Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397263.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_86.0, 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: 8461613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 85630 characters in sequence are not A, C, G, or T
File 14 of 18
Found at i:6309002 original size:34 final size:32
Alignment explanation
Indices: 6308950--6309020 Score: 106
Period size: 34 Copynumber: 2.2 Consensus size: 32
6308940 ACGGCCTAAG
* *
6308950 AAAGAGAGGAGAAGAGAACCAATTGGAGGGCT
1 AAAGAGAGGAGAAAAGAACCAATTGAAGGGCT
6308982 AAAGAGGAGGGAGAAAAGAACCAATTGAAGGGCT
1 AAAGA-GA-GGAGAAAAGAACCAATTGAAGGGCT
6309016 AAAGA
1 AAAGA
6309021 AGACAAGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 5 0.14
33 2 0.06
34 28 0.80
ACGTcount: A:0.48, C:0.08, G:0.35, T:0.08
Consensus pattern (32 bp):
AAAGAGAGGAGAAAAGAACCAATTGAAGGGCT
Found at i:6309349 original size:33 final size:33
Alignment explanation
Indices: 6309252--6309350 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
6309242 TTTACTAGTA
* * *
6309252 AAGCAACTGAAGCTGCTGGTGCTGCACCAAGGG
1 AAGCTACTGAAGCTGCTGGTGGTGCACCAAGTG
* *
6309285 AAGCTGCTGAAGCTACTGGTGGTGCACCAAGTG
1 AAGCTACTGAAGCTGCTGGTGGTGCACCAAGTG
* *
6309318 AAGCTACTAAAGCTGTTGGTGGTGCACCAAGTG
1 AAGCTACTGAAGCTGCTGGTGGTGCACCAAGTG
6309351 TTGCTACAGC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.20
Consensus pattern (33 bp):
AAGCTACTGAAGCTGCTGGTGGTGCACCAAGTG
Found at i:6310383 original size:2 final size:2
Alignment explanation
Indices: 6310376--6310412 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6310366 ATGATTTTGC
*
6310376 AT AT AT AT AT AT AG 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 AT A
6310413 AAAGGCTGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6331333 original size:14 final size:14
Alignment explanation
Indices: 6331302--6331347 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
6331292 CCTTCACACC
6331302 TCTTTTTCTCTCTT-
1 TCTTTTTCTCT-TTA
6331316 TCTTTTTCTCTTTA
1 TCTTTTTCTCTTTA
*
6331330 TC-TTCTCT-TTTA
1 TCTTTTTCTCTTTA
6331342 TCTTTT
1 TCTTTT
6331348 ATTTGTACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 6 0.21
13 9 0.32
14 13 0.46
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (14 bp):
TCTTTTTCTCTTTA
Found at i:6331340 original size:19 final size:18
Alignment explanation
Indices: 6331312--6331349 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
6331302 TCTTTTTCTC
6331312 TCTTTCTTTT-TCTCTTTA
1 TCTTTCTTTTATCT-TTTA
6331330 TCTTCTCTTTTATCTTTTA
1 TCTT-TCTTTTATCTTTTA
6331349 T
1 T
6331350 TTGTACTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 11 0.61
20 3 0.17
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (18 bp):
TCTTTCTTTTATCTTTTA
Found at i:6331518 original size:16 final size:17
Alignment explanation
Indices: 6331489--6331524 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
6331479 ATCTTTTTTA
6331489 ATTTATATTATTTAACT
1 ATTTATATTATTTAACT
6331506 ATTTATA-TATTTAACT
1 ATTTATATTATTTAACT
6331522 ATT
1 ATT
6331525 GTGTGAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTATATTATTTAACT
Found at i:6331559 original size:21 final size:21
Alignment explanation
Indices: 6331535--6331579 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
6331525 GTGTGAAATC
*
6331535 TTATATATTATA-TTTATATAT
1 TTATACATTATAGTTT-TATAT
*
6331556 TTATGCATTATAGTTTTATAT
1 TTATACATTATAGTTTTATAT
6331577 TTA
1 TTA
6331580 ATTTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (21 bp):
TTATACATTATAGTTTTATAT
Found at i:6331994 original size:19 final size:17
Alignment explanation
Indices: 6331957--6331995 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
6331947 TATTTATATG
*
6331957 TTATATAAAATTATCTA
1 TTATATAAAATTAACTA
6331974 TTATATAAAATTCAACATA
1 TTATATAAAATT-AAC-TA
6331993 TTA
1 TTA
6331996 GCTTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
18 2 0.11
19 5 0.26
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (17 bp):
TTATATAAAATTAACTA
Found at i:6333991 original size:17 final size:17
Alignment explanation
Indices: 6333969--6334004 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6333959 GATTTTAAAC
6333969 TTAATTAAATCTCACAA
1 TTAATTAAATCTCACAA
* *
6333986 TTAATTCAATTTCACAA
1 TTAATTAAATCTCACAA
6334003 TT
1 TT
6334005 TTATAGTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAATTAAATCTCACAA
Found at i:6337753 original size:17 final size:17
Alignment explanation
Indices: 6337718--6337751 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6337708 TATAAAAATC
*
6337718 ATATTTTATTCATATTT
1 ATATATTATTCATATTT
6337735 ATATATTATATCATATT
1 ATATATTAT-TCATATT
6337752 ATGTATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATATTATTCATATTT
Found at i:6338355 original size:22 final size:21
Alignment explanation
Indices: 6338319--6338359 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
6338309 TAGTTATGTA
6338319 TAAATTAAATATATATAATAT
1 TAAATTAAATATATATAATAT
*
6338340 TAAATTATTATATATATAAT
1 TAAATTA-AATATATATAAT
6338360 TAATGATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAATTAAATATATATAATAT
Found at i:6338361 original size:20 final size:19
Alignment explanation
Indices: 6338307--6338362 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 19
6338297 AAGTTATAGT
*
6338307 AATAGTTATGTATA-AATTA
1 AATA-TTATATATATAATTA
6338326 AATA-TATATA-AT-ATTA
1 AATATTATATATATAATTA
6338342 AATTATTATATATATAATTA
1 AA-TATTATATATATAATTA
6338362 A
1 A
6338363 TGATACAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
16 7 0.23
17 7 0.23
18 6 0.19
19 6 0.19
20 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (19 bp):
AATATTATATATATAATTA
Found at i:6338710 original size:33 final size:32
Alignment explanation
Indices: 6338659--6338724 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 32
6338649 TAATAATACT
*
6338659 TATGTATAAATTAAATATATGTATAT-ATAATA
1 TATGTATAAATTAAATATATATAT-TCATAATA
*
6338691 TATGTATACAATTATATATATATATTCATAATA
1 TATGTATA-AATTAAATATATATATTCATAATA
6338724 T
1 T
6338725 TTTATATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 9 0.30
33 21 0.70
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (32 bp):
TATGTATAAATTAAATATATATATTCATAATA
Found at i:6339611 original size:22 final size:22
Alignment explanation
Indices: 6339584--6339634 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
6339574 CAAATAATTT
*
6339584 TACAAAAAAGAATAT-TGAAAAA
1 TACAAAAAA-AATATATAAAAAA
* *
6339606 TTCAAATAAAATATATAAAAAA
1 TACAAAAAAAATATATAAAAAA
6339628 TACAAAA
1 TACAAAA
6339635 GTAGAATGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.22
Consensus pattern (22 bp):
TACAAAAAAAATATATAAAAAA
Found at i:6345827 original size:27 final size:27
Alignment explanation
Indices: 6345759--6346391 Score: 304
Period size: 27 Copynumber: 23.6 Consensus size: 27
6345749 CATCACGGGC
* * * *
6345759 GTTCCAAGTATAGAAGCACCTAGAGGC
1 GTTCCAAGTACAGAAGCGCCTAGGGGT
* * *
6345786 GATT-TAAGTATAGAAGCGTCTAGGGGT
1 G-TTCCAAGTACAGAAGCGCCTAGGGGT
* * * * *
6345813 GTTCCAAGCACAGAAACGCCCAAGGGC
1 GTTCCAAGTACAGAAGCGCCTAGGGGT
* * * * * *
6345840 ATTCCAAGTATAGAAGTGTAC-AAGGGA
1 GTTCCAAGTACAGAAGCG-CCTAGGGGT
** * * * * *
6345867 GTTCCAAGCGCAAAAGCACCCACGGGC
1 GTTCCAAGTACAGAAGCGCCTAGGGGT
* * *
6345894 GTTCCAAGTATAGAAGCACCTAGGAGT
1 GTTCCAAGTACAGAAGCGCCTAGGGGT
* *
6345921 GTTTCAAGTACAGAAACGCCTA-GGGT
1 GTTCCAAGTACAGAAGCGCCTAGGGGT
* * *
6345947 GTTCCAATTACAAAAGCGCAC-AGTGGT
1 GTTCCAAGTACAGAAGCGC-CTAGGGGT
* * *
6345974 GTTCCTTAAGCACAAAAACGCCTA-GGGT
1 GTTCC--AAGTACAGAAGCGCCTAGGGGT
* * *
6346002 GTTCCAAGTACAAAATGC-AC-AGGGGC
1 GTTCCAAGTACAGAA-GCGCCTAGGGGT
* * * **
6346028 GTTCCAACTACAGAAGCACCCAGGGAC
1 GTTCCAAGTACAGAAGCGCCTAGGGGT
* *
6346055 GTTCCAAGTATAGAAGCGCCTAGGGGG
1 GTTCCAAGTACAGAAGCGCCTAGGGGT
* * * *
6346082 GTTCCAAGCACAGAAACGTCC-AAGGGC
1 GTTCCAAGTACAGAAGCG-CCTAGGGGT
* * *
6346109 GTTCCAAGTATAGAAGC-ACTCAGGGGA
1 GTTCCAAGTACAGAAGCGCCT-AGGGGT
* * * *
6346136 GTTCCAAGTGCAGAAGCACCCAGGGGC
1 GTTCCAAGTACAGAAGCGCCTAGGGGT
* * *
6346163 GTTCCAAGTATAGAAGCACCTA-GAGT
1 GTTCCAAGTACAGAAGCGCCTAGGGGT
** * *
6346189 GTTCCAAACACAGAAACGCCTA-GGTT
1 GTTCCAAGTACAGAAGCGCCTAGGGGT
* * * * *
6346215 GTTCCAAGTATAGAAGCACCCAAGGGC
1 GTTCCAAGTACAGAAGCGCCTAGGGGT
* * *
6346242 GTTCTAAGCT-CAGAAGCGCCCA-GGGA
1 GTTCCAAG-TACAGAAGCGCCTAGGGGT
* *
6346268 GTTCCAAGTTCAGAAGCACCTAGGGGT
1 GTTCCAAGTACAGAAGCGCCTAGGGGT
* *
6346295 GTTCTAAGTACAGAAGCACCTAGGGGT
1 GTTCCAAGTACAGAAGCGCCTAGGGGT
* * * * *
6346322 GTTCCAAGCACAAAAACACCTA-GAGT
1 GTTCCAAGTACAGAAGCGCCTAGGGGT
* * * *
6346348 GTTCCAAGTACAGAAACGCATAGAGGC
1 GTTCCAAGTACAGAAGCGCCTAGGGGT
* *
6346375 GTTTCAAGTGCAGAAGC
1 GTTCCAAGTACAGAAGC
6346392 ACCCAGGGAC
Statistics
Matches: 457, Mismatches: 127, Indels: 44
0.73 0.20 0.07
Matches are distributed among these distances:
25 5 0.01
26 127 0.28
27 297 0.65
28 16 0.04
29 12 0.03
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (27 bp):
GTTCCAAGTACAGAAGCGCCTAGGGGT
Found at i:6345852 original size:54 final size:54
Alignment explanation
Indices: 6345791--6346366 Score: 392
Period size: 54 Copynumber: 10.8 Consensus size: 54
6345781 GAGGCGATTT
** *
6345791 AAGTATAGAAGCGTCTAGGGGTGTTCCAAGCACAGAAACGCCCAAGGGCATTCC
1 AAGTATAGAAGCACCTAGGGGTGTTCCAAGCACAGAAACGCCCAAGGGCGTTCC
* * * * * *
6345845 AAGTATAGAAGTGTA-C-AAGGGAGTTCCAAGCGCA-AAAGCACCCACGGGCGTTCC
1 AAGTATAGAA--GCACCTAGGGGTGTTCCAAGCACAGAAA-CGCCCAAGGGCGTTCC
* * * * *
6345899 AAGTATAGAAGCACCTAGGAGTGTTTCAAGTACAGAAACG-CCTAGGGTGTTCC
1 AAGTATAGAAGCACCTAGGGGTGTTCCAAGCACAGAAACGCCCAAGGGCGTTCC
* * * * * * * *
6345952 AATTACAAAAGCGCAC-AGTGGTGTTCCTTAAGCACAAAAACG-CCTAGGGTGTTCC
1 AAGTATAGAAGCAC-CTAGGGGTGTTCC--AAGCACAGAAACGCCCAAGGGCGTTCC
* * * * *
6346007 AAGTACAAAATGCA-C-AGGGGCGTTCCAA-CTACAGAAGCACCC-AGGGACGTTCC
1 AAGTATAGAA-GCACCTAGGGGTGTTCCAAGC-ACAGAAACGCCCAAGGG-CGTTCC
* * *
6346060 AAGTATAGAAGCGCCTAGGGGGGTTCCAAGCACAGAAACGTCCAAGGGCGTTCC
1 AAGTATAGAAGCACCTAGGGGTGTTCCAAGCACAGAAACGCCCAAGGGCGTTCC
* ** * * *
6346114 AAGTATAGAAGCA-CTCAGGGGAGTTCCAAGTGCAGAAGCACCCAGGGGCGTTCC
1 AAGTATAGAAGCACCT-AGGGGTGTTCCAAGCACAGAAACGCCCAAGGGCGTTCC
* * * **
6346168 AAGTATAGAAGCACCTA-GAGTGTTCCAAACACAGAAACG-CCTAGGTTGTTCC
