Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 204 of 292
Found at i:60622613 original size:23 final size:23
Alignment explanation
Indices: 60622587--60622652 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
60622577 ATTATTACAC
60622587 ATTAAGATATTTTTATGTAACAA
1 ATTAAGATATTTTTATGTAACAA
*
60622610 ATTAA-A-A-TTTCAT-T-ACAA
1 ATTAAGATATTTTTATGTAACAA
60622628 ATTAAGATATTTTTATG-ATACAA
1 ATTAAGATATTTTTATGTA-ACAA
60622651 AT
1 AT
60622653 ACATACTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
18 9 0.26
19 2 0.06
20 6 0.17
21 6 0.17
22 1 0.03
23 11 0.31
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (23 bp):
ATTAAGATATTTTTATGTAACAA
Found at i:60635584 original size:6 final size:6
Alignment explanation
Indices: 60635573--60635604 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
60635563 TAATTATTAG
*
60635573 TTTTAT TTTTAT TTTAAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
60635605 CTCTCTGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:60635594 original size:12 final size:12
Alignment explanation
Indices: 60635563--60635604 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
60635553 TTTTAAAATA
*
60635563 TAATTATTAGTTT
1 TAATTTTTA-TTT
60635576 T-ATTTTTATTT
1 TAATTTTTATTT
60635587 TAATTTTTATTT
1 TAATTTTTATTT
*
60635599 TTATTT
1 TAATTT
60635605 CTCTCTGGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 4 0.15
12 21 0.81
13 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (12 bp):
TAATTTTTATTT
Found at i:60639548 original size:12 final size:12
Alignment explanation
Indices: 60639533--60639562 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
60639523 CGATTTTAAA
60639533 AAATTTTTTACT
1 AAATTTTTTACT
*
60639545 AAATATTTTACT
1 AAATTTTTTACT
60639557 AAATTT
1 AAATTT
60639563 ATGATTTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (12 bp):
AAATTTTTTACT
Found at i:60641368 original size:38 final size:38
Alignment explanation
Indices: 60641312--60641408 Score: 106
Period size: 38 Copynumber: 2.6 Consensus size: 38
60641302 TTATCAATTG
* * * * *
60641312 CATGTTCAGCATGCCTACTGTTACTGTTGAACCGATTA
1 CATGTTAAGCATGTCTACTGTTACTATTAAACCGAATA
* **
60641350 CATGTTAAGCATGTCTACTGCTACTATTAAATTGAATA
1 CATGTTAAGCATGTCTACTGTTACTATTAAACCGAATA
*
60641388 CAT-TTAAGCATGTCTATTGTT
1 CATGTTAAGCATGTCTACTGTT
60641409 TTTACATGAT
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
37 16 0.33
38 33 0.67
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (38 bp):
CATGTTAAGCATGTCTACTGTTACTATTAAACCGAATA
Found at i:60645063 original size:13 final size:13
Alignment explanation
Indices: 60645047--60645074 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
60645037 CCGATAAATT
60645047 TACTTTTAATTTA
1 TACTTTTAATTTA
60645060 TACTTTTAATTTA
1 TACTTTTAATTTA
60645073 TA
1 TA
60645075 GGCACAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (13 bp):
TACTTTTAATTTA
Found at i:60652947 original size:15 final size:15
Alignment explanation
Indices: 60652927--60652956 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
60652917 TATTTTTTCC
60652927 TTTACCTTTTCATAT
1 TTTACCTTTTCATAT
*
60652942 TTTACCTTTTTATAT
1 TTTACCTTTTCATAT
60652957 ATTATATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTACCTTTTCATAT
Found at i:60654252 original size:17 final size:17
Alignment explanation
Indices: 60654225--60654264 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
60654215 AAAAATATTT
*
60654225 TTTTATAAT--TTTGTA
1 TTTTATAATCATTTTTA
60654240 TTTT-TAATCATTTTTA
1 TTTTATAATCATTTTTA
60654256 TTTTATAAT
1 TTTTATAAT
60654265 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 4 0.19
15 4 0.19
16 9 0.43
17 4 0.19
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTATAATCATTTTTA
Found at i:60654266 original size:14 final size:15
Alignment explanation
Indices: 60654224--60654269 Score: 58
Period size: 14 Copynumber: 3.0 Consensus size: 15
60654214 AAAAAATATT
60654224 TTTTTATAATTTTGTA
1 TTTTTATAATTTT-TA
*
60654240 TTTTTAATCATTTTTA
1 TTTTT-ATAATTTTTA
60654256 -TTTTATAATTTTTA
1 TTTTTATAATTTTTA
60654270 AAAAAAGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 9 0.33
15 4 0.15
16 7 0.26
17 7 0.26
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTTTATAATTTTTA
Found at i:60655567 original size:13 final size:13
Alignment explanation
Indices: 60655549--60655577 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
60655539 AATATATTAT
60655549 AATACTTATAATA
1 AATACTTATAATA
60655562 AATACTTATAATA
1 AATACTTATAATA
60655575 AAT
1 AAT
60655578 TTTTTTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (13 bp):
AATACTTATAATA
Found at i:60655639 original size:24 final size:23
Alignment explanation
Indices: 60655612--60655686 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 23
60655602 TTTAGGATTC
60655612 AAATAATATTTTTATTACTTTATA
1 AAATAATATTTTTATTA-TTTATA
* * *
60655636 AAATACACA-ATTTATTTTTTATA
1 AAATA-ATATTTTTATTATTTATA
* *
60655659 ATATAAT-TTTTTAGTATTTATA
1 AAATAATATTTTTATTATTTATA
*
60655681 ATATAA
1 AAATAA
60655687 GAAGTTTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
22 18 0.44
23 10 0.24
24 11 0.27
25 2 0.05
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (23 bp):
AAATAATATTTTTATTATTTATA
Found at i:60658000 original size:14 final size:14
Alignment explanation
Indices: 60657981--60658009 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
60657971 TGAAAGATAA
60657981 ATTTTATTAAAACT
1 ATTTTATTAAAACT
60657995 ATTTTATTAAAACT
1 ATTTTATTAAAACT
60658009 A
1 A
60658010 AGTAAATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTTATTAAAACT
Found at i:60658731 original size:13 final size:15
Alignment explanation
Indices: 60658703--60658734 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
60658693 TATTAAATAT
60658703 TTTTTTATTATGTAA
1 TTTTTTATTATGTAA
60658718 TTTTTT-TTAT-TAA
1 TTTTTTATTATGTAA
60658731 TTTT
1 TTTT
60658735 GCATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 4 0.24
15 6 0.35
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTTTTATTATGTAA
Found at i:60664084 original size:59 final size:59
Alignment explanation
Indices: 60663933--60664073 Score: 185
Period size: 60 Copynumber: 2.4 Consensus size: 59
60663923 TTTTCAGAAA
*
60663933 ATAAAGGATATATTGATCATTTAAGCGTTTTAATATATTTGGATATTTTTATAAAAAAATT
1 ATAAAGG-TATATTGATCATTTAA-CCTTTTAATATATTTGGATATTTTTATAAAAAAATT
** ** **
60663994 ATTTATTTATATTGATCATTTAAGCCTTTTAATATATTTGGATATTTTTATAAAAAGTTT
1 ATAAAGGTATATTGATCATTTAA-CCTTTTAATATATTTGGATATTTTTATAAAAAAATT
60664054 A-AAAGGTATATTGATCATTT
1 ATAAAGGTATATTGATCATTT
60664074 CATTCTTTTA
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
59 15 0.22
60 51 0.74
61 3 0.04
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.48
Consensus pattern (59 bp):
ATAAAGGTATATTGATCATTTAACCTTTTAATATATTTGGATATTTTTATAAAAAAATT
Found at i:60670881 original size:23 final size:24
Alignment explanation
Indices: 60670855--60670899 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
60670845 CACAAAAATA
60670855 CAAACTAATAT-TATTTTAATATC
1 CAAACTAATATATATTTTAATATC
* * *
60670878 CAAATTTATCTATATTTTAATA
1 CAAACTAATATATATTTTAATA
60670900 AAATATTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (24 bp):
CAAACTAATATATATTTTAATATC
Found at i:60670912 original size:24 final size:23
Alignment explanation
Indices: 60670881--60670926 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
60670871 TAATATCCAA
60670881 ATTTATCTATAT-TTTAATAAAAT
1 ATTTATCTATATATTTAA-AAAAT
*
60670904 ATTTAATCTTTATATTTAAAAAA
1 ATTT-ATCTATATATTTAAAAAA
60670927 GTTAAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 11 0.55
25 5 0.25
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTTATCTATATATTTAAAAAAT
Found at i:60673666 original size:13 final size:14
Alignment explanation
Indices: 60673648--60673676 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
60673638 GGGTTTCAGG
60673648 TTTTATTTTT-TAT
1 TTTTATTTTTGTAT
60673661 TTTTATTTTTGTAT
1 TTTTATTTTTGTAT
60673675 TT
1 TT
60673677 GCTTAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTATTTTTGTAT
Found at i:60676556 original size:18 final size:18
Alignment explanation
Indices: 60676528--60676591 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
60676518 TAATAAACTA
60676528 TTAAT-ATAAATTATTAT
1 TTAATAATAAATTATTAT
60676545 TTAATAATAAATGT-TTAT
1 TTAATAATAAAT-TATTAT
* *
60676563 TAAAATAATAATTTA-TA-
1 T-TAATAATAAATTATTAT
60676580 TTAATAATAAAT
