Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 21 of 33
Found at i:3332278 original size:8 final size:9
Alignment explanation
Indices: 3332265--3332328 Score: 55
Period size: 8 Copynumber: 7.3 Consensus size: 9
3332255 AAAATATCAT
3332265 ATAATA-AA
1 ATAATATAA
3332273 ATAATATAA
1 ATAATATAA
3332282 ATAAAATATAA
1 AT--AATATAA
3332293 AT-ATATAA
1 ATAATATAA
*
3332301 AT-ATATTA
1 ATAATATAA
* *
3332309 A-AATTTAT
1 ATAATATAA
3332317 ATAATATAA
1 ATAATATAA
3332326 ATA
1 ATA
3332329 TAAGTTAGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
8 24 0.53
9 12 0.27
11 9 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATAATATAA
Found at i:3332303 original size:25 final size:26
Alignment explanation
Indices: 3332263--3332331 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 26
3332253 ATAAAATATC
*
3332263 ATAT-AATAAAAT-AATATAAATAAA
1 ATATAAATAATATAAATATAAATAAA
*
3332287 ATATAAAT-ATATAAATAT-ATTAAA
1 ATATAAATAATATAAATATAAATAAA
* *
3332311 ATTTATATAATATAAATATAA
1 ATATAAATAATATAAATATAA
3332332 GTTAGATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
24 18 0.49
25 18 0.49
26 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATAAATAATATAAATATAAATAAA
Found at i:3336454 original size:21 final size:21
Alignment explanation
Indices: 3336415--3336463 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
3336405 TTAAATAATA
* * *
3336415 AATATAATATGTTGCATATTT
1 AATATAACATGTTGAATATAT
*
3336436 AATATAACATGTTTAATATAT
1 AATATAACATGTTGAATATAT
3336457 ATATATA
1 A-ATATA
3336464 TATATTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (21 bp):
AATATAACATGTTGAATATAT
Found at i:3336479 original size:25 final size:24
Alignment explanation
Indices: 3336451--3336512 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
3336441 AACATGTTTA
3336451 ATATATATATATATATATTATATTT
1 ATAT-TATATATATATATTATATTT
*
3336476 ATATT-TAATAATTTATATTATATTT
1 ATATTAT-AT-ATATATATTATATTT
3336501 ATACTTATATAT
1 ATA-TTATATAT
3336513 GATTGATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
23 1 0.03
24 3 0.09
25 23 0.72
26 4 0.12
27 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
ATATTATATATATATATTATATTT
Found at i:3337954 original size:19 final size:19
Alignment explanation
Indices: 3337930--3337991 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
3337920 TTATTATTTT
*
3337930 ATAAATATAAAAATCATAA
1 ATAAATATAAAAATTATAA
*
3337949 ATAAATA-AATAATTTATAA
1 ATAAATATAA-AAATTATAA
*
3337968 ATTAAATTATAAATATTATAA
1 A-TAAA-TATAAAAATTATAA
3337989 ATA
1 ATA
3337992 TTTTTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.06
19 15 0.43
20 6 0.17
21 10 0.29
22 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAATATAAAAATTATAA
Found at i:3338165 original size:21 final size:21
Alignment explanation
Indices: 3338122--3338167 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3338112 TATTTGTAAT
* *
3338122 TTATTTATTATAATTTTATAA
1 TTATTTATTATAATTATAAAA
3338143 TTATTTAATTATAA-TATAAAA
1 TTATTT-ATTATAATTATAAAA
3338164 TTAT
1 TTAT
3338168 ATATAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTTATTATAATTATAAAA
Found at i:3345190 original size:22 final size:22
Alignment explanation
Indices: 3345165--3345208 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3345155 TTATTATAAA
*
3345165 ATATAATAATAAAATTACCATG
1 ATATAATAATAAAATTAACATG
** *
3345187 ATATGTTAATATAATTAACATG
1 ATATAATAATAAAATTAACATG
3345209 TGTATCGATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (22 bp):
ATATAATAATAAAATTAACATG
Found at i:3346132 original size:31 final size:32
Alignment explanation
Indices: 3346051--3346134 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 32
3346041 TGTGTATTTA
3346051 AATT-TTTATATATTTATATAAATTTTAATTAATT
1 AATTATTTATATA-TT-T-TAAATTTTAATTAATT
* * *
3346085 AATTAATTA-ATTTTTTAAATTTTAA-TATTT
1 AATTATTTATATATTTTAAATTTTAATTAATT
*
3346115 TATTATTTATATATTTTAAA
1 AATTATTTATATATTTTAAA
3346135 AATATTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
30 11 0.26
31 19 0.45
32 1 0.02
33 2 0.05
34 6 0.14
35 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
AATTATTTATATATTTTAAATTTTAATTAATT
Found at i:3349291 original size:20 final size:20
Alignment explanation
Indices: 3349268--3349305 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3349258 TAAAAAGGCA
*
3349268 AATAATGAGCTTAAAAAAAT
1 AATAATGAGCCTAAAAAAAT
*
3349288 AATAATGTGCCTAAAAAA
1 AATAATGAGCCTAAAAAA
3349306 GCTAAGTACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.24
Consensus pattern (20 bp):
AATAATGAGCCTAAAAAAAT
Found at i:3349760 original size:61 final size:61
Alignment explanation
Indices: 3349695--3349892 Score: 184
Period size: 61 Copynumber: 3.1 Consensus size: 61
3349685 TAGCAAAATC
3349695 AAATATATAATATATATAATGAGAGTAACTAATACTAATTCAATTGGTGAATTTATCAAAA
1 AAATATATAATATATATAATGAGAGTAACTAATACTAATTCAATTGGTGAATTTATCAAAA
* * ** * * * * * * *
3349756 AAATATTTAA-ATAAATTTTGTATTA-TAAGTTAAGTAACATCAATTTATTTGATGAGAATATAA
1 AAATATATAATATATATAATG-A-GAGTAA-CTAA-T-AC-T-AATTCAATTG--GTGAATTTAT
3349819 CAAAA
57 CAAAA
3349824 TCAAATATATAATATATATAATGAGAGTAACTAATACTAATTCAATTGGTGAATTTATCAAAA
1 --AAATATATAATATATATAATGAGAGTAACTAATACTAATTCAATTGGTGAATTTATCAAAA
3349887 AAATAT
1 AAATAT
3349893 TTAAATAAAT
Statistics
Matches: 102, Mismatches: 22, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
60 7 0.07
61 19 0.19
62 4 0.04
63 13 0.13
64 2 0.02
65 9 0.09
66 9 0.09
67 2 0.02
68 13 0.13
69 4 0.04
70 13 0.13
71 7 0.07
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (61 bp):
AAATATATAATATATATAATGAGAGTAACTAATACTAATTCAATTGGTGAATTTATCAAAA
Found at i:3349870 original size:131 final size:131
Alignment explanation
Indices: 3349631--3349904 Score: 521
Period size: 131 Copynumber: 2.1 Consensus size: 131
3349621 GTTAATGTTA
* * *
3349631 TTAATTAAATTTTGTGTTATAAGTTAAGTAACATCAATTTATTTGATGAGAATATAGCAAAATCA
1 TTAAATAAATTTTGTATTATAAGTTAAGTAACATCAATTTATTTGATGAGAATATAACAAAATCA
3349696 AATATATAATATATATAATGAGAGTAACTAATACTAATTCAATTGGTGAATTTATCAAAAAAATA
66 AATATATAATATATATAATGAGAGTAACTAATACTAATTCAATTGGTGAATTTATCAAAAAAATA
3349761 T
131 T
3349762 TTAAATAAATTTTGTATTATAAGTTAAGTAACATCAATTTATTTGATGAGAATATAACAAAATCA
1 TTAAATAAATTTTGTATTATAAGTTAAGTAACATCAATTTATTTGATGAGAATATAACAAAATCA
3349827 AATATATAATATATATAATGAGAGTAACTAATACTAATTCAATTGGTGAATTTATCAAAAAAATA
66 AATATATAATATATATAATGAGAGTAACTAATACTAATTCAATTGGTGAATTTATCAAAAAAATA
3349892 T
131 T
3349893 TTAAATAAATTT
1 TTAAATAAATTT
3349905 AAAATATAAT
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 140 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (131 bp):
TTAAATAAATTTTGTATTATAAGTTAAGTAACATCAATTTATTTGATGAGAATATAACAAAATCA
AATATATAATATATATAATGAGAGTAACTAATACTAATTCAATTGGTGAATTTATCAAAAAAATA
T
Found at i:3354067 original size:16 final size:15
Alignment explanation
Indices: 3354043--3354076 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3354033 TGTACAATTT
*
3354043 AATTGTGTAATTATGA
1 AATTCTGTAATTAT-A
3354059 AATTCTGTAATTATA
1 AATTCTGTAATTATA
3354074 AAT
1 AAT
3354077 AGTTTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (15 bp):
AATTCTGTAATTATA
Found at i:3358780 original size:14 final size:14
Alignment explanation
Indices: 3358761--3358842 Score: 60
Period size: 16 Copynumber: 5.5 Consensus size: 14
3358751 ATTATAATTA
3358761 TATTTAAAATTTTT
1 TATTTAAAATTTTT
3358775 TATTT-AAATTTTAAT
1 TATTTAAAATTTT--T
* *
3358790 ATATTAATAAATTATAT
1 -TATTTA-AAATT-TTT
3358807 TATTT-AAATTTTT
1 TATTTAAAATTTTT
*
3358820 TATATATAATATTTTT
1 TAT-T-TAAAATTTTT
3358836 TATTTAA
1 TATTTAA
