Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012247.1 Kokia drynarioides strain JFW-HI SEQ_127248, 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: 110606
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:590 original size:31 final size:29
Alignment explanation
Indices: 351--833 Score: 373
Period size: 29 Copynumber: 17.0 Consensus size: 29
341 AAAGTCCCTA
351 AACTTCCAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* *
380 AACTTCCAAAAATCCCATTTTTAACCCCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
**
409 AAACTTCCAAAAATTCCATTTTTACCCCTA
1 -AACTTCCAAAAATTCCATTTTTACCCCCG
* *
439 AACTTTCCAAAAATCCCATTTTTAACCCC-
1 AAC-TTCCAAAAATTCCATTTTTACCCCCG
*
468 -A-----AAAAATT-CATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* **
490 AACTTCCAAAAA-TCTCATTTTAACCCCAA
1 AACTTCCAAAAATTC-CATTTTTACCCCCG
* *
519 AACTTTCAAAAATTCTATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* *
548 AACTTTCAAAAATTCCATTTATTGA-CCTCG
1 AACTTCCAAAAATTCCATTT-TT-ACCCCCG
*
578 AAACTTCTAAAAATTCCATTTTTACCCCCG
1 -AACTTCCAAAAATTCCATTTTTACCCCCG
*
608 AACTTCCAAAAATCCCATTTTT-------
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* *
630 AAC-CCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
***
658 AACTTCCAAAAA-TCTCATTTTTAACCCTAA
1 AACTTCCAAAAATTC-CATTTTT-ACCCCCG
* *
688 AACTTTCAAAAATTCTATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
** *
717 AACTTCCAAAAACACCATTTTTTA-CCTCG
1 AACTTCCAAAAATTCCA-TTTTTACCCCCG
* ** *
746 AAACTTCCAATAACACCATTTTTTA-CCCTG
1 -AACTTCCAAAAATTCCA-TTTTTACCCCCG
* *
776 AAACTTCCAAAAATCCCATTTTTA-CCCCA
1 -AACTTCCAAAAATTCCATTTTTACCCCCG
* *
805 AATTTTCCCAAAATTACCA-TTTTACCCCC
1 AA-CTTCCAAAAATT-CCATTTTTACCCCC
834 AGGAATCCGA
Statistics
Matches: 368, Mismatches: 54, Indels: 63
0.76 0.11 0.13
Matches are distributed among these distances:
21 27 0.07
22 9 0.02
23 1 0.00
27 1 0.00
28 13 0.04
29 159 0.43
30 137 0.37
31 21 0.06
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCCCG
Found at i:601 original size:139 final size:139
Alignment explanation
Indices: 351--738 Score: 348
Period size: 139 Copynumber: 2.8 Consensus size: 139
341 AAAGTCCCTA
* **
351 AACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAACTTC
1 AACTTCCAAAAATTCCATTTTAACCCCAAAACTTCCAAAAATCCCATTTTTAACCCCGAAACTTC
*
416 CAAAAATTCCATTTTTACCCCTAAACTTTCCAAAAATCCCATTTTTAACCCCAAAAAATTCATTT
66 CAAAAATTCCATTTTTACCCCGAAACTTTCCAAAAATCCCATTTTTAACCCCAAAAAATTCATTT
481 TTACCCTCG
131 TTACCCTCG
* * * *
490 AACTTCCAAAAA-TCTCATTTTAACCCCAAAACTTTCAAAAATTCTATTTTTACCCCCG-AACTT
1 AACTTCCAAAAATTC-CATTTTAACCCCAAAACTTCCAAAAATCCCATTTTTAACCCCGAAACTT
* * * * ** *
553 TCAAAAATTCCATTTATTGACCTCGAAAC-TTCTAAAAATTCCATTTTT-ACCCC-CGAACTTCC
65 CCAAAAATTCCATTT-TT-ACCCCGAAACTTTCCAAAAATCCCATTTTTAACCCCAAAAAATT-C
**** **
615 AAAAAT-CCCATTTTT
127 ATTTTTACCC---TCG
* * * * **
630 AAC-CCCAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATCTCATTTTTAACCCTAAAACTT
1 AACTTCCAAAAATTCCATTTTAACCC-CAAAACTTCCAAAAATCCCATTTTTAACCCCGAAACTT
* *
693 TCAAAAATTCTATTTTTACCCCCG-AAC-TTCCAAAAA-CACCATTTTT
65 CCAAAAATTCCATTTTTA-CCCCGAAACTTTCCAAAAATC-CCATTTTT
739 TACCTCGAAA
Statistics
Matches: 202, Mismatches: 35, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
137 7 0.03
138 49 0.24
139 112 0.55
140 34 0.17
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (139 bp):
AACTTCCAAAAATTCCATTTTAACCCCAAAACTTCCAAAAATCCCATTTTTAACCCCGAAACTTC
CAAAAATTCCATTTTTACCCCGAAACTTTCCAAAAATCCCATTTTTAACCCCAAAAAATTCATTT
TTACCCTCG
Found at i:635 original size:168 final size:169
Alignment explanation
Indices: 350--806 Score: 699
Period size: 168 Copynumber: 2.7 Consensus size: 169
340 GAAAGTCCCT
* * * *
350 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAACTT
1 AAACTTTCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATACCATTTTTAACCTCGAAACTT
*
415 CCAAAAATTCCATTTTTACCCCTAAACTTTCCAAAAATCCCATTTTTAACCCCAAAAAATT-CAT
66 CCAAAAATTCCATTTTTACCCCTGAAC-TTCCAAAAATCCCATTTTTAACCCCAAAAAATTCCAT
479 TTTTACCCTCGAACTTCCAAAAATCTCA-TTTTAACCCCA
130 TTTTACCCTCGAACTTCCAAAAATCTCATTTTTAACCCCA
* * *
518 AAACTTTCAAAAATTCTATTTTTACCCCCGAACTTTCAAAAATTCCATTTATTGACCTCGAAACT
1 AAACTTTCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATACCATTT-TTAACCTCGAAACT
* *
583 TCTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC-AAAAATTCCAT
65 TCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACCCCAAAAAATTCCAT
*
647 TTTTACCCTCGAACTTCCAAAAATCTCATTTTTAACCCTA
130 TTTTACCCTCGAACTTCCAAAAATCTCATTTTTAACCCCA
* *
687 AAACTTTCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAACACCATTTTTTACCTCGAAACTT
1 AAACTTTCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATACCATTTTTAACCTCGAAACTT
* **
752 CCAATAACACCATTTTTTA-CCCTGAAACTTCCAAAAATCCCATTTTT-ACCCCAAA
66 CCAAAAATTCCA-TTTTTACCCCTG-AACTTCCAAAAATCCCATTTTTAACCCCAAA
807 TTTTCCCAAA
Statistics
Matches: 264, Mismatches: 19, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
167 7 0.03
168 133 0.50
169 124 0.47
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.32
Consensus pattern (169 bp):
AAACTTTCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATACCATTTTTAACCTCGAAACTT
CCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACCCCAAAAAATTCCATT
TTTACCCTCGAACTTCCAAAAATCTCATTTTTAACCCCA
Found at i:645 original size:50 final size:53
Alignment explanation
Indices: 357--738 Score: 357
Period size: 59 Copynumber: 6.8 Consensus size: 53
347 CCTAAACTTC
357 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAACTT
1 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAA-CCC---AC-T
**
415 CCAAAAATTCCATTTTTACCCCTAAACTTTCCAAAAATCCCATTTTTAACCC-C-
1 -CAAAAATTCCATTTTTACCCCCGAAC-TTCCAAAAATCCCATTTTTAACCCACT
* * *
468 AAAAAATT-CATTTTTACCCTCGAACTTCCAAAAATCTCA-TTTTAACCCCAAAACTTT
1 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAA-CCC---AC--T
* * * *
525 CAAAAATTCTATTTTTACCCCCGAACTTTCAAAAATTCCATTTATTGACCTCGAAACTT
1 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTT-TTAACC-C---AC-T
584 CTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAA-CC-C-
1 C-AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCACT
* *
635 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTAACCCTAAAACTTT
1 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCC----AC--T
*
694 CAAAAATTCTATTTTTACCCCCGAACTTCCAAAAA-CACCATTTTT
