Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000096.1 Hibiscus syriacus cultivar Beakdansim tig00000179_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: 70440
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:6575 original size:55 final size:55
Alignment explanation
Indices: 6489--6594 Score: 194
Period size: 55 Copynumber: 1.9 Consensus size: 55
6479 TTTTTTTTCT
*
6489 TATCTATGTTTTTTCACCACCCTATATTCATGTACTTGAAAATGTGTTGGAACTA
1 TATCTATGTTTTTTCACCACCCTATAATCATGTACTTGAAAATGTGTTGGAACTA
*
6544 TATCTATGTTTTTTCACCACCCTATAATCATGTACTTGAGAATGTGTTGGA
1 TATCTATGTTTTTTCACCACCCTATAATCATGTACTTGAAAATGTGTTGGA
6595 GCTTGGAACT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (55 bp):
TATCTATGTTTTTTCACCACCCTATAATCATGTACTTGAAAATGTGTTGGAACTA
Found at i:12560 original size:35 final size:35
Alignment explanation
Indices: 12521--12653 Score: 178
Period size: 35 Copynumber: 3.8 Consensus size: 35
12511 AGATGAACAA
12521 TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCAC
* * * *
12556 TTGAATCGAAAGTGCTGATGTTTCATTTCGTTCTTC
1 TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTC-AC
*
12592 TTGAATCGAAAGTG-TCGATGCTTCCTTCCATTCAC
1 TTGAATCGAAAGTGCT-GATGCTTCCTTCCGTTCAC
* *
12627 TTGAATCAAAAGTGCCGATGCTTCCTT
1 TTGAATCGAAAGTGCTGATGCTTCCTT
12654 TCATTATTCT
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
35 56 0.67
36 28 0.33
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.37
Consensus pattern (35 bp):
TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCAC
Found at i:12639 original size:71 final size:71
Alignment explanation
Indices: 12521--12664 Score: 209
Period size: 71 Copynumber: 2.0 Consensus size: 71
12511 AGATGAACAA
* * * * *
12521 TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCTGATGTTTCATTTCG
1 TTGAATCGAAAGTGCTGATGCTTCCTTCCATTCACTTGAATCAAAAGTGCCGATGCTTCATTTCA
*
12586 TTCTTC
66 TTATTC
*
12592 TTGAATCGAAAGTG-TCGATGCTTCCTTCCATTCACTTGAATCAAAAGTGCCGATGCTTCCTTTC
1 TTGAATCGAAAGTGCT-GATGCTTCCTTCCATTCACTTGAATCAAAAGTGCCGATGCTTCATTTC
12656 ATTATTC
65 ATTATTC
12663 TT
1 TT
12665 ATTAACCTTC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 1 0.02
71 64 0.98
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (71 bp):
TTGAATCGAAAGTGCTGATGCTTCCTTCCATTCACTTGAATCAAAAGTGCCGATGCTTCATTTCA
TTATTC
Found at i:15525 original size:59 final size:59
Alignment explanation
Indices: 15433--15549 Score: 216
Period size: 59 Copynumber: 2.0 Consensus size: 59
15423 AGAGTTCATC
*
15433 TTAATTTATTATACTGGACATGTATATTCATTAACCTTGCATCATATTTCAATCAATAT
1 TTAATCTATTATACTGGACATGTATATTCATTAACCTTGCATCATATTTCAATCAATAT
*
15492 TTAATCTATTATATTGGACATGTATATTCATTAACCTTGCATCATATTTCAATCAATA
1 TTAATCTATTATACTGGACATGTATATTCATTAACCTTGCATCATATTTCAATCAATA
15550 AATTTATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (59 bp):
TTAATCTATTATACTGGACATGTATATTCATTAACCTTGCATCATATTTCAATCAATAT
Found at i:19879 original size:14 final size:14
Alignment explanation
Indices: 19840--19881 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
19830 TTTTAGTTAG
19840 CTTTATTTTTACTGT
1 CTTTATTTTT-CTGT
19855 CTTTAATTTTTCT-T
1 CTTT-ATTTTTCTGT
