Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013882.1 Kokia drynarioides strain JFW-HI SEQ_128910, 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: 183984
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 272 characters in sequence are not A, C, G, or T
Found at i:509 original size:98 final size:98
Alignment explanation
Indices: 110--1195 Score: 1275
Period size: 98 Copynumber: 11.2 Consensus size: 98
100 ACCATGGAGA
* * * * * *
110 CATGAAGGGAAAGATTTAAGCCGTAACGGCGGATCCAATACCACGAAGACA-CAAGGAAAAGGTT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGAAGGGAAAGGTT
* * *
174 TAAGTCGCAATGACAAACCTAGTACCTCAG-AG
66 TAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
* * *
206 ACATGAAGGGAAAGATCTAAGCCGCAACGGC-AGATCCAGTACCACGAAGACA-CAAGGGAAAGG
1 -CATGAAGGGAAAGATTTAAGCCGCAACGGCGA-ATCCAGTACCACGAAGATATGAAGGGAAAGG
* *
269 TTTAAGTCGCAATGGCAAACCTAGTACCTCAG-AG
64 TTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
* * * ** * *
303 ACATGAAGGGAAAGATCTAAGCCGCAACGACGGATATAGTACCACGAAGACA-CAAGGGAAAGGT
1 -CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGAAGGGAAAGGT
* *
367 TTAAGTCGTAATGGCGAACCTAGTACCTCAG-AG
65 TTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
* * * * * *
400 ACATGAAGGGAAAAATCTAAGCCGTAATGGCGGATCCAGTACCACGAAGATTTGAAGGGAAAGGT
1 -CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGAAGGGAAAGGT
* * *
465 TTAAGTCGTAATGGCGAACCTTGTACCTCAAAAA
65 TTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
** * * *
499 CATGAAGGGAAAGATTTAAGTTGCAACGGCGAATCCA--A-TACGAGGATATAAAGGGAAAGGTT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGAAGGGAAAGGTT
561 TAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
66 TAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
* * * *
594 CATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAATACCAC-AAGGATATAAAGGGAAAAGT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAA-GATATGAAGGGAAAGGT
* * * *
658 TTAAGTCGTAACGGCAAACCTTGTACCTAAGAAG
65 TTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
* * * *
692 CATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCCAGTACCACAAAGACATGGAGGGAAAGGTT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGAAGGGAAAGGTT
* * * *
757 TAAGTCGCAACGACGACCCTTGTACCTTAGAAG
66 TAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
* *
790 CATGAAGGGAAAGATTTAAGACGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGAAGGGAAAGGTT
* * *
855 TAAGTCGCAATGGCAAACCTTGTACCTTAAAAG
66 TAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
* *
888 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAGGATATAAAGGGAAAAGT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAA-GATATGAAGGGAAAGGT
* * * *
952 TTAAGTTGCAACGACGAACCTTGTACCTAAGAAG
65 TTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
* *
986 C-TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGATATGGAGGGAAAGGTT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGAAGGGAAAGGTT
* * *
1050 TAAGTTGCAACGACGAACCTTGTACCT-AGGAAG
66 TAAGTCGCAATGGCGAACCTTGTACCTCA-GAAG
* **
1083 CATGAAGAGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGGGGGAAAGG-T
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGAAGGGAAAGGTT
** * * * *
1147 TACAACCGCAACGGTGAACCTTGTACCTTAGAAA
66 TA-AGTCGCAATGGCGAACCTTGTACCTCAGAAG
* *
1181 CATGACGAGAAAGAT
1 CATGAAGGGAAAGAT
1196 CTAACTCACG
Statistics
Matches: 883, Mismatches: 91, Indels: 29
0.88 0.09 0.03
Matches are distributed among these distances:
95 86 0.10
96 2 0.00
97 318 0.36
98 473 0.54
99 4 0.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (98 bp):
CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGAAGGGAAAGGTT
TAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
Found at i:1144 original size:49 final size:49
Alignment explanation
Indices: 82--1131 Score: 746
Period size: 49 Copynumber: 21.6 Consensus size: 49
72 AGGTTGAGGC
* * * *
82 CGCAACGGCGAA-CCCGATACCATGGAGACATGAAGGGAAAGATTTAAGC
1 CGCAACGGCGAATCCAG-TACCACGAAGACATGAAGGGAAAGATTTAAGT
* * * * * *
131 CGTAACGGCGGATCCAATACCACGAAGACA-CAAGGAAAAGGTTTAAGT
1 CGCAACGGCGAATCCAGTACCACGAAGACATGAAGGGAAAGATTTAAGT
* * * * * *
179 CGCAATGAC-AAACCTAGTACCTC-AGAGACATGAAGGGAAAGATCTAAGC
1 CGCAACGGCGAATCC-AGTACCACGA-AGACATGAAGGGAAAGATTTAAGT
* *
228 CGCAACGGC-AGATCCAGTACCACGAAGACA-CAAGGGAAAGGTTTAAGT
1 CGCAACGGCGA-ATCCAGTACCACGAAGACATGAAGGGAAAGATTTAAGT
* * * * *
276 CGCAATGGC-AAACCTAGTACCTC-AGAGACATGAAGGGAAAGATCTAAGC
1 CGCAACGGCGAATCC-AGTACCACGA-AGACATGAAGGGAAAGATTTAAGT
* * ** * *
325 CGCAACGACGGATATAGTACCACGAAGACA-CAAGGGAAAGGTTTAAGT
1 CGCAACGGCGAATCCAGTACCACGAAGACATGAAGGGAAAGATTTAAGT
* * * * * *
373 CGTAATGGCGAA-CCTAGTACCTC-AGAGACATGAAGGGAAAAATCTAAGC
1 CGCAACGGCGAATCC-AGTACCACGA-AGACATGAAGGGAAAGATTTAAGT
* * * ** *
422 CGTAATGGCGGATCCAGTACCACGAAGATTTGAAGGGAAAGGTTTAAGT
1 CGCAACGGCGAATCCAGTACCACGAAGACATGAAGGGAAAGATTTAAGT
* * * * * *
471 CGTAATGGCGAA-CCTTGTACCTCAAAAACATGAAGGGAAAGATTTAAGT
1 CGCAACGGCGAATCC-AGTACCACGAAGACATGAAGGGAAAGATTTAAGT
* * * * * *
520 TGCAACGGCGAATCCA--A-TACGAGGATATAAAGGGAAAGGTTTAAGT
1 CGCAACGGCGAATCCAGTACCACGAAGACATGAAGGGAAAGATTTAAGT
* * *
566 CGCAATGGCGAA-CCTTGTACCTCAGAAG-CATGAAGGGAAAGATTTAAGT
1 CGCAACGGCGAATCC-AGTACCAC-GAAGACATGAAGGGAAAGATTTAAGT
* * *
615 CGCAACGGCGAATCCAATACCAC-AAGGATATAAAGGGAAA-AGTTTAAGT
1 CGCAACGGCGAATCCAGTACCACGAA-GACATGAAGGGAAAGA-TTTAAGT
* * * * *
664 CGTAACGGC-AAACCTTGTACCTAAGAAG-CATGAAGGGAAAGATTTAAGC
1 CGCAACGGCGAATCC-AGTACC-ACGAAGACATGAAGGGAAAGATTTAAGT
* * * *
713 CGCAACAGCGAATCCAGTACCACAAAGACATGGAGGGAAAGGTTTAAGT
1 CGCAACGGCGAATCCAGTACCACGAAGACATGAAGGGAAAGATTTAAGT
* * * *
762 CGCAACGACG-ACCCTTGTACCTTA-GAAG-CATGAAGGGAAAGATTTAAGA
