Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007925.1 Hibiscus syriacus cultivar Beakdansim tig00110331_pilon, 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: 1316088
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 7
Found at i:2339 original size:2 final size:2
Alignment explanation
Indices: 2332--2357 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2322 CAAACTATCC
2332 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
2358 TCCAGTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4761 original size:21 final size:21
Alignment explanation
Indices: 4704--4764 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
4694 CATATGAAAC
*
4704 TTGTCCCGAAGGACCAATGTA
1 TTGTCCCGAAGGACCTATGTA
* * *
4725 TTGTCCCAAAAGACCTCTGTA
1 TTGTCCCGAAGGACCTATGTA
*
4746 TTGTCTCGAAGGACCTATG
1 TTGTCCCGAAGGACCTATG
4765 AAACCCTCGA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGTA
Found at i:4854 original size:18 final size:17
Alignment explanation
Indices: 4827--4860 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4817 ACATGGGCAT
*
4827 TATCATTTGTTCATTTCA
1 TATCACTTGTT-ATTTCA
4845 TATCACTTGTTATTTC
1 TATCACTTGTTATTTC
4861 TCTTCTGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.21, C:0.18, G:0.06, T:0.56
Consensus pattern (17 bp):
TATCACTTGTTATTTCA
Found at i:8354 original size:2 final size:2
Alignment explanation
Indices: 8347--8388 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
8337 CAAACTATCC
8347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8389 TCCAGTCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10549 original size:18 final size:18
Alignment explanation
Indices: 10526--10560 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
10516 TTTATGTCAT
10526 ATATCA-ATTCACATATAC
1 ATATCACATTCA-ATATAC
10544 ATATCACATTCAATATA
1 ATATCACATTCAATATA
10561 TTTATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATCACATTCAATATAC
Found at i:11571 original size:21 final size:21
Alignment explanation
Indices: 11546--11585 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
11536 TTTCATTTAG
11546 GGGGGAATC-GATACCCCCTCA
1 GGGGGAATCTG-TACCCCCTCA
11567 GGGGGAATCTGTACCCCCT
1 GGGGGAATCTGTACCCCCT
11586 GCACAATCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.20, C:0.33, G:0.30, T:0.17
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTCA
Found at i:12395 original size:3 final size:3
Alignment explanation
Indices: 12387--12509 Score: 160
Period size: 3 Copynumber: 40.7 Consensus size: 3
12377 ATTTTCTATT
12387 TAA TAA TAA TAA T-A TATA TAA T-A TATA TAA TTAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA -TAA TAA TAA TAA TAA
* * * * *
12433 TAT TTA TAA TAA TAA TAA TAA TAA TGA TAA TGA TAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12481 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
12510 GAATGAAAAA
Statistics
Matches: 105, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.04
3 92 0.88
4 9 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:12703 original size:45 final size:44
Alignment explanation
Indices: 12630--12798 Score: 221
Period size: 45 Copynumber: 3.8 Consensus size: 44
12620 GATGGAAATG
*
12630 TTGAAAAAATCATGCACTGAAGGGCTTACAGATGACCCGAAGATT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAG-TT
* *
12675 TTGAAAACATCATGCACTCAAGGTCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAA-GTT
* * **
12720 TTGAAAACATCATACACTGAAGGGCTTACAAATGACCAAAATGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAA-GTT
* * *
12765 TTGCAAATATCATGCACTGAAGGTCTTACAGATG
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATG
12799 TGGGAAATAG
Statistics
Matches: 108, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 107 0.99
46 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.25
Consensus pattern (44 bp):
TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGTT
Found at i:12788 original size:90 final size:90
Alignment explanation
Indices: 12630--12798 Score: 250
Period size: 90 Copynumber: 1.9 Consensus size: 90
12620 GATGGAAATG
* * **
12630 TTGAAAAAATCATGCACTGAAGGGCTTACAGATGACCCGAAGATTTTGAAAACATCATGCACTCA
1 TTGAAAAAATCATACACTGAAGGGCTTACAAATGACCAAAAGATTTTGAAAACATCATGCACTCA
12695 AGGTCTTACAGATGACCCGAAGGTT
66 AGGTCTTACAGATGACCCGAAGGTT
* * * *
12720 TTGAAAACATCATACACTGAAGGGCTTACAAATGACCAAAATG-TTTTGCAAATATCATGCACTG
1 TTGAAAAAATCATACACTGAAGGGCTTACAAATGACCAAAA-GATTTTGAAAACATCATGCACTC
12784 AAGGTCTTACAGATG
65 AAGGTCTTACAGATG
12799 TGGGAAATAG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
90 69 0.99
91 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.25
Consensus pattern (90 bp):
TTGAAAAAATCATACACTGAAGGGCTTACAAATGACCAAAAGATTTTGAAAACATCATGCACTCA
AGGTCTTACAGATGACCCGAAGGTT
Found at i:13494 original size:22 final size:22
Alignment explanation
Indices: 13448--13513 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
13438 AAATCCAATA
* *
13448 AATCTTTCATCTTTGAA-AAGAG
1 AATCTATCATCTTTGAAGAA-TG
*
13470 AATCTATCATCTTTGTAGAATG
1 AATCTATCATCTTTGAAGAATG
*
13492 AATCTATTATCTTTGAAGAATG
1 AATCTATCATCTTTGAAGAATG
13514 TAGATGTAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
22 36 0.95
23 2 0.05
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAATG
Found at i:13940 original size:52 final size:53
Alignment explanation
Indices: 13879--14009 Score: 158
Period size: 54 Copynumber: 2.5 Consensus size: 53
13869 CACTGGTTCA
* * *
13879 TAAAACATTTGATAACACATTTATTCA-GT-TGTGGCTTCTGCACAGATGTTTG
1 TAAAACATTTGACAATACATTCA-TCATGTCTGTGGCTTCTGCACAGATGTTTG
* * * * *
13931 TAAAACATTTGACAATACATTCATCATTTCCTGTGGTTTCTGCCCAGGTTTTTG
1 TAAAACATTTGACAATACATTCATCATGT-CTGTGGCTTCTGCACAGATGTTTG
13985 TAAAACATTTGACAATACATTCATC
1 TAAAACATTTGACAATACATTCATC
14010 CTTTCATATG
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
51 3 0.04
52 21 0.31
54 44 0.65
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (53 bp):
TAAAACATTTGACAATACATTCATCATGTCTGTGGCTTCTGCACAGATGTTTG
Found at i:13986 original size:54 final size:54
Alignment explanation
Indices: 13908--14033 Score: 189
Period size: 54 Copynumber: 2.3 Consensus size: 54
13898 TTTATTCAGT
* * *
13908 TGTGGCTTCTGCACAGATGTTTGTAAAACATTTGACAATACATTCATCATTTCC
1 TGTGGTTTCTGCCCAGATGTTTGTAAAACATTTGACAATACATTCATCATTTCA
* * *
13962 TGTGGTTTCTGCCCAGGTTTTTGTAAAACATTTGACAATACATTCATCCTTTCA
1 TGTGGTTTCTGCCCAGATGTTTGTAAAACATTTGACAATACATTCATCATTTCA
*
14016 TATGGTTTCTGCCCAGAT
1 TGTGGTTTCTGCCCAGAT
14034 TTCTGGTTAG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.39
Consensus pattern (54 bp):
TGTGGTTTCTGCCCAGATGTTTGTAAAACATTTGACAATACATTCATCATTTCA
Found at i:15036 original size:75 final size:75
Alignment explanation
Indices: 14913--15082 Score: 232
Period size: 75 Copynumber: 2.3 Consensus size: 75
14903 GATGTGGGCC
** * * * *
14913 TTCAGCATGCCCCAACATTTACTGGTACAAGCGTTCAAAATACGTCAACATTCCTAATTCTTATT
1 TTCAGCATGCCCCAACATTTACTAATACAAACATTCAAAATACATCAACATTCCTAATTCTGATT
*
14978 TAAATGAGCT
66 AAAATGAGCT
* * * * *
14988 TTCAGTATGTCCCAACATTTGCTAATACAAACATTCAAAATACATCAACATTCTTGATTCTGATT
1 TTCAGCATGCCCCAACATTTACTAATACAAACATTCAAAATACATCAACATTCCTAATTCTGATT
15053 AAAATGAGCT
66 AAAATGAGCT
15063 TTCAGCATGCCCCAACATTT
1 TTCAGCATGCCCCAACATTT
15083 TCTTCTTGCT
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 81 1.00
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTTACTAATACAAACATTCAAAATACATCAACATTCCTAATTCTGATT
AAAATGAGCT
Found at i:17454 original size:14 final size:13
Alignment explanation
Indices: 17431--17464 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
17421 CTTGATTCAA
*
17431 TTTTTTTCTTTTC
1 TTTTTTTCTTTCC
17444 TTTTCTTTCTTTCC
1 TTTT-TTTCTTTCC
17458 TTTTTTT
1 TTTTTTT
17465 TTCATTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTCTTTCC
Found at i:17467 original size:15 final size:15
Alignment explanation
Indices: 17431--17483 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
17421 CTTGATTCAA
*
17431 TTTTTTTCTTTTC-T
1 TTTTTTTCTTTCCTT
*
17445 TTTCTTTCTTTCCTT
1 TTTTTTTCTTTCCTT
* *
17460 TTTTTTTCATTCATT
1 TTTTTTTCTTTCCTT
17475 TTTTTTTCT
1 TTTTTTTCT
17484 GTTTTTCTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 11 0.34
15 21 0.66
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTCTTTCCTT
Found at i:20060 original size:21 final size:21
Alignment explanation
Indices: 20036--20076 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
20026 AAAAGTACGA
20036 ATGCAAAATGAAAATGCAAAG
1 ATGCAAAATGAAAATGCAAAG
*
20057 ATGCAAAATGCAAATGCAAA
1 ATGCAAAATGAAAATGCAAA
