Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005189.1 Hibiscus syriacus cultivar Beakdansim tig00011718_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1183632
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:236571 original size:19 final size:18
Alignment explanation
Indices: 236541--236576 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
236531 AAAATAAATA
236541 ATAAAATTAAAATCATTT
1 ATAAAATTAAAATCATTT
236559 ATAAAATTTAAAATCATT
1 ATAAAA-TTAAAATCATT
236577 AAAAAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAAATTAAAATCATTT
Found at i:236582 original size:18 final size:18
Alignment explanation
Indices: 236528--236582 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
236518 TAATATATAT
* *
236528 TTTAAAATAAATAATAAAA
1 TTTAAAATCATTAA-AAAA
*
236547 -TTAAAATCATTTATAAAA
1 TTTAAAATCA-TTAAAAAA
236565 TTTAAAATCATTAAAAAA
1 TTTAAAATCATTAAAAAA
236583 GTTTGGCCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 19 0.63
19 11 0.37
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTAAAATCATTAAAAAA
Found at i:236733 original size:28 final size:31
Alignment explanation
Indices: 236702--236759 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
236692 TGTTTTGATT
236702 ATTAAAATT-TTAAATT-TT-TAAAATAATA
1 ATTAAAATTATTAAATTATTATAAAATAATA
*
236730 ATTAAATTTATTAAATTATTATAAAATAAT
1 ATTAAAATTATTAAATTATTATAAAATAAT
236760 TACTATGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 8 0.31
29 7 0.27
30 2 0.08
31 9 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
ATTAAAATTATTAAATTATTATAAAATAATA
Found at i:236760 original size:28 final size:28
Alignment explanation
Indices: 236702--236761 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
236692 TGTTTTGATT
*
236702 ATTAAAATTTTAAATTTTTAAAATAATA
1 ATTAAAATTTTAAATTATTAAAATAATA
* *
236730 ATTAAATTTATTAAATTATTATAA-AATA
1 ATTAAAATT-TTAAATTATTAAAATAATA
236758 ATTA
1 ATTA
236762 CTATGATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTAAAATTTTAAATTATTAAAATAATA
Found at i:237874 original size:31 final size:31
Alignment explanation
Indices: 237839--237911 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
237829 GTTAACATGT
237839 AGTGACCACT-TCTTAAATAAATAAAAATAAA
1 AGTGACCA-TATCTTAAATAAATAAAAATAAA
* * *
237870 AGTGATCATATCTTAATTAAATAAAAATGAA
1 AGTGACCATATCTTAAATAAATAAAAATAAA
* *
237901 TGTGAACATAT
1 AGTGACCATAT
237912 AAATTTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.30
Consensus pattern (31 bp):
AGTGACCATATCTTAAATAAATAAAAATAAA
Found at i:245206 original size:3 final size:3
Alignment explanation
Indices: 245198--245277 Score: 135
Period size: 3 Copynumber: 26.7 Consensus size: 3
245188 AACATATGAT
245198 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A TATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
*
245243 ATA ATA ATA TTA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
245278 GATGATGATG
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 1 0.01
3 71 0.97
4 1 0.01
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:248522 original size:98 final size:99
Alignment explanation
Indices: 248305--248553 Score: 310
Period size: 98 Copynumber: 2.5 Consensus size: 99
248295 ATAATGTCTT
* * *
248305 CTCGACCTTAAAACATATGCATGGATCCTCTTAACCCCG-TCTTTTTCCA--TCATATATAAAAT
1 CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTT-CATTTCATATATAAAAT
* *
248367 GTATTTTGCATTCCGTCTAGATACTAGTATAACTTCTA
65 GTATTTAGCATTCCGTATAGATACTAG---AACTTCTA
* * * *
248405 CTCGACCTTAAAAGATATGCGTGGATTCTCTTAGCCCTGTTCTTTTTCATTTTATGTATAAAATG
1 CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCATTTCATATATAAAATG
*
248470 TATTTAGCATTCTGTATAGATA-TACG-ACTTCTA
66 TATTTAGCATTCCGTATAGATACTA-GAACTTCTA
* *
248503 GTCGACCTTAAAAGATATGCATGTATTCTCTTAGCCCCGTTCTTTTTCATT
1 CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCATT
248554 ATGCATGAAA
Statistics
Matches: 131, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
98 54 0.41
100 36 0.27
101 9 0.07
102 32 0.24
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (99 bp):
CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCATTTCATATATAAAATG
TATTTAGCATTCCGTATAGATACTAGAACTTCTA
Found at i:249404 original size:28 final size:28
Alignment explanation
Indices: 249364--249421 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
249354 GTTTATATAC
249364 GATCCTGTTAAAGAGGAAGGGGAAGGAG
1 GATCCTGTTAAAGAGGAAGGGGAAGGAG
*
249392 GATCCTGTTAAAGAGGGAGGGGAAGGAG
1 GATCCTGTTAAAGAGGAAGGGGAAGGAG
249420 GA
1 GA
249422 GGGAATATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.34, C:0.07, G:0.45, T:0.14
Consensus pattern (28 bp):
GATCCTGTTAAAGAGGAAGGGGAAGGAG
Found at i:252828 original size:98 final size:99
Alignment explanation
Indices: 252611--252859 Score: 310
Period size: 98 Copynumber: 2.5 Consensus size: 99
252601 ATAATGTCTT
* * *
252611 CTCGACCTTAAAACATATGCATGGATCCTCTTAACCCCG-TCTTTTTCCA--TCATATATAAAAT
1 CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTT-CATTTCATATATAAAAT
* *
252673 GTATTTTGCATTCCGTCTAGATACTAGTATAACTTCTA
65 GTATTTAGCATTCCGTATAGATACTAG---AACTTCTA
* * * *
252711 CTCGACCTTAAAAGATATGCGTGGATTCTCTTAGCCCTGTTCTTTTTCATTTTATGTATAAAATG
1 CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCATTTCATATATAAAATG
*
252776 TATTTAGCATTCTGTATAGATA-TACG-ACTTCTA
66 TATTTAGCATTCCGTATAGATACTA-GAACTTCTA
* *
252809 GTCGACCTTAAAAGATATGCATGTATTCTCTTAGCCCCGTTCTTTTTCATT
1 CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCATT
252860 ATGCATGAAA
Statistics
Matches: 131, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
98 54 0.41
100 36 0.27
101 9 0.07
102 32 0.24
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (99 bp):
CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCATTTCATATATAAAATG
TATTTAGCATTCCGTATAGATACTAGAACTTCTA
Found at i:253712 original size:28 final size:28
Alignment explanation
Indices: 253672--253729 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
253662 GTTTATATAC
253672 GATCCTGTTAAAGAGGAAGGGGAAGGAG
1 GATCCTGTTAAAGAGGAAGGGGAAGGAG
*
253700 GATCCTGTTAAAGAGGGAGGGGAAGGAG
1 GATCCTGTTAAAGAGGAAGGGGAAGGAG
253728 GA
1 GA
253730 GGGAATATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.34, C:0.07, G:0.45, T:0.14
Consensus pattern (28 bp):
GATCCTGTTAAAGAGGAAGGGGAAGGAG
Found at i:257123 original size:98 final size:98
Alignment explanation
Indices: 256913--257159 Score: 299
Period size: 98 Copynumber: 2.5 Consensus size: 98
256903 ATAATGTCTT
* * *
256913 CTCGACCTTAAAACATATGCATGGATCCTCTTAACCCCG-TCTTTTTCCA--TCATATATAAAAT
1 CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTT-CATTTCATATATAAAAT
*
256975 GTATTTGCATTCCGTCTAGATACTAGTATAACTTCTA
65 GTATTTGCATTCCGTATAGATACTAG---AACTTCTA
* * * *
257012 CTCGACCTT-AAAGATATGCGTGGATTCTCTTAGCCCTGTTCTTTTTCATTTTATGTATAAAATG
1 CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCATTTCATATATAAAATG
*
257076 TATTTAGCATTCTGTATAGATA-TACG-ACTTCTA
66 TATTT-GCATTCCGTATAGATACTA-GAACTTCTA
* *
257109 GTCGACCTTAAAAGATATGCATGTATTCTCTTAGCCCCGTTCTTTTTCATT
1 CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCATT
257160 ATGCATGAAA
Statistics
Matches: 129, Mismatches: 13, Indels: 13
0.83 0.08 0.08
Matches are distributed among these distances:
97 15 0.12
98 64 0.50
99 16 0.12
100 19 0.15
101 15 0.12
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (98 bp):
CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCATTTCATATATAAAATG
TATTTGCATTCCGTATAGATACTAGAACTTCTA
Found at i:258013 original size:28 final size:28
Alignment explanation
Indices: 257973--258030 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
257963 GGTTATATAC
257973 GATCCTGTTAAAGAGGAAGGGGAAGGAG
1 GATCCTGTTAAAGAGGAAGGGGAAGGAG
*
258001 GATCCTGTTAAAGAGGGAGGGGAAGGAG
1 GATCCTGTTAAAGAGGAAGGGGAAGGAG
258029 GA
1 GA
258031 GGGAATATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.34, C:0.07, G:0.45, T:0.14
Consensus pattern (28 bp):
GATCCTGTTAAAGAGGAAGGGGAAGGAG
Found at i:261453 original size:97 final size:97
Alignment explanation
Indices: 261225--261484 Score: 323
Period size: 97 Copynumber: 2.7 Consensus size: 97
261215 ATAATGTCTT
* * * * *
261225 CTCGACCTTAAAACATATGCATGGATCCTCTTAACCCCG-TCTTTTTCCATCATATAT-AAATGT
1 CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTT-CATTATGTATAAAATGT
* *
261288 ATTTTGCATTCCGTCTAGATACTAGTATAACTTCTA
65 ATTTAGCATTCCGTATAGATACTAG---AACTTCTA
* *
261324 CTCGACCTTAAAAGATATGCGTGGATTCTCTTAGCCCTGTTCTTTTTCATTTTATGTATAAAATG
1 CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCA--TTATGTATAAAATG
*
261389 TATTTAGCATTCTGTATAGATA-TACG-ACTTCTA
64 TATTTAGCATTCCGTATAGATACTA-GAACTTCTA
*
261422 GTCGACCTT-AAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCATTATGTATAAAATGT
1 CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCATTATGTATAAAATGT
261485 CTTTTTCTAT
Statistics
Matches: 143, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
95 15 0.10
97 37 0.26
98 15 0.10
99 36 0.25
100 7 0.05
101 8 0.06
102 25 0.17
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (97 bp):
CTCGACCTTAAAAGATATGCATGGATTCTCTTAGCCCCGTTCTTTTTCATTATGTATAAAATGTA
TTTAGCATTCCGTATAGATACTAGAACTTCTA
Found at i:262326 original size:28 final size:29
Alignment explanation
Indices: 262286--262344 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
262276 GTTTATTTAC
262286 GATCCTGTTAAAGA-GGAAGGGGAAGGAG
1 GATCCTGTTAAAGAGGGAAGGGGAAGGAG
*
262314 GATCCTGTTAAAGAGGGGAGGGGAAGGAG
1 GATCCTGTTAAAGAGGGAAGGGGAAGGAG
262343 GA
1 GA
262345 GGGAATATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.34, C:0.07, G:0.46, T:0.14
Consensus pattern (29 bp):
GATCCTGTTAAAGAGGGAAGGGGAAGGAG
Found at i:267554 original size:2 final size:2
Alignment explanation
Indices: 267547--267586 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
267537 ATATACAAAC
* * *
267547 AT AT AT AT AT AT AC AA AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
267587 GTTCGTTCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:267558 original size:18 final size:18
Alignment explanation
Indices: 267531--267577 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
267521 GAGATGGTAC
*
267531 ATATACATATACAAACAT
1 ATATATATATACAAACAT
267549 ATATATATATACAAACAT
1 ATATATATATACAAACAT
267567 ATATATATATA
1 ATATATATATA
267578 TATATATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATATATATACAAACAT
Found at i:269286 original size:20 final size:21
Alignment explanation
Indices: 269261--269312 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
269251 TTTTCCCAAT
269261 TCGCAATGCGAATAAGT-AAA
1 TCGCAATGCGAATAAGTAAAA
* **
269281 TCGCAACGCGAATTGGTAAAA
1 TCGCAATGCGAATAAGTAAAA
269302 TCGCAATGCGA
1 TCGCAATGCGA
269313 TACTGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATAAGTAAAA
Found at i:269325 original size:41 final size:41
Alignment explanation
Indices: 269298--269389 Score: 148
Period size: 41 Copynumber: 2.2 Consensus size: 41
269288 GCGAATTGGT
*
269298 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
269339 AAAATCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
269380 AGAATCGCAA
1 AAAATCGCAA
269390 TGCGCTTTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.18
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:269326 original size:20 final size:20
Alignment explanation
Indices: 269301--269375 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
269291 AATTGGTAAA
*
269301 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
269321 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
269342 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
269362 TTCGCAACGAGATA
1 ATCGCAACGCGATA
269376 ATACAGAATC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 2 0.04
20 26 0.58
21 15 0.33
22 2 0.04
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:269347 original size:21 final size:20
Alignment explanation
Indices: 269299--269389 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
269289 CGAATTGGTA
* *
269299 AAATCGCAATGCGATACTGAC
1 AAATCGCAACGCGATAAT-AC
*
269320 -TATCGCAACGCGATAATAC
1 AAATCGCAACGCGATAATAC
*
269339 AAAATCGCAACGCGATACTGAC
1 -AAATCGCAACGCGATAAT-AC
** *
269361 -TTTCGCAACGAGATAATAC
1 AAATCGCAACGCGATAATAC
269380 AGAATCGCAA
1 A-AATCGCAA
269390 TGCGCTTTTC
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
19 4 0.07
20 27 0.50
21 21 0.39
22 2 0.04
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGATAATAC
Found at i:269724 original size:20 final size:20
Alignment explanation
Indices: 269696--269756 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
269686 GACATTCATT
269696 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAAAA
*
269716 TGGCTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAAAA
*
269736 TGACTATCGCAACGAGAAAA
1 TGACTATCGCAACGCGAAAA
269756 T
1 T
269757 TGCAATGCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.16
Consensus pattern (20 bp):
TGACTATCGCAACGCGAAAA
Found at i:269816 original size:19 final size:19
Alignment explanation
Indices: 269775--269839 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
269765 GAAATGAAAA
269775 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
269791 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
269808 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
269827 TCGCATTGCGATT
1 TCGCATTGCGATT
269840 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.25
16 3 0.07
17 3 0.07
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:269998 original size:14 final size:14
Alignment explanation
Indices: 269979--270015 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
269969 CATCAATTAA
269979 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
269993 ACAAATCATCTTTT
1 ACAAATCAACATTT
270007 ACAAATCAA
1 ACAAATCAA
270016 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:271908 original size:20 final size:20
Alignment explanation
Indices: 271885--271952 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
271875 GAAACTTAAA
271885 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
271905 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
* **
271925 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
271944 ATCGCAACG
1 ATCGCAACG
271953 ACAAAATCGC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 13 0.31
20 29 0.69
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:271960 original size:14 final size:14
Alignment explanation
Indices: 271941--271998 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
271931 ATGCGAAATG
271941 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
271955 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
271971 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
271987 AAAATCGCAACG
1 AAAATCGCAACG
271999 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:271983 original size:32 final size:33
Alignment explanation
Indices: 271925--272003 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
271915 GAAAATGGCT
271925 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
271958 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
271990 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
272004 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:272559 original size:18 final size:18
Alignment explanation
Indices: 272533--272577 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
272523 GTCGATCAGA
*
272533 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
272551 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
272569 TGATGGCTC
1 TGATGGCTC
272578 CCGAAATGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:273922 original size:20 final size:19
Alignment explanation
Indices: 273897--273950 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
273887 AATAGCTTCT
273897 GAAAATGAAAATCGCAACAC
1 GAAAAT-AAAATCGCAACAC
* *
273917 GAAAATAACTATCGCAACGC
1 GAAAATAA-AATCGCAACAC
*
273937 GAAACTAAAATCGC
1 GAAAATAAAATCGC
273951 GTTGCGATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.50, C:0.22, G:0.15, T:0.13
Consensus pattern (19 bp):
GAAAATAAAATCGCAACAC
Found at i:274463 original size:20 final size:20
Alignment explanation
Indices: 274415--274467 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
274405 GGTTATGTAT
*
274415 TATCGCGTTGCGAAAGTTAG
1 TATCGCGTTGCGAAAGTCAG
* *
274435 AACCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
274455 TATCTCGTTGCGA
1 TATCGCGTTGCGA
274468 TTTTGTATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:274501 original size:20 final size:19
Alignment explanation
Indices: 274476--274545 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
274466 GATTTTGTAT
274476 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGT-AG
*
274496 TATCGCATTGC-AT--TAC
1 TATCGCATTGCGATAGTAG
*
274512 TATCGCAATGCGATAGTCAG
1 TATCGCATTGCGATAGT-AG
274532 TATCGCATTGCGAT
1 TATCGCATTGCGAT
274546 TTTCCCAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
16 11 0.26
17 3 0.07
19 3 0.07
20 25 0.60
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (19 bp):
TATCGCATTGCGATAGTAG
Found at i:274656 original size:21 final size:21
Alignment explanation
Indices: 274616--274656 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
274606 ACTGTAGACC
** *
274616 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
274637 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
274657 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:274975 original size:16 final size:16
Alignment explanation
Indices: 274954--274985 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
274944 TGTAACGTCC
*
