Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011158.1 Kokia drynarioides strain JFW-HI SEQ_126132, 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: 302748
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 168 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:2886 original size:14 final size:14
Alignment explanation
Indices: 2866--2904 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2856 TATTAAAAAT
* *
2866 CCATAACTCACTAA
1 CCATAACCCAATAA
*
2880 CCCTAACCCAATAA
1 CCATAACCCAATAA
2894 CCATAACCCAA
1 CCATAACCCAA
2905 CTAGAAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (14 bp):
CCATAACCCAATAA
Found at i:13893 original size:41 final size:41
Alignment explanation
Indices: 13808--13912 Score: 122
Period size: 41 Copynumber: 2.6 Consensus size: 41
13798 GTGGAGATAG
* * *
13808 TGATTCAGGCTTTGTGCCTAACAGGCTTTGTGCCGATGAGT
1 TGATTCAGGCTTTGTGCCTAGCAAGCTTTGTGCCGATGAAT
* * *
13849 TGATTTAGGTTTTGTGCCTAGCAAGTTTTGTGCCGGA-GAAT
1 TGATTCAGGCTTTGTGCCTAGCAAGCTTTGTGCC-GATGAAT
* *
13890 TGATGCATGCTTTGTGCCTAGCA
1 TGATTCAGGCTTTGTGCCTAGCA
13913 GGCCTCGTGT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 51 0.96
42 2 0.04
ACGTcount: A:0.18, C:0.17, G:0.29, T:0.36
Consensus pattern (41 bp):
TGATTCAGGCTTTGTGCCTAGCAAGCTTTGTGCCGATGAAT
Found at i:16065 original size:17 final size:17
Alignment explanation
Indices: 16033--16071 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
16023 TAACTACCTC
**
16033 CTAACTAATTCTCTAAA
1 CTAACTAATTAACTAAA
16050 CTAACTAATTAACTAAA
1 CTAACTAATTAACTAAA
*
16067 TTAAC
1 CTAAC
16072 AACAGTTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CTAACTAATTAACTAAA
Found at i:22907 original size:9 final size:9
Alignment explanation
Indices: 22895--22924 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
22885 AATTTTATTA
*
22895 TTAAAACTT
1 TTAAAATTT
22904 TTAAAATTT
1 TTAAAATTT
22913 TTAAAATTT
1 TTAAAATTT
22922 TTA
1 TTA
22925 TTAAGCTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (9 bp):
TTAAAATTT
Found at i:23308 original size:21 final size:22
Alignment explanation
Indices: 23284--23325 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
23274 GACACTTTTA
23284 AATTAAAATTAAATTA-AAAAT
1 AATTAAAATTAAATTAGAAAAT
**
23305 AATTTTAATTAAATTAGAAAA
1 AATTAAAATTAAATTAGAAAA
23326 AAAAAAATTT
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:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AATTAAAATTAAATTAGAAAAT
Found at i:34927 original size:25 final size:25
Alignment explanation
Indices: 34889--34936 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
34879 ATTTCCGCAT
34889 AAAAAATGGGTTTTTC-TTTTACCA
1 AAAAAATGGGTTTTTCATTTTACCA
34913 AAAAAATGGGTTTTTCATTTTACC
1 AAAAAATGGGTTTTTCATTTTACC
34937 TTGCCTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (25 bp):
AAAAAATGGGTTTTTCATTTTACCA
Found at i:35644 original size:3 final size:3
Alignment explanation
Indices: 35636--35670 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
35626 TTTTTACATA
*
35636 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
35671 AATTTAATGA
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:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:38132 original size:31 final size:31
Alignment explanation
Indices: 38097--38159 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
38087 AACAAATCGA
*
38097 TGACTTAAATAAAAACTTTTGAATAATTTAG
1 TGACTTAAATAAAAACTTTAGAATAATTTAG
*
38128 TGACTTAAATGAAAACTTTAGAATAATTTAG
1 TGACTTAAATAAAAACTTTAGAATAATTTAG
38159 T
1 T
38160 AATCGTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.38
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTAGAATAATTTAG
Found at i:39762 original size:25 final size:26
Alignment explanation
Indices: 39729--39779 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
39719 TTTTTAACTC
39729 TTTTTTATT-TTTACTCTAT-TTCTCT
1 TTTTTTATTCTTT-CTCTATCTTCTCT
*
39754 TTTTTTATTCTTTCTCTTTCTTCTCT
1 TTTTTTATTCTTTCTCTATCTTCTCT
39780 CTACTCCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTTTATTCTTTCTCTATCTTCTCT
Found at i:43890 original size:13 final size:14
Alignment explanation
Indices: 43867--43901 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
43857 GGGTGGCAAT
43867 GAAGAGGGAAGGGG
1 GAAGAGGGAAGGGG
43881 GAAG-GGGAA-GGG
1 GAAGAGGGAAGGGG
43893 GAAGAGGGA
1 GAAGAGGGA
43902 TTTTCCCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 9 0.45
14 4 0.20
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (14 bp):
GAAGAGGGAAGGGG
Found at i:44838 original size:46 final size:46
Alignment explanation
Indices: 44735--44853 Score: 157
Period size: 46 Copynumber: 2.6 Consensus size: 46
44725 AGTTGTAGCA
* * * * *
44735 AATTTTGATTAACCTTTATGGCACATTCTGTTTAATCTTTGTGGCG
1 AATTTTGATTAGCCTTTGTGGCACATTCTATTTAACCTTTGTGACG
* *
44781 AATTTTAATTAGCCTTTGTGGCACATTCTATTTAGCCTTTGTGACG
1 AATTTTGATTAGCCTTTGTGGCACATTCTATTTAACCTTTGTGACG
* *
44827 AATTTTGATTAGTCTTTGTGGCGCATT
1 AATTTTGATTAGCCTTTGTGGCACATT
44854 TTGTATGCTG
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.45
Consensus pattern (46 bp):
AATTTTGATTAGCCTTTGTGGCACATTCTATTTAACCTTTGTGACG
Found at i:44856 original size:23 final size:23
Alignment explanation
Indices: 44736--44873 Score: 100
Period size: 23 Copynumber: 5.9 Consensus size: 23
44726 GTTGTAGCAA
* * *
44736 ATTTTGATTAACCTTTATGGCAC
1 ATTTTGATTAGCCTTTGTGGCGC
* * ** *
44759 ATTCTGTTTAATCTTTGTGGCGA
1 ATTTTGATTAGCCTTTGTGGCGC
* *
44782 ATTTTAATTAGCCTTTGTGGCAC
1 ATTTTGATTAGCCTTTGTGGCGC
* * *
44805 ATTCT-ATTTAGCCTTTGTGACGA
1 ATTTTGA-TTAGCCTTTGTGGCGC
*
44828 ATTTTGATTAGTCTTTGTGGCGC
1 ATTTTGATTAGCCTTTGTGGCGC
44851 ATTTTGTATGCT-GCCTTTGTGGC
1 ATTTTG-AT--TAGCCTTTGTGGC
44874 ATATTCTATT
Statistics
Matches: 88, Mismatches: 22, Indels: 8
0.75 0.19 0.07
Matches are distributed among these distances:
22 1 0.01
23 73 0.83
24 3 0.03
25 10 0.11
26 1 0.01
ACGTcount: A:0.18, C:0.16, G:0.20, T:0.46
Consensus pattern (23 bp):
ATTTTGATTAGCCTTTGTGGCGC
Found at i:47169 original size:23 final size:23
Alignment explanation
Indices: 47143--47200 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
47133 GCATACGGTG
47143 ACGCCGCGATGAGGAGCATGACA
1 ACGCCGCGATGAGGAGCATGACA
47166 ACGCCGCGATGAGGAGCATGACA
1 ACGCCGCGATGAGGAGCATGACA
*
47189 ACGTCGCGATGA
1 ACGCCGCGATGA
47201 TGCGACTCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.29, C:0.26, G:0.34, T:0.10
Consensus pattern (23 bp):
ACGCCGCGATGAGGAGCATGACA
Found at i:49566 original size:18 final size:19
Alignment explanation
Indices: 49525--49566 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
49515 CACTCCATTT
* *
49525 TAAAATTAAAAGATAAAAG
1 TAAATTTAAAAAATAAAAG
49544 T-AATTTAAAAAATAAAA-
1 TAAATTTAAAAAATAAAAG
49561 TAAATT
1 TAAATT
49567 GCATGAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 18 0.90
19 1 0.05
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
TAAATTTAAAAAATAAAAG
Found at i:52001 original size:49 final size:48
Alignment explanation
Indices: 51948--52563 Score: 389
Period size: 49 Copynumber: 12.6 Consensus size: 48
51938 TTAGGGTATA
* * *
51948 AGATTTGCCGTTGTGGCTTCAATCTTTCCCTTCATGTCTTTGTGGTACT
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-CTTTGTGGTACT
* * * * *
51997 AGATTTGTCGTTGCGGCTTAAATCTTTCCTTTCATGCTTCTGAGGTACA
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTT-TGTGGTACT
* * * * * * *
52046 AGGTTCGCTGTTGCGACTTAAACCTTTCCCTTTATATCTTTGTGGTAGT
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT-GCTTTGTGGTACT
* **
52095 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTAAA
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTT-TGTGGTACT
* * * * * * *
52144 AGGTTCGCCGTTACGACTTAAA-CTTTTCCTT-TTGTATCTTCGTGGTATT
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG---CTTTGTGGTACT
* * * *
52193 AGATTCGTCGTTGCGGCTTAAATTTTTCCTTTCATGCTTTTGAGGTA-T
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGC-TTTGTGGTACT
* * * ** * * * *
52241 AAGGTTCGCCATTACGATTTAAA-CATTTCCTTTTATAACTTCGTGGTACT
1 -AGATTCGCCGTTGCGGCTTAAATC-TTTCCCTTCAT-GCTTTGTGGTACT
* * * * * *
52291 AGATTTGTCGTTACAGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACA
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTT-TGTGGTACT
* * * * * *
52340 AGATTCGTCGTTGTGACTTAAACCTTTCCCTTTGTAT-CTTCGTGGTACT
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCC-TT-CATGCTTTGTGGTACT
** * * *
52389 AGATTCATCGTTGCGGCTTGAATCTTTCCCTTCATGCTTCTGAGGTACA
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTT-TGTGGTACT
* * * * *
52438 AGGTTCGCCGTTGCGACTTAAA-CTTTTCCCTTTATATCTTCGTGGTACT
1 AGATTCGCCGTTGCGGCTTAAATC-TTTCCCTTCAT-GCTTTGTGGTACT
** * * * * *
52487 AGATTCATCATTGCGGCTTGAATCTTTCCCTTCATACTTCTGAGGTACA
1 AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTT-TGTGGTACT
* * * *
52536 AGGTTCACCGTTGCGACTTAAACCTTTC
1 AGATTCGCCGTTGCGGCTTAAATCTTTC
52564 TCTCCAAACC
Statistics
Matches: 428, Mismatches: 116, Indels: 46
0.73 0.20 0.08
Matches are distributed among these distances:
47 4 0.01
48 28 0.07
49 368 0.86
50 24 0.06
51 4 0.01
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (48 bp):
AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTGTGGTACT
Found at i:52090 original size:98 final size:98
Alignment explanation
Indices: 51971--52563 Score: 826
Period size: 98 Copynumber: 6.1 Consensus size: 98
51961 TGGCTTCAAT
* * * * *
51971 CTTTCCCTTCATGTCTTTGTGGTACTAGATTTGTCGTTGCGGCTTAAATCTTTCCTTTCATGCTT
1 CTTTCCCTTTATATCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
*
52036 CTGAGGTACAAGGTTCGCTGTTGCGACTTAAAC
66 CTGAGGTACAAGGTTCGCCGTTGCGACTTAAAC
* * *
52069 CTTTCCCTTTATATCTTTGTGGTAGTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
1 CTTTCCCTTTATATCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
* *
52134 CTGAGGTAAAAGGTTCGCCGTTACGACTTAAAC
66 CTGAGGTACAAGGTTCGCCGTTGCGACTTAAAC
* * * * * *
52167 TTTTCCTTTTGTATCTTCGTGGTATTAGATTCGTCGTTGCGGCTTAAATTTTTCCTTTCATGCTT
1 CTTTCCCTTTATATCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
* * * * *
52232 TTGAGGTATAAGGTTCGCCATTACGATTTAAAC
66 CTGAGGTACAAGGTTCGCCGTTGCGACTTAAAC
* * * * * *
52265 ATTTCCTTTTATAACTTCGTGGTACTAGATTTGTCGTTACAGCTTAAATCTTTCCCTTCATGCTT
1 CTTTCCCTTTATATCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
* * *
52330 CTGAGGTACAAGATTCGTCGTTGTGACTTAAAC
