Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007545.1 Hibiscus syriacus cultivar Beakdansim tig00021147_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: 59117
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:109 original size:54 final size:54
Alignment explanation
Indices: 1--270 Score: 392
Period size: 54 Copynumber: 5.1 Consensus size: 54
*
1 GAAGAAA-AGGGGAGCGAACCCGTAA-AAG-A-TTTTTTGAGTTCTATACTTCCT
1 GAAGAAAGA-GGGAGCGAACCCGTAAGAAGAAGATTTTTGAGTTCTATACTTCCT
* * *
52 GAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATATTCGAGTTCTATACTCCCT
1 GAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATTTTTGAGTTCTATACTTCCT
* *
106 GAAG-AAGA-GGAGCGAACCCGTAAGAAGAAGATTCTCGAGTTCTATACTTCCT
1 GAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATTTTTGAGTTCTATACTTCCT
*
158 GAAGAAAG-GGGAGGGAACCCGTAAGAAGAAGATTTTTGAGTTCTATACTTCCT
1 GAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATTTTTGAGTTCTATACTTCCT
* * *
211 GAAGAAAGAGGGAACGAACCCGTAAGAATAAGATTTTTGAGTTCTATACTCCCT
1 GAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATTTTTGAGTTCTATACTTCCT
265 GAAGAA
1 GAAGAA
271 TAGGGAACGA
Statistics
Matches: 198, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
51 23 0.12
52 49 0.25
53 57 0.29
54 69 0.35
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (54 bp):
GAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATTTTTGAGTTCTATACTTCCT
Found at i:349 original size:55 final size:55
Alignment explanation
Indices: 240--657 Score: 513
Period size: 55 Copynumber: 7.7 Consensus size: 55
230 CCGTAAGAAT
* * *
240 AAGATT-TTTGAGT-TCTATACTCCCTGAAG-AATAGGGAAC-GAACACGATTGTTG
1 AAGATTGTTCGAGTCTC-ATACTCTCTGAAGAAATAGGGAGCAG-ACACGATTGTTG
* * * *
293 AAGATTGTTCGAGTCTTATACTCTCTGAA-AGAATAGGGAGAAGACACAATTATTG
1 AAGATTGTTCGAGTCTCATACTCTCTGAAGA-AATAGGGAGCAGACACGATTGTTG
* *
348 AAGATTGTTCGAGTCTCATACTCTCTGAA-AGAATAGGGGGAGCAGACACAATTATTG
1 AAGATTGTTCGAGTCTCATACTCTCTGAAGA-AATA--GGGAGCAGACACGATTGTTG
*
405 AAGATTGTTCAAGTCTCATACTCTCTGAA-AGAATAGGGAGCAGACA--ATTGTTG
1 AAGATTGTTCGAGTCTCATACTCTCTGAAGA-AATAGGGAGCAGACACGATTGTTG
*
458 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
513 AAGATTGTTCGAGTCTCATA--CTCTGAAGAAATAGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
** *
566 AAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAAAGAGCA-ACACGATTATTG
1 AAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
*
620 AAGATTATTCGAGT-TCTATACTGC-CTGAAAGAAATAGG
1 AAGATTGTTCGAGTCTC-ATACT-CTCTG-AAGAAATAGG
658 AGTGAACCCA
Statistics
Matches: 330, Mismatches: 20, Indels: 28
0.87 0.05 0.07
Matches are distributed among these distances:
53 109 0.33
54 50 0.15
55 117 0.35
56 1 0.00
57 53 0.16
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (55 bp):
AAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
Found at i:563 original size:108 final size:108
Alignment explanation
Indices: 240--633 Score: 509
