Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold158
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: 1811518
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 13
Found at i:569520 original size:20 final size:20
Alignment explanation
Indices: 569495--569573 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
569485 GTATCGATAC
569495 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
569515 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
569540 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
569560 CATGTATCGATACA
1 AATGTATCGATACA
569574 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:573441 original size:21 final size:21
Alignment explanation
Indices: 573412--573456 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
573402 AAGTTTTCAT
*
573412 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
573432 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
573454 TTT
1 TTT
573457 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:575688 original size:13 final size:13
Alignment explanation
Indices: 575670--575695 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
575660 CAATTTTTTG
575670 TGTATCGATACAT
1 TGTATCGATACAT
575683 TGTATCGATACAT
1 TGTATCGATACAT
575696 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:575755 original size:21 final size:21
Alignment explanation
Indices: 575731--575806 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
575721 CTACAAAGAA
575731 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
575752 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
575772 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
575793 ATGTATCGATACAT
1 ATGTATCGATACAT
575807 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:575776 original size:20 final size:20
Alignment explanation
Indices: 575751--575824 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
575741 ACATCTTTTT
575751 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
575771 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
575792 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
575812 CATGTATCGATAC
1 CATGTATCGATAC
575825 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:575788 original size:41 final size:41
Alignment explanation
Indices: 575731--575824 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
575721 CTACAAAGAA
575731 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
575772 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
575813 ATGTATCGATAC
1 ATGTATCGATAC
575825 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:576496 original size:3 final size:3
Alignment explanation
Indices: 576490--576524 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
576480 TTATTTATGT
576490 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
576525 GAAATCTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:576909 original size:24 final size:20
Alignment explanation
Indices: 576868--576909 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
576858 AAATTCAAAT
576868 ATAAATTATAAAATAATAAA
1 ATAAATTATAAAATAATAAA
* *
576888 ATAAA-TATATAATAATTAA
1 ATAAATTATAAAATAATAAA
576907 ATA
1 ATA
576910 CATCTTAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATTATAAAATAATAAA
Found at i:577014 original size:15 final size:14
Alignment explanation
Indices: 576996--577025 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
576986 TTATAAAAAA
576996 AAATTAATAAACTAT
1 AAATTAATAAA-TAT
577011 AAATTAATAAATAT
1 AAATTAATAAATAT
577025 A
1 A
577026 TATTTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATTAATAAATAT
Found at i:578270 original size:41 final size:41
Alignment explanation
Indices: 578156--578270 Score: 117
Period size: 41 Copynumber: 2.7 Consensus size: 41
578146 ATATTGAATA
* * *
578156 ATAAAATATATATTAAA-ATTTTAATCATTAAAATTAAATTTAT
1 ATAAAATAT-TTTTAAATATTTTAAT-AATAAAATT-AATTAAT
* * *
578199 ATTAAATATTATTAAAATATTTTAAAAATAAAATT-ATTAAT
1 ATAAAATATT-TTTAAATATTTTAATAATAAAATTAATTAAT
578240 ATAAAAATATTTTTAAATATTTTAATAATAA
1 AT-AAAATATTTTTAAATATTTTAATAATAA
578271 CGCCTATGGG
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
41 25 0.42
42 8 0.13
43 20 0.33
44 7 0.12
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (41 bp):
ATAAAATATTTTTAAATATTTTAATAATAAAATTAATTAAT
Found at i:579102 original size:15 final size:15
Alignment explanation
Indices: 579084--579113 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
579074 TTTATATAAA
579084 TTTTAATATTTTTAT
1 TTTTAATATTTTTAT
*
579099 TTTTTATATTTTTAT
1 TTTTAATATTTTTAT
579114 ATAATTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTAATATTTTTAT
Found at i:579112 original size:8 final size:8
Alignment explanation
Indices: 579065--579125 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
579055 GGGGTTTTGT
579065 TATTTTT-
1 TATTTTTA
579072 TATTTATATA
1 TATTT-T-TA
* *
579082 AATTTTAA
1 TATTTTTA
579090 TATTTTTA
1 TATTTTTA
579098 T-TTTTTA
1 TATTTTTA
579105 TATTTTTA
1 TATTTTTA
**
579113 TATAATTA
1 TATTTTTA
579121 TATTT
1 TATTT
579126 ATATTAAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
7 12 0.29
8 24 0.57
9 2 0.05
10 4 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TATTTTTA
Found at i:579226 original size:20 final size:18
Alignment explanation
Indices: 579188--579229 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
579178 TGACTCACAA
579188 ATAAAAAATAAAAAAATT
1 ATAAAAAATAAAAAAATT
*
579206 ATAAAAATTAATAATAAATT
1 ATAAAAAATAA-AA-AAATT
579226 ATAA
1 ATAA
579230 TATTATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 2 0.10
20 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAAAAATAAAAAAATT
Found at i:580028 original size:28 final size:25
Alignment explanation
Indices: 579949--580032 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 25
579939 TTTATTATAT
*
579949 TTATTATAATTATAAATATAATAAATA
1 TTATTATAA-T-TAAATATAAAAAATA
579976 TTATTATAATTAAATATAATAAAATA
1 TTATTATAATTAAATATAA-AAAATA
* *
580002 TTACTTTTAATATTAATAATAAAAAATA
1 TTA-TTATAAT-TAAAT-ATAAAAAATA
580030 TTA
1 TTA
580033 AAATTATTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
25 9 0.18
26 9 0.18
27 15 0.30
28 13 0.26
29 4 0.08
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (25 bp):
TTATTATAATTAAATATAAAAAATA
Found at i:580199 original size:12 final size:12
Alignment explanation
Indices: 580182--580207 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
580172 ATGGTCTATC
580182 TATTATGATAGG
1 TATTATGATAGG
580194 TATTATGATAGG
1 TATTATGATAGG
580206 TA
1 TA
580208 GTATTTGGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (12 bp):
TATTATGATAGG
Found at i:582008 original size:4 final size:4
Alignment explanation
Indices: 582001--582054 Score: 55
Period size: 4 Copynumber: 14.5 Consensus size: 4
581991 AATTTTAATT
*
582001 TTTA TTTA -TTA -TTA TTTTA TTTA TTTA -TTA -TTA ATTA -TTA TTTA
1 TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
582045 TTTA TTTA TT
1 TTTA TTTA TT
582055 CATCTGTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
3 15 0.33
4 28 0.61
5 3 0.07
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:582035 original size:36 final size:34
Alignment explanation
Indices: 581980--582046 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 34
581970 TTAAGGTTAG
*
581980 ATTTTTTTTTTAATTTTAATTTTTATTTATTATT
1 ATTTTTTTTTTAATTTTAATTATTATTTATTATT
582014 ATTTTATTTATTT-ATTATTAATTATTATTTATT
1 ATTTT-TTT-TTTAATT-TTAATTATTATTTATT
582047 TATTTATTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
35 6 0.21
36 18 0.62
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (34 bp):
ATTTTTTTTTTAATTTTAATTATTATTTATTATT
Found at i:582044 original size:25 final size:26
Alignment explanation
Indices: 581998--582054 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 26
581988 TTTAATTTTA
*
581998 ATTT-TTATTTATTATTATTTTATTT
1 ATTTATTATTAATTATTATTTTATTT
582023 ATTTATTATTAATTATTA-TTTATTT
1 ATTTATTATTAATTATTATTTTATTT
582048 ATTTATT
1 ATTTATT
582055 CATCTGTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 18 0.60
26 12 0.40
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (26 bp):
ATTTATTATTAATTATTATTTTATTT
Found at i:582192 original size:20 final size:19
Alignment explanation
Indices: 582156--582202 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
582146 AAACTCTAAC
*
582156 ATAAAATTTGATTTTTTGT
1 ATAAAATTTGATCTTTTGT
* *
582175 ATAATAATTTTATCTTTTTT
1 ATAA-AATTTGATCTTTTGT
582195 ATAAAATT
1 ATAAAATT
582203 AAAATAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (19 bp):
ATAAAATTTGATCTTTTGT
Found at i:583084 original size:15 final size:15
Alignment explanation
Indices: 583034--583084 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 15
583024 TTTAATATTT
583034 TAATTTTTT-A-AAA
1 TAATTTTTTAATAAA
*
583047 TAATTTATTAATAAA
1 TAATTTTTTAATAAA
* *
583062 TAATTTTTTTATTCAA
1 TAA-TTTTTTAATAAA
583078 TAATTTT
1 TAATTTT
583085 AAAAAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 8 0.26
14 1 0.03
15 10 0.32
16 12 0.39
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATTTTTTAATAAA
Found at i:583117 original size:11 final size:10
Alignment explanation
Indices: 583079--583125 Score: 67
Period size: 10 Copynumber: 4.6 Consensus size: 10
583069 TTTATTCAAT
583079 AATTTTAAAA
1 AATTTTAAAA
583089 AATTTTAAAA
1 AATTTTAAAA
583099 AATTTTAAAA
1 AATTTTAAAA
*
583109 AATCATTAAAA
1 AAT-TTTAAAA
*
583120 GATTTT
1 AATTTT
583126 TAGTAATGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
10 25 0.76
11 8 0.24
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (10 bp):
AATTTTAAAA
Found at i:586698 original size:20 final size:20
Alignment explanation
Indices: 586673--586711 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
586663 TTATGGCGTG
586673 AGGAGAGATGATTTGGAGTA
1 AGGAGAGATGATTTGGAGTA
586693 AGGAGAGATGATTTGGAGT
1 AGGAGAGATGATTTGGAGT
586712 TATGTGTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.41, T:0.26
Consensus pattern (20 bp):
AGGAGAGATGATTTGGAGTA
Found at i:587756 original size:10 final size:11
Alignment explanation
Indices: 587737--587765 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
587727 TTTTAAAGTA
587737 AAATATAATAT
1 AAATATAATAT
587748 AAA-ATAATAT
1 AAATATAATAT
587758 AAATATAA
1 AAATATAA
587766 AATGAAGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAATATAATAT
Found at i:587764 original size:16 final size:15
Alignment explanation
Indices: 587738--587768 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
587728 TTTAAAGTAA
587738 AATATAATATAAAAT
1 AATATAATATAAAAT
587753 AATATAAATATAAAAT
1 AATAT-AATATAAAAT
587769 GAAGACATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATATAATATAAAAT
Found at i:590687 original size:19 final size:19
Alignment explanation
Indices: 590663--590723 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
590653 TTATGTACGT
*
590663 ATATTTATTATATTATAAG
1 ATATTTATTATATTATAAA
590682 ATATTTATTAATATT-TAAA
