Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 112 of 161
Found at i:35600673 original size:5 final size:5
Alignment explanation
Indices: 35600663--35600733 Score: 62
Period size: 5 Copynumber: 14.6 Consensus size: 5
35600653 GTAAAAATAT
* *
35600663 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TCATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA T-ATTA
35600709 -A-TA TATTA TATTA TATTA TA-TA TAT
1 TATTA TATTA TATTA TATTA TATTA TAT
35600734 ACATAAAACA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
3 4 0.07
4 8 0.15
5 32 0.58
6 10 0.18
7 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (5 bp):
TATTA
Found at i:35600715 original size:19 final size:19
Alignment explanation
Indices: 35600691--35600733 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
35600681 ATTATGTTTT
35600691 TATATTATATTATCATTA-A
1 TATATTATATTAT-ATTATA
35600710 TATATTATATTATATTATA
1 TATATTATATTATATTATA
35600729 TATAT
1 TATAT
35600734 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:35600766 original size:18 final size:19
Alignment explanation
Indices: 35600738--35600777 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
35600728 ATATATACAT
*
35600738 AAAACAAAAGAAAGAATAG
1 AAAACAAAAGAAAGAAAAG
35600757 AAAA-AAAAGAAAGAAAAG
1 AAAACAAAAGAAAGAAAAG
35600775 AAA
1 AAA
35600778 CAGAATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAACAAAAGAAAGAAAAG
Found at i:35611420 original size:45 final size:44
Alignment explanation
Indices: 35611371--35611521 Score: 180
Period size: 45 Copynumber: 3.4 Consensus size: 44
35611361 CCCGAAGTGG
**
35611371 TGCCATAATATCTTTCAACTATGGTCTTAATTCATTCAAATTTAA
1 TGCCATAATATCTTTCAACTATGGTCTT-ATTCATTCAGGTTTAA
* * *
35611416 TGCCATAATATCTTTCAACTAGGGTCTTACTT-GTTCTGGTTTAA
1 TGCCATAATATCTTTCAACTATGGTCTTA-TTCATTCAGGTTTAA
* *
35611460 TGCCATAGTATCTTTCAACTATGGTCTT-TCTCATTTCAGGTATAA
1 TGCCATAATATCTTTCAACTATGGTCTTAT-TCA-TTCAGGTTTAA
*
35611505 TGCCATGATATCTTTCA
1 TGCCATAATATCTTTCA
35611522 GTCATGGTCT
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 35 0.39
45 53 0.59
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.42
Consensus pattern (44 bp):
TGCCATAATATCTTTCAACTATGGTCTTATTCATTCAGGTTTAA
Found at i:35612333 original size:14 final size:15
Alignment explanation
Indices: 35612307--35612339 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
35612297 AGTCAACTAA
35612307 AATTTTGTTTTGTTT
1 AATTTTGTTTTGTTT
35612322 AATTTT-TTTTGTTT
1 AATTTTGTTTTGTTT
35612336 AATT
1 AATT
35612340 ATCAATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (15 bp):
AATTTTGTTTTGTTT
Found at i:35616444 original size:12 final size:12
Alignment explanation
Indices: 35616427--35616462 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
35616417 GAAAAGAAAA
35616427 TAAAATCTAATT
1 TAAAATCTAATT
35616439 TAAAATCTAATT
1 TAAAATCTAATT
35616451 TAAAATCTAATT
1 TAAAATCTAATT
35616463 CAAACTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAAATCTAATT
Found at i:35621808 original size:20 final size:21
Alignment explanation
Indices: 35621767--35621810 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
35621757 ATTAATACTC
*
35621767 AATAATTACTAAAGTTTCAAA
1 AATAATTACTAAAGTTCCAAA
35621788 AATAATTACT-AAG-TCCAAA
1 AATAATTACTAAAGTTCCAAA
35621807 AATA
1 AATA
35621811 TTTTTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.41
20 3 0.14
21 10 0.45
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.30
Consensus pattern (21 bp):
AATAATTACTAAAGTTCCAAA
Found at i:35624009 original size:63 final size:63
Alignment explanation
Indices: 35623916--35624058 Score: 207
Period size: 63 Copynumber: 2.3 Consensus size: 63
35623906 GCTACACGAC
* * * *
35623916 CATGTG-CCAGGCCGTGTTACTCACTATTTTGGAATTAGAGTCACGCGGGCCAAGGACACGGG
1 CATGTGTCCAGGCCGTGTAACTCACTATTTTGGAATTAGAGTCACACAGACCAAGGACACGGG
* *
35623978 CATGTGTCCAGGCCGTGTAACTCACTTTTTTGGAATTAGAGTCACACAGACCAGGGACACGGG
1 CATGTGTCCAGGCCGTGTAACTCACTATTTTGGAATTAGAGTCACACAGACCAAGGACACGGG
**
35624041 TGTGTGTCCAGGCCGTGT
1 CATGTGTCCAGGCCGTGT
35624059 GAGAGGTATT
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
62 6 0.08
63 66 0.92
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (63 bp):
CATGTGTCCAGGCCGTGTAACTCACTATTTTGGAATTAGAGTCACACAGACCAAGGACACGGG
Found at i:35625696 original size:10 final size:10
Alignment explanation
Indices: 35625660--35625722 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
35625650 TTTTTATTTT
35625660 TATTAAATTA
1 TATTAAATTA
*
35625670 TATTTAA-TA
1 TATTAAATTA
35625679 -A-T-AATTA
1 TATTAAATTA
35625686 TATTAAATTA
1 TATTAAATTA
*
35625696 TGATTAAACTATT
1 T-ATTAAA-T-TA
35625709 TATTAAATTA
1 TATTAAATTA
35625719 TATT
1 TATT
35625723 TAATAATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
6 2 0.05
7 3 0.07
8 2 0.05
9 3 0.07
10 17 0.40
11 7 0.16
12 7 0.16
13 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (10 bp):
TATTAAATTA
Found at i:35625716 original size:23 final size:25
Alignment explanation
Indices: 35625658--35625741 Score: 102
Period size: 26 Copynumber: 3.4 Consensus size: 25
35625648 TATTTTTATT
35625658 TTTATTAAATTATATTTAATAATAA
1 TTTATTAAATTATATTTAATAATAA
*
35625683 TTATATTAAATTATGA-TTAA-ACT-A
1 TT-TATTAAATTAT-ATTTAATAATAA
35625707 TTTATTAAATTATATTTAATAATAA
1 TTTATTAAATTATATTTAATAATAA
*
35625732 TCCTATTAAA
1 T-TTATTAAA
35625742 ATTTAATGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
22 1 0.02
23 15 0.30
24 5 0.10
25 6 0.12
26 22 0.44
27 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (25 bp):
TTTATTAAATTATATTTAATAATAA
Found at i:35626214 original size:5 final size:6
Alignment explanation
Indices: 35626198--35626222 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35626188 GTTGATAATA
35626198 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
35626223 AAAATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:35626410 original size:16 final size:17
Alignment explanation
Indices: 35626374--35626410 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
35626364 AATTTTATTT
35626374 TAATAATAAATTTTAAA
1 TAATAATAAATTTTAAA
35626391 -AATAA-AAATTTTAAA
1 TAATAATAAATTTTAAA
35626406 TAATA
1 TAATA
35626411 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:35634620 original size:12 final size:12
Alignment explanation
Indices: 35634605--35634634 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
35634595 TAGTATCTAT
*
35634605 TTTAAATTTTAA
1 TTTAAATATTAA
35634617 TTTAAATATTAA
1 TTTAAATATTAA
35634629 TTTAAA
1 TTTAAA
35634635 AATACATACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTAAATATTAA
Found at i:35638107 original size:38 final size:38
Alignment explanation
Indices: 35638065--35638140 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
35638055 AACCATTTCA
35638065 TAATTACGTAATGTGATTATATTATTAATCTAAAAGAT
1 TAATTACGTAATGTGATTATATTATTAATCTAAAAGAT
35638103 TAATTACGTAATGTGATTATATTATTAATCTAAAAGAT
1 TAATTACGTAATGTGATTATATTATTAATCTAAAAGAT
35638141 GTGCAGGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (38 bp):
TAATTACGTAATGTGATTATATTATTAATCTAAAAGAT
Found at i:35639326 original size:21 final size:19
Alignment explanation
Indices: 35639294--35639343 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
35639284 TTTGCTTAAA
*
35639294 AAAATATGAATTATATATTT
1 AAAATATAAATTATAT-TTT
35639314 AAAATATTAAATTATATTTT
1 AAAATA-TAAATTATATTTT
35639334 AAAATA-AAAT
1 AAAATATAAAT
35639344 AATGCAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 4 0.14
20 15 0.54
21 9 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AAAATATAAATTATATTTT
Found at i:35639420 original size:21 final size:21
Alignment explanation
Indices: 35639396--35639507 Score: 77
Period size: 21 Copynumber: 5.2 Consensus size: 21
35639386 TATAATTGTA
35639396 TTAATATTTAATTATAAATAT
1 TTAATATTTAATTATAAATAT
*
35639417 TTAATAATTATATT-TAAATAT
1 TTAATATTTA-ATTATAAATAT
* * *
35639438 TTAAAATATAATT-TATATAT
1 TTAATATTTAATTATAAATAT
* * *
35639458 TTTA-ATTAAATTTTATAAATAA
1 TTAATATTTAA--TTATAAATAT
*
35639480 TTAATATTAATTACTTATAAATAT
1 TTAATA-T--TTAATTATAAATAT
35639504 TTAA
1 TTAA
35639508 AATTAATATT
Statistics
Matches: 69, Mismatches: 14, Indels: 13
0.72 0.15 0.14
Matches are distributed among these distances:
19 4 0.06
20 12 0.17
21 25 0.36
22 11 0.16
23 1 0.01
24 14 0.20
26 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAATATTTAATTATAAATAT
Found at i:35639452 original size:33 final size:33
Alignment explanation
Indices: 35639415--35639514 Score: 86
Period size: 33 Copynumber: 3.1 Consensus size: 33
35639405 AATTATAAAT
35639415 ATTTAATAATTATATTTAAATATTTAAAATATA
1 ATTTAATAATTATATTTAAATATTTAAAATATA
* * *
35639448 ATTT-ATATATTTTAATTAAAT-TTTATAA-ATA
1 ATTTAATA-ATTATATTTAAATATTTAAAATATA
35639479 A-TTAAT-ATTAATTACTTATAAATATTTAAAAT-TA
1 ATTTAATAATT-A-TA-TT-TAAATATTTAAAATATA
35639513 AT
1 AT
35639515 ATTTCATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
29 3 0.06
30 2 0.04
31 8 0.15
32 10 0.19
33 20 0.38
34 9 0.17
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (33 bp):
ATTTAATAATTATATTTAAATATTTAAAATATA
Found at i:35639457 original size:20 final size:21
Alignment explanation
Indices: 35639410--35639518 Score: 68
Period size: 21 Copynumber: 5.0 Consensus size: 21
35639400 TATTTAATTA
35639410 TAAATATTTAATAATTATATT
1 TAAATATTTAATAATTATATT
35639431 TAAATATTTAA-AA-TATAATT
1 TAAATATTTAATAATTAT-ATT
* *
35639451 TATATATTTTAATTAAATT-T-TA
1 TAAATA-TTTAA-T-AATTATATT
*
35639473 TAAATAATTAAT-ATTAATTACTT
1 TAAATATTTAATAATT-A-TA-TT
35639496 ATAAATATTTAA-AATTAATATT
1 -TAAATATTTAATAATT-ATATT
35639518 T
1 T
35639519 CATATATTAA
Statistics
Matches: 69, Mismatches: 6, Indels: 26
0.68 0.06 0.26
Matches are distributed among these distances:
18 3 0.04
19 3 0.04
20 11 0.16
21 22 0.32
22 8 0.12
23 3 0.04
24 18 0.26
25 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATATTTAATAATTATATT
Found at i:35643653 original size:25 final size:25
Alignment explanation
Indices: 35643622--35643724 Score: 90
Period size: 24 Copynumber: 4.2 Consensus size: 25
35643612 CTTATGATCA
*
35643622 TCCCGATAATTGGCTCTCGTAAGCT
1 TCCCGATAATTGGCTCTCGTGAGCT
*
35643647 TCTCGATTAA-TGGCTCTCCG-GAGCT
1 TCCCGA-TAATTGGCTCT-CGTGAGCT
*
35643672 TCCCGAT-ATTGGCTCTCATGAGCT
1 TCCCGATAATTGGCTCTCGTGAGCT
* * *
35643696 TCCC-A-AATTTAGCTCACTTGAGCT
1 TCCCGATAA-TTGGCTCTCGTGAGCT
35643720 TCCCG
1 TCCCG
35643725 TTTATGGCTT
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
23 4 0.06
24 34 0.53
25 21 0.33
26 5 0.08
ACGTcount: A:0.18, C:0.30, G:0.19, T:0.32
