Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009069.1 Hibiscus syriacus cultivar Beakdansim tig00112496_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: 530156
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:418551 original size:21 final size:21
Alignment explanation
Indices: 418527--418593 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
418517 TCATTCCTTG
418527 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
418548 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
418569 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
418590 AGAG
1 AGAG
418594 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:418551 original size:42 final size:42
Alignment explanation
Indices: 418505--418593 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
418495 CCTATTGTTG
* *
418505 AAGAGGCCCCTATCATTCCTTG-AGA-GTCCCCTCCCACCGTTC
1 AAGAGGCCACTATCA-TCCTTGAAGAGGT-CCCTCCCACCATTC
* *
418547 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCATCCTTGAAGAGGTCCCTCCCACCATTC
418589 AAGAG
1 AAGAG
418594 CCCGATTCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 5 0.12
42 34 0.83
43 2 0.05
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.21
Consensus pattern (42 bp):
AAGAGGCCACTATCATCCTTGAAGAGGTCCCTCCCACCATTC
Found at i:419965 original size:14 final size:14
Alignment explanation
Indices: 419946--419981 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
419936 ATTGTTTAAT
419946 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
419960 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
419974 TGATTTGT
1 TGATTTGT
419982 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:420110 original size:19 final size:18
Alignment explanation
Indices: 420088--420179 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
420078 AAAAATTACT
420088 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAAT-AAA
*
420107 ATCGCAA--CG--ATATA
1 ATCGCAATGCGAAATAAA
420121 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAAT-AAA
*
420140 ATCGCAA--CG--ACAAA
1 ATCGCAATGCGAAATAAA
* *
420154 ATTGCAACGCGAAACTAAA
1 ATCGCAATGCGAAA-TAAA
420173 ATCGCAA
1 ATCGCAA
420180 CGACAAAATC
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 18 0.32
15 3 0.05
16 4 0.07
17 4 0.07
18 3 0.05
19 25 0.44
ACGTcount: A:0.48, C:0.21, G:0.16, T:0.15
Consensus pattern (18 bp):
ATCGCAATGCGAAATAAA
Found at i:420130 original size:33 final size:32
Alignment explanation
Indices: 420088--420193 Score: 149
Period size: 33 Copynumber: 3.2 Consensus size: 32
420078 AAAAATTACT
* *
420088 ATCGCAATGCGAAATGAAAATCGCAACGATATA
1 ATCGCAATGCGAAAT-AAAATCGCAACGACAAA
420121 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAAT-AAAATCGCAACGACAAA
* *
420154 ATTGCAACGCGAAACTAAAATCGCAACGACAAA
1 ATCGCAATGCGAAA-TAAAATCGCAACGACAAA
420187 ATCGCAA
1 ATCGCAA
420194 CGTGAAACTA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 65 0.98
34 1 0.02
ACGTcount: A:0.48, C:0.22, G:0.16, T:0.14
Consensus pattern (32 bp):
ATCGCAATGCGAAATAAAATCGCAACGACAAA
Found at i:420160 original size:14 final size:14
Alignment explanation
Indices: 420137--420195 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
420127 ATGCGAAATA
420137 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
420151 AAAATTGCAACGCGAAAC
1 AAAATCGCAA--CG--AC
420169 TAAAATCGCAACGAC
1 -AAAATCGCAACGAC
420184 AAAATCGCAACG
1 AAAATCGCAACG
420196 TGAAACTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.55
15 2 0.05
16 2 0.05
17 2 0.05
18 2 0.05
19 9 0.24
ACGTcount: A:0.49, C:0.25, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:420180 original size:19 final size:18
Alignment explanation
Indices: 420088--420210 Score: 58
Period size: 19 Copynumber: 7.3 Consensus size: 18
420078 AAAAATTACT
420088 ATCGCAATGCGAAA-TGAAA
1 ATCGCAA-GCGAAACT-AAA
*
420107 ATCGCAA-CG--A-TATA
1 ATCGCAAGCGAAACTAAA
420121 ATCGCAATGCGAAA-TAAAA
1 ATCGCAA-GCGAAACT-AAA
420140 ATCGCAA-CG--AC-AAA
1 ATCGCAAGCGAAACTAAA
*
420154 ATTGCAACGCGAAACTAAA
1 ATCGCAA-GCGAAACTAAA
420173 ATCGCAA-CG--AC-AAA
1 ATCGCAAGCGAAACTAAA
*
420187 ATCGCAACGTGAAACTAAA
1 ATCGCAA-GCGAAACTAAA
*
420206 TTCGC
1 ATCGC
420211 GTTGCGATTT
Statistics
Matches: 82, Mismatches: 6, Indels: 32
0.68 0.05 0.27
Matches are distributed among these distances:
14 28 0.34
15 5 0.06
16 5 0.06
17 6 0.07
18 6 0.07
19 32 0.39
ACGTcount: A:0.46, C:0.22, G:0.16, T:0.15
Consensus pattern (18 bp):
ATCGCAAGCGAAACTAAA
Found at i:420194 original size:33 final size:33
Alignment explanation
Indices: 420088--420205 Score: 148
Period size: 33 Copynumber: 3.5 Consensus size: 33
420078 AAAAATTACT
* * * *
420088 ATCGCAATGCGAAATGAAAATCGCAACGATATA
1 ATCGCAACGCGAAATAAAAATCGCAACGACAAA
*
420121 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATAAAAATCGCAACGACAAA
*
420154 ATTGCAACGCGAAACT-AAAATCGCAACGACAAA
1 ATCGCAACGCGAAA-TAAAAATCGCAACGACAAA
*
420187 ATCGCAACGTGAAACTAAA
1 ATCGCAACGCGAAA-TAAA
420206 TTCGCGTTGC
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
33 73 0.96
34 3 0.04
ACGTcount: A:0.48, C:0.21, G:0.16, T:0.14
Consensus pattern (33 bp):
ATCGCAACGCGAAATAAAAATCGCAACGACAAA
Found at i:420228 original size:19 final size:19
Alignment explanation
Indices: 420206--420336 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
420196 TGAAACTAAA
*
420206 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
420225 TTCGCTTTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
* *
420241 CTCG--TTGTGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
420258 TTCGCATTGTGATTGTC--
1 TTCGCATTGCGATTTTCAT
420275 -TCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
420291 TTCGCATTGCGATTGTC--
1 TTCGCATTGCGATTTTCAT
420308 -T--CATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
420324 TTCGCATTGCGAT
1 TTCGCATTGCGAT
420337 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 11, Indels: 30
0.68 0.09 0.24
Matches are distributed among these distances:
14 26 0.30
16 10 0.12
17 10 0.12
19 40 0.47
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:420253 original size:33 final size:33
Alignment explanation
Indices: 420210--420336 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
420200 ACTAAATTCG
* **
420210 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTGTCT
* *
420243 CGTTGTGATTTTCATTTCGCATTGTGATTGTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTGTCT
420276 CGTTGCGATTTTCATTTCGCATTGCGATTGTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTGTCT
*
420309 CATTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
420337 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 86 1.00
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTGTCT
Found at i:420402 original size:20 final size:20
Alignment explanation
Indices: 420330--420402 Score: 51
Period size: 20 Copynumber: 3.6 Consensus size: 20
420320 TCATTTCGCA
* * *
420330 TTGCGATAGTAATTTCCGCG
1 TTGCGATAGTCATTTCAGTG
* *
420350 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCAG-TG
*
420370 ATTGCGA-ACGTCATTTCTGTG
1 -TTGCGATA-GTCATTTCAGTG
420391 TTGCGATAGTCA
1 TTGCGATAGTCA
420403 AATGATTGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.08
20 22 0.55
21 12 0.30
22 3 0.08
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCATTTCAGTG
Found at i:422890 original size:24 final size:24
Alignment explanation
Indices: 422853--422906 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
422843 CTGAAACATC
* *
422853 ATCAAAATCTGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
*
422877 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
422901 ATCAAA
1 ATCAAA
422907 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:422920 original size:24 final size:24
