Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007894.1 Hibiscus syriacus cultivar Beakdansim tig00110279_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: 1425917
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:263839 original size:12 final size:12
Alignment explanation
Indices: 263818--263851 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
263808 GGTTGTGGGT
*
263818 TTTGAGATTGTG
1 TTTGATATTGTG
263830 TTTGATATTGTG
1 TTTGATATTGTG
*
263842 TTTGGTATTG
1 TTTGATATTG
263852 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:264699 original size:19 final size:20
Alignment explanation
Indices: 264658--264730 Score: 85
Period size: 19 Copynumber: 3.6 Consensus size: 20
264648 TTAAATTCGT
* *
264658 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTGAAATTCTA
*
264678 GTTTCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCTA
**
264697 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-CTA
264718 GTTGCGAATTTGA
1 GTTGCGAATTTGA
264731 GTTTTGTGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.37
20 16 0.35
21 13 0.28
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCTA
Found at i:264761 original size:20 final size:20
Alignment explanation
Indices: 264697--264832 Score: 109
Period size: 20 Copynumber: 6.8 Consensus size: 20
264687 TTGAAATTCA
*
264697 GTTGCGAATTTGA-AATTCCGC
1 GTTGCGAATTTGACTA-T-CGC
* * * *
264718 GTTGCGAATTTGAGTTTTGT
1 GTTGCGAATTTGACTATCGC
*
264738 GTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
* *
264758 GTTGCGAATTTTACT-TCTGT
1 GTTGCGAATTTGACTATC-GC
* *
264778 GTTGCG-ATTT-ACAAATTCAC
1 GTTGCGAATTTGAC-TA-TCGC
264798 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
264818 GTTGCGAATTTGACT
1 GTTGCGAATTTGACT
264833 TATGTGTTGC
Statistics
Matches: 91, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
18 2 0.02
19 6 0.07
20 60 0.66
21 21 0.23
22 2 0.02
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:264859 original size:20 final size:20
Alignment explanation
Indices: 264776--264904 Score: 113
Period size: 20 Copynumber: 6.5 Consensus size: 20
264766 TTTTACTTCT
264776 GTGTTGCGATTTACAAATTC
1 GTGTTGCGATTTACAAATTC
** *
264796 ACGTTGCGAATTTGAC-TA-TC
1 GTGTTGCG-ATTT-ACAAATTC
* **
264816 GCGTTGCGAATTTGACTTA-T-
1 GTGTTGCG-ATTT-ACAAATTC
264836 GTGTTGCGATTTACAAATTC
1 GTGTTGCGATTTACAAATTC
*
264856 GTGTTGCGATTTACAGATTC
1 GTGTTGCGATTTACAAATTC
*
264876 GTGTTGCGATTTACAGATTC
1 GTGTTGCGATTTACAAATTC
*
264896 GCGTTGCGA
1 GTGTTGCGA
264905 AATTGGAAAC
Statistics
Matches: 95, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
18 3 0.03
19 5 0.05
20 77 0.81
21 8 0.08
22 2 0.02
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (20 bp):
GTGTTGCGATTTACAAATTC
Found at i:264862 original size:60 final size:60
Alignment explanation
Indices: 264736--264864 Score: 213
Period size: 60 Copynumber: 2.1 Consensus size: 60
264726 TTTGAGTTTT
* * *
264736 GTGTTGCAAATTTGACTATCGCGTTGCGAATTTTACTTCTGTGTTGCGATTTACAAATTC
1 GTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTC
**
264796 ACGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTC
1 GTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTC
264856 GTGTTGCGA
1 GTGTTGCGA
264865 TTTACAGATT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (60 bp):
GTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTC
Found at i:264945 original size:20 final size:20
Alignment explanation
Indices: 264892--264945 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
264882 CGATTTACAG
264892 ATTCGCGTTGCGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
* *
264912 A-ACTGGGTTGCGAAATTGGA
1 ATTC-GCGTTGCGAAATTGGA
*
264932 ATTCGCGTTACGAA
1 ATTCGCGTTGCGAA
264946 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:270591 original size:32 final size:31
Alignment explanation
Indices: 270551--270618 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
270541 AATATATATG
*
270551 ATCA-TTTTAGTTTTTATTTAATTAGGAT-AT
1 ATCACTTTTA-TTTTTATTTAATTAAGATGAT
270581 ACTCACTTTTATTTTTATTTAATTAAGATGAT
1 A-TCACTTTTATTTTTATTTAATTAAGATGAT
270613 ATCACT
1 ATCACT
270619 AAGGGTTAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
30 1 0.03
31 25 0.74
32 8 0.24
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.53
Consensus pattern (31 bp):
ATCACTTTTATTTTTATTTAATTAAGATGAT
Found at i:271609 original size:16 final size:16
Alignment explanation
Indices: 271573--271618 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
271563 AATCAAAATA
*
271573 CAAAATAATTCAAGCT
1 CAAAATAATTCAAACT
271589 C-AAATAA-TCGAAACT
1 CAAAATAATTC-AAACT
*
271604 CAAAATAACTCAAAC
1 CAAAATAATTCAAAC
271619 AAAATGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 11 0.42
17 2 0.08
ACGTcount: A:0.54, C:0.22, G:0.04, T:0.20
Consensus pattern (16 bp):
CAAAATAATTCAAACT
Found at i:274681 original size:19 final size:19
Alignment explanation
Indices: 274641--274682 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
274631 ATTTCTTTTA
**
274641 TTTTCTTTTCATGTTTTCG
1 TTTTCTTTTCATGTTTAAG
274660 TTTTCGTTTTCAT-TTTAAG
1 TTTTC-TTTTCATGTTTAAG
274679 TTTT
1 TTTT
274683 TAAACATGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.10, C:0.12, G:0.10, T:0.69
Consensus pattern (19 bp):
TTTTCTTTTCATGTTTAAG
Found at i:276411 original size:21 final size:21
Alignment explanation
Indices: 276386--276448 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
276376 ATGTAGTCCT
276386 TTATTAGTATTTATTTTTATA
1 TTATTAGTATTTATTTTTATA
* *
276407 TTATTTGTCA--TATTTGTATA
1 TTATTAGT-ATTTATTTTTATA
*
276427 TTA-TAATATTATATTTTTATA
1 TTATTAGTATT-TATTTTTATA
276448 T
1 T
276449 AGTTTAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 12 0.36
21 17 0.52
22 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (21 bp):
TTATTAGTATTTATTTTTATA
Found at i:280246 original size:22 final size:22
Alignment explanation
Indices: 280189--280247 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
280179 ACGCGATTCT
280189 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
280211 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
280232 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
280248 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:280288 original size:40 final size:40
Alignment explanation
Indices: 280232--280327 Score: 165
Period size: 40 Copynumber: 2.4 Consensus size: 40
280222 GCGATTTTCC
280232 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
* * *
280272 GACTATTGCAACGCGAATATGTAAATCGCAATGCGATTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
280312 GACTATCGCAATGCGA
1 GACTATCGCAATGCGA
280328 TTCTGACTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (40 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
Found at i:280328 original size:20 final size:20
Alignment explanation
Indices: 280232--280337 Score: 108
Period size: 20 Copynumber: 5.3 Consensus size: 20
280222 GCGATTTTCC
280232 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGAATAT
* *
280252 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAATGCGAATAT
* *
280272 GACTATTGCAACGCGAATAT
1 GACTATCGCAATGCGAATAT
* *
280292 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGAATAT
* *
280312 GACTATCGCAATGCGATTCT
1 GACTATCGCAATGCGAATAT
280332 GACTAT
1 GACTAT
280338 TACAACGCGA
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.03
20 66 0.94
21 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (20 bp):
GACTATCGCAATGCGAATAT
Found at i:280347 original size:20 final size:20
Alignment explanation
Indices: 280304--280363 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
280294 AAATCGCAAT
* * *
280304 GCGATTATGACTATCGCAAT
1 GCGATTCTGACTATCACAAC
*
280324 GCGATTCTGACTATTACAAC
1 GCGATTCTGACTATCACAAC
*
280344 GCGATTCTGACTGTCACAAC
1 GCGATTCTGACTATCACAAC
280364 ACTGAATTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (20 bp):
GCGATTCTGACTATCACAAC
Found at i:283500 original size:18 final size:18
Alignment explanation
Indices: 283477--283512 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
283467 AAGCAAAAGG
*
283477 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
283495 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
283513 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:283715 original size:20 final size:20
Alignment explanation
Indices: 283690--283930 Score: 211
Period size: 20 Copynumber: 12.7 Consensus size: 20
283680 CACATTCATT
*
283690 TGACTATCGCAACGTGAATA
1 TGACTATCGCAACGCGAATA
283710 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
283730 TGACTATTGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
283747 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*
283764 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAATA
*
283784 TGACTATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
283801 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*** *
283818 TGACTATCGCAACATAAAAA
1 TGACTATCGCAACGCGAATA
*
283838 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
*
283858 TGACTATCGCAACTCGAA-A
1 TGACTATCGCAACGCGAATA
* *
283877 TGACTATCGCAATGCGAATT
1 TGACTATCGCAACGCGAATA
* * *
283897 TGATTATCGCAACGGGAATT
1 TGACTATCGCAACGCGAATA
283917 TGACTATCGCAACG
1 TGACTATCGCAACG
283931 AGAAAATCGC
Statistics
Matches: 180, Mismatches: 28, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
