Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005467.1 Hibiscus syriacus cultivar Beakdansim tig00012524_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: 580209
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 3 of 3
Found at i:482431 original size:45 final size:45
Alignment explanation
Indices: 482342--482519 Score: 297
Period size: 45 Copynumber: 4.0 Consensus size: 45
482332 GTAACCATGC
482342 AAATAAGCTTACGAGCTTATGGAAT-AATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
482386 AAATAAGCTTACGAGC-TATTGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTA-TGGAATAAATGGTAAGTATATTGGTA
*
482431 AAATAAGATTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
482476 AAATAAGCTTACGAGCTTATGGGATTAAATGGTTAGTATATTGG
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGG
482520 GTAAGAAATG
Statistics
Matches: 126, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
43 2 0.02
44 22 0.17
45 79 0.63
46 23 0.18
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:482480 original size:24 final size:24
Alignment explanation
Indices: 482408--482481 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
482398 GAGCTATTGG
482408 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
482432 AATAAGAT--TACGAGCT-TA-TGG---
1 AATAA-ATGGTA--AG-TATATTGGTAA
482453 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
482477 AATAA
1 AATAA
482482 GCTTACGAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 22
0.64 0.00 0.36
Matches are distributed among these distances:
19 1 0.03
20 6 0.15
21 8 0.21
22 2 0.05
23 2 0.05
24 13 0.33
25 6 0.15
26 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.20, T:0.31
Consensus pattern (24 bp):
AATAAATGGTAAGTATATTGGTAA
Found at i:482938 original size:12 final size:12
Alignment explanation
Indices: 482921--482945 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
482911 TTTGCTAAAA
482921 TTACTGTAGCAG
1 TTACTGTAGCAG
482933 TTACTGTAGCAG
1 TTACTGTAGCAG
482945 T
1 T
482946 GCATCGATGC
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:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (12 bp):
TTACTGTAGCAG
Found at i:485269 original size:21 final size:21
Alignment explanation
Indices: 485182--485270 Score: 56
Period size: 21 Copynumber: 4.2 Consensus size: 21
485172 TTCTATGCGG
* *
485182 TCCTTCGGGATATATATGTTA
1 TCCTTCGGAACATATATGTTA
**
485203 TCCGTT-GGAACATATATGCGA
1 TCC-TTCGGAACATATATGTTA
* * * *
485224 TTCTTCGGGACACATAT-TTGG
1 TCCTTCGGAACATATATGTT-A
* *
485245 TCCTTTGGAATATATATGTTA
1 TCCTTCGGAACATATATGTTA
485266 TCCTT
1 TCCTT
485271 GAGGAGTGGT
Statistics
Matches: 48, Mismatches: 16, Indels: 8
0.67 0.22 0.11
Matches are distributed among these distances:
20 2 0.04
21 42 0.88
22 4 0.08
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (21 bp):
TCCTTCGGAACATATATGTTA
Found at i:485313 original size:21 final size:21
Alignment explanation
Indices: 485283--485333 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
485273 GGAGTGGTCA
*
485283 TTCAGGACATATATGTATTCC
1 TTCAGGACATATATGTAGTCC
* * *
485304 TTCGGGACATCTATGTGGTCC
1 TTCAGGACATATATGTAGTCC
485325 TTCAGGACA
1 TTCAGGACA
485334 AAGTCTATGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (21 bp):
TTCAGGACATATATGTAGTCC
Found at i:490360 original size:21 final size:19
Alignment explanation
Indices: 490328--490366 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
490318 TGAAAAAATA
490328 TGATGAATAATATCGATAT
1 TGATGAATAATATCGATAT
490347 TGATGCAATTAATATCGATA
1 TGATG-AA-TAATATCGATA
490367 CTGCTATGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 2 0.11
21 11 0.61
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (19 bp):
TGATGAATAATATCGATAT
Found at i:490876 original size:54 final size:54
Alignment explanation
Indices: 490808--491043 Score: 312
Period size: 54 Copynumber: 4.4 Consensus size: 54
490798 TGTTGCTACG
* *
490808 ACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAAAAAGTTTATGAACA
1 ACCGTATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACA
* * *
490862 ACCGTATCGGCACTAAGTGTG-AAACCAAAAGAATTCATAATAAGTTTATGAACG
1 ACCGTATCGGCACTAAGTGTGCAACCCACAA-AATTCATAATAAGTTTATGAACA
** ** *
490916 ACCGTATCAACACTAAGTGTGCAACCCACGTAATTCATAATAAGTTTATGAACG
1 ACCGTATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACA
* * *
490970 ATCGTATCGGCACTAAGCGTGCAACCCACAGAATTCATAATAAGTTTATGAACA
1 ACCGTATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACA
* * *
491024 TCTGTATCGGCACTACGTGT
1 ACCGTATCGGCACTAAGTGT
491044 AAACCCCAAA
Statistics
Matches: 157, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
53 7 0.04
54 145 0.92
55 5 0.03
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (54 bp):
ACCGTATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACA
Found at i:491038 original size:108 final size:108
Alignment explanation
Indices: 490805--491022 Score: 346
