Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003080.1 Hibiscus syriacus cultivar Beakdansim tig00006427_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: 50755
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:628 original size:52 final size:53
Alignment explanation
Indices: 416--619 Score: 266
Period size: 50 Copynumber: 4.0 Consensus size: 53
406 CCGAATGACG
*
416 CTATGTGTGCAACTTAAGAAATTCATAATGAGTT-T--ATTTCCGTATTAGCA
1 CTATGTGTGCAACTTAAGAAATTCATAATGAGTTATGAATTTCCGTATTGGCA
466 CTATGTGTGCAAC-TAAGAAATTCATAATGAGTTTATGAA-TTCCG--TTGGCA
1 CTATGTGTGCAACTTAAGAAATTCATAATGAG-TTATGAATTTCCGTATTGGCA
* **
516 CTATGTGTGC-ACTTAAGAAATTCATAATGAGTTATGAATTTCGGTATTGATA
1 CTATGTGTGCAACTTAAGAAATTCATAATGAGTTATGAATTTCCGTATTGGCA
* *
568 CTATGTGTG-AAC-TAAGAAATTGATAATGAGTTTATGAATTTCTGTATTGGCA
1 CTATGTGTGCAACTTAAGAAATTCATAATGAG-TTATGAATTTCCGTATTGGCA
620 TTGGGTGTGC
Statistics
Matches: 136, Mismatches: 8, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
49 27 0.20
50 52 0.38
51 18 0.13
52 38 0.28
53 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.37
Consensus pattern (53 bp):
CTATGTGTGCAACTTAAGAAATTCATAATGAGTTATGAATTTCCGTATTGGCA
Found at i:13402 original size:20 final size:21
Alignment explanation
Indices: 13323--13405 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 21
13313 TCAGAACCCC
* *
13323 ATGGGGGTATCGATTCCC-CT
1 ATGGGGGGATCGATTCCCTCA
* *
13343 GTGGGGGGATCGGTTCCCCTTCA
1 ATGGGGGGATCGATT-CCC-TCA
* *
13366 AAGGGGGAATCTG-TTCCCTC-
1 ATGGGGGGATC-GATTCCCTCA
13386 ATGGGGGGATCGATTCCCTC
1 ATGGGGGGATCGATTCCCTC
13406 TGCACCAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
19 1 0.02
20 28 0.57
21 5 0.10
22 3 0.06
23 11 0.22
24 1 0.02
ACGTcount: A:0.14, C:0.25, G:0.34, T:0.27
Consensus pattern (21 bp):
ATGGGGGGATCGATTCCCTCA
Found at i:17175 original size:22 final size:21
Alignment explanation
Indices: 17133--17172 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17123 GAGCTTATTT
*
17133 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
17154 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
17173 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:17642 original size:12 final size:12
Alignment explanation
Indices: 17625--17650 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17615 TCCAATGTTT
17625 TTCTTCTTCTCC
1 TTCTTCTTCTCC
17637 TTCTTCTTCTCC
1 TTCTTCTTCTCC
17649 TT
1 TT
17651 TGGTGTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCTTCTTCTCC
Found at i:18725 original size:18 final size:18
Alignment explanation
Indices: 18699--18742 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
18689 GTGAAGTATG
* *
18699 AATGGTGTTGTTGTGGAA
1 AATGTTGTTGTCGTGGAA
*
18717 AATGTTGTTGTCGTGGTA
1 AATGTTGTTGTCGTGGAA
*
18735 AGTGTTGT
1 AATGTTGT
18743 AAGGTTAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.02, G:0.36, T:0.43
Consensus pattern (18 bp):
AATGTTGTTGTCGTGGAA
Found at i:20860 original size:860 final size:860
Alignment explanation
Indices: 18458--20987 Score: 4332
Period size: 860 Copynumber: 3.0 Consensus size: 860
18448 GGAAAATATT
* *
18458 TGATTTGATCTCGATTATATGTTTCGAGTCATATATGAGAATGCCCGATCGTGATTCTAGTAAGA
1 TGATATGATATCGATTATATGTTTCGAGTCATATATGAGAATG-CCGATCGTGATTCTAGTAAGA
* * *
18523 AACCCCGTAATGATAGCTTGAACTCTGAAATTGCATAAATACAAACATAATAAGGAACATGATAT
65 AACCCCGTAATGATAGCTTGAACTCTGAAATTGCATAAATATAAACATAAGAAGGAAAATGATAT
*
18588 GAAATAATAATTGAAATGATGGAATGAAAAGAATGAGGGAGTTGTTTGAAGGTGATGGAAGAGTG
130 GAAATAATAATTGAAATGATGGAATGAAAAGAATGAGGAAGTTGTTTGAAGGTGATGGAAGAGTG
*
18653 ATGGTTGTTGTGGTTTAATGATAATGAAAATAGATGGTGAAGTATGAATGGTGTTGTTGTGGAAA
195 ATGGTTGTTGTGGTTTAATGATAATGAAAATAGATGGTGAAGTATGAATGGTGTT-ATGTGGAAA
18718 ATGTTGTTGTCGTGGTAAGTGTTGTAAGGTTAAAGCGGATTGTGACCCGTTAGCTATTTGGAGCT
259 ATGTT-TTGTCGTGGTAAGTGTTGTAAGGTTAAAGCGGATTGTGACCCGTTAGCTATTTGGAGCT
* *
18783 AAGAACCAACAATATAAAAGATGGAATCGAAATGGTAGTGTATGGAATGTGACCCACTAGCTATA
323 AAGAACCAACAATATAAAAGATGGAATCGAAATGGTAGGGTATGGAACGTGACCCACTAGCTATA
* * *
18848 GATGAGCTAGGAACTAAGGGTATAACAAAAGGAAATGGATAAAGACTACAAGACTATCTTGAAGC
388 GATGAGCTAGGAACCAACGGTATAACAAAAGGAAATGGATGAAGACTACAAGACTATCTTGAAGC
* * *
18913 CGATAAAGTTCTACAATAGAACAAGAATGAAAGCAACCTCTCAAAGATGTTTTATATATTCAAAT
453 CGATAAAGTTCTACAAGAAAACAAGAATGAAAGAAACCTCTCAAAGATGTTTTATATATTCAAAT
* *
18978 GTGTTTCTACAAATGATCCCAAATGTGCCTATTTATAGTATTTCTAAGAAGCATATG-AAAGACT
518 GTGTGTCTACAAATGATCCCAAAGGTGCCTATTTATAGTATTTCTAAGAAGCATATGAAAAGACT
* * *
19042 TAAAAGATGAAAACATTTTCATCAATTTAGCAATAAAATGCACTTGAATGCTTTGTCTTCTTATC
583 CAAAAGATGAAAACATTCTCATCAATTTAGCAATAAAATGCACTTGAATGCTTTGTCTTCTTTTC
* * * *
