Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007530.1 Hibiscus syriacus cultivar Beakdansim tig00021026_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: 82465
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:331 original size:2 final size:2
Alignment explanation
Indices: 324--383 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
314 ACAGTTGAGC
324 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
366 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
384 TCTTTCACGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5233 original size:31 final size:31
Alignment explanation
Indices: 5195--5269 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
5185 ATTGCACGTC
5195 TAGTACCTAAACTATCAGTTTTGGTTCATTT
1 TAGTACCTAAACTATCAGTTTTGGTTCATTT
* *
5226 TAGTACCTAAATTATTAGTTTTGGTTCATTT
1 TAGTACCTAAACTATCAGTTTTGGTTCATTT
*
5257 TAGTACATAAACT
1 TAGTACCTAAACT
5270 TTCAATATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.45
Consensus pattern (31 bp):
TAGTACCTAAACTATCAGTTTTGGTTCATTT
Found at i:5704 original size:40 final size:42
Alignment explanation
Indices: 5606--5705 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 42
5596 GGGGATAAAT
** *
5606 GTAACTGAAAATGTTATATAAAATATAATATTTTGGATTGGAC
1 GTAACT-AAAATGTTATATAAAATATAATATTTTAAATTGCAC
5649 GTAATCTAAAATGTTA-A-AAAA-ATAATATTTTAAATTGCAC
1 GTAA-CTAAAATGTTATATAAAATATAATATTTTAAATTGCAC
*
5689 TTAACTAAAAGTGTTAT
1 GTAACTAAAA-TGTTAT
5706 TTTTAATAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
39 6 0.12
40 24 0.48
41 4 0.08
42 1 0.02
43 13 0.26
44 2 0.04
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (42 bp):
GTAACTAAAATGTTATATAAAATATAATATTTTAAATTGCAC
Found at i:14055 original size:26 final size:27
Alignment explanation
Indices: 14006--14056 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
13996 AGGTCTGATT
*
14006 TAATATTTAAATTTTTAAAATTATATC
1 TAATATTTAAATTTTGAAAATTATATC
* *
14033 TAATATTT-AGTTTTGAAACTTATA
1 TAATATTTAAATTTTGAAAATTATA
14057 AGATTATCGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (27 bp):
TAATATTTAAATTTTGAAAATTATATC
Found at i:14110 original size:23 final size:24
Alignment explanation
Indices: 14084--14135 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
14074 ATTTAAACTA
*
14084 TTAATTTTGATATATTTT-AAAAC
1 TTAATTTTCATATATTTTCAAAAC
* * *
14107 TTAAATTTCATTTTTTTTCAAAAC
1 TTAATTTTCATATATTTTCAAAAC
14131 TTAAT
1 TTAAT
14136 ATTAAATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.54
Consensus pattern (24 bp):
TTAATTTTCATATATTTTCAAAAC
Found at i:30173 original size:20 final size:22
Alignment explanation
Indices: 30128--30185 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
30118 GCATGGGTAG
30128 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
30152 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
30172 TGCATCGATACACT
1 TGCATCGATGCACT
30186 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:32157 original size:64 final size:64
Alignment explanation
Indices: 32104--32267 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 64
32094 CGGTGCACCA
*
32104 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * * **
32168 CTTGTGCATCGATACATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** *
32233 AGAATGCATC-AGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGA-TGCATGAAATGCATTCGATGTTT
32268 CAATTAATTC
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 32 0.38
65 52 0.62
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:32242 original size:19 final size:17
Alignment explanation
Indices: 32218--32264 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
32208 ATATTCAGAG
32218 TGCATCGATGCATGGAGAA
1 TGCATCGATGCAT-G-GAA
32237 TGCATC-AGTGCATGGAA
1 TGCATCGA-TGCATGGAA
32254 TGCATTCGATG
1 TGCA-TCGATG
32265 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (17 bp):
TGCATCGATGCATGGAA
Found at i:32498 original size:20 final size:21
Alignment explanation
Indices: 32475--32514 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
32465 GAATCGAATA
32475 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
32495 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
32515 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:38754 original size:22 final size:21
Alignment explanation
Indices: 38712--38751 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
38702 AAGTTTGTTT
38712 TCATTTTTCAATTTTAAAACA
1 TCATTTTTCAATTTTAAAACA
38733 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
38752 ACAGTTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:40731 original size:64 final size:64
Alignment explanation
Indices: 40678--40841 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
40668 CGGTGCACCA
*
40678 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * **
40742 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * * *
40807 AGAATGCATCGGTGCATGGAATACATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
40842 CAATTAATTC
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
64 32 0.38
65 53 0.62
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:41081 original size:20 final size:21
Alignment explanation
Indices: 41058--41097 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
41048 GAATCGAATA
41058 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
41078 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
41098 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:41620 original size:23 final size:23
Alignment explanation
Indices: 41594--41653 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
41584 ATGGCACTTT
*
41594 GGTGCATTTCTACGCGGCACTAC
1 GGTGCATTTCTACGCGGAACTAC
* * * *
41617 GGTGCAATTCTATGTGGAACTTC
1 GGTGCATTTCTACGCGGAACTAC
*
41640 GGTGCATTTATACG
1 GGTGCATTTCTACG
41654 AGTTGTGGTG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.32
Consensus pattern (23 bp):
GGTGCATTTCTACGCGGAACTAC
Found at i:43003 original size:21 final size:21
Alignment explanation
Indices: 42979--43020 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
42969 ATGCTTTACC
42979 TCAATTCACTCTTGAATTGAG
1 TCAATTCACTCTTGAATTGAG
43000 TCAATTCACTCTTGAATTGAG
1 TCAATTCACTCTTGAATTGAG
43021 GGGAGGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (21 bp):
TCAATTCACTCTTGAATTGAG
Found at i:44128 original size:17 final size:19
Alignment explanation
Indices: 44106--44146 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
44096 GAGAGAAAGA
44106 GAAGAAAGA-AAG-TGAAG
1 GAAGAAAGAGAAGATGAAG
44123 GAAG-AAGAGAAGATGAAG
1 GAAGAAAGAGAAGATGAAG
44141 G-AGAAA
1 GAAGAAA
44147 AGGAGTCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.19
17 9 0.43
18 8 0.38
ACGTcount: A:0.59, C:0.00, G:0.37, T:0.05
Consensus pattern (19 bp):
GAAGAAAGAGAAGATGAAG
Found at i:50730 original size:34 final size:34
Alignment explanation
Indices: 50687--50783 Score: 176
Period size: 34 Copynumber: 2.9 Consensus size: 34
50677 CATCATCCGT
*
50687 CGAGTCATTCCAGGTAGCTTCAAACTCATGATGA
1 CGAGACATTCCAGGTAGCTTCAAACTCATGATGA
*
50721 CGAGCCATTCCAGGTAGCTTCAAACTCATGATGA
1 CGAGACATTCCAGGTAGCTTCAAACTCATGATGA
50755 CGAGACATTCCAGGTAGCTTCAAACTCAT
1 CGAGACATTCCAGGTAGCTTCAAACTCAT
50784 CATTAGCAGT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 61 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (34 bp):
CGAGACATTCCAGGTAGCTTCAAACTCATGATGA
Found at i:52496 original size:21 final size:21
Alignment explanation
Indices: 52472--52515 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
52462 TATCCCAATC
*
52472 GGGTTAAAATTCGTTAAGTTT
1 GGGTTAAAATTCGTGAAGTTT
52493 GGGTTAAAATTCGTGAAGTTT
1 GGGTTAAAATTCGTGAAGTTT
52514 GG
1 GG
52516 ATCAAATGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.05, G:0.30, T:0.39
Consensus pattern (21 bp):
GGGTTAAAATTCGTGAAGTTT
Found at i:57839 original size:19 final size:19
Alignment explanation
Indices: 57815--57859 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
57805 ACAAACATCA
*
57815 TCAGATTCTGGCAGTGAAT
1 TCAGATTCTAGCAGTGAAT
**
57834 TCAGATTCTAGTTGTGAAT
1 TCAGATTCTAGCAGTGAAT
57853 TCAGATT
1 TCAGATT
57860 TCATTAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (19 bp):
TCAGATTCTAGCAGTGAAT
Found at i:58183 original size:32 final size:32
Alignment explanation
Indices: 58147--58222 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 32
58137 AGGCGTGAGG
* *
58147 GCCTACCCAAGGGAGTATCTTAGGGCCTAAGA
1 GCCTACCCAAGGAAGTATATTAGGGCCTAAGA
* *
58179 GCCTACCCAAAGAAGTATATTAGGGCCTTAGA
1 GCCTACCCAAGGAAGTATATTAGGGCCTAAGA
58211 GCCTACCCAAGG
1 GCCTACCCAAGG
58223 TCACCTTAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.18
Consensus pattern (32 bp):
GCCTACCCAAGGAAGTATATTAGGGCCTAAGA
Found at i:61977 original size:22 final size:22
Alignment explanation
Indices: 61952--62002 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
61942 CACCACAGCT
*
61952 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
61974 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
61996 CGTAGAA
1 CGTAGAA
62003 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:62003 original size:22 final size:22
Alignment explanation
Indices: 61960--62004 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
61950 CTCGTATAAA
61960 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
61982 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
62004 T
1 T
62005 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:62727 original size:67 final size:67
Alignment explanation
Indices: 62610--62759 Score: 212
Period size: 67 Copynumber: 2.2 Consensus size: 67
62600 TTTTCTCATG
* * *
62610 GGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGTATCGGTT-CCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAA-ATCATATACGA
62675 TG-A
64 TGAA
* * * *
62678 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTG
1 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATG
62743 AA
66 AA
62745 GGGGTATCGGTTCCC
1 GGGGTATCGGTTCCC
62760 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
66 10 0.14
67 53 0.72
68 11 0.15
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.27
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATG
AA
Found at i:62778 original size:20 final size:20
Alignment explanation
Indices: 62740--62779 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
62730 ATCATATTCG
* *
62740 TTGAAGGGGTATCGGTTCCC
1 TTGAAGGGGTACCGATTCCC
*
62760 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
62780 CTAACCCAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (20 bp):
TTGAAGGGGTACCGATTCCC
Found at i:62781 original size:66 final size:65
Alignment explanation
Indices: 62625--62781 Score: 183
Period size: 67 Copynumber: 2.4 Consensus size: 65
62615 ATCGGTTCCC
* *
62625 CCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGATGAGGGGTATCGGTT
1 CCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGATGAGGGGTATCGGTT
* * * *
62690 CCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTTGAAGGGGTATCG
1 --CCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGATG-AGGGGTATCG
62754 GTT
63 GTT
* *
62757 -CCCTTGAATGGGTACCGATTCCCCT
1 CCCCCTG--GGGGTACCGATTCCCCT
62782 AACCCAGAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 5 0.06
66 26 0.33
67 48 0.61
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (65 bp):
CCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGATGAGGGGTATCGGTT
Found at i:68836 original size:22 final size:22
Alignment explanation
Indices: 68811--68861 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
68801 CACCACAGCT
*
68811 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
68833 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
68855 CGTAGAA
1 CGTAGAA
68862 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:68862 original size:22 final size:22
Alignment explanation
Indices: 68819--68863 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
68809 CTCGTATAAA
68819 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
68841 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
68863 T
1 T
68864 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:69616 original size:67 final size:68
Alignment explanation
Indices: 69470--69621 Score: 216
Period size: 68 Copynumber: 2.2 Consensus size: 68
69460 TTTTCTCATG
* * *
69470 GGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGTATCGGTT-CCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGA
*
69535 TGAG
65 TGAA
* * * *
69539 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
69603 GAA
66 GAA
69606 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
69622 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
67 27 0.36
68 37 0.49
69 11 0.15
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.26
Consensus pattern (68 bp):
GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
GAA
Found at i:69631 original size:21 final size:21
Alignment explanation
Indices: 69601--69643 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
69591 ATCATATTCG
* *
69601 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
69622 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
69643 T
1 T
69644 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:69633 original size:67 final size:67
Alignment explanation
Indices: 69470--69643 Score: 199
Period size: 67 Copynumber: 2.6 Consensus size: 67
69460 TTTTCTCATG
* * *
69470 GGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGTATCGGTT--CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGA
*
69535 TGAG
64 TGAA
* * * *
69539 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
69603 GAA
65 GAA
* *
69606 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
69644 AACCCAGAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
65 6 0.06
67 39 0.42
68 37 0.40
69 11 0.12
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.27
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGATG
AA
Found at i:72075 original size:25 final size:25
Alignment explanation
Indices: 72044--72091 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
72034 TGATTTTTGG
*
72044 ATTAAGCTATTATATAGAGAATTTT
1 ATTAAGCTATTAGATAGAGAATTTT
72069 ATTAAGCTATTAGATAGAGAATT
1 ATTAAGCTATTAGATAGAGAATT
72092 AATCTACTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.40
Consensus pattern (25 bp):
ATTAAGCTATTAGATAGAGAATTTT
Found at i:72483 original size:21 final size:21
Alignment explanation
Indices: 72457--72496 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
72447 CAGAACCCCA
*
72457 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
72478 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
72497 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Done.