Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007547.1 Hibiscus syriacus cultivar Beakdansim tig00021149_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: 72016
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4495 original size:95 final size:96
Alignment explanation
Indices: 4300--4495 Score: 216
Period size: 95 Copynumber: 2.1 Consensus size: 96
4290 CCGTTGAGGC
* * * * * *
4300 AGTATCGATACCATTATAAGGGTATCGATCCCATGTAAACATCAAATCTAATTTTGGCATTGATA
1 AGTATCGATACCATGATAAGGGTATCGATACCATGGAAACATCAAAGCTAATTTCGGCATCGATA
** * *
4365 CCTTAAGGGGGTATAGATATCATAGTATAGT
66 CCGGAAGGGGGTATAGATAACATAGTATAGA
* ** *
4396 AGTATCGATACCATGATAAGGGTATCGATACCA-GGAAATATTGAAGCTAATTTCGGTATCGATA
1 AGTATCGATACCATGATAAGGGTATCGATACCATGGAAACATCAAAGCTAATTTCGGCATCGATA
* * *
4460 TCGGAAGGGGGTGTCTG-TAACATAGTATAGA
66 CCGGAAGGGGGTAT-AGATAACATAGTATAGA
4491 AGTAT
1 AGTAT
4496 TAGTACTAGG
Statistics
Matches: 82, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
95 50 0.61
96 32 0.39
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.30
Consensus pattern (96 bp):
AGTATCGATACCATGATAAGGGTATCGATACCATGGAAACATCAAAGCTAATTTCGGCATCGATA
CCGGAAGGGGGTATAGATAACATAGTATAGA
Found at i:4979 original size:47 final size:47
Alignment explanation
Indices: 4910--5270 Score: 514
Period size: 47 Copynumber: 7.7 Consensus size: 47
4900 AAATCAAATT
* * *
4910 CATAAATGAAAACGCATGAAAGGACGCATTAAGGCATGAAATGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGC
*
4957 CATAATTGAAAATGCATGAAAGGATGCATTAATGG-ATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAA-GGCATGAAATGATGC
*
5004 CATAATTGAAAATGCATTAAAGGATGCATTAAGGCATGAAATGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGC
*
5051 CATAATGGATAAA-GCATGAAAGGATGCATTAAGGCATGAAATGATG-
1 CATAATTGA-AAATGCATGAAAGGATGCATTAAGGCATGAAATGATGC
*
5097 CATTATTGAAAATGCATG-AAGGATGCATTAAGGCATGAAATGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGC
* * * *
5143 CACAATGGAAAATGCCTGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGC
* *
5190 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGT
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGC
* * *
5237 CATATATATTAAAATGCATGAATGGATGTATTAA
1 CATA-AT-TGAAAATGCATGAAAGGATGCATTAA
5271 TATGTGAAAA
Statistics
Matches: 283, Mismatches: 23, Indels: 14
0.88 0.07 0.04
Matches are distributed among these distances:
45 30 0.11
46 28 0.10
47 195 0.69
48 7 0.02
49 23 0.08
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.23
Consensus pattern (47 bp):
CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGC
Found at i:5009 original size:20 final size:20
Alignment explanation
Indices: 4967--5235 Score: 99
Period size: 20 Copynumber: 11.8 Consensus size: 20
4957 CATAATTGAA
4967 AATGCATGAAAGGATGCATT
1 AATGCATGAAAGGATGCATT
*
4987 AATGGATGAAAGGATGCCATAATT
1 AATGCATGAAAGGATG-C---ATT
*
5011 GAAAATGCATTAAAGGATGCATT
1 ---AATGCATGAAAGGATGCATT
* *
5034 AAGGCATGAAATGATGCCATAATGGAT
1 AATGCATGAAAGGATG-C---AT---T
*
5061 AAAGCATGAAAGGATGCATT
1 AATGCATGAAAGGATGCATT
* *
5081 AAGGCATGAAATGATGCATTATT
1 AATGCATGAAAGGATGC---ATT
5104 GAAAATGCATG-AAGGATGCATT
