Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009157.1 Hibiscus syriacus cultivar Beakdansim tig00112683_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: 96534
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7628 original size:20 final size:20
Alignment explanation
Indices: 7584--7638 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 20
7574 AAGTAGATTT
7584 TATTATTGTTTTA-TAATGTA
1 TATTATT-TTTTATTAATGTA
*
7604 AATTATTTTTTATTATAT-TA
1 TATTATTTTTTATTA-ATGTA
*
7624 TATTAATTTTATATT
1 TATT-ATTTTTTATT
7639 TAATTATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 5 0.17
20 13 0.45
21 11 0.38
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (20 bp):
TATTATTTTTTATTAATGTA
Found at i:8003 original size:18 final size:18
Alignment explanation
Indices: 7982--8017 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
7972 GAAATTTGAA
*
7982 TTAAAAAACCGTTAAAAT
1 TTAAAAAACCATTAAAAT
*
8000 TTAAAAACCCATTAAAAT
1 TTAAAAAACCATTAAAAT
8018 AATTAGCTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.14, G:0.03, T:0.28
Consensus pattern (18 bp):
TTAAAAAACCATTAAAAT
Found at i:8645 original size:28 final size:29
Alignment explanation
Indices: 8588--8681 Score: 102
Period size: 29 Copynumber: 3.3 Consensus size: 29
8578 TATTTTATTG
* * *
8588 AGTCCATCAACTATTAAAAATTATAAAAT
1 AGTCCCTCAATTATTAAAAGTTATAAAAT
* * *
8617 AGTCTCTTAATTATTAAAAGTTA-CAAAT
1 AGTCCCTCAATTATTAAAAGTTATAAAAT
*
8645 AGTCCCTCGATTATTAAAAGTTATAAAAT
1 AGTCCCTCAATTATTAAAAGTTATAAAAT
8674 CA-TCCCTC
1 -AGTCCCTC
8682 GACTATAGGG
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
28 24 0.45
29 28 0.53
30 1 0.02
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (29 bp):
AGTCCCTCAATTATTAAAAGTTATAAAAT
Found at i:8683 original size:29 final size:29
Alignment explanation
Indices: 8599--8683 Score: 102
Period size: 28 Copynumber: 3.0 Consensus size: 29
8589 GTCCATCAAC
* * **
8599 TATTAAAAATTATAAAATAGTCTCTTAAT
1 TATTAAAAGTTATAAAATAGTCCCTCGAT
*
8628 TATTAAAAGTTA-CAAATAGTCCCTCGAT
1 TATTAAAAGTTATAAAATAGTCCCTCGAT
8656 TATTAAAAGTTATAAAATCA-TCCCTCGA
1 TATTAAAAGTTATAAAAT-AGTCCCTCGA
8684 CTATAGGGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
28 24 0.50
29 23 0.48
30 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (29 bp):
TATTAAAAGTTATAAAATAGTCCCTCGAT
Found at i:14126 original size:16 final size:18
Alignment explanation
Indices: 14105--14139 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
14095 TTTACTCATT
14105 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
14121 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
14139 T
1 T
14140 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:17334 original size:15 final size:15
Alignment explanation
Indices: 17309--17414 Score: 51
Period size: 14 Copynumber: 6.9 Consensus size: 15
17299 AGATCCAATC
17309 AAGAACAAAAAG-AA
1 AAGAACAAAAAGCAA
17323 AAGAAGCAAAAAGCAAAA
1 AAGAA-CAAAAAGC--AA
* * *
17341 AAAAAAAACAAAGAAA
1 AAGAACAA-AAAGCAA
*
17357 AAGAAACAAGAA-CAA
1 AAG-AACAAAAAGCAA
17372 AAGAA-AAAAGAGC-A
1 AAGAACAAAA-AGCAA
* *
17386 AA-ATCAAAAAGAAA
1 AAGAACAAAAAGCAA
*
17400 AAGGGACAAAAAGCA
1 AA-GAACAAAAAGCA
17415 CATGCAAAGA
Statistics
Matches: 67, Mismatches: 13, Indels: 22
0.66 0.13 0.22
Matches are distributed among these distances:
13 6 0.09
14 18 0.27
15 13 0.19
16 14 0.21
17 6 0.09
18 10 0.15
ACGTcount: A:0.75, C:0.09, G:0.15, T:0.01
Consensus pattern (15 bp):
AAGAACAAAAAGCAA
Found at i:17367 original size:7 final size:7
Alignment explanation
Indices: 17315--17401 Score: 57
Period size: 7 Copynumber: 11.6 Consensus size: 7
17305 AATCAAGAAC
17315 AAAAAGA
1 AAAAAGA
*
17322 AAAGAAGC
1 AAA-AAGA
17330 AAAAAGCA
1 AAAAAG-A
*
17338 AAAAAAA
1 AAAAAGA
*
17345 AAAACAAA
1 AAAA-AGA
17353 GAAAAAGA
1 -AAAAAGA
*
17361 AACAAGA
1 AAAAAGA
17368 ACAAAAGA
1 A-AAAAGA
17376 AAAAAGA
1 AAAAAGA
* **
17383 GCAAAATC
1 -AAAAAGA
17391 AAAAAGA
1 AAAAAGA
17398 AAAA
1 AAAA
17402 GGGACAAAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
7 32 0.52
8 26 0.42
9 4 0.06
ACGTcount: A:0.78, C:0.08, G:0.13, T:0.01
Consensus pattern (7 bp):
