Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003112.1 Hibiscus syriacus cultivar Beakdansim tig00006507_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: 642031
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:488712 original size:30 final size:30
Alignment explanation
Indices: 488676--488733 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
488666 CACATGCATG
*
488676 CATGCACGCTTCAGACGTCCAGGCCCCCCA
1 CATGCACGATTCAGACGTCCAGGCCCCCCA
488706 CATGCACGATTCAGACGTCCAGGCCCCC
1 CATGCACGATTCAGACGTCCAGGCCCCC
488734 ATGCAACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.21, C:0.45, G:0.21, T:0.14
Consensus pattern (30 bp):
CATGCACGATTCAGACGTCCAGGCCCCCCA
Found at i:491517 original size:2 final size:2
Alignment explanation
Indices: 491510--491563 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
491500 TAATATAGAA
491510 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
491552 AT AT AT AT AT AT
1 AT AT AT AT AT AT
491564 GTGTGTGTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:491658 original size:2 final size:2
Alignment explanation
Indices: 491647--491687 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
491637 AATAAGTATG
491647 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
491688 AAGGTTCCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:493897 original size:32 final size:31
Alignment explanation
Indices: 493845--493949 Score: 133
Period size: 31 Copynumber: 3.4 Consensus size: 31
493835 AGGCTTGAGA
*
493845 GCCTACCCAAGAAAGTTCTCGGGGCCACAAG
1 GCCTACCCAAGAAAGATCTCGGGGCCACAAG
*
493876 GCCTACCCCAAGAGAA-ATCTCGGGGCCACAGG
1 GCCTA-CCCAAGA-AAGATCTCGGGGCCACAAG
* *
493908 GCCTACCCAAGAAAGATCTCGGAGCCGC-AG
1 GCCTACCCAAGAAAGATCTCGGGGCCACAAG
493938 AGCCTACCCAAG
1 -GCCTACCCAAG
493950 GGTTGCCTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
30 3 0.05
31 34 0.52
32 26 0.40
33 2 0.03
ACGTcount: A:0.30, C:0.34, G:0.26, T:0.10
Consensus pattern (31 bp):
GCCTACCCAAGAAAGATCTCGGGGCCACAAG
Found at i:495662 original size:25 final size:24
Alignment explanation
Indices: 495611--495663 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
495601 CAGGACATCG
*
495611 AAAAACATAAAATAGGGCTATTCA
1 AAAAACATAAAATAAGGCTATTCA
*
495635 AAAAACATAAAATAAGGCTATTCG
1 AAAAACATAAAATAAGGCTATTCA
495659 AAAAA
1 AAAAA
495664 TTTGACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.19
Consensus pattern (24 bp):
AAAAACATAAAATAAGGCTATTCA
Found at i:497342 original size:28 final size:28
Alignment explanation
Indices: 497308--497371 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
497298 TTTGAGAGAA
497308 AATGTTGGAATTAAACTTGATTTTTTTT
1 AATGTTGGAATTAAACTTGATTTTTTTT
497336 AATGTTGGAATTAAACTTGATTTTTTTT
1 AATGTTGGAATTAAACTTGATTTTTTTT
497364 AATGTTGG
1 AATGTTGG
497372 CGAACTATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.52
Consensus pattern (28 bp):
AATGTTGGAATTAAACTTGATTTTTTTT
Found at i:500930 original size:24 final size:20
Alignment explanation
Indices: 500898--500955 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
500888 GCATAGGTAG
500898 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
500922 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
500942 TGTATCGATGCACT
1 TGCATCGATGCACT
500956 TCAAGGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:505258 original size:24 final size:20
Alignment explanation
Indices: 505231--505288 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
505221 GCATGGGTAG
505231 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
505255 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
505275 TGTATCGATGCACT
1 TGCATCGATGCACT
505289 TTAAGGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:508858 original size:32 final size:31
Alignment explanation
Indices: 508810--508894 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 31
508800 CAAAAAGCTT
*
508810 GGGGCC-CAAGAGCCTACCCAAGAAAGTTCTC
1 GGGGCCAC-AGAGCCTACCCAAGAAAGATCTC
* *
508841 GGGGCCACGGAGGCCTACCTAAGAAAGATCTC
1 GGGGCCACAGA-GCCTACCCAAGAAAGATCTC
*
508873 GGGGCCGCAGAGCCTACCCAAG
1 GGGGCCACAGAGCCTACCCAAG
508895 GGAGGTTCGT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 18 0.39
32 28 0.61
ACGTcount: A:0.27, C:0.32, G:0.31, T:0.11
Consensus pattern (31 bp):
GGGGCCACAGAGCCTACCCAAGAAAGATCTC
Found at i:509046 original size:12 final size:12
Alignment explanation
Indices: 509029--509063 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
509019 ACCAATATAT
509029 CAGAAATTAGAA
1 CAGAAATTAGAA
*
509041 CAGAAATCAGAA
1 CAGAAATTAGAA
509053 CAGAAATTAGA
1 CAGAAATTAGA
509064 GAAAACATCC
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:0.57, C:0.11, G:0.17, T:0.14
Consensus pattern (12 bp):
CAGAAATTAGAA
Found at i:513894 original size:24 final size:24
Alignment explanation
Indices: 513867--513913 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
513857 ATTAAAAATG
*
513867 TAAGAGATGTAAAATTAGATAATT
1 TAAGAGATATAAAATTAGATAATT
513891 TAAGAGATATAAAATTAGATAAT
1 TAAGAGATATAAAATTAGATAAT
513914 CAATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (24 bp):
TAAGAGATATAAAATTAGATAATT
Found at i:517180 original size:66 final size:66
Alignment explanation
Indices: 517054--517183 Score: 170
Period size: 66 Copynumber: 2.0 Consensus size: 66
517044 TAGGTCCATA
* ** * * *
517054 AGGAATTACCAGTCGGTGTTGAACCTATAAAAGGAATTACCAGCAACGACTAAACTTGCCAGAGA
1 AGGAATTACCAGTCGGGGTAAAACCTATAAAAGAAATTACCAGCAACAACTAAACCTGCCAGAGA
517119 T
66 T
* ** *
517120 AGGAATTACCAGTCGGGGTAAAACCTATACAAGAAATTACCAGCAGTAACTGAACCTGCCAGAG
1 AGGAATTACCAGTCGGGGTAAAACCTATAAAAGAAATTACCAGCAACAACTAAACCTGCCAGAG
517184 TCGTCATTCA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (66 bp):
AGGAATTACCAGTCGGGGTAAAACCTATAAAAGAAATTACCAGCAACAACTAAACCTGCCAGAGA
T
Found at i:520099 original size:194 final size:194
Alignment explanation
Indices: 519743--520105 Score: 455
Period size: 194 Copynumber: 1.9 Consensus size: 194
519733 GTCGCGAAAG
* * ** *
519743 TATCGATACCTTACACATATGTATCAATACATGACAATTTAACAGGTTGAAGTTTTGACAAAACC
1 TATCGATACCTTACACACATGTATCAATACATGACAATATAACAGGTTGAAAATTTGAAAAAACC
* * * * *
519808 GGTTCAGTTTGACAAAACCGTTAAAGAGACCAGAATGGTTGAAATTTGTATCGATATTTTTATAA
66 GGTTCAATATGACAAAACCGGTAAAGAGACCAGAATGGTTGAAA-TAGTATCGATACTTTTATAA
* *
519873 GTATATGCACCAAAGTATCGGTACTTTAGGAATTTAAAATAATTGCAATAATAGCGCCTATAAAA
130 GTATATGCACCAAAGTATCGATACTTTAGGAATTGAAAATAATTGCAATAATAGCGCCTATAAAA
* * * *
519938 TATCGATACCTTATACACATGTATCGATACATGACAATATAACATGTT-AAAATTTGAAAAAATC
1 TATCGATACCTTACACACATGTATCAATACATGACAATATAACAGGTTGAAAATTTGAAAAAACC
* * *
520002 GGTTTCAATATGACAAAACCGGTAAAGTACTATCGGATAT-GTT-AAA-AGTATCGATACTTTTA
66 GG-TTCAATATGACAAAACCGGTAAAG-A-GACCAGA-ATGGTTGAAATAGTATCGATACTTTTA
* * *
520064 TAAGTATATGTATCATAGTATCGATACTTTAGGAATTGAAAA
127 TAAGTATATGCACCAAAGTATCGATACTTTAGGAATTGAAAA
520106 AAAAATGAAA
Statistics
Matches: 142, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
194 65 0.46
195 64 0.45
196 4 0.03
197 7 0.05
198 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (194 bp):
TATCGATACCTTACACACATGTATCAATACATGACAATATAACAGGTTGAAAATTTGAAAAAACC
GGTTCAATATGACAAAACCGGTAAAGAGACCAGAATGGTTGAAATAGTATCGATACTTTTATAAG
TATATGCACCAAAGTATCGATACTTTAGGAATTGAAAATAATTGCAATAATAGCGCCTATAAAA
Found at i:521639 original size:199 final size:200
Alignment explanation
Indices: 521377--521829 Score: 617
Period size: 200 Copynumber: 2.3 Consensus size: 200
521367 TCGGTACCTA
* * * *
521377 ATAATAGGTGTAAACATAAAGA-ATCAATACTCTTTGTATATGTATCGATTCTTTTAGTCCAGTA
1 ATAATAGGTGTAAACATAAA-ATATCGATACTATTTGTATAAGTATCGATACTTTTAGTCCAGTA
* ** * *
521441 TGTTTCTC-AACAATTTGCACACACAAAGTATCAATACATGTATAACAAGTATTGATACTTATAA
65 TGCTTCTCAAACAACATGCACACACAAAGTATCAATACACGTATAACAAGTATCGATACTTATAA
* * *
521505 TTTTGAAATCGATTACTTTAAAGTTATAGGAAAATTTACAATGTAAAC-AGTAAAAATCTATCGA
130 TTTCGAAACCGATTACTTTAAAGTAATAGGAAAATTTACAATGTAAACGA-TAAAAATCTATCGA
521569 TTTAATG
194 TTTAATG
*
521576 ATAATAGGTGTAAACATAAAATATCGATACTATTTGTGTAAGTATCGATACTTTTAGTCCAGTAT
1 ATAATAGGTGTAAACATAAAATATCGATACTATTTGTATAAGTATCGATACTTTTAGTCCAGTAT
* * * * * *
521641 GCTTCTCAAACAACATGCACGCAGAAAGTATCGATATACGTATCATAAGTATCGATACTTATAAT
66 GCTTCTCAAACAACATGCACACACAAAGTATCAATACACGTATAACAAGTATCGATACTTATAAT
* * *
521706 TTCGAAACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGATCAAAATCTATCGGTT
131 TTCGAAACCGATTACTTTAAAGTAATAGGAAAATTTACAATGTAAACGATAAAAATCTATCGATT
521771 TAATG
196 TAATG
* * * * *
521776 ATAATAGGCGTAAACATAAAGTTTCGATACTTTTTGTATAGGTATCGATA-TTTT
1 ATAATAGGTGTAAACATAAAATATCGATACTATTTGTATAAGTATCGATACTTTT
521830 CGATCTAAAC
Statistics
Matches: 223, Mismatches: 28, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
198 1 0.00
199 68 0.30
200 153 0.69
201 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (200 bp):
ATAATAGGTGTAAACATAAAATATCGATACTATTTGTATAAGTATCGATACTTTTAGTCCAGTAT
GCTTCTCAAACAACATGCACACACAAAGTATCAATACACGTATAACAAGTATCGATACTTATAAT
TTCGAAACCGATTACTTTAAAGTAATAGGAAAATTTACAATGTAAACGATAAAAATCTATCGATT
TAATG
Found at i:522172 original size:108 final size:108
Alignment explanation
Indices: 521983--522396 Score: 273
Period size: 108 Copynumber: 3.7 Consensus size: 108
521973 ATGTACACTG
* * * *
521983 TAATATGTTGATAATACTGATAACAAATCAAGTAATTAATCGATTATGTTA-CTGCCGGATTTCT
1 TAATATGTTGATAATACTGATAACAAATTAAATAATTAATCGATTATGTTATC-GTCAGATTTCT
* * *
522047 AAGGA-TCTATCAGCTTAAACTTTGGTAACATTTTAGGTTTTACC
65 AA-GACCCCATCAACTTAAACTTTGGTAACATTTTAGGTTTTACC
* * *
522091 TAATATGTTGATAATACTGATAATAAATTAAATAATTAA-CATATTTTGTTATCGTCAGATTTCT
1 TAATATGTTGATAATACTGATAACAAATTAAATAATTAATC-GATTATGTTATCGTCAGATTTCT
* * * * * *
522155 AAGACCCCATCAACTTAAAAAATGTGCT-ACCTATTACGTTACATAAGCGCTACC
65 AAGACCCCATCAACTT--AAACTTTGGTAACATTTTAGGTT---T------TACC
* ** **** * ** *
522209 TAATATGTT-ATTATGGTTGATAATGTTTTGAGGAATTAATCGGTTATGTTATCGTCAGATTTCT
1 TAATATGTTGATAAT-ACTGATAACAAATTAAATAATTAATCGATTATGTTATCGTCAGATTTCT
* * * * * * **
522273 AAGGCTCCATCAGCTTAAACTTTAGCAACATTTTTGGCGTTACC
65 AAGACCCCATCAACTTAAACTTTGGTAACATTTTAGGTTTTACC
* * ** *
522317 TAATATGTTGATAATACTGATAACAAATTAAATAATTAA-CATATTTTGTTATTATCGGATTTCT
1 TAATATGTTGATAATACTGATAACAAATTAAATAATTAATC-GATTATGTTATCGTCAGATTTCT
*
522381 AAGGCCCCATCAACTT
65 AAGACCCCATCAACTT
522397 TAAAAAGGCG
Statistics
Matches: 227, Mismatches: 60, Indels: 38
0.70 0.18 0.12
Matches are distributed among these distances:
107 4 0.02
108 122 0.54
109 14 0.06
110 7 0.03