1 AAGTATAGAAGCACCTAGGGGTGTTCCAAGCACAGAAACGCCCAAGGGCGTTCC
* * * * * * *
6346220 AAGTATAGAAGCACCCAAGGGCGTTCTAAGCTCAGAAGCGCCC-AGGGAGTTCC
1 AAGTATAGAAGCACCTAGGGGTGTTCCAAGCACAGAAACGCCCAAGGGCGTTCC
* * * * * * *
6346273 AAGT-TCAGAAGCACCTAGGGGTGTTCTAAGTACAGAAGCACCTAGGGGTGTTCC
1 AAGTAT-AGAAGCACCTAGGGGTGTTCCAAGCACAGAAACGCCCAAGGGCGTTCC
* * * * * *
6346327 AAGCACAAAAACACCTA-GAGTGTTCCAAGTACAGAAACGC
1 AAGTATAGAAGCACCTAGGGGTGTTCCAAGCACAGAAACGC
6346367 ATAGAGGCGT
Statistics
Matches: 410, Mismatches: 88, Indels: 49
0.75 0.16 0.09
Matches are distributed among these distances:
51 1 0.00
52 42 0.10
53 142 0.35
54 178 0.43
55 44 0.11
56 3 0.01
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.17
Consensus pattern (54 bp):
AAGTATAGAAGCACCTAGGGGTGTTCCAAGCACAGAAACGCCCAAGGGCGTTCC
Found at i:6346005 original size:28 final size:26
Alignment explanation
Indices: 6345912--6346016 Score: 95
Period size: 26 Copynumber: 3.9 Consensus size: 26
6345902 TATAGAAGCA
* * *
6345912 CCTAGGAGTGTTTCAAGTACAGAAACG
1 CCTAGG-GTGTTCCAAGCACAAAAACG
** *
6345939 CCTAGGGTGTTCCAATTACAAAAGCG
1 CCTAGGGTGTTCCAAGCACAAAAACG
6345965 CAC-AGTGGTGTTCCTTAAGCACAAAAACG
1 C-CTAG-GGTGTTCC--AAGCACAAAAACG
*
6345994 CCTAGGGTGTTCCAAGTACAAAA
1 CCTAGGGTGTTCCAAGCACAAAA
6346017 TGCACAGGGG
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
26 28 0.43
27 15 0.23
28 9 0.14
29 13 0.20
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (26 bp):
CCTAGGGTGTTCCAAGCACAAAAACG
Found at i:6346320 original size:159 final size:160
Alignment explanation
Indices: 6346055--6346411 Score: 407
Period size: 159 Copynumber: 2.2 Consensus size: 160
6346045 ACCCAGGGAC
* * * * *
6346055 GTTCCAAGTATAGAAGCGCCTAGGGGGGTTCCAAGCACAGAAACGTCCAAGGGCGTTCCAAGTAT
1 GTTCCAAGTATAGAAGCACCCAAGGGCGTTCCAAGCACAGAAACGTCCAAGGGAGTTCCAAGTAT
* * * * *
6346120 AGAAGCACTCAGGGGAGTTCCAAGTGCAGAAGCACCCAGGGGCGTTCCAAGTATAGAAGCACCTA
66 AGAAGCACTCAGGGGAGTTCCAAGTACAGAAGCACCCAGGGGCGTTCCAAGCACAAAAACACCTA
6346185 GAGTGTTCCAAACACAGAAACGCCTAGGTT
131 GAGTGTTCCAAACACAGAAACGCCTAGGTT
* * * *
6346215 GTTCCAAGTATAGAAGCACCCAAGGGCGTTCTAAGCTCAGAAGCG-CCCAGGGAGTTCCAAGT-T
1 GTTCCAAGTATAGAAGCACCCAAGGGCGTTCCAAGCACAGAAACGTCCAAGGGAGTTCCAAGTAT
* * * *
6346278 CAGAAGCAC-CTAGGGGTGTTCTAAGTACAGAAGCACCTAGGGGTGTTCCAAGCACAAAAACACC
66 -AGAAGCACTC-AGGGGAGTTCCAAGTACAGAAGCACCCAGGGGCGTTCCAAGCACAAAAACACC
** * **
6346342 TAGAGTGTTCCAAGTACAGAAACGCATAGAGGC
129 TAGAGTGTTCCAAACACAGAAACGCCTAG-GTT
* ** *
6346375 GTTTCAAGTGCAGAAGCACCC-AGGGACGTTACAAGCA
1 GTTCCAAGTATAGAAGCACCCAAGGG-CGTTCCAAGCA
6346412 TGGAACAACT
Statistics
Matches: 164, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
158 2 0.01
159 97 0.59
160 65 0.40
ACGTcount: A:0.32, C:0.24, G:0.27, T:0.17
Consensus pattern (160 bp):
GTTCCAAGTATAGAAGCACCCAAGGGCGTTCCAAGCACAGAAACGTCCAAGGGAGTTCCAAGTAT
AGAAGCACTCAGGGGAGTTCCAAGTACAGAAGCACCCAGGGGCGTTCCAAGCACAAAAACACCTA
GAGTGTTCCAAACACAGAAACGCCTAGGTT
Found at i:6346350 original size:53 final size:52
Alignment explanation
Indices: 6345880--6346362 Score: 274
Period size: 53 Copynumber: 9.0 Consensus size: 52
6345870 CCAAGCGCAA
* * *
6345880 AAGCACCCACGGGCGTTCCAAGTATAGAAGCACCTAGGAGTGTTTCAAGTACAG
1 AAGCACCCA-GGGTGTTCCAAGTACAGAAGCACCTA-GAGTGTTCCAAGTACAG
* * * * * * * * *
6345934 AAACGCCTAGGGTGTTCCAATTACAAAAGCGCAC-AGTGGTGTTCCTTAAGCACAA
1 AAGCACCCAGGGTGTTCCAAGTACAGAAGCAC-CTAG-AGTGTTCC--AAGTACAG
* * * * * * *
6345989 AAACGCCTAGGGTGTTCCAAGTACAAAATGCA-C-AGGGGCGTTCCAACTACAG
1 AAGCACCCAGGGTGTTCCAAGTACAGAA-GCACCTA-GAGTGTTCCAAGTACAG
* * * * * *
6346041 AAGCACCCAGGGACGTTCCAAGTATAGAAGCGCCTAGGGGGGTTCCAAGCACAG
1 AAGCACCCAGGG-TGTTCCAAGTACAGAAGCACCTA-GAGTGTTCCAAGTACAG
* * * * * * * *
6346095 AAACGTCCAAGGGCGTTCCAAGTATAGAAGCA-CTCAGGGGAGTTCCAAGTGCAG
1 AAGC-ACCCAGGGTGTTCCAAGTACAGAAGCACCT-A-GAGTGTTCCAAGTACAG
* * **
6346149 AAGCACCCAGGGGCGTTCCAAGTATAGAAGCACCTAGAGTGTTCCAAACACAG
1 AAGCACCCA-GGGTGTTCCAAGTACAGAAGCACCTAGAGTGTTCCAAGTACAG
* * * * * * * * *
6346202 AAACGCCTAGGTTGTTCCAAGTATAGAAGCACCCAAGGGCGTTCTAAGCT-CAG
1 AAGCACCCAGGGTGTTCCAAGTACAGAAGCA-CCTAGAGTGTTCCAAG-TACAG
* * * * *
6346255 AAGCGCCCAGGGAGTTCCAAGTTCAGAAGCACCTAGGGGTGTTCTAAGTACAG
1 AAGCACCCAGGGTGTTCCAAGTACAGAAGCACCTA-GAGTGTTCCAAGTACAG
* * * *
6346308 AAGCACCTAGGGGTGTTCCAAGCACAAAAACACCTAGAGTGTTCCAAGTACAG
1 AAGCACCCA-GGGTGTTCCAAGTACAGAAGCACCTAGAGTGTTCCAAGTACAG
6346361 AA
1 AA
6346363 ACGCATAGAG
Statistics
Matches: 340, Mismatches: 71, Indels: 37
0.76 0.16 0.08
Matches are distributed among these distances:
52 41 0.12
53 139 0.41
54 116 0.34
55 42 0.12
56 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (52 bp):
AAGCACCCAGGGTGTTCCAAGTACAGAAGCACCTAGAGTGTTCCAAGTACAG
Found at i:6346410 original size:80 final size:78
Alignment explanation
Indices: 6346059--6346411 Score: 269
Period size: 80 Copynumber: 4.4 Consensus size: 78
6346049 AGGGACGTTC
* * * * * * * * * *
6346059 CAAGTATAGAAGCGCCTAGGGGGGTTCCAAGCACAGAAACGTCCAAGGGCGTTCCAAGTATAG-A
1 CAAGTACAGAAGCACCCAGGGGCGTTCCAAGCACAGAAGC-ACCTAGAGTGTTCCAAGTACAGAA
*
6346123 A-GCACTCAGGGGAGTTC
65 ACGC-CT-A-GGG-GTTT
* * * **
6346140 CAAGTGCAGAAGCACCCAGGGGCGTTCCAAGTATAGAAGCACCTAGAGTGTTCCAAACACAGAAA
1 CAAGTACAGAAGCACCCAGGGGCGTTCCAAGCACAGAAGCACCTAGAGTGTTCCAAGTACAGAAA
* *
6346205 CGCCTAGGTTGTTC
66 CGCCTAGG-GGTTT
* * * * * * * * * *
6346219 CAAGTATAGAAGCACCCAAGGGCGTTCTAAGCTCAGAAGCGCCCAGGGAGTTCCAAGTTCAGAAG
1 CAAGTACAGAAGCACCCAGGGGCGTTCCAAGCACAGAAGCACCTAGAGTGTTCCAAGTACAGAAA
*
6346284 CACCTAGGGGTGTT
66 CGCCTAGGGGT-TT
* * * *
6346298 CTAAGTACAGAAGCACCTAGGGGTGTTCCAAGCACAAAAACACCTAGAGTGTTCCAAGTACAGAA
1 C-AAGTACAGAAGCACCCAGGGGCGTTCCAAGCACAGAAGCACCTAGAGTGTTCCAAGTACAGAA
*
6346363 ACGCATAGAGGCGTTT
65 ACGCCTAG-GG-GTTT
* * *
6346379 CAAGTGCAGAAGCACCCAGGGACGTTACAAGCA
1 CAAGTACAGAAGCACCCAGGGGCGTTCCAAGCA
6346412 TGGAACAACT
Statistics
Matches: 210, Mismatches: 55, Indels: 15
0.75 0.20 0.05
Matches are distributed among these distances:
78 2 0.01
79 65 0.31
80 98 0.47
81 41 0.20
82 4 0.02
ACGTcount: A:0.32, C:0.24, G:0.27, T:0.17
Consensus pattern (78 bp):
CAAGTACAGAAGCACCCAGGGGCGTTCCAAGCACAGAAGCACCTAGAGTGTTCCAAGTACAGAAA
CGCCTAGGGGTTT
Found at i:6362823 original size:26 final size:27
Alignment explanation
Indices: 6362791--6362841 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
6362781 CAATTTAAAA
*
6362791 AAATTTAA-AAAGTTTTTATTTTTTTG
1 AAATTTAATAAAGTTTTTATATTTTTG
*
6362817 AAATTTAATCAAGTTTTTATATTTT
1 AAATTTAATAAAGTTTTTATATTTT
6362842 AATTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (27 bp):
AAATTTAATAAAGTTTTTATATTTTTG
Found at i:6362852 original size:26 final size:27
Alignment explanation
Indices: 6362791--6362854 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
6362781 CAATTTAAAA
* *
6362791 AAATTTAA-AAAGTTTTTATTTTTTTG
1 AAATTTAATCAAGTTTTTATTATTTTG
6362817 AAATTTAATCAAGTTTTTA-TATTTT-
1 AAATTTAATCAAGTTTTTATTATTTTG
*
6362842 AATTTTAAATCAA
1 AAATTT-AATCAA
6362855 ATAAACTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 5 0.15
26 19 0.58
27 9 0.27
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (27 bp):
AAATTTAATCAAGTTTTTATTATTTTG
Found at i:6369863 original size:14 final size:14
Alignment explanation
Indices: 6369844--6369890 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
6369834 TCCAATGGGT
6369844 GTGTTTTTTAAAAA
1 GTGTTTTTTAAAAA
*
6369858 GTGTTTTTT-TAAA
1 GTGTTTTTTAAAAA
*
6369871 G-GTATTTTAAAAA
1 GTGTTTTTTAAAAA
6369884 GTGTTTT
1 GTGTTTT
6369891 AAAATTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 6 0.22
13 8 0.30
14 13 0.48
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
GTGTTTTTTAAAAA
Found at i:6373571 original size:12 final size:12
Alignment explanation
Indices: 6373552--6373599 Score: 80
Period size: 12 Copynumber: 4.0 Consensus size: 12
6373542 CAGAATAGTT
6373552 TCTTGCTGCCTC
1 TCTTGCTGCCTC
6373564 -CTTTGCTGCCTC
1 TC-TTGCTGCCTC
6373576 TCTTGCTGCCTC
1 TCTTGCTGCCTC
6373588 TCTTGCTGCCTC
1 TCTTGCTGCCTC
6373600 AAAAATCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 1 0.03
12 32 0.94
13 1 0.03
ACGTcount: A:0.00, C:0.42, G:0.17, T:0.42
Consensus pattern (12 bp):
TCTTGCTGCCTC
Found at i:6374279 original size:21 final size:21
Alignment explanation
Indices: 6374244--6374286 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
6374234 CTCTTAAAGT
6374244 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAA-CTAA
*
6374266 AATTT-AACTAAAATAACTAA
1 AATTTAAAATAAAATAACTAA
6374286 A
1 A
6374287 TTAATCACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (21 bp):
AATTTAAAATAAAATAACTAA
Found at i:6378045 original size:18 final size:18
Alignment explanation
Indices: 6378022--6378061 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6378012 AGTTTCACAA
* *
6378022 ATAATTTATAAGTAACAC
1 ATAATTCATAAATAACAC
*
6378040 ATAATTCATAAATAACTC
1 ATAATTCATAAATAACAC
6378058 ATAA
1 ATAA
6378062 ATTAACGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.33
Consensus pattern (18 bp):
ATAATTCATAAATAACAC
Found at i:6385613 original size:4 final size:4
Alignment explanation
Indices: 6385604--6385629 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
6385594 ACATTCCCCT
6385604 TGAA TGAA TGAA TGAA TGAA TGAA TG
1 TGAA TGAA TGAA TGAA TGAA TGAA TG
6385630 CTGTTCATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (4 bp):
TGAA
Found at i:6395312 original size:22 final size:22
Alignment explanation
Indices: 6395287--6395328 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
6395277 TTAAAAAGTC
6395287 CCTAATAAAGCATGAGATATAG
1 CCTAATAAAGCATGAGATATAG
6395309 CCTAATAAAGCATGAGATAT
1 CCTAATAAAGCATGAGATAT
6395329 GAAAGGGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (22 bp):
CCTAATAAAGCATGAGATATAG
Found at i:6398732 original size:6 final size:6
Alignment explanation
Indices: 6398721--6398752 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
6398711 ACACGACAAG
*
6398721 GGGAAA GGGAAA GGGAAA GGGAAA GGAAAA GG
1 GGGAAA GGGAAA GGGAAA GGGAAA GGGAAA GG
6398753 CTTGGGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GGGAAA
Found at i:6407534 original size:18 final size:19
Alignment explanation
Indices: 6407507--6407550 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
6407497 AATAAGATTT