274954 ATATTTTTAAAAAAAT
1 ATATTTTAAAAAAAAT
274970 ATATTTTAAAAAAAAT
1 ATATTTTAAAAAAAAT
274986 CTAGATGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATTTTAAAAAAAAT
Found at i:279468 original size:59 final size:59
Alignment explanation
Indices: 279373--279490 Score: 191
Period size: 59 Copynumber: 2.0 Consensus size: 59
279363 AACACTCGTC
* * *
279373 GGCCTGACATTACTTATCTTATCAAATCTTTCATTAACTTATACGGATTGTTCTAATTT
1 GGCCTGACATTACTTATCTTATCAAAGCTTTAATTAACTTACACGGATTGTTCTAATTT
* *
279432 GGCCTGCCATTGCTTATCTTATCAAAGCTTTAATTAACTTACACGGATTGTTCTAATTT
1 GGCCTGACATTACTTATCTTATCAAAGCTTTAATTAACTTACACGGATTGTTCTAATTT
279491 AAGTATAGAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.42
Consensus pattern (59 bp):
GGCCTGACATTACTTATCTTATCAAAGCTTTAATTAACTTACACGGATTGTTCTAATTT
Found at i:283463 original size:30 final size:31
Alignment explanation
Indices: 283422--283497 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
283412 TTCAAAATAC
* *
283422 ATAAAATATGGTCACTTTCATTTTTA-TTAA
1 ATAAGATATGGTCACTTTCATTTTAATTTAA
**
283452 ATAAGATATGGTCACTTTTGTTTTAATTTAA
1 ATAAGATATGGTCACTTTCATTTTAATTTAA
*
283483 TTAAGATATGGTCAC
1 ATAAGATATGGTCAC
283498 CATAGGTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 22 0.55
31 18 0.45
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (31 bp):
ATAAGATATGGTCACTTTCATTTTAATTTAA
Found at i:283819 original size:27 final size:27
Alignment explanation
Indices: 283744--283845 Score: 93
Period size: 27 Copynumber: 3.7 Consensus size: 27
283734 GTATAAATAC
* * *
283744 TTAACTTAAATTCATAATATTTTATATATA
1 TTAACTTAATTTAAAAATA-TTT-TAT-TA
*
283774 TTAACTT-A-TTAAATATATTTTATTA
1 TTAACTTAATTTAAAAATATTTTATTA
283799 TTAACTTAATTTAAAAATATTTTATT-
1 TTAACTTAATTTAAAAATATTTTATTA
* *
283825 TTTATTTGAATTTAAAAATAT
1 TTAACTT-AATTTAAAAATAT
283846 ATATTTTATT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
25 9 0.14
26 9 0.14
27 31 0.49
28 6 0.10
29 1 0.02
30 7 0.11
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (27 bp):
TTAACTTAATTTAAAAATATTTTATTA
Found at i:283853 original size:31 final size:31
Alignment explanation
Indices: 283815--283900 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 31
283805 TAATTTAAAA
283815 ATATTTTATTTTTATTTGAATTTAAAAATAT
1 ATATTTTATTTTTATTTGAATTTAAAAATAT
*
283846 ATATTTTATTTTTA-TCGAAACTTGTAAAAATAT
1 ATATTTTATTTTTATTTG-AA-TT-TAAAAATAT
*
283879 ATA-TTTA-TTTTATTTTAATTTA
1 ATATTTTATTTTTATTTGAATTTA
283901 TTAAAAGGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
29 2 0.04
30 4 0.08
31 23 0.48
32 7 0.15
33 12 0.25
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.57
Consensus pattern (31 bp):
ATATTTTATTTTTATTTGAATTTAAAAATAT
Found at i:284747 original size:6 final size:6
Alignment explanation
Indices: 284738--284786 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
284728 ATTAAAAAAA
284738 TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT
1 TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT
284786 T
1 T
284787 GTTCACATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TATAAT
Found at i:286608 original size:13 final size:13
Alignment explanation
Indices: 286590--286622 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
286580 AGTCAAAGAA
286590 AGTCAACGGTCAC
1 AGTCAACGGTCAC
286603 AGTCAACGGTCAC
1 AGTCAACGGTCAC
*
286616 GGTCAAC
1 AGTCAAC
286623 AGTCGGGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.15
Consensus pattern (13 bp):
AGTCAACGGTCAC
Found at i:286638 original size:17 final size:17
Alignment explanation
Indices: 286616--286673 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
286606 CAACGGTCAC
286616 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
286633 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
286650 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
286667 GGTCAAC
1 GGTCAAC
286674 CCGGTTCAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:286691 original size:19 final size:19
Alignment explanation
Indices: 286667--286737 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
286657 AGTCGGGTCG
*
286667 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
286686 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
* * *
286705 AGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
286725 GGTCAAACCGGTT
1 GGTCAAACCGGTT
286738 TTCCAGCAGC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 31 0.67
20 15 0.33
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:286697 original size:9 final size:9
Alignment explanation
Indices: 286667--286736 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
286657 AGTCGGGTCG
*
286667 GGTCAACCC
1 GGTCAAACC
*
286676 GGTTCAGACC
1 GG-TCAAACC
286686 GGTCAAACC
1 GGTCAAACC
*
286695 GGTTCAGACC
1 GG-TCAAACC
*
286705 AGTCAAACC
1 GGTCAAACC
*
286714 GGTTCAAAACT
1 GG-TC-AAACC
286725 GGTCAAACC
1 GGTCAAACC
286734 GGT
1 GGT
286737 TTTCCAGCAG
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
9 24 0.50
10 18 0.38
11 6 0.12
ACGTcount: A:0.29, C:0.30, G:0.24, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:293878 original size:13 final size:14
Alignment explanation
Indices: 293860--293889 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
293850 GTCAAAGAAA
293860 GTCAACGGTC-ACG
1 GTCAACGGTCAACG
293873 GTCAACGGTCAACG
1 GTCAACGGTCAACG
293887 GTC
1 GTC
293890 GGGTCGGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:293901 original size:17 final size:17
Alignment explanation
Indices: 293879--293936 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
293869 CACGGTCAAC
293879 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
293896 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
293913 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
293930 GGTCAAC
1 GGTCAAC
293937 CCCGGTTCAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:293906 original size:7 final size:7
Alignment explanation
Indices: 293860--293889 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
293850 GTCAAAGAAA
293860 GTCAACG
1 GTCAACG
293867 GTC-ACG
1 GTCAACG
293873 GTCAACG
1 GTCAACG
293880 GTCAACG
1 GTCAACG
293887 GTC
1 GTC
293890 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:293962 original size:19 final size:19
Alignment explanation
Indices: 293938--294001 Score: 101
Period size: 19 Copynumber: 3.3 Consensus size: 19
293928 CGGGTCAACC
293938 CCGGTTCAGACCGGTCAAA
1 CCGGTTCAGACCGGTCAAA
293957 CCGGTTCAGACCGGTCAAA
1 CCGGTTCAGACCGGTCAAA
* *
293976 CCGGTTCAAAACTGGTCAAA
1 CCGGTTC-AGACCGGTCAAA
293996 CCGGTT
1 CCGGTT
294002 TTCCAGCAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
19 26 0.62
20 16 0.38
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.19
Consensus pattern (19 bp):
CCGGTTCAGACCGGTCAAA
Found at i:293969 original size:10 final size:10
Alignment explanation
Indices: 293938--294001 Score: 71
Period size: 9 Copynumber: 6.6 Consensus size: 10
293928 CGGGTCAACC
*
293938 CCGGTTCAGA
1 CCGGTTCAAA
293948 CCGG-TCAAA
1 CCGGTTCAAA
*
293957 CCGGTTCAGA
1 CCGGTTCAAA
293967 CCGG-TCAAA
1 CCGGTTCAAA
293976 CCGGTTCAAAA
1 CCGGTTC-AAA
*
293987 CTGG-TCAAA
1 CCGGTTCAAA
293996 CCGGTT
1 CCGGTT
294002 TTCCAGCAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
9 22 0.49
10 17 0.38
11 6 0.13
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.19
Consensus pattern (10 bp):
CCGGTTCAAA
Found at i:294897 original size:31 final size:31
Alignment explanation
Indices: 294862--294932 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
294852 GCAAATGGTA
* *
294862 CTTCGACTATTGGGTATTGTTTTGTTAAGTC
1 CTTCGACTATAGAGTATTGTTTTGTTAAGTC
* * *
294893 CTTCGATTATAGAGTGTTGTTTTGTTGAGTC
1 CTTCGACTATAGAGTATTGTTTTGTTAAGTC
*
294924 CCTCGACTA
1 CTTCGACTA
294933 GTAAAAATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.45
Consensus pattern (31 bp):
CTTCGACTATAGAGTATTGTTTTGTTAAGTC
Found at i:308069 original size:20 final size:20
Alignment explanation
Indices: 308044--308098 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
308034 TTTACATTTA
308044 GGGAACCGATTCCCCATAGG
1 GGGAACCGATTCCCCATAGG
308064 GGGAACCGATTCCCCATAGG
1 GGGAACCGATTCCCCATAGG
*
308084 GGGTACCGATTCCCC
1 GGGAACCGATTCCCC
308099 CCACGCTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16
Consensus pattern (20 bp):
GGGAACCGATTCCCCATAGG
Found at i:313858 original size:21 final size:21
Alignment explanation
Indices: 313832--313871 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
313822 CCCCCTTTGA
*
313832 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
313853 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
313872 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:323602 original size:23 final size:24
Alignment explanation
Indices: 323576--323635 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 24