1 ---AATGCATGAAAGGATGCATT
* * *
5126 AAGGCATGAAATGATGCCACAATGGAA
1 AATGCATGAAAGGATG---C-AT---T
*
5153 AATGCCTGAAAGGATGCATT
1 AATGCATGAAAGGATGCATT
*
5173 AAGGCATGAAAGGATGCCATAATT
1 AATGCATGAAAGGATG-C---ATT
5197 GAAAATGCATGAAAGGATGCATT
1 ---AATGCATGAAAGGATGCATT
* *
5220 AAGGCATGAAAAGATG
1 AATGCATGAAAGGATG
5236 TCATATATAT
Statistics
Matches: 190, Mismatches: 24, Indels: 70
0.67 0.08 0.25
Matches are distributed among these distances:
19 7 0.04
20 78 0.41
21 3 0.02
22 3 0.02
23 14 0.07
24 11 0.06
25 7 0.04
26 10 0.05
27 57 0.30
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.22
Consensus pattern (20 bp):
AATGCATGAAAGGATGCATT
Found at i:5165 original size:139 final size:140
Alignment explanation
Indices: 4917--5271 Score: 509
Period size: 139 Copynumber: 2.5 Consensus size: 140
4907 ATTCATAAAT
* * *
4917 GAAAACGCATGAAAGGACGCATTAAGGCATGAAATGATGCCATAATTGAAAATGCATGAAAGGAT
1 GAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCCATTATTGAAAATGCATG-AAGGAT
* * * *
4982 GCATTAATGGATGAAAGGATGCCATAATTGAAAATGCATTAAAGGATGCATTAAGGCATGAAATG
65 GCATTAATGGATGAAAGGATGCCACAATGGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGG
5047 ATGCCATAATG
130 ATGCCATAATG
5058 GATAAA-GCATGAAAGGATGCATTAAGGCATGAAATGATG-CATTATTGAAAATGCATGAAGGAT
1 GA-AAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCCATTATTGAAAATGCATGAAGGAT
* *
5121 GCATTAA-GGCATGAAATGATGCCACAATGGAAAATGCCTGAAAGGATGCATTAAGGCATGAAAG
65 GCATTAATGG-ATGAAAGGATGCCACAATGGAAAATGCATGAAAGGATGCATTAAGGCATGAAAG
*
5185 GATGCCATAATT
129 GATGCCATAATG
* * *
5197 GAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGTCATATATATTAAAATGCATGAATGG
1 GAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCCAT-TAT-TGAAAATGCATGAA-GG
*
5262 ATGTATTAAT
63 ATGCATTAAT
5272 ATGTGAAAAT
Statistics
Matches: 194, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
138 5 0.03
139 106 0.55
140 20 0.10
141 37 0.19
142 16 0.08
143 10 0.05
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.23
Consensus pattern (140 bp):
GAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCCATTATTGAAAATGCATGAAGGATG
CATTAATGGATGAAAGGATGCCACAATGGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGA
TGCCATAATG
Found at i:9735 original size:2 final size:2
Alignment explanation
Indices: 9722--9756 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
9712 TTTCATAAAT
*
9722 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9757 TGTAGATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13502 original size:91 final size:91
Alignment explanation
Indices: 13347--13519 Score: 251
Period size: 91 Copynumber: 1.9 Consensus size: 91
13337 TTGCATTGGA
* *
13347 TTTTATCCTAAAATGTTTAACTGTTTACTCTAAAAAGTTAAACAATTGGTAATAATCTTGGTTAC
1 TTTTAACCTAAAATGTTTAACTGTATACTCTAAAAAGTTAAACAATTGGTAATAATCTTGGTTAC
*
13412 AACGGAGAATGTTACATTGCGGCCGG
66 AACCGAGAATGTTACATTGCGGCCGG
* ** *
13438 TTTTAACCTAAAATG-TTACCATGTATACTCTAAAAAGTTCCATAATTGGTAATAAT-TTCGGTT
1 TTTTAACCTAAAATGTTTAAC-TGTATACTCTAAAAAGTTAAACAATTGGTAATAATCTT-GGTT
13501 ACAACCGAGAATGTTACAT
64 ACAACCGAGAATGTTACAT
13520 GAGTTTCTTG
