Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold105
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: 2918491
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 41655 characters in sequence are not A, C, G, or T
File 1 of 16
Found at i:3780 original size:158 final size:158
Alignment explanation
Indices: 3591--3982 Score: 509
Period size: 158 Copynumber: 2.5 Consensus size: 158
3581 AAGATATTTT
* *
3591 ATATTATT-TTTTTTAATCTTTTATATTCTTATGGGTATCTGTAAGGGTATAAAAGA-TTCTGAA
1 ATATTATTCATTTTTAATCTTTTATATTCTTATGGGTATCTGTAAGGGTATAAAAGATTTC-AAA
* * *
3654 AA-TTTTTCATATCTTTTCGAGTTTC-ATT-AAGATATGAAATGATATTTTTCTAAAATAAATAA
65 AACTTTTT-ATATCTTTTCGAGCTTCTATTAAAG-TACGAAATGATATTTTTCAAAAATAAAT-A
* *
3716 AAATTAAATTAGCACTCTAATTATTAAAACAA
127 AAATTAAATTAACACTCTAATAATTAAAACAA
* *
3748 ATATTATTCATTTTTAATCTTTGATATTCTTATGGGTATCCGTAAGGGTATAAAAGATTTCAAAA
1 ATATTATTCATTTTTAATCTTTTATATTCTTATGGGTATCTGTAAGGGTATAAAAGATTTCAAAA
3813 ACTTTTTATATCTTTTCGAGCTTCTATTAAAGTACGAAATGATATTTTTCAAAAATAAATAAAAT
66 ACTTTTTATATCTTTTCGAGCTTCTATTAAAGTACGAAATGATATTTTTCAAAAATAAATAAAAT
* * *
3878 TGAATTAACACTCTCATAATTAAAATAA
131 TAAATTAACACTCTAATAATTAAAACAA
* * * *
3906 ATATTA--CGTTTTTAATCTTTTATATTCCTATGGGTGTCTGT--GGAGTATAAAGGATCTT-AA
1 ATATTATTCATTTTTAATCTTTTATATTCTTATGGGTATCTGTAAGG-GTATAAAAGAT-TTCAA
3966 AAACTTTTTA-ATCTTTT
64 AAACTTTTTATATCTTTT
3983 TGGGTCTCAT
Statistics
Matches: 210, Mismatches: 18, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
154 9 0.04
155 22 0.10
156 32 0.15
157 8 0.04
158 99 0.47
159 37 0.18
160 3 0.01
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.43
Consensus pattern (158 bp):
ATATTATTCATTTTTAATCTTTTATATTCTTATGGGTATCTGTAAGGGTATAAAAGATTTCAAAA
ACTTTTTATATCTTTTCGAGCTTCTATTAAAGTACGAAATGATATTTTTCAAAAATAAATAAAAT
TAAATTAACACTCTAATAATTAAAACAA
Found at i:4028 original size:158 final size:156
Alignment explanation
Indices: 3591--4043 Score: 413
Period size: 158 Copynumber: 2.9 Consensus size: 156
3581 AAGATATTTT
** * * * *
3591 ATATTATTTTTTTTAATCTTTTATATTCTTATGGGTATCTGTAAGGGTATAAAAGA-TTCTGAAA
1 ATATTATCATTTTTAATCTTTGATATTCCTATGGGTATCCGT-AGGGTATAAAAGATTTC-AAAA
* * * * **
3655 A-TTTTTCATATCTTTTCGAGTTTC-ATT-AAGATATGAAATGATATTTTTCTAAAATAAATAAA
64 ACTTTTT-ATATCTTTTCGAGCTTCTATTAAAG-TACGAAAGGACATTTTTAAAAAATAAAT-AA
* *
3717 AATTAAATTAGCACTCTAATTATTAAAACAA
126 AATTAAATTAACACTCTAATAATTAAAACAA
*
3748 ATATTATTCATTTTTAATCTTTGATATTCTTATGGGTATCCGTAAGGGTATAAAAGATTTCAAAA
1 ATATTA-TCATTTTTAATCTTTGATATTCCTATGGGTATCCGT-AGGGTATAAAAGATTTCAAAA
* * *
3813 ACTTTTTATATCTTTTCGAGCTTCTATTAAAGTACGAAATGATATTTTTCAAAAATAAATAAAAT
64 ACTTTTTATATCTTTTCGAGCTTCTATTAAAGTACGAAAGGACATTTTTAAAAAATAAATAAAAT
* * *
3878 TGAATTAACACTCTCATAATTAAAATAA
129 TAAATTAACACTCTAATAATTAAAACAA
* * * * *
3906 ATATTA-CGTTTTTAATCTTTTATATTCCTATGGGTGTCTGT-GGAGTATAAAGGATCTT-AAAA
1 ATATTATCATTTTTAATCTTTGATATTCCTATGGGTATCCGTAGG-GTATAAAAGAT-TTCAAAA
* * * * *
3968 ACTTTTTA-ATCTTTTTG-G-GTCTCATTAAGGTATGGAAAGGGCATTTCTTGAAAATGAATAAA
64 ACTTTTTATATCTTTTCGAGCTTCT-ATTAAAGTA-CGAAAGGACATTT-TT-AAAA--AATAAA
*
4030 TAAAATAAAATTAA
123 TAAAATTAAATTAA
4044 TCCTTATACA
Statistics
Matches: 254, Mismatches: 29, Indels: 25
0.82 0.09 0.08
Matches are distributed among these distances:
152 3 0.01
153 9 0.04
154 19 0.07
155 24 0.09
156 35 0.14
157 6 0.02
158 118 0.46
159 37 0.15
160 3 0.01
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.42
Consensus pattern (156 bp):
ATATTATCATTTTTAATCTTTGATATTCCTATGGGTATCCGTAGGGTATAAAAGATTTCAAAAAC
TTTTTATATCTTTTCGAGCTTCTATTAAAGTACGAAAGGACATTTTTAAAAAATAAATAAAATTA
AATTAACACTCTAATAATTAAAACAA
Found at i:15821 original size:19 final size:19
Alignment explanation
Indices: 15797--15835 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
15787 TGGCCCTAGT
15797 TCGGAAAGTGAAGAAGAGG
1 TCGGAAAGTGAAGAAGAGG
15816 TCGGAAAGTGAAGAAGAGG
1 TCGGAAAGTGAAGAAGAGG
15835 T
1 T
15836 AGACAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.41, T:0.13
Consensus pattern (19 bp):
TCGGAAAGTGAAGAAGAGG
Found at i:18184 original size:20 final size:20
Alignment explanation
Indices: 18149--18199 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
18139 AATAATAAAT
*
18149 TATAATTATTAAAATTAATA
1 TATAATTATAAAAATTAATA
*
18169 TA-AATATATAAAAATTCATA
1 TATAAT-TATAAAAATTAATA
18189 TATAATTATAA
1 TATAATTATAA
18200 TATTATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.11
20 21 0.78
21 3 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TATAATTATAAAAATTAATA
Found at i:18206 original size:16 final size:19
Alignment explanation
Indices: 18187--18227 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
18177 TAAAAATTCA
18187 TATATAA-TTA-TA-ATAT
1 TATATAATTTAGTATATAT
18203 TATATAATTTAGTATATAT
1 TATATAATTTAGTATATAT
18222 TATATA
1 TATATA
18228 TAAAATTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 3 0.14
18 2 0.09
19 10 0.45
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TATATAATTTAGTATATAT
Found at i:21814 original size:29 final size:28
Alignment explanation
Indices: 21782--21840 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
21772 TTAGAGTGTT
*
21782 ATTTTGAATATTTAGAGGTGAAATTGTAA
1 ATTTTGAAAATTTAG-GGTGAAATTGTAA
*
21811 ATTTTGAAAATTTAGGGTTAAATTGTAA
1 ATTTTGAAAATTTAGGGTGAAATTGTAA
21839 AT
1 AT
21841 AAGGCAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (28 bp):
ATTTTGAAAATTTAGGGTGAAATTGTAA
Found at i:21849 original size:29 final size:29
Alignment explanation
Indices: 21791--21849 Score: 66
Period size: 28 Copynumber: 2.0 Consensus size: 29
21781 TATTTTGAAT
***
21791 ATTTAGAGGTGAAATTGTAAATTTTGAAA
1 ATTTAGAGGTGAAATTGTAAATAAGGAAA
*
21820 ATTTAG-GGTTAAATTGTAAATAAGGCAAA
1 ATTTAGAGGTGAAATTGTAAATAAGG-AAA
21849 A
1 A
21850 GTAAAAGGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (29 bp):
ATTTAGAGGTGAAATTGTAAATAAGGAAA
Found at i:22281 original size:157 final size:157
Alignment explanation
Indices: 21904--22288 Score: 492
Period size: 158 Copynumber: 2.4 Consensus size: 157
21894 TATATTATTT
* * *
21904 TTTTTAATCTTTTATATTCTTATGGGTATCTGTAAGGGTATAAAAGATTCTGAAAATTTTTTATA
1 TTTTTAATCTTTTATATTCCTATGGGTATCTGTAAGGGTAT-AAAGATT-TAAAAACTTTTTATA
* * ** *
21969 TCTTTTCGAGTTTCCATTAAGATATGAAATGATATTTTTTTAAAATAAATAAAAATTAAATTAGC
64 TCTTTTCGAGCTTCCATTAAGATACGAAATGATATTTTTCAAAAATAAATAAAAATTAAATTAAC
* *
22034 ACTCTAATTATTAAAATAAATATTATTCA
129 ACTCTAATAATTAAAATAAATATTATGCA
* ** *
22063 TTTTTAATCTTTGATATTTGTATGGGTATCCGTAAGGGTATAAAGATTTCAAAAACTTTTTATAT
1 TTTTTAATCTTTTATATTCCTATGGGTATCTGTAAGGGTATAAAGATTT-AAAAACTTTTTATAT
* *
22128 CTTTTCGAGCTTCTATTAA-AGTACGAAATGATATTTTTCAAAAATAAAT-AAAATTGAATTAAC
65 CTTTTCGAGCTTCCATTAAGA-TACGAAATGATATTTTTCAAAAATAAATAAAAATTAAATTAAC
* *
22191 ACTCTCATAATTAAAATAAATATTA-GCG
129 ACTCTAATAATTAAAATAAATATTATGCA
* *
22219 TTTTTAATCTTTTATATTCCTATGGGTGTCTGT-CGGAGTATAAAGGATCTTAAAAACTTTTTA-
1 TTTTTAATCTTTTATATTCCTATGGGTATCTGTAAGG-GTATAAA-GAT-TTAAAAACTTTTTAT
22282 ATCTTTT
63 ATCTTTT
22289 TGGGTCTAAT
Statistics
Matches: 198, Mismatches: 23, Indels: 13
0.85 0.10 0.06
Matches are distributed among these distances:
155 2 0.01
156 43 0.22
157 52 0.26
158 64 0.32
159 37 0.19
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (157 bp):
TTTTTAATCTTTTATATTCCTATGGGTATCTGTAAGGGTATAAAGATTTAAAAACTTTTTATATC
TTTTCGAGCTTCCATTAAGATACGAAATGATATTTTTCAAAAATAAATAAAAATTAAATTAACAC
TCTAATAATTAAAATAAATATTATGCA
Found at i:22507 original size:17 final size:17
Alignment explanation
Indices: 22488--22528 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
22478 TATTTTCAAA
22488 AAAATAAAAT-ATAAAT
1 AAAATAAAATAATAAAT
*
22504 AAAATAAAGTAATAAAT
1 AAAATAAAATAATAAAT
22521 AAAATAAA
1 AAAATAAA
22529 TACATATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (17 bp):
AAAATAAAATAATAAAT
Found at i:36570 original size:27 final size:29
Alignment explanation
Indices: 36540--36603 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 29
36530 TTATTAAAAT
36540 TAATATA-AATAGTATAAAATTCA-TATA
1 TAATATATAATAGTATAAAATTCAGTATA
* * *
36567 TAAT-TATAATATTATATAATTTAGTATA
1 TAATATATAATAGTATAAAATTCAGTATA
*
36595 TATTATATA
1 TAATATATA
36604 TAAAATTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 2 0.07
27 17 0.57
28 7 0.23
29 4 0.13
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (29 bp):
