Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006858.1 Hibiscus syriacus cultivar Beakdansim tig00017449_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: 109664
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:8206 original size:2 final size:2
Alignment explanation
Indices: 8194--8237 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
8184 TATGAAAATA
8194 AT AT A- 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
8235 AT A
1 AT A
8238 GTGAATCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11513 original size:36 final size:37
Alignment explanation
Indices: 11473--11620 Score: 151
Period size: 36 Copynumber: 4.1 Consensus size: 37
11463 TGAGAGAAGG
* * *
11473 AAAATTTGTTTCAAGAG-AAACACTTTCAAATGAGAT
1 AAAATTTGTTTTAAGAGAAAACAATCTCAAATGAGAT
*
11509 AAAATTTGTTTTAAG-GAAAACAATCTCAAGTGAGAT
1 AAAATTTGTTTTAAGAGAAAACAATCTCAAATGAGAT
* * ** *
11545 AGAATATGTTTTAAGA-AAAATGATCTAAAATGAGAT
1 AAAATTTGTTTTAAGAGAAAACAATCTCAAATGAGAT
* * * *
11581 GAAATTAGTTTTAATA-AAAACAATCTCAAGTGAGAT
1 AAAATTTGTTTTAAGAGAAAACAATCTCAAATGAGAT
11617 AAAA
1 AAAA
11621 ATCTGAGTGA
Statistics
Matches: 90, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
35 1 0.01
36 89 0.99
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (37 bp):
AAAATTTGTTTTAAGAGAAAACAATCTCAAATGAGAT
Found at i:11885 original size:97 final size:97
Alignment explanation
Indices: 11776--12010 Score: 323
Period size: 97 Copynumber: 2.4 Consensus size: 97
11766 GTTGATCCAA
*
11776 CTCAAGTTAGATAAAAATCTGAGTGAAATGATAATGAAGTTTAGATTTCAAGGGAAACTGTCTCA
1 CTCAAGTGAGATAAAAATCTGAGTGAAATGATAATGAAGTTTAGATTTCAAGGGAAACTGTCTCA
11841 AGTGAGACAAAATCAGTTTTAAGAAAGAA-AAT
66 AGTGAGACAAAATCAGTTTTAAGAAA-AACAAT
* * * * * * *
11873 CTCAAGTGAGATAAATATCCGAGTGAAATGATATTGAATTTTGGATTTCAATGGAAACTTTCTCA
1 CTCAAGTGAGATAAAAATCTGAGTGAAATGATAATGAAGTTTAGATTTCAAGGGAAACTGTCTCA
**
11938 AGTGAGACAAAATTTGTTTTAAGAAAAACAAT
66 AGTGAGACAAAATCAGTTTTAAGAAAAACAAT
* *
11970 CTCAAGTGAGAT-AAAATCTTGAGTAAAATGATTATG-AGTTT
1 CTCAAGTGAGATAAAAATC-TGAGTGAAATGATAATGAAGTTT
12011 TAGGGAAACT
Statistics
Matches: 120, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
96 11 0.09
97 109 0.91
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (97 bp):
CTCAAGTGAGATAAAAATCTGAGTGAAATGATAATGAAGTTTAGATTTCAAGGGAAACTGTCTCA
AGTGAGACAAAATCAGTTTTAAGAAAAACAAT
Found at i:12472 original size:18 final size:18
Alignment explanation
Indices: 12447--12491 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
12437 CTTCTCTAAA
12447 GCTTGACTTCTCATTTAT
1 GCTTGACTTCTCATTTAT
*
12465 GTTTGACTTCTCATTTAT
1 GCTTGACTTCTCATTTAT
12483 GCTTGACTT
1 GCTTGACTT
12492 TTCGAATATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.20, G:0.13, T:0.51
Consensus pattern (18 bp):
GCTTGACTTCTCATTTAT
Found at i:17566 original size:18 final size:19
Alignment explanation
Indices: 17533--17572 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
17523 ACACGTAACA
*
17533 AGATAAAAGGAAATCAGGTT
1 AGATAAAA-GAAATCAAGTT
17553 AGATAAAA-AAATCAAGTT
1 AGATAAAAGAAATCAAGTT
17571 AG
1 AG
17573 TAAGAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
20 8 0.42
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (19 bp):
AGATAAAAGAAATCAAGTT
Found at i:18738 original size:19 final size:19
Alignment explanation
Indices: 18714--18750 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
18704 GTGCCATAGT
*
18714 ATAGAAGTATCGATACTAG
1 ATAGAAGTACCGATACTAG
18733 ATAGAAGTACCGATACTA
1 ATAGAAGTACCGATACTA
18751 TGGAGCCTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (19 bp):
ATAGAAGTACCGATACTAG
Found at i:19186 original size:47 final size:47
Alignment explanation
Indices: 19132--19415 Score: 410
Period size: 47 Copynumber: 6.1 Consensus size: 47
19122 AAATCAAATT
* * *
19132 CATAATTGAAAATACATGAAAGGATGCACTAAGGCATGAATGGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
19179 CATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAATGGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
19226 CATAATTAAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGT
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
19273 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGAATTC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
19320 CATAATTGAAAATGCATGAAAGGAAGCATTAA-ACATG-AACGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
19365 CATAATTGAAAATGCATGAAAAGGATTCATTAAGGCATGAAAGGATGC
1 CATAATTGAAAATGCATG-AAAGGATGCATTAAGGCATGAAAGGATGC
19413 CAT
1 CAT
19416 GTTTATTAAA
Statistics
Matches: 212, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
45 22 0.10
46 16 0.08
47 164 0.77
48 10 0.05
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (47 bp):
CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:19204 original size:27 final size:26
Alignment explanation
Indices: 19165--19299 Score: 82
Period size: 27 Copynumber: 5.5 Consensus size: 26
19155 ATGCACTAAG
19165 GCATGAATGGATGCCATAATTGAAAAT
1 GCATGAATGGATGCCATAATT-AAAAT
*
19192 GCATGAAAT-GATG-C---ATT--AAG
1 GCATG-AATGGATGCCATAATTAAAAT
19212 GCATGAATGGATGCCATAATTAAAAAT
1 GCATGAATGGATGCCATAATT-AAAAT
*
19239 GCATGAAAT-GATG-C---ATT--AAG
1 GCATG-AATGGATGCCATAATTAAAAT
* *
19259 GCATGAAAGGATGTCATAATTGAAAAT
1 GCATGAATGGATGCCATAATT-AAAAT
*
19286 GCATGAAAGGATGC
1 GCATGAATGGATGC
19300 ATTAAGGCAT
Statistics
Matches: 84, Mismatches: 6, Indels: 36
0.67 0.05 0.29
Matches are distributed among these distances:
19 5 0.06
20 22 0.26
21 2 0.02
23 6 0.07
24 6 0.07
26 2 0.02
27 35 0.42
28 6 0.07
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (26 bp):
GCATGAATGGATGCCATAATTAAAAT
Found at i:19217 original size:20 final size:20
Alignment explanation
Indices: 19192--19312 Score: 64
Period size: 20 Copynumber: 5.3 Consensus size: 20
19182 AATTGAAAAT
19192 GCATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
*
19212 GCATG-AATGGATGCCATAATTAAAAAT
1 GCATGAAAT-GATG-C---ATT---AAG
19239 GCATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
* *
19259 GCATGAAAGGATGTCATAATTGAAAAT
1 GCATGAAATGATG-C---ATT---AAG
*
19286 GCATGAAAGGATGCATTAAG
1 GCATGAAATGATGCATTAAG
19306 GCATGAA
1 GCATGAA
19313 CGAATTCCAT
Statistics
Matches: 80, Mismatches: 5, Indels: 32
0.68 0.04 0.27
Matches are distributed among these distances:
19 3 0.04
20 32 0.40
21 2 0.03
23 6 0.08
24 6 0.08
26 2 0.03
27 26 0.32
28 3 0.04
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (20 bp):
GCATGAAATGATGCATTAAG
Found at i:25509 original size:21 final size:22
Alignment explanation
Indices: 25469--25519 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 22
25459 CCTTAAGGGG
*
25469 GTATCGGTACCATAGTATAGTA
