACATTAATAT--TA-ACA---TATT
1 AACTATAATTTATATTAATATAGTATATAGTTTATA
*
906841 AACTATAGTTTATATTAATATAGTATATAGT
1 AACTATAATTTATATTAATATAGTATATAGT
906872 ATTGTCGTAA
Statistics
Matches: 81, Mismatches: 9, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
30 21 0.26
32 2 0.02
33 4 0.05
34 2 0.02
35 1 0.01
36 50 0.62
37 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (36 bp):
AACTATAATTTATATTAATATAGTATATAGTTTATA
Found at i:906864 original size:15 final size:16
Alignment explanation
Indices: 906836--906869 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
906826 TAATATTAAC
*
906836 ATATTAACTATAGTTT
1 ATATTAACTATAGTAT
906852 ATATTAA-TATAGTAT
1 ATATTAACTATAGTAT
906867 ATA
1 ATA
906870 GTATTGTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (16 bp):
ATATTAACTATAGTAT
Found at i:907974 original size:14 final size:15
Alignment explanation
Indices: 907944--907982 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
907934 TGATCTAAGG
*
907944 ACTATAATATATAAA
1 ACTAAAATATATAAA
907959 ACTAAAATAT-TAAA
1 ACTAAAATATATAAA
907973 ACTCAAAATA
1 ACT-AAAATA
907983 AGATAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (15 bp):
ACTAAAATATATAAA
Found at i:910700 original size:14 final size:15
Alignment explanation
Indices: 910681--910709 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
910671 AATATATTGA
910681 ATAATAA-AATATTT
1 ATAATAATAATATTT
910695 ATAATAATAATATTT
1 ATAATAATAATATTT
910710 TAAATCCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATAATAATATTT
Found at i:911203 original size:15 final size:17
Alignment explanation
Indices: 911169--911203 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
911159 TAATGTGACT
911169 AAAATATAAATACTAAA
1 AAAATATAAATACTAAA
911186 AAAAT-TAAATACTTAAA
1 AAAATATAAATAC-TAAA
911203 A
1 A
911204 TCAAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATATAAATACTAAA
Found at i:912235 original size:3 final size:3
Alignment explanation
Indices: 912227--912256 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
912217 TAACCAAAAT
912227 TAA TAA TAA TAA TAA TAA TAA TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
912257 TTTCTAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:915115 original size:10 final size:10
Alignment explanation
Indices: 915102--915126 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
915092 TAAGAAAAAC
915102 AAAAAAAAGA
1 AAAAAAAAGA
915112 AAAAAAAAGA
1 AAAAAAAAGA
915122 AAAAA
1 AAAAA
915127 GATGGATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:915599 original size:1 final size:1
Alignment explanation
Indices: 915595--915697 Score: 62
Period size: 1 Copynumber: 103.0 Consensus size: 1
915585 AAAAGGAGAT
* * * * * * * * *
915595 AAAAAAAGAAAAAAGAAAAAAAGAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * * * *
915660 AGGAAAAAGAAAAAAGAAAAGAAAAAAAGAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
915698 GAAACGAAAT
Statistics
Matches: 72, Mismatches: 30, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (1 bp):
A
Found at i:915608 original size:7 final size:7
Alignment explanation
Indices: 915596--915701 Score: 142
Period size: 7 Copynumber: 14.4 Consensus size: 7
915586 AAAGGAGATA
915596 AAAAAAG
1 AAAAAAG
915603 AAAAAAG
1 AAAAAAG
915610 AAAAAAAGAG
1 --AAAAA-AG
915620 AAAAAAG
1 AAAAAAG
915627 AAAAAAG
1 AAAAAAG
915634 AAAAAAG
1 AAAAAAG
915641 AAAAAAG
1 AAAAAAG
915648 AAAAAAG
1 AAAAAAG
915655 AAAAAAG
1 AAAAAAG
