Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004711.1 Hibiscus syriacus cultivar Beakdansim tig00010618_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: 90175
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:54 original size:23 final size:23
Alignment explanation
Indices: 5--72 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1 TATA
*
5 TGGCACTACGGTGC-ATTCTATG
1 TGGCACTACGGTGCAATTCTACG
* *
27 CGGCACTCCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
50 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
73 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 12 0.31
23 27 0.69
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:2342 original size:21 final size:21
Alignment explanation
Indices: 2293--2345 Score: 99
Period size: 20 Copynumber: 2.6 Consensus size: 21
2283 TCTGGCTTAG
2293 AGTATCGATACCCTTATGAAC
1 AGTATCGATACCCTTATGAAC
2314 AG-ATCGATACCCTTATGAAC
1 AGTATCGATACCCTTATGAAC
2334 AGTATCGATACC
1 AGTATCGATACC
2346 TCTTGGGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (21 bp):
AGTATCGATACCCTTATGAAC
Found at i:2436 original size:20 final size:21
Alignment explanation
Indices: 2400--2450 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
2390 ATTGATAGTG
* *
2400 GTATCGATA-CTATAAGGGTA
1 GTATCGATACCTAGAAGGATA
*
2420 GTATCGATACCT-GAAGGATG
1 GTATCGATACCTAGAAGGATA
*
2440 GTATTGATACC
1 GTATCGATACC
2451 CTTAAAACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (21 bp):
GTATCGATACCTAGAAGGATA
Found at i:2533 original size:53 final size:54
Alignment explanation
Indices: 2429--2556 Score: 159
Period size: 53 Copynumber: 2.4 Consensus size: 54
2419 AGTATCGATA
* *
2429 CCTGAAGGATGGTATTGATACCCTTAAAACATCGAATGCCAGATTGGTATCAGTAC
1 CCTG-AGGA-GGTATCGATACCCTTAAAACATCGAATGCCAGATTGATATCAGTAC
* ** **
2485 CCTGAGGAGGTATCGATACCCTT-GAACATCGAATGTTATTTTGATATCAGTAC
1 CCTGAGGAGGTATCGATACCCTTAAAACATCGAATGCCAGATTGATATCAGTAC
*
2538 CATGAGGAGGTATCGATAC
1 CCTGAGGAGGTATCGATAC
2557 AATTGAAGGG
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
53 42 0.66
54 14 0.22
55 4 0.06
56 4 0.06
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (54 bp):
CCTGAGGAGGTATCGATACCCTTAAAACATCGAATGCCAGATTGATATCAGTAC
Found at i:2967 original size:21 final size:21
Alignment explanation
Indices: 2941--2991 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
2931 ATTTTATGGA
*
2941 AATGTGAACTTTGAACAAGTG
1 AATGTGAACTTTAAACAAGTG
*
2962 AATGTGAACTTTAAACCAGTG
1 AATGTGAACTTTAAACAAGTG
2983 AATGTGAAC
1 AATGTGAAC
2992 AAACTCTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (21 bp):
AATGTGAACTTTAAACAAGTG
Found at i:3219 original size:23 final size:23
Alignment explanation
Indices: 3165--3221 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
3155 GAGACAAATA
* *
3165 TGGCACTTCGATGTAAACCTATG
1 TGGCACTTCGGTGCAAACCTATG
3188 TGGCACTTCGGTGCAAACCTATG
1 TGGCACTTCGGTGCAAACCTATG
3211 TGGTC-CTTCGG
1 TGG-CACTTCGG
3222 GACAATTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAAACCTATG
Found at i:11312 original size:72 final size:71
Alignment explanation
Indices: 11223--11360 Score: 231
Period size: 72 Copynumber: 1.9 Consensus size: 71
11213 ACAAGAAATA
*
11223 AAGACTTCGGTGAGAATCTGAATGTTAGTGGTGCAATCAATGTGATGATAACAAATGATCAAGAA
1 AAGACTTCGGTGAGAATCTGAATGTTAGTGGTGCAACCAATGTGATGATAACAAATGATCAAGAA
11288 CAGATG
66 CAGATG
* * *
11294 AAGACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGCAACTGATCAAGA
1 AAGACTTC-GGTGAGAATCTGAATGTTAGTGGTGCAACCAATGTGATGATAACAAATGATCAAGA
11359 AC
65 AC
11361 CTGTTAGGGG
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 8 0.13
72 54 0.87
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.25
Consensus pattern (71 bp):
AAGACTTCGGTGAGAATCTGAATGTTAGTGGTGCAACCAATGTGATGATAACAAATGATCAAGAA
CAGATG
Found at i:14898 original size:125 final size:125
Alignment explanation
Indices: 14676--14924 Score: 311
Period size: 125 Copynumber: 2.0 Consensus size: 125
14666 TACCCACATT
* *** *
14676 GGGGCATGACTAAACCCACATCATGTTGATATGAAAAGATTTGGACCAAGGAGTCATGAAGAATG
1 GGGGCATGACTAAACCCACATCATGTTGAGATGAAAAGATTCACACCAAGAAGTCATGAAGAATG
* * *
14741 AGCCTTACAAATTGAGATGATGGGGCATTTTGAAGGCCCGTACCAGTATGAGATAATGTC
66 AGCCTTACAAATTGAGATGATGGAGCATTTTGAAGGCCCGTACCAGAATAAGATAATGTC
* * * *
14801 GGGGCATGACTGAACCCACATTATGTTGAGATGATAAGGTTCACACCAAGAAGTCATTGAA-AAT
1 GGGGCATGACTAAACCCACATCATGTTGAGATGAAAAGATTCACACCAAGAAGTCA-TGAAGAAT
* * * * * * *
14865 GAGCCTTATAATTTGAGGTGTTTGAGCATTTTGAAGGCTCGTACCTGAATAAGATAATGT
65 GAGCCTTACAAATTGAGATGATGGAGCATTTTGAAGGCCCGTACCAGAATAAGATAATGT
14925 TGCGGCATTA
Statistics
Matches: 104, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
125 100 0.96
126 4 0.04
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (125 bp):
