Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008194.1 Hibiscus syriacus cultivar Beakdansim tig00110813_pilon, whole genome shotgun sequence
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: 2426039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 13
Found at i:999691 original size:2 final size:2
Alignment explanation
Indices: 999684--999719 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
999674 AGACAAGTTC
999684 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
999720 CAGTATAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:999902 original size:14 final size:14
Alignment explanation
Indices: 999872--999901 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
999862 CCTAAGATAA
999872 TTTATTAGATATTT
1 TTTATTAGATATTT
999886 TTTATTA-ATATTT
1 TTTATTAGATATTT
999899 TTT
1 TTT
999902 TTATGTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTATTAGATATTT
Found at i:1000138 original size:21 final size:22
Alignment explanation
Indices: 1000105--1000154 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
1000095 ATTTTTAATT
* * *
1000105 TTAATAATTGAAAGTTTAGGTGA
1 TTAA-AATCGAAAATTTAGATGA
1000128 -TAAAATCGAAAATTTAGATGA
1 TTAAAATCGAAAATTTAGATGA
1000149 TTAAAA
1 TTAAAA
1000155 AATATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (22 bp):
TTAAAATCGAAAATTTAGATGA
Found at i:1015266 original size:314 final size:314
Alignment explanation
Indices: 1014697--1015325 Score: 1222
Period size: 314 Copynumber: 2.0 Consensus size: 314
1014687 CATTCCCTAT
*
1014697 GGTCAATAACATAGATGCTTATCTTGGAAGTTATTCATCTTTCAATCCATTGTCTGAAGATTTGG
1 GGTCAATAACATAGATGCTTATCTTGGAAGTTATTCATCTTTCAATCCATTGTCTGAAGATTTGC
1014762 GCTAATTAAGCCTCCAAATCTCAATCAAGTATTCAGTAGAAGACAAACGTATAAGGTGACAGGAA
66 GCTAATTAAGCCTCCAAATCTCAATCAAGTATTCAGTAGAAGACAAACGTATAAGGTGACAGGAA
*
1014827 GACAATTAAGGACAGCTACTAGAAGAAAGGCTTATTTAGTAGATGCCACTTAAGAAAAGAGTTCT
131 GACAATTAAGGACAGCTACTACAAGAAAGGCTTATTTAGTAGATGCCACTTAAGAAAAGAGTTCT
1014892 CAACACATAATAACAGCACATTGATCACTAAGACACTTTATCAATAATTCCCCCCATCAAATATC
196 CAACACATAATAACAGCACATTGATCACTAAGACACTTTATCAATAATTCCCCCCATCAAATATC
1014957 AATATCACAATCTTTTCAAAAGATTAAACACTTAGCAAAGACGGAAATGGGAAA
261 AATATCACAATCTTTTCAAAAGATTAAACACTTAGCAAAGACGGAAATGGGAAA
*
1015011 GGTCAATAACATAGATGCTTATCTTGGAAGTTATTCATCTTTCAATCCATTGTCTGAAGGTTTGC
1 GGTCAATAACATAGATGCTTATCTTGGAAGTTATTCATCTTTCAATCCATTGTCTGAAGATTTGC
1015076 GCTAATTAAGCCTCCAAATCTCAATCAAGTATTCAGTAGAAGACAAACGTATAAGGTGACAGGAA
66 GCTAATTAAGCCTCCAAATCTCAATCAAGTATTCAGTAGAAGACAAACGTATAAGGTGACAGGAA
*
1015141 GACAATTAAGGACAGCTACTACAAGAAAGGCTTATTTAGTAGATGCCTCTTAAGAAAAGAGTTCT
131 GACAATTAAGGACAGCTACTACAAGAAAGGCTTATTTAGTAGATGCCACTTAAGAAAAGAGTTCT
1015206 CAACACATAATAACAGCACATTGATCACTAAGACACTTTATCAATAATTCCCCCCATCAAATATC
196 CAACACATAATAACAGCACATTGATCACTAAGACACTTTATCAATAATTCCCCCCATCAAATATC
1015271 AATATCACAATCTTTTCAAAAGATTAAACACTTAGCAAAGACGGAAATGGGAAA
261 AATATCACAATCTTTTCAAAAGATTAAACACTTAGCAAAGACGGAAATGGGAAA
1015325 G
1 G
1015326 AATGATAACT
Statistics
Matches: 311, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
314 311 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (314 bp):
GGTCAATAACATAGATGCTTATCTTGGAAGTTATTCATCTTTCAATCCATTGTCTGAAGATTTGC
GCTAATTAAGCCTCCAAATCTCAATCAAGTATTCAGTAGAAGACAAACGTATAAGGTGACAGGAA
GACAATTAAGGACAGCTACTACAAGAAAGGCTTATTTAGTAGATGCCACTTAAGAAAAGAGTTCT
CAACACATAATAACAGCACATTGATCACTAAGACACTTTATCAATAATTCCCCCCATCAAATATC
AATATCACAATCTTTTCAAAAGATTAAACACTTAGCAAAGACGGAAATGGGAAA
Found at i:1018752 original size:14 final size:14
Alignment explanation
Indices: 1018715--1018758 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1018705 TTCAAATAAT
* *
1018715 TTAAATTAAACAAC
1 TTAAATTAAAAAAA
* *
1018729 TCAAACTAAAAAAA
1 TTAAATTAAAAAAA
1018743 TTAAATTAAAAAAA
1 TTAAATTAAAAAAA
1018757 TT
1 TT
1018759 TTATTCACTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (14 bp):
TTAAATTAAAAAAA
Found at i:1027424 original size:99 final size:98
Alignment explanation
Indices: 1027293--1027496 Score: 318
Period size: 99 Copynumber: 2.1 Consensus size: 98
1027283 CTGGAACTGG
*
1027293 GAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCCGTCTTGAGTCC
1 GAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCCGTCTTGAGTCC
*
1027358 AATATCCTTCGTTGTGAAGTTAAAATTGACTCT
66 AATATCATTCGTTGTGAAGTTAAAATTGACTCT
* ** *
1027391 GAAAGTTGTTTGTTGACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTC
1 GAAA-TTGTTTGTTGACAATCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCCGTCTTGAGTC
* **
1027456 CAATATCATTCGTTGTGAAGTTGAAATTGGTTCT
65 CAATATCATTCGTTGTGAAGTTAAAATTGACTCT
1027490 GAAATTG
1 GAAATTG
1027497 GGAAGCCCCT
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 7 0.07
99 89 0.93
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (98 bp):
GAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCCGTCTTGAGTCC
AATATCATTCGTTGTGAAGTTAAAATTGACTCT
Found at i:1028641 original size:16 final size:16
Alignment explanation
Indices: 1028620--1028663 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
1028610 TGAACCCACC
1028620 TTATTTTCTTTTATTT
1 TTATTTTCTTTTATTT
*
1028636 TTATTTTTCTTTTGTTT
1 TTA-TTTTCTTTTATTT
*
1028653 TT-TTCTCTTTT
1 TTATTTTCTTTT
1028664 CCTTTTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.32
16 3 0.12
17 14 0.56
ACGTcount: A:0.07, C:0.09, G:0.02, T:0.82
Consensus pattern (16 bp):
TTATTTTCTTTTATTT
Found at i:1028729 original size:75 final size:75
Alignment explanation
Indices: 1028645--1028788 Score: 202
Period size: 75 Copynumber: 1.9 Consensus size: 75
1028635 TTTATTTTTC
* * * * *
1028645 TTTTGTTTTTTT-CTCTTTTCCTTTTCTTTTTTTTT-CAATTTAGGGTGCCTTTTCGGGTTTTCA
1 TTTTATTTTTTTCCT-TTTTCCTTTTCTTTTTTTTTCCAACTTAGGGCGCCCTCTCGGGTTTTCA
1028708 CCCTAAACAAT
65 CCCTAAACAAT
* *
1028719 TTTTATTTTTTTCCTTTTTCTTTTTCTTTTTTTTTCCAACTTAGGGCGCCCTCTCGGGTTTTCAT
1 TTTTATTTTTTTCCTTTTTCCTTTTCTTTTTTTTTCCAACTTAGGGCGCCCTCTCGGGTTTTCAC
1028784 CCTAA
66 CCTAA
1028789 GCGAAGTACT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
74 30 0.49
75 31 0.51
ACGTcount: A:0.11, C:0.21, G:0.10, T:0.58
Consensus pattern (75 bp):
TTTTATTTTTTTCCTTTTTCCTTTTCTTTTTTTTTCCAACTTAGGGCGCCCTCTCGGGTTTTCAC
CCTAAACAAT
Found at i:1028744 original size:74 final size:75
Alignment explanation
Indices: 1028645--1028788 Score: 202
Period size: 74 Copynumber: 1.9 Consensus size: 75
1028635 TTTATTTTTC
* * * * *
1028645 TTTTGTTTTTTTCTCTTTTCCTTTTCTTTTTTTTT-CAATTTAGGGTGCCTTTTCGGGTTTTCAC
1 TTTTATTTTTTTCTCTTTTCCTTTTCTTTTTTTTTCCAACTTAGGGCGCCCTCTCGGGTTTTCAC
1028709 CCTAAACAAT
66 CCTAAACAAT
*
1028719 TTTTATTTTTTTC-CTTTTTCTTTTTCTTTTTTTTTCCAACTTAGGGCGCCCTCTCGGGTTTTCA
1 TTTTATTTTTTTCTC-TTTTCCTTTTCTTTTTTTTTCCAACTTAGGGCGCCCTCTCGGGTTTTCA
*
1028783 TCCTAA
65 CCCTAA
1028789 GCGAAGTACT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
73 1 0.02
74 31 0.51
75 29 0.48
ACGTcount: A:0.11, C:0.21, G:0.10, T:0.58
Consensus pattern (75 bp):
TTTTATTTTTTTCTCTTTTCCTTTTCTTTTTTTTTCCAACTTAGGGCGCCCTCTCGGGTTTTCAC
CCTAAACAAT
Found at i:1039621 original size:2 final size:2
Alignment explanation
Indices: 1039614--1039640 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1039604 GTATGCTAAA
1039614 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1039641 AGGGAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1043505 original size:20 final size:20
Alignment explanation
Indices: 1043482--1043520 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1043472 TTTTAAGTTG
*
1043482 TAATTAAGTATTGATATTTT
1 TAATTAAGTATCGATATTTT
1043502 TAATTAAGTATCGATATTT
1 TAATTAAGTATCGATATTT
1043521 GTCGTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (20 bp):
TAATTAAGTATCGATATTTT
Found at i:1048539 original size:43 final size:43
Alignment explanation
Indices: 1048333--1048533 Score: 258
Period size: 43 Copynumber: 4.7 Consensus size: 43
1048323 ACCATATCTT
* * *
1048333 TTGCGGTGTTTATGGGAAAAACGCCGCTAAATCTCAAGACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
* *
1048376 TTGCGGCATTTGTGGGAAAAACGCCACTAAATCTCAACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
* *
1048419 TTGCGGCGTTTGTGGGAAAAACTCCGCCAAATCTCAACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
** ** *
1048462 TTGCAACGTTTGTTTGAAAAACGCCGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
* * * *
1048505 TTACGACGTTTGTTGGATAAACGCCGCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTA
1048534 TATATCGTTA
Statistics
Matches: 138, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 138 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (43 bp):
TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
Found at i:1048547 original size:43 final size:43
Alignment explanation
Indices: 1048347--1048558 Score: 217
Period size: 43 Copynumber: 4.9 Consensus size: 43
1048337 GGTGTTTATG
* * * * * *
1048347 GGAAAAACGCCGCTAAATCTCAAGACCTATTGCGGCATTTGTG
1 GGAAAAACGCCGCTAAATATCAACACCTATTACGACGTTTGTT
* * * * *
1048390 GGAAAAACGCCACTAAATCTCAACACCTATTGCGGCGTTTGTG
1 GGAAAAACGCCGCTAAATATCAACACCTATTACGACGTTTGTT
* * * * *
1048433 GGAAAAACTCCGCCAAATCTCAACACCTATTGCAACGTTTGTT
1 GGAAAAACGCCGCTAAATATCAACACCTATTACGACGTTTGTT
*
1048476 TGAAAAACGCCGCTAAATATCAACACCTATTACGACGTTTGTT
1 GGAAAAACGCCGCTAAATATCAACACCTATTACGACGTTTGTT
* * *** *
1048519 GGATAAACGCCGCTATATATCGTTACCTATTACGGCGTTT
1 GGAAAAACGCCGCTAAATATCAACACCTATTACGACGTTT
1048559 TTTGTTACCA
Statistics
Matches: 147, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 147 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (43 bp):
GGAAAAACGCCGCTAAATATCAACACCTATTACGACGTTTGTT
Found at i:1052915 original size:18 final size:18
Alignment explanation
Indices: 1052892--1052949 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
1052882 CTTTAATTTG
1052892 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTTTCT
*
1052910 TTTATTTAATTACTATT-T
1 TTTATTTAATTA-TTTTCT
* *
1052928 ATTATTTTATTATTTTCAT
1 TTTATTTAATTATTTTC-T
1052947 TTT
1 TTT
1052950 TTATAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.09
18 23 0.72
19 6 0.19
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTTTCT
Found at i:1052940 original size:36 final size:39
Alignment explanation
Indices: 1052893--1052971 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 39
1052883 TTTAATTTGT
*
1052893 TTATTTAATTATTTTC-TTTTATT-TAATTA-CTA-TTTA
1 TTATTTAATTATTTTCATTTT-TTATAAATATCTATTTTA
*