66 CTGAGGTACAAGGTTCGCCGTTGCGACTTAAAC
* * *
52363 CTTTCCCTTTGTATCTTCGTGGTACTAGATTCATCGTTGCGGCTTGAATCTTTCCCTTCATGCTT
1 CTTTCCCTTTATATCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
52428 CTGAGGTACAAGGTTCGCCGTTGCGACTTAAAC
66 CTGAGGTACAAGGTTCGCCGTTGCGACTTAAAC
* * * * *
52461 TTTTCCCTTTATATCTTCGTGGTACTAGATTCATCATTGCGGCTTGAATCTTTCCCTTCATACTT
1 CTTTCCCTTTATATCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
*
52526 CTGAGGTACAAGGTTCACCGTTGCGACTTAAAC
66 CTGAGGTACAAGGTTCGCCGTTGCGACTTAAAC
52559 CTTTC
1 CTTTC
52564 TCTCCAAACC
Statistics
Matches: 439, Mismatches: 56, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
98 439 1.00
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.40
Consensus pattern (98 bp):
CTTTCCCTTTATATCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
CTGAGGTACAAGGTTCGCCGTTGCGACTTAAAC
Found at i:71405 original size:23 final size:24
Alignment explanation
Indices: 71342--71406 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 24
71332 TAAATAAATA
* *
71342 AAATTAAAATAC-ATAAAAATATT
1 AAATTAAAATTCTATTAAAATATT
* * *
71365 AAAATAAAATTTTAATTAAACTA-T
1 AAATTAAAATTCT-ATTAAAATATT
71389 AAATTAAAATTCTATTAA
1 AAATTAAAATTCTATTAA
71407 TACAATTAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
23 14 0.42
24 12 0.36
25 7 0.21
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATTAAAATTCTATTAAAATATT
Found at i:72332 original size:19 final size:20
Alignment explanation
Indices: 72304--72341 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
72294 NAAAAAACTA
72304 AAAATAATTT-TCAAAATTTT
1 AAAATAATTTAT-AAAATTTT
72324 AAAAT-ATTTATAAAATTT
1 AAAATAATTTATAAAATTT
72342 ATATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATAATTTATAAAATTTT
Found at i:76301 original size:17 final size:18
Alignment explanation
Indices: 76279--76314 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
76269 GAGATAGACA
76279 AAAAAAATAA-AAAGAAG
1 AAAAAAATAATAAAGAAG
76296 AAAAAAATAATAAAGAAG
1 AAAAAAATAATAAAGAAG
76314 A
1 A
76315 GTGATAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (18 bp):
AAAAAAATAATAAAGAAG
Found at i:80431 original size:17 final size:16
Alignment explanation
Indices: 80409--80440 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
80399 AAATCCAATT
80409 GAACCAAGTCCAAACCC
1 GAACCAAGT-CAAACCC
80426 GAACCAAGTCAAACC
1 GAACCAAGTCAAACC
80441 GTTGACCGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.44, C:0.38, G:0.12, T:0.06
Consensus pattern (16 bp):
GAACCAAGTCAAACCC
Found at i:80509 original size:27 final size:26
Alignment explanation
Indices: 80464--80528 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
80454 TAATCGATCG
* * *
80464 TTGACTGTTAACCGTTGACTATTGACT
1 TTGACT-TTGACCATTGACCATTGACT
* *
80491 GTTGATTTTGACCATTGACCGTTGACT
1 -TTGACTTTGACCATTGACCATTGACT
80518 TTGACTTTGAC
1 TTGACTTTGAC
80529 TCGTTAACTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
26 10 0.32
27 16 0.52
28 5 0.16
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (26 bp):
TTGACTTTGACCATTGACCATTGACT
Found at i:80533 original size:20 final size:20
Alignment explanation
Indices: 80478--80539 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
80468 CTGTTAACCG
*
80478 TTGACTATTGACT-GTTGATT
1 TTGACT-TTGACTCGTTGACT
*
80498 TTGACCATTGAC-CGTTGACT
1 TTGA-CTTTGACTCGTTGACT
*
80518 TTGACTTTGACTCGTTAACT
1 TTGACTTTGACTCGTTGACT
80538 TT
1 TT
80540 TTCCAAGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 6 0.17
20 28 0.80
21 1 0.03
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.45
Consensus pattern (20 bp):
TTGACTTTGACTCGTTGACT
Found at i:85188 original size:227 final size:227
Alignment explanation
Indices: 84793--85241 Score: 810
Period size: 227 Copynumber: 2.0 Consensus size: 227
84783 GCCTCTCGGT
84793 AGTTGAAATCGCATGAGATTAACTACCCTACTCATGATCTTGAGCTTGCTGCAGTAATCTTCGCT
1 AGTTGAAATCGCATGAGATTAACTACCCTACTCATGATCTTGAGCTTGCTGCAGTAATCTTCGCT
84858 CTTAAAATTTGAAGACACTATATCTACGGGGAGAAGTGTTATATCTTTACTGATCATAAGAGCTT
66 CTTAAAATTTGAAGACACTATATCTACGGGGAGAAGTGTTATATCTTTACTGATCATAAGAGCTT
84923 GAAGTATTTGCTTAATCAGAAGGAGCTAACGTCGTTGGTTAGAACTCCTTAAGGACTATGATTGT
131 GAAGTATTTGCTTAATCAGAAGGAGCTAACGTCGTTGGTTAGAACTCCTTAAGGACTATGATTGT
*
84988 GAGATTGAGTATTACCCTGGTAAGGTTTCGAC
196 GAGATTGAGTATCACCCTGGTAAGGTTTCGAC
* *
85020 AGTTGAAATCGCATGAGATTAATTACCCTACTCATGATCTTGAGCTTGCTGCAGTAATCTTCGTT
1 AGTTGAAATCGCATGAGATTAACTACCCTACTCATGATCTTGAGCTTGCTGCAGTAATCTTCGCT
* *
85085 CTTAAAATTTGAAGACACTATCTCTATGGGGAGAAGTGTTATAT-TTTCACTGATCATAAGAGCT
66 CTTAAAATTTGAAGACACTATATCTACGGGGAGAAGTGTTATATCTTT-ACTGATCATAAGAGCT
* *
85149 TGAAGTATTTTCTTACTCAGAAGGAGCTAACGTCGTTGGTTAGAACTCCTTAAGGACTATGATTG
130 TGAAGTATTTGCTTAATCAGAAGGAGCTAACGTCGTTGGTTAGAACTCCTTAAGGACTATGATTG
*
85214 TGAGATTGAGTATCACCTTGGTAAGGTT
195 TGAGATTGAGTATCACCCTGGTAAGGTT
85242 AATATGGTTA
Statistics
Matches: 213, Mismatches: 8, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
226 3 0.01
227 210 0.99
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (227 bp):
AGTTGAAATCGCATGAGATTAACTACCCTACTCATGATCTTGAGCTTGCTGCAGTAATCTTCGCT
CTTAAAATTTGAAGACACTATATCTACGGGGAGAAGTGTTATATCTTTACTGATCATAAGAGCTT
GAAGTATTTGCTTAATCAGAAGGAGCTAACGTCGTTGGTTAGAACTCCTTAAGGACTATGATTGT
GAGATTGAGTATCACCCTGGTAAGGTTTCGAC
Found at i:87474 original size:11 final size:11
Alignment explanation
Indices: 87458--87532 Score: 51
Period size: 11 Copynumber: 6.8 Consensus size: 11
87448 ACCAAGTCAA
87458 ACCGTTGACCG
1 ACCGTTGACCG
*
87469 ACCGTTGATCG
1 ACCGTTGACCG
** * *
87480 GTCGTTAATCG
1 ACCGTTGACCG
*
87491 ACCATTGACCG
1 ACCGTTGACCG
* **
87502 ATCGTTGACTA
1 ACCGTTGACCG
* *
87513 ATCGTTGATCG
1 ACCGTTGACCG
87524 ACCGTTGAC
1 ACCGTTGAC
87533 TTTGATCGTT
Statistics
Matches: 46, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
11 46 1.00
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (11 bp):
ACCGTTGACCG
Found at i:87551 original size:20 final size:20
Alignment explanation
Indices: 87523--87616 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 20
87513 ATCGTTGATC
87523 GACCGTTGACTTTGATCGTT
1 GACCGTTGACTTTGATCGTT
* *
87543 GACCATTGACTATTGGTCGTT
1 GACCGTTGACT-TTGATCGTT
*
87564 GACCGTTGACTTTGACCGTT
1 GACCGTTGACTTTGATCGTT
* *
87584 GATCGTTGACTTTGA-CTTT
1 GACCGTTGACTTTGATCGTT
*
87603 GACCCTTTGACTTT
1 GA-CCGTTGACTTT
87617 TTTCAAAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
19 5 0.08
20 40 0.63
21 18 0.29
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.40
Consensus pattern (20 bp):
GACCGTTGACTTTGATCGTT
Found at i:90972 original size:9 final size:8
Alignment explanation
Indices: 90942--90969 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
90932 CTAAATTTGT
90942 AAAATAAA
1 AAAATAAA
90950 AAAATAAA
1 AAAATAAA
90958 AAAATAAA
1 AAAATAAA
90966 AAAA
1 AAAA
90970 ATATATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:95798 original size:99 final size:99
Alignment explanation
Indices: 95627--95824 Score: 387
Period size: 99 Copynumber: 2.0 Consensus size: 99
95617 GATCTTTCCG
95627 AAAAAGGCAACCCCAAATGCCATGCAACTAAATGAGGAAAACTTAAGGGGTCTAAGTTTAAAAAT
1 AAAAAGGCAACCCCAAATGCCATGCAACTAAATGAGGAAAACTTAAGGGGTCTAAGTTTAAAAAT
95692 TGGAACAACAGATAAAAATGTCTTTTATCATTTA
66 TGGAACAACAGATAAAAATGTCTTTTATCATTTA
*
95726 AAAAAGGCAACCCCAAATGTCATGCAACTAAATGAGGAAAACTTAAGGGGTCTAAGTTTAAAAAT
1 AAAAAGGCAACCCCAAATGCCATGCAACTAAATGAGGAAAACTTAAGGGGTCTAAGTTTAAAAAT
95791 TGGAACAACAGATAAAAATGTCTTTTATCATTTA
66 TGGAACAACAGATAAAAATGTCTTTTATCATTTA
95825 CATTATGCTG
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (99 bp):
AAAAAGGCAACCCCAAATGCCATGCAACTAAATGAGGAAAACTTAAGGGGTCTAAGTTTAAAAAT
TGGAACAACAGATAAAAATGTCTTTTATCATTTA
Found at i:100518 original size:2 final size:2
Alignment explanation
Indices: 100511--100535 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
100501 TCAACCAACA
100511 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 A
100536 ACAACCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:100701 original size:24 final size:22
Alignment explanation
Indices: 100670--100717 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
100660 AGCAATATTG
*
100670 AAATAACATTAAAAAATAGCAAC
1 AAATAACA-CAAAAAATAGCAAC
*
100693 AAATCAACACGAAAAATAGCAAC
1 AAAT-AACACAAAAAATAGCAAC
100716 AA
1 AA
100718 GCCAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.65, C:0.17, G:0.06, T:0.12
Consensus pattern (22 bp):
AAATAACACAAAAAATAGCAAC
Found at i:100752 original size:22 final size:22
Alignment explanation
Indices: 100682--100752 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
100672 ATAACATTAA
* *
100682 AAAATAGCAACAAATCAACACG
1 AAAATAGCAACAAAACAACAAG
** * *
100704 AAAAATAGCAACAAGCCAATAAA
1 -AAAATAGCAACAAAACAACAAG
*
100727 AAAATTGCAACAAAACAACAAG
1 AAAATAGCAACAAAACAACAAG
100749 AAAA
1 AAAA
100753 CAACATCAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
22 21 0.55
23 17 0.45
ACGTcount: A:0.65, C:0.18, G:0.08, T:0.08
Consensus pattern (22 bp):
AAAATAGCAACAAAACAACAAG
Found at i:100752 original size:23 final size:23
Alignment explanation
Indices: 100681--100752 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
100671 AATAACATTA
* *
100681 AAAAATAGCAACAAATCAACACG
1 AAAAATAGCAACAAAACAACAAG
** *
100704 AAAAATAGCAACAAGCCAATAA-
1 AAAAATAGCAACAAAACAACAAG
*
100726 AAAAATTGCAACAAAACAACAAG
1 AAAAATAGCAACAAAACAACAAG
100749 AAAA
1 AAAA
100753 CAACATCAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 18 0.45
23 22 0.55
ACGTcount: A:0.65, C:0.18, G:0.08, T:0.08
Consensus pattern (23 bp):
AAAAATAGCAACAAAACAACAAG
Found at i:101080 original size:353 final size:335
Alignment explanation
Indices: 100259--100946 Score: 903
Period size: 350 Copynumber: 2.0 Consensus size: 335
100249 AACAAAATAA
* * * * * ** * *
100259 TAGTAATATAATAGTGAAATGACATCGAAATGGTAGCGGAACAATATTAAAAGTAGTAGTGAAAT
1 TAGTAAAACAATAGAGAAAT-ACATCGAAATGGTAGC-GAACAGTATCAAAACCAATATTGAAAT
* * * * * *
100324 AGCATTAAAAAATAGCAACAAATCAACACGAAAAACAGCAACAAGCCAGTAAAGAAATTGCAACA
64 AACAATAAAAAATAGCAACAAATCAAAACGAAAAATA--AACAA-CCAATAAAAAAATTGCAACA
*
100389 AAACAAGGAAACAACATCAAAACACAATAGCAAAACGTGCCAAAAAAGCAATAAAACAACTTTTA
126 AAACAAGAAAACAACATCAAAACACAATAGCAAAACGTGCCAAAAAAGCAATAAAACAACTTTTA
*
100454 AATAGCAACAAAATAACGTCGAAAGAGCGGCAACATGCAAAATGTAATCAACCAACAATATATAT
191 AATAGCAACAAAAGAACGTCGAAAGAGCGGCAACATGCAAAATGTAATCAACCAAC---------