6407507 TTTCTCTCCC-CTAAATAC
1 TTTCTCTCCCTCTAAATAC
* *
6407525 TTTCTTTCCCTCTGAATAC
1 TTTCTCTCCCTCTAAATAC
6407544 TTTCTCT
1 TTTCTCT
6407551 TATATTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.16, C:0.34, G:0.02, T:0.48
Consensus pattern (19 bp):
TTTCTCTCCCTCTAAATAC
Found at i:6428931 original size:14 final size:15
Alignment explanation
Indices: 6428912--6428941 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
6428902 GTGAATGAAT
6428912 AATGAAAAG-ATAAA
1 AATGAAAAGAATAAA
6428926 AATGAAAAGAATAAA
1 AATGAAAAGAATAAA
6428941 A
1 A
6428942 GGAATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (15 bp):
AATGAAAAGAATAAA
Found at i:6433077 original size:23 final size:23
Alignment explanation
Indices: 6433047--6433101 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
6433037 TCTTAATATA
6433047 ATGAATATTCAAGGAGGAGTGTT
1 ATGAATATTCAAGGAGGAGTGTT
6433070 ATGAATATTCAAGGAGGAGTGTT
1 ATGAATATTCAAGGAGGAGTGTT
6433093 ATGAATATT
1 ATGAATATT
6433102 TTTTTGAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (23 bp):
ATGAATATTCAAGGAGGAGTGTT
Found at i:6433154 original size:17 final size:17
Alignment explanation
Indices: 6433132--6433173 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
6433122 TTATGTATAT
6433132 TTAGATTTGGATGTAA-A
1 TTAGATTTGGATG-AAGA
6433149 TTAGA-TTGGATGAAGA
1 TTAGATTTGGATGAAGA
6433165 TTATGATTT
1 TTA-GATTT
6433174 AATTTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.09
16 11 0.50
17 7 0.32
18 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (17 bp):
TTAGATTTGGATGAAGA
Found at i:6433899 original size:17 final size:18
Alignment explanation
Indices: 6433867--6433900 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6433857 TAAGAGAGTC
*
6433867 ATTAAGAAAAATTTTTAG
1 ATTAAGAAAAAATTTTAG
6433885 ATTAA-AAAAAATTTTA
1 ATTAAGAAAAAATTTTA
6433901 AATTTTGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
ATTAAGAAAAAATTTTAG
Found at i:6435019 original size:17 final size:18
Alignment explanation
Indices: 6434988--6435022 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6434978 GAAAAAGGGC
*
6434988 AAAAAAGAATAAAGAAAA
1 AAAAAACAATAAAGAAAA
6435006 AAAAAACAAT-AAGAAAA
1 AAAAAACAATAAAGAAAA
6435023 CAATTCTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.83, C:0.03, G:0.09, T:0.06
Consensus pattern (18 bp):
AAAAAACAATAAAGAAAA
Found at i:6435661 original size:29 final size:30
Alignment explanation
Indices: 6435627--6435701 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
6435617 TCATTAATCA
**
6435627 AAAAAATTT-ATTTAATTTAA-AATAAAAAT
1 AAAAAATTTAATTTAACGTAATAA-AAAAAT
*
6435656 ATAAAAATTTAATTAAACGTAATAAAAAAAT
1 A-AAAAATTTAATTTAACGTAATAAAAAAAT
6435687 -AAAAATTTAATTTAA
1 AAAAAATTTAATTTAA
6435702 ACTTTTTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 15 0.38
30 8 0.21
31 14 0.36
32 2 0.05
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (30 bp):
AAAAAATTTAATTTAACGTAATAAAAAAAT
Found at i:6435664 original size:30 final size:29
Alignment explanation
Indices: 6435636--6435701 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
6435626 AAAAAAATTT
*
6435636 ATTTAATTTAA---AATAAAAATATAAAA
1 ATTTAATTTAACGTAATAAAAAAATAAAA
*
6435662 ATTTAATTAAACGTAATAAAAAAATAAAA
1 ATTTAATTTAACGTAATAAAAAAATAAAA
6435691 ATTTAATTTAA
1 ATTTAATTTAA
6435702 ACTTTTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.29
29 24 0.71
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (29 bp):
ATTTAATTTAACGTAATAAAAAAATAAAA
Found at i:6435702 original size:30 final size:29
Alignment explanation
Indices: 6435647--6435703 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
6435637 TTTAATTTAA
*
6435647 AATAAAAATATAAAAATTTAATTAAACGT
1 AATAAAAAAATAAAAATTTAATTAAACGT
6435676 AATAAAAAAATAAAAATTTAATTTAAAC
1 AATAAAAAAATAAAAATTTAA-TTAAAC
6435704 TTTTTATACG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (29 bp):
AATAAAAAAATAAAAATTTAATTAAACGT
Found at i:6435933 original size:18 final size:18
Alignment explanation
Indices: 6435910--6435945 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
6435900 CCATGCCTAT
6435910 GGGATATGGCTCTAAGGA
1 GGGATATGGCTCTAAGGA
6435928 GGGATATGGCTCTAAGGA
1 GGGATATGGCTCTAAGGA
6435946 AGGGTGGGGG
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:0.28, C:0.11, G:0.39, T:0.22
Consensus pattern (18 bp):
GGGATATGGCTCTAAGGA
Found at i:6436522 original size:18 final size:19
Alignment explanation
Indices: 6436484--6436523 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
6436474 GCGTTTCTTT
*
6436484 TTTAAGTATTTCATTTGTC
1 TTTAAATATTTCATTTGTC
*
6436503 TTTAAATATTT-ATTTTTC
1 TTTAAATATTTCATTTGTC
6436521 TTT
1 TTT
6436524 GACATAGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTAAATATTTCATTTGTC
Found at i:6442836 original size:33 final size:33
Alignment explanation
Indices: 6442785--6442861 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
6442775 TCATAACAAA
** *
6442785 TTAGCATGTTACATCATCATTAAATATAATAT-
1 TTAGCATGCCACAACATCATTAAATATAATATG
*
6442817 TTCAGCATGCCACAACATCATTAATTATAATATG
1 TT-AGCATGCCACAACATCATTAAATATAATATG
6442851 TTAGCATGCCA
1 TTAGCATGCCA
6442862 TGTCAGTGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
32 2 0.05
33 35 0.90
34 2 0.05
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (33 bp):
TTAGCATGCCACAACATCATTAAATATAATATG
Found at i:6442965 original size:30 final size:30
Alignment explanation
Indices: 6442929--6442985 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
6442919 TTATTAGAGT
6442929 TTATTT-GATTTAAAATAAAAGTATAAGAAC
1 TTATTTGGA-TTAAAATAAAAGTATAAGAAC
*
6442959 TTATTTGGATTAAAATGAAAGTATAAG
1 TTATTTGGATTAAAATAAAAGTATAAG
6442986 GGCTTGATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (30 bp):
TTATTTGGATTAAAATAAAAGTATAAGAAC
Found at i:6448619 original size:103 final size:103
Alignment explanation
Indices: 6448440--6448636 Score: 268
Period size: 103 Copynumber: 1.9 Consensus size: 103
6448430 CCTTTGCCAT
* * * * ** * *
6448440 AGGTATTGGTACTTTTGATCCATAATGGTTTTTACATGAAAGGTGTTGATACTCCTTTATAAAGG
1 AGGTATCGATACTTTTGATCCAGAATGATTTTTACATGAAAGGCATTAAGACTCCTTTATAAAGG
*
6448505 TATTAATACTTTTACTCTAGAACACCCTTGAAGTCCAA
66 TATCAATACTTTTACTCTAGAACACCCTTGAAGTCCAA
* ** * *
6448543 AGGTATCGATACTTTTGATCTAGAATGATTTTTGGATGAAAGGCATTAAGACTTCTTTATAAGGG
1 AGGTATCGATACTTTTGATCCAGAATGATTTTTACATGAAAGGCATTAAGACTCCTTTATAAAGG
6448608 TATCAATACTTTTACTCTAGAACACCCTT
66 TATCAATACTTTTACTCTAGAACACCCTT
6448637 AGAGTACTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
103 80 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (103 bp):
AGGTATCGATACTTTTGATCCAGAATGATTTTTACATGAAAGGCATTAAGACTCCTTTATAAAGG
TATCAATACTTTTACTCTAGAACACCCTTGAAGTCCAA
Found at i:6451969 original size:4 final size:4
Alignment explanation
Indices: 6451960--6452028 Score: 56
Period size: 4 Copynumber: 17.2 Consensus size: 4
6451950 AAAGTCGATC
6451960 CTTT CTTT CTTT -TTCT CCTTT CCTTT CTTT -TTT CTTT -TTT CTTCT
1 CTTT CTTT CTTT CTT-T -CTTT -CTTT CTTT CTTT CTTT CTTT CTT-T
* *
6452005 CCTT CTTT CTTT GTTT CTTT -TTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT C
6452029 CTTTTTCTAG
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
3 11 0.20
4 32 0.59
5 9 0.17
6 2 0.04
ACGTcount: A:0.00, C:0.26, G:0.01, T:0.72
Consensus pattern (4 bp):
CTTT
Found at i:6451987 original size:18 final size:17
Alignment explanation
Indices: 6451958--6452016 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
6451948 CCAAAGTCGA
6451958 TCCTTTCTTTCTTTTTC
1 TCCTTTCTTTCTTTTTC
6451975 TCCTTTCCTTTCTTTTT-
1 TCCTTT-CTTTCTTTTTC
* *
6451992 T-CTTT-TTTCTTCTCC
1 TCCTTTCTTTCTTTTTC
*
6452007 TTCTTTCTTT
1 TCCTTTCTTT
6452017 GTTTCTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 7 0.19
15 1 0.03
16 8 0.22
17 10 0.28
18 10 0.28
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (17 bp):
TCCTTTCTTTCTTTTTC
Found at i:6451996 original size:29 final size:28
Alignment explanation
Indices: 6451961--6452028 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 28
6451951 AAGTCGATCC
6451961 TTTCTTTCTTT-TTCTCCTTTCCTTTCTTT-
1 TTTCTTT-TTTCTTCTCC-TT-CTTTCTTTG
6451990 TTTCTTTTTTCTTCTCCTTCTTTCTTTG
1 TTTCTTTTTTCTTCTCCTTCTTTCTTTG
6452018 TTTCTTTTTTC
1 TTTCTTTTTTC
6452029 CTTTTTCTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
27 8 0.22
28 16 0.43
29 13 0.35
ACGTcount: A:0.00, C:0.25, G:0.01, T:0.74
Consensus pattern (28 bp):
TTTCTTTTTTCTTCTCCTTCTTTCTTTG
Found at i:6452000 original size:19 final size:18
Alignment explanation
Indices: 6451958--6451991 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6451948 CCAAAGTCGA
6451958 TCCTTT-CTTTCTTTTTC
1 TCCTTTCCTTTCTTTTTC
6451975 TCCTTTCCTTTCTTTTT
1 TCCTTTCCTTTCTTTTT
6451992 TCTTTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
TCCTTTCCTTTCTTTTTC
Found at i:6452023 original size:8 final size:7
Alignment explanation
Indices: 6451960--6452036 Score: 57
Period size: 7 Copynumber: 10.3 Consensus size: 7
6451950 AAAGTCGATC
6451960 CTTTCTTT
1 CTTT-TTT
6451968 CTTTTTCT
1 CTTTTT-T
6451976 CCTTTCCTTT
1 -CTTT--TTT
6451986 CTTTTTT
1 CTTTTTT
6451993 CTTTTTT
1 CTTTTTT
* *
6452000 C-TTCTC
1 CTTTTTT
*
6452006 CTTCTTT
1 CTTTTTT
6452013 CTTTGTTT
1 CTTT-TTT
6452021 CTTTTTT
1 CTTTTTT
*
6452028 CCTTTTT
1 CTTTTTT
6452035 CT
1 CT
6452037 AGGGTGAAGC
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
6 4 0.07
7 28 0.51
8 12 0.22
9 8 0.15
10 1 0.02
11 2 0.04
ACGTcount: A:0.00, C:0.26, G:0.01, T:0.73
Consensus pattern (7 bp):
CTTTTTT
Found at i:6453717 original size:36 final size:35
Alignment explanation
Indices: 6453628--6453717 Score: 81
Period size: 36 Copynumber: 2.5 Consensus size: 35
6453618 CAAGCAATGG
*
6453628 CCCTTACATCAACTTTTTCACAAGATCAAATGATAA
1 CCCTTACATC-ACTTTTTCACAAGATCAAACGATAA
* * * ** * *
6453664 TCCTTACAATTATTTTTTCACGGGATTAAGCGATAA
1 CCCTTAC-ATCACTTTTTCACAAGATCAAACGATAA
6453700 CCCTTACATCAGCTTTTT
1 CCCTTACATCA-CTTTTT
6453718 AAAGGGATCG
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
35 3 0.07
36 36 0.88
37 2 0.05
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (35 bp):
CCCTTACATCACTTTTTCACAAGATCAAACGATAA
Found at i:6460081 original size:21 final size:22
Alignment explanation
