Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold324
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: 2336777
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 10 of 16
Found at i:1405366 original size:48 final size:48
Alignment explanation
Indices: 1405256--1405449 Score: 311
Period size: 48 Copynumber: 4.0 Consensus size: 48
1405246 TTTAGCCTAC
*
1405256 TTAATCTTAAATTTTATATAATTCAGATCAGTTAACTTTTAAGAGAAAA
1 TTAATCTTAAATTTTATATAATTCAGATCAGTTAAC-ATTAAGAGAAAA
* * *
1405305 TTCACCTTAAATTTTATATAATTCAAATCAGTTAAC-TCTAAGAGAAAA
1 TTAATCTTAAATTTTATATAATTCAGATCAGTTAACAT-TAAGAGAAAA
1405353 TTAATCTTAAATTTTATATAATTCAGATCAGTTAACATTAAGAGAAAA
1 TTAATCTTAAATTTTATATAATTCAGATCAGTTAACATTAAGAGAAAA
*
1405401 TTAATCTTAAATTTT-TATAATTCAGATCAGTTAACATTAAGAAAAAA
1 TTAATCTTAAATTTTATATAATTCAGATCAGTTAACATTAAGAGAAAA
1405448 TT
1 TT
1405450 GCTTTCAAGA
Statistics
Matches: 136, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
47 34 0.25
48 68 0.50
49 34 0.25
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (48 bp):
TTAATCTTAAATTTTATATAATTCAGATCAGTTAACATTAAGAGAAAA
Found at i:1405385 original size:97 final size:95
Alignment explanation
Indices: 1405256--1405449 Score: 309
Period size: 97 Copynumber: 2.0 Consensus size: 95
1405246 TTTAGCCTAC
* *
1405256 TTAATCTTAAATTTTATATAATTCAGATCAGTTAACTTTTAAGAGAAAATTCACCTTAAATTTTA
1 TTAATCTTAAATTTTATATAATTCAGATCAGTTAAC-ATTAAGAGAAAATTAACCTTAAATTTT-
*
1405321 TATAATTCAAATCAGTTAAC-TCTAAGAGAAAA
64 TATAATTCAAATCAGTTAACAT-TAAGAAAAAA
*
1405353 TTAATCTTAAATTTTATATAATTCAGATCAGTTAACATTAAGAGAAAATTAATCTTAAATTTTTA
1 TTAATCTTAAATTTTATATAATTCAGATCAGTTAACATTAAGAGAAAATTAACCTTAAATTTTTA
*
1405418 TAATTCAGATCAGTTAACATTAAGAAAAAA
66 TAATTCAAATCAGTTAACATTAAGAAAAAA
1405448 TT
1 TT
1405450 GCTTTCAAGA
Statistics
Matches: 91, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
95 30 0.33
96 25 0.27
97 36 0.40
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (95 bp):
TTAATCTTAAATTTTATATAATTCAGATCAGTTAACATTAAGAGAAAATTAACCTTAAATTTTTA
TAATTCAAATCAGTTAACATTAAGAAAAAA
Found at i:1408238 original size:22 final size:23
Alignment explanation
Indices: 1408187--1408241 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
1408177 TTAATTCATT
*
1408187 TAAAAGAAT-TATATAAAATTTA
1 TAAAAAAATATATATAAAATTTA
*
1408209 -AAATAAAATATATAT-ATATTTA
1 TAAA-AAAATATATATAAAATTTA
1408231 TAAAAAAATAT
1 TAAAAAAATAT
1408242 TAGTGTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 3 0.11
22 17 0.61
23 8 0.29
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
TAAAAAAATATATATAAAATTTA
Found at i:1408299 original size:60 final size:59
Alignment explanation
Indices: 1408207--1408337 Score: 176
Period size: 60 Copynumber: 2.2 Consensus size: 59
1408197 ATATAAAATT
* ** *
1408207 TAAAA-TAAAATATATATATATTTATAAAAAAATATTAGTGTCTTTTATTATTTTTTAA
1 TAAAATTAAAATATATATAAATTTATAAAAAAATATTAGCATCTTTTATTATTTTTAAA
*
1408265 -AAAATTAAAATATAAATATAAATTTATAAAAAAATATTGGCATCTTTTATTATTTTTAAA
1 TAAAATTAAAATAT--ATATAAATTTATAAAAAAATATTAGCATCTTTTATTATTTTTAAA
1408325 TTAAAATTAAAAT
1 -TAAAATTAAAAT
1408338 TTTAAAATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
57 4 0.06
58 8 0.13
60 40 0.63
62 11 0.17
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.44
Consensus pattern (59 bp):
TAAAATTAAAATATATATAAATTTATAAAAAAATATTAGCATCTTTTATTATTTTTAAA
Found at i:1408417 original size:102 final size:104
Alignment explanation
Indices: 1408263--1408485 Score: 308
Period size: 102 Copynumber: 2.1 Consensus size: 104
1408253 ATTATTTTTT
* * * *
1408263 AAAAAATTAAAATATAAATATAAATTTATAAAAAAATATTGGCATCTTTTATTATTTTTAAATTA
1 AAAAAATTAAAATA-AAAAATAAACTTATAAAAAAATATTGACATCTCTTATTATTTTTAAATTA
1408328 AAATTAAA-ATTTTAAAATTTTAAATATA-TTTTTAATAA
65 AAATTAAATATTTTAAAATTTTAAATATATTTTTTAATAA
* *
1408366 AAAACAATTAAAATAAAAAATATACTT-TAAAAAAATATTGATATCTCTTATTATTTTTAAATTA
1 AAAA-AATTAAAATAAAAAATAAACTTATAAAAAAATATTGACATCTCTTATTATTTTTAAATTA
* *
1408430 AAATTAAATTTTTTAAAATTTTTAATATATTTTTTAATCAA
65 AAATTAAATATTTTAAAATTTTAAATATATTTTTTAAT-AA
* *
1408471 TAATAATTAAAATAA
1 AAAAAATTAAAATAA
1408486 CATTATCTTT
Statistics
Matches: 106, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
102 42 0.40
103 31 0.29
104 29 0.27
105 4 0.04
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (104 bp):
AAAAAATTAAAATAAAAAATAAACTTATAAAAAAATATTGACATCTCTTATTATTTTTAAATTAA
AATTAAATATTTTAAAATTTTAAATATATTTTTTAATAA
Found at i:1408807 original size:15 final size:14
Alignment explanation
Indices: 1408778--1408810 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1408768 TACAAAAATG
*
1408778 TATTAATTTTAATA
1 TATTAAATTTAATA
1408792 TATTAAATTT-ATA
1 TATTAAATTTAATA
1408805 TATTAA
1 TATTAA
1408811 GTCGATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATTAAATTTAATA
Found at i:1408905 original size:11 final size:11
Alignment explanation
Indices: 1408856--1408905 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
1408846 TCTAATTTAT
1408856 TAAAATATAATA
1 TAAAATATAA-A
1408868 TAAAATAT-AA
1 TAAAATATAAA
1408878 -AAAATATAAA
1 TAAAATATAAA
*
1408888 AAAAATATAAA
1 TAAAATATAAA
*
1408899 TATAATA
1 TAAAATA
1408906 CATATATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 7 0.21
10 3 0.09
11 16 0.47
12 8 0.24
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAAATATAAA
Found at i:1409866 original size:8 final size:8
Alignment explanation
Indices: 1409853--1409883 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
1409843 ATATGCCTTC
1409853 AAATAAAA
1 AAATAAAA
1409861 AAATAAAA
1 AAATAAAA
1409869 AAATAAAA
1 AAATAAAA
1409877 AAA-AAAA
1 AAATAAAA
1409884 CTTGCCCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.17
8 19 0.83
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAATAAAA
Found at i:1414554 original size:2 final size:2
Alignment explanation
Indices: 1414549--1414574 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1414539 ATTGTGTGTG
1414549 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1414575 GTAAGACTTG
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):
TA
Found at i:1415902 original size:14 final size:16
Alignment explanation
Indices: 1415885--1415922 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1415875 TATTTTATTT
1415885 AAAT-TTAAT-TATAA
1 AAATATTAATATATAA
1415899 AAATATTAATATATAA
1 AAATATTAATATATAA
1415915 AATATATT
1 AA-ATATT
1415923 TTTAATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 5 0.24
16 7 0.33
17 5 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATTAATATATAA
Found at i:1415945 original size:12 final size:12
Alignment explanation
Indices: 1415924--1415953 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1415914 AAATATATTT
*
1415924 TTAATAATTAAA
1 TTAATTATTAAA
1415936 TTAATTATTAAA
1 TTAATTATTAAA
1415948 TTAATT
1 TTAATT
1415954 TAAATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TTAATTATTAAA
Found at i:1415956 original size:22 final size:21
Alignment explanation
Indices: 1415931--1415980 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
1415921 TTTTTAATAA
1415931 TTAAATTAATTATTAAATT-AAT
1 TTAAATTAA-T-TTAAATTAAAT
*
1415953 TTAAATTTAATTTGAATTAAAT
1 TTAAA-TTAATTTAAATTAAAT
1415975 TTAAAT
1 TTAAAT
1415981 AAAAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 7 0.28