*
100519 ATATATATATATATATAACAACCAATCAACATATTTTTTTAACAAGCTATAAATTGTAACCTAAA
247 A-ATATATATATATATAACAACCAATCAACATATTTTTTTAACAAGCTATAAATCGTAACCTAAA
*
100584 TTAATTGTCAACAATTAAAAAGTAG
311 CTAATTGTCAACAATTAAAAAGTAG
* * * * *
100609 TAGTAATATAATAGTGAAATGACATCGAAATGGTAGCGGAACAGTATTAAAAGCAATATTGAAAT
1 TAGTAAAACAATAGAGAAAT-ACATCGAAATGGTAGC-GAACAGTATCAAAACCAATATTGAAAT
* *
100674 AACATTAAAAAATAGCAACAAATCAACACGAAAAATAGCAACAAGCCAATAAAAAAATTGCAACA
64 AACAATAAAAAATAGCAACAAATCAAAACGAAAAATA--AACAA-CCAATAAAAAAATTGCAAC-
100739 AAACAACAAGAAAACAACATCAAAACACAATAGCAAAACGTGCCAAAAAAGCAATAAAACAACTT
125 -AA-AACAAGAAAACAACATCAAAACACAATAGCAAAACGTGCCAAAAAAGCAATAAAACAACTT
100804 TTAAATAGCAACAAAAGAACGTCGAAAGAGCGGCAACATGCAAAATGTAATCAACCAAC-A-ATA
188 TTAAATAGCAACAAAAGAACGTCGAAAGAGCGGCAACATGCAAAATGTAATCAACCAACAATATA
*
100867 TATATATATAACAACCAATCAACATATTTTTTTAACAAGCTATAAATCGTAACCTATACTAATTG
253 TATATATATAACAACCAATCAACATATTTTTTTAACAAGCTATAAATCGTAACCTAAACTAATTG
*
100932 TCAACAATTGAAAAG
318 TCAACAATTAAAAAG
100947 GTAACTTAGA
Statistics
Matches: 321, Mismatches: 14, Indels: 15
0.92 0.04 0.04
Matches are distributed among these distances:
341 79 0.25
342 1 0.00
350 121 0.38
352 2 0.01
353 118 0.37
ACGTcount: A:0.52, C:0.16, G:0.12, T:0.20
Consensus pattern (335 bp):
TAGTAAAACAATAGAGAAATACATCGAAATGGTAGCGAACAGTATCAAAACCAATATTGAAATAA
CAATAAAAAATAGCAACAAATCAAAACGAAAAATAAACAACCAATAAAAAAATTGCAACAAAACA
AGAAAACAACATCAAAACACAATAGCAAAACGTGCCAAAAAAGCAATAAAACAACTTTTAAATAG
CAACAAAAGAACGTCGAAAGAGCGGCAACATGCAAAATGTAATCAACCAACAATATATATATATA
TAACAACCAATCAACATATTTTTTTAACAAGCTATAAATCGTAACCTAAACTAATTGTCAACAAT
TAAAAAGTAG
Found at i:104774 original size:52 final size:52
Alignment explanation
Indices: 104696--104932 Score: 366
Period size: 52 Copynumber: 4.6 Consensus size: 52
104686 AATGTAAAAG
104696 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* * *
104748 GGTCCGATGACTACGTTTCATCGTGAGTATATGAATCCTTTACAGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* * * * * *
104800 GGTTCGATTACTATGTATTATTGTGAGTATATGAATTCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* * *
104852 GGTCCGATGACTATGTGTCATCATGAGTATATGAATCTTTTACGGATTGTGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
104904 GGTCCGATGACTATGTGTCATCGTGAGTA
1 GGTCCGATGACTATGTGTCATCGTGAGTA
104933 CTAAAGGAAA
Statistics
Matches: 164, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 164 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
Found at i:105732 original size:21 final size:21
Alignment explanation
Indices: 105684--105733 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
105674 AAGACTTGTT
* *
105684 TCGGTAAAAGAGTCACCTGTA
1 TCGGTAGAAGAGTCACATGTA
*
105705 TCGGTAGAATAGTCACATGTA
1 TCGGTAGAAGAGTCACATGTA
105726 TCGGTAGA
1 TCGGTAGA
105734 GATCTGCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (21 bp):
TCGGTAGAAGAGTCACATGTA
Found at i:113862 original size:29 final size:29
Alignment explanation
Indices: 113817--113952 Score: 182
Period size: 29 Copynumber: 4.7 Consensus size: 29
113807 TCAGATTCGG
*
113817 CCACAAAGGCTCACATATAACAAAATCAA
1 CCACAAAGGCTCTCATATAACAAAATCAA
*
113846 CCACAAAGGCTCTCATATAACAAAATCAG
1 CCACAAAGGCTCTCATATAACAAAATCAA
* *
113875 CCACAAAGGGTCTCATATAGCAAAATCAA
1 CCACAAAGGCTCTCATATAACAAAATCAA
* * *
113904 CCATAAAGGCTCTTATATAACAAAATCAG
1 CCACAAAGGCTCTCATATAACAAAATCAA
* **
113933 TCACAAACACTCTCATATAA
1 CCACAAAGGCTCTCATATAA
113953 TAGAATTAGT
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 92 1.00
ACGTcount: A:0.46, C:0.26, G:0.09, T:0.19
Consensus pattern (29 bp):
CCACAAAGGCTCTCATATAACAAAATCAA
Found at i:113899 original size:58 final size:58
Alignment explanation
Indices: 113790--113939 Score: 196
Period size: 58 Copynumber: 2.6 Consensus size: 58
113780 ACAGAGATAG
* * * *
113790 CCACAAAGGCTC-CAT-TATCAGATTCGGCCACAAAGGCTCACATATAACAAAATCAA
1 CCACAAAGGCTCTCATATAACAAAATCAGCCACAAAGGCTCACATATAACAAAATCAA
* * *
113846 CCACAAAGGCTCTCATATAACAAAATCAGCCACAAAGGGTCTCATATAGCAAAATCAA
1 CCACAAAGGCTCTCATATAACAAAATCAGCCACAAAGGCTCACATATAACAAAATCAA
* * *
113904 CCATAAAGGCTCTTATATAACAAAATCAGTCACAAA
1 CCACAAAGGCTCTCATATAACAAAATCAGCCACAAA
113940 CACTCTCATA
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
56 12 0.15
57 3 0.04
58 67 0.82
ACGTcount: A:0.44, C:0.26, G:0.11, T:0.19
Consensus pattern (58 bp):
CCACAAAGGCTCTCATATAACAAAATCAGCCACAAAGGCTCACATATAACAAAATCAA
Found at i:113963 original size:29 final size:29
Alignment explanation
Indices: 113830--113968 Score: 116
Period size: 29 Copynumber: 4.8 Consensus size: 29
113820 CAAAGGCTCA
** **
113830 CATATAACAAAATCAACCACAAAGGCTCT
1 CATATAACAAAATCAGTCACAAACACTCT
* ***
113859 CATATAACAAAATCAGCCACAAAGGGTCT
1 CATATAACAAAATCAGTCACAAACACTCT
* ** * **
113888 CATATAGCAAAATCAACCATAAAGGCTCT
1 CATATAACAAAATCAGTCACAAACACTCT
*
113917 TATATAACAAAATCAGTCACAAACACTCT
1 CATATAACAAAATCAGTCACAAACACTCT
* * *
113946 CATATAATAGAATTAGTCACAAA
1 CATATAACAAAATCAGTCACAAA
113969 GGCTCCTTCT
Statistics
Matches: 93, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 93 1.00
ACGTcount: A:0.47, C:0.23, G:0.09, T:0.21
Consensus pattern (29 bp):
CATATAACAAAATCAGTCACAAACACTCT
Found at i:116168 original size:195 final size:195
Alignment explanation
Indices: 115771--116217 Score: 497
Period size: 195 Copynumber: 2.3 Consensus size: 195
115761 GAAACTGATG
* * *
115771 CGATGGTTGAGGTACCGCATATGTTACGAGTCCTCGACAGCTCGTGTGAGTAGCATCATGAGTCG
1 CGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGACAGCTCGTGTGAGCAGCATCATGACTCG
* * *
115836 AGAAATGAGAAAAGAATCCAAGAATGGATTGCAGGCCCTACGATGGCTGAGATTTATGCATAAGT
66 AGAAATGAGAAAAGAATCCAAGAATGGATTACAGGCCCTACGATGGCTGAGATCTATGCATAAGC
* * * * * *
115901 GTATATTCTTGATTGCTCGTGTGAGCAGCATCATTAGGGAACAGTTATATACACATATATCGTAT
131 GTATACTCTCGATAGCTCGTGTGAGCAGCATCATTAGGGAACAGTTATATACACAAACACCGTAT
* * * * * *
115966 CGATGGCTGAGGTACCGTATATGTTGCGAGTCCTCAACAGTTCGTGTGAGCAGTATCGTGACTCG
1 CGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGACAGCTCGTGTGAGCAGCATCATGACTCG
* * * * * * * * * *
116031 AGAAA-GAGATATGGATCCTA-AATGGATTATAGGCCTTACGATGGTTGGGA-CTATGCTTTA-C
66 AGAAATGAGAAAAGAATCCAAGAATGGATTACAGGCCCTACGATGGCTGAGATCTATGCATAAGC
* * *
116092 GTATACTCTCGATAGCTCGTGTGAGCAGCATCGTTCGGGAATAGTTTATAGTACAGACAAACACC
131 GTATACTCTCGATAGCTCGTGTGAGCAGCATCATTAGGGAACAG-TTATA-TAC--ACAAACACC
116157 GTAT
192 GTAT
* * ** * *
116161 TGATGGCTGGGGTACCGCATACATTACGAGTCCTCGACAGCTCATGTGAGAAGCATC
1 CGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGACAGCTCGTGTGAGCAGCATC
116218 GAGTACTGTT
Statistics
Matches: 206, Mismatches: 42, Indels: 8
0.80 0.16 0.03
Matches are distributed among these distances:
191 38 0.18
192 12 0.06
193 28 0.14
194 11 0.05
195 117 0.57
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (195 bp):
CGATGGCTGAGGTACCGCATATGTTACGAGTCCTCGACAGCTCGTGTGAGCAGCATCATGACTCG
AGAAATGAGAAAAGAATCCAAGAATGGATTACAGGCCCTACGATGGCTGAGATCTATGCATAAGC
GTATACTCTCGATAGCTCGTGTGAGCAGCATCATTAGGGAACAGTTATATACACAAACACCGTAT
Found at i:121049 original size:22 final size:22
Alignment explanation
Indices: 121021--121065 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
121011 TACTCTCGAT
*
121021 AAAATAGCAACATCGATTAAAC
1 AAAATAGCAAAATCGATTAAAC
121043 AAAATAGCAAAATCGATTAAAC
1 AAAATAGCAAAATCGATTAAAC
121065 A
1 A
121066 TTATTAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.58, C:0.16, G:0.09, T:0.18
Consensus pattern (22 bp):
AAAATAGCAAAATCGATTAAAC
Found at i:121301 original size:22 final size:21
Alignment explanation
Indices: 121272--121317 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
121262 GTAGAGGGAA
* * *
121272 TAAAAAAATAATAATATCGAT
1 TAAAAAAACAACAACATCGAT
121293 TAAACAAAACAACAACATCGAT
1 TAAA-AAAACAACAACATCGAT
121315 TAA
1 TAA
121318 GCATGATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.61, C:0.13, G:0.04, T:0.22
Consensus pattern (21 bp):
TAAAAAAACAACAACATCGAT
Found at i:123735 original size:19 final size:17
Alignment explanation
Indices: 123703--123741 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
123693 CTAAACAAAC
123703 AAACAAAAAATTAAATA
1 AAACAAAAAATTAAATA
123720 AAACAAAACTAATTAAATA
1 AAACAAAA--AATTAAATA
123739 AAA
1 AAA
123742 AACTAAGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.40
19 12 0.60
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (17 bp):
AAACAAAAAATTAAATA
Found at i:126844 original size:75 final size:74
Alignment explanation
Indices: 126721--126894 Score: 303
Period size: 75 Copynumber: 2.3 Consensus size: 74
126711 TATTTGTGAT
* *
126721 GACTGATGAAGTTGAACAATGAAATCTATGAAGAGATGCAACAAATTCCTTGATCTTTGATAAAA
1 GACTGATGAAGTTGAACGATGAAATCTATCAAGAGATGCAACAAATTCCTTGATCTTTGAT-AAA
*
126786 AAGCGTTGTA
65 AAGCGTCGTA
126796 GACTGATGAAGTTGAACGATGAAATCTATCAAGAGATGCAACAAATTCCTTGATCTTTGATAAAA
1 GACTGATGAAGTTGAACGATGAAATCTATCAAGAGATGCAACAAATTCCTTGATCTTTGATAAAA
126861 AGCGTCGTA
66 AGCGTCGTA
*
126870 GACTAATGAAGTTGAACGATGAAAT
1 GACTGATGAAGTTGAACGATGAAAT
126895 TTGACCGTTG
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
74 36 0.38
75 59 0.62
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.27
Consensus pattern (74 bp):
GACTGATGAAGTTGAACGATGAAATCTATCAAGAGATGCAACAAATTCCTTGATCTTTGATAAAA
AGCGTCGTA
Found at i:133915 original size:32 final size:32
Alignment explanation
Indices: 133874--133937 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
133864 CCTTCTTTAG
133874 GTACTTCATTTCCTATAACGCATTATGTTAAT
1 GTACTTCATTTCCTATAACGCATTATGTTAAT
133906 GTACTTCATTTCCTATAACGCATTATGTTAAT
1 GTACTTCATTTCCTATAACGCATTATGTTAAT
133938 TATGACGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (32 bp):
GTACTTCATTTCCTATAACGCATTATGTTAAT
Found at i:135104 original size:24 final size:25
Alignment explanation
Indices: 135068--135123 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
135058 AGACTACCAA
*
135068 AGCAACTTCTAAA-TAAAACTC-AAG
1 AGCAA-TTCTAAAGAAAAACTCAAAG
135092 AGCAATTCTTAAAGAAAAACTCAAAG
1 AGCAATTC-TAAAGAAAAACTCAAAG
135118 AG-AATT
1 AGCAATT
135124 ATTATTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 3 0.11
24 9 0.32
25 11 0.39
26 5 0.18
ACGTcount: A:0.52, C:0.16, G:0.11, T:0.21
Consensus pattern (25 bp):
AGCAATTCTAAAGAAAAACTCAAAG
Found at i:148930 original size:2 final size:2
Alignment explanation