1052929 TTATTTTATTATTTTCATTTTTTATAAATATCTATTTTA
1 TTATTTAATTATTTTCATTTTTTATAAATATCTATTTTA
1052968 TTAT
1 TTAT
1052972 ACATTTTCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
36 17 0.46
37 9 0.24
38 3 0.08
39 8 0.22
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (39 bp):
TTATTTAATTATTTTCATTTTTTATAAATATCTATTTTA
Found at i:1057708 original size:14 final size:15
Alignment explanation
Indices: 1057691--1057719 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1057681 GTATATAGAT
1057691 ATAATTA-TAAATAA
1 ATAATTATTAAATAA
1057705 ATAATTATTAAATAA
1 ATAATTATTAAATAA
1057720 CTTTCCGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAATTATTAAATAA
Found at i:1059940 original size:15 final size:17
Alignment explanation
Indices: 1059914--1059957 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
1059904 CGATATTTAA
*
1059914 AAAATATTTTAAT-ATT
1 AAAATTTTTTAATAATT
*
1059930 -TAATTTTTTAATAATT
1 AAAATTTTTTAATAATT
1059946 AAAATTTTTTAA
1 AAAATTTTTTAA
1059958 ATAGATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 10 0.43
16 3 0.13
17 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AAAATTTTTTAATAATT
Found at i:1064925 original size:18 final size:18
Alignment explanation
Indices: 1064878--1064930 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
1064868 AGGGATTTAC
**
1064878 AGTGGTCCTTCAAGACAT
1 AGTGGTCCTTCGGGACAT
1064896 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1064914 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
1064931 AACATTCAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1070997 original size:60 final size:57
Alignment explanation
Indices: 1070871--1070997 Score: 125
Period size: 58 Copynumber: 2.2 Consensus size: 57
1070861 AAAAATTGTG
* * *
1070871 TGAATTGATAAATTCATATTTTTTTAAAAAAATAATTATAATTTAATGAATTAAAAGA
1 TGAATTTATAAATTCATATTTTTTTAAAAAAATAATTATAATTTAA-GAAATAAAACA
* * *
1070929 TTAA-TTATAAAGTT-ATAATTTTTTTAAAAAAATACTTTTATAATTTTAA-AAATAAATCA
1 TGAATTTATAAA-TTCAT-ATTTTTTTAAAAAAATA--ATTATAA-TTTAAGAAATAAAACA
1070988 TGAATTTATA
1 TGAATTTATA
1070998 TATATAATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
57 8 0.14
58 22 0.39
59 10 0.18
60 11 0.20
61 5 0.09
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (57 bp):
TGAATTTATAAATTCATATTTTTTTAAAAAAATAATTATAATTTAAGAAATAAAACA
Found at i:1080312 original size:18 final size:17
Alignment explanation
Indices: 1080291--1080405 Score: 54
Period size: 18 Copynumber: 6.5 Consensus size: 17
1080281 CTTTAGGTAG
*
1080291 TTTTAAAATTTTATTTTA
1 TTTTAAAATTTT-TATTA
*
1080309 TTTTGAAATTTTTATTA
1 TTTTAAAATTTTTATTA
*** *
1080326 TTTTTTTA-TTTTAGTAA
1 TTTTAAAATTTTTA-TTA
*
1080343 CTTTTAATATTTTTATATA
1 -TTTTAAAATTTTTAT-TA
* *
1080362 TTTCAATAATATTTA-TA
1 TTTTAA-AATTTTTATTA
* * *
1080379 TTTTTAAAATTATAATAA
1 -TTTTAAAATTTTTATTA
1080397 TTTTAAAAT
1 TTTTAAAAT
1080406 CCTTAAATTT
Statistics
Matches: 73, Mismatches: 17, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
16 5 0.07
17 27 0.37
18 29 0.40
19 12 0.16
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (17 bp):
TTTTAAAATTTTTATTA
Found at i:1080355 original size:25 final size:25
Alignment explanation
Indices: 1080304--1080356 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
1080294 TAAAATTTTA
* *
1080304 TTTTATTTTGAAATTTTTATTATTT
1 TTTTATTTTGAAACTTTTAATATTT
*
1080329 TTTTATTTTAGTAACTTTTAATATTT
1 TTTTATTTT-GAAACTTTTAATATTT
1080355 TT
1 TT
1080357 ATATATTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (25 bp):
TTTTATTTTGAAACTTTTAATATTT
Found at i:1080395 original size:26 final size:26
Alignment explanation
Indices: 1080344--1080401 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
1080334 TTTTAGTAAC
*
1080344 TTTTAATATTTTTATATATTTCAATAA
1 TTTT-ATATTTTTATAAATTTCAATAA
1080371 TATTTATATTTTTA-AAATTAT-AATAA
1 T-TTTATATTTTTATAAATT-TCAATAA
1080397 TTTTA
1 TTTTA
1080402 AAATCCTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
25 4 0.14
26 10 0.36
27 11 0.39
28 3 0.11
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTTATATTTTTATAAATTTCAATAA
Found at i:1090572 original size:34 final size:34
Alignment explanation
Indices: 1090525--1090590 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
1090515 CTTTTTTGGC
* *
1090525 AATGATAACTTTTAAAAATTATTTTATATAATGA
1 AATGATAAATTTTAAAAATTATTGTATATAATGA
* *
1090559 AATGATAAATTTTAAAATTTATTGTGTATAAT
1 AATGATAAATTTTAAAAATTATTGTATATAAT
1090591 AAAGCTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (34 bp):
AATGATAAATTTTAAAAATTATTGTATATAATGA
Found at i:1102662 original size:22 final size:22
Alignment explanation
Indices: 1102634--1102975 Score: 452
Period size: 22 Copynumber: 15.6 Consensus size: 22
1102624 AATTATTTAA
1102634 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
1102656 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
1102678 AATTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
1102700 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
1102722 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
* *
1102744 AATTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
*
1102766 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
1102788 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
1102810 ATTTATTTTAAAATATCGATTG
1 ATTTATTTTAAAATATGGATTG
*
1102832 ATTTATTTTAAAATATGTATTG
1 ATTTATTTTAAAATATGGATTG
1102854 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
1102876 ATTTATTATAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
***
1102898 ATTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATGGATTG
1102919 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
1102941 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
1102963 ATTTATTTTAAAA
1 ATTTATTTTAAAA
1102976 AATTTATTAT
Statistics
Matches: 273, Mismatches: 46, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
21 18 0.07
22 255 0.93
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:1102725 original size:66 final size:65
Alignment explanation
Indices: 1102634--1102975 Score: 504
Period size: 66 Copynumber: 5.2 Consensus size: 65
1102624 AATTATTTAA
* *
1102634 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAAAAAAATTATTTTAAAATATGGATT
1 ATTTATTTTAAAATAT-GATTGATTTATTTTAAAATATGAAAAAATTTATTTTAAAATATAGATT
1102699 G
65 G
*
1102700 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGAAAAAAATTATTTTAAAATATAGATT
1 ATTTATTTTAAAATAT-GATTGATTTATTTTAAAATATGAAAAAATTTATTTTAAAATATAGATT
1102765 G
65 G
*
1102766 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGAAAAAATTTATTTTAAAATATCGATT
1 ATTTATTTTAAAATAT-GATTGATTTATTTTAAAATATGAAAAAATTTATTTTAAAATATAGATT
1102831 G
65 G
* *** *
1102832 ATTTATTTTAAAATATGTATTGATTTATTTTAAAATATGGATTGATTTATTATAAAATATAGATT
1 ATTTATTTTAAAATATG-ATTGATTTATTTTAAAATATGAAAAAATTTATTTTAAAATATAGATT
1102897 G
65 G
*** * ***
1102898 ATTTATTTTAAAATATGAAAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGATTGATTTATTTTAAAATATGAAAAAATTTATTTTAAAATATAGATTG
1102963 ATTTATTTTAAAA
1 ATTTATTTTAAAA
1102976 AATTTATTAT
Statistics
Matches: 261, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
65 58 0.22
66 203 0.78
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (65 bp):
ATTTATTTTAAAATATGATTGATTTATTTTAAAATATGAAAAAATTTATTTTAAAATATAGATTG
Found at i:1103056 original size:31 final size:31
Alignment explanation
Indices: 1102999--1103057 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1102989 AGTTGTATGG
*
1102999 ATTATTTAAATTTCAATATTATAAAACTAAA
1 ATTATTTAAATTTCAATATTACAAAACTAAA
* *
1103030 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAATATTACAAAACT
1103058 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAATATTACAAAACTAAA
Found at i:1105146 original size:20 final size:20
Alignment explanation
Indices: 1105118--1105155 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1105108 ACTCAAACTC
1105118 CAATAAAATTTACATTATCT
1 CAATAAAATTTACATTATCT
* *
1105138 CAATTAAATTTACGTTAT
1 CAATAAAATTTACATTAT
1105156 GAACTAAATA
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:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (20 bp):
CAATAAAATTTACATTATCT
Found at i:1116686 original size:25 final size:24
Alignment explanation
Indices: 1116635--1116687 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1116625 GCAAAGTGAC
*
1116635 TATATTTTTAATTAATAAATTATA
1 TATATTTTTAATTAATAAATTAAA
*
1116659 TATATTTTTAA-TAATTTAATCTAAA
1 TATATTTTTAATTAA-TAAAT-TAAA
1116684 TATA
1 TATA
1116688 AAATGAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 3 0.12
24 15 0.60
25 7 0.28
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TATATTTTTAATTAATAAATTAAA
Found at i:1116758 original size:18 final size:17
Alignment explanation
Indices: 1116737--1116784 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1116727 TAATTAATTT
*
1116737 AATATTAATATAAAATGA
1 AATACTAATAT-AAATGA
*
1116755 AATACTCATATAAATGA
1 AATACTAATATAAATGA
* *
1116772 AACACTAAAATAA
1 AATACTAATATAA
1116785 TTTGATTGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.27
Consensus pattern (17 bp):
AATACTAATATAAATGA
Found at i:1117248 original size:32 final size:32
Alignment explanation
Indices: 1117212--1117290 Score: 140
Period size: 32 Copynumber: 2.5 Consensus size: 32
1117202 CAAGAGTTAA
1117212 GAGTATTTTAATAAACCTTGACGAGAGAATGT
1 GAGTATTTTAATAAACCTTGACGAGAGAATGT
* *
1117244 GAGTACTTTAATAAACCTTGAGGAGAGAATGT
1 GAGTATTTTAATAAACCTTGACGAGAGAATGT
1117276 GAGTATTTTAATAAA
1 GAGTATTTTAATAAA
1117291 TTATTTTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.32
Consensus pattern (32 bp):
GAGTATTTTAATAAACCTTGACGAGAGAATGT
Found at i:1119032 original size:28 final size:28
Alignment explanation
Indices: 1118992--1119048 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1118982 CGCCACGCTA
*
1118992 GAAAGAGCATTTCAGGGAACGT-GCCTTT
1 GAAAGAGCATTTCAGGAAAC-TCGCCTTT
*
1119020 GAAAGAGTATTTCAGGAAACTCGCCTTT
1 GAAAGAGCATTTCAGGAAACTCGCCTTT
1119048 G
1 G
1119049 CTTTTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (28 bp):
GAAAGAGCATTTCAGGAAACTCGCCTTT
Found at i:1119812 original size:138 final size:137
Alignment explanation
Indices: 1119478--1120144 Score: 909
Period size: 138 Copynumber: 4.8 Consensus size: 137
1119468 ATCACATGTG
*
1119478 ACTATTCATGTCAGTACCTATCATGTTTGATGGGACGCAGTAAAGTGGTGAAAGCGCGTTTCA--
1 ACTATTCATGTCAGTACCTATCATGTTTGA-GGGACGCAGCAAAGTGGTGAAAGCGCGTTTCAGG
* * * *