1 TTAATAATAAAT
60676592 ATTTTGTAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
16 9 0.23
17 6 0.15
18 14 0.36
19 10 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATAATAAATTATTAT
Found at i:60676588 original size:19 final size:20
Alignment explanation
Indices: 60676546--60676589 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
60676536 AATTATTATT
60676546 TAATAATAAATGTTTATTAA
1 TAATAATAAATGTTTATTAA
60676566 -AATAAT-AAT-TTATATTAA
1 TAATAATAAATGTT-TATTAA
60676584 TAATAA
1 TAATAA
60676590 ATATTTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.09
18 9 0.41
19 11 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
TAATAATAAATGTTTATTAA
Found at i:60677058 original size:2 final size:2
Alignment explanation
Indices: 60677051--60677087 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
60677041 ATGTACTCTC
60677051 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 A
60677088 ATAATGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60677153 original size:18 final size:19
Alignment explanation
Indices: 60677130--60677176 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
60677120 AAATATTTTC
60677130 TTAATTATAAAA-TAAATT
1 TTAATTATAAAAGTAAATT
*
60677148 TTAATTGTTAAAAGTAAATT
1 TTAATT-ATAAAAGTAAATT
*
60677168 GT-ATTATAA
1 TTAATTATAA
60677177 GATTTTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 9 0.38
19 8 0.33
20 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (19 bp):
TTAATTATAAAAGTAAATT
Found at i:60682433 original size:22 final size:22
Alignment explanation
Indices: 60682403--60682458 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
60682393 AATTATTCTG
60682403 TAATATTTAAATTTAGAA-AAATT
1 TAAT-TTTAAATTTA-AATAAATT
*
60682426 TAATTTTAATTTTAAATAAATT
1 TAATTTTAAATTTAAATAAATT
* *
60682448 AAATTTAAAAT
1 TAATTTTAAAT
60682459 GATACGAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.07
22 22 0.79
23 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TAATTTTAAATTTAAATAAATT
Found at i:60682757 original size:24 final size:29
Alignment explanation
Indices: 60682702--60682764 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
60682692 AAAATTTACA
*
60682702 TAAATAAATAAATTTTATTATTAATGTAT
1 TAAATAAATAAATGTTATTATTAATGTAT
60682731 TAAAT-AAT-AATGTTATT-TTAA-GT-T
1 TAAATAAATAAATGTTATTATTAATGTAT
60682755 TAAAATAAAT
1 T-AAATAAAT
60682765 TATTTGTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 2 0.06
25 6 0.19
26 7 0.23
27 8 0.26
28 3 0.10
29 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (29 bp):
TAAATAAATAAATGTTATTATTAATGTAT
Found at i:60683469 original size:23 final size:24
Alignment explanation
Indices: 60683415--60683469 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
60683405 AATTAATTTA
*
60683415 AAAGTAAATAAAAATAAGCAATGC
1 AAAGTAAATAAAAATAAACAATGC
* *
60683439 AAATTAAAT-CAAATAAACAAT-C
1 AAAGTAAATAAAAATAAACAATGC
60683461 AATAGTAAA
1 AA-AGTAAA
60683470 CCCTAGGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 3 0.12
23 15 0.58
24 8 0.31
ACGTcount: A:0.64, C:0.09, G:0.07, T:0.20
Consensus pattern (24 bp):
AAAGTAAATAAAAATAAACAATGC
Found at i:60685173 original size:13 final size:13
Alignment explanation
Indices: 60685155--60685180 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60685145 TTTGGGTAGC
60685155 TCTTTTTCTTTTT
1 TCTTTTTCTTTTT
60685168 TCTTTTTCTTTTT
1 TCTTTTTCTTTTT
60685181 ACCCCTTTAA
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TCTTTTTCTTTTT
Found at i:60687069 original size:22 final size:22
Alignment explanation
Indices: 60687044--60687085 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
60687034 ATAAGCTCAT
*
60687044 TTACATTCAATTAATAAATGTA
1 TTACATTCAATCAATAAATGTA
60687066 TTACATTCAATCAATAAATG
1 TTACATTCAATCAATAAATG
60687086 AGAATTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (22 bp):
TTACATTCAATCAATAAATGTA
Found at i:60687528 original size:11 final size:11
Alignment explanation
Indices: 60687512--60687536 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
60687502 TGTTGAACTT
60687512 CTAAATTATCA
1 CTAAATTATCA
60687523 CTAAATTATCA
1 CTAAATTATCA
60687534 CTA
1 CTA
60687537 GAATGAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (11 bp):
CTAAATTATCA
Found at i:60690815 original size:11 final size:11
Alignment explanation
Indices: 60690801--60690845 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
60690791 AGATAAATAT
60690801 TATTTTATTAA
1 TATTTTATTAA
*
60690812 TATTTTAATAATA
1 TATTTT-ATTA-A
*
60690825 TATTTTATTAT
1 TATTTTATTAA
60690836 TATTTTATTA
1 TATTTTATTA
60690846 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:60690828 original size:24 final size:24
Alignment explanation
Indices: 60690796--60690851 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
60690786 TAATTAGATA
60690796 AATATTATTTTATTAATATTTTAAT
1 AATA-TATTTTATTAATATTTTAAT
* *
60690821 AATATATTTTATTATTATTTTATT
1 AATATATTTTATTAATATTTTAAT
*
60690845 AGTATAT
1 AATATAT
60690852 AAAGAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AATATATTTTATTAATATTTTAAT
Found at i:60691211 original size:25 final size:25
Alignment explanation
Indices: 60691183--60691233 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
60691173 CATGAAAATA
60691183 ATGTTATTTATAGTAGAGTTTTCTT
1 ATGTTATTTATAGTAGAGTTTTCTT
60691208 ATGTTATTTATAGTAGAGTTTTCTT
1 ATGTTATTTATAGTAGAGTTTTCTT
60691233 A
1 A
60691234 CATAAGGTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.04, G:0.16, T:0.55
Consensus pattern (25 bp):
ATGTTATTTATAGTAGAGTTTTCTT
Found at i:60693056 original size:46 final size:46
Alignment explanation
Indices: 60693004--60693277 Score: 410
Period size: 46 Copynumber: 6.0 Consensus size: 46
60692994 AGTGTGCTCT
*
60693004 CTGATATGAAAT-ATGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGA-ATAAGACCATGGTTGAAAGATACCATGGCAAC
60693050 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
60693096 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* *
60693142 GTGATATGAAATGAATAAGACCATGGTTGAAAAATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* *
60693188 GTGACATGAAAAT-AATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
60693234 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGATACTATGGCA
1 CTGATATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCA
60693278 TTATGTCAAA
Statistics
Matches: 216, Mismatches: 9, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
45 6 0.03
46 205 0.95
47 5 0.02
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:60695758 original size:46 final size:46
Alignment explanation
Indices: 60695706--60695881 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
60695696 TGGTTGAGCA
*
60695706 TCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
60695752 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
60695797 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
60695845 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
60695882 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.58
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:60695862 original size:93 final size:93
Alignment explanation
Indices: 60695703--60695873 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
60695693 GGATGGTTGA
* **
60695703 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
60695768 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
60695796 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
60695861 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
60695874 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:60697981 original size:13 final size:13
Alignment explanation
Indices: 60697963--60697990 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
60697953 TAAATGTATG
60697963 AATTATGTATGTT
1 AATTATGTATGTT
60697976 AATTATGTATGTT
1 AATTATGTATGTT
60697989 AA
1 AA
60697991 ATGATGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
AATTATGTATGTT
Found at i:60700154 original size:53 final size:53
Alignment explanation
Indices: 60699984--60700187 Score: 160
Period size: 53 Copynumber: 3.8 Consensus size: 53
60699974 AGGGTTTAAG
* * * * * * *
60699984 GATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGC-AA
1 GATACCATGTAAGACCATGTCAAGACATGACAATGGTAAG-TTCATAAGGCAAA
* * * * * * * * *
60700037 GTAAATCATGTAAGACTATGTCAAGACATGGCATTGATAAACTACGATAAGGTAAA
1 G-ATACCATGTAAGACCATGTCAAGACATGACAATGGT-AAGTTC-ATAAGGCAAA
* * * *
60700093 GATCCCATGTAAGACCAT-TCCAAGGCATGACAATGGTGAGTTCATAAGGCAAG