323566 ATTAAATATT
323576 AAATATAATTTTAAAA-AAATTAA
1 AAATATAATTTTAAAACAAATTAA
* * *
323599 AAATTTAAATATTAAAACGAATTAA
1 AAATAT-AATTTTAAAACAAATTAA
*
323624 AATTATTAATTT
1 AAATA-TAATTT
323636 ATATACTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
23 5 0.18
24 9 0.32
25 13 0.46
26 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATATAATTTTAAAACAAATTAA
Found at i:323848 original size:20 final size:19
Alignment explanation
Indices: 323820--323858 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
323810 CATGTCATCC
*
323820 ATATATTAAATTATAATTAT
1 ATATATTAAAATAT-ATTAT
*
323840 ATATTTTAAAATATATTAT
1 ATATATTAAAATATATTAT
323859 TAATGTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATATTAAAATATATTAT
Found at i:335030 original size:2 final size:2
Alignment explanation
Indices: 335023--335054 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
335013 TAATCACATC
335023 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
335055 GCTAACAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:337960 original size:26 final size:26
Alignment explanation
Indices: 337871--337960 Score: 62
Period size: 26 Copynumber: 3.5 Consensus size: 26
337861 TTTAAATTAT
* *
337871 ATTTACACTTATATATGAATTATATCA
1 ATTTAAAC-TATATATGAATCATATCA
* **
337898 ATTTCAACTATA-ATGAATTCCA-AAAA
1 ATTTAAACTATATATGAA-T-CATATCA
*
337924 ATATT--ATTATATATGAATCATATCA
1 AT-TTAAACTATATATGAATCATATCA
337949 ATTTAAACTATA
1 ATTTAAACTATA
337961 ATAAAGATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 15
0.66 0.13 0.21
Matches are distributed among these distances:
24 4 0.09
25 15 0.32
26 19 0.40
27 9 0.19
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (26 bp):
ATTTAAACTATATATGAATCATATCA
Found at i:337978 original size:20 final size:20
Alignment explanation
Indices: 337953--337999 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
337943 ATATCAATTT
*
337953 AAACTATAA-TAAAGATATAA
1 AAACTATAATTAAA-AAATAA
*
337973 AAACTACAATTAAAAAATAA
1 AAACTATAATTAAAAAATAA
337993 AAA-TATA
1 AAACTATA
338000 TTTTATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 3 0.13
20 16 0.70
21 4 0.17
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.23
Consensus pattern (20 bp):
AAACTATAATTAAAAAATAA
Found at i:338092 original size:14 final size:13
Alignment explanation
Indices: 338058--338082 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
338048 ATTTATTTTA
338058 AAATAATTAAAAT
1 AAATAATTAAAAT
338071 AAATAATTAAAA
1 AAATAATTAAAA
338083 GTAATAAATT
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAATTAAAAT
Found at i:341626 original size:18 final size:18
Alignment explanation
Indices: 341600--341644 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
341590 TCACGGAATG
341600 TAAGATTACCAGCGGGAA
1 TAAGATTACCAGCGGGAA
* * *
341618 TAGGATTACCGGCGGTAA
1 TAAGATTACCAGCGGGAA
341636 TAAGATTAC
1 TAAGATTAC
341645 TGAGAATGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.22
Consensus pattern (18 bp):
TAAGATTACCAGCGGGAA
Found at i:343541 original size:21 final size:22
Alignment explanation
Indices: 343499--343541 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
343489 ATTTGGTTCA
*
343499 TGTTACTTATATTTTATCAATT
1 TGTTACTTATATTTTATAAATT
343521 TGTT-CTTA-ATTTTAATAAATT
1 TGTTACTTATATTTT-ATAAATT
343542 AAAATAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 10 0.53
22 4 0.21
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (22 bp):
TGTTACTTATATTTTATAAATT
Found at i:352047 original size:27 final size:26
Alignment explanation
Indices: 352017--352082 Score: 105
Period size: 27 Copynumber: 2.5 Consensus size: 26
352007 TGGTAGAAAA
352017 AATAACAAAACCGATAAAACGTCCAAT
1 AATAACAAAACCGATAAAACG-CCAAT
* *
352044 AATAACAAAACTGGTAAAACGCCAAT
1 AATAACAAAACCGATAAAACGCCAAT
352070 AATAACAAAACCG
1 AATAACAAAACCG
352083 GTAGAAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
26 17 0.47
27 19 0.53
ACGTcount: A:0.56, C:0.21, G:0.09, T:0.14
Consensus pattern (26 bp):
AATAACAAAACCGATAAAACGCCAAT
Found at i:352075 original size:26 final size:27
Alignment explanation
Indices: 352017--352085 Score: 113
Period size: 26 Copynumber: 2.6 Consensus size: 27
352007 TGGTAGAAAA
*
352017 AATAACAAAACCGATAAAACGTCCAAT
1 AATAACAAAACCGGTAAAACGTCCAAT
*
352044 AATAACAAAACTGGTAAAACG-CCAAT
1 AATAACAAAACCGGTAAAACGTCCAAT
352070 AATAACAAAACCGGTA
1 AATAACAAAACCGGTA
352086 GAAATAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 20 0.51
27 19 0.49
ACGTcount: A:0.55, C:0.20, G:0.10, T:0.14
Consensus pattern (27 bp):
AATAACAAAACCGGTAAAACGTCCAAT
Found at i:356302 original size:20 final size:19
Alignment explanation
Indices: 356274--356314 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
356264 TTGAGGCTGC
*
356274 AAGAGCAATATCAGTACTTG
1 AAGAACAATATCAGTA-TTG
*
356294 AAGAACAATATCGGTATTG
1 AAGAACAATATCAGTATTG
356313 AA
1 AA
356315 TAAACAGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (19 bp):
AAGAACAATATCAGTATTG
Found at i:356320 original size:20 final size:20
Alignment explanation
Indices: 356279--356320 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
356269 GCTGCAAGAG
*
356279 CAATATCAGTACTTGAAGAA
1 CAATATCAGTACTTGAAAAA
*
356299 CAATATCGGTA-TTGAATAAA
1 CAATATCAGTACTTGAA-AAA
356319 CA
1 CA
356321 GTACCGGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.26
Consensus pattern (20 bp):
CAATATCAGTACTTGAAAAA
Found at i:356726 original size:15 final size:15
Alignment explanation
Indices: 356706--356735 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
356696 CTTCTTTTGA
356706 GAAATGATCTCTAAT
1 GAAATGATCTCTAAT
*
356721 GAAATGATGTCTAAT
1 GAAATGATCTCTAAT
356736 TTCTATGTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (15 bp):
GAAATGATCTCTAAT
Found at i:359939 original size:21 final size:21
Alignment explanation
Indices: 359915--359969 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
359905 TAAAAGAAGC
359915 TTTAAGATCATCAAGTTTCTT
1 TTTAAGATCATCAAGTTTCTT
359936 TTTAAGATCATCAAGTTTCTT
1 TTTAAGATCATCAAGTTTCTT
*
359957 TTTATGATCATCA
1 TTTAAGATCATCA
359970 TGAACCTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (21 bp):
TTTAAGATCATCAAGTTTCTT
Found at i:360609 original size:15 final size:16
Alignment explanation
Indices: 360570--360630 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 16
360560 ACCAATATTT
*
360570 TTCTTCTTT-TTCAT-
1 TTCTTTTTTCTTCATC
360584 TTCCTTATTTTCTTCATC
1 TT-CTT-TTTTCTTCATC
*
360602 TT-TTTTTTCTTGATC
1 TTCTTTTTTCTTCATC
*
360617 TTCTTCTTTCTTCA
1 TTCTTTTTTCTTCA
360631 CCATCATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 2 0.05
15 15 0.39
16 14 0.37
17 5 0.13
18 2 0.05
ACGTcount: A:0.08, C:0.23, G:0.02, T:0.67
Consensus pattern (16 bp):
TTCTTTTTTCTTCATC
Found at i:362148 original size:21 final size:23
Alignment explanation
Indices: 362122--362170 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
362112 AAAAAGGTAA
362122 TATCGGTACCAC-CACTAAG-AG
1 TATCGGTACCACACACTAAGTAG
*
362143 TATCGGTACTACTACACTAAGTAG
1 TATCGGTACCAC-ACACTAAGTAG
362167 TATC
1 TATC
362171 AATATTGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 11 0.46
23 7 0.29
24 6 0.25
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (23 bp):
TATCGGTACCACACACTAAGTAG
Found at i:370214 original size:40 final size:40
Alignment explanation
Indices: 370158--370291 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 40
370148 TATTAAAATT
*
370158 TAAAT-AATCCATACAACTACAATAATAAATTATTTAAAA
1 TAAATCAATCTATACAACTACAATAATAAATTATTTAAAA
* **
370197 TAAATCAATCTATACAACTACAATAATAAATCAATTTATATTT
1 TAAATCAATCTATACAACTACAATAATAAAT-TATTTA-A-AA
* * *
370240 TAAAATAAATCAAT-CCA-TAC-A-AATAAATTATTTAAAA
1 T-AAATCAATCTATACAACTACAATAATAAATTATTTAAAA
*
370277 TAAATCAATATATAC
1 TAAATCAATCTATAC
370292 TAACAAATTA
Statistics
Matches: 76, Mismatches: 13, Indels: 14
0.74 0.13 0.14
Matches are distributed among these distances:
36 9 0.12
37 2 0.03
38 1 0.01
39 10 0.13
40 31 0.41
41 6 0.08
42 4 0.05
43 3 0.04
44 10 0.13
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (40 bp):
TAAATCAATCTATACAACTACAATAATAAATTATTTAAAA
Found at i:370277 original size:32 final size:32
Alignment explanation
Indices: 370238--370655 Score: 332
Period size: 32 Copynumber: 14.7 Consensus size: 32
370228 CAATTTATAT
*
370238 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
** *
370270 TTTAAAATAAATCAATATATACTAACAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
370302 TTTAAAATAAATCAAT-C--A-T--T--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
370324 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
370356 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
370378 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
*
370408 --T--AATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
370436 TTTAAAATAAATCAATACATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
370466 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
370484 TTTAAAATAAATCAATCTATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
370516 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
370548 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
370570 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
370602 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
370634 TTTAAAATAAATCAATTCATAC
1 TTTAAAATAAATCAATCCATAC
370656 AACTACACTA
Statistics
Matches: 316, Mismatches: 18, Indels: 104
0.72 0.04 0.24
Matches are distributed among these distances:
20 1 0.00
22 61 0.19
23 6 0.02
24 5 0.02
25 1 0.00
26 40 0.13
27 3 0.01
28 10 0.03
29 1 0.00
30 5 0.02
31 5 0.02
32 178 0.56
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:370328 original size:54 final size:54
Alignment explanation
Indices: 370270--370880 Score: 367
Period size: 54 Copynumber: 11.2 Consensus size: 54
370260 AAATAAATTA
*
370270 TTTAAAATAAATCAATATATACTAACAAATTATTTAAAATAAATCAAT-CATTAT
1 TTTAAAATAAATCAATATATACTAATAAATTATTTAAAATAAATCAATCCA-TAT
*
370324 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATATATACTAATAAATTATTTAAAATAAATCAATCCATAT
** * * ** **
370378 TTTAAAATAAATCAATCCATAC-AACTACAA-TAATAAATCAATTCATACTAATAAAT-T
1 TTTAAAATAAATCAATATATACTAA-TA-AATTATTTAA--AATAAAT-C-AATCCATAT
* *
370435 ATTTAAAATAAATCAATACATAC-AACTACA--A--T--AATAAATCAATCCATAT
1 -TTTAAAATAAATCAATATATACTAA-TAAATTATTTAAAATAAATCAATCCATAT
* *
370484 TTTAAAATAAATCAATCTATACAAATAAATTATTTAAAATAAATCAATCCATA-
1 TTTAAAATAAATCAATATATACTAATAAATTATTTAAAATAAATCAATCCATAT
* * * * * * * **
370537 CTAATAAATTATTTAAAATA-AATCAATCCA-TATTTTAAAATAAATCAATCCATACTAATAAAT
1 TTTA-AAATAAATCAATATATACT-AATAAATTA-TTTAAAATAAATCAAT-C---C--AT--A-
370600 T
54 T
** * *
370601 ATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACA
1 -TTTAAAATAAATCAATATATACTAATAAATTATTTAAAATAAATCAATCCATA-T
** ** * * * *
370657 ACTACACTAATAAATCAATCCATATTTTAAAATAAATTAATCTATACT-AATAAAT---TA-
1 TTTA-A--AATAAATCAAT--ATATACT--AATAAATT-ATTTAAAATAAATCAATCCATAT
*
370714 TTTAAAATAAATCAAT-TCATAC-AACTACA--A--T--AATAAATCAATCCATAT
1 TTTAAAATAAATCAATAT-ATACTAA-TAAATTATTTAAAATAAATCAATCCATAT
*
370762 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATATATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *
370816 TTTAAAATAAATCAATACATACTAATAAAATATTTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATATATACTAATAAATTA-TTTAAAATAAATCAATCCATAT
*
370871 TTTATAATAA
1 TTTAAAATAA
370881 TTTATTTTAA
Statistics
Matches: 435, Mismatches: 66, Indels: 111
0.71 0.11 0.18
Matches are distributed among these distances:
43 2 0.00
44 6 0.01
45 1 0.00
47 3 0.01
48 51 0.12
49 9 0.02
50 10 0.02
51 1 0.00
52 4 0.01
53 7 0.02
54 180 0.41
55 38 0.09
56 9 0.02
57 5 0.01
58 45 0.10
59 2 0.00
60 6 0.01
62 15 0.03
63 6 0.01
64 29 0.07
65 6 0.01
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
TTTAAAATAAATCAATATATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:370330 original size:22 final size:21
Alignment explanation
Indices: 370298--370340 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
370288 ATACTAACAA
370298 ATTATTTAAAATAAATCAATC
1 ATTATTTAAAATAAATCAATC
370319 ATTATTTTAAAATAAATCAATC
1 ATTA-TTTAAAATAAATCAATC
370341 TATACTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTATTTAAAATAAATCAATC
Found at i:370382 original size:22 final size:22
Alignment explanation
Indices: 370356--370398 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
370346 TAATAAATTA
370356 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
370378 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
370399 CAACTACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:370412 original size:26 final size:26
Alignment explanation
Indices: 370383--370482 Score: 103
Period size: 26 Copynumber: 3.6 Consensus size: 26
370373 CATATTTTAA
370383 AATAAATCAATCCATACAACTACAAT
1 AATAAATCAATCCATACAACTACAAT
* *
370409 AATAAATCAATTCATACTAA-TAAATTATTT
1 AATAAATCAATCCATAC-AACTACA--A--T
*
370439 AAAATAAATCAATACATACAACTACAAT
1 --AATAAATCAATCCATACAACTACAAT
370467 AATAAATCAATCCATA
1 AATAAATCAATCCATA
370483 TTTTAAAATA
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
26 34 0.56
27 2 0.03
28 2 0.03
30 2 0.03
31 2 0.03
32 19 0.31
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (26 bp):
AATAAATCAATCCATACAACTACAAT
Found at i:370574 original size:22 final size:22
Alignment explanation
Indices: 370548--370590 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
370538 TAATAAATTA
370548 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
370570 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
370591 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:370599 original size:22 final size:22
Alignment explanation
Indices: 370550--370598 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
370540 ATAAATTATT
**
370550 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
370572 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
370595 TAAA
1 TAAA
370599 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:370614 original size:246 final size:246
Alignment explanation
Indices: 370179--370880 Score: 898
Period size: 246 Copynumber: 2.9 Consensus size: 246
370169 TACAACTACA
*
370179 ATAATAAATTATTTAAAATAAATCAAT-CTATACAACTACAATAATAAATCAATTTATATTTTAA
1 ATAATAAATTATTTAAAATAAATCAATACTATACAACTACAATAATAAATCAATTCATATTTTAA
* * *
370243 AATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATATATACTAACAAATTATTTAAA
66 AATAAATCAATCAATACAAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTATTTAAA
*
370308 ATAAATCAAT-CATTATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
131 ATAAATCAATCCA-TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
370372 CCATATTTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATTCAT
195 CCATATTTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCAT
*
370424 ACTAATAAATTATTTAAAATAAATCAATAC-ATACAACTACAATAATAAATCAATCCATATTTTA
1 A-TAATAAATTATTTAAAATAAATCAATACTATACAACTACAATAATAAATCAATTCATATTTTA
* *
370488 AAATAAATCAATCTATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
65 AAATAAATCAATCAATACAAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTATTTAA
370553 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
130 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
370618 CCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACACTAATAAATCAATCCAT
195 -C---C--AT--A-T-TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCAT
** * * * * **
370680 ATTTTAAA--A--T-AAATTAATCTATACTAATA-AATTATTTAA-AATAAATCAATTCATACAA
1 ATAATAAATTATTTAAAATAAATCAATACT-ATACAACTA--CAATAATAAATCAATTCATA-TT
* * * *
370738 CTACAAT-AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCTATACTAATAAATTATT
62 TTAAAATAAATCAATCAATACAAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTATT
* *
370796 TAAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAAATATTTTAAAATAAAT
127 TAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA-TTTAAAATAAAT
*
370861 CAATCCATATTTTATAATAA
191 CAATCCATATTTTAAAATAA
370881 TTTATTTTAA
Statistics
Matches: 410, Mismatches: 28, Indels: 46
0.85 0.06 0.10
Matches are distributed among these distances:
237 9 0.02
238 1 0.00
239 1 0.00
241 2 0.00
243 1 0.00
245 1 0.00
246 264 0.64
247 21 0.05
248 1 0.00
250 15 0.04
251 6 0.01
252 29 0.07
253 8 0.02
254 1 0.00
255 6 0.01
256 44 0.11
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (246 bp):
ATAATAAATTATTTAAAATAAATCAATACTATACAACTACAATAATAAATCAATTCATATTTTAA
AATAAATCAATCAATACAAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTATTTAAA
ATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
CATATTTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCAT
Found at i:370693 original size:278 final size:275
Alignment explanation
Indices: 370238--370814 Score: 810
Period size: 278 Copynumber: 2.1 Consensus size: 275
370228 CAATTTATAT
* *
370238 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATATATACTAACAAATTAT
1 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATATATACTAACAAATAAA
* *
370303 TTAAAATAAATCAATCATTATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAAT
66 TCAAAATAAATCAA-CATTATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
***
370368 CAATCCATATTTTAAAATAAATCAATCCATACAACTACAATAATAAATCAAT-TCATACTAATAA
130 CAATCCATAAACTAAAATAAATCAATCCAT--AACTACAATAATAAATCAATCT-ATACTAATAA
370432 ATTATTTAAAATAAATCAATACATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATC
192 ATTATTTAAAATAAATCAATACATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATC
370497 AATCTATACAAATAAATTA
257 AATCTATACAAATAAATTA
* * *