1119541 GGGGGCGTCTTCCCTTTTTTGTTAGAGAATATGTTATAATTTCCCTATTATGTGTGATGTCCCCC
65 GGGGGCGCCTTCCTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTATGTGTGATGTCCCCC
1119606 GT-AGGGC
130 GTGAGGGC
* *
1119613 ACTATTCATGTCAGTATCTATCTTGTTTGAGGAGACGCAGCAAAGTGGTGAAAGCGCGTTTCAGG
1 ACTATTCATGTCAGTACCTATCATGTTTGAGG-GACGCAGCAAAGTGGTGAAAGCGCGTTTCAGG
1119678 GGGGGCGCCTTCCTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTATGTGTGATGTCCCAC
65 GGGGGCGCCTTCCTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTATGTGTGATGTCCC-C
* * *
1119743 GGTGA-AGT
129 CGTGAGGGC
* *
1119751 ACTATTCATGTCAATACCTATCATGTTTGATGGGACGCACCAAAGTGGTGAAAGCGCGTTTCA--
1 ACTATTCATGTCAGTACCTATCATGTTTGA-GGGACGCAGCAAAGTGGTGAAAGCGCGTTTCAGG
* * * *
1119814 GGGGGCGCCTTCCCCTTCTTGTGTTAGAGAATAGGTTATAATTGCCCAATTATGTGTGATATCCC
65 GGGGGCGCCTT--CCTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTATGTGTGATGTCCC
*
1119879 CCTGTG-GGGA
128 CC-GTGAGGGC
*
1119889 ACTATTCATGTCAGTACCTATCATGTTTGAGGAGACGCAACAAAGTGGTGAAAGCGCGTTTCAGG
1 ACTATTCATGTCAGTACCTATCATGTTTGAGG-GACGCAGCAAAGTGGTGAAAGCGCGTTTCAGG
* * * *
1119954 GGGCGCACCTTCATTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTATGTATGATGTCCCC
65 GGGGGCGCCTTC-CTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTATGTGTGATGTCCCC
*
1120019 CGTCAGGGC
129 CGTGAGGGC
* *
1120028 ACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCATCAATGTGGTGAAAGCGCGTTTCAGG
1 ACTATTCATGTCAGTACCTATCATGTTTGA-GGGACGCAGCAAAGTGGTGAAAGCGCGTTTCAGG
* * * **
1120093 GGGTGTGTCTTCCCTTTTTTT-CCAGAGAATAGGTTATAATTGCCCTATTATG
65 GGGGGCGCCTT-CCTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTATG
1120145 CTTGAAATTT
Statistics
Matches: 473, Mismatches: 42, Indels: 31
0.87 0.08 0.06
Matches are distributed among these distances:
134 2 0.00
135 57 0.12
136 11 0.02
137 62 0.13
138 202 0.43
139 127 0.27
140 12 0.03
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (137 bp):
ACTATTCATGTCAGTACCTATCATGTTTGAGGGACGCAGCAAAGTGGTGAAAGCGCGTTTCAGGG
GGGGCGCCTTCCTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTATGTGTGATGTCCCCCG
TGAGGGC
Found at i:1120048 original size:277 final size:272
Alignment explanation
Indices: 1119478--1120144 Score: 996
Period size: 277 Copynumber: 2.4 Consensus size: 272
1119468 ATCACATGTG
**
1119478 ACTATTCATGTCAGTACCTATCATGTTTGATGGGACGCAGTAAAGTGGTGAAAGCGCGTTTCAGG
1 ACTATTCATGTCAGTACCTATCATGTTTGATGGGACGCACCAAAGTGGTGAAAGCGCGTTTCAGG
* * *
1119543 GGGCGTCTTCCCTTTTTTGTTAGAGAATATGTTATAATTTCCCTATTATGTGTGATGTCCCCCGT
66 GGGCGTCTTCCC-TTTTTGTTAGAGAATAGGTTATAATTGCCCTATTATGTGTGATATCCCCCGT
* * * *
1119608 AGGGCACTATTCATGTCAGTATCTATCTTGTTTGAGGAGACGCAGCAAAGTGGTGAAAGCGCGTT
130 AGGGAACTATTCATGTCAGTACCTATCATGTTTGAGGAGACGCAACAAAGTGGTGAAAGCGCGTT
* * *
1119673 TCAGGGGGGGCGCCTTCCTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTATGTGTGATGT
195 TCAGGGGGCGCACCTTCCTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTATGTATGATGT
* * *
1119738 CCCACGGTGAAGT
260 CCCACCGTCAAGC
*
1119751 ACTATTCATGTCAATACCTATCATGTTTGATGGGACGCACCAAAGTGGTGAAAGCGCGTTTCAGG
1 ACTATTCATGTCAGTACCTATCATGTTTGATGGGACGCACCAAAGTGGTGAAAGCGCGTTTCAGG
* *
1119816 GGGCGCCTTCCCCTTCTTGTGTTAGAGAATAGGTTATAATTGCCCAATTATGTGTGATATCCCCC
66 GGGCGTCTT-CCCTT-TT-TGTTAGAGAATAGGTTATAATTGCCCTATTATGTGTGATATCCCCC
*
1119881 TGTGGGGAACTATTCATGTCAGTACCTATCATGTTTGAGGAGACGCAACAAAGTGGTGAAAGCGC
128 -GTAGGGAACTATTCATGTCAGTACCTATCATGTTTGAGGAGACGCAACAAAGTGGTGAAAGCGC
*
1119946 GTTTCAGGGGGCGCACCTTCATTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTATGTATG
192 GTTTCAGGGGGCGCACCTTC-CTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTATGTATG
*
1120011 ATGTCCC-CCGTCAGGGC
256 ATGTCCCACCGTCA-AGC
* * *
1120028 ACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCATCAATGTGGTGAAAGCGCGTTTCAGG
1 ACTATTCATGTCAGTACCTATCATGTTTGATGGGACGCACCAAAGTGGTGAAAGCGCGTTTCA-G
*
1120093 GGGTGTGTCTTCCCTTTTT-TTCCAGAGAATAGGTTATAATTGCCCTATTATG
65 GGG-GCGTCTTCCCTTTTTGTT--AGAGAATAGGTTATAATTGCCCTATTATG
1120145 CTTGAAATTT
Statistics
Matches: 356, Mismatches: 28, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
273 72 0.20
274 5 0.01
275 44 0.12
276 82 0.23
277 139 0.39
278 9 0.03
279 5 0.01
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (272 bp):
ACTATTCATGTCAGTACCTATCATGTTTGATGGGACGCACCAAAGTGGTGAAAGCGCGTTTCAGG
GGGCGTCTTCCCTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTATGTGTGATATCCCCCGTA
GGGAACTATTCATGTCAGTACCTATCATGTTTGAGGAGACGCAACAAAGTGGTGAAAGCGCGTTT
CAGGGGGCGCACCTTCCTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTATGTATGATGTC
CCACCGTCAAGC
Found at i:1120169 original size:20 final size:21
Alignment explanation
Indices: 1120146--1120192 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
1120136 CCTATTATGC
*
1120146 TTGAAATTT-ATGTTAGAGTG
1 TTGAAATTTGATGTTAGAATG
1120166 TTG-AATTTGATGTTAGAATG
1 TTGAAATTTGATGTTAGAATG
1120186 -TGAAATT
1 TTGAAATT
1120193 GGATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (21 bp):
TTGAAATTTGATGTTAGAATG
Found at i:1121179 original size:42 final size:42
Alignment explanation
Indices: 1121133--1121216 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
1121123 AATACTGCGA
* *
1121133 AGATGACATATGAA-CTAGTGGGCTTGGCATATACCCTTGTGG
1 AGATGAAATATGAACCT-GTGGGCTGGGCATATACCCTTGTGG
*
1121175 AGATGAAATATGAACCTGTGGGCTGGGCATGTACCCTTGTGG
1 AGATGAAATATGAACCTGTGGGCTGGGCATATACCCTTGTGG
1121217 CATTATCATC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 36 0.95
43 2 0.05
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (42 bp):
AGATGAAATATGAACCTGTGGGCTGGGCATATACCCTTGTGG
Found at i:1123030 original size:13 final size:13
Alignment explanation
Indices: 1123000--1123032 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1122990 TTAATAAAAA
1123000 ATAAAATATTATTT
1 ATAAAA-ATTATTT
1123014 -TAAAAATTATTT
1 ATAAAAATTATTT
1123026 ATAAAAA
1 ATAAAAA
1123033 AATATAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATAAAAATTATTT
Found at i:1123048 original size:35 final size:35
Alignment explanation
Indices: 1122979--1123048 Score: 81
Period size: 35 Copynumber: 2.0 Consensus size: 35
1122969 AATAATTATA
* *
1122979 TAAATATTATTTTAATAAAAAATAAAATATTATTT
1 TAAAAATTATTTTAATAAAAAATAAAATACTATTT
*
1123014 TAAAAATTATTTATAA-AAAAATATAACA-ACTATTT
1 TAAAAATTATTT-TAATAAAAA-ATAAAATACTATTT
1123049 AGAAAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
35 22 0.73
36 8 0.27
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (35 bp):
TAAAAATTATTTTAATAAAAAATAAAATACTATTT
Found at i:1123442 original size:29 final size:28
Alignment explanation
Indices: 1123398--1123452 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
1123388 ACCTCACACG
1123398 AAAGGATGTTAGTTAGAGAAATATTAGTC
1 AAAGGATGTTAGTTAGAG-AATATTAGTC
* * *
1123427 AAAGGGTGTTATTTAGAGTATATTAG
1 AAAGGATGTTAGTTAGAGAATATTAG
1123453 GTTCATAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (28 bp):
AAAGGATGTTAGTTAGAGAATATTAGTC
Found at i:1125983 original size:229 final size:228
Alignment explanation
Indices: 1125572--1126021 Score: 785
Period size: 229 Copynumber: 2.0 Consensus size: 228
1125562 GTAAATTATC
* * *
1125572 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTTATTATTATCTTTAG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTTATTATTATATTTAG
**
1125637 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
66 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
*
1125702 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
131 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
1125767 GAAACATAAATTACATAACTTTCAAAAAAGTATA
196 GAAACATAAATTACATAACTTT-AAAAAAGTATA
*
1125801 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATA-TTTATTATTATATTTG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTTATTATTATATTTA
*
1125865 GTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
65 GTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
* *
1125930 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAAT
130 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAAT
1125995 TGAAACATAAATTACATAACTTTAAAA
195 TGAAACATAAATTACATAACTTTAAAA
1126022 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
228 4 0.02
229 197 0.94
230 9 0.04
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTTATTATTATATTTAG
TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
GAAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:1126110 original size:20 final size:20
Alignment explanation
Indices: 1126087--1126136 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1126077 CGATATACCA
1126087 GGTAAAATTATGATAAAACC
1 GGTAAAATTATGATAAAACC
*
1126107 GGTAACAA-AATGATAAAACC
1 GGTAA-AATTATGATAAAACC
1126127 GGTAAAATTA
1 GGTAAAATTA
1126137 AAAGTGTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (20 bp):
GGTAAAATTATGATAAAACC
Found at i:1126277 original size:20 final size:19
Alignment explanation
Indices: 1126254--1126300 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1126244 CGATATAACA
*
1126254 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
1126274 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
1126294 GGTAAAA
1 GGTAAAA
1126301 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:1128657 original size:33 final size:33
Alignment explanation
Indices: 1128615--1128680 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1128605 AAATAGATGG
*
1128615 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
1128648 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1128681 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1130536 original size:19 final size:19
Alignment explanation
Indices: 1130473--1130535 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
1130463 AATGTCGAGT
*
1130473 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGATTTA
1130492 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
1130511 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
1130530 T-ATTTT
1 TAATTTT
1130536 TTTATGTGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 5 0.12
19 38 0.88
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:1131507 original size:198 final size:199
Alignment explanation
Indices: 1130618--1131839 Score: 2164
Period size: 200 Copynumber: 6.1 Consensus size: 199
1130608 TTAAGGGTCA
* * *** *
1130618 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