3358843 TATATTTATA
Statistics
Matches: 54, Mismatches: 5, Indels: 18
0.70 0.06 0.23
Matches are distributed among these distances:
13 12 0.22
14 14 0.26
15 3 0.06
16 18 0.33
17 1 0.02
18 5 0.09
19 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTTAAAATTTTT
Found at i:3358843 original size:14 final size:14
Alignment explanation
Indices: 3358761--3358845 Score: 66
Period size: 14 Copynumber: 5.7 Consensus size: 14
3358751 ATTATAATTA
*
3358761 TATTTAAAATTTTT
1 TATTTAATATTTTT
*
3358775 TATTTAA-ATTTTAA
1 TATTTAATATTTT-T
*
3358789 TATATTAATAAATTATAT
1 TAT-TTAAT--ATT-TTT
3358807 TATTTAA-ATTTTT
1 TATTTAATATTTTT
3358820 TATATATAATATTTTT
1 TAT-T-TAATATTTTT
3358836 TATTTAATAT
1 TATTTAATAT
3358846 ATTTATATAG
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
13 10 0.17
14 20 0.34
15 8 0.14
16 9 0.16
17 4 0.07
18 6 0.10
19 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTTAATATTTTT
Found at i:3364364 original size:2 final size:2
Alignment explanation
Indices: 3364359--3364388 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3364349 CTCTCTCTCT
3364359 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3364389 TCTGCATGGT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3366790 original size:22 final size:23
Alignment explanation
Indices: 3366736--3366790 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
3366726 TATGTTAGAA
* *
3366736 TTTTATTGATATTTAACTAATTT
1 TTTTATTTATTTTTAACTAATTT
* *
3366759 TTTTA-ATATTTTTAA-TTATTT
1 TTTTATTTATTTTTAACTAATTT
3366780 TTTTATTTATT
1 TTTTATTTATT
3366791 ATAATTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 10 0.38
22 11 0.42
23 5 0.19
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTATTTATTTTTAACTAATTT
Found at i:3366797 original size:18 final size:21
Alignment explanation
Indices: 3366748--3366798 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
3366738 TTATTGATAT
*
3366748 TTAACTAATTTTTTTAATATTT
1 TTAA-TAATTTTTTTAATATTA
*
3366770 TTAATTATTTTTTT-AT-TTA
1 TTAATAATTTTTTTAATATTA
3366789 TT-ATAATTTT
1 TTAATAATTTT
3366799 AAAAGTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 7 0.27
19 4 0.15
20 2 0.08
21 9 0.35
22 4 0.15
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTAATAATTTTTTTAATATTA
Found at i:3366815 original size:15 final size:14
Alignment explanation
Indices: 3366797--3366850 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 14
3366787 TATTATAATT
3366797 TTAAAAGTATAAAGA
1 TTAAAA-TATAAAGA
*
3366812 TTAAAATATTAAA-T
1 TTAAAATA-TAAAGA
3366826 TTAATAATATAAAGA
1 TTAA-AATATAAAGA
*
3366841 TTTAAATATA
1 TTAAAATATA
3366851 TTTTTTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 16 0.48
15 17 0.52
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (14 bp):
TTAAAATATAAAGA
Found at i:3366836 original size:29 final size:31
Alignment explanation
Indices: 3366787--3366849 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
3366777 TTTTTTTATT
3366787 TATTATAATTTTAAAAGTATAAAGATTAAAA
1 TATTATAATTTTAAAAGTATAAAGATTAAAA
*
3366818 TATTA-AA-TTTAATAA-TATAAAGATTTAAA
1 TATTATAATTTTAA-AAGTATAAAGATTAAAA
3366847 TAT
1 TAT
3366850 ATTTTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 21 0.70
30 4 0.13
31 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (31 bp):
TATTATAATTTTAAAAGTATAAAGATTAAAA
Found at i:3366848 original size:14 final size:14
Alignment explanation
Indices: 3366804--3366850 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
3366794 ATTTTAAAAG
*
3366804 TATAAAGATTAAAA
1 TATAAAGATTTAAA
*
3366818 TATTAA-ATTTAATAA
1 TATAAAGATTT-A-AA
3366833 TATAAAGATTTAAA
1 TATAAAGATTTAAA
3366847 TATA
1 TATA
3366851 TTTTTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 3 0.11
14 12 0.44
15 8 0.30
16 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (14 bp):
TATAAAGATTTAAA
Found at i:3366857 original size:29 final size:28
Alignment explanation
Indices: 3366794--3366868 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 28
3366784 ATTTATTATA
3366794 ATTTTAA-AAGTATAAAGATTAAAATATT
1 ATTTTAATAA-TATAAAGATTAAAATATT
*
3366822 AAATTTAATAATATAAAGATTTAAATATATT
1 -ATTTTAATAATATAAAGA-TTAAA-ATATT
3366853 -TTTTATTATAATATAA
1 ATTTTA--ATAATATAA
3366869 TAATTGCAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 18 0.46
30 7 0.18
31 14 0.36
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (28 bp):
ATTTTAATAATATAAAGATTAAAATATT
Found at i:3368261 original size:28 final size:26
Alignment explanation
Indices: 3368230--3368294 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
3368220 AAGAATATAA
3368230 AAAATAAAATATGATATAATAAAAAAAT
1 AAAATAAAATATGAT-T-ATAAAAAAAT
* *
3368258 AAAAT-GAATTTGATTATAAAAAAAT
1 AAAATAAAATATGATTATAAAAAAAT
3368283 AATAA-AAAATAT
1 AA-AATAAAATAT
3368295 TATGACCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
25 12 0.39
26 7 0.23
27 7 0.23
28 5 0.16
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (26 bp):
AAAATAAAATATGATTATAAAAAAAT
Found at i:3369327 original size:12 final size:12
Alignment explanation
Indices: 3369310--3369336 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3369300 TTAAGTAAAA
3369310 AATATATTTTTT
1 AATATATTTTTT
3369322 AATATATTTTTT
1 AATATATTTTTT
3369334 AAT
1 AAT
3369337 CAATTCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
AATATATTTTTT
Found at i:3369398 original size:28 final size:28
Alignment explanation
Indices: 3369361--3369436 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
3369351 TTAAGTTTTT
3369361 AAATAATATTAATTAATTAATTT-AAACAA
1 AAAT-ATATTAATTAATTAATTTCAAA-AA
* * *
3369390 AAATATATTAATAAATTTATTTCAAAAT
1 AAATATATTAATTAATTAATTTCAAAAA
*
3369418 TAATATA-TAATTGAATTAA
1 AAATATATTAATT-AATTAA
3369437 AAATAAGTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 4 0.10
28 28 0.72
29 7 0.18
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (28 bp):
AAATATATTAATTAATTAATTTCAAAAA
Found at i:3369493 original size:22 final size:22
Alignment explanation
Indices: 3369467--3369517 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
3369457 AATACATTTA
*
3369467 AATTATAATATAA-TTTAATAAT
1 AATTA-AAGATAATTTTAATAAT
*
3369489 AATTAAAGATAATTTTAATATT
1 AATTAAAGATAATTTTAATAAT
3369511 AATTAAA
1 AATTAAA
3369518 ATTTTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTAAAGATAATTTTAATAAT
Found at i:3376856 original size:16 final size:17
Alignment explanation
Indices: 3376831--3376869 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
3376821 AATATAATTA
3376831 TAAA-ATAT-AATTTTT
1 TAAATATATAAATTTTT
3376846 TAAATATATAAAATTTTT
1 TAAATATAT-AAATTTTT
3376864 TAAATA
1 TAAATA
3376870 ATTAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 4 0.19
18 13 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAATATATAAATTTTT
Found at i:3377521 original size:2 final size:2
Alignment explanation
Indices: 3377509--3377551 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
3377499 ATAGAAATTC
3377509 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3377550 AT
1 AT
3377552 CCAACTTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3379442 original size:7 final size:7
Alignment explanation
Indices: 3379430--3379459 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
3379420 AAATTTCAAC
3379430 ATTATTA
1 ATTATTA
3379437 ATTATTA
1 ATTATTA
3379444 ATTATTA
1 ATTATTA
3379451 ATTATTA
1 ATTATTA
3379458 AT
1 AT
3379460 AATGAGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTATTA
Found at i:3379795 original size:19 final size:20
Alignment explanation
Indices: 3379761--3379816 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