19869 CATTTATTTTTCT
1 C-TTTATTTTTCT
19882 AGGTACATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 10 0.40
15 9 0.36
16 6 0.24
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.69
Consensus pattern (14 bp):
CTTTATTTTTCTGT
Found at i:21580 original size:78 final size:78
Alignment explanation
Indices: 21468--21684 Score: 343
Period size: 78 Copynumber: 2.8 Consensus size: 78
21458 ACCGTTGAAC
*
21468 AGGGGGGAATCGGTACC-CCT-T-GGGGGGGAATCGGTTCCCTCTGAGCATACTGGAATTCTCGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGGAATCGGTTCCCTCTGAGCATACTGGAATTCTCGG
21530 AACAAAAATGTTT
66 AACAAAAATGTTT
*
21543 AGGGGGGAATCGGTTCCTCCTATGGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGGAATCGGTTCCCTCTGAGCATACTGGAATTCTCGG
21608 AACAAAAATGTTT
66 AACAAAAATGTTT
21621 AGGGGGGAATCGGTTCCTCCTATGGGGGGGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 AGGGGGGAATCGGTTCCTCCTAT----GGGGGGGGAATCGGTTCCCTCTGAGCATA-CTGGAATT
21685 TTTGGCTTTG
Statistics
Matches: 131, Mismatches: 3, Indels: 9
0.92 0.02 0.06
Matches are distributed among these distances:
75 16 0.12
76 3 0.02
77 1 0.01
78 76 0.58
81 1 0.01
82 34 0.26
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.24
Consensus pattern (78 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGGGAATCGGTTCCCTCTGAGCATACTGGAATTCTCGG
AACAAAAATGTTT
Found at i:24312 original size:21 final size:20
Alignment explanation
Indices: 24282--24340 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
24272 AGAACCCCAT
* *
24282 GGGGGTATCGATTCCC-CTG
1 GGGGGGATCGATTCCCTCAG
*
24301 TGGGGGGAATCGGTTCCCTCAG
1 -GGGGGG-ATCGATTCCCTCAG
24323 GGGGGGATCGATTCCCTC
1 GGGGGGATCGATTCCCTC
24341 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 16 0.48
21 15 0.45
22 2 0.06
ACGTcount: A:0.12, C:0.25, G:0.39, T:0.24
Consensus pattern (20 bp):
GGGGGGATCGATTCCCTCAG
Found at i:30212 original size:78 final size:78
Alignment explanation
Indices: 30097--30309 Score: 380
Period size: 78 Copynumber: 2.8 Consensus size: 78
30087 ACCGTTGAAC
30097 AGGGGGGAATCGGTTCC-CCT-T-GGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGG
30159 AACAAAAATGTTT
66 AACAAAAATGTTT
30172 AGGGGGGAATCGGTTCCTCCTATGGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGG
30237 AACAAAAATGTTT
66 AACAAAAATGTTT
*
30250 AGGGGGGAATCGGTTCCTCCTATGGGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGGAATCGGTTCCCTCCGAGCATA-CTGGAATT
30310 TTTGGCTTTG
Statistics
Matches: 133, Mismatches: 1, Indels: 5
0.96 0.01 0.04
Matches are distributed among these distances:
75 17 0.13
76 3 0.02
77 2 0.02
78 111 0.83
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (78 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGG
AACAAAAATGTTT
Found at i:38491 original size:8 final size:9
Alignment explanation
Indices: 38471--38502 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
38461 AAGTGGACAC
38471 TTTTTGGAT
1 TTTTTGGAT
38480 TTTTTGGAT
1 TTTTTGGAT
38489 TTTTTGGAT
1 TTTTTGGAT
38498 TTTTT
1 TTTTT
38503 ATGGTTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.09, C:0.00, G:0.19, T:0.72
Consensus pattern (9 bp):
TTTTTGGAT