112 1 0.00
114 1 0.00
116 5 0.02
117 10 0.04
118 62 0.27
119 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.38
Consensus pattern (108 bp):
TAATATGTTGATAATACTGATAACAAATTAAATAATTAATCGATTATGTTATCGTCAGATTTCTA
AGACCCCATCAACTTAAACTTTGGTAACATTTTAGGTTTTACC
Found at i:522380 original size:226 final size:226
Alignment explanation
Indices: 522016--522485 Score: 692
Period size: 226 Copynumber: 2.1 Consensus size: 226
522006 CAAATCAAGT
* * * * *
522016 AATTAATCGATTATGTTACTGCCGGATTTCTAAGGATCTATCAGCTTAAACTTTGGTAACATTTT
1 AATTAATCGGTTATGTTACTGCCAGATTTCTAAGGATCCATCAGCTTAAACTTTAGCAACATTTT
** * *
522081 AGGTTTTACCTAATATGTTGATAATACTGATAATAAATTAAATAATTAACATATTTTGTTATCGT
66 AGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAATAATTAACATATTTTGTTATCAT
* *
522146 CAGATTTCTAAGACCCCATCAACTTAAAAAATGTGCTACCTATTACGTTACATAAGCGCTACCTA
131 CAGATTTCTAAGACCCCATCAACTTAAAAAAGGCGCTACCTATTACGTTACATAAGCGCTACCTA
* * *
522211 ATATGTTATTATGGTTGATAATGTTTTG-AGG
196 ATATATTATTATGATTAATAATG-TTTGCAGG
* *
522242 AATTAATCGGTTATGTTA-TCGTCAGATTTCTAAGGCTCCATCAGCTTAAACTTTAGCAACATTT
1 AATTAATCGGTTATGTTACT-GCCAGATTTCTAAGGATCCATCAGCTTAAACTTTAGCAACATTT
* *
522306 TTGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAATAATTAACATATTTTGTTATTA
65 TAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAATAATTAACATATTTTGTTATCA
* * * *
522371 TCGGATTTCTAAGGCCCCATCAACTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGTTACCT
130 TCAGATTTCTAAGACCCCATCAACTTAAAAAAGGCGCTACCTATTACGTTACATAAGCGCTACCT
*
522436 AATATATTATTATGATTAATAATGTTTGCAGT
195 AATATATTATTATGATTAATAATGTTTGCAGG
*
522468 AATTAACCGGTTATGTTA
1 AATTAATCGGTTATGTTA
522486 AAGTCAATAT
Statistics
Matches: 218, Mismatches: 24, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
225 5 0.02
226 213 0.98
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (226 bp):
AATTAATCGGTTATGTTACTGCCAGATTTCTAAGGATCCATCAGCTTAAACTTTAGCAACATTTT
AGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAATAATTAACATATTTTGTTATCAT
CAGATTTCTAAGACCCCATCAACTTAAAAAAGGCGCTACCTATTACGTTACATAAGCGCTACCTA
ATATATTATTATGATTAATAATGTTTGCAGG
Found at i:524049 original size:3 final size:3
Alignment explanation
Indices: 524043--524110 Score: 109
Period size: 3 Copynumber: 22.0 Consensus size: 3
524033 TTTTTTATAT
*
524043 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
524091 TTA TTA TTTA TTA TATA TTA
1 TTA TTA -TTA TTA T-TA TTA
524111 CAGGCCCAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
3 55 0.90
4 6 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:525462 original size:3 final size:3
Alignment explanation
Indices: 525449--525507 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
525439 TTATTTGCAA
* * *
525449 TAT TAT T-T TAT TAT TAT TAT TGCT T-T AAT TAT TAT T-T CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
*
525492 TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT T
525508 TATATAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
2 4 0.09
3 39 0.87
4 2 0.04
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:525467 original size:26 final size:28
Alignment explanation
Indices: 525438--525499 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
525428 TATTTTAATC
*
525438 ATTATTTGC-AA-TATTATTTTATTATT
1 ATTATTTGCTAATTATTATTTCATTATT
525464 ATTA-TTGCTTTAATTATTATTTCATTATT
1 ATTATTTGC--TAATTATTATTTCATTATT
525493 ATTATTT
1 ATTATTT
525500 TTATTATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 4 0.13
26 4 0.13
28 2 0.07
29 18 0.60
30 2 0.07
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (28 bp):
ATTATTTGCTAATTATTATTTCATTATT
Found at i:525505 original size:26 final size:28
Alignment explanation
Indices: 525449--525507 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
525439 TTATTTGCAA
*
525449 TATTATTTTATTATTATTATTGCTTTAAT
1 TATTATTTCATTATTATTATT-CTTTAAT
525478 TATTATTTCATTATTATTATT-TTT-AT
1 TATTATTTCATTATTATTATTCTTTAAT
525504 TATT
1 TATT
525508 TATATAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 6 0.21
27 3 0.10
29 20 0.69
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (28 bp):
TATTATTTCATTATTATTATTCTTTAAT
Found at i:527847 original size:8 final size:7
Alignment explanation
Indices: 527823--527864 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
527813 TTTTCATACA
527823 TGCA-TT
1 TGCATTT
527829 TGCATTT
1 TGCATTT
527836 TGCATCTT
1 TGCAT-TT
527844 TGCATTT
1 TGCATTT
* *
527851 TTCATTG
1 TGCATTT
527858 TGCATTT
1 TGCATTT
527865 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:527847 original size:15 final size:14
Alignment explanation
Indices: 527823--527864 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
527813 TTTTCATACA
527823 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
527836 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
527851 TTCATTGTGCATTT
1 TGCATTTTGCATTT
527865 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:527960 original size:27 final size:27
Alignment explanation
Indices: 527924--527983 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
527914 CATTCACATA
527924 TTTACATTTGCATTTACATTTGCATTT
1 TTTACATTTGCATTTACATTTGCATTT
* * *
527951 TTTACGTTTGTATTTACATTTTCA-TT
1 TTTACATTTGCATTTACATTTGCATTT
527977 TTTACAT
1 TTTACAT
527984 AATTACATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTACATTTGCATTTACATTTGCATTT
Found at i:527977 original size:12 final size:12
Alignment explanation
Indices: 527923--527950 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
527913 ACATTCACAT
527923 ATTTACATTTGC
1 ATTTACATTTGC
527935 ATTTACATTTGC
1 ATTTACATTTGC
527947 ATTT
1 ATTT
527951 TTTACGTTTG
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:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:532384 original size:114 final size:114
Alignment explanation
Indices: 532183--532390 Score: 389
Period size: 114 Copynumber: 1.8 Consensus size: 114
532173 GTGCCACGTT
532183 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
**
532248 GTTTGGTATTAACCCCAAAACCAATCATTAGATTTGAAAGACGAATTTG
66 GTTTGGTAGGAACCCCAAAACCAATCATTAGATTTGAAAGACGAATTTG
532297 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
*
532362 GTTTGGTAGGAACCCCAGAACCAATCATT
66 GTTTGGTAGGAACCCCAAAACCAATCATT
532391 GGAATTAAAA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 91 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
GTTTGGTAGGAACCCCAAAACCAATCATTAGATTTGAAAGACGAATTTG
Found at i:534959 original size:22 final size:22
Alignment explanation
Indices: 534928--534982 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
534918 ATCTATACTC
*
534928 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
534950 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
534972 TTCAAAGATGA
1 TTCAAAGATGA
534983 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:535759 original size:113 final size:113
Alignment explanation
Indices: 535390--536388 Score: 1292
Period size: 113 Copynumber: 8.8 Consensus size: 113
535380 GATTTAAATC
* * ** * * *
535390 CATCATTCAATGGATCAACAGTGCCAAATAGAGTTCATAATAAGAAGAACTCATCTAAAGAAGGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* *
535455 AGAAGAAGTTGATAATAAGAAGAACTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * * * *
535503 CATCATTCGATAGATCAGCATTACCAGGTCGAGTTCATAATGAGAATAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG-A--A
*
535568 AGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATT
63 AGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * * *
535619 CATCATTCGATTGATTAGCAGTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
*
535684 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * *
535732 CATCATTCGATCGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
*
535797 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGTTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * * * * *
535845 CATCACTAGATGGATCAACATTTCCA-GAAGGTGTTCGTAATGAGAAGAACTCATCTGAAGAAAG
1 CATCATTCGATGGATCAACATTGCCAGGTA-GAGTTCATAATGAGAAGAACTCATCTGAAGAAAG
* *
535909 AAGAAGAAATTCATAATGAGAAGAACTTGTTCAACTTTTCGTTTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * * * * *
535958 CATCACTAGATGGATCAACTTTTCCAGAG-AGAGTTTATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTCGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAG
*
536022 AAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTCGCTTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * * *
536071 CATCATTCGATTGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG-AAGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-
* *
536135 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * ** * * *
536184 CATCACTCGGTGGATCAGTAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* ** *
536249 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTT-GCTCAAATA
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAATT
* ** * * * *
536297 CATCACTT-GATGGATCAACATTTCCA-AAAGGTGTTCATAATGAGAAGAACCCGTCTGAAG-AG
1 CATCA-TTCGATGGATCAACATTGCCAGGTA-GAGTTCATAATGAGAAGAACTCATCTGAAGAAA
*
536359 GAAGAAGGAGTTCATAATGAGAAGAACTTG
64 GAAGAAGAAGTTCATAATGAGAAGAACTTG
536389 CTTAACCTTT
Statistics
Matches: 794, Mismatches: 80, Indels: 25
0.88 0.09 0.03
Matches are distributed among these distances:
112 34 0.04
113 646 0.81
114 10 0.01
115 2 0.00
116 102 0.13
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
Found at i:536632 original size:3 final size:3
Alignment explanation
Indices: 536626--536693 Score: 118
Period size: 3 Copynumber: 22.0 Consensus size: 3
536616 GTTTTTTTAT
536626 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
536674 TTA TTA TTTA TTA TATA TTA
1 TTA TTA -TTA TTA T-TA TTA
536694 CAGGCCCAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
3 57 0.90
4 6 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:538063 original size:3 final size:3
Alignment explanation
Indices: 538050--538108 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
538040 TTATTTGCAA
* * *
538050 TAT TAT T-T TAT TAT TAT TAT TGCT T-T AAT TAT TAT T-T CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
*
538093 TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT T
538109 TATATAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
2 4 0.09
3 39 0.87
4 2 0.04
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:538068 original size:26 final size:28
Alignment explanation
Indices: 538039--538100 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