GGGGCATGACTAAACCCACATCATGTTGAGATGAAAAGATTCACACCAAGAAGTCATGAAGAATG
AGCCTTACAAATTGAGATGATGGAGCATTTTGAAGGCCCGTACCAGAATAAGATAATGTC
Found at i:16176 original size:37 final size:37
Alignment explanation
Indices: 16126--16239 Score: 176
Period size: 37 Copynumber: 3.1 Consensus size: 37
16116 AAAGCCAAGT
*
16126 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTGAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
*
16163 CTTCACCAAAGAGTAGTGAAGCAAA-CCATCTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
* * *
16199 CTTCACCGAAGAGTAGTGAAGCATATCCTTTTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
16236 CTTC
1 CTTC
16240 TCAGAAGAGT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
36 32 0.46
37 38 0.54
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (37 bp):
CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
Found at i:16691 original size:54 final size:54
Alignment explanation
Indices: 16626--16981 Score: 441
Period size: 54 Copynumber: 6.6 Consensus size: 54
16616 ATAGTAAAGC
*
16626 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
16680 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGAGAGCGAACCAGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
16734 AGAAGAATATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTT
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
16788 AGAAGAAGATTGTTCGAGTTCTATACTCCCT-GAAGTAAGAGGGAGCGAACCCGTA
1 AGAAGAAGA-TGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTA
* * *
16843 AGAAGAAGTTATTCGAGTTCTATACTCCCT-GAAGCAAA-AGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAG-AG-AAAGAGGGAGCGAACCCGTA
* * * * * * *
16897 AGAAGAAGATGTTCGAGTTCTATACTCTCT-GAAGGAATAGAGAGCGGACCCGTT
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTA
** * *
16951 TTATGAAGATTGTTCGAGTTCTATACTCCCT
1 AGAAGAAGA-TGTTCGAGTTCCATACTCCCT
16982 GAACGGATAG
Statistics
Matches: 272, Mismatches: 25, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
53 2 0.01
54 200 0.74
55 70 0.26
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (54 bp):
AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
Found at i:16816 original size:163 final size:163
Alignment explanation
Indices: 16626--16984 Score: 485
Period size: 163 Copynumber: 2.2 Consensus size: 163
16616 ATAGTAAAGC
*
16626 AGAAGAAGA-TGTTCGAGTTCCATACTCCCT-AGAGAAAGAAGGAGCGAACCCGTAAGAAGAAGA
1 AGAAGAAGATTGTTCGAGTTCTATACTCCCTGA-AGAAAGAAGGAGCGAACCCGTAAGAAGAAGA
* *
16689 TGTTCGAGTTCCATACTCCCT-AGAG-AAAGAGAGAGCGAACCAGTAAGAAGAATATGTTCGAGT
65 TATTCGAGTTCCATACTCCCTGA-AGCAAA-AGAGAGCGAACCAGTAAGAAGAAGATGTTCGAGT
*
16752 TCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTT
128 TCCATACTCCCTGA-AGAAAGAGAGAGCGAACCCGTT
* * *
16788 AGAAGAAGATTGTTCGAGTTCTATACTCCCTGAAGTAAGAGGGAGCGAACCCGTAAGAAGAAGTT
1 AGAAGAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAAGGAGCGAACCCGTAAGAAGAAGAT
* * * *
16853 ATTCGAGTTCTATACTCCCTGAAGCAAAAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTCT
66 ATTCGAGTTCCATACTCCCTGAAGCAAAAGAGAGCGAACCAGTAAGAAGAAGATGTTCGAGTTCC
* * * *
16918 ATACTCTCTGAAGGAATAGAGAGCGGACCCGTT
131 ATACTCCCTGAAGAAAGAGAGAGCGAACCCGTT
** *
16951 TTATGAAGATTGTTCGAGTTCTATACTCCCTGAA
1 AGAAGAAGATTGTTCGAGTTCTATACTCCCTGAA
16985 CGGATAGGGA
Statistics
Matches: 174, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
162 9 0.05
163 159 0.91
164 6 0.03
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (163 bp):
AGAAGAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAAGGAGCGAACCCGTAAGAAGAAGAT
ATTCGAGTTCCATACTCCCTGAAGCAAAAGAGAGCGAACCAGTAAGAAGAAGATGTTCGAGTTCC
ATACTCCCTGAAGAAAGAGAGAGCGAACCCGTT
Found at i:16868 original size:109 final size:107
Alignment explanation
Indices: 16626--16983 Score: 461
Period size: 109 Copynumber: 3.3 Consensus size: 107
16616 ATAGTAAAGC
* *
16626 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTAAGAAGAAGATG
1 AGAAGAAGTTGTTCGAGTTCCATACTCCCT-GAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATG
* * *
16691 TTCGAGTTCCATACTCCCT-AGAGAAAGAGAGAGCGAACCAGTA
65 TTCGAGTTCTATACTCCCTGA-AGGAAGAGAGAGCGAACCCGTA
*
16734 AGAAGAA-TATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTAGAAGAAGAT
1 AGAAGAAGT-TGTTCGAGTTCCATACTCCCT-GAGAAAGAGGGAGCGAACCCGTAAGAAGAAGA-
* *
16798 TGTTCGAGTTCTATACTCCCTGAAGTAAGAGGGAGCGAACCCGTA
63 TGTTCGAGTTCTATACTCCCTGAAGGAAGAGAGAGCGAACCCGTA
* *
16843 AGAAGAAGTTATTCGAGTTCTATACTCCCTGAAGCAAA-AGGGAGCGAACCCGTAAGAAGAAGAT
1 AGAAGAAGTTGTTCGAGTTCCATACTCCCTG-AG-AAAGAGGGAGCGAACCCGTAAGAAGAAGAT
* * * *
16907 GTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTT
64 GTTCGAGTTCTATACTCCCTGAAGGAAGAGAGAGCGAACCCGTA
** * *
16951 TTATGAAGATTGTTCGAGTTCTATACTCCCTGA
1 AGAAGAAG-TTGTTCGAGTTCCATACTCCCTGA