1 GTATCGATACCATAGTATAGTA
25491 GTATCGATACCAT-GTATAGTA
1 GTATCGATACCATAGTATAGTA
25512 GTATCGAT
1 GTATCGAT
25520 GTGGTAAGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (22 bp):
GTATCGATACCATAGTATAGTA
Found at i:25633 original size:20 final size:20
Alignment explanation
Indices: 25597--25634 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25587 GTACCATATT
*
25597 ATAGAAGTAATGGTACTAGG
1 ATAGAAGTAATGATACTAGG
25617 ATAGAAGT-ATCGATACTA
1 ATAGAAGTAAT-GATACTA
25635 TAGAGCCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (20 bp):
ATAGAAGTAATGATACTAGG
Found at i:26101 original size:20 final size:20
Alignment explanation
Indices: 26076--26149 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
26066 AATTGAAAAT
*
26076 GCATGAAAGTATGCATTAAG
1 GCATGAAAGGATGCATTAAG
26096 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
26116 GCATGAAAGGATACATTAAG
1 GCATGAAAGGATGCATTAAG
*
26136 GCATGAACGGATGC
1 GCATGAAAGGATGC
26150 CATAATTGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.20
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:26166 original size:27 final size:27
Alignment explanation
Indices: 26136--26221 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 27
26126 ATACATTAAG
26136 GCATGAACGGATGCCATAATTGAAAAT
1 GCATGAACGGATGCCATAATTGAAAAT
*
26163 GCATGAA-GTGATG-C---ATT---AAG
1 GCATGAACG-GATGCCATAATTGAAAAT
*
26183 GCATGAACGAATGCCATAATTGAAAAT
1 GCATGAACGGATGCCATAATTGAAAAT
*
26210 GCATGAAAGGAT
1 GCATGAACGGAT
26222 TCATTAAGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 18
0.66 0.07 0.26
Matches are distributed among these distances:
20 12 0.27
21 2 0.04
23 3 0.07
24 3 0.07
26 2 0.04
27 23 0.51
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (27 bp):
GCATGAACGGATGCCATAATTGAAAAT
Found at i:26185 original size:47 final size:47
Alignment explanation
Indices: 26116--26510 Score: 527
Period size: 47 Copynumber: 8.7 Consensus size: 47
26106 ATGCATTAAG
*
26116 GCATGAAAGGATACATTAAGGCATGAACGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
*
26163 GCATG-AAGTGATGCATTAAGGCATGAACGAATGCCATAATTGAAAAT
1 GCATGAAAG-GATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
* *
26210 GCATGAAAGGATTCATTAAGTCATGAACGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
* *
26257 GCATGAAAGGATGCATTAAGGCATCAACGGATACCATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
26304 GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
*
26351 GCAT-----GATGCATTAAGGCATGAAC-GAT--TATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
* *
26390 ACATGAAAAGGAGGCATTAAGGCATGAA-GGATGCC---A-TG-AAA-
1 GCATG-AAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
26431 G-ATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
* * * *
26477 GCATGAAAATGATGCATTAATGCATAAATGGATG
1 GCATG-AAAGGATGCATTAAGGCATGAACGGATG
26511 TGTTAATACG
Statistics
Matches: 307, Mismatches: 21, Indels: 39
0.84 0.06 0.11
Matches are distributed among these distances:
39 36 0.12
40 10 0.03
41 3 0.01
42 22 0.07
43 3 0.01
44 3 0.01
45 23 0.07
46 4 0.01
47 176 0.57
48 27 0.09
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.23
Consensus pattern (47 bp):
GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
Found at i:26254 original size:94 final size:95
Alignment explanation
Indices: 26017--26510 Score: 614
Period size: 94 Copynumber: 5.5 Consensus size: 95
26007 AAATTAAATT
* *
26017 CATAATTGAAAATGCATGAAATGATGCATT-AGGCATGAAAGGATGCCATAATTGAAAATGCATG
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
*
26081 AAAGT-ATGCATTAAGGCATGAAAGGATG-
66 AAAGTGATGCATTAAGGCATGAACGGATGC
* *
26109 C---ATT---AAGGCATGAAAGGATACATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
*
26168 -AAGTGATGCATTAAGGCATGAACGAATGC
66 AAAGTGATGCATTAAGGCATGAACGGATGC
* *
26197 CATAATTGAAAATGCATGAAAGGATTCATTAAGTCATGAACGGATGCCATAATTGAAAATGCATG
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
* *
26262 AAAG-GATGCATTAAGGCATCAACGGATAC
66 AAAGTGATGCATTAAGGCATGAACGGATGC
26291 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGC---
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
26353 --A-TGATGCATTAAGGCATGAAC-GAT--
66 AAAGTGATGCATTAAGGCATGAACGGATGC
* * *
26377 TATAATTGAAAATACATGAAAAGGAGGCATTAAGGCATGAA-GGATGCC---A-TG-AAA-G-AT
1 CATAATTGAAAATGCATG-AAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCAT
26434 GAAAG-GATGCATTAAGGCATGAACGGATGC
65 GAAAGTGATGCATTAAGGCATGAACGGATGC
* * * *
26464 CATAATTGAAAATGCATGAAAATGATGCATTAATGCATAAATGGATG
1 CATAATTGAAAATGCATG-AAAGGATGCATTAAGGCATGAACGGATG
26511 TGTTAATACG
Statistics
Matches: 356, Mismatches: 24, Indels: 48
0.83 0.06 0.11
Matches are distributed among these distances:
80 1 0.00
81 3 0.01
82 2 0.01
83 1 0.00
84 20 0.06
85 3 0.01
86 44 0.12
87 110 0.31
88 9 0.03
89 22 0.06
91 3 0.01
92 1 0.00
94 134 0.38
95 3 0.01
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.23
Consensus pattern (95 bp):
CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
AAAGTGATGCATTAAGGCATGAACGGATGC
Found at i:26269 original size:27 final size:27
Alignment explanation
Indices: 26231--26356 Score: 100
Period size: 27 Copynumber: 5.2 Consensus size: 27
26221 TTCATTAAGT
26231 CATGAACGGATGCCATAATTGAAAATG
1 CATGAACGGATGCCATAATTGAAAATG
* *
26258 CATGAAAGGATG-C---ATT---AAGG
1 CATGAACGGATGCCATAATTGAAAATG
* *
26278 CATCAACGGATACCATAATTGAAAATG
1 CATGAACGGATGCCATAATTGAAAATG
* *
26305 CATGAAAGGATG-C---ATT---AAGG
1 CATGAACGGATGCCATAATTGAAAATG
26325 CATGAACGGATGCCATAATTGAAAATG
1 CATGAACGGATGCCATAATTGAAAATG
26352 CATGA
1 CATGA
26357 TGCATTAAGG
Statistics
Matches: 73, Mismatches: 12, Indels: 28
0.65 0.11 0.25
Matches are distributed among these distances:
20 26 0.36
21 2 0.03
23 6 0.08
24 6 0.08
26 2 0.03
27 31 0.42
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (27 bp):
CATGAACGGATGCCATAATTGAAAATG
Found at i:26395 original size:39 final size:41
Alignment explanation
Indices: 26037--26482 Score: 221
Period size: 47 Copynumber: 10.1 Consensus size: 41
26027 AATGCATGAA
* *
26037 ATGATGCATT-AGGCATGAAAGGATGCCATAATTGAAAATGC
1 ATGATGCATTAAGGCATGAACGGAT-CCATAATTGAAAATAC
* * ** *
26078 ATGAAAGTATGCATTAAGGCATGAAAGGATGCATTAA--G-GCATGAA
1 AT----G-ATGCATTAAGGCATGAACGGATCCA-TAATTGAAAAT-AC
* * *
26123 AGGATACATTAAGGCATGAACGGATGCCATAATTGAAAATGCATGA
1 ATGATGCATTAAGGCATGAACGGAT-CCATAATTGAAAAT--A--C
* *
26169 AGTGATGCATTAAGGCATGAACGAATGCCATAATTGAAAATGC
1 A-TGATGCATTAAGGCATGAACGGAT-CCATAATTGAAAATAC
* * *
26212 ATGAAAGGATTCATTAAGTCATGAACGGATGCCATAATTGAAAATGC
1 AT-----GATGCATTAAGGCATGAACGGAT-CCATAATTGAAAATAC
* *
26259 ATGAAAGGATGCATTAAGGCATCAACGGATACCATAATTGAAAATGC