Consensus pattern (25 bp):
TCCCGATAATTGGCTCTCGTGAGCT
Found at i:35643694 original size:24 final size:24
Alignment explanation
Indices: 35643622--35643699 Score: 84
Period size: 25 Copynumber: 3.2 Consensus size: 24
35643612 CTTATGATCA
* *
35643622 TCCCGATAATTGGCTCTCGTAAGCT
1 TCCCGAT-ATTGGCTCTCATGAGCT
* * **
35643647 TCTCGATTAATGGCTCTCCGGAGCT
1 TCCCGA-TATTGGCTCTCATGAGCT
35643672 TCCCGATATTGGCTCTCATGAGCT
1 TCCCGATATTGGCTCTCATGAGCT
35643696 TCCC
1 TCCC
35643700 AAATTTAGCT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
24 19 0.44
25 23 0.53
26 1 0.02
ACGTcount: A:0.17, C:0.31, G:0.21, T:0.32
Consensus pattern (24 bp):
TCCCGATATTGGCTCTCATGAGCT
Found at i:35643809 original size:25 final size:25
Alignment explanation
Indices: 35643667--35643809 Score: 85
Period size: 25 Copynumber: 5.8 Consensus size: 25
35643657 TGGCTCTCCG
* *
35643667 GAGCTTCCCGATAT-TGGCTCTCAT
1 GAGCTTCCCGTTATATGGCTCACAT
** * * *
35643691 GAGCTTCCC-AAATTTAGCTCACTT
1 GAGCTTCCCGTTATATGGCTCACAT
***
35643715 GAGCTTCCCGTT-TATGGCTTGTAT
1 GAGCTTCCCGTTATATGGCTCACAT
* * * ** *
35643739 GAGTTTCCCGATAAATGGCTTGCAA
1 GAGCTTCCCGTTATATGGCTCACAT
* **
35643764 GAGCTTCCCATTATACAGCTCACAT
1 GAGCTTCCCGTTATATGGCTCACAT
*
35643789 GAGCTTCCCGTTACATGGCTC
1 GAGCTTCCCGTTATATGGCTC
35643810 GGAANGGGCA
Statistics
Matches: 86, Mismatches: 30, Indels: 5
0.71 0.25 0.04
Matches are distributed among these distances:
23 3 0.03
24 41 0.48
25 42 0.49
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCACAT
Found at i:35651076 original size:45 final size:45
Alignment explanation
Indices: 35651026--35651118 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
35651016 CATTAAATGC
*
35651026 TTACTCTATTTTATTTCCTCTGTTTTATAGTAACTTGGAAGGTCG
1 TTACTCTATTTTATTTCCCCTGTTTTATAGTAACTTGGAAGGTCG
*
35651071 TTACTCTGTTTTATTTCCCCTGTTTTATAGTAACTTGGAAGGTCG
1 TTACTCTATTTTATTTCCCCTGTTTTATAGTAACTTGGAAGGTCG
35651116 TTA
1 TTA
35651119 AGGTTGGAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.48
Consensus pattern (45 bp):
TTACTCTATTTTATTTCCCCTGTTTTATAGTAACTTGGAAGGTCG
Found at i:35660039 original size:38 final size:38
Alignment explanation
Indices: 35659997--35660077 Score: 92
Period size: 37 Copynumber: 2.1 Consensus size: 38
35659987 ATATCCCAAT
*
35659997 TAAAAAATTTATATAAATTATTTTCTTACATGTGTAA-C
1 TAAAAAA-ATATATAAATTATTTTCTTACATGTGTAACC
* * * **
35660035 TAAAAAAATCTATCAATTGTTTTCTTTTATGTGTAACC
1 TAAAAAAATATATAAATTATTTTCTTACATGTGTAACC
35660073 TAAAA
1 TAAAA
35660078 GGTTTAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
37 23 0.64
38 13 0.36
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (38 bp):
TAAAAAAATATATAAATTATTTTCTTACATGTGTAACC
Found at i:35662663 original size:22 final size:22
Alignment explanation
Indices: 35662622--35662681 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
35662612 TTCAATGAAA
35662622 CTGGAAATTG--TTGCATTTGTT
1 CTGGAAATTGTTTTG-ATTTGTT
* *
35662643 -TTGATATTGTTCTTGATTTGTT
1 CTGGAAATTGTT-TTGATTTGTT
35662665 CTGGAAATTGTTTTGAT
1 CTGGAAATTGTTTTGAT
35662682 AGTCTGTTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
20 7 0.23
22 12 0.39
23 12 0.39
ACGTcount: A:0.18, C:0.07, G:0.22, T:0.53
Consensus pattern (22 bp):
CTGGAAATTGTTTTGATTTGTT
Found at i:35662709 original size:46 final size:46
Alignment explanation
Indices: 35662652--35662817 Score: 125
Period size: 46 Copynumber: 3.3 Consensus size: 46
35662642 TTTGATATTG
35662652 TTCTTGATTTGTTCTGGAAATTGTTTTGATAGTCTGTTGGAAATTA
1 TTCTTGATTTGTTCTGGAAATTGTTTTGATAGTCTGTTGGAAATTA
* ** * * * * *
35662698 TTCTTGATTTGTTAGTGAGTAGAATATGAAACTGGAAATTGTTGCATTTGTTTTGATATTG
1 TTCTTGATTTGTT-CTG-G-A-AAT-TG--TTTTG--ATAG-T-C---TG-TTGGAAATTA
35662759 TTCTTGATTTGTTCTGGAAATTGTTTTGATAGTCTGTTGGAAATTA
1 TTCTTGATTTGTTCTGGAAATTGTTTTGATAGTCTGTTGGAAATTA
35662805 TTCTTGATTTGTT
1 TTCTTGATTTGTT
35662818 AGTGAGTAGA
Statistics
Matches: 89, Mismatches: 16, Indels: 30
0.66 0.12 0.22
Matches are distributed among these distances:
46 33 0.37
47 4 0.04
48 1 0.01
49 1 0.01
50 4 0.04
51 3 0.03
52 3 0.03
53 2 0.02
54 2 0.02
55 3 0.03
56 3 0.03
57 4 0.04
58 1 0.01
59 1 0.01
60 4 0.04
61 20 0.22
ACGTcount: A:0.22, C:0.06, G:0.22, T:0.50
Consensus pattern (46 bp):
TTCTTGATTTGTTCTGGAAATTGTTTTGATAGTCTGTTGGAAATTA
Found at i:35662770 original size:22 final size:22
Alignment explanation
Indices: 35662729--35662788 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
35662719 GAATATGAAA
35662729 CTGGAAATTG--TTGCATTTGTT
1 CTGGAAATTGTTTTG-ATTTGTT
* *
35662750 -TTGATATTGTTCTTGATTTGTT
1 CTGGAAATTGTT-TTGATTTGTT
35662772 CTGGAAATTGTTTTGAT
1 CTGGAAATTGTTTTGAT
35662789 AGTCTGTTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
20 7 0.23
22 12 0.39
23 12 0.39
ACGTcount: A:0.18, C:0.07, G:0.22, T:0.53
Consensus pattern (22 bp):
CTGGAAATTGTTTTGATTTGTT
Found at i:35662802 original size:107 final size:107
Alignment explanation
Indices: 35662616--35662845 Score: 460
Period size: 107 Copynumber: 2.1 Consensus size: 107
35662606 GCTGTTTTCA
35662616 ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTGA
1 ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTGA
35662681 TAGTCTGTTGGAAATTATTCTTGATTTGTTAGTGAGTAGAAT
66 TAGTCTGTTGGAAATTATTCTTGATTTGTTAGTGAGTAGAAT
35662723 ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTGA
1 ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTGA
35662788 TAGTCTGTTGGAAATTATTCTTGATTTGTTAGTGAGTAGAAT
66 TAGTCTGTTGGAAATTATTCTTGATTTGTTAGTGAGTAGAAT
35662830 ATGAAACTGGAAATTG
1 ATGAAACTGGAAATTG
35662846 CAAGTATAGT
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 123 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.46
Consensus pattern (107 bp):
ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTGA
TAGTCTGTTGGAAATTATTCTTGATTTGTTAGTGAGTAGAAT
Found at i:35666985 original size:44 final size:44
Alignment explanation
Indices: 35666859--35666986 Score: 109
Period size: 44 Copynumber: 2.8 Consensus size: 44
35666849 ATGATTTTAG
* *
35666859 TAAATTCATATAAGAACATTTTTTATTAAGAATTTTATGAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAGAA-TTT-T-AAATTATA
* * * **
35666906 TATCATT-AT-TAA-ATTATATTTAATATTAATTATTTTAAATTATA
1 TA-AATTCATATAAGA--AAATTTATTATTAAGAATTTTAAATTATA
*
35666950 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTA
35666987 TGAAATTATA
Statistics
Matches: 63, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
43 3 0.05
44 29 0.46
45 5 0.08
46 7 0.11
47 16 0.25
48 3 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (44 bp):
TAAATTCATATAAGAAAATTTATTATTAAGAATTTTAAATTATA
Found at i:35667208 original size:15 final size:15
Alignment explanation
Indices: 35667173--35667224 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
35667163 TTAAGAATTT
*
35667173 TATTAAATTAT-ATA
1 TATTTAATTATAATA
35667187 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
35667201 TATTTAATAATAAT-
1 TATTTAATTATAATA
35667215 TATGTTAATT
1 TAT-TTAATT
35667225 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:35667295 original size:61 final size:60
Alignment explanation
Indices: 35667228--35667415 Score: 195
Period size: 61 Copynumber: 3.1 Consensus size: 60
35667218 GTTAATTTAT
35667228 ATTTTATAGTATCATATATTATGATTTGAGTAAATTTATATAAGAATATTGATTATTAAGA
1 ATTTTATA-TATCATATATTATGATTTGAGTAAATTTATATAAGAATATTGATTATTAAGA
* * * * ** * * * * *
35667289 ATTTTATTAAATTATATATTTTAATTAAAATATATTTA-ATAATAAT-TATG-TTA-AAATA
1 ATTTTA-TATATCATATATTATGATTTGAGTAAATTTATATAAGAATAT-TGATTATTAAGA
*
35667347 TATTTTATAATATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGA
1 -ATTTTAT-ATATCATATATTATGATTTGAGTAAATTTATATAAGAATATTGATTATTAAGA
35667409 ATTTTAT
1 ATTTTAT
35667416 TAAATTATAT
Statistics
Matches: 96, Mismatches: 23, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
58 4 0.04
59 31 0.32
60 18 0.19
61 38 0.40
62 5 0.05
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (60 bp):
ATTTTATATATCATATATTATGATTTGAGTAAATTTATATAAGAATATTGATTATTAAGA
Found at i:35667317 original size:18 final size:17
Alignment explanation
Indices: 35667289--35667323 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35667279 ATTATTAAGA
*
35667289 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
35667306 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
35667324 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:35667372 original size:120 final size:120
Alignment explanation
Indices: 35667159--35667467 Score: 573
Period size: 120 Copynumber: 2.6 Consensus size: 120
35667149 NNNNNNNNNN
* *
35667159 ATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAT
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
* * *
35667224 TTATATTTTATAGTATCATATATTATGATTTGAGTAAATTTATATAAGAATATTG
66 ATATATTTTATAATATCATATATTATGATTTGAGTAAATTCATATAAGAATATTG
35667279 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
35667344 ATATATTTTATAATATCATATATTATGATTTGAGTAAATTCATATAAGAATATTG
66 ATATATTTTATAATATCATATATTATGATTTGAGTAAATTCATATAAGAATATTG
35667399 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
35667464 ATAT
66 ATAT
35667468 GATTAAATTA
Statistics
Matches: 184, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 184 1.00
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (120 bp):
ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
ATATATTTTATAATATCATATATTATGATTTGAGTAAATTCATATAAGAATATTG
Found at i:35667426 original size:61 final size:61
Alignment explanation
Indices: 35667159--35667428 Score: 220
Period size: 59 Copynumber: 4.5 Consensus size: 61
35667149 NNNNNNNNNN
* * * * *
35667159 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG
1 ATTATTAAGAATTTTATTAAATTATATATTATGATT-TGAGTAAATTTATATAAGAATAT-TG
* * * *
35667219 -TTAATTTA-TATTTTA-TAGTATCATATATTATGATTTGAGTAAATTTATATAAGAATATTG
1 ATT-ATTAAGAATTTTATTA-AATTATATATTATGATTTGAGTAAATTTATATAAGAATATTG
* * ** * * *
35667279 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTA-ATAATAAT-TATG
1 ATTATTAAGAATTTTATTAAATTATATATTATGATTTGAGTAAATTTATATAAGAATAT-TG
* * * *
35667339 -TTA-AAATATATTTTA-TAATATCATATATTATGATTTGAGTAAATTCATATAAGAATATTG
1 ATTATTAAGA-ATTTTATTAA-ATTATATATTATGATTTGAGTAAATTTATATAAGAATATTG
35667399 ATTATTAAGAATTTTATTAAATTATATATT
1 ATTATTAAGAATTTTATTAAATTATATATT
35667429 TTAATTAAAA
Statistics
Matches: 160, Mismatches: 34, Indels: 31
0.71 0.15 0.14
Matches are distributed among these distances:
58 9 0.06
59 59 0.37
60 35 0.22
61 49 0.31
62 8 0.05
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (61 bp):
ATTATTAAGAATTTTATTAAATTATATATTATGATTTGAGTAAATTTATATAAGAATATTG
