Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 1 of 163
Found at i:9877 original size:26 final size:25
Alignment explanation
Indices: 9839--9895 Score: 89
Period size: 26 Copynumber: 2.3 Consensus size: 25
9829 TCCAAGGACA
9839 CAGAGTTGCGAGTTATAACTTTTGTG
1 CAGAGTTGCGAGTTATAAC-TTTGTG
*
9865 CAGAGTTGTGAGTTATAACTTTGTG
1 CAGAGTTGCGAGTTATAACTTTGTG
9890 CA-AGTT
1 CAGAGTT
9896 TTGCTGGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 4 0.13
25 8 0.27
26 18 0.60
ACGTcount: A:0.25, C:0.11, G:0.26, T:0.39
Consensus pattern (25 bp):
CAGAGTTGCGAGTTATAACTTTGTG
Found at i:21184 original size:6 final size:6
Alignment explanation
Indices: 21173--21198 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
21163 TGAATGGGTA
21173 CTAGTT CTAGTT CTAGTT CTAGTT CT
1 CTAGTT CTAGTT CTAGTT CTAGTT CT
21199 GGTACTTGGG
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:0.15, C:0.19, G:0.15, T:0.50
Consensus pattern (6 bp):
CTAGTT
Found at i:27669 original size:13 final size:13
Alignment explanation
Indices: 27651--27675 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27641 CACACGTATA
27651 AAAAGAATATATC
1 AAAAGAATATATC
27664 AAAAGAATATAT
1 AAAAGAATATAT
27676 ATATATGCAC
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:0.64, C:0.04, G:0.08, T:0.24
Consensus pattern (13 bp):
AAAAGAATATATC
Found at i:30841 original size:159 final size:159
Alignment explanation
Indices: 30552--30888 Score: 611
Period size: 159 Copynumber: 2.1 Consensus size: 159
30542 AGAAAATGAC
* * *
30552 AAAAAAAAGTGCTAATCCTAACCCAACAAGTAGATCCAGTGGAAAAGAAGATGTTATCCATCCTA
1 AAAAAAAAGTGCTAATCCTAACCCAACAAATAGATCCAATGAAAAAGAAGATGTTATCCATCCTA
30617 AGGGTTCCGGGTTCGAGCACCTATGTGTGCCTTGTCAAAAGGTTAAAAAAGTATGAACAAATACT
66 AGGGTTCCGGGTTCGAGCACCTATGTGTGCCTTGTCAAAAGGTTAAAAAAGTATGAACAAATACT
30682 ACCATGTAATCACATCGATATATTTAAAA
131 ACCATGTAATCACATCGATATATTTAAAA
30711 AAAAAAAAGTGCTAATCCTAACCCAACAAATAGATCCAATGAAAAAGAAGATGTTATCCATCCTA
1 AAAAAAAAGTGCTAATCCTAACCCAACAAATAGATCCAATGAAAAAGAAGATGTTATCCATCCTA
* *
30776 AGGGTTCCGGGTTCGAGCACCTGTGTGTGTCTTGTCAAAAGGTTAAAAAAGTATGAACAAATACT
66 AGGGTTCCGGGTTCGAGCACCTATGTGTGCCTTGTCAAAAGGTTAAAAAAGTATGAACAAATACT
*
30841 ACCATGTAATCACATCGGTATATTTAAAA
131 ACCATGTAATCACATCGATATATTTAAAA
*
30870 AAAAAGAAGTGCTAATCCT
1 AAAAAAAAGTGCTAATCCT
30889 TCCACATCAA
Statistics
Matches: 171, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
159 171 1.00
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (159 bp):
AAAAAAAAGTGCTAATCCTAACCCAACAAATAGATCCAATGAAAAAGAAGATGTTATCCATCCTA
AGGGTTCCGGGTTCGAGCACCTATGTGTGCCTTGTCAAAAGGTTAAAAAAGTATGAACAAATACT
ACCATGTAATCACATCGATATATTTAAAA
Found at i:40603 original size:25 final size:25
Alignment explanation
Indices: 40575--40625 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
40565 ACATCAAAAT
* *
40575 GGGCATTTAATAGTATAATTTTAAA
1 GGGCATTTAATAGCATAATTGTAAA
40600 GGGCATTTAATAGCATAATTGTAAA
1 GGGCATTTAATAGCATAATTGTAAA
40625 G
1 G
40626 CTAAGACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (25 bp):
GGGCATTTAATAGCATAATTGTAAA
Found at i:41318 original size:20 final size:20
Alignment explanation
Indices: 41295--41333 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
41285 ATAAATGATA
41295 TTAA-TATCATTCTATAAAAT
1 TTAATTATCATTCTA-AAAAT
41315 TTAATTATCATTCTAAAAA
1 TTAATTATCATTCTAAAAA
41334 CTTTGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATTATCATTCTAAAAAT
Found at i:41937 original size:21 final size:23
Alignment explanation
Indices: 41904--41954 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
41894 CAACCTTTAT
*
41904 GTTTTATT-TTATTTTC-AA-AA
1 GTTTAATTATTATTTTCTAATAA
41924 GTTTAATTATTATTTTCTAATAA
1 GTTTAATTATTATTTTCTAATAA
41947 -TTTAATTA
1 GTTTAATTA
41955 AAGTTATACT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 7 0.26
21 8 0.30
22 10 0.37
23 2 0.07
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (23 bp):
GTTTAATTATTATTTTCTAATAA
Found at i:42753 original size:24 final size:24
Alignment explanation
Indices: 42704--42754 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
42694 AATTGATTTT
* * *
42704 TTATTAAAAAATTATTTATTTTTA
1 TTATTAAAAAATTAGTCATTTATA
42728 TTATT-AAAAATTAGTCATTGTATA
1 TTATTAAAAAATTAGTCATT-TATA
42752 TTA
1 TTA
42755 ATATGAGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TTATTAAAAAATTAGTCATTTATA
Found at i:44504 original size:41 final size:41
Alignment explanation
Indices: 44447--44542 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
44437 GAATTTTATT
*
44447 TTAACAATAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
44488 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
44529 TTGACAAGAATTCT
1 TTAACAAGAATTCT
44543 CTATGAACAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.36, C:0.29, G:0.05, T:0.29
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:53748 original size:16 final size:16
Alignment explanation
Indices: 53697--53756 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
53687 TTATCTCATC
* *
53697 ATTTAAAGTTACTATT
1 ATTTAAAATAACTATT
*
53713 ATTTAAAAATAGCT-TAT
1 ATTT-AAAATAACTAT-T
*
53730 ATTTAGAATAACTATT
1 ATTTAAAATAACTATT
53746 ATTTAAAATAA
1 ATTTAAAATAA
53757 TTGTTCTTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 23 0.66
17 12 0.34
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (16 bp):
ATTTAAAATAACTATT
Found at i:53846 original size:42 final size:42
Alignment explanation
Indices: 53799--53886 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
53789 CGTCATCTAA
53799 AATAGCTTTTATTTAGAGTAGTTTTGGTTTCTTTTTATTTAG
1 AATAGCTTTTATTTAGAGTAGTTTTGGTTTCTTTTTATTTAG
53841 AATAGCTTTTATTTAGAGTAGTTTTGGTTTCTTTTTATTTAG
1 AATAGCTTTTATTTAGAGTAGTTTTGGTTTCTTTTTATTTAG
53883 AATA
1 AATA
53887 ATTTTGGTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.56
Consensus pattern (42 bp):
AATAGCTTTTATTTAGAGTAGTTTTGGTTTCTTTTTATTTAG
Found at i:69053 original size:5 final size:5
Alignment explanation
Indices: 69047--69099 Score: 63
Period size: 5 Copynumber: 10.8 Consensus size: 5
69037 CGTATTATGT
* * * *
69047 CATGT CATGT CATGT CATGT CATG- CATGC CATGC CATGC CATGC CATGC
1 CATGC CATGC CATGC CATGC CATGC CATGC CATGC CATGC CATGC CATGC
69096 CATG
1 CATG
69100 GACTCTGATG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.09
5 43 0.91
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (5 bp):
CATGC
Found at i:69079 original size:24 final size:24
Alignment explanation
Indices: 69047--69095 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
69037 CGTATTATGT
* * * *
69047 CATGTCATGTCATGTCATGTCATG
1 CATGCCATGCCATGCCATGCCATG
69071 CATGCCATGCCATGCCATGCCATG
1 CATGCCATGCCATGCCATGCCATG
69095 C
1 C
69096 CATGGACTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (24 bp):
CATGCCATGCCATGCCATGCCATG
Found at i:71996 original size:29 final size:29
Alignment explanation
Indices: 71954--72324 Score: 247
Period size: 29 Copynumber: 12.8 Consensus size: 29
71944 AATCGAGGTC
71954 AAAAATGGAATTTTGGGAAATTCGGGGGT
1 AAAAATGGAATTTTGGGAAATTCGGGGGT
**
71983 -AAAATGGTAATTTTGGTGAAA-TC-GAAGT
1 AAAAATGG-AATTTTGG-GAAATTCGGGGGT
* *
72011 CAAAATGGAATCTT-GGAAAGTTCGGGGGT
1 AAAAATGGAATTTTGGGAAA-TTCGGGGGT
* *
72040 -AAAATGGTAATTTTGATGAAA-TCGGGGTT
1 AAAAATGG-AATTTTG-GGAAATTCGGGGGT
*
72069 AAAAATGGAATTTT-AGAAAGTTCGGGGGT
1 AAAAATGGAATTTTGGGAAA-TTCGGGGGT
*
72098 -AAAATGGTAAATTTTGGTGAAA-TC-GAGGT
1 AAAAATGG--AATTTTGG-GAAATTCGGGGGT
*
72127 CAAAAATGGAATCTT-GGAAAGTTCGGGGGT
1 -AAAAATGGAATTTTGGGAAA-TTCGGGGGT
* * *
72157 -AAAATGGTAATTTTGATGAAA-TCGAGGTT
1 AAAAATGG-AATTTTG-GGAAATTCGGGGGT
* *
72186 AAAAATGGAATTTT-AGAAAGTTCGGCGGT
1 AAAAATGGAATTTTGGGAAA-TTCGGGGGT
*
72215 -AAAATGGTAATTTTTGGTGAAA-TCGGGGTT
1 AAAAATGG-AA-TTTTGG-GAAATTCGGGGGT
*
72245 AAAAATGGAATTTTGGAAAAGTTCGGGGGT
1 AAAAATGGAATTTTGGGAAA-TTCGGGGGT
* * * * *
72275 -GAAATGGTAATTTTTGG-AAGTCGAGGTT
1 AAAAATGG-AATTTTGGGAAATTCGGGGGT
*
72303 AAAAATGGAATTTTGGAAAATT
1 AAAAATGGAATTTTGGGAAATT
72325 TAGGGACCTA
Statistics
Matches: 268, Mismatches: 37, Indels: 74
0.71 0.10 0.20
Matches are distributed among these distances:
26 4 0.01
27 13 0.05
28 62 0.23
29 103 0.38
30 56 0.21
31 22 0.08
32 8 0.03
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.30
Consensus pattern (29 bp):
AAAAATGGAATTTTGGGAAATTCGGGGGT
Found at i:72013 original size:58 final size:58
Alignment explanation
Indices: 71924--72321 Score: 577
Period size: 58 Copynumber: 6.8 Consensus size: 58
71914 TCGCAAGGGC
* *
71924 AAAATGGTAATTTTCGATGAAATCGAGGTCAAAAATGGAATTTTGGGAAA-TTCGGGGGT
1 AAAATGGTAATTTT-GGTGAAATCGAGGTTAAAAATGGAATTTT-GGAAAGTTCGGGGGT
* * *
71983 AAAATGGTAATTTTGGTGAAATCGAAG-TCAAAATGGAATCTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
* * *
72040 AAAATGGTAATTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGGT
1 AAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
* *
72098 AAAATGGTAAATTTTGGTGAAATCGAGGTCAAAAATGGAATCTTGGAAAGTTCGGGGGT
1 AAAATGGT-AATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
* * *
72157 AAAATGGTAATTTTGATGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTCGGCGGT
1 AAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
*
72215 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAAGTTCGGGGGT
1 AAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGG-AAAGTTCGGGGGT
* * *
72275 GAAATGGTAATTTTTG-GAAGTCGAGGTTAAAAATGGAATTTTGGAAA
1 AAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAA
72322 ATTTAGGGAC
Statistics
Matches: 305, Mismatches: 29, Indels: 12
0.88 0.08 0.03
Matches are distributed among these distances:
56 5 0.02
57 48 0.16
58 127 0.42
59 104 0.34
60 21 0.07
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.30
Consensus pattern (58 bp):
AAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
Found at i:72171 original size:117 final size:117
Alignment explanation
Indices: 71924--72321 Score: 617
Period size: 117 Copynumber: 3.4 Consensus size: 117
71914 TCGCAAGGGC
* *
71924 AAAATGGTAATTTTCGATGAAATCGAGGTCAAAAATGGAATTTTGGGAAA-TTCGGGGGTAAAAT
1 AAAATGGTAATTTT-GATGAAATCGAGGTTAAAAATGGAATTTT-AGAAAGTTCGGGGGTAAAAT
*
71988 GGT-AATTTTGGTGAAATCGAAGTC-AAAATGGAATCTTGGAAAGTTCGGGGGT
64 GGTAAATTTTGGTGAAATCGAGGTCAAAAATGGAATCTTGGAAAGTTCGGGGGT
*
72040 AAAATGGTAATTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGGTAAAATGG
1 AAAATGGTAATTTTGATGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTCGGGGGTAAAATGG
72105 TAAATTTTGGTGAAATCGAGGTCAAAAATGGAATCTTGGAAAGTTCGGGGGT
66 TAAATTTTGGTGAAATCGAGGTCAAAAATGGAATCTTGGAAAGTTCGGGGGT
*
72157 AAAATGGTAATTTTGATGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTCGGCGGTAAAATGG
1 AAAATGGTAATTTTGATGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTCGGGGGTAAAATGG
* * * *
72222 TAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAAGTTCGGGGGT
66 TAAATTTTGGTGAAATCGAGGTCAAAAATGGAATCTTGG-AAAGTTCGGGGGT
* * *
72275 GAAATGGTAATTTT--TGGAAGTCGAGGTTAAAAATGGAATTTTGGAAA
1 AAAATGGTAATTTTGAT-GAAATCGAGGTTAAAAATGGAATTTTAGAAA
72322 ATTTAGGGAC
Statistics
Matches: 264, Mismatches: 13, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
114 4 0.02
115 44 0.17
116 35 0.13
117 155 0.59
118 26 0.10
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.30
Consensus pattern (117 bp):
AAAATGGTAATTTTGATGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTCGGGGGTAAAATGG
TAAATTTTGGTGAAATCGAGGTCAAAAATGGAATCTTGGAAAGTTCGGGGGT
Found at i:73511 original size:15 final size:15
Alignment explanation
Indices: 73486--73524 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
73476 CATTTTTTAT
*
73486 TATTATTAATAATTAA
1 TATT-TTAATAAATAA
73502 TATTTTAATAAATAA
1 TATTTTAATAAATAA
73517 TATATTTA
1 TAT-TTTA
73525 TTATTATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTTTAATAAATAA
Found at i:74361 original size:50 final size:50
Alignment explanation
Indices: 74298--74397 Score: 121
Period size: 50 Copynumber: 2.0 Consensus size: 50
74288 TGTTTGGACT
* *
74298 TTTAATATTTAAATCATTTTAATCCAAAATAAATTCAAACTTAACATAAA
1 TTTAATATTTAAATCATTTAAATCCAAAATAAATTCAAACTTAAAATAAA
* ** * *
74348 TTTAA-ATTCTAAATGATTTAAATTTAAAATAAATTTAAATTTAAAATAAA
1 TTTAATATT-TAAATCATTTAAATCCAAAATAAATTCAAACTTAAAATAAA
74398 CTAAGATTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 3 0.07
50 39 0.93
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.40
Consensus pattern (50 bp):
TTTAATATTTAAATCATTTAAATCCAAAATAAATTCAAACTTAAAATAAA
Found at i:74385 original size:17 final size:17
Alignment explanation
Indices: 74323--74410 Score: 92
Period size: 17 Copynumber: 5.2 Consensus size: 17
74313 ATTTTAATCC
* *
74323 AAAATAAATTCAAACTT
1 AAAATAAATTTAAATTT
*
74340 AACATAAATTTAAATTCT
1 AAAATAAATTTAAATT-T
*
74358 -AAAT-GATTTAAATTT
1 AAAATAAATTTAAATTT
74373 AAAATAAATTTAAATTT
1 AAAATAAATTTAAATTT
*
74390 AAAATAAA-CTAAGATTT
1 AAAATAAATTTAA-ATTT
74407 AAAA
1 AAAA
74411 ATTAAAAGTT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
15 1 0.02
16 16 0.27
17 42 0.70
18 1 0.02
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (17 bp):
AAAATAAATTTAAATTT
Found at i:74389 original size:23 final size:23
Alignment explanation
Indices: 74363--74409 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
74353 ATTCTAAATG
*
74363 ATTTAAATTTAAAATAA-ATTTAA
1 ATTTAAA-ATAAAATAAGATTTAA
*
74386 ATTTAAAATAAACTAAGATTTAA
1 ATTTAAAATAAAATAAGATTTAA
74409 A
1 A
74410 AATTAAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (23 bp):
ATTTAAAATAAAATAAGATTTAA
Found at i:83724 original size:6 final size:6
Alignment explanation
Indices: 83713--83742 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
83703 GCAAGGTTCT
83713 CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA
1 CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA
83743 TTTTCTAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCTCA
Found at i:99465 original size:20 final size:19
Alignment explanation
Indices: 99435--99479 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
99425 TGATTTTATG
99435 ATTTTTTTATTTTTAAATA
1 ATTTTTTTATTTTTAAATA
**
99454 ATTTTTTGTATTTTTTTATA
1 ATTTTTT-TATTTTTAAATA
99474 ATTTTT
1 ATTTTT
99480 ACATATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
ATTTTTTTATTTTTAAATA
Found at i:100032 original size:17 final size:17
Alignment explanation
Indices: 100010--100042 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
100000 TTTTTAATAA
*
100010 AATCCATATTTGATTGC
1 AATCCATATTTCATTGC
100027 AATCCATATTTCATTG
1 AATCCATATTTCATTG
100043 TTTTAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.42
Consensus pattern (17 bp):
AATCCATATTTCATTGC
Found at i:100424 original size:13 final size:13
Alignment explanation
Indices: 100406--100432 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
100396 TCATCACTTC
100406 ACTACACTATCAT
1 ACTACACTATCAT
100419 ACTACACTATCAT
1 ACTACACTATCAT
100432 A
1 A
100433 AAAAACATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.30, G:0.00, T:0.30
Consensus pattern (13 bp):
ACTACACTATCAT
Found at i:101988 original size:19 final size:18
Alignment explanation
Indices: 101938--101991 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
101928 TATATATAGT
*
101938 TACATAAAAA-TGAAAAA
1 TACATAAAAATTCAAAAA
*
101955 TA-TTAAAAATCTCAAGAAA
1 TACATAAAAAT-TCAA-AAA
101974 TACATAAAAATTCAAAAA
1 TACATAAAAATTCAAAAA
101992 ATATTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
16 6 0.20
17 2 0.07
18 6 0.20
19 9 0.30
20 7 0.23
ACGTcount: A:0.65, C:0.09, G:0.04, T:0.22
Consensus pattern (18 bp):
TACATAAAAATTCAAAAA
Found at i:103470 original size:9 final size:9
Alignment explanation
Indices: 103456--103481 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
103446 TAATTTTCGA
103456 ATTCGAATT
1 ATTCGAATT
103465 ATTCGAATT
1 ATTCGAATT
103474 ATTCGAAT
1 ATTCGAAT
103482 AAACCGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (9 bp):
ATTCGAATT
Found at i:103748 original size:58 final size:58
Alignment explanation
Indices: 103630--103749 Score: 179
Period size: 58 Copynumber: 2.1 Consensus size: 58
103620 ATCCATCAAC
* ** * *
103630 AAACTAAACTCAAATATTTTTAAACCCAAATATAATTTTATTGTTCAAAAATACTTAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCTCAAAAACACTCAT
103688 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCT-AAATAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCTCAAA-AACACTCAT
103746 AAAC
1 AAAC
103750 AACTCCTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 3 0.05
58 53 0.95
ACGTcount: A:0.47, C:0.17, G:0.01, T:0.34
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCTCAAAAACACTCAT
Found at i:107592 original size:31 final size:31
Alignment explanation
Indices: 107550--107619 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
107540 AAAAATATTA
* * *
107550 ATTTTCTTTTTAGGCACTATTGTTGAAAATC
1 ATTTTCATTTTAGGCACTATCGTTAAAAATC
*
107581 ATTTTCATTTTAGGCACTATCGTTAAAAATT
1 ATTTTCATTTTAGGCACTATCGTTAAAAATC
107612 ATTTTCAT
1 ATTTTCAT
107620 ATTGGTCACT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.49
Consensus pattern (31 bp):
ATTTTCATTTTAGGCACTATCGTTAAAAATC
Found at i:122529 original size:21 final size:21
Alignment explanation
Indices: 122496--122539 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
122486 ATATCCCAAT
* *
122496 CTACCTGAATCAATTATTCAC
1 CTACCCGAATCAATTAATCAC
*
122517 CTACCCGAGTCAATTAATCAC
1 CTACCCGAATCAATTAATCAC
122538 CT
1 CT
122540 CATAGACCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.32, G:0.07, T:0.30
Consensus pattern (21 bp):
CTACCCGAATCAATTAATCAC
Found at i:129082 original size:2 final size:2
Alignment explanation
Indices: 129075--129105 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
129065 CTTGTAATTA
129075 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 A
129106 ATTAACCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:138748 original size:29 final size:30
Alignment explanation
Indices: 138703--138762 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
138693 TGGGTTAATG
*
138703 TGCAATTGTATATAT-AAACTTTGATTTGA
1 TGCAATTGTATACATAAAACTTTGATTTGA
* *
138732 TGCAATTTTATACATAAAATTTTGATTTGA
1 TGCAATTGTATACATAAAACTTTGATTTGA
138762 T
1 T