20077 TGCAAATGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.12, G:0.17, T:0.15
Consensus pattern (21 bp):
ATGCAAAATGAAAATGCAAAG
Found at i:21759 original size:5 final size:5
Alignment explanation
Indices: 21749--21792 Score: 63
Period size: 5 Copynumber: 8.6 Consensus size: 5
21739 AAATTATAGC
21749 AAAAT AAAAT ACATAA- AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT A-A-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
21793 TAATATGGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 2 0.06
5 30 0.83
6 2 0.06
7 2 0.06
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:24790 original size:3 final size:3
Alignment explanation
Indices: 24782--24863 Score: 98
Period size: 3 Copynumber: 27.7 Consensus size: 3
24772 ATTTTCTATT
* *
24782 TAA TAA TAA TAA T-A TATA TAA T-A TATA TAA CAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA
*
24827 TAA T-A TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
24864 GAATGAAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
2 6 0.09
3 57 0.83
4 6 0.09
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:25110 original size:7 final size:7
Alignment explanation
Indices: 25098--25122 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
25088 ATAAGGTGAG
25098 TCTCTCT
1 TCTCTCT
25105 TCTCTCT
1 TCTCTCT
25112 TCTCTCT
1 TCTCTCT
25119 TCTC
1 TCTC
25123 ATTGGCAGAA
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:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (7 bp):
TCTCTCT
Found at i:25603 original size:33 final size:33
Alignment explanation
Indices: 25541--25603 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
25531 TTTAAGGCAT
* *
25541 ACTACGTAAGCTGAGAGGTGAGTAGGGTGGTAC
1 ACTACGTAAGCTGAGAGGGGAGTAAGGTGGTAC
25574 ACTACGTGAA-CTGAGAGGCGGA-TAAGGTGG
1 ACTACGT-AAGCTGAGAGG-GGAGTAAGGTGG
25604 CACATACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
33 22 0.85
34 4 0.15
ACGTcount: A:0.29, C:0.13, G:0.40, T:0.19
Consensus pattern (33 bp):
ACTACGTAAGCTGAGAGGGGAGTAAGGTGGTAC
Found at i:25885 original size:9 final size:9
Alignment explanation
Indices: 25873--25897 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
25863 CAAATTTTCC
25873 AAATATTAG
1 AAATATTAG
25882 AAATATTAG
1 AAATATTAG
25891 AAATATT
1 AAATATT
25898 GTCCCGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (9 bp):
AAATATTAG
Found at i:30765 original size:32 final size:32
Alignment explanation
Indices: 30729--30796 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
30719 GCTTTTGGTT
* *
30729 AGATGAAAAAAGTTTGTTGTGTAAGAGATTGA
1 AGATGAAAAAAGTGTGTTATGTAAGAGATTGA
**
30761 AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
1 AGATGAAAAAAGTGTGTTATGTAAGAGATTGA
30793 AGAT
1 AGAT
30797 CATGTTCACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (32 bp):
AGATGAAAAAAGTGTGTTATGTAAGAGATTGA
Found at i:32013 original size:56 final size:58
Alignment explanation
Indices: 31924--32117 Score: 152
Period size: 61 Copynumber: 3.3 Consensus size: 58
31914 AAAATTAGGT
* * * *
31924 ACTTATTTTGA-AAAAAATTATTTTAGG-GATTTAAAGA-AAAATGGTA-TAGTTTAAGG
1 ACTTATTTTGACAAAAAAGTAGTTAAGGTG-TTTAAAGATAAAAT-ATATTAGTTTAAGG
* * *
31980 ACTTATTTTGACAAAAAA-TAGTTAAGGTGTTTAAAGTGATTACATATATTAGTTTAAGT
1 ACTTATTTTGACAAAAAAGTAGTTAAGGTGTTTAAA--GATAAAATATATTAGTTTAAGG
* *
32039 A-TCTAATTTGACAAAAAAAGTAGTTAAGGTGTTTAAAG-TAATTACATATATTAGTTTAAGT
1 ACT-TATTTTGAC-AAAAAAGTAGTTAAGGTGTTTAAAGATAA--A-ATATATTAGTTTAAGG
*
32100 A-TCTAATTTGACAAAAAA
1 ACT-TATTTTGACAAAAAA
32118 AATAATTTAG
Statistics
Matches: 117, Mismatches: 9, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
56 24 0.21
57 7 0.06
58 7 0.06
59 22 0.19
60 12 0.10
61 45 0.38
ACGTcount: A:0.43, C:0.05, G:0.15, T:0.38
Consensus pattern (58 bp):
ACTTATTTTGACAAAAAAGTAGTTAAGGTGTTTAAAGATAAAATATATTAGTTTAAGG
Found at i:32074 original size:61 final size:60
Alignment explanation
Indices: 31986--32118 Score: 241
Period size: 61 Copynumber: 2.2 Consensus size: 60
31976 AAGGACTTAT
*
31986 TTTGAC-AAAAAATAGTTAAGGTGTTTAAAGTGATTACATATATTAGTTTAAGTATCTAA
1 TTTGACAAAAAAATAGTTAAGGTGTTTAAAGTAATTACATATATTAGTTTAAGTATCTAA
32045 TTTGACAAAAAAAGTAGTTAAGGTGTTTAAAGTAATTACATATATTAGTTTAAGTATCTAA
1 TTTGACAAAAAAA-TAGTTAAGGTGTTTAAAGTAATTACATATATTAGTTTAAGTATCTAA
32106 TTTGACAAAAAAA
1 TTTGACAAAAAAA
32119 ATAATTTAGG
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
59 6 0.08
60 6 0.08
61 59 0.83
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (60 bp):
TTTGACAAAAAAATAGTTAAGGTGTTTAAAGTAATTACATATATTAGTTTAAGTATCTAA
Found at i:40417 original size:8 final size:7
Alignment explanation
Indices: 40393--40434 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
40383 TTTTCATACA
40393 TGCA-TT
1 TGCATTT
40399 TGCATTT
1 TGCATTT
40406 TGCATCTT
1 TGCAT-TT
40414 TGCATTT
1 TGCATTT
* *
40421 TTCATTG
1 TGCATTT
40428 TGCATTT
1 TGCATTT
40435 ATACTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:40417 original size:15 final size:14
Alignment explanation
Indices: 40393--40434 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
40383 TTTTCATACA
40393 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
40406 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
40421 TTCATTGTGCATTT
1 TGCATTTTGCATTT
40435 ATACTCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:40504 original size:12 final size:12
Alignment explanation
Indices: 40487--40514 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
40477 ACATTCACAT
40487 ATTTACATTTGC
1 ATTTACATTTGC
40499 ATTTACATTTGC
1 ATTTACATTTGC
40511 ATTT
1 ATTT
40515 TTTTACGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:44777 original size:114 final size:114
Alignment explanation
Indices: 44577--44796 Score: 386
Period size: 114 Copynumber: 1.9 Consensus size: 114
44567 CACATTCTCG
*
44577 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* * *
44642 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAATTTGCTCA
*
44691 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
*
44756 GGTAGGAACCCCAGAACCAATCATTGAAATTGAAAGATGAA
66 GGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAA
44797 ATGCATGATC
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 100 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAATTTGCTCA
Found at i:47335 original size:22 final size:22
Alignment explanation
Indices: 47308--47362 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
47298 ATCTACACTC
47308 TTTAAAGATGATAGATTCTCTT
1 TTTAAAGATGATAGATTCTCTT
47330 TTTAAAGATGATAGATTCTCTT
1 TTTAAAGATGATAGATTCTCTT
*
47352 TTCAAAGATGA
1 TTTAAAGATGA
47363 AAGCTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.42
Consensus pattern (22 bp):
TTTAAAGATGATAGATTCTCTT
Found at i:48297 original size:76 final size:76
Alignment explanation
Indices: 48040--48288 Score: 428
Period size: 76 Copynumber: 3.3 Consensus size: 76
48030 CTATTTCTCA
48040 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
48105 AGA-CTTAGAGT
66 A-ACCTTAGAGT
48116 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
48181 ATCCTTAGGGT
66 AACCTTAGAGT
*
48192 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
48257 AACCTTCGAGT
66 AACCTTAGAGT
* *
48268 CAGCTGTAAGCCCTACAGTGC
1 CATCTGTAAGTCCTACAGTGC
48289 GGAATGTTTT
Statistics
Matches: 163, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
76 163 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.33
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTAGAGT
Found at i:48367 original size:17 final size:17
Alignment explanation
Indices: 48322--48370 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
48312 CCAGGCAGAG
48322 TTCATAATGAGAAG-AA
1 TTCATAATGAGAAGAAA
* *
48338 CTCAT-CTGAAGAAGAAA
1 TTCATAATG-AGAAGAAA
48355 TTCATAATGAGAAGAA
1 TTCATAATGAGAAGAA
48371 TTTTTTGAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
15 2 0.08
16 9 0.35
17 13 0.50
18 2 0.08
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.22
Consensus pattern (17 bp):
TTCATAATGAGAAGAAA
Found at i:48372 original size:16 final size:16
Alignment explanation
Indices: 48322--48372 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
48312 CCAGGCAGAG
48322 TTCATAATGAGAAGAA
1 TTCATAATGAGAAGAA
* *
48338 CTCAT-CTGAAGAAGAAA
1 TTCATAATG-AGAAG-AA
48355 TTCATAATGAGAAGAA
1 TTCATAATGAGAAGAA
48371 TT
1 TT
48373 TTTTGAACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 2 0.07
16 13 0.46
17 11 0.39
18 2 0.07
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (16 bp):
TTCATAATGAGAAGAA
Found at i:48479 original size:93 final size:93
Alignment explanation
Indices: 48382--48649 Score: 491