538029 TATTTTAATC
*
538039 ATTATTTGC-AA-TATTATTTTATTATT
1 ATTATTTGCTAATTATTATTTCATTATT
538065 ATTA-TTGCTTTAATTATTATTTCATTATT
1 ATTATTTGC--TAATTATTATTTCATTATT
538094 ATTATTT
1 ATTATTT
538101 TTATTATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 4 0.13
26 4 0.13
28 2 0.07
29 18 0.60
30 2 0.07
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (28 bp):
ATTATTTGCTAATTATTATTTCATTATT
Found at i:538106 original size:26 final size:28
Alignment explanation
Indices: 538050--538108 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
538040 TTATTTGCAA
*
538050 TATTATTTTATTATTATTATTGCTTTAAT
1 TATTATTTCATTATTATTATT-CTTTAAT
538079 TATTATTTCATTATTATTATT-TTT-AT
1 TATTATTTCATTATTATTATTCTTTAAT
538105 TATT
1 TATT
538109 TATATAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 6 0.21
27 3 0.10
29 20 0.69
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (28 bp):
TATTATTTCATTATTATTATTCTTTAAT
Found at i:539470 original size:32 final size:32
Alignment explanation
Indices: 539433--539532 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 32
539423 GGTGCGCACA
* *
539433 TGTGTACCTAAATTGAAACGAGTGCCTATGTG
1 TGTGTACCTAAATTTAAACGAGCGCCTATGTG
* * * *
539465 TGTGTACCTTAATTTAAATGAGGGCTTATGTG
1 TGTGTACCTAAATTTAAACGAGCGCCTATGTG
** *
539497 TGTGTGTCTGAATTTAAACGAGCGCCTATGTG
1 TGTGTACCTAAATTTAAACGAGCGCCTATGTG
539529 TGTG
1 TGTG
539533 CGTGCGCGTG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (32 bp):
TGTGTACCTAAATTTAAACGAGCGCCTATGTG
Found at i:539599 original size:32 final size:32
Alignment explanation
Indices: 539548--539644 Score: 158
Period size: 32 Copynumber: 3.0 Consensus size: 32
539538 GCGTGCGTGC
* *
539548 GTACCTGAACTCAAACAAGCGCCTATGTATGT
1 GTACTTGAATTCAAACAAGCGCCTATGTATGT
539580 GTACTTGAATTCAAACAAGCGCCTATGTATGT
1 GTACTTGAATTCAAACAAGCGCCTATGTATGT
* *
539612 GTACTTGAATTCAAACAAGTGCCTATGTGTGT
1 GTACTTGAATTCAAACAAGCGCCTATGTATGT
539644 G
1 G
539645 CGCGCGCGTG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (32 bp):
GTACTTGAATTCAAACAAGCGCCTATGTATGT
Found at i:539816 original size:58 final size:57
Alignment explanation
Indices: 539703--539826 Score: 142
Period size: 56 Copynumber: 2.1 Consensus size: 57
539693 CGCGCGCTCA
* * *
539703 TGCGTGCGTGTATACCTGAATTCAAACGAGCACATGTGTGCGTGCGTTCGTGTGTGCG
1 TGCGTGTGTGTATA-CTGAATTCAAACGAGCACATGTGTGCGTGCGTGCGCGTGTGCG
* * * *
539761 TGCGTGTGTGTAT-CTGAATTCAAATGAGCGCTTGTGTGTGTGCGTGCGCACGTGTGCG
1 TGCGTGTGTGTATACTGAATTCAAACGAGCACATGTGTGCGTGCGTGCG--CGTGTGCG
*
539819 TGTGTGTG
1 TGCGTGTG
539827 CATCTGTATG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
56 30 0.54
58 26 0.46
ACGTcount: A:0.15, C:0.18, G:0.35, T:0.32
Consensus pattern (57 bp):
TGCGTGTGTGTATACTGAATTCAAACGAGCACATGTGTGCGTGCGTGCGCGTGTGCG
Found at i:540203 original size:27 final size:27
Alignment explanation
Indices: 540165--540221 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
540155 CTCCCTCCCT
*
540165 CAATATAAATATATAATATATATTTTA
1 CAATATAAATATATAATATATATTTCA
*
540192 CAATATAAATATATATTATATATTTCA
1 CAATATAAATATATAATATATATTTCA
540219 CAA
1 CAA
540222 GGTGTAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (27 bp):
CAATATAAATATATAATATATATTTCA
Found at i:543762 original size:3 final size:3
Alignment explanation
Indices: 543754--543866 Score: 199
Period size: 3 Copynumber: 37.7 Consensus size: 3
543744 TTTTTATCCA
543754 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
543802 TAT TAT TAC TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
543850 TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
543867 AATATATTAA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 104 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:543906 original size:20 final size:19
Alignment explanation
Indices: 543865--543909 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
543855 CTATTATTAT
* *
543865 TAAATATATTAAATACATA
1 TAAATATATTAAAAACAAA
*
543884 TAAATATTATTAAAAATAAA
1 TAAATA-TATTAAAAACAAA
543904 TAAATA
1 TAAATA
543910 ATAAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATATATTAAAAACAAA
Found at i:558111 original size:83 final size:83
Alignment explanation
Indices: 557972--558755 Score: 1387
Period size: 83 Copynumber: 9.5 Consensus size: 83
557962 GACAGAATCA
*
557972 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAATCATTGAATTTG
558037 GAAGATGAATGTGCCAAT
66 GAAGATGAATGTGCCAAT
*
558055 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTTGACAAAACCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAATCATTGAATTTG
558120 GAAGATGAATGTGCCAAT
66 GAAGATGAATGTGCCAAT
558138 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAATCATTGAATTTG
*
558203 GAAGATGAATGTGTTC-AT
66 GAAGATGAATGTG-CCAAT
*
558221 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAATCATTGAATTTG
558286 GAAGATGAATGTGCCAAT
66 GAAGATGAATGTGCCAAT
*
558304 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAATCATGGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAATCATTGAATTTG
558369 GAAGATGAATGTGCCAAT
66 GAAGATGAATGTGCCAAT
*
558387 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAATCATTGAATTTG
558452 GAAGATGAATGTGCCAAT
66 GAAGATGAATGTGCCAAT
*
558470 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAATCATGGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAATCATTGAATTTG
558535 GAAGATGAATGTGCCAAT
66 GAAGATGAATGTGCCAAT
558553 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAATCATTGAATTTG
*
558618 GAAGATGAATGTGTTC-AT
66 GAAGATGAATGTG-CCAAT
* * * *
558636 AGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTTGACAAAA-CAATCATTGAGTTTA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAATCATTGAATTTG
* *
558700 AAAGATGAATGTGTTC-AT
66 GAAGATGAATGTG-CCAAT
558718 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
558756 ATTCAGTAGG
Statistics
Matches: 678, Mismatches: 20, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
82 68 0.10
83 608 0.90
84 2 0.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (83 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAATCATTGAATTTG
GAAGATGAATGTGCCAAT
Found at i:559685 original size:113 final size:113
Alignment explanation
Indices: 559472--561045 Score: 2983
Period size: 113 Copynumber: 14.0 Consensus size: 113
559462 CAAAGATTCA
* * *
559472 AATTTATCATTTGAAGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
559537 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
559585 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
559650 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
559698 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
559763 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
559811 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
559876 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
559924 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
559989 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
560037 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
560102 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
560150 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
560215 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
560263 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
560328 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
560376 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
560441 AGGAAGAAGAAGTTCATAATGA-AAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
560488 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
560553 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
560601 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
560666 ATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
560714 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTTATAATGAGAAAAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
560779 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
560827 AATTCATCACTTGATGGATCATTTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
560892 AAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * *
560940 AATCCATCAATTGATGGATTATCTTTTCCGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
561004 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA-CTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
561046 GGCATAATTC
Statistics
Matches: 1438, Mismatches: 22, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
111 5 0.00
112 176 0.12
113 1257 0.87
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
AATTCATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:561372 original size:3 final size:3
Alignment explanation
Indices: 561364--561514 Score: 256
Period size: 3 Copynumber: 51.7 Consensus size: 3
561354 TTTTTATCCA
561364 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
561412 TAT TAT TAT TAT TAT TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
561458 TAT TAT TAT TAC TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
561505 TA- TAT TAT TA
1 TAT TAT TAT TA
561515 AATATATTAA
Statistics
Matches: 140, Mismatches: 4, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
2 8 0.06
3 132 0.94
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:561553 original size:19 final size:19
Alignment explanation
Indices: 561513--561566 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
561503 ATTATATTAT
* * *
561513 TAAATATATTAAATACATA
1 TAAATATATTAAAAATAAA
561532 TAAATATATTAAAAATAAA
1 TAAATATATTAAAAATAAA
*
561551 TAAATA-ATAAAAAATA
1 TAAATATATTAAAAATA
561567 TAATTACAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 9 0.29
19 22 0.71
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAATATATTAAAAATAAA
Found at i:568199 original size:20 final size:19
Alignment explanation
Indices: 568174--568227 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
568164 GCGAAATAAA
568174 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
568194 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
568214 AATCGCAACGCGAT
1 AATCGCAACGCGAT
568228 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:568238 original size:21 final size:21
Alignment explanation
Indices: 568212--568309 Score: 78
Period size: 21 Copynumber: 4.7 Consensus size: 21
568202 ATCAGTTCCC
568212 AGAATCGCAACGCGATTATGA
1 AGAATCGCAACGCGATTATGA
*
568233 AGAATCGCAATGCGA-TA-GTA
1 AGAATCGCAACGCGATTATG-A
** * **
568253 CA-AATTCGCATTGCGATTTTCC
1 -AGAA-TCGCAACGCGATTATGA
*