138763 CTAATTCTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.47
Consensus pattern (30 bp):
TGCAATTGTATACATAAAACTTTGATTTGA
Found at i:138987 original size:29 final size:29
Alignment explanation
Indices: 138947--139014 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
138937 GAGTTTTATG
*
138947 TATATAA--TTACACTAAATTAGAATTCA
1 TATATAATTTTACACTAAATTAAAATTCA
* *
138974 TATATAATTTTACATTAAATTAAAATTTA
1 TATATAATTTTACACTAAATTAAAATTCA
*
139003 TGTATAATTTTA
1 TATATAATTTTA
139015 AAATTTATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 7 0.20
29 28 0.80
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (29 bp):
TATATAATTTTACACTAAATTAAAATTCA
Found at i:139559 original size:27 final size:27
Alignment explanation
Indices: 139520--139571 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
139510 GTCACACCCT
*
139520 TCCTTTTTCATTCTGACTTTTACCTCG
1 TCCTTTTTAATTCTGACTTTTACCTCG
139547 TCCTTTTTAATTCTGACTTTTACCT
1 TCCTTTTTAATTCTGACTTTTACCT
139572 TTTTCATCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (27 bp):
TCCTTTTTAATTCTGACTTTTACCTCG
Found at i:145505 original size:14 final size:15
Alignment explanation
Indices: 145488--145519 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
145478 ATTAAAATAA
145488 TTTAATTTTATT-AT
1 TTTAATTTTATTAAT
145502 TTTAATTTTATTAAT
1 TTTAATTTTATTAAT
145517 TTT
1 TTT
145520 GAAAGTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTAATTTTATTAAT
Found at i:147227 original size:31 final size:30
Alignment explanation
Indices: 147177--147261 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 30
147167 ATAAAGACCT
*
147177 AACC-TTTCAAAATGATCAAATAAGGGTCA
1 AACCTTTTCAAAATGCTCAAATAAGGGTCA
147206 AACCTTTTCGAAAATGCTCAAATAAGGGTCA
1 AACCTTTTC-AAAATGCTCAAATAAGGGTCA
147237 AACCTTTTCAAAAGTGCTCAAATAA
1 AACCTTTTCAAAA-TGCTCAAATAA
147262 TGGCTTCTCA
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
29 4 0.08
30 8 0.15
31 40 0.77
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (30 bp):
AACCTTTTCAAAATGCTCAAATAAGGGTCA
Found at i:150162 original size:22 final size:22
Alignment explanation
Indices: 150134--150178 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
150124 TTGGGTGGCT
150134 AACATTAATTGAACCCATCTAG
1 AACATTAATTGAACCCATCTAG
150156 AACATTAATTGAACCCATCTAG
1 AACATTAATTGAACCCATCTAG
150178 A
1 A
150179 TGGGTGGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (22 bp):
AACATTAATTGAACCCATCTAG
Found at i:150846 original size:24 final size:23
Alignment explanation
Indices: 150783--150846 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
150773 TGGATCTTAA
150783 ATGTTTAAATTTGAGTTTAATTTAT
1 ATGTTTAAATTT-A-TTTAATTTAT
** *
150808 AT-TTTAAATAGATTTAATTTTTT
1 ATGTTTAAATTTATTTAA-TTTAT
*
150831 TTGTTTAAATTTATTT
1 ATGTTTAAATTTATTT
150847 TTCAAACTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
22 5 0.16
23 6 0.19
24 18 0.58
25 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (23 bp):
ATGTTTAAATTTATTTAATTTAT
Found at i:154163 original size:32 final size:33
Alignment explanation
Indices: 154127--154200 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
154117 AATTTTTATG
* *
154127 AAATATTTT-CAAGAAATTTAT-CAAACACCAAA
1 AAATATTTTAC-ACAAATATATCCAAACACCAAA
* *
154159 AAATATTTTACACAAATATATCCAAACACTAGA
1 AAATATTTTACACAAATATATCCAAACACCAAA
154192 AAATATTTT
1 AAATATTTT
154201 TTACAGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 17 0.47
33 19 0.53
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (33 bp):
AAATATTTTACACAAATATATCCAAACACCAAA
Found at i:155970 original size:42 final size:42
Alignment explanation
Indices: 155923--156004 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
155913 AAAGGAGTTG
* *
155923 TTTATGAGTGTTATTTAGGAATAAAATTATATTTGGGTTTAA
1 TTTATGAGTGTTATTTAAGAATAAAATTATATTTGAGTTTAA
* *
155965 TTTATGAGTGTTTTTTAAGAATGAAATTATATTTGAGTTT
1 TTTATGAGTGTTATTTAAGAATAAAATTATATTTGAGTTT
156005 TAAAATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (42 bp):
TTTATGAGTGTTATTTAAGAATAAAATTATATTTGAGTTTAA
Found at i:160493 original size:27 final size:27
Alignment explanation
Indices: 160445--160513 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
160435 CCAAGGTTAA
* **
160445 AAAGAGTTCAAAAAAAAATTCAGTTTTT
1 AAAGGGTTC-AAAAAAAATTCAACTTTT
*
160473 AAGGGGTTCAAAAAAAATTCAACTTTT
1 AAAGGGTTCAAAAAAAATTCAACTTTT
160500 AAAGGGTTCAAAAA
1 AAAGGGTTCAAAAA
160514 TATTTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 29 0.81
28 7 0.19
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (27 bp):
AAAGGGTTCAAAAAAAATTCAACTTTT
Found at i:167497 original size:21 final size:18
Alignment explanation
Indices: 167473--167572 Score: 57
Period size: 20 Copynumber: 5.3 Consensus size: 18
167463 AAAAAATCAT
*
167473 TAAAAATATCTATAAAAATTG
1 TAAAAATAT-T-T-AAAATTA
167494 TAAAAATATTTAAAATTA
1 TAAAAATATTTAAAATTA
*
167512 T-AAAA-A-TTAAAATAA
1 TAAAAATATTTAAAATTA
*
167527 CTGAAAAA-ATTAAAAAATGTA
1 -T-AAAAATATT-TAAAAT-TA
167548 -AACAAATATTTAAAAATTA
1 TAA-AAATATTT-AAAATTA
167567 TAAAAA
1 TAAAAA
167573 AAATCCATGA
Statistics
Matches: 64, Mismatches: 5, Indels: 22
0.70 0.05 0.24
Matches are distributed among these distances:
15 8 0.12
16 2 0.03
17 4 0.06
18 14 0.22
19 10 0.16
20 16 0.25
21 10 0.16
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (18 bp):
TAAAAATATTTAAAATTA
Found at i:167572 original size:9 final size:9
Alignment explanation
Indices: 167483--167572 Score: 55
Period size: 9 Copynumber: 9.9 Consensus size: 9
167473 TAAAAATATC
167483 TATAAAAAT
1 TATAAAAAT
*
167492 TGTAAAAA-
1 TATAAAAAT
*
167500 TATTTAAAAT
1 TA-TAAAAAT
167510 TATAAAAAT
1 TATAAAAAT
167519 TA-AAATAACT
1 TATAAA-AA-T
*
167529 GA-AAAAAT
1 TATAAAAAT
167537 TA-AAAAAT
1 TATAAAAAT
167545 GTA-AACAAAT
1 -TATAA-AAAT
*
167555 ATTTAAAAAT
1 -TATAAAAAT
167565 TATAAAAA
1 TATAAAAA
167573 AAATCCATGA
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
8 12 0.18
9 35 0.54
10 16 0.25
11 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.30
Consensus pattern (9 bp):
TATAAAAAT
Found at i:168142 original size:29 final size:30
Alignment explanation
Indices: 168081--168148 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
168071 ACTACTAAAA
* * *
168081 TAGTCACTTTTGTTTGTCTCATGTTATATTT
1 TAGTCACTTATGTTTG-CACATGTTACATTT
*
168112 TAGTCACTTATGTTTG-ACATGTTACGTTT
1 TAGTCACTTATGTTTGCACATGTTACATTT
168141 TAGTCACT
1 TAGTCACT
168149 AATTTTATCG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.55
31 15 0.45
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.51
Consensus pattern (30 bp):
TAGTCACTTATGTTTGCACATGTTACATTT
Found at i:168640 original size:31 final size:29
Alignment explanation
Indices: 168571--168641 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
168561 AAACGATAAC
**
168571 ATAAGTGACTAAAATGTAACATTTCAAAT
1 ATAAGTGACTAAAATGTAACAAGTCAAAT
*
168600 ATAAATGACTAAAATGTAACCTAAGTCAAAT
1 ATAAGTGACTAAAATGTAA-C-AAGTCAAAT
168631 A-AACGTGACTA
1 ATAA-GTGACTA
168642 TTTTTATAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 18 0.51
30 3 0.09
31 14 0.40
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (29 bp):
ATAAGTGACTAAAATGTAACAAGTCAAAT
Found at i:173914 original size:23 final size:23
Alignment explanation
Indices: 173871--173924 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
173861 AATTCTGAAT
* * *
173871 TTCGAGTTTATCAAGTCAAGTTA
1 TTCGAGTTAATCAAATCAAGTAA
173894 TTCGAGTTAACTCAAAT-AAGTAA
1 TTCGAGTTAA-TCAAATCAAGTAA
*
173917 ATCGAGTT
1 TTCGAGTT
173925 TCGAGTTGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (23 bp):
TTCGAGTTAATCAAATCAAGTAA
Found at i:174078 original size:19 final size:19
Alignment explanation
Indices: 174056--174110 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 19
174046 AATTACAAAA
174056 AAAAATT-AAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
174074 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
174093 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
174111 GTTTTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:182676 original size:6 final size:6
Alignment explanation
Indices: 182665--182715 Score: 77
Period size: 6 Copynumber: 8.5 Consensus size: 6
182655 TGATCAAAAT
*
182665 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TG-AAG TTGAAAT TGAAAG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG -TGAAAG TGAAAG
182713 TGA
1 TGA
182716 TATGAATTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 3 0.07
6 36 0.88
7 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:186607 original size:9 final size:10
Alignment explanation
Indices: 186561--186611 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
186551 GCTTGTAAGA
186561 TCTGTTTTTC
1 TCTGTTTTTC
*
186571 TCTGTTACGTTC
1 TCTGTT--TTTC
* *
186583 TTTCTTTTTC
1 TCTGTTTTTC
186593 TCTGTTTTTC
1 TCTGTTTTTC
186603 T-TGTTTTTC
1 TCTGTTTTTC
186612 CCGAATTGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
9 8 0.24
10 18 0.55
12 7 0.21
ACGTcount: A:0.02, C:0.20, G:0.10, T:0.69
Consensus pattern (10 bp):
TCTGTTTTTC
