Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 1 of 345
Found at i:3629 original size:75 final size:73
Alignment explanation
Indices: 3541--3710 Score: 213
Period size: 75 Copynumber: 2.3 Consensus size: 73
3531 GGTTTTCCTC
*** * * **
3541 ATTGAAATACCATACCTACATTTTTTAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
3605 TCAGTATGG
65 TCAGTATGG
*
3614 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
3679 CTCAGTATGG
64 CTCAGTATGG
3689 A-TG--ATACCATACCTACATTTCA
1 ATTGAAATACCATACCTACATTTCA
3711 TACTTTGCCA
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
70 19 0.22
73 3 0.03
74 7 0.08
75 57 0.66
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:3710 original size:35 final size:35
Alignment explanation
Indices: 3546--3710 Score: 188
Period size: 35 Copynumber: 4.6 Consensus size: 35
3536 TCCTCATTGA
*** *
3546 AATACCATACCTACATTTTTTAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
3581 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
3621 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
3656 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
3691 GATACCATACCTACATTTCA
1 AATACCATACCTACATTTCA
3711 TACTTTGCCA
Statistics
Matches: 116, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
35 86 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:5245 original size:23 final size:24
Alignment explanation
Indices: 5219--5264 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5209 ATATTTTCAA
5219 ATTAA-ATTTT-ACAAATAATATAT
1 ATTAAGATTTTGA-AAATAATATAT
*
5242 ATTAAGTTTTTGAAAATAATATA
1 ATTAAGATTTTGAAAATAATATA
5265 AAATTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 14 0.70
25 1 0.05
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (24 bp):
ATTAAGATTTTGAAAATAATATAT
Found at i:5393 original size:16 final size:16
Alignment explanation
Indices: 5374--5406 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5364 AAACATTACC
5374 AATT-TAAATATTATTT
1 AATTGTAAATATT-TTT
5390 AATTGTAAATATTTTT
1 AATTGTAAATATTTTT
5406 A
1 A
5407 CTTATAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
AATTGTAAATATTTTT
Found at i:10824 original size:19 final size:19
Alignment explanation
Indices: 10774--10824 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
10764 ATTTATTATA
* *
10774 TTTTA-TAATATTTATAAG
1 TTTTATTAATTTTTTTAAG
*
10792 TTTTCTTAATTTTTTTAAG
1 TTTTATTAATTTTTTTAAG
10811 TTTATATTAATTTT
1 TTT-TATTAATTTT
10825 AATATTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 4 0.15
19 14 0.52
20 9 0.33
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (19 bp):
TTTTATTAATTTTTTTAAG
Found at i:10854 original size:9 final size:9
Alignment explanation
Indices: 10757--10873 Score: 55
Period size: 9 Copynumber: 12.4 Consensus size: 9
10747 GGTTTGTTAA
10757 TTTTATAAT
1 TTTTATAAT
10766 TTATTAT-A-
1 TT-TTATAAT
10774 TTTTATAAT
1 TTTTATAAT
*
10783 ATTTATAAGT
1 TTTTATAA-T
10793 TTTCT-TAAT
1 TTT-TATAAT
*
10802 TTTTTTAAGT
1 TTTTATAA-T
*
10812 TTATATTAAT
1 TTTTA-TAAT
10822 TTTAATATTAAT
1 TTT--TA-TAAT
10834 ATTTT-T-AT
1 -TTTTATAAT
10842 TTTTATAAT
1 TTTTATAAT
* *
10851 TTTTCTGAT
1 TTTTATAAT
*
10860 TTTTTTAAT
1 TTTTATAAT
10869 ATTTT
1 -TTTT
10874 TATGAGAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 27
0.70 0.07 0.22
Matches are distributed among these distances:
7 8 0.09
8 7 0.08
9 34 0.40
10 21 0.25
11 5 0.06
12 7 0.08
13 3 0.04
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Found at i:20042 original size:38 final size:38
Alignment explanation
Indices: 19944--20063 Score: 143
Period size: 38 Copynumber: 3.1 Consensus size: 38
19934 TTTAAGCTCA
* *
19944 GATATAATACCAGCACTAGGCTTGCGGGATTTAACCCG
1 GATATAATACCAGCACTAAGCCTGCGGGATTTAACCCG
* * * *
19982 GATATAATAACAACACGAAGCCTGCGAGATTTAACCCG
1 GATATAATACCAGCACTAAGCCTGCGGGATTTAACCCG
*
20020 GATATAATACCAGCA-TATAGCCTGCGGGTCTTTAAGCCCG
1 GATATAATACCAGCACTA-AGCCTGCGGG-ATTTAA-CCCG
20060 GATA
1 GATA
20064 CACATCAAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
37 1 0.01
38 54 0.79
39 5 0.07
40 8 0.12
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.23
Consensus pattern (38 bp):
GATATAATACCAGCACTAAGCCTGCGGGATTTAACCCG
Found at i:22603 original size:47 final size:46
Alignment explanation
Indices: 22499--22626 Score: 134
Period size: 47 Copynumber: 2.7 Consensus size: 46
22489 TCACACATTA
* * *
22499 CACACCGAAGCCATAGCCCAACTATGGTCTTACA-AGGATCACATAT
1 CACACCGATGCCATATCCCAA-TATGGTCTTATACAGGATCACATAT
** *
22545 CACACTAATGCCATATCCCAGATATGGTCTTATACAGTAGT-ACATAT
1 CACACCGATGCCATATCCCA-ATATGGTCTTATACAGGA-TCACATAT
* *
22592 CACACCGATGCCATATCTCAAACATGGTCTTATAC
1 CACACCGATGCCATATC-CCAATATGGTCTTATAC
22627 GGAAGCACAT
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
46 27 0.40
47 38 0.56
48 3 0.04
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (46 bp):
CACACCGATGCCATATCCCAATATGGTCTTATACAGGATCACATAT
Found at i:30693 original size:13 final size:13
Alignment explanation
Indices: 30675--30700 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30665 ATTTAATTCT
30675 TCATAAAATTTTA
1 TCATAAAATTTTA
30688 TCATAAAATTTTA
1 TCATAAAATTTTA
30701 ACAAAGAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TCATAAAATTTTA
Found at i:32143 original size:26 final size:26
Alignment explanation
Indices: 32114--32166 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
32104 TCTGATCACA
32114 AGTTAAACGTGAAAGTTGATTATAAC
1 AGTTAAACGTGAAAGTTGATTATAAC
*
32140 AGTTAAATGTGAAAGTTGATTATAAC
1 AGTTAAACGTGAAAGTTGATTATAAC
32166 A
1 A
32167 CCAATCCCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (26 bp):
AGTTAAACGTGAAAGTTGATTATAAC
Found at i:33496 original size:23 final size:23
Alignment explanation
Indices: 33464--33507 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
33454 ACTACCATTT
33464 TCTAAATAAAATAATAATAAATC
1 TCTAAATAAAATAATAATAAATC
* *
33487 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
33508 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATC
Found at i:42575 original size:19 final size:19
Alignment explanation
Indices: 42522--42578 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 19
42512 GCATCTTTTC
* **
42522 ATGTTTTA-AAATTCTTTC
1 ATGTTTTAGAAATTATTAA
*
42540 ATGTTTTCAGTAATTATTAA
1 ATGTTTT-AGAAATTATTAA
42560 ATGTTTTAGAAATTATTAA
1 ATGTTTTAGAAATTATTAA
42579 TCTCTTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 7 0.22
19 12 0.38
20 13 0.41
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (19 bp):
ATGTTTTAGAAATTATTAA
Found at i:43202 original size:11 final size:12
Alignment explanation
Indices: 43175--43202 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
43165 TTAAAACTAG
43175 TTTTTGTTTGAC
1 TTTTTGTTTGAC
43187 TTTTTGTTTGAC
1 TTTTTGTTTGAC
43199 TTTT
1 TTTT
43203 AACACTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.14, T:0.71
Consensus pattern (12 bp):
TTTTTGTTTGAC
Found at i:58078 original size:36 final size:36
Alignment explanation
Indices: 58008--58078 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
57998 TTTGGTATCG
*
58008 AAATTAAATTTTATACTTTTATAATTTTAAAAAATT
1 AAATTAAATTTTATACTTTTATAATATTAAAAAATT
*
58044 AAATTAAATTATTATTA-TTTTATAA-ATTATAAAAT
1 AAATTAAATT-TTA-TACTTTTATAATATTAAAAAAT
58079 GAATACTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 18 0.58
37 11 0.35
38 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (36 bp):
AAATTAAATTTTATACTTTTATAATATTAAAAAATT
Found at i:61687 original size:15 final size:15
Alignment explanation
Indices: 61667--61696 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61657 AATAATAATT
