Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_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: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 43 of 43
Found at i:9741098 original size:49 final size:49
Alignment explanation
Indices: 9740827--9741097 Score: 391
Period size: 49 Copynumber: 5.5 Consensus size: 49
9740817 AGTATAACAA
* *
9740827 TGCATTTCGGCATAAAAGGTACCACAAATGAAAGTTAAATGCATAACGG
1 TGCATTTCAGCATAAAAGGTGCCACAAATGAAAGTTAAATGCATAACGG
* *
9740876 TGCATTTCAACATAAAAGGTGCCACAAATGAAAGTTAAATGCATAACAG
1 TGCATTTCAGCATAAAAGGTGCCACAAATGAAAGTTAAATGCATAACGG
* *
9740925 TGCATTTC-GACATAAAATGTGCCGCAAATGAAAGTTAAATGCATAACGG
1 TGCATTTCAG-CATAAAAGGTGCCACAAATGAAAGTTAAATGCATAACGG
* * **
9740974 AGAATTTCAAAAATAAAAGGTGCCACAAATGAAAGTTAAATGCATAACGG
1 TGCATTTC-AGCATAAAAGGTGCCACAAATGAAAGTTAAATGCATAACGG
* * *
9741024 TGCATTTCGGCATAAAAGGTACCACTAATGAAAGTTAAATGCATAACGG
1 TGCATTTCAGCATAAAAGGTGCCACAAATGAAAGTTAAATGCATAACGG
*
9741073 TGCATTTCAGCATAAAATGTGCCAC
1 TGCATTTCAGCATAAAAGGTGCCAC
9741098 TCATGTTATT
Statistics
Matches: 195, Mismatches: 24, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
49 153 0.78
50 42 0.22
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (49 bp):
TGCATTTCAGCATAAAAGGTGCCACAAATGAAAGTTAAATGCATAACGG
Found at i:9741131 original size:99 final size:98
Alignment explanation
Indices: 9740820--9741097 Score: 439
Period size: 99 Copynumber: 2.8 Consensus size: 98
9740810 AAGCTAAAGT
*
9740820 ATAACAATGCATTTCGGCATAAAAGGTACCACAAATGAAAGTTAAATGCATAACGGTGCATTTCA
1 ATAACAGTGCATTTCGGCATAAAAGGTACCACAAATGAAAGTTAAATGCATAACGGTGCATTTCA
9740885 ACATAAAAGGTGCCACAAATGAAAGTTAAATGC
66 ACATAAAAGGTGCCACAAATGAAAGTTAAATGC
* * * * * *
9740918 ATAACAGTGCATTTCGACATAAAATGTGCCGCAAATGAAAGTTAAATGCATAACGGAGAATTTCA
1 ATAACAGTGCATTTCGGCATAAAAGGTACCACAAATGAAAGTTAAATGCATAACGGTGCATTTC-
*
9740983 AAAATAAAAGGTGCCACAAATGAAAGTTAAATGC
65 AACATAAAAGGTGCCACAAATGAAAGTTAAATGC
* *
9741017 ATAACGGTGCATTTCGGCATAAAAGGTACCACTAATGAAAGTTAAATGCATAACGGTGCATTTCA
1 ATAACAGTGCATTTCGGCATAAAAGGTACCACAAATGAAAGTTAAATGCATAACGGTGCATTTCA
* *
9741082 GCATAAAATGTGCCAC
66 ACATAAAAGGTGCCAC
9741098 TCATGTTATT
Statistics
Matches: 160, Mismatches: 19, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
98 71 0.44
99 89 0.56
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.23
Consensus pattern (98 bp):
ATAACAGTGCATTTCGGCATAAAAGGTACCACAAATGAAAGTTAAATGCATAACGGTGCATTTCA
ACATAAAAGGTGCCACAAATGAAAGTTAAATGC
Found at i:9746271 original size:15 final size:15
Alignment explanation
Indices: 9746251--9746289 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
9746241 TAGAGAAAAT
*
9746251 AAGAAATTGCGTAAC
1 AAGAAATTGCATAAC
*
9746266 AAGAAATTGCATAGC
1 AAGAAATTGCATAAC
9746281 AAGTAAATT
1 AAG-AAATT
9746290 CCTTTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.23
Consensus pattern (15 bp):
AAGAAATTGCATAAC
Found at i:9747441 original size:49 final size:49
Alignment explanation
Indices: 9747388--9747632 Score: 400
Period size: 49 Copynumber: 5.0 Consensus size: 49
9747378 AATGCTCTAA
* * *
9747388 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTACCACA
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACT
* *
9747437 AATGAAAGTTAAATGCATAACGGTACATTTCGACATAAAAGGTGCGACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACT
9747486 AATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACT
* * *
9747535 AATGAAAGTTAAATGCATAACGGTGTATTTCGGCATAAAAGGTGTCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACT
* *
9747584 AATGAAAGTTAAATGCATAACGGTGCATTTCGACCTAAAAGGTGTCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACT
9747633 CATGTTATTC
Statistics
Matches: 183, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 183 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (49 bp):
AATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACT
Found at i:9748162 original size:21 final size:22
Alignment explanation
Indices: 9748121--9748164 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
9748111 ATAATCTTTG
*
9748121 TATTATGTTATAAAGAATGTTT
1 TATTATATTATAAAGAATGTTT
*
9748143 TATTATATTATTAA-AATGTTT
1 TATTATATTATAAAGAATGTTT
9748164 T
1 T
9748165 GTTTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (22 bp):
TATTATATTATAAAGAATGTTT
Found at i:9749782 original size:91 final size:91
Alignment explanation
Indices: 9749624--9749793 Score: 245
Period size: 91 Copynumber: 1.9 Consensus size: 91
9749614 TTGTTTAAGA
9749624 TCTTTTATGCAGGCCTTAAACAAATATGTTAAATATTAATTCCATGTCAACTATTTGACATCTTT
1 TCTTTTATGCAGGCCTTAAACAAATATGTTAAATATTAATTCCATGTCAACTATTTGACATCTTT
9749689 TGTTGGTGTATTTTATGATCTTTCAT
66 TGTTGGTGTATTTTATGATCTTTCAT
* * * * *
9749715 TCTTTTATGTAGGCCTTAAACAAATATGTTAAGTA-TATATTCCTTGTCAACTGTTTTACAT-TA
1 TCTTTTATGCAGGCCTTAAACAAATATGTTAAATATTA-ATTCCATGTCAACTATTTGACATCT-
* *
9749778 TTTGTTGTTGTTTTTT
64 TTTGTTGGTGTATTTT
9749794 TCTTGAAGGT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
90 3 0.04
91 67 0.96
ACGTcount: A:0.26, C:0.13, G:0.12, T:0.49
Consensus pattern (91 bp):
TCTTTTATGCAGGCCTTAAACAAATATGTTAAATATTAATTCCATGTCAACTATTTGACATCTTT
TGTTGGTGTATTTTATGATCTTTCAT
Found at i:9753502 original size:2 final size:2
Alignment explanation
Indices: 9753490--9753535 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
9753480 TTATTTGTCA
9753490 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9753531 AT AT A
1 AT AT A
9753536 ATTTACAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9753726 original size:26 final size:26
Alignment explanation
Indices: 9753692--9753741 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
9753682 AATGATGCTC
9753692 AATGCGTGTCATAAATGA-GCGTCACA
1 AATGCGTGTCATAAAT-ACGCGTCACA
*
9753718 AATGTGTGTCATAAATACGCGTCA
1 AATGCGTGTCATAAATACGCGTCA
9753742 TAGATTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (26 bp):
AATGCGTGTCATAAATACGCGTCACA
Found at i:9760711 original size:20 final size:19
Alignment explanation
Indices: 9760673--9760720 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
9760663 TAATTTCTAT
9760673 AAAGAAAAAAAGGAAAAAA
1 AAAGAAAAAAAGGAAAAAA
* * *
9760692 ATAGAAAAATAATGAGAAAA
1 AAAGAAAAA-AAGGAAAAAA
9760712 AAAGAAAAA
1 AAAGAAAAA
9760721 GAAAAAAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (19 bp):
AAAGAAAAAAAGGAAAAAA
Found at i:9760733 original size:31 final size:31
Alignment explanation
Indices: 9760675--9760734 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
9760665 ATTTCTATAA
*
9760675 AGAAAAAAAGGAAAAAAATAGAAAAATAATG
1 AGAAAAAAAGGAAAAAAATAAAAAAATAATG
9760706 AGAAAAAAA-GAAAAAGAA-AAAAGAAATAA
1 AGAAAAAAAGGAAAAA-AATAAAA-AAATAA
9760735 AAAGTTGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (31 bp):
AGAAAAAAAGGAAAAAAATAAAAAAATAATG
Found at i:9762368 original size:130 final size:130
Alignment explanation
Indices: 9762119--9762357 Score: 284
Period size: 130 Copynumber: 1.8 Consensus size: 130
9762109 CCTAAAGAGT
* * **
9762119 AGTGGAACATATACTATTTCTTTCATATTTGGTCTTCCTGAAAAGCAGCGAAGCAAGTCAAGTTC
1 AGTGAAACATATACTATTTCTTTCAGATTTGGTCTTCCTGAAAAGCAGCGAAGCAAACCAAGTTC
* * *
9762184 GATTCAATGTTCCCTAAAGAGCAGCGAAGTGAATCAATAATTTTCAAGATCTGATTACCCGAAAA
66 GATTCAATCTTCCCTAAAGAGCAGCGAAGCGAATCAAAAATTTTCAAGATCTGATTACCCGAAAA
* ** * * *
9762249 AGTGAAACATATTCT-TCTTCTTTCAGATTTGGTCTTTTTGAAGAGTAGCGGAGCAAACCAAGTT
1 AGTGAAACATATACTAT-TTCTTTCAGATTTGGTCTTCCTGAAAAGCAGCGAAGCAAACCAAGTT
* * * * * *
9762313 TGATTTAATCTTCTCTGAAGAGCAGTGAAGCGGAT-AAAAATTTTC
65 CGATTCAATCTTCCCTAAAGAGCAGCGAAGCGAATCAAAAATTTTC
9762358 TCGAGTCTGA
Statistics
Matches: 89, Mismatches: 19, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