Found at i:193869 original size:23 final size:22
Alignment explanation
Indices: 193834--193878 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
193824 GTCCTTTATT
193834 TTAAATTAATTTTTAAAAGATAA
1 TTAAATTAATTTTTAAAA-ATAA
* *
193857 TTAATTTACTTTTTAAAAATAA
1 TTAAATTAATTTTTAAAAATAA
193879 AAATTGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TTAAATTAATTTTTAAAAATAA
Found at i:193913 original size:25 final size:24
Alignment explanation
Indices: 193868--193914 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
193858 TAATTTACTT
*
193868 TTTAAAAATAAAAATTGATAATAA
1 TTTAAAAATAAAAACTGATAATAA
193892 TTTAAAAA-AAAAACTGA-AATAA
1 TTTAAAAATAAAAACTGATAATAA
193914 T
1 T
193915 CCAATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.27
23 8 0.36
24 8 0.36
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
TTTAAAAATAAAAACTGATAATAA
Found at i:196249 original size:26 final size:26
Alignment explanation
Indices: 196200--196251 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
196190 TTAACAATCT
*
196200 TAAATTTTGAAAATTTGAAAGTATAAC
1 TAAATTTTGAAAA-TTAAAAGTATAAC
196227 TAAATTTCTGAAAA-TAAAAGTATAA
1 TAAATTT-TGAAAATTAAAAGTATAA
196252 AAACTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 10 0.43
27 7 0.30
28 6 0.26
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.35
Consensus pattern (26 bp):
TAAATTTTGAAAATTAAAAGTATAAC
Found at i:200151 original size:2 final size:2
Alignment explanation
Indices: 200146--200172 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
200136 TATATATATA
200146 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
200173 TTGACAATCA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:201602 original size:32 final size:32
Alignment explanation
Indices: 201558--201624 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
201548 ATTGAGGATT
* *
201558 CAAGACTGGCCCAGATAGCAATCTCCCTTGAA
1 CAAGACTAGCCCAGAGAGCAATCTCCCTTGAA
*
201590 CAAGACTAGCCCAGAGAGTAATCTCCCTTGAA
1 CAAGACTAGCCCAGAGAGCAATCTCCCTTGAA
201622 CAA
1 CAA
201625 TACTGAAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.30, G:0.18, T:0.18
Consensus pattern (32 bp):
CAAGACTAGCCCAGAGAGCAATCTCCCTTGAA
Found at i:203606 original size:7 final size:7
Alignment explanation
Indices: 203594--203618 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
203584 TAGCTGATAA
203594 AACATTG
1 AACATTG
203601 AACATTG
1 AACATTG
203608 AACATTG
1 AACATTG
203615 AACA
1 AACA
203619 AATGAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (7 bp):
AACATTG
Found at i:209357 original size:23 final size:23
Alignment explanation
Indices: 209330--209378 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
209320 TTTTTTCATC
*
209330 TATTTTACGAATAATTCAACAAT
1 TATTTTACGAATAATTAAACAAT
* *
209353 TATTTTACTAATAATTAAATAAT
1 TATTTTACGAATAATTAAACAAT
209376 TAT
1 TAT
209379 AATAAGAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTTTACGAATAATTAAACAAT
Found at i:212567 original size:30 final size:31
Alignment explanation
Indices: 212523--212580 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
212513 ATAATTTTTT
* *
212523 ATCACTTAACTAT-AAAAAATTATAAAAATA
1 ATCACCTAACTATAAAAAAATTACAAAAATA
*
212553 ATCACCTAATTATAAAAAAATTACAAAA
1 ATCACCTAACTATAAAAAAATTACAAAA
212581 TGATCATCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (31 bp):
ATCACCTAACTATAAAAAAATTACAAAAATA
Found at i:212954 original size:24 final size:24
Alignment explanation
Indices: 212927--212977 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
212917 AAAGCAAAAC
212927 TAAAAAAATATTAATAAACCAAAT
1 TAAAAAAATATTAATAAACCAAAT
212951 TAAAAAAATATTAATAAACCAAAT
1 TAAAAAAATATTAATAAACCAAAT
212975 TAA
1 TAA
212978 CAATGTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (24 bp):
TAAAAAAATATTAATAAACCAAAT
Found at i:232333 original size:119 final size:119
Alignment explanation
Indices: 232155--232441 Score: 429
Period size: 119 Copynumber: 2.4 Consensus size: 119
232145 ATATAAAAAC
*
232155 ACACCAAGCTAAGCTTTAAACATGTCCA--ATTCTTACATATAAACTGGTTTAGTCCTAATTTAA
1 ACACCAAGCTAAGCTTTAAACATGTCCAGTTTTCTTACATATAAACTGGTTTAGTCCTAATTTAA
* *
232218 AACACTAAAACAAACAGTAAACAGTAAAACACTA-AGCTCCAGCTTAGATTACAG
66 AACACTAAAACAAACAGTAAACAGTAAAACACTAGA-CTACAGCTTAGACTACAG
*
232272 ACACCAAGCTAAGCTTTAAACATGTCCAGTTTTTTTACATATAAACTGGTTTAGTCCTAATTTAA
1 ACACCAAGCTAAGCTTTAAACATGTCCAGTTTTCTTACATATAAACTGGTTTAGTCCTAATTTAA
* * * *
232337 AACACTAAAACAAACAGTCAACAGTAAAACACTAGATTATAGTTTAGACTACAG
66 AACACTAAAACAAACAGTAAACAGTAAAACACTAGACTACAGCTTAGACTACAG
* * *
232391 ACACCAAGCTAAAGC-TTAACCATGTCCAGTTTTGTTACATATAAACCGGTT
1 ACACCAAGCT-AAGCTTTAAACATGTCCAGTTTTCTTACATATAAACTGGTT
232442 CAGTTCTTCC
Statistics
Matches: 155, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
117 28 0.18
119 122 0.79
120 5 0.03
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (119 bp):
ACACCAAGCTAAGCTTTAAACATGTCCAGTTTTCTTACATATAAACTGGTTTAGTCCTAATTTAA
AACACTAAAACAAACAGTAAACAGTAAAACACTAGACTACAGCTTAGACTACAG
Found at i:242194 original size:102 final size:102
Alignment explanation
Indices: 242017--242211 Score: 318
Period size: 102 Copynumber: 1.9 Consensus size: 102
242007 TGAATCAAAA
* *
242017 TTTCCCGTATCATTTTACATATTTCTTAAATGCATAGAAATTTCAAGGTCATAACATGTAAAATT
1 TTTCCCGGATCATTTTACATATTTCTTAAATGCATAGAAAATTCAAGGTCATAACATGTAAAATT
*
242082 TATTAAGAATTTTGTGGTAGGATTGAAATTAAATTAT
66 TATTAAGAATTTTGTGGTAGGATCGAAATTAAATTAT
* *
242119 TTTCCCGGATCATTTTATATATTTCTTTAATGCATAGAAAATTCAAGGTCATAACATGTAAAATT
1 TTTCCCGGATCATTTTACATATTTCTTAAATGCATAGAAAATTCAAGGTCATAACATGTAAAATT
* * *
242184 TGTTAGGAATTTTGTGTTAGGATCGAAA
66 TATTAAGAATTTTGTGGTAGGATCGAAA
242212 AAAAGTAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 85 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (102 bp):
TTTCCCGGATCATTTTACATATTTCTTAAATGCATAGAAAATTCAAGGTCATAACATGTAAAATT
TATTAAGAATTTTGTGGTAGGATCGAAATTAAATTAT
Found at i:243259 original size:118 final size:115
Alignment explanation
Indices: 243049--243259 Score: 314
Period size: 118 Copynumber: 1.8 Consensus size: 115
243039 GGATATACCC
* * *
243049 AAATCCCATATTTTTGGAATAATCTAATATATTAGATTGAAATTGTTCATATAACCTTCTTTTGA
1 AAATCCCAAATCTTTGGAATAAGCTAATATATTAGATTGAAATTGTTCATATAACCTTCTTTTGA
* * * **
243114 ACCGCATTGATGATCCTTTTTTGAGTTATTATGGGTAACAGGGATTCCCA
66 ACCCCATTGACGATCCATTTTCAAGTTATTATGGGTAACAGGGATTCCCA
*
243164 AAATCCCAAATCTTTGGAATAAGGTAATAGTGTATTAGATTGAAATTGTTCATATAACCTTCTTT
1 AAATCCCAAATCTTTGGAATAAGCTAATA---TATTAGATTGAAATTGTTCATATAACCTTCTTT
243229 TGAACCCCATTGACGATCCATTTTCAAGTTA
63 TGAACCCCATTGACGATCCATTTTCAAGTTA
243260 CCATTTGTTG
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
115 25 0.30
118 59 0.70
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (115 bp):
AAATCCCAAATCTTTGGAATAAGCTAATATATTAGATTGAAATTGTTCATATAACCTTCTTTTGA
ACCCCATTGACGATCCATTTTCAAGTTATTATGGGTAACAGGGATTCCCA
Found at i:244849 original size:17 final size:17
Alignment explanation
Indices: 244829--244883 Score: 76
Period size: 17 Copynumber: 3.3 Consensus size: 17
244819 TTTAAATTTG
*
244829 TTTTGAGTTTCAAGTTA
1 TTTTGAGTTTTAAGTTA
* *
244846 TTTTG-TTTTTAATTTA
1 TTTTGAGTTTTAAGTTA
244862 TTTTGAGTTTTAAGTTA
1 TTTTGAGTTTTAAGTTA
244879 TTTTG
1 TTTTG
244884 TTTTCATGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 13 0.41
17 19 0.59
ACGTcount: A:0.20, C:0.02, G:0.15, T:0.64
Consensus pattern (17 bp):
TTTTGAGTTTTAAGTTA
Found at i:244866 original size:33 final size:33
Alignment explanation
Indices: 244823--244887 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
244813 TTTGGATTTA
*
244823 AATTTGTTTTGAGTTTCAAGTTATTTTGTTTTT
1 AATTTATTTTGAGTTTCAAGTTATTTTGTTTTT
*
244856 AATTTATTTTGAGTTTTAAGTTATTTTGTTTT
1 AATTTATTTTGAGTTTCAAGTTATTTTGTTTT
244888 CATGTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.20, C:0.02, G:0.14, T:0.65
Consensus pattern (33 bp):
AATTTATTTTGAGTTTCAAGTTATTTTGTTTTT
Found at i:248763 original size:60 final size:60
Alignment explanation
Indices: 248687--248801 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
248677 AATTTTGGCG
*
248687 AAATCGAGGTTAAAAATAAAATTTTGAAAAGTTTAAGGGTAAAATGGCAATTTTTGGTAA
1 AAATCGAGGTCAAAAATAAAATTTTGAAAAGTTTAAGGGTAAAATGGCAATTTTTGGTAA
* * * * *
248747 AAATCGGGGTCAAAAATAGAATTTTGGAAATTTTAAGGGTAAAATGGTAATTTTT
1 AAATCGAGGTCAAAAATAAAATTTTGAAAAGTTTAAGGGTAAAATGGCAATTTTT
248802 AGAAAGTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.43, C:0.03, G:0.21, T:0.33
Consensus pattern (60 bp):
AAATCGAGGTCAAAAATAAAATTTTGAAAAGTTTAAGGGTAAAATGGCAATTTTTGGTAA
Found at i:248847 original size:90 final size:87
Alignment explanation
Indices: 248752--249020 Score: 276
Period size: 90 Copynumber: 3.0 Consensus size: 87
248742 GGTAAAAATC
248752 GGGGTCAAAAATAGAATTTTGGAAATTTTAAGGGTAAAATGGTAATTTTTAGAAAGTTTTAGGGT
1 GGGGTC-AAAAT-GAATTTTGGAAATTTTAAGGGTAAAAT-GTAATTTTTAGAAAGTTTTAGGGT
248817 TAAAATATAATTTTGAAAAAGTTTA
63 TAAAATATAATTTTGAAAAAGTTTA
* * * * * *
248842 GGGGTCAAAATGTCATTTTTAGAAAATCTTAAGGTTAAAATATAA-TTTTGGAAAAG-TTTAGGG
1 GGGGTCAAAATG--AATTTT-GGAAATTTTAAGGGTAAAATGTAATTTTTAG-AAAGTTTTA-GG
* * * *
