Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006841.1 Hibiscus syriacus cultivar Beakdansim tig00017392_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: 66560
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3255 original size:21 final size:21
Alignment explanation
Indices: 3231--3271 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3221 ATTGCCTCAG
3231 GCGAAGGGCACACACAAAAAA
1 GCGAAGGGCACACACAAAAAA
3252 GCGAAGGGCACACACAAAAA
1 GCGAAGGGCACACACAAAAA
3272 CACTAGCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.24, G:0.24, T:0.00
Consensus pattern (21 bp):
GCGAAGGGCACACACAAAAAA
Found at i:5601 original size:205 final size:202
Alignment explanation
Indices: 5251--5656 Score: 744
Period size: 205 Copynumber: 2.0 Consensus size: 202
5241 ACAGTCTATA
5251 AAGACAATATACAGAATGAAAAGAATCTCAAAGAAAATTTAACATCCTGATAACATTGCTGGATG
1 AAGACAATATACAGAATGAAAAGAATCTCAAAGAAAATTTAACATCCTGATAACATTGCTGGATG
5316 TCAGTCATCTAAAGCCAATTCTTTCGTAACTAGCAATCCTTTTTTTTTTATTTGCAACTCATGAA
66 TCAGTCATCTAAAGCCAATTCTTTCGTAACTAGCAATCCTTTTTTTTTTATTTGCAACTCATGAA
5381 TGTTAATTGTATTCAAGAACACCCATTTATCTAGTCAAACTTAAATTAGGGTTGCTAAAATGTAA
131 TGTTAATTGTATTCAAGAACACCCATTTATCTAGTC-AACTTAAATTAGGGTTGCTAAAATGTAA
5446 GACAATGT
195 GACAATGT
*
5454 AAGACAATATACAGAATGAAAAGGATCTCAAAGAAAATTTAACAT-CTGATAACATTGCTGGATC
1 AAGACAATATACAGAATGAAAAGAATCTCAAAGAAAATTTAACATCCTGATAACATTGCTGG---
5518 ATGTCAGTCATCTAAAGCCAATTCTTTCGTAAACTAGCAATCC-TTTTTTTTTATTTGCAACTCA
63 ATGTCAGTCATCTAAAGCCAATTCTTTCGT-AACTAGCAATCCTTTTTTTTTTATTTGCAACTCA
5582 TGAATGTTAATTGTATTCAAGAACACCCATTTATCTAGTCAACTTAAATTAGGGTTGCTAAAATG
127 TGAATGTTAATTGTATTCAAGAACACCCATTTATCTAGTCAACTTAAATTAGGGTTGCTAAAATG
5647 TAAGACAATG
192 TAAGACAATG
5657 AAATTATATT
Statistics
Matches: 198, Mismatches: 1, Indels: 7
0.96 0.00 0.03
Matches are distributed among these distances:
202 16 0.08
203 44 0.22
204 35 0.18
205 91 0.46
206 12 0.06
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (202 bp):
AAGACAATATACAGAATGAAAAGAATCTCAAAGAAAATTTAACATCCTGATAACATTGCTGGATG
TCAGTCATCTAAAGCCAATTCTTTCGTAACTAGCAATCCTTTTTTTTTTATTTGCAACTCATGAA
TGTTAATTGTATTCAAGAACACCCATTTATCTAGTCAACTTAAATTAGGGTTGCTAAAATGTAAG
ACAATGT
Found at i:9960 original size:33 final size:33
Alignment explanation
Indices: 9871--10214 Score: 278
Period size: 33 Copynumber: 10.1 Consensus size: 33
9861 CTTTTTTCTC
* * **
9871 AAAACATTTTTGACAAAGTATAATATATAGTTTCA
1 AAAACA-TTTTGA-AAATTATATTATATAGTTTTG
* * * *
9906 AAAACGGTTTTTCAAAA-TATATTGTATAATTTTG
1 AAAAC--ATTTTGAAAATTATATTATATAGTTTTG
* *
9940 AAAACATTTTTAAAATTATATAATATATAGTTTCG
1 AAAACATTTTGAAAATTATAT--TATATAGTTTTG
*
9975 AAAACA-TTT----A-TATATTATATAGTTTTT
1 AAAACATTTTGAAAATTATATTATATAGTTTTG
*
10002 AAAAGTCATTTTGAAAATATATATAATATATAGTTTTT
1 AAAA--CATTTTGAAAAT-TATAT--TATATAGTTTTG
10040 AAAACATTTTGAAAATTATATATAGTATATAGTTTTG
1 AAAACATTTTGAAAA-T-TATAT--TATATAGTTTTG
*
10077 AAAACATTTTGAAAATTATAATATATAGTTTTG
1 AAAACATTTTGAAAATTATATTATATAGTTTTG
*
10110 AAAACATTTTGAAAATTATAATATATAGTTTTG
1 AAAACATTTTGAAAATTATATTATATAGTTTTG
10143 AAAACATTTTTGAAAA-TAT-TTATATA-TTATAT-
1 AAAACA-TTTTGAAAATTATATTATATAGTT-T-TG
* *
10175 AAGACATTTTGAAAATATATATAATATATAGTTTTT
1 AAAACATTTTGAAAAT-TATAT--TATATAGTTTTG
10211 AAAA
1 AAAA
10215 AATATTTTTG
Statistics
Matches: 262, Mismatches: 20, Indels: 53
0.78 0.06 0.16
Matches are distributed among these distances:
27 14 0.05
29 7 0.03
30 4 0.02
31 11 0.04
32 20 0.08
33 63 0.24
34 31 0.12
35 28 0.11
36 32 0.12
37 36 0.14
38 16 0.06
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (33 bp):
AAAACATTTTGAAAATTATATTATATAGTTTTG
Found at i:10044 original size:65 final size:62
Alignment explanation
Indices: 9922--10159 Score: 201
Period size: 70 Copynumber: 3.5 Consensus size: 62
9912 GTTTTTCAAA
* *
9922 ATATATTGTATAATTTTGAAAACATTTTTAAAATTATATAATATATAGTTTCGAAAACATTT
1 ATATATTATATAATTTTGAAAACATTTTGAAAATTATATAATATATAGTTTCGAAAACATTT
* * **
9984 ATATATTATATAGTTTTTAAAAGTCATTTTGAAAATATATATAATATATAGTTTTTAAAACATTT
1 ATATATTATATAATTTTGAAAA--CATTTTGAAAAT-TATATAATATATAGTTTCGAAAACA-TT
10049 T
62 T
*
10050 GAAAATTATATATAGTATATAGTTTTGAAAACATTTTGAAAA-T-TATAATATATAGTTTTGAAA
1 ----A-TATAT-TA-TATA-A-TTTTGAAAACATTTTGAAAATTATATAATATATAGTTTCGAAA
10113 ACATTTT
57 ACA-TTT
* *
10120 GAAAATTATAATATATAGTTTTGAAAACATTTTTGAAAAT
1 ----A-TATATTATATAATTTTGAAAACA-TTTTGAAAAT
10160 ATTTATATAT
Statistics
Matches: 150, Mismatches: 11, Indels: 24
0.81 0.06 0.13
Matches are distributed among these distances:
62 19 0.13
64 11 0.07
65 23 0.15
66 14 0.09
67 9 0.06
68 4 0.03
69 2 0.01
70 37 0.25
71 6 0.04
72 2 0.01
73 15 0.10
75 8 0.05
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (62 bp):
ATATATTATATAATTTTGAAAACATTTTGAAAATTATATAATATATAGTTTCGAAAACATTT
Found at i:10069 original size:37 final size:35
Alignment explanation
Indices: 9983--10336 Score: 291
Period size: 33 Copynumber: 9.9 Consensus size: 35
9973 CGAAAACATT
9983 TATATAT-TATATAGTTTTTAAAAGTCATTTTGAAAA
1 TATATATATATATAGTTTTTAAAA--CATTTTGAAAA
10019 TATATATAATATATAGTTTTTAAAACATTTTGAAAA
1 TATATAT-ATATATAGTTTTTAAAACATTTTGAAAA
*
10055 TTATATATAGTATATAGTTTTGAAAACATTTTGAAAA
1 -TATATATA-TATATAGTTTTTAAAACATTTTGAAAA
*
10092 T-TATA-ATATATAGTTTTGAAAACATTTTGAAAA
1 TATATATATATATAGTTTTTAAAACATTTTGAAAA
*
10125 T-TATA-ATATATAGTTTTGAAAACATTTTTGAAAA
1 TATATATATATATAGTTTTTAAAACA-TTTTGAAAA
* * *
10159 TAT-T-TATATAT--TATATAAGACATTTTGAAAA
1 TATATATATATATAGTTTTTAAAACATTTTGAAAA
* **
10190 TATATATAATATATAGTTTTTAAAAAATATTTTTGAAGT
1 TATATAT-ATATATAGTTTTT--AAAACA-TTTTGAAAA
* * *
10229 TATATATATTGTATATGTTTTTAAAAACGTTTCTTAAAA
1 TATATATA-TATATA-GTTTTT-AAAACATTT-TGAAAA
***
10268 TACGTATA-ATATATAGTTAAAAAAAAGCATTTTGAAAA
1 TA--TATATATATATAGTT-TTTAAAA-CATTTTGAAAA
*
10306 GT-TATATATTATATA-TTTTTGAAAAAATTTT
1 -TATATATA-TATATAGTTTTT-AAAACATTTT
