Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000235.1 Hibiscus syriacus cultivar Beakdansim tig00000405_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: 589249
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:530335 original size:84 final size:84
Alignment explanation
Indices: 530189--530374 Score: 255
Period size: 84 Copynumber: 2.2 Consensus size: 84
530179 TCTTGAAACA
* * * *
530189 AAAGACCTTTGAGTTCGACTACGCTTAGCTCCAAGGCACATCAGTTGCAGCATAACTCAAGGCTA
1 AAAGACCTTAGAGTTCGACTACGCTCAGCTCAAAGGCACATCAGTTGCAGCATAACTCAAGGCGA
*
530254 GAAGGGTTATCTACCAACC
66 GAAGGGATATCTACCAACC
* ** * *
530273 AAAGACCTTAGAGTTTGACTACGCTCAGCTCAAAGGCACATCTTTTGCAGCATAGCTTAAGGCGA
1 AAAGACCTTAGAGTTCGACTACGCTCAGCTCAAAGGCACATCAGTTGCAGCATAACTCAAGGCGA
*
530338 GAAGGGATATCTGCCAACC
66 GAAGGGATATCTACCAACC
* *
530357 AAAGACCCTCGAGTTCGA
1 AAAGACCTTAGAGTTCGA
530375 TTACATTCAA
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (84 bp):
AAAGACCTTAGAGTTCGACTACGCTCAGCTCAAAGGCACATCAGTTGCAGCATAACTCAAGGCGA
GAAGGGATATCTACCAACC
Found at i:530394 original size:84 final size:84
Alignment explanation
Indices: 530189--530399 Score: 224
Period size: 84 Copynumber: 2.5 Consensus size: 84
530179 TCTTGAAACA
* * * * * * *
530189 AAAGACCTTTGAGTTCGACTACGCTTAGCTCCAAGGCACATCAGTTGCAGCATAACTCAAGGCTA
1 AAAGACCCTAGAGTTCGACTACACTCAACTCAAAGGCACATCAGTTGCAGCATAACTCAAGGCGA
*
530254 GAAGGGTTATCTACCAACC
66 GAAGGGATATCTACCAACC
* * * * ** * *
530273 AAAGACCTTAGAGTTTGACTACGCTCAGCTCAAAGGCACATCTTTTGCAGCATAGCTTAAGGCGA
1 AAAGACCCTAGAGTTCGACTACACTCAACTCAAAGGCACATCAGTTGCAGCATAACTCAAGGCGA
*
530338 GAAGGGATATCTGCCAACC
66 GAAGGGATATCTACCAACC
* * * * *
530357 AAAGACCCTCGAGTTCGATTACATTCAACTCAGAGGCAAATCA
1 AAAGACCCTAGAGTTCGACTACACTCAACTCAAAGGCACATCA
530400 AATTTACAAC
Statistics
Matches: 106, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
84 106 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (84 bp):
AAAGACCCTAGAGTTCGACTACACTCAACTCAAAGGCACATCAGTTGCAGCATAACTCAAGGCGA
GAAGGGATATCTACCAACC
Found at i:530436 original size:86 final size:85
Alignment explanation
Indices: 530189--530436 Score: 205
Period size: 84 Copynumber: 2.9 Consensus size: 85
530179 TCTTGAAACA
* * * * * * * * * * * *
530189 AAAGACCTTTGAGTTCGACTACGCTTAGCTCCAAGGCACATCAGTTGCAGCATAAC-TCAAGGCT
1 AAAGACCCTAGAGTTCGACTACACTCAACTCAAAGGCAAATCATTTACAACATAGCTTCAAGGCA
* *
530253 AGAAGGGTTATCTACCAACC
66 AGAAGGGATATCTGCCAACC
* * * * * * * * *
530273 AAAGACCTTAGAGTTTGACTACGCTCAGCTCAAAGGCACATCTTTTGCAGCATAGCTT-AAGGCG
1 AAAGACCCTAGAGTTCGACTACACTCAACTCAAAGGCAAATCATTTACAACATAGCTTCAAGGCA
530337 AGAAGGGATATCTGCCAACC
66 AGAAGGGATATCTGCCAACC
* * * *
530357 AAAGACCCTCGAGTTCGATTACATTCAACTCAGAGGCAAATCAAATTTACAACATAG-TTCAAGG
1 AAAGACCCTAGAGTTCGACTACACTCAACTCAAAGGCAAATC--ATTTACAACATAGCTTCAAGG
*
530421 CAAGAAGGGCTATCTG
64 CAAGAAGGGATATCTG
530437 TCAATAAATT
Statistics
Matches: 136, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
84 105 0.77
85 3 0.02
86 28 0.21
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (85 bp):
AAAGACCCTAGAGTTCGACTACACTCAACTCAAAGGCAAATCATTTACAACATAGCTTCAAGGCA