Found at i:35667437 original size:18 final size:17
Alignment explanation
Indices: 35667409--35667443 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35667399 ATTATTAAGA
*
35667409 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
35667426 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
35667444 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:35667697 original size:16 final size:16
Alignment explanation
Indices: 35667676--35667724 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
35667666 TTGATTTGCT
35667676 ATTACGCTTCTATTCC
1 ATTACGCTTCTATTCC
35667692 ATTACGCCTT-TATTCC
1 ATTACG-CTTCTATTCC
35667708 ATTACGCTTCTATTCC
1 ATTACGCTTCTATTCC
35667724 A
1 A
35667725 ATACAGCGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.10
16 25 0.81
17 3 0.10
ACGTcount: A:0.20, C:0.31, G:0.06, T:0.43
Consensus pattern (16 bp):
ATTACGCTTCTATTCC
Found at i:35667901 original size:39 final size:40
Alignment explanation
Indices: 35667845--35667949 Score: 106
Period size: 44 Copynumber: 2.5 Consensus size: 40
35667835 TTTCCTTATG
* *
35667845 CTATTACACCTCCATTCCATTCAACCAAACACA-TGA-ATA
1 CTATTACGCCTCTATTCCATTCAACCAAACA-ATTGATATA
* *
35667884 CTATTACGCCTCTATTCCATTACATTCAACCAAACAATTGATTTG
1 CTATTACGCCTCTATT-C----CATTCAACCAAACAATTGATATA
35667929 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
35667950 ACGCCTCTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
39 14 0.25
40 5 0.09
43 1 0.02
44 18 0.33
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.33
Consensus pattern (40 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAATTGATATA
Found at i:35667918 original size:44 final size:45
Alignment explanation
Indices: 35667855--35667951 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 45
35667845 CTATTACACC
*
35667855 TCCATTCCATTCAACCAAACACA-TGA-ATACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATTGATATACTATTACGCCTCTAT
* *
35667899 TCCATTACATTCAACCAAACAATTGATTTGCTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAATTGATATACTATTACGCCTCTAT
35667944 TCCATTAC
1 TCCATTAC
35667952 GCCTCTATTC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.48
45 24 0.50
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATTGATATACTATTACGCCTCTAT
Found at i:35667948 original size:255 final size:255
Alignment explanation
Indices: 35667492--35667963 Score: 874
Period size: 255 Copynumber: 1.9 Consensus size: 255
35667482 TTACTGATAT
*
35667492 TAATTATCTTATTAAAATTTAATAACAATAACAATAATCATTTATCTAAACAAATTTCTGCTAAG
1 TAATAATCTTATTAAAATTTAATAACAATAACAATAATCATTTATCTAAACAAATTTCTGCTAAG
*
35667557 GGTATTCTAGTCATTTTAGTTTTTTTCCCTTATGCTATACACCTCCATTCCATTTAACCAAACAC
66 GGTATTCTAGTCATTTTAGTTTTTTTCCCTTATGCTATACACCTCCATTCCATTCAACCAAACAC
* *
35667622 AAGAATACTATTATGCCTCTATTCCATTACATTCAACCAAACAATTGATTTGCTATTACGCTTCT
131 AAGAATACTATTACGCCTCTATTCCATTACATTCAACCAAACAATTGATTTGCTATTACGCCTCT
*
35667687 ATTCCATTACGCCTTTATTCCATTACGCTTCTATTCCAATACAGCGAACCAAACGTGCCC
196 ATTCCATTACGCCTCTATTCCATTACGCTTCTATTCCAATACAGCGAACCAAACGTGCCC
35667747 TAATAATCTTATTAAAATTTAATAACAATAACAATAATCATTTATCTAAACAAATTTCTGCTAAG
1 TAATAATCTTATTAAAATTTAATAACAATAACAATAATCATTTATCTAAACAAATTTCTGCTAAG
35667812 GGTATTCTAGTCATTTTAGTTTTTTT-CCTTATGCTATTACACCTCCATTCCATTCAACCAAACA
66 GGTATTCTAGTCATTTTAGTTTTTTTCCCTTATGCTA-TACACCTCCATTCCATTCAACCAAACA
*
35667876 CATGAATACTATTACGCCTCTATTCCATTACATTCAACCAAACAATTGATTTGCTATTACGCCTC
130 CAAGAATACTATTACGCCTCTATTCCATTACATTCAACCAAACAATTGATTTGCTATTACGCCTC
35667941 TATTCCATTACGCCTCTATTCCA
195 TATTCCATTACGCCTCTATTCCA
35667964 ATACAGCAAA
Statistics
Matches: 210, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
254 10 0.05
255 200 0.95
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (255 bp):
TAATAATCTTATTAAAATTTAATAACAATAACAATAATCATTTATCTAAACAAATTTCTGCTAAG
GGTATTCTAGTCATTTTAGTTTTTTTCCCTTATGCTATACACCTCCATTCCATTCAACCAAACAC
AAGAATACTATTACGCCTCTATTCCATTACATTCAACCAAACAATTGATTTGCTATTACGCCTCT
ATTCCATTACGCCTCTATTCCATTACGCTTCTATTCCAATACAGCGAACCAAACGTGCCC
Found at i:35667952 original size:16 final size:16
Alignment explanation
Indices: 35667931--35667963 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
35667921 TTGATTTGCT
35667931 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
35667947 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
35667963 A
1 A
35667964 ATACAGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:35669638 original size:3 final size:3
Alignment explanation
Indices: 35669630--35669695 Score: 62
Period size: 3 Copynumber: 22.3 Consensus size: 3
35669620 ATTAGTTTAA
* * * *
35669630 TAT TAT TAT TAA T-T TAT TGT TAT TAT TAT TAT TAC TAT TAT TAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
35669677 TTT TAC TAT TAT TTT TAT T
1 TAT TAT TAT TAT TAT TAT T
35669696 TTTTTTCTTA
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
2 1 0.02
3 47 0.98
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:35669696 original size:18 final size:18
Alignment explanation
Indices: 35669625--35669698 Score: 78
Period size: 18 Copynumber: 4.2 Consensus size: 18
35669615 TACTAATTAG
* *
35669625 TTTAATATTATTATTA-A
1 TTTACTATTATTATTATT
* *
35669642 TTTATTGTTATTATTATT
1 TTTACTATTATTATTATT
* *
35669660 ATTACTATTATTATAATT
1 TTTACTATTATTATTATT
*
35669678 TTTACTATTATTTTTATT
1 TTTACTATTATTATTATT
35669696 TTT
1 TTT
35669699 TTTCTTATCA
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
17 14 0.30
18 32 0.70
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (18 bp):
TTTACTATTATTATTATT
Found at i:35671737 original size:47 final size:47
Alignment explanation
Indices: 35671658--35671749 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 47
35671648 TATAGAGATC
* * *
35671658 AAATTTAGAATTCTAATTCTAATAGACGTCAAAATGCTAAAACTATA
1 AAATATAGAATTCTAATTCTAATAGACATCAAAATACTAAAACTATA
*
35671705 AAATATAGAATTCTAATTCTAATAGGCATCAAAATACTAAAACTA
1 AAATATAGAATTCTAATTCTAATAGACATCAAAATACTAAAACTA
35671750 GAATTTTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.30
Consensus pattern (47 bp):
AAATATAGAATTCTAATTCTAATAGACATCAAAATACTAAAACTATA
Found at i:35675949 original size:15 final size:15
Alignment explanation
Indices: 35675929--35675958 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
35675919 AGGGATGTAC
35675929 CTCTATTTTCACTAA
1 CTCTATTTTCACTAA
35675944 CTCTATTTTCACTAA
1 CTCTATTTTCACTAA
35675959 GATCGGCGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (15 bp):
CTCTATTTTCACTAA
Found at i:35680734 original size:35 final size:35
Alignment explanation
Indices: 35680651--35680765 Score: 83
Period size: 35 Copynumber: 3.3 Consensus size: 35
35680641 TGAACTGTTA
* * * ** *
35680651 CAAATTTTTGAATTTAATCAAACCTTGAACTTAAT
1 CAAATTTTTAAACTTAAGCAAATTTTGAACTTAAG
**
35680686 C--ATGTTTTAAACTTTAAG-AAATTTTGGGCTTAAG
1 CAAAT-TTTTAAAC-TTAAGCAAATTTTGAACTTAAG
* * *
35680720 CGAATTTTTGAACTTAAGCATATTTTGAACTTAAG
1 CAAATTTTTAAACTTAAGCAAATTTTGAACTTAAG
*
35680755 CAAATTCTTAA
1 CAAATTTTTAA
35680766 TTTGAGTAGG
Statistics
Matches: 60, Mismatches: 15, Indels: 10
0.71 0.18 0.12
Matches are distributed among these distances:
33 2 0.03
34 23 0.38
35 33 0.55
36 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (35 bp):
CAAATTTTTAAACTTAAGCAAATTTTGAACTTAAG
Found at i:35680745 original size:17 final size:17
Alignment explanation
Indices: 35680675--35680756 Score: 69
Period size: 17 Copynumber: 4.8 Consensus size: 17
35680665 TAATCAAACC
* *
35680675 TTGAACTTAATCATGTT
1 TTGAACTTAAGCATATT
* *
35680692 TTAAACTTTAAG-AAATT
1 TTGAAC-TTAAGCATATT
**
35680709 TTGGGCTTAAGCGA-ATTT
1 TTGAACTTAAGC-ATA-TT
35680727 TTGAACTTAAGCATATT
1 TTGAACTTAAGCATATT
35680744 TTGAACTTAAGCA
1 TTGAACTTAAGCA
35680757 AATTCTTAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
16 5 0.10
17 28 0.55
18 18 0.35
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (17 bp):
TTGAACTTAAGCATATT
Found at i:35681154 original size:124 final size:124
Alignment explanation
Indices: 35680997--35681257 Score: 360
Period size: 124 Copynumber: 2.1 Consensus size: 124
35680987 TCATGAACTA
* * *
35680997 GTAAACCTTTATAACATCAGCTGGGAACCTAGGTCCACTAACTGTGTTGGAGCTGCAAGCTCTTA
1 GTAAACCTTTATAACATCAGCTGGGAACATAGGTCCACTAACTGTGTTGGAGATACAAGCTCTTA
* **
35681062 AAATATTAGCTGGGAGCATAGGTCCGCTAGTTGTTTTTGGAGGCTACGACCATAAACCG
66 AAATATTAGCTGGGAGCATAGGTCCGCTAGCTGTTTTTAAAGGCTACGACCATAAACCG
* ** *
35681121 GTAAACCTTTATAACATCAGCTGGGAACATAGGTCCGCTAGTTGTGTTGGAGATACAAGCTTTTA
1 GTAAACCTTTATAACATCAGCTGGGAACATAGGTCCACTAACTGTGTTGGAGATACAAGCTCTTA
* * * * * *
35681186 GAATATTAGCTGGGAGCTTAGGTCTGCTAGCTGTTTTTAAAGGTTACGATCATAAATCG
66 AAATATTAGCTGGGAGCATAGGTCCGCTAGCTGTTTTTAAAGGCTACGACCATAAACCG
**
35681245 ACAAACCTTTATA
1 GTAAACCTTTATA
35681258 TAATACAAAG
Statistics
Matches: 119, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
124 119 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (124 bp):
GTAAACCTTTATAACATCAGCTGGGAACATAGGTCCACTAACTGTGTTGGAGATACAAGCTCTTA
AAATATTAGCTGGGAGCATAGGTCCGCTAGCTGTTTTTAAAGGCTACGACCATAAACCG
Found at i:35686940 original size:4 final size:4
Alignment explanation
Indices: 35686933--35687000 Score: 50
Period size: 4 Copynumber: 16.0 Consensus size: 4
35686923 GAATAAATAA
* *
35686933 AAAG AAAG AAACG AAACG AAACG AAACG AAAC AAA- AAGAA AAAG AAAG
1 AAAG AAAG AAA-G AAA-G AAA-G AAA-G AAAG AAAG AA-AG AAAG AAAG
35686981 AAAG AAAG AAAAG AAA- AAAG
1 AAAG AAAG -AAAG AAAG AAAG
35687001 GGAAGGAAGG
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
3 5 0.09
4 27 0.47
5 25 0.44
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:35686950 original size:5 final size:5
Alignment explanation
Indices: 35686936--35686964 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
35686926 TAAATAAAAA
35686936 GAAA- GAAAC GAAAC GAAAC GAAAC GAAAC
1 GAAAC GAAAC GAAAC GAAAC GAAAC GAAAC
35686965 AAAAAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.62, C:0.17, G:0.21, T:0.00
Consensus pattern (5 bp):
GAAAC
Found at i:35686960 original size:15 final size:14
Alignment explanation
Indices: 35686936--35686996 Score: 54
Period size: 15 Copynumber: 4.3 Consensus size: 14
35686926 TAAATAAAAA
35686936 GAAAGAAACGAAAC
1 GAAAGAAACGAAAC
35686950 GAAACGAAACGAAAC
1 GAAA-GAAACGAAAC
* *
35686965 AAAAAGAAAAAGAAA-
1 -GAAAG-AAACGAAAC
*
35686980 GAAAGAAA-GAAAA
1 GAAAGAAACGAAAC
35686993 GAAA
1 GAAA
35686997 AAAGGGAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
12 4 0.10
13 7 0.17
14 8 0.20
15 11 0.28
16 10 0.25
ACGTcount: A:0.72, C:0.08, G:0.20, T:0.00
Consensus pattern (14 bp):