1 CGCAACGGCGAATCC-AGTACC--ACGAAGACATGAAGGGAAAGATTTAAGT
* * *
811 CGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTTTAAGT
1 CGCAACGGCGAATCCAGTACCACGAAGACATGAAGGGAAAGATTTAAGT
* * * * *
860 CGCAATGGC-AAACCTTGTACCTTA-AAAG-CATGAAGGGAAAGATTTAAGC
1 CGCAACGGCGAATCC-AGTACC--ACGAAGACATGAAGGGAAAGATTTAAGT
* *
909 CGCAACGGCGAATCCAGTACCAC-AAGGATATAAAGGGAAA-AGTTTAAGT
1 CGCAACGGCGAATCCAGTACCACGAA-GACATGAAGGGAAAGA-TTTAAGT
* * * * *
958 TGCAACGACGAA-CCTTGTACCTAAGAAG-C-TGAAGGGAAAGATTTAAGC
1 CGCAACGGCGAATCC-AGTACC-ACGAAGACATGAAGGGAAAGATTTAAGT
* * * *
1006 CGCAACGGCGAATCCAATACCACGAAGATATGGAGGGAAAGGTTTAAGT
1 CGCAACGGCGAATCCAGTACCACGAAGACATGAAGGGAAAGATTTAAGT
* * * * * *
1055 TGCAACGACGAA-CCTTGTACCTAGGAAG-CATGAAGAGAAAGATTTAAGC
1 CGCAACGGCGAATCC-AGTACC-ACGAAGACATGAAGGGAAAGATTTAAGT
1104 CGCAACGGCGAATCCAGTACCACGAAGA
1 CGCAACGGCGAATCCAGTACCACGAAGA
1132 TATGGGGGGA
Statistics
Matches: 764, Mismatches: 179, Indels: 116
0.72 0.17 0.11
Matches are distributed among these distances:
45 2 0.00
46 31 0.04
47 21 0.03
48 164 0.21
49 493 0.65
50 47 0.06
51 6 0.01
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (49 bp):
CGCAACGGCGAATCCAGTACCACGAAGACATGAAGGGAAAGATTTAAGT
Found at i:1168 original size:195 final size:195
Alignment explanation
Indices: 110--1195 Score: 1273
Period size: 195 Copynumber: 5.6 Consensus size: 195
100 ACCATGGAGA
* * * * * *
110 CATGAAGGGAAAGATTTAAGCCGTAACGGCGGATCCAATACCACGAAGACA-CAAGGAAAAGGTT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAAAGGGAAAGGTT
* * * * *
174 TAAGTCGCAATGACAAACCTAGTACCTCAG-AGACATGAAGGGAAAGATCTAAGCCGCAACGGC-
66 TAAGTCGCAACGGCGAACCTTGTACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCG
* * *
237 AGATCCAGTACCACGAAGACA-CAAGGGAAAGGTTTAAGTCGCAATGGCAAACCTAGTACCTCAG
130 A-ATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAATGGCAAACCTTGTACCT-AG
301 -AG
193 AAG
* * * ** * *
303 ACATGAAGGGAAAGATCTAAGCCGCAACGACGGATATAGTACCACGAAGACA-CAAGGGAAAGGT
1 -CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAAAGGGAAAGGT
* * * * * * *
367 TTAAGTCGTAATGGCGAACCTAGTACCTCAG-AGACATGAAGGGAAAAATCTAAGCCGTAATGGC
65 TTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGC
* * * * *
431 GGATCCAGTACCACGAAGATTTGAAGGGAAAGGTTTAAGTCGTAATGGCGAACCTTGTACCTCAA
129 GAATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAATGGCAAACCTTGTACCT-AG
*
496 AAA
193 AAG
** * *
499 CATGAAGGGAAAGATTTAAGTTGCAACGGCGAATCCA--A-TACGAGGATATAAAGGGAAAGGTT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAAAGGGAAAGGTT
* *
561 TAAGTCGCAATGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGTCGCAACGGCGA
66 TAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGA
* * * * *
626 ATCCAATACCAC-AAGGATATAAAGGGAAAAGTTTAAGTCGTAACGGCAAACCTTGTACCTAAGA
131 ATCCAGTACCACGAA-GATATGAAGGGAAAGGTTTAAGTCGCAATGGCAAACCTTGTACCT-AGA
690 AG
194 AG
* * * **
692 CATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCCAGTACCACAAAGACATGGAGGGAAAGGTT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAAAGGGAAAGGTT
* * * *
757 TAAGTCGCAACGACGACCCTTGTACCTTAGAAGCATGAAGGGAAAGATTTAAGACGCAACGGCGA
66 TAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGA
* *
822 ATCCAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAATGGCAAACCTTGTACCTTAAAA
131 ATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAATGGCAAACCTTGTACC-TAGAA
887 G
195 G
*
888 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAGGATATAAAGGGAAAAGT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAA-GATATAAAGGGAAAGGT
* * *
952 TTAAGTTGCAACGACGAACCTTGTACCTAAGAAGC-TGAAGGGAAAGATTTAAGCCGCAACGGCG
65 TTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCG
* * * * * *
1016 AATCCAATACCACGAAGATATGGAGGGAAAGGTTTAAGTTGCAACGACGAACCTTGTACCTAGGA
130 AATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAATGGCAAACCTTGTACCTA-GA
1081 AG
194 AG
* ***
1083 CATGAAGAGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGGGGGAAAGG-T
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAAAGGGAAAGGTT
** * * * * *
1147 TACAACCGCAACGGTGAACCTTGTACCTTAGAAACATGACGAGAAAGAT
66 TA-AGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGAT
1196 CTAACTCACG
Statistics
Matches: 776, Mismatches: 100, Indels: 30
0.86 0.11 0.03
Matches are distributed among these distances:
192 9 0.01
193 155 0.20
194 138 0.18
195 237 0.31
196 234 0.30
197 3 0.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (195 bp):
CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAAAGGGAAAGGTT
TAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGA
ATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAATGGCAAACCTTGTACCTAGAAG
Found at i:1485 original size:39 final size:39
Alignment explanation
Indices: 1420--1563 Score: 198
Period size: 39 Copynumber: 3.7 Consensus size: 39
1410 TCACCAACCA
*
1420 ATCTCTTACCCCGAGCCTGAGTCAGATTGTAGCCATTCG
1 ATCTCTTACCCCGAGCCTGAGGCAGATTGTAGCCATTCG
* *
1459 ATCTTTTACCCCGAGCCTGGGGCAGATTGTAGCCATTCG
1 ATCTCTTACCCCGAGCCTGAGGCAGATTGTAGCCATTCG
* * * * ** *
1498 ATCTTTTACCCCGAGCCTGGGGCAAATTGCAATCGTTCG
1 ATCTCTTACCCCGAGCCTGAGGCAGATTGTAGCCATTCG
1537 ATCTCTTACCCCGAGCCTGAGGCAGAT
1 ATCTCTTACCCCGAGCCTGAGGCAGAT
1564 CATCATCAGC
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 94 1.00
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGAGGCAGATTGTAGCCATTCG
Found at i:1585 original size:78 final size:78
Alignment explanation
Indices: 1408--1585 Score: 187
Period size: 78 Copynumber: 2.3 Consensus size: 78
1398 AGTGAAGTTA
* * * * *
1408 CATCACCAACCAATCTCTTACCCCGAGCCTGAGTCAGATTGTAGCCATTCGATCTTTTACCCCGA
1 CATCACCAACCAATCTCTTACCCCGAGCCTGAGGCAAATTGCAACCATTCGATCTCTTACCCCGA