TAATATATAATAGTATAAAATTCAGTATA
Found at i:36584 original size:16 final size:19
Alignment explanation
Indices: 36563--36603 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
36553 ATAAAATTCA
36563 TATATAA-TTA-TA-ATAT
1 TATATAATTTAGTATATAT
36579 TATATAATTTAGTATATAT
1 TATATAATTTAGTATATAT
36598 TATATA
1 TATATA
36604 TAAAATTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 3 0.14
18 2 0.09
19 10 0.45
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TATATAATTTAGTATATAT
Found at i:36679 original size:19 final size:18
Alignment explanation
Indices: 36651--36686 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
36641 TTTATTTTAA
36651 AAAATAAATAATTAAAATT
1 AAAATAAAT-ATTAAAATT
*
36670 AAAATTAATATTAAAAT
1 AAAATAAATATTAAAAT
36687 ATTAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATAAATATTAAAATT
Found at i:40183 original size:29 final size:28
Alignment explanation
Indices: 40149--40208 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
40139 GTTAGAGTGT
*
40149 ATTTTGAATATTTAGAGGTGAAATTGTAA
1 ATTTTGAAAATTTAG-GGTGAAATTGTAA
*
40178 ATTTTGAAAATTTAGGGTTAAATTGTAA
1 ATTTTGAAAATTTAGGGTGAAATTGTAA
40206 ATT
1 ATT
40209 AAGGCAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.43
Consensus pattern (28 bp):
ATTTTGAAAATTTAGGGTGAAATTGTAA
Found at i:40573 original size:158 final size:158
Alignment explanation
Indices: 40260--40652 Score: 482
Period size: 157 Copynumber: 2.5 Consensus size: 158
40250 AAGATATTTT
* *
40260 ATATTATT-TTTTTTAATCTTTTATATTCTTATGGGTATCTGTAAGGGTATAAAAGA-TTCTGAA
1 ATATTATTCATTTTTAATCTTTTATATT-TTATGGGTATCTGTAAGGGTATAAAAGATTTC-AAA
* * **
40323 AA-TTTTTATATC-TTTCGAGTTTCCATTAAGATATGAAATGATATTTTTTTAAAATAAATAAAA
64 AACTTTTTATATCTTTTCGAGCTTCCATTAAGATACGAAATGATATTTTTCAAAAATAAATAAAA
* *
40386 ATTAAATTAGCACTCTAATTATTAAAATAA
129 ATTAAATTAACACTCTAATAATTAAAATAA
* *
40416 ATATTATTCATTTTTAATCTTTGATATTTGTATGGGTATCCGTAAGGGTATAAAAGATTTCAAAA
1 ATATTATTCATTTTTAATCTTTTATATTT-TATGGGTATCTGTAAGGGTATAAAAGATTTCAAAA
*
40481 ACTTTTTATATCTTTTCGAGCTTCTATTAA-AGTACGAAATGATATTTTTCAAAAATAAAT-AAA
65 ACTTTTTATATCTTTTCGAGCTTCCATTAAGA-TACGAAATGATATTTTTCAAAAATAAATAAAA
* *
40544 ATTGAATTAACACTCTCATAATTAAAATAA
129 ATTAAATTAACACTCTAATAATTAAAATAA
* * * * * *
40574 ATATTA-GCGTTTTTAATCTTTTATATTCCTATGGGTGTCTGT-CGGAGTATAAAGGATCTT-AA
1 ATATTATTCATTTTTAATCTTTTATATT-TTATGGGTATCTGTAAGG-GTATAAAAGAT-TTCAA
40636 AAACTTTTTA-ATCTTTT
63 AAACTTTTTATATCTTTT
40653 TGGGTCTAAT
Statistics
Matches: 207, Mismatches: 21, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
156 18 0.09
157 98 0.47
158 51 0.25
159 40 0.19
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (158 bp):
ATATTATTCATTTTTAATCTTTTATATTTTATGGGTATCTGTAAGGGTATAAAAGATTTCAAAAA
CTTTTTATATCTTTTCGAGCTTCCATTAAGATACGAAATGATATTTTTCAAAAATAAATAAAAAT
TAAATTAACACTCTAATAATTAAAATAA
Found at i:40881 original size:17 final size:16
Alignment explanation
Indices: 40851--40891 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
40841 ATATTTTCAA
40851 AAAATAAAATATAAAT
1 AAAATAAAATATAAAT
*
40867 AAAATAAAGTAATAAAT
1 AAAATAAAAT-ATAAAT
40884 AAAATAAA
1 AAAATAAA
40892 TACATATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (16 bp):
AAAATAAAATATAAAT
Found at i:54390 original size:17 final size:18
Alignment explanation
Indices: 54370--54408 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
54360 AATATAATAA
54370 TAAAGTAATTA-TATATT
1 TAAAGTAATTATTATATT
*
54387 TAAATTAATTATTTATATT
1 TAAAGTAATTA-TTATATT
54406 TAA
1 TAA
54409 TATTGTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
19 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TAAAGTAATTATTATATT
Found at i:54929 original size:20 final size:20
Alignment explanation
Indices: 54899--54944 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
54889 AATTATTAAT
*
54899 TTATTAAAATTAATATA-AA
1 TTATAAAAATTAATATATAA
*
54918 TATATAAAAATTCATATATAA
1 T-TATAAAAATTAATATATAA
54939 TTATAA
1 TTATAA
54945 TATTATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 19 0.83
21 3 0.13
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TTATAAAAATTAATATATAA
Found at i:54951 original size:16 final size:19
Alignment explanation
Indices: 54932--54972 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
54922 TAAAAATTCA
54932 TATATAA-TTA-TA-ATAT
1 TATATAATTTAGTATATAT
54948 TATATAATTTAGTATATAT
1 TATATAATTTAGTATATAT
54967 TATATA
1 TATATA
54973 TAAAATTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 3 0.14
18 2 0.09
19 10 0.45
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TATATAATTTAGTATATAT
Found at i:58836 original size:159 final size:158
Alignment explanation
Indices: 58642--59036 Score: 502
Period size: 159 Copynumber: 2.5 Consensus size: 158
58632 AGATATTTTT
* *
58642 ATATTATT-TTTTTTAATCTTTTATATTCTTATGGGTATCTGTAAGGGTATAAAAGA-TTCTGAA
1 ATATTATTCATTTTTAATCTTTTATATTCTTATGGGTATCTGTAAGGGTATAAAAGATTTC-AAA
* * *
58705 AA-TTTTTCATATCTTTTCGAG-TTTTCATT-AAGATATGAAATGATATTTTTCTAAAATAAATA
65 AACTTTTT-ATATCTTTTCGAGCTTCT-ATTAAAG-TACGAAATGATATTTTTCAAAAATAAAT-
* *
58767 AAAATTAAATTAGCACTCTAATTATTAAAACAA
126 AAAATTAAATTAACACTCTAATAATTAAAACAA
* *
58800 ATATTATTCATTTTTAATCTTTGATATTCTTATGGGTATCCGTAAGGGTATAAAAGATTTCAAAA
1 ATATTATTCATTTTTAATCTTTTATATTCTTATGGGTATCTGTAAGGGTATAAAAGATTTCAAAA
58865 ACTTTTTATATCTTTTCGAGCTTCTATTAAAGTACGAAATGATATTTTTCAAAAATAAATAAAAT
66 ACTTTTTATATCTTTTCGAGCTTCTATTAAAGTACGAAATGATATTTTTCAAAAATAAATAAAAT
* * *
58930 TGAATTAACACTCTCATAATTAAAATAA
131 TAAATTAACACTCTAATAATTAAAACAA
* * * * * *
58958 ATATTA-ACGTTTTTAATCTTTTATATTCCTATGGGTGTCTGT-TGGAGTATAAAGGATCTT-AA
1 ATATTATTCATTTTTAATCTTTTATATTCTTATGGGTATCTGTAAGG-GTATAAAAGAT-TTCAA
59020 AAACTTTTTA-ATCTTTT
64 AAACTTTTTATATCTTTT
59037 TGGGTCTCAT
Statistics
Matches: 210, Mismatches: 20, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
156 9 0.04
157 52 0.25
158 44 0.21
159 91 0.43
160 14 0.07
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (158 bp):
ATATTATTCATTTTTAATCTTTTATATTCTTATGGGTATCTGTAAGGGTATAAAAGATTTCAAAA
ACTTTTTATATCTTTTCGAGCTTCTATTAAAGTACGAAATGATATTTTTCAAAAATAAATAAAAT
TAAATTAACACTCTAATAATTAAAACAA
Found at i:59256 original size:17 final size:17
Alignment explanation
Indices: 59236--59277 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
59226 TATTTTCAAA
59236 AAAATAAAAAAATAAAT
1 AAAATAAAAAAATAAAT
**
59253 AAAATAAAGTAATAAAT
1 AAAATAAAAAAATAAAT
59270 AAAATAAA
1 AAAATAAA
59278 TACATATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (17 bp):
AAAATAAAAAAATAAAT
Found at i:72788 original size:17 final size:18
Alignment explanation
Indices: 72768--72806 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
72758 AATATAATAA
72768 TAAAGTAATTA-TATATT
1 TAAAGTAATTATTATATT
*
72785 TAAATTAATTATTTATATT
1 TAAAGTAATTA-TTATATT
72804 TAA
1 TAA
72807 TATTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
19 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TAAAGTAATTATTATATT
Found at i:73326 original size:20 final size:20
Alignment explanation
Indices: 73296--73341 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
73286 AATTATTAAT
*
73296 TTATTAAAATTAATATA-AA
1 TTATAAAAATTAATATATAA
*
73315 TATATAAAAATTCATATATAA
1 T-TATAAAAATTAATATATAA
73336 TTATAA
1 TTATAA
73342 TATTATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 19 0.83
21 3 0.13
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TTATAAAAATTAATATATAA
Found at i:73348 original size:28 final size:27
Alignment explanation
Indices: 73313--73378 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 27
73303 AATTAATATA
73313 AATA-TATAAAAATTCATATATAATTAT
1 AATATTATAAAAATTCA-ATATAATTAT
* * *
73340 AATATTAT-ATAATTTAATATATTTAT
1 AATATTATAAAAATTCAATATAATTAT
*
73366 ATTATATATAAAA
1 AATAT-TATAAAA
73379 TTTATTATTG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
26 13 0.42
27 13 0.42
28 5 0.16
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
AATATTATAAAAATTCAATATAATTAT
Found at i:73366 original size:16 final size:16
Alignment explanation
Indices: 73329--73359 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
73319 TAAAAATTCA
73329 TATATAATTATAATAT
1 TATATAATTATAATAT
73345 TATATAATT-TAATAT
1 TATATAATTATAATAT
73360 ATTTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATAATTATAATAT
Found at i:73366 original size:26 final size:27