Indices: 148923--148965 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
148913 ATTTAGTATT
148923 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
148965 T
1 T
148966 TTATTATTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:154045 original size:20 final size:19
Alignment explanation
Indices: 153973--154053 Score: 69
Period size: 19 Copynumber: 4.2 Consensus size: 19
153963 TGAAAACTAT
*
153973 TAAATTTTAAT-AAAAATA
1 TAAATTTTTATAAAAAATA
*
153991 TAGAATTTAT-TAAAAAAT-
1 TA-AATTTTTATAAAAAATA
* *
154009 TAAATTTTTTTGTAAAAATTA
1 TAAA--TTTTTATAAAAAATA
154030 TAAATTTTTATAAAAAATTA
1 TAAATTTTTATAAAAAA-TA
154050 TAAA
1 TAAA
154054 ATGCATAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
17 2 0.04
18 5 0.10
19 26 0.52
20 13 0.26
21 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TAAATTTTTATAAAAAATA
Found at i:154561 original size:93 final size:91
Alignment explanation
Indices: 154420--154596 Score: 250
Period size: 93 Copynumber: 1.9 Consensus size: 91
154410 AAAAAAAATC
* * * * *
154420 AGGGGTTTAATTGCTTTTTTTTTTTAATTTGAGAGCTTTTTTATGCATTTTGA-AAGTTCAAGTA
1 AGGGGCTTAATTACTTTTTTTTTTTAATTTGAGAGCTTTATGATGCATTTTGACAA-TTCAAATA
154484 CTCAATTAAGTGCAAAAAAAAATTTGT
65 CTCAATTAAGTGCAAAAAAAAATTTGT
*
154511 AGGGGCTTAATTACTTTTTTTTTTTTAAATTTGAG-GATCTTATGATGCATTTTGACAATTCAAA
1 AGGGGCTTAATTAC-TTTTTTTTTTT-AATTTGAGAGCT-TTATGATGCATTTTGACAATTCAAA
154575 TACTCAATTAAGTGCAAAAAAA
63 TACTCAATTAAGTGCAAAAAAA
154597 TGTAAGAACT
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
91 12 0.16
92 13 0.17
93 49 0.64
94 2 0.03
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (91 bp):
AGGGGCTTAATTACTTTTTTTTTTTAATTTGAGAGCTTTATGATGCATTTTGACAATTCAAATAC
TCAATTAAGTGCAAAAAAAAATTTGT
Found at i:163983 original size:39 final size:38
Alignment explanation
Indices: 163929--164006 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 38
163919 AATGAAAAGG
* *
163929 AAATAAATGAAATAGAAATAGATAAATAATATAAACATA
1 AAATAAATAAAATAGAAATAGATAAAT-ATATAAAAATA
* *
163968 AAATAAATAAAATAGAAATATATTAATATATAAAAATA
1 AAATAAATAAAATAGAAATAGATAAATATATAAAAATA
164006 A
1 A
164007 TATTAATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
38 11 0.31
39 24 0.69
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (38 bp):
AAATAAATAAAATAGAAATAGATAAATATATAAAAATA
Found at i:164008 original size:27 final size:25
Alignment explanation
Indices: 163968--164028 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
163958 TATAAACATA
163968 AAATAAATAAAATAGAAATATATTAAT
1 AAATAAA-AAAATAGAAATATATT-AT
* **
163995 ATATAAAAATAATATTAATATATTAT
1 AAATAAAAA-AATAGAAATATATTAT
164021 AAATAAAA
1 AAATAAAA
164029 TATATAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 11 0.38
27 18 0.62
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (25 bp):
AAATAAAAAAATAGAAATATATTAT
Found at i:164025 original size:11 final size:11
Alignment explanation
Indices: 163954--164087 Score: 59
Period size: 11 Copynumber: 12.5 Consensus size: 11
163944 AAATAGATAA
*
163954 ATAATATAAAC
1 ATAATATAAAT
*
163965 ATAAAATAAAT
1 ATAATATAAAT
* *
163976 AAAATAGAAAT
1 ATAATATAAAT
163987 AT-AT-T-AAT
1 ATAATATAAAT
163995 AT-ATA-AAA-
1 ATAATATAAAT
*
164003 ATAATATTAAT
1 ATAATATAAAT
*
164014 ATATTATAAAT
1 ATAATATAAAT
*
164025 AAAATATATAA-
1 ATAATATA-AAT
*
164036 ATGAATTCTAATAT
1 AT-AA-TATAA-AT
*
164050 ATAATAAAAAT
1 ATAATATAAAT
* **
164061 CTATATATGTAT
1 ATA-ATATAAAT
164073 ATAATA-AAAT
1 ATAATATAAAT
164083 ATAAT
1 ATAAT
164088 TAATATTTTT
Statistics
Matches: 89, Mismatches: 23, Indels: 23
0.66 0.17 0.17
Matches are distributed among these distances:
8 9 0.10
9 5 0.06
10 11 0.12
11 41 0.46
12 15 0.17
13 6 0.07
14 2 0.02
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:164030 original size:22 final size:19
Alignment explanation
Indices: 163987--164031 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 19
163977 AAATAGAAAT
*
163987 ATATTAATATATAAAAATA
1 ATATTAATATATAAAAAAA
164006 ATATTAATATATTATAAATAAA
1 ATATTAATATA-TA-AAA-AAA
164028 ATAT
1 ATAT
164032 ATAAATGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 11 0.50
20 2 0.09
21 3 0.14
22 6 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATTAATATATAAAAAAA
Found at i:166862 original size:18 final size:18
Alignment explanation
Indices: 166841--166912 Score: 53
Period size: 18 Copynumber: 4.2 Consensus size: 18
166831 AATATTTTTT
166841 TTTATATAAAACATCATA
1 TTTATATAAAACATCATA
* *
166859 TTTA-A-ACAA-ATCA-C
1 TTTATATAAAACATCATA
* * *
166873 TTTAAAAAAAACATTTATA
1 TTTATATAAAACA-TCATA
*
166892 TTTATTTAAAACATCATA
1 TTTATATAAAACATCATA
166910 TTT
1 TTT
166913 GAAAAAAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
14 4 0.10
15 5 0.12
16 6 0.15
17 2 0.05
18 13 0.32
19 10 0.25
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTATATAAAACATCATA
Found at i:166867 original size:50 final size:51
Alignment explanation
Indices: 166808--166921 Score: 122
Period size: 51 Copynumber: 2.2 Consensus size: 51
166798 AAGATACAAG
* * * * *
166808 ATTTGAACAAAACAATAT-AAATAAATATTTTTTTTTATATAAAACATCAT
1 ATTTAAACAAAACAATATAAAAAAAACATTTATATTTATATAAAACATCAT
* * * *
166858 ATTTAAACAAATCACTTTAAAAAAAACATTTATATTTATTTAAAACATCAT
1 ATTTAAACAAAACAATATAAAAAAAACATTTATATTTATATAAAACATCAT
*
166909 ATTTGAAAAAAAA
1 ATTT-AAACAAAA
166922 AACAAACTAT
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
50 14 0.27
51 31 0.61
52 6 0.12
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.37
Consensus pattern (51 bp):
ATTTAAACAAAACAATATAAAAAAAACATTTATATTTATATAAAACATCAT
Found at i:171384 original size:50 final size:50
Alignment explanation
Indices: 171327--171456 Score: 136
Period size: 50 Copynumber: 2.6 Consensus size: 50
171317 ATATGAAATA
* *
171327 TTTATATAAGAT-TCAATATTTGAACAAAACAATATAAATAAATATTTATT
1 TTTATATAAAATATC-ATATTTAAACAAAACAATATAAATAAATATTTATT
* * * ** *
171377 TTTATATAAAATATCATATTTAAACAAATCATTTTAAATAAATATAAATA
1 TTTATATAAAATATCATATTTAAACAAAACAATATAAATAAATATTTATT
* * *
171427 TTTATTTAAAACATCATATTTGAAAAAAAA
1 TTTATATAAAATATCATATTT-AAACAAAA
171457 GAAGAAGATA
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
50 58 0.88
51 8 0.12
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.39
Consensus pattern (50 bp):
TTTATATAAAATATCATATTTAAACAAAACAATATAAATAAATATTTATT
Found at i:171398 original size:18 final size:18
Alignment explanation
Indices: 171377--171447 Score: 53
Period size: 18 Copynumber: 4.2 Consensus size: 18
171367 AATATTTATT
171377 TTTATATAAAATATCATA
1 TTTATATAAAATATCATA
*
171395 TTTA-A-ACAA-ATCAT-
1 TTTATATAAAATATCATA
* *
171409 TTTAAAT-AAATATAAATA
1 TTTATATAAAATAT-CATA
* *
171427 TTTATTTAAAACATCATA
1 TTTATATAAAATATCATA
171445 TTT
1 TTT
171448 GAAAAAAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
14 4 0.10
15 8 0.20
16 5 0.12
17 3 0.08
18 15 0.38
19 5 0.12
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTATATAAAATATCATA
Found at i:172710 original size:13 final size:13
Alignment explanation
Indices: 172692--172721 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
172682 TTTACACTCA
172692 AGAACAAGTGACC
1 AGAACAAGTGACC
172705 AGAACAAGTGACC
1 AGAACAAGTGACC
172718 AGAA
1 AGAA
172722 TTCTTTCTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.20, G:0.23, T:0.07
Consensus pattern (13 bp):
AGAACAAGTGACC
Found at i:183655 original size:14 final size:14
Alignment explanation
Indices: 183630--183665 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
183620 GAAAAAACCT
183630 AATTCGAATACTTCA
1 AATTC-AATACTTCA
*
183645 TATTCAATACTTCA
1 AATTCAATACTTCA
183659 AATTCAA
1 AATTCAA
183666 AAAAAGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (14 bp):
AATTCAATACTTCA
Found at i:186822 original size:31 final size:32
Alignment explanation
Indices: 186770--186847 Score: 79
Period size: 32 Copynumber: 2.4 Consensus size: 32
186760 AAAATTATTG
* ** *
186770 TTTTGGAAAATTTTAACTTTTTTT-TTTATATA
1 TTTTGG-AATTTTTAACTTTTTTTAAATATAAA
186802 TTTTGGAATTTTTAGA-TTTTTTTAAATATAAA
1 TTTTGGAATTTTTA-ACTTTTTTTAAATATAAA
*
186834 TTTTGAAATTTTTA
1 TTTTGGAATTTTTA
186848 TTAATATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 14 0.36
32 25 0.64
ACGTcount: A:0.31, C:0.01, G:0.08, T:0.60
Consensus pattern (32 bp):
TTTTGGAATTTTTAACTTTTTTTAAATATAAA
Found at i:186853 original size:24 final size:24
Alignment explanation
Indices: 186808--186854 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
186798 TATATTTTGG
* * *
186808 AATTTTTAGATTTTTTTAAATATA
1 AATTTTGAAATTTTTATAAATATA
*
186832 AATTTTGAAATTTTTATTAATAT
1 AATTTTGAAATTTTTATAAATAT
186855 TTTGAATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
AATTTTGAAATTTTTATAAATATA
Found at i:186876 original size:19 final size:19
Alignment explanation
Indices: 186853--186903 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
186843 TTTTATTAAT
*
186853 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAATC
* * *
186872 GTTTTAAATTTTTTAAAATC
1 ATTTTGAA-TTTTAAAAATC
186892 ATTTTGAATTTT
1 ATTTTGAATTTT
186904 TTGTAATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATC
Found at i:188056 original size:58 final size:58
Alignment explanation
Indices: 187992--188106 Score: 185
Period size: 58 Copynumber: 2.0 Consensus size: 58
187982 CCAAATTCAA
*
187992 GCCTAGCAAATAGAACTAAATTTTTAGTTGAGCTTAGCCTGAACTTGAACCCAACTCG
1 GCCTAGCAAATAGAACTAAATTTTTAGTTGAGCTTAGCCTGAACCTGAACCCAACTCG
* * * *
188050 GCCTAGCAAATGGACCTAAATTTTTAGTTGAGCTTGGCTTGAACCTGAACCCAACTC
1 GCCTAGCAAATAGAACTAAATTTTTAGTTGAGCTTAGCCTGAACCTGAACCCAACTC
188107 AACCTATAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (58 bp):
GCCTAGCAAATAGAACTAAATTTTTAGTTGAGCTTAGCCTGAACCTGAACCCAACTCG
Found at i:194752 original size:17 final size:17
Alignment explanation
Indices: 194730--194768 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
194720 AGGTGGAGAA
* *
194730 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
*
194747 CTTGTTTGTAGAGAATT
1 CTTGTTCGTAGAGAATT
194764 CTTGT
1 CTTGT
194769 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:196007 original size:29 final size:29
Alignment explanation
Indices: 195925--196201 Score: 203
Period size: 29 Copynumber: 9.6 Consensus size: 29
195915 AAACTGCACA
* * **
195925 ACAAAGGCATTTCCTTT-CCAAAGATAACC
1 ACAAAGGCATTT-CTTTAACAGAGATTGCC
* *
195954 ACAAAGGC-TTCCTTTAA-AAAGGATTGCC