568275 AGAATCGCAACGCGAATATGA
1 AGAATCGCAACGCGATTATGA
568296 A-AATCGCAACGCGA
1 AGAATCGCAACGCGA
568310 ACATATAAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
19 1 0.02
20 18 0.30
21 38 0.63
22 3 0.05
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.20
Consensus pattern (21 bp):
AGAATCGCAACGCGATTATGA
Found at i:568302 original size:20 final size:20
Alignment explanation
Indices: 568277--568810 Score: 239
Period size: 20 Copynumber: 26.5 Consensus size: 20
568267 GATTTTCCAG
** *
568277 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
**
568297 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-CGTA
* * *
568317 AATCGCAACTCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * *
568336 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCCGT-A
* *
568358 AATTGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
**
568378 AATCGCAACGAC-AATATGTAA
1 AATCGCAACG-CGAATCCGT-A
*
568399 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* * *
568419 AATCACAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
568439 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
* * * *
568459 AATCGTAATGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
568479 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
568499 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
*
568520 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
568540 AATCGCAACGCG-AT-CGATA
1 AATCGCAACGCGAATCCG-TA
* *
568559 ATTCGCAACGCGATCTCCGGT-
1 AATCGCAACGCGA-ATCC-GTA
** **
568580 -ATCGCAAATCAGTTTCC--A
1 AATCGCAACGC-GAATCCGTA
* * *
568598 GATTCGCAACGCGATTCTG-A
1 -AATCGCAACGCGAATCCGTA
* ** * *
568618 CTATCGCATTGCGATTTCC-CA
1 -AATCGCAACGCGA-ATCCGTA
*** * *
568639 AATTCGCGTTGTGATTTTCC-TA
1 AA-TCGCAACGCGA--ATCCGTA
* * *
568661 ATTCGCAATGCGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
568681 AATCGCAACGCGATTACGTA
1 AATCGCAACGCGAATCCGTA
* *
568701 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATCCGTA
* * *
568721 AATCGCAATGCGATTGCGTA
1 AATCGCAACGCGAATCCGTA
** *
568741 AATCGCAATACGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
568761 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
568781 AATCGCAATGCGAATCTGTA
1 AATCGCAACGCGAATCCGTA
568801 AATCGCAACG
1 AATCGCAACG
568811 AGATTCTGAC
Statistics
Matches: 400, Mismatches: 88, Indels: 52
0.74 0.16 0.10
Matches are distributed among these distances:
18 2 0.00
19 22 0.05
20 292 0.73
21 73 0.18
22 10 0.03
23 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:568453 original size:40 final size:41
Alignment explanation
Indices: 568338--568549 Score: 311
Period size: 41 Copynumber: 5.2 Consensus size: 41
568328 GATTCTGACT
* * *
568338 ATCGCAACGAGTATCCGTAAAATTGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
568379 ATCGCAACGACAATATGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
568420 ATCACAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
568460 ATCGTAATGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
568500 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
568541 ATCGCAACG
1 ATCGCAACG
568550 CGATCGATAA
Statistics
Matches: 152, Mismatches: 18, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
40 71 0.47
41 81 0.53
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:568527 original size:121 final size:119
Alignment explanation
Indices: 568357--568574 Score: 348
Period size: 121 Copynumber: 1.8 Consensus size: 119
568347 AGTATCCGTA
* *
568357 AAATTGCAACGCGTATCCGTAAATCGCAACGACAATATGTAAAATCGCAACGCGTATCCGTAAAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAAT
568422 CACAACGAGAATACG-TAAATCGCAACGCGTATCTGTAAATCGTAATGAGAATACGT
66 CACAACGAG-AT-CGATAAATCGCAACGCG-ATCTGTAAATCGTAATGAGAATACGT
*
568478 AAATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAAT
* * *
568543 CGCAACGCGATCGATAATTCGCAACGCGATCT
66 CACAACGAGATCGATAAATCGCAACGCGATCT
568575 CCGGTATCGC
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
119 6 0.07
120 15 0.17
121 69 0.77
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (119 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAAT
CACAACGAGATCGATAAATCGCAACGCGATCTGTAAATCGTAATGAGAATACGT
Found at i:568654 original size:21 final size:21
Alignment explanation
Indices: 568621--568673 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
568611 ATTCTGACTA
568621 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * * *
568642 TCGCGTTGTGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
568663 TCGCAATGCGA
1 TCGCATTGCGA
568674 ATACGTAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:569682 original size:24 final size:24
Alignment explanation
Indices: 569655--569708 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
569645 GTATTTGAAA
569655 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
569679 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
569703 TTTGAT
1 TTTGAT
569709 GATTTTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:571629 original size:20 final size:21
Alignment explanation
Indices: 571604--571691 Score: 103
Period size: 20 Copynumber: 4.4 Consensus size: 21
571594 CAACGCGGAA
571604 ATCGCAACAC-GAATATGACT
1 ATCGCAACACGGAATATGACT
571624 ATCGCAACACGGAA-ATGACT
1 ATCGCAACACGGAATATGACT
**
571644 ATCGCAATGCGGAAT-TGACT
1 ATCGCAACACGGAATATGACT
** *
571664 ATCGCAATGCGGAA-ATGATT
1 ATCGCAACACGGAATATGACT
571684 ATCGCAAC
1 ATCGCAAC
571692 GAGAGAATCG
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
20 58 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACACGGAATATGACT
Found at i:571663 original size:40 final size:41
Alignment explanation
Indices: 571614--571690 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 41
571604 ATCGCAACAC
571614 GAATATGACTATCGCAACACGGAAATGACTATCGCAATGCG
1 GAATATGACTATCGCAACACGGAAATGACTATCGCAATGCG
** *
571655 GAAT-TGACTATCGCAATGCGGAAATGATTATCGCAA
1 GAATATGACTATCGCAACACGGAAATGACTATCGCAA
571691 CGAGAGAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 29 0.88
41 4 0.12
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (41 bp):
GAATATGACTATCGCAACACGGAAATGACTATCGCAATGCG
Found at i:571725 original size:19 final size:19
Alignment explanation
Indices: 571697--571803 Score: 134
Period size: 19 Copynumber: 5.8 Consensus size: 19
571687 GCAACGAGAG
571697 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
571716 AATCGTAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
571735 AATCGTAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
571754 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
571768 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
571788 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
571804 TAGTTTCGCG
Statistics
Matches: 77, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
14 8 0.10
16 5 0.06
17 2 0.03
18 3 0.04
19 48 0.62
20 11 0.14
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:571748 original size:38 final size:35
Alignment explanation
Indices: 571664--571803 Score: 144
Period size: 34 Copynumber: 3.9 Consensus size: 35
571654 GGAATTGACT
** *
571664 ATCGCAATGCGGAAATGATTATCGCAA-CGAGA-GA
1 ATCGCAATGC-GAAATGAAAATCGCAAGCGAAATGA
*
571698 ATCGCAATGCGAAATGAAAATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG--A
* *
571736 ATCGTAATGCGAAATGAAAATCGCAA-CG-AGTGA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
571769 ATCGCAATGCGAAAATGAAAATCGCAACGCGAAAT
1 ATCGCAATGCG-AAATGAAAATCGCAA-GCGAAAT
571804 TAGTTTCGCG
Statistics
Matches: 88, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
33 24 0.27
34 25 0.28
35 7 0.08
36 5 0.06
37 2 0.02
38 25 0.28
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (35 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
Found at i:571760 original size:71 final size:73
Alignment explanation
Indices: 571664--571803 Score: 212
Period size: 71 Copynumber: 1.9 Consensus size: 73
571654 GGAATTGACT
** * *
571664 ATCGCAATGCGGAAATGATTATCGCAACGAGAGAATCGCAATGCG-AAATGAAAATCGTAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAAAATCGCAACGCG
571728 AAATGAAA
66 AAATGAAA
* *
571736 ATCGTAATGC-GAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAAATCGCAACGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAAAATCGCAACGCG
571800 AAAT
66 AAAT
571804 TAGTTTCGCG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
71 31 0.51
72 30 0.49
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (73 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAAAATCGCAACGCG
AAATGAAA
Found at i:571869 original size:33 final size:33
Alignment explanation
Indices: 571812--571896 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
571802 ATTAGTTTCG
*
571812 CGTTGCTATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
571846 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
571879 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
571897 TGCGTTGAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 34 0.72
34 13 0.28
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:572028 original size:14 final size:14
Alignment explanation
Indices: 572009--572045 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
571999 CATCAATTAA
572009 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
572023 ACAAATCATCTTTT
1 ACAAATCAACATTT
572037 ACAAATCAA
1 ACAAATCAA
572046 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:573454 original size:21 final size:22
Alignment explanation
Indices: 573404--573481 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 22
573394 AATGTTGGGA
* *
573404 GGGACCTCTTCAAC-GATGACAG
1 GGGA-CTCTTGAACGGATGATAG
* * *
573426 TGGCCTCTTGAACGG-TGGTAG
1 GGGACTCTTGAACGGATGATAG
*
573447 GGGACTCTTG-AGGGATGATAG
1 GGGACTCTTGAACGGATGATAG
*
573468 GGGCCTCTTGAACG
1 GGGACTCTTGAACG
573482 ATAGGGGAGG
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
20 3 0.07
21 34 0.81
22 5 0.12
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.23
Consensus pattern (22 bp):
GGGACTCTTGAACGGATGATAG
Found at i:573506 original size:42 final size:41
Alignment explanation
Indices: 573401--573508 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 41
573391 TAGAATGTTG
* * * *
573401 GGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGGT
1 GGAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGAT
* ** *
573442 GGTAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGAT
1 GG-AGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGAT
573484 AGG-GGAGGCCTCTTGAACGATGACA
1 -GGAGG-GGCCTCTTGAACGATGACA
573509 CGTGAGTCGG
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
41 4 0.08
42 46 0.88
43 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (41 bp):
GGAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGAT
Found at i:574001 original size:20 final size:20
Alignment explanation
Indices: 573970--574056 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
573960 GAAACTTAAA
*
573970 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
573990 ATCACAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
574010 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
574030 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
574050 ATCGCAA
1 ATCGCAA
574057 CGAGAGAATC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:574134 original size:19 final size:19
Alignment explanation
Indices: 574100--574137 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
574090 CGCGATTATA
*
574100 GTTTCGCGTTGCGATTTTG
1 GTTTCGCATTGCGATTTTG
*
574119 GTTTCGCATTGTGATTTTG
1 GTTTCGCATTGCGATTTTG
574138 TCATTGCGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.13, G:0.29, T:0.50
Consensus pattern (19 bp):
GTTTCGCATTGCGATTTTG
Found at i:574169 original size:19 final size:19
Alignment explanation
Indices: 574141--574186 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
574131 GATTTTGTCA
*
574141 TTGCGGTTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
**
574160 TTGCGATTTTCATTTCTTG
1 TTGCGATTTTCATTTCGCG
574179 TTGCGATT
1 TTGCGATT
574187 CTCTTGTTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.17, G:0.22, T:0.52
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:574451 original size:94 final size:94
Alignment explanation
Indices: 574303--574682 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
574293 ATGGATTGCA
* *
574303 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
574367 TTAGCAGAATTGGCAACAACCGAACAAAT
66 TTAGCAGAATTGACAGCAACCGAACAAAT
*
574396 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTCAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
574461 TTAGCAGAATTGACAGCAACCGAACAAAT
66 TTAGCAGAATTGACAGCAACCGAACAAAT
574490 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
574555 TTAGCAGAATTGACAGCAACCGAATAAAT
66 TTAGCAGAATTGACAGCAACCGAACAAAT
*
574584 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * * *
574648 TTTAGTAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGACAGCAACCGAACAAAT
574678 TTACT
1 TTACT
574683 AAGCAATCTA
Statistics
Matches: 273, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
93 23 0.08
94 250 0.92
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGACAGCAACCGAACAAAT
Found at i:576439 original size:19 final size:19
Alignment explanation
Indices: 576387--576457 Score: 97
Period size: 20 Copynumber: 3.6 Consensus size: 19
576377 TGAAATGAAA
576387 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGA-AATGACT
576407 ATCGCAACGCAGAAATGACT
1 ATCGCAACG-AGAAATGACT
* **
576427 ATCGCAACGAGAAATTAAA
1 ATCGCAACGAGAAATGACT
576446 ATCGCAACGAGA
1 ATCGCAACGAGA
576458 TAATCGCAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
19 19 0.40
20 25 0.53
21 3 0.06
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAACGAGAAATGACT
Found at i:576483 original size:19 final size:19
Alignment explanation
Indices: 576378--576485 Score: 91
Period size: 20 Copynumber: 5.8 Consensus size: 19
576368 TCTTTTGGTT
*
576378 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
576397 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
576417 AGAAATGACTATCGCAACGA
1 -GAAATGAAAATCGCAACGC
*
576437 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
576454 G--A-GATAATCGCAACGC
1 GAAATGAAAATCGCAACGC
576470 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
576486 TACGATTTTG
Statistics
Matches: 71, Mismatches: 11, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 1 0.01
18 1 0.01
19 25 0.35
20 30 0.42
21 2 0.03
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:576534 original size:33 final size:33
Alignment explanation
Indices: 576488--576610 Score: 201
Period size: 33 Copynumber: 3.7 Consensus size: 33
576478 AATCGCAATA
** *
576488 CGATTTTGGTTTCGCGTTGCGATTATCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
* *
576521 TGATTTTCATTTCGCGTTGTGATTCTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
576554 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
576587 CGATTTTCATTTCGCGTTGCGATT
1 CGATTTTCATTTCGCGTTGCGATT
576611 TTCATTTCTC
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 83 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
Found at i:576540 original size:19 final size:19
Alignment explanation
Indices: 576516--576658 Score: 117
Period size: 19 Copynumber: 7.9 Consensus size: 19
576506 GCGATTATCT
*
576516 CGTTGTGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* *
576535 CGTTGTGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
576549 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
576568 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
576582 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
576601 CGTTGCGATTTTCATTTCTCT
1 CGTTGCGATTTTCA-TT-TCG
**
576622 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
576642 TGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
576659 TCATGTTGTG
Statistics
Matches: 100, Mismatches: 12, Indels: 24
0.74 0.09 0.18
Matches are distributed among these distances:
14 19 0.19
16 6 0.06
17 6 0.06
19 37 0.37
20 15 0.15
21 17 0.17
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.49
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:576558 original size:14 final size:14
Alignment explanation
Indices: 576535--576591 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
576525 TTTCATTTCG
*
576535 CGTTGTGATTCTCT
1 CGTTGCGATTCTCT
*
576549 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
576568 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
576582 CGTTGCGATT
1 CGTTGCGATT
576592 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:576637 original size:40 final size:41
Alignment explanation
Indices: 576576--576658 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
576566 CGCGTTGCGA
**
576576 TTCTCTCGTTGCGATTTTCA-TTTCGCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATTTTCAT
*
576616 TTCTCTCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATTTTCAT
576657 TT
1 TT
576659 TCATGTTGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 18 0.46
41 21 0.54
ACGTcount: A:0.11, C:0.20, G:0.18, T:0.51
Consensus pattern (41 bp):
TTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATTTTCAT
Found at i:576648 original size:20 final size:20
Alignment explanation
Indices: 576583--576673 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
576573 CGATTCTCTC
*
576583 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
576602 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCGT
**
576622 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCGT
*
576643 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCGT
*
576663 GTTGTGATTTT
1 GTTGCGATTTT
576674 AAGTTTAGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
19 13 0.21
20 31 0.51
21 17 0.28
ACGTcount: A:0.12, C:0.16, G:0.20, T:0.52
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:577255 original size:20 final size:20
Alignment explanation
Indices: 577230--577423 Score: 239
Period size: 20 Copynumber: 9.6 Consensus size: 20
577220 CTTTAAAAAT
577230 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
577250 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
577270 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
577291 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
577311 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
577331 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
577351 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
577371 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
577392 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
577413 CTCGTTGCGAT
1 CGCGTTGCGAT
577424 AGTCAGAATC
Statistics
Matches: 148, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
20 95 0.64
21 53 0.36
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:577289 original size:41 final size:40
Alignment explanation
Indices: 577230--577423 Score: 239
Period size: 41 Copynumber: 4.8 Consensus size: 40
577220 CTTTAAAAAT
*
577230 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTACGGATA
* * * *
577270 TGTCGTTGCGATTTACGGATACGCATTGCGATTTACGTATT
1 CG-CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATA
* *
577311 CTCGTTGCGATTTACAGATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATA
* *
577351 CGCGTTGCGATTTTACGTAT-TGTCGTTGCGATTTACGGATA
1 CGCGTTGCGA-TTTACGGATACG-CGTTGCGATTTACGGATA
*
577392 CGCGTTGCGATTTTACGGATACTCGTTGCGAT
1 CGCGTTGCGA-TTTACGGATACGCGTTGCGAT
577424 AGTCAGAATC
Statistics
Matches: 134, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
40 54 0.40
41 80 0.60
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (40 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATA
Found at i:577437 original size:41 final size:39
Alignment explanation
Indices: 577227--577446 Score: 228
Period size: 41 Copynumber: 5.4 Consensus size: 39
577217 GTGCTTTAAA
577227 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACG
1 AATCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTACG
* * *
577267 TATTGTCGTTGCGATTTACGGATACGCATTGCGATTTACG
1 AATCG-CGTTGCGATTTACGGATACGCGTTGCGATTTACG
* * *
577307 TATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACG
1 -AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTACG
* * *
577347 GATACGCGTTGCGATTTTACGTAT-TGTCGTTGCGATTTACG
1 AAT-CGCGTTGCGA-TTTACGGATACG-CGTTGCGATTTACG
* * *
577388 GATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAG
1 AAT-CGCGTTGCGA-TTTACGGATACGCGTTGCGAT-TTAC-G
577430 AATCGCGTTGCGATTTA
1 AATCGCGTTGCGATTTA
577447 TATGTTCGCG
Statistics
Matches: 152, Mismatches: 20, Indels: 16
0.81 0.11 0.09
Matches are distributed among these distances:
39 1 0.01
40 55 0.36
41 92 0.61
42 4 0.03
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (39 bp):
AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTACG
Found at i:577439 original size:61 final size:61
Alignment explanation
Indices: 577273--577483 Score: 216