10337 ATATAGATTA
Statistics
Matches: 265, Mismatches: 27, Indels: 52
0.77 0.08 0.15
Matches are distributed among these distances:
31 12 0.05
32 8 0.03
33 52 0.20
34 24 0.09
35 5 0.02
36 32 0.12
37 40 0.15
38 42 0.16
39 39 0.15
40 7 0.03
41 4 0.02
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (35 bp):
TATATATATATATAGTTTTTAAAACATTTTGAAAA
Found at i:10167 original size:135 final size:134
Alignment explanation
Indices: 9914--10214 Score: 338
Period size: 135 Copynumber: 2.3 Consensus size: 134
9904 CAAAAACGGT
* *
9914 TTTTCAAAATATAT-T-GTATA-A-TTTTGAAAACATTTTTAAAATTATATAATATATAGTTTCG
1 TTTTGAAAATATATATAGTATATAGTTTTGAAAACATTTTGAAAATTATATAATATATAGTTTCG
* * *
9975 AAAACATTTATATATTATATAGTTTTTAAAAGTCATTTTGAAAATATATATAATATATAGTT-TT
66 AAAACATTTATATAATATATAGTTTTGAAAAG-CATTTTGAAAATATATAT-ATATATA-TTATA
10039 TAAAACA
128 TAAAACA
*
10046 TTTTGAAAATTATATATAGTATATAGTTTTGAAAACATTTTGAAAA-T-TATAATATATAGTTTT
1 TTTTGAAAA-TATATATAGTATATAGTTTTGAAAACATTTTGAAAATTATATAATATATAGTTTC
10109 GAAAACATTTTGAAAATTATAATATATAGTTTTGAAAA-CATTTTTG-AAA-ATAT-T-TATATA
65 GAAAACA-TTT----A-TATAATATATAGTTTTGAAAAGCA-TTTTGAAAATATATATATATATA
*
10169 TTATATAAGACA
123 TTATATAAAACA
* *
10181 TTTTGAAAATATATATAATATATAGTTTTTAAAA
1 TTTTGAAAATATATATAGTATATAGTTTTGAAAA
10215 AATATTTTTG
Statistics
Matches: 147, Mismatches: 9, Indels: 24
0.82 0.05 0.13
Matches are distributed among these distances:
132 8 0.05
133 5 0.03
134 26 0.18
135 49 0.33
136 5 0.03
137 20 0.14
138 4 0.03
139 5 0.03
140 6 0.04
141 19 0.13
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (134 bp):
TTTTGAAAATATATATAGTATATAGTTTTGAAAACATTTTGAAAATTATATAATATATAGTTTCG
AAAACATTTATATAATATATAGTTTTGAAAAGCATTTTGAAAATATATATATATATATTATATAA
AACA
Found at i:10244 original size:70 final size:69
Alignment explanation
Indices: 9983--10245 Score: 229
Period size: 70 Copynumber: 3.8 Consensus size: 69
9973 CGAAAACATT
* * * *
9983 TATATATTATATAGTTTTTAAAAGTCA-TTTTGAAAATATATATAATATATAGT-TTTTAAAACA
1 TATATAATATATAGTTTTGAAAA--CATTTTTG-AAAT-TATAT-ATAT-T-GTATATGAAAACA
10046 TTTTGAAAATTA
59 TTTTGAAAA-TA
* * *
10058 TATATAGTATATAGTTTTGAAAACA-TTTTGAAAATTATAATATATAGT-TTTGAAAACATTTTG
1 TATATAATATATAGTTTTGAAAACATTTTTG-AAATTAT-ATATATTGTATATGAAAACATTTTG
10121 -AAA-A
64 AAAATA
* * *
10125 T-TATAATATATAGTTTTGAAAACATTTTTGAAAATATTTATATAT-TATAT-AAGACATTTTGA
1 TATATAATATATAGTTTTGAAAACATTTTTGAAATTATATATAT-TGTATATGAAAACATTTTGA
10187 AAATA
65 AAATA
* * *
10192 TATATAATATATAGTTTTTAAAAAATATTTTTGAAGTTATATATATTGTATATG
1 TATATAATATATAG-TTTT-GAAAACATTTTTGAAATTATATATATTGTATATG
10246 TTTTTAAAAA
Statistics
Matches: 162, Mismatches: 15, Indels: 26
0.80 0.07 0.13
Matches are distributed among these distances:
65 16 0.10
66 33 0.20
67 9 0.06
68 12 0.07
69 8 0.05
70 42 0.26
72 7 0.04
73 14 0.09
75 21 0.13
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (69 bp):
TATATAATATATAGTTTTGAAAACATTTTTGAAATTATATATATTGTATATGAAAACATTTTGAA
AATA
Found at i:10351 original size:3 final size:3
Alignment explanation
Indices: 10343--10397 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
10333 TTTTATATAG
*
10343 ATT ATT ATT ATTT ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
10389 ATT ATT ATT
1 ATT ATT ATT
10398 TCCTATTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:11537 original size:23 final size:22
Alignment explanation
Indices: 11499--11554 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
11489 ATTCTTATTT
* *
11499 TATTTTATTTATTTATTATTA-
1 TATTTTTTTTAATTATTATTAG
11520 TCATGTTTTTTTAATTATTATTAG
1 T-AT-TTTTTTTAATTATTATTAG
11544 TATTTTTTTTA
1 TATTTTTTTTA
11555 CCTCATATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 1 0.03
22 10 0.33
23 18 0.60
24 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (22 bp):
TATTTTTTTTAATTATTATTAG
Found at i:11549 original size:20 final size:20
Alignment explanation
Indices: 11504--11551 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
11494 TATTTTATTT
11504 TATTTATTTATTATTATCATG
1 TATTT-TTTATTATTATCATG
*
11525 T-TTTTTTAATTATTATTA-G
1 TATTTTTT-ATTATTATCATG
11544 TATTTTTT
1 TATTTTTT
11552 TTACCTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 18 0.75
21 1 0.04
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (20 bp):
TATTTTTTATTATTATCATG
Found at i:14911 original size:5 final size:5
Alignment explanation
Indices: 14629--14903 Score: 452
Period size: 5 Copynumber: 55.2 Consensus size: 5
14619 TTTAGTCCTT
14629 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
14679 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
14729 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
*
14779 -TAT- TTATA TTATA TT-TA TTATA TTATA TTATA TATTTA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA T-TATA TTATA TTATA
14827 TTATATA TTATA TTATA -TAT- TTATA TTATA TTATA TTATA TTATA TTATA
1 -T-TATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* *
14877 TTATA TTATA TTACTT TTATA ATATA T
1 TTATA TTATA TTA-TA TTATA TTATA T
14904 ATTTTATTCA
Statistics
Matches: 255, Mismatches: 6, Indels: 18
0.91 0.02 0.06
Matches are distributed among these distances:
4 16 0.06
5 225 0.88
6 10 0.04
7 4 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:14976 original size:15 final size:15
Alignment explanation
Indices: 14958--14996 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
14948 TTTAATCCTT
*
14958 TTTTATTTTCTTTTG
1 TTTTATTTTCTTTTA
*
14973 TTTTATTGTCTTTTA
1 TTTTATTTTCTTTTA
14988 TATTTATTT
1 T-TTTATTT
14997 ATTTTTTCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.77
Consensus pattern (15 bp):
TTTTATTTTCTTTTA
Found at i:19062 original size:95 final size:95
Alignment explanation
Indices: 18895--19070 Score: 255
Period size: 95 Copynumber: 1.9 Consensus size: 95
18885 ATATATATAA
* * * * *