1 ACAAAGGCATTTCTTTAACAGA-GATTGCC
* *
195982 ACAAAGGCATTTCTTTAATATAGATTGCC
1 ACAAAGGCATTTCTTTAACAGAGATTGCC
* * *
196011 ACAAAGGGATTTCGTTT-ATAGAGATTGAC
1 ACAAAGGCATTTC-TTTAACAGAGATTGCC
*
196040 ACAAAGGCATTTCCATT-ACAGAGATTGCC
1 ACAAAGGCATTT-CTTTAACAGAGATTGCC
*** *
196069 ACAAAGATGTTTCCTTT-ACAGAGATTACC
1 ACAAAGGCATTT-CTTTAACAGAGATTGCC
*
196098 ACAAAGGCATTTCCTTT-ACAAAGATTGCC
1 ACAAAGGCATTT-CTTTAACAGAGATTGCC
* *
196127 ACAAAGGCATTTCTTTAACAAAGATTACC
1 ACAAAGGCATTTCTTTAACAGAGATTGCC
** * *
196156 ACAAAGGTGTTTCCTTT-ACAAAGATTTCC
1 ACAAAGGCATTT-CTTTAACAGAGATTGCC
* *
196185 ATAAAGGC-GTTCTTTAA
1 ACAAAGGCATTTCTTTAA
196202 GAGGTTCATT
Statistics
Matches: 209, Mismatches: 30, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
27 11 0.05
28 22 0.11
29 166 0.79
30 10 0.05
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (29 bp):
ACAAAGGCATTTCTTTAACAGAGATTGCC
Found at i:196100 original size:87 final size:87
Alignment explanation
Indices: 195925--196192 Score: 260
Period size: 87 Copynumber: 3.1 Consensus size: 87
195915 AAACTGCACA
* * * * *
195925 ACAAAGGCATTTCCTTTCCAAAGA-TAACCACAAAGGC-TTCCTTTAA-AAAGGATTGCCACAAA
1 ACAAAGGCATTTCCTTTACAAAGATTGA-CACAAAGGCATTTCATTAACAAA-GATTACCACAAA
*** *
195987 GGCATTT-CTTTA-ATATAGATTGCC
64 GATGTTTCCTTTACA-A-AGATTACC
* * * * * *
196011 ACAAAGGGATTTCGTTTATAGAGATTGACACAAAGGCATTTCCATT-ACAGAGATTGCCACAAAG
1 ACAAAGGCATTTCCTTTACAAAGATTGACACAAAGGCATTT-CATTAACAAAGATTACCACAAAG
*
196075 ATGTTTCCTTTACAGAGATTACC
65 ATGTTTCCTTTACAAAGATTACC
* * *
196098 ACAAAGGCATTTCCTTTACAAAGATTGCCACAAAGGCATTTCTTTAACAAAGATTACCACAAAGG
1 ACAAAGGCATTTCCTTTACAAAGATTGACACAAAGGCATTTCATTAACAAAGATTACCACAAAGA
*
196163 TGTTTCCTTTACAAAGATTTCC
66 TGTTTCCTTTACAAAGATTACC
*
196185 ATAAAGGC
1 ACAAAGGC
196193 GTTCTTTAAG
Statistics
Matches: 149, Mismatches: 26, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
86 31 0.21
87 107 0.72
88 10 0.07
89 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (87 bp):
ACAAAGGCATTTCCTTTACAAAGATTGACACAAAGGCATTTCATTAACAAAGATTACCACAAAGA
TGTTTCCTTTACAAAGATTACC
Found at i:196192 original size:58 final size:57
Alignment explanation
Indices: 195925--196201 Score: 271
Period size: 58 Copynumber: 4.8 Consensus size: 57
195915 AAACTGCACA
* ** * *
195925 ACAAAGGCATTTCCTTTCCAAAGATAACCACAAAGGCTTCCTTTAA-AAAGGATTGCC
1 ACAAAGGCATTTCCTTTACAAAGATTGCCACAAAGGCTTTCTTTAACAAA-GATTACC
* * *
195982 ACAAAGGCATTT-CTTTA-ATATAGATTGCCACAAAGGGATTTCGTTT-ATAGAGATTGA-C
1 ACAAAGGCATTTCCTTTACA-A-AGATTGCCACAAA-GGCTTTC-TTTAACAAAGATT-ACC
* * *
196040 ACAAAGGCATTTCCATTACAGAGATTGCCACAAAGATG-TTTCCTTT-ACAGAGATTACC
1 ACAAAGGCATTTCCTTTACAAAGATTGCCACAAAG--GCTTT-CTTTAACAAAGATTACC
196098 ACAAAGGCATTTCCTTTACAAAGATTGCCACAAAGGCATTTCTTTAACAAAGATTACC
1 ACAAAGGCATTTCCTTTACAAAGATTGCCACAAAGGC-TTTCTTTAACAAAGATTACC
** * * *
196156 ACAAAGGTGTTTCCTTTACAAAGATTTCCATAAAGGCGTTCTTTAA
1 ACAAAGGCATTTCCTTTACAAAGATTGCCACAAAGGCTTTCTTTAA
196202 GAGGTTCATT
Statistics
Matches: 187, Mismatches: 18, Indels: 30
0.80 0.08 0.13
Matches are distributed among these distances:
55 1 0.01
56 6 0.03
57 37 0.20
58 131 0.70
59 11 0.06
60 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (57 bp):
ACAAAGGCATTTCCTTTACAAAGATTGCCACAAAGGCTTTCTTTAACAAAGATTACC
Found at i:199097 original size:24 final size:25
Alignment explanation
Indices: 199050--199100 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
199040 GTGATAATTT
*
199050 TAAAATAAAATTATTATTTTTTGAATA
1 TAAAATAAAATTATTA--TCTTGAATA
199077 TAAAATAAAATTATTA-CTTGAATA
1 TAAAATAAAATTATTATCTTGAATA
199101 GAATTCTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
27 16 0.70
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (25 bp):
TAAAATAAAATTATTATCTTGAATA
Found at i:199170 original size:12 final size:12
Alignment explanation
Indices: 199137--199170 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
199127 AAATTGTGAT
199137 AATTATAATTTA
1 AATTATAATTTA
199149 AATT-TAAATTTA
1 AATTAT-AATTTA
199161 AATTATAATT
1 AATTATAATT
199171 ATTAGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.05
12 18 0.90
13 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTATAATTTA
Found at i:199353 original size:21 final size:22
Alignment explanation
Indices: 199314--199354 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
199304 TGTTGAATAT
199314 TTTAAAAATGTTTTAATTATGA
1 TTTAAAAATGTTTTAATTATGA
* *
199336 TTTAGAAAT-TTTTTATTAT
1 TTTAAAAATGTTTTAATTAT
199355 AATATTTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (22 bp):
TTTAAAAATGTTTTAATTATGA
Found at i:201109 original size:32 final size:31
Alignment explanation
Indices: 201034--201111 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 31
201024 TTGATCCAAT
* *
201034 TTGGTACTCAAACTTGAAACTTTTTCTTAAT
1 TTGGTACTTAAACTTGAAACTTTTTCTTAAG
* * * *
201065 TTAGTACCTAAACTTGATAATTTTTTTTTAAG
1 TTGGTACTTAAACTTGA-AACTTTTTCTTAAG
201097 TTGGTACTTAAACTT
1 TTGGTACTTAAACTT
201112 TTCGTGAACC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 14 0.37
32 24 0.63
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.47
Consensus pattern (31 bp):
TTGGTACTTAAACTTGAAACTTTTTCTTAAG
Found at i:201643 original size:22 final size:24
Alignment explanation
Indices: 201612--201662 Score: 79
Period size: 22 Copynumber: 2.2 Consensus size: 24
201602 AGTTGGAAAT
201612 TTTTAAATTAA-TTTTTTT-AAAC
1 TTTTAAATTAATTTTTTTTAAAAC
*
201634 TTTTAGATTAATTTTTTTTAAAAC
1 TTTTAAATTAATTTTTTTTAAAAC
201658 TTTTA
1 TTTTA
201663 CTTCAATGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 10 0.38
23 7 0.27
24 9 0.35
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTTAAATTAATTTTTTTTAAAAC
Found at i:202039 original size:2 final size:2
Alignment explanation
Indices: 202032--202070 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
202022 TTTTAAACTA
202032 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
202071 CTTCTTCTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:202557 original size:25 final size:25
Alignment explanation
Indices: 202528--202589 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
202518 AACAAACATT
* * *
202528 TTTTTTTTAAAATTTTAATCTTTTTA
1 TTTTTTTCAAAA-GTTAATATTTTTA
*
202554 TTTTTTTCATAAGTTAATATTTTTA
1 TTTTTTTCAAAAGTTAATATTTTTA
202579 TTTTTGTTCAA
1 TTTTT-TTCAA
202590 CCAATTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 16 0.53
26 14 0.47
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (25 bp):
TTTTTTTCAAAAGTTAATATTTTTA
Found at i:202768 original size:20 final size:20
Alignment explanation
Indices: 202740--202791 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
202730 TATGTTCGAG
* *
202740 ATTTAAGGTTTATGATTTGA
1 ATTTAAGGTTTAAGATTTAA
* *
202760 TTTTGAGGTTTAAGATTTAA
1 ATTTAAGGTTTAAGATTTAA
202780 ATTTAAGGTTTA
1 ATTTAAGGTTTA
202792 GAGGTTCGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (20 bp):
ATTTAAGGTTTAAGATTTAA
Found at i:203080 original size:9 final size:9
Alignment explanation
Indices: 203068--203107 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
203058 AAAATTAAAT
203068 AAATATTAA
1 AAATATTAA
*
203077 AAATATGAA
1 AAATATTAA
*
203086 AAATGTTAA
1 AAATATTAA
203095 AAATGATTAA
1 AAAT-ATTAA
203105 AAA
1 AAA
203108 GTGTTTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (9 bp):
AAATATTAA
Found at i:203080 original size:18 final size:18
Alignment explanation
Indices: 203057--203098 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
203047 GTATTTTAAA
203057 AAAAAT-TAAATAAATATT
1 AAAAATATAAA-AAATATT
* *
203075 AAAAATATGAAAAATGTT
1 AAAAATATAAAAAATATT
203093 AAAAAT
1 AAAAAT
203099 GATTAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (18 bp):
AAAAATATAAAAAATATT
Found at i:203357 original size:16 final size:17
Alignment explanation
Indices: 203332--203377 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
203322 TCTTCAATTT
203332 TTTAATATTTTTA-AAA
1 TTTAATATTTTTATAAA
* *
203348 TTTAA-AATTTTATAAT
1 TTTAATATTTTTATAAA
203364 TTTAATATTTTTAT
1 TTTAATATTTTTAT
203378 CCGATTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 6 0.24
16 12 0.48
17 7 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAATATTTTTATAAA
Found at i:206285 original size:51 final size:51
Alignment explanation
Indices: 206172--206359 Score: 227
Period size: 51 Copynumber: 3.6 Consensus size: 51
206162 ATTTCGTTTA
* * ** *
206172 ATACTCAAGATGACA-TATAGTCATCAGACCTCTTGTTCCATATAGGAATTCAT
1 ATACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGG-ATTCAT
* *
206225 ATACTCACGATGACACTTAGTCATC-GAGCCTTTAATCCATCATGGATTCAT
1 ATACTCACGATGACACTTAGTCATCGGA-CCTTTAATCCATAAAGGATTCAT
* *
206276 GTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCAT
* *
206327 TTACTCACGATGACACTTAGTTATCGGACCTTT
1 ATACTCACGATGACACTTAGTCATCGGACCTTT
206360 TCGTTTATAA
Statistics
Matches: 120, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
51 81 0.68
52 13 0.11
53 25 0.21
54 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (51 bp):
ATACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCAT
Found at i:218712 original size:41 final size:42
Alignment explanation
Indices: 218664--218756 Score: 152
Period size: 41 Copynumber: 2.2 Consensus size: 42
218654 CAGTATGAGT
*
218664 TTGGTATTCGCCAATGGGTGAATTGTGTAAGGTCTATTTATG
1 TTGGTATTCGCCAATGGGTGAATTGTGTAAGGTCTACTTATG
* *
218706 TT-GTATTCGCTAATGGGTGAATTGTGTAAGGTCTACTTGTG
1 TTGGTATTCGCCAATGGGTGAATTGTGTAAGGTCTACTTATG
218747 TTGGTATTCG
1 TTGGTATTCG
218757 GTAATGGGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 38 0.81
42 9 0.19
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (42 bp):
TTGGTATTCGCCAATGGGTGAATTGTGTAAGGTCTACTTATG
Found at i:220574 original size:120 final size:119
Alignment explanation
Indices: 220373--220604 Score: 322
Period size: 120 Copynumber: 1.9 Consensus size: 119
220363 TATAATTCAA
* * *
220373 AATTTCATCTTCATGTCTGTATCAACTTTGTTACCAGTATAAGATGATGCTCACATGAGCTGTCG
1 AATTTCATCTTCATGTCTGTATCAACTTTATTACCAATATAAGATGATGCTCACACGAGCTGTCG
* * * *
220438 AGGACTTGCAACATATGCGGTACCCCAGCCATCGATACGGTATGCTATAATCTAG
66 AGGAATCGCAACATATGCGGTACCCCAGCCATCAATACAGTAT-CTATAATCTAG
* ** *
220493 AATTTCAT-TCTCATGTTTGTATCAACTTTATTACCAATATTCGATGCTGCTCACACGAGCTGTC
1 AATTTCATCT-TCATGTCTGTATCAACTTTATTACCAATATAAGATGATGCTCACACGAGCTGTC
* *
220557 GAGGAATCGCAACATATGTGGTACCTCAGCCATCAATACAGTATCTAT