Period size: 93 Copynumber: 2.9 Consensus size: 93
48372 TTTTTGAACC
*
48382 TTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAATAAATC
1 TTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAAATC
48447 ATCTGAAGAAGGAAGAATTTGTACAACT
66 ATCTGAAGAAGGAAGAATTTGTACAACT
* *
48475 TTTTGCTTAAATTCATCACTTGATGGATTAATTTTTCCAGAGAAAGTTCATAATGAGAAGAAATC
1 TTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAAATC
*
48540 ATCTGAAGAAGGAAGAATTTGTATAACT
66 ATCTGAAGAAGGAAGAATTTGTACAACT
*
48568 TTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTC
1 TTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAAATC
48633 ATCTGAAGAAGGAAGAA
66 ATCTGAAGAAGGAAGAA
48650 GAAGTTCATA
Statistics
Matches: 168, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 168 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (93 bp):
TTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAAATC
ATCTGAAGAAGGAAGAATTTGTACAACT
Found at i:48729 original size:113 final size:113
Alignment explanation
Indices: 48551--48900 Score: 540
Period size: 113 Copynumber: 3.1 Consensus size: 113
48541 TCTGAAGAAG
* *
48551 GAAGAATTTGTATAACTTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTT
1 GAAGAACTTGTACAACTTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTT
*
48616 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
66 CATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGA
* * ** ** *
48664 GAAGAACTTGTACAACTTTTTGCTTAAATTCATCA-TTCGGTGGATCAGCAGTTCCAGTTAGAGT
1 GAAGAACTTGTACAACTTTTTGCTTAAATTCATCACTT-GATGGATCAACTTTTCCAGAGAAAGT
*
48728 TCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCATAATGA
65 TCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGA
* * *
48777 GAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTT
1 GAAGAACTTGTACAACTTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTT
*
48842 CAGAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGA
66 CATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGA
*
48890 GAAGAGCTTGT
1 GAAGAACTTGT
48901 TCGACCTTTT
Statistics
Matches: 210, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
112 2 0.01
113 206 0.98
114 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (113 bp):
GAAGAACTTGTACAACTTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTT
CATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGA
Found at i:50643 original size:2 final size:2
Alignment explanation
Indices: 50636--50681 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
50626 TATATCAGTC
50636 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50678 AT AT
1 AT AT
50682 TTGTTTAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57760 original size:18 final size:19
Alignment explanation
Indices: 57734--57772 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
57724 CGATTAATTG
* *
57734 AATCGAATATTATAT-TTA
1 AATCAAATATAATATCTTA
57752 AATCAAATATAATATCTTA
1 AATCAAATATAATATCTTA
57771 AA
1 AA
57773 ATTAATTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (19 bp):
AATCAAATATAATATCTTA
Found at i:63536 original size:8 final size:9
Alignment explanation
Indices: 63518--63552 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
63508 TAAAGACAGT
63518 AAATAAAAA
1 AAATAAAAA
63527 AAATAAAAA
1 AAATAAAAA
63536 AAATAAGAAGA
1 AAATAA-AA-A
63547 AAATAA
1 AAATAA
63553 TCCTCACGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 2 0.08
11 7 0.29
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (9 bp):
AAATAAAAA
Found at i:81928 original size:74 final size:71
Alignment explanation
Indices: 81850--81992 Score: 223
Period size: 71 Copynumber: 2.0 Consensus size: 71
81840 AAAATCTATC
*
81850 AAATTTAAAACAAAATTATTTAAAAAGTTAACAAGAAAAAAAATATATTTTTAATAGTCCAAGGT
1 AAATTTAAAACAAAATTATTTAAAAA-TTAACAAG--AAAAAATATATTTTTAATAGTCAAAGGT
81915 GAATATATA
63 GAATATATA
* * *
81924 AAATTTAAAACAAAATTATTTAAAAATTAACATGAAAATATATATTTTTAATAGTCAAAGGTGAT
1 AAATTTAAAACAAAATTATTTAAAAATTAACAAGAAAAAATATATTTTTAATAGTCAAAGGTGAA
81989 TATA
66 TATA
81993 AGTGATGATA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
71 32 0.49
73 7 0.11
74 26 0.40
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.34
Consensus pattern (71 bp):
AAATTTAAAACAAAATTATTTAAAAATTAACAAGAAAAAATATATTTTTAATAGTCAAAGGTGAA
TATATA
Found at i:82780 original size:2 final size:2
Alignment explanation
Indices: 82773--82800 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
82763 TTTATTAATT
82773 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
82801 AATAAGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:82953 original size:17 final size:16
Alignment explanation
Indices: 82917--82964 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
82907 TCTAAAAAAA
82917 TTAAAATATATATAAT
1 TTAAAATATATATAAT
* *
82933 TTAAAATATTTATTTAT
1 TTAAAATATATA-TAAT
82950 TTAAAA-ATATCATAA
1 TTAAAATATAT-ATAA
82965 AGTGGACATC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 16 0.62
17 10 0.38
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAAAATATATATAAT
Found at i:84524 original size:3 final size:3
Alignment explanation
Indices: 84516--84652 Score: 100
Period size: 3 Copynumber: 46.0 Consensus size: 3
84506 CTGTAATATG
*
84516 TAA TAA TAA TATA TAT TAA TAA TAA TAA -AA -AA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * *
84560 TATT TAT TAA TAA TAA TAA AAA T-A TAA TAA AAA TTA TTA TTA TTA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
84605 TAA TAA TTA TAA CAA TTA TAA CAA TTA TAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
84653 AACGGGCAAA
Statistics
Matches: 108, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
2 6 0.06
3 97 0.90
4 5 0.05
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:84537 original size:16 final size:16
Alignment explanation
Indices: 84511--84577 Score: 71
Period size: 16 Copynumber: 3.9 Consensus size: 16
84501 TGGGCCTGTA
84511 ATATGTAATAATAATAT
1 ATAT-TAATAATAATAT
*
84528 ATATTAATAATAATAAAAA
1 ATATTAATAATAAT---AT
*
84547 ATAATAATAATAATAT
1 ATATTAATAATAATAT
*
84563 TTATTAATAATAATA
1 ATATTAATAATAATA
84578 AAAATATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
16 24 0.57
17 4 0.10
19 14 0.33
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (16 bp):
ATATTAATAATAATAT
Found at i:85135 original size:120 final size:118
Alignment explanation
Indices: 84986--85549 Score: 506
Period size: 112 Copynumber: 4.9 Consensus size: 118
84976 AACTTCAATA
* * *
84986 TGTGATGAATTAAAGGC-AAGATTGAACAAGTTCTTCTCATTATTAACTTATT-TTCCTTCTTCA
1 TGTGATGAATTAAA--CAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
85049 GATGAGTTC-TCTCATTATGAACACT-TCTGGAAATGTTGATGTTGATCTATCTCCTTC
64 GATGAGTTCTTCTCATTATGAACTCTCTCTGGAAATGTTGATGTTGATCTA--T-C-TC
*
85106 TGTGATAGAATTAAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCC-TCTTCAG
1 TGTGAT-GAATTAAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * * *
85170 ATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA-----A-GTTGATCCATC-G
65 ATGAGTTCTTCTCATTATGAACTCTCTCTGGAAATGTTGATGTTGATCTATCTC
* *
85217 AGTGATGAATTCAAACAAAAGGTTTGAACAA---------ATTATGAATTTCTTCTTCCTTCTTC
1 TGTGATGAATT-AAAC-AAAGG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* * * *
85273 AGATGTGTTCTTCTCATTATGAACTCTAC-CTGGAAATGTTAATGCTGATTTATCTCCTTC
63 AGATGAGTTCTTCTCATTATGAACTCT-CTCTGGAAATGTTGATGTTGATCTA--T-C-TC
* * ** * *
85333 TGTGATAGAGTCATGCAAAGGTTGAACAAGTTTTTCTCATTATGAACTTCTTATTCC-TCTTCAG
1 TGTGAT-GAATTAAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * *
85397 ATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGA---T--TC-ATCT-
65 ATGAGTTCTTCTCATTATGAACTCTCTCTGGAAATGTTGATGTTGATCTATCTC
*
85444 AGTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
1 TGTGATGAA-TTAAAC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* *
85509 GATGAGTTCTTCTCATTATGAACT-TCTTTGGAAACGTTGAT
64 GATGAGTTCTTCTCATTATGAACTCTCTCTGGAAATGTTGAT
85550 CCATTGAGTA
Statistics
Matches: 367, Mismatches: 41, Indels: 79
0.75 0.08 0.16
Matches are distributed among these distances:
104 17 0.05
105 36 0.10
106 1 0.00
110 8 0.02
111 23 0.06
112 59 0.16
113 40 0.11
114 11 0.03
115 5 0.01
116 16 0.04
117 5 0.01
119 2 0.01
120 52 0.14
121 27 0.07
122 48 0.13
123 17 0.05
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (118 bp):
TGTGATGAATTAAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
TGAGTTCTTCTCATTATGAACTCTCTCTGGAAATGTTGATGTTGATCTATCTC
Found at i:85329 original size:227 final size:226
Alignment explanation
Indices: 85024--85532 Score: 745
Period size: 227 Copynumber: 2.2 Consensus size: 226