Alignment explanation
Indices: 73313--73382 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
73303 AATTAATATA
*
73313 AATATATA-AAAATTCATATATAATTAT
1 AATATATATAAAATTTA-ATATAATTAT
* *
73340 AATAT-TATATAATTTAATATATTTAT
1 AATATATATAAAATTTAATATAATTAT
*
73366 ATTATATATAAAATTTA
1 AATATATATAAAATTTA
73383 TTATTGAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 15 0.42
27 21 0.58
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (27 bp):
AATATATATAAAATTTAATATAATTAT
Found at i:79382 original size:16 final size:17
Alignment explanation
Indices: 79356--79392 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
79346 GAAATAAAAT
79356 TAATCAAAATTTTATTA
1 TAATCAAAATTTTATTA
79373 TAAT-AAAATTTTATTA
1 TAATCAAAATTTTATTA
79389 TAAT
1 TAAT
79393 TAATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATCAAAATTTTATTA
Found at i:79403 original size:19 final size:18
Alignment explanation
Indices: 79363--79416 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 18
79353 AATTAATCAA
79363 AATTTTATTATAA-TAA-
1 AATTTTATTATAATTAAT
79379 AATTTTATTATAATTAATT
1 AATTTTATTATAATTAA-T
*
79398 ATTTTTAGTTA-AATTAAT
1 AATTTTA-TTATAATTAAT
79416 A
1 A
79417 TTATTTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 13 0.39
17 3 0.09
18 2 0.06
19 12 0.36
20 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
AATTTTATTATAATTAAT
Found at i:79847 original size:10 final size:9
Alignment explanation
Indices: 79832--79923 Score: 53
Period size: 9 Copynumber: 9.8 Consensus size: 9
79822 ATAAATTATT
79832 AATTTATTAA
1 AATTTA-TAA
79842 AATTTATATA
1 AATTTATA-A
*
79852 AATATATAA
1 AATTTATAA
*
79861 AATTTTTAA
1 AATTTATAA
79870 AATAATTATAA
1 AAT--TTATAA
*
79881 TATTT-TAA
1 AATTTATAA
*
79889 AATAT-TAA
1 AATTTATAA
*
79897 AATGATTATAT
1 AAT--TTATAA
* *
79908 TATATATAA
1 AATTTATAA
79917 AATTTAT
1 AATTTAT
79924 TGTTAAATTT
Statistics
Matches: 62, Mismatches: 14, Indels: 13
0.70 0.16 0.15
Matches are distributed among these distances:
8 12 0.19
9 24 0.39
10 15 0.24
11 11 0.18
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (9 bp):
AATTTATAA
Found at i:79863 original size:19 final size:18
Alignment explanation
Indices: 79839--79923 Score: 75
Period size: 19 Copynumber: 4.6 Consensus size: 18
79829 ATTAATTTAT
79839 TAAAATTTATATAAATATA
1 TAAAATTTATA-AAATATA
*
79858 TAAAATTTTTAAAATAATTA
1 TAAAATTTATAAAAT-A-TA
*
79878 TAATATTT-TAAAATAT-
1 TAAAATTTATAAAATATA
**
79894 TAAAATGATTATATTATATA
1 TAAAAT--TTATAAAATATA
79914 TAAAATTTAT
1 TAAAATTTAT
79924 TGTTAAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
16 5 0.09
17 1 0.02
18 11 0.20
19 23 0.42
20 15 0.27
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (18 bp):
TAAAATTTATAAAATATA
Found at i:80026 original size:17 final size:17
Alignment explanation
Indices: 80002--80037 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
79992 AAATATTTTA
80002 ATTTTTAAAAA-TAATT
1 ATTTTTAAAAATTAATT
80018 ATTTATTAAAAATTAATT
1 ATTT-TTAAAAATTAATT
80036 AT
1 AT
80038 ATAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 7 0.39
18 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTTAAAAATTAATT
Found at i:80047 original size:20 final size:18
Alignment explanation
Indices: 80006--80052 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
79996 ATTTTAATTT
*
80006 TTAAAAA-TAATTATTTA
1 TTAAAAATTAATTATTAA
80023 TTAAAAATTAATTATATAAA
1 TTAAAAATTAATTAT-T-AA
*
80043 TTAAAGATTA
1 TTAAAAATTA
80053 TTTAACTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 7 0.28
19 1 0.04
20 10 0.40
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TTAAAAATTAATTATTAA
Found at i:85288 original size:18 final size:18
Alignment explanation
Indices: 85265--85300 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
85255 CTAAATTTTA
85265 GAGTCTCA-AAAGCCAAAT
1 GAGTCTCAGAAA-CCAAAT
85283 GAGTCTCAGAAACCAAAT
1 GAGTCTCAGAAACCAAAT
85301 CAAATCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (18 bp):
GAGTCTCAGAAACCAAAT
Found at i:86486 original size:459 final size:459
Alignment explanation
Indices: 85628--86517 Score: 1548
Period size: 459 Copynumber: 1.9 Consensus size: 459
85618 TACTATCTAC
85628 AAACACCAACCCTTCCACAACAACAATCACTACACTCCCTGTGCAATCTATGTTCCCTTACATAC
1 AAACACCAACCCTTCCACAACAACAATCACTACACTCCCTGTGCAATCTATGTTCCCTTACATAC
* *
85693 AGCAGCAAATGCCTTTAGGAGGATGGCCACAACTACTAAACTTTTACCAAAACTTACTTGTATCC
66 AGCAGCAAATGCCTTTAAGAGGATGGCCACAACTACCAAACTTTTACCAAAACTTACTTGTATCC
*
85758 ATCTTATCATCGCCACAACAAAAATACATAATACTTGACCTAAACACTATGGCCAATATAACACC
131 ATCTCATCATCGCCACAACAAAAATACATAATACTTGACCTAAACACTATGGCCAATATAACACC
*
85823 AGGAAGCCCCTCAACTCCAGTAAACATCGCTCAAGGCACTAATCCAATGACCATGCCCAGAAACT
196 AGGAAGCCCCTCAACTCCAGTAAACATCGCTCAAGGCACAAATCCAATGACCATGCCCAGAAACT
* ** * *
85888 CAATAGTGGCGACCAACCCCTGGGAGTCTTAAGTCTGCCCGTCACACATCCTTCTGCCAGACTAT
261 CAACAGTGGCGACCAACCCCTGGGAGTCACAAGTCTGCCCGTCACACATCCCTCTGCCAAACTAT
* * * *
85953 TATAGTAATTATATAGCTTAAATGCAGGCTATGACCAACTACATAATCGCCTAACAAGCCATCAT
326 TATAGTAATTATATAGCTCAAATGCAGGCTATGACCAACCACATAACCGCCCAACAAGCCATCAT
86018 ACAACAGCTCCTACAAAAGCAAGAAAAGCAAAACCCTCCAGTAGAAAAGCAGGAAAAGTAAGAAA
391 ACAACAGCTCCTACAAAAGCAAGAAAAGCAAAACCCTCCAGTAGAAAAGCAGGAAAAGTAAGAAA
86083 AGCA
456 AGCA
* * *
86087 AAACACCAACTCTTTCACAACAACAATCACTACATTCCCTGTGCAATCTATGTTCCCTTACATAC
1 AAACACCAACCCTTCCACAACAACAATCACTACACTCCCTGTGCAATCTATGTTCCCTTACATAC
*
86152 AGCAGCAAATGCCTTTAAGAGGATGGCCACAACTGCCAAACTTTTACCAAAACTTACTTGTATCC
66 AGCAGCAAATGCCTTTAAGAGGATGGCCACAACTACCAAACTTTTACCAAAACTTACTTGTATCC
* *
86217 ATCTCATCATCGCCATAACAAAAATACATAATACTTGACCTAAACACTATGGCCAATATAACATC
131 ATCTCATCATCGCCACAACAAAAATACATAATACTTGACCTAAACACTATGGCCAATATAACACC
*
86282 AGGAAGCCCCTCAACTCCAGTAAACATCGCTCAAGGCACAAATCCAATGCCCATGCCCA-AAACC
196 AGGAAGCCCCTCAACTCCAGTAAACATCGCTCAAGGCACAAATCCAATGACCATGCCCAGAAA-C
*
86346 TCAACAGTGGCGACCAACCCTTGGGAGTCACAAGTCTGCCCGTCACACATCCCTCTGCCAAACTA
260 TCAACAGTGGCGACCAACCCCTGGGAGTCACAAGTCTGCCCGTCACACATCCCTCTGCCAAACTA
*
86411 TTATAGTAATTATATAGCTCAAATGCAGGCTATGACCAACCACGTAACCGCCCAACAAGCCATCA
325 TTATAGTAATTATATAGCTCAAATGCAGGCTATGACCAACCACATAACCGCCCAACAAGCCATCA
* *
86476 TACAACAGCTCCTATAAAAGTAAGAAAAGCAAAACCCTCCAG
390 TACAACAGCTCCTACAAAAGCAAGAAAAGCAAAACCCTCCAG
86518 CACAGGCAAA
Statistics
Matches: 406, Mismatches: 24, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
458 3 0.01
459 403 0.99
ACGTcount: A:0.37, C:0.30, G:0.13, T:0.21
Consensus pattern (459 bp):
AAACACCAACCCTTCCACAACAACAATCACTACACTCCCTGTGCAATCTATGTTCCCTTACATAC
AGCAGCAAATGCCTTTAAGAGGATGGCCACAACTACCAAACTTTTACCAAAACTTACTTGTATCC
ATCTCATCATCGCCACAACAAAAATACATAATACTTGACCTAAACACTATGGCCAATATAACACC
AGGAAGCCCCTCAACTCCAGTAAACATCGCTCAAGGCACAAATCCAATGACCATGCCCAGAAACT
CAACAGTGGCGACCAACCCCTGGGAGTCACAAGTCTGCCCGTCACACATCCCTCTGCCAAACTAT
TATAGTAATTATATAGCTCAAATGCAGGCTATGACCAACCACATAACCGCCCAACAAGCCATCAT
ACAACAGCTCCTACAAAAGCAAGAAAAGCAAAACCCTCCAGTAGAAAAGCAGGAAAAGTAAGAAA
AGCA
Found at i:89914 original size:422 final size:422
Alignment explanation
Indices: 89130--89943 Score: 1520
Period size: 422 Copynumber: 1.9 Consensus size: 422
89120 CAAAGGATGA
*
89130 GACTTTTTGTTATCAGGTAATGCCTTTCGGCTTAAAGAACGCTGGTGCAACGTATCAACGGTTGG
1 GACTTTTTGTTACCAGGTAATGCCTTTCGGCTTAAAGAACGCTGGTGCAACGTATCAACGGTTGG
*
89195 TAAATAAATTTTTAAAGAACAAATCGGGCGGTCGATGAAAGTATACATGGACGACATGCTGGTCA
66 TAAATAAATTTTTAAAGAACAAATCGGGCAGTCGATGAAAGTATACATGGACGACATGCTGGTCA
* *
89260 AAAGCGACACCATTGAACGGCATATCAATGACCTGACCGAAGCTTTTACCGTTCTTCGAAGGTAC
131 AAAGCGACACCATTGAACGGCACATCAATGACCTGACCGAAGCTTTTACCATTCTTCGAAGGTAC
* *
89325 AATATGAAGTTAAACCCATTGAAGTGTACGTTTGGGGTGGTAGCTGGTAAATTTCTAGAATTCAT
196 AATATGAAGTTAAACCCATTGAAGTGTACATTTGGGGTGGCAGCTGGTAAATTTCTAGAATTCAT
89390 GGTGTCGTCTAGAGGAATAGAGGCAAACCTAGAAAATATCAAAACCATAATAGAGATGACCCCGC
261 GGTGTCGTCTAGAGGAATAGAGGCAAACCTAGAAAATATCAAAACCATAATAGAGATGACCCCGC
*
89455 CTAAGTTGACAAAAGAAGTACAAAAGCTCATAGGAAGAGTGGCTGCCTTAAACCAGTTCATCTCC
326 CTAAGTTGACAAAAAAAGTACAAAAGCTCATAGGAAGAGTGGCTGCCTTAAACCAGTTCATCTCC
89520 AAGCTTTTACTAGTTCATCTCCAAGCTCATAG
391 AAGCTTTTACTAGTTCATCTCCAAGCTCATAG
* * *
89552 GACTTTTTGTTACCATGTAATGCCTTTCGGCTTGAAGAATGCTGGTGCAACGTATCAACGGTTGG
1 GACTTTTTGTTACCAGGTAATGCCTTTCGGCTTAAAGAACGCTGGTGCAACGTATCAACGGTTGG
*
89617 TAAATAAATTTTTAAAGAACAAATCGGGCAGTCGATGAAAGTATACATGGATGACATGCTGGTCA
