Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009078.1 Hibiscus syriacus cultivar Beakdansim tig00112517_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: 829977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:719403 original size:124 final size:123
Alignment explanation
Indices: 719183--719473 Score: 378
Period size: 124 Copynumber: 2.4 Consensus size: 123
719173 TGGATCAGCT
*
719183 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT---GAAGAATAAGAAGTTCACAATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCACAATGAGAA
* * * * * * *
719245 GATCTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAACC
66 GAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
*
719303 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG-AAGAAGAAGTTCACAATGAGA
* * * *
719368 AGAGCTTATTCAACCTTTTGAATGACTCTATCACAGAATGAAATAGGTCAACATCATCC
65 AGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
* *
719427 ---CCAGCGGAAAGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAA
1 TTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AAGAAGAA
719474 TTTATTCAAC
Statistics
Matches: 150, Mismatches: 15, Indels: 10
0.86 0.09 0.06
Matches are distributed among these distances:
120 36 0.24
121 4 0.03
122 36 0.24
123 7 0.05
124 67 0.45
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (123 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCACAATGAGAA
GAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
Found at i:719618 original size:3 final size:3
Alignment explanation
Indices: 719612--719663 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
719602 TTCATTTAAA
* *
719612 TAT TAT T-T ATAT TAT CAT TAT TAT TAT AAT TAT TAT TAT TAT T-T
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
719656 TAT TAT TA
1 TAT TAT TA
719664 ATAAATCATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 3 0.07
3 38 0.90
4 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:721021 original size:3 final size:3
Alignment explanation
Indices: 721013--721047 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
721003 TTATTTACAA
*
721013 TAT TAT TAT TAT TAT TATT TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT T
721048 TATATAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:721036 original size:16 final size:16
Alignment explanation
Indices: 721015--721050 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
721005 ATTTACAATA
721015 TTATTATTATTATTAT
1 TTATTATTATTATTAT
*
721031 TTATTATTTTTATTAT
1 TTATTATTATTATTAT
721047 TTAT
1 TTAT
721051 ATAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:721082 original size:16 final size:16
Alignment explanation
Indices: 721048--721079 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
721038 TTTTATTATT
721048 TATATAAATAAATAAA
1 TATATAAATAAATAAA
721064 TATATATAATAAATAA
1 TATATA-AATAAATAA
721080 TATTTGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TATATAAATAAATAAA
Found at i:721358 original size:27 final size:27
Alignment explanation
Indices: 721320--721374 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
721310 ATATTTCTAA
721320 ATAAATAAATATTGTATTT-ATAAATAT
1 ATAAATAAATATT-TATTTCATAAATAT
* *
721347 ATAAATTAATATTTATTTCATAATTAT
1 ATAAATAAATATTTATTTCATAAATAT
721374 A
1 A
721375 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
ATAAATAAATATTTATTTCATAAATAT
Found at i:723760 original size:43 final size:43
Alignment explanation
Indices: 723690--723939 Score: 227
Period size: 43 Copynumber: 5.7 Consensus size: 43
723680 ACTAAAGTTC
* * *** *
723690 GCGGCGTTTGGTAACAAAAAACGCCGCAATAGGTAACGATATATA
1 GCGGCGTTT-GT-TCAACAAACGCCGCAATAGGTGTTGATATTTA
**
723735 GCGGCGTTTGTTGGACAAACGCCGCAATAGGTGTTGATATTTA
1 GCGGCGTTTGTTCAACAAACGCCGCAATAGGTGTTGATATTTA
* *
723778 GCGGCGTTTGTCCAACAAACACCGCAATAGGTGTTGATATTTA
1 GCGGCGTTTGTTCAACAAACGCCGCAATAGGTGTTGATATTTA
* *
723821 GCTGCGTTT-TTCCAACAAACGCCGCAATAGGTGTTGAGATTTA
1 GCGGCGTTTGTT-CAACAAACGCCGCAATAGGTGTTGATATTTA
* * * * * * *
