Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009238.1 Hibiscus syriacus cultivar Beakdansim tig00112864_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: 1094141
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 4 of 5
Found at i:716560 original size:21 final size:21
Alignment explanation
Indices: 716530--716585 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
716520 GATTCTGACT
716530 ATCGCATTGCGATTTCCCAAA
1 ATCGCATTGCGATTTCCCAAA
* * *
716551 ATCGCGTTGCGATTTTCCTAA
1 ATCGCATTGCGATTTCCCAAA
*
716572 ATCGCAATGCGATT
1 ATCGCATTGCGATT
716586 ACGTAAATCG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (21 bp):
ATCGCATTGCGATTTCCCAAA
Found at i:717369 original size:20 final size:20
Alignment explanation
Indices: 717344--717432 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
717334 CAACGCGGAA
717344 ATCGCAACG-GGAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
717364 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
717384 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
* *
717404 ATCGCAATGCAGAAATGACT
1 ATCGCAACGCGGAAATGACT
717424 ATCGCAACG
1 ATCGCAACG
717433 AGAGAATCGC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 57 0.93
21 4 0.07
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:717461 original size:33 final size:33
Alignment explanation
Indices: 717404--717498 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
717394 GGAATTGACT
**
717404 ATCGCAATGCAGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
717438 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
717471 ATCGCAATGCGAAAATGAAAATCGCAAC
1 ATCGCAATGCG-AAATGAAAATCGCAAC
717499 TCGAAATTAG
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:717575 original size:33 final size:33
Alignment explanation
Indices: 717514--717609 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
717504 ATTAGTTTCG
*
717514 CGTTGCGATTTTCATTTTTGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
**
717548 CGTTGCGATTTTCATTTCGCATTGCGATTTTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
** *
717581 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
717610 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 31 0.56
34 24 0.44
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:717813 original size:33 final size:33
Alignment explanation
Indices: 717751--717846 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 33
717741 ATTAGTTTCG
*
717751 CGTTGCGATTTTCATTTTCGCATTACGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
* *
717785 CGTTACGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
* ** *
717818 CATTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
717847 AGTCTGTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 30 0.57
34 23 0.43
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:717895 original size:237 final size:237
Alignment explanation
Indices: 717480--717954 Score: 887
Period size: 237 Copynumber: 2.0 Consensus size: 237
717470 AATCGCAATG
* * *
717480 CGAAAATGAAAATCGCAACTCGAAATTAGTTTCGCGTTGCGATTTTCATTTTTGCATTGCGATTC
1 CGAAAATGAAAATCGCAACGCGAAATTAGTTTCGCGTTGCGATTTTCATTTTCGCATTACGATTC
* * *
717545 ACTCGTTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGTCATTTCCGCGTTGCGAT
66 ACTCGTTACGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCATTTCCGCGTTGCGAT
717610 AGTCTGTTTTGCATTCAACATAATGCAAATTGAAATCAACAAATCAACTATTACATTTCAATCAA
131 AGTCTGTTTTGCATTCAACATAATGCAAATTGAAATCAACAAATCAACTATTACATTTCAATCAA
717675 TTAAACAAGCACAAATATTATGTACACATCAATTAAACAAAT
196 TTAAACAAGCACAAATATTATGTACACATCAATTAAACAAAT
717717 CGAAAATGAAAATCGCAACGCGAAATTAGTTTCGCGTTGCGATTTTCATTTTCGCATTACGATTC
1 CGAAAATGAAAATCGCAACGCGAAATTAGTTTCGCGTTGCGATTTTCATTTTCGCATTACGATTC
717782 ACTCGTTACGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCATTTCCGCGTTGCGAT
66 ACTCGTTACGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCATTTCCGCGTTGCGAT
*
717847 AGTCTGTTTTGCATTCAACATAATGCAGATTGAAATCAACAAATCAACTATTACATTTCAATCAA
131 AGTCTGTTTTGCATTCAACATAATGCAAATTGAAATCAACAAATCAACTATTACATTTCAATCAA
717912 TTAAACAAGCACAAATATTATGTACACATCAATTAAACAAAT
196 TTAAACAAGCACAAATATTATGTACACATCAATTAAACAAAT
717954 C
1 C
717955 AACATTTACA
Statistics
Matches: 231, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
237 231 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (237 bp):
CGAAAATGAAAATCGCAACGCGAAATTAGTTTCGCGTTGCGATTTTCATTTTCGCATTACGATTC
ACTCGTTACGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCATTTCCGCGTTGCGAT
AGTCTGTTTTGCATTCAACATAATGCAAATTGAAATCAACAAATCAACTATTACATTTCAATCAA
TTAAACAAGCACAAATATTATGTACACATCAATTAAACAAAT
Found at i:717967 original size:14 final size:14
Alignment explanation
Indices: 717948--717984 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
717938 CATCAATTAA
717948 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
717962 ACAAATCATCTTTT
1 ACAAATCAACATTT
717976 ACAAATCAA
1 ACAAATCAA
717985 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:719944 original size:20 final size:20
Alignment explanation
Indices: 719919--720017 Score: 146
Period size: 20 Copynumber: 5.0 Consensus size: 20
719909 AATAGAATCT
*
719919 GAAAATGACTATCGTAATGC
1 GAAAATGACTATCGCAATGC
719939 GAAAATGACTATCGCAATGC
1 GAAAATGACTATCGCAATGC
* *
719959 AAAAATGACTATCGTAATGC
1 GAAAATGACTATCGCAATGC
719979 GAAAATGACTATCGCAATGC
1 GAAAATGACTATCGCAATGC
*
719999 -AAATTTGACTATCGCAATG
1 GAAA-ATGACTATCGCAATG
720018 AGAGAATCAC
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
19 3 0.04
20 69 0.96
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.24
Consensus pattern (20 bp):
GAAAATGACTATCGCAATGC
Found at i:719975 original size:40 final size:40
Alignment explanation
Indices: 719920--720017 Score: 169
Period size: 40 Copynumber: 2.5 Consensus size: 40
719910 ATAGAATCTG
719920 AAAATGACTATCGTAATGCGAAAATGACTATCGCAATGCA
1 AAAATGACTATCGTAATGCGAAAATGACTATCGCAATGCA
719960 AAAATGACTATCGTAATGCGAAAATGACTATCGCAATGCA
1 AAAATGACTATCGTAATGCGAAAATGACTATCGCAATGCA
** *
720000 AATTTGACTATCGCAATG
1 AAAATGACTATCGTAATG
720018 AGAGAATCAC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (40 bp):
AAAATGACTATCGTAATGCGAAAATGACTATCGCAATGCA
Found at i:720080 original size:34 final size:37
Alignment explanation
Indices: 720041--720148 Score: 123
Period size: 40 Copynumber: 2.8 Consensus size: 37
720031 GCGATTTTCA
*
720041 TTTCGCATTGCGAT-TC-TTTCG-TTGCGATAGTAAT
1 TTTCGCATTGCGATATCATTTCGATTACGATAGTAAT
*
720075 TTTCGCATTGCGATAGTCATTTTCGCATTACGATAGTCAT
1 TTTCGCATTGCGATA-TCA-TTTCG-ATTACGATAGTAAT
720115 TTTCGCATTGCGATAGTCATTTTCGCATTACGAT
1 TTTCGCATTGCGATA-TCA-TTTCG-ATTACGAT
720149 TCTCTCGTTG
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
34 14 0.21
36 2 0.03
38 5 0.08
40 45 0.68
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (37 bp):
TTTCGCATTGCGATATCATTTCGATTACGATAGTAAT
Found at i:720087 original size:20 final size:20
Alignment explanation
Indices: 720062--720205 Score: 201
Period size: 20 Copynumber: 7.5 Consensus size: 20
720052 GATTCTTTCG
*
720062 TTGCGATAGTAATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
720082 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
720102 TTACGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
720122 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
720142 TTACGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
720156 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
720176 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
720196 TTGCGATAGT
1 TTGCGATAGT
720206 AAACTATTCT
Statistics
Matches: 110, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
14 6 0.05
16 6 0.05
18 6 0.05
20 92 0.84
