Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold60
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: 3815296
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18690 characters in sequence are not A, C, G, or T
File 8 of 21
Found at i:1065941 original size:16 final size:16
Alignment explanation
Indices: 1065920--1065960 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1065910 AACATCAATT
1065920 ACAGATTTTAGAAATC
1 ACAGATTTTAGAAATC
* *
1065936 ACAGATTTTTGGAATC
1 ACAGATTTTAGAAATC
*
1065952 ACATATTTT
1 ACAGATTTT
1065961 CAACCCATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (16 bp):
ACAGATTTTAGAAATC
Found at i:1066441 original size:14 final size:16
Alignment explanation
Indices: 1066413--1066444 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1066403 AAATGAAATT
1066413 ATTTTTTAATATTTTA
1 ATTTTTTAATATTTTA
1066429 ATTTTTT-AT-TTTTA
1 ATTTTTTAATATTTTA
1066443 AT
1 AT
1066445 ATATCTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTTTAATATTTTA
Found at i:1069441 original size:24 final size:24
Alignment explanation
Indices: 1069401--1069453 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 24
1069391 CTACATTTTT
1069401 TTTATATTTATATTTAAATTATTA
1 TTTATATTTATATTTAAATTATTA
*
1069425 TTTATAATTTTTA-TT-AA-T-TTA
1 TTTAT-ATTTATATTTAAATTATTA
1069446 TTTATATT
1 TTTATATT
1069454 ATTTAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.11
21 8 0.30
22 1 0.04
23 2 0.07
24 7 0.26
25 6 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTATATTTATATTTAAATTATTA
Found at i:1070481 original size:317 final size:313
Alignment explanation
Indices: 1069887--1070514 Score: 945
Period size: 317 Copynumber: 2.0 Consensus size: 313
1069877 AATAAGTAAA
* *
1069887 AAGTTAATATATTTCCTTCACACGACCAACAAACACAATAAATAACTTGTAATATAAGAAAAAAT
1 AAGTTAATACATTTCCTTCACACAACCAACAAACACAATAAATAACTTGTAATATAAGAAAAAAT
* *
1069952 CTCAAAAATTAAAAAAAAATTAAAACTTATTAGAAGCAAATAATTTGATAGGAAGAAGAAACCTC
66 CCCAAAAATTAAAAAAAAA-TAAAACTTATTAGAAGCAAATAATTTGATAGGAAGAAAAAACCTC
*
1070017 AATTAAAAATAAAGTTATGATAACATTTAAATATAATAATTATAAGATGAAGTAAAAAAAAATAA
130 AATGAAAAATAAAGTTATGATAACATTTAAATATAATAATTATAAGATGAAGTAAAAAAAAATAA
* * * *
1070082 GCATTTTATACCTAAACTACCAATAACCTTTCACTGATAAACCTAGTACATGAAAATAAATCATA
195 ACATTTTATACCTAAACCACCAATAACCTTTCACTGATAAAACTAGTACATGAAAATAAACCATA
* * *
1070147 AAATTAATAAAAGACCATATCCTATGCACACAGAATATGTTCAGATACAAAGTAG
260 AAATTAATAAAAGACCATATCCTATACACACAAAATAGGTTCA-ATACAAAGTAG
* * *
1070202 AAGTTAATACCTTTCCTTCACATAACCAACAAACACAATAAATAATTTGTAATATAAGAAAAAAT
1 AAGTTAATACATTTCCTTCACACAACCAACAAACACAATAAATAACTTGTAATATAAGAAAAAAT
* * *
1070267 CCCAATAATTAAAAACAAAA-AAGACTTGTTAGAAGCAAATAATTTGATAAGGAA-AAAAAACCT
66 CCCAAAAATTAAAAA-AAAATAAAACTTATTAGAAGCAAATAATTTGAT-AGGAAGAAAAAACCT
* *
1070330 CAATGAAAAATGAAGTTATGATAACATTTAAATATAATAATTATTAGATGAAGTAATAAAAAAAA
129 CAATGAAAAATAAAGTTATGATAACATTTAAATATAATAATTATAAGATGAAG---TAAAAAAAA
* * * *
1070395 ATAAACATTTTATATCTAAACCACCAATAACCTTTCATTGATAAAATTGGTACATGAAAATAAAC
191 ATAAACATTTTATACCTAAACCACCAATAACCTTTCACTGATAAAACTAGTACATGAAAATAAAC
* *
1070460 CATGAAATTAATAAAAGACCATATCCTATATACACAAAATAGGTTCAATACAAAG
256 CATAAAATTAATAAAAGACCATATCCTATACACACAAAATAGGTTCAATACAAAG
1070515 CAGTTATTAT
Statistics
Matches: 282, Mismatches: 26, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
314 84 0.30
315 78 0.28
316 12 0.04
317 108 0.38
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.26
Consensus pattern (313 bp):
AAGTTAATACATTTCCTTCACACAACCAACAAACACAATAAATAACTTGTAATATAAGAAAAAAT
CCCAAAAATTAAAAAAAAATAAAACTTATTAGAAGCAAATAATTTGATAGGAAGAAAAAACCTCA
ATGAAAAATAAAGTTATGATAACATTTAAATATAATAATTATAAGATGAAGTAAAAAAAAATAAA
CATTTTATACCTAAACCACCAATAACCTTTCACTGATAAAACTAGTACATGAAAATAAACCATAA
AATTAATAAAAGACCATATCCTATACACACAAAATAGGTTCAATACAAAGTAG
Found at i:1071159 original size:6 final size:6
Alignment explanation
Indices: 1071137--1071176 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
1071127 TTTTTCTATT
*
1071137 TTTTTC TTTAT- TTTTTC TTTTTC TTTTTC TCTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC TTTT
1071177 GATTACTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.13
6 20 0.67
7 6 0.20
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:1071163 original size:13 final size:12
Alignment explanation
Indices: 1071123--1071176 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
1071113 TTCATTTCCC
1071123 TTTTTTTTTCTAT
1 TTTTTTTTTCT-T
*
1071136 TTTTTTCTTTATT
1 TTTTTT-TTTCTT
1071149 TTTTCTTTTTCTT
1 TTTT-TTTTTCTT
*
1071162 TTTCTCTTTTCTT
1 TTT-TTTTTTCTT
1071175 TT
1 TT
1071177 GATTACTAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
13 28 0.80
14 7 0.20
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:1071176 original size:12 final size:11
Alignment explanation
Indices: 1071117--1071176 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
1071107 TTTTTTTTCA
*
1071117 TTTCCCTTTTT
1 TTTCTCTTTTT
1071128 TTT-TCTATTTT
1 TTTCTCT-TTTT
1071139 TTTCT-TTATTT
1 TTTCTCTT-TTT
*
1071150 TTTCTTTTTCTT
1 TTTCTCTTT-TT
1071162 TTTCTCTTTTCT
1 TTTCTCTTTT-T
1071174 TTT
1 TTT
1071177 GATTACTAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
10 3 0.07
11 21 0.51
12 17 0.41
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTCTCTTTTT
Found at i:1071176 original size:25 final size:26
Alignment explanation
Indices: 1071122--1071176 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
1071112 TTTCATTTCC
*
1071122 CTTTTTTTTTCTATTTTTTTCTTTAT
1 CTTTTTTTTTCTATTTTTCTCTTTAT
*
1071148 -TTTTTCTTTT-TCTTTTTCTCTTT-T
1 CTTTTT-TTTTCTATTTTTCTCTTTAT
1071172 CTTTT
1 CTTTT
1071177 GATTACTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
24 1 0.04
25 20 0.80
26 4 0.16
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.82
Consensus pattern (26 bp):
CTTTTTTTTTCTATTTTTCTCTTTAT
Found at i:1072065 original size:21 final size:21
Alignment explanation
Indices: 1072041--1072080 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1072031 TATCCAATTC
*
1072041 AAATCGAAGAAAAAACTCTCT
1 AAATCAAAGAAAAAACTCTCT
1072062 AAATCAAAGAAAAAACTCT
1 AAATCAAAGAAAAAACTCT
1072081 AAATGTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.17, G:0.07, T:0.17
Consensus pattern (21 bp):
AAATCAAAGAAAAAACTCTCT
Found at i:1074954 original size:21 final size:23
Alignment explanation
Indices: 1074930--1074973 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
1074920 TAATGCGTAA
1074930 AATTTAAATTTT-AA-TTTAATT
1 AATTTAAATTTTAAATTTTAATT
*
1074951 AATTTTAATTTTAAATTTTAATT
1 AATTTAAATTTTAAATTTTAATT
1074974 TTAATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 2 0.10
23 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AATTTAAATTTTAAATTTTAATT
Found at i:1074956 original size:15 final size:13
Alignment explanation
Indices: 1074932--1074988 Score: 69
Period size: 13 Copynumber: 4.1 Consensus size: 13
1074922 ATGCGTAAAA
1074932 TTTAAATTTTAAT
1 TTTAAATTTTAAT
*
1074945 TTAATTAATTTTAAT
1 TT--TAAATTTTAAT
1074960 TTTAAATTTTAAT
1 TTTAAATTTTAAT
1074973 TTTAATATTTATAAT
1 TTTAA-ATTT-TAAT
1074988 T
1 T
1074989 ATTTTTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
13 17 0.45
14 4 0.11
15 17 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTAAATTTTAAT
Found at i:1074983 original size:7 final size:6
Alignment explanation
Indices: 1074930--1074983 Score: 60
Period size: 6 Copynumber: 9.2 Consensus size: 6
1074920 TAATGCGTAA
*
1074930 AATTTA AATTTT AA-TTT AA--TT AATTTT AATTTT AAATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT -AATTTT AATTTT
1074976 AATATTT A
1 AAT-TTT A