723864 GCGGCGTTT-TTCCCACAAACACCGCAAAAGAT-CTGGTATATA
1 GCGGCGTTTGTT-CAACAAACGCCGCAATAGGTGTTGATATTTA
* * *
723906 GCGGCGTTTTTTTAGAACAAACGCCGCAAAAGGT
1 GCGGCG-TTTGTT-CAACAAACGCCGCAATAGGT
723940 CATATCTATA
Statistics
Matches: 172, Mismatches: 30, Indels: 7
0.82 0.14 0.03
Matches are distributed among these distances:
42 13 0.08
43 130 0.76
44 20 0.12
45 9 0.05
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Consensus pattern (43 bp):
GCGGCGTTTGTTCAACAAACGCCGCAATAGGTGTTGATATTTA
Found at i:723959 original size:86 final size:86
Alignment explanation
Indices: 723727--723939 Score: 275
Period size: 86 Copynumber: 2.5 Consensus size: 86
723717 AATAGGTAAC
* * *
723727 GATATATAGCGGCGTTTGTTGGACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCCA
1 GATATATAGCGGCGTTTTTTGAACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCA
* * *
723792 ACAAACACCGCAATAGGTGTT
66 ACAAACACCGCAAAAGATGCT
* * ** * *
723813 GATATTTAGCTGCGTTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
1 GATATATAGCGGCGTTTTTTGAACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCA
723878 ACAAACACCGCAAAAGAT-CT
66 ACAAACACCGCAAAAGATGCT
* *
723898 GGTATATAGCGGCGTTTTTTTAGAACAAACGCCGCAAAAGGT
1 GATATATAGCGGCG-TTTTTT-GAACAAACGCCGCAATAGGT
723940 CATATCTATA
Statistics
Matches: 107, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
85 12 0.11
86 77 0.72
87 18 0.17
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (86 bp):
GATATATAGCGGCGTTTTTTGAACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCA
ACAAACACCGCAAAAGATGCT
Found at i:727606 original size:52 final size:52
Alignment explanation
Indices: 727519--727730 Score: 388
Period size: 52 Copynumber: 4.1 Consensus size: 52
727509 TAACAACAAA
*
727519 ATACATTATAATTTAGAAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAG-AAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
727572 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
*
727624 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAGCAGTCTTCAAC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
*
727676 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
727728 ATA
1 ATA
727731 TTGTTCAGTA
Statistics
Matches: 155, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
52 139 0.90
53 16 0.10
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (52 bp):
ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
Found at i:728922 original size:80 final size:81
Alignment explanation
Indices: 728821--728973 Score: 204
Period size: 80 Copynumber: 1.9 Consensus size: 81
728811 ATTTACCACT
* ** * *
728821 CTATTGCGGCATTTTGGTATAAACGCCGCTAAATGT-TAAATATATTGCGGCG-TTTTAGCTA-A
1 CTATTACGGCATTTTACTATAAACACAGCTAAATGTCT-AATATATTGCGGCGTTTTTA-CTATA
728883 AACGCCGCTACATGTCTA
64 AACGCCGCTACATGTCTA
* *
728901 CTATTACGGCATTTTACTATAAACACAGCTACATGTCTACTATATTGCGGCGTTTTTACTATAAA
1 CTATTACGGCATTTTACTATAAACACAGCTAAATGTCTAATATATTGCGGCGTTTTTACTATAAA
728966 CGCCGCTA
66 CGCCGCTA
728974 TTGTTTAACC
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
80 46 0.73
81 17 0.27
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (81 bp):
CTATTACGGCATTTTACTATAAACACAGCTAAATGTCTAATATATTGCGGCGTTTTTACTATAAA
CGCCGCTACATGTCTA
Found at i:728932 original size:39 final size:40
Alignment explanation
Indices: 728822--728966 Score: 125
Period size: 41 Copynumber: 3.6 Consensus size: 40
728812 TTTACCACTC
** * * * *
728822 TATTGCGGCATTTTGGTATAAACGCCGCTAAATGT-TAAATA
1 TATTGCGGCATTTTACTATAAACACAGCTACATGTCT--ACA
* * *
728863 TATTGCGGCGTTTTAGCTA-AAACGCCGCTACATGTCTAC-
1 TATTGCGGCATTTTA-CTATAAACACAGCTACATGTCTACA
*
728902 TATTACGGCATTTTACTATAAACACAGCTACATGTCTACTA
1 TATTGCGGCATTTTACTATAAACACAGCTACATGTCTAC-A
*
728943 TATTGCGGCGTTTTTACTATAAAC
1 TATTGCGGC-ATTTTACTATAAAC
728967 GCCGCTATTG
Statistics
Matches: 87, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
38 3 0.03
39 31 0.36
40 1 0.01
41 36 0.41
42 16 0.18
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (40 bp):
TATTGCGGCATTTTACTATAAACACAGCTACATGTCTACA