129 10 0.11
130 79 0.89
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Consensus pattern (130 bp):
AGTGAAACATATACTATTTCTTTCAGATTTGGTCTTCCTGAAAAGCAGCGAAGCAAACCAAGTTC
GATTCAATCTTCCCTAAAGAGCAGCGAAGCGAATCAAAAATTTTCAAGATCTGATTACCCGAAAA
Found at i:9762519 original size:128 final size:128
Alignment explanation
Indices: 9762269--9762519 Score: 288
Period size: 128 Copynumber: 2.0 Consensus size: 128
9762259 ATTCTTCTTC
** * * * * * *
9762269 TTTCAGATTTGGTCTTTTTGAAGAGTAGCGGAGCAAACCAAGTTTGATTTAATCTTCTCTGAAGA
1 TTTCAGATTTAATCTTCTTGAAGAGCAGCGAAGCAAACCAAGTTTGATTCAACCTTCCCTGAAGA
* ** * * * * * *
9762334 GCAGTGAAGCGGATAAAAATTTTCTCGAGTCTGATCTCTCTTAAACAGTGTATGAGTATATTA
66 ACAACGAAGCAGATAAAAATTTTCTCGAGTCTAAACTCCCCTAAACAATGTATGAGTATATTA
*
9762397 TTTCAGATTTAATCTTCTTGAAGAGCAGCGAAGCAAATCAAGTTTGATTCAACCTTCCCTGAAGA
1 TTTCAGATTTAATCTTCTTGAAGAGCAGCGAAGCAAACCAAGTTTGATTCAACCTTCCCTGAAGA
* * * *
9762462 ACAACGAAGTAGATCAAAATTTTTTCGAGTCTAAACTCCCCTAAAGAATAGTA-GAGTA
66 ACAACGAAGCAGATAAAAATTTTCTCGAGTCTAAACTCCCCTAAACAAT-GTATGAGTA
9762520 GACCCGCCTT
Statistics
Matches: 100, Mismatches: 22, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
128 97 0.97
129 3 0.03
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (128 bp):
TTTCAGATTTAATCTTCTTGAAGAGCAGCGAAGCAAACCAAGTTTGATTCAACCTTCCCTGAAGA
ACAACGAAGCAGATAAAAATTTTCTCGAGTCTAAACTCCCCTAAACAATGTATGAGTATATTA
Found at i:9776555 original size:25 final size:26
Alignment explanation
Indices: 9776527--9776577 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
9776517 AAACTCAACA
*
9776527 TTTTTTATTTGCCTTAGCA-ATTTTT
1 TTTTTTATTTACCTTAGCATATTTTT
* *
9776552 TTTTTTGTTTACCTTTGCATATTTTT
1 TTTTTTATTTACCTTAGCATATTTTT
9776578 ATTACCTCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.14, C:0.12, G:0.08, T:0.67
Consensus pattern (26 bp):
TTTTTTATTTACCTTAGCATATTTTT
Found at i:9790929 original size:12 final size:12
Alignment explanation
Indices: 9790912--9790939 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
9790902 AATTTTTGGC
9790912 TTTTTTGGTTTT
1 TTTTTTGGTTTT
9790924 TTTTTTGGTTTT
1 TTTTTTGGTTTT
9790936 TTTT
1 TTTT
9790940 GCCTTTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (12 bp):
TTTTTTGGTTTT
Found at i:9790971 original size:10 final size:10
Alignment explanation
Indices: 9790921--9790979 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
9790911 CTTTTTTGGT
9790921 TTTTTTTTTG
1 TTTTTTTTTG
*
9790931 GTTTTTTTTG
1 TTTTTTTTTG
**
9790941 -CCTTTTTTG
1 TTTTTTTTTG
* *
9790950 CCTTCTTTTTG
1 -TTTTTTTTTG
9790961 TTTTTTTTTG
1 TTTTTTTTTG
9790971 TTTTTTTTT
1 TTTTTTTTT
9790980 TAAAAAATAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
9 7 0.18
10 26 0.67
11 6 0.15
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.81
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:9790978 original size:9 final size:9
Alignment explanation
Indices: 9790922--9790978 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
9790912 TTTTTTGGTT
9790922 TTTTTTTTGG
1 TTTTTTTT-G
9790932 TTTTTTTTG
1 TTTTTTTTG
**
9790941 CCTTTTTTG
1 TTTTTTTTG
*
9790950 CCTTCTTTTTG
1 --TTTTTTTTG
9790961 TTTTTTTTTG
1 -TTTTTTTTG
9790971 TTTTTTTT
1 TTTTTTTT
9790979 TTAAAAAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
9 16 0.42
10 16 0.42
11 6 0.16
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.81
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:9804149 original size:22 final size:22
Alignment explanation
Indices: 9804123--9804171 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
9804113 AGGAAATCGA
9804123 TTCCCATTCAAAGGGGAATAGG
1 TTCCCATTCAAAGGGGAATAGG
* * * *
9804145 TTCCCCTTCAAGGGGGTATCGG
1 TTCCCATTCAAAGGGGAATAGG
9804167 TTCCC
1 TTCCC
9804172 TCTGCCCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