AAAAAGA
Found at i:17373 original size:28 final size:27
Alignment explanation
Indices: 17308--17388 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 27
17298 AAGATCCAAT
* *
17308 CAAGAACAAAAAGAAAAGAAGCAAAAAG
1 CAAGAACAAAAAAAAAAGAA-CAAAAAA
*
17336 CAA-AAAAAAAAAACAAAGAA-AAAGAAA
1 CAAGAACAAAAAAA-AAAGAACAAA-AAA
*
17363 CAAGAACAAAAGAAAAAAGAGCAAAA
1 CAAGAACAAAA-AAAAAAGAACAAAA
17389 TCAAAAAGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
26 3 0.07
27 13 0.30
28 21 0.49
29 6 0.14
ACGTcount: A:0.77, C:0.10, G:0.14, T:0.00
Consensus pattern (27 bp):
CAAGAACAAAAAAAAAAGAACAAAAAA
Found at i:17379 original size:34 final size:33
Alignment explanation
Indices: 17317--17380 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
17307 TCAAGAACAA
*
17317 AAAGAAAAGAAGCAAAAAGCAAAAAAAAAAAAC
1 AAAGAAAAGAAACAAAAAGCAAAAAAAAAAAAC
* *
17350 AAAGAAAAAGAAACAAGAA-CAAAAGAAAAAA
1 AAAG-AAAAGAAACAAAAAGCAAAAAAAAAAA
17381 GAGCAAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 15 0.56
34 12 0.44
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (33 bp):
AAAGAAAAGAAACAAAAAGCAAAAAAAAAAAAC
Found at i:18054 original size:22 final size:22
Alignment explanation
Indices: 18029--18077 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
18019 CCATCAATCT
* *
18029 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
18051 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
18073 TTTGA
1 TTTGA
18078 CCAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:19051 original size:36 final size:36
Alignment explanation
Indices: 19008--19289 Score: 303
Period size: 36 Copynumber: 8.0 Consensus size: 36
18998 AGTAGAAGAG
19008 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
19044 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
19080 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
19116 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
19152 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
** * ** * *
19181 TTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
19218 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
19253 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
19290 ACCTTTGAAT
Statistics
Matches: 203, Mismatches: 31, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 6 0.03
36 140 0.69
37 34 0.17
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:19281 original size:138 final size:137
Alignment explanation
Indices: 19028--19352 Score: 427
Period size: 138 Copynumber: 2.4 Consensus size: 137
19018 CTTGAGACAG
* *
19028 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
* *
19093 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
*
19158 GAATATG
131 GAATATA
* * ** * * * * *
19165 TTTTCTTTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* * *
19230 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACCT
65 TGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAACAT
*
19294 TTGAATTTA
129 TTGAATATA
* * * *
19303 TTTCCCCTAAAACAAATTTTATCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
19353 CAAAATCTTC
Statistics
Matches: 158, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
137 48 0.30
138 110 0.70
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
GAATATA
Found at i:19382 original size:67 final size:68
Alignment explanation
Indices: 19264--19420 Score: 203
Period size: 68 Copynumber: 2.4 Consensus size: 68
19254 TTTCGTCTAT
* **
19264 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAACA-AATTTTATC
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTATC
19326 TCC
66 TCC
* * * * *
19329 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTATC
19394 TCC
66 TCC
* *
19397 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
19421 ACAGATATCT
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 28 0.36
68 31 0.40
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTATC
TCC
Found at i:20248 original size:105 final size:105
Alignment explanation
Indices: 20064--21000 Score: 1454
Period size: 105 Copynumber: 9.0 Consensus size: 105
20054 GCACTCGAGG
* * * *