GAAAGAAACGAAAC
Found at i:35688008 original size:39 final size:40
Alignment explanation
Indices: 35687888--35688021 Score: 98
Period size: 39 Copynumber: 3.4 Consensus size: 40
35687878 GACTTCGAGT
* * * * *
35687888 CGATGAGACACTAGGTGTTAATTTACTACTTTGGATTAATT
1 CGATGAGACACTAGGTGTCAATTTATTACTTCGAATT-ATC
* * * * *
35687929 CGATGAGGCAGTGGGTGTCAA--T-TTACTTC-AGTTTAAC
1 CGATGAGACACTAGGTGTCAATTTATTACTTCGA-ATTATC
*
35687966 CGATGAGACA-TTGGTGTCAATTTATTACTTCGAATTATC
1 CGATGAGACACTAGGTGTCAATTTATTACTTCGAATTATC
* *
35688005 CGATGAGGCACTGGGTG
1 CGATGAGACACTAGGTG
35688022 CCAAACTGGT
Statistics
Matches: 71, Mismatches: 16, Indels: 13
0.71 0.16 0.13
Matches are distributed among these distances:
36 9 0.13
37 10 0.14
38 8 0.11
39 21 0.30
40 6 0.08
41 17 0.24
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (40 bp):
CGATGAGACACTAGGTGTCAATTTATTACTTCGAATTATC
Found at i:35691839 original size:5 final size:5
Alignment explanation
Indices: 35691782--35691835 Score: 81
Period size: 5 Copynumber: 10.8 Consensus size: 5
35691772 ATTATTAAGT
* * *
35691782 ATATT ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATT ATATT
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
35691832 ATAT
1 ATAT
35691836 TATAATAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (5 bp):
ATATG
Found at i:35695404 original size:27 final size:27
Alignment explanation
Indices: 35695365--35695423 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
35695355 TTATTTGTGT
35695365 AGATCCAACCAGACCTCGTACGGAGTA
1 AGATCCAACCAGACCTCGTACGGAGTA
** *
35695392 AGATCCAGTCAGACCTCGTACGGAGTT
1 AGATCCAACCAGACCTCGTACGGAGTA
35695419 AGATC
1 AGATC
35695424 GAGGCAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.19
Consensus pattern (27 bp):
AGATCCAACCAGACCTCGTACGGAGTA
Found at i:35702354 original size:40 final size:41
Alignment explanation
Indices: 35702286--35702373 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 41
35702276 ATTTTATCTG
* * *
35702286 AATTTTTGTAAATATTTTGTAGTGTTAATTATAAGTTTTAT
1 AATTTTTGTAAATATTTTATAGTATTAATTATAAGTCTTAT
* * * *
35702327 -ATTTTTGTGAATCTTTTATATTATTAATTATAGGTCTTAT
1 AATTTTTGTAAATATTTTATAGTATTAATTATAAGTCTTAT
35702367 AATTTTT
1 AATTTTT
35702374 ATTTCCATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 33 0.85
41 6 0.15
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.58
Consensus pattern (41 bp):
AATTTTTGTAAATATTTTATAGTATTAATTATAAGTCTTAT
Found at i:35702466 original size:34 final size:34
Alignment explanation
Indices: 35702423--35702523 Score: 148
Period size: 34 Copynumber: 3.0 Consensus size: 34
35702413 CTGCTATTAG
*
35702423 AGTTTTAAGTTTTATTATTTTTGTTTCATTTTGT
1 AGTTTTAAGTCTTATTATTTTTGTTTCATTTTGT
* *
35702457 AGTTTTAAGTCTTATTATATTTGTTTCATTTTTT
1 AGTTTTAAGTCTTATTATTTTTGTTTCATTTTGT
* * *
35702491 AGTTTTAAGCCTTATCATTTTTGTCTCATTTTG
1 AGTTTTAAGTCTTATTATTTTTGTTTCATTTTG
35702524 GTGAATATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.19, C:0.08, G:0.11, T:0.62
Consensus pattern (34 bp):
AGTTTTAAGTCTTATTATTTTTGTTTCATTTTGT
Found at i:35706015 original size:20 final size:21
Alignment explanation
Indices: 35705990--35706029 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
35705980 TTTTCAATGA
35705990 ATTTTTATTTATA-AAATTAG
1 ATTTTTATTTATATAAATTAG
*
35706010 ATTTTTATTTTTATAAATTA
1 ATTTTTATTTATATAAATTA
35706030 AATAAAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
ATTTTTATTTATATAAATTAG
Found at i:35709163 original size:33 final size:33
Alignment explanation
Indices: 35709126--35709190 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
35709116 ACTATATTTT
35709126 AAATATTTAAATATTTGTAATTAAT-ATTTTAAA
1 AAATATTT-AATATTTGTAATTAATGATTTTAAA
** *
35709159 AAATATTTTTTATTTTTAATTAATGATTTTAA
1 AAATATTTAATATTTGTAATTAATGATTTTAA
35709191 CACAATTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (33 bp):
AAATATTTAATATTTGTAATTAATGATTTTAAA
Found at i:35716656 original size:24 final size:23
Alignment explanation
Indices: 35716612--35716656 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
35716602 ATGAAACATT
*
35716612 ATTCTTGCAAATCATGAATAGTA
1 ATTCTTGCAAATCATCAATAGTA
* *
35716635 ATTCTTGGCAAGTCATCTATAG
1 ATTCTT-GCAAATCATCAATAG
35716657 CGCAACATCT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 6 0.33
24 12 0.67
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (23 bp):
ATTCTTGCAAATCATCAATAGTA
Found at i:35717958 original size:27 final size:27
Alignment explanation
Indices: 35717864--35717958 Score: 111
Period size: 27 Copynumber: 3.5 Consensus size: 27
35717854 TATTTCTCTT
* * *
35717864 AGTGTTCACCATAAGTTCTATTCCTTT-
1 AGTGTTCGCCATACGTACTATT-CTTTC
* * *
35717891 AGAGTTCGCCATATGTACTATTCCTTC
1 AGTGTTCGCCATACGTACTATTCTTTC
*
35717918 TGTGTTCGCCATACGTACTATTCTTTC
1 AGTGTTCGCCATACGTACTATTCTTTC
35717945 AGTGTTCGCCATAC
1 AGTGTTCGCCATAC
35717959 TTACCATTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 3 0.05
27 54 0.95
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (27 bp):
AGTGTTCGCCATACGTACTATTCTTTC
Found at i:35718084 original size:27 final size:26
Alignment explanation
Indices: 35718054--35718128 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 26
35718044 AAGGCATTTT
*
35718054 TTTCTATGATCACCACAAAGGCTCCCA
1 TTTC-ATGATTACCACAAAGGCTCCCA
* *
35718081 TTTCACAGATTACCACAAAGGCTTCCA
1 TTTCA-TGATTACCACAAAGGCTCCCA
*
35718108 TTTCATAGATTTCCACAAAGG
1 TTTCAT-GATTACCACAAAGG
35718129 TTTTCATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.02
27 40 0.98
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (26 bp):
TTTCATGATTACCACAAAGGCTCCCA
Found at i:35718136 original size:27 final size:27
Alignment explanation
Indices: 35718065--35718137 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
35718055 TTCTATGATC
*
35718065 ACCACAAAGGCTCCCATTTCACAGATT
1 ACCACAAAGGCTTCCATTTCACAGATT
*
35718092 ACCACAAAGGCTTCCATTTCATAGATT
1 ACCACAAAGGCTTCCATTTCACAGATT
* * *
35718119 TCCACAAAGGTTTTCATTT
1 ACCACAAAGGCTTCCATTT
35718138 TCTGGCATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (27 bp):
ACCACAAAGGCTTCCATTTCACAGATT
Found at i:35720703 original size:134 final size:133
Alignment explanation
Indices: 35720462--35721059 Score: 641
Period size: 134 Copynumber: 4.5 Consensus size: 133
35720452 GGATAAGTTA
* * *
35720462 TAGAGTTCATCAATTTACGATCGCAACTCTATTCAAACAGTTCGCTGATTTACAATCACAACTGA
1 TAGAGTTCA-CTATTTACAATCGCAACTCTATTCAAACAGTTCACTGATTTACAATCACAACTGA
* * *
35720527 TATTATCAAAGCTCATTGATTTA-TATTCATAGCTT-AGATTCATTGATTTACT-ATCATAAACG
65 TATTATTAAAGCTCATTGATTTACGA-TCACAGCTTAAG-TTCATTGATTTA-TGATCATAAACG
*
35720589 ATTCACT
127 GTTCACT
* * * * *
35720596 TAGAGTTCACCTATTTACAATTGCAACTCTATTCAAACATTTCACTAATTTACGATCACAATTGA
1 TAGAGTTCA-CTATTTACAATCGCAACTCTATTCAAACAGTTCACTGATTTACAATCACAACTGA
* * * * *
35720661 TATTATTAAAGCTCATTGATTTATGTTCACAGGTTAAGTTCATTGATTTATGATCATGAATGGTT
65 TATTATTAAAGCTCATTGATTTACGATCACAGCTTAAGTTCATTGATTTATGATCATAAACGGTT
35720726 CACT
130 CACT
* * * * *
35720730 TAGAGGTT-ACTAATTTACAATCACAACTCCATTCAAACAGTTCGCTTATTTACGATCACAACTG
1 TAGA-GTTCACT-ATTTACAATCGCAACTCTATTCAAACAGTTCACTGATTTACAATCACAACTG
** * * * *
35720794 ATATTATTAAAGCTTGTTTATTTACGATCACAGCTTAAGTTCATTGATTTACGATCATGAATGGT
64 ATATTATTAAAGCTCATTGATTTACGATCACAGCTTAAGTTCATTGATTTATGATCATAAACGGT
35720859 TCACT
129 TCACT
* ** * * * *
35720864 TAGAGTTTACTGATTTACGTTTGCAACT-TCGTTCAAACAGTTCATTGATTTACAATTACAACTG
1 TAGAGTTCACT-ATTTACAATCGCAACTCT-ATTCAAACAGTTCACTGATTTACAATCACAACTG
* * * * *
35720928 ATATTATTAAAACTCGTTGATTTACGATCATAGCTTAAGTTCATTAATTTATGATCATAAAC-TT
64 ATATTATTAAAGCTCATTGATTTACGATCACAGCTTAAGTTCATTGATTTATGATCATAAACGGT
35720992 TCACT
129 TCACT
* * * ** * *
35720997 TAAAGTTCACCGATTTATAATCAAAACTTTATTCAAACAGTTCACTGATTTATAATCACAACT
1 TAGAGTTCA-CTATTTACAATCGCAACTCTATTCAAACAGTTCACTGATTTACAATCACAACT
35721060 TGTAACAGCC
Statistics
Matches: 390, Mismatches: 65, Indels: 19
0.82 0.14 0.04
Matches are distributed among these distances:
133 58 0.15
134 327 0.84
135 5 0.01
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (133 bp):
TAGAGTTCACTATTTACAATCGCAACTCTATTCAAACAGTTCACTGATTTACAATCACAACTGAT
ATTATTAAAGCTCATTGATTTACGATCACAGCTTAAGTTCATTGATTTATGATCATAAACGGTTC
ACT
Found at i:35720950 original size:268 final size:267
Alignment explanation
Indices: 35720465--35721059 Score: 707
Period size: 268 Copynumber: 2.2 Consensus size: 267
35720455 TAAGTTATAG
* * *
35720465 AGTTCATCAATTTACGATCGCAACTCTATTCAAACAGTTCGCTGATTTACAATCACAACTGATAT
1 AGTTCACCAATTTACAATCACAACTCTATTCAAACAGTTCGCTGATTTACAATCACAACTGATAT
* * *
35720530 TATCAAAGCTCATTGATTTATATTCATAGCTTAGATTCATTGATTTACTATCATAAACGATTCAC
66 TATCAAAGCTCATTGATTTAGATTCACAGCTTAGATTCATTGATTTACGATCATAAACGATTCAC
* * *
35720595 TTAGAGTTCACCTATTTACAATTGCAACTCTATTCAAACATTTCACTAATTTACGATCACAATTG
131 TTAGAGTTCACCTATTTACAATTGCAACTCTATTCAAACAGTTCACTAATTTACAATCACAACTG
* * * * * *
35720660 ATATTATTAAAGCTCATTGATTTATGTTCACAGGTTAAGTTCATTGATTTATGATCATGAA-TGG
196 ATATTATTAAAACTCATTGATTTACGATCACAGCTTAAGTTCATTAATTTATGATCATAAACT--
35720724 TTCACTTAGA
259 TTCACTTA-A
* * * * *
35720734 GGTT-ACTAATTTACAATCACAACTCCATTCAAACAGTTCGCTTATTTACGATCACAACTGATAT
1 AGTTCACCAATTTACAATCACAACTCTATTCAAACAGTTCGCTGATTTACAATCACAACTGATAT
* ** * * * *
35720798 TATTAAAGCTTGTTTATTTACGA-TCACAGCTTA-AGTTCATTGATTTACGATCATGAATGGTTC
66 TATCAAAGCTCATTGATTTA-GATTCACAGCTTAGA-TTCATTGATTTACGATCATAAACGATTC
* ** * * * *
35720861 ACTTAGAGTTTA-CTGATTTACGTTTGCAACT-TCGTTCAAACAGTTCATTGATTTACAATTACA
129 ACTTAGAGTTCACCT-ATTTACAATTGCAACTCT-ATTCAAACAGTTCACTAATTTACAATCACA
* *
35720924 ACTGATATTATTAAAACTCGTTGATTTACGATCATAGCTTAAGTTCATTAATTTATGATCATAAA
192 ACTGATATTATTAAAACTCATTGATTTACGATCACAGCTTAAGTTCATTAATTTATGATCATAAA
35720989 CTTTCACTTAA
257 CTTTCACTTAA
* * * * * *
35721000 AGTTCACCGATTTATAATCAAAACTTTATTCAAACAGTTCACTGATTTATAATCACAACT
1 AGTTCACCAATTTACAATCACAACTCTATTCAAACAGTTCGCTGATTTACAATCACAACT
35721060 TGTAACAGCC
Statistics
Matches: 273, Mismatches: 47, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
266 4 0.01
267 57 0.21
268 207 0.76
269 5 0.02
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (267 bp):
AGTTCACCAATTTACAATCACAACTCTATTCAAACAGTTCGCTGATTTACAATCACAACTGATAT
TATCAAAGCTCATTGATTTAGATTCACAGCTTAGATTCATTGATTTACGATCATAAACGATTCAC
TTAGAGTTCACCTATTTACAATTGCAACTCTATTCAAACAGTTCACTAATTTACAATCACAACTG
ATATTATTAAAACTCATTGATTTACGATCACAGCTTAAGTTCATTAATTTATGATCATAAACTTT
CACTTAA
Found at i:35722548 original size:24 final size:24
Alignment explanation
Indices: 35722520--35722567 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