TTCCCATTCAAAGGGGAATAGG
Found at i:9804172 original size:21 final size:21
Alignment explanation
Indices: 9804091--9804172 Score: 58
Period size: 22 Copynumber: 3.8 Consensus size: 21
9804081 CAGAACTCAT
* *
9804091 GGGGGTATCGATTCCC-TAAA
1 GGGGGAATCGATTCCCTTCAA
*
9804111 GGAGGAAATCGATTCCCATTCAA
1 GG-GGGAATCGATTCCC-TTCAA
* * *
9804134 AGGGGAATAGGTTCCCCTTCAA
1 GGGGGAATCGATT-CCCTTCAA
* *
9804156 GGGGGTATCGGTTCCCT
1 GGGGGAATCGATTCCCT
9804173 CTGCCCTATA
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
20 2 0.04
21 16 0.33
22 23 0.48
23 7 0.15
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTTCAA
Found at i:9808085 original size:22 final size:22
Alignment explanation
Indices: 9808041--9808085 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
9808031 AAATTGAAAT
* *
9808041 TTTCTTTTTTGATACTTTCAAA
1 TTTCATTTTTGAGACTTTCAAA
9808063 TTTCATTTTTGAGA-TTTCTAAA
1 TTTCATTTTTGAGACTTTC-AAA
9808085 T
1 T
9808086 CCTTCTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.58
Consensus pattern (22 bp):
TTTCATTTTTGAGACTTTCAAA
Found at i:9812241 original size:12 final size:13
Alignment explanation
Indices: 9812214--9812246 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
9812204 ATATTATAAT
*
9812214 TTTTCAAACTTAG
1 TTTTCAAACATAG
9812227 TTTTCAAA-ATAG
1 TTTTCAAACATAG
9812239 TTTTCAAA
1 TTTTCAAA
9812247 TTTGCCCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:9815485 original size:13 final size:13
Alignment explanation
Indices: 9815467--9815492 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9815457 GTTTTCACGT
9815467 ATACACTTTGAAA
1 ATACACTTTGAAA
9815480 ATACACTTTGAAA
1 ATACACTTTGAAA
9815493 CACTTATCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
ATACACTTTGAAA
Found at i:9821518 original size:15 final size:15
Alignment explanation
Indices: 9821498--9821538 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
9821488 TCGGTTGTGT
9821498 TGATGCAAGAAATGG
1 TGATGCAAGAAATGG
9821513 TGATGCAAGAAATGG
1 TGATGCAAGAAATGG
*
9821528 TGATGGAAGAA
1 TGATGCAAGAA
9821539 TTCATTTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.34, T:0.20
Consensus pattern (15 bp):
TGATGCAAGAAATGG
Found at i:9846105 original size:22 final size:22
Alignment explanation
Indices: 9846077--9846128 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
9846067 TTTTACCATA
*
9846077 TTTTGAAATATTTTCATAAGTT
1 TTTTGAAATATTTTCATAAATT
9846099 TTTTGAAATATTTTCATAAATT
1 TTTTGAAATATTTTCATAAATT
*
9846121 TTATGAAA
1 TTTTGAAA
9846129 ATGGGTTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (22 bp):
TTTTGAAATATTTTCATAAATT
Found at i:9851501 original size:2 final size:2
Alignment explanation
Indices: 9851496--9851520 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9851486 TGTGTGTGTG
9851496 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 T
9851521 TTATGAAATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9870050 original size:33 final size:33
Alignment explanation
Indices: 9870013--9870078 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
9870003 GTAGTAGCCA
9870013 GAGTATGAAG-TCAGGGAAAAGAGCCAAAACATC
1 GAGTATGAAGAT-AGGGAAAAGAGCCAAAACATC
*
9870046 GAGTATGAAGATAGGGAAAAGAGCCAGAACATC
1 GAGTATGAAGATAGGGAAAAGAGCCAAAACATC
9870079 TTCAGTTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.45, C:0.14, G:0.29, T:0.12
Consensus pattern (33 bp):
GAGTATGAAGATAGGGAAAAGAGCCAAAACATC
Found at i:9877969 original size:12 final size:12
Alignment explanation
Indices: 9877946--9877978 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
9877936 GCACACAAAC
9877946 AAATAGAAAAATA
1 AAATA-AAAAATA
9877959 AAATAAAAAATA
1 AAATAAAAAATA
9877971 AAATAAAA
1 AAATAAAA
9877979 CTTGGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:9881524 original size:2 final size:2