14 15 0.08
15 2 0.01
16 2 0.01
17 8 0.04
18 2 0.01
19 18 0.10
20 133 0.74
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:283767 original size:54 final size:54
Alignment explanation
Indices: 283695--283913 Score: 244
Period size: 54 Copynumber: 4.0 Consensus size: 54
283685 TCATTTGACT
* * * * *
283695 ATCGCAACGTGAATATGACTATCGCAACGCGAATATGACTATTGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGGGATA
283749 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGGGATA
*** *
283803 ATCGCAATGCGAAAATGACTATCGCAACATAAAAATGACTATCGCAACGCGAATTTGA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACG-GGA--T-A
* ** *
283861 CTATCGCAACT-CG-AAATGACTATCGCAATGCGAATTTGATTATCGCAACGGGA
1 --ATCGCAA-TGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGGGA
283914 ATTTGACTAT
Statistics
Matches: 141, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
54 95 0.67
55 2 0.01
57 1 0.01
58 3 0.02
59 30 0.21
60 9 0.06
61 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (54 bp):
ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGGGATA
Found at i:284105 original size:36 final size:34
Alignment explanation
Indices: 284065--284144 Score: 114
Period size: 30 Copynumber: 2.4 Consensus size: 34
284055 TCAACTTTTA
284065 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAA--ACAAATAAGAATTATTTACAC
284101 ATCAATT----AAACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAACAAATAAGAATTATTTACAC
284131 ATCAATTAAACAAA
1 ATCAATTAAACAAA
284145 TCAACTCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
30 28 0.70
32 2 0.05
34 3 0.08
36 7 0.17
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (34 bp):
ATCAATTAAACAAACAAATAAGAATTATTTACAC
Found at i:284114 original size:30 final size:30
Alignment explanation
Indices: 284080--284145 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
284070 TTAAACAAGC
284080 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
284110 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
284140 ACAAAT
1 ACAAAT
284146 CAACTCTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.29
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:285616 original size:42 final size:42
Alignment explanation
Indices: 285537--285629 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
285527 CCTCTTCAAC
* * *
285537 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
285579 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
285621 GATGACAGG
1 GATGACAGG
285630 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:286151 original size:20 final size:20
Alignment explanation
Indices: 286126--286201 Score: 143
Period size: 20 Copynumber: 3.8 Consensus size: 20
286116 TCGCAACACG
286126 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
286146 AATGACTATCACAACGCGAA
1 AATGACTATCGCAACGCGAA
286166 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
286186 AATGACTATCGCAACG
1 AATGACTATCGCAACG
286202 AGAGAATCAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.41, C:0.25, G:0.18, T:0.16
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:288211 original size:20 final size:20
Alignment explanation
Indices: 288188--288260 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
288178 GAAACTTAAA
*
288188 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
288208 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
**
288228 ATCGCAACGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
288247 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
288261 CTAAAATCGC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.33
20 30 0.67
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:288252 original size:19 final size:19
Alignment explanation
Indices: 288185--288271 Score: 86
Period size: 20 Copynumber: 4.5 Consensus size: 19
288175 TCTGAAACTT
*
288185 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
** *
288205 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAA-ATG
**
288225 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
288244 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAA-TG
288263 AAAATCGCA
1 AAAATCGCA
288272 TTGCGATTCT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
19 28 0.48
20 30 0.52
ACGTcount: A:0.44, C:0.24, G:0.17, T:0.15
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:288683 original size:22 final size:22
Alignment explanation
Indices: 288657--288699 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
288647 GAGATAGACG
288657 GATTTCGCCGGAGATGGGGACT
1 GATTTCGCCGGAGATGGGGACT
*
288679 GATTTCGTCGGAGATGGGGAC
1 GATTTCGCCGGAGATGGGGAC
288700 GTATATCGCC
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:0.19, C:0.16, G:0.42, T:0.23
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACT
Found at i:288906 original size:20 final size:20
Alignment explanation
Indices: 288873--288987 Score: 131
Period size: 20 Copynumber: 5.7 Consensus size: 20
288863 GCGCTTTGAA
*
288873 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
288893 CATCGCGTTACGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
288913 AAATCGCGTTGCGATAGTCAA
1 -AATCGCGTTGCGATAGTCAG
* *
288934 AATCTCGTTGCGATAGTGAG
1 AATCGCGTTGCGATAGTCAG
* *
288954 AATCGCTTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* *
288974 ACTCGCATTGCGAT
1 AATCGCGTTGCGAT
288988 TTACATATTC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 62 0.78
21 17 0.22
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:288929 original size:41 final size:41
Alignment explanation
Indices: 288872--288972 Score: 132
Period size: 41 Copynumber: 2.5 Consensus size: 41
288862 GGCGCTTTGA
**
288872 AAATCGCATTGCGATAGTCAGCATCGCGTTACGATAGTCAG
1 AAATCGCATTGCGATAGTCAAAATCGCGTTACGATAGTCAG
* * * *
288913 AAATCGCGTTGCGATAGTCAAAATCTCGTTGCGATAGTGAG
1 AAATCGCATTGCGATAGTCAAAATCGCGTTACGATAGTCAG
*
288954 -AATCGCTTTGCGATAGTCA
1 AAATCGCATTGCGATAGTCA
288973 TACTCGCATT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 18 0.34
41 35 0.66
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (41 bp):
AAATCGCATTGCGATAGTCAAAATCGCGTTACGATAGTCAG
Found at i:289121 original size:19 final size:19
Alignment explanation
Indices: 289097--289147 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
289087 CGATACCGGA
*
289097 GATCGCGTTGCGAATTATC
1 GATCGCATTGCGAATTATC
289116 GATCGCATTGCGAATTATC
1 GATCGCATTGCGAATTATC
289135 GATCGCATTGCGA
1 GATCGCATTGCGA
289148 TTTAGTTGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (19 bp):
GATCGCATTGCGAATTATC
Found at i:292373 original size:174 final size:169
Alignment explanation
Indices: 292148--292515 Score: 444
Period size: 169 Copynumber: 2.1 Consensus size: 169
292138 TTTAGTACCA
* * * * * *
292148 AAACTATCAGTTTTTGTATGCTTTAGTA-CATAAATTT-TCATTTTGTTCAAAACTCAACGTTAA
1 AAACTATCAATTTTGGTCTGTTTTAGTATC-TAAATTTCT-TTTTTATTCAAAACTCAACGTTAA
* * *
292211 ATTTTGAATATGG-TACTAAAATGAAACAAAAACTAAATTTTTTTAATGAC-GG-GCTAAAATGA
64 ATTTTGAA-AGGGATACTAAAATG----AAAAA--AAA-GTTTTTAATGACGGGAGCTAAAATAA
292273 AACATGA-TCTCTACATTTTATTTTAGGGCAAATTACACATTTAATACAT
121 AACAT-ACTCTCTACATTTTATTTTAGGGCAAATTACACATTTAATACAT
*
292322 ATACTATCAATTTTGG-CTTGTTTTAGTATCTAAATTTCTTTTTTATTCAAAACTCAACGTTAAA
1 AAACTATCAATTTTGGTC-TGTTTTAGTATCTAAATTTCTTTTTTATTCAAAACTCAACGTTAAA
*
292386 TTTTGAACGGGATACTAAAATGAAAAAAAAGTTTTTAATGACGGGAGCTAAAATAAAACATACTC
65 TTTTGAAAGGGATACTAAAATGAAAAAAAAGTTTTTAATGACGGGAGCTAAAATAAAACATACTC
* * *
292451 TCTATATTTTATTTTAGGGTAAATTACACATTTAATACTT
130 TCTACATTTTATTTTAGGGCAAATTACACATTTAATACAT
*
292491 AAACTATCGATTTTGGTCTGTTTTA
1 AAACTATCAATTTTGGTCTGTTTTA
292516 ATTCCTAAAC
Statistics
Matches: 170, Mismatches: 16, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
167 11 0.06
168 6 0.04
169 74 0.44
170 6 0.04
173 2 0.01
174 69 0.41
175 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.39
Consensus pattern (169 bp):
AAACTATCAATTTTGGTCTGTTTTAGTATCTAAATTTCTTTTTTATTCAAAACTCAACGTTAAAT
TTTGAAAGGGATACTAAAATGAAAAAAAAGTTTTTAATGACGGGAGCTAAAATAAAACATACTCT
CTACATTTTATTTTAGGGCAAATTACACATTTAATACAT
Found at i:294800 original size:37 final size:37
Alignment explanation
Indices: 294749--294845 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
294739 CCTTTTCGTC
* *
294749 CTACTAGGATTCAAACTCTTAAAACTAGGATAGAATT
1 CTACTAGGATTCAAACTCATAAAAATAGGATAGAATT
* * *
294786 TTACTAGGATTCAAACTCATAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCATAAAAATAGGATAGAATT
* * *
294823 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCATAAA
294846 GATATGATCC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCATAAAAATAGGATAGAATT
Found at i:295412 original size:2 final size:2
Alignment explanation
Indices: 295392--295430 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
295382 TTTTTAATAC
* *
295392 TA TA TT TA T- TA TT 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
295431 ATGTTTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:295651 original size:16 final size:19
Alignment explanation
Indices: 295637--295686 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
295627 TTTTTTATTT
295637 ATATTA-TATTATATTTTC
1 ATATTATTATTATATTTTC
295655 ATATTATTATTATTATTGTT-
1 ATATTATTATTA-TATT-TTC
295675 ATGATTATTATT
1 AT-ATTATTATT
295687 TTTCTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.21
19 5 0.18
20 6 0.21
21 11 0.39
