Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold73
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: 1308442
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.31
Warning! 157727 characters in sequence are not A, C, G, or T
File 8 of 9
Found at i:936299 original size:24 final size:23
Alignment explanation
Indices: 936272--936332 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
936262 AAAAAATTTA
*
936272 AATTTATTTTTATTTGATTATACG
1 AATTTATTTTTATTTGATGATA-G
** *
936296 AATTTAAATTT-TTT-ATGATAT
1 AATTTATTTTTATTTGATGATAG
936317 AATTTATTTTTATTTG
1 AATTTATTTTTATTTG
936333 TATAAATTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
21 9 0.31
22 8 0.28
23 3 0.10
24 9 0.31
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.61
Consensus pattern (23 bp):
AATTTATTTTTATTTGATGATAG
Found at i:936322 original size:21 final size:21
Alignment explanation
Indices: 936296--936350 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
936286 TGATTATACG
936296 AATTTAAATTTTTTATG-ATA
1 AATTTAAATTTTTTATGTATA
*
936316 TAATTT--ATTTTTATTTGTATA
1 -AATTTAAATTTTT-TATGTATA
936337 AATTTAAATTTTTT
1 AATTTAAATTTTTT
936351 TGTCGATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
19 6 0.21
20 8 0.28
21 9 0.31
22 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
AATTTAAATTTTTTATGTATA
Found at i:936352 original size:20 final size:21
Alignment explanation
Indices: 936296--936353 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
936286 TGATTATACG
936296 AATTTAAATTTTTTATG-ATAT
1 AATTTAAATTTTTT-TGTATAT
*
936317 AATTT-ATTTTTATTTGTATA-
1 AATTTAAATTTT-TTTGTATAT
936337 AATTTAAATTTTTTTGT
1 AATTTAAATTTTTTTGT
936354 CGATTATAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
AATTTAAATTTTTTTGTATAT
Found at i:936392 original size:68 final size:70
Alignment explanation
Indices: 936218--936400 Score: 196
Period size: 70 Copynumber: 2.6 Consensus size: 70
936208 TTTAAGTATT
* *
936218 ATTATATGAATTAAAATTT-TATAAAATATGATTTATTTTTATTTAAAAAATTTAAATTTATTTT
1 ATTATAAGAATTTAAATTTCT-TAAAATATGATTTATTTTTATTTAAAAAATTTAAATTTATTTT
* *
936282 TATTTG
65 TAGTCG
* * ** * * *
936288 ATTATACGAATTTAAATTTTTTATGATATAATTTATTTTTATTTGTATAAATTTAAA-TT-TTTT
1 ATTATAAGAATTTAAATTTCTTAAAATATGATTTATTTTTATTT-AAAAAATTTAAATTTATTTT
936351 T-GTCG
65 TAGTCG
*
936356 ATTATAAGAGTTTAAATTATCTTAAAATATGA-TTATTTTTATTTA
1 ATTATAAGAATTTAAATT-TCTTAAAATATGATTTATTTTTATTTA
936401 TAAGATTAAT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
68 30 0.32
69 14 0.15
70 39 0.41
71 11 0.12
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (70 bp):
ATTATAAGAATTTAAATTTCTTAAAATATGATTTATTTTTATTTAAAAAATTTAAATTTATTTTT
AGTCG
Found at i:936768 original size:19 final size:20
Alignment explanation
Indices: 936746--936788 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
936736 ATTTATTTTT
936746 TTAAGATT-AAT-TATAGGAG
1 TTAAGATTGAATATA-AGGAG
936765 TTAAGATTGAATATAAGGAG
1 TTAAGATTGAATATAAGGAG
936785 TTAA
1 TTAA
936789 TTTTGTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.36
20 12 0.55
21 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (20 bp):
TTAAGATTGAATATAAGGAG
Found at i:936785 original size:20 final size:19
Alignment explanation
Indices: 936746--936788 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
936736 ATTTATTTTT
936746 TTAAGATTAATTATAGGAG
1 TTAAGATTAATTATAGGAG
936765 TTAAGATTGAA-TATAAGGAG
1 TTAAGATT-AATTAT-AGGAG
936785 TTAA
1 TTAA
936789 TTTTGTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (19 bp):
TTAAGATTAATTATAGGAG
Found at i:937464 original size:28 final size:29
Alignment explanation
Indices: 937440--937496 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
937430 ATATATTTAT
**
937440 TTTAAAAAAAATTTATT-AAATTATTTGA
1 TTTAAAAAAAATAAATTAAAATTATTTGA
*
937468 TTTAAAATAAATAAATTAAAATTATTTGA
1 TTTAAAAAAAATAAATTAAAATTATTTGA
937497 AAAAATTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (29 bp):
TTTAAAAAAAATAAATTAAAATTATTTGA
Found at i:938354 original size:2 final size:2
Alignment explanation
Indices: 938347--938385 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
938337 GAATTTTGTT
*
938347 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
938386 TCATTATGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:942039 original size:18 final size:18
Alignment explanation
Indices: 942016--942062 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
942006 GTTCTCAATC
*
942016 ACTAGTTTTTCTTACTAA
1 ACTAGTTTTTCTTACAAA
942034 ACTAGTTTTTCTTACAAA
1 ACTAGTTTTTCTTACAAA
*
942052 ACTAGATTTTC
1 ACTAGTTTTTC
942063 GACAGAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.47
Consensus pattern (18 bp):
ACTAGTTTTTCTTACAAA
Found at i:943560 original size:2 final size:2
Alignment explanation
Indices: 943553--943597 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
943543 GGCGTGCAGG
943553 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
943595 TC T
1 TC T
943598 TTGTCCACCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:945504 original size:16 final size:17
Alignment explanation
Indices: 945483--945539 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 17
945473 GTCATAATCG
945483 TATTTAAATT-ATTTTA
1 TATTTAAATTAATTTTA
*
945499 TATTTATATTAATTTTAA
1 TATTTAAATTAATTTT-A
*
945517 TAAATTAATAATTAATTTTA
1 T--ATTTA-AATTAATTTTA
945537 TAT
1 TAT
945540 AACTTATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
16 9 0.27
17 5 0.15
18 4 0.12
20 6 0.18
21 9 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTAAATTAATTTTA
Found at i:945548 original size:21 final size:20
Alignment explanation
Indices: 945502--945548 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
945492 TATTTTATAT
945502 TTAT-ATTAATTTTAATAAA
1 TTATAATTAATTTTAATAAA
*
945521 TTAATAATTAATTTTATATAAC
1 TT-ATAATTAATTTTA-ATAAA
945543 TTATAA
1 TTATAA
945549 AACATTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.08
20 2 0.08
21 14 0.58
22 6 0.25
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATAATTAATTTTAATAAA
Found at i:945715 original size:8 final size:8
Alignment explanation
Indices: 945704--945790 Score: 52
Period size: 8 Copynumber: 9.9 Consensus size: 8
945694 TTAATAATTC
945704 ATATATTT
1 ATATATTT
945712 ATATCATATTT
1 ATA---TATTT
*
945723 ATTTATTTT
1 ATATA-TTT
945732 ATTATATTT
1 A-TATATTT
945741 A-ATAATTTT
1 ATAT-A-TTT
945750 AATATATTT
1 -ATATATTT
945759 ATATATTT
1 ATATATTT
945767 ATATTATATT
1 ATA-TAT-TT
*
945777 -TATATAT
1 ATATATTT
945784 ATATATT
1 ATATATT
945791 ATTATGTCCA
Statistics
Matches: 63, Mismatches: 4, Indels: 24
0.69 0.04 0.26
Matches are distributed among these distances:
7 3 0.05
8 25 0.40
9 19 0.30
10 7 0.11
11 9 0.14
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (8 bp):
ATATATTT
Found at i:945734 original size:9 final size:10
Alignment explanation
Indices: 945705--945795 Score: 68
Period size: 9 Copynumber: 9.3 Consensus size: 10
945695 TAATAATTCA
945705 TATATTTATAT
1 TATATTT-TAT
*
945716 CATA-TTTAT
1 TATATTTTAT
945725 T-TATTTTAT
1 TATATTTTAT
*
945734 TATA-TTTAA
1 TATATTTTAT
*
945743 TA-ATTTTAA
1 TATATTTTAT
945752 TATA-TTTA-
1 TATATTTTAT
945760 TATATTTATAT
1 TATATTT-TAT
945771 TATATTTATAT
1 TATATTT-TAT
*
945782 ATATATATTAT
1 -TATATTTTAT
945793 TAT
1 TAT
945796 GTCCATGTGA
Statistics
Matches: 68, Mismatches: 4, Indels: 17
0.76 0.04 0.19
Matches are distributed among these distances:
8 7 0.10
9 28 0.41
10 10 0.15
11 17 0.25
12 6 0.09
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (10 bp):
TATATTTTAT
Found at i:945740 original size:18 final size:19
Alignment explanation