1 GATACCATGTAAGACCATGT-CAAGACATGACAATGGTAAGTTCATAAGGCAAA
*
60700146 GATACCATGTAAGACCATGTCAAGACATGTCAATGGTAAGTT
1 GATACCATGTAAGACCATGTCAAGACATGACAATGGTAAGTT
60700188 TAAAAAGGAT
Statistics
Matches: 116, Mismatches: 29, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
53 45 0.39
54 35 0.30
55 33 0.28
56 3 0.03
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (53 bp):
GATACCATGTAAGACCATGTCAAGACATGACAATGGTAAGTTCATAAGGCAAA
Found at i:60705994 original size:12 final size:12
Alignment explanation
Indices: 60705981--60706063 Score: 66
Period size: 14 Copynumber: 6.8 Consensus size: 12
60705971 CATAGTTTTT
*
60705981 TTCTCTTCTCTT
1 TTCTCTTCTCTC
*
60705993 TTTTCTT-TCT-
1 TTCTCTTCTCTC
60706003 TTCT-TTCTCTC
1 TTCTCTTCTCTC
60706014 -TCTCTCTCTCTC
1 TTCTCT-TCTCTC
60706026 TCTCTCTCTCTCTC
1 T-TCTCT-TCTCTC
60706040 TCTCTCTCTCTCTC
1 T-TCTCT-TCTCTC
60706054 TCTCTCTTCT
1 T-TCTCTTCT
60706064 TTTCTTTTTG
Statistics
Matches: 63, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
9 2 0.03
10 9 0.14
11 4 0.06
12 12 0.19
13 3 0.05
14 33 0.52
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (12 bp):
TTCTCTTCTCTC
Found at i:60706013 original size:2 final size:2
Alignment explanation
Indices: 60706008--60706060 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
60705998 TTTCTTTCTT
60706008 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
60706050 TC TC TC TC TC T
1 TC TC TC TC TC T
60706061 TCTTTTCTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:60707161 original size:25 final size:25
Alignment explanation
Indices: 60707127--60707177 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
60707117 GTAAAGAGAA
60707127 GGAAGACTGATTCTAATTTGATCTG
1 GGAAGACTGATTCTAATTTGATCTG
*
60707152 GGAATACTGATTCTAATTTGATCTG
1 GGAAGACTGATTCTAATTTGATCTG
60707177 G
1 G
60707178 CAGTTTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (25 bp):
GGAAGACTGATTCTAATTTGATCTG
Found at i:60707323 original size:87 final size:87
Alignment explanation
Indices: 60707170--60707391 Score: 282
Period size: 87 Copynumber: 2.5 Consensus size: 87
60707160 GATTCTAATT
** * * *
60707170 TGATCTGGCAGTTTAACTGCAACTTATCGGTACAGTGGTTTACCGCATTGTACCACTTGTACGTC
1 TGATCTGGCAGTTTAACTGCAACTTATCGGTACAGCAGTTTACCGCACTATACCACATGTACGTC
60707235 AGCTTTGCTGCATACTATTATC
66 AGCTTTGCTGCATACTATTATC
* * * * *
60707257 TGATCTGGTAGTTTAACTGTAACTTATAGGTACAGCAGTTTACCGCACTATACCGCATGTATGTC
1 TGATCTGGCAGTTTAACTGCAACTTATCGGTACAGCAGTTTACCGCACTATACCACATGTACGTC
* * *
60707322 AGTTTTGTTGCGTACTATTATC
66 AGCTTTGCTGCATACTATTATC
* * * *
60707344 TGATCTAGCAGTTTAAACTGCAACATATCTGTGCAGCAGTTTACCGCA
1 TGATCTGGCAGTTT-AACTGCAACTTATCGGTACAGCAGTTTACCGCA
60707392 ATGCACTGTA
Statistics
Matches: 114, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
87 86 0.75
88 28 0.25
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.35
Consensus pattern (87 bp):
TGATCTGGCAGTTTAACTGCAACTTATCGGTACAGCAGTTTACCGCACTATACCACATGTACGTC
AGCTTTGCTGCATACTATTATC
Found at i:60709207 original size:25 final size:25
Alignment explanation
Indices: 60709066--60709207 Score: 80
Period size: 25 Copynumber: 5.7 Consensus size: 25
60709056 TTTTATAATC
* * **
60709066 AGAATAACATTTCATTATCAGAACC
1 AGAATGACATTTCATTATTAGAATA
* *
60709091 GGAATGACATTTGATTATTAGAATTA
1 AGAATGACATTTCATTATTAGAA-TA
* * *
60709117 A-AGTGACATTTTATTATCA-AATCA
1 AGAATGACATTTCATTATTAGAAT-A
* *
60709141 A-AATGGCATATCA-TATTCAGAATCA
1 AGAATGACATTTCATTATT-AGAAT-A
*
60709166 AG-ATGATATTT-ATTTATTAGAATA
1 AGAATGACATTTCA-TTATTAGAATA
*
60709190 AGAATAACATTTCATTAT
1 AGAATGACATTTCATTAT
60709208 CAAATCAGAA
Statistics
Matches: 88, Mismatches: 20, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
23 4 0.05
24 17 0.19
25 62 0.70
26 5 0.06
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (25 bp):
AGAATGACATTTCATTATTAGAATA
Found at i:60716120 original size:17 final size:17
Alignment explanation
Indices: 60716100--60716132 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
60716090 GATATCAGGA
*
60716100 TAAAATTTTAATATTAT
1 TAAAATTTAAATATTAT
60716117 TAAAATTTAAATATTA
1 TAAAATTTAAATATTA
60716133 AAAACATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAAATTTAAATATTAT
Found at i:60719082 original size:12 final size:12
Alignment explanation
Indices: 60719065--60719089 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60719055 TGACCTCAAA
60719065 TGAACTTTTGTT
1 TGAACTTTTGTT
60719077 TGAACTTTTGTT
1 TGAACTTTTGTT
60719089 T
1 T
60719090 TGGTTGACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TGAACTTTTGTT
Found at i:60719410 original size:3 final size:3
Alignment explanation
Indices: 60719402--60719452 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
60719392 TTATCATATT
60719402 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
60719450 TAA
1 TAA
60719453 AGAATTACAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:60722789 original size:51 final size:51
Alignment explanation
Indices: 60722729--60722837 Score: 200
Period size: 51 Copynumber: 2.1 Consensus size: 51
60722719 ACCAAGGTTA
*
60722729 GTTGAGGACTTAAATGTAATATTTTCAAAATTATCGGGTTGGTGTTGCGAT
1 GTTGAGGACTTAAATGTAATATTTTCAAAATTATCGGGTTGGTGTTGCAAT
*
60722780 GTTGAGGACTTAAATGTAATATTTTCAAAATTGTCGGGTTGGTGTTGCAAT
1 GTTGAGGACTTAAATGTAATATTTTCAAAATTATCGGGTTGGTGTTGCAAT
60722831 GTTGAGG
1 GTTGAGG
60722838 GTATCACATC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.27, C:0.07, G:0.28, T:0.39
Consensus pattern (51 bp):
GTTGAGGACTTAAATGTAATATTTTCAAAATTATCGGGTTGGTGTTGCAAT
Found at i:60724299 original size:60 final size:60
Alignment explanation
Indices: 60724234--60724354 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
60724224 AGGCTGTTTG
*
60724234 GGGCTTTGTTTTGTAGGGGAAAAAAAATCTCAAACCTTGCTTGCTGATGTATGTATGCAT
1 GGGCTTTGTTTTGTAGGGGAAAAAAAATCTCAAACCTTGCTTGCTGATGTATGCATGCAT
60724294 GGGCTTTGTTTTGTAGGGGAAAAAAAATCTCAAACCTTGCTTGCTGATGTATGCATGCAT
1 GGGCTTTGTTTTGTAGGGGAAAAAAAATCTCAAACCTTGCTTGCTGATGTATGCATGCAT
60724354 G
1 G
60724355 CATGCATGCA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (60 bp):
GGGCTTTGTTTTGTAGGGGAAAAAAAATCTCAAACCTTGCTTGCTGATGTATGCATGCAT
Found at i:60728096 original size:39 final size:39
Alignment explanation
Indices: 60728029--60728155 Score: 164
Period size: 39 Copynumber: 3.2 Consensus size: 39
60728019 GGACTTTAGC
* * *
60728029 CCGGACATATTTCTAGCACGTAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCTAGCACATAGCCTGCGGACCTTAAGT
* * *
60728068 CCGAATATAATTCTAGAACATAGGCTGCGGACCTTAAGT
1 CCGGATATAATTCTAGCACATAGCCTGCGGACCTTAAGT
* * *
60728107 CCGGATATAATTCCAGCACATAGCCTGCTGACCTTTAAGC
1 CCGGATATAATTCTAGCACATAGCCTGCGGACC-TTAAGT
60728147 CCGGATATA
1 CCGGATATA
60728156 CGTCAAATAT
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 61 0.81
40 14 0.19
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.25
Consensus pattern (39 bp):
CCGGATATAATTCTAGCACATAGCCTGCGGACCTTAAGT
Found at i:60743253 original size:2 final size:2
Alignment explanation
Indices: 60743246--60743282 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
60743236 TTCCAACAAC
60743246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60743283 CAAAAACCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60744689 original size:27 final size:27
Alignment explanation
Indices: 60744658--60744713 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
60744648 CCCTACTACC
*
60744658 CCAACATCACCGGACACAAATCCGACT
1 CCAACATCACCAGACACAAATCCGACT
* * *
60744685 CCAACATTACCAGACACTAATCCGGCT
1 CCAACATCACCAGACACAAATCCGACT
60744712 CC
1 CC
60744714 CACCGGCCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.41, G:0.11, T:0.14
Consensus pattern (27 bp):
CCAACATCACCAGACACAAATCCGACT
Found at i:60744737 original size:24 final size:24
Alignment explanation
Indices: 60744710--60744761 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
60744700 ACTAATCCGG
60744710 CTCCCACCGGCCCTACCACGACTC
1 CTCCCACCGGCCCTACCACGACTC
* * *
60744734 CTCCGACTGGCCCTACCATGACTC
1 CTCCCACCGGCCCTACCACGACTC
60744758 CTCC
1 CTCC
60744762 GACTGGGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.15, C:0.54, G:0.13, T:0.17
Consensus pattern (24 bp):
CTCCCACCGGCCCTACCACGACTC
Found at i:60744762 original size:24 final size:24
Alignment explanation
Indices: 60744718--60744833 Score: 97
Period size: 24 Copynumber: 4.8 Consensus size: 24
60744708 GGCTCCCACC
60744718 GGCCCTACCACGACTCCTCCGACT
1 GGCCCTACCACGACTCCTCCGACT