AGAAGGGATATCTGCCAACC
Found at i:530988 original size:3 final size:3
Alignment explanation
Indices: 530976--531037 Score: 63
Period size: 3 Copynumber: 19.3 Consensus size: 3
530966 AAAAAACATT
530976 TTA TTA -TA TTA TTA TTTA TTTA TTA TTA TTA TTA CTTA TTA TTAA TTAA
1 TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA -TTA TTA TT-A TT-A
*
531025 TTA ATA TTA TTA T
1 TTA TTA TTA TTA T
531038 ATTTGTGCAG
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 2 0.04
3 34 0.64
4 17 0.32
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:531017 original size:27 final size:26
Alignment explanation
Indices: 530976--531037 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 26
530966 AAAAAACATT
* *
530976 TTATTA-TATTATTATTTATTTATTA
1 TTATTATTATTATTATTAATTAATTA
531001 TTATTATTACTTATTATTAATTAATTA
1 TTATTATTA-TTATTATTAATTAATTA
*
531028 ATATTATTAT
1 TTATTATTAT
531038 ATTTGTGCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.19
26 3 0.09
27 23 0.72
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (26 bp):
TTATTATTATTATTATTAATTAATTA
Found at i:533846 original size:51 final size:51
Alignment explanation
Indices: 533739--533848 Score: 159
Period size: 51 Copynumber: 2.2 Consensus size: 51
533729 CCGGAAAATT
* *
533739 CGGGTACCCGATTGTCGGGACACGAACCGACAAATCAACTACCCGAATATC
1 CGGGTACCCGATTGTCGGGACACGAACCGACAAATCAACTACCCAAAGATC
* **
533790 CGGGTACCCGGTTGTCGGGACACGGGCCGACAAATCAACTACCCAAAGA-C
1 CGGGTACCCGATTGTCGGGACACGAACCGACAAATCAACTACCCAAAGATC
533840 CTGGGTACC
1 C-GGGTACC
533849 TGGATTTGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
50 2 0.04
51 51 0.96
ACGTcount: A:0.28, C:0.32, G:0.25, T:0.15
Consensus pattern (51 bp):
CGGGTACCCGATTGTCGGGACACGAACCGACAAATCAACTACCCAAAGATC
Found at i:534418 original size:98 final size:95
Alignment explanation
Indices: 534297--534471 Score: 235
Period size: 98 Copynumber: 1.8 Consensus size: 95
534287 TTAACTTATG
*
534297 AAATATATTTTATTATTATCTTAACTAAAATTATATATTTTAATCATATCTTAA-TTTCAAAAAC
1 AAATATATTTTATTATTACCTTAACTAAAA-TATATATTTTAATCATATCTTAACTTT-AAAAA-
*
534361 TTTTTTTGTTATTTTAAACTCATCTTAACTTTAA
63 TTTTATT-TTATTTTAAACTCATCTTAACTTTAA
* * * * * *
534395 AAATATTTTTTATTCTTACCTTAACTTAAATATATATTTTATTCTTATCTTAACTTTTAAAATTT
1 AAATATATTTTATTATTACCTTAACTAAAATATATATTTTAATCATATCTTAACTTTAAAAATTT
534460 TATTTTATTTTA
66 TATTTTATTTTA
534472 TTTTTATCTT
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
95 8 0.12
96 6 0.09
97 25 0.37
98 29 0.43
ACGTcount: A:0.35, C:0.10, G:0.01, T:0.54
Consensus pattern (95 bp):
AAATATATTTTATTATTACCTTAACTAAAATATATATTTTAATCATATCTTAACTTTAAAAATTT
TATTTTATTTTAAACTCATCTTAACTTTAA
Found at i:534621 original size:30 final size:30
Alignment explanation
Indices: 534382--534619 Score: 158
Period size: 30 Copynumber: 7.8 Consensus size: 30
534372 TTTTAAACTC
* *
534382 ATCTTAACTTTAAAAATATTTTTTATTCTT
1 ATCTTAACTTAAAAAATATATTTTATTCTT
* *
534412 ACCTTAACTT-AAATATATATTTTATTCTT
1 ATCTTAACTTAAAAAATATATTTTATTCTT
* * *
534441 ATCTTAACTTTTAAAATTTTATTTTATTTTATTTTT
1 ATCTTAAC--TTAAAA----AATATATTTTATTCTT