66 TAAATAAATTTTTAAAGAACAAATCGGGCAGTCGATGAAAGTATACATGGACGACATGCTGGTCA
89682 AAAGCGACACCATTGAACGGCACATCAATGACCTGACCGAAGCTTTTACCATTCTTCGAAGGTAC
131 AAAGCGACACCATTGAACGGCACATCAATGACCTGACCGAAGCTTTTACCATTCTTCGAAGGTAC
*
89747 AATATGAAGTTAAACCCATTGAAGTGTACATTTGGGGTGGCAGTTGGTAAATTTCTAGAATTCAT
196 AATATGAAGTTAAACCCATTGAAGTGTACATTTGGGGTGGCAGCTGGTAAATTTCTAGAATTCAT
89812 GGTGTCGTCTAGAGGAATAGAGGCAAACCTAGAAAATATCAAAACCATAATAGAGATGACCCCGC
261 GGTGTCGTCTAGAGGAATAGAGGCAAACCTAGAAAATATCAAAACCATAATAGAGATGACCCCGC
89877 CTAAGTTGACAAAAAAAGTACAAAAGCTCATAGGAAGAGTGGCTGCCTTAAACCAGTTCATCTCC
326 CTAAGTTGACAAAAAAAGTACAAAAGCTCATAGGAAGAGTGGCTGCCTTAAACCAGTTCATCTCC
89942 AA
391 AA
89944 ACTTGTGGAC
Statistics
Matches: 380, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
422 380 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (422 bp):
GACTTTTTGTTACCAGGTAATGCCTTTCGGCTTAAAGAACGCTGGTGCAACGTATCAACGGTTGG
TAAATAAATTTTTAAAGAACAAATCGGGCAGTCGATGAAAGTATACATGGACGACATGCTGGTCA
AAAGCGACACCATTGAACGGCACATCAATGACCTGACCGAAGCTTTTACCATTCTTCGAAGGTAC
AATATGAAGTTAAACCCATTGAAGTGTACATTTGGGGTGGCAGCTGGTAAATTTCTAGAATTCAT
GGTGTCGTCTAGAGGAATAGAGGCAAACCTAGAAAATATCAAAACCATAATAGAGATGACCCCGC
CTAAGTTGACAAAAAAAGTACAAAAGCTCATAGGAAGAGTGGCTGCCTTAAACCAGTTCATCTCC
AAGCTTTTACTAGTTCATCTCCAAGCTCATAG
Found at i:95760 original size:18 final size:18
Alignment explanation
Indices: 95737--95772 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
95727 CTAAATCTTA
95737 GAGTCTCACAAACCAAAT
1 GAGTCTCACAAACCAAAT
*
95755 GAGTCTCATAAACCAAAT
1 GAGTCTCACAAACCAAAT
95773 CTATATAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.19
Consensus pattern (18 bp):
GAGTCTCACAAACCAAAT
Found at i:99604 original size:15 final size:16
Alignment explanation
Indices: 99584--99616 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
99574 AAAATGAATG
99584 ATATTAATT-AATATT
1 ATATTAATTAAATATT
99599 ATATTAATTAAATATT
1 ATATTAATTAAATATT
99615 AT
1 AT
99617 TTTTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATTAATTAAATATT
Found at i:99670 original size:13 final size:13
Alignment explanation
Indices: 99654--99678 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
99644 ATTAAATTAA
99654 ATTTTAAAATTTT
1 ATTTTAAAATTTT
99667 ATTTTAAAATTT
1 ATTTTAAAATTT
99679 AATGTATTTT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTTAAAATTTT
Found at i:104196 original size:2 final size:2
Alignment explanation
Indices: 104189--104229 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
104179 CATTTGTACC
*
104189 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
104230 CCTTTTGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:111802 original size:27 final size:27
Alignment explanation
Indices: 111742--111852 Score: 95
Period size: 28 Copynumber: 4.1 Consensus size: 27
111732 TTTAAAATTT
111742 ATATAATATAAAT-TATTAATA-TATTA
1 ATATAATATAAATATA-TAATATTATTA
* *
111768 AAATTAATATAAATATATAATATTTTTA
1 ATA-TAATATAAATATATAATATTATTA
* *
111796 ATATAATTATAAA-ATAATAAAATATATAA
1 ATATAA-TATAAATAT-ATAATAT-TATTA
* *
111825 ATATGACATAAATATATAA-ATTATTA
1 ATATAATATAAATATATAATATTATTA
111851 AT
1 AT
111853 TTTAATTAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
26 8 0.12
27 22 0.32
28 29 0.42
29 10 0.14
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (27 bp):
ATATAATATAAATATATAATATTATTA
Found at i:111838 original size:56 final size:53
Alignment explanation
Indices: 111776--111880 Score: 133
Period size: 56 Copynumber: 1.9 Consensus size: 53
111766 TAAAATTAAT
*
111776 ATAAATATATAATATTTTTAA-TATAATTATAAAATAATAA-AATATATAAATATGAC
1 ATAAATATATAA-ATTATTAATTATAA-T-TAAAATAA-AATAATA-ATAAATATGAC
*
111832 ATAAATATATAAATTATTAATTTTAATTAAAATAAAATAATAATAAATA
1 ATAAATATATAAATTATTAATTATAATTAAAATAAAATAATAATAAATA
111881 AAACTATTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
53 9 0.20
54 12 0.27
55 8 0.18
56 16 0.36
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (53 bp):
ATAAATATATAAATTATTAATTATAATTAAAATAAAATAATAATAAATATGAC
Found at i:112724 original size:15 final size:15
Alignment explanation
Indices: 112704--112732 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
112694 TTGGTTTTGA
112704 GTTGGATTATTTCGG
1 GTTGGATTATTTCGG
112719 GTTGGATTATTTCG
1 GTTGGATTATTTCG
112733 AGTTATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.31, T:0.48
Consensus pattern (15 bp):
GTTGGATTATTTCGG
Found at i:112802 original size:16 final size:16
Alignment explanation
Indices: 112782--112869 Score: 81
Period size: 16 Copynumber: 5.5 Consensus size: 16
112772 TTTAAGTTTA
112782 AGTCATTTCGGGTTCG
1 AGTCATTTCGGGTTCG
* **
112798 GGTCACTTT-GAATTCG
1 AGTCA-TTTCGGGTTCG
112814 AGTCATTTCGGGTTCG
1 AGTCATTTCGGGTTCG
* **
112830 GGTCACTTT-GAATTCG
1 AGTCA-TTTCGGGTTCG
112846 AGTCATTTCGGGTTCG
1 AGTCATTTCGGGTTCG
*
112862 AGTTATTT
1 AGTCATTT
112870 TAGATTCGGG
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
15 6 0.11
16 43 0.78
17 6 0.11
ACGTcount: A:0.16, C:0.17, G:0.27, T:0.40
Consensus pattern (16 bp):
AGTCATTTCGGGTTCG
Found at i:112877 original size:32 final size:32
Alignment explanation
Indices: 112755--112861 Score: 162
Period size: 32 Copynumber: 3.3 Consensus size: 32
112745 TTCGAGTTGT
* * **
112755 TTTCAGGTTCGGGTCA-TTTTAAGTTTAAGTCA
1 TTTCGGGTTCGGGTCACTTTGAA-TTCGAGTCA
112787 TTTCGGGTTCGGGTCACTTTGAATTCGAGTCA
1 TTTCGGGTTCGGGTCACTTTGAATTCGAGTCA
112819 TTTCGGGTTCGGGTCACTTTGAATTCGAGTCA
1 TTTCGGGTTCGGGTCACTTTGAATTCGAGTCA
112851 TTTCGGGTTCG
1 TTTCGGGTTCG
112862 AGTTATTTTA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 65 0.93
33 5 0.07
ACGTcount: A:0.16, C:0.17, G:0.27, T:0.40
Consensus pattern (32 bp):
TTTCGGGTTCGGGTCACTTTGAATTCGAGTCA
Found at i:113867 original size:21 final size:22
Alignment explanation
Indices: 113820--113878 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 22
113810 TATAATCACA
* *
113820 TATTATATAACTAATTCAAAAG
1 TATTATATTACTAATTTAAAAG
*
113842 T-TTATATTA-TAATTTATAAG
1 TATTATATTACTAATTTAAAAG
* *
113862 TATTATTTTATTAATTT
1 TATTATATTACTAATTT
113879 TATGTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 10 0.32
21 14 0.45
22 7 0.23
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (22 bp):
TATTATATTACTAATTTAAAAG
Found at i:113980 original size:16 final size:16
Alignment explanation
Indices: 113961--114028 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
113951 TGTTCGAATT
* *
113961 ATTTCAGATTCGGGTC
1 ATTTCGGATTCGAGTC
* *
113977 ATTTCGGGTTTGAGTC
1 ATTTCGGATTCGAGTC
* *
113993 ATTTCGGATTCGGGTT
1 ATTTCGGATTCGAGTC
114009 ATTTC-GAGTTCGAGTC
1 ATTTCGGA-TTCGAGTC
114025 ATTT
1 ATTT
114029 TGAATTTAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
15 2 0.05
16 39 0.95
ACGTcount: A:0.16, C:0.15, G:0.26, T:0.43
Consensus pattern (16 bp):
ATTTCGGATTCGAGTC
Found at i:113997 original size:32 final size:32
Alignment explanation
Indices: 113936--114028 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 32
113926 CAGAATAATT
* * *
113936 ATTCGTGTCATTTC-ATGTTCGAATTATTTCAG
1 ATTCGGGTCATTTCGA-GTTCGAGTCATTTCAG
* * *
113968 ATTCGGGTCATTTCGGGTTTGAGTCATTTCGG
1 ATTCGGGTCATTTCGAGTTCGAGTCATTTCAG
*
114000 ATTCGGGTTATTTCGAGTTCGAGTCATTT
1 ATTCGGGTCATTTCGAGTTCGAGTCATTT
114029 TGAATTTAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.17, C:0.15, G:0.24, T:0.44
Consensus pattern (32 bp):
ATTCGGGTCATTTCGAGTTCGAGTCATTTCAG
Found at i:114645 original size:2 final size:2
Alignment explanation
Indices: 114633--114667 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
114623 AGGTGATTAT
*
114633 TC TC TC GC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
114668 TCATTCCCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.49, G:0.03, T:0.49
Consensus pattern (2 bp):
TC
Found at i:116160 original size:18 final size:17
Alignment explanation
Indices: 116094--116159 Score: 52
Period size: 16 Copynumber: 4.1 Consensus size: 17
116084 TCATTATTTA
*
116094 AAATTTTATATATTTAT
1 AAATTTTATATATATAT
**
116111 AAAAATTA-ATATA-A-
1 AAATTTTATATATATAT
116125 AAATAATTTATAT-TATAT
1 AAAT--TTTATATATATAT
116143 AAATTTTA-ATATATAT
1 AAATTTTATATATATAT
116159 A
1 A
116160 TTTTTAGGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 13
0.68 0.09 0.23
Matches are distributed among these distances:
14 3 0.08
15 3 0.08