1 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATC-CCATTTTT
739 TACCTCGAAA
Statistics
Matches: 275, Mismatches: 24, Indels: 48
0.79 0.07 0.14
Matches are distributed among these distances:
49 6 0.02
50 60 0.22
51 17 0.06
52 7 0.03
53 1 0.00
54 1 0.00
55 1 0.00
56 1 0.00
57 8 0.03
58 28 0.10
59 77 0.28
60 68 0.25
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (53 bp):
CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCACT
Found at i:754 original size:109 final size:110
Alignment explanation
Indices: 525--738 Score: 303
Period size: 109 Copynumber: 2.0 Consensus size: 110
515 CCAAAACTTT
* * * *
525 CAAAAATTCTATTTTTACCCCCGAACTTTCAAAAATTCCATTTATTGACCTCGAAACTTCTAAAA
1 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTATTAACCTCAAAACTTCTAAAA
590 ATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCC
66 ATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCC
*
635 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAA-TCTCATTT-TTAACC-CTAAAACTT-TCA
1 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTC-CATTTATTAACCTC-AAAACTTCT-A
*
696 AAAATTCTATTTTTACCCCCGAACTTCCAAAAA-CACCATTTTT
63 AAAATTCCATTTTTACCCCCGAACTTCCAAAAATC-CCATTTTT
739 TACCTCGAAA
Statistics
Matches: 94, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
108 3 0.03
109 54 0.57
110 37 0.39
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.34
Consensus pattern (110 bp):
CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTATTAACCTCAAAACTTCTAAAA
ATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCC
Found at i:812 original size:29 final size:28
Alignment explanation
Indices: 634--832 Score: 143
Period size: 30 Copynumber: 6.8 Consensus size: 28
624 ATTTTTAACC
* *
634 CCAAAAATTCCATTTTTACCCTCGAACTT
1 CCAAAAATCCCATTTTTACCC-CAAACTT
* *
663 CCAAAAATCTCATTTTTAACCCTAAAACTT
1 CCAAAAATCCCATTTTT-ACCC-CAAACTT
* * * *
693 TCAAAAATTCTATTTTTACCCCCGAACTT
1 CCAAAAATCCCATTTTTA-CCCCAAACTT
*
722 CCAAAAA-CACCATTTTTTACCTCGAAACTT
1 CCAAAAATC-CCA-TTTTTACC-CCAAACTT
* *
752 CCAATAA-CACCATTTTTTACCCTGAAACTT
1 CCAAAAATC-CCA-TTTTTACCC-CAAACTT
*
782 CCAAAAATCCCATTTTTACCCCAAATTTT
1 CCAAAAATCCCATTTTTACCCCAAA-CTT
* *
811 CCCAAAATTACCA-TTTTACCCC
1 -CCAAAAATCCCATTTTTACCCC
833 CAGGAATCCG
Statistics
Matches: 140, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
28 3 0.02
29 52 0.37
30 84 0.60
31 1 0.01
ACGTcount: A:0.34, C:0.31, G:0.02, T:0.33
Consensus pattern (28 bp):
CCAAAAATCCCATTTTTACCCCAAACTT
Found at i:2300 original size:17 final size:16
Alignment explanation
Indices: 2274--2316 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
2264 ATTTTGAAAT
2274 TAAATTTAAATTTAAAA
1 TAAA-TTAAATTTAAAA
2291 TAAATATAAATTTAAAA
1 TAAAT-TAAATTTAAAA
2308 TAAATTAAA
1 TAAATTAAA
2317 AAGGGGCCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATTAAATTTAAAA
Found at i:3844 original size:5 final size:5
Alignment explanation
Indices: 3834--3858 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3824 TCAATGGTGT
3834 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
3859 ATTCAACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:5385 original size:49 final size:49
Alignment explanation
Indices: 5313--5485 Score: 193
Period size: 49 Copynumber: 3.5 Consensus size: 49
5303 GTGACATGAA
* * *
5313 ACTTGAACCTGTGACTGCATAACCACCGCCAATTGGGAGTTCGAGTTAT
1 ACTTGAACCCGTGACTGCATAACCACCGCCAACTGGGAGCTCGAGTTAT
* * *
5362 ACTTGAACCCATGACTGCATAACCACCGTCAACTGGGAGCTCTAGTTAT
1 ACTTGAACCCGTGACTGCATAACCACCGCCAACTGGGAGCTCGAGTTAT
*** ** * * *
5411 ACTTGAACCCGTGACCATATAACCACCGTGAACTAGGAGCCCTAGTTAT
1 ACTTGAACCCGTGACTGCATAACCACCGCCAACTGGGAGCTCGAGTTAT
* * *
5460 ACTTGAACTCGTGACCGTATAACCAC
1 ACTTGAACCCGTGACTGCATAACCAC
5486 AATGAACTAA
Statistics
Matches: 109, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 109 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (49 bp):
ACTTGAACCCGTGACTGCATAACCACCGCCAACTGGGAGCTCGAGTTAT
Found at i:5492 original size:49 final size:49
Alignment explanation
Indices: 5356--5501 Score: 193
Period size: 49 Copynumber: 3.0 Consensus size: 49
5346 TGGGAGTTCG
* * * * * *
5356 AGTTATACTTGAACCCATGACTGCATAACCACCGTCAACTGGGAGCTCT
1 AGTTATACTTGAACCCGTGACCGTATAACCACCGTGAACTAGGAGCCCT
*
5405 AGTTATACTTGAACCCGTGACCATATAACCACCGTGAACTAGGAGCCCT
1 AGTTATACTTGAACCCGTGACCGTATAACCACCGTGAACTAGGAGCCCT
* ** *
5454 AGTTATACTTGAACTCGTGACCGTATAACCACAATGAACTAAGAGCCC
1 AGTTATACTTGAACCCGTGACCGTATAACCACCGTGAACTAGGAGCCC
5502 AAGCTGCAAC
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 85 1.00
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (49 bp):
AGTTATACTTGAACCCGTGACCGTATAACCACCGTGAACTAGGAGCCCT
Found at i:18102 original size:14 final size:13
Alignment explanation
Indices: 18075--18099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18065 ATAATTACTT
18075 ATTAAATTTTTTA
1 ATTAAATTTTTTA
18088 ATTAAATTTTTT
1 ATTAAATTTTTT
18100 TAAGGTTAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTAAATTTTTTA
Found at i:19047 original size:21 final size:21
Alignment explanation
Indices: 19006--19048 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
18996 TTATTTTGAA
*
19006 TTATATTTATGTTTAATTTTT
1 TTATATTTATGTTTAAGTTTT
*
19027 TTATATTATAT-TTTACGTTTT
1 TTATATT-TATGTTTAAGTTTT
19048 T
1 T
19049 ATGAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (21 bp):
TTATATTTATGTTTAAGTTTT
Found at i:23104 original size:4 final size:4
Alignment explanation
Indices: 23091--23133 Score: 54
Period size: 4 Copynumber: 11.0 Consensus size: 4
23081 AAAATTGAAG
*
23091 GAAA -AAA GAAA GAAAA AAAA GAAA GAAA GAAA GAAA G-AA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
23134 AAGGAAGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 6 0.18
4 25 0.74
5 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:23123 original size:25 final size:25
Alignment explanation
Indices: 23091--23151 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
23081 AAAATTGAAG
23091 GAAA-AAAGAAAGAAAAAAAAGAAA
1 GAAAGAAAGAAAGAAAAAAAAGAAA
* *
23115 GAAAGAAAGAAAGAAGAAAAAGGAA
1 GAAAGAAAGAAAGAAAAAAAAGAAA
*
23140 GAAGGAGAAGAA
1 GAAAGA-AAGAA
23152 GGGGGAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 4 0.12
25 23 0.72
26 5 0.16
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (25 bp):
GAAAGAAAGAAAGAAAAAAAAGAAA
Found at i:23133 original size:7 final size:7
Alignment explanation