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:722105 original size:20 final size:20
Alignment explanation
Indices: 722082--722135 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
722072 GAAACTTTAA
*
722082 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
722102 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
722122 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
722136 TGAAAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:722204 original size:20 final size:20
Alignment explanation
Indices: 722159--722207 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
722149 GCGATTCTCT
722159 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* ** *
722179 CATTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCAAATTCG
722199 CGTTGCGAT
1 CGTTGCGAT
722208 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:722598 original size:22 final size:22
Alignment explanation
Indices: 722537--722598 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
722527 TGACCGTTAA
* *
722537 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
722559 T-ATTATCGTC---G-TGGGGAC
1 TGATT-TCGTCGGAGATGGGGAC
722577 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
722599 GAATGTCGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 12 0.38
19 4 0.12
21 4 0.12
22 12 0.38
ACGTcount: A:0.19, C:0.16, G:0.37, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:723408 original size:15 final size:16
Alignment explanation
Indices: 723388--723425 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
723378 ATATTTAGCT
* *
723388 GGGCGGGCGGATG-TG
1 GGGCGGGCGAATGCGG
723403 GGGCGGGCGAATGCGG
1 GGGCGGGCGAATGCGG
723419 GGGCGGG
1 GGGCGGG
723426 TAATGTCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.08, C:0.16, G:0.68, T:0.08
Consensus pattern (16 bp):
GGGCGGGCGAATGCGG
Found at i:723690 original size:20 final size:20
Alignment explanation
Indices: 723665--723703 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
723655 GCTATGTAAA
*
723665 TCGCATTGCGATTTACGTAT
1 TCGCATTACGATTTACGTAT
723685 TCGCATTACGATTTACGTA
1 TCGCATTACGATTTACGTA
723704 AATCGCAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (20 bp):
TCGCATTACGATTTACGTAT
Found at i:723759 original size:62 final size:62
Alignment explanation
Indices: 723693--723819 Score: 227
Period size: 62 Copynumber: 2.0 Consensus size: 62
723683 ATTCGCATTA
723693 CGATTTACGTAAATCGCAACGCGAATTTGGGAAATCACAATGCGATAGTCAGAATCGCGTTG
1 CGATTTACGTAAATCGCAACGCGAATTTGGGAAATCACAATGCGATAGTCAGAATCGCGTTG
* * *
723755 CGATTTACGTAAATCGCAACGCGGATTTGGGAAATCGCAATGTGATAGTCAGAATCGCGTTG
1 CGATTTACGTAAATCGCAACGCGAATTTGGGAAATCACAATGCGATAGTCAGAATCGCGTTG
723817 CGA
1 CGA
723820 ACCTGGAAAC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (62 bp):
CGATTTACGTAAATCGCAACGCGAATTTGGGAAATCACAATGCGATAGTCAGAATCGCGTTG
Found at i:724397 original size:19 final size:19
Alignment explanation
Indices: 724373--724410 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
724363 CCTTGCTATT
724373 AAGTATTAGAGGGGATAAA
1 AAGTATTAGAGGGGATAAA
724392 AAGTATTAGAGGGGATAAA
1 AAGTATTAGAGGGGATAAA
724411 CGAGTCATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.32, T:0.21
Consensus pattern (19 bp):
AAGTATTAGAGGGGATAAA
Found at i:724622 original size:32 final size:31
Alignment explanation
Indices: 724586--724645 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
724576 TGATTTTTGG
* *
724586 GTCGGGTTAATATCATATCAGTTAGATTTCAA
1 GTCGGGTCAATATCAAATCAGTT-GATTTCAA
*
724618 GTCGGGTCAATATCAAATCGGTTGATTT
1 GTCGGGTCAATATCAAATCAGTTGATTT
724646 TCGATTTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 5 0.20
32 20 0.80
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (31 bp):
GTCGGGTCAATATCAAATCAGTTGATTTCAA
Found at i:725129 original size:19 final size:17
Alignment explanation
Indices: 725087--725129 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
725077 ATAAATATAA
725087 TATTATTTCCTTTATTT
1 TATTATTTCCTTTATTT
*
725104 TAGTTATTTTCTATTATTTT
1 TA-TTATTTCCT-TTA-TTT
725124 TATTAT
1 TATTAT
725130 AAATCTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 8 0.36
19 7 0.32
20 5 0.23
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTTCCTTTATTT
Found at i:725292 original size:17 final size:19
Alignment explanation
Indices: 725244--725304 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 19
725234 AAGTAAACTT
*
725244 TATATTATTTTTATTATAAA
1 TATAATATTTTTATT-TAAA
*
725264 TATAATATTTTTATTTAAT
1 TATAATATTTTTATTTAAA
725283 TATAA-A-TTTTATTTAAA
1 TATAATATTTTTATTTAAA
725300 T-TAAT
1 TATAAT
725305 TTATTATCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 3 0.08
17 11 0.30
18 1 0.03
19 8 0.22
20 14 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATAATATTTTTATTTAAA
Found at i:725311 original size:17 final size:17
Alignment explanation
Indices: 725245--725311 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
725235 AGTAAACTTT
*
725245 ATATTATTTTTATTATAA
1 ATATAATTTTTATT-TAA
725263 ATATAATATTTTTATTTAA
1 ATAT-A-ATTTTTATTTAA
* *
725282 TTATAAATTTTATTTAA
1 ATATAATTTTTATTTAA
725299 AT-TAATTTATTAT
1 ATATAATTT-TTAT
725312 CCAGTTCGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
16 5 0.12
17 16 0.39
18 5 0.12
19 6 0.15
20 9 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATAATTTTTATTTAA
Found at i:725435 original size:22 final size:23
Alignment explanation
Indices: 725404--725451 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
725394 TGGTTCGGGT
*
725404 TTTTCGGTTCGGGTTAATTTAAG
1 TTTTCGGTTCCGGTTAATTTAAG
* *
725427 TTTT-GGTTCCGGTTACTTTCAG
1 TTTTCGGTTCCGGTTAATTTAAG
725449 TTT
1 TTT
725452 CGCTAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.12, C:0.12, G:0.23, T:0.52
Consensus pattern (23 bp):
TTTTCGGTTCCGGTTAATTTAAG
Found at i:727410 original size:33 final size:33
Alignment explanation
Indices: 727373--727438 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
727363 TTATTTAATA
727373 ACTTTAATCCCATAGTTATTGAGATTAGTGATG
1 ACTTTAATCCCATAGTTATTGAGATTAGTGATG
727406 ACTTTAATCCCATAGTTATTGAGATTAGTGATG
1 ACTTTAATCCCATAGTTATTGAGATTAGTGATG
727439 GTTTTTGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (33 bp):
ACTTTAATCCCATAGTTATTGAGATTAGTGATG
Found at i:728095 original size:17 final size:17
Alignment explanation
Indices: 728075--728109 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
728065 TTGATTTTTA
*
728075 TTTTTGTTTGGGTTTGC
1 TTTTGGTTTGGGTTTGC
*
728092 TTTTGGTTTGTGTTTGC
1 TTTTGGTTTGGGTTTGC
728109 T
1 T
728110 GATTTTAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.06, G:0.29, T:0.66
Consensus pattern (17 bp):
TTTTGGTTTGGGTTTGC
Found at i:730929 original size:27 final size:27
Alignment explanation
Indices: 730899--730965 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 27
730889 CCTAAACCCG
730899 AAACCGACCCGAATATCACACTTAAAA
1 AAACCGACCCGAATATCACACTTAAAA
* *
730926 AAACCCAACTCGAATATCACACTTAAAA
1 AAA-CCGACCCGAATATCACACTTAAAA
*
730954 AACCCGACCCGA
1 AAACCGACCCGA
730966 CCCGAATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 10 0.29
28 24 0.71
ACGTcount: A:0.46, C:0.33, G:0.07, T:0.13
Consensus pattern (27 bp):
AAACCGACCCGAATATCACACTTAAAA
Found at i:733251 original size:59 final size:58
Alignment explanation
Indices: 733148--733277 Score: 138
Period size: 59 Copynumber: 2.2 Consensus size: 58
733138 TTGAATGACA
*
733148 ATTTTGTAACTTTTAAAAGTCAAGAGACTTAACAAAACAACACCCTATAATCGGAGACC
1 ATTTTGTAACTTTTAAAAGTCAAGAGACTAAACAAAACAACACCCTATAATCGG-GACC
** **** * *
733207 ATTTTGTAACTTTTAATTGTCGAA-AGACTAAACAAAGTTGCACCCTGTAGTCGGGACC
1 ATTTTGTAACTTTTAAAAGTC-AAGAGACTAAACAAAACAACACCCTATAATCGGGACC