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
90 6 0.08
91 67 0.92
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (91 bp):
TTTTAACCTAAAATGTTTAACTGTATACTCTAAAAAGTTAAACAATTGGTAATAATCTTGGTTAC
AACCGAGAATGTTACATTGCGGCCGG
Found at i:17365 original size:95 final size:96
Alignment explanation
Indices: 17186--17375 Score: 240
Period size: 95 Copynumber: 2.0 Consensus size: 96
17176 AGGCAATATC
* * * * **
17186 GATACCACTATAAGGGTATCGATACCATGCAAACATCAAATCTAATTTTGGTATCGATACCTTAA
1 GATACCACTATAAGGGTATCGATACCAAGCAAACATCAAACCTAATTTCGGTATCGACACCGGAA
* * *
17251 GGGGGTATCAGTACCATAGTATAGTAGTATG
66 GGGGGCATCAGTACAATAGTATAGAAGTATG
* *
17282 GATACCA-TGATAAGGGTATCGATACCAAG-AAATATCGAACCTAATTTCGGTATCGACACCGGA
1 GATACCACT-ATAAGGGTATCGATACCAAGCAAACATCAAACCTAATTTCGGTATCGACACCGGA
* *
17345 AGGGGGCATCGGTACAATAGTTTAGAAGTAT
65 AGGGGGCATCAGTACAATAGTATAGAAGTAT
17376 TGGTACTAGG
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
95 54 0.68
96 26 0.32
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (96 bp):
GATACCACTATAAGGGTATCGATACCAAGCAAACATCAAACCTAATTTCGGTATCGACACCGGAA
GGGGGCATCAGTACAATAGTATAGAAGTATG
Found at i:17396 original size:95 final size:96
Alignment explanation
Indices: 17186--17401 Score: 222
Period size: 95 Copynumber: 2.3 Consensus size: 96
17176 AGGCAATATC
** * * * * * **
17186 GATACCACTATAAGGGTATCGATACCATGCAAACATCAAATCTAATTTTGGTATCGATACCTTAA
1 GATACCAGGATAAGAGTATCGATACCAAGCAAACATCAAACCTAATTTCGGTATCGACACCGGAA
* * *
17251 GGGGGTATCAGTACCATAGTATAGTAGTATG
66 GGGGGCATCAGTACAATAGTATAGAAGTATG
* * * *
17282 GATACCATGATAAGGGTATCGATACCAAG-AAATATCGAACCTAATTTCGGTATCGACACCGGAA
1 GATACCAGGATAAGAGTATCGATACCAAGCAAACATCAAACCTAATTTCGGTATCGACACCGGAA
* *
17346 GGGGGCATCGGTACAATAGTTTAGAAGTATTG
66 GGGGGCATCAGTACAATAGTATAGAAGTA-TG
*
17378 G-TACTAGGAT-AGTAGTATCGATAC
1 GATACCAGGATAAG-AGTATCGATAC
17402 TATAAAGCCT
Statistics
Matches: 100, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
94 2 0.02
95 69 0.69
96 29 0.29
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (96 bp):
GATACCAGGATAAGAGTATCGATACCAAGCAAACATCAAACCTAATTTCGGTATCGACACCGGAA
GGGGGCATCAGTACAATAGTATAGAAGTATG
Found at i:18381 original size:24 final size:23
Alignment explanation
Indices: 18325--18392 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
18315 CAAAACAGAG
* *
18325 TCCATGTCAAGTATCATATAAAA
1 TCCAGGTCAAATATCATATAAAA
* *
18348 TTCAGATCAAATATCATATCAAAA
1 TCCAGGTCAAATATCATAT-AAAA
*
18372 TCCAGGTCAAA-ATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
18393 CTATTTATAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 3 0.08
23 21 0.57
24 13 0.35
ACGTcount: A:0.47, C:0.18, G:0.09, T:0.26
Consensus pattern (23 bp):
TCCAGGTCAAATATCATATAAAA
Found at i:19114 original size:29 final size:28
Alignment explanation
Indices: 19072--19143 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
19062 GTTGACCATT
19072 TTACACAAATAGCACCCTTTTTA-AAATAA
1 TTAC-CAAATAGCACCC-TTTTAGAAATAA
*
19101 TTACCAATATAGCACCCTTTTAGAATTAA
1 TTACCAA-ATAGCACCCTTTTAGAAATAA
*
19130 TTCCCAAAATAGCA
1 TTACC-AAATAGCA
19144 TCAAAACGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 8 0.21