** * * *
534477 ATCTTAACTTATTACATTTATTATATTCTT
1 ATCTTAACTTAAAAAATATATTTTATTCTT
** * ** ** *
534507 AAATTAAATTATTAAATATATACTATTTTT
1 ATCTTAACTTAAAAAATATATTTTATTCTT
* * ** *
534537 ACCTTAAATTATTAAATATTTTTTATTCTT
1 ATCTTAACTTAAAAAATATATTTTATTCTT
*
534567 AT-TGTAACTTAAAATATATATTTTATTCTT
1 ATCT-TAACTTAAAAAATATATTTTATTCTT
534597 ATCTTAACTTAAAAAAT-TATTTT
1 ATCTTAACTTAAAAAATATATTTT
534620 TACTTTTATT
Statistics
Matches: 164, Mismatches: 35, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
29 31 0.19
30 103 0.63
31 3 0.02
32 3 0.02
34 4 0.02
36 20 0.12
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.55
Consensus pattern (30 bp):
ATCTTAACTTAAAAAATATATTTTATTCTT
Found at i:536481 original size:21 final size:21
Alignment explanation
Indices: 536457--536527 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
536447 GAAAAACAGA
536457 AAATAAAATTAATAAAATAAT
1 AAATAAAATTAATAAAATAAT
* *
536478 AAATAGTAA-TAATAATATAAT
1 AAATA-AAATTAATAAAATAAT
*
536499 GAAATAATATT-ATAAATATAAT
1 -AAATAAAATTAATAAA-ATAAT
*
536521 ATATAAA
1 AAATAAA
536528 TAATATATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 26 0.67
22 13 0.33
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (21 bp):
AAATAAAATTAATAAAATAAT
Found at i:536504 original size:13 final size:12
Alignment explanation
Indices: 536467--536701 Score: 97
Period size: 12 Copynumber: 19.8 Consensus size: 12
536457 AAATAAAATT
*
536467 AATAAAATAATA
1 AATAATATAATA
*
536479 AAT-A-GTAAT-
1 AATAATATAATA
536488 AATAATATAATGA
1 AATAATATAAT-A
*
536501 AATAATATTATA
1 AATAATATAATA
536513 AAT-ATAATATATA
1 AATAAT-ATA-ATA
536526 AATAATAT-ATA
1 AATAATATAATA
*
536537 TAT-ATAT-ATA
1 AATAATATAATA
536547 AACTAATAT-AT-
1 AA-TAATATAATA
*
536558 AAT-ATATACTA
1 AATAATATAATA
536569 AATATATATATATA
1 AATA-ATATA-ATA
536583 ATATAATAT-AT-
1 A-ATAATATAATA
536594 AATAATAATAAT-
1 AATAAT-ATAATA
536606 AATAATAT-ATA
1 AATAATATAATA
* * *
536617 TATTATATACTA
1 AATAATATAATA
* *
536629 TATCATATAATA
1 AATAATATAATA
* *
536641 TACAATAT-AT-
1 AATAATATAATA
536651 AATATATATAATA
1 AATA-ATATAATA
*
536664 TATATATATATATA
1 AATA-ATATA-ATA
*
536678 TATATATATATATA
1 AATA-ATATA-ATA
*
536692 TATATATATA
1 AATA-ATATA
536702 CCATAATATA
Statistics
Matches: 182, Mismatches: 18, Indels: 44
0.75 0.07 0.18
Matches are distributed among these distances:
9 7 0.04
10 24 0.13
11 35 0.19
12 45 0.25
13 32 0.18
14 36 0.20
15 3 0.02
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (12 bp):
AATAATATAATA
Found at i:536516 original size:22 final size:21
Alignment explanation
Indices: 536457--536699 Score: 99
Period size: 22 Copynumber: 10.9 Consensus size: 21
536447 GAAAAACAGA
*
536457 AAATAAAATTAATAAA-ATAAT
1 AAATAATATT-ATAAATATAAT
* *
536478 AAATAGTAATA-ATAATATAAT
1 AAATAATATTATA-AATATAAT
536499 GAAATAATATTATAAATATAAT
1 -AAATAATATTATAAATATAAT
* *
536521 ATATAAATAATATATATATATATAT
1 AAAT-AAT-AT-TATAAATATA-AT
*
536546 AAACTAATA-TATAATATATACT
1 AAA-TAATATTATAA-ATATAAT
536568 AAAT-ATATATATATAATATAAT
1 AAATAATAT-TATA-AATATAAT
*
536590 ATATAATA--AT-AATAATAAT
1 AAATAATATTATAAAT-ATAAT