19107 TTCAAAGTTGGATGAATATTCTAGATCATTTTGGGGATGAATCTAGACAATTTGAAGATGGATTT
648 TTCAAAGTTGGATGAATAATCTAGATCATTTTGGGGATGAATCTAGACAATTTAAAGCTGAATTT
19172 GGCCTTAATTTCGTCCAAGGGGTGGAAGACTCTTGCTATTCCATGCTG-AAATTATCTTGATAAG
713 GGCCTTAATTTCGTCCAAGGGGTGGAAGACTCTTGCTATTCCATGCTGAAAATTATCTTGATAAG
*
19236 TGAATTAAATCACCTTTCATTGCATGCTCCCTTGAAGAATATGAACAACCCTTGAACTTAGATGA
778 TGAATTAAATCACCCTTCATTGCATGCTCCCTTGAAGAATATGAACAACCCTTGAACTTAGATGA
*
19301 TAACAATCAGTTTTGAAA
843 TAACAATCAGCTTTGAAA
* * *
19319 TGATATGATCTCGATTATATGTTTCGAGTCATATATGAGAATACCCGATCGTGATTGTAGTAAGA
1 TGATATGATATCGATTATATGTTTCGAGTCATATATGAGAAT-GCCGATCGTGATTCTAGTAAGA
19384 AACCCCGTAATGATAGCTTGAACTCTGAAATTGCATAAATATAAACATAAGAAGGAAAATGATAT
65 AACCCCGTAATGATAGCTTGAACTCTGAAATTGCATAAATATAAACATAAGAAGGAAAATGATAT
*
19449 GAAATAATAATTGAAATGATGGAATGAAAAGAATGAGGAAGTTGTTTGAAGGTAATGGAAGAGTG
130 GAAATAATAATTGAAATGATGGAATGAAAAGAATGAGGAAGTTGTTTGAAGGTGATGGAAGAGTG
19514 ATGGTTGTTGT-GTTTAATGATAATGAAAATAGATGGTGAAGTATG-A-------A--TGG----
195 ATGGTTGTTGTGGTTTAATGATAATGAAAATAGATGGTGAAGTATGAATGGTGTTATGTGGAAAA
*
19564 TG--TTGTCGTGGTAAGTGTTGTAAGGTTAAAGCGGATTGTGACCCATTAGCTATTTGGAGCTAA
260 TGTTTTGTCGTGGTAAGTGTTGTAAGGTTAAAGCGGATTGTGACCCGTTAGCTATTTGGAGCTAA
19627 GAACCAACAATATAAAAGATGGAATCGAAATGGTAGGGTATGGAACGTGACCCACTAGCTATAGA
325 GAACCAACAATATAAAAGATGGAATCGAAATGGTAGGGTATGGAACGTGACCCACTAGCTATAGA
* * *
19692 TGAGCTAGGAACCAATGGTATAACAAAGGGAAATGGATGAAGTCTACAAGACTATCTTGAAGCCG
390 TGAGCTAGGAACCAACGGTATAACAAAAGGAAATGGATGAAGACTACAAGACTATCTTGAAGCCG
*
19757 ATAAAGTTCTACAAG-AAACAAGAATG-AAGAAACCTCTCAAAGATGTTTTATATATTCAAATAT
455 ATAAAGTTCTACAAGAAAACAAGAATGAAAGAAACCTCTCAAAGATGTTTTATATATTCAAATGT
19820 GTGTCTACAAATGATCCCAAAGGTGCCTATTTATAGTATTTCTAAGAAGCATATGAAAAGACTCA
520 GTGTCTACAAATGATCCCAAAGGTGCCTATTTATAGTATTTCTAAGAAGCATATGAAAAGACTCA
*
19885 AAAGATGAAAACATTCTCATCAATTTATCAATAAAATGCACTTGAATGCTTTGTCTTCTTTTCTT
585 AAAGATGAAAACATTCTCATCAATTTAGCAATAAAATGCACTTGAATGCTTTGTCTTCTTTTCTT
* * *
19950 CAAAGTTGGATGAATACTCTAGATCATTTTGGGGATGAATCTACACAATTTAAAGCTAAATTTGG
650 CAAAGTTGGATGAATAATCTAGATCATTTTGGGGATGAATCTAGACAATTTAAAGCTGAATTTGG
* *
20015 CCTTAATTTCGTCCAAGGGGTGGAAGACTCTTGCTATTCCATGCTGAAAATTATCTTGATAATTA
715 CCTTAATTTCGTCCAAGGGGTGGAAGACTCTTGCTATTCCATGCTGAAAATTATCTTGATAAGTG
* *
20080 AATTAAATCACCCTTCATTGCATGCTCCCTTGAAGAATATGAATAGCCCTTGAACTTAGATGATA
780 AATTAAATCACCCTTCATTGCATGCTCCCTTGAAGAATATGAACAACCCTTGAACTTAGATGATA
20145 ACAATCAGCTTTGAAA
845 ACAATCAGCTTTGAAA
*
20161 TGATATGATATCGA-T-TATGTTTCGATTCATATATGAGAATGCCGATCGTGATTCTAGTAAGAA
1 TGATATGATATCGATTATATGTTTCGAGTCATATATGAGAATGCCGATCGTGATTCTAGTAAGAA
20224 ACCCCGTAATGATAGCTTGAACTCTGAAATTGCATAAATATAAACATAAGAAGGAAAATGATATG
66 ACCCCGTAATGATAGCTTGAACTCTGAAATTGCATAAATATAAACATAAGAAGGAAAATGATATG
20289 AAATAATAATTGAAATGATGGAATGAAAAGAATGAGGAAGTTGTTTGAAGGTGATGGAAGAGTGA
131 AAATAATAATTGAAATGATGGAATGAAAAGAATGAGGAAGTTGTTTGAAGGTGATGGAAGAGTGA
*
20354 TAGTTGTTGTGGTTTAATGATAATGAAAATAGATGGTGAAGTATGAATGGTGTTATCGTGGAAAA
196 TGGTTGTTGTGGTTTAATGATAATGAAAATAGATGGTGAAGTATGAATGGTGTTAT-GTGGAAAA
* *
20419 TGTTTTTGTCGTGGTAAGTGTTGCAAGGTTAAAGCGGATTGTGACCCGTTAGCTATTTAGAGCTA
260 TG-TTTTGTCGTGGTAAGTGTTGTAAGGTTAAAGCGGATTGTGACCCGTTAGCTATTTGGAGCTA
* * *
20484 AGAACCAACAATATAAAACATAGAATCGAAATGGTAGGGTATGGAACGTGACCCACTAGCTATAA
324 AGAACCAACAATATAAAAGATGGAATCGAAATGGTAGGGTATGGAACGTGACCCACTAGCTATAG
*
20549 ATGAGCTAGGAACCAACGATATAACAAAAGGAAATGGATGAAGACTACAAGACTATCTTGAAGCC
389 ATGAGCTAGGAACCAACGGTATAACAAAAGGAAATGGATGAAGACTACAAGACTATCTTGAAGCC
20614 GATAAAGTTCTACAAGAAAACAAGAATGAAAGAAACCTCTCAAAGATGTTTTATATATTCAAATG
454 GATAAAGTTCTACAAGAAAACAAGAATGAAAGAAACCTCTCAAAGATGTTTTATATATTCAAATG
20679 TGTGTCTACAAATGATCCCAAAGGTGCCTATTTATAGTATTTCTAAGAAGCATATGAAAAGACTC
519 TGTGTCTACAAATGATCCCAAAGGTGCCTATTTATAGTATTTCTAAGAAGCATATGAAAAGACTC
* *
20744 AAAATATGAAAACATTCTCATCAATTTAGCAATAAAATGCACTTGAATGCTTTGTCTTATTTTCT
584 AAAAGATGAAAACATTCTCATCAATTTAGCAATAAAATGCACTTGAATGCTTTGTCTTCTTTTCT
20809 TCAAAGTTGGATGAATAATCTAGATCATTTTGGGGATGAATCTAGACAATTTAAAGCTGAATTTG
649 TCAAAGTTGGATGAATAATCTAGATCATTTTGGGGATGAATCTAGACAATTTAAAGCTGAATTTG
* * * *
20874 GCCTTAATTTCGTCCAAGGGGTTGAAGACTCTTGCTTTTCCATGCTGAAACTTGTCTTGATAAGT
714 GCCTTAATTTCGTCCAAGGGGTGGAAGACTCTTGCTATTCCATGCTGAAAATTATCTTGATAAGT
20939 GAATTAAATCACCCTTCATTGCATGCTCCCTTGAAGAATATGAACAACC
779 GAATTAAATCACCCTTCATTGCATGCTCCCTTGAAGAATATGAACAACC
20988 AGCTTTGAAT
Statistics
Matches: 1575, Mismatches: 70, Indels: 49
0.93 0.04 0.03
Matches are distributed among these distances:
839 159 0.10
840 146 0.09
841 187 0.12
842 303 0.19
845 2 0.00
848 1 0.00
849 3 0.00
851 3 0.00
855 2 0.00