Found at i:732016 original size:18 final size:19
Alignment explanation
Indices: 731982--732022 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
731972 GTTTATCTCC
731982 TTAACATTTTTACCTTTTT
1 TTAACATTTTTACCTTTTT
732001 TTAACATTTTTA-CTTTTT
1 TTAACATTTTTACCTTTTT
732019 TTAA
1 TTAA
732023 TAGAATTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63
Consensus pattern (19 bp):
TTAACATTTTTACCTTTTT
Found at i:732488 original size:22 final size:22
Alignment explanation
Indices: 732463--732504 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
732453 GAAATGATAC
* *
732463 AAAAACGTGTCACAAAGACAAA
1 AAAAACATGCCACAAAGACAAA
*
732485 AAAAATATGCCACAAAGACA
1 AAAAACATGCCACAAAGACA
732505 GAATTATTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.19, G:0.12, T:0.10
Consensus pattern (22 bp):
AAAAACATGCCACAAAGACAAA
Found at i:736200 original size:23 final size:24
Alignment explanation
Indices: 736159--736211 Score: 99
Period size: 23 Copynumber: 2.2 Consensus size: 24
736149 TATTCTTTAA
736159 AAATTTCAAATTTTCATATAATTT
1 AAATTTCAAATTTTCATATAATTT
736183 AAATTTCAAA-TTTCATATAATTT
1 AAATTTCAAATTTTCATATAATTT
736206 AAATTT
1 AAATTT
736212 ATAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 19 0.66
24 10 0.34
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (24 bp):
AAATTTCAAATTTTCATATAATTT
Found at i:736409 original size:59 final size:58
Alignment explanation
Indices: 736324--736501 Score: 175
Period size: 58 Copynumber: 3.1 Consensus size: 58
736314 ATCATATATC
736324 CCCAAACTATGACTCTCATTTC-AAATTAGTCCCTAAATTTTTAAACATTTCACTTTCAT
1 CCCAAACTATGACTCTC-TTTCTAAATTAGTCCCTAAA-TTTTAAACATTTCACTTTCAT
** * * * * *
736383 CTTAAACTATGACTATCTTTCTAAATTAGT-CCTCAAACTTTGAATATTTCATTTTCAT
1 CCCAAACTATGACTCTCTTTCTAAATTAGTCCCT-AAATTTTAAACATTTCACTTTCAT
* * * * *
736441 CCCAAACTATGAATCTCATTCTAAATT-GGCCCTAAACTTTTAAATC-TTCCAATTTCAT
1 CCCAAACTATGACTCTCTTTCTAAATTAGTCCCTAAA-TTTTAAA-CATTTCACTTTCAT
736499 CCC
1 CCC
736502 CAAATTCATT
Statistics
Matches: 96, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
57 4 0.04
58 67 0.70
59 25 0.26
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.39
Consensus pattern (58 bp):
CCCAAACTATGACTCTCTTTCTAAATTAGTCCCTAAATTTTAAACATTTCACTTTCAT
Found at i:744227 original size:17 final size:17
Alignment explanation
Indices: 744193--744228 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
744183 TTTCTTTTTG
* *
744193 ATTTATTATTATTTAAA
1 ATTTATTATTAATAAAA
744210 ATTTATTATTAATAAAA
1 ATTTATTATTAATAAAA
744227 AT
1 AT
744229 ATAAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATTATTAATAAAA
Found at i:745089 original size:29 final size:29
Alignment explanation
Indices: 745054--745135 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
745044 AAACTAAATT
*
745054 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
745083 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
745112 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
745136 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:746442 original size:15 final size:15
Alignment explanation
Indices: 746419--746448 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
746409 ACGAGGCTGG
746419 AATTACAACAATAAC
1 AATTACAACAATAAC
*
746434 AATTCCAACAATAAC
1 AATTACAACAATAAC
746449 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTACAACAATAAC
Found at i:749841 original size:29 final size:29
Alignment explanation
Indices: 749806--749887 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
749796 AAACTAAATT
*
749806 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
749835 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
*
749864 GATATCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
749888 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:757330 original size:30 final size:30
Alignment explanation
Indices: 757257--757330 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
757247 TAGGCTGCCT
* *
757257 GGAGGAGGAGGAGGTGGTGGTCGTCCACCA