Period size: 108 Copynumber: 2.0 Consensus size: 108
490795 ATATGTTGCT
490805 ACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAAAAAGTTTATGAACAACCGTATC
1 ACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAAAAAGTTTATGAACAACCGTATC
*
490870 GGCACTAAGTGTGAAACCAAAAGAATTCATAATAAGTTTATGA
66 GGCACTAAGCGTGAAACCAAAAGAATTCATAATAAGTTTATGA
* ** * * *
490913 ACGACCGTATCAACACTAAGTGTGCAACCCACGTAATTCATAATAAGTTTATGAACGATCGTATC
1 ACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAAAAAGTTTATGAACAACCGTATC
* * *
490978 GGCACTAAGCGTGCAACCCACAGAATTCATAATAAGTTTATGA
66 GGCACTAAGCGTGAAACCAAAAGAATTCATAATAAGTTTATGA
491021 AC
1 AC
491023 ATCTGTATCG
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 100 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (108 bp):
ACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAAAAAGTTTATGAACAACCGTATC
GGCACTAAGCGTGAAACCAAAAGAATTCATAATAAGTTTATGA
Found at i:491603 original size:20 final size:20
Alignment explanation
Indices: 491540--491605 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
491530 ACATGGAACA
491540 CCATGAGTCTCCTCTTACCC
1 CCATGAGTCTCCTCTTACCC
* *
491560 CTACGAGTCTCCTCTTACCC
1 CCATGAGTCTCCTCTTACCC
*
491580 CCATGAGTCTCCTCTTGCCC
1 CCATGAGTCTCCTCTTACCC
491600 CCATGA
1 CCATGA
491606 TCTACCCTGC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.15, C:0.44, G:0.12, T:0.29
Consensus pattern (20 bp):
CCATGAGTCTCCTCTTACCC
Found at i:492553 original size:12 final size:12
Alignment explanation
Indices: 492538--492576 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
492528 AAACTGAAGT
492538 AAAGGAAAAAGG
1 AAAGGAAAAAGG
*
492550 AAAGGAAAAAGA
1 AAAGGAAAAAGG
* *
492562 AAAAGAAAATGG
1 AAAGGAAAAAGG
492574 AAA
1 AAA
492577 CTTTTATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.03
Consensus pattern (12 bp):
AAAGGAAAAAGG
Found at i:500106 original size:2 final size:2
Alignment explanation
Indices: 500101--500130 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
500091 TGTGTAAAAG
500101 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
500131 CATTTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:509101 original size:18 final size:18
Alignment explanation
Indices: 509078--509112 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
509068 ACTGAAAATT
509078 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
509096 TGTCCCGAAGGATCACT
1 TGTCCCGAAGGACCACT
509113 TATAATCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:509918 original size:15 final size:15
Alignment explanation
Indices: 509898--509931 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
509888 GTATTGGTAC
509898 CTGATGAATCGATAT
1 CTGATGAATCGATAT
509913 CTGATGAATCGATAT
1 CTGATGAATCGATAT
509928 -TGAT
1 CTGAT
509932 TCCCCTTGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (15 bp):
CTGATGAATCGATAT
Found at i:520621 original size:10 final size:10
Alignment explanation
Indices: 520606--520633 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
520596 TTTAATTCAA
520606 GAATTATGGT
1 GAATTATGGT
520616 GAATTATGGT
1 GAATTATGGT
520626 GAATTATG
1 GAATTATG
520634 AGAGATGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (10 bp):
GAATTATGGT
Found at i:520838 original size:19 final size:19
Alignment explanation
Indices: 520814--520866 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
520804 CGAATGCCAT
520814 TAGTGCATCGATGCATAAG
1 TAGTGCATCGATGCATAAG
*
520833 TAGTGCATCGATACATAAG
1 TAGTGCATCGATGCATAAG
520852 TAGTGCATCGATGCA
1 TAGTGCATCGATGCA
520867 CCCCCTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (19 bp):
TAGTGCATCGATGCATAAG
Found at i:524018 original size:15 final size:15
Alignment explanation
Indices: 523998--524029 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
523988 TGTGCGTGCT
523998 ATATGACCAACCCCC
1 ATATGACCAACCCCC
*
524013 ATATGACCAGCCCCC
1 ATATGACCAACCCCC
524028 AT
1 AT
524030 GCTCAAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.44, G:0.09, T:0.16
Consensus pattern (15 bp):
ATATGACCAACCCCC
Found at i:526417 original size:22 final size:22
Alignment explanation
Indices: 526392--526442 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
526382 CCCAATGCTT
526392 GCTAGCTAGCTCCCACACTCAA
1 GCTAGCTAGCTCCCACACTCAA
526414 GCTAGCTAGCTCCCACACTCAA
1 GCTAGCTAGCTCCCACACTCAA
526436 GCTAGCT
1 GCTAGCT
526443 TGAATGATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.39, G:0.16, T:0.20
Consensus pattern (22 bp):
GCTAGCTAGCTCCCACACTCAA
Found at i:530882 original size:21 final size:20
Alignment explanation
Indices: 530846--530889 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
530836 TATTTAAACC
530846 ATACATAAATAATAAATAAA
1 ATACATAAATAATAAATAAA
*
530866 ATACATACATAAATAAATAAA
1 ATACATAAAT-AATAAATAAA
530887 ATA
1 ATA
530890 TTCTTCGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (20 bp):
ATACATAAATAATAAATAAA