18895 TAAAGCTTGAGTTGTCCCTCTAGAGCAATTTGTTAAACGCCCCGGCTTTATGGATAATATTTGGC
1 TAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAAGATTTAGC
*
18960 TAGCCTGATAAAGGTGATTATACTATACAT
66 TAACCTGATAAAGGTGATTATACTATACAT
* * *
18990 TAAAGCTTGAGCTGTCTCTCTA-AGGTAATTGGTTAAACTCCCCGACTTTATGGATAAGATTTAG
1 TAAAGCTTGAGCTGTCCCTCTAGA-GCAATTGGTTAAACGCCCCGACTTTATGGATAAGATTTAG
19054 CTAACCTGATAAAGGTG
65 CTAACCTGATAAAGGTG
19071 TTTACATATT
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
94 1 0.01
95 70 0.99
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (95 bp):
TAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAAGATTTAGC
TAACCTGATAAAGGTGATTATACTATACAT
Found at i:20574 original size:165 final size:163
Alignment explanation
Indices: 20262--21331 Score: 1047
Period size: 165 Copynumber: 6.5 Consensus size: 163
20252 TATCTTCCAA
* * *
20262 CCAAAGACCTTCGAGTTCGACTA-AGCTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAG
1 CCAAAGACCTTCGAGTTCGACTACA-CTCAGC-TCAAAGGCACATCATTTGCAGCATAACTCAAG
* * *
20326 GCTAA-AAGGGTTATCTGTCACCAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCACATC
64 GC-AAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATC
* * * *
20390 ATTTGCAACATAGCTTAAGTCGAGAAGGGCTATCTG
128 ATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTG
* * * *
20426 CCAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACCAACATTTGCAGCATAACTTAAGG
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCA-CATCATTTGCAGCATAACTCAAGG
* ** *
20491 CAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTATGCTCAGCTCCAAGGCATATCA
65 CAAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCA
*
20556 TTTACAGCATAACTTAAGTCGAGAAGGGATATCTG
129 TTTACAGCATAACTTAAGTCGAGAAGGGTTATCTG
* * * * * * * * * * * **
20591 TCAAAGACCCTCAATTTCGATTATACTTAGCTTCGAGGGCACATCAATTACAATATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACACTCAGC-TCAAAGGCACATCATTTGCAGCATAACTCAAGG
* * * * * * * *
20656 CTAGAAGGGTTATCTGTCACTAAAAGACCTTCAAGTTCAACTACGCTCAGCTCCAAGGCATATAA
65 CAAGAAGGGTTATCTGCCAC-CAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCA
20721 TTTACAGCATAACTTAAGTCGAGAAGGGTTATCTG
129 TTTACAGCATAACTTAAGTCGAGAAGGGTTATCTG
* * * * * * * *
20756 CCAACAAAAAACCTTTGAGTTTGACTACGCTCAGCTCAATGACACATCATTTGCAGCATAGCTTA
1 -C--C-AAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCA
* * * * * * * *
20821 AGTCGAGAAGGGTTATCTG---CCAAAGACCCTCAAGTTCGATTATACTCAGCTTCGAGGGCACA
62 AGGCAAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACA
* * *
20883 TCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
126 TCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTG
* * * * *
20921 TCACCAAAGGACCTTCGAGTTTGACTACGCTCAGCTCTAAGGCATATCATTTGCAGCATAACTTA
1 ---CCAAA-GACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCA
* * * * * *
20986 AGTCAAAAAGGGTTATCTGCCAACCAAAGACCTTAGAGTTTGACTACACTCAGTTCTAAGGCACA
62 AGGCAAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACA
* *
21051 TCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG
126 TCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTG
* * *
21089 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTC-GAGGCACATCATTTGCAGCATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACACTCAGC-TCAAAGGCACATCATTTGCAGCATAACTCAAGG
* * * * * *
21153 CTAGAAGGGTTATCTGCCAACAAAGACCTTTGGGTTCGATTACACTCAGCT-CAACGACACATCA
65 CAAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAA-GGCACATCA
* * * * * * *
21217 TTTGCGGTATAACTCAAGGCTAGAAGGGTTATTTG
129 TTTACAGCATAACTTAAGTCGAGAAGGGTTATCTG
* * * * * * * *
21252 CCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACGTCATCTACAACATAGCTCAAGGC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGC
*
21317 AAGAAGGGCTATCTG
66 AAGAAGGGTTATCTG
21332 TCAATAAAAT
Statistics
Matches: 749, Mismatches: 136, Indels: 43
0.81 0.15 0.05
Matches are distributed among these distances:
162 4 0.01
163 137 0.18
164 155 0.21
165 321 0.43
166 7 0.01
167 1 0.00
168 81 0.11
169 43 0.06
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (163 bp):
CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGC
AAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATT
TACAGCATAACTTAAGTCGAGAAGGGTTATCTG
Found at i:20581 original size:84 final size:82
Alignment explanation
Indices: 20222--21331 Score: 1002
Period size: 84 Copynumber: 13.4 Consensus size: 82
20212 AATTTTTTCT
* * *
20222 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTAAG
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATC-TGC-ACCAAAGACCTTCGAGTTCGACTACG
* *
20287 CTCAGCTTCGAGGGCACATC
64 CTCAGC-TCCAAGGCACATC
* * * *
20307 ATTTACAGCATAACTCAAGGCTAAAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCAACTACGC
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG-CACCAAAGACCTTCGAGTTCGACTACGC
20372 TCAGCTCCAAGGCACATC
65 TCAGCTCCAAGGCACATC
* * * * * * *
20390 ATTTGCAACATAGCTTAAGTCGAGAAGGGCTATCTG--CCAAAGACCTTCGAGTTCGATTACACT
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
* * *
20453 CAACTCAAAGGCACCAAC
66 CAGCTCCAAGGCA-CATC
* * *
20471 ATTTGCAGCATAACTTAAGGCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTATG
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACG
*
20536 CTCAGCTCCAAGGCATATC
64 CTCAGCTCCAAGGCACATC
* * * * * * * * * **
20555 ATTTACAGCATAACTTAAGTCGAGAAGGGATATCTG--TCAAAGACCCTCAATTTCGATTATACT
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
* * *
20618 TAGCTTCGAGGGCACATC
66 CAGC-TCCAAGGCACATC
* * ** * * * *
20636 AATTACAATATAACTCAAGGCTAGAAGGGTTATCTGTCACTAAAAGACCTTCAAGTTCAACTACG
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG-CAC-CAAAGACCTTCGAGTTCGACTACG
* *
20701 CTCAGCTCCAAGGCATATA
64 CTCAGCTCCAAGGCACATC
* * * * * * *
20720 ATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAAACCTTTGAGTTTGACTACG
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACG
*
20785 CTCAGCT-CAATGACACATC
64 CTCAGCTCCAA-GGCACATC
* * * * * * **
20804 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG--CCAAAGACCCTCAAGTTCGATTATACT
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
* *
20867 CAGCTTCGAGGGCACATC
66 CAGC-TCCAAGGCACATC
* * *
20885 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGGACCTTCGAGTTTGACTACG
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG-CACCAAA-GACCTTCGAGTTCGACTACG
* *
20950 CTCAGCTCTAAGGCATATC
64 CTCAGCTCCAAGGCACATC
* * * * * *
20969 ATTTGCAGCATAACTTAAGTCAAAAAGGGTTATCTGCCAACCAAAGACCTTAGAGTTTGACTACA
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACG
* *
21034 CTCAGTTCTAAGGCACATC
64 CTCAGCTCCAAGGCACATC
* * * * * *
21053 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG--CCAAAGACCCTCGAGTTCGATTACACT
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
* *
21116 CAGCTTCGAGGCACATC
66 CAGCTCCAAGGCACATC
* * * * * *
21133 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTTGGGTTCGATTACAC
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG-CACCAAAGACCTTCGAGTTCGACTACGC
*
21198 TCAGCT-CAACGACACATC
65 TCAGCTCCAA-GGCACATC
* * * * *
21216 ATTTGCGGTATAACTCAAGGCTAGAAGGGTTATTTG--CCAAAGACCTTTGAGTTCGACTACGCT
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
*
21279 CAGCTCCAAGGCACGTC
66 CAGCTCCAAGGCACATC
* * * * * * *
21296 ATCTACAACATAGCTCAAGGCAAGAAGGGCTATCTG
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG
21332 TCAATAAAAT
Statistics
Matches: 839, Mismatches: 161, Indels: 55
0.80 0.15 0.05
Matches are distributed among these distances:
80 209 0.25
81 115 0.14
82 3 0.00
83 110 0.13
84 285 0.34
85 117 0.14
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (82 bp):
ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
CAGCTCCAAGGCACATC
Found at i:20731 original size:249 final size:246
Alignment explanation
Indices: 20222--21335 Score: 1213
Period size: 249 Copynumber: 4.5 Consensus size: 246
20212 AATTTTTTCT
* * * * *
20222 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTAAG
1 ATTTGCAGCATAACTTAAGGCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACG
* * * * * * *
20287 CTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAAAAGGGTTATCTGTCACCAAAG
66 CTCAGC-TCCAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGT---CAAAG
* * * * * * * * * * * *
20352 ACCTTCGAGTTCAACTACGCTCAGC-TCCAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAA
127 ACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAA
* * * *
20416 GGGCTATCTGCC-AAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACCA-A
192 GGGTTATCTGCCAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCA-CATA
*
20470 CATTTGCAGCATAACTTAAGGCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTAT
1 -ATTTGCAGCATAACTTAAGGCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTAC
* *
20535 GCTCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGATATCTGTCAAAGACC
65 GCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGTCAAAGACC
* * * * *
20600 CTCAATTTCGATTATACTTAGCTTCGAGGGCACATCAATTACAATATAACTCAAGGCTAGAAGGG
130 CTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGG
* * * *
20665 TTATCTGTCACTAAAAGACCTTCAAGTTCAACTACGCTCAGCTCCAAGGCATATA
195 TTATCTG-C-C-AAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATA
* * * * * *
20720 ATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAAACCTTTGAGTTTGACTACG
1 ATTTGCAGCATAACTTAAGGCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACG
* * * * *
20785 CTCAGCT-CAATGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACC
66 CTCAGCTCCAA-GGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGTCAAAGACC
* *
20849 CTCAAGTTCGATTATACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGG
130 CTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGG
* * * * * *
20914 TTATCTGTCACCAAAGGACCTTCGAGTTTGACTACGCTCAGCTCTAAGGCATATC
195 TTATCTG---CCAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATA
* * * *
20969 ATTTGCAGCATAACTTAAGTCAAAAAGGGTTATCTGCCAACCAAAGACCTTAGAGTTTGACTACA
1 ATTTGCAGCATAACTTAAGGCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACG
* * * *
21034 CTCAGTTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
66 CTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGTCAAAGACCC
* * *
21099 TCGAGTTCGATTACACTCAGCTTCGA-GGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGT
131 TCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGT
* * * * *
21163 TATCTGCCAACAAAGACCTTTGGGTTCGATTACACTCAGCT-CAACGACACATC
196 TATCTGCC-A-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAA-GGCACATA
* * * * * * *
21216 ATTTGCGGTATAACTCAAGGCTAGAAGGGTTATTTG----CCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGGCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACG
* * * * * * *
21277 CTCAGCTCCAAGGCACGTCATCTACAACATAGCTCAAGGCAAGAAGGGCTATCTGTCAA
66 CTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGTCAA
21336 TAAAATTATC
Statistics
Matches: 744, Mismatches: 108, Indels: 32
0.84 0.12 0.04
Matches are distributed among these distances:
243 70 0.09
245 24 0.03
246 42 0.06
247 60 0.08
248 89 0.12
249 422 0.57
250 36 0.05
251 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (246 bp):
ATTTGCAGCATAACTTAAGGCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACG
CTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGCTATCTGTCAAAGACCC
TCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGT
TATCTGCCAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATA
Found at i:21988 original size:35 final size:34
Alignment explanation
Indices: 21902--22177 Score: 188
Period size: 37 Copynumber: 8.1 Consensus size: 34
21892 ATATATCTAT
** *
21902 ATATATATATTATATAGTTTGTAAATGATTTTTTAAA
1 ATATATATA-TATATAGTTT-TAAAACA-TTTTGAAA
* *
