Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014694.1 Kokia drynarioides strain JFW-HI SEQ_129733, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 570195
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 173 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:169 original size:41 final size:42
Alignment explanation
Indices: 112--215 Score: 133
Period size: 41 Copynumber: 2.5 Consensus size: 42
102 TAATTACATT
*
112 TAATTAAATATTTAATTATT-AAAACAATCCAAATATTTAAA
1 TAATTAAATATTTAATTATTAAAAACAACCCAAATATTTAAA
* * *
153 TAATTAATTATTTAATTATTAAAAATAACCCAAATATTTAAT
1 TAATTAAATATTTAATTATTAAAAACAACCCAAATATTTAAA
*
195 TAA--AAATATTTTATTAGTTAA
1 TAATTAAATATTTAATTA-TTAA
216 TTATATTTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
40 11 0.20
41 23 0.42
42 21 0.38
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (42 bp):
TAATTAAATATTTAATTATTAAAAACAACCCAAATATTTAAA
Found at i:171 original size:71 final size:67
Alignment explanation
Indices: 42--172 Score: 172
Period size: 70 Copynumber: 1.9 Consensus size: 67
32 ATATTTAAAT
* * *
42 ATTTAATTAATTATTTATTAAAAACAACCCAAATATTTAATTAAAAAATATTTTATTATTTAATT
1 ATTTAATTAAATATTTATTAAAAACAACCCAAATATTTAAATAAAAAATATTTAATTATTTAATT
107 AC
66 AC
* * *
109 ATTTAATTAAATATTTAATTATTAAAACAATCCAAATATTTAAATAATTAATTATTTAATTATT
1 ATTTAATTAAATATTT-ATTA--AAAACAACCCAAATATTTAAATAA-AAAATATTTAATTATT
173 AAAAATAACC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
67 15 0.28
68 4 0.07
70 22 0.41
71 13 0.24
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (67 bp):
ATTTAATTAAATATTTATTAAAAACAACCCAAATATTTAAATAAAAAATATTTAATTATTTAATT
AC
Found at i:199 original size:112 final size:113
Alignment explanation
Indices: 1--308 Score: 539
Period size: 112 Copynumber: 2.7 Consensus size: 113
1 ATTAAATATTTAATAATTAAAAACAATCCAAATATTTAAATATTTAATTAATTATTTATTAAAAA
1 ATTAAATATTTAATAATTAAAAACAATCCAAATATTTAAATATTTAATTAATTATTTATTAAAAA
*
66 CAACCCAAATATTTAATTAAAAAATATTTTATTATTTAATTACATTTA
66 CAACCCAAATATTTAATTAAAAAATATTTTATTAGTTAATTACATTTA
* * * *
114 ATTAAATATTTAATTATT-AAAACAATCCAAATATTTAAATAATTAATTATTTAATTATTAAAAA
1 ATTAAATATTTAATAATTAAAAACAATCCAAATATTTAAATATTTAATTAATTATTTATTAAAAA
* *
178 TAACCCAAATATTTAATT-AAAAATATTTTATTAGTTAATTATATTTA
66 CAACCCAAATATTTAATTAAAAAATATTTTATTAGTTAATTACATTTA
225 ATTAAATATTTAATAATTAAAAACAATCCAAATATTTAAATATTTAATTAATTATTTATTAAAAA
1 ATTAAATATTTAATAATTAAAAACAATCCAAATATTTAAATATTTAATTAATTATTTATTAAAAA
290 CAACCCAAATATTTAATTA
66 CAACCCAAATATTTAATTA
309 TTTAATTACA
Statistics
Matches: 181, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
111 44 0.24
112 120 0.66
113 17 0.09
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (113 bp):
ATTAAATATTTAATAATTAAAAACAATCCAAATATTTAAATATTTAATTAATTATTTATTAAAAA
CAACCCAAATATTTAATTAAAAAATATTTTATTAGTTAATTACATTTA
Found at i:299 original size:42 final size:44
Alignment explanation
Indices: 232--406 Score: 212
Period size: 42 Copynumber: 3.9 Consensus size: 44
222 TTAATTAAAT
* *
232 ATTTAATAATTAAAAACAATCCAAATATTTAAATATTTAATTA-
1 ATTTAATTATTAAAAACAATCCAAATATTTAATTATTTAATTAC
* *
275 A-TTATTTATTAAAAACAACCCAAATATTTAATTATTTAATTAC
1 ATTTAATTATTAAAAACAATCCAAATATTTAATTATTTAATTAC
*
318 ATTTAATTATT-AAAACAATCCAAATATTTAATTAATTAATTATTTAAC
1 ATTTAATTATTAAAAACAATCCAAATATTTAATT-A-T--TTAATT-AC
* *
366 TAGTTAATTATTAACAACAATCCAAATATTTAATTATTTAA
1 -ATTTAATTATTAAAAACAATCCAAATATTTAATTATTTAA
407 AAACAATCCA
Statistics
Matches: 113, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
42 37 0.33
43 23 0.20
44 9 0.08
45 1 0.01
46 3 0.03
47 5 0.04
48 3 0.03
49 11 0.10
50 21 0.19
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.42
Consensus pattern (44 bp):
ATTTAATTATTAAAAACAATCCAAATATTTAATTATTTAATTAC
Found at i:312 original size:8 final size:8
Alignment explanation
Indices: 299--377 Score: 50
Period size: 8 Copynumber: 9.5 Consensus size: 8
289 ACAACCCAAA
299 TATTTAAT
1 TATTTAAT
307 TATTTAAT
1 TATTTAAT
315 TACATTTAAT
1 T--ATTTAAT
* *
325 TATTAAAAC
1 TATT-TAAT
* ** *
334 AATCCAAA
1 TATTTAAT
342 TATTTAAT
1 TATTTAAT
*
350 TAATTAAT
1 TATTTAAT
*
358 TATTTAAC
1 TATTTAAT
*
366 TAGTTAAT
1 TATTTAAT
374 TATT
1 TATT
378 AACAACAATC
Statistics
Matches: 52, Mismatches: 16, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
8 40 0.77
9 4 0.08
10 8 0.15
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.49
Consensus pattern (8 bp):
TATTTAAT
Found at i:354 original size:112 final size:107
Alignment explanation
Indices: 1--356 Score: 428
Period size: 112 Copynumber: 3.2 Consensus size: 107
1 ATTAAATATTTAATAATTAAAAACAATCCAAATATTTAAATATTTAATTAATTATTTATTAAAAA
1 ATTAAATATTTAATAATTAAAAACAATCCAAATATTTAAATATTTAATTAATTATTTATTAAAAA
** *
66 CAACCCAAATATTTAATTAAAAAATATTTTATTATTTAATTACATTTA
66 CAACCCAAATATTTAATTAAATTATATTTAATTA-TTAA--A-A--TA
* * * *
114 ATTAAATATTTAATTATT-AAAACAATCCAAATATTTAAATAATTAATTATTTAATTATTAAAAA
1 ATTAAATATTTAATAATTAAAAACAATCCAAATATTTAAATATTTAATTAATTATTTATTAAAAA
* * *
178 TAACCCAAATATTTAATTAAA-AATATTTTATTAGTTAATTATATTTA
66 CAACCCAAATATTTAATTAAATTATATTTAATTA-TTAA--A-A--TA
225 ATTAAATATTTAATAATTAAAAACAATCCAAATATTTAAATATTTAATTAATTATTTATTAAAAA
1 ATTAAATATTTAATAATTAAAAACAATCCAAATATTTAAATATTTAATTAATTATTTATTAAAAA
* *
290 CAACCCAAATATTTAATTATTTAATTACATTTAATTATTAAAACA
66 CAACCCAAATATTTAATTA---AATTATATTTAATTATTAAAATA
*
335 ATCCAAATATTTAATTAATTAA
1 AT-TAAATATTTAA-TAATTAA
357 TTATTTAACT
Statistics
Matches: 219, Mismatches: 17, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
110 3 0.01
111 51 0.23
112 132 0.60
113 18 0.08
115 6 0.03
116 9 0.04
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (107 bp):
ATTAAATATTTAATAATTAAAAACAATCCAAATATTTAAATATTTAATTAATTATTTATTAAAAA
CAACCCAAATATTTAATTAAATTATATTTAATTATTAAAATA
Found at i:363 original size:16 final size:16
Alignment explanation
Indices: 302--377 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
292 ACCCAAATAT
302 TTAATTATTTAATTACA
1 TTAATTATTTAATTA-A
* **
319 TTTAATTATTAAAACAA
1 -TTAATTATTTAATTAA
* *
336 TCCAAATATTTAATTAA
1 T-TAATTATTTAATTAA
* *
353 TTAATTATTTAACTAG
1 TTAATTATTTAATTAA
369 TTAATTATT
1 TTAATTATT
378 AACAACAATC
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
16 21 0.47
17 12 0.27
18 12 0.27
ACGTcount: A:0.43, C:0.07, G:0.01, T:0.49
Consensus pattern (16 bp):
TTAATTATTTAATTAA
Found at i:392 original size:50 final size:50
Alignment explanation
Indices: 302--406 Score: 158
Period size: 50 Copynumber: 2.1 Consensus size: 50
292 ACCCAAATAT
* *
302 TTAATTATTTAATTACATTTAATTATTAAAACAATCCAAATATTTAATTAA
1 TTAATTATTTAACTA-AGTTAATTATTAAAACAATCCAAATATTTAATTAA
*
353 TTAATTATTTAACT-AGTTAATTATTAACAACAATCCAAATATTTAATTAT
1 TTAATTATTTAACTAAGTTAATTATTAA-AACAATCCAAATATTTAATTAA
403 TTAA
1 TTAA
407 AAACAATCCA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
49 12 0.24
50 25 0.50
51 13 0.26
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.45
Consensus pattern (50 bp):
TTAATTATTTAACTAAGTTAATTATTAAAACAATCCAAATATTTAATTAA
Found at i:410 original size:77 final size:75
Alignment explanation
Indices: 318--477 Score: 205
Period size: 77 Copynumber: 2.1 Consensus size: 75
308 ATTTAATTAC
* *
318 ATTTAATTATTAAAACAATCCAAATATTTAATTAATTAA-TTATTTAACTAGTTAATTATTAACA
1 ATTTAATTATTAAAACAATCCAAATAATTAATTAATTAATTTA-ATAACTAGTTAATTATTAACA
*
382 ACAATCCAAAT
65 ACAACCCAAAT
* * * *
393 ATTTAATTATTTAAAAACAATCCAAATAATTAATTATTTAGTTTAATAATTAGTTATTTATTAAC
1 ATTTAATTA-TT-AAAACAATCCAAATAATTAATTAATTAATTTAATAACTAGTTAATTATTAAC
*
458 AATAACCCAAAT
64 AACAACCCAAAT
*
470 ACTTAATT
1 ATTTAATT
478 CAAAATATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
75 9 0.12
76 2 0.03
77 59 0.81
78 3 0.04
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (75 bp):
ATTTAATTATTAAAACAATCCAAATAATTAATTAATTAATTTAATAACTAGTTAATTATTAACAA
CAACCCAAAT
Found at i:6339 original size:21 final size:21
Alignment explanation
Indices: 6321--6362 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6311 CTTAAAGCGG
*
6321 AGGTAGCAACGAGGGAAGCAA
1 AGGTAGCAACGAGGCAAGCAA
*
6342 AGGTAGCAGCGAGGCAAGCAA
1 AGGTAGCAACGAGGCAAGCAA
6363 GGAAGCAGAG
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:0.40, C:0.17, G:0.38, T:0.05
Consensus pattern (21 bp):
AGGTAGCAACGAGGCAAGCAA
Found at i:6726 original size:43 final size:43
Alignment explanation
Indices: 6660--6837 Score: 158
Period size: 44 Copynumber: 4.1 Consensus size: 43
6650 AATCTGTTAA
** * * *
6660 TTTAGCGGTGTTTATGGGGAAAGCGTCGCTAAAGACCATGTTT
1 TTTAGCGGCATTTGTGGGGAAAGCGCCGCTAAAGACCATGTTC
* *
6703 TTTAGCGGCATTTGTGGGTAAAGCGCCGTTAAAGACCATGTTC
1 TTTAGCGGCATTTGTGGGGAAAGCGCCGCTAAAGACCATGTTC
* * * ** *
6746 TTTAGCGGCATTTGTTTGGAAAAGTGCCATTGAAGACCATGTTC
1 TTTAGCGGCATTTG-TGGGGAAAGCGCCGCTAAAGACCATGTTC
* * * * ** *
6790 TTTAGCGACGTTTGTTTGGAAAAGTACCACTAAAGACCATGTTC
1 TTTAGCGGCATTTG-TGGGGAAAGCGCCGCTAAAGACCATGTTC
6834 TTTA
1 TTTA
6838 CCGACGTTTT
Statistics
Matches: 117, Mismatches: 17, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
43 50 0.43
44 67 0.57
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (43 bp):
TTTAGCGGCATTTGTGGGGAAAGCGCCGCTAAAGACCATGTTC
Found at i:6792 original size:44 final size:44
Alignment explanation
Indices: 6689--6837 Score: 201
Period size: 44 Copynumber: 3.4 Consensus size: 44
6679 AAAGCGTCGC
* * * * *
6689 TAAAGACCATGTTTTTTAGCGGCATTTG-TGGGTAAAGCGCCGT
1 TAAAGACCATGTTCTTTAGCGGCATTTGTTTGGAAAAGTGCCAT
6732 TAAAGACCATGTTCTTTAGCGGCATTTGTTTGGAAAAGTGCCAT
1 TAAAGACCATGTTCTTTAGCGGCATTTGTTTGGAAAAGTGCCAT
* * * * *
6776 TGAAGACCATGTTCTTTAGCGACGTTTGTTTGGAAAAGTACCAC
1 TAAAGACCATGTTCTTTAGCGGCATTTGTTTGGAAAAGTGCCAT
6820 TAAAGACCATGTTCTTTA
1 TAAAGACCATGTTCTTTA
6838 CCGACGTTTT
Statistics
Matches: 94, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
43 27 0.29
44 67 0.71
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (44 bp):
TAAAGACCATGTTCTTTAGCGGCATTTGTTTGGAAAAGTGCCAT
Found at i:13296 original size:40 final size:40
Alignment explanation
Indices: 13245--13325 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