Found at i:530900 original size:16 final size:16
Alignment explanation
Indices: 530881--530939 Score: 118
Period size: 16 Copynumber: 3.7 Consensus size: 16
530871 TACATAAATA
530881 AATAAAATATTCTTCG
1 AATAAAATATTCTTCG
530897 AATAAAATATTCTTCG
1 AATAAAATATTCTTCG
530913 AATAAAATATTCTTCG
1 AATAAAATATTCTTCG
530929 AATAAAATATT
1 AATAAAATATT
530940 AAAAGTTATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.37
Consensus pattern (16 bp):
AATAAAATATTCTTCG
Found at i:530963 original size:13 final size:12
Alignment explanation
Indices: 530945--530991 Score: 62
Period size: 13 Copynumber: 3.9 Consensus size: 12
530935 ATATTAAAAG
530945 TTATAAAAATATA
1 TTAT-AAAATATA
530958 TTAT-AAAT-TA
1 TTATAAAATATA
530968 TTATAAAATATA
1 TTATAAAATATA
530980 TTTATAAAATAT
1 -TTATAAAATAT
530992 TAAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 6 0.19
11 8 0.26
12 2 0.06
13 15 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TTATAAAATATA
Found at i:530971 original size:23 final size:24
Alignment explanation
Indices: 530945--530999 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
530935 ATATTAAAAG
*
530945 TTATAAAAATATA-TTATAAATTA
1 TTATAAAAATATATTTATAAAATA
530968 TTAT-AAAATATATTTATAAAATA
1 TTATAAAAATATATTTATAAAATA
*
530991 TTAAAAAAA
1 TTATAAAAA
531000 AATTAAACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 8 0.29
23 16 0.57
24 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TTATAAAAATATATTTATAAAATA
Found at i:543896 original size:35 final size:35
Alignment explanation
Indices: 543855--543929 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
543845 TTCATGTTCA
*
543855 AAATTCCAAAACACTTCAATTATATTATAAACCCC
1 AAATTCCAAAACACTTCAATTACATTATAAACCCC
* * * *
543890 AAATTCCAAAATACTTTAATTACATTCTAAACCCT
1 AAATTCCAAAACACTTCAATTACATTATAAACCCC
543925 AAATT
1 AAATT
543930 AAAGTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTATAAACCCC
Found at i:543980 original size:35 final size:35
Alignment explanation
Indices: 543925--544003 Score: 122
Period size: 35 Copynumber: 2.3 Consensus size: 35
543915 TCTAAACCCT
* * *
543925 AAATTAAAGTATTTTAGAATTTAGGATTTAAAATG
1 AAATTGAATTATTTTAGAATTTAGGATTTAAAATA
*
543960 TAATTGAATTATTTTAGAATTTAGGATTTAAAATA
1 AAATTGAATTATTTTAGAATTTAGGATTTAAAATA
543995 AAATTGAAT
1 AAATTGAAT
544004 ATTGTTGCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTAGGATTTAAAATA
Found at i:544722 original size:11 final size:11
Alignment explanation
Indices: 544699--544747 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
544689 TATTTATAAT
*
544699 TTTTTTAA-AA
1 TTTTTTAATTA
544709 TTTTTTAATTA
1 TTTTTTAATTA
544720 TTTTTTATATTA
1 TTTTTTA-ATTA
*
544732 TTATTTAATTAA
1 TTTTTTAATT-A
544744 TTTT
1 TTTT
544748 ATTCAACTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 8 0.24
11 11 0.33
12 14 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTTAATTA
Found at i:544724 original size:12 final size:11
Alignment explanation
Indices: 544699--544747 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
544689 TATTTATAAT
*
544699 TTTTTTAA-AA
1 TTTTTTAATTA
544709 TTTTTTAATTA
1 TTTTTTAATTA
544720 TTTTTTATATTA
1 TTTTTTA-ATTA
*
544732 TTATTTAATTA
1 TTTTTTAATTA
*
544743 ATTTT
1 TTTTT
544748 ATTCAACTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 8 0.24
11 15 0.45
12 10 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTTAATTA
Found at i:545561 original size:19 final size:19
Alignment explanation
Indices: 545530--545570 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
545520 AAATAATAAT
*
545530 AATATAAATAATATTTTAA
1 AATATAAATAATAATTTAA
545549 AATATTAAA-AATAATTTAA
1 AATA-TAAATAATAATTTAA
545568 AAT
1 AAT
545571 GCCACTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATATAAATAATAATTTAA
Found at i:546517 original size:42 final size:40
Alignment explanation
Indices: 546468--546616 Score: 122
Period size: 41 Copynumber: 3.6 Consensus size: 40
546458 CCACAAACGA
* *
546468 TACTTTAGTGGCGTTTCTTAAACAAACGCCGCGATAGTATAG
1 TACTTTAGCGGCGTTT-TTATACAAACGCCGCGATAG-ATAG
* * * * * *
546510 TACTTTAGCAGCGCTTTTATATAAATGCCGCAATAGGGATCG
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCGATA--GATAG
* ** *
546552 T--TTATAGTGGCGTTTTTCCACAAACGCCGTGATAGATTAG
1 TACTT-TAGCGGCGTTTTTATACAAACGCCGCGATAGA-TAG
546592 TACTTTAGCGGCGTTTTTATACAAA
1 TACTTTAGCGGCGTTTTTATACAAA
546617 TGCCACAAAA
Statistics
Matches: 80, Mismatches: 21, Indels: 13
0.70 0.18 0.11
Matches are distributed among these distances:
39 2 0.03
40 5 0.06
41 53 0.66
42 19 0.24
43 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (40 bp):
TACTTTAGCGGCGTTTTTATACAAACGCCGCGATAGATAG
Found at i:546676 original size:82 final size:82
Alignment explanation
Indices: 546473--546698 Score: 262
Period size: 82 Copynumber: 2.8 Consensus size: 82
546463 AACGATACTT
* * * *
546473 TAGTGGCGTTTCTT-AAACAAACGCCGCGATAGTATAGTACTTTAGCAGCGCTTTTATATAAATG