Indices: 945707--945792 Score: 95
Period size: 18 Copynumber: 4.6 Consensus size: 19
945697 ATAATTCATA
*
945707 TATTTATATCATATTTATT
1 TATTTATATTATATTTATT
*
945726 TATTT-TATTATATTTAAT
1 TATTTATATTATATTTATT
* * *
945744 AATTT-TAATATATTTATA
1 TATTTATATTATATTTATT
*
945762 TATTTATATTATATTTATA
1 TATTTATATTATATTTATT
*
945781 TATATATATTAT
1 TATTTATATTAT
945793 TATGTCCATG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
18 29 0.51
19 28 0.49
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTATATTATATTTATT
Found at i:945741 original size:45 final size:48
Alignment explanation
Indices: 945692--945787 Score: 121
Period size: 47 Copynumber: 2.0 Consensus size: 48
945682 TTGTTTTTAA
*
945692 ATTTAATAA-TTCATATATTTATATCATATT-TATT-TATTT-TAT-TAT
1 ATTTAATAATTTAATATATTTATAT-AT-TTATATTATATTTATATATAT
945737 ATTTAATAATTTTAATATATTTATATATTTATATTATATTTATATATAT
1 ATTTAATAA-TTTAATATATTTATATATTTATATTATATTTATATATAT
945786 AT
1 AT
945788 ATTATTATGT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
45 11 0.25
46 6 0.14
47 19 0.43
48 3 0.07
49 5 0.11
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (48 bp):
ATTTAATAATTTAATATATTTATATATTTATATTATATTTATATATAT
Found at i:945776 original size:19 final size:19
Alignment explanation
Indices: 945704--945792 Score: 112
Period size: 19 Copynumber: 4.8 Consensus size: 19
945694 TTAATAATTC
*
945704 ATATATTTATATCATATTT
1 ATATATTTATATTATATTT
*
945723 ATTTATTT-TATTATATTT
1 ATATATTTATATTATATTT
*
945741 A-ATAATTT-TAATATATTT
1 ATAT-ATTTATATTATATTT
945759 ATATATTTATATTATATTT
1 ATATATTTATATTATATTT
*
945778 ATATATATATATTAT
1 ATATATTTATATTAT
945793 TATGTCCATG
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
17 1 0.02
18 28 0.46
19 32 0.52
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATATTTATATTATATTT
Found at i:946234 original size:2 final size:2
Alignment explanation
Indices: 946223--946254 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
946213 AATTCTGCAA
946223 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
946255 AACCACCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:949130 original size:17 final size:16
Alignment explanation
Indices: 949093--949171 Score: 63
Period size: 17 Copynumber: 4.8 Consensus size: 16
949083 TCCTATGTTA
*
949093 AAATTAAAATATAATT
1 AAATTAAAATTTAATT
949109 AAATTTAAAATTTAATT
1 AAA-TTAAAATTTAATT
* * *
949126 TAATTAATTTATATAATT
1 AAATTAA--AATTTAATT
*
949144 -AATTAATATTTAA-T
1 AAATTAAAATTTAATT
949158 AAATTTAAAATTTA
1 AAA-TTAAAATTTA
949172 TAATATTTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 1 0.02
15 8 0.15
16 16 0.31
17 20 0.38
18 7 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTAAAATTTAATT
Found at i:949131 original size:33 final size:32
Alignment explanation
Indices: 949094--949157 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 32
949084 CCTATGTTAA
949094 AATTAA-AATATAATTAAATTTAAAATTTAATTT
1 AATTAATAATATAATT-AA-TTAAAATTTAATTT
* *
949127 AATTAATTTATATAATTAATTAATATTTAAT
1 AATTAA-TAATATAATTAATTAAAATTTAAT
949158 AAATTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 17 0.63
34 2 0.07
35 8 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
AATTAATAATATAATTAATTAAAATTTAATTT
Found at i:949132 original size:22 final size:22
Alignment explanation
Indices: 949090--949171 Score: 60
Period size: 23 Copynumber: 3.5 Consensus size: 22
949080 ATCTCCTATG
* *
949090 TTAAAATTAAAATATAATTAAAT
1 TTAAAATT-TAATTTAATTAAAT
949113 TTAAAATTTAATTTAATT-AAT
1 TTAAAATTTAATTTAATTAAAT
949134 TTATATAATTAATTAATATTTAA-TAAAT
1 TTA-A-AA-T--TT-A-ATTTAATTAAAT
949162 TTAAAATTTA
1 TTAAAATTTA
949172 TAATATTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
21 6 0.12
22 10 0.20
23 12 0.24
24 1 0.02
25 1 0.02
26 4 0.08
27 3 0.06
28 12 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAAAATTTAATTTAATTAAAT
Found at i:950817 original size:20 final size:20
Alignment explanation
Indices: 950758--950820 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
950748 AGTTTGGATT
* *
950758 TATTTAATTAAATTTGAATTA
1 TATTTATTTATATTT-AATTA
* **
950779 TTATTTATTAATA-AAAATTA
1 -TATTTATTTATATTTAATTA
950799 TATTTATTTATATTTAATTA
1 TATTTATTTATATTTAATTA
950819 TA
1 TA
950821 AAATATATTA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 11 0.34
20 12 0.38
22 9 0.28
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TATTTATTTATATTTAATTA
Found at i:950835 original size:15 final size:17
Alignment explanation
Indices: 950807--950840 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
950797 TATATTTATT
950807 TATATTTAATTATAAAA
1 TATATTTAATTATAAAA
950824 TATA-TTAA-TATAAAA
1 TATATTTAATTATAAAA
950839 TA
1 TA
950841 AAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 4 0.24
17 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATATTTAATTATAAAA
Found at i:953153 original size:21 final size:21
Alignment explanation
Indices: 953110--953153 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
953100 TGATGCATTA
* * **
953110 TTGGATGAGAGAATACATTTT
1 TTGGATGAAAAAATACAACTT
953131 TTGGATGAAAAAATACAACTT
1 TTGGATGAAAAAATACAACTT
953152 TT
1 TT
953154 AATAACCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (21 bp):
TTGGATGAAAAAATACAACTT
Found at i:954049 original size:16 final size:16
Alignment explanation
Indices: 954005--954051 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
953995 ATTTATAAAT
*
954005 TAAAAATTAAA-TAAA
1 TAAAAATTAAATTTAA
* * *
954020 TCAAGATCAAATTTAA
1 TAAAAATTAAATTTAA
954036 TAAAAATTAAATTTAA
1 TAAAAATTAAATTTAA
954052 ATTAAATTAA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (16 bp):
TAAAAATTAAATTTAA
Found at i:954385 original size:13 final size:13
Alignment explanation
Indices: 954367--954391 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
954357 GTCTCTCTCC
954367 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
954380 TTTTTTTCTTTT
1 TTTTTTTCTTTT
954392 AAGCCCTGAA
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTTTCTTTTT
Found at i:955934 original size:20 final size:20
Alignment explanation
Indices: 955905--956056 Score: 62
Period size: 20 Copynumber: 8.1 Consensus size: 20
955895 TAATTATTTA
*
955905 TATAAATATATTTATTATAT
1 TATAATTATATTTATTATAT
* *
955925 TATAATTATATTTAAAATATTT
1 TATAATTATATTT--ATTATAT
* * * * *
955947 TTTATTTATATTAATTTTAA
1 TATAATTATATTTATTATAT
955967 TA-AATTAATAATTTATT-TA-
1 TATAATT-AT-ATTTATTATAT
**
955986 TATAA--AT-TTTAAAATA-
1 TATAATTATATTTATTATAT
956002 TATAATTATA-TT-TTATAT
1 TATAATTATATTTATTATAT
*
956020 TAT-ATTA-A-TTATTTTA-
1 TATAATTATATTTATTATAT
956036 TATATATTATATTTA-TATAT
1 TATA-ATTATATTTATTATAT
956056 T
1 T
956057 TATATGTAAT
Statistics
Matches: 97, Mismatches: 19, Indels: 32
0.66 0.13 0.22
Matches are distributed among these distances:
15 4 0.04
16 13 0.13
17 13 0.13
18 11 0.11
19 9 0.09
20 26 0.27
21 6 0.06
22 15 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATAATTATATTTATTATAT
Found at i:955982 original size:31 final size:35
Alignment explanation
Indices: 955946--956070 Score: 111
Period size: 31 Copynumber: 3.6 Consensus size: 35
955936 TTAAAATATT
955946 TTTTATTTATATTAATTTTAATAA-AT-TAA-TA-A
1 TTTTATTTATATTAATTTTAA-AATATATAATTATA
*
955978 -TTTATTTATATAAATTTTAAAATATATAATTATA
1 TTTTATTTATATTAATTTTAAAATATATAATTATA
**
956012 TTTTATATTATATTAATTATT-TTATATAT-ATTATA
1 TTTTAT-TTATATTAATT-TTAAAATATATAATTATA
956047 TTTATATATTTATATGTAATTTTA
1 -TT-T-TATTTATAT-TAATTTTA
956071 TTAAGTTTAT
Statistics
Matches: 77, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
30 2 0.03
31 21 0.27
32 3 0.04
33 2 0.03
34 1 0.01
35 11 0.14
36 18 0.23
37 11 0.14
38 8 0.10