13235 CATAGGTAGG
13245 AACAATAATTGCCTTCCCAAGAAGTATGTTCACAATAACA
1 AACAATAATTGCCTTCCCAAGAAGTATGTTCACAATAACA
13285 AACAATAATTGCCTTCCCAAGAAGTATGTTCACAATAACA
1 AACAATAATTGCCTTCCCAAGAAGTATGTTCACAATAACA
13325 A
1 A
13326 TTGATTTTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (40 bp):
AACAATAATTGCCTTCCCAAGAAGTATGTTCACAATAACA
Found at i:23211 original size:30 final size:30
Alignment explanation
Indices: 23175--23238 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
23165 AGTTTGAGCA
* * *
23175 AGGTGGAGGGACAATAGGAGGAGTATCCTT
1 AGGTGGAGGGACAATAGGAGCAATATCCTC
*
23205 AGGTGGAGGGACAATATGAGCAATATCCTC
1 AGGTGGAGGGACAATAGGAGCAATATCCTC
23235 AGGT
1 AGGT
23239 TCTTGAAAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.36, T:0.20
Consensus pattern (30 bp):
AGGTGGAGGGACAATAGGAGCAATATCCTC
Found at i:31986 original size:24 final size:26
Alignment explanation
Indices: 31959--32010 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
31949 TAAAAATTGA
31959 TAAATG-T-TATTTTCCATCGAAACG
1 TAAATGTTATATTTTCCATCGAAACG
31983 TAAATGTTAGTATTTTCCATCGAAACG
1 TAAATGTTA-TATTTTCCATCGAAACG
32010 T
1 T
32011 TCTCAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 6 0.24
25 1 0.04
27 18 0.72
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (26 bp):
TAAATGTTATATTTTCCATCGAAACG
Found at i:36644 original size:24 final size:23
Alignment explanation
Indices: 36614--36669 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
36604 CTTTATCTCA
36614 CACGAGCCAAGAATGGTAAGCTCT
1 CACGAGCC-AGAATGGTAAGCTCT
* *
36638 CACGAGCTCATAATGGTTAGCTCT
1 CACGAGC-CAGAATGGTAAGCTCT
*
36662 TACGAGCC
1 CACGAGCC
36670 CAGTCCAGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 26 0.93
25 1 0.04
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (23 bp):
CACGAGCCAGAATGGTAAGCTCT
Found at i:44560 original size:45 final size:45
Alignment explanation
Indices: 44469--44570 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 45
44459 ATGGAGTTAT
* * ** *
44469 ATGCTG-GAAGCATGACTAGTGTGAACATGAATTTTGTGAGTACTA
1 ATGCTGCG-AGCATGACTAGTGCGAACATGAATGTTACGAGCACTA
*
44514 ATGCTGCGAGCATGACTAGTGCGAACATGAATGTTACGAGCGCTA
1 ATGCTGCGAGCATGACTAGTGCGAACATGAATGTTACGAGCACTA
*
44559 ATGTTGCGAGCA
1 ATGCTGCGAGCA
44571 CTGATGCTAC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
45 48 0.98
46 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.26
Consensus pattern (45 bp):
ATGCTGCGAGCATGACTAGTGCGAACATGAATGTTACGAGCACTA
Found at i:44593 original size:30 final size:30
Alignment explanation
Indices: 44559--44630 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
44549 ACGAGCGCTA
44559 ATGTTGCGAGCACTGATGCTACAAACATTG
1 ATGTTGCGAGCACTGATGCTACAAACATTG
*
44589 ATGTTGCGAGCACTGATGCTGCAAACATTG
1 ATGTTGCGAGCACTGATGCTACAAACATTG
44619 ATGTTGCGAGCA
1 ATGTTGCGAGCA
44631 TGGATGAAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (30 bp):
ATGTTGCGAGCACTGATGCTACAAACATTG
Found at i:44605 original size:15 final size:15
Alignment explanation
Indices: 44544--44630 Score: 66
Period size: 15 Copynumber: 5.8 Consensus size: 15
44534 GCGAACATGA
* * *
44544 ATGTTACGAGCGCTA
1 ATGTTGCGAGCACTG
44559 ATGTTGCGAGCACTG
1 ATGTTGCGAGCACTG
* * * * *
44574 ATGCTACAAACATTG
1 ATGTTGCGAGCACTG
44589 ATGTTGCGAGCACTG
1 ATGTTGCGAGCACTG
* * * *
44604 ATGCTGCAAACATTG
1 ATGTTGCGAGCACTG
44619 ATGTTGCGAGCA
1 ATGTTGCGAGCA
44631 TGGATGAAGA
Statistics
Matches: 52, Mismatches: 20, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
15 52 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (15 bp):
ATGTTGCGAGCACTG
Found at i:44636 original size:15 final size:14
Alignment explanation
Indices: 44518--44632 Score: 52
Period size: 15 Copynumber: 7.7 Consensus size: 14
44508 GTACTAATGC
44518 TGCGAGCATGACTAG-
1 TGCGAGCATGA-T-GT
*
44533 TGCGAACATGAATGT
1 TGCGAGCATG-ATGT
* * *
44548 TACGAGCGCTAATGT
1 TGCGAGC-ATGATGT
*
44563 TGCGAGCACTGATGC
1 TGCGAGCA-TGATGT
* * *
44578 TACAAACATTGATGT
1 TGCGAGCA-TGATGT
*
44593 TGCGAGCACTGATGC
1 TGCGAGCA-TGATGT
* *
44608 TGCAAACATTGATGT
1 TGCGAGCA-TGATGT
44623 TGCGAGCATG
1 TGCGAGCATG
44633 GATGAAGAAC
Statistics
Matches: 71, Mismatches: 25, Indels: 9
0.68 0.24 0.09
Matches are distributed among these distances:
14 3 0.04
15 66 0.93
16 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (14 bp):
TGCGAGCATGATGT
Found at i:44985 original size:82 final size:82
Alignment explanation
Indices: 44910--45073 Score: 240
Period size: 82 Copynumber: 2.0 Consensus size: 82
44900 TTAGCGGTGT
* * *
44910 CGAAGTTAAATTGTAATTTTTATCATAGTAAAAATGTAA-TTTTTAAATGATTAGATCAAAATTT
1 CGAAGTTAAATTGTAATTTTTATCATAGTAAAAAAG-AATTTTTTAAATGATTAAATAAAAATTT
44974 TATCATTTTTAGGAGGGC
65 TATCATTTTTAGGAGGGC
* * *
44992 CGAAGTTAAATTTTAATTTTTATGATATTAAAAAAGAATTTTTTAAATGATTAAATAAAAATTTT
1 CGAAGTTAAATTGTAATTTTTATCATAGTAAAAAAGAATTTTTTAAATGATTAAATAAAAATTTT
* *
45057 ATCAATTTTAGGGGGGC
66 ATCATTTTTAGGAGGGC
45074 AAATTGCAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 2 0.03
82 71 0.97
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.41
Consensus pattern (82 bp):
CGAAGTTAAATTGTAATTTTTATCATAGTAAAAAAGAATTTTTTAAATGATTAAATAAAAATTTT
ATCATTTTTAGGAGGGC
Found at i:45541 original size:19 final size:18
Alignment explanation
Indices: 45490--45562 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 18
45480 AATCTTTTAC
*
45490 ATATTTAAAATTTT-ATA
1 ATATTTAAATTTTTAATA
45507 ATATTTACAATGTTTTAATA
1 ATATTTA-AAT-TTTTAATA
45527 ATATTTAATATTTTTAATA
1 ATATTTAA-ATTTTTAATA
* *
45546 ATTTTTACAATGTTTAA
1 ATATTTA-AATTTTTAA
45563 AATTTTTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
17 7 0.15
18 2 0.04
19 26 0.54
20 13 0.27
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
ATATTTAAATTTTTAATA
Found at i:45544 original size:9 final size:10
Alignment explanation
Indices: 45519--45578 Score: 63
Period size: 9 Copynumber: 6.3 Consensus size: 10
45509 ATTTACAATG
45519 TTTTAATAAT
1 TTTTAATAAT
*
45529 ATTTAAT-AT
1 TTTTAATAAT
45538 TTTTAATAAT
1 TTTTAATAAT
*
45548 TTTT-ACAAT
1 TTTTAATAAT
*
45557 GTTTAA-AAT
1 TTTTAATAAT
*
45566 TTTTTATAAT
1 TTTTAATAAT
45576 TTT
1 TTT
45579 GCACTCATCT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
9 22 0.54
10 19 0.46
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:45571 original size:10 final size:9
Alignment explanation
Indices: 45450--45569 Score: 64
Period size: 10 Copynumber: 12.8 Consensus size: 9
45440 CAAAACTATT
45450 AATTTTTATA
1 AATTTTTA-A
*
45460 AATTTATATA
1 AATTTTTA-A
*
45470 AATTATTAA
1 AATTTTTAA
45479 TAATCTTTT-A
1 -AAT-TTTTAA
* *
45489 CATATTTAA
1 AATTTTTAA
*
45498 AA-TTTTAT
1 AATTTTTAA
* *
45506 AATATTTAC
1 AATTTTTAA
45515 AATGTTTTAA
1 AAT-TTTTAA
*
45525 TAATATTTAA
1 -AATTTTTAA
*
45535 TATTTTTAA
1 AATTTTTAA
*
45544 TAATTTTTAC
1 -AATTTTTAA
*
45554 AATGTTTAA
1 AATTTTTAA
45563 AATTTTT
1 AATTTTT
45570 TATAATTTTG
Statistics
Matches: 82, Mismatches: 21, Indels: 15
0.69 0.18 0.13
Matches are distributed among these distances:
8 9 0.11
9 32 0.39
10 35 0.43
11 6 0.07
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (9 bp):
AATTTTTAA
Found at i:49879 original size:22 final size:21
Alignment explanation
Indices: 49836--49877 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
49826 ATCCCAAACC
*
49836 CCCAAACATTTTTACTTTTCT
1 CCCAAACACTTTTACTTTTCT
*
49857 CCCAAA-ACTTTTACTTCTCT
1 CCCAAACACTTTTACTTTTCT
49877 C
1 C
49878 TCATCCCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.24, C:0.33, G:0.00, T:0.43
Consensus pattern (21 bp):
CCCAAACACTTTTACTTTTCT
Found at i:50330 original size:17 final size:17
Alignment explanation
Indices: 50285--50366 Score: 60
Period size: 17 Copynumber: 4.6 Consensus size: 17
50275 TTATATCTAC
*
50285 TATTTATATTATTAAAT
1 TATTTATATTATTGAAT
* * *
50302 TAAAATTCATATTTTTGTAT
1 T---ATTTATATTATTGAAT
50322 TATTTATATTATTGAAT
1 TATTTATATTATTGAAT
*
50339 TATTTA-ATCATATT-AAA
1 TATTTATAT--TATTGAAT
50356 TATTTATATTA
1 TATTTATATTA
50367 AAATTTAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
16 4 0.08
17 28 0.55
18 6 0.12
20 13 0.25
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTTATATTATTGAAT
Found at i:50342 original size:20 final size:20
Alignment explanation
Indices: 50285--50342 Score: 50
Period size: 20 Copynumber: 3.0 Consensus size: 20
50275 TTATATCTAC
* *
50285 TATTTATATTATTAAATTAA
1 TATTTATATTATTGAATTAT
* * *
50305 AATTCATATTTTTG---TAT
1 TATTTATATTATTGAATTAT
50322 TATTTATATTATTGAATTAT
1 TATTTATATTATTGAATTAT
50342 T
1 T
50343 TAATCATATT
Statistics
Matches: 27, Mismatches: 8, Indels: 6
0.66 0.20 0.15
Matches are distributed among these distances:
17 13 0.48
20 14 0.52
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (20 bp):
TATTTATATTATTGAATTAT
Found at i:53335 original size:19 final size:18
Alignment explanation
Indices: 53308--53354 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 18
53298 TAAATATGTA
53308 TTTTT-AATTAAATTCTAT
1 TTTTTAAATTAAATT-TAT
53326 TTTTTAAATTTAAATTTAT
1 TTTTTAAA-TTAAATTTAT
53345 TGTTTTAAAT
1 T-TTTTAAAT
53355 GGTAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.19
19 7 0.27
20 14 0.54
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTTAAATTAAATTTAT
Found at i:53340 original size:20 final size:20
Alignment explanation
Indices: 53315--53354 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
53305 GTATTTTTAA
53315 TTAAATTCTATT-TTTTAAAT
1 TTAAATT-TATTGTTTTAAAT
53335 TTAAATTTATTGTTTTAAAT
1 TTAAATTTATTGTTTTAAAT
53355 GGTAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (20 bp):
TTAAATTTATTGTTTTAAAT
Found at i:53648 original size:93 final size:96
Alignment explanation
Indices: 53522--53695 Score: 248
Period size: 95 Copynumber: 1.8 Consensus size: 96
53512 TCTTTTTTAT
53522 TCAATCATTTAAGAAAAAAAAACATTTACCATAAAAATACT-AATTCCAATCAAT-A-ATTTAAT
1 TCAATCATTTAAG-AAAAAAAACATTTACCATAAAAATACTAAATT-CAATCAATCATATTTAAT
*
53584 AAAGTTACCTAAATTAATTTATTGTTTATTCAA
64 AAAATTACCTAAATTAATTTATTGTTTATTCAA
* * * *