1130683 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1130748 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1130813 AATG
196 AATG
1130817 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
*
1130882 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1130947 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1131012 TAATG
195 TAATG
1131017 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
*
1131082 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1131147 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1131212 TAATG
195 TAATG
* *** *
1131217 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
1131282 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1131346 TAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1131410 AATG
196 AATG
1131414 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
*
1131478 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1131543 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1131608 TAATG
195 TAATG
* *** * *
1131613 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
1131678 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
1131742 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1131807 AATG
196 AATG
*
1131811 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
1131840 CTAATTTAAA
Statistics
Matches: 988, Mismatches: 30, Indels: 11
0.96 0.03 0.01
Matches are distributed among these distances:
196 18 0.02
197 119 0.12
198 245 0.25
199 196 0.20
200 410 0.41
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:1131566 original size:396 final size:398
Alignment explanation
Indices: 1130618--1131839 Score: 2243
Period size: 396 Copynumber: 3.1 Consensus size: 398
1130608 TTAAGGGTCA
* * *** *
1130618 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
1130682 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1130747 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
* ***
1130812 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGT
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGT
* *
1130877 GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
260 GCATCAATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
1130942 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
324 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
1131007 CTAAATAATG
389 CTAAATAATG
1131017 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1131082 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1131147 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1131212 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
1131277 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
1131342 AATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
326 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
1131406 AAATAATG
391 AAATAATG
1131414 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1131478 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1131543 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1131608 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
*
1131673 AATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
* *
1131738 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCT
326 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
1131803 AAATAATG
391 AAATAATG
*
1131811 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
1131840 CTAATTTAAA
Statistics
Matches: 802, Mismatches: 19, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
396 307 0.38
397 171 0.21
398 53 0.07
399 79 0.10
400 192 0.24
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (398 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
AAATAATG
Found at i:1133323 original size:18 final size:18
Alignment explanation
Indices: 1133300--1133361 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
1133290 ATCGGTCGCA
* * *
1133300 GAAGATGAAGCTGACGAT
1 GAAGATGACGATGATGAT
1133318 GAAGATGACGATGATGAT
1 GAAGATGACGATGATGAT
*
1133336 GATGATGACGATGATGAT
1 GAAGATGACGATGATGAT
1133354 GAAGATGA
1 GAAGATGA
1133362 TGATCCAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (18 bp):
GAAGATGACGATGATGAT
Found at i:1133324 original size:6 final size:6
Alignment explanation
Indices: 1133300--1133361 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
1133290 ATCGGTCGCA
* * * * * *
1133300 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
*
1133348 GATGAT GAAGAT GA
1 GAAGAT GAAGAT GA
1133362 TGATCCAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:1133335 original size:3 final size:3
Alignment explanation
Indices: 1133315--1133365 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
1133305 TGAAGCTGAC
* * * *
1133315 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAT GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1133363 GAT
1 GAT
1133366 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:1133362 original size:12 final size:12
Alignment explanation
Indices: 1133303--1133365 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
1133293 GGTCGCAGAA
* *
1133303 GATGAAGCTGAC
1 GATGAAGATGAT
*
1133315 GATGAAGATGAC
1 GATGAAGATGAT
*
1133327 GATGATGATGAT
1 GATGAAGATGAT
*
1133339 GATGACGATGAT
1 GATGAAGATGAT
1133351 GATGAAGATGAT
1 GATGAAGATGAT
1133363 GAT
1 GAT
1133366 CCAAACAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:1135242 original size:183 final size:184
Alignment explanation
Indices: 1134727--1135576 Score: 1604
Period size: 182 Copynumber: 4.7 Consensus size: 184
1134717 CTTTCAACAT
**
1134727 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1134792 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
1134857 AATGTGTCGATACGATTTCAAAAAGTGTCGACA-TTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
1134910 ATTATAATGTAATAGATAATTTTGT-ATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1134974 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
1135038 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
1135092 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1135157 GGTCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
1135221 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
1135275 ATTATAATGTAATAGATAA-TTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1135339 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTAC-TTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
1135403 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
1135457 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1135522 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
1135577 CCATTTAAAA
Statistics
Matches: 655, Mismatches: 6, Indels: 11
0.97 0.01 0.02
Matches are distributed among these distances:
181 33 0.05
182 346 0.53
183 265 0.40
184 11 0.02
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:1135407 original size:365 final size:365
Alignment explanation
Indices: 1134727--1135576 Score: 1598
Period size: 365 Copynumber: 2.3 Consensus size: 365
1134717 CTTTCAACAT
**
1134727 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1134792 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
1134857 AATGTGTCGATACGATTTCAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAA
1134922 TAGATAATTTTGTATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTA
196 TAGATAATTTTGTATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTA
1134987 TATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATGTGTCGATACA
261 TATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATGTGTCGATACA
1135052 ATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
326 ATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
1135092 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1135157 GGTCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
1135221 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACA-TTTACACATCGGAACCCATAATTATAATGTA
1135286 ATAGATAA-TTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACC
195 ATAGATAATTTTGT-ATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACC
1135350 TATATCGACACTTTTTAATATTGTGTCGGTAC-TTATGTCCATATTGGAAGAAAAATGTGTCGAT
259 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AAAATGTGTCGAT
1135414 ACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
323 ACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
1135457 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1135522 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
1135577 CCATTTAAAA
Statistics
Matches: 475, Mismatches: 6, Indels: 7
0.97 0.01 0.01
Matches are distributed among these distances:
364 96 0.20
365 347 0.73
366 32 0.07
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (365 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAA
TAGATAATTTTGTATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTA
TATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATGTGTCGATACA
ATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:1138156 original size:23 final size:23
Alignment explanation
Indices: 1138125--1138187 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1138115 ATAGGTAAAC
*
1138125 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1138148 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1138171 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
1138188 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1138195 original size:23 final size:23
Alignment explanation
Indices: 1138125--1138197 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1138115 ATAGGTAAAC
* * **
1138125 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
1138148 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
1138171 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
1138194 ATAT
1 ATAT
1138198 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:1138585 original size:23 final size:23
Alignment explanation
Indices: 1138554--1138616 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1138544 ATAGGTAAAC
*
1138554 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1138577 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1138600 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
1138617 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1138624 original size:23 final size:23
Alignment explanation
Indices: 1138554--1138626 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1138544 ATAGGTAAAC
* * **
