Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_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: 11700749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 50
Found at i:2176 original size:13 final size:13
Alignment explanation
Indices: 2154--2183 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2144 ACTAAACACC
2154 TTTC-ACATACCT
1 TTTCAACATACCT
2166 TTTCAACATACCT
1 TTTCAACATACCT
2179 TTTCA
1 TTTCA
2184 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:7854 original size:15 final size:15
Alignment explanation
Indices: 7807--7856 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
7797 TTTCATATGT
7807 TATACTATAGTTATTA
1 TATA-TATAGTTATTA
*
7823 TCATATATATATATATTA
1 T-ATATATA-GT-TATTA
7841 TATATATAGTTATTA
1 TATATATAGTTATTA
7856 T
1 T
7857 GATAATAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 6 0.21
16 6 0.21
17 11 0.38
18 6 0.21
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (15 bp):
TATATATAGTTATTA
Found at i:9483 original size:18 final size:18
Alignment explanation
Indices: 9460--9530 Score: 74
Period size: 18 Copynumber: 4.0 Consensus size: 18
9450 AAAATTAGAG
*
9460 TACAAAAAGAAAAGAAAA
1 TACAAAAAAAAAAGAAAA
* *
9478 TACAAAAAGAAGA-AAAA
1 TACAAAAAAAAAAGAAAA
*
9495 TTCAAAAAAAAAAGAAAA
1 TACAAAAAAAAAAGAAAA
*
9513 GA-AAAAAAAAGAAGAAAA
1 TACAAAAAAAA-AAGAAAA
9531 AGTCAAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
17 22 0.49
18 23 0.51
ACGTcount: A:0.79, C:0.04, G:0.11, T:0.06
Consensus pattern (18 bp):
TACAAAAAAAAAAGAAAA
Found at i:9522 original size:37 final size:40
Alignment explanation
Indices: 9463--9539 Score: 124
Period size: 37 Copynumber: 2.0 Consensus size: 40
9453 ATTAGAGTAC
*
9463 AAAAAGAAAAGAAAATACAAAAAGAAGAAAAATTCAAAAA
1 AAAAAGAAAAGAAAATACAAAAAGAAGAAAAAGTCAAAAA
9503 AAAAAGAAAAG-AAA-A-AAAAAGAAGAAAAAGTCAAAAA
1 AAAAAGAAAAGAAAATACAAAAAGAAGAAAAAGTCAAAAA
9540 TAGAAAGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
37 21 0.58
38 1 0.03
39 3 0.08
40 11 0.31
ACGTcount: A:0.79, C:0.04, G:0.12, T:0.05
Consensus pattern (40 bp):
AAAAAGAAAAGAAAATACAAAAAGAAGAAAAAGTCAAAAA
Found at i:9531 original size:19 final size:19
Alignment explanation
Indices: 9481--9532 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 19
9471 AAGAAAATAC
**
9481 AAAAAGAAGAAAAATTCAAA
1 AAAAAGAAGAAAAA-GAAAA
9501 AAAAA-AAG-AAAAGAAAA
1 AAAAAGAAGAAAAAGAAAA
9518 AAAAAGAAGAAAAAG
1 AAAAAGAAGAAAAAG
9533 TCAAAAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 8 0.29
18 7 0.25
19 8 0.29
20 5 0.18
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.04
Consensus pattern (19 bp):
AAAAAGAAGAAAAAGAAAA
Found at i:9538 original size:19 final size:19
Alignment explanation
Indices: 9481--9544 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
9471 AAGAAAATAC
*
9481 AAAAAGAAGAAAAATTCAA
1 AAAAAGAAGAAAAAGTCAA
* **
9500 AAAAAAAAG-AAAAGAAAA
1 AAAAAGAAGAAAAAGTCAA
9518 AAAAAGAAGAAAAAGTCAA
1 AAAAAGAAGAAAAAGTCAA
*
9537 AAATAGAA
1 AAAAAGAA
9545 AGCAAGCCAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
18 14 0.39
19 22 0.61
ACGTcount: A:0.78, C:0.03, G:0.12, T:0.06
Consensus pattern (19 bp):
AAAAAGAAGAAAAAGTCAA
Found at i:12444 original size:2 final size:2
Alignment explanation
Indices: 12437--12466 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12427 AGTTATTATC
12437 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12467 GTTATTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13834 original size:16 final size:16
Alignment explanation
Indices: 13798--13845 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
13788 CTTTTCTATC
13798 TTTATTT-CATTTCTT
1 TTTATTTCCATTTCTT
*
13813 TCTATTTCCATTAT-TT
1 TTTATTTCCATT-TCTT
13829 TTTATTATCCATTTCTT
1 TTTATT-TCCATTTCTT
13846 AAGTCCACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 6 0.22
16 12 0.44
17 9 0.33
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATTTCCATTTCTT
Found at i:14126 original size:34 final size:33
Alignment explanation
Indices: 14084--14151 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 33
14074 AGTACATAAG
* * *
14084 AAAAGAAAATACAAAAAGAAGAAAAATTCAGAAA
1 AAAAGAAAAGAAAAAAAGAAGAAAAAGTCA-AAA
14118 AAAAGAAAAGAAAAAAAGAAGAAAAAGTCAAAA
1 AAAAGAAAAGAAAAAAAGAAGAAAAAGTCAAAA
14151 A
1 A
14152 TAGAAAGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
33 4 0.13
34 27 0.87
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.06
Consensus pattern (33 bp):
AAAAGAAAAGAAAAAAAGAAGAAAAAGTCAAAA
Found at i:14129 original size:13 final size:13
Alignment explanation
Indices: 14113--14137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14103 AGAAAAATTC
14113 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
14126 AGAAAAAAAGAA
1 AGAAAAAAAGAA
14138 GAAAAAGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:22031 original size:24 final size:24
Alignment explanation
Indices: 21976--22024 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
21966 AGTGCAAAAG
* *
21976 AAAGAAAAGAAAAAGAAGAATCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
*
22000 AAAGCAAAGAAAAAG-TGAAGCAA
1 AAAGCAAAGAAAAAGAAGAAGCAA
22023 AA
1 AA
22025 TTGCAAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.71, C:0.06, G:0.18, T:0.04
Consensus pattern (24 bp):
AAAGCAAAGAAAAAGAAGAAGCAA
Found at i:22214 original size:24 final size:25
Alignment explanation
Indices: 22170--22219 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
22160 TTTCTATTTC
*
22170 ATTTCATTTTCTTTCATCTTTTCTT
1 ATTTCATTTACTTTCATCTTTTCTT
22195 ATTTCA-TTACTTT-ATCCTTTTCTT
1 ATTTCATTTACTTTCAT-CTTTTCTT
22219 A
1 A
22220 ACATTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 2 0.09
24 15 0.65
25 6 0.26
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (25 bp):
ATTTCATTTACTTTCATCTTTTCTT
Found at i:30195 original size:17 final size:18
Alignment explanation
Indices: 30173--30210 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
30163 ACCTATAGTT
30173 CACATC-TATATAATATG
1 CACATCATATATAATATG
*
30190 CACATCATTATATTATATG
1 CACATCA-TATATAATATG
30209 CA
1 CA
30211 TTATATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.37
Consensus pattern (18 bp):
CACATCATATATAATATG
Found at i:31050 original size:21 final size:19
Alignment explanation
Indices: 31010--31061 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
31000 CGGCCAAGAA
*
31010 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
31029 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCA-TT-AAAAT
*
31050 CATATATTTTCA
1 CATGTATTTTCA
31062 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 16 0.55
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:31766 original size:29 final size:27
Alignment explanation
Indices: 31727--31797 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 27
31717 TTGGAGTGCA
31727 AAAAG-AAAGAAAAAGACAAAAGAAG-AG
1 AAAAGAAAAGAAAAAGA-AAAA-AAGAAG
31754 AAAA-AAATCAG-AAAAGAAAAAAAGAAG
1 AAAAGAAA--AGAAAAAGAAAAAAAGAAG
31781 AAAAGAAAAGAAAAAGA
1 AAAAGAAAAGAAAAAGA
31798 GAAAGCAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
26 5 0.13
27 22 0.58
28 9 0.24
29 2 0.05
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.01
Consensus pattern (27 bp):
AAAAGAAAAGAAAAAGAAAAAAAGAAG
Found at i:31771 original size:5 final size:5
Alignment explanation
Indices: 31744--31794 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
31734 AGAAAAAGAC
* *
31744 AAAAG AAGAG AAAA- AAATCAG AAAAG AAAAA AAGAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAA--AG AAAAG AAAAG AA-AAG AAAAG AAAAG
31791 AAAA
1 AAAA
31795 AGAGAAAGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 3 0.08
5 27 0.71
6 5 0.13
7 3 0.08
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:31782 original size:16 final size:15
Alignment explanation
Indices: 31726--31802 Score: 66
Period size: 16 Copynumber: 4.7 Consensus size: 15
31716 ATTGGAGTGC
31726 AAAAAG-AAAGAAAAA
1 AAAAAGAAAAG-AAAA
*
31741 GACAAAAGAAGAGAAAA
1 -A-AAAAGAAAAGAAAA
*
31758 AAATCAGAAAAGAAAA
1 AAA-AAGAAAAGAAAA
31774 AAAGAAGAAAAGAAAA
1 AAA-AAGAAAAGAAAA
31790 GAAAAAGAGAAAG
1 -AAAAAGA-AAAG
31803 CAAGCCAAGG
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
15 2 0.04
16 30 0.59
17 16 0.31
18 3 0.06
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.01
Consensus pattern (15 bp):
AAAAAGAAAAGAAAA
Found at i:34327 original size:17 final size:18
Alignment explanation
Indices: 34305--34342 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
34295 ACCTATAGTT
34305 CACATC-TATATAATATG
1 CACATCATATATAATATG
*
34322 CACATCATTATATTATATG
1 CACATCA-TATATAATATG
34341 CA
1 CA
34343 TTATATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.37
Consensus pattern (18 bp):
CACATCATATATAATATG
Found at i:35173 original size:19 final size:21
Alignment explanation
Indices: 35149--35200 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
35139 CGGCCAAGAG
*
35149 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
35168 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
35189 CATGTATTTTCA
1 CATGTATTTTCA
35201 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:46410 original size:23 final size:23
Alignment explanation
Indices: 46360--46429 Score: 86
Period size: 24 Copynumber: 3.0 Consensus size: 23
46350 ACACATGCCT
* *
46360 TACATCAAGTGGCATCAGAAGCCT
1 TACATCAAGTGGTATCAG-AGCCA
*
46384 TACATCAAGTGGTATAAGAGCCA
1 TACATCAAGTGGTATCAGAGCCA
*
46407 TACATCAAGCGGTAATCAGAGCC
1 TACATCAAGTGGT-ATCAGAGCC
46430 TTGGTAGAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 16 0.40
24 24 0.60
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (23 bp):
TACATCAAGTGGTATCAGAGCCA
Found at i:47869 original size:24 final size:25
Alignment explanation
Indices: 47823--47877 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
47813 ACAGTTATGC
*
47823 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
47847 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
47872 CA-TTGA
1 CACTTGA
47878 GGCTCTAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:54024 original size:19 final size:21
Alignment explanation