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (35 bp):
TTTTATTTATATTAATTTTAAAATATATAATTATA
Found at i:956045 original size:23 final size:23
Alignment explanation
Indices: 955999--956061 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
955989 AAATTTTAAA
*
955999 ATATATAATTATATT-T-TATATT
1 ATAT-TAATTATTTTATATATATT
956021 ATATTAATTATTTTATATATATT
1 ATATTAATTATTTTATATATATT
*
956044 ATATTTA-TATATTTATAT
1 ATATTAATTAT-TTTATAT
956062 GTAATTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
21 9 0.25
22 8 0.22
23 19 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATATTAATTATTTTATATATATT
Found at i:956725 original size:5 final size:5
Alignment explanation
Indices: 956715--956843 Score: 55
Period size: 5 Copynumber: 27.2 Consensus size: 5
956705 ATTAACTTTA
* * *
956715 AATAT AATAT AAT-T -ATAT AATAT AAATAT AAAAT AAAAT AA-A- AAAAT
1 AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT AATAT
* * * *
956762 AATAT AAAAT AA-A- AA-AT AATAT AATAA AAT-T TATAT TATAT AAATTAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT -AA-TAT
* * *
956810 GAATAT ATTAA AAT-T TATAT AA-AT AA-AT AATAT A
1 -AATAT AATAT AATAT AATAT AATAT AATAT AATAT A
956844 TTAAATATGA
Statistics
Matches: 98, Mismatches: 14, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
3 7 0.07
4 19 0.19
5 58 0.59
6 9 0.09
7 5 0.05
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:956734 original size:13 final size:13
Alignment explanation
Indices: 956716--956902 Score: 65
Period size: 13 Copynumber: 14.5 Consensus size: 13
956706 TTAACTTTAA
*
956716 ATATAATATAATT
1 ATATAATATAAAT
956729 ATATAATATAAAT
1 ATATAATATAAAT
*
956742 ATAAAATA-AAAT
1 ATATAATATAAAT
* *
956754 A-AAAAAAT-AAT
1 ATATAATATAAAT
* *
956765 ATAAAATAAAAAAT
1 ATATAAT-ATAAAT
956779 AATATAATA-AAATTT
1 -ATATAATATAAA--T
*
956794 ATATTATATAAAT
1 ATATAATATAAAT
*
956807 -TATGAATATATTAAA
1 ATAT-AATATA--AAT
*
956822 AT-TTATATAAAT
1 ATATAATATAAAT
*
956834 AAATAATATATTAA-
1 ATATAATATA--AAT
* *
956848 ATATGATTACAAAT
1 ATAT-AATATAAAT
956862 -TATAATATATAA-
1 ATATAATATA-AAT
*
956874 A-ATTATAT-AA-
1 ATATAATATAAAT
*
956884 ATATAATAAAAAT
1 ATATAATATAAAT
956897 ATATAA
1 ATATAA
956903 ATTATCATTT
Statistics
Matches: 131, Mismatches: 21, Indels: 44
0.67 0.11 0.22
Matches are distributed among these distances:
10 3 0.02
11 14 0.11
12 27 0.21
13 48 0.37
14 19 0.15
15 19 0.15
16 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (13 bp):
ATATAATATAAAT
Found at i:956778 original size:30 final size:29
Alignment explanation
Indices: 956731--956791 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
956721 ATATAATTAT
*
956731 ATAATATAAATATAAAATAAAATAAAAAA
1 ATAATATAAATAAAAAATAAAATAAAAAA
* *
956760 ATAATATAAAATAAAAAATAATATAATAAA
1 ATAATAT-AAATAAAAAATAAAATAAAAAA
956790 AT
1 AT
956792 TTATATTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (29 bp):
ATAATATAAATAAAAAATAAAATAAAAAA
Found at i:956898 original size:27 final size:26
Alignment explanation
Indices: 956729--956907 Score: 88
Period size: 27 Copynumber: 6.8 Consensus size: 26
956719 TAATATAATT
* *
956729 ATATAATATAAATATAAAATAAAATAA
1 ATATAATA-AAATATAAAATTATATAA
* * * *
956756 A-A-AA-ATAATATAAAATAAAAAATA
1 ATATAATAAAATATAAAATTATATA-A
* *
956780 ATATAATAAAAT-TTATATTATATAA
1 ATATAATAAAATATAAAATTATATAA
*
956805 AT-T-ATGAATATATTAAAATTTATATAA
1 ATATAAT-AAAATA-TAAAA-TTATATAA
* *
956832 ATA-AATAATATATTAAA-TATGATTACA
1 ATATAATAAAATATAAAATTAT-A-TA-A
* *
956859 A-ATTATAATATATAAAATTATATAA
1 ATATAATAAAATATAAAATTATATAA
956884 ATATAATAAAAATATATAAATTAT
1 ATATAAT-AAAATATA-AAATTAT
956908 CATTTAATAT
Statistics
Matches: 118, Mismatches: 16, Indels: 35
0.70 0.09 0.21
Matches are distributed among these distances:
23 17 0.14
24 11 0.09
25 9 0.08
26 26 0.22
27 43 0.36
28 12 0.10
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (26 bp):
ATATAATAAAATATAAAATTATATAA
Found at i:956926 original size:56 final size:51
Alignment explanation
Indices: 956812--956935 Score: 126
Period size: 56 Copynumber: 2.3 Consensus size: 51
956802 TAAATTATGA
* *
956812 ATATAT-TAAAATTTATATAAATAAATAATATATTAAATATGATTACAAATT
1 ATATATATAAAA-TTATATAAATAAATAAAATATTAAATATCATTACAAATT
*
956863 ATAATATATAAAATTATATAAATATAATAAAAATATATAAATTATCATTTA-ATATAT
1 AT-ATATATAAAATTATATAAATA-AAT-AAAATAT-TAAA-TATCA-TTACAAAT-T
956920 ATATATATAAACATTA
1 ATATATATAAA-ATTA
956936 AAATTATATT
Statistics
Matches: 61, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
51 2 0.03
52 15 0.25
53 8 0.13
54 6 0.10
55 4 0.07
56 16 0.26
57 10 0.16
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (51 bp):
ATATATATAAAATTATATAAATAAATAAAATATTAAATATCATTACAAATT
Found at i:956935 original size:29 final size:25
Alignment explanation
Indices: 956796--956935 Score: 104
Period size: 27 Copynumber: 5.2 Consensus size: 25
956786 TAAAATTTAT
956796 ATTATATAAAT-TATGAATATATTAAA
1 ATTATATAAATATAT-AATATA-TAAA
*
956822 ATTTATATAAATAAATAATATATTAAA
1 A-TTATATAAATATATAATATA-TAAA
* *
956849 TATGATTACAAAT-TATAATATATAAA
1 -ATTA-TATAAATATATAATATATAAA
*
956875 ATTATATAAATATAATAAAAATATATAA
1 ATTATATAAATAT-AT-AATATATA-AA
*
956903 ATTATCATTTAATATATATATATATAAA
1 ATTAT-A-TAAATATATA-ATATATAAA
956931 CATTA
1 -ATTA
956936 AAATTATATT
Statistics
Matches: 93, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
24 6 0.06
25 4 0.04
26 7 0.08
27 38 0.41
28 19 0.20
29 13 0.14
30 6 0.06
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (25 bp):
ATTATATAAATATATAATATATAAA
Found at i:963343 original size:3 final size:3
Alignment explanation
Indices: 963319--963357 Score: 51
Period size: 3 Copynumber: 12.0 Consensus size: 3
963309 ATGACATTCG
963319 ATT ATT GATT ACTT ATTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT -ATT A-TT A-TT ATT ATT ATT ATT ATT ATT ATT
963358 TTTTTCTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
3 24 0.73
4 9 0.27
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:963842 original size:23 final size:22
Alignment explanation
Indices: 963816--963858 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
963806 TTGTTTATTT
963816 AAATAAATT-TTTAAAGATAAATC
1 AAAT-AATTATTTAAA-ATAAATC
*
963839 AAATTATTATTTAAAATAAA
1 AAATAATTATTTAAAATAAA
963859 AATTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
AAATAATTATTTAAAATAAATC
Found at i:963932 original size:27 final size:25
Alignment explanation
Indices: 963852--963935 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 25
963842 TTATTATTTA
963852 AAATAAAAATTTATTTAAATACAAATT
1 AAATAAAAATTTATTTAAATA-AAA-T
963879 AAAAAATAAAAATTTATTTAAATAAAAT
1 ---AAATAAAAATTTATTTAAATAAAAT
963907 AAATATAAAATCTTACTTTAAA-AAAAT
1 AAATA-AAAAT-TTA-TTTAAATAAAAT
963934 AA
1 AA
963936 TAGTTAAGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
25 5 0.10
26 5 0.10
27 10 0.20
28 7 0.14
29 3 0.06
30 21 0.41
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (25 bp):
AAATAAAAATTTATTTAAATAAAAT
Found at i:965480 original size:2 final size:2
Alignment explanation
Indices: 965473--965498 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
965463 CTACACAGAC
965473 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
965499 GTGGAAATCA
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:965964 original size:19 final size:20
Alignment explanation
Indices: 965942--965983 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
965932 TCTTATTCTA
*
965942 TTTATTATTTATT-TATAAT
1 TTTATTATTTATTAAATAAT
*
965961 TTTATTTTTTATTAAATAAT
1 TTTATTATTTATTAAATAAT
965981 TTT
1 TTT
965984 TTTTAGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATTATTTATTAAATAAT
Found at i:966171 original size:11 final size:10
Alignment explanation
Indices: 966156--966226 Score: 63
Period size: 11 Copynumber: 6.7 Consensus size: 10
966146 ATTAGACATG
966156 ATATAAATAA
1 ATATAAATAA
*
966166 GATATAAAATTA
1 -ATAT-AAATAA
*
966178 TTA-AAATAA
1 ATATAAATAA
966187 ATATGAAATAA
1 ATAT-AAATAA
*
966198 AAATAATATAA
1 ATATAA-ATAA
966209 ATATAATATAA
1 ATATAA-ATAA
966220 ATATAAA
1 ATATAAA
966227 ATATCTTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
9 7 0.14
10 3 0.06
11 35 0.70
12 5 0.10
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (10 bp):
ATATAAATAA
Found at i:966236 original size:27 final size:25
Alignment explanation
Indices: 966158--966263 Score: 85
Period size: 27 Copynumber: 4.0 Consensus size: 25
966148 TAGACATGAT
966158 ATAA-ATAAGATATAAAAT-TATTAAA
1 ATAATATAA-ATATAAAATAT-TTAAA
*
966183 ATAAATATGAAATA-AAAATAATATAAA
1 AT-AATAT-AAATATAAAAT-ATTTAAA
966210 TATAATATAAATATAAAATATCTTAAA
1 -ATAATATAAATATAAAATAT-TTAAA
*
966237 ATTTATATAAATAT-AAATATTTTAAA
1 A-TAATATAAATATAAAATA-TTTAAA
966263 A
1 A
966264 ATTATTATAA
Statistics
Matches: 68, Mismatches: 3, Indels: 19
0.76 0.03 0.21
Matches are distributed among these distances:
25 2 0.03
26 26 0.38
27 35 0.51
28 5 0.07
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (25 bp):
ATAATATAAATATAAAATATTTAAA
Found at i:966264 original size:27 final size:25
Alignment explanation
Indices: 966214--966283 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 25
966204 TATAAATATA
966214 ATATAAATATAAAATATCTTAAAATTT
1 ATATAAATAT-AAATATCTTAAAA-TT
*
966241 ATATAAATATAAATATTTTAAAAATT
1 ATATAAATATAAATATCTT-AAAATT
966267 AT-TATAATATAATATAT
1 ATATA-AATATAA-ATAT
966284 AGCTATGGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
25 2 0.05
26 19 0.49
27 18 0.46
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (25 bp):
ATATAAATATAAATATCTTAAAATT
Found at i:966441 original size:29 final size:30
Alignment explanation
Indices: 966383--966462 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 30
966373 AAATAAAATA
*
966383 ATTAAAATATATATAATATAAACACATAAT
1 ATTAAAATTTATATAATATAAACACATAAT
*
966413 -TTAAAATTTATATAATATAAACTA-TTAAT
1 ATTAAAATTTATATAATATAAAC-ACATAAT
*
966442 ATACTAAAATTTATAAAATAT
1 AT--TAAAATTTATATAATAT
966463 TTTAAATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
29 25 0.58
30 2 0.05
32 16 0.37
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (30 bp):
ATTAAAATTTATATAATATAAACACATAAT
Found at i:966456 original size:32 final size:29
Alignment explanation
Indices: 966380--966434 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
966370 AATAAATAAA
*
966380 ATAA-TTAAAATATATATAATATAAACAC
1 ATAATTTAAAATTTATATAATATAAACAC
966408 ATAATTTAAAATTTATATAATATAAAC
1 ATAATTTAAAATTTATATAATATAAAC
966435 TATTAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (29 bp):
ATAATTTAAAATTTATATAATATAAACAC
Found at i:966493 original size:10 final size:10
Alignment explanation
Indices: 966439--966504 Score: 50
Period size: 9 Copynumber: 6.9 Consensus size: 10
966429 ATAAACTATT
*
966439 AATATACTAA
1 AATATAATAA
*
966449 AAT-TTATAA
1 AATATAATAA
* *
966458 AATAT-TTTA
1 AATATAATAA
*
966467 AATATAATTAT
1 AATATAA-TAA
966478 AATATAATAA
1 AATATAATAA
966488 AATAT-AT-A
1 AATATAATAA
966496 AATATAATA
1 AATATAATA
966505 TTATTACACA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
8 6 0.14
9 18 0.42
10 11 0.26
11 8 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (10 bp):
AATATAATAA
Found at i:966501 original size:18 final size:18
Alignment explanation
Indices: 966422--966504 Score: 55
Period size: 18 Copynumber: 4.4 Consensus size: 18
966412 TTTAAAATTT
966422 ATATAATATAAACTAT-T-A
1 ATATAATA-AAA-TATATAA
* *
966440 ATATACTAAAATTTATAA
1 ATATAATAAAATATATAA
* *
966458 A-ATATTTTAAATATAATTATA
1 ATATA-ATAAAATAT-A-TA-A
966479 ATATAATAAAATATATAA
1 ATATAATAAAATATATAA
966497 ATATAATA
1 ATATAATA
966505 TTATTACACA
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
16 2 0.04
17 7 0.14
18 24 0.47
19 3 0.06
20 3 0.06
21 9 0.18
22 3 0.06
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATAATAAAATATATAA
Found at i:968725 original size:16 final size:16
Alignment explanation
Indices: 968704--968734 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
968694 TAAAATTATC
*
968704 TTTAATTATTGTTAAA
1 TTTAATTATTATTAAA
968720 TTTAATTATTATTAA
1 TTTAATTATTATTAA
968735 GTTATTCTAA
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:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TTTAATTATTATTAAA
Found at i:969084 original size:25 final size:27
Alignment explanation
Indices: 969041--969090 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
969031 TATCTTTAAA
**
969041 ATTTTTAAAATAATGATAAT-TAATTT
1 ATTTTTAAAATAAAAATAATATAATTT
969067 ATTTTT-AAATAAAAATAATATAAT
1 ATTTTTAAAATAAAAATAATATAAT
969091 ATGTTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
ATTTTTAAAATAAAAATAATATAATTT
Found at i:970602 original size:16 final size:17
Alignment explanation
Indices: 970529--970608 Score: 78
Period size: 16 Copynumber: 4.7 Consensus size: 17
970519 AACATGAATA
970529 TATAAATATATCAAA-ATT
1 TATAAATATA--AAATATT
*
970547 TATAAAATATAAATTATT
1 TAT-AAATATAAAATATT
*
970565 TACAAAT-TAAAAT-TT
1 TATAAATATAAAATATT
970580 ATATAAATATAAAATATT
1 -TATAAATATAAAATATT
970598 T-TAAATATAAA
1 TATAAATATAAA
970609 TTTATTATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
15 2 0.04
16 21 0.40
17 13 0.25
18 10 0.19
19 7 0.13
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TATAAATATAAAATATT
Found at i:970610 original size:32 final size:33
Alignment explanation
Indices: 970541--970626 Score: 101
Period size: 32 Copynumber: 2.7 Consensus size: 33
970531 TAAATATATC
*
970541 AAAATTTATA-AAATATAAATTATTTACAAATT
1 AAAATTTATATAAATATAAAATATTTACAAATT
*
970573 AAAATTTATATAAATATAAAATATTT-TAAA-T
1 AAAATTTATATAAATATAAAATATTTACAAATT
*
970604 ATAAATTTAT-TATA-ATAAAATAT
1 A-AAATTTATATAAATATAAAATAT
970627 ATGAATATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
30 9 0.18
31 5 0.10
32 21 0.43
33 14 0.29
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (33 bp):
AAAATTTATATAAATATAAAATATTTACAAATT
Found at i:970778 original size:2 final size:2
Alignment explanation
Indices: 970773--970799 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
970763 GAGATTGAAC
970773 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
970800 AAAGTAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:971395 original size:10 final size:10
Alignment explanation
Indices: 971367--971400 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
971357 AATTATTATG
*
971367 TAAAATATAA
1 TAAAATATTA
971377 TAAAATATTA
1 TAAAATATTA
*
971387 TAAAATATTT
1 TAAAATATTA
971397 TAAA
1 TAAA
971401 TTTATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAAAATATTA
Found at i:972580 original size:2 final size:2
Alignment explanation
Indices: 972573--972606 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
972563 TGTATGTGAA
972573 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
972607 TTTGACGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:972918 original size:24 final size:24
Alignment explanation
Indices: 972886--972938 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
972876 CGCACCTAAA
*
972886 TCAAGCCCCACTACGCCTGGAACT
1 TCAAGCCCCACCACGCCTGGAACT
972910 TCAAGCCCCACCACGCCTGGAACT
1 TCAAGCCCCACCACGCCTGGAACT
972934 TCAAG
1 TCAAG
972939 TCCTCCTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.26, C:0.42, G:0.17, T:0.15
Consensus pattern (24 bp):
TCAAGCCCCACCACGCCTGGAACT