858 196 0.12
859 12 0.01
860 364 0.23
861 197 0.13
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (860 bp):
TGATATGATATCGATTATATGTTTCGAGTCATATATGAGAATGCCGATCGTGATTCTAGTAAGAA
ACCCCGTAATGATAGCTTGAACTCTGAAATTGCATAAATATAAACATAAGAAGGAAAATGATATG
AAATAATAATTGAAATGATGGAATGAAAAGAATGAGGAAGTTGTTTGAAGGTGATGGAAGAGTGA
TGGTTGTTGTGGTTTAATGATAATGAAAATAGATGGTGAAGTATGAATGGTGTTATGTGGAAAAT
GTTTTGTCGTGGTAAGTGTTGTAAGGTTAAAGCGGATTGTGACCCGTTAGCTATTTGGAGCTAAG
AACCAACAATATAAAAGATGGAATCGAAATGGTAGGGTATGGAACGTGACCCACTAGCTATAGAT
GAGCTAGGAACCAACGGTATAACAAAAGGAAATGGATGAAGACTACAAGACTATCTTGAAGCCGA
TAAAGTTCTACAAGAAAACAAGAATGAAAGAAACCTCTCAAAGATGTTTTATATATTCAAATGTG
TGTCTACAAATGATCCCAAAGGTGCCTATTTATAGTATTTCTAAGAAGCATATGAAAAGACTCAA
AAGATGAAAACATTCTCATCAATTTAGCAATAAAATGCACTTGAATGCTTTGTCTTCTTTTCTTC
AAAGTTGGATGAATAATCTAGATCATTTTGGGGATGAATCTAGACAATTTAAAGCTGAATTTGGC
CTTAATTTCGTCCAAGGGGTGGAAGACTCTTGCTATTCCATGCTGAAAATTATCTTGATAAGTGA
ATTAAATCACCCTTCATTGCATGCTCCCTTGAAGAATATGAACAACCCTTGAACTTAGATGATAA
CAATCAGCTTTGAAA
Found at i:23868 original size:20 final size:20
Alignment explanation
Indices: 23843--23958 Score: 109
Period size: 20 Copynumber: 6.0 Consensus size: 20
23833 AAACCATTAA
23843 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
*
23863 GGGGGAATCTGT--TCCC--
1 GGGGGAATCTGTACCCCCTG
23879 -GGGGAATC-GATACCCCCTGG
1 GGGGGAATCTG-TACCCCCT-G
* *
23899 GGGAGGAATCTATTCCCCCTG
1 GGG-GGAATCTGTACCCCCTG
* *
23920 GGAGGAATCTATACCCCCTG
1 GGGGGAATCTGTACCCCCTG
*
23940 GGGGGAATCTGTTCCCCCT
1 GGGGGAATCTGTACCCCCT
23959 AGGCAATCTG
Statistics
Matches: 78, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
14 1 0.01
15 9 0.12
17 3 0.04
18 3 0.04
20 44 0.56
21 5 0.06
22 13 0.17
ACGTcount: A:0.17, C:0.29, G:0.32, T:0.22
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:27450 original size:20 final size:21
Alignment explanation
Indices: 27411--27457 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
27401 GAGTTTATTT
27411 TCATTTTTCAATTTTGAAAAA
1 TCATTTTTCAATTTTGAAAAA
27432 TCATTTTT-ATATTTT-AAAAA
1 TCATTTTTCA-ATTTTGAAAAA
*
27452 TAATTT
1 TCATTT
27458 CTCATAATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAAAA
Found at i:29472 original size:21 final size:20
Alignment explanation
Indices: 29448--29561 Score: 100
Period size: 21 Copynumber: 5.9 Consensus size: 20
29438 AAACCATTAA
*
29448 GGGGTGAATCTGTACCCCTG
1 GGGGGGAATCTGTACCCCTG
*
29468 GGGGGGAATCTGT-TCCC--
1 GGGGGGAATCTGTACCCCTG
29485 --GGGGAATC-GATACCCCCTG
1 GGGGGGAATCTG-TA-CCCCTG
*
29504 GGGGGGAATCTGTTCCCCCT-
1 GGGGGGAATCTG-TACCCCTG
29524 -GGGGGAATCTGTACCCTCTG
1 GGGGGGAATCTGTACCC-CTG
*
29544 GGGGGGAATCTGTTCCCC
1 GGGGGGAATCTGTACCCC
29562 CTAGGCAATC
Statistics
Matches: 76, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
14 1 0.01
15 9 0.12
17 3 0.04
18 4 0.05
19 16 0.21
20 13 0.17
21 28 0.37
22 2 0.03
ACGTcount: A:0.14, C:0.27, G:0.36, T:0.23
Consensus pattern (20 bp):
GGGGGGAATCTGTACCCCTG
Found at i:29545 original size:40 final size:39
Alignment explanation
Indices: 29448--29563 Score: 161
Period size: 40 Copynumber: 3.0 Consensus size: 39
29438 AAACCATTAA
29448 GGGGTGAATCTGTACCCCTGGGGGGGAATCTGTT--CCC-
1 GGGG-GAATCTGTACCCCTGGGGGGGAATCTGTTCCCCCT
29485 -GGGGAATC-GATACCCCCTGGGGGGGAATCTGTTCCCCCT
1 GGGGGAATCTG-TA-CCCCTGGGGGGGAATCTGTTCCCCCT
29524 GGGGGAATCTGTACCCTCTGGGGGGGAATCTGTTCCCCCT
1 GGGGGAATCTGTACCC-CTGGGGGGGAATCTGTTCCCCCT
29564 AGGCAATCTG
Statistics
Matches: 71, Mismatches: 0, Indels: 13
0.85 0.00 0.15
Matches are distributed among these distances:
34 1 0.01
35 7 0.10
36 23 0.32
38 3 0.04
39 3 0.04
40 33 0.46
41 1 0.01
ACGTcount: A:0.14, C:0.28, G:0.35, T:0.23
Consensus pattern (39 bp):
GGGGGAATCTGTACCCCTGGGGGGGAATCTGTTCCCCCT
Found at i:30003 original size:32 final size:31
Alignment explanation
Indices: 29967--30035 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 31
29957 GTTTTTGGTT
* *
29967 AGATGAAAGGAGTTTGTTGTGTAAGTGATTGA
1 AGATGAAAGGAGTGTGTTGTGTAAGAGA-TGA
29999 AGATGAAAGGAGTGTGTTGTGTAAGAGATGA
1 AGATGAAAGGAGTGTGTTGTGTAAGAGATGA
30030 A-ATGAA
1 AGATGAA
30036 TGTGTTATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 5 0.14
31 4 0.11
32 26 0.74
ACGTcount: A:0.36, C:0.00, G:0.35, T:0.29
Consensus pattern (31 bp):
AGATGAAAGGAGTGTGTTGTGTAAGAGATGA
Found at i:30027 original size:25 final size:25
Alignment explanation
Indices: 29999--30047 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
29989 AAGTGATTGA
* *
29999 AGATGAAAGGAGTGTGTTGTGTAAG
1 AGATGAAAGGAATGTGTTATGTAAG
*
30024 AGATGAAATGAATGTGTTATGTAA
1 AGATGAAAGGAATGTGTTATGTAA
30048 AAATATTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.31