53617 TCAATCATTTAAG-AAGAAAACATTTATCATAAAAATATTAAATTCAATCCATCATATTTAATAA
1 TCAATCATTTAAGAAAAAAAACATTTACCATAAAAATACTAAATTCAATCAATCATATTTAATAA
*
53681 AATTGCCTAAATTAA
66 AATTACCTAAATTAA
53696 ATATGATTTA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
93 30 0.43
94 5 0.07
95 35 0.50
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (96 bp):
TCAATCATTTAAGAAAAAAAACATTTACCATAAAAATACTAAATTCAATCAATCATATTTAATAA
AATTACCTAAATTAATTTATTGTTTATTCAA
Found at i:53896 original size:19 final size:18
Alignment explanation
Indices: 53845--53901 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 18
53835 AAAGTGTGTC
*
53845 TTCTTTTAATTAAATTTTA
1 TTCTTTAAATTAAA-TTTA
53864 TT-TTTAAAATTTAAATTTA
1 TTCTTT-AAA-TTAAATTTA
53883 TTCCTTTAAATTAATATTT
1 TT-CTTTAAATTAA-ATTT
53902 TAAGAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
18 3 0.09
19 14 0.44
20 12 0.38
21 3 0.09
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (18 bp):
TTCTTTAAATTAAATTTA
Found at i:53978 original size:9 final size:9
Alignment explanation
Indices: 53964--54009 Score: 65
Period size: 9 Copynumber: 5.0 Consensus size: 9
53954 TGTGGACAAC
*
53964 ATAATTTAT
1 ATAATTTAA
53973 ATAATTTAA
1 ATAATTTAA
53982 ATAATTTAA
1 ATAATTTAA
*
53991 ATAATTAAA
1 ATAATTTAA
54000 ATCAATTTAA
1 AT-AATTTAA
54010 CACTTGTCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (9 bp):
ATAATTTAA
Found at i:56157 original size:30 final size:30
Alignment explanation
Indices: 56117--56174 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
56107 AAAAAATATA
*
56117 ATTTTAAAAAGATTAAATTAAAATTTTATT
1 ATTTTAAAAAGATTAAAATAAAATTTTATT
* *
56147 ATTTTTAAAAGATTAAAATATAATTTTA
1 ATTTTAAAAAGATTAAAATAAAATTTTA
56175 ATTTTATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (30 bp):
ATTTTAAAAAGATTAAAATAAAATTTTATT
Found at i:67938 original size:341 final size:339
Alignment explanation
Indices: 67316--68337 Score: 1780
Period size: 341 Copynumber: 3.0 Consensus size: 339
67306 TATTTTTGAT
* * * * *
67316 AAATTTGGCATAATGGTGAAGAATTTTTAAATTTTTTAGCATAAAACCGTTAAGTTCTATAAGTT
1 AAATTTGGCATAATGATGAGGAATTTTTAAATTTTTTAGCATGAAACCATTAAGTTCTATAGGTT
* *
67381 ACACTAAGTATATATAGAAAGGAATTGTTGATACCAAATGATGTGATTGATATGAGTAAATAAAC
66 ACACTAAGTATAGATAGAAAGGAATTGTTGATACCAAATGATGTGAATGATATGAGTAAATAAAC
*
67446 ATGCTAGTATATATGATAGATAGTAATTTTGGGATTGTGTGACTAAATTGATATTTGTGCATATT
131 ATGCTAGTATATATGATAGATAGTAATTTTGGGATTATGTGACTAAATTGATATTTGTGCATATT
**
67511 GAGGTGTTTAAGGATGACCTAAGGCATTGTTTGGTTACATCTAGAGCTAAAAAATTAGACCTTAA
196 GAGGTGTTTAA-GATGACCTAAGGCATTGTTTGGTTACATCTAGAGCTAAAAAGCTAGACCTTAA
* *
67576 AATGAATTCCCAATTAATACCCGTCTTTAAGTCTTATGACCTTTCTTGATGAAGTACATTACAAG
260 AATGAATTCCCAATTAATACCCGTCTTTGAGCCTTATGACCTTTCTTGATGAAGTACATTACAAG
67641 CCTCTAAAGCCTAAA
325 CCTCTAAAGCCTAAA
*
67656 AAATTTGGCACAATGATGAGGAATTTTTAAATTTTTTAGCATGAAACCATTAAGTTCTATAGGTT
1 AAATTTGGCATAATGATGAGGAATTTTTAAATTTTTTAGCATGAAACCATTAAGTTCTATAGGTT
* * * *
67721 ACACTAAGTATAGATAGAAAGGAATTATTGATACCAAATAATATGAATGATATGAGTAAAAAAAA
66 ACACTAAGTATAGATAGAAAGGAATTGTTGATACCAAATGATGTGAATGATATGAGT-AAATAAA
67786 CATGCTAGTATATATGATAGATAGTAATTTTGGGATTATGTGACTAAATTGATATTTGTGCATAT
130 CATGCTAGTATATATGATAGATAGTAATTTTGGGATTATGTGACTAAATTGATATTTGTGCATAT
*
67851 TGAGGTGTTTAACGATGACCTATGGCATTGTTTGGTTACATCTAGAGCTAAAAAGCTAGACCTTA
195 TGAGGTGTTTAA-GATGACCTAAGGCATTGTTTGGTTACATCTAGAGCTAAAAAGCTAGACCTTA
67916 AAATGAATTCCCAATTAATACCCGTCTTTGAGCCTTATGACCTTTCTTGATGAAGTACATTACAA
259 AAATGAATTCCCAATTAATACCCGTCTTTGAGCCTTATGACCTTTCTTGATGAAGTACATTACAA
67981 GCCTCTAAAGCCTAAA
324 GCCTCTAAAGCCTAAA
67997 AAATTTGGCATAATGATGAGGAATTTTT-AATTTTTTAGCATGAAACCATTAAGTTCTATAGGTT
1 AAATTTGGCATAATGATGAGGAATTTTTAAATTTTTTAGCATGAAACCATTAAGTTCTATAGGTT
*
68061 ACACTAAGTATAGATAGAAAGGAATTGTTGATACCAAATGATGTGAATGATATTAGTAAATAAAC
66 ACACTAAGTATAGATAGAAAGGAATTGTTGATACCAAATGATGTGAATGATATGAGTAAATAAAC
68126 ATGCTAGTATATATGATAGATAGTAATTTTGGGATTATGTGACTAAATTGATATTTGTGCATATT
131 ATGCTAGTATATATGATAGATAGTAATTTTGGGATTATGTGACTAAATTGATATTTGTGCATATT
* * *
68191 GAGGTGTTT--GATGACCTAAGGCATTGTTTAGTTACATCTAGAGCAAAAAAGCTAGACCTTATA
196 GAGGTGTTTAAGATGACCTAAGGCATTGTTTGGTTACATCTAGAGCTAAAAAGCTAGACCTTAAA
* *
68254 ATGAATTCCCAATTAATACCCATCTTTGAGCCTTATGACCTTTCTTGATGAACTACATTACAAGC
261 ATGAATTCCCAATTAATACCCGTCTTTGAGCCTTATGACCTTTCTTGATGAAGTACATTACAAGC
68319 CTCTAAAGCCTAAA
326 CTCTAAAGCCTAAA
68333 AAATT
1 AAATT
68338 ATTTGTGTGT
Statistics
Matches: 650, Mismatches: 31, Indels: 6
0.95 0.05 0.01
Matches are distributed among these distances:
336 132 0.20
339 81 0.12
340 200 0.31
341 237 0.36
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (339 bp):
AAATTTGGCATAATGATGAGGAATTTTTAAATTTTTTAGCATGAAACCATTAAGTTCTATAGGTT
ACACTAAGTATAGATAGAAAGGAATTGTTGATACCAAATGATGTGAATGATATGAGTAAATAAAC
ATGCTAGTATATATGATAGATAGTAATTTTGGGATTATGTGACTAAATTGATATTTGTGCATATT
GAGGTGTTTAAGATGACCTAAGGCATTGTTTGGTTACATCTAGAGCTAAAAAGCTAGACCTTAAA
ATGAATTCCCAATTAATACCCGTCTTTGAGCCTTATGACCTTTCTTGATGAAGTACATTACAAGC
CTCTAAAGCCTAAA
Found at i:69176 original size:18 final size:18
Alignment explanation
Indices: 69149--69190 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
69139 CTCAAGCTCC
69149 TTTG-TTTTCTTGCTTTA
1 TTTGCTTTTCTTGCTTTA
* *
69166 TTTGCTTTTCTTGTTTTG
1 TTTGCTTTTCTTGCTTTA
69184 TTTGCTT
1 TTTGCTT
69191 GAGGACAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.02, C:0.12, G:0.14, T:0.71
Consensus pattern (18 bp):
TTTGCTTTTCTTGCTTTA
Found at i:76584 original size:21 final size:22
Alignment explanation
Indices: 76545--76586 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
76535 ATCTGTAGTT
*
76545 TCATGACTTGTATTAGTAGAAA
1 TCATGACTTGTATCAGTAGAAA
*
76567 TCAT-ACTTGTATCGGTAGAA
1 TCATGACTTGTATCAGTAGAA
76587 CTAGCACAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (22 bp):
TCATGACTTGTATCAGTAGAAA
Found at i:82673 original size:23 final size:22
Alignment explanation
Indices: 82641--82684 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
82631 ACTTCTATAG
*
82641 TTTTACTTTTAAAATTTTAAAAA
1 TTTTAATTTTAAAA-TTTAAAAA
*
82664 TTTTAATTTTTAAATTTAAAA
1 TTTTAATTTTAAAATTTAAAA
82685 TACAAGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTAATTTTAAAATTTAAAAA
Found at i:82819 original size:14 final size:13
Alignment explanation
Indices: 82801--82846 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
82791 AATTTGAATT
82801 TTAAAATTTAAAA
1 TTAAAATTTAAAA
82814 TGTAAAAATTTAAAA
1 T-T-AAAATTTAAAA
* *
82829 TTAAAATATGAAA
1 TTAAAATTTAAAA
82842 TTAAA
1 TTAAA
82847 TTCTGTTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 15 0.52
14 2 0.07
15 12 0.41
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (13 bp):
TTAAAATTTAAAA
Found at i:82823 original size:15 final size:14
Alignment explanation
Indices: 82803--82834 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
82793 TTTGAATTTT
82803 AAAATTTAAAATGTA
1 AAAATTTAAAAT-TA
82818 AAAATTTAAAATTA
1 AAAATTTAAAATTA
82832 AAA
1 AAA
82835 TATGAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
AAAATTTAAAATTA
Found at i:85462 original size:19 final size:19
Alignment explanation
Indices: 85425--85462 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
85415 ATTAACCATT
*
85425 TTTTGCAATTGAAATAATA
1 TTTTGCAATTGAAAAAATA
85444 TTTTGCACATT-AAAAAATA
1 TTTTGCA-ATTGAAAAAATA
85463 CAAGAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (19 bp):
TTTTGCAATTGAAAAAATA
Found at i:86863 original size:12 final size:12
Alignment explanation
Indices: 86846--86870 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
86836 GAAAGATTAT
86846 TTATCCAAAAAA
1 TTATCCAAAAAA
86858 TTATCCAAAAAA
1 TTATCCAAAAAA
86870 T
1 T
86871 AAAGAGAAGG
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:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (12 bp):
TTATCCAAAAAA
Found at i:103868 original size:31 final size:32
Alignment explanation
Indices: 103830--103889 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
103820 TTTTTTCAAT
*
103830 TCAATTAAG-CCTTTGAACATTAAAATTACAC
1 TCAATTAAGTCATTTGAACATTAAAATTACAC
* *
103861 TCAATTAAGTTATTTGATCATTAAAATTA
1 TCAATTAAGTCATTTGAACATTAAAATTA
103890 AAGGTCAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 9 0.36
32 16 0.64
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (32 bp):
TCAATTAAGTCATTTGAACATTAAAATTACAC
Found at i:104011 original size:10 final size:10
Alignment explanation
Indices: 103992--104184 Score: 55
Period size: 10 Copynumber: 19.5 Consensus size: 10
103982 TTTTATACTT
*
103992 AAAATCATTA
1 AAAATTATTA
104002 AAAATTATTA
1 AAAATTATTA
*
104012 AAATATATAAATA
1 AAA-AT-T-ATTA
*
104025 TAAATTATTA
1 AAAATTATTA
*
104035 AAATATT-TTT
1 AAA-ATTATTA
*
104045 AAATTTA-TA
1 AAAATTATTA
* *
104054 AAAGATTGTAA
1 AAA-ATTATTA
*
104065 AAAATTATAA
1 AAAATTATTA
** *
104075 AAAAAAATGTT
1 AAAATTAT-TA
* * *
104086 AACATAATAA
1 AAAATTATTA
104096 AAAATTA-TA
1 AAAATTATTA
* *
104105 TAAATTATGA
1 AAAATTATTA
* *
104115 AAAA-AATAA
1 AAAATTATTA
*
104124 AAAATT-GTA
1 AAAATTATTA
104133 AAAATT-TTGA
1 AAAATTATT-A
104143 AAAATGT-TT-
1 AAAAT-TATTA
*
104152 AAAA-TATTG
1 AAAATTATTA
104161 AAAATTATT-
1 AAAATTATTA
*
104170 AAAACTATTA
1 AAAATTATTA
104180 AAAAT
1 AAAAT
104185 GGAAAAGTGC
Statistics
Matches: 133, Mismatches: 34, Indels: 32
0.67 0.17 0.16
Matches are distributed among these distances:
7 1 0.01
8 2 0.02
9 44 0.33
10 59 0.44
11 19 0.14
12 3 0.02
13 5 0.04
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (10 bp):
AAAATTATTA
Found at i:104054 original size:33 final size:33
Alignment explanation
Indices: 103993--104055 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
103983 TTTATACTTA
103993 AAATCATTAAAAATTATTAAAATATATAAATAT
1 AAATCATTAAAAATTATTAAAATATATAAATAT
* * *
104026 AAATTATTAAAATATT-TTTAAATTTATAAA
1 AAATCATTAAAA-ATTATTAAAATATATAAA
104056 AGATTGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 23 0.88
34 3 0.12
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (33 bp):
AAATCATTAAAAATTATTAAAATATATAAATAT
Found at i:104137 original size:28 final size:28