35722510 TCTCGATATA
*
35722520 TGGCTATCCGGAGCT-CCTGATTAT
1 TGGCTATCCAGAGCTACCTG-TTAT
*
35722544 TGGCTATTCAGAGCTACCTGTTAT
1 TGGCTATCCAGAGCTACCTGTTAT
35722568 AAGCTCGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (24 bp):
TGGCTATCCAGAGCTACCTGTTAT
Found at i:35722592 original size:25 final size:24
Alignment explanation
Indices: 35722554--35722666 Score: 75
Period size: 25 Copynumber: 4.6 Consensus size: 24
35722544 TGGCTATTCA
* *
35722554 GAGCTACCTGTTATAAGCTCGCAT
1 GAGCTTCCCGTTATAAGCTCGCAT
* **
35722578 GAGCTTCCCAGTTAT-GGCTCTTAT
1 GAGCTTCCC-GTTATAAGCTCGCAT
** * *
35722602 GAGCTTTTCGTTATATAGCCCGGAT
1 GAGCTTCCCGTTATA-AGCTCGCAT
* * * *
35722627 AAGCTTCCCGATATATGACTCACAT
1 GAGCTTCCCGTTATAAG-CTCGCAT
35722652 GAGCTTCCCGTTATA
1 GAGCTTCCCGTTATA
35722667 TGACTCGAGA
Statistics
Matches: 64, Mismatches: 21, Indels: 7
0.70 0.23 0.08
Matches are distributed among these distances:
23 5 0.08
24 21 0.33
25 38 0.59
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (24 bp):
GAGCTTCCCGTTATAAGCTCGCAT
Found at i:35745932 original size:15 final size:16
Alignment explanation
Indices: 35745887--35745934 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
35745877 TTAATAAATG
35745887 AAATAGAATATAAA-AT
1 AAATA-AATATAAATAT
*
35745903 TAATAAATATTAAATAT
1 AAATAAATA-TAAATAT
35745920 AAAT-AATATAAATAT
1 AAATAAATATAAATAT
35745935 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 11 0.39
16 12 0.43
17 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
AAATAAATATAAATAT
Found at i:35746955 original size:28 final size:28
Alignment explanation
Indices: 35746915--35746974 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
35746905 AGTTATCTCA
35746915 AGACATGGAGCCCATGTCTTGAGACTCG
1 AGACATGGAGCCCATGTCTTGAGACTCG
35746943 AGACATGGAGCCCATGTCTTGAGACTCG
1 AGACATGGAGCCCATGTCTTGAGACTCG
35746971 AGAC
1 AGAC
35746975 CTCTAAAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (28 bp):
AGACATGGAGCCCATGTCTTGAGACTCG
Found at i:35747147 original size:110 final size:109
Alignment explanation
Indices: 35746953--35747177 Score: 414
Period size: 110 Copynumber: 2.1 Consensus size: 109
35746943 AGACATGGAG
*
35746953 CCCATGTCTTGAGACTCGAGACCTCTAAAACCAAGTTTTGGCTACTGACTTCCATGTCCCTAGTC
1 CCCATGTCTTGAGACTCGAGACCTCTAAAACCAAATTTTGGCTACTGACTTCCATGTCCCTAGTC
35747018 ACTAGGGCCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACA
66 ACTAGGGCCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACA
*
35747062 CTCCATGTCTTGAGACTCGAGACCTCTAAAACCAAATTTTGGCTACTGACTTCCATGTCCCTGGT
1 C-CCATGTCTTGAGACTCGAGACCTCTAAAACCAAATTTTGGCTACTGACTTCCATGTCCCTAGT
*
35747127 CACTAGGGTCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACA
65 CACTAGGGCCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACA
35747172 CCCATG
1 CCCATG
35747178 GTATGTCTCG
Statistics
Matches: 112, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
109 6 0.05
110 106 0.95
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (109 bp):
CCCATGTCTTGAGACTCGAGACCTCTAAAACCAAATTTTGGCTACTGACTTCCATGTCCCTAGTC
ACTAGGGCCATGTCTTAAGACTTTACCCTGTATGTCTCTAGACA
Found at i:35747536 original size:40 final size:40
Alignment explanation
Indices: 35747492--35747633 Score: 149
Period size: 40 Copynumber: 3.5 Consensus size: 40
35747482 TAGGTCGAGT
* *
35747492 ATTAGCGGCGCTTTTTAAAAAACGCCGCTATAGATCAAGC
1 ATTAGCGGTGCTTTTCAAAAAACGCCGCTATAGATCAAGC
* * ** *
35747532 ATTAGTGATGCTTTTTGAAAAACGCTGCTATAGATCAAGC
1 ATTAGCGGTGCTTTTCAAAAAACGCCGCTATAGATCAAGC
* * * * *
35747572 ATTAGCGGTGCTTCTCGAAAAATGCCACTATAGATCGAGC
1 ATTAGCGGTGCTTTTCAAAAAACGCCGCTATAGATCAAGC
** *
35747612 ATTAATGGGGCTTTTCAAAAAA
1 ATTAGCGGTGCTTTTCAAAAAA
35747634 TGCCACAAAA
Statistics
Matches: 84, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 84 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (40 bp):
ATTAGCGGTGCTTTTCAAAAAACGCCGCTATAGATCAAGC
Found at i:35747719 original size:114 final size:115
Alignment explanation
Indices: 35747571--35747862 Score: 361
Period size: 114 Copynumber: 2.5 Consensus size: 115
35747561 ATAGATCAAG
* * ** * ** * *
35747571 CATTAGCGGTGCTTCTCGAAAAATGCCACTATAGATCGAGCATTAATGGGGCTTTTCAAAAAATG
1 CATTAGCGGCGCTTTTTAAAAAATGCCACAATAGATCGAGCATTAGCGGCGCTTTTCAAAAAACG
*
35747636 CCACAAAAAAGTTGAGCAAAAC-ACGACGTTTGTTGTTGAGCTTTAGTGA
66 CCACAAAAAAGTTGAGCAAAACGACGACGTTTGTTATTGAGCTTTAGTGA
* * * **
35747685 CATTAGCGGCGCTTTTTAAAAAATGCCACAATAGATTGAGCATTAGCGACGATTTTTGAAAAACG
1 CATTAGCGGCGCTTTTTAAAAAATGCCACAATAGATCGAGCATTAGCGGCGCTTTTCAAAAAACG
* * *
35747750 CCGCAAAAAAGTTGAGCAAAACGACGTCGTTTGTTATTGAGCTTTAGTGG
66 CCACAAAAAAGTTGAGCAAAACGACGACGTTTGTTATTGAGCTTTAGTGA
* ** * *
35747800 CATTAGCAGCGCTTTTTAAAAAACACCGCAATAGATCGAGAATTAGCGGCGCTTTGTCAAAAA
1 CATTAGCGGCGCTTTTTAAAAAATGCCACAATAGATCGAGCATTAGCGGCGCTTT-TCAAAAA
35747863 CCGCTGCTAT
Statistics
Matches: 148, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
114 72 0.49
115 71 0.48
116 5 0.03
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (115 bp):
CATTAGCGGCGCTTTTTAAAAAATGCCACAATAGATCGAGCATTAGCGGCGCTTTTCAAAAAACG
CCACAAAAAAGTTGAGCAAAACGACGACGTTTGTTATTGAGCTTTAGTGA
Found at i:35747765 original size:41 final size:40
Alignment explanation
Indices: 35747685--35747767 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
35747675 GCTTTAGTGA
* * * * *
35747685 CATTAGCGGCGCTTTTTAAAAAATGCCACAATAGATTGAG
1 CATTAGCGACGATTTTTAAAAAACGCCACAAAAAATTGAG
* *
35747725 CATTAGCGACGATTTTTGAAAAACGCCGCAAAAAAGTTGAG
1 CATTAGCGACGATTTTTAAAAAACGCCACAAAAAA-TTGAG
35747766 CA
1 CA
35747768 AAACGACGTC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
40 28 0.80
41 7 0.20
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.24
Consensus pattern (40 bp):
CATTAGCGACGATTTTTAAAAAACGCCACAAAAAATTGAG
Found at i:35747862 original size:40 final size:41
Alignment explanation
Indices: 35747801--35747895 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
35747791 CTTTAGTGGC
* * *
35747801 ATTAGCAGCGCTTTTTAAAAAACAC-C-GCAATAGATCGAGA
1 ATTAGCGGCGCTTTGTAAAAAAC-CGCTGCAATAGATAGAGA
* * *
35747841 ATTAGCGGCGCTTTGTCAAAAACCGCTGCTATAGATAGAGC
1 ATTAGCGGCGCTTTGTAAAAAACCGCTGCAATAGATAGAGA
*
35747882 ATTAGCGGTGCTTT
1 ATTAGCGGCGCTTT
35747896 TTGGAAAAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
39 1 0.02
40 21 0.46
41 24 0.52
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (41 bp):
ATTAGCGGCGCTTTGTAAAAAACCGCTGCAATAGATAGAGA
Found at i:35747862 original size:115 final size:113
Alignment explanation
Indices: 35747596--35747863 Score: 338
Period size: 115 Copynumber: 2.3 Consensus size: 113
35747586 TCGAAAAATG
* ** * *
35747596 CCACTATAGATCGAGCATTAATGGGGCTTTTCAAAAAATGCCACAAAAAAGTTGAGCAAAACACG
1 CCACAATAGATCGAGCATTAGCGGCGCTTTTC-AAAAACGCCACAAAAAAGTTGAGCAAAACACG
* * **
35747661 ACGTTTGTTGTTGAGCTTTAGTGACATTAGCGGCGCTTTTTAAAAAATG
65 ACGTTTGTTATTGAGCTTTAGTGACATTAGCAGCGCTTTTTAAAAAACA
* * * * *
35747710 CCACAATAGATTGAGCATTAGCGACGATTTTTGAAAAACGCCGCAAAAAAGTTGAGCAAAACGAC
1 CCACAATAGATCGAGCATTAGCGGCG-CTTTTCAAAAACGCCACAAAAAAGTTGAGCAAAAC-AC
* *
35747775 GTCGTTTGTTATTGAGCTTTAGTGGCATTAGCAGCGCTTTTTAAAAAACA
64 GACGTTTGTTATTGAGCTTTAGTGACATTAGCAGCGCTTTTTAAAAAACA
* *
35747825 CCGCAATAGATCGAGAATTAGCGGCGCTTTGTCAAAAAC
1 CCACAATAGATCGAGCATTAGCGGCGCTTT-TCAAAAAC
35747864 CGCTGCTATA
Statistics
Matches: 129, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
114 50 0.39
115 79 0.61
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (113 bp):
CCACAATAGATCGAGCATTAGCGGCGCTTTTCAAAAACGCCACAAAAAAGTTGAGCAAAACACGA
CGTTTGTTATTGAGCTTTAGTGACATTAGCAGCGCTTTTTAAAAAACA
Found at i:35748072 original size:157 final size:156
Alignment explanation
Indices: 35747715--35748128 Score: 552
Period size: 157 Copynumber: 2.7 Consensus size: 156
35747705 AAATGCCACA
* * * * *
35747715 ATAGATTGAGCATTAGCGACGATTTTTGAAAAACGCCGCAAAAAAGTTGAGCAAAACGACGTCGT
1 ATAGATAGAGCATTAGCGGCGCTTTTCGAAAAACGCCTCAAAAAAGTTGAGCAAAACGACGTCGT
* *
35747780 TTGTTATTGAGCTTTAGTGGCATTAGCAGCGCTTTTTAAAAAACACCGCAATAGATCGAGAATTA
66 TTGTTGTTGAGCTTTAGTGGCATTAGCAGCACTTTTTAAAAAACACCGCAATAGATCGAGAATTA
* * **
35747845 GCGGCGCTTTGTCAAAAACCGCTGCT
131 GCGACACTTTGTCAAAAACAACTGCT
* * *
35747871 ATAGATAGAGCATTAGCGGTGCTTTTTGGAAAAACGCCAT-AAAAAAGTTGAGCAAAACAACGTC
1 ATAGATAGAGCATTAGCGGCGC-TTTTCGAAAAACGCC-TCAAAAAAGTTGAGCAAAACGACGTC
35747935 GTTTGTTGTTGAGCTTTAGTGGCATTAGCAGCACTTTTATAAAAAA-ATGCCGCAATAGATCGAG
64 GTTTGTTGTTGAGCTTTAGTGGCATTAGCAGCACTTTT-TAAAAAACA--CCGCAATAGATCGAG
* *
35747999 AATTAGTGACAC-TTGTGGAAAAA-AACTGCT
126 AATTAGCGACACTTTGT-CAAAAACAACTGCT
* * *
35748029 ATAGATCGAGCATTAGCGGCGCTTTTCGCAAAATGCCTCAAAAAAGTTGAG-AAAACGACGTCGT
1 ATAGATAGAGCATTAGCGGCGCTTTTCGAAAAACGCCTCAAAAAAGTTGAGCAAAACGACGTCGT
*
35748093 TTGTTGTTGAGCTTTAGTGGCATTAGCGGCA-TTTTT
66 TTGTTGTTGAGCTTTAGTGGCATTAGCAGCACTTTTT
35748129 GGTATAAATG
Statistics
Matches: 229, Mismatches: 22, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
154 1 0.00
155 4 0.02
156 61 0.27
157 98 0.43
158 36 0.16
159 29 0.13
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.28
Consensus pattern (156 bp):
ATAGATAGAGCATTAGCGGCGCTTTTCGAAAAACGCCTCAAAAAAGTTGAGCAAAACGACGTCGT
TTGTTGTTGAGCTTTAGTGGCATTAGCAGCACTTTTTAAAAAACACCGCAATAGATCGAGAATTA
GCGACACTTTGTCAAAAACAACTGCT
Found at i:35748265 original size:14 final size:14
Alignment explanation
Indices: 35748248--35748287 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
35748238 TAAAGTTTTG
*
35748248 AGTTTAGGGTTTAT
1 AGTTTATGGTTTAT
*
35748262 AGTTTATAGTTTAT
1 AGTTTATGGTTTAT
35748276 AGTTTATGGTTT
1 AGTTTATGGTTT
35748288 GGGGTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (14 bp):
AGTTTATGGTTTAT
Found at i:35748266 original size:7 final size:7
Alignment explanation
Indices: 35748256--35748287 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
35748246 TGAGTTTAGG
35748256 GTTTATA
1 GTTTATA
35748263 GTTTATA
1 GTTTATA
35748270 GTTTATA
1 GTTTATA
*
35748277 GTTTATG
1 GTTTATA
35748284 GTTT
1 GTTT
35748288 GGGGTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (7 bp):
GTTTATA
Found at i:35748470 original size:7 final size:7
Alignment explanation
Indices: 35748460--35748677 Score: 98
Period size: 7 Copynumber: 31.1 Consensus size: 7
35748450 GTAATATATA
35748460 TTTAGGG
1 TTTAGGG
*
35748467 TTTAAGG
1 TTTAGGG
35748474 TTTAGGG
1 TTTAGGG
*
35748481 TATA-GG
1 TTTAGGG
* *
35748487 TTTATGA
1 TTTAGGG
35748494 TTTAGGG
1 TTTAGGG
*
35748501 TTTAAGG
1 TTTAGGG
*
35748508 TTTAAGG
1 TTTAGGG
* *
35748515 TTTATGA
1 TTTAGGG
*
35748522 TTTAGTG
1 TTTAGGG
* *
35748529 TTAAGAG
1 TTTAGGG
*
