Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000191.1 Hibiscus syriacus cultivar Beakdansim tig00000341_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: 123283
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:5097 original size:21 final size:21
Alignment explanation
Indices: 5039--5105 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
5029 CACACACTTA
* * *
5039 TATATATATATTTATATA-AC
1 TATATGTATACTTATATACAT
5059 TATAATGTATACTTATATACAT
1 TAT-ATGTATACTTATATACAT
5081 TATATGTATACTTATATAC-T
1 TATATGTATACTTATATACAT
5101 TATAT
1 TATAT
5106 AACTATAAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 9 0.21
21 29 0.69
22 4 0.10
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.49
Consensus pattern (21 bp):
TATATGTATACTTATATACAT
Found at i:5126 original size:28 final size:29
Alignment explanation
Indices: 5053--5136 Score: 84
Period size: 28 Copynumber: 3.0 Consensus size: 29
5043 TATATATTTA
* * *
5053 TATAACTATA-ATGTATACTTATATACAT
1 TATAAGTATACATATATACTTATATACAC
* *
5081 TATATGTATACTTATATACTTATATA-AC
1 TATAAGTATACATATATACTTATATACAC
*
5109 TATAAGTATAACAT-TATACATATATACA
1 TATAAGTAT-ACATATATACTTATATACA
5137 TACATACATA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
28 28 0.62
29 17 0.38
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.42
Consensus pattern (29 bp):
TATAAGTATACATATATACTTATATACAC
Found at i:5141 original size:4 final size:4
Alignment explanation
Indices: 5124--5153 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
5114 GTATAACATT
*
5124 ATAC ATAT ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
5154 GCATCATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (4 bp):
ATAC
Found at i:5309 original size:21 final size:21
Alignment explanation
Indices: 5267--5309 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
5257 AAATGAATAA
* *
5267 TTCAGTTCATTTTTTATTAAT
1 TTCAGTTCATATTTTATCAAT
5288 TTCAGTTTCATATTTTA-CAAT
1 TTCAG-TTCATATTTTATCAAT
5309 T
1 T
5310 ATTTGGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.58
Consensus pattern (21 bp):
TTCAGTTCATATTTTATCAAT
Found at i:27957 original size:65 final size:64
Alignment explanation
Indices: 27871--28012 Score: 176
Period size: 65 Copynumber: 2.2 Consensus size: 64
27861 TTGTTTAGGG
* * * * **
27871 TGCATCGATGCACATGCAGTGCATCAATGCATGAATTTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCAATGCATCAACATTAAATA-AAAACATCGAATAGGATTTA
* * ** *
27936 TGCTTCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCAATGCATCAACATTAAATAAAAACATCGAATAGGATTTA
28000 TGCATCGATGCAT
1 TGCATCGATGCAT
28013 GGTGTAGTGC
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
64 31 0.48
65 34 0.52
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAAGGAGTGCATCAATGCATCAACATTAAATAAAAACATCGAATAGGATTTA
Found at i:28010 original size:64 final size:66
Alignment explanation
Indices: 27908--28032 Score: 193
Period size: 64 Copynumber: 1.9 Consensus size: 66
27898 TGCATGAATT
*
27908 TTAAATAGAAAACATCGAATAGGATTTATGCTTCGATGCATAAG-G-AGTGCATCGATGCATCCC
1 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCAT-AGTGTAGTGCATCGATGCATCCC
27971 CA
65 CA
* *
27973 TTAAATA-CAAACATCGAATAGGATTTATGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAGTGTAGTGCATCGATGCAT
28033 ACCTTCATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
63 1 0.02
64 32 0.58
65 22 0.40
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (66 bp):
TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAGTGTAGTGCATCGATGCATCCCC
A
Found at i:29468 original size:21 final size:21
Alignment explanation
Indices: 29442--29504 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
29432 GTCGAGGGTT
29442 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
*
29463 TCATAGGTCCTTCGGGACATAT
1 TCATAGGTCCTTCGGGACA-AC
* *
29485 TCACAAGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
29505 ATTTCATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:29497 original size:22 final size:21
Alignment explanation
Indices: 29448--29504 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 21
29438 GGTTTCATAG
* *
29448 GTCCTTCGGGACAACTCATAG
1 GTCCTTCGGGACAACTCACAA
*
29469 GTCCTTCGGGACATATTCACAA
1 GTCCTTCGGGACA-ACTCACAA
29491 GTCCTTCGGGACAA
1 GTCCTTCGGGACAA
29505 ATTTCATATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 14 0.44
22 18 0.56
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (21 bp):
GTCCTTCGGGACAACTCACAA
Found at i:38473 original size:20 final size:20
Alignment explanation
Indices: 38450--38487 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38440 TAAAATTTAA