*
536609 AATATATATATTATATACTAT-AT
1 AA-ATA-ATATTATA-AATATAAT
* *
536632 CATATAATA-TACAATATATAAT
1 -AAATAATATTATAA-ATATAAT
*
536654 ATATATAATATATATATATATATAT
1 A-A-ATAATAT-TATAAATATA-AT
* *
536679 ATATATATATATATATATATA
1 AAATA-ATAT-TATAAATATA
536700 TACCATAATA
Statistics
Matches: 171, Mismatches: 21, Indels: 57
0.69 0.08 0.23
Matches are distributed among these distances:
18 3 0.02
19 7 0.04
20 12 0.07
21 26 0.15
22 46 0.27
23 28 0.16
24 33 0.19
25 15 0.09
26 1 0.01
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (21 bp):
AAATAATATTATAAATATAAT
Found at i:536718 original size:2 final size:2
Alignment explanation
Indices: 536505--536701 Score: 187
Period size: 2 Copynumber: 105.5 Consensus size: 2
536495 TAATGAAATA
* *
536505 AT AT -T AT AA AT AT A- AT AT AT AA AT A- 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
* *
536544 AT AA ACT A- AT AT AT A- AT AT AT ACT AA AT AT AT AT AT AT A- AT
1 AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
536585 AT A- AT AT AT A- AT A- AT A- AT A- AT A- AT A- 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
*
536620 -T AT AT ACT AT AT CAT AT A- AT AT AC A- AT AT AT A- AT AT AT AT
1 AT AT AT A-T AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
536660 A- 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
536701 A
1 A
536702 CCATAATATA
Statistics
Matches: 164, Mismatches: 9, Indels: 44
0.76 0.04 0.20
Matches are distributed among these distances:
1 18 0.11
2 139 0.85
3 7 0.04
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:536908 original size:29 final size:29
Alignment explanation
Indices: 536861--536917 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
536851 TGATTCGTGT
* * * *
536861 TGTATATATTATTATTAAATTATTTAAAA
1 TGTATATACTATGAATAAATTAGTTAAAA
536890 TGTATATACTATGAATAAATTAGTTAAA
1 TGTATATACTATGAATAAATTAGTTAAA
536918 TTTTAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (29 bp):
TGTATATACTATGAATAAATTAGTTAAAA
Found at i:541744 original size:8 final size:8
Alignment explanation
Indices: 541732--541820 Score: 63
Period size: 8 Copynumber: 11.1 Consensus size: 8
541722 TAATTCTTCG
541732 ACTCTTAA
1 ACTCTTAA
*
541740 TCTCTTAA
1 ACTCTTAA
541748 ACTCTTAA
1 ACTCTTAA
** *
541756 GTTCTCAA
1 ACTCTTAA
*
541764 ACTCTCAA
1 ACTCTTAA
*
541772 ACTCTGAA
1 ACTCTTAA
* *
541780 ACTATCAA
1 ACTCTTAA
*
541788 ACTCTCAA
1 ACTCTTAA
*
541796 ACT-TTCGA
1 ACTCTT-AA
541804 ACTCTTAA
1 ACTCTTAA
*
541812 ATTCTTAA
1 ACTCTTAA
541820 A
1 A
541821 ATGACTCATA
Statistics
Matches: 64, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
7 1 0.02
8 61 0.95
9 2 0.03
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (8 bp):
ACTCTTAA
Found at i:543071 original size:43 final size:43
Alignment explanation
Indices: 543012--543406 Score: 426
Period size: 43 Copynumber: 9.2 Consensus size: 43
543002 TGAGAACAAA
* * *
543012 AAACACCGCAATAGGTCAATATCTATTA-CGGCGTTTTTTGA-AC
1 AAACGCCGCAAAAGGTC-ATATCTA-TAGCGGCGTTTTTGGATAC
*
543055 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGA-AT