Found at i:38716 original size:50 final size:50
Alignment explanation
Indices: 38654--38764 Score: 195
Period size: 50 Copynumber: 2.2 Consensus size: 50
38644 CCTTCCATAT
*
38654 TCTTCCATAAGGTTCCACACATCTCCAGAATATTCCAGAGGAGTCCACAC
1 TCTTCCACAAGGTTCCACACATCTCCAGAATATTCCAGAGGAGTCCACAC
* *
38704 TCTTCCACAAGGTTCCACACATCTCCAGAATATTTCAGAGGATTCCACAC
1 TCTTCCACAAGGTTCCACACATCTCCAGAATATTCCAGAGGAGTCCACAC
38754 TCTTCCACAAG
1 TCTTCCACAAG
38765 CTTCTAGAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.30, C:0.32, G:0.13, T:0.25
Consensus pattern (50 bp):
TCTTCCACAAGGTTCCACACATCTCCAGAATATTCCAGAGGAGTCCACAC
Found at i:41472 original size:9 final size:9
Alignment explanation
Indices: 41458--41488 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
41448 TACCCTTTAT
41458 GGGTTGTAA
1 GGGTTGTAA
41467 GGGTTGTAA
1 GGGTTGTAA
41476 GGGTTGTAA
1 GGGTTGTAA
41485 GGGT
1 GGGT
41489 GAAAGCACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.48, T:0.32
Consensus pattern (9 bp):
GGGTTGTAA
Found at i:43939 original size:2 final size:2
Alignment explanation
Indices: 43932--43995 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
43922 GTAATTATGA
43932 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
43974 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
43996 GAGGATTATC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47786 original size:24 final size:24
Alignment explanation
Indices: 47751--47820 Score: 95
Period size: 24 Copynumber: 2.8 Consensus size: 24
47741 GTGAAGGTGG
47751 TAAACTGATTGTAGCTAAAAATAA
1 TAAACTGATTGTAGCTAAAAATAA
*
47775 TAAACTGGTTGTAGCTAAAAATAAGA
1 TAAACTGATTGTAGCTAAAAAT-A-A
* *
47801 AAAATTGATTGTAGCTAAAA
1 TAAACTGATTGTAGCTAAAA
47821 GAAACAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 21 0.52
25 1 0.03
26 18 0.45
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.29
Consensus pattern (24 bp):
TAAACTGATTGTAGCTAAAAATAA
Found at i:53739 original size:17 final size:18
Alignment explanation
Indices: 53705--53737 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
53695 TTTTGTTTGT
53705 AATTTATTTAAGTATTTA
1 AATTTATTTAAGTATTTA
53723 AATTT-TTTAA-TATTT
1 AATTTATTTAAGTATTT
53738 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
AATTTATTTAAGTATTTA
Found at i:55001 original size:21 final size:20
Alignment explanation
Indices: 54968--55006 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
54958 TAGATTTAAT
54968 TAAAATTTATAACTCATAAC
1 TAAAATTTATAACTCATAAC
*
54988 TAAATATTTTTAACTCATA
1 TAAA-ATTTATAACTCATA
55007 TTACAACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAATTTATAACTCATAAC
Found at i:65500 original size:5 final size:5
Alignment explanation
Indices: 65476--65641 Score: 66
Period size: 5 Copynumber: 33.8 Consensus size: 5
65466 ATAAAAAGTC
* * ***
65476 AAAAG AAAAT -AAAT ACAAAT AAAAT ATAAAT -AAAT AATAT CGTGAT
1 AAAAT AAAAT AAAAT A-AAAT AAAAT A-AAAT AAAAT AAAAT -AAAAT
* * *
65522 AATAAT AAAAT -AAAT AAGAT AAAAAT AAAAT AATAT AATGAA- AAAAA
1 AA-AAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AA--AAT AAAAT
* ** * *
65569 AAAAT GAAAT AAAAT AAAAT AGTTAT ATAA- AAAAT AAAAT -AAAT AATA-