61667 ATAATAGTAAAAATA
1 ATAATAGTAAAAATA
*
61682 ATAATAGTAATAATA
1 ATAATAGTAAAAATA
61697 GCTAAGTGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
ATAATAGTAAAAATA
Found at i:62096 original size:3 final size:3
Alignment explanation
Indices: 62090--62198 Score: 71
Period size: 3 Copynumber: 36.3 Consensus size: 3
62080 ATAGTTGTAG
* * * * * * *
62090 TAA TAA TAA TAG TAA GAA AAA TAG TGA TAA T-A TAA CAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * **
62137 T-A TAA CAA -AA GAA TAA TAA TAA TAA TAA TTG TAA TGGAGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T--A-A TAA TAA
62183 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
62199 GATACTAAGA
Statistics
Matches: 81, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
2 6 0.07
3 71 0.88
4 1 0.01
5 1 0.01
6 2 0.02
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:62134 original size:20 final size:21
Alignment explanation
Indices: 62095--62134 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
62085 TGTAGTAATA
*
62095 ATAATAGTAAGAAAAATAGTG
1 ATAATAGTAACAAAAATAGTG
*
62116 ATAATA-TAACAATAATAGT
1 ATAATAGTAACAAAAATAGT
62135 AATATAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.57, C:0.03, G:0.12, T:0.28
Consensus pattern (21 bp):
ATAATAGTAACAAAAATAGTG
Found at i:63363 original size:33 final size:33
Alignment explanation
Indices: 63319--63387 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
63309 AGTGTCAGAC
63319 GCGTGGAGCGTGGTGACCAAGGCTGAGGGGCAT
1 GCGTGGAGCGTGGTGACCAAGGCTGAGGGGCAT
* * * *
63352 GCGTGGGGCGTGGTGGCCAAGGTTGAGGGGTAT
1 GCGTGGAGCGTGGTGACCAAGGCTGAGGGGCAT
63385 GCG
1 GCG
63388 GCGGCTGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.14, C:0.16, G:0.52, T:0.17
Consensus pattern (33 bp):
GCGTGGAGCGTGGTGACCAAGGCTGAGGGGCAT
Found at i:66523 original size:24 final size:26
Alignment explanation
Indices: 66496--66547 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
66486 AAAATGAGAA
66496 TTTTATA-ATTT-AATTTAAATAATT
1 TTTTATATATTTAAATTTAAATAATT
*
66520 TTTTATATTTTTTAAATTTAAATAATT
1 TTTTATA-TATTTAAATTTAAATAATT
66547 T
1 T
66548 ATAATCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
26 3 0.12
27 14 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTATATATTTAAATTTAAATAATT
Found at i:66557 original size:27 final size:27
Alignment explanation
Indices: 66507--66558 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
66497 TTTATAATTT
* *
66507 AATTTAAATAATTTTTTATATTTTTTA
1 AATTTAAATAATTTATAATATTTTTTA
*
66534 AATTTAAATAATTTATAATCTTTTT
1 AATTTAAATAATTTATAATATTTTT
66559 ATTTGTAGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (27 bp):
AATTTAAATAATTTATAATATTTTTTA
Found at i:70981 original size:30 final size:30
Alignment explanation
Indices: 70945--71005 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
70935 TGGTTAGTAC
70945 AGTGTTCAAAACTTGAAATACAAGTTCTAT
1 AGTGTTCAAAACTTGAAATACAAGTTCTAT
70975 AGTGTTCAAAACTTGAAATACAAGTTCTAT
1 AGTGTTCAAAACTTGAAATACAAGTTCTAT
71005 A
1 A
71006 TTGCTATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (30 bp):
AGTGTTCAAAACTTGAAATACAAGTTCTAT
Found at i:71261 original size:15 final size:16
Alignment explanation
Indices: 71243--71277 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
71233 TATTTTTTTC
71243 TGTTTTCTT-AGAACT
1 TGTTTTCTTCAGAACT
*
71258 TGTTTTCTTCAGAAGT
1 TGTTTTCTTCAGAACT
71274 TGTT
1 TGTT
71278 AAAGAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.54
Consensus pattern (16 bp):
TGTTTTCTTCAGAACT
Found at i:87791 original size:12 final size:12
Alignment explanation
Indices: 87774--87798 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
87764 TTTAAATCAA
87774 GTATTACAAAGC
1 GTATTACAAAGC
87786 GTATTACAAAGC
1 GTATTACAAAGC
87798 G
1 G
87799 GTGGAGATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (12 bp):
GTATTACAAAGC
Found at i:93405 original size:16 final size:16
Alignment explanation
Indices: 93384--93415 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
93374 TCCTTTTGCC
93384 GTCTCTCTCTGTCTCT
1 GTCTCTCTCTGTCTCT
*
93400 GTCTCTGTCTGTCTCT
1 GTCTCTCTCTGTCTCT
93416 TTTTTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.34, G:0.16, T:0.50
Consensus pattern (16 bp):
GTCTCTCTCTGTCTCT
Found at i:98917 original size:3 final size:3
Alignment explanation
Indices: 98856--98905 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
98846 TTGCGTTCCT
*
98856 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
98904 TT
1 TT
98906 TTGTCATTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:106178 original size:25 final size:25
Alignment explanation
Indices: 106154--106202 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
106144 AATATTTAAT
106154 TTATTT-TATAT-TAGATAAATATAA
1 TTATTTATATATGTA-ATAAATATAA
*
106178 TTATTTATATATGTAATATATATAA
1 TTATTTATATATGTAATAAATATAA
106203 ATATGAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 14 0.64
26 2 0.09
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (25 bp):
TTATTTATATATGTAATAAATATAA
Found at i:106997 original size:31 final size:32
Alignment explanation
Indices: 106951--107012 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
106941 TCCCACGGAA
* *
106951 GTTTTTTTTTTATTAA-AAATTGAATT-ATATT
1 GTTTATTTTTCATTAATAAATT-AATTCATATT
106982 GTTTATTTTTCATTAATAAATTAATTCATAT
1 GTTTATTTTTCATTAATAAATTAATTCATAT
107013 ATCTTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (32 bp):
GTTTATTTTTCATTAATAAATTAATTCATATT
Found at i:110190 original size:29 final size:30
Alignment explanation
Indices: 110151--110210 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
110141 GTGTTAATAA
**
110151 TTTGTAAAAAATT-GAGTAAATTAAAATTT
1 TTTGTAAAAAATTAGACAAAATTAAAATTT
* *
110180 TTTGTATAAAATTATACAAAATTAAAATTT
1 TTTGTAAAAAATTAGACAAAATTAAAATTT
110210 T
1 T
110211 AATTATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (30 bp):
TTTGTAAAAAATTAGACAAAATTAAAATTT
Found at i:124863 original size:30 final size:30
Alignment explanation
Indices: 124828--124888 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
124818 ATTTTATGGT
124828 TAATTTTATTATTATTTTAAAGATATTTGC
1 TAATTTTATTATTATTTTAAAGATATTTGC
* *
124858 TAATTTTGTTATTATTTTAGAGATATTTGC
1 TAATTTTATTATTATTTTAAAGATATTTGC
124888 T
1 T
124889 TGTTAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (30 bp):
TAATTTTATTATTATTTTAAAGATATTTGC
Found at i:125359 original size:31 final size:32
Alignment explanation
Indices: 125298--125359 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
125288 TTTAGTGTAA
* *
125298 TTATACATATGAAACTTTGATTGTGGTTCAAAT
1 TTATACATA-GAAACTTTAATTGTGATTCAAAT
*
125331 TTATACATA-AAACTTTAATTTTGATTCAA
1 TTATACATAGAAACTTTAATTGTGATTCAA
125360 TTATATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 17 0.65
33 9 0.35
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (32 bp):
TTATACATAGAAACTTTAATTGTGATTCAAAT
Found at i:129496 original size:18 final size:18
Alignment explanation
Indices: 129473--129508 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
129463 TAATCTCTCT
129473 TTTATGATATTTTTACGG
1 TTTATGATATTTTTACGG
129491 TTTATGATATTTTTACGG
1 TTTATGATATTTTTACGG
129509 AACAGACAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.17, T:0.56
Consensus pattern (18 bp):
TTTATGATATTTTTACGG
Found at i:145161 original size:3 final size:3
Alignment explanation
Indices: 145155--145184 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
145145 TTCTCTTGTT
*
145155 TTA TTA TTA TTA TGA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