85014 AGTTCTTCTC
* * * * *
85024 ATTATTAACTTATT-TTCCTTCTTCAGATGAGTTC-TCTCATTATGAACACTTCTGGAAATGTTG
1 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCCTGGAAATGTTA
* *
85087 ATGTTGATCTATCTCCTTCTGTGATAGAATTAAACAAAGGTTGAACAAGTTCTTCTCATTATGAA
66 ATGCTGATCTATCTCCTTCTGTGATAGAATCAAACAAAGGTTGAACAAGTTCTTCTCATTATGAA
*
85152 CTTCTTTTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCG
131 CTTCTTATTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCG
85217 AGTGATGAATTCAAACAAAAGGTTTGAACAA-
196 AGTGATGAATTCAAACAAAAGG-TTGAACAAT
* *
85248 ATTATGAATTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATTATGAACTCTACCTGGAAATGTT
1 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-CCTGGAAATGTT
* * ** *
85313 AATGCTGATTTATCTCCTTCTGTGATAGAGTCATGCAAAGGTTGAACAAGTTTTTCTCATTATGA
65 AATGCTGATCTATCTCCTTCTGTGATAGAATCAAACAAAGGTTGAACAAGTTCTTCTCATTATGA
*
85378 ACTTCTTATTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATTCATC
130 ACTTCTTATTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATC
* *
85443 TAGTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCT
195 GAGTGATGAATTCAAACAAAAGGTTGAACAA-------T
85482 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 -ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
85533 TCTTTGGAAA
Statistics
Matches: 253, Mismatches: 20, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
224 11 0.04
225 19 0.08
226 23 0.09
227 152 0.60
235 48 0.19
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (226 bp):
ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCCTGGAAATGTTA
ATGCTGATCTATCTCCTTCTGTGATAGAATCAAACAAAGGTTGAACAAGTTCTTCTCATTATGAA
CTTCTTATTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCG
AGTGATGAATTCAAACAAAAGGTTGAACAAT
Found at i:86757 original size:18 final size:18
Alignment explanation
Indices: 86720--86757 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
86710 TATGTGAAAG
*
86720 AATAAATTGAATTTCGAA
1 AATAAATTGAATTTCAAA
86738 AATAAATTGAATTTCAAA
1 AATAAATTGAATTTCAAA
86756 AA
1 AA
86758 GATATTCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (18 bp):
AATAAATTGAATTTCAAA
Found at i:87156 original size:18 final size:18
Alignment explanation
Indices: 87124--87174 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
87114 TTTTTCATCA
*
87124 TTTTTCATTTCATTTAATT
1 TTTTTC-TTTTATTTAATT
*
87143 TTTTTCTTTTATTTTTATT
1 TTTTTCTTTTA-TTTAATT
*
87162 TTATT-TTTTATTT
1 TTTTTCTTTTATTT
87175 TTTCTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 3 0.11
18 9 0.32
19 16 0.57
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTCTTTTATTTAATT
Found at i:87157 original size:30 final size:30
Alignment explanation
Indices: 87110--87182 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
87100 CATTTTCTAT
* *
87110 ATATTTTTTC-ATCATTTTTCATTTCATTTA
1 ATATTTTTTCTTTTATTTTT-ATTTCATTTA
* *
87140 AT-TTTTTTCTTTTATTTTTATTTTATTTT
1 ATATTTTTTCTTTTATTTTTATTTCATTTA
*
87169 TTATTTTTTCTTTT
1 ATATTTTTTCTTTT
87183 TTTCTTCTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 16 0.44
30 20 0.56
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.75
Consensus pattern (30 bp):
ATATTTTTTCTTTTATTTTTATTTCATTTA
Found at i:87182 original size:12 final size:12
Alignment explanation
Indices: 87142--87175 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
87132 TTCATTTAAT
*
87142 TTTTTTCTTTTA
1 TTTTTTATTTTA
87154 -TTTTTATTTTA
1 TTTTTTATTTTA
87165 TTTTTTATTTT
1 TTTTTTATTTT
87176 TTCTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTATTTTA
Found at i:97904 original size:28 final size:26
Alignment explanation
Indices: 97849--97916 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 26
97839 TAAAAACATT
*
97849 AAAAAATAATATATATAAATATTATG
1 AAAAAATAATATATATAAAAATTATG
*
97875 AAAATAATAAGTATATATAAAAATTTTG
1 AAAA-AATAA-TATATATAAAAATTATG
*
97903 AAAAAAAAAT-TATA
1 AAAAAATAATATATA
97917 AATTAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 4 0.11
26 5 0.14
27 9 0.24
28 19 0.51
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.32
Consensus pattern (26 bp):
AAAAAATAATATATATAAAAATTATG
Found at i:98573 original size:17 final size:16
Alignment explanation
Indices: 98533--98584 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
98523 TTATCTAAAA
98533 ATAA-TTAAAATATAT
1 ATAATTTAAAATATAT
*
98548 ATAATTTAAAATATTT
1 ATAATTTAAAATATAT
*
98564 ATTTATTTAAAA-ATAT
1 A-TAATTTAAAATATAT
98580 CATAA
1 -ATAA
98585 AATGGACATC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.13
16 16 0.53
17 10 0.33
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATTTAAAATATAT
Found at i:100140 original size:3 final size:3
Alignment explanation
Indices: 100132--100244 Score: 86
Period size: 3 Copynumber: 38.0 Consensus size: 3
100122 CTGTAATATG
* * *
100132 TAA TAA TAA TATT TAT TAA TAA TAA TAA AAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * *
100177 TAA TAA T-A TAA TTA TTA TTA TTA TAA TTA TAA CAA TTA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
100224 TAA TAA TAA AAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
100245 AACGGTCAAA
Statistics
Matches: 89, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
2 4 0.04
3 83 0.93
4 2 0.02
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:100170 original size:17 final size:17
Alignment explanation
Indices: 100148--100181 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
100138 TAATATTTAT
100148 TAATAATAATAAAAATA
1 TAATAATAATAAAAATA
*
100165 TAATAATAATAATAATA
1 TAATAATAATAAAAATA
100182 ATATAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAATAATAATAAAAATA
Found at i:101891 original size:6 final size:6
Alignment explanation
Indices: 101880--101913 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
101870 CCTATGTTGC
**
101880 ACGGAT ACGGAT ACGGGG ACGGAT ACGGAT ACGG
1 ACGGAT ACGGAT ACGGAT ACGGAT ACGGAT ACGG
101914 GGACAGATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.41, T:0.12
Consensus pattern (6 bp):
ACGGAT
Found at i:101903 original size:18 final size:18
Alignment explanation
Indices: 101880--101925 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
101870 CCTATGTTGC
101880 ACGGATACGGATACGGGG
1 ACGGATACGGATACGGGG
101898 ACGGATACGGATACGGGG
1 ACGGATACGGATACGGGG
*
101916 ACAGATACGG
1 ACGGATACGG
101926 GGATGGGGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.17, G:0.41, T:0.11
Consensus pattern (18 bp):
ACGGATACGGATACGGGG
Found at i:107720 original size:24 final size:24
Alignment explanation
Indices: 107675--107721 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
107665 TCAGAAGATG
* *
107675 CTTTACCTTAGTTATAAGAGGATC
1 CTTTACCTTAGTAACAAGAGGATC
* *
107699 CTTTAGCTTAGTAACAATAGGAT
1 CTTTACCTTAGTAACAAGAGGAT
107722 AGTTCACACG
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:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (24 bp):
CTTTACCTTAGTAACAAGAGGATC
Found at i:109781 original size:17 final size:17
Alignment explanation
Indices: 109759--109813 Score: 110
Period size: 17 Copynumber: 3.2 Consensus size: 17
109749 CCACTGCTTC
109759 TGCAATGTCTAGTCTTG
1 TGCAATGTCTAGTCTTG
109776 TGCAATGTCTAGTCTTG
1 TGCAATGTCTAGTCTTG
109793 TGCAATGTCTAGTCTTG
1 TGCAATGTCTAGTCTTG
109810 TGCA
1 TGCA
109814 TATCATAGCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (17 bp):
TGCAATGTCTAGTCTTG
Found at i:120407 original size:12 final size:12
Alignment explanation
Indices: 120390--120419 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
120380 TGAACTTAAC
120390 GAGCAATGAGAT
1 GAGCAATGAGAT
120402 GAGCAATGAGAT
1 GAGCAATGAGAT
120414 GAGCAA
1 GAGCAA
120420 CGAGCTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.10, G:0.33, T:0.13
Consensus pattern (12 bp):
GAGCAATGAGAT
Found at i:121509 original size:14 final size:16
Alignment explanation
Indices: 121480--121527 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 16
121470 TTAATTATTT
121480 TTAAG-ATTCAATTGAA
1 TTAAGTATTC-ATTGAA
121496 TTAA-TATT-ATTGAA
1 TTAAGTATTCATTGAA
121510 --AAGTATTCATTGAA
1 TTAAGTATTCATTGAA
121524 TTAA
1 TTAA
121528 ATAAAATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
12 2 0.07
13 4 0.15
14 12 0.44
16 9 0.33
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (16 bp):
TTAAGTATTCATTGAA
Found at i:121884 original size:14 final size:15
Alignment explanation
Indices: 121867--121905 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
121857 TTGATTTTCG
121867 TTAA-CCCCTTTTGT
1 TTAAGCCCCTTTTGT
*
121881 TTAAGTCCCTTTTGT
1 TTAAGCCCCTTTTGT
*
121896 TTAAGTCCCT
1 TTAAGCCCCT