1 ATATTTATT-ATATTATAAA
590701 ATA-TTA-TATATTTATAAA
1 ATATTTATTATA-TTATAAA
590719 ATATT
1 ATATT
590724 ATTTAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
16 3 0.08
17 3 0.08
18 10 0.27
19 16 0.43
20 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATATTTATTATATTATAAA
Found at i:590740 original size:18 final size:18
Alignment explanation
Indices: 590663--590745 Score: 63
Period size: 19 Copynumber: 4.8 Consensus size: 18
590653 TTATGTACGT
*
590663 ATATTTAT-TATATTATAAG
1 ATATTTATAT-TATT-TAAA
*
590682 ATATTTATTAATATTTAAA
1 ATATTTA-TATTATTTAAA
*
590701 ATA-TTATA-TATTTATA
1 ATATTTATATTATTTAAA
590717 A-A---ATATTATTTAAA
1 ATATTTATATTATTTAAA
590731 ATATTTATATTATTT
1 ATATTTATATTATTT
590746 TTATATTATA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
13 3 0.06
14 8 0.15
15 2 0.04
16 8 0.15
17 2 0.04
18 12 0.23
19 13 0.25
20 5 0.09
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (18 bp):
ATATTTATATTATTTAAA
Found at i:590744 original size:21 final size:21
Alignment explanation
Indices: 590720--590798 Score: 55
Period size: 21 Copynumber: 4.0 Consensus size: 21
590710 ATTTATAAAA
590720 TATTATTTAAAATATTTATAT
1 TATTATTTAAAATATTTATAT
590741 TATT-TTT---ATA-TTATA-
1 TATTATTTAAAATATTTATAT
* * * *
590756 TAATATTTTAATTATTTTTAAT
1 TATTATTTAAAATATTTAT-AT
*
590778 TA-TATTTAAAATAATTATAT
1 TATTATTTAAAATATTTATAT
590798 T
1 T
590799 TATTCAAACA
Statistics
Matches: 44, Mismatches: 7, Indels: 15
0.67 0.11 0.23
Matches are distributed among these distances:
15 3 0.07
16 8 0.18
17 3 0.07
19 2 0.05
20 9 0.20
21 17 0.39
22 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTATTTAAAATATTTATAT
Found at i:590755 original size:39 final size:37
Alignment explanation
Indices: 590663--590763 Score: 98
Period size: 39 Copynumber: 2.6 Consensus size: 37
590653 TTATGTACGT
*
590663 ATATTTATTATATTATAAGATATTTATTAATATTTAAA
1 ATATTT-TTATATTATAAAATATTTATTAATATTTAAA
* *
590701 ATA-TTATATATTTATAAAATA-TTATTTAAAATATTTATA
1 ATATTTTTATA-TTATAAAATATTTA-TT--AATATTTAAA
* *
590740 TTATTTTTATATTATATAATATTT
1 ATATTTTTATATTATAAAATATTT
590764 TAATTATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
36 7 0.14
37 13 0.25
38 3 0.06
39 20 0.39
40 8 0.16
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (37 bp):
ATATTTTTATATTATAAAATATTTATTAATATTTAAA
Found at i:590757 original size:18 final size:17
Alignment explanation
Indices: 590663--590764 Score: 55
Period size: 18 Copynumber: 5.4 Consensus size: 17
590653 TTATGTACGT
590663 ATATTTATTATA-TTATAA
1 ATATTT-TTATATTTAT-A
*
590681 GATATTTATTAATATTTAAA
1 -ATATTT-TT-ATATTTATA
*
590701 ATA-TTATATATTTATAAA
1 ATATTTTTATATTTAT--A
590719 ATATTATTTAAAATATTTATA
1 ATATT-TTT---ATATTTATA
*
590740 TTATTTTTATATTATATA
1 ATATTTTTATATT-TATA
590758 ATATTTT
1 ATATTTT
590765 AATTATTTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 21
0.71 0.06 0.22
Matches are distributed among these distances:
16 7 0.10
17 6 0.09
18 16 0.24
19 13 0.19
20 9 0.13
21 8 0.12
23 8 0.12
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (17 bp):
ATATTTTTATATTTATA
Found at i:590763 original size:36 final size:33
Alignment explanation
Indices: 590686--590772 Score: 83
Period size: 36 Copynumber: 2.7 Consensus size: 33
590676 TATAAGATAT
590686 TTAT-TAATATTTAAAATA-TTATATATTTATA
1 TTATATAATATTTAAAATATTTATATATTTATA
* *
590717 --AAATATTATTTAAAATATTTATATTATTTTTATA
1 TTATATAATATTTAAAATATTTATA-TA--TTTATA
* *
590751 TTATATAATATTTTAATTATTT
1 TTATATAATATTTAAAATATTT
590773 TTAATTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
29 1 0.02
30 13 0.30
31 5 0.12
32 2 0.05
34 6 0.14
36 16 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
TTATATAATATTTAAAATATTTATATATTTATA
Found at i:590769 original size:27 final size:29
Alignment explanation
Indices: 590719--590798 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
590709 TATTTATAAA
*
590719 ATATTATTTAAAATATTTATATTATTTTT
1 ATATTATATAAAATATTTATATTATTTTT
*
590748 ATATTATATAATAT-TTTA-ATTATTTTT
1 ATATTATATAAAATATTTATATTATTTTT
*
590775 A-ATTATATTTAAAATAATTATATT
1 ATATTATA--TAAAATATTTATATT
590799 TATTCAAACA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
26 6 0.14
27 10 0.23
28 9 0.21
29 15 0.35
30 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
ATATTATATAAAATATTTATATTATTTTT
Found at i:591351 original size:20 final size:20
Alignment explanation
Indices: 591326--591400 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
591316 TTTTACCCAG
*
591326 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCATCA
*
591346 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCATCA
591366 ATGTATCGATACATTCATCA
1 ATGTATCGATACATTCATCA
591386 ATGTATCGATACATT
1 ATGTATCGATACATT
591401 TTGTCTTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTCATCA
Found at i:602018 original size:21 final size:21
Alignment explanation
Indices: 601992--602068 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
601982 ATATTATCCA
601992 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
602013 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
602034 AATGTATCGATACA-TTATACA
1 AATGTATCGATACATTTGTA-G
602055 AATGTATCGATACA
1 AATGTATCGATACA
602069 AGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:602174 original size:20 final size:20
Alignment explanation
Indices: 602149--602203 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
602139 GCCAAGGAAA
*
602149 TGTATCGATACATTTTTCTG
1 TGTATCGATACATTTATCTG
** *
602169 TGTATCGATACATGGATCTT
1 TGTATCGATACATTTATCTG
602189 TGTATCGATACATTT
1 TGTATCGATACATTT
602204 GGGAATTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTTATCTG
Found at i:610817 original size:57 final size:57
Alignment explanation
Indices: 610729--611413 Score: 889
Period size: 57 Copynumber: 11.9 Consensus size: 57
610719 CGTTCATCTC
610729 TTCAAAGCCCACAAGTCAGTGGCA-CTCTTTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCT-TTTCAAAGCCCACAAGTTAGTGGCACTCTT
* * * *
610786 TTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAATCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCACTCTT
* * *
610843 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCACTCTT
* * *
610899 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAGCCCACAAGTTAGTGGCACTCTT
610956 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCAC-CTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAGCCCACAAGTTAGTGGCACTCTT
* * *
611013 TTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCATAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCACTCTT
* *
611070 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCA-TCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCACTCTT
* * * * *
611126 TTCAAAGCCCATAAGTCAGTAGCACTCTTTTCAAAGCCTACAAGTGAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAGCCCACAAGTTAGTGGCACTCTT
* * *
611183 TTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCATAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCACTCTT
* * * * * * *
611240 TTCAAAGCCTACAAGTCAGTGGCACCCTTTCAAAGCCCATAAGTCAATGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCACTCTT
* * * *
611296 TTCAAAGCTCACAAGTCAGTGGAACTCTTTTCAAAGCCCACAAGCTAGTGGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAGCCCACAAGTTAGTGG-CACTCTT
* *
611355 TTCAAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCTACATAAGTTAGTGGCAC
1 TTCAAAGCCCACA--AGTCAGTGGC-A-TCTTTTCAAAGCC--CACAAGTTAGTGGCAC
611414 ATTTTTTTTA
Statistics
Matches: 552, Mismatches: 61, Indels: 24
0.87 0.10 0.04
Matches are distributed among these distances:
56 129 0.23
57 370 0.67
58 3 0.01
59 14 0.03
61 8 0.01
62 15 0.03
63 2 0.00
64 11 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (57 bp):
TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCACTCTT
Found at i:610874 original size:85 final size:85
Alignment explanation
Indices: 610729--611413 Score: 910
Period size: 85 Copynumber: 8.0 Consensus size: 85
610719 CGTTCATCTC
*
610729 TTCAAAGCCCACAAGTCAGTGGCA-CTCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACCT-TTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAG
* *
610793 CCCACAAGTTAGTGGCA-TCCT
64 CCCACAAGTCAGTGGCACTCTT
* *
610814 TTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGC
* *
610879 CCACAAGTTAGTGGCA-TCCT
65 CCACAAGTCAGTGGCACTCTT
* *
610899 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGC
610964 CCACAAGTCAGTGGCACTCTT
65 CCACAAGTCAGTGGCACTCTT
* * *
610985 TTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
*
611050 CATAAGTCAGTGGCACTCTT
66 CACAAGTCAGTGGCACTCTT
* * *
611070 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
* *
611135 CATAAGTCAGTAGCACTCTT
66 CACAAGTCAGTGGCACTCTT
* * * * *
611155 TTCAAAGCCTACAAGTGAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
*
611220 CATAAGTCAGTGGCACTCTT
66 CACAAGTCAGTGGCACTCTT
* * * * * *
611240 TTCAAAGCCTACAAGTCAGTGGCACCCTTTCAAAGCCCATAAGTCAATGGCACCCTTTCAAAGCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
*
611305 CACAAGTCAGTGGAACTCTT
66 CACAAGTCAGTGGCACTCTT
* *
611325 TTCAAAGCCCACAAG-CTAGTGGTAACTCTTTTCAAAGCCCACACGAGTCGGTGGCAACTCTTTT
1 TTCAAAGCCCACAAGTC-AGTGG-CAC-CTTTTCAAAGCCCACA--AGTCAGTGGC-AC-CTTTT
* *
611389 CAAAGCCTACATAAGTTAGTGGCAC
59 CAAAGCC--CACAAGTCAGTGGCAC
611414 ATTTTTTTTA
Statistics
Matches: 549, Mismatches: 39, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
84 1 0.00
85 445 0.81
86 54 0.10
87 16 0.03
89 8 0.01
90 2 0.00
91 10 0.02
93 13 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (85 bp):
TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
CACAAGTCAGTGGCACTCTT
Found at i:610985 original size:142 final size:142
Alignment explanation
Indices: 610729--611413 Score: 930
Period size: 142 Copynumber: 4.8 Consensus size: 142
610719 CGTTCATCTC
*
610729 TTCAAAGCCCACAAGTCAGTGGCA-CTCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCATC-CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
* * *
610793 CCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAG
65 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAG
610858 TCAGTGGCACCCT
130 TCAGTGGCACCCT
*
610871 TTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
*
610936 CCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGT
66 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGT
* *
611001 TAGTGGCACCTT
131 CAGTGGCACCCT
* * *
611013 TTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCATAAGTCAGTGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
* *
611078 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCA-TCTTTTCAAAGCCCATAAGT
66 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGT
* *
611142 CAGTAGCACTCTT
131 CAGTGGCAC-CCT
* * * *
611155 TTCAAAGCCTACAAGTGAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCA-TCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
* * * * *
611219 CCATAAGTCAGTGGCACTCTTTTCAAAGCCTACAAGTCAGTGGCAC-CCTTTCAAAGCCCATAAG
66 CCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAG
*