145185 CACATTTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:149772 original size:110 final size:111
Alignment explanation
Indices: 149575--149798 Score: 396
Period size: 110 Copynumber: 2.0 Consensus size: 111
149565 TAGGCAACTC
*
149575 AAATTTATCTAAGTTTAATGTTAGTGATCATAAATACATAATAGGATGAGAGTTCATTTAATTGA
1 AAATTTATCTAAGTTTAATGTTAGTGATCATAAATACATAATAGGAAGAGAGTTCATTTAATTGA
*
149640 GCCAATCCATATTAGCTTCTTCAAGCTTTTTCATATATTTTAATTT
66 GCCAATCCATATTAGCTCCTTCAAGCTTTTTCATATATTTTAATTT
* *
149686 AAATTTATCTAAGTTT-GTGTTAGTGATCATAAATACATAATAGGAAGAGAGTTCTTTTAATTGA
1 AAATTTATCTAAGTTTAATGTTAGTGATCATAAATACATAATAGGAAGAGAGTTCATTTAATTGA
*
149750 GTCAATCCATATTAGCTCCTTCAAGCTTTTTCATATATTTTAATTT
66 GCCAATCCATATTAGCTCCTTCAAGCTTTTTCATATATTTTAATTT
149796 AAA
1 AAA
149799 GTATATGAGA
Statistics
Matches: 108, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
110 92 0.85
111 16 0.15
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (111 bp):
AAATTTATCTAAGTTTAATGTTAGTGATCATAAATACATAATAGGAAGAGAGTTCATTTAATTGA
GCCAATCCATATTAGCTCCTTCAAGCTTTTTCATATATTTTAATTT
Found at i:164754 original size:12 final size:12
Alignment explanation
Indices: 164737--164770 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
164727 CTCTCTTTCT
164737 CCTCTTCCTCCC
1 CCTCTTCCTCCC
* *
164749 CCTCTTCATCCT
1 CCTCTTCCTCCC
164761 CCTCTTCCTC
1 CCTCTTCCTC
164771 ATCATCTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.03, C:0.59, G:0.00, T:0.38
Consensus pattern (12 bp):
CCTCTTCCTCCC
Found at i:164778 original size:24 final size:24
Alignment explanation
Indices: 164735--164782 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
164725 CTCTCTCTTT
* *
164735 CTCCTCTTCCTCCCCCTCTTCATC
1 CTCCTCTTCCTCACCATCTTCATC
*
164759 CTCCTCTTCCTCATCATCTTCATC
1 CTCCTCTTCCTCACCATCTTCATC
164783 TTCGTCCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.08, C:0.52, G:0.00, T:0.40
Consensus pattern (24 bp):
CTCCTCTTCCTCACCATCTTCATC
Found at i:168147 original size:28 final size:28
Alignment explanation
Indices: 168086--168183 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
168076 TCACAAATTG
** * *
168086 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
168115 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
168143 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
168171 GCACTAAGTGTGC
1 GCACTAAGTGTGC
168184 GGGCTTATTG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:170009 original size:35 final size:35
Alignment explanation
Indices: 169982--170147 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
169972 CATGGCAAAG
*
169982 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
170017 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
170052 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
170092 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
170127 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
170148 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:170101 original size:75 final size:75
Alignment explanation
Indices: 169982--170152 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
169972 CATGGCAAAG
** *
169982 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
170041 CCATACTGAGC
65 CCATACCGAGC
170052 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
170117 CATACCGAGT
66 CATACCGAGC
**
170127 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
170153 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:177503 original size:35 final size:35
Alignment explanation
Indices: 177476--177641 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
177466 CATGGCAAAG
*
177476 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
177511 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
177546 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
177586 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
177621 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
177642 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:177595 original size:75 final size:75
Alignment explanation
Indices: 177476--177646 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
177466 CATGGCAAAG
** *
177476 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
177535 CCATACTGAGC
65 CCATACCGAGC
177546 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
177611 CATACCGAGT
66 CATACCGAGC
**
177621 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
177647 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:178921 original size:13 final size:13
Alignment explanation
Indices: 178903--178927 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
178893 AATAATTATT
178903 AAATTATTTAAAA
1 AAATTATTTAAAA
178916 AAATTATTTAAA
1 AAATTATTTAAA
178928 TAATTAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTATTTAAAA
Found at i:178934 original size:21 final size:22
Alignment explanation
Indices: 178878--178935 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
178868 GTTATTCAAC
*
178878 TTTAAAAAATTATAAAATAATTA
1 TTTAAATAATTA-AAAATAATTA
*
178901 -TTAAATTATTTAAAAA-AATTA
1 TTTAAA-TAATTAAAAATAATTA
178922 TTTAAATAATTAAA
1 TTTAAATAATTAAA
178936 TTATTTGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 12 0.40
22 14 0.47
23 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTAAATAATTAAAAATAATTA
Found at i:180255 original size:17 final size:18
Alignment explanation
Indices: 180229--180263 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
180219 TACAGGAAGA
180229 AAGAAGATGAT-GAGAAT
1 AAGAAGATGATCGAGAAT
*
180246 AAGAATATGATCGAGAAT
1 AAGAAGATGATCGAGAAT
180264 CCTTTGGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.51, C:0.03, G:0.26, T:0.20
Consensus pattern (18 bp):
AAGAAGATGATCGAGAAT
Found at i:191242 original size:18 final size:18
Alignment explanation
Indices: 191219--191257 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
191209 GTTGAAAAGG
*
191219 TTACAAAGAAAAACAAAA
1 TTACAAAAAAAAACAAAA
*
191237 TTACAAAAAAAAACTAAA
1 TTACAAAAAAAAACAAAA
191255 TTA
1 TTA
191258 TATAACTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.69, C:0.10, G:0.03, T:0.18
Consensus pattern (18 bp):
TTACAAAAAAAAACAAAA
Found at i:195676 original size:137 final size:140
Alignment explanation
Indices: 195427--195710 Score: 484
Period size: 137 Copynumber: 2.0 Consensus size: 140
195417 TTATGTAAGG
** * *
195427 CAAACACATATATGAAATTAGAATACCTTGTAATTACATTGTAATTATTACCCTAATAATTAACC
1 CAAACACATATATGAAATTAGAATACCTTACAATGACATCGTAATTATTACCCTAATAATTAACC
* *
195492 TTTCTTGCAATTACTATCTAAACACACCCTAAACATTTATTTCTAAATCCTCAGACATATGTTTG
66 TTTCTTGCAATAACTATCAAAACACACCCTAAACATTTATTTCTAAATCCTCAGACATATGTTTG
195557 CTTTTTCATC
131 CTTTTTCATC
*
195567 CAAACACATATATGAAATTAGAATA-C-TACAA-GGCATCGTAATTATTACCCTAATAATTAACC
1 CAAACACATATATGAAATTAGAATACCTTACAATGACATCGTAATTATTACCCTAATAATTAACC
195629 TTTCTTGCAATAACTATCAAAACACACCCTAAACATTTATTTCTAAATCCTCAGACATATGTTTG
66 TTTCTTGCAATAACTATCAAAACACACCCTAAACATTTATTTCTAAATCCTCAGACATATGTTTG
195694 CTTTTTCATC
131 CTTTTTCATC
195704 CAAACAC
1 CAAACAC
195711 TTGTTGTTTC
Statistics
Matches: 137, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
137 108 0.79
138 3 0.02
139 1 0.01
140 25 0.18
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (140 bp):
CAAACACATATATGAAATTAGAATACCTTACAATGACATCGTAATTATTACCCTAATAATTAACC
TTTCTTGCAATAACTATCAAAACACACCCTAAACATTTATTTCTAAATCCTCAGACATATGTTTG
CTTTTTCATC
Found at i:198252 original size:26 final size:26
Alignment explanation
Indices: 198223--198275 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