*
60744742 GGCCCTACCATGACTCCTCCGACT
1 GGCCCTACCACGACTCCTCCGACT
** * * *
60744766 GGGACAACCACAACTCCTCCAACT
1 GGCCCTACCACGACTCCTCCGACT
** * * *
60744790 GGGACAACCACAACTCCTCCAACT
1 GGCCCTACCACGACTCCTCCGACT
** * *
60744814 GGGACAACCACAACTCCTCC
1 GGCCCTACCACGACTCCTCC
60744834 AACAGGGACA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 85 1.00
ACGTcount: A:0.26, C:0.45, G:0.15, T:0.15
Consensus pattern (24 bp):
GGCCCTACCACGACTCCTCCGACT
Found at i:60744834 original size:24 final size:24
Alignment explanation
Indices: 60744754--60744872 Score: 211
Period size: 24 Copynumber: 5.0 Consensus size: 24
60744744 CCCTACCATG
*
60744754 ACTCCTCCGACTGGGACAACCACA
1 ACTCCTCCAACTGGGACAACCACA
60744778 ACTCCTCCAACTGGGACAACCACA
1 ACTCCTCCAACTGGGACAACCACA
60744802 ACTCCTCCAACTGGGACAACCACA
1 ACTCCTCCAACTGGGACAACCACA
*
60744826 ACTCCTCCAACAGGGACAACCACA
1 ACTCCTCCAACTGGGACAACCACA
*
60744850 ACTCCTCCAACAGGGACAACCAC
1 ACTCCTCCAACTGGGACAACCAC
60744873 GAGTCCAGGA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 93 1.00
ACGTcount: A:0.34, C:0.42, G:0.13, T:0.11
Consensus pattern (24 bp):
ACTCCTCCAACTGGGACAACCACA
Found at i:60748066 original size:22 final size:21
Alignment explanation
Indices: 60748024--60748066 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
60748014 CTCAAAATAT
* *
60748024 ATGAAAAAATCTTTTTAAAAA
1 ATGAAAAAATCATGTTAAAAA
*
60748045 ATGAAAATAATCATGTTGAAAA
1 ATGAAAA-AATCATGTTAAAAA
60748067 CATTCCCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (21 bp):
ATGAAAAAATCATGTTAAAAA
Found at i:60750350 original size:20 final size:20
Alignment explanation
Indices: 60750293--60750355 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
60750283 TTTATTCATA
*
60750293 TAATAAATTA-TTAATATAAT
1 TAATAAATTATTTAATAT-TT
*
60750313 TAATATAA--ATTTATTATTT
1 TAATA-AATTATTTAATATTT
60750332 TAATAAATTATTTAATATTT
1 TAATAAATTATTTAATATTT
60750352 TAAT
1 TAAT
60750356 TTTATTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.06
19 7 0.19
20 25 0.69
21 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATAAATTATTTAATATTT
Found at i:60750392 original size:16 final size:17
Alignment explanation
Indices: 60750364--60750400 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
60750354 ATTTTATTTT
60750364 AATAATAAATTTTAAAA
1 AATAATAAATTTTAAAA
*
60750381 AATAAT-AATTTTAAAT
1 AATAATAAATTTTAAAA
60750397 AATA
1 AATA
60750401 TTCTTCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAATAAATTTTAAAA
Found at i:60752448 original size:29 final size:31
Alignment explanation
Indices: 60752400--60752463 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
60752390 TTTATAGTTA
*
60752400 TTTAATTAGATAATTATTATT-TATTTAATAT
1 TTTAATAAGATAATTATTATTAT-TTTAATAT
*
60752431 TTTAATAAGAT-ATT-TTATTATTTTATTAT
1 TTTAATAAGATAATTATTATTATTTTAATAT
60752460 TTTA
1 TTTA
60752464 TTATTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.53
30 4 0.13
31 10 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (31 bp):
TTTAATAAGATAATTATTATTATTTTAATAT
Found at i:60752452 original size:8 final size:8
Alignment explanation
Indices: 60752441--60752481 Score: 82
Period size: 8 Copynumber: 5.1 Consensus size: 8
60752431 TTTAATAAGA
60752441 TATTTTAT
1 TATTTTAT
60752449 TATTTTAT
1 TATTTTAT
60752457 TATTTTAT
1 TATTTTAT
60752465 TATTTTAT
1 TATTTTAT
60752473 TATTTTAT
1 TATTTTAT
60752481 T
1 T
60752482 TAGTCTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:60757854 original size:60 final size:59
Alignment explanation
Indices: 60757721--60757857 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 59
60757711 CAGTGTTAAT
* *
60757721 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGTCCCTTACAGTATCAGAGTATAT
1 TGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGTCCCTTACAG-ATCAGAGTATAC
* *
60757782 TGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAG-CCCTATTACA-AGTC-GAGATATAC
1 TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGTCCC--TTACAGA-TCAGAG-TATAC
60757842 TGGGTCCT-GCCCATAT
1 TGGG-CCTAGCCCATAT
60757858 TAACATAGTT
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
59 7 0.10
60 46 0.69
61 14 0.21
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (59 bp):
TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGTCCCTTACAGATCAGAGTATAC
Found at i:60758224 original size:27 final size:26
Alignment explanation
Indices: 60758194--60758259 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
60758184 GTCAAAATTA
*
60758194 ACCTTAGGGGTATAACGGTCATTTTAC
1 ACCTTAGGGGTATAACGGTAATTTT-C
* * *
60758221 ACC-TAAGGGTAAAATGGTAATTTTC
1 ACCTTAGGGGTATAACGGTAATTTTC
*
60758246 ATACTTAGGGGTAT
1 A-CCTTAGGGGTAT
60758260 TTTAGTAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
25 2 0.07
26 18 0.60
27 10 0.33
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (26 bp):
ACCTTAGGGGTATAACGGTAATTTTC
Found at i:60760406 original size:19 final size:18
Alignment explanation
Indices: 60760369--60760412 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
60760359 ATACATGCAG
60760369 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
60760386 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
60760405 TACTAATT
1 TAATAATT
60760413 AATATATCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:60762263 original size:28 final size:27
Alignment explanation
Indices: 60762162--60762263 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 27
60762152 TCAGTGTTAA
* *
60762162 CTGGGCCTTAGCCCATATCAATATTAAT
1 CTGGGCC-TAGCCCATATCAGTATCAAT
*
60762190 CTGGGCCATAGCCCCT-TACAGTATCAGAGTAT
1 CTGGGCC-TAGCCCATAT-CAGTATC--A--AT
*
60762222 ATTGGGCCTAGCCCATATCAGTATCAAT
1 -CTGGGCCTAGCCCATATCAGTATCAAT
60762250 CTGGGCCGTAGCCC
1 CTGGGCC-TAGCCC
60762264 TATTACAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
27 7 0.12
28 27 0.46
30 2 0.03
32 16 0.27
33 7 0.12
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (27 bp):
CTGGGCCTAGCCCATATCAGTATCAAT
Found at i:60762296 original size:60 final size:59
Alignment explanation
Indices: 60762161--60762299 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 59
60762151 ATCAGTGTTA
* *
60762161 ACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTATCAGAGTAT
1 ACTGGGCCTT-GCCCATATCAATATCAATCTGGGCCATAGCCCATTACAG-ATCAGAGTAT
* * * *
60762222 ATTGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACA-AGTC-GAGATAT
1 ACTGGGCCTTGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTACAGA-TCAGAG-TAT
*
60762282 ACTGGGTCTTGCCCATAT
1 ACTGGGCCTTGCCCATAT
60762300 TAACATAGTT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
59 4 0.06
60 49 0.74
61 13 0.20
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (59 bp):
ACTGGGCCTTGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGATCAGAGTAT
Found at i:60763897 original size:19 final size:18
Alignment explanation
Indices: 60763860--60763903 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
60763850 ATACATGCAG
60763860 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
60763877 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
60763896 TACTAATT
1 TAATAATT
60763904 AAAATTTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:60768140 original size:18 final size:18
Alignment explanation
Indices: 60768104--60768200 Score: 86
Period size: 18 Copynumber: 5.4 Consensus size: 18
60768094 AGTTTCATTT
* * *
60768104 AGTAACATTCAATCATTC
1 AGTAACAATCAGTTATTC
* * *
60768122 AGTAGCAATTAGTTGTTC
1 AGTAACAATCAGTTATTC
* * *
60768140 AGCAACAATCATTTACTC
1 AGTAACAATCAGTTATTC
*
60768158 AGTAGCAATCAGTTATTC
1 AGTAACAATCAGTTATTC
*
60768176 AGTAACAATCAATTATTC
1 AGTAACAATCAGTTATTC
*
60768194 AATAACA
1 AGTAACA
60768201 GCCAGTCATT
Statistics
Matches: 60, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (18 bp):
AGTAACAATCAGTTATTC
Found at i:60769592 original size:19 final size:18
Alignment explanation
Indices: 60769570--60769616 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 18
60769560 TATTCTGTTA
60769570 CTTTGTTTCTTTTCTATTT
1 CTTTGTTTCTTTT-TATTT
*
60769589 CTTTATTTCTTTTTATTT
1 CTTTGTTTCTTTTTATTT
60769607 CATTTGTTTC
1 C-TTTGTTTC
60769617 ATTTATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.09, C:0.15, G:0.04, T:0.72
Consensus pattern (18 bp):
CTTTGTTTCTTTTTATTT
Found at i:60769660 original size:21 final size:21
Alignment explanation
Indices: 60769630--60769670 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
60769620 TATTTTATAA
*
60769630 TAATATTATAATAATATAATT