1 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGTTTTTGGATAC
* * * * *
543098 AAACGCCGCACAAA-GTTATGATATATAGCGGCGTTTCTAGA-AA
1 AAACGCCGCA-AAAGGTCAT-ATCTATAGCGGCGTTTTTGGATAC
* *
543141 AAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGATAC
* * * * *
543184 AAACGCCGCAAAAGATAAGACCTATA-CTGGCGTTTTTAGA-AC
1 AAACGCCGCAAAAGGTCATATCTATAGC-GGCGTTTTTGGATAC
* * *
543226 AAACGCCGTAAAAGGTCATACCTATAGCGGCGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGATAC
* * * *
543269 AAACGCCGCAAAAGGTCAGATATATAGCGGCATTTTTTGATAC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGATAC
* *
543312 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGATAC
* ** *
543355 AAACGTCGCAAAAGGTCGGATATATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGATAC
543398 AAACGCCGC
1 AAACGCCGC
543407 TAATTACCAT
Statistics
Matches: 302, Mismatches: 42, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
42 61 0.20
43 238 0.79
44 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGATAC
Found at i:543172 original size:128 final size:127
Alignment explanation
Indices: 543009--543389 Score: 446
Period size: 128 Copynumber: 3.0 Consensus size: 127
542999 GTTTGAGAAC
* * *
543009 AAAAAACACCGCAATAGGTCAATATCTATTA-CGGCGTTTTTTGA-ACAAACGCCGCAAAAGGTC
1 AAAAAACGCCGCAAAAGGTC-AGATCTA-TAGCGGCGTTTTTTGATACAAACGCCGCAAAAGGTC
* *
543072 GATATCTATAGCGGCGTTTTTGGAATAAACGCCGCACAAAGTTATGATATATAGCGGCGTTTCTA
64 -AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCA-AAAGTTATGATATATAGCGGCGTTTCTA
543137 G
127 G
* * * *
543138 AAAAAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGATAAG
1 AAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTGATACAAACGCCGCAAAAGGTCAG
* * * * ** * *
543203 ACCTATA-CTGGCGTTTTTAGAACAAACGCCGTAAAAGGTCAT-ACCTATAGCGGCGTTTTTGG
66 ATCTATAGC-GGCGTTTTTGGAACAAACGCCGCAAAA-GTTATGATATATAGCGGCGTTTCTAG
* * *
543265 ACACAAACGCCGCAAAAGGTCAGATATATAGCGGCATTTTTTGATACAAACGCCGCAAAAGGTCA
1 A-AAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTGATACAAACGCCGCAAAAGGTCA
* * **
543330 GATCTATAGCGGCGTTTTTGGACACAAACGTCGCAAAAGGTCGGATATATAGCGGCGTTT
65 GATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGTTATGATATATAGCGGCGTTT
543390 TTGGATACAA
Statistics
Matches: 210, Mismatches: 34, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
127 23 0.11
128 125 0.60
129 62 0.30
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (127 bp):
AAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTGATACAAACGCCGCAAAAGGTCAG
ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGTTATGATATATAGCGGCGTTTCTAG
Found at i:546041 original size:41 final size:41
Alignment explanation
Indices: 545991--546375 Score: 346
Period size: 41 Copynumber: 9.4 Consensus size: 41
545981 TTTGCGGTAC
* * *
545991 AAACGCCACTAAAGTACGAGTCTTTTGCGGTGTTTTTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTATAA
* * * * *
546032 AAACACCACTAAAGTACAAGTCTATAGCGACGTTTGTAAACAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT-T-TATAA
* *
546075 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAAACAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT-T-TATAA
