Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005354.1 Hibiscus syriacus cultivar Beakdansim tig00012158_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: 70080
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:14762 original size:78 final size:77
Alignment explanation
Indices: 14673--14833 Score: 297
Period size: 78 Copynumber: 2.1 Consensus size: 77
14663 CACGTAGATA
14673 TATTATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTTATATACTAATA
1 TATTATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTA-TTTTTTT-TATACTAATA
14738 TCTTGTTTAAACG-
64 TCTTGTTTAAACGT
14751 TATTATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTTATACTAATATC
1 TATTATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTTATACTAATATC
14816 TTGTTTAAACGT
66 TTGTTTAAACGT
14828 TATTAT
1 TATTAT
14834 ATATATATAT
Statistics
Matches: 82, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
76 23 0.28
77 13 0.16
78 46 0.56
ACGTcount: A:0.20, C:0.12, G:0.07, T:0.60
Consensus pattern (77 bp):
TATTATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTTATACTAATATC
TTGTTTAAACGT
Found at i:14915 original size:19 final size:21
Alignment explanation
Indices: 14891--14929 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
14881 TATTACTATA
14891 ATTATTATT-TA-ATTTTTCT
1 ATTATTATTATATATTTTTCT
14910 ATTATTATTATATATTTTTC
1 ATTATTATTATATATTTTTC
14930 CCTCTCTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTATTATTATATATTTTTCT
Found at i:14916 original size:22 final size:21
Alignment explanation
Indices: 14886--14929 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
14876 TTTTGTATTA
*
14886 CTATAATTATTATTTAATTTTT
1 CTATAATTATTATAT-ATTTTT
*
14908 CTATTATTATTATATATTTTT
1 CTATAATTATTATATATTTTT
14929 C
1 C
14930 CCTCTCTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (21 bp):
CTATAATTATTATATATTTTT
Found at i:25686 original size:1 final size:1
Alignment explanation
Indices: 25680--25708 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
25670 TCCTAAGTTG
25680 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25709 CGTTTGGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:26693 original size:56 final size:56
Alignment explanation
Indices: 26607--26712 Score: 203
Period size: 56 Copynumber: 1.9 Consensus size: 56
26597 TTCTCAATTT
*
26607 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTTTTACC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTTTTACC
26663 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
26713 AAGTTCAACT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (56 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTTTTACC
Found at i:26759 original size:161 final size:161
Alignment explanation
Indices: 26494--26817 Score: 648
Period size: 161 Copynumber: 2.0 Consensus size: 161
26484 ATCTTTGCAG
26494 GTTTTACCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCA
1 GTTTTACCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCA
26559 ACTTCACGACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAACT
66 ACTTCACGACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAACT
26624 TCACAACGAAGGATATTGGACTCCAGACGAC
131 TCACAACGAAGGATATTGGACTCCAGACGAC
26655 GTTTTACCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCA
1 GTTTTACCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCA
26720 ACTTCACGACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAACT
66 ACTTCACGACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAACT
26785 TCACAACGAAGGATATTGGACTCCAGACGAC
131 TCACAACGAAGGATATTGGACTCCAGACGAC
26816 GT
1 GT
26818 AAGTTCAACT
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
161 163 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (161 bp):
GTTTTACCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCA
ACTTCACGACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAACT
TCACAACGAAGGATATTGGACTCCAGACGAC
Found at i:26917 original size:106 final size:106
Alignment explanation
Indices: 26665--27231 Score: 915
Period size: 106 Copynumber: 5.4 Consensus size: 106
26655 GTTTTACCCA
*
26665 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACGAC
* * * *
26730 GAAGGGACCGCTGGTTGTCAACGAA-CATTTCTCAATTTCA
66 GAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
26770 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACGAC
26835 GAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
66 GAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
* *
26876 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACGGC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACGAC
26941 GAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
66 GAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
*
26982 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACGAC
27047 GAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
66 GAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
* * *
27088 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCAC--AAGCTCAACTTCACG
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC-G-ACGTAAGTTCAACTTCACG
* * ** * * * *
27151 ACGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTCCA
64 ACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
*
27194 GAACCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
27232 TGAACAATAC
Statistics
Matches: 439, Mismatches: 20, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
105 88 0.20
106 348 0.79
107 1 0.00
108 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (106 bp):
GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGTAAGTTCAACTTCACGAC
GAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCG
Found at i:29149 original size:78 final size:76
Alignment explanation
Indices: 29059--29213 Score: 283
Period size: 78 Copynumber: 2.0 Consensus size: 76
29049 CACGTAGATA
29059 TATTATCGTTCGTACTTCTTTTCATTTATTTTCATTTCATTTTGTATTTTTTTTATATACTAATA