Alignment explanation
Indices: 104091--104146 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
104081 ATGTTAACAT
*
104091 AATAAAAAATTATATAAATTATGAAAAA
1 AATAAAAAATTATAAAAATTATGAAAAA
* *
104119 AATAAAAAATTGTAAAAATTTTGAAAAA
1 AATAAAAAATTATAAAAATTATGAAAAA
104147 TGTTTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (28 bp):
AATAAAAAATTATAAAAATTATGAAAAA
Found at i:107533 original size:366 final size:366
Alignment explanation
Indices: 106861--107596 Score: 1157
Period size: 366 Copynumber: 2.0 Consensus size: 366
106851 ACACACGGCT
* * * *
106861 TGTGACACAGGTAGTCACACGGTTGTGTGCCATTTTGAAATGCACTGCAGGGTACTTGAGCAGAC
1 TGTGACACAGGTAGTCACACGGTCGTGTGCCATTTTGAAATGCACTGCAAGGTACATGAGCAAAC
* ** * *
106926 ACACAGGCTGAGACATTGTCGTGTGGCCCATTTATGTATAGACACACGGGCTAGCACACGGTCCC
66 ACACAAGCTGAGACACAGTCATGTGGCCCATTTATGTATAGACACAAGGGCTAGCACACGGTCCC
* *
106991 ACACACAGGCATGTGGTGTAAGTCAGTAGAGTTATTTCTAGTATGAACACTGACGGGCACACGTG
131 ACACACAGGCATATGGTGTAAGTCAGTAGAGTTATTTCTAGTATGAACACGGACGGGCACACGTG
* ** *
107056 ATGTTACACGGTCGTGTGACCCTATTTCGAACGCATACACGGGTGAGCACACGAGCTAGTACACG
196 ATGCTACACGACCATGTGACCCTATTTCGAACGCATACACGGGTGAGCACACGAGCTAGTACACG
* * *
107121 ATCGTGTGCCCCTGTTTCACATAATTTTTCTAATTTTTCTCAAACTTTCTAGTTGTTTTCAATTT
261 ACCGTGTGCCCCTGTTTCACATAATTTTTCTAATTTTTCTCAAACTTTCTAATTATTTTCAATTT
*
107186 AGTTCCTAGTTGTATCTAAGCTATTCTTAAGGGCTTTAATG
326 AGTTCCTAGTTGTATCTAAGCTATTCTTAAGGGCTTTAATA
* * * *
107227 TGTGACATAGGTAGTCACACGGTCGTGTGCCATTTTGAAATGTAGTGCAAGGTACATGGGCAAAC
1 TGTGACACAGGTAGTCACACGGTCGTGTGCCATTTTGAAATGCACTGCAAGGTACATGAGCAAAC
* * * **
107292 ACACAAGCTGGGACACAGTCATGTGGCCTATTTTTGTATAGACACAAGGTTTAGCACACGGTCCC
66 ACACAAGCTGAGACACAGTCATGTGGCCCATTTATGTATAGACACAAGGGCTAGCACACGGTCCC
* * *
107357 ACACACGGGCATATGGTGTAAGTCAGTAGAGTTATTTCTAGTATGAACACGGGCGGGCACATGTG
131 ACACACAGGCATATGGTGTAAGTCAGTAGAGTTATTTCTAGTATGAACACGGACGGGCACACGTG
* *
107422 ATGCTACACGACCATGTGACCCTATTTCGAAGGCATACACGGGTGAGCACACGGGCTAGTACACG
196 ATGCTACACGACCATGTGACCCTATTTCGAACGCATACACGGGTGAGCACACGAGCTAGTACACG
* *
107487 ACCGTGTGCCCTTGTTTCACATAATTTTTCTAATTTTTCTCAAACTTTTTAATTATTTTCAATTT
261 ACCGTGTGCCCCTGTTTCACATAATTTTTCTAATTTTTCTCAAACTTTCTAATTATTTTCAATTT
107552 AGTTCCTAGTTGTATCTAAGCTATTCTTAAGGGCTTTAATA
326 AGTTCCTAGTTGTATCTAAGCTATTCTTAAGGGCTTTAATA
107593 TGTG
1 TGTG
107597 TTTTGAGGGT
Statistics
Matches: 335, Mismatches: 35, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
366 335 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (366 bp):
TGTGACACAGGTAGTCACACGGTCGTGTGCCATTTTGAAATGCACTGCAAGGTACATGAGCAAAC
ACACAAGCTGAGACACAGTCATGTGGCCCATTTATGTATAGACACAAGGGCTAGCACACGGTCCC
ACACACAGGCATATGGTGTAAGTCAGTAGAGTTATTTCTAGTATGAACACGGACGGGCACACGTG
ATGCTACACGACCATGTGACCCTATTTCGAACGCATACACGGGTGAGCACACGAGCTAGTACACG
ACCGTGTGCCCCTGTTTCACATAATTTTTCTAATTTTTCTCAAACTTTCTAATTATTTTCAATTT
AGTTCCTAGTTGTATCTAAGCTATTCTTAAGGGCTTTAATA
Found at i:107920 original size:18 final size:18
Alignment explanation
Indices: 107880--107932 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
107870 TTTTCAGTTG
*
107880 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
*
107898 CAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
107916 TAATTAA--AAATTTATT
1 TAATTAATTAAATTTATT
107932 T
1 T
107933 TTATCCTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 10 0.32
17 7 0.23
18 14 0.45
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:111347 original size:23 final size:23
Alignment explanation
Indices: 111317--111466 Score: 103
Period size: 23 Copynumber: 6.4 Consensus size: 23
111307 ATGCTAGCGC
111317 GCTTACTGTTTCGCA-TTTCGTGT
1 GCTTACTGTTTCGCACTTT-GTGT
111340 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
* ** * *
111363 GCCTACTGATTT-GTGCTATGTGC
1 GCTTACTG-TTTCGCACTTTGTGT
* * *
111386 GCCTACTGATT-GCACTGTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
* * *
111408 GCCTACTGGATT-GCACTGTGTGT
1 GCTTACT-GTTTCGCACTTTGTGT
111431 GCTTACTGTTTCCCCAGCAC-TTGTGT
1 GCTTACTGTTT---C-GCACTTTGTGT
111457 GCTTACTGTT
1 GCTTACTGTT
111467 AAGTACTTCG
Statistics
Matches: 106, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
22 19 0.18
23 62 0.58
24 6 0.06
26 15 0.14
27 4 0.04
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.41
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTTGTGT
Found at i:111438 original size:45 final size:46
Alignment explanation
Indices: 111336--111438 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 46
111326 TTCGCATTTC
* * **
111336 GTGTGCTTACTGTTTCGCACTTTGTGTGCCTACTGATTTGTGCTAT
1 GTGTGCTTACTGATTCGCACTGTGTGTGCCTACTGATTTGCACTAT
* * *
111382 GTGCGCCTACTGATT-GCACTGTGTGTGCCTACTGGA-TTGCACTGT
1 GTGTGCTTACTGATTCGCACTGTGTGTGCCTACT-GATTTGCACTAT
111427 GTGTGCTTACTG
1 GTGTGCTTACTG
111439 TTTCCCCAGC
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
45 33 0.70
46 14 0.30
ACGTcount: A:0.12, C:0.21, G:0.27, T:0.40
Consensus pattern (46 bp):
GTGTGCTTACTGATTCGCACTGTGTGTGCCTACTGATTTGCACTAT
Found at i:114319 original size:6 final size:6
Alignment explanation
Indices: 114308--114354 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
114298 CCGAGTCCCG
*
114308 CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCGCA CCCTC
1 CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTC
114355 GCCTACGAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.15, C:0.68, G:0.02, T:0.15
Consensus pattern (6 bp):
CCCTCA
Found at i:116465 original size:20 final size:20
Alignment explanation
Indices: 116427--116466 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
116417 ATACATTAAA
*
116427 TAAAAAAATAAATCTTAATT
1 TAAAAAAATAAATCATAATT
116447 TAAAGAAAATAAA-CATAATT
1 TAAA-AAAATAAATCATAATT
116467 ATCTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (20 bp):
TAAAAAAATAAATCATAATT
Found at i:117504 original size:29 final size:31
Alignment explanation
Indices: 117472--117541 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
117462 TTTAATGTGT
117472 AATTGTATACATG-AACTTTAATT-TGGTGC
1 AATTGTATACATGAAACTTTAATTATGGTGC
* ** * *
117501 AATTATACCCGTGAAACTTTAATTATGGTTC
1 AATTGTATACATGAAACTTTAATTATGGTGC
*
117532 AAATGTATAC
1 AATTGTATAC
117542 TTAAAATTTT
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
29 9 0.30
30 10 0.33
31 11 0.37
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (31 bp):
AATTGTATACATGAAACTTTAATTATGGTGC
Found at i:117847 original size:14 final size:14
Alignment explanation
Indices: 117802--117848 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
117792 TTTTAAAATA
117802 ATTAAAATTATT-T
1 ATTAAAATTATTAT
* *
117815 TTTAAAATATAAATAT
1 ATTAAAAT-T-ATTAT
117831 ATTAAAATTATTAT
1 ATTAAAATTATTAT
117845 ATTA
1 ATTA
117849 TTTTTTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
13 7 0.26
14 9 0.33
15 3 0.11
16 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTAAAATTATTAT
Found at i:117872 original size:38 final size:38
Alignment explanation
Indices: 117785--117865 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 38
117775 TGTCACGTCA
* *
117785 ATAAATGTTTTAAAATAATTAAAATTATTTTTTAAAAT
1 ATAAATATATTAAAATAATTAAAATTATTTTTTAAAAT
* * *
117823 ATAAATATATTAAAATTATT-ATATTATTTTTTTGAAAT
1 ATAAATATATTAAAATAATTAAAATTA-TTTTTTAAAAT
117861 ATAAA
1 ATAAA
117866 ATTATTATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 5 0.14
38 32 0.86
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (38 bp):
ATAAATATATTAAAATAATTAAAATTATTTTTTAAAAT
Found at i:118385 original size:28 final size:29
Alignment explanation
Indices: 118329--118386 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
118319 CAATTTGATC
* * * *
118329 AAAAAAAAATTAAGTGTGAAAGTGCTCCA
1 AAAAAAAAATTAAGAGTCAAAATGATCCA
118358 AAAAAAAAATTAAGAGTCAAAAT-ATCCA
1 AAAAAAAAATTAAGAGTCAAAATGATCCA
118386 A
1 A
118387 CACTTAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.19
Consensus pattern (29 bp):
AAAAAAAAATTAAGAGTCAAAATGATCCA
Found at i:123452 original size:27 final size:28
Alignment explanation
Indices: 123422--123479 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
123412 TTTTATGTTC
* *
123422 TTTTGATTTTCCTTTT-TTTTT-CTTTAT
1 TTTTGATTCT-CTTTTGTTTTTCCTCTAT
*
123449 TTTTTATTCTCTTTTGTTTTTCCTCTAT
1 TTTTGATTCTCTTTTGTTTTTCCTCTAT
123477 TTT
1 TTT
123480 CCTCTCTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 5 0.19
27 13 0.50
28 8 0.31
ACGTcount: A:0.07, C:0.14, G:0.03, T:0.76
Consensus pattern (28 bp):
TTTTGATTCTCTTTTGTTTTTCCTCTAT
Found at i:132521 original size:12 final size:12
Alignment explanation
Indices: 132504--132530 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
132494 TTCGTCGTAG
132504 TCATCATCATAA
1 TCATCATCATAA
132516 TCATCATCATAA
1 TCATCATCATAA
132528 TCA
1 TCA
132531 AGTCCATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.33
Consensus pattern (12 bp):
TCATCATCATAA
Found at i:134239 original size:25 final size:23
Alignment explanation
Indices: 134205--134260 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 23
134195 ATGTGTTGTA
134205 ATATAATTATATATTATAAAAAATG
1 ATATAATTATATA-TA-AAAAAATG
* *
134230 ATATACTTATTTATAAAAAAAT-
1 ATATAATTATATATAAAAAAATG
134252 ACTATAATT
1 A-TATAATT
134261 TATTTTCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 1 0.04
23 13 0.48
24 2 0.07
25 11 0.41
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATAATTATATATAAAAAAATG
Found at i:134957 original size:30 final size:29
Alignment explanation
Indices: 134907--134988 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 29
134897 TTTTGGATGA
*
134907 CTTAAAAGTTGGAGAATTTTTTTAGGCCC
1 CTTAAAAGTTGGAAAATTTTTTTAGGCCC
* *
134936 CTTAAAAGTTGGGAAAATTTTTTTTTGGGCCT
1 CTTAAAAGTT-GGAAAA--TTTTTTTAGGCCC
134968 CTTAAAAGTT-GAAAATTTTTT
1 CTTAAAAGTTGGAAAATTTTTT
134989 GGACCTCTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
28 6 0.13
29 10 0.21
30 10 0.21
32 21 0.45
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (29 bp):
CTTAAAAGTTGGAAAATTTTTTTAGGCCC
Found at i:144985 original size:17 final size:15