1138554 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
1138577 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
1138600 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
1138623 ATAT
1 ATAT
1138627 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:1139233 original size:9 final size:9
Alignment explanation
Indices: 1139203--1139245 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
1139193 TACGATCATT
1139203 TATTTTAAA
1 TATTTTAAA
* *
1139212 TTTTTTTAA
1 TATTTTAAA
*
1139221 -ATTTTATA
1 TATTTTAAA
1139229 TATTTTAAA
1 TATTTTAAA
1139238 TATTTTAA
1 TATTTTAA
1139246 TTGAAAATCT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
8 5 0.19
9 22 0.81
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAA
Found at i:1154101 original size:28 final size:28
Alignment explanation
Indices: 1154063--1154189 Score: 114
Period size: 28 Copynumber: 4.4 Consensus size: 28
1154053 AAGCTTTATA
*
1154063 TTTAATTTTATATTATAAATATTAATTT
1 TTTAATATTATATTATAAATATTAATTT
*
1154091 TTTAATATTATATTATAGATATTAATTTT
1 TTTAATATTATATTATAAATATTAA-TTT
* * * *
1154120 AATATTAATTTTTAAATAAATTAAATATCAATTT
1 --T-TTAA-TATTATAT-TA-TAAATATTAATTT
*
1154154 TTTAATATTATATTATAGATATTAA--T
1 TTTAATATTATATTATAAATATTAATTT
1154180 TTTAATATTA
1 TTTAATATTA
1154190 ATTTTTTTAA
Statistics
Matches: 80, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
26 11 0.14
28 31 0.39
29 4 0.05
30 6 0.08
31 5 0.06
32 5 0.06
33 6 0.08
34 4 0.05
35 8 0.10
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (28 bp):
TTTAATATTATATTATAAATATTAATTT
Found at i:1154157 original size:63 final size:63
Alignment explanation
Indices: 1154078--1154249 Score: 283
Period size: 63 Copynumber: 2.7 Consensus size: 63
1154068 TTTTATATTA
1154078 TAAATATTAATTTTTTAATATTATATTATAGATATTAATTTTAATATTAA-TTTTTAAATAAAT
1 TAAATA-TAATTTTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAAT
1154141 TAAATATCAATTTTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTTAAATAAAT
1 TAAATAT-AATTTTTTAATATTATATTATAGATATTAATTTTAATATTAA-TTTTTTAAATAAAT
*
1154206 TAAATATTATCTTTTTAATATTATATTATAGATATTTAATTTTA
1 TAAATATAAT-TTTTTAATATTATATTATAGATA-TTAATTTTA
1154250 TATCATATAA
Statistics
Matches: 103, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
62 1 0.01
63 48 0.47
64 2 0.02
65 43 0.42
66 9 0.09
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (63 bp):
TAAATATAATTTTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAAT
Found at i:1154304 original size:20 final size:19
Alignment explanation
Indices: 1154244--1154305 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
1154234 TAGATATTTA
*
1154244 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
1154263 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
1154281 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
1154301 ATTTT
1 ATTTT
1154306 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:1154967 original size:31 final size:31
Alignment explanation
Indices: 1154908--1154968 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
1154898 ATAGTTATAT
* * **
1154908 AAATTATTTAAATTTTAATATTGTAAAACTA
1 AAATTATTTAAATATCAATATTACAAAACTA
*
1154939 AAATTATTTAAATATCAGTATTACAAAACT
1 AAATTATTTAAATATCAATATTACAAAACT
1154969 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (31 bp):
AAATTATTTAAATATCAATATTACAAAACTA
Found at i:1161373 original size:22 final size:22
Alignment explanation
Indices: 1161345--1161389 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1161335 TTGGTCCTTG
1161345 TATTTTAATATATGTGTATGTT
1 TATTTTAATATATGTGTATGTT
1161367 TATTTTAATATATGTGTATGTT
1 TATTTTAATATATGTGTATGTT
1161389 T
1 T
1161390 CATATTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (22 bp):
TATTTTAATATATGTGTATGTT
Found at i:1161916 original size:21 final size:23
Alignment explanation
Indices: 1161878--1161921 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1161868 TTTTTTGAAA
1161878 ATTTTTACAAAATATTCA-TTTT
1 ATTTTTACAAAATATTCAGTTTT
* *
1161900 ATTTTT-CAATATTTTCAGTTTT
1 ATTTTTACAAAATATTCAGTTTT
1161922 TCTTGCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (23 bp):
ATTTTTACAAAATATTCAGTTTT
Found at i:1162506 original size:16 final size:17
Alignment explanation
Indices: 1162480--1162517 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
1162470 ATACATATCA
1162480 ATTTTTGTCTTAATAA-T
1 ATTTTTGTCTTAA-AATT
1162497 ATTTTT-TCTTAAAATT
1 ATTTTTGTCTTAAAATT
1162513 ATTTT
1 ATTTT
1162518 AAAATACGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 2 0.10
16 12 0.60
17 6 0.30
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (17 bp):
ATTTTTGTCTTAAAATT
Found at i:1171646 original size:13 final size:13
Alignment explanation
Indices: 1171626--1171673 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
1171616 CGAAAATAAC
1171626 AAAATAATAAAAT
1 AAAATAATAAAAT
*
1171639 AGAATAATATAAAAT
1 AAAAT-A-ATAAAAT
*
1171654 AAAATAATAATAT
1 AAAATAATAAAAT
1171667 AAAATAA
1 AAAATAA
1171674 AGTATAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 17 0.57
14 2 0.07
15 11 0.37
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (13 bp):
AAAATAATAAAAT
Found at i:1171652 original size:15 final size:15
Alignment explanation
Indices: 1171618--1171662 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
1171608 GGTAAAAACG
1171618 AAAATAACAA-AATAAT
1 AAAATAA-AATAAT-AT
*
1171634 AAAATAGAATAATAT
1 AAAATAAAATAATAT
1171649 AAAATAAAATAATA
1 AAAATAAAATAATA
1171663 ATATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAATAAAATAATAT
Found at i:1171662 original size:18 final size:19
Alignment explanation
Indices: 1171631--1171674 Score: 72
Period size: 18 Copynumber: 2.3 Consensus size: 19
1171621 ATAACAAAAT
1171631 AATAAAATAGAATAATATAA
1 AATAAAATA-AATAATATAA
1171651 AATAAAAT-AATAATATAA
1 AATAAAATAAATAATATAA
1171669 AATAAA
1 AATAAA
1171675 GTATAATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 16 0.67
20 8 0.33
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (19 bp):
AATAAAATAAATAATATAA
Found at i:1171928 original size:2 final size:2
Alignment explanation
Indices: 1171921--1171966 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
1171911 AATGCTAATA
*
1171921 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AA AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1171960 AT A- AT AT
1 AT AT AT AT
1171967 TTGGAAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 4 0.11
2 34 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1173728 original size:105 final size:105
Alignment explanation
Indices: 1173536--1173996 Score: 724
Period size: 105 Copynumber: 4.4 Consensus size: 105
1173526 GTATTGTTCC
* ** ** * * *
1173536 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGATTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
* * * * * *
1173601 CCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGGTCTA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1173642 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1173707 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1173747 TAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAGATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
1173812 CAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1173852 GAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1173917 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1173957 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1173997 GGTAGGACCT
Statistics
Matches: 328, Mismatches: 27, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
105 286 0.87
106 42 0.13
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1183950 original size:23 final size:24
Alignment explanation
Indices: 1183924--1183978 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
1183914 CGAAAATAAC
*
1183924 AAAATAATAA-AA-TAGAATAATAT
1 AAAATAATAACAATTA-AATAAAAT
*
1183947 AAAATAA-AACAATTATATAAAAT
1 AAAATAATAACAATTAAATAAAAT
1183970 AAAATAATA
1 AAAATAATA
1183979 TCATATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 2 0.07
23 22 0.81
24 3 0.11
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (24 bp):
AAAATAATAACAATTAAATAAAAT
Found at i:1183988 original size:18 final size:17
Alignment explanation
Indices: 1183916--1183993 Score: 65
Period size: 18 Copynumber: 4.6 Consensus size: 17
1183906 GGTAAAAACG
1183916 AAAATAACAA-AATA-AT
1 AAAATAA-AATAATATAT
*
1183932 AAAATAGAAT-A-ATAT
1 AAAATAAAATAATATAT
*
1183947 AAAATAAAACAATTATAT
1 AAAATAAAATAA-TATAT
1183965 AAAATAAAATAATATCAT
1 AAAATAAAATAATAT-AT
* *
1183983 ATAATATAATA
1 AAAATAAAATA
1183994 GTAAAGAACC
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 1 0.02
15 13 0.26
16 7 0.14
17 3 0.06
18 26 0.52
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.27
Consensus pattern (17 bp):
AAAATAAAATAATATAT
Found at i:1188967 original size:17 final size:18
Alignment explanation
Indices: 1188934--1188967 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1188924 ATTCAGAAAA
*
1188934 TAAAATTGATATTTATAT
1 TAAAATTGATATGTATAT
1188952 TAAAATT-ATATGTATA
1 TAAAATTGATATGTATA
1188968 CATCATGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
TAAAATTGATATGTATAT
Found at i:1192864 original size:30 final size:30
Alignment explanation
Indices: 1192820--1192876 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1192810 TATGATTTTA
*
1192820 AAAAAATAAAAGTTTCGATACTAAACATAT
1 AAAAAATAAAAGTTTAGATACTAAACATAT
* * *
1192850 AAAAACTAATAGTTTAGGTACTAAACA
1 AAAAAATAAAAGTTTAGATACTAAACA
1192877 CATCGTTTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.54, C:0.11, G:0.09, T:0.26
Consensus pattern (30 bp):
AAAAAATAAAAGTTTAGATACTAAACATAT
Found at i:1194808 original size:45 final size:45
Alignment explanation
Indices: 1194744--1194881 Score: 222
Period size: 45 Copynumber: 3.1 Consensus size: 45
1194734 AGCCTTTAAA
*
1194744 ATTTCAACTCTAGCATACTTTTCTGTTGATAATACACCCATATGC
1 ATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCATATGC
*
1194789 ATTTCAACTCTAGCATACTTTTTTGTTGATAATGCACCCATATGC
1 ATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCATATGC
* * * *
1194834 ATTTCAACTCTAGCATATTTTTCTGTTTATAATGTATCCATATGC
1 ATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCATATGC
1194879 ATT
1 ATT
1194882 ATTCTTTTAT
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 86 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (45 bp):
ATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCATATGC
Found at i:1196877 original size:31 final size:31
Alignment explanation
Indices: 1196842--1196964 Score: 97
Period size: 32 Copynumber: 3.9 Consensus size: 31
1196832 GAGTCGAGGA
*
1196842 TTACCTATGTCTTTCGAGACATATGGATAGT
1 TTACCTATGTCTTTCGAGACATATGGACAGT
** * *
1196873 TTACCTATGTCCCTCGGGACATATGGACAGGA
1 TTACCTATGTCTTTCGAGACATATGGACA-GT
* * *
1196905 TTACCTATGTCCTTT-GGGTCATATGGACAAT
1 TTACCTATGT-CTTTCGAGACATATGGACAGT
* *
1196936 GTTACCTTATGT-TCTTCAAAACATATGGA
1 -TTACC-TATGTCT-TTCGAGACATATGGA
1196965 TAGGTCCTTC
Statistics
Matches: 72, Mismatches: 14, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
31 26 0.36
32 31 0.43
33 15 0.21
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (31 bp):
TTACCTATGTCTTTCGAGACATATGGACAGT
Found at i:1196914 original size:32 final size:32
Alignment explanation
Indices: 1196838--1196933 Score: 122
Period size: 32 Copynumber: 3.0 Consensus size: 32
1196828 CCAAGAGTCG
* * *
1196838 AGGATTACCTATGTCTTTCGAGACATATGGAT
1 AGGATTACCTATGTCCTTCGGGACATATGGAC
* *
1196870 A-GTTTACCTATGTCCCTCGGGACATATGGAC
1 AGGATTACCTATGTCCTTCGGGACATATGGAC
* *
1196901 AGGATTACCTATGTCCTTTGGGTCATATGGAC
1 AGGATTACCTATGTCCTTCGGGACATATGGAC
1196933 A
1 A
1196934 ATGTTACCTT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
31 26 0.48
32 28 0.52
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (32 bp):
AGGATTACCTATGTCCTTCGGGACATATGGAC
Found at i:1196941 original size:32 final size:32
Alignment explanation
Indices: 1196842--1196947 Score: 101
Period size: 32 Copynumber: 3.3 Consensus size: 32
1196832 GAGTCGAGGA
* * *
1196842 TTACCTATGT-CTTTCGAGACATATGGATAGT-
1 TTACCTATGTCCTTT-GGGACATATGGACAATG
* * *
1196873 TTACCTATGTCCCTCGGGACATATGGAC-AGG
1 TTACCTATGTCCTTTGGGACATATGGACAATG
*
1196904 ATTACCTATGTCCTTTGGGTCATATGGACAATG
1 -TTACCTATGTCCTTTGGGACATATGGACAATG
1196937 TTACCTTATGT
1 TTACC-TATGT
1196948 TCTTCAAAAC
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
31 21 0.35
32 32 0.53
33 7 0.12
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.36
Consensus pattern (32 bp):
TTACCTATGTCCTTTGGGACATATGGACAATG
Found at i:1197994 original size:20 final size:22
Alignment explanation
Indices: 1197969--1198020 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
1197959 TGGCTCTTCA
1197969 GTATCGATA-T-CCCTACTATG
1 GTATCGATACTACCCTACTATG
1197989 GTATCGATACTACCCTACTATG
1 GTATCGATACTACCCTACTATG
*
1198011 ATATCGATAC
1 GTATCGATAC
1198021 CAAAATTAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 9 0.31
21 1 0.03
22 19 0.66
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (22 bp):
GTATCGATACTACCCTACTATG
Found at i:1198109 original size:18 final size:18
Alignment explanation
Indices: 1198086--1198133 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1198076 ACTACGCTAT
1198086 GGTACCGATACCCCCTTC
1 GGTACCGATACCCCCTTC
1198104 GGTACCGATACCCCCTTC
1 GGTACCGATACCCCCTTC
*
1198122 GGTATCGATACC
1 GGTACCGATACC
1198134 AAAATTAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.19, C:0.40, G:0.19, T:0.23
Consensus pattern (18 bp):
GGTACCGATACCCCCTTC
Found at i:1199565 original size:2 final size:2
Alignment explanation
Indices: 1199558--1199589 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1199548 TATTTGCTTG
1199558 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
1199590 CACCATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1202116 original size:119 final size:119
Alignment explanation
Indices: 1201905--1202140 Score: 454
Period size: 119 Copynumber: 2.0 Consensus size: 119
1201895 TCCATGGATT
*
1201905 TTCTATACAACATAATATTGCCCTAATTTTAATAAGTGATATACACATAATAATCTTTTTCAAAA
1 TTCTATACAACATAATATTGCCCTAATTTTAATAAGTGATATACACATAATAATCTTCTTCAAAA
1201970 AAAACCTCGAATAATAAAAGATGTGTTATTTTGTATGAACAGTCATCGGGAACG
66 AAAACCTCGAATAATAAAAGATGTGTTATTTTGTATGAACAGTCATCGGGAACG
1202024 TTCTATACAACATAATATTGCCCTAATTTTAATAAGTGATATACACATAATAATCTTCTTCAAAA
1 TTCTATACAACATAATATTGCCCTAATTTTAATAAGTGATATACACATAATAATCTTCTTCAAAA
*
1202089 AAAACCTCGAATAATAAAAGATGTGTTATTTTGTATTAACAGTCATCGGGAA
66 AAAACCTCGAATAATAAAAGATGTGTTATTTTGTATGAACAGTCATCGGGAA
1202141 TGTGATCCTC
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 115 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (119 bp):
TTCTATACAACATAATATTGCCCTAATTTTAATAAGTGATATACACATAATAATCTTCTTCAAAA
AAAACCTCGAATAATAAAAGATGTGTTATTTTGTATGAACAGTCATCGGGAACG
Found at i:1203621 original size:14 final size:14
Alignment explanation
Indices: 1203604--1203649 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1203594 GTATTTAAAA
*
1203604 TTTATAGTTTATGT
1 TTTATAGTTTATAT
* *
1203618 TTTAAAGTTTAAAT
1 TTTATAGTTTATAT
*
1203632 TTTATATTTTATAT
1 TTTATAGTTTATAT
1203646 TTTA
1 TTTA
1203650 ATATATAACG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTATAGTTTATAT
Found at i:1203630 original size:28 final size:28
Alignment explanation
Indices: 1203597--1203650 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1203587 TTTAATAGTA
*
1203597 TTTAAAATTTATAGTTTATGTTTTAAAG
1 TTTAAAATTTATAGTTTATATTTTAAAG
* *
1203625 TTTAAATTTTATATTTTATATTTTAA
1 TTTAAAATTTATAGTTTATATTTTAA
1203651 TATATAACGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (28 bp):
TTTAAAATTTATAGTTTATATTTTAAAG
Found at i:1203650 original size:21 final size:21
Alignment explanation
Indices: 1203597--1203642 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1203587 TTTAATAGTA
* * * *
1203597 TTTAAAATTTATAGTTTATGT
1 TTTAAAGTTTAAATTTTATAT
1203618 TTTAAAGTTTAAATTTTATAT
1 TTTAAAGTTTAAATTTTATAT
1203639 TTTA
1 TTTA
1203643 TATTTTAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (21 bp):
TTTAAAGTTTAAATTTTATAT
Found at i:1207871 original size:16 final size:17
Alignment explanation
Indices: 1207845--1207877 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1207835 TCAAACAATC
1207845 ATTTATTTATTTAAATA
1 ATTTATTTATTTAAATA
*
1207862 ATTT-TTTATTTGAATA
1 ATTTATTTATTTAAATA
1207878 TGAATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
ATTTATTTATTTAAATA
Found at i:1207954 original size:19 final size:18
Alignment explanation
Indices: 1207932--1207978 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
1207922 AATGATAAAT
* *
1207932 TTAATTTTTAATCTTTTTG
1 TTAATATTTAAT-TTTTAG
1207951 TTAATATTTAATTTTTAG
1 TTAATATTTAATTTTTAG
1207969 TTAA-ATTTAA
1 TTAATATTTAA
1207979 CACTTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 6 0.23
18 9 0.35
19 11 0.42
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (18 bp):
TTAATATTTAATTTTTAG
Found at i:1215744 original size:29 final size:31
Alignment explanation
Indices: 1215712--1215770 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
1215702 CAAATTACCA
1215712 TTAACCG-AAT-TAACCGAACTTTTTTTTCT
1 TTAACCGTAATCTAACCGAACTTTTTTTTCT
1215741 TTAACCGTTAATCTAACCGAACTTTTTTTT
1 TTAACCG-TAATCTAACCGAACTTTTTTTT
1215771 GAAAATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 7 0.26
31 3 0.11
32 17 0.63
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.46
Consensus pattern (31 bp):
TTAACCGTAATCTAACCGAACTTTTTTTTCT
Found at i:1217769 original size:123 final size:123
Alignment explanation
Indices: 1217550--1217795 Score: 492
Period size: 123 Copynumber: 2.0 Consensus size: 123
1217540 TGGTGGTTTC
1217550 CGAGAGATGAATATGATATGCAGTAAGAGAGGACCACCAGCCATGATTGTCCTCTGGGAAAATGT
1 CGAGAGATGAATATGATATGCAGTAAGAGAGGACCACCAGCCATGATTGTCCTCTGGGAAAATGT
1217615 AATTATTTACTCTCTTTTGTCTCTTTGTGCCGATTCACTAGGATTTCTTCATTGATTT
66 AATTATTTACTCTCTTTTGTCTCTTTGTGCCGATTCACTAGGATTTCTTCATTGATTT
1217673 CGAGAGATGAATATGATATGCAGTAAGAGAGGACCACCAGCCATGATTGTCCTCTGGGAAAATGT
1 CGAGAGATGAATATGATATGCAGTAAGAGAGGACCACCAGCCATGATTGTCCTCTGGGAAAATGT
1217738 AATTATTTACTCTCTTTTGTCTCTTTGTGCCGATTCACTAGGATTTCTTCATTGATTT
66 AATTATTTACTCTCTTTTGTCTCTTTGTGCCGATTCACTAGGATTTCTTCATTGATTT
1217796 TAACCCAAAA
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 123 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (123 bp):
CGAGAGATGAATATGATATGCAGTAAGAGAGGACCACCAGCCATGATTGTCCTCTGGGAAAATGT
AATTATTTACTCTCTTTTGTCTCTTTGTGCCGATTCACTAGGATTTCTTCATTGATTT
Found at i:1217888 original size:47 final size:47
Alignment explanation
Indices: 1217820--1217913 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
1217810 TTTCAGATAT
1217820 ATGATGATGGGTTTATTCACTACAGAATTGGGTTGGGACGGGCTTGG
1 ATGATGATGGGTTTATTCACTACAGAATTGGGTTGGGACGGGCTTGG
1217867 ATGATGATGGGTTTATTCACTACAGAATTGGGTTGGGACGGGCTTGG
1 ATGATGATGGGTTTATTCACTACAGAATTGGGTTGGGACGGGCTTGG
1217914 TCATACACGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.21, C:0.11, G:0.36, T:0.32
Consensus pattern (47 bp):
ATGATGATGGGTTTATTCACTACAGAATTGGGTTGGGACGGGCTTGG
Found at i:1220838 original size:3 final size:3
Alignment explanation
Indices: 1220830--1220859 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1220820 TAATGCTGTA
1220830 ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1220860 CTATGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1223616 original size:206 final size:207
Alignment explanation
Indices: 1223261--1223674 Score: 821
Period size: 206 Copynumber: 2.0 Consensus size: 207
1223251 TGGTTAAAAG
1223261 ATTTAGTTAATACTTTTCATTTTTCCTAGATCGTGGGTTTAATATGCATTAAGAGTATTTTTTTA
1 ATTTAGTTAATACTTTTCATTTTTCCTAGATCGTGGGTTTAATATGCATTAAGAGTATTTTTTTA
1223326 ACCACTGTATACAAACTGTTTAACAAAAATCAGTATAAAAAGTCAATTTTTAAATAATTTTAATG
66 ACCACTGTATACAAACTGTTTAACAAAAATCAGTATAAAAAGTCAATTTTTAAATAATTTTAATG
1223391 ATTATTTTTAATTTGTATCAATGTCTCATCGGCAGTAATAAAATTTTAGAATATATTAAGAAACG
131 ATTATTTTTAATTTGTATCAATGTCTCATCGGCAGTAATAAAATTTTAGAATATATTAAGAAACG
1223456 AAAACAAACAAA
196 AAAACAAACAAA
1223468 ATTTAGTTAATACTTTTCATTTTTCCTAGATCGTGGGTTTAATATGCATTAAGAGTA-TTTTTTA
1 ATTTAGTTAATACTTTTCATTTTTCCTAGATCGTGGGTTTAATATGCATTAAGAGTATTTTTTTA
1223532 ACCACTGTATACAAACTGTTTAACAAAAATCAGTATAAAAAGTCAATTTTTAAATAATTTTAATG
66 ACCACTGTATACAAACTGTTTAACAAAAATCAGTATAAAAAGTCAATTTTTAAATAATTTTAATG
1223597 ATTATTTTTAATTTGTATCAATGTCTCATCGGCAGTAATAAAATTTTAGAATATATTAAGAAACG
131 ATTATTTTTAATTTGTATCAATGTCTCATCGGCAGTAATAAAATTTTAGAATATATTAAGAAACG
1223662 AAAACAAACAAA
196 AAAACAAACAAA
1223674 A
1 A
1223675 AATGATGATT
Statistics
Matches: 207, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
206 150 0.72
207 57 0.28
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (207 bp):
ATTTAGTTAATACTTTTCATTTTTCCTAGATCGTGGGTTTAATATGCATTAAGAGTATTTTTTTA