121906 AAAATGGCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.15, C:0.26, G:0.10, T:0.49
Consensus pattern (15 bp):
TTAAGCCCCTTTTGT
Found at i:121892 original size:15 final size:15
Alignment explanation
Indices: 121872--121905 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
121862 TTTCGTTAAC
121872 CCCTTTTGTTTAAGT
1 CCCTTTTGTTTAAGT
121887 CCCTTTTGTTTAAGT
1 CCCTTTTGTTTAAGT
121902 CCCT
1 CCCT
121906 AAAATGGCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.12, C:0.26, G:0.12, T:0.50
Consensus pattern (15 bp):
CCCTTTTGTTTAAGT
Found at i:125960 original size:33 final size:32
Alignment explanation
Indices: 125923--125991 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
125913 GTATCAAACC
* *
125923 ATTTAACTCATTATAAATTGTATTATAAAATT
1 ATTTAACCCATTATAAACTGTATTATAAAATT
*
125955 GATTTAACCCATTATAAACTGTATTATAAGATT
1 -ATTTAACCCATTATAAACTGTATTATAAAATT
125988 ATTT
1 ATTT
125992 GTGTAGCACC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 4 0.12
33 29 0.88
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.45
Consensus pattern (32 bp):
ATTTAACCCATTATAAACTGTATTATAAAATT
Found at i:126921 original size:20 final size:18
Alignment explanation
Indices: 126877--126924 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
126867 GATACAATTA
**
126877 GTATCGATACTGAGGTGG
1 GTATCGATACTGAGGAAG
*
126895 GTTTCGATACTGTGAGGAAG
1 GTATCGATAC--TGAGGAAG
126915 GTATCGATAC
1 GTATCGATAC
126925 CATTGATTCC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 9 0.38
20 15 0.62
ACGTcount: A:0.25, C:0.12, G:0.33, T:0.29
Consensus pattern (18 bp):
GTATCGATACTGAGGAAG
Found at i:127086 original size:94 final size:95
Alignment explanation
Indices: 126912--127089 Score: 207
Period size: 94 Copynumber: 1.9 Consensus size: 95
126902 TACTGTGAGG
* * *
126912 AAGGTATCGATACCATTGATTCCAGAATGCAGAAATGGTATCAATACTATAATAGAGTATTGGTA
1 AAGGTATCGATACCATGGATTCCAGAATGCAGAAATGGTATCAATACTATAAGAGAGTATCGGTA
* *
126977 CCATAGTATAAAAGTATCGGTATTAAGAGA
66 CCACAATATAAAAGTATCGGTATTAAGAGA
* * * * ** *
127007 AAGGTATTGCTACCATGGA-TCTAGAATGTAGAAATGGTATTGATACTGA-AAGGGAGTATCGGT
1 AAGGTATCGATACCATGGATTCCAGAATGCAGAAATGGTATCAATACT-ATAAGAGAGTATCGGT
* *
127070 ATCACAATATAGAAGTATCG
65 ACCACAATATAAAAGTATCG
127090 ATACCATGGT
Statistics
Matches: 68, Mismatches: 14, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
94 51 0.75
95 17 0.25
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.28
Consensus pattern (95 bp):
AAGGTATCGATACCATGGATTCCAGAATGCAGAAATGGTATCAATACTATAAGAGAGTATCGGTA
CCACAATATAAAAGTATCGGTATTAAGAGA
Found at i:127495 original size:54 final size:54
Alignment explanation
Indices: 127429--128038 Score: 803
Period size: 54 Copynumber: 11.2 Consensus size: 54
127419 TTGTGATTAC
* * *
127429 CGTATTGACACTATGTGTACAACCTAAGAAATGCATAATGAGTTTATGAATTTT
1 CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTT
127483 CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAA-TTT
1 CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTT
127536 CTGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTT
1 C-GTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTT
* ** *
127591 CCTATTGGCACTATGTGTGCAAATTAAGAAATTCATAATGAGTTTATGAATTTC
1 CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTT
127645 CGTATAT-GCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTT
1 CGTAT-TGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTT
* * * * *
127699 CGTATTGGCATTATGTGTGCAACTTTAGAAATTCATAACGTGTTTATGAATTTT
1 CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTT
*
127753 CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTC
1 CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTT
* *
127807 CGTATTGGCACTGTGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTC
1 CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTT
* * * * *
127861 CGTATTGACACTGTGTATGCAACTTATAAGAAATTCATAATGAGTTTATGAATTTC
1 CGTATTGGCACTATGTGTGCAAC--CTAAGAAATTCATAATGAGTTTATGAATTTT
* * * * * *
127917 CGTATTGACACTGTGTGTACAACTTAAGAAATTCATAATAAGGTTATGAA-TTT
1 CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTT
* ** * *** * * * * *
127970 CTATATTGGCACTGGGTGTGCAAACTACTTAATTTATAGTAAATTTGTGAATTTAT
1 C-GTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTT-T
128026 CGTATTGGCACTA
1 CGTATTGGCACTA
128039 CAGGTGCAAA
Statistics
Matches: 499, Mismatches: 48, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
53 8 0.02
54 421 0.84
55 17 0.03
56 53 0.11
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (54 bp):
CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTT
Found at i:130494 original size:20 final size:21
Alignment explanation
Indices: 130454--130494 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
130444 TTTTTTGCCA
* *
130454 GGTTTTGAAACCCCCTTAGGT
1 GGTTTCGAAACCCCCTAAGGT
130475 GGTTTCGAAA-CCCCTAAGGT
1 GGTTTCGAAACCCCCTAAGGT
130495 AGTATCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
GGTTTCGAAACCCCCTAAGGT
Found at i:138725 original size:29 final size:31
Alignment explanation
Indices: 138692--138772 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
138682 AAATGGATTT
* *
138692 GTTTAATGACCAAAATA-AAAATTTTG-AAA
1 GTTTAGTGACCAAAATATAAAATTTGGAAAA
* *
138721 GTTTAGTGACCAAAGTATAAACTTTGGAAAA
1 GTTTAGTGACCAAAATATAAAATTTGGAAAA
*
138752 GTTTAGGGACCAAAATGATAA
1 GTTTAGTGACCAAAAT-ATAA
138773 TTTAAATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 15 0.35
30 7 0.16
31 17 0.40
32 4 0.09
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (31 bp):
GTTTAGTGACCAAAATATAAAATTTGGAAAA
Found at i:141411 original size:2 final size:2
Alignment explanation
Indices: 141404--141460 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
141394 ATTTTAACAT
141404 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
141446 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
141461 TTGAAGAATG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:146509 original size:2 final size:2
Alignment explanation
Indices: 146502--146608 Score: 74
Period size: 2 Copynumber: 50.5 Consensus size: 2
146492 TAGTTCATTC
* * * *
146502 AT AT AT AT AA ACT AT TT AT AT AGT AT AT AT AA ACT AT AT AA ACT
1 AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT A-T AT AT AT A-T
*
146546 AT AGT AT AT AT TT AT AT ACT AT AT AT AT -T AT AT AT -T AT AT AT
1 AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
*
146588 AT AT AA ACT AT AT ACT AT AT A
1 AT AT AT A-T AT AT A-T AT AT A
146609 GTTTACATAT
Statistics
Matches: 83, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
1 2 0.02
2 69 0.83
3 12 0.14
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:146509 original size:30 final size:31
Alignment explanation
Indices: 146444--146509 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
146434 AACAATTATA
* *
146444 ATATATTAATAAACCATATATTTTATATAAT
1 ATATATTAATAAACCATATAGTTCATATAAT
* * *
146475 -TATATTAATAAACTATGTAGTTCAT-TCAT
1 ATATATTAATAAACCATATAGTTCATATAAT
146504 ATATAT
1 ATATAT
146510 AAACTATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (31 bp):
ATATATTAATAAACCATATAGTTCATATAAT
Found at i:146541 original size:13 final size:13
Alignment explanation
Indices: 146536--146653 Score: 73
Period size: 13 Copynumber: 9.1 Consensus size: 13
146526 ATATATAAAC
146536 TATATAAACTATA
1 TATATAAACTATA
**
146549 GTATAT-ATTTATA
1 -TATATAAACTATA
*
146562 TACTATATA-TAT-
1 TA-TATAAACTATA
*
146574 TATATATTA-TATA
1 TATATA-AACTATA
146587 TATATAAACTATA
1 TATATAAACTATA
* * *
146600 TACTATATAGTTTA
1 TA-TATAAACTATA
* * *
146614 CATATGAAGTATA
1 TATATAAACTATA
*
146627 TATAAAAACTATA
1 TATATAAACTATA
146640 TATATAAACTATA
1 TATATAAACTATA
146653 T
1 T
146654 GTTTTTCGTT
Statistics
Matches: 81, Mismatches: 17, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
11 4 0.05
12 10 0.12
13 53 0.65
14 14 0.17
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (13 bp):
TATATAAACTATA
Found at i:146543 original size:31 final size:30
Alignment explanation
Indices: 146505--146601 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 30
146495 TTCATTCATA
146505 TATATAAACTATTTA-TATAGTATATATAAAC
1 TATATAAACTA-TTAGTATA-TATATATAAAC
* *
146536 TATATAAACTA-TAGTATATATTTATATAC
1 TATATAAACTATTAGTATATATATATAAAC
* * *
146565 TATATATATTATATATTATATATATATAAAC
1 TATATAAACTAT-TAGTATATATATATAAAC
146596 TATATA
1 TATATA
146602 CTATATAGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
29 20 0.36
30 4 0.07
31 32 0.57
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (30 bp):
TATATAAACTATTAGTATATATATATAAAC
Found at i:146555 original size:7 final size:6