*
1473 GCCTGGGGCAGAT
66 GCCTGAGGCAGAT
** ** * * * * *
1486 TGT-AGCCATTCGATCTTTTACCCCGAGCCTGGGGCAAATTGCAATCGTTCGATCTCTTACCCCG
1 CATCA-CCAACCAATCTCTTACCCCGAGCCTGAGGCAAATTGCAACCATTCGATCTCTTACCCCG
1550 AGCCTGAGGCAGAT
65 AGCCTGAGGCAGAT
* *
1564 CATCATCAGCCAATCTCTTACC
1 CATCACCAACCAATCTCTTACC
1586 TGATCATGGA
Statistics
Matches: 76, Mismatches: 22, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
77 1 0.01
78 74 0.97
79 1 0.01
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.26
Consensus pattern (78 bp):
CATCACCAACCAATCTCTTACCCCGAGCCTGAGGCAAATTGCAACCATTCGATCTCTTACCCCGA
GCCTGAGGCAGAT
Found at i:2794 original size:16 final size:15
Alignment explanation
Indices: 2773--2821 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
2763 TGTCCAAGGC
2773 AATATATATATGTAAA
1 AATATATATAT-TAAA
2789 AATATATATATATAAA
1 AATATATATAT-TAAA
*
2805 TAAAATATATATTAAA
1 -AATATATATATTAAA
2821 A
1 A
2822 CCCAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 1 0.03
16 19 0.63
17 10 0.33
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
AATATATATATTAAA
Found at i:2799 original size:20 final size:19
Alignment explanation
Indices: 2774--2816 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
2764 GTCCAAGGCA
**
2774 ATATATATATGTA-AAAAT
1 ATATATATATAAATAAAAT
2792 ATATATATATAAATAAAAT
1 ATATATATATAAATAAAAT
2811 ATATAT
1 ATATAT
2817 TAAAACCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATATATATATAAATAAAAT
Found at i:3562 original size:30 final size:30
Alignment explanation
Indices: 3528--3844 Score: 219
Period size: 29 Copynumber: 10.8 Consensus size: 30
3518 AAAAGGTCCT
* *
3528 TAAACTATCTAAAAATTACATTTTAACCCC
1 TAAACTTTCCAAAAATTACATTTTAACCCC
* *
3558 TAAACTTT-AAAGAAATTACATTTTAA-CCT
1 TAAACTTTCCAA-AAATTACATTTTAACCCC
* * **
3587 TAAACTTTTCAAGAATTACA-TTTAAAACC
1 TAAACTTTCCAAAAATTACATTTTAACCCC
** *
3616 TAATTTTTCCAAAAATTACATTTTGACCCC
1 TAAACTTTCCAAAAATTACATTTTAACCCC
*
3646 -AAACTTTCCAAAAATTACATTTTGA--CC
1 TAAACTTTCCAAAAATTACATTTTAACCCC
* * *
3673 TCAATTTTCCAAAAATTACATTTTTACCCC
1 TAAACTTTCCAAAAATTACATTTTAACCCC
* *
3703 CAAACTTTCC-AAAATTACATTTTTTA-CCC
1 TAAACTTTCCAAAAATTACA-TTTTAACCCC
** *
3732 TAATTTTTTCAAAAATTACAATTTT-ACCCC
1 TAAACTTTCCAAAAATTAC-ATTTTAACCCC
* * * *
3762 TCGAACTTTTC-AAAATTCCATTTTTGA-CCC
1 T-AAACTTTCCAAAAATTACA-TTTTAACCCC
** *
3792 TAATTTTTCC-AAAATTACCATTTTACCCCC
1 TAAACTTTCCAAAAATTA-CATTTTAACCCC
* * *
3822 AAAAC-ATCCAAAAATTCCATTTT
1 TAAACTTTCCAAAAATTACATTTT
3845 GACCTCAACT
Statistics
Matches: 228, Mismatches: 42, Indels: 35
0.75 0.14 0.11
Matches are distributed among these distances:
27 2 0.01
28 27 0.12
29 103 0.45
30 88 0.39
31 8 0.04
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.38
Consensus pattern (30 bp):
TAAACTTTCCAAAAATTACATTTTAACCCC
Found at i:3864 original size:58 final size:58
Alignment explanation
Indices: 3539--3878 Score: 272
Period size: 58 Copynumber: 5.8 Consensus size: 58
3529 AAACTATCTA
* ** * * ** *
3539 AAAATTACA-TTTTAACCCCTAAACTTTAAAGAAATTA-CATTTTAACCTTAAACTTTTC
1 AAAATTACATTTTTGA-CCCTAATTTTTCAA-AAATTACCATTTTACCCCCAAACTTTCC
** *
3597 AAGAATTACA-TTTAAAACCTAATTTTTCCAAAAATTA-CATTTTGA-CCCCAAACTTTCC
1 AA-AATTACATTTTTGACCCTAATTTTT-CAAAAATTACCATTTT-ACCCCCAAACTTTCC
*
3655 AAAAATTACA-TTTTGA-CCTCAATTTTCCAAAAATTA-CATTTTTACCCCCAAACTTTCC
1 -AAAATTACATTTTTGACCCT-AATTTTTCAAAAATTACCA-TTTTACCCCCAAACTTTCC
* * * *
3713 AAAATTACATTTTTTACCCTAATTTTTTCAAAAATTACAATTTTACCCCTCGAACTTTTC
1 AAAATTACATTTTTGACCCTAA-TTTTTCAAAAATTACCATTTTACCCC-CAAACTTTCC
* * *
3773 AAAATTCCATTTTTGACCCTAATTTTTCCAAAATTACCATTTTACCCCCAAAAC-ATCC
1 AAAATTACATTTTTGACCCTAATTTTTCAAAAATTACCATTTTACCCCC-AAACTTTCC
* * *
3831 AAAAATTCCA-TTTTGA-CCTCAA-CTTTCATAAAATTACCGTTTTACCCC
1 -AAAATTACATTTTTGACCCT-AATTTTTCA-AAAATTACCATTTTACCCC
3879 TTAATGTCTA
Statistics
Matches: 240, Mismatches: 26, Indels: 32
0.81 0.09 0.11
Matches are distributed among these distances:
57 31 0.13
58 102 0.43
59 78 0.32
60 29 0.12
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.37
Consensus pattern (58 bp):
AAAATTACATTTTTGACCCTAATTTTTCAAAAATTACCATTTTACCCCCAAACTTTCC
Found at i:3953 original size:28 final size:29
Alignment explanation
Indices: 3905--3986 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 29
3895 TCATTTTTGA
3905 CCTCGAACTGTCCCAAAATTATCATTTTAT
1 CCTCGAACTGT-CCAAAATTATCATTTTAT
*
3935 CCTCGAA-TGTCCAAAATTACCATTTTAT
1 CCTCGAACTGTCCAAAATTATCATTTTAT
* * * *
3963 CC-CCAAGTATCCAAAAATATCATT
1 CCTCGAACTGTCCAAAATTATCATT
3987 GTCAACTCTG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
27 3 0.07
28 33 0.72
29 3 0.07
30 7 0.15
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (29 bp):
CCTCGAACTGTCCAAAATTATCATTTTAT
Found at i:6826 original size:12 final size:12
Alignment explanation
Indices: 6769--6826 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
6759 ATAACATCCA
6769 AACAACAAAAAT
1 AACAACAAAAAT
* *
6781 AGCAATAAAAAT
1 AACAACAAAAAT
* *
6793 AACAGCAAAAAC
1 AACAACAAAAAT
*
6805 AAC-ACGAAAAT
1 AACAACAAAAAT
6816 AACAACCAAAA
1 AACAA-CAAAA
6827 CAGTGAAAAG
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
11 8 0.24
12 22 0.65
13 4 0.12
ACGTcount: A:0.69, C:0.19, G:0.05, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:7452 original size:11 final size:11
Alignment explanation
Indices: 7387--7456 Score: 52
Period size: 11 Copynumber: 6.0 Consensus size: 11
7377 CTAATATCTC
7387 TAAAATAATAA
1 TAAAATAATAA
*
7398 CAAAATTAATAA
1 TAAAA-TAATAA
*
7410 TAAAATAAGAA
1 TAAAATAATAA
*
7421 TTATACAATATTCAA
1 -TA-A-AATAAT-AA
*
7436 -ATAATAATAA
1 TAAAATAATAA
7446 TAAAATAATAA
1 TAAAATAATAA
7457 CAACACGACA