ACCACTGTATACAAACTGTTTAACAAAAATCAGTATAAAAAGTCAATTTTTAAATAATTTTAATG
ATTATTTTTAATTTGTATCAATGTCTCATCGGCAGTAATAAAATTTTAGAATATATTAAGAAACG
AAAACAAACAAA
Found at i:1225998 original size:13 final size:13
Alignment explanation
Indices: 1225980--1226018 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1225970 TCTGAAGCAG
1225980 TCATACGACTGCA
1 TCATACGACTGCA
1225993 TCATACGACTGCA
1 TCATACGACTGCA
1226006 TCATACGACTGCA
1 TCATACGACTGCA
1226019 AAACAAGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (13 bp):
TCATACGACTGCA
Found at i:1234815 original size:3 final size:3
Alignment explanation
Indices: 1234807--1234854 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
1234797 ATAATTATCT
* * *
1234807 TTA TTA TTA ATA TTA TTG TTA TTA GTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
1234853 TT
1 TT
1234855 TAAAACCAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1240287 original size:32 final size:32
Alignment explanation
Indices: 1240213--1240287 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
1240203 GCATCTTTAA
* *
1240213 AGATTCAACAATAAATGTTAGGGCATATTTGG
1 AGATTCAACATTAAATATTAGGGCATATTTGG
* * *
1240245 AGATTTAACATTGAATATTGGGGCATATTTGG
1 AGATTCAACATTAAATATTAGGGCATATTTGG
*
1240277 GGATTCAACAT
1 AGATTCAACAT
1240288 CCTGATGCAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (32 bp):
AGATTCAACATTAAATATTAGGGCATATTTGG
Found at i:1241343 original size:64 final size:65
Alignment explanation
Indices: 1241267--1241390 Score: 189
Period size: 64 Copynumber: 1.9 Consensus size: 65
1241257 ATGCATGATT
* * *
1241267 TTAAATAGAAAACATCGAATAGGA-TTTATGCATCGATGCATAAGTAGTGCATCAATGCATCCCC
1 TTAAATAGAAAACATCGAAT-GCATTTTATGCACCGATGCACAAGTAGTGCATCAATGCATCCCC
1241331 A
65 A
*
1241332 TTAAATA-AAAACATCGAATGCATTTTATGCACCGATGCACAAGTAGTGCATCGATGCAT
1 TTAAATAGAAAACATCGAATGCATTTTATGCACCGATGCACAAGTAGTGCATCAATGCAT
1241391 ACATTCATTG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
63 2 0.04
64 45 0.83
65 7 0.13
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (65 bp):
TTAAATAGAAAACATCGAATGCATTTTATGCACCGATGCACAAGTAGTGCATCAATGCATCCCCA
Found at i:1241905 original size:17 final size:19
Alignment explanation
Indices: 1241883--1241918 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1241873 GATTTACATG
1241883 AATACATGT-ATAT-ATAT
1 AATACATGTGATATGATAT
1241900 AATACATGTGATATGATAT
1 AATACATGTGATATGATAT
1241919 GAGATATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (19 bp):
AATACATGTGATATGATAT
Found at i:1242088 original size:31 final size:30
Alignment explanation
Indices: 1242049--1242122 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
1242039 GTCGAGGGTT
**
1242049 TTACCTATG-TCTTTCGAGACATATGGACAA
1 TTACCTATGTTCTAACGA-ACATATGGACAA
*
1242079 TATACCTATGTTCTAAGGAACATATGGACAA
1 T-TACCTATGTTCTAACGAACATATGGACAA
*
1242110 TTACCTAGGTTCT
1 TTACCTATGTTCT
1242123 TTGGGACCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 12 0.32
31 21 0.55
32 5 0.13
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (30 bp):
TTACCTATGTTCTAACGAACATATGGACAA
Found at i:1243169 original size:21 final size:21
Alignment explanation
Indices: 1243145--1243209 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 21
1243135 AGGGCCATCC
1243145 ATGATTTCAACTCCATGACGG
1 ATGATTTCAACTCCATGACGG
* * *
1243166 ATGATATCATAC-CCACGAATC-C
1 ATGATTTCA-ACTCCATG-A-CGG
*
1243188 ACGATTTCAACTCCATGACGG
1 ATGATTTCAACTCCATGACGG
1243209 A
1 A
1243210 GGATATTGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 10
0.65 0.14 0.20
Matches are distributed among these distances:
20 1 0.03
21 16 0.50
22 14 0.44
23 1 0.03
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (21 bp):
ATGATTTCAACTCCATGACGG
Found at i:1243194 original size:43 final size:43
Alignment explanation
Indices: 1243141--1243285 Score: 184
Period size: 43 Copynumber: 3.4 Consensus size: 43
1243131 ACGAAGGGCC
* * *
1243141 ATCCATGATTTCAACTCCATGACGGATGATATCATACCCACGA
1 ATCCACGATTTCAACTCCATGACGGAGGATATCGTACCCACGA
* *
1243184 ATCCACGATTTCAACTCCATGACGGAGGATATTGTACCCACGG
1 ATCCACGATTTCAACTCCATGACGGAGGATATCGTACCCACGA
* * *
1243227 ATCCACGATTTCAACTCCACGACAGAGGATATCGTCCCCAC-A
1 ATCCACGATTTCAACTCCATGACGGAGGATATCGTACCCACGA
* *
1243269 CAACCACGGTTTCAACT
1 -ATCCACGATTTCAACT
1243286 TCACGGTAAA
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
43 89 1.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCATGACGGAGGATATCGTACCCACGA
Found at i:1243479 original size:43 final size:43
Alignment explanation
Indices: 1243396--1243514 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 43
1243386 ACCATCCATG
* * **
1243396 ATTTTAACTCCACAACGGAGGATATCGTACCCACGGATCCACA
1 ATTTTAACTCCACGACGGAGGATATCGTGCCCACACATCCACA
* *
1243439 ATTTCAACTCCACGACGGAGGATATCGTGCCCACACATCCACG
1 ATTTTAACTCCACGACGGAGGATATCGTGCCCACACATCCACA
** *
1243482 ATTTTAACAT-CACGACAAAGGATTTCGTGCCCA
1 ATTTTAAC-TCCACGACGGAGGATATCGTGCCCA
1243515 TCAACAATAT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 64 0.98
44 1 0.02
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (43 bp):
ATTTTAACTCCACGACGGAGGATATCGTGCCCACACATCCACA
Found at i:1243717 original size:36 final size:36
Alignment explanation
Indices: 1243662--1243767 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
1243652 CTTTAAAAAT
* *
1243662 GTTTCCCTTCAAACGAATTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATA
* *
1243698 GTTTCCCTTGAAATAAATTTTTTCTCTCTTGAGATA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATA
* *
1243734 GTTTCCCTTGGAACAAATTTTGTCTCCCTTGAGA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA
1243768 CAATTTCTCT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATA
Found at i:1243780 original size:36 final size:36
Alignment explanation
Indices: 1243662--1243784 Score: 156
Period size: 36 Copynumber: 3.4 Consensus size: 36
1243652 CTTTAAAAAT
** *
1243662 GTTTCCCTTCAAACGAATTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGGAACAAATTTTGTCTCTCTTGAGATA
* * *
1243698 GTTTCCCTTGAAATAAATTTTTTCTCTCTTGAGATA
1 GTTTCCCTTGGAACAAATTTTGTCTCTCTTGAGATA
* *
1243734 GTTTCCCTTGGAACAAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGGAACAAATTTTGTCTCTCTTGAGATA
* *
1243770 ATTTCTCTTGGAACA
1 GTTTCCCTTGGAACA
1243785 TAAACTTTGA
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 76 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (36 bp):
GTTTCCCTTGGAACAAATTTTGTCTCTCTTGAGATA
Found at i:1243808 original size:29 final size:30
Alignment explanation
Indices: 1243762--1243845 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 30
1243752 TTTGTCTCCC
* * * *
1243762 TTGAGACAATTTCTCTTGGAACATAAA-CT
1 TTGAAACAGTTTCCCTTGAAACATAAATCT
*
1243791 TTGAAA-ACGTTTCCCTTGAAACACAAAATCT
1 TTGAAACA-GTTTCCCTTGAAACA-TAAATCT
*
1243822 TTGAATCAGTTTCCCTTGAAACAT
1 TTGAAACAGTTTCCCTTGAAACAT
1243846 GTTTTTGTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
28 1 0.02
29 17 0.39
30 3 0.07
31 22 0.50
32 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (30 bp):
TTGAAACAGTTTCCCTTGAAACATAAATCT
Found at i:1243913 original size:94 final size:93
Alignment explanation
Indices: 1243733--1243973 Score: 283
Period size: 94 Copynumber: 2.5 Consensus size: 93
1243723 CTCTTGAGAT
* * * * *
1243733 AGTTTCCCTTGGAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGGAACATAAACTTTGAAAA
1 AGTTTCCCTTGAAAC-AGTTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACTTTG--AA
1243798 CGTTTCCCTTGAAACACAAAATCTTTGAATC
63 CGTTTCCCTTGAAACACAAAATCTTTGAATC
* * *
1243829 AGTTTCCCTTGAAACATGTTTTTGTCTCCCTTGAGACGGTTTCCCTTGAAACA-AAATTTTG-TC
1 AGTTTCCCTTGAAACA-G-TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACTTTGAAC
*
1243892 GGTTTCCCTTGAAACATAAAATCTTTGAATC
64 -GTTTCCCTTGAAACACAAAATCTTTGAATC
* *
1243923 A-TTTCCCCTTGAAACGAGTTTTGTCTCTCTTGAGACAGTGTCCC-TGAAACA
1 AGTTT-CCCTTGAAAC-AGTTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
1243974 CCTACATTTG
Statistics
Matches: 128, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
92 7 0.05
93 27 0.21
94 41 0.32
95 2 0.02
96 21 0.16
97 30 0.23
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (93 bp):
AGTTTCCCTTGAAACAGTTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACTTTGAACGT
TTCCCTTGAAACACAAAATCTTTGAATC
Found at i:1244125 original size:33 final size:33
Alignment explanation
Indices: 1244017--1244131 Score: 92
Period size: 33 Copynumber: 3.4 Consensus size: 33
1244007 TTTGTCTTTC
*
1244017 TTGAGATCGTTTCTCATGGAACAACAACCAA-A-CT
1 TTGAGATCGTTTCTCAT-GAA-AA-AACAAATATCT
* * * *
1244051 TTGAGAT-GTTTCTCTTGAAACAAATCCTATTTTCT
1 TTGAGATCGTTTCTCATGAAA-AAA--CAAATATCT
*
1244086 TTGAGATCGTTTCTCATGAAAGAACAAATATCT
1 TTGAGATCGTTTCTCATGAAAAAACAAATATCT
*
1244119 TTGAGATAGTTTC
1 TTGAGATCGTTTC
1244132 CCTTTAAACG
Statistics
Matches: 65, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
31 3 0.05
32 4 0.06
33 28 0.43
34 7 0.11
35 11 0.17
36 12 0.18
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (33 bp):
TTGAGATCGTTTCTCATGAAAAAACAAATATCT
Found at i:1244158 original size:69 final size:67
Alignment explanation
Indices: 1243980--1244160 Score: 174
Period size: 69 Copynumber: 2.6 Consensus size: 67
1243970 AACACCTACA
* *
1243980 TTTGAGATTGTTTCCCTTGAAACATGTTTTGTCT-TTCTTGAGATCGTTTCTCATGGAACAACAA
1 TTTGAGA-TGTTTCCCTTGAAACA-ATTTTGTCTCTT-TTGAGATCGTTTCTCATGAAACAACAA
1244044 CCAAAC
63 -CAAAC
* *
1244050 TTTGAGATGTTTCTCTTGAAACAAATCCTATT-T-TC-TTTGAGATCGTTTCTCATGAAAGAACA
1 TTTGAGATGTTTCCCTTGAAAC-AAT--T-TTGTCTCTTTTGAGATCGTTTCTCATGAAACAACA
*
1244112 A-ATATC
62 ACA-AAC
*
1244118 TTTGAGATAGTTTCCCTTTAAACGAATTTTGTCTCTTTTGAGA
1 TTTGAGAT-GTTTCCCTTGAAAC-AATTTTGTCTCTTTTGAGA
1244161 CAGCTTCTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
66 2 0.02
67 3 0.03
68 12 0.13
69 62 0.67
70 10 0.11
71 2 0.02
72 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (67 bp):
TTTGAGATGTTTCCCTTGAAACAATTTTGTCTCTTTTGAGATCGTTTCTCATGAAACAACAACAA
AC
Found at i:1244458 original size:129 final size:129
Alignment explanation
Indices: 1244231--1244685 Score: 527
Period size: 129 Copynumber: 3.5 Consensus size: 129
1244221 TGGCATGCCG
* * * * *
1244231 TCCTCATAACATAGGAACCGTGTCATCACCTGACCTGATCTCCGCATCACGTAGGAGCCGTGTCA
1 TCCTCATCACATAAGAACCGTGTCATCACCCGACCTGATCTCCTCATCACGTAAGAGCCGTGTCA
* * * * * * * * *
1244296 ACCCCAGTTAACCAGTTATCCTCATTATGTAGGAATCGTATTATCACCTTTAGATAGCCTACCG