Period size: 108 Copynumber: 3.6 Consensus size: 108
230 CCGTAAGAAT
* * * *
240 AAGATT-TTTGAGT-TCTATACTCCCTGAAG-AATAGGGAAC-GAACACGATTGTTGAAGATTGT
1 AAGATTGTTCGAGTCTC-ATACTCTCTGAAGAAATAGGGAGCAG-ACACGATTATTGAAGATTGT
* * *
301 TCGAGTCTTATACTCTCTGAAAGAATAGGGAGAAGACACAATTATTG
64 TCGAGTCTCATAC-CTCTGAAAGAATAGGGAGCAGACAC-ATTGTTG
*
348 AAGATTGTTCGAGTCTCATACTCTCTGAA-AGAATAGGGGGAGCAGACACAATTATTGAAGATTG
1 AAGATTGTTCGAGTCTCATACTCTCTGAAGA-AATA--GGGAGCAGACACGATTATTGAAGATTG
*
412 TTCAAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA-ATTGTTG
63 TTCGAGTCTCATAC-CTCTGAAAGAATAGGGAGCAGACACATTGTTG
* *
458 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
1 AAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATTGTTC
523 GAGTCTCATA-CTCTG-AAGAAATAGGGAGCAGACACGATTGTTG
66 GAGTCTCATACCTCTGAAAG-AATAGGGAGCAGACAC-ATTGTTG
** *
566 AAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAAAGAGCA-ACACGATTATTGAAGATTATTC
1 AAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATTGTTC
630 GAGT
66 GAGT
634 TCTATACTGC
Statistics
Matches: 257, Mismatches: 18, Indels: 23
0.86 0.06 0.08
Matches are distributed among these distances:
105 3 0.01
106 20 0.08
107 24 0.09
108 89 0.35
109 17 0.07
110 44 0.17
111 1 0.00
112 58 0.23
113 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (108 bp):
AAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATTGTTC
GAGTCTCATACCTCTGAAAGAATAGGGAGCAGACACATTGTTG
Found at i:2783 original size:12 final size:12
Alignment explanation
Indices: 2766--2790 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2756 CATGTGTATC
2766 CCGTCACTGTCA
1 CCGTCACTGTCA
2778 CCGTCACTGTCA
1 CCGTCACTGTCA
2790 C
1 C
2791 AAAAATGGAT
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:0.16, C:0.44, G:0.16, T:0.24
Consensus pattern (12 bp):
CCGTCACTGTCA
Found at i:6766 original size:5 final size:5
Alignment explanation
Indices: 6756--6822 Score: 59
Period size: 5 Copynumber: 13.2 Consensus size: 5
6746 AACAATTAAA
* *
6756 AAAAT AAAAT AATAA- AACAA- ATAAT AAAAT AAAGAT AACAT AAAAT
1 AAAAT AAAAT AA-AAT AA-AAT AAAAT AAAAT AAA-AT AAAAT AAAAT
6802 -AAAT AAAAT AAACAT AAAAT A
1 AAAAT AAAAT AAA-AT AAAAT A
6823 TAAGGACCTA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
4 6 0.12
5 35 0.67
6 11 0.21
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:6771 original size:16 final size:17
Alignment explanation
Indices: 6752--6809 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
6742 TTTAAACAAT
6752 TAAAA-AAATAAAATAA
1 TAAAACAAATAAAATAA
6768 TAAAACAAATAATAA-AA
1 TAAAACAAATAA-AATAA
*
6785 TAAAGATAACATAAAATAAA
1 TAAA-ACAA-ATAAAAT-AA
6805 TAAAA
1 TAAAA
6810 TAAACATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
16 5 0.14
17 12 0.34
18 7 0.20
19 5 0.14
20 6 0.17
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.19
Consensus pattern (17 bp):
TAAAACAAATAAAATAA
Found at i:6773 original size:25 final size:25