733265 ATTTATGT-ACTTT
1 ATTT-TGTAACTTT
733278 ACCCTAGAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 13 0.22
59 45 0.75
60 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (58 bp):
ATTTTGTAACTTTTAAAAGTCAAGAGACTAAACAAAACAACACCCTATAATCGGGACC
Found at i:736643 original size:14 final size:15
Alignment explanation
Indices: 736611--736645 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
736601 TTTCAGATTT
*
736611 TCACATTGTTTAGTA
1 TCACATAGTTTAGTA
736626 TCACATAGTTTA-TA
1 TCACATAGTTTAGTA
736640 TCACAT
1 TCACAT
736646 GTTCACGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (15 bp):
TCACATAGTTTAGTA
Found at i:736656 original size:22 final size:23
Alignment explanation
Indices: 736626--736668 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
736616 TTGTTTAGTA
*
736626 TCACATAGTT-TATATCACATGT
1 TCACATAGTTCGATATCACATGT
*
736648 TCACGTAGTTCGATATCACAT
1 TCACATAGTTCGATATCACAT
736669 AATTTATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (23 bp):
TCACATAGTTCGATATCACATGT
Found at i:736665 original size:37 final size:37
Alignment explanation
Indices: 736624--736727 Score: 172
Period size: 37 Copynumber: 2.8 Consensus size: 37
736614 CATTGTTTAG
* *
736624 TATCACATAGTTTATATCACATGTTCACGTAGTTCGA
1 TATCACATAGTTTATATCACATGTTCACATAATTCGA
* *
736661 TATCACATAATTTATATCACATGTTCACATAATTCGG
1 TATCACATAGTTTATATCACATGTTCACATAATTCGA
736698 TATCACATAGTTTATATCACATGTTCACAT
1 TATCACATAGTTTATATCACATGTTCACAT
736728 GTTCATGTAG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (37 bp):
TATCACATAGTTTATATCACATGTTCACATAATTCGA
Found at i:739854 original size:58 final size:59
Alignment explanation
Indices: 739747--739862 Score: 137
Period size: 58 Copynumber: 2.0 Consensus size: 59
739737 ATAGTTGAAT
* * *
739747 GACCATTTTGTAACTTTTAAAAGTCGAGGGACTTAACAAAACAACACCCTATAGTCGGG
1 GACCATTTTATAACTTTTAAAAGTCGAGGGACTAAACAAAACAACACCCTATACTCGGG
*** **
739806 GACCATTTTATAACTTTTAGCTGTCG-GGGACTAAACAAAGA-TGCACCCTATACTCGG
1 GACCATTTTATAACTTTTAAAAGTCGAGGGACTAAACAAA-ACAACACCCTATACTCGG
739863 AGATTATTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
58 25 0.52
59 23 0.48
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (59 bp):
GACCATTTTATAACTTTTAAAAGTCGAGGGACTAAACAAAACAACACCCTATACTCGGG
Found at i:740875 original size:28 final size:28
Alignment explanation
Indices: 740843--740899 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
740833 GAATAAAATA
740843 TCACCCATATGGAAAAGTAAATGTATTC
1 TCACCCATATGGAAAAGTAAATGTATTC
740871 TCACCCATATGGAAAAGTAAATGTATTC
1 TCACCCATATGGAAAAGTAAATGTATTC
740899 T
1 T
740900 AATATTTTAT
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:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (28 bp):
TCACCCATATGGAAAAGTAAATGTATTC
Found at i:742731 original size:23 final size:23
Alignment explanation
Indices: 742701--742745 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
742691 TCGAGGGTTT
* *
742701 TACGCGGTCCTTTGGGACATTTC
1 TACGCGGTCCTTCGAGACATTTC
742724 TACGCGGTCCTTCGAGACATTT
1 TACGCGGTCCTTCGAGACATTT
742746 ATGTGGTCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.33
Consensus pattern (23 bp):
TACGCGGTCCTTCGAGACATTTC
Found at i:770999 original size:2 final size:2
Alignment explanation
Indices: 770992--771030 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
770982 TATACCTGCA
770992 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
771031 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:771035 original size:2 final size:2
Alignment explanation
Indices: 771030--771068 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
771020 ATATATATAT
771030 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
771069 TCCTGCTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:772498 original size:6 final size:6
Alignment explanation
Indices: 772487--772513 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
772477 GATGATAAAT
772487 GGGGAC GGGGAC GGGGAC GGGGAC GGG
1 GGGGAC GGGGAC GGGGAC GGGGAC GGG
772514 TTTGGTAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.70, T:0.00
Consensus pattern (6 bp):
GGGGAC
Found at i:772580 original size:12 final size:13
Alignment explanation
Indices: 772536--772579 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
772526 CGCCCCGATT
772536 ACCCGATTACCCG
1 ACCCGATTACCCG
*
772549 CCCCGATTACCCG
1 ACCCGATTACCCG
772562 -CCCGA-TACCCG
1 ACCCGATTACCCG
772573 ACCCGAT
1 ACCCGAT
772580 AAATATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 6 0.21
12 10 0.36
13 12 0.43
ACGTcount: A:0.20, C:0.50, G:0.16, T:0.14
Consensus pattern (13 bp):
ACCCGATTACCCG
Found at i:772722 original size:12 final size:12
Alignment explanation
Indices: 772707--772741 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
772697 CGATTCTCGG
*
772707 CCCAATACCCTA
1 CCCAATACCCGA
*
772719 CCCAATACCCGG
1 CCCAATACCCGA
772731 CCCAATACCCG
1 CCCAATACCCG
772742 TTTAAATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.29, C:0.51, G:0.09, T:0.11
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:773828 original size:31 final size:31
Alignment explanation
Indices: 773704--773849 Score: 129
Period size: 31 Copynumber: 4.7 Consensus size: 31
773694 TATCTATGAC
* *
773704 CTTTAGATAAAAT-GCTAATTTAATC-CTTAAA
1 CTTTAGATAAAATATC-AATTTGA-CGCTTAAA
* *
773735 TTTTAGATAAAAATAAT-AATTTGACACTTAAA
1 CTTTAGAT-AAAAT-ATCAATTTGACGCTTAAA
* * *
773767 CTTT-GTATAAAGTATCAGTTTGATGCTTAAA
1 CTTTAG-ATAAAATATCAATTTGACGCTTAAA
* *
773798 CTTTAGATAAAATATCAATTTTACGTTTAAA
1 CTTTAGATAAAATATCAATTTGACGCTTAAA
*
773829 ATTTAGATAAAATATCAATTT
1 CTTTAGATAAAATATCAATTT
773850 TCCTGCCACT
Statistics
Matches: 94, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
30 2 0.02
31 69 0.73
32 23 0.24
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.40
Consensus pattern (31 bp):
CTTTAGATAAAATATCAATTTGACGCTTAAA
Found at i:777633 original size:10 final size:10
Alignment explanation
Indices: 777620--777648 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
777610 GTTCAATCGT
777620 GGTTGAACCC
1 GGTTGAACCC
777630 GGTTGAACCC
1 GGTTGAACCC
777640 GGTTGAACC
1 GGTTGAACC
777649 AGTGAACCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.28, G:0.31, T:0.21
Consensus pattern (10 bp):
GGTTGAACCC
Found at i:778001 original size:45 final size:43
Alignment explanation
Indices: 777892--778013 Score: 147
Period size: 45 Copynumber: 2.7 Consensus size: 43
777882 TTTAATGAAA
**
777892 ATAATATTTGTGAAATTTACCTATTAATGTTAAGGTTATGTAAT
1 ATAATATTTGTGAAATTTAAATATTAAT-TTAAGGTTATGTAAT
* * *
777936 ATAATAATATAT-ATATTTTAAATATTAATATTAAGGTTATGTAAT
1 ATAAT-ATTTGTGA-AATTTAAATATTAAT-TTAAGGTTATGTAAT
777981 ATTAATATTTGTGAAATTTAAATATTAATTTAA
1 A-TAATATTTGTGAAATTTAAATATTAATTTAA
778014 AACTAAAAGT
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
44 10 0.15
45 50 0.77
46 5 0.08
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (43 bp):
ATAATATTTGTGAAATTTAAATATTAATTTAAGGTTATGTAAT
Found at i:780311 original size:21 final size:22
Alignment explanation
Indices: 780278--780320 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
780268 TTCTACCGTT
* * *
780278 GATTATTATGATGTTTATGTGA
1 GATTATTACGATGCTGATGTGA
780300 GATT-TTACGATGCTGATGTGA
1 GATTATTACGATGCTGATGTGA
780321 TAATTTATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.44
Consensus pattern (22 bp):
GATTATTACGATGCTGATGTGA
Found at i:780587 original size:83 final size:82
Alignment explanation
Indices: 780451--780773 Score: 406
Period size: 83 Copynumber: 4.0 Consensus size: 82
780441 CAATGAATTA
* * * *
780451 TCACGTCAATACTGTAACGGTTAATAAAGAAAAACGTTGGTCAAATGCTCATATTAAGTTTGTTT