198213 TATAAAGTCG
198223 ATAGTATTTTGTATTAGTTTCATTTT
1 ATAGTATTTTGTATTAGTTTCATTTT
198249 ATAGTATTTTGTATTAGTTTCATTTT
1 ATAGTATTTTGTATTAGTTTCATTTT
198275 A
1 A
198276 GTTATGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.25, C:0.04, G:0.11, T:0.60
Consensus pattern (26 bp):
ATAGTATTTTGTATTAGTTTCATTTT
Found at i:199585 original size:25 final size:25
Alignment explanation
Indices: 199518--199585 Score: 61
Period size: 26 Copynumber: 2.7 Consensus size: 25
199508 CAAAGAGAGT
*
199518 GAAGAA-AAGGAAAAAGAAAAAGAAC
1 GAAGAAGAAGGGAAAA-AAAAAGAAC
*
199543 -AA-AAGAAGGAGATGAAAAAAAAGACC
1 GAAGAAGAAGG-GA--AAAAAAAAGAAC
199569 GAAGAAGAAGGGAAAAA
1 GAAGAAGAAGGGAAAAA
199586 GGAAGAGAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
23 2 0.06
24 6 0.17
25 5 0.14
26 8 0.23
27 7 0.20
28 7 0.20
ACGTcount: A:0.68, C:0.04, G:0.26, T:0.01
Consensus pattern (25 bp):
GAAGAAGAAGGGAAAAAAAAAGAAC
Found at i:201302 original size:53 final size:53
Alignment explanation
Indices: 201161--201311 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
201151 ACAAGTGTGC
* **
201161 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
201214 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
201267 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
201312 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:208819 original size:53 final size:53
Alignment explanation
Indices: 208678--208828 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
208668 ACAAGTGTGC
* **
208678 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
208731 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
208784 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
208829 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:216502 original size:32 final size:32
Alignment explanation
Indices: 216461--216521 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
216451 AAACACTCTC
* *
216461 TCTTTTGTAAAACATTCCTTTTACTTTTATTA
1 TCTTTTGTAAAACATCCCTATTACTTTTATTA
*
216493 TCTTTTGTAAAACCTCCCTATTACTTTTA
1 TCTTTTGTAAAACATCCCTATTACTTTTA
216522 ATAAAATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.03, T:0.52
Consensus pattern (32 bp):
TCTTTTGTAAAACATCCCTATTACTTTTATTA
Found at i:217018 original size:20 final size:20
Alignment explanation
Indices: 216953--217018 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
216943 CTCTTTCAAA
* *
216953 AAAAAATTCAACATGATTTT
1 AAAAAATTCAAAATAATTTT
* **
216973 TAAAAATTTGAAATAATTTT
1 AAAAAATTCAAAATAATTTT
216993 AAAAAATTCAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTT-T
217013 AAAAAA
1 AAAAAA
217019 ATATAAAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 4 0.11
20 33 0.89
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.35
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:217080 original size:21 final size:19
Alignment explanation
Indices: 217056--217100 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
217046 TATATATTTT
*
217056 AAAAAACTTAAAAATTCTAA
1 AAAAAAATTAAAAATT-TAA
* *
217076 AAAAATATTTAAAATTTAA
1 AAAAAAATTAAAAATTTAA
217095 AAAAAA
1 AAAAAA
217101 CAAAATAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAAAATTAAAAATTTAA
Found at i:218461 original size:12 final size:12
Alignment explanation
Indices: 218444--218468 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
218434 TGTGGTACCT
218444 CTTCAATATCTA
1 CTTCAATATCTA
218456 CTTCAATATCTA
1 CTTCAATATCTA
218468 C
1 C
218469 AACAAACAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (12 bp):
CTTCAATATCTA
Found at i:230099 original size:20 final size:20
Alignment explanation
Indices: 230062--230099 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
230052 TGATGGGGAG
*
230062 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
230082 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
230100 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:232057 original size:46 final size:46
Alignment explanation
Indices: 232005--232324 Score: 489
Period size: 46 Copynumber: 7.0 Consensus size: 46
231995 AGTGTGCTCT
*
232005 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
232051 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
232097 CTGATATGAAATGTGTAAGACAATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
232143 CTGATATGAAATGTGTAAGACCATGGTTGAAAAATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
232189 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ***
232235 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
232281 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
232325 TCATGTCAAA
Statistics
Matches: 255, Mismatches: 18, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
45 1 0.00
46 254 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:236607 original size:44 final size:44
Alignment explanation
Indices: 236541--236627 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
236531 TTTGTATTAG
* *
236541 ATATTATAATTATTTAAGTTTATTTTTACCTAA-TTAATATTTAA
1 ATATTATAATTATTAAACTTTATTTTTA-CTAATTTAATATTTAA
*
236585 ATATTGTAATTATTAAACTTTATTTTTACTAATTTAATATTTA
1 ATATTATAATTATTAAACTTTATTTTTACTAATTTAATATTTA
236628 GATACTACTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
43 4 0.10
44 35 0.90
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (44 bp):
ATATTATAATTATTAAACTTTATTTTTACTAATTTAATATTTAA
Found at i:270965 original size:40 final size:39
Alignment explanation
Indices: 270921--271123 Score: 133
Period size: 40 Copynumber: 5.3 Consensus size: 39
270911 GGTTTATCCA
*
270921 ACTAGAGCTGGGCTCACAATTATTATCATCGGTATATCTG
1 ACTAGAGCTGGG-TCACAATTATTATCGTCGGTATATCTG
* * * **
270961 ACTAGCA-CTGGGT-GCAA--A-TATCGTTGGTTTATCCA
1 ACTAG-AGCTGGGTCACAATTATTATCGTCGGTATATCTG
* * *
270996 ACTAGAGCTTGGCTCACAATTATTATCGTCGATATATTTG
1 ACTAGAGC-TGGGTCACAATTATTATCGTCGGTATATCTG
* * **
271036 ACTAGCA-CTGGGTGCA-AA-TATCAT--T-GGTTTATCCA
1 ACTAG-AGCTGGGT-CACAATTATTATCGTCGGTATATCTG
*
271071 ACTAGAGCTGGGTTCACAATTATTATCGTCGGTATATTTG
1 ACTAGAGCTGGG-TCACAATTATTATCGTCGGTATATCTG
271111 ACTAGCA-CTGGGT
1 ACTAG-AGCTGGGT
271124 GCAAATATCG
Statistics
Matches: 120, Mismatches: 26, Indels: 35
0.66 0.14 0.19
Matches are distributed among these distances:
34 2 0.02
35 35 0.29
36 9 0.08
37 8 0.07
38 8 0.07
39 10 0.08
40 45 0.38
41 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (39 bp):
ACTAGAGCTGGGTCACAATTATTATCGTCGGTATATCTG
Found at i:270987 original size:75 final size:75
Alignment explanation
Indices: 270885--271197 Score: 441
Period size: 75 Copynumber: 4.2 Consensus size: 75
270875 CGGTTAATCC
* * * * * *
270885 GACTAGCGCTGGGCGGAATTATGGTTGGTTTATCCAACTAGAGCTGGGCTCACAATTATTATCAT
1 GACTAGCACTGGGTGCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACAATTATTATCGT
270950 CGGTATATCT
66 CGGTATATCT
*
270960 GACTAGCACTGGGTGCAAATATCGTTGGTTTATCCAACTAGAGCTTGGCTCACAATTATTATCGT
1 GACTAGCACTGGGTGCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACAATTATTATCGT
* *
271025 CGATATATTT
66 CGGTATATCT
* *
271035 GACTAGCACTGGGTGCAAATATCATTGGTTTATCCAACTAGAGCTGGGTTCACAATTATTATCGT
1 GACTAGCACTGGGTGCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACAATTATTATCGT
*
271100 CGGTATATTT
66 CGGTATATCT
* * *
271110 GACTAGCACTGGGTGCAAATATCGTTAGTTTATCCAATTAGAGCTGGGCTCAC-ATTCAATATCG
1 GACTAGCACTGGGTGCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACAATT-ATTATCG
*
271174 TCGGT-TAGTCC
65 TCGGTATA-TCT
*
271185 GACTAGCGCTGGG
1 GACTAGCACTGGG
271198 CGTAAATTCC
Statistics
Matches: 215, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
74 5 0.02
75 210 0.98