Alignment explanation
Indices: 422869--422920 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
422859 ATCTGAGTAT
* * *
422869 TGACCAATATCAAAGTCCGAGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
422893 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
422917 TGAC
1 TGAC
422921 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:423704 original size:20 final size:21
Alignment explanation
Indices: 423679--423730 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
423669 TTTTCCCAAT
*
423679 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
423699 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
423720 TCGCAATGCGA
1 TCGCAATGCGA
423731 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:423865 original size:40 final size:40
Alignment explanation
Indices: 423781--423866 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
423771 ATACTGACTT
* ***
423781 TCGCAACGAGATTCTGACTTTCGCAACGCGATTCTGACTT
1 TCGCAACGAGATTCTGACTTTCGCAACGAGATTCTGAAAA
423821 TCGCAACGAGATTCTGACTTTCGCAACGAGATTCTGAAAA
1 TCGCAACGAGATTCTGACTTTCGCAACGAGATTCTGAAAA
423861 TCGCAA
1 TCGCAA
423867 TCATCTTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.27
Consensus pattern (40 bp):
TCGCAACGAGATTCTGACTTTCGCAACGAGATTCTGAAAA
Found at i:423866 original size:20 final size:20
Alignment explanation
Indices: 423761--423857 Score: 167
Period size: 20 Copynumber: 4.8 Consensus size: 20
423751 TAATACAAAA
* *
423761 TCGCAACGCGATACTGACTT
1 TCGCAACGAGATTCTGACTT
423781 TCGCAACGAGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
*
423801 TCGCAACGCGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
423821 TCGCAACGAGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
423841 TCGCAACGAGATTCTGA
1 TCGCAACGAGATTCTGA
423858 AAATCGCAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 73 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGAGATTCTGACTT
Found at i:424162 original size:14 final size:14
Alignment explanation
Indices: 424143--424196 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
424133 GAAAATCGCA
424143 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
424157 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
424174 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
424190 TTGCGAT
1 TTGCGAT
424197 AATCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:424162 original size:33 final size:33
Alignment explanation
Indices: 424125--424195 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
424115 AAAATCGCAA
424125 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
424158 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
424191 TGCGA
1 TGCGA
424196 TAATCAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:425662 original size:40 final size:42
Alignment explanation
Indices: 425618--425704 Score: 133
Period size: 40 Copynumber: 2.1 Consensus size: 42
425608 CCTCTTCAAC
*
425618 GATGAAAGTGGCCTCTTGAACG-GTGG-GGGGACTCTTGAGG
1 GATGAAAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
425658 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGAAAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
425700 GATGA
1 GATGA
425705 CAGGTGAGTC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
40 20 0.48
41 3 0.07
42 19 0.45
ACGTcount: A:0.22, C:0.14, G:0.41, T:0.23
Consensus pattern (42 bp):
GATGAAAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:425673 original size:21 final size:21
Alignment explanation
Indices: 425644--425704 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
425634 TGAACGGTGG
*
425644 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
425665 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
425686 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
425705 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:426071 original size:20 final size:20
Alignment explanation
Indices: 426046--426098 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
426036 GAAGAATAGT
*
426046 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
426066 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* *
426086 TGACTATCGCAAC
1 TTACTTTCGCAAC
426099 GCGGAAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:426099 original size:20 final size:20
Alignment explanation
Indices: 426052--426138 Score: 86
Period size: 20 Copynumber: 4.4 Consensus size: 20
426042 TAGTTTACTT
* * * *
426052 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
426072 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
426092 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
426112 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
426131 TCGCAACG
1 TCGCAACG
426139 ATAAAATCGC
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
19 13 0.23
20 43 0.77
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:426133 original size:19 final size:18
Alignment explanation
Indices: 426111--426207 Score: 75
Period size: 19 Copynumber: 5.7 Consensus size: 18
426101 GGAAATGGCT
426111 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAAT-AAA
426130 ATCGCAA--CG--ATAAA
1 ATCGCAATGCGAAATAAA
426144 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAAT-AAA
*
426163 ATCGCAA--CG--ACAAA
1 ATCGCAATGCGAAATAAA
* *
426177 ATCGCAACGCGAAACACAA
1 ATCGCAATGCGAAATA-AA
*
426196 ATCGCATTGCGA
1 ATCGCAATGCGA
426208 TTTTCATTTC
Statistics
Matches: 65, Mismatches: 3, Indels: 20
0.74 0.03 0.23
Matches are distributed among these distances:
14 20 0.31
15 3 0.05
16 4 0.06
17 4 0.06
18 5 0.08
19 29 0.45
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (18 bp):
ATCGCAATGCGAAATAAA
Found at i:426146 original size:14 final size:14
Alignment explanation
Indices: 426127--426185 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
426117 ATGCGAAATG
426127 AAAATCGCAACGAT
1 AAAATCGCAACGAT
426141 AAAATCGCAATGCGAAAT
1 AAAATCGCAA--CG--AT
*
426159 AAAAATCGCAACGAC
1 -AAAATCGCAACGAT
426174 AAAATCGCAACG
1 AAAATCGCAACG
426186 CGAAACACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 22 0.56
15 1 0.03
16 2 0.05
17 2 0.05
18 2 0.05
19 10 0.26
ACGTcount: A:0.51, C:0.22, G:0.15, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAT
Found at i:426153 original size:33 final size:33
Alignment explanation
Indices: 426111--426201 Score: 137
Period size: 33 Copynumber: 2.8 Consensus size: 33
426101 GGAAATGGCT
* *
426111 ATCGCAATGCGAAATGAAAATCGCAACGATAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
426144 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
* * *
426177 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAATGCGAAATAAAAATCGCA
426202 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.48, C:0.23, G:0.16, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATAAAAATCGCAACGACAAA
Found at i:426219 original size:19 final size:19
Alignment explanation
Indices: 426197--426249 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
426187 GAAACACAAA
426197 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
426216 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
426235 TCGCATTGCGATTTT
1 TCGCATTGCGATTTT
426250 GTCGTTACGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:426832 original size:18 final size:18
Alignment explanation
Indices: 426809--426856 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
426799 CGGGTCGATC
426809 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
426827 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
426845 AGGTGATGGCTC
1 AGGTGATGGCTC
426857 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:428223 original size:20 final size:20