Indices: 6460046--6460089 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
6460036 CTCTTAAAGT
6460046 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
6460068 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
6460089 A
1 A
6460090 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:6464090 original size:75 final size:75
Alignment explanation
Indices: 6463976--6464125 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
6463966 TAACATATCA
6463976 TTCACCTAGGGTAATATACTCCTAGGGGTTCATCATAACTTTTGACATCTTAGTCTAGGCACACA
1 TTCACCTAGGGTAATATACTCCTAGGGGTTCATCATAACTTTTGACATCTTAGTCTAGGCACACA
6464041 CAACATAGGC
66 CAACATAGGC
6464051 TTCACCTAGGGTAATATACTCCTAGGGGTTCATCATAACTTTTGACATCTTAGTCTAGGCACACA
1 TTCACCTAGGGTAATATACTCCTAGGGGTTCATCATAACTTTTGACATCTTAGTCTAGGCACACA
6464116 CAACATAGGC
66 CAACATAGGC
6464126 CACTTATGTG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (75 bp):
TTCACCTAGGGTAATATACTCCTAGGGGTTCATCATAACTTTTGACATCTTAGTCTAGGCACACA
CAACATAGGC
Found at i:6465470 original size:55 final size:55
Alignment explanation
Indices: 6465409--6465551 Score: 178
Period size: 66 Copynumber: 2.4 Consensus size: 55
6465399 TTAATTTACA
6465409 TAAAAAATTGAGGCTGTTACAACTCACATGTCATCCTTGGCTTCCCAAGTCACCT
1 TAAAAAATTGAGGCTGTTACAACTCACATGTCATCCTTGGCTTCCCAAGTCACCT
6465464 TAAAAAATTGAGGGTGTTACAATAGCGTTACAACTCACATGTCATCCTTGGCTTCCCAAGTCACC
1 TAAAAAATTGA--G-G---C--T---GTTACAACTCACATGTCATCCTTGGCTTCCCAAGTCACC
6465529 T
55 T
*
6465530 TAAAAAATTGAGGGTGTTACAA
1 TAAAAAATTGAGGCTGTTACAA
6465552 TAGCGCTATT
Statistics
Matches: 76, Mismatches: 1, Indels: 22
0.77 0.01 0.22
Matches are distributed among these distances:
55 18 0.24
57 1 0.01
58 2 0.03
61 1 0.01
63 2 0.03
64 1 0.01
66 51 0.67
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (55 bp):
TAAAAAATTGAGGCTGTTACAACTCACATGTCATCCTTGGCTTCCCAAGTCACCT
Found at i:6465506 original size:66 final size:66
Alignment explanation
Indices: 6465424--6465556 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
6465414 AATTGAGGCT
6465424 GTTACAACTCACATGTCATCCTTGGCTTCCCAAGTCACCTTAAAAAATTGAGGGTGTTACAATAG
1 GTTACAACTCACATGTCATCCTTGGCTTCCCAAGTCACCTTAAAAAATTGAGGGTGTTACAATAG
6465489 C
66 C
6465490 GTTACAACTCACATGTCATCCTTGGCTTCCCAAGTCACCTTAAAAAATTGAGGGTGTTACAATAG
1 GTTACAACTCACATGTCATCCTTGGCTTCCCAAGTCACCTTAAAAAATTGAGGGTGTTACAATAG
6465555 C
66 C
6465556 G
1 G
6465557 CTATTGTGCC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (66 bp):
GTTACAACTCACATGTCATCCTTGGCTTCCCAAGTCACCTTAAAAAATTGAGGGTGTTACAATAG
C
Found at i:6471883 original size:14 final size:14
Alignment explanation
Indices: 6471843--6471885 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
6471833 TAATACAGAG
6471843 AAATTAGTATATTTT
1 AAATTAGT-TATTTT
* *
6471858 -ATTTAATTATTTT
1 AAATTAGTTATTTT
6471871 AAATTAGTTATTTT
1 AAATTAGTTATTTT
6471885 A
1 A
6471886 GATGAGTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (14 bp):
AAATTAGTTATTTT
Found at i:6475137 original size:19 final size:19
Alignment explanation
Indices: 6475113--6475217 Score: 70
Period size: 19 Copynumber: 5.2 Consensus size: 19
6475103 TGATTCCAAC
6475113 TTTTAATAAAATATTAATA
1 TTTTAATAAAATATTAATA
*
6475132 TTTTAACATATTAATATTAA-A
1 TTTT-A-ATA-AAATATTAATA
*
6475153 TTATAAATAAAATATTAATA
1 TT-TTAATAAAATATTAATA
* *
6475173 GTTTAAAAAAATAAAAATTAA-A
1 TTTTAATAAAAT----ATTAATA
*
6475195 TTATAAATAAAATATTAATA
1 TT-TTAATAAAATATTAATA
6475215 TTT
1 TTT
6475218 AAATTATAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
19 26 0.39
20 9 0.14
21 7 0.11
22 11 0.17
23 13 0.20
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (19 bp):
TTTTAATAAAATATTAATA
Found at i:6475206 original size:42 final size:41
Alignment explanation
Indices: 6475117--6475220 Score: 154
Period size: 42 Copynumber: 2.5 Consensus size: 41
6475107 TCCAACTTTT
* * * * *
6475117 AATAAAATATTAATATTTTAACATATTAATATTAAATTATA
1 AATAAAATATTAATATTTAAAAAAATAAAAATTAAATTATA
6475158 AATAAAATATTAATAGTTTAAAAAAATAAAAATTAAATTATA
1 AATAAAATATTAATA-TTTAAAAAAATAAAAATTAAATTATA
6475200 AATAAAATATTAATATTTAAA
1 AATAAAATATTAATATTTAAA
6475221 TTATAAATTA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 21 0.37
42 36 0.63
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (41 bp):
AATAAAATATTAATATTTAAAAAAATAAAAATTAAATTATA
Found at i:6475346 original size:28 final size:28
Alignment explanation
Indices: 6475314--6475388 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 28
6475304 TTATATATCA
*
6475314 AATATTAATAATTAAATAATCAATTATT
1 AATATTAATAATTAAATAACCAATTATT
* * *
6475342 AATATT-TTAAATAAATTACCAATTATT
1 AATATTAATAATTAAATAACCAATTATT
* *
6475369 AATATTTAAAAATAAAATAA
1 AATA-TTAATAATTAAATAA
6475389 ATAAAATAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
27 21 0.58
28 8 0.22
29 7 0.19
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (28 bp):
AATATTAATAATTAAATAACCAATTATT
Found at i:6475396 original size:14 final size:14
Alignment explanation
Indices: 6475377--6475403 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6475367 TTAATATTTA
6475377 AAAATAAAATAAAT
1 AAAATAAAATAAAT
6475391 AAAATAAAATAAA
1 AAAATAAAATAAA
6475404 AAATTAATCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:6475578 original size:65 final size:65
Alignment explanation
Indices: 6475429--6475585 Score: 160
Period size: 65 Copynumber: 2.4 Consensus size: 65
6475419 ATATTTAGAT
6475429 TAAATAAAATATTAATATTTTAAA-TAAATAATCAATTATTAATATTTAAAAATATAATAAAATA
1 TAAAT-AAATATTAATA-TTTAAATTAAATAA-CAATTATTAATATTTAAAAATATAATAAAATA
6475493 AAA
63 AAA
* * * * * *
6475496 TAATTTATCATAATAATATTTAAATTAAATAA-AA-TATTAATATTTTAAAATATTAAT-GACTA
1 TAA-ATA-AATATTAATATTTAAATTAAATAACAATTATTAATATTTAAAAATA-TAATAAAATA
6475558 AATTA
63 AA--A
6475563 TAAATAAATATTAATATTTAAAT
1 TAAATAAATATTAATATTTAAAT
6475586 GGTCAATTAT
Statistics
Matches: 75, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
65 37 0.49
66 8 0.11
67 14 0.19
68 16 0.21
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.41
Consensus pattern (65 bp):
TAAATAAATATTAATATTTAAATTAAATAACAATTATTAATATTTAAAAATATAATAAAATAAAA
Found at i:6475665 original size:64 final size:60
Alignment explanation
Indices: 6475596--6475821 Score: 190
Period size: 64 Copynumber: 3.6 Consensus size: 60
6475586 GGTCAATTAT
*
6475596 TAATATCTTAAATAAACTATCAATTATTAATATTTAAAAAATAAAATAAAATAATTAATCATAA
1 TAATAT-TTAAATAAA-TA--AATTATTAATATTTAAAAAATAAATTAAAATAATTAATCATAA
* * * *
6475660 TAATATTTAAATTAA-AAA-TATTAATATTTTAAAATATTAATGATTAAATTATAAATAA-AATA
1 TAATATTTAAATAAATAAATTATTAATA-TTTAAAA-AATAA--ATTAAA--ATAATTAATCATA
*
6475722 T
60 A
** * *
6475723 TAATATTT-AATTTATCAATTATTAATATTTAAATTAAATTAAATTAAAATAATTGATCATAA
1 TAATATTTAAATAAATAAATTATTAATATTTAAA--AAA-TAAATTAAAATAATTAATCATAA
* *
6475785 TAATATTTAAATTAAATAAAATATTAATATTTTAAAA
1 TAATATTTAAA-TAAATAAATTATTAATATTTAAAAA
6475822 TATTAATGAT
Statistics
Matches: 130, Mismatches: 18, Indels: 30
0.73 0.10 0.17
Matches are distributed among these distances:
58 8 0.06
59 9 0.07
60 4 0.03
61 7 0.05
62 23 0.18
63 35 0.27
64 40 0.31
65 4 0.03
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (60 bp):
TAATATTTAAATAAATAAATTATTAATATTTAAAAAATAAATTAAAATAATTAATCATAA
Found at i:6475676 original size:42 final size:42
Alignment explanation
Indices: 6475629--6475800 Score: 110
Period size: 42 Copynumber: 4.1 Consensus size: 42
6475619 TTATTAATAT
6475629 TTAAAAAATAAAATAAAATAATTAATCATAATAATATTTAAA
1 TTAAAAAATAAAATAAAATAATTAATCATAATAATATTTAAA
* *
6475671 TTAAAAATATTAATATTTTAAAAT-ATTAATGAT--TAA-ATTATAAA
1 TTAAAAA-A-TAA-A--ATAAAATAATTAATCATAATAATATT-TAAA
* * ** * *
6475715 -TAAAATAT-TAAT-ATTTAATTTATCAATTATTAATATTTAAA
1 TTAAAAAATAAAATAAAATAATTAATC-A-TAATAATATTTAAA
* * *
6475756 TT--AAATTAAATTAAAATAATTGATCATAATAATATTTAAA
1 TTAAAAAATAAAATAAAATAATTAATCATAATAATATTTAAA
6475796 TTAAA
1 TTAAA
6475801 TAAAATATTA
Statistics
Matches: 96, Mismatches: 17, Indels: 34
0.65 0.12 0.23
Matches are distributed among these distances:
36 2 0.02
37 6 0.06
38 1 0.01
39 2 0.02
40 18 0.19
41 11 0.11
42 22 0.23
43 9 0.09
44 10 0.10
45 1 0.01
46 8 0.08
47 6 0.06
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (42 bp):
TTAAAAAATAAAATAAAATAATTAATCATAATAATATTTAAA
Found at i:6475756 original size:148 final size:152
Alignment explanation
Indices: 6475438--6475761 Score: 498
Period size: 148 Copynumber: 2.1 Consensus size: 152
6475428 TTAAATAAAA
*
6475438 TATTAATATTTTAAATAAATAATCAATTATTAATATTTAAAAATATAATAAAATAAAATAATTTA
1 TATTAATA-TTTAAATAAATAATCAATTATTAATATTT-AAAATATAATAAAATAAAATAATTAA
6475503 TCATAATAATATTTAAATTAAATAAAATATTAATATTTTAAAATATTAATGACTAAATTATAAAT
64 TCATAATAATATTTAAATT-AATAAAATATTAATATTTTAAAATATTAATGACTAAATTATAAAT
*
6475568 AAATATTAATATTTAAATGGTCAAT
128 AAATATTAATATTTAAATGATCAAT
6475593 TATTAATATCTTAAATAAACT-ATCAATTATTAATATTT-AAA-A-AATAAAATAAAATAATTAA
1 TATTAATAT-TTAAATAAA-TAATCAATTATTAATATTTAAAATATAATAAAATAAAATAATTAA
*
6475654 TCATAATAATATTTAAATT-A-AAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATA
64 TCATAATAATATTTAAATTAATAAAATATTAATATTTTAAAATATTAATGACTAAATTATAAAT-
* *
6475717 AAATATTAATATTTAATTTATCAAT
128 AAATATTAATATTTAAATGATCAAT
6475742 TATTAATATTTAAATTAAAT
1 TATTAATATTTAAA-TAAAT
6475762 TAAATTAAAA
Statistics
Matches: 160, Mismatches: 5, Indels: 15
0.89 0.03 0.08
Matches are distributed among these distances:
148 47 0.29
149 36 0.22
151 37 0.23
152 1 0.01
153 3 0.02
154 1 0.01
155 34 0.21
156 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (152 bp):
TATTAATATTTAAATAAATAATCAATTATTAATATTTAAAATATAATAAAATAAAATAATTAATC
ATAATAATATTTAAATTAATAAAATATTAATATTTTAAAATATTAATGACTAAATTATAAATAAA
TATTAATATTTAAATGATCAAT
Found at i:6475769 original size:22 final size:21
Alignment explanation
Indices: 6475660--6475763 Score: 81
Period size: 22 Copynumber: 5.0 Consensus size: 21
6475650 TTAATCATAA
* *
6475660 TAATATTTAAATTAAAAATAT
1 TAATATTTAAATTACAATTAT
* * *
6475681 TAATATTTTAAAATATTAATGAT
1 TAATA-TTTAAATTA-CAATTAT
*
6475704 TAA-ATTATAAA-TA-AAATAT
1 TAATATT-TAAATTACAATTAT
*
6475723 TAATATTTAATTTATCAATTAT
1 TAATATTTAAATTA-CAATTAT
6475745 TAATATTTAAATTA-AATTA
1 TAATATTTAAATTACAATTA
6475764 AATTAAAATA
Statistics
Matches: 67, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