Found at i:974691 original size:17 final size:18
Alignment explanation
Indices: 974671--974739 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 18
974661 ATTTTTAAAA
974671 AAAATTAATTTAAA-ATT
1 AAAATTAATTTAAATATT
974688 AAAA--AATTATAAATATT
1 AAAATTAATT-TAAATATT
974705 AAAATATAATTTTTAAATTTATT
1 AAAAT-TAA--TTTAAA--TATT
974728 AAATATTAATTT
1 AAA-ATTAATTT
974740 TAAAAATAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
15 4 0.10
16 4 0.10
17 11 0.26
20 2 0.05
21 7 0.17
22 2 0.05
23 10 0.24
24 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATTAATTTAAATATT
Found at i:974751 original size:23 final size:22
Alignment explanation
Indices: 974698--974747 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
974688 AAAAAATTAT
974698 AAATATTAAAATATAATTTTTAA
1 AAATATTAAAATATAA-TTTTAA
**
974721 ATTTATT-AAATATTAATTTTAA
1 AAATATTAAAATA-TAATTTTAA
974743 AAATA
1 AAATA
974748 ATTATATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATATTAAAATATAATTTTAA
Found at i:975393 original size:14 final size:14
Alignment explanation
Indices: 975376--975420 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
975366 AAAAGTTATA
975376 TATATATTTAAATT
1 TATATATTTAAATT
*
975390 TATATATTTATA-T
1 TATATATTTAAATT
*
975403 T-TATATTTAAATA
1 TATATATTTAAATT
975416 TATAT
1 TATAT
975421 TAAATATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 9 0.35
13 3 0.12
14 14 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATATATTTAAATT
Found at i:975395 original size:20 final size:20
Alignment explanation
Indices: 975372--975420 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
975362 TTTTAAAAGT
975372 TATATATATATTTAAATTTA
1 TATATATATATTTAAATTTA
* *
975392 TATATTTATATTTATATTTA
1 TATATATATATTTAAATTTA
*
975412 AATATATAT
1 TATATATAT
975421 TAAATATGAA
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATATATATATTTAAATTTA
Found at i:975400 original size:26 final size:26
Alignment explanation
Indices: 975371--975420 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
975361 TTTTTAAAAG
*
975371 TTATATATATATTTAAATTTATATAT
1 TTATATATATATTTAAATATATATAT
*
975397 TTATATTTATATTTAAATATATAT
1 TTATATATATATTTAAATATATAT
975421 TAAATATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTATATATATATTTAAATATATATAT
Found at i:976074 original size:13 final size:13
Alignment explanation
Indices: 976056--976080 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
976046 TTTTTATAAA
976056 AATATTTATATTT
1 AATATTTATATTT
976069 AATATTTATATT
1 AATATTTATATT
976081 CGTATATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:977390 original size:37 final size:39
Alignment explanation
Indices: 977342--977449 Score: 106
Period size: 37 Copynumber: 2.9 Consensus size: 39
977332 TGAATTAGAT
977342 TAAATTTTAAAAATTATTTTATTATTTAAAATAATA-TAA
1 TAAA-TTTAAAAATTATTTTATTATTTAAAATAATATTAA
* * *
977381 -AAATTTAAAAAATA-TTT-TTATATTAATAT-TTATTAA
1 TAAATTTAAAAATTATTTTATTAT-TTAAAATAATATTAA
977417 TAAA-TTAAATAATT-TTTTATTATTT-AAATAATA
1 TAAATTTAAA-AATTATTTTATTATTTAAAATAATA
977450 ATTATTATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
35 6 0.11
36 20 0.36
37 23 0.41
38 7 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (39 bp):
TAAATTTAAAAATTATTTTATTATTTAAAATAATATTAA
Found at i:978252 original size:11 final size:10
Alignment explanation
Indices: 978225--978276 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
978215 ATAAAAATTA
978225 AATTAAATAT
1 AATTAAATAT
978235 AATTAAAGTAT
1 AATTAAA-TAT
* *
978246 GATTAAAACAT
1 AATT-AAATAT
978257 AATTAAATAT
1 AATTAAATAT
*
978267 -ATTTAATAT
1 AATTAAATAT
978276 A
1 A
978277 TCCAGACATA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 8 0.24
10 12 0.35
11 11 0.32
12 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (10 bp):
AATTAAATAT
Found at i:978667 original size:3 final size:3
Alignment explanation
Indices: 978659--978687 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
978649 ATTTATTTAT
978659 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
978688 TGCAGAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:979288 original size:3 final size:3
Alignment explanation
Indices: 979280--979308 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
979270 AGGAAAATGG
979280 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
979309 AGTAATTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:979639 original size:15 final size:15
Alignment explanation
Indices: 979621--979651 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
979611 TAATTAAAGG
979621 AAATATAAATTGGCT
1 AAATATAAATTGGCT
979636 AAATATAAATTGGCT
1 AAATATAAATTGGCT
979651 A
1 A
979652 TCTTATTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.32
Consensus pattern (15 bp):
AAATATAAATTGGCT
Found at i:979675 original size:2 final size:2
Alignment explanation
Indices: 979668--979720 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
979658 TGTTATGCCC
979668 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
979710 TA TA TA TA TA T
1 TA TA TA TA TA T
979721 TTGAAGAAGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:980884 original size:19 final size:18
Alignment explanation
Indices: 980848--980917 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 18
980838 TAAAATATTG
980848 ATATATATTTATATTATTTTT
1 ATAT-TATTT-TA-TATTTTT
980869 CATATTATTTTATATTTTT
1 -ATATTATTTTATATTTTT
*
980888 ATTATTTTTTTATATTTTT
1 A-TATTATTTTATATTTTT
*
980907 -TAATATTTTAT
1 ATATTATTTTAT
980918 TCATGTCATA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
17 9 0.20
18 1 0.02
19 23 0.52
20 2 0.05
21 5 0.11
22 4 0.09
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (18 bp):
ATATTATTTTATATTTTT
Found at i:980907 original size:28 final size:28
Alignment explanation
Indices: 980851--980915 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
980841 AATATTGATA
*
980851 TATATTTATATTATTTTTCATATTATTT
1 TATATTTTTATTATTTTTCATATTATTT
*
980879 TATATTTTTATTATTTTTTTATATT-TTT
1 TATATTTTTATTA-TTTTTCATATTATTT
980907 TAATATTTT
1 T-ATATTTT
980916 ATTCATGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 16 0.48
29 17 0.52
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (28 bp):
TATATTTTTATTATTTTTCATATTATTT
Found at i:980915 original size:10 final size:10
Alignment explanation
Indices: 980864--980915 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
980854 ATTTATATTA
*
980864 TTTTTCATAT
1 TTTTTAATAT
980874 TATTTT-ATA-
1 T-TTTTAATAT
*
980883 TTTTTATTAT
1 TTTTTAATAT
*
980893 TTTTTTATAT
1 TTTTTAATAT
980903 TTTTTAATAT
1 TTTTTAATAT
980913 TTT
1 TTT
980916 ATTCATGTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 4 0.11
9 3 0.09
10 24 0.69
11 4 0.11
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTAATAT
Found at i:980916 original size:28 final size:27
Alignment explanation
Indices: 980851--980918 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 27
980841 AATATTGATA
980851 TATATTTATATTATTTTTCATATTATTT
1 TATATTT-TATTATTTTTCATATTATTT
*
980879 TATATTTTTATTATTTTTTTATATT-TTT
1 TATA-TTTTATTA-TTTTTCATATTATTT
980907 TAATATTTTATT
1 T-ATATTTTATT
980919 CATGTCATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 20 0.56
29 16 0.44
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (27 bp):
TATATTTTATTATTTTTCATATTATTT
Found at i:982389 original size:69 final size:69
Alignment explanation
Indices: 982305--982438 Score: 216
Period size: 69 Copynumber: 1.9 Consensus size: 69
982295 CCATCATCTT
* *
982305 CCTCTCCTTCTCCCTCTCCCTCATCGTCACCGTCACCACTAACGCCAACACCACCATCCTTTTCC
1 CCTCTCCTTCTCCCTCTCCCTCATCGTCACCGTCACCACCAACGCCAACACCACCATCCTCTTCC