Consensus pattern (25 bp):
AGATGAAAGGAATGTGTTATGTAAG
Found at i:32663 original size:27 final size:27
Alignment explanation
Indices: 32633--32693 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
32623 GAGGACTAAC
*
32633 TTTTAAATTTAAATTAAAAATAATATAT
1 TTTTAAA-TTAAATTAAAAATAAAATAT
* *
32661 TTTTAAATTAAGTTAATAATAAAATAT
1 TTTTAAATTAAATTAAAAATAAAATAT
*
32688 ATTTAA
1 TTTTAA
32694 TAAGTCAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
TTTTAAATTAAATTAAAAATAAAATAT
Found at i:32734 original size:27 final size:26
Alignment explanation
Indices: 32669--32741 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 26
32659 ATTTTTAAAT
*
32669 TAAGTTAATA-ATAAAATATATTTAA
1 TAAGTTAATATATAAAAAATATTTAA
* **
32694 TAAGTCAAT-T-TAAAAAATATTTCT
1 TAAGTTAATATATAAAAAATATTTAA
32718 TAAAGTTAATATATAAAAAATATT
1 T-AAGTTAATATATAAAAAATATT
32742 ATGAATTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
24 12 0.31
25 15 0.38
26 1 0.03
27 11 0.28
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (26 bp):
TAAGTTAATATATAAAAAATATTTAA
Found at i:34366 original size:41 final size:43
Alignment explanation
Indices: 34310--34437 Score: 120
Period size: 43 Copynumber: 3.0 Consensus size: 43
34300 TAAAAACACC
* **
34310 GCAAAAAGTCAAGATCTATA-AATGTTTTTTTAAACAAACG-CT
1 GCAAAAGGTC-AGATCTATACAATGTTTTTGGAAACAAACGCCT
** *
34352 GCAAAAGGTCAGATCTATAGCGGTGTTTTTGGATACAAACGCCT
1 GCAAAAGGTCAGATCTATA-CAATGTTTTTGGAAACAAACGCCT
* *
34396 -CAAAAGGTCAGATCTATAGCGGA-GTTTTTGGATACAAACGCC
1 GCAAAAGGTCAGATCTATA-C-AATGTTTTTGGAAACAAACGCC
34438 GTTAATTACC
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
41 9 0.12
42 9 0.12
43 54 0.72
44 3 0.04
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.27
Consensus pattern (43 bp):
GCAAAAGGTCAGATCTATACAATGTTTTTGGAAACAAACGCCT
Found at i:34437 original size:43 final size:44
Alignment explanation
Indices: 34343--34437 Score: 167
Period size: 43 Copynumber: 2.2 Consensus size: 44
34333 GTTTTTTTAA
*
34343 ACAAACG-CTGCAAAAGGTCAGATCTATAGCGGTGTTTTTGGAT
1 ACAAACGCCTGCAAAAGGTCAGATCTATAGCGGAGTTTTTGGAT
34386 ACAAACGCCT-CAAAAGGTCAGATCTATAGCGGAGTTTTTGGAT
1 ACAAACGCCTGCAAAAGGTCAGATCTATAGCGGAGTTTTTGGAT
34429 ACAAACGCC
1 ACAAACGCC
34438 GTTAATTACC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
43 48 0.96
44 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (44 bp):
ACAAACGCCTGCAAAAGGTCAGATCTATAGCGGAGTTTTTGGAT
Found at i:38823 original size:16 final size:15
Alignment explanation
Indices: 38798--38838 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
38788 ATCCTTAAAA
*
38798 AGATAAAAAAATGTT
1 AGATAAAAAAATATT
38813 AGATAAAAAAATATT
1 AGATAAAAAAATATT
*
38828 AAATAAAAAAA
1 AGATAAAAAAA
38839 ATAAGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (15 bp):
AGATAAAAAAATATT
Found at i:40344 original size:29 final size:26
Alignment explanation
Indices: 40259--40353 Score: 82
Period size: 29 Copynumber: 3.3 Consensus size: 26
40249 ACCCATATAA
*
40259 TATATATTTTAAAAATATTTTAAAATT
1 TATATATTTTAAAAATTTTTTAAAA-T
*
40286 ATATATTATAGTTTAAAAATATTTTCAAAAT
1 -TATA-TAT--TTTAAAAAT-TTTTTAAAAT
*
40317 TATATAGTTTTCAAAAATGTTTTTAAAAC
1 TATATA-TTTT-AAAAAT-TTTTTAAAAT
40346 TATATATT
1 TATATATT
40354 ACATAAGTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
28 9 0.16
29 25 0.45
30 5 0.09
31 10 0.18
32 7 0.12
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (26 bp):
TATATATTTTAAAAATTTTTTAAAAT
Found at i:40381 original size:36 final size:36
Alignment explanation
Indices: 40315--40573 Score: 241
Period size: 36 Copynumber: 7.2 Consensus size: 36
40305 TATTTTCAAA
*
40315 ATTATAT-AGTTTTCAAAAATGTTTTTAAAACTATAT
1 ATTATATAAGTTTTC-AAAATGTTTTAAAAACTATAT
* * *
40351 ATTACATAAGTTTTCAAAATGATTTCAAAACTATAT
1 ATTATATAAGTTTTCAAAATGTTTTAAAAACTATAT
** *
40387 AATATATATGTGTTTTAAAAATGTTTTAAAAAC----T
1 -AT-TATATAAGTTTTCAAAATGTTTTAAAAACTATAT
40421 A-TATAT-A-TTTTCAAAATGTTTTAAAAACTATAT
1 ATTATATAAGTTTTCAAAATGTTTTAAAAACTATAT
* * * * *
40454 AATATATATATTTTTAAAAATATTTTAAAAATTATAT
1 ATTATATA-AGTTTTCAAAATGTTTTAAAAACTATAT
*
40491 ATTATATTTA-TTTTCAAAATGTTTTAAAAACTATAT
1 ATTATA-TAAGTTTTCAAAATGTTTTAAAAACTATAT
*
40527 -TATATATAAATGTTTTCAAACATGTTTTCAAAACTATAT
1 AT-TATAT-AA-GTTTTCAAA-ATGTTTTAAAAACTATAT
40566 ATTATATA
1 ATTATATA
40574 TATACAATAT
Statistics
Matches: 184, Mismatches: 21, Indels: 34
0.77 0.09 0.14
Matches are distributed among these distances:
29 20 0.11
31 5 0.03
33 3 0.02
34 6 0.03
35 2 0.01
36 54 0.29
37 38 0.21
38 33 0.18
39 22 0.12
40 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (36 bp):
ATTATATAAGTTTTCAAAATGTTTTAAAAACTATAT