21939 GTATGTATATAATATATAGCTTTAAAACATTTTGAAA
1 --ATATATAT-ATATATAGTTTTAAAACATTTTGAAA
**
21976 ATATATATAATATATAGTTAAAAAAACATTTTTGAAA
1 ATATATAT-ATATATAGTT-TTAAAACA-TTTTGAAA
*
22013 ACTATATA-CTATATAGTTTTTAAAACATTTTG---
1 A-TATATATATATATAG-TTTTAAAACATTTTGAAA
22045 --A-A-A-A-ATATAGTTTTAAAAACATTTTTGAAA
1 ATATATATATATATAGTTTT-AAAACA-TTTTGAAA
22075 ACTATATATATAT-T--TTTTAAAACATTTTGAAA
1 A-TATATATATATATAGTTTTAAAACATTTTGAAA
*
22107 ATAAATATATATATAGTTTTTGAAAAACATTTTGAAA
1 ATATATATATATATAG-TTTT--AAAACATTTTGAAA
*
22144 CATATATATATA-AT--TTTTAAAACATTTTTAAA
1 -ATATATATATATATAGTTTTAAAACATTTTGAAA
22176 AT
1 AT
22178 CATAGTTTTT
Statistics
Matches: 197, Mismatches: 16, Indels: 56
0.73 0.06 0.21
Matches are distributed among these distances:
25 4 0.02
26 12 0.06
27 6 0.03
28 1 0.01
29 1 0.01
31 12 0.06
32 23 0.12
33 7 0.04
34 9 0.05
35 27 0.14
36 21 0.11
37 36 0.18
38 21 0.11
39 16 0.08
40 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (34 bp):
ATATATATATATATAGTTTTAAAACATTTTGAAA
Found at i:22019 original size:36 final size:33
Alignment explanation
Indices: 21944--22176 Score: 157
Period size: 35 Copynumber: 7.0 Consensus size: 33
21934 TTAAAGTATG
21944 TATATAATATATAGCTTTAAAACATTTTGAAAATA
1 TATATAATATATAG-TTTAAAACATTTTGAAAA-A
* *
21979 TATATAATATATAGTTAAAAAAACATTTTTGAAAAC
1 TATATAATATATAGTT--TAAAACA-TTTTGAAAAA
*
22015 TATATACTATATAGTTTTTAAAACATTTTGAAAAA
1 TATATAATATATAG--TTTAAAACATTTTGAAAAA
*
22050 TATAGT--T-T-TA----AAAACATTTTTGAAAAC
1 TATA-TAATATATAGTTTAAAACA-TTTTGAAAAA
**
22077 TATAT-ATATATTTTTTAAAACATTTTG-AAAA
1 TATATAATATATAGTTTAAAACATTTTGAAAAA
* *
22108 TAAATATATATATAGTTTTTGAAAAACATTTTGAAACA
1 TATATA-ATATATAG--TTT--AAAACATTTTGAAAAA
* *
22146 TATAT-ATATA-ATTTTTAAAACATTTTTAAAA
1 TATATAATATATA-GTTTAAAACATTTTGAAAA
22177 TCATAGTTTT
Statistics
Matches: 160, Mismatches: 16, Indels: 47
0.72 0.07 0.21
Matches are distributed among these distances:
26 7 0.04
27 14 0.09
28 1 0.01
29 1 0.01
31 7 0.04
32 20 0.12
33 13 0.08
34 6 0.04
35 31 0.19
36 31 0.19
37 20 0.12
38 9 0.06
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (33 bp):
TATATAATATATAGTTTAAAACATTTTGAAAAA
Found at i:22080 original size:27 final size:26
Alignment explanation
Indices: 22023--22080 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
22013 ACTATATACT
*
22023 ATATAGTTTTTAAAACATTTTGAAAA
1 ATATAGTTTTAAAAACATTTTGAAAA
22049 ATATAGTTTTAAAAACATTTTTGAAAA
1 ATATAGTTTTAAAAACA-TTTTGAAAA
*
22076 CTATA
1 ATATA
22081 TATATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 16 0.55
27 13 0.45
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (26 bp):
ATATAGTTTTAAAAACATTTTGAAAA
Found at i:22106 original size:131 final size:128
Alignment explanation
Indices: 21959--22297 Score: 413
Period size: 131 Copynumber: 2.6 Consensus size: 128
21949 AATATATAGC
21959 TTTAAAACATTTTGAAAATATATATAATATATAG-TTAAAAAAACATTTTTGAAAACTATATACT
1 TTTAAAACATTTTGAAAATATATATAATATATAGTTTAAAAAAACA-TTTTGAAAACTATATA-T
22023 ATATAGTTTTTAAAACATTTTGAAAAAT-ATAG-TTTTAAAAACATTTTTGAAAACTATATATAT
64 ATATAGTTTTTAAAACATTTT-AAAAATCATAGTTTTTAAAAACATTTTTGAAAA-T-TATATA-
22086 ATTT
125 ATTT
* **
22090 TTTAAAACATTTTGAAAATAAATAT-ATATATAGTTTTTGAAAAACATTTTG-AAAC-ATATATA
1 TTTAAAACATTTTGAAAATATATATAATATATAG-TTTAAAAAAACATTTTGAAAACTATATATA
* * *
22152 TATAATTTTTAAAACATTTTTAAAATCATAGTTTTTAAAAACATTTTTGAAAATTATATAGTTT
65 TATAGTTTTTAAAACATTTTAAAAATCATAGTTTTTAAAAACATTTTTGAAAATTATATAATTT
*
22216 TTTAAAACTATTTTTGAAAATGTATATATAATATATAGTTTTTAAAAGAAACAGTTTT-AAAAAT
1 TTTAAAAC-A-TTTTGAAAA--TATATATAATATATAG--TTTAAAA-AAACA-TTTTGAAAACT
*
22280 GTATATTATATAGTTTTT
58 ATATA-TATATAGTTTTT
22298 GTTTTTATGT
Statistics
Matches: 181, Mismatches: 12, Indels: 25
0.83 0.06 0.11
Matches are distributed among these distances:
126 11 0.06
127 12 0.07
128 35 0.19
129 26 0.14
130 18 0.10
131 37 0.20
132 15 0.08
133 5 0.03
134 7 0.04
135 4 0.02
136 11 0.06
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (128 bp):
TTTAAAACATTTTGAAAATATATATAATATATAGTTTAAAAAAACATTTTGAAAACTATATATAT
ATAGTTTTTAAAACATTTTAAAAATCATAGTTTTTAAAAACATTTTTGAAAATTATATAATTT
Found at i:22152 original size:69 final size:68
Alignment explanation
Indices: 22049--22262 Score: 229
Period size: 69 Copynumber: 3.2 Consensus size: 68
22039 ATTTTGAAAA
22049 ATATAG-TTTTAAAAACATTTTTGAAAACTATATATATATTTTTTAAAACATTTTGAAAATAAAT
1 ATATAGTTTTTAAAAACATTTTTGAAAA-TATATATATATTTTTTAAAACATTTTGAAAATAAAT
22113 ATAT
65 ATAT
*
22117 ATATAGTTTTTGAAAAACA-TTTTGAAACATATATATATAATTTTTAAAACATTTT-----T-AA
1 ATATAGTTTTT-AAAAACATTTTTGAAA-ATATATATATATTTTTTAAAACATTTTGAAAATAAA
22175 -A-AT
64 TATAT
* *
22178 -CATAGTTTTTAAAAACATTTTTGAAAAT-TATATA-GTTTTTTAAAACTATTTTTGAAAATGTA
1 ATATAGTTTTTAAAAACATTTTTGAAAATATATATATATTTTTTAAAAC-A-TTTTGAAAA--TA
*
22240 TATATAAT
62 AATAT-AT
22248 ATATAGTTTTTAAAA
1 ATATAGTTTTTAAAA
22263 GAAACAGTTT
Statistics
Matches: 122, Mismatches: 6, Indels: 33
0.76 0.04 0.20
Matches are distributed among these distances:
57 10 0.08
58 7 0.06
59 13 0.11
60 17 0.14
61 2 0.02
62 1 0.01
63 2 0.02
64 1 0.01
66 1 0.01
67 1 0.01
68 7 0.06
69 37 0.30
70 10 0.08
71 13 0.11
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (68 bp):
ATATAGTTTTTAAAAACATTTTTGAAAATATATATATATTTTTTAAAACATTTTGAAAATAAATA
TAT
Found at i:22183 original size:128 final size:130
Alignment explanation
Indices: 21959--22262 Score: 417
Period size: 131 Copynumber: 2.3 Consensus size: 130
21949 AATATATAGC
**
21959 TTTAAAACATTTTGAAAATATATATAATATATAG-TTAAAAAAACATTTTTGAAAACTATATACT
1 TTTAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAAACATTTTTGAAAACTATATACT
*
22023 ATATAGTTTTTAAAACATTTTGAAAAATATAG-TTTTAAAAACATTTTTGAAAACTATATATATA
66 ATATAATTTTTAAAACATTTTGAAAAATATAGTTTTTAAAAACATTTTTGAAAA-T-TATATA-A
22087 TTT
128 TTT
*
22090 TTTAAAACATTTTGAAAATAAATAT-ATATATAGTTTTTGAAAAACA-TTTTG-AAAC-ATATA-