Alignment explanation
Indices: 6745--6818 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 25
6735 TGAACTATTT
*
6745 AAACAATTAAAAAAATAAA-ATAATA
1 AAACAA-TAAAAAAATAAACATAACA
* *
6770 AAACAAATAATAAAATAAAGATAACA
1 AAAC-AATAAAAAAATAAACATAACA
*
6796 TAA-AATAAATAAAATAAACATAA
1 AAACAATAAA-AAAATAAACATAA
6819 AATATAAGGA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
24 5 0.12
25 27 0.66
26 9 0.22
ACGTcount: A:0.74, C:0.05, G:0.01, T:0.19
Consensus pattern (25 bp):
AAACAATAAAAAAATAAACATAACA
Found at i:6805 original size:20 final size:20
Alignment explanation
Indices: 6756--6822 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
6746 AACAATTAAA
*
6756 AAAATAAA-ATAATAAAACA-
1 AAAATAAATAAAAT-AAACAT
6775 AATAATAAAATAAAGAT-AACAT
1 AA-AAT-AAATAAA-ATAAACAT
6797 AAAATAAATAAAATAAACAT
1 AAAATAAATAAAATAAACAT
6817 AAAATA
1 AAAATA
6823 TAAGGACCTA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
19 4 0.10
20 21 0.51
21 10 0.24
22 4 0.10
23 2 0.05
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.19
Consensus pattern (20 bp):
AAAATAAATAAAATAAACAT
Found at i:11862 original size:28 final size:28
Alignment explanation
Indices: 11805--11862 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
11795 GTTTTTGTTA
** *
11805 TTTTTTTACTTTCTTTTGTTATTTTCTT
1 TTTTTTTACTTTCTTTTGTTACATTATT
*
11833 TTTTTTTCCTTTTCTTTT-TTACATTATT
1 TTTTTTTAC-TTTCTTTTGTTACATTATT
11861 TT
1 TT
11863 CTCTTATTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.09, C:0.12, G:0.02, T:0.78
Consensus pattern (28 bp):
TTTTTTTACTTTCTTTTGTTACATTATT
Found at i:14423 original size:5 final size:5
Alignment explanation
Indices: 14413--14478 Score: 64
Period size: 5 Copynumber: 13.2 Consensus size: 5
14403 ACAATTTAAA
* * * *
14413 AAAAT AAAAT --AAT AAAAT AAAGT AAAAT AAAGAC AACAT AAAAT AAATT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT
14462 AAAAT AAACAT AAAAT A
1 AAAAT AAA-AT AAAAT A
14479 TGAGAACCTA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
3 3 0.06
5 38 0.78
6 8 0.16
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:16646 original size:42 final size:41
Alignment explanation
Indices: 16545--16647 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 41
16535 AAATCCTACC
* * * *
16545 CGAAAGTCTTATGGATGGCCCGAAGGACTTATCATCATACT
1 CGAAAGACTTATAGATGGCCCAAAGGACTTAGCATCATACT
* * *
16586 CGAAAGACTTATAAATGGCTCAAAGGACTTACGCATCATGCT
1 CGAAAGACTTATAGATGGCCCAAAGGACTTA-GCATCATACT
16628 CGAAAGACTTACT-GATGGCC
1 CGAAAGACTTA-TAGATGGCC
16648 TGAAGAACTT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 26 0.51
42 24 0.47
43 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.24
Consensus pattern (41 bp):
CGAAAGACTTATAGATGGCCCAAAGGACTTAGCATCATACT
Found at i:16658 original size:42 final size:42
Alignment explanation
Indices: 16545--16665 Score: 131
Period size: 42 Copynumber: 2.9 Consensus size: 42
16535 AAATCCTACC
* * *