22 14 0.56
23 4 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTAAATTAATTTAAATTAAAT
Found at i:1415962 original size:16 final size:15
Alignment explanation
Indices: 1415931--1415980 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
1415921 TTTTTAATAA
1415931 TTAAATTAATT--A-
1 TTAAATTAATTAAAT
1415943 TTAAATTAATTTAAAT
1 TTAAATTAA-TTAAAT
*
1415959 TTAATTTGAATTAAAT
1 TTAAATT-AATTAAAT
1415975 TTAAAT
1 TTAAAT
1415981 AAAAAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 9 0.29
13 2 0.06
15 1 0.03
16 17 0.55
17 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TTAAATTAATTAAAT
Found at i:1415964 original size:11 final size:11
Alignment explanation
Indices: 1415943--1415980 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1415933 AAATTAATTA
1415943 TTAAA-TTAAT
1 TTAAATTTAAT
1415953 TTAAATTTAAT
1 TTAAATTTAAT
* *
1415964 TTGAATTAAAT
1 TTAAATTTAAT
1415975 TTAAAT
1 TTAAAT
1415981 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:1416008 original size:6 final size:5
Alignment explanation
Indices: 1415929--1416008 Score: 51
Period size: 5 Copynumber: 15.8 Consensus size: 5
1415919 TATTTTTAAT
* * *
1415929 AATTA AATTA ATTATTA AATTA ATTTA AATTTA ATTTG AATTA AATTTA
1 AATTA AATTA A--ATTA AATTA AATTA AA-TTA AATTA AATTA AA-TTA
*
1415978 AA-TA AA--A AATTA AA-AA AATTA AATTA TAATT
1 AATTA AATTA AATTA AATTA AATTA AATTA -AATT
1416009 CGACATAGAC
Statistics
Matches: 59, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
3 3 0.05
4 7 0.12
5 31 0.53
6 13 0.22
7 5 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (5 bp):
AATTA
Found at i:1418565 original size:3 final size:3
Alignment explanation
Indices: 1418557--1418601 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
1418547 TTAATGCATG
1418557 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA
1418602 ATTAATATGC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1418708 original size:26 final size:26
Alignment explanation
Indices: 1418662--1418753 Score: 73
Period size: 28 Copynumber: 3.5 Consensus size: 26
1418652 ATAACTATAG
1418662 ATATAAA--TATATTATTAATATATCAA
1 ATATAAATTTATATT-TT-ATATATCAA
*
1418688 ATATAAATTTATATTTTATATTATTAA
1 ATATAAATTTATATTTTATA-TATCAA
* * *
1418715 TTTATAAATTTATATTTGAT-TGTCCAA
1 -ATATAAATTTATATTTTATATAT-CAA
*
1418742 AAATAAATTTAT
1 ATATAAATTTAT
1418754 GTACCATCAT
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
26 22 0.41
27 9 0.17
28 23 0.43
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (26 bp):
ATATAAATTTATATTTTATATATCAA
Found at i:1418835 original size:34 final size:37
Alignment explanation
Indices: 1418765--1418836 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 37
1418755 TACCATCATT
**
1418765 AAATTATAAAACAATATTTTATTAATAAATAAAAATA
1 AAATTATAAAACAATATTTTAAAAATAAATAAAAATA
*
1418802 AAATTAT-AAA-AATA-TTTAAAAATAAATATAAATA
1 AAATTATAAAACAATATTTTAAAAATAAATAAAAATA
1418836 A
1 A
1418837 TTATTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 18 0.56
35 4 0.12
36 3 0.09
37 7 0.22
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (37 bp):
AAATTATAAAACAATATTTTAAAAATAAATAAAAATA
Found at i:1418841 original size:24 final size:24
Alignment explanation
Indices: 1418794--1418874 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 24
1418784 TATTAATAAA
1418794 TAAAAATAAAATTATAAA-AA-TATT
1 TAAAAAT-AAA-TATAAATAATTATT
1418818 TAAAAATAAATATAAATAATTATT
1 TAAAAATAAATATAAATAATTATT
** *
1418842 T-TTAATAAATAATAAATAATTAAT
1 TAAAAATAAAT-ATAAATAATTATT
*
1418866 TAATAATAA
1 TAAAAATAA
1418875 CTAATTTATA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
22 6 0.12
23 12 0.24
24 25 0.51
25 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TAAAAATAAATATAAATAATTATT
Found at i:1418870 original size:18 final size:18
Alignment explanation
Indices: 1418843--1418880 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1418833 ATAATTATTT
1418843 TTAATAAATAATAAATAA
1 TTAATAAATAATAAATAA
* *
1418861 TTAATTAATAATAACTAA
1 TTAATAAATAATAAATAA
1418879 TT
1 TT
1418881 TATATATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAATAAATAATAAATAA
Found at i:1419201 original size:17 final size:16
Alignment explanation
Indices: 1419181--1419245 Score: 51
Period size: 18 Copynumber: 3.9 Consensus size: 16
1419171 TCTATTTATA
1419181 TTAAATATATATTATTT
1 TTAAA-ATATATTATTT
* *
1419198 TTAATATCATAATTATAT
1 TTAAAAT-AT-ATTATTT
* *
1419216 TTAAAATGT-TTATATA
1 TTAAAATATATTAT-TT
1419232 TTAAAATATATTAT
1 TTAAAATATATTAT
1419246 AATAATTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
15 4 0.11
16 10 0.27
17 11 0.30
18 12 0.32
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (16 bp):
TTAAAATATATTATTT
Found at i:1419246 original size:17 final size:17
Alignment explanation
Indices: 1419173--1419246 Score: 66
Period size: 17 Copynumber: 4.4 Consensus size: 17
1419163 AAATTTAATC
1419173 TATT-TATATTAAATATA
1 TATTATATATTAAA-ATA
* *
1419190 TATTAT-TTTTAATATCA
1 TATTATATATTAAAAT-A
*
1419207 TAATTATAT-TTAAAATG
1 T-ATTATATATTAAAATA
1419224 T-TTATATATTAAAATA
1 TATTATATATTAAAATA
1419240 TATTATA
1 TATTATA
1419247 ATAATTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
15 6 0.13
16 10 0.22
17 17 0.37
18 12 0.26
19 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (17 bp):
TATTATATATTAAAATA
Found at i:1419276 original size:25 final size:25
Alignment explanation
Indices: 1419236--1419311 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 25
1419226 TATATATTAA
*
1419236 AATATATTATA--ATAATT-TTTTAT
1 AATATATTATATTTTAATTATTTT-T
1419259 AATATATTATATTTTAATTATTTTT
1 AATATATTATATTTTAATTATTTTT
* *
1419284 -ATATAATATATATTTATATTATATTT
1 AATATATTATAT-TTTA-ATTATTTTT
1419310 AA
1 AA
1419312 AATTATTGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
23 11 0.25
24 10 0.23
25 10 0.23
26 12 0.27
27 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
AATATATTATATTTTAATTATTTTT
Found at i:1419301 original size:15 final size:15
Alignment explanation
Indices: 1419243--1419307 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
1419233 TAAAATATAT
*
1419243 TATAATA-AT-TTTT
1 TATAATATATATTTA
1419256 TATAATATATTATATT-
1 TATAATATA-TAT-TTA
*
1419272 T-TAAT-TATTTTTA
1 TATAATATATATTTA
1419285 TATAATATATATTTA
1 TATAATATATATTTA
*
1419300 TATTATAT
1 TATAATAT
1419308 TTAAAATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
12 2 0.05
13 10 0.24
14 7 0.17
15 19 0.45
16 2 0.05
17 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATAATATATATTTA
Found at i:1419308 original size:28 final size:28
Alignment explanation
Indices: 1419228--1419309 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 28
1419218 AAAATGTTTA
* *
1419228 TATATTAAAATATA-TTATAATA-ATTTT
1 TATA-TAATATATATTTATATTATATTTT
* *
1419255 T-TATAATATAT-TATATTTTAATTATTTT
1 TATATAATATATATTTATATT-A-TATTTT
1419283 TATATAATATATATTTATATTATATTT
1 TATATAATATATATTTATATTATATTT
1419310 AAAATTATTG
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
25 11 0.26
26 3 0.07
27 1 0.02
28 11 0.26
29 11 0.26
30 6 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TATATAATATATATTTATATTATATTTT
Found at i:1419612 original size:11 final size:11
Alignment explanation
Indices: 1419590--1419639 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