611283 TCAATGGCACCCT
130 TCAGTGGCACCCT
* * * *
611296 TTCAAAGCTCACAAGTCAGTGGAACTCTTTTCAAAGCCCACAAG-CTAGTGGTAACTCTTTTCAA
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTC-AGTGG-CACTCTTTTCAA
* * * *
611360 AGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCTACATAAGTTAGTGGCAC
63 AGCCCACA--AGTCAGTGGC-AC-CCTTTCAAAGCC--CACAAGTCAGTGGCAC
611414 ATTTTTTTTA
Statistics
Matches: 488, Mismatches: 42, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
141 76 0.16
142 357 0.73
143 2 0.00
144 16 0.03
146 9 0.02
147 15 0.03
149 13 0.03
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (142 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGT
CAGTGGCACCCT
Found at i:613211 original size:16 final size:16
Alignment explanation
Indices: 613192--613231 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
613182 ATTAAATGAG
613192 TTCAAACACATGATTT
1 TTCAAACACATGATTT
*
613208 TTCAAAGACATGATTT
1 TTCAAACACATGATTT
613224 TTCAAACA
1 TTCAAACA
613232 AAAATGACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.35
Consensus pattern (16 bp):
TTCAAACACATGATTT
Found at i:615845 original size:19 final size:20
Alignment explanation
Indices: 615812--615859 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
615802 TATTATGTCA
615812 AAAATATTTAATTTTTTAATG
1 AAAAT-TTTAATTTTTTAATG
* *
615833 -AAATTTTATTTTTTTTATG
1 AAAATTTTAATTTTTTAATG
615852 AAAATTTT
1 AAAATTTT
615860 GTTAGAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
AAAATTTTAATTTTTTAATG
Found at i:617283 original size:24 final size:24
Alignment explanation
Indices: 617216--617283 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
617206 AAACATAAGT
* * *
617216 TGATCACCAAAATCAAACACATGA
1 TGATTACCAAAATCAAGCACATAA
* * *
617240 TGATTGCCAAAACCAGGCACA-AA
1 TGATTACCAAAATCAAGCACATAA
617263 CTGATTACCAAAATCAAGCAC
1 -TGATTACCAAAATCAAGCAC
617284 TTGCACATGA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
23 1 0.03
24 33 0.97
ACGTcount: A:0.46, C:0.26, G:0.12, T:0.16
Consensus pattern (24 bp):
TGATTACCAAAATCAAGCACATAA
Found at i:617568 original size:40 final size:40
Alignment explanation
Indices: 617513--617607 Score: 190
Period size: 40 Copynumber: 2.4 Consensus size: 40
617503 GGCCGGCTTA
617513 AAGAAAATTAAGCTTAGTTGTCCACCAAGTACCTATCTTT
1 AAGAAAATTAAGCTTAGTTGTCCACCAAGTACCTATCTTT
617553 AAGAAAATTAAGCTTAGTTGTCCACCAAGTACCTATCTTT
1 AAGAAAATTAAGCTTAGTTGTCCACCAAGTACCTATCTTT
617593 AAGAAAATTAAGCTT
1 AAGAAAATTAAGCTT
617608 TCAACCCATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.32
Consensus pattern (40 bp):
AAGAAAATTAAGCTTAGTTGTCCACCAAGTACCTATCTTT
Found at i:621898 original size:3 final size:3
Alignment explanation
Indices: 621883--621923 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
621873 AAAATTACAC
*
621883 TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
621924 AAGGTGTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:622374 original size:2 final size:2
Alignment explanation
Indices: 622367--622392 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
622357 GAGTGCAAAA
622367 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
622393 TAATTTATCA
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:622892 original size:117 final size:119
Alignment explanation
Indices: 622731--622957 Score: 370
Period size: 119 Copynumber: 1.9 Consensus size: 119
622721 ATTCATATTC
* * *
622731 CTTATAATTATTATTTATAATTAATAAAAAATTAAAAATTTTATG-AAA-ATATATATATATTAT
1 CTTATAATTACTAGTTATAATTAATAAAAAATTAAAAAATTTATGTAAATATATATATATATTAT
622794 AATTAAATTTAAATAAAATTTTTTAATTATTAAATATCATTTCAAATCCAACAA
66 AATTAAATTTAAATAAAATTTTTTAATTATTAAATATCATTTCAAATCCAACAA
* *
622848 CTTATAATTACT-GTTATAATTAATAAAAAATTAAAAAAATTTATGTAAATATTTATATATTTTA
1 CTTATAATTACTAGTTATAATTAATAAAAAATT-AAAAAATTTATGTAAATATATATATATATTA
*
622912 TAATTAAATTTAAATAATATTTTTTAATTATTAAATATCATTTCAA
65 TAATTAAATTTAAATAAAATTTTTTAATTATTAAATATCATTTCAA
622958 GCCCCGTTGA
Statistics
Matches: 101, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
116 19 0.19
117 22 0.22
118 3 0.03
119 57 0.56
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (119 bp):
CTTATAATTACTAGTTATAATTAATAAAAAATTAAAAAATTTATGTAAATATATATATATATTAT
AATTAAATTTAAATAAAATTTTTTAATTATTAAATATCATTTCAAATCCAACAA
Found at i:624044 original size:2 final size:2
Alignment explanation
Indices: 624037--624068 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
624027 GTGATAAAGA
624037 AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
624069 TGGAATTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:624856 original size:13 final size:15
Alignment explanation
Indices: 624827--624861 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
624817 AAAAAATAAC
624827 ATTAATAAAATATTT
1 ATTAATAAAATATTT
624842 ATTAATAAAAT-TTAT
1 ATTAATAAAATATT-T
624857 ATTAA
1 ATTAA
624862 CATATGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAATAAAATATTT
Found at i:625258 original size:147 final size:156
Alignment explanation
Indices: 625053--625349 Score: 373
Period size: 147 Copynumber: 1.9 Consensus size: 156
625043 GACTCTCACA
* * *
625053 TTAGTATGCAAAATGTAATTTATGAAAATAATGGTAGAAAATAGTAAAAGAAAAAAAAGG-T-TT
1 TTAGCATGCAAAATGTAATGTATGAAAATAATGGTAGAAAATAGAAAAAGAAAAAAAAGGATATT
*
625116 CTTTATCTTTTC-CTTT-CAT-GA-TTT-TTTT-T-TTGGGGGTTTAATTTGCCCTAAAAAGGCC
66 CTTTACCTTTTCTCTTTACATAGAGTTTATTTTGTGTTGGGGGTTTAATTTGCCCTAAAAAGGCC
625174 AAATTAAAAGAACCTTCACCTCCCAG
131 AAATTAAAAGAACCTTCACCTCCCAG
*
625200 TTAGCATGCAAAATGTAATGTATGAAAATAATGGTAGAAAA-ACGAAAATAG-TAAAAAAGGATA
1 TTAGCATGCAAAATGTAATGTATGAAAATAATGGTAGAAAATA-GAAAA-AGAAAAAAAAGGATA
* * * *
625263 TTCTTTACCTTTTCTTTTTGAGATAAGAGTTTTGAATTTTGTGTTTGGGGTTTAATTTGCCCTAT
64 TTCTTTACCTTTTCTCTTT-ACAT-AGAG-TTT--ATTTTGTGTTGGGGGTTTAATTTGCCCTAA
625328 AAAGGCCAAATTAAAAGAACCT
124 AAAGGCCAAATTAAAAGAACCT
625350 CCATTGGTGT
Statistics
Matches: 125, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
146 1 0.01
147 51 0.41
148 3 0.02
149 13 0.10
150 3 0.02
152 2 0.02
154 2 0.02
156 3 0.02
159 4 0.03
160 1 0.01
161 42 0.34
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.35
Consensus pattern (156 bp):
TTAGCATGCAAAATGTAATGTATGAAAATAATGGTAGAAAATAGAAAAAGAAAAAAAAGGATATT
CTTTACCTTTTCTCTTTACATAGAGTTTATTTTGTGTTGGGGGTTTAATTTGCCCTAAAAAGGCC
AAATTAAAAGAACCTTCACCTCCCAG
Found at i:630215 original size:30 final size:30
Alignment explanation
Indices: 630177--630247 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
630167 TTTTATATAA
*
630177 ATTA-TAAATTTTTAATT-TTATTAAATTAT
1 ATTATTAAATTTTT-ATTATTAATAAATTAT
630206 ATTATTAAATTTTTATTATTAATAAATTAT
1 ATTATTAAATTTTTATTATTAATAAATTAT
*
630236 GTTACTTAAATT
1 ATTA-TTAAATT
630248 GATTTTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 7 0.19
30 23 0.62
31 7 0.19
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (30 bp):
ATTATTAAATTTTTATTATTAATAAATTAT
Found at i:630219 original size:24 final size:24
Alignment explanation
Indices: 630147--630223 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
630137 ATATTTTAGG
* *
630147 TTATTAAATT-TAA-TGTGAATTT
1 TTATTAAATTATAATTTTAAATTT
*
630169 TTATATAAATTATAAATTTTTAA-TT
1 TTAT-TAAATTAT-AATTTTAAATTT
630194 TTATTAAATTAT-ATTATTAAATTT
1 TTATTAAATTATAATT-TTAAATTT
630218 TTATTA
1 TTATTA
630224 TTAATAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
22 7 0.15
23 10 0.22
24 17 0.37
25 8 0.17
26 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (24 bp):
TTATTAAATTATAATTTTAAATTT
Found at i:630224 original size:14 final size:13
Alignment explanation
Indices: 630194--630260 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 13
630184 ATTTTTAATT
630194 TTATTAAATTATA
1 TTATTAAATTATA
630207 TTATTAAATTTTTATTA
1 TTATTAAA---TTA-TA
* *
630224 TTAATAAATTATG
1 TTATTAAATTATA
*
630237 TTACTTAAATTGATT
1 TTA-TTAAATT-ATA
630252 TTATTAAAT
1 TTATTAAAT
630261 AATTATAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
13 12 0.27
14 15 0.34
15 5 0.11
16 3 0.07
17 9 0.20
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (13 bp):
TTATTAAATTATA
Found at i:630256 original size:31 final size:30
Alignment explanation
Indices: 630177--630267 Score: 82
Period size: 30 Copynumber: 3.0 Consensus size: 30
630167 TTTTATATAA
* *
630177 ATTA-TAAATTTTTAATT-TTATTAAATTAT
1 ATTATTAAATTATT-ATTATTAATAAATTAT
*
630206 ATTATTAAATTTTTATTATTAATAAATTAT
1 ATTATTAAATTATTATTATTAATAAATTAT
*
630236 GTTACTTAAATTGATT-TTATTAA-ATAATTAT
1 ATTA-TTAAATT-ATTATTATTAATA-AATTAT
630267 A
1 A
630268 ATAAAAAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
29 7 0.13
30 24 0.45
31 20 0.38
32 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (30 bp):
ATTATTAAATTATTATTATTAATAAATTAT
Found at i:631878 original size:21 final size:18
Alignment explanation
Indices: 631841--631880 Score: 53
Period size: 21 Copynumber: 2.1 Consensus size: 18
631831 TGTATGATAT
631841 TTAAATTTAAAATAAATA
1 TTAAATTTAAAATAAATA
631859 TTAAATATTATAATATAAATA
1 TTAAAT-TTA-AA-ATAAATA
631880 T
1 T
631881 ATTTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 3 0.16
20 2 0.11
21 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAATTTAAAATAAATA
Found at i:632705 original size:2 final size:2
Alignment explanation
Indices: 632698--632754 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
632688 ATAAATTGGC
632698 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
632740 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
632755 TTTATAATAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:632764 original size:10 final size:11
Alignment explanation
Indices: 632698--632766 Score: 59
Period size: 12 Copynumber: 6.0 Consensus size: 11
632688 ATAAATTGGC
*
632698 TATATATATATA
1 TATATATAT-TT
*
632710 TATATATATATA
1 TATATATAT-TT
*
632722 TATATATATATA
1 TATATATAT-TT
*
632734 TATATATATATA
1 TATATATAT-TT
632746 TATATATATTT
1 TATATATATTT
632757 TATA-ATATTT
1 TATATATATTT
632767 AAATTTGTAT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
10 6 0.11
11 5 0.09
12 45 0.80
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TATATATATTT
Found at i:633188 original size:2 final size:2
Alignment explanation
Indices: 633181--633219 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
633171 TGTTTGTGAA
633181 AT AT AT 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 AT AT AT A
633220 AAAGAGCTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:633894 original size:17 final size:17
Alignment explanation
Indices: 633872--633907 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
633862 TTTTTAATTT
*
633872 TTGTATTTATTACTATA
1 TTGTATTTATTACAATA
633889 TTGTATTTATTACAATA
1 TTGTATTTATTACAATA
633906 TT
1 TT
633908 AAATTTTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (17 bp):
TTGTATTTATTACAATA
Found at i:635434 original size:6 final size:6
Alignment explanation
Indices: 635423--635450 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
635413 TTCATATCCT
635423 CATTTG CATTTG CATTTG CATTTG CATT