38450 TTTAAATATATA-AATTATAT
1 TTTAAATAT-TAGAATTATAT
*
38470 TTTAGATATTAGAATTAT
1 TTTAAATATTAGAATTAT
38488 TGAAACGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTAAATATTAGAATTATAT
Found at i:41336 original size:13 final size:13
Alignment explanation
Indices: 41318--41347 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41308 TTAAAAAAAG
41318 TTAAAAATATTAT
1 TTAAAAATATTAT
*
41331 TTAAAAATATTTT
1 TTAAAAATATTAT
41344 TTAA
1 TTAA
41348 GAAAAACATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAAAAATATTAT
Found at i:42712 original size:10 final size:10
Alignment explanation
Indices: 42697--42722 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
42687 TAAAGCATAT
42697 GTCTTATGAA
1 GTCTTATGAA
42707 GTCTTATGAA
1 GTCTTATGAA
42717 GTCTTA
1 GTCTTA
42723 CCTCATAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (10 bp):
GTCTTATGAA
Found at i:50993 original size:49 final size:49
Alignment explanation
Indices: 50933--51033 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
50923 TTAATGAGTA
*
50933 TGAATAGTAAGTGACTTGAAGTTTTATTTTGAAGTATTAAAGTTAACAT
1 TGAATAATAAGTGACTTGAAGTTTTATTTTGAAGTATTAAAGTTAACAT
*
50982 TGAATAATAAGTGACTTGACGTTTTATTTTGAAGTATTAAAGTTAACAT
1 TGAATAATAAGTGACTTGAAGTTTTATTTTGAAGTATTAAAGTTAACAT
51031 TGA
1 TGA
51034 TGTTGTGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.41
Consensus pattern (49 bp):
TGAATAATAAGTGACTTGAAGTTTTATTTTGAAGTATTAAAGTTAACAT
Found at i:53523 original size:63 final size:64
Alignment explanation
Indices: 53450--53579 Score: 192
Period size: 63 Copynumber: 2.0 Consensus size: 64
53440 AACATACCTC
* *
53450 TTGGTTGTTGCATT-TTCATCACAATCTCAATCAA-TGTAATATGTGAGGCCATTTTGTTGATAG
1 TTGGTTGTTGC-TTCTTCATCACAATCTCAATCAATTGTAATACGTGAGACCATTTTGTTGATAG
*
53513 TTGGTTGTTGCTTCTTCATCACAATCTCAATCAATGTTGTAATCCGTGAGACCATTTTGTTGATA
1 TTGGTTGTTGCTTCTTCATCACAATCTCAATCAA--TTGTAATACGTGAGACCATTTTGTTGATA
53578 G
64 G
53579 T
1 T
53580 ATCATTGTCC
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
62 2 0.03
63 31 0.52
66 27 0.45
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (64 bp):
TTGGTTGTTGCTTCTTCATCACAATCTCAATCAATTGTAATACGTGAGACCATTTTGTTGATAG
Found at i:68020 original size:182 final size:181
Alignment explanation
Indices: 67712--68257 Score: 806
Period size: 182 Copynumber: 3.0 Consensus size: 181
67702 GAAAGTGTCG
* * *
67712 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAGTAGTTTTAGCGCTTATAAAGTGTCAATATTT
1 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAGTAGTTTTAGCGCCTATAAAGTGTCGATACTT
* * * * *
67777 TATAACAATGGATCGATTCACAACGATATAATAGATAAAAATATGACAAAACTGGTCTCTAAAGG
66 TATAAAAATGTATCGATCCACAACGATATAACAG-TAAAAATATGACAAAACTGGTCTCTAAAAG
* *
67842 ACAAAACCGGTATAGAGCGACCGAATATATTGAAAGTGTCGATATTTTAATA
130 ACAAAACCGGTATAGAGCGACTGGATATATTGAAAGTGTCGATATTTTAATA
* *
67894 TAAGTATCTACACTTTGTGAATTTAAAAGAGAAGTAGTTTTAGCGCCTATAAAGTGACGATACTT
1 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAGTAGTTTTAGCGCCTATAAAGTGTCGATACTT
* *
67959 TATAAAAATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCGATCTCTAAAAG
66 TATAAAAATGTATCGATCCACAACGATATAACA-GTAAAAATATGACAAAACTGGTCTCTAAAAG
* * *
68024 ACAAAATCAGTATAGAGCGACTGGATATATTGAAAGTGTCGATACTTTAATA
130 ACAAAACCGGTATAGAGCGACTGGATATATTGAAAGTGTCGATATTTTAATA
* * *
68076 TAAGTATCGACACTTAT-TGAATTTAAAAGAGAAGCAGTTTTAGCACCTATAAAATGTCGATACT
1 TAAGTATCGACACTT-TGTGAATTTAAAAGAGAAGTAGTTTTAGCGCCTATAAAGTGTCGATACT
* * * *
68140 TTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACTGGTCTCGAAAT
65 TTATAAAAATGTATCGATCCACAACGATATAACA-GTAAAAATATGACAAAACTGGTCTCTAAAA
* * *
68205 GACAAAACCGGTAAAGCGCTACTGGATATATTGAAAGTGTCGATATTTTAATA
129 GACAAAACCGGTATAGAGCGACTGGATATATTGAAAGTGTCGATATTTTAATA
68258 AGTACGCGTA
Statistics
Matches: 327, Mismatches: 35, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
182 325 0.99
183 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.29
Consensus pattern (181 bp):
TAAGTATCGACACTTTGTGAATTTAAAAGAGAAGTAGTTTTAGCGCCTATAAAGTGTCGATACTT
TATAAAAATGTATCGATCCACAACGATATAACAGTAAAAATATGACAAAACTGGTCTCTAAAAGA
CAAAACCGGTATAGAGCGACTGGATATATTGAAAGTGTCGATATTTTAATA
Found at i:70248 original size:19 final size:22
Alignment explanation
Indices: 70200--70248 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
70190 TTTTGTTTGT
70200 TTTTATATAAAATGATAGTATAA
1 TTTTATATAAAAT-ATAGTATAA
70223 TTATTATATAAAAT-TA-TA-AA
1 TT-TTATATAAAATATAGTATAA
70243 TTTTAT
1 TTTTAT
70249 TATAGATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 4 0.16
20 4 0.16
21 2 0.08
22 2 0.08