1419580 TTTAATTAAT
1419590 TAATATTAAATA
1 TAATA-TAAATA
1419602 TAATATAAATA
1 TAATATAAATA
*
1419613 TAAAATAAATA
1 TAATATAAATA
*
1419624 -ATTA-AAATA
1 TAATATAAATA
1419633 TAATATA
1 TAATATA
1419640 TATGATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
9 5 0.16
10 5 0.16
11 17 0.53
12 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATATAAATA
Found at i:1419618 original size:18 final size:17
Alignment explanation
Indices: 1419591--1419657 Score: 54
Period size: 16 Copynumber: 4.1 Consensus size: 17
1419581 TTAATTAATT
*
1419591 AATATTAAATATAATATA
1 AATA-TAAAAATAATATA
1419609 AATAT-AAAATAA-AT-
1 AATATAAAAATAATATA
1419623 AAT-TAAAATATAATATA
1 AATATAAAA-ATAATATA
*
1419640 TATGATAAAAAT-ATATA
1 AAT-ATAAAAATAATATA
1419657 A
1 A
1419658 TTATTTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
13 1 0.03
14 6 0.15
15 6 0.15
16 8 0.20
17 8 0.20
18 6 0.15
19 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (17 bp):
AATATAAAAATAATATA
Found at i:1419651 original size:33 final size:31
Alignment explanation
Indices: 1419597--1419660 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
1419587 AATTAATATT
1419597 AAATATAATATAAATATAAAATAAATAATTA
1 AAATATAATATAAATATAAAATAAATAATTA
* *
1419628 AAATATAATATATATGATAAAAATATATAATTA
1 AAATATAATATAAAT-AT-AAAATAAATAATTA
1419661 TTTTAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 14 0.48
32 2 0.07
33 13 0.45
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (31 bp):
AAATATAATATAAATATAAAATAAATAATTA
Found at i:1419681 original size:33 final size:33
Alignment explanation
Indices: 1419597--1419681 Score: 86
Period size: 33 Copynumber: 2.6 Consensus size: 33
1419587 AATTAATATT
*
1419597 AAATATAATATA-AATAT-AAAATAAATAATTA
1 AAATAAAATATATAATATAAAAATAAATAATTA
* *
1419628 AAATATAATATAT-ATGATAAAAATATATAATTA
1 AAATAAAATATATAAT-ATAAAAATAAATAATTA
***
1419661 TTTTAAAATATATAATATAAA
1 AAATAAAATATATAATATAAA
1419682 TTATTAATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
31 14 0.31
32 2 0.04
33 27 0.60
34 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (33 bp):
AAATAAAATATATAATATAAAAATAAATAATTA
Found at i:1419727 original size:20 final size:20
Alignment explanation
Indices: 1419561--1419728 Score: 62
Period size: 20 Copynumber: 8.3 Consensus size: 20
1419551 GCTAATAATA
*
1419561 AAATAAATAAATAAATATATT
1 AAATAAATATA-AAATATATT
* * * *
1419582 TAATTAAT-TAATATTAAATAT
1 AAATAAATATAA-AATATAT-T
*
1419603 AATATAAATATAAAATA-AAT
1 AA-ATAAATATAAAATATATT
* * *
1419623 AATTAAAATATAATATATATG
1 AAAT-AAATATAAAATATATT
* *
1419644 ATAA-AAATATATAATTATTTT
1 A-AATAAATATA-AAATATATT
* * *
1419665 AAA-ATATATAATATAAATT
1 AAATAAATATAAAATATATT
* *
1419684 -ATTAATATATTAAAT-T-TT
1 AAATAA-ATATAAAATATATT
*
1419702 ACATAAATATAAAATATATT
1 AAATAAATATAAAATATATT
1419722 AAATAAA
1 AAATAAA
1419729 ATTAAGATTC
Statistics
Matches: 102, Mismatches: 32, Indels: 27
0.63 0.20 0.17
Matches are distributed among these distances:
18 11 0.11
19 12 0.12
20 50 0.49
21 17 0.17
22 9 0.09
23 3 0.03
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (20 bp):
AAATAAATATAAAATATATT
Found at i:1419977 original size:13 final size:13
Alignment explanation
Indices: 1419959--1419986 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1419949 TTGATTCAAA
1419959 TTAAAATAAAATT
1 TTAAAATAAAATT
1419972 TTAAAATAAAATT
1 TTAAAATAAAATT
1419985 TT
1 TT
1419987 TATAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TTAAAATAAAATT
Found at i:1420239 original size:13 final size:13
Alignment explanation
Indices: 1420229--1420253 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1420219 TAAAAATTAT
1420229 AATTTAAAATTTG
1 AATTTAAAATTTG
1420242 AATTTAAAATTT
1 AATTTAAAATTT
1420254 TGACAACATA
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:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
AATTTAAAATTTG
Found at i:1420565 original size:16 final size:17
Alignment explanation
Indices: 1420544--1420575 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1420534 CTCAAAGTAG
1420544 ATAAAT-AATTTAATTT
1 ATAAATAAATTTAATTT
1420560 ATAAATAAATTTAATT
1 ATAAATAAATTTAATT
1420576 AATCATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAATAAATTTAATTT
Found at i:1422868 original size:13 final size:13
Alignment explanation
Indices: 1422852--1422884 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1422842 TAATTTTAAA
*
1422852 AAATTTAAAATTT
1 AAATTTAAAATAT
1422865 AAATTT-AAATAT
1 AAATTTAAAATAT
1422877 AAATTTAA
1 AAATTTAA
1422885 CCTAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATTTAAAATAT
Found at i:1425702 original size:13 final size:13
Alignment explanation
Indices: 1425684--1425708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1425674 TTCAGCCCAA
1425684 AAAGAAAAAAAAG
1 AAAGAAAAAAAAG
1425697 AAAGAAAAAAAA
1 AAAGAAAAAAAA
1425709 AAATTTATGT
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAG
Found at i:1426328 original size:16 final size:17
Alignment explanation
Indices: 1426296--1426328 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1426286 ATCAATATTA
1426296 TTTAATAAAATATAATT
1 TTTAATAAAATATAATT
*
1426313 TTTATTAAAA-ATAATT
1 TTTAATAAAATATAATT
1426329 AAAAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAATAAAATATAATT
Found at i:1426344 original size:16 final size:17
Alignment explanation
Indices: 1426320--1426352 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1426310 ATTTTTATTA
1426320 AAAATAATTAAAAATAT
1 AAAATAATTAAAAATAT
1426337 AAAA-AATTAAAAATAT
1 AAAATAATTAAAAATAT
1426353 CATTAACTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATAATTAAAAATAT
Found at i:1426515 original size:15 final size:16
Alignment explanation
Indices: 1426495--1426524 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1426485 TTATAAAAAA
1426495 AAAGAAAAAG-GAAAG
1 AAAGAAAAAGAGAAAG
1426510 AAAGAAAAAGAGAAA
1 AAAGAAAAAGAGAAA
1426525 AAATTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAGAGAAAG
Found at i:1427005 original size:18 final size:18
Alignment explanation
Indices: 1426975--1427029 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 18
1426965 TTATTTTATA
1426975 TAATTT-ATCAAAATATTT
1 TAATTTAAT-AAAATATTT
*
1426993 TAATTTAATAAAA-AATT
1 TAATTTAATAAAATATTT
*
1427010 TATATATTAATAATATATTT
1 TA-AT-TTAATAAAATATTT
1427030 ATATTATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 5 0.17
18 12 0.40
19 10 0.33
20 3 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTTAATAAAATATTT
Found at i:1427019 original size:19 final size:18
Alignment explanation
Indices: 1426984--1427071 Score: 63
Period size: 19 Copynumber: 4.7 Consensus size: 18
1426974 ATAATTTATC
*
1426984 AAAATATTTTA-ATTTAAT
1 AAAAAATTTTATA-TTAAT
1427002 AAAAAATTTATATATTAAT
1 AAAAAATTT-TATATTAAT
* * **
1427021 AATATATTTATATTATTTTT
1 AAAAAATTT-TA-TATTAAT
1427041 AAATAAATTTTAT-TTAAT
1 AAA-AAATTTTATATTAAT
*
1427059 TAAAAATTTTATA
1 AAAAAATTTTATA
1427072 AATATTAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
17 9 0.16
18 13 0.24
19 18 0.33
20 10 0.18
21 5 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAAAATTTTATATTAAT
Found at i:1429299 original size:74 final size:74
Alignment explanation
Indices: 1429178--1429330 Score: 297