16545 CGAAAGTCTTATGGATGGCCCGAAGGACTTA-TCATCATACT
1 CGAAAGACTTATAGATGGCCTGAAGGACTTACTCATCATACT
* * * *
16586 CGAAAGACTTATAAATGG-CTCAAAGGACTTACGCATCATGCT
1 CGAAAGACTTATAGATGGCCT-GAAGGACTTACTCATCATACT
*
16628 CGAAAGACTTACT-GATGGCCTGAAGAACTTACTCATCA
1 CGAAAGACTTA-TAGATGGCCTGAAGGACTTACTCATCA
16666 AGAAACCGAT
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
40 1 0.02
41 24 0.37
42 37 0.57
43 3 0.05
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (42 bp):
CGAAAGACTTATAGATGGCCTGAAGGACTTACTCATCATACT
Found at i:17926 original size:6 final size:5
Alignment explanation
Indices: 17893--17956 Score: 60
Period size: 5 Copynumber: 12.6 Consensus size: 5
17883 AAACAATTTA
* *
17893 AAAAT AAAAT AAAAT AAAA- AATAA- AAAAGT AAAAT AAAGAC AACAT
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AAAA-T AAAAT AAA-AT AAAAT
*
17939 AAAAT AAATT AAAAT AAA
1 AAAAT AAAAT AAAAT AAA
17957 CTTAAAATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
4 4 0.08
5 38 0.78
6 7 0.14
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:20170 original size:42 final size:41
Alignment explanation
Indices: 20076--20188 Score: 140
Period size: 41 Copynumber: 2.7 Consensus size: 41
20066 GCCCGAAGGT
* *
20076 CTTATGGATGGCCCGAAGGACTTA-TCATCTTACTCGAAAGA
1 CTTATAGATGGCCC-AAGGACTTACTCATCATACTCGAAAGA
* * *
20117 CTTATAAATGGCCCATAGGACTTACACATCATGCTCGAAAGA
1 CTTATAGATGGCCCA-AGGACTTACTCATCATACTCGAAAGA
20159 CTTACT-GATGGCCCAAGGACTTACTCATCA
1 CTTA-TAGATGGCCCAAGGACTTACTCATCA
20189 AGAAACCGTT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
40 1 0.02
41 34 0.55
42 26 0.42
43 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (41 bp):
CTTATAGATGGCCCAAGGACTTACTCATCATACTCGAAAGA
Found at i:20297 original size:254 final size:259
Alignment explanation
Indices: 19830--20370 Score: 783
Period size: 254 Copynumber: 2.1 Consensus size: 259
19820 GTACCATAAA
* ** *
19830 AAGGTCTTATCATCTTGCTCGAAAATGTTATAAATGGCCCGAAAGACTTACGTATCATGCTCGGA
1 AAGGTCTTATCATCTTGCTCGAAAATCTTATAAATGGCCCGAAAGACTTACACATCATGCTCGAA
* *
19895 AGACATACTGATGACCCGACGGAATAACTCATCAAGAAACCTTTAAAAATCAAGCTTAGTTTCTT
66 AGACATACTGATGACCCGAAGGAATAACTCATCAAGAAACCGTTAAAAATCAAGCTTAG--T-TT
19960 AGTTGTCATCAAGGAACCCCTACATATTATGTTGGTCCCTCGAGTGAGGTATTGTTGATTCAACT
128 A-TTGTCATCAAGGAACCCCTACATATTATGTTGGTCCCTCGAGTGAGGTATTGTTGATTCAACT
*
20025 CCATATATGATTAATCGAGTAC-ATAAAATGTTGAAAA-AT-CTGCCCGAAGGTCTTATGGATGG
192 CCATATATGATGAATCGAGTACGA-AAAATGTTGAAAACATCCTGCCCGAAGGTCTTATGGATGG
20087 CCCG
256 CCCG
* * *
20091 AAGGACTTATCATCTTACTCGAAAGA-CTTATAAATGGCCC-ATAGGACTTACACATCATGCTCG
1 AAGGTCTTATCATCTTGCTCGAAA-ATCTTATAAATGGCCCGA-AAGACTTACACATCATGCTCG
* * * * * *
20154 AAAGACTTACTGATGGCCC-AAGGACTTACTCATCAAGAAACCGTTGAAAATTAAGCTTAG-TT-
64 AAAGACATACTGATGACCCGAAGGAATAACTCATCAAGAAACCGTTAAAAATCAAGCTTAGTTTA
*
20216 TTGTCATCAAGGAACCCCTACATATTATGTTGGTCCCTCGAGTGAGGTGTTGTTGATTCAACTCC
129 TTGTCATCAAGGAACCCCTACATATTATGTTGGTCCCTCGAGTGAGGTATTGTTGATTCAACTCC