1074984 TAATTATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
4 4 0.09
5 5 0.12
6 24 0.56
7 10 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
AATTTT
Found at i:1074994 original size:19 final size:18
Alignment explanation
Indices: 1074946--1074993 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
1074936 AATTTTAATT
1074946 TAATTAATTTTAATTTTA
1 TAATTAATTTTAATTTTA
1074964 -AATTTTAATTTTAATATTTA
1 TAA--TTAATTTTAAT-TTTA
1074984 TAATT-ATTTT
1 TAATTAATTTT
1074994 TTTATTCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 2 0.08
18 5 0.19
19 13 0.50
20 4 0.15
21 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TAATTAATTTTAATTTTA
Found at i:1075305 original size:22 final size:22
Alignment explanation
Indices: 1075224--1075306 Score: 59
Period size: 22 Copynumber: 3.9 Consensus size: 22
1075214 AATTATAAAT
*
1075224 ATTAATATTTAAATTTTAAATT-T
1 ATTAAT-TTTAAATTTT-AATTAA
*
1075247 ATTAATATT--ATTTT--TTAA
1 ATTAATTTTAAATTTTAATTAA
* **
1075265 ATATAATTATAAAAATTAATTAA
1 AT-TAATTTTAAATTTTAATTAA
1075288 ATTAATTTTAAATTTTAAT
1 ATTAATTTTAAATTTTAAT
1075307 GACATATGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 13
0.67 0.13 0.19
Matches are distributed among these distances:
17 2 0.04
18 2 0.04
19 5 0.11
20 5 0.11
21 3 0.07
22 16 0.36
23 12 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTAATTTTAAATTTTAATTAA
Found at i:1075546 original size:13 final size:13
Alignment explanation
Indices: 1075528--1075560 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
1075518 ATAAATTTAA
1075528 AATATTATTTTTT
1 AATATTATTTTTT
1075541 AATATTA--TTTT
1 AATATTATTTTTT
1075552 AATATTATT
1 AATATTATT
1075561 AAACATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
11 11 0.61
13 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
AATATTATTTTTT
Found at i:1075705 original size:20 final size:19
Alignment explanation
Indices: 1075683--1075762 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 19
1075673 TATGAAAAAG
*
1075683 TATTTTTAAATAAAATAATG
1 TATTTTTAAATAAAA-AATA
*
1075703 TATTTTTAGATAAAAAATA
1 TATTTTTAAATAAAAAATA
**
1075722 TATTTTTTTATAAAAAAATA
1 TATTTTTAAAT-AAAAAATA
1075742 TAATTTTTAATAATAAAAAAT
1 T-ATTTTT-A-AATAAAAAAT
1075763 TATCATACTT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
19 12 0.24
20 23 0.46
21 6 0.12
22 7 0.14
23 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
TATTTTTAAATAAAAAATA
Found at i:1075727 original size:39 final size:40
Alignment explanation
Indices: 1075683--1075759 Score: 95
Period size: 39 Copynumber: 1.9 Consensus size: 40
1075673 TATGAAAAAG
* *
1075683 TATTTTTAAATAAAATAATGT-ATTTTTAGATAA-AAAATA
1 TATTTTTAAATAAAAAAATATAATTTTTA-ATAATAAAATA
**
1075722 TATTTTTTTATAAAAAAATATAATTTTTAATAATAAAA
1 TATTTTTAAATAAAAAAATATAATTTTTAATAATAAAA
1075760 AATTATCATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 21 0.66
40 11 0.34
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (40 bp):
TATTTTTAAATAAAAAAATATAATTTTTAATAATAAAATA
Found at i:1078268 original size:20 final size:19
Alignment explanation
Indices: 1078243--1078281 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1078233 TAATTTTTTA
*
1078243 AAAATTTATTTTTTAAATTT
1 AAAATTTA-TATTTAAATTT
1078263 AAAATTTATATTTAAATTT
1 AAAATTTATATTTAAATTT
1078282 TTTAAATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AAAATTTATATTTAAATTT
Found at i:1079388 original size:13 final size:13
Alignment explanation
Indices: 1079370--1079397 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1079360 AATTTTTTTG
1079370 AATATTTATATTT
1 AATATTTATATTT
1079383 AATATTTATATTT
1 AATATTTATATTT
1079396 AA
1 AA
1079398 CATATATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:1080971 original size:139 final size:139
Alignment explanation
Indices: 1080720--1081001 Score: 519
Period size: 139 Copynumber: 2.0 Consensus size: 139
1080710 CTATATTCAA
*
1080720 TGTCTCATTGATAAGATCATAGCTTAGTCCTTCAGGGCAAGAGAAGAACATGTAAAAAAAATGTT
1 TGTCTCATTGATAAGATCATAACTTAGTCCTTCAGGGCAAGAGAAGAACATGTAAAAAAAATGTT
* *
1080785 AACTCTATGCAATAAGGAAACTCAAATGTGATCTTAGTGTCAGTAACAGCATTAACATAGTAAGT
66 AACTCTATGCAACAAGGAAACTCAAATGTGATCTTAGTGTCAATAACAGCATTAACATAGTAAGT
*
1080850 AGATGAGAG
131 AAATGAGAG
*
1080859 TGTCTCATTGATAAGATCATAACTTAGTCCTTGAGGGCAAGAGAAGAACATGTAAAAAAAATGTT
1 TGTCTCATTGATAAGATCATAACTTAGTCCTTCAGGGCAAGAGAAGAACATGTAAAAAAAATGTT
1080924 AACTCTATGCAACAAGGAAACTCAAATGTGATCTTAGTGTCAATAACAGCATTAACATAGTAAGT
66 AACTCTATGCAACAAGGAAACTCAAATGTGATCTTAGTGTCAATAACAGCATTAACATAGTAAGT
1080989 AAATGAGAG
131 AAATGAGAG
1080998 TGTC
1 TGTC
1081002 ATGGCCTAAT
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 138 1.00
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (139 bp):
TGTCTCATTGATAAGATCATAACTTAGTCCTTCAGGGCAAGAGAAGAACATGTAAAAAAAATGTT
AACTCTATGCAACAAGGAAACTCAAATGTGATCTTAGTGTCAATAACAGCATTAACATAGTAAGT
AAATGAGAG
Found at i:1083090 original size:21 final size:21
Alignment explanation
Indices: 1083064--1083111 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1083054 GTATCTTTGA
*
1083064 ATGAAATAATGCATTGGTTGG
1 ATGAAAGAATGCATTGGTTGG
**
1083085 ATGAAAGAATGCATTTTTTGG
1 ATGAAAGAATGCATTGGTTGG
1083106 ATGAAA
1 ATGAAA
1083112 AAATACAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (21 bp):
ATGAAAGAATGCATTGGTTGG
Found at i:1083124 original size:21 final size:21
Alignment explanation
Indices: 1083081--1083124 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1083071 AATGCATTGG
* * **
1083081 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAAAATACAACTT
1083102 TTGGATGAAAAAATACAACTT
1 TTGGATGAAAAAATACAACTT
1083123 TT
1 TT
1083125 AATAATCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (21 bp):
TTGGATGAAAAAATACAACTT
Found at i:1083617 original size:22 final size:22
Alignment explanation
Indices: 1083592--1083667 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
1083582 AGTTTTAGGC
*
1083592 AATATAAATTAACTTATGTAAT
1 AATACAAATTAACTTATGTAAT
* **
1083614 AATACAAATCATAAGTT-T-TAGGC
1 AATACAAAT--TAACTTATGTA-AT
*
1083637 AATATAAATTAACTTATGTAAT
1 AATACAAATTAACTTATGTAAT
1083659 AATACAAAT
1 AATACAAAT
1083668 CATAAATTTA
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
21 5 0.12
22 19 0.47
23 11 0.28
24 5 0.12
ACGTcount: A:0.50, C:0.08, G:0.07, T:0.36
Consensus pattern (22 bp):
AATACAAATTAACTTATGTAAT
Found at i:1083629 original size:45 final size:45
Alignment explanation
Indices: 1083580--1083701 Score: 228
Period size: 45 Copynumber: 2.7 Consensus size: 45
1083570 ATGTTCATCT
1083580 TAAGTTTTAGGCAATATAAATTAACTTATGTAATAATACAAATCA
1 TAAGTTTTAGGCAATATAAATTAACTTATGTAATAATACAAATCA
1083625 TAAGTTTTAGGCAATATAAATTAACTTATGTAATAATACAAATCA
1 TAAGTTTTAGGCAATATAAATTAACTTATGTAATAATACAAATCA
*
1083670 TAA-ATTTAGGCAATATAAATTAACTTATGTAA
1 TAAGTTTTAGGCAATATAAATTAACTTATGTAA
1083702 GAGAGAGAGA
Statistics
Matches: 76, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
44 28 0.37
45 48 0.63
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (45 bp):
TAAGTTTTAGGCAATATAAATTAACTTATGTAATAATACAAATCA
Found at i:1083708 original size:2 final size:2
Alignment explanation
Indices: 1083701--1083828 Score: 256
Period size: 2 Copynumber: 64.0 Consensus size: 2
1083691 AACTTATGTA
1083701 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1083743 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1083785 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1083827 AG
1 AG
1083829 GAGGAATTAA
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 126 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1085397 original size:23 final size:22