3379751 AGTATCCGAA
*
3379761 TTTAAATATTTATTTTTATT
1 TTTAAATATATATTTTTATT
*
3379781 TTTAAAT-TATATTTTTATA
1 TTTAAATATATATTTTTATT
**
3379800 TAAAAATATATATTTTT
1 TTTAAATATATATTTTT
3379817 TAAATTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTAAATATATATTTTTATT
Found at i:3379811 original size:20 final size:20
Alignment explanation
Indices: 3379764--3379816 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
3379754 ATCCGAATTT
* * **
3379764 AAATATTTATTTTTATTTTT
1 AAATATATATTTTTATATAA
3379784 AAAT-TATATTTTTATATAA
1 AAATATATATTTTTATATAA
3379803 AAATATATATTTTT
1 AAATATATATTTTT
3379817 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
AAATATATATTTTTATATAA
Found at i:3380498 original size:7 final size:6
Alignment explanation
Indices: 3380469--3380497 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3380459 TATTCTGTAT
3380469 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
3380498 TTATTCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:3382284 original size:55 final size:56
Alignment explanation
Indices: 3382171--3382288 Score: 202
Period size: 55 Copynumber: 2.1 Consensus size: 56
3382161 TAAAGATTGA
*
3382171 ATGCATGATTGGCATGTTTTGGATCTTTACGATACACAAGCCACTGCTGCGTGATC
1 ATGCATGATTGGCATGTTTTGGATCTTTACGATACACAAGCCACTGCTGCATGATC
* *
3382227 ATGCATGATTGGCATGTTTTGGATC-TTATGATACACAGGCCACTGCTGCATGATC
1 ATGCATGATTGGCATGTTTTGGATCTTTACGATACACAAGCCACTGCTGCATGATC
3382282 ATGCATG
1 ATGCATG
3382289 CGCCACGTTG
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
55 34 0.58
56 25 0.42
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (56 bp):
ATGCATGATTGGCATGTTTTGGATCTTTACGATACACAAGCCACTGCTGCATGATC
Found at i:3382330 original size:4 final size:4
Alignment explanation
Indices: 3382315--3382343 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
3382305 TGCATGTTTC
3382315 TTAA TT-A TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
3382344 CTCGAGCTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (4 bp):
TTAA
Found at i:3383365 original size:216 final size:217
Alignment explanation
Indices: 3382908--3383381 Score: 555
Period size: 216 Copynumber: 2.2 Consensus size: 217
3382898 TTCTACATCA
* * *
3382908 TTTAAATCATAAATTATTTAT-AGTCTTCTATTCAAGTTGAGCCTTTACACCTATTATCAATTGA
1 TTTAAATCATAAATTACTTATGA-TTTTATATTCAAGTTGAGCCTTTACACCTATTATCAATTGA
* * * * ** * *
3382972 TTTTAGGTTAGACATTTAATATGATATCAGAGTTTAAGTTTTATTCTGTTTTTTATTTTTATTTA
65 TTTTAGATTAAACATTTAACATGATATCAAAACTTAAGTTATATTCTGTTTTTTATTCTTATTTA
* * * * *
3383037 TTATCATTTTTGAGTTTTTCACACAATAAGCTCTTCTGTCTTTGCCTATATGTGATGTGATCCAT
130 TTATCATTTTCGAGTTTGTCACACAATAAACTCTTCTGTCTTTGCCTACACGTGATGTGATCCAT
*
3383102 TAAAGTAGTGGTATTACACATCG
195 TAAAGTAGTGGTATTACACATAG
* * * * *
3383125 TTTAAATCATAAATTACTTATGATTTTTTATTTAATTTGAGCCTTTACACTTATTATCAGTTGAT
1 TTTAAATCATAAATTACTTATGATTTTATATTCAAGTTGAGCCTTTACACCTATTATCAATTGAT
** * * *
3383190 TTTAGATTAAATGTTTAACATGATATGAAAACTTAAGTTATGTTTTG-TTTTTATTCTTATTTAT
66 TTTAGATTAAACATTTAACATGATATCAAAACTTAAGTTATATTCTGTTTTTTATTCTTATTTAT
*
3383254 TATTC-TTTTCGAGTTTGTCACACAATAAACTCTTTTGTCTTTGCCTACACGTGATGTGA-CCTA
131 TA-TCATTTTCGAGTTTGTCACACAATAAACTCTTCTGTCTTTGCCTACACGTGATGTGATCC-A
* * *
3383317 TTAAAGTGGTGTTATTACATATAAG
194 TTAAAGTAGTGGTATTACACAT-AG
* * *
3383342 -TTAAATGATGAATT-GTCTATGATTTTATATTCAAGTTGAG
1 TTTAAATCATAAATTACT-TATGATTTTATATTCAAGTTGAG
3383382 TTTCTTCATC
Statistics
Matches: 216, Mismatches: 36, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
215 3 0.01
216 118 0.55
217 94 0.44
218 1 0.00
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.47
Consensus pattern (217 bp):
TTTAAATCATAAATTACTTATGATTTTATATTCAAGTTGAGCCTTTACACCTATTATCAATTGAT
TTTAGATTAAACATTTAACATGATATCAAAACTTAAGTTATATTCTGTTTTTTATTCTTATTTAT
TATCATTTTCGAGTTTGTCACACAATAAACTCTTCTGTCTTTGCCTACACGTGATGTGATCCATT
AAAGTAGTGGTATTACACATAG
Found at i:3384544 original size:24 final size:25
Alignment explanation
Indices: 3384492--3384545 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
3384482 CTTCTTATTT
*
3384492 AAATAAAATTTGTGTACTGGTAAAAA
1 AAATAAAATTTGTGTAAT-GTAAAAA
*
3384518 AAATACAATTTGTGTAAT-TAAAAA
1 AAATAAAATTTGTGTAATGTAAAAA
3384542 AAAT
1 AAAT
3384546 TATGAACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 10 0.38
26 16 0.62
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.31
Consensus pattern (25 bp):
AAATAAAATTTGTGTAATGTAAAAA
Found at i:3385333 original size:74 final size:75
Alignment explanation
Indices: 3385250--3385389 Score: 212
Period size: 74 Copynumber: 1.9 Consensus size: 75
3385240 TTATTAATAA
* ***
3385250 TAAAAATATAATTAATAAACATAGAGTTTTCATCGGTTCAAAAGATT-TTTCATATATATA-ATA
1 TAAAAATATAATTAATAAACATAGAATTTTCATCAAATCAAAAGATTCTTT-ATATATATATATA
3385313 TAATAATAATT
65 TAATAATAATT
*
3385324 TAAAAATATAATTAATAAACATAGAATTTTTATCAAATCAAAAGATTCTTTATATATATATATAT
1 TAAAAATATAATTAATAAACATAGAATTTTCATCAAATCAAAAGATTCTTTATATATATATATAT
3385389 A
66 A
3385390 TATATATTCT
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
74 51 0.86
75 8 0.14
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.39
Consensus pattern (75 bp):
TAAAAATATAATTAATAAACATAGAATTTTCATCAAATCAAAAGATTCTTTATATATATATATAT
AATAATAATT
Found at i:3392286 original size:4 final size:4
Alignment explanation
Indices: 3392277--3392310 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
3392267 ATTATGAGCA
3392277 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
3392311 GCACTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:3393059 original size:22 final size:21
Alignment explanation
Indices: 3393002--3393059 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
3392992 TATGATTTAT
3393002 ATTA-ATAAAAAAGTAAATATA
1 ATTATATAAAAAA-TAAATATA
3393023 ATTAT-TAAATTAAATAAATATAA
1 ATTATATAAA--AAATAAATAT-A
3393046 ATTATATAAAAAAT
1 ATTATATAAAAAAT
3393060 TATAAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
21 8 0.25
22 11 0.34
23 9 0.28
24 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
ATTATATAAAAAATAAATATA
Found at i:3393835 original size:2 final size:2
Alignment explanation
Indices: 3393828--3393871 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3393818 GTGCATGCAT
3393828 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3393870 CA
1 CA
3393872 TATATATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3393876 original size:2 final size:2
Alignment explanation
Indices: 3393871--3393916 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3393861 ACACACACAC
3393871 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3393913 AT AT
1 AT AT
3393917 CTTCAATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3406295 original size:47 final size:47
Alignment explanation
Indices: 3406241--3406335 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
3406231 TCTACTCCTT
*
3406241 AGAGATTTCTTCTCAACATTCCCAAAAATTTTCGCAGGCAATCAATA
1 AGAGATTTCTTCTCAACATTCCCAAAAATTTTCACAGGCAATCAATA
*
3406288 AGAGATTTCTTCTCAACATTTCCAAAAATTTTCACAGGCAATCAATA
1 AGAGATTTCTTCTCAACATTCCCAAAAATTTTCACAGGCAATCAATA
3406335 A
1 A
3406336 CATTTTTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (47 bp):
AGAGATTTCTTCTCAACATTCCCAAAAATTTTCACAGGCAATCAATA
Found at i:3407455 original size:52 final size:52
Alignment explanation
Indices: 3407382--3407485 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 52
3407372 CCCAATATCT
* * *
3407382 GATATTCATACTCAAAACTGTGAACAAGTGTCTCATATTCAACTTTTTACAA
1 GATATTCATACACAAAACTGTGAACAAGTATCTCACATTCAACTTTTTACAA
* *
3407434 GATATTCATTCACAAATCTGTGAACAAGTATCTCACATTCAACTTTTTACAA