Period size: 61 Copynumber: 3.5 Consensus size: 61
577263 TACGTATTGT
* * *
577273 CGTTGCGATTTACGGATACGCATTGCGAT-TTACGTATTC-TCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATGTCACG-AATCGTCGTTGCGATTTACAGATACG
* * * * *
577333 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATGTCACGAATCGTCGTTGCGATTTACAGATACG
* * *
577394 CGTTGCGATTTTACGGATACTCGTTGCGATAGTCA-GAATCG-CGTTGCGATTTATATG-TTCG
1 CGTTGCGA-TTTACGGATACGCGTTGCGAT-GTCACGAATCGTCGTTGCGATTTACA-GATACG
* ** *
577455 CGTTGCGATTTTCATATTCGCGTTGCGAT
1 CGTTGCGATTTACGGATACGCGTTGCGAT
577484 TCTGGAAAAT
Statistics
Matches: 128, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
60 45 0.35
61 56 0.44
62 25 0.20
63 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (61 bp):
CGTTGCGATTTACGGATACGCGTTGCGATGTCACGAATCGTCGTTGCGATTTACAGATACG
Found at i:577455 original size:20 final size:20
Alignment explanation
Indices: 577432--577484 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
577422 ATAGTCAGAA
*
577432 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
577452 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
577472 TCGCGTTGCGATT
1 TCGCGTTGCGATT
577485 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:577476 original size:40 final size:41
Alignment explanation
Indices: 577229--577484 Score: 215
Period size: 41 Copynumber: 6.3 Consensus size: 41
577219 GCTTTAAAAA
* *
577229 TCGCGTTGCGATTTA-CGGATACGCGTTGCGATTTTACGTAT
1 TCGCGTTGCGATTTATAGGATACGCGTTGCGA-TTTACGGAT
* * *
577270 T-GTCGTTGCGATTTA-CGGATACGCATTGCGATTTACGTAT
1 TCG-CGTTGCGATTTATAGGATACGCGTTGCGATTTACGGAT
* *
577310 TCTCGTTGCGATTTACA-GATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATAGGATACGCGTTGCGATTTACGGAT
* * *
577350 ACGCGTTGCGATTT-TACG-TATTGTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATAGGATA-CG-CGTTGCGATTTACGGAT
* * * * *
577391 ACGCGTTGCGATTT-TACGGATACTCGTTGCGATAGT-CAGAA
1 TCGCGTTGCGATTTATA-GGATACGCGTTGCGAT-TTACGGAT
* * * **
577432 TCGCGTTGCGATTTATATG-TTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTATAGGATACGCGTTGCGATTTACGGAT
577472 TCGCGTTGCGATT
1 TCGCGTTGCGATT
577485 CTGGAAAATC
Statistics
Matches: 182, Mismatches: 22, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
39 4 0.02
40 85 0.47
41 87 0.48
42 4 0.02
43 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (41 bp):
TCGCGTTGCGATTTATAGGATACGCGTTGCGATTTACGGAT
Found at i:577479 original size:101 final size:101
Alignment explanation
Indices: 577227--577484 Score: 364
Period size: 101 Copynumber: 2.6 Consensus size: 101
577217 GTGCTTTAAA
577227 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
1 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
* * *
577292 GCATTGCGATTTACGTATTCTCGTTGCGATTTACAG
66 GCATTGCGATTTACGGATACTCGTTGCGATGTACAG
577328 -ATACGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 AAT-CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
*
577392 CGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAG
65 CGCATTGCGA-TTTACGGATACTCGTTGCGAT-GTACAG
** * *
577430 AATCGCGTTGCGATTTATATG-TTCGCGTTGCGATTTT-CATATTCG-CGTTGCGATT
1 AATCGCGTTGCGATTTA-CGGATACGCGTTGCGATTTTACGTATT-GTCGTTGCGATT
577485 CTGGAAAATC
Statistics
Matches: 143, Mismatches: 8, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
100 2 0.01
101 85 0.59
102 52 0.36
103 4 0.03
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (101 bp):
AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
GCATTGCGATTTACGGATACTCGTTGCGATGTACAG
Found at i:577545 original size:42 final size:42
Alignment explanation
Indices: 577452--577545 Score: 95
Period size: 42 Copynumber: 2.3 Consensus size: 42
577442 ATTTATATGT
* *
577452 TCGCGTTGCG-ATTTTCATATTCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
** * *
577493 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTCTTCATAA
1 TCGCGTTGCGAATTT-TCA-TATTCGCATTGCGATTCTGCAAAA
577535 TCGCGTTGCGA
1 TCGCGTTGCGA
577546 TTCTGGGAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
41 8 0.19
42 31 0.74
43 3 0.07
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
Found at i:577583 original size:20 final size:19
Alignment explanation
Indices: 577534--577587 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
577524 ATTCTTCATA
577534 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
577553 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
577574 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
577588 TTTATTTTGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:579169 original size:3 final size:3
Alignment explanation
Indices: 579161--579194 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
579151 ACGAGTACAA
579161 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
579195 TGAAATGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:588350 original size:26 final size:26
Alignment explanation
Indices: 588270--588350 Score: 65
Period size: 26 Copynumber: 3.0 Consensus size: 26
588260 ACCGACCCGG
* *
588270 TGACATTTTGAGAATTATTGTGAAAAA
1 TGACATTTCGAGAATTTTTGT-AAAAA
** * *
588297 TGTGATATTCTGGGAATTATTT-TGAAAA
1 TGACAT-TTC-GAGAATT-TTTGTAAAAA
588325 TGACATTTCGAGAATTTTTGTAAAAA
1 TGACATTTCGAGAATTTTTGTAAAAA
588351 ATGATGGAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
25 3 0.08
26 11 0.28
27 7 0.17
28 10 0.25
29 7 0.17
30 2 0.05
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.40
Consensus pattern (26 bp):
TGACATTTCGAGAATTTTTGTAAAAA
Found at i:588401 original size:29 final size:28
Alignment explanation
Indices: 588362--588451 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 28
588352 TGATGGAATT
* *
588362 TTTTTTAAAAAAGATGACATTTCGGGAA
1 TTTTTTGAAAAAGATGACATTTCGGAAA
588390 TTTTTGTGAAAAATG-TGACA-TTCTGGAAA
1 TTTTT-TGAAAAA-GATGACATTTC-GGAAA
* * * *
588419 TTATTTTGAAAAATATGATATTTTGGTAA
1 TT-TTTTGAAAAAGATGACATTTCGGAAA
588448 TTTT
1 TTTT
588452 CGAATGTGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
28 10 0.20
29 34 0.68
30 6 0.12
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.43
Consensus pattern (28 bp):
TTTTTTGAAAAAGATGACATTTCGGAAA
Found at i:592034 original size:23 final size:23
Alignment explanation
Indices: 592007--592076 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
591997 GTCACCACAG
* * *
592007 CTCATATAAATGCACCGAAGTGC
1 CTCATAGAATTGCACCGTAGTGC
592030 CTCATAGAATTGCACCGTAGTGC
1 CTCATAGAATTGCACCGTAGTGC
* *
592053 CGCGTAGAATTGCACCGTAGTGC
1 CTCATAGAATTGCACCGTAGTGC
592076 C
1 C
592077 ATATAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (23 bp):
CTCATAGAATTGCACCGTAGTGC
Found at i:592264 original size:103 final size:103
Alignment explanation
Indices: 592096--592413 Score: 582
Period size: 103 Copynumber: 3.1 Consensus size: 103
592086 TGTCCATAAA
592096 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
592161 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
*
592199 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCATCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
*
592264 TTCACACATGTTCCAAAGAATGCATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
* * * *
592302 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCATAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
592367 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
592405 GACCACATA
1 GACCACATA
592414 GACCCTCGAC
Statistics
Matches: 207, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 207 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
Found at i:593615 original size:21 final size:21
Alignment explanation
Indices: 593591--593636 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
593581 TTTTTGTTCG
* *
593591 CTTGAA-GAGGTATCGGTTCCT
1 CTTGAATG-GGTATCGATTCCC
593612 CTTGAATGGGTATCGATTCCC
1 CTTGAATGGGTATCGATTCCC
593633 CTTG
1 CTTG
593637 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (21 bp):
CTTGAATGGGTATCGATTCCC
Found at i:597601 original size:23 final size:23
Alignment explanation
Indices: 597574--597641 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
597564 GTCACCACAG
*
597574 CTCATATAAATGCACCGAAGTGC
1 CTCATAGAAATGCACCGAAGTGC
* *
597597 CTCATAGAATTGCACCGTAGTGC
1 CTCATAGAAATGCACCGAAGTGC
* * * *
597620 CGCGTAGAATTGCACCGTAGTG
1 CTCATAGAAATGCACCGAAGTG
597642 ACATATAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (23 bp):
CTCATAGAAATGCACCGAAGTGC
Found at i:597831 original size:103 final size:103
Alignment explanation
Indices: 597660--597980 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
597650 TAATGTCCAT
*
597660 AAGGACCATATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
597725 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
597763 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
597828 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
597866 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
597931 GACTTCACACATGTTCCAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
597969 AAGGACCACATA
1 AAGGACCACATA
597981 GACCCTCGAC
Statistics
Matches: 213, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 213 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:604319 original size:29 final size:30
Alignment explanation
Indices: 604133--604319 Score: 153
Period size: 29 Copynumber: 6.6 Consensus size: 30
604123 ACCCGACCCA
*
604133 GTGACATTTTGGGAATTA-TTGTGAAAAAG
1 GTGACATTTTGGGAATTATTTTTGAAAAAG
*
604162 GTGACATTCTGGGAATTA-TTTTGAAAAA-
1 GTGACATTTTGGGAATTATTTTTGAAAAAG
* * * *
604190 ATGACATTTCGGGAATT-TTTGTGAAAAAAT
1 GTGACATTTTGGGAATTATTTTTG-AAAAAG
*
604220 GTGACA-TTT-GG-ATTTTTTTTGAAAAA-
1 GTGACATTTTGGGAATTATTTTTGAAAAAG
* ** * *
604246 -TGATATTTCAGGAATT-TTTATGAAAAAT
1 GTGACATTTTGGGAATTATTTTTGAAAAAG
* *
604274 GTGACATTCTGTGAATTATTTTTG-AAAAG
1 GTGACATTTTGGGAATTATTTTTGAAAAAG
*
604303 GTGACATTTTGGTAATT
1 GTGACATTTTGGGAATT
604320 TTCGAATTTA
Statistics
Matches: 126, Mismatches: 22, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
25 4 0.03
26 2 0.02
27 20 0.16
28 28 0.22
29 62 0.49
30 10 0.08
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (30 bp):
GTGACATTTTGGGAATTATTTTTGAAAAAG
Found at i:607259 original size:7 final size:7
Alignment explanation
Indices: 607247--607293 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
607237 TATGTGATAA
607247 GGTTTAG
1 GGTTTAG
*
607254 GGTTTAT
1 GGTTTAG
607261 GGTTTAG
1 GGTTTAG
*
607268 AGTTTAG
1 GGTTTAG
*
607275 GGTTTAT
1 GGTTTAG
607282 GGTTTAG
1 GGTTTAG