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (19 bp):
ATATTATTATTATATTTTC
Found at i:295735 original size:4 final size:4
Alignment explanation
Indices: 295722--295751 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
295712 TATATTTTAA
295722 TATT TCATT TATT TATT TATT TATT TATT T
1 TATT T-ATT TATT TATT TATT TATT TATT T
295752 TTCCTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:300039 original size:21 final size:21
Alignment explanation
Indices: 300015--300076 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
300005 AACAAAAAGG
300015 GAAAAAATAAACAAAAAAG-AA
1 GAAAAAA-AAACAAAAAAGAAA
* *
300036 GAAAACAAAAGAAAAAAGAAA
1 GAAAAAAAAACAAAAAAGAAA
* *
300057 GAACAAAAATC-AAAAAGAAA
1 GAAAAAAAAACAAAAAAGAAA
300077 AAGGGACAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 19 0.56
21 15 0.44
ACGTcount: A:0.79, C:0.06, G:0.11, T:0.03
Consensus pattern (21 bp):
GAAAAAAAAACAAAAAAGAAA
Found at i:300040 original size:19 final size:19
Alignment explanation
Indices: 300005--300078 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 19
299995 ATTCAATCAG
* *
300005 AACAAAAAGGGAAAAAA-TA
1 AACAAAAA-AGAAAAAACAA
300024 AACAAAAAAGAAGAAAACAA
1 AACAAAAAAGAA-AAAACAA
* *
300044 AAGAAAAAAGAAAGAACAA
1 AACAAAAAAGAAAAAACAA
300063 AA-ATCAAAAAGAAAAA
1 AACA--AAAAAGAAAAA
300079 GGGACAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
18 4 0.09
19 20 0.43
20 22 0.48
ACGTcount: A:0.78, C:0.07, G:0.12, T:0.03
Consensus pattern (19 bp):
AACAAAAAAGAAAAAACAA
Found at i:300057 original size:11 final size:11
Alignment explanation
Indices: 300015--300064 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
300005 AACAAAAAGG
*
300015 GAAAAAATAAA
1 GAAAAAAGAAA
*
300026 CAAAAAAG-AA
1 GAAAAAAGAAA
*
300036 GAAAACA-AAA
1 GAAAAAAGAAA
300046 GAAAAAAGAAA
1 GAAAAAAGAAA
300057 GAACAAAA
1 GAA-AAAA
300065 ATCAAAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 15 0.48
11 12 0.39
12 4 0.13
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:300077 original size:13 final size:13
Alignment explanation
Indices: 300023--300078 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
300013 GGGAAAAAAT
300023 AAACAAAAAAGAAGA
1 AAAC-AAAAAGAA-A
300038 AAAC-AAAAGAAA
1 AAACAAAAAGAAA
* *
300050 AAAGAAAGAACAAA
1 AAACAAA-AAGAAA
*
300064 AATCAAAAAGAAA
1 AAACAAAAAGAAA
300077 AA
1 AA
300079 GGGACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 4 0.12
13 16 0.47
14 10 0.29
15 4 0.12
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.02
Consensus pattern (13 bp):
AAACAAAAAGAAA
Found at i:300759 original size:22 final size:22
Alignment explanation
Indices: 300686--300762 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
300676 GCTACCCCAT
* *
300686 CAAACCATTGAGCATTAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
300708 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
300730 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
300752 CAAACCTTTGA
1 CAAACCTTTGA
300763 CCAAACATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.22
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:300982 original size:24 final size:24
Alignment explanation
Indices: 300954--301014 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
300944 GGGACAATAT
*
300954 TTTCAAAACTTTTAATTAAACATC
1 TTTCAAAACTCTTAATTAAACATC
*
300978 TTTCAAAACTCTTGATTAAACATC
1 TTTCAAAACTCTTAATTAAACATC
**
301002 TTTTGAAACTCTT
1 TTTCAAAACTCTT
301015 TATTGATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.43
Consensus pattern (24 bp):
TTTCAAAACTCTTAATTAAACATC
Found at i:301780 original size:106 final size:106
Alignment explanation
Indices: 301590--302223 Score: 982
Period size: 106 Copynumber: 6.0 Consensus size: 106
301580 ATATCGTGCT
* * * *
301590 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
301655 AATTTCAGAGCCAATTTCAACTTCACAACGAAGAATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
301696 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTACC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT-CC
*
301760 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
301802 ACTCTAGACAACGCAAGTTCAACATCACAACGAATGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
301867 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
301908 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
301973 AATTTCAGAGCCAATTTCAACTTCATAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
** ** * *
302014 ACTTAAGACAACGCAAGTTCAACTTCACGACGAAGGGACAACTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
302079 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
302120 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
302185 AATTTCAGAGCCAATTTCAACTTTACAACGAAGGATATT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
302224 TGTAACACCC
Statistics
Matches: 482, Mismatches: 44, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
105 2 0.00
106 478 0.99
107 2 0.00
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:303010 original size:30 final size:30
Alignment explanation
Indices: 302974--303035 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
302964 GAAGGACCTT
* *
302974 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
303004 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
303034 TC
1 TC
303036 TATATGTTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:303825 original size:64 final size:64
Alignment explanation
Indices: 303717--303891 Score: 228
Period size: 64 Copynumber: 2.7 Consensus size: 64
303707 TAATGAAGGT
* * * ** *
303717 ATGCATCGATGCATTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATT-ACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-GTCATTATTAAC-GG
303780 G
64 G
* * *
303781 ATGCATCGATGCACTCCTTATGCATCGATGCATCAATTGCATTCGATGTTTCATTATTAACGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTGTCATTATTAACGGG
*
303845 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGAT
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGAT
303892 ATATTTATTT
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
63 1 0.01
64 95 0.97
65 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTGTCATTATTAACGGG
Found at i:303914 original size:64 final size:64
Alignment explanation
Indices: 303717--303940 Score: 211
Period size: 64 Copynumber: 3.5 Consensus size: 64
303707 TAATGAAGGT
* * * * ** * * * ** *
303717 ATGCATCGATGCATTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATCAATTGCATTCGATAT-TTCATTATTAAAGAG
* * * *
303781 ATGCATCGATGCACTCCTTATGCATCGATGCATCAATTGCATTCGATGTTTCATTATTAACGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATCAATTGCATTCGATATTTCATTATTAAAGAG
* *
303845 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATATATTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCATCAATTGCATTCGATAT-TTCATTATTAAAGAG
** *
303908 AGTGCATCGATGCACTACCAATGCATCGGTGCA
1 A-TGCATCGATGCACTACTTATGCATCGATGCA
303941 CATTCAAACA
Statistics
Matches: 137, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
63 3 0.02
64 129 0.94
65 5 0.04
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATCAATTGCATTCGATATTTCATTATTAAAGAG
Found at i:307660 original size:30 final size:30
Alignment explanation
Indices: 307624--307687 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
307614 GAAGGACCTG
* *
307624 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
307654 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
307684 TCCA
1 TCCA
307688 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:308475 original size:64 final size:64
Alignment explanation
Indices: 308367--308541 Score: 226
Period size: 64 Copynumber: 2.7 Consensus size: 64
308357 TAATGAAGGT
* * * ** * **
308367 ATGCATCGATGCATTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTATTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-GTCATTATTAACGGG
* * *
308431 ATGCATCGATGCACTCCTTATGCATCGATGCATCAATTGCATTCGATGTTTCATTATTAACGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTGTCATTATTAACGGG
*
308495 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGAT
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGAT
308542 ATATTTATTT
Statistics
Matches: 97, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
63 1 0.01
64 96 0.99
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTGTCATTATTAACGGG
Found at i:308564 original size:64 final size:64
Alignment explanation
Indices: 308367--308590 Score: 211
Period size: 64 Copynumber: 3.5 Consensus size: 64
308357 TAATGAAGGT
* * * * ** * * * ** *
308367 ATGCATCGATGCATTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTATTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATCAATTGCATTCGATAT-TTCATTATTAAAGAG
* * * *
308431 ATGCATCGATGCACTCCTTATGCATCGATGCATCAATTGCATTCGATGTTTCATTATTAACGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATCAATTGCATTCGATATTTCATTATTAAAGAG
* *
308495 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATATATTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCATCAATTGCATTCGATAT-TTCATTATTAAAGAG
** *
308558 AGTGCATCGATGCACTACCAATGCATCGGTGCA
1 A-TGCATCGATGCACTACTTATGCATCGATGCA
308591 CATTCAAACA
Statistics
Matches: 137, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
63 3 0.02
64 129 0.94
65 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATCAATTGCATTCGATATTTCATTATTAAAGAG
Found at i:309547 original size:106 final size:106