1 TTTAAAACATTTTGAAAATATATATAATATATAGTTTTT-AAAAACATTTTTGAAAACTATATAC
* *
22150 TATATAATTTTTAAAACATTTT-TAAAATCATAGTTTTTAAAAACATTTTTGAAAATTATATAGT
65 TATATAATTTTTAAAACATTTTGAAAAAT-ATAGTTTTTAAAAACATTTTTGAAAATTATATAAT
22214 TT
129 TT
22216 TTTAAAACTATTTTTGAAAATGTATATATAATATATAGTTTTTAAAA
1 TTTAAAAC-A-TTTTGAAAA--TATATATAATATATAGTTTTTAAAA
22263 GAAACAGTTT
Statistics
Matches: 157, Mismatches: 7, Indels: 19
0.86 0.04 0.10
Matches are distributed among these distances:
126 11 0.07
127 12 0.08
128 35 0.22
129 26 0.17
130 22 0.14
131 44 0.28
132 7 0.04
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.44
Consensus pattern (130 bp):
TTTAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAAACATTTTTGAAAACTATATACT
ATATAATTTTTAAAACATTTTGAAAAATATAGTTTTTAAAAACATTTTTGAAAATTATATAATTT
Found at i:22200 original size:60 final size:59
Alignment explanation
Indices: 22119--22236 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 59
22109 AAATATATAT
*
22119 ATAGTTTTTGAAAAACATTTTGAAACATATATATA-TAATTTTTAAAAC-ATTTTT-AAAATC
1 ATAGTTTTTAAAAAACATTTTGAAA-AT-TATATAGT--TTTTTAAAACTATTTTTGAAAATC
22179 ATAGTTTTT-AAAAACATTTTTGAAAATTATATAGTTTTTTAAAACTATTTTTGAAAAT
1 ATAGTTTTTAAAAAACA-TTTTGAAAATTATATAGTTTTTTAAAACTATTTTTGAAAAT
22237 GTATATATAA
Statistics
Matches: 54, Mismatches: 0, Indels: 9
0.86 0.00 0.14
Matches are distributed among these distances:
57 10 0.19
58 12 0.22
59 15 0.28
60 17 0.31
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (59 bp):
ATAGTTTTTAAAAAACATTTTGAAAATTATATAGTTTTTTAAAACTATTTTTGAAAATC
Found at i:22211 original size:96 final size:93
Alignment explanation
Indices: 21997--22211 Score: 226
Period size: 96 Copynumber: 2.3 Consensus size: 93
21987 ATATAGTTAA
* *
21997 AAAAACATTTTTGAAAACTATATACTATATAGTTTTTAAAACATTTTGAAAAATATAGTTTTAAA
1 AAAAACATTTTTGAAAATTATATACTATATAGTTTTTAAAACATTTTGAAAAATATAATTTTAAA
*
22062 AACATTTTTGAAAACTATATATATATTTTT
66 AACATTTTT-AAAAC-ATACATATATTTTT
* *
22092 TAAAACA-TTTTGAAAATAAATATA-TATATAGTTTTTGAAAAACATTTTGAAACATATATATAT
1 AAAAACATTTTTGAAAAT-TATATACTATATAGTTTTT--AAAACATTTTG--A-A-A-A-ATAT
* *
22155 AATTTTTAAAACATTTTT-AAA-AT-CATA-GTTTTT
57 AATTTTAAAAACATTTTTAAAACATACATATATTTTT
22188 AAAAACATTTTTGAAAATTATATA
1 AAAAACATTTTTGAAAATTATATA
22212 GTTTTTTAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
94 21 0.21
95 11 0.11
96 27 0.27
97 13 0.13
98 3 0.03
99 1 0.01
100 4 0.04
101 1 0.01
102 20 0.20
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.43
Consensus pattern (93 bp):
AAAAACATTTTTGAAAATTATATACTATATAGTTTTTAAAACATTTTGAAAAATATAATTTTAAA
AACATTTTTAAAACATACATATATTTTT
Found at i:22250 original size:39 final size:40
Alignment explanation
Indices: 22206--22291 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 40
22196 TTTTGAAAAT
* * *
22206 TATATAGTTTTT-TA-AAACTATTTTTGAAAATGTATATATAA
1 TATATAGTTTTTAAAGAAAC-AGTTTTAAAAATGTATAT-T-A
22247 TATATAGTTTTTAAAAGAAACAGTTTTAAAAATGTATATTA
1 TATATAGTTTTT-AAAGAAACAGTTTTAAAAATGTATATTA
22288 TATA
1 TATA
22292 GTTTTTGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
41 17 0.44
42 1 0.03
43 17 0.44
44 4 0.10
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.45
Consensus pattern (40 bp):
TATATAGTTTTTAAAGAAACAGTTTTAAAAATGTATATTA
Found at i:23329 original size:5 final size:5
Alignment explanation
Indices: 23321--23503 Score: 149
Period size: 5 Copynumber: 37.2 Consensus size: 5
23311 TCCTTTTGTT
23321 TTATA TTATA TTATA TTATA TTATA TTATA -TATA -TATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * * * * * *
23369 TTATA TTATA TTACA TTACA TTACA TTACA TTACA TTACA TTACA TTACA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * * * * * *
23419 TTACA TTACA TTACA TTACA TTACA TTACA TTACA TTACA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * *
23469 TTAT- TTTTG TTAT- TAATA TTACTT TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTA-TA TTATA TTATA T
23504 ATTTTATTCA
Statistics
Matches: 166, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
4 14 0.08
5 148 0.89
6 4 0.02
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.52
Consensus pattern (5 bp):
TTATA
Found at i:23505 original size:18 final size:19
Alignment explanation
Indices: 23465--23506 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
23455 TACATTATAT
* *
23465 TATATTATTTTTGTTATTA
1 TATATTACTTTTGATATTA
23484 -ATATTACTTTT-ATATTA
1 TATATTACTTTTGATATTA
23501 TATATT
1 TATATT
23507 TTATTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TATATTACTTTTGATATTA
Found at i:29675 original size:24 final size:25
Alignment explanation
Indices: 29629--29689 Score: 85
Period size: 23 Copynumber: 2.6 Consensus size: 25
29619 TAGTAATTTA
29629 AATTTTATA--TTAATTTTTAAAAT
1 AATTTTATATTTTAATTTTTAAAAT
*
29652 ATTTTTATATTTTAATTTTT-AAAT
1 AATTTTATATTTTAATTTTTAAAAT
29676 AATTTTAT-TTTTAA
1 AATTTTATATTTTAA
29690 AATATTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 14 0.41
24 11 0.32
25 9 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
AATTTTATATTTTAATTTTTAAAAT
Found at i:29697 original size:24 final size:24
Alignment explanation
Indices: 29648--29701 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
29638 TTAATTTTTA
* * *
29648 AAATATTTTTATATTTTAATTTTT
1 AAATAATTTTATATTTTAAATATT
29672 AAATAATTTTAT-TTTTAAAATATT
1 AAATAATTTTATATTTT-AAATATT
29696 AAATAA
1 AAATAA
29702 ATCTCTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
AAATAATTTTATATTTTAAATATT
Found at i:30641 original size:128 final size:128
Alignment explanation
Indices: 30406--30646 Score: 342
Period size: 128 Copynumber: 1.9 Consensus size: 128
30396 AAATATAAGT
* * * * * *
30406 TATAAGATTTTGAAGTGATAAAATTACAGTTAATTTTAAAATTAAATATGACTCTAATTAATTTA
1 TATAAGATTTTGAAGAGAAAAAAGTACAATTAAATTTAAAATTAAATAGGACTCTAATTAATTTA