1 CATTTG CATTTG CATTTG CATTTG CATT
635451 GAATCTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.50
Consensus pattern (6 bp):
CATTTG
Found at i:636669 original size:18 final size:18
Alignment explanation
Indices: 636646--636680 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
636636 AATCATATAA
636646 TTAT-AATTTGGATTTTTT
1 TTATAAATTT-GATTTTTT
636664 TTATAAATTTGATTTTT
1 TTATAAATTTGATTTTT
636681 ATGAAATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (18 bp):
TTATAAATTTGATTTTTT
Found at i:637263 original size:23 final size:25
Alignment explanation
Indices: 637227--637273 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
637217 TCATTAAACA
*
637227 TTTTATGTGAAATTTATGTAATTTT
1 TTTTATGTGAAATTGATGTAATTTT
637252 TTTTAT-TG-AATTGATGTAATTT
1 TTTTATGTGAAATTGATGTAATTT
637274 ATGACAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.62
24 2 0.10
25 6 0.29
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.60
Consensus pattern (25 bp):
TTTTATGTGAAATTGATGTAATTTT
Found at i:638163 original size:12 final size:11
Alignment explanation
Indices: 638143--638175 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
638133 TGTATGCAAG
638143 AAGAAAAAAAA
1 AAGAAAAAAAA
638154 AAGAAAAAAAA
1 AAGAAAAAAAA
638165 AAGAAATAAAA
1 AAGAAA-AAAA
638176 GGAAGAGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:638466 original size:24 final size:24
Alignment explanation
Indices: 638407--638454 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
638397 ACCTTATTGG
638407 TTAACAAATGCACATACGCTAGCT
1 TTAACAAATGCACATACGCTAGCT
638431 TTAACAAATGCACATACGCTAGCT
1 TTAACAAATGCACATACGCTAGCT
638455 GTTCACCCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (24 bp):
TTAACAAATGCACATACGCTAGCT
Found at i:642102 original size:20 final size:20
Alignment explanation
Indices: 642077--642122 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
642067 CATTTCTATT
642077 GATACACA-TGAAAATGCATC
1 GATACACATTG-AAATGCATC
* *
642097 GATACATATTGTAATGCATC
1 GATACACATTGAAATGCATC
642117 GATACA
1 GATACA
642123 TTATGTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.26
Consensus pattern (20 bp):
GATACACATTGAAATGCATC
Found at i:642223 original size:21 final size:21
Alignment explanation
Indices: 642190--642248 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
642180 TCATATATAG
* *
642190 GAATATATTGATACAATTCCA
1 GAATGTATCGATACAATTCCA
642211 GAATGTATCGATAC-A-TCCA
1 GAATGTATCGATACAATTCCA
*
642230 AAATTGTATCGATACAATT
1 GAA-TGTATCGATACAATT
642249 AGCCCAACGA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 6 0.19
20 12 0.38
21 13 0.41
22 1 0.03
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (21 bp):
GAATGTATCGATACAATTCCA
Found at i:642860 original size:13 final size:13
Alignment explanation
Indices: 642842--642866 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
642832 TTCAACGATT
642842 TGTATCGATACAA
1 TGTATCGATACAA
642855 TGTATCGATACA
1 TGTATCGATACA
642867 TTTTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:642947 original size:13 final size:13
Alignment explanation
Indices: 642929--642953 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
642919 ATTACTCAAA
642929 TGTATCGATACAT
1 TGTATCGATACAT
642942 TGTATCGATACA
1 TGTATCGATACA
642954 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:643018 original size:52 final size:52
Alignment explanation
Indices: 642962--643090 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
642952 CACTGATCTT
* * *
642962 TGTATCGATACATGCAGGCAAATTTGCTCAGATGTATTGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
643014 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
643066 TGTATCGATACATGAAGGTAAATTT
1 TGTATCGATACATGCAGGCAAATTT
643091 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:653505 original size:16 final size:16
Alignment explanation
Indices: 653484--653514 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
653474 TTTCATGATC
653484 TATGAAATTATGCTTT
1 TATGAAATTATGCTTT
*
653500 TATGAAATTGTGCTT
1 TATGAAATTATGCTT
653515 ATATTTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.48
Consensus pattern (16 bp):
TATGAAATTATGCTTT
Found at i:654194 original size:20 final size:21
Alignment explanation
Indices: 654171--654223 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
654161 TGCATATGAA
654171 AATGTATTGATACA-TAT-TG
1 AATGTATTGATACATTATGTG
*
654190 CAATGTATCGATACATTATGTG
1 -AATGTATTGATACATTATGTG
*
654212 AAAGTATTGATA
1 AATGTATTGATA
654224 TAAGTCATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 13 0.46
21 13 0.46
22 2 0.07
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (21 bp):
AATGTATTGATACATTATGTG
Found at i:654223 original size:21 final size:20
Alignment explanation
Indices: 654174--654223 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
654164 ATATGAAAAT
*
654174 GTATTGATACATATTGCAAT
1 GTATTGATACATATTGCAAA
*
654194 GTATCGATACATTATGTG-AAA
1 GTATTGATACA-TAT-TGCAAA
654215 GTATTGATA
1 GTATTGATA
654224 TAAGTCATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 10 0.40
21 13 0.52
22 2 0.08
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (20 bp):
GTATTGATACATATTGCAAA
Found at i:654298 original size:21 final size:21
Alignment explanation
Indices: 654250--654351 Score: 113
Period size: 21 Copynumber: 4.9 Consensus size: 21
654240 GCTACCCTTC
654250 GAATGTATCGATACACATAT--A
1 GAATGTATCGATACA-AT-TCCA
654271 GGAATGTATCGATACAATTCCA
1 -GAATGTATCGATACAATTCCA
654293 GAATGTATCGATACAATTCCA
1 GAATGTATCGATACAATTCCA
* *
654314 GAATTTATCGATAC-A-TCTA
1 GAATGTATCGATACAATTCCA
*
654333 GAATTGTATTGATACAATT
1 GAA-TGTATCGATACAATT
654352 AGCCCAACCA
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
19 6 0.08
20 11 0.15
21 37 0.52
22 17 0.24
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (21 bp):
GAATGTATCGATACAATTCCA
Found at i:654350 original size:41 final size:42
Alignment explanation
Indices: 654250--654351 Score: 113
Period size: 41 Copynumber: 2.4 Consensus size: 42
654240 GCTACCCTTC
654250 GAATGTATCGATACACATAT--AGGAATGTATCGATACAATTCCA
1 GAATGTATCGATACA-AT-TCCA-GAATGTATCGATACAATTCCA
* *
654293 GAATGTATCGATACAATTCCAGAATTTATCGATAC-A-TCTA
1 GAATGTATCGATACAATTCCAGAATGTATCGATACAATTCCA
*
654333 GAATTGTATTGATACAATT
1 GAA-TGTATCGATACAATT
654352 AGCCCAACCA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
40 6 0.11
41 16 0.30
42 15 0.28
43 16 0.30
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (42 bp):
GAATGTATCGATACAATTCCAGAATGTATCGATACAATTCCA
Found at i:658230 original size:52 final size:51
Alignment explanation
Indices: 658089--658237 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
658079 CGAAATATGA
*
658089 AAATTTGCCTGCATGTATCGATACATTGAATTGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
658141 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
658193 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
658238 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:658244 original size:13 final size:13
Alignment explanation
Indices: 658226--658250 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
658216 CAAAGATCAG
658226 TGTATCGATACAA
1 TGTATCGATACAA
658239 TGTATCGATACA
1 TGTATCGATACA
658251 TTTTTTGGCA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:658312 original size:13 final size:13
Alignment explanation
Indices: 658294--658318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
658284 AAAAAAAATA
658294 TGTATCGATACAT
1 TGTATCGATACAT
658307 TGTATCGATACA
1 TGTATCGATACA
658319 ATACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:659318 original size:43 final size:43
Alignment explanation
Indices: 659257--659442 Score: 192
Period size: 48 Copynumber: 4.1 Consensus size: 43
659247 TAAAGATGGA
659257 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * * *
659300 AAAGGTGCTAATGTGCTGATTCAAGGTCAGCTACATTGTACTTAAAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T---T
* * *
659347 ATGAAGGTGCCAATTTGCTGATTTAAGGCCAGCGATATTGGACTT
1 A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
659392 AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTT
1 --A---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
659440 AAA
1 AAA
659443 AGGAGACGCC
Statistics
Matches: 116, Mismatches: 18, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
43 38 0.33
44 1 0.01
45 1 0.01
46 1 0.01
47 3 0.03
48 39 0.34
49 33 0.28
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:659387 original size:92 final size:94
Alignment explanation
Indices: 659214--659434 Score: 293
Period size: 92 Copynumber: 2.3 Consensus size: 94
659204 AAAGGATGTC
659214 AATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTC
1 AATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG-AAAGGTGCCAATATGCTGATTC
*
659279 AAGGCCAGCTATATTGGACTTAAAGGTGCT
65 AAGGCCAGCGATATTGGACTTAAAGGTGCT
* * * * *
659309 AATGTGCTGATTCAAGGTCAGCTACATTGTACTTAAATAT-G-AAGGTGCCAATTTGCTGATTTA
1 AATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATATGCTGATTCA
*
659372 AGGCCAGCGATATTGGACTTAAAGGCAAGGTGCC
66 AGGCCAGCGATATTGGACTT--A---AAGGTGCT
* *
659406 AATATGCTGATTCAAGGCCAGCTATATTG
1 AATGTGCTGATTCAAGGCCAGCTACATTG
659435 GGCTTAAAAG
Statistics
Matches: 111, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
92 39 0.35
94 2 0.02
95 37 0.33
97 33 0.30
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (94 bp):
AATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATATGCTGATTCA
AGGCCAGCGATATTGGACTTAAAGGTGCT
Found at i:659533 original size:60 final size:59
Alignment explanation
Indices: 659486--660127 Score: 338
Period size: 57 Copynumber: 10.9 Consensus size: 59
659476 AGGTTTGCAT
* * *
659486 CACTGACTTGTGGGCTTTT-AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTAACTTGTGGGCTTTTAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGC
* *
659544 CACTAACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGC---TG-GAAGAGTGC
1 CACTAACTTGTGGGCTTTT-AAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGC
* * * * * * *
659600 TA-TAGAGTTGTGAGCTTTGGAAAA-GATGCCA-TCGACTTGTGGGC-TTCGAAAAAGGGTGC
1 CACTA-ACTTGTGGGCTTT-TAAAAGGGTGCCACT-AACTTGTGGGCTTTTG-AAAAGGGTGC
* * * * *
659659 CACTGATTTGTGGGC-TTT-GAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTAACTTGTGGGCTTTTAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGC
*** *
659716 CACTAACTTGTGGGCTTTTGAAAAATATGGCACTAACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTAACTTGTGGGCTTTT-AAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGC
** * * * * *
659776 CACTAACTTGTGGGC-TGAAAAAGAAAAAGAGTGCTA-TAGAGTTGTGAGCTTTGGAAAA-GATG
1 CACTAACTTGTGGGCTTTTAAAAG-----G-GTGCCACTA-ACTTGTGGGCTTTTGAAAAGGGTG
659838 C
59 C
** ** * * *
659839 CACCGACTTGTGGGCTTCGAAAAAGGGTGCCACTGATTTGTGGGC-TTTG--AAGGTTGC
1 CACTAACTTGTGGGCTT-TTAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGC
* *** **
659896 CACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTGAAAAAGAAAAATAGTGC
1 CACTAACTTGTGGGCTTTT-AAAAGGGTGCCACTAACTTGTGGGCT---TTTG-AAAAGGGTGC
* * * * * ** *
659960 TA-TAGAGTTGTGAGCTTTGGAAAA-GATGCCACCGACTTGTGGGC-TTCGAAAAAGGGTGC
1 CACTA-ACTTGTGGGCTTT-TAAAAGGGTGCCACTAACTTGTGGGCTTTTG-AAAAGGGTGC
* * * * * * ***
660019 CACTGATTTGTGGGC-TTT-GAAGGTTGCCACTGACTTATGGGCTTTTGAAAAAAAATGC
1 CACTAACTTGTGGGCTTTTAAAAGGGTGCCACTAACTTGTGGGCTTTTG-AAAAGGGTGC
* * *** * *
660077 CACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGACTTTTGAA
1 CACTAACTTGTGGGCTTTTAAAAGGGTGCCACTAACTTGTGGGCTTTTGAA
660128 GGGTGATGAA
Statistics
Matches: 448, Mismatches: 94, Indels: 83
0.72 0.15 0.13
Matches are distributed among these distances:
54 1 0.00
55 18 0.04
56 29 0.06
57 103 0.23
58 61 0.14
59 53 0.12
60 97 0.22
61 1 0.00
63 37 0.08
64 41 0.09
65 7 0.02
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.29
Consensus pattern (59 bp):
CACTAACTTGTGGGCTTTTAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGC
Found at i:659545 original size:30 final size:30
Alignment explanation
Indices: 659486--660127 Score: 454
Period size: 30 Copynumber: 21.7 Consensus size: 30
659476 AGGTTTGCAT
*
659486 CACTGACTTGTGGGCTTTT--AAAGGTTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
659514 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
*
659544 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
* * *
659574 CACTAACTTGTGGGC---TG-GAAGAGTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
* * * * *
659600 TA-TAGAGTTGTGAGCTTTGGAAAA-GATGC
1 CACT-GACTTGTGGGCTTTTGAAAAGGGTGC
*
659629 CA-TCGACTTGTGGGC-TTCGAAAAAGGGTGC
1 CACT-GACTTGTGGGCTTTTG-AAAAGGGTGC
* *
659659 CACTGATTTGTGGGC-TTTG--AAGGTTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
659686 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
* *** *
659716 CACTAACTTGTGGGCTTTTGAAAAATATGG
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
*
659746 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
* *** *
659776 CACTAACTTGTGGGCTGAAAAAGAAAAAGAGTGC
1 CACTGACTTGTGGGCT---TTTG-AAAAGGGTGC
* * * * *
659810 TA-TAGAGTTGTGAGCTTTGGAAAA-GATGC
1 CACT-GACTTGTGGGCTTTTGAAAAGGGTGC
* *
659839 CACCGACTTGTGGGC-TTCGAAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTG-AAAAGGGTGC
* *
659869 CACTGATTTGTGGGC-TTTG--AAGGTTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
659896 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
* *** **
659926 CACTAACTTGTGGGCTGAAAAAGAAAAATAGTGC
1 CACTGACTTGTGGGCT---TTTG-AAAAGGGTGC
* * * * *
659960 TA-TAGAGTTGTGAGCTTTGGAAAA-GATGC
1 CACT-GACTTGTGGGCTTTTGAAAAGGGTGC
* *
659989 CACCGACTTGTGGGC-TTCGAAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTG-AAAAGGGTGC
* *
660019 CACTGATTTGTGGGC-TTTG--AAGGTTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
* ***
660046 CACTGACTTATGGGCTTTTGAAAAAAAATGC
1 CACTGACTTGTGGGCTTTTG-AAAAGGGTGC
***
660077 CACTGACTTGTGGGC-TTTGAAAAATATGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
*
660106 CACTGACTTGTGGACTTTTGAA
1 CACTGACTTGTGGGCTTTTGAA
660128 GGGTGATGAA
Statistics
Matches: 487, Mismatches: 90, Indels: 72
0.75 0.14 0.11
Matches are distributed among these distances:
25 1 0.00
26 16 0.03
27 64 0.13
28 40 0.08
29 76 0.16
30 227 0.47
31 22 0.05
33 4 0.01
34 37 0.08
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.29
Consensus pattern (30 bp):
CACTGACTTGTGGGCTTTTGAAAAGGGTGC
Found at i:659875 original size:210 final size:202
Alignment explanation
Indices: 659462--659941 Score: 766
Period size: 210 Copynumber: 2.3 Consensus size: 202
659452 CACCAACTTG
* *
659462 TGTGGGCTTTTGAGAGGTTTGCATCACTGACTTGTGGGCTTTT--AAAGGTTGCCACTGACTTGT
1 TGTGGGC-TTTGA-AGG-TTGC--CACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGT
* *
659525 GGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
61 GGGCTTTTGAAAAAGATGCCACTAACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
*
659590 GGAAGAGTGCTATAGAGTTGTGAGCTTTGGAAAAGATGCCATCGACTTGTGGGCTTCGAAAAAGG
126 GGAAGAGTGCTATAGAGTTGTGAGCTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGAAAAAGG
659655 GTGCCACTGATT
191 GTGCCACTGATT
659667 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
* *
659732 TTTGAAAAATATGGCACTAACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTGAAAA
66 TTTGAAAAAGATGCCACTAACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTG----
659797 AGAAAAAGAGTGCTATAGAGTTGTGAGCTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGAAAA
127 -G---AAGAGTGCTATAGAGTTGTGAGCTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGAAAA
659862 AGGGTGCCACTGATT
188 AGGGTGCCACTGATT
659877 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
659942 GAAAAAGAAA
Statistics
Matches: 258, Mismatches: 7, Indels: 15
0.92 0.03 0.05
Matches are distributed among these distances:
200 19 0.07
202 84 0.33
203 3 0.01
204 5 0.02
205 7 0.03
207 1 0.00
210 139 0.54
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (202 bp):
TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
TTTGAAAAAGATGCCACTAACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTGGAAG
AGTGCTATAGAGTTGTGAGCTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGAAAAAGGGTGCC
ACTGATT
Found at i:659944 original size:150 final size:150
Alignment explanation
Indices: 659683--660092 Score: 642
Period size: 150 Copynumber: 2.7 Consensus size: 150
659673 CTTTGAAGGT
* * * * ** *
659683 TGCCACTGACTTGTGGGCTTTTG-AAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAATATGGC
1 TGCCACCGACTTGTGGGC-TTCGAAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGGT-TGCC
*
659747 ACTAACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTGAAAAAGAAAAAGAGTGCTA
62 ACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTGAAAAAGAAAAAGAGTGCTA
659812 TAGAGTTGTGAGCTTTGGAAAAGA
127 TAGAGTTGTGAGCTTTGGAAAAGA
659836 TGCCACCGACTTGTGGGCTTCGAAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTG
1 TGCCACCGACTTGTGGGCTTCGAAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTG
*
659901 ACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTGAAAAAGAAAAATAGTGCTATAGA
66 ACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTGAAAAAGAAAAAGAGTGCTATAGA
659966 GTTGTGAGCTTTGGAAAAGA
131 GTTGTGAGCTTTGGAAAAGA
659986 TGCCACCGACTTGTGGGCTTCGAAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTG
1 TGCCACCGACTTGTGGGCTTCGAAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTG
* *** *
660051 ACTTATGGGCTTTTGAAAAAAAATGCCACTGACTTGTGGGCT
66 ACTTGTGGGCTTTTG-AAAAGGGTGCCACTAACTTGTGGGCT
660093 TTGAAAAATA
Statistics
Matches: 241, Mismatches: 14, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
150 169 0.70
151 25 0.10
152 7 0.03
153 40 0.17
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.28
Consensus pattern (150 bp):
TGCCACCGACTTGTGGGCTTCGAAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTG
ACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTGAAAAAGAAAAAGAGTGCTATAGA
GTTGTGAGCTTTGGAAAAGA
Found at i:660109 original size:210 final size:207
Alignment explanation
Indices: 659462--660127 Score: 649
Period size: 210 Copynumber: 3.2 Consensus size: 207
659452 CACCAACTTG
* *
659462 TGTGGGCTTTTGAGAGGTTTGCATCACTGACTTGTGGGCTTTT--AAAGGTTGCCACTGACTTGT
1 TGTGGGC-TTTGA-AGG-TTGC--CACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGT
*** *** * * * * *
659525 GGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
61 GGGCTAAAGAAAAATATGGCACTAACTTGTGAGCTTTGGAAAAGGATGCCACCAACTTGTGGGCT
* * * *
659590 ---G--GAAGAGTGCTATAGAGTTGTGAGCTTTGGAAAAGATGCCATCGACTTGTGGGCTTCGAA
126 AAAGAAAAAGAGTGCCATAGAGTTGTGAGCTTTGGAAAAGATGCCACCGACTTATGGGCTTCGAA
***
659650 AAAGGGTGCCACTGATT
191 AAAAAATGCCACTGATT
659667 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
*** * * * *
659732 TTTGAAAAATATGGCACTAACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTGAAAA
66 AAAGAAAAATATGGCACTAACTTGTGAGCTTTGGAAAAGGATGCCACCAACTTGTGGGCT---AA
* *
659797 AGAAAAAGAGTGCTATAGAGTTGTGAGCTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGAAAA
128 AGAAAAAGAGTGCCATAGAGTTGTGAGCTTTGGAAAAGATGCCACCGACTTATGGGCTTCGAAAA
***
659862 AGGGTGCCACTGATT
193 AAAATGCCACTGATT
659877 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
* *
659942 GAAAAAGAAAAATA-GTGCTA-TAGAGTTGTGAGCTTTGGAAAA-GATGCCACCGACTTGTGGGC
66 ---AAAGAAAAATATG-GC-ACTA-ACTTGTGAGCTTTGGAAAAGGATGCCACCAACTTGTGGGC
** * * * * * * *
660004 T-TCGAAAAAGGGTGCCACT-GATTTGTGGGCTTT-G-AAGGTTGCCACTGACTTATGGGCTTTT
125 TAAAGAAAAAGAGTGCCA-TAGAGTTGTGAGCTTTGGAAAAGATGCCACCGACTTATGGGC-TTC
*
660065 GAAAAAAAATGCCACTGACT
188 GAAAAAAAATGCCACTGATT
** *
660085 TGTGGGCTTTGAAAAATATGCCACTGACTTGTGGACTTTTGAA
1 TGTGGGCTTTG-AAGGT-TGCCACTGACTTGTGGGCTTTTGAA
660128 GGGTGATGAA
Statistics
Matches: 406, Mismatches: 35, Indels: 35
0.85 0.07 0.07
Matches are distributed among these distances:
200 19 0.05
202 83 0.20
203 3 0.01
204 5 0.01
205 7 0.02
207 19 0.05
208 31 0.08
209 27 0.07
210 164 0.40
212 1 0.00
213 30 0.07
214 17 0.04
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.29
Consensus pattern (207 bp):
TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
AAAGAAAAATATGGCACTAACTTGTGAGCTTTGGAAAAGGATGCCACCAACTTGTGGGCTAAAGA
AAAAGAGTGCCATAGAGTTGTGAGCTTTGGAAAAGATGCCACCGACTTATGGGCTTCGAAAAAAA
ATGCCACTGATT
Found at i:661572 original size:1 final size:1
Alignment explanation
Indices: 661566--661691 Score: 117
Period size: 1 Copynumber: 126.0 Consensus size: 1
661556 TTCGGACCCC
* * * * * * * *
661566 TTTTTTTTGTTTTTGTTTGTTTTTGTTTTGTTTTTTTTTGTTTTTTTGTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * *
661631 TTGTTTTTTTGTTTTTTTGTTTTTTTTTGTTTTGTTTTTTTTTGTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
661692 GGAGGACGCC
Statistics
Matches: 95, Mismatches: 30, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 95 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (1 bp):
T
Found at i:661584 original size:10 final size:9
Alignment explanation
Indices: 661566--661691 Score: 143
Period size: 9 Copynumber: 13.8 Consensus size: 9
661556 TTCGGACCCC
661566 TTTTTTTTG
1 TTTTTTTTG
661575 TTTTTGTTTG
1 TTTTT-TTTG
661585 TTTTTGTTTTG
1 -TTTT-TTTTG
661596 TTTTTTTT-
1 TTTTTTTTG
661604 TGTTTTTTTG
1 T-TTTTTTTG
661614 TTTTTTTTG
1 TTTTTTTTG
*
661623 TTTTTTTTT
1 TTTTTTTTG
661632 TGTTTTTTTG
1 T-TTTTTTTG
661642 -TTTTTTTG
1 TTTTTTTTG
661650 TTTTTTTT-
1 TTTTTTTTG
* *
661658 TGTTTTGT-
1 TTTTTTTTG
661666 TTTTTTTTG
1 TTTTTTTTG
661675 TTTTTTTTTG
1 -TTTTTTTTG
661685 TTTTTTT
1 TTTTTTT
661692 GGAGGACGCC
Statistics
Matches: 102, Mismatches: 6, Indels: 18
0.81 0.05 0.14
Matches are distributed among these distances:
8 21 0.21
9 47 0.46
10 25 0.25
11 8 0.08
12 1 0.01
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:677365 original size:10 final size:10
Alignment explanation
Indices: 677350--677374 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
677340 ATAATCAAAT
677350 AAGTGGCATA
1 AAGTGGCATA
677360 AAGTGGCATA
1 AAGTGGCATA
677370 AAGTG
1 AAGTG
677375 CCATTATGGT
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:0.40, C:0.08, G:0.32, T:0.20