Alignment explanation
Indices: 309362--310426 Score: 1554
Period size: 106 Copynumber: 10.1 Consensus size: 106
309352 GGATGTTACA
* *
309362 ATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
1 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
* *
309427 ATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGTAGG
66 ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
309468 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
1 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
309533 ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
66 ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
* * * * *
309574 ATATTGGACTCCAGACAACGC-AGTTCAACTTTACGAAGAAGGGACTGCTGGTTGTCAACAAACA
1 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
* * *
309638 ACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAATG
66 ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
* * * *
309679 ATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAATGGACCGCTGGTTGTCAACAAACA
1 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
* * *
309744 ATTTCCAAATTTCAGAGCCAATTTCAACTTCACAGTGAAGG
66 ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
309785 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
1 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
* *
309850 ACTTCCCAATTTCAGAGCTAATTTCAACTTCACAGGGAAGG
66 ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
* *
309891 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACA
1 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
* * *
309956 ACTTCTCAATTTTAGAGCCAATTTCAACTTCACAACGAAGG
66 ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
*
309997 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
1 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
* * *
310062 ATTTCCCAATTCCAGAGCCAATTTCAACTTCACAGCGTAGG
66 ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
*
310103 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACA
1 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
* *
310168 ACTTCCCAATTTCAGAGCCAATTTCAACTTCTCAGCGAATG
66 ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
* * * * * * * *
310209 ATCTTGGACCCAAGACAACACAAGCTCAACTTCCCGACGAAGGG-TCGACTGATTGTCAA-CAA-
1 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAAC
* *
310271 AA-TT-TC-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGG
65 AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
* * * ** * *
310309 ATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAATA
1 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
* ** * *
310374 ATTTCCCGGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGG
66 ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGG
310415 ATATTGGACTCA
1 ATATTGGACTCA
310427 GAACAATGCT
Statistics
Matches: 869, Mismatches: 80, Indels: 20
0.90 0.08 0.02
Matches are distributed among these distances:
100 76 0.09
101 5 0.01
102 3 0.00
103 4 0.00
104 3 0.00
105 102 0.12
106 676 0.78
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
Found at i:311111 original size:37 final size:37
Alignment explanation
Indices: 311061--311199 Score: 206
Period size: 37 Copynumber: 3.8 Consensus size: 37
311051 TTTCGTCCTA
311061 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTTG
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTTG
311098 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTTG
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTTG
* * * * *
311135 CTAGGATTCAAACTCTTAAAAATATGATAGAGTTCTA
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTTG
* * *
311172 CTATGATTTAAACTCCTAAAGATAGGAT
1 CTAGGATTCAAACTCCTAAAAATAGGAT
311200 CCACAAGCAC
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 92 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTTG
Found at i:311750 original size:2 final size:2
Alignment explanation
Indices: 311734--311785 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
311724 TTTTTAATAC
* *
311734 TA TA TT TA T- TA TA TA TA TA TA TA GA 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
311775 TA TA TA TA TA T
1 TA TA TA TA TA T
311786 TTAAATTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:311981 original size:16 final size:16
Alignment explanation
Indices: 311962--312020 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
311952 GTTTTTGGTT
311962 TTTTTATATTATATTA
1 TTTTTATATTATATTA
*
311978 TTTTCATATTACTATTTA
1 TTTTTATATTA-TA-TTA
* *
311996 TTGTTATAAT-TATTA
1 TTTTTATATTATATTA
*
312011 TTTTTCTATT
1 TTTTTATATT
312021 TTACTCATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
15 10 0.29
16 12 0.35
17 2 0.06
18 10 0.29
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTTTATATTATATTA
Found at i:312065 original size:4 final size:4
Alignment explanation
Indices: 312052--312139 Score: 63
Period size: 4 Copynumber: 21.2 Consensus size: 4
312042 TATATATTAA
* *
312052 TATT TCATT TATT TATT TATT TATT TATT TATT T-TT TCTTT TATTT TTTT
1 TATT T-ATT TATT TATT TATT TATT TATT TATT TATT T-ATT TA-TT TATT
* * * *
312102 TACT TATT TTTAT TCTT CATT T-TT TCATT TATT TATT T
1 TATT TATT TAT-T TATT TATT TATT T-ATT TATT TATT T
312140 TTTCCCTCTA
Statistics
Matches: 67, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
3 6 0.09
4 45 0.67
5 16 0.24
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:318201 original size:3 final size:3
Alignment explanation
Indices: 318193--318230 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
318183 CCAATTTTAT
318193 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
318231 CGAATGATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:320245 original size:31 final size:31
Alignment explanation
Indices: 320205--320278 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
320195 TAATTTTGTT
320205 ATAATCGTTAGTGACCATTTTATTACATATCG
1 ATAA-CGTTAGTGACCATTTTATTACATATCG
320237 ATAACGTTAGTGACCATTTTATTACATATCG
1 ATAACGTTAGTGACCATTTTATTACATATCG
320268 ATAACGTTAGT
1 ATAACGTTAGT
320279 AGCCGTTGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 38 0.90
32 4 0.10
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (31 bp):
ATAACGTTAGTGACCATTTTATTACATATCG
Found at i:320419 original size:3 final size:3
Alignment explanation
Indices: 320411--320435 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
320401 TTAGAATTAT
320411 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
320436 ATATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:322524 original size:60 final size:60
Alignment explanation
Indices: 322415--322528 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
322405 TTGTAAGATA
* * * ** *
322415 TTGCTTTATTGAGTTCATTGACTATTAAAAGTTACCAAATGGTCCCTCGACTATAGAGAG
1 TTGCTTTATTGAGTCCATTGACTATTAAAAGCTACAAAATAATCACTCGACTATAGAGAG
* * *
322475 TTGCTTTGTTGAGTCCCTTGACTATTAAAAGCTACAAAATAATTACTCGACTAT
1 TTGCTTTATTGAGTCCATTGACTATTAAAAGCTACAAAATAATCACTCGACTAT
322529 TCATTATGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (60 bp):
TTGCTTTATTGAGTCCATTGACTATTAAAAGCTACAAAATAATCACTCGACTATAGAGAG
Found at i:329275 original size:33 final size:36
Alignment explanation
Indices: 329233--329300 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
329223 GTGATCGATC
329233 GTTTGGTTTGCTC-A-AT-ATAGTTGCATTTTGTCG
1 GTTTGGTTTGCTCAATATGATAGTTGCATTTTGTCG
329266 GTTTGGTTTGCTCAATATGATAGTTGCATTTTGTC
1 GTTTGGTTTGCTCAATATGATAGTTGCATTTTGTC
329301 AGCCTTTAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 13 0.41
34 1 0.03
35 2 0.06
36 16 0.50
ACGTcount: A:0.16, C:0.12, G:0.24, T:0.49
Consensus pattern (36 bp):
GTTTGGTTTGCTCAATATGATAGTTGCATTTTGTCG
Found at i:331305 original size:21 final size:21
Alignment explanation
Indices: 331281--331347 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
331271 GGGGTTTAAG
*
331281 GTTTATGATTTAGGATTTAGA
1 GTTTATGATTTAGGATTGAGA
* *
331302 GTTTAAGATTTAGGATTGAGT
1 GTTTATGATTTAGGATTGAGA
* *
331323 GTTTATGGTTTAGGATAG-GA
1 GTTTATGATTTAGGATTGAGA
331343 GTTTA
1 GTTTA
331348 GGGTTTAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 6 0.15
21 33 0.85
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.45
Consensus pattern (21 bp):
GTTTATGATTTAGGATTGAGA
Found at i:332287 original size:2 final size:2
Alignment explanation
Indices: 332280--332345 Score: 87
Period size: 2 Copynumber: 33.0 Consensus size: 2
332270 TAAATGTAAC
* * *
332280 AT AT AT AT GT AT AT AT AT AT AT AT AT GT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
332322 AT AT AT AT GT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
332346 TGACATATTG
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (2 bp):
AT
Found at i:332310 original size:24 final size:24
Alignment explanation
Indices: 332281--332345 Score: 112
Period size: 24 Copynumber: 2.6 Consensus size: 24
332271 AAATGTAACA
332281 TATATATGTATATATATATATATATG
1 TATATATG--TATATATATATATATG
332307 TATATATGTATATATATATATATG
1 TATATATGTATATATATATATATG
332331 TATATATGTATATAT
1 TATATATGTATATAT
332346 TGACATATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
24 31 0.79
26 8 0.21
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (24 bp):
TATATATGTATATATATATATATG
Found at i:332353 original size:16 final size:16
Alignment explanation
Indices: 332282--332353 Score: 67
Period size: 18 Copynumber: 4.4 Consensus size: 16
332272 AATGTAACAT