Indices: 54000--54051 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
53990 CGGCCAAGAG
*
54000 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
54019 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
54040 CATGTATTTTCA
1 CATGTATTTTCA
54052 AAGGGTTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:54800 original size:8 final size:8
Alignment explanation
Indices: 54789--54823 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
54779 GAGAAAAATT
54789 AGAAAAGA
1 AGAAAAGA
54797 AGAAAAGA
1 AGAAAAGA
54805 AGAAAAGAAA
1 AGAAAAG--A
54815 AGAAAAGA
1 AGAAAAGA
54823 A
1 A
54824 AAAGAGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 17 0.68
10 8 0.32
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:54812 original size:13 final size:13
Alignment explanation
Indices: 54789--54832 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
54779 GAGAAAAATT
54789 AGAAAAGAAGAAA
1 AGAAAAGAAGAAA
54802 AGAAGAA-AAGAAA
1 AGAA-AAGAAGAAA
54815 AGAAAAGAA-AAA
1 AGAAAAGAAGAAA
54827 GAGAAA
1 -AGAAA
54833 GCAAGCCAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 5 0.18
13 21 0.75
14 2 0.07
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAGAAA
Found at i:58234 original size:12 final size:12
Alignment explanation
Indices: 58207--58241 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
58197 TGGACTAAAG
58207 GTAGCTGGGA-A
1 GTAGCTGGGAGA
58218 GTAGCTGGGAGA
1 GTAGCTGGGAGA
58230 GTAGCTGAGGAG
1 GTAGCTG-GGAG
58242 CTGAGGAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 10 0.45
12 8 0.36
13 4 0.18
ACGTcount: A:0.26, C:0.09, G:0.49, T:0.17
Consensus pattern (12 bp):
GTAGCTGGGAGA
Found at i:61371 original size:14 final size:14
Alignment explanation
Indices: 61349--61381 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
61339 TCAAAAAAAG
61349 AAAAA-AAAAGAAA
1 AAAAAGAAAAGAAA
61362 AAAAAGAAAAGAAA
1 AAAAAGAAAAGAAA
*
61376 GAAAAG
1 AAAAAG
61382 TTGAAGCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAGAAA
Found at i:61372 original size:5 final size:5
Alignment explanation
Indices: 61344--61381 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
61334 AGCACTCAAA
*
61344 AAAAG AAAAA AAAAG AAAA- AAAAG AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
61382 TTGAAGCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:61381 original size:9 final size:9
Alignment explanation
Indices: 61341--61380 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
61331 GTAAGCACTC
61341 AAAAAAAGAA
1 AAAAAAAG-A
61351 AAAAAAAGA
1 AAAAAAAGA
61360 AAAAAAAGA
1 AAAAAAAGA
*
61369 AAAGAAAGA
1 AAAAAAAGA
61378 AAA
1 AAA
61381 GTTGAAGCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:83995 original size:11 final size:13
Alignment explanation
Indices: 83963--83992 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
83953 TGGCCAAAGA
83963 TGAAAAGGTATGT
1 TGAAAAGGTATGT
83976 TGAAAAGGTATG-
1 TGAAAAGGTATGT
83988 TGAAA
1 TGAAA
83993 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:97290 original size:15 final size:15
Alignment explanation
Indices: 97270--97344 Score: 132
Period size: 15 Copynumber: 5.0 Consensus size: 15
97260 TAATAAGGTT
97270 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
97285 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
97300 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
97315 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
97330 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
97345 TGAATTGATT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:97389 original size:32 final size:31
Alignment explanation
Indices: 97285--97799 Score: 194
Period size: 32 Copynumber: 17.4 Consensus size: 31
97275 TTTTAAAATA
* * *
97285 ATTTATTTTAAAATAATTTATTATA--AAATA
1 ATTTATTTT-AAATAATTTATTATATGGATTG
*
97315 ATTTATTTTAAAATAATTTATTATAAAATATGAATTG
1 ATTTATTTT-AAATAATTTA-T-T---ATATGGATTG
97352 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
97384 ATTTA-TTT---TAA---A--ATATGGATTG
1 ATTTATTTTAAATAATTTATTATATGGATTG
*
97406 ATTTATTTTATATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
97438 ATTTA-TTT---TAA---A--ATATGGATTG
1 ATTTATTTTAAATAATTTATTATATGGATTG
*
97460 ATTTATTTTAAATAATTTATTAGTATGGGTTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
* *
97492 ATTTATTTTAAAATATGGATTGATT-TAT-TATTG
1 ATTTATTTT-AAATA---ATTTATTATATGGATTG
* * * ** * * * *
97525 TAGTTGTATGGATTAATTTATTTTAAAT-AATTT
1 -ATTTATTTTAAATAATTTA--TTATATGGATTG
* ** * ** *
97558 ATTAGTATGGATTGATTTATTTTAAAATATGAATTG
1 ATT--TAT---TTTAAATAATTTATTATATGGATTG
97594 ATTTA-TTT---TAA---A--ATATGGATTG
1 ATTTATTTTAAATAATTTATTATATGGATTG
* *
97616 ATTTATTTTAAATAATTTATTATTATAGATTA
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
97648 ATTTATTTT--A-AA---A-TATA--GATTG
1 ATTTATTTTAAATAATTTATTATATGGATTG
97670 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
97702 ATTTA-TTT--A-AA---A--ATATGGATTG
1 ATTTATTTTAAATAATTTATTATATGGATTG
*
97724 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
*
97756 ATTTATTTTAAATATTTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
97788 ATTTATTTTAAA
1 ATTTATTTTAAA
97800 ATATGGATTG
Statistics
Matches: 377, Mismatches: 36, Indels: 142
0.68 0.06 0.26
Matches are distributed among these distances:
22 69 0.18
23 15 0.04
24 4 0.01
25 8 0.02
26 12 0.03
27 2 0.01
28 9 0.02
29 9 0.02
30 29 0.08
31 15 0.04
32 125 0.33
33 16 0.04
34 13 0.03
35 7 0.02
36 23 0.06
37 21 0.06
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (31 bp):
ATTTATTTTAAATAATTTATTATATGGATTG
Found at i:97396 original size:54 final size:54
Alignment explanation
Indices: 97330--97911 Score: 632
Period size: 54 Copynumber: 10.8 Consensus size: 54
97320 TTTTAAAATA
* *
97330 ATTTATTATAAAATATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
*
97384 ATTTATTTTAAAATATGGATTGATTTATTTTATATAATTTATTAGTATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
*
97438 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGGTTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
* *
97492 ATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTG
** ** * ** * * * *
97540 ATTTATTTT-AAATAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGAATTG
1 ATTTATTTTAAAAT-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTG
* * *
97594 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTATTATAGATTA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
*
97648 ATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
* *
97702 ATTTATTTAAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
** ** * ** * * *
97756 ATTTATTTT-AAATATTTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTG
1 ATTTATTTTAAAATA-TGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTG
*** * *
97810 ATTTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATGTATTG
1 ATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
97868 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
97912 TCATAGTTGT
Statistics
Matches: 436, Mismatches: 69, Indels: 46
0.79 0.13 0.08
Matches are distributed among these distances:
47 4 0.01
48 25 0.06
49 3 0.01
50 5 0.01
51 1 0.00
52 5 0.01
53 16 0.04
54 315 0.72
55 20 0.05
56 10 0.02
57 12 0.03
58 18 0.04
59 2 0.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:97400 original size:22 final size:22
Alignment explanation
Indices: 97375--97471 Score: 86
Period size: 22 Copynumber: 4.0 Consensus size: 22
97365 AATTTATTAG
97375 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
97397 TATGGATTGATTTATTTTATATAA
1 TATGGATTGATTTATTTTA-A-AA
* *
97421 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-T-GGATTGA-T---TTATTTTAAAA
97451 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
97472 TAATTTATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
22 29 0.48
23 1 0.02
24 2 0.03
25 1 0.02
26 7 0.11
27 2 0.03
28 7 0.11
29 1 0.02
30 2 0.03
31 1 0.02
32 8 0.13
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:97549 original size:80 final size:77
Alignment explanation
Indices: 97429--97678 Score: 369
Period size: 76 Copynumber: 3.2 Consensus size: 77
97419 AATTTATTAG
*
97429 TATGGATTGATTTA-TTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGGTTGA
1 TATGGATTGATTTATTTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
97493 TTTATTTTAAAA
66 TTTATTTTAAAA
*** *
97505 TATGGATTGATTTATTATTGTAGTTGTATGGATTAATTTATTTTAAATAATTTATTAGTATGGAT
1 TATGGATTGATTTATT-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGAT
97570 TGATTTATTTTAAAA
63 TGATTTATTTTAAAA
* * * *
97585 TATGAATTGATTTA-TTTTAAAATATGGATTGATTTATTTTAAATAATTTATTATTATAGATTAA
1 TATGGATTGATTTATTTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
97649 TTTATTTTAAAA
66 TTTATTTTAAAA
*
97661 TATAGATTGATTTATTTT
1 TATGGATTGATTTATTTT
97679 AAATAATTTA
Statistics
Matches: 154, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
76 76 0.49
77 6 0.04
78 4 0.03
79 3 0.02
80 65 0.42
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (77 bp):
TATGGATTGATTTATTTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
TTTATTTTAAAA
Found at i:97579 original size:22 final size:22
Alignment explanation
Indices: 97563--97627 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
97553 AATTTATTAG
97563 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
97585 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
97607 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
97628 TAATTTATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:97655 original size:22 final size:22
Alignment explanation
Indices: 97639--97681 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
97629 AATTTATTAT
97639 TATAGATTAATTTATTTTAAAA
1 TATAGATTAATTTATTTTAAAA
*
97661 TATAGATTGATTTATTTTAAA
1 TATAGATTAATTTATTTTAAA
97682 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
TATAGATTAATTTATTTTAAAA
Found at i:97875 original size:22 final size:22
Alignment explanation
Indices: 97859--97901 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
97849 AATTTATTAG
*
97859 TATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
97881 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