370516 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT-TTTA-AAATA
1 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT--ATATACTAACAAATA
*
370579 AATCAATCCATACTAAT-AA-ATTA-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAA
64 AATCAA--AATA--AATCAACATTATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAA
* * ** *
370641 TAAATCAATTCATACAACTACACTAATAAATCAATCCAT-ATTTTAA-AATAAATTAATCTATAC
125 TAAATCAATCCATA-AACTA-A--AATAAATCAATCCATAACTACAATAATAAATCAATCTATAC
*
370704 TAATAAATTATTTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCCATATTTTAAAA
186 TAATAAATTATTTAAAATAAATCAATACATACAACTACAATAATAAATCAATCCATATTTTAAAA
*
370769 TAAATCAATCTATACTAATAAATTA
251 TAAATCAATCTATACAAATAAATTA
370794 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
370815 TTTTAAAATA
Statistics
Matches: 270, Mismatches: 18, Indels: 22
0.87 0.06 0.07
Matches are distributed among these distances:
278 229 0.85
279 13 0.05
280 8 0.03
281 2 0.01
282 18 0.07
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (275 bp):
TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATATATACTAACAAATAAA
TCAAAATAAATCAACATTATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATC
AATCCATAAACTAAAATAAATCAATCCATAACTACAATAATAAATCAATCTATACTAATAAATTA
TTTAAAATAAATCAATACATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
TATACAAATAAATTA
Found at i:370735 original size:80 final size:80
Alignment explanation
Indices: 370516--370814 Score: 411
Period size: 80 Copynumber: 3.7 Consensus size: 80
370506 AAATAAATTA
* * *** *
370516 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAA
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAAT-A
* * *
370580 ATCAATCCATACTAATAAATT
65 ATAAATCAAT-C-CAT--A-T
* *
370601 ATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACACTA
1 -TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAATA
370666 ATAAATCAATCCATAT
65 ATAAATCAATCCATAT
*
370682 TTTAAAATAAATTAATCTATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAATAA
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAATAA
370747 TAAATCAATCCATAT
66 TAAATCAATCCATAT
*
370762 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATTCATA
370815 TTTTAAAATA
Statistics
Matches: 198, Mismatches: 14, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
80 128 0.65
81 1 0.01
82 1 0.01
84 2 0.01
85 1 0.01
86 61 0.31
87 4 0.02
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (80 bp):
TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAATAA
TAAATCAATCCATAT
Found at i:370801 original size:32 final size:30
Alignment explanation
Indices: 370762--370865 Score: 107
Period size: 32 Copynumber: 3.6 Consensus size: 30
370752 CAATCCATAT
370762 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATC-ATACTAATAAA-TA
370794 TTTAAAATAAATCAATC---C--AT--AT-
1 TTTAAAATAAATCAATCATACTAATAAATA
370816 TTTAAAATAAATCAATACATACTAATAAAATA
1 TTTAAAATAAATCAAT-CATACTAAT-AAATA
370848 TTTTAAAATAAATCAATC
1 -TTTAAAATAAATCAATC
370866 CATATTTTAT
Statistics
Matches: 61, Mismatches: 0, Indels: 22
0.73 0.00 0.27
Matches are distributed among these distances:
22 16 0.26
23 2 0.03
24 1 0.02
26 3 0.05
28 3 0.05
31 2 0.03
32 18 0.30
33 16 0.26
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.36
Consensus pattern (30 bp):
TTTAAAATAAATCAATCATACTAATAAATA
Found at i:370820 original size:22 final size:22
Alignment explanation
Indices: 370794--370836 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
370784 TAATAAATTA
*
370794 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATACATAT
370816 TTTAAAATAAATCAATACATA
1 TTTAAAATAAATCAATACATA
370837 CTAATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATACATAT
Found at i:370851 original size:33 final size:35
Alignment explanation
Indices: 370812--370897 Score: 113
Period size: 33 Copynumber: 2.5 Consensus size: 35
370802 AAATCAATCC
370812 ATATTTTAAAATAAATCAATACATA-CTAATAA-A
1 ATATTTTAAAATAAATCAATACATATCTAATAATA
* * *
370845 ATATTTTAAAATAAATCAATCCATATTTTATAATA
1 ATATTTTAAAATAAATCAATACATATCTAATAATA
370880 ATTTATTTTAAAATAAAT
1 A--TATTTTAAAATAAAT
370898 TATTTTATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
33 24 0.52
34 5 0.11
35 2 0.04
37 15 0.33
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (35 bp):
ATATTTTAAAATAAATCAATACATATCTAATAATA
Found at i:370888 original size:15 final size:15
Alignment explanation
Indices: 370868--370912 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
370858 AATCAATCCA
*
370868 TATTTTATAATAATT
1 TATTTTATAATAAAT
*
370883 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
370898 TATTTTATAATAAAT
1 TATTTTATAATAAAT
370913 AACCTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTTATAATAAAT
Found at i:371397 original size:30 final size:31
Alignment explanation
Indices: 371353--371415 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
371343 CCGCTGTTAA
*
371353 AAATTTAATGCG-TTTAGTACCTAAACTATC
1 AAATTTAATGCGTTTTAATACCTAAACTATC
* * * *
371383 AAATTTGATTCGTTTTAATATCTAAACTTTC
1 AAATTTAATGCGTTTTAATACCTAAACTATC
371414 AA
1 AA
371416 TTCTTTTCGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (31 bp):
AAATTTAATGCGTTTTAATACCTAAACTATC
Found at i:377278 original size:4 final size:4
Alignment explanation
Indices: 377269--377299 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
377259 CCATCAAAAC
377269 CAAA CAAA CAAA CAAA CAAA CAAA CAAA CAA
1 CAAA CAAA CAAA CAAA CAAA CAAA CAAA CAA
377300 TGAACCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.26, G:0.00, T:0.00
Consensus pattern (4 bp):
CAAA
Found at i:379299 original size:5 final size:5
Alignment explanation
Indices: 379289--379316 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
379279 ATGAGAGAAC
379289 GGTGG GGTGG GGTGG GGTGG GGTGG GGT
1 GGTGG GGTGG GGTGG GGTGG GGTGG GGT
379317 TTAGGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.79, T:0.21
Consensus pattern (5 bp):
GGTGG
Found at i:379597 original size:2 final size:2
Alignment explanation
Indices: 379590--379646 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
379580 TTAGTTAAAC
379590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
379632 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
379647 CATTTTCACT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:385226 original size:44 final size:42
Alignment explanation
Indices: 385165--385253 Score: 108
Period size: 44 Copynumber: 2.1 Consensus size: 42
385155 GTAAAGTTAC
* *
385165 ACATACAAAATAACCCAA-TATTCAAAACACACAGAGCTTAAA
1 ACATACAAAATAACCCAACT-TACAAAACACACAAAGCTTAAA
* *
385207 ACATACACAACATAACCCAACTTACAAAACATACAAAGCTTATA
1 ACATACA-AA-ATAACCCAACTTACAAAACACACAAAGCTTAAA
385251 ACA
1 ACA
385254 CACCTTGATG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
42 7 0.17
43 2 0.05
44 30 0.75
45 1 0.03
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (42 bp):
ACATACAAAATAACCCAACTTACAAAACACACAAAGCTTAAA
Found at i:387397 original size:31 final size:33
Alignment explanation
Indices: 387341--387404 Score: 87
Period size: 31 Copynumber: 1.9 Consensus size: 33
387331 GTCCACTGTG
*
387341 AGACTAAAACTAATTAAAAATTTAGATATTAAAAT
1 AGACTAAAACTAATT--AAATTTAGATACTAAAAT
387376 AGACTAAAACTAA-T-AATTTAGATACTAAA
1 AGACTAAAACTAATTAAATTTAGATACTAAA
387405 CACTTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 14 0.50
34 1 0.04
35 13 0.46
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.30
Consensus pattern (33 bp):
AGACTAAAACTAATTAAATTTAGATACTAAAAT
Found at i:388858 original size:2 final size:2
Alignment explanation
Indices: 388853--388887 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
388843 CCGAAAACCC
388853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
388888 ATAGGCATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:394341 original size:15 final size:15
Alignment explanation
Indices: 394321--394351 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
394311 TTTAAATTTA
394321 AAATATAAAAAAATT
1 AAATATAAAAAAATT
*
394336 AAATATAAAAATATT
1 AAATATAAAAAAATT
394351 A
1 A
394352 TTAATTATTA
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATATAAAAAAATT
Found at i:400435 original size:14 final size:14
Alignment explanation
Indices: 400416--400456 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
400406 TCTCTATATA
400416 TATATATGTGTGTG
1 TATATATGTGTGTG
400430 TATATATGTGTGTG
1 TATATATGTGTGTG
400444 TATATATGTGTGT
1 TATATATGTGTGT
400457 ATCTGTGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (14 bp):
TATATATGTGTGTG
Found at i:400435 original size:16 final size:16
Alignment explanation
Indices: 400412--400456 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
400402 TCTCTCTCTA
*
400412 TATATATATATGTGTG
1 TATATATATGTGTGTG
*
400428 TGTATATATGTGTGTG
1 TATATATATGTGTGTG