* *
546118 AAACGCCACTAAAGTAAGAGT-TATAGCAGCGTTTTTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTATAA
* * * * *
546158 AAACACCAGTAAAGTATGAGT-TATAGCAGCGCTTTTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTATAA
* *
546198 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTATAA
* * * * * * *
546239 AAACGCCCCTAAAGAACGATTCTATACCGGCATTTGTGTAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTATAA
** * * * * *
546280 AAACGCCACTACAA-TATTAATCTTTAGCAGCGTTTGTATAC
1 AAACGCCACTA-AAGTACGAGTCTATAGCGGCGTTTTTATAA
* * * * *
546321 AAACGCCACTAAAGTAAGA-TCTTTTGCGGCGTTTGTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTATAA
*
546361 AAACGCCTCTAAAGT
1 AAACGCCACTAAAGT
546376 TAGGTTTTTT
Statistics
Matches: 290, Mismatches: 49, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
40 92 0.32
41 120 0.41
42 15 0.05
43 63 0.22
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTATAA
Found at i:546220 original size:123 final size:124
Alignment explanation
Indices: 545991--546375 Score: 405
Period size: 123 Copynumber: 3.1 Consensus size: 124
545981 TTTGCGGTAC
* * * * *
545991 AAACGCCACTAAAGTACGAGTCTTTTGCGGTGTTTTTATAAAAACACCACTAAAGTACAAGTCTA
1 AAACGCCACTAAAGTAAGAGTCTATAGCGGCGTTTTTATAAAAACACCACTAAAGTATAAGTCTA
* *
546056 TAGC-GACGTTTGTAAACAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAAACAA
66 TAGCAG-CGTTTGT--ATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGT-AACAA
* * *
546118 AAACGCCACTAAAGTAAGAGT-TATAGCAGCGTTTTTATAAAAACACCAGTAAAGTATGAGT-TA
1 AAACGCCACTAAAGTAAGAGTCTATAGCGGCGTTTTTATAAAAACACCACTAAAGTATAAGTCTA
*
546181 TAGCAGCGCTTT-TATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGT-ATAA
66 TAGCAGCG-TTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTAACAA
* * * * * * *
546239 AAACGCCCCTAAAG-AACGATTCTATACCGGCATTTGTGTAAAAACGCCACTACAA-TATTAA-T
1 AAACGCCACTAAAGTAA-GAGTCTATAGCGGCGTTTTTATAAAAACACCACTA-AAGTA-TAAGT
* * * *
546301 CTTTAGCAGCGTTTGTATACAAACGCCACTAAAGTAAGA-TCTTTTGCGGCGTTTGTATAC--
63 CTATAGCAGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTA-ACAA
*
546361 AAACGCCTCTAAAGT
1 AAACGCCACTAAAGT
546376 TAGGTTTTTT
Statistics
Matches: 220, Mismatches: 27, Indels: 26
0.81 0.10 0.10
Matches are distributed among these distances:
120 2 0.01
121 19 0.09
122 58 0.26
123 74 0.34
124 1 0.00
125 9 0.04
126 37 0.17
127 20 0.09
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (124 bp):
AAACGCCACTAAAGTAAGAGTCTATAGCGGCGTTTTTATAAAAACACCACTAAAGTATAAGTCTA
TAGCAGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTAACAA
Found at i:547973 original size:31 final size:32
Alignment explanation
Indices: 547937--548025 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
547927 AAGGGGGCAC
* *
547937 CTTGGGGCCA-GAAAGCTTACCCAAGAAAGTT
1 CTTGGGGCCACGAAAGCCTACCCAAGAAAGAT
* *
547968 CTTGGGGCCACGGAGGCCTACCCAAGAAAGAT
1 CTTGGGGCCACGAAAGCCTACCCAAGAAAGAT
* *
548000 CTTGGGGGC-CGTATAGCCTACCCAAG
1 CTTGGGGCCACG-AAAGCCTACCCAAG
548026 GGTCACCTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 12 0.25
32 36 0.75
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (32 bp):