Period size: 74 Copynumber: 2.1 Consensus size: 74
1429168 TCTATGTAAA
*
1429178 CATCCTCCATTTTGGTACCTTGTCAACTTTTTGTGTTTCCGACCTAAAACCAATCAGCTATGTGT
1 CATCCTACATTTTGGTACCTTGTCAACTTTTTGTGTTTCCGACCTAAAACCAATCAGCTATGTGT
1429243 GGCAGATTT
66 GGCAGATTT
1429252 CATCCTACATTTTGGTACCTTGTCAACTTTTTGTGTTTCCGACCTAAAACCAATCAGCTATGTGT
1 CATCCTACATTTTGGTACCTTGTCAACTTTTTGTGTTTCCGACCTAAAACCAATCAGCTATGTGT
1429317 GGCAGATTT
66 GGCAGATTT
1429326 CATCC
1 CATCC
1429331 CAAATCTAAG
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (74 bp):
CATCCTACATTTTGGTACCTTGTCAACTTTTTGTGTTTCCGACCTAAAACCAATCAGCTATGTGT
GGCAGATTT
Found at i:1436440 original size:3 final size:3
Alignment explanation
Indices: 1436432--1436485 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
1436422 ATACAATACA
* *
1436432 AAT AAT AAT AAT AAT AAT AAT AAT AAAT ATT AAT AAT TAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
1436478 AAT AAT AA
1 AAT AAT AA
1436486 AGAAAAAGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1436759 original size:16 final size:18
Alignment explanation
Indices: 1436740--1436783 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
1436730 TAAAATTATC
1436740 AATAATTACATTA-TA-A
1 AATAATTACATTACTATA
1436756 AAT-ATTGACATTACTATA
1 AATAATT-ACATTACTATA
1436774 AATAA-TACAT
1 AATAATTACAT
1436784 GCATTCTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 3 0.12
16 9 0.38
17 6 0.25
18 5 0.21
19 1 0.04
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.36
Consensus pattern (18 bp):
AATAATTACATTACTATA
Found at i:1436848 original size:17 final size:18
Alignment explanation
Indices: 1436803--1436849 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
1436793 TAACAGTTGC
*
1436803 ATTTAATTTATTTATTAT
1 ATTTAATATATTTATTAT
*
1436821 -TTTAGAAATATTT-TTAT
1 ATTTA-ATATATTTATTAT
1436838 ATTTAATATATT
1 ATTTAATATATT
1436850 ATTTTTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTTAATATATTTATTAT
Found at i:1437242 original size:44 final size:44
Alignment explanation
Indices: 1437194--1437281 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
1437184 GAAAATACTA
* *
1437194 AAAATTTATTTGTATCGTAATTTCATATGTTACTAATAATTTAT
1 AAAATTTATTTGTACCATAATTTCATATGTTACTAATAATTTAT
*
1437238 AAAATTTATTTGTACCATAGTTTCATATGTTACTAATAATTTAT
1 AAAATTTATTTGTACCATAATTTCATATGTTACTAATAATTTAT
1437282 GAACACAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (44 bp):
AAAATTTATTTGTACCATAATTTCATATGTTACTAATAATTTAT
Found at i:1437810 original size:27 final size:28
Alignment explanation
Indices: 1437768--1437835 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 28
1437758 AAGTAATAAA
1437768 AAATTATTTT-A--TAAAATTTAAATTT
1 AAATTATTTTAATTTAAAATTTAAATTT
1437793 AAATT-TTTTAATTTAAAATTTAAATTT
1 AAATTATTTTAATTTAAAATTTAAATTT
* *
1437820 ATATTATTTTATTTTA
1 AAATTATTTTAATTTA
1437836 TTTAATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
24 4 0.11
25 6 0.16
27 18 0.49
28 9 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
AAATTATTTTAATTTAAAATTTAAATTT
Found at i:1437858 original size:24 final size:23
Alignment explanation
Indices: 1437822--1437866 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
1437812 TTAAATTTAT
*
1437822 ATTATTTTATTTTATTTAATTAA
1 ATTATTATATTTTATTTAATTAA
1437845 ATTATTATATTTTTATTTAATT
1 ATTATTATA-TTTTATTTAATT
1437867 CACATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTATTATATTTTATTTAATTAA
Found at i:1437885 original size:29 final size:29
Alignment explanation
Indices: 1437826--1437890 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
1437816 ATTTATATTA
* * * *
1437826 TTTTATTTTATTTAATTAAATTATTATAT
1 TTTTATTTAATTCAATAAAATAATTATAT
1437855 TTTTATTTAATTCACATAAAATAATTA-AT
1 TTTTATTTAATTCA-ATAAAATAATTATAT
1437884 TTATTAT
1 TT-TTAT
1437891 AAGTTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTTATTTAATTCAATAAAATAATTATAT
Found at i:1438238 original size:15 final size:15
Alignment explanation
Indices: 1438203--1438244 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1438193 TTTAATATTT
*
1438203 TAAAATTTATATAATA
1 TAAAAATTAT-TAATA
1438219 T--AAATTATTAATA
1 TAAAAATTATTAATA
1438232 TAAAAATTATTAA
1 TAAAAATTATTAA
1438245 AAATAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 6 0.26
14 6 0.26
15 10 0.43
16 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAAATTATTAATA
Found at i:1438443 original size:27 final size:26
Alignment explanation
Indices: 1438386--1438445 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 26
1438376 CTATTAATTT
1438386 AATATTTT-ATTTTTTATAATAAATA
1 AATATTTTAATTTTTTATAATAAATA
*
1438411 AA-ATTTTAATTTTTT-TAATTAATA
1 AATATTTTAATTTTTTATAATAAATA
1438435 ATATTATTTTA
1 A-A-TATTTTA
1438446 TATATTATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 14 0.47
25 10 0.33
27 6 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
AATATTTTAATTTTTTATAATAAATA
Found at i:1438490 original size:27 final size:30
Alignment explanation
Indices: 1438428--1438490 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
1438418 AATTTTTTTA
*
1438428 ATTAATAATATTATTTTATATATTATTCAT
1 ATTAATAATATTATATTATATATTATTCAT
* *
1438458 AATAATAATA-TATATTATGTATTATT-AT
1 ATTAATAATATTATATTATATATTATTCAT
1438486 -TTAAT
1 ATTAAT
1438491 TTGATAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 4 0.14
28 2 0.07
29 14 0.48
30 9 0.31
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (30 bp):
ATTAATAATATTATATTATATATTATTCAT
Found at i:1438734 original size:2 final size:2
Alignment explanation
Indices: 1438727--1438768 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1438717 ACCAGGAGGA
*
1438727 AG AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1438769 TGAGGGAAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1440000 original size:13 final size:13
Alignment explanation
Indices: 1439982--1440007 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1439972 AGGGATTTTT
1439982 TTTTTTTTTAATA
1 TTTTTTTTTAATA
1439995 TTTTTTTTTAATA
1 TTTTTTTTTAATA
1440008 AGACATCTGT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTAATA
Found at i:1440892 original size:14 final size:14
Alignment explanation
Indices: 1440873--1440902 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1440863 AACAAGTATT
*
1440873 TTCAGCATAGGTAC
1 TTCAGCATAAGTAC
1440887 TTCAGCATAAGTAC
1 TTCAGCATAAGTAC
1440901 TT
1 TT
1440903 TGGTTCAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (14 bp):
TTCAGCATAAGTAC
Found at i:1440943 original size:14 final size:14
Alignment explanation
Indices: 1440877--1440965 Score: 63
Period size: 14 Copynumber: 6.2 Consensus size: 14
1440867 AGTATTTTCA
* **
1440877 GCATAGGTACTTCA
1 GCATAAGTACTTTG
1440891 GCATAAGTACTTTG
1 GCATAAGTACTTTG
* *
1440905 G-TTCAGGTACTTTCG
1 GCAT-AAGTACTTT-G
*
1440920 GCATAGGTACTTTG
1 GCATAAGTACTTTG
*
1440934 ACATAAGTACCTTTG
1 GCATAAGTA-CTTTG
* *
1440949 GCACAAGTACATTG
1 GCATAAGTACTTTG
1440963 GCA
1 GCA
1440966 CGTTTCTTGG
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
13 1 0.02
14 35 0.58
15 23 0.38
16 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (14 bp):
GCATAAGTACTTTG
Found at i:1445307 original size:15 final size:16
Alignment explanation
Indices: 1445287--1445316 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1445277 CTTTCGATTT