1 AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT
65617 AAAAT -AAA- AAAAT -AAAT -AAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
65642 AGGACTAATA
Statistics
Matches: 122, Mismatches: 21, Indels: 36
0.68 0.12 0.20
Matches are distributed among these distances:
4 38 0.31
5 59 0.48
6 24 0.20
7 1 0.01
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:65543 original size:9 final size:9
Alignment explanation
Indices: 65525--65641 Score: 75
Period size: 9 Copynumber: 12.8 Consensus size: 9
65515 TCGTGATAAT
65525 AATAAAATA
1 AATAAAATA
*
65534 AATAAGATAAA
1 AATAA-A-ATA
65545 AATAAAAT-
1 AATAAAATA
*
65553 AATATAATGA
1 AATAAAAT-A
*
65563 AA-AAAAAA
1 AATAAAATA
*
65571 AATGAAATAA
1 AATAAAAT-A
65581 AATAAAATA
1 AATAAAATA
*
65590 GTTATATAAA-A
1 --AATA-AAATA
65601 AATAAAATA
1 AATAAAATA
65610 AATAATAA-A
1 AATAA-AATA
65619 AATAAAA-A
1 AATAAAATA
65627 AAT-AAATA
1 AATAAAATA
65635 AATAAAA
1 AATAAAA
65642 AGGACTAATA
Statistics
Matches: 85, Mismatches: 10, Indels: 26
0.70 0.08 0.21
Matches are distributed among these distances:
7 3 0.04
8 23 0.27
9 31 0.36
10 14 0.16
11 11 0.13
12 3 0.04
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AATAAAATA
Found at i:65579 original size:42 final size:41
Alignment explanation
Indices: 65492--65587 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 41
65482 AAATAAATAC
* ** * *
65492 AAATAAAATATAAATAAATAATATCGTGATAATAATAAAAT
1 AAATAAAATAAAAATAAATAATATAATGATAAAAAAAAAAT
*
65533 AAATAAGATAAAAATAAAATAATATAATGA-AAAAAAAAAAT
1 AAATAAAATAAAAAT-AAATAATATAATGATAAAAAAAAAAT
65574 GAAATAAAATAAAA
1 -AAATAAAATAAAA
65588 TAGTTATATA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
41 22 0.48
42 24 0.52
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (41 bp):
AAATAAAATAAAAATAAATAATATAATGATAAAAAAAAAAT
Found at i:65580 original size:21 final size:20
Alignment explanation
Indices: 65528--65587 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
65518 TGATAATAAT
*
65528 AAAATAAATAAGATAAAAAT
1 AAAATAAATAAGATAAAAAA
65548 AAAATAATATAATGA-AAAAAA
1 AAAATAA-ATAA-GATAAAAAA
*
65569 AAAATGAAATAAAATAAAA
1 AAAAT-AAATAAGATAAAA
65588 TAGTTATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 8 0.24
21 22 0.65
22 4 0.12
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAATAAATAAGATAAAAAA
Found at i:65653 original size:56 final size:56
Alignment explanation
Indices: 65520--65641 Score: 153
Period size: 56 Copynumber: 2.2 Consensus size: 56
65510 TAATATCGTG
* * *
65520 ATAATAATAAAATAAATAAGAT-AAAAATAAAATAATATAATGAAAAAAAAAAATGAA
1 ATAA-AATAAAAT-AGTAATATAAAAAATAAAATAATATAATAAAAAAAAAAAATGAA
*
65577 ATAAAATAAAATAGTTATATAAAAAATAAAATAA-ATAATAAAAATAAAAAAAT-AA
1 ATAAAATAAAATAGTAATATAAAAAATAAAATAATATAATAAAAA-AAAAAAATGAA
65632 AT-AAATAAAA
1 ATAAAATAAAA
65642 AGGACTAATA
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
54 8 0.14
55 18 0.31
56 29 0.49
57 4 0.07
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (56 bp):
ATAAAATAAAATAGTAATATAAAAAATAAAATAATATAATAAAAAAAAAAAATGAA
Found at i:66443 original size:16 final size:15
Alignment explanation