Indices: 23091--23169 Score: 51
Period size: 7 Copynumber: 12.0 Consensus size: 7
23081 AAAATTGAAG
*
23091 GAAAAAA
1 GAAAGAA
23098 GAAAGAA
1 GAAAGAA
*
23105 -AAAAAA
1 GAAAGAA
23111 GAAAGAA
1 GAAAGAA
*
23118 -AGA-AA
1 GAAAGAA
23123 GAAAGAA
1 GAAAGAA
23130 GAAA-AA
1 GAAAGAA
*
23136 GGAAGAA
1 GAAAGAA
*
23143 G-GAGAA
1 GAAAGAA
* **
23149 GAAGGGG
1 GAAAGAA
23156 GAAAGAA
1 GAAAGAA
23163 GAAAGAA
1 GAAAGAA
23170 AAAAAGATAA
Statistics
Matches: 53, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
5 2 0.04
6 19 0.36
7 32 0.60
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (7 bp):
GAAAGAA
Found at i:23143 original size:13 final size:13
Alignment explanation
Indices: 23093--23176 Score: 73
Period size: 13 Copynumber: 6.5 Consensus size: 13
23083 AATTGAAGGA
*
23093 AAAAAGAAAGAAA
1 AAAAAGAAAGAAG
23106 AAAAAGAAAGAA-
1 AAAAAGAAAGAAG
*
23118 AGAAAGAAAGAAG
1 AAAAAGAAAGAAG
*
23131 AAAAAGGAAGAAG
1 AAAAAGAAAGAAG
* * * **
23144 GAGAAGAAGGGGG
1 AAAAAGAAAGAAG
23157 AAAGAAGAAAGAA-
1 AAA-AAGAAAGAAG
23170 AAAAAGA
1 AAAAAGA
23177 TAATGTGTTT
Statistics
Matches: 55, Mismatches: 14, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
12 15 0.27
13 34 0.62
14 6 0.11
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAGAAG
Found at i:23860 original size:16 final size:16
Alignment explanation
Indices: 23815--23864 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
23805 TAAACCTAAC
*
23815 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
23831 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
23845 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
23861 TAAT
1 TAAT
23865 ATCCCATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:25233 original size:43 final size:43
Alignment explanation
Indices: 25151--25233 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
25141 ATTAACATGT
* *
25151 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTCAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTCAC
* *
25194 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGT
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGT
25234 TATTAATTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 3 0.09
43 32 0.91
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTCAC
Found at i:29045 original size:4 final size:4
Alignment explanation
Indices: 29025--29090 Score: 64
Period size: 4 Copynumber: 16.2 Consensus size: 4
29015 AACACATTAC
* * *
29025 CTTT CTTT -TCTT C-TT CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT
1 CTTT CTTT CT-TT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
29073 CTTTT CTTT CTTT CTTT C
1 C-TTT CTTT CTTT CTTT C
29091 CCATTTATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
3 4 0.08
4 40 0.78
5 7 0.14
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:29084 original size:17 final size:18
Alignment explanation
Indices: 29025--29090 Score: 80
Period size: 17 Copynumber: 3.5 Consensus size: 18
29015 AACACATTAC
29025 CTTTCTTTTCTTCTTCTTT
1 CTTTC-TTTCTTCTTCTTT
*
29044 CTTTCCTCTCCTTCTTCCTTT
1 CTTT-CT-TTCTTCTT-CTTT
29065 CTTTCTTTCTT-TTCTTT
1 CTTTCTTTCTTCTTCTTT
29082 CTTTCTTTC
1 CTTTCTTTC
29091 CCATTTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
17 13 0.31
18 2 0.05
19 9 0.21
20 10 0.24
21 8 0.19
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (18 bp):
CTTTCTTTCTTCTTCTTT
Found at i:32342 original size:13 final size:13
Alignment explanation
Indices: 32310--32370 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 13
32300 ATAAAAGGGG
32310 AAAAAATTAAAAT
1 AAAAAATTAAAAT
*
32323 ATAAAAATTAAATT
1 A-AAAAATTAAAAT
**
32337 AAAAAATGCAAAT
1 AAAAAATTAAAAT
**
32350 AATAAAACAAAAAT
1 AA-AAAATTAAAAT
32364 AAAAAAT
1 AAAAAAT
32371 GGCTAAAGTA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
13 16 0.42
14 22 0.58
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.21
Consensus pattern (13 bp):
AAAAAATTAAAAT
Found at i:34363 original size:18 final size:17
Alignment explanation
Indices: 34336--34369 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
34326 TCAACCATAT
34336 TAAATCCATGAAAAATC
1 TAAATCCATGAAAAATC
34353 TAAATTCCATGAAAAAT
1 TAAA-TCCATGAAAAAT
34370 AAGTTAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (17 bp):
TAAATCCATGAAAAATC
Found at i:39022 original size:17 final size:18
Alignment explanation
Indices: 39000--39033 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
38990 AAGGCTTTTT
39000 TTAAATAAT-ATAAAAAA
1 TTAAATAATCATAAAAAA
39017 TTAAATAATCATAAAAA
1 TTAAATAATCATAAAAA
39034 TGAGGTGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TTAAATAATCATAAAAAA
Found at i:39687 original size:27 final size:27
Alignment explanation
Indices: 39636--39688 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
39626 CTTAGCAATT
* *
39636 TGAGAAAAAAAAAATAGTTTAAGAAAC
1 TGAGAAAAAAAAAAAACTTTAAGAAAC
*
39663 TGAGAAAAAAAAAAAACTTTTAGAAA
1 TGAGAAAAAAAAAAAACTTTAAGAAA
39689 GCAACATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.64, C:0.04, G:0.13, T:0.19
Consensus pattern (27 bp):
TGAGAAAAAAAAAAAACTTTAAGAAAC
Found at i:39892 original size:21 final size:20
Alignment explanation
Indices: 39859--39911 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
39849 TTTTGTTGTT
39859 ATATTTTTATAAATATG-ATCTA
1 ATATTTTT-TAAATA-GAAT-TA
39881 ATATTTTTTAAATAGAAATTA
1 ATATTTTTTAAATAG-AATTA
39902 ATATTTTTTA
1 ATATTTTTTA
39912 TTTTTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 1 0.03
21 18 0.62
22 10 0.34
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (20 bp):
ATATTTTTTAAATAGAATTA
Found at i:43579 original size:30 final size:31
Alignment explanation
Indices: 43545--43605 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 31
43535 ACCCATGTTA
43545 TAATTGT-AATTTAAAAAATATATATATTTT
1 TAATTGTAAATTTAAAAAATATATATATTTT
* * *
43575 TAATTTTAAAATTTAATAATTATATATATTT
1 TAATTGT-AAATTTAAAAAATATATATATTT
43606 CATTTATCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 6 0.23
32 20 0.77
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (31 bp):
TAATTGTAAATTTAAAAAATATATATATTTT
Found at i:47675 original size:21 final size:20
Alignment explanation
Indices: 47603--47676 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
47593 TTTTTTTGGA
*
47603 GTTATTTTTGTTGTTTTGCT
1 GTTATTTTTGTTGTTTGGCT
*
47623 GTTATTTTTGCTACTGTTTTGGTT
1 GTTATTTTTG-T--TG-TTTGGCT