16 19 0.50
17 9 0.24
18 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTTTATATATATAT
Found at i:120134 original size:17 final size:18
Alignment explanation
Indices: 120114--120148 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
120104 ATACACTTAA
120114 AATAAAAAT-TATTTATT
1 AATAAAAATATATTTATT
120131 AATAAAAATATATTTATT
1 AATAAAAATATATTTATT
120149 TTATATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAAAAATATATTTATT
Found at i:121886 original size:1 final size:1
Alignment explanation
Indices: 121882--121906 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
121872 TTATAACCCT
121882 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
121907 AATCCCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:123566 original size:2 final size:2
Alignment explanation
Indices: 123559--123586 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
123549 TATTTCAATA
123559 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
123587 TCTATTCCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:124135 original size:25 final size:25
Alignment explanation
Indices: 124080--124129 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
124070 AAATTTATTT
*
124080 ATTATTTATATTAAATTAATAAATA
1 ATTATTTAAATTAAATTAATAAATA
124105 ATTATTTAAATTTAAATTAAATAAA
1 ATTATTTAAA-TTAAATT-AATAAA
124130 ATTATTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
26 7 0.32
27 6 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTATTTAAATTAAATTAATAAATA
Found at i:124343 original size:53 final size:53
Alignment explanation
Indices: 124233--124343 Score: 136
Period size: 53 Copynumber: 2.1 Consensus size: 53
124223 ACAAATAAAT
* * * *
124233 AAATAATAAATTTAAAAATTTAAATTTAATTTTTACAAAAGTAAAGTCAATTT
1 AAATAAAAAATTTAAAAATTTAAATTTAATTTTTACAAAAATAAAGTAAATTA
* *
124286 AAATAAAAAATTTAAATATTTAAATTT-ATTATTTATAAAAATAATA-TAAATTA
1 AAATAAAAAATTTAAAAATTTAAATTTAATT-TTTACAAAAATAA-AGTAAATTA
124339 AAATA
1 AAATA
124344 TGAATATACG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
52 3 0.06
53 46 0.92
54 1 0.02
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (53 bp):
AAATAAAAAATTTAAAAATTTAAATTTAATTTTTACAAAAATAAAGTAAATTA
Found at i:125637 original size:18 final size:17
Alignment explanation
Indices: 125610--125646 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
125600 AATAATTATG
125610 ATATAATAAAAATATAA
1 ATATAATAAAAATATAA
*
125627 ATATAAATAAATATATAA
1 ATAT-AATAAAAATATAA
125645 AT
1 AT
125647 GATTAATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATAATAAAAATATAA
Found at i:138028 original size:21 final size:20
Alignment explanation
Indices: 137977--138019 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
137967 AATTCAAAAT
*
137977 AATTAATAATTATTTTTAAA
1 AATTAATAAATATTTTTAAA
*
137997 AAATAATAAATA-TTTTAAA
1 AATTAATAAATATTTTTAAA
138016 AATT
1 AATT
138020 TTAATAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTAATAAATATTTTTAAA
Found at i:138501 original size:2 final size:2
Alignment explanation
Indices: 138496--138533 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
138486 TGAAAAAAAA
* *
138496 AT AT AT AT AT AT AT AT AG AT AG AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
138534 TCAGTTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:138610 original size:23 final size:23
Alignment explanation
Indices: 138584--138641 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
138574 AATATTAAAA
138584 ATATTATATTAATATTTATAATT
1 ATATTATATTAATATTTATAATT
* * *
138607 ATATT-TAAATAATTTTTTTAATT
1 ATATTAT-ATTAATATTTATAATT
138630 AT-TTA-ATTAATA
1 ATATTATATTAATA
138642 ATTCAAGTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
21 5 0.18
22 3 0.11
23 20 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATATTATATTAATATTTATAATT
Found at i:138628 original size:32 final size:32
Alignment explanation
Indices: 138549--138635 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 32
138539 TTAAATCCGT
* *
138549 AAAATTTTATTTTATTATTTAAAATAATATTA
1 AAAATATTATTTTAATATTTAAAATAATATTA
* * *
138581 AAAATATTATATTAATATTTATAATTATATTTA
1 AAAATATTATTTTAATATTTAAAATAATA-TTA
138614 AATAAT-TT-TTTTAATTATTTAA
1 AA-AATATTATTTTAA-TATTTAA
138636 TTAATAATTC
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
32 29 0.64
33 13 0.29
34 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
AAAATATTATTTTAATATTTAAAATAATATTA
Found at i:139553 original size:19 final size:18
Alignment explanation
Indices: 139511--139556 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
139501 ATTTTATAAT
*
139511 TTAATTTAAATAAAAATA
1 TTAATTTAAGTAAAAATA
*
139529 TT--TTTAAGTAGTAAATA
1 TTAATTTAAGTA-AAAATA
139546 TTAATTTAAGT
1 TTAATTTAAGT
139557 GGGACGACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 7 0.30
17 7 0.30
18 2 0.09
19 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (18 bp):
TTAATTTAAGTAAAAATA
Found at i:140147 original size:15 final size:16
Alignment explanation
Indices: 140124--140161 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
140114 TTTGTAATGA
*
140124 ATTAAAATAA-TAAAT
1 ATTATAATAATTAAAT
140139 ATTATAATAATTAAAT
1 ATTATAATAATTAAAT
*
140155 AGTATAA
1 ATTATAA
140162 AAAATAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTATAATAATTAAAT
Found at i:140162 original size:25 final size:25
Alignment explanation
Indices: 140107--140153 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
140097 AGTTAACGTA
* *
140107 AATAAATTTTGTAATGAATTAAAAT
1 AATAAATATTATAATGAATTAAAAT
140132 AATAAATATTATAAT-AATTAAA
1 AATAAATATTATAATGAATTAAA
140154 TAGTATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
AATAAATATTATAATGAATTAAAAT
Found at i:140859 original size:15 final size:14
Alignment explanation
Indices: 140838--140866 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
140828 GAGACATAAA
140838 ATTTTTTTTTTAAG
1 ATTTTTTTTTTAAG
140852 ATTTTTTTTTTAAG
1 ATTTTTTTTTTAAG
140866 A
1 A
140867 GTTTATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (14 bp):
ATTTTTTTTTTAAG
Found at i:141161 original size:22 final size:22
Alignment explanation
Indices: 141133--141177 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
141123 TAAATATTAA
141133 AAAAT-AAATAAATAATATAATT
1 AAAATAAAATAAA-AATATAATT
141155 AAAATAAAATAAAAATATAATT
1 AAAATAAAATAAAAATATAATT
141177 A
1 A
141178 TATTTCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATAAAATAAAAATATAATT
Found at i:143312 original size:27 final size:28
Alignment explanation
Indices: 143277--143335 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 28
143267 ATTTTTTAAA
143277 TTATAATTAAATTTAA-AGTATT-ATATAT
1 TTATAATTAAATTTAACA-TATTAATA-AT
*
143305 TTAT-ATTAATTTTAACATATTAATAAT
1 TTATAATTAAATTTAACATATTAATAAT
143332 TTAT
1 TTAT
143336 TATATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
TTATAATTAAATTTAACATATTAATAAT
Found at i:149434 original size:17 final size:17
Alignment explanation
Indices: 149412--149458 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
149402 TAGTTAAAAA
*
149412 TTATAAAATAATTATTT
1 TTATAAAATAAATATTT
149429 TTATAAAATAAATA-TT
1 TTATAAAATAAATATTT
* *
149445 TAATAAATTAAATA
1 TTATAAAATAAATA
149459 ATTACATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTATAAAATAAATATTT
Found at i:149519 original size:22 final size:20
Alignment explanation
Indices: 149487--149529 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 20
149477 ATTAAATTAA
149487 ATAATAATAAA-ATAATTATT
1 ATAATAATAAATAT-ATTATT
149507 ATAATAAATTAAATATATTATT
1 ATAAT-AA-TAAATATATTATT
149529 A
1 A
149530 ATATATTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.25
21 2 0.10
22 11 0.55
23 2 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAATAATAAATATATTATT
Found at i:150160 original size:21 final size:20
Alignment explanation
Indices: 150124--150166 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
150114 CATTAATTTA
150124 AATTTTA-ATTAAAATATCT
1 AATTTTATATTAAAATATCT
* *
150143 AATTTTATTATTATAATATTT
1 AATTTTA-TATTAAAATATCT
150164 AAT
1 AAT
150167 CTTAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
21 13 0.65
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTTTATATTAAAATATCT
Found at i:150175 original size:21 final size:21
Alignment explanation
Indices: 150131--150175 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