Indices: 66417--66446 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
66407 ATGTGTGACC
66417 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
66432 GGTCAGTCCCGGGAT
1 GGTCA-TCCCGGGAT
66447 AACGGCCGGC
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:66770 original size:29 final size:27
Alignment explanation
Indices: 66681--66780 Score: 83
Period size: 29 Copynumber: 3.4 Consensus size: 27
66671 ATTCCAAAAT
66681 ATATATATATATATTTCAAAATATTTTTTAAA
1 ATATAT-TATAT-TTTCAAAATA---TTTAAA
* * * *
66713 TTATATTATATTTTAAAAAAATTCCAAA
1 ATATATTATATTTTCAAAATATT-TAAA
66741 ACTATATTATATTTTCAAAATGATTTAAA
1 A-TATATTATATTTTCAAAAT-ATTTAAA
*
66770 AAATATTATAT
1 ATATATTATAT
66781 AAGTTTTCAA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
27 2 0.04
28 12 0.21
29 21 0.38
30 11 0.20
31 5 0.09
32 5 0.09
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (27 bp):
ATATATTATATTTTCAAAATATTTAAA
Found at i:66807 original size:35 final size:36
Alignment explanation
Indices: 66757--66979 Score: 178
Period size: 35 Copynumber: 6.1 Consensus size: 36
66747 TTATATTTTC
*
66757 AAAATGATTTAAAAA-ATATTATATAAGTTTTCAAA
1 AAAATGTTTTAAAAATATATTATATAAGTTTTCAAA
66792 AAAATGTTTTCAAAAACTATATATTATATAAGTTTTCAAA
1 AAAATGTTTT--AAAA--ATATATTATATAAGTTTTCAAA
* *
66832 AAGA--TTTTAAAAACTATATTATATATA-TTTTC--T
1 AAAATGTTTTAAAAA-TATATTATATA-AGTTTTCAAA
*
66865 AAAATGTTTTAAAAACTATATTATGT-AGTTTTC--A
1 AAAATGTTTTAAAAA-TATATTATATAAGTTTTCAAA
66899 AAAATGTTTTAAAAATATTATTATATACA-TTTTCAAA
1 AAAATGTTTTAAAAATA-TATTATATA-AGTTTTCAAA
** * *
66936 AATGTTTTTTAAAACCTATATATTATATACGTTTTTTCAAA
1 AAAATGTTTTAAAA---ATATATTATATAAG--TTTTCAAA
66977 AAA
1 AAA
66980 CCGTTTGCAA
Statistics
Matches: 155, Mismatches: 12, Indels: 36
0.76 0.06 0.18
Matches are distributed among these distances:
33 6 0.04
34 28 0.18
35 49 0.32
36 6 0.04
37 16 0.10
38 4 0.03
39 10 0.06
40 26 0.17
41 10 0.06
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (36 bp):
AAAATGTTTTAAAAATATATTATATAAGTTTTCAAA
Found at i:66876 original size:108 final size:103
Alignment explanation
Indices: 66743--66964 Score: 274
Period size: 106 Copynumber: 2.1 Consensus size: 103
66733 ATTCCAAAAC
66743 TATAT-TATATTTTCAAAATGATTTAAAAA-ATATTATATAAGTTTTCAAAAAAATGTTTTCAAA
1 TATATATATATTTTCAAAATGATTTAAAAACATATTATAT-AGTTTTC--AAAAATGTTTT-AAA
66806 AACTATATATTATATA-AGTTTTCAAAAA-G-ATTTTAAAAACTA
62 AA-TAT-TATTATATACA-TTTTCAAAAATGTATTTTAAAAACTA
* *
66848 TATTATATATATTTTCTAAAATGTTTTAAAAACTATATTATGTAGTTTTCAAAAATGTTTTAAAA
1 TA-TATATATATTTTC-AAAATGATTTAAAAAC-ATATTATATAGTTTTCAAAAATGTTTTAAAA
* *
66913 ATATTATTATATACATTTTCAAAAATGTTTTTTAAAACCTA
63 ATATTATTATATACATTTTCAAAAATGTATTTTAAAAACTA
66954 TATATTATATA
1 TATA-TATATA
66965 CGTTTTTTCA
Statistics
Matches: 104, Mismatches: 4, Indels: 17
0.83 0.03 0.14
Matches are distributed among these distances:
104 19 0.18
105 9 0.09
106 27 0.26
107 20 0.19
108 14 0.13
109 7 0.07
110 8 0.08
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.45
Consensus pattern (103 bp):
TATATATATATTTTCAAAATGATTTAAAAACATATTATATAGTTTTCAAAAATGTTTTAAAAATA
TTATTATATACATTTTCAAAAATGTATTTTAAAAACTA
Found at i:68004 original size:84 final size:84