29 28 0.74
30 2 0.05
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31
Consensus pattern (28 bp):
TTACCAAATAGCACCCTTTTAGAAATAA
Found at i:19204 original size:18 final size:18
Alignment explanation
Indices: 19181--19240 Score: 104
Period size: 18 Copynumber: 3.4 Consensus size: 18
19171 CACCGGTCAA
19181 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
19199 CGGGTCGGGTCAAC-AGT
1 CGGGTCGGGTCAACGGGT
19216 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
19234 CGGGTCG
1 CGGGTCG
19241 TGACCGGTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.41
18 23 0.59
ACGTcount: A:0.12, C:0.23, G:0.48, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:19239 original size:13 final size:13
Alignment explanation
Indices: 19175--19204 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
19165 GAATAGCACC
19175 GGTCAACGGGTCG
1 GGTCAACGGGTCG
19188 GGTCAACGGGTCG
1 GGTCAACGGGTCG
19201 GGTC
1 GGTC
19205 GGGTCAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:19263 original size:10 final size:10
Alignment explanation
Indices: 19243--19297 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
19233 TCGGGTCGTG
19243 ACCGGTC-AA
1 ACCGGTCAAA
19252 ACCGGTCAAA
1 ACCGGTCAAA
19262 ACCGGTTCAAA
1 ACCGG-TCAAA
*
19273 ACCGGT-TAA
1 ACCGGTCAAA
19282 ACCGGTCAAA
1 ACCGGTCAAA
19292 ACCGGT
1 ACCGGT
19298 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:19298 original size:19 final size:19
Alignment explanation
Indices: 19243--19298 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
19233 TCGGGTCGTG
*
19243 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
19262 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
19282 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
19299 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:25571 original size:24 final size:24
Alignment explanation
Indices: 25539--25602 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
25529 AGAGTCCATG
* *
25539 TCAAGTATCATATAAAAATTCAGA
1 TCAAATATCATATAAAAATCCAGA
* * *
25563 TCAAATATCATATCAGAATCCAGG
1 TCAAATATCATATAAAAATCCAGA
* *
25587 TCAAAAATCAGATAAA
1 TCAAATATCATATAAA
25603 CTATTTATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (24 bp):
TCAAATATCATATAAAAATCCAGA
Found at i:26327 original size:29 final size:28
Alignment explanation
Indices: 26285--26356 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
26275 GTTGACCATT
26285 TTACACAAATAGCACCCTTTTTA-AAATAA
1 TTAC-CAAATAGCACCC-TTTTAGAAATAA
*
26314 TTACCAATATAGCACCCTTTTAGAATTAA
1 TTACCAA-ATAGCACCCTTTTAGAAATAA
*
26343 TTCCCAAAATAGCA
1 TTACC-AAATAGCA
26357 TCAAAACCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 8 0.21
29 28 0.74
30 2 0.05
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31
Consensus pattern (28 bp):
TTACCAAATAGCACCCTTTTAGAAATAA
Found at i:26409 original size:13 final size:13
Alignment explanation
Indices: 26387--26417 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
26377 AGAATAGCAC
26387 CGGG-CAACGGGT
1 CGGGTCAACGGGT
26399 CGGGTCAACGGGT
1 CGGGTCAACGGGT
26412 CGGGTC
1 CGGGTC