16984 ACGGATAGGG
Statistics
Matches: 223, Mismatches: 20, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
108 105 0.47
109 113 0.51
110 5 0.02
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (107 bp):
AGAAGAAGTTGTTCGAGTTCCATACTCCCTGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGT
TCGAGTTCTATACTCCCTGAAGGAAGAGAGAGCGAACCCGTA
Found at i:17008 original size:54 final size:53
Alignment explanation
Indices: 16628--17051 Score: 325
Period size: 54 Copynumber: 7.8 Consensus size: 53
16618 AGTAAAGCAG
* * **
16628 AAGAAGA-TGTTCGAGTTCCATACTCCCT--AGAGAAAGAAGGAGCGAACCCGTAAG
1 AAGAAGATTGTTCGAGTTCTATACTCCCTGAAG-GATAG--GGAGCGAACCCGT-TT
* * *
16682 AAGAAGA-TGTTCGAGTTCCATACTCCCT--AGAGAAAGAGAGAGCGAACCAG--T
1 AAGAAGATTGTTCGAGTTCTATACTCCCTGAAG-GATAG-G-GAGCGAACCCGTTT
* * * *
16733 AAGAAGAATATGTTCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTAG
1 AAGAAG-AT-TGTTCGAGTTCTATACTCCCTGA-AG-GATAGGGAGCGAACCCGTT-T
* *
16790 AAGAAGATTGTTCGAGTTCTATACTCCCTGAAGTAAGAGGGAGCGAACCCG--T
1 AAGAAGATTGTTCGAGTTCTATACTCCCTGAAG-GATAGGGAGCGAACCCGTTT
* * * **
16842 AAGAAGAAGTTATTCGAGTTCTATACTCCCTGAAGCAAAAGGGAGCGAACCCGTAAG
1 AAGAAG-A-TTGTTCGAGTTCTATACTCCCTGAAG-GATAGGGAGCGAACCCGT-TT
* * *
16899 AAGAAGA-TGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT
1 AAGAAGATTGTTCGAGTTCTATACTCCCTGAAGG-ATAGGGAGCGAACCCG-TTT
* *
16953 ATGAAGATTGTTCGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTT
1 AAGAAGATTGTTCGAGTTCTATACTCCCTGAA-GGATAGGGAGCGAACCCGTTT
* *
17007 ATTGAAGATTGATCGAG-TCTTATACTCCCTGAAGGAATAGGGAGC
1 A-AGAAGATTGTTCGAGTTC-TATACTCCCTGAAGG-ATAGGGAGC
17052 AGACTTATCA
Statistics
Matches: 323, Mismatches: 25, Indels: 43
0.83 0.06 0.11
Matches are distributed among these distances:
51 6 0.02
52 7 0.02
53 3 0.01
54 168 0.52
55 115 0.36
56 12 0.04
57 12 0.04
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (53 bp):
AAGAAGATTGTTCGAGTTCTATACTCCCTGAAGGATAGGGAGCGAACCCGTTT
Found at i:17081 original size:55 final size:55
Alignment explanation
Indices: 16901--17055 Score: 171
Period size: 55 Copynumber: 2.9 Consensus size: 55
16891 CCCGTAAGAA
* * *
16901 GAAGA-TGTTCGAGT-TCTATACTCTCTGAA-GGAATAGAGAGCGGACCCGTTT-TAT
1 GAAGATTGTTCGAGTCTCTATACTCCCTGAACGG-ATAGGGAGCAGA-CCGTTTAT-T
*
16955 GAAGATTGTTCGAGT-TCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTATT
1 GAAGATTGTTCGAGTCTCTATACTCCCTGAACGGATAGGGAGCAGA-CCGTTTATT
*
17010 GAAGATTGATCGAGTCT-TATACTCCCTGAA-GGAATAGGGAGCAGAC
1 GAAGATTGTTCGAGTCTCTATACTCCCTGAACGG-ATAGGGAGCAGAC
17056 TTATCATTTG
Statistics
Matches: 92, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
54 8 0.09
55 80 0.87
56 4 0.04
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTCTATACTCCCTGAACGGATAGGGAGCAGACCGTTTATT
Found at i:19407 original size:12 final size:12
Alignment explanation
Indices: 19366--19407 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
19356 CATTTGTTTT
19366 TTAAATTAAAAA
1 TTAAATTAAAAA
*
19378 -TCAATTGAAAAA
1 TTAAATT-AAAAA
19390 TGTAAATTAAAAA
1 T-TAAATTAAAAA
19403 TTAAA
1 TTAAA
19408 GTGGTTTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 5 0.20
12 9 0.36
13 6 0.24
14 5 0.20
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (12 bp):
TTAAATTAAAAA
Found at i:19995 original size:14 final size:14
Alignment explanation
Indices: 19959--19996 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
19949 TTTTGAAAAT
19959 AAAAAATTAATTGA
1 AAAAAATTAATTGA
* *
19973 AATAGATTAATTGA
1 AAAAAATTAATTGA
19987 AAAAAATTAA
1 AAAAAATTAA
19997 ACTCATGTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (14 bp):
AAAAAATTAATTGA
Found at i:22467 original size:13 final size:13
Alignment explanation
Indices: 22449--22485 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
22439 ATAAAATTGT
22449 AAAAAATTAATTA
1 AAAAAATTAATTA
22462 AAAAAATTAATTA
1 AAAAAATTAATTA
*
22475 AAAAATTTAAT
1 AAAAAATTAAT
22486 AATAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAAATTAATTA
Found at i:23223 original size:81 final size:82
Alignment explanation
Indices: 23088--23251 Score: 321
Period size: 81 Copynumber: 2.0 Consensus size: 82
23078 TGTCATTGAA
23088 TAATAAAAATTCTACAAATGTTAAATTATAAATTTATTCTTAAACTATTTTATATTTAC-AAAAA
1 TAATAAAAATTCTACAAATGTTAAATTATAAATTTATTCTTAAACTATTTTATATTTACAAAAAA
23152 AATCTATAATTAAAATT
66 AATCTATAATTAAAATT
23169 TAATAAAAATTCTACAAATGTTAAATTATAAATTTATTCTTAAACTATTTTATATTTACAAAAAA
1 TAATAAAAATTCTACAAATGTTAAATTATAAATTTATTCTTAAACTATTTTATATTTACAAAAAA
23234 AATCTATAATTAAAATT
66 AATCTATAATTAAAATT
23251 T
1 T
23252 TATATGAAGT
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 59 0.72
82 23 0.28
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (82 bp):
TAATAAAAATTCTACAAATGTTAAATTATAAATTTATTCTTAAACTATTTTATATTTACAAAAAA