*
332282 ATATATGTATATATATAT
1 ATATATGTATATAT-T-G
332300 ATATATGTATATA-TG
1 ATATATGTATATATTG
*
332315 -TATATATATATATATG
1 ATATATGTATATAT-TG
332331 TATATATGTATATATTG
1 -ATATATGTATATATTG
*
332348 ACATAT
1 ATATAT
332354 TGGGACCTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
14 11 0.24
16 8 0.17
17 2 0.04
18 25 0.54
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (16 bp):
ATATATGTATATATTG
Found at i:336284 original size:222 final size:222
Alignment explanation
Indices: 335898--336341 Score: 888
Period size: 222 Copynumber: 2.0 Consensus size: 222
335888 TTAAAAAACA
335898 TTTTGTCTTAATTTGTTATATCAAAATATTATAAAACATGATTCAACATAAAGCAACAACCGGCT
1 TTTTGTCTTAATTTGTTATATCAAAATATTATAAAACATGATTCAACATAAAGCAACAACCGGCT
335963 GACGTCGTATGTCGCCATGGCGAGGACATGAAAGGCTAAGATTAACGGACTAGGCCATAAACCGG
66 GACGTCGTATGTCGCCATGGCGAGGACATGAAAGGCTAAGATTAACGGACTAGGCCATAAACCGG
336028 AGAGCATAGCCGATACTCCATGTGAAAATGTCCCTCCAAGTCTCAAGTACGCAAAATATGCATGC
131 AGAGCATAGCCGATACTCCATGTGAAAATGTCCCTCCAAGTCTCAAGTACGCAAAATATGCATGC
336093 TTCACGTCCTGCATTGTAGGATCAGAG
196 TTCACGTCCTGCATTGTAGGATCAGAG
336120 TTTTGTCTTAATTTGTTATATCAAAATATTATAAAACATGATTCAACATAAAGCAACAACCGGCT
1 TTTTGTCTTAATTTGTTATATCAAAATATTATAAAACATGATTCAACATAAAGCAACAACCGGCT
336185 GACGTCGTATGTCGCCATGGCGAGGACATGAAAGGCTAAGATTAACGGACTAGGCCATAAACCGG
66 GACGTCGTATGTCGCCATGGCGAGGACATGAAAGGCTAAGATTAACGGACTAGGCCATAAACCGG
336250 AGAGCATAGCCGATACTCCATGTGAAAATGTCCCTCCAAGTCTCAAGTACGCAAAATATGCATGC
131 AGAGCATAGCCGATACTCCATGTGAAAATGTCCCTCCAAGTCTCAAGTACGCAAAATATGCATGC
336315 TTCACGTCCTGCATTGTAGGATCAGAG
196 TTCACGTCCTGCATTGTAGGATCAGAG
336342 GATGCCCTGA
Statistics
Matches: 222, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
222 222 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.25
Consensus pattern (222 bp):
TTTTGTCTTAATTTGTTATATCAAAATATTATAAAACATGATTCAACATAAAGCAACAACCGGCT
GACGTCGTATGTCGCCATGGCGAGGACATGAAAGGCTAAGATTAACGGACTAGGCCATAAACCGG
AGAGCATAGCCGATACTCCATGTGAAAATGTCCCTCCAAGTCTCAAGTACGCAAAATATGCATGC
TTCACGTCCTGCATTGTAGGATCAGAG
Found at i:338345 original size:16 final size:16
Alignment explanation
Indices: 338324--338373 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
338314 TATTACTCTT
338324 TTTTTTATATTATATA
1 TTTTTTATATTATATA
338340 TTTTTTAT-TATATATA
1 TTTTTTATAT-TATATA
* *
338356 TCTTATATCATTATATA
1 TTTTTTAT-ATTATATA
338373 T
1 T
338374 AGTAGATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 1 0.03
16 20 0.69
17 7 0.24
18 1 0.03
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTTATATTATATA
Found at i:338478 original size:35 final size:40
Alignment explanation
Indices: 338407--338481 Score: 97
Period size: 38 Copynumber: 2.0 Consensus size: 40
338397 GTTTACTATG
338407 TATATATTTGTTCTGAATATTATATTTTATACGTTTTTATA
1 TATATATTTGTTCTGAATATTATATTTTATA-GTTTTTATA
*
338448 TATATATTT-TT-T-AATATTCTATTTT-T-GTTTTTAT
1 TATATATTTGTTCTGAATATTATATTTTATAGTTTTTAT
338482 TTATTTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
35 8 0.24
37 1 0.03
38 12 0.36
39 1 0.03
40 2 0.06
41 9 0.27
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64
Consensus pattern (40 bp):
TATATATTTGTTCTGAATATTATATTTTATAGTTTTTATA
Found at i:338515 original size:17 final size:16
Alignment explanation
Indices: 338477--338534 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
338467 TATTTTTGTT
*
338477 TTTATTTATTTATATATA
1 TTTATTT-TTTCTAT-TA
*
338495 TTATATTTTTACT-TTA
1 TT-TATTTTTTCTATTA
338511 TTTATTTTTTCTATTA
1 TTTATTTTTTCTATTA
338527 TTT-TTTTT
1 TTTATTTTT
338535 CTTAATATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
15 14 0.40
16 10 0.29
17 1 0.03
18 5 0.14
19 5 0.14
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATTTTTTCTATTA
Found at i:338668 original size:20 final size:19
Alignment explanation
Indices: 338645--338682 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
338635 TATTTTTATT
338645 CTTTTTTAATTTCTTTTACC
1 CTTTTTTAATTT-TTTTACC
*
338665 CTTTTTTTATTTTTTTAC
1 CTTTTTTAATTTTTTTAC
338683 TCCATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (19 bp):
CTTTTTTAATTTTTTTACC
Found at i:338749 original size:10 final size:9
Alignment explanation
Indices: 338745--338810 Score: 51
Period size: 10 Copynumber: 6.9 Consensus size: 9
338735 ATTTTGTTTA
338745 TTTTTATTAT
1 TTTTTATT-T
338755 TTTTTATTAT
1 TTTTTATT-T
*
338765 TTTTTATGT
1 TTTTTATTT
* *
338774 GTTTTGTTAT
1 TTTTTATT-T
*
338784 TTTTCATTT
1 TTTTTATTT
338793 TTTCTTATTT
1 TTT-TTATTT
*
338803 TATTTATT
1 TTTTTATT
338811 ATTCTCACGT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
9 15 0.33
10 30 0.67
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (9 bp):
TTTTTATTT
Found at i:338764 original size:19 final size:19
Alignment explanation
Indices: 338714--338813 Score: 68
Period size: 19 Copynumber: 5.3 Consensus size: 19
338704 ATCTGTGTCT
**
338714 TTATTTTTTAACA-TTTTA
1 TTATTTTTTATTATTTTTA
*
338732 TTCATTTTGT-TTATTTTTA
1 TT-ATTTTTTATTATTTTTA
338751 TTATTTTTTATTA-TTTT-
1 TTATTTTTTATTATTTTTA
*
338768 TTATGTGTTTTGTTATTTTTCA
1 TTAT-T-TTTTATTATTTTT-A
338790 TT-TTTTCTTATT-TTATTTA
1 TTATTTT-TTATTATT-TTTA
338809 TTATT
1 TTATT
338814 CTCACGTTTG
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
17 4 0.06
18 14 0.22
19 30 0.46
20 14 0.22
21 1 0.02
22 2 0.03
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.74
Consensus pattern (19 bp):
TTATTTTTTATTATTTTTA
Found at i:338778 original size:29 final size:28
Alignment explanation
Indices: 338746--338813 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
338736 TTTTGTTTAT
*
338746 TTTTATTATTTTTTATTATTTT-TTATGTG
1 TTTTATTATTTTTCATT-TTTTCTTAT-TG
* *
338775 TTTTGTTATTTTTCATTTTTTCTTATTT
1 TTTTATTATTTTTCATTTTTTCTTATTG
338803 TATTTATTATT
1 T-TTTATTATT
338814 CTCACGTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 6 0.18
29 27 0.82
ACGTcount: A:0.16, C:0.03, G:0.04, T:0.76
Consensus pattern (28 bp):
TTTTATTATTTTTCATTTTTTCTTATTG
Found at i:338781 original size:39 final size:38
Alignment explanation
Indices: 338736--338809 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 38
338726 ATTTTATTCA
*
338736 TTTTGTTTATTTTT-ATTATTTT-TTATTATTTTTTATGTG
1 TTTTG-TTATTTTTCATT-TTTTCTTATT-TTATTTATGTG
338775 TTTTGTTATTTTTCATTTTTTCTTATTTTATTTAT
1 TTTTGTTATTTTTCATTTTTTCTTATTTTATTTAT
338810 TATTCTCACG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
38 19 0.59
39 13 0.41
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (38 bp):
TTTTGTTATTTTTCATTTTTTCTTATTTTATTTATGTG
Found at i:341833 original size:11 final size:11
Alignment explanation
Indices: 341817--341842 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
341807 AATTAGTGGC
341817 ATGTAATTATT
1 ATGTAATTATT
341828 ATGTAATTATT
1 ATGTAATTATT
341839 ATGT
1 ATGT
341843 TTTATTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (11 bp):
ATGTAATTATT
Found at i:344917 original size:69 final size:69
Alignment explanation
Indices: 344794--344931 Score: 190
Period size: 69 Copynumber: 2.0 Consensus size: 69
344784 GATTTAAACT
* *
344794 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAACCACTTCATTTGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
344859 TCAA
66 TCAA
* * * *
344863 ATGAGATTGATCAAGCACAATCA-TTTCTGAATTACTGCATCAC-TCTACTCGAAGATCATGGAG
1 ATGAGATTGATCAAGCACAATCATTTTC-GAATCACTGAACCACTTC-ACTCGAAGATCATAGAG
344926 CATCAA
64 CATCAA
344932 GAGAGAGACA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
68 6 0.10
69 55 0.90
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
TCAA
Found at i:345953 original size:32 final size:31
Alignment explanation
Indices: 345870--345975 Score: 113
Period size: 32 Copynumber: 3.3 Consensus size: 31
345860 ATCTTTGAAG
* * *
345870 ATTCAACATCAAATGTTGAGACATTTTTTTA
1 ATTCAACATCAAATGTTGGGGCATTTTTTGA
*
345901 GATTTAACATCAAATGTTGGGGCATTTTTTGA
1 -ATTCAACATCAAATGTTGGGGCATTTTTTGA
* * **
345933 TATTCAACATCGAATATTGGGGCATCTTTGGGA
1 -ATTCAACATCAAATGTTGGGGCAT-TTTTTGA
345966 ATTCAACATC
1 ATTCAACATC
345976 CTGATGCAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 58 0.92
33 5 0.08
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (31 bp):
ATTCAACATCAAATGTTGGGGCATTTTTTGA
Found at i:346747 original size:106 final size:106
Alignment explanation
Indices: 346595--346912 Score: 503
Period size: 106 Copynumber: 3.0 Consensus size: 106
346585 GTGCCACCCG
* * * *
346595 AGACAACACAAGTTCAACTTCACAACGAAGGGACGACTAGTTGTCAACAAATAATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTT
346660 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
*
346701 AGACACCACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTT
* * *
346766 CCA-AACCAATTTCAACTTCACAGCGAAGAATATTGGACTCG
66 -CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* * *
346807 AGACAACACAAGTTCAACTTCACAGCGAATGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTT
* *
346872 CAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
346913 GAACAATACA
Statistics
Matches: 193, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
105 2 0.01
106 189 0.98
107 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
Found at i:347683 original size:36 final size:36
Alignment explanation
Indices: 347620--347705 Score: 140
Period size: 36 Copynumber: 2.4 Consensus size: 36
347610 TTTGAATACA
* *
347620 GTTTCTCTTG-AA-ACATAAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