248905 GTTAAAATGTAATTTTTTAGAAAGTTTT
61 GTTAAAATATAA-TTTTGAAAAAGTTTA
* * *
248933 GGGGTC-AAAT-AATTTTGGAAAAGTTCAGGAGGGTCAAAATGTAATTTTTAGAAAGTTTTAGGA
1 GGGGTCAAAATGAATTTTGG-AAATTTTA--AGGGT-AAAATGTAATTTTTAGAAAGTTTTAGGG
248996 TTAAAATATAATTTTGAAAAAGTTT
62 TTAAAATATAATTTTGAAAAAGTTT
249021 GAGGATTAAA
Statistics
Matches: 145, Mismatches: 22, Indels: 25
0.76 0.11 0.13
Matches are distributed among these distances:
86 1 0.01
87 10 0.07
88 1 0.01
89 30 0.21
90 59 0.41
91 44 0.30
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (87 bp):
GGGGTCAAAATGAATTTTGGAAATTTTAAGGGTAAAATGTAATTTTTAGAAAGTTTTAGGGTTAA
AATATAATTTTGAAAAAGTTTA
Found at i:248878 original size:60 final size:59
Alignment explanation
Indices: 248759--249084 Score: 367
Period size: 60 Copynumber: 5.5 Consensus size: 59
248749 ATCGGGGTCA
* * *
248759 AAAATAGAATTTTGG-AAATTTTAAGGGT-AAAATGGTAATTTTTAGAAAGTTTTAGGGTT
1 AAAATATAATTTTGGAAAAGTTTAGGGGTCAAAAT-GTAATTTTTAGAAAG-TTTAGGGTT
* * * *
248818 AAAATATAATTTTGAAAAAGTTTAGGGGTCAAAATGTCATTTTTAGAAAATCTTAAGGTT
1 AAAATATAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTTAGAAAGT-TTAGGGTT
* * *
248878 AAAATATAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTTTAGAAAGTTTTGGGGT
1 AAAATATAATTTTGGAAAAGTTTAGGGGTCAAAATGTAA-TTTTTAGAAAGTTTAGGGTT
* * *
248938 -CAA-ATAATTTTGGAAAAGTTCAGGAGGGTCAAAATGTAATTTTTAGAAAGTTTTAGGATT
1 AAAATATAATTTTGGAAAAGTTTA-G-GGGTCAAAATGTAATTTTTAGAAAG-TTTAGGGTT
* * * *
248998 AAAATATAATTTTGAAAAAGTTT-GAGGATTAAAATGTAATTTTTAGAAAGTTTTAGGGTC
1 AAAATATAATTTTGGAAAAGTTTAG-GGGTCAAAATGTAATTTTTAGAAAG-TTTAGGGTT
*
249058 GAAATATAATTTTGGAAAAGTTT-GGGG
1 AAAATATAATTTTGGAAAAGTTTAGGGG
249085 ACCTCTAAGG
Statistics
Matches: 228, Mismatches: 30, Indels: 18
0.83 0.11 0.07
Matches are distributed among these distances:
58 18 0.08
59 30 0.13
60 146 0.64
61 18 0.08
62 16 0.07
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.37
Consensus pattern (59 bp):
AAAATATAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTTAGAAAGTTTAGGGTT
Found at i:248943 original size:120 final size:119
Alignment explanation
Indices: 248759--249084 Score: 414
Period size: 120 Copynumber: 2.7 Consensus size: 119
248749 ATCGGGGTCA
* * * * *
248759 AAAATAGAATTTTGG-AAATTTTAAGGG-TAAAATGGTAATTTTTAGAAAGTTTTAGGGTTAAAA
1 AAAATATAATTTTGGAAAAGTTTAGGGGTTAAAAT-GTAATTTTTAGAAAGTTTT-GGGGTCAAA
* *
248822 TATAATTTTGAAAAAGTTTAGGGGTCAAAATGTCATTTTTAGAAAATCTTAAGG-TT
64 TATAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTTAGAAAAT-TTAAGGATT
248878 AAAATATAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTTTAGAAAGTTTTGGGGTC-AA-
1 AAAATATAATTTTGGAAAAGTTTAGGGGTTAAAATGTAA-TTTTTAGAAAGTTTTGGGGTCAAAT
* * *
248941 ATAATTTTGGAAAAGTTCAGGAGGGTCAAAATGTAATTTTTAGAAAGTTTTAGGATT
65 ATAATTTTGGAAAAGTTTA-G-GGGTCAAAATGTAATTTTTAGAAAATTTAAGGATT
* * *
248998 AAAATATAATTTTGAAAAAGTTT-GAGGATTAAAATGTAATTTTTAGAAAGTTTTAGGGTCGAAA
1 AAAATATAATTTTGGAAAAGTTTAG-GGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGTC-AAA
249062 TATAATTTTGGAAAAGTTT-GGGG
64 TATAATTTTGGAAAAGTTTAGGGG
249085 ACCTCTAAGG
Statistics
Matches: 183, Mismatches: 14, Indels: 20
0.84 0.06 0.09
Matches are distributed among these distances:
118 17 0.09
119 46 0.25
120 80 0.44
121 23 0.13
122 17 0.09
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.37
Consensus pattern (119 bp):
AAAATATAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAATA
TAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTTAGAAAATTTAAGGATT
Found at i:249078 original size:30 final size:30
Alignment explanation
Indices: 248759--249080 Score: 209
Period size: 30 Copynumber: 10.8 Consensus size: 30
248749 ATCGGGGTCA
*
248759 AAAATAGAATTTTGG-AAA-TTTTAAGGG-T
1 AAAATATAATTTTGGAAAAGTTTT-AGGGTT
* *
248787 AAAATGGTAATTTT-TAGAAAGTTTTAGGGTT
1 AAAAT-ATAATTTTGGA-AAAGTTTTAGGGTT
* *
248818 AAAATATAATTTTGAAAAAG-TTTAGGGGTC
1 AAAATATAATTTTGGAAAAGTTTTA-GGGTT
* * * * *
248848 AAAATGTCATTTTTAGAAAA-TCTTAAGGTT
1 AAAATAT-AATTTTGGAAAAGTTTTAGGGTT
248878 AAAATATAATTTTGGAAAAG-TTTAGGGGTT
1 AAAATATAATTTTGGAAAAGTTTTA-GGGTT
* ** *
248908 AAAATGTAATTTTTTAGAAAGTTTT-GGGGT
1 AAAATATAATTTTGGA-AAAGTTTTAGGGTT
* ** *
248938 -CAA-ATAATTTTGGAAAAGTTCAGGAGGGTC
1 AAAATATAATTTTGGAAAAGTT--TTAGGGTT
* * *
248968 AAAATGTAATTTT-TAGAAAGTTTTAGGATT
1 AAAATATAATTTTGGA-AAAGTTTTAGGGTT
* * *
248998 AAAATATAATTTTGAAAAAGTTTGAGGATT
1 AAAATATAATTTTGGAAAAGTTTTAGGGTT
* * *
249028 AAAATGTAATTTT-TAGAAAGTTTTAGGGTC
1 AAAATATAATTTTGGA-AAAGTTTTAGGGTT
*
249058 GAAATATAATTTTGGAAAAGTTT
1 AAAATATAATTTTGGAAAAGTTT
249081 GGGGACCTCT
Statistics
Matches: 224, Mismatches: 48, Indels: 42
0.71 0.15 0.13
Matches are distributed among these distances:
27 6 0.03
28 13 0.06
29 26 0.12
30 131 0.58
31 32 0.14
32 16 0.07
ACGTcount: A:0.40, C:0.02, G:0.20, T:0.38
Consensus pattern (30 bp):
AAAATATAATTTTGGAAAAGTTTTAGGGTT
Found at i:250611 original size:35 final size:35
Alignment explanation
Indices: 250572--250653 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
250562 GGAATTTGGA
*
250572 TTCAAAATAAATTTAAATTTAAAATAATTTTAAAC
1 TTCAAAATAAATTTAAATTTAAAATAAATTTAAAC
* *
250607 TTC-AAATAAGTTTTAAATTTATAATAAATTTAAAC
1 TTCAAAATAA-ATTTAAATTTAAAATAAATTTAAAC
*
250642 TT-AAAATGAATT
1 TTCAAAATAAATT
250654 AAAAATCTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
34 8 0.20
35 32 0.80
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (35 bp):
TTCAAAATAAATTTAAATTTAAAATAAATTTAAAC
Found at i:250622 original size:18 final size:17
Alignment explanation
Indices: 250575--250653 Score: 86
Period size: 17 Copynumber: 4.5 Consensus size: 17
250565 ATTTGGATTC
* *
250575 AAAATAAATTTAAATTT
1 AAAATAATTTTAAACTT
250592 AAAATAATTTTAAACTT
1 AAAATAATTTTAAACTT
* *
250609 CAAATAAGTTTTAAATTT
1 AAAATAA-TTTTAAACTT
* *
250627 ATAATAAATTTAAACTT
1 AAAATAATTTTAAACTT
250644 AAAATGAATT
1 AAAAT-AATT
250654 AAAAATCTAA
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
17 33 0.66
18 17 0.34
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.41
Consensus pattern (17 bp):
AAAATAATTTTAAACTT
Found at i:251397 original size:16 final size:16
Alignment explanation
Indices: 251376--251414 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
251366 GTAAGTCTTC
251376 TCGTTTCACTCACTCT
1 TCGTTTCACTCACTCT
251392 TCGTTTCACTCACTCT
1 TCGTTTCACTCACTCT
*
251408 TGGTTTC
1 TCGTTTC
251415 GATTCGGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.10, C:0.33, G:0.10, T:0.46
Consensus pattern (16 bp):
TCGTTTCACTCACTCT
Found at i:262110 original size:25 final size:25
Alignment explanation
Indices: 262076--262127 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
262066 TCGTTAGCGA
262076 GTCATTCTATGCATTTAGACATGGT
1 GTCATTCTATGCATTTAGACATGGT
262101 GTCATTCTATGCATTTAGACATGGT
1 GTCATTCTATGCATTTAGACATGGT
262126 GT
1 GT
262128 TGTCAATGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.40
Consensus pattern (25 bp):
GTCATTCTATGCATTTAGACATGGT
Found at i:262767 original size:19 final size:19
Alignment explanation
Indices: 262738--262775 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
262728 ATCCTATCGG
262738 GATATAATAAAATATAAAAA
1 GATATAATAAAAT-TAAAAA
262758 GATA-AATAAAATTAAAAA
1 GATATAATAAAATTAAAAA
262776 AAATACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
GATATAATAAAATTAAAAA
Found at i:262776 original size:19 final size:20
Alignment explanation
Indices: 262738--262790 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
262728 ATCCTATCGG
262738 GATATAATAAAA-TATAAAAA
1 GATA-AATAAAATTATAAAAA
262758 GATAAATAAAATTA-AAAAA
1 GATAAATAAAATTATAAAAA
* *
262777 AATACATAATAATT
1 GATAAATAA-AATT
262791 TTTTAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (20 bp):
GATAAATAAAATTATAAAAA
Found at i:262776 original size:20 final size:20
Alignment explanation
Indices: 262738--262790 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
262728 ATCCTATCGG
*
262738 GATATAATAAAA-TATAAAAA
1 GATA-AATAAAATTAAAAAAA
262758 GATAAATAAAATTAAAAAAA
1 GATAAATAAAATTAAAAAAA
*
262778 -ATACATAATAATT
1 GATAAATAA-AATT
262791 TTTTAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (20 bp):
GATAAATAAAATTAAAAAAA
Found at i:272636 original size:23 final size:23
Alignment explanation
Indices: 272610--272730 Score: 138
Period size: 23 Copynumber: 5.2 Consensus size: 23
272600 ACACTAGCGC
272610 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
272633 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
*
272656 GCTCTCTATTATTAGCACTGTGTGT
1 GCTCTC--TGATTAGCACTGTGTGT
* *
272681 GCTCTCCGATTAGCA-TTTCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
272704 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
272727 GCTC
1 GCTC
272731 AGTACTTTGT
Statistics
Matches: 83, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
22 5 0.06
23 56 0.67
24 3 0.04
25 16 0.19
26 3 0.04
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:272702 original size:46 final size:47
Alignment explanation
Indices: 272610--272730 Score: 147
Period size: 48 Copynumber: 2.6 Consensus size: 47
272600 ACACTAGCGC
* * *