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
10 2 0.04
11 23 0.51
12 12 0.27
13 2 0.04
14 4 0.09
15 2 0.04
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:12224 original size:5 final size:5
Alignment explanation
Indices: 12211--12240 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
12201 TTGTATGGAT
*
12211 TACAC TACAA TACAA TACAA TACAA TACAA
1 TACAA TACAA TACAA TACAA TACAA TACAA
12241 ACCATACCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (5 bp):
TACAA
Found at i:19034 original size:16 final size:18
Alignment explanation
Indices: 19003--19042 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
18993 TTTCAATTGT
19003 AATTAATTTAAAATTTTC
1 AATTAATTTAAAATTTTC
*
19021 AATTAA-TT-AAATTTTT
1 AATTAATTTAAAATTTTC
19037 AATTAA
1 AATTAA
19043 AAATTTATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.62
17 2 0.10
18 6 0.29
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTAATTTAAAATTTTC
Found at i:21199 original size:23 final size:23
Alignment explanation
Indices: 21166--21212 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
21156 TAATTCTCAA
* * *
21166 ATATATTTAAACAATTAAATGTT
1 ATATATATAAAAAAATAAATGTT
21189 ATATATATAAAAAAATAAATGTT
1 ATATATATAAAAAAATAAATGTT
21212 A
1 A
21213 ATAATTTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (23 bp):
ATATATATAAAAAAATAAATGTT
Found at i:21799 original size:6 final size:6
Alignment explanation
Indices: 21788--21819 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
21778 CACACACCTC
*
21788 TCATCT TCATCT TCATCT TCATCT TCTTCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TC
21820 CCTTTTGATT
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:0.12, C:0.34, G:0.00, T:0.53
Consensus pattern (6 bp):
TCATCT
Found at i:22087 original size:14 final size:14
Alignment explanation
Indices: 22070--22100 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
22060 TTAGGTTTAA
22070 AAATTTAATTAATT
1 AAATTTAATTAATT
*
22084 AAATTTATTTAATT
1 AAATTTAATTAATT
22098 AAA
1 AAA
22101 AATCTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:22228 original size:20 final size:20
Alignment explanation
Indices: 22195--22234 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
22185 GATCACTTCG
22195 TAACAAAATAATAACATAAA
1 TAACAAAATAATAACATAAA
*
22215 TAACTAAAAT-ATAACCTAAA
1 TAAC-AAAATAATAACATAAA
22235 GCAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (20 bp):
TAACAAAATAATAACATAAA
Found at i:31547 original size:6 final size:6
Alignment explanation
Indices: 31538--31588 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
31528 CTCGATAGGT
* *
31538 ATAGAG ATAGAG ATAAAG ATAGCG ATAGAG ATAGAG ATAGAG ATAGAG
1 ATAGAG ATAGAG ATAGAG ATAGAG ATAGAG ATAGAG ATAGAG ATAGAG
31586 ATA
1 ATA
31589 ATCATAATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.51, C:0.02, G:0.29, T:0.18
Consensus pattern (6 bp):
ATAGAG
Found at i:39161 original size:18 final size:17
Alignment explanation
Indices: 39133--39172 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
39123 CCACCTCGTG
39133 GAAAACGATCCCTGCTA
1 GAAAACGATCCCTGCTA
39150 GAAAAGCGATCCCTGCTA
1 GAAAA-CGATCCCTGCTA
39168 GAAAA
1 GAAAA
39173 TTTGCCGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (17 bp):
GAAAACGATCCCTGCTA
Found at i:45999 original size:21 final size:22
Alignment explanation
Indices: 45944--46000 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
45934 TTATTTTTGT
*
45944 AAATATTTTAAA-AAAATTTAA
1 AAATATTTTAAATAAAATTAAA
* * *
45965 AAATATACTAAAATTAAA-TAAA
1 AAATAT-TTTAAATAAAATTAAA
45987 AAATATTTTAAATA
1 AAATATTTTAAATA
46001 TTTTTGAATA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
21 11 0.41
22 13 0.48
23 3 0.11
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATATTTTAAATAAAATTAAA
Found at i:46032 original size:20 final size:19
Alignment explanation
Indices: 45988--46025 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
45978 TTAAATAAAA
*
45988 AATATTTTAAATATTTTTG
1 AATATTTTAAATATTCTTG
46007 AATATTTGTAAATATTCTT
1 AATATTT-TAAATATTCTT
46026 ATATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (19 bp):
AATATTTTAAATATTCTTG
Found at i:47337 original size:19 final size:20
Alignment explanation
Indices: 47300--47342 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
47290 GGATGATTTT
* *
47300 TTTAAAATTTAAAGTTAAA-
1 TTTAAAATATAAAGATAAAC
*
47319 TTTAAAATATATAGATAAAC
1 TTTAAAATATAAAGATAAAC
47339 TTTA
1 TTTA
47343 TCTTTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (20 bp):
TTTAAAATATAAAGATAAAC
Found at i:55968 original size:21 final size:21
Alignment explanation
Indices: 55944--55988 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
55934 AAAAGTATTT
55944 AAAAAAGTATAAAAATTATAA
1 AAAAAAGTATAAAAATTATAA
* * * *
55965 AAAATAGTTTTAAAATTTTAA
1 AAAAAAGTATAAAAATTATAA
55986 AAA
1 AAA
55989 CTAATTAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAAAAGTATAAAAATTATAA
Found at i:57148 original size:29 final size:30
Alignment explanation
Indices: 57109--57165 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
57099 CATCCAAAAT
57109 TGTAATGTTATACAT-AAACTTTGATTTTG
1 TGTAATGTTATACATAAAACTTTGATTTTG
* * *
57138 TGTAATTTTATATATAAAATTTTGATTT
1 TGTAATGTTATACATAAAACTTTGATTT
57166 GATTCAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.53
Consensus pattern (30 bp):
TGTAATGTTATACATAAAACTTTGATTTTG
Found at i:58562 original size:17 final size:17
Alignment explanation
Indices: 58542--58574 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
58532 TTAAAAATTA
58542 TAAAAA-TATAAATTTAT
1 TAAAAATTAT-AATTTAT
58559 TAAAAATTATAATTTA
1 TAAAAATTATAATTTA