1 TAGTGGCGTTT-TTCCAACAAACGCCGCGATAGAATAGTACTTTAGC-GCGTTTTTATACAAATG
* * *
546537 CCGCAATAGGGATCGTTTA
64 CCACAAAAGGGATCGTTCA
* *
546556 TAGTGGCGTTTTTCC-ACAAACGCCGTGATAGATTAGTACTTTAGCGGCGTTTTTATACAAATGC
1 TAGTGGCGTTTTTCCAACAAACGCCGCGATAGAATAGTACTTTAGC-GCGTTTTTATACAAATGC
*
546620 CACAAAAGGGTTCGTTCA
65 CACAAAAGGGATCGTTCA
* * * * *
546638 TAGTGGCGTTTTTCCAACAAATGTCGCGATA-AAGAGTACTTTTGCG-TTTTTTATACAAATG
1 TAGTGGCGTTTTTCCAACAAACGCCGCGATAGAATAGTACTTTAGCGCGTTTTTATACAAATG
546699 TCGTAATAGG
Statistics
Matches: 123, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
80 14 0.11
81 1 0.01
82 85 0.69
83 23 0.19
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (82 bp):
TAGTGGCGTTTTTCCAACAAACGCCGCGATAGAATAGTACTTTAGCGCGTTTTTATACAAATGCC
ACAAAAGGGATCGTTCA
Found at i:547960 original size:16 final size:16
Alignment explanation
Indices: 547926--547967 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
547916 TCGTTCATTT
547926 AATAAAT-AA-ACGAA
1 AATAAATGAACACGAA
*
547940 CATAAATGAACACGAA
1 AATAAATGAACACGAA
*
547956 AATAAACGAACA
1 AATAAATGAACA
547968 AATTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 6 0.26
15 2 0.09
16 15 0.65
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (16 bp):
AATAAATGAACACGAA
Found at i:548047 original size:10 final size:10
Alignment explanation
Indices: 548032--548106 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
548022 CATTTAATAA
548032 ATAAACGAAC
1 ATAAACGAAC
548042 ATAAACGAAC
1 ATAAACGAAC
548052 ----ACGAAC
1 ATAAACGAAC
548058 ATAAACGAAC
1 ATAAACGAAC
** *
548068 ACGAAC-ATAA
1 ATAAACGA-AC
548078 ATGAACACGAAC
1 AT-AA-ACGAAC
548090 ATAAACGAAC
1 ATAAACGAAC
548100 ATAAACG
1 ATAAACG
548107 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:548057 original size:16 final size:16
Alignment explanation
Indices: 548036--548100 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
548026 TAATAAATAA
548036 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
548052 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
548068 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
548084 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
548100 A
1 A
548101 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:548348 original size:11 final size:11
Alignment explanation
Indices: 548308--548357 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
548298 AAAAATTAAG
*
548308 AGCTCGATTAA
1 AGCTCGATTCA
* *
548319 AACTCGATACTCG
1 AGCTCGAT--TCA
548332 AGCTCGATTCA
1 AGCTCGATTCA
548343 AGCTCGATTCA
1 AGCTCGATTCA
548354 AGCT
1 AGCT
548358 TGGCATTGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
11 24 0.75
13 8 0.25
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:548427 original size:16 final size:16
Alignment explanation
Indices: 548406--548438 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
548396 TCCCCATCTT
548406 CTTTTATATAAGTTGC
1 CTTTTATATAAGTTGC
548422 CTTTTATATAAGTTGC
1 CTTTTATATAAGTTGC
548438 C
1 C
548439 AACCCCGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48
Consensus pattern (16 bp):
CTTTTATATAAGTTGC
Found at i:548920 original size:14 final size:14
Alignment explanation
Indices: 548901--548947 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
548891 AATGAAACAT
*
548901 AAACGAGCATAACC
1 AAACGAACATAACC
*
548915 AAACGAACGTAACC
1 AAACGAACATAACC
*
548929 GAACGAACATAACC
1 AAACGAACATAACC
*
548943 GAACG
1 AAACG
548948 TTCACGAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.49, C:0.28, G:0.17, T:0.06
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:551968 original size:19 final size:19
Alignment explanation
Indices: 551946--552001 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
551936 TTCTATAATA
551946 TTAAAAATATAATTATGTT
1 TTAAAAATATAATTATGTT
* *
551965 TTAAAAAT-T-ATCTATAATA
1 TTAAAAATATAAT-TAT-GTT
551984 TT-AAAATATAATTATGTT
1 TTAAAAATATAATTATGTT
552002 CTACCTCCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 9
0.69 0.10 0.21
Matches are distributed among these distances:
17 2 0.07
18 10 0.34
19 15 0.52
20 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (19 bp):
TTAAAAATATAATTATGTT
Found at i:551999 original size:37 final size:38
Alignment explanation
Indices: 551927--552001 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
551917 ATTTTTTTAC
* *
551927 TTAAAATTTTTCTATAATATTAAAAATATAATTATGTT
1 TTAAAAATTATCTATAATATTAAAAATATAATTATGTT
551965 TTAAAAATTATCTATAATATT-AAAATATAATTATGTT
1 TTAAAAATTATCTATAATATTAAAAATATAATTATGTT
552002 CTACCTCCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 16 0.46
38 19 0.54
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (38 bp):
TTAAAAATTATCTATAATATTAAAAATATAATTATGTT
Found at i:553092 original size:110 final size:112
Alignment explanation
Indices: 552908--553118 Score: 345
Period size: 110 Copynumber: 1.9 Consensus size: 112
552898 GCTTACACGG
* * *