23 2 0.08
24 11 0.44
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (22 bp):
TTTTATATAAAATATAGTATAA
Found at i:70764 original size:33 final size:33
Alignment explanation
Indices: 70722--70788 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
70712 AAATAGATGG
*
70722 AGTGGTGAAAGGAGTTGAGGTGTTGAGAGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGAGGTGA
*
70755 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGAGGTGA
70788 A
1 A
70789 CTTAAGATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.48, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTGTTGAGAGGTGA
Found at i:71276 original size:18 final size:18
Alignment explanation
Indices: 71253--71291 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
71243 AAAAAAAAAT
71253 GAAGAAGAAAAGAGGGAG
1 GAAGAAGAAAAGAGGGAG
71271 GAAGAAGAAAAGAGGGAG
1 GAAGAAGAAAAGAGGGAG
71289 GAA
1 GAA
71292 ATGAGGAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (18 bp):
GAAGAAGAAAAGAGGGAG
Found at i:72870 original size:19 final size:19
Alignment explanation
Indices: 72846--72913 Score: 127
Period size: 19 Copynumber: 3.6 Consensus size: 19
72836 AATGTAGGGT
*
72846 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGATTTA
72865 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
72884 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
72903 TAATTTTGTAT
1 TAATTTTGTAT
72914 GTGAATATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.54
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:73554 original size:199 final size:199
Alignment explanation
Indices: 73264--74420 Score: 1530
Period size: 199 Copynumber: 5.8 Consensus size: 199
73254 GTAAACATAT
* * *
73264 GTGTCGATACATTTATAAAAAATATCGATCCCAAAAGCATCGAAACCCGTAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* ** * * *
73329 GGTAATTTTGTAATATAACCGATATAAATATACCAAATTTATGTGAGAATAGGTCTACATAATGT
66 GGTAAATTTACAATGTAACCGATATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGT
* * *
73394 ATCGACACTTTCTCATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGATGAACGC
131 ATCGACACTTT-TGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGC
**
73459 AT-TT
195 ATAAA
* * *
73463 GTGTCGATATATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAATATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * * * *
73528 GATAAATTTACAATGTAACTGATATAACTATAACGGTTTTATGAGAAAATAGGTCTACATAATGT
66 GGTAAATTTACAATGTAACCGATATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGT
* * * * * * *
73593 ATCGACACTTATGGAATTTGTGTCGATACTGTTTGTTCAGAAGGAATGCCCAAAAGGGTGCACCC
131 ATCGACACTT-TTGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGC
73658 ATAAA
195 ATAAA
* * * * * *
73663 GTGTCGATACATTTTATGAAAAGTGTCGATCCGAAAAACATTGAAACCCCTAATTATAATATAAT
1 GTGTCGATACA-TTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
* * ** * * *
73728 AAGTAATTTTTTAATATAACCGGTATAAATATACC-AGTTTTATGTGAGAATATGTCTACATAAT
65 AGGTAAATTTACAATGTAACCGATATAAATATACCGA-TTTTATGTGAGAATAGGTCTACATAAT
* *
73792 GTTTCGACACTTTTTAATTTTGTGTCGATACTTTTTTGTCCAGAATGAATGCCCAAAATGGTGAA
129 GTATCGACACTTTTGAA-TTTGTGTCGATAC-TTTTTGTCCAGAATGAATGCCCAAAATGGTGAA
73857 CGCATAAA
192 CGCATAAA
* * *
73865 GTGTCGATACATTTATAAAACGTATCGATCCCAAAAATATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
73930 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAAATTTACAATGTAACCGATATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGT
* *
73995 GTCGACACTTTTGAATTTGTGCCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCA
131 ATCGACACTTTTGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCA
74060 TAAA
196 TAAA
* * * **
74064 GTGTCGATACATATA-AAAAAATATCGATCCCAAAAACCTCGAAACTGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * *
74128 GGTAAATTTACAATGTACCCGATTTAAATATATCGATTTTATGTGAGAATATGTCTACATAATGT
66 GGTAAATTTACAATGTAACCGATATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGT
* * * *
74193 GTCGACACTTTTGAATTTGTGTCGATACTTTTTTTCTAGAATGAATGTCCAAAATGGTGAACGCA
131 ATCGACACTTTTGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCA
74258 TAAA
196 TAAA
* * * * * * *
74262 GTGTCGATACATATATAAAAACTATCTATCTCAAAAACATTGAAATCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* **
74327 GGTAAATTTACAATGTAACCGATATAAATATATCGATTTTATGTGAGAATAGGTGAACATAATGT
66 GGTAAATTTACAATGTAACCGATATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGT
74392 ATCGACACGTTTT-AGATTTGTGTCGATAC
131 ATCGACAC-TTTTGA-ATTTGTGTCGATAC
74421 AATTTTAAAT
Statistics
Matches: 837, Mismatches: 111, Indels: 19
0.87 0.11 0.02
Matches are distributed among these distances:
198 183 0.22