Found at i:40423 original size:29 final size:29
Alignment explanation
Indices: 40399--40454 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
40389 TATATATGTG
40399 TTTTAAAAATGTTTTAAAAACTATATATA
1 TTTTAAAAATGTTTTAAAAACTATATATA
*
40428 TTTTCAAAATGTTTTAAAAACTATATA
1 TTTTAAAAATGTTTTAAAAACTATATA
40455 ATATATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (29 bp):
TTTTAAAAATGTTTTAAAAACTATATATA
Found at i:40512 original size:73 final size:75
Alignment explanation
Indices: 40420--40576 Score: 237
Period size: 73 Copynumber: 2.1 Consensus size: 75
40410 TTTTAAAAAC
*
40420 TATATATATTTTCAAAATGTTTTAAAAACTATATAATATATATAT-TTTT-AAAAATATTTTAAA
1 TATATATATTTTCAAAATGTTTTAAAAACTATATAATATATAAATGTTTTCAAAAATATTTTAAA
*
40483 AATTATATAT
66 AACTATATAT
* * * * *
40493 TATATTTATTTTCAAAATGTTTTAAAAACTATATTATATATAAATGTTTTCAAACATGTTTTCAA
1 TATATATATTTTCAAAATGTTTTAAAAACTATATAATATATAAATGTTTTCAAAAATATTTTAAA
40558 AACTATATAT
66 AACTATATAT
40568 TATATATAT
1 TATATATAT
40577 ACAATATTAT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
73 42 0.57
74 4 0.05
75 28 0.38
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.48
Consensus pattern (75 bp):
TATATATATTTTCAAAATGTTTTAAAAACTATATAATATATAAATGTTTTCAAAAATATTTTAAA
AACTATATAT
Found at i:41313 original size:84 final size:81
Alignment explanation
Indices: 41190--42073 Score: 908
Period size: 84 Copynumber: 10.7 Consensus size: 81
41180 TTGAATATAA
* * *
41190 TCGAACTCGAAGGTC-TTT-AGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
1 TCGAACTCGAAGGTCTTTTGTGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
*
41253 CGTTGAGCTGAGTGTAG
66 C-TTGAGCTGAGCGTAG
* * * * *
41270 TCGAACTCAAAGGTCTTTTGTTTGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTTG--TGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
41335 GCCTTGGAGCTGAGCGTAG
64 GCCTT-GAGCTGAGCGTAG
* * * * * *
41354 TCGAACTCGAAGGTCTTTGGTTGGCCGATAACCCTTCTAGACTTAAGTTGTACTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTTG-T-GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
41419 GCCTTGGAGCTGAGCGTAG
64 GCCTT-GAGCTGAGCGTAG
*
41438 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTG-T-GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * *
41503 GCCCTCGAAGCTGAGTGTAA
64 G-CCTTG-AGCTGAGCGTAG
** * *
41523 TCGAACTCGGGGGTC-TTTG-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
1 TCGAACTCGAAGGTCTTTTGTGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
41586 CGTTGAGCTGAGCGTAG
66 C-TTGAGCTGAGCGTAG
* * * * * *
41603 TCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTT-GT-GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* *
41668 GCCTTCGAAGCTGAGTGTAA
64 GCCTT-G-AGCTGAGCGTAG
* * *
41688 TCGAACTCG-GGAGTC-TTTG-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TCGAACTCGAAG-GTCTTTTGTGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
41750 CCTTGGAGCTGAGCGTAG
65 CCTT-GAGCTGAGCGTAG
* * *
41768 TCGAACTCAAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTG-T-GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * *
41833 GCCCTCGAAGCTGAGTGTAA
64 G-CCTTG-AGCTGAGCGTAG
** * * *
41853 TCGAACTCGGGGGTC-TTTG-GCAGATAGCCTTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
1 TCGAACTCGAAGGTCTTTTGTGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
41916 CGTTGAGCTGAGCGTAG
66 C-TTGAGCTGAGCGTAG
* * * * * *
41933 TCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTT-GT-GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * *
41998 GCCCTCGAAGCTAAGTGTAA
64 G-CCTTG-AGCTGAGCGTAG
* ** * *
42018 TCGAACTTGGGGGTC-TTTG-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
1 TCGAACTCGAAGGTCTTTTGTGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
42074 AGTTTGTTTA
Statistics
Matches: 674, Mismatches: 100, Indels: 59
0.81 0.12 0.07
Matches are distributed among these distances:
80 83 0.12
81 168 0.25
82 2 0.00
83 8 0.01
84 319 0.47
85 94 0.14
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (81 bp):
TCGAACTCGAAGGTCTTTTGTGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
CTTGAGCTGAGCGTAG
Found at i:41618 original size:165 final size:165
Alignment explanation
Indices: 41187--42073 Score: 1298
Period size: 165 Copynumber: 5.4 Consensus size: 165
41177 AAGTTGAATA
** *
41187 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * * *
41252 CCGTTGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTTGCAGACAACCCTTCTAGACTTAAG
66 CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTCGCAGATAACCCTTCTAGACTTAAG
* * * * *
41317 TTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCG
131 TTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
* ** * * * * * *
41351 TAGTCGAACTCGAAGGTCTTTGGTTGGCCGATAACCCTTCTAGACTTAAGTTGTACTGCAAATGA
1 TAATCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
* * * *
41416 TATGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGAC
62 TGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTCGCAGATAACCCTTCTAGAC
41480 TTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
126 TTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
41520 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * *
41585 CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGA
66 CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTTCGCAGATAACCCTTCTAGACTTAA
* *
41649 GTTATGCTGTAAATGATGTGCCTTCGAAGCTGAGTG
130 GTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
*
41685 TAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * *
41750 CC-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAA
66 CCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTCGCAGATAACCCTTCTAGACTTAA
41814 GTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
130 GTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
*
41850 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCTTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * *
41915 CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGA
66 CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTTCGCAGATAACCCTTCTAGACTTAA
* *
41979 GTTATGCTGTAAATGATGTGCCCTCGAAGCTAAGTG
130 GTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
*
42015 TAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
42074 AGTTTGTTTA
Statistics
Matches: 652, Mismatches: 59, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
164 24 0.04
165 472 0.72
166 15 0.02
167 3 0.00
168 111 0.17
169 27 0.04
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTCGCAGATAACCCTTCTAGACTTAAG
TTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
Found at i:41840 original size:330 final size:330
Alignment explanation
Indices: 41187--42073 Score: 1436
Period size: 330 Copynumber: 2.7 Consensus size: 330
41177 AAGTTGAATA
** *
41187 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * ** * * *
41252 CCGTTGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTTGCAGACAACCCTTCTAGACTTAAG
66 CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
* * * * * * * *
41317 TTGTGCTGCAAATGATATGCCTT-GGAGCTGAGCGTAGTCGAACTC-GAAGGTCTTTGGTTGGCC
131 TTATGCTGTAAATGATGTGCCTTCGAAGCTGAGTGTAATCGAACTCGGGA-GTC--T--TTGGCA
* * * * *
41380 GATAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACT
191 GATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACT
* *
41445 CGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCG
256 CAAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCG
41510 AAGCTGAGTG
321 AAGCTGAGTG
41520 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
41585 CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
41650 TTATGCTGTAAATGATGTGCCTTCGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAG
131 TTATGCTGTAAATGATGTGCCTTCGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAG
*
41715 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
196 CCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
41780 GTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCT
261 GTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCT
41845 GAGTG
326 GAGTG
*
41850 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCTTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
41915 CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
* * * *
41980 TTATGCTGTAAATGATGTGCCCTCGAAGCTAAGTGTAATCGAACTTGGGGGTCTTTGGCAGATAG
131 TTATGCTGTAAATGATGTGCCTTCGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAG
42045 CCCTTCTCGACTTAAGCTATGCTGCAAAT
196 CCCTTCTCGACTTAAGCTATGCTGCAAAT
42074 AGTTTGTTTA
Statistics
Matches: 521, Mismatches: 31, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
330 356 0.68
332 1 0.00
333 140 0.27
334 22 0.04
335 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (330 bp):
TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
TTATGCTGTAAATGATGTGCCTTCGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAG
CCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
GTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCT
GAGTG
Found at i:43418 original size:95 final size:95
Alignment explanation
Indices: 43245--43443 Score: 328
Period size: 95 Copynumber: 2.1 Consensus size: 95
43235 GGACATCCCA
* * * *
43245 ATATGTAAACACCTTTATCAGGTTAGCTGAAATCTTATCCATAAAGCTGGGGCGTTTAACCAATT