* * *
47647 ATTGTTTTTTGTTGTTTGGGT
1 GTT-ATTTTTGTTGTTTGGCT
47668 GTTATTTTT
1 GTTATTTTT
47677 ATGCATTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
20 15 0.36
21 9 0.21
22 2 0.05
23 2 0.05
24 8 0.19
25 6 0.14
ACGTcount: A:0.07, C:0.04, G:0.22, T:0.68
Consensus pattern (20 bp):
GTTATTTTTGTTGTTTGGCT
Found at i:48432 original size:165 final size:163
Alignment explanation
Indices: 48253--48586 Score: 632
Period size: 165 Copynumber: 2.0 Consensus size: 163
48243 CAAATACACT
48253 TAAAAACATTAAAACAAACATTAAAAAATAAACAAATTTAAAATACATTAAAAATTCTTTATATT
1 TAAAAACATTAAAACAAACATTAAAAAATAAACAAATTTAAAATACATTAAAAATTCTTTATATT
48318 AAGATTTCAAATAAAGTAGTAGAAAAATTAACAATAAAACATAAGTTCTACAATATTCAAATAAT
66 AAGATTTCAAATAAAGTAGTAGAAAAATTAACAATAAAACATAAGTTCTACAATATTCAAATAAT
48383 ATTAAAAAAGACAATAAAACAATAGTAAAAACGCA
131 ATTAAAAAAGACAAT-AAA-AATAGTAAAAACGCA
48418 TAAAAACATTAAAACAAACATTAAAAAATAAACAAATTTAAAATACATTAAAAATTCTTTATATT
1 TAAAAACATTAAAACAAACATTAAAAAATAAACAAATTTAAAATACATTAAAAATTCTTTATATT
* *
48483 AAGATTTCAAATAAATTAGTAGAAAAATTAACAATAAAACATAAGTTCTACAATTTTCAAATAAT
66 AAGATTTCAAATAAAGTAGTAGAAAAATTAACAATAAAACATAAGTTCTACAATATTCAAATAAT
48548 ATTAAAAAAGACAATAAAAATAGTAAAAACGCA
131 ATTAAAAAAGACAATAAAAATAGTAAAAACGCA
48581 TAAAAA
1 TAAAAA
48587 TAACATCTAA
Statistics
Matches: 167, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
163 21 0.13
164 3 0.02
165 143 0.86
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.27
Consensus pattern (163 bp):
TAAAAACATTAAAACAAACATTAAAAAATAAACAAATTTAAAATACATTAAAAATTCTTTATATT
AAGATTTCAAATAAAGTAGTAGAAAAATTAACAATAAAACATAAGTTCTACAATATTCAAATAAT
ATTAAAAAAGACAATAAAAATAGTAAAAACGCA
Found at i:48574 original size:21 final size:19
Alignment explanation
Indices: 48545--48588 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
48535 ATTTTCAAAT
*
48545 AATATTAAAAAAGACAATAAA
1 AATAGTAAAAAAG-C-ATAAA
*
48566 AATAGTAAAAACGCATAAA
1 AATAGTAAAAAAGCATAAA
48585 AATA
1 AATA
48589 ACATCTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
20 1 0.05
21 11 0.52
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.18
Consensus pattern (19 bp):
AATAGTAAAAAAGCATAAA
Found at i:48613 original size:12 final size:12
Alignment explanation
Indices: 48596--48620 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48586 ATAACATCTA
48596 AACAATCAAAAT
1 AACAATCAAAAT
48608 AACAATCAAAAT
1 AACAATCAAAAT
48620 A
1 A
48621 GCAGCAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (12 bp):
AACAATCAAAAT
Found at i:48630 original size:12 final size:12
Alignment explanation
Indices: 48603--48698 Score: 85
Period size: 12 Copynumber: 8.3 Consensus size: 12
48593 CTAAACAATC
48603 AAAATAACAATC-
1 AAAATAACAA-CA
* *
48615 AAAATAGCAGCA
1 AAAATAACAACA
*
48627 AAAATAACAGC-
1 AAAATAACAACA
*
48638 AAAACAACAAC-
1 AAAATAACAACA
48649 -AAA-AACAACA
1 AAAATAACAACA
*
48659 AAAATAGCAACA
1 AAAATAACAACA
*
48671 AAAACAACAACA
1 AAAATAACAACA
*
48683 AAAATAACAGCA
1 AAAATAACAACA
48695 AAAA
1 AAAA
48699 CAATACCCAA
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
9 6 0.09
10 3 0.04
11 13 0.19
12 48 0.69
ACGTcount: A:0.70, C:0.19, G:0.05, T:0.06
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:48631 original size:24 final size:22
Alignment explanation
Indices: 48614--48701 Score: 88
Period size: 21 Copynumber: 3.9 Consensus size: 22
48604 AAATAACAAT
* * *
48614 CAAAATAGCAGCAAAAATAACA
1 CAAAATAACAACAAAAACAACA
*
48636 GCAAAACAACAACAAAAACAACA
1 -CAAAATAACAACAAAAACAACA
*
48659 -AAAATAGCAACAAAAACAACAA
1 CAAAATAACAACAAAAACAAC-A
*
48681 CAAAAATAACAGCAAAAACAA
1 C-AAAATAACAACAAAAACAA
48702 TACCCAAACA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
21 18 0.33
22 1 0.02
23 18 0.33
24 17 0.31
ACGTcount: A:0.69, C:0.20, G:0.06, T:0.05
Consensus pattern (22 bp):
CAAAATAACAACAAAAACAACA
Found at i:48631 original size:44 final size:44
Alignment explanation
Indices: 48582--48701 Score: 127
Period size: 44 Copynumber: 2.7 Consensus size: 44
48572 AAAAACGCAT
* * * *
48582 AAAAATAACATCTAAACAATCAA-AATAACAATC-AAAATAGCAGC
1 AAAAATAACAGCAAAACAA-CAACAAAAACAA-CAAAAATAGCAAC
48626 AAAAATAACAGCAAAACAACAACAAAAACAACAAAAATAGCAAC
1 AAAAATAACAGCAAAACAACAACAAAAACAACAAAAATAGCAAC
* * * *
48670 AAAAACAACAACAAAAATAACAGCAAAAACAA
1 AAAAATAACAGC-AAAACAACAACAAAAACAA
48702 TACCCAAACA
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
43 4 0.06
44 44 0.68
45 17 0.26
ACGTcount: A:0.68, C:0.19, G:0.04, T:0.08
Consensus pattern (44 bp):
AAAAATAACAGCAAAACAACAACAAAAACAACAAAAATAGCAAC
Found at i:48657 original size:9 final size:9
Alignment explanation
Indices: 48643--48701 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
48633 ACAGCAAAAC
48643 AACAACAAA
1 AACAACAAA
48652 AACAACAAA
1 AACAACAAA
* *
48661 AATAGCAACA
1 AACAACAA-A
*
48671 AA-AACAAC
1 AACAACAAA
48679 AACAA-AAA
1 AACAACAAA
*
48687 TAACAGCAAA
1 -AACAACAAA
48697 AACAA
1 AACAA
48702 TACCCAAACA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
8 4 0.10
9 29 0.74
10 6 0.15
ACGTcount: A:0.73, C:0.20, G:0.03, T:0.03
Consensus pattern (9 bp):
AACAACAAA
Found at i:48680 original size:33 final size:32
Alignment explanation
Indices: 48596--48691 Score: 102
Period size: 33 Copynumber: 2.8 Consensus size: 32
48586 ATAACATCTA
* *
48596 AACAATCAAAATAACAATCAAAATAGCAGCAAAAAT
1 AACAA-CAAAACAACAA-CAAAA-A-CAACAAAAAT
*
48632 AACAGCAAAACAACAACAAAAACAACAAAAAT
1 AACAACAAAACAACAACAAAAACAACAAAAAT
* *
48664 AGCAACAAAAACAACAACAAAAATAACA
1 AACAAC-AAAACAACAACAAAAACAACA
48692 GCAAAAACAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
32 13 0.25
33 21 0.40
34 5 0.09
35 10 0.19
36 4 0.08
ACGTcount: A:0.69, C:0.20, G:0.04, T:0.07
Consensus pattern (32 bp):
AACAACAAAACAACAACAAAAACAACAAAAAT
Found at i:48691 original size:21 final size:21
Alignment explanation
Indices: 48615--48701 Score: 75
Period size: 23 Copynumber: 3.9 Consensus size: 21
48605 AATAACAATC
* * *
48615 AAAATAGCAGCAAAAATAACA
1 AAAATAACAACAAAAACAACA
*
48636 GCAAAACAACAACAAAAACAACA
1 --AAAATAACAACAAAAACAACA
*
48659 AAAATAGCAACAAAAACAACAACA
1 AAAATAACAAC--AAA-AACAACA
*
48683 AAAATAACAGCAAAAACAA
1 AAAATAACAACAAAAACAA
48702 TACCCAAACA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
21 14 0.26
22 3 0.06
23 20 0.38
24 16 0.30
ACGTcount: A:0.70, C:0.20, G:0.06, T:0.05
Consensus pattern (21 bp):
AAAATAACAACAAAAACAACA
Found at i:48711 original size:56 final size:55