1445287 CTTTTTC-TTTCTTTC
1 CTTTTTCATTTCTTTC
1445302 CTTTTTCATTTCTTT
1 CTTTTTCATTTCTTT
1445317 GATCAAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.73
Consensus pattern (16 bp):
CTTTTTCATTTCTTTC
Found at i:1445741 original size:15 final size:17
Alignment explanation
Indices: 1445709--1445745 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1445699 GTTATTATCG
1445709 AATATGAATATATATTT
1 AATATGAATATATATTT
1445726 AATATGAATAT-T-TTT
1 AATATGAATATATATTT
1445741 AATAT
1 AATAT
1445746 TTTTATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.40
16 1 0.05
17 11 0.55
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (17 bp):
AATATGAATATATATTT
Found at i:1448438 original size:15 final size:14
Alignment explanation
Indices: 1448420--1448459 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
1448410 TCGATTATTT
1448420 TATTATTTAATAAAA
1 TATTA-TTAATAAAA
*
1448435 TATTATTAATAATA
1 TATTATTAATAAAA
1448449 TATTAATTAAT
1 TATT-ATTAAT
1448460 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTATTAATAAAA
Found at i:1450317 original size:2 final size:2
Alignment explanation
Indices: 1450312--1450338 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1450302 TATTGTTTTA
1450312 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1450339 CCACTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1458715 original size:23 final size:25
Alignment explanation
Indices: 1458671--1458720 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
1458661 ATTAATTGTT
* *
1458671 ATTAAATTTTAAATAATTATAATTA
1 ATTAAATTTAAAATAATCATAATTA
1458696 ATTAAA-TTAAAATAA-CATAATTA
1 ATTAAATTTAAAATAATCATAATTA
1458719 AT
1 AT
1458721 ATATTCATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 9 0.39
24 8 0.35
25 6 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTAAATTTAAAATAATCATAATTA
Found at i:1459582 original size:12 final size:13
Alignment explanation
Indices: 1459560--1459595 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1459550 TTATATTATT
1459560 TTTAATT-AAATA
1 TTTAATTAAAATA
1459572 TTT-ATTAAAAT-
1 TTTAATTAAAATA
1459583 TTTAATTAAAATA
1 TTTAATTAAAATA
1459596 AATATTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTAATTAAAATA
Found at i:1466013 original size:2 final size:2
Alignment explanation
Indices: 1466006--1466032 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1465996 GTACTTGTAT
1466006 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1466033 TCAATTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1466441 original size:44 final size:45
Alignment explanation
Indices: 1466380--1466483 Score: 117
Period size: 45 Copynumber: 2.3 Consensus size: 45
1466370 TAATATTTAA
1466380 TTTTTTAATT-TTATATTAAATATT-ATA-TTATT-AAAATATAAAT
1 TTTTTTAATTATT-TATTAAAT-TTAATATTTATTCAAAATATAAAT
* * *
1466423 TTTTATTAATTATTTATTATATTTAATATTTATTCAATATTTAAAT
1 TTTT-TTAATTATTTATTAAATTTAATATTTATTCAAAATATAAAT
*
1466469 TTTTTTAAATATTTA
1 TTTTTTAATTATTTA
1466484 AAAAAATTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
43 6 0.12
44 16 0.31
45 17 0.33
46 13 0.25
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (45 bp):
TTTTTTAATTATTTATTAAATTTAATATTTATTCAAAATATAAAT
Found at i:1466464 original size:18 final size:17
Alignment explanation
Indices: 1466428--1466484 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
1466418 TAAATTTTTA
1466428 TTAATTATTTATT-ATAT
1 TTAA-TATTTATTAATAT
1466445 TTAATATTTATTCAATAT
1 TTAATATTTATT-AATAT
*
1466463 TTAA-ATTTTTTTAAATAT
1 TTAATA-TTTATT-AATAT
1466481 TTAA
1 TTAA
1466485 AAAAATTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 8 0.23
17 5 0.14
18 22 0.63
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TTAATATTTATTAATAT
Found at i:1469552 original size:2 final size:2
Alignment explanation
Indices: 1469545--1469587 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1469535 TGTAACATAG
1469545 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1469587 A
1 A
1469588 AAAGCAATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1470060 original size:9 final size:11
Alignment explanation
Indices: 1470038--1470064 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1470028 TCATATCCGA
1470038 ATATGTATTAT
1 ATATGTATTAT
1470049 ATATGTATTAT
1 ATATGTATTAT
1470060 ATATG
1 ATATG
1470065 GATCAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (11 bp):
ATATGTATTAT
Found at i:1471421 original size:7 final size:7
Alignment explanation
Indices: 1471409--1471440 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
1471399 TAATTTAATA
1471409 AAATTTT
1 AAATTTT
1471416 AAATTTT
1 AAATTTT
1471423 AAA-TTT
1 AAATTTT
1471429 AAA-TTT
1 AAATTTT
1471435 AAATTT
1 AAATTT
1471441 AGATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AAATTTT
Found at i:1471431 original size:6 final size:6
Alignment explanation
Indices: 1471413--1471471 Score: 66
Period size: 6 Copynumber: 9.7 Consensus size: 6
1471403 TTAATAAAAT
* * *
1471413 TTTAAA TTTTAAA TTTAAA TTTAAA TTTAGA TTT-AA TTTGAT TTGTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
1471462 TTTAAA TTTA
1 TTTAAA TTTA
1471472 TTGTTCACTC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
5 4 0.09
6 31 0.69
7 10 0.22
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:1471440 original size:36 final size:37
Alignment explanation
Indices: 1471391--1471472 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 37
1471381 ATGGATAGAG
1471391 TTAAA-TTATAATTTA-ATAAAATTTTAAATTT-TAAAT
1 TTAAATTTATAATTTAGATAAAA-TTT-AATTTGTAAAT
** *
1471427 TTAAATTTA-AATTTAGATTTAATTTGATTTGTAAAT
1 TTAAATTTATAATTTAGATAAAATTTAATTTGTAAAT
1471463 TTAAATTTAT
1 TTAAATTTAT
1471473 TGTTCACTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
35 4 0.10
36 28 0.72
37 7 0.18
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (37 bp):
TTAAATTTATAATTTAGATAAAATTTAATTTGTAAAT
Found at i:1474971 original size:21 final size:21
Alignment explanation
Indices: 1474945--1474986 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1474935 AATTAAATTT
1474945 AAAAAAAGAAAAGACAAAAAA
1 AAAAAAAGAAAAGACAAAAAA
* *
1474966 AAAAAACGAAAAGATAAAAAA
1 AAAAAAAGAAAAGACAAAAAA
1474987 GAGAATCTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.83, C:0.05, G:0.10, T:0.02
Consensus pattern (21 bp):
AAAAAAAGAAAAGACAAAAAA
Found at i:1475494 original size:15 final size:16
Alignment explanation
Indices: 1475474--1475506 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1475464 TCCATTGAAA
1475474 TTTAAAT-ATTTTAAT
1 TTTAAATAATTTTAAT
1475489 TTTAAATAATTTTAAT
1 TTTAAATAATTTTAAT
1475505 TT
1 TT
1475507 ATTATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAAATAATTTTAAT
Found at i:1475507 original size:15 final size:14
Alignment explanation
Indices: 1475472--1475507 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
1475462 CATCCATTGA
1475472 AATTTAAATATTTT
1 AATTTAAATATTTT
1475486 AATTTTAAATAATTTT
1 AA-TTTAAAT-ATTTT
1475502 AATTTA
1 AATTTA
1475508 TTATGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 11 0.55
16 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATTTAAATATTTT
Found at i:1475544 original size:15 final size:15
Alignment explanation
Indices: 1475524--1475570 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1475514 AAAATAAAAG