20064 CAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCTCAATTTCA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCA
20128 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
64 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
20170 CAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
20235 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
20275 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * *
20340 GCCAATTTCAACTTTACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
20380 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAGCAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
20445 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
20485 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
20550 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
20590 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAATAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
20655 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * *
20695 CAATGCAAGGTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
20760 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
20800 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * *
20860 TTCAATTTCAACTTCATAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
** * * * * * * ** *
20900 CAACATAAGTTCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
* *
20965 AGCCAATTTCAACTTCACGACGGAGGATATTGGACT
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
21001 TGGAACAATG
Statistics
Matches: 778, Mismatches: 46, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
100 80 0.10
101 3 0.00
102 3 0.00
103 4 0.01
104 3 0.00
105 610 0.78
106 73 0.09
107 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:21594 original size:34 final size:36
Alignment explanation
Indices: 21548--21649 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
21538 TTTCGTCATA
*
21548 CTAGGATTCAAACTCCTAAAAATATGATAGAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
21584 -T-GGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
21618 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
21650 GTTCTACTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 31 0.52
35 1 0.02
36 1 0.02
37 27 0.45
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:21673 original size:37 final size:37
Alignment explanation
Indices: 21546--21683 Score: 147
Period size: 37 Copynumber: 3.8 Consensus size: 37
21536 TTTTTCGTCA
* *
21546 TACTAGGATTCAAACTCCTAAAAATATGATAGAATT-
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* *
21582 T--TTGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* * *
21617 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
** * * *
21654 TACTATTATTTAAATTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
21684 CCACAAGCAC
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
34 30 0.35
35 1 0.01
36 1 0.01
37 54 0.63
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
Found at i:22204 original size:20 final size:20
Alignment explanation
Indices: 22179--22216 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22169 ATTATTATTA
22179 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
22199 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
22217 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:22248 original size:16 final size:18
Alignment explanation
Indices: 22227--22261 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
22217 TTTACTCATT
22227 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
22243 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
22261 T
1 T
22262 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:24207 original size:42 final size:42
Alignment explanation
Indices: 24147--24362 Score: 182
Period size: 42 Copynumber: 5.1 Consensus size: 42
24137 TAAAGTGAAA
** * *
24147 TTTTTGTAATAAACACCGCAATAGTCATGCACCTTAGCGACG
1 TTTTTGTAATAAATGCCGCAATAGTCATGCACTTTAGTGACG
* * * * *
24189 TTTTTGTAATAAATACCGCAATAATCATGTATTTTAGTGACA
1 TTTTTGTAATAAATGCCGCAATAGTCATGCACTTTAGTGACG
** * * * **
24231 TTTTTAAAATAAACGCCGCAACAGTCATGCACCTTAGTGATT