Consensus pattern (10 bp):
AAGTGGCATA
Found at i:679857 original size:97 final size:97
Alignment explanation
Indices: 679732--679972 Score: 340
Period size: 97 Copynumber: 2.5 Consensus size: 97
679722 ATTGAAAAAT
* * *
679732 GGGGTTGGAGTATCCATTTGGAGGAATGGGGTTGGAGTGTCCCTGATGATGATAATTTAAGTGAG
1 GGGGTTGGAGTATCCACTTGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAG
679797 AATAAAATTTAAACTTTGATGCATTTAAAAGC
66 AATAAAATTTAAACTTTGATGCATTTAAAAGC
* * *
679829 GGGGTTGGAGAATCCCCTTGGAGGAATGGGGTTGAAGTGTCCCCGATGATGACAATTTAAGTGAG
1 GGGGTTGGAGTATCCACTTGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAG
* **
679894 AATAAGATTTAAACTTTGATGTGTTTAAAAGC
66 AATAAAATTTAAACTTTGATGCATTTAAAAGC
* * * * *
679926 GGGGTTAGAGTAT-CTCTTCGGAGGAATAGGGTTGGAGTATTCCCGAT
1 GGGGTTGGAGTATCCACTT-GGAGGAATGGGGTTGGAGTGTCCCCGAT
679973 AAATAAAATT
Statistics
Matches: 127, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
96 4 0.03
97 123 0.97
ACGTcount: A:0.29, C:0.10, G:0.31, T:0.30
Consensus pattern (97 bp):
GGGGTTGGAGTATCCACTTGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAG
AATAAAATTTAAACTTTGATGCATTTAAAAGC
Found at i:682199 original size:20 final size:19
Alignment explanation
Indices: 682176--682250 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 19
682166 AAAAAGACAG
682176 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
*
682195 GAATGTATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
682216 CATATATCGATACATTGAA
1 AATGTATCGATACATTGAA
682235 ACATGTATCGATACAT
1 A-ATGTATCGATACAT
682251 CTAGGTAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:682284 original size:71 final size:71
Alignment explanation
Indices: 682196--682332 Score: 229
Period size: 71 Copynumber: 1.9 Consensus size: 71
682186 TACATTGAAG
*
682196 AATGTATCGATACATTCATACATATATCGATACATTGAAACATGTATCGATACATCTAGGTAAAA
1 AATGTATCGATACATTCATACATATATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAA
682261 AGACAA
66 AGACAA
* * **
682267 AATGTATCGATATATTCATACATGTATCGATTTATTGAAAAATGTATCGATACATCTAGGTAAAA
1 AATGTATCGATACATTCATACATATATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAA
682332 A
66 A
682333 TGTAACTTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (71 bp):
AATGTATCGATACATTCATACATATATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAA
AGACAA
Found at i:682293 original size:20 final size:20
Alignment explanation
Indices: 682265--682318 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
682255 GTAAAAAGAC
682265 AAAATGTATCGATATATTCA
1 AAAATGTATCGATATATTCA
* * * *
682285 TACATGTATCGATTTATTGA
1 AAAATGTATCGATATATTCA
682305 AAAATGTATCGATA
1 AAAATGTATCGATA
682319 CATCTAGGTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (20 bp):
AAAATGTATCGATATATTCA
Found at i:682315 original size:91 final size:89
Alignment explanation
Indices: 682148--682321 Score: 215
Period size: 91 Copynumber: 1.9 Consensus size: 89
682138 ACATTATTCA
* * *
682148 ATGTATCGATATCTGGGTAAAAAGACAGAATGTATCGATACATTGAAGAATGTATCGATACATTC
1 ATGTATCGATATCTAGGTAAAAAGACAAAATGTATCGATACATTCAAGAATGTATCGATACATTC
* *
682213 ATACATATATCGATACATTGAAAC
66 AAAAATATATCGATACATTGAAAC
* * **
682237 ATGTATCGATACATCTAGGTAAAAAGACAAAATGTATCGATATATTCATA-CATGTATCGATTTA
1 ATGTATCGAT--ATCTAGGTAAAAAGACAAAATGTATCGATACATTCA-AGAATGTATCGATACA
* *
682301 TTGAAAAATGTATCGATACAT
63 TTCAAAAATATATCGATACAT
682322 CTAGGTAAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
89 10 0.14
91 60 0.85
92 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (89 bp):
ATGTATCGATATCTAGGTAAAAAGACAAAATGTATCGATACATTCAAGAATGTATCGATACATTC
AAAAATATATCGATACATTGAAAC
Found at i:683080 original size:45 final size:47
Alignment explanation
Indices: 682981--683090 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 47
682971 CTAATGTGCC
* *
682981 AATTCAAGGCCATCGACATTGGGCTAAGGGAAAAATGGACCAATGTGCT
1 AATTCAAGGCCAACGACATTGGGCTAA--GAAAAATGGACCAATATGCT
* *
683030 GATTCAAGGCCAACGACATTGGGCT-A-ATAAATGTG-CCAATATGCT
1 AATTCAAGGCCAACGACATTGGGCTAAGAAAAATG-GACCAATATGCT
*
683075 AATTCAATGCCAACGA
1 AATTCAAGGCCAACGA
683091 TATTAGACTT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
45 29 0.54
46 1 0.02
48 1 0.02
49 23 0.43
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (47 bp):
AATTCAAGGCCAACGACATTGGGCTAAGAAAAATGGACCAATATGCT
Found at i:683245 original size:30 final size:30
Alignment explanation
Indices: 683171--683261 Score: 105
Period size: 32 Copynumber: 3.0 Consensus size: 30
683161 AAAAAAAAGA
* * *
683171 TGCCACTAACTTGTTTGGGCTTTGAAAAGAGT
1 TGCCACCAACTTGTGTGGGCTTT-AAAAG-GG
683203 TGCCACCAACTTGTGTGGGCTTTAAAAGGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGG
* *
683233 TGCCATCGAC-T-TGTGGGCTTTAAAAGGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGG
683261 T
1 T
683262 ATGCCACTGA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 18 0.33
29 1 0.02
30 9 0.17
31 5 0.09
32 21 0.39
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.31
Consensus pattern (30 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGGG
Found at i:683255 original size:28 final size:28
Alignment explanation
Indices: 683171--683673 Score: 453
Period size: 28 Copynumber: 17.7 Consensus size: 28
683161 AAAAAAAAGA
* *
683171 TGCCACTAACTTGTTTGGGCTTTGAAAAGAGT
1 TGCCACTGACTTG--TGGGCTTTG-AAAG-GG
** *
683203 TGCCACCAACTTGTGTGGGCTTTAAAAGGG
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGGG
*
683233 TGCCA-TCGACTTGTGGGCTTTAAAAGGG
1 TGCCACT-GACTTGTGGGCTTTGAAAGGG
*
683261 TATGCCACTGACTTGT-AGCTTTGAAAGGG
1 --TGCCACTGACTTGTGGGCTTTGAAAGGG
* * *
683290 TACAACTGACTTGTGGGCTTTGAAGGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGG
* * *
683318 TACCACTGTCTTGTGGGTTTTGAGAA-GG
1 TGCCACTGACTTGTGGGCTTTGA-AAGGG
* **
683346 TGCCACTGACTTATAAGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGG
* * *
683374 TGCCACTGATTTGTAGGCTTT-AGATGGG
1 TGCCACTGACTTGTGGGCTTTGA-AAGGG
*
683402 TGCCACTGACTTGTAGGCTTT-AGAAGGG
1 TGCCACTGACTTGTGGGCTTTGA-AAGGG
* * * *
683430 TGCCACTAATTTGTGGGCTTTGGAACGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGG
* *
683458 TGCCACTGATTTGTAGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGG
* *
683486 TACCACTGACTTGTGGACTTTGGAAA-GG
1 TGCCACTGACTTGTGGGCTTT-GAAAGGG
* * *
683514 TGCCACTGATTTATAGG-TTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGG
* *
683541 TACCACTGACTTGTGGGCTTTGGAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGG
* *
683569 TGCCACTGATTTGTGGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGG
* * *
683597 TGCCACTAACTTATGGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGG
* *
683625 TGCCACTAACTTGTGGGCTTTGGAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGG
* *
683653 ATGCCACTAACTTATGGGCTT
1 -TGCCACTGACTTGTGGGCTT
683674 ACCTAAATGA
Statistics
Matches: 395, Mismatches: 61, Indels: 33
0.81 0.12 0.07
Matches are distributed among these distances:
26 4 0.01
27 33 0.08
28 277 0.70
29 36 0.09
30 20 0.05
31 5 0.01
32 17 0.04
33 1 0.00
34 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGG
Found at i:684806 original size:15 final size:14
Alignment explanation
Indices: 684788--684880 Score: 52
Period size: 14 Copynumber: 6.6 Consensus size: 14
684778 TCTGGACCCT
684788 TTTTTTGTTTGTTTG
1 TTTTTTGTTT-TTTG
*
684803 TTTTTTTTTTTTTTG
1 -TTTTTTGTTTTTTG
* *
684818 CTTTTGGTTTTTCTG
1 TTTTTTGTTTTT-TG
684833 TTTTTT-TTGTTTT-
1 TTTTTTGTT-TTTTG
684846 TTTATTT-TTTTCTTG
1 TTT-TTTGTTTT-TTG
* *
684861 -GTTTT-TTTTTTA
1 TTTTTTGTTTTTTG
684873 TTTTTTGT
1 TTTTTTGT
684881 ACGAAGGACG
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
12 2 0.03
13 16 0.26
14 21 0.34
15 13 0.21
16 9 0.15
ACGTcount: A:0.02, C:0.03, G:0.12, T:0.83
Consensus pattern (14 bp):
TTTTTTGTTTTTTG
Found at i:684842 original size:39 final size:38
Alignment explanation
Indices: 684799--684880 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 38
684789 TTTTTGTTTG
684799 TTTGTTTTTTT-TTTTTTTGCTTTTGGTTTTTCTGTT-TTT
1 TTTGTTTTTTTATTTTTTT-C--TTGGTTTTTCTGTTATTT
* *
684838 TTTGTTTTTTTATTTTTTTCTTGGTTTTTTTTTTATTT
1 TTTGTTTTTTTATTTTTTTCTTGGTTTTTCTGTTATTT
684876 TTTGT
1 TTTGT
684881 ACGAAGGACG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
37 12 0.31
38 8 0.21
39 12 0.31
40 7 0.18
ACGTcount: A:0.02, C:0.04, G:0.11, T:0.83
Consensus pattern (38 bp):
TTTGTTTTTTTATTTTTTTCTTGGTTTTTCTGTTATTT
Found at i:696418 original size:97 final size:92
Alignment explanation
Indices: 696252--696445 Score: 255
Period size: 97 Copynumber: 2.1 Consensus size: 92
696242 TTTTTGATTG
* *
696252 AAAAATGGGGTTAGAGGATCCTCTCGGAGGAATGGGAGTGTCCCCGATGATGACAATTTAAGTGA
1 AAAAGTGGGGTTAGAGGATCCTCTCGGAGGAATGGGAGTGTCCCCGATGATGAAAATTTAAGTGA
696317 GAATAAAATTTAAACTTTGATGCT-TTT
66 GAATAAAATTTAAACTTTGATG-TGTTT
* * * *
696344 AAAAGTGGGGTTTGAGTATCTTCTCGGAGGAATAGGGTTGAAGTGTCCCTGATGATGAAAATTTA
1 AAAAGTGGGGTTAGAGGATCCTCTCGGAGGAAT--GG--G-AGTGTCCCCGATGATGAAAATTTA
* *
696409 AGTGGGAATAAGATTTAAACTTTGATGTGTTT
61 AGTGAGAATAAAATTTAAACTTTGATGTGTTT
696441 AAAAG
1 AAAAG
696446 CGGTTAGAGT
Statistics
Matches: 88, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
92 29 0.33
94 2 0.02
96 2 0.02
97 55 0.62
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.31
Consensus pattern (92 bp):
AAAAGTGGGGTTAGAGGATCCTCTCGGAGGAATGGGAGTGTCCCCGATGATGAAAATTTAAGTGA
GAATAAAATTTAAACTTTGATGTGTTT
Found at i:698725 original size:20 final size:20
Alignment explanation
Indices: 698692--698764 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
698682 GTAAAAAGAT
*
698692 AGAATGTATCGATACATTAA
1 AGAATATATCGATACATTAA
* *
698712 AGAATATATTGATACATTCAT
1 AGAATATATCGATACATT-AA
* *
698733 A-CATGTATCGATACATTAA
1 AGAATATATCGATACATTAA
* *
698752 AAAATGTATCGAT
1 AGAATATATCGAT
698765 GCATCTGGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 2 0.05
20 39 0.91
21 2 0.05
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (20 bp):
AGAATATATCGATACATTAA
Found at i:698811 original size:20 final size:20
Alignment explanation
Indices: 698782--698827 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
698772 GGTAAAAAGA
*
698782 CAAA-ATGTATCGATGCATT
1 CAAACATGTATCGATACATT
* *
698801 CATACATGTATTGATACATT
1 CAAACATGTATCGATACATT
698821 CAAACAT
1 CAAACAT
698828 TCAAAAATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (20 bp):
CAAACATGTATCGATACATT
Found at i:698813 original size:91 final size:89
Alignment explanation
Indices: 698646--698827 Score: 249
Period size: 91 Copynumber: 2.0 Consensus size: 89
698636 TTTTAACTAG
* * *
698646 ATGTATCGATACATTGAAATGTATCGATACATCTGGGTAAAAAGATAGAATGTATCGATACATTA
1 ATGTATCGATACATTAAAATGTATCGATACATCTGGGTAAAAAGACAAAATGTATCGATACATTA
*
698711 AAGAATATATTGATACATTCATAC
66 AAGAATATATTGATACATTCAAAC
* *
698735 ATGTATCGATACATTAAAAAATGTATCGATGCATCTGGGTAAAAAGACAAAATGTATCGATGCAT
1 ATGTATCGATACATT--AAAATGTATCGATACATCTGGGTAAAAAGACAAAATGTATCGATACAT
* * *
698800 TCATA-CATGTATTGATACATTCAAAC
64 T-AAAGAATATATTGATACATTCAAAC
698826 AT
1 AT
698828 TCAAAAATGT