1 GGAGGTGGAGGTGGTGGTGGTCGTCCACCA
* * * *
757287 GGAGGTGGCGGTGGTGGTGGTGGTGCACCG
1 GGAGGTGGAGGTGGTGGTGGTCGTCCACCA
757317 GGTA-GTGGAGGTGG
1 GG-AGGTGGAGGTGG
757331 AGCGGGAAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.14, C:0.12, G:0.57, T:0.18
Consensus pattern (30 bp):
GGAGGTGGAGGTGGTGGTGGTCGTCCACCA
Found at i:765997 original size:3 final size:3
Alignment explanation
Indices: 765989--766054 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
765979 TCATTTAAAT
** * *
765989 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
766035 TTA TTA -TA TT- TTA TTTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA
766055 AATATTACAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 4 0.08
3 41 0.80
4 6 0.12
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:766010 original size:18 final size:18
Alignment explanation
Indices: 765983--766018 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
765973 ATTTTTTCAT
*
765983 TTAAATTTATTATTATTA
1 TTAAAATTATTATTATTA
766001 TTAAAATTATTATTATTA
1 TTAAAATTATTATTATTA
766019 GTATTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAAAATTATTATTATTA
Found at i:775350 original size:114 final size:114
Alignment explanation
Indices: 775150--775372 Score: 356
Period size: 114 Copynumber: 2.0 Consensus size: 114
775140 TGCTATGTGA
* * *
775150 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGG
* * * *
775215 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGC
66 TTCGGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAATTTGC
*
775264 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGG
* *
775329 TTCGGTAGGAATCCCATAACCAATCATTGAAATTGAAAGATGAA
66 TTCGGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAA
775373 CTGCATGATC
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGG
TTCGGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAATTTGC
Found at i:777407 original size:54 final size:54
Alignment explanation
Indices: 777322--777476 Score: 256
Period size: 54 Copynumber: 2.9 Consensus size: 54
777312 GAAATCTTGG
*
777322 CAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAACATTTGAA
1 CAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAACATCTGAA
* * *
777376 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAG
1 CAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAACATCTGAA
* *
777430 CAGAAGCCACAGGAAAGGATGAATGCACTGTCAAATGTTTTACGAAC
1 CAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAAC
777477 CTGTTATTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (54 bp):
CAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAACATCTGAA
Found at i:777869 original size:22 final size:22
Alignment explanation
Indices: 777843--777941 Score: 171
Period size: 22 Copynumber: 4.5 Consensus size: 22
777833 ATCTACACTC
777843 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
777865 TTCAAATATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
777887 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
777909 TTTAAAGATGATATATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
777931 TTCAAAGATGA
1 TTCAAAGATGA
777942 AAGCTTTATG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 72 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:778773 original size:76 final size:76
Alignment explanation
Indices: 778615--779328 Score: 1297
Period size: 76 Copynumber: 9.4 Consensus size: 76
778605 CTATTTCTCA
*
778615 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTT-GGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
778679 AGCCTTAGGGT
66 AGCCTTAGGGT
778690 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
778755 AGCCTTAGGGT
66 AGCCTTAGGGT
778766 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
778831 AAGCCTTAGGGT
65 AAGCCTTAGGGT
778843 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
778908 AGCCTTAGGGT
66 AGCCTTAGGGT
778919 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
778984 AGCCTTAGGGT
66 AGCCTTAGGGT
*