* * *
30471 ATTTTGATTAAATAGAATTATAATTAAAATTTAATTTAATAAAATTATATTTTTTTCACTTAG
66 ATTTTGATTAAATAAAATTATAACTAAAATTAAATTTAATAAAATTATATTTTTTTCACTTAG
*
30534 TATAAGATTTTGAAGAGAAAAAAGTATAATTAAATTTAAAATTAAATAGGACTCTAATTAATTTA
1 TATAAGATTTTGAAGAGAAAAAAGTACAATTAAATTTAAAATTAAATAGGACTCTAATTAATTTA
* *
30599 ATTTTGTTTAAATAAAATTATGACT-AAATTCAAATCTT-ATAAAATTAT
66 ATTTTGATTAAATAAAATTATAACTAAAATT-AAAT-TTAATAAAATTAT
30647 GAAAAAAAAT
Statistics
Matches: 99, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
127 5 0.05
128 92 0.93
129 2 0.02
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (128 bp):
TATAAGATTTTGAAGAGAAAAAAGTACAATTAAATTTAAAATTAAATAGGACTCTAATTAATTTA
ATTTTGATTAAATAAAATTATAACTAAAATTAAATTTAATAAAATTATATTTTTTTCACTTAG
Found at i:32729 original size:19 final size:20
Alignment explanation
Indices: 32705--32756 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
32695 AATATACTTT
*
32705 TATGAACAGTAA-AATACGG
1 TATGAACAGTAACAATACCG
*
32724 TATGAACAGTGAACATTACCG
1 TATGAACAGT-AACAATACCG
32745 TATGAACAGTAA
1 TATGAACAGTAA
32757 TGAACAGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 10 0.34
20 4 0.14
21 15 0.52
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.23
Consensus pattern (20 bp):
TATGAACAGTAACAATACCG
Found at i:36260 original size:21 final size:19
Alignment explanation
Indices: 36203--36254 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
36193 ATATATGTTT
**
36203 TATGAACAGTAAAATATGG
1 TATGAACAGTAAAATACCG
*
36222 TATGAATAGTGAACAATACCG
1 TATGAACAGT-AA-AATACCG
36243 TATGAACAGTAA
1 TATGAACAGTAA
36255 TGAATAGTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 9 0.33
20 4 0.15
21 14 0.52
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (19 bp):
TATGAACAGTAAAATACCG
Found at i:36345 original size:21 final size:21
Alignment explanation
Indices: 36321--36361 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
36311 ATAAATTATA
36321 CATCGATGCACTGCTATAGTG
1 CATCGATGCACTGCTATAGTG
36342 CATCGATGCACTGCTATAGT
1 CATCGATGCACTGCTATAGT
36362 ACTACTACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (21 bp):
CATCGATGCACTGCTATAGTG
Found at i:37115 original size:24 final size:24
Alignment explanation
Indices: 37088--37158 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
37078 CACCACAGCT
* *
37088 CGTATAAATTGCACTGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* *
37112 CGTAGAATTTGCACCGAAGTGCCG
1 CGTAGAAATTGCACCGAAGTGCCA
*
37136 CGTAGAAA-TGCACCGTAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
37159 TATAAGATTG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 13 0.32
24 27 0.68
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:39943 original size:23 final size:23
Alignment explanation
Indices: 39917--39991 Score: 105
Period size: 23 Copynumber: 3.2 Consensus size: 23
39907 TCCTTATGGA
* * *
39917 CAATTTTATATGGCACTACGGTG
1 CAATTCTATGTGGCACTTCGGTG
*
39940 CAATTCTATGCGGCACTTCGGTG
1 CAATTCTATGTGGCACTTCGGTG
39963 CAAATTCTATGTGGCACTTCGGTG
1 C-AATTCTATGTGGCACTTCGGTG
39987 CAATT
1 CAATT
39992 TATACGAGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 24 0.52
24 22 0.48
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (23 bp):
CAATTCTATGTGGCACTTCGGTG
Found at i:39973 original size:24 final size:24
Alignment explanation
Indices: 39928--39989 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
39918 AATTTTATAT
*
39928 GGCACTACGGTGC-AATTCTATGC
1 GGCACTTCGGTGCAAATTCTATGC
*
39951 GGCACTTCGGTGCAAATTCTATGT
1 GGCACTTCGGTGCAAATTCTATGC
39975 GGCACTTCGGTGCAA
1 GGCACTTCGGTGCAA
39990 TTTATACGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 12 0.33
24 24 0.67
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.27
Consensus pattern (24 bp):
GGCACTTCGGTGCAAATTCTATGC
Found at i:40306 original size:24 final size:24
Alignment explanation
Indices: 40279--40333 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
40269 GATATCGAAA
40279 AGCAGAAAGATCCAATATAAGCTC
1 AGCAGAAAGATCCAATATAAGCTC
*
40303 AGCAGAAATATCCAATATAAGCTC
1 AGCAGAAAGATCCAATATAAGCTC
*
40327 AACAGAA
1 AGCAGAA
40334 CAACATATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.49, C:0.20, G:0.15, T:0.16
Consensus pattern (24 bp):
AGCAGAAAGATCCAATATAAGCTC
Found at i:40610 original size:21 final size:21
Alignment explanation
Indices: 40549--40603 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
40539 CTGAAGTTAT
40549 TGTAGCAGTGCATCGGTACAC
1 TGTAGCAGTGCATCGGTACAC
40570 TGTAGCAGTGCATCGGTACAC
1 TGTAGCAGTGCATCGGTACAC
40591 TGTAGCAGTGCAT
1 TGTAGCAGTGCAT
40604 TGATACAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (21 bp):
TGTAGCAGTGCATCGGTACAC
Found at i:44006 original size:2 final size:2
Alignment explanation
Indices: 43999--44056 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
43989 TTTAAATAAA
43999 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
44041 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
44057 GTCGGAACCG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44515 original size:13 final size:14
Alignment explanation
Indices: 44483--44516 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
44473 TAAATAGGAT
44483 AAATAAAGGAAAAG
1 AAATAAAGGAAAAG
*
44497 AAATAAAGGGAAA-
1 AAATAAAGGAAAAG
44510 AAATAAA
1 AAATAAA
44517 AAATAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.09
Consensus pattern (14 bp):
AAATAAAGGAAAAG
Found at i:44536 original size:23 final size:23
Alignment explanation
Indices: 44510--44553 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
44500 TAAAGGGAAA
44510 AAATAAA-AAATAAAACATATATT
1 AAATAAATAAATAAAA-ATATATT
44533 AAATAAATAAATAAAAATATA
1 AAATAAATAAATAAAAATATA
44554 CATATATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (23 bp):
AAATAAATAAATAAAAATATATT
Found at i:44627 original size:25 final size:25