1 TCACGTCAATACCGTAACAG---ATAAAAAAAAACGTTGATCAAATGCTCATATTAAGTTTGTTT
780516 TCTTAACTAAAGAATTTCAT
63 TCTTAACTAAAGAATTTCAT
* * * * *
780536 TCACGTCAATACCGTAACAGACAATAAAAAAATGTTGGTAAAATGCTCATATTAAGTTTTTTTTC
1 TCACGTCAATACCGTAACAGATAA-AAAAAAACGTTGATCAAATGCTCATATTAAGTTTGTTTTC
780601 TTAACTAAAGAATTTCAT
65 TTAACTAAAGAATTTCAT
* * *
780619 TCACGTCAATACCGT---A-ATAAAGAAAAACGTTGATCAAATGCTCATATTAATTTTATTTTCT
1 TCACGTCAATACCGTAACAGATAAAAAAAAACGTTGATCAAATGCTCATATTAAGTTTGTTTTCT
780680 TAACTAAAGAATTTCAT
66 TAACTAAAGAATTTCAT
* * * * * *
780697 TCACGTCAATACCGTAAC-GGTAAAAAAAAATGTTAATCAAATACTCATATTAAATTTGGTTT-T
1 TCACGTCAATACCGTAACAGATAAAAAAAAACGTTGATCAAATGCTCATATTAAGTTTGTTTTCT
780760 TAACTAAAGAATTT
66 TAACTAAAGAATTT
780774 TATTGATAAA
Statistics
Matches: 211, Mismatches: 22, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
78 67 0.32
79 3 0.01
80 16 0.08
81 35 0.17
82 3 0.01
83 69 0.33
85 18 0.09
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (82 bp):
TCACGTCAATACCGTAACAGATAAAAAAAAACGTTGATCAAATGCTCATATTAAGTTTGTTTTCT
TAACTAAAGAATTTCAT
Found at i:780692 original size:78 final size:78
Alignment explanation
Indices: 780472--780773 Score: 383
Period size: 78 Copynumber: 3.8 Consensus size: 78
780462 CTGTAACGGT
* * *
780472 TAATAAAGAAAAACGTTGGTCAAATGCTCATATTAAGTTTGTTTTCTTAACTAAAGAATTTCATT
1 TAATAAAAAAAAACGTTGATCAAATGCTCATATTAATTTTGTTTTCTTAACTAAAGAATTTCATT
780537 CACGTCAATACCG
66 CACGTCAATACCG
* * * *
780550 TAACAGACAATAAAAAAATGTTGGTAAAATGCTCATATTAAGTTTT-TTTTCTTAACTAAAGAAT
1 T---A-ATAA-AAAAAAACGTTGATCAAATGCTCATATTAA-TTTTGTTTTCTTAACTAAAGAAT
780614 TTCATTCACGTCAATACCG
60 TTCATTCACGTCAATACCG
* *
780633 TAATAAAGAAAAACGTTGATCAAATGCTCATATTAATTTTATTTTCTTAACTAAAGAATTTCATT
1 TAATAAAAAAAAACGTTGATCAAATGCTCATATTAATTTTGTTTTCTTAACTAAAGAATTTCATT
780698 CACGTCAATACCG
66 CACGTCAATACCG
* * * * *
780711 TAACGGTAAAAAAAAATGTTAATCAAATACTCATATTAAATTTGGTTT-TTAACTAAAGAATTT
1 TAA---TAAAAAAAAACGTTGATCAAATGCTCATATTAATTTTGTTTTCTTAACTAAAGAATTT
780774 TATTGATAAA
Statistics
Matches: 197, Mismatches: 17, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
77 4 0.02
78 67 0.34
79 3 0.02
80 16 0.08
81 36 0.18
82 3 0.02
83 65 0.33
84 3 0.02
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (78 bp):
TAATAAAAAAAAACGTTGATCAAATGCTCATATTAATTTTGTTTTCTTAACTAAAGAATTTCATT
CACGTCAATACCG
Found at i:793321 original size:18 final size:20
Alignment explanation
Indices: 793298--793335 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
793288 AATTATCATA
793298 TATTTT-TA-AAAAATTATG
1 TATTTTCTATAAAAATTATG
793316 TATTTTCTATTAAAAATTAT
1 TATTTTCTA-TAAAAATTAT
793336 TTTCGCCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
21 9 0.53
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
TATTTTCTATAAAAATTATG
Found at i:793973 original size:21 final size:21
Alignment explanation
Indices: 793949--793992 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
793939 ATCATCTTTT
*
793949 AATTT-TACATTATAAATATTA
1 AATTTGTACATCATAAAT-TTA
*
793970 AATTTGTACCTCATAAATTTA
1 AATTTGTACATCATAAATTTA
793991 AA
1 AA
793993 ATTATTTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (21 bp):
AATTTGTACATCATAAATTTA
Found at i:794083 original size:97 final size:99
Alignment explanation
Indices: 793974--794165 Score: 259
Period size: 97 Copynumber: 2.0 Consensus size: 99
793964 ATATTAAATT
* *
793974 TGTACCTCATAAATTTAAAA-TTATTTGATATCG-TATTATAAAATTATGAATGTAT-AATTTTA
1 TGTACCTCATAAA-TTAAAATTTAGTTGATA-CGATATTATAAAATTATGAATATATGAATTTTA
794036 AATTACATTTA-ATTATTAAATAAAAGTTAATTTTG
64 AATTACATTTATATTATTAAATAAAAGTTAATTTTG
* *
794071 TGTACCAT-ATAAATTAAAATTTAGTTGATACGATATTATAAAATTATGGATATATGATTTTTAA
1 TGTACC-TCATAAATTAAAATTTAGTTGATACGATATTATAAAATTATGAATATATGAATTTTAA
* * *
794135 ATTAGATTTATTTTTTTAAATAAAAGTTAAT
65 ATTACATTTATATTATTAAATAAAAGTTAAT
794166 GCTTAAATCA
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
96 8 0.10
97 40 0.48
98 17 0.20
99 18 0.22
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (99 bp):
TGTACCTCATAAATTAAAATTTAGTTGATACGATATTATAAAATTATGAATATATGAATTTTAAA
TTACATTTATATTATTAAATAAAAGTTAATTTTG
Found at i:805872 original size:33 final size:33
Alignment explanation
Indices: 805835--805900 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
805825 TACATTGGCA
*** *
805835 GGTTTTAGGCCATTTTTCCACAAATGGCTTCCG
1 GGTTTTAGGCCACCGTTCCACAAATGGATTCCG
805868 GGTTTTAGGCCACCGTTCCACAAATGGATTCCG
1 GGTTTTAGGCCACCGTTCCACAAATGGATTCCG
805901 AAGGAGATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.32
Consensus pattern (33 bp):
GGTTTTAGGCCACCGTTCCACAAATGGATTCCG
Found at i:810023 original size:18 final size:19
Alignment explanation
Indices: 810000--810039 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
809990 TTTCAGGCTT
* *
810000 AGGATGA-TCGTCGGTGGG
1 AGGATGATTCGCCAGTGGG
810018 AGGATGATTCGCCAGTGGG
1 AGGATGATTCGCCAGTGGG
810037 AGG
1 AGG
810040 TCCATGTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.20, C:0.12, G:0.47, T:0.20
Consensus pattern (19 bp):
AGGATGATTCGCCAGTGGG
Found at i:810381 original size:53 final size:53
Alignment explanation
Indices: 810301--810411 Score: 177
Period size: 53 Copynumber: 2.1 Consensus size: 53
810291 TTATTTATCA
* * *
810301 GTAATGATATCTTCCGTGACCGTTATTGAAAGACTGTGATACTCATAATCATT
1 GTAATGATATCTTCCGTGACCATTATTGAAAGACTGCGATACTCATAATCACT
* *
810354 GTAATGATATTTTCCGTGACCATTATTGAAAGATTGCGATACTCATAATCACT
1 GTAATGATATCTTCCGTGACCATTATTGAAAGACTGCGATACTCATAATCACT
810407 GTAAT
1 GTAAT
810412 AGCGTCTGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (53 bp):
GTAATGATATCTTCCGTGACCATTATTGAAAGACTGCGATACTCATAATCACT
Found at i:810739 original size:84 final size:87
Alignment explanation
Indices: 810618--810789 Score: 323
Period size: 84 Copynumber: 2.0 Consensus size: 87
810608 ATATTTTAGA
810618 TATTTATTTTACAAATAAATTTAATGAAAATTGAGACTAAAGAAAGTAAAGATGATAAATCT-AA
1 TATTTATTTTACAAATAAATTTAATGAAAATTGAGACTAAAGAAAGTAAAGATGATAAATCTAAA
810682 A-ATAAAAAGA-TTTTAAGATT
66 ATATAAAAAGATTTTTAAGATT
810702 TATTTATTTTACAAATAAATTTAATGAAAATTGAGACTAAAGAAAGTAAAGATGATAAATCTAAA
1 TATTTATTTTACAAATAAATTTAATGAAAATTGAGACTAAAGAAAGTAAAGATGATAAATCTAAA
810767 ATATAAAAAGATTTTTAAGATT
66 ATATAAAAAGATTTTTAAGATT
810789 T
1 T
810790 TAATTTTATA
Statistics
Matches: 85, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
84 62 0.73
85 3 0.04
86 9 0.11
87 11 0.13
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.34
Consensus pattern (87 bp):
TATTTATTTTACAAATAAATTTAATGAAAATTGAGACTAAAGAAAGTAAAGATGATAAATCTAAA
ATATAAAAAGATTTTTAAGATT
Found at i:812225 original size:3 final size:3
Alignment explanation
Indices: 812217--812253 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
812207 AAACTTTATG
812217 TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
812254 TACTACTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:812243 original size:17 final size:17
Alignment explanation
Indices: 812221--812253 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
812211 TTTATGTAAT
812221 AATAATAATAATAATAA
1 AATAATAATAATAATAA
812238 AATAATAATAATAATA
1 AATAATAATAATAATA
812254 TACTACTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAATAATAATAATAA
Found at i:813069 original size:20 final size:20
Alignment explanation
Indices: 813040--813081 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
813030 TAATTAAAGC
*
813040 AACACAACTAGATTGAATAG
1 AACACAACTAAATTGAATAG
*
813060 AACACGACTAAATTGAATAG
1 AACACAACTAAATTGAATAG
813080 AA
1 AA
813082 ATAAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.19
Consensus pattern (20 bp):
AACACAACTAAATTGAATAG
Found at i:814066 original size:68 final size:67
Alignment explanation