35748536 TTTAGCG
1 TTTAGGG
* *
35748543 TTTATAGT
1 TTTA-GGG
*
35748551 TTTATGG
1 TTTAGGG
*
35748558 TGTA-GG
1 TTTAGGG
*
35748564 TTTATGG
1 TTTAGGG
***
35748571 TTTAATC
1 TTTAGGG
**
35748578 TTTATTG
1 TTTAGGG
35748585 TTTAGGG
1 TTTAGGG
35748592 TTTAGGG
1 TTTAGGG
**
35748599 TTTAGAA
1 TTTAGGG
*
35748606 TTTAGGT
1 TTTAGGG
35748613 TTTAGGG
1 TTTAGGG
**
35748620 TTTAAAG
1 TTTAGGG
**
35748627 TTTATAG
1 TTTAGGG
35748634 TTTAGGG
1 TTTAGGG
* *
35748641 TCTAAAGG
1 T-TTAGGG
*
35748649 CTTAGGG
1 TTTAGGG
*
35748656 TTTATGG
1 TTTAGGG
*
35748663 TTTAGTG
1 TTTAGGG
35748670 TTTAGGG
1 TTTAGGG
35748677 T
1 T
35748678 CTGATTTTAA
Statistics
Matches: 156, Mismatches: 51, Indels: 8
0.73 0.24 0.04
Matches are distributed among these distances:
6 10 0.06
7 138 0.88
8 8 0.05
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:35749368 original size:22 final size:23
Alignment explanation
Indices: 35749328--35749370 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
35749318 ACTCTTTTTC
* *
35749328 AAAAGGTTGATGGTTAAATTTGA
1 AAAAGATTGATGGTCAAATTTGA
35749351 AAAAGATTGA-GGTCAAATTT
1 AAAAGATTGATGGTCAAATTT
35749371 AACTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.33
Consensus pattern (23 bp):
AAAAGATTGATGGTCAAATTTGA
Found at i:35750317 original size:19 final size:20
Alignment explanation
Indices: 35750293--35750333 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
35750283 CCTTTACATG
*
35750293 TTACATCCTT-TTGTCTTTT
1 TTACATACTTATTGTCTTTT
*
35750312 TTACATAGTTATTGTCTTTT
1 TTACATACTTATTGTCTTTT
35750332 TT
1 TT
35750334 GGACATTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (20 bp):
TTACATACTTATTGTCTTTT
Found at i:35752521 original size:43 final size:43
Alignment explanation
Indices: 35752466--35752631 Score: 176
Period size: 43 Copynumber: 3.9 Consensus size: 43
35752456 TGAAAAAAAT
* * **
35752466 CGCTAAAAGTCATTTTCTATAGTGGCGTTTGTGATAAAAGCGC
1 CGCTAAAGGTCATTTTCTTTACCGGCGTTTGTGATAAAAGCGC
**
35752509 CGCTAAAGGTCATACTCTTTACCGGCGTTTGTGATAAAAGCGC
1 CGCTAAAGGTCATTTTCTTTACCGGCGTTTGTGATAAAAGCGC
* * * *
35752552 CGTTAAAGGTCATGTTT-TTTAGCAGCGTTTGTGAT-AAAGCAC
1 CGCTAAAGGTCAT-TTTCTTTACCGGCGTTTGTGATAAAAGCGC
* * *
35752594 CAG-TAAAGGTCATGTTCTTTACTGGCGTCTGTGATAAA
1 C-GCTAAAGGTCATTTTCTTTACCGGCGTTTGTGATAAA
35752632 GCACCAGTTA
Statistics
Matches: 102, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
41 2 0.02
42 31 0.30
43 68 0.67
44 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (43 bp):
CGCTAAAGGTCATTTTCTTTACCGGCGTTTGTGATAAAAGCGC
Found at i:35753992 original size:70 final size:70
Alignment explanation
Indices: 35753908--35754112 Score: 394
Period size: 70 Copynumber: 2.9 Consensus size: 70
35753898 ATTTAATCCC
*
35753908 TGTAC-TTCTTTTGGGTCTTTTTTTGTCCAATGTACTTTCCAAATTTTAACATATTATCATATAA
1 TGTACTTTTTTTTGGGTCTTTTTTTGTCCAATGTACTTTCCAAATTTTAACATATTATCATATAA
35753972 TTCCG
66 TTCCG
35753977 TGTACTTTTTTTTGGGTCTTTTTTTGTCCAATGTACTTTCCAAATTTTAACATATTATCATATAA
1 TGTACTTTTTTTTGGGTCTTTTTTTGTCCAATGTACTTTCCAAATTTTAACATATTATCATATAA
35754042 TTCCG
66 TTCCG
35754047 TGTACTTTTTTTTGGGTCTTTTTTTGTCCAATGTACTTTCCAAATTTTAACATATTATCATATAA
1 TGTACTTTTTTTTGGGTCTTTTTTTGTCCAATGTACTTTCCAAATTTTAACATATTATCATATAA
35754112 T
66 T
35754113 ATCATGTCAG
Statistics
Matches: 134, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
69 5 0.04
70 129 0.96
ACGTcount: A:0.23, C:0.16, G:0.10, T:0.51
Consensus pattern (70 bp):
TGTACTTTTTTTTGGGTCTTTTTTTGTCCAATGTACTTTCCAAATTTTAACATATTATCATATAA
TTCCG
Found at i:35756406 original size:10 final size:9
Alignment explanation
Indices: 35756351--35756420 Score: 50
Period size: 10 Copynumber: 7.1 Consensus size: 9
35756341 CTTACACAGT
35756351 ATTATAAAA
1 ATTATAAAA
*
35756360 ATTTTAGAAA
1 ATTATA-AAA
*
35756370 ACTATAGTAAA
1 ATTATA--AAA
35756381 ATTATTAAAA
1 ATTA-TAAAA
*
35756391 TTTTATAAAGA
1 -ATTATAAA-A
35756402 ATTATAAAA
1 ATTATAAAA
*
35756411 ATAATAAAA
1 ATTATAAAA
35756420 A
1 A
35756421 ATAGTTTATT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
9 15 0.31
10 21 0.44
11 10 0.21
12 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (9 bp):
ATTATAAAA
Found at i:35770250 original size:46 final size:47
Alignment explanation
Indices: 35770192--35770297 Score: 124
Period size: 47 Copynumber: 2.3 Consensus size: 47
35770182 TTGATATATG
* * * *
35770192 TTAGGATTAGAATAATA-AAATTCTAGTTTTAGTATTTTGATGCCTA
1 TTAGAATTAGAATAATATAAATTATAGTTTTAGCATTTTGACGCCTA
** ** *
35770238 TTAGAATTAGAATTCTATATTTTATAGTTTTAGCATTTTGACGTCTA
1 TTAGAATTAGAATAATATAAATTATAGTTTTAGCATTTTGACGCCTA
35770285 TTAGAATTAGAAT
1 TTAGAATTAGAAT
35770298 TCTAAATTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
46 14 0.28
47 36 0.72
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (47 bp):
TTAGAATTAGAATAATATAAATTATAGTTTTAGCATTTTGACGCCTA
Found at i:35770276 original size:47 final size:47
Alignment explanation
Indices: 35770215--35770306 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 47
35770205 AATAAAATTC
* * *
35770215 TAGTTTTAGTATTTTGATGCCTATTAGAATTAGAATTCTATATTTTA
1 TAGTTTTAGCATTTTGACGCCTATTAGAATTAGAATTCTAAATTTTA
*
35770262 TAGTTTTAGCATTTTGACGTCTATTAGAATTAGAATTCTAAATTT
1 TAGTTTTAGCATTTTGACGCCTATTAGAATTAGAATTCTAAATTT
35770307 GATCTCTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (47 bp):
TAGTTTTAGCATTTTGACGCCTATTAGAATTAGAATTCTAAATTTTA
Found at i:35772281 original size:3 final size:3
Alignment explanation
Indices: 35772269--35772334 Score: 62
Period size: 3 Copynumber: 22.3 Consensus size: 3
35772259 TAAGAAAAAA
* * * * * *
35772269 AAT AAA AAT AAT AGT AAA AAT TAT AAT AAT AGT AAT AAT AAT AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
35772317 AAT AA- ATT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
35772335 TTAAACTAAT
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
2 1 0.02
3 47 0.98
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:35772287 original size:18 final size:18
Alignment explanation
Indices: 35772266--35772339 Score: 78
Period size: 18 Copynumber: 4.2 Consensus size: 18
35772256 TGATAAGAAA
*
35772266 AAAAATAAAAATAATAGT
1 AAAAATAATAATAATAGT
*
35772284 AAAAATTATAATAATAGT
1 AAAAATAATAATAATAGT
* * *
35772302 AATAATAATAATAACAAT
1 AAAAATAATAATAATAGT
* *
35772320 -AAATTAATAATAATATT
1 AAAAATAATAATAATAGT
35772337 AAA
1 AAA
35772340 CTAATTAGTA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
17 13 0.29
18 32 0.71
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (18 bp):
AAAAATAATAATAATAGT
Found at i:35773332 original size:18 final size:17
Alignment explanation
Indices: 35773309--35773342 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
35773299 TATTTCGATA
35773309 TTTTAATAAAATGTAATC
1 TTTTAA-AAAATGTAATC
*
35773327 TTTTAAATAATGTAAT
1 TTTTAAAAAATGTAAT
35773343 ATGATTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (17 bp):
TTTTAAAAAATGTAATC
Found at i:35773422 original size:11 final size:11
Alignment explanation
Indices: 35773404--35773436 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
35773394 TACACGAATG
35773404 AATAACAAACA
1 AATAACAAACA
*
35773415 ATTAACAAACA
1 AATAACAAACA
35773426 AAT-ACAAACA
1 AATAACAAACA
35773436 A
1 A
35773437 GCATAACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.70, C:0.18, G:0.00, T:0.12
Consensus pattern (11 bp):
AATAACAAACA
Found at i:35775122 original size:25 final size:25
Alignment explanation
Indices: 35775094--35775150 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
35775084 AGCTTATGTG
35775094 AGCATACCAATTTACAGCTCGTGAA
1 AGCATACCAATTTACAGCTCGTGAA
* *
35775119 AGCATACCGATTTACAGCTCGTGAG
1 AGCATACCAATTTACAGCTCGTGAA
35775144 AGCATAC
1 AGCATAC
35775151 ATGTACAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (25 bp):
AGCATACCAATTTACAGCTCGTGAA
Found at i:35777425 original size:255 final size:255
Alignment explanation
Indices: 35776974--35777483 Score: 939
Period size: 255 Copynumber: 2.0 Consensus size: 255
35776964 TAGTAACGAG
*
35776974 TGGTACAAGGCCTGTATCTGAGGGCCAGGGAAGAGAGGCTAAGGAAGCTAATCGACTGTTTAACG
1 TGGTACAAGGCCTATATCTGAGGGCCAGGGAAGAGAGGCTAAGGAAGCTAATCGACTGTTTAACG
* * *
35777039 TCATAGCAATAATGTGCAAGCGTATACTATCAATGCAAGTATAGTAGACAGATGTGAGTTTGTCG
66 TCACAGCAATAATGTGCAAGCGTACACTATCAATGCAAGTATAGTAGACAGATGTGAGTCTGTCG
* *
35777104 AAAATCGATCCCATAGGGATGGTAGTCTTTTGTCTATTAATGTTAGTGCAATAACTATATATAAA
131 AAAATCGATCCCATAGGGATGATAGTCTTTTGTCTATTAATGTCAGTGCAATAACTATATATAAA
*
35777169 TGAGATAATTTGTGAGGATAGTTGTCGATGCAATAACTTGAAAACAATAAAATAAAATAT
196 TGAGATAAATTGTGAGGATAGTTGTCGATGCAATAACTTGAAAACAATAAAATAAAATAT
*
35777229 TGGTACAAGGCCTATATCTGAGGGCTAGGGAAGAGAGGCTAAGGAAGCTAATCGACTGTTTAACG
1 TGGTACAAGGCCTATATCTGAGGGCCAGGGAAGAGAGGCTAAGGAAGCTAATCGACTGTTTAACG
*
35777294 TCACAGCAATAATGTGCAAGCGTACACTATCGATGCAAGTATAGTAGACAGATGTGAGTCTGTCG
66 TCACAGCAATAATGTGCAAGCGTACACTATCAATGCAAGTATAGTAGACAGATGTGAGTCTGTCG
35777359 AAAATCGATCCCATAGGGATGATAGTCTTTTGTCTATTAATGTCAGTGCAATAACTATATATAAA
131 AAAATCGATCCCATAGGGATGATAGTCTTTTGTCTATTAATGTCAGTGCAATAACTATATATAAA
35777424 TGAGATAAATTGTGAGGATAGTTGTCGATGCAATAACTTGAAAACAATAAAATAAAATAT
196 TGAGATAAATTGTGAGGATAGTTGTCGATGCAATAACTTGAAAACAATAAAATAAAATAT
35777484 GATAATGATA
Statistics
Matches: 246, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
255 246 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (255 bp):
TGGTACAAGGCCTATATCTGAGGGCCAGGGAAGAGAGGCTAAGGAAGCTAATCGACTGTTTAACG
TCACAGCAATAATGTGCAAGCGTACACTATCAATGCAAGTATAGTAGACAGATGTGAGTCTGTCG
AAAATCGATCCCATAGGGATGATAGTCTTTTGTCTATTAATGTCAGTGCAATAACTATATATAAA
TGAGATAAATTGTGAGGATAGTTGTCGATGCAATAACTTGAAAACAATAAAATAAAATAT
Found at i:35778347 original size:66 final size:66
Alignment explanation
Indices: 35778259--35778384 Score: 171
Period size: 66 Copynumber: 1.9 Consensus size: 66
35778249 TTATCCGGAA
* ** * *
35778259 AGCTATCAGGTGAGGCGACAATTCTAGATGAAATCTGGAGTTAACTCTTGGAGCGACATTGCAGG
1 AGCTATCAGGTGAGGCGACAATTCTAGACGAAATCTGGAACTAACTCATGCAGCGACATTGCAGG
35778324 C
66 C
* * * *
35778325 AGCTGTCAGGTGTGGCGACAATTCTGGACGCAATCTGGAACTAACTCATGCAGCGACATT
1 AGCTATCAGGTGAGGCGACAATTCTAGACGAAATCTGGAACTAACTCATGCAGCGACATT
35778385 AATGCAATAA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 51 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (66 bp):
AGCTATCAGGTGAGGCGACAATTCTAGACGAAATCTGGAACTAACTCATGCAGCGACATTGCAGG
C
Found at i:35782531 original size:15 final size:16
Alignment explanation
Indices: 35782513--35782545 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
35782503 GAAAAATTCA
35782513 TTATTTGTG-AATTTG
1 TTATTTGTGCAATTTG
*