1 TTTTTGTAATAAATGCCGCAATAGTCATGCACTTTAGTGACG
* * *
24273 TTTTTGTAA-AACATGCTGCAATAGTCATACACTTTAGTGATG
1 TTTTTGTAATAA-ATGCCGCAATAGTCATGCACTTTAGTGACG
** * * * * *
24315 TTTTTACAATAAATGCCGTAACAATCATGCACTTTAGCGGCG
1 TTTTTGTAATAAATGCCGCAATAGTCATGCACTTTAGTGACG
24357 TTTTTG
1 TTTTTG
24363 ATAAACATCG
Statistics
Matches: 135, Mismatches: 37, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
41 2 0.01
42 131 0.97
43 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (42 bp):
TTTTTGTAATAAATGCCGCAATAGTCATGCACTTTAGTGACG
Found at i:24281 original size:84 final size:84
Alignment explanation
Indices: 24140--24390 Score: 249
Period size: 84 Copynumber: 3.0 Consensus size: 84
24130 ACTCTTATAA
** * *
24140 AGTGAAATTTTTGTAATAAACACCGCAATAGTCATGCACCTTAGCGACGTTTTTGTAATAA-ATA
1 AGTGAAATTTTTAAAATAAACGCCGCAACAGTCATGCACCTTAGCGACGTTTTTGTAA-AACATA
** *
24204 CCGCAATAATCATGTATTTT
65 CCGCAATAATCATACACTTT
* * ** *
24224 AGTGACATTTTTAAAATAAACGCCGCAACAGTCATGCACCTTAGTGATTTTTTTGTAAAACATGC
1 AGTGAAATTTTTAAAATAAACGCCGCAACAGTCATGCACCTTAGCGACGTTTTTGTAAAACATAC
* *
24289 TGCAATAGTCATACACTTT
66 CGCAATAATCATACACTTT
** * * * * * *
24308 AGTGATGTTTTTACAATAAATGCCGTAACAATCATGCACTTTAGCGGCGTTTTTG-ATAAACAT-
1 AGTGAAATTTTTAAAATAAACGCCGCAACAGTCATGCACCTTAGCGACGTTTTTGTA-AAACATA
*
24371 -CGTAATAATCATACACTTT
65 CCGCAATAATCATACACTTT
24390 A
1 A
24391 ATGGTCTTTT
Statistics
Matches: 137, Mismatches: 28, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
82 17 0.12
83 3 0.02
84 117 0.85
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (84 bp):
AGTGAAATTTTTAAAATAAACGCCGCAACAGTCATGCACCTTAGCGACGTTTTTGTAAAACATAC
CGCAATAATCATACACTTT
Found at i:24401 original size:40 final size:41
Alignment explanation
Indices: 24322--24450 Score: 115
Period size: 40 Copynumber: 3.1 Consensus size: 41
24312 ATGTTTTTAC
* * *
24322 AATAAA-TGCCGTAACAATCATGCACTTTAGCGGCGTTTTTG
1 AATAAACT-CCGTAATAATCATACACTTTAACGGCGTTTTTG
*
24363 -ATAAACAT-CGTAATAATCATACACTTTAATGGTC-TTTTTG
1 AATAAAC-TCCGTAATAATCATACACTTTAACGG-CGTTTTTG
* * *
24403 TAATAAACTCCGCAATAATTATACACTTTGACGG-GTTTTTG
1 -AATAAACTCCGTAATAATCATACACTTTAACGGCGTTTTTG
24444 CAATAAA
1 -AATAAA
24451 TGCTGCAACT
Statistics
Matches: 72, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
40 31 0.43
41 14 0.19
42 27 0.38
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (41 bp):
AATAAACTCCGTAATAATCATACACTTTAACGGCGTTTTTG
Found at i:26976 original size:21 final size:21
Alignment explanation
Indices: 26946--26991 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
26936 AGCGACACTT
* *
26946 AAAAAGACCGCTATGTAACTA
1 AAAAACACCGCTATATAACTA
*
26967 AAAAACACCGCTATATGACTA
1 AAAAACACCGCTATATAACTA
26988 AAAA
1 AAAA
26992 TGTCGCTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.20, G:0.11, T:0.17
Consensus pattern (21 bp):
AAAAACACCGCTATATAACTA
Found at i:30305 original size:22 final size:22
Alignment explanation
Indices: 30277--30324 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
30267 TGTTTTACTA
30277 CTTTCGAATA-GAAAAATAATAG
1 CTTTCGAATATG-AAAATAATAG
*
30299 CTTTCGAATATGAAAGTAATAG
1 CTTTCGAATATGAAAATAATAG
30321 CTTT
1 CTTT
30325 TGAAAACGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (22 bp):
CTTTCGAATATGAAAATAATAG
Found at i:31899 original size:18 final size:17
Alignment explanation
Indices: 31853--31900 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
31843 ATCCTAATTA
* *
31853 AAAAATAAAATAAAAAT
1 AAAATTAAAATAAAAAG
31870 AAAATTACAAATAATAAAG
1 AAAATTA-AAATAA-AAAG
*
31889 GAAATTAAAATA
1 AAAATTAAAATA
31901 TTCAAGGATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 6 0.23
18 11 0.42
19 9 0.35
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (17 bp):
AAAATTAAAATAAAAAG
Found at i:33635 original size:44 final size:44
Alignment explanation
Indices: 33450--33742 Score: 128
Period size: 44 Copynumber: 6.7 Consensus size: 44
33440 TGAAAATGTC
* * * *
33450 GATCCACCTCCTTCTGAGATGGAATCGAACG-AGATGTTGGTGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAATGAAG-TATTGATGCT
* * * *
33494 GATCTACCTCCTTTTGTGATAGAATC-AAGTAAAAG-ATTGATGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAA-T-GAAGTATTGATGCT