Indices: 813951--814086 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 67
813941 CAGAAATCAC
813951 AGTTTACCCGTCGGCCTAGAGAACATCGGCCTCGGTTTAAGAGGGATTCTGAAAGCGAGCGCGAT
1 AGTTTACCCGTCGGCCTAGAGAACATCGGCCTCGGTTTAAGAGGGATTCTGAAAGCGAGCGCGAT
814016 AA
66 AA
814018 AGTTTATCCCGTCGGCCTAGAGAACATCGGCCTCGGTTTAAGAGGGATTCTGAAAGCGAGCGCGA
1 AGTTTA-CCCGTCGGCCTAGAGAACATCGGCCTCGGTTTAAGAGGGATTCTGAAAGCGAGCGCGA
814083 TAA
65 TAA
814086 A
1 A
814087 TGCGACGGTA
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
67 6 0.09
68 62 0.91
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.21
Consensus pattern (67 bp):
AGTTTACCCGTCGGCCTAGAGAACATCGGCCTCGGTTTAAGAGGGATTCTGAAAGCGAGCGCGAT
AA
Found at i:818612 original size:28 final size:28
Alignment explanation
Indices: 818580--818634 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
818570 TTGTCGTTAC
* *
818580 TTTCAAGCACTGCCTTGACAACATAATG
1 TTTCAAGCACTGACTCGACAACATAATG
* *
818608 TTTCAAGCATTGACTCGACGACATAAT
1 TTTCAAGCACTGACTCGACAACATAAT
818635 ATAAATTGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.29
Consensus pattern (28 bp):
TTTCAAGCACTGACTCGACAACATAATG
Found at i:818854 original size:29 final size:30
Alignment explanation
Indices: 818821--818878 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
818811 ATGCCTCTTT
* * *
818821 TTCCAGTTTAGTGTCTAAC-GTTTATTTCA
1 TTCCAATTTAGTGCCTAACACTTTATTTCA
*
818850 TTCCAATTTGGTGCCTAACACTTTATTTC
1 TTCCAATTTAGTGCCTAACACTTTATTTC
818879 GTTACTCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.47
Consensus pattern (30 bp):
TTCCAATTTAGTGCCTAACACTTTATTTCA
Found at i:822724 original size:194 final size:199
Alignment explanation
Indices: 822331--822729 Score: 601
Period size: 199 Copynumber: 2.0 Consensus size: 199
822321 TGAACTGTAC
* *
822331 AAATTAGATCGAAAGGGTAGCCATTGCCTCTACGATACCTAATCCTGATTAATCAATTAATAAAT
1 AAATTAGATCGAAAGGGTAGCCATCGCCTCTACGATACCTAATCCAGATTAATCAATTAATAAAT
*
822396 CACATATCAATGATTATACATAAAAATACAACACCAAAATTTGACCTAATTTGAATATTTTTTAA
66 CACATACCAATGATTATACATAAAAATACAACACCAAAATTTGACCTAATTTGAATATTTTTTAA
*
822461 TTATAATAAATTATATTTTATATAACTCGATGTAACTTATAATATAGAAATATATATACTATTAT
131 TTATAATAAATTATATTTTATATAACTCGATGTAACTTATAATATAGAAATATATATAATATTAT
822526 GCTT
196 GCTT
* * * ** *
822530 AAATTAGATTGAAAGTGTAGCCCTCGCCTCTACGATATTTAATCCAGATTAATCAGTTAATAAAT
1 AAATTAGATCGAAAGGGTAGCCATCGCCTCTACGATACCTAATCCAGATTAATCAATTAATAAAT
* * * ** * * *
822595 CATATGCCATTGATTATATTTAGACATAC-ACATCAAAATTTGACCTAATTTGAATATTTTTTAA
66 CACATACCAATGATTATACATAAAAATACAACACCAAAATTTGACCTAATTTGAATATTTTTTAA
822659 TTATAATAAA-T-TA-TTT-TATAACTCGATGTAACTTATAATATAGAAATATATATAATATTAT
131 TTATAATAAATTATATTTTATATAACTCGATGTAACTTATAATATAGAAATATATATAATATTAT
822720 GCTT
196 GCTT
822724 AAATTA
1 AAATTA
822730 AGCTATTTAT
Statistics
Matches: 182, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
194 54 0.30
195 3 0.02
196 2 0.01
197 1 0.01
198 44 0.24
199 78 0.43
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.38
Consensus pattern (199 bp):
AAATTAGATCGAAAGGGTAGCCATCGCCTCTACGATACCTAATCCAGATTAATCAATTAATAAAT
CACATACCAATGATTATACATAAAAATACAACACCAAAATTTGACCTAATTTGAATATTTTTTAA
TTATAATAAATTATATTTTATATAACTCGATGTAACTTATAATATAGAAATATATATAATATTAT
GCTT
Found at i:825050 original size:41 final size:41
Alignment explanation
Indices: 824991--825072 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
824981 AACATGCAAA
* *
824991 CATTGATTGATTTGCATCTCTTTAATTTTTAGATTTTGTCT
1 CATTGATTGATTTGCATCTCTATAATTTATAGATTTTGTCT
* * **
825032 CATTGTTTGATTTTCATCTCTATGGTTTATAGATTTTGTCT
1 CATTGATTGATTTGCATCTCTATAATTTATAGATTTTGTCT
825073 TTTCTCTTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.18, C:0.12, G:0.13, T:0.56
Consensus pattern (41 bp):
CATTGATTGATTTGCATCTCTATAATTTATAGATTTTGTCT
Found at i:825092 original size:3 final size:3
Alignment explanation
Indices: 825084--825108 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
825074 TTCTCTTGTT
825084 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
825109 ACATGATAAC
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:825482 original size:28 final size:30
Alignment explanation
Indices: 825424--825483 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
825414 GGGGCCATTT
* *
825424 TGCTCCAAAATAAAACAATGAAGGCTAAAA
1 TGCTCCAAAATAAAACAATAAAGGATAAAA
*
825454 TGCTCCAAAA-CAAA-AATAAAGGATAAAA
1 TGCTCCAAAATAAAACAATAAAGGATAAAA
825482 TG
1 TG
825484 ACCATATGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 14 0.52
29 3 0.11
30 10 0.37
ACGTcount: A:0.55, C:0.15, G:0.13, T:0.17
Consensus pattern (30 bp):
TGCTCCAAAATAAAACAATAAAGGATAAAA
Found at i:827065 original size:18 final size:18
Alignment explanation
Indices: 827009--827056 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
826999 TATGTGGCAT
*
827009 TGTTATGTCAGCGTGCGA
1 TGTTATGTAAGCGTGCGA
827027 TGTTATGTAAGCGTGCGA
1 TGTTATGTAAGCGTGCGA
827045 TGTTATGTAAGC
1 TGTTATGTAAGC
827057 TTGTCATGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.21, C:0.12, G:0.31, T:0.35
Consensus pattern (18 bp):
TGTTATGTAAGCGTGCGA
Found at i:837361 original size:14 final size:14
Alignment explanation
Indices: 837344--837371 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
837334 AGCATAACAA
837344 AATTATATAACTAT
1 AATTATATAACTAT
837358 AATTATATAACTAT
1 AATTATATAACTAT
837372 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:838365 original size:16 final size:16
Alignment explanation
Indices: 838344--838376 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
838334 TAATAAATAG
838344 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
838360 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
838376 A
1 A
838377 AATTTTTTTT
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:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:838457 original size:10 final size:10
Alignment explanation
Indices: 838442--838516 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
838432 CATTTAATAA
838442 ATAAACGAAC
1 ATAAACGAAC
838452 ATAAACGAAC
1 ATAAACGAAC
838462 ----ACGAAC
1 ATAAACGAAC
838468 ATAAACGAAC
1 ATAAACGAAC
** *
838478 ACGAAC-ATAA
1 ATAAACGA-AC
838488 ATGAACACGAAC
1 AT-AA-ACGAAC
838500 ATAAACGAAC
1 ATAAACGAAC
838510 ATAAACG
1 ATAAACG
838517 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:838467 original size:16 final size:16
Alignment explanation
Indices: 838446--838510 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
838436 TAATAAATAA
838446 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
838462 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
838478 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
838494 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
838510 A
1 A
838511 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:839271 original size:14 final size:14
Alignment explanation
Indices: 839254--839309 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
839244 AATGAACATA
839254 AACGAACATAATCG
1 AACGAACATAATCG
839268 AACGAACAT-A---
1 AACGAACATAATCG
* *
839278 AACAAACATAACCG
1 AACGAACATAATCG
839292 AACGAACATAATCG
1 AACGAACATAATCG
839306 AACG
1 AACG
839310 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:839274 original size:24 final size:24
Alignment explanation
Indices: 839234--839308 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
839224 GATTGAATTA
*
839234 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
839258 AACATAATCGAACGAACATAAACA
1 AACATAATCGAACGAACATAAACG
* *
839282 AACATAACCGAACGAACATAATCG
1 AACATAATCGAACGAACATAAACG
839306 AAC
1 AAC
839309 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:841740 original size:17 final size:17