272610 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGTGCT
1 GCTCTATGATTAGCACTGTGTGTGCTCTCCGATTAGCAC-TCTCGTG-T
* *
272659 -CTCTATTATTAGCACTGTGTGTGCTCTCCGATTAGCA-TTTCGTGT
1 GCTCTATGATTAGCACTGTGTGTGCTCTCCGATTAGCACTCTCGTGT
* *
272704 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTATGATTAGCACTGTGTGTGCTC
272731 AGTACTTTGT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
45 1 0.02
46 29 0.46
48 33 0.52
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.40
Consensus pattern (47 bp):
GCTCTATGATTAGCACTGTGTGTGCTCTCCGATTAGCACTCTCGTGT
Found at i:272764 original size:23 final size:23
Alignment explanation
Indices: 272729--272822 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
272719 CTTTGTGTGC
*
272729 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
272752 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
272775 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
272800 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
272822 T
1 T
272823 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:277171 original size:20 final size:20
Alignment explanation
Indices: 277148--277190 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
277138 CAAAATATAG
277148 TTTAAACAAAAAAAATATTT
1 TTTAAACAAAAAAAATATTT
* **
277168 TTTAAATATTAAAAATATTT
1 TTTAAACAAAAAAAATATTT
277188 TTT
1 TTT
277191 TGTTAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAACAAAAAAAATATTT
Found at i:282537 original size:25 final size:26
Alignment explanation
Indices: 282491--282557 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
282481 AGCTTATATA
282491 TATTTTATAAATTTTAAAATATTTTC
1 TATTTTATAAATTTTAAAATATTTTC
* * *
282517 TATTTT-TAATTTTTTATATATTTATTTC
1 TATTTTATAA-ATTTTA-AAATAT-TTTC
282545 TATTTTTATAAAT
1 TA-TTTTATAAAT
282558 ATTTGATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
25 3 0.09
26 11 0.34
27 4 0.12
28 6 0.19
29 5 0.16
30 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (26 bp):
TATTTTATAAATTTTAAAATATTTTC
Found at i:282551 original size:22 final size:22
Alignment explanation
Indices: 282500--282561 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 22
282490 ATATTTTATA
*
282500 AATTTTA-AAATATTTTCTATTTTT
1 AATTTTATAAATA--TT-TATTTCT
* *
282524 AATTTTTTATATATTTATTTCT
1 AATTTTATAAATATTTATTTCT
*
282546 ATTTTTATAAATATTT
1 AATTTTATAAATATTT
282562 GATAAAACGT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
22 19 0.61
23 2 0.06
24 6 0.19
25 4 0.13
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (22 bp):
AATTTTATAAATATTTATTTCT
Found at i:296801 original size:14 final size:14
Alignment explanation
Indices: 296782--296817 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
296772 GTTCAAGTTT
296782 AATTTGAAATTTAA
1 AATTTGAAATTTAA
296796 AATTTGAAATTTAA
1 AATTTGAAATTTAA
296810 AATTTGAA
1 AATTTGAA
296818 TATTGATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (14 bp):
AATTTGAAATTTAA
Found at i:300378 original size:83 final size:83
Alignment explanation
Indices: 300239--300400 Score: 279
Period size: 83 Copynumber: 2.0 Consensus size: 83
300229 ATGGATGAAA
*
300239 GAGCAAATTAGTCATTGTAGTTAGATCAAAGAGCAAATTGATCCATTCTAATAAGAATTTCACAC
1 GAGCAAATTAGTCATTGTAGTTAGATCAAAGAGCAAACTGATCCATTCTAATAAGAATTTCACAC
300304 ATTTGTAATGTTAAGAAT
66 ATTTGTAATGTTAAGAAT
** * *
300322 GAGCAAATTAGTCATTGTAGTTAGATCAAAGAGCAAACTGATCTTTTCTATTAAGAATTTCATAC
1 GAGCAAATTAGTCATTGTAGTTAGATCAAAGAGCAAACTGATCCATTCTAATAAGAATTTCACAC
300387 ATTTGTAATGTTAA
66 ATTTGTAATGTTAA
300401 AAACTGACGT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 74 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (83 bp):
GAGCAAATTAGTCATTGTAGTTAGATCAAAGAGCAAACTGATCCATTCTAATAAGAATTTCACAC
ATTTGTAATGTTAAGAAT
Found at i:311838 original size:2 final size:2
Alignment explanation
Indices: 311831--311865 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
311821 TATTATTCCA
311831 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 A
311866 CTTTTTACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:315721 original size:12 final size:12
Alignment explanation
Indices: 315706--315754 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
315696 GGAGGCAGAG
*
315706 GATGAGGGTGAT
1 GATGATGGTGAT
315718 GATGATGGTGAT
1 GATGATGGTGAT
*
315730 GGTGATGGTGAT
1 GATGATGGTGAT
* *
315742 GGTGATGATGAT
1 GATGATGGTGAT
315754 G
1 G
315755 CTATTTCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.22, C:0.00, G:0.47, T:0.31
Consensus pattern (12 bp):
GATGATGGTGAT
Found at i:315723 original size:6 final size:6
Alignment explanation
Indices: 315712--315754 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
315702 AGAGGATGAG
* *
315712 GGTGAT GATGAT GGTGAT GGTGAT GGTGAT GGTGAT GATGAT G
1 GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT G
315755 CTATTTCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.33
Consensus pattern (6 bp):
GGTGAT
Found at i:316733 original size:277 final size:267
Alignment explanation
Indices: 316081--316767 Score: 765
Period size: 276 Copynumber: 2.5 Consensus size: 267
316071 TTTAATGTAA
* *
316081 TTATCGGATACCAAACAAGAAGAATGGTGCAGTATATGATTTGATTGAAAGGGAGGGGTATTTTG
1 TTATCGGATACC--A-AATAAGAATGGTGCAATATATGATTTGATTGAAAGGGAGGGGTATTTTG
* * **
316146 GCTTGAAAAATTATATTTGTTAATGTTAGGCCAAATATGCACTTCATTTATAAATATAAATAAGT
63 GCTTGAAAAATTATATTTGTTAATTTTAGGCCGAATATGCACTTTGTTTATAAATATAAATAAGT
* * * * * *
316211 AGATTAGTAATGTTTGGGTAGTGTTGGCAAAGATTGAGGGCTTGGGATTTTAAGTGTTTAGGTTC
128 AGATAAATAAGGTTTGGGTAGTATTGGCAAAGATTGAGGGCTTGGGATATTAAGTGTCTAGGTTC
* * * * * *
316276 TGAGTTCTATTATGTGTATTTATGTGTGAGTTTTCAGTCTAGATTTTGTTCTGATTTAAGTTTCA
193 GGAGTCCTATTATGTGCATTTATGTGTGAGTTCTCAGTCTAGATTTTATTCTGATTTAAGTTCCA
* *
316341 CTATGTGTAT
258 CCATGTATAT
* *
316351 TTATCGGATACCAAATGAGAAGAATGGTGCAACTGCAATATATGATTTGATTG-AAGGGAAAGGT
1 TTATCGGATACCAAAT---AAGAAT-G-G----TGCAATATATGATTTGATTGAAAGGG-AGGGG
* *
316415 TATTTTGGCTTGAAAAATCATATTTGTTAATTTTGGGCCGAATATGCACTTTGTTTATAAAATAT
56 TATTTTGGCTTGAAAAATTATATTTGTTAATTTTAGGCCGAATATGCACTTTGTTTAT-AAATAT
* * *
316480 AAACAAGTAGATAAATAAGGTTTTGGTAGTATTGGCAAAGGCTGAGGGCTTGCGGGCTTGGGATA
120 AAATAAGTAGATAAATAAGGTTTGGGTAGTATTGGCAAA----GA----TTGAGGGCTTGGGATA
*
316545 TTAAGTGTCTAGGTT-GGAGTCCTATTGTGTGCATTTACATGTGTGAGTTC-CTAGTCTAGATTT
177 TTAAGTGTCTAGGTTCGGAGTCCTATTATGTGCATTT--ATGTGTGAGTTCTC-AGTCTAGATTT
*
316608 TATTCTGGTTTAAGTTCCACCATGTATAAT
239 TATTCTGATTTAAGTTCCACCATGTAT-AT
* * *
316638 TT-TCGGAT-TCAAACT-AGAATGGTGCAATATATGATTTGACTGAAAGGGAGGGGTATTTTGGT
1 TTATCGGATACCAAA-TAAGAATGGTGCAATATATGATTTGATTGAAAGGGAGGGGTATTTTGGC
* * *
316700 TTGAAAATTTTGTATTTGTTAATTTTAGGCCGAATATGCACTTTGTTTTTAAATATAAATAAGTA
65 TTGAAAA-ATTATATTTGTTAATTTTAGGCCGAATATGCACTTTGTTTATAAATATAAATAAGTA
316765 GAT
129 GAT
316768 GAGTAACGAT
Statistics
Matches: 351, Mismatches: 40, Indels: 46
0.80 0.09 0.11
Matches are distributed among these distances:
267 2 0.01
268 1 0.00
270 18 0.05
271 1 0.00
272 1 0.00
275 5 0.01
276 128 0.36
277 81 0.23
280 1 0.00
281 3 0.01
282 5 0.01
284 17 0.05
285 33 0.09
286 51 0.15
287 4 0.01
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (267 bp):
TTATCGGATACCAAATAAGAATGGTGCAATATATGATTTGATTGAAAGGGAGGGGTATTTTGGCT
TGAAAAATTATATTTGTTAATTTTAGGCCGAATATGCACTTTGTTTATAAATATAAATAAGTAGA
TAAATAAGGTTTGGGTAGTATTGGCAAAGATTGAGGGCTTGGGATATTAAGTGTCTAGGTTCGGA
GTCCTATTATGTGCATTTATGTGTGAGTTCTCAGTCTAGATTTTATTCTGATTTAAGTTCCACCA
TGTATAT
Found at i:320612 original size:22 final size:21
Alignment explanation
Indices: 320587--320628 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
320577 TTTGAAGGGG
*
320587 TTAATTATAATTTTATCATATA
1 TTAATTAAAATTTTAT-ATATA
320609 TTAATTAAAATTTTATATAT
1 TTAATTAAAATTTTATATAT
320629 TTTGAGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAATTAAAATTTTATATATA
Found at i:324176 original size:17 final size:16
Alignment explanation
Indices: 324136--324173 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
324126 GAATATGATA
*
324136 TTATTAAATTTTATAT
1 TTATTTAATTTTATAT
324152 TTATTTAATTTT-TAT
1 TTATTTAATTTTATAT
324167 TTGATTT
1 TT-ATTT
324174 TAAATATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTATTTAATTTTATAT
Found at i:353668 original size:22 final size:22
Alignment explanation
Indices: 353643--353686 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
353633 CCAATTTGAT
353643 CCAAACCCAAAATGACCAAACA
1 CCAAACCCAAAATGACCAAACA
* *
353665 CCAAATCCAAAATGACCCAACA
1 CCAAACCCAAAATGACCAAACA
353687 TGAAGTGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.36, G:0.05, T:0.07
Consensus pattern (22 bp):
CCAAACCCAAAATGACCAAACA
Found at i:355232 original size:48 final size:48
Alignment explanation
Indices: 355157--355343 Score: 141
Period size: 48 Copynumber: 3.9 Consensus size: 48
355147 ACTCGAACGA
355157 GGACGTGAAGTAGAAGCATT-GGATCGTACTTTGTGTTTTGATGGAGAAGG
1 GGACG-GAA-TAGAAGCATTAGG-TCGTACTTTGTGTTTTGATGGAGAAGG
* * * *
355207 GGACGGAATAGAAGCACTGGGTCGTACTTTGT-TTTTCA---ATGAAGA
1 GGACGGAATAGAAGCATTAGGTCGTACTTTGTGTTTTGATGGA-GAAGG
* * * * * * * *