*
607289 AGTTT
1 GGTTT
607294 TATGTGATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (7 bp):
GGTTTAG
Found at i:607272 original size:21 final size:21
Alignment explanation
Indices: 607248--607293 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
607238 ATGTGATAAG
607248 GTTTAGGGTTTATGGTTTAGA
1 GTTTAGGGTTTATGGTTTAGA
607269 GTTTAGGGTTTATGGTTTAGA
1 GTTTAGGGTTTATGGTTTAGA
607290 GTTT
1 GTTT
607294 TATGTGATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (21 bp):
GTTTAGGGTTTATGGTTTAGA
Found at i:607332 original size:28 final size:28
Alignment explanation
Indices: 607277--607351 Score: 123
Period size: 28 Copynumber: 2.6 Consensus size: 28
607267 GAGTTTAGGG
*
607277 TTTATGGTTTAGAGTTTTATGTGATATGA
1 TTTAAGGTTTAGAG-TTTATGTGATATGA
607306 TTTAAGGTTTAGAGTTTATGTGATATGA
1 TTTAAGGTTTAGAGTTTATGTGATATGA
*
607334 TTTAAGGTTTAGGGTTTA
1 TTTAAGGTTTAGAGTTTA
607352 GATTTATATG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 31 0.70
29 13 0.30
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (28 bp):
TTTAAGGTTTAGAGTTTATGTGATATGA
Found at i:610507 original size:11 final size:11
Alignment explanation
Indices: 610491--610551 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
610481 AAATTCGAGT
*
610491 TCGAGCTTGAA
1 TCGAGCTTAAA
*
610502 TCGAGCTCAAAA
1 TCGAGCT-TAAA
*
610514 TCGAGCTTGAA
1 TCGAGCTTAAA
*
610525 TCGAGCTCAAAA
1 TCGAGCT-TAAA
*
610537 TCGAGCTTCAA
1 TCGAGCTTAAA
610548 TCGA
1 TCGA
610552 ACTCTTGAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 22 0.55
12 18 0.45
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (11 bp):
TCGAGCTTAAA
Found at i:610517 original size:12 final size:12
Alignment explanation
Indices: 610500--610543 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
610490 TTCGAGCTTG
610500 AATCGAGCTCAA
1 AATCGAGCTCAA
**
610512 AATCGAGCT-TG
1 AATCGAGCTCAA
610523 AATCGAGCTCAA
1 AATCGAGCTCAA
610535 AATCGAGCT
1 AATCGAGCT
610544 TCAATCGAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (12 bp):
AATCGAGCTCAA
Found at i:610521 original size:23 final size:23
Alignment explanation
Indices: 610491--610551 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
610481 AAATTCGAGT
610491 TCGAGCTTGAATCGAGCTCAAAA
1 TCGAGCTTGAATCGAGCTCAAAA
610514 TCGAGCTTGAATCGAGCTCAAAA
1 TCGAGCTTGAATCGAGCTCAAAA
*
610537 TCGAGCTTCAATCGA
1 TCGAGCTTGAATCGA
610552 ACTCTTGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (23 bp):
TCGAGCTTGAATCGAGCTCAAAA
Found at i:610588 original size:16 final size:16
Alignment explanation
Indices: 610564--610595 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
610554 TCTTGAATTT
*
610564 TTTTTGAGTTCGAGTC
1 TTTTCGAGTTCGAGTC
610580 TTTTCGAGTTCGAGTC
1 TTTTCGAGTTCGAGTC
610596 GAGCTTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.16, G:0.25, T:0.47
Consensus pattern (16 bp):
TTTTCGAGTTCGAGTC
Found at i:610842 original size:8 final size:8
Alignment explanation
Indices: 610829--610858 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
610819 TCTATTGGAG
610829 TTTAAAAA
1 TTTAAAAA
610837 TTTAAAAA
1 TTTAAAAA
610845 TTT-AAAA
1 TTTAAAAA
610852 TTTAAAA
1 TTTAAAA
610859 CTAGGTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TTTAAAAA
Found at i:613646 original size:20 final size:20
Alignment explanation
Indices: 613623--613674 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
613613 AACGCGATCC
613623 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
613643 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
613663 CCAAAATCGCAA
1 CCAGAATCGCAA
613675 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:613755 original size:20 final size:20
Alignment explanation
Indices: 613730--613923 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
613720 GATTTTCCAT
* *
613730 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
613750 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
613770 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
613790 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
613810 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
613830 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
613850 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
613870 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
613891 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
613911 AATCGCAACGCGA
1 AATCGCAACGCGA
613924 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:613775 original size:40 final size:39
Alignment explanation
Indices: 613726--613923 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
613716 TTGCGATTTT
* ** *
613726 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
613764 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
613805 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
613845 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
613884 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
613924 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:613813 original size:60 final size:60
Alignment explanation
Indices: 613730--613922 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
613720 GATTTTCCAT
* ** * *
613730 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
613790 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
613850 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
613911 AATCGCAACGCG
1 AATCGCAACGCG
613923 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:614343 original size:33 final size:33
Alignment explanation
Indices: 614304--614374 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
614294 TTCACTTAGA
*
614304 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
614337 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
614370 TTTCA
1 TTTCA
614375 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:614532 original size:33 final size:33
Alignment explanation
Indices: 614495--614565 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
614485 AGAATGACTG
**
614495 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
*
614528 TCGCAATGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
614561 TCGCA
1 TCGCA
614566 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.44, C:0.24, G:0.23, T:0.10
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:614583 original size:19 final size:19
Alignment explanation
Indices: 614561--614658 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
614551 GAAACCAAAA
*
614561 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
614580 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
614594 TCTCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
614613 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
614627 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
614646 TCGCGTTGCGATT
1 TCGCGTTGCGATT
614659 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 19 0.31
16 5 0.08
17 6 0.10
19 31 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:614612 original size:33 final size:33
Alignment explanation
Indices: 614566--614680 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
614556 CAAAATCGCA
614566 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
614599 TTGTGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
614632 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
614665 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
614681 AACCAAAAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:614635 original size:14 final size:14
Alignment explanation
Indices: 614583--614672 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
614573 TTTCATTTCG
614583 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
614597 CGTTGTGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
614616 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
614630 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
614647 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
614663 CGTTGCGATT
1 CGTTGCGATT
614673 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 27 0.44
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 17 0.27
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:616796 original size:93 final size:93
Alignment explanation
Indices: 616378--616941 Score: 1098
Period size: 93 Copynumber: 6.1 Consensus size: 93
616368 TAGATTGCTT
*
616378 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
616443 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
616471 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
616535 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
616563 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
616627 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
616654 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
616719 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
616747 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
616812 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
616840 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
616905 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
616933 AGTAAATTT
1 AGTAAATTT
616942 ATCCATTCAA
Statistics
Matches: 468, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
91 79 0.17
92 116 0.25
93 273 0.58
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:617025 original size:19 final size:19
Alignment explanation
Indices: 616985--617113 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
616975 TAGTTTACTT
* *
616985 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
617005 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
617024 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
617043 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
617057 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
617076 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
617090 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
617109 TCGCA
1 TCGCA
617114 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:617064 original size:33 final size:32
Alignment explanation
Indices: 617021--617113 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
617011 CGCGAAACCA
**
617021 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
617053 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
617086 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
617114 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:617111 original size:52 final size:52