19 10 0.15
20 10 0.15
21 9 0.13
22 31 0.46
23 7 0.10
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (21 bp):
TAATATTTAAATTACAATTAT
Found at i:6475797 original size:276 final size:282
Alignment explanation
Indices: 6475429--6475936 Score: 782
Period size: 276 Copynumber: 1.8 Consensus size: 282
6475419 ATATTTAGAT
6475429 TAAATAAAATATTAATATTTTAAATAAATAATCAATTATTAATATTTAAAAATATAATAAAATAA
1 TAAATAAAATATTAATATTTTAAAT--ATAATCAATTATTAATATTTAAAAATATAATAAAATAA
*
6475494 AATAATTTATCATAATAATATTTAAATTAAATAAAATATTAATATTTTAAAATATTAATGACTAA
64 AATAATTGATCATAATAATATTTAAATTAAATAAAATATTAATATTTTAAAATATTAATGACTAA
* *
6475559 ATTATAAAT-AAATATTAATATTTAAATGGTCAATTATTAATATCTTAAATAAACTATC-A-ATT
129 ATTATAAATGAAATATTAATATTTAAATGATCAATTAGTAATATCTTAAATAAA-T-TCTAGATT
*
6475621 ATTAATATTTAAAAAATAAAAT-AAAATAATTAATCATAATAATATTTAAATTAAAAATATTAAT
192 ATTAATATTTAAAAAATAAAATGAAAATAAATAATCATAATAATATTTAAATTAAAAATATTAAT
6475685 ATTTTAAAATATTAATGATTAAATTA
257 ATTTTAAAATATTAATGATTAAATTA
* * *
6475711 TAAATAAAATATTAATA-TTT-AAT-TTATCAATTATTAATATTT-AAATTA-AATTAAATTAAA
1 TAAATAAAATATTAATATTTTAAATATAATCAATTATTAATATTTAAAAATATAA-TAAAATAAA
*
6475771 ATAATTGATCATAATAATATTTAAATTAAATAAAATATTAATATTTTAAAATATTAATGATTAAA
65 ATAATTGATCATAATAATATTTAAATTAAATAAAATATTAATATTTTAAAATATTAATGACTAAA
* * * *
6475836 TTATAAATGAAATATTTATATTTAAATGATTAATTAGTAATATTTTAATTAAATTCTAGATTATT
130 TTATAAATGAAATATTAATATTTAAATGATCAATTAGTAATATCTTAAATAAATTCTAGATTATT
* *
6475901 AATATTTAAAAAATATAATGAAAATAAATAGTCATA
195 AATATTTAAAAAATAAAATGAAAATAAATAATCATA
6475937 TAAATAATAA
Statistics
Matches: 207, Mismatches: 14, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
275 4 0.02
276 86 0.42
277 80 0.39
278 14 0.07
280 3 0.01
281 3 0.01
282 17 0.08
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (282 bp):
TAAATAAAATATTAATATTTTAAATATAATCAATTATTAATATTTAAAAATATAATAAAATAAAA
TAATTGATCATAATAATATTTAAATTAAATAAAATATTAATATTTTAAAATATTAATGACTAAAT
TATAAATGAAATATTAATATTTAAATGATCAATTAGTAATATCTTAAATAAATTCTAGATTATTA
ATATTTAAAAAATAAAATGAAAATAAATAATCATAATAATATTTAAATTAAAAATATTAATATTT
TAAAATATTAATGATTAAATTA
Found at i:6475828 original size:128 final size:125
Alignment explanation
Indices: 6475608--6475890 Score: 428
Period size: 128 Copynumber: 2.3 Consensus size: 125
6475598 ATATCTTAAA
*
6475608 TAAACTATCAATTATTAATATTTAAA--AAA-TAAAATAAAATAATTAATCATAATAATATTTAA
1 TAAATTATCAATTATTAATATTTAAATTAAATTAAAATAAAATAATTAATCATAATAATATTTAA
6475670 ATTAAAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATAAAATATTAATATT
66 ATTAAAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATAAAATATTAATATT
* * *
6475730 TAATTTATCAATTATTAATATTTAAATTAAATTAAATTAAAATAATTGATCATAATAATATTTAA
1 TAAATTATCAATTATTAATATTTAAATTAAATTAAAATAAAATAATTAATCATAATAATATTTAA
* *
6475795 ATTAAATAAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATGAAATATTTATATT
66 ATT--A-AAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATAAAATATTAATATT
* * * *
6475858 TAAATGATTAATTAGTAATATTTTAATTAAATT
1 TAAATTATCAATTATTAATATTTAAATTAAATT
6475891 CTAGATTATT
Statistics
Matches: 144, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
122 24 0.17
124 3 0.02
125 34 0.24
127 1 0.01
128 82 0.57
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (125 bp):
TAAATTATCAATTATTAATATTTAAATTAAATTAAAATAAAATAATTAATCATAATAATATTTAA
ATTAAAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATAAAATATTAATATT
Found at i:6475843 original size:42 final size:41
Alignment explanation
Indices: 6475664--6475858 Score: 162
Period size: 42 Copynumber: 4.6 Consensus size: 41
6475654 TCATAATAAT
6475664 ATTTAAATTAAAAATATTAATATTTTAAAATATTAATGATTAA
1 ATTTAAA-T-AAAATATTAATATTTTAAAATATTAATGATTAA
** * *
6475707 ATTATAAATAAAATATTAATA-TTTAATTTATCAATTATTAA
1 ATT-TAAATAAAATATTAATATTTTAAAATATTAATGATTAA
* * * ** *
6475748 TATTTAAATTAAATTAAATTAAAATAATTGATCATAATAAT-ATTTAA
1 -ATTTAAA-TAAA--ATATT--AATATTTTAAAATATTAATGA-TTAA
6475795 A-TTAAATAAAATATTAATATTTTAAAATATTAATGATTAA
1 ATTTAAATAAAATATTAATATTTTAAAATATTAATGATTAA
* *
6475835 ATTATAAATGAAATATTTATATTT
1 ATT-TAAATAAAATATTAATATTT
6475859 AAATGATTAA
Statistics
Matches: 121, Mismatches: 19, Indels: 25
0.73 0.12 0.15
Matches are distributed among these distances:
40 19 0.16
41 22 0.18
42 41 0.34
43 4 0.03
44 12 0.10
45 5 0.04
46 6 0.05
47 12 0.10
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (41 bp):
ATTTAAATAAAATATTAATATTTTAAAATATTAATGATTAA
Found at i:6475929 original size:128 final size:128
Alignment explanation
Indices: 6475614--6475930 Score: 337
Period size: 128 Copynumber: 2.5 Consensus size: 128
6475604 TAAATAAACT
* * * * * ** *
6475614 ATCAATTATTAATATTTAAA--AAA-TAAAATAAAATAATTAATCATAATAAT-ATTTAAAT-TA
1 ATCAATTAGTAATATTTAAATTAAATTAAATTAAAATAATTGATAAAAATAATAATGAAAATAAA
* *
6475674 -AAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATAAAATATTAATATTTAATTT
66 TAAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATG
* * * * * *
6475736 ATCAATTATTAATATTTAAATTAAATTAAATTAAAATAATTGATCATAATAATATTTAAATTAAA
1 ATCAATTAGTAATATTTAAATTAAATTAAATTAAAATAATTGATAAAAATAATAATGAAAATAAA
* *
6475801 TAAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATGAAATATTTATATTTAAATG
66 TAAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATG
* * * * *
6475864 ATTAATTAGTAATATTTTAATTAAATTCTAGATTATTAAT-ATTTA-AAAAAT-ATAATGAAAAT
1 ATCAATTAGTAATATTTAAATTAAA-T-TAAATTA-AAATAATTGATAAAAATAATAATGAAAAT
6475926 AAATA
63 AAATA
6475931 GTCATATAAA
Statistics
Matches: 165, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
122 20 0.12
124 3 0.02
125 25 0.15
126 5 0.03
127 1 0.01
128 93 0.56
129 5 0.03
130 10 0.06
131 3 0.02
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.42
Consensus pattern (128 bp):
ATCAATTAGTAATATTTAAATTAAATTAAATTAAAATAATTGATAAAAATAATAATGAAAATAAA
TAAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATG
Found at i:6482441 original size:28 final size:28
Alignment explanation
Indices: 6482363--6482600 Score: 237
Period size: 29 Copynumber: 8.3 Consensus size: 28
6482353 GGTAGCTTTT
* * *
6482363 ACATATTTGCCTTAATATAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
* * *
6482391 GCATGTTTTATCTTAATATAGACAAGAAA
1 ACATG-TTTGTCTTAATTTAGACAAGAAA
* *
6482420 ATATGTTTGTCTTAAATTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
* *
6482448 CCACAT-TTTGTTTTAATTTAGATAAGAAA
1 --ACATGTTTGTCTTAATTTAGACAAGAAA
* *
6482477 ATATGTTTGTCTTAATTTAGACAAAAAAA
1 ACATGTTTGTCTTAATTTAGAC-AAGAAA
6482506 ACATGTTTGTCTTAATTTCAGACAAGAAGA
1 ACATGTTTGTCTTAATTT-AGACAAGAA-A
* * *
6482536 ATATGTTTTATCTTAATCTAGACAAGAAA
1 ACATG-TTTGTCTTAATTTAGACAAGAAA
* *
6482565 ACATATTTGT-TTCAATTTAGACAAGATA
1 ACATGTTTGTCTT-AATTTAGACAAGAAA
6482593 ACATGTTT
1 ACATGTTT
6482601 TATTTTAACT
Statistics
Matches: 173, Mismatches: 28, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
27 5 0.03
28 62 0.36
29 74 0.43
30 21 0.12
31 11 0.06
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.37
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:6482464 original size:57 final size:57
Alignment explanation
Indices: 6482401--6482600 Score: 228
Period size: 57 Copynumber: 3.5 Consensus size: 57
6482391 GCATGTTTTA
*
6482401 TCTTAATATAGACAAGAAAATATGTTTGTCTTAAATTAGACAAGAAACCACAT-TTTG
1 TCTTAATTTAGACAAGAAAATATGTTTGTCTTAAATTAGACAAGAAA-CACATATTTG
* * * * * *
6482458 TTTTAATTTAGATAAGAAAATATGTTTGTCTTAATTTAGACAAAAAAAACATGTTTG
1 TCTTAATTTAGACAAGAAAATATGTTTGTCTTAAATTAGACAAGAAACACATATTTG
*
6482515 TCTTAATTTCAGACAAGAAGAATATGTTTTATCTT-AATCTAGACAAGAAA-ACATATTTG
1 TCTTAATTT-AGACAAGAA-AATATG-TTTGTCTTAAAT-TAGACAAGAAACACATATTTG
* *
6482574 T-TTCAATTTAGACAAGATAACATGTTT
1 TCTT-AATTTAGACAAGAAAATATGTTT
6482601 TATTTTAACT
Statistics
Matches: 123, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
56 7 0.06
57 59 0.48
58 18 0.15
59 22 0.18
60 17 0.14
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (57 bp):
TCTTAATTTAGACAAGAAAATATGTTTGTCTTAAATTAGACAAGAAACACATATTTG
Found at i:6482797 original size:18 final size:17
Alignment explanation
Indices: 6482762--6482795 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
6482752 ATAATAACAA
6482762 AATAAGAGTTATTATTT
1 AATAAGAGTTATTATTT
6482779 AATAAGGAGTT-TTATTT
1 AATAA-GAGTTATTATTT
6482796 TATCAAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (17 bp):
AATAAGAGTTATTATTT
Found at i:6493531 original size:17 final size:16
Alignment explanation
Indices: 6493502--6493542 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
6493492 CTACAAAAAC
*
6493502 ATAAAACTTAACTTAA
1 ATAAAACTAAACTTAA
6493518 ATAATAACTAAACTTAAA
1 ATAA-AACTAAACTT-AA
6493536 ATAAAAC
1 ATAAAAC
6493543 ATCATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 12 0.55
18 6 0.27
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAACTAAACTTAA
Found at i:6497458 original size:71 final size:69
Alignment explanation
Indices: 6497323--6497458 Score: 150
Period size: 71 Copynumber: 1.9 Consensus size: 69
6497313 CATAATGCTT
* * **
6497323 TCCCAAGGCATTTTGGACACTTAGTATCGATACTCCTTTCTGAGGTATCAATACTTTTTATACAA
1 TCCCAAGCCATTTTGGACACTAAGTATCGATACTCCTTTCT-AGGTATCAATACTTTCGATACAA
6497388 CATGC
65 CATGC
* * *
6497393 TCCCTAAGCCATTTTGGTCACTAAGTATCGATACCTTCCTTT-T-GGTCATTAATACTTTCGCTA
1 TCCC-AAGCCATTTTGGACACTAAGTATCGATA-C-TCCTTTCTAGGT-ATCAATACTTTCGATA
6497456 CAA
62 CAA
6497459 AATGAGTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
70 7 0.13
71 40 0.73
72 2 0.04
73 6 0.11
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (69 bp):
TCCCAAGCCATTTTGGACACTAAGTATCGATACTCCTTTCTAGGTATCAATACTTTCGATACAAC
ATGC
Found at i:6499457 original size:84 final size:84
Alignment explanation
Indices: 6499286--6499462 Score: 212
Period size: 84 Copynumber: 2.1 Consensus size: 84
6499276 AAATAAAAAC
* * * *
6499286 CATCCTCATGCTTAACCCATAGTGTATATGAAATTCTTAACACATACATCTCTTGGCATTCATTT
1 CATCCTCATGCTTAACCCATAGTGTACATCAAATTCTCAACACATACATCTCATGGCATTCATTT
* *
6499351 CATAGTTTATCTAATAACT
66 CATAGTTCATCTAATAAAT
* * * * *
6499370 CATCCTCATGCTTATCTCGTAGTGTACATCATATTCTCAACATATACATCTCATGGCATTCATTT
1 CATCCTCATGCTTAACCCATAGTGTACATCAAATTCTCAACACATACATCTCATGGCATTCATTT
* *
6499435 CATA-TCTCATTTCATAAAT
66 CATAGT-TCATCTAATAAAT
*
6499454 CATCATCAT
1 CATCCTCAT