Alignment explanation
Indices: 146502--146608 Score: 74
Period size: 7 Copynumber: 16.8 Consensus size: 6
146492 TAGTTCATTC
* * * *
146502 ATATAT ATAAACT ATTTAT ATAGTAT ATATAA ACTATAT AAACTAT AGTATAT
1 ATATAT ATATA-T ATATAT ATA-TAT ATATAT A-TATAT ATA-TAT A-TATAT
* *
146555 ATTTAT ATACTAT ATATAT -TATAT AT-TAT ATATAT ATAAACT ATATACT
1 ATATAT ATA-TAT ATATAT ATATAT ATATAT ATATAT ATATA-T ATATA-T
146604 ATATA
1 ATATA
146609 GTTTACATAT
Statistics
Matches: 80, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
5 10 0.12
6 28 0.35
7 41 0.51
8 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.45
Consensus pattern (6 bp):
ATATAT
Found at i:146600 original size:38 final size:40
Alignment explanation
Indices: 146558--146645 Score: 112
Period size: 38 Copynumber: 2.3 Consensus size: 40
146548 AGTATATATT
* * *
146558 TATATACTATATA-TATTATATAT-TA-TATATATATAAAC
1 TATATACTATATAGT-TTACATATGAAGTATATATAAAAAC
146596 TATATACTATATAGTTTACATATGAAGTATATATAAAAAC
1 TATATACTATATAGTTTACATATGAAGTATATATAAAAAC
146636 TATATA-TATA
1 TATATACTATA
146646 AACTATATGT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
38 20 0.45
39 6 0.14
40 18 0.41
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (40 bp):
TATATACTATATAGTTTACATATGAAGTATATATAAAAAC
Found at i:146608 original size:9 final size:8
Alignment explanation
Indices: 146502--146608 Score: 74
Period size: 9 Copynumber: 12.6 Consensus size: 8
146492 TAGTTCATTC
146502 ATATATAT
1 ATATATAT
* *
146510 AAACTATTT
1 ATA-TATAT
146519 ATATAGTAT
1 ATATA-TAT
*
146528 ATATAAACT
1 ATATATA-T
*
146537 ATATAAACT
1 ATATATA-T
146546 ATAGTATAT
1 ATA-TATAT
*
146555 ATTTATAT
1 ATATATAT
146563 ACTATATAT
1 A-TATATAT
146572 AT-TATAT
1 ATATATAT
146579 AT-TATAT
1 ATATATAT
*
146586 ATATATAA
1 ATATATAT
146594 ACTATATACT
1 A-TATATA-T
146604 ATATA
1 ATATA
146609 GTTTACATAT
Statistics
Matches: 81, Mismatches: 10, Indels: 15
0.76 0.09 0.14
Matches are distributed among these distances:
7 14 0.17
8 17 0.21
9 46 0.57
10 4 0.05
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.45
Consensus pattern (8 bp):
ATATATAT
Found at i:146618 original size:29 final size:29
Alignment explanation
Indices: 146525--146618 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
146515 ATTTATATAG
* *
146525 TATATATAAACTATATAAACTATAGTATA
1 TATATATAAACTATATATACTATAGTTTA
* * * *
146554 TATTTATATACTATATATATTATATATTATA
1 TATATATAAACTATATATACTATA-GTT-TA
146585 TATATATAAACTATATACTA-TATAGTTTA
1 TATATATAAACTATATA-TACTATAGTTTA
*
146614 CATAT
1 TATAT
146619 GAAGTATATA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
29 26 0.50
30 3 0.06
31 21 0.40
32 2 0.04
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (29 bp):
TATATATAAACTATATATACTATAGTTTA
Found at i:148034 original size:20 final size:18
Alignment explanation
Indices: 148011--148102 Score: 65
Period size: 18 Copynumber: 5.3 Consensus size: 18
148001 ATTTATATAG
148011 TATATACTATATATATAAAC
1 TATATA-TATATATAT-AAC
*
148031 TATAT-TGTATATAT-AC
1 TATATATATATATATAAC
*
148047 TATATAGTTTATATATGAAC
1 TATATA-TATATATAT-AAC
148067 --TATATATA-A-A-AAC
1 TATATATATATATATAAC
*
148080 TCTATATATATATA-AAC
1 TATATATATATATATAAC
148097 TATATA
1 TATATA
148103 CACTATAACT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
13 3 0.05
15 9 0.15
16 9 0.15
17 12 0.20
18 20 0.33
20 7 0.12
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (18 bp):
TATATATATATATATAAC
Found at i:148089 original size:17 final size:17
Alignment explanation
Indices: 148067--148102 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
148057 ATATATGAAC
*
148067 TATATATAAAAACTCTA
1 TATATATAAAAACTATA
*
148084 TATATATATAAACTATA
1 TATATATAAAAACTATA
148101 TA
1 TA
148103 CACTATAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (17 bp):
TATATATAAAAACTATA
Found at i:148217 original size:27 final size:27
Alignment explanation
Indices: 148187--148241 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
148177 ATATATATCA
** *
148187 ACTACATACTATAGTTGATATTTATAT
1 ACTACATAAGATAGTTGATACTTATAT
* *
148214 ACTATATAAGATAGTTTATACTTATAT
1 ACTACATAAGATAGTTGATACTTATAT
148241 A
1 A
148242 ATTTATACTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (27 bp):
ACTACATAAGATAGTTGATACTTATAT
Found at i:148248 original size:27 final size:27
Alignment explanation
Indices: 148197--148248 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
148187 ACTACATACT
* *
148197 ATAGTTGATATTTATATACTATATAAG
1 ATAGTTGATACTTATATAATATATAAG
* *
148224 ATAGTTTATACTTATATAATTTATA
1 ATAGTTGATACTTATATAATATATA
148249 CTATATAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (27 bp):
ATAGTTGATACTTATATAATATATAAG
Found at i:148259 original size:15 final size:15
Alignment explanation
Indices: 148228--148256 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
148218 TATAAGATAG
148228 TTTATACTTATATAA
1 TTTATACTTATATAA
148243 TTTATAC-TATATAA
1 TTTATACTTATATAA
148257 ATTCAAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTATACTTATATAA
Found at i:148286 original size:15 final size:15
Alignment explanation
Indices: 148268--148301 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
148258 TTCAAAGTAT
148268 ATACTATAT-GTGTGA
1 ATACTATATAGT-TGA
148283 ATACTATATAGTTGA
1 ATACTATATAGTTGA
148298 ATAC
1 ATAC
148302 ATTAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (15 bp):
ATACTATATAGTTGA
Found at i:149162 original size:23 final size:23
Alignment explanation
Indices: 149128--149194 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
149118 CACCACAGCT
*
149128 CGTATAAATGCACCGAAGTGTCA-
1 CGTAGAAATGCACCGAAGTG-CAG
* *
149151 CGTAGAATTGCACCGTAGTGCAG
1 CGTAGAAATGCACCGAAGTGCAG
*
149174 CGTAGAAATACACCGAAGTGC
1 CGTAGAAATGCACCGAAGTGC
149195 CATATAAGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
22 2 0.05
23 35 0.95
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCAG
Found at i:154114 original size:23 final size:23
Alignment explanation
Indices: 154071--154131 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
154061 CTCGTATAAA
*
154071 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* *
154094 TGCACCGTAGTG-CAGCATAGAAA
1 TGCACCGAAGTGCCA-CATAGAAT
* *
154117 TACACCAAAGTGCCA
1 TGCACCGAAGTGCCA
154132 TATAAGGTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 2 0.07
23 26 0.87
24 2 0.07
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.16
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:154524 original size:14 final size:14
Alignment explanation
Indices: 154505--154547 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
154495 CTTTTTCTTT
*
154505 CATATATCTCATGG
1 CATATATCACATGG
154519 CATATATCACATGG
1 CATATATCACATGG
154533 CATATATCACATGG
1 CATATATCACATGG
154547 C
1 C
154548 TCTTTATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (14 bp):
CATATATCACATGG
Found at i:156441 original size:18 final size:18
Alignment explanation
Indices: 156418--156468 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
156408 ATATGAACTA
156418 TATATAAAAACTATAGTT
1 TATATAAAAACTATAGTT
156436 TATATAAAAACTATAGTT
1 TATATAAAAACTATAGTT
*
156454 TATATATAAACTATA
1 TATATAAAAACTATA
156469 TATTATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (18 bp):
TATATAAAAACTATAGTT
Found at i:156470 original size:20 final size:19
Alignment explanation
Indices: 156416--156526 Score: 72
Period size: 20 Copynumber: 5.8 Consensus size: 19
156406 ACATATGAAC
*
156416 TATATATAAAAACTATAGTT
1 TATATATAAATA-TATAGTT
156436 TATATA-AAA-ACTATAGTT
1 TATATATAAATA-TATAGTT
156454 TATATATAAACTATATA--T
1 TATATATAAA-TATATAGTT
** * *
156472 TATAT-TTGATATTTA-TA
1 TATATATAAATATATAGTT
156489 TACTATATAATATATATAGTT
1 TA-TATATAA-ATATATAGTT
*
156510 TATATATGAACTATATA
1 TATATAT-AAATATATA
156527 TATATAAACT
Statistics
Matches: 73, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
16 5 0.07
17 4 0.05
18 24 0.33
19 7 0.10
20 27 0.37
21 6 0.08
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.45
Consensus pattern (19 bp):
TATATATAAATATATAGTT
Found at i:156474 original size:18 final size:18
Alignment explanation
Indices: 156418--156540 Score: 73
Period size: 18 Copynumber: 6.9 Consensus size: 18
156408 ATATGAACTA
*
156418 TATATAAAAACTATAGT-T
1 TATATATAAACTATA-TAT
*
156436 TATATAAAAACTATAGT-T
1 TATATATAAACTATA-TAT
156454 TATATATAAACTATATAT
1 TATATATAAACTATATAT
** *
156472 TATAT-TTGA-TATTTAT
1 TATATATAAACTATATAT
156488 ATACTATATAATA-TATATAGTT
1 -TA-TATATAA-ACTATATA--T
*
156510 TATATATGAAC--TATA-
1 TATATATAAACTATATAT
156525 TATATATAAACTATAT
1 TATATATAAACTATAT