347654 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
347690 GTTTCTCTTGAAACAC
1 GTTTCTCTTGAAACAC
347706 CAAACCCTCG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
34 10 0.21
35 2 0.04
36 36 0.75
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (36 bp):
GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
Found at i:348916 original size:18 final size:19
Alignment explanation
Indices: 348884--348936 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
348874 TTATACGTTT
348884 TTATATATATTTTTTAATA
1 TTATATATATTTTTTAATA
* * *
348903 TTCTAT-TTTTTTTTATTA
1 TTATATATATTTTTTAATA
348921 TTATATATATTTTTTA
1 TTATATATATTTTTTA
348937 TTTTATTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATATATATTTTTTAATA
Found at i:348952 original size:37 final size:37
Alignment explanation
Indices: 348844--348957 Score: 97
Period size: 37 Copynumber: 3.0 Consensus size: 37
348834 ATTTTTTTCC
* * * *
348844 ATTATGTATATTTTTT-TCTTAATTTATATTTTATACGTT
1 ATTATATATATTTTTTATATTATTTTAT-TTTTTTA--TT
* * *
348883 TTTATATATATTTTTTAATATTCTATT-TTTTTTTATT
1 ATTATATATATTTTTT-ATATTATTTTATTTTTTTATT
*
348920 ATTATATATATTTTTTATTTTATTTTATTTTTTCTATT
1 ATTATATATATTTTTTATATTATTTTATTTTTT-TATT
348958 TTTTTTCTTA
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
36 7 0.12
37 23 0.38
38 4 0.07
39 20 0.33
40 1 0.02
41 5 0.08
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (37 bp):
ATTATATATATTTTTTATATTATTTTATTTTTTTATT
Found at i:348962 original size:17 final size:17
Alignment explanation
Indices: 348911--348952 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
348901 TATTCTATTT
*
348911 TTTTTTATTATTATATATA
1 TTTTTTATT-TTAT-TTTA
348930 TTTTTTATTTTATTTTA
1 TTTTTTATTTTATTTTA
348947 TTTTTT
1 TTTTTT
348953 CTATTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
18 4 0.18
19 9 0.41
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTATTTTATTTTA
Found at i:349049 original size:33 final size:33
Alignment explanation
Indices: 348983--349049 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
348973 ATGTATATCT
* *
348983 TTATTTTTATTTGTTTTACTTAGTATATATTTA
1 TTATTTTTATTTGTTTTACGTAGAATATATTTA
349016 TTATTTTTATTTGTTTTA-GTA-AATACTACTTTA
1 TTATTTTTATTTGTTTTACGTAGAATA-TA-TTTA
349049 T
1 T
349050 ATGTACACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 3 0.10
32 4 0.13
33 23 0.77
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.64
Consensus pattern (33 bp):
TTATTTTTATTTGTTTTACGTAGAATATATTTA
Found at i:349090 original size:7 final size:8
Alignment explanation
Indices: 349062--349102 Score: 55
Period size: 8 Copynumber: 4.8 Consensus size: 8
349052 GTACACATTA
349062 TTTTTATT
1 TTTTTATT
349070 ATTTTTAATTT
1 -TTTTT-A-TT
349081 TTTTTATT
1 TTTTTATT
349089 TTTTTATT
1 TTTTTATT
349097 TTTTTA
1 TTTTTA
349103 CTCCATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.53
9 6 0.20
10 6 0.20
11 2 0.07
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTATT
Found at i:349102 original size:16 final size:19
Alignment explanation
Indices: 349062--349101 Score: 66
Period size: 17 Copynumber: 2.2 Consensus size: 19
349052 GTACACATTA
349062 TTTTTATTATTTTTAATTT
1 TTTTTATTATTTTTAATTT
349081 TTTTTATT-TTTTT-ATTT
1 TTTTTATTATTTTTAATTT
349098 TTTT
1 TTTT
349102 ACTCCATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.38
18 5 0.24
19 8 0.38
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTTATTATTTTTAATTT
Found at i:349230 original size:26 final size:25
Alignment explanation
Indices: 349174--349234 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
349164 ATTTTTATTA
349174 TTTTATTATTATTTTTTACGTGTTT
1 TTTTATTATTATTTTTTACGTGTTT
* * *
349199 TGTTATTTTTCATTTTTT-CTTGTTT
1 TTTTATTATT-ATTTTTTACGTGTTT
349224 TATTTATTATT
1 T-TTTATTATT
349235 CTCACGTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 15 0.52
26 14 0.48
ACGTcount: A:0.15, C:0.05, G:0.07, T:0.74
Consensus pattern (25 bp):
TTTTATTATTATTTTTTACGTGTTT
Found at i:351780 original size:36 final size:36
Alignment explanation
Indices: 351740--351812 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
351730 TAAGCCATTT
351740 GTTTATGATTTCTCTAAAAAAGCGAATAAAAGGTCA
1 GTTTATGATTTCTCTAAAAAAGCGAATAAAAGGTCA
351776 GTTTATGATTTCTCTAAAAAAGCGAATAAAAGGTCA
1 GTTTATGATTTCTCTAAAAAAGCGAATAAAAGGTCA
351812 G
1 G
351813 CCAATCAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (36 bp):
GTTTATGATTTCTCTAAAAAAGCGAATAAAAGGTCA
Found at i:355410 original size:23 final size:23
Alignment explanation
Indices: 355383--355434 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
355373 GTCTGGACGA
355383 AGCAAATAATTTACAAAGTAAGC
1 AGCAAATAATTTACAAAGTAAGC
355406 AGCAAATAATTTACAAAGTAAGC
1 AGCAAATAATTTACAAAGTAAGC
355429 AGCAAA
1 AGCAAA
355435 ACAATTTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.19
Consensus pattern (23 bp):
AGCAAATAATTTACAAAGTAAGC
Found at i:356169 original size:29 final size:29
Alignment explanation
Indices: 356127--356184 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
356117 GGGAAGAATG
356127 TGGAATTTTATATCATAATAAAACTTATA
1 TGGAATTTTATATCATAATAAAACTTATA
* *
356156 TGGAATTTTATATCATAGTACAACTTATA
1 TGGAATTTTATATCATAATAAAACTTATA
356185 AAATTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (29 bp):
TGGAATTTTATATCATAATAAAACTTATA
Found at i:360040 original size:81 final size:82
Alignment explanation
Indices: 359944--360093 Score: 212
Period size: 81 Copynumber: 1.8 Consensus size: 82
359934 ACTTTAGCGG
* * * *
359944 CGTTTCTTAAACAAACGCCGCTATAGAGTAGTACTATAGCGGCATTTTTATATAAACGCCGCAAT
1 CGTTTCTTAAACAAACGCCACAACAGAGTAGTACTATAGCGGCATTTTTATACAAACGCCGCAAT
360009 AGGTACATATGTAATGA
66 AGGTACATATGTAATGA
* * * * *
360026 CGTTT-TTCAACAAACGCCACAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCTGCAAT
1 CGTTTCTTAAACAAACGCCACAACAGAGTAGTACTATAGCGGCATTTTTATACAAACGCCGCAAT
360090 AGGT
66 AGGT
360094 CCATCTATAG
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
81 54 0.92
82 5 0.08
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (82 bp):
CGTTTCTTAAACAAACGCCACAACAGAGTAGTACTATAGCGGCATTTTTATACAAACGCCGCAAT
AGGTACATATGTAATGA
Found at i:360073 original size:41 final size:41
Alignment explanation
Indices: 359933--360295 Score: 175
Period size: 41 Copynumber: 8.8 Consensus size: 41
359923 CACAAAATGA
* *
359933 TACTTTAGCGGCGTTTCTTAAACAAACGCCGCTATAGAGTAG
1 TACTTTAGCGGCGTTT-TTATACAAACGCCGCAATAGAGTAG
* * * *
359975 TACTATAGCGGCATTTTTATATAAACGCCGCAATAG-GTACA
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTA-G
* ** * * *
360016 TA-TGTAATGACGTTTTTCA-ACAAACGCCACAACAGAGTAG
1 TACTTTAGCGGCGTTTTT-ATACAAACGCCGCAATAGAGTAG
* *
360056 TACTTTAGCGGCGTTTTTATACAAACTCTGCAATAG-GTCCA-
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGT--AG
* * * * * * *
360097 T-CTATAGTGGCATTTTTTTCTGACAAACGCCGCAAAAGATTTG
1 TACTTTAGCGGC--GTTTTTAT-ACAAACGCCGCAATAGAGTAG
* * * * **
360140 TACTTTAGCGGTGTTTTTATAAAAATGCCACAATAGAGTTC
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTAG
* * * * * * * * * *
360181 TCCTATAGTGGCTTTTTTTCTAATAAACGCTGCAACATATTAG
1 TACTTTAGCGGC-GTTTTTAT-ACAAACGCCGCAATAGAGTAG
* * * * *
360224 AACTTTAGTGGCGTTTTTACACAAACGCCGCAA-AAAATATG
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTA-G
*
360265 TACTTTAGCGGCGTTTTCT-TAAAAACGCCGC
1 TACTTTAGCGGCGTTTT-TATACAAACGCCGC
360296 TATAAAATGA
Statistics
Matches: 232, Mismatches: 72, Indels: 35
0.68 0.21 0.10
Matches are distributed among these distances:
40 43 0.19
41 107 0.46
42 39 0.17
43 35 0.15
44 8 0.03
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (41 bp):
TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTAG
Found at i:360113 original size:81 final size:82
Alignment explanation
Indices: 359953--360256 Score: 254
Period size: 84 Copynumber: 3.7 Consensus size: 82
359943 GCGTTTCTTA
* * * * * * *
359953 AACAAACGCCGCTATAGAGTAGTACTATAGCGGCATTTTTATATAAACGCCGCAATAGGTACATA
1 AACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCCGCAATAGGTACATC
* * * *
360018 TGTAATGACGTTTTTC-
66 TATAGTGGCATTTTTCT
* * *
360034 AACAAACGCCACAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCTGCAATAGGTCCATC
1 AACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCCGCAATAGGTACATC
360099 TATAGTGGCATTTTTTTCT
66 TATAGTGGCA--TTTTTCT
* * * * * * * *
360118 GACAAACGCCGCAAAAGATTTGTACTTTAGCGGTGTTTTTATA-AAAATGCCACAATAGAGTTC-
1 AACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACT-CCGCAATAG-GTACA
*
360181 TCCTATAGTGGCTTTTTTTCT
64 T-CTATAGTGGC-ATTTTTCT
* * * * * * * *
360202 AATAAACGCTGCAACATATTAGAACTTTAGTGGCGTTTTTACACAAACGCCGCAA
1 AACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCCGCAA
360257 AAAATATGTA
Statistics
Matches: 177, Mismatches: 38, Indels: 13
0.78 0.17 0.06
Matches are distributed among these distances:
81 61 0.34
83 10 0.06
84 90 0.51
85 16 0.09
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (82 bp):
AACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCCGCAATAGGTACATC
TATAGTGGCATTTTTCT
Found at i:364788 original size:21 final size:21
Alignment explanation
Indices: 364764--364822 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
364754 TGATTTATTA
**
364764 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
364785 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