199 331 0.40
200 44 0.05
201 233 0.28
202 46 0.05
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (199 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGATATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGT
ATCGACACTTTTGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCA
TAAA
Found at i:77250 original size:18 final size:18
Alignment explanation
Indices: 77229--77265 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
77219 GTAATTGGAG
77229 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
77247 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
77265 T
1 T
77266 ATAAATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:77272 original size:24 final size:24
Alignment explanation
Indices: 77221--77273 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
77211 TTTCATATGT
* * *
77221 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
77245 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
77269 AATTT
1 AATTT
77274 TGGCTCTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:78054 original size:201 final size:200
Alignment explanation
Indices: 77645--78980 Score: 1417
Period size: 201 Copynumber: 6.8 Consensus size: 200
77635 TAAAGTTTCC
* * * *
77645 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACTGAA-AATTATAA
1 CATAAAGTGTCGATATATTTATAAAAAGTATCGATCCCAAAAATATCGAAAC-CAATAATTATAA
* * *
77709 TGTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTTTGAAAAAATAGAT-ATA
65 TGTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGTGA-A
* * * ** * * *
77773 CATAATGTATCAAAACTTGTGGAA-TTTGTGTCGATACTTTTGGTCCACAAGGAATGCCCAAAAA
129 CATAATGTGTCGACACTT-TTTAATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCC-AAAA
* * *
77837 AGGTGCACC
192 TGGTGAACG
* * *
77846 CATAAAGTGTCGATATATTTTTAAAAAGAATCGATCCCAAAAATATCGAAACAAATAATTATAAT
1 CATAAAGTGTCGATATATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCAATAATTATAAT
* * *
77911 GTAATAGATAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGTA-AGAATAGGTGTAC
66 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATG-AGAAAATAGGTGAAC
* *
77975 ATAATGTGTCGACACTTTTTGAATTTTGTATCGATACTTTTTGTCTAGAATGAATGCCCAAAATG
130 ATAATGTGTCGACACTTTTT-AATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATG
78040 GTGAACG
194 GTGAACG
* * * **
78047 TATAAAGTGTCAATACATTTATAAAAAGTATCGATCCCAAAAATATCGAAATAAATAATTATAAT
1 CATAAAGTGTCGATATATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCAATAATTATAAT
* * * * * *
78112 ATAATAGGTAAATTTATAATGTACCCAATATAAATATTCCGGTTTTATGAGAAAATAGGGGAACA
66 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGTGAACA
* *
78177 TAATGTGTCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGTCCAAAATGGT
131 TAATGTGTCGACACTTTTTAATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGT
78242 GAACG
196 GAACG
* * *
78247 CATAAAGTGTCGATACATTTATAAAAGGTATCGATCCCAAAAATATTGAAACCAATAATTATAAT
1 CATAAAGTGTCGATATATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCAATAATTATAAT
* *
78312 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGATTTTATGAGAAAATAGGGGAACA
66 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGTGAACA
* * * **** * * * *
78377 TAAGGTGTTGACAC----T--TTTTGT-CCAGA-A-TGAAGGCCCAAAATG-GTGAACGCATAAA
131 TAATGTGTCGACACTTTTTAATTTTGTGTC-GATACTTTTTGTCCAGAATGAATG--CCCA-AAA
**
78432 --GTG-TTG
192 TGGTGAACG
* * *
78438 -AT--A----C-AT-T-TATA-AAA-AGTATTGATCCCAAAAACATCGAAACCAATAATTATAAT
1 CATAAAGTGTCGATATATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCAATAATTATAAT
*
78491 GTAATAGGTAAATTTACAATGTAACCAATATAAATATACCGGTTTTATGAGAAAATAAGG-GAAC
66 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAAT-AGGTGAAC
* * * **
78555 ATAATGTGTTGACACTTTTTAAATATGTGTCGATACTTTTTGTCCAGAATGAATGCAAAAAATGG
130 ATAATGTGTCGACACTTTTTAATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGG
78620 TGAACG
195 TGAACG
* * * *
78626 CATAAAGTGCCGATATATTTATAAAAAGTATCGATCCCAAAAATATTGAAACCGAT-AGT-T-A-
1 CATAAAGTGTCGATATATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCAATAATTATAAT
* ** * *
78687 -TAAT--GT-AA-TTACAATGTAACC-GATATAAATGTATTGGTTTTATGAGAAAATAGTTAAAC
66 GTAATAGGTAAATTTACAATGTAACCAG-TATAAATATACCGGTTTTATGAGAAAATAGGTGAAC
* * * * *
78746 ATAACGTATCGACACGTTTTAGA-TTTGTGTCGATACTTTTTGTCCAAAATGAATG-CCAAAAGG
130 ATAATGTGTCGACACTTTTTA-ATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATG
*
78809 GTTGCACG
194 G-TGAACG
* * * * **
78817 CATAAAGTGTTGATATATTTTTAAAAAGAATCGATCCCAAAAACATCGAAACTGATAATTATAAT
1 CATAAAGTGTCGATATATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCAATAATTATAAT
* *