Alignment explanation
Indices: 144963--145010 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 15
144953 CAAAAATTTC
144963 TTCCTTCTCTCCTTTTT
1 TTCCTTCT-T-CTTTTT
144980 TTCCTTCTTCTTTTT
1 TTCCTTCTTCTTTTT
144995 TTCTCTTCCTTCTTTT
1 TTC-CTT-CTTCTTTT
145011 CTTGTTTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.31
16 4 0.14
17 16 0.55
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TTCCTTCTTCTTTTT
Found at i:144995 original size:14 final size:17
Alignment explanation
Indices: 144974--145010 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
144964 TCCTTCTCTC
144974 CTTTTTTTC-CTT-CTT
1 CTTTTTTTCTCTTCCTT
144989 CTTTTTTTCTCTTCCTT
1 CTTTTTTTCTCTTCCTT
145006 CTTTT
1 CTTTT
145011 CTTGTTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 9 0.45
16 3 0.15
17 8 0.40
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (17 bp):
CTTTTTTTCTCTTCCTT
Found at i:145011 original size:14 final size:14
Alignment explanation
Indices: 144967--145012 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
144957 AATTTCTTCC
144967 TTCTC-TCCTTTTT
1 TTCTCTTCCTTTTT
144980 TTC-CTTCTTCTTTTT
1 TTCTCTTC--CTTTTT
*
144995 TTCTCTTCCTTCTT
1 TTCTCTTCCTTTTT
145009 TTCT
1 TTCT
145013 TGTTTCTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 1 0.04
13 5 0.18
14 9 0.32
15 9 0.32
16 4 0.14
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCTCTTCCTTTTT
Found at i:145020 original size:21 final size:20
Alignment explanation
Indices: 144980--145025 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 20
144970 TCTCCTTTTT
144980 TTCCTTCTTCTTTTTTTCTC
1 TTCCTTCTTCTTTTTTTCTC
145000 TTCCTTCTT-TTCTTGTTTCTC
1 TTCCTTCTTCTT-TT-TTTCTC
145021 TTCCT
1 TTCCT
145026 CAATATCCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.08
20 11 0.46
21 11 0.46
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.67
Consensus pattern (20 bp):
TTCCTTCTTCTTTTTTTCTC
Found at i:145023 original size:17 final size:18
Alignment explanation
Indices: 144959--145023 Score: 52
Period size: 17 Copynumber: 3.9 Consensus size: 18
144949 GTGACAAAAA
*
144959 TTTCTTC-CTTCTCTCCT
1 TTTCTTCTCTTCTCTTCT
*
144976 TTT-TT-TCCT-TCTTCT
1 TTTCTTCTCTTCTCTTCT
*
144991 TTTTTTCTCTTC-CTTCT
1 TTTCTTCTCTTCTCTTCT
*
145008 TTTCTTGT-TTCTCTTC
1 TTTCTTCTCTTCTCTTC
145024 CTCAATATCC
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
15 8 0.21
16 9 0.24
17 21 0.55
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTCTTCTCTTCTCTTCT
Found at i:150331 original size:32 final size:31
Alignment explanation
Indices: 150295--150359 Score: 121
Period size: 32 Copynumber: 2.1 Consensus size: 31
150285 TCTTTAGCTT
150295 ACTTAGTTTTATCATTATTTGATTGCTTATAC
1 ACTTAGTTTTATCATTATTTGATTGC-TATAC
150327 ACTTAGTTTTATCATTATTTGATTGCTATAC
1 ACTTAGTTTTATCATTATTTGATTGCTATAC
150358 AC
1 AC
150360 ATATAGTACG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 7 0.21
32 26 0.79
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (31 bp):
ACTTAGTTTTATCATTATTTGATTGCTATAC
Found at i:150773 original size:6 final size:6
Alignment explanation
Indices: 150764--150789 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
150754 ATTCCAATCA
150764 CACTTT CACTTT CACTTT CACTTT CA
1 CACTTT CACTTT CACTTT CACTTT CA
150790 ATTTTGATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.00, T:0.46
Consensus pattern (6 bp):
CACTTT
Found at i:152229 original size:31 final size:31
Alignment explanation
Indices: 152191--152253 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
152181 TATTTTCATA
152191 TTTTATCTAATTTTATTTCTCTCAAATTCTC
1 TTTTATCTAATTTTATTTCTCTCAAATTCTC
152222 TTTTATCTAATTTTATTTCTCTCAAATTCTC
1 TTTTATCTAATTTTATTTCTCTCAAATTCTC
152253 T
1 T
152254 AGATTTCTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTTATCTAATTTTATTTCTCTCAAATTCTC
Found at i:159621 original size:26 final size:26
Alignment explanation
Indices: 159592--159646 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
159582 GCTACAACTT
159592 TGAACAAGTTCCTGCAACGACAATTC
1 TGAACAAGTTCCTGCAACGACAATTC
* * *
159618 TGAACAAGTTCTTGCAGCGATAATTC
1 TGAACAAGTTCCTGCAACGACAATTC
159644 TGA
1 TGA
159647 GCGCAATGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (26 bp):
TGAACAAGTTCCTGCAACGACAATTC
Found at i:161300 original size:24 final size:24
Alignment explanation
Indices: 161273--161343 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
161263 CCCAGACAAA
*
161273 TTAGCTCTCACGAGCCCA-AGATGG
1 TTAGCTCTTACGAGCCCAGA-ATGG
*
161297 TTAGCTATTACGAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
* *
161321 TTAGCTCTTACGAGTCCATAATG
1 TTAGCTCTTACGAGCCCAGAATG
161344 CTTAACCAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
24 40 0.98
25 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.27
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATGG
Found at i:163665 original size:34 final size:34
Alignment explanation
Indices: 163622--163691 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
163612 TGTATTGCAA
163622 AAATCTTTTTCAACTTTCTTCTTCTGTTGGAATT
1 AAATCTTTTTCAACTTTCTTCTTCTGTTGGAATT
163656 AAATCTTTTTCAACTTTCTTCTTCTGTTGGAATT
1 AAATCTTTTTCAACTTTCTTCTTCTGTTGGAATT
163690 AA
1 AA
163692 TTCCATGGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.09, T:0.51
Consensus pattern (34 bp):
AAATCTTTTTCAACTTTCTTCTTCTGTTGGAATT
Found at i:164558 original size:8 final size:8
Alignment explanation
Indices: 164547--164597 Score: 75
Period size: 8 Copynumber: 6.1 Consensus size: 8
164537 CATTACATAT
164547 ATATACAC
1 ATATACAC
*
164555 ATATATAC
1 ATATACAC
164563 ATATACACAC
1 ATAT--ACAC
164573 ATATACAC
1 ATATACAC
164581 ATATACAC
1 ATATACAC
164589 ATATACAC
1 ATATACAC
164597 A
1 A
164598 CATATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
8 32 0.82
10 7 0.18
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (8 bp):
ATATACAC
Found at i:164558 original size:10 final size:10
Alignment explanation
Indices: 164540--164605 Score: 63
Period size: 10 Copynumber: 7.2 Consensus size: 10
164530 ATTCTCACAT
*
164540 TACATATATA
1 TACACATATA
164550 TACACATATA
1 TACACATATA
164560 T--AC--ATA
1 TACACATATA
*
164566 TACACACATA
1 TACACATATA
164576 TACAC--ATA
1 TACACATATA
164584 TACACATATA
1 TACACATATA
*
164594 CACACATATA
1 TACACATATA
164604 TA
1 TA
164606 TATGTGTGTG
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
6 4 0.09
8 12 0.26
10 31 0.66
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (10 bp):
TACACATATA
Found at i:164572 original size:18 final size:18
Alignment explanation
Indices: 164535--164603 Score: 86
Period size: 18 Copynumber: 3.9 Consensus size: 18
164525 AGATCATTCT
* *
164535 CACAT-TACATATATATA
1 CACATATACACATATACA
*
164552 CACATATATACATATACA
1 CACATATACACATATACA
164570 CACATATACACATATACA
1 CACATATACACATATACA
* *
164588 CATATACACACATATA
1 CACATATACACATATA
164604 TATATGTGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
17 5 0.11
18 40 0.89
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (18 bp):
CACATATACACATATACA
Found at i:164625 original size:10 final size:10
Alignment explanation
Indices: 164610--164705 Score: 104
Period size: 10 Copynumber: 10.6 Consensus size: 10
164600 TATATATATG
164610 TGTGTGTATA
1 TGTGTGTATA
164620 TGTGTGTATA
1 TGTGTGTATA
164630 --TGTGTATA
1 TGTGTGTATA
164638 --TGTGTATA
1 TGTGTGTATA
164646 TGTGTGTATA
1 TGTGTGTATA
164656 TGTGTGTATA
1 TGTGTGTATA
164666 ----TGTATA
1 TGTGTGTATA
*
164672 TATGTGTATA
1 TGTGTGTATA
164682 --TGTGTATA
1 TGTGTGTATA
*
164690 TGTGTATATA
1 TGTGTGTATA
164700 TGTGTG
1 TGTGTG
164706 AATACTAAGT
Statistics
Matches: 76, Mismatches: 2, Indels: 16
0.81 0.02 0.17
Matches are distributed among these distances:
6 6 0.08
8 24 0.32
10 46 0.61
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (10 bp):
TGTGTGTATA
Found at i:164629 original size:26 final size:26
Alignment explanation
Indices: 164612--164704 Score: 123
Period size: 26 Copynumber: 3.6 Consensus size: 26
164602 TATATATGTG
*
164612 TGTGTATATGTGTGTATATGTGTATA
1 TGTGTATATGTGTGTATATGTATATA
* *
164638 TGTGTATATGTGTGTATATGTGTGTA
1 TGTGTATATGTGTGTATATGTATATA
* * *
164664 TATGTATATATGTGTATATGTGTATA
1 TGTGTATATGTGTGTATATGTATATA
*
164690 TGTGTATATATGTGT
1 TGTGTATATGTGTGT
164705 GAATACTAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 62 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.51
Consensus pattern (26 bp):
TGTGTATATGTGTGTATATGTATATA
Found at i:164633 original size:8 final size:8
Alignment explanation
Indices: 164612--164698 Score: 111
Period size: 8 Copynumber: 10.1 Consensus size: 8
164602 TATATATGTG
164612 TGTGTATA
1 TGTGTATA
164620 TGTGTGTATA
1 --TGTGTATA
164630 TGTGTATA
1 TGTGTATA
164638 TGTGTATA
1 TGTGTATA
164646 TGTGTGTATA
1 --TGTGTATA
164656 TGTGTGTATA
1 --TGTGTATA
*
164666 TGTATATA
1 TGTGTATA
164674 TGTGTATA
1 TGTGTATA
164682 TGTGTATA
1 TGTGTATA
164690 TGTGTATA
1 TGTGTATA
164698 T
1 T
164699 ATGTGTGAAT
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
8 47 0.64
10 26 0.36
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (8 bp):
TGTGTATA
Found at i:166025 original size:2 final size:2
Alignment explanation
Indices: 166018--166045 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
166008 TTGTATAATA
166018 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
166046 TTCTTTTCCC
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:167062 original size:714 final size:711
Alignment explanation
Indices: 165566--167667 Score: 3267
Period size: 707 Copynumber: 3.0 Consensus size: 711
165556 TTCCTACAGC
* * * * *
165566 GACAATTCTAGGCGCAATTCTAAATAGACTCATGCAACGATATTAGTAGTAAAATATGATAAAAT
1 GACAATTCTGGGCGTAATTCTGAATGGACTCATGCAACGACATTAGTAGTAAAATATGATAAAAT
* *
165631 TAAAGGGAACTTAGCTAAGGTCTATTGAGTTAGAAAATGAAATGAACTAACTTAAAAATTGCTAA
66 TAAAGGCAACTTAGCTAAGGTCCATTGAGTTAGAAAATGAAATGAACTAACTTAAAAATTGCTAA
* * * *
165696 AATGTGTGCTAAGAATGACCAAATGGGAACAACTTAAACAATATGTAGGGAGAAATGCATGGTTC
131 AATGTGTGTTAAGAATGACTAAATGGGAACAACTTAAACAATAAGTAGGGAGAAATTCATGGTTC