1 AT-----GATGCATTAAGGCATGAACGGAT-CCATAATTGAAAATAC
*
26306 ATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGC
1 AT-----GATGCATTAAGGCATGAACGGAT-CCATAATTGAAAATAC
*
26353 ATGATGCATTAAGGCATGAAC-GAT-TATAATTGAAAATAC
1 ATGATGCATTAAGGCATGAACGGATCCATAATTGAAAATAC
* *
26392 ATGAAAAGGAGGCATTAAGGCATGAA-GGATGCC---A-TGAAAGATGAA
1 AT------GATGCATTAAGGCATGAACGGAT-CCATAATTGAAA-AT-AC
* *
26437 AGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGC
1 ATGATGCATTAAGGCATGAACGGAT-CCATAATTGAAAATAC
26479 ATGA
1 ATGA
26483 AAATGATGCA
Statistics
Matches: 332, Mismatches: 36, Indels: 73
0.75 0.08 0.17
Matches are distributed among these distances:
39 32 0.10
40 30 0.09
41 8 0.02
42 24 0.07
43 11 0.03
44 11 0.03
45 25 0.08
46 11 0.03
47 180 0.54
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.22
Consensus pattern (41 bp):
ATGATGCATTAAGGCATGAACGGATCCATAATTGAAAATAC
Found at i:26441 original size:20 final size:21
Alignment explanation
Indices: 26411--26466 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
26401 AGGCATTAAG
26411 GCATG-AAGGATGCCATGAAA
1 GCATGAAAGGATGCCATGAAA
* *
26431 G-ATGAAAGGATG-CATTAAG
1 GCATGAAAGGATGCCATGAAA
*
26450 GCATGAACGGATGCCAT
1 GCATGAAAGGATGCCAT
26467 AATTGAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 9 0.30
20 18 0.60
21 3 0.10
ACGTcount: A:0.38, C:0.14, G:0.30, T:0.18
Consensus pattern (21 bp):
GCATGAAAGGATGCCATGAAA
Found at i:28260 original size:13 final size:13
Alignment explanation
Indices: 28226--28264 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
28216 GTGTGAGAAA
28226 TCTAAATTT-AAG
1 TCTAAATTTAAAG
*
28238 GCTAAATTTAAAG
1 TCTAAATTTAAAG
*
28251 TCTAAGTTTAAAG
1 TCTAAATTTAAAG
28264 T
1 T
28265 GTAAGGTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (13 bp):
TCTAAATTTAAAG
Found at i:29584 original size:55 final size:55
Alignment explanation
Indices: 29491--29687 Score: 227
Period size: 55 Copynumber: 3.5 Consensus size: 55
29481 TGCAAGGCCC
* * *
29491 AAAAATAGGGGCCTCAAAATCGAATATATCTATTAGTTGTTGCTATTAATAAGCAT
1 AAAAATAGGGGCC-CAAAATCGAGTATATCTATCAGTTGTTGCTATTAAAAAGCAT
* *
29547 AAAATTAGGGGCCCAAAATCGAGTATATATATCAGTTGTTGCTATTAAAAAGCAT
1 AAAAATAGGGGCCCAAAATCGAGTATATCTATCAGTTGTTGCTATTAAAAAGCAT
* * * * *
29602 AAAAATAGGAGTCTCGAAATCGAGTATATCTATCAATTGTTGCCATTAAGAAA-CAT
1 AAAAATAGG-GGCCCAAAATCGAGTATATCTATCAGTTGTTGCTATTAA-AAAGCAT
* * *
29658 -AAAATAGGGGTCCCATAATCAAATATATCT
1 AAAAATAGGGG-CCCAAAATCGAGTATATCT
29688 CTATTTATCA
Statistics
Matches: 120, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
54 1 0.01
55 68 0.57
56 48 0.40
57 3 0.03
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (55 bp):
AAAAATAGGGGCCCAAAATCGAGTATATCTATCAGTTGTTGCTATTAAAAAGCAT
Found at i:29899 original size:31 final size:31
Alignment explanation
Indices: 29861--29923 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
29851 TCTCATAAAA
*
29861 TAGGGGTCTCGAAATTGAATATATATATCAG
1 TAGGGGTCCCGAAATTGAATATATATATCAG
* *
29892 TAGGGGTCCCGAAATTGAGTATATCTATCAG
1 TAGGGGTCCCGAAATTGAATATATATATCAG
29923 T
1 T
29924 TGTTGCATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (31 bp):
TAGGGGTCCCGAAATTGAATATATATATCAG
Found at i:29976 original size:55 final size:56
Alignment explanation
Indices: 29892--30029 Score: 208
Period size: 56 Copynumber: 2.5 Consensus size: 56
29882 TATATATCAG
* *
29892 TAGGGGTCCCGAAATTGAGTATATCTATCAGTTGTTG-CATTAAGAAGCATAAAAA
1 TAGGGGTCCCGAAATCGAGTATATCTATCAATTGTTGCCATTAAGAAGCATAAAAA
29947 TAGGGGTCCCGAAATCGAGTATATCTATCAATTGTTGCCATTAAGAAGCATAAAAA
1 TAGGGGTCCCGAAATCGAGTATATCTATCAATTGTTGCCATTAAGAAGCATAAAAA
** *
30003 TAAAGGTCCC-AGAATCGAATATATCTA
1 TAGGGGTCCCGA-AATCGAGTATATCTA
30030 GAAAATAGGG
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
55 36 0.47
56 40 0.53
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (56 bp):
TAGGGGTCCCGAAATCGAGTATATCTATCAATTGTTGCCATTAAGAAGCATAAAAA
Found at i:30679 original size:16 final size:16
Alignment explanation
Indices: 30654--30708 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
30644 CTAGAATGTT
*
30654 TATGAGGGAATTGAAA
1 TATGAAGGAATTGAAA
*
30670 TATGAAGGAATTGGAA
1 TATGAAGGAATTGAAA
* *
30686 TCTGTCAGGAATTGAAA
1 TATG-AAGGAATTGAAA
*
30703 TCTGAA
1 TATGAA
30709 TCTAAAACAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 18 0.56
17 14 0.44
ACGTcount: A:0.40, C:0.05, G:0.27, T:0.27
Consensus pattern (16 bp):
TATGAAGGAATTGAAA
Found at i:31296 original size:15 final size:14
Alignment explanation
Indices: 31261--31453 Score: 85
Period size: 14 Copynumber: 13.1 Consensus size: 14
31251 AAAGGCAGTG
*
31261 AAGATAAATAAACTA
1 AAGA-AAATAAAATA
31276 AAGAAAATAAAATA
1 AAGAAAATAAAATA
*
31290 AAGGAAATAAAAATA
1 AAGAAAAT-AAAATA
*
31305 AATGAAAAACAAAAT-
1 AA-G-AAAATAAAATA
*
31320 AAGATAAAGAAAACATAAA
1 AAGA-AAA-TAAA-AT--A
*
31339 AATAAAATAAAGATA
1 AAGAAAATAAA-ATA
*
31354 AAAACTAAATAAAATA
1 AAGA--AAATAAAATA
*
31370 AAGAACAT-AAA-A
1 AAGAAAATAAAATA
* *
31382 AACAAAA-GAAATA
1 AAGAAAATAAAATA
31395 AA-AAAATAAAGATA
1 AAGAAAATAAA-ATA
*
31409 AA-TAAATAAAATA
1 AAGAAAATAAAATA
**
31422 ATCAAAATAAAGATA
1 AAGAAAATAAA-ATA
31437 AAGAGCAAA-AAAATA
1 AAGA--AAATAAAATA
31452 AA
1 AA
31454 AATTAAAAGA
Statistics
Matches: 140, Mismatches: 19, Indels: 38
0.71 0.10 0.19
Matches are distributed among these distances:
12 13 0.09
13 13 0.09
14 42 0.30
15 31 0.22
16 17 0.12
17 18 0.13
18 3 0.02
19 3 0.02
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (14 bp):
AAGAAAATAAAATA
Found at i:31344 original size:44 final size:42
Alignment explanation
Indices: 31294--31419 Score: 113
Period size: 44 Copynumber: 3.0 Consensus size: 42
31284 AAAATAAAGG
31294 AAATAAAAATAAATGAAAAACAAAATAAGATAAAGAAAACATAA
1 AAATAAAAATAAATGAAAAACAAAATAAGATAAAG--AACATAA
* *
31338 AAAT-AAAATAAA-GATAAAAACTAAATAAAATAAAGAACATAA
1 AAATAAAAATAAATG--AAAAACAAAATAAGATAAAGAACATAA
* * *
31380 AAA-ACAAAAGAAAT-AAAAA-AATA-AAGATAAATAA-ATAA
1 AAATA-AAAATAAATGAAAAACAAAATAAGATAAAGAACATAA
31418 AA
1 AA
31420 TAATCAAAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
38 6 0.09
39 9 0.13
40 2 0.03
41 5 0.07
42 11 0.16
43 15 0.21
44 22 0.31
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (42 bp):
AAATAAAAATAAATGAAAAACAAAATAAGATAAAGAACATAA
Found at i:31354 original size:17 final size:17
Alignment explanation
Indices: 31334--31422 Score: 56
Period size: 19 Copynumber: 4.9 Consensus size: 17
31324 TAAAGAAAAC
31334 ATAAAAATAAAATAAAG
1 ATAAAAATAAAATAAAG
31351 ATAAAAACT-AAATAAA-
1 ATAAAAA-TAAAATAAAG
* *
31367 ATAAAGAACATAAAAAACAAA
1 AT-AA-AA-ATAAAATA-AAG
* *
31388 AGAAATAAAAAAATAAAG
1 ATAAA-AATAAAATAAAG
31406 ATAAATAAATAAAATAA
1 AT-AA-AAATAAAATAA