Alignment explanation
Indices: 1085362--1085421 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
1085352 AACCCTTACC
*
1085362 ATTATTTAAAATAATATTAAAA
1 ATTATTTTAAATAATATTAAAA
* *
1085384 ATTATTTTAGAATAATATTTATA
1 ATTATTTTA-AATAATATTAAAA
1085407 ATTAATTTTAAATAA
1 ATT-ATTTTAAATAA
1085422 ACAATAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.24
23 19 0.58
24 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTATTTTAAATAATATTAAAA
Found at i:1085404 original size:12 final size:12
Alignment explanation
Indices: 1085364--1085418 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
1085354 CCCTTACCAT
1085364 TATTTAAAATAA
1 TATTTAAAATAA
* *
1085376 TATTAAAAATTA
1 TATTTAAAATAA
*
1085388 T-TTTAGAATAA
1 TATTTAAAATAA
*
1085399 TATTTATAATTAA
1 TATTTA-AAATAA
1085412 T-TTTAAA
1 TATTTAAA
1085419 TAAACAATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
11 10 0.29
12 19 0.56
13 5 0.15
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (12 bp):
TATTTAAAATAA
Found at i:1089831 original size:2 final size:2
Alignment explanation
Indices: 1089826--1089863 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1089816 CACACACGTG
1089826 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
1089864 AAAGCGCGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1094419 original size:2 final size:2
Alignment explanation
Indices: 1094412--1094451 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1094402 GTTTAGTCCT
1094412 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
1094452 AAAGCACGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1097235 original size:20 final size:19
Alignment explanation
Indices: 1097199--1097237 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1097189 TCAATTTTTT
*
1097199 ATTTATATTTATTTTTAAA
1 ATTTATATTTATATTTAAA
*
1097218 ATTTAATATTTGTATTTAAA
1 ATTT-ATATTTATATTTAAA
1097238 CTCTTTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTTATATTTATATTTAAA
Found at i:1098637 original size:2 final size:2
Alignment explanation
Indices: 1098630--1098666 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1098620 AAACAAAAAC
1098630 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1098667 ATGAGAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1100662 original size:16 final size:14
Alignment explanation
Indices: 1100639--1100673 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1100629 TAAAAATATA
1100639 TTTTTAATTTTAATT
1 TTTTTAA-TTTAATT
1100654 TTTTGTAATTTAATT
1 TTTT-TAATTTAATT
1100669 TTTTT
1 TTTTT
1100674 CATTAAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.05
15 15 0.79
16 3 0.16
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTTAATTTAATT
Found at i:1100778 original size:14 final size:14
Alignment explanation
Indices: 1100761--1100790 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1100751 TTATATAATA
*
1100761 TAAAAATATTATTT
1 TAAAAATAATATTT
1100775 TAAAAATAATATTT
1 TAAAAATAATATTT
1100789 TA
1 TA
1100791 TTTAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAAAATAATATTT
Found at i:1100798 original size:30 final size:32
Alignment explanation
Indices: 1100759--1100839 Score: 82
Period size: 30 Copynumber: 2.7 Consensus size: 32
1100749 AATTATATAA
*
1100759 TATAAAAATATTATTTTAAA-AATAATA-TTT
1 TATATAAATATTATTTTAAATAATAATATTTT
* **
1100789 TATTTAAATA-TATTTTTAAATTTTAATATTTT
1 TATATAAATATTA-TTTTAAATAATAATATTTT
1100821 TATATAAAT-TT-TTTTAAAT
1 TATATAAATATTATTTTAAAT
1100840 GTTAAATCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
29 2 0.05
30 23 0.55
31 5 0.12
32 12 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TATATAAATATTATTTTAAATAATAATATTTT
Found at i:1100819 original size:31 final size:30
Alignment explanation
Indices: 1100781--1100844 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
1100771 ATTTTAAAAA
* *
1100781 TAATA-TTTTATTTAAATATATTTTTAAATTT
1 TAATATTTTTATATAAAT-T-TTTTTAAATGT
1100812 TAATATTTTTATATAAATTTTTTTAAATGT
1 TAATATTTTTATATAAATTTTTTTAAATGT
1100842 TAA
1 TAA
1100845 ATCAACCTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 13 0.43
31 6 0.20
32 11 0.37
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (30 bp):
TAATATTTTTATATAAATTTTTTTAAATGT
Found at i:1101280 original size:2 final size:2
Alignment explanation
Indices: 1101273--1101307 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1101263 GCATGTGTAC
1101273 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1101308 AACATTCAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1102137 original size:15 final size:15
Alignment explanation
Indices: 1102117--1102147 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1102107 GGATTTCCCC
1102117 TTTTTTTT-CTTTTT
1 TTTTTTTTCCTTTTT
1102131 TTTTTTTTCCTTTTT
1 TTTTTTTTCCTTTTT
1102146 TT
1 TT
1102148 CTTACCCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTTTCCTTTTT
Found at i:1102319 original size:14 final size:14
Alignment explanation
Indices: 1102302--1102352 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
1102292 ATTTGAGGTT
1102302 TTTTATATTTAAAA
1 TTTTATATTTAAAA
* *
1102316 TTTTAATAATT-GAA
1 TTTT-ATATTTAAAA
1102330 TTTTA-ATTTAAAA
1 TTTTATATTTAAAA
*
1102343 TTTGATATTT
1 TTTTATATTT
1102353 TATTAATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
12 3 0.10
13 7 0.24
14 14 0.48
15 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (14 bp):
TTTTATATTTAAAA
Found at i:1102468 original size:13 final size:13
Alignment explanation
Indices: 1102452--1102476 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1102442 TTTTGAACTC
1102452 TCTTTTTTTTTTT
1 TCTTTTTTTTTTT
1102465 TCTTTTTTTTTT
1 TCTTTTTTTTTT
1102477 AAATACTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TCTTTTTTTTTTT
Found at i:1102652 original size:11 final size:11
Alignment explanation
Indices: 1102636--1102733 Score: 56
Period size: 11 Copynumber: 8.7 Consensus size: 11
1102626 ATTAACATAA
1102636 ATATAATAAAT
1 ATATAATAAAT
*
1102647 ATATAATAATT
1 ATATAATAAAT
* * *
1102658 TTAAAATTAAT
1 ATATAATAAAT
* *
1102669 ATAAATATAAAA
1 ATATA-ATAAAT
**
1102681 ATATTTTAAAT
1 ATATAATAAAT
*
1102692 ATA-ATTATAAT
1 ATATAATA-AAT
*
1102703 ATAATAAAAAAT
1 AT-ATAATAAAT
1102715 ATATATATAAAT
1 ATATA-ATAAAT
1102727 ATA-AATA
1 ATATAATA
1102734 CGATAAATTT
Statistics
Matches: 66, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
10 6 0.09
11 37 0.56
12 21 0.32
13 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATAATAAAT
Found at i:1102675 original size:6 final size:6
Alignment explanation
Indices: 1102666--1102733 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 6
1102656 TTTTAAAATT
* * * * *
1102666 AATATA AATATA AAAAT- ATTTTA AATATA ATTAT- AATAT- AATAAAA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AAT-ATA
*
1102712 AATATA TATATA AATATA AATA
1 AATATA AATATA AATATA AATA
1102734 CGATAAATTT
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
5 9 0.19
6 35 0.74
7 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
AATATA
Found at i:1102686 original size:28 final size:30
Alignment explanation
Indices: 1102641--1102733 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 30
1102631 CATAAATATA
*
1102641 ATAAATAT-ATAATAATTTTAAA-ATTAA-T
1 ATAAATATAAAAATAATTTTAAATA-TAATT
1102669 ATAAATATAAAAAT-ATTTTAAATATAATT
1 ATAAATATAAAAATAATTTTAAATATAATT
* * * *
1102698 AT-AATATAATAAA-AAATATATATATAAAT
1 ATAAATATAA-AAATAATTTTAAATATAATT
1102727 ATAAATA
1 ATAAATA
1102734 CGATAAATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
28 26 0.48
29 24 0.44
30 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