*
915662 GAAAAAG
1 AAAAAAG
915669 AAAAAAG
1 AAAAAAG
915676 AAAAGAA-
1 AAAA-AAG
915683 AAAAAGAG
1 AAAAA-AG
915691 AAAAAAAG
1 -AAAAAAG
915699 AAA
1 AAA
915702 CGAAATTGAA
Statistics
Matches: 90, Mismatches: 2, Indels: 14
0.85 0.02 0.13
Matches are distributed among these distances:
6 1 0.01
7 68 0.76
8 9 0.10
9 10 0.11
10 2 0.02
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:918123 original size:52 final size:52
Alignment explanation
Indices: 918023--918126 Score: 154
Period size: 52 Copynumber: 2.0 Consensus size: 52
918013 GGCCCATTTT
* ** *
918023 AGACAGAAATGATCCATGTGAGGCATCTTGAAGGCTCACATTAGCATGAAAA
1 AGACAGAAATAATCCATGTGAGGCATCTTGAAGGCTCACACCAACATGAAAA
* *
918075 AGACAGAAGTAATCCATGTGGGGCATCTTGAAGGCTCACACCAACATGAAAA
1 AGACAGAAATAATCCATGTGAGGCATCTTGAAGGCTCACACCAACATGAAAA
918127 GGTTGGGATA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (52 bp):
AGACAGAAATAATCCATGTGAGGCATCTTGAAGGCTCACACCAACATGAAAA
Found at i:918164 original size:172 final size:171
Alignment explanation
Indices: 917863--918238 Score: 610
Period size: 172 Copynumber: 2.2 Consensus size: 171
917853 GGTCTATATT
917863 ATCCATGTGGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGAGGCA
1 ATCCATGTGGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGAGGCA
* *
917928 TCTTGAAGACTCACACCAACATGAAAAGGTTGGGATATTTTGAAAGTCCATTTCAAAAAGAAATA
66 TCTTGAAGACTCACACCAACATGAAAAGGTTGGGATATTTTAAAAATCCATTTCAAAAAGAAATA
*
917993 GAATGTTAG-GGCATTTTGAAGGCCCATTTTAGACAGAAATG
131 GAATGTT-GTGGCATTTTGAAGGCCCATTTCAGACAGAAATG
* *
918034 ATCCATGTGAGGCATCTTGAAGGCTCACATTAGCATGAAAAAGACAGAAGTAATCCATGTGGGGC
1 ATCCATGTG-GGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGAGGC
* * **
918099 ATCTTGAAGGCTCACACCAACATGAAAAGGTTGGGATATTTTAAAAATCTATTTCAACCAGAAAT
65 ATCTTGAAGACTCACACCAACATGAAAAGGTTGGGATATTTTAAAAATCCATTTCAAAAAGAAAT
918164 AGAATGTTGTGGCATTTTGAAGGCCCATTTCAGACAGAAATG
130 AGAATGTTGTGGCATTTTGAAGGCCCATTTCAGACAGAAATG
* * *
918206 ATCTATGTGGGGCATTTTGAAGGCTCATATCAG
1 ATCCATGT-GGGCATCTTGAAGGCTCACATCAG
918239 TAAGAAACAA
Statistics
Matches: 189, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
171 10 0.05
172 178 0.94
173 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (171 bp):
ATCCATGTGGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGAGGCA
TCTTGAAGACTCACACCAACATGAAAAGGTTGGGATATTTTAAAAATCCATTTCAAAAAGAAATA
GAATGTTGTGGCATTTTGAAGGCCCATTTCAGACAGAAATG
Found at i:918194 original size:41 final size:40
Alignment explanation
Indices: 918149--918238 Score: 94
Period size: 42 Copynumber: 2.2 Consensus size: 40
918139 TTAAAAATCT
*
918149 ATTTCA-ACCAGAAATAGA-ATGTTGTGGCATTTTGAAGGCCC
1 ATTTCAGA-CAGAAAT-GATATG-TGGGGCATTTTGAAGGCCC
*
918190 ATTTCAGACAGAAATGATCTATGTGGGGCATTTTGAAGGCTC
1 ATTTCAGACAGAAATGA--TATGTGGGGCATTTTGAAGGCCC
*
918232 ATATCAG
1 ATTTCAG
918239 TAAGAAACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
40 2 0.05
41 13 0.31
42 24 0.57
43 3 0.07
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (40 bp):
ATTTCAGACAGAAATGATATGTGGGGCATTTTGAAGGCCC
Found at i:918630 original size:54 final size:54
Alignment explanation
Indices: 918546--918654 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
918536 CACTGACAAG
* *
918546 AAATCTGGGCAGAAGCCACGGGAAAAGATGAATGTGTTGTCAAATGTTTTATGA
1 AAATCTGGGCAGAAGCCACAGGAAAAGATGAATGTGTTGCCAAATGTTTTATGA
* * *
918600 AAATCTGGGCAGAGGCTACAGGAAATGATGAATGTGTTGCCAAATGTTTTATGA
1 AAATCTGGGCAGAAGCCACAGGAAAAGATGAATGTGTTGCCAAATGTTTTATGA