* * * * * * ** * *** **
33538 GATTCAACTCCTTATGCGATGGATTTGAACAAAATAAAAATATT
1 GATCCACCTCCTTCTGTGATGGAATCGAATGAAGTATTGATGCT
* * * *
33582 AATCCACCTCCTTCTGTGATGGAATCGAATGAGGTGTTGGTGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAATGAAGTATTGATGCT
* * * * *
33626 GATCTACCTCTTTTTGTGATAGAATCGAGCA-AAAG-ATTGATGCT
1 GATCCACCTCCTTCTGTGATGGAATCGA--ATGAAGTATTGATGCT
* * * * * *** **
33670 GATCCAACTCCTTATGTGATGGATTTGAATGAAATAAAAATATT
1 GATCCACCTCCTTCTGTGATGGAATCGAATGAAGTATTGATGCT
*
33714 GATCCATCTCCTTCTGTGATGGAATCGAA
1 GATCCACCTCCTTCTGTGATGGAATCGAA
33743 CGAGGTGTCG
Statistics
Matches: 172, Mismatches: 68, Indels: 18
0.67 0.26 0.07
Matches are distributed among these distances:
42 1 0.01
43 7 0.04
44 157 0.91
45 4 0.02
46 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (44 bp):
GATCCACCTCCTTCTGTGATGGAATCGAATGAAGTATTGATGCT
Found at i:33679 original size:132 final size:132
Alignment explanation
Indices: 33451--33796 Score: 525
Period size: 132 Copynumber: 2.6 Consensus size: 132
33441 GAAAATGTCG
* * *
33451 ATCCACCTCCTTCTGAGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTTTGTGATAG
1 ATCCACCTCCTTCTGTGATGGAATCGAACGAGGTGTTGGTGCTGATCTACCTCTTTTTGTGATAG
* *
33516 AATCAAGTAAAAGATTGATGCTGATTCAACTCCTTATGCGATGGATTTGAACAAAATAAAAATAT
66 AATCAAGCAAAAGATTGATGCTGATCCAACTCCTTATGCGATGGATTTGAACAAAATAAAAATAT
33581 TA
131 TA
*
33583 ATCCACCTCCTTCTGTGATGGAATCGAATGAGGTGTTGGTGCTGATCTACCTCTTTTTGTGATAG
1 ATCCACCTCCTTCTGTGATGGAATCGAACGAGGTGTTGGTGCTGATCTACCTCTTTTTGTGATAG
* * **
33648 AATCGAGCAAAAGATTGATGCTGATCCAACTCCTTATGTGATGGATTTGAATGAAATAAAAATAT
66 AATCAAGCAAAAGATTGATGCTGATCCAACTCCTTATGCGATGGATTTGAACAAAATAAAAATAT
*
33713 TG
131 TA
* * * *
33715 ATCCATCTCCTTCTGTGATGGAATCGAACGAGGTGTCGGTGTTGATCTACCT-TCTTCTGTGATA
1 ATCCACCTCCTTCTGTGATGGAATCGAACGAGGTGTTGGTGCTGATCTACCTCT-TTTTGTGATA
*
33779 GAATTAAGCAAAAG-TTGA
65 GAATCAAGCAAAAGATTGA
33797 ATAATCTCTT
Statistics
Matches: 195, Mismatches: 18, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
131 5 0.03
132 190 0.97
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (132 bp):
ATCCACCTCCTTCTGTGATGGAATCGAACGAGGTGTTGGTGCTGATCTACCTCTTTTTGTGATAG
AATCAAGCAAAAGATTGATGCTGATCCAACTCCTTATGCGATGGATTTGAACAAAATAAAAATAT
TA
Found at i:34033 original size:118 final size:111
Alignment explanation
Indices: 33806--34066 Score: 326
Period size: 118 Copynumber: 2.3 Consensus size: 111
33796 AATAATCTCT
* * * *
33806 TCATTATGAATTCTCTACTGGAAATGTTGATTCACCTCCTTTTGTGATGGATGAACATTGAACAA
1 TCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTATGTGATGGATGAACATTGAACAA
* * *
33871 GTTCTTCTCATTATGAACTTCTTATCTCTAATCGAATGAGTTCTTC
66 GTTCTTCTCATTATGAACTTATTATCCCTAATCGAATGAATTCTTC
*
33917 TCATTATGAACCCTCCACTGGAAAATGTTGATCCACCTCCTTATGTGATGGAATCGAACCAAGGT
1 TCATTATGAACTCTCCACTGG-AAATGTTGATCCACCTCCTTATGTGATGG-AT-GAA-C-A--T
* * * *
33982 TGAACAAGTTCTTTTCGTTATGAACTTATTCTCCCTCATC-AGATGAATTCTTC
59 TGAACAAGTTCTTCTCATTATGAACTTATTATCCCTAATCGA-ATGAATTCTTC
*
34035 TCATTATGAACTCTCCATTGGAAATGTTGATC
1 TCATTATGAACTCTCCACTGGAAATGTTGATC
34067 GGTTTATCTT
Statistics
Matches: 128, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
111 18 0.14
112 27 0.21
113 2 0.02
114 3 0.02
115 1 0.01
116 1 0.01
117 12 0.09
118 64 0.50
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (111 bp):
TCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTATGTGATGGATGAACATTGAACAA
GTTCTTCTCATTATGAACTTATTATCCCTAATCGAATGAATTCTTC
Found at i:34559 original size:39 final size:39
Alignment explanation
Indices: 34499--34811 Score: 391
Period size: 39 Copynumber: 8.0 Consensus size: 39
34489 TCAAAGATTT
* *
34499 TGTTTCAAGGGAAAC-AGTCTCAAGAGAGACAAAA-CTTTC
1 TGTTTCGAGGGAAACTA-TCTCAAGAGAGATAAAATC-TTC
* *
34538 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATTTTC
1 TGTTTCGAGGGAAACTATCTCAAGAGAGATAAAATCTTC
*
34577 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAGAGAGATAAAATCTTC
* * * *
34616 TTTTTCGAGGAAAACTATCTCAA-ACGAGACAAAATCTTA
1 TGTTTCGAGGGAAACTATCTCAAGA-GAGATAAAATCTTC
* * *
34655 TGTTTCGATGGAAACTATATCAAGCA-AGATAAAATCTTA