Alignment explanation
Indices: 9881517--9881568 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
9881507 TGAATGAATA
* *
9881517 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
9881559 AT AT AC AT AT
1 AT AT AT AT AT
9881569 TATGTTTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:9884225 original size:45 final size:45
Alignment explanation
Indices: 9884136--9884618 Score: 794
Period size: 45 Copynumber: 10.8 Consensus size: 45
9884126 ATAAGCATGC
9884136 AAATAAGCTTA-GAAGCTTATGGAAT-AATGGTAAGTATATTGGTA
1 AAATAAGCTTACG-AGCTTATGGAATAAATGGTAAGTATATTGGTA
*
9884180 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
9884225 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
9884270 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATACTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
9884315 AAATAAGCTTATGAGCTTATGGAATAAATGTTAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
9884360 AAATAAGCTTACGAG-TTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
9884404 AAATAAGCTTACGAGCTTATGAAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
9884449 AAATAAGCTTATGAGCTTATGGAATAATTGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
9884494 AAATAAGCTTATGAGCTTATGGAATAAAAGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
9884539 AAATAAGCTTACGATCTTATGGAATAAATGGTAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
9884584 AAATAAGCTTACGAGCTCATAGG-ATAAATGATAAG
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAG
9884619 AAATTTTATA
Statistics
Matches: 412, Mismatches: 23, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
44 65 0.16
45 345 0.84
46 2 0.00
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:9884529 original size:224 final size:224
Alignment explanation
Indices: 9884136--9884600 Score: 790
Period size: 224 Copynumber: 2.1 Consensus size: 224
9884126 ATAAGCATGC
9884136 AAATAAGCTTA-GAAGCTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTACG-AGCTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
*
9884200 GGAATAAATGGTAAGTATATGGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
65 GAAATAAATGGTAAGTATATGGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
* *
9884265 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATACTGGTAAAATAAGCTTATGAG
130 TGGTAAAATAAGCTTACGAGCTTATGGAATAAAAGGTAAGTATACTGGTAAAATAAGCTTACGAG
* *
9884330 CTTATGGAATAAATGTTAAGTATATGGGTA
195 CTTATGGAATAAATGGTAAGTATATGGATA
9884360 AAATAAGCTTACGAG-TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTACGAGCTTATGGAAT-AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
* * *
9884424 GAAATAAATGGTAAGTATATTGGTAAAATAAGCTTATGAGCTTATGGAATAATTGGTAAGTATAT
65 GAAATAAATGGTAAGTATATGGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
* * *
9884489 TGGTAAAATAAGCTTATGAGCTTATGGAATAAAAGGTAAGTATATTGGTAAAATAAGCTTACGAT
130 TGGTAAAATAAGCTTACGAGCTTATGGAATAAAAGGTAAGTATACTGGTAAAATAAGCTTACGAG
*
9884554 CTTATGGAATAAATGGTAAGTATATTGATA
195 CTTATGGAATAAATGGTAAGTATATGGATA
9884584 AAATAAGCTTACGAGCT
1 AAATAAGCTTACGAGCT
9884601 CATAGGATAA
Statistics
Matches: 226, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
223 9 0.04
224 215 0.95
225 2 0.01
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (224 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
AAATAAATGGTAAGTATATGGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATT
GGTAAAATAAGCTTACGAGCTTATGGAATAAAAGGTAAGTATACTGGTAAAATAAGCTTACGAGC
TTATGGAATAAATGGTAAGTATATGGATA
Found at i:9887440 original size:12 final size:11
Alignment explanation
Indices: 9887426--9887496 Score: 63
Period size: 12 Copynumber: 6.1 Consensus size: 11
9887416 ATAAAGAATA
*
9887426 AAAAGAAAATG
1 AAAAGAAAAAG
*
9887437 AAAATGAAGAAG
1 AAAA-GAAAAAG
*
9887449 AAGAAGAAGAAG
1 AA-AAGAAAAAG
9887461 AAGAAGAAAAATAG