1475524 TTAATTAAAATAGAT
1 TTAATTAAAATAGAT
1475539 TTAATT-AAATA-A-
1 TTAATTAAAATAGAT
* *
1475551 TTAATTAAATTTGAT
1 TTAATTAAAATAGAT
1475566 TTAAT
1 TTAAT
1475571 CAGTTCGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 6 0.22
13 4 0.15
14 6 0.22
15 11 0.41
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (15 bp):
TTAATTAAAATAGAT
Found at i:1475782 original size:22 final size:22
Alignment explanation
Indices: 1475754--1475816 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
1475744 TTAATCTAAA
* *
1475754 AAGTCCATTTAAATCTAAATTC
1 AAGTCCATCTAAATTTAAATTC
1475776 AAGTCCATCTAAATTTAAATTC
1 AAGTCCATCTAAATTTAAATTC
*
1475798 AAGTCTATCTAAATTTAAA
1 AAGTCCATCTAAATTTAAA
1475817 CAGAAACAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.37
Consensus pattern (22 bp):
AAGTCCATCTAAATTTAAATTC
Found at i:1475992 original size:44 final size:44
Alignment explanation
Indices: 1475932--1476023 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 44
1475922 AATACTAAAT
*
1475932 TTAATTAAATTAATTTTTAATTTAAACAAATCGAATCAATCAAA
1 TTAATTAAATTAATTTTTAATTTAAACAAATCAAATCAATCAAA
* *
1475976 TTAATTAAATTAATTTTTAATTTAAACAAATCAAATCGATGAAA
1 TTAATTAAATTAATTTTTAATTTAAACAAATCAAATCAATCAAA
1476020 TTAA
1 TTAA
1476024 CTTTTTACTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (44 bp):
TTAATTAAATTAATTTTTAATTTAAACAAATCAAATCAATCAAA
Found at i:1477161 original size:22 final size:22
Alignment explanation
Indices: 1477132--1477176 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1477122 ATATTAAAAA
*
1477132 TTTTTAATTTTATT-TTAATTT
1 TTTTTAATTATATTATTAATTT
1477153 TTTTATAATTATATTAATTAATTT
1 TTTT-TAATTATATT-ATTAATTT
1477177 ATGACACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 9 0.45
24 7 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTTAATTATATTATTAATTT
Found at i:1481261 original size:20 final size:20
Alignment explanation
Indices: 1481235--1481302 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
1481225 AATGTTTTTT
1481235 TATAATTATTATTTTAAATAA
1 TATAATT-TTATTTTAAATAA
*
1481256 -ATAATTTATATATTTAATTAA
1 TATAATTT-TAT-TTTAAATAA
*
1481277 TATTAATTTTATTTT-AATTA
1 TA-TAATTTTATTTTAAATAA
1481297 TATAAT
1 TATAAT
1481303 ATTTTTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
19 5 0.12
20 14 0.35
21 11 0.28
22 4 0.10
23 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATAATTTTATTTTAAATAA
Found at i:1481306 original size:21 final size:20
Alignment explanation
Indices: 1481235--1481312 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 20
1481225 AATGTTTTTT
* *
1481235 TATAATTATTATTTTAAATA
1 TATAATTTTTATTTTAATTA
* *
1481255 AATAATTTATATATTTAATTAA
1 TATAATTTTTAT-TTTAATT-A
1481277 TATTAA-TTTTATTTTAATTA
1 TA-TAATTTTTATTTTAATTA
1481297 TATAATATTTTTATTT
1 TAT-A-ATTTTTATTT
1481313 ATTTTAATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
19 1 0.02
20 13 0.28
21 14 0.30
22 15 0.33
23 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATAATTTTTATTTTAATTA
Found at i:1481312 original size:42 final size:43
Alignment explanation
Indices: 1481237--1481339 Score: 104
Period size: 42 Copynumber: 2.4 Consensus size: 43
1481227 TGTTTTTTTA
* *
1481237 TAATTATTATTTTAAATAAATAATTTATATATTTA-ATTAATAT
1 TAATT-TTATTTTAATTATATAATTTATATATTTATATTAATAT
* * *
1481280 TAATTTTATTTTAATTATATAATATT-TTTATTTATTTTAATTT
1 TAATTTTATTTTAATTATATAAT-TTATATATTTATATTAATAT
**
1481323 TAATAAT-TTTTAATTAT
1 TAATTTTATTTTAATTAT
1481340 TTATTAACTT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
42 33 0.65
43 18 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (43 bp):
TAATTTTATTTTAATTATATAATTTATATATTTATATTAATAT
Found at i:1481313 original size:21 final size:20
Alignment explanation
Indices: 1481266--1481313 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1481256 ATAATTTATA
*
1481266 TATTTAATTAATATTAATTT
1 TATTTAATTAATAATAATTT
*
1481286 TATTTTAATTATATAATATTTT
1 TA-TTTAATTA-ATAATAATTT
1481308 TATTTA
1 TATTTA
1481314 TTTTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 12 0.50
22 10 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTAATTAATAATAATTT
Found at i:1481317 original size:26 final size:25
Alignment explanation
Indices: 1481284--1481341 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
1481274 TAATATTAAT
1481284 TTTATTTTAATTATATAAT-ATTTTTA
1 TTTATTTTAATT-T-TAATAATTTTTA
1481310 TTTATTTTAATTTTAATAATTTTTA
1 TTTATTTTAATTTTAATAATTTTTA
*
1481335 ATTATTT
1 TTTATTT
1481342 ATTAACTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 4 0.13
25 14 0.47
26 12 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTATTTTAATTTTAATAATTTTTA
Found at i:1481330 original size:46 final size:41
Alignment explanation
Indices: 1481231--1481332 Score: 96
Period size: 46 Copynumber: 2.3 Consensus size: 41
1481221 TAGTAATGTT
*
1481231 TTTTTATAATTATTATTTTAAATAAATAATTTATATATTTAA
1 TTTTAATAATT-TTATTTTAAATAAATAATTTATATATTTAA
* * * *
1481273 TTAATATTAATTTTATTTTAATTATATAATATTTTTATTTATTTTAA
1 TT-TTAATAATTTTATTTTAA--ATA-AATA-ATTTATATA-TTTAA
1481320 TTTTAATAATTTT
1 TTTTAATAATTTT
1481333 TAATTATTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
42 11 0.23
43 6 0.13
44 3 0.06
45 4 0.09
46 16 0.34
47 7 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (41 bp):
TTTTAATAATTTTATTTTAAATAAATAATTTATATATTTAA
Found at i:1481379 original size:21 final size:21
Alignment explanation
Indices: 1481355--1481397 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1481345 AACTTTTCAA
1481355 ATATATT-ATATTAATATATTT
1 ATATATTAAT-TTAATATATTT
*
1481376 ATATTTTAATTTAATATATTT
1 ATATATTAATTTAATATATTT
1481397 A
1 A
1481398 ACAATCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATATTAATTTAATATATTT
Found at i:1481408 original size:34 final size:33
Alignment explanation
Indices: 1481374--1481465 Score: 85
Period size: 34 Copynumber: 2.7 Consensus size: 33
1481364 ATTAATATAT
1481374 TTATATTTTAATTTAATATATTTAACAATCATA
1 TTATATTTTAATTTAATATATTTAACAATCATA
* * * * * * *
1481407 TTATTTTTTCACTATAATTTATTTTATAATCACCA
1 TTATATTTT-AATTTAATATATTTAACAATCA-TA
*
1481442 TTATATTTAAATTTAAATATATTT
1 TTATATTTTAATTT-AATATATTT
1481466 TTTATTATTA
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
33 8 0.18
34 20 0.45
35 16 0.36
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (33 bp):
TTATATTTTAATTTAATATATTTAACAATCATA
Found at i:1481507 original size:33 final size:34
Alignment explanation
Indices: 1481469--1481532 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
1481459 TATATTTTTT
* *
1481469 ATTATTAATTTTAATA-TTATAATATTTAATCTC
1 ATTATTAATGTAAATAGTTATAATATTTAATCTC
*
1481502 ATTATTAATGTAAATAGTTATTATATTTAAT
1 ATTATTAATGTAAATAGTTATAATATTTAAT
1481533 TATTTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 14 0.52
34 13 0.48
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (34 bp):
ATTATTAATGTAAATAGTTATAATATTTAATCTC
Found at i:1481556 original size:25 final size:24
Alignment explanation
Indices: 1481519--1481567 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1481509 ATGTAAATAG
* * *
1481519 TTATTATATTTAATTATTTTTAATC
1 TTATTAAAATTAATT-TTGTTAATC
1481544 TTATTAAAATTAATTTTGTTAATC
1 TTATTAAAATTAATTTTGTTAATC
1481568 GTCTAAATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (24 bp):