Alignment explanation
Indices: 67547--68327 Score: 873
Period size: 84 Copynumber: 9.5 Consensus size: 84
67537 GACTCGACAA
* * * * * *
67547 TTTTGTTGACAGATAGCCCCTCTTA-CCTTGAGCTATGCTGCAAATGATGGCGCCTTTGAGCTGA
1 TTTTGTTGGCAGATAACCCTTC-TAGCCTTGAGTTATGCTGCAAATGAT-GTGCCTTGGAGCTGA
* *
67611 GTGTAATCG-ACTCGGAGGTC
64 GTGTAGTCGAACTCGAAGGTC
* * * * *
67631 ---T-TTGGCAGATAACCCTTCTTGCCTTGAGCTATACTGCAAATGATGGTGCCTTTGAGTTGAG
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT-GTGCCTTGGAGCTGAG
* *
67692 TGTAATCGAACTCAAAGG--
65 TGTAGTCGAACTCGAAGGTC
* * * *
67710 -TAT-TTGGCAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGGTGCCTTTGAGCTGAT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT-GTGCCTTGGAGCTGAG
*
67773 TGTAATCGAACTCGAAGGTC
65 TGTAGTCGAACTCGAAGGTC
* *
67793 -TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATG-TG-TAATGATGTGCCTTGGAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGT
* *
67855 GTA-TTGAACTTGAAGGT-
66 GTAGTCGAACTCGAAGGTC
* * * *
67872 TTTTGGTTGGCAGAT--CCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCTTGGAGCTGAG
1 TTTT-GTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAG
67935 TGTAGTCGAACTCGAAGGTC
65 TGTAGTCGAACTCGAAGGTC
* * *
67955 TTTTGTTAGCATATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTACCTTGGAGCTGA--
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGT
*
68018 G-CGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * * * *
68036 TTTGGTTGGAAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGT
* *
68101 GTAGTCAAACTTGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * *
68120 TTTTGTTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGT
68185 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * ** *
68204 TTTTGGTGGCAAATAACCCTTCTTGCCTTGGGCTATATTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGT
*
68269 GTAGTCGAACTCAAAGGTC
66 GTAGTCGAACTCGAAGGTC
*
68288 TTTGGTTGGCAGATAAACCCTTCTAGCCTTGAGTTATGCT
1 TTTTGTTGGCAGAT-AACCCTTCTAGCCTTGAGTTATGCT
68328 ACCAATTGTT
Statistics
Matches: 598, Mismatches: 80, Indels: 37
0.84 0.11 0.05
Matches are distributed among these distances:
79 19 0.03
80 75 0.13
81 203 0.34
82 27 0.05
83 9 0.02
84 245 0.41
85 20 0.03
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (84 bp):
TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGT
GTAGTCGAACTCGAAGGTC
Found at i:68082 original size:165 final size:165
Alignment explanation
Indices: 67577--68327 Score: 859
Period size: 165 Copynumber: 4.6 Consensus size: 165
67567 TCTTACCTTG
* * * *
67577 AGCTATGCTGCAAATGATGGCGCCTTTGAGCTGAGTGTAATCG-ACTCGGAGGTC-TTTG--GCA
1 AGCTATGCTGCAAATGAT-GTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGCA
* * * * * *
67638 GATAACCCTTCTTGCCTTGAGCTATACTGCAAATGATGGTGCCTTTGAGTTGAGTGTAATCGAAC
65 GATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT-GTGCCTTGGAGCTGAGCG--ATCGAAC
* * * * *
67703 TCAAAGG--TAT--TTGGCAGATAACCCTTCTCGCCTTG
127 TCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTA
* * * *
67738 AGTTATGCTGCAAATGATGGTGCCTTTGAGCTGATTGTAATCGAACTCGAAGGTC-TTTGTTGAC
1 AGCTATGCTGCAAATGAT-GTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTG-C