31423 TCAAAATAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
16 2 0.04
17 16 0.29
18 7 0.13
19 23 0.42
20 6 0.11
21 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.04, T:0.16
Consensus pattern (17 bp):
ATAAAAATAAAATAAAG
Found at i:31418 original size:22 final size:22
Alignment explanation
Indices: 31390--31432 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
31380 AAAACAAAAG
31390 AAATAAAAAAAT-AAAGATAAAT
1 AAATAAAAAAATCAAA-ATAAAT
*
31412 AAATAAAATAATCAAAATAAA
1 AAATAAAAAAATCAAAATAAA
31433 GATAAAGAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (22 bp):
AAATAAAAAAATCAAAATAAAT
Found at i:31429 original size:18 final size:18
Alignment explanation
Indices: 31330--31432 Score: 54
Period size: 17 Copynumber: 5.7 Consensus size: 18
31320 AAGATAAAGA
*
31330 AAACATAAA-AATAAAAT
1 AAACATAAATAAAAAAAT
*
31347 AAAGATAAAAACTAAATAAAAT
1 AAACAT--AAA-TAAA-AAAAT
* * *
31369 AAAGA-ACAT-AAAAAAC
1 AAACATAAATAAAAAAAT
*
31385 AAA-AGAAATAAAAAAAT
1 AAACATAAATAAAAAAAT
*
31402 AAAGATAAATAAATAAAAT
1 AAACATAAATAAA-AAAAT
*
31421 AATCA-AAATAAA
1 AAACATAAATAAA
31433 GATAAAGAGC
Statistics
Matches: 68, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
15 1 0.01
16 10 0.15
17 16 0.24
18 16 0.24
19 13 0.19
21 2 0.03
22 10 0.15
ACGTcount: A:0.76, C:0.05, G:0.04, T:0.16
Consensus pattern (18 bp):
AAACATAAATAAAAAAAT
Found at i:31447 original size:28 final size:27
Alignment explanation
Indices: 31315--31478 Score: 78
Period size: 28 Copynumber: 6.0 Consensus size: 27
31305 AATGAAAAAC
*
31315 AAAAT-AAGATAAAGAAAACATAAAAAT-
1 AAAATAAAGATAAAG-AAATA-AAAAATA
*
31342 AAAATAAAGATAAA-AACTAAATAAAATAA
1 AAAATAAAGATAAAGAAAT-AA-AAAAT-A
* *
31371 AGAACATAAA-A-AACA-AAAGAAATAA-A
1 A-AA-ATAAAGATAA-AGAAATAAAAAATA
* *
31397 AAAATAAAGATAAATAAATAAAATAATC
1 AAAATAAAGATAAAGAAATAAAA-AATA
*
31425 AAAATAAAGATAAAGAGCA-AAAAAATA
1 AAAATAAAGATAAAGA-AATAAAAAATA
*
31452 AAAATTAAAAGA-AAAGAAA-AGAAAATA
1 AAAA-T-AAAGATAAAGAAATAAAAAATA
31479 CTAATAATTG
Statistics
Matches: 108, Mismatches: 13, Indels: 32
0.71 0.08 0.21
Matches are distributed among these distances:
24 5 0.05
25 4 0.04
26 13 0.12
27 28 0.26
28 36 0.33
29 11 0.10
30 6 0.06
31 5 0.05
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (27 bp):
AAAATAAAGATAAAGAAATAAAAAATA
Found at i:31541 original size:4 final size:4
Alignment explanation
Indices: 31498--31525 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
31488 GTACTTACAT
31498 AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA
31526 CAAATGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:31568 original size:17 final size:17
Alignment explanation
Indices: 31498--31569 Score: 58
Period size: 17 Copynumber: 4.1 Consensus size: 17
31488 GTACTTACAT
31498 AATAAATA-AATAAAT-A
1 AATAAATATAA-AAATAA
*
31514 AATAAATAAATACAAATGAA
1 AATAAAT--ATAAAAAT-AA
* *
31534 AATAAATATATAATTAA
1 AATAAATATAAAAATAA
*
31551 AATTAATATAAAAATAA
1 AATAAATATAAAAATAA
31568 AA
1 AA
31570 AAACAAAACA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
16 7 0.16
17 18 0.40
18 11 0.24
19 1 0.02
20 8 0.18
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (17 bp):
AATAAATATAAAAATAA
Found at i:36804 original size:21 final size:22
Alignment explanation
Indices: 36779--36820 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
36769 ATTCAAAGAT
36779 ATTAAT-ACATATTAAAATTTA
1 ATTAATAACATATTAAAATTTA
* *
36800 ATTAATAATATATTTAAATTT
1 ATTAATAACATATTAAAATTT
36821 TACAAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTAATAACATATTAAAATTTA
Found at i:39388 original size:63 final size:64
Alignment explanation
Indices: 39239--39398 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 64
39229 GAATTAATTG
* * * *** * *
39239 AACATCGAATGCATTCCATGCACCGATACACTCTCCATTCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACGCT-AATATTTTCAA
*
39304 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACAGGCT-AT-TTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCAC--GCTAATATTTTCA
39366 A
64 A
39367 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
39399 CTTGGTCCAC
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 32 0.39
64 5 0.06
65 44 0.53
67 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACGCTAATATTTTCAA
Found at i:47954 original size:19 final size:19
Alignment explanation
Indices: 47930--47968 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
47920 TCGAATGCAT
47930 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
47949 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
47968 T
1 T
47969 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:48093 original size:64 final size:65
Alignment explanation
Indices: 47916--48078 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
47906 GAATTAATTG
* * * *
47916 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
47981 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
48044 A
65 A
48045 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
48079 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:49037 original size:8 final size:7
Alignment explanation
Indices: 49024--49068 Score: 51
Period size: 6 Copynumber: 6.7 Consensus size: 7
49014 AATATTAGCC
49024 ATATAT-
1 ATATATA
49030 ATATAT-
1 ATATATA
49036 ATATATA
1 ATATATA
*
49043 ATA-GTA
1 ATATATA
49049 ATAGTATA
1 ATA-TATA
49057 ATATATA
1 ATATATA
49064 ATATA
1 ATATA
49069 ATAAAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 17 0.50
7 12 0.35
8 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (7 bp):
ATATATA
Found at i:49070 original size:12 final size:12
Alignment explanation
Indices: 49024--49071 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 12
49014 AATATTAGCC
49024 ATATATATATATA
1 ATATA-ATATATA
49037 TATATAATAGTAATA
1 -ATATAATA-T-ATA
*
49052 GTATAATATATA
1 ATATAATATATA
49064 ATATAATA
1 ATATAATA
49072 AAAATAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 10 0.33
13 4 0.13
14 13 0.43
15 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (12 bp):
ATATAATATATA
Found at i:49077 original size:26 final size:28
Alignment explanation
Indices: 49025--49077 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
49015 ATATTAGCCA
**
49025 TATATATATATATATATAATAGTAATAG
1 TATATATATATATATATAATAAAAATAG
49053 TATA-ATATATA-ATATAATAAAAATA
1 TATATATATATATATATAATAAAAATA
49078 AATAAAAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 7 0.30
28 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (28 bp):
TATATATATATATATATAATAAAAATAG
Found at i:49078 original size:21 final size:21
Alignment explanation
Indices: 49036--49074 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