1 GATATTCATACACAAAACTGTGAACAAGTATCTCACATTCAACTTTTTACAA
3407486 TATCAACAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.35
Consensus pattern (52 bp):
GATATTCATACACAAAACTGTGAACAAGTATCTCACATTCAACTTTTTACAA
Found at i:3414029 original size:12 final size:12
Alignment explanation
Indices: 3414012--3414041 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3414002 ATTTATAAAA
3414012 TATTAATATTTT
1 TATTAATATTTT
3414024 TATTAATATTTT
1 TATTAATATTTT
*
3414036 AATTAA
1 TATTAA
3414042 ATTAATATTA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTAATATTTT
Found at i:3414063 original size:18 final size:18
Alignment explanation
Indices: 3414024--3414073 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
3414014 TTAATATTTT
*
3414024 TATTAATATT-TTAATTA
1 TATTAATATTATGAATTA
*
3414041 AATTAATATTATGAATTA
1 TATTAATATTATGAATTA
*
3414059 TATTAATTTTATGAA
1 TATTAATATTATGAA
3414074 AATTTTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (18 bp):
TATTAATATTATGAATTA
Found at i:3414276 original size:57 final size:56
Alignment explanation
Indices: 3414168--3414273 Score: 146
Period size: 55 Copynumber: 1.9 Consensus size: 56
3414158 AAACTTTTAA
* * *
3414168 ATTTTTATATTTATATTAAAAATTATATTGTTTAATTAAATATATGATTTTATTAT
1 ATTTTTATATTTATATTAAAAATTATAGTATTTAATTAAATATATAATTTTATTAT
3414224 ATTTATTATATTTAATATT-AAAATTAT-GTATTT-ATTAAATATATAATTTT
1 ATTT-TTATATTT-ATATTAAAAATTATAGTATTTAATTAAATATATAATTTT
3414274 TTAAAATCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
55 16 0.36
56 8 0.18
57 16 0.36
58 5 0.11
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (56 bp):
ATTTTTATATTTATATTAAAAATTATAGTATTTAATTAAATATATAATTTTATTAT
Found at i:3416566 original size:419 final size:419
Alignment explanation
Indices: 3415788--3416620 Score: 1666
Period size: 419 Copynumber: 2.0 Consensus size: 419
3415778 AGTACCATAA
3415788 ACGATTGTTAGTGATCGAGATGGGCGATTTACGGGACAGTTTTGGACGGAGTTGTTCAAGTTATT
1 ACGATTGTTAGTGATCGAGATGGGCGATTTACGGGACAGTTTTGGACGGAGTTGTTCAAGTTATT
3415853 GGGGTCAGACTTGAACTTTTCCGCTAGTGTGCATCCTCAAACAGATGGGCAGACCGAGAGAGTGA
66 GGGGTCAGACTTGAACTTTTCCGCTAGTGTGCATCCTCAAACAGATGGGCAGACCGAGAGAGTGA
3415918 ATGCTTTATTGGAGGTTTATTTCAGACACTATGTGAGTGCAACACAGTGTGACTGGCCAAAGTTG
131 ATGCTTTATTGGAGGTTTATTTCAGACACTATGTGAGTGCAACACAGTGTGACTGGCCAAAGTTG
3415983 TTGGATGTGGCCCAATTTTCTTATAACTTGCAACGAAGTGAGGCCACAAATCAGAGTCCATTCGA
196 TTGGATGTGGCCCAATTTTCTTATAACTTGCAACGAAGTGAGGCCACAAATCAGAGTCCATTCGA
3416048 GATAGTAACTAGGCAACAACCGTTCGCACCTAGTGCTATTGCGACAGGTTACACGTGACCAAATC
261 GATAGTAACTAGGCAACAACCGTTCGCACCTAGTGCTATTGCGACAGGTTACACGTGACCAAATC
3416113 CAGCAGCTTACAAGTTCGCTAAGGCATGGGAAGAGCAGATTGACTTAGCCAGGGTTTGTACTTGA
326 CAGCAGCTTACAAGTTCGCTAAGGCATGGGAAGAGCAGATTGACTTAGCCAGGGTTTGTACTTGA
3416178 GTTGCCAGCAAAACTCAAGATACACCTCG
391 GTTGCCAGCAAAACTCAAGATACACCTCG
3416207 ACGATTGTTAGTGATCGAGATGGGCGATTTACGGGACAGTTTTGGACGGAGTTGTTCAAGTTATT
1 ACGATTGTTAGTGATCGAGATGGGCGATTTACGGGACAGTTTTGGACGGAGTTGTTCAAGTTATT
3416272 GGGGTCAGACTTGAACTTTTCCGCTAGTGTGCATCCTCAAACAGATGGGCAGACCGAGAGAGTGA
66 GGGGTCAGACTTGAACTTTTCCGCTAGTGTGCATCCTCAAACAGATGGGCAGACCGAGAGAGTGA
3416337 ATGCTTTATTGGAGGTTTATTTCAGACACTATGTGAGTGCAACACAGTGTGACTGGCCAAAGTTG
131 ATGCTTTATTGGAGGTTTATTTCAGACACTATGTGAGTGCAACACAGTGTGACTGGCCAAAGTTG
3416402 TTGGATGTGGCCCAATTTTCTTATAACTTGCAACGAAGTGAGGCCACAAATCAGAGTCCATTCGA
196 TTGGATGTGGCCCAATTTTCTTATAACTTGCAACGAAGTGAGGCCACAAATCAGAGTCCATTCGA
3416467 GATAGTAACTAGGCAACAACCGTTCGCACCTAGTGCTATTGCGACAGGTTACACGTGACCAAATC
261 GATAGTAACTAGGCAACAACCGTTCGCACCTAGTGCTATTGCGACAGGTTACACGTGACCAAATC
3416532 CAGCAGCTTACAAGTTCGCTAAGGCATGGGAAGAGCAGATTGACTTAGCCAGGGTTTGTACTTGA
326 CAGCAGCTTACAAGTTCGCTAAGGCATGGGAAGAGCAGATTGACTTAGCCAGGGTTTGTACTTGA
3416597 GTTGCCAGCAAAACTCAAGATACA
391 GTTGCCAGCAAAACTCAAGATACA
3416621 TCCCGTTTTT
Statistics
Matches: 414, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
419 414 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (419 bp):
ACGATTGTTAGTGATCGAGATGGGCGATTTACGGGACAGTTTTGGACGGAGTTGTTCAAGTTATT
GGGGTCAGACTTGAACTTTTCCGCTAGTGTGCATCCTCAAACAGATGGGCAGACCGAGAGAGTGA
ATGCTTTATTGGAGGTTTATTTCAGACACTATGTGAGTGCAACACAGTGTGACTGGCCAAAGTTG
TTGGATGTGGCCCAATTTTCTTATAACTTGCAACGAAGTGAGGCCACAAATCAGAGTCCATTCGA
GATAGTAACTAGGCAACAACCGTTCGCACCTAGTGCTATTGCGACAGGTTACACGTGACCAAATC
CAGCAGCTTACAAGTTCGCTAAGGCATGGGAAGAGCAGATTGACTTAGCCAGGGTTTGTACTTGA
GTTGCCAGCAAAACTCAAGATACACCTCG
Found at i:3417335 original size:20 final size:19
Alignment explanation
Indices: 3417293--3417338 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
3417283 ATTCCTCTCT
*
3417293 ATTTTTT-TTTATCTCTAA
1 ATTTTTTATTTAACTCTAA
3417311 ATTTTTTATTTAACTCTAA
1 ATTTTTTATTTAACTCTAA
3417330 ACTTTTTTA
1 A-TTTTTTA
3417339 ACTTTAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.28
19 11 0.44
20 7 0.28
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTTATTTAACTCTAA
Found at i:3417451 original size:29 final size:29
Alignment explanation
Indices: 3417418--3417476 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3417408 CCGAGTCGTG
3417418 ACACTTTCAGAATAAAATTCAAATAAAAA
1 ACACTTTCAGAATAAAATTCAAATAAAAA
3417447 ACACTTTCAGAATAAAATTCAAATAAAAA
1 ACACTTTCAGAATAAAATTCAAATAAAAA
3417476 A
1 A
3417477 TAAAAAAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.24
Consensus pattern (29 bp):
ACACTTTCAGAATAAAATTCAAATAAAAA
Found at i:3417576 original size:6 final size:6
Alignment explanation
Indices: 3417565--3417594 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3417555 TAAAACCATC
3417565 TCTTCG TCTTCG TCTTCG TCTTCG TCTTCG
1 TCTTCG TCTTCG TCTTCG TCTTCG TCTTCG
3417595 ACTGAGTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.17, T:0.50
Consensus pattern (6 bp):
TCTTCG
Found at i:3417603 original size:18 final size:18
Alignment explanation
Indices: 3417565--3417603 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3417555 TAAAACCATC
* **
3417565 TCTTCGTCTTCGTCTTCG
1 TCTTCGTCTTCGACTGAG
3417583 TCTTCGTCTTCGACTGAG
1 TCTTCGTCTTCGACTGAG
3417601 TCT
1 TCT
3417604 GAGTGTGACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.05, C:0.31, G:0.18, T:0.46
Consensus pattern (18 bp):
TCTTCGTCTTCGACTGAG
Found at i:3423167 original size:2 final size:2
Alignment explanation
Indices: 3423160--3423203 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3423150 TCATTTATGC
3423160 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
3423202 TA
1 TA
3423204 GATTATTCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3426558 original size:5 final size:5
Alignment explanation
Indices: 3426548--3426588 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
3426538 ACACCATGCA
*
3426548 ATAAT ATAAT ATAAT ATAAATT AAAAT ATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT AT-AA-T ATAAT ATAAT ATAAT ATAA
3426589 AAATAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 26 0.81
6 4 0.12
7 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:3426577 original size:17 final size:17
Alignment explanation
Indices: 3426555--3426616 Score: 71
Period size: 16 Copynumber: 3.8 Consensus size: 17
3426545 GCAATAATAT
3426555 AATATAATATAAATTAA
1 AATATAATATAAATTAA
3426572 AATATAATAT-AATATAA
1 AATATAATATAAAT-TAA
3426589 AA-ATAATATTAAA-TAA
1 AATATAATA-TAAATTAA
3426605 AAT-TAA-ATAAAT
1 AATATAATATAAAT
3426617 ATTTTAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
14 4 0.10
15 1 0.03
16 17 0.43
17 16 0.40
18 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATATAATATAAATTAA
Found at i:3426602 original size:10 final size:10