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (75 bp):
GACTAGCACTGGGTGCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACAATTATTATCGT
CGGTATATCT
Found at i:272600 original size:46 final size:46
Alignment explanation
Indices: 272426--272607 Score: 240
Period size: 46 Copynumber: 4.0 Consensus size: 46
272416 TTTAACATGA
* * * * *
272426 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACTATGGTCTTACACA-TTTCATATCAGGT
* ** * * *
272472 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATATCAGGT
*
272518 TGCCATGGTATCTTTCAACTATGGTTTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATATCAGGT
272564 TGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATATCAG
272608 AGAGTACACT
Statistics
Matches: 121, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
45 4 0.03
46 117 0.97
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.42
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATATCAGGT
Found at i:274749 original size:13 final size:12
Alignment explanation
Indices: 274733--274783 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 12
274723 TTCTTTCTTT
274733 ATATACTAATAAA
1 ATATA-TAATAAA
274746 ATAT-TAATAAA
1 ATATATAATAAA
*
274757 ATATATTATTAAA
1 ATATA-TAATAAA
*
274770 ATAT-TAATGAA
1 ATATATAATAAA
274781 ATA
1 ATA
274784 ATATTTATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 19 0.58
13 14 0.42
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (12 bp):
ATATATAATAAA
Found at i:274755 original size:11 final size:11
Alignment explanation
Indices: 274739--274783 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
274729 CTTTATATAC
274739 TAATAAAATAT
1 TAATAAAATAT
274750 TAATAAAATATAT
1 TAAT-AAA-ATAT
*
274763 TATTAAAATAT
1 TAATAAAATAT
*
274774 TAATGAAATA
1 TAATAAAATA
274784 ATATTTATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:274769 original size:24 final size:24
Alignment explanation
Indices: 274733--274788 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
274723 TTCTTTCTTT
*
274733 ATATACTAATAAAATATTAATAAA
1 ATATATTAATAAAATATTAATAAA
* *
274757 ATATATTATTAAAATATTAATGAA
1 ATATATTAATAAAATATTAATAAA
274781 ATAATATT
1 AT-ATATT
274789 TATCTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
ATATATTAATAAAATATTAATAAA
Found at i:282321 original size:30 final size:31
Alignment explanation
Indices: 282264--282344 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 31
282254 TCTTTCGGGA
*
282264 TTTTGGAAATTTTCAATTAAGCTCTTCAA-AG
1 TTTT-GAAATTTTCAATTAAGCCCTTCAAGAG
* *
282295 TTTTGAAATTTTTAATT-AGACCCTTCAAGAT
1 TTTTGAAATTTTCAATTAAG-CCCTTCAAGAG
*
282326 TTCTTGAAATTCTC-ATTAA
1 TT-TTGAAATTTTCAATTAA
282345 ATCCATTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
29 2 0.05
30 19 0.46
31 10 0.24
32 10 0.24
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (31 bp):
TTTTGAAATTTTCAATTAAGCCCTTCAAGAG
Found at i:286904 original size:39 final size:41
Alignment explanation
Indices: 286846--286928 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 41
286836 ATGTGAAAAA
* *
286846 CATACAAGTCCATAAGCCTAACCTAT-TCCCAAAATGGAAC
1 CATACAAGTCCATAAGCCTAACCTATGTCCAAAAATAGAAC
* * *
286886 CATACGAG-CCATATGCCTAACCTATGTGCAAAAATAGAAC
1 CATACAAGTCCATAAGCCTAACCTATGTCCAAAAATAGAAC
286926 CAT
1 CAT
286929 TAAGAGTCCA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 16 0.43
40 21 0.57
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.20
Consensus pattern (41 bp):
CATACAAGTCCATAAGCCTAACCTATGTCCAAAAATAGAAC
Found at i:300589 original size:26 final size:25
Alignment explanation
Indices: 300498--300589 Score: 71
Period size: 29 Copynumber: 3.4 Consensus size: 25
300488 ATTTATGTGA
300498 ATTAAAAAT--TAAATTGTATTTTTT
1 ATTAAAAATAGTAAATTG-ATTTTTT
*
300522 ATTTAAAAAATAAGTAAATTAATTTTATAT
1 A-TT-AAAAAT-AGTAAATTGATTTT-T-T
300552 ATTAGATCAAATAGTAAATTGATTCTTTT
1 ATTA-A--AAATAGTAAATTGATT-TTTT
300581 ATTAAAAAT
1 ATTAAAAAT
300590 TCTTATCAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
24 1 0.02
25 2 0.04
26 10 0.18
28 7 0.13
29 15 0.27
30 14 0.25
31 6 0.11
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (25 bp):
ATTAAAAATAGTAAATTGATTTTTT
Found at i:303510 original size:6 final size:6
Alignment explanation
Indices: 303496--303546 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
303486 GAAAGATGAC
* * * *
303496 GGTGGT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GATCAT GGTGGT
1 GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT
303544 GGT
1 GGT
303547 CATGATGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.14, C:0.02, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTGAT
Found at i:303549 original size:12 final size:12
Alignment explanation
Indices: 303501--303555 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
303491 ATGACGGTGG
*
303501 TGGTGATGGTGA
1 TGGTGATGGTCA
*
303513 TGGTGATGGTGA
1 TGGTGATGGTCA
*
303525 TGGTGATGATCA
1 TGGTGATGGTCA
*
303537 TGGTGGTGGTCA
1 TGGTGATGGTCA
*
303549 TGATGAT
1 TGGTGAT
303556 AATAATGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.18, C:0.04, G:0.44, T:0.35
Consensus pattern (12 bp):
TGGTGATGGTCA
Found at i:303551 original size:18 final size:18
Alignment explanation
Indices: 303501--303552 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
303491 ATGACGGTGG
* * *
303501 TGGTGATGGTGATGGTGA
1 TGGTGATGGTCATGATCA
*
303519 TGGTGATGGTGATGATCA
1 TGGTGATGGTCATGATCA
*
303537 TGGTGGTGGTCATGAT
1 TGGTGATGGTCATGAT
303553 GATAATAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.17, C:0.04, G:0.44, T:0.35
Consensus pattern (18 bp):
TGGTGATGGTCATGATCA
Found at i:310521 original size:10 final size:10
Alignment explanation
Indices: 310506--310530 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
310496 GTTTTATTAT
310506 TTATTTTGTA
1 TTATTTTGTA
310516 TTATTTTGTA
1 TTATTTTGTA
310526 TTATT
1 TTATT
310531 ACACATCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (10 bp):
TTATTTTGTA
Found at i:311108 original size:31 final size:32
Alignment explanation
Indices: 311069--311147 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 32
311059 CATTGTCAGC
* *
311069 TATTATAAAAAATTATAA-AAAATATTAATTAA
1 TATTATAAAAAATTA-AATAAAAAATTAAATAA
311101 -ATTAT-AAAAATTAAATAAAAAATTAAATAA
1 TATTATAAAAAATTAAATAAAAAATTAAATAA
*
311131 TATTA-AAAAAATGAAAT
1 TATTATAAAAAATTAAAT
311148 TAACCCTTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 2 0.05
30 20 0.49
31 19 0.46
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (32 bp):
TATTATAAAAAATTAAATAAAAAATTAAATAA
Found at i:311123 original size:21 final size:21
Alignment explanation
Indices: 311073--311141 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
311063 GTCAGCTATT
*
311073 ATAAAAAATTATAAAAAAT-A
1 ATAAAAAATTATAAAAATTAA
* *
311093 TTAATTAAATTATAAAAATTAA
1 ATAA-AAAATTATAAAAATTAA
311115 ATAAAAAATTA-AATAATATTAA
1 ATAAAAAATTATAA-AA-ATTAA
311137 A-AAAA
1 ATAAAA
311142 TGAAATTAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
20 5 0.12
21 25 0.62
22 10 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAAAAAATTATAAAAATTAA
Found at i:311286 original size:21 final size:22
Alignment explanation
Indices: 311250--311291 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
311240 AGAAATTATA
* *
311250 AAAAATAATAATAATT-TAGAC
1 AAAAATAAAAAAAATTATAGAC
311271 AAAAATAAAAAAAATTATAGA
1 AAAAATAAAAAAAATTATAGA
311292 GCTTTTTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (22 bp):
AAAAATAAAAAAAATTATAGAC
Found at i:311959 original size:23 final size:24
Alignment explanation