ATAAATATAAAAATAATTTTAAATATAATT
Found at i:1110545 original size:29 final size:29
Alignment explanation
Indices: 1110513--1110571 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1110503 TTTTTTTTGG
1110513 GAATCATTCGCTGTTTTTAGGCCTTGTTT
1 GAATCATTCGCTGTTTTTAGGCCTTGTTT
1110542 GAATCATTCGCTGTTTTTAGGCCTTGTTT
1 GAATCATTCGCTGTTTTTAGGCCTTGTTT
1110571 G
1 G
1110572 GAAATTCAAA
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:0.14, C:0.17, G:0.22, T:0.47
Consensus pattern (29 bp):
GAATCATTCGCTGTTTTTAGGCCTTGTTT
Found at i:1115579 original size:2 final size:2
Alignment explanation
Indices: 1115572--1115617 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1115562 AGCCTGTCCT
1115572 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
1115614 TA TA
1 TA TA
1115618 AAATATGCAT
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):
TA
Found at i:1118263 original size:17 final size:18
Alignment explanation
Indices: 1118157--1118266 Score: 73
Period size: 19 Copynumber: 5.7 Consensus size: 18
1118147 TTATATTTAC
1118157 ATATTTT-TATGTTATAATA
1 ATATTTTATAT-TT-TAATA
1118176 ATATTTTATATTTATACATA
1 ATATTTTATATTT-TA-ATA
* *
1118196 A-ATTTTAAAATATTAATA
1 ATATTTT-ATATTTTAATA
1118214 ATTTATATTCTATAAATTTTAATA
1 A--TAT-TT-TAT--ATTTTAATA
*
1118238 ATTTTTTATATTTTAAT-
1 ATATTTTATATTTTAATA
1118255 ATATTTTATATT
1 ATATTTTATATT
1118267 ATATTTTAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
17 11 0.15
18 12 0.16
19 19 0.25
20 14 0.19
21 4 0.05
22 5 0.07
23 1 0.01
24 9 0.12
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (18 bp):
ATATTTTATATTTTAATA
Found at i:1118269 original size:22 final size:18
Alignment explanation
Indices: 1118160--1118284 Score: 70
Period size: 18 Copynumber: 6.2 Consensus size: 18
1118150 TATTTACATA
* *
1118160 TTTTTATGTTATAATAAT
1 TTTTTATATTTTAATAAT
* *
1118178 ATTTTATATTTATACATAAA
1 TTTTTATATTT-TA-ATAAT
* * *
1118198 TTTTAAAATATTAATAATT
1 TTTTTATATTTTAATAA-T
1118217 TATATTCTATAAATTTTAATAAT
1 T-T-TT-TAT--ATTTTAATAAT
1118240 TTTTTATATTTTAATATATT
1 TTTTTATATTTTAATA-A-T
1118260 TTATATTATATTTTAATTAAT
1 TT-T-TTATATTTTAA-TAAT
1118281 TTTT
1 TTTT
1118285 ATTTCTTATA
Statistics
Matches: 82, Mismatches: 12, Indels: 25
0.69 0.10 0.21
Matches are distributed among these distances:
18 21 0.26
19 7 0.09
20 19 0.23
21 8 0.10
22 14 0.17
23 4 0.05
24 9 0.11
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (18 bp):
TTTTTATATTTTAATAAT
Found at i:1118271 original size:12 final size:11
Alignment explanation
Indices: 1118243--1118283 Score: 59
Period size: 10 Copynumber: 3.8 Consensus size: 11
1118233 TAATAATTTT
1118243 TTATATTTTAA
1 TTATATTTTAA
1118254 -TATATTTTATA
1 TTATATTTTA-A
1118265 TTATATTTTAA
1 TTATATTTTAA
1118276 TTA-ATTTT
1 TTATATTTT
1118284 TATTTCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 14 0.50
11 5 0.18
12 9 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATATTTTAA
Found at i:1118572 original size:18 final size:18
Alignment explanation
Indices: 1118538--1118575 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1118528 TCTTAGGAAG
1118538 AAGAAAAACAGGAAAAGA
1 AAGAAAAACAGGAAAAGA
*
1118556 AAGAAGAAA-AGGGAAAGA
1 AAGAA-AAACAGGAAAAGA
1118574 AA
1 AA
1118576 TGGCAAGAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (18 bp):
AAGAAAAACAGGAAAAGA
Found at i:1121004 original size:10 final size:10
Alignment explanation
Indices: 1120989--1121017 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
1120979 AATTGGATTC
1120989 TTTGTTTTGT
1 TTTGTTTTGT
1120999 TTTGTTTTG-
1 TTTGTTTTGT
1121008 TTTGTTTTGT
1 TTTGTTTTGT
1121018 CCATAGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (10 bp):
TTTGTTTTGT
Found at i:1121013 original size:4 final size:5
Alignment explanation
Indices: 1120989--1121017 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1120979 AATTGGATTC
1120989 TTTGT TTTGT TTTGT TTTG- TTTGT TTTGT
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT
1121018 CCATAGTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (5 bp):
TTTGT
Found at i:1125238 original size:14 final size:14
Alignment explanation
Indices: 1125219--1125246 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1125209 TATTTGTATT
1125219 TCTTTTTCTTTTTA
1 TCTTTTTCTTTTTA
1125233 TCTTTTTCTTTTTA
1 TCTTTTTCTTTTTA
1125247 AAGATTGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (14 bp):
TCTTTTTCTTTTTA
Found at i:1130673 original size:9 final size:9
Alignment explanation
Indices: 1130659--1130691 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1130649 TTCAATGGAG
1130659 ATTTTTCTC
1 ATTTTTCTC
1130668 ATTTTTCTC
1 ATTTTTCTC
1130677 ATTTCTT-TC
1 ATTT-TTCTC
1130686 ATTTTT
1 ATTTTT
1130692 TTTTCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (9 bp):
ATTTTTCTC
Found at i:1134779 original size:2 final size:2
Alignment explanation
Indices: 1134772--1134805 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1134762 AATTATTTCA
1134772 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
1134806 TTCTTAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1135119 original size:42 final size:43
Alignment explanation
Indices: 1135066--1135148 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 43
1135056 TATTTTTTTG
*
1135066 AAAAAATGTTGACATTTTTC-ATAGAAAATTAAAGATATTTTCT
1 AAAAAATGTTGACA-TTTTCAATAGAAAACTAAAGATATTTTCT
* * *
1135109 AAAAAA-GTTGAGATTTTCAATGGAAAACTGAAGATATTTT
1 AAAAAATGTTGACATTTTCAATAGAAAACTAAAGATATTTT
1135149 TAATGTTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 5 0.14
42 24 0.69
43 6 0.17
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (43 bp):
AAAAAATGTTGACATTTTCAATAGAAAACTAAAGATATTTTCT
Found at i:1135330 original size:23 final size:24
Alignment explanation
Indices: 1135290--1135335 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1135280 TTATTTTAAT
1135290 ATTTTTAATAAAATTAATAATATA
1 ATTTTTAATAAAATTAATAATATA
*
1135314 ATTTTTAATAATA-TAATAATAT
1 ATTTTTAATAAAATTAATAATAT
1135336 TTTAAATTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTTTTAATAAAATTAATAATATA
Found at i:1140955 original size:48 final size:47
Alignment explanation
Indices: 1140857--1140956 Score: 121
Period size: 48 Copynumber: 2.1 Consensus size: 47
1140847 AAGTGGTGGC
** * *
1140857 TGTGGTGCAGGATGTGGAAACATAGCAAGAGCGGTAGCTGTGGTGGT
1 TGTGGTGCAGGATGCAGAAACATAGCAAGAGCGGTAGCTGTGGCGAT
* *
1140904 TGTGGTGCAGGATGCAGAAACATGATG-AAGAGTGGTAGTTGTGGCGAT
1 TGTGGTGCAGGATGCAGAAACAT-A-GCAAGAGCGGTAGCTGTGGCGAT
1140952 TGTGG
1 TGTGG
1140957 AAGCATGCTG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
47 21 0.47
48 23 0.51
49 1 0.02
ACGTcount: A:0.24, C:0.09, G:0.42, T:0.25
Consensus pattern (47 bp):
TGTGGTGCAGGATGCAGAAACATAGCAAGAGCGGTAGCTGTGGCGAT
Found at i:1142947 original size:24 final size:24
Alignment explanation
Indices: 1142894--1142948 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
1142884 TAGAATAAAG
1142894 TATTATAA-TTTGATAATAAAAAAT
1 TATTA-AATTTTGATAATAAAAAAT
* * *
1142918 TA-TAAATTTTGATATTTAAAATT
1 TATTAAATTTTGATAATAAAAAAT
1142941 TATTAAAT
1 TATTAAAT
1142949 ATTAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 2 0.08
23 17 0.65
24 7 0.27
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
TATTAAATTTTGATAATAAAAAAT
Found at i:1144750 original size:2 final size:2
Alignment explanation
Indices: 1144743--1144772 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1144733 TGTGCAGACT
1144743 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1144773 TTCATTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1152773 original size:2 final size:2