982370 CCTC
66 CCTC
* *
982374 CCTCTTCC-TCTCCCTCTCCCTCATTGTCATCGTCACCACCAACGCCAACACCACCATCCTCTTC
1 CCTC-TCCTTCTCCCTCTCCCTCATCGTCACCGTCACCACCAACGCCAACACCACCATCCTCTTC
982438 C
65 C
982439 TCACCTTCAC
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
69 57 0.95
70 3 0.05
ACGTcount: A:0.16, C:0.53, G:0.04, T:0.26
Consensus pattern (69 bp):
CCTCTCCTTCTCCCTCTCCCTCATCGTCACCGTCACCACCAACGCCAACACCACCATCCTCTTCC
CCTC
Found at i:982406 original size:75 final size:69
Alignment explanation
Indices: 982301--982438 Score: 170
Period size: 75 Copynumber: 1.9 Consensus size: 69
982291 AACACCATCA
* *
982301 TCTTCCTCTCCTTCTCCCTCTCCCTCATCGTCACCGTCACCACTAACGCCAACACCACCATCCTT
1 TCTTCCTCTCCCTCTCCCTCTCCCTCATCGTCA-C--CA-C-C-AACGCCAACACCACCATCCTC
982366 TTCCCCTCCC
60 TTCCCCTCCC
**
982376 TCTTCCTCTCCCTCTCCCTCAT-TGTCATCGTCACCACCAACGCCAACACCACCATCCTCTTCC
1 TCTTCCTCTCCCTCTCCCTC-TCCCTCATCGTCACCACCAACGCCAACACCACCATCCTCTTCC
982439 TCACCTTCAC
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
69 24 0.41
70 1 0.02
71 1 0.02
72 2 0.03
74 1 0.02
75 28 0.48
76 1 0.02
ACGTcount: A:0.16, C:0.52, G:0.04, T:0.28
Consensus pattern (69 bp):
TCTTCCTCTCCCTCTCCCTCTCCCTCATCGTCACCACCAACGCCAACACCACCATCCTCTTCCCC
TCCC
Found at i:984632 original size:17 final size:15
Alignment explanation
Indices: 984604--984639 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
984594 TATTAATGCA
984604 AATTTAAATTTAAAT
1 AATTTAAATTTAAAT
984619 AATTTAAAATTTTAAAT
1 AATTT-AAA-TTTAAAT
984636 AATT
1 AATT
984640 CGAGATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 3 0.16
17 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTAAATTTAAAT
Found at i:989351 original size:22 final size:22
Alignment explanation
Indices: 989293--989389 Score: 62
Period size: 21 Copynumber: 4.5 Consensus size: 22
989283 TTAAAATATT
989293 TTATATTTATATAAAATTTAATAA
1 TTATA-TTATATAAAA-TTAATAA
* *
989317 TAATA-TATTTAAAA-TAATAAA
1 TTATATTATATAAAATTAAT-AA
*
989338 TTATATTATAT-AAATT-TTAA
1 TTATATTATATAAAATTAATAA
* * *
989358 -TATATTTATATTAATTTTAT-A
1 TTATA-TTATATAAAATTAATAA
989379 TTATATTATAT
1 TTATATTATAT
989390 TTTAATAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
19 4 0.07
20 12 0.20
21 21 0.36
22 18 0.31
24 4 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTATATTATATAAAATTAATAA
Found at i:989361 original size:14 final size:14
Alignment explanation
Indices: 989300--989362 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
989290 ATTTTATATT
*
989300 TATATAAAATTTAA
1 TATATAAATTTTAA
989314 TA-ATAATATATTTAA
1 TATATAA-AT-TTTAA
* * *
989329 AATAATAAATTATAT
1 TAT-ATAAATTTTAA
989344 TATATAAATTTTAA
1 TATATAAATTTTAA
989358 TATAT
1 TATAT
989363 TTATATTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
13 4 0.11
14 17 0.45
15 11 0.29
16 2 0.05
17 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:989378 original size:17 final size:17
Alignment explanation
Indices: 989358--989393 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
989348 TAAATTTTAA
989358 TATATTTATATTA-ATTT
1 TATA-TTATATTATATTT
989375 TATATTATATTATATTT
1 TATATTATATTATATTT
989392 TA
1 TA
989394 ATAATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATATTATATTATATTT
Found at i:989400 original size:16 final size:17
Alignment explanation
Indices: 989365--989405 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
989355 TAATATATTT
*
989365 ATATTA-ATTTTATATT
1 ATATTATATTTTATATA
989381 ATATTATATTTTA-ATA
1 ATATTATATTTTATATA
*
989397 ATATAATAT
1 ATATTATAT
989406 AAAAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATTATATTTTATATA
Found at i:990586 original size:12 final size:11
Alignment explanation
Indices: 990564--990623 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
990554 AATTTAATCG
990564 TAAAAAT-ATA
1 TAAAAATAATA
990574 TAAAAATTAATA
1 TAAAAA-TAATA
*
990586 TATAAATAATA
1 TAAAAATAATA
***
990597 TTTTAATAATA
1 TAAAAATAATA
990608 TAATAAATAATA
1 TAA-AAATAATA
990620 -AAAA
1 TAAAA
990624 TATGTATTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
10 8 0.20
11 18 0.44
12 15 0.37
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:990595 original size:11 final size:11
Alignment explanation
Indices: 990567--990619 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
990557 TTAATCGTAA
*
990567 AAAT-ATATAA
1 AAATAATATAT
990577 AAATTAATATAT
1 AAA-TAATATAT
*
990589 AAATAATATTT
1 AAATAATATAT
*
990600 TAATAATATAAT
1 AAATAATAT-AT
990612 AAATAATA
1 AAATAATA
990620 AAAATATGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 3 0.09
11 16 0.46
12 16 0.46
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAATAATATAT
Found at i:990597 original size:23 final size:23
Alignment explanation
Indices: 990567--990623 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
990557 TTAATCGTAA
990567 AAAT-ATATAAAAATTAATAT-AT
1 AAATAATATAAAAA-TAATATAAT
***
990589 AAATAATATTTTAATAATATAAT
1 AAATAATATAAAAATAATATAAT
990612 AAATAATA-AAAA
1 AAATAATATAAAA
990624 TATGTATTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
AAATAATATAAAAATAATATAAT
Found at i:992158 original size:20 final size:21
Alignment explanation
Indices: 992133--992183 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
992123 ATCTGTTGAA
*
992133 TTTAAAAATA-ATTATATTTT
1 TTTAAAAATAGATAATATTTT
**
992153 TTTAAATTTAGATAATATTTT
1 TTTAAAAATAGATAATATTTT
992174 TTTATAAAAT
1 TTTA-AAAAT
992184 TTGATATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 8 0.33
21 13 0.54
22 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTAAAAATAGATAATATTTT
Found at i:992181 original size:23 final size:24
Alignment explanation
Indices: 992140--992189 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
992130 GAATTTAAAA
992140 ATAATTATATTTTTTT-AAATTTAG
1 ATAATTATATTTTTTTAAAATTT-G
992164 ATAA-TAT-TTTTTTATAAAATTTG
1 ATAATTATATTTTTT-TAAAATTTG
992187 ATA
1 ATA
992190 TAAAATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.25
23 8 0.33
24 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (24 bp):
ATAATTATATTTTTTTAAAATTTG
Found at i:992548 original size:12 final size:12
Alignment explanation
Indices: 992501--992550 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
992491 ATTAAAAAAT
992501 ATTTTAA-ATTTA
1 ATTTTAATA-TTA
*
992513 TTTTTAAT-TTA
1 ATTTTAATATTA
*
992524 ATTATATATATTA
1 ATTTTA-ATATTA
992537 ATTTTAATATTA
1 ATTTTAATATTA
992549 AT
1 AT
992551 ATATTATGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
11 7 0.23
12 16 0.52
13 8 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTTTAATATTA
Found at i:992566 original size:25 final size:24
Alignment explanation
Indices: 992510--992572 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
992500 TATTTTAAAT
992510 TTATTTTTAATTTAATTATATATA
1 TTATTTTTAATTTAATTATATATA
* *
992534 TTAATTTTAATATTAA-TATATTATG
1 TTATTTTTAAT-TTAATTATA-TATA
992559 TTATTTTT-ATTTAA
1 TTATTTTTAATTTAA
992573 AAATTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 4 0.12
24 16 0.47
25 14 0.41
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTATTTTTAATTTAATTATATATA
Found at i:993002 original size:15 final size:17
Alignment explanation
Indices: 992971--993003 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
992961 AAATTTTTAT
992971 TATTTTATAATTAAAAA
1 TATTTTATAATTAAAAA
992988 TATTTTA-AA-TAAAAA
1 TATTTTATAATTAAAAA
993003 T
1 T
993004 GATGAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATTTTATAATTAAAAA
Found at i:994204 original size:23 final size:24
Alignment explanation
Indices: 994169--994213 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
994159 GTTCATTTAA