97902 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:97961 original size:31 final size:31
Alignment explanation
Indices: 97926--97984 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
97916 AGTTGTATGG
* *
97926 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
97957 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
97985 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:100636 original size:417 final size:418
Alignment explanation
Indices: 99982--100824 Score: 1424
Period size: 417 Copynumber: 2.0 Consensus size: 418
99972 CCTTATCTTG
*
99982 CAAAATTATTTCCCAAATTATTTATTAATAAAAATCCCGCATCGTTTTCTTGTGACATTTGTTGT
1 CAAAATTATTTCCCAAATTATTTATTAATAAAAATCCCGCATCGTTTTCTTGTGACATTTGTTCT
*
100047 CTTGCAAAACGCATTCAGAGCTCTTATCCTCTTTCTCCCTCCCGCTCAGCTACCTTTTTCCTTAA
66 CTTGCAAAACACATTCAGAGCTCTTATCCTC--TCTCCCTCCCGCTCAGCTACCTTTTTCCTTAA
* *
100112 TTCATAGTGATATTTGGGGACCTTCACGGGTTACGGGTTTACATGAAATTCGTTGGTTTATTACT
129 TTCATAGTGACATTTGGGGACCTTCACGGGTTACAGGTTTACATGAAATTCGTTGGTTTATTACT
*
100177 TTAATTGATGACCACTCTCGTACCACTTGGACCTTTCTTATGAAGGAAAAATCTAAGTCTTGCAT
194 TTAATTGATGACCACTCTCGTACCACTTGGACCTTTCTTATGAAGGAAAAATCTAAGTCGTGCAT
100242 CATCTTCAAACAATTCCACAAAATGGTTGAATCACAATTCCAAAGTTCCATTGGCATCCTGAAAT
259 CATCTTCAAACAATTCCACAAAATGGTTGAATCACAATTCCAAAGTTCCATTGGCATCCTGAAAT
*
100307 ATGATAATGTGGGGAAATACCTCTCTCAGTCGTTAGGATATTTCTTCCAGG-AAA-AGAATAGTT
324 ATGATAATGTGGGGAAATACCTCTCTCAGTCGTTAGGATATTTCTTCCAGGAAAACAGAATAGTC
100370 CATCTCAC-TTCTTGTGTCGACACTCCACAA
389 CATCTCACTTTC-TGTGTCGACACTCCACAA
100400 CAAAATTATTTCCCAAATTATTTATTAATAAAAATCCCGCATCGTTTTCTTGTGACATTTGTTCT
1 CAAAATTATTTCCCAAATTATTTATTAATAAAAATCCCGCATCGTTTTCTTGTGACATTTGTTCT
* *
100465 CTTGCAAAACACATTCAGAGCTCTTATCCTC-CTCTCTCCCGCTCAGCTAAACCTTTTTTCTTAA
66 CTTGCAAAACACATTCAGAGCTCTTATCCTCTCTCCCTCCCGCTCAGCT--ACCTTTTTCCTTAA
*
100529 TTCATAGTGACATTTGGGGACCTTCACGGGTTACAGGTTTACATGGAATTCGTTGGTTTATTACT
129 TTCATAGTGACATTTGGGGACCTTCACGGGTTACAGGTTTACATGAAATTCGTTGGTTTATTACT
* * * * *
100594 TTTATTGATGACCACTCTCGTACCACTTGGACTTTTCTTATGAAGGACAAATCTGAGTCGTGTAT
194 TTAATTGATGACCACTCTCGTACCACTTGGACCTTTCTTATGAAGGAAAAATCTAAGTCGTGCAT
*
100659 CATCTTCAAACAATTCCACTAAATGGTTGAATCACAATTCCAAAGTTCCATTGGCATCCTGAAAT
259 CATCTTCAAACAATTCCACAAAATGGTTGAATCACAATTCCAAAGTTCCATTGGCATCCTGAAAT
* * *
100724 CTGATAATGTGGGGGAATACCTCTCTCAGTCGTTAGGATCTTTCTTCCAGGAAAACAGAATAGTC
324 ATGATAATGTGGGGAAATACCTCTCTCAGTCGTTAGGATATTTCTTCCAGGAAAACAGAATAGTC
* * *
100789 CATCTCACTTTCTGTGTTGACACTCTATAA
389 CATCTCACTTTCTGTGTCGACACTCCACAA
100819 CAAAAT
1 CAAAAT
100825 GGGGTCACCG
Statistics
Matches: 399, Mismatches: 21, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
415 16 0.04
417 246 0.62
418 97 0.24
419 37 0.09
420 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (418 bp):
CAAAATTATTTCCCAAATTATTTATTAATAAAAATCCCGCATCGTTTTCTTGTGACATTTGTTCT
CTTGCAAAACACATTCAGAGCTCTTATCCTCTCTCCCTCCCGCTCAGCTACCTTTTTCCTTAATT
CATAGTGACATTTGGGGACCTTCACGGGTTACAGGTTTACATGAAATTCGTTGGTTTATTACTTT
AATTGATGACCACTCTCGTACCACTTGGACCTTTCTTATGAAGGAAAAATCTAAGTCGTGCATCA
TCTTCAAACAATTCCACAAAATGGTTGAATCACAATTCCAAAGTTCCATTGGCATCCTGAAATAT
GATAATGTGGGGAAATACCTCTCTCAGTCGTTAGGATATTTCTTCCAGGAAAACAGAATAGTCCA
TCTCACTTTCTGTGTCGACACTCCACAA
Found at i:105048 original size:17 final size:16
Alignment explanation
Indices: 105026--105087 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 16
105016 AAATTGGAGT
105026 ACAAAAAGAAAGAAAAG
1 ACAAAAAG-AAGAAAAG
105043 ACAAAAAGAAGAAAA-
1 ACAAAAAGAAGAAAAG
105058 ATTCAGAAAAGAAG-AAA-
1 A--CA-AAAAGAAGAAAAG
*
105075 ATAAAAAGAAGAA
1 ACAAAAAGAAGAA
105088 TTTCAAAAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 8 0.20
15 3 0.08
16 7 0.17
17 14 0.35
18 8 0.20
ACGTcount: A:0.74, C:0.05, G:0.16, T:0.05
Consensus pattern (16 bp):
ACAAAAAGAAGAAAAG
Found at i:105095 original size:14 final size:14
Alignment explanation
Indices: 105045--105087 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 14
105035 AAGAAAAGAC
105045 AAAAAGAAGAAAAATT
1 AAAAAGAAG-AAAA-T
105061 CAGAAAAGAAGAAAAT
1 -A-AAAAGAAGAAAAT
105077 AAAAAGAAGAA
1 AAAAAGAAGAA
105088 TTTCAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 10 0.40
15 1 0.04
16 1 0.04
17 5 0.20
18 8 0.32
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.07
Consensus pattern (14 bp):
AAAAAGAAGAAAAT
Found at i:111638 original size:5 final size:5
Alignment explanation
Indices: 111628--111653 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
111618 CAGCCTCTCA
111628 AGCTC AGCTC AGCTC AGCTC AGCTC A
1 AGCTC AGCTC AGCTC AGCTC AGCTC A
111654 ATTCCATTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.38, G:0.19, T:0.19
Consensus pattern (5 bp):
AGCTC
Found at i:111730 original size:2 final size:2
Alignment explanation
Indices: 111723--111758 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
111713 TGCAGATTCC
111723 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
111759 TGTCGAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118438 original size:13 final size:13
Alignment explanation
Indices: 118413--118464 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
118403 AATGACGCGC
*
118413 AATGCGCGACATA
1 AATGCGCGTCATA
*
118426 AATGCACGTCATA
1 AATGCGCGTCATA
* * *
118439 AATACGTGTTATA
1 AATGCGCGTCATA
118452 AATGCGCGTCATA
1 AATGCGCGTCATA
118465 GATTTATGAC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:122620 original size:4 final size:4
Alignment explanation
Indices: 122611--122645 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
122601 CAACTTTTTC
122611 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
122646 AGGGTGTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:123439 original size:29 final size:28
Alignment explanation
Indices: 123407--123487 Score: 67
Period size: 29 Copynumber: 2.8 Consensus size: 28
123397 TTTTATCTCC
123407 AAACTATGACTCATTCTAAATTAGTCCTT
1 AAACTATGACTCATTCTAAATTA-TCCTT
* * *
123436 AAACTTTTGA-ACATTCTAAGTTCATCCTT
1 AAAC-TATGACTCATTCTAAATT-ATCCTT
* *
123465 AAACTGA-CACTCTTTCTAAATTA
1 AAACT-ATGACTCATTCTAAATTA
123488 ATCCCCAAAC
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
28 3 0.08
29 32 0.80
30 5 0.12
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (28 bp):
AAACTATGACTCATTCTAAATTATCCTT
Found at i:123469 original size:58 final size:58
Alignment explanation
Indices: 123358--123501 Score: 130
Period size: 58 Copynumber: 2.5 Consensus size: 58
123348 AACGGTAGCC
* * * * ** * * *
123358 CTCATTTTAAGTTGGTCCTTAAGCTTTTGATTATTCTAATTTTATCTCCAAACT-ATGA
1 CTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCTAAGTTCATCTCCAAACTGA-CA
*
123416 CTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCTAAGTTCATC-CTTAAACTGACA
1 CTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCTAAGTTCATCTC-CAAACTGACA
* * **
123474 CTCTTTCTAAATTAATCCCCAAACTTTT
1 CTCATTCTAAATTAGTCCTTAAACTTTT
123502 TAAAATTCCA
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
57 1 0.01
58 68 0.97
59 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (58 bp):
CTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCTAAGTTCATCTCCAAACTGACA
Found at i:128569 original size:9 final size:9
Alignment explanation
Indices: 128557--128594 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
128547 TAATAAAAAA
128557 TAAAAAATT
1 TAAAAAATT
128566 TAAAAAATT
1 TAAAAAATT
*
128575 T-AATAATT
1 TAAAAAATT
*
128583 TAGAAAATT
1 TAAAAAATT
128592 TAA
1 TAA
128595 GAGACTCTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (9 bp):
TAAAAAATT
Found at i:128582 original size:17 final size:17
Alignment explanation
Indices: 128562--128594 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
128552 AAAAATAAAA
128562 AATTTAAAAAATTTAAT
1 AATTTAAAAAATTTAAT
*
128579 AATTTAGAAAATTTAA
1 AATTTAAAAAATTTAA
128595 GAGACTCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AATTTAAAAAATTTAAT
Found at i:128778 original size:2 final size:2
Alignment explanation
Indices: 128738--128764 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
128728 ATAGTTCAGT
128738 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
128765 TCTATTTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:137429 original size:35 final size:35
Alignment explanation
Indices: 137388--137482 Score: 131
Period size: 35 Copynumber: 2.7 Consensus size: 35
137378 AGAAACTCAA
137388 CATAATTGTATACATAACAAAAACCCTAACAAACT
1 CATAATTGTATACATAACAAAAACCCTAACAAACT
137423 CATAATTGTATGA-ATAA-AATAAACCCTAACAAACT
1 CATAATTGTAT-ACATAACAA-AAACCCTAACAAACT
* *
137458 CATAATTGCATGCATAACAGAAAAC
1 CATAATTGTATACATAACA-AAAAC
137483 TCTAGCAGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
34 2 0.04
35 44 0.83
36 6 0.11
37 1 0.02
ACGTcount: A:0.51, C:0.20, G:0.06, T:0.23
Consensus pattern (35 bp):
CATAATTGTATACATAACAAAAACCCTAACAAACT
Found at i:148127 original size:20 final size:21
Alignment explanation
Indices: 148077--148126 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
148067 GAGGGAACCA
*
148077 ATTCCCCCCCAGGGGGTACCG
1 ATTCCCCCCTAGGGGGTACCG
148098 ATTCCCCCCTAGGGGGTACCG
1 ATTCCCCCCTAGGGGGTACCG
148119 ATTCCCCC
1 ATTCCCCC
148127 TGTTTAACGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.14, C:0.44, G:0.24, T:0.18
Consensus pattern (21 bp):
ATTCCCCCCTAGGGGGTACCG
Found at i:151141 original size:2 final size:2
Alignment explanation
Indices: 151079--151126 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
151069 TTTATATCAA
151079 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
151121 AT AT AT
1 AT AT AT
151127 TAACTCTATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:151944 original size:3 final size:3
Alignment explanation
Indices: 151936--151963 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
151926 ATGGATCTTT
151936 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
151964 GTCATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:153966 original size:25 final size:24
Alignment explanation
Indices: 153926--153989 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 24
153916 CACCGAAGTG
*
153926 CCACATAG-ATTTGTCCCAAAAGA
1 CCACGTAGAATTTGTCCCAAAAGA
* **