Alignment explanation
Indices: 1152766--1152790 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1152756 TTCTTGCAAC
1152766 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 A
1152791 AAGGCAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1152937 original size:2 final size:2
Alignment explanation
Indices: 1152930--1152963 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1152920 TTCCTGCTCA
1152930 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
1152964 CGTACCTGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1153501 original size:18 final size:18
Alignment explanation
Indices: 1153478--1153513 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1153468 TAAGTTTCAG
* *
1153478 TATTTATATTTATATATA
1 TATTTAAATTTAAATATA
1153496 TATTTAAATTTAAATATA
1 TATTTAAATTTAAATATA
1153514 ATGATATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTAAATTTAAATATA
Found at i:1153572 original size:20 final size:21
Alignment explanation
Indices: 1153540--1153578 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1153530 AGATTTAATT
*
1153540 TTTAAAAAGTAAATATATTTA
1 TTTAAAAAGTAAAAATATTTA
1153561 TTTAAAAA-TAAAAATATT
1 TTTAAAAAGTAAAAATATT
1153579 CATAAATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (21 bp):
TTTAAAAAGTAAAAATATTTA
Found at i:1154089 original size:17 final size:17
Alignment explanation
Indices: 1154067--1154100 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1154057 AATAATTAAA
*
1154067 TTATAATTAAATAATTT
1 TTATAATAAAATAATTT
*
1154084 TTATAATAAAATTATTT
1 TTATAATAAAATAATTT
1154101 AATAAATTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATAATAAAATAATTT
Found at i:1154121 original size:18 final size:18
Alignment explanation
Indices: 1154095--1154136 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1154085 TATAATAAAA
* *
1154095 TTATTTAATAAATTGATT
1 TTATATAATAAATTAATT
1154113 TTATATAATAAATTAATT
1 TTATATAATAAATTAATT
1154131 TTATAT
1 TTATAT
1154137 CATTTTGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TTATATAATAAATTAATT
Found at i:1154840 original size:17 final size:18
Alignment explanation
Indices: 1154809--1154842 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1154799 TATTAATACG
1154809 AAAACATTTAGTTTTAAT
1 AAAACATTTAGTTTTAAT
*
1154827 AAAA-ATTTATTTTTAA
1 AAAACATTTAGTTTTAA
1154843 GTTATGATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
AAAACATTTAGTTTTAAT
Found at i:1155394 original size:15 final size:16
Alignment explanation
Indices: 1155365--1155450 Score: 97
Period size: 16 Copynumber: 5.4 Consensus size: 16
1155355 ATCCAAATCA
1155365 AAAATAATTTAAATTC
1 AAAATAATTTAAATTC
*
1155381 AAAA-AATTTTAATTC
1 AAAATAATTTAAATTC
*
1155396 AAAATAACTTAAATAT-
1 AAAATAATTTAAAT-TC
*
1155412 AAAATAATTTAAATTT
1 AAAATAATTTAAATTC
*
1155428 AAAATATTTTAAACTT-
1 AAAATAATTTAAA-TTC
1155444 AAAATAA
1 AAAATAA
1155451 CCCTATTCTA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
15 15 0.25
16 42 0.70
17 3 0.05
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATAATTTAAATTC
Found at i:1156611 original size:5 final size:5
Alignment explanation
Indices: 1156598--1156648 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
1156588 AAATGATATT
*
1156598 ATTTG ATTTA ATTTTA ATTTA ATTTTA A-TT- ATTTA ATTTA ATTTTA
1 ATTTA ATTTA A-TTTA ATTTA A-TTTA ATTTA ATTTA ATTTA A-TTTA
1156644 ATTTA
1 ATTTA
1156649 GATAGTAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
3 1 0.03
4 4 0.10
5 20 0.50
6 15 0.38
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (5 bp):
ATTTA
Found at i:1156615 original size:6 final size:6
Alignment explanation
Indices: 1156604--1156647 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
1156594 TATTATTTGA
1156604 TTTAAT TTTAA- TTTAAT TTTAATT ATTTAA- TTTAAT TTTAAT TT
1 TTTAAT TTTAAT TTTAAT TTTAA-T -TTTAAT TTTAAT TTTAAT TT
1156648 AGATAGTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 10 0.29
6 18 0.53
7 1 0.03
8 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTAAT
Found at i:1156619 original size:11 final size:11
Alignment explanation
Indices: 1156603--1156648 Score: 71
Period size: 11 Copynumber: 4.5 Consensus size: 11
1156593 ATATTATTTG
1156603 ATTTAATTTTA
1 ATTTAATTTTA
1156614 ATTTAATTTTA
1 ATTTAATTTTA
1156625 A-TT-A-TTTA
1 ATTTAATTTTA
1156633 ATTTAATTTTA
1 ATTTAATTTTA
1156644 ATTTA
1 ATTTA
1156649 GATAGTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 5 0.16
9 3 0.09
10 3 0.09
11 21 0.66
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTTAATTTTA
Found at i:1156634 original size:19 final size:19
Alignment explanation
Indices: 1156610--1156646 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1156600 TTGATTTAAT
1156610 TTTAATTTAATTTTAATTA
1 TTTAATTTAATTTTAATTA
1156629 TTTAATTTAATTTTAATT
1 TTTAATTTAATTTTAATT
1156647 TAGATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTAATTTAATTTTAATTA
Found at i:1157064 original size:20 final size:20
Alignment explanation
Indices: 1157039--1157098 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
1157029 ATTCAATATT
1157039 ATTAAAAAAAT-TTATATTAA
1 ATTAAAAAAATATTAT-TTAA
* *
1157059 ATTAAAAATATATTATTTTA
1 ATTAAAAAAATATTATTTAA
1157079 ATT--AAAAATATTACTTTAA
1 ATTAAAAAAATATTA-TTTAA
1157098 A
1 A
1157099 ACAAATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
18 9 0.26
19 5 0.15
20 16 0.47
21 4 0.12
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTAAAAAAATATTATTTAA
Found at i:1157074 original size:21 final size:19
Alignment explanation
Indices: 1157039--1157090 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
1157029 ATTCAATATT
*
1157039 ATTAAAAAAATTTATATTAA
1 ATTAAAAATATTTAT-TTAA
*
1157059 ATTAAAAATATATTATTTTA
1 ATTAAAAATAT-TTATTTAA
1157079 ATTAAAAATATT
1 ATTAAAAATATT
1157091 ACTTTAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 24 0.83
21 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTAAAAATATTTATTTAA
Found at i:1157091 original size:18 final size:19
Alignment explanation
Indices: 1157043--1157097 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
1157033 AATATTATTA
*
1157043 AAAAAAT-TTATATTAAATT
1 AAAAAATATTAT-TTTAATT
1157062 AAAAATATATTATTTTAATT
1 AAAAA-ATATTATTTTAATT
*
1157082 -AAAAATATTACTTTAA
1 AAAAAATATTATTTTAA
1157098 AACAAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 11 0.34
19 9 0.28
20 8 0.25
21 4 0.12
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAAAATATTATTTTAATT
Found at i:1157573 original size:2 final size:2
Alignment explanation
Indices: 1157566--1157590 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1157556 ATCCATTAGC
1157566 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
1157591 ATGCAAAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1157683 original size:16 final size:17
Alignment explanation
Indices: 1157664--1157732 Score: 62
Period size: 16 Copynumber: 4.5 Consensus size: 17
1157654 AGTTTTAATT
1157664 TAATTAATTA-ATTTAA
1 TAATTAATTATATTTAA
*
1157680 TAATT-TTTATATTT-A
1 TAATTAATTATATTTAA
1157695 T-A-T-ATTATATTTAA
1 TAATTAATTATATTTAA
* *
1157709 T-ATTAAATATAATTAA
1 TAATTAATTATATTTAA
1157725 TAATTAAT
1 TAATTAAT
1157733 AAAAATATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
13 9 0.21
14 4 0.09
15 6 0.14
16 19 0.44
17 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAATTAATTATATTTAA
Found at i:1158727 original size:26 final size:29
Alignment explanation
Indices: 1158702--1158761 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
1158692 TATTATTAAT
* *
1158702 TTTTAA-ATTTATTATTAAAATATAATTA