Alignment explanation
Indices: 428175--428233 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
428165 AATAGTTTCT
* *
428175 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
428195 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
428215 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
428234 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:428523 original size:22 final size:22
Alignment explanation
Indices: 428496--428539 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
428486 GATGGAGATA
428496 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
428518 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
428540 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:428824 original size:41 final size:41
Alignment explanation
Indices: 428705--428842 Score: 161
Period size: 41 Copynumber: 3.4 Consensus size: 41
428695 CGCTTTGAAA
* * *
428705 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * ** * * *
428746 ATTGCGTTGCAAAATT-AAGTATCGCGTTGTGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* *
428786 ATCGAGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
428827 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
428843 CCAAATTCGC
Statistics
Matches: 76, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 31 0.41
41 45 0.59
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:428839 original size:20 final size:20
Alignment explanation
Indices: 428725--428838 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
428715 GATTATGTAT
*
428725 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
428745 TATTGCGTTGCAAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
428765 TATCGCGTTGTGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
428785 TATCGAGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
428806 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
428826 TATCGCGTTGCGA
1 TATCGCGTTGCGA
428839 TTTTCCAAAT
Statistics
Matches: 73, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
19 3 0.04
20 55 0.75
21 13 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:428857 original size:21 final size:20
Alignment explanation
Indices: 428828--428879 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
428818 ATAGTCAGTA
* *
428828 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
**
428849 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACAAAT
428869 TCGCATTGCGA
1 TCGCATTGCGA
428880 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:428858 original size:41 final size:41
Alignment explanation
Indices: 428765--428860 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
428755 CAAAATTAAG
* * * ** *
428765 TATCGCGTTGTGAAAGTCAGTATCGAGTTGCGATTTTGTAT
1 TATCGCATTGCGATAGTCAGTATCGAGTTGCGATTTTCAAA
* *
428806 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAA
1 TATCGCATTGCGATAGTCAGTATCGAGTTGCGATTTT-CAAA
428848 T-TCGCATTGCGAT
1 TATCGCATTGCGAT
428861 TTACTTATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (41 bp):
TATCGCATTGCGATAGTCAGTATCGAGTTGCGATTTTCAAA
Found at i:428921 original size:21 final size:22
Alignment explanation
Indices: 428869--428921 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
428859 ATTTACTTAT
*
428869 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGAAAAA
**
428890 TCGCAACGCGAAATT-GAAAAA
1 TCGCATTGCGAAATTGGAAAAA
428911 TCGCATTGCGA
1 TCGCATTGCGA
428922 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGAAAAA
Found at i:435221 original size:44 final size:44
Alignment explanation
Indices: 435193--435279 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
435183 GAATTTAAAT
*
435193 TTTAGAGTTTAAAGTTCAAATAAATAAAATAATATAATTAAAGA
1 TTTAAAGTTTAAAGTTCAAATAAATAAAATAATATAATTAAAGA
* *
435237 TTTAAATTTTAAAGTTTAAATAAATAAAA-ATATATAAATTAAA
1 TTTAAAGTTTAAAGTTCAAATAAATAAAATA-ATAT-AATTAAA
435280 CAGTAAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 1 0.03
44 30 0.79
45 7 0.18
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (44 bp):
TTTAAAGTTTAAAGTTCAAATAAATAAAATAATATAATTAAAGA
Found at i:435287 original size:44 final size:44
Alignment explanation
Indices: 435200--435289 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 44
435190 AATTTTAGAG
* *
435200 TTTAAAGTTCAAATAAATAAAATAATATAATTAAAGATTTAAAT
1 TTTAAAGTTCAAATAAATAAAATAATATAATTAAACATGTAAAT
*
435244 TTTAAAGTTTAAATAAATAAAA-ATATATAAATTAAACA-GTAAAT
1 TTTAAAGTTCAAATAAATAAAATA-ATAT-AATTAAACATGTAAAT
435288 TT
1 TT
435290 AAATATATGT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 32 0.78
45 8 0.20
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (44 bp):
TTTAAAGTTCAAATAAATAAAATAATATAATTAAACATGTAAAT
Found at i:444780 original size:24 final size:24
Alignment explanation
Indices: 444722--444816 Score: 84
Period size: 24 Copynumber: 4.0 Consensus size: 24
444712 ATTTCCGACT
* * *
444722 TGAATTATGCTCTGA-TACATGACC
1 TGAATTATGTTCTGATTTC-TGATC
*
444746 TGAATTTTGTTCTGATTTCTGATC
1 TGAATTATGTTCTGATTTCTGATC
* * * *
444770 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTATGTTCTGATTTCTGATC
* *
444794 TGAATTATGTTTTAATTTCTGAT
1 TGAATTATGTTCTGATTTCTGAT
444817 ATCTCCGTTT
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
24 54 0.96
25 2 0.04
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (24 bp):
TGAATTATGTTCTGATTTCTGATC
Found at i:444804 original size:12 final size:12
Alignment explanation
Indices: 444745--444804 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
444735 GATACATGAC
*
444745 CTGAATTTTGTT
1 CTGAATTCTGTT
* *
444757 CTGATTTCTGAT
1 CTGAATTCTGTT
*
444769 CTGGATTCTGTT
1 CTGAATTCTGTT
444781 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
*
444793 CTGAATTATGTT
1 CTGAATTCTGTT
444805 TTAATTTCTG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 2 0.05
12 35 0.90
13 2 0.05
ACGTcount: A:0.17, C:0.13, G:0.18, T:0.52
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:451487 original size:137 final size:132
Alignment explanation
Indices: 451299--451569 Score: 391
Period size: 137 Copynumber: 2.0 Consensus size: 132
451289 TGGTCAAGTT
* * *
451299 AAGAGTTTCTTGTAAGACCTTTTATTCAGGGTTGTGTCTAAATCCACAGCCAGCAGCTTTTAAGT
1 AAGAGTTTCTTGTAAGACCTTTTATTCAGGGTTGTGCCTAAACCCACAGCCAACAGCTTTTAAGT
* * *
451364 TGGAT-CAGAGCAACCACCATGCCAATACATAATTTTATAAATGCAGCCACTTTTAATGAAAACA
66 TGGATCCA-AGCAACCACCACG-CAATACATAATTATATAAATGCA--C-C-TCTAATGAAAACA
*
451428 CTTTCGTG
125 CTTTCATG
*
451436 AAGAGTTTCTTGTAAGACCTTTTATTCAGGGTTGTGCCTAAACCCACAGCCAATAGCTTTTAAGT
1 AAGAGTTTCTTGTAAGACCTTTTATTCAGGGTTGTGCCTAAACCCACAGCCAACAGCTTTTAAGT
* *
451501 TGGATCCAAGCAACCACCACGCAATATATAATTATGTAAATGCACCTCTAATGAAAACACTTTCA
66 TGGATCCAAGCAACCACCACGCAATACATAATTATATAAATGCACCTCTAATGAAAACACTTTCA
451566 TG
131 TG
451568 AA
1 AA
451570 CGGGATGCTC
Statistics
Matches: 123, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
132 21 0.17
133 1 0.01
134 1 0.01
136 20 0.16
137 78 0.63
138 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (132 bp):
AAGAGTTTCTTGTAAGACCTTTTATTCAGGGTTGTGCCTAAACCCACAGCCAACAGCTTTTAAGT
TGGATCCAAGCAACCACCACGCAATACATAATTATATAAATGCACCTCTAATGAAAACACTTTCA
TG
Found at i:457766 original size:13 final size:14
Alignment explanation
Indices: 457730--457770 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
457720 TAAACCCCAA
457730 AAATCTCTAAA-CTC
1 AAATCTCTAAATC-C
457744 AAATCTCTAAATCC
1 AAATCTCTAAATCC
457758 AAA-CTCTAAATCC
1 AAATCTCTAAATCC
457771 CTAATTTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.38
14 15 0.58
15 1 0.04
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (14 bp):
AAATCTCTAAATCC
Found at i:458956 original size:3 final size:3
Alignment explanation