1 TAATAATATAATAATATAATT
* *
60769651 TAATAATATACTTATATAAT
1 TAATAATATAATAATATAAT
60769671 AAATATATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATAATATAATAATATAATT
Found at i:60769669 original size:13 final size:13
Alignment explanation
Indices: 60769626--60769671 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
60769616 CATTTATTTT
60769626 ATAATAATATTATA
1 ATAAT-ATATTATA
60769640 ATAATATAATT-TA
1 ATAATAT-ATTATA
60769653 ATAATATACTTAT-
1 ATAATATA-TTATA
60769666 ATAATA
1 ATAATA
60769672 AATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.03
13 19 0.66
14 9 0.31
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
ATAATATATTATA
Found at i:60769766 original size:5 final size:5
Alignment explanation
Indices: 60769756--60769788 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
60769746 ATATTACATA
*
60769756 ATAAT ATAAT ATAAT ATAAT ATAAT TTAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
60769789 TTTTATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:60769793 original size:10 final size:10
Alignment explanation
Indices: 60769756--60769813 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
60769746 ATATTACATA
*
60769756 ATAATATAAT
1 ATAATTTAAT
*
60769766 ATAATATAAT
1 ATAATTTAAT
60769776 ATAATTTAAT
1 ATAATTTAAT
60769786 AT-ATTT--T
1 ATAATTTAAT
*
60769793 ATAATTAAAT
1 ATAATTTAAT
60769803 AATATATTTAA
1 -ATA-ATTTAA
60769814 AACATAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
7 3 0.08
8 3 0.08
9 4 0.10
10 22 0.55
11 3 0.08
12 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATAATTTAAT
Found at i:60770339 original size:16 final size:16
Alignment explanation
Indices: 60770318--60770349 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
60770308 AAAATAAACT
60770318 CAATTAAACAATGAAA
1 CAATTAAACAATGAAA
60770334 CAATTAAACAATGAAA
1 CAATTAAACAATGAAA
60770350 ATATAAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (16 bp):
CAATTAAACAATGAAA
Found at i:60774911 original size:18 final size:18
Alignment explanation
Indices: 60774888--60774952 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
60774878 TTAATTTATT
60774888 TAATAATAATGCTAATAA
1 TAATAATAATGCTAATAA
60774906 TAATAATAAT-CTAAT-A
1 TAATAATAATGCTAATAA
* *
60774922 TAAAACCATAATGTTAATTAA
1 TAATA--ATAATGCTAA-TAA
*
60774943 TAATTATAAT
1 TAATAATAAT
60774953 AATTTAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
16 5 0.13
17 5 0.13
18 15 0.39
19 8 0.21
20 1 0.03
21 4 0.11
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (18 bp):
TAATAATAATGCTAATAA
Found at i:60774932 original size:21 final size:20
Alignment explanation
Indices: 60774908--60774976 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
60774898 GCTAATAATA
60774908 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
60774929 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
60774948 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
60774969 ATAATAAT
1 ATAATAAT
60774977 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:60780056 original size:22 final size:20
Alignment explanation
Indices: 60780016--60780064 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
60780006 CAGTTTAAAA
60780016 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
* *
60780036 TATATAAATTTATTAATATA
1 TATAAAAATTTATTAATATG
*
60780056 TGTAAAAAT
1 TATAAAAAT
60780065 AACTTTTACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:60794251 original size:16 final size:16
Alignment explanation
Indices: 60794230--60794261 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
60794220 AATCCCAGCC
60794230 CAGTTTTAGTTTGCAT
1 CAGTTTTAGTTTGCAT
60794246 CAGTTTTAGTTTGCAT
1 CAGTTTTAGTTTGCAT
60794262 TAGTGAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (16 bp):
CAGTTTTAGTTTGCAT
Found at i:60812905 original size:46 final size:47
Alignment explanation
Indices: 60812831--60812941 Score: 107
Period size: 48 Copynumber: 2.3 Consensus size: 47
60812821 GTACCCATAC
* * * * *
60812831 CATGGCCCCGTAGCCAAATCAATGTAACT-TATCTGAAGAACTATTAT
1 CATGG-CCCGAAGCCAAATCAATATAACTCCATCCGAAGAACTAATAT
** **
60812878 CATGGCCCGAAGCCAAATCGGTATAACTCGCATCCGAAGTGCTAATAT
1 CATGGCCCGAAGCCAAATCAATATAACTC-CATCCGAAGAACTAATAT
*
60812926 CATGGCCTGAAGCCAA
1 CATGGCCCGAAGCCAA
60812942 CTCTACTTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
46 19 0.37
47 5 0.10
48 28 0.54
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (47 bp):
CATGGCCCGAAGCCAAATCAATATAACTCCATCCGAAGAACTAATAT
Found at i:60814698 original size:26 final size:26
Alignment explanation
Indices: 60814661--60814744 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
60814651 TGATACAAAT
* *
60814661 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
60814687 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
60814713 TGATAATGAGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
60814739 TGATAA
1 TGATAA
60814745 GAATTTCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:60846837 original size:31 final size:31
Alignment explanation
Indices: 60846802--60846865 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
60846792 AAATATTAGT
60846802 CCGTAAGTTAATTTACTTATCACATATAAGG
1 CCGTAAGTTAATTTACTTATCACATATAAGG
60846833 CCGTAAGTTAATTTACTTATCACATATAAGG
1 CCGTAAGTTAATTTACTTATCACATATAAGG
60846864 CC
1 CC
60846866 AGACATAGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (31 bp):
CCGTAAGTTAATTTACTTATCACATATAAGG
Found at i:60847566 original size:19 final size:19
Alignment explanation
Indices: 60847542--60847582 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
60847532 TATTTTAAAG
60847542 TTATTTAGGCAGATAAATC
1 TTATTTAGGCAGATAAATC
**
60847561 TTATTTAGTTAGATAAATC
1 TTATTTAGGCAGATAAATC
60847580 TTA
1 TTA
60847583 GAATAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (19 bp):
TTATTTAGGCAGATAAATC
Found at i:60854066 original size:24 final size:24
Alignment explanation
Indices: 60854037--60854086 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
60854027 AAATCAGAGT
*
60854037 AAGCATCAGAAAGTCTAGACACAG
1 AAGCATCAGAAAGTCTAAACACAG
60854061 AAGCATCAGAAAGTCTAAACACAG
1 AAGCATCAGAAAGTCTAAACACAG
60854085 AA
1 AA
60854087 CTCCATACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.20, G:0.18, T:0.12
Consensus pattern (24 bp):
AAGCATCAGAAAGTCTAAACACAG
Found at i:60862207 original size:19 final size:19
Alignment explanation
Indices: 60862183--60862222 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
60862173 ATTATTTTTG
60862183 ATCAAATAAAATT-AAATTA
1 ATCAAAT-AAATTAAAATTA
*
60862202 ATCAAATTAATTAAAATTA
1 ATCAAATAAATTAAAATTA
60862221 AT
1 AT
60862223 ATGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:60876489 original size:21 final size:21
Alignment explanation
Indices: 60876463--60876503 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
60876453 ACAAGTACGA
60876463 ATACTTACCGTAAGCAAAATT
1 ATACTTACCGTAAGCAAAATT
*
60876484 ATACTTACCTTAAGCAAAAT
1 ATACTTACCGTAAGCAAAAT
60876504 ATAAACAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (21 bp):
ATACTTACCGTAAGCAAAATT
Found at i:60877900 original size:18 final size:18
Alignment explanation
Indices: 60877886--60878075 Score: 200
Period size: 18 Copynumber: 10.6 Consensus size: 18
60877876 TATTAATCAA
* *
60877886 TTATTCAGTAATAATCAT
1 TTATTCAGTAACAGTCAT
60877904 TTATTCAGTAACAGTCAT
1 TTATTCAGTAACAGTCAT
** *
60877922 TTATTCAGTCCCAGTCAA
1 TTATTCAGTAACAGTCAT
* * * *
60877940 TTATCCAGTAATAATCAG
1 TTATTCAGTAACAGTCAT
*
60877958 TTATTCAGTAATAGTCAT
1 TTATTCAGTAACAGTCAT
* *
60877976 TTATTTAGTCACAGTCAT
1 TTATTCAGTAACAGTCAT
* * *
60877994 TTATTCAGTAATAATCAG
1 TTATTCAGTAACAGTCAT
60878012 TTATTCAGTAACAGTCAT
1 TTATTCAGTAACAGTCAT
* *
60878030 TTATTCAGTAACAGTTAA
1 TTATTCAGTAACAGTCAT
* * *
60878048 TTATTCAGTAGCAGACAG
1 TTATTCAGTAACAGTCAT
60878066 TTATTCAGTA
1 TTATTCAGTA
60878076 CCTTTATTTT
Statistics
Matches: 141, Mismatches: 31, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 141 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAT
Found at i:60877943 original size:54 final size:54
Alignment explanation
Indices: 60877882--60878075 Score: 282
Period size: 54 Copynumber: 3.6 Consensus size: 54
60877872 TTAGTATTAA
* *
60877882 TCAATTATTCAGTAATAATCATTTATTCAGTAACAGTCATTTATTCAGTCCCAG
1 TCAATTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTCACAG
* * *
60877936 TCAATTATCCAGTAATAATCAGTTATTCAGTAATAGTCATTTATTTAGTCACAG