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
89 15 0.19
91 64 0.79
92 2 0.02
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (89 bp):
ATGTATCGATACATTAAAATGTATCGATACATCTGGGTAAAAAGACAAAATGTATCGATACATTA
AAGAATATATTGATACATTCAAAC
Found at i:700233 original size:78 final size:78
Alignment explanation
Indices: 700151--700298 Score: 192
Period size: 78 Copynumber: 1.9 Consensus size: 78
700141 CCAGATGATG
**
700151 AAAAATTTAATATTTTAGAAACA-AAAACAAGGTTGGAGTATCCTTTC-AAAAATAACAAGGTTG
1 AAAAATTTAATATTTT-GAAA-ATAAAACAAGGTTGGAGTATCC-CCCAAAAAATAACAAGGTTG
*
700214 GAGTATCCTCAAGATA
63 AAGTATCCTCAAGATA
** * *
700230 AAAAATTTAATATTTTGAAAATAAAATGATGTTGGAGTATCCCCCAAAAAATAACAGGGTTGAAG
1 AAAAATTTAATATTTTGAAAATAAAACAAGGTTGGAGTATCCCCCAAAAAATAACAAGGTTGAAG
700295 TATC
66 TATC
700299 TACTTGAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
77 2 0.03
78 42 0.70
79 16 0.27
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.28
Consensus pattern (78 bp):
AAAAATTTAATATTTTGAAAATAAAACAAGGTTGGAGTATCCCCCAAAAAATAACAAGGTTGAAG
TATCCTCAAGATA
Found at i:700291 original size:28 final size:28
Alignment explanation
Indices: 700260--700329 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
700250 ATAAAATGAT
700260 GTTGGAGTATCCCCCAAAAAATAACAGG
1 GTTGGAGTATCCCCCAAAAAATAACAGG
* ** *** *
700288 GTTGAAGTATCTACTTGAAAATAATAGG
1 GTTGGAGTATCCCCCAAAAAATAACAGG
700316 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
700330 AAGATAAAAA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (28 bp):
GTTGGAGTATCCCCCAAAAAATAACAGG
Found at i:700291 original size:106 final size:107
Alignment explanation
Indices: 700176--700390 Score: 283
Period size: 106 Copynumber: 2.0 Consensus size: 107
700166 TAGAAACAAA
* * *
700176 AACAAGGTTGGAGTATCCT-TTCAAAAATAACAAGGTTGGAGTATCCTCAAGAT-AAAAAATTTA
1 AACAAGGTTGAAGTAT-CTATT-AAAAATAACAAGGTTGGAGTATCCCCAAGATAAAAAAAATTA
* *
700239 ATATTTTGAAAAT-AAAATGATGTTGGAGTATCCCCCAAAAAAT
64 ATATTTTGAAAATAAAAACGAGGTTGGAGTATCCCCCAAAAAAT
* * * *
700282 AACAGGGTTGAAGTATCTACTTGAAAATAATAGGGTTGGAGTATCCCCAAGATAAAAAAAATTAA
1 AACAAGGTTGAAGTATCTA-TTAAAAATAACAAGGTTGGAGTATCCCCAAGATAAAAAAAATTAA
**
700347 TATTTTGAAAATAAAAACGAGGTTGGAGTATCCCCTTAAAAAT
65 TATTTTGAAAATAAAAACGAGGTTGGAGTATCCCCCAAAAAAT
700390 A
1 A
700391 GCGAGGTTAG
Statistics
Matches: 94, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
105 2 0.02
106 41 0.44
107 24 0.26
108 27 0.29
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (107 bp):
AACAAGGTTGAAGTATCTATTAAAAATAACAAGGTTGGAGTATCCCCAAGATAAAAAAAATTAAT
ATTTTGAAAATAAAAACGAGGTTGGAGTATCCCCCAAAAAAT
Found at i:700874 original size:79 final size:79
Alignment explanation
Indices: 700305--700912 Score: 480
Period size: 79 Copynumber: 7.7 Consensus size: 79
700295 TATCTACTTG
* * ** * *
700305 AAAATAATAGGGTTGGAGTATCCC-CAAGATAAAAAAAATTAATATTTTGAAAATAAAAACGAGG
1 AAAATAACAGGGTTGGAGTA-CCCTCAAGAT-GAAAATTTTAATATTTTGAAAATAAAAATGGGG
* *
700369 TTGGAGTATCCCCTTA
64 TTAGAGTATCCCCTCA
* * ** ** *
700385 AAAATAGC-GAGGTTAGAGTA-CCTCCAAGATGAAGCTTTTAATATTTCAAAAATAAATATGGGG
1 AAAATAACAG-GGTTGGAGTACCCT-CAAGATGAAAATTTTAATATTTTGAAAATAAAAATGGGG
* * **
700448 TTGGAGTATCTCCTTG
64 TTAGAGTATCCCCTCA
* ** * * * * *
700464 GAAATAAGGGGGTTAGAGTATCCTCTAGATGAAAAATTTAATATTTTGAAAATAAGAAA-AGGGT
1 AAAATAACAGGGTTGGAGTACCCTCAAGATGAAAATTTTAATATTTTGAAAATAA-AAATGGGGT
* *
700528 TGGAGTATCCCCTAA
65 TAGAGTATCCCCTCA
* * * ** *
700543 AAAATAACAGGGTTGGAGTACCCTCGAGATAAAAATTTTAATATTTTAAAAATAAAAACAGAGTT
1 AAAATAACAGGGTTGGAGTACCCTCAAGATGAAAATTTTAATATTTTGAAAATAAAAATGGGGTT
* *
700608 TGAGTATCCCTTCA
66 AGAGTATCCCCTCA
* ** * * ** *
700622 AAAATAA-TGGGATTGGAACACCCTCGAGATGAAAATTTTAATATTTCGACGATAAAAATGAGGT
1 AAAATAACAGGG-TTGGAGTACCCTCAAGATGAAAATTTTAATATTTTGAAAATAAAAATGGGGT
*
700686 TAGAGTATCCCCTAA
65 TAGAGTATCCCCTCA
* * ** * ** *
700701 AAAATAA-TGGAATT-TTGTA-TCTCCAAGATGAAAATTTTAATATTTTGATGATGAAAATGGGG
1 AAAATAACAGG-GTTGGAGTACCCT-CAAGATGAAAATTTTAATATTTTGAAAATAAAAATGGGG
* * *
700763 TTAGAGTTTTCCCTCG
64 TTAGAGTATCCCCTCA
*
700779 AAAATAAC-GAGATTGGAGTACCCTCAAGATGAAAATTTTAATATTTTGAAAATAAAAATGGGGT
1 AAAATAACAG-GGTTGGAGTACCCTCAAGATGAAAATTTTAATATTTTGAAAATAAAAATGGGGT
* *
700843 TAGAGTATCCTCTCT
65 TAGAGTATCCCCTCA
* * * *
700858 GAATTAACAGGGTTGGAGTATCCCT-AATATGAAAAATTTAATATTTTGAAAATAA
1 AAAATAACAGGGTTGGAGTA-CCCTCAAGATGAAAATTTTAATATTTTGAAAATAA
700913 CAAGGTTGTA
Statistics
Matches: 425, Mismatches: 87, Indels: 33
0.78 0.16 0.06
Matches are distributed among these distances:
77 2 0.00
78 66 0.16
79 323 0.76
80 34 0.08
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (79 bp):
AAAATAACAGGGTTGGAGTACCCTCAAGATGAAAATTTTAATATTTTGAAAATAAAAATGGGGTT
AGAGTATCCCCTCA
Found at i:703391 original size:52 final size:51
Alignment explanation
Indices: 703313--703440 Score: 157
Period size: 52 Copynumber: 2.5 Consensus size: 51
703303 AATAGCCCGC
* * *
703313 ATGTATCGATACATTGAAGAATATATCCATACATTTAGGTCTAAAACTCAAA
1 ATGTATCGATACAATGAAAAATATATCCATACATTTAGGT-TAAAACCCAAA
* * * *
703365 ATGTATCAATACAATGAAAAATATATCGATATATTTAGGTTAAAACCCATA
1 ATGTATCGATACAATGAAAAATATATCCATACATTTAGGTTAAAACCCAAA
* * *
703416 ATGTATCGGTACGATAAAAAATATA
1 ATGTATCGATACAATGAAAAATATA
703441 ATGATGCATT
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
51 30 0.46
52 35 0.54
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (51 bp):
ATGTATCGATACAATGAAAAATATATCCATACATTTAGGTTAAAACCCAAA
Found at i:703533 original size:20 final size:21
Alignment explanation
Indices: 703508--703561 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
703498 CATTTTAGAC
*
703508 ATGTATCAATACATTCACT-T
1 ATGTATCGATACATTCACTAT
*
703528 ATGTATTGATACATTCACTAT
1 ATGTATCGATACATTCACTAT
*
703549 TTGTATCGATACA
1 ATGTATCGATACA
703562 AATTATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATTCACTAT
Found at i:704439 original size:62 final size:62
Alignment explanation
Indices: 704373--704814 Score: 494
Period size: 62 Copynumber: 7.2 Consensus size: 62
704363 TGTCATGCTT
* ** *
704373 TTTGAGGACTAAAAGATGCCAACGGCTTGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTC
1 TTTGAGGACTAAAAGGTGCCAACAACTCGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTC
** * * * *
704435 TTTGAGGACTAAAAAATG-CTACTAACTCTTGTGGGCTTTAAAAAGAAAAAGGTGCCCTATTC
1 TTTGAGGACTAAAAGGTGCCAAC-AACTCGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTC
* * * * * *
704497 TTTTAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAACGAAAAAGATGTCTTGCTC
1 TTTGAGGACTAAAAGGTGCCAACAACTCGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTC
* * * * *
704559 TTTGAAGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAAGAAAAAAGTGTCATGCTC
1 TTTGAGGACTAAAAGGTGCCAACAACTCGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTC
* * * * *
704620 TTTGAAGACTAAAATGTGCCAACAACTCATGTGGGCTTTAAAAAGAAAAAGATGTCCTACTT
1 TTTGAGGACTAAAAGGTGCCAACAACTCGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTC
* * * **
704682 TTTGAGGATTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCATCCTACTC
1 TTTGAGGACTAAAAGGTGCCAACAACTCGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTC
* * * * * ** *
704744 TTTGAGGACTAAAAGGTG-CATCAACTCGTGTGGGTTTTTAAAAGGAATAGGCATCCTTCTC
1 TTTGAGGACTAAAAGGTGCCAACAACTCGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTC
*
704805 TTTGAAGACT
1 TTTGAGGACT
704815 TTAAAAAGGA
Statistics
Matches: 324, Mismatches: 53, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
61 102 0.31
62 220 0.68
63 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (62 bp):
TTTGAGGACTAAAAGGTGCCAACAACTCGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTC
Found at i:704697 original size:185 final size:185
Alignment explanation
Indices: 704328--704787 Score: 548
Period size: 185 Copynumber: 2.5 Consensus size: 185
704318 AAGGGATGCT
* * * * *
704328 ACCAACTTGTGTGGACTTTGAAAAGGAAAAAAAAGTGTCATGCTTTTTGAGGACTAAAAGATGCC
1 ACCAACTTGTGTGGGCTTT-AAAAAG-AAAAAGA-TGTCATGCTCTTTGAGGACTAAAAGGTGCC
** * * * * *
704393 AACGGCTTGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTCTTTGAGGACTAAAAAATGCTACT
63 AACAACTCGTGTGGGCTTT-AAAAGAAAAAAGTGTCATACTCTTTGAAGACTAAAAAATGCAACT
* * *
704458 AACTCTTGTGGGCTTTAAAAAGAAAAAGGTGCCCTATTCTTTTAGGACTAAAAGGTGCC
127 AACTCATGTGGGCTTTAAAAAGAAAAAGATGCCCTATTCTTTGAGGACTAAAAGGTGCC
* * * * *
704517 ACCAACTCGTGTGGGCTTTAAAACGAAAAAGATGTCTTGCTCTTTGAAGACTAAAAGGTGCCACC
1 ACCAACTTGTGTGGGCTTTAAAAAGAAAAAGATGTCATGCTCTTTGAGGACTAAAAGGTGCCAAC
* **
704582 AACTCGTGTGGGCTTTAAAAGAAAAAAGTGTCATGCTCTTTGAAGACTAAAATGTGCCAAC-AAC
66 AACTCGTGTGGGCTTTAAAAGAAAAAAGTGTCATACTCTTTGAAGACTAAAAAATG-CAACTAAC
* *
704646 TCATGTGGGCTTTAAAAAGAAAAAGATGTCCTACTT-TTTGAGGATTAAAAGGTGCC
130 TCATGTGGGCTTTAAAAAGAAAAAGATGCCCTA-TTCTTTGAGGACTAAAAGGTGCC
*** * * *
704702 ACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAAGGTG-CATC
1 ACCAACTTGTGTGGGCTTTAAAAAGAAAAAGATGTCATGCTCTTTGAGGACTAAAAGGTGCCAAC
*
704766 AACTCGTGTGGGTTTTTAAAAG
66 AACTCGTGTGGG-CTTTAAAAG
704788 GAATAGGCAT
Statistics
Matches: 234, Mismatches: 34, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
184 15 0.06
185 145 0.62
186 46 0.20
187 6 0.03
188 5 0.02
189 17 0.07
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (185 bp):
ACCAACTTGTGTGGGCTTTAAAAAGAAAAAGATGTCATGCTCTTTGAGGACTAAAAGGTGCCAAC
AACTCGTGTGGGCTTTAAAAGAAAAAAGTGTCATACTCTTTGAAGACTAAAAAATGCAACTAACT
CATGTGGGCTTTAAAAAGAAAAAGATGCCCTATTCTTTGAGGACTAAAAGGTGCC
Found at i:704809 original size:123 final size:124
Alignment explanation
Indices: 704328--704814 Score: 503
Period size: 123 Copynumber: 3.9 Consensus size: 124
704318 AAGGGATGCT
* * * * * * *
704328 ACCAACTTGTGTGGACTTTGAAAAGGAAAAAAAAGTGTCATGCTTTTTGAGGACTAAAAGATGCC
1 ACCAACTTGTGTGGGCTTT-AAAA--AGAAAAAGGTGTCCTACTCTTTGAGGACTAAAAGGTGCC
** * * ** *
704393 AACGGCTTGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTCTTTGAGGACTAAAAAATGCT
63 AACAACTCGTGTGGGCTTTAAAAAGAAAAAGGTATCCTACTCTTTGAGGACTAAAAGGTGCC
* * * * *
704455 ACTAACTCT-TGTGGGCTTTAAAAAGAAAAAGGTGCCCTATTCTTTTAGGACTAAAAGGTGCCAC
1 ACCAACT-TGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTCTTTGAGGACTAAAAGGTGCCAA
* * * * * *
704519 CAACTCGTGTGGGCTTTAAAACGAAAAAGATGTCTTGCTCTTTGAAGACTAAAAGGTGCC
65 CAACTCGTGTGGGCTTTAAAAAGAAAAAGGTATCCTACTCTTTGAGGACTAAAAGGTGCC
* * * * * *
704579 ACCAACTCGTGTGGGCTTT-AAAAGAAAAAAGTGTCATGCTCTTTGAAGACTAAAATGTGCCAAC
1 ACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTCTTTGAGGACTAAAAGGTGCCAAC
* * * * *
704643 AACTCATGTGGGCTTTAAAAAGAAAAAGATGTCCTACTTTTTGAGGATTAAAAGGTGCC
66 AACTCGTGTGGGCTTTAAAAAGAAAAAGGTATCCTACTCTTTGAGGACTAAAAGGTGCC
** *
704702 ACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAAGGTG-CATC
1 ACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTCTTTGAGGACTAAAAGGTGCCAAC
* * * * * * *
704766 AACTCGTGTGGGTTTTTAAAAGGAATAGGCATCCTTCTCTTTGAAGACT
66 AACTCGTGTGGGCTTTAAAAAGAAAAAGGTATCCTACTCTTTGAGGACT
704815 TTAAAAAGGA
Statistics
Matches: 295, Mismatches: 62, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
123 146 0.49