* *
20281 ATATGTGATGAATCGAGTACGAAAAATGTTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCTC
194 ATATATGATGAATCGAGTACGAAAAATGTTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCC
20346 G
259 G
*
20347 AAGGTTTTATCATCTTGCTCGAAA
1 AAGGTCTTATCATCTTGCTCGAAA
20371 CACTACAAGA
Statistics
Matches: 253, Mismatches: 22, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
254 95 0.38
255 3 0.01
256 49 0.19
260 36 0.14
261 69 0.27
262 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (259 bp):
AAGGTCTTATCATCTTGCTCGAAAATCTTATAAATGGCCCGAAAGACTTACACATCATGCTCGAA
AGACATACTGATGACCCGAAGGAATAACTCATCAAGAAACCGTTAAAAATCAAGCTTAGTTTATT
GTCATCAAGGAACCCCTACATATTATGTTGGTCCCTCGAGTGAGGTATTGTTGATTCAACTCCAT
ATATGATGAATCGAGTACGAAAAATGTTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCG
Found at i:25201 original size:57 final size:58
Alignment explanation
Indices: 25082--25225 Score: 182
Period size: 57 Copynumber: 2.5 Consensus size: 58
25072 AAGAAATTAC
* * * * **
25082 TCATCAATAAAACCTTGAAAATCAAGCTTATTTTCTTATAAAAATTCATTGAAAATCG
1 TCATCAAGAAACCCTTGAAAATCAGGCTTAGTTTCTTATAAAAATTCATTGAAAATAA
* * * * *
25140 TCATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTT-TAAAAATTCTTTGGAGATAA
1 TCATCAAGAAACCCTTGAAAATCAGGCTTAGTTTCTTATAAAAATTCATTGAAAATAA
25197 TCATCAAGAAACCCTTGAAAATCAGGCTT
1 TCATCAAGAAACCCTTGAAAATCAGGCTT
25226 GGTTCCTAAA
Statistics
Matches: 73, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
57 42 0.58
58 31 0.42
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (58 bp):
TCATCAAGAAACCCTTGAAAATCAGGCTTAGTTTCTTATAAAAATTCATTGAAAATAA
Found at i:25378 original size:42 final size:42
Alignment explanation
Indices: 25260--25378 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 42
25250 ATCCTGCACG
* *
25260 AAGATCTTATGGATGGCCCGAAGGACTT-ATCATCTTGCTTGA
1 AAGA-CTTATAGATGGCCCGAAGGACTTAATCATCATGCTTGA
* * * ** * *
25302 AACACTTATAAATGACATGAAGGATTTAAGCATCATGCTTGA
1 AAGACTTATAGATGGCCCGAAGGACTTAATCATCATGCTTGA
* * *
25344 AAGACTTATTGATGGCCCAAATGACTTAATCATCA
1 AAGACTTATAGATGGCCCGAAGGACTTAATCATCA
25379 AGAAAACCTT
Statistics
Matches: 57, Mismatches: 19, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
41 17 0.30
42 40 0.70
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (42 bp):
AAGACTTATAGATGGCCCGAAGGACTTAATCATCATGCTTGA
Found at i:26401 original size:173 final size:173
Alignment explanation
Indices: 26111--26456 Score: 584
Period size: 173 Copynumber: 2.0 Consensus size: 173
26101 AGTTTAAATC
* * * *
26111 TCATGATCTTAATGACATCTGGTTTAGATAATGCTCCAATGTGGGTACTCATGGCTCTTTTCATG
1 TCATGATCTTAACGACATCTGGTTTAGATAATGCCCCAATATGGGTACTCATGGCTCTCTTCATG
** *
26176 CCAAAATCTTAATCTCGAATGGTTTCACTCTGGTGTCACTAATCAGCAATGTTATCGAATAGACT
66 AAAAAATCTTAATATCGAATGGTTTCACTCTGGTGTCACTAATCAGCAATGTTATCGAATAGACT
26241 AAGGGCTTCTCTTCACGATGACATAACCAAATGAACACTTAAA
131 AAGGGCTTCTCTTCACGATGACATAACCAAATGAACACTTAAA
*