6499463 AACATGGGAG
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
83 1 0.01
84 77 0.99
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.38
Consensus pattern (84 bp):
CATCCTCATGCTTAACCCATAGTGTACATCAAATTCTCAACACATACATCTCATGGCATTCATTT
CATAGTTCATCTAATAAAT
Found at i:6512602 original size:29 final size:30
Alignment explanation
Indices: 6512534--6512602 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
6512524 GAATAATAAT
6512534 ATTTATTTGATCTAAAATAAAAATATAAAA
1 ATTTATTTGATCTAAAATAAAAATATAAAA
* * *
6512564 ATTCGA-TTGATC-ATAATAAAAGA-ATAAGA
1 ATT-TATTTGATCTAAAATAAAA-ATATAAAA
6512593 ATTTATTTGA
1 ATTTATTTGA
6512603 CTTCTTTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
28 1 0.03
29 20 0.62
30 10 0.31
31 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (30 bp):
ATTTATTTGATCTAAAATAAAAATATAAAA
Found at i:6523137 original size:21 final size:21
Alignment explanation
Indices: 6523112--6523164 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
6523102 TTGAGGAACA
6523112 TAGTCGACCCTAAAAACATTG
1 TAGTCGACCCTAAAAACATTG
* * **
6523133 TAGTCGACCTTAACAATGTTG
1 TAGTCGACCCTAAAAACATTG
6523154 TAGTCGACCCT
1 TAGTCGACCCT
6523165 CAAGCTTCAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (21 bp):
TAGTCGACCCTAAAAACATTG
Found at i:6530021 original size:36 final size:35
Alignment explanation
Indices: 6529917--6530105 Score: 136
Period size: 35 Copynumber: 5.3 Consensus size: 35
6529907 TTAATTATTT
* * *
6529917 AATTAAATTAATTAGGC-CTAATAAATTAATTAAAC
1 AATTTAATCAATTAGGCTC-AATCAATTAATTAAAC
* * * * *
6529952 GATTTAATTAATGAAGCGCAA-CAACTTAATTAAAC
1 AATTTAATCAATTAGGCTCAATCAA-TTAATTAAAC
*
6529987 AATTTCAATCAATTAGGCTCAATGAATTAATTAAA-
1 AATTT-AATCAATTAGGCTCAATCAATTAATTAAAC
* * * *
6530022 AATTTTTAATCAATTAGGCCCAATGACTTAATTAAAT
1 AA--TTTAATCAATTAGGCTCAATCAATTAATTAAAC
* *
6530059 AATTTAA-CTAATTAAGCTCAA-CAACTTAATTATAC
1 AATTTAATC-AATTAGGCTCAATCAA-TTAATTAAAC
6530094 AATTTTAATCAA
1 AA-TTTAATCAA
6530106 GTACTTGTGA
Statistics
Matches: 124, Mismatches: 19, Indels: 21
0.76 0.12 0.13
Matches are distributed among these distances:
34 4 0.03
35 56 0.45
36 56 0.45
37 8 0.06
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (35 bp):
AATTTAATCAATTAGGCTCAATCAATTAATTAAAC
Found at i:6532343 original size:60 final size:60
Alignment explanation
Indices: 6532109--6532627 Score: 358
Period size: 60 Copynumber: 8.7 Consensus size: 60
6532099 TACAATAATC
* * * * * * * * *
6532109 AAATCGAA-CTCATTGTAAGATAAGTCGGGCCTAGATTTAGTCTAGGAATTCTGAAATTTT
1 AAATCGAACCT-ATTATGAGATAAGTCGAGCCTAGATTAAGTTTAGGAGTTTTAAAATATT
* * * * * * *
6532169 AAAATCGAACCTGTTGTGAGATAGGTTGAGCCTAAATTAAGTCTAGGAGTTTTAAAATTTT
1 -AAATCGAACCTATTATGAGATAAGTCGAGCCTAGATTAAGTTTAGGAGTTTTAAAATATT
* * * * * *
6532230 ATAATCGAACTTGTCATGAGATAGGTAGAGCCTAGATTAAGTCTT-GGAATTTTAAAATATT
1 A-AATCGAACCTATTATGAGATAAGTCGAGCCTAGATTAAGT-TTAGGAGTTTTAAAATATT
* * * * * *
6532291 AAATTGAACCTATTTTGAGATAAGTTGAGCCTAGATGAATTTTAAGAGTTTTAAAATATT
1 AAATCGAACCTATTATGAGATAAGTCGAGCCTAGATTAAGTTTAGGAGTTTTAAAATATT
* * * * *
6532351 AAATTGAACCTATTTTGAGATAATAAGTCGAGTCTAGAATTAAGTTTAGGAATTTCAAAATATT
1 AAATCGAACCTATTATGAG---ATAAGTCGAGCCTAG-ATTAAGTTTAGGAGTTTTAAAATATT
* * * ** *
6532415 AAATTGAACCTATGATGAGATAAGTCAAGTTTAGATTAAGTCTAGGAGTTTTAAAATATT
1 AAATCGAACCTATTATGAGATAAGTCGAGCCTAGATTAAGTTTAGGAGTTTTAAAATATT
* * * * * *
6532475 AAATCAAACCAATTATGATATAGGTCGAGCCTAGATTAAG-CTAGAAG---T----TATT
1 AAATCGAACCTATTATGAGATAAGTCGAGCCTAGATTAAGTTTAGGAGTTTTAAAATATT
* * * * * * *
6532527 AAATCGAATCTGTTGTGAGAT-AGGCTAAGCCTAGATTAAGTCTAGGAGTTTCAAAATATT
1 AAATCGAACCTATTATGAGATAAGTC-GAGCCTAGATTAAGTTTAGGAGTTTTAAAATATT
*** * * *
6532587 AAATCGAACCTATTGCAAGATAAATAGAGCCTTGATTAAGT
1 AAATCGAACCTATTATGAGATAAGTCGAGCCTAGATTAAGT
6532628 CAAAAATTGT
Statistics
Matches: 367, Mismatches: 73, Indels: 37
0.77 0.15 0.08
Matches are distributed among these distances:
51 2 0.01
52 32 0.09
53 6 0.02
56 1 0.00
59 8 0.02
60 153 0.42
61 111 0.30
62 3 0.01
63 13 0.04
64 38 0.10
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.34
Consensus pattern (60 bp):
AAATCGAACCTATTATGAGATAAGTCGAGCCTAGATTAAGTTTAGGAGTTTTAAAATATT
Found at i:6534440 original size:25 final size:25
Alignment explanation
Indices: 6534412--6534459 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
6534402 TGGTCACAAC
* * *
6534412 CACGAATACCAACTCGTGGCCTTGT
1 CACGAATAACAACCCGCGGCCTTGT
*
6534437 CACGTATAACAACCCGCGGCCTT
1 CACGAATAACAACCCGCGGCCTT
6534460 ACCACATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (25 bp):
CACGAATAACAACCCGCGGCCTTGT
Found at i:6549664 original size:15 final size:16
Alignment explanation
Indices: 6549644--6549674 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
6549634 GGTCATGCAT
6549644 AAAACCAAA-AATAAA
1 AAAACCAAACAATAAA
6549659 AAAACCAAACAATAAA
1 AAAACCAAACAATAAA
6549675 TTATGATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.77, C:0.16, G:0.00, T:0.06
Consensus pattern (16 bp):
AAAACCAAACAATAAA
Found at i:6551455 original size:19 final size:20
Alignment explanation
Indices: 6551417--6551456 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
6551407 TTAAAATATT
6551417 AAATAAAAGAAAAATATAAA
1 AAATAAAAGAAAAATATAAA
6551437 AAATAAATA-AAAAAT-TAAA
1 AAATAAA-AGAAAAATATAAA
6551456 A
1 A
6551457 GGGTGGAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 13 0.68
21 1 0.05
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (20 bp):
AAATAAAAGAAAAATATAAA
Found at i:6558695 original size:16 final size:16
Alignment explanation
Indices: 6558674--6558704 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6558664 AATCAAGGCC
6558674 TTATAATTATAACTAT
1 TTATAATTATAACTAT
*
6558690 TTATAATTATGACTA
1 TTATAATTATAACTA
6558705 AAACTCAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (16 bp):
TTATAATTATAACTAT
Found at i:6562367 original size:58 final size:58
Alignment explanation
Indices: 6562302--6562411 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 58
6562292 CTTTGCATGC
* * * * *
6562302 ATAGCATTTATTAAATCA-CATAAAATAGATTTATCTCTTGCATACTACTTTGTGTTGT
1 ATAGCATTTATTAAAT-AGCATAAAATAAATCTATCACATGCAAACTACTTTGTGTTGT
*
6562360 ATAGCATTTATTAAATAGTATAAAATAAATCTATCACATGCAAACTACTTTG
1 ATAGCATTTATTAAATAGCATAAAATAAATCTATCACATGCAAACTACTTTG
6562412 GATGATTATG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 1 0.02
58 44 0.98
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (58 bp):
ATAGCATTTATTAAATAGCATAAAATAAATCTATCACATGCAAACTACTTTGTGTTGT
Found at i:6576647 original size:85 final size:84
Alignment explanation
Indices: 6576550--6576708 Score: 214
Period size: 85 Copynumber: 1.9 Consensus size: 84
6576540 CCAATCATTA
* * * * *
6576550 ATTCTAGCATATTGCGAATAATTTTATTTGAAAATCCAAA-T-AATAATTCTAAACATTAATTCC
1 ATTCTAGCATATTACCAATAATTTTAATTGAAAATCCAAATTGAA-AA-TCCAAACAATAATTCC
6576613 CAAACATAATTCTTAATGTCTG
64 C-AACATAATTCTTAATGTCTG
* *
6576635 ATTCTAGCATATTACCAATCATTTTAATTGAAAATCCAAATTGAAAATCCAAACAATAATTCTCA
1 ATTCTAGCATATTACCAATAATTTTAATTGAAAATCCAAATTGAAAATCCAAACAATAATTCCCA
6576700 ACATAATTC
66 ACATAATTC
6576709 CCAAGCATAA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
84 10 0.15
85 50 0.77
86 3 0.05
87 2 0.03
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (84 bp):
ATTCTAGCATATTACCAATAATTTTAATTGAAAATCCAAATTGAAAATCCAAACAATAATTCCCA
ACATAATTCTTAATGTCTG
Found at i:6576678 original size:13 final size:13
Alignment explanation
Indices: 6576660--6576687 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6576650 CAATCATTTT
6576660 AATTGAAAATCCA
1 AATTGAAAATCCA
6576673 AATTGAAAATCCA
1 AATTGAAAATCCA
6576686 AA
1 AA
6576688 CAATAATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (13 bp):
AATTGAAAATCCA
Found at i:6576744 original size:97 final size:98
Alignment explanation
Indices: 6576577--6576762 Score: 284
Period size: 97 Copynumber: 1.9 Consensus size: 98
6576567 ATAATTTTAT
* *
6576577 TTGAAAATCCAAATAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGTCTGATTCTAG
1 TTGAAAATCCAAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGTCTAATTCTAG
*
6576642 CATATTACCAATCATTTTAATTGAAAATCCAAA
66 CATATTACAAATCATTTTAATTGAAAATCCAAA
* * * *
6576675 TTGAAAATCCAAACAATAATTCTCAACA-TAATTCCCAAGCATAATTTTTAATGTTTAATTCTAG
1 TTGAAAATCCAAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGTCTAATTCTAG
* *
6576739 CATATTGCAAATTATTTTAATTGA
66 CATATTACAAATCATTTTAATTGA
6576763 TTATTAAAAC
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
97 53 0.67
98 26 0.33
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (98 bp):
TTGAAAATCCAAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGTCTAATTCTAG
CATATTACAAATCATTTTAATTGAAAATCCAAA
Found at i:6584381 original size:21 final size:22
Alignment explanation
Indices: 6584346--6584391 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
6584336 TTAATTATTT
* *
6584346 TAATTATTATATATTTTTAACA
1 TAATTAATATATATTATTAACA
*
6584368 TAATTAAT-TATATTATTATCA
1 TAATTAATATATATTATTAACA
6584389 TAA
1 TAA
6584392 AATTACGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATTAATATATATTATTAACA
Found at i:6594443 original size:31 final size:32
Alignment explanation
Indices: 6594386--6594445 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
6594376 TTTTCGAAAG
*
6594386 GATCAACCATAACCTTACACTACCTTTCATGA
1 GATCAACCATAACCTCACACTACCTTTCATGA
* *
6594418 GATCAAGCATAA-CTCACGCTACCTTTCA
1 GATCAACCATAACCTCACACTACCTTTCA
6594446 AGGGATCGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 14 0.56
32 11 0.44
ACGTcount: A:0.33, C:0.32, G:0.08, T:0.27
Consensus pattern (32 bp):
GATCAACCATAACCTCACACTACCTTTCATGA
Found at i:6595866 original size:2 final size:2
Alignment explanation
Indices: 6595859--6595885 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6595849 CAAGCATCTA
6595859 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6595886 GATGAATGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6596559 original size:21 final size:22
Alignment explanation
Indices: 6596521--6596561 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
6596511 TTACATTTTG
* *
6596521 TCTACTATTTATCTATAGATGT
1 TCTACTATGTATCGATAGATGT
6596543 TCTAC-ATGTATCGATAGAT
1 TCTACTATGTATCGATAGAT