1 AA-AAG-AAAA-AG
9887475 AAAAG-AAAAG
1 AAAAGAAAAAG
9887485 AAAAGAAAAAG
1 AAAAGAAAAAG
9887496 A
1 A
9887497 GAAAAAAATG
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
10 7 0.13
11 13 0.25
12 20 0.38
13 8 0.15
14 4 0.08
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:9887449 original size:18 final size:17
Alignment explanation
Indices: 9887428--9887507 Score: 69
Period size: 18 Copynumber: 4.6 Consensus size: 17
9887418 AAAGAATAAA
9887428 AAGAAAATGAAAATGAAG
1 AAGAAAATGAAAA-GAAG
9887446 AAGAAGAA-GAAGAAGAAG
1 AAGAA-AATGAA-AAGAAG
9887464 AAGAAAAATAGAAAAGAA-
1 AAG-AAAAT-GAAAAGAAG
9887482 AAGAAAA-GAAAA-AGAG
1 AAGAAAATGAAAAGA-AG
*
9887498 AAAAAAATGA
1 AAGAAAATGA
9887508 TGAGAGATGA
Statistics
Matches: 53, Mismatches: 1, Indels: 17
0.75 0.01 0.24
Matches are distributed among these distances:
14 1 0.02
15 6 0.11
16 6 0.11
17 6 0.11
18 20 0.38
19 11 0.21
20 3 0.06
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (17 bp):
AAGAAAATGAAAAGAAG
Found at i:9887450 original size:3 final size:3
Alignment explanation
Indices: 9887442--9887496 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
9887432 AAATGAAAAT
9887442 GAA GAA GAA GAA GAA GAA GAA GAA GAA -AA -ATA GAA -AA GAA -AA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA
*
9887484 GAA -AA GAA AAA GA
1 GAA GAA GAA GAA GA
9887497 GAAAAAAATG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 9 0.20
3 35 0.78
4 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:9887527 original size:2 final size:2
Alignment explanation
Indices: 9887522--9887585 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
9887512 AGATGATTAA
9887522 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9887564 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
9887586 TCACTTGTGG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9891549 original size:45 final size:45
Alignment explanation
Indices: 9891460--9891943 Score: 756
Period size: 45 Copynumber: 10.8 Consensus size: 45
9891450 GTAAGCATGC
*
9891460 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
9891504 AAATAAGCTTACGAGATTATAGAATAAATGGTAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
9891549 AAATAAGCTTACGAACTTATGGAATAAATGGTAAGTATATTAGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
9891594 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
9891639 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
9891684 AAATAAGATTATGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
9891729 AAATAAGCTTACGAGCTTATGCAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
9891774 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
9891819 AAATAAGCTCATGAGCTTATGGAATAAAAGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
9891864 AAATAAACTTACGAGCTTATGGAATAAATGGTAAGTGTATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
9891909 AAATAAGCCTACGAGCTCATAGG-ATAAATGATAAG
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAG
9891944 AAATTTTATA
Statistics
Matches: 406, Mismatches: 32, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
44 23 0.06
45 381 0.94
46 2 0.00
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:9891778 original size:24 final size:24
Alignment explanation
Indices: 9891751--9891824 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
9891741 GAGCTTATGC
9891751 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
* ** *
9891775 AATAAGCTTATGAGCT-TA-TGG---
1 AATAA-ATGGTAAG-TATATTGGTAA
9891796 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
9891820 AATAA
1 AATAA
9891825 GCTCATGAGC
Statistics
Matches: 35, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
19 1 0.03
20 6 0.17
21 8 0.23
24 13 0.37
25 6 0.17
26 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.32
Consensus pattern (24 bp):