1 TTTTAAGATATATTATCAAAATATAATTA
*
1158730 TTTTAAGATATATTATCAAAATATTATTA
1 TTTTAAGATATATTATCAAAATATAATTA
1158759 TTT
1 TTT
1158762 CATATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (29 bp):
TTTTAAGATATATTATCAAAATATAATTA
Found at i:1158833 original size:23 final size:23
Alignment explanation
Indices: 1158788--1158833 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1158778 ATATTCATAC
*
1158788 TTTATATAATAAAAAAATTTATA
1 TTTATATAATAAAAAAATGTATA
*
1158811 TTTATATTATAAAATAAA-GTATA
1 TTTATATAATAAAA-AAATGTATA
1158834 AATATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTATATAATAAAAAAATGTATA
Found at i:1158918 original size:14 final size:14
Alignment explanation
Indices: 1158899--1158953 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 14
1158889 AAATTAATAA
1158899 AATAATAAAATTTT
1 AATAATAAAATTTT
*
1158913 AATAAT-ATATTTT
1 AATAATAAAATTTT
1158926 AA-AATAATAATATTT
1 AATAATAA-AAT-TTT
1158941 AGATAATAAAATT
1 A-ATAATAAAATT
1158954 AAATATTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
12 3 0.09
13 9 0.26
14 8 0.24
15 5 0.15
16 4 0.12
17 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
AATAATAAAATTTT
Found at i:1159511 original size:21 final size:21
Alignment explanation
Indices: 1159485--1159526 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1159475 TTATTATTAA
*
1159485 AATTATTAAAATTTTATTTTT
1 AATTATTAAAATTTAATTTTT
1159506 AATTATTAAAATTTAATTTTT
1 AATTATTAAAATTTAATTTTT
1159527 TGTTAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTATTAAAATTTAATTTTT
Found at i:1159612 original size:37 final size:38
Alignment explanation
Indices: 1159571--1159663 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 38
1159561 AATAAAAACC
* * * *
1159571 AAATTCAACTTGATAATTTACTTAAATAATTTAAAA-T
1 AAATTAAACTTGATAATTGAATTAAATAATTCAAAATT
* * *
1159608 AAATTAAATTTGATAAATGAATTGAATAATTCAAAATT
1 AAATTAAACTTGATAATTGAATTAAATAATTCAAAATT
*
1159646 AAGTTAAACTTGATAATT
1 AAATTAAACTTGATAATT
1159664 AATAAACAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
37 29 0.64
38 16 0.36
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.39
Consensus pattern (38 bp):
AAATTAAACTTGATAATTGAATTAAATAATTCAAAATT
Found at i:1161103 original size:2 final size:2
Alignment explanation
Indices: 1161096--1161122 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1161086 AGCTTTTGTT
1161096 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 T
1161123 CATGCTGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1162909 original size:18 final size:17
Alignment explanation
Indices: 1162844--1162910 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
1162834 TTTAATATTT
1162844 TAAA-ATTTTATATAAAAA
1 TAAATATTTT-TA-AAAAA
* *
1162862 TATTATATTTTAAAAAAA
1 TA-AATATTTTTAAAAAA
1162880 TAAAT-TTATTTAAAAAA
1 TAAATATT-TTTAAAAAA
1162897 TAAATAATTTTTAA
1 TAAAT-ATTTTTAA
1162911 TTTTAATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
16 2 0.05
17 15 0.38
18 14 0.35
19 4 0.10
20 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATATTTTTAAAAAA
Found at i:1163526 original size:12 final size:13
Alignment explanation
Indices: 1163498--1163538 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
1163488 GATATAGATA
*
1163498 ATAAAAATTAATT
1 ATAAATATTAATT
1163511 -TAAAT-TTAATT
1 ATAAATATTAATT
1163522 ATAAATATTAA-T
1 ATAAATATTAATT
1163534 ATAAA
1 ATAAA
1163539 ATAATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 6 0.24
12 15 0.60
13 4 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATAAATATTAATT
Found at i:1165908 original size:16 final size:16
Alignment explanation
Indices: 1165887--1165921 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1165877 TGGATAGTGA
1165887 CTTCTTGTCTTTTAAT
1 CTTCTTGTCTTTTAAT
1165903 CTTCTTGTCTTTTAAT
1 CTTCTTGTCTTTTAAT
1165919 CTT
1 CTT
1165922 TGAATAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.20, G:0.06, T:0.63
Consensus pattern (16 bp):
CTTCTTGTCTTTTAAT
Found at i:1165982 original size:18 final size:19
Alignment explanation
Indices: 1165954--1165992 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
1165944 GTAATCTCTC
1165954 TAAATTTTTTTTAAGTATT
1 TAAATTTTTTTTAAGTATT
1165973 TAAA-TTTTTTTAAGTATT
1 TAAATTTTTTTTAAGTATT
1165991 TA
1 TA
1165993 TGTTTGATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TAAATTTTTTTTAAGTATT
Found at i:1167034 original size:2 final size:2
Alignment explanation
Indices: 1167027--1167059 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1167017 ACTACAAGTA
1167027 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
1167060 CACACACTGT
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:1168984 original size:20 final size:20
Alignment explanation
Indices: 1168959--1168996 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1168949 AAAAATATCT
1168959 TAAATTATTT-TATTTTTAAA
1 TAAATT-TTTATATTTTTAAA
1168979 TAAATTTTTATATTTTTA
1 TAAATTTTTATATTTTTA
1168997 TTGTACGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TAAATTTTTATATTTTTAAA
Found at i:1168992 original size:25 final size:26
Alignment explanation
Indices: 1168964--1169028 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 26
1168954 TATCTTAAAT
*
1168964 TATTTTATTT-TTAAATAAATTTTTA
1 TATTTTATTTAGTAAATAAATTTTTA
1168989 TATTTTTATTGTACGTAAATAAATTTTTA
1 TA-TTTTATT-TA-GTAAATAAATTTTTA
*
1169018 TCTTTTGATTT
1 TATTTT-ATTT
1169029 GTATCTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
25 2 0.06
26 7 0.21
27 1 0.03
28 5 0.15
29 18 0.55
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (26 bp):
TATTTTATTTAGTAAATAAATTTTTA
Found at i:1169007 original size:29 final size:30
Alignment explanation
Indices: 1168975--1169048 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
1168965 ATTTTATTTT
*
1168975 TAAATAAATTTTTATATTTTTA-TTGTA-C
1 TAAATAAATTTTTATATTTTGATTTGTATC
*
1169003 GTAAATAAATTTTTATCTTTTGATTTGTATC
1 -TAAATAAATTTTTATATTTTGATTTGTATC
*
1169034 TAAATAAGTTTTTAT
1 TAAATAAATTTTTAT
1169049 TATGAAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 20 0.50
30 19 0.47
31 1 0.03
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (30 bp):
TAAATAAATTTTTATATTTTGATTTGTATC
Found at i:1169095 original size:28 final size:27
Alignment explanation
Indices: 1169059--1169113 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
1169049 TATGAAATTT
**
1169059 TAATTTATATTAAGGTTTACTTAAATA
1 TAATTTATATTAAAATTTACTTAAATA
*
1169086 TAATTATATATTAAAATTTATTTAAATA
1 TAATT-TATATTAAAATTTACTTAAATA
1169114 CAAGTTAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (27 bp):
TAATTTATATTAAAATTTACTTAAATA
Found at i:1169134 original size:30 final size:30
Alignment explanation
Indices: 1169098--1169160 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1169088 ATTATATATT
* *
1169098 AAAATTTATT-TAAATACAAGTTAAAGATTA
1 AAAATTTATTAT-AATACAAATTAAAAATTA
*
1169128 AAAATTTATTATGATACAAATTAAAAATTA
1 AAAATTTATTATAATACAAATTAAAAATTA
1169158 AAA
1 AAA
1169161 CAATATTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (30 bp):
AAAATTTATTATAATACAAATTAAAAATTA
Found at i:1169168 original size:30 final size:30
Alignment explanation
Indices: 1169111--1169168 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1169101 ATTTATTTAA
* * *
1169111 ATACAAGTTAAAGATTAAAAATTTATTATG
1 ATACAAATTAAAAATTAAAAATATATTATG
1169141 ATACAAATTAAAAATTAAAACA-ATATTA
1 ATACAAATTAAAAATTAAAA-ATATATTA
1169169 ATACGTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (30 bp):
ATACAAATTAAAAATTAAAAATATATTATG
Found at i:1169902 original size:21 final size:22
Alignment explanation