6596562 AGCCTCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (22 bp):
TCTACTATGTATCGATAGATGT
Found at i:6608229 original size:28 final size:28
Alignment explanation
Indices: 6608188--6608243 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
6608178 GCTGAACCCT
* *
6608188 CCTTTCTCTTCTT-CTTCTTCTCTTTCTC
1 CCTTTCTCTCCTTCCTTCTT-TCGTTCTC
6608216 CCTTTCTCTCCTTCCTTCTTTCGTTCTC
1 CCTTTCTCTCCTTCCTTCTTTCGTTCTC
6608244 TTCCTTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.00, C:0.41, G:0.02, T:0.57
Consensus pattern (28 bp):
CCTTTCTCTCCTTCCTTCTTTCGTTCTC
Found at i:6608260 original size:17 final size:17
Alignment explanation
Indices: 6608219--6608260 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
6608209 CTTTCTCCCT
*
6608219 TTCTCTC-CTTCCTTCT
1 TTCTCTCTCTTCCTTCA
6608235 TTCGT-TCTCTTCCTTCA
1 TTC-TCTCTCTTCCTTCA
6608252 TTCTCTCTC
1 TTCTCTCTC
6608261 CTTCTCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.02, C:0.40, G:0.02, T:0.55
Consensus pattern (17 bp):
TTCTCTCTCTTCCTTCA
Found at i:6609013 original size:11 final size:11
Alignment explanation
Indices: 6608999--6609028 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
6608989 ATAATTAAAA
6608999 TATTATTATTT
1 TATTATTATTT
6609010 TATTATTATTT
1 TATTATTATTT
6609021 TATTATTA
1 TATTATTA
6609029 AAATATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTATTATTT
Found at i:6613181 original size:33 final size:33
Alignment explanation
Indices: 6613144--6613208 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
6613134 GTCACATTAG
* * *
6613144 CATGTTATCTCATCATCAATTATAATATGTTAA
1 CATGTCATATCATCATCAATTATAACATGTTAA
*
6613177 CATGTCATATCATCATCAATTATGACATGTTA
1 CATGTCATATCATCATCAATTATAACATGTTA
6613209 GCAAGTCACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (33 bp):
CATGTCATATCATCATCAATTATAACATGTTAA
Found at i:6614055 original size:21 final size:19
Alignment explanation
Indices: 6614031--6614074 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
6614021 GAATAAGATC
*
6614031 TTCTTACTCTCTCTAAATACT
1 TTCTT-CTC-CTCTAAACACT
*
6614052 TTCTTTTCCTCTAAACACT
1 TTCTTCTCCTCTAAACACT
6614071 TTCT
1 TTCT
6614075 CTTATATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 2 0.10
21 5 0.24
ACGTcount: A:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (19 bp):
TTCTTCTCCTCTAAACACT
Found at i:6614770 original size:51 final size:51
Alignment explanation
Indices: 6614715--6614846 Score: 174
Period size: 51 Copynumber: 2.6 Consensus size: 51
6614705 GAATCTAAAA
* * *
6614715 ATAATTTTACCACTAGAAGTGAATGGATAATTATATTATTAAAATATAAGG
1 ATAATTTTACCACCAGAAGTGAATGGATAATTATATCATCAAAATATAAGG
* * * * *
6614766 ATAATTTTACCACCAGAAGTGCATAGATAATTTTATCATCAGAATCTAAGG
1 ATAATTTTACCACCAGAAGTGAATGGATAATTATATCATCAAAATATAAGG
* *
6614817 ATAATTTTACCACCAGAAATGGATGGATAA
1 ATAATTTTACCACCAGAAGTGAATGGATAA
6614847 ATTTACCAAC
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 70 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32
Consensus pattern (51 bp):
ATAATTTTACCACCAGAAGTGAATGGATAATTATATCATCAAAATATAAGG
Found at i:6614825 original size:25 final size:25
Alignment explanation
Indices: 6614690--6614834 Score: 100
Period size: 25 Copynumber: 5.7 Consensus size: 25
6614680 AATTCTATGA
**
6614690 ATAATTTTACCATCAGAATCTAAAA
1 ATAATTTTACCATCAGAATCTAAGG
*
6614715 ATAATTTTACCA-CTAGAAGT-GAATGG
1 ATAATTTTACCATC-AGAA-TCTAA-GG
* ** * * *
6614741 ATAATTATATTATTAAAATATAAGG
1 ATAATTTTACCATCAGAATCTAAGG
*
6614766 ATAATTTTACCACCAGAAGTGC-ATA-G
1 ATAATTTTACCATCAGAA-T-CTA-AGG
*
6614792 ATAATTTTATCATCAGAATCTAAGG
1 ATAATTTTACCATCAGAATCTAAGG
*
6614817 ATAATTTTACCACCAGAA
1 ATAATTTTACCATCAGAA
6614835 ATGGATGGAT
Statistics
Matches: 90, Mismatches: 20, Indels: 20
0.69 0.15 0.15
Matches are distributed among these distances:
24 3 0.03
25 52 0.58
26 34 0.38
27 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.32
Consensus pattern (25 bp):
ATAATTTTACCATCAGAATCTAAGG
Found at i:6614851 original size:26 final size:26
Alignment explanation
Indices: 6614764--6614870 Score: 101
Period size: 26 Copynumber: 4.2 Consensus size: 26
6614754 TAAAATATAA
* *
6614764 GGATAATTTTACCACCAGAAGTGCAT
1 GGATAATTTTACCACCAGAAATGGAT
* * * ** *
6614790 AGATAATTTTATCATCAG-AATCTAA
1 GGATAATTTTACCACCAGAAATGGAT
6614815 GGATAATTTTACCACCAGAAATGGAT
1 GGATAATTTTACCACCAGAAATGGAT
* *
6614841 GGATAAATTTACCAACA-AAAGTGGAT
1 GGATAATTTTACCACCAGAAA-TGGAT
6614867 GGAT
1 GGAT
6614871 GCCTTAACCC
Statistics
Matches: 64, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
25 21 0.33
26 43 0.67
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (26 bp):
GGATAATTTTACCACCAGAAATGGAT
Found at i:6614991 original size:28 final size:27
Alignment explanation
Indices: 6614933--6615010 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 27
6614923 TATGTAGATC
6614933 ACCCACCAAAAGTGGAT-ATATACTTGTA
1 ACCCA-CAAAAGTGGATGA-ATACTTGTA
* *
6614961 ACCTATCAAAAGTGGATGAATA-TTTTCA
1 ACCCA-CAAAAGTGGATGAATACTTGT-A
*
6614989 ACCCACAAAAAATGGATGAATA
1 ACCCAC-AAAAGTGGATGAATA
6615011 ATGAAAAGAC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
27 4 0.10
28 37 0.88
29 1 0.02
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (27 bp):
ACCCACAAAAGTGGATGAATACTTGTA
Found at i:6618560 original size:115 final size:114
Alignment explanation
Indices: 6618357--6618579 Score: 258
Period size: 115 Copynumber: 1.9 Consensus size: 114
6618347 AATAAGGGGT
* * * * * * *
6618357 AAGTGTACATTTAAGGTGTATTTATATTTTACTTGACCATGTTCTTTCATGTGTGAAAAAAAAGC
1 AAGTGTACATTTAAGGTGTATTTATATTTTACCTAACCAAGTTCTTGCACGTGTCAAAAAAAAAC
* *
6618422 CTATATGACACCCTAAATTTTATATATTTATATATATTTAAATTAATGAA
66 CTATATGACACCCTAAA-TTTATATATATATATATATATAAATTAATGAA
*
6618472 AAGTGTACTTTTAATGG-GTATTTATATTTTACCTAACCAAGTT-TGTGCACGTGTACAATAAAA
1 AAGTGTACATTTAA-GGTGTATTTATATTTTACCTAACCAAGTTCT-TGCACGTGT-CAA-AAAA
6618535 AAACCTATAT-ACCATCCC-AAA-TTATATATATATATATATATAAAT
62 AAACCTATATGA-CA-CCCTAAATTTATATATATATATATATATAAAT
6618580 CCAAGGCTAT
Statistics
Matches: 92, Mismatches: 10, Indels: 12
0.81 0.09 0.11
Matches are distributed among these distances:
114 1 0.01
115 65 0.71
116 5 0.05
117 18 0.20
118 3 0.03
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.39
Consensus pattern (114 bp):
AAGTGTACATTTAAGGTGTATTTATATTTTACCTAACCAAGTTCTTGCACGTGTCAAAAAAAAAC
CTATATGACACCCTAAATTTATATATATATATATATATAAATTAATGAA
Found at i:6619135 original size:11 final size:11
Alignment explanation
Indices: 6619101--6619129 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
6619091 GCAAAATGCA
6619101 AATTCAAATGT
1 AATTCAAATGT
6619112 AATTCAAATGT
1 AATTCAAATGT
6619123 AATTCAA
1 AATTCAA
6619130 TCGTAAGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (11 bp):
AATTCAAATGT
Found at i:6623844 original size:21 final size:20
Alignment explanation
Indices: 6623811--6623851 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
6623801 ATAGACTGGG
*
6623811 AAAAAAATTTAAATCATTTT
1 AAAAAAATTTAAATAATTTT
*
6623831 AAAAAATTTCTAAATAATTTT
1 AAAAAAATT-TAAATAATTTT
6623852 CATCAATAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAAAATTTAAATAATTTT
Found at i:6624839 original size:11 final size:11
Alignment explanation
Indices: 6624805--6624833 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
6624795 GCAAAAGGCA
6624805 AATTCAAATGT
1 AATTCAAATGT
6624816 AATTCAAATGT
1 AATTCAAATGT
6624827 AATTCAA
1 AATTCAA
6624834 TCGTAAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (11 bp):
AATTCAAATGT
Found at i:6625507 original size:2 final size:2
Alignment explanation
Indices: 6625500--6625524 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6625490 TACAAAACCC
6625500 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6625525 ACCTACTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6637353 original size:2 final size:2
Alignment explanation
Indices: 6637346--6637380 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
6637336 GAGCTAGGCG
* *
6637346 AT AT AT AT AC AT AC 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
6637381 AAGGATCAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:6643419 original size:2 final size:2
Alignment explanation
Indices: 6643412--6643452 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
6643402 GCGTTTGAGG
6643412 AT AT AT 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 AT AT AT A
6643453 AAGATCAATG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6647764 original size:14 final size:14
Alignment explanation
Indices: 6647745--6647794 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
6647735 CTTTCTTGTA
6647745 TTTTCTCCTTTCTT
1 TTTTCTCCTTTCTT
*
6647759 TTTTCTACTTT-TT
1 TTTTCTCCTTTCTT
6647772 CTTATTCT-CTTTCTT
1 -TT-TTCTCCTTTCTT
*
6647787 TTTCCTCC
1 TTTTCTCC
6647795 CTTTTCTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 5 0.17
14 19 0.63
15 6 0.20
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTCTCCTTTCTT
Found at i:6647799 original size:28 final size:29
Alignment explanation
Indices: 6647747--6647802 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
6647737 TTCTTGTATT
* *
6647747 TTCTCCTTTCTTTTTTCTACTTTTTCTTA
1 TTCTCCTTTCTTTTTCCTACCTTTTCTTA
*
6647776 TTCT-CTTTCTTTTTCCTCCCTTTTCTT
1 TTCTCCTTTCTTTTTCCTACCTTTTCTT
6647803 CTTCATTGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.68
Consensus pattern (29 bp):
TTCTCCTTTCTTTTTCCTACCTTTTCTTA
Found at i:6657587 original size:49 final size:51
Alignment explanation
Indices: 6657504--6657599 Score: 142
Period size: 50 Copynumber: 1.9 Consensus size: 51
6657494 AGTTTGGTGG
*
6657504 CTGTGAGTGACCGAAGCATATACCTTGACACGTGGCGCCATA-TTGGGCTC
1 CTGTGAGTGACCGAAGCACATACCTTGACACGTGGCGCCATAGTTGGGCTC
* * *
6657554 CTGTGAGTGACCGGAGCACA-GCCTTGACACGTGGCGCTATAGTTGG
1 CTGTGAGTGACCGAAGCACATACCTTGACACGTGGCGCCATAGTTGG
6657600 TGGCTTAGGC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 19 0.46
50 22 0.54
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.23
Consensus pattern (51 bp):
CTGTGAGTGACCGAAGCACATACCTTGACACGTGGCGCCATAGTTGGGCTC
Found at i:6658337 original size:10 final size:10
Alignment explanation
Indices: 6658322--6658365 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