78882 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACA
66 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGTGAACA
* * *
78947 TAATGTATCGACACTTTTAAATTTT-TATCGATAC
131 TAATGTGTCGACACTTTTTAATTTTGTGTCGATAC
78981 ATTTAAATAA
Statistics
Matches: 953, Mismatches: 131, Indels: 104
0.80 0.11 0.09
Matches are distributed among these distances:
179 107 0.11
180 6 0.01
181 3 0.00
183 3 0.00
184 1 0.00
185 9 0.01
186 4 0.00
187 12 0.01
188 4 0.00
189 2 0.00
190 10 0.01
191 146 0.15
192 17 0.02
193 7 0.01
194 11 0.01
195 5 0.01
196 7 0.01
197 2 0.00
198 6 0.01
199 16 0.02
200 271 0.28
201 273 0.29
202 31 0.03
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.31
Consensus pattern (200 bp):
CATAAAGTGTCGATATATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCAATAATTATAAT
GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGTGAACA
TAATGTGTCGACACTTTTTAATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGT
GAACG
Found at i:78306 original size:200 final size:199
Alignment explanation
Indices: 77645--78980 Score: 1545
Period size: 200 Copynumber: 6.8 Consensus size: 199
77635 TAAAGTTTCC
* * *
77645 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACTGAA-AATTATAA
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAATATCGAAAC-CAATAATTATAA
* * **
77709 TGTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTTTGAAAAAATA-GATATA
65 TGTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGGGA-A
* * * * ** * * * *
77773 CATAATGTATCAAAACTTGTGGAATTTGTGTCGATACTTTTGGTCCACAAGGAATGCCCAAAAAA
129 CATAATGTGTCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATG-CC-AAAAT
* *
77838 GGTGCACC
192 GGTGAACG
* * * *
77846 CATAAAGTGTCGATATATTTTTAAAAAGAATCGATCCCAAAAATATCGAAACAAATAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCAATAATTATAAT
* * * *
77911 GTAATAGATAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGTA-AGAATAGGTGTAC
66 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATG-AGAAAATAGGGGAAC
* * *
77975 ATAATGTGTCGACACTTTTTGAATTTTGTATCGATACTTTTTGTCTAGAATGAATGCCCAAAATG
130 ATAATGTGTCGACACTTTTT-AAATTTGTGTCGATACTTTTTGTCCAGAATGAATG-CCAAAATG
78040 GTGAACG
193 GTGAACG
* * **
78047 TATAAAGTGTCAATACATTTATAAAAAGTATCGATCCCAAAAATATCGAAATAAATAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCAATAATTATAAT
* * * * *
78112 ATAATAGGTAAATTTATAATGTACCCAATATAAATATTCCGGTTTTATGAGAAAATAGGGGAACA
66 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGGGAACA
78177 TAATGTGTCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGTCCAAAATGGT
131 TAATGTGTCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATG-CCAAAATGGT
78242 GAACG
195 GAACG
* *
78247 CATAAAGTGTCGATACATTTATAAAAGGTATCGATCCCAAAAATATTGAAACCAATAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCAATAATTATAAT
*
78312 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGATTTTATGAGAAAATAGGGGAACA
66 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGGGAACA
* * * **
78377 TAAGGTGTTGACAC---TT---TTTGT-CCAGA-A-------T---GAA-G--GCCCAAAATGGT
131 TAATGTGTCGACACTTTTTAAATTTGTGTC-GATACTTTTTGTCCAGAATGAATGCCAAAATGGT
78421 GAACG
195 GAACG
* * *
78426 CATAAAGTGTTGATACATTTATAAAAAGTATTGATCCCAAAAACATCGAAACCAATAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCAATAATTATAAT
* *
78491 GTAATAGGTAAATTTACAATGTAACCAATATAAATATACCGGTTTTATGAGAAAATAAGGGAACA
66 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGGGAACA
* * *
78556 TAATGTGTTGACACTTTTTAAATATGTGTCGATACTTTTTGTCCAGAATGAATGCAAAAAATGGT
131 TAATGTGTCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGC-CAAAATGGT
78621 GAACG
195 GAACG
* * * * *
78626 CATAAAGTGCCGATATATTTATAAAAAGTATCGATCCCAAAAATATTGAAACCGAT-AGT-T-A-
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCAATAATTATAAT
* ** ***
78687 -TAAT--GT-AA-TTACAATGTAACC-GATATAAATGTATTGGTTTTATGAGAAAATAGTTAAAC
66 GTAATAGGTAAATTTACAATGTAACCAG-TATAAATATACCGGTTTTATGAGAAAATAGGGGAAC
* * * * * *
78746 ATAACGTATCGACACGTTTTAGATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGT
130 ATAATGTGTCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAATGG-
*
78811 TGCACG
194 TGAACG
* * * * * **
78817 CATAAAGTGTTGATATATTTTTAAAAAGAATCGATCCCAAAAACATCGAAACTGATAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCAATAATTATAAT
* **
78882 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACA
66 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGGGAACA
* * *
78947 TAATGTATCGACAC-TTTTAAATTTTTATCGATAC
131 TAATGTGTCGACACTTTTTAAATTTGTGTCGATAC
78981 ATTTAAATAA
Statistics
Matches: 976, Mismatches: 119, Indels: 82
0.83 0.10 0.07