AATCTATAATTAAAATT
Found at i:29430 original size:4 final size:4
Alignment explanation
Indices: 29421--29483 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
29411 AAAAAATCAT
29421 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
29469 TCTG TCTG TCTG TCT
1 TCTG TCTG TCTG TCT
29484 ATCTATTATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.00, C:0.25, G:0.24, T:0.51
Consensus pattern (4 bp):
TCTG
Found at i:34391 original size:32 final size:31
Alignment explanation
Indices: 34346--34447 Score: 107
Period size: 31 Copynumber: 3.2 Consensus size: 31
34336 AATTATTTTT
* * *
34346 AAATAATTATAAAATAA-TAATTAAATTTTATT
1 AAATTATTATAAAACAAGT-ATTAAA-TTTATA
*
34378 AAGTTATTATAAAACAAGTATTAAATTTATA
1 AAATTATTATAAAACAAGTATTAAATTTATA
* * *
34409 AAATTATTATAAAACAATTCTTAAACTTATAA
1 AAATTATTATAAAACAAGTATTAAATTTAT-A
34441 AAATTAT
1 AAATTAT
34448 CTTTATTTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
31 31 0.52
32 28 0.47
33 1 0.02
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (31 bp):
AAATTATTATAAAACAAGTATTAAATTTATA
Found at i:44794 original size:3 final size:3
Alignment explanation
Indices: 44786--44836 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
44776 TTATGTAAAC
44786 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
44834 ATA
1 ATA
44837 GGGGCATACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:45017 original size:2 final size:2
Alignment explanation
Indices: 45010--45052 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
45000 CAAGTTAATA
45010 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
45052 A
1 A
45053 GATAGCCCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59053 original size:14 final size:14
Alignment explanation
Indices: 59034--59060 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
59024 AAGGTCAACG
59034 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
59048 GTCGGGTCGGGTC
1 GTCGGGTCGGGTC
59061 TGACCGGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.22, G:0.52, T:0.22
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:59077 original size:9 final size:9
Alignment explanation
Indices: 59063--59125 Score: 72
Period size: 10 Copynumber: 6.7 Consensus size: 9
59053 GTCGGGTCTG
59063 ACCGGTCAA
1 ACCGGTCAA
* *
59072 ATCGGTTCAG
1 ACCGG-TCAA
59082 ACCGGTCAA
1 ACCGGTCAA
*
59091 ACCGGTTCGA
1 ACCGG-TCAA
59101 ACCGGTCAA
1 ACCGGTCAA
59110 ACCGGTCAAA
1 ACCGGTC-AA
59120 ACCGGT
1 ACCGGT
59126 TTTTCCAGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
9 22 0.49
10 23 0.51
ACGTcount: A:0.29, C:0.30, G:0.25, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:59103 original size:10 final size:10
Alignment explanation
Indices: 59063--59126 Score: 64
Period size: 9 Copynumber: 6.7 Consensus size: 10
59053 GTCGGGTCTG
59063 ACCGG-TCAA
1 ACCGGTTCAA
* *
59072 ATCGGTTCAG
1 ACCGGTTCAA
59082 ACCGG-TCAA
1 ACCGGTTCAA
*
59091 ACCGGTTCGA
1 ACCGGTTCAA
59101 ACCGG-TCAA
1 ACCGGTTCAA
59110 ACCGG-TCAAA
1 ACCGGTTC-AA
59120 ACCGGTT
1 ACCGGTT
59127 TTTCCAGCAG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
9 22 0.49
10 22 0.49
11 1 0.02
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:59122 original size:19 final size:19
Alignment explanation
Indices: 59063--59125 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
59053 GTCGGGTCTG
* *
59063 ACCGGTCAAATCGGTTCAG
1 ACCGGTCAAACCGGTTCAA
*
59082 ACCGGTCAAACCGGTTCGA
1 ACCGGTCAAACCGGTTCAA
59101 ACCGGTCAAACCGG-TCAAA
1 ACCGGTCAAACCGGTTC-AA
59120 ACCGGT
1 ACCGGT
59126 TTTTCCAGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 2 0.05
19 37 0.95
ACGTcount: A:0.29, C:0.30, G:0.25, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAA
Found at i:66383 original size:37 final size:37
Alignment explanation
Indices: 66328--66398 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
66318 TCTAAAATTT
* *
66328 GTTAAATGTTAGGGTAAAGTAAACGAAATTATTAATC
1 GTTAAAGGTTAGGATAAAGTAAACGAAATTATTAATC
*
66365 GTTAAAGGTTAGGATAAAGTAAATGAAATTATTA
1 GTTAAAGGTTAGGATAAAGTAAACGAAATTATTA
66399 TTCGACTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.32
Consensus pattern (37 bp):
GTTAAAGGTTAGGATAAAGTAAACGAAATTATTAATC
Found at i:66935 original size:28 final size:28
Alignment explanation
Indices: 66885--66941 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
66875 CTCTTCGCTT
* *
66885 ACATTATGTCGTCGAATCTATACTTGAA
1 ACATTATGTCGTCGAAGCAATACTTGAA
* *
66913 ACATTATGTCGTTGAGGCAATACTTGAA
1 ACATTATGTCGTCGAAGCAATACTTGAA
66941 A
1 A
66942 GCAAGACCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (28 bp):
ACATTATGTCGTCGAAGCAATACTTGAA
Found at i:67454 original size:44 final size:41
Alignment explanation
Indices: 67377--67458 Score: 110