*
400444 TATATATGTGTGT
1 TATATATATGTGT
400457 ATCTGTGTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (16 bp):
TATATATATGTGTGTG
Found at i:400465 original size:12 final size:12
Alignment explanation
Indices: 400418--400465 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
400408 TCTATATATA
400418 TATATGTGTGTG
1 TATATGTGTGTG
400430 TATATATGTGTGTG
1 --TATATGTGTGTG
*
400444 TATATATGTGTG
1 TATATGTGTGTG
*
400456 TATCTGTGTG
1 TATATGTGTG
400466 GTGGGGGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
12 19 0.61
14 12 0.39
ACGTcount: A:0.19, C:0.02, G:0.29, T:0.50
Consensus pattern (12 bp):
TATATGTGTGTG
Found at i:402170 original size:10 final size:10
Alignment explanation
Indices: 402155--402224 Score: 56
Period size: 10 Copynumber: 6.7 Consensus size: 10
402145 ACACACTGGG
402155 CATCCGAGGC
1 CATCCGAGGC
402165 CATCCGACCGAGGC
1 CAT-C--C-GAGGC
402179 CAT-CGAGAG-
1 CATCCGAG-GC
402188 CATCCGAGGC
1 CATCCGAGGC
*
402198 CATCCG-GGAA
1 CATCCGAGG-C
402208 CATCCGAGGC
1 CATCCGAGGC
402218 CATCCGA
1 CATCCGA
402225 CCGAGGCCAT
Statistics
Matches: 49, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
9 9 0.18
10 28 0.57
11 3 0.06
13 1 0.02
14 8 0.16
ACGTcount: A:0.24, C:0.37, G:0.29, T:0.10
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:402177 original size:14 final size:14
Alignment explanation
Indices: 402158--402243 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 14
402148 CACTGGGCAT
402158 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
402172 CCGAGGCCATCGAGAGCA
1 CCGAGGCCATC---CG-A
402190 TCCGAGGCCATCCGGGAA
1 -CCGAGGCCATCC--G-A
402208 CATCCGAGGCCATCCGA
1 C--C-GAGGCCATCCGA
402225 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
402239 ACGAG
1 CCGAG
402244 CTATGCGAGG
Statistics
Matches: 58, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 27 0.47
15 1 0.02
17 4 0.07
18 4 0.07
19 12 0.21
20 10 0.17
ACGTcount: A:0.24, C:0.37, G:0.30, T:0.08
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:402213 original size:20 final size:20
Alignment explanation
Indices: 402172--402224 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
402162 GGCCATCCGA
*
402172 CCGAGGCCAT-CGAGAGCAT
1 CCGAGGCCATCCGAGAACAT
*
402191 CCGAGGCCATCCGGGAACAT
1 CCGAGGCCATCCGAGAACAT
402211 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
402225 CCGAGGCCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.25, C:0.36, G:0.30, T:0.09
Consensus pattern (20 bp):
CCGAGGCCATCCGAGAACAT
Found at i:402238 original size:10 final size:10
Alignment explanation
Indices: 402172--402224 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
402162 GGCCATCCGA
402172 CCGAGGCCAT
1 CCGAGGCCAT
402182 -CGAGAG-CAT
1 CCGAG-GCCAT
402191 CCGAGGCCAT
1 CCGAGGCCAT
*
402201 CCG-GGAACAT
1 CCGAGG-CCAT
402211 CCGAGGCCAT
1 CCGAGGCCAT
402221 CCGA
1 CCGA
402225 CCGAGGCCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
9 10 0.28
10 24 0.67
11 2 0.06
ACGTcount: A:0.25, C:0.36, G:0.30, T:0.09
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:409872 original size:21 final size:21
Alignment explanation
Indices: 409845--409979 Score: 234
Period size: 21 Copynumber: 6.4 Consensus size: 21
409835 CAAAATCGCA
409845 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
* *
409866 TTACGATAGCAATGTTCACCG
1 TTGCGATAGCACTGTTCACCG
*
409887 TTACGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
409908 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
409929 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
*
409950 TTGCGATAGCACTGTTCACCA
1 TTGCGATAGCACTGTTCACCG
409971 TTGCGATAG
1 TTGCGATAG
409980 TGATCAAAAT
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 109 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (21 bp):
TTGCGATAGCACTGTTCACCG
Found at i:410688 original size:21 final size:21
Alignment explanation
Indices: 410662--410717 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
410652 GCAATGTGAG
410662 CAGTGCTATCGCAACGATGAA
1 CAGTGCTATCGCAACGATGAA
* * *
410683 CAGTGCTATCACAACGGTGAG
1 CAGTGCTATCGCAACGATGAA
410704 CAGTGCTATCGCAA
1 CAGTGCTATCGCAA
410718 TGCGATTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (21 bp):
CAGTGCTATCGCAACGATGAA
Found at i:410733 original size:21 final size:21
Alignment explanation
Indices: 410709--410765 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
410699 GTGAGCAGTG
*
410709 CTATCGCAATGCGATTTTGGA
1 CTATCGCAATGCGATTTTAGA
* *
410730 CTATCGCATTGCGAATTTAGA
1 CTATCGCAATGCGATTTTAGA
**
410751 AAATCGCAATGCGAT
1 CTATCGCAATGCGAT
410766 AGTCAAAATC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (21 bp):
CTATCGCAATGCGATTTTAGA
Found at i:412002 original size:24 final size:24
Alignment explanation
Indices: 411970--412018 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
411960 ATTACCAACA
* *
411970 TCTGTTTGTCCCGATGTTAATATC
1 TCTGATTGTCCCGAGGTTAATATC
* *
411994 TCTGATTGTCTCGAGGTTATTATC
1 TCTGATTGTCCCGAGGTTAATATC
412018 T
1 T
412019 TTGTTGTAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.47
Consensus pattern (24 bp):
TCTGATTGTCCCGAGGTTAATATC
Found at i:414751 original size:59 final size:60
Alignment explanation
Indices: 414686--414806 Score: 156
Period size: 59 Copynumber: 2.0 Consensus size: 60
414676 AACATAATGA
* * *
414686 ATAGTCGG-ATGACCATCTTGTAAATTTTAATAGTC-AGGGACTCAACAAAATAACATCTT
1 ATAGTCGGAAT-ACCATCTTATAAATTTTAATAGTCAAGAGAATCAACAAAATAACATCTT
* * * *
414745 ATAGTCGGAATACCATTTTATAACTTTTAATAGTCAAGAGAATCAACAAAGTAATATCTT
1 ATAGTCGGAATACCATCTTATAAATTTTAATAGTCAAGAGAATCAACAAAATAACATCTT
414805 AT
1 AT
414807 GGTCAGTGAA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 29 0.55
60 24 0.45
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (60 bp):
ATAGTCGGAATACCATCTTATAAATTTTAATAGTCAAGAGAATCAACAAAATAACATCTT
Found at i:414820 original size:60 final size:59
Alignment explanation
Indices: 414710--414831 Score: 142
Period size: 60 Copynumber: 2.1 Consensus size: 59
414700 ATCTTGTAAA
* *
414710 TTTTAATAGTCAGGGACTCAACAAAATAACATCTTATAGTCGGAATACCATTT-TATAAC
1 TTTTAATAGTCAGAGAATCAACAAAATAACATCTTATAGTCGGAATACCATTTATAT-AC
* * *
414769 TTTTAATAGTCAAGAGAATCAACAAAGTAATATCTTATGGTCAGTG-A-ACCATTTATATAC
1 TTTTAATAGTC-AGAGAATCAACAAAATAACATCTTATAGTC-G-GAATACCATTTATATAC
414829 TTT
1 TTT
414832 ACCCTAAAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
59 11 0.20
60 37 0.69
61 5 0.09
62 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (59 bp):
TTTTAATAGTCAGAGAATCAACAAAATAACATCTTATAGTCGGAATACCATTTATATAC
Found at i:418743 original size:29 final size:28
Alignment explanation
Indices: 418706--418788 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 28
418696 TAAAGTGTAA
418706 GTATCATATTAAATCTTTTAAAAGTACAT
1 GTATCATATTAAAT-TTTTAAAAGTACAT
* * * * *
418735 GTATTATATTAGATATTTTCATAGTACAA
1 GTATCATATTAAAT-TTTTAAAAGTACAT
*
418764 GTATCACATTAAATATTTTTAAAAG
1 GTATCATATT-AA-ATTTTTAAAAG
418789 ATAGATATTA
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
29 31 0.76
30 8 0.20
31 2 0.05
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.42
Consensus pattern (28 bp):
GTATCATATTAAATTTTTAAAAGTACAT
Found at i:418753 original size:60 final size:59
Alignment explanation
Indices: 418674--418822 Score: 153
Period size: 58 Copynumber: 2.5 Consensus size: 59
418664 TGATAGTAAA
* * ** *
418674 AGTATTATATTATACATTTTATTAAAGTGTAAGTATCATATTAAAT-CTTTTAAAAGTAC
1 AGTATTATATTAGATATTTTATTAAAGTACAAGTATCACATTAAATACTTTTAAAAG-AC
* *
418733 ATGTATTATATTAGATATTTTCA-T--AGTACAAGTATCACATTAAATATTTTTAAAAGAT
1 A-GTATTATATTAGATATTTT-ATTAAAGTACAAGTATCACATTAAATACTTTTAAAAGAC
* *
418791 AGATATTATATTGGATATTTTATAAAAGTACA
1 AG-TATTATATTAGATATTTTATTAAAGTACA
418823 TGTACAAAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
57 2 0.03
58 37 0.50
59 10 0.14
60 24 0.32
61 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (59 bp):
AGTATTATATTAGATATTTTATTAAAGTACAAGTATCACATTAAATACTTTTAAAAGAC
Found at i:419180 original size:26 final size:26
Alignment explanation
Indices: 419125--419180 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
419115 CCCTTAATTT
* * *
419125 TTTTTATTTATAATTAGGGTCCTCAT
1 TTTTTATTTATAATTAGGGCCCTAAA
419151 TTTTTATTT-TCAATTAGGGCCCTAAA
1 TTTTTATTTAT-AATTAGGGCCCTAAA
419177 TTTT
1 TTTT
419181 ATAATTTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.54
Consensus pattern (26 bp):
TTTTTATTTATAATTAGGGCCCTAAA
Found at i:419346 original size:94 final size:93
Alignment explanation
Indices: 419178--419362 Score: 205
Period size: 94 Copynumber: 2.0 Consensus size: 93
419168 GGCCCTAAAT
** * * * *
419178 TTTATAATTTCCTAAAATTTTTAGTTTTTAGCCATCTTTTTTCATTTCTCTTATTAATTATCTAA
1 TTTATAATTTAATAAAATATTTAGTTTTTAGCCA-CTTTTTCCATTTCTCGTATTAATCATCTAA
* *
419243 TTTTGAATTAAATTTAACTAAT-TTTTATA