150121 TTAAATTTTA
* *
150131 ATTAAAATATCTAATTTTATT
1 ATTAAAATATCTAATCTTAAT
* *
150152 ATTATAATATTTAATCTTAAT
1 ATTAAAATATCTAATCTTAAT
150173 ATT
1 ATT
150176 TTTATTATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTAAAATATCTAATCTTAAT
Found at i:151000 original size:20 final size:21
Alignment explanation
Indices: 150962--151003 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
150952 TAATATTTAA
150962 ATTTTTAATAAAAAATTTAAAT
1 ATTTTTAAT-AAAAATTTAAAT
*
150984 ATTTTTAAT-AAATTTTAAAT
1 ATTTTTAATAAAAATTTAAAT
151004 TTCACTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTTTAATAAAAATTTAAAT
Found at i:151836 original size:13 final size:14
Alignment explanation
Indices: 151808--151853 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
151798 TCAATGAAGA
151808 TATT-TAAT-TTTAT
1 TATTATAATATTT-T
151821 TATTATAATA-TTT
1 TATTATAATATTTT
*
151834 TATCATAATATTTT
1 TATTATAATATTTT
151848 TATTAT
1 TATTAT
151854 TTTTAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 14 0.50
14 14 0.50
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTATAATATTTT
Found at i:152268 original size:20 final size:20
Alignment explanation
Indices: 152209--152269 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 20
152199 ATATATTTTT
152209 AATTATTTATTTACAATATTTAA
1 AATTATTT-TTT--AATATTTAA
* *
152232 TATT-TATTTTAA-A-TTAA
1 AATTATTTTTTAATATTTAA
152249 AATTATTTTTTAATATTTAA
1 AATTATTTTTTAATATTTAA
152269 A
1 A
152270 TTTAATTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
17 7 0.23
18 8 0.26
19 3 0.10
20 5 0.16
21 3 0.10
22 2 0.06
23 3 0.10
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTATTTTTTAATATTTAA
Found at i:152475 original size:17 final size:17
Alignment explanation
Indices: 152453--152486 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
152443 GTCGAGCATC
152453 CATCACTGAAAAATATA
1 CATCACTGAAAAATATA
152470 CATCACTGAAAAATATA
1 CATCACTGAAAAATATA
152487 AAGAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.06, T:0.24
Consensus pattern (17 bp):
CATCACTGAAAAATATA
Found at i:153271 original size:14 final size:14
Alignment explanation
Indices: 153254--153289 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
153244 TATTTAATTA
*
153254 AATTAAGTAAAATC
1 AATTAAATAAAATC
153268 AATTAAATAAAATC
1 AATTAAATAAAATC
153282 AATATAAA
1 AAT-TAAA
153290 ATTAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.28
Consensus pattern (14 bp):
AATTAAATAAAATC
Found at i:154135 original size:2 final size:2
Alignment explanation
Indices: 154128--154153 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
154118 GACAACATAG
154128 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
154154 TAATTGCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:157122 original size:22 final size:22
Alignment explanation
Indices: 157097--157138 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
157087 ATTTTAAATT
157097 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAATT-TAAAAATATA
157119 TAAATATTAATTTAAAAATA
1 TAAATATTAATTTAAAAATA
157139 ATTTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTAATTTAAAAATATA
Found at i:157141 original size:34 final size:34
Alignment explanation
Indices: 157062--157170 Score: 87
Period size: 36 Copynumber: 3.1 Consensus size: 34
157052 ATTTATGTAG
* * *
157062 TTAAAAATTATTATTTAAAA-ATA-AAATTTTAAAT
1 TTAAAAATAATTA-TAAAAATATATAAATATT-AAT
**
157096 TTAAATTTAATTATAAAAATATATAAATATTAAT
1 TTAAAAATAATTATAAAAATATATAAATATTAAT
* * * *
157130 TTAAAAATAATTTTTTAATAATTTATAAATAGTAAT
1 TTAAAAATAA--TTATAAAAATATATAAATATTAAT
157166 TTAAA
1 TTAAA
157171 TTTTTTAAAC
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
33 5 0.08
34 24 0.40
35 6 0.10
36 25 0.42
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (34 bp):
TTAAAAATAATTATAAAAATATATAAATATTAAT
Found at i:159115 original size:12 final size:12
Alignment explanation
Indices: 159098--159122 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
159088 TACACTGTTA
159098 CGCCTGGGCACC
1 CGCCTGGGCACC
159110 CGCCTGGGCACC
1 CGCCTGGGCACC
159122 C
1 C
159123 TCTTTGTTAA
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:0.08, C:0.52, G:0.32, T:0.08
Consensus pattern (12 bp):
CGCCTGGGCACC
Found at i:159351 original size:15 final size:15
Alignment explanation
Indices: 159323--159356 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
159313 ATATTAATTT
159323 TTTAAAATATTTATAA
1 TTTAAAATATTTAT-A
159339 TTTAAAA-ATTTATA
1 TTTAAAATATTTATA
159353 TTTA
1 TTTA
159357 TATTCATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 6 0.33
16 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAAAATATTTATA
Found at i:160506 original size:16 final size:15
Alignment explanation
Indices: 160475--160535 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
160465 TTTAAAAATT
*
160475 ATTTAAAAATTTTAA
1 ATTTAAAAAATTTAA
**
160490 ATTTATATTAATTTAA
1 ATTTA-AAAAATTTAA
160506 ATATTAAAAAATTTAA
1 AT-TTAAAAAATTTAA
160522 ATTTAAAATAATTT
1 ATTTAAAA-AATTT
160536 GAATATAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
15 11 0.29
16 24 0.63
17 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTAAAAAATTTAA
Found at i:160513 original size:32 final size:32
Alignment explanation
Indices: 160477--160541 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
160467 TAAAAATTAT
* * *
160477 TTAAAAATTTTAAATTTATATTAATTTAAATA
1 TTAAAAAATTTAAATTTAAAATAATTTAAATA
*
160509 TTAAAAAATTTAAATTTAAAATAATTTGAATA
1 TTAAAAAATTTAAATTTAAAATAATTTAAATA
160541 T
1 T
160542 AAATTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (32 bp):
TTAAAAAATTTAAATTTAAAATAATTTAAATA
Found at i:160544 original size:16 final size:16
Alignment explanation
Indices: 160498--160544 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
160488 AAATTTATAT
160498 TAATTTAAATATTAAAA
1 TAATTTAAATA-TAAAA
*
160515 -AATTTAAATTTAAAA
1 TAATTTAAATATAAAA
*
160530 TAATTTGAATATAAA
1 TAATTTAAATATAAA
160545 TTTTTTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
TAATTTAAATATAAAA
Found at i:161392 original size:17 final size:17
Alignment explanation
Indices: 161372--161448 Score: 52
Period size: 17 Copynumber: 4.4 Consensus size: 17
161362 TATTTTTTTA
161372 ATTTATTAAATAATATT
1 ATTTATTAAATAATATT
* * *
161389 ATTTTTTATATCAATAGCT
1 ATTTATTAAAT-AATA-TT
*
161408 ATTTATTTAAAAAAATATT
1 ATTTA-TT-AAATAATATT
161427 -TTTATTAAA-AA-ATT
1 ATTTATTAAATAATATT
161441 ATTATATT
1 ATT-TATT
161449 TAATGTTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 13
0.70 0.10 0.19
Matches are distributed among these distances:
14 3 0.06
15 4 0.09
16 7 0.15
17 11 0.23
18 8 0.17
19 6 0.13
20 6 0.13
21 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (17 bp):
ATTTATTAAATAATATT
Found at i:161451 original size:17 final size:16
Alignment explanation
Indices: 161407--161451 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
161397 TATCAATAGC
161407 TATTTATTTAAAAAAA
1 TATTTATTTAAAAAAA
* *
161423 TATTTTTATTAAAAAAT
1 TATTTAT-TTAAAAAAA
161440 TATTATATTTAA
1 TATT-TATTTAA
161452 TGTTTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 6 0.25
17 16 0.67
18 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTTATTTAAAAAAA
Found at i:169740 original size:14 final size:15
Alignment explanation
Indices: 169717--169759 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
169707 ATAATTTTGT
169717 AAATAA-ATTTTTTA
1 AAATAATATTTTTTA
*
169731 TAA-AATATTTTTTA
1 AAATAATATTTTTTA
*
169745 AAATAATTTTTTTTA
1 AAATAATATTTTTTA
169760 CGAATACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 2 0.08
14 12 0.50
15 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AAATAATATTTTTTA
Found at i:169757 original size:15 final size:14
Alignment explanation
Indices: 169700--169759 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
169690 AGAATATTAA
169700 AAAAAATATAATTTTGT
1 AAAAAATAT--TTTT-T
*
169717 AAATAA-ATTTTTT
1 AAAAAATATTTTTT
*
169730 ATAAAATATTTTTT
1 AAAAAATATTTTTT
*
169744 AAAATAATTTTTTTT
1 AAAA-AATATTTTTT
169759 A
1 A
169760 CGAATACATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
13 5 0.14
14 14 0.39
15 10 0.28
16 2 0.06
17 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
AAAAAATATTTTTT
Found at i:170227 original size:22 final size:22