1 TATTATCGTTCGTACTTCTTTTCATTTATTTTCATTTCATTTTGTA-TTTTTTT-TATACTAATA
29124 TCTTGTTTAAACG
64 TCTTGTTTAAACG
*
29137 TATTATCGTTCGTACTTCTTTTCGTTTATTTTCATTTCATTTTGTATTTTTTTTATACTAATATC
1 TATTATCGTTCGTACTTCTTTTCATTTATTTTCATTTCATTTTGTATTTTTTTTATACTAATATC
29202 TTGTTTAAACG
66 TTGTTTAAACG
29213 T
1 T
29214 TATTTATATA
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
76 24 0.32
77 7 0.09
78 45 0.59
ACGTcount: A:0.21, C:0.13, G:0.07, T:0.59
Consensus pattern (76 bp):
TATTATCGTTCGTACTTCTTTTCATTTATTTTCATTTCATTTTGTATTTTTTTTATACTAATATC
TTGTTTAAACG
Found at i:36939 original size:43 final size:43
Alignment explanation
Indices: 36877--36959 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
36867 TCTAATCTCA
* *
36877 AAAGTGACAATTCATAAATACACCAAACTAACATATTACAGCC
1 AAAGTGACAATCCACAAATACACCAAACTAACATATTACAGCC
*
36920 AAAGTTACAATCCACAAATACACCAAACTAACATATTACA
1 AAAGTGACAATCCACAAATACACCAAACTAACATATTACA
36960 ACATTTCTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.51, C:0.24, G:0.05, T:0.20
Consensus pattern (43 bp):
AAAGTGACAATCCACAAATACACCAAACTAACATATTACAGCC
Found at i:44143 original size:2 final size:2
Alignment explanation
Indices: 44136--44175 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
44126 ACTCTACATG
44136 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
44176 CACATATAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48791 original size:13 final size:13
Alignment explanation
Indices: 48764--48802 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
48754 ATTTTAGTAG
**
48764 TTGATTTGACCAA
1 TTGATTTGATTAA
48777 TTGATTTGATTAA
1 TTGATTTGATTAA
*
48790 TTAATTTGATTAA
1 TTGATTTGATTAA
48803 CTGTTTATAT
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:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (13 bp):
TTGATTTGATTAA
Found at i:50946 original size:20 final size:20
Alignment explanation
Indices: 50923--50970 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
50913 GTTACAATAT
50923 CGCAACGCGAATAGGT-AAAC
1 CGCAACGCGAATA-GTAAAAC
* *
50943 CGCAACGTGAATAGTAAAAT
1 CGCAACGCGAATAGTAAAAC
50963 CGCAACGC
1 CGCAACGC
50971 TAATTACCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.40, C:0.25, G:0.23, T:0.12
Consensus pattern (20 bp):
CGCAACGCGAATAGTAAAAC
Found at i:51023 original size:20 final size:20
Alignment explanation
Indices: 50998--51046 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
50988 AAACAGTACT
50998 ATCGCAACGAGAATAGAAAA
1 ATCGCAACGAGAATAGAAAA
* * *
51018 ATCGCAATGCGAATAGTAAA
1 ATCGCAACGAGAATAGAAAA
*
51038 ATTGCAACG
1 ATCGCAACG
51047 CTAATTATCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGAATAGAAAA
Found at i:51047 original size:77 final size:77
Alignment explanation
Indices: 50920--51083 Score: 256
Period size: 77 Copynumber: 2.1 Consensus size: 77
50910 CAGGTTACAA
* ** *
50920 TATCGCAACGCGAATAGGTAAACCGCAACGTGAATAGTAAAATCGCAACGCTAATTACCGATATA
1 TATCGCAACGAGAATAGAAAAACCGCAACGCGAATAGTAAAATCGCAACGCTAATTACCGATATA