26418 GGGTCAACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.13, C:0.26, G:0.48, T:0.13
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:26417 original size:18 final size:18
Alignment explanation
Indices: 26394--26453 Score: 104
Period size: 18 Copynumber: 3.4 Consensus size: 18
26384 CACCGGGCAA
26394 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
26412 CGGGTCGGGTCAAC-AGT
1 CGGGTCGGGTCAACGGGT
26429 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
26447 CGGGTCG
1 CGGGTCG
26454 TGACCGGTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.41
18 23 0.59
ACGTcount: A:0.12, C:0.23, G:0.48, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:26476 original size:10 final size:10
Alignment explanation
Indices: 26456--26531 Score: 111
Period size: 10 Copynumber: 7.6 Consensus size: 10
26446 TCGGGTCGTG
26456 ACCGGTC-AA
1 ACCGGTCAAA
26465 ACCGGTCAAA
1 ACCGGTCAAA
26475 ACCGGTTCAAA
1 ACCGG-TCAAA
26486 ACCGGTCAAA
1 ACCGGTCAAA
26496 ACCGGTTCAAA
1 ACCGG-TCAAA
*
26507 ACCGGT-TAA
1 ACCGGTCAAA
26516 ACCGGTCAAA
1 ACCGGTCAAA
26526 ACCGGT
1 ACCGGT
26532 TTCCAGCGTT
Statistics
Matches: 61, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
9 15 0.25
10 26 0.43
11 20 0.33
ACGTcount: A:0.36, C:0.29, G:0.21, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:26489 original size:21 final size:20
Alignment explanation
Indices: 26456--26531 Score: 111
Period size: 21 Copynumber: 3.8 Consensus size: 20
26446 TCGGGTCGTG
26456 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGTCAAA
26475 ACCGGTTCAAAACCGGTCAAA
1 ACCGG-TCAAAACCGGTCAAA
*
26496 ACCGGTTCAAAACCGGT-TAA
1 ACCGG-TCAAAACCGGTCAAA
26516 ACCGGTCAAAACCGGT
1 ACCGGTCAAAACCGGT
26532 TTCCAGCGTT
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
19 16 0.30
20 9 0.17
21 29 0.54
ACGTcount: A:0.36, C:0.29, G:0.21, T:0.14
Consensus pattern (20 bp):
ACCGGTCAAAACCGGTCAAA
Found at i:27422 original size:47 final size:47
Alignment explanation
Indices: 27349--27765 Score: 505
Period size: 47 Copynumber: 8.7 Consensus size: 47
27339 AAATCAAATT
* * *
27349 CATAATGGAAAATGCATGGAAGGATGCATTAAGGGATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
27396 CATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
27443 CACAA-TGCAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGC
1 CATAATTG-AAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * **
27490 CACAATGGAAAATGCATGAAATCATGCATTAAGGCATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
27537 CATAATTGAAAATGCATGAAAGGATGCCATAATTGAAAATGCATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAGGATG-C---ATT---AAGGCATGAAAGGATGC
*
27591 CATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * * * *
27638 CACAATGGAAAATGCCTAAAAGGACGCATTAAGGCATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * * * *
27685 CATAATTGAAAACGCATTAAAGGATGAATTAAGGCATGAAATGATGT
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
27732 CATATATATTAAAATGCAT-AAATGGATGTATTAA
1 CATA-AT-TGAAAATGCATGAAA-GGATGCATTAA
27766 TATGTGAAAA
Statistics
Matches: 326, Mismatches: 32, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
46 2 0.01