Alignment explanation
Indices: 616985--617113 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
616975 TAGTTTACTT
**
616985 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
617037 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
617090 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
617114 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:617131 original size:19 final size:19
Alignment explanation
Indices: 617109--617243 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
617099 GAAACCAAAA
*
617109 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
617128 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
617144 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
617161 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
617177 T--CGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
**
617194 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
617213 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
617233 TCGTGTTGCGA
1 TCGCGTTGCGA
617244 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 11, Indels: 21
0.75 0.09 0.17
Matches are distributed among these distances:
14 15 0.16
16 10 0.11
17 11 0.12
19 46 0.49
20 12 0.13
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:617150 original size:14 final size:14
Alignment explanation
Indices: 617131--617187 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
617121 TTTCATTTCG
617131 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
617145 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
617162 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
617178 CGTTGCGATT
1 CGTTGCGATT
617188 TTAATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:617156 original size:33 final size:33
Alignment explanation
Indices: 617114--617206 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
617104 CAAAATCGCA
*
617114 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
617147 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
617180 TTGCGATTTTAATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
617207 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:619186 original size:14 final size:14
Alignment explanation
Indices: 619167--619202 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
619157 ATTGTTTAAT
619167 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
619181 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
619195 TGATTTGT
1 TGATTTGT
619203 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:619325 original size:19 final size:19
Alignment explanation
Indices: 619309--619410 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
619299 AAAAATGACT
619309 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
619328 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
619347 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
619361 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
619380 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
619400 ATCGCAATGCG
1 ATCGCAATGCG
619411 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:619463 original size:19 final size:19
Alignment explanation
Indices: 619439--619745 Score: 376
Period size: 19 Copynumber: 17.4 Consensus size: 19
619429 GATTATCTCG
619439 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
619458 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
619477 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
619491 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
619510 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
619529 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
619548 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
619567 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
619581 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
619600 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
619619 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
619633 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
619652 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
619671 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
619685 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
619705 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
619719 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
619738 TTGCGATT
1 TTGCGATT
619746 GTATTTTCCG
Statistics
Matches: 252, Mismatches: 10, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
14 35 0.14
16 31 0.12
17 27 0.11
18 3 0.01
19 144 0.57
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:619514 original size:71 final size:71
Alignment explanation
Indices: 619439--619678 Score: 373
Period size: 71 Copynumber: 3.4 Consensus size: 71
619429 GATTATCTCG
619439 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
619504 TTCGCA
66 TTCGCA
*
619510 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
*
619573 TTC-TGTCG--
61 TTCATTTCGCA
*
619581 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
619646 TTCGCA
66 TTCGCA
619652 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
619679 CTCTCGTTGC
Statistics
Matches: 154, Mismatches: 5, Indels: 20
0.86 0.03 0.11
Matches are distributed among these distances:
66 6 0.04
68 7 0.05
69 6 0.04
71 115 0.75
73 6 0.04
74 8 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:619589 original size:142 final size:137
Alignment explanation
Indices: 619401--619745 Score: 516
Period size: 142 Copynumber: 2.5 Consensus size: 137
619391 GAAATGAAAA
*
619401 TCGCAATGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTT-TAATTTCGCATTGCGATT-T-TCGTTGCGATTTTCATTTCGCATTGCGAT
*
619465 TTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
63 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
*
619530 TGCGATTTTCATT
128 TGCGA--TTC-TC
619543 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATT-T-TCGTTGCGATTTTCATTTCGCATTGCGATT
619608 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
64 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
619673 GCGATTCTC
129 GCGATTCTC
* * *
619682 TCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCGTTGCGAT
1 TCGCATTGCGATTTTAATTT-CGCATTGCGATTTTC--GTTGCGATTTTCATTTCGCATTGCGAT
619745 T
63 T
619746 GTATTTTCCG
Statistics
Matches: 191, Mismatches: 8, Indels: 12
0.91 0.04 0.06
Matches are distributed among these distances:
136 2 0.01
137 15 0.08
138 38 0.20
139 4 0.02
140 3 0.02
142 126 0.66
143 3 0.02
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (137 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTTTCGTTGCGATTTTCATTTCGCATTGCGATTTT
CATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
GATTCTC
Found at i:619684 original size:52 final size:52
Alignment explanation
Indices: 619439--619717 Score: 388
Period size: 52 Copynumber: 5.2 Consensus size: 52
619429 GATTATCTCG
*
619439 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
*
619491 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
619548 TTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
619600 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
619652 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
619705 TTGCGATTTTCAT
1 TTGCGATTTTCAT
619718 GTTGGGATTT
Statistics
Matches: 217, Mismatches: 4, Indels: 11
0.94 0.02 0.05
Matches are distributed among these distances:
52 161 0.74
53 17 0.08
54 7 0.03
55 8 0.04
57 24 0.11
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:622042 original size:12 final size:12
Alignment explanation
Indices: 622025--622049 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
622015 TCTTCGGGGA
622025 CTTTTTCTTCTT
1 CTTTTTCTTCTT
622037 CTTTTTCTTCTT
1 CTTTTTCTTCTT
622049 C
1 C
622050 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:622257 original size:24 final size:24
Alignment explanation
Indices: 622223--622269 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
622213 CTGAAACATC
622223 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
622247 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
622270 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:622978 original size:20 final size:20
Alignment explanation
Indices: 622950--623318 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
622940 AAATTTCAGT
* * * *
622950 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
622970 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
622990 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
623010 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
623030 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
623050 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
623070 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
623090 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
623110 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
623130 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
623150 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
623170 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
623190 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
623210 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
623230 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
623250 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
623270 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
623290 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
623310 GTTGCGATT
1 GTTGCGATT
623319 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:623841 original size:84 final size:83
Alignment explanation
Indices: 623742--623905 Score: 265
Period size: 84 Copynumber: 2.0 Consensus size: 83
623732 TATATTTTTA
*
623742 TTTATATCACATGTTTCATGTATCGGACAAAAATTGATTGTCTTTTTCGTCTTTTTCCTATCCTT
1 TTTATATCACATGTTTCATGTATCGGACAAAAATTGATTGTC-TTTTCGTCTTTTTCCTATCATT
623807 GTTAACACAAAAATATTTG
65 GTTAACACAAAAATATTTG
* * *
623826 TTTATGTCACATGTTTCATTTATCGGATAAAAATTGATTGTCTTTTCGTCTTTTTCCTATCATTG
1 TTTATATCACATGTTTCATGTATCGGACAAAAATTGATTGTCTTTTCGTCTTTTTCCTATCATTG
* *
623891 TTAACATAAGAATAT
66 TTAACACAAAAATAT
623906 GCAAAGAGGT
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
83 35 0.47
84 39 0.53
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.46
Consensus pattern (83 bp):
TTTATATCACATGTTTCATGTATCGGACAAAAATTGATTGTCTTTTCGTCTTTTTCCTATCATTG
TTAACACAAAAATATTTG
Done.