Alignment explanation
Indices: 3426547--3426619 Score: 51
Period size: 10 Copynumber: 6.9 Consensus size: 10
3426537 AACACCATGC
3426547 AATAATA-TA
1 AATAATATTA
3426556 ATATAATA-TA
1 A-ATAATATTA
*
3426566 AATTAAAATATA
1 AA-TAATAT-TA
*
3426578 ATATAATATAAA
1 A-ATAATAT-TA
3426590 AATAATATTA
1 AATAATATTA
*
3426600 AATAAAATTA
1 AATAATATTA
3426610 AATAAATATT
1 AAT-AATATT
3426620 TTAAAAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
9 2 0.04
10 26 0.50
11 12 0.23
12 11 0.21
13 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AATAATATTA
Found at i:3426638 original size:16 final size:16
Alignment explanation
Indices: 3426609--3426656 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
3426599 AAATAAAATT
*
3426609 AAATAAATATTTTAAA
1 AAATAAATAATTTAAA
*
3426625 AAATATATAATTTAAA
1 AAATAAATAATTTAAA
** *
3426641 TTATTAATAATTTAAA
1 AAATAAATAATTTAAA
3426657 TTTTATATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATAAATAATTTAAA
Found at i:3426666 original size:16 final size:17
Alignment explanation
Indices: 3426628--3426666 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
3426618 TTTTAAAAAA
3426628 TATATAATTTAAATTAT
1 TATATAATTTAAATTAT
3426645 TA-ATAATTTAAATT-T
1 TATATAATTTAAATTAT
3426660 TATATAA
1 TATATAA
3426667 ATATAACCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.14
16 16 0.76
17 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATAATTTAAATTAT
Found at i:3426736 original size:17 final size:19
Alignment explanation
Indices: 3426701--3426754 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
3426691 TATTATAATA
3426701 AAATATATAAATATAATTT
1 AAATATATAAATATAATTT
*
3426720 AAATATATGAAT-T-ATTT
1 AAATATATAAATATAATTT
* * *
3426737 AAATTTAAAAATTTAATT
1 AAATATATAAATATAATT
3426755 ATTTTATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 13 0.45
18 2 0.07
19 14 0.48
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
AAATATATAAATATAATTT
Found at i:3426741 original size:23 final size:22
Alignment explanation
Indices: 3426715--3426788 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
3426705 ATATAAATAT
*
3426715 AATTTAAATATATGAATTATTTA
1 AATTTAAATAT-TTAATTATTTA
*
3426738 AATTTAAAAATTTAATTATTT-
1 AATTTAAATATTTAATTATTTA
* *
3426759 TA-TTAAATATTTTTTATTATTTA
1 AATTTAAATA--TTTAATTATTTA
3426782 AATTTAA
1 AATTTAA
3426789 TTCAACAATC
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
20 6 0.15
21 1 0.02
22 19 0.46
23 11 0.27
24 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (22 bp):
AATTTAAATATTTAATTATTTA
Found at i:3427526 original size:2 final size:2
Alignment explanation
Indices: 3427519--3427556 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3427509 AACATGCAAA
*
3427519 AG AG AG AG AG AA 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
3427557 GGGGAGATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3427888 original size:2 final size:2
Alignment explanation
Indices: 3427881--3427911 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3427871 TAAATTAATC
*
3427881 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3427912 GTCTCTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3429027 original size:18 final size:20
Alignment explanation
Indices: 3428992--3429031 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
3428982 ATACATATTT
3428992 ATTAAAATATATTTTTAAAA
1 ATTAAAATATATTTTTAAAA
3429012 ATTAAAAT-TA-TTTTAAAA
1 ATTAAAATATATTTTTAAAA
3429030 AT
1 AT
3429032 AAATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.50
19 2 0.10
20 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAAAATATATTTTTAAAA
Found at i:3430934 original size:19 final size:20
Alignment explanation
Indices: 3430890--3430934 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
3430880 ATATTTTTAA
3430890 ATTTTTTTATCAATTTAATT
1 ATTTTTTTATCAATTTAATT
* *
3430910 AATTTTTTAT-TATTTAATT
1 ATTTTTTTATCAATTTAATT
3430929 -TTTTTT
1 ATTTTTT
3430935 AATTTTATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 9 0.41
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTTTTTATCAATTTAATT
Found at i:3430939 original size:15 final size:15
Alignment explanation
Indices: 3430903--3430939 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3430893 TTTTTATCAA
3430903 TTTAA-TTAATTTTT
1 TTTAATTTAATTTTT
3430917 TATT-ATTTAATTTTT
1 T-TTAATTTAATTTTT
3430932 TTTAATTT
1 TTTAATTT
3430940 TATGATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTAATTTAATTTTT
Found at i:3431239 original size:3 final size:3
Alignment explanation
Indices: 3431224--3431265 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
3431214 CATGGAAACA
*
3431224 AAT AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3431266 TTTGATATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3434477 original size:2 final size:2
Alignment explanation
Indices: 3434472--3434497 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3434462 TCAAAAAATA
3434472 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
3434498 TCTTTTTTCT
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:3435397 original size:2 final size:2
Alignment explanation
Indices: 3435390--3435418 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3435380 TATTTAACTT
3435390 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
3435419 CTTTACTAAT
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:3436359 original size:19 final size:18
Alignment explanation
Indices: 3436322--3436371 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
3436312 ATTAAATCAG
**
3436322 ATTTAAAATTATTTTATT
1 ATTTAAAATTATTAAATT
3436340 ATTTAAAATATATTAAATT
1 ATTTAAAAT-TATTAAATT
3436359 ATTTAAAATTATT
1 ATTTAAAATTATT
3436372 TATAAGTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTAAAATTATTAAATT
Found at i:3436367 original size:10 final size:10
Alignment explanation
Indices: 3436322--3436373 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
3436312 ATTAAATCAG
3436322 ATTTAAAATT
1 ATTTAAAATT
*
3436332 ATTT--TATT
1 ATTTAAAATT
3436340 ATTTAAAA-T
1 ATTTAAAATT
3436349 ATATT-AAATT
1 AT-TTAAAATT
3436359 ATTTAAAATT
1 ATTTAAAATT
3436369 ATTTA
1 ATTTA
3436374 TAAGTTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
8 7 0.20
9 8 0.23
10 20 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATTTAAAATT
Found at i:3436960 original size:15 final size:14
Alignment explanation
Indices: 3436940--3436985 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
3436930 GTTATTGTAT
3436940 TTGAAAAAAAATTA
1 TTGAAAAAAAATTA
3436954 GTTG-AAAAAAA-TA
1 -TTGAAAAAAAATTA
*
3436967 CTTTAAAAAAAATTA
1 -TTGAAAAAAAATTA
3436982 TTGA
1 TTGA
3436986 GAGAAATGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 4 0.15
14 17 0.65
15 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (14 bp):
TTGAAAAAAAATTA
Found at i:3436999 original size:28 final size:28
Alignment explanation
Indices: 3436937--3436999 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
3436927 ATTGTTATTG
*
3436937 TATTTGAAAAAAAATTAGTTGAAAAAAA
1 TATTTTAAAAAAAATTAGTTGAAAAAAA
* * *
3436965 TACTTTAAAAAAAATTA-TTGAGAGAAA
1 TATTTTAAAAAAAATTAGTTGAAAAAAA
3436992 TGATTTTA
1 T-ATTTTA
3437000 TAAATATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 9 0.31
28 20 0.69
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (28 bp):
TATTTTAAAAAAAATTAGTTGAAAAAAA
Found at i:3437353 original size:19 final size:19
Alignment explanation
Indices: 3437311--3437359 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
3437301 TATAGGTATA
*
3437311 ATATAA-AAATA-TAATAT
1 ATATAATAAATATTAAAAT