364806 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
364823 ATTGGAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.05, G:0.20, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:365065 original size:43 final size:43
Alignment explanation
Indices: 365018--365243 Score: 283
Period size: 43 Copynumber: 5.3 Consensus size: 43
365008 ACCAGATCTT
* * *
365018 TTGCGGTGTTTGTGGGAAAAACGTCGCTAAATCTCAAGACCTA
1 TTGCGGTGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
* * * *
365061 TTGCGGCGTTTGTGGAAAAAACGCCGCTAAATCTCAACACTTA
1 TTGCGGTGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
*
365104 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
1 TTGCGGTGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
* *
365147 TTGCGGTGTTTGTTGGACAAACGCCGCTAAATATCAACACCTA
1 TTGCGGTGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
* * * ***
365190 TTGCGGCT-TTTGTTGGACAAACGCCGCTATATATCGTTACCTA
1 TTGCGG-TGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
*
365233 TTGCGGCGTTT
1 TTGCGGTGTTT
365244 TTTGTTACCA
Statistics
Matches: 165, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
43 164 0.99
44 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (43 bp):
TTGCGGTGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
Found at i:365071 original size:86 final size:87
Alignment explanation
Indices: 364975--365243 Score: 269
Period size: 86 Copynumber: 3.1 Consensus size: 87
364965 ATATGACATT
* * * *
364975 TTGCGGCGTTTGTTCTAAAAAAAACCGCTATATAC-CAGA-TCTT-TTGCGGTGTTTGTGGGAAA
1 TTGCGGCGTTTGTTCGAAAAAAAACCGCTAAAT-CTCA-ACACTTATTGCGGCGTTTGTGGGAAA
* * *
365037 AACGTCGCTAAATCTCAAGACCTA
64 AACGCCGCTAAATATCAACACCTA
* **
365061 TTGCGGCGTTTG-TGGAAAAAACGCCGCTAAATCTCAACACTTATTGCGGCGTTTGTGGGAAAAA
1 TTGCGGCGTTTGTTCGAAAAAAAACCGCTAAATCTCAACACTTATTGCGGCGTTTGTGGGAAAAA
365125 CGCCGCTAAATATCAACACCTA
66 CGCCGCTAAATATCAACACCTA
* * * ** * * * * *
365147 TTGCGGTGTTTGTT-GGACAAACGCCGCTAAATATCAACACCTATTGCGGCTTTTGTTGGACAAA
1 TTGCGGCGTTTGTTCGAAAAAAAACCGCTAAATCTCAACACTTATTGCGGCGTTTGTGGGAAAAA
* ***
365211 CGCCGCTATATATCGTTACCTA
66 CGCCGCTAAATATCAACACCTA
365233 TTGCGGCGTTT
1 TTGCGGCGTTT
365244 TTTGTTACCA
Statistics
Matches: 156, Mismatches: 23, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
84 2 0.01
85 20 0.13
86 133 0.85
87 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (87 bp):
TTGCGGCGTTTGTTCGAAAAAAAACCGCTAAATCTCAACACTTATTGCGGCGTTTGTGGGAAAAA
CGCCGCTAAATATCAACACCTA
Found at i:365124 original size:129 final size:129
Alignment explanation
Indices: 364975--365218 Score: 303
Period size: 129 Copynumber: 1.9 Consensus size: 129
364965 ATATGACATT
* * * * * * *
364975 TTGCGGCGTTTGTTCTAAAAAAAACCGCTATATA-CCAGATCTTTTGCGGTGTTTGTGGGAAAAA
1 TTGCGGCGTTTGTGC-GAAAAAAACCGCTAAATATCAACACCTATTGCGGTGTTTGTGGGAAAAA
* * *
365039 CGTCGCTAAATCTCAAGACCTATTGCGGCGTTTG-TGGAAAAAACGCCGCTAAATCTCAACACTT
65 CGCCGCTAAATATCAACACCTATTGCGGCGTTTGTTGG-AAAAACGCCGCTAAATCTCAACACTT
365103 A
129 A
* ** * *
365104 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTATTGCGGTGTTTGTTGGACAAAC
1 TTGCGGCGTTTGTGCGAAAAAAACCGCTAAATATCAACACCTATTGCGGTGTTTGTGGGAAAAAC
* *
365169 GCCGCTAAATATCAACACCTATTGCGGCTTTTGTTGGACAAACGCCGCTA
66 GCCGCTAAATATCAACACCTATTGCGGCGTTTGTTGGAAAAACGCCGCTA
365219 TATATCGTTA
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
128 14 0.15
129 79 0.82
130 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (129 bp):
TTGCGGCGTTTGTGCGAAAAAAACCGCTAAATATCAACACCTATTGCGGTGTTTGTGGGAAAAAC
GCCGCTAAATATCAACACCTATTGCGGCGTTTGTTGGAAAAACGCCGCTAAATCTCAACACTTA
Found at i:373441 original size:23 final size:23
Alignment explanation
Indices: 373406--373457 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
373396 GTCATCCGAC
* *
373406 CGAGGCCATCCGAACGAGCTATG
1 CGAGGGCAACCGAACGAGCTATG
*
373429 CGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCAACCGAACGAGCTATG
373452 CGAGGG
1 CGAGGG
373458 AATCCGAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.27, G:0.38, T:0.10
Consensus pattern (23 bp):
CGAGGGCAACCGAACGAGCTATG
Found at i:373464 original size:23 final size:24
Alignment explanation
Indices: 373413--373465 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
373403 GACCGAGGCC
*
373413 ATCCGAACGAGCTATGCGAGGGCA
1 ATCCGAGCGAGCTATGCGAGGGCA
373437 A-CCGAGCGAGCTATGCGAGGG-A
1 ATCCGAGCGAGCTATGCGAGGGCA
373459 ATCCGAG
1 ATCCGAG
373466 GGAAGCCGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 2 0.07
23 24 0.89
24 1 0.04
ACGTcount: A:0.28, C:0.25, G:0.36, T:0.11
Consensus pattern (24 bp):
ATCCGAGCGAGCTATGCGAGGGCA
Found at i:373516 original size:29 final size:29
Alignment explanation
Indices: 373483--373567 Score: 152
Period size: 29 Copynumber: 2.9 Consensus size: 29
373473 GAGCGAGGGT
*
373483 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
373512 AGGTCGCCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
*
373541 AGGTCACCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
373568 TGTGTTGGGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.21, C:0.31, G:0.36, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:373783 original size:11 final size:11
Alignment explanation
Indices: 373769--373821 Score: 58
Period size: 11 Copynumber: 5.1 Consensus size: 11
373759 CAACATTACA
373769 AAATAATTATT
1 AAATAATTATT
* *
373780 AAATTATTATA
1 AAATAATTATT
373791 AAATAATTATT
1 AAATAATTATT
*
373802 -AA-AATTATC
1 AAATAATTATT
373811 AAAT-ATTATT
1 AAATAATTATT
373821 A
1 A
373822 TCATAACTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
9 6 0.18
10 10 0.29
11 18 0.53
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
AAATAATTATT
Found at i:373788 original size:22 final size:23
Alignment explanation
Indices: 373763--373809 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
373753 CCATCACAAC
373763 ATTACAAAATAATTATT-AAATT
1 ATTACAAAATAATTATTAAAATT
*
373785 ATTATAAAATAATTATTAAAATT
1 ATTACAAAATAATTATTAAAATT
373808 AT
1 AT
373810 CAAATATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTACAAAATAATTATTAAAATT
Found at i:373822 original size:22 final size:21
Alignment explanation
Indices: 373763--373821 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 21
373753 CCATCACAAC
*
373763 ATTACAAAATAATTATTAAATT
1 ATTATAAAATAATTATTAAA-T
373785 ATTATAAAATAATTATTAAA-
1 ATTATAAAATAATTATTAAAT
*
373805 ATTATCAAAT-ATTATTA
1 ATTATAAAATAATTATTA
373822 TCATAACTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 7 0.20
20 9 0.26
22 19 0.54
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTATAAAATAATTATTAAAT
Found at i:374389 original size:15 final size:15
Alignment explanation
Indices: 374369--374434 Score: 69
Period size: 15 Copynumber: 4.4 Consensus size: 15
374359 TTCACTCTCA
*
374369 TCATCATCGTCGTCG
1 TCATCATCGTCATCG
* *
374384 TCATCATCCTCATCC
1 TCATCATCGTCATCG
*
374399 TCATCCTCGTCATCG
1 TCATCATCGTCATCG
* * *
374414 TCTTCCTCATCATCG
1 TCATCATCGTCATCG
374429 TCATCA
1 TCATCA
374435 CTCTCAACAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.17, C:0.39, G:0.09, T:0.35
Consensus pattern (15 bp):
TCATCATCGTCATCG
Found at i:374411 original size:21 final size:21
Alignment explanation
Indices: 374387--374433 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
374377 GTCGTCGTCA
*
374387 TCATCCTCATCCTCATCCTCG
1 TCATCCTCATCCTCATCATCG
* *
374408 TCATCGTCTTCCTCATCATCG
1 TCATCCTCATCCTCATCATCG
374429 TCATC
1 TCATC
374434 ACTCTCAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.43, G:0.06, T:0.36
Consensus pattern (21 bp):
TCATCCTCATCCTCATCATCG
Found at i:375526 original size:21 final size:21
Alignment explanation
Indices: 375483--375528 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
375473 AAGGAATATT
* *
375483 AATATTAATATTAATAATAAA
1 AATACTAATAATAATAATAAA
* *
375504 AATACTAATAATAATATTTAA
1 AATACTAATAATAATAATAAA
375525 AATA
1 AATA
375529 TTTTTTTCAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AATACTAATAATAATAATAAA
Found at i:375721 original size:84 final size:84
Alignment explanation
Indices: 375580--375746 Score: 273
Period size: 84 Copynumber: 2.0 Consensus size: 84
375570 CTCTTTACAC
* *
375580 ATTCTTGTGTTAACAAGGATAAGACAAAGAAGAAAAAGATAACTAATTTTTGTCCGATAAATGAA
1 ATTCTTGTGTTAACAAAGATAAGACAAAGAAGAAAAAGAAAACTAATTTTTGTCCGATAAATGAA
375645 ACATGTGACATAAACAAAT
66 ACATGTGACATAAACAAAT
* * *
375664 ATTCTTGTGTTAATAAAGATATGACAAAGACGAAAAAGACAAAC-AATTTTTGTCCGATAAATGA
1 ATTCTTGTGTTAACAAAGATAAGACAAAGAAGAAAAAGA-AAACTAATTTTTGTCCGATAAATGA
375728 AACATGTGACATAAACAAA
65 AACATGTGACATAAACAAA
375747 AATATATCTG
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
84 74 0.96
85 3 0.04
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (84 bp):
ATTCTTGTGTTAACAAAGATAAGACAAAGAAGAAAAAGAAAACTAATTTTTGTCCGATAAATGAA
ACATGTGACATAAACAAAT
Found at i:375766 original size:17 final size:17
Alignment explanation
Indices: 375744--375778 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
375734 TGACATAAAC
*
375744 AAAAATATATCTGATAA
1 AAAAATATATCCGATAA
375761 AAAAATATATCCGATAA
1 AAAAATATATCCGATAA
375778 A
1 A
375779 TTTTACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAAATATATCCGATAA
Found at i:375932 original size:16 final size:16
Alignment explanation
Indices: 375911--375943 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
375901 AGTAAAGCCT
375911 AATTCCCTTCCCAATC
1 AATTCCCTTCCCAATC