552908 TTGATGAAAACACATAAATTGAAATGGTAAGGAGAGAGAGAGAGTTGTTTGATTTTCTTTAAAAG
1 TTGATAAAAACACAGAAATTGAAAAGGTAAGGAGAGAGAGAGAGTTGTTTGATTTTCTTTAAAAG
552973 CTCTCATAAAAAGATAACCAAATAAGAAACAAATTTAGCTTACAAAA
66 CTCTCATAAAAAGATAACCAAATAAGAAACAAATTTAGCTTACAAAA
*
553020 TTGATAAAAACACAGAAATTGAAAAGGT-AGG-TAGAGAGAGAGTTGTTTGATTTTCTTTAAAAG
1 TTGATAAAAACACAGAAATTGAAAAGGTAAGGAGAGAGAGAGAGTTGTTTGATTTTCTTTAAAAG
* * *
553083 CTCTCATAAAAAGATGACCAAATAAGGAATAAATTT
66 CTCTCATAAAAAGATAACCAAATAAGAAACAAATTT
553119 GATGAAATAT
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
110 64 0.70
111 3 0.03
112 25 0.27
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (112 bp):
TTGATAAAAACACAGAAATTGAAAAGGTAAGGAGAGAGAGAGAGTTGTTTGATTTTCTTTAAAAG
CTCTCATAAAAAGATAACCAAATAAGAAACAAATTTAGCTTACAAAA
Found at i:554712 original size:57 final size:57
Alignment explanation
Indices: 554417--554692 Score: 435
Period size: 57 Copynumber: 4.8 Consensus size: 57
554407 ATGGCACTGA
* *
554417 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTTCGAATGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATGGGCACTTT
*
554474 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATGGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATGGGCACTTT
* * * * *
554531 GGGTGCAAAAAGTTAAGAAACTCATAATTTGTTTATGAATTTTCATATGGCCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATGGGCACTTT
* * * *
554588 GTGTGTAAAAAGTTAAGAAATTCATAATTTGTTTATTAATTTCCATATGGGTACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATGGGCACTTT
*
554645 GGGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTAT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTAT
554693 AAAAACTTTA
Statistics
Matches: 199, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 199 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (57 bp):
GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATGGGCACTTT
Found at i:555008 original size:68 final size:68
Alignment explanation
Indices: 554899--555574 Score: 1000
Period size: 68 Copynumber: 10.0 Consensus size: 68
554889 AGATTCATGA
*
554899 CCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGGCTTTG
1 CCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
554964 AGG
66 AGG
* * * *
554967 CCTAGTCGTGTATTTGACAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGGCTAAGTGCATTTG
1 CCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
*
555032 AGT
66 AGG
*
555035 CCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1 CCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
555100 AGG
66 AGG
* * * * **
555103 CCTAGCTATGTATTTGACAGAAATGTGTCAATTATGATAGTTAGATGAAAGGCTAAGTGCCTTTG
1 CCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
555168 AGG
66 AGG
* * * * *
555171 CATAGCTGTGCATTTGACA-AAATGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTTCCTTTG
1 CCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
555235 AGG
66 AGG
** * * *
555238 CCTAACTGTGCATTTGACAGAAAGGTTTCAATTATGCAAGTTATATGAAAGGCTAAGTGCCTTTG
1 CCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
555303 AGG
66 AGG
* *
555306 CATAGTTGTGCATTTGACAGAAAGGTGTCAATTATG-CAGTTAGATGAAAGGCTAAATGCCTTTG
1 CCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
555370 AGG
66 AGG
* * *
555373 CATA-TATGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAAGCTAAGTGCCTTT
1 CCTAGT-TGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
555437 GAGG
65 GAGG
* * *
555441 TCTAGTTGTGCATTTGAAAGAAAAGTGTCAATTATG-CAGTTAGATGAAAGGCTAAGTGCCTTTG
1 CCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
555505 AGG
66 AGG
* * * *
555508 CATAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTG
1 CCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
555573 AG
66 AG
555575 TAAAAGATTA
Statistics
Matches: 549, Mismatches: 54, Indels: 10
0.90 0.09 0.02
Matches are distributed among these distances:
66 1 0.00
67 184 0.34
68 363 0.66
69 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.31
Consensus pattern (68 bp):
CCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
AGG
Found at i:555269 original size:135 final size:136
Alignment explanation
Indices: 554901--555574 Score: 982
Period size: 135 Copynumber: 5.0 Consensus size: 136
554891 ATTCATGACC
*
554901 TAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGGCTTTGAG
1 TAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
* * * *
554966 GCCT-AGTCGTGTATTTGACAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGGCTAAGTGCATT
66 GCCTAACT-GTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
* *
555030 TGAGTCC
130 TGAGGCA
*
555037 TAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
1 TAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
* * * * **
555102 GCCTAGCTATGTATTTGACAGAAATGTGTCAATTATGATAGTTAGATGAAAGGCTAAGTGCCTTT
66 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
555167 GAGGCA
131 GAGGCA
* * * *