*
994169 TTTTAAATTATTTT-AATTTAAAT
1 TTTTAAATCATTTTAAATTTAAAT
*
994192 TTTTAAGTCATTTTAAATTTAA
1 TTTTAAATCATTTTAAATTTAA
994214 TACGTGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTTAAATCATTTTAAATTTAAAT
Found at i:994819 original size:19 final size:20
Alignment explanation
Indices: 994795--994833 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
994785 GATCATAATT
994795 TTTTATTATAATAA-AATAA
1 TTTTATTATAATAATAATAA
*
994814 TTTTATTATTATAATAATAA
1 TTTTATTATAATAATAATAA
994834 ATAATTGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTATTATAATAATAATAA
Found at i:994825 original size:22 final size:23
Alignment explanation
Indices: 994789--994839 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
994779 TAATGAGATC
994789 ATAATTTTTTATTATAAT-A-AA
1 ATAATTTTTTATTATAATAATAA
994810 ATAATTTTATTATTATAATAATAA
1 ATAATTTT-TTATTATAATAATAA
994834 ATAATT
1 ATAATT
994840 GCTATTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.30
22 10 0.37
23 1 0.04
24 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATAATTTTTTATTATAATAATAA
Found at i:994845 original size:25 final size:22
Alignment explanation
Indices: 994789--994846 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
994779 TAATGAGATC
*
994789 ATAATT-TTTTATTATAATAAA
1 ATAATTCTATTATTATAATAAA
*
994810 ATAATTTTATTATTATAATAATAA
1 ATAATTCTATTATTATAAT-A-AA
994834 ATAATTGCTATTA
1 ATAATT-CTATTA
994847 ATGCTCTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 6 0.19
22 11 0.35
23 1 0.03
24 8 0.26
25 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
ATAATTCTATTATTATAATAAA
Found at i:999576 original size:15 final size:14
Alignment explanation
Indices: 999558--999592 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
999548 TTACTCAACA
999558 TAAATTAAAAAAATT
1 TAAATT-AAAAAATT
*
999573 TAAATTTAAAAATT
1 TAAATTAAAAAATT
999587 TAAATT
1 TAAATT
999593 GCAATCTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATTAAAAAATT
Found at i:999585 original size:14 final size:14
Alignment explanation
Indices: 999566--999592 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
999556 CATAAATTAA
999566 AAAAATTTAAATTT
1 AAAAATTTAAATTT
999580 AAAAATTTAAATT
1 AAAAATTTAAATT
999593 GCAATCTAAC
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAAATTTAAATTT
Found at i:1002520 original size:32 final size:29
Alignment explanation
Indices: 1002466--1002525 Score: 84
Period size: 32 Copynumber: 2.0 Consensus size: 29
1002456 ATCTCAATCC
*
1002466 AATTTATTATAATAATAATTTTTTATTTA
1 AATTTATTATAAAAATAATTTTTTATTTA
1002495 AATTTAATTATTAAAAATATATTTTTTATTT
1 AATTT-ATTA-TAAAAATA-ATTTTTTATTT
1002526 TTTTCATGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 5 0.19
30 4 0.15
31 7 0.26
32 11 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
AATTTATTATAAAAATAATTTTTTATTTA
Found at i:1003524 original size:30 final size:30
Alignment explanation
Indices: 1003490--1003555 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
1003480 TATTGTATAT
*
1003490 AAATAAAACTCTAACTTCTAATTTTTATTA
1 AAATAAAACTCTAACTTCTAATTTATATTA
* * * * *
1003520 AAATAAAATTTTAATTTTTAATTTATATTC
1 AAATAAAACTCTAACTTCTAATTTATATTA
1003550 AAATAA
1 AAATAA
1003556 TTCGTAACAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (30 bp):
AAATAAAACTCTAACTTCTAATTTATATTA
Found at i:1004246 original size:2 final size:2
Alignment explanation
Indices: 1004239--1004269 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1004229 ATTGTCAGCC
1004239 TA 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 TA T
1004270 GAAGTGTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1004773 original size:2 final size:2
Alignment explanation
Indices: 1004768--1004800 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1004758 AATTCAACAG
*
1004768 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1004801 ATGAGTTCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1009505 original size:2 final size:2
Alignment explanation
Indices: 1009498--1009528 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1009488 TACTCAAAAT
1009498 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1009529 TATATATGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1011206 original size:19 final size:19
Alignment explanation
Indices: 1011184--1011239 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 19
1011174 AACATGATAT
1011184 AAATTTTTAAATATATAAA
1 AAATTTTTAAATATATAAA
1011203 AAA--TTTAAATATAAATAAA
1 AAATTTTTAAATAT--ATAAA
*
1011222 ATATTTTTTTAAATATAT
1 A-A-ATTTTTAAATATAT
1011240 CATATTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
17 9 0.30
19 9 0.30
20 1 0.03
21 2 0.07
23 9 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATTTTTAAATATATAAA
Found at i:1011772 original size:17 final size:16
Alignment explanation
Indices: 1011728--1011772 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
1011718 TTTATTTAGA
*
1011728 TTATATTTATGTCATTT
1 TTATA-TTATATCATTT
*
1011745 TTATATAATATCATATT
1 TTATATTATATCAT-TT
1011762 TTATATTATAT
1 TTATATTATAT
1011773 TTAAATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (16 bp):
TTATATTATATCATTT
Found at i:1012340 original size:26 final size:29
Alignment explanation
Indices: 1012286--1012364 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 29
1012276 TTGAATTATT
*
1012286 ATTTATTTAATAAAAATAATATTTATTTAA
1 ATTTAATTAATAAAAATAATA-TTATTTAA
* *
1012316 ATTTAATT-ATAAAAATAATATTTTAATTAT
1 ATTTAATTAATAAAAATAATA--TTATTTAA
* *
1012346 TTTTAAATAATAAAAATAA
1 ATTTAATTAATAAAAATAA
1012365 ATTTACTTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 12 0.29
30 20 0.48
31 10 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTTAATTAATAAAAATAATATTATTTAA
Found at i:1012362 original size:31 final size:31
Alignment explanation
Indices: 1012274--1012368 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 31
1012264 AATCGATTTG
* **
1012274 ATTTGAATTATTATTTATTTAATAAAAATAAT
1 ATTTTAATTATT-TTTAAATAATAAAAATAAT
* ** *
1012306 A-TTTATTTAAATTT-AATTATAAAAATAAT
1 ATTTTAATTATTTTTAAATAATAAAAATAAT
1012335 ATTTTAATTATTTTTAAATAATAAAAATAA-
1 ATTTTAATTATTTTTAAATAATAAAAATAAT
1012365 ATTT
1 ATTT
1012369 ACTTGAATCA
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
29 13 0.26
30 17 0.34
31 19 0.38
32 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTTTAATTATTTTTAAATAATAAAAATAAT
Found at i:1013441 original size:18 final size:17
Alignment explanation
Indices: 1013413--1013459 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
1013403 AATAATAAGT
1013413 TAAAAAA-AAATTTAGA
1 TAAAAAATAAATTTAGA
**
1013429 TAAAAAATTAAATTTATT
1 TAAAAAA-TAAATTTAGA
1013447 TAAAAAATAAATT
1 TAAAAAATAAATT
1013460 AAGCTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 7 0.26
17 6 0.22
18 14 0.52
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
TAAAAAATAAATTTAGA
Found at i:1014425 original size:19 final size:19
Alignment explanation
Indices: 1014394--1014441 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
1014384 TAAATTTCAT
* *
1014394 TAAAATTAA-AATTA-AAT
1 TAAAAATAATAATTATAAA
1014411 TAATAAATAATAATTATAAA
1 TAA-AAATAATAATTATAAA
1014431 TAAAAATAATA
1 TAAAAATAATA
1014442 TTTTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 3 0.12
18 5 0.19
19 13 0.50
20 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAATAATAATTATAAA
Found at i:1014449 original size:19 final size:21
Alignment explanation
Indices: 1014405--1014449 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
1014395 AAAATTAAAA
1014405 TTAAATTAATAAATAATAATT
1 TTAAATTAATAAATAATAATT
* *
1014426 ATAAA-TAA-AAATAATATTT