65 TTTTAAATTAAATCTAA-TAATGTTTTATA
* *
419272 TTTATAATTTAATAAAATATTTAGTTTTT-GACC-CTATTTTCCATTTCTCGTATTTATACATTT
1 TTTATAATTTAATAAAATATTTAGTTTTTAG-CCACT-TTTTCCATTTCTCGTATTAAT-CATCT
*
419335 ATTTTTAAATTAAATCTAATAATGTTTT
63 AATTTTAAATTAAATCTAATAATGTTTT
419363 TCTTTTTTTA
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
92 2 0.03
93 23 0.30
94 51 0.67
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (93 bp):
TTTATAATTTAATAAAATATTTAGTTTTTAGCCACTTTTTCCATTTCTCGTATTAATCATCTAAT
TTTAAATTAAATCTAATAATGTTTTATA
Found at i:419624 original size:18 final size:18
Alignment explanation
Indices: 419601--419636 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
419591 TTCGCTCAGA
419601 GCCTCGAAAATGTCTGGG
1 GCCTCGAAAATGTCTGGG
419619 GCCTCGAAAATGTCTGGG
1 GCCTCGAAAATGTCTGGG
419637 ACGGCTCTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (18 bp):
GCCTCGAAAATGTCTGGG
Found at i:420484 original size:10 final size:10
Alignment explanation
Indices: 420467--420558 Score: 157
Period size: 10 Copynumber: 9.2 Consensus size: 10
420457 GATAATAAAC
*
420467 CTCTCTCTCC
1 CTCTCTCTCT
* *
420477 CTCCCTCTCC
1 CTCTCTCTCT
420487 CTCTCTCTCT
1 CTCTCTCTCT
420497 CTCTCTCTCT
1 CTCTCTCTCT
420507 CTCTCTCTCT
1 CTCTCTCTCT
420517 CTCTCTCTCT
1 CTCTCTCTCT
420527 CTCTCTCTCT
1 CTCTCTCTCT
420537 CTCTCTCTCT
1 CTCTCTCTCT
420547 CTCTCTCTCT
1 CTCTCTCTCT
420557 CT
1 CT
420559 TACCACTAAT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 79 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (10 bp):
CTCTCTCTCT
Found at i:420488 original size:6 final size:6
Alignment explanation
Indices: 420467--420558 Score: 157
Period size: 6 Copynumber: 15.3 Consensus size: 6
420457 GATAATAAAC
* * *
420467 CTCTCT CTCCCT CCCTCT CCCTCT CTCTCT CTCTCT CTCTCT CTCTCT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
420515 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CT
420559 TACCACTAAT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 82 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (6 bp):
CTCTCT
Found at i:420494 original size:4 final size:4
Alignment explanation
Indices: 420467--420558 Score: 157
Period size: 4 Copynumber: 23.0 Consensus size: 4
420457 GATAATAAAC
* * *
420467 CTCT CTCT CCCT CCCT CTCC CTCT CTCT CTCT CTCT CTCT CTCT CTCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
420515 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
420559 TACCACTAAT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 84 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (4 bp):
CTCT
Found at i:426598 original size:76 final size:76
Alignment explanation
Indices: 426396--426600 Score: 267
Period size: 75 Copynumber: 2.7 Consensus size: 76
426386 CCGTTGTACA
* * *
426396 AGGGGGGAATCGGTACCCCCT-TGGGGGG-ATCGGTTCCCTCCGAGC-ATACTGGAATTCTCGGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAAT-CTGGAAATCTCGGA
** *
426458 ACAAAACTGTTT
65 ACAAAACCATTC
426470 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAG-AATTCTGGAAATCTCGGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAA-TCTGGAAATCTCGGA
* *
426533 GCCAAACCATTC
65 ACAAAACCATTC
* *
426545 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGATTCCCTCTGAGCAATCTGGAA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAA
426601 TTTTTGGCTT
Statistics
Matches: 115, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
74 24 0.21
75 61 0.53
76 28 0.24
77 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.23
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGAA
CAAAACCATTC
Found at i:433343 original size:117 final size:118
Alignment explanation
Indices: 433123--433344 Score: 299
Period size: 117 Copynumber: 1.9 Consensus size: 118
433113 CTTTCAAATC
*
433123 AAAATTTTCTTTTTCAATACTTTCAAATTTTATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTT
1 AAAATTTTCTTTTTCAATACTTTCAAATTTTATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* *
433188 CATTTTGATTTTCAAAATCTATTTTCGTTTCTAGAAGAAGTTTGTTTAATTTG
66 CATTTTGATTTTCAAAATCTATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
* * * *
433241 AAAA-TTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACT-CTTTTCTCAACAT
1 AAAATTTTCTTTTTCAATA-CTTTCAAATTTTATTTTTGAAAGCTCTAAATCCTTCT-TCAACAT
* * *
433303 TTCATTTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
64 TTCATTTTGATTTTCAAAATCTATTTTAG-TTTCTAAAAGAAG
433345 ATCATTTTTA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
116 5 0.05
117 78 0.86
118 8 0.09
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (118 bp):
AAAATTTTCTTTTTCAATACTTTCAAATTTTATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
CATTTTGATTTTCAAAATCTATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
Found at i:434852 original size:76 final size:76
Alignment explanation
Indices: 434651--434854 Score: 279
Period size: 75 Copynumber: 2.7 Consensus size: 76
434641 CGTTGTACAA
* * * *
434651 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGC-ATACTGGAATTCTCGGAAC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAAT-CTGGAAATCTCGGAAC
** *
434714 AAAACTGTTTAG
65 AAAACCATTCAG
* * *
434726 GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGAACA
434790 AAACCATTCAG
66 AAACCATTCAG
*
434801 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAA
434855 TTTTTGGCTT
Statistics
Matches: 114, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
75 82 0.72
76 32 0.28
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.23
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGAACA
AAACCATTCAG
Found at i:435789 original size:22 final size:22
Alignment explanation
Indices: 435764--435814 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
435754 TCTAAACCAT
435764 TTGACATAAAACGCTCACACCC
1 TTGACATAAAACGCTCACACCC
435786 TTGACATAAAACGCTCACACCC
1 TTGACATAAAACGCTCACACCC
*
435808 TTAACAT
1 TTGACAT
435815 TTTTGATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.33, G:0.08, T:0.22
Consensus pattern (22 bp):
TTGACATAAAACGCTCACACCC
Found at i:438432 original size:21 final size:20
Alignment explanation
Indices: 438395--438435 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
438385 CTATAGAAAA
* *
438395 TATATTTTTTATTTTTTAAT
1 TATAATTTTTATATTTTAAT
438415 TATAATTTTTATCATTTTAAT
1 TATAATTTTTAT-ATTTTAAT
438436 ACATAATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TATAATTTTTATATTTTAAT
Found at i:438441 original size:22 final size:20
Alignment explanation
Indices: 438400--438447 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
438390 GAAAATATAT
* *
438400 TTTTTATTTTTTAATTATAA
1 TTTTTATATTTTAATCATAA
438420 TTTTTATCATTTTAATACATAA
1 TTTTTAT-ATTTTAAT-CATAA
*
438442 TCTTTA
1 TTTTTA
438448 AAAAATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 7 0.30
21 7 0.30
22 9 0.39
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTATATTTTAATCATAA
Found at i:439134 original size:31 final size:31
Alignment explanation
Indices: 439036--439126 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
439026 CAATTTAAGG
439036 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
439067 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
439098 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
439127 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:439290 original size:21 final size:21
Alignment explanation
Indices: 439266--439307 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
439256 ATTTGAATAT
**
439266 TATGAAGGGGTATTGATTCCC
1 TATGAAGGGGTACCGATTCCC
439287 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
439308 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:439370 original size:21 final size:21
Alignment explanation
Indices: 439336--439375 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
439326 TTTGAGTAGA
*
439336 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
439358 AAAAT-ATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
439376 ATATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 1 0.06
22 5 0.29
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:439629 original size:34 final size:32
Alignment explanation
Indices: 439590--439659 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
439580 TTTTGTAAAG
*
439590 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
439624 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
439656 GGGA
1 GGGA
439660 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:443377 original size:17 final size:17
Alignment explanation
Indices: 443355--443388 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
443345 CCGGTCCATT
443355 TGAACTGGACCATTGAC
1 TGAACTGGACCATTGAC
* *
443372 TGAACTTGACCGTTGAC
1 TGAACTGGACCATTGAC
443389 CGTTTATACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (17 bp):
TGAACTGGACCATTGAC
Done.