153949 CCACGTAGAAATTTGTCCCGATGGA
1 CCACGTAG-AATTTGTCCCAAAAGA
153974 CCACGTAGAATTTGTC
1 CCACGTAGAATTTGTC
153990 ATGAAGGACC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.20
24 8 0.23
25 20 0.57
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (24 bp):
CCACGTAGAATTTGTCCCAAAAGA
Found at i:153998 original size:24 final size:24
Alignment explanation
Indices: 153886--154007 Score: 83
Period size: 24 Copynumber: 5.1 Consensus size: 24
153876 CTGCTCATAT
153886 AATTTG-CACTGAAGTG-CCACGTAG
1 AATTTGTCAC-GAAG-GACCACGTAG
* *
153910 AATATG-CACCGAAGTG-CCACATAG
1 AATTTGTCA-CGAAG-GACCACGTAG
* * *
153934 -ATTTGTCCCAAAAGACCACGTAG
1 AATTTGTCACGAAGGACCACGTAG
* *
153957 AAATTTGTCCCGATGGACCACGTAG
1 -AATTTGTCACGAAGGACCACGTAG
* *
153982 AATTTGTCATGAAGGACCGCGTAG
1 AATTTGTCACGAAGGACCACGTAG
154006 AA
1 AA
154008 CCCTCGACTT
Statistics
Matches: 79, Mismatches: 14, Indels: 10
0.77 0.14 0.10
Matches are distributed among these distances:
22 1 0.01
23 14 0.18
24 43 0.54
25 21 0.27
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (24 bp):
AATTTGTCACGAAGGACCACGTAG
Found at i:154154 original size:14 final size:15
Alignment explanation
Indices: 154135--154173 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
154125 ATCACTTAGC
*
154135 ACATTTTCATATA-G
1 ACATTTTCACATAGG
154149 ACATTTTCACATAGG
1 ACATTTTCACATAGG
*
154164 ATATTTTCAC
1 ACATTTTCAC
154174 TTATAACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (15 bp):
ACATTTTCACATAGG
Found at i:160293 original size:25 final size:24
Alignment explanation
Indices: 160264--160337 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 24
160254 TGCCACATAT
160264 ATTTGTTCCGAATGACCGCGTAGAA
1 ATTTGTTCCGAA-GACCGCGTAGAA
* * *
160289 ATTTGTCCCAAAGGACCACGTAG-A
1 ATTTGTTCCGAA-GACCGCGTAGAA
160313 ATTTG-TCTCGAAGTACCGCGTAGAA
1 ATTTGTTC-CGAAG-ACCGCGTAGAA
160338 CCCTCGACTC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
23 2 0.05
24 17 0.44
25 20 0.51
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (24 bp):
ATTTGTTCCGAAGACCGCGTAGAA
Found at i:160334 original size:24 final size:24
Alignment explanation
Indices: 160277--160337 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
160267 TGTTCCGAAT
160277 GACCGCGTAGAAATTTGTCCCAAAG
1 GACCGCGTAG-AATTTGTCCCAAAG
* * *
160302 GACCACGTAGAATTTGTCTCGAAG
1 GACCGCGTAGAATTTGTCCCAAAG
*
160326 TACCGCGTAGAA
1 GACCGCGTAGAA
160338 CCCTCGACTC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
24 22 0.71
25 9 0.29
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (24 bp):
GACCGCGTAGAATTTGTCCCAAAG
Found at i:164786 original size:20 final size:19
Alignment explanation
Indices: 164761--164799 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
164751 ATCAGTCATG
164761 GGGTATCGATACCAACAGGT
1 GGGTATCGATACCAA-AGGT
164781 GGGTATCGATACCAAAGGT
1 GGGTATCGATACCAAAGGT
164800 TATGTACCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.21
Consensus pattern (19 bp):
GGGTATCGATACCAAAGGT
Found at i:172823 original size:21 final size:19
Alignment explanation
Indices: 172785--172833 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
172775 ATACTTGTAA
* *
172785 TTTTATAATTTTATTTTAT
1 TTTTATATTTTTATTTTAC
172804 TTTTATATTTTTAAATTTTAC
1 TTTTATATTTTT--ATTTTAC
*
172825 TTTTCTATT
1 TTTTATATT
172834 AATAATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 11 0.44
21 14 0.56
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTATATTTTTATTTTAC
Found at i:175556 original size:31 final size:31
Alignment explanation
Indices: 175518--175581 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
175508 AATATATAAT
* *
175518 ATGTGATCATTTTCGTTTTTAGTTCATTAAG
1 ATGTGATCATGTTCGTTATTAGTTCATTAAG
* *
175549 ATGTGATCATGTTCGTTATTATTTTATTAAG
1 ATGTGATCATGTTCGTTATTAGTTCATTAAG
175580 AT
1 AT
175582 ATGGTCACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.52
Consensus pattern (31 bp):
ATGTGATCATGTTCGTTATTAGTTCATTAAG
Found at i:183532 original size:12 final size:12
Alignment explanation
Indices: 183515--183548 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
183505 GATTTTCATA
183515 TGTTCAAGTTCT
1 TGTTCAAGTTCT
183527 TGTTCAAGTTCT
1 TGTTCAAGTTCT
183539 TGTTCAAGTT
1 TGTTCAAGTT
183549 TGAGCTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.50
Consensus pattern (12 bp):
TGTTCAAGTTCT
Found at i:194105 original size:36 final size:35
Alignment explanation
Indices: 194065--194229 Score: 115
Period size: 36 Copynumber: 4.5 Consensus size: 35
194055 TTTATGTATG
*
194065 TATATATTATATAGTTTGCAAATGATTTTAGAAATATA
1 TATATAATATATAGTTTG-AAATGATTTTAG-AA-ATA
*
194103 TATATAATATATAGTTTTTGAAA-GA-TTTCGAAA-A
1 TATATAATATATAG--TTTGAAATGATTTTAGAAATA
* **
194137 CTTATATAATATATAGTTTTTAAAACATTTT-GAAAATA
1 --TATATAATATATAG-TTTGAAATGATTTTAG-AAATA
* *
194175 TATATAATATATAGTTTTTAAAAT-ATTTTGAAAAAATA
1 TATATAATATATAG--TTTGAAATGATTTT--AGAAATA
194213 TATATAATATATAGTTT
1 TATATAATATATAGTTT
194230 TTAAAAACAT
Statistics
Matches: 108, Mismatches: 7, Indels: 26
0.77 0.05 0.18
Matches are distributed among these distances:
34 1 0.01
35 8 0.07
36 40 0.37
37 17 0.16
38 35 0.32
39 3 0.03
40 4 0.04
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (35 bp):
TATATAATATATAGTTTGAAATGATTTTAGAAATA
Found at i:194116 original size:38 final size:35
Alignment explanation
Indices: 194065--194252 Score: 157
Period size: 38 Copynumber: 5.1 Consensus size: 35
194055 TTTATGTATG
*
194065 TATATATTATATAGTTTGCAAATGATTTTAGAAATATA
1 TATATAATATATAGTTTG-AAATGATTTT-GAAA-ATA
*
194103 TATATAATATATAGTTTTTGAAA-GATTTCGAAAACT-
1 TATATAATATATAG--TTTGAAATGATTTTGAAAA-TA
* **
194139 TATATAATATATAGTTTTTAAAACATTTTGAAAATA
1 TATATAATATATAG-TTTGAAATGATTTTGAAAATA
*
194175 TATATAATATATAGTTTTTAAAAT-ATTTTGAAAAAATA
1 TATATAATATATAG--TTTGAAATGATTTTG--AAAATA
* **
194213 TATATAATATATAGTTTTTAAAAACATTTTGAAAATA
1 TATATAATATATAG--TTTGAAATGATTTTGAAAATA
194250 TAT
1 TAT
194253 GTAAAATCTT
Statistics
Matches: 133, Mismatches: 8, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
35 8 0.06
36 44 0.33
37 21 0.16
38 47 0.35
39 9 0.07
40 4 0.03
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (35 bp):
TATATAATATATAGTTTGAAATGATTTTGAAAATA
Found at i:194150 original size:74 final size:74
Alignment explanation
Indices: 194065--194252 Score: 236
Period size: 74 Copynumber: 2.5 Consensus size: 74
194055 TTTATGTATG
* ** *
194065 TATATATTATATAGTTTGCAAATGATTTTAGAAATATATATATAATATATAGTTTTTGAAAGATT
1 TATATAATATATAGTTTGCAAAACATTTT-GAAA-ATATATATAATATATAGTTTTTAAAAGATT
*
194130 TCG-AAAACT-
64 TCGAAAAAATA
** * *
194139 TATATAATATATAGTTTTTAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAATATTTT
1 TATATAATATATAGTTTGCAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAAGATTTC
194204 GAAAAAATA
66 GAAAAAATA
**
194213 TATATAATATATAGTTTTTAAAAACATTTTGAAAATATAT
1 TATATAATATATAG-TTTGCAAAACATTTTGAAAATATAT
194253 GTAAAATCTT
Statistics
Matches: 101, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
72 30 0.30
73 9 0.09
74 38 0.38
75 24 0.24
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (74 bp):
TATATAATATATAGTTTGCAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAAGATTTC
GAAAAAATA
Found at i:195992 original size:40 final size:41
Alignment explanation
Indices: 195940--196039 Score: 166
Period size: 40 Copynumber: 2.5 Consensus size: 41
195930 ATGTTTCCCT
*
195940 TTTTTCTTTTTGCATTAATTCACGCACGCATGC-TTCCCCC
1 TTTTTCTCTTTGCATTAATTCACGCACGCATGCTTTCCCCC
*
195980 TTTTTCTCTTTGCATCAATTCACGCACGCATGCTTTCCCCC
1 TTTTTCTCTTTGCATTAATTCACGCACGCATGCTTTCCCCC
*
196021 TTTTTCTCTTTGAATTAAT
1 TTTTTCTCTTTGCATTAAT
196040 GCTACCAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
40 31 0.56
41 24 0.44
ACGTcount: A:0.16, C:0.30, G:0.09, T:0.45
Consensus pattern (41 bp):
TTTTTCTCTTTGCATTAATTCACGCACGCATGCTTTCCCCC
Found at i:202978 original size:2 final size:2
Alignment explanation
Indices: 202971--202997 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
202961 TCAATCTACA
202971 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
202998 ATTTAGACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:203084 original size:13 final size:13
Alignment explanation
Indices: 203066--203095 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
203056 AACGACACGC
*
203066 AATGTAAGTCGTA
1 AATGTAAGTCATA
203079 AATGTAAGTCATA
1 AATGTAAGTCATA
203092 AATG
1 AATG
203096 CGTGTCATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (13 bp):
AATGTAAGTCATA
Found at i:203185 original size:13 final size:13
Alignment explanation
Indices: 203169--203256 Score: 113
Period size: 13 Copynumber: 6.8 Consensus size: 13
203159 GCGCAATGTA
203169 CGTCATAAATGCG
1 CGTCATAAATGCG
*
203182 CGTCATAAATGCA
1 CGTCATAAATGCG
* *
203195 CGTTATAAATGTG
1 CGTCATAAATGCG
*
203208 CGTCATAAATGCA
1 CGTCATAAATGCG
203221 CGTCATAAATGCG
1 CGTCATAAATGCG
* *
203234 TGTCATAACTGCG
1 CGTCATAAATGCG
*
203247 CATCATAAAT
1 CGTCATAAAT
203257 TTATGACACA
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 62 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (13 bp):
CGTCATAAATGCG
Found at i:203192 original size:26 final size:26
Alignment explanation
Indices: 203163--203256 Score: 125
Period size: 26 Copynumber: 3.6 Consensus size: 26
203153 AATGACGCGC
*
203163 AATGTACGTCATAAATGCGCGTCATA
1 AATGCACGTCATAAATGCGCGTCATA
* *
203189 AATGCACGTTATAAATGTGCGTCATA
1 AATGCACGTCATAAATGCGCGTCATA
*
203215 AATGCACGTCATAAATGCGTGTCATA
1 AATGCACGTCATAAATGCGCGTCATA
* * *
203241 ACTGCGCATCATAAAT
1 AATGCACGTCATAAAT
203257 TTATGACACA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 59 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (26 bp):
AATGCACGTCATAAATGCGCGTCATA
Found at i:203470 original size:17 final size:17
Alignment explanation
Indices: 203448--203500 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
203438 AATTAAGAGT
203448 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
203465 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
203482 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
203499 TA
1 TA
203501 ACTTTATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:204928 original size:85 final size:85
Alignment explanation
Indices: 204720--206200 Score: 1806
Period size: 85 Copynumber: 17.5 Consensus size: 85
204710 CCAATTTGAC
* * *
204720 CTGTCAA-AAA-ACCTTCGAGTTCGATTACACTCACCTCAAAGACATATCCAATTTACAGCATAG
1 CTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAG
*
204783 CTCAAGGCGAGAAGGGTTGT
66 CTCAAGGCGAGAAGGGTTAT
* * * * *
204803 -TGTCAACCAATACCTTCGAGTTCGATTACACTCAACTCAAAGGCACATCCAATTTACAACATAA
1 CTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAG
204867 CTCAAGGCGAGAAGGGTTAT
66 CTCAAGGCGAGAAGGGTTAT
* * * * * * *
204887 CTGTCAACCAAGACCTTCAAGTTCGAGTACACTCAGTTCAAAGGCATATCCAATTTATAACATAA
1 CTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCAT-A
* * *
204952 G-TAAAGGCGAGAAGGGCTGT
65 GCTCAAGGCGAGAAGGGTTAT
* * *
204972 CTGTCAACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGTATA
1 CTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATA
205037 GCTCAAGGCGAGAAGGGTTAT
65 GCTCAAGGCGAGAAGGGTTAT
* * *
205058 CTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGTTGAAAGATGCA-AT--AATTTATAGCA
1 CTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAG--GCACATCCAATTTACAGCA
*
205120 TAACTCAAGGCGAGAAGGGTTAT
63 TAGCTCAAGGCGAGAAGGGTTAT
* * *
205143 CTGTCAACAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACATCAAATTTACAGCATGG
1 CTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAG
205208 CTCAAGGCGAGAA-GGTCTAT
66 CTCAAGGCGAGAAGGGT-TAT
* * * * * *
205228 CTGTCAACAAAAGTCCTTCGAGTTCGAGTATACTCAGCTCAAAGGCACGTCCAATTTAAAGCACA
1 CTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATA
205293 GCTCAAGGCGAGAAGGGTTAT
65 GCTCAAGGCGAGAAGGGTTAT
* * *
205314 CTGTCAAC-ATGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTATAGCATAG
1 CTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAG
*
205378 CTCAAGACGAGAAGGGTTAT
66 CTCAAGGCGAGAAGGGTTAT
* *
205398 CTGTCAACAAAAGACCTTTGA-TTCGATTACACT-AGCTCAAAGGCGCATCCAATTTACAGCATA
1 CTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATA
* * *
205461 ACTCAAGGCGATAAGGTTTAT
65 GCTCAAGGCGAGAAGGGTTAT
* * * *
205482 CTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGATCAAAGGTACATCAAATTTACAGCATAG
1 CTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAG
* *
205547 CTCAAGGCGAGATGGGCTAT
66 CTCAAGGCGAGAAGGGTTAT
* * * * *
205567 CTATCAACAAAAGACCTTTGAGTTTGATTACACTCAGCTTAAAGGCACATCCAATTTACAACATA
1 CTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATA
* *
205632 ACTCAAGGTGAGAAGGGTTAT
65 GCTCAAGGCGAGAAGGGTTAT
* * * * * *
205653 ATGTCAACCAATACCTTCGAGTTTGATTACACTCAGCTCAAAGGTACATCAAATTTACAGCATAG
1 CTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAG
*
205718 CTCAAGGCGAGAAGGGCTAT
66 CTCAAGGCGAGAAGGGTTAT
* * **
205738 CTGTCAATAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAATGTGCATCCAATTTACAGCATA
1 CTGTCAA-CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATA
* * *
205803 ACTCAAGACAAGAA-GGTTAT
65 GCTCAAGGCGAGAAGGGTTAT
* * * * * *
205823 CTATCAACCAAGACCTTCAAGTTTGATTACACTCAGCTCAAAGGCACGTCCAATTTACAACATAG
1 CTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAG
*
205888 TTCAAGGCGAGAA-GGTTAT
66 CTCAAGGCGAGAAGGGTTAT
* * * *
205907 CTGTCAACAAAAGACCTTCGAGTTCGATTAAACTCAACTCAAAGGCGCATCCAATCTACAGCATA
1 CTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATA
* * * **
205972 ACTCAAGGCAATAAATGTTAT
65 GCTCAAGGCGAGAAGGGTTAT
* * * *
205993 CCGTCAATC-AAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGTACATCAAATTTACAGCATA
1 CTGTCAA-CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATA
206057 GCTCAAGGCGAGAAGGG-TAT
65 GCTCAAGGCGAGAAGGGTTAT
* ** *
206077 -TGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATGTCAAATTTACAGCATA
1 CTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATA
*
206141 ACTCAAGGCGAGAAGGGTTAT
65 GCTCAAGGCGAGAAGGGTTAT
* ** * * * *
206162 CTGTTAGTAAAAACTTTCGAGTTCGATTCCATTCAGCTC
1 CTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTC
206201 GATGACACAT
Statistics
Matches: 1198, Mismatches: 173, Indels: 52
0.84 0.12 0.04
Matches are distributed among these distances:
82 10 0.01
83 19 0.02
84 381 0.32
85 448 0.37
86 331 0.28
87 6 0.01
88 3 0.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (85 bp):
CTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAG
CTCAAGGCGAGAAGGGTTAT
Found at i:206213 original size:680 final size:682
Alignment explanation
Indices: 204724--206200 Score: 2040
Period size: 680 Copynumber: 2.2 Consensus size: 682
204714 TTTGACCTGT
* * * *
204724 CAAAAAACCTTCGAGTTCGATTACACTCACCTCAAAGACATATCCAATTTACAGCATAGCTCAAG
1 CAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCCAATTTACAGCATAACTCAAG
* * * *
204789 GCGAGAAGGGTTGT-TGTCAACCAATACCTTCGAGTTCGATTACACTCAACTCAAAGGCACATCC
66 GCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCA
* * *
204853 AATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCAAGTTCGAGTACA
131 AATTTACAACATAACTCAAGGCGAGAAGGGCTATCTATCAACAAAGACCTTCAAGTTCGAGTACA
* * * * *
204918 CTCAGTTCAAAGGCATATCCAATTTATAACATAAGTAAAGGCGAGAAGGGCTGTCTGTCAACAAA
196 CTCAGTTCAAAGGCACATCCAATTTACAACATAACTAAAGGCGAGAAGGGCTATATGTCAACAAA
* *
204983 AGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGTATAGCTCAAGGCGA
261 AGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGCGA
* * *
205048 GAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGTTGAAAGATGCAATAATT
326 GAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGATGCAATAATT
* * * * *
205113 TATAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCA
391 TACAGCATAACTCAAGACAAGAAGGGTTATCTATCAACAAAGACCTTCAAGTTCGATTACACTCA
* * *
205178 ACTCAAAGGCACATCAAATTTACAGCATGGCTCAAGGCGAGAAGGTCTATCTGTCAACAAAAGTC
456 ACTCAAAGGCACATCAAATTTACAACATAGCTCAAGGCGAGAAGGTCTATCTGTCAACAAAAGAC
* * * * * * *
205243 CTTCGAGTTCGAGTATACTCAGCTCAAAGGCACGTCCAATTTAAAGCACAGCTCAAGGCGAGAAG
521 CTTCGAGTTCGAGTAAACTCAACTCAAAGGCACATCCAATCTAAAGCACAACTCAAGGCAAGAAA
* * *
205308 GGTTATCTGTCAACATGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTATAG
586 GGTTATCCGTCAACAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAG
205373 CATAGCTCAAGACGAGAAGGGTTATCTGTCAA
651 CATAGCTCAAGACGAGAAGGGTTATCTGTCAA
* **
205405 CAAAAGACCTTTGA-TTCGATTACACT-AGCTCAAAGGCGCATCCAATTTACAGCATAACTCAAG
1 CAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCCAATTTACAGCATAACTCAAG
* * * * *
205468 GCGATAAGGTTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGATCAAAGGTACATCA
66 GCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCA
* * * ** * *
205533 AATTTACAGCATAGCTCAAGGCGAGATGGGCTATCTATCAACAAAAGACCTTTGAGTTTGATTAC
131 AATTTACAACATAACTCAAGGCGAGAAGGGCTATCTATCAAC-AAAGACCTTCAAGTTCGAGTAC
* * *
205598 ACTCAGCTT-AAAGGCACATCCAATTTACAACATAACTCAAGGTGAGAAGGGTTATATGTCAAC-
195 ACTCAG-TTCAAAGGCACATCCAATTTACAACATAACTAAAGGCGAGAAGGGCTATATGTCAACA
* * * *
205661 CAATACCTTCGAGTTTGATTACACTCAGCTCAAAGGTACATCAAATTTACAGCATAGCTCAAGGC
259 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGC
*
205726 GAGAAGGGCTATCTGTCAATAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAATG-TGC-ATC
324 GAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAA-GATGCAAT-
* *
205789 CAATTTACAGCATAACTCAAGACAAGAA-GGTTATCTATCAACCAAGACCTTCAAGTTTGATTAC
387 -AATTTACAGCATAACTCAAGACAAGAAGGGTTATCTATCAACAAAGACCTTCAAGTTCGATTAC
* * * *
205853 ACTCAGCTCAAAGGCACGTCCAATTTACAACATAGTTCAAGGCGAGAAGGT-TATCTGTCAACAA
451 ACTCAACTCAAAGGCACATCAAATTTACAACATAGCTCAAGGCGAGAAGGTCTATCTGTCAACAA
* * * *
205917 AAGACCTTCGAGTTCGATTAAACTCAACTCAAAGGCGCATCCAATCTACAGCATAACTCAAGGCA
516 AAGACCTTCGAGTTCGAGTAAACTCAACTCAAAGGCACATCCAATCTAAAGCACAACTCAAGGCA
* * * *
205982 ATAAATGTTATCCGTCAATCAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGTACATCAAAT
581 AGAAAGGTTATCCGTCAA-CAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAAT
*
206047 TTACAGCATAGCTCAAGGCGAGAAGGG-TAT-TGTCAA
645 TTACAGCATAGCTCAAGACGAGAAGGGTTATCTGTCAA
* * *
206083 CAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATGTCAAATTTACAGCATAACTCAAG
1 CAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCCAATTTACAGCATAACTCAAG
* *** * * *
206148 GCGAGAAGGGTTATCTGTTAGTAAAAACTTTCGAGTTCGATTCCATTCAGCTC
66 GCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTACACTCAGCTC
206201 GATGACACAT
Statistics
Matches: 694, Mismatches: 93, Indels: 19
0.86 0.12 0.02
Matches are distributed among these distances:
678 19 0.03
679 140 0.20
680 427 0.62
681 106 0.15
682 2 0.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (682 bp):
CAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCCAATTTACAGCATAACTCAAG
GCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCA
AATTTACAACATAACTCAAGGCGAGAAGGGCTATCTATCAACAAAGACCTTCAAGTTCGAGTACA
CTCAGTTCAAAGGCACATCCAATTTACAACATAACTAAAGGCGAGAAGGGCTATATGTCAACAAA
AGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGCGA
GAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGATGCAATAATT
TACAGCATAACTCAAGACAAGAAGGGTTATCTATCAACAAAGACCTTCAAGTTCGATTACACTCA
ACTCAAAGGCACATCAAATTTACAACATAGCTCAAGGCGAGAAGGTCTATCTGTCAACAAAAGAC
CTTCGAGTTCGAGTAAACTCAACTCAAAGGCACATCCAATCTAAAGCACAACTCAAGGCAAGAAA
GGTTATCCGTCAACAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAG
CATAGCTCAAGACGAGAAGGGTTATCTGTCAA
Found at i:206987 original size:39 final size:39
Alignment explanation
Indices: 206944--207203 Score: 300
Period size: 39 Copynumber: 6.7 Consensus size: 39
206934 TTTTAGAAAT
206944 ATATATATAATATATAGTTTTTAAAAT-TATTTTGAAAAA
1 ATATATATAATATATAGTTTTTAAAATAT-TTTTGAAAAA
* *
206983 ATATATATAATATATAGTTTTTAAAA-ACATTTTGAAAAT
1 ATATATATAATATATAGTTTTTAAAATA-TTTTTGAAAAA
* * * *
207022 ATATGTATAATATATA-TTTTTTAAACATTTTTGAAAAC
1 ATATATATAATATATAGTTTTTAAAATATTTTTGAAAAA
* * *
207060 TTATATATAATATATAGTTTTTAAAACATTTTTG--AAT
1 ATATATATAATATATAGTTTTTAAAATATTTTTGAAAAA
* *
207097 ATATATATATTATATAGGTTTTTAAAATATTTTTGAAAAC
1 ATATATATAATATATA-GTTTTTAAAATATTTTTGAAAAA
*
207137 TTATATATAATATATAGTTTTTAAAATATTTTTG--AAA
1 ATATATATAATATATAGTTTTTAAAATATTTTTGAAAAA
* * *
207174 CTATATATATTGTATAGTTTTTGAAAATAT
1 ATATATATAATATATAGTTTTT-AAAATAT
207204 ATATTATATA
Statistics
Matches: 193, Mismatches: 20, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
37 37 0.19
38 55 0.28
39 85 0.44
40 16 0.08
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.48
Consensus pattern (39 bp):
ATATATATAATATATAGTTTTTAAAATATTTTTGAAAAA
Found at i:207002 original size:77 final size:77
Alignment explanation
Indices: 206933--207203 Score: 358
Period size: 77 Copynumber: 3.5 Consensus size: 77
206923 TTTGCAAATG
* **
206933 ATTTTAGAAATATATATATAATATATAGTTTTTAAAATTATTTTGAAAAAATATATATAATATAT
1 ATTTTTGAAATATATATATAATATATAGTTTTTAAAA-TATTTTGAAAACTTATATATAATATAT
206998 AGTTTTTAAAAAC
65 AGTTTTTAAAAAC
* *
207011 A-TTTTGAAAATATATGTATAATATATATTTTTTAAACAT-TTTTGAAAACTTATATATAATATA
1 ATTTTTG-AAATATATATATAATATATAGTTTTTAAA-ATATTTTGAAAACTTATATATAATATA
207074 TAGTTTTT-AAAAC
64 TAGTTTTTAAAAAC
*
207087 ATTTTTG-AATATATATATATTATATAGGTTTTTAAAATATTTTTGAAAACTTATATATAATATA
1 ATTTTTGAAATATATATATAATATATA-GTTTTTAAAATA-TTTTGAAAACTTATATATAATATA
*
207151 TAGTTTTT-AAAAT
64 TAGTTTTTAAAAAC
*
207164 ATTTTTGAAACTATATATAT--TGTATAGTTTTTGAAAATAT
1 ATTTTTGAAA-TATATATATAATATATAGTTTTT-AAAATAT
207204 ATATTATATA
Statistics
Matches: 174, Mismatches: 10, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
75 19 0.11
76 21 0.12
77 93 0.53
78 31 0.18
79 10 0.06
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (77 bp):
ATTTTTGAAATATATATATAATATATAGTTTTTAAAATATTTTGAAAACTTATATATAATATATA
GTTTTTAAAAAC
Found at i:207208 original size:24 final size:24
Alignment explanation
Indices: 207162--207239 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 24
207152 AGTTTTTAAA
*
207162 ATATTTTTGAAACTATATATATTGT
1 ATATTTTTGAAAC-ATATATATTAT
207187 ATAGTTTTTGAAA-ATATATATTAT
1 ATA-TTTTTGAAACATATATATTAT
207211 ATATTTTCTGAAACAT-TAT-TTAT
1 ATATTTT-TGAAACATATATATTAT
*
207234 TTATTT
1 ATATTT
207240 ATTTATTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
23 13 0.27
24 21 0.44
25 5 0.10
26 9 0.19
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (24 bp):
ATATTTTTGAAACATATATATTAT
Found at i:208443 original size:4 final size:4
Alignment explanation
Indices: 208430--208462 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
208420 TTTGATTTAC
208430 ATTT ATTTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT
208463 TCCCTTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:208462 original size:49 final size:49
Alignment explanation
Indices: 208398--208512 Score: 128
Period size: 49 Copynumber: 2.4 Consensus size: 49
208388 TTGGTTTTCA
* * *
208398 TATTTATTTAATATTTTTTCATTTTGATTTACATTTATTTTA-TTTATT
1 TATTTATTTATTATTTTTCCATTTTCATTTACATTTATTTTATTTTATT
* * * **
208446 TATTTATTTATTTATTTTCCCTTTTTCCTTTTGATTTATTTTATTTTATT
1 TATTTATTTA-TTATTTTTCCATTTTCATTTACATTTATTTTATTTTATT
208496 T-TTTA-TTATTATTTTTC
1 TATTTATTTATTATTTTTC
208513 TATTATTATT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
47 8 0.14
48 13 0.23
49 28 0.50
50 7 0.12
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (49 bp):
TATTTATTTATTATTTTTCCATTTTCATTTACATTTATTTTATTTTATT
Found at i:208500 original size:17 final size:18
Alignment explanation
Indices: 208480--208533 Score: 76
Period size: 17 Copynumber: 3.1 Consensus size: 18
208470 TTCCTTTTGA
208480 TTTATT-TTATTTTATTT
1 TTTATTATTATTTTATTT
*
208497 TTTATTATTATTTT-TCT
1 TTTATTATTATTTTATTT
*
208514 ATTATTATTATTTTATTT
1 TTTATTATTATTTTATTT
208532 TT
1 TT
208534 CCCTTTTCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 21 0.68
18 10 0.32
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTATTATTATTTTATTT
Found at i:210777 original size:27 final size:25
Alignment explanation
Indices: 210747--210817 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 25
210737 AAACACAATA
210747 TTAAAAATTTAAACGAACATAAATGCC
1 TTAAAAA--TAAACGAACATAAATGCC
*
210774 TTAAAAAATAAACGAACATGAATGCC
1 TT-AAAAATAAACGAACATAAATGCC
210800 TTCAAAAATAAACGAACA
1 TT-AAAAATAAACGAACA
210818 AACAAAAACA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 34 0.83
27 2 0.05
28 5 0.12
ACGTcount: A:0.55, C:0.15, G:0.08, T:0.21
Consensus pattern (25 bp):
TTAAAAATAAACGAACATAAATGCC
Found at i:210779 original size:26 final size:26
Alignment explanation
Indices: 210756--210817 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
210746 ATTAAAAATT
*
210756 TAAACGAACATAAATGCCTTAAAAAA
1 TAAACGAACATAAATGCCTTCAAAAA
*
210782 TAAACGAACATGAATGCCTTCAAAAA
1 TAAACGAACATAAATGCCTTCAAAAA
210808 TAAACGAACA
1 TAAACGAACA
210818 AACAAAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.55, C:0.18, G:0.10, T:0.18
Consensus pattern (26 bp):
TAAACGAACATAAATGCCTTCAAAAA
Found at i:215143 original size:24 final size:25
Alignment explanation
Indices: 215111--215170 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
215101 TATGTGATTT
*
215111 ATATATTATAATT-ATT-TTTTACAA
1 ATAT-TTATAATTAATTGTTTTAAAA
215135 ATAATTTAT-ATTAATTGTTTTAAAA
1 AT-ATTTATAATTAATTGTTTTAAAA
215160 ATATTTA-AATT
1 ATATTTATAATT
215171 TTATATTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
23 3 0.10
24 17 0.55
25 11 0.35
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (25 bp):
ATATTTATAATTAATTGTTTTAAAA
Found at i:216529 original size:22 final size:21
Alignment explanation
Indices: 216485--216541 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
216475 TCTAGGCTTA
* *
216485 ATAGTATCGGTAC-CTCTACT
1 ATAGTATCGATACTCTATACT
216505 ATAGTATCGATACTTCTATACT
1 ATAGTATCGATAC-TCTATACT
216527 ATAGTATCGATACTC
1 ATAGTATCGATACTC
216542 CCTTTCAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 12 0.36
21 2 0.06
22 19 0.58
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (21 bp):
ATAGTATCGATACTCTATACT
Found at i:218456 original size:106 final size:106
Alignment explanation
Indices: 218321--218523 Score: 273
Period size: 106 Copynumber: 1.9 Consensus size: 106
218311 TAAGGGTTAG
* * * * * *
218321 GGTTAGAGAAGATAAACATAGATAGAAGATGGAGAGACTTAG-TTTGGGTTTAGGGTTAATAGAT
1 GGTTAAAGAAGATAAACAAAGACAAAAGATGAAGAGAC-TAGATTTGGGTTTAGGGTTAATAAAT
* *
218385 ATAAATAGAGATAGAAGATGAAGAGGCTCGGTTTGGATTTAA
65 ATAAATAGAGACAGAAGATGAAGAGGCTAGGTTTGGATTTAA
* * * * *
218427 GGTTAAAGAAGATGAACAAAGACAAAAGATGAAGAGGCTCGATTTGGGTTTGGGGTTAGTAAATA
1 GGTTAAAGAAGATAAACAAAGACAAAAGATGAAGAGACTAGATTTGGGTTTAGGGTTAATAAATA
218492 TAAATAGAGACAGAAGATGAAGAGGCTAGGTT
66 TAAATAGAGACAGAAGATGAAGAGGCTAGGTT
218524 AAGATTTGGG
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
105 2 0.02
106 81 0.98
ACGTcount: A:0.40, C:0.05, G:0.31, T:0.25
Consensus pattern (106 bp):
GGTTAAAGAAGATAAACAAAGACAAAAGATGAAGAGACTAGATTTGGGTTTAGGGTTAATAAATA
TAAATAGAGACAGAAGATGAAGAGGCTAGGTTTGGATTTAA
Found at i:218530 original size:106 final size:106
Alignment explanation
Indices: 218363--218573 Score: 291
Period size: 106 Copynumber: 2.0 Consensus size: 106
218353 AGAGACTTAG
* * * **
218363 TTTGGGTTTAGGGTTAATAGATATAAATAGAGATAGAAGATGAAGAGGCTCGGTTTGGATTTAAG
1 TTTGGGTTTAGGGTTAATAAATATAAATAGAGACAGAAGATGAAGAGGCTAGGTTAAGATTT-AG
218428 G-TTAAAGAAGATGAACAAAGACA-AAAGATGAAGAGGCTCGA
65 GATTAAAGAAGATGAACAAAGACAGAAAG-TGAAGAGGCTCGA
* * *
218469 TTTGGGTTTGGGGTTAGTAAATATAAATAGAGACAGAAGATGAAGAGGCTAGGTTAAGATTTGGG
1 TTTGGGTTTAGGGTTAATAAATATAAATAGAGACAGAAGATGAAGAGGCTAGGTTAAGATTTAGG
* * *
218534 ATTAGAGAAGATGATCAGAGACAGAAAGTGAAGAGGCTCG
66 ATTAAAGAAGATGAACAAAGACAGAAAGTGAAGAGGCTCG
218574 GTTAGAGTTT
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
105 2 0.02
106 86 0.93
107 4 0.04
ACGTcount: A:0.39, C:0.06, G:0.31, T:0.24
Consensus pattern (106 bp):
TTTGGGTTTAGGGTTAATAAATATAAATAGAGACAGAAGATGAAGAGGCTAGGTTAAGATTTAGG
ATTAAAGAAGATGAACAAAGACAGAAAGTGAAGAGGCTCGA
Found at i:218532 original size:53 final size:54
Alignment explanation
Indices: 218320--218586 Score: 190
Period size: 53 Copynumber: 5.0 Consensus size: 54
218310 ATAAGGGTTA
* * * * * ** * * *
218320 GGGTTAG-AGAAGATAAACATAGATAGAAGATGGAGAGACTTAGTTTGGGTTTA
1 GGGTTAGTAGAAGATAAATAGAGACAGAAGATGAAGAGGCTCGGTTTAGATTTG
* * * * *
218373 GGGTTAATAG-ATATAAATAGAGATAGAAGATGAAGAGGCTCGGTTTGGATTTA
1 GGGTTAGTAGAAGATAAATAGAGACAGAAGATGAAGAGGCTCGGTTTAGATTTG
* * * * * * * * *
218426 AGGTTA-AAGAAGATGAACAAAGACAAAAGATGAAGAGGCTCGATTTGGGTTTG
1 GGGTTAGTAGAAGATAAATAGAGACAGAAGATGAAGAGGCTCGGTTTAGATTTG
* * *
218479 GGGTTAGTA-AATATAAATAGAGACAGAAGATGAAGAGGCTAGGTTAAGATTTG
1 GGGTTAGTAGAAGATAAATAGAGACAGAAGATGAAGAGGCTCGGTTTAGATTTG
* *
218532 GGATTAG-AGAAGAT-GATCAGAGACAGAA-AGTGAAGAGGCTCGG-TTAGAGTTTG
1 GGGTTAGTAGAAGATAAAT-AGAGACAGAAGA-TGAAGAGGCTCGGTTTAGA-TTTG
218585 GG
1 GG
218587 TTTGGGTTAG
Statistics
Matches: 170, Mismatches: 37, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
52 10 0.06
53 157 0.92
54 3 0.02
ACGTcount: A:0.39, C:0.05, G:0.32, T:0.24
Consensus pattern (54 bp):
GGGTTAGTAGAAGATAAATAGAGACAGAAGATGAAGAGGCTCGGTTTAGATTTG
Found at i:219408 original size:33 final size:33
Alignment explanation
Indices: 219371--219612 Score: 295
Period size: 33 Copynumber: 7.5 Consensus size: 33
219361 TAATAAATTA
219371 ATATAGTTTATATATACTAATGAACTATATAAT
1 ATATAGTTTATATATACTAATGAACTATATAAT
*
219404 ATATAGTTTATATATACT-AT--A-TAGTTTAA-
1 ATATAGTTTATATATACTAATGAACTA-TATAAT
* * *
219433 ATATA--CTA-ATGA-ACTGTATGAACTATATACT
1 ATATAGTTTATAT-ATACT-AATGAACTATATAAT
219464 ATATAGTTTATATATACTAATGAACTATATAAT
1 ATATAGTTTATATATACTAATGAACTATATAAT
* * * *
219497 ATATAATTTATATTTACTAATGAACAATATACT
1 ATATAGTTTATATATACTAATGAACTATATAAT
* *
219530 ATGTAGTTTACATATACTAATGAACTATATAAT
1 ATATAGTTTATATATACTAATGAACTATATAAT
*
219563 ATATAGTTTATATATACTAATGAACTTTATAAT
1 ATATAGTTTATATATACTAATGAACTATATAAT
219596 ATATAGTTTATATATAC
1 ATATAGTTTATATATAC
219613 ACTACATAGT
Statistics
Matches: 177, Mismatches: 20, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
26 5 0.03
27 3 0.02
28 2 0.01
29 7 0.04
30 9 0.05
31 7 0.04
32 2 0.01
33 137 0.77
34 5 0.03
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (33 bp):
ATATAGTTTATATATACTAATGAACTATATAAT
Found at i:219417 original size:42 final size:41
Alignment explanation
Indices: 219371--219509 Score: 127
Period size: 42 Copynumber: 3.1 Consensus size: 41
219361 TAATAAATTA
219371 ATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACT
1 ATATAGTTTATATATACTAATGAAC--TAT-ATA-ATA---TATAT-T--T
* * *
219422 ATATAGTTTAAATATACTAATGAACTGTATGAACTATATA-CT
1 ATATAGTTTATATATACTAATGAACTATAT-AA-TATATATTT
219464 ATATAGTTTATATATACTAATGAACTATATAATATATAATTT
1 ATATAGTTTATATATACTAATGAACTATATAATATAT-ATTT
219506 ATAT
1 ATAT
219510 TTACTAATGA
Statistics
Matches: 78, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
40 5 0.06
41 3 0.04
42 34 0.44
46 4 0.05
48 3 0.04
49 5 0.06
51 24 0.31
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (41 bp):
ATATAGTTTATATATACTAATGAACTATATAATATATATTT
Found at i:219438 original size:18 final size:18
Alignment explanation
Indices: 219397--219440 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
219387 CTAATGAACT
* *
219397 ATATAATATATAGTTTAT
1 ATATACTATATAGTTTAA
219415 ATATACTATATAGTTTAA
1 ATATACTATATAGTTTAA
219433 ATATACTA
1 ATATACTA
219441 ATGAACTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
ATATACTATATAGTTTAA
Found at i:219669 original size:2 final size:2
Alignment explanation
Indices: 219664--219714 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
219654 CTATATAGTT
219664 TA TA TA TA T- TA TA T- TA -A 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
219703 TA TA TA TA TA TA
1 TA TA TA TA TA TA
219715 AACAAATTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:220571 original size:30 final size:30
Alignment explanation
Indices: 220518--220796 Score: 160
Period size: 30 Copynumber: 9.3 Consensus size: 30
220508 GGTTTAAAAA
*
220518 TATCTTAAC--ATTAAAAAATATTTTATTTT
1 TATCTTAACTTATT-AAATATATTTTATTTT
* * *
220547 TTTCTTAACTTATTTAATATATTTTATTCT
1 TATCTTAACTTATTAAATATATTTTATTTT
* ** *
220577 TATCTTAACTAAAAAAATATATTTTATATT
1 TATCTTAACTTATTAAATATATTTTATTTT
* * * *
220607 TATTTTAACTTATTACATATATTATATTCT
1 TATCTTAACTTATTAAATATATTTTATTTT
* * *
220637 TAACTTAAATTATTAAATATATTATATTTT
1 TATCTTAACTTATTAAATATATTTTATTTT
* * * *
220667 TACCTCAATTTATTAAATAT-TATTTATTCT
1 TATCTTAACTTATTAAATATAT-TTTATTTT
* * * * *
220697 TA-CATTGACTTAATATATATA-TATATATAT
1 TATC-TTAACTTATTAAATATATTTTAT-TTT
* *
220727 TATTTTAA-TT-TTAAAATGTATATTTTATTCT
1 TATCTTAACTTATT-AAA--TATATTTTATTTT
* * ** *
220758 TATTTTAATTTAAGAAATATA-TTTAATTT
1 TATCTTAACTTATTAAATATATTTTATTTT
220787 TATCTTAACT
1 TATCTTAACT
220797 ATAAAAAAAT
Statistics
Matches: 189, Mismatches: 48, Indels: 26
0.72 0.18 0.10
Matches are distributed among these distances:
28 1 0.01
29 32 0.17
30 130 0.69
31 17 0.09
32 9 0.05
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (30 bp):
TATCTTAACTTATTAAATATATTTTATTTT
Found at i:220615 original size:60 final size:59
Alignment explanation
Indices: 220518--220796 Score: 210
Period size: 60 Copynumber: 4.7 Consensus size: 59
220508 GGTTTAAAAA
* *
220518 TATCTTAACATT-AAAAA-ATATTTTATTTTTTTCTTAACTTATTTAATATATTTTATTCT
1 TATCTTAAC-TTAAAAAATATATTTTATTTTATT-TTAACTTATTAAATATATTTTATTCT
* * *
220577 TATCTTAACTAAAAAAATATATTTTATATTTATTTTAACTTATTACATATATTATATTCT
1 TATCTTAACTTAAAAAATATATTTTAT-TTTATTTTAACTTATTAAATATATTTTATTCT
* * ** * ** * *
220637 TAACTTAAATTATTAAATATATTATATTTTTACCTCAATTTATTAAATAT-TATTTATTCT
1 TATCTTAACTTAAAAAATATATTTTA-TTTTATTTTAACTTATTAAATATAT-TTTATTCT
* * * * *
220697 TA-CATTGACTTAATATATATATATATATATTATTTTAA-TT-TTAAAATGTATATTTTATTCT
1 TATC-TTAACTTAAAAAATATAT-TTTATTTTATTTTAACTTATT-AAA--TATATTTTATTCT
* * * * *
220758 TATTTTAATTTAAGAAATATATTTAATTTTATCTTAACT
1 TATCTTAACTTAAAAAATATATTTTATTTTATTTTAACT
220797 ATAAAAAAAT
Statistics
Matches: 173, Mismatches: 34, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
58 3 0.02
59 21 0.12
60 110 0.64
61 38 0.22
62 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (59 bp):
TATCTTAACTTAAAAAATATATTTTATTTTATTTTAACTTATTAAATATATTTTATTCT
Found at i:221925 original size:44 final size:44
Alignment explanation
Indices: 221826--221918 Score: 168
Period size: 44 Copynumber: 2.1 Consensus size: 44
221816 TACTACCCTG
221826 AGTATCAATACCAAAAATGACTTTGATGTTTTGAAAATTAGTTT
1 AGTATCAATACCAAAAATGACTTTGATGTTTTGAAAATTAGTTT
* *
221870 AGTATCAATACCAAAAATGGCTTTGATGTTTTGAAAATTATTTT
1 AGTATCAATACCAAAAATGACTTTGATGTTTTGAAAATTAGTTT
221914 AGTAT
1 AGTAT
221919 TGATACCTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.40
Consensus pattern (44 bp):
AGTATCAATACCAAAAATGACTTTGATGTTTTGAAAATTAGTTT
Found at i:234541 original size:22 final size:22
Alignment explanation
Indices: 234498--234541 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
234488 TTCCATTCAA
* *
234498 CATCAACACCATCAACATCTTC
1 CATCAACACCACCAACAACTTC
* *
234520 CATCAAGACCACCATCAACTTC
1 CATCAACACCACCAACAACTTC
234542 ATAATTCCGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.41, G:0.02, T:0.20
Consensus pattern (22 bp):
CATCAACACCACCAACAACTTC
Found at i:247119 original size:20 final size:22
Alignment explanation
Indices: 247081--247120 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
247071 GTTTTGCAGA
247081 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
247103 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
247121 AGATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:247723 original size:21 final size:21
Alignment explanation
Indices: 247699--247738 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
247689 CAACAATTGG
247699 AAACAATTAGTATCCTTTTGA
1 AAACAATTAGTATCCTTTTGA
* * *
247720 AAACTATTGGTATCTTTTT
1 AAACAATTAGTATCCTTTT
247739 TATTAAACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (21 bp):
AAACAATTAGTATCCTTTTGA
Found at i:250093 original size:45 final size:45
Alignment explanation
Indices: 250011--250199 Score: 245
Period size: 45 Copynumber: 4.2 Consensus size: 45
250001 ATTTTATTTG
* * *
250011 CTTATCCAATAT-TTTACCATTTATTAACCATAAGCTCGTAAGTTTAT
1 CTTA-CCAATATACTTACCATTTA-T-CCCATAAGCTCGTAAGCTTAT
* *
250058 TTTACCAAAATACTTACCATTTATCCCATAAGCTCGTAAGCTTAT
1 CTTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTAT
* * * * *
250103 CTTACCATTATACTTACCATTTGTTCCATAAGCTCATAATCTTAT
1 CTTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTAT
*
250148 TTTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTAT
1 CTTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTAT
250193 CTTACCA
1 CTTACCA
250200 TTTGTTCCAT
Statistics
Matches: 122, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
45 102 0.84
46 7 0.06
47 13 0.11
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (45 bp):
CTTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTAT
Found at i:250148 original size:90 final size:91
Alignment explanation
Indices: 250024--250201 Score: 297
Period size: 90 Copynumber: 2.0 Consensus size: 91
250014 ATCCAATATT
*
250024 TTACCATTTATTAACCATAAGCTCGTAAGTTTATTTTACCAAAATACTTACCATTTATCCCATAA
1 TTACCATTTATT-ACCATAAGCTCATAAGTTTATTTTACCAAAATACTTACCATTTATCCCATAA
250089 GCTCGTAAGCTTATCTTACCATTATAC
65 GCTCGTAAGCTTATCTTACCATTATAC
* *
250116 TTACCATTTGTT-CCATAAGCTCATAA-TCTTATTTTACCAATATACTTACCATTTATCCCATAA
1 TTACCATTTATTACCATAAGCTCATAAGT-TTATTTTACCAAAATACTTACCATTTATCCCATAA
250179 GCTCGTAAGCTTATCTTACCATT
65 GCTCGTAAGCTTATCTTACCATT
250202 TGTTCCATAA
Statistics
Matches: 82, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
89 1 0.01
90 70 0.85
92 11 0.13
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (91 bp):
TTACCATTTATTACCATAAGCTCATAAGTTTATTTTACCAAAATACTTACCATTTATCCCATAAG
CTCGTAAGCTTATCTTACCATTATAC
Found at i:250197 original size:33 final size:33
Alignment explanation
Indices: 250160--250247 Score: 158
Period size: 33 Copynumber: 2.7 Consensus size: 33
250150 TACCAATATA
* *
250160 CTTACCATTTATCCCATAAGCTCGTAAGCTTAT
1 CTTACCATTTGTTCCATAAGCTCGTAAGCTTAT
250193 CTTACCATTTGTTCCATAAGCTCGTAAGCTTAT
1 CTTACCATTTGTTCCATAAGCTCGTAAGCTTAT
250226 CTTACCATTTGTTCCATAAGCT
1 CTTACCATTTGTTCCATAAGCT
250248 TATTTTACCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.25, C:0.26, G:0.10, T:0.39
Consensus pattern (33 bp):
CTTACCATTTGTTCCATAAGCTCGTAAGCTTAT
Found at i:250212 original size:25 final size:25
Alignment explanation
Indices: 250184--250257 Score: 67
Period size: 33 Copynumber: 2.6 Consensus size: 25
250174 CATAAGCTCG
250184 TAAGCTTATCTTACCATTTGTTCCA
1 TAAGCTTATCTTACCATTTGTTCCA
250209 TAAGCTCGTAAGCTTATCTTACCATTTGTTCCA
1 TAA----G----CTTATCTTACCATTTGTTCCA
*
250242 TAAGCTTATTTTACCA
1 TAAGCTTATCTTACCA
250258 ATATACTTGC
Statistics
Matches: 40, Mismatches: 1, Indels: 16
0.70 0.02 0.28
Matches are distributed among these distances:
25 14 0.35
29 2 0.05
33 24 0.60
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (25 bp):
TAAGCTTATCTTACCATTTGTTCCA
Found at i:251843 original size:29 final size:28
Alignment explanation
Indices: 251777--251844 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
251767 AGGTTCTTCA
* *
251777 TCAATTTTCCAAAATTTACGAATTGATC
1 TCAATTTTTCAAAATTTACGAAATGATC
* * *
251805 TCCAACTTTTCAAAATTTATGAAATGGTCC
1 T-CAATTTTTCAAAATTTACGAAATGAT-C
251835 TCAATTTTTC
1 TCAATTTTTC
251845 TAAGGCTTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 1 0.03
29 29 0.91
30 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.41
Consensus pattern (28 bp):
TCAATTTTTCAAAATTTACGAAATGATC
Found at i:254568 original size:20 final size:20
Alignment explanation
Indices: 254545--254631 Score: 58
Period size: 19 Copynumber: 4.3 Consensus size: 20
254535 TCTCTCATCA
254545 TTTTTTTCTTCTTTCTATCT
1 TTTTTTTCTTCTTTCTATCT
* *
254565 TTTTCTTCTTTCTTTTTATTTCT
1 TTTTTTTC-TTCTTTCTA--TCT
254588 TTTTCTATT-TT-TTTCTAT-T
1 TTTT-T-TTCTTCTTTCTATCT
*
254607 TTTTTCATCTTCTTT-T-TCT
1 TTTTT-TTCTTCTTTCTATCT
254626 TTTTTT
1 TTTTTT
254632 AGCTTTTATG
Statistics
Matches: 52, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
18 3 0.06
19 14 0.27
20 11 0.21
21 8 0.15
22 5 0.10
23 9 0.17
25 2 0.04
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTTTCTTCTTTCTATCT
Found at i:254599 original size:9 final size:10
Alignment explanation
Indices: 254556--254631 Score: 57
Period size: 10 Copynumber: 7.2 Consensus size: 10
254546 TTTTTTCTTC
*
254556 TTTCTATCTT
1 TTTCTATTTT
254566 TTTCT-TCTTT
1 TTTCTAT-TTT
*
254576 CTTTTTATTTCTT
1 -TTTCTA-TT-TT
254589 TTTCTATTTT
1 TTTCTATTTT
254599 TTTCTATTTT
1 TTTCTATTTT
*
254609 TTTCATCTTCTT
1 TTTC-TATT-TT
254621 TTTCT-TTTT
1 TTTCTATTTT
254630 TT
1 TT
254632 AGCTTTTATG