26284 TCATGATCTTAACGACATCTGGTTTAGGTAATGCCCCAATATGGGTACTCATGGCTCTCTTCATG
1 TCATGATCTTAACGACATCTGGTTTAGATAATGCCCCAATATGGGTACTCATGGCTCTCTTCATG
*
26349 AAAAAATCTTAATATCGAATGGTTTCACTCTGGTGTCACTAATCATCAATGTTATCGAATAGACT
66 AAAAAATCTTAATATCGAATGGTTTCACTCTGGTGTCACTAATCAGCAATGTTATCGAATAGACT
* * *
26414 GAGGGCTTCTCTTCACGATGCCATAACCAGATGAACACTTAAA
131 AAGGGCTTCTCTTCACGATGACATAACCAAATGAACACTTAAA
26457 AAGTGATCAA
Statistics
Matches: 161, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
173 161 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (173 bp):
TCATGATCTTAACGACATCTGGTTTAGATAATGCCCCAATATGGGTACTCATGGCTCTCTTCATG
AAAAAATCTTAATATCGAATGGTTTCACTCTGGTGTCACTAATCAGCAATGTTATCGAATAGACT
AAGGGCTTCTCTTCACGATGACATAACCAAATGAACACTTAAA
Found at i:31479 original size:231 final size:225
Alignment explanation
Indices: 31021--31492 Score: 691
Period size: 231 Copynumber: 2.1 Consensus size: 225
31011 CATATATTCA
* *
31021 GGTCGGGTCGGGTAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTAATATTTGGGT
1 GGTCGGGTCGGGTAAACTTTATTTTGGTCGGGTCAGGTCGATTTTTTTAAGTGTAATA-TT--GT
* *
31086 CGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATA
63 CGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTAATA
* * *
31151 TATTCAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCCAATTAAGTCACTGTTT
128 TATTCAGGAATAATTACAATAATACCCATCTATATATAATTGTTATTCCAATTAAGTCACTGTTT
31216 TTATTGAATAAAAATAATTTTTTTATTATTTCG
193 TTATTGAATAAAAATAATTTTTTTATTATTTCG
*
31249 GGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAGGTC-ATTTTTTTAAGTGTGATA-T-TCG
1 GGTCGGGTCGGGT-AAACTTTATTTTGGTCGGGTCAGGTCGATTTTTTTAAGTGTAATATTGTCG
* *
31311 GGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCCACTCGAACCAAAAAATGTATAATTTTA
65 GGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGA---C-C-CG----AAAAAATATATAATTTTA
*
31376 CCTAATATATTTAGGAATAATTACAATAATACCCATCTATATAT-ATTGTTATTCCAATTAAGTC
121 CCTAATATATTCAGGAATAATTACAATAATACCCATCTATATATAATTGTTATTCCAATTAAGTC
*
31440 ACTGTTTTTATTGAATAAAAATAGTTTTTTTATTATTTCG
186 ACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCG
31480 GGTCGGGTCGGGT
1 GGTCGGGTCGGGT
31493 TTCTAATTCA
Statistics
Matches: 222, Mismatches: 12, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
223 36 0.16
226 2 0.01
227 1 0.00
228 31 0.14
229 25 0.11
231 70 0.32
232 57 0.26
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (225 bp):
GGTCGGGTCGGGTAAACTTTATTTTGGTCGGGTCAGGTCGATTTTTTTAAGTGTAATATTGTCGG
GTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTAATATAT
TCAGGAATAATTACAATAATACCCATCTATATATAATTGTTATTCCAATTAAGTCACTGTTTTTA
TTGAATAAAAATAATTTTTTTATTATTTCG
Found at i:31548 original size:231 final size:218
Alignment explanation
Indices: 31077--31554 Score: 532
Period size: 231 Copynumber: 2.1 Consensus size: 218
31067 TTAAGTGTAA
* * *
31077 TATTTGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTT
1 TATTTTGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTT
* * * *
31142 TACCTTATATATTCAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCCAATTAAG
66 TACCTAATATATTCAGGAATAATTACAATAATACCCATCTATATATAATTGTTATTCCAATTAAG
* *
31207 TCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGGTGAAACTTTAT
131 TCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGGTCAAACTTCAT
** * ***
31272 TTTGGTCGGGTCAGGTCATTTTTT
196 AAT-GTCGGGTCAGATCATAACTT
* **
31296 TAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCCACTCGAACCAAA
1 T-A-T-T-TTGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGA---C-C-CG----AAA
* *
31361 AAATGTATAATTTTACCTAATATATTTAGGAATAATTACAATAATACCCATCTATATAT-ATTGT
53 AAATATATAATTTTACCTAATATATTCAGGAATAATTACAATAATACCCATCTATATATAATTGT
*
31425 TATTCCAATTAAGTCACTGTTTTTATTGAATAAAAATAGTTTTTTTATTATTTCGGGTCGGGTCG
118 TATTCCAATTAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCG
*
31490 GGTTTCTAA-TTCATAAAT-TCGGGTCAGATCGGATGAAACTT
183 GG--TCAAACTTCAT-AATGTCGGGTCAGATC--AT--AACTT
*
31531 TATTTTGGTCAGGTCGGG-TCGGGT
1 TATTTTGGTCGGGTCGGGTTCGGGT
31555 GGACCAAAAA
Statistics
Matches: 213, Mismatches: 26, Indels: 29
0.79 0.10 0.11
Matches are distributed among these distances:
219 1 0.00
220 1 0.00
221 1 0.00
222 1 0.00
223 36 0.17
226 1 0.00
227 1 0.00
228 2 0.01
230 6 0.03
231 90 0.42
232 62 0.29
233 7 0.03
234 1 0.00
235 3 0.01
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (218 bp):
TATTTTGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTT
TACCTAATATATTCAGGAATAATTACAATAATACCCATCTATATATAATTGTTATTCCAATTAAG
TCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGGTCAAACTTCAT
AATGTCGGGTCAGATCATAACTT
Found at i:38864 original size:8 final size:8
Alignment explanation
Indices: 38851--38877 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
38841 AAAAGTACAT
38851 TGTTATTC
1 TGTTATTC
38859 TGTTATTC
1 TGTTATTC
38867 TGTTATTC
1 TGTTATTC
38875 TGT
1 TGT
38878 GCTTCAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.15, T:0.63
Consensus pattern (8 bp):
TGTTATTC
Found at i:39060 original size:35 final size:35
Alignment explanation
Indices: 39008--39145 Score: 170
Period size: 35 Copynumber: 3.9 Consensus size: 35
38998 TGAATAAGAA
* *
39008 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGT
* * * *
39043 GAACGGAAGAAAACATCGACACTTTCGATTCATGAA
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAG-T
* *
39079 GAACGAAAGGAAGCATCGACACTTTCAATTCAAGT
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGT
*
39114 GAACGGAAGGAAGCTTC-AGCACTTTCGATTCA
1 GAACGGAAGGAAGCATCGA-CACTTTCGATTCA
39146 GTTGTTCATC
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
34 1 0.01
35 56 0.65
36 29 0.34
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20
Consensus pattern (35 bp):
GAACGGAAGGAAGCATCGACACTTTCGATTCAAGT
Found at i:39092 original size:71 final size:71
Alignment explanation
Indices: 39005--39145 Score: 221