*
3437328 ATTTAATAAATATTAAAAT
1 ATATAATAAATATTAAAAT
3437347 ATATAATAAATAT
1 ATATAATAAATAT
3437360 GTTTGATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 5 0.19
18 5 0.19
19 17 0.63
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATAATAAATATTAAAAT
Found at i:3437978 original size:19 final size:20
Alignment explanation
Indices: 3437941--3437978 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3437931 TCAATAAAAT
*
3437941 TTTTAAATATAATAAATATC
1 TTTTAAATATAAAAAATATC
3437961 TTTTAAAT-TAAAAAATAT
1 TTTTAAATATAAAAAATAT
3437979 TTAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTTAAATATAAAAAATATC
Found at i:3438177 original size:3 final size:3
Alignment explanation
Indices: 3438169--3438198 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3438159 ACTAATTCTT
3438169 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3438199 ATCTTCAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3454375 original size:2 final size:2
Alignment explanation
Indices: 3454370--3454398 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3454360 TTCTTCTTCT
3454370 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3454399 TTGATAAATT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3459956 original size:3 final size:3
Alignment explanation
Indices: 3459950--3459980 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3459940 TATTATTATT
3459950 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
3459981 ATCTTGCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:3461015 original size:20 final size:18
Alignment explanation
Indices: 3460990--3461033 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3460980 ATAATTTATA
3460990 TTATATAAAATTTATTATTT
1 TTATATAAAA--TATTATTT
*
3461010 TTATATATAATATTATTT
1 TTATATAAAATATTATTT
3461028 TT-TATA
1 TTATATA
3461034 TGATATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 10 0.43
20 9 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATAAAATATTATTT
Found at i:3461033 original size:17 final size:18
Alignment explanation
Indices: 3461002--3461039 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3460992 ATATAAAATT
3461002 TATTATTTTTATATATAA
1 TATTATTTTTATATATAA
*
3461020 TATTATTTTT-TATATGA
1 TATTATTTTTATATATAA
3461037 TAT
1 TAT
3461040 AATTACATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TATTATTTTTATATATAA
Found at i:3461042 original size:22 final size:23
Alignment explanation
Indices: 3460984--3461042 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 23
3460974 ATTTCAATAA
*
3460984 TTTATATTATATAAAATTTATTAT
1 TTTATA-TATATAATATTTATTAT
3461008 TTT-TATATATAATA-TTATT-T
1 TTTATATATATAATATTTATTAT
3461028 TTTATATGATATAAT
1 TTTATAT-ATATAAT
3461043 TACATTATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.12
21 8 0.25
22 15 0.47
23 2 0.06
24 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTATATATATAATATTTATTAT
Found at i:3461889 original size:29 final size:28
Alignment explanation
Indices: 3461823--3461889 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
3461813 AATTTTATAG
3461823 TAATATTAAATATTTTATAATTAAATTAA
1 TAAT-TTAAATATTTTATAATTAAATTAA
** *
3461852 -AATAAAAATATTTT-TTATTATTAATTAA
1 TAATTTAAATATTTTATAATTA--AATTAA
3461880 TAATTTAAAT
1 TAATTTAAAT
3461890 CAAAGTAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
26 5 0.17
27 9 0.30
28 9 0.30
29 7 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TAATTTAAATATTTTATAATTAAATTAA
Found at i:3465100 original size:79 final size:79
Alignment explanation
Indices: 3464975--3465212 Score: 399
Period size: 79 Copynumber: 3.0 Consensus size: 79
3464965 AAAATTCTGG
* * * *
3464975 TTCTTTATATAAGGTTGTAAAT-TTATTTATAGATAAGGTGAAAATTATCAAGATACTGATAACT
1 TTCTTTCTGTAAGGTTG-AAATGTAACTTATAGATAAGGTGAAAATTATCAAGATACTGATAACT
3465039 TTAGGGCAGTAAAAT
65 TTAGGGCAGTAAAAT
3465054 TTCTTTCTGTAAGGTTGAAATGTAACTTATAGATAAGGTGAAAATTATCAAGATACTGATAACTT
1 TTCTTTCTGTAAGGTTGAAATGTAACTTATAGATAAGGTGAAAATTATCAAGATACTGATAACTT
3465119 TAGGGCAGTAAAAT
66 TAGGGCAGTAAAAT
*
3465133 TTCTTTCTGTGAGGTTGAAATGTAACTTATAGATAAGGTGAAAATTATCAAGATACTGATAACTT
1 TTCTTTCTGTAAGGTTGAAATGTAACTTATAGATAAGGTGAAAATTATCAAGATACTGATAACTT
3465198 TAGGG-AGGTAAAAT
66 TAGGGCA-GTAAAAT
3465212 T
1 T
3465213 CAGAATTAAT
Statistics
Matches: 152, Mismatches: 5, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
78 5 0.03
79 147 0.97
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.36
Consensus pattern (79 bp):
TTCTTTCTGTAAGGTTGAAATGTAACTTATAGATAAGGTGAAAATTATCAAGATACTGATAACTT
TAGGGCAGTAAAAT
Found at i:3465749 original size:28 final size:29
Alignment explanation
Indices: 3465677--3465751 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 29
3465667 CACGTGATGC
* **
3465677 AATAAAAAATATAATTAAAATATAATATA
1 AATATAAAATATTTTTAAAATATAATATA
** *
3465706 AATATATGAT-TATTTTAAAATAT-ATGTA
1 AATATAAAATAT-TTTTAAAATATAATATA
3465734 AATATAAAATATTTTTAA
1 AATATAAAATATTTTTAA
3465752 CATTATTATG
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
28 19 0.53
29 17 0.47
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (29 bp):
AATATAAAATATTTTTAAAATATAATATA
Found at i:3466435 original size:3 final size:3
Alignment explanation
Indices: 3466429--3466470 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
3466419 GATGATGATG
3466429 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3466471 GTAGTAGTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3467886 original size:21 final size:20
Alignment explanation
Indices: 3467847--3467901 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
3467837 ATAATTTTTT
*
3467847 ATATAATTAATATTTTAATA
1 ATATAATTATTATTTTAATA
3467867 A-ATTAATTATTATATTTAATA
1 ATA-TAATTATTAT-TTTAATA
3467888 ATATAATTA-TATTT
1 ATATAATTATTATTT
3467902 ATTATACATA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.10
20 13 0.42
21 14 0.45
22 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATAATTATTATTTTAATA
Found at i:3467914 original size:21 final size:18
Alignment explanation
Indices: 3467847--3467902 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 18
3467837 ATAATTTTTT
3467847 ATATAATTAATATTTTAATAA
1 ATATAATT-ATA-TTTAAT-A
*
3467868 ATTAATTATTATATTTAATA
1 A-T-ATAATTATATTTAATA
3467888 ATATAATTATATTTA
1 ATATAATTATATTTA
3467903 TTATACATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 12 0.39
19 1 0.03
20 2 0.06
21 7 0.23
22 4 0.13
23 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATAATTATATTTAATA
Found at i:3468160 original size:2 final size:2
Alignment explanation
Indices: 3468153--3468191 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
3468143 AAGGTCTTTC
* *
3468153 AT AT AT AT AT AT AT AT AT AT AT AT GAT AT TT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
3468192 TAGTATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (2 bp):
AT
Found at i:3468244 original size:29 final size:29
Alignment explanation
Indices: 3468212--3468285 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
3468202 TTAATTAATT
3468212 TTTATATGTTATTATAATTT-TTTAT-ATAA
1 TTTATAT-TTATT-TAATTTATTTATCATAA
* *
3468241 TTTATATTTATTTAATTTATTTATCGTAT
1 TTTATATTTATTTAATTTATTTATCATAA
3468270 TTTATATTTTATTTAA
1 TTTATA-TTTATTTAA
3468286 ATAAATAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 6 0.15
28 10 0.25
29 15 0.38
30 9 0.22
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (29 bp):
TTTATATTTATTTAATTTATTTATCATAA
Found at i:3468256 original size:15 final size:15
Alignment explanation
Indices: 3468212--3468260 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3468202 TTAATTAATT