66 ACCCCAGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTACCA
* * * * *
1244360 TCCTCATCACATAAGAACCGTGCCATCACCCGACCTAATCTCCTCATCACGTAGGAGTCTTGTCA
1 TCCTCATCACATAAGAACCGTGTCATCACCCGACCTGATCTCCTCATCACGTAAGAGCCGTGTCA
*
1244425 ACCCCAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCC-AGCCA
66 ACCCCAGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTA-CCA
* * * * * *
1244489 TTCTCATCACGTAGGAACTGTGTCTTCATCCGACCTGATCTCCTCATCACGTAAGAGCCGTGTCA
1 TCCTCATCACATAAGAACCGTGTCATCACCCGACCTGATCTCCTCATCACGTAAGAGCCGTGTCA
* * * * * * **
1244554 ACCCTAGATAACCAGTCGTCTTCATCACATAGGAACCATGTTATCACCCTCAGATGGTTTACCA
66 ACCCCAGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTACCA
* ** * *
1244618 TCCTCATCACAT-AGAAACCGTGTCATCGCCCGATATGATCTCTTCATCACGTAAGAGTCGTGTC
1 TCCTCATCACATAAG-AACCGTGTCATCACCCGACCTGATCTCCTCATCACGTAAGAGCCGTGTC
1244682 AACC
65 AACC
1244686 TTTAGACGAC
Statistics
Matches: 274, Mismatches: 49, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
128 2 0.01
129 271 0.99
130 1 0.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (129 bp):
TCCTCATCACATAAGAACCGTGTCATCACCCGACCTGATCTCCTCATCACGTAAGAGCCGTGTCA
ACCCCAGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCTACCA
Found at i:1245504 original size:145 final size:146
Alignment explanation
Indices: 1245239--1245521 Score: 337
Period size: 145 Copynumber: 1.9 Consensus size: 146
1245229 TCGGATTCTC
* *
1245239 GCCGGTGATCGGGATCTCCAATCAACATTCCGAACAGTCAAAAGTTGCGCAAGCCCAGCACAGAC
1 GCCGGCGATCGGGATCTCCAATCAACATTCCGAACAGTCAAAAGTTGCGCAAGACCAGCACAGAC
** * *
1245304 AACATACTGAAAATTCAGGACAATCAGACGGTGGACAGCGGCGGATCGGTAAAAAT-AAGCTGAA
66 AACATACTGAAAATTCAGGACAATCAGACGGTGGACAGCGGCACATCGGAAAAAATAAAGCCGAA
1245368 CGGTTTTTGGCCTCTT
131 CGGTTTTTGGCCTCTT
* ** *
1245384 GCCGGCGATCGGGAT-TACCGATCAACA-TCTCGAA-AGGTCAAAAGTTGCGTGAGACCAGCA-T
1 GCCGGCGATCGGGATCT-CCAATCAACATTC-CGAACA-GTCAAAAGTTGCGCAAGACCAGCACA
* * *
1245445 GAACAACATACTGAAAATTCAGGACGATCGGACGGTGGAC-GATGGCACATC-GAAGAAAATAAA
63 G-ACAACATACTGAAAATTCAGGACAATCAGACGGTGGACAG-CGGCACATCGGAA-AAAATAAA
*
1245508 TCCGAACGGTTTTT
125 GCCGAACGGTTTTT
1245522 AACCTTTTTA
Statistics
Matches: 117, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
144 8 0.07
145 95 0.81
146 14 0.12
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (146 bp):
GCCGGCGATCGGGATCTCCAATCAACATTCCGAACAGTCAAAAGTTGCGCAAGACCAGCACAGAC
AACATACTGAAAATTCAGGACAATCAGACGGTGGACAGCGGCACATCGGAAAAAATAAAGCCGAA
CGGTTTTTGGCCTCTT
Found at i:1255483 original size:20 final size:20
Alignment explanation
Indices: 1255454--1255491 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1255444 TTTCAAAGAA
1255454 ATGCACCGATGCACCAATCT
1 ATGCACCGATGCACCAATCT
*
1255474 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
1255492 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCT
Found at i:1255571 original size:65 final size:64
Alignment explanation
Indices: 1255502--1255661 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 64
1255492 GAATAAATTG
* * *
1255502 AACATCAAATGCATTTTATGCATCGATGCACACA-CCATGCATCGATGCACTCAGG-TTTTTATG
1 AACATCAAATGCATTTCATGCATCGATGCACA-AGACATGCATCGATGCACTCAGGCTATTT-TG
1255565 AA
64 -A
* *
1255567 AACATCAAATGCATTTGATGCATCGATGCACAAGACGTGCATCGATGCACTCAGGCTATTTTGA
1 AACATCAAATGCATTTCATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTTTGA
* * * *
1255631 AACATCGAATGCACTTCATACATCGTTGCAC
1 AACATCAAATGCATTTCATGCATCGATGCAC
1255662 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 28 0.33
65 52 0.62
66 4 0.05
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCAAATGCATTTCATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTTTGA
Found at i:1257071 original size:211 final size:211
Alignment explanation
Indices: 1256707--1257128 Score: 844
Period size: 211 Copynumber: 2.0 Consensus size: 211
1256697 GCCATCTATA
1256707 TCGTATTTTGTGCTCTTAGACCAGATGAATATGGAAGAGTTTCATCTTGTACAACCGCCAAAGAA
1 TCGTATTTTGTGCTCTTAGACCAGATGAATATGGAAGAGTTTCATCTTGTACAACCGCCAAAGAA
1256772 ATATGGGATAAACTACAAGTCACTCATTAAGGCACCGACGAGGTAAAAAAATCTAAAATTAATCT
66 ATATGGGATAAACTACAAGTCACTCATTAAGGCACCGACGAGGTAAAAAAATCTAAAATTAATCT
1256837 TCTAACACATAGCTATAAAAATTTCATGATGAAACCAAATAAAAACATCAAAGCCATGACAGATA
131 TCTAACACATAGCTATAAAAATTTCATGATGAAACCAAATAAAAACATCAAAGCCATGACAGATA
1256902 GATTTTCAACGATTGT
196 GATTTTCAACGATTGT
1256918 TCGTATTTTGTGCTCTTAGACCAGATGAATATGGAAGAGTTTCATCTTGTACAACCGCCAAAGAA
1 TCGTATTTTGTGCTCTTAGACCAGATGAATATGGAAGAGTTTCATCTTGTACAACCGCCAAAGAA
1256983 ATATGGGATAAACTACAAGTCACTCATTAAGGCACCGACGAGGTAAAAAAATCTAAAATTAATCT
66 ATATGGGATAAACTACAAGTCACTCATTAAGGCACCGACGAGGTAAAAAAATCTAAAATTAATCT
1257048 TCTAACACATAGCTATAAAAATTTCATGATGAAACCAAATAAAAACATCAAAGCCATGACAGATA
131 TCTAACACATAGCTATAAAAATTTCATGATGAAACCAAATAAAAACATCAAAGCCATGACAGATA
1257113 GATTTTCAACGATTGT
196 GATTTTCAACGATTGT
1257129 CAATGGTCTC
Statistics
Matches: 211, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
211 211 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.27
Consensus pattern (211 bp):
TCGTATTTTGTGCTCTTAGACCAGATGAATATGGAAGAGTTTCATCTTGTACAACCGCCAAAGAA
ATATGGGATAAACTACAAGTCACTCATTAAGGCACCGACGAGGTAAAAAAATCTAAAATTAATCT
TCTAACACATAGCTATAAAAATTTCATGATGAAACCAAATAAAAACATCAAAGCCATGACAGATA
GATTTTCAACGATTGT
Found at i:1265662 original size:48 final size:48
Alignment explanation
Indices: 1265591--1265687 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
1265581 GCTTTTGTAG
1265591 AAAATTGAAAAGATTTGCACAGTGATTTAGAGTGGTTCGACTTTCTCA
1 AAAATTGAAAAGATTTGCACAGTGATTTAGAGTGGTTCGACTTTCTCA
1265639 AAAATTGAAAAGATTTGCACAGTGATTTAGAGTGGTTCGACTTTCTCA
1 AAAATTGAAAAGATTTGCACAGTGATTTAGAGTGGTTCGACTTTCTCA
1265687 A
1 A
1265688 CCAAAGTCTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (48 bp):
AAAATTGAAAAGATTTGCACAGTGATTTAGAGTGGTTCGACTTTCTCA
Found at i:1266367 original size:64 final size:63
Alignment explanation
Indices: 1266284--1266492 Score: 235
Period size: 65 Copynumber: 3.2 Consensus size: 63
1266274 TTCACTAAGA
* *
1266284 GTGCATCGATGCATGAAATGCATTCGTTGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGG-TG
* * * *
1266348 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAATCTCTA-AGTGCATCGATGCATAGTA
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGT-
*
1266412 T
63 G
* **
1266413 GTGCATCGATGCATGAAATGTATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATA-TCCA-GAGTGCATCGATGCATGG--
1266476 TG
62 TG
1266478 GTGCATCGATGCATG
1 GTGCATCGATGCATG
1266493 GATTGGTGTA
Statistics
Matches: 122, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
62 2 0.02
63 7 0.06
64 43 0.35
65 63 0.52
66 7 0.06
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTG
Found at i:1266481 original size:20 final size:20
Alignment explanation
Indices: 1266456--1266511 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1266446 ATTTATTCCA
1266456 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
1266476 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
* *
1266496 TGGTGTATCGGTGCAT
1 TGGTGCATCGATGCAT
1266512 CACTTGGCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32
Consensus pattern (20 bp):
TGGTGCATCGATGCATGGAT
Found at i:1267685 original size:6 final size:6
Alignment explanation
Indices: 1267674--1267700 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1267664 ATAAAATATA
1267674 ATAATT ATAATT ATAATT ATAATT ATA
1 ATAATT ATAATT ATAATT ATAATT ATA
1267701 GAAAATCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATAATT
Found at i:1270618 original size:23 final size:22
Alignment explanation
Indices: 1270590--1270650 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 22
1270580 TTTAAATAAA
1270590 TAATAATTATATAAATATTATTT
1 TAATAATTATATAAATATTA-TT
* *
1270613 TAATAA--AAATAAA-AATATT
1 TAATAATTATATAAATATTATT
*
1270632 TATATAATTATATTAATAT
1 TA-ATAATTATATAAATAT
1270651 AAAATATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
19 4 0.14
20 7 0.24
21 6 0.21
22 5 0.17
23 7 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATAATTATATAAATATTATT
Found at i:1270642 original size:32 final size:37
Alignment explanation
Indices: 1270583--1270671 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 37
1270573 TAATAAATTT
*
1270583 AAATAAATAATAATTATATAAATATTATTTTAATA-A
1 AAATAAATAATAATTATATAAATATTATATTAATATA
*
1270619 AAATAAA-AAT-ATT-TATATA-ATTATATTAATATA
1 AAATAAATAATAATTATATAAATATTATATTAATATA
*
1270652 AAAT--ATAATAATTATTTAAA
1 AAATAAATAATAATTATATAAA
1270672 AAAATAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
31 1 0.02
32 14 0.31
33 13 0.29
34 7 0.16
35 3 0.07
36 7 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (37 bp):
AAATAAATAATAATTATATAAATATTATATTAATATA
Found at i:1270675 original size:21 final size:24
Alignment explanation
Indices: 1270635--1270677 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1270625 AAATATTTAT
1270635 ATAATTATATTAATATAAAATATA
1 ATAATTATATTAATATAAAATATA
1270659 ATAATTAT-TTAA-A-AAAATA
1 ATAATTATATTAATATAAAATA
1270678 ATAACTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 4 0.21
24 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATAATTATATTAATATAAAATATA
Found at i:1275178 original size:23 final size:23
Alignment explanation
Indices: 1275148--1275193 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1275138 GATAAATCCA
1275148 ACTTATAGAATTACAAGTTTCTT
1 ACTTATAGAATTACAAGTTTCTT
1275171 ACTTATAGAATTACAAGTTTCTT
1 ACTTATAGAATTACAAGTTTCTT
1275194 CTCTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (23 bp):
ACTTATAGAATTACAAGTTTCTT
Found at i:1277757 original size:17 final size:17
Alignment explanation
Indices: 1277735--1277776 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
1277725 ACTCCCACTG
1277735 CTTGTGCAATGTCTGGT
1 CTTGTGCAATGTCTGGT
1277752 CTTGTGCAATGTCTGGT
1 CTTGTGCAATGTCTGGT
1277769 CTTGTGCA
1 CTTGTGCA
1277777 TATCATAGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.12, C:0.19, G:0.29, T:0.40
Consensus pattern (17 bp):
CTTGTGCAATGTCTGGT
Found at i:1283238 original size:14 final size:14
Alignment explanation
Indices: 1283228--1283268 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1283218 GGTTTTATAT
1283228 TTTGGGATTTAGTG
1 TTTGGGATTTAGTG
*
1283242 TTTGGGATTTTAGGG
1 TTTGGGA-TTTAGTG
*
1283257 TTTGTGATTTAG
1 TTTGGGATTTAG
1283269 AGTTAGGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.15, C:0.00, G:0.34, T:0.51
Consensus pattern (14 bp):
TTTGGGATTTAGTG
Done.