918654 A
1 A
918655 CCATTGATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.27
Consensus pattern (54 bp):
AAATCTGGGCAGAAGCCACAGGAAAAGATGAATGTGTTGCCAAATGTTTTATGA
Found at i:919101 original size:22 final size:22
Alignment explanation
Indices: 919076--919128 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
919066 AACTTATCCC
* **
919076 TTTCTTTTTCTGTTATTGTTGA
1 TTTCTTCTTCTGTTATTACTGA
919098 TTTCTTCTTCTGTTATTACTGA
1 TTTCTTCTTCTGTTATTACTGA
919120 TTTCTTCTT
1 TTTCTTCTT
919129 ATACACCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.09, C:0.15, G:0.09, T:0.66
Consensus pattern (22 bp):
TTTCTTCTTCTGTTATTACTGA
Found at i:923737 original size:3 final size:3
Alignment explanation
Indices: 923729--923778 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
923719 AACTATTAAG
923729 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AA- ATAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
923772 AAT AAT A
1 AAT AAT A
923779 TTTATTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 5 0.12
3 37 0.86
4 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:924186 original size:22 final size:21
Alignment explanation
Indices: 924162--924203 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
924152 AAAAAGAAAA
924162 AAAAT-AAACCAAAAAATACCC
1 AAAATCAAACC-AAAAATACCC
924183 AAAATCGAAACCAAAAATACC
1 AAAATC-AAACCAAAAATACC
924204 TCCATAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.64, C:0.24, G:0.02, T:0.10
Consensus pattern (21 bp):
AAAATCAAACCAAAAATACCC
Found at i:924852 original size:8 final size:9
Alignment explanation
Indices: 924822--924851 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
924812 AATAACATAA
924822 AAAATAAAT
1 AAAATAAAT
924831 AAAATAAAT
1 AAAATAAAT
924840 AAAA-AAAT
1 AAAATAAAT
924848 AAAA
1 AAAA
924852 AGAAACTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAATAAAT
Found at i:924861 original size:23 final size:21
Alignment explanation
Indices: 924811--924864 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
924801 TTATTAGACC
*
924811 AAATAACAT-AAAAAATAAATA
1 AAATAA-ATAAAAAAATAAAAA
924832 AAATAAATAAAAAAATAAAAA
1 AAATAAATAAAAAAATAAAAA
924853 GAAACTAAATAA
1 -AAA-TAAATAA
924865 TAAACCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 17 0.59
22 3 0.10
23 7 0.24
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.17
Consensus pattern (21 bp):
AAATAAATAAAAAAATAAAAA
Found at i:924892 original size:12 final size:12
Alignment explanation
Indices: 924811--924905 Score: 52
Period size: 12 Copynumber: 7.7 Consensus size: 12
924801 TTATTAGACC
* *
924811 AAATAACATAAA
1 AAATAATATAAT
*
924823 AAATAAATAAAAT
1 AAAT-AATATAAT
* *
924836 AAATAAAAAAAT
1 AAATAATATAAT
*
924848 AAA-AAGA-AACT
1 AAATAATATAA-T
*
924859 AAATAATA-AACC
1 AAATAATATAA-T
924871 ATAATAATATAAT
1 A-AATAATATAAT
924884 AAATAATATATAT
1 AAATAATATA-AT
924897 AATATAATA
1 AA-ATAATA
924906 CTATAATATA
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
10 2 0.03
11 7 0.10
12 30 0.44
13 21 0.31
14 8 0.12
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (12 bp):
AAATAATATAAT
Found at i:924911 original size:26 final size:26
Alignment explanation
Indices: 924874--924929 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
924864 ATAAACCATA
924874 ATAATATAATAA-ATAATATATATA-AT
1 ATAATATAATAATAT-ATAT-TATACAT
924900 ATAATACT-ATAATATATATTATACAT
1 ATAATA-TAATAATATATATTATACAT
924926 ATAA