Alignment explanation
Indices: 48625--48750 Score: 132
Period size: 56 Copynumber: 2.3 Consensus size: 55
48615 AAAATAGCAG
*
48625 CAAAAATAACAGC-AAAACAACAACAAAAACAACAAAAATAGCAACAAAAACAACAA
1 CAAAAATAACAGCAAAAACAACAACAAAAACAACAAAAAAAGCAAC-AAAACAAC-A
* ** ** * *
48681 CAAAAATAACAGCAAAAACAA-TACCCAAACAGTAAAAAAAGTATCAAAACAACA
1 CAAAAATAACAGCAAAAACAACAACAAAAACAACAAAAAAAGCAACAAAACAACA
*
48735 -AAAAATAACATCAAAA
1 CAAAAATAACAGCAAAA
48751 CAGCAAAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
53 15 0.25
54 1 0.02
55 8 0.13
56 29 0.48
57 7 0.12
ACGTcount: A:0.69, C:0.20, G:0.04, T:0.07
Consensus pattern (55 bp):
CAAAAATAACAGCAAAAACAACAACAAAAACAACAAAAAAAGCAACAAAACAACA
Found at i:48769 original size:22 final size:21
Alignment explanation
Indices: 48707--48782 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
48697 AACAATACCC
* *
48707 AAACAGTAAAAAA-AGTATCA
1 AAACAGCAAAAAATAGCATCA
* *
48727 AAACAACAAAAAATAACATCA
1 AAACAGCAAAAAATAGCATCA
48748 AAACAGCAAAAAATAGCAATCA
1 AAACAGCAAAAAATAGC-ATCA
*
48770 AAACAGTAAAAAA
1 AAACAGCAAAAAA
48783 AACAACACCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.23
21 20 0.43
22 16 0.34
ACGTcount: A:0.68, C:0.14, G:0.07, T:0.11
Consensus pattern (21 bp):
AAACAGCAAAAAATAGCATCA
Found at i:50048 original size:30 final size:29
Alignment explanation
Indices: 49976--50053 Score: 93
Period size: 30 Copynumber: 2.7 Consensus size: 29
49966 TAGACGAAGT
* * *
49976 CAAAAATGTGATTTTTTGATGCTCTGGGG
1 CAAAAATGTAATTTTTGGATGCTCGGGGG
* **
50005 TAAAACGGTAATTTTTGGATGCTCGGGGGG
1 CAAAAATGTAATTTTTGGATGCTC-GGGGG
50035 CAAAAATGTAATTTTTGGA
1 CAAAAATGTAATTTTTGGA
50054 CATTTTTGGG
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 19 0.49
30 20 0.51
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (29 bp):
CAAAAATGTAATTTTTGGATGCTCGGGGG
Found at i:50049 original size:29 final size:28
Alignment explanation
Indices: 49976--50049 Score: 67
Period size: 29 Copynumber: 2.5 Consensus size: 28
49966 TAGACGAAGT
* * *
49976 CAAAAATGTGATTTTTTGATGCTCTGGGG
1 CAAAAATGT-AATTTTGGATGCTCGGGGG
* **
50005 TAAAACGGTAATTTTTGGATGCTCGGGGGG
1 CAAAAATGTAA-TTTTGGATGCTC-GGGGG
50035 CAAAAATGTAATTTT
1 CAAAAATGTAATTTT
50050 TGGACATTTT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
28 1 0.03
29 21 0.62
30 12 0.35
ACGTcount: A:0.28, C:0.09, G:0.27, T:0.35
Consensus pattern (28 bp):
CAAAAATGTAATTTTGGATGCTCGGGGG
Found at i:50194 original size:29 final size:30
Alignment explanation
Indices: 50037--50196 Score: 122
Period size: 30 Copynumber: 5.5 Consensus size: 30
50027 TCGGGGGGCA
*
50037 AAAAT-GTAATTTTTGGACATTTTTGGGGGT
1 AAAATGGTAATTTTTAGACA-TTTTGGGGGT
* * * *
50067 AAAATGGTAATTTTTAAAAAGTTT-AGGGT
1 AAAATGGTAATTTTTAGACATTTTGGGGGT
*
50096 AAAAAAT-GTAATTTTTGGACA-TTTGGGGG-
1 --AAAATGGTAATTTTTAGACATTTTGGGGGT
* *
50125 -AAATGGTAATTTTTAGA-ATTTTTGAGGT
1 AAAATGGTAATTTTTAGACATTTTGGGGGT
* *
50153 CAAAAAT-GAAATTTTTAGACA-TTCGGGGGT
1 --AAAATGGTAATTTTTAGACATTTTGGGGGT
50183 AAAATGGTAATTTT
1 AAAATGGTAATTTT
50197 GAAAAGTTAG
Statistics
Matches: 101, Mismatches: 17, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
26 5 0.05
27 17 0.17
28 5 0.05
29 14 0.14
30 39 0.39
31 21 0.21
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (30 bp):
AAAATGGTAATTTTTAGACATTTTGGGGGT
Found at i:50209 original size:29 final size:28
Alignment explanation
Indices: 50177--50419 Score: 122
Period size: 30 Copynumber: 8.4 Consensus size: 28
50167 TTAGACATTC
50177 GGGGGTAAAATGGTAATTTTGAAAAGTTA
1 GGGGGTAAAATGG-AATTTTGAAAAGTTA
* * *
50206 GGGGTTTAAAAATGGAATTTTGGAGAA-TTT
1 GGGG-GT-AAAATGGAATTTT-GAAAAGTTA
** * *
50236 GAGGGCAAAAATGTAATTTTTAGAAAGTTA
1 G-GGGGTAAAATGGAATTTTGA-AAAGTTA
* *
50266 -AGGGTCAAAAATGGAATTTTGGAAAATTTA
1 GGGGGT--AAAATGGAATTTT-GAAAAGTTA
* *
50296 -GGGGTAAAATGTAATTTTTGAAAAGTTT
1 GGGGGTAAAATGGAA-TTTTGAAAAGTTA
* * *
50324 GGGGTTAAAATGGAATTTT-AGGATGTTTA
1 GGGGGTAAAATGGAATTTTGA-AAAG-TTA
* *
50353 -GGGGTAAAAATGTAATTTTTAGAAAA-TTT
1 GGGGGT-AAAATGGAA-TTTT-GAAAAGTTA
* *
50382 GGGGTTAAAAATGGAATTTTG-GAAGTTA
1 GGGGGT-AAAATGGAATTTTGAAAAGTTA
*
50410 GAGGGTAAAA
1 GGGGGTAAAA
50420 ATATAAATTT
Statistics
Matches: 160, Mismatches: 35, Indels: 40
0.68 0.15 0.17
Matches are distributed among these distances:
27 7 0.04
28 35 0.22
29 50 0.31
30 51 0.32
31 16 0.10
32 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.28, T:0.33
Consensus pattern (28 bp):
GGGGGTAAAATGGAATTTTGAAAAGTTA
Found at i:50217 original size:59 final size:58
Alignment explanation
Indices: 50036--50401 Score: 286
Period size: 59 Copynumber: 6.2 Consensus size: 58
50026 CTCGGGGGGC
* * * *
50036 AAAAATGTAATTTTTGGACATTTTTGGGGGTAAAATGGTAATTTTTAAAAAGTTTA-GGGTA
1 AAAAATGGAATTTTTAGACA--TTTGGGGGTAAAAT-GTAATTTTTGAAAAG-TTAGGGGTT
* * ** * * *
50097 AAAAATGTAATTTTTGGACATTTGGGGG--AAATGGTAATTTTT-AGAATTTTTGAGGTC
1 AAAAATGGAATTTTTAGACATTTGGGGGTAAAAT-GTAATTTTTGA-AAAGTTAGGGGTT
* *
50154 AAAAATGAAATTTTTAGACATTCGGGGGTAAAATGGTAA-TTTTGAAAAGTTAGGGGTTT
1 AAAAATGGAATTTTTAGACATTTGGGGGTAAAAT-GTAATTTTTGAAAAGTTAGGGG-TT
* ** * *
50213 AAAAATGGAATTTTGGAGA-ATTTGAGGGCAAAAATGTAATTTTT-AGAAAGTTAAGGGTC
1 AAAAATGGAATTTT-TAGACATTTG-GGGGTAAAATGTAATTTTTGA-AAAGTTAGGGGTT
* * * *
50272 AAAAATGGAA-TTTTGGAAAATTTAGGGGTAAAATGTAATTTTTGAAAAGTTTGGGGTT
1 AAAAATGGAATTTTTAG-ACATTTGGGGGTAAAATGTAATTTTTGAAAAGTTAGGGGTT
** * *
50330 -AAAATGGAA-TTTTAGGATGTTTAGGGGTAAAAATGTAATTTTTAGAAAA-TTTGGGGTT
1 AAAAATGGAATTTTTA-GACATTTGGGGGT-AAAATGTAATTTTT-GAAAAGTTAGGGGTT
50388 AAAAATGGAATTTT
1 AAAAATGGAATTTT
50402 GGAAGTTAGA
Statistics
Matches: 256, Mismatches: 31, Indels: 37
0.79 0.10 0.11
Matches are distributed among these distances:
56 3 0.01
57 68 0.27
58 66 0.26
59 71 0.28
60 28 0.11
61 20 0.08
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (58 bp):
AAAAATGGAATTTTTAGACATTTGGGGGTAAAATGTAATTTTTGAAAAGTTAGGGGTT
Found at i:50225 original size:30 final size:29
Alignment explanation
Indices: 50183--50421 Score: 165
Period size: 29 Copynumber: 8.2 Consensus size: 29
50173 ATTCGGGGGT
50183 AAAATGGTAATTTTGAAAAGTTAGGGGTTTA
1 AAAATGG-AATTTTGAAAAGTTAGGGG-TTA
* * *
50214 AAAATGGAATTTTGGAGAA-TTTGAGGG-CA
1 AAAATGGAATTTT-GAAAAGTTAG-GGGTTA
* * * *
50243 AAAATGTAATTTTTAGAAAGTTAAGGGTCA
1 AAAATGGAATTTTGA-AAAGTTAGGGGTTA
*
50273 AAAATGGAATTTTGGAAAATTTAGGGG-T-
1 AAAATGGAATTTT-GAAAAGTTAGGGGTTA
* *