AATAAATGGTAAGTATATTGGTAA
Found at i:9899291 original size:53 final size:53
Alignment explanation
Indices: 9899161--9899318 Score: 228
Period size: 53 Copynumber: 3.0 Consensus size: 53
9899151 GTGTACTTTT
**
9899161 GGCACTATGTGTATATCCATGGTATTCATAATGAGTTTGTGAATTA-CATTTC
1 GGCACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTC
* * * * *
9899213 GGCATTATATGTGCATCCATTGTATTCATTATGAGTTTGTGAATAACCATTTC
1 GGCACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTC
* *
9899266 GGCACTATGTGTGCACCCATGGTATTCATAATGAGGTTGTGAATTACCATTTC
1 GGCACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTC
9899319 ATTACATTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
52 39 0.43
53 52 0.57
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.39
Consensus pattern (53 bp):
GGCACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTC
Found at i:9906088 original size:53 final size:53
Alignment explanation
Indices: 9906031--9906178 Score: 224
Period size: 53 Copynumber: 2.8 Consensus size: 53
9906021 GAAACTATGT
*
9906031 GTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGGCATTATAA
1 GTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGGCACTATAA
* * **
9906084 GTGCATCCATTGTATTCATAATGAGTTTGTGAATAACCATTTCGGCACTATGT
1 GTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGGCACTATAA
* * *
9906137 GTGCACCCATGGTATTCATAATAAGGTTGTGAATTACCATTT
1 GTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTT
9906179 TGTTACATTT
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 85 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (53 bp):
GTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGGCACTATAA
Found at i:9919755 original size:14 final size:13
Alignment explanation
Indices: 9919736--9919775 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 13
9919726 TTGAACCCCC
9919736 TTTTATTTTATTTT
1 TTTTATTTT-TTTT
9919750 TTTTATTTCTTTTT
1 TTTTATTT-TTTTT
9919764 TTTTCATTTTTT
1 TTTT-ATTTTTT
9919776 CTTTCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTATTTTTTTT
Found at i:9919762 original size:12 final size:11
Alignment explanation
Indices: 9919747--9919793 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
9919737 TTTATTTTAT
9919747 TTTTTTTATTTC
1 TTTTTTT-TTTC
9919759 -TTTTTTTTTC
1 TTTTTTTTTTC
*
9919769 ATTTTTTCTTTC
1 -TTTTTTTTTTC
9919781 TTTTTTCTTTTC
1 TTTTTT-TTTTC
9919793 T
1 T
9919794 CATTTCCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 4 0.13
11 12 0.40
12 14 0.47
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:9919767 original size:18 final size:18
Alignment explanation
Indices: 9919736--9919791 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
9919726 TTGAACCCCC
*
9919736 TTTTATTTTATTTTT-TTT
1 TTTTCTTTT-TTTTTCTTT
* *
9919754 ATTTCTTTTTTTTTCATT
1 TTTTCTTTTTTTTTCTTT
9919772 TTTTCTTTCTTTTTTCTTT
1 TTTTCTTT-TTTTTTCTTT
9919791 T
1 T
9919792 CTCATTTCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 5 0.16
18 16 0.52
19 10 0.32
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTCTTTTTTTTTCTTT
Found at i:9919775 original size:26 final size:26
Alignment explanation
Indices: 9919746--9919798 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
9919736 TTTTATTTTA
*
9919746 TTTTT-TTTATTTCTTT-TTTTTTCAT
1 TTTTTCTTTATTT-TTTCTTTTCTCAT
*
9919771 TTTTTCTTTCTTTTTTCTTTTCTCAT
1 TTTTTCTTTATTTTTTCTTTTCTCAT
9919797 TT
1 TT
9919799 CCATTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (26 bp):
TTTTTCTTTATTTTTTCTTTTCTCAT
Found at i:9919787 original size:11 final size:11
Alignment explanation
Indices: 9919748--9919790 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
9919738 TTATTTTATT
*
9919748 TTTTTTATTTC
1 TTTTTTCTTTC
9919759 TTTTTT-TTTC
1 TTTTTTCTTTC
9919769 ATTTTTTCTTTC
1 -TTTTTTCTTTC
9919781 TTTTTTCTTT
1 TTTTTTCTTT