355252 GGATGGAGTAGAAACAATAGGTCGTGCTTTGTCTTTAGATGGAGAACG
1 GGACGGAATAGAAGCATTAGGTCGTACTTTGTGTTTTGATGGAGAAGG
* ** * **
355300 GGACAGAGCAGAAGCATTAAGTCGTACTTTGTGTCCTGATGGAG
1 GGACGGAATAGAAGCATTAGGTCGTACTTTGTGTTTTGATGGAG
355344 GTGATGGAAT
Statistics
Matches: 107, Mismatches: 24, Indels: 14
0.74 0.17 0.10
Matches are distributed among these distances:
44 1 0.01
45 30 0.28
46 4 0.04
47 5 0.05
48 56 0.52
49 6 0.06
50 5 0.05
ACGTcount: A:0.28, C:0.12, G:0.33, T:0.28
Consensus pattern (48 bp):
GGACGGAATAGAAGCATTAGGTCGTACTTTGTGTTTTGATGGAGAAGG
Found at i:360176 original size:20 final size:21
Alignment explanation
Indices: 360153--360192 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
360143 AAAATATTAA
*
360153 AAAATAACAAAATTC-AAAAT
1 AAAATAAAAAAATTCTAAAAT
360173 AAAATAAAAAAATTCTAAAA
1 AAAATAAAAAAATTCTAAAA
360193 AAAGAGTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAATAAAAAAATTCTAAAAT
Found at i:365212 original size:32 final size:32
Alignment explanation
Indices: 365169--365239 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
365159 CAACTTGCAA
365169 AACTT-AACCTCTCAACAACTACTAACACGGG
1 AACTTAAACCTCTCAACAACTACTAACACGGG
365200 AACTTAAACCTCTCAACAACTACTAACACGGG
1 AACTTAAACCTCTCAACAACTACTAACACGGG
365232 AACTTAAA
1 AACTTAAA
365240 ATACGATGGC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
31 5 0.13
32 34 0.87
ACGTcount: A:0.42, C:0.30, G:0.08, T:0.20
Consensus pattern (32 bp):
AACTTAAACCTCTCAACAACTACTAACACGGG
Found at i:368055 original size:15 final size:17
Alignment explanation
Indices: 368019--368058 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
368009 GGATTTATTG
368019 AAATATATTAATTAAATT
1 AAAT-TATTAATTAAATT
368037 -AATTATT-ATT-AATT
1 AAATTATTAATTAAATT
368051 AAATTATT
1 AAATTATT
368059 CGAAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.19
15 10 0.48
16 4 0.19
17 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTATTAATTAAATT
Found at i:368125 original size:29 final size:27
Alignment explanation
Indices: 368067--368126 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
368057 TTCGAAATAT
* * *
368067 ATTTTTTTAATAGTTAATCAAATTGTA
1 ATTTTTTTAATAATTAATCAAATCGAA
368094 ATTTTTTTAAATATATTAATCAAATCGAA
1 ATTTTTTT-AATA-ATTAATCAAATCGAA
368123 ATTT
1 ATTT
368127 AAATATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 8 0.29
28 4 0.14
29 16 0.57
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (27 bp):
ATTTTTTTAATAATTAATCAAATCGAA
Found at i:380805 original size:16 final size:16
Alignment explanation
Indices: 380784--380815 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
380774 AATTTTTTTC
380784 TCCCCCTTCGTGAGAG
1 TCCCCCTTCGTGAGAG
380800 TCCCCCTTCGTGAGAG
1 TCCCCCTTCGTGAGAG
380816 AACCAGAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.38, G:0.25, T:0.25
Consensus pattern (16 bp):
TCCCCCTTCGTGAGAG
Found at i:380916 original size:18 final size:18
Alignment explanation
Indices: 380893--380933 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
380883 TTTTCTTTTA
380893 TATTATATAATAAAATAT
1 TATTATATAATAAAATAT
* * *
380911 TATTATTTATTATAATAT
1 TATTATATAATAAAATAT
380929 TATTA
1 TATTA
380934 ATTAATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTATATAATAAAATAT
Found at i:380942 original size:18 final size:18
Alignment explanation
Indices: 380900--380942 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
380890 TTATATTATA
* *
380900 TAATAAAATATTATTATT
1 TAATATAATATTATTAAT
*
380918 TATTATAATATTATTAAT
1 TAATATAATATTATTAAT
380936 TAATATA
1 TAATATA
380943 TCTTTTAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATATAATATTATTAAT
Found at i:381616 original size:70 final size:67
Alignment explanation
Indices: 381490--381622 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 67
381480 ATAAACAATA
* * *
381490 TAATGGTTTTGCCTTTTAACTTAATAGGTAAACATTTATCAAAATGACATAATTTTACCTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAAGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
381555 CT
66 CT
** *
381557 TAATGGTTTTGACTTTTAACTTTAGAAAGGGTAAACATTTATCAAAACGATGTAGTTTTACCTTT
1 TAATGGTTTTGACTTTTAAC-TTA-AAA-GGTAAACATTTATCAAAACGACATAATTTTACCTTT
381622 T
63 T
381623 CTTATTTGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 19 0.33
68 3 0.05
69 2 0.04
70 33 0.58
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAAGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
CT
Found at i:388293 original size:28 final size:28
Alignment explanation
Indices: 388249--388303 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
388239 AATCGGTTTA
*
388249 AATAAAAAAATCATTAAAATTTTTAAAT
1 AATAAAAAAATCATTAAAAATTTTAAAT
*
388277 AATAAAAAATAT-TTTAAAAATTTTAAA
1 AATAAAAAA-ATCATTAAAAATTTTAAA
388304 ATCCAATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (28 bp):
AATAAAAAAATCATTAAAAATTTTAAAT
Found at i:398116 original size:51 final size:52
Alignment explanation
Indices: 398012--398117 Score: 178
Period size: 52 Copynumber: 2.1 Consensus size: 52
398002 AATCTACAAA
398012 CTTGATTCTAAAAAATCTAACCATCAACATTTATACATCATATCAATTTAGT
1 CTTGATTCTAAAAAATCTAACCATCAACATTTATACATCATATCAATTTAGT
* * *
398064 CTTGATTCTAAAAAATCTAACCCTCAACATTTATACATTATGT-AATTTAGT
1 CTTGATTCTAAAAAATCTAACCATCAACATTTATACATCATATCAATTTAGT
398115 CTT
1 CTT
398118 TTATAATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 11 0.22
52 40 0.78
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.39
Consensus pattern (52 bp):
CTTGATTCTAAAAAATCTAACCATCAACATTTATACATCATATCAATTTAGT
Found at i:400282 original size:29 final size:29
Alignment explanation
Indices: 400249--400307 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
400239 TAATTATGCC
400249 TTTATAATTTCATTAAGAAATCCAAATAA
1 TTTATAATTTCATTAAGAAATCCAAATAA
400278 TTTATAATTTCATTAAGAAATCCAAATAA
1 TTTATAATTTCATTAAGAAATCCAAATAA
400307 T
1 T
400308 ACAATTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.39
Consensus pattern (29 bp):
TTTATAATTTCATTAAGAAATCCAAATAA
Found at i:405826 original size:31 final size:29
Alignment explanation
Indices: 405751--405826 Score: 71
Period size: 31 Copynumber: 2.5 Consensus size: 29
405741 GAATCCAATA
*
405751 AAAATTTCATGTACAAAATTACACAAAATC
1 AAAA-TTCATGTATAAAATTACACAAAATC
* ** * *
405781 AAAATTTACATATAAAATTATACATTAATTC
1 AAAATTCATGTATAAAATTACACA--AAATC
405812 AAAATTCATGTATAA
1 AAAATTCATGTATAA
405827 TTTTAAGATT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
29 15 0.43
30 4 0.11
31 16 0.46
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATTCATGTATAAAATTACACAAAATC
Found at i:416590 original size:9 final size:9
Alignment explanation
Indices: 416570--416621 Score: 54
Period size: 10 Copynumber: 5.8 Consensus size: 9
416560 TAAACATTAT
416570 AAAAATTC-
1 AAAAATTCA
416578 -AAAATTCA
1 AAAAATTCA
*
416586 AAAAATTATA
1 AAAAATT-CA
416596 AAAAATTCA
1 AAAAATTCA
*
416605 TAAAAATTAA
1 -AAAAATTCA
416615 AAAAATT
1 AAAAATT
416622 AGCATTTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
7 7 0.19
9 14 0.38
10 16 0.43
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAAATTCA
Found at i:416602 original size:19 final size:19
Alignment explanation
Indices: 416578--416621 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
416568 ATAAAAATTC
416578 AAAATTCA-AAAAATTATAA
1 AAAATTCATAAAAATTA-AA
416597 AAAATTCATAAAAATTAAA
1 AAAATTCATAAAAATTAAA
416616 AAAATT
1 AAAATT
416622 AGCATTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAATTCATAAAAATTAAA
Found at i:416622 original size:9 final size:9
Alignment explanation
Indices: 416578--416622 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
416568 ATAAAAATTC
*
416578 AAAATTCAA
1 AAAATTAAA
416587 AAAATTATAA
1 AAAATTA-AA
*
416597 AAAATTCATA
1 AAAATT-AAA
416607 AAAATTAAA
1 AAAATTAAA
416616 AAAATTA
1 AAAATTA
416623 GCATTTTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 15 0.48
10 15 0.48
11 1 0.03
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAATTAAA
Found at i:416767 original size:31 final size:32
Alignment explanation
Indices: 416701--416767 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
416691 TTAAAAAAAC
* **
416701 AATTCAATTTTTTTTTGAAAGGTTGATGGTGA
1 AATTCAATTTTTTTTTGAAAGGTTGAGGGCCA
*
416733 AATTCGATTTTTTTTTGAAA-GTCT-AGGGCCA
1 AATTCAATTTTTTTTTGAAAGGT-TGAGGGCCA
416764 AATT
1 AATT
416768 TAGTTGAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
31 10 0.33
32 20 0.67
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.45
Consensus pattern (32 bp):
AATTCAATTTTTTTTTGAAAGGTTGAGGGCCA
Found at i:432347 original size:29 final size:29
Alignment explanation
Indices: 432301--432372 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
432291 AAAGTAAAGA
* *
432301 GACTAAATTCTTACAAATAGATATATAGG
1 GACTAAATTCTTACAAATACAAATATAGG
* *
432330 GACTAAATTCTTAGAAATACAAATATATG
1 GACTAAATTCTTACAAATACAAATATAGG
*
432359 GACTAAATTATTAC
1 GACTAAATTCTTAC
432373 TTTTCAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (29 bp):
GACTAAATTCTTACAAATACAAATATAGG
Found at i:444739 original size:86 final size:86
Alignment explanation