50985 GGTAAACAGTAC
66 GGTAAACAGTAC
* * * *
50997 TATCGCAACGAGAATAGAAAAATCGCAATGCGAATAGTAAAATTGCAACGCTAATTATCGATATA
1 TATCGCAACGAGAATAGAAAAACCGCAACGCGAATAGTAAAATCGCAACGCTAATTACCGATATA
51062 GGTAAACAGTAC
66 GGTAAACAGTAC
51074 TATCGCAACG
1 TATCGCAACG
51084 CTAATTACCG
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (77 bp):
TATCGCAACGAGAATAGAAAAACCGCAACGCGAATAGTAAAATCGCAACGCTAATTACCGATATA
GGTAAACAGTAC
Found at i:51347 original size:20 final size:20
Alignment explanation
Indices: 51322--51368 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
51312 GTAATTAGCG
51322 TTGCGATTTTACTATTCGCA
1 TTGCGATTTTACTATTCGCA
* * *
51342 TTGCGATTTTCCTATTCTCG
1 TTGCGATTTTACTATTCGCA
51362 TTGCGAT
1 TTGCGAT
51369 AGTACTGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (20 bp):
TTGCGATTTTACTATTCGCA
Found at i:51394 original size:77 final size:76
Alignment explanation
Indices: 51284--51445 Score: 220
Period size: 77 Copynumber: 2.1 Consensus size: 76
51274 GTGAAAATAA
* * *
51284 CGTTGCGATAGTAATGTTACATATATCGGTAATTAGCGTTGCG-ATTTTACTATTCGCATTGCGA
1 CGTTGCGATAGTAATGTTACATATATCGGTAATTAGCGTTGCGAATTTGA-AAATCGCATTGCGA
51348 TTTTCCTATTCT-
65 TTTTCCTATT-TG
* * * *
51360 CGTTGCGATAGTACTGTTTGCCTATATCGGTAATTAGCGTTGTGAATTTGAAAATCGCATTGCGA
1 CGTTGCGATAGTAATG-TTACATATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCATTGCGA
51425 TTTTCCTATTTG
65 TTTTCCTATTTG
51437 CGTTGCGAT
1 CGTTGCGAT
51446 TTTGGAACAT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
76 16 0.21
77 55 0.72
78 5 0.07
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.41
Consensus pattern (76 bp):
CGTTGCGATAGTAATGTTACATATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCATTGCGAT
TTTCCTATTTG
Found at i:58520 original size:454 final size:452
Alignment explanation
Indices: 57289--58650 Score: 2260
Period size: 453 Copynumber: 3.0 Consensus size: 452
57279 AACCATTCAT
* * *
57289 ATATTACAAACCGAATTAAAATCATACAAGTTTCATACTCAGTATAT-AAAAAATCAAATATGAC
1 ATATTACAAACCGAATTAAAATCA-ACAAGTTCCAGACTCAGTATATAAAAAAATCAAATGTGAC
* * * * *
57353 CTACATGTCCCCTAATCACACATTGTATCGTACTCTACAAGCAAAGCCAAAAGACCTCTCAATAT
65 CTACATGCCCCCTAATCACACATTGTATCGTACTCTGCAAGCAAAGCC-AAAGAACTCCCAATAC
* * *
57418 TGAAGTTGTTAGCTACACTGGATCGATTCTTTTAACATGAAATGGTGAGTAAAGAGTGAGCTTTG
129 TAAAGTTGTTAGCTGCACTGGATCAATTCTTTTAACATGAAATGGTGAGTAAAGAGTGAGCTTTG
* * * *
57483 GGAAGCTGAGTAATACAAAACTACTAGATGAATGCAATAGGCCATCATGTATAAGTAAAACATGA
194 GGAAGCTCAATAATACAGAACTACCAGATGAATGCAATAGGCCATCATGTATAAGTAAAACATGA
57548 ATTTTCTTAACGATACAAACATCATCAGGTTCTATGACGAGCTCAGATTTCATTAATCATTTCTT
259 ATTTTCTTAACGATACAAACATCATCAGGTTCTATGACGAGCTCAGATTTCATTAATCATTTCTT
*
57613 CAAGTAATAGTCAAGAAATCAAAATCTAAAGGAAATATTCAGAAAGAGACTCAACAGATTGAGAT
324 CAAGTAATAGTCAAGAAATCAAAATCTGAAGGAAATATTCAGAAAGAGACTCAACAGATTGAGAT
57678 GAAGATTCTAGTGTGTTCCCTCCAAACCAGAATAAATGTAATCATAGTTTAAAAACAATAGTAG
389 GAAGATTCTAGTGTGTTCCCTCCAAACCAGAATAAATGTAATCATAGTTTAAAAACAATAGTAG
* *