50301 AAAATGTAATTTTTGAAAAGTTTGGGGTT-
1 AAAATGGAA-TTTTGAAAAGTTAGGGGTTA
* *
50330 AAAATGGAATTTT-AGGATGTTTAGGGG-TA
1 AAAATGGAATTTTGA-AAAG-TTAGGGGTTA
* *
50359 AAAATGTAATTTTTAGAAAA-TTTGGGGTTA
1 AAAATGGAA-TTTT-GAAAAGTTAGGGGTTA
*
50389 AAAATGGAATTTTG-GAAGTTAGAGGG-TA
1 AAAATGGAATTTTGAAAAGTTAG-GGGTTA
50417 AAAAT
1 AAAAT
50422 ATAAATTTTG
Statistics
Matches: 164, Mismatches: 27, Indels: 37
0.72 0.12 0.16
Matches are distributed among these distances:
27 3 0.02
28 38 0.23
29 58 0.35
30 48 0.29
31 16 0.10
32 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTGAAAAGTTAGGGGTTA
Found at i:50363 original size:58 final size:58
Alignment explanation
Indices: 50178--50433 Score: 285
Period size: 58 Copynumber: 4.4 Consensus size: 58
50168 TAGACATTCG
*
50178 GGGGT-AAAATGGTAA-TTTTGAAAAGTTAGGGGTTTAAAAATGGAATTTTGGAGAATTT-
1 GGGGTAAAAAT-GTAATTTTTGAAAAGTTAGGGG-TTAAAAATGGAATTTTGGA-AGTTTA
* * * *
50236 GAGGGCAAAAATGTAATTTTT-AGAAAGTTAAGGGTCAAAAATGGAATTTTGGAAAATTTA
1 G-GGGTAAAAATGTAATTTTTGA-AAAGTTAGGGGTTAAAAATGGAATTTTGG-AAGTTTA
* *
50296 GGGGT-AAAATGTAATTTTTGAAAAGTTTGGGGTT-AAAATGGAATTTTAGGATGTTTA
1 GGGGTAAAAATGTAATTTTTGAAAAGTTAGGGGTTAAAAATGGAATTTT-GGAAGTTTA
*
50353 GGGGTAAAAATGTAATTTTTAGAAAA-TTTGGGGTTAAAAATGGAATTTTGGAAG-TTA
1 GGGGTAAAAATGTAATTTTT-GAAAAGTTAGGGGTTAAAAATGGAATTTTGGAAGTTTA
* *
50410 GAGGGTAAAAATATAAATTTTGAA
1 G-GGGTAAAAATGTAATTTTTGAA
50434 GACTCAGGGG
Statistics
Matches: 174, Mismatches: 12, Indels: 25
0.82 0.06 0.12
Matches are distributed among these distances:
57 30 0.17
58 71 0.41
59 52 0.30
60 21 0.12
ACGTcount: A:0.39, C:0.01, G:0.26, T:0.34
Consensus pattern (58 bp):
GGGGTAAAAATGTAATTTTTGAAAAGTTAGGGGTTAAAAATGGAATTTTGGAAGTTTA
Found at i:50402 original size:116 final size:113
Alignment explanation
Indices: 50062--50405 Score: 354
Period size: 116 Copynumber: 2.9 Consensus size: 113
50052 GACATTTTTG
* * * * * *
50062 GGGGTAAAATGGTAATTTTTAAAAAGTTTAGGGTAAAAAATGTAATTTTTGGACATTTGGGG-GA
1 GGGGTAAAATGGTAATTTTTGAAAAGTTTGGGGT-TAAAATGGAA-TTTTGGA-GTTTGGGGAAA
** * * * * *
50126 AATGGTAATTTTTAGAATTTTTGAGGTCAAAAATGAAATTTT-TAGACATTCG
63 AAT-GTAATTTTTAGAAAATTTGGGGTCAAAAATGGAATTTTGGA-AAATTCA
*
50178 GGGGTAAAATGGTAA-TTTTGAAAAGTTAGGGGTTTAAAAATGGAATTTTGGAGAATTTGAGGGC
1 GGGGTAAAATGGTAATTTTTGAAAAGTTTGGGG-TT-AAAATGGAATTTTGGAG--TTTG-GGG-
* ** *
50242 AAAAATGTAATTTTTAGAAAGTTAAGGGTCAAAAATGGAATTTTGGAAAATTTA
60 AAAAATGTAATTTTTAGAAAATTTGGGGTCAAAAATGGAATTTTGGAAAATTCA
50296 GGGGTAAAAT-GTAATTTTTGAAAAGTTTGGGGTTAAAATGGAATTTTAGGATGTTTAGGGGTAA
1 GGGGTAAAATGGTAATTTTTGAAAAGTTTGGGGTTAAAATGGAATTTT-GGA-GTTT-GGGG-AA
*
50360 AAATGTAATTTTTAGAAAATTTGGGGTTAAAAATGGAATTTTGGAA
62 AAATGTAATTTTTAGAAAATTTGGGGTCAAAAATGGAATTTTGGAA
50406 GTTAGAGGGT
Statistics
Matches: 193, Mismatches: 23, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
115 21 0.11
116 91 0.47
117 13 0.07
118 63 0.33
119 5 0.03
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.35
Consensus pattern (113 bp):
GGGGTAAAATGGTAATTTTTGAAAAGTTTGGGGTTAAAATGGAATTTTGGAGTTTGGGGAAAAAT
GTAATTTTTAGAAAATTTGGGGTCAAAAATGGAATTTTGGAAAATTCA
Found at i:58037 original size:87 final size:87
Alignment explanation
Indices: 57903--59048 Score: 1525
Period size: 87 Copynumber: 13.1 Consensus size: 87
57893 TGAAATATTT
* * * **
57903 TTTTTTATGTGAATGACAATTCAGTACTAGCTAACATAATTATTTGATGTTGAAATCGTGTCTTA
1 TTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGATGTTGAAATCGTGTCTTA
57968 GTATCCAATCACACTTGAAATG
66 GTATCCAATCACACTTGAAATG
* * * *
57990 TTTTTGATGTGAATCACGATTTAGTACTATCTAACATAATTGCTTGATGCTGAAATCGTGTCTTT
1 TTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGATGTTGAAATCGTGTCTTA
*
58055 GCATCCAATCACACTTGAAATG
66 GTATCCAATCACACTTGAAATG
* * * * * *
58077 TTTCTGATGTGAA-CGCGATTCAGTACTATTTAACATAATTGCTTGATATTGGAA-CAGTGTCTT
1 TTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGATGTTGAAATC-GTGTCTT
*
58140 AATATCCAATCACACTTGAAATG
65 AGTATCCAATCACACTTGAAATG
* * * *
58163 TTTTTTTATGTGAATCACGATTCAGTATTATTTAACATAATTGTTTGATGTT-AGAATCGTGTTT
1 -TTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGATGTTGA-AATCGTGTCT
58227 TAGTATCCAATCACACTTGAAATG
64 TAGTATCCAATCACACTTGAAATG
* * * *
58251 TTTTTTTTATGTGAATCACAATTCAGTACTACCTAACATAATTGTTTGATGCTGAAATCGTGTCT
1 --TTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGATGTTGAAATCGTGTCT
*
58316 TAGTATCCAATCACATTTGAAATG
64 TAGTATCCAATCACACTTGAAATG
* * * *
58340 TTTTTGATATGAATCACGATTCAGTACTATCTAACATAATTGCTTGAT-CTGAAATCGTGTCTTT
1 TTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGATGTTGAAATCGTGTCTTA
*
58404 GCATCCAATCACACTTGAAATG
66 GTATCCAATCACACTTGAAATG
* * * * * * *
58426 TTTCTGATGTGAATCGCGATTCAGTACTATTTAACATAATTGCTTGATATTGGAACCGTGTCTTA
1 TTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGATGTTGAAATCGTGTCTTA
*
58491 ATATCCAATCACACTTGAAATG
66 GTATCCAATCACACTTGAAATG
*
58513 TTTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGATGTT-AGAATCGTGTTT
1 -TTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGATGTTGA-AATCGTGTCT
*
58577 TAGTATCCAATCACACTTTAAATG
64 TAGTATCCAATCACACTTGAAATG
* * * *
58601 TTTTTTTTTTATGTGAATCACAATTCAGTACTACCTAACATAATTGTTTGATGCTGAAATCGTGT
1 ----TTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGATGTTGAAATCGTGT
*
58666 CTTAGTATCCAATCACATTTGAAATG
62 CTTAGTATCCAATCACACTTGAAATG
* * * * *
58692 TTTTTGATATGAATCACGATTCAGTACTATCTAACATAATTGCTTGATGCTGAAATTGTGTCTTT
1 TTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGATGTTGAAATCGTGTCTTA
*
58757 GCATCCAATCACACTTGAAATG
66 GTATCCAATCACACTTGAAATG
* * * *
58779 TTTTTGATGTGAATCGCGATTCAGTACTATCTAACATAATTGCTTGATATTGGAA-CTGTGTCTT
1 TTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGATGTTGAAATC-GTGTCTT
*
58843 AATATCCAATCACACTTGAAATG
65 AGTATCCAATCACACTTGAAATG
* *
58866 TTTTTTTATGTAAATCACGATTCAGTACTATCTAACATAATTGCTTGATGTT-AGAATCGTGTTT
1 -TTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGATGTTGA-AATCGTGTCT
58930 TAGTATCCAATCACACTTGAAATG
64 TAGTATCCAATCACACTTGAAATG
* *
58954 TTTTTTTTATGTGAATCATGATTCAGTACTATCTAACATAATTGCTTGATGTT-AGAATCGTGTT
1 --TTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGATGTTGA-AATCGTGTC
*
59018 TTTGTATCCAATCACACTTGAAATG
63 TTAGTATCCAATCACACTTGAAATG
59043 TTTTTT
1 TTTTTT
59049 TTATGTAAAA
Statistics
Matches: 941, Mismatches: 99, Indels: 38
0.87 0.09 0.04
Matches are distributed among these distances:
85 1 0.00
86 141 0.15