124 129 0.44
126 4 0.01
127 15 0.05
128 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (124 bp):
ACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTCTTTGAGGACTAAAAGGTGCCAAC
AACTCGTGTGGGCTTTAAAAAGAAAAAGGTATCCTACTCTTTGAGGACTAAAAGGTGCC
Found at i:704824 original size:35 final size:35
Alignment explanation
Indices: 704783--704849 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
704773 GTGGGTTTTT
* *
704783 AAAAGGAATAGGCATCCTTCTCTTTGAAGACTTTA
1 AAAAGGAAAAGGCATCCTACTCTTTGAAGACTTTA
*
704818 AAAAGGAAAAGGTATCCTACTCTTTGAAGACT
1 AAAAGGAAAAGGCATCCTACTCTTTGAAGACT
704850 AAAAAGTGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.28
Consensus pattern (35 bp):
AAAAGGAAAAGGCATCCTACTCTTTGAAGACTTTA
Found at i:704828 original size:96 final size:97
Alignment explanation
Indices: 704717--704911 Score: 268
Period size: 97 Copynumber: 2.0 Consensus size: 97
704707 CTTGTGTGGG
* * *
704717 CTTTAAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAAGGTG-CA-TCAACTCGTGTGGGTT
1 CTTTAAAAAGAAAAAGGCATCCTACTCTTTGAAGACTAAAAAGTGCCACT-AACTCGTGTGGGCT
* *
704780 TTTAAAAGGAATAGGCATCCTTCTCTTTGAAGA
65 TTAAAAAGGAAAAGGCATCCTTCTCTTTGAAGA
* * *
704813 CTTTAAAAAGGAAAAGGTATCCTACTCTTTGAAGACTAAAAAGTGCCACTAACTTGTGTGGGCTT
1 CTTTAAAAAGAAAAAGGCATCCTACTCTTTGAAGACTAAAAAGTGCCACTAACTCGTGTGGGCTT
** *
704878 TAAAAAGGAAAAGGTGTCTTTCTCTTTGAAGA
66 TAAAAAGGAAAAGGCATCCTTCTCTTTGAAGA
704910 CT
1 CT
704912 AAATGGTGCC
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
96 41 0.48
97 44 0.51
98 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.30
Consensus pattern (97 bp):
CTTTAAAAAGAAAAAGGCATCCTACTCTTTGAAGACTAAAAAGTGCCACTAACTCGTGTGGGCTT
TAAAAAGGAAAAGGCATCCTTCTCTTTGAAGA
Found at i:704880 original size:62 final size:62
Alignment explanation
Indices: 704813--705013 Score: 269
Period size: 62 Copynumber: 3.2 Consensus size: 62
704803 TCTTTGAAGA
* * *
704813 CTTTAAAAAGGAAAAGGTATCCTACTCTTTGAAGACTAAAAAGTGCCACTAACTTGTGTGGG
1 CTTTAAAAAGGAAAAGGTGTCCTACTCTTTGAAGACTAAAAGGTGCCACCAACTTGTGTGGG
* * * *
704875 CTTTAAAAAGGAAAAGGTGTCTTTCTCTTTGAAGACTAAATGGTGCCACCAACTTGTATGGG
1 CTTTAAAAAGGAAAAGGTGTCCTACTCTTTGAAGACTAAAAGGTGCCACCAACTTGTGTGGG
* ** *
704937 CTTCAAAAAGGAAAAGACGTCCTGCTCTTT-AAGGACTAAAAGGTGCCACCAACTTGTGTGGG
1 CTTTAAAAAGGAAAAGGTGTCCTACTCTTTGAA-GACTAAAAGGTGCCACCAACTTGTGTGGG
* *
704999 CTTTTAAAAGAAAAA
1 CTTTAAAAAGGAAAA
705014 AAAGGATGCC
Statistics
Matches: 121, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
61 2 0.02
62 119 0.98
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (62 bp):
CTTTAAAAAGGAAAAGGTGTCCTACTCTTTGAAGACTAAAAGGTGCCACCAACTTGTGTGGG
Found at i:705089 original size:30 final size:30
Alignment explanation
Indices: 705017--705252 Score: 208
Period size: 30 Copynumber: 7.9 Consensus size: 30
705007 AGAAAAAAAA
* * *
705017 GGATGCCACTAAGTGATGGACTTTGATAA-
1 GGATGCCACTGAGTCATGGACTTTGAGAAG
* * *
705046 GGATGCCATTGAGTCATAGACTTTGAGATG
1 GGATGCCACTGAGTCATGGACTTTGAGAAG
* ** *
705076 GTATGCCACTGAGTTGTGGGCTTTGAGAAG
1 GGATGCCACTGAGTCATGGACTTTGAGAAG
*
705106 GGATACCACTGAGTCATGGACTTTG-GAATG
1 GGATGCCACTGAGTCATGGACTTTGAGAA-G
** * * *
705136 GGATGCCACTGAGTTGTGAATTTTGAGATG
1 GGATGCCACTGAGTCATGGACTTTGAGAAG
* * * *
705166 GGATGCCACTGAGTTATGAACTTTGAAAAA
1 GGATGCCACTGAGTCATGGACTTTGAGAAG
* *
705196 GGATGCCACTGAGTCGTAGACTTTGAGAA-
1 GGATGCCACTGAGTCATGGACTTTGAGAAG
* * * *
705225 GAATGCCACTAAATCGTGGACTTTGAGA
1 GGATGCCACTGAGTCATGGACTTTGAGA
705253 TAATTACTTT
Statistics
Matches: 166, Mismatches: 38, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
29 50 0.30
30 114 0.69
31 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (30 bp):
GGATGCCACTGAGTCATGGACTTTGAGAAG
Found at i:711689 original size:79 final size:79
Alignment explanation
Indices: 711588--712230 Score: 524
Period size: 79 Copynumber: 8.1 Consensus size: 79
711578 CTAAATACGG
* * * *
711588 GGTTGGAGTATCCCTGATGATAAAAATTTTAATATTTTGGAAATGAAAA-GAGGGTTGGAGTATC
1 GGTTGGAGTATCCCCGA-GATAAAAATTTTAATATTTCGAAAATAAAAATGAGGGTTGGAGTATC
* *
711652 CTCTAAAAAATAACCA
65 CCCTCAAAAATAA-CA
* * * *
711668 GGTTGGAGTATCCCCGAGATAAAAATTTTAATATTTTGAAAATAAAAATGA-AGTTAGAGTATCT
1 GGTTGGAGTATCCCCGAGATAAAAATTTTAATATTTCGAAAATAAAAATGAGGGTTGGAGTATCC
* *
711732 CTTTAAAAATAACA
66 CCTCAAAAATAACA
* * * *
711746 GGGTTGGAATATCCCCTAGATGAAAATTTTAATATTTCAAAAATAAAAATG-GGGTTGGAGTATC
1 -GGTTGGAGTATCCCCGAGATAAAAATTTTAATATTTCGAAAATAAAAATGAGGGTTGGAGTATC
* * *
711810 CCTTTAGAAATAACAA
65 CCCTCAAAAATAAC-A
* * * * *
711826 GGTT-GAGGTATTCTCGAGATAAAAAATTTAATATTT-TAGAAATAAAAA-CAGGGTTGGAGTAT
1 GGTTGGA-GTATCCCCGAGATAAAAATTTTAATATTTCGA-AAATAAAAATGAGGGTTGGAGTAT
* **
711888 CCCCTCAGAAATAATG
64 CCCCTCAAAAATAACA
* * *
711904 GGATTGGAGCA-CCCTCGAGATGAAAATTTTAGTATTTCGAAAATAAAAATGTA--GTTGGAGTA
1 GG-TTGGAGTATCCC-CGAGATAAAAATTTTAATATTTCGAAAATAAAAATG-AGGGTTGGAGTA
*
711966 TCCCCTTAAAAATAACA
63 TCCCCTCAAAAATAACA
* * * * *
711983 GGGTTGAAGTATCCTCGAGATGAAAATTTTAATCTTTCGAAAATAAAAATG-GGGTTGGATTATC
1 -GGTTGGAGTATCCCCGAGATAAAAATTTTAATATTTCGAAAATAAAAATGAGGGTTGGAGTATC
* **
712047 TCCTCGGAAATAACAA
65 CCCTCAAAAATAAC-A
* * * * * *
712063 GGTTGAAGTA-CCCTTGAGACAAAAA-TTTAATATTTCAAAAATAAGAAT-AGGGTTAGAGTATC
1 GGTTGGAGTATCCC-CGAGATAAAAATTTTAATATTTCGAAAATAAAAATGAGGGTTGGAGTATC
**
712125 CCCTCAAAAATAATGG
65 CCCTCAAAAATAA-CA
* * * * * * * *
712141 GGTAGGAGTATCCTCAAGATGAAAAA-TTTAATATTTTGAAACTTAAAACGA-GGTTAGAGTATC
1 GGTTGGAGTATCCCCGAGAT-AAAAATTTTAATATTTCGAAAATAAAAATGAGGGTTGGAGTATC
* *
712204 ACCTCGAAAATAACA
65 CCCTCAAAAATAACA
*
712219 GAGTTAGAGTAT
1 G-GTTGGAGTAT
712231 TTTTAAGAAA
Statistics
Matches: 454, Mismatches: 84, Indels: 51
0.77 0.14 0.09
Matches are distributed among these distances:
78 63 0.14
79 362 0.80
80 28 0.06
81 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.29
Consensus pattern (79 bp):
GGTTGGAGTATCCCCGAGATAAAAATTTTAATATTTCGAAAATAAAAATGAGGGTTGGAGTATCC
CCTCAAAAATAACA
Found at i:712028 original size:237 final size:236
Alignment explanation
Indices: 711588--712219 Score: 743
Period size: 237 Copynumber: 2.7 Consensus size: 236
711578 CTAAATACGG
* * * * *
711588 GGTTGGAGTATCCCT-GATGATAAAAATTTTAATATTTTGGAAATGAAAAGAGGGTTGGAGTATC
1 GGTTGAAGTA-CCCTCGA-GATAAAAAATTTAATATTTTAGAAATAAAAACAGGGTTGGAGTATC
* * ** *
711652 CTCTAAAAAATAACCAGGTTGGAGTATCCC-CGAGATAAAAATTTTAATATTTTGAAAATAAAAA
64 CCCTCAAAAATAA-TGGGTTGGAGTA-CCCTCGAGATGAAAATTTTAATATTTTGAAAATAAAAA
* * *
711716 TGAAGTTAGAGTATCTCTTTAAAAATAACAGGGTTGGAATATCCCCTAGATGAAAATTTTAATAT
127 TGAAGTTAGAGTATCCCCTTAAAAATAACAGGGTTGGAATATCCCCGAGATGAAAATTTTAATAT
*
711781 TTCAAAAATAAAAATGGGGTTGGAGTATC-CCTTTAGAAATAACAA
192 TTCAAAAATAAAAATGGGGTTGGAGTATCTCC-TCAGAAATAACAA
* **
711826 GGTTGAGGTATTCTCGAGATAAAAAATTTAATATTTTAGAAATAAAAACAGGGTTGGAGTATCCC
1 GGTTGAAGTACCCTCGAGATAAAAAATTTAATATTTTAGAAATAAAAACAGGGTTGGAGTATCCC
* * * * *
711891 CTCAGAAATAATGGGATTGGAGCACCCTCGAGATGAAAATTTTAGTATTTCGAAAATAAAAATGT
66 CTCAAAAATAATGGG-TTGGAGTACCCTCGAGATGAAAATTTTAATATTTTGAAAATAAAAATGA
* * *
711956 AGTTGGAGTATCCCCTTAAAAATAACAGGGTT-GAAGTATCCTCGAGATGAAAATTTTAATCTTT
130 AGTTAGAGTATCCCCTTAAAAATAACAGGGTTGGAA-TATCCCCGAGATGAAAATTTTAATATTT
* * *
712020 CGAAAATAAAAATGGGGTTGGATTATCTCCTCGGAAATAACAA
194 CAAAAATAAAAATGGGGTTGGAGTATCTCCTCAGAAATAACAA
* * * * * * *
712063 GGTTGAAGTACCCTTGAGA-CAAAAATTTAATATTTCAAAAATAAGAATAGGGTTAGAGTATCCC
1 GGTTGAAGTACCCTCGAGATAAAAAATTTAATATTTTAGAAATAAAAACAGGGTTGGAGTATCCC
* * * * * * *
712127 CTCAAAAATAATGGGGTAGGAGTATCCTCAAGATGAAAAATTTAATATTTTGAAACTTAAAACGA
66 CTCAAAAATAAT-GGGTTGGAGTACCCTCGAGATGAAAATTTTAATATTTTGAAAATAAAAATGA
* * **
712192 GGTTAGAGTATCACCTCGAAAATAACAG
130 AGTTAGAGTATCCCCTTAAAAATAACAG
712220 AGTTAGAGTA
Statistics
Matches: 333, Mismatches: 55, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
236 119 0.36
237 202 0.61
238 12 0.04
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (236 bp):
GGTTGAAGTACCCTCGAGATAAAAAATTTAATATTTTAGAAATAAAAACAGGGTTGGAGTATCCC
CTCAAAAATAATGGGTTGGAGTACCCTCGAGATGAAAATTTTAATATTTTGAAAATAAAAATGAA
GTTAGAGTATCCCCTTAAAAATAACAGGGTTGGAATATCCCCGAGATGAAAATTTTAATATTTCA
AAAATAAAAATGGGGTTGGAGTATCTCCTCAGAAATAACAA
Found at i:712317 original size:51 final size:52
Alignment explanation
Indices: 712245--712354 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 52
712235 AAGAAAAAAA
*
712245 TTAATA-TTTCAAAATTAAAAAC-AGGATTGGAGTATCCTCGAGATGAAAATT
1 TTAATATTTTCAAAATTAAAAACAAGG-TTGGAGGATCCTCGAGATGAAAATT
* * *
712296 TTAATATTTTGAAAA-TAAAAACAAGGTTGGAGGATCCTTGTGATGAAAATT
1 TTAATATTTTCAAAATTAAAAACAAGGTTGGAGGATCCTCGAGATGAAAATT
*
712347 TTGATATT
1 TTAATATT
712355 ATAGAAGTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
51 42 0.81
52 10 0.19
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (52 bp):
TTAATATTTTCAAAATTAAAAACAAGGTTGGAGGATCCTCGAGATGAAAATT
Found at i:716155 original size:10 final size:10
Alignment explanation
Indices: 716128--716163 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
716118 GATGTCTGGA
*
716128 ATATATAAAC
1 ATATATATAC
716138 ATATATATAC
1 ATATATATAC
*
716148 ATATATATAT
1 ATATATATAC
716158 ATATAT
1 ATATAT
716164 GTATATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATATAC
Found at i:717477 original size:13 final size:13
Alignment explanation
Indices: 717459--717483 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
717449 CATAAAATGT
717459 TGTATCGATACAA
1 TGTATCGATACAA
717472 TGTATCGATACA
1 TGTATCGATACA
717484 TATTTTCATG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:717481 original size:33 final size:33
Alignment explanation
Indices: 717439--717508 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
717429 TTCAACGATT
**
717439 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATCATGTATCGATACAA
***
717472 TGTATCGATACATATTTTCATGTATCGATACAA
1 TGTATCGATACATAAAATCATGTATCGATACAA
717505 TGTA
1 TGTA
717509 AGCTACTGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (33 bp):
TGTATCGATACATAAAATCATGTATCGATACAA
Found at i:717567 original size:13 final size:13
Alignment explanation
Indices: 717549--717573 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
717539 ATTACTCACA
717549 TGTATCGATACAT
1 TGTATCGATACAT
717562 TGTATCGATACA
1 TGTATCGATACA
717574 CTAATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:717638 original size:52 final size:52
Alignment explanation
Indices: 717582--717706 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
717572 CACTAATCTT
*
717582 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
717634 TGTATCGATACATGCAGGCAAATTTGTCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
717686 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
717707 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:721778 original size:13 final size:13
Alignment explanation
Indices: 721760--721785 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
721750 TACAGCAAGT
721760 ATGTATCGATACA
1 ATGTATCGATACA
721773 ATGTATCGATACA
1 ATGTATCGATACA
721786 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Done.