57742 AAATTACAAATCGAATTAAAATCAACAAGTTCCAGACTCAGTATATAAAAAAATCAAATGTGACC
1 ATATTACAAACCGAATTAAAATCAACAAGTTCCAGACTCAGTATATAAAAAAATCAAATGTGACC
* * *
57807 TACATGCCCCCTAATCACACATTATACCGTACTCTGTAAGCAAAGCCAAAGTAACTCCCAATACT
66 TACATGCCCCCTAATCACACATTGTATCGTACTCTGCAAGCAAAGCCAAAG-AACTCCCAATACT
* *
57872 AAAGTTGTTAACTGCACTGGATCAATTCTTTTAACATGAAATGATGAGTAAAGAGTGAGCTTTGG
130 AAAGTTGTTAGCTGCACTGGATCAATTCTTTTAACATGAAATGGTGAGTAAAGAGTGAGCTTTGG
** *
57937 GAAGCTCAATAATACAGAACTGTCAGATGAATGCAATAGGCCATCATGTATAAGTAAAGCATGAA
195 GAAGCTCAATAATACAGAACTACCAGATGAATGCAATAGGCCATCATGTATAAGTAAAACATGAA
58002 TTTTCTTAACGATACAAACATCATCAGGTTCTATGACGAGCTCAGATTTCATTAATCATTTCTTC
260 TTTTCTTAACGATACAAACATCATCAGGTTCTATGACGAGCTCAGATTTCATTAATCATTTCTTC
* *
58067 AGGTAATAGTCAAGAAATCAAAATCTGAAGGAAATATTCAGAAAGAGACTCAACATATTGAGATG
325 AAGTAATAGTCAAGAAATCAAAATCTGAAGGAAATATTCAGAAAGAGACTCAACAGATTGAGATG
*
58132 AAGATTCTAGTGTATTCCCTCCAAACCAGAATAAATGTAATCATAGTTTAAAAACAATAGTAG
390 AAGATTCTAGTGTGTTCCCTCCAAACCAGAATAAATGTAATCATAGTTTAAAAACAATAGTAG
*
58195 ATATTACAAACCGAATTAAAATCAACAAGTTCCAGACTCAGTATATAAAAAAAATCAAATGTTAC
1 ATATTACAAACCGAATTAAAATCAACAAGTTCCAGACTCAGTATAT-AAAAAAATCAAATGTGAC
58260 CTACATGCCCCCTAATCACACATTGTATCGTACTCTGCAAGCAAAGCCAAATGAACTCCCAATAC
65 CTACATGCCCCCTAATCACACATTGTATCGTACTCTGCAAGCAAAGCCAAA-GAACTCCCAATAC
58325 TAAAG-TGTTTAGCTGCACTGGATCAATTCTTTTAACATGAAATGGTGAGTAAAGAGTGAGCTTT
129 TAAAGTTG-TTAGCTGCACTGGATCAATTCTTTTAACATGAAATGGTGAGTAAAGAGTGAGCTTT
* *
58389 GGGAAGCTCAATAATACAGAACTACCAGATGAATGCAATAGGTCATAATGTATAAGTAAAACATG
193 GGGAAGCTCAATAATACAGAACTACCAGATGAATGCAATAGGCCATCATGTATAAGTAAAACATG
* * * * * *
58454 AATTTTCTAAATGATAAAAACATCATCAGGTTCTACGACGAGATCATATTTCATTAATCATTTCT
258 AATTTTCTTAACGATACAAACATCATCAGGTTCTATGACGAGCTCAGATTTCATTAATCATTTCT
* * * *
58519 TCATGTAACAGTCAGGAAATCAAAATCTGAAGGAAATATTCAGAGAGAGAGACTCAAGAGATTGA
323 TCAAGTAATAGTCAAGAAATCAAAATCTGAAGGAAATATTCAGA-A-AGAGACTCAACAGATTGA
58584 GATGAAGATTCTAGTGTGTTCCCTCCAAACCAGAATAAATGTAATCATAGTTTAAAAACAATAGT
386 GATGAAGATTCTAGTGTGTTCCCTCCAAACCAGAATAAATGTAATCATAGTTTAAAAACAATAGT
58649 AG
451 AG
58651 TTTATTTCAG
Statistics
Matches: 848, Mismatches: 54, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
452 24 0.03
453 444 0.52
454 296 0.35
455 2 0.00
456 82 0.10
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.27
Consensus pattern (452 bp):
ATATTACAAACCGAATTAAAATCAACAAGTTCCAGACTCAGTATATAAAAAAATCAAATGTGACC
TACATGCCCCCTAATCACACATTGTATCGTACTCTGCAAGCAAAGCCAAAGAACTCCCAATACTA
AAGTTGTTAGCTGCACTGGATCAATTCTTTTAACATGAAATGGTGAGTAAAGAGTGAGCTTTGGG
AAGCTCAATAATACAGAACTACCAGATGAATGCAATAGGCCATCATGTATAAGTAAAACATGAAT
TTTCTTAACGATACAAACATCATCAGGTTCTATGACGAGCTCAGATTTCATTAATCATTTCTTCA
AGTAATAGTCAAGAAATCAAAATCTGAAGGAAATATTCAGAAAGAGACTCAACAGATTGAGATGA
AGATTCTAGTGTGTTCCCTCCAAACCAGAATAAATGTAATCATAGTTTAAAAACAATAGTAG
Found at i:60095 original size:27 final size:27
Alignment explanation
Indices: 60065--60157 Score: 125
Period size: 27 Copynumber: 3.5 Consensus size: 27