1 TTAAATTAATAAATAATAATT
1014445 TTAAA
1 TTAAA
1014450 AAATTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 14 0.67
20 3 0.14
21 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAATTAATAAATAATAATT
Found at i:1019632 original size:20 final size:18
Alignment explanation
Indices: 1019594--1019634 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
1019584 ATTAATATAT
*
1019594 TAAAATTTATATAAATTA
1 TAAAATTTAAATAAATTA
1019612 TAAAATTTTAAATATAATTA
1 TAAAA-TTTAAATA-AATTA
1019632 TAA
1 TAA
1019635 TTTATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 7 0.35
20 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATTTAAATAAATTA
Found at i:1020021 original size:18 final size:18
Alignment explanation
Indices: 1019963--1020024 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 18
1019953 TATGGGAAGT
*
1019963 TTTAAAAATTTTAAATTA
1 TTTAATAATTTTAAATTA
* **
1019981 TTTTATTAATTAAAAAATTTTA
1 -TTTAATAATT-TTAAA--TTA
1020003 TTTAATAATTTTAAATTA
1 TTTAATAATTTTAAATTA
1020021 TTTA
1 TTTA
1020025 TTTATTTAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
18 7 0.21
19 8 0.24
20 6 0.18
21 9 0.27
22 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTAATAATTTTAAATTA
Found at i:1021287 original size:17 final size:16
Alignment explanation
Indices: 1021226--1021295 Score: 56
Period size: 16 Copynumber: 4.5 Consensus size: 16
1021216 TTAAATTTTT
1021226 TTTAAAATTT--TTTA
1 TTTAAAATTTAATTTA
* * *
1021240 TTTTAAATTGAATTGA
1 TTTAAAATTTAATTTA
* *
1021256 -GTAAGATTTAATTTAA
1 TTTAAAATTTAATTT-A
*
1021272 TTTAAAATTTATTTTA
1 TTTAAAATTTAATTTA
1021288 TTTAAAAT
1 TTTAAAAT
1021296 AATATTAAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
14 8 0.20
15 9 0.22
16 13 0.32
17 11 0.27
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (16 bp):
TTTAAAATTTAATTTA
Found at i:1023362 original size:4 final size:4
Alignment explanation
Indices: 1023353--1023385 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1023343 GATTACGTAG
1023353 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1023386 ATGAAGTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:1023839 original size:44 final size:44
Alignment explanation
Indices: 1023766--1023899 Score: 232
Period size: 44 Copynumber: 3.0 Consensus size: 44
1023756 AGATACAAAT
* * * *
1023766 AAAAGTAAGTTTTTTGAATTAATTAAGACAATATATTTTGTCGA
1 AAAACTAAGCTTTTTGAATTAGTTGAGACAATATATTTTGTCGA
1023810 AAAACTAAGCTTTTTGAATTAGTTGAGACAATATATTTTGTCGA
1 AAAACTAAGCTTTTTGAATTAGTTGAGACAATATATTTTGTCGA
1023854 AAAACTAAGCTTTTTGAATTAGTTGAGACAATATATTTTGTCGA
1 AAAACTAAGCTTTTTGAATTAGTTGAGACAATATATTTTGTCGA
1023898 AA
1 AA
1023900 CATCTCCAAA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 86 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (44 bp):
AAAACTAAGCTTTTTGAATTAGTTGAGACAATATATTTTGTCGA
Found at i:1026113 original size:19 final size:19
Alignment explanation
Indices: 1026089--1026186 Score: 60
Period size: 19 Copynumber: 5.1 Consensus size: 19
1026079 TTAATATTTA
1026089 AAAATTTATATATTTATAT
1 AAAATTTATATATTTATAT
*
1026108 AAAATTT-TATAAATTA-AT
1 AAAATTTATAT-ATTTATAT
** **
1026126 AAGTTTTATTATATAAATTAT
1 AAAATTTA-TATATTTA-TAT
1026147 AACATATTTATATATTTATAT
1 AA-A-ATTTATATATTTATAT
* *
1026168 TATATTTATAT-TTTA-AT
1 AAAATTTATATATTTATAT
1026185 AA
1 AA
1026187 TTTATTTCAT
Statistics
Matches: 59, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
17 3 0.05
18 14 0.24
19 21 0.36
20 3 0.05
21 8 0.14
22 6 0.10
23 4 0.07
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (19 bp):
AAAATTTATATATTTATAT
Found at i:1026193 original size:19 final size:19
Alignment explanation
Indices: 1026092--1026182 Score: 60
Period size: 20 Copynumber: 4.7 Consensus size: 19
1026082 ATATTTAAAA
* *
1026092 ATTTATATATTTATATAAA
1 ATTTATATATTTATATTAT
* * *
1026111 ATTTTATAAATTAATAAGTTTT
1 A-TTTATATATTTAT-A-TTAT
* **
1026133 A-TTATATAAATTATAACAT
1 ATTTATAT-ATTTATATTAT
1026152 ATTTATATATTTATATTAT
1 ATTTATATATTTATATTAT
1026171 ATTTATAT-TTTA
1 ATTTATATATTTA
1026183 ATAATTTATT
Statistics
Matches: 53, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
18 4 0.08
19 19 0.36
20 23 0.43
21 5 0.09
22 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (19 bp):
ATTTATATATTTATATTAT
Found at i:1030916 original size:7 final size:7
Alignment explanation
Indices: 1030906--1030930 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1030896 ATTATATTTA
1030906 AAAAAAT
1 AAAAAAT
1030913 AAAAAAT
1 AAAAAAT
1030920 AAAAAAT
1 AAAAAAT
1030927 AAAA
1 AAAA
1030931 TAAATGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:1031358 original size:2 final size:2
Alignment explanation
Indices: 1031353--1031377 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1031343 AAATGGAAAA
1031353 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1031378 TCGAAATCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1031672 original size:7 final size:7
Alignment explanation
Indices: 1031646--1031698 Score: 51
Period size: 6 Copynumber: 8.1 Consensus size: 7
1031636 GCGACAAAAT
1031646 TTTATTA
1 TTTATTA
1031653 TTT-TTA
1 TTTATTA
*
1031659 ATT-TTA
1 TTTATTA
1031665 TTTATTA
1 TTTATTA
*
1031672 -TTAATA
1 TTTATTA
*
1031678 TTTATGA
1 TTTATTA
1031685 TTTA-TA
1 TTTATTA
1031691 TTTATTA
1 TTTATTA
1031698 T
1 T
1031699 AATTTATTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 20 0.54
7 17 0.46
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (7 bp):
TTTATTA
Found at i:1031675 original size:16 final size:16
Alignment explanation
Indices: 1031643--1031682 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1031633 AATGCGACAA
*
1031643 AATTTTA-TTATTTTT
1 AATTTTATTTATTATT
1031658 AATTTTATTTATTATT
1 AATTTTATTTATTATT
1031674 AATATTTAT
1 AAT-TTTAT
1031683 GATTTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.32
16 10 0.45
17 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTTTATTTATTATT
Found at i:1031681 original size:13 final size:13
Alignment explanation
Indices: 1031663--1031698 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1031653 TTTTTAATTT
1031663 TATTTATTATTAA
1 TATTTATTATTAA
* *
1031676 TATTTATGATTTA
1 TATTTATTATTAA
1031689 TATTTATTAT
1 TATTTATTAT
1031699 AATTTATTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (13 bp):
TATTTATTATTAA
Found at i:1194875 original size:2 final size:2
Alignment explanation
Indices: 1194863--1194910 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1194853 TAATACTGTA
1194863 AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1194904 AG AG AG A
1 AG AG AG A
1194911 ATGATAACTG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1195914 original size:2 final size:2
Alignment explanation
Indices: 1195907--1195936 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1195897 TAACAATTGC
1195907 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
1195937 TATTCGTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1196638 original size:2 final size:2
Alignment explanation
Indices: 1196631--1196659 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1196621 TACTTATGAT
1196631 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
1196660 GGAGAGGTGT
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:1197820 original size:22 final size:22
Alignment explanation
Indices: 1197792--1197834 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1197782 AGGTTGTAAA
1197792 ATATTAAAATTTAAATTTTAAT
1 ATATTAAAATTTAAATTTTAAT
* *
1197814 ATATTAAATTTTAATTTTTAA
1 ATATTAAAATTTAAATTTTAA
1197835 AATAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATTAAAATTTAAATTTTAAT
Done.