1 ATATATAATCACCTTTATCAGGCTAGCTGAAATATTATCCATAAAGCTGGGGCGTTTAACCAATT
*
43310 GCCTTAGAGGGACAGCTCAAGCTTTATTGT
66 GCCTTAGAGGGACAACTCAAGCTTTATTGT
43340 ATAGTATAATCACCTTTATCAGGCTAGCTG-AATATTATCCATAAAGCTGGGGCGTTTAACCAAT
1 ATA-TATAATCACCTTTATCAGGCTAGCTGAAATATTATCCATAAAGCTGGGGCGTTTAACCAAT
*
43404 TGCTTTAGAGGGACAACTCAAGCTTTATTGT
65 TGCCTTAGAGGGACAACTCAAGCTTTATTGT
43435 ATATATAAT
1 ATATATAAT
43444 AGTGTAATCT
Statistics
Matches: 97, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
94 6 0.06
95 68 0.70
96 23 0.24
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (95 bp):
ATATATAATCACCTTTATCAGGCTAGCTGAAATATTATCCATAAAGCTGGGGCGTTTAACCAATT
GCCTTAGAGGGACAACTCAAGCTTTATTGT
Found at i:46984 original size:14 final size:14
Alignment explanation
Indices: 46961--46999 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
46951 ATCCTTAAAA
*
46961 AGAT-AAAAATGTT
1 AGATAAAAAATATT
46974 AGATAAAAAATATT
1 AGATAAAAAATATT
*
46988 AAATAAAAAATA
1 AGATAAAAAATA
47000 AGATTAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.26
Consensus pattern (14 bp):
AGATAAAAAATATT
Found at i:47149 original size:13 final size:13
Alignment explanation
Indices: 47125--47163 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
47115 TAGGGAAACC
*
47125 AAAAAGAAATAAA
1 AAAAAAAAATAAA
*
47138 ACAAAAAAATAAA
1 AAAAAAAAATAAA
47151 AAAAAAAAATAAA
1 AAAAAAAAATAAA
47164 TGAAAGATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.87, C:0.03, G:0.03, T:0.08
Consensus pattern (13 bp):
AAAAAAAAATAAA
Found at i:48177 original size:16 final size:15
Alignment explanation
Indices: 48151--48180 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
48141 TGTTGTGGCC
48151 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
48166 GGTCAGTCCCGGGAT
1 GGTCA-TCCCGGGAT
48181 CTTCGACCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.27, G:0.40, T:0.20
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:48404 original size:2 final size:2
Alignment explanation
Indices: 48397--48425 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
48387 ACAAATAATA
48397 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48426 TTTCCAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48467 original size:20 final size:20
Alignment explanation
Indices: 48438--48475 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48428 TCCAAAACCC
*
48438 ATATAATATATTTTAAAATT
1 ATATAATATAGTTTAAAATT
*
48458 ATATATTATAGTTTAAAA
1 ATATAATATAGTTTAAAA
48476 ATATTTTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
ATATAATATAGTTTAAAATT
Found at i:48508 original size:26 final size:26
Alignment explanation
Indices: 48473--48539 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
48463 TTATAGTTTA
* * *
48473 AAAATATTTTCAAAATTATATTTTTC
1 AAAATGTTTTCAAAATTATATATTAC
* *
48499 AAAATGTTTTTAAAACTATATATTAC
1 AAAATGTTTTCAAAATTATATATTAC
*
48525 ATAA-GTTTTCAAAAT
1 AAAATGTTTTCAAAAT
48540 GATTTCAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
25 9 0.27
26 24 0.73
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (26 bp):
AAAATGTTTTCAAAATTATATATTAC
Found at i:48536 original size:36 final size:34
Alignment explanation
Indices: 48487--48738 Score: 221
Period size: 35 Copynumber: 7.3 Consensus size: 34
48477 TATTTTCAAA
*
48487 ATTATAT-TTTTCAAAATGTTTTTAAAACTATAT
1 ATTATATATTTTCAAAATGTTTTAAAAACTATAT
* * *
48520 ATTACATAAGTTTTCAAAATGATTTCAAAACTATAT
1 ATTATAT-A-TTTTCAAAATGTTTTAAAAACTATAT
* *
48556 AATATATATGTGTTTTAAAAATGTTTT-AAAAC----T
1 -AT-TATA--TATTTTCAAAATGTTTTAAAAACTATAT
*
48589 A-TATATATTTTCAAAATGTTTTAAAAACTATGT
1 ATTATATATTTTCAAAATGTTTTAAAAACTATAT
* * * *
48622 AATATATATTTTTAAAATATTTTAAAAATTATAT
1 ATTATATATTTTCAAAATGTTTTAAAAACTATAT
*
48656 ATTTATTTATTTTCAAAATGTTTTAAAAACTATATT
1 A-TTATATATTTTCAAAATGTTTTAAAAACTATA-T
* *
48692 ATATATAAATGTTTTCAAACATGTTTTCAAAACTATAT
1 AT-TAT--ATATTTTCAAA-ATGTTTTAAAAACTATAT
48730 ATTATATAT
1 ATTATATAT
48739 ATACTTTTAA
Statistics
Matches: 178, Mismatches: 22, Indels: 36
0.75 0.09 0.15
Matches are distributed among these distances:
28 15 0.08
29 5 0.03
30 4 0.02
32 1 0.01
33 9 0.05
34 29 0.16
35 31 0.17
36 29 0.16
37 10 0.06
38 28 0.16
39 16 0.09
40 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (34 bp):
ATTATATATTTTCAAAATGTTTTAAAAACTATAT
Found at i:48591 original size:28 final size:29
Alignment explanation
Indices: 48568--48657 Score: 92
Period size: 34 Copynumber: 3.0 Consensus size: 29
48558 TATATATGTG
48568 TTTTAAAAATGTTTT-AAAACTATATATA
1 TTTTAAAAATGTTTTAAAAACTATATATA
*
48596 TTTTCAAAATGTTTTAAAAACTATGTAATATATA
1 TTTTAAAAATGTTTTAAAAAC----T-ATATATA
* * *
48630 TTTTTAAAATATTTTAAAAATTATATAT
1 TTTTAAAAATGTTTTAAAAACTATATAT
48658 TTATTTATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
28 14 0.27
29 11 0.21
30 1 0.02
33 1 0.02
34 25 0.48
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTTAAAAATGTTTTAAAAACTATATATA
Found at i:48596 original size:135 final size:135
Alignment explanation
Indices: 48457--48767 Score: 310
Period size: 135 Copynumber: 2.3 Consensus size: 135
48447 ATTTTAAAAT
* *
48457 TATATATTATA-GTTTAAAAATATTTTCAAAATTATATTTTTCAAAATGTTTTTAAAACTATATA
1 TATATATTATACGTTTAAAAATATTTTCAAAA-TATATTTTT-AAAATATTTTAAAAACTATATA
* **
48521 -TTACATAAGTTTTCAAAATGATTTCAAAACTATATAATATATATGTGTTTT-AAAAATGTTTT-
64 TTTA-ATAA-TTTTCAAAATGATTTAAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTC
48583 AAAACTATA
127 AAAACTATA
* * * * * *
48592 TATATTTTCAAAATGTTTTAAAAACTA-TGT-AATATATATTTTTAAAATATTTTAAAAATTATA
1 TATATATT--ATACG-TTTAAAAA-TATTTTCAAAATATATTTTTAAAATATTTTAAAAACTATA
* * * * *
48655 TATTTATTTATTTTCAAAATGTTTTAAAAACTATATTATATATAAATGTTTTCAAACATGTTTTC
62 TATTTAATAATTTTCAAAATGATTTAAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTC
48720 AAAACTATA
127 AAAACTATA
* * *
48729 TATTATATATATACTTTTAAAAAATGTTTTCAAACTATA
1 TA-TATAT-TATACGTTT-AAAAATATTTTCAAAATATA
48768 CAATATATAT
Statistics
Matches: 140, Mismatches: 23, Indels: 23
0.75 0.12 0.12
Matches are distributed among these distances:
135 44 0.31
136 35 0.25
137 34 0.24
138 14 0.10
139 11 0.08
140 2 0.01
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (135 bp):
TATATATTATACGTTTAAAAATATTTTCAAAATATATTTTTAAAATATTTTAAAAACTATATATT
TAATAATTTTCAAAATGATTTAAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTCAAAA
CTATA
Found at i:48674 original size:35 final size:34
Alignment explanation
Indices: 48489--48738 Score: 208
Period size: 36 Copynumber: 7.2 Consensus size: 34
48479 TTTTCAAAAT
* *
48489 TATAT-TTTTCAAAATGTTTTTAAAACTATATAT
1 TATATATTTTCAAAATGTTTTAAAAACTATATAA
* * *
48522 TACATAAGTTTTCAAAATGATTTCAAAACTATATAA
1 TATAT-A-TTTTCAAAATGTTTTAAAAACTATATAA
*
48558 TATATATGTGTTTTAAAAATGTTTT-AAAAC----T-A
1 TATATA----TTTTCAAAATGTTTTAAAAACTATATAA
*
48590 TATATATTTTCAAAATGTTTTAAAAACTATGTAA
1 TATATATTTTCAAAATGTTTTAAAAACTATATAA
* * * *
48624 TATATATTTTTAAAATATTTTAAAAATTATATATT
1 TATATATTTTCAAAATGTTTTAAAAACTATATA-A
*
48659 TATTTATTTTCAAAATGTTTTAAAAACTATATTATA
1 TATATATTTTCAAAATGTTTTAAAAACTATA-TA-A
* * *
48695 TATAAATGTTTTCAAACATGTTTTCAAAACTATATAT
1 TAT--ATATTTTCAAA-ATGTTTTAAAAACTATATAA
48732 TATATAT
1 TATATAT
48739 ATACTTTTAA
Statistics
Matches: 177, Mismatches: 23, Indels: 32
0.76 0.10 0.14
Matches are distributed among these distances:
28 14 0.08
29 5 0.03
32 7 0.04
33 6 0.03
34 30 0.17
35 31 0.18
36 35 0.20
37 8 0.05
38 25 0.14
39 16 0.09
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (34 bp):
TATATATTTTCAAAATGTTTTAAAAACTATATAA
Found at i:48725 original size:39 final size:38
Alignment explanation
Indices: 48588--48776 Score: 137
Period size: 39 Copynumber: 5.1 Consensus size: 38
48578 GTTTTAAAAC
* * *
48588 TATATATA-TTTTCAAAATGTTTTAAAAACTATGTA-A
1 TATAAATACTTTTCAAAATGTTTTCAAAACTATATATA
* * *
48624 TAT--ATA-TTTTTAAAATATTTT-AAAAAT-TATATA
1 TATAAATACTTTTCAAAATGTTTTCAAAACTATATATA
* ** *
48657 TTTATTTA-TTTTCAAAATGTTTTAAAAACTATATTATA
1 TATAAATACTTTTCAAAATGTTTTCAAAACTATA-TATA
*
48695 TATAAAT-GTTTTCAAACATGTTTTCAAAACTATATATTA
1 TATAAATACTTTTCAAA-ATGTTTTCAAAACTATATA-TA
* * *
48734 TATATATACTTTTAAAAAATGTTTTC-AAACTATACAATA
1 TATAAATACTTTT-CAAAATGTTTTCAAAACTATA-TATA
48773 TATA
1 TATA
48777 TATATATATA
Statistics
Matches: 124, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
32 3 0.02
33 8 0.06
34 16 0.13
35 15 0.12
36 8 0.06
37 2 0.02
38 18 0.15
39 38 0.31
40 13 0.10
41 3 0.02
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (38 bp):
TATAAATACTTTTCAAAATGTTTTCAAAACTATATATA
Found at i:49249 original size:39 final size:39
Alignment explanation
Indices: 49166--49309 Score: 164
Period size: 40 Copynumber: 3.6 Consensus size: 39
49156 TAGAATTTAT
* * *
49166 GAGTCTTTAGCGGCGTTGTAAAGAAACGCCACTAAAGT-C
1 GAGTCTATAGCGGCGTTGTATA-AAACGCCACTAATGTAC
* * * *
49205 AAGTCTATAGCGGTGTTGTATAAAACGCTACCAATGTAC
1 GAGTCTATAGCGGCGTTGTATAAAACGCCACTAATGTAC
* * *
49244 GAGTCTATAGAGACGTTTGTATAAAATGCCACTAATGTAC
1 GAGTCTATAGCGGCG-TTGTATAAAACGCCACTAATGTAC
49284 GAGTCTATAGCGGCGTTTGTATAAAA
1 GAGTCTATAGCGGCG-TTGTATAAAA
49310 ACACTGCTAA
Statistics
Matches: 87, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
38 12 0.14
39 30 0.34
40 45 0.52
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.28
Consensus pattern (39 bp):
GAGTCTATAGCGGCGTTGTATAAAACGCCACTAATGTAC
Done.