60055 TCTTTTAGTC
60065 ATTTTAGTTATTTAAATATCGAAGGTT
1 ATTTTAGTTATTTAAATATCGAAGGTT
* * *
60092 ATTTTAGTTATTTAAAAATC-AGGGGT
1 ATTTTAGTTATTTAAATATCGAAGGTT
* *
60118 ATTTTAGTCATTTAAATATCGAATGTT
1 ATTTTAGTTATTTAAATATCGAAGGTT
*
60145 ATTTTAATTATTT
1 ATTTTAGTTATTT
60158 CCCAGCTAGA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
26 22 0.40
27 33 0.60
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.49
Consensus pattern (27 bp):
ATTTTAGTTATTTAAATATCGAAGGTT
Found at i:62150 original size:224 final size:225
Alignment explanation
Indices: 61762--62211 Score: 861
Period size: 224 Copynumber: 2.0 Consensus size: 225
61752 TTCTTTTATC
61762 TGAAATTAGGGTTGTGACAATTTGTGTTATGTTCGTGTTATTTTTGTGTAATGTTATATATTCGT
1 TGAAATTAGGGTTGTGACAATTTGTGTTATGTTCGTGTTATTTTTGTGTAATGTTATATATTCGT
61827 GTATCCACTCAAATCTTTTGTTAATTGTTTTTCTAATCAAAGTTAGGTAAAATTGAGTGCTGAAG
66 GTATCCACTCAAATCTTTTGTTAATTGTTTTTCTAATCAAAGTTAGGTAAAATTGAGTGCTGAAG
61892 ACAATTTCTAAATTTGTAGTTTGTTTTTGTCATATAGATTGTTTTAATTCTCA-ATATGCAACAA
131 ACAATTTCTAAATTTGTAGTTTGTTTTTGTCATATAGATTGTTTTAATTCTCAGATATGCAACAA
61956 TC-TGTTACTTGTTCATGAAC-TAACATTT
196 TCATGTTACTTGTTCATGAACTTAACATTT
61984 TGAAATTAGGGTTGTGACAATTTGTGTTATGTTCGTGTTATTTTTGTGTAATGTTATATATTCGT
1 TGAAATTAGGGTTGTGACAATTTGTGTTATGTTCGTGTTATTTTTGTGTAATGTTATATATTCGT
62049 GTATCCAAGCTCAAATCTTTTGTTAATTGTTTTTCTAATCAAAGTTAGGTAAAATTGAGTGCTGA
66 GTATCC-A-CTCAAATCTTTTGTTAATTGTTTTTCTAATCAAAGTTAGGTAAAATTGAGTGCTGA
62114 AGACAATTTCTAAATTTGTAGTTTGTTTTTGTCATATAGATTGTTTTAATTCTCAGATATGCAAC
129 AGACAATTTCTAAATTTGTAGTTTGTTTTTGTCATATAGATTGTTTTAATTCTCAGATATGCAAC
62179 AATCATGTTACTTGTTCATGAACTTAACATTT
194 AATCATGTTACTTGTTCATGAACTTAACATTT
62211 T
1 T
62212 TGTTCAATTC
Statistics
Matches: 223, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
222 71 0.32
223 1 0.00
224 111 0.50
225 13 0.06
226 18 0.08
227 9 0.04
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (225 bp):
TGAAATTAGGGTTGTGACAATTTGTGTTATGTTCGTGTTATTTTTGTGTAATGTTATATATTCGT
GTATCCACTCAAATCTTTTGTTAATTGTTTTTCTAATCAAAGTTAGGTAAAATTGAGTGCTGAAG
ACAATTTCTAAATTTGTAGTTTGTTTTTGTCATATAGATTGTTTTAATTCTCAGATATGCAACAA
TCATGTTACTTGTTCATGAACTTAACATTT
Found at i:63450 original size:20 final size:20
Alignment explanation
Indices: 63425--63478 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
63415 TAATCCTATT
63425 CACTGGTAATCTTACATTCC
1 CACTGGTAATCTTACATTCC
63445 CACTGGTAATCTTACATTCC
1 CACTGGTAATCTTACATTCC
63465 CACTGGTAATCTTA
1 CACTGGTAATCTTA
63479 TATTTCGTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (20 bp):
CACTGGTAATCTTACATTCC
Found at i:64873 original size:18 final size:18
Alignment explanation
Indices: 64850--64885 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
64840 GTGCTTTCGG
64850 CTTGTGTTTCTATGCATA
1 CTTGTGTTTCTATGCATA
64868 CTTGTGTTTCTATGCATA
1 CTTGTGTTTCTATGCATA
64886 GTACTAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (18 bp):
CTTGTGTTTCTATGCATA
Done.