58575 ATTTCCTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAAATTATAATTTAT
Found at i:63056 original size:63 final size:62
Alignment explanation
Indices: 62955--63073 Score: 148
Period size: 63 Copynumber: 1.9 Consensus size: 62
62945 GTTTCCCATG
* * *** *
62955 GAGGAAGTACCCGATCATACTGAAGCCAAAGGTGAGGATTTGAGTACCAGACCGCTTGTTGCA
1 GAGGAAGAACCCGAGCATACTGAAGCCAAAGCAAAGGATTCGAGTACCAGA-CGCTTGTTGCA
* * *
63018 GAGGAAGAACCTGAGCATTCTGAAGCCAAAGCAAAGGATTCGAGTACCGGACGCTT
1 GAGGAAGAACCCGAGCATACTGAAGCCAAAGCAAAGGATTCGAGTACCAGACGCTT
63074 CTCGGGGAGG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
62 5 0.11
63 42 0.89
ACGTcount: A:0.32, C:0.21, G:0.29, T:0.18
Consensus pattern (62 bp):
GAGGAAGAACCCGAGCATACTGAAGCCAAAGCAAAGGATTCGAGTACCAGACGCTTGTTGCA
Found at i:68037 original size:13 final size:14
Alignment explanation
Indices: 68012--68047 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
68002 GAATTTTTAA
68012 AATAAATTATAATT
1 AATAAATTATAATT
*
68026 ATTAAATT-TAATT
1 AATAAATTATAATT
68039 AATAAATTA
1 AATAAATTA
68048 AAAATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATAAATTATAATT
Found at i:72799 original size:18 final size:19
Alignment explanation
Indices: 72778--72815 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
72768 ATCTTATTGT
72778 TAATAATTTA-TTTATTTA
1 TAATAATTTAGTTTATTTA
*
72796 TAATAATTTAGTTTTTTTA
1 TAATAATTTAGTTTATTTA
72815 T
1 T
72816 TTGGTGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TAATAATTTAGTTTATTTA
Found at i:74489 original size:8 final size:8
Alignment explanation
Indices: 74478--74502 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
74468 AAAGTTAAAA
74478 TTTTAATT
1 TTTTAATT
74486 TTTTAATT
1 TTTTAATT
74494 TTTTAATT
1 TTTTAATT
74502 T
1 T
74503 AAAAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTAATT
Found at i:77967 original size:9 final size:9
Alignment explanation
Indices: 77940--77978 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
77930 ATATGTTACC
77940 AATTCGGTT
1 AATTCGGTT
*
77949 AATTTTGGTT
1 AA-TTCGGTT
77959 AATTCGGTT
1 AATTCGGTT
*
77968 AATTCAGTT
1 AATTCGGTT
77977 AA
1 AA
77979 ATGAACATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (9 bp):
AATTCGGTT
Found at i:79667 original size:21 final size:21
Alignment explanation
Indices: 79641--79681 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
79631 TAAGTTTAAT
*
79641 TAAAAAATTGTTATAAAATCA
1 TAAAAAATTATTATAAAATCA
79662 TAAAAAATTATTATAAAATC
1 TAAAAAATTATTATAAAATC
79682 TCGATTCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAAAAATTATTATAAAATCA
Found at i:81962 original size:7 final size:7
Alignment explanation
Indices: 81952--81977 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
81942 ACCTCAAATT
81952 TTGAACC
1 TTGAACC
81959 TTGAACC
1 TTGAACC
81966 TTGAACC
1 TTGAACC
81973 TTGAA
1 TTGAA
81978 TCTTATGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (7 bp):
TTGAACC
Found at i:82052 original size:40 final size:41
Alignment explanation
Indices: 82002--82079 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 41
81992 TCTCGAATCG
* *
82002 TAAATCATGAACCAC-AAACCTCAAATCC-AAATCCTAAACA
1 TAAACCATGAACC-CTAAACATCAAATCCTAAATCCTAAACA
*
82042 TAAACCATGAACCCTAAACATTAAATCCTAAATCCTAA
1 TAAACCATGAACCCTAAACATCAAATCCTAAATCCTAA
82080 TCGAGTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 1 0.03
40 23 0.70
41 9 0.27
ACGTcount: A:0.49, C:0.28, G:0.03, T:0.21
Consensus pattern (41 bp):
TAAACCATGAACCCTAAACATCAAATCCTAAATCCTAAACA
Found at i:85137 original size:8 final size:8
Alignment explanation
Indices: 85124--85152 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
85114 GTTCACAGTA
85124 ACATTACT
1 ACATTACT
85132 ACATTACT
1 ACATTACT
85140 ACATTACT
1 ACATTACT
85148 ACATT
1 ACATT
85153 TGCATGATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (8 bp):
ACATTACT
Found at i:88120 original size:18 final size:17
Alignment explanation
Indices: 88084--88118 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
88074 TCTTTAAATG
88084 ATAAATAATATTAAAAA
1 ATAAATAATATTAAAAA
88101 ATAAATTAA-ATTAAAAA
1 ATAAA-TAATATTAAAAA
88118 A
1 A
88119 ATTATCCGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAATAATATTAAAAA
Found at i:88808 original size:26 final size:26
Alignment explanation
Indices: 88779--88842 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
88769 TGATTTTATG
88779 TATAAATTTATTCTCCCGCCTAATAA
1 TATAAATTTATTCTCCCGCCTAATAA
88805 TATAAATTTATTCTCCCGCCTAATAA
1 TATAAATTTATTCTCCCGCCTAATAA
88831 TATAAATTTATT
1 TATAAATTTATT
88843 AATACACCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (26 bp):
TATAAATTTATTCTCCCGCCTAATAA
Found at i:89134 original size:19 final size:20
Alignment explanation
Indices: 89100--89137 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
89090 AATTTTTGCA
89100 TATCTTTCCTTCTTCTTTCT
1 TATCTTTCCTTCTTCTTTCT
*
89120 TATCTTTTC-TCTTCTTTC
1 TATCTTTCCTTCTTCTTTC
89138 CCTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.66
Consensus pattern (20 bp):
TATCTTTCCTTCTTCTTTCT
Found at i:90265 original size:6 final size:6
Alignment explanation
Indices: 90250--90296 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
90240 TGAAGCAGTG
* *
90250 GCTCCA GCTCCC GCTCCA GCTCCA GCTCCG GCTCCA GCTCCA GCTCC
1 GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA GCTCC
90297 GGTTCTGGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.11, C:0.53, G:0.19, T:0.17
Consensus pattern (6 bp):
GCTCCA
Found at i:90308 original size:18 final size:18
Alignment explanation
Indices: 90250--90298 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
90240 TGAAGCAGTG