1 TCAATTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTCACAG
* *
60877990 TCATTTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTAACAG
1 TCAATTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTCACAG
* **
60878044 TTAATTATTCAGTAGCAGA-CAGTTATTCAGTA
1 TCAATTATTCAGTAATA-ATCAGTTATTCAGTA
60878076 CCTTTATTTT
Statistics
Matches: 125, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
54 124 0.99
55 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (54 bp):
TCAATTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTCACAG
Found at i:60878502 original size:17 final size:18
Alignment explanation
Indices: 60878468--60878502 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
60878458 TCAGCTAATC
*
60878468 ATATATATTTTCAGTTCA
1 ATATATATTTTCAATTCA
60878486 ATATATA-TTTCAATTCA
1 ATATATATTTTCAATTCA
60878503 CTTTACATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.49
Consensus pattern (18 bp):
ATATATATTTTCAATTCA
Found at i:60879343 original size:19 final size:19
Alignment explanation
Indices: 60879319--60879355 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
60879309 CCAATTTTTC
*
60879319 CTTTTTCTTTCTTTCCTTT
1 CTTTTTCCTTCTTTCCTTT
60879338 CTTTTTCCTTCTTTCCTT
1 CTTTTTCCTTCTTTCCTT
60879356 CCCCTGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTTTCCTTCTTTCCTTT
Found at i:60881862 original size:13 final size:13
Alignment explanation
Indices: 60881844--60881868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60881834 CTTAATAGGT
60881844 AATTGAACTTGAA
1 AATTGAACTTGAA
60881857 AATTGAACTTGA
1 AATTGAACTTGA
60881869 TATCGAAATT
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:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
AATTGAACTTGAA
Found at i:60882078 original size:392 final size:391
Alignment explanation
Indices: 60881346--60882139 Score: 1387
Period size: 392 Copynumber: 2.0 Consensus size: 391
60881336 AAGTGATTTT
60881346 TGGAAAAA-T-TAATATTGATCAAGTAAAATAAAACCAATCAAATTAATTACAATTAATATGATA
1 TGGAAAAATTATAATATTGATCAAGTAAAATAAAACCAATCAAATTAATTACAATTAATATGATA
60881409 TTTTTGGAAATTAATTTTCAAGTCAAACAATTGGCTCAATGGTAATTGAACTTGAAAATTGAACC
66 TTTTTGGAAATTAATTTTCAAGTCAAACAATTGGCTCAATGGTAATTGAACTTGAAAATTGAACC
60881474 TGATATCAAAATTTGGGCCCAAGAACCCAAAACCGAGATCGATACCTAAAAACTAGTCGAATCAA
131 TGATATCAAAATTTGGGCCCAAGAACCCAAAACCGAGATCGATACCTAAAAACTAGTCGAATCAA
* * *
60881539 GTCTGGTACATGAAACTAGGCTTGGACTAGACCGATCGGACCTTCACTAGGCTTGGATCGAATCG
196 GTCTGGTACATGAAACTAGGCTTGGACCAGACCGATCGGACCGTCACTAGGCCTGGATCGAATCG
* * *
60881604 GCTACAGTCGACCCAGCTCGAGTTTTCGTGAGGGTGTCGTACCTGCGATGGCACCACCGGACACG
261 GCAACAGTCGACCCAGCTCGAGTTTTCGTGAGGGTGTCGCACCTGCAATGGCACCACCGGACACG
** *
60881669 ATGGTGACGGCGATGACGATGACATCATTCTAGTGGCCAACGGGTGGTCCTTCGATGATTGAGCA
326 ACAGTGACGGCGATGACGATGACAACATTCTAGTGGCCAACGGGTGGTCCTTCGATGATTGAGCA
60881734 G
391 G
* *
60881735 TGGAAAAATTATAATATTGATCAAGTAAAATTAAATCAATCAAATTAATTACAATTAATATGATA
1 TGGAAAAATTATAATATTGATCAAGTAAAATAAAACCAATCAAATTAATTACAATTAATATGATA
*
60881800 TTTTTGGAAATTAATTTTCAAGTCAAACAATTGGCTTAATAGGTAATTGAACTTGAAAATTGAAC
66 TTTTTGGAAATTAATTTTCAAGTCAAACAATTGGCTCAAT-GGTAATTGAACTTGAAAATTGAAC
* * * *
60881865 TTGATATCGAAATTTGGGCCCAAGAACCCAAAATCGAGATCGATGCCTAAAAACTAGTCGAATCA
130 CTGATATCAAAATTTGGGCCCAAGAACCCAAAACCGAGATCGATACCTAAAAACTAGTCGAATCA
*
60881930 AGTCTGGTACGTGAAACTAGGCTTGGACCAGACCGATCGGACCGTCACTAGGCCTGGATCGAATC
195 AGTCTGGTACATGAAACTAGGCTTGGACCAGACCGATCGGACCGTCACTAGGCCTGGATCGAATC
60881995 GGCAACAGTCGACCCAGCTCGAGTTTTCGTGAGGGTGTCGCACCTGCAATGGCACCACCGGACAC
260 GGCAACAGTCGACCCAGCTCGAGTTTTCGTGAGGGTGTCGCACCTGCAATGGCACCACCGGACAC
*
60882060 GACAGTG-CTGGCGATGACGATGACAACATTCTAGTGGCCAGCGGGTGGTCCTTCGATGATTGAG
325 GACAGTGAC-GGCGATGACGATGACAACATTCTAGTGGCCAACGGGTGGTCCTTCGATGATTGAG
60882124 CAG
389 CAG
60882127 TGGAAAAATTATA
1 TGGAAAAATTATA
60882140 CTCTTACCAG
Statistics
Matches: 383, Mismatches: 18, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
389 8 0.02
390 1 0.00
391 92 0.24
392 282 0.74
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (391 bp):
TGGAAAAATTATAATATTGATCAAGTAAAATAAAACCAATCAAATTAATTACAATTAATATGATA
TTTTTGGAAATTAATTTTCAAGTCAAACAATTGGCTCAATGGTAATTGAACTTGAAAATTGAACC
TGATATCAAAATTTGGGCCCAAGAACCCAAAACCGAGATCGATACCTAAAAACTAGTCGAATCAA
GTCTGGTACATGAAACTAGGCTTGGACCAGACCGATCGGACCGTCACTAGGCCTGGATCGAATCG
GCAACAGTCGACCCAGCTCGAGTTTTCGTGAGGGTGTCGCACCTGCAATGGCACCACCGGACACG
ACAGTGACGGCGATGACGATGACAACATTCTAGTGGCCAACGGGTGGTCCTTCGATGATTGAGCA
G
Found at i:60884398 original size:20 final size:21
Alignment explanation
Indices: 60884365--60884405 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
60884355 ATAAAAGTAC
60884365 AATAGGTATCGATACTTTTTG
1 AATAGGTATCGATACTTTTTG
*
60884386 AATA-GTATTGATACTTTTTG
1 AATAGGTATCGATACTTTTTG
60884406 CTTTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.46
Consensus pattern (21 bp):
AATAGGTATCGATACTTTTTG
Found at i:60900760 original size:13 final size:13
Alignment explanation
Indices: 60900710--60900771 Score: 79
Period size: 13 Copynumber: 4.8 Consensus size: 13
60900700 TTTGGCAATA
60900710 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* *
60900723 TTTTTAAAAAGTG
1 CTTTTGAAAAGTG
* *
60900736 CTATGGAAAAGTG
1 CTTTTGAAAAGTG
*
60900749 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
60900762 CTTTTGAAAA
1 CTTTTGAAAA
60900772 TTTTAGGTGT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:60901723 original size:16 final size:17
Alignment explanation
Indices: 60901696--60901729 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
60901686 TAAGAGTATG
60901696 TACATAATATATATATT
1 TACATAATATATATATT
60901713 TACATATATATATATAT
1 TACATA-ATATATATAT
60901730 ATAATTAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
TACATAATATATATATT
Found at i:60902442 original size:24 final size:23
Alignment explanation
Indices: 60902404--60902458 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
60902394 AATACATGTT
*
60902404 CATAATAT-ATATAAAACGTATA
1 CATAATATAATATAAAACATATA
* *
60902426 TATAATATAATATTAAAACATTTA
1 CATAATATAATA-TAAAACATATA
60902450 CATAATATA
1 CATAATATA
60902459 TACACATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 7 0.26
23 3 0.11
24 17 0.63
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (23 bp):
CATAATATAATATAAAACATATA
Found at i:60902578 original size:2 final size:2
Alignment explanation
Indices: 60902531--60902559 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
60902521 AAGATATACT
60902531 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60902560 TAAAGATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60903070 original size:3 final size:3
Alignment explanation
Indices: 60903062--60903171 Score: 161
Period size: 3 Copynumber: 37.0 Consensus size: 3
60903052 GAGTACATAC
*
60903062 TAA TAA TAA TAA TAA GAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
60903110 TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA GAA TAA TAA T-A TCAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
*
60903158 TAA T-A TAA AAA TAA
1 TAA TAA TAA TAA TAA
60903172 CAAGGATATT
Statistics
Matches: 96, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
2 4 0.04
3 90 0.94
4 2 0.02
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:60905043 original size:44 final size:45
Alignment explanation
Indices: 60904945--60905044 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 45
60904935 TTCTTTTGCG
** * * * *
60904945 ACTTCAGAAAGACAAGATTTGATATCCTTGATCAGCTCCCCTGCA
1 ACTTCAGGGAGACAAGATTTGACATCCTTGACCAGCTCCACTACA
* * *
60904990 ACTTTAGGGAGACAAGATTTG-CATCTTTGACCTGCTCCACTACA
1 ACTTCAGGGAGACAAGATTTGACATCCTTGACCAGCTCCACTACA
60905034 ACTTCAGGGAG
1 ACTTCAGGGAG
60905045 GCCAAATCCG
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
44 27 0.60
45 18 0.40
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (45 bp):
ACTTCAGGGAGACAAGATTTGACATCCTTGACCAGCTCCACTACA
Found at i:60905312 original size:14 final size:14
Alignment explanation
Indices: 60905289--60905319 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
60905279 AGTTGATTTA
*
60905289 AAAAATATAAATTG
1 AAAAACATAAATTG
60905303 AAAAACATAAATTG
1 AAAAACATAAATTG
60905317 AAA
1 AAA
60905320 TTACCTCAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (14 bp):
AAAAACATAAATTG
Found at i:60905477 original size:14 final size:14
Alignment explanation
Indices: 60905458--60905484 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
60905448 TTAATTTTTG