CTTGGGGCCACGAAAGCCTACCCAAGAAAGAT
Found at i:557640 original size:19 final size:19
Alignment explanation
Indices: 557616--557660 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
557606 ATTTATGCAC
*
557616 CAATGCATAGATAGTGCAT
1 CAATGCATAGATAGTACAT
*
557635 CGATGCATAGATAGTACAT
1 CAATGCATAGATAGTACAT
557654 CAATGCA
1 CAATGCA
557661 CCCGTCAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (19 bp):
CAATGCATAGATAGTACAT
Found at i:561484 original size:64 final size:63
Alignment explanation
Indices: 561409--561570 Score: 166
Period size: 63 Copynumber: 2.6 Consensus size: 63
561399 ATTATTCAAG
* * **
561409 GTGCATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATCA
1 GTGCATCGATGCACAAGAAGTGCATCGATGCAC-CCACTAAAATAAAAACATCGAATGTCATCA
** * * ** *
561473 GTGCATCGATGCACAAGTGGTGCATCTATGCACCCACTAAAATACAAACATCGAATGGGATTTA
1 GTGCATCGATGCACAAGAAGTGCATCGATGCACCCACTAAAATAAAAACATCGAATGTCA-TCA
* *
561537 -TGCACCGATGCA-TAGATAGTGCATCGATGCACCC
1 GTGCATCGATGCACAAGA-AGTGCATCGATGCACCC
561571 GTCAAGGGAT
Statistics
Matches: 80, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
62 2 0.03
63 48 0.60
64 30 0.38
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (63 bp):
GTGCATCGATGCACAAGAAGTGCATCGATGCACCCACTAAAATAAAAACATCGAATGTCATCA
Found at i:561583 original size:35 final size:35
Alignment explanation
Indices: 561543--561624 Score: 155
Period size: 35 Copynumber: 2.3 Consensus size: 35
561533 TTTATGCACC
561543 GATGCATAGATAGTGCATCGATGCACCCGTCAAGG
1 GATGCATAGATAGTGCATCGATGCACCCGTCAAGG
561578 GATGCATAGATAGTGCATCGATGCACCCGTCAAGG
1 GATGCATAGATAGTGCATCGATGCACCCGTCAAGG
*
561613 GATGCATCGATA
1 GATGCATAGATA
561625 CATGGTGTAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (35 bp):
GATGCATAGATAGTGCATCGATGCACCCGTCAAGG
Found at i:572963 original size:31 final size:30
Alignment explanation
Indices: 572928--572997 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
572918 AGTTTCAAAA
572928 GTAACAAATCAGTCACTAACATTATCAATTT
1 GTAACAAAT-AGTCACTAACATTATCAATTT
* * *
572959 GTAACAAAATGGTTACTAACATTATCGATTT
1 GTAAC-AAATAGTCACTAACATTATCAATTT
572990 GTAACAAA
1 GTAACAAA
572998 ATGATCACTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 3 0.09
31 28 0.80
32 4 0.11
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (30 bp):
GTAACAAATAGTCACTAACATTATCAATTT
Found at i:572998 original size:31 final size:31
Alignment explanation
Indices: 572942--573000 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
572932 CAAATCAGTC
572942 ACTAACATTATCAATTTGTAACAAAATGGTT
1 ACTAACATTATCAATTTGTAACAAAATGGTT
*
572973 ACTAACATTATCGATTTGTAACAAAATG
1 ACTAACATTATCAATTTGTAACAAAATG
573001 ATCACTCCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (31 bp):
ACTAACATTATCAATTTGTAACAAAATGGTT
Found at i:573022 original size:31 final size:30
Alignment explanation
Indices: 572940--573006 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 30
572930 AACAAATCAG
*
572940 TCACTAACATTATCAATTTGTAACAAAATGG
1 TCACTAACATTATC-ATTTGTAACAAAATGA
*
572971 TTACTAACATTATCGATTTGTAACAAAATGA