375927 AATTCCCTTCCCAATC
1 AATTCCCTTCCCAATC
375943 A
1 A
375944 TTGAAAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.42, G:0.00, T:0.30
Consensus pattern (16 bp):
AATTCCCTTCCCAATC
Found at i:376166 original size:9 final size:9
Alignment explanation
Indices: 376154--376188 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
376144 TTACAAATAT
376154 AAAAAATCC
1 AAAAAATCC
*
376163 AAAAAATTCA
1 AAAAAA-TCC
376173 AAAAAATCC
1 AAAAAATCC
376182 AAAAAAT
1 AAAAAAT
376189 TACAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAAAATCC
Found at i:376178 original size:19 final size:20
Alignment explanation
Indices: 376154--376198 Score: 83
Period size: 19 Copynumber: 2.3 Consensus size: 20
376144 TTACAAATAT
376154 AAAAAATCCAAAAAATT-CA
1 AAAAAATCCAAAAAATTACA
376173 AAAAAATCCAAAAAATTACA
1 AAAAAATCCAAAAAATTACA
376193 AAAAAA
1 AAAAAA
376199 AAATAATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.73, C:0.13, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAAAATCCAAAAAATTACA
Found at i:377162 original size:27 final size:27
Alignment explanation
Indices: 377128--377190 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
377118 GCATCAAACG
*
377128 CGGCCAGTTGCTTTGGAAATCATCTTA
1 CGGCCAGTCGCTTTGGAAATCATCTTA
*
377155 CGGCCAGTCGTTTTGGAAATCATCTTA
1 CGGCCAGTCGCTTTGGAAATCATCTTA
377182 CGGCCAGTC
1 CGGCCAGTC
377191 AGCACCAGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.30
Consensus pattern (27 bp):
CGGCCAGTCGCTTTGGAAATCATCTTA
Found at i:379276 original size:3 final size:3
Alignment explanation
Indices: 379268--379292 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
379258 GCTCAGGTAA
379268 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
379293 GTGCTCTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:379904 original size:15 final size:15
Alignment explanation
Indices: 379884--379921 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
379874 CTTAAGTGTG
379884 TAAATGAACCGAGCT
1 TAAATGAACCGAGCT
*
379899 TAAATGAATCGAGCT
1 TAAATGAACCGAGCT
*
379914 TGAATGAA
1 TAAATGAA
379922 GAAGATTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (15 bp):
TAAATGAACCGAGCT
Found at i:380507 original size:97 final size:97
Alignment explanation
Indices: 380341--380549 Score: 357
Period size: 97 Copynumber: 2.2 Consensus size: 97
380331 GAGTTTATTC
* * *
380341 ATGAACATAAACGAATCGAACATACCTCTTCTCATGTTCGTTCGTTTATTAAATGAACATAAATT
1 ATGAACATAAACGAACCGAACATACCTCTTCTCATGTTCGATCGTTTATTAAATGAACATAAAAT
380406 TTTTGTTCATGCTCATTTATTTAGCTTAACAA
66 TTTTGTTCATGCTCATTTATTTAGCTTAACAA
*
380438 ATGAACATAAACGAACCGAACATACCTCTGT-TCGTGTTCGATCGTTTATTAAATGAACATAAAA
1 ATGAACATAAACGAACCGAACATACCTCT-TCTCATGTTCGATCGTTTATTAAATGAACATAAAA
*
380502 TTTTTGTTCATGCTCATTTATTTAGTTTAACAA
65 TTTTTGTTCATGCTCATTTATTTAGCTTAACAA
380535 ATGAACATAAACGAA
1 ATGAACATAAACGAA
380550 AACGAATAGT
Statistics
Matches: 106, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
97 105 0.99
98 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.36
Consensus pattern (97 bp):
ATGAACATAAACGAACCGAACATACCTCTTCTCATGTTCGATCGTTTATTAAATGAACATAAAAT
TTTTGTTCATGCTCATTTATTTAGCTTAACAA
Found at i:384937 original size:16 final size:16
Alignment explanation
Indices: 384916--384948 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
384906 TATAAAACAC
384916 AGTAATTGTTTTACAT
1 AGTAATTGTTTTACAT
384932 AGTAATTGTTTTACAT
1 AGTAATTGTTTTACAT
384948 A
1 A
384949 TGCACCTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (16 bp):
AGTAATTGTTTTACAT
Found at i:392732 original size:33 final size:32
Alignment explanation
Indices: 392682--392796 Score: 167
Period size: 32 Copynumber: 3.6 Consensus size: 32
392672 TAACATGTCT
* *
392682 GAGGGACTAAAATTGAATGGGAGTCAACGATC
1 GAGGGACTAAAATTGAATGAGAGTTAACGATC
392714 GAGGGACTAAAAATTGAATGAGAGTTAACGATC
1 GAGGGACT-AAAATTGAATGAGAGTTAACGATC
** * *
392747 GAAAGATTAAAATTGAATAAGAGTTAACGATC
1 GAGGGACTAAAATTGAATGAGAGTTAACGATC
392779 GAGGGACTAAAATTGAAT
1 GAGGGACTAAAATTGAAT
392797 AAATCAATAA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
32 46 0.63
33 27 0.37
ACGTcount: A:0.43, C:0.09, G:0.26, T:0.22
Consensus pattern (32 bp):
GAGGGACTAAAATTGAATGAGAGTTAACGATC
Found at i:396008 original size:20 final size:21
Alignment explanation
Indices: 395975--396014 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
395965 GATTTAAGGG
395975 TAAACTATACA-TTTAGTATT
1 TAAACTATACATTTTAGTATT
395995 TAAACTATTA-ATTTTAGTAT
1 TAAACTA-TACATTTTAGTAT
396015 GTTTTAGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (21 bp):
TAAACTATACATTTTAGTATT
Found at i:396791 original size:2 final size:2
Alignment explanation
Indices: 396734--396776 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
396724 AAATATTATT
396734 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
396776 T
1 T
396777 TCATAATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:397415 original size:31 final size:31
Alignment explanation
Indices: 397380--397453 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
397370 ACGCGTTTAG
*
397380 TACCTAAA-TTATCAATTTCGATCCGTTATAA
1 TACCTAAACTT-TCAATATCGATCCGTTATAA
* *
397411 TACCTAAACTTTCAATATCGATCCGTTTTAG
1 TACCTAAACTTTCAATATCGATCCGTTATAA
397442 TACCTAAACTTT
1 TACCTAAACTTT
397454 TAACTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
31 37 0.95
32 2 0.05
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (31 bp):
TACCTAAACTTTCAATATCGATCCGTTATAA
Found at i:406343 original size:31 final size:31
Alignment explanation
Indices: 406281--406352 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
406271 AATTTAAAAA
*
406281 ATAATATTTTAATCACTTACGTTATCTATTT
1 ATAATATTTTAATCACTTACGTTATCGATTT
* * *
406312 ATAATGTTTTAGTCACTTATGTTAGT-GATTT
1 ATAATATTTTAATCACTTACGTTA-TCGATTT
*
406343 ATAACATTTT
1 ATAATATTTT
406353 GAAGTAGATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (31 bp):
ATAATATTTTAATCACTTACGTTATCGATTT
Found at i:406629 original size:31 final size:31
Alignment explanation
Indices: 406594--406652 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
406584 GACCAAAACG
**
406594 TTATAAATCTATAATGTAAGTGAGCAAATCA
1 TTATAAATAGATAATGTAAGTGAGCAAATCA
* *
406625 TTATAAATAGATAATGTAGGTGATCAAA
1 TTATAAATAGATAATGTAAGTGAGCAAA
406653 ATGTACTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32
Consensus pattern (31 bp):
TTATAAATAGATAATGTAAGTGAGCAAATCA
Found at i:410845 original size:31 final size:31
Alignment explanation
Indices: 410810--410868 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
410800 GACCAAAACG
**
410810 TTATAAATCTATAATGTAAGTGAGCAAATCA
1 TTATAAATAGATAATGTAAGTGAGCAAATCA
* *
410841 TTATAAATAGATAATGTAGGTGATCAAA
1 TTATAAATAGATAATGTAAGTGAGCAAA
410869 ATGTACTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32
Consensus pattern (31 bp):
TTATAAATAGATAATGTAAGTGAGCAAATCA
Found at i:413213 original size:30 final size:29
Alignment explanation
Indices: 413109--413229 Score: 147
Period size: 29 Copynumber: 4.1 Consensus size: 29
413099 TGTGAGAACT
* * *
413109 CTAAACTCTAAGGA-CTAAAGTATAAAAAA
1 CTAAAGTCTAGGGACCT-AAGTGTAAAAAA
413138 CTAAAGTCTAGGGACCTAAGTGTAAAAAA
1 CTAAAGTCTAGGGACCTAAGTGTAAAAAA
*
413167 CTAAAGTCTA-GGACCTATGTGTAAAAAA
1 CTAAAGTCTAGGGACCTAAGTGTAAAAAA
* *
413195 TCTAAAGTTTAGGGACCTAAGTGTGAAAAAT
1 -CTAAAGTCTAGGGACCTAAGTGT-AAAAAA
413226 CTAA
1 CTAA
413230 TCCTAGAGGG
Statistics
Matches: 81, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
28 17 0.21
29 42 0.52
30 17 0.21
31 5 0.06
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.24
Consensus pattern (29 bp):
CTAAAGTCTAGGGACCTAAGTGTAAAAAA
Found at i:414562 original size:3 final size:3
Alignment explanation
Indices: 414542--414579 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
414532 TTTTGTAATT
414542 TAA TAA -AA TAA TATA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
414580 AAAATGGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.12
3 25 0.78
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:415585 original size:28 final size:28
Alignment explanation
Indices: 415553--415609 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
415543 AATACCAAGG
415553 GTGTGAGTATTCAATGTCAAATGATTGA
1 GTGTGAGTATTCAATGTCAAATGATTGA
415581 GTGTGAGTATTCAATGTCAAATGATTGA
1 GTGTGAGTATTCAATGTCAAATGATTGA
415609 G
1 G
415610 ATTTATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.07, G:0.26, T:0.35
Consensus pattern (28 bp):
GTGTGAGTATTCAATGTCAAATGATTGA
Found at i:418468 original size:61 final size:59
Alignment explanation
Indices: 418421--418601 Score: 274
Period size: 62 Copynumber: 3.0 Consensus size: 59
418411 ATATAAACGG
*
418421 TCACTTAATTATAAGATATAATTATATTAAATCTTCGACTATTAAAAATTATAAAATGA
1 TCACTTAATTATAAGATATAATTATATTAAATCATCGACTATTAAAAATTATAAAATGA
*
418480 TCCTCTCTTAATTATAAGATATAATTATATTAAATCATCGACTATT-AAAATTATAAAATGA
1 ---TCACTTAATTATAAGATATAATTATATTAAATCATCGACTATTAAAAATTATAAAATGA
*
418541 TCATCTCTTAATTATAAGATATAATTATATTAAATCCTCGACTATTAAAAATTATAAAATG
1 TCA---CTTAATTATAAGATATAATTATATTAAATCATCGACTATTAAAAATTATAAAATG
418602 GTCATCTAAC
Statistics
Matches: 111, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
58 2 0.02
61 54 0.49
62 55 0.50
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.39
Consensus pattern (59 bp):
TCACTTAATTATAAGATATAATTATATTAAATCATCGACTATTAAAAATTATAAAATGA
Done.