60905458 AAAAGCAGAAATTA
1 AAAAGCAGAAATTA
60905472 AAAAGCAGAAATT
1 AAAAGCAGAAATT
60905485 GAAATTACCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (14 bp):
AAAAGCAGAAATTA
Found at i:60905528 original size:87 final size:87
Alignment explanation
Indices: 60905149--60905549 Score: 358
Period size: 87 Copynumber: 4.6 Consensus size: 87
60905139 AAAAGTAGAT
* * * * * * *
60905149 CTCAGCGTGCCCCGAGACTTAACTTACCTCTCGTAATATGAGTTGATTTTTGAAAAATATAGATT
1 CTCAGCGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATT
** *
60905214 GGAAAAAAATAGAAATTGAAAATAC
65 -G-AAAAAGCAGAAATTGAAATTAC
* *
60905239 CTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTAAAAAATATAAATT
1 CTCAGCGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATT
*
60905302 GAAAAA-CATAAATTGAAATTAC
65 GAAAAAGCAGAAATTGAAATTAC
** * * *
60905324 CTCAGCGTGCCTCGAGGCTCAACTCACCTCTTACAATATGAGTTGGTCTTTTTG--AAACTTAAT
1 CTCAGCGTGCCT-GAGGCTCAACTCACCTCTCGCAATATGAGTT-G-ATTTTTGAAAAACATAAA
* **
60905387 TTG-AAAAGTAGATTTTGAAA--A-
63 TTGAAAAAGCAGAAATTGAAATTAC
* ** **** * * *
60905408 -ACAGAAAT-TAAAAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAAAAGCAGAAATT
1 CTCAG-CGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATT
60905471 -AAAAAGCAGAAATTGAAATTAC
65 GAAAAAGCAGAAATTGAAATTAC
60905493 CTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
1 CTCAGCGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
60905550 AAAATGGAAT
Statistics
Matches: 246, Mismatches: 49, Indels: 35
0.75 0.15 0.11
Matches are distributed among these distances:
80 6 0.02
82 49 0.20
83 3 0.01
84 5 0.02
85 53 0.22
86 13 0.05
87 59 0.24
88 15 0.06
89 3 0.01
90 40 0.16
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (87 bp):
CTCAGCGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTG
AAAAAGCAGAAATTGAAATTAC
Found at i:60911313 original size:46 final size:46
Alignment explanation
Indices: 60911260--60911487 Score: 307
Period size: 46 Copynumber: 5.0 Consensus size: 46
60911250 GCTCTCTGAA
* * *
60911260 ATGAAATGAGTAAGACCATGATTGAAAGACACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
60911306 ATGAAATGTA-TAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATG-AGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
60911352 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** **
60911398 GGGAAATGAAAAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
60911444 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
60911488 TCAAAGATAA
Statistics
Matches: 163, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
45 1 0.01
46 161 0.99
47 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.20
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:60922288 original size:16 final size:15
Alignment explanation
Indices: 60922264--60922315 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
60922254 AATTAAGACC
60922264 TTTTAAAATTTAAAAA
1 TTTT-AAATTTAAAAA
* *
60922280 TTATTAAATATATAAA
1 TT-TTAAATTTAAAAA
*
60922296 TTTTAAAATTATAAAA
1 TTTTAAATTTA-AAAA
60922312 TTTT
1 TTTT
60922316 TATTAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 7 0.24
16 20 0.69
17 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTTAAATTTAAAAA
Found at i:60935386 original size:11 final size:12
Alignment explanation
Indices: 60935356--60935388 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
60935346 CGACCCGCCA
60935356 ATATTAATTTTT
1 ATATTAATTTTT
60935368 ATATTAATTTTT
1 ATATTAATTTTT
60935380 ATA-TAATTT
1 ATATTAATTT
60935389 AAAAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:60935544 original size:30 final size:30
Alignment explanation
Indices: 60935510--60935572 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
60935500 ATTTAACAAG
*
60935510 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
*
60935540 CAAATATCTTTAAAATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
60935570 CAA
1 CAA
60935573 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATATCTCTAAAATAATAACAAAATTAA
Found at i:60935627 original size:22 final size:22
Alignment explanation
Indices: 60935602--60935644 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
60935592 TATCCAAATA
60935602 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
60935624 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
60935645 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:60935648 original size:11 final size:11
Alignment explanation
Indices: 60935609--60935649 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
60935599 ATAATAACAA
60935609 CAAAATAGTAG
1 CAAAATAGTAG
* *
60935620 CAACATAATAG
1 CAAAATAGTAG
*
60935631 TAAAATAGTAG
1 CAAAATAGTAG
60935642 CAAAATAG
1 CAAAATAG
60935650 GGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:60936236 original size:15 final size:15
Alignment explanation
Indices: 60936215--60936250 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
60936205 AGGGTATGAT
60936215 AAAATATTAAAAATA
1 AAAATATTAAAAATA
* *
60936230 TAAATATTTAAAATA
1 AAAATATTAAAAATA
60936245 AAAATA
1 AAAATA
60936251 CGTAATGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATATTAAAAATA
Found at i:60938682 original size:17 final size:19
Alignment explanation
Indices: 60938649--60938683 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
60938639 TAGGATCGTG
60938649 TATTTCTCTAGTAATTTTT
1 TATTTCTCTAGTAATTTTT
60938668 TATTT-TCTA-TAATTTT
1 TATTTCTCTAGTAATTTT
60938684 AAAATACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.23, C:0.09, G:0.03, T:0.66
Consensus pattern (19 bp):
TATTTCTCTAGTAATTTTT
Found at i:60940888 original size:33 final size:33
Alignment explanation
Indices: 60940851--60940917 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
60940841 TTATTATTAG
60940851 AAATGATAAAAATAAAAGAAAATAAAAAGGATA
1 AAATGATAAAAATAAAAGAAAATAAAAAGGATA
* ** *
60940884 AAATGATAAAATTAAATTAAATTAAAAAGGATA
1 AAATGATAAAAATAAAAGAAAATAAAAAGGATA
60940917 A
1 A
60940918 TTTGATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (33 bp):
AAATGATAAAAATAAAAGAAAATAAAAAGGATA
Found at i:60941184 original size:21 final size:20
Alignment explanation
Indices: 60941155--60941207 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
60941145 TTTCTTTTTG
60941155 AAAAATAAAATTAATTATAA
1 AAAAATAAAATTAATTATAA
* * *
60941175 AAAAAGTAAATTTATTTTTAA
1 AAAAA-TAAAATTAATTATAA
60941196 AAAATATAAAAT
1 AAAA-ATAAAAT
60941208 GAGTTATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 5 0.19
21 21 0.78
22 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAAATAAAATTAATTATAA
Found at i:60943545 original size:101 final size:103
Alignment explanation
Indices: 60943440--60943673 Score: 355
Period size: 108 Copynumber: 2.2 Consensus size: 103
60943430 ACACTGATCA
* *
60943440 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCT-AC-CACTTATCACTTATCACTT
1 CATTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTCACTCACTTATCACTTATCACTT
60943503 GTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTAT
66 GTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTAT
* *
60943541 CATTTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCACTTATCACTTAT
1 CATTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCT--CAC---TCACTTATCACTTAT
* *
60943606 CACTTGTCATTGATCAGATAAGAGTAGCTAAGTTACCACTTAT
61 CACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTAT
60943649 CATTTGTCACTTATCACTGATCAGA
1 CATTTGTCACTTATCACTGATCAGA
60943674 AGTACTCAAA
Statistics
Matches: 120, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
101 38 0.32
104 2 0.02
108 80 0.67
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.33
Consensus pattern (103 bp):
CATTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTCACTCACTTATCACTTATCACTT
GTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTAT
Found at i:60943597 original size:7 final size:7
Alignment explanation
Indices: 60943585--60943610 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
60943575 CTGAGGCTAC
60943585 CACTTAT
1 CACTTAT
60943592 CACTTAT
1 CACTTAT
60943599 CACTTAT
1 CACTTAT
60943606 CACTT
1 CACTT
60943611 GTCATTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (7 bp):
CACTTAT
Found at i:60943609 original size:58 final size:57
Alignment explanation
Indices: 60943443--60943671 Score: 234
Period size: 51 Copynumber: 4.2 Consensus size: 57
60943433 CTGATCACAT
* *
60943443 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCT---AC----CACTTATCAC