Alignment explanation
Indices: 841727--841760 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
841717 ATAATATTCG
*
841727 TATTAAATATATATTAA
1 TATTAAAGATATATTAA
841744 TATTAAAGATATATTAA
1 TATTAAAGATATATTAA
841761 CCGATCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TATTAAAGATATATTAA
Found at i:842113 original size:17 final size:17
Alignment explanation
Indices: 842091--842126 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
842081 AAAGTAAAGG
*
842091 GATCTTTTGGTTATTTT
1 GATCTTTCGGTTATTTT
842108 GATCTTTCGGTTATTTT
1 GATCTTTCGGTTATTTT
842125 GA
1 GA
842127 CATTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.08, G:0.19, T:0.58
Consensus pattern (17 bp):
GATCTTTCGGTTATTTT
Found at i:844528 original size:17 final size:17
Alignment explanation
Indices: 844515--844549 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
844505 ATAATATTCG
*
844515 TATTAAATATATATTAA
1 TATTAAAGATATATTAA
844532 TATTAAAGATATATTAA
1 TATTAAAGATATATTAA
844549 T
1 T
844550 TGATCAAATC
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:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TATTAAAGATATATTAA
Found at i:844730 original size:17 final size:17
Alignment explanation
Indices: 844708--844757 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
844698 AGTAGAGGGA
844708 TCTTTCGGTTATTTTGG
1 TCTTTCGGTTATTTTGG
* *
844725 TCTTTCGATTATTTTGT
1 TCTTTCGGTTATTTTGG
844742 TCTTTCGGTTATTTTG
1 TCTTTCGGTTATTTTG
844758 ACATTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.08, C:0.12, G:0.18, T:0.62
Consensus pattern (17 bp):
TCTTTCGGTTATTTTGG
Found at i:847066 original size:12 final size:13
Alignment explanation
Indices: 847040--847069 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
847030 TTTTAATTCC
847040 ATGTTTAATGTTG
1 ATGTTTAATGTTG
847053 ATGTTTAATG-TG
1 ATGTTTAATGTTG
847065 ATGTT
1 ATGTT
847070 GGTATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (13 bp):
ATGTTTAATGTTG
Found at i:849235 original size:17 final size:17
Alignment explanation
Indices: 849195--849229 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
849185 GAAAGTAGAG
849195 GACATTTCGATTATTTT
1 GACATTTCGATTATTTT
849212 GACATTTCGATTATTTT
1 GACATTTCGATTATTTT
849229 G
1 G
849230 TGATTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.51
Consensus pattern (17 bp):
GACATTTCGATTATTTT
Found at i:851939 original size:28 final size:28
Alignment explanation
Indices: 851907--851964 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
851897 TTTCGTCCTA
* *
851907 TAAAACTTTACATGTTCAAATTCGCTCC
1 TAAAACTTTACAAGTTCAAATTCACTCC
* *
851935 TAAAATTTTATAAGTTCAAATTCACTCC
1 TAAAACTTTACAAGTTCAAATTCACTCC
851963 TA
1 TA
851965 CACAAATTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (28 bp):
TAAAACTTTACAAGTTCAAATTCACTCC
Found at i:852362 original size:23 final size:21
Alignment explanation
Indices: 852332--852378 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 21
852322 CTGGAAATGT
852332 TAAAAAAACATTAATGTTTTAGG
1 TAAAAAAA-A-TAATGTTTTAGG
*
852355 TAAAAAAAATAATGTTTTTGG
1 TAAAAAAAATAATGTTTTAGG
852376 TAA
1 TAA
852379 TTTTTTTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.61
22 1 0.04
23 8 0.35
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (21 bp):
TAAAAAAAATAATGTTTTAGG
Found at i:862248 original size:2 final size:2
Alignment explanation
Indices: 862241--862265 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
862231 TAATTATTCA
862241 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
862266 CAGAATTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:863769 original size:29 final size:30
Alignment explanation
Indices: 863699--863757 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
863689 AATTTAAGGT
863699 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAC
863730 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
863758 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAC
Found at i:863873 original size:15 final size:15
Alignment explanation
Indices: 863853--863882 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
863843 ATTGCCCAGG
863853 GGGTACAGATACCCC
1 GGGTACAGATACCCC
863868 GGGTACAGATACCCC
1 GGGTACAGATACCCC
863883 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:863910 original size:22 final size:21
Alignment explanation
Indices: 863847--863904 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
863837 TTCAAGATTG
863847 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
863865 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
863883 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
863904 C
1 C
863905 TGCAGGTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
15 11 0.32
18 7 0.21
21 16 0.47
ACGTcount: A:0.24, C:0.38, G:0.28, T:0.10
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:863982 original size:20 final size:21
Alignment explanation
Indices: 863938--863980 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
863928 AACAGAATGT
863938 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
863959 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
863980 C
1 C
863981 AGTTCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.44, G:0.28, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:864042 original size:21 final size:21
Alignment explanation
Indices: 864016--864058 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
864006 ATTTGAATAT
* *
864016 TATGAAGGGGTATCGATTCCC
1 TATGAAGAGGTACCGATTCCC
864037 TATGAAGAGGTACCGATTCCC
1 TATGAAGAGGTACCGATTCCC
864058 T
1 T
864059 CTATTCTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (21 bp):
TATGAAGAGGTACCGATTCCC
Found at i:864124 original size:20 final size:22
Alignment explanation
Indices: 864086--864125 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
864076 TTTGAGTATA
864086 AAAATCATCCCCAAACGGCTCT
1 AAAATCATCCCCAAACGGCTCT
864108 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
864126 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCT
Found at i:864379 original size:34 final size:34
Alignment explanation
Indices: 864340--864443 Score: 167
Period size: 34 Copynumber: 3.1 Consensus size: 34
864330 TTTTGTAAAG
864340 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
864374 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
* * *
864408 GGGAAATGTTCTAGTTTAGCCCG-G-AAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
864440 GGGA
1 GGGA
864444 GTTGTAAGGT
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
32 11 0.16
33 1 0.01
34 55 0.82
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (34 bp):
GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
Found at i:865605 original size:34 final size:33
Alignment explanation
Indices: 865543--865614 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 33
865533 CCTTACAAAC
* *
865543 TCCCTAGTTTTTCCGGGCTAAACTAGAACC-TT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTTT
*
865575 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTTT
865610 TCCCT
1 TCCCT
865615 TTACAAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 15 0.44
35 7 0.21
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.33
Consensus pattern (33 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTTT
Found at i:865852 original size:20 final size:22
Alignment explanation
Indices: 865827--865866 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
865817 AGTCGTATAT
865827 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
865847 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
865867 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:865918 original size:21 final size:21