47 250 0.77
48 7 0.02
49 19 0.06
50 3 0.01
51 3 0.01
53 1 0.00
54 41 0.13
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (47 bp):
CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:27434 original size:20 final size:20
Alignment explanation
Indices: 27409--27489 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 20
27399 AATTGAAAAT
*
27409 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
27429 GCATGAAAGGATGCCACAATGCAAAAT
1 GCATGAAAGGATG---C-AT---TAAG
*
27456 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
27476 GCATGAAAGGATGC
1 GCATGAAAGGATGC
27490 CACAATGGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
20 27 0.57
23 3 0.06
24 3 0.06
27 14 0.30
ACGTcount: A:0.41, C:0.14, G:0.26, T:0.20
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:27460 original size:27 final size:26
Alignment explanation
Indices: 27384--27661 Score: 154
Period size: 27 Copynumber: 11.3 Consensus size: 26
27374 GCATTAAGGG
*
27384 ATGAAAGGATGCCATAATTGAAAATGC
1 ATGAAAGGATGCCACAA-TGAAAATGC
* * *
27411 ATGAAATGATG---C-AT--TAAGGC
1 ATGAAAGGATGCCACAATGAAAATGC
27431 ATGAAAGGATGCCACAATGCAAAATGC
1 ATGAAAGGATGCCACAATG-AAAATGC
* * *
27458 ATGAAATGATG---C-AT--TAAGGC
1 ATGAAAGGATGCCACAATGAAAATGC
27478 ATGAAAGGATGCCACAATGGAAAATGC
1 ATGAAAGGATGCCACAAT-GAAAATGC
** * *
27505 ATGAAATCATG---C-AT--TAAGGC
1 ATGAAAGGATGCCACAATGAAAATGC
*
27525 ATGAAAGGATGCCATAATTGAAAATGC
1 ATGAAAGGATGCCACAA-TGAAAATGC
*
27552 ATGAAAGGATGCCATAATTGAAAATGC
1 ATGAAAGGATGCCACAA-TGAAAATGC
* *
27579 ATGAAAGGATGCCATAATTAAAAATGC
1 ATGAAAGGATGCCACAA-TGAAAATGC
* *
27606 ATGAAAGGATG---C-AT--TAAGGC
1 ATGAAAGGATGCCACAATGAAAATGC
27626 ATGAAAGGATGCCACAATGGAAAATGC
1 ATGAAAGGATGCCACAAT-GAAAATGC
* *
27653 CTAAAAGGA
1 ATGAAAGGA
27662 CGCATTAAGG
Statistics
Matches: 193, Mismatches: 30, Indels: 56
0.69 0.11 0.20
Matches are distributed among these distances:
20 56 0.29
22 2 0.01
23 9 0.05
24 9 0.05
25 1 0.01
27 116 0.60
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.20
Consensus pattern (26 bp):
ATGAAAGGATGCCACAATGAAAATGC
Found at i:27507 original size:74 final size:74
Alignment explanation
Indices: 27429--27661 Score: 249
Period size: 74 Copynumber: 3.1 Consensus size: 74
27419 ATGCATTAAG
*
27429 GCATGAAAGGATGCCACAATGCAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCACA
1 GCATGAAAGGATGCCATAATGCAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCACA
27494 ATGGAAAAT
66 ATGGAAAAT
** * * ** * * *
27503 GCATGAAATCATG-CATTAAGGCATGAAA-GGATGCCATAATTG-A-AAATGCATGAAAGGATGC
1 GCATGAAAGGATGCCA-TAATGCA--AAATGCATGAAATGA-TGCATTAAGGCATGAAAGGATGC
* *
27564 CATAATTGAAAAT
62 CACAATGGAAAAT
** *
27577 GCATGAAAGGATGCCATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCACA
1 GCATGAAAGGATGCCATAATGCAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCACA
27642 ATGGAAAAT
66 ATGGAAAAT
* *
27651 GCCTAAAAGGA
1 GCATGAAAGGA
27662 CGCATTAAGG
Statistics
Matches: 123, Mismatches: 28, Indels: 16
0.74 0.17 0.10
Matches are distributed among these distances:
72 5 0.04
73 9 0.07
74 94 0.76
75 10 0.08
76 5 0.04
ACGTcount: A:0.44, C:0.13, G:0.24, T:0.19