1 TTATCACTTATCACTGATCAGATAAGAGTAGCT-AAGCTACCACTTATCACTTATCAC
*
60943494 TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTAT--C--AT---
1 TTATCACTTATCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCACTTATCAC
* * *
60943544 TTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCACTTATCAC
1 TTATCACTTATCACTGATCAGATAAGAGTAGCT-AAGCTACCACTTATCACTTATCAC
* * * * *
60943602 TTATCACTTGTCATTGATCAGATAAGAGTAGCTAAGTTACCACTTATCATTTGTCAC
1 TTATCACTTATCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCACTTATCAC
*
60943659 TTATCACTGATCA
1 TTATCACTTATCA
60943672 GAAGTACTCA
Statistics
Matches: 148, Mismatches: 15, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
50 35 0.24
51 45 0.30
53 5 0.03
55 3 0.02
57 31 0.21
58 29 0.20
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (57 bp):
TTATCACTTATCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCACTTATCAC
Found at i:60947901 original size:15 final size:15
Alignment explanation
Indices: 60947880--60947916 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
60947870 ACAACGCGAT
60947880 AACGTAAGTAACTAA
1 AACGTAAGTAACTAA
* *
60947895 GACGTAAGTAATTAA
1 AACGTAAGTAACTAA
60947910 AACGTAA
1 AACGTAA
60947917 TATTTTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (15 bp):
AACGTAAGTAACTAA
Found at i:60951122 original size:18 final size:17
Alignment explanation
Indices: 60951095--60951129 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
60951085 TTATTGTTTC
60951095 TCTAATATAATAATAGT
1 TCTAATATAATAATAGT
*
60951112 TCTATATATAATAGTAGT
1 TCTA-ATATAATAATAGT
60951130 ACATTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (17 bp):
TCTAATATAATAATAGT
Found at i:60951376 original size:20 final size:20
Alignment explanation
Indices: 60951309--60951394 Score: 59
Period size: 20 Copynumber: 4.2 Consensus size: 20
60951299 ATATTATGTA
* *
60951309 ATATTATATATTTTATTATAAT
1 ATATAATATAGTTTATTAT--T
* *
60951331 ATATAATATAATAATAGTTA-T
1 ATATAATATAGT-TTA-TTATT
60951352 ATATAATAGTAGTTT-TTATT
1 ATATAATA-TAGTTTATTATT
* *
60951372 ATATATTATTGTTTATTATT
1 ATATAATATAGTTTATTATT
60951392 ATA
1 ATA
60951395 CTGATTGAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
19 8 0.15
20 16 0.31
21 10 0.19
22 13 0.25
23 2 0.04
24 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
ATATAATATAGTTTATTATT
Found at i:60951594 original size:230 final size:240
Alignment explanation
Indices: 60951068--60951698 Score: 618
Period size: 240 Copynumber: 2.6 Consensus size: 240
60951058 ATGCCATATA
* * * * * * * *
60951068 ATGTAATACTATATATTTTATTGT-TTCTCTAATATAATAATAGTTCTATAT-ATAATAG-TAGT
1 ATGTAATATTATATATTTTATTATAATATATAATATAATAATAGTTATATATAATAGTAGATATT
* * * * * *
60951130 A-CATTATATATTA---ATTATTATTATATTAGTTGAAATATGTTTTAAGTCCCTATATTTTTC-
66 ATTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAGTCCCTATACTTTTCG
* *
60951190 ATACATTTGAAAGTTAACCCTCCTACTATATTATATAATGCTATATCACATCATATAGTATATAA
131 A-ACATTTAAAAGTTAACACTCCTACTATATTATATAATGCTATATCACATCA-ATAGTATATAA
* * * * * **
60951255 TATAGTAATAGTTTATATATATGTATATATGATTGAACATTATAATATT
194 TATAGT-ATA-TATATATATACGCATAAATGATTAAACATTATAATAGC
60951304 ATGTAATATTATATATTTTATTATAATATATAATATAATAATAGTTATATATAATAGTAG-T-TT
1 ATGTAATATTATATATTTTATTATAATATATAATATAATAATAGTTATATATAATAGTAGATATT
* * *
60951367 -TTATTATATATTATTGTTTATTATTATACTGATTGAAATATGCTGTAAGTCCCTATACTATTCG
66 ATTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAGTCCCTATACTTTTCG
* *
60951431 AACATTTAAAAGTTAATACTCCTACTATATTATATAATGCTATATCATATC-ATA-TAT-TAATA
131 AACATTTAAAAGTTAACACTCCTACTATATTATATAATGCTATATCACATCAATAGTATATAATA
* *
60951493 -A-T-T-TATATATATACGCATAAATTATTAAATATTATAATAGC
196 TAGTATATATATATATACGCATAAATGATTAAACATTATAATAGC
* * * *
60951534 ATGTAAT-TCTATCTCTTTTATTATAATCTATATTATAATAATAGTTACT-TATAATAGTAGTAC
1 ATGTAATAT-TATATATTTTATTATAATATATAATATAATAATAGTTA-TATATAATAGTAG---
* *
60951597 ATTATATATTACTTATTATATATTATTGTTTATTATTATACTAATTAAAATATGCTTTAAGTCCT
61 -----ATATTA-TTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAGTCCC
* * * * *
60951662 TATAGTTTTCGTACATTTAAAAATTAGCCCTCCTACT
120 TATACTTTTCGAACATTTAAAAGTTAACACTCCTACT
60951699 GTATCTAATG
Statistics
Matches: 329, Mismatches: 45, Indels: 36
0.80 0.11 0.09
Matches are distributed among these distances:
229 1 0.00
230 81 0.25
231 1 0.00
232 1 0.00
234 1 0.00
235 1 0.00
236 27 0.08
237 38 0.12
238 10 0.03
239 1 0.00
240 87 0.26
241 1 0.00
242 79 0.24
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (240 bp):
ATGTAATATTATATATTTTATTATAATATATAATATAATAATAGTTATATATAATAGTAGATATT
ATTATTATATATTATTGTTTATTATTATACTAATTGAAATATGCTTTAAGTCCCTATACTTTTCG
AACATTTAAAAGTTAACACTCCTACTATATTATATAATGCTATATCACATCAATAGTATATAATA
TAGTATATATATATATACGCATAAATGATTAAACATTATAATAGC
Found at i:60951601 original size:16 final size:17
Alignment explanation
Indices: 60951565--60951602 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
60951555 TATAATCTAT
60951565 ATTATAATAATAGTTAC
1 ATTATAATAATAGTTAC
*
60951582 -TTATAATAGTAG-TAC
1 ATTATAATAATAGTTAC
60951597 ATTATA
1 ATTATA
60951603 TATTACTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (17 bp):
ATTATAATAATAGTTAC
Found at i:60951736 original size:2 final size:2
Alignment explanation
Indices: 60951711--60951781 Score: 78
Period size: 2 Copynumber: 36.0 Consensus size: 2
60951701 ATCTAATGCC
*
60951711 AT AT CAT AT -T AT CAT AT A- AT AT AT AT -T A- AT AGT TT AT AT
1 AT AT -AT AT AT AT -AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
60951750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60951782 GCATCGATGA
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
1 4 0.07
2 51 0.85
3 5 0.08
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60951881 original size:30 final size:26
Alignment explanation
Indices: 60951839--60951915 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 26
60951829 TTATGATCTA
* *
60951839 TATTTTAATAATAGTTATGTATGTATT
1 TATTTTAGTAATAGTTATATAT-TATT
60951866 AATATTTTTAGTAATAGTTATATATTATT
1 --TA-TTTTAGTAATAGTTATATATTATT
*
60951895 TATTTTATGTAATAGTAATAT
1 TATTTTA-GTAATAGTTATAT
60951916 TCTAATTTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
26 5 0.12
27 14 0.33
29 6 0.14
30 18 0.42
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (26 bp):
TATTTTAGTAATAGTTATATATTATT
Found at i:60951906 original size:27 final size:29
Alignment explanation
Indices: 60951837--60951915 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 29
60951827 TATTATGATC
* *
60951837 TATATTTTA-ATAATAGTTATGTATGTAT
1 TATATTTTATGTAATAGTTATATATGTAT
60951865 TAATATTTT-TAGTAATAGTTATATAT-TAT
1 T-ATATTTTAT-GTAATAGTTATATATGTAT
*
60951894 T-TATTTTATGTAATAGTAATAT
1 TATATTTTATGTAATAGTTATAT
60951916 TCTAATTTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 18 0.41
28 2 0.05
29 11 0.25
30 13 0.30
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (29 bp):
TATATTTTATGTAATAGTTATATATGTAT
Found at i:60956957 original size:16 final size:17
Alignment explanation
Indices: 60956911--60956985 Score: 61
Period size: 16 Copynumber: 4.6 Consensus size: 17
60956901 AGTAGATATT
*
60956911 TATTAT-TTATAAAAGA
1 TATTATATTATAAAATA
60956927 TATT-TATTAATAAAATA
1 TATTATATT-ATAAAATA
60956944 -ATTATATTATAAAAT-
1 TATTATATTATAAAATA
* * *
60956959 TTTTATGTAAT-AAATA
1 TATTATATTATAAAATA
*
60956975 TATTAAATTAT
1 TATTATATTAT
60956986 GACAAGTGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
15 5 0.11
16 30 0.65
17 11 0.24
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TATTATATTATAAAATA
Found at i:60956970 original size:32 final size:33
Alignment explanation
Indices: 60956911--60956985 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 33
60956901 AGTAGATATT
60956911 TATTAT-TTATAAAAGATATTTATTAATAAA-A
1 TATTATATTATAAAAGATATTTATTAATAAATA
*
60956942 TAATTATATTAT-AAA-ATTTTTATGTAATAAATA
1 T-ATTATATTATAAAAGATATTTAT-TAATAAATA
*
60956975 TATTAAATTAT
1 TATTATATTAT
60956986 GACAAGTGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
31 8 0.21
32 24 0.63
33 6 0.16
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (33 bp):
TATTATATTATAAAAGATATTTATTAATAAATA
Found at i:60957055 original size:15 final size:17
Alignment explanation
Indices: 60957035--60957066 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
60957025 AAATATTTGA
60957035 TATTAA-TTAA-ATATT
1 TATTAAGTTAACATATT
60957050 TATTAAGTTAACATATT
1 TATTAAGTTAACATATT
60957067 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TATTAAGTTAACATATT
Done.