Indices: 311907--311959 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
311897 AAAAATTATT
311907 ATATTTTACAAATATTGATGAAAA
1 ATATTTTACAAATATTGATGAAAA
* * *
311931 AGATTTTA-AAATTTTGCT-AAATA
1 ATATTTTACAAATATTGATGAAA-A
311954 ATATTT
1 ATATTT
311960 AATGCCATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 3 0.12
23 14 0.58
24 7 0.29
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (24 bp):
ATATTTTACAAATATTGATGAAAA
Found at i:312737 original size:12 final size:12
Alignment explanation
Indices: 312720--312750 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
312710 TGCTGTGTTA
312720 CTTCCTTTCCTT
1 CTTCCTTTCCTT
312732 CTTCCTTTCCTT
1 CTTCCTTTCCTT
312744 CTTCCTT
1 CTTCCTT
312751 GTCATCCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (12 bp):
CTTCCTTTCCTT
Found at i:316980 original size:5 final size:5
Alignment explanation
Indices: 316970--317003 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
316960 AAATTTGTGA
316970 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
317004 AACACACAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:317179 original size:25 final size:25
Alignment explanation
Indices: 317149--317230 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
317139 TCTAGTAAGA
317149 ATAAAATACATTATTCTAATAAAAT
1 ATAAAATACATTATTCTAATAAAAT
* * *
317174 ATAAAATAGATGGAGTT-TAATAAGAT
1 ATAAAATACAT-TA-TTCTAATAAAAT
* * *
317200 TTAAAAAACTTTATTCTAA-AATAAT
1 ATAAAATACATTATTCTAATAA-AAT
317225 ATAAAA
1 ATAAAA
317231 GAAGTGTAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
24 4 0.09
25 21 0.49
26 16 0.37
27 2 0.05
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (25 bp):
ATAAAATACATTATTCTAATAAAAT
Found at i:321234 original size:31 final size:31
Alignment explanation
Indices: 321168--321234 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
321158 GGATAAATAT
* *
321168 TAATTTTATATATAAATTTTGATTTAATGTG
1 TAATTTGATATATAAATTTTGATTTAATGTA
321199 TAATTTGATATATGAATATTTTGATTT-A-GTA
1 TAATTTGATATAT-AA-ATTTTGATTTAATGTA
321230 TAATT
1 TAATT
321235 ATTTAGGTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 19 0.59
32 3 0.09
33 10 0.31
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (31 bp):
TAATTTGATATATAAATTTTGATTTAATGTA
Found at i:323292 original size:20 final size:21
Alignment explanation
Indices: 323259--323304 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
323249 TAGAGATAAT
* *
323259 ATTTATATTTTTTTAATTTAA
1 ATTTATATTATTTTAAGTTAA
*
323280 ATTT-TATTATTTTCAGTTAA
1 ATTTATATTATTTTAAGTTAA
323300 ATTTA
1 ATTTA
323305 ACCTTTAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTTATATTATTTTAAGTTAA
Found at i:323430 original size:10 final size:10
Alignment explanation
Indices: 323411--323464 Score: 53
Period size: 10 Copynumber: 5.8 Consensus size: 10
323401 CGCATAACAA
323411 TTTATATATT
1 TTTATATATT
*
323421 TTTATGTATT
1 TTTATATATT
*
323431 TTTTTA-ATT
1 TTTATATATT
323440 TTT-T-TATT
1 TTTATATATT
*
323448 TTTAAATATT
1 TTTATATATT
323458 TTT-TATA
1 TTTATATA
323465 AGTTTTAGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
8 7 0.19
9 9 0.25
10 20 0.56
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTATATATT
Found at i:323439 original size:27 final size:27
Alignment explanation
Indices: 323409--323461 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
323399 CTCGCATAAC
**
323409 AATTTATATATTTTTATGTATTTTTTT
1 AATTTATATATTTTTAAATATTTTTTT
* *
323436 AATTTTTTTATTTTTAAATATTTTTT
1 AATTTATATATTTTTAAATATTTTTT
323462 ATAAGTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (27 bp):
AATTTATATATTTTTAAATATTTTTTT
Found at i:323449 original size:17 final size:18
Alignment explanation
Indices: 323427--323463 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
323417 TATTTTTATG
*
323427 TATTTTTTTAAT-TTTTT
1 TATTTTTTAAATATTTTT
323444 TA-TTTTTAAATATTTTT
1 TATTTTTTAAATATTTTT
323461 TAT
1 TAT
323464 AAGTTTTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 3
0.81 0.05 0.14
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TATTTTTTAAATATTTTT
Found at i:323470 original size:27 final size:27
Alignment explanation
Indices: 323417--323470 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
323407 ACAATTTATA
** *
323417 TATTTTTATGTATTTTTTTAATTTTTT
1 TATTTTTAAATATTTTTTTAATGTTTT
323444 TATTTTTAAATATTTTTTATAA-GTTTT
1 TATTTTTAAATATTTTTT-TAATGTTTT
323471 AGATTATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (27 bp):
TATTTTTAAATATTTTTTTAATGTTTT
Found at i:325792 original size:17 final size:19
Alignment explanation
Indices: 325753--325793 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
325743 CATTATCATT
325753 TTTATTTTCGTTTTAAAGA
1 TTTATTTTCGTTTTAAAGA
325772 -TTATTTTC-TTTTAAA-A
1 TTTATTTTCGTTTTAAAGA
325788 TTTATT
1 TTTATT
325794 ATTATCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 1 0.05
17 12 0.57
18 8 0.38
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTATTTTCGTTTTAAAGA
Found at i:329861 original size:35 final size:35
Alignment explanation
Indices: 329815--329886 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
329805 TATTGTTAAA
329815 AAATTTCATCTATTTATGTGATTAAAAATTAATAT
1 AAATTTCATCTATTTATGTGATTAAAAATTAATAT
329850 AAATTTCATCTATTTATGTGATTAAAAATTAATAT
1 AAATTTCATCTATTTATGTGATTAAAAATTAATAT
329885 AA
1 AA
329887 TGTATCAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (35 bp):
AAATTTCATCTATTTATGTGATTAAAAATTAATAT
Found at i:331316 original size:27 final size:26
Alignment explanation
Indices: 331279--331336 Score: 107
Period size: 27 Copynumber: 2.2 Consensus size: 26
331269 ATGGCATGTC
331279 ATACACTATTATCTTATTATTTTATT
1 ATACACTATTATCTTATTATTTTATT
331305 ATACACCTATTATCTTATTATTTTATT
1 ATACA-CTATTATCTTATTATTTTATT
331332 ATACA
1 ATACA
331337 TGCTAATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 5 0.16
27 26 0.84
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (26 bp):
ATACACTATTATCTTATTATTTTATT
Found at i:334479 original size:19 final size:19
Alignment explanation
Indices: 334452--334489 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
334442 TATATGTGAC
334452 TTTAAAAAATAAT-TTAAAA
1 TTTAAAAAA-AATATTAAAA
*
334471 TTTATAAAAAATATTAAAA
1 TTTAAAAAAAATATTAAAA
334490 AAATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TTTAAAAAAAATATTAAAA
Found at i:336755 original size:19 final size:19
Alignment explanation
Indices: 336731--336768 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
336721 TTTGATCCTT
336731 TAAAATTTATAAAGATATA
1 TAAAATTTATAAAGATATA
336750 TAAAATTTATAAAGATATA
1 TAAAATTTATAAAGATATA
336769 GACTATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (19 bp):
TAAAATTTATAAAGATATA
Found at i:344112 original size:15 final size:15
Alignment explanation
Indices: 344092--344142 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
344082 ATTGATTTCT
344092 ATATATTATCATAAG
1 ATATATTATCATAAG
***
344107 ATATATTA--ATTTCT
1 ATATATTATCA-TAAG
344121 ATATATTATCATAAG
1 ATATATTATCATAAG
344136 ATATATT
1 ATATATT
344143 TGACAGATCA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 1 0.04
14 9 0.33
15 16 0.59
16 1 0.04
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (15 bp):
ATATATTATCATAAG
Found at i:344120 original size:29 final size:29
Alignment explanation
Indices: 344080--344142 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
344070 TTACATTTAA
*
344080 ATATTGATTTCTATATATTATCATAAGAT
1 ATATTAATTTCTATATATTATCATAAGAT
344109 ATATTAATTTCTATATATTATCATAAGAT
1 ATATTAATTTCTATATATTATCATAAGAT
344138 ATATT
1 ATATT
344143 TGACAGATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (29 bp):