Indices: 458948--458974 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
458938 ACCACAACAT
458948 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
458975 TACTATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:459593 original size:23 final size:23
Alignment explanation
Indices: 459548--459594 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
459538 AACTATCTTT
* * *
459548 ATAATATAACAATGATATATAAA
1 ATAAAATAACAATAAAATATAAA
*
459571 ATAAAATAACAATAAAATTTAAA
1 ATAAAATAACAATAAAATATAAA
459594 A
1 A
459595 CCTAATATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (23 bp):
ATAAAATAACAATAAAATATAAA
Found at i:477505 original size:9 final size:9
Alignment explanation
Indices: 477493--477531 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
477483 AAGAAGAAAT
477493 AAAAGAGAA
1 AAAAGAGAA
477502 AAAATGAGAA
1 AAAA-GAGAA
*
477512 AAATGAGAA
1 AAAAGAGAA
477521 AAAA-AGAA
1 AAAAGAGAA
477529 AAA
1 AAA
477532 TGATGGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 7 0.26
9 12 0.44
10 8 0.30
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (9 bp):
AAAAGAGAA
Found at i:477513 original size:8 final size:9
Alignment explanation
Indices: 477501--477614 Score: 72
Period size: 8 Copynumber: 13.6 Consensus size: 9
477491 ATAAAAGAGA
477501 AAAAATGAG
1 AAAAATGAG
477510 AAAAATGAG
1 AAAAATGAG
*
477519 AAAAA-AAG
1 AAAAATGAG
477527 AAAAATGATGG
1 AAAAATGA--G
477538 AAAAATG-G
1 AAAAATGAG
477546 --AAA-GA-
1 AAAAATGAG
477551 AAAAATG-G
1 AAAAATGAG
**
477559 AAAAGGGAAG
1 AAAAATG-AG
477569 AAAAA--ATG
1 AAAAATGA-G
477577 AAAAATGA-
1 AAAAATGAG
477585 AAAAA-GAG
1 AAAAATGAG
*
477593 AAAAATGAA
1 AAAAATGAG
477602 AAAAATGA-
1 AAAAATGAG
477610 AAAAA
1 AAAAA
477615 AAAGAAATAA
Statistics
Matches: 84, Mismatches: 6, Indels: 31
0.69 0.05 0.26
Matches are distributed among these distances:
5 1 0.01
6 3 0.04
7 6 0.07
8 35 0.42
9 25 0.30
10 6 0.07
11 8 0.10
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (9 bp):
AAAAATGAG
Found at i:477581 original size:9 final size:9
Alignment explanation
Indices: 477569--477615 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
477559 AAAAGGGAAG
477569 AAAAAATG-
1 AAAAAATGA
477577 -AAAAATG-
1 AAAAAATGA
477584 AAAAAA-GA
1 AAAAAATGA
*
477592 GAAAAATGA
1 AAAAAATGA
477601 AAAAAATGA
1 AAAAAATGA
477610 AAAAAA
1 AAAAAA
477616 AAGAAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
7 8 0.24
8 10 0.29
9 16 0.47
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.09
Consensus pattern (9 bp):
AAAAAATGA
Found at i:479017 original size:51 final size:51
Alignment explanation
Indices: 478956--479417 Score: 656
Period size: 51 Copynumber: 8.9 Consensus size: 51
478946 AATTCGTTTA
*
478956 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAGGTTCG
1 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
*
479007 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCTGACAAGTTCG
1 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
479058 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
1 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
479109 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
1 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
479160 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
1 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
479211 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGGA-AAGTTCG
1 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGC-GGACAAGTTCG
* * * ** **
479262 TAGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTTA
1 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
* * * * * **
479313 TTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACTCATTTTA
1 TTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC-AAGTTCG
* * *
479369 TTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACA
1 TTGAAGATTG----AGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
479418 CGTTTTATGA
Statistics
Matches: 378, Mismatches: 22, Indels: 18
0.90 0.05 0.04
Matches are distributed among these distances:
50 3 0.01
51 294 0.78
52 4 0.01
53 2 0.01
54 2 0.01
55 31 0.08
56 42 0.11
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (51 bp):
TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
Found at i:479393 original size:56 final size:56
Alignment explanation
Indices: 479272--479495 Score: 228
Period size: 55 Copynumber: 4.1 Consensus size: 56
479262 TAGAAGATTG
* * * * * *
479272 AGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC-C-TGTTTATTGAAGATTTTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCGGACTCGT-TTTATTGAAGATTGTTCA
*
479327 AGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACTCATTTTATTGAAGATTGTTCA
1 AGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTTATTGAAGATTGTTCA
* * * * *
479383 AGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAGGATTGTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTTATTGAAGATTGTTCA
* * *
479438 AGTCTTATACT-TCCTGAAGGAATAGGGAGCAGG-CTCGTTAT-TTGAAGATTTTTCA
1 AGTCTTATACTCT-CTGAAGGAATAGAGAGC-GGACTCGTTTTATTGAAGATTGTTCA
479493 AGT
1 AGT
479496 ATTTATCCTG
Statistics
Matches: 142, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.01
55 85 0.60
56 54 0.38
57 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (56 bp):
AGTCTTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTTATTGAAGATTGTTCA
Found at i:479447 original size:111 final size:110
Alignment explanation
Indices: 479272--479495 Score: 260
Period size: 111 Copynumber: 2.0 Consensus size: 110
479262 TAGAAGATTG
* * *
479272 AGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATAC
1 AGTCCTATACTCCCTGAAAGAATAGAGAGCAGACCTGTTTATTGAAGATTGTTCGAGTTCTATAC
*
479337 -TCTCTGAAGGAATAGAGAGC-GGACTCATTTTATTGAAGATTGTTCA
66 TTC-CTGAAGGAATAGAGAGCAGG-CTCATTAT-TTGAAGATTGTTCA
* * * *
479383 AGTCTTATACTCTCTGAATGAATAGAGAGCAGACAC-GTTT-TATGAGGATTGTTCGAG-TCTTA
1 AGTCCTATACTCCCTGAAAGAATAGAGAGCAGAC-CTGTTTAT-TGAAGATTGTTCGAGTTC-TA
* * *
479445 TACTTCCTGAAGGAATAGGGAGCAGGCTCGTTATTTGAAGATTTTTCA
63 TACTTCCTGAAGGAATAGAGAGCAGGCTCATTATTTGAAGATTGTTCA
479493 AGT
1 AGT
479496 ATTTATCCTG
Statistics
Matches: 97, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
110 19 0.20
111 73 0.75
112 5 0.05
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (110 bp):
AGTCCTATACTCCCTGAAAGAATAGAGAGCAGACCTGTTTATTGAAGATTGTTCGAGTTCTATAC
TTCCTGAAGGAATAGAGAGCAGGCTCATTATTTGAAGATTGTTCA
Found at i:483870 original size:17 final size:17
Alignment explanation
Indices: 483845--483887 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
483835 ATATATTTTT
*
483845 AATTAAAAATATA-AAA
1 AATTTAAAATATATAAA
483861 ATATTTAAAATATATAAA
1 A-ATTTAAAATATATAAA
483879 AATTTAAAA
1 AATTTAAAA
483888 CTTTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 19 0.79
18 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTTAAAATATATAAA
Found at i:484260 original size:25 final size:25
Alignment explanation
Indices: 484194--484263 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
484184 GAGCGGTGAT
*
484194 TAGTATCATTATAAATATTTTTTCA
1 TAGTATCATTATAAATGTTTTTTCA
484219 TAGTATCATTATAAATGTTTTTTCA
1 TAGTATCATTATAAATGTTTTTTCA
484244 TAGTATCATTATAAATGTTT
1 TAGTATCATTATAAATGTTT
484264 AAAATATTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (25 bp):
TAGTATCATTATAAATGTTTTTTCA
Found at i:484968 original size:20 final size:20
Alignment explanation
Indices: 484945--484996 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
484935 AACGCGATCC
484945 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
484965 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
484985 CCAAAATCGCAA