Consensus pattern (74 bp):
GCATGAAAGGATGCCATAATGCAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCACA
ATGGAAAAT
Found at i:27647 original size:148 final size:141
Alignment explanation
Indices: 27352--27730 Score: 542
Period size: 148 Copynumber: 2.6 Consensus size: 141
27342 TCAAATTCAT
* *
27352 AATGGAAAATGCATGGAAGGATGCATTAAGGGATGAAAGGATGCCATAATTGAAAATGCATGAAA
1 AATGGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAATGCATGAAA
* * *
27417 TGATGCATTAAGGCATGAAAGGATGCCACAATGCAAAATGCATGAAATGATGCATTAAGGCATGA
66 GGATGCATTAAGGCATGAAAGGATGCCACAATGAAAAATGCATGAAAGGATGCATTAAGGCATGA
27482 AAGGATGCCAC
131 AAGGATGCCAC
**
27493 AATGGAAAATGCATGAAATCATGCATTAAGGCATGAAAGGATGCCATAATTGAAAATGCATGAAA
1 AATGGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAATGCATGAAA
* * *
27558 GGATGCCATAATTGAAAATGCATGAAAGGATGCCATAATTAAAAATGCATGAAAGGATGCATTAA
66 GGATG-C---ATT---AAGGCATGAAAGGATGCCACAATGAAAAATGCATGAAAGGATGCATTAA
27623 GGCATGAAAGGATGCCAC
124 GGCATGAAAGGATGCCAC
* * * * *
27641 AATGGAAAATGCCTAAAAGGACGCATTAAGGCATGAAAGGATGCCATAATTGAAAACGCATTAAA
1 AATGGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAATGCATGAAA
* *
27706 GGATGAATTAAGGCATGAAATGATG
66 GGATGCATTAAGGCATGAAAGGATG
27731 TCATATATAT
Statistics
Matches: 211, Mismatches: 20, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
141 79 0.37
142 1 0.00
144 3 0.01
145 3 0.01
148 125 0.59
ACGTcount: A:0.43, C:0.12, G:0.25, T:0.20
Consensus pattern (141 bp):
AATGGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAATGCATGAAA
GGATGCATTAAGGCATGAAAGGATGCCACAATGAAAAATGCATGAAAGGATGCATTAAGGCATGA
AAGGATGCCAC
Found at i:27681 original size:195 final size:197
Alignment explanation
Indices: 27384--27759 Score: 569
Period size: 195 Copynumber: 1.9 Consensus size: 197
27374 GCATTAAGGG
* *
27384 ATGAAAGGATGCCATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCACAAT
1 ATGAAAGGATGCCATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCACAAT
* * * * *
27449 GCAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCACAATGGAAAATGCATGAAATCA
66 GCAAAATGCATAAAAGGACGCATTAAGGCATGAAAGGATGCCACAATGGAAAACGCATGAAAGCA
*
27514 TGCATTAAGGCATGAAAGGATGCCATA-AT-TGAAAATGCATGAAA-GGATGCCATAATTGAAAA
131 TGAATTAAGGCATGAAAGGATGCCATATATATGAAAATGCAT-AAATGGATGCCATAATTGAAAA
27576 TGC
195 TGC
27579 ATGAAAGGATGCCATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCACAAT
1 ATGAAAGGATGCCATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCACAAT
* * * * * *
27644 GGAAAATGCCTAAAAGGACGCATTAAGGCATGAAAGGATGCCATAATTGAAAACGCATTAAAGGA
66 GCAAAATGCATAAAAGGACGCATTAAGGCATGAAAGGATGCCACAATGGAAAACGCATGAAAGCA
* * *
27709 TGAATTAAGGCATGAAATGATGTCATATATATTAAAATGCATAAATGGATG
131 TGAATTAAGGCATGAAAGGATGCCATATATATGAAAATGCATAAATGGATG
27760 TATTAATATG
Statistics
Matches: 161, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
195 141 0.88
196 5 0.03
197 15 0.09
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.22
Consensus pattern (197 bp):
ATGAAAGGATGCCATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCACAAT
GCAAAATGCATAAAAGGACGCATTAAGGCATGAAAGGATGCCACAATGGAAAACