Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003850.1 Hibiscus syriacus cultivar Beakdansim tig00008262_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: 524162
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:12 original size:6 final size:6
Alignment explanation
Indices: 2--969 Score: 388
Period size: 6 Copynumber: 165.8 Consensus size: 6
1 T
* * * *
2 AGAAGG AGAAGG AGAAGG AGAAAG AGAATG AGAAGA AGAAGG AGAATG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * *
50 AGAA-- A-AAGA AGAAGA AGAAGA AGAAGA AGAAAG AGAAGG AGAA-G
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * ** * **
94 AGAAGAAG AGAAGG AGAATG AGAA-A AGAATG AGAAAA AGAATG AGAATT
1 AGAAG--G AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * *
143 AGAAGG AGAA-- A-AATG AGAAGA AGAAAG AGAA-- A-AAGA AGAAGA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * *
185 AGAATG AGAAGG AGAATG AGAAGA AGAAGG AGAAGAATG AGGAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAG---G AGAAGG AGAAGG
* * * * * ** * * *
236 AGGAGG AGAAGA AGAAAG AGAA-A ACAACA ACAAGA AGAAGA AGTTAA--
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AG--AAGG
* ** * * * * * ** * * *
283 AGAAGA AGAAAA AGAAGA ACAAGA ACAAGA AGAATA AAAAGA AGAAGA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * * * * *
331 AGAAGA ATAAGA AGAAGA AGAAGA AGAAGA AGAAGG AGGAGG GGGAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * * *
379 AGGAGG AGGAGG AGGAGG AGGAGG AG-AGG AGGAGG AGGAGG AGGAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * *
426 AGGAGG AGGAGG AGAAGG AGGAGG AGAATG AGAAGG AGAAGG AGAATG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * *
474 AGAAGG AGAAGA AGAAGG AGAATG AGGAA-A AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG A-GAAGG AGAAGG AGAAGG AGAAGG
* * ** ** * * *
522 AGAAGG AGAAGA AGAAGG AGAATG AGAAAA AGAAAA AGAAGA ATAAGA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * *
570 AGGAGA AGAAGG AGAATG AGAATG AGAATG AGAA-G A-AA-G AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
** * * * *
615 AGAAAA AGAAGA AGAAGG AGAAGA AGAAGA AGAAGA AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * *
663 AGAATG AGAAGA AGGAGG AGAATG AGAAGG AGAATG AGAA-- A-AATG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * **
708 AGAAGG ACAATG AGAA-- A-AAGG ATAAGA AGAAAG AGAAAA AGAA-G
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
** * * * * * * * * *
752 A-AAAA AAAAGA AAAAGA AGAAGA AGAAGA AGAATG AGAATG AGAAGA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * *
799 AGAAGA AGAAGG AGAAGA AGAAGA ATG-AGA AGGAGG AGAAGG AGGAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG A-GAAGG AGAAGG AGAAGG AGAAGG
* * *
847 AGAAGA AGAA-G A-AAGA AGAAGG AG-A-- AGAAGG AGAAGA AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * *
890 AGAATG AGAAGG AGAAGG AGGAGA AGGAGC AGAAGG AGAA-G -G-AGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * *
935 AGAAGG AGAAGA AGAAGA AGAAGA AGAAGA AGAAG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAG
970 TGTGCATGTG
Statistics
Matches: 787, Mismatches: 131, Indels: 88
0.78 0.13 0.09
Matches are distributed among these distances:
3 13 0.02
4 18 0.02
5 37 0.05
6 702 0.89
7 4 0.01
8 8 0.01
9 5 0.01
ACGTcount: A:0.57, C:0.01, G:0.39, T:0.03
Consensus pattern (6 bp):
AGAAGG
Found at i:159 original size:21 final size:21
Alignment explanation
Indices: 7--237 Score: 136
Period size: 21 Copynumber: 10.7 Consensus size: 21
1 TAGAAG
*
7 GAGAAGGAGAAGGAGAAAGAGAAT
1 GAGAAGAAGAAGGAG-AA-A-AAT
31 GAGAAGAAGAAGGAG---AAT
1 GAGAAGAAGAAGGAGAAAAAT
* * *
49 GAGAAAAAGAAGAAGAAGAA-
1 GAGAAGAAGAAGGAGAAAAAT
*
69 GAAGAAGAAGAAAGAGAAGGAGAA-
1 G-AGAAGAAGAAGGAGAA--A-AAT
* * *
93 GAGAAGAAG-AGAAGGAGAAT
1 GAGAAGAAGAAGGAGAAAAAT
*
113 GAGAA-AAGAATGAGAAAAAGAAT
1 GAGAAGAAGAA-G-GAGAAA-AAT
**
136 GAGAATTAGAAGGAGAAAAAT
1 GAGAAGAAGAAGGAGAAAAAT
*
157 GAGAAGAAGAAAGAGAAAAA-
1 GAGAAGAAGAAGGAGAAAAAT
*
177 GAAGAAGAAGAATGAGAAGGAGAAT
1 G-AGAAGAAGAAGGAGAA--A-AAT
*
202 GAGAAGAAGAAGGAGAAGAAT
1 GAGAAGAAGAAGGAGAAAAAT
* *
223 GAGGAGGAGAAGGAG
1 GAGAAGAAGAAGGAG
238 GAGGAGAAGA
Statistics
Matches: 164, Mismatches: 25, Indels: 39
0.72 0.11 0.17
Matches are distributed among these distances:
18 16 0.10
19 5 0.03
20 8 0.05
21 67 0.41
22 11 0.07
23 18 0.11
24 38 0.23
25 1 0.01
ACGTcount: A:0.59, C:0.00, G:0.36, T:0.05
Consensus pattern (21 bp):
GAGAAGAAGAAGGAGAAAAAT
Found at i:1276 original size:2 final size:2
Alignment explanation
Indices: 1269--1308 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1259 AACATCAGAC
1269 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
1309 TAAAAAACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21195 original size:33 final size:33
Alignment explanation
Indices: 21167--21242 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
21157 GGTTGGTTAA
21167 AAACAAAAGGTTGA-TGGATTGGCTGTTGGGAAG
1 AAACAAAAGGTT-ATTGGATTGGCTGTTGGGAAG
21200 AAACAAAAGGTTATTGGATTGGCTGTTGGGAAG
1 AAACAAAAGGTTATTGGATTGGCTGTTGGGAAG
*
21233 AAACAGAAGG
1 AAACAAAAGG
21243 AGACTCCTGG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 1 0.02
33 40 0.98
ACGTcount: A:0.37, C:0.07, G:0.34, T:0.22
Consensus pattern (33 bp):
AAACAAAAGGTTATTGGATTGGCTGTTGGGAAG
Found at i:23447 original size:2 final size:2
Alignment explanation
Indices: 23438--23481 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
23428 TTTTTTTTAA
*
23438 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23479 AT A
1 AT A
23482 GTTTATATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23581 original size:4 final size:4
Alignment explanation
Indices: 23567--23678 Score: 59
Period size: 4 Copynumber: 27.2 Consensus size: 4
23557 TACTCTGTTC
* * * *
23567 TTAT CTTAT TTAT TTAT CTAT TTAT TTAA TTAT TTAA TTAT TT-T TTCT
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * *
23615 TCTCT TTAT TT-T TATAT TTCCT CTAT CT-T TGAT TTAT TTACT CATAT
1 T-TAT TTAT TTAT T-TAT TT-AT TTAT TTAT TTAT TTAT TTA-T -TTAT
23662 TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT T
23679 CATGTATATA
Statistics
Matches: 84, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
3 6 0.07
4 62 0.74
5 14 0.17
6 2 0.02
ACGTcount: A:0.22, C:0.10, G:0.01, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:36728 original size:106 final size:101
Alignment explanation
Indices: 36541--36940 Score: 469
Period size: 106 Copynumber: 3.9 Consensus size: 101
36531 GGGAATCGTG
*
36541 AACACAAGCTCAACTTCACAGCAAAGGGGCGGCTGACTGT--CAACTTCCCAATTTCAGAGCCAA
1 AACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCACAACTTCCCAATTTCAGAGCCAA
* *
36604 TTTCAACTTCACAACGAAGGATATTGGACTCAAGAA
66 TTTCAACTTCACGACGAAGGATATTGGACTCAAGAC
* *
36640 AACACAAGCTCAACTTAACAGCGAATGGGCGGCTGACTGTCAACAAACAACTTCCCAATTTCAGA
1 AACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGT---C--ACAACTTCCCAATTTCAGA
* *
36705 GCAAATTTCAACTTCAC-AGCGAAGGATATTGGACCCAAGAC
61 GCCAATTTCAACTTCACGA-CGAAGGATATTGGACTCAAGAC
* *
36746 AACACAAGCTCAACTTCAC-GACGAAGGGGCGGCTGATTGTCA-AA-TT--C-A-TTCAGAGTCA
1 AACACAAGCTCAACTTCACAG-CGAAGGGGCGGCTGACTGTCACAACTTCCCAATTTCAGAGCCA
* *
36804 ATTTCAACTTCACGATGAAGGATATTAGACTCAAGAC
65 ATTTCAACTTCACGACGAAGGATATTGGACTCAAGAC
* * *
36841 AGCACAAGCTCAACTTCACAGCGAAGTGGCGGCTGACTGTCAACAAACAATTTCCCAGTTTCAGA
1 AACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTC-AC-AAC---TTCCCAATTTCAGA
* * *
36906 ACCAATTTCAACTTCACGTCGGAGGATATTGGACT
61 GCCAATTTCAACTTCACGACGAAGGATATTGGACT
36941 AGGAGCAATA
Statistics
Matches: 255, Mismatches: 24, Indels: 37
0.81 0.08 0.12
Matches are distributed among these distances:
95 76 0.30
96 4 0.02
97 1 0.00
98 2 0.01
99 39 0.15
100 2 0.01
101 1 0.00
102 2 0.01
103 1 0.00
104 1 0.00
105 2 0.01
106 124 0.49
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.21
Consensus pattern (101 bp):
AACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCACAACTTCCCAATTTCAGAGCCAA
TTTCAACTTCACGACGAAGGATATTGGACTCAAGAC
Found at i:36800 original size:201 final size:204
Alignment explanation
Indices: 36541--36939 Score: 585
Period size: 201 Copynumber: 2.0 Consensus size: 204
36531 GGGAATCGTG
*
36541 AACACAAGCTCAACTTCACAGCAAAGGGGCGGCTGACTGTCAACTTCCCAATTTCAGAGCCAATT
1 AACACAAGCTCAACTTCACAGCAAAGGGGCGGCTGACTGTCAAATT-CCAATTTCAGAGCCAATT
*
36606 TCAACTTCACAACGAAGGATATTGGACTCAAGAAAACACAAGCTCAACTTAACAGCGAA-TGGGC
65 TCAACTTCACAACGAAGGATATTAGACTCAAGAAAACACAAGCTCAACTTAACAGCGAAGT-GGC
*
36670 GGCTGACTGTCAACAAACAACTTCCCAATTTCAGAGCAAATTTCAACTTCACAG-CGAAGGATAT
129 GGCTGACTGTCAACAAACAACTTCCCAATTTCAGAACAAATTTCAACTTCAC-GTCGAAGGATAT
36734 TGGACCCAAGAC
193 TGGACCCAAGAC
* * *
36746 AACACAAGCTCAACTTCAC-GACGAAGGGGCGGCTGATTGTCAAATT-C-A-TTCAGAGTCAATT
1 AACACAAGCTCAACTTCACAG-CAAAGGGGCGGCTGACTGTCAAATTCCAATTTCAGAGCCAATT
* * * * *
36807 TCAACTTCACGATGAAGGATATTAGACTCAAGACAGCACAAGCTCAACTTCACAGCGAAGTGGCG
65 TCAACTTCACAACGAAGGATATTAGACTCAAGAAAACACAAGCTCAACTTAACAGCGAAGTGGCG
* * * *
36872 GCTGACTGTCAACAAACAATTTCCCAGTTTCAGAACCAATTTCAACTTCACGTCGGAGGATATTG
130 GCTGACTGTCAACAAACAACTTCCCAATTTCAGAACAAATTTCAACTTCACGTCGAAGGATATTG
36937 GAC
195 GAC
36940 TAGGAGCAAT
Statistics
Matches: 176, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
200 1 0.01
201 130 0.74
202 2 0.01
203 1 0.01
204 1 0.01
205 41 0.23
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (204 bp):
AACACAAGCTCAACTTCACAGCAAAGGGGCGGCTGACTGTCAAATTCCAATTTCAGAGCCAATTT
CAACTTCACAACGAAGGATATTAGACTCAAGAAAACACAAGCTCAACTTAACAGCGAAGTGGCGG
CTGACTGTCAACAAACAACTTCCCAATTTCAGAACAAATTTCAACTTCACGTCGAAGGATATTGG
ACCCAAGAC
Found at i:36866 original size:95 final size:95
Alignment explanation
Indices: 36699--36883 Score: 268
Period size: 95 Copynumber: 1.9 Consensus size: 95
36689 ACTTCCCAAT
*
36699 TTCAGAGCAAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCAAATTTCAACTTCACAGCGAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCA
*
36764 CGACGAAGGGGCGGCTGATTGTCAAATTCA
66 CGACGAAGGGGCGGCTGACTGTCAAATTCA
* * *
36794 TTCAGAGTC-AATTTCAACTTCAC-GATGAAGGATATTAGACTCAAGACAGCACAAGCTCAACTT
1 TTCAGAG-CAAATTTCAACTTCACAG-CGAAGGATATTAGACCCAAGACAACACAAGCTCAACTT
*
36857 CAC-AGCGAAGTGGCGGCTGACTGTCAA
64 CACGA-CGAAGGGGCGGCTGACTGTCAA
36884 CAAACAATTT
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
94 2 0.02
95 78 0.96
96 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (95 bp):
TTCAGAGCAAATTTCAACTTCACAGCGAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCA
CGACGAAGGGGCGGCTGACTGTCAAATTCA
Found at i:37516 original size:2 final size:2
Alignment explanation
Indices: 37504--37554 Score: 56
Period size: 2 Copynumber: 26.5 Consensus size: 2
37494 TCCATACAAA
37504 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AGT AT -T AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
37544 AT GAT AT -T AT A
1 AT -AT AT AT AT A
37555 AGTTATAGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
1 4 0.09
2 35 0.81
3 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39028 original size:2 final size:2
Alignment explanation
Indices: 39023--39060 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
39013 AAATATTTAT
39023 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
39061 GTTTATATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41628 original size:22 final size:22
Alignment explanation
Indices: 41603--41653 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
41593 CAAAAATGAG
41603 ATTAAAATGGCTTTGATACCAT
1 ATTAAAATGGCTTTGATACCAT
41625 ATTAAAATGGCTTTGATACCAT
1 ATTAAAATGGCTTTGATACCAT
41647 ATTAAAA
1 ATTAAAA
41654 ACAATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (22 bp):
ATTAAAATGGCTTTGATACCAT
Found at i:43998 original size:38 final size:38
Alignment explanation
Indices: 43934--44009 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
43924 ACCTGTTTTA
* *
43934 GTCTTTCAGCTGAAAACCCTCGGAGCCCATCTGCTACT
1 GTCTTCCAGCTGAAAACCCTCGGAGCCCATCCGCTACT
43972 GTCTTCCAGCT-AAAAGCCCT-GAGAGCCCATCCGCTACT
1 GTCTTCCAGCTGAAAA-CCCTCG-GAGCCCATCCGCTACT
44010 TCAAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 5 0.15
38 29 0.85
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (38 bp):
GTCTTCCAGCTGAAAACCCTCGGAGCCCATCCGCTACT
Found at i:46419 original size:19 final size:18
Alignment explanation
Indices: 46392--46436 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
46382 AAAAATTTCG
*
46392 ATACATTCTACAAGTATCA
1 ATACTTTCTA-AAGTATCA
*
46411 ATACTTTCTAGAGTATCA
1 ATACTTTCTAAAGTATCA
46429 ATACTTTC
1 ATACTTTC
46437 GAGTCTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.38
Consensus pattern (18 bp):
ATACTTTCTAAAGTATCA
Found at i:55582 original size:22 final size:22
Alignment explanation
Indices: 55553--55596 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
55543 TAATAATTGA
*
55553 AAATAATT-ATAAAAATAAAAT
1 AAATAATTCAAAAAAATAAAAT
55574 AAATAAATTCAAAAAAATAAAAT
1 AAAT-AATTCAAAAAAATAAAAT
55597 TTTAAACTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 4 0.20
23 12 0.60
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (22 bp):
AAATAATTCAAAAAAATAAAAT
Found at i:56819 original size:348 final size:348
Alignment explanation
Indices: 56182--56885 Score: 1408
Period size: 348 Copynumber: 2.0 Consensus size: 348
56172 ATGTTCGAAC
56182 TAATCAATAGCTTTTTATTTTCATTTTTCTGCCATAATGTAAAACATAATATGTAAAACATTTTG
1 TAATCAATAGCTTTTTATTTTCATTTTTCTGCCATAATGTAAAACATAATATGTAAAACATTTTG
56247 AAAACAAGTAATAAATCTGGGGTTTGCTATAGTGGTTGAGGTGCTGCTTGAAACTCACTTGATCC
66 AAAACAAGTAATAAATCTGGGGTTTGCTATAGTGGTTGAGGTGCTGCTTGAAACTCACTTGATCC
56312 TTGGTTTGTTTCTTCTCAGCGCCCAGTTACATTTTGTTTCATTTCCCCTTTAAAAAGGTGGCAAC
131 TTGGTTTGTTTCTTCTCAGCGCCCAGTTACATTTTGTTTCATTTCCCCTTTAAAAAGGTGGCAAC
56377 TTGATTGGTGGAAATATCATTCAATTAAAGTATTAAAAATAATTTTAAAAAAGCCACTCATTTAT
196 TTGATTGGTGGAAATATCATTCAATTAAAGTATTAAAAATAATTTTAAAAAAGCCACTCATTTAT
56442 GTCACAACACGTGTAATGAAACATGTCACATTTGACTTGTGTCGTCACATGATTTGAGGGTTAAA
261 GTCACAACACGTGTAATGAAACATGTCACATTTGACTTGTGTCGTCACATGATTTGAGGGTTAAA
56507 TATATTGAATTAATTTAAAATTA
326 TATATTGAATTAATTTAAAATTA
56530 TAATCAATAGCTTTTTATTTTCATTTTTCTGCCATAATGTAAAACATAATATGTAAAACATTTTG
1 TAATCAATAGCTTTTTATTTTCATTTTTCTGCCATAATGTAAAACATAATATGTAAAACATTTTG
56595 AAAACAAGTAATAAATCTGGGGTTTGCTATAGTGGTTGAGGTGCTGCTTGAAACTCACTTGATCC
66 AAAACAAGTAATAAATCTGGGGTTTGCTATAGTGGTTGAGGTGCTGCTTGAAACTCACTTGATCC
56660 TTGGTTTGTTTCTTCTCAGCGCCCAGTTACATTTTGTTTCATTTCCCCTTTAAAAAGGTGGCAAC
131 TTGGTTTGTTTCTTCTCAGCGCCCAGTTACATTTTGTTTCATTTCCCCTTTAAAAAGGTGGCAAC
56725 TTGATTGGTGGAAATATCATTCAATTAAAGTATTAAAAATAATTTTAAAAAAGCCACTCATTTAT
196 TTGATTGGTGGAAATATCATTCAATTAAAGTATTAAAAATAATTTTAAAAAAGCCACTCATTTAT
56790 GTCACAACACGTGTAATGAAACATGTCACATTTGACTTGTGTCGTCACATGATTTGAGGGTTAAA
261 GTCACAACACGTGTAATGAAACATGTCACATTTGACTTGTGTCGTCACATGATTTGAGGGTTAAA
56855 TATATTGAATTAATTTAAAATTA
326 TATATTGAATTAATTTAAAATTA
56878 TAATCAAT
1 TAATCAAT
56886 TTGATAGAAT
Statistics
Matches: 356, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
348 356 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (348 bp):
TAATCAATAGCTTTTTATTTTCATTTTTCTGCCATAATGTAAAACATAATATGTAAAACATTTTG
AAAACAAGTAATAAATCTGGGGTTTGCTATAGTGGTTGAGGTGCTGCTTGAAACTCACTTGATCC
TTGGTTTGTTTCTTCTCAGCGCCCAGTTACATTTTGTTTCATTTCCCCTTTAAAAAGGTGGCAAC
TTGATTGGTGGAAATATCATTCAATTAAAGTATTAAAAATAATTTTAAAAAAGCCACTCATTTAT
GTCACAACACGTGTAATGAAACATGTCACATTTGACTTGTGTCGTCACATGATTTGAGGGTTAAA
TATATTGAATTAATTTAAAATTA
Found at i:66337 original size:16 final size:16
Alignment explanation
Indices: 66312--66354 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
66302 ACAGAGCCTC
66312 TGAATCATTCAACATT
1 TGAATCATTCAACATT
*
66328 TGAATTATTCAACATT
1 TGAATCATTCAACATT
66344 TGAATCATTCA
1 TGAATCATTCA
66355 GCGCTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (16 bp):
TGAATCATTCAACATT
Found at i:72698 original size:21 final size:21
Alignment explanation
Indices: 72673--72717 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
72663 CTAATGTTCA
72673 TTAGTTGGGACTAATACATAT
1 TTAGTTGGGACTAATACATAT
72694 TTAGTTGGGACTAATACATAT
1 TTAGTTGGGACTAATACATAT
72715 TTA
1 TTA
72718 TGACGTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (21 bp):
TTAGTTGGGACTAATACATAT
Found at i:79481 original size:15 final size:15
Alignment explanation
Indices: 79457--79490 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
79447 CCGTAGGACC
*
79457 ACTACATCCCGAAGG
1 ACTACATCCCGAAAG
*
79472 ACTACGTCCCGAAAG
1 ACTACATCCCGAAAG
79487 ACTA
1 ACTA
79491 TTATACTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAAG
Found at i:80072 original size:64 final size:63
Alignment explanation
Indices: 80003--80159 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 63
79993 TAATGAAGGT
* **
80003 ATGCATCGATGCACTACTTGTGCATCGGTGC-ATAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCGAT-AAATGCATTCGATCGTTTTATT-TTAA-AA
80066 G
63 G
* * * * *
80067 ATGCATCGATGCA-TGCCTTATGCATCGATGCGCTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCGATAAATGCATTCGATCGTTTTATTTTAAAAG
*
80130 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
80160 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
63 3 0.04
64 65 0.84
65 9 0.12
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCGATAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:85272 original size:15 final size:15
Alignment explanation
Indices: 85248--85281 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
85238 CCATAGGACC
*
85248 ACTACATCCCGAAGG
1 ACTACATCCCGAAAG
*
85263 ACTACGTCCCGAAAG
1 ACTACATCCCGAAAG
85278 ACTA
1 ACTA
85282 TTATACCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAAG
Found at i:85408 original size:29 final size:29
Alignment explanation
Indices: 85372--85446 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
85362 ATGTTCATTT
*
85372 ACTCATGTTATTTCTCTTGTGATCATATA
1 ACTCATGTCATTTCTCTTGTGATCATATA
*
85401 ACTCATGTCATTTCTCTTGTGATCATGTA
1 ACTCATGTCATTTCTCTTGTGATCATATA
*
85430 GCTCATGTCATGTTCTC
1 ACTCATGTCAT-TTCTC
85447 ATATCACATA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 37 0.88
30 5 0.12
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.45
Consensus pattern (29 bp):
ACTCATGTCATTTCTCTTGTGATCATATA
Found at i:85892 original size:64 final size:63
Alignment explanation
Indices: 85823--85979 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 63
85813 TAATGAAGGT
* **
85823 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAA-AA
85886 G
63 G
* * * *
85887 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
*
85950 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
85980 ACACCTTCAA
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
63 3 0.04
64 66 0.85
65 9 0.12
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:93206 original size:15 final size:15
Alignment explanation
Indices: 93186--93216 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
93176 ATGGTATGAT
93186 AAATAAATGTCTGAA
1 AAATAAATGTCTGAA
93201 AAATAAATGTCTGAA
1 AAATAAATGTCTGAA
93216 A
1 A
93217 GAGCGAAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (15 bp):
AAATAAATGTCTGAA
Found at i:105991 original size:22 final size:23
Alignment explanation
Indices: 105961--106012 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
105951 ACCACCAGTA
*
105961 TTTTTTATTGTCT-T-TTTTCTT
1 TTTTTTATTCTCTCTATTTTCTT
105982 TTTTTATATTCTCTCTATTTTCTT
1 TTTTT-TATTCTCTCTATTTTCTT
106006 TTATTTT
1 TT-TTTT
106013 TTAATTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.19
22 7 0.27
23 1 0.04
24 10 0.38
25 3 0.12
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTTTTATTCTCTCTATTTTCTT
Found at i:106441 original size:21 final size:21
Alignment explanation
Indices: 106407--106450 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
106397 ATTATGTGCT
* * *
106407 AAATTTACGTTTGTTATTGTA
1 AAATTTACGATTGTAATTATA
*
106428 AAATTTATGATTGTAATTATA
1 AAATTTACGATTGTAATTATA
106449 AA
1 AA
106451 TCTTTATTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (21 bp):
AAATTTACGATTGTAATTATA
Found at i:109409 original size:11 final size:12
Alignment explanation
Indices: 109391--109419 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
109381 AAGCTAAAAG
109391 ATATATGTATGT
1 ATATATGTATGT
109403 A-ATATGTATGT
1 ATATATGTATGT
109414 ATATAT
1 ATATAT
109420 ATATACATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (12 bp):
ATATATGTATGT
Found at i:130922 original size:20 final size:20
Alignment explanation
Indices: 130838--131034 Score: 166
Period size: 20 Copynumber: 9.8 Consensus size: 20
130828 AATGACTAAT
**
130838 AAATTCGCAACGCGAACTCC
1 AAATTCGCAACGCGATTTCC
* * *
130858 AATTTCGCAACAC-AGTTTCA
1 AAATTCGCAACGCGA-TTTCC
* **
130878 AAATTCGCAACGCGTATATGT
1 AAATTCGCAACGCG-ATTTCC
130899 AAA-TCGCAACGCGATTTTCC
1 AAATTCGCAACGCGA-TTTCC
*
130919 AAATTCACAACGCGATTTCC
1 AAATTCGCAACGCGATTTCC
*
130939 AAATTCACAACGCGATTTCC
1 AAATTCGCAACGCGATTTCC
* *
130959 AAATTCACAACGCGATTTTC
1 AAATTCGCAACGCGATTTCC
* *
130979 AAATTTGCAACACTGAATTT-C
1 AAATTCGCAACGC-G-ATTTCC
* * *
131000 AAATCCGCAACTCGATTTCT
1 AAATTCGCAACGCGATTTCC
*
131020 GAATTCGCAACGCGA
1 AAATTCGCAACGCGA
131035 ATTTTGTTTT
Statistics
Matches: 144, Mismatches: 25, Indels: 16
0.78 0.14 0.09
Matches are distributed among these distances:
19 6 0.04
20 106 0.74
21 27 0.19
22 5 0.03
ACGTcount: A:0.34, C:0.27, G:0.13, T:0.26
Consensus pattern (20 bp):
AAATTCGCAACGCGATTTCC
Found at i:131003 original size:61 final size:61
Alignment explanation
Indices: 130905--131039 Score: 148
Period size: 61 Copynumber: 2.2 Consensus size: 61
130895 ATGTAAATCG
* *
130905 CAACGCGATTTTCCAAATTCACAACGCGATTTCCAAATTCACAACGCGATTTCCAAATTCA
1 CAACGCGATTTTCCAAATTCACAACACGATTTCCAAATCCACAACGCGATTTCCAAATTCA
** * * ** *
130966 CAACGCGATTTT-CAAATTTGCAACACTGAATTT-CAAATCCGCAACTCGATTTCTGAATTCG
1 CAACGCGATTTTCCAAATTCACAACAC-G-ATTTCCAAATCCACAACGCGATTTCCAAATTCA
131027 CAACGCGAATTTT
1 CAACGCG-ATTTT
131040 GTTTTCGCAA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
60 11 0.18
61 42 0.68
62 9 0.15
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.29
Consensus pattern (61 bp):
CAACGCGATTTTCCAAATTCACAACACGATTTCCAAATCCACAACGCGATTTCCAAATTCA
Found at i:131066 original size:20 final size:20
Alignment explanation
Indices: 130838--131070 Score: 161
Period size: 20 Copynumber: 11.6 Consensus size: 20
130828 AATGACTAAT
** *
130838 AAATTCGCAACGCGAACTCC
1 AAATTCGCAACGCGATTTTC
* * *
130858 AATTTCGCAACAC-AGTTTC
1 AAATTCGCAACGCGATTTTC
*
130877 AAAATTCGCAACGCGTATATGT-
1 -AAATTCGCAACGCG-AT-TTTC
130899 AAA-TCGCAACGCGATTTTCC
1 AAATTCGCAACGCGATTTT-C
* *
130919 AAATTCACAACGCGATTTCC
1 AAATTCGCAACGCGATTTTC
* *
130939 AAATTCACAACGCGATTTCC
1 AAATTCGCAACGCGATTTTC
*
130959 AAATTCACAACGCGATTTTC
1 AAATTCGCAACGCGATTTTC
* * *
130979 AAATTTGCAACACTGAATTTC
1 AAATTCGCAACGC-GATTTTC
* *
131000 AAATCCGCAACTCGA-TTTC
1 AAATTCGCAACGCGATTTTC
*
131019 TGAATTCGCAACGCGAATTTT-
1 -AAATTCGCAACGCG-ATTTTC
*** *
131040 GTTTTCGCAACTCGATTTTC
1 AAATTCGCAACGCGATTTTC
*
131060 GAATTCGCAAC
1 AAATTCGCAAC
131071 ATGTTTTATT
Statistics
Matches: 173, Mismatches: 28, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
18 2 0.01
19 14 0.08
20 118 0.68
21 33 0.19
22 4 0.02
23 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.28
Consensus pattern (20 bp):
AAATTCGCAACGCGATTTTC
Found at i:131873 original size:12 final size:12
Alignment explanation
Indices: 131852--131885 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
131842 ACCACATTTC
*
131852 CAATACCAAACA
1 CAATATCAAACA
131864 CAATATCAAACA
1 CAATATCAAACA
*
131876 CAATCTCAAA
1 CAATATCAAA
131886 ACCCACAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:132038 original size:24 final size:24
Alignment explanation
Indices: 132011--132064 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
132001 GTATTCAAAA
*
132011 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTAGGTCAATACCCGGAC
* *
132035 TTTGATCTAGGTCAATACTCGGAT
1 TTTGATCTAGGTCAATACCCGGAC
132059 TTTGAT
1 TTTGAT
132065 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATCTAGGTCAATACCCGGAC
Found at i:134913 original size:207 final size:206
Alignment explanation
Indices: 134551--135160 Score: 967
Period size: 207 Copynumber: 2.9 Consensus size: 206
134541 TCCAAATACA
*
134551 TTCATGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTAC
1 TTCACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTAC
* *
134616 ACATCTAAAACCAATAAACATCAAATTATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACC
66 ACATCTAAAACCAACAAACAACAAATTATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACC
*
134681 AAAAAGTATATAACAGTTAACAACACTTGCATAAACTTGCTAATAACAACTGGTTGTTTATGCAC
131 AACAAGTATATAACAGTTAACAACACTTGCATAAACTT-CTAATAACAACTGGTTGTTTATGCAC
134746 AAATACATCAAT
195 AAATACATCAAT
*
134758 TTCACGTAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTAC
1 TTCACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTAC
134823 ACATCTAAAACCAACAAACAACAAATTATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACC
66 ACATCTAAAACCAACAAACAACAAATTATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACC
* * *
134888 AACAAGTATATAACAGTTAACAACACTTGCACAAACTTACCAATAATAACTGGTTGTTTATGCAC
131 AACAAGTATATAACAGTTAACAACACTTGCATAAACTT-CTAATAACAACTGGTTGTTTATGCAC
134953 AAATACATCAAT
195 AAATACATCAAT
* * *
134965 TTCACGCAGCTCACTTCAGGATTAACCTACAGAAACCAAACATTTGCTCAAACAACACTTTTTAT
1 TTCACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTAC
* * *
135030 ACGTCTAAAACCAACAAACAACAAATTATTAAATTTTAGGTACTT-AACCAAACATTTTCAAACC
66 ACATCTAAAACCAACAAACAACAAATTATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACC
* * * *
135094 AACAAAG-AGTATATA-TGTTAACAACGCTTGC-TCAAACTTATCAATAACAAATGGTTGTTTAT
131 AAC-AAGTA-TATA-ACAGTTAACAACACTTGCAT-AAACTTCT-AATAACAACTGGTTGTTTAT
135156 GCACA
191 GCACA
135161 CTTTCAGCCG
Statistics
Matches: 375, Mismatches: 23, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
206 23 0.06
207 351 0.94
208 1 0.00
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (206 bp):
TTCACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTAC
ACATCTAAAACCAACAAACAACAAATTATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACC
AACAAGTATATAACAGTTAACAACACTTGCATAAACTTCTAATAACAACTGGTTGTTTATGCACA
AATACATCAAT
Found at i:136273 original size:21 final size:21
Alignment explanation
Indices: 136247--136306 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
136237 GTGAATCGGG
* **
136247 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGACAGGGAC
*
136268 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATGACAGGGAC
*
136289 CTCTTGAATGATGACAGG
1 CTCTTGAACGATGACAGG
136307 TGAAGCGGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGACAGGGAC
Found at i:136455 original size:4 final size:4
Alignment explanation
Indices: 136446--136487 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
136436 GGGCCGCTAA
* * *
136446 AAAT AAAT AAAT ACAT AAAT CAGT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
136488 TGCCGAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:136734 original size:21 final size:21
Alignment explanation
Indices: 136710--136755 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
136700 ACCATTGTCG
*
136710 TCACGTAAAGTACCGACCTCA
1 TCACGCAAAGTACCGACCTCA
*
136731 TCACGCAAAGTACTGACCTCA
1 TCACGCAAAGTACCGACCTCA
136752 TCAC
1 TCAC
136756 ATAACTCCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.35, G:0.13, T:0.20
Consensus pattern (21 bp):
TCACGCAAAGTACCGACCTCA
Found at i:138181 original size:19 final size:19
Alignment explanation
Indices: 138129--138190 Score: 88
Period size: 20 Copynumber: 3.2 Consensus size: 19
138119 GAGTAGTTAT
*
138129 CGAAACTTAAATTCGCAACG
1 CGAAAC-TAAAATCGCAACG
*
138149 CGAAAATGAAAATCGCAACG
1 CGAAACT-AAAATCGCAACG
138169 CGAAACTAAAATCGCAACG
1 CGAAACTAAAATCGCAACG
138188 CGA
1 CGA
138191 TTTTCGTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 16 0.42
20 22 0.58
ACGTcount: A:0.45, C:0.24, G:0.18, T:0.13
Consensus pattern (19 bp):
CGAAACTAAAATCGCAACG
Found at i:138576 original size:22 final size:22
Alignment explanation
Indices: 138551--138604 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
138541 AAGATAGACT
* *
138551 GATTTCGCCGGAGATGGTGATG
1 GATTTCGCCGGAGATGGGGACG
*
138573 GATTTTGCCGGAGATGGGGACG
1 GATTTCGCCGGAGATGGGGACG
*
138595 GATGTCGCCG
1 GATTTCGCCG
138605 TAGAGAGGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.17, C:0.17, G:0.43, T:0.24
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACG
Found at i:138793 original size:20 final size:20
Alignment explanation
Indices: 138770--138861 Score: 69
Period size: 21 Copynumber: 4.5 Consensus size: 20
138760 TGACTTCTGT
*
138770 GTTGCGAATTACAAATTCGC
1 GTTGCGAATTACAAAATCGC
* **
138790 GTTGTGAATTTGAAAATCGC
1 GTTGCGAATTACAAAATCGC
*
138810 GTTACGAATTTGA-AAAATCGC
1 GTTGCGAA-TT-ACAAAATCGC
* **
138831 GTTGTGAATTTGGAAAATCGC
1 GTTGCGAA-TTACAAAATCGC
*
138852 GTTACGAATT
1 GTTGCGAATT
138862 TGGAAACTAT
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
20 24 0.42
21 33 0.58
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.33
Consensus pattern (20 bp):
GTTGCGAATTACAAAATCGC
Found at i:138864 original size:21 final size:21
Alignment explanation
Indices: 138786--138867 Score: 112
Period size: 21 Copynumber: 4.0 Consensus size: 21
138776 AATTACAAAT
**
138786 TCGCGTTGTGAATTT-GAAAA
1 TCGCGTTACGAATTTGGAAAA
*
138806 TCGCGTTACGAATTTGAAAAA
1 TCGCGTTACGAATTTGGAAAA
**
138827 TCGCGTTGTGAATTTGGAAAA
1 TCGCGTTACGAATTTGGAAAA
138848 TCGCGTTACGAATTTGGAAA
1 TCGCGTTACGAATTTGGAAA
138868 CTATATTGCG
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 13 0.25
21 40 0.75
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (21 bp):
TCGCGTTACGAATTTGGAAAA
Found at i:139096 original size:20 final size:21
Alignment explanation
Indices: 139071--139115 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
139061 AGATTTCGAC
139071 ATTTGGTTACA-AGTTGATTT
1 ATTTGGTTACATAGTTGATTT
*
139091 ATTTGGTTACATCGTTGATTT
1 ATTTGGTTACATAGTTGATTT
139112 ATTT
1 ATTT
139116 ATATATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.22, C:0.07, G:0.18, T:0.53
Consensus pattern (21 bp):
ATTTGGTTACATAGTTGATTT
Found at i:140164 original size:3 final size:3
Alignment explanation
Indices: 140156--140198 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
140146 AAATAAAATA
*
140156 TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
140199 TAGATAAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:140406 original size:3 final size:3
Alignment explanation
Indices: 140398--140456 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
140388 TTGTCGGTAT
*
140398 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TCA -TA TCT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA T-TA TTA TTA TTA
140443 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
140457 TATTTTTAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
2 2 0.04
3 44 0.88
4 4 0.08
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:141968 original size:15 final size:15
Alignment explanation
Indices: 141931--141968 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
141921 GGTATTTAGT
* *
141931 GGGCGGGCGGATGTG
1 GGGCGGGTGGATGCG
141946 GGGCGGGTGGATGCG
1 GGGCGGGTGGATGCG
141961 GGGCGGGT
1 GGGCGGGT
141969 AAGGTCTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.13, G:0.68, T:0.13
Consensus pattern (15 bp):
GGGCGGGTGGATGCG
Found at i:142240 original size:17 final size:17
Alignment explanation
Indices: 142198--142275 Score: 93
Period size: 17 Copynumber: 4.5 Consensus size: 17
142188 ATAATCTATG
142198 TCTGATAACTGTAAAGCA
1 TCTGATAACTGTAAA-CA
*
142216 CCTGATAACTGTAAACA
1 TCTGATAACTGTAAACA
* *
142233 TATGATAACTGTAAATA
1 TCTGATAACTGTAAACA
**
142250 TCTGATAACTAAAAATCA
1 TCTGATAACTGTAAA-CA
142268 TCTGATAA
1 TCTGATAA
142276 TTATAAATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
17 28 0.55
18 23 0.45
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (17 bp):
TCTGATAACTGTAAACA
Found at i:142274 original size:35 final size:34
Alignment explanation
Indices: 142198--142293 Score: 102
Period size: 35 Copynumber: 2.8 Consensus size: 34
142188 ATAATCTATG
* * **
142198 TCTGATAACTGTAAAGCACCTGATAACTGTAAACA
1 TCTGATAACTGTAAA-TATCTGATAACTAAAAACA
*
142233 TATGATAACTGTAAATATCTGATAACTAAAAATCA
1 TCTGATAACTGTAAATATCTGATAACTAAAAA-CA
* * *
142268 TCTGATAATTATAAATATCTAATAAC
1 TCTGATAACTGTAAATATCTGATAAC
142294 GGTGAAGTGT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
34 13 0.25
35 38 0.75
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (34 bp):
TCTGATAACTGTAAATATCTGATAACTAAAAACA
Found at i:142292 original size:17 final size:17
Alignment explanation
Indices: 142198--142293 Score: 84
Period size: 17 Copynumber: 5.5 Consensus size: 17
142188 ATAATCTATG
* *
142198 TCTGATAACTGTAAAGCA
1 TCTGATAACTATAAA-TA
* * *
142216 CCTGATAACTGTAAACA
1 TCTGATAACTATAAATA
* *
142233 TATGATAACTGTAAATA
1 TCTGATAACTATAAATA
*
142250 TCTGATAACTAAAAATCA
1 TCTGATAACTATAAAT-A
*
142268 TCTGATAATTATAAATA
1 TCTGATAACTATAAATA
*
142285 TCTAATAAC
1 TCTGATAAC
142294 GGTGAAGTGT
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
17 37 0.56
18 29 0.44
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (17 bp):
TCTGATAACTATAAATA
Found at i:143359 original size:16 final size:18
Alignment explanation
Indices: 143328--143371 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
143318 AATTTAAACT
*
143328 TAAATATAAAATTCGATA
1 TAAAAATAAAATTCGATA
143346 -AAAAATAAAA-TCGATA
1 TAAAAATAAAATTCGATA
*
143362 TAAAACTAAA
1 TAAAAATAAA
143372 TCGTATTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.25
Consensus pattern (18 bp):
TAAAAATAAAATTCGATA
Found at i:150904 original size:13 final size:13
Alignment explanation
Indices: 150886--150911 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
150876 TCACCTAATC
150886 TAACTGAGAAAAG
1 TAACTGAGAAAAG
150899 TAACTGAGAAAAG
1 TAACTGAGAAAAG
150912 GTTTGAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (13 bp):
TAACTGAGAAAAG
Found at i:153480 original size:18 final size:19
Alignment explanation
Indices: 153430--153496 Score: 91
Period size: 19 Copynumber: 3.6 Consensus size: 19
153420 CATTATGTCC
*
153430 TTCCACGTTACTGTTCTAA
1 TTCCACATTACTGTTCTAA
**
153449 TTCCACCGTACTGTTCTAA
1 TTCCACATTACTGTTCTAA
153468 TTCCA-ATTACTGTTCTAA
1 TTCCACATTACTGTTCTAA
*
153486 TTCGACATTAC
1 TTCCACATTAC
153497 ACTCCAGAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
18 15 0.36
19 27 0.64
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.40
Consensus pattern (19 bp):
TTCCACATTACTGTTCTAA
Found at i:155793 original size:21 final size:22
Alignment explanation
Indices: 155763--155803 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
155753 AGGTACTATG
155763 GTTTTGTGA-TTTAGTAAAATT
1 GTTTTGTGATTTTAGTAAAATT
*
155784 GTTTTTTGATTTTAGTAAAA
1 GTTTTGTGATTTTAGTAAAA
155804 GATAGAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (22 bp):
GTTTTGTGATTTTAGTAAAATT
Found at i:157691 original size:17 final size:17
Alignment explanation
Indices: 157669--157712 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
157659 CAAGAGTCTG
157669 AAAAGAAAGGAAAAATA
1 AAAAGAAAGGAAAAATA
157686 AAAAGAAAGGAAAAATA
1 AAAAGAAAGGAAAAATA
157703 AAAAGAAAGG
1 AAAAGAAAGG
157713 CTTCGGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (17 bp):
AAAAGAAAGGAAAAATA
Found at i:158083 original size:17 final size:17
Alignment explanation
Indices: 158052--158095 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
158042 TCAACAAAAA
158052 AATCACCAA-CTATATC
1 AATCACCAATCTATATC
158068 AATCACCAATCTATATC
1 AATCACCAATCTATATC
*
158085 AATCATCAATC
1 AATCACCAATC
158096 ATGCAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (17 bp):
AATCACCAATCTATATC
Found at i:161333 original size:28 final size:30
Alignment explanation
Indices: 161292--161361 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
161282 TGAAAATGTA
161292 TAATAAA-AT-AAATAAT-TAT-TAAAAAG
1 TAATAAATATAAAATAATATATATAAAAAG
* *
161318 TAA-AAATAATAAAATAATATATATTAATAG
1 TAATAAAT-ATAAAATAATATATATAAAAAG
161348 TAATAAATATAAAA
1 TAATAAATATAAAA
161362 AGGGGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
25 3 0.08
26 3 0.08
27 2 0.06
28 7 0.19
29 3 0.08
30 14 0.39
31 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (30 bp):
TAATAAATATAAAATAATATATATAAAAAG
Found at i:161408 original size:18 final size:18
Alignment explanation
Indices: 161387--161428 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
161377 ATTATTTTTA
*
161387 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
161405 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
161423 AAATAA
1 AAATAA
161429 GCAAATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:162086 original size:12 final size:12
Alignment explanation
Indices: 162071--162098 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
162061 TACCTAAAAA
162071 AAATAATATTCT
1 AAATAATATTCT
162083 AAATAATATTCT
1 AAATAATATTCT
162095 AAAT
1 AAAT
162099 CCTAATTAAA
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:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATAATATTCT
Found at i:162104 original size:73 final size:75
Alignment explanation
Indices: 162021--162212 Score: 264
Period size: 76 Copynumber: 2.6 Consensus size: 75
162011 TAAAACATCT
* * **
162021 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAA-AAA-ATAATAT-TCT
1 TAAATCCTAATTAAAATAC-TAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
*
162083 AAATAATATTC
65 AAATAATATCC
*
162094 TAAATCCTAATTAAAATACTAAAACATATTTAAACTAAAATACTTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAAC-TATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
162159 AAATAATATCC
65 AAATAATATCC
* *
162170 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
1 TAAATCCTAATTAAAATACTAAAA-CTATTTAAACTAAAATAC
162213 AAAGATAAAA
Statistics
Matches: 106, Mismatches: 8, Indels: 7
0.88 0.07 0.06
Matches are distributed among these distances:
72 6 0.06
73 40 0.38
74 3 0.03
75 6 0.06
76 50 0.47
77 1 0.01
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.30
Consensus pattern (75 bp):
TAAATCCTAATTAAAATACTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAA
AATAATATCC
Found at i:162152 original size:25 final size:24
Alignment explanation
Indices: 162105--162152 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
162095 AAATCCTAAT
* **
162105 TAAAATACTAAAACATATTTAAAC
1 TAAAATACTAAAACAAAGATAAAC
162129 TAAAATACTTAAAACAAAGATAAA
1 TAAAATAC-TAAAACAAAGATAAA
162153 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.25
Consensus pattern (24 bp):
TAAAATACTAAAACAAAGATAAAC
Found at i:162236 original size:76 final size:73
Alignment explanation
Indices: 162021--162248 Score: 248
Period size: 76 Copynumber: 3.1 Consensus size: 73
162011 TAAAACATCT
* * *
162021 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAAAAA-ATAATATTCT-
1 TAAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATA-CAAAAAAAATATAATATT-TA
*
162083 AAATAATATTC
63 AAATAATATCC
* * * *
162094 TAAATCCTAATTAAAATACTAAAACATATTTAAACTAAAATACTTAAAACAAAGATAAAATA-TA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC--AAAA-AAA-ATATAATATTT
162158 AAAATAATATCC
62 AAAATAATATCC
* *
162170 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAA-A-AAAATATAATATTTAA
*
162235 AATATTATCC
64 AATAATATCC
162245 TAAA
1 TAAA
162249 CTTGAGTTTA
Statistics
Matches: 132, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
72 6 0.05
73 34 0.26
74 12 0.09
75 23 0.17
76 52 0.39
77 5 0.04
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (73 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAAAAAATATAATATTTAAAA
TAATATCC
Found at i:163787 original size:3 final size:3
Alignment explanation
Indices: 163739--163774 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
163729 TTTTTAAAAG
*
163739 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
163775 TGATAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 29 0.97
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:173212 original size:15 final size:15
Alignment explanation
Indices: 173192--173227 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
173182 TCCCGAAGAA
173192 TTTCCAATTGTTGAG
1 TTTCCAATTGTTGAG
173207 TTTCCAATTGTTGAG
1 TTTCCAATTGTTGAG
173222 TTTCCA
1 TTTCCA
173228 TAGTCGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (15 bp):
TTTCCAATTGTTGAG
Found at i:175015 original size:22 final size:19
Alignment explanation
Indices: 174957--175018 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
174947 AAAACCAAAA
174957 CCCC-AGGGGGTATCGATT
1 CCCCTAGGGGGTATCGATT
* *
174975 CCCCTAGGAGGAATCGATT
1 CCCCTAGGGGGTATCGATT
174994 CCCCTTCAAGGGGGTATCGATT
1 CCCC-T--AGGGGGTATCGATT
175016 CCC
1 CCC
175019 TCTGCCCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.11
19 16 0.44
20 1 0.03
22 15 0.42
ACGTcount: A:0.19, C:0.31, G:0.27, T:0.23
Consensus pattern (19 bp):
CCCCTAGGGGGTATCGATT
Found at i:180897 original size:22 final size:23
Alignment explanation
Indices: 180853--180898 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
180843 CCATTCAGGA
180853 GGGAATCGGTACCCCCTTGGGGG
1 GGGAATCGGTACCCCCTTGGGGG
*
180876 GGGAATCGGTTCCCCCTTGGGGG
1 GGGAATCGGTACCCCCTTGGGGG
180899 AAAGCGGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.11, C:0.26, G:0.43, T:0.20
Consensus pattern (23 bp):
GGGAATCGGTACCCCCTTGGGGG
Found at i:180906 original size:21 final size:22
Alignment explanation
Indices: 180859--180910 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
180849 AGGAGGGAAT
* * *
180859 CGGTACCCCCTTGGGGGGGGAAT
1 CGGTTCCCCCTT-GGGGGGAAAG
180882 CGGTTCCCCCTT-GGGGGAAAG
1 CGGTTCCCCCTTGGGGGGAAAG
180903 CGGTTCCC
1 CGGTTCCC
180911 TCTGGACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 15 0.58
23 11 0.42
ACGTcount: A:0.12, C:0.31, G:0.38, T:0.19
Consensus pattern (22 bp):
CGGTTCCCCCTTGGGGGGAAAG
Found at i:189820 original size:22 final size:22
Alignment explanation
Indices: 189779--189859 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
189769 CTCGTATAAA
189779 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
189802 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
189824 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
189846 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
189860 ATATAATGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 45 0.79
23 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:189855 original size:13 final size:13
Alignment explanation
Indices: 189793--189855 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
189783 CCGAAGTGCC
189793 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
189806 CC---GAAGTGC-
1 CCGTAGAATTGCA
189815 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
189828 CC---GAAGTGC-
1 CCGTAGAATTGCA
189837 CCGTAGAATTGCA
1 CCGTAGAATTGCA
189850 CCGTAG
1 CCGTAG
189856 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:190109 original size:149 final size:149
Alignment explanation
Indices: 189839--190141 Score: 579
Period size: 149 Copynumber: 2.0 Consensus size: 149
189829 CGAAGTGCCC
*
189839 GTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
1 GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
189904 ATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATAC
66 ATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATAC
189969 ATATGTCCTAAAGAACCGA
131 ATATGTCCTAAAGAACCGA
*
189988 GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTTCTTAAGAATC
1 GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
190053 ATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATAC
66 ATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATAC
*
190118 ATATGTCCTAAAGAACCGC
131 ATATGTCCTAAAGAACCGA
190137 GTAGA
1 GTAGA
190142 CCCTCTACCC
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (149 bp):
GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
ATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATAC
ATATGTCCTAAAGAACCGA
Found at i:190256 original size:24 final size:26
Alignment explanation
Indices: 190229--190289 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 26
190219 TATCGCGTAG
190229 ACATAGTAT-TTT-CATACCTTTATC
1 ACATAGTATATTTACATACCTTTATC
190253 ACATAGGCATATCATTTACATACCTTTATC
1 ACATA-G--TAT-ATTTACATACCTTTATC
190283 ACATAGT
1 ACATAGT
190290 TCATATAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
24 5 0.16
25 1 0.03
27 4 0.13
29 4 0.13
30 17 0.55
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (26 bp):
ACATAGTATATTTACATACCTTTATC
Found at i:190758 original size:67 final size:67
Alignment explanation
Indices: 190644--190794 Score: 221
Period size: 67 Copynumber: 2.3 Consensus size: 67
190634 TTTTTCTCAT
* * * *
190644 GGGGGAATCGGTTCGCCCCTGTGGGTATCGATTCCCCACAAGCATTCTGGAATTTCATATACGAT
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACAAGCATTCTGGAAATTCATATACGAT
190709 GA
66 GA
* * * * *
190711 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATCCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACAAGCATTCTGGAAATTCATATACGAT
190776 GA
66 GA
190778 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
190795 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
67 75 1.00
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACAAGCATTCTGGAAATTCATATACGAT
GA
Found at i:196602 original size:21 final size:22
Alignment explanation
Indices: 196541--196620 Score: 126
Period size: 22 Copynumber: 3.6 Consensus size: 22
196531 CTCGTATAAA
*
196541 TGCACCAAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
196564 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
196586 TGCACCGAAGT-CCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
196607 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
196621 ATATAATGAT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
21 20 0.37
22 23 0.43
23 11 0.20
ACGTcount: A:0.26, C:0.30, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:196881 original size:144 final size:143
Alignment explanation
Indices: 196602--196888 Score: 508
Period size: 144 Copynumber: 2.0 Consensus size: 143
196592 GAAGTCCCGT
*
196602 AGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAGAATCATA
1 AGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAGAATCATA
196667 TACATATACTATGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATCATA
66 TACATATACTATGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATCATA
196732 TTCCTAAAGAACCG
131 TTCCT-AAGAACCG
196746 AGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCAT
1 AGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTT-AGAATCAT
196811 ATACA-ATACTAT-GGATCAAGTAT-TGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATACA
65 ATACATATACTATGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATAT-CA
196873 TATGTCCTAAGAACCG
129 TAT-TCCTAAGAACCG
196889 CGTAGACCCT
Statistics
Matches: 139, Mismatches: 1, Indels: 7
0.95 0.01 0.05
Matches are distributed among these distances:
142 36 0.26
143 24 0.17
144 66 0.47
145 13 0.09
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (143 bp):
AGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAGAATCATA
TACATATACTATGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATCATA
TTCCTAAGAACCG
Found at i:197516 original size:65 final size:67
Alignment explanation
Indices: 197404--197551 Score: 201
Period size: 65 Copynumber: 2.2 Consensus size: 67
197394 TTTTTCTCAT
* *
197404 GGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCACAAGCATTCTGGAATTTCATATACGAT
1 GGGGTATCGG-TCCCCCCCTGGGGGTATCGATTCCCCACAAGCATTCTGGAAATTCATATACGAT
197469 GA-
65 GAG
* * * * *
197471 GGGGTATCGGTCCCCCCCT-GGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATCCGTTG
1 GGGGTATCGGTCCCCCCCTGGGGGTATCGATTCCCCACAAGCATTCTGGAAATTCATATACGATG
197535 AG
66 AG
*
197537 GGGGTATCGTTCCCC
1 GGGGTATCGGTCCCC
197552 TTGAATGGGT
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
65 40 0.56
66 23 0.32
67 9 0.12
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTCCCCCCCTGGGGGTATCGATTCCCCACAAGCATTCTGGAAATTCATATACGATG
AG
Found at i:198492 original size:13 final size:13
Alignment explanation
Indices: 198471--198504 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
198461 TATCTTATTT
*
198471 TTATTTTTAGGAA
1 TTATATTTAGGAA
198484 TTATATTTAGGAA
1 TTATATTTAGGAA
*
198497 TCATATTT
1 TTATATTT
198505 TATTTTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (13 bp):
TTATATTTAGGAA
Found at i:200200 original size:32 final size:33
Alignment explanation
Indices: 200159--200249 Score: 107
Period size: 32 Copynumber: 2.8 Consensus size: 33
200149 CCTAAGGTGA
*
200159 CCCTTGGGTAGGCTCTTAGGCTC-CTAGATG-TT
1 CCCTTGGGTAGGCTCTTAGGC-CACAAGATGCTT
* *
200191 CCCTTGGGTAAGCTCTCAGGCCACAAGATGCTT
1 CCCTTGGGTAGGCTCTTAGGCCACAAGATGCTT
* *
200224 -CCTTAGGTAGGCTCTTAGGACACAAG
1 CCCTTGGGTAGGCTCTTAGGCCACAAG
200250 GTATTACTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 1 0.02
32 47 0.94
33 2 0.04
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.27
Consensus pattern (33 bp):
CCCTTGGGTAGGCTCTTAGGCCACAAGATGCTT
Found at i:201540 original size:2 final size:2
Alignment explanation
Indices: 201535--201560 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
201525 ATTAAATTCC
201535 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
201561 ATAAGTTATT
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):
TA
Found at i:205210 original size:383 final size:383
Alignment explanation
Indices: 204503--205265 Score: 1508
Period size: 383 Copynumber: 2.0 Consensus size: 383
204493 ACAAAGACAT
204503 AGATAAACGTGCCATAGAGGCAGAACTATTCTTATTAAAAAAACTAAAAAAGAACAAAGAGAAAA
1 AGATAAACGTGCCATAGAGGCAGAACTATTCTTATTAAAAAAACTAAAAAAGAACAAAGAGAAAA
204568 GAAAATCGACGGTCGACAAACAACATCAAAATTAATACCGCCGTCGGCTAATAAAATAAAAAAAT
66 GAAAATCGACGGTCGACAAACAACATCAAAATTAATACCGCCGTCGGCTAATAAAATAAAAAAAT
204633 AACATAATCTATAAAAAGCGACAAAAACTCAAAGTAAAAAAAAATCTCATATGTTGTACAAAAAT
131 AACATAATCTATAAAAAGCGACAAAAACTCAAAGTAAAAAAAAATCTCATATGTTGTACAAAAAT
204698 ATTTTTGCAAACATATTTTACATTTCCACCAATTATCATATGTTGAAATATTTTTTTGTGAATAT
196 ATTTTTGCAAACATATTTTACATTTCCACCAATTATCATATGTTGAAATATTTTTTTGTGAATAT
204763 ATATATTTTTATTTAAAATATTTTTGTTCACCTTATGGATATGTTAAAATCTAGTATATATTTAC
261 ATATATTTTTATTTAAAATATTTTTGTTCACCTTATGGATATGTTAAAATCTAGTATATATTTAC
204828 TTTTTTGATAATTTTATGAAATAAAATTATAATTATGATTAAAAATATATTTATTCAG
326 TTTTTTGATAATTTTATGAAATAAAATTATAATTATGATTAAAAATATATTTATTCAG
*
204886 AGATAAACGTGCCATAGAGGCAGAACTATTCTTATTAAAAAAATTAAAAAAGAACAAAGAGAAAA
1 AGATAAACGTGCCATAGAGGCAGAACTATTCTTATTAAAAAAACTAAAAAAGAACAAAGAGAAAA
*
204951 GAAAATCGACGGTCGACAACCAACATCAAAATTAATACCGCCGTCGGCTAATAAAATAAAAAAAT
66 GAAAATCGACGGTCGACAAACAACATCAAAATTAATACCGCCGTCGGCTAATAAAATAAAAAAAT
205016 AACATAATCTATAAAAAGCGACAAAAACTCAAAGTAAAAAAAAATCTCATATGTTGTACAAAAAT
131 AACATAATCTATAAAAAGCGACAAAAACTCAAAGTAAAAAAAAATCTCATATGTTGTACAAAAAT
205081 ATTTTTGCAAACATATTTTACATTTCCACCAATTATCATATGTTGAAATATTTTTTTGTGAATAT
196 ATTTTTGCAAACATATTTTACATTTCCACCAATTATCATATGTTGAAATATTTTTTTGTGAATAT
205146 ATATATTTTTATTTAAAATATTTTTGTTCACCTTATGGATATGTTAAAATCTAGTATATATTTAC
261 ATATATTTTTATTTAAAATATTTTTGTTCACCTTATGGATATGTTAAAATCTAGTATATATTTAC
205211 TTTTTTGATAATTTTATGAAATAAAATTATAATTATGATTAAAAATATATTTATT
326 TTTTTTGATAATTTTATGAAATAAAATTATAATTATGATTAAAAATATATTTATT
205266 TAATTAGGAT
Statistics
Matches: 378, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
383 378 1.00
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (383 bp):
AGATAAACGTGCCATAGAGGCAGAACTATTCTTATTAAAAAAACTAAAAAAGAACAAAGAGAAAA
GAAAATCGACGGTCGACAAACAACATCAAAATTAATACCGCCGTCGGCTAATAAAATAAAAAAAT
AACATAATCTATAAAAAGCGACAAAAACTCAAAGTAAAAAAAAATCTCATATGTTGTACAAAAAT
ATTTTTGCAAACATATTTTACATTTCCACCAATTATCATATGTTGAAATATTTTTTTGTGAATAT
ATATATTTTTATTTAAAATATTTTTGTTCACCTTATGGATATGTTAAAATCTAGTATATATTTAC
TTTTTTGATAATTTTATGAAATAAAATTATAATTATGATTAAAAATATATTTATTCAG
Found at i:207248 original size:2 final size:2
Alignment explanation
Indices: 207243--207296 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
207233 TTCTCTCTTA
207243 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
207285 AT AT AT AT AT AT
1 AT AT AT AT AT AT
207297 TAAATTATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:211772 original size:17 final size:18
Alignment explanation
Indices: 211750--211784 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
211740 AAGGGATTTT
*
211750 TATTTT-TATTTTTAAAA
1 TATTTTATAATTTTAAAA
211767 TATTTTATAATTTTAAAA
1 TATTTTATAATTTTAAAA
211785 AATTAAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTTATAATTTTAAAA
Found at i:212000 original size:29 final size:31
Alignment explanation
Indices: 211943--212001 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
211933 TGATATTGTT
211943 ATTATTTTATAATTTTCTAAAAAATTTAATG
1 ATTATTTTATAATTTTCTAAAAAATTTAATG
*
211974 ATTATTTTAT-ATTTT-TAAAAATTTTAAT
1 ATTATTTTATAATTTTCTAAAAAATTTAAT
212002 AAGGGTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 12 0.44
30 5 0.19
31 10 0.37
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (31 bp):
ATTATTTTATAATTTTCTAAAAAATTTAATG
Found at i:214020 original size:19 final size:19
Alignment explanation
Indices: 213998--214036 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
213988 TATCAATCAC
213998 ATAAAGAAAT-ATAAATAAA
1 ATAAAGAAATAAT-AATAAA
*
214017 ATAAAGTAATAATAATAAA
1 ATAAAGAAATAATAATAAA
214036 A
1 A
214037 AATGAACCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
ATAAAGAAATAATAATAAA
Found at i:223929 original size:280 final size:280
Alignment explanation
Indices: 223428--223986 Score: 1001
Period size: 280 Copynumber: 2.0 Consensus size: 280
223418 TATTACCGAT
** *
223428 GATACTTCTGACTGAAATTAACGACGAACGGCAACGATTCATGACGAAAGATTTGAGGGGTTTTG
1 GATACTTCCAACTGAAATTAACGACGAACGGCAACGATTCACGACGAAAGATTTGAGGGGTTTTG
* *
223493 TTCCTCGCTCGACAACGAACTCGATGGTGGTTTCGGCTCATCGATCGAAGGTCGGACGGTGAGTA
66 TTCCTCACTCGACAACGAACTCGATGGTGGTTCCGGCTCATCGATCGAAGGTCGGACGGTGAGTA
223558 GATCGGAGTTGAAAATTGTTGACCGGGAGAGGAATTATGAGTGTATTTCTGCAGAAATACACGGG
131 GATCGGAGTTGAAAATTGTTGACCGGGAGAGGAATTATGAGTGTATTTCTGCAGAAATACACGGG
223623 GAAATGGGGGTTTATATTAACTTCTAAAGAAAAATGGTAAAATCATGAGTTTAGCCACTGAATTT
196 GAAATGGGGGTTTATATTAACTTCTAAAGAAAAATGGTAAAATCATGAGTTTAGCCACTGAATTT
223688 CCTGCACTTCTTAAAACGGC
261 CCTGCACTTCTTAAAACGGC
* *
223708 GATACTTCCAACTGAAATTAACGACGAACGGCGACGATTCACGACGAAAGGTTTGAGGGGTTTTG
1 GATACTTCCAACTGAAATTAACGACGAACGGCAACGATTCACGACGAAAGATTTGAGGGGTTTTG
*
223773 TTCCTCACTCGACAACGAACTCGATGGTGGTTCCGGCTCGTCGATCGAAGGTCGGACGGTGAGTA
66 TTCCTCACTCGACAACGAACTCGATGGTGGTTCCGGCTCATCGATCGAAGGTCGGACGGTGAGTA
* *
223838 GATCGGAGTTGAAAATTGTTGATCGGGAGAGGAATTATGAGTGTATTTCTGCATAAATACACGGG
131 GATCGGAGTTGAAAATTGTTGACCGGGAGAGGAATTATGAGTGTATTTCTGCAGAAATACACGGG
* *
223903 GAAATGGGGGTTTATATTAACTTCTAAAGAAAAATGGTAAAATCATGATTTTGGCCACTGAATTT
196 GAAATGGGGGTTTATATTAACTTCTAAAGAAAAATGGTAAAATCATGAGTTTAGCCACTGAATTT
*
223968 CCTGTACTTCTTAAAACGG
261 CCTGCACTTCTTAAAACGG
223987 TCTGCTAACT
Statistics
Matches: 266, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
280 266 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (280 bp):
GATACTTCCAACTGAAATTAACGACGAACGGCAACGATTCACGACGAAAGATTTGAGGGGTTTTG
TTCCTCACTCGACAACGAACTCGATGGTGGTTCCGGCTCATCGATCGAAGGTCGGACGGTGAGTA
GATCGGAGTTGAAAATTGTTGACCGGGAGAGGAATTATGAGTGTATTTCTGCAGAAATACACGGG
GAAATGGGGGTTTATATTAACTTCTAAAGAAAAATGGTAAAATCATGAGTTTAGCCACTGAATTT
CCTGCACTTCTTAAAACGGC
Found at i:229290 original size:14 final size:14
Alignment explanation
Indices: 229271--229303 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
229261 TGGGGAGTAA
*
229271 TCCCTGTAAATAAT
1 TCCCTGCAAATAAT
229285 TCCCTGCAAATAAT
1 TCCCTGCAAATAAT
229299 TCCCT
1 TCCCT
229304 ACATAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (14 bp):
TCCCTGCAAATAAT
Found at i:230688 original size:21 final size:21
Alignment explanation
Indices: 230662--230706 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
230652 GATTTCTGGG
* *
230662 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
230683 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
230704 CAA
1 CAA
230707 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:232023 original size:17 final size:18
Alignment explanation
Indices: 231989--232041 Score: 99
Period size: 17 Copynumber: 3.0 Consensus size: 18
231979 AGGAATGATA
231989 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
232007 TGTGGTCCTTC-GGACAT
1 TGTGGTCCTTCGGGACAT
232024 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
232042 ATATGTATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 17 0.50
18 17 0.50
ACGTcount: A:0.11, C:0.23, G:0.32, T:0.34
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:232134 original size:138 final size:138
Alignment explanation
Indices: 231886--232154 Score: 520
Period size: 138 Copynumber: 1.9 Consensus size: 138
231876 CGAGGGTCTA
*
231886 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
231951 GATCCTTGGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCT
66 GATCCTTGACATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCT
232016 TCGGACAT
131 TCGGACAT
232024 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
232089 GATCCTTGACATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCT
66 GATCCTTGACATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCT
232154 T
131 T
232155 TGGGACATAT
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
138 129 1.00
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (138 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCTTGACATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCT
TCGGACAT
Found at i:232150 original size:18 final size:18
Alignment explanation
Indices: 232127--232162 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
232117 AGGAATGATA
232127 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
*
232145 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTCGGGACAT
232163 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:232232 original size:121 final size:120
Alignment explanation
Indices: 232007--232266 Score: 450
Period size: 121 Copynumber: 2.1 Consensus size: 120
231997 TTCGGGACAT
232007 TGTGGTCCTTCGGACATTGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTC
1 TGTGGTCCTTCGGACATTGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTC
*
232072 TGGTGAGACACATACTTGATCCTTGACATATGTATATGATTCTTAAGGAATGATA
66 TGGTGAGACACATACTTGATCCTAGACATATGTATATGATTCTTAAGGAATGATA
*
232127 TGTGGTCCTTCGGGACATTGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGT
1 TGTGGTCCTTC-GGACATTGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGT
*
232192 CTGGTGAGACACATACTTGATCCCTAG-TATATGTATATGATTCTTAAGGAATGATA
65 CTGGTGAGACACATACTTGAT-CCTAGACATATGTATATGATTCTTAAGGAATGATA
*
232248 TGTGGTCCTTATGGACATT
1 TGTGGTCCTT-CGGACATT
232267 ATTATATGGC
Statistics
Matches: 133, Mismatches: 4, Indels: 5
0.94 0.03 0.04
Matches are distributed among these distances:
120 11 0.08
121 118 0.89
122 4 0.03
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.37
Consensus pattern (120 bp):
TGTGGTCCTTCGGACATTGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTC
TGGTGAGACACATACTTGATCCTAGACATATGTATATGATTCTTAAGGAATGATA
Found at i:232304 original size:23 final size:23
Alignment explanation
Indices: 232274--232333 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
232264 ATTATTATAT
232274 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
232297 GGCACTACGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
*
232320 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
232334 TGTATATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:232341 original size:23 final size:23
Alignment explanation
Indices: 232264--232341 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
232254 CCTTATGGAC
*
232264 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
232288 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* *
232311 ATTCTATGTGGCACTTCGGTGC-
1 ATTATATGTGGCACTACGGTGCA
232333 ATGTATATG
1 AT-TATATG
232342 AGCTGTGGTG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
22 2 0.04
23 40 0.89
24 3 0.07
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:237617 original size:18 final size:18
Alignment explanation
Indices: 237594--237629 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
237584 AGGAATTATA
*
237594 TGTGGTCTTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
237612 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
237630 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:237631 original size:62 final size:62
Alignment explanation
Indices: 237565--237752 Score: 162
Period size: 62 Copynumber: 3.1 Consensus size: 62
237555 TGATCCTTGG
*
237565 CATATGTATATGATTCTTAAGGAATTATATGTGGTCTTTCGGGACATTGTGGTCCTTCGGGA
1 CATATGTATATGATTCTTAAGGAATCATATGTGGTCTTTCGGGACATTGTGGTCCTTCGGGA
* * * * * *
237627 CATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGTCTGGT-GAGACACATACT-TGATCCTT-
1 CATATGTATATGATTCTTAAGGAATCATATGTG--GTCT-TTCG-G-GACAT--TGTGGTCCTTC
237684 --GA
59 GGGA
* *
237686 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGA
1 CATATGTATATGATTCTTAAGGAATCATATGTGGTCTTTCGGGACATTGTGGTCCTTCGGGA
237748 CATAT
1 CATAT
237753 ATGTATTCTT
Statistics
Matches: 94, Mismatches: 15, Indels: 34
0.66 0.10 0.24
Matches are distributed among these distances:
57 6 0.06
58 5 0.05
59 24 0.26
60 10 0.11
61 10 0.11
62 28 0.30
63 5 0.05
64 6 0.06
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.37
Consensus pattern (62 bp):
CATATGTATATGATTCTTAAGGAATCATATGTGGTCTTTCGGGACATTGTGGTCCTTCGGGA
Found at i:237705 original size:121 final size:121
Alignment explanation
Indices: 237491--237854 Score: 649
Period size: 121 Copynumber: 3.0 Consensus size: 121
237481 CGAGGGTCTA
237491 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* * *
237556 GATCCTTGGCATATGTATATGATTCTTAAGGAATTATATGTGGTCTTTCGGGACAT
66 GATCCTTGACATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
237612 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
237677 GATCCTTGACATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCTTGACATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
237733 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* * **
237798 GATCCCT-AGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCTTGA-CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
237854 T
1 T
237855 ATTATATGGC
Statistics
Matches: 235, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
120 1 0.00
121 234 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCTTGACATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:237738 original size:18 final size:18
Alignment explanation
Indices: 237715--237750 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
237705 AGGAATGATA
237715 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
237733 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
237751 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:237911 original size:23 final size:23
Alignment explanation
Indices: 237857--237929 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
237847 TGGACATTAT
237857 TATATGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
***
237880 TACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
**
237903 TATATGGCACTTTGGTGC-ATT-
1 TATATGGCACTACGGTGCAATTC
237924 TATATG
1 TATATG
237930 AGCTGTGGTG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 6 0.14
22 3 0.07
23 33 0.79
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAATTC
Found at i:245916 original size:17 final size:18
Alignment explanation
Indices: 245884--245918 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
245874 TATTTTTTAA
245884 AATATGTTTATAAAATTT
1 AATATGTTTATAAAATTT
245902 AATATGTTT-TAAAATTT
1 AATATGTTTATAAAATTT
245919 TCTATTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
AATATGTTTATAAAATTT
Found at i:247064 original size:284 final size:292
Alignment explanation
Indices: 246510--247087 Score: 1055
Period size: 284 Copynumber: 2.0 Consensus size: 292
246500 TATGGGTTGC
246510 TCAAGTAGGTATACTTTATTTATTCCTACATTACGTCCTTTTTTTAAAATAAAATTTTCTCTCCC
1 TCAAGTAGGTATACTTTATTTATTCCTA-ATTACGTCCTTTTTTTAAAATAAAATTTTCTCTCCC
246575 CTCTTCCTCTCTCTCTTCTTTTTATAATTTTGTAGGGTTTTTTTTATAGATTTAAATTTTTCTTT
65 CTCTTCCTCTCTCTCTTCTTTTTATAATTTTGTAGGGTTTTTTTTATAGATTTAAATTTTTCTTT
246640 TTTTTCTTTGTTTAGCGGCAAAGGCAACGGTTTTAATATTAGTTAACTTTCATCGGTTCTATTTT
130 TTTTTCTTTGTTTAGCGGCAAAGGCAACGGTTTTAATATTAGTTAACTTTCATCGGTTCTATTTT
246705 CTCTTTGTTTCTTAGGTTTTTTCAATAAAAATAATTATTTCTTTATGTCATGTTTTTCTCTACCT
195 CTCTTTGTTTCTTAGGTTTTTTCAATAAAAATAATTATTTCTTTATGTCATGTTTTTCTCTACCT
246770 TTATGCAACGTTTTTCGTTTTCTTTCTCGGTCA
260 TTATGCAACGTTTTTCGTTTTCTTTCTCGGTCA
246803 TCAAGTAGGTATACTTTA-TTATTCCT-ATTACGTCC-TTTTTTAAAATAAAATTTTCTCTCCCC
1 TCAAGTAGGTATACTTTATTTATTCCTAATTACGTCCTTTTTTTAAAATAAAATTTTCTCTCCCC
246865 -C-TCCTCTCTCTCTTC-TTTT-TAATTTTGTAGGG-TTTTTTTATAGATTTAAATTTTTCTTTT
66 TCTTCCTCTCTCTCTTCTTTTTATAATTTTGTAGGGTTTTTTTTATAGATTTAAATTTTTCTTTT
* * *
246925 TTTTCTTTGTTTAGCGGCAAAGGCAACGGTTTTAATATTATTTACCTTTCATTGGTTCTATTTTC
131 TTTTCTTTGTTTAGCGGCAAAGGCAACGGTTTTAATATTAGTTAACTTTCATCGGTTCTATTTTC
*
246990 TCTTTGTTTTTTAGGTTTTTTCAATAAAAATAATTATTTCTTTATGTCATGTTTTTCTCTACCTT
196 TCTTTGTTTCTTAGGTTTTTTCAATAAAAATAATTATTTCTTTATGTCATGTTTTTCTCTACCTT
247055 TATGCAACGTTTTTCGTTTTCTTTCTCGGTCA
261 TATGCAACGTTTTTCGTTTTCTTTCTCGGTCA
247087 T
1 T
247088 TTTTTGAATA
Statistics
Matches: 281, Mismatches: 4, Indels: 9
0.96 0.01 0.03
Matches are distributed among these distances:
284 187 0.67
285 13 0.05
286 4 0.01
287 14 0.05
288 1 0.00
289 27 0.10
290 9 0.03
292 8 0.03
293 18 0.06
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.53
Consensus pattern (292 bp):
TCAAGTAGGTATACTTTATTTATTCCTAATTACGTCCTTTTTTTAAAATAAAATTTTCTCTCCCC
TCTTCCTCTCTCTCTTCTTTTTATAATTTTGTAGGGTTTTTTTTATAGATTTAAATTTTTCTTTT
TTTTCTTTGTTTAGCGGCAAAGGCAACGGTTTTAATATTAGTTAACTTTCATCGGTTCTATTTTC
TCTTTGTTTCTTAGGTTTTTTCAATAAAAATAATTATTTCTTTATGTCATGTTTTTCTCTACCTT
TATGCAACGTTTTTCGTTTTCTTTCTCGGTCA
Found at i:250492 original size:2 final size:2
Alignment explanation
Indices: 250487--250516 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
250477 ATTTTTTTAT
250487 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
250517 AAAGATCGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:250686 original size:2 final size:2
Alignment explanation
Indices: 250679--250719 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
250669 GTATCCCATT
250679 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
250720 TTATTATAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:254118 original size:29 final size:29
Alignment explanation
Indices: 254076--254143 Score: 111
Period size: 29 Copynumber: 2.3 Consensus size: 29
254066 AAATACAATG
254076 AATAGTCGGGTGACCATTTTATAACTT-TT
1 AATAGTCGGGTGACCATTTTATAA-TTGTT
*
254105 AATAGTTGGGTGACCATTTTATAATTGTT
1 AATAGTCGGGTGACCATTTTATAATTGTT
254134 AATAGTCGGG
1 AATAGTCGGG
254144 ACTCAACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 2 0.06
29 34 0.94
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (29 bp):
AATAGTCGGGTGACCATTTTATAATTGTT
Found at i:265627 original size:18 final size:18
Alignment explanation
Indices: 265604--265640 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
265594 GAGAGGTGTT
*
265604 AGAGTCCTAGTTAAGTTA
1 AGAGTCCTAGCTAAGTTA
265622 AGAGTCCTAGCTAAGTTA
1 AGAGTCCTAGCTAAGTTA
265640 A
1 A
265641 CTTTATCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.30
Consensus pattern (18 bp):
AGAGTCCTAGCTAAGTTA
Found at i:270866 original size:15 final size:15
Alignment explanation
Indices: 270846--270880 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
270836 AATGTCATTG
270846 TGTTTTATGGTAAAA
1 TGTTTTATGGTAAAA
270861 TGTTTTATGGTAAAA
1 TGTTTTATGGTAAAA
270876 TGTTT
1 TGTTT
270881 GGATGAGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (15 bp):
TGTTTTATGGTAAAA
Found at i:281775 original size:2 final size:2
Alignment explanation
Indices: 281768--281829 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
281758 TATGCATACA
281768 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
281810 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
281830 CCCAATTTCC
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):
AT
Found at i:281970 original size:36 final size:37
Alignment explanation
Indices: 281922--282001 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 37
281912 AAAAAAAATC
* * *
281922 AATTTCCCTCTAAATTCTTAATTTCCAACT-TCCCAA
1 AATTTCCATCTAAATTATCAATTTCCAACTGTCCCAA
**
281958 AATTTCCATCTAAATTATCAATTTCCCTCTGGTCCCAA
1 AATTTCCATCTAAATTATCAATTTCCAACT-GTCCCAA
281996 AATTTC
1 AATTTC
282002 TCAATTTCCC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 25 0.68
38 12 0.32
ACGTcount: A:0.30, C:0.29, G:0.03, T:0.39
Consensus pattern (37 bp):
AATTTCCATCTAAATTATCAATTTCCAACTGTCCCAA
Found at i:282099 original size:2 final size:2
Alignment explanation
Indices: 282092--282126 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
282082 CTCATTTTGA
282092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
282127 ATTAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:285201 original size:85 final size:84
Alignment explanation
Indices: 285059--285226 Score: 248
Period size: 85 Copynumber: 2.0 Consensus size: 84
285049 GCATATACTC
* * *
285059 TTTGACACACAATGTGTGTCATCTTCATTTATGACGGGGGTTTCAATGTCACGCAATGTA-AGTC
1 TTTGACACACAATGTGTGTCATCTTCATTTATAACGGGGGCTTCAATGACACGCAATG-AGAGTC
*
285123 ATAAATGCGTGTCATAAATT
65 ATAAATGCGCGTCATAAATT
* * *
285143 TTTGACACACAAATGTGTGTCGTCTTCATTTATAACGGGGGCTTCAATGACGCGCAATGAGCGTC
1 TTTGACACAC-AATGTGTGTCATCTTCATTTATAACGGGGGCTTCAATGACACGCAATGAGAGTC
285208 ATAAATGCGCGTCATAAAT
65 ATAAATGCGCGTCATAAAT
285227 GTGTGTCATA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
84 11 0.15
85 64 0.85
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (84 bp):
TTTGACACACAATGTGTGTCATCTTCATTTATAACGGGGGCTTCAATGACACGCAATGAGAGTCA
TAAATGCGCGTCATAAATT
Found at i:285219 original size:13 final size:13
Alignment explanation
Indices: 285198--285252 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
285188 AATGACGCGC
*
285198 AATGAGCGTCATA
1 AATGCGCGTCATA
285211 AATGCGCGTCATA
1 AATGCGCGTCATA
* *
285224 AATGTGTGTCATA
1 AATGCGCGTCATA
*
285237 AATGCGCGTCGTA
1 AATGCGCGTCATA
285250 AAT
1 AAT
285253 TTATGTCGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:285227 original size:26 final size:26
Alignment explanation
Indices: 285198--285252 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
285188 AATGACGCGC
285198 AATGAGCGTCATAAATGCGCGTCATA
1 AATGAGCGTCATAAATGCGCGTCATA
* * *
285224 AATGTGTGTCATAAATGCGCGTCGTA
1 AATGAGCGTCATAAATGCGCGTCATA
285250 AAT
1 AAT
285253 TTATGTCGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (26 bp):
AATGAGCGTCATAAATGCGCGTCATA
Found at i:285259 original size:26 final size:26
Alignment explanation
Indices: 285205--285259 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
285195 CGCAATGAGC
*
285205 GTCATAAATGCGCGTCATAAATGTGT
1 GTCATAAATGCGCGTCATAAATGTAT
* *
285231 GTCATAAATGCGCGTCGTAAATTTAT
1 GTCATAAATGCGCGTCATAAATGTAT
285257 GTC
1 GTC
285260 GCACAGTTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (26 bp):
GTCATAAATGCGCGTCATAAATGTAT
Found at i:290800 original size:19 final size:18
Alignment explanation
Indices: 290776--290811 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
290766 AACTTGTTGT
*
290776 TATATATGTAATGTTAATA
1 TATATACGTAAT-TTAATA
290795 TATATACGTAATTTAAT
1 TATATACGTAATTTAAT
290812 CAAAATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (18 bp):
TATATACGTAATTTAATA
Found at i:291468 original size:27 final size:27
Alignment explanation
Indices: 291408--291507 Score: 104
Period size: 27 Copynumber: 3.9 Consensus size: 27
291398 AATAAATTAA
* *
291408 AATAA-AAAATATTTTTAAATGAAAAT
1 AATAATAAAATATTTTTAAATTAAATT
*
291434 AA-ACATAAAATATTTTTAAATTAAGTT
1 AATA-ATAAAATATTTTTAAATTAAATT
*
291461 AATAATAAAATATATTT-AA-TAAATT
1 AATAATAAAATATTTTTAAATTAAATT
*
291486 AAT-ATAAAAT-GTTTTAAATTAA
1 AATAATAAAATATTTTTAAATTAA
291508 TATATATAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
23 3 0.05
24 9 0.15
25 12 0.19
26 5 0.08
27 32 0.52
28 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (27 bp):
AATAATAAAATATTTTTAAATTAAATT
Found at i:291625 original size:15 final size:15
Alignment explanation
Indices: 291605--291635 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
291595 AATTATATAA
*
291605 AAAATTTAAAATTCT
1 AAAATTTAAAAATCT
291620 AAAATTTAAAAATCT
1 AAAATTTAAAAATCT
291635 A
1 A
291636 TAATATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAATTTAAAAATCT
Found at i:291825 original size:39 final size:39
Alignment explanation
Indices: 291781--291886 Score: 117
Period size: 39 Copynumber: 2.7 Consensus size: 39
291771 TTTTAAAAAT
* *
291781 AATTTAGAACGCTA-ATGTGAAATAATTTAATAAATTAAG
1 AATTTAGAACGTTATA-GTGAAATAATTTAAGAAATTAAG
* * *
291820 AATTTAGAACGTTATGGTGTCAA-AATTTAAGAAATTAGG
1 AATTTAGAACGTTATAGTG-AAATAATTTAAGAAATTAAG
* *
291859 ATTTTAGAATGTTATAGTGAAATAATTT
1 AATTTAGAACGTTATAGTGAAATAATTT
291887 GAGAGTTATG
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
38 2 0.04
39 51 0.93
40 2 0.04
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (39 bp):
AATTTAGAACGTTATAGTGAAATAATTTAAGAAATTAAG
Found at i:294796 original size:18 final size:19
Alignment explanation
Indices: 294761--294801 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
294751 TTTTTATTAA
*
294761 ATTTGATTTTGAT-TTTTT
1 ATTTGATTTTGATGTTTTG
*
294779 ATTTGATTTTTATGTTTTG
1 ATTTGATTTTGATGTTTTG
294798 ATTT
1 ATTT
294802 TGTAGTTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.17, C:0.00, G:0.12, T:0.71
Consensus pattern (19 bp):
ATTTGATTTTGATGTTTTG
Found at i:295015 original size:3 final size:3
Alignment explanation
Indices: 295009--295040 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
294999 CAACAACAAC
295009 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
295041 ATATATAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:304001 original size:20 final size:20
Alignment explanation
Indices: 303907--304275 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
303897 GATTTTCCAT
* ** *
303907 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
303927 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
303947 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
303967 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
303987 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
304007 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
304027 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
304047 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
304067 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
304087 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
304107 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
304127 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
304147 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
304167 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
304187 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
304207 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
304227 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
304247 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
304267 AATCACAAC
1 AATCGCAAC
304276 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:304988 original size:24 final size:24
Alignment explanation
Indices: 304949--304995 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
304939 AAATTTGGTC
304949 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
304973 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
304996 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:305187 original size:12 final size:12
Alignment explanation
Indices: 305170--305194 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
305160 ATATAATCCT
305170 GAAGAAGAAAAA
1 GAAGAAGAAAAA
305182 GAAGAAGAAAAA
1 GAAGAAGAAAAA
305194 G
1 G
305195 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:307520 original size:19 final size:19
Alignment explanation
Indices: 307498--307823 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
307488 CGGAAAATAC
*
307498 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
307517 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
307531 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
307551 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
307565 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
307584 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
307603 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
307617 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
307636 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
307655 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
307669 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
307688 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
307707 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
307726 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
307745 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
307764 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
307778 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
307797 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
307816 AATCGCAA
1 AATCGCAA
307824 CGAGATAATC
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 50 0.19
15 3 0.01
16 13 0.05
17 12 0.04
18 4 0.01
19 174 0.65
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:307585 original size:33 final size:34
Alignment explanation
Indices: 307498--307823 Score: 321
Period size: 33 Copynumber: 9.2 Consensus size: 34
307488 CGGAAAATAC
* *
307498 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
307531 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
307565 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
307603 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
307636 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
307669 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
307707 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
307745 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
307777 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
307816 AATCGCAA
1 AATCGCAA
307824 CGAGATAATC
Statistics
Matches: 257, Mismatches: 12, Indels: 43
0.82 0.04 0.14
Matches are distributed among these distances:
32 2 0.01
33 111 0.43
34 32 0.12
35 9 0.04
36 6 0.02
37 4 0.02
38 91 0.35
39 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:307759 original size:161 final size:157
Alignment explanation
Indices: 307526--307845 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
307516 AAATCCCAAC
*
307526 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
307591 ATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
66 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
307656 ATCGCAACGAGAGAATCGCAATGCGAA
131 ATCGCAACGAGAGAATCGCAATGCGAA
*
307683 ATGAAAATCGCAATGC-GAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGC-A-ACG--A-GAAAATCGCAATGCGAAATGAAAA
307747 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
61 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
*
307812 TGAAAATCGCAACGAGATAATCGCAATGCGAA
126 TGAAAATCGCAACGAGAGAATCGCAATGCGAA
307844 AT
1 AT
307846 TATAAACGCA
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 13 0.08
157 17 0.11
158 3 0.02
160 1 0.01
161 120 0.78
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (157 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
ATCGCAACGAGAGAATCGCAATGCGAA
Done.