* * *
165761 TTTCTGGTACTATCACATCCCCCAAACTTGAGTTTTTACTTATCCTCAAGTAAAATAGAAACTAG
196 TTTCTAGTACTATCACA-CCCCCAAACTTGAGTTTTTACTTGTCCTCAAGTAAAACAGAAACTAG
* * * ** *
165826 CAAGGCTATACAAAAATTTGTCAAGAAAAAAAATCATTCTAGCAACTTGAATCATCTAAAATTCC
260 -AAGACTATACAAAAATTTATCAAGACAAATGATCATTCTAGCAACTTGAATCATCTAAAATTTC
* * * *
165891 AATGAATGAATAACATTCCAATGATAGAATATCGCGCAGACAATTCATAAGCATGAATAACTAAG
324 AATGAATGAATCACATTCCAATGACAGAATATTGCGCCGACAATTCATAAGCATGAATAACTAAG
*
165956 ATTG--------C-AA-C---ATCATGCTTCAAATCCTACATTCTATCTACCAATACAACATTTA
389 ATTGCAACTTATCAAAGCTAGATCATGCTTCAAATCTTACATTCTATCTACCAATACAACATTTA
* *
166008 TTGTATAATAATATATATATATATATATATATATATATTTCTTTTCCCCTTTTTTTTATGTGACT
454 TTG-----T-ATA-ATA-ATATATACATATATCT-T-TTTCTTTT-CCC-TTTTTTTATGTGACT
* *
166073 GAGGGATGTCGTTGCATTACTATACCCTTTGTTCTTAAGAAGTAATGATGGAGTGCAACAAACCC
507 GAGGGATGACGTTGCATTACTATACCCTTTGTTCTTGAGAAGTAATGATGGAGTGCAACAAA-CC
* * *
166138 CTAGGGACTATGTAA-T-TGCATCGACACACACTCTTGCAGCGACAGCCTTTGGCTAGATTCATT
571 CAAGGGAGTACGTAATTATGCA--GACACACACTCTTGCAGCGACAGCCTTTGGCTAGATTCATT
*
166201 TTTCTAACACTTGCATTGGAGTGTTCCCCCTTAAACAGTTCACAATTCTGGGCGGAATTCTGGAC
634 TTTCTAACACTTGCATTGGAGTGTTCCCCCTTAAACAGTTCACAATTCTGGGCGCAATTCTGGAC
166266 ATCATCATGCAGT
699 ATCATCATGCAGT
166279 GACAATTCTGGGCGTAATTCTGAATGGACTCATGCAACGACATTAGTAGTAAAATATGATAAAAT
1 GACAATTCTGGGCGTAATTCTGAATGGACTCATGCAACGACATTAGTAGTAAAATATGATAAAAT
166344 TAAAGGCAACTTAGCTAAGGTCCATTGAGTTAGAAAATGAAATGAACTAACTTAAAAATTGCTAA
66 TAAAGGCAACTTAGCTAAGGTCCATTGAGTTAGAAAATGAAATGAACTAACTTAAAAATTGCTAA
*
166409 AATGTGTGTTAAGAATGACTAAATGGGAACAAATTAAACAATAAGTAGGGAGAAATTCATGGTTC
131 AATGTGTGTTAAGAATGACTAAATGGGAACAACTTAAACAATAAGTAGGGAGAAATTCATGGTTC
166474 TTTCTAGTACTATCACACCCCCAAACTTGAGTTTTTACTTGTCCTCAAGTAAAACAGAAACTAGT
196 TTTCTAGTACTATCACACCCCCAAACTTGAGTTTTTACTTGTCCTCAAGTAAAACAGAAACTAG-
166539 AAGACTATACAAAAATTTATCAAGACAAATGATCATTCTAGCAACTTGAATCATCTAAAATTTCA
260 AAGACTATACAAAAATTTATCAAGACAAATGATCATTCTAGCAACTTGAATCATCTAAAATTTCA
166604 ATGAATGAATCACATTCCAATGACAGAATATTGCGCCGACAATTCATAAGCATGAATAACTAAGA
325 ATGAATGAATCACATTCCAATGACAGAATATTGCGCCGACAATTCATAAGCATGAATAACTAAGA
166669 TTGCAACTTAATCAAAGCTAGAATCATGCTTCAAATCTTACATTCTATCTACCAATACAACATTT
390 TTGCAACTT-ATCAAAGCTAG-ATCATGCTTCAAATCTTACATTCTATCTACCAATACAACATTT
*
166734 ATTGTATAATAATATATACATATATCTTTTTCTTTTCCCTTTTTTTATGTGATTGAGGGATGACG
453 ATTGTATAATAATATATACATATATCTTTTTCTTTTCCCTTTTTTTATGTGACTGAGGGATGACG
* *
166799 TTGCATTACTATACTCTTTGTTCTTGAGAAGTAACGATGGAGTGCAACAAACCCAAGGGAGTACG
518 TTGCATTACTATACCCTTTGTTCTTGAGAAGTAATGATGGAGTGCAACAAACCCAAGGGAGTACG
* * * *
166864 TAATTATGCAGACACACACTATTGCAGCGATAGCCATTGACTAGATTCATTTTTCTAACACTTGC
583 TAATTATGCAGACACACACTCTTGCAGCGACAGCCTTTGGCTAGATTCATTTTTCTAACACTTGC
* * *
166929 ATTGGAGTGTTCCCTCTTAAACAATTCACAATTCTGGGCGCAATTTTGGACATCATCATGCAGT
648 ATTGGAGTGTTCCCCCTTAAACAGTTCACAATTCTGGGCGCAATTCTGGACATCATCATGCAGT
* * *
166993 GACAATTTTGGGTGTAATTCTGAATGGACTCATGCAGCGACATTAGTAGTAAAATATGATAAAAT
1 GACAATTCTGGGCGTAATTCTGAATGGACTCATGCAACGACATTAGTAGTAAAATATGATAAAAT
*
167058 TAAAGGCAACTTAGCTAAGGTCCATTGAGTTAGCAAATGAAATGAACTAACTTAAAAATTGCTAA
66 TAAAGGCAACTTAGCTAAGGTCCATTGAGTTAGAAAATGAAATGAACTAACTTAAAAATTGCTAA
*
167123 AATGTGTGTTAAGAAAGACTAAATGGGAACAACTTAAACAATAAGTAGGGAGAAATTCATGGTTC
131 AATGTGTGTTAAGAATGACTAAATGGGAACAACTTAAACAATAAGTAGGGAGAAATTCATGGTTC
* * *
167188 TTTCTAGTACTGTCACATCCCCAAACTTGAGTTTTTTACTAGTCCTCAAGTAAAACAG-----A-
196 TTTCTAGTACTATCACACCCCCAAACTTGAG-TTTTTACTTGTCCTCAAGTAAAACAGAAACTAG
167247 AA-ACTATACAAAAATTTATCAAGACAAATGATCATTCTAGCAACTTGAATCATCTAAAATTTCA
260 AAGACTATACAAAAATTTATCAAGACAAATGATCATTCTAGCAACTTGAATCATCTAAAATTTCA
* *
167311 ATGAATGAATCATATTCCAATGACAGAATATTGCACCGACAATTCATAAGCATGAATAACTAAGA
325 ATGAATGAATCACATTCCAATGACAGAATATTGCGCCGACAATTCATAAGCATGAATAACTAAGA
167376 TTGCAACTTCATCAAAGCTAGCATCATGCTTCAAATCTTACATTCTATCTACCAATACAACATTT
390 TTGCAACTT-ATCAAAGCTAG-ATCATGCTTCAAATCTTACATTCTATCTACCAATACAACATTT
* *
167441 ATTATACAATAATATATACATATATCTTTTTCTTTTCCCTTTTTTTATGTGACTGAGGGATGACG
453 ATTGTATAATAATATATACATATATCTTTTTCTTTTCCCTTTTTTTATGTGACTGAGGGATGACG
* * * *
167506 TTGCATTATTATACCCTTTGTTCTTGAGAAGTATTGATAGAGTGCAACAATCCCAAGGGAGTACG
518 TTGCATTACTATACCCTTTGTTCTTGAGAAGTAATGATGGAGTGCAACAAACCCAAGGGAGTACG
* * *
167571 TAATTATGTAGACACACACTCTTGCAGCGACAGGCTTTGGCTAGATTCATTTTTCTAACATTTGC
583 TAATTATGCAGACACACACTCTTGCAGCGACAGCCTTTGGCTAGATTCATTTTTCTAACACTTGC
*
167636 ATTGGAGTGTACCCCCTTAAACAGTTCACAAT
648 ATTGGAGTGTTCCCCCTTAAACAGTTCACAAT
167668 ACACCCACAT
Statistics
Matches: 1294, Mismatches: 77, Indels: 42
0.92 0.05 0.03
Matches are distributed among these distances:
707 396 0.31
708 2 0.00
710 1 0.00
712 168 0.13
713 199 0.15
714 343 0.27
715 98 0.08
716 7 0.01
717 8 0.01
718 1 0.00
719 14 0.01
720 3 0.00
721 4 0.00
722 3 0.00
723 1 0.00
727 46 0.04
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (711 bp):
GACAATTCTGGGCGTAATTCTGAATGGACTCATGCAACGACATTAGTAGTAAAATATGATAAAAT
TAAAGGCAACTTAGCTAAGGTCCATTGAGTTAGAAAATGAAATGAACTAACTTAAAAATTGCTAA
AATGTGTGTTAAGAATGACTAAATGGGAACAACTTAAACAATAAGTAGGGAGAAATTCATGGTTC
TTTCTAGTACTATCACACCCCCAAACTTGAGTTTTTACTTGTCCTCAAGTAAAACAGAAACTAGA
AGACTATACAAAAATTTATCAAGACAAATGATCATTCTAGCAACTTGAATCATCTAAAATTTCAA
TGAATGAATCACATTCCAATGACAGAATATTGCGCCGACAATTCATAAGCATGAATAACTAAGAT
TGCAACTTATCAAAGCTAGATCATGCTTCAAATCTTACATTCTATCTACCAATACAACATTTATT
GTATAATAATATATACATATATCTTTTTCTTTTCCCTTTTTTTATGTGACTGAGGGATGACGTTG
CATTACTATACCCTTTGTTCTTGAGAAGTAATGATGGAGTGCAACAAACCCAAGGGAGTACGTAA
TTATGCAGACACACACTCTTGCAGCGACAGCCTTTGGCTAGATTCATTTTTCTAACACTTGCATT
GGAGTGTTCCCCCTTAAACAGTTCACAATTCTGGGCGCAATTCTGGACATCATCATGCAGT
Found at i:168910 original size:38 final size:38
Alignment explanation
Indices: 168868--168941 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
168858 GGTTTTAGAA
* *
168868 GATGATGGATACAGGAGACTCAAGGAGACTAAAAAACT
1 GATGATGGACAAAGGAGACTCAAGGAGACTAAAAAACT
*
168906 GATGATGGACAAAGGAGACTCAAGGAGGCTAAAAAA
1 GATGATGGACAAAGGAGACTCAAGGAGACTAAAAAA
168942 TTTCTTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.46, C:0.12, G:0.28, T:0.14
Consensus pattern (38 bp):
GATGATGGACAAAGGAGACTCAAGGAGACTAAAAAACT
Found at i:172322 original size:26 final size:26
Alignment explanation
Indices: 172288--172345 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
172278 ACACAACAAT
* *
172288 AATTTTGAACAAGTTCATGTAGCGAC
1 AATTCTGAACAAGTTCATGCAGCGAC
* *
172314 AATTCTGAACAAGTTCTTGCAGCGAT
1 AATTCTGAACAAGTTCATGCAGCGAC
172340 AATTCT
1 AATTCT
172346 AGTCGCAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (26 bp):
AATTCTGAACAAGTTCATGCAGCGAC
Found at i:172776 original size:2 final size:2
Alignment explanation
Indices: 172769--172800 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
172759 TTGTACAGTA
172769 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
172801 TTATGTGACT
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:173399 original size:17 final size:17
Alignment explanation
Indices: 173357--173401 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
173347 CATTAATTTA
*
173357 CAATGACAAATGGAAATG
1 CAATGAC-AATGCAAATG
*
173375 CAAAGACAATGCAAATG
1 CAATGACAATGCAAATG
*
173392 CAGTGACAAT
1 CAATGACAAT
173402 TATAATGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.16
Consensus pattern (17 bp):
CAATGACAATGCAAATG
Found at i:173490 original size:6 final size:6
Alignment explanation
Indices: 173479--173509 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
173469 GTATGCATGA
173479 AAAACT AAAACT AAAACT AAAA-T AAAACT AA
1 AAAACT AAAACT AAAACT AAAACT AAAACT AA
173510 CTCAATTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAACT
Found at i:183557 original size:26 final size:26
Alignment explanation
Indices: 183519--183581 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
183509 GCTTATACAG
*
183519 CGACAACTT-TGAACAAGTTCTTGTAA
1 CGACAA-TTCTGAACAAGTTCTTGCAA
*
183545 CGACAATTCTGAACAAGTTCTTGCAG
1 CGACAATTCTGAACAAGTTCTTGCAA
*
183571 TGACAATTCTG
1 CGACAATTCTG
183582 GGCGTAATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 2 0.06
26 31 0.94
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (26 bp):
CGACAATTCTGAACAAGTTCTTGCAA
Found at i:185263 original size:24 final size:24
Alignment explanation
Indices: 185232--185287 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
185222 CCAGACAAAA
185232 TTAGCTCTCACG-AGCCCA-AGATGG
1 TTAGCTCTCACGCA-CCCAGA-ATGG
*
185256 TTAGCTCTTACGCACCCAGAATGG
1 TTAGCTCTCACGCACCCAGAATGG
185280 TTAGCTCT
1 TTAGCTCT
185288 TATGAGTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (24 bp):
TTAGCTCTCACGCACCCAGAATGG
Found at i:196262 original size:22 final size:20
Alignment explanation
Indices: 196236--196284 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 20
196226 ATTTTTAAAA
196236 TTTTAACTTTTTTAATATATAT
1 TTTTAA-TTTTTTAATATAT-T
*
196258 TTTTAGATTTTTTTATATATT
1 TTTTA-ATTTTTTAATATATT
196279 TTTTAA
1 TTTTAA
196285 AAATATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 6 0.24
22 17 0.68
23 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTAATTTTTTAATATATT
Found at i:196317 original size:20 final size:21
Alignment explanation
Indices: 196278--196338 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
196268 TTTTATATAT
*
196278 TTTTTAAAAATATAATTTTGAAA
1 TTTTTGAAAAT-T-ATTTTGAAA
196301 TTTTT-ATAAA-TATTTTG-AA
1 TTTTTGA-AAATTATTTTGAAA
196320 TTTTTGAAAATTATTTTGA
1 TTTTTGAAAATTATTTTGA
196339 TTTTTTTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
19 10 0.29
20 14 0.41
21 1 0.03
22 1 0.03
23 8 0.24
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTTTGAAAATTATTTTGAAA
Found at i:196323 original size:19 final size:20
Alignment explanation
Indices: 196278--196343 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 20
196268 TTTTATATAT
*
196278 TTTTTAAAAATATAATTTTGAAA
1 TTTTTGAAAAT-T-ATTTTG-AA
196301 TTTTT-ATAAA-TATTTTGAA
1 TTTTTGA-AAATTATTTTGAA
196320 TTTTTGAAAATTATTTTG-A
1 TTTTTGAAAATTATTTTGAA