1 CCAGAATCGCAA
484997 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:485135 original size:60 final size:60
Alignment explanation
Indices: 485052--485244 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
485042 GATTTTCCAT
* ** * * *
485052 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGTA
* * ***
485112 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGTA
* **
485172 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGTA
485233 AATCGCAACGCG
1 AATCGCAACGCG
485245 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 80 0.71
61 32 0.29
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGTA
Found at i:485146 original size:20 final size:20
Alignment explanation
Indices: 485052--485244 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
485042 GATTTTCCAT
* ** *
485052 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
485072 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
485092 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
485112 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
485132 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
485152 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
485172 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
485192 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
*
485213 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
485233 AATCGCAACGCG
1 AATCGCAACGCG
485245 ATATTTAAAG
Statistics
Matches: 143, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 16 0.11
22 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:485661 original size:32 final size:32
Alignment explanation
Indices: 485623--485691 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
485613 ATTTCACTTA
*
485623 GATTTCATTTCGCGTTACGATTCTGTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
* *
485655 GATTTCATTTCGCGTTGCTATTCTCTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
485687 GATTT
1 GATTT
485692 TCAAGTTAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (32 bp):
GATTTCATTTCGCGTTACGATTCTCTCGTTGC
Found at i:485672 original size:18 final size:18
Alignment explanation
Indices: 485623--485672 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
485613 ATTTCACTTA
*
485623 GATTTCATTTCGCGTTAC
1 GATTTCATTTCGCGTTGC
*
485641 GA-TTC-TGT--CGTTGC
1 GATTTCATTTCGCGTTGC
485655 GATTTCATTTCGCGTTGC
1 GATTTCATTTCGCGTTGC
485673 TATTCTCTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.28
15 3 0.12
16 4 0.16
17 3 0.12
18 8 0.32
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (18 bp):
GATTTCATTTCGCGTTGC
Found at i:485834 original size:14 final size:14
Alignment explanation
Indices: 485815--485869 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
485805 AGAATGACTG
485815 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
485829 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
485848 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
485862 TCGCAACG
1 TCGCAACG
485870 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:485852 original size:33 final size:33
Alignment explanation
Indices: 485815--485885 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
485805 AGAATGACTG
**
485815 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
485848 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
485881 TCGCA
1 TCGCA
485886 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:485903 original size:19 final size:19
Alignment explanation
Indices: 485881--485978 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
485871 GAAACCAAAA
*
485881 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
485900 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
485914 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
485933 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
485947 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
485966 TCGCGTTGCGATT
1 TCGCGTTGCGATT
485979 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:485922 original size:14 final size:14
Alignment explanation
Indices: 485903--485992 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
485893 TTTCATTTCG
485903 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
485917 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
485936 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
485950 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
485967 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
485983 CGTTGCGATT
1 CGTTGCGATT
485993 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:485928 original size:33 final size:33
Alignment explanation
Indices: 485886--486000 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
485876 CAAAATCGCA
485886 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
485919 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
485952 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
485985 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
486001 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:488026 original size:93 final size:93
Alignment explanation
Indices: 487693--488347 Score: 1266
Period size: 93 Copynumber: 7.1 Consensus size: 93
487683 TAGATTGCTT
*
487693 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
487758 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
487786 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
487850 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
487877 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
487942 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
487970 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
488035 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
488063 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AA-A-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
488125 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
488153 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
488218 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
488246 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
488311 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
488339 AGTAAATTT
1 AGTAAATTT
488348 ATCCATTCAA
Statistics
Matches: 556, Mismatches: 1, Indels: 10
0.98 0.00 0.02
Matches are distributed among these distances:
90 87 0.16
91 75 0.13
92 41 0.07
93 353 0.63
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:488215 original size:183 final size:186
Alignment explanation
Indices: 487693--488347 Score: 1266
Period size: 183 Copynumber: 3.5 Consensus size: 186
487683 TAGATTGCTT
*
487693 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
487758 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
487823 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTC-TTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
487877 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
487942 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
488007 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
488063 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AA-A-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
488125 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
488190 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
488246 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
488311 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
488348 ATCCATTCAA
Statistics
Matches: 465, Mismatches: 1, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
183 180 0.39
184 157 0.34
185 22 0.05
186 106 0.23
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:488288 original size:276 final size:277