65 GAGGAATCGCAACATATGCGGTACCCCAGCCATCAATACAGTATCTAT
220605 GCATATAATT
Statistics
Matches: 98, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
119 5 0.05
120 93 0.95
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (119 bp):
AATTTCATCTTCATGTCTGTATCAACTTTATTACCAATATAAGATGATGCTCACACGAGCTGTCG
AGGAATCGCAACATATGCGGTACCCCAGCCATCAATACAGTATCTATAATCTAG
Found at i:220948 original size:13 final size:13
Alignment explanation
Indices: 220930--220965 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
220920 ATTTAACATT
220930 ACGAATTTACCGG
1 ACGAATTTACCGG
220943 ACGAATTTACCGG
1 ACGAATTTACCGG
220956 ACGAATTTAC
1 ACGAATTTAC
220966 AATTAAAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (13 bp):
ACGAATTTACCGG
Found at i:224242 original size:13 final size:13
Alignment explanation
Indices: 224224--224251 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
224214 CTCAGAGAGG
224224 AATAGTCTTGATA
1 AATAGTCTTGATA
224237 AATAGTCTTGATA
1 AATAGTCTTGATA
224250 AA
1 AA
224252 CATTCTCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (13 bp):
AATAGTCTTGATA
Found at i:224767 original size:31 final size:31
Alignment explanation
Indices: 224701--224789 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 31
224691 TAGTAGACTC
* * * * * *
224701 TATCTGTTATGTGTTTATTGTCCCAGTGGAC
1 TATCTATTTTGTGTTTACTGTCCCAGCGAAA
224732 TATCTATTTTGTGTTTACTGTCCCAGCGAAA
1 TATCTATTTTGTGTTTACTGTCCCAGCGAAA
224763 TATCTCTATTTTGTGTTTACTGTCCCA
1 TA--TCTATTTTGTGTTTACTGTCCCA
224790 ATGGACTTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
31 27 0.54
33 23 0.46
ACGTcount: A:0.18, C:0.19, G:0.17, T:0.46
Consensus pattern (31 bp):
TATCTATTTTGTGTTTACTGTCCCAGCGAAA
Found at i:226278 original size:10 final size:9
Alignment explanation
Indices: 226258--226439 Score: 72
Period size: 10 Copynumber: 19.2 Consensus size: 9
226248 TGATAATAAA
226258 ATAAAAATT
1 ATAAAAATT
226267 ATAAAAATTT
1 ATAAAAA-TT
*
226277 ATTAAAATTT
1 A-TAAAAATT
*
226287 AATAAAAA-C
1 -ATAAAAATT
226296 ATAAAAATAT
1 ATAAAAAT-T
* *
226306 TTAAAAGTT
1 ATAAAAATT
*
226315 ATTAAAATT
1 ATAAAAATT
226324 ATAAAAAATT
1 AT-AAAAATT
226334 AT-AAAATAT
1 ATAAAAAT-T
*
226343 ATAGAAA-T
1 ATAAAAATT
226351 A-AAAAATAT
1 ATAAAAAT-T
*
226360 ATATAAATT
1 ATAAAAATT
* *
226369 TTATAAATT
1 ATAAAAATT
226378 AGTAAGAAAATT
1 A-T-A-AAAATT
*
226390 ATTTAAAATGT
1 A-TAAAAAT-T
226401 A-AATAAA-T
1 ATAA-AAATT
226409 AT-AAAATT
1 ATAAAAATT
*
226417 CGTAAAAAATTT
1 -AT-AAAAA-TT
226429 ATAAAAATT
1 ATAAAAATT
226438 AT
1 AT
226440 CGAGTCTCTC
Statistics
Matches: 130, Mismatches: 21, Indels: 44
0.67 0.11 0.23
Matches are distributed among these distances:
7 7 0.05
8 18 0.14
9 36 0.28
10 46 0.35
11 14 0.11
12 9 0.07
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (9 bp):
ATAAAAATT
Found at i:226285 original size:19 final size:18
Alignment explanation
Indices: 226261--226439 Score: 59
Period size: 19 Copynumber: 9.4 Consensus size: 18
226251 TAATAAAATA
226261 AAAATTATAAAAATTTATT
1 AAAATTATAAAAATTTA-T
*
226280 AAAATTTAATAAAAA--CAT
1 AAAA-TT-ATAAAAATTTAT
* * *
226298 AAAAATATTTAAAAGTTATT
1 AAAATTA-TAAAAATTTA-T
*
226318 AAAATTATAAAAAATTAT
1 AAAATTATAAAAATTTAT
* *
226336 AAAATATATAGAAA--TAA
1 AAAAT-TATAAAAATTTAT
*
226353 AAAATATATATAAATTT-T
1 AAAAT-TATAAAAATTTAT
*
226371 ATAAATTAGTAAGAAAATTATTT
1 A-AAATTA-T-A-AAAATT-TAT
226394 AAAATGTA-AATAAA--TAT
1 AAAAT-TATAA-AAATTTAT
*
226411 AAAATTCGTAAAAAATTTAT
1 AAAATT-AT-AAAAATTTAT
226431 AAAAATTAT
1 -AAAATTAT
226440 CGAGTCTCTC
Statistics
Matches: 122, Mismatches: 15, Indels: 45
0.67 0.08 0.25
Matches are distributed among these distances:
16 2 0.02
17 28 0.23
18 17 0.14
19 30 0.25
20 18 0.15
21 18 0.15
22 5 0.04
23 4 0.03
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (18 bp):
AAAATTATAAAAATTTAT
Found at i:226303 original size:38 final size:38
Alignment explanation
Indices: 226250--226331 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
226240 ACGAAAGTTG
*
226250 ATAATAAAATAAAAAT-TATAAAAATTTATTAAAATT-TA
1 ATAA-AAAATAAAAATAT-TAAAAAGTTATTAAAATTATA
*
226288 ATAAAAACATAAAAATATTTAAAAGTTATTAAAATTATA
1 ATAAAAA-ATAAAAATATTAAAAAGTTATTAAAATTATA
226327 A-AAAA
1 ATAAAA
226332 TTATAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
37 3 0.08
38 32 0.82
39 4 0.10
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (38 bp):
ATAAAAAATAAAAATATTAAAAAGTTATTAAAATTATA
Found at i:226310 original size:28 final size:27
Alignment explanation
Indices: 226258--226414 Score: 97
Period size: 28 Copynumber: 5.5 Consensus size: 27
226248 TGATAATAAA
*
226258 ATAAAAATTATAAAAATTTATTAAAATTT
1 ATAAAAA-TATAAAAATAT-TTAAAATTT
* *
226287 AATAAAAACATAAAAATATTTAAAAGTT
1 -ATAAAAATATAAAAATATTTAAAATTT
* *
226315 ATTAAAATTATAAAAA-ATTATAAAATAT
1 A-TAAAAATATAAAAATATT-TAAAATTT
* *
226343 ATAGAAATA-AAAAATATATATAAATTT
1 ATAAAAATATAAAAATATTTA-AAATTT
* *
226370 -TATAAATTAGTAAGAAAATTATTTAAAATGT
1 ATA-AAAATA-T-A-AAAA-TATTTAAAATTT
226401 A-AATAAATATAAAA
1 ATAA-AAATATAAAA
226415 TTCGTAAAAA
Statistics
Matches: 99, Mismatches: 16, Indels: 26
0.70 0.11 0.18
Matches are distributed among these distances:
26 9 0.09
27 21 0.21
28 30 0.30
29 10 0.10
30 10 0.10
31 14 0.14
32 5 0.05
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (27 bp):
ATAAAAATATAAAAATATTTAAAATTT
Found at i:226338 original size:38 final size:39
Alignment explanation
Indices: 226270--226344 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 39
226260 AAAAATTATA
*
226270 AAAATTTATTAAAATTTAATAAAAACATAAAA-ATATTT
1 AAAAGTTATTAAAATTTAATAAAAACATAAAATATATTT
**
226308 AAAAGTTATTAAAATTATAA-AAAATTATAAAATATAT
1 AAAAGTTATTAAAATT-TAATAAAAACATAAAATATAT
226345 AGAAATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 25 0.78
39 7 0.22
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (39 bp):
AAAAGTTATTAAAATTTAATAAAAACATAAAATATATTT
Found at i:226821 original size:19 final size:18
Alignment explanation
Indices: 226798--226852 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 18
226788 AATTCTTTAC
226798 AATTTTTTATAACTTTTGT
1 AATTTTTTATAACTTTT-T
*
226817 GA-TTTTTATGAA-TTTTT
1 AATTTTTTAT-AACTTTTT
226834 AATATTTTTCATAACTTTT
1 AAT-TTTTT-ATAACTTTT
226853 ATTTATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
17 2 0.07
18 11 0.38
19 10 0.34
20 6 0.21
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (18 bp):
AATTTTTTATAACTTTTT
Found at i:226853 original size:19 final size:19
Alignment explanation
Indices: 226801--226863 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
226791 TCTTTACAAT
*
226801 TTTTTATAACTTTT-GTGA
1 TTTTTATAACTTTTAATGA
*
226819 TTTTTATGAATTTTTAAT-A
1 TTTTTAT-AACTTTTAATGA
* *
226838 TTTTTCATAACTTTTATTTA
1 TTTTT-ATAACTTTTAATGA
226858 TTTTTA
1 TTTTTA
226864 ATTTTTATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
18 7 0.19
19 21 0.57
20 9 0.24
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTTATAACTTTTAATGA
Found at i:227970 original size:17 final size:19
Alignment explanation
Indices: 227934--227970 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
227924 ATTCATGTTG
227934 ATATTATTTAAATTTATAT
1 ATATTATTTAAATTTATAT
* *
227953 ATATTTTTTAATTTTATA
1 ATATTATTTAAATTTATA
227971 CTGCTTTAAT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTATTTAAATTTATAT
Found at i:229261 original size:17 final size:16
Alignment explanation
Indices: 229215--229263 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
229205 AAAGTTTGAA
229215 AAGATTATTCTTATTT
1 AAGATTATTCTTATTT
229231 AAGATT-TT-TT-TTT
1 AAGATTATTCTTATTT
*
229244 ATGAATTATTCTTATTT
1 AAG-ATTATTCTTATTT
229261 AAG
1 AAG
229264 CTTTGAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
13 5 0.19
14 5 0.19
15 4 0.15
16 8 0.30
17 5 0.19
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (16 bp):
AAGATTATTCTTATTT
Found at i:229630 original size:14 final size:14
Alignment explanation
Indices: 229611--229638 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
229601 ATAATAATCC
229611 TCAAACAAATAGAA
1 TCAAACAAATAGAA
229625 TCAAACAAATAGAA
1 TCAAACAAATAGAA
229639 AAGTTCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (14 bp):
TCAAACAAATAGAA
Found at i:229958 original size:76 final size:76
Alignment explanation
Indices: 229867--230037 Score: 256
Period size: 76 Copynumber: 2.3 Consensus size: 76
229857 TAGGGTTTAG
* * *
229867 GGATTGATTTTTATGCATCAAGAT-GAAAAATGATCATGTCTCATATTTTCTCTCCTCTCATCAT
1 GGATTGATTTTTATGCATCAAGATAG-AAAACGATCATCTCTCATATTTTCGCTCCTCTCATCAT
229931 TTCAATTTGGAA
65 TTCAATTTGGAA
*
229943 GGATTGATTTTTATGCATCAAGATAGAAAACGATCATCTCTCTTATTTTCGCTCCTCTCATCATT
1 GGATTGATTTTTATGCATCAAGATAGAAAACGATCATCTCTCATATTTTCGCTCCTCTCATCATT
230008 TCAATTTGGAA
66 TCAATTTGGAA
** *
230019 ACACTGATTTTTATG-ATCA
1 GGATTGATTTTTATGCATCA
230038 TCTCTCTTAT
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
75 4 0.05
76 82 0.94
77 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (76 bp):
GGATTGATTTTTATGCATCAAGATAGAAAACGATCATCTCTCATATTTTCGCTCCTCTCATCATT
TCAATTTGGAA
Found at i:230040 original size:59 final size:59
Alignment explanation
Indices: 229974--230097 Score: 230
Period size: 59 Copynumber: 2.1 Consensus size: 59
229964 GATAGAAAAC
229974 GATCATCTCTCTTATTTTCGCTCCTCTCATCATTTCAATTTGGAAACACTGATTTTTAT
1 GATCATCTCTCTTATTTTCGCTCCTCTCATCATTTCAATTTGGAAACACTGATTTTTAT
*
230033 GATCATCTCTCTTATTTTCTCTCCTCTCATCATTTCAATTTGGAAACACTGATTTTTAT
1 GATCATCTCTCTTATTTTCGCTCCTCTCATCATTTCAATTTGGAAACACTGATTTTTAT
230092 GCATCA
1 G-ATCA
230098 AGAAAGAAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
59 59 0.94
60 4 0.06
ACGTcount: A:0.23, C:0.24, G:0.08, T:0.45
Consensus pattern (59 bp):
GATCATCTCTCTTATTTTCGCTCCTCTCATCATTTCAATTTGGAAACACTGATTTTTAT
Found at i:230119 original size:77 final size:76
Alignment explanation
Indices: 230031--230291 Score: 326
Period size: 76 Copynumber: 3.4 Consensus size: 76
230021 ACTGATTTTT
* * *
230031 ATGATCATCTCTCTTATTTTCTCTCCTCTCATCATTTCAATTTGGAAACACTGATTTTTATGCAT
1 ATGATCATCTCTCTTATTTTCTCTCCTCTCATCATTCCAATTTGGAAAGATTGATTTTTATGCAT
* *
230096 CAAGAAAGAAAA
66 C-AGGATGAAAA
* * * * *
230108 ATGATCATCTCTCTTATTTTCTTTCCACTAATCATTCCAATTTGGAATGATTTATTTTTATGCAT
1 ATGATCATCTCTCTTATTTTCTCTCCTCTCATCATTCCAATTTGGAAAGATTGATTTTTATGCAT
*
230173 CAGGATGTAAA
66 CAGGATGAAAA
* * *