1 TGTTTCGAGGGAAACTATCTCAAG-AGAGATAAAATCTTC
* * *
34694 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATATTT
1 TGTTTCGAGGGAAACTATCTCAAGAGAGATAAAATCTTC
* * *
34733 TATTTCGAGGGAAACTATCTGAAGCGAGATAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAGAGAGATAAAATCTTC
*
34772 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAGAGAGATAAAATCTTC
34811 T
1 T
34812 TTAAAAACAA
Statistics
Matches: 242, Mismatches: 26, Indels: 12
0.86 0.09 0.04
Matches are distributed among these distances:
38 1 0.00
39 239 0.99
40 1 0.00
41 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (39 bp):
TGTTTCGAGGGAAACTATCTCAAGAGAGATAAAATCTTC
Found at i:34905 original size:76 final size:75
Alignment explanation
Indices: 34814--35051 Score: 320
Period size: 76 Copynumber: 3.1 Consensus size: 75
34804 AATCTTCTTT
* *
34814 AAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAAACCGACTCAAGCGAGACAAAT
1 AAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAAA-CGTCTCAAGTGAGACAAAT
34879 CTTGTTTTAAG
65 CTTGTTTTAAG
* * *
34890 AAAAACAATCTTGAGTGAAAT-AAATCTTCTTGTTTCGAGTAAAAACTGTCTCAAGTGAGAAAAA
1 AAAAACAATCTTGAGTGAAATGAAAT-GTCTTCTTTCGAGTAAAAAC-GTCTCAAGTGAGACAAA
34954 TCTTGTTTTAAG
64 TCTTGTTTTAAG
* * *
34966 AAAAACAAACTTGAGTCAAATGAAATGTTTTCTTTCGAGTAAAATA-GTCTCAAGTGAGACAAAG
1 AAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAA-ACGTCTCAAGTGAGACAAA-
*
35030 TC-TATTTTAAG
64 TCTTGTTTTAAG
*
35041 AAAAATAATCT
1 AAAAACAATCT
35052 CTAGTGAGAT
Statistics
Matches: 143, Mismatches: 14, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
75 38 0.27
76 100 0.70
77 5 0.03
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (75 bp):
AAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAAACGTCTCAAGTGAGACAAATC
TTGTTTTAAG
Found at i:35064 original size:151 final size:146
Alignment explanation
Indices: 34758--35066 Score: 374
Period size: 151 Copynumber: 2.1 Consensus size: 146
34748 TATCTGAAGC
** *
34758 GAGATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTTTAAAAACAAT
1 GAGAT-AAATCTTCTGTTTCGAGAAAAACTATCTCAAGCGAGATAAAATCTTCTTTAAAAACAAA
* *
34823 CTTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAAACCGACTCAAGCGAGACAAATCTTGTTTTA
65 CTTGAGTCAAATGAAATGTCTTCTTTCGAGTAAAAA-CGACTCAAGCGAGACAAATCTTATTTTA
34888 AGAAAAACAATCTTGAGT
129 AGAAAAACAATCTTGAGT
* * * *
34906 GAAATAAATCTTCTTGTTTCGAGTAAAAACTGTCTCAAGTGAGA-AAAATCTTGTTTTAAGAAAA
1 GAGATAAATCTTC-TGTTTCGAG-AAAAACTATCTCAAGCGAGATAAAATCTT-CTTT---AAAA
* * *
34970 ACAAACTTGAGTCAAATGAAATGTTTTCTTTCGAGTAAAATA-GTCTCAAGTGAGACAAAGTC-T
60 ACAAACTTGAGTCAAATGAAATGTCTTCTTTCGAGTAAAA-ACGACTCAAGCGAGACAAA-TCTT
*
35033 ATTTTAAGAAAAATAATCTCT-AGT
123 ATTTTAAGAAAAACAATCT-TGAGT
35057 GAGATAAATC
1 GAGATAAATC
35067 CTATGTATTA
Statistics
Matches: 138, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
147 8 0.06
148 21 0.15
149 19 0.14
151 45 0.33
152 44 0.32
153 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (146 bp):
GAGATAAATCTTCTGTTTCGAGAAAAACTATCTCAAGCGAGATAAAATCTTCTTTAAAAACAAAC
TTGAGTCAAATGAAATGTCTTCTTTCGAGTAAAAACGACTCAAGCGAGACAAATCTTATTTTAAG
AAAAACAATCTTGAGT
Found at i:48866 original size:14 final size:12
Alignment explanation
Indices: 48842--48879 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
48832 ATTAACTTGC
48842 TGATTTT-TTTT
1 TGATTTTCTTTT
48853 TGCATTTCTCTTTT
1 TG-ATTT-TCTTTT
48867 TGATTTTCTTTT
1 TGATTTTCTTTT
48879 T
1 T
48880 ATTGAATGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.08
12 11 0.46
13 5 0.21
14 6 0.25
ACGTcount: A:0.08, C:0.11, G:0.08, T:0.74
Consensus pattern (12 bp):
TGATTTTCTTTT
Found at i:63090 original size:14 final size:14
Alignment explanation
Indices: 63071--63103 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
63061 GTGCTTTCAA
63071 CTTTTCTTTCTT-TT
1 CTTTTCTTT-TTCTT
63085 CTTTTCTTTTTCTT
1 CTTTTCTTTTTCTT
63099 CTTTT
1 CTTTT
63104 TTGGAGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTCTTTTTCTT
Found at i:67875 original size:24 final size:24
Alignment explanation
Indices: 67843--67958 Score: 144
Period size: 24 Copynumber: 4.8 Consensus size: 24
67833 TTCGATTTGA