555173 TAGCTGTGCATTTGACA-AAATGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTTCCTTTGAG
1 TAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
* * *
555237 GCCTAACTGTGCATTTGACAGAAAGGTTTCAATTATGCAAGTTATATGAAAGGCTAAGTGCCTTT
66 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
555302 GAGGCA
131 GAGGCA
*
555308 TAGTTGTGCATTTGACAGAAAGGTGTCAATTATG-CAGTTAGATGAAAGGCTAAATGCCTTTGAG
1 TAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
* * *
555372 GCATATA-TGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAAGCTAAGTGCCTT
66 GCCTA-ACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
555436 TGAGGTC-
130 TGAGG-CA
* *
555443 TAGTTGTGCATTTGAAAGAAAAGTGTCAATTATG-CAGTTAGATGAAAGGCTAAGTGCCTTTGAG
1 TAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
* ** * * *
555507 GCATAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTT
66 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
555572 GAG
131 GAG
555575 TAAAAGATTA
Statistics
Matches: 490, Mismatches: 43, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
135 334 0.68
136 155 0.32
137 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.31
Consensus pattern (136 bp):
TAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
GAGGCA
Found at i:555293 original size:203 final size:202
Alignment explanation
Indices: 554901--555574 Score: 1003
Period size: 203 Copynumber: 3.3 Consensus size: 202
554891 ATTCATGACC
* *
554901 TAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGGCTTTGAG
1 TAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAG
* * * * *
554966 GCCTAGTCGTGTATTTGACAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGGCTAAGTGCATTT
66 GCATAGT-GTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCTTT
* *
555031 GAGTCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
130 GAGGCCTAGTTGTGCATTTGACAGAAAAGTGTCAATTATG-CAGTTAGATGAAAGGCTAAGTGCC
*
555096 TTTGAGGCC
194 TTTGAGGCA
* * * * ** *
555105 TAGCTATGTATTTGACAGAAATGTGTCAATTATGATAGTTAGATGAAAGGCTAAGTGCCTTTGAG
1 TAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAG
* *
555170 GCATAGCTGTGCATTTGACA-AAATGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTTCCTTT
66 GCATAG-TGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCTTT
** * * *
555234 GAGGCCTAACTGTGCATTTGACAGAAAGGTTTCAATTATGCAAGTTATATGAAAGGCTAAGTGCC
130 GAGGCCTAGTTGTGCATTTGACAGAAAAGTGTCAATTATGC-AGTTAGATGAAAGGCTAAGTGCC
555299 TTTGAGGCA
194 TTTGAGGCA
555308 TAGTTGTGCATTTGACAGAAAGGTGTCAATTATG-CAGTTAGATGAAAGGCTAAATGCCTTTGAG
1 TAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAG
* *
555372 GCATATATGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAA-AGCTAAGTGCCTT
66 GCATA-GTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGA-CTAAGTGCCTT
* *
555436 TGAGGTCTAGTTGTGCATTTGAAAGAAAAGTGTCAATTATGCAGTTAGATGAAAGGCTAAGTGCC
129 TGAGGCCTAGTTGTGCATTTGACAGAAAAGTGTCAATTATGCAGTTAGATGAAAGGCTAAGTGCC
555501 TTTGAGGCA
194 TTTGAGGCA
* *
555510 TAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAG
1 TAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAG
555575 TAAAAGATTA
Statistics
Matches: 424, Mismatches: 40, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
202 112 0.26
203 237 0.56
204 74 0.17
205 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.31
Consensus pattern (202 bp):
TAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAG
GCATAGTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCTTTG
AGGCCTAGTTGTGCATTTGACAGAAAAGTGTCAATTATGCAGTTAGATGAAAGGCTAAGTGCCTT
TGAGGCA
Found at i:555810 original size:45 final size:46
Alignment explanation
Indices: 555696--555818 Score: 194
Period size: 47 Copynumber: 2.7 Consensus size: 46
555686 ACGTTGTACC
* *
555696 AAAGGAATGAAATGATGCCATAAATGAAATATATAATAGCGTATAA
1 AAAGGCATGAAATGATGCCATAAATGAAATGTATAATAGCGTATAA
* *
555742 AAAGGGCATGAAAGGATGGCATAAATGAAATGTATAATAGCGTAT-A
1 AAA-GGCATGAAATGATGCCATAAATGAAATGTATAATAGCGTATAA
555788 AAAGGCATGAAATGATGCCATAAATGAAATG
1 AAAGGCATGAAATGATGCCATAAATGAAATG
555819 CATATGGGTT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
45 26 0.37
46 7 0.10
47 37 0.53
ACGTcount: A:0.49, C:0.07, G:0.22, T:0.22
Consensus pattern (46 bp):
AAAGGCATGAAATGATGCCATAAATGAAATGTATAATAGCGTATAA
Found at i:555855 original size:45 final size:45
Alignment explanation
Indices: 555801--555913 Score: 172
Period size: 45 Copynumber: 2.5 Consensus size: 45
555791 GGCATGAAAT
*
555801 GATGCCATAAATGAAATGCATATGGGTTCATTATTGGCACAAAAG
1 GATGCCATAAATGAAATGCATATGGGTGCATTATTGGCACAAAAG
* * *
555846 GATGTCATAATTGAAATGCATATGGGTGCATTATTGGCATAAAAG
1 GATGCCATAAATGAAATGCATATGGGTGCATTATTGGCACAAAAG
*
555891 AATGCCATAAATGAAAATGCATA
1 GATGCCATAAATG-AAATGCATA
555914 ATAACGCATT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
45 51 0.85
46 9 0.15
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (45 bp):
GATGCCATAAATGAAATGCATATGGGTGCATTATTGGCACAAAAG