Indices: 1169878--1169922 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1169868 TTTTATTTAA
1169878 ATTAATTTAAAA-ATTAATTTT
1 ATTAATTTAAAATATTAATTTT
* *
1169899 ATTATTTTAAAATATTATTTTT
1 ATTAATTTAAAATATTAATTTT
1169921 AT
1 AT
1169923 ATTAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTAATTTAAAATATTAATTTT
Found at i:1169920 original size:14 final size:14
Alignment explanation
Indices: 1169898--1169939 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1169888 AAATTAATTT
1169898 TATTA-TTTTAAAA
1 TATTATTTTTAAAA
* *
1169911 TATTATTTTTATAT
1 TATTATTTTTAAAA
*
1169925 TAATATTTTTAAAA
1 TATTATTTTTAAAA
1169939 T
1 T
1169940 TAAATTTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTATTTTTAAAA
Found at i:1169963 original size:16 final size:16
Alignment explanation
Indices: 1169934--1169996 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
1169924 TTAATATTTT
* *
1169934 TAAAATTAAATTTAAA
1 TAAAAATAATTTTAAA
1169950 TAAAAATAATTTTATTAA
1 TAAAAATAATTTTA--AA
1169968 TAAATAATAA-TTTAAA
1 TAAA-AATAATTTTAAA
*
1169984 TTAAAA-AATTTTA
1 TAAAAATAATTTTA
1169997 TCTAAATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
14 2 0.05
15 6 0.15
16 17 0.43
18 10 0.25
19 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAAATAATTTTAAA
Found at i:1170251 original size:11 final size:11
Alignment explanation
Indices: 1170231--1170271 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 11
1170221 TAATCGATAA
1170231 TTTA-TATATT
1 TTTATTATATT
1170241 TTTATTATATT
1 TTTATTATATT
*
1170252 TATATTA-ATT
1 TTTATTATATT
1170262 TTTATT-TATT
1 TTTATTATATT
1170272 AATTATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 15 0.56
11 12 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATTATATT
Found at i:1170345 original size:9 final size:8
Alignment explanation
Indices: 1170311--1170439 Score: 52
Period size: 9 Copynumber: 15.5 Consensus size: 8
1170301 TAAAATTTTG
1170311 ATATA-TT
1 ATATATTT
1170318 ATA-ATTT
1 ATATATTT
*
1170325 TTATTATTT
1 ATA-TATTT
*
1170334 ATAT-TTA
1 ATATATTT
1170341 ATATATTT
1 ATATATTT
1170349 ATATATTAT
1 ATATATT-T
* *
1170358 GTTTATTTT
1 ATATA-TTT
*
1170367 TTATATTAT
1 ATATATT-T
1170376 ATCATATTT
1 AT-ATATTT
*
1170385 -TATATTA
1 ATATATTT
1170392 ATAT-TTT
1 ATATATTT
*
1170399 AATTATTTTT
1 -A-TATATTT
1170409 ATATAATTAT
1 ATAT-ATT-T
*
1170419 ATTTATTTT
1 ATATA-TTT
*
1170428 ATATAATT
1 ATATATTT
1170436 ATAT
1 ATAT
1170440 TATATTTAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 29
0.68 0.11 0.21
Matches are distributed among these distances:
6 1 0.01
7 20 0.22
8 26 0.28
9 29 0.32
10 16 0.17
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.63
Consensus pattern (8 bp):
ATATATTT
Found at i:1170370 original size:35 final size:35
Alignment explanation
Indices: 1170324--1170391 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 35
1170314 TATTATAATT
1170324 TTTATTATTTATATT-TAAT-ATATTTATATATTATG
1 TTTATTATTTATATTAT-ATCATATTT-TATATTATG
*
1170359 TTTATTTTTTATATTATATCATATTTTATATTA
1 TTTATTATTTATATTATATCATATTTTATATTA
1170392 ATATTTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 23 0.77
36 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (35 bp):
TTTATTATTTATATTATATCATATTTTATATTATG
Found at i:1170387 original size:12 final size:12
Alignment explanation
Indices: 1170329--1170415 Score: 52
Period size: 13 Copynumber: 7.1 Consensus size: 12
1170319 TAATTTTTAT
*
1170329 TATTTATATTTAA
1 TATTT-TATATAA
*
1170342 TATATTTATATAT
1 TAT-TTTATATAA
* **
1170355 TATGTTTATTTTT
1 TAT-TTTATATAA
* *
1170368 TATATTATATCA
1 TATTTTATATAA
1170380 TATTTTATATTAA
1 TATTTTATA-TAA
*
1170393 TATTTTA-ATTA
1 TATTTTATATAA
1170404 T-TTTTATATAA
1 TATTTTATATAA
1170415 T
1 T
1170416 TATATTTATT
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
10 5 0.09
11 7 0.12
12 14 0.24
13 30 0.52
14 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (12 bp):
TATTTTATATAA
Found at i:1170442 original size:38 final size:40
Alignment explanation
Indices: 1170321--1170454 Score: 104
Period size: 41 Copynumber: 3.4 Consensus size: 40
1170311 ATATATTATA
* **
1170321 ATTTTTAT-TATTTATATTTAATATATT-TATATATTATGTTT
1 ATTTTTATATAATTATATTT-AT-T-TTATATATATTATAATT
* *
1170362 ATTTTT-TAT-ATTATATCATATTTTATATTAATATTTTAATT
1 ATTTTTATATAATTATAT-TTATTTTATA-T-ATATTATAATT
1170403 ATTTTTATATAATTATATTTATTTTATATA-ATTAT-ATT
1 ATTTTTATATAATTATATTTATTTTATATATATTATAATT
*
1170441 ATATTTA-A-AATTAT
1 ATTTTTATATAATTAT
1170455 CATATAAATT
Statistics
Matches: 78, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
36 6 0.08
37 1 0.01
38 11 0.14
39 7 0.09
40 11 0.14
41 23 0.29
42 12 0.15
43 7 0.09
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.63
Consensus pattern (40 bp):
ATTTTTATATAATTATATTTATTTTATATATATTATAATT
Found at i:1170465 original size:62 final size:60
Alignment explanation
Indices: 1170346--1170466 Score: 145
Period size: 62 Copynumber: 2.0 Consensus size: 60
1170336 ATTTAATATA
* * * * * *
1170346 TTTATATATTATGTTTATTTTTTATATTATATCATATTTTATATTAATATTTTAATTATT
1 TTTATATATTATATTTATTTTATATATTATATCATATTTAAAATTAATATATAAATTATT
*
1170406 TTTATATAATTATATTTATTTTATATAATTATATTATATTTAAAATT-ATCATATAAATTAT
1 TTTATAT-ATTATATTTATTTTATAT-ATTATATCATATTTAAAATTAAT-ATATAAATTAT
1170467 ATATTAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
60 7 0.14
61 18 0.35
62 26 0.51
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (60 bp):
TTTATATATTATATTTATTTTATATATTATATCATATTTAAAATTAATATATAAATTATT
Found at i:1170755 original size:21 final size:22
Alignment explanation
Indices: 1170709--1170755 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1170699 CTACAGAAAG
** *
1170709 AAAATTACAAAAACAGTGGAAG
1 AAAATTACAAAAACAGTCCAAA
1170731 AAAATTACAAAAACAG-CCAAA
1 AAAATTACAAAAACAGTCCAAA
1170752 AAAA
1 AAAA
1170756 GATGAATTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.66, C:0.13, G:0.11, T:0.11
Consensus pattern (22 bp):
AAAATTACAAAAACAGTCCAAA
Found at i:1171043 original size:24 final size:24
Alignment explanation
Indices: 1171016--1171062 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1171006 GATGTGCAAG
1171016 AAATAAT-TAAAATATAAAATAAAA
1 AAATAATAT-AAATATAAAATAAAA
1171040 AAATAATATAAATATAAAATAAA
1 AAATAATATAAATATAAAATAAA
1171063 TATATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (24 bp):
AAATAATATAAATATAAAATAAAA
Found at i:1171058 original size:19 final size:19
Alignment explanation
Indices: 1171026--1171095 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
1171016 AAATAATTAA
1171026 AATATAAA-ATAAAAAAAT
1 AATATAAATATAAAAAAAT
1171044 AATATAAATATAAAATAAAT
1 AATATAAATATAAAA-AAAT
*
1171064 -ATATAAATATATTAAAAAT
1 AATATAAATATA-AAAAAAT
*
1171083 TATAT-AATATAAA
1 AATATAAATATAAA
1171096 TTATTAGTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
18 9 0.20
19 27 0.59
20 10 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AATATAAATATAAAAAAAT
Found at i:1171060 original size:13 final size:12
Alignment explanation
Indices: 1171023--1171070 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
1171013 AAGAAATAAT
1171023 TAAAATATAAAA
1 TAAAATATAAAA
1171035 TAAAA-A-AATAA
1 TAAAATATAA-AA
1171046 TATAAATATAAAA
1 TA-AAATATAAAA
1171059 TAAATATATAAA
1 TAAA-ATATAAA
1171071 TATATTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
10 2 0.06
11 5 0.16
12 10 0.32
13 12 0.39
14 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
TAAAATATAAAA
Found at i:1171069 original size:24 final size:24
Alignment explanation
Indices: 1171025--1171096 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 24
1171015 GAAATAATTA
* *
1171025 AAATATAAAATAAAAAAATAATAT