230184 ATGATCATCTCTCTTATTTTCTCCCCCCTTATCATTCCAATTT-GAAAGGATTGATTTTTATGCA
1 ATGATCATCTCTCTTATTTTCTCTCCTCTCATCATTCCAATTTGGAAA-GATTGATTTTTATGCA
*
230248 TTAGGATGAAAA
65 TCAGGATGAAAA
** * *
230260 ATGATTTTCTCTCTTATGTTCTTTCCTCTCAT
1 ATGATCATCTCTCTTATTTTCTCTCCTCTCAT
230292 TCTTCTTCCC
Statistics
Matches: 157, Mismatches: 26, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
75 3 0.02
76 96 0.61
77 58 0.37
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (76 bp):
ATGATCATCTCTCTTATTTTCTCTCCTCTCATCATTCCAATTTGGAAAGATTGATTTTTATGCAT
CAGGATGAAAA
Found at i:230717 original size:35 final size:38
Alignment explanation
Indices: 230648--230718 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
230638 TTTAATATAA
* * *
230648 AATAATTATATTAAGAATATTATTAAATTATATTTAAT
1 AATAAATATATTAAGAATATGATTAAAATATATTTAAT
230686 AATAAATATATTAA-AATATGA-TAAAAT-TATTTA
1 AATAAATATATTAAGAATATGATTAAAATATATTTA
230719 TTTTTATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 6 0.20
36 5 0.17
37 6 0.20
38 13 0.43
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (38 bp):
AATAAATATATTAAGAATATGATTAAAATATATTTAAT
Found at i:230984 original size:30 final size:30
Alignment explanation
Indices: 230948--231004 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
230938 ATTTTTAGCT
230948 AAATTTGA-CATTCAACCTTTTAAAATAGTC
1 AAATTTGACCATT-AACCTTTTAAAATAGTC
*
230978 AAATTTGACCATTAACCTTTTGAAATA
1 AAATTTGACCATTAACCTTTTAAAATA
231005 CTAACTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (30 bp):
AAATTTGACCATTAACCTTTTAAAATAGTC
Found at i:233678 original size:17 final size:17
Alignment explanation
Indices: 233656--233723 Score: 66
Period size: 17 Copynumber: 3.9 Consensus size: 17
233646 TTAAACCTTT
233656 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAAGA
233673 TTAAATTTATTTTAA-A
1 TTAAATTTATTTTAAGA
*** *
233689 TTTTAAATTTAAAATAAGT
1 --TTAAATTTATTTTAAGA
233708 TTAAATTTACTTTTAA
1 TTAAATTTA-TTTTAA
233724 ATTTAAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
16 1 0.03
17 24 0.60
18 15 0.38
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTTAAGA
Found at i:233695 original size:35 final size:36
Alignment explanation
Indices: 233654--233733 Score: 108
Period size: 35 Copynumber: 2.2 Consensus size: 36
233644 AATTAAACCT
***
233654 TTTTAAATTTATTTTAAGATTAAATTTA-TTTTAAA
1 TTTTAAATTTAAAATAAGATTAAATTTACTTTTAAA
*
233689 TTTTAAATTTAAAATAAGTTTAAATTTACTTTTAAA
1 TTTTAAATTTAAAATAAGATTAAATTTACTTTTAAA
*
233725 TTTAAAATT
1 TTTTAAATT
233734 AATAAAAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 24 0.62
36 15 0.38
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (36 bp):
TTTTAAATTTAAAATAAGATTAAATTTACTTTTAAA
Found at i:233700 original size:24 final size:24
Alignment explanation
Indices: 233664--233728 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
233654 TTTTAAATTT
*
233664 ATTTTAAGA-TTAAATTTATTTTAA
1 ATTTTAA-ATTTAAATTTAGTTTAA
* *
233688 ATTTTAAATTTAAAATAAGTTTAA
1 ATTTTAAATTTAAATTTAGTTTAA
**
233712 A-TTTACTTTTAAATTTA
1 ATTTTAAATTTAAATTTA
233729 AAATTAATAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
23 13 0.39
24 20 0.61
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (24 bp):
ATTTTAAATTTAAATTTAGTTTAA
Found at i:233701 original size:6 final size:6
Alignment explanation
Indices: 233655--233735 Score: 53
Period size: 6 Copynumber: 13.8 Consensus size: 6
233645 ATTAAACCTT
* *
233655 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAA TTTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA
* * ** *
233702 -ATAAG TTTAAA TTTACT TTTAAA TTTAAA ATTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
233736 TAAAAATCCA
Statistics
Matches: 56, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
5 12 0.21
6 38 0.68
7 6 0.11
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:234307 original size:2 final size:2
Alignment explanation
Indices: 234300--234331 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
234290 ATTTGTTTTA
234300 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
234332 TTGAAGCGCT
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:235547 original size:30 final size:30
Alignment explanation
Indices: 235446--235746 Score: 210
Period size: 30 Copynumber: 10.1 Consensus size: 30
235436 AAGGCCTTCG
* *
235446 AACTTTTTAAAAATTACATTTTAACCCCCTCA
1 AACTTTCTAAAAATTACATTTTTA--CCCTCA
* * * *
235478 AACTATCCAAAAATTACATTTTGACCCTCG
1 AACTTTCTAAAAATTACATTTTTACCCTCA
* *
235508 AAC-TTCTAAAAATTATATTTTAACCCTCA
1 AACTTTCTAAAAATTACATTTTTACCCTCA
* * * * *
235537 AACTTTCTAAAAATTCCAATTGTGCCCTCG
1 AACTTTCTAAAAATTACATTTTTACCCTCA
* * * * *
235567 TACTTTCCAAAAATTCCATTTTTGCCC-CG
1 AACTTTCTAAAAATTACATTTTTACCCTCA
*
235596 TAC-TTC-ACAAAATTACATTTTTTTACCCTCA
1 AACTTTCTA-AAAATTACA--TTTTTACCCTCA
235627 AACTTT-TAAAAAATTACA-TTTTACCCTCA
1 AACTTTCT-AAAAATTACATTTTTACCCTCA
* * *
235656 AAC-TTCCAAAAATTACGTTTTTA-CCTCG
1 AACTTTCTAAAAATTACATTTTTACCCTCA
* * *
235684 AATTTTCCT-AAAATAACATTTTTACCTCTAA
1 AACTTT-CTAAAAATTACATTTTTACC-CTCA
* *
235715 AACTTTC-CAAAATTACATTTTAACCC-CA
1 AACTTTCTAAAAATTACATTTTTACCCTCA
235743 AACT
1 AACT
235747 CTCCAAAACT
Statistics
Matches: 216, Mismatches: 38, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
27 1 0.00
28 33 0.15
29 64 0.30
30 76 0.35
31 10 0.05
32 31 0.14
33 1 0.00
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.37
Consensus pattern (30 bp):
AACTTTCTAAAAATTACATTTTTACCCTCA
Found at i:236131 original size:97 final size:97
Alignment explanation
Indices: 236015--236190 Score: 273
Period size: 97 Copynumber: 1.8 Consensus size: 97
236005 ACAATATTCT
* * *
236015 TTTATTTTGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGATTTTTCTTCAAACCGGGAT
1 TTTATTTTGGGTTTTGAAAATTTGTGACTTAACTTACTAGGCACGACTTTTCTTCAAACCGAGAT
236080 AATCGAATACCCTTAAATCGAGGCAATGTTTC
66 AATCGAATACCCTTAAATCGAGGCAATGTTTC
* ** *
236112 TTTATCTTT-GGTTTTGAAAATTTGTGACTTAACTTATTAGGTGCGACTTTTCTTCAAATCGAGA
1 TTTAT-TTTGGGTTTTGAAAATTTGTGACTTAACTTACTAGGCACGACTTTTCTTCAAACCGAGA
236176 TAATCGAATACCCTT
65 TAATCGAATACCCTT
236191 TTCCAAGGCT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
97 68 0.96
98 3 0.04
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (97 bp):
TTTATTTTGGGTTTTGAAAATTTGTGACTTAACTTACTAGGCACGACTTTTCTTCAAACCGAGAT
AATCGAATACCCTTAAATCGAGGCAATGTTTC
Found at i:245408 original size:3 final size:3
Alignment explanation
Indices: 245395--245457 Score: 99
Period size: 3 Copynumber: 21.0 Consensus size: 3
245385 TTATGATATC
* * *
245395 GAA GCA GAA GAA GAA AAA GAA GAA TAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
245443 GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA
245458 AGGGATGATC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:247824 original size:209 final size:209
Alignment explanation
Indices: 247463--248450 Score: 1392
Period size: 209 Copynumber: 4.7 Consensus size: 209
247453 CAATGAGGTG
* * * * * * * * * *
247463 GTCATCTTCCTAATAAGATACAGAGAAGTATACCAACTCAATCAAACAAAGCTCGATGTGAGTGA
1 GTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAAAGTGAG-CA
* ***
247528 AA-CTTCGAACCCTAACTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAGCAGTTACC
65 AATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTACC
* *
247592 TTCCTGATGAGATACAAAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGCGGATC
130 TTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATC
*
247657 AAAACAAGTGATACA
195 AAAACAAGTGATGCA
* * *
247672 GTCATCTTCTTGATGAGTTACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAA
1 GTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAAAGTGAGCAA
* * * *
247737 ATCTTCGAACCCTAACTTCTTGATTAGATACTGAGAAGCAAGTCGAAGCAATAAAACGGTTACCT
66 ATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTACCT
247802 TCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCA
131 TCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCA
247867 AAACAAGTGATGCA
196 AAACAAGTGATGCA
247881 GTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAAAGTGAGCAA
1 GTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAAAGTGAGCAA
* *
247946 ATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGTGGTTACCT
66 ATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTACCT
* * *
248011 TCCTGATGAGATACAAAGAAGTGAATCAGAACCGTCTTCCTGATGAGACACAGAGAAGTGGATCA
131 TCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCA
*
248076 AAACAAGTGATGCG
196 AAACAAGTGATGCA
* * *
248090 GTCAGCTTCCTGATGAGATACTGACAAGTAGACCAAATCAATGAAATC-AGACTCAAAGTGAGCA
1 GTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAG-CTCAAAGTGAGCA
* * * *
248154 AATCTTTGAACCCTAGCTTCCTGATAAGATACTGAGAAG-TAGATCGAAGCAATAAATTGGTTAC
65 AATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAAG-TCGAAGCAATAAAATGGTTAC
* * * ** * *
248218 CTT-CTCGATGAGATATAGAGAAGTAAACTAGATTTGTCTTCCTAATGAGACACAGAGAAGTTGA
129 CTTCCT-GATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGA
*
248282 TCAAAACAAGTGATGCG
193 TCAAAACAAGTGATGCA
* * * *
248299 GCCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAATGAAACCAAAGCTCAATGTGAGCA
1 GTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACC-AAGCTCAAAGTGAGCA
* * * * *
248364 AAACTTCGAA-CCTCAGCTCCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCAT
65 AATCTTCGAACCCT-AGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAC
*
248428 CTTCCTGATGAGATACGGAGAAG
129 CTTCCTGATGAGATACAGAGAAG
248451 AAGATTAAGA
Statistics
Matches: 701, Mismatches: 69, Indels: 17
0.89 0.09 0.02
Matches are distributed among these distances:
208 8 0.01
209 609 0.87
210 79 0.11
211 5 0.01
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (209 bp):
GTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAAAGTGAGCAA
ATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTACCT
TCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCA
AAACAAGTGATGCA
Found at i:248845 original size:23 final size:23
Alignment explanation
Indices: 248819--248920 Score: 75
Period size: 23 Copynumber: 4.4 Consensus size: 23
248809 ATTAAACTTT
248819 TTTAAATTTATTTTAAGA-TTAAA
1 TTTAAATTTATTTTAA-ATTTAAA
* *
248842 TTTAATTTTGTTTTAAATTTAAA
1 TTTAAATTTATTTTAAATTTAAA
* **
248865 -TTAAGTTTAAATTTT-GTTTTAAA
1 TTTAAATTT--ATTTTAAATTTAAA
* * **
248888 TTTAAATTAAGTTTAAATTTACT
1 TTTAAATTTATTTTAAATTTAAA
248911 TTTAAATTTA
1 TTTAAATTTA