156541 TGCTGAGCTC
Statistics
Matches: 86, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
15 10 0.12
16 6 0.07
17 8 0.09
18 45 0.52
19 2 0.02
20 12 0.14
21 2 0.02
22 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (18 bp):
TATATATAAACTATATAT
Found at i:156488 original size:29 final size:29
Alignment explanation
Indices: 156447--156532 Score: 76
Period size: 29 Copynumber: 3.0 Consensus size: 29
156437 ATATAAAAAC
*
156447 TATAGTTTATATATAAACTATATATTATATT
1 TATAG-TT-TATATAAACTATATATTATATA
156478 TGATA-TTTATAT--ACTATATA--ATATA
1 T-ATAGTTTATATAAACTATATATTATATA
156503 TATAGTTTATATATGAACTATATA-TATATA
1 TATAGTTTATATA--AACTATATATTATATA
156533 AACTATATTG
Statistics
Matches: 47, Mismatches: 1, Indels: 15
0.75 0.02 0.24
Matches are distributed among these distances:
24 3 0.06
25 12 0.26
27 8 0.17
29 13 0.28
30 7 0.15
31 1 0.02
32 3 0.06
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (29 bp):
TATAGTTTATATAAACTATATATTATATA
Found at i:156528 original size:15 final size:15
Alignment explanation
Indices: 156408--156540 Score: 66
Period size: 15 Copynumber: 8.9 Consensus size: 15
156398 TACAGTTTAC
*
156408 ATATGAACTATATAT
1 ATATAAACTATATAT
156423 A-A-AAACTATAGTTTAT
1 ATATAAACTATA---TAT
*
156439 ATAAAAACTATAGTTTAT
1 ATATAAACTATA---TAT
156457 ATATAAACTATATAT
1 ATATAAACTATATAT
*
156472 -TAT--A-TTTGATAT
1 ATATAAACTAT-ATAT
* *
156484 TTATATACTATATA-
1 ATATAAACTATATAT
* *
156498 ATATATA-TAGTTTAT
1 ATATAAACTA-TATAT
*
156513 ATATGAACTATATAT
1 ATATAAACTATATAT
156528 ATATAAACTATAT
1 ATATAAACTATAT
156541 TGCTGAGCTC
Statistics
Matches: 95, Mismatches: 10, Indels: 26
0.73 0.08 0.20
Matches are distributed among these distances:
11 2 0.02
12 5 0.05
13 12 0.13
14 13 0.14
15 29 0.31
16 8 0.08
17 1 0.01
18 25 0.26
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (15 bp):
ATATAAACTATATAT
Found at i:157278 original size:18 final size:18
Alignment explanation
Indices: 157255--157291 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
157245 CTAACATGCA
* *
157255 AACTATATAGTATATACT
1 AACTATATAATATAAACT
157273 AACTATATAATATAAACT
1 AACTATATAATATAAACT
157291 A
1 A
157292 TGTAATATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.35
Consensus pattern (18 bp):
AACTATATAATATAAACT
Found at i:157285 original size:16 final size:16
Alignment explanation
Indices: 157255--157315 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
157245 CTAACATGCA
157255 AACTATATAGTATATACT
1 AACTATATA--ATATACT
157273 AACTATATAATATA--
1 AACTATATAATATACT
*
157287 AACTATGTAATATACT
1 AACTATATAATATACT
* *
157303 AATTATTTAATAT
1 AACTATATAATAT
157316 CAAATATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
14 13 0.34
16 16 0.42
18 9 0.24
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (16 bp):
AACTATATAATATACT
Found at i:157335 original size:27 final size:28
Alignment explanation
Indices: 157280--157362 Score: 80
Period size: 30 Copynumber: 2.9 Consensus size: 28
157270 ACTAACTATA
*
157280 TAATAT-AAACTATGTAATATACTAATTATT
1 TAATATCAAACTA--TAATATGC-AATTATT
157310 TAATATCAAA-TATAATATGCAATTATT
1 TAATATCAAACTATAATATGCAATTATT
* *
157337 TGATATGAAACTATATGATATGCAAT
1 TAATATCAAACTATA--ATATGCAAT
157363 GCAACTGTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
27 15 0.33
28 11 0.24
30 17 0.37
31 3 0.07
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (28 bp):
TAATATCAAACTATAATATGCAATTATT
Found at i:157360 original size:30 final size:27
Alignment explanation
Indices: 157294--157362 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 27
157284 ATAAACTATG
*
157294 TAATATACTAATTATTTAATATCAAATA
1 TAATATGC-AATTATTTAATATCAAATA
* *
157322 TAATATGCAATTATTTGATATGAAACTA
1 TAATATGCAATTATTTAATATCAAA-TA
157350 TATGATATGCAAT
1 TA--ATATGCAAT
157363 GCAACTGTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 15 0.43
28 11 0.31
30 9 0.26
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (27 bp):
TAATATGCAATTATTTAATATCAAATA
Found at i:157756 original size:12 final size:12
Alignment explanation
Indices: 157727--157760 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
157717 ATTGTAATAA
157727 ATCAAATGTTAT
1 ATCAAATGTTAT
*
157739 -TCAAATTTTAT
1 ATCAAATGTTAT
157750 ATCAAATGTTA
1 ATCAAATGTTA
157761 CTTACATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (12 bp):
ATCAAATGTTAT
Found at i:164728 original size:23 final size:23
Alignment explanation
Indices: 164702--164756 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
164692 TAAGCTACCA
164702 AAAGGCAGAGAAAAATATGTCAC
1 AAAGGCAGAGAAAAATATGTCAC
* * *
164725 AAAGACAGAGATAAATATGTCAT
1 AAAGGCAGAGAAAAATATGTCAC
164748 AAAGGCAGA
1 AAAGGCAGA
164757 TAACATGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.11, G:0.22, T:0.15
Consensus pattern (23 bp):
AAAGGCAGAGAAAAATATGTCAC
Found at i:166534 original size:39 final size:40
Alignment explanation
Indices: 166449--166534 Score: 104
Period size: 43 Copynumber: 2.1 Consensus size: 40
166439 AATCAATTAT
*
166449 AATAAAACAAACAGACTATATAAATATACAATTTACACTTTAC
1 AATAAAACAAACAGACTATATAAAAATACAATTTACAC--T-C
*
166492 AATAAAACAAACATA-TCATATAAAAATACAATTTACAC-C
1 AATAAAACAAACAGACT-ATATAAAAATACAATTTACACTC
166531 AATA
1 AATA
166535 GATGCGATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
39 5 0.12
42 1 0.03
43 34 0.85
ACGTcount: A:0.57, C:0.16, G:0.01, T:0.26
Consensus pattern (40 bp):
AATAAAACAAACAGACTATATAAAAATACAATTTACACTC
Found at i:178030 original size:31 final size:30
Alignment explanation
Indices: 177960--178032 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
177950 AGTTTTAAAA
* *
177960 GTAACAAATTAGTCACTAACATATCAATTT
1 GTAACAAAATAGTCACTAACATATCAATCT
* *
177990 GTAACAAAATAGTCACTAATATTATCGATCT
1 GTAACAAAATAGTCACTAACA-TATCAATCT
*
178021 GTAATAAAATAG
1 GTAACAAAATAG
178033 CCGCTCAACC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 19 0.51
31 18 0.49
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (30 bp):
GTAACAAAATAGTCACTAACATATCAATCT
Found at i:178806 original size:31 final size:31
Alignment explanation
Indices: 178745--178819 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
178735 AACAGTGGAC
* * *
178745 TGACAATTTTGTT-TAAATTGACAACGTTAG
1 TGACTATTTTGTTATAAATCGACAACATTAG
*
178775 TGACTATTTTGTTATAAATCGATAACATTAG
1 TGACTATTTTGTTATAAATCGACAACATTAG
*
178806 T-AATATATTTGTTA
1 TGACTAT-TTTGTTA
178820 ATTTTAAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 16 0.42
31 22 0.58
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (31 bp):
TGACTATTTTGTTATAAATCGACAACATTAG
Found at i:180588 original size:2 final size:2
Alignment explanation
Indices: 180581--180632 Score: 88
Period size: 2 Copynumber: 26.0 Consensus size: 2
180571 AAATTGTGTA
180581 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
180623 -T CAT AT AT AT
1 AT -AT AT AT AT
180633 TTGTAACACC
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 46 0.96
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:181623 original size:20 final size:21
Alignment explanation
Indices: 181598--181647 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
181588 TGGTGTGTAG
181598 TATCGATACTT-CTTGACCAA
1 TATCGATACTTGCTTGACCAA
* *
181618 TATCGATA-TTGTTTGACCAG
1 TATCGATACTTGCTTGACCAA
181638 TATCGATACT
1 TATCGATACT
181648 CTCGGGCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 23 0.88
21 1 0.04
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (21 bp):
TATCGATACTTGCTTGACCAA
Found at i:182041 original size:14 final size:14
Alignment explanation
Indices: 182022--182055 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
182012 CATTTAAATG
*
182022 ATGAACGAATACAA
1 ATGAACGAACACAA
*
182036 ATGAACGAACATAA
1 ATGAACGAACACAA
182050 ATGAAC
1 ATGAAC
182056 ATAAATGAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (14 bp):
ATGAACGAACACAA
Found at i:182387 original size:14 final size:14
Alignment explanation
Indices: 182368--182449 Score: 59
Period size: 14 Copynumber: 6.1 Consensus size: 14
182358 AGATTGGACT
182368 AAACATAAATGAAC
1 AAACATAAATGAAC
182382 AAACAT--A--AAC
1 AAACATAAATGAAC
*
182392 AAACA-AAAGTAAAC
1 AAACATAAA-TGAAC
*
182406 GAAACATAAACGAAC
1 -AAACATAAATGAAC
*
182421 AAACATAAACGAAC
1 AAACATAAATGAAC
*
182435 ATAA-ATGAATGAAC
1 A-AACATAAATGAAC
182449 A
1 A
182450 TAAACGAACA
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
10 8 0.14
11 1 0.02
12 1 0.02
14 33 0.59
15 10 0.18
16 3 0.05
ACGTcount: A:0.65, C:0.16, G:0.09, T:0.11
Consensus pattern (14 bp):
AAACATAAATGAAC
Found at i:182449 original size:24 final size:24