Period size: 71 Copynumber: 2.0 Consensus size: 71
38995 AGGTGAATAA
* *
39005 GAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGGAAGAAAACATC-GACACTTTC
1 GAAGAACGAAAGGAAGCATCGACACTTTCAATTCAAGTGAACGGAAGAAAACATCAG-CACTTTC
39069 GATTCAT
65 GATTCAT
* * *
39076 GAAGAACGAAAGGAAGCATCGACACTTTCAATTCAAGTGAACGGAAGGAAGCTTCAGCACTTTCG
1 GAAGAACGAAAGGAAGCATCGACACTTTCAATTCAAGTGAACGGAAGAAAACATCAGCACTTTCG
39141 ATTCA
66 ATTCA
39146 GTTGTTCATC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
71 63 0.98
72 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (71 bp):
GAAGAACGAAAGGAAGCATCGACACTTTCAATTCAAGTGAACGGAAGAAAACATCAGCACTTTCG
ATTCAT
Found at i:40323 original size:16 final size:16
Alignment explanation
Indices: 40299--40333 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40289 GATGAATAAA
* *
40299 TTTATTTTAATTTATT
1 TTTAGTTTAATATATT
40315 TTTAGTTTAATATATT
1 TTTAGTTTAATATATT
40331 TTT
1 TTT
40334 CTCAACAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTAGTTTAATATATT
Found at i:41179 original size:32 final size:33
Alignment explanation
Indices: 41130--41199 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 33
41120 AATAATTTAC
*
41130 TTTAAAATTTTTAACTATTGAATTATTTAGAAT
1 TTTAAAATTTTTAACTATTGAATCATTTAGAAT
41163 TTTAAAA-TTTTAACTATTGAATCATTTAGAAT
1 TTTAAAATTTTTAACTATTGAATCATTTAGAAT
41195 TTTAA
1 TTTAA
41200 TTTTTTATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 29 0.81
33 7 0.19
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (33 bp):
TTTAAAATTTTTAACTATTGAATCATTTAGAAT
Found at i:41642 original size:16 final size:16
Alignment explanation
Indices: 41621--41660 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
41611 AAAATTTAAT
* *
41621 TTTTATTCATTATTTA
1 TTTTATTAATTATATA
41637 TTTTATTAATTATATA
1 TTTTATTAATTATATA
41653 TTTATATT
1 TTT-TATT
41661 TATTTTTACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTATTAATTATATA
Found at i:41645 original size:26 final size:26
Alignment explanation
Indices: 41616--41666 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
41606 ATCTTAAAAT
*
41616 TTAATT-TTTATTCATTATTTATTTTA
1 TTAATTATATATTCA-TATTTATTTTA
*
41642 TTAATTATATATTTATATTTATTTT
1 TTAATTATATATTCATATTTATTTT
41667 TACGTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (26 bp):
TTAATTATATATTCATATTTATTTTA
Found at i:54645 original size:35 final size:35
Alignment explanation
Indices: 54588--54679 Score: 118
Period size: 34 Copynumber: 2.7 Consensus size: 35
54578 AACAAAATTT
*
54588 CTTAACGAGAACGAGT-GAAGCAAAA-TTTATCGAG
1 CTTAACGAGAACGAGTCG-AGCAAAATTTTAACGAG
54622 CTTAACGAGCAACGAGTCGAGCAAAATTTTAACGAG
1 CTTAACGAG-AACGAGTCGAGCAAAATTTTAACGAG
* *
54658 CTTTACGAG-TCGAGTCGAGCAA
1 CTTAACGAGAACGAGTCGAGCAA
54680 TAAATATATT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
34 21 0.40
35 14 0.27
36 17 0.33
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (35 bp):
CTTAACGAGAACGAGTCGAGCAAAATTTTAACGAG
Done.