49026 ATATATATAT
**
49036 ATATATAATAGTAATAGTATA
1 ATATATAATAGTAATAAAATA
49057 ATATATAATA-TAATAAAA
1 ATATATAATAGTAATAAAA
49075 ATAAATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (21 bp):
ATATATAATAGTAATAAAATA
Found at i:49324 original size:16 final size:13
Alignment explanation
Indices: 49284--49317 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
49274 TTTTATTGAT
49284 ATTTTTTTCCTTC
1 ATTTTTTTCCTTC
49297 ATTTTTTTCCTTC
1 ATTTTTTTCCTTC
49310 ATTTTTTT
1 ATTTTTTT
49318 TTTCCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTTTTTTCCTTC
Found at i:55796 original size:14 final size:15
Alignment explanation
Indices: 55772--55804 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
55762 AAGTAAGTGC
55772 ATTCAAATTATTTTG
1 ATTCAAATTATTTTG
55787 ATTC-AATTATTTTG
1 ATTCAAATTATTTTG
55801 ATTC
1 ATTC
55805 GTAGGATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (15 bp):
ATTCAAATTATTTTG
Found at i:57292 original size:15 final size:15
Alignment explanation
Indices: 57272--57342 Score: 74
Period size: 15 Copynumber: 4.7 Consensus size: 15
57262 TATGCTATCT
57272 TATGTGAATATGATC
1 TATGTGAATATGATC
*
57287 TATGTGAGTACATG-TC
1 TATGTGA--ATATGATC
*
57303 TATGTG-ATATAATC
1 TATGTGAATATGATC
*
57317 TATGTGAATATGATA
1 TATGTGAATATGATC
*
57332 TATGTTAATAT
1 TATGTGAATAT
57343 ATGTCTATGT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
13 3 0.07
14 8 0.17
15 23 0.50
16 8 0.17
17 4 0.09
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (15 bp):
TATGTGAATATGATC
Found at i:57758 original size:23 final size:23
Alignment explanation
Indices: 57728--57771 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
57718 GAGTCGATGG
57728 TTCTACGCAATCCTTCGGGACAA
1 TTCTACGCAATCCTTCGGGACAA
* *
57751 TTCTACGCAGTCTTTCGGGAC
1 TTCTACGCAATCCTTCGGGAC
57772 TACTTGTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (23 bp):
TTCTACGCAATCCTTCGGGACAA
Found at i:63541 original size:103 final size:104
Alignment explanation
Indices: 63409--63616 Score: 312
Period size: 103 Copynumber: 2.0 Consensus size: 104
63399 CATGTATCAA
*
63409 AACATTTAATGATTCTATACTAAACATATATATAATAAGATTGTATATATAATATTAAATACAAA
1 AACATTTAATGATTCCATACTAAACATATATATAATAAGATTGTATATATAATATTAAATACAAA
*
63474 GCCA-TTTTAACACAC-AAAATTATTATATTACACGTGAT
66 GCCACTTTT-ACACACGAAAATTATTATATTACACATGAT
* * **
63512 AACATTTAATGATTCCATATTAAAGATATATATAATAAGATTGTATATATAATATTAAATGTAAA
1 AACATTTAATGATTCCATACTAAACATATATATAATAAGATTGTATATATAATATTAAATACAAA
* *
63577 GCCACTTTTGCACACGTATAATTATTATATTACACATGAT
66 GCCACTTTTACACACG-AAAATTATTATATTACACATGAT
63617 TAAAAAGCAT
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
103 69 0.73
104 4 0.04
105 21 0.22
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (104 bp):
AACATTTAATGATTCCATACTAAACATATATATAATAAGATTGTATATATAATATTAAATACAAA
GCCACTTTTACACACGAAAATTATTATATTACACATGAT
Found at i:64729 original size:3 final size:3
Alignment explanation
Indices: 64721--64756 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
64711 CATGTAAAAT
64721 ATA ATA ATA ATA ATTA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA
64757 TTAAAATACG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:64764 original size:16 final size:16
Alignment explanation
Indices: 64715--64757 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 16
64705 GGCCTGCATG
64715 TAAAATATAATAATAA
1 TAAAATATAATAATAA
64731 TAATTAATAATAATAATAA
1 TAA--AAT-ATAATAATAA
64750 TAAAATAT
1 TAAAATAT
64758 TAAAATACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 5 0.21
17 3 0.12
18 3 0.12
19 13 0.54
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAAATATAATAATAA
Found at i:65394 original size:111 final size:111
Alignment explanation
Indices: 64915--66040 Score: 1633
Period size: 111 Copynumber: 10.1 Consensus size: 111
64905 ACTGTCACTC
* * *
64915 AGGGAATATCAGATCT-GGAGATGTTGATTCATTGAATCAGAGTAGACTTGTTCCACTGTCACTC
1 AGGGAATATCAGATCTGGGAGA-GTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTC
*
64979 AGGGAATATCAAATCTTGAAAGAGAGAGATCTGTTCCGCTTCCTCTG
65 AGGGAATATCAAATCTTGAAAGAAAGAGATCTGTTCCGCTTCCTCTG
* * *
65026 AGGGAATATCAGATATGGGAGAGTTGATCCATTGAATC-GGGCAGATTTGTTCCGCTGTCACTCA
1 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
*
65090 GGGAATATCAAATCTTGAAATAAAGAGAGATCTGTTCCGCTTCCTCTG
66 GGGAATATCAAATCTTGAAA-GAA-AGAGATCTGTTCCGCTTCCTCTG
* * *
65138 AGGGAATATCAGATATGGGAGAGTTGATCCATTGAATC-GGGCAGATTTGTTCCGCTGTCACTCA
1 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
*
65202 GGGAATATCAAATCTTGAAAGAAAGAGAGATCTGTTCCGCTTCCTTTG
66 GGGAATATCAAATCTTGAAAG-AA-AGAGATCTGTTCCGCTTCCTCTG
* * * * *
65250 AGGGAATATCAGATCTGGGAGAATTGATCCATTGAATCGGGGCAGATTTGTTCTGCTGTCACTCA
1 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
*
65315 GGGAATATCAAATCTTGAAAGAAAGAGATTTGTTCCGCTTCCTCTG
66 GGGAATATCAAATCTTGAAAGAAAGAGATCTGTTCCGCTTCCTCTG
* * *
65361 AGGGAATATCAGATATGGGAGAGTTGATCCATTGAATCGGGGTAGATTTGTTCCGCTGTCACTCA
1 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
* * * *
65426 AGGAATATCAAATCTTG-AA-AAAGAGGAATTTGTTTCGCTTCTTCTG
66 GGGAATATCAAATCTTGAAAGAAAGA-G-ATCTGTTCCGCTTCCTCTG
*
65472 ATGGAATATCAGATCTGGGCA-AGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTC
1 AGGGAATATCAGATCTGGG-AGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTC
* * * *
65536 AGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCTGCTTCCTCTG
65 AGGGAATATCAAATCTTGAAAGAAAGAGATCTGTTCCGCTTCCTCTG
* *
65583 AGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAGACTTATTCCGCTGTCACTCA
1 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
* * *
65648 GGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTTCCTCTG
66 GGGAATATCAAATCTTGAAAGAAAGAGATCTGTTCCGCTTCCTCTG
* * *
65694 AGGGAATATCATATCTGGGAAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTATCACTCA
1 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
* *
65759 GGGAATATCGAATCTTGAAAGAGATG-GATCTGTTCCGCTTCCTCTG
66 GGGAATATCAAATCTTGAAAGA-AAGAGATCTGTTCCGCTTCCTCTG
* * *
65805 AGGGAATATCA-ATTCTGGGAAAGTTGATTCATTGAATCAGGGTAGACTTGTTCCACTGTCACTC
1 AGGGAATATCAGA-TCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTC
* *
65869 AGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCGCTTCCTCTG
65 AGGGAATATCAAATCTTGAAAGAAAGAGATCTGTTCCGCTTCCTCTG
*
65916 AGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
1 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
* * *
65981 GGGAATATCAAATCTTGAAA-AAA-ATGATATGTTCCACTTCTTCTG
66 GGGAATATCAAATCTTGAAAGAAAGA-GATCTGTTCCGCTTCCTCTG
66026 AAGGGAATATCAGAT
1 -AGGGAATATCAGAT
66041 AGATGGATTT
Statistics
Matches: 943, Mismatches: 55, Indels: 34