35782528 TTATTTTTGCAATTTG
1 TTATTTGTGCAATTTG
35782544 TT
1 TT
35782546 TTATTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.64
Consensus pattern (16 bp):
TTATTTGTGCAATTTG
Found at i:35787201 original size:26 final size:26
Alignment explanation
Indices: 35787165--35787216 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
35787155 TTTTGGTCAC
35787165 AAGTACATATTCGTTGTAGTAGACTA
1 AAGTACATATTCGTTGTAGTAGACTA
35787191 AAGTACATATTCGTTGTAGTAGACTA
1 AAGTACATATTCGTTGTAGTAGACTA
35787217 TGTGTCTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (26 bp):
AAGTACATATTCGTTGTAGTAGACTA
Found at i:35797508 original size:29 final size:28
Alignment explanation
Indices: 35797481--35797533 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
35797471 TTATATAATT
35797481 TATA-TCATA-TAAAAAATAAATTTATAA
1 TATACTCATATTAAAAAA-AAATTTATAA
*
35797508 TATACTCATATTAAAAAAATATTTAT
1 TATACTCATATTAAAAAAAAATTTAT
35797534 TGCCAACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 12 0.52
29 7 0.30
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.40
Consensus pattern (28 bp):
TATACTCATATTAAAAAAAAATTTATAA
Found at i:35833699 original size:183 final size:183
Alignment explanation
Indices: 35833391--35833754 Score: 613
Period size: 183 Copynumber: 2.0 Consensus size: 183
35833381 CTAAACCATC
* *
35833391 ACCCTACATTTTATTTCATCTCATTTGCATTTAGGTTACTTTGCATCTAGTTAATTAATTTAATT
1 ACCCTACATTTTATTTCATCTCATTTGCATTTAGGTTAATTTGAATCTAGTTAATTAATTTAATT
* *
35833456 TTAACATTTATCAATTCAAAATTGTTGTGTTTTCTTTACCAGCTTGTAAATCCATAATTTTGCAA
66 TTAACATCTATCAATTCAAAATTGTTGTGTTTTCTTTACCAACTTGTAAATCCATAATTTTGCAA
* *
35833521 TTATTTGATTAACAAATATAGTCCATGTGGAGACGATAACTCTTTTACTTATT
131 TTATGTGATTAACAAATATAATCCATGTGGAGACGATAACTCTTTTACTTATT
35833574 ACCCTACATTTTATTTCATCTCATTTGCATTTAGGTTAATTTGAATCTAGTTAATTAATTTAATT
1 ACCCTACATTTTATTTCATCTCATTTGCATTTAGGTTAATTTGAATCTAGTTAATTAATTTAATT
* * * *
35833639 TTAACATCTATCACTTCAAAATAT-TTTTGTTTTCTTTGCCAACTTGTAAATTCATAATTTTGCA
66 TTAACATCTATCAATTCAAAAT-TGTTGTGTTTTCTTTACCAACTTGTAAATCCATAATTTTGCA
*
35833703 ATTATGTGATTAACAAATATAATCCTTGTGGAGACGATAACTCTTTTACTTA
130 ATTATGTGATTAACAAATATAATCCATGTGGAGACGATAACTCTTTTACTTA
35833755 CTTATTACTT
Statistics
Matches: 169, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
183 168 0.99
184 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.45
Consensus pattern (183 bp):
ACCCTACATTTTATTTCATCTCATTTGCATTTAGGTTAATTTGAATCTAGTTAATTAATTTAATT
TTAACATCTATCAATTCAAAATTGTTGTGTTTTCTTTACCAACTTGTAAATCCATAATTTTGCAA
TTATGTGATTAACAAATATAATCCATGTGGAGACGATAACTCTTTTACTTATT
Found at i:35834591 original size:15 final size:15
Alignment explanation
Indices: 35834567--35834598 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
35834557 TATGCATGCA
*
35834567 AAATATAAAAGACAT
1 AAATACAAAAGACAT
35834582 AAATACAAAAGACAT
1 AAATACAAAAGACAT
35834597 AA
1 AA
35834599 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:35837286 original size:35 final size:35
Alignment explanation
Indices: 35837207--35837402 Score: 182
Period size: 35 Copynumber: 5.6 Consensus size: 35
35837197 GTACATCATC
* * **
35837207 AGTCCAACC-ATAACACGTCGATGCTCATAACAGCT
1 AGTCCAACCGA-AACACGCCAATGCTCATAAGGGCT
* * ** *
35837242 AATCTAACCGAAACATTCCAATGTTCATAAGGGCT
1 AGTCCAACCGAAACACGCCAATGCTCATAAGGGCT
* * *
35837277 AGTCCAACCGTAACATGCAAATGCTCATAAGGGCT
1 AGTCCAACCGAAACACGCCAATGCTCATAAGGGCT
*
35837312 AGTCCAACCGTAACACGCCAATGCTCATAA-GGCTT
1 AGTCCAACCGAAACACGCCAATGCTCATAAGGGC-T
* * *
35837347 AGTCCAATC-ATAACACACCAATGCTCATAAGAGCT
1 AGTCCAACCGA-AACACGCCAATGCTCATAAGGGCT
* *
35837382 AATCTAACCGAAACACGCCAA
1 AGTCCAACCGAAACACGCCAA
35837403 ACAGAGAGTA
Statistics
Matches: 131, Mismatches: 25, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
34 3 0.02
35 124 0.95
36 4 0.03
ACGTcount: A:0.37, C:0.29, G:0.15, T:0.20
Consensus pattern (35 bp):
AGTCCAACCGAAACACGCCAATGCTCATAAGGGCT
Found at i:35837321 original size:70 final size:70
Alignment explanation
Indices: 35837207--35837402 Score: 225
Period size: 70 Copynumber: 2.8 Consensus size: 70
35837197 GTACATCATC
* * * ** *
35837207 AGTCCAACCATAACACGTC-GATGCTCATAACAGCTAATCTAACCGAAACATTCCAATGTTCATA
1 AGTCCAACCATAACAC-ACAAATGCTCATAAGAGCTAATCTAACCGAAACACGCCAATGCTCATA
35837271 AGGGC-T
65 A-GGCTT
* ** * * * *
35837277 AGTCCAACCGTAACATGCAAATGCTCATAAGGGCTAGTCCAACCGTAACACGCCAATGCTCATAA
1 AGTCCAACCATAACACACAAATGCTCATAAGAGCTAATCTAACCGAAACACGCCAATGCTCATAA
35837342 GGCTT
66 GGCTT
* *
35837347 AGTCCAATCATAACACACCAATGCTCATAAGAGCTAATCTAACCGAAACACGCCAA
1 AGTCCAACCATAACACACAAATGCTCATAAGAGCTAATCTAACCGAAACACGCCAA
35837403 ACAGAGAGTA
Statistics
Matches: 103, Mismatches: 21, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
69 4 0.04
70 99 0.96
ACGTcount: A:0.37, C:0.29, G:0.15, T:0.20
Consensus pattern (70 bp):
AGTCCAACCATAACACACAAATGCTCATAAGAGCTAATCTAACCGAAACACGCCAATGCTCATAA
GGCTT
Found at i:35844732 original size:35 final size:35
Alignment explanation
Indices: 35844681--35844834 Score: 175
Period size: 35 Copynumber: 4.4 Consensus size: 35
35844671 AGTACATTGT
**
35844681 TAATCCAACC-ATAACACGCTGATGCTCATAAGAGC
1 TAATCCAACCGA-AACACGCCAATGCTCATAAGAGC
* * *
35844716 TAATCCAACCGAAACACGTCAGTGCTTATAAGAGC
1 TAATCCAACCGAAACACGCCAATGCTCATAAGAGC
* * * * *
35844751 TAGTCCAATCGTAATACGCCAATGCTCATAAGAGT
1 TAATCCAACCGAAACACGCCAATGCTCATAAGAGC
* **
35844786 TAATACAACCTTAACACGCCAATGCTCATAAGAGC
1 TAATCCAACCGAAACACGCCAATGCTCATAAGAGC
35844821 TAATCCAACCGAAA
1 TAATCCAACCGAAA
35844835 TGCACCAAAC
Statistics
Matches: 96, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
35 95 0.99
36 1 0.01
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.21
Consensus pattern (35 bp):
TAATCCAACCGAAACACGCCAATGCTCATAAGAGC
Found at i:35847377 original size:21 final size:21
Alignment explanation
Indices: 35847353--35847393 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
35847343 AGATGGCTTT
35847353 AACTAAATTAAAAGAATTAAA
1 AACTAAATTAAAAGAATTAAA
* **
35847374 AACTCAATTGTAAGAATTAA
1 AACTAAATTAAAAGAATTAA
35847394 TTGACAGAGG
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:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (21 bp):
AACTAAATTAAAAGAATTAAA
Found at i:35850084 original size:21 final size:21
Alignment explanation
Indices: 35850060--35850174 Score: 54
Period size: 21 Copynumber: 5.2 Consensus size: 21
35850050 CACTATACCG
35850060 GAAATGAATAAGACCATAGTT
1 GAAATGAATAAGACCATAGTT
* ***
35850081 GAAA-GACAATATGACACTATACCG
1 GAAATG--AATAAGAC-C-ATAGTT
*
35850105 GAAATGAATAAAACCATAGTT
1 GAAATGAATAAGACCATAGTT
* * ***
35850126 GAAA-GACACTATGGCACTATACCG
1 GAAATGA-A-TA-AG-ACCATAGTT
35850150 GAAATGAATAAGACCATAGTT
1 GAAATGAATAAGACCATAGTT
35850171 GAAA
1 GAAA
35850175 GACACTATGG
Statistics
Matches: 64, Mismatches: 20, Indels: 20
0.62 0.19 0.19
Matches are distributed among these distances:
20 3 0.05
21 21 0.33
22 11 0.17
23 9 0.14
24 17 0.27
25 3 0.05
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20
Consensus pattern (21 bp):
GAAATGAATAAGACCATAGTT
Found at i:35850205 original size:90 final size:89
Alignment explanation
Indices: 35850022--35850211 Score: 283
Period size: 90 Copynumber: 2.1 Consensus size: 89
35850012 TTGAAAAACG
*
35850022 AATAAGACCATATTTGAAAGACACATGGCACTATACCGGAAATGAATAAGACCATAGTTGAAAGA
1 AATAAGACCATAGTTGAAAGACACATGGCACTATACCGGAAATGAATAAGACCATAGTTGAAAGA
* *
35850087 CAATATGACACTATACCGGAAATG
66 CAATATGACACTATACCGAAAATA
*
35850111 AATAAAACCATAGTTGAAAGACACTATGGCACTATACCGGAAATGAATAAGACCATAGTTGAAAG
1 AATAAGACCATAGTTGAAAGACAC-ATGGCACTATACCGGAAATGAATAAGACCATAGTTGAAAG
* * **
35850176 ACACTATGGCA-TCATGTCGAAAATA
65 ACAATATGACACT-ATACCGAAAATA
35850201 AATAAGACCAT
1 AATAAGACCAT
35850212 GCCCATAAGA
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
89 23 0.26
90 67 0.74
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (89 bp):
AATAAGACCATAGTTGAAAGACACATGGCACTATACCGGAAATGAATAAGACCATAGTTGAAAGA
CAATATGACACTATACCGAAAATA
Found at i:35850211 original size:45 final size:45
Alignment explanation
Indices: 35850021--35850186 Score: 289
Period size: 45 Copynumber: 3.7 Consensus size: 45
35850011 CTTGAAAAAC
*
35850021 GAATAAGACCATATTTGAAAGACAC-ATGGCACTATACCGGAAAT
1 GAATAAGACCATAGTTGAAAGACACTATGGCACTATACCGGAAAT
* *
35850065 GAATAAGACCATAGTTGAAAGACAATATGACACTATACCGGAAAT
1 GAATAAGACCATAGTTGAAAGACACTATGGCACTATACCGGAAAT
*
35850110 GAATAAAACCATAGTTGAAAGACACTATGGCACTATACCGGAAAT
1 GAATAAGACCATAGTTGAAAGACACTATGGCACTATACCGGAAAT
35850155 GAATAAGACCATAGTTGAAAGACACTATGGCA
1 GAATAAGACCATAGTTGAAAGACACTATGGCA
35850187 TCATGTCGAA
Statistics
Matches: 114, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
44 23 0.20
45 91 0.80
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.20
Consensus pattern (45 bp):
GAATAAGACCATAGTTGAAAGACACTATGGCACTATACCGGAAAT
Found at i:35850222 original size:90 final size:90
Alignment explanation
Indices: 35850038--35850231 Score: 259
Period size: 90 Copynumber: 2.2 Consensus size: 90
35850028 ACCATATTTG
35850038 AAAGACAC-ATGGCACTATACCGGAAATGAATAAGACCATAGTTGAAAGACAATATGACACTATA
1 AAAGACACTATGGCACTATACCGGAAATGAATAAGACCATAGTTGAAAGACAATATGACACTATA
* * ***
35850102 CCGGAAATGAATAAAACCATAGTTG
66 CCGAAAATAAATAAAACCATAGCCC
* *
35850127 AAAGACACTATGGCACTATACCGGAAATGAATAAGACCATAGTTGAAAGACACTATGGCA-TCAT
1 AAAGACACTATGGCACTATACCGGAAATGAATAAGACCATAGTTGAAAGACAATATGACACT-AT
** *
35850191 GTCGAAAATAAATAAGACCAT-GCCC
65 ACCGAAAATAAATAAAACCATAGCCC
35850216 ATAAGACACTATGGCA
1 A-AAGACACTATGGCA
35850232 TTCTTGAATA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
89 11 0.12
90 81 0.88
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (90 bp):
AAAGACACTATGGCACTATACCGGAAATGAATAAGACCATAGTTGAAAGACAATATGACACTATA
CCGAAAATAAATAAAACCATAGCCC
Found at i:35860093 original size:5 final size:5
Alignment explanation
Indices: 35860085--35860115 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
35860075 TGAGATGAAT
35860085 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
35860116 ATATTTGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:35864441 original size:18 final size:20
Alignment explanation
Indices: 35864409--35864446 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
35864399 TAAAAATTCA
*
35864409 CAAAAATATTTTAAA-AAAT
1 CAAAAATATTGTAAACAAAT
35864428 CAAAAA-ATTGTAAACAAAT
1 CAAAAATATTGTAAACAAAT
35864447 TCATAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.63, C:0.08, G:0.03, T:0.26
Consensus pattern (20 bp):
CAAAAATATTGTAAACAAAT
Found at i:35864467 original size:21 final size:18