248921 AAATTAATAA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
22 12 0.20
23 38 0.63
24 10 0.17
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (23 bp):
TTTAAATTTATTTTAAATTTAAA
Found at i:248862 original size:29 final size:29
Alignment explanation
Indices: 248830--248927 Score: 144
Period size: 29 Copynumber: 3.3 Consensus size: 29
248820 TTAAATTTAT
*
248830 TTTAAGATTAAATTT-AATTTTGTTTTAAA
1 TTTAA-ATTAAGTTTAAATTTTGTTTTAAA
248859 TTTAAATTAAGTTTAAATTTTGTTTTAAA
1 TTTAAATTAAGTTTAAATTTTGTTTTAAA
**
248888 TTTAAATTAAGTTTAAATTTACTTTTAAA
1 TTTAAATTAAGTTTAAATTTTGTTTTAAA
248917 TTTAAAATTAA
1 TTT-AAATTAA
248928 TAAAAGTCCA
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
28 8 0.12
29 49 0.77
30 7 0.11
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (29 bp):
TTTAAATTAAGTTTAAATTTTGTTTTAAA
Found at i:248868 original size:5 final size:6
Alignment explanation
Indices: 248819--248927 Score: 66
Period size: 6 Copynumber: 18.8 Consensus size: 6
248809 ATTAAACTTT
* ***
248819 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AA TTTTGT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *** * **
248865 -TTAAG TTTAAA TTTTGT TTTAAA TTTAAA -TTAAG TTTAAA TTTACT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
248911 TTTAAA TTTAAA ATTAA
1 TTTAAA TTTAAA TTTAA
248928 TAAAAGTCCA
Statistics
Matches: 75, Mismatches: 22, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
5 18 0.24
6 57 0.76
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:248873 original size:17 final size:17
Alignment explanation
Indices: 248819--248908 Score: 68
Period size: 17 Copynumber: 5.6 Consensus size: 17
248809 ATTAAACTTT
**
248819 TTTAAATTTATTTTAAG
1 TTTAAATTTAAATTAAG
* **
248836 ATTAAATTT-AATTTTG
1 TTTAAATTTAAATTAAG
248852 TTTTAAATTTAAATTAAG
1 -TTTAAATTTAAATTAAG
248870 TTTAAA-TT---TT--G
1 TTTAAATTTAAATTAAG
248881 TTTTAAATTTAAATTAAG
1 -TTTAAATTTAAATTAAG
248899 TTTAAATTTA
1 TTTAAATTTA
248909 CTTTTAAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
11 1 0.02
12 6 0.11
13 4 0.07
16 7 0.12
17 32 0.57
18 6 0.11
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTAAATTTAAATTAAG
Found at i:250653 original size:29 final size:29
Alignment explanation
Indices: 250599--250893 Score: 181
Period size: 29 Copynumber: 10.1 Consensus size: 29
250589 CCCAGAAGGC
* * * *
250599 CCTCGAACTTTCTAAAAAGTATATTTTGA
1 CCTCAAACTTTCTAAAAATTACATTTTTA
**
250628 CCTCAAACTTTCTAAAAATTACATTTACA
1 CCTCAAACTTTCTAAAAATTACATTTTTA
* * * *
250657 CCCCTAAACTTTTTAATAATTACATTTTAA
1 CCTC-AAACTTTCTAAAAATTACATTTTTA
* * *
250687 CCCCTAAACTTTCCAAAAATTACATTTTAA
1 CCTC-AAACTTTCTAAAAATTACATTTTTA
*
250717 CCCCTAAACTTGT-T-AAAATTACA-TTTTA
1 CCTC-AAACTT-TCTAAAAATTACATTTTTA
* * * * *
250745 CCCTTAAACTCTCCAAAAATTATATTTTTGCC
1 -CCTCAAACTTTCTAAAAATTACATTTTT--A
* *
250777 CCTTAAACTTT-TAAAAATTACATTTTCA
1 CCTCAAACTTTCTAAAAATTACATTTTTA
* *
250805 CCCTCGAACTTTC-AAAAATTCCATTTTTA
1 -CCTCAAACTTTCTAAAAATTACATTTTTA
* * * *
250834 CCCTCATAC-TTCCAAAAATCACGTTTTTA
1 -CCTCAAACTTTCTAAAAATTACATTTTTA
* ** *
250863 CCTCGAA-TTTCCCAAAATAACATTTTTA
1 CCTCAAACTTTCTAAAAATTACATTTTTA
250891 CCT
1 CCT
250894 TTAAAACTTT
Statistics
Matches: 214, Mismatches: 40, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
27 1 0.00
28 37 0.17
29 89 0.42
30 76 0.36
31 11 0.05
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
CCTCAAACTTTCTAAAAATTACATTTTTA
Found at i:250705 original size:60 final size:57
Alignment explanation
Indices: 250632--250830 Score: 222
Period size: 59 Copynumber: 3.4 Consensus size: 57
250622 TTTTGACCTC
*
250632 AAACTTTCTAAAAATTACATTTACACCCCTAAACTTTTTAATAATTACATTTTAACCCCT
1 AAACTTTCCAAAAATTACATTTA-ACCCCTAAACTTTTTAA-AATTACATTTT-ACCCCT
* *
250692 AAACTTTCCAAAAATTACATTTTAACCCCTAAACTTGTTAAAATTACATTTTACCCTT
1 AAACTTTCCAAAAATTACA-TTTAACCCCTAAACTTTTTAAAATTACATTTTACCCCT
* * ** *
250750 AAACTCTCCAAAAATTATATTTTTGCCCCTTAAACTTTTAAAAATTACATTTT-CACCCT
1 AAACTTTCCAAAAATTACA-TTTAACCCC-TAAACTTTTTAAAATTACATTTTAC-CCCT
* *
250809 CGAACTTT-CAAAAATTCCATTT
1 -AAACTTTCCAAAAATTACATTT
250831 TTACCCTCAT
Statistics
Matches: 121, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
58 34 0.28
59 44 0.36
60 39 0.32
61 4 0.03
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (57 bp):
AAACTTTCCAAAAATTACATTTAACCCCTAAACTTTTTAAAATTACATTTTACCCCT
Found at i:250802 original size:30 final size:29
Alignment explanation
Indices: 250604--250836 Score: 195
Period size: 30 Copynumber: 7.9 Consensus size: 29
250594 AAGGCCCTCG
* * * *
250604 AACTTTCTAAAAAGTATATTTTGACCTC-A
1 AACTTT-TAAAAATTACATTTTTACCCCTA
**
250633 AACTTTCTAAAAATTACATTTACACCCCTA
1 AACTTT-TAAAAATTACATTTTTACCCCTA
* *
250663 AACTTTTTAATAATTACATTTTAACCCCTA
1 AAC-TTTTAAAAATTACATTTTTACCCCTA
* *
250693 AACTTTCCAAAAATTACATTTTAACCCCTA
1 AACTTT-TAAAAATTACATTTTTACCCCTA
*
250723 AACTTGTT-AAAATTACA-TTTTACCCTTA
1 AACTT-TTAAAAATTACATTTTTACCCCTA
** * *
250751 AACTCTCCAAAAATTATATTTTTGCCCCTTA
1 AACT-TTTAAAAATTACATTTTTACCCC-TA
* *
250782 AACTTTTAAAAATTACATTTTCA-CCCTCG
1 AACTTTTAAAAATTACATTTTTACCCCT-A
* *
250811 AACTTTCAAAAATTCCATTTTTACCC
1 AACTTTTAAAAATTACATTTTTACCC
250837 TCATACTTCC
Statistics
Matches: 167, Mismatches: 27, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
28 14 0.08
29 67 0.40
30 76 0.46
31 10 0.06
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.38
Consensus pattern (29 bp):
AACTTTTAAAAATTACATTTTTACCCCTA
Found at i:250815 original size:88 final size:87
Alignment explanation
Indices: 250604--250919 Score: 221
Period size: 88 Copynumber: 3.6 Consensus size: 87
250594 AAGGCCCTCG
* * * * * * *
250604 AACTTTCTAAAAAGTATATTTTGACCTC-AAACTTTCTAAAAATTACATTTACACCCCTAAACTT
1 AACTTTCCAAAAATTACATTTTAACCCCTAAACTTTC-AAAAATTACATTT-TACCCTTAAAC-T
** *
250668 TTTAATAATTACATTTTAACCCCTA
63 TCCAAAAATTACATTTTAACCCCTA
*
250693 AACTTTCCAAAAATTACATTTTAACCCCTAAACTTGT-TAAAATTACATTTTACCCTTAAACTCT
1 AACTTTCCAAAAATTACATTTTAACCCCTAAACTT-TCAAAAATTACATTTTACCCTTAAACT-T
* **
250757 CCAAAAATTATATTTTTGCCCCTTA
64 CCAAAAATTACATTTTAACCCC-TA
* * * * * *
250782 AACTTT-TAAAAATTACATTTTCA-CCCTCGAACTTTCAAAAATTCCATTTTTACCCTCATACTT
1 AACTTTCCAAAAATTACATTTTAACCCCT-AAACTTTCAAAAATTACA-TTTTACCCTTAAACTT
* * * * *
250845 CCAAAAATCACGTTTTTACCTC-G
64 CCAAAAATTACATTTTAACCCCTA
* * * ** * *
250868 AA-TTTCCCAAAATAACATTTTTACCTTTAAAACTTTCCAAAATTGCATTTTA
1 AACTTTCCAAAAATTACATTTTAACCCCT-AAACTTTCAAAAATTACATTTTA
250920 ACTCCAAACT
Statistics
Matches: 181, Mismatches: 37, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
85 3 0.02
86 20 0.11
87 23 0.13
88 72 0.40
89 56 0.31
90 6 0.03
91 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (87 bp):
AACTTTCCAAAAATTACATTTTAACCCCTAAACTTTCAAAAATTACATTTTACCCTTAAACTTCC
AAAAATTACATTTTAACCCCTA
Found at i:251297 original size:96 final size:97
Alignment explanation
Indices: 251179--251369 Score: 280
Period size: 96 Copynumber: 2.0 Consensus size: 97
251169 AAAATATTTA
251179 AAATCGAGGCAATATTCTTTTAT-TTATGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGA
1 AAATCGAGGCAATATTCTTTTATCTT-TGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGA
* *
251243 TTTTTCTTCAACT-GAGATAATCGAATACCCTT
65 ATTTTCTTCAAATCGAGATAATCGAATACCCTT
* * **
251275 AAATCGAGGCAATGTT-TCTTTATCTTTGGTTTTGAAAATTTGTGCTTTAACTTACTAGGGGCGA
1 AAATCGAGGCAATATTCT-TTTATCTTTGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGA
*
251339 ATTTTCTTCAAATCGGGATAATCGAATACCC
65 ATTTTCTTCAAATCGAGATAATCGAATACCC
251370 GTTTTAGAGG
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
95 1 0.01
96 66 0.78
97 18 0.21
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (97 bp):
AAATCGAGGCAATATTCTTTTATCTTTGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAA
TTTTCTTCAAATCGAGATAATCGAATACCCTT
Found at i:253700 original size:26 final size:26
Alignment explanation
Indices: 253671--253722 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
253661 AAAAAAAGAA
*
253671 GAAATATGAGAAGGTTTAAAAAAATT
1 GAAATAAGAGAAGGTTTAAAAAAATT
*
253697 GAAATAAGAGAAGGTTTTAAAAAATT
1 GAAATAAGAGAAGGTTTAAAAAAATT
253723 AAGATTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (26 bp):
GAAATAAGAGAAGGTTTAAAAAAATT
Found at i:254947 original size:48 final size:48
Alignment explanation
Indices: 254876--254984 Score: 155
Period size: 48 Copynumber: 2.3 Consensus size: 48
254866 TTAGGTGAGA
* *
254876 GTTTAGATAAGGGCAATCCTATCAATAGCAACCCAGATATAAGAAAGG
1 GTTTAGATAAGGGCAATCCTATCAATAACAACCCAAATATAAGAAAGG
* * * * *
254924 GTTTAGATAAGTGTAATCCTATCAATAATAGCCCAAATATAAGAGAGG
1 GTTTAGATAAGGGCAATCCTATCAATAACAACCCAAATATAAGAAAGG
254972 GTTTAGATAAGGG
1 GTTTAGATAAGGG
254985 TGTGAATATA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (48 bp):
GTTTAGATAAGGGCAATCCTATCAATAACAACCCAAATATAAGAAAGG
Found at i:255087 original size:27 final size:27
Alignment explanation
Indices: 255055--255107 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
255045 AGAAGGAGGG
255055 GAGGAAGCTATTCCAAAGAGAGATAGA
1 GAGGAAGCTATTCCAAAGAGAGATAGA
* * * *
255082 GAGGAAGTTGTTCCAGAGGGAGATAG
1 GAGGAAGCTATTCCAAAGAGAGATAG
255108 TGATAGTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.36, T:0.17
Consensus pattern (27 bp):
GAGGAAGCTATTCCAAAGAGAGATAGA
Found at i:259979 original size:17 final size:18
Alignment explanation
Indices: 259954--259995 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
259944 GAGTTAAACG
*
259954 AATCAAGTT-TTTGAGTT
1 AATCAAGTTATTCGAGTT
*
259971 AATCGAGTTATTCGAGTT
1 AATCAAGTTATTCGAGTT
259989 AACTCAA
1 AA-TCAA
259996 ATTTTTTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 8 0.40
18 9 0.45
19 3 0.15
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
AATCAAGTTATTCGAGTT
Found at i:260151 original size:17 final size:17
Alignment explanation
Indices: 260129--260196 Score: 83
Period size: 17 Copynumber: 4.3 Consensus size: 17
260119 TTTTTACTTT
260129 TCCCTCAAAACTTTTAC
1 TCCCTCAAAACTTTTAC
260146 TCCCTCAAAACTTTTAC
1 TCCCTCAAAACTTTTAC
**
260163 TCCCTC-CCAC-TTT-C
1 TCCCTCAAAACTTTTAC
260177 T--CTCAAAACTTTTAC
1 TCCCTCAAAACTTTTAC
260192 TCCCT
1 TCCCT
260197 TCTCATCCCA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
12 3 0.07
13 2 0.05
14 5 0.12
15 5 0.12
16 2 0.05
17 25 0.60
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.37
Consensus pattern (17 bp):
TCCCTCAAAACTTTTAC
Done.