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
9 5 0.09
10 25 0.45
11 10 0.18
12 12 0.22
13 3 0.05
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTCTATTTT
Found at i:254608 original size:17 final size:17
Alignment explanation
Indices: 254544--254603 Score: 88
Period size: 17 Copynumber: 3.6 Consensus size: 17
254534 ATCTCTCATC
254544 ATTTTTTTCTTCTTTCT
1 ATTTTTTTCTTCTTTCT
*
254561 ATCTTTTTCTTCTTTCT
1 ATTTTTTTCTTCTTTCT
254578 -TTTTATTTCTT-TTTCT
1 ATTTT-TTTCTTCTTTCT
254594 ATTTTTTTCT
1 ATTTTTTTCT
254604 ATTTTTTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
16 13 0.33
17 26 0.67
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (17 bp):
ATTTTTTTCTTCTTTCT
Found at i:254619 original size:26 final size:25
Alignment explanation
Indices: 254556--254632 Score: 61
Period size: 26 Copynumber: 3.0 Consensus size: 25
254546 TTTTTTCTTC
254556 TTTCTATCTT-TTTCTTCTTTCTTTTTA
1 TTTC-ATCTTCTTT-TT-TTTCTTTTTA
* *
254583 TTTCTTTTTCTATTTTTTTCTATTTT-
1 TTTCATCTTCT-TTTTTTTCT-TTTTA
*
254609 TTTCATCTTCTTTTTCTT-TTTTTA
1 TTTCATCTTCTTTTTTTTCTTTTTA
254633 GCTTTTATGC
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
23 4 0.10
24 1 0.02
25 6 0.15
26 17 0.41
27 11 0.27
28 2 0.05
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTCATCTTCTTTTTTTTCTTTTTA
Found at i:257293 original size:45 final size:45
Alignment explanation
Indices: 257225--257461 Score: 305
Period size: 45 Copynumber: 5.3 Consensus size: 45
257215 TTTACCATTT
* * * *
257225 ATAAGCTTATTTTACCAAAATACTTACCATTTATCCCACATGGTC
1 ATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGCTC
* * * *
257270 ATAAGCTTATCTTACCATTATACTTACCATTTGTTCCATAAGCTC
1 ATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGCTC
257315 ATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGCTC
1 ATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGCTC
* * * * *
257360 GTAAGCTTATCTTACCATTATACTTACCATTTGTTCCATAAGCTC
1 ATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGCTC
* * *
257405 ATAAGCTTATTTTACCAATATACTT-GCAATTATTCCATAAGCTC
1 ATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGCTC
* *
257449 GTAAGATTATTTT
1 ATAAGCTTATTTT
257462 CTAGTTTAAC
Statistics
Matches: 167, Mismatches: 25, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
44 27 0.16
45 140 0.84
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39
Consensus pattern (45 bp):
ATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGCTC
Found at i:257378 original size:90 final size:90
Alignment explanation
Indices: 257225--257458 Score: 380
Period size: 90 Copynumber: 2.6 Consensus size: 90
257215 TTTACCATTT
* * * * *
257225 ATAAGCTTATTTTACCAAAATACTTACCATTTATCCCACATGGTCATAAGCTTATCTTACCATTA
1 ATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATCTTACCATTA
257290 TACTTACCATTTGTTCCATAAGCTC
66 TACTTACCATTTGTTCCATAAGCTC
257315 ATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATCTTACCATTA
1 ATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATCTTACCATTA
257380 TACTTACCATTTGTTCCATAAGCTC
66 TACTTACCATTTGTTCCATAAGCTC
* * * *
257405 ATAAGCTTATTTTACCAATATACTT-GCAATTATTCCATAAGCTCGTAAGATTAT
1 ATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTAT
257459 TTTCTAGTTT
Statistics
Matches: 135, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 25 0.19
90 110 0.81
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (90 bp):
ATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATCTTACCATTA
TACTTACCATTTGTTCCATAAGCTC
Found at i:257691 original size:61 final size:61
Alignment explanation
Indices: 257570--257691 Score: 156
Period size: 61 Copynumber: 2.0 Consensus size: 61
257560 GTAGTGCTAA
* * *
257570 ACCTGCACTAAGCTTACGCCATAATGCTAATCCGGACAATACACATAAGGTCGTGCCCACC
1 ACCTACACTAAGCTTACGCCATAATGCTAATCCGGACAATACACATAAGGTAGTACCCACC
* * * * *
257631 ACCTACACTAAGCTTATGCTATAGTGCTAATCCGGAC-ATGATACATAAGGTAGTATCCACC
1 ACCTACACTAAGCTTACGCCATAATGCTAATCCGGACAAT-ACACATAAGGTAGTACCCACC
257692 TTTCCCTCAC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 2 0.04
61 50 0.96
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (61 bp):
ACCTACACTAAGCTTACGCCATAATGCTAATCCGGACAATACACATAAGGTAGTACCCACC
Found at i:258997 original size:29 final size:28
Alignment explanation
Indices: 258931--258998 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
258921 AGATTCTTCA
* **
258931 TCAATTTTCCAAAATTTATGACTTGCTC
1 TCAATTTTTCAAAATTTATGAAATGCTC
* *
258959 TCCAACTTTTCAAAATTTATGAAATGGTCC
1 T-CAATTTTTCAAAATTTATGAAATGCT-C
258989 TCAATTTTTC
1 TCAATTTTTC
258999 TATGGCTTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 1 0.03
29 29 0.91
30 2 0.06
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (28 bp):
TCAATTTTTCAAAATTTATGAAATGCTC
Found at i:259444 original size:17 final size:18
Alignment explanation
Indices: 259411--259445 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
259401 ACCAAATATT
*
259411 TTAATACTTATTAATTCC
1 TTAATACTTAATAATTCC
259429 TTAATAC-TAATAATTCC
1 TTAATACTTAATAATTCC
259446 AACATTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAATACTTAATAATTCC
Found at i:260147 original size:29 final size:28
Alignment explanation
Indices: 260077--260147 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 28
260067 CCTAGGTTCT
*
260077 TCATCAATTTTCCAAAATTTATGAATTGA
1 TCATCAATTTT-CAAAATTTATGAAATGA
*
260106 TC-TCCAACTTTTCAAAATTTATGAAATGG
1 TCAT-CAA-TTTTCAAAATTTATGAAATGA
260135 TCATCAATGTTTC
1 TCATCAAT-TTTC
260148 TAAGGCTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
28 2 0.06
29 29 0.81
30 5 0.14
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (28 bp):
TCATCAATTTTCAAAATTTATGAAATGA
Found at i:262887 original size:17 final size:16
Alignment explanation
Indices: 262865--262919 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 16
262855 CTCATCATTA
262865 TTTTTTCATCTTTCTAT
1 TTTTTTC-TCTTTCTAT
262882 TTTTTTCTTCTTTCT-T
1 TTTTTTC-TCTTTCTAT
*
262898 TTTATTTCTTTTTCTAT
1 TTT-TTTCTCTTTCTAT
262915 TTTTT
1 TTTTT
262920 CACCTTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 12 0.35
17 22 0.65
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTCTCTTTCTAT
Found at i:262928 original size:31 final size:32
Alignment explanation
Indices: 262875--262939 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
262865 TTTTTTCATC
* *
262875 TTTCTATTTTTTTCTTCTTTCTTTTTATTTCTT
1 TTTCTATTTTTTTCTACCTTCTTTTTATTT-TT
*
262908 TTTCTA-TTTTTTC-ACCTTCTTTTTCTTTTT
1 TTTCTATTTTTTTCTACCTTCTTTTTATTTTT
262938 TT
1 TT
262940 AGCTCTTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 4 0.14
31 12 0.41
32 7 0.24
33 6 0.21
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (32 bp):
TTTCTATTTTTTTCTACCTTCTTTTTATTTTT
Found at i:265497 original size:40 final size:40
Alignment explanation
Indices: 265442--265563 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
265432 TACAGGTTTA
265442 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
265482 TAATACACTTCGGTGTATATGGTGGGCACGACATTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
265522 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
265562 TA
1 TA
265564 GCACTACGGT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:265718 original size:44 final size:44
Alignment explanation
Indices: 265668--265785 Score: 130
Period size: 47 Copynumber: 2.6 Consensus size: 44
265658 GTAAGCATAC
*
265668 AAATAAGCTTACGAGCTTTTGGAATAATGACAAGTATATAT-GAA
1 AAATAAGCTTACGAGCTTATGGAATAATGACAAGTAT-TATGGAA
* ** * *
265712 AAATAAGCTTACAAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--T-AATGACAAGTATTATGGAA
*
265759 AAATAAGCTTACGAGCTTATGGGATAA
1 AAATAAGCTTACGAGCTTATGGAATAA
265786 ATGGTAAGAG
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
44 24 0.39
45 1 0.02
46 3 0.05
47 34 0.55
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGACAAGTATTATGGAA
Found at i:266262 original size:22 final size:22
Alignment explanation
Indices: 266237--266289 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
266227 AAAGGGGTAC
266237 CGATTCCCCTGCTACAGGGAAT
1 CGATTCCCCTGCTACAGGGAAT
266259 CGATTCCCCTGCTACAGGGAAT
1 CGATTCCCCTGCTACAGGGAAT
266281 CGATTCCCC
1 CGATTCCCC
266290 CACTGTTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.23
Consensus pattern (22 bp):
CGATTCCCCTGCTACAGGGAAT
Found at i:268654 original size:6 final size:6
Alignment explanation
Indices: 268615--268703 Score: 71
Period size: 6 Copynumber: 15.3 Consensus size: 6
268605 ATATTATAAG
* *
268615 AAGAAA AA-AAA ACAGAAG AAGAAA AA-AAA TAGAAA AAGAAA AAGAAA
1 AAGAAA AAGAAA A-AGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* * * *
268662 ACG-AA GA-AAA AAGAAA ACGAGA AAG-AA AAGAAA AAGAGAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGA-AA AA
268704 AAATGAGAGA
Statistics
Matches: 64, Mismatches: 12, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
5 17 0.27
6 40 0.62
7 7 0.11
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.01
Consensus pattern (6 bp):
AAGAAA
Found at i:268654 original size:35 final size:34
Alignment explanation
Indices: 268615--268706 Score: 100
Period size: 34 Copynumber: 2.7 Consensus size: 34
268605 ATATTATAAG
268615 AAGAAAAAAAAACAGAAGAAGAAAA-AAAATAGAAA
1 AAGAAAAAAAAACAGAAGAA-AAAAGAAAA-AGAAA
* *
268650 AAGAAAAAGAAAAC-GAAGAAAAAAGAAAACGAGA
1 AAGAAAAA-AAAACAGAAGAAAAAAGAAAAAGAAA
*
268684 AAGAAAAGAAAAAGAGAA-AAAAA
1 AAGAAAA-AAAAACAGAAGAAAAA
268707 TGAGAGATGA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
34 23 0.46
35 22 0.44
36 5 0.10
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.01
Consensus pattern (34 bp):
AAGAAAAAAAAACAGAAGAAAAAAGAAAAAGAAA
Found at i:268672 original size:16 final size:15
Alignment explanation
Indices: 268653--268705 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 15
268643 ATAGAAAAAG
268653 AAAAAGAAAACGAAGA
1 AAAAAGAAAACG-AGA
268669 AAAAAGAAAACGAGAA
1 AAAAAGAAAACGAG-A
*
268685 AGAAAAGAAAAAGAGA
1 A-AAAAGAAAACGAGA
268701 AAAAA
1 AAAAA
268706 ATGAGAGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
15 6 0.18
16 16 0.47
17 12 0.35
ACGTcount: A:0.77, C:0.04, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAACGAGA
Done.