ATATTAATTTCTATATATTATCATAAGAT
Found at i:348162 original size:15 final size:15
Alignment explanation
Indices: 348142--348171 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
348132 AGTAGTTTTG
348142 ATGCAAATTATTGCA
1 ATGCAAATTATTGCA
348157 ATGCAAATTATTGCA
1 ATGCAAATTATTGCA
348172 GACTAACAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
ATGCAAATTATTGCA
Found at i:355257 original size:57 final size:56
Alignment explanation
Indices: 355169--355336 Score: 177
Period size: 57 Copynumber: 3.0 Consensus size: 56
355159 GATATAATAC
* *
355169 CTTAAGCCGAGGGGACTGACGAACAACTGGTGATAA-AAGATCTGGCTTT-GCTACTTT
1 CTTAAGCCGAGGGGACCGACGAACAACTGGTGATAAGAAG-TCT-GATTTGGCTAC-TT
* *
355226 CTTAAGCCGAGGGGACCGATGAACAACTGGTGATAAGATGTCTGATTTGGCTACTT
1 CTTAAGCCGAGGGGACCGACGAACAACTGGTGATAAGAAGTCTGATTTGGCTACTT
* * * *
355282 CTTTAAGCCGAGTGGACCAACG-AC--CTGGTGAT-AGAATATCTGATTTGACTACTT
1 C-TTAAGCCGAGGGGACCGACGAACAACTGGTGATAAGAA-GTCTGATTTGGCTACTT
355336 C
1 C
355337 CTTGGGATTT
Statistics
Matches: 97, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
53 3 0.03
54 24 0.25
56 9 0.09
57 59 0.61
58 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (56 bp):
CTTAAGCCGAGGGGACCGACGAACAACTGGTGATAAGAAGTCTGATTTGGCTACTT
Found at i:357954 original size:27 final size:27
Alignment explanation
Indices: 357906--357958 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
357896 TGTATTCAAC
* *
357906 ATCCTCAAATTATAATTTTTTTAATTA
1 ATCCTCAAATTATAAATATTTTAATTA
357933 ATCCTCAAACTT-TAAATATTTTAATT
1 ATCCTCAAA-TTATAAATATTTTAATT
357959 GCATTTCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (27 bp):
ATCCTCAAATTATAAATATTTTAATTA
Found at i:358093 original size:6 final size:7
Alignment explanation
Indices: 358076--358110 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
358066 TTCTTTCTTT
358076 TTTTTAA
1 TTTTTAA
358083 TTTTTAA
1 TTTTTAA
358090 TTTTTAA
1 TTTTTAA
* *
358097 TTTTCAC
1 TTTTTAA
358104 TTTTTAA
1 TTTTTAA
358111 AAGTTATGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTTTAA
Found at i:358259 original size:12 final size:12
Alignment explanation
Indices: 358242--358286 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
358232 TATAACATCG
358242 ATAATTAAAAAT
1 ATAATTAAAAAT
358254 ATAATT-AAAAT
1 ATAATTAAAAAT
358265 AT--TTAAAAAT
1 ATAATTAAAAAT
*
358275 -TAATTTAAAAT
1 ATAATTAAAAAT
358286 A
1 A
358287 AATATCATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
9 3 0.11
10 5 0.18
11 14 0.50
12 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAATTAAAAAT
Found at i:358270 original size:21 final size:21
Alignment explanation
Indices: 358246--358286 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
358236 ACATCGATAA
358246 TTAAAAATATAA-TTAAAATAT
1 TTAAAAAT-TAATTTAAAATAT
358267 TTAAAAATTAATTTAAAATA
1 TTAAAAATTAATTTAAAATA
358287 AATATCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TTAAAAATTAATTTAAAATAT
Found at i:371722 original size:22 final size:22
Alignment explanation
Indices: 371679--371721 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
371669 ACGTACAATA
* *
371679 ATTAATTTTTAATAGTAAAAAT
1 ATTAATTTTTAACAATAAAAAT
371701 ATTAATTTTTGAACAATAAAA
1 ATTAATTTTT-AACAATAAAA
371722 TTAATTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (22 bp):
ATTAATTTTTAACAATAAAAAT
Found at i:372516 original size:21 final size:22
Alignment explanation
Indices: 372470--372510 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
372460 TAAAATTTTT
* *
372470 TTTAAAATGTTGTTAAATAATA
1 TTTAAAATGTTATGAAATAATA
372492 TTTAAAA-GTTATGAAATAA
1 TTTAAAATGTTATGAAATAA
372511 AGTTTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (22 bp):
TTTAAAATGTTATGAAATAATA
Found at i:374764 original size:37 final size:39
Alignment explanation
Indices: 374723--374801 Score: 135
Period size: 37 Copynumber: 2.1 Consensus size: 39
374713 TATTTTTAAC
*
374723 AAAATAAAATAAAATATAATCT-AATTC-TTAATATAAG
1 AAAATAAAATAAAATATAATCTAAATTCTTTAACATAAG
374760 AAAATAAAATAAAATATAATCTAAATTCTTTAACATAAG
1 AAAATAAAATAAAATATAATCTAAATTCTTTAACATAAG
374799 AAA
1 AAA
374802 GTCCAAGACA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
37 22 0.56
38 5 0.13
39 12 0.31
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (39 bp):
AAAATAAAATAAAATATAATCTAAATTCTTTAACATAAG
Found at i:376477 original size:3 final size:3
Alignment explanation
Indices: 376469--376495 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
376459 TGAAAAATAA
376469 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
376496 TATCTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:385566 original size:28 final size:29
Alignment explanation
Indices: 385517--385572 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
385507 TTATAATTTT
*
385517 TATTTTAAATTAATTTTAAAATTTTAAAA
1 TATTTTAAATTAATTTTAAAATTATAAAA
385546 TATTTT-AATTACATTTT-AAATTATAAA
1 TATTTTAAATTA-ATTTTAAAATTATAAA
385573 TGGTATATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
TATTTTAAATTAATTTTAAAATTATAAAA
Found at i:387199 original size:29 final size:30
Alignment explanation
Indices: 387153--387216 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
387143 TTGACCTTAC
* *
387153 TTGATTCTTTTTAATAGTAAAAAGATTAAA
1 TTGATTCTATTTAATAGTAAAAAGACTAAA
* * *
387183 TTGATTC-ATTTATTAGTAGAAAGACTAAT
1 TTGATTCTATTTAATAGTAAAAAGACTAAA
387212 TTGAT
1 TTGAT
387217 AAGACCTCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (30 bp):
TTGATTCTATTTAATAGTAAAAAGACTAAA
Found at i:390673 original size:51 final size:51
Alignment explanation
Indices: 390560--390659 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
390550 TATAATAAAG
* * * *
390560 GTCACTCAATTAT-GTTTTTTTATTACTTAACAATGAAAAATTATAAAATA
1 GTCATTCAATTATAATTTTTTTATCACCTAACAATGAAAAATTATAAAATA
**
390610 GTCATTCAATTATAATTTTTTTATCACCTAATTATGAAAAATTATAAAAT
1 GTCATTCAATTATAATTTTTTTATCACCTAACAATGAAAAATTATAAAAT
390660 GATCATCTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 12 0.28
51 31 0.72
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (51 bp):
GTCATTCAATTATAATTTTTTTATCACCTAACAATGAAAAATTATAAAATA
Found at i:400364 original size:48 final size:48
Alignment explanation
Indices: 400293--400394 Score: 204
Period size: 48 Copynumber: 2.1 Consensus size: 48
400283 AGCTTTAGGG
400293 ACCAAAGTGGACCTAATTGCCAAGTTCAAGGACTAAAAGTTATATTAA
1 ACCAAAGTGGACCTAATTGCCAAGTTCAAGGACTAAAAGTTATATTAA
400341 ACCAAAGTGGACCTAATTGCCAAGTTCAAGGACTAAAAGTTATATTAA
1 ACCAAAGTGGACCTAATTGCCAAGTTCAAGGACTAAAAGTTATATTAA
400389 ACCAAA
1 ACCAAA
400395 TGTATATAAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.24
Consensus pattern (48 bp):
ACCAAAGTGGACCTAATTGCCAAGTTCAAGGACTAAAAGTTATATTAA
Found at i:409171 original size:16 final size:17
Alignment explanation
Indices: 409150--409199 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
409140 TCTGTAAAAG
*
409150 AAACATAAAT-AAACCA
1 AAACATAAATCAAAACA
*
409166 AAACATGAATCAAAACA
1 AAACATAAATCAAAACA
*
409183 AAA-ATCAAAACAAAACA
1 AAACAT-AAATCAAAACA
409200 TTATTGATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.70, C:0.18, G:0.02, T:0.10
Consensus pattern (17 bp):
AAACATAAATCAAAACA
Found at i:409181 original size:12 final size:12
Alignment explanation
Indices: 409173--409197 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
409163 CCAAAACATG
409173 AATCAAAACAAA
1 AATCAAAACAAA
409185 AATCAAAACAAA
1 AATCAAAACAAA
409197 A
1 A
409198 CATTATTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.16, G:0.00, T:0.08
Consensus pattern (12 bp):
AATCAAAACAAA