Alignment explanation
Indices: 44599--44667 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
44589 AAGCAAACAT
44599 AAAACAAAGAAATGAAAATTATTTA
1 AAAACAAAGAAATGAAAATTATTTA
*
44624 AAAACAAAGAAATGAAAATTGTTTA
1 AAAACAAAGAAATGAAAATTATTTA
*
44649 AAAACAAAGAAATAAAAAT
1 AAAACAAAGAAATGAAAAT
44668 AAAACATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.20
Consensus pattern (25 bp):
AAAACAAAGAAATGAAAATTATTTA
Found at i:44771 original size:2 final size:2
Alignment explanation
Indices: 44764--44801 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
44754 AATCAAAGGA
44764 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
44802 GCATATAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44820 original size:3 final size:3
Alignment explanation
Indices: 44812--44879 Score: 68
Period size: 3 Copynumber: 22.0 Consensus size: 3
44802 GCATATAGGT
* *
44812 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAGA -AA TAA TAA TAGC T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA
44857 TATA TATA TAA TAA TAA TAA TAA
1 TA-A TA-A TAA TAA TAA TAA TAA
44880 ATGACGTATA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
2 2 0.04
3 45 0.80
4 9 0.16
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:47003 original size:110 final size:110
Alignment explanation
Indices: 46855--47058 Score: 293
Period size: 110 Copynumber: 1.9 Consensus size: 110
46845 TGGGAAATTG
* * ** * *
46855 TTTGTTGACAGTCAGCTGCCCCTTCGCTGTGAAGTTGAGCTTGTACTGTCTCGAGTCTAATATCC
1 TTTGTTGACAATCAACCACCCCTTCGCTGTGAAGTTGAGCTTGTACTGTCTCGAGTCCAATATCA
*
46920 TTCGTTGTGAAGTTGAAATTGACTTTGAATGAAACTAAAAAGTTA
66 TTCGCTGTGAAGTTGAAATTGACTTTGAATGAAACTAAAAAGTTA
** *
46965 TTTGTTGACAATCAACCACCCCTTCG-TCGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATC
1 TTTGTTGACAATCAACCACCCCTTCGCT-GTGAAGTTGAGCTTGTACTGTCTCGAGTCCAATATC
*
47029 ATTCGCTGTGAAGTTGAAATTGCCTTTGAA
65 ATTCGCTGTGAAGTTGAAATTGACTTTGAA
47059 ATTGGGAAGC
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
109 1 0.01
110 81 0.99
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.36
Consensus pattern (110 bp):
TTTGTTGACAATCAACCACCCCTTCGCTGTGAAGTTGAGCTTGTACTGTCTCGAGTCCAATATCA
TTCGCTGTGAAGTTGAAATTGACTTTGAATGAAACTAAAAAGTTA
Found at i:48179 original size:15 final size:15
Alignment explanation
Indices: 48152--48193 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
48142 ACCCACCTTA
*
48152 TTTTTCTTATTCT-T
1 TTTTTCTTTTTCTCT
48166 TTTGTTCTTTTTCTCT
1 TTT-TTCTTTTTCTCT
48182 TTTTTCCTTTTT
1 TTTTT-CTTTTT
48194 TCAATTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 3 0.12
15 11 0.46
16 10 0.42
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTTTCTTTTTCTCT
Found at i:50542 original size:18 final size:18
Alignment explanation
Indices: 50519--50557 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
50509 ACCGGTCACA
*
50519 ACCCGACCTAACCCGTTG
1 ACCCGACCCAACCCGTTG
*
50537 ACCCGACCCGACCCGTTG
1 ACCCGACCCAACCCGTTG
50555 ACC
1 ACC
50558 GTTGACCCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.49, G:0.18, T:0.13
Consensus pattern (18 bp):
ACCCGACCCAACCCGTTG
Found at i:50566 original size:15 final size:15
Alignment explanation
Indices: 50546--50579 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
50536 GACCCGACCC
*
50546 GACCCGTTGACCGTT
1 GACCCGTTAACCGTT
50561 GACCCGTTAACCGTT
1 GACCCGTTAACCGTT
50576 GACC
1 GACC
50580 GGCGTTGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (15 bp):
GACCCGTTAACCGTT
Found at i:51893 original size:18 final size:18
Alignment explanation
Indices: 51867--51901 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
51857 GGACTGAAGG
* *
51867 AAATGATAAGATTGGATT
1 AAATAATAAGATCGGATT
51885 AAATAATAAGATCGGAT
1 AAATAATAAGATCGGAT
51902 GGAAGGAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.03, G:0.20, T:0.29
Consensus pattern (18 bp):
AAATAATAAGATCGGATT
Found at i:53117 original size:24 final size:24
Alignment explanation
Indices: 53090--53157 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
53080 TTCGATTTGA
* *
53090 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACCTGG
53114 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
*
53138 ATTTTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
53158 ATGAATTATG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:53174 original size:24 final size:24
Alignment explanation
Indices: 53094--53167 Score: 94
Period size: 24 Copynumber: 3.1 Consensus size: 24
53084 ATTTGAATTC
* * *
53094 TGATCTGATACTTGACTTGGATTC
1 TGATATGATACTTGACATGGATTA
* *
53118 TGATATGATACTTGACCTGGATTT
1 TGATATGATACTTGACATGGATTA
*
53142 TGATATGATACTTGACATGAATTA
1 TGATATGATACTTGACATGGATTA
53166 TG
1 TG
53168 TTTTGATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTA
Found at i:53337 original size:43 final size:43
Alignment explanation
Indices: 53276--53367 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
53266 GGGCTTTACT
* *
53276 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
1 TGGTGTATTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
53319 TGGTGTATTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTATTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
53362 TGGTGT
1 TGGTGT
53368 GTTCGGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.17, C:0.11, G:0.36, T:0.36
Consensus pattern (43 bp):
TGGTGTATTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
Found at i:63068 original size:13 final size:14
Alignment explanation
Indices: 63050--63083 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
63040 GATAAAGGAT
63050 AAATAAAGGG-AAA
1 AAATAAAGGGAAAA
63063 AAATAAAGGGAAAA
1 AAATAAAGGGAAAA
63077 AAATAAA
1 AAATAAA
63084 AAATAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.09
Consensus pattern (14 bp):
AAATAAAGGGAAAA
Done.