Alignment explanation
Indices: 865894--865936 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
865884 CCCAGAATAG
*
865894 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
865915 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
865936 A
1 A
865937 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:866012 original size:21 final size:20
Alignment explanation
Indices: 865972--866009 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
865962 CTGTTGAACA
865972 GGGGGGAATCGATACCCCTG
1 GGGGGGAATCGATACCCCTG
*
865992 GGGGGGAATCGGTACCCC
1 GGGGGGAATCGATACCCC
866010 CTGAACATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.26, G:0.42, T:0.13
Consensus pattern (20 bp):
GGGGGGAATCGATACCCCTG
Found at i:866072 original size:20 final size:20
Alignment explanation
Indices: 866047--866125 Score: 87
Period size: 20 Copynumber: 4.1 Consensus size: 20
866037 AAAACCTGCA
866047 GGGGGTATCTGTACCCCCTG
1 GGGGGTATCTGTACCCCCTG
866067 GGGGGTATCTGTA--CCC--
1 GGGGGTATCTGTACCCCCTG
866083 -GGGGTATCTGTACCCCCTGGG
1 GGGGGTATCTGTACCCCCT--G
* *
866104 GGGGGAATCTATACCCCCTG
1 GGGGGTATCTGTACCCCCTG
866124 GG
1 GG
866126 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
18 3 0.06
20 16 0.32
22 16 0.32
ACGTcount: A:0.13, C:0.28, G:0.37, T:0.23
Consensus pattern (20 bp):
GGGGGTATCTGTACCCCCTG
Found at i:866088 original size:15 final size:15
Alignment explanation
Indices: 866068--866097 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
866058 TACCCCCTGG
866068 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
866083 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
866098 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:866108 original size:22 final size:22
Alignment explanation
Indices: 866083--866125 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
866073 ATCTGTACCC
* *
866083 GGGGTATCTGTACCCCCTGGGG
1 GGGGAATCTATACCCCCTGGGG
866105 GGGGAATCTATACCCCCTGGG
1 GGGGAATCTATACCCCCTGGG
866126 CAATCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.28, G:0.37, T:0.21
Consensus pattern (22 bp):
GGGGAATCTATACCCCCTGGGG
Found at i:866247 original size:29 final size:31
Alignment explanation
Indices: 866215--866274 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
866205 AAACTTTGAA
866215 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
866244 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
866275 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:867861 original size:3 final size:3
Alignment explanation
Indices: 867853--867890 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
867843 TACGTCCTCA
* *
867853 TTC TTC TTC TTC TTC TTC TTC TTG TTT TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
867891 CCTTTCTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:868941 original size:34 final size:33
Alignment explanation
Indices: 868879--868950 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 33
868869 CCTTACAAAC
* *
868879 TCCCTAGTTTTTCCGGGCTAAACTAGAACC-TT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTTT
*
868911 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTTT
868946 TCCCT
1 TCCCT
868951 TTACAAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 15 0.44
35 7 0.21
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.33
Consensus pattern (33 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTTT
Found at i:869188 original size:20 final size:22
Alignment explanation
Indices: 869163--869202 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
869153 AGTCGTATAT
869163 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
869183 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
869203 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:869254 original size:21 final size:21
Alignment explanation
Indices: 869230--869272 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
869220 CCCAGAATAG
*
869230 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
869251 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
869272 A
1 A
869273 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:869349 original size:21 final size:20
Alignment explanation
Indices: 869308--869345 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
869298 CTGTTGAACA
869308 GGGGGGAATCGGTACCCCTG
1 GGGGGGAATCGGTACCCCTG
869328 GGGGGGAATCGGTACCCC
1 GGGGGGAATCGGTACCCC
869346 CTGGACATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.45, T:0.13
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCTG
Found at i:869408 original size:21 final size:21
Alignment explanation
Indices: 869383--869461 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
869373 AAAACCTGCA
869383 GGGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
869404 GGGGGTATCTGTA--CCC---
1 GGGGGTATCTGTACCCCCTGG
869420 -GGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
* *
869440 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
869461 G
1 G
869462 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 32 0.64
ACGTcount: A:0.13, C:0.28, G:0.37, T:0.23
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:869424 original size:36 final size:36
Alignment explanation
Indices: 869384--869455 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
869374 AAACCTGCAG
* *
869384 GGGGTATCTGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
869420 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
869456 CCTGGGCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.14, C:0.28, G:0.35, T:0.24
Consensus pattern (36 bp):
GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
Found at i:869425 original size:15 final size:15
Alignment explanation
Indices: 869405--869434 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
869395 ACCCCCTGGG
869405 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
869420 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
869435 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:869583 original size:29 final size:31
Alignment explanation
Indices: 869551--869610 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
869541 AAACTTTGAA
869551 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
869580 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
869611 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:869669 original size:19 final size:20
Alignment explanation
Indices: 869645--869692 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
869635 AGTTCAACAC
*
869645 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
869664 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
869684 TTTTGAAAA
1 TTTTGAAAA
869693 AGGATTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:871027 original size:29 final size:30
Alignment explanation
Indices: 870956--871015 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
870946 CAATTTAAGG
870956 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
870987 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
871016 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:871130 original size:21 final size:21
Alignment explanation
Indices: 871105--871168 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
871095 TTCAAGATTA
* *
871105 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
871126 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
871147 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
871168 C
1 C
871169 TGCAGGTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.22, C:0.38, G:0.28, T:0.12
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:871242 original size:20 final size:21
Alignment explanation