Alignment explanation
Indices: 170168--170215 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
170158 ATTTTAAAAA
* *
170168 TTTTAAAATCTAATTTATTTTAT
1 TTTTAAAAT-TCATTTAATTTAT
170191 TTTTAAAATTCATTTAATTTAT
1 TTTTAAAATTCATTTAATTTAT
170213 TTT
1 TTT
170216 ATGAATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTAAAATTCATTTAATTTAT
Found at i:174545 original size:39 final size:39
Alignment explanation
Indices: 174490--174595 Score: 106
Period size: 39 Copynumber: 2.6 Consensus size: 39
174480 TTATTTTTAT
*
174490 AATTAATATTTTAAATTTATATATAATAAAATAAAAAATA
1 AATTAA-ATTTTAAATTTATATAAAATAAAATAAAAAATA
* * * * **
174530 AATTAGATTTTAAATTTTTTTAAAATTACTTAAAAAATA
1 AATTAAATTTTAAATTTATATAAAATAAAATAAAAAATA
174569 AATTAAATTTATATAA-TTATATCAAAA
1 AATTAAATTT-TA-AATTTATAT-AAAA
174596 AATATTTTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
39 36 0.68
40 11 0.21
41 6 0.11
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (39 bp):
AATTAAATTTTAAATTTATATAAAATAAAATAAAAAATA
Found at i:174986 original size:15 final size:14
Alignment explanation
Indices: 174967--175007 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 14
174957 GTATTCGTAA
174967 AAAAAAATTATTTT
1 AAAAAAATTATTTT
174981 -AAAAAA-TATTTT
1 AAAAAAATTATTTT
174993 ACAAAAAATCTATTT
1 A-AAAAAAT-TATTT
175008 ACAAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 6 0.26
13 6 0.26
14 6 0.26
16 5 0.22
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAAAAATTATTTT
Found at i:175008 original size:15 final size:14
Alignment explanation
Indices: 174968--175013 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
174958 TATTCGTAAA
*
174968 AAAAAATTATTT-T
1 AAAAAATTATTTAC
174981 AAAAAA-TATTTTAC
1 AAAAAATTA-TTTAC
174995 AAAAAATCTATTTAC
1 AAAAAAT-TATTTAC
175010 AAAA
1 AAAA
175014 TTAATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 2 0.07
13 9 0.32
14 6 0.21
15 9 0.32
16 2 0.07
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAAAATTATTTAC
Found at i:175294 original size:22 final size:23
Alignment explanation
Indices: 175247--175294 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
175237 TGAAAATTTG
*
175247 TTATTTTATTTATTTAAAATATA
1 TTATTTTATATATTTAAAATATA
175270 TTATTTTATAT-TTTACAAATA-A
1 TTATTTTATATATTTA-AAATATA
175292 TTA
1 TTA
175295 AAATTACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATTTTATATATTTAAAATATA
Found at i:177821 original size:15 final size:14
Alignment explanation
Indices: 177798--177833 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 14
177788 ATAAAATCTT
177798 TTAATATTAAATTAAA
1 TTAA-ATTAAATT-AA
177814 TTAAATTAAATTAA
1 TTAAATTAAATTAA
177828 TTAAAT
1 TTAAAT
177834 ATATGACACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 8 0.40
16 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAAATTAAATTAA
Found at i:177831 original size:4 final size:5
Alignment explanation
Indices: 177798--177833 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
177788 ATAAAATCTT
177798 TTAATA TTAAA TTAAA TTAAA TTAAA TT-AA TTAAA T
1 TTAA-A TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA T
177834 ATATGACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.14
5 21 0.72
6 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:180244 original size:13 final size:14
Alignment explanation
Indices: 180226--180258 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
180216 TTTTATTAAT
180226 TATAAATAATA-AA
1 TATAAATAATATAA
180239 TATAAATAATATAA
1 TATAAATAATATAA
180253 -ATAAAT
1 TATAAAT
180259 TAAATCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 17 0.89
14 2 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TATAAATAATATAA
Found at i:180287 original size:10 final size:10
Alignment explanation
Indices: 180233--180288 Score: 53
Period size: 9 Copynumber: 5.6 Consensus size: 10
180223 AATTATAAAT
*
180233 AATAAATATA
1 AATAAATTTA
*
180243 AAT-AATATA
1 AATAAATTTA
180252 AATAAA-TTA
1 AATAAATTTA
*
180261 AATCATATTTAA
1 AAT-AAATTT-A
180273 AATAAATTTA
1 AATAAATTTA
180283 AATAAA
1 AATAAA
180289 AAATTTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 14 0.36
10 14 0.36
11 7 0.18
12 4 0.10
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (10 bp):
AATAAATTTA
Found at i:185593 original size:19 final size:19
Alignment explanation
Indices: 185569--185610 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
185559 AATGATGGGC
185569 CATTTAAT-TTCCACATTGG
1 CATTTAATCTTCC-CATTGG
*
185588 CATTTAATCTTTCCATTGG
1 CATTTAATCTTCCCATTGG
185607 CATT
1 CATT
185611 ACTAATTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (19 bp):
CATTTAATCTTCCCATTGG
Found at i:193174 original size:2 final size:2
Alignment explanation
Indices: 193169--193218 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
193159 ATATATATAT
*
193169 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
193211 GG AG AG AG
1 AG AG AG AG
193219 TGGGAGAGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:194825 original size:26 final size:26
Alignment explanation
Indices: 194767--194837 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 26
194757 TTAACGTTGA
* *
194767 ATTT-ATTTAAT-AATTAAATTATTT
1 ATTTAATTTAATAAATTTAATTATTG
*
194791 ATTTCATTTAATAAATTTAATT-TTG
1 ATTTAATTTAATAAATTTAATTATTG
*
194816 ATTTGAATTTATTTAAATTTAA
1 ATTT-AATTTA-ATAAATTTAA
194838 ATATAATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
24 4 0.10
25 13 0.33
26 13 0.33
27 9 0.23
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.56
Consensus pattern (26 bp):
ATTTAATTTAATAAATTTAATTATTG
Found at i:194855 original size:55 final size:56
Alignment explanation
Indices: 194763--194869 Score: 132
Period size: 55 Copynumber: 1.9 Consensus size: 56
194753 TTGGTTAACG
194763 TTGAATTTATTTAATAATTAAATTATTTATTTCATTTA-ATAAATTTAATTTTGAT
1 TTGAATTTATTTAATAATTAAATTATTTATTTCATTTAGATAAATTTAATTTTGAT
* * *
194818 TTGAATTTATTTAA-ATTTAAATATAATATT-TTT-ATTTAGATTAATTTCATTT
1 TTGAATTTATTTAATAATTAAAT-T-AT-TTATTTCATTTAGATAAATTTAATTT
194870 AAATCATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
54 7 0.16
55 20 0.44
56 16 0.36
57 2 0.04
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (56 bp):
TTGAATTTATTTAATAATTAAATTATTTATTTCATTTAGATAAATTTAATTTTGAT
Found at i:200464 original size:75 final size:76
Alignment explanation
Indices: 200359--200508 Score: 212
Period size: 75 Copynumber: 2.0 Consensus size: 76
200349 TTATATCAAT
* * * *
200359 GGTGAAGAGACAGAAATACACAAACCCAGTAACTATGGAACGGTTAGAGATTAATCCATCTTCTC
1 GGTGAAGAGACA-AAATACACAAACCCAGTAACTATGAAACGGTTAAAAATTAAACCATCTTCTC
*
200424 GGTGAAGAACAC
65 GGGGAAGAACAC
* * *
200436 GGTGAAGAGAC-AAATACACAAACCCAGTAACTATGAAAGGGTTAAAAATTAAACGATTTTCTCG
1 GGTGAAGAGACAAAATACACAAACCCAGTAACTATGAAACGGTTAAAAATTAAACCATCTTCTCG
200500 GGGAAGAAC
66 GGGAAGAAC
200509 TTACCACGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
75 54 0.83
77 11 0.17
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.19
Consensus pattern (76 bp):
GGTGAAGAGACAAAATACACAAACCCAGTAACTATGAAACGGTTAAAAATTAAACCATCTTCTCG
GGGAAGAACAC
Found at i:201650 original size:19 final size:20
Alignment explanation
Indices: 201599--201667 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
201589 AAAAATATTT
* *
201599 TAATTTATAATAAATAAAAAA
1 TAATTAATAAT-ATTAAAAAA
201620 TAATTAATAATATTAAAAAA
1 TAATTAATAATATTAAAAAA
* *
201640 TTATTTA-AATATTAATAAAA
1 TAATTAATAATATTAA-AAAA
201660 T-ATTAATA
1 TAATTAATA
201668 TATAATGTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.29
20 19 0.46
21 10 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATTAATAATATTAAAAAA
Found at i:201670 original size:19 final size:18
Alignment explanation
Indices: 201613--201670 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 18
201603 TTATAATAAA
201613 TAAAAAATAATTAATAATAT
1 TAAAAAAT-ATTAAT-ATAT
201633 TAAAAAATTATTTAA-ATAT
1 TAAAAAA-TA-TTAATATAT
201652 TAATAAAATATTAATATAT
1 TAA-AAAATATTAATATAT
201671 AATGTAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.12
19 13 0.38
20 12 0.35
21 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAAAATATTAATATAT
Found at i:201762 original size:20 final size:20
Alignment explanation
Indices: 201734--201800 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
201724 ATTTAAAGGT
*
201734 ATTTTTATATAAAATTTAAA