Matches are distributed among these distances:
179 150 0.15
182 3 0.00
183 3 0.00
185 6 0.01
186 3 0.00
190 6 0.01
191 145 0.15
192 4 0.00
193 6 0.01
194 8 0.01
195 4 0.00
196 7 0.01
197 4 0.00
198 3 0.00
199 22 0.02
200 299 0.31
201 270 0.28
202 33 0.03
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.31
Consensus pattern (199 bp):
CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCAATAATTATAAT
GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGGGAACA
TAATGTGTCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAATGGTG
AACG
Found at i:78510 original size:179 final size:179
Alignment explanation
Indices: 78210--78574 Score: 631
Period size: 179 Copynumber: 2.0 Consensus size: 179
78200 TTGTGTCGAT
* * *
78210 ACTTTTTGTCCAGAATGAATGTCCAAAATGGTGAACGCATAAAGTGTCGATACATTTATAAAAGG
1 ACTTTTTGTCCAGAATGAAGGCCCAAAATGGTGAACGCATAAAGTGTCGATACATTTATAAAAAG
* * *
78275 TATCGATCCCAAAAATATTGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTAACCAG
66 TATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTAACCAA
*
78340 TATAAATATACCGATTTTATGAGAAAATAGGGGAACATAAGGTGTTGAC
131 TATAAATATACCGATTTTATGAGAAAATAAGGGAACATAAGGTGTTGAC
*
78389 ACTTTTTGTCCAGAATGAAGGCCCAAAATGGTGAACGCATAAAGTGTTGATACATTTATAAAAAG
1 ACTTTTTGTCCAGAATGAAGGCCCAAAATGGTGAACGCATAAAGTGTCGATACATTTATAAAAAG
*
78454 TATTGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTAACCAA
66 TATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTAACCAA
* *
78519 TATAAATATACCGGTTTTATGAGAAAATAAGGGAACATAATGTGTTGAC
131 TATAAATATACCGATTTTATGAGAAAATAAGGGAACATAAGGTGTTGAC
78568 ACTTTTT
1 ACTTTTT
78575 AAATATGTGT
Statistics
Matches: 175, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
179 175 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (179 bp):
ACTTTTTGTCCAGAATGAAGGCCCAAAATGGTGAACGCATAAAGTGTCGATACATTTATAAAAAG
TATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTAACCAA
TATAAATATACCGATTTTATGAGAAAATAAGGGAACATAAGGTGTTGAC
Found at i:78820 original size:191 final size:190
Alignment explanation
Indices: 78389--78968 Score: 644
Period size: 191 Copynumber: 2.9 Consensus size: 190
78379 AGGTGTTGAC
* *
78389 ACTTTTTGTCCAGAATGAAGGCCCAAAATGGTGAACGCATAAAGTGTTGATACATTTATAAAAAG
1 ACTTTTTGTCCAGAATGAATG-CCAAAATGGTGAACGCATAAAGTGTTGATATATTTATAAAAAG
* *
78454 TATTGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTAACCAA
65 TATCGATCCCAAAAACATCGAAACCGATAA-T-T-A--TAAT--GT-AA-TTACAATGTAACCAA
* * * * *
78519 TATAAATATACCGGTTTTATGAGAAAATAAGGGAACATAATGTGTTGACACTTTTTAAATATGTG
121 TATAAATATACCGGTTTTATGAGAAAATAAGGAAACATAACGTATCGACACGTTTTAAATATGTG
78584 TCGAT
186 TCGAT
* **
78589 ACTTTTTGTCCAGAATGAATGCAAAAAATGGTGAACGCATAAAGTGCCGATATATTTATAAAAAG
1 ACTTTTTGTCCAGAATGAATGC-CAAAATGGTGAACGCATAAAGTGTTGATATATTTATAAAAAG
* * * * *
78654 TATCGATCCCAAAAATATTGAAACCGATAGTTATAATGTAATTACAATGTAACCGATATAAATGT
65 TATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATTACAATGTAACCAATATAAATAT
** * * *
78719 ATTGGTTTTATGAGAAAAT-AGTTAAACATAACGTATCGACACGTTTTAGATTTGTGTCGAT
130 ACCGGTTTTATGAGAAAATAAG-GAAACATAACGTATCGACACGTTTTAAATATGTGTCGAT
* * * *
78780 ACTTTTTGTCCAAAATGAATGCCAAAAGGGTTGCACGCATAAAGTGTTGATATATTTTTAAAAAG
1 ACTTTTTGTCCAGAATGAATGCCAAAATGG-TGAACGCATAAAGTGTTGATATATTTATAAAAAG
* * *
78845 AATCGATCCCAAAAACATCGAAACTGATAATTATAATGTAATAGGTAAATTTACAATGTAACCAG
65 TATCGATCCCAAAAACATCGAAACCGATAA-T-T-A--TAAT--GT-AA-TTACAATGTAACCAA
* * *
78910 TATAAATATACCGGTTTTATGAGAGAAT-AGGTCAACATAATGTATCGACAC-TTTTAAAT
121 TATAAATATACCGGTTTTATGAGAAAATAAGG-AAACATAACGTATCGACACGTTTTAAAT
78969 TTTTATCGAT
Statistics
Matches: 323, Mismatches: 44, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
190 8 0.02
191 146 0.45
192 3 0.01
193 3 0.01
194 1 0.00
195 4 0.01
196 4 0.01
197 1 0.00
198 3 0.01
199 11 0.03
200 139 0.43
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (190 bp):
ACTTTTTGTCCAGAATGAATGCCAAAATGGTGAACGCATAAAGTGTTGATATATTTATAAAAAGT
ATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATTACAATGTAACCAATATAAATATA
CCGGTTTTATGAGAAAATAAGGAAACATAACGTATCGACACGTTTTAAATATGTGTCGAT
Found at i:78949 original size:570 final size:577
Alignment explanation
Indices: 77803--78964 Score: 1583
Period size: 570 Copynumber: 2.0 Consensus size: 577
77793 GGAATTTGTG
* * * * *
77803 TCGATACTTTTGGTCCACAAGGAATGCCCAAAAAAGGTGCACCCATAAAGTGTCGATATATTTTT
1 TCGACACTTTTGGTCCACAAGGAAGGCCCAAAAAAGGTGAACCCATAAAGTGTCGATACATTTAT
*
77868 AAAAAGAATCGATCCCAAAAATATCGAAACAAATAATTATAATGTAATAGATAAATTTACAATGT
66 AAAAAGAATCGATCCCAAAAACATCGAAACAAATAATTATAATGTAATAGATAAATTTACAATGT
* * *