TTATTAAAATTAATTTTGTTAATC
Found at i:1482124 original size:15 final size:17
Alignment explanation
Indices: 1482104--1482143 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1482094 ATATATTTTG
*
1482104 AAAAATTAAA-TAA-AT
1 AAAAATAAAATTAATAT
1482119 AAAAATAAAATTAATAT
1 AAAAATAAAATTAATAT
1482136 AAAAATAA
1 AAAAATAA
1482144 TTATATCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 3 0.14
17 10 0.45
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAAATAAAATTAATAT
Found at i:1483083 original size:25 final size:25
Alignment explanation
Indices: 1483059--1483107 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1483049 ATAGGATATA
*
1483059 AATATAATTTAAAT-ATATAATTAT
1 AATAAAATTTAAATAATATAATTAT
* *
1483083 ATTAAAATTTATATAATATAATTAT
1 AATAAAATTTAAATAATATAATTAT
1483108 TAATGTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AATAAAATTTAAATAATATAATTAT
Found at i:1483095 original size:18 final size:19
Alignment explanation
Indices: 1483054--1483106 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1483044 TTAAAATAGG
*
1483054 ATATAAATATAATTTAAAT
1 ATATAAATATAATTAAAAT
*
1483073 ATATAATTAT-ATTAAAAT
1 ATATAAATATAATTAAAAT
*
1483091 TTATATAATATAATTA
1 ATATA-AATATAATTA
1483107 TTAATGTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 11 0.39
19 13 0.46
20 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATAAATATAATTAAAAT
Found at i:1484251 original size:20 final size:21
Alignment explanation
Indices: 1484218--1484256 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1484208 GATTCAAATC
* *
1484218 AATTACAAACAAAA-TTTTAA
1 AATTAAAAAAAAAACTTTTAA
1484238 AATTAAAAAAAAAACTTTT
1 AATTAAAAAAAAAACTTTT
1484257 TTTTATCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (21 bp):
AATTAAAAAAAAAACTTTTAA
Found at i:1484538 original size:23 final size:24
Alignment explanation
Indices: 1484506--1484552 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1484496 AAGATTAACT
1484506 TTAAAAAA-TTGACTATTTTTATA
1 TTAAAAAATTTGACTATTTTTATA
* * *
1484529 TTAAATAATTTTATTATTTTTATA
1 TTAAAAAATTTGACTATTTTTATA
1484553 ATTTTTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TTAAAAAATTTGACTATTTTTATA
Found at i:1486690 original size:59 final size:59
Alignment explanation
Indices: 1486598--1486715 Score: 200
Period size: 59 Copynumber: 2.0 Consensus size: 59
1486588 ATTGAGGACT
* *
1486598 TTTATGGTAGTTTTGTCTATATGAATTTCATGGACTCTAACCATTTAAAGAAATAAAAG
1 TTTATGATAGTTTTGTCTATATGAATTTCATGGACTCTAACCATTCAAAGAAATAAAAG
* *
1486657 TTTATGATAGTTTTGTCTATATGAATTTCATGGACTCTAACTATTCAAAGAAATCAAAG
1 TTTATGATAGTTTTGTCTATATGAATTTCATGGACTCTAACCATTCAAAGAAATAAAAG
1486716 AAACTTTATC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (59 bp):
TTTATGATAGTTTTGTCTATATGAATTTCATGGACTCTAACCATTCAAAGAAATAAAAG
Found at i:1502107 original size:2 final size:2
Alignment explanation
Indices: 1502100--1502136 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1502090 CCAGATGTAC
1502100 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1502137 CCATTTGATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1503065 original size:2 final size:2
Alignment explanation
Indices: 1503058--1503089 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1503048 AAACAACAAA
1503058 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1503090 TTCAGATCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1503169 original size:2 final size:2
Alignment explanation
Indices: 1503162--1503195 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1503152 CAAATCCAAC
1503162 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1503196 CAAATGAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1506156 original size:3 final size:3
Alignment explanation
Indices: 1506148--1506176 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1506138 GGGACCGCTT
1506148 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1506177 TCCTTTGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:1508067 original size:3 final size:3
Alignment explanation
Indices: 1508059--1508085 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1508049 TTAGATCAAG
1508059 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1508086 TATTTATTTT
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:1510555 original size:13 final size:13
Alignment explanation
Indices: 1510501--1510556 Score: 62
Period size: 12 Copynumber: 4.5 Consensus size: 13
1510491 GTTCACTTAC
1510501 TATTATTATTA-T
1 TATTATTATTATT
*
1510513 TATTATTATT-CT
1 TATTATTATTATT
1510525 TATTATTATTATT
1 TATTATTATTATT
* * *
1510538 AATTATTTTTGTT
1 TATTATTATTATT
1510551 TATTAT
1 TATTAT
1510557 AATAATTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
12 21 0.57
13 16 0.43
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:1510556 original size:3 final size:3
Alignment explanation
Indices: 1510501--1510544 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
1510491 GTTCACTTAC
*
1510501 TAT TAT TAT TAT TAT TAT TAT TCT TAT TAT TAT TAT TAAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT T
1510545 TTTGTTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1510564 original size:19 final size:20
Alignment explanation
Indices: 1510530--1510568 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1510520 ATTCTTATTA
*
1510530 TTATTATTAATTATTTTTGT
1 TTATTATTAATAATTTTTGT
1510550 TTATTA-TAATAATTTTTGT
1 TTATTATTAATAATTTTTGT
1510569 CGTTTCATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
TTATTATTAATAATTTTTGT
Found at i:1511611 original size:12 final size:12
Alignment explanation
Indices: 1511591--1511650 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
1511581 TGTAAATTTT
*
1511591 AAATGATATAAA
1 AAATAATATAAA
1511603 AAATAATATAAA
1 AAATAATATAAA
*
1511615 ATAA-AATATAAT
1 A-AATAATATAAA
*
1511627 ATATAATA-AAA
1 AAATAATATAAA
1511638 AATATTAATATAA
1 AA-A-TAATATAA
1511651 TGTAAATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
11 4 0.11
12 25 0.66
13 7 0.18
14 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (12 bp):
AAATAATATAAA
Found at i:1511620 original size:17 final size:17
Alignment explanation
Indices: 1511598--1511641 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
1511588 TTTAAATGAT
1511598 ATAAAAAATAATATAAA
1 ATAAAAAATAATATAAA
* *
1511615 ATAAAATATAATATATA
1 ATAAAAAATAATATAAA
1511632 ATAAAAAATA
1 ATAAAAAATA
1511642 TTAATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAAAAAATAATATAAA
Found at i:1511659 original size:31 final size:30
Alignment explanation
Indices: 1511590--1511664 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
1511580 TTGTAAATTT
1511590 TAAATGATATAAAAAATAATATAAAATAAAA
1 TAAAT-ATATAAAAAATAATATAAAATAAAA
* **
1511621 TATAATATATAATAAAA-AATATTAATATAATG
1 TA-AATATATAA-AAAATAATA-TAAAATAAAA
1511653 TAAATATATAAA
1 TAAATATATAAA
1511665 TATATTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
30 1 0.03
31 21 0.55
32 16 0.42
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (30 bp):
TAAATATATAAAAAATAATATAAAATAAAA
Found at i:1511661 original size:19 final size:18
Alignment explanation
Indices: 1511614--1511680 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
1511604 AATAATATAA
*
1511614 AATAAAATATAAT-ATAT