67843 ATTCTGATATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
67867 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
* * * * *
67891 ATTTTGATCTGATACTTAACTTAG
1 ATTCTGATATGATACTTGACATGG
* *
67915 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
*
67939 ATTTTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
67959 TTGATTTATT
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.01
24 77 0.97
25 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:73040 original size:24 final size:24
Alignment explanation
Indices: 72922--73037 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
72912 TTTTATTTAA
72922 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
72946 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
* *
72970 ATTCTGATCTGATACTTGACTTTG
1 ATTCTGATCTGATACTTGACATGG
* *
72994 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
73018 ATTTTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
73038 CTGATTTTTG
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 82 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:75561 original size:6 final size:6
Alignment explanation
Indices: 75550--75574 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
75540 TAAGGTTCAT
75550 GTTTGA GTTTGA GTTTGA GTTTGA G
1 GTTTGA GTTTGA GTTTGA GTTTGA G
75575 GCTTCAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (6 bp):
GTTTGA
Found at i:78466 original size:12 final size:12
Alignment explanation
Indices: 78429--78467 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
78419 ATATGATATT
78429 TGACATGGATTC
1 TGACATGGATTC
*
78441 TGATAT-GATATC
1 TGACATGGAT-TC
78453 TGACATGGATTC
1 TGACATGGATTC
78465 TGA
1 TGA
78468 TTTGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:78531 original size:24 final size:24
Alignment explanation
Indices: 78417--78528 Score: 163
Period size: 24 Copynumber: 4.7 Consensus size: 24
78407 ATTTGAATTT
*
78417 TGATATGATATTTGACATGGATTC
1 TGATATGATACTTGACATGGATTC
78441 TGATATGATA-TCTGACATGGATTC
1 TGATATGATACT-TGACATGGATTC
* *
78465 TGATTTGATACTTGACTTGGATTC
1 TGATATGATACTTGACATGGATTC
* *
78489 TGATATGATACTTGACCTGGATTT
1 TGATATGATACTTGACATGGATTC
78513 TGATATGATACTTGAC
1 TGATATGATACTTGAC
78529 CTGATTTATA
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.41
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTC
Found at i:79917 original size:45 final size:45
Alignment explanation
Indices: 79848--79972 Score: 171
Period size: 45 Copynumber: 2.8 Consensus size: 45
79838 ATTCAAGATT
79848 TTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTA-T-ACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * **
79895 TTACCATTTATCCCATAAGCTCGTAAGCTTATCTTACCATTATAC
1 TTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* *
79940 TTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 TTACCATTTATACCATAAGCTCGTAAGCTTATTT
79973 GTGTGGTTAT
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
44 25 0.35
45 35 0.49
46 1 0.01
47 10 0.14
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.38
Consensus pattern (45 bp):
TTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:84318 original size:93 final size:93
Alignment explanation
Indices: 84199--84389 Score: 292
Period size: 93 Copynumber: 2.1 Consensus size: 93
84189 AAGATGATGA
* * * * * *
84199 ATAAGAATGATTAAAATTGAACGAATCGATACCGTAAGAGATCAAAATCATTCTTTTTGTAAATC
1 ATAAGAATAACTAAAATCGAACGAATCGATACAGTAAAAGATCAAAATCATTCTTTTTGTAAATA
*
84264 GATAACCAAAATCAGTCATATAAAAAAT
66 GATAACCAAAATCAGTCATACAAAAAAT
84292 ATAAGAATAACTAAAATCGAACGAATCGATACAGTAAAAGATCAAAATCATTCTTTTTGTAAATA
1 ATAAGAATAACTAAAATCGAACGAATCGATACAGTAAAAGATCAAAATCATTCTTTTTGTAAATA
* * *
84357 GGTAATCAAAATCAGTCATACCAAAAAT
66 GATAACCAAAATCAGTCATACAAAAAAT
84385 ATAAG
1 ATAAG
84390 GGGTTATCCG
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.27
Consensus pattern (93 bp):
ATAAGAATAACTAAAATCGAACGAATCGATACAGTAAAAGATCAAAATCATTCTTTTTGTAAATA
GATAACCAAAATCAGTCATACAAAAAAT
Found at i:84475 original size:3 final size:3
Alignment explanation
Indices: 84467--84491 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