77933 AACCAGTATAAATATACCGGTTTTATGTAAGAATAGGTGTACATAATGTGTCGACACTTTTTGAA
131 AACCAATATAAATATACCGGTTTTATGTAAAAATAGGTGAACATAATGTGTCGACACTTTTTGAA
* * * ** * *
77998 TTTTGTATCGATACTTTTTGTCTAGAATGAATGCCCAAAATGGTGAACGTATAAAGTGTCAATAC
196 ATATGTATCGATACTTTTTGTCCAGAATGAATGCAAAAAATGGTGAACGCATAAAGTGCCAATAC
*
78063 ATTTATAAAAAGTATCGATCCCAAAAATATCGAAATAAATAATTATAATATAATAGGTAAATTTA
261 ATTTATAAAAAGTATCGATCCCAAAAATATCGAAACAAATAA-TAT-ATATAATA-GTAAATTTA
* * * * * *
78128 TAATGTACCCAATATAAATATTCCGGTTTTATGAGAAAATAGGGGAACATAATGTGTCGACACTT
323 CAATGTAACCAATATAAATATT-CGGTTTTATGAGAAAATAGGGAAACATAACGTATCGACACGT
* *
78193 TTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGTCCAAAATGGTGAACGCATAAAGTGTC
387 TTTAAATTTGTGTCGATACTTTTTGTCCAAAATGAATGTCCAAAAGGGTGAACGCATAAAGTGTC
* * * *
78258 GATACATTTATAAAAGGTATCGATCCCAAAAATATTGAAACCAATAATTATAATGTAATAGGTAA
452 GATACATTTATAAAAAGAATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAGGTAA
* *
78323 ATTTACAATGTAACCAGTATAAATATACCGATTTTATGAGAAAATAGGGGAACATAAGGTG
517 ATTTACAATGTAACCAGTATAAATATACCGATTTTATGAGAAAATAGGGCAACATAAGGTA
* * * * * * *
78384 TTGACACTTTTTGTCCAGAATGAAGGCCC-AAAATGGTGAACGCATAAAGTGTTGATACATTTAT
1 TCGACACTTTTGGTCCACAAGGAAGGCCCAAAAAAGGTGAACCCATAAAGTGTCGATACATTTAT
* * * *
78448 AAAAAGTATTGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGT
66 AAAAAGAATCGATCCCAAAAACATCGAAACAAATAATTATAATGTAATAGATAAATTTACAATGT
*
78513 AACCAATATAAATATACCGGTTTTATG-AGAAAATAAGG-GAACATAATGTGTTGACACTTTTT-
131 AACCAATATAAATATACCGGTTTTATGTA-AAAAT-AGGTGAACATAATGTGTCGACACTTTTTG
* *
78575 AAATATGTGTCGATACTTTTTGTCCAGAATGAATGCAAAAAATGGTGAACGCATAAAGTGCCGAT
194 AAATATGTATCGATACTTTTTGTCCAGAATGAATGCAAAAAATGGTGAACGCATAAAGTGCCAAT
* * ** *
78640 ATATTTATAAAAAGTATCGATCCCAAAAATATTGAAACCGAT-A-GT-TATAAT-GT-AA-TTAC
259 ACATTTATAAAAAGTATCGATCCCAAAAATATCGAAACAAATAATATATATAATAGTAAATTTAC
* **
78699 AATGTAACCGATATAAATGTATT-GGTTTTATGAGAAAATAGTTAAACATAACGTATCGACACGT
324 AATGTAACCAATATAAA--TATTCGGTTTTATGAGAAAATAGGGAAACATAACGTATCGACACGT
* *
78763 TTTAGATTTGTGTCGATACTTTTTGTCCAAAATGAATG-CCAAAAGGGTTGCACGCATAAAGTGT
387 TTTAAATTTGTGTCGATACTTTTTGTCCAAAATGAATGTCCAAAAGGG-TGAACGCATAAAGTGT
* * * **
78827 TGATATATTTTTAAAAAGAATCGATCCCAAAAACATCGAAACTGATAATTATAATGTAATAGGTA
451 CGATACATTTATAAAAAGAATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAGGTA
* * * *
78892 AATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGTA
516 AATTTACAATGTAACCAGTATAAATATACCGATTTTATGAGAAAATAGGGCAACATAAGGTA
78954 TCGACACTTTT
1 TCGACACTTTT
78965 AAATTTTTAT
Statistics
Matches: 511, Mismatches: 65, Indels: 21
0.86 0.11 0.04
Matches are distributed among these distances:
569 8 0.02
570 226 0.44
571 2 0.00
572 6 0.01
574 6 0.01
576 1 0.00
578 1 0.00
579 94 0.18
580 141 0.28
581 26 0.05
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (577 bp):
TCGACACTTTTGGTCCACAAGGAAGGCCCAAAAAAGGTGAACCCATAAAGTGTCGATACATTTAT
AAAAAGAATCGATCCCAAAAACATCGAAACAAATAATTATAATGTAATAGATAAATTTACAATGT
AACCAATATAAATATACCGGTTTTATGTAAAAATAGGTGAACATAATGTGTCGACACTTTTTGAA
ATATGTATCGATACTTTTTGTCCAGAATGAATGCAAAAAATGGTGAACGCATAAAGTGCCAATAC
ATTTATAAAAAGTATCGATCCCAAAAATATCGAAACAAATAATATATATAATAGTAAATTTACAA
TGTAACCAATATAAATATTCGGTTTTATGAGAAAATAGGGAAACATAACGTATCGACACGTTTTA
AATTTGTGTCGATACTTTTTGTCCAAAATGAATGTCCAAAAGGGTGAACGCATAAAGTGTCGATA
CATTTATAAAAAGAATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTT
ACAATGTAACCAGTATAAATATACCGATTTTATGAGAAAATAGGGCAACATAAGGTA
Found at i:83460 original size:199 final size:199
Alignment explanation
Indices: 83070--83748 Score: 815
Period size: 199 Copynumber: 3.4 Consensus size: 199
83060 ACCTATATAT
* * * *
83070 GTGTCGATACATTTTCTAAAAGTATC-AACCCAAAAAATATCGAAACCAATAATTATAATGTAAT
1 GTGTCGATACATTAT-TAAAAGTATCGATCCC-AAAAACATCGAAACCGATAATTATAATGTAAT
* * * * * *
83134 AGGTAAATTAACAATGTAATCGGTATAAATATATCGG-TTAATTAGAAAATATGTCAACAT-ATG
64 AGGTAAATTTACAATGTAATCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCATCATAATG
* *
83197 TATCGACACTTGTGT-AATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCA
129 TATCGACACTTGT-TAAATTTGTGTCGATACTTTTTGTCCAGAATGAAT-ACCAAACGAGGTGCA
83261 CGCATAAA
192 CGCATAAA
* * *
83269 GTGTCGATACAGTTATTAAAAGTATTGATCCCAATAAA-ATTGAAACCGATATTTATAATGTAAT
1 GTGTCGATACA-TTATTAAAAGTATCGATCCCAA-AAACATCGAAACCGATAATTATAATGTAAT
* * *
83333 ATGTAAATTTATAATGTAATCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCATCATAAAG
64 AGGTAAATTTACAATGTAATCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCATCATAATG
* * *
83398 TATTGACACTTGTTAAATTTGTGTCGATA-TATTTTGTCCATAATGAATACCAAATG-GGTGCAC
129 TATCGACACTTGTTAAATTTGTGTCGATACT-TTTTGTCCAGAATGAATACCAAACGAGGTGCAC