Alignment explanation
Indices: 182383--182461 Score: 97
Period size: 24 Copynumber: 3.2 Consensus size: 24
182373 TAAATGAACA
*
182383 AACATAAACAAACAAA-AGTAAACG
1 AACATAAACGAACAAACA-TAAACG
182407 AAACATAAACGAACAAACATAAACG
1 -AACATAAACGAACAAACATAAACG
* **
182432 AACATAAATGAATGAACATAAACG
1 AACATAAACGAACAAACATAAACG
182456 AACATA
1 AACATA
182462 TTATCGAACG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
24 27 0.55
25 21 0.43
26 1 0.02
ACGTcount: A:0.63, C:0.16, G:0.09, T:0.11
Consensus pattern (24 bp):
AACATAAACGAACAAACATAAACG
Found at i:184503 original size:2 final size:2
Alignment explanation
Indices: 184493--184521 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
184483 AACTTAAAAT
184493 TA TA T- 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
184522 ATAAACCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:187061 original size:2 final size:2
Alignment explanation
Indices: 187056--187102 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
187046 ATTGAAGTTA
187056 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
187098 AT AT A
1 AT AT A
187103 CATGTAATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:187196 original size:15 final size:15
Alignment explanation
Indices: 187174--187221 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
187164 CTTTTAATAG
187174 AAATAAATTTAGAAT
1 AAATAAATTTAGAAT
187189 -AATAAAATTCT-GAAT
1 AAAT-AAATT-TAGAAT
*
187204 AAATAAATTCAGAAT
1 AAATAAATTTAGAAT
187219 AAA
1 AAA
187222 AACCCTAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
14 3 0.11
15 21 0.75
16 4 0.14
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.29
Consensus pattern (15 bp):
AAATAAATTTAGAAT
Found at i:187240 original size:14 final size:14
Alignment explanation
Indices: 187221--187249 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
187211 TTCAGAATAA
187221 AAACCCTAAGGTTT
1 AAACCCTAAGGTTT
187235 AAACCCTAAGGTTT
1 AAACCCTAAGGTTT
187249 A
1 A
187250 TGGTAACTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (14 bp):
AAACCCTAAGGTTT
Found at i:197391 original size:16 final size:17
Alignment explanation
Indices: 197360--197392 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
197350 GATAATTTTG
197360 TATTCAATGACTATATTA
1 TATTCAAT-ACTATATTA
197378 TATTCAAT-CTATATT
1 TATTCAATACTATATT
197393 TTAGTGACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (17 bp):
TATTCAATACTATATTA
Found at i:202460 original size:24 final size:24
Alignment explanation
Indices: 202433--202526 Score: 102
Period size: 24 Copynumber: 4.0 Consensus size: 24
202423 TTCGATTTGA
* *
202433 ATTCTGTTATGATATC-TGACCTAG
1 ATTCTGATATGATA-CATGACCTGG
* * *
202457 ATTCTGATCTGGTAC-TGACATGG
1 ATTCTGATATGATACATGACCTGG
202480 ATTCTGATATGATACATGACCTGG
1 ATTCTGATATGATACATGACCTGG
* *
202504 ATTATGATATGATACTTGACCTG
1 ATTCTGATATGATACATGACCTG
202527 AATTATGTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 20 0.34
24 39 0.66
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACATGACCTGG
Found at i:202546 original size:24 final size:24
Alignment explanation
Indices: 202484--202533 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
202474 ACATGGATTC
* *
202484 TGATATGATACATGACCTGGATTA
1 TGATATGATACTTGACCTGAATTA
202508 TGATATGATACTTGACCTGAATTA
1 TGATATGATACTTGACCTGAATTA
202532 TG
1 TG
202534 TTTTGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (24 bp):
TGATATGATACTTGACCTGAATTA
Found at i:204519 original size:2 final size:2
Alignment explanation
Indices: 204514--204575 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
204504 CAAAAAAATT
204514 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
204556 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
204576 ACTCACACTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:206475 original size:16 final size:16
Alignment explanation
Indices: 206454--206484 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
206444 TGAACCATTG
206454 CTTGAAGGACCTATTT
1 CTTGAAGGACCTATTT
206470 CTTGAAGGACCTATT
1 CTTGAAGGACCTATT
206485 GAGGTTGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (16 bp):
CTTGAAGGACCTATTT
Found at i:207132 original size:18 final size:18
Alignment explanation
Indices: 207109--207169 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
207099 CTACAATCGA
207109 TTCATCCTCCTTTGGTCG
1 TTCATCCTCCTTTGGTCG
* ***
207127 TTCATCCTTCTTCAATCG
1 TTCATCCTCCTTTGGTCG
207145 TTCA-CCTCCTTTGGTCG
1 TTCATCCTCCTTTGGTCG
207162 ATTCATCC
1 -TTCATCC
207170 ACCGTAGAGA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
17 9 0.27
18 22 0.67
19 2 0.06
ACGTcount: A:0.11, C:0.34, G:0.11, T:0.43
Consensus pattern (18 bp):
TTCATCCTCCTTTGGTCG
Found at i:207154 original size:35 final size:38
Alignment explanation
Indices: 207097--207169 Score: 116
Period size: 35 Copynumber: 2.0 Consensus size: 38
207087 TCCTCCTACG
207097 TTCTACAATCGATTCATCCTCCTTTGGTCG-TTCATCC
1 TTCTACAATCGATTCATCCTCCTTTGGTCGATTCATCC
*
207134 TTCTTCAATCG-TTCA-CCTCCTTTGGTCGATTCATCC
1 TTCTACAATCGATTCATCCTCCTTTGGTCGATTCATCC
207170 ACCGTAGAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 13 0.38
36 11 0.32
37 10 0.29
ACGTcount: A:0.15, C:0.33, G:0.11, T:0.41
Consensus pattern (38 bp):
TTCTACAATCGATTCATCCTCCTTTGGTCGATTCATCC
Found at i:209206 original size:15 final size:15
Alignment explanation
Indices: 209174--209228 Score: 83
Period size: 15 Copynumber: 3.5 Consensus size: 15
209164 AGAGCCTTTT
209174 AATCATTCAGACTGCTA
1 AATCATTCAG--TGCTA
209191 AATCATTCAGTGCTA
1 AATCATTCAGTGCTA
209206 AATCATTCAGTGCTA
1 AATCATTCAGTGCTA
*
209221 AACCATTC
1 AATCATTC
209229 TGTTTTAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
15 27 0.73
17 10 0.27
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.31
Consensus pattern (15 bp):
AATCATTCAGTGCTA
Found at i:212242 original size:22 final size:22
Alignment explanation
Indices: 212216--212258 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
212206 GAGATGTTAT
212216 AGTTTTAATGCAAGAGTTACAG
1 AGTTTTAATGCAAGAGTTACAG
* *
212238 AGTTTTATTGCATGAGTTACA
1 AGTTTTAATGCAAGAGTTACA
212259 AACTGATGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (22 bp):
AGTTTTAATGCAAGAGTTACAG
Found at i:218061 original size:22 final size:21
Alignment explanation
Indices: 218025--218096 Score: 83
Period size: 22 Copynumber: 3.4 Consensus size: 21
218015 TTATTGAGTT
218025 GTTAC-AAGTTTAATGCAAGA
1 GTTACAAAGTTTAATGCAAGA
218045 GTTACAAAGCTTTAATGCAAGA
1 GTTACAAAG-TTTAATGCAAGA
* * * *
218067 GTTACAGAGTTGTATTGTATGA
1 GTTACAAAGTT-TAATGCAAGA
218089 GTTACAAA
1 GTTACAAA
218097 CTATTGGATT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
20 5 0.11
21 5 0.11
22 34 0.77
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.32
Consensus pattern (21 bp):
GTTACAAAGTTTAATGCAAGA
Found at i:218732 original size:39 final size:39
Alignment explanation
Indices: 218673--218751 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
218663 CGTTAACGCA
*
218673 AAGTTTGATTTAAGTCCCTAAATCGTCCAGCCATGAATT
1 AAGTTTGATTAAAGTCCCTAAATCGTCCAGCCATGAATT
* *
218712 AAGTTTGGTTAAAGTTCCTAAATCGTCCAGCCATGAATT
1 AAGTTTGATTAAAGTCCCTAAATCGTCCAGCCATGAATT
218751 A
1 A
218752 TTTCCAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (39 bp):
AAGTTTGATTAAAGTCCCTAAATCGTCCAGCCATGAATT
Found at i:222706 original size:31 final size:31
Alignment explanation
Indices: 222668--222740 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
222658 TATTACAGCA
* *
222668 ATAATTGCTAATTATATTTAAAGACCAAGTT
1 ATAATTGCTAATTACATTTAAACACCAAGTT
*
222699 ATAATTGCTAATTACATTTAAACACTAAGTT
1 ATAATTGCTAATTACATTTAAACACCAAGTT
222730 ATAATTAGCTA
1 ATAATT-GCTA
222741 TAATTGCTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
31 34 0.89
32 4 0.11
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.38
Consensus pattern (31 bp):
ATAATTGCTAATTACATTTAAACACCAAGTT
Found at i:225339 original size:59 final size:59
Alignment explanation
Indices: 225232--225348 Score: 139
Period size: 59 Copynumber: 2.0 Consensus size: 59
225222 GCCAAGTGAC
* * * *
225232 TATTTTATAACTTTTAATAGTCAGAGGCTAAGCAAAGTAGTTTTCTATAGTTGAGAGAT
1 TATTTTATAACTTTCAATAGTCAGAGGCTAAGCAAAATAGTTTCCTATAGTCGAGAGAT
* * *
225291 TATTTTGTAACTTTCAATAGTTAGTGGACTTAA-CAAAATAG-TTCCTATAGTCGAGAGA
1 TATTTTATAACTTTCAATAGTCAGAGG-C-TAAGCAAAATAGTTTCCTATAGTCGAGAGA
225349 CCATTTGTGC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
59 38 0.78
60 8 0.16
61 3 0.06
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (59 bp):
TATTTTATAACTTTCAATAGTCAGAGGCTAAGCAAAATAGTTTCCTATAGTCGAGAGAT
Done.