6658312 TTTCCTATTT
6658322 TAAAATTTAA
1 TAAAATTTAA
*
6658332 TAAAATTTACTT
1 TAAAATTTA--A
*
6658344 TAATATTTAA
1 TAAAATTTAA
6658354 TAAAATTTAA
1 TAAAATTTAA
6658364 TA
1 TA
6658366 TTTGATAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 20 0.71
12 8 0.29
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (10 bp):
TAAAATTTAA
Found at i:6658351 original size:22 final size:22
Alignment explanation
Indices: 6658320--6658362 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
6658310 TGTTTCCTAT
6658320 TTTAAAATTTAATAAAATTTAC
1 TTTAAAATTTAATAAAATTTAC
*
6658342 TTTAATATTTAATAAAATTTA
1 TTTAAAATTTAATAAAATTTA
6658363 ATATTTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTAAAATTTAATAAAATTTAC
Found at i:6658364 original size:17 final size:17
Alignment explanation
Indices: 6658342--6658374 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6658332 TAAAATTTAC
6658342 TTTAATATTTAATAAAA
1 TTTAATATTTAATAAAA
*
6658359 TTTAATATTTGATAAA
1 TTTAATATTTAATAAA
6658375 GAAAAAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATATTTAATAAAA
Found at i:6663784 original size:23 final size:23
Alignment explanation
Indices: 6663754--6663800 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
6663744 TATTAATTTG
6663754 ATGTTTTTTCCTTCCATCCTCAA
1 ATGTTTTTTCCTTCCATCCTCAA
6663777 ATGTTTTTTCCTTCCATCCTCAA
1 ATGTTTTTTCCTTCCATCCTCAA
6663800 A
1 A
6663801 GACTTCCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.30, G:0.04, T:0.47
Consensus pattern (23 bp):
ATGTTTTTTCCTTCCATCCTCAA
Found at i:6664363 original size:22 final size:23
Alignment explanation
Indices: 6664324--6664370 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
6664314 ATTTCTATGC
* *
6664324 ATTACTATGATAACTAAG-CTAA
1 ATTACTATCAAAACTAAGTCTAA
*
6664346 ATTACTATCAAAATTAAGTCTAA
1 ATTACTATCAAAACTAAGTCTAA
6664369 AT
1 AT
6664371 AACTCTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (23 bp):
ATTACTATCAAAACTAAGTCTAA
Found at i:6665352 original size:34 final size:31
Alignment explanation
Indices: 6665282--6665357 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 31
6665272 TCATAGTAAT
6665282 ATAATATATTAAAATTTTATATATATACATA
1 ATAATATATTAAAATTTTATATATATACATA
* * * *
6665313 TTAATATGTTATAATTATTATACCTATATATATA
1 ATAATATATTAAAATT-TTATA--TATATACATA
6665347 ATAATAATATT
1 ATAAT-ATATT
6665358 TTGTAATAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
31 13 0.37
32 5 0.14
34 13 0.37
35 4 0.11
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (31 bp):
ATAATATATTAAAATTTTATATATATACATA
Found at i:6666087 original size:22 final size:21
Alignment explanation
Indices: 6666059--6666114 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
6666049 TTTAGGGTTA
*
6666059 AACTTATAATATA-CATATATTT
1 AACTTATAATA-AGCA-ATACTT
*
6666081 AATTTATACATAAGCAATACTT
1 AACTTATA-ATAAGCAATACTT
6666103 AACTTATAATAA
1 AACTTATAATAA
6666115 ACTTCACTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 4 0.14
22 20 0.69
23 5 0.17
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (21 bp):
AACTTATAATAAGCAATACTT
Found at i:6666475 original size:103 final size:103
Alignment explanation
Indices: 6666368--6666559 Score: 339
Period size: 103 Copynumber: 1.9 Consensus size: 103
6666358 TATATTGTTT
* * *
6666368 TTGTAATCTTTATAGTCTATATAGTAAAGTTTAATATGAATATACTACAAGTTTATTATTATTAA
1 TTGTAATATTTATAGTCTATATAGTAAAGTTTAATATGAATATAATAAAAGTTTATTATTATTAA
6666433 TAAAATATAAAATGTTTAAATTTTGTTGATATAAGGAC
66 TAAAATATAAAATGTTTAAATTTTGTTGATATAAGGAC
* *
6666471 TTGTAATATTTATAGTTTATATAGTAAAGTTTAATATGAATATAATAAAAGTTTATTATTCTTAA
1 TTGTAATATTTATAGTCTATATAGTAAAGTTTAATATGAATATAATAAAAGTTTATTATTATTAA
6666536 TAAAATATAAAATGTTTAAATTTT
66 TAAAATATAAAATGTTTAAATTTT
6666560 ATTGTGTGTG
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 84 1.00
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (103 bp):
TTGTAATATTTATAGTCTATATAGTAAAGTTTAATATGAATATAATAAAAGTTTATTATTATTAA
TAAAATATAAAATGTTTAAATTTTGTTGATATAAGGAC
Found at i:6669101 original size:2 final size:2
Alignment explanation
Indices: 6669085--6669144 Score: 52
Period size: 2 Copynumber: 31.0 Consensus size: 2
6669075 AAAGGCAATA
* * * *
6669085 AT AT AT AG AT GT AT AT A- AC AT -T AT AT AT AC 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
* *
6669125 CT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
6669145 TAATGTTGAA
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6675228 original size:27 final size:27
Alignment explanation
Indices: 6675197--6675250 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
6675187 GCTTAACTTC
*
6675197 TAATTGCATGTAGCAATAGAGAAATTA
1 TAATTACATGTAGCAATAGAGAAATTA
* * *
6675224 TAATTACGTGTAGTAGTAGAGAAATTA
1 TAATTACATGTAGCAATAGAGAAATTA
6675251 AGTGCAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (27 bp):
TAATTACATGTAGCAATAGAGAAATTA
Found at i:6679275 original size:2 final size:2
Alignment explanation
Indices: 6679270--6679301 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6679260 ATCACAAATC
*
6679270 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6679302 CCAGCTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6689648 original size:805 final size:799
Alignment explanation
Indices: 6687920--6689533 Score: 2674
Period size: 805 Copynumber: 2.0 Consensus size: 799
6687910 TACTTGTGGT
* * * * * *
6687920 AGGTTACAAGTATACATACACTTTTAGTGAGTGATCCACATATGATGGGTT-ATCTAGTTCTAGT
1 AGGTGACAAGTATAAATACACTTTTAATGAGTGATCCACATATGATGAGTTAATC-ACTTCAAGT
* * * * * *
6687984 GGATTATCCACTTGTTAGTGGGTTAGTGGCTTAAAGCACCCATCAATTTCTGATTGTAAAATTAT
65 GGATTA-CCA-TTG-GAGTGGATTAAT-GCCTAAAG-ACCTATCAA-TTCTAATTGTAAAATTAT
* * *
6688049 CTATCCACTTCTGGTAGCAAAATTATCTTTAGATTCTGTTGGTGAAGTTATCCATTTACTTTGGT
124 CTATCCACTTCTGGTAGCAAAATTATCTTTAGATTCTATTGGTAAAATTATCCATTTACTTTGGT
*
6688114 AGTAAAATTAGAATTAAAATTGTGATAGTGTAAACTATTATAGTCGTCATAATTATTAAATGATG
189 AGTAAAATTAGAATTAAAATAGTGATAGTGTAAACTATTATAGTCGTCATAATTATTAAATGATG
6688179 TTACATTCACTTCAAGAAATGGATGGATTCATGACTAAGACCATAATTATTAAATGGTGCCGCAT
254 TTACATTCACTTCAAGAAATGGATGGATTCATGACTAAGACCATAATTATTAAATGGTGCCGCAT
*
6688244 TCACTTCAGGAAATGCATGGATTTATAATTTTTATTAGCTCGTTTGTCACATTTACTTTAAGGAA
319 TCACTTCAGGAAATGCATGGATTTATAATTTTTATTAGCTCGTTTGTCACATTCACTTTAAGGAA
* *
6688309 TGGACATTATGATTTTTTGTTAATAATTATATAATAGTAAATTCACTTTTCAATTAAGGGACAAG
384 CGGACATTATGATTTTTTGTTAATAATTATATAATAGTAAATTCACTTTTCAATCAAGGGACAAG
*
6688374 ATATAAGATATACAACATAATAGTAAAATTCATATTAATTTTGATTTTTAGGGAATGAAAATACC
449 ATATAAGATATAAAACATAATAGTAAAATTCATATTAATTTTGATTTTTAGGGAATGAAAATACC
*
6688439 AAAGAGATATCGAGTCACTTATTTAATTTTTGAAAATCAGAAAAAAAAAAAACAACCTTTATGAG
514 AAAGAGATATCGAGTCACTTACTTAATTTTTGAAAATCAGAAAAAAAAAAAACAACCTTTATGAG
6688504 AAGATGAAAAAATAATACTAACACTTACCTAATTTGCTAAAACCAAAAATTGAAACCCAATTATT
579 AAGATGAAAAAATAATACTAACACTTACCTAATTTGCTAAAACCAAAAATTGAAACCCAATTATT
6688569 GATTGAAGCTTGAGATATTAGAGAATCATGCTAATAGTGTGTTATGAAATAAATATGAAGGAACA
644 GATTGAAGCTTGAGATATTAGAGAATCATGCTAATAGTGTGTTATGAAATAAATATGAAGGAACA
6688634 ACTATAAGAGAAATATAAAAATAAGTATTTAAGGGAAAGAAAGTATTTAAAGGGAATAAGAATAT
709 ACTATAAGAGAAATATAAAAATAAGTATTTAAGGGAAAGAAAGTATTTAAAGGGAATAAGAATAT
* *
6688699 CTTATTCAAGTGTGTATTTACCAAGT
774 CTTATTCAAATGTGTATTTACCAAGA
* * * * * * *
6688725 AGGTTACAAGTATACATACACTTTTAGTGGGTGATCCACATATGATGGGTTATTCACTTCTAGTG
1 AGGTGACAAGTATAAATACACTTTTAATGAGTGATCCACATATGATGAGTTAATCACTTCAAGTG
** * * *
6688790 GATTATCCACTTTTTAGTGGGTTAGTGGCTTAAAGCACCTATCAATTTCTAATTGTAAAATTATC
66 GATTA-CCA--TTGGAGTGGATTAAT-GCCTAAAG-ACCTATCAA-TTCTAATTGTAAAATTATC
*
6688855 TATCCACTTCTGGTAGCAAAATTATCTTTATATTCTATTGGTAAAATTATCCATTTACTTTGGTA
125 TATCCACTTCTGGTAGCAAAATTATCTTTAGATTCTATTGGTAAAATTATCCATTTACTTTGGTA
* *
6688920 GTAAAATTAGAATTAAACTAGTGATAGTGTAAACTATTATAGTCGTCATAATTGTTAAATGATGT
190 GTAAAATTAGAATTAAAATAGTGATAGTGTAAACTATTATAGTCGTCATAATTATTAAATGATGT
* *
6688985 TGCATTCACTTCAAGAAATGGATGGATTCATGATTAAGACCATAATTATTAAATGGTGCCGCATT
255 TACATTCACTTCAAGAAATGGATGGATTCATGACTAAGACCATAATTATTAAATGGTGCCGCATT
*
6689050 CACTTCAGGAAATGGATGGATTTATAATTTTTTATTAGCTCGTTTGTCACATTCACTTTAAGGAA
320 CACTTCAGGAAATGCATGGATTTATAA-TTTTTATTAGCTCGTTTGTCACATTCACTTTAAGGAA
6689115 CGGACATTATGA-TTTTTGTTAATAATTATATAATAGTAAATTCACTTTTCAATCAAGGGACAAG
384 CGGACATTATGATTTTTTGTTAATAATTATATAATAGTAAATTCACTTTTCAATCAAGGGACAAG
*
6689179 ATATAAGATATAAAACATAATAGTAAAATTCATATTAATTTTGATTTTTAGGGAATGAAAATACT
449 ATATAAGATATAAAACATAATAGTAAAATTCATATTAATTTTGATTTTTAGGGAATGAAAATACC
*
6689244 AAAGAGATATCGAGTCACTTACTTGATTTTTGAAAATCAGAAATAAAAAAAAACAACCTTTATGA
514 AAAGAGATATCGAGTCACTTACTTAATTTTTGAAAATCAGAAA-AAAAAAAAACAACCTTTATGA
6689309 GAAGATGAAAAAATAATACTAACACTTACCTAATTTGCTAAAACCAAAAATTGAAACCCAATTAT
578 GAAGATGAAAAAATAATACTAACACTTACCTAATTTGCTAAAACCAAAAATTGAAACCCAATTAT
6689374 TGATTGAAGCTTGAGATATTAGAGAATCATGCTAATAGTGTGTTATGAAATAAATATGAAGGAAC
643 TGATTGAAGCTTGAGATATTAGAGAATCATGCTAATAGTGTGTTATGAAATAAATATGAAGGAAC
*
6689439 AACTATAAGAGAAATATAAAAATAAGTATTTAAGGGAAAGAAAGTATTTAGAGGGAATAAGAATA
708 AACTATAAGAGAAATATAAAAATAAGTATTTAAGGGAAAGAAAGTATTTAAAGGGAATAAGAATA
6689504 TCTTATTCAAATGTGTATTTACCAATGA
773 TCTTATTCAAATGTGTATTTACCAA-GA
6689532 AG
1 AG
6689534 TGAATGGGCC
Statistics
Matches: 777, Mismatches: 27, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
805 484 0.62
806 290 0.37
807 3 0.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (799 bp):
AGGTGACAAGTATAAATACACTTTTAATGAGTGATCCACATATGATGAGTTAATCACTTCAAGTG
GATTACCATTGGAGTGGATTAATGCCTAAAGACCTATCAATTCTAATTGTAAAATTATCTATCCA
CTTCTGGTAGCAAAATTATCTTTAGATTCTATTGGTAAAATTATCCATTTACTTTGGTAGTAAAA
TTAGAATTAAAATAGTGATAGTGTAAACTATTATAGTCGTCATAATTATTAAATGATGTTACATT
CACTTCAAGAAATGGATGGATTCATGACTAAGACCATAATTATTAAATGGTGCCGCATTCACTTC
AGGAAATGCATGGATTTATAATTTTTATTAGCTCGTTTGTCACATTCACTTTAAGGAACGGACAT
TATGATTTTTTGTTAATAATTATATAATAGTAAATTCACTTTTCAATCAAGGGACAAGATATAAG
ATATAAAACATAATAGTAAAATTCATATTAATTTTGATTTTTAGGGAATGAAAATACCAAAGAGA
TATCGAGTCACTTACTTAATTTTTGAAAATCAGAAAAAAAAAAAACAACCTTTATGAGAAGATGA
AAAAATAATACTAACACTTACCTAATTTGCTAAAACCAAAAATTGAAACCCAATTATTGATTGAA
GCTTGAGATATTAGAGAATCATGCTAATAGTGTGTTATGAAATAAATATGAAGGAACAACTATAA
GAGAAATATAAAAATAAGTATTTAAGGGAAAGAAAGTATTTAAAGGGAATAAGAATATCTTATTC
AAATGTGTATTTACCAAGA
Done.