1 ATAA
924930 ATTTTTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
25 4 0.15
26 20 0.74
27 3 0.11
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (26 bp):
ATAATATAATAATATATATTATACAT
Found at i:924964 original size:28 final size:28
Alignment explanation
Indices: 924924--925050 Score: 139
Period size: 28 Copynumber: 4.3 Consensus size: 28
924914 TATATTATAC
* *
924924 ATATAAATTTTTTCAAAAACTATATATT
1 ATATATATGTTTTCAAAAACTATATATT
924952 ATATATATGTTTTCAAAAATTATATACTATATATT
1 ATATATATGTTTTC---AA--A-A-ACTATATATT
924987 ATATATATGTTTTCAAAAACTATATATT
1 ATATATATGTTTTCAAAAACTATATATT
* *
925015 ATATATACGTTTTCAAATA-TATATATAT
1 ATATATATGTTTTCAAAAACTATATAT-T
925043 ATATATAT
1 ATATATAT
925051 ATATATTAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
27 7 0.08
28 47 0.55
29 1 0.01
30 1 0.01
31 2 0.02
32 2 0.02
33 1 0.01
34 1 0.01
35 24 0.28
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.47
Consensus pattern (28 bp):
ATATATATGTTTTCAAAAACTATATATT
Found at i:924986 original size:35 final size:34
Alignment explanation
Indices: 924942--925056 Score: 145
Period size: 35 Copynumber: 3.5 Consensus size: 34
924932 TTTTTCAAAA
924942 ACTATATATTATATATATGTTTTCAAAAATTATAT
1 ACTATATATTATATATATGTTTTCAAAAA-TATAT
924977 ACTATATATTATATATATGTTTTC---AA-A-A-
1 ACTATATATTATATATATGTTTTCAAAAATATAT
* *
925005 ACTATATATTATATATACGTTTTCAAATATATAT
1 ACTATATATTATATATATGTTTTCAAAAATATAT
925039 A-TATATATATATATATAT
1 ACTATATAT-TATATATAT
925057 TAAATAGTAC
Statistics
Matches: 70, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
28 23 0.33
29 1 0.01
30 1 0.01
31 1 0.01
32 3 0.04
33 8 0.11
34 9 0.13
35 24 0.34
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (34 bp):
ACTATATATTATATATATGTTTTCAAAAATATAT
Found at i:924991 original size:63 final size:64
Alignment explanation
Indices: 924911--925055 Score: 215
Period size: 63 Copynumber: 2.3 Consensus size: 64
924901 TAATACTATA
* * *
924911 ATATATAT-TATACATATAAATTTTTTCAAAAACTATATATTATATATATGTTTTCAAAAAT-T
1 ATATATATATATATATATAAATGTTTTCAAAAACTATATATTATATATACGTTTTCAAAAATAT
* *
924973 ATATACTATATAT-TATATATATGTTTTCAAAAACTATATATTATATATACGTTTTCAAATATAT
1 ATATA-TATATATATATATAAATGTTTTCAAAAACTATATATTATATATACGTTTTCAAAAATAT
925037 ATATATATATATATATATA
1 ATATATATATATATATATA
925056 TTAAATAGTA
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
62 5 0.07
63 54 0.73
64 15 0.20
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (64 bp):
ATATATATATATATATATAAATGTTTTCAAAAACTATATATTATATATACGTTTTCAAAAATAT
Found at i:925036 original size:2 final size:2
Alignment explanation
Indices: 925031--925056 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
925021 ACGTTTTCAA
925031 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
925057 TAAATAGTAC
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:949934 original size:13 final size:13
Alignment explanation
Indices: 949918--949946 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
949908 TTTTTGTGTG
949918 TTTTTTTTCTTTA
1 TTTTTTTTCTTTA
949931 TTTTTTTTCTTTA
1 TTTTTTTTCTTTA
949944 TTT
1 TTT
949947 ACTTTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTCTTTA
Found at i:950943 original size:102 final size:102
Alignment explanation
Indices: 950762--950967 Score: 331
Period size: 102 Copynumber: 2.0 Consensus size: 102
950752 GTCACGGGAT
* * * *
950762 AACTCTACCTAACTAGCTCAGGGGTGGAATGTTTGCTCCCTTTCACTTAGAGTGTGGGATGTTAG
1 AACTCTACCTAACTAGCTCAGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGAGATGGTAG
* *
950827 TGTGATGAGCTGACTCCCCTTAAAGTATGCTTAAAAA
66 TGTGATAAGATGACTCCCCTTAAAGTATGCTTAAAAA
* * *
950864 AACTCTACTTCACTAGCTCGGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGAGATGGTAG
1 AACTCTACCTAACTAGCTCAGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGAGATGGTAG
950929 TGTGATAAGATGACTCCCCTTAAAGTATGCTTAAAAA
66 TGTGATAAGATGACTCCCCTTAAAGTATGCTTAAAAA
950966 AA
1 AA
950968 GAGTTGAAGT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 95 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (102 bp):
AACTCTACCTAACTAGCTCAGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGAGATGGTAG
TGTGATAAGATGACTCCCCTTAAAGTATGCTTAAAAA
Found at i:955337 original size:14 final size:14
Alignment explanation
Indices: 955318--955349 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
955308 GGAAATTAGC
*
955318 CTTAGCTTTACTCA
1 CTTAGCTTGACTCA
955332 CTTAGCTTGACTCA
1 CTTAGCTTGACTCA
955346 CTTA
1 CTTA
955350 CCCGTCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.28, G:0.09, T:0.41
Consensus pattern (14 bp):
CTTAGCTTGACTCA
Found at i:955757 original size:4 final size:4
Alignment explanation
Indices: 955748--955779 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
955738 GAAAAGAAAA
955748 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
955780 GGTGGGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:956057 original size:42 final size:42
Alignment explanation
Indices: 955974--956056 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 42
955964 ATAAAAATAT
*
955974 ATAAAACCCCAAAAAAAATAGCTAAATTAAAAAAAAGAAAAA
1 ATAAAAACCCAAAAAAAATAGCTAAATTAAAAAAAAGAAAAA
* *
956016 ATAAAAACCC-AAAAAATTAGCTAAATT-ATAAAAAGAAAAA
1 ATAAAAACCCAAAAAAAATAGCTAAATTAAAAAAAAGAAAAA
956056 A
1 A
956057 ACGATTATGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 13 0.34
41 16 0.42
42 9 0.24
ACGTcount: A:0.70, C:0.11, G:0.05, T:0.14
Consensus pattern (42 bp):
ATAAAAACCCAAAAAAAATAGCTAAATTAAAAAAAAGAAAAA
Found at i:957327 original size:20 final size:20
Alignment explanation
Indices: 957302--957351 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
957292 ATGTTGGACC
957302 AAATAACAT-AAAAAGAAAGA
1 AAATAA-ATAAAAAAGAAAGA
957322 AAATAAATAAAAAAGAAA-A
1 AAATAAATAAAAAAGAAAGA
957341 TAAAT-AATAAA
1 -AAATAAATAAA
957352 CCATAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (20 bp):
AAATAAATAAAAAAGAAAGA
Found at i:957338 original size:16 final size:16
Alignment explanation
Indices: 957317--957347 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
957307 ACATAAAAAG
957317 AAAGAAAATAAATAAA
1 AAAGAAAATAAATAAA
957333 AAAGAAAATAAATAA
1 AAAGAAAATAAATAA
957348 TAAACCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (16 bp):
AAAGAAAATAAATAAA
Found at i:957367 original size:2 final size:2
Alignment explanation
Indices: 957360--957419 Score: 53
Period size: 2 Copynumber: 33.0 Consensus size: 2
957350 AACCATAATA
957360 AT AT AT AT A- AT AT A- AT ACT AT A- AT AT AT A- AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
*
957398 AT AT -T AT AT AT A- AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
957420 TTTCAAAAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
1 7 0.15
2 39 0.81
3 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:957371 original size:22 final size:25
Alignment explanation
Indices: 957339--957398 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