Alignment explanation
Indices: 487693--488347 Score: 1278
Period size: 276 Copynumber: 2.4 Consensus size: 277
487683 TAGATTGCTT
*
487693 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
487758 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
487823 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTGGTTGAAAGTAAATTTGT
131 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTGGTTGAAAGTAAATTTGT
487888 TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGT
196 TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGT
487953 TTTGTCTTTTGGTTGAA
261 TTTGTCTTTTGGTTGAA
487970 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
488035 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
488100 GTGTATTCTTTAACACTGTG-AA-ATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
131 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTC-TTTGGTTGAAAGTAAATTTG
488163 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
195 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
488228 TTTTGTCTTTTGGTTGAA
260 TTTTGTCTTTTGGTTGAA
488246 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
488311 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
488348 ATCCATTCAA
Statistics
Matches: 376, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
275 20 0.05
276 207 0.55
277 149 0.40
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (277 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTGGTTGAAAGTAAATTTGT
TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGT
TTTGTCTTTTGGTTGAA
Found at i:488431 original size:19 final size:19
Alignment explanation
Indices: 488391--488519 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
488381 TAGTTTACTT
* *
488391 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
488411 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
488430 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
488449 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
488463 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
488482 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
488496 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
488515 TCGCA
1 TCGCA
488520 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:488470 original size:33 final size:32
Alignment explanation
Indices: 488427--488519 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
488417 CGCGAAACCA
**
488427 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
488459 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
488492 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
488520 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:488517 original size:52 final size:52
Alignment explanation
Indices: 488391--488519 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
488381 TAGTTTACTT
**
488391 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
488443 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
488496 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
488520 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:488537 original size:19 final size:19
Alignment explanation
Indices: 488515--488648 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
488505 GAAACCAAAA
*
488515 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
488534 TCGCGTTGCGA--TT-ATT
1 TCGCGTTGCGATTTTCATT
488550 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
* *
488566 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
488582 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
488599 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
488618 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
488638 TCGTGTTGCGA
1 TCGCGTTGCGA
488649 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
14 15 0.16
15 2 0.02
16 13 0.14
17 7 0.07
18 7 0.07
19 39 0.41
20 12 0.13
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:488556 original size:14 final size:14
Alignment explanation
Indices: 488537--488592 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
488527 TTTCATTTCG
488537 CGTTGCGATTATTT
1 CGTTGCGATTATTT
488551 CGTTGCGATTTCATTT
1 CGTTGCGA-TT-ATTT
* *
488567 CGCATTGCGATTCTGT
1 CG--TTGCGATTATTT
488583 CGTTGCGATT
1 CGTTGCGATT
488593 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 16 0.44
15 2 0.06
16 10 0.28
17 2 0.06
18 6 0.17
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTATTT
Found at i:488601 original size:33 final size:33
Alignment explanation
Indices: 488520--488611 Score: 150
Period size: 32 Copynumber: 2.8 Consensus size: 33
488510 CAAAATCGCA
*
488520 TTGCGATTTTCATTTCGCGTTGCGATTATTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTATGTCG
* *
488553 TTGCGA-TTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTATGTCG
488585 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
488612 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.54
33 25 0.46
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTATGTCG
Found at i:490568 original size:14 final size:14
Alignment explanation
Indices: 490549--490584 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
490539 ATTGTTTAAT
490549 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
490563 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
490577 TGATTTGT
1 TGATTTGT
490585 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:490706 original size:19 final size:19
Alignment explanation
Indices: 490690--490791 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
490680 CAAAATGACT
490690 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
490709 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
490728 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
490742 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
490761 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
490781 ATCGCAATGCG
1 ATCGCAATGCG
490792 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:490850 original size:19 final size:19
Alignment explanation
Indices: 490820--491106 Score: 329
Period size: 19 Copynumber: 16.4 Consensus size: 19
490810 GATTATCTCG
490820 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
490838 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
490857 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
490871 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
490890 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
490909 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
490928 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
490942 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
490961 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
490980 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
490994 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
491013 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
491032 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
491046 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
491066 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
491080 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
491099 TTGCGATT
1 TTGCGATT
491107 GTATTTTCCG
Statistics
Matches: 232, Mismatches: 10, Indels: 53
0.79 0.03 0.18
Matches are distributed among these distances:
14 35 0.15
16 31 0.13
17 27 0.12
18 9 0.04
19 118 0.51
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:490904 original size:52 final size:49
Alignment explanation
Indices: 490798--491074 Score: 303
Period size: 52 Copynumber: 5.3 Consensus size: 49
490788 TGCGTTTATA
490798 ATTTCGCATTGCGATTATC--TCG-TTGCGATTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATT-TCTTTCGATTGCGA-TTC-TTTCG--TTGCGATTTTC