1 TCACTAACATTATC-ATTTGTAACAAAATGA
573002 TCACT
1 TCACT
573007 CCACCATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.34
Consensus pattern (30 bp):
TCACTAACATTATCATTTGTAACAAAATGA
Found at i:574088 original size:31 final size:31
Alignment explanation
Indices: 574045--574171 Score: 209
Period size: 31 Copynumber: 4.1 Consensus size: 31
574035 GTCCTGAAGG
* * *
574045 ACCTATCCATATGTTCCGAAGAACATAGGTA
1 ACCTGTCCATATGTCCCGAAGGACATAGGTA
574076 ACCTGTCCATATGTCCCGAAGGACATAGGTA
1 ACCTGTCCATATGTCCCGAAGGACATAGGTA
574107 ACCTGTCCATATGTCCCGAAGGACATAGGTA
1 ACCTGTCCATATGTCCCGAAGGACATAGGTA
* *
574138 AACTGTCCATATGTCCTGAAGGACATAGGTA
1 ACCTGTCCATATGTCCCGAAGGACATAGGTA
574169 ACC
1 ACC
574172 CTCGACTCTT
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 90 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (31 bp):
ACCTGTCCATATGTCCCGAAGGACATAGGTA
Found at i:574538 original size:31 final size:31
Alignment explanation
Indices: 574502--574563 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
574492 ATGACTTATC
*
574502 ACACTAACATATACTTATACAAATCATGTAA
1 ACACTAAAATATACTTATACAAATCATGTAA
574533 ACACTAAAATATACTTATACAAATCATGTAA
1 ACACTAAAATATACTTATACAAATCATGTAA
574564 CATACATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (31 bp):
ACACTAAAATATACTTATACAAATCATGTAA
Found at i:575581 original size:10 final size:10
Alignment explanation
Indices: 575566--575595 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
575556 CTTCACGTAT
575566 GAAGAAGAAA
1 GAAGAAGAAA
575576 GAAGAAGAAA
1 GAAGAAGAAA
575586 GAAGAAGAAA
1 GAAGAAGAAA
575596 CAAGTTCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAA
Found at i:576114 original size:30 final size:31
Alignment explanation
Indices: 576080--576151 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
576070 TGGAGTGACT
* * * *
576080 ATTTTGTTACAATTC-ATAACGTTAGTGATC
1 ATTTTGTTACAAATCAATAACATTAGTAACC
576110 ATTTTGTTACAAATCAATAACATTAGTAACC
1 ATTTTGTTACAAATCAATAACATTAGTAACC
*
576141 AATTTGTTACA
1 ATTTTGTTACA
576152 TTTGAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 14 0.39
31 22 0.61
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (31 bp):
ATTTTGTTACAAATCAATAACATTAGTAACC
Found at i:582860 original size:22 final size:21
Alignment explanation
Indices: 582835--582887 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
582825 TACTCAGGAA
*
582835 AGTATCGATACCTCATA-TAAGG
1 AGTATCGATACCTCAAACT-A-G
*
582857 AGTATCAATA-CTCAAACTAG
1 AGTATCGATACCTCAAACTAG
582877 AGTATCGATAC
1 AGTATCGATAC
582888 TAGCCCTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 10 0.38
21 6 0.23
22 10 0.38
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (21 bp):
AGTATCGATACCTCAAACTAG
Found at i:582939 original size:19 final size:19
Alignment explanation
Indices: 582915--582954 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
582905 CCTTTAATAA
582915 GTCAGTAATATCCCTAGAG
1 GTCAGTAATATCCCTAGAG
582934 GTCAGTAATATCCCTAGAG
1 GTCAGTAATATCCCTAGAG
582953 GT
1 GT
582955 TTGTATCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (19 bp):
GTCAGTAATATCCCTAGAG
Done.