957329 TAAAAAAGAA
*
957339 AATAAATAATAA-ACCATAATA-AT
1 AATATATAATAATACCATAATATAT
*
957362 -ATATATAATATAATACTATAATATAT
1 AATATAT-A-ATAATACCATAATATAT
957388 AATATATAATA
1 AATATATAATA
957399 TATTATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
22 5 0.17
23 1 0.03
24 4 0.13
25 11 0.37
26 3 0.10
27 6 0.20
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (25 bp):
AATATATAATAATACCATAATATAT
Found at i:957372 original size:7 final size:7
Alignment explanation
Indices: 957357--957414 Score: 82
Period size: 7 Copynumber: 8.1 Consensus size: 7
957347 ATAAACCATA
957357 ATAATAT
1 ATAATAT
957364 AT-ATAAT
1 ATAAT-AT
957371 ATAATACT
1 ATAATA-T
957379 ATAATAT
1 ATAATAT
957386 ATAATAT
1 ATAATAT
957393 ATAATAT
1 ATAATAT
*
957400 ATTATAT
1 ATAATAT
957407 ATAATAT
1 ATAATAT
957414 A
1 A
957415 CATATTTTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
6 2 0.04
7 35 0.76
8 9 0.20
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (7 bp):
ATAATAT
Found at i:957433 original size:28 final size:28
Alignment explanation
Indices: 957402--957455 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
957392 TATAATATAT
957402 TATATATAATATACATATTTTCAAAAAG
1 TATATATAATATACATATTTTCAAAAAG
* * *
957430 TATATATTATATATATGTTTTCAAAA
1 TATATATAATATACATATTTTCAAAA
957456 TGTTTTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (28 bp):
TATATATAATATACATATTTTCAAAAAG
Found at i:957445 original size:39 final size:39
Alignment explanation
Indices: 957390--957484 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
957380 TAATATATAA
* * *
957390 TATATAATATATTATATATAAT-ATACATATTTTCAAAAAG
1 TATATATTATA-TATATATAATCA-AAATATTTTCAAAAAC
* ** *
957430 TATATATTATATATATGTTTTCAAAATGTTTTCAAAAAC
1 TATATATTATATATATATAATCAAAATATTTTCAAAAAC
957469 TATATATTATATATAT
1 TATATATTATATATAT
957485 GTTTACAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
39 36 0.77
40 11 0.23
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.46
Consensus pattern (39 bp):
TATATATTATATATATATAATCAAAATATTTTCAAAAAC
Found at i:957485 original size:39 final size:39
Alignment explanation
Indices: 957419--957494 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
957409 AATATACATA
* *
957419 TTTTCAAAAAGTATATATTATATATATGTTTTCAAAATG
1 TTTTCAAAAACTATATATTATATATATGTTTACAAAATG
957458 TTTTCAAAAACTATATATTATATATATGTTTACAAAA
1 TTTTCAAAAACTATATATTATATATATGTTTACAAAA
957495 AAATTATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (39 bp):
TTTTCAAAAACTATATATTATATATATGTTTACAAAATG
Found at i:960162 original size:28 final size:30
Alignment explanation
Indices: 960088--960152 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
960078 CTTTCGATTG
* *
960088 TCTCTATTCTTCATCATTCGGCCATGGTCT
1 TCTCTCTTCTCCATCATTCGGCCATGGTCT
960118 TCTCTCTTCTCCATCATTCGGCCATGAG-CT
1 TCTCTCTTCTCCATCATTCGGCCATG-GTCT
960148 TCTCT
1 TCTCT
960153 TCTCCCTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.12, C:0.34, G:0.12, T:0.42
Consensus pattern (30 bp):
TCTCTCTTCTCCATCATTCGGCCATGGTCT
Found at i:960562 original size:20 final size:20
Alignment explanation
Indices: 960516--960562 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
960506 TGATTAAAAA
* * *
960516 TTATATGATTTACTTTTTGT
1 TTATATTATTTAATTTTTAT
960536 TTATATTATTTAATTTTTAT
1 TTATATTATTTAATTTTTAT
960556 TTATATT
1 TTATATT
960563 TATTGAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (20 bp):
TTATATTATTTAATTTTTAT
Done.