Period size: 44 Copynumber: 1.9 Consensus size: 41
67367 GCAACGCGAT
* * *
67377 TTTGAAAAATGTGTTGCGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGATAATGAAAAAGTGTTGCGAGAG
67418 TTTGAAAAACGTGTTGTTGCGATAATGAAAAAGTGTTGCGA
1 TTTGAAAAA--TG-TGTTGCGATAATGAAAAAGTGTTGCGA
67459 TAGTAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 9 0.26
43 2 0.06
44 24 0.69
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAATGAAAAAGTGTTGCGAGAG
Found at i:67468 original size:19 final size:19
Alignment explanation
Indices: 67381--67467 Score: 77
Period size: 19 Copynumber: 4.3 Consensus size: 19
67371 CGCGATTTTG
67381 AAAAATGTGTTGCGATAGT
1 AAAAATGTGTTGCGATAGT
* *
67400 TAAAATGTGTTGCGAGAGTTT
1 AAAAATGTGTTGCGATAG--T
*
67421 GAAAAACGTGTTGTTGCGATAAT
1 -AAAAA--TG-TGTTGCGATAGT
67444 GAAAAA-GTGTTGCGATAGT
1 -AAAAATGTGTTGCGATAGT
67463 AAAAA
1 AAAAA
67468 ATCCAAAATA
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
18 5 0.09
19 27 0.48
20 1 0.02
21 1 0.02
22 4 0.07
23 7 0.12
24 2 0.04
25 9 0.16
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.30
Consensus pattern (19 bp):
AAAAATGTGTTGCGATAGT
Found at i:69269 original size:2 final size:2
Alignment explanation
Indices: 69258--69286 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
69248 CATTAATTAG
69258 AT AT -T 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
69287 TAATTTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:70917 original size:16 final size:16
Alignment explanation
Indices: 70872--70909 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
70862 TTCGAACAAG
70872 CATGCGAATTAGATAT
1 CATGCGAATTAGATAT
70888 CATGCGAATTAGATAT
1 CATGCGAATTAGATAT
70904 CATGCG
1 CATGCG
70910 GTTAAGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (16 bp):
CATGCGAATTAGATAT
Found at i:80604 original size:19 final size:17
Alignment explanation
Indices: 80564--80700 Score: 91
Period size: 17 Copynumber: 7.7 Consensus size: 17
80554 AAGAAATGAA
* *
80564 AAAAAAGAAAGAAAAAAG
1 AAAAATGAAA-AAAAAGG
80582 -AAAATGAAAAAAAGGAGG
1 AAAAATGAAAAAAA--AGG
* *
80600 AAAAATGAAAGAAAATG
1 AAAAATGAAAAAAAAGG
*
80617 AAAAATGAGAAAAAAAAATG
1 AAAAAT--G-AAAAAAAAGG
*
80637 AAAAATGGTGAAAAAAA-G
1 AAAAAT-G-AAAAAAAAGG
* *
80655 AAAAATGAAGAAAAATG
1 AAAAATGAAAAAAAAGG
80672 AAAAATGAAAAAAGAA-G
1 AAAAATGAAAAAA-AAGG
*
80689 AAAAAAGAAAAA
1 AAAAATGAAAAA
80701 GAAATAAAAG
Statistics
Matches: 99, Mismatches: 12, Indels: 17
0.77 0.09 0.13
Matches are distributed among these distances:
16 10 0.10
17 42 0.42
18 11 0.11
19 21 0.21
20 15 0.15
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.07
Consensus pattern (17 bp):
AAAAATGAAAAAAAAGG
Found at i:80628 original size:55 final size:55
Alignment explanation
Indices: 80549--80714 Score: 153
Period size: 55 Copynumber: 2.9 Consensus size: 55
80539 ATATTTCGCT
**
80549 TGAAGAAGAAATGAAAAAAAAGAAAGAAAAAAGAAAATGAAAAAAAGGAGGAAAAA
1 TGAAGAA-AAATGAAAAATGAGAAAGAAAAAAGAAAATGAAAAAAAGGAGGAAAAA
*
80605 TGAA-AGAAAATGAAAAATGAGAAA-AAAAAATGAAAAATGGTGAAAAAA--A-GAAAAA
1 TGAAGA-AAAATGAAAAATGAGAAAGAAAAAA-G-AAAAT-G-AAAAAAAGGAGGAAAAA
* *
80660 TGAAGAAAAATGAAAAATGAAAAAAGAAGAAAAAAGAAAAAGAAATAAAAGGAGG
1 TGAAGAAAAATGAAAAATG---AGA-AAGAAAAAAGAAAATGAAA-AAAAGGAGG
80715 GTTCAAGATG
Statistics
Matches: 89, Mismatches: 6, Indels: 26
0.74 0.05 0.21
Matches are distributed among these distances:
54 6 0.07
55 40 0.45
56 14 0.16
57 6 0.07
58 12 0.13
59 4 0.04
60 7 0.08
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.08
Consensus pattern (55 bp):
TGAAGAAAAATGAAAAATGAGAAAGAAAAAAGAAAATGAAAAAAAGGAGGAAAAA
Found at i:80632 original size:29 final size:30
Alignment explanation
Indices: 80578--80639 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
80568 AAGAAAGAAA
**
80578 AAAGAAAATGAAAAAAAGG-AGGAAAAATG
1 AAAGAAAATGAAAAAAAGGAAAAAAAAATG
*
80607 AAAGAAAATG-AAAAATGAGAAAAAAAAATG
1 AAAGAAAATGAAAAAAAG-GAAAAAAAAATG
80637 AAA
1 AAA
80640 AATGGTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 11 0.39
30 11 0.39
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (30 bp):
AAAGAAAATGAAAAAAAGGAAAAAAAAATG
Found at i:80635 original size:13 final size:12
Alignment explanation
Indices: 80557--80641 Score: 64
Period size: 13 Copynumber: 6.8 Consensus size: 12
80547 CTTGAAGAAG
80557 AAATGAAAAAAA
1 AAATGAAAAAAA
*
80569 AGAAAGAAAAAAGA
1 A-AATGAAAAAA-A
80583 AAATGAAAAAAA
1 AAATGAAAAAAA
** * **
80595 GGAGGAAAAATG
1 AAATGAAAAAAA
*
80607 AAA-GAAAATGAA
1 AAATGAAAA-AAA
80619 AAATGAGAAAAAA
1 AAATGA-AAAAAA
80632 AAATGAAAAA
1 AAATGAAAAA
80642 TGGTGAAAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
11 5 0.09
12 17 0.31
13 28 0.51
14 5 0.09
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (12 bp):
AAATGAAAAAAA