83461 GCATAAA
193 GCATAAA
* *
83468 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTACAATGTGATA
1 GTGTCGATACA-TTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
** * ** * * * *
83533 TATAACTTTACAATGTACCCGATAGAAATATACCGGTTTTATGAAAAAATAGGTC-TAAATAATG
65 GGTAAATTTACAATGTAATCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAT-CATAATG
* * *
83597 TATCGACACTCT-TTAAGTTTGTGTCGATACTTTTT-TCCAGAATGAATGCCCAACGAGGTGCAC
129 TATCGACACT-TGTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATACCAAACGAGGTGCAC
83660 GCATAAA
193 GCATAAA
*
83667 GTGTCGATACA-T-TTAAAATTGTATCGATCCAAAAAACACATCGAAACCGATAATTATAATGTA
1 GTGTCGATACATTATTAAAA--GTATCGATCC-CAAAA-ACATCGAAACCGATAATTATAATGTA
*
83730 ATAGGTAAATTTGCAATGT
62 ATAGGTAAATTTACAATGT
83749 TACAGGTATG
Statistics
Matches: 415, Mismatches: 49, Indels: 31
0.84 0.10 0.06
Matches are distributed among these distances:
196 6 0.01
197 1 0.00
198 30 0.07
199 257 0.62
200 78 0.19
201 43 0.10
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (199 bp):
GTGTCGATACATTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
GTAAATTTACAATGTAATCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCATCATAATGTA
TCGACACTTGTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATACCAAACGAGGTGCACGCA
TAAA
Found at i:83900 original size:23 final size:23
Alignment explanation
Indices: 83850--83894 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
83840 TATCTATTTT
*
83850 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
83873 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
83895 TGTTATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:106356 original size:43 final size:47
Alignment explanation
Indices: 106298--106403 Score: 114
Period size: 50 Copynumber: 2.3 Consensus size: 47
106288 ATAACTAAAG
* *
106298 AATAACATATTAATAAACT-AAACA-TGTTTTAA-C-CC-TAATTCCT
1 AATAAAATAATAAT-AACTAAAACATTGTTTTAACCACCTTAATTCCT
*
106341 AATAAAATAATAATAACTAAAAATATTGTTTTAACCCAACCTTAATTCCT
1 AATAAAATAATAATAACT-AAAACATTGTTTTAA-CC-ACCTTAATTCCT
106391 AATAAAATAATAA
1 AATAAAATAATAA
106404 ATCTGATCCT
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
42 4 0.08
43 12 0.23
44 4 0.08
45 8 0.15
47 1 0.02
49 2 0.04
50 21 0.40
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (47 bp):
AATAAAATAATAATAACTAAAACATTGTTTTAACCACCTTAATTCCT
Found at i:108641 original size:27 final size:27
Alignment explanation
Indices: 108611--108678 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
108601 CTATTATATT
108611 AATTAAAATAATTTTTCATATTCTAAA
1 AATTAAAATAATTTTTCATATTCTAAA
*
108638 AATTAAAATGATTTTTCATATTCTAAA
1 AATTAAAATAATTTTTCATATTCTAAA
108665 AATTAAAATGAATT
1 AATTAAAAT-AATT
108679 GATTTTAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 35 0.92
28 3 0.08
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (27 bp):
AATTAAAATAATTTTTCATATTCTAAA
Found at i:113172 original size:20 final size:21
Alignment explanation
Indices: 113147--113186 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
113137 TTCCTTGGCA
*
113147 TGAATT-TTTTTTTTTATTGT
1 TGAATTATTTTTTTATATTGT
113167 TGAATTATTTTTTTATATTG
1 TGAATTATTTTTTTATATTG
113187 CAGTCTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (21 bp):
TGAATTATTTTTTTATATTGT
Found at i:114178 original size:17 final size:17
Alignment explanation
Indices: 114158--114190 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
114148 AATTTCTTTT
*
114158 AATTTTATACATATTTC
1 AATTTTACACATATTTC
114175 AATTTTACACATATTT
1 AATTTTACACATATTT
114191 GAGAGCGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTTTACACATATTTC
Found at i:115433 original size:11 final size:11
Alignment explanation
Indices: 115417--115466 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 11
115407 TTAGAGTTAA
115417 TTAAAATATGT
1 TTAAAATATGT
115428 TTAAAATA--T
1 TTAAAATATGT
*
115437 TTAAAATGTGT
1 TTAAAATATGT
*
115448 TTAAAGT-T-T
1 TTAAAATATGT
115457 TTAAAATATG
1 TTAAAATATG
115467 AAAAACACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
9 15 0.47
10 2 0.06
11 15 0.47
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (11 bp):
TTAAAATATGT
Found at i:115440 original size:20 final size:20
Alignment explanation
Indices: 115417--115466 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
115407 TTAGAGTTAA
115417 TTAAAATATGTTTAAAATAT
1 TTAAAATATGTTTAAAATAT
* * *
115437 TTAAAATGTGTTTAAAGTTT
1 TTAAAATATGTTTAAAATAT
115457 TTAAAATATG
1 TTAAAATATG
115467 AAAAACACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (20 bp):
TTAAAATATGTTTAAAATAT
Done.