87 336 0.36
88 216 0.23
89 166 0.18
90 1 0.00
91 79 0.08
92 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (87 bp):
TTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGATGTTGAAATCGTGTCTTA
GTATCCAATCACACTTGAAATG
Found at i:58551 original size:350 final size:351
Alignment explanation
Indices: 57886--59047 Score: 2033
Period size: 350 Copynumber: 3.3 Consensus size: 351
57876 TGTTGGAACT
* * * *
57886 TCACACTTGAAATATTTTTTTTTATGTGAATGACAATTCAGTACTAGCTAACATAATTATTTGAT
1 TCACACTTGAAAT-GTTTTTTTTATGTGAATCACAATTCAGTACTACCTAACATAATTGTTTGAT
* * *
57951 GTTGAAATCGTGTCTTAGTATCCAATCACACTTGAAATGTTTTTGATGTGAATCACGATTTAGTA
65 GCTGAAATCGTGTCTTAGTATCCAATCACACTTGAAATGTTTTTGATATGAATCACGATTCAGTA
58016 CTATCTAACATAATTGCTTGATGCTGAAATCGTGTCTTTGCATCCAATCACACTTGAAATGTTTC
130 CTATCTAACATAATTGCTTGATGCTGAAATCGTGTCTTTGCATCCAATCACACTTGAAATGTTTC
58081 TGATGTGAA-CGCGATTCAGTACTATTTAACATAATTGCTTGATATTGGAACAGTGTCTTAATAT
195 TGATGTGAATCGCGATTCAGTACTATTTAACATAATTGCTTGATATTGGAACAGTGTCTTAATAT
* * *
58145 CCAATCACACTTGAAATGTTTTTTTATGTGAATCACGATTCAGTATTATTTAACATAATTGTTTG
260 CCAATCACACTTGAAATGTTTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTG
58210 ATGTTAGAATCGTGTTTTAGTATCCAA
325 ATGTTAGAATCGTGTTTTAGTATCCAA
58237 TCACACTTGAAATGTTTTTTTTATGTGAATCACAATTCAGTACTACCTAACATAATTGTTTGATG
1 TCACACTTGAAATGTTTTTTTTATGTGAATCACAATTCAGTACTACCTAACATAATTGTTTGATG
*
58302 CTGAAATCGTGTCTTAGTATCCAATCACATTTGAAATGTTTTTGATATGAATCACGATTCAGTAC
66 CTGAAATCGTGTCTTAGTATCCAATCACACTTGAAATGTTTTTGATATGAATCACGATTCAGTAC
58367 TATCTAACATAATTGCTTGAT-CTGAAATCGTGTCTTTGCATCCAATCACACTTGAAATGTTTCT
131 TATCTAACATAATTGCTTGATGCTGAAATCGTGTCTTTGCATCCAATCACACTTGAAATGTTTCT
*
58431 GATGTGAATCGCGATTCAGTACTATTTAACATAATTGCTTGATATTGGAACCGTGTCTTAATATC
196 GATGTGAATCGCGATTCAGTACTATTTAACATAATTGCTTGATATTGGAACAGTGTCTTAATATC
58496 CAATCACACTTGAAATGTTTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGA
261 CAATCACACTTGAAATGTTTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGA
58561 TGTTAGAATCGTGTTTTAGTATCCAA
326 TGTTAGAATCGTGTTTTAGTATCCAA
*
58587 TCACACTTTAAATGTTTTTTTTTTATGTGAATCACAATTCAGTACTACCTAACATAATTGTTTGA
1 TCACACTTGAAATG--TTTTTTTTATGTGAATCACAATTCAGTACTACCTAACATAATTGTTTGA
*
58652 TGCTGAAATCGTGTCTTAGTATCCAATCACATTTGAAATGTTTTTGATATGAATCACGATTCAGT
64 TGCTGAAATCGTGTCTTAGTATCCAATCACACTTGAAATGTTTTTGATATGAATCACGATTCAGT
*
58717 ACTATCTAACATAATTGCTTGATGCTGAAATTGTGTCTTTGCATCCAATCACACTTGAAATGTTT
129 ACTATCTAACATAATTGCTTGATGCTGAAATCGTGTCTTTGCATCCAATCACACTTGAAATGTTT
* * *
58782 TTGATGTGAATCGCGATTCAGTACTATCTAACATAATTGCTTGATATTGGAACTGTGTCTTAATA
194 CTGATGTGAATCGCGATTCAGTACTATTTAACATAATTGCTTGATATTGGAACAGTGTCTTAATA
*
58847 TCCAATCACACTTGAAATGTTTTTTTATGTAAATCACGATTCAGTACTATCTAACATAATTGCTT
259 TCCAATCACACTTGAAATGTTTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTT
58912 GATGTTAGAATCGTGTTTTAGTATCCAA
324 GATGTTAGAATCGTGTTTTAGTATCCAA
** * *
58940 TCACACTTGAAATGTTTTTTTTATGTGAATCATGATTCAGTACTATCTAACATAATTGCTTGATG
1 TCACACTTGAAATGTTTTTTTTATGTGAATCACAATTCAGTACTACCTAACATAATTGTTTGATG
* * *
59005 -TTAGAATCGTGTTTTTGTATCCAATCACACTTGAAATGTTTTT
66 CTGA-AATCGTGTCTTAGTATCCAATCACACTTGAAATGTTTTT
59048 TTTATGTAAA
Statistics
Matches: 779, Mismatches: 27, Indels: 10
0.95 0.03 0.01
Matches are distributed among these distances:
349 51 0.07
350 288 0.37
351 96 0.12
352 137 0.18
353 207 0.27
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (351 bp):
TCACACTTGAAATGTTTTTTTTATGTGAATCACAATTCAGTACTACCTAACATAATTGTTTGATG
CTGAAATCGTGTCTTAGTATCCAATCACACTTGAAATGTTTTTGATATGAATCACGATTCAGTAC
TATCTAACATAATTGCTTGATGCTGAAATCGTGTCTTTGCATCCAATCACACTTGAAATGTTTCT
GATGTGAATCGCGATTCAGTACTATTTAACATAATTGCTTGATATTGGAACAGTGTCTTAATATC
CAATCACACTTGAAATGTTTTTTTATGTGAATCACGATTCAGTACTATCTAACATAATTGCTTGA
TGTTAGAATCGTGTTTTAGTATCCAA
Found at i:60092 original size:24 final size:22
Alignment explanation
Indices: 60028--60092 Score: 53
Period size: 24 Copynumber: 2.8 Consensus size: 22
60018 AATAAATAGT
*
60028 TATTATTAAAATATTAATATTAAA
1 TATTATTTAAA-ATT-ATATTAAA
60052 TATT-TTTCAATAA-TATATTAAGAA
1 TATTATTT-AA-AATTATATT-A-AA
60076 TATTATTTAAAATTATA
1 TATTATTTAAAATTATA
60093 ATTTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
22 5 0.15
23 6 0.18
24 19 0.56
25 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TATTATTTAAAATTATATTAAA
Found at i:60109 original size:13 final size:14
Alignment explanation
Indices: 60075--60116 Score: 59
Period size: 13 Copynumber: 2.9 Consensus size: 14
60065 TATATTAAGA
60075 ATATTATTTAAAATT
1 ATATT-TTTAAAATT
60090 ATAATTTTTAAAATT
1 AT-ATTTTTAAAATT
60105 -TATTTTTAAAAT
1 ATATTTTTAAAAT
60117 AAAATTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 11 0.42
14 1 0.04
15 11 0.42
16 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATTTTTAAAATT
Found at i:67034 original size:58 final size:58
Alignment explanation
Indices: 66926--67035 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 58
66916 TTAGGAATAC
* **
66926 AATTATATTTGAGTTTAAAAATATTTGGGTTTAATTTATAAGTGTTTTTTAAGATTGA
1 AATTATATTTGAGTTCAAAAATATTTGGGTTTAATTTATAAGTGGGTTTTAAGATTGA
* * *
66984 AATTATATTTGGGTTCAAAAATATTTGGGTTTAGTTTGATGA-TGGGTTTTAA
1 AATTATATTTGAGTTCAAAAATATTTGGGTTTAATTT-ATAAGTGGGTTTTAA
67036 ATATTAGGAG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 42 0.93
59 3 0.07
ACGTcount: A:0.32, C:0.01, G:0.19, T:0.48
Consensus pattern (58 bp):
AATTATATTTGAGTTCAAAAATATTTGGGTTTAATTTATAAGTGGGTTTTAAGATTGA
Found at i:67240 original size:23 final size:23
Alignment explanation
Indices: 67197--67241 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
67187 TTGAAAATTA
**
67197 AACTCGATTCGTTTAACTCGAAT
1 AACTCGATTCGAATAACTCGAAT
*
67220 AACTCGATTCGAATAATTCGAA
1 AACTCGATTCGAATAACTCGAA
67242 ATTCGAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCGAAT
Found at i:75939 original size:5 final size:5
Alignment explanation
Indices: 75929--76057 Score: 61
Period size: 5 Copynumber: 25.8 Consensus size: 5
75919 AAACATAACT
* * * *
75929 TATCA TATCA TAACA TATCA TGTTGA -ATCA TATCA TATCA TAACA TATCA
1 TATCA TATCA TATCA TATCA T-ATCA TATCA TATCA TATCA TATCA TATCA
* * * *
75979 TATTGA -ATCA AATCA TAAT-A TAACA TATCA TATCA AATCGA -ATCGA
1 TA-TCA TATCA TATCA T-ATCA TATCA TATCA TATCA TATC-A TATC-A
* * * **
76025 -ATCA AATCA AATCA TAACA TAAAA TATCA TATC
1 TATCA TATCA TATCA TATCA TATCA TATCA TATC
76058 TTACCCCCCA