Indices: 444585--445128 Score: 676
Period size: 86 Copynumber: 6.3 Consensus size: 86
444575 GGTTTTATTC
* * * * * * * *
444585 GTCTTTCTTAGGTATAAGTTGTTCTATCAAGGTTCTTTTTGCTAGTGGTTCTATATTATCTGGCT
1 GTCTTTCTTAGGTGTAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGGTTCTATACTATCCGGGT
* *
444650 TTAATTATCTTATTGATGTTT
66 TTAATCATCCTATTGATGTTT
* * * * * *
444671 GCCTTTATTAGGTGTAGGTTGCTCTATCAAGGTTTCTTTTGTTATTGGTTCTATAATATCTGGGT
1 GTCTTTCTTAGGTGTAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGGTTCTATACTATCCGGGT
* *
444736 TTAATTATCCTATTGATGTTC
66 TTAATCATCCTATTGATGTTT
* * *
444757 GTCTTTCTTAGATGTAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGGTTCTATACTGTCCAGGT
1 GTCTTTCTTAGGTGTAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGGTTCTATACTATCCGGGT
* *
444822 TTAATCGTCTTATTGATGTTT
66 TTAATCATCCTATTGATGTTT
* * * * *
444843 ATCTTTCTTAAGTGTAGGTTGTTCTATCAAGGTTCCTTTTGTTATTGGTTCTATACTGTCCGGGT
1 GTCTTTCTTAGGTGTAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGGTTCTATACTATCCGGGT
* *
444908 TTAATCGTCCTATTGATGATT
66 TTAATCATCCTATTGATGTTT
* * *
444929 GTCTTTCTTAAGTGTAGGTTGCTCTATCAAGGTTCCTTTTGCAATTGGTTCTATACTGTCCGGGT
1 GTCTTTCTTAGGTGTAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGGTTCTATACTATCCGGGT
*
444994 TTAATCGTCCTATTGATGTTT
66 TTAATCATCCTATTGATGTTT
* * * * * *
445015 GTCTTTCTTAGATGTAGGTTGCTTTATCAA-GTTCCTTTAGCTATTGGTTCTGTGCTATCTGGGT
1 GTCTTTCTTAGGTGTAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGGTTCTATACTATCCGGGT
*
445079 TTAATCATCCTATTGATGTTC
66 TTAATCATCCTATTGATGTTT
* * **
445100 GTATTTCTTAGATGTAGGCAGCTCTATCA
1 GTCTTTCTTAGGTGTAGGTTGCTCTATCA
445129 GGGTAATAAG
Statistics
Matches: 404, Mismatches: 54, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
85 72 0.18
86 332 0.82
ACGTcount: A:0.18, C:0.15, G:0.20, T:0.48
Consensus pattern (86 bp):
GTCTTTCTTAGGTGTAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGGTTCTATACTATCCGGGT
TTAATCATCCTATTGATGTTT
Found at i:453313 original size:19 final size:19
Alignment explanation
Indices: 453277--453313 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
453267 TCATTATACT
* *
453277 AATTTATAATTTTTTTTAA
1 AATTTATAATTCTCTTTAA
453296 AATTTATAATTCTCTTTA
1 AATTTATAATTCTCTTTA
453314 GTTGTTAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTATAATTCTCTTTAA
Found at i:462198 original size:42 final size:41
Alignment explanation
Indices: 462139--462218 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 41
462129 GTTATGGCCG
*
462139 CTCCTCTTTAACGGCTAGCTTTTCTATCAAATGGGTCCTTCT
1 CTCCTCCTTAACGGCTAGCTTTTCTATC-AATGGGTCCTTCT
*
462181 CTCCTCCTTAACGGCTAGCTTTTCTATCTATGGGTCCT
1 CTCCTCCTTAACGGCTAGCTTTTCTATCAATGGGTCCT
462219 ACTATACACA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 9 0.25
42 27 0.75
ACGTcount: A:0.15, C:0.30, G:0.15, T:0.40
Consensus pattern (41 bp):
CTCCTCCTTAACGGCTAGCTTTTCTATCAATGGGTCCTTCT
Found at i:463654 original size:14 final size:15
Alignment explanation
Indices: 463623--463653 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
463613 TGGATCTGTT
463623 AATAAATATTTAAAA
1 AATAAATATTTAAAA
463638 AATAAATATTTAAAA
1 AATAAATATTTAAAA
463653 A
1 A
463654 TCAGAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAAATATTTAAAA
Found at i:465428 original size:111 final size:112
Alignment explanation
Indices: 465207--465435 Score: 293
Period size: 111 Copynumber: 2.0 Consensus size: 112
465197 GTTGAAGTTA
*
465207 AAATGATTCTTACCATGATGTCAATGAACTAAGATATTAAATGCCCGACATTTTAGTAAGCTAAA
1 AAATAATTCTTACCATGATGTCAATGAACTAAGATATTAAATGCCCGAC----T--TAAGCTAAA
* *
465272 CATCGATAAATCTCAATCCAATCTTTAAGCAGTAAGGACAGCTACAGGTCAAG
60 CATCAATAAATCTCAATCCAATCTTTAAGCAGTAAGGACAGCTACAAGTCAAG
* *
465325 AAATAATTCTTACCATGATGTCAATGATCTAAGGTATTAAATGCCCGAC-TAAGCTAAACATCAA
1 AAATAATTCTTACCATGATGTCAATGAACTAAGATATTAAATGCCCGACTTAAGCTAAACATCAA
* * *
465389 TATA-C-CATGATCCACTCTTTAGGCAGTAAGGACAGCTACAAGTCAAG
66 TAAATCTCA--ATCCAATCTTTAAGCAGTAAGGACAGCTACAAGTCAAG
465436 CTATATAACT
Statistics
Matches: 101, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
109 2 0.02
110 1 0.01
111 52 0.51
118 46 0.46
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (112 bp):
AAATAATTCTTACCATGATGTCAATGAACTAAGATATTAAATGCCCGACTTAAGCTAAACATCAA
TAAATCTCAATCCAATCTTTAAGCAGTAAGGACAGCTACAAGTCAAG
Found at i:465591 original size:147 final size:147
Alignment explanation
Indices: 465324--465667 Score: 503
Period size: 147 Copynumber: 2.3 Consensus size: 147
465314 TACAGGTCAA
* * * *
465324 GAAAT-AATTCTTACCATGATGTCAATGATCTAAGGTATTAAATGCCCGACTAAGCTAAACATCA
1 GAAATGAA-TCTTACTATGATGTCAATGAACTAAGCTATTGAATGCCCGACTAAGCTAAACATCA
* * *
465388 ATATACCATGATCCACTCTTTAGGCAGTAAGGACAGCTACAAGTCAAGCTATATAACTAACTTGA
65 ATATACCATAATCCAATCTTTAGGCAGCAAGGACAGCTACAAGTCAAGCTATATAACTAACTTGA
* **
465453 ACGTTAGCCAATTCATTT
130 ACCTTAGCCAACGCATTT
465471 GAAATGAATCTTACTATGATGTCAATGAACTAAGCTATTGAATGCCCGACTAAGCTAAACAT-AG
1 GAAATGAATCTTACTATGATGTCAATGAACTAAGCTATTGAATGCCCGACTAAGCTAAACATCA-
* * *
465535 ATATACCATAATCCAATCTTTATGCAGCAAGGACAGCTATAAGTCAAGCTATATAACTAGCTTGA
65 ATATACCATAATCCAATCTTTAGGCAGCAAGGACAGCTACAAGTCAAGCTATATAACTAACTTGA
* *
465600 ACCTTATCCAGCGCATTT
130 ACCTTAGCCAACGCATTT
* *
465618 GAAATGATTCTTACTATGATGCCAATGAACTAAGCTATTGAATGCCCGAC
1 GAAATGAATCTTACTATGATGTCAATGAACTAAGCTATTGAATGCCCGAC
465668 GCCCCAACTA
Statistics
Matches: 178, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
146 1 0.01
147 175 0.98
148 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (147 bp):
GAAATGAATCTTACTATGATGTCAATGAACTAAGCTATTGAATGCCCGACTAAGCTAAACATCAA
TATACCATAATCCAATCTTTAGGCAGCAAGGACAGCTACAAGTCAAGCTATATAACTAACTTGAA
CCTTAGCCAACGCATTT
Found at i:474312 original size:28 final size:28
Alignment explanation
Indices: 474272--474329 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
474262 AAGGCCAACG
*
474272 TTTTTTAAAAGGCTGAAATTTTGGGAAC
1 TTTTTTAAAAGGCTGAAACTTTGGGAAC
*
474300 TTTTTTTAAAGGCTGAAACTTTGGGAAC
1 TTTTTTAAAAGGCTGAAACTTTGGGAAC
474328 TT
1 TT
474330 AGTCCCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (28 bp):
TTTTTTAAAAGGCTGAAACTTTGGGAAC
Found at i:476264 original size:24 final size:24
Alignment explanation
Indices: 476207--476268 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
476197 CATCTATTTT
476207 TACGGTTAAAAATTGACCCTTATG
1 TACGGTTAAAAATTGACCCTTATG
** *
476231 TTTGGTTAAAAATTGACCCTTGTG
1 TACGGTTAAAAATTGACCCTTATG
*
476255 TACGGATAAAAATT
1 TACGGTTAAAAATT
476269 TTAACGGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (24 bp):
TACGGTTAAAAATTGACCCTTATG
Found at i:477444 original size:48 final size:45
Alignment explanation
Indices: 477343--477450 Score: 135
Period size: 48 Copynumber: 2.3 Consensus size: 45
477333 ATGTCTTGAT
* * * * **
477343 GTGGAAAATGACCATACCAAACAAAGATAATGAGCATGTCCTAAG
1 GTGGAAAATGACCATACCAAAAAAAAAAAAAGAGCACATCCTAAG
477388 GTGGAAAATGACCATACCAAAAAAAAAAAAAGGAGAGCACATCCTAAG
1 GTGGAAAATGACCATACC-AAAAAAAAAAAA--AGAGCACATCCTAAG
477436 GTGGAAAATGACCAT
1 GTGGAAAATGACCAT
477451 TAAGGAAACG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
45 18 0.33
46 9 0.17
48 27 0.50
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (45 bp):
GTGGAAAATGACCATACCAAAAAAAAAAAAAGAGCACATCCTAAG
Found at i:480351 original size:2 final size:2
Alignment explanation
Indices: 480344--480399 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
480334 TTATGGGGGC
* * *
480344 CA CA CA CA CA CA AA CA TA CA CA CA CA CG CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
* * *
480386 TA CA TA AA CA CA CA
1 CA CA CA CA CA CA CA
480400 TTTACATATT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.52, C:0.41, G:0.02, T:0.05
Consensus pattern (2 bp):
CA
Found at i:496066 original size:20 final size:21
Alignment explanation
Indices: 496023--496077 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
496013 TATCAAAAGA
* *
496023 TATATTAATTAATAATATTAT
1 TATAATAAATAATAATATTAT
496044 TATAATAAATAATAATA-TAT
1 TATAATAAATAATAATATTAT
* *
496064 TATTATTAATAATA
1 TATAATAAATAATA
496078 TAAAATATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATAATAAATAATAATATTAT
Found at i:496073 original size:24 final size:24
Alignment explanation
Indices: 496032--496086 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
496022 ATATATTAAT
496032 TAATAATATTATTATAATAA-ATAA
1 TAAT-ATATTATTATAATAATATAA
496056 TAATATATTATTATTAATAATATAA
1 TAATATATTATTA-TAATAATATAA
496081 -AATATA
1 TAATATA
496087 AGAAAAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.31
24 16 0.55
25 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAATATATTATTATAATAATATAA
Found at i:502913 original size:17 final size:19
Alignment explanation
Indices: 502886--502924 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
502876 GATATGTGAC
502886 AAAAATGAGAA-TGAAGTG
1 AAAAATGAGAATTGAAGTG
502904 AAAAAT-AGAATTGAAGTG
1 AAAAATGAGAATTGAAGTG
502922 AAA
1 AAA
502925 TTTGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.59, C:0.00, G:0.23, T:0.18
Consensus pattern (19 bp):
AAAAATGAGAATTGAAGTG
Done.