1 ATTTATATATAAAATTTAAA
* * *
201754 ATTTATATATCACATGT---
1 ATTTATATATAAAATTTAAA
*
201771 ATTTTTATATAAAATTTAAA
1 ATTTATATATAAAATTTAAA
201791 ATTTATATAT
1 ATTTATATAT
201801 CACATCATAC
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
17 13 0.37
20 22 0.63
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (20 bp):
ATTTATATATAAAATTTAAA
Found at i:201782 original size:37 final size:37
Alignment explanation
Indices: 201732--201805 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
201722 TAATTTAAAG
201732 GTATTTTTATATAAAATTTAAAATTTATATATCACAT
1 GTATTTTTATATAAAATTTAAAATTTATATATCACAT
201769 GTATTTTTATATAAAATTTAAAATTTATATATCACAT
1 GTATTTTTATATAAAATTTAAAATTTATATATCACAT
201806 CATACGTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (37 bp):
GTATTTTTATATAAAATTTAAAATTTATATATCACAT
Found at i:201836 original size:19 final size:21
Alignment explanation
Indices: 201812--201865 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 21
201802 ACATCATACG
201812 TAAATATTTTATT-AATA-T-T
1 TAAATATTTT-TTAAATATTAT
201831 TAAATAATTTTTTAAATATTAT
1 TAAAT-ATTTTTTAAATATTAT
201853 TAAATATTTTTTA
1 TAAATATTTTTTA
201866 TTCAATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
19 7 0.23
20 9 0.29
21 9 0.29
22 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAAATATTTTTTAAATATTAT
Found at i:207355 original size:3 final size:3
Alignment explanation
Indices: 207341--207378 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
207331 AAAACGCGAT
* *
207341 TTA TTC TTA TTA TTA TTC TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
207379 CAGAGGAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:207358 original size:12 final size:12
Alignment explanation
Indices: 207341--207378 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
207331 AAAACGCGAT
207341 TTATTCTTATTA
1 TTATTCTTATTA
207353 TTATTCTTATTA
1 TTATTCTTATTA
*
207365 TTATTATTATTA
1 TTATTCTTATTA
207377 TT
1 TT
207379 CAGAGGAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATTCTTATTA
Found at i:209045 original size:13 final size:13
Alignment explanation
Indices: 209014--209092 Score: 56
Period size: 13 Copynumber: 6.2 Consensus size: 13
209004 ATTAGACATC
209014 TTTAAATTTAATA
1 TTTAAATTTAATA
**
209027 -TTAAATTTGTTA
1 TTTAAATTTAATA
209039 TTTAAA-TTAA-A
1 TTTAAATTTAATA
** *
209050 TTTAAATAAAATT
1 TTTAAATTTAATA
209063 TTATAATATTTAATA
1 TT-TAA-ATTTAATA
* *
209078 TTTATATTTATTA
1 TTTAAATTTAATA
209091 TT
1 TT
209093 ATTTGATTTT
Statistics
Matches: 49, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
11 7 0.14
12 14 0.29
13 16 0.33
14 5 0.10
15 7 0.14
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (13 bp):
TTTAAATTTAATA
Found at i:209182 original size:19 final size:18
Alignment explanation
Indices: 209151--209201 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 18
209141 TTTATTTTAC
209151 TTATATATTTATTTATATAT
1 TTATAT-TTTATTTATAT-T
209171 TTA-ATTTTTATTTATATT
1 TTATA-TTTTATTTATATT
209189 TTATATTTTATTT
1 TTATATTTTATTT
209202 TAAAAAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 12 0.41
19 13 0.45
20 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATATTTTATTTATATT
Found at i:209202 original size:12 final size:12
Alignment explanation
Indices: 209151--209203 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 12
209141 TTTATTTTAC
209151 TTATATATTTATT
1 TTATAT-TTTATT
*
209164 TATATATTTAATT
1 T-TATATTTTATT
209177 TT-TATTTATATT
1 TTATATTT-TATT
209189 TTATATTTTATT
1 TTATATTTTATT
209201 TTA
1 TTA
209204 AAAAAATGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
11 5 0.14
12 13 0.37
13 12 0.34
14 5 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTATATTTTATT
Found at i:209203 original size:19 final size:19
Alignment explanation
Indices: 209151--209203 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 19
209141 TTTATTTTAC
209151 TTATATATTTATTTATATATT
1 TTATAT-TTTATTT-TATATT
*
209172 TAAT-TTTTA-TTTATATT
1 TTATATTTTATTTTATATT
209189 TTATATTTTATTTTA
1 TTATATTTTATTTTA
209204 AAAAAATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 9 0.32
18 7 0.25
19 8 0.29
20 1 0.04
21 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATATTTTATTTTATATT
Found at i:211871 original size:28 final size:27
Alignment explanation
Indices: 211818--211897 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
211808 ATTTGCACCA
211818 TTTTT-TTCAATTTATATTTAATTTAT
1 TTTTTATTCAATTTATATTTAATTTAT
* *
211844 TTTCTTATTCAATTTTTGATTTCA-TTAT
1 TTT-TTATTCAATTTAT-ATTTAATTTAT
* *
211872 TTTTTATTATAATTTCATTTTTAATT
1 TTTTTATT-CAATTT-ATATTTAATT
211898 GTTTTTAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
26 3 0.07
27 7 0.17
28 25 0.60
29 7 0.17
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.68
Consensus pattern (27 bp):
TTTTTATTCAATTTATATTTAATTTAT
Found at i:212195 original size:10 final size:10
Alignment explanation
Indices: 212180--212212 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
212170 ATTAATTTAA
212180 TTTTATATAT
1 TTTTATATAT
212190 TTTTATA-AT
1 TTTTATATAT
212199 TTTTATATTAT
1 TTTTATA-TAT
212210 TTT
1 TTT
212213 AATAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 7 0.33
11 5 0.24
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTATATAT
Found at i:212204 original size:19 final size:20
Alignment explanation
Indices: 212180--212217 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
212170 ATTAATTTAA
*
212180 TTTTATA-TATTTTTATAAT
1 TTTTATATTATTTTAATAAT
212199 TTTTATATTATTTTAATAA
1 TTTTATATTATTTTAATAA
212218 ATTAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTATATTATTTTAATAAT
Found at i:212445 original size:19 final size:19
Alignment explanation
Indices: 212423--212472 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
212413 ATATTATATA
*
212423 AAAATTTATATAAATTTAT
1 AAAATTAATATAAATTTAT
*
212442 AAAATTAAT-TTAATTT-T
1 AAAATTAATATAAATTTAT
*
212459 -ATATTAATATAAAT
1 AAAATTAATATAAAT
212473 AAATTATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.27
17 5 0.19
18 6 0.23
19 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AAAATTAATATAAATTTAT
Found at i:212534 original size:16 final size:17
Alignment explanation
Indices: 212515--212547 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
212505 TATAATATAA
212515 TTTAAAAT-CAAATATT
1 TTTAAAATGCAAATATT
*
212531 TTTAAATTGCAAATATT
1 TTTAAAATGCAAATATT
212548 CAATCTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTAAAATGCAAATATT
Found at i:215060 original size:1 final size:1
Alignment explanation
Indices: 215054--215080 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
215044 CATTCAAATG
215054 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
215081 GCATGCATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:217678 original size:28 final size:28
Alignment explanation
Indices: 217619--217675 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
217609 AAAAAAATCC
* *
217619 ATTTTAACAAATTAATGTATAGATTAAA
1 ATTTTAAAAAATTAATGTATAAATTAAA
217647 ATTTTAAAAAATTAAT-TCATAAAATTAAA
1 ATTTTAAAAAATTAATGT-AT-AAATTAAA
217676 TTTGTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 1 0.04
28 17 0.68
29 7 0.28
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (28 bp):
ATTTTAAAAAATTAATGTATAAATTAAA
Found at i:221479 original size:4 final size:4
Alignment explanation
Indices: 221470--221500 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
221460 TCTTTGTATC
221470 TTTA TTTA TTTA TTTA TTTA TTTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
221501 AGTTGTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:223271 original size:2 final size:2
Alignment explanation
Indices: 223264--223296 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
223254 TTTATATGAT
223264 TA TA 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 TA TA T
223297 GTATTGATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:223394 original size:2 final size:2
Alignment explanation
Indices: 223375--223411 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
223365 CCGTAGTTCT
* *
223375 TC TC TT TC TC TA TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
223412 GAAACATTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.03, C:0.43, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Done.