Statistics
Matches: 97, Mismatches: 19, Indels: 16
0.73 0.14 0.12
Matches are distributed among these distances:
4 6 0.06
5 84 0.87
6 7 0.07
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.32
Consensus pattern (5 bp):
TATCA
Found at i:75942 original size:15 final size:15
Alignment explanation
Indices: 75922--76013 Score: 77
Period size: 15 Copynumber: 6.1 Consensus size: 15
75912 TCATACGAAA
*
75922 CATAACTTATCATAT
1 CATAACATATCATAT
*
75937 CATAACATATCATGT
1 CATAACATATCATAT
75952 --TGAATCATATCATAT
1 CAT-AA-CATATCATAT
75967 CATAACATATCATAT
1 CATAACATATCATAT
*
75982 --TGAATCAAATCATAAT
1 CAT-AA-CATATCAT-AT
75998 -ATAACATATCATAT
1 CATAACATATCATAT
76012 CA
1 CA
76014 AATCGAATCG
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
13 2 0.03
14 6 0.10
15 47 0.75
16 6 0.10
17 2 0.03
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (15 bp):
CATAACATATCATAT
Found at i:75965 original size:30 final size:30
Alignment explanation
Indices: 75929--76011 Score: 132
Period size: 30 Copynumber: 2.8 Consensus size: 30
75919 AAACATAACT
*
75929 TATCATATCATAACATATCATGTTGAATCA
1 TATCATATCATAACATATCATATTGAATCA
75959 TATCATATCATAACATATCATATTGAATCA
1 TATCATATCATAACATATCATATTGAATCA
*
75989 AATCATAAT-ATAACATATCATAT
1 TATCAT-ATCATAACATATCATAT
76012 CAAATCGAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
30 48 0.96
31 2 0.04
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.36
Consensus pattern (30 bp):
TATCATATCATAACATATCATATTGAATCA
Found at i:76006 original size:40 final size:40
Alignment explanation
Indices: 75954--76045 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
75944 TATCATGTTG
* * *
75954 AATCATATCATATCATAACATATC-ATATTGAATCAAATCA
1 AATCATAACATATCATAACAAATCGA-ATCGAATCAAATCA
*
75994 TAAT-ATAACATATCATATCAAATCGAATCGAATCAAATCA
1 -AATCATAACATATCATAACAAATCGAATCGAATCAAATCA
76034 AATCATAACATA
1 AATCATAACATA
76046 AAATATCATA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
39 3 0.07
40 38 0.84
41 4 0.09
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.29
Consensus pattern (40 bp):
AATCATAACATATCATAACAAATCGAATCGAATCAAATCA
Found at i:76013 original size:25 final size:25
Alignment explanation
Indices: 75955--76057 Score: 76
Period size: 25 Copynumber: 4.3 Consensus size: 25
75945 ATCATGTTGA
* *
75955 ATCATATCATATCATAACATATCAT
1 ATCATATCAAATCATAACATAACAT
* *
75980 ATTGA-ATCAAATCATAATATAACAT
1 A-TCATATCAAATCATAACATAACAT
*
76005 ATCATATCAAATC--GA-AT--CGA-
1 ATCATATCAAATCATAACATAAC-AT
* *
76025 ATCAAATCAAATCATAACATAAAAT
1 ATCATATCAAATCATAACATAACAT
76050 ATCATATC
1 ATCATATC
76058 TTACCCCCCA
Statistics
Matches: 59, Mismatches: 10, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
20 13 0.22
21 1 0.02
22 3 0.05
23 3 0.05
24 3 0.05
25 34 0.58
26 2 0.03
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.30
Consensus pattern (25 bp):
ATCATATCAAATCATAACATAACAT
Found at i:85447 original size:30 final size:33
Alignment explanation
Indices: 85413--85480 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
85403 AGGAAGAGAA
85413 AGGATA-GG-GAAGAAGGGGAAGGAGGAGGA-G
1 AGGATAGGGAGAAGAAGGGGAAGGAGGAGGAGG
*
85443 AGGATAGGGAAGAAGAAGGGGGAGGAGGAGGAGG
1 AGGATAGGG-AGAAGAAGGGGAAGGAGGAGGAGG
85477 AGGA
1 AGGA
85481 GAGTTGAGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 6 0.18
31 2 0.06
33 20 0.61
34 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.57, T:0.03
Consensus pattern (33 bp):
AGGATAGGGAGAAGAAGGGGAAGGAGGAGGAGG
Found at i:103085 original size:1 final size:1
Alignment explanation
Indices: 103034--103065 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
103024 TTCATTTGGG
103034 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
103066 NNNNNNNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:103086 original size:1 final size:1
Alignment explanation
Indices: 103076--103104 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
103066 NNNNNNNNNN
103076 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
103105 CAGGATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:107909 original size:264 final size:264
Alignment explanation
Indices: 107439--107972 Score: 1023
Period size: 264 Copynumber: 2.0 Consensus size: 264
107429 TAAATATATT
107439 TATAAATAAATTAATACAAAAATTAAATGAGATTTTAGTGAAAATATAAATTTATTTAAATTTTG
1 TATAAATAAATTAATACAAAAATTAAATGAGATTTTAGTGAAAATATAAATTTATTTAAATTTTG
107504 GTTCGCATGCGTTCAAAATTATTTCATGAAAAGAAAATTGAACTATAGAAGAGAATGAGAAGGAG
66 GTTCGCATGCGTTCAAAATTATTTCATGAAAAGAAAATTGAACTATAGAAGAGAATGAGAAGGAG
* *
107569 AGCTTTAGATTGGCACAAGTAGTACAAACAGAGAAGGTCATACAACAATGATTTTAATAGCCCGT
131 AGCTTTAGATTGGCACAAGTAGTACAAACAGAGAAGATCATACAACAATGATTTTAATAGCCCAT
107634 TGACTTAAATGAAAACTTTCAAATAGTTTAGTAATCATTTTTTAACCTTTTGAAGTTGAATGGCT
196 TGACTTAAATGAAAACTTTCAAATAGTTTAGTAATCATTTTTTAACCTTTTGAAGTTGAATGGCT
107699 AAAA
261 AAAA
107703 TATAAATAAATTAATACAAAAATTAAATGAGATTTTAGTGAAAATATAAATTTATTTAAATTTTG
1 TATAAATAAATTAATACAAAAATTAAATGAGATTTTAGTGAAAATATAAATTTATTTAAATTTTG
107768 GTTCGCATGCGTTCAAAATTATTTCATGAAAAGAAAATTGAACTATAGAAGAGAATGAGAAGGAG
66 GTTCGCATGCGTTCAAAATTATTTCATGAAAAGAAAATTGAACTATAGAAGAGAATGAGAAGGAG
107833 AGCTTTAGATTGGCACAAGTAGTACAAACAGAGAAGATCATACAACAATGATTTTAATAGCCCAT
131 AGCTTTAGATTGGCACAAGTAGTACAAACAGAGAAGATCATACAACAATGATTTTAATAGCCCAT
* *
107898 TGACTTAAATGAAAACTTTCAAATAGTTTAGTGATCATTTTTTAACCTTTTGAAGTTGAGTGGCT
196 TGACTTAAATGAAAACTTTCAAATAGTTTAGTAATCATTTTTTAACCTTTTGAAGTTGAATGGCT
107963 AAAA
261 AAAA
*
107967 TGTAAA
1 TATAAA
107973 GTTACTAATA
Statistics
Matches: 265, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
264 265 1.00
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (264 bp):
TATAAATAAATTAATACAAAAATTAAATGAGATTTTAGTGAAAATATAAATTTATTTAAATTTTG
GTTCGCATGCGTTCAAAATTATTTCATGAAAAGAAAATTGAACTATAGAAGAGAATGAGAAGGAG
AGCTTTAGATTGGCACAAGTAGTACAAACAGAGAAGATCATACAACAATGATTTTAATAGCCCAT
TGACTTAAATGAAAACTTTCAAATAGTTTAGTAATCATTTTTTAACCTTTTGAAGTTGAATGGCT
AAAA
Found at i:109465 original size:19 final size:18
Alignment explanation
Indices: 109441--109483 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
109431 TATAATTTTA
* *
109441 AAAAATTATTATTATTAT
1 AAAAATTATTAGTATGAT
109459 AACAAATTATTAGTATGAT
1 AA-AAATTATTAGTATGAT
109478 AAAAAT
1 AAAAAT
109484 ATTTTCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (18 bp):
AAAAATTATTAGTATGAT
Done.