0.91 0.05 0.03
Matches are distributed among these distances:
109 5 0.01
110 67 0.07
111 641 0.68
112 181 0.19
113 49 0.05
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (111 bp):
AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
GGGAATATCAAATCTTGAAAGAAAGAGATCTGTTCCGCTTCCTCTG
Found at i:66220 original size:34 final size:34
Alignment explanation
Indices: 66169--66441 Score: 429
Period size: 34 Copynumber: 8.0 Consensus size: 34
66159 ATGACCCAAA
* * * *
66169 GGATTTAAGCATCATGCTCGAAAGACTTACAGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
*
66203 GGATTTGATCATTATGCTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
* *
66237 AGATTTGATCATCATGCTCGAAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
66271 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
* *
66305 GGTTTTGATCATCATGCTCGAAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
*
66339 GGATTTGATCATCATGCTCGGAAGACTTATTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
* *
66373 GGATTTGATCATCATGCTCGTAAGACTTAATGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
*
66407 GGATTTGATCATCATACTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
66441 G
1 G
66442 ACCCGAAGGA
Statistics
Matches: 219, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 219 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (34 bp):
GGATTTGATCATCATGCTCGGAAGACTTACTGAT
Found at i:69089 original size:11 final size:11
Alignment explanation
Indices: 69073--69111 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
69063 TCAATCTTCC
69073 TTATTCTTTTT
1 TTATTCTTTTT
69084 TTATTC--TTT
1 TTATTCTTTTT
69093 TTATTCTTTTT
1 TTATTCTTTTT
*
69104 TTTTTCTT
1 TTATTCTT
69112 CTTTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 9 0.36
11 16 0.64
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (11 bp):
TTATTCTTTTT
Found at i:69096 original size:20 final size:21
Alignment explanation
Indices: 69067--69122 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
69057 CCCTTTTCAA
*
69067 TCTTCCTTATTCTTTTTTTAT
1 TCTTCTTTATTCTTTTTTTAT
*
69088 TCTT-TTTATTCTTTTTTTTT
1 TCTTCTTTATTCTTTTTTTAT
69108 TCTTCTTTATT-TTTT
1 TCTTCTTTATTCTTTT
69123 GGCGAAGTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 22 0.69
21 10 0.31
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (21 bp):
TCTTCTTTATTCTTTTTTTAT
Found at i:69113 original size:14 final size:15
Alignment explanation
Indices: 69083--69122 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
69073 TTATTCTTTT
69083 TTTATTCTTTTTATTC
1 TTTATT-TTTTTATTC
*
69099 TTT-TTTTTTTCTTC
1 TTTATTTTTTTATTC
69113 TTTATTTTTT
1 TTTATTTTTT
69123 GGCGAAGTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 11 0.50
15 8 0.36
16 3 0.14
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTATTTTTTTATTC
Found at i:74959 original size:14 final size:14
Alignment explanation
Indices: 74942--74970 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
74932 TAATCCCTGT
74942 AAATAATTCCCTAC
1 AAATAATTCCCTAC
74956 AAATAATTCCCTAC
1 AAATAATTCCCTAC
74970 A
1 A
74971 TAGAAATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATAATTCCCTAC
Found at i:77722 original size:103 final size:107
Alignment explanation
Indices: 77569--77773 Score: 303
Period size: 103 Copynumber: 2.0 Consensus size: 107
77559 CATGTATCAA
* *
77569 AACATTTAATGATTCTATACTAAACATATATATATAATAAGATTGTATATATAATATTAAATACA
1 AACATTTAATGATTCCATACTAAACAGATATATATAATAAGATTGTATATATAATATTAAATACA
*
77634 AAGCC-GTTTTAACACACA-A-AATTATTATATTACACGTGAT
66 AAGCCACTTTT-ACACACATATAATTATTATATTACACGTGAT
* **
77674 AACATTTAATGATTCCATA-TTAA-AGATATATATAATAAGATTGTATATATAATATTAAATGTA
1 AACATTTAATGATTCCATACTAAACAGATATATATAATAAGATTGTATATATAATATTAAATACA
*
77737 AAGCCACTTTTGCACACATATAATTATTATATTACAC
66 AAGCCACTTTTACACACATATAATTATTATATTACAC
77774 ATAATTAAAA
Statistics
Matches: 90, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
103 48 0.53
104 8 0.09
105 34 0.38
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (107 bp):
AACATTTAATGATTCCATACTAAACAGATATATATAATAAGATTGTATATATAATATTAAATACA
AAGCCACTTTTACACACATATAATTATTATATTACACGTGAT
Found at i:78859 original size:3 final size:3
Alignment explanation
Indices: 78851--78895 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
78841 CATGTAAAAT
78851 ATA ATA ATA ATA ATA ATA ATTA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
78896 TTAAAAGACG
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:78876 original size:19 final size:19
Alignment explanation
Indices: 78852--78889 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
78842 ATGTAAAATA
78852 TAATAATAATAATAATAAT
1 TAATAATAATAATAATAAT
78871 TAATAATAATAATAATAAT
1 TAATAATAATAATAATAAT
78890 AAAATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAATAATAATAATAATAAT
Found at i:79880 original size:14 final size:15
Alignment explanation
Indices: 79855--79887 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
79845 TTTTTAAATA
79855 AATTATAAATATATT
1 AATTATAAATATATT
*
79870 AATTA-AAATATTTT
1 AATTATAAATATATT
79884 AATT
1 AATT
79888 CTTTTCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTATAAATATATT
Found at i:85011 original size:23 final size:22
Alignment explanation
Indices: 84959--85011 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
84949 ATATTACAAA
*
84959 AATATTTATTTATTTTTTAAAAT
1 AATA-TTAATTATTTTTTAAAAT
84982 -ATAATTAATTATTTGTTTAAAAT
1 AAT-ATTAATTATTT-TTTAAAAT
85005 AATATTA
1 AATATTA
85012 TTTTTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 11 0.42
23 13 0.50
24 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
AATATTAATTATTTTTTAAAAT
Found at i:85183 original size:19 final size:22
Alignment explanation
Indices: 85122--85183 Score: 83
Period size: 23 Copynumber: 2.9 Consensus size: 22
85112 ATAATTTAAA
* *
85122 AAATAATATTATTTCAAATAAAT
1 AAATAATATGATTTTAAA-AAAT
85145 AAATAATATGATTTTAAAAAAT
1 AAATAATATGATTTTAAAAAAT
85167 AAATAA-AT-ATTTTAAAA
1 AAATAATATGATTTTAAAA
85184 TATTTTCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 9 0.24
21 2 0.05
22 10 0.27
23 16 0.43
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
AAATAATATGATTTTAAAAAAT
Found at i:85203 original size:34 final size:34
Alignment explanation
Indices: 85164--85239 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 34
85154 GATTTTAAAA
* *
85164 AATAAATAAATATT-TTAAAATATTTTCATAATATT
1 AATAAATAAA-ATTCTTAAAATAATTTAATAAT-TT
*
85199 -ATAAATAAAATTCTTAGAATAATTTAATAATTT
1 AATAAATAAAATTCTTAAAATAATTTAATAATTT
85232 AATAAATA
1 AATAAATA
85240 CATACAAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 5 0.14
34 31 0.86
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (34 bp):
AATAAATAAAATTCTTAAAATAATTTAATAATTT
Found at i:105097 original size:13 final size:13
Alignment explanation
Indices: 105073--105108 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
105063 CGACAGAAGA
105073 AAGAAA-TTTTTT
1 AAGAAATTTTTTT
105085 AAGAAATTTTTTT
1 AAGAAATTTTTTT
105098 AAGAACATTTT
1 AAGAA-ATTTT
105109 AGTCCAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 6 0.27
13 11 0.50
14 5 0.23
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (13 bp):
AAGAAATTTTTTT
Found at i:107760 original size:36 final size:36
Alignment explanation
Indices: 107712--108200 Score: 575
Period size: 36 Copynumber: 13.8 Consensus size: 36
107702 AACTATTTCC
* *
107712 AAAACACTATATAATATATATTTTTTCAAAAAT-TTTT
1 AAAA-ACTATATATTATATA-ATTTTCAAAAATGTTTT
*
107749 AAAATCTATATATTATATAATTTT-AAAAATGTTTT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
* **
107784 CAAAAACTATATATTATATAGTTTTC-AAAATAATTT
1 -AAAAACTATATATTATATAATTTTCAAAAATGTTTT
*
107820 AAAAACTATATATTATAT-ATATTTC-TAAATGTTTT
1 AAAAACTATATATTATATAAT-TTTCAAAAATGTTTT
*
107855 -AAAAC--TATATT-TATAATTTTCAAAAATGTATT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
* *
107887 AAAAACTATGTAATATAT-ATTTTCAAAAATG-TTT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
*
107921 -AAAACTATATATTATATATATTTTCTAAAATGTTTT
1 AAAAACTATATATTATATA-ATTTTCAAAAATGTTTT
107957 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
107993 AAAAACTATATATTATATAATTTTCAAAAATGTTTTT
1 AAAAACTATATATTATATAATTTTCAAAAATG-TTTT
* * * *
108030 AAAAACTTTGTAATATAT-TTTTTCAAAAATGTTTT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
*
108065 -AAAAC--TATA-TATAT-ATTTTCTAAAATGTTTT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
* *
108096 AAATACTATATTTTATATAATTTTCAAAAATGTTTT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
* *
108132 AAAAACTATATAATATAT-ATATTCAAAAATGTTTT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT
108167 AAAAAAACTATATATTATATACATATTTCAAAAA
1 --AAAAACTATATATTATATA-AT-TTTCAAAAA
108201 CCGTTTGCAA
Statistics
Matches: 391, Mismatches: 36, Indels: 47
0.82 0.08 0.10
Matches are distributed among these distances:
31 27 0.07
32 23 0.06
33 20 0.05
34 22 0.06
35 91 0.23
36 140 0.36
37 58 0.15
39 2 0.01
40 8 0.02
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (36 bp):
AAAAACTATATATTATATAATTTTCAAAAATGTTTT
Found at i:108239 original size:139 final size:136
Alignment explanation
Indices: 107818--108239 Score: 368
Period size: 139 Copynumber: 3.1 Consensus size: 136
107808 TCAAAATAAT
* *
107818 TTAAAA-ACTATATATTATAT-ATATTTC-TAAATGTTTT-AAAACTATAT--T-TATAATTTTC
1 TTAAAATACTATATATTATATAAT-TTTCAAAAATGTTTTAAAAACTATATAATATATAATATTC
* * * *
107876 AAAAATGTATT-AAAAACTATGTAATAT-ATATTTTCAAAAATGTTT-AAAACTATATATTATAT
65 AAAAATGTTTTAAAAAACTTTATAATATAATA-TTTCAAAAACGTTTGAAAAC----TA-TATAT
* *
107938 ATATTTTCTAAAA
124 ATATTGTATAAAA
* *
107951 TGTTTTAAAA-ACTATATATTATATAATTTTCAAAAATGTTTTAAAAACTATATATTATATAATT
1 ----TTAAAATACTATATATTATATAATTTTCAAAAATGTTTTAAAAACTATATAATATATAATA
* * * * * *
108015 TTCAAAAATGTTTTTAAAAACTTTGTAATATATTTTTTCAAAAATGTTTTAAAACTATATATATA
62 TTCAAAAATGTTTTAAAAAACTTTATAATATAATATTTCAAAAACGTTTGAAAACTATATATATA
* *
108080 TTTTCTAAAA
127 TTGTATAAAA
* *
108090 TGTTTTAAATACTATATTTTATATAATTTTCAAAAATGTTTTAAAAACTATATAATATAT-ATAT
1 ---TTAAAATACTATATATTATATAATTTTCAAAAATGTTTTAAAAACTATATAATATATAATAT
* *
108154 TCAAAAATGTTTTAAAAAAACTATATATTATATACATATTTCAAAAACCGTTTGCAAACTATA-A
63 TCAAAAATGTTTT-AAAAAACT-T-TATAATATA-ATATTTCAAAAA-CGTTTGAAAACTATATA
108218 TATATATGTATAAAA
123 TATAT-TGTATAAAA
108233 -TAAAATA
1 TTAAAATA
108240 TGGACGAAAA
Statistics
Matches: 247, Mismatches: 22, Indels: 30
0.83 0.07 0.10
Matches are distributed among these distances:
137 24 0.10
138 33 0.13
139 89 0.36
140 3 0.01
141 8 0.03
142 36 0.15
143 48 0.19
144 6 0.02
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (136 bp):
TTAAAATACTATATATTATATAATTTTCAAAAATGTTTTAAAAACTATATAATATATAATATTCA
AAAATGTTTTAAAAAACTTTATAATATAATATTTCAAAAACGTTTGAAAACTATATATATATTGT
ATAAAA
Found at i:109065 original size:84 final size:84
Alignment explanation
Indices: 108764--109648 Score: 687
Period size: 84 Copynumber: 10.7 Consensus size: 84
108754 GCTCTTCTTA
* * * * * * * *
108764 CCTTGAGCTATGTTGTAAATTTGATTTGCCTTTGAGCTTAGTGTAATCGAACTTGAAGGTC---T
1 CCTTGAGCTATGCTGCAAA--TGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
* *
108826 -TTAGCAGATAGCCCTTCTCG
64 GTTAGCAGATAACCCTTCTAG
* * * * * * * *
108846 ACTTAATCTATGCTGCAAATAACAGTGCCTTGGAGTTGAGCGTAATCGAAC-CG-AGG--TTTTG
1 CCTTGAGCTATGCTGCAAATGA-TGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
* *
108907 TT-GACGGATAACCTTTCTAG
65 TTAG-CAGATAACCCTTCTAG
** * * * *
108927 CCTTGATTTATGCTG-TAATGAT-AGCCTTAAAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGT
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
*
108990 TAGCAGATAACCCCTCTAG
66 TAGCAGATAACCCTTCTAG
* * * *
109009 CCTTGAGTTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGT
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* * *
109074 TGGCAGATAGCCCTTCTCG
66 TAGCAGATAACCCTTCTAG
* * * * ** * *
109093 ACTTAAGCTATTCTGCAAATAATGGTGCCTCT-GAGCTGAGTATAATCAAACTCGAAGGTC-TTT
1 CCTTGAGCTATGCTGCAAATGAT-GTGCCT-TAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
*
109156 G---GAAGATAACCCTTCTAG
64 GTTAGCAGATAACCCTTCTAG
* * * * *
109174 CCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGT
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* *
109239 TGGAAGATAACCCTTCTCA-
66 TAGCAGATAACCCTTCT-AG
* * * * * *
109258 ACTTAAGCTATGTTACAAATGATGTGCTTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
109323 TAGCA-ATAACCCTTCTCA-
66 TAGCAGATAACCCTTCT-AG
** * ** ** * *
109341 ATTTAAGCTATGCAACAAATGATAGTGCCTCTA-AGCTGAGTATAATCGAACTCGAATGTC---T
1 CCTTGAGCTATGCTGCAAATGAT-GTGCCT-TAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
*
109402 -TTAGTAGATAACCCTTCTAG
64 GTTAGCAGATAACCCTTCTAG
* * * *
109422 CCTTGAGTTATGCTTCAAATGATGTGCCTTTA-AGATGAGCGTAGTCGAACTCGGAGGTCTTTTG
1 CCTTGAGCTATGCTGCAAATGATGTGCC-TTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
* * *
109486 TTAGCAAATAACCTTTCTTG
65 TTAGCAGATAACCCTTCTAG
* * * * *
109506 CCTTGAGCTATGTTGCAAATGGTGTGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGTC-TTTGC
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* * *
109570 TGGCAGATAGCCCTTCTCG
66 TAGCAGATAACCCTTCTAG
* **
109589 -CTTAAGCTA-GCTGCAAATGATGGTGCCTCT-GAGCTGAGTATA-TCGAACTCGAAGGTCTTT
1 CCTTGAGCTATGCTGCAAATGAT-GTGCCT-TAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
109649 GGTAGATAAC