196339 TTTTT
1 TTTTT
196344 TTTGTAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
19 16 0.40
20 14 0.35
21 1 0.03
22 1 0.03
23 8 0.20
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (20 bp):
TTTTTGAAAATTATTTTGAA
Found at i:196336 original size:76 final size:75
Alignment explanation
Indices: 196206--196345 Score: 171
Period size: 77 Copynumber: 1.9 Consensus size: 75
196196 AATTAGCTTC
* * *
196206 AAAAATTATTATTTTAGAAAATTTTTAAAATTTTAACTTTTTTAATATATATTTTTAGATTTTTT
1 AAAAATTATAATTTTAGAAAATTTTTAAAATTTTAACTTTTTGAAAATATA-TTTT-GATTTTTT
196271 TATATATTTTTT
64 TATATATTTTTT
*
196283 AAAAA-TATAATTTT-GAAATTTTTATAAATATTTTGAA-TTTTTGAAAAT-TATTTTGATTTTT
1 AAAAATTATAATTTTAGAAAATTTT-TAAA-ATTTT-AACTTTTTGAAAATATATTTTGATTTTT
196344 TT
63 TT
196346 TGTAATTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
74 9 0.16
75 12 0.21
76 14 0.25
77 19 0.34
78 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (75 bp):
AAAAATTATAATTTTAGAAAATTTTTAAAATTTTAACTTTTTGAAAATATATTTTGATTTTTTTA
TATATTTTTT
Found at i:196436 original size:9 final size:9
Alignment explanation
Indices: 196422--196448 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
196412 ACACCAATCT
196422 GTTATTCGA
1 GTTATTCGA
196431 GTTATTCGA
1 GTTATTCGA
196440 GTTATTCGA
1 GTTATTCGA
196449 ATTGTGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (9 bp):
GTTATTCGA
Found at i:199732 original size:6 final size:6
Alignment explanation
Indices: 199721--199756 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
199711 CGGGAAGGCA
199721 AAGTCG AAGTCG AAGTCG AAGTCG AAGTCG AAGTCG
1 AAGTCG AAGTCG AAGTCG AAGTCG AAGTCG AAGTCG
199757 CCTCCTGAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (6 bp):
AAGTCG
Found at i:203117 original size:16 final size:16
Alignment explanation
Indices: 203096--203132 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
203086 TCTAAAATAA
*
203096 TCTCTTTAGAGAACTT
1 TCTCTTTAGACAACTT
*
203112 TCTCTTTATACAACTT
1 TCTCTTTAGACAACTT
203128 TCTCT
1 TCTCT
203133 CGAATTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.05, T:0.49
Consensus pattern (16 bp):
TCTCTTTAGACAACTT
Found at i:205564 original size:28 final size:28
Alignment explanation
Indices: 205524--205577 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
205514 AATGAGCATC
*
205524 ATGACCTTTGGGTCAACAGGGAGTAAGA
1 ATGACCTTTGGGTCAACAAGGAGTAAGA
205552 ATGACCTTTGGGTCAACAAGGAGTAA
1 ATGACCTTTGGGTCAACAAGGAGTAA
205578 ATCAGATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (28 bp):
ATGACCTTTGGGTCAACAAGGAGTAAGA
Found at i:219459 original size:36 final size:36
Alignment explanation
Indices: 219403--219531 Score: 148
Period size: 36 Copynumber: 3.8 Consensus size: 36
219393 GGCGTCAACT
* * *
219403 TCATGAACTTTAGGTGAACAGGGAGTAAAATGAGCA
1 TCATGACCTTTGGGTCAACAGGGAGTAAAATGAGCA
219439 TCATGACCTTTGGGTCAACAGGGAGTAAAATGAGCA
1 TCATGACCTTTGGGTCAACAGGGAGTAAAATGAGCA
* * *
219475 TCAAGTCCTTTGGGTTAACAGGGAGT---A--AG--
1 TCATGACCTTTGGGTCAACAGGGAGTAAAATGAGCA
219504 -CATGACCTTTGGGTCAACAGGGAGTAAA
1 TCATGACCTTTGGGTCAACAGGGAGTAAA
219532 TCAGATATCG
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
28 22 0.27
31 2 0.02
33 1 0.01
36 56 0.69
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (36 bp):
TCATGACCTTTGGGTCAACAGGGAGTAAAATGAGCA
Found at i:224767 original size:49 final size:48
Alignment explanation
Indices: 224714--225149 Score: 158
Period size: 49 Copynumber: 9.0 Consensus size: 48
224704 TCATCCCTTC
* * *
224714 AGGGTGTAAGATTCACCATTACAACTTCAATCTTTCTCATCTTATCTAT
1 AGGGTATAAGATTCACCATTACAGCCTCAATCTTTC-CATCTTATCTAT
* ** * ** * * ** *
224763 AGGGTATAAGGTTTTCCGTTATGGCCTCAACCTTTCCCTTCACATCTCT
1 AGGGTATAAGATTCACCATTACAGCCTCAATCTTT-CCATCTTATCTAT
* *
224812 AGGGTATAAGATTCACCATTGCAGCCTCAATCTTTCCATCTTATCTCT
1 AGGGTATAAGATTCACCATTACAGCCTCAATCTTTCCATCTTATCTAT
* * * * * * * ** * * **
224860 AAGGTACAAGGTTCGCCGTTGCGGCCTTGACCTTTCCCTTCACATCTCA-
1 AGGGTATAAGATTCACCATTACAGCCTCAATCTTT-CCATCTTATCT-AT
* * * * * *
224909 AGGGTATAAGATTTACTATTGCAACCTCAATCTTTTCATCTTATCTCT
1 AGGGTATAAGATTCACCATTACAGCCTCAATCTTTCCATCTTATCTAT
** * * * * * * * **
224957 AAAGTATAAGGTTCACCGTTGCGGCCTCGACCTTTCCCTTCACATCTCA-
1 AGGGTATAAGATTCACCATTACAGCCTCAATCTTT-CCATCTTATCT-AT
** * * * *
225006 AGGGTATAAGATTTGCTATTGCAGCCTCAATCTTTTCATCTTATCTCTT
1 AGGGTATAAGATTCACCATTACAGCCTCAATCTTTCCATCTTATCT-AT
** ** * * * * ** *
225055 AAAGTATAAGATTCGTCATTGCGGCCTCGAAAT-TTCCCTTCAGATCTTT
1 AGGGTATAAGATTCACCATTACAGCCTC--AATCTTTCCATCTTATCTAT
**** *
225104 AGGGTATAAGATTTGGTATTGCAGCCTCAATCTTTCCATCTTATCT
1 AGGGTATAAGATTCACCATTACAGCCTCAATCTTTCCATCTTATCT
225150 CTAAGGTTCA
Statistics
Matches: 271, Mismatches: 106, Indels: 21
0.68 0.27 0.05
Matches are distributed among these distances:
47 3 0.01
48 86 0.32
49 169 0.62
50 10 0.04
51 3 0.01
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (48 bp):
AGGGTATAAGATTCACCATTACAGCCTCAATCTTTCCATCTTATCTAT
Found at i:224893 original size:97 final size:97
Alignment explanation
Indices: 224740--225176 Score: 561
Period size: 97 Copynumber: 4.5 Consensus size: 97
224730 CATTACAACT
* * ** ** *
224740 TCAATCTTTCTCATCTTATCTATAGGGTATAAGGTTTTCCGTTATGGCCTCAACCTTTCCCTTCA
1 TCAATCTTTC-CATCTTATCTCTAAGGTATAAGGTTCGCCGTTGCGGCCTCGACCTTTCCCTTCA
* * *
224805 CATCTCTAGGGTATAAGATTCACCATTGCAGCC
65 CATCTCAAGGGTATAAGATTTACTATTGCAGCC
* *
224838 TCAATCTTTCCATCTTATCTCTAAGGTACAAGGTTCGCCGTTGCGGCCTTGACCTTTCCCTTCAC
1 TCAATCTTTCCATCTTATCTCTAAGGTATAAGGTTCGCCGTTGCGGCCTCGACCTTTCCCTTCAC
*
224903 ATCTCAAGGGTATAAGATTTACTATTGCAACC
66 ATCTCAAGGGTATAAGATTTACTATTGCAGCC
* * *
224935 TCAATCTTTTCATCTTATCTCTAAAGTATAAGGTTCACCGTTGCGGCCTCGACCTTTCCCTTCAC
1 TCAATCTTTCCATCTTATCTCTAAGGTATAAGGTTCGCCGTTGCGGCCTCGACCTTTCCCTTCAC
*
225000 ATCTCAAGGGTATAAGATTTGCTATTGCAGCC
66 ATCTCAAGGGTATAAGATTTACTATTGCAGCC
* * * * * **
225032 TCAATCTTTTCATCTTATCTCTTAAAGTATAAGATTCGTCATTGCGGCCTCGAAATTTCCCTTCA
1 TCAATCTTTCCATCTTATCTC-TAAGGTATAAGGTTCGCCGTTGCGGCCTCGACCTTTCCCTTCA
* ** **
225097 GATCTTTAGGGTATAAGATTTGGTATTGCAGCC
65 CATCTCAAGGGTATAAGATTTACTATTGCAGCC
* *
225130 TCAATCTTTCCATCTTATCTCTAAGGT-TCAAGATTCGCCGTTACGGC
1 TCAATCTTTCCATCTTATCTCTAAGGTAT-AAGGTTCGCCGTTGCGGC
225177 TTCAAATTTT
Statistics
Matches: 302, Mismatches: 35, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
96 1 0.00
97 205 0.68
98 96 0.32
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (97 bp):
TCAATCTTTCCATCTTATCTCTAAGGTATAAGGTTCGCCGTTGCGGCCTCGACCTTTCCCTTCAC
ATCTCAAGGGTATAAGATTTACTATTGCAGCC
Found at i:225236 original size:97 final size:98
Alignment explanation
Indices: 225146--225478 Score: 351
Period size: 97 Copynumber: 3.4 Consensus size: 98
225136 TTTCCATCTT
* * * * *
225146 ATCTCTAAGGTTCAAGATTCGCCGTTACGGCTTCAAAT-TTTACCATCACGTCTCTAAGGTACAG
1 ATCTCTATGGTACAAGATTCGCCGTTGCGGCTTCAAATCTTTACCATCACGGCTCTAAGGTACAA
*
225210 GATTT-GTCGTTGTGGCTTCAACCTTTCCCTCGC
66 G-TTTCGCCGTTGTGGCTTCAACCTTTCCCTCGC
* * *
225243 ATCTTTATGGTACAAGATTCACCGTTGCGGCTTC-AATCTTTCCCATCACGGCTCTAAGGTACAA
1 ATCTCTATGGTACAAGATTCGCCGTTGCGGCTTCAAATCTTTACCATCACGGCTCTAAGGTACAA
225307 GTTTCGCCGTTGTGGCTTCAACCTTTCCCTCGC
66 GTTTCGCCGTTGTGGCTTCAACCTTTCCCTCGC
* * * * *
225340 ATCTCCATGGTACAAGATTCGCCATTGCGGCTTC-AATCTTT-CTCATTATGCCTCTAAGGTACA
1 ATCTCTATGGTACAAGATTCGCCGTTGCGGCTTCAAATCTTTAC-CATCACGGCTCTAAGGTAC-
** **
225403 AAG-TTCATCGTTACGGCTTCAACCTTTCCCTC-C
64 AAGTTTCGCCGTTGTGGCTTCAACCTTTCCCTCGC
* * * *
225436 ATATCTTTAAGGCATCAA-ATTCACCGTTGCGGCTTC-AATCTTT
1 --ATCTCTATGGTA-CAAGATTCGCCGTTGCGGCTTCAAATCTTT
225479 CCCTTCAAAC
Statistics
Matches: 203, Mismatches: 26, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
96 8 0.04
97 158 0.78
98 34 0.17
99 3 0.01
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (98 bp):
ATCTCTATGGTACAAGATTCGCCGTTGCGGCTTCAAATCTTTACCATCACGGCTCTAAGGTACAA
GTTTCGCCGTTGTGGCTTCAACCTTTCCCTCGC
Found at i:225479 original size:49 final size:48
Alignment explanation
Indices: 224789--225482 Score: 235
Period size: 49 Copynumber: 14.3 Consensus size: 48
224779 CGTTATGGCC
* * * * * *
224789 TCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTCACCATTGCAGCC
1 TCAACCTTTCCCTCCA-ATCTCTAAGGTACAAGATTCACCGTTGCGGCT
* * ** * *
224838 TCAATCTTTCCATCTTATCTCTAAGGTACAAGGTTCGCCGTTGCGGCCT
1 TCAACCTTTCCCTCCAATCTCTAAGGTACAAGATTCACCGTTGCGG-CT
* * * * ** ** *
224887 T-GACCTTTCCCTTCACATCTC-AAGGGTATAAGATTTACTATTGCAACC
1 TCAACCTTTCCCTCCA-ATCTCTAA-GGTACAAGATTCACCGTTGCGGCT
* * * ** * * * *
224935 TCAATCTTTTCATCTTATCTCTAAAGTATAAGGTTCACCGTTGCGGCC
1 TCAACCTTTCCCTCCAATCTCTAAGGTACAAGATTCACCGTTGCGGCT
* * * ** ** * *
224983 TCGACCTTTCCCTTCACATCTC-AAGGGTATAAGATTTGCTATTGCAGCC
1 TCAACCTTTCCCTCCA-ATCTCTAA-GGTACAAGATTCACCGTTGCGGCT
* * * ** * * ** * *
225032 TCAATCTTTTCATCTTATCTCTTAAAGTATAAGATTCGTCATTGCGGCC
1 TCAACCTTTCCCTCCAATCTC-TAAGGTACAAGATTCACCGTTGCGGCT
* * * * * ***** * *
225081 TCGAA-ATTTCCCTTCAGATCTTTAGGGTATAAGATTTGGTATTGCAGCC
1 TC-AACCTTTCCCTCCA-ATCTCTAAGGTACAAGATTCACCGTTGCGGCT
* * ** * * *
225130 TCAATCTTTCCATCTTATCTCTAAGGTTCAAGATTCGCCGTTACGGCT
1 TCAACCTTTCCCTCCAATCTCTAAGGTACAAGATTCACCGTTGCGGCT
** * * * *** *
225178 TCAAATTTTACCAT-CACGTCTCTAAGGTACAGGATTTGTCGTTGTGGCT
1 TCAACCTTT-CCCTCCA-ATCTCTAAGGTACAAGATTCACCGTTGCGGCT
* *
225227 TCAACCTTTCCCTCGC-ATCTTTATGGTACAAGATTCACCGTTGCGGCT
1 TCAACCTTTCCCTC-CAATCTCTAAGGTACAAGATTCACCGTTGCGGCT
* ** * * *
225275 TCAATCTTTCCCAT-CACGGCTCTAAGGTACAAGTTTCGCCGTTGTGGCT
1 TCAACCTTTCCC-TCCA-ATCTCTAAGGTACAAGATTCACCGTTGCGGCT
* * * *
225324 TCAACCTTTCCCTCGC-ATCTCCATGGTACAAGATTCGCCATTGCGGCT
1 TCAACCTTTCCCTC-CAATCTCTAAGGTACAAGATTCACCGTTGCGGCT
* * *
225372 TCAATCTTT--CT-CATTATGCCTCTAAGGTACAA-AGTTCATCGTTACGGCT
1 TCAACCTTTCCCTCCA--AT--CTCTAAGGTACAAGA-TTCACCGTTGCGGCT
* *
225421 TCAACCTTTCCCTCCATATCTTTAAGGCATCAA-ATTCACCGTTGCGGCT
1 TCAACCTTTCCCTCCA-ATCTCTAAGGTA-CAAGATTCACCGTTGCGGCT
*
225470 TCAATCTTTCCCT
1 TCAACCTTTCCCT
225483 TCAAACCTGT
Statistics
Matches: 467, Mismatches: 147, Indels: 62
0.69 0.22 0.09
Matches are distributed among these distances:
44 1 0.00