3468212 TTTATATGTTATTATAA
1 TTTATAT-TTATT-TAA
*
3468229 -TT-T-TTTATATAA
1 TTTATATTTATTTAA
3468241 TTTATATTTATTTAA
1 TTTATATTTATTTAA
3468256 TTTAT
1 TTTAT
3468261 TTATCGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
12 3 0.11
13 6 0.22
14 2 0.07
15 14 0.52
16 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTATATTTATTTAA
Found at i:3468258 original size:9 final size:10
Alignment explanation
Indices: 3468212--3468264 Score: 51
Period size: 9 Copynumber: 5.5 Consensus size: 10
3468202 TTAATTAATT
3468212 TTTATATGTTA
1 TTTATAT-TTA
3468223 -TTATAATTT-
1 TTTAT-ATTTA
*
3468232 TTTATA-TAA
1 TTTATATTTA
3468241 TTTATATTTA
1 TTTATATTTA
3468251 TTTA-ATTTA
1 TTTATATTTA
3468260 TTTAT
1 TTTAT
3468265 CGTATTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
8 1 0.03
9 16 0.46
10 16 0.46
11 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTATATTTA
Found at i:3468393 original size:27 final size:26
Alignment explanation
Indices: 3468341--3468393 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
3468331 CTATTTACTT
*
3468341 AATATAAAAAAATTTAATTATTAAATA
1 AATATAAAAAAAATTAATTA-TAAATA
3468368 AATATTAAAAAATAATTAATTA-AAAT
1 AATA-TAAAAAA-AATTAATTATAAAT
3468394 GATAGCGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 8 0.35
28 7 0.30
29 8 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
AATATAAAAAAAATTAATTATAAATA
Found at i:3471481 original size:2 final size:2
Alignment explanation
Indices: 3471474--3471512 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3471464 TTCTTATTAT
* *
3471474 AC AC AC AC AC AC AC AC AC GC AC GC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3471513 TATTTCAGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.49, G:0.05, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3473103 original size:18 final size:18
Alignment explanation
Indices: 3473062--3473104 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
3473052 TTTATTATTT
3473062 AATTAAAATCAAAAATTAA
1 AATT-AAATCAAAAATTAA
*
3473081 AATTAAAT-AAAATTTAA
1 AATTAAATCAAAAATTAA
3473098 ATATTAA
1 A-ATTAA
3473105 TTTTTATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 9 0.41
19 4 0.18
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTAAATCAAAAATTAA
Found at i:3476729 original size:29 final size:29
Alignment explanation
Indices: 3476695--3476767 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 29
3476685 GTTGATTTTT
*
3476695 AAATAAATTATTAAAATATTATTAATTTA
1 AAATAAAATATTAAAATATTATTAATTTA
*
3476724 AAATAAAATATTAAAATATTATTATTTTA
1 AAATAAAATATTAAAATATTATTAATTTA
*
3476753 ATTAATAAAAAATTA
1 A--AATAAAATATTA
3476768 TTAAATTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
29 28 0.72
31 11 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AAATAAAATATTAAAATATTATTAATTTA
Found at i:3476776 original size:23 final size:23
Alignment explanation
Indices: 3476735--3476778 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3476725 AATAAAATAT
* **
3476735 TAAAATATTATTATTTTAATTAA
1 TAAAAAATTATTAAATTAATTAA
3476758 TAAAAAATTATTAAATTAATT
1 TAAAAAATTATTAAATTAATT
3476779 GACAAATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAAAAATTATTAAATTAATTAA
Found at i:3477215 original size:21 final size:20
Alignment explanation
Indices: 3477181--3477219 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3477171 TATGTCGATG
3477181 TATAATTTAAATAATATTTAA
1 TATAATTTAAATAA-ATTTAA
**
3477202 TATAATTTTCATAAATTT
1 TATAATTTAAATAAATTT
3477220 TGATATGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
TATAATTTAAATAAATTTAA
Found at i:3477254 original size:11 final size:11
Alignment explanation
Indices: 3477191--3477313 Score: 60
Period size: 11 Copynumber: 11.0 Consensus size: 11
3477181 TATAATTTAA
*
3477191 ATAATATTTAAT
1 ATAAT-TTTGAT
*
3477203 ATAATTTTCAT
1 ATAATTTTGAT
3477214 A-AATTTTGAT
1 ATAATTTTGAT
* *
3477224 ATGATTTTAAT
1 ATAATTTTGAT
3477235 ATTTAAATTTTGAT
1 A--T-AATTTTGAT
3477249 ATAATTTTG-T
1 ATAATTTTGAT
*
3477259 TTAATATTTGAT
1 ATAAT-TTTGAT
*
3477271 -TCGATTTT-A-
1 AT-AATTTTGAT
*
3477280 ATAACTTTT-TT
1 ATAA-TTTTGAT
*
3477291 ATAATCTTTAAT
1 ATAAT-TTTGAT
3477303 ATAATTTTGAT
1 ATAATTTTGAT
3477314 GATTATTGAT
Statistics
Matches: 87, Mismatches: 12, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
9 1 0.01
10 21 0.24
11 41 0.47
12 15 0.17
13 1 0.01
14 8 0.09
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (11 bp):
ATAATTTTGAT
Found at i:3477496 original size:21 final size:21
Alignment explanation
Indices: 3477391--3477497 Score: 65
Period size: 21 Copynumber: 5.0 Consensus size: 21
3477381 AATACAGTTT
*
3477391 TAATAACTTTTAATATAATTTA
1 TAATAA-TTTTAATATCATTTA
* * **
3477413 GTAATTATTTTAATAACACCTA
1 -TAATAATTTTAATATCATTTA
* *
3477435 TAATAATTTTAATAACTTTTTA
1 TAATAATTTTAATATC-ATTTA
* **
3477457 TACT-ATTTCGATAAT-ATTTA
1 TAATAATTTTAAT-ATCATTTA
*
3477477 TAATAATTTTGATATCATTTA
1 TAATAATTTTAATATCATTTA
3477498 ATATAATAAT
Statistics
Matches: 64, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
20 9 0.14
21 33 0.52
22 17 0.27
23 5 0.08
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (21 bp):
TAATAATTTTAATATCATTTA
Found at i:3478552 original size:10 final size:10
Alignment explanation
Indices: 3478537--3478569 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3478527 TTTAAATATA
3478537 TAAAAAAATT
1 TAAAAAAATT
3478547 T-AAAAAATT
1 TAAAAAAATT
*
3478556 TATAAAAATT
1 TAAAAAAATT
3478566 TAAA
1 TAAA
3478570 TATACGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAAAAAATT
Found at i:3478553 original size:9 final size:9
Alignment explanation
Indices: 3478539--3478569 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
3478529 TAAATATATA
3478539 AAAAAATTT
1 AAAAAATTT
3478548 AAAAAATTT
1 AAAAAATTT
3478557 ATAAAAATTT
1 A-AAAAATTT
3478567 AAA
1 AAA
3478570 TATACGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAAAATTT
Found at i:3480268 original size:2 final size:2
Alignment explanation
Indices: 3480261--3480288 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3480251 CATATACATT
3480261 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3480289 GATATGGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3483188 original size:23 final size:23
Alignment explanation
Indices: 3483137--3483189 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
3483127 TTATAATATT
*
3483137 TAAAAATTTTTATTAATTTAAAAA
1 TAAAAATATTTATT-ATTTAAAAA
*
3483161 T-AAAATATTTATT-TTTAAACTA
1 TAAAAATATTTATTATTTAAA-AA
3483183 TAAAAAT
1 TAAAAAT
3483190 TAAAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 6 0.24
22 2 0.08
23 16 0.64
24 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAAAATATTTATTATTTAAAAA
Found at i:3483493 original size:3 final size:3
Alignment explanation
Indices: 3483485--3483513 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3483475 AGAAAAAACA
3483485 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3483514 ACAGTTAGCT
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:3483529 original size:3 final size:3
Alignment explanation
Indices: 3483523--3483557 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3483513 AACAGTTAGC
3483523 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3483558 TGTTTTTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3484769 original size:95 final size:95
Alignment explanation
Indices: 3484612--3484790 Score: 322
Period size: 95 Copynumber: 1.9 Consensus size: 95
3484602 CTCCTTCAAC
*
3484612 TATATATATTATATGCAAGTTTCTTGCACTTCTTCTCCTTCTATCTTAATTGATATTTATATATA