490849 ATTTCGCATTGCGA-TTCTTTCG-TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTCTTTCGATTGCGA--TTC-TTTCG--TTGCGATTTTC
* *
490901 ATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTC
1 ATTTCGCATTGCGA-TTT-CTTTCG-ATTGCGATTCTTTCGTTGCGATTTTC
*
490953 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC-TTTCG-ATTGCGATTCTTTCGTTGCGATTTTC
*
491005 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC-TTTCG-ATTGCGATTCTTTCGTTGCGATTTTC
491057 ATTTCCGCATTGCGATTT
1 ATTT-CGCATTGCGATTT
491075 TCATGTTGGG
Statistics
Matches: 212, Mismatches: 4, Indels: 19
0.90 0.02 0.08
Matches are distributed among these distances:
49 2 0.01
50 1 0.00
51 23 0.11
52 156 0.74
53 10 0.05
54 6 0.03
55 8 0.04
57 6 0.03
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (49 bp):
ATTTCGCATTGCGATTTCTTTCGATTGCGATTCTTTCGTTGCGATTTTC
Found at i:490905 original size:71 final size:71
Alignment explanation
Indices: 490820--491106 Score: 357
Period size: 71 Copynumber: 4.1 Consensus size: 71
490810 GATTATCTCG
490820 TTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
490884 TTCGCA
66 TTCGCA
* *
490890 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
490955 TTCGCA
66 TTCGCA
*
490961 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATT
491021 TTCATTTCGCA
61 TTCATTTCGCA
* *
491032 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTTTC--GTTGCGATTTT
*
491090 CATTTCGCG
63 CATTTCGCA
491099 TTGCGATT
1 TTGCGATT
491107 GTATTTTCCG
Statistics
Matches: 192, Mismatches: 9, Indels: 33
0.82 0.04 0.14
Matches are distributed among these distances:
66 12 0.06
67 27 0.14
68 14 0.07
69 13 0.07
70 8 0.04
71 112 0.58
72 6 0.03
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:493406 original size:12 final size:12
Alignment explanation
Indices: 493389--493413 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
493379 TCTTCGGGGA
493389 CTTTTTCTTCTT
1 CTTTTTCTTCTT
493401 CTTTTTCTTCTT
1 CTTTTTCTTCTT
493413 C
1 C
493414 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:493620 original size:22 final size:24
Alignment explanation
Indices: 493588--493632 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
493578 CTGAAACATC
493588 ATCAAAATCC-G-TATTGACCAAT
1 ATCAAAATCCGGATATTGACCAAT
*
493610 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
493633 GACCAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 1 0.05
24 10 0.50
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:494342 original size:20 final size:20
Alignment explanation
Indices: 494314--494682 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
494304 AAATTTCAGT
* * * *
494314 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
494334 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
494354 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
494374 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
494394 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
494414 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
494434 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
494454 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
494474 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
494494 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
494514 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
494534 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
494554 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
494574 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
494594 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
494614 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
494634 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
494654 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
494674 GTTGCGATT
1 GTTGCGATT
494683 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:496795 original size:2 final size:2
Alignment explanation
Indices: 496788--496816 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
496778 CAAATCTCGT
496788 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
496817 GTATGTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:502770 original size:17 final size:17
Alignment explanation
Indices: 502750--502810 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
502740 TTCCTGTATC
502750 GTTCCTTTTACTGTACT
1 GTTCCTTTTACTGTACT
* *
502767 GTTCATTTTTCTGTACT
1 GTTCCTTTTACTGTACT
502784 GATT--TATTTACTGTACCT
1 G-TTCCT-TTTACTGTA-CT
502802 -TTCCTTTTA
1 GTTCCTTTTA
502811 TTACAATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 3 0.08
17 28 0.78
18 5 0.14
ACGTcount: A:0.15, C:0.20, G:0.10, T:0.56
Consensus pattern (17 bp):
GTTCCTTTTACTGTACT
Found at i:502792 original size:18 final size:17
Alignment explanation
Indices: 502750--502799 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
502740 TTCCTGTATC
*
502750 GTTCCTTTTACTGTACT
1 GTTCATTTTACTGTACT
*
502767 GTTCATTTTTCTGTACT
1 GTTCATTTTACTGTACT
*
502784 GATTTA-TTTACTGTAC
1 G-TTCATTTTACTGTAC
502800 CTTTCCTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 25 0.89
18 3 0.11
ACGTcount: A:0.16, C:0.18, G:0.12, T:0.54
Consensus pattern (17 bp):
GTTCATTTTACTGTACT
Found at i:502813 original size:333 final size:331
Alignment explanation
Indices: 502209--502840 Score: 1016
Period size: 333 Copynumber: 1.9 Consensus size: 331
502199 TAATACTATA
502209 CATAAAATATATGTAACATCTATAATCAAATTTATTCTAAAACAAGTTATTTGGTTGTTATCTAC
1 CATAAAATATATGTAACATCTATAATCAAATTTATTCTAAAACAAGTTATTTGGTTGTTATCTAC
* * * * * **
502274 CGTCACACGACCTCCCACTGATTTACACTATGTTTATAATATTTTATTGTAAAATGCATTTTTAA
66 CGCCACACGACCTCCCACTAATTTACACTATGTTTATAACATTTTACTGTAAAATGAATAATTAA
* * *
502339 ACTTATACAGTTTTTTATCATATACTTACTCTTTTTACTGTACTAATCTTTTCACTATATTATTC
131 ACTTATACAGTTCTTTATCATATACTTACTATTTTTACTGTACTAATATTTTCACTATATTATTC
**
502404 TTTTTCCTATATCGTTCCTTTCACTGTACTGTTTCTTTTTCTATACTGATTTATTTACTGTTTCT
196 TTTTTCCTATATCGTTCCTTTCACTGTACTGTTTCTTTTTCTATACTGATTTATTTACTGTACCT
* *
502469 TTCCTTTTATTACACTATTTCTCTTATTGTATTATATCTTTTACTGTTATGTATCTGACGTTGTA
261 TTCCTTTTATTACAATATTTCTCTTATTATATTATATCTTTTACTGTTATGTATCTGACGTTGTA
502534 CTATTT
326 CTATTT
* * *
502540 CATAAAATATATGTAACATCTATAATCAGATTTATTCTAAAACATGTTTATTTGGTTGTTGTCTA
1 CATAAAATATATGTAACATCTATAATCAAATTTATTCTAAAACAAG-TTATTTGGTTGTTATCTA
502605 CCGCCACACGACCTCCCACTAATTTACACTATGTTTATAACATTTTACTGTAAAATGTAATAATT
65 CCGCCACACGACCTCCCACTAATTTACACTATGTTTATAACATTTTACTGTAAAATG-AATAATT
*
502670 AAACTTGTACAGTTCTTTATCATATACTTACTATTTTT-CATGTACTAATATTTTCACTATATTA
129 AAACTTATACAGTTCTTTATCATATACTTACTATTTTTAC-TGTACTAATATTTTCACTATATTA
* * *
502734 TTCTTTTTCCTGTATCGTTCCTTTTACTGTACTG-TTCATTTTTCTGTACTGATTTATTTACTGT
193 TTCTTTTTCCTATATCGTTCCTTTCACTGTACTGTTTC-TTTTTCTATACTGATTTATTTACTGT
*
502798 ACCTTTCCTTTTATTACAATATTTCTCTTATTATATTGTATCT
257 ACCTTTCCTTTTATTACAATATTTCTCTTATTATATTATATCT
502841 GATGTTGTAC
Statistics
Matches: 275, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
331 44 0.16
332 74 0.27
333 157 0.57
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.48
Consensus pattern (331 bp):
CATAAAATATATGTAACATCTATAATCAAATTTATTCTAAAACAAGTTATTTGGTTGTTATCTAC
CGCCACACGACCTCCCACTAATTTACACTATGTTTATAACATTTTACTGTAAAATGAATAATTAA
ACTTATACAGTTCTTTATCATATACTTACTATTTTTACTGTACTAATATTTTCACTATATTATTC
TTTTTCCTATATCGTTCCTTTCACTGTACTGTTTCTTTTTCTATACTGATTTATTTACTGTACCT
TTCCTTTTATTACAATATTTCTCTTATTATATTATATCTTTTACTGTTATGTATCTGACGTTGTA
CTATTT
Found at i:503067 original size:65 final size:63
Alignment explanation
Indices: 502961--503148 Score: 223
Period size: 65 Copynumber: 2.9 Consensus size: 63
502951 GACTTTTACA