Found at i:80649 original size:21 final size:20
Alignment explanation
Indices: 80557--80694 Score: 85
Period size: 19 Copynumber: 7.0 Consensus size: 20
80547 CTTGAAGAAG
**
80557 AAATGAAAAAAAAGAAAGAAA
1 AAATGAAAAATGAGAAA-AAA
80578 AAA-G-AAAATGA-AAAAAA
1 AAATGAAAAATGAGAAAAAA
** * *
80595 GGAGGAAAAAT--G-AAAGA
1 AAATGAAAAATGAGAAAAAA
80612 AAATGAAAAATGAGAAAAAA
1 AAATGAAAAATGAGAAAAAA
**
80632 AAATGAAAAATG-GTGAAAA
1 AAATGAAAAATGAGAAAAAA
80651 AAA-GAAAAATGAAGAAAAATGAA
1 AAATGAAAAATG-AG-AAAA--AA
*
80674 AAATGAAAAAAGAAGAAAAAA
1 AAATGAAAAATG-AGAAAAAA
80695 GAAAAAGAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 24
0.71 0.11 0.19
Matches are distributed among these distances:
17 16 0.18
18 12 0.13
19 19 0.21
20 18 0.20
21 7 0.08
23 9 0.10
24 10 0.11
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (20 bp):
AAATGAAAAATGAGAAAAAA
Found at i:80665 original size:10 final size:10
Alignment explanation
Indices: 80549--80673 Score: 60
Period size: 10 Copynumber: 13.4 Consensus size: 10
80539 ATATTTCGCT
80549 TGAAGAAGAAA
1 TGAAGAA-AAA
80560 TGAA-AAAAA
1 TGAAGAAAAA
*
80569 AGAA-AGAAAA
1 TGAAGA-AAAA
80579 --AAG-AAAA
1 TGAAGAAAAA
80586 TGAA-AAAAA
1 TGAAGAAAAA
* *
80595 GGAGGAAAAA
1 TGAAGAAAAA
80605 TGAA-AGAAAA
1 TGAAGA-AAAA
80615 T---GAAAAA
1 TGAAGAAAAA
80622 TG-AGAAAAA
1 TGAAGAAAAA
**
80631 AAAATGAAAAA
1 TGAA-GAAAAA
**
80642 TGGTGAAAAA
1 TGAAGAAAAA
80652 --AAGAAAAA
1 TGAAGAAAAA
80660 TGAAGAAAAA
1 TGAAGAAAAA
80670 TGAA
1 TGAA
80674 AAATGAAAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 29
0.67 0.10 0.22
Matches are distributed among these distances:
7 9 0.10
8 9 0.10
9 22 0.25
10 37 0.43
11 10 0.11
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (10 bp):
TGAAGAAAAA
Found at i:82037 original size:37 final size:38
Alignment explanation
Indices: 81987--82060 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 38
81977 AATTCAATCT
81987 TAAGCCTTCACGGAAGAGTAGTGAAGCAAA-TCATTTA
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAACTCATTTA
*
82024 TAAGCCTTCACGGAAGAGTTGTGAAGCAAACTCATTT
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAACTCATTT
82061 TATGAAGATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 29 0.83
38 6 0.17
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.26
Consensus pattern (38 bp):
TAAGCCTTCACGGAAGAGTAGTGAAGCAAACTCATTTA
Found at i:82242 original size:55 final size:55
Alignment explanation
Indices: 82069--82479 Score: 369
Period size: 55 Copynumber: 7.7 Consensus size: 55
82059 TTTATGAAGA
* ** * *
82069 TCGAGTCCTATACTCTCTGAAGGAATATAGAGCGGACCCGTTTGCTGAAGA----
1 TCGAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * *
82120 TCGAGTCCTATACTCTCTGAAGGAATAGAGAGC-GACCCGTTT-TATGAAGATTGT
1 TCGAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACACGTTTGT-TGAAGATTGT
* * ** *
82174 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACTTGTTTGTTGAAAATTGT
1 TCGAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * *
82229 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGATACGTTTATTGAAGA---T
1 TCGAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* ** * * * *
82281 T-GAGT-CTTTTTTCTCTGAAGAAATAGGGAGCAGAC-CGTTTGTTGAAGATTAT
1 TCGAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * ** *
82333 TCGAGTCTTATACTCCCTGAACGAACAGGGAGCAAACACGTTTATTGAAGATTGT
1 TCGAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * * **
82388 TTGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGCCGAAGATTGT
1 TCGAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * * *
82443 CCAAGTCTTATACTCCCTAAAAGAATAGGGAGCGGAC
1 TCGAGTCCTATACTCCCTGAAGGAATAGGGAGCGGAC
82480 CCGTCGTTTG
Statistics
Matches: 299, Mismatches: 48, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
49 12 0.04
50 39 0.13
51 36 0.12
52 4 0.01
53 4 0.01
54 50 0.17
55 153 0.51
56 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (55 bp):
TCGAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
Found at i:82440 original size:159 final size:160
Alignment explanation
Indices: 82069--82441 Score: 457
Period size: 159 Copynumber: 2.3 Consensus size: 160
82059 TTTATGAAGA
** * *
82069 TCGAGTCCTATACTCTCTGAAGGAATATAGAGCGGACCCGTTTGCTGAAGATCGAGTCCTATACT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGCTGAAGATTGAGTCCTATACT
* *
82134 CTCTGAAGGAATAGAGAGCGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCCCTGAACGAA
66 CTCTGAAGAAATAGAGAGCGACCCGTTTTATGAAGATTATTCGAGTTCTATACTCCCTGAACGAA
* ** ** *
82199 TAGGGAGCGGACTTGTTTGTTGAAAATTGT
131 CAGGGAGCAAACACGTTTATTGAAAATTGT
* ** * **
82229 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGATACGTTTATTGAAGATTGAGT-CTTTTTT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGCTGAAGATTGAGTCCTATACT
*