1 TATATATATTATATGCAAGTTTCTTGCACTTCTTCTCCTTCTATCTTAATTGATATATATATATA
*
3484677 CACTTGGAGGATTTTATGGTTATATATATA
66 CACCTGGAGGATTTTATGGTTATATATATA
*
3484707 TATATATATTATATGCAAGTTTCTTGCACTTCTTCTCCTTCTATCTTAATTGATGTATATATATA
1 TATATATATTATATGCAAGTTTCTTGCACTTCTTCTCCTTCTATCTTAATTGATATATATATATA
*
3484772 CACCTGGAGGGTTTTATGG
66 CACCTGGAGGATTTTATGG
3484791 ATACGCTCTA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 80 1.00
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (95 bp):
TATATATATTATATGCAAGTTTCTTGCACTTCTTCTCCTTCTATCTTAATTGATATATATATATA
CACCTGGAGGATTTTATGGTTATATATATA
Found at i:3486228 original size:15 final size:16
Alignment explanation
Indices: 3486194--3486237 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
3486184 AATAGATTCA
*
3486194 ATTTAAAA-TTTTAAT
1 ATTTAAAATTTTTTAT
3486209 ATTTAAAATTTTTTAT
1 ATTTAAAATTTTTTAT
*
3486225 -TTTATAATTTTTT
1 ATTTAAAATTTTTT
3486238 TAAATAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 20 0.77
16 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTAAAATTTTTTAT
Found at i:3486394 original size:2 final size:2
Alignment explanation
Indices: 3486381--3486410 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
3486371 AATTTAATTC
3486381 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
3486411 TCATTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3489141 original size:2 final size:2
Alignment explanation
Indices: 3489134--3489190 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
3489124 AATTATTAAA
*
3489134 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
3489176 AG AG AG AG AA AG AG A
1 AG AG AG AG AG AG AG A
3489191 TTAGATAGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3492953 original size:4 final size:4
Alignment explanation
Indices: 3492928--3492977 Score: 75
Period size: 4 Copynumber: 12.5 Consensus size: 4
3492918 ATAATCTTTC
*
3492928 AAGA AA-A AAGGA AAGC AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AA-GA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
3492976 AA
1 AA
3492978 CATTGAAGAC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 3 0.07
4 36 0.86
5 3 0.07
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:3495047 original size:2 final size:2
Alignment explanation
Indices: 3495040--3495072 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3495030 AGGATTTAAA
3495040 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3495073 ATAGGATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3499406 original size:2 final size:2
Alignment explanation
Indices: 3499401--3499433 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3499391 TGTGTGTATC
*
3499401 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3499434 GTTGATAAAT
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:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3500380 original size:3 final size:3
Alignment explanation
Indices: 3500374--3500406 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3500364 CAAATAATAT
3500374 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3500407 GAATTGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3502305 original size:2 final size:2
Alignment explanation
Indices: 3502298--3502331 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3502288 TGTGTATAAT
3502298 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
3502332 CACACCAGGA
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):
TA
Found at i:3503750 original size:6 final size:6
Alignment explanation
Indices: 3503742--3503774 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
3503732 GCTGTTGCAA
*
3503742 TTATTA TTATTT TTATTT TTATTT TTATTT TTA
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTA
3503775 AAGATAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TTATTT
Found at i:3505188 original size:27 final size:27
Alignment explanation
Indices: 3505161--3505231 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 27
3505151 TGATTTGAAT
3505161 TTAAAATAAATAT-TTTATAATTTAAA
1 TTAAAATAAATATATTTATAATTTAAA
* * *
3505187 TTAAATTAAATTTATTTATTATTT-AA
1 TTAAAATAAATATATTTATAATTTAAA
*
3505213 TTAATAA-AAATTTATTTAT
1 TTAA-AATAAATATATTTAT
3505232 TTAAATTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 29 0.74
27 10 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TTAAAATAAATATATTTATAATTTAAA
Found at i:3506146 original size:26 final size:27
Alignment explanation
Indices: 3506094--3506147 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 27
3506084 TATTTTTTTA
* *
3506094 AAAATAAATTTTTTATTTTTATTATAT
1 AAAATAAATTTTTAATTTATATTATAT
3506121 AAAA-AAA-TTTTAATTTATATTCATAT
1 AAAATAAATTTTTAATTTATATT-ATAT
3506147 A
1 A
3506148 TATCAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.50
26 8 0.33
27 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
AAAATAAATTTTTAATTTATATTATAT
Found at i:3508804 original size:16 final size:17
Alignment explanation
Indices: 3508771--3508814 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
3508761 ATTTTATAAG
*
3508771 TATTTATTTTATGTAAA
1 TATTTATTTAATGTAAA
3508788 TATTTATTTAATG-AAA
1 TATTTATTTAATGTAAA
3508804 TATTTTATTTA
1 TA-TTTATTTA
3508815 TACTTCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
TATTTATTTAATGTAAA
Found at i:3514217 original size:17 final size:17
Alignment explanation
Indices: 3514197--3514230 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3514187 GTTTTCATTT
3514197 TTTTATGTAATATTTTA
1 TTTTATGTAATATTTTA
*
3514214 TTTTATGTTATATTTTA
1 TTTTATGTAATATTTTA
3514231 ATTATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
TTTTATGTAATATTTTA
Found at i:3515710 original size:16 final size:18
Alignment explanation
Indices: 3515684--3515728 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
3515674 TTAGACAGAA
3515684 AAAAATA-ATAAT-AA-T
1 AAAAATATATAATAAAGT
3515699 AAAAATATATAATAAAGT
1 AAAAATATATAATAAAGT
*
3515717 ATAAATATATAA
1 AAAAATATATAA
3515729 ATATTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 7 0.27
16 5 0.19
17 2 0.08
18 12 0.46
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAAATATATAATAAAGT
Found at i:3515714 original size:13 final size:15
Alignment explanation
Indices: 3515684--3515713 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
3515674 TTAGACAGAA
3515684 AAAAATAATAATAAT
1 AAAAATAATAATAAT
3515699 AAAAATATATAATAA
1 AAAAATA-ATAATAA
3515714 AGTATAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAATAATAATAAT
Found at i:3517730 original size:15 final size:15
Alignment explanation
Indices: 3517712--3517759 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
3517702 TAAATTGGTT
3517712 AGATATAAATTTTAA
1 AGATATAAATTTTAA
*
3517727 AGATAAAAATTATTAA
1 AGATATAAATT-TTAA
3517743 A-ATAATAATATTTTAA
1 AGAT-ATAA-ATTTTAA
3517759 A
1 A
3517760 ATTAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 12 0.43
16 13 0.46
17 3 0.11
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (15 bp):
AGATATAAATTTTAA
Found at i:3517766 original size:22 final size:20
Alignment explanation
Indices: 3517738--3517802 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
3517728 GATAAAAATT
3517738 ATTAAAATAATAATATTTTAAA
1 ATTAAAATAAT-AT-TTTTAAA
*
3517760 ATTAAAATTATATTTTTAAA
1 ATTAAAATAATATTTTTAAA
* * * *
3517780 AATAATAT-TTATTTTTAAT
1 ATTAAAATAATATTTTTAAA
3517799 ATTA
1 ATTA
3517803 TTAAATTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
19 12 0.32
20 13 0.35
21 2 0.05
22 10 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTAAAATAATATTTTTAAA
Done.