*
90250 GCTCCAGCTCCCGCTCCA
1 GCTCCAGCTCCGGCTCCA
90268 GCTCCAGCTCCGGCTCCA
1 GCTCCAGCTCCGGCTCCA
90286 GCTCCAGCTCCGG
1 GCTCCAGCTCCGG
90299 TTCTGGCTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.10, C:0.51, G:0.22, T:0.16
Consensus pattern (18 bp):
GCTCCAGCTCCGGCTCCA
Found at i:100292 original size:210 final size:210
Alignment explanation
Indices: 99996--100375 Score: 561
Period size: 210 Copynumber: 1.8 Consensus size: 210
99986 AAAATCGATT
* * *
99996 TTTTTTATTCTTTGGTACAATTTATTAGCCCAAGCTCATAAAATATAACCCTAATGGATGCTGAC
1 TTTTTTATTCTTTGATACAATTTATTAGCCCAAGCTCATAAAATACAACCCAAATGGATGCTGAC
* *
100061 TTGAATGCAAAATTTAATGTCGTTGGAATCGTATCGATTGGATTAAAAATTGATGAATGTATTGG
66 TTGAATGCAAAATTCAATGTCGTTGGAATCGGATCGATTGGATTAAAAATTGATGAATGTATTGG
*
100126 TTCAGACAAAAGTATTGAAACAGGTTTTGAGTGAATTATTTGAAACTGTCTCGGAACCTGTTGAA
131 TTCAGACAAAAGCATTGAAACAGGTTTTGAGTGAATTATTTGAAACTGTCTCGGAACCTGTTGAA
100191 TCGATCAAAAAACCG
196 TCGATCAAAAAACCG
* *
100206 TTTTTTATTCTTTGATACAATTTATTAGGCCCAA-TTCATAAAATCCAACCCAAACT-GATG-TG
1 TTTTTTATTCTTTGATACAATTTATTA-GCCCAAGCTCATAAAATACAACCCAAA-TGGATGCT-
* * * *
100268 GAGTTGAATTTC-AAATTCAATGTCGTTGGAATCGGATTGATTGGATTAAAAATTGATGGATGTA
63 GACTTGAA-TGCAAAATTCAATGTCGTTGGAATCGGATCGATTGGATTAAAAATTGATGAATGTA
* * *
100332 TTGGTTTAGACAAAGGCATTGAAACGGGTTTTGAGTGAATTATT
127 TTGGTTCAGACAAAAGCATTGAAACAGGTTTTGAGTGAATTATT
100376 CGGAACCTCC
Statistics
Matches: 151, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
209 1 0.01
210 141 0.93
211 9 0.06
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (210 bp):
TTTTTTATTCTTTGATACAATTTATTAGCCCAAGCTCATAAAATACAACCCAAATGGATGCTGAC
TTGAATGCAAAATTCAATGTCGTTGGAATCGGATCGATTGGATTAAAAATTGATGAATGTATTGG
TTCAGACAAAAGCATTGAAACAGGTTTTGAGTGAATTATTTGAAACTGTCTCGGAACCTGTTGAA
TCGATCAAAAAACCG
Found at i:103098 original size:20 final size:20
Alignment explanation
Indices: 103061--103100 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
103051 ATTAATTCAA
*
103061 ATTATTTTTATATTAATTTT
1 ATTATTTTTATATAAATTTT
103081 ATTATTTTTATCA-AAATTTT
1 ATTATTTTTAT-ATAAATTTT
103101 GCTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTATTTTTATATAAATTTT
Found at i:116851 original size:21 final size:21
Alignment explanation
Indices: 116827--116869 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
116817 TAAAAAAAAA
* *
116827 TGTTATTATTTTTTATTGTTT
1 TGTTATTATTTTTCATTATTT
*
116848 TGTTATTGTTTTTCATTATTT
1 TGTTATTATTTTTCATTATTT
116869 T
1 T
116870 ACTATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.02, G:0.09, T:0.74
Consensus pattern (21 bp):
TGTTATTATTTTTCATTATTT
Found at i:116855 original size:11 final size:11
Alignment explanation
Indices: 116827--116859 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
116817 TAAAAAAAAA
*
116827 TGTTATTATTT
1 TGTTATTGTTT
116838 T-TTATTGTTT
1 TGTTATTGTTT
116848 TGTTATTGTTT
1 TGTTATTGTTT
116859 T
1 T
116860 TCATTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (11 bp):
TGTTATTGTTT
Found at i:117063 original size:9 final size:10
Alignment explanation
Indices: 117047--117078 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
117037 TGGGAACATT
117047 TATTTTAATG
1 TATTTTAATG
117057 T-TTTTAATG
1 TATTTTAATG
117066 TATTTT-ATG
1 TATTTTAATG
117075 TATT
1 TATT
117079 ATATTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (10 bp):
TATTTTAATG
Found at i:117351 original size:59 final size:60
Alignment explanation
Indices: 117232--117363 Score: 169
Period size: 59 Copynumber: 2.2 Consensus size: 60
117222 TCAATAAACT
** * * *
117232 AAGTTCAAGTACCTAATTGAATTAAAATAAACTTTAGGTGCTAAATTGAACCTTAAAGCC
1 AAGTTCAAGTACCTAATTGAACCAAAATAAACCTTAGGTGATAAATTGAACCTCAAAGCC
* * *
117292 AAGTTCAAGTACCTAATTGGACCAAAA-AAACCTTAGGT-ATCAATATGAACCTCGAAGCC
1 AAGTTCAAGTACCTAATTGAACCAAAATAAACCTTAGGTGATAAAT-TGAACCTCAAAGCC
117351 AAGTTCAAGTACC
1 AAGTTCAAGTACC
117364 AAAATATATA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
58 4 0.06
59 35 0.56
60 24 0.38
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (60 bp):
AAGTTCAAGTACCTAATTGAACCAAAATAAACCTTAGGTGATAAATTGAACCTCAAAGCC
Found at i:129459 original size:30 final size:29
Alignment explanation
Indices: 129418--129484 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
129408 TTACTTATTT
*
129418 AAAAAATACACTAT-GAAGTTTAAAAATTAA
1 AAAAAAAACACTATCGAA--TTAAAAATTAA
* *
129448 AAAAAAAACACTATCTAATTAAAATTTAA
1 AAAAAAAACACTATCGAATTAAAAATTAA
129477 AAAAAAAA
1 AAAAAAAA
129485 TTTATATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 18 0.55
30 13 0.39
31 2 0.06
ACGTcount: A:0.66, C:0.07, G:0.03, T:0.24
Consensus pattern (29 bp):
AAAAAAAACACTATCGAATTAAAAATTAA
Found at i:135977 original size:30 final size:31
Alignment explanation
Indices: 135937--136002 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
135927 AAAAAATATA
*
135937 ATTT-AATTATTAAATTATTC-AAATATTTT
1 ATTTAAATTATTAAACTATTCAAAATATTTT
*
135966 ATTTAAATTATTAAACTATTCAAAATTTTTT
1 ATTTAAATTATTAAACTATTCAAAATATTTT
135997 ATTTAA
1 ATTTAA
136003 GTCACTAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 4 0.12
30 15 0.45
31 14 0.42
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (31 bp):
ATTTAAATTATTAAACTATTCAAAATATTTT
Found at i:136095 original size:33 final size:33
Alignment explanation
Indices: 136053--136115 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
136043 AAGTTCTAAA
136053 CAACAATTCGACAACCGATATAATGTATCCAAG
1 CAACAATTCGACAACCGATATAATGTATCCAAG
136086 CAACAATTCGACAACCGATATAATGTATCC
1 CAACAATTCGACAACCGATATAATGTATCC
136116 GTACTCATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.22
Consensus pattern (33 bp):