1 AAATATAAAATAAATATATAATAT
1171049 AAATATAAAATAAATATATAA-AT
1 AAATATAAAATAAATATATAATAT
* *
1171072 --ATATTAAA-AATTATATAATAT
1 AAATATAAAATAAATATATAATAT
1171093 AAAT
1 AAAT
1171097 TATTAGTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 9 0.22
21 9 0.22
23 4 0.10
24 19 0.46
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATATAAAATAAATATATAATAT
Found at i:1171681 original size:75 final size:75
Alignment explanation
Indices: 1171531--1171689 Score: 187
Period size: 75 Copynumber: 2.1 Consensus size: 75
1171521 GTAACCATAA
* * * *
1171531 TGAGTGTTGGCAATCAAGATTTCATCTTTTTAGAGATCAGGATTTATGTGGCGAGCACAAGTCTA
1 TGAGTGTTGGCAATCAAGATTTCATCTTTTTAGAGACCAGGATTTAAGTGACGAGCACAAGTATA
*
1171596 GCAACTAGAG
66 GCAACCAGAG
* * * *
1171606 TGAGTGTTGGTAATCAAGATTTCGTCTTTTT-GGGAACCAGGATTTAAGTGACGAGCATAAGTAT
1 TGAGTGTTGGCAATCAAGATTTCATCTTTTTAGAG-ACCAGGATTTAAGTGACGAGCACAAGTAT
*
1171670 -GACAGCCAGAG
65 AG-CAACCAGAG
*
1171681 TGAATGTTG
1 TGAGTGTTG
1171690 ATGATCAGGG
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
74 3 0.04
75 68 0.96
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (75 bp):
TGAGTGTTGGCAATCAAGATTTCATCTTTTTAGAGACCAGGATTTAAGTGACGAGCACAAGTATA
GCAACCAGAG
Found at i:1172475 original size:11 final size:11
Alignment explanation
Indices: 1172459--1172527 Score: 61
Period size: 11 Copynumber: 6.1 Consensus size: 11
1172449 TTTGGATGCA
1172459 ATAAAAAATAT
1 ATAAAAAATAT
1172470 ATAAAAAATATT
1 ATAAAAAATA-T
*
1172482 TTAAATTAAATAT
1 ATAAA--AAATAT
*
1172495 -TAATAAATA-
1 ATAAAAAATAT
1172504 ATAAATAAATAT
1 ATAAA-AAATAT
*
1172516 TTAAAAAATAT
1 ATAAAAAATAT
1172527 A
1 A
1172528 ATTAAAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
10 8 0.17
11 21 0.45
12 12 0.26
13 1 0.02
14 5 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAAAAAATAT
Found at i:1172513 original size:21 final size:21
Alignment explanation
Indices: 1172459--1172533 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 21
1172449 TTTGGATGCA
*
1172459 ATAAA-AAATATATAAAAAAT
1 ATAAATAAATATTTAAAAAAT
*
1172479 ATTTTAAATTAAATA-TTAATAAAT
1 A---TAAA-TAAATATTTAAAAAAT
1172503 AATAAATAAATATTTAAAAAAT
1 -ATAAATAAATATTTAAAAAAT
*
1172525 ATAATTAAA
1 ATAAATAAA
1172534 ATAAAAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
20 1 0.02
21 14 0.32
22 12 0.27
23 4 0.09
24 7 0.16
25 6 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAATAAATATTTAAAAAAT
Found at i:1172535 original size:22 final size:21
Alignment explanation
Indices: 1172485--1172546 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1172475 AAATATTTTA
*
1172485 AATTAAATATTAATAAATAAT
1 AATTAAATATTAAAAAATAAT
*
1172506 AAATAAATATTTAAAAAAT-AT
1 AATTAAATA-TTAAAAAATAAT
1172527 AATTAAA-A-TAAAAATATAAT
1 AATTAAATATTAAAAA-ATAAT
1172547 TGCATTTCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
18 6 0.17
19 2 0.06
20 3 0.09
21 16 0.46
22 8 0.23
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AATTAAATATTAAAAAATAAT
Found at i:1173177 original size:22 final size:20
Alignment explanation
Indices: 1173125--1173195 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
1173115 TTATTATAAT
* *
1173125 TATATATAT-AATTATTATA
1 TATATATATAAATTTTTAAA
*
1173144 TATTTATATAAATTTTAATAAA
1 TATATATATAAATTTT--TAAA
*
1173166 TATATATGTAAATTTTTAAA
1 TATATATATAAATTTTTAAA
*
1173186 TATTTATATA
1 TATATATATA
1173196 TTTATATTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 8 0.19
20 17 0.40
22 17 0.40
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (20 bp):
TATATATATAAATTTTTAAA
Found at i:1173186 original size:30 final size:29
Alignment explanation
Indices: 1173152--1173208 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
1173142 TATATTTATA
1173152 TAAAT-TTTAATAAATATATATGTAAATTTT
1 TAAATATTT-ATAAATATATAT-TAAATTTT
* *
1173182 TAAATATTTATATATTTATATTAAATT
1 TAAATATTTATAAATATATATTAAATT
1173209 AAGTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.25
30 15 0.62
31 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (29 bp):
TAAATATTTATAAATATATATTAAATTTT
Found at i:1173242 original size:18 final size:18
Alignment explanation
Indices: 1173216--1173254 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1173206 ATTAAGTAAT
*
1173216 TTTTTATTTTATATTATA
1 TTTTAATTTTATATTATA
*
1173234 TTTTAATTTTTTATTATA
1 TTTTAATTTTATATTATA
1173252 TTT
1 TTT
1173255 ATATTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTAATTTTATATTATA
Found at i:1173245 original size:25 final size:24
Alignment explanation
Indices: 1173212--1173259 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
1173202 TTAAATTAAG
*
1173212 TAATTTTTTATTTTATATTATATTT
1 TAATTTTTTATTATAT-TTATATTT
1173237 TAATTTTTTATTATATTTATATT
1 TAATTTTTTATTATATTTATATT
1173260 AAATAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (24 bp):
TAATTTTTTATTATATTTATATTT
Found at i:1173406 original size:21 final size:22
Alignment explanation
Indices: 1173382--1173426 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1173372 TTTTAACGTG
1173382 AAAATTTAAA-ATAAAAAATAA
1 AAAATTTAAATATAAAAAATAA
* *
1173403 AAAATTTAAATTTTAAAAATAA
1 AAAATTTAAATATAAAAAATAA
1173425 AA
1 AA
1173427 TGGGAGACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATTTAAATATAAAAAATAA
Found at i:1174064 original size:34 final size:32
Alignment explanation
Indices: 1174021--1174084 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 32
1174011 TTCCTTCAGC
*
1174021 AAATCAATCTGATCTTATATTTAAAAAAAAAAAA
1 AAATCAATCTGATCTTAGA--TAAAAAAAAAAAA
1174055 AAATCAATCTGATCTTAGATAAAAAAAAAA
1 AAATCAATCTGATCTTAGATAAAAAAAAAA
1174085 TCCAATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 11 0.38
34 18 0.62
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27
Consensus pattern (32 bp):
AAATCAATCTGATCTTAGATAAAAAAAAAAAA
Found at i:1175818 original size:2 final size:2
Alignment explanation
Indices: 1175813--1175845 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1175803 ATATATATAT
1175813 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1175846 TGTTTAACCA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1176630 original size:27 final size:25
Alignment explanation
Indices: 1176584--1176634 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
1176574 AAACAAGGTA
1176584 TAAATATTAATATAAAATATTTTTT
1 TAAATATTAATATAAAATATTTTTT
1176609 TAAA-ATTAATAATGAAACATATTTTT
1 TAAATATTAAT-AT-AAA-ATATTTTT
1176635 AAATTTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.26
25 6 0.26
26 3 0.13
27 8 0.35
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
TAAATATTAATATAAAATATTTTTT
Found at i:1179386 original size:8 final size:8
Alignment explanation
Indices: 1179350--1179415 Score: 50
Period size: 8 Copynumber: 8.6 Consensus size: 8
1179340 ATATATTCAA
1179350 ATATAAAT
1 ATATAAAT
1179358 ATA-AAA-
1 ATATAAAT
*
1179364 ATATAATT
1 ATATAAAT
* *
1179372 TTTTAAAT
1 ATATAAAT
1179380 ATATAAA-
1 ATATAAAT
*
1179387 AAATTAAAT
1 ATA-TAAAT
*
1179396 ATATTAAT
1 ATATAAAT
1179404 AT-TAAAT
1 ATATAAAT
1179411 ATATA
1 ATATA
1179416 TTCGATACTT
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
6 3 0.07
7 13 0.30
8 25 0.58
9 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Found at i:1179409 original size:15 final size:16
Alignment explanation
Indices: 1179374--1179415 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
1179364 ATATAATTTT
1179374 TTAAATATATAAAAAA
1 TTAAATATATAAAAAA
* *
1179390 TTAAATATAT-TAATA
1 TTAAATATATAAAAAA
1179405 TTAAATATATA
1 TTAAATATATA
1179416 TTCGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAATATATAAAAAA
Done.