9919791 TCTCATTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.13
11 22 0.73
12 4 0.13
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:9928398 original size:2 final size:2
Alignment explanation
Indices: 9928391--9928416 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9928381 GAATGATAGG
9928391 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
9928417 GCTCATGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9939643 original size:19 final size:17
Alignment explanation
Indices: 9939609--9939641 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9939599 AGTTGGAATA
9939609 ATGTTTTAGAATATATT
1 ATGTTTTAGAATATATT
*
9939626 ATGTTTTAGTATATAT
1 ATGTTTTAGAATATAT
9939642 ATCAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (17 bp):
ATGTTTTAGAATATATT
Found at i:9939860 original size:94 final size:97
Alignment explanation
Indices: 9939740--9939929 Score: 287
Period size: 94 Copynumber: 2.0 Consensus size: 97
9939730 TAGGTAAGAG
*
9939740 ATAAATCATATTAAAATATACCGTCTCTTGCATGTGCCTTGTTATATGTTGCTCTTACATTGTTT
1 ATAAATCATATT-AAATATACCGTCTCTTCCATGTGCCTTGTTATATGTTGCTCTTACATTGTTT
9939805 A-TTTTTCCGCTCTTAAATTCTTAAGATGCTCA
65 ATTTTTTCCGCTCTTAAATTCTTAAGATGCTCA
* * ** *
9939837 ATAAATCATATT-AA-ATACTGTCTCTTCCGTGTTTCTTGTTATATGTTGCTCTTGCATTGTTTA
1 ATAAATCATATTAAATATACCGTCTCTTCCATGTGCCTTGTTATATGTTGCTCTTACATTGTTTA
*
9939900 TTTTTTCCGCTCTTAAATTCTTGAGATGCT
66 TTTTTTCCGCTCTTAAATTCTTAAGATGCT
9939930 TGATGATCAA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
94 43 0.51
95 30 0.35
97 12 0.14
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (97 bp):
ATAAATCATATTAAATATACCGTCTCTTCCATGTGCCTTGTTATATGTTGCTCTTACATTGTTTA
TTTTTTCCGCTCTTAAATTCTTAAGATGCTCA
Found at i:9943506 original size:20 final size:21
Alignment explanation
Indices: 9943481--9943526 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
9943471 AATACAATTA
*
9943481 TAATATT-ACACTTACCTCAC
1 TAATATTAACACTCACCTCAC
9943501 TAATATTACACACTCACCTCAC
1 TAATATTA-ACACTCACCTCAC
9943523 TAAT
1 TAAT
9943527 GTTCTCTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.30
22 16 0.70
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATATTAACACTCACCTCAC
Found at i:9944070 original size:22 final size:22
Alignment explanation
Indices: 9944044--9944091 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
9944034 AATACAATTA
*
9944044 TAATATTACACACTTACCTCAC
1 TAATATTACACACTCACCTCAC
9944066 TAATATTACACACTCACCTCAC
1 TAATATTACACACTCACCTCAC
9944088 TAAT
1 TAAT
9944092 GTTCTCTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (22 bp):
TAATATTACACACTCACCTCAC
Found at i:9947165 original size:36 final size:36
Alignment explanation
Indices: 9947123--9947198 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
9947113 TTATAGCTAA
*
9947123 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
9947159 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
9947195 AAAA
1 AAAA
9947199 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:9951682 original size:15 final size:15
Alignment explanation
Indices: 9951662--9951691 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9951652 ACCACGTGCT
9951662 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
9951677 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
9951692 GATTGTGATA
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:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:9952154 original size:36 final size:36
Alignment explanation
Indices: 9952112--9952187 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
9952102 TTATAGCTAA
*
9952112 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
9952148 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
9952184 AAAA
1 AAAA
9952188 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Done.