82293 CTCTGAAGAAATAGGGAGCAGA-CCGTTTGT-TGAAGATTATTCGAG-TCTTATACTCCCTGAAC
66 CTCTGAAGAAATAGAGAGC-GACCCGTTT-TATGAAGATTATTCGAGTTC-TATACTCCCTGAAC
*
82355 GAACAGGGAGCAAACACGTTTATTGAAGATTGT
128 GAACAGGGAGCAAACACGTTTATTGAAAATTGT
* * * * * *
82388 TTGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGCCGAAGATTG
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGCTGAAGATTG
82442 TCCAAGTCTT
Statistics
Matches: 181, Mismatches: 29, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
158 2 0.01
159 126 0.70
160 53 0.29
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (160 bp):
TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGCTGAAGATTGAGTCCTATACT
CTCTGAAGAAATAGAGAGCGACCCGTTTTATGAAGATTATTCGAGTTCTATACTCCCTGAACGAA
CAGGGAGCAAACACGTTTATTGAAAATTGT
Found at i:83793 original size:64 final size:64
Alignment explanation
Indices: 83750--83870 Score: 197
Period size: 64 Copynumber: 1.9 Consensus size: 64
83740 ACTCTTTTAA
83750 AATAAAGACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAAT
1 AATAAA-ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAAT
* ** *
83815 AATGAAACATCGAATGCAATTGGTGCATCGATGCATAAGGAGTGCATCGATGCATC
1 AATAAAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATC
83871 AGGAGTGCAT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
64 47 0.90
65 5 0.10
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (64 bp):
AATAAAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAAT
Found at i:83913 original size:104 final size:102
Alignment explanation
Indices: 83774--83973 Score: 251
Period size: 104 Copynumber: 1.9 Consensus size: 102
83764 ATGCAATTCA
** * *
83774 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATGA-AACATCGAATGCAATTGG
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCAACAATAAT-ACAACATCGAATACAATTGA
*
83838 TGCATCGATGCATAAGGAGTGCATCGATGCATCAGGAG
65 TGCACCGATGCATAAGGAGTGCATCGATGCATCAGGAG
* **
83876 TGCATCGATGCATCCCAAG-AGTGCATCGATGCATCCCAACAATAATACTACATCGAATACCTTT
1 TGCATCGATGCAT---AAGTAGTGCATCGATGCATCCCAACAATAATACAACATCGAATACAATT
* * *
83940 TATGCACCGATGCATCAGTAGTGCATCGATGCAT
63 GATGCACCGATGCATAAGGAGTGCATCGATGCAT
83974 ACCTTCATTA
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
102 13 0.16
103 1 0.01
104 66 0.80
105 3 0.04
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (102 bp):
TGCATCGATGCATAAGTAGTGCATCGATGCATCCCAACAATAATACAACATCGAATACAATTGAT
GCACCGATGCATAAGGAGTGCATCGATGCATCAGGAG
Found at i:83914 original size:21 final size:19
Alignment explanation
Indices: 83837--83910 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
83827 AATGCAATTG
83837 GTGCATCGATGCAT-AAGGA
1 GTGCATCGATGCATCAA-GA
*
83856 GTGCATCGATGCATCAGGA
1 GTGCATCGATGCATCAAGA
83875 GTGCATCGATGCATCCCAAGA
1 GTGCATCGATGCAT--CAAGA
83896 GTGCATCGATGCATC
1 GTGCATCGATGCATC
83911 CCAACAATAA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
19 31 0.62
20 1 0.02
21 18 0.36
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (19 bp):
GTGCATCGATGCATCAAGA
Found at i:84350 original size:29 final size:29
Alignment explanation
Indices: 84308--84410 Score: 181
Period size: 29 Copynumber: 3.6 Consensus size: 29
84298 TGATATGAAG
84308 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
84337 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
*
84366 TGACATGAGATACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
*
84395 TGATATGAG-TACATGA
1 TGACATGAGCTACATGA
84411 ACATATGAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
28 7 0.10
29 65 0.90
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:87444 original size:40 final size:39
Alignment explanation
Indices: 87389--87511 Score: 192
Period size: 40 Copynumber: 3.1 Consensus size: 39
87379 GAAAATTCTT
* *
87389 AACGAACTTGGAAAATCGCAACGCGAACTTCGACTACCGC
1 AACGAATTTGGAAAATCGCAACGCGAACTT-GACTATCGC
* *
87429 AACGAATTTGAAAAATCGCAACGTGAACTTGGACTATCGC
1 AACGAATTTGGAAAATCGCAACGCGAACTT-GACTATCGC
87469 AACGAATTTGGAAAATCGCAACGCGAACTTGACTATCGC
1 AACGAATTTGGAAAATCGCAACGCGAACTTGACTATCGC
87508 AACG
1 AACG
87512 CGAACTTGGA
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
39 13 0.17
40 63 0.83
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (39 bp):
AACGAATTTGGAAAATCGCAACGCGAACTTGACTATCGC
Found at i:87448 original size:19 final size:19
Alignment explanation
Indices: 87389--87585 Score: 91
Period size: 19 Copynumber: 10.2 Consensus size: 19
87379 GAAAATTCTT
*
87389 AACGAACTTGGAAAATCGC
1 AACGAATTTGGAAAATCGC
* * ** *
87408 AACGCGAACTTCGACTACCGC
1 AA--CGAATTTGGAAAATCGC
*
87429 AACGAATTTGAAAAATCGC
1 AACGAATTTGGAAAATCGC
* **
87448 AACGTGAACTTGGACTATCGC
1 AAC--GAATTTGGAAAATCGC
87469 AACGAATTTGGAAAATCGC
1 AACGAATTTGGAAAATCGC
* **
87488 AACGCGAACTT-GACTATCGC
1 AA--CGAATTTGGAAAATCGC