CAACAATTCGACAACCGATATAATGTATCCAAG
Found at i:136474 original size:43 final size:43
Alignment explanation
Indices: 136413--136499 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
136403 TAATTTTTTT
136413 CAAAAAAATAAAACTCAAGCTAAAACAAATCGA-TCCAACCCAA
1 CAAAAAAATAAAACTCAAGCTAAAACAAATCGACT-CAACCCAA
136456 CAAAAAAATAAAACTCAAGCTAAAACAAATCGACTCAACCCAA
1 CAAAAAAATAAAACTCAAGCTAAAACAAATCGACTCAACCCAA
136499 C
1 C
136500 CTGTGTTGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.57, C:0.26, G:0.05, T:0.11
Consensus pattern (43 bp):
CAAAAAAATAAAACTCAAGCTAAAACAAATCGACTCAACCCAA
Found at i:140373 original size:26 final size:26
Alignment explanation
Indices: 140344--140395 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
140334 AAAATGTAAG
* * *
140344 GTTTAGATAAAATTATTATACGAAAT
1 GTTTACATAAAATAAATATACGAAAT
*
140370 GTTTACATGAAATAAATATACGAAAT
1 GTTTACATAAAATAAATATACGAAAT
140396 TGATATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.35
Consensus pattern (26 bp):
GTTTACATAAAATAAATATACGAAAT
Found at i:143707 original size:41 final size:41
Alignment explanation
Indices: 143662--143742 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
143652 TTTAAAATTT
143662 GGATTATTTTGATTAC-ATGTTCAGATCAATTCATAATTAAA
1 GGATTATTTTGATT-CTATGTTCAGATCAATTCATAATTAAA
*
143703 GGATTATTTTGGTTCTATGTTCAGATCAATTCATAATTAA
1 GGATTATTTTGATTCTATGTTCAGATCAATTCATAATTAA
143743 TTTATTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (41 bp):
GGATTATTTTGATTCTATGTTCAGATCAATTCATAATTAAA
Found at i:149301 original size:13 final size:13
Alignment explanation
Indices: 149285--149323 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
149275 AAAAATTATT
149285 AAAAAAAGAAACA
1 AAAAAAAGAAACA
*
149298 AAAAAAAAAAACA
1 AAAAAAAGAAACA
149311 AAACAAAATGAAA
1 AAA-AAAA-GAAA
149324 ACCTCTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 15 0.68
14 4 0.18
15 3 0.14
ACGTcount: A:0.85, C:0.08, G:0.05, T:0.03
Consensus pattern (13 bp):
AAAAAAAGAAACA
Found at i:154720 original size:3 final size:3
Alignment explanation
Indices: 154712--154739 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
154702 TGCATGCATG
154712 TGT TGT TGT TGT TGT TGT TGT TGT TGT T
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT T
154740 TATGTAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TGT
Found at i:155531 original size:15 final size:15
Alignment explanation
Indices: 155503--155533 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
155493 GGAAATATAA
*
155503 TAAAATTTTATATTT
1 TAAAATGTTATATTT
155518 TAAAATGTTATATTT
1 TAAAATGTTATATTT
155533 T
1 T
155534 TTTTATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TAAAATGTTATATTT
Found at i:155962 original size:23 final size:24
Alignment explanation
Indices: 155934--155994 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
155924 ATTATTTTTT
**
155934 ATATAAAAATAAAATT-TTTAAAA
1 ATATAAAAATAAAATTGACTAAAA
* *
155957 ATATAATATATGAAATTGACTAAAA
1 ATATAA-AAATAAAATTGACTAAAA
*
155982 ATATTAAAATAAA
1 ATATAAAAATAAA
155995 TGTTTCCTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
23 6 0.21
24 13 0.45
25 10 0.34
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (24 bp):
ATATAAAAATAAAATTGACTAAAA
Found at i:156345 original size:22 final size:22
Alignment explanation
Indices: 156320--156367 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
156310 ATAAAAATAT
*
156320 AATAACGA-AATAGTAGCAAAAC
1 AATAAC-ATAATAGTAACAAAAC
156342 AATAACATAATAGTAACAAAAC
1 AATAACATAATAGTAACAAAAC
156364 AATA
1 AATA
156368 GTACACAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.62, C:0.12, G:0.08, T:0.17
Consensus pattern (22 bp):
AATAACATAATAGTAACAAAAC
Found at i:157557 original size:6 final size:6
Alignment explanation
Indices: 157546--157594 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
157536 GTCTTTTTTA
* * *
157546 GTATAT GTATAT GTATTT GTATAT GTACAT GTATAT GTATAT GCATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
157594 G
1 G
157595 CAAGTGCTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (6 bp):
GTATAT
Found at i:164155 original size:128 final size:128
Alignment explanation
Indices: 164020--164275 Score: 503
Period size: 128 Copynumber: 2.0 Consensus size: 128
164010 AAATATATAG
164020 TTATTAATTTATATATACTTTTATTATCATTATATATATTTTTTTAAAATTGTAAATATAAACAT
1 TTATTAATTTATATATACTTTTATTATCATTATATATATTTTTTTAAAATTGTAAATATAAACAT
*
164085 ATATTTTTAATATTTATATTAAATATTTAATTTACGTATTATATAATTTACAAGGAAAACAAA
66 ATATTTTTAATATTTACATTAAATATTTAATTTACGTATTATATAATTTACAAGGAAAACAAA
164148 TTATTAATTTATATATACTTTTATTATCATTATATATATTTTTTTAAAATTGTAAATATAAACAT
1 TTATTAATTTATATATACTTTTATTATCATTATATATATTTTTTTAAAATTGTAAATATAAACAT
164213 ATATTTTTAATATTTACATTAAATATTTAATTTACGTATTATATAATTTACAAGGAAAACAAA
66 ATATTTTTAATATTTACATTAAATATTTAATTTACGTATTATATAATTTACAAGGAAAACAAA
164276 CATACTATAA
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 127 1.00
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (128 bp):
TTATTAATTTATATATACTTTTATTATCATTATATATATTTTTTTAAAATTGTAAATATAAACAT
ATATTTTTAATATTTACATTAAATATTTAATTTACGTATTATATAATTTACAAGGAAAACAAA
Found at i:167826 original size:22 final size:20
Alignment explanation
Indices: 167783--167822 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
167773 TTCGGTTTAT
*
167783 ATATTAAATAAATTATTAAA
1 ATATAAAATAAATTATTAAA
167803 AT-TAAAATAAATTATTAAA
1 ATATAAAATAAATTATTAAA
167822 A
1 A
167823 AAATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATAAAATAAATTATTAAA
Found at i:167833 original size:19 final size:18
Alignment explanation
Indices: 167788--167831 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