Found at i:409496 original size:59 final size:59
Alignment explanation
Indices: 409420--409539 Score: 161
Period size: 59 Copynumber: 2.0 Consensus size: 59
409410 GGCAACTATC
* *
409420 CCCACTTGAGGCCTGAACTTTTTTTTACTCCAAGTTAGGCCCTGAACTTGGTAATT-TT
1 CCCACTTGAGGCCTGAACTTTTTTTTACTCCAAATTAGGCCATGAACTTGGTAATTGTT
* ** * *
409478 CCCACATTGAGGCTTGAACTTTTTTTTTGTCTAAATTAGTCCATGAACTTGGTAATTGTT
1 CCCAC-TTGAGGCCTGAACTTTTTTTTACTCCAAATTAGGCCATGAACTTGGTAATTGTT
409538 CC
1 CC
409540 TATGTTAAGG
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
58 5 0.09
59 44 0.83
60 4 0.08
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.40
Consensus pattern (59 bp):
CCCACTTGAGGCCTGAACTTTTTTTTACTCCAAATTAGGCCATGAACTTGGTAATTGTT
Found at i:425346 original size:27 final size:27
Alignment explanation
Indices: 425273--425348 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 27
425263 CTTCAAAATG
* **
425273 AAATTTAGTTTCTATATTTTTATTTTTAA
1 AAATTTAGTCT-TA-ATTTTTAGATTTAA
*
425302 AAATTTAGTCTTACTTTTTAGATTTAA
1 AAATTTAGTCTTAATTTTTAGATTTAA
*
425329 AAATTTTGAT-TTAATTTTTA
1 AAATTTAG-TCTTAATTTTTA
425349 ATATTTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 27 0.68
28 3 0.08
29 10 0.25
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (27 bp):
AAATTTAGTCTTAATTTTTAGATTTAA
Found at i:426590 original size:136 final size:137
Alignment explanation
Indices: 426346--426618 Score: 460
Period size: 136 Copynumber: 2.0 Consensus size: 137
426336 AACTACGTGT
426346 GTTGGCCTAATGGTCAAGGTGTTCACTACCCTAGATATGGCTTGAGTTCAAGTCACACTTGTCGG
1 GTTGGCCTAATGGTCAAGGTGTTCACTACCCTAGATATGGCTTGAGTTCAAGTCACACTTGTCGG
* * *
426411 GTTGTTGTTTAGGGCTTTTGCGCTCCTCTTATAATTCATCCAAAAATAATAA-ATCTGGAATAGC
66 ATTATTGTTTAGAGCTTTTGCGCTCCTCTTATAATTCATCCAAAAATAATAATATCTGGAATAGC
426475 ATTGGGA
131 ATTGGGA
* * * *
426482 GTTGGCCTAATGGTCAATGTGTTCATTGCCCTAGGTATGG-TCTGAGTTCAAGTCACACTTGTCG
1 GTTGGCCTAATGGTCAAGGTGTTCACTACCCTAGATATGGCT-TGAGTTCAAGTCACACTTGTCG
426546 GATTATTGTTTAGAGCTTTTGCGCTCCTCTTATAATTCATCCAAAAATAATAATATCTGGAATAG
65 GATTATTGTTTAGAGCTTTTGCGCTCCTCTTATAATTCATCCAAAAATAATAATATCTGGAATAG
426611 CATTGGGA
130 CATTGGGA
426619 ATATGTGGTG
Statistics
Matches: 128, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
135 1 0.01
136 108 0.84
137 19 0.15
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (137 bp):
GTTGGCCTAATGGTCAAGGTGTTCACTACCCTAGATATGGCTTGAGTTCAAGTCACACTTGTCGG
ATTATTGTTTAGAGCTTTTGCGCTCCTCTTATAATTCATCCAAAAATAATAATATCTGGAATAGC
ATTGGGA
Found at i:429720 original size:2 final size:2
Alignment explanation
Indices: 429713--429741 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
429703 TTTCTAAAAC
429713 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
429742 GTAAATTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:434010 original size:3 final size:3
Alignment explanation
Indices: 434002--434059 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
433992 GCAAGATTGG
434002 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
434050 TTA TTA TTA T
1 TTA TTA TTA T
434060 GTAGAGCTAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:437353 original size:2 final size:2
Alignment explanation
Indices: 437346--437377 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
437336 CCATCACATT
437346 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
437378 AAAGCCTAGG
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:442467 original size:18 final size:18
Alignment explanation
Indices: 442444--442490 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
442434 GGATATGTTC
442444 TTTCTTTTTGATCCCCCT
1 TTTCTTTTTGATCCCCCT
* * *
442462 TTTCTTTTTCTATCTCCTT
1 TTTCTTTTT-GATCCCCCT
442481 TTTCTTTTTG
1 TTTCTTTTTG
442491 GGTTGTAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.04, C:0.26, G:0.04, T:0.66
Consensus pattern (18 bp):
TTTCTTTTTGATCCCCCT
Found at i:447989 original size:21 final size:22
Alignment explanation
Indices: 447966--448006 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
447956 GTTTTTATTT
447966 TTTTA-TCAAA-TTGGTCTTTC
1 TTTTAGTCAAATTTGGTCTTTC
*
447986 TTTTAGTTAAATTTGGTCTTT
1 TTTTAGTCAAATTTGGTCTTT
448007 TACTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
22 9 0.50
ACGTcount: A:0.20, C:0.10, G:0.12, T:0.59
Consensus pattern (22 bp):
TTTTAGTCAAATTTGGTCTTTC
Found at i:448017 original size:22 final size:22
Alignment explanation
Indices: 447958--448020 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
447948 TTTTTAATGT
*
447958 TTTTATTTTTTTATCAAATTGGTC
1 TTTTACTTTTTTA--AAATTGGTC
*
447982 -TTT-CTTTTAGTTAAATTTGGTC
1 TTTTACTTTT--TTAAAATTGGTC
448004 TTTTACTTTTTTAAAAT
1 TTTTACTTTTTTAAAAT
448021 AGTTAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
22 18 0.56
23 6 0.19
24 8 0.25
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.62
Consensus pattern (22 bp):
TTTTACTTTTTTAAAATTGGTC
Found at i:448707 original size:19 final size:19
Alignment explanation
Indices: 448683--448722 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
448673 TAGTTTCCAC
448683 ATCTAAATAATTATATTAT
1 ATCTAAATAATTATATTAT
448702 ATCTAAATAATTATATTAT
1 ATCTAAATAATTATATTAT
448721 AT
1 AT
448723 ACACGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
ATCTAAATAATTATATTAT
Found at i:451974 original size:16 final size:16
Alignment explanation
Indices: 451955--451988 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
451945 TATGTTTAAA
*
451955 TAAAGTTATTAGTATT
1 TAAAGTTATTAATATT
451971 TAAAGTTATTAATATT
1 TAAAGTTATTAATATT
451987 TA
1 TA
451989 TTTATAAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
TAAAGTTATTAATATT
Found at i:457377 original size:16 final size:16
Alignment explanation
Indices: 457346--457378 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
457336 ATCTTATAAA
457346 TAATAAAAGTAGAAAT
1 TAATAAAAGTAGAAAT
457362 TAATATAAAGTA-AAAT
1 TAATA-AAAGTAGAAAT
457378 T
1 T
457379 GTATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (16 bp):
TAATAAAAGTAGAAAT
Found at i:457687 original size:30 final size:30
Alignment explanation
Indices: 457653--457709 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
457643 CAAGACCAAA
457653 TTTATGTAA-AAAAA-AATCTATTAATAATAT
1 TTTAT-TAATAAAAATAATCT-TTAATAATAT
457683 TTTATTAATAAAAATAATCTTTAATAA
1 TTTATTAATAAAAATAATCTTTAATAA
457710 ATGAAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
29 3 0.12
30 17 0.68
31 5 0.20
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (30 bp):
TTTATTAATAAAAATAATCTTTAATAATAT
Found at i:460097 original size:42 final size:42
Alignment explanation
Indices: 460050--460177 Score: 186
Period size: 42 Copynumber: 3.0 Consensus size: 42
460040 TAATTATTCC
* * *
460050 TTTCTTAATTTACCTAGCTTCCTTTATTATTATGAATATAAT
1 TTTCTTAAATTACCTAACTTCCTTTATTATTATGAATAGAAT
*
460092 TTTCTTAAATTACCTAACTTCCTCTATTATTATGAATAGAACT
1 TTTCTTAAATTACCTAACTTCCTTTATTATTATGAATAGAA-T
* *
460135 TTT-TTAAATTACCTAACTTCCTTTGTTGTTATGAATAGAAT
1 TTTCTTAAATTACCTAACTTCCTTTATTATTATGAATAGAAT
460176 TT
1 TT
460178 GGCTTTTTCA
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
41 3 0.04
42 71 0.91
43 4 0.05
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.49
Consensus pattern (42 bp):
TTTCTTAAATTACCTAACTTCCTTTATTATTATGAATAGAAT
Found at i:466350 original size:3 final size:3
Alignment explanation
Indices: 466342--466372 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
466332 AATATGTTAT
466342 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
466373 GCATATTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.