84457 ATAATACAAT
84467 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
84492 AACCCTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:88530 original size:15 final size:15
Alignment explanation
Indices: 88510--88551 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
88500 TTTCAGAACT
88510 AATAATCAATAAAAC
1 AATAATCAATAAAAC
88525 AATAATCAATAAAAC
1 AATAATCAATAAAAC
88540 AATAATCAATAA
1 AATAATCAATAA
88552 TCAGAGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (15 bp):
AATAATCAATAAAAC
Found at i:88534 original size:7 final size:7
Alignment explanation
Indices: 88510--88554 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
88500 TTTCAGAACT
88510 AATAATC
1 AATAATC
*
88517 AATAAAAC
1 AAT-AATC
88525 AATAATC
1 AATAATC
*
88532 AATAAAAC
1 AAT-AATC
88540 AATAATC
1 AATAATC
88547 AATAATC
1 AATAATC
88554 A
1 A
88555 GAGTTTATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 20 0.62
8 12 0.38
ACGTcount: A:0.64, C:0.13, G:0.00, T:0.22
Consensus pattern (7 bp):
AATAATC
Found at i:92041 original size:21 final size:22
Alignment explanation
Indices: 92012--92056 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
92002 TTAGACACCC
*
92012 AAATCAATTGTCATTTTAATAA
1 AAATCAATTGTAATTTTAATAA
* *
92034 AAAT-AATTTTAATTTTATTAA
1 AAATCAATTGTAATTTTAATAA
92055 AA
1 AA
92057 CGTCTTAGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (22 bp):
AAATCAATTGTAATTTTAATAA
Found at i:95910 original size:13 final size:12
Alignment explanation
Indices: 95892--95921 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
95882 AACTCTTCTT
95892 TTATTATTTATTA
1 TTATTATTTA-TA
95905 TTATTATTTATA
1 TTATTATTTATA
95917 TTATT
1 TTATT
95922 TTATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTATTATTTATA
Found at i:95941 original size:11 final size:11
Alignment explanation
Indices: 95925--95983 Score: 70
Period size: 11 Copynumber: 5.5 Consensus size: 11
95915 TATTATTTTA
95925 TTTTTTTTCAT
1 TTTTTTTTCAT
95936 TTTTTTTTCA-
1 TTTTTTTTCAT
95946 --TTTTTTCAT
1 TTTTTTTTCAT
95955 TTTCATTTTTCAT
1 TTT--TTTTTCAT
*
95968 TTTTCTTTCAT
1 TTTTTTTTCAT
95979 TTTTT
1 TTTTT
95984 CATTTTTCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
8 8 0.20
11 22 0.54
13 11 0.27
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTTTCAT
Found at i:95969 original size:32 final size:33
Alignment explanation
Indices: 95928--95998 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 33
95918 TATTTTATTT
*
95928 TTTTTCATTTTTTTTTCATTTTTTCA-TTTTCA
1 TTTTTCATTTTTCTTTCATTTTTTCATTTTTCA
*
95960 TTTTTCATTTTTCTTTCATTTTTTCATTTTTCT
1 TTTTTCATTTTTCTTTCATTTTTTCATTTTTCA
95993 TTTTTC
1 TTTTTC
95999 TCTATCTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 25 0.69
33 11 0.31
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (33 bp):
TTTTTCATTTTTCTTTCATTTTTTCATTTTTCA
Found at i:95972 original size:7 final size:7
Alignment explanation
Indices: 95928--95998 Score: 66
Period size: 7 Copynumber: 10.9 Consensus size: 7
95918 TATTTTATTT
95928 TTTTTCA
1 TTTTTCA
95935 -TTTT--
1 TTTTTCA
95939 TTTTTCA
1 TTTTTCA
95946 TTTTTTCA
1 -TTTTTCA
95954 -TTTTCA
1 TTTTTCA
95960 TTTTTCA
1 TTTTTCA
95967 TTTTTC-
1 TTTTTCA
95973 --TTTCA
1 TTTTTCA
95978 TTTTTTCA
1 -TTTTTCA
*
95986 TTTTTCT
1 TTTTTCA
95993 TTTTTC
1 TTTTTC
95999 TCTATCTTCA
Statistics
Matches: 54, Mismatches: 1, Indels: 18
0.74 0.01 0.25
Matches are distributed among these distances:
4 4 0.07
5 4 0.07
6 10 0.19
7 24 0.44
8 12 0.22
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCA
Found at i:95991 original size:19 final size:19
Alignment explanation
Indices: 95927--95994 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
95917 TTATTTTATT
*
95927 TTTTTTCATTTTTTTTTCA
1 TTTTTTCATTTTTCTTTCA
95946 TTTTTTCA----T-TTTCA
1 TTTTTTCATTTTTCTTTCA
95960 -TTTTTCATTTTTCTTTCA
1 TTTTTTCATTTTTCTTTCA
95978 TTTTTTCATTTTTCTTT
1 TTTTTTCATTTTTCTTT
95995 TTTCTCTATC
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 7 0.16
14 5 0.12
15 1 0.02
17 1 0.02
18 5 0.12
19 24 0.56
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTTCATTTTTCTTTCA
Done.