Statistics
Matches: 648, Mismatches: 121, Indels: 68
0.77 0.14 0.08
Matches are distributed among these distances:
78 21 0.03
79 5 0.01
80 78 0.12
81 137 0.21
82 73 0.11
83 62 0.10
84 238 0.37
85 33 0.05
86 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (84 bp):
CCTTGAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
TAGCAGATAACCCTTCTAG
Found at i:109427 original size:248 final size:247
Alignment explanation
Indices: 108757--109662 Score: 1014
Period size: 248 Copynumber: 3.7 Consensus size: 247
108747 ACATATAGCT
* * * * * * *
108757 CTTCTTACCTTGAGCTATGTTGTAAATTTGATTTGCCTTTGAGCTTAGTGTAATCGAACTTGAAG
1 CTTC-TACCTTGAGCTATGTTGCAAA--TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * * ** *
108822 GTC---T-TTAGCAGATAGCCCTTCTCGACTTAATCTATGCTGCAAATAACAGTGCCT-TGGAGT
63 GTCTTTTGTTGGCAGATAGCCCTTCTC-ACTTAAGCTATGCTGCAAATGATGGTGCCTCT-GAGC
** * * * *
108882 TGAGCGTAATCGAAC-CG-AGGT-TTTGTTGACGGATAACCTTTCTAGCCTTGATTTATGCTG-T
126 TGAGTATAATCGAACTCGAAGGTCTTTGGT-A--GATAACCCTTCTAGCCTTGAGTTATGCTGCA
* * * *
108943 AATGAT-AGCCTTAAAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGTTAGCAGATAACC
188 AATGATGTGCCTTAAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGAAGATAACC
* * ** * *
109002 CCTCTAGCCTTGAGTTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCAAACTCGAAGGT
1 CTTCTA-CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
* * *
109067 CTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATAATGGTGCCTCTGAGCTGA
65 CTTTTGTTGGCAGATAGCCCTTCTC-ACTTAAGCTATGCTGCAAATGATGGTGCCTCTGAGCTGA
* *
109132 GTATAATCAAACTCGAAGGTCTTTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
129 GTATAATCGAACTCGAAGGTCTTTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
** * * *
109197 GTGCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTTGGAAGATAACC
194 GTGCCTTAAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGAAGATAACC
* * * *
109251 CTTCTCAACTTAAGCTATGTTACAAATGATGTGCTTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
1 CTTCT-ACCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
* * * ** * *
109316 CTTTTGTTAGCA-ATAACCCTTCTCAATTTAAGCTATGCAACAAATGATAGTGCCTCTAAGCTGA
65 CTTTTGTTGGCAGATAGCCCTTCTC-ACTTAAGCTATGCTGCAAATGATGGTGCCTCTGAGCTGA
* * *
109380 GTATAATCGAACTCGAATGTCTTTAGTAGATAACCCTTCTAGCCTTGAGTTATGCTTCAAATGAT
129 GTATAATCGAACTCGAAGGTCTTTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
* * * *
109445 GTGCCTTTAAGATGAGCGTAGTCGAACTCGGAGGTCTTTTGTTAGCAA-ATAACC
194 GTGCCTTAAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTT-GGAAGATAACC
* * * *
109499 TTTCTTGCCTTGAGCTATGTTGCAAATGGTGTGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGT
1 CTTC-TACCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
* *
109564 C-TTTGCTGGCAGATAGCCCTTCTCGCTTAAGCTA-GCTGCAAATGATGGTGCCTCTGAGCTGAG
65 CTTTTGTTGGCAGATAGCCCTTCTCACTTAAGCTATGCTGCAAATGATGGTGCCTCTGAGCTGAG
109627 TAT-ATCGAACTCGAAGGTCTTTGGTAGATAACCCTT
130 TATAATCGAACTCGAAGGTCTTTGGTAGATAACCCTT
109663 AA
Statistics
Matches: 557, Mismatches: 89, Indels: 30
0.82 0.13 0.04
Matches are distributed among these distances:
243 33 0.06
244 2 0.00
245 49 0.09
246 28 0.05
247 103 0.18
248 221 0.40
249 116 0.21
250 5 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (247 bp):
CTTCTACCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
TTTTGTTGGCAGATAGCCCTTCTCACTTAAGCTATGCTGCAAATGATGGTGCCTCTGAGCTGAGT
ATAATCGAACTCGAAGGTCTTTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
GCCTTAAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGAAGATAACC
Found at i:109544 original size:164 final size:166
Alignment explanation
Indices: 108785--109648 Score: 693
Period size: 165 Copynumber: 5.3 Consensus size: 166
108775 GTTGTAAATT
* * * * * * * * *
108785 TGATTTGCCTTTGAGCTTAGTGTAATCGAACTTGAAGGTC---T-TTAGCAGATAGCCCTTCTCG
1 TGATGTGCCTTTAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTAGCAAATAACCCTTCTAG
* * * * * * * *
108846 ACTTAATCTATGCTGCAAATAACAGTGCCTTGGAGTTGAGCGTAATCGAAC-CG-AGGT-TTT-G
66 CCTTGAGCTATGCTGCAAATGA-TGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGG
* * * **
108907 TTGACGGATAACCTTTCTAGCCTTGATTTATGCTGT--AA
130 TTGA--GATAACCCTTCTAGACTTAAGCTATGCT-TCAAA
* * * * *
108945 TGAT-AGCCTTAAAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGTTAGCAGATAACCCCTCTAG
1 TGATGTGCCTTTAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTAGCAAATAACCCTTCTAG
* * *
109009 CCTTGAGTTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGT
66 CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGT
* * * *
109074 TGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAA
131 T-G-AGATAACCCTTCTAGACTTAAGCTATGCTTCAAA
* * * ** * *
109112 TAATGGTGCCTCTGAGCTGAGTATAATCAAACTCGAAGGTC-TTTG---G-AAGATAACCCTTCT
1 TGAT-GTGCCTTTAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTAGCAA-ATAACCCTTCT
* *
109172 AGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTG
64 AGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTG
109237 GTTGGAAGATAACCCTTCTCA-ACTTAAGCTATG-TTACAAA
129 GTT-G-AGATAACCCTTCT-AGACTTAAGCTATGCTT-CAAA
*
109277 TGATGTG-CTTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTAGC-AATAACCCTTCTC
1 TGATGTGCCTTT-AAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTAGCAAATAACCCTTCT-
** * ** * ** * * *
109340 A-ATTTAAGCTATGCAACAAATGATAGTGCCTCT-AAGCTGAGTATAATCGAACTCGAATGTCTT
64 AGCCTTGAGCTATGCTGCAAATGAT-GTGCCT-TGGAGCTGAGCGTAGTCAAACTCGAAGGTCTT
* * * *
109403 TAG-T-AGATAACCCTTCTAGCCTTGAGTTATGCTTCAAA
127 TGGTTGAGATAACCCTTCTAGACTTAAGCTATGCTTCAAA
* * * *
109441 TGATGTGCCTTTAAGATGAGCGTAGTCGAACTCGGAGGTCTTTTGTTAGCAAATAACCTTTCTTG
1 TGATGTGCCTTTAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTAGCAAATAACCCTTCTAG
* * ** *
109506 CCTTGAGCTATGTTGCAAATGGTGTGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGCT
66 CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGT
* * * *
109571 GGCAGATAGCCCTTCTCG-CTTAAGCTA-GCTGCAAA
131 TG-AGATAACCCTTCTAGACTTAAGCTATGCTTCAAA
* * **
109606 TGATGGTGCCTCTGAGCTGAGTATA-TCGAACTCGAAGGTCTTT
1 TGAT-GTGCCTTTAAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
109649 GGTAGATAAC
Statistics
Matches: 566, Mismatches: 102, Indels: 67
0.77 0.14 0.09
Matches are distributed among these distances:
159 29 0.05
160 4 0.01
162 24 0.04
163 40 0.07
164 132 0.23
165 176 0.31
166 45 0.08
167 48 0.08
168 41 0.07
169 27 0.05
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (166 bp):
TGATGTGCCTTTAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTAGCAAATAACCCTTCTAG
CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGT
TGAGATAACCCTTCTAGACTTAAGCTATGCTTCAAA
Done.