* * * *
502961 ATATTCAATTATTATTTCACCTCATGCACCATAAATGTACATGATTCATATGACTGATATGTACT
1 ATATTCAATTATCATCT-ACCTCATGCACCACAAA-GTACATGAGTCATATGACTGATATGTACT
* * *
503026 ATATTCAATTATCACTCTACCTCATGTACCACAAAGATACATGAGTCATATGAGTGATTTGTACT
1 ATATTCAATTATCA-TCTACCTCATGCACCACAAAG-TACATGAGTCATATGACTGATATGTACT
* * * *
503091 GTATACAATTATCATTCCACCTCATGCACCACAAAGGTACATGAGTCATATTACTGAT
1 ATATTCAATTATCA-TCTACCTCATGCACCACAAA-GTACATGAGTCATATGACTGAT
503149 CTGCACCACA
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
64 1 0.01
65 102 0.96
66 3 0.03
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (63 bp):
ATATTCAATTATCATCTACCTCATGCACCACAAAGTACATGAGTCATATGACTGATATGTACT
Found at i:503161 original size:35 final size:35
Alignment explanation
Indices: 503115--503186 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
503105 TTCCACCTCA
503115 TGCACCACAAAGGTACATGAGTCATATTACTGATC
1 TGCACCACAAAGGTACATGAGTCATATTACTGATC
503150 TGCACCACAAAGGTACATGAGTCATATTACTGATC
1 TGCACCACAAAGGTACATGAGTCATATTACTGATC
503185 TG
1 TG
503187 TATTGTATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (35 bp):
TGCACCACAAAGGTACATGAGTCATATTACTGATC
Found at i:503226 original size:100 final size:100
Alignment explanation
Indices: 503053--503241 Score: 288
Period size: 100 Copynumber: 1.9 Consensus size: 100
503043 TACCTCATGT
* * * *
503053 ACCACAAAGATACATGAGTCATATGAGTGATTTGTACTGTATACAATTATCATTCCACCTCATGC
1 ACCACAAAGATACATGAGTCATATGACTGATCTGTACTGTATACAATTATCACTCCACCCCATGC
*
503118 ACCACAAAGGTACATGAGTCATATTACTGATCTGC
66 ACCACAAAGGTACATGAATCATATTACTGATCTGC
* * * * *
503153 ACCACAAAGGTACATGAGTCATATTACTGATCTGTATTGTATTCAATTATCACTCTACCCCATGC
1 ACCACAAAGATACATGAGTCATATGACTGATCTGTACTGTATACAATTATCACTCCACCCCATGC
503218 ACCACAAAGGTACATGAATCATAT
66 ACCACAAAGGTACATGAATCATAT
503242 GAATGATATG
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 79 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (100 bp):
ACCACAAAGATACATGAGTCATATGACTGATCTGTACTGTATACAATTATCACTCCACCCCATGC
ACCACAAAGGTACATGAATCATATTACTGATCTGC
Found at i:503257 original size:165 final size:165
Alignment explanation
Indices: 502985--503305 Score: 489
Period size: 165 Copynumber: 1.9 Consensus size: 165
502975 TTTCACCTCA
* * * *
502985 TGCACCATAAATGTACATGATTCATATGACTGATATGTACTATATTCAATTATCACTCTACCTCA
1 TGCACCACAAAGGTACATGAGTCATATGACTGATATGTACTATATTCAATTATCACTCTACCCCA
* * * * *
503050 TGTACCACAAAGATACATGAGTCATATGAGTGATTTGTACTGTATACAATTATCATTCCACCTCA
66 TGCACCACAAAGATACATGAATCATATGAATGATATGTACTGTATACAATTATCACTCCACCTCA
*
503115 TGCACCACAAAGGTACATGAGTCATATTACTGATC
131 TGCACCAAAAAGGTACATGAGTCATATTACTGATC
* * * *
503150 TGCACCACAAAGGTACATGAGTCATATTACTGATCTGTATTGTATTCAATTATCACTCTACCCCA
1 TGCACCACAAAGGTACATGAGTCATATGACTGATATGTACTATATTCAATTATCACTCTACCCCA
* **
503215 TGCACCACAAAGGTACATGAATCATATGAATGATATGTACTGTATTTAATTATCACTCCACCTCA
66 TGCACCACAAAGATACATGAATCATATGAATGATATGTACTGTATACAATTATCACTCCACCTCA
503280 TGCACCAAAAAGGTACATGAGTCATA
131 TGCACCAAAAAGGTACATGAGTCATA
503306 GGAGTAATAT
Statistics
Matches: 139, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
165 139 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (165 bp):
TGCACCACAAAGGTACATGAGTCATATGACTGATATGTACTATATTCAATTATCACTCTACCCCA
TGCACCACAAAGATACATGAATCATATGAATGATATGTACTGTATACAATTATCACTCCACCTCA
TGCACCAAAAAGGTACATGAGTCATATTACTGATC
Found at i:503316 original size:65 final size:65
Alignment explanation
Indices: 503150--503305 Score: 231
Period size: 65 Copynumber: 2.4 Consensus size: 65
503140 ATTACTGATC
* * * * *
503150 TGCACCACAAAGGTACATGAGTCATATTACTGATCTGTATTGTATTCAATTATCACTCTACCCCA
1 TGCACCACAAAGGTACATGAGTCATATGAATGATATGTACTGTATTCAATTATCACTCCACCCCA
* * *
503215 TGCACCACAAAGGTACATGAATCATATGAATGATATGTACTGTATTTAATTATCACTCCACCTCA
1 TGCACCACAAAGGTACATGAGTCATATGAATGATATGTACTGTATTCAATTATCACTCCACCCCA
*
503280 TGCACCAAAAAGGTACATGAGTCATA
1 TGCACCACAAAGGTACATGAGTCATA
503306 GGAGTAATAT
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 81 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.29
Consensus pattern (65 bp):
TGCACCACAAAGGTACATGAGTCATATGAATGATATGTACTGTATTCAATTATCACTCCACCCCA
Found at i:505326 original size:18 final size:18
Alignment explanation
Indices: 505302--505345 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
505292 ATAATATGTT
*
505302 AACACATATACTCATG-CA
1 AACACATA-AATCATGACA
*
505320 CACACATAAATCATGACA
1 AACACATAAATCATGACA
505338 AACACATA
1 AACACATA
505346 CTTCTATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.50, C:0.27, G:0.05, T:0.18
Consensus pattern (18 bp):
AACACATAAATCATGACA
Found at i:511096 original size:129 final size:132
Alignment explanation
Indices: 510739--511129 Score: 711
Period size: 132 Copynumber: 3.0 Consensus size: 132
510729 GCCTGGTTCA
*
510739 TTTCATTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAG-TTGATCTTCAGCA
1 TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
* *
510803 AGCGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTAAGCGTTC
66 AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGCGTTC
510868 TT
131 TT
510870 TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
1 TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
510935 AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGCG-T-
66 AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGCGTTC
510998 TT
131 TT
511000 TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCT-CCTGCTAGTTTGATCTTCAGCA
1 TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
*
511064 AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTT-CTCAGCCTCAGTATGAAGGTTTACGTGTTC
66 AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGCGTTC
511128 TT
131 TT
511130 CTGACAATAA
Statistics
Matches: 253, Mismatches: 4, Indels: 7
0.96 0.02 0.03
Matches are distributed among these distances:
128 26 0.10
129 57 0.23
130 46 0.18
131 51 0.20
132 73 0.29
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (132 bp):
TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGCGTTC
TT
Found at i:512834 original size:29 final size:29
Alignment explanation
Indices: 512779--512835 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
512769 TATCATTAAA
512779 TTTTATCAAACTATTACAAAATTATATTTT
1 TTTTATCAAACTATTAC-AAATTATATTTT
512809 TTTTATCAAACTATTAC-AATCTATATT
1 TTTTATCAAACTATTACAAAT-TATATT
512836 CTTATAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 3 0.12
29 6 0.23
30 17 0.65
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (29 bp):
TTTTATCAAACTATTACAAATTATATTTT
Found at i:515752 original size:41 final size:43
Alignment explanation
Indices: 515695--515780 Score: 140
Period size: 41 Copynumber: 2.0 Consensus size: 43
515685 CGTGTAGCGC
*
515695 TAGACAAGGTTGGCAAGGTTTTAAGTTTT-A-AGTTTTAACCT
1 TAGACAAGGTTGGCAAGGTTTTAACTTTTAACAGTTTTAACCT
515736 TAGACAAGGTTGGCAAGGTTTTAACTTTTAACTAGTTTTAACCT
1 TAGACAAGGTTGGCAAGGTTTTAACTTTTAAC-AGTTTTAACCT
515780 T
1 T
515781 TGTAGACTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
41 28 0.68
42 1 0.02
44 12 0.29
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.40
Consensus pattern (43 bp):
TAGACAAGGTTGGCAAGGTTTTAACTTTTAACAGTTTTAACCT
Found at i:515775 original size:17 final size:20
Alignment explanation
Indices: 515753--515796 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
515743 GGTTGGCAAG
515753 GTTTTAA-CTTT-TA-ACTA
1 GTTTTAACCTTTGTAGACTA
515770 GTTTTAACCTTTGTAGACTA
1 GTTTTAACCTTTGTAGACTA
*
515790 ATTTTAA
1 GTTTTAA
515797 TATATAATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 7 0.30
18 4 0.17
19 2 0.09
20 10 0.43
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (20 bp):
GTTTTAACCTTTGTAGACTA
Done.