1 AATAAAATATATTAATAT
*
1511631 AATAAAAAATATTAATAT
1 AATAAAATATATTAATAT
* *
1511649 AATGTAAATATATAAATAT
1 AAT-AAAATATATTAATAT
*
1511668 ATTAAAATTATAT
1 AATAAAA-TATAT
1511681 ATGATTTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
17 11 0.28
18 10 0.25
19 19 0.47
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (18 bp):
AATAAAATATATTAATAT
Found at i:1511696 original size:19 final size:19
Alignment explanation
Indices: 1511616--1511701 Score: 60
Period size: 17 Copynumber: 4.8 Consensus size: 19
1511606 TAATATAAAA
* *
1511616 TAAAATATAATATATAATA
1 TAAAATATTATATATAATT
* *
1511635 AAAAATATTA-ATATAATG
1 TAAAATATTATATATAATT
*
1511653 T-AAATA-TATAAAT-ATAT
1 TAAAATATTATATATAAT-T
*
1511670 T-AAA-ATTATATATGATT
1 TAAAATATTATATATAATT
1511687 TAAAATATTA-ATATA
1 TAAAATATTATATATA
1511702 TCAATATTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
16 5 0.09
17 20 0.38
18 16 0.30
19 12 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
TAAAATATTATATATAATT
Found at i:1511728 original size:19 final size:19
Alignment explanation
Indices: 1511696--1511744 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1511686 TTAAAATATT
*
1511696 AATATATCAATATTTATAAA
1 AATATATAAATATTT-TAAA
1511716 AATATA-AAATATTTTAAA
1 AATATATAAATATTTTAAA
*
1511734 TATATATAAAT
1 AATATATAAAT
1511745 TATCTGATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 9 0.35
19 11 0.42
20 6 0.23
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATATAAATATTTTAAA
Found at i:1512284 original size:44 final size:44
Alignment explanation
Indices: 1512230--1512331 Score: 195
Period size: 44 Copynumber: 2.3 Consensus size: 44
1512220 AAAATAAAAT
1512230 TATATAGATATAATACAAAATTGGATCAAATTCATGTTTGTGTA
1 TATATAGATATAATACAAAATTGGATCAAATTCATGTTTGTGTA
*
1512274 TATATAGATATAATATAAAATTGGATCAAATTCATGTTTGTGTA
1 TATATAGATATAATACAAAATTGGATCAAATTCATGTTTGTGTA
1512318 TATATAGATATAAT
1 TATATAGATATAAT
1512332 GAAAACATTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.40
Consensus pattern (44 bp):
TATATAGATATAATACAAAATTGGATCAAATTCATGTTTGTGTA
Found at i:1512494 original size:20 final size:21
Alignment explanation
Indices: 1512465--1512508 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1512455 AAATAAAATC
1512465 TTTTCCTTTT-TTTCTTACAT
1 TTTTCCTTTTCTTTCTTACAT
* *
1512485 TTTTCTTTTTCTTTCTTTCAT
1 TTTTCCTTTTCTTTCTTACAT
1512506 TTT
1 TTT
1512509 CATTCCTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTCCTTTTCTTTCTTACAT
Found at i:1512910 original size:2 final size:2
Alignment explanation
Indices: 1512897--1512930 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1512887 ATTAACATCC
*
1512897 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1512931 GTCAACAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1513856 original size:2 final size:2
Alignment explanation
Indices: 1513849--1513885 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1513839 TGAAAGACAA
1513849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1513886 ATGAGAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1513989 original size:15 final size:17
Alignment explanation
Indices: 1513969--1514001 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1513959 AACATAAAGT
1513969 AAATTAAT-T-TTTTTA
1 AAATTAATATCTTTTTA
1513984 AAATTAATATCTTTTTA
1 AAATTAATATCTTTTTA
1514001 A
1 A
1514002 TTATCAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATTAATATCTTTTTA
Found at i:1514248 original size:3 final size:3
Alignment explanation
Indices: 1514242--1514298 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
1514232 GTAGTAGTAG
1514242 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1514290 TAA TAA TAA
1 TAA TAA TAA
1514299 AAGAAACTGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1515664 original size:16 final size:16
Alignment explanation
Indices: 1515643--1515680 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
1515633 TTATTACCAA
*
1515643 AATTTTTTAAAAATAT
1 AATTTTTTAAAAAAAT
1515659 AA--TTTTAAAAAAAT
1 AATTTTTTAAAAAAAT
1515673 AATTTTTT
1 AATTTTTT
1515681 TATTTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
14 13 0.68
16 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTTTTAAAAAAAT
Found at i:1515666 original size:14 final size:14
Alignment explanation
Indices: 1515647--1515678 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1515637 TACCAAAATT
*
1515647 TTTTAAAAATATAA
1 TTTTAAAAAAATAA
1515661 TTTTAAAAAAATAA
1 TTTTAAAAAAATAA
1515675 TTTT
1 TTTT
1515679 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTTAAAAAAATAA
Found at i:1515710 original size:22 final size:22
Alignment explanation
Indices: 1515658--1515716 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
1515648 TTTAAAAATA
** *
1515658 TAATTTTAAAAAAATAATTTTT
1 TAATTTTTTAAAAATAATTTAT
*
1515680 TTATTTTTTAAAAATAA-TTAT
1 TAATTTTTTAAAAATAATTTAT
*
1515701 TAATTATTTTTAAAAT
1 TAATT-TTTTAAAAAT
1515717 TTTGTAATGT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 7 0.23
22 23 0.77
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TAATTTTTTAAAAATAATTTAT
Found at i:1517503 original size:30 final size:30
Alignment explanation
Indices: 1517463--1517523 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
1517453 TTTTTAGATA
1517463 AATTTAAATATTAAATA-TATTTTTAATTTT
1 AATTTAAATA-TAAATATTATTTTTAATTTT
* * *
1517493 AATTTTAATATCATTATTATTTTTAATTTT
1 AATTTAAATATAAATATTATTTTTAATTTT
1517523 A
1 A
1517524 TCAAAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (30 bp):
AATTTAAATATAAATATTATTTTTAATTTT
Found at i:1517516 original size:24 final size:23
Alignment explanation
Indices: 1517476--1517523 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
1517466 TTAAATATTA
*
1517476 AATATATTTTTAATTTTAATTTT
1 AATATATTATTAATTTTAATTTT
*
1517499 AATATCATTATTATTTTTAATTTT
1 AATAT-ATTATTAATTTTAATTTT
1517523 A
1 A
1517524 TCAAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
AATATATTATTAATTTTAATTTT
Found at i:1517886 original size:22 final size:24
Alignment explanation
Indices: 1517860--1517905 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
1517850 GATTATCAAG
1517860 TTTAATTATTT-ATA-AATTATTA
1 TTTAATTATTTAATATAATTATTA
1517882 TTTAATTATTTAATATAATTATTA
1 TTTAATTATTTAATATAATTATTA
1517906 ACTTTTCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 11 0.50
23 3 0.14
24 8 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTAATTATTTAATATAATTATTA
Found at i:1518076 original size:20 final size:19
Alignment explanation
Indices: 1518028--1518070 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1518018 AATTTTTAAG
*
1518028 ATAATACATATTTTTAAAAT
1 ATAATAAAT-TTTTTAAAAT
1518048 ATAATAAATTTTTTAAAA-
1 ATAATAAATTTTTTAAAAT
1518066 ATAAT
1 ATAAT
1518071 TAAAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 9 0.41
20 8 0.36
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATAAATTTTTTAAAAT
Found at i:1519726 original size:21 final size:20
Alignment explanation
Indices: 1519696--1519734 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1519686 ATAAAATTAT
1519696 TTATATTTAT-ATTTAAAAAA
1 TTATATTTATCA-TTAAAAAA
1519716 TTATAATTTATCATTAAAA
1 TTAT-ATTTATCATTAAAA
1519735 TCATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATATTTATCATTAAAAAA
Done.