Alignment explanation
Indices: 35864399--35864468 Score: 50
Period size: 21 Copynumber: 3.4 Consensus size: 18
35864389 GTATAATTCA
35864399 TAAAAATTCACAAAAATATTT
1 TAAAAATT--CAAAAA-ATTT
*
35864420 TAAAAAATCAAAAAATTGT
1 TAAAAATTCAAAAAATT-T
*
35864439 AAACAAATTCATAAAAACTTT
1 TAA-AAATTCA-AAAAA-TTT
35864460 TAGAAAATT
1 TA-AAAATT
35864469 TATTTATGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
18 3 0.08
19 9 0.22
20 6 0.15
21 19 0.47
22 3 0.08
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.30
Consensus pattern (18 bp):
TAAAAATTCAAAAAATTT
Found at i:35865243 original size:42 final size:42
Alignment explanation
Indices: 35865196--35865296 Score: 134
Period size: 42 Copynumber: 2.4 Consensus size: 42
35865186 ACATGCCTAA
35865196 GACACACGCCCGTGT-CTCAGGC-CGTGTAACATTCGAAATAGG
1 GACACACGCCCGTGTCCT-A-GCTCGTGTAACATTCGAAATAGG
**
35865238 GACACACGGTCGTGTCCTAGCTCGTGTAACATTCGAAATAGG
1 GACACACGCCCGTGTCCTAGCTCGTGTAACATTCGAAATAGG
* *
35865280 GACACACGGCTGTGTCC
1 GACACACGCCCGTGTCC
35865297 CAACCTGTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
41 2 0.04
42 49 0.92
43 2 0.04
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.21
Consensus pattern (42 bp):
GACACACGCCCGTGTCCTAGCTCGTGTAACATTCGAAATAGG
Found at i:35865373 original size:12 final size:12
Alignment explanation
Indices: 35865356--35865385 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
35865346 TGCCACATGC
35865356 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
35865368 CCGTGTGCTAGG
1 CCGTGTGCCAGG
35865380 CCGTGT
1 CCGTGT
35865386 AACTGTCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:35866304 original size:35 final size:35
Alignment explanation
Indices: 35866241--35866360 Score: 134
Period size: 35 Copynumber: 3.4 Consensus size: 35
35866231 ACGTTGTCAG
* *
35866241 TCCAACC-ATAACACGCCGATGCTCATAAGAGTTAA
1 TCCAACCGA-AACACGCCAATGCTCATAAGAGCTAA
* * * * *
35866276 TCCAATCGAAACATGCCAGTGCTTATAAGAGCTAG
1 TCCAACCGAAACACGCCAATGCTCATAAGAGCTAA
* *
35866311 TCCAACCGTAACACGCCAATGCTCACAAGAGCTAA
1 TCCAACCGAAACACGCCAATGCTCATAAGAGCTAA
*
35866346 TCCAACCAAAACACG
1 TCCAACCGAAACACG
35866361 TCAAACAAAA
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
35 67 0.99
36 1 0.01
ACGTcount: A:0.38, C:0.30, G:0.15, T:0.17
Consensus pattern (35 bp):
TCCAACCGAAACACGCCAATGCTCATAAGAGCTAA
Found at i:35870419 original size:28 final size:28
Alignment explanation
Indices: 35870387--35870443 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
35870377 TGTTACAATA
35870387 TAACTAATTCCATATTCTTTAGATTTTT
1 TAACTAATTCCATATTCTTTAGATTTTT
35870415 TAACTAATTCCATATTCTTTAGATTTTT
1 TAACTAATTCCATATTCTTTAGATTTTT
35870443 T
1 T
35870444 CTTCAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.04, T:0.54
Consensus pattern (28 bp):
TAACTAATTCCATATTCTTTAGATTTTT
Found at i:35870953 original size:84 final size:84
Alignment explanation
Indices: 35870852--35871013 Score: 297
Period size: 84 Copynumber: 1.9 Consensus size: 84
35870842 TCATCTCATC
* *
35870852 ATATTTATTTAAGGTATTCATGTTTATTAAGTAGTTGAGCATTTATTATTGACATTTATTGTATA
1 ATATTTATTTAAGGTATTCATGTTTATTAAGAAGTTGAGCATTTATTATTGACATTTATTGCATA
35870917 TTTAAGAGAAAAATTTGAA
66 TTTAAGAGAAAAATTTGAA
*
35870936 ATATTTATTTAAGGTATTCATGTTTATTAAGAAGTTGAGCATTTATTATTGATATTTATTGCATA
1 ATATTTATTTAAGGTATTCATGTTTATTAAGAAGTTGAGCATTTATTATTGACATTTATTGCATA
35871001 TTTAAGAGAAAAA
66 TTTAAGAGAAAAA
35871014 CCTAAAAGCT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.36, C:0.04, G:0.14, T:0.46
Consensus pattern (84 bp):
ATATTTATTTAAGGTATTCATGTTTATTAAGAAGTTGAGCATTTATTATTGACATTTATTGCATA
TTTAAGAGAAAAATTTGAA
Found at i:35871558 original size:208 final size:208
Alignment explanation
Indices: 35871191--35871815 Score: 984
Period size: 208 Copynumber: 3.0 Consensus size: 208
35871181 GACAATGAAC
* * *
35871191 AATAAGGCTTTTGTTGATAAAATGAGACAAAACTCAATAAATGTGCATATTTACTCAATGTGGCT
1 AATATGGCTTTTGTTGATAAAATGAGACAAAACTCAGTAAAGGTGCATATTTACTCAATGTGGCT
* * * *
35871256 TAATCTTATTAAATAAGGAAAATTGGTTAAATTAAGTTATTAAGACTAAATGTAGCATTTATGCG
66 TAATCTTATTAAATAACGAAAATGGGTTAAATTAAGTTATTAAGACTAATTGTAGCATTTATGTG
* * * *
35871321 GGTATTAGAAATTTTGAAGGTATGATATATTATTATGTTTAAATTATTAAGATGGTGAAACATAA
131 GGTATTAGAAATTTTGAAGTTATGATATATTATTATGCTTAAATGATTAAGATGGTGAAATATAA
35871386 TATAACGAACTTA
196 TATAACGAACTTA
* *
35871399 AATGTGGCTTTTGTTGATAAAAAT-AGACAAAACTCAGTAAAGGTGCATATTTACTCTATGTGGC
1 AATATGGCTTTTGTTGAT-AAAATGAGACAAAACTCAGTAAAGGTGCATATTTACTCAATGTGGC
* *
35871463 TTAATCTTATGAAATAACGAAAATGGGTTAAATTAAGTTATTAAGACCAATTGTAGCATTTATGT
65 TTAATCTTATTAAATAACGAAAATGGGTTAAATTAAGTTATTAAGACTAATTGTAGCATTTATGT
* * * * * *
35871528 GGGTATTAGAAATTTGGAAGTTAGGATATATTATCATGCTTAAATGGTTAAGATAGTGAAATGTA
130 GGGTATTAGAAATTTTGAAGTTATGATATATTATTATGCTTAAATGATTAAGATGGTGAAATATA
*
35871593 ATATAACGAACTGA
195 ATATAACGAACTTA
* *
35871607 AATATGGTTTTTGTTGATAAAATGAGGCAAAACTCAGTAAAGGTGCATATTTACTCAATGTGGCT
1 AATATGGCTTTTGTTGATAAAATGAGACAAAACTCAGTAAAGGTGCATATTTACTCAATGTGGCT
*
35871672 TAATCTTATTAAATAACAAAAATGGGTTAAATTAAGTTATTAAGACTAATTGTAGCATTTATGTG
66 TAATCTTATTAAATAACGAAAATGGGTTAAATTAAGTTATTAAGACTAATTGTAGCATTTATGTG
*
35871737 GGTATTAGAAATTTTGAAGTTATGATATATTATTATGCTTAAATGATTAAGATGATGAAATATAA
131 GGTATTAGAAATTTTGAAGTTATGATATATTATTATGCTTAAATGATTAAGATGGTGAAATATAA
*
35871802 TATAATGAA-TTA
196 TATAACGAACTTA
35871814 AA
1 AA
35871816 ATGATAACAA
Statistics
Matches: 377, Mismatches: 38, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
207 9 0.02
208 363 0.96
209 5 0.01
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.36
Consensus pattern (208 bp):
AATATGGCTTTTGTTGATAAAATGAGACAAAACTCAGTAAAGGTGCATATTTACTCAATGTGGCT
TAATCTTATTAAATAACGAAAATGGGTTAAATTAAGTTATTAAGACTAATTGTAGCATTTATGTG
GGTATTAGAAATTTTGAAGTTATGATATATTATTATGCTTAAATGATTAAGATGGTGAAATATAA
TATAACGAACTTA
Found at i:35872964 original size:26 final size:26
Alignment explanation
Indices: 35872922--35873005 Score: 116
Period size: 26 Copynumber: 3.2 Consensus size: 26
35872912 AGATTATTAA
*
35872922 AATTCTTCTAAAAGAAAACTTAAGAGG
1 AATTCTT-TAAAAGAAAACTCAAGAGG
*
35872949 AATTTTTTAAAAGAAAACTCAAGAGG
1 AATTCTTTAAAAGAAAACTCAAGAGG
35872975 AATTCTTTAAAAGAAAAACTCAA-AGAG
1 AATTCTTTAAAAG-AAAACTCAAGAG-G
35873002 AATT
1 AATT
35873006 TTATTAACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
26 32 0.62
27 20 0.38
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.26
Consensus pattern (26 bp):
AATTCTTTAAAAGAAAACTCAAGAGG
Found at i:35878383 original size:57 final size:56
Alignment explanation
Indices: 35878320--35878482 Score: 202
Period size: 57 Copynumber: 2.9 Consensus size: 56
35878310 ATAAATGAGA
* *
35878320 AATCATTTGGAAATTATTATGATTTTCTTCAAAATGAAAATAAAAATAAAAAATTGG
1 AATCATTTGGAAATTATTATGATTTTCTCCAAAATGAAAATGAAAATAAAAAATT-G
* * *
35878377 AATCATTT-GAAATTGATTATGATTTTCACCAAAATAAAAATGAAAATAGAGAAATTG
1 AATCATTTGGAAATT-ATTATGATTTTCTCCAAAATGAAAATGAAAATA-AAAAATTG
* * * * *
35878434 AATCATTTGAAAATAAATGTGGTTTTCTCCAAAATGAAAATGAAAATAA
1 AATCATTTGGAAATTATTATGATTTTCTCCAAAATGAAAATGAAAATAA
35878483 CCTGAAAAAT
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
56 7 0.08
57 74 0.81
58 10 0.11
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.33
Consensus pattern (56 bp):
AATCATTTGGAAATTATTATGATTTTCTCCAAAATGAAAATGAAAATAAAAAATTG
Found at i:35885830 original size:7 final size:7
Alignment explanation
Indices: 35885818--35885854 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
35885808 TCTCTATCTT
35885818 TGCCTGC
1 TGCCTGC
35885825 TGCCTGC
1 TGCCTGC
35885832 TGCCTGC
1 TGCCTGC
35885839 TGCCTGC
1 TGCCTGC
35885846 TGCCTGC
1 TGCCTGC
35885853 TG
1 TG
35885855 GGTTTGATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.00, C:0.41, G:0.30, T:0.30
Consensus pattern (7 bp):
TGCCTGC
Found at i:35892461 original size:27 final size:27
Alignment explanation
Indices: 35892431--35892508 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 27
35892421 GATATGAAAC
35892431 ATTAAATAAAATAAACTTCCTGTAAAA
1 ATTAAATAAAATAAACTTCCTGTAAAA
* * *
35892458 ATT-AAT--AAT-CA-TAT-ATG-AAAC
1 ATTAAATAAAATAAACT-TCCTGTAAAA
35892479 ATTAAATAAAATAAACTTCCTGTAAAA
1 ATTAAATAAAATAAACTTCCTGTAAAA
35892506 ATT
1 ATT
35892509 TTGCATCTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
21 6 0.16
22 6 0.16
23 2 0.05
24 6 0.16
25 2 0.05
26 6 0.16
27 9 0.24
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.32
Consensus pattern (27 bp):
ATTAAATAAAATAAACTTCCTGTAAAA
Found at i:35892465 original size:48 final size:48
Alignment explanation
Indices: 35892407--35892508 Score: 188
Period size: 48 Copynumber: 2.1 Consensus size: 48
35892397 AAGAACAATG
35892407 AAAAA-TAATAATCAGATATGAAACATTAAATAAAATAAACTTCCTGT
1 AAAAATTAATAATCAGATATGAAACATTAAATAAAATAAACTTCCTGT
*
35892454 AAAAATTAATAATCATATATGAAACATTAAATAAAATAAACTTCCTGT
1 AAAAATTAATAATCAGATATGAAACATTAAATAAAATAAACTTCCTGT
35892502 AAAAATT
1 AAAAATT
35892509 TTGCATCTTG
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 5 0.09
48 48 0.91
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.29
Consensus pattern (48 bp):
AAAAATTAATAATCAGATATGAAACATTAAATAAAATAAACTTCCTGT
Found at i:35892921 original size:17 final size:19
Alignment explanation
Indices: 35892881--35892921 Score: 50
Period size: 17 Copynumber: 2.2 Consensus size: 19
35892871 ATTATATAAT
35892881 AAAATAAAGTATAATAAAAC
1 AAAATAAAGTAT-ATAAAAC
*
35892901 AAAAT-AAGTAT-TAAAAG
1 AAAATAAAGTATATAAAAC
35892918 AAAA
1 AAAA
35892922 AGAAATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 9 0.45
19 6 0.30
20 5 0.25
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (19 bp):
AAAATAAAGTATATAAAAC
Found at i:35892972 original size:13 final size:13
Alignment explanation
Indices: 35892956--35892990 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
35892946 ACAAAAATTT
35892956 GAAAGAAAAGAAA
1 GAAAGAAAAGAAA
*
35892969 GAAATAAAAGAAA
1 GAAAGAAAAGAAA
35892982 G-AAGAAAAG
1 GAAAGAAAAG
35892991 GAGACGCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (13 bp):
GAAAGAAAAGAAA
Found at i:35896259 original size:11 final size:11
Alignment explanation
Indices: 35896243--35896279 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 11
35896233 ATTTTAAAAG
35896243 TTTTATAACTT
1 TTTTATAACTT
35896254 TTTTATAACTTT
1 TTTTATAAC-TT
35896266 TGTTTATAACTT
1 T-TTTATAACTT
35896278 TT
1 TT
35896280 ATGGTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.42
12 6 0.25
13 8 0.33
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.65
Consensus pattern (11 bp):
TTTTATAACTT
Done.