* * *
67802 AGATAACCCTTCTAGCCTTGAGTTATG-TG-TAATGATGTGCCTTGGAGCTGAGTGTATTGAACT
64 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCG-ATCGAACT
* * *
67865 TGAAGGTTTTTGGTTGGCAGAT--CCCTTCTCGACTTA
128 CGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTA
* *
67901 AGTTATGCTACAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTAGCA
1 AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTT-GCA
* *
67966 TATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTACCTTGGAGCTGAGCG-TCGAACTCG
65 GATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGATCGAACTCG
68030 AAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTA
130 AAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTA
* * * * *
68066 AGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCAAACTTGAAGGTCTTTTGTTGGTA
1 AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTT-GCA
*
68131 GATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
65 GATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCG-A-TCGAACT
* * *
68196 CGAAGGTCTTTTGG-TGGCAA-ATAACCCTTCTTGCCTTG
128 CGAAGGTC-TTTGGTTGG-AAGATAACCCTTCTCGACTTA
* ** * * *
68234 GGCTATATTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCA
1 AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTT-GCA
68299 GATAAACCCTTCTAGCCTTGAGTTATGCT
65 GAT-AACCCTTCTAGCCTTGAGTTATGCT
68328 ACCAATTGTT
Statistics
Matches: 518, Mismatches: 52, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
161 51 0.10
162 63 0.12
163 95 0.18
164 6 0.01
165 179 0.35
168 92 0.18
169 32 0.06
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (165 bp):
AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGCAG
ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGATCGAACTCGA
AGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTA
Found at i:69679 original size:95 final size:97
Alignment explanation
Indices: 69441--69692 Score: 290
Period size: 95 Copynumber: 2.7 Consensus size: 97
69431 GGCTAGCTGG
* * *
69441 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTATAGGGACAGCTCAA--TATCATTGTATATA
1 ATCCATAAAGCCGAGG-GTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCT-TTATTGTATATA
*
69504 TATTATAACTGCCTTTATCAGGCTAGCTAATATT
64 TATTATAACTACCTTTATCAGGCTAGCTAATATT
* *
69538 A-CAAT-AAGCC-AGGGTTTAACC-ATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-TA
1 ATCCATAAAGCCGAGGGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTGTATATATA
* * *
69598 -TA-ATC-ACCTTTATCTGGCTTAGCTAAATCTT
66 TTATAACTACCTTTATCAGGC-TAGCT-AATATT
* * *
69629 ATCCATAAAGCCGTGGGTTTAACCAATTTCTTTAGAGGGACAGCTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCGAGGGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTGTATATAT
69693 GTAATATTAT
Statistics
Matches: 132, Mismatches: 14, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
89 11 0.08
90 7 0.05
91 8 0.06
92 26 0.20
93 23 0.17
94 13 0.10
95 39 0.30
96 4 0.03
97 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (97 bp):
ATCCATAAAGCCGAGGGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTGTATATATA
TTATAACTACCTTTATCAGGCTAGCTAATATT
Done.