Found at i:559049 original size:24 final size:24
Alignment explanation
Indices: 558980--559049 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
558970 AATCTTATAT
*
558980 GGCACTACGGTGC-ATTTCTACGC
1 GGCACTTCGGTGCAATTTCTACGC
* *
559003 GGCACTTCGGTGCAAATTCTACGT
1 GGCACTTCGGTGCAATTTCTACGC
* *
559027 GGCATTTCGGTGCAATTTATACG
1 GGCACTTCGGTGCAATTTCTACG
559050 AGTTGTGGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 12 0.30
24 28 0.70
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (24 bp):
GGCACTTCGGTGCAATTTCTACGC
Found at i:564897 original size:16 final size:17
Alignment explanation
Indices: 564865--564898 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
564855 ATAAAGGTGT
564865 ATATGTGAAATAATATG
1 ATATGTGAAATAATATG
*
564882 ATATGTGATA-AATATG
1 ATATGTGAAATAATATG
564898 A
1 A
564899 AAAAATAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (17 bp):
ATATGTGAAATAATATG
Found at i:564999 original size:24 final size:24
Alignment explanation
Indices: 564965--565032 Score: 127
Period size: 24 Copynumber: 2.8 Consensus size: 24
564955 GAGTAGAGGG
*
564965 TCTACGCGGTCCTTCGGGACAAAT
1 TCTACGTGGTCCTTCGGGACAAAT
564989 TCTACGTGGTCCTTCGGGACAAAT
1 TCTACGTGGTCCTTCGGGACAAAT
565013 TCTACGTGGTCCTTCGGGAC
1 TCTACGTGGTCCTTCGGGAC
565033 GTATATGTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (24 bp):
TCTACGTGGTCCTTCGGGACAAAT
Found at i:566695 original size:57 final size:57
Alignment explanation
Indices: 566615--566796 Score: 285
Period size: 57 Copynumber: 3.2 Consensus size: 57
566605 ATGGCACTAA
566615 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTTCGTATGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTTCGTATGGGCACTTT
* *
566672 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATGGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTTCGTATGGGCACTTT
* ** *
566729 GGGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAA-TTTCTGTATAAGAACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTTC-GTATGGGCACTTT
*
566786 ATGTGCAAAAA
1 GTGTGCAAAAA
566797 CTATGAAATA
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
56 3 0.03
57 111 0.97
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (57 bp):
GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTTCGTATGGGCACTTT
Found at i:567073 original size:68 final size:68
Alignment explanation
Indices: 566964--567293 Score: 525
Period size: 68 Copynumber: 4.9 Consensus size: 68
566954 TCATGGCCTA
* * * *
566964 GCATTTGACAGAAATGTATCAATTATGCTAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAGT
1 GCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAGC
567029 TGT
66 TGT
* * *
567032 GCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGTCTTTGAGGCTTAGT
1 GCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAGC
567097 TGT
66 TGT
* * *
567100 GCATTTGACAGAAATGTGTCAATTATGCTAGTCAGATGAAAGGCTAAGTGCCTTTGAGGCCTAGC
1 GCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAGC
*
567165 TAT
66 TGT
567168 GCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAGC
1 GCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAGC
567233 TGT
66 TGT
* * * *
567236 ACATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAG
1 GCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
567294 TAAAAGATTA
Statistics
Matches: 242, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 242 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (68 bp):
GCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAGC
TGT
Found at i:567561 original size:46 final size:46
Alignment explanation
Indices: 567394--567613 Score: 345
Period size: 47 Copynumber: 4.8 Consensus size: 46
567384 GCATAACGTT
* *
567394 GTATCAAA-GGCATGAAAGGATGCCATAAATGAAATGTATAATAGC
1 GTATAAAAGGGCATGAAAGGATGTCATAAATGAAATGTATAATAGC
*
567439 GTATAAAAAGGGCATGAAAGGATGTCATAAATGAAATGTATAATAGT
1 GTAT-AAAAGGGCATGAAAGGATGTCATAAATGAAATGTATAATAGC
* *
567486 GTATAAAAAGGGCATGAAAAGATGCCATAAATGAAATGTATAATAGC
1 GTAT-AAAAGGGCATGAAAGGATGTCATAAATGAAATGTATAATAGC
*
567533 GTATAAAAGGGCATGAAAGGATGTCATAAATGAAATGTATAATAAC
1 GTATAAAAGGGCATGAAAGGATGTCATAAATGAAATGTATAATAGC
*
567579 GTATAAAA-TGCATGAAAGGATGTCATAAATGAAAT
1 GTATAAAAGGGCATGAAAGGATGTCATAAATGAAAT
567614 ACATATGGGT
Statistics
Matches: 163, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
45 30 0.18
46 50 0.31
47 83 0.51
ACGTcount: A:0.47, C:0.07, G:0.22, T:0.24
Consensus pattern (46 bp):
GTATAAAAGGGCATGAAAGGATGTCATAAATGAAATGTATAATAGC
Found at i:567566 original size:93 final size:92
Alignment explanation
Indices: 567394--567613 Score: 361
Period size: 93 Copynumber: 2.4 Consensus size: 92
567384 GCATAACGTT
*
567394 GTATCAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGCGTATAAAAAGGGCATGAAAG
1 GTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGCGTATAAAAAGGGCATGAAAG
**
567459 GATGTCATAAATGAAATGTATAATAGT
66 GATGTCATAAATGAAATGTATAATAAC
*
567486 GTATAAAAAGGGCATGAAAAGATGCCATAAATGAAATGTATAATAGCGTAT-AAAAGGGCATGAA
1 GTAT-AAAA-GGCATGAAAGGATGCCATAAATGAAATGTATAATAGCGTATAAAAAGGGCATGAA
567550 AGGATGTCATAAATGAAATGTATAATAAC
64 AGGATGTCATAAATGAAATGTATAATAAC
* *
567579 GTATAAAATGCATGAAAGGATGTCATAAATGAAAT
1 GTATAAAAGGCATGAAAGGATGCCATAAATGAAAT
567614 ACATATGGGT
Statistics
Matches: 119, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
91 24 0.20
92 8 0.07
93 47 0.39
94 40 0.34
ACGTcount: A:0.47, C:0.07, G:0.22, T:0.24
Consensus pattern (92 bp):
GTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGCGTATAAAAAGGGCATGAAAG
GATGTCATAAATGAAATGTATAATAAC
Found at i:567696 original size:45 final size:45
Alignment explanation
Indices: 567592--567707 Score: 126
Period size: 45 Copynumber: 2.6 Consensus size: 45
567582 TAAAATGCAT
* * *
567592 GAAAGGATGTCATAAATGAAATACATATGGGTGCACTATTCGTAC
1 GAAAGGATGACATAAATGAAATGCATATGGGTGCACTATTCGCAC
* * * *
567637 GAAAGGATGACATAATTGAAATGCATATGGGTGCATTATTGGCAT
1 GAAAGGATGACATAAATGAAATGCATATGGGTGCACTATTCGCAC
**
567682 G-AAGGAATTCCATAAATGAAAATGCA
1 GAAAGG-ATGACATAAATG-AAATGCA
567708 GAATATCGCA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
44 4 0.07
45 48 0.81
46 7 0.12
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (45 bp):
GAAAGGATGACATAAATGAAATGCATATGGGTGCACTATTCGCAC
Found at i:571553 original size:2 final size:2
Alignment explanation
Indices: 571546--571582 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
571536 ATTTAAAAAT
571546 TA TA TA TA TA TA TA TA TA TA TA -A 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
571583 AATCAGGTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:572450 original size:2 final size:2
Alignment explanation
Indices: 572443--572473 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
572433 GTATTTTTAG
572443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
572474 TATTTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:573038 original size:60 final size:60
Alignment explanation
Indices: 572877--573040 Score: 247
Period size: 60 Copynumber: 2.7 Consensus size: 60
572867 AACTCTTATT
*
572877 TAAATTAGTCCTTAAACTTTTGAATATTCTAATTTTATCCCCAAATTATGACCCTCATTC
1 TAAATTAGTCCTTAAACTTTTGAATATTCTAATTTTATCCCTAAATTATGACCCTCATTC
* * * ** * *
572937 TACATTAGTCCTTAAATTTTTCAGCATTCTAATTTCATCCCTAAATTATGACCCTCTTTC
1 TAAATTAGTCCTTAAACTTTTGAATATTCTAATTTTATCCCTAAATTATGACCCTCATTC
*
572997 TAAATTAGTTCTTAAACTTTTGAATATTCTAATTTTATCCCTAA
1 TAAATTAGTCCTTAAACTTTTGAATATTCTAATTTTATCCCTAA
573041 TTAATCCAAA
Statistics
Matches: 89, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 89 1.00
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (60 bp):
TAAATTAGTCCTTAAACTTTTGAATATTCTAATTTTATCCCTAAATTATGACCCTCATTC
Found at i:575493 original size:2 final size:2
Alignment explanation
Indices: 575488--575534 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
575478 GAGTCAAAAA
575488 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
575530 AT AT A
1 AT AT A
575535 AATAATAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:576986 original size:16 final size:16
Alignment explanation
Indices: 576965--576996 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
576955 TCGTTAAGAA
*
576965 CTCGAGTCGAGTCGAG
1 CTCGAGTCCAGTCGAG
576981 CTCGAGTCCAGTCGAG
1 CTCGAGTCCAGTCGAG
576997 TCCATTCGAT
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:0.19, C:0.28, G:0.34, T:0.19
Consensus pattern (16 bp):
CTCGAGTCCAGTCGAG
Found at i:579038 original size:45 final size:45
Alignment explanation
Indices: 578964--579101 Score: 199
Period size: 44 Copynumber: 3.1 Consensus size: 45
578954 CATTTCTTAT
* * * *
578964 CAATCTACTTACTATTTATCCCA-AAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTAC
579008 CAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTAC
* * *
579053 CAATACACTTGCCA-TTGTTCCATAAGTTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTAC
579097 CAATA
1 CAATA
579102 CTTGCCATTG
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
44 53 0.62
45 33 0.38
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (45 bp):
CAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:579102 original size:44 final size:43
Alignment explanation
Indices: 578987--579115 Score: 206
Period size: 44 Copynumber: 3.0 Consensus size: 43
578977 ATTTATCCCA
*
578987 AAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTTCCAT
1 AAGCTCGTAAGCTTATTTTACCAATA-ACTTGCCA-TTGTTCCAT
579032 AAGCTCGTAAGCTTATTTTACCAATACACTTGCCATTGTTCCAT
1 AAGCTCGTAAGCTTATTTTACCAATA-ACTTGCCATTGTTCCAT
*
579076 AAGTTCGTAAGCTTATTTTACCAAT-ACTTGCCATTGTTCC
1 AAGCTCGTAAGCTTATTTTACCAATAACTTGCCATTGTTCC
579116 TAAACCATAT
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
42 15 0.19
44 33 0.41
45 33 0.41
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (43 bp):
AAGCTCGTAAGCTTATTTTACCAATAACTTGCCATTGTTCCAT
Done.