46 2 0.00
47 3 0.01
48 177 0.38
49 263 0.56
50 14 0.03
51 5 0.01
52 2 0.00
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.35
Consensus pattern (48 bp):
TCAACCTTTCCCTCCAATCTCTAAGGTACAAGATTCACCGTTGCGGCT
Found at i:227482 original size:3 final size:3
Alignment explanation
Indices: 227474--227500 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
227464 GGTCATCCAT
227474 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
227501 AATATTGTAG
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:241476 original size:21 final size:21
Alignment explanation
Indices: 241444--241490 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
241434 AGTTGGTACG
* *
241444 AAGGAAAGAAAGAGGAAGCAC
1 AAGGAAAGAAAGAAGAAACAC
241465 AAGGACAA-AAAGAAGAAACAC
1 AAGGA-AAGAAAGAAGAAACAC
241486 AAGGA
1 AAGGA
241491 GGAAGGAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.62, C:0.11, G:0.28, T:0.00
Consensus pattern (21 bp):
AAGGAAAGAAAGAAGAAACAC
Found at i:242243 original size:13 final size:13
Alignment explanation
Indices: 242225--242255 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
242215 ATGTTGAATA
242225 AGAAAAGAAAAAG
1 AGAAAAGAAAAAG
242238 AGAAAAGAAAAAG
1 AGAAAAGAAAAAG
242251 A-AAAA
1 AGAAAA
242256 CTGCTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAAAAG
Found at i:243778 original size:21 final size:20
Alignment explanation
Indices: 243739--243778 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
243729 TTCTTGCATC
*
243739 TCTTTCTACATTTGTTCCAA
1 TCTTTCTACATTTGATCCAA
*
243759 TCTTTCTATCCTTTGATCCA
1 TCTTTCTA-CATTTGATCCA
243779 TTGCATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.17, C:0.28, G:0.05, T:0.50
Consensus pattern (20 bp):
TCTTTCTACATTTGATCCAA
Found at i:244941 original size:3 final size:3
Alignment explanation
Indices: 244933--244967 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
244923 CCAAAATCAA
*
244933 AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
244968 ATAGTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:248400 original size:14 final size:14
Alignment explanation
Indices: 248381--248409 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
248371 GGTAATCGAG
248381 TATGAATCAACACC
1 TATGAATCAACACC
248395 TATGAATCAACACC
1 TATGAATCAACACC
248409 T
1 T
248410 TTTCTATGAT
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:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (14 bp):
TATGAATCAACACC
Found at i:251680 original size:51 final size:51
Alignment explanation
Indices: 251625--251727 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
251615 TATATATGAA
251625 AAGATAAATTAATAATTTTATAATTGAATTGATGTTCAAGTGATCAGTAAC
1 AAGATAAATTAATAATTTTATAATTGAATTGATGTTCAAGTGATCAGTAAC
251676 AAGATAAATTAATAATTTTATAATTGAATTGATGTTCAAGTGATCAGTAAC
1 AAGATAAATTAATAATTTTATAATTGAATTGATGTTCAAGTGATCAGTAAC
251727 A
1 A
251728 TCAAATTAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.37
Consensus pattern (51 bp):
AAGATAAATTAATAATTTTATAATTGAATTGATGTTCAAGTGATCAGTAAC
Found at i:254247 original size:30 final size:30
Alignment explanation
Indices: 254211--254270 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
254201 GCTGGAGTAA
254211 GATAATCCTCAAAACCAGTAGCTTCGTCGC
1 GATAATCCTCAAAACCAGTAGCTTCGTCGC
254241 GATAATCCTCAAAACCAGTAGCTTCGTCGC
1 GATAATCCTCAAAACCAGTAGCTTCGTCGC
254271 CATTTTGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (30 bp):
GATAATCCTCAAAACCAGTAGCTTCGTCGC
Found at i:258460 original size:21 final size:21
Alignment explanation
Indices: 258435--258475 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
258425 CATTGTAAAA
* *
258435 TTTAAAATTTTTATTTTCAAT
1 TTTAAAATTTTAAATTTCAAT
258456 TTTAAAATTTTAAATTTCAA
1 TTTAAAATTTTAAATTTCAA
258476 AACATCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTAAAATTTTAAATTTCAAT
Found at i:264783 original size:49 final size:49
Alignment explanation
Indices: 264721--264817 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
264711 TTCATATAGA
264721 ACTACACTTCTTTTATTTCA-TT-TTGATTAGAATAAGGTGTTTCAACCTT
1 ACTACACTTCTTTTA-TT-AGTTATTGATTAGAATAAGGTGTTTCAACCTT
*
264770 ACTACA-TTACTTTTATTAGTTATTGATTAGAATAAGGTTTTTCAACCT
1 ACTACACTT-CTTTTATTAGTTATTGATTAGAATAAGGTGTTTCAACCT
264818 ATAAATAGAC
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
47 1 0.02
48 6 0.14
49 37 0.84
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.46
Consensus pattern (49 bp):
ACTACACTTCTTTTATTAGTTATTGATTAGAATAAGGTGTTTCAACCTT
Found at i:268425 original size:43 final size:43
Alignment explanation
Indices: 268362--268443 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
268352 TGGAATGGGT
268362 CTGCTCACACGAGTTATGGGTCAAGATGTTAGACTACACGATG
1 CTGCTCACACGAGTTATGGGTCAAGATGTTAGACTACACGATG
* *
268405 CTGCTCACACGAGTTGTGGGTCGAGATGTTAGACTACAC
1 CTGCTCACACGAGTTATGGGTCAAGATGTTAGACTACAC
268444 TGTGGAGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (43 bp):
CTGCTCACACGAGTTATGGGTCAAGATGTTAGACTACACGATG
Found at i:269029 original size:13 final size:13
Alignment explanation
Indices: 269013--269037 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
269003 TTCATTTCTA
269013 TTTTTCCTTTTTC
1 TTTTTCCTTTTTC
269026 TTTTTCCTTTTT
1 TTTTTCCTTTTT
269038 AAATCAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCCTTTTTC
Found at i:281416 original size:17 final size:17
Alignment explanation
Indices: 281391--281425 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
281381 GGAAGTGCCT
*
281391 AAAAAGGAAGAGAAAAG
1 AAAAAGGAAGAAAAAAG
*
281408 AAAAGGGAAGAAAAAAG
1 AAAAAGGAAGAAAAAAG
281425 A
1 A
281426 GAAATAAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
AAAAAGGAAGAAAAAAG
Found at i:281918 original size:3 final size:3
Alignment explanation
Indices: 281910--281954 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
281900 CTGTTGGTCT
* *
281910 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGG AGA AGA AAA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
281955 TAAGGAAGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:282485 original size:17 final size:17
Alignment explanation
Indices: 282465--282502 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
282455 TTGTCATTGT
*
282465 ATTTTAGTTGTT-GTTGC
1 ATTTTACTTGTTAGTT-C
282482 ATTTTACTTGTTAGTTC
1 ATTTTACTTGTTAGTTC
282499 ATTT
1 ATTT
282503 GCATTGTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.61
Consensus pattern (17 bp):
ATTTTACTTGTTAGTTC
Found at i:293416 original size:14 final size:15
Alignment explanation
Indices: 293399--293432 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
293389 AGAAAATGAG
293399 AAAAAG-AAAGAAAA
1 AAAAAGAAAAGAAAA
*
293413 AAAAAGAAAAGAAGA
1 AAAAAGAAAAGAAAA
293428 AAAAA
1 AAAAA
293433 TGTTTGCTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAGAAAA
Found at i:295952 original size:13 final size:13
Alignment explanation
Indices: 295936--295960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
295926 TTCATTTCTA
295936 TTTTTCCTTTTTC
1 TTTTTCCTTTTTC
295949 TTTTTCCTTTTT
1 TTTTTCCTTTTT
295961 AAATCAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCCTTTTTC
Found at i:299886 original size:20 final size:20
Alignment explanation
Indices: 299846--299903 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
299836 GTAGAAGCAT
* * *
299846 ACTTGTATCGATGGAACTGA
1 ACTTGTATCGGTAGAAGTGA
299866 ACTTGTATCGGTAGAAGTGA
1 ACTTGTATCGGTAGAAGTGA
* * *
299886 AGTTCTACCGGTAGAAGT
1 ACTTGTATCGGTAGAAGT
299904 CCCAAGGTAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (20 bp):
ACTTGTATCGGTAGAAGTGA
Found at i:300115 original size:20 final size:20
Alignment explanation
Indices: 300090--300140 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
300080 GTCTTCAAGG
300090 TATCGGTAGAACTGAAGTTA
1 TATCGGTAGAACTGAAGTTA
* * *
300110 TATCGGTAAAAGTGAAGTTC
1 TATCGGTAGAACTGAAGTTA
*
300130 TACCGGTAGAA
1 TATCGGTAGAA
300141 GTCCCAAGCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.27
Consensus pattern (20 bp):
TATCGGTAGAACTGAAGTTA
Found at i:312634 original size:38 final size:39
Alignment explanation
Indices: 312556--312634 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 39
312546 TAAAATTAAG
** *
312556 TTTTTAAAATATAAAAATTATTAAAATTATTGTATTATT
1 TTTTTAAAATATAAAAATTATTAAAATTATTAAATAATT
*
312595 TTTTTGAAATAT-AAAATTATTAAAATTATTAAATAATT
1 TTTTTAAAATATAAAAATTATTAAAATTATTAAATAATT
312633 TT
1 TT
312635 AATCTCATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 25 0.69
39 11 0.31
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (39 bp):
TTTTTAAAATATAAAAATTATTAAAATTATTAAATAATT
Found at i:313678 original size:20 final size:19
Alignment explanation
Indices: 313618--313682 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
313608 ATTATTTTAA
313618 TAATTTTATATTTCAAAAAT
1 TAATTTTATATTT-AAAAAT
* * *
313638 TAATATAATAATTT--TAA-
1 TAATTTTAT-ATTTAAAAAT
313655 TAATTTTATATTTAAAAAAT
1 TAATTTTATATTT-AAAAAT
313675 TAATTTTA
1 TAATTTTA
313683 AATCATTTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
16 4 0.12
17 7 0.21
18 2 0.06
19 2 0.06
20 15 0.44
21 4 0.12
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATTTTATATTTAAAAAT
Found at i:316527 original size:35 final size:35
Alignment explanation
Indices: 316465--316615 Score: 169
Period size: 35 Copynumber: 4.3 Consensus size: 35
316455 ACTAACTAAG
* *
316465 CTCATATGAGCATAATATTACTAGGAATCTTGAAGAA
1 CTCATATGAG-TTAA-ATTACTGGGAATCTTGAAGAA
*
316502 CTCATATAAGTTAAATTACTGGGAATCTTGAAGAA
1 CTCATATGAGTTAAATTACTGGGAATCTTGAAGAA
* *
316537 CTCGTATGAGTTAAATTACTGGGAATCTTGAAGAG
1 CTCATATGAGTTAAATTACTGGGAATCTTGAAGAA
** * * * *
316572 CTTGTATGAGCTGAATTACTGGGAAACTTAAAGAA
1 CTCATATGAGTTAAATTACTGGGAATCTTGAAGAA
*
316607 ATCAT-TGAG
1 CTCATATGAG
316616 ATATGAATGT
Statistics
Matches: 99, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
34 4 0.04
35 83 0.84
36 3 0.03
37 9 0.09
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (35 bp):
CTCATATGAGTTAAATTACTGGGAATCTTGAAGAA
Done.