Indices: 871202--871244 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
871192 AACAGAATGT
871202 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
871223 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
871244 C
1 C
871245 TGTTCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.44, G:0.28, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:871306 original size:21 final size:21
Alignment explanation
Indices: 871280--871322 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
871270 ATTTGAATAT
* *
871280 TATGAAGGGGTATCGATTCCC
1 TATGAAGAGGTACCGATTCCC
871301 TATGAAGAGGTACCGATTCCC
1 TATGAAGAGGTACCGATTCCC
871322 T
1 T
871323 CTATTCTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (21 bp):
TATGAAGAGGTACCGATTCCC
Found at i:871388 original size:20 final size:22
Alignment explanation
Indices: 871350--871389 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
871340 TTGGAGTATA
871350 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
871372 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
871390 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:871643 original size:34 final size:34
Alignment explanation
Indices: 871604--871707 Score: 167
Period size: 34 Copynumber: 3.1 Consensus size: 34
871594 TTTTGTAAAG
*
871604 GGGAAATGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
871638 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
* *
871672 GGGAAAGGTTCTAGTTTAGCCCG-G-AAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
871704 GGGA
1 GGGA
871708 GTTGTAAGGT
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
32 11 0.16
33 1 0.01
34 55 0.82
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (34 bp):
GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
Found at i:874789 original size:2 final size:2
Alignment explanation
Indices: 874782--874814 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
874772 AATATGGGTA
874782 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
874815 AGGGCAGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:876153 original size:3 final size:3
Alignment explanation
Indices: 876145--876171 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
876135 AGTTCGGAGA
876145 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
876172 GGTGAAATCA
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):
AAT
Found at i:886668 original size:31 final size:31
Alignment explanation
Indices: 886630--886785 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
886620 CCCGAAGGAC
* * *
886630 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
886661 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
886692 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
886723 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
886754 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
886785 C
1 C
886786 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:887026 original size:23 final size:24
Alignment explanation
Indices: 887000--887046 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
886990 ATATACTTGT
*
887000 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
887023 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
887047 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:887708 original size:21 final size:21
Alignment explanation
Indices: 887678--887722 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
887668 ATTCTTTCGT
* *
887678 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
887699 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
887720 TTG
1 TTG
887723 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:890720 original size:31 final size:31
Alignment explanation
Indices: 890682--890837 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
890672 CCCGAAGGAC
* * *
890682 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
* *
890713 CAGTCCATATGTCCCGAAGGACATAAGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
890744 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
890775 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
890806 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
890837 C
1 C
890838 CCTCAACCCT
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
31 112 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:891079 original size:23 final size:24
Alignment explanation
Indices: 891053--891099 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
891043 ATATACTTGT
*
891053 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
891076 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
891100 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:891761 original size:21 final size:21
Alignment explanation
Indices: 891731--891775 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
891721 ATTCTTTCGT
* *
891731 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
891752 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
891773 TTG
1 TTG
891776 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:892782 original size:24 final size:25
Alignment explanation
Indices: 892723--892786 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 25
892713 AATTCGGGCT
*
892723 GACTACATCTTAATTAAATAGAAAC
1 GACTATATCTTAATTAAATAGAAAC
*
892748 GGAAGTAATATCTTAATTAAATAGAAAC
1 -G-ACT-ATATCTTAATTAAATAGAAAC
892776 -ACTATATCTTA
1 GACTATATCTTA
892787 TGATTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 8 0.24
25 2 0.06
26 1 0.03
27 2 0.06
28 20 0.61
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (25 bp):
GACTATATCTTAATTAAATAGAAAC
Found at i:893090 original size:10 final size:10
Alignment explanation
Indices: 893077--893157 Score: 69
Period size: 10 Copynumber: 7.7 Consensus size: 10
893067 ACACGCTGGG
893077 CATCCGAGGC
1 CATCCGAGGC
893087 CATCCGACCGAGGC
1 CAT-C--C-GAGGC
*
893101 TATCCGAGAG-
1 CATCCGAG-GC
893111 CATCCGAGGC
1 CATCCGAGGC
893121 CATCCGAGAG-
1 CATCCGAG-GC
893131 CATCCGAGAG-
1 CATCCGAG-GC
893141 CATCCGAGGC
1 CATCCGAGGC
893151 CATCCGA
1 CATCCGA
893158 ACGAGCTATG
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
9 2 0.03
10 46 0.75
11 4 0.07
13 2 0.03
14 7 0.11
ACGTcount: A:0.25, C:0.36, G:0.28, T:0.11
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:893119 original size:20 final size:19
Alignment explanation
Indices: 893094--893157 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 19
893084 GGCCATCCGA
893094 CCGAGGCTATCCGAGAGCAT
1 CCGAGGC-ATCCGAGAGCAT
893114 CCGAGGCCATCCGAGAGCAT
1 CCGAGG-CATCCGAGAGCAT
893134 CCGAGAGCATCCGAG-GCCAT
1 CCGAG-GCATCCGAGAG-CAT
893154 CCGA
1 CCGA
893158 ACGAGCTATG
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
19 1 0.02
20 38 0.93
21 2 0.05
ACGTcount: A:0.25, C:0.34, G:0.30, T:0.11
Consensus pattern (19 bp):
CCGAGGCATCCGAGAGCAT
Found at i:893200 original size:33 final size:32
Alignment explanation
Indices: 893075--893228 Score: 152
Period size: 33 Copynumber: 4.8 Consensus size: 32
893065 CAACACGCTG
*
893075 GGCATCCGAGGCCATCCGACCGAGGCTATCCGA
1 GGCATCCGAGGCCATCCGAGCGA-GCTATCCGA
893108 GAGCATCCGAGGCCATCCGA--GAGC-ATCCGA
1 G-GCATCCGAGGCCATCCGAGCGAGCTATCCGA
* *
893138 GAGCATCCGAGGCCATCCGAACGAGCTATGCGA
1 G-GCATCCGAGGCCATCCGAGCGAGCTATCCGA
* * * *
893171 TGGCATCCGAGGGCAACCGAGCGAGCTATGCTA
1 -GGCATCCGAGGCCATCCGAGCGAGCTATCCGA
* * *
893204 GGGAATCCGAGGGCAGCCGAGCGAG
1 -GGCATCCGAGGCCATCCGAGCGAG
893229 GGTAGGTCGC
Statistics
Matches: 108, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
30 26 0.24
31 2 0.02
32 6 0.06
33 55 0.51
34 19 0.18
ACGTcount: A:0.25, C:0.31, G:0.34, T:0.11
Consensus pattern (32 bp):
GGCATCCGAGGCCATCCGAGCGAGCTATCCGA
Done.