* ** *
87508 AACGCGAACTTGGACTATCAC
1 AA--CGAATTTGGAAAATCGC
* *
87529 AACGAATTT---AGA-C-T
1 AACGAATTTGGAAAATCGC
*
87543 AACGTAATTTGGAAAATCAC
1 AACG-AATTTGGAAAATCGC
87563 AACGAATTTGGAAAATCGC
1 AACGAATTTGGAAAATCGC
87582 AACG
1 AACG
87586 CGAACTTGGA
Statistics
Matches: 137, Mismatches: 28, Indels: 26
0.72 0.15 0.14
Matches are distributed among these distances:
14 4 0.03
15 6 0.04
16 1 0.01
18 2 0.01
19 56 0.41
20 22 0.16
21 46 0.34
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (19 bp):
AACGAATTTGGAAAATCGC
Found at i:87525 original size:21 final size:21
Alignment explanation
Indices: 87391--87532 Score: 132
Period size: 21 Copynumber: 7.0 Consensus size: 21
87381 AAATTCTTAA
**
87391 CGAACTTGGAAAATCGCAACG
1 CGAACTTGGACTATCGCAACG
* *
87412 CGAACTTCGACTACCGCAA--
1 CGAACTTGGACTATCGCAACG
* * **
87431 CGAATTTGAAAAATCGCAACG
1 CGAACTTGGACTATCGCAACG
*
87452 TGAACTTGGACTATCGCAA--
1 CGAACTTGGACTATCGCAACG
* **
87471 CGAATTTGGAAAATCGCAACG
1 CGAACTTGGACTATCGCAACG
87492 CGAACTT-GACTATCGCAACG
1 CGAACTTGGACTATCGCAACG
*
87512 CGAACTTGGACTATCACAACG
1 CGAACTTGGACTATCGCAACG
87533 AATTTAGACT
Statistics
Matches: 93, Mismatches: 23, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
19 28 0.30
20 18 0.19
21 47 0.51
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.19
Consensus pattern (21 bp):
CGAACTTGGACTATCGCAACG
Found at i:87594 original size:21 final size:19
Alignment explanation
Indices: 87389--87595 Score: 93
Period size: 21 Copynumber: 10.6 Consensus size: 19
87379 GAAAATTCTT
87389 AACGAACTTGGAAAATCGC
1 AACGAACTTGGAAAATCGC
* ** *
87408 AACGCGAACTTCGACTACCGC
1 AA--CGAACTTGGAAAATCGC
* *
87429 AACGAATTTGAAAAATCGC
1 AACGAACTTGGAAAATCGC
**
87448 AACGTGAACTTGGACTATCGC
1 AAC--GAACTTGGAAAATCGC
*
87469 AACGAATTTGGAAAATCGC
1 AACGAACTTGGAAAATCGC
**
87488 AACGCGAACTT-GACTATCGC
1 AA--CGAACTTGGAAAATCGC
** *
87508 AACGCGAACTTGGACTATCAC
1 AA--CGAACTTGGAAAATCGC
* * *
87529 AACGAA-TT--TAGA-C-T
1 AACGAACTTGGAAAATCGC
* *
87543 AACGTAATTTGGAAAATCAC
1 AACG-AACTTGGAAAATCGC
*
87563 AACGAATTTGGAAAATCGC
1 AACGAACTTGGAAAATCGC
87582 AACGCGAACTTGGA
1 AA--CGAACTTGGA
87596 CTATCGCAAA
Statistics
Matches: 143, Mismatches: 30, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
14 4 0.03
15 3 0.02
16 3 0.02
18 4 0.03
19 52 0.36
20 22 0.15
21 55 0.38
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (19 bp):
AACGAACTTGGAAAATCGC
Found at i:87929 original size:2 final size:2
Alignment explanation
Indices: 87922--87966 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
87912 TATATTATTA
*
87922 AT AT AT AT AT AT AT AT AG AT AT -T AT AT -T 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
87962 AT AT A
1 AT AT A
87967 ATTAATAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:88791 original size:20 final size:20
Alignment explanation
Indices: 88768--88853 Score: 52
Period size: 21 Copynumber: 4.0 Consensus size: 20
88758 GAGTAGCTTA
88768 AAAAATATATTATAATTTTT
1 AAAAATATATTATAATTTTT
88788 AAAAA-A-ATTA-AATTATTAT
1 AAAAATATATTATAATT-TT-T
* *
88807 AATTAACATTTATGTATTGATTTTT
1 AA--AA-ATATAT-TA-TAATTTTT
*
88832 AAAGAATATAATATAATTTTT
1 AAA-AATATATTATAATTTTT
88853 A
1 A
88854 TTGTATTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 21
0.66 0.07 0.28
Matches are distributed among these distances:
17 4 0.08
18 6 0.12
19 4 0.08
20 5 0.10
21 10 0.20
22 3 0.06
23 5 0.10
24 3 0.06
25 5 0.10
26 2 0.04
27 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (20 bp):
AAAAATATATTATAATTTTT
Found at i:89227 original size:17 final size:17
Alignment explanation
Indices: 89195--89227 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
89185 GTAGTTAATT
89195 ATTT-TTATATTAAAAA
1 ATTTATTATATTAAAAA
89211 ATTTATTATAATTAAAA
1 ATTTATTAT-ATTAAAA
89228 TTTTAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTATTATATTAAAAA
Found at i:89243 original size:30 final size:29
Alignment explanation
Indices: 89197--89255 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
89187 AGTTAATTAT
*
89197 TTTTATATTAAAAAATTTATTATAATTAAAA
1 TTTTATATTAAAAAATTAATTA-AA-TAAAA
*
89228 TTTTA-ATTTAAAAATTAATTAAATAAAA
1 TTTTATATTAAAAAATTAATTAAATAAAA
89256 GATTTCTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 5 0.19
29 2 0.08
30 14 0.54
31 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TTTTATATTAAAAAATTAATTAAATAAAA
Found at i:89394 original size:18 final size:16
Alignment explanation
Indices: 89363--89397 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
89353 TCTTAATACA
89363 AATAATAAATAAAGTT
1 AATAATAAATAAAGTT
89379 AATAATAAGGATAAAGTT
1 AATAATAA--ATAAAGTT
89397 A
1 A
89398 TAAATGGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (16 bp):
AATAATAAATAAAGTT
Done.