778995 CATCTGTAAGTCCTACAGTGCATGATGTTTCCGAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
779060 AGCCTTAGGGT
66 AGCCTTAGGGT
779071 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
779136 AGCCTTAGGGT
66 AGCCTTAGGGT
*
779147 CATCTGTAAGTCCTACAGTGCATGGTGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
779212 A-CCTTCGTGT
66 AGCCTTAGGGT
* *
779222 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTAGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* *
779287 AAACCTTCGGGT
65 AAGCCTTAGGGT
* *
779299 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
779329 TCAACATTTC
Statistics
Matches: 622, Mismatches: 13, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
75 108 0.17
76 403 0.65
77 111 0.18
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:779467 original size:3 final size:3
Alignment explanation
Indices: 779459--779526 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
779449 TCATTTAAAT
** * *
779459 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
779507 TTA TTA TATA TTA TTTA TTA
1 TTA TTA T-TA TTA -TTA TTA
779527 AATATTACAA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:780542 original size:21 final size:21
Alignment explanation
Indices: 780516--780560 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
780506 GATTTCTGGG
* *
780516 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
780537 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
780558 CAA
1 CAA
780561 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:784732 original size:21 final size:21
Alignment explanation
Indices: 784706--784750 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
784696 GATTTCTGGG
* *
784706 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
784727 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
784748 CAA
1 CAA
784751 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:788918 original size:21 final size:21
Alignment explanation
Indices: 788892--788936 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
788882 GATTTCTGGG
* *
788892 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
788913 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
788934 CAA
1 CAA
788937 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:808751 original size:60 final size:60
Alignment explanation
Indices: 808656--808773 Score: 191
Period size: 60 Copynumber: 2.0 Consensus size: 60
808646 TCTCGAAGAC
** *
808656 TAGGAAGGAGCCTGATGATGGTGGGTTGGATGGAGAAGGGGATACTGGGAACAGAAGAAA
1 TAGGAAGGAGCCTGATGATGGTGCATTGGAAGGAGAAGGGGATACTGGGAACAGAAGAAA
* *
808716 TAGGAAGGAGCCTGATGATGGTGCATTGGAAGGAGAAGTGGATACTGGGAATAGAAGA
1 TAGGAAGGAGCCTGATGATGGTGCATTGGAAGGAGAAGGGGATACTGGGAACAGAAGA
808774 TCTAATTTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.34, C:0.07, G:0.42, T:0.18
Consensus pattern (60 bp):
TAGGAAGGAGCCTGATGATGGTGCATTGGAAGGAGAAGGGGATACTGGGAACAGAAGAAA
Found at i:820837 original size:32 final size:32
Alignment explanation
Indices: 820749--820847 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 32
820739 AGTTTATGAT
* * *
820749 AATTGAAATACTTAAATACTTACAAGTTCGCTA
1 AATTCAAATACTTAAA-ACTTCCAAGTTCGATA
*
820782 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
1 AATTCAAATACTT-AAAACTTCCAAGTTCGATA
820815 AATTCAAATACTTAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAACTTCCAAGTTCGATA
820847 A
1 A
820848 TTGAAACAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
32 19 0.32
33 38 0.63
34 3 0.05
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.32
Consensus pattern (32 bp):
AATTCAAATACTTAAAACTTCCAAGTTCGATA
Found at i:829857 original size:21 final size:21
Alignment explanation
Indices: 829816--829858 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
829806 TTTGTTGGGT
*
829816 TTTGGAACTAGCGCAGTTGGA
1 TTTGGAACTAGCGCAGATGGA
**
829837 TTTGGAACTAGTTCAGATGGA
1 TTTGGAACTAGCGCAGATGGA
829858 T
1 T
829859 GTAAAATATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.33
Consensus pattern (21 bp):
TTTGGAACTAGCGCAGATGGA
Done.