167778 TTTATATATT
167788 AAATAAATTATTAAAATTA
1 AAATAAATTATTAAAA-TA
167807 AAATAAATTATTAAAA-A
1 AAATAAATTATTAAAATA
167824 AATATAAA
1 AA-ATAAA
167832 ATCTAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.12
18 5 0.21
19 16 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATAAATTATTAAAATA
Found at i:167914 original size:2 final size:2
Alignment explanation
Indices: 167907--167937 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
167897 TGACTCGTTT
*
167907 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
167938 TTGAACAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:172609 original size:20 final size:19
Alignment explanation
Indices: 172571--172616 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
172561 TTGGGATCAA
172571 GATTCAAGGTTTAAAATTT
1 GATTCAAGGTTTAAAATTT
* *
172590 GATTCTAAGGTTTGAGATTT
1 GATTC-AAGGTTTAAAATTT
172610 GAATTCA
1 G-ATTCA
172617 GATTTCAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 5 0.22
20 14 0.61
21 4 0.17
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.41
Consensus pattern (19 bp):
GATTCAAGGTTTAAAATTT
Found at i:175327 original size:89 final size:89
Alignment explanation
Indices: 175176--175340 Score: 251
Period size: 89 Copynumber: 1.9 Consensus size: 89
175166 ACTTCAAAGG
* * *
175176 AGAGAAGCTGAAGAAACTGAAGTAAGGTACTGAATATGATCGAATGGGGTTGTAGAGTTGCTTGT
1 AGAGAAGCTGAAGAAACTGAAGTAAGGTACTGAAAATGATCAAATGGGGTTGTAGAGTTGCTTAT
*
175241 TCTACATATGGGGACTTGAAGAGA
66 TCCACATATGGGGACTTGAAGAGA
* * *
175265 AGAGAAGCTTATGAAACTGAAGTGAA-TTACTGAAAATGATCAAATGGGGTTGTAGAGTTGCTTA
1 AGAGAAGCTGAAGAAACTGAAGT-AAGGTACTGAAAATGATCAAATGGGGTTGTAGAGTTGCTTA
175329 TTCCACATATGG
65 TTCCACATATGG
175341 AGGAGGCAGG
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
89 66 0.97
90 2 0.03
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.27
Consensus pattern (89 bp):
AGAGAAGCTGAAGAAACTGAAGTAAGGTACTGAAAATGATCAAATGGGGTTGTAGAGTTGCTTAT
TCCACATATGGGGACTTGAAGAGA
Found at i:177589 original size:2 final size:2
Alignment explanation
Indices: 177584--177614 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
177574 TAAAACTTTA
177584 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 A
177615 AAAGTCATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:177932 original size:30 final size:27
Alignment explanation
Indices: 177882--177963 Score: 91
Period size: 30 Copynumber: 3.0 Consensus size: 27
177872 AGCTCCACTC
177882 ATATTATTTTTATTTATTTAA-AATATT
1 ATATTATTTTTATTTATTTAATAAT-TT
177909 ATATTATTTTATATTAATATTTAATAATTT
1 ATATTATTTT-TATT--TATTTAATAATTT
177939 ATA-TATTTTTTATTTA-TTAA-AATTT
1 ATATTA-TTTTTATTTATTTAATAATTT
177964 TGTATACAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
25 5 0.10
26 4 0.08
27 12 0.24
28 4 0.08
29 6 0.12
30 16 0.32
31 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
ATATTATTTTTATTTATTTAATAATTT
Found at i:178878 original size:22 final size:22
Alignment explanation
Indices: 178830--178879 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
178820 AATGTTTACA
* *
178830 TTAAAATAATATTATATAATAT
1 TTAAAATAACATAATATAATAT
*
178852 ATAAAAGTAACATAATATAA-AT
1 TTAAAA-TAACATAATATAATAT
178874 TTAAAA
1 TTAAAA
178880 ACAGATCAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
TTAAAATAACATAATATAATAT
Found at i:181465 original size:29 final size:29
Alignment explanation
Indices: 181432--181595 Score: 177
Period size: 30 Copynumber: 5.6 Consensus size: 29
181422 ATGAAAATAA
* *
181432 AATTTTAGAAAAGCTCAGGGTCAAAATGT
1 AATTTTAGAAAAGTTTAGGGTCAAAATGT
* *
181461 GATTTTGGAAAAGTTTAGGGGTCAAAATGT
1 AATTTTAGAAAAGTTTA-GGGTCAAAATGT
* * * * *
181491 GATTTTGGAAAATTTTAAGGTCAAAGTGT
1 AATTTTAGAAAAGTTTAGGGTCAAAATGT
181520 AATTTTAGAAAAGTTTAGGTGTCAAAATGT
1 AATTTTAGAAAAGTTTAGG-GTCAAAATGT
* * *
181550 AATTTT-GAAAAATTTTAGTGGTTAAAATAT
1 AATTTTAG-AAAAGTTTAG-GGTCAAAATGT
181580 AATTTTAGAAAAGTTT
1 AATTTTAGAAAAGTTT
181596 TGGGGTTTTT
Statistics
Matches: 114, Mismatches: 16, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
29 39 0.34
30 73 0.64
31 2 0.02
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.37
Consensus pattern (29 bp):
AATTTTAGAAAAGTTTAGGGTCAAAATGT
Found at i:181496 original size:59 final size:58
Alignment explanation
Indices: 181432--181601 Score: 160
Period size: 59 Copynumber: 2.9 Consensus size: 58
181422 ATGAAAATAA
* * *
181432 AATTTTAGAAAAGCTCAGGGTCAAAATGTGATTTTGGAAAAGTTTAGGGGTCAAAATGT
1 AATTTT-GAAAAGCTCAAGGTCAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATGT
* ** * * *
181491 GATTTTGGAAAATTTTAAGGTCAAAGTGTAATTTTAGAAAAGTTTAGGTGTCAAAATGT
1 AATTTT-GAAAAGCTCAAGGTCAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATGT
** * * * * *
181550 AATTTTGAAAAATTTTAGTGGTTAAAATATAATTTTAGAAAAGTTTTGGGGT
1 AATTTTG-AAAAGCTCA-AGGTCAAAATGTAATTTTAGAAAAGTTTAGGGGT
181602 TTTTTGGTCA
Statistics
Matches: 92, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
58 1 0.01
59 63 0.68
60 28 0.30
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (58 bp):
AATTTTGAAAAGCTCAAGGTCAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATGT
Found at i:183949 original size:23 final size:23
Alignment explanation
Indices: 183921--183984 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
183911 ACGTCTCGTG
*
183921 CTCTCTGTTATTAGCACTGTGTGTG
1 CTCTCTG--ATTAGCACTGTGTGTA
* *
183946 CTCTCTGATTAGTACTTTGTGTA
1 CTCTCTGATTAGCACTGTGTGTA
183969 CTCTCT-ATTTAGCACT
1 CTCTCTGA-TTAGCACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 26 0.76
25 7 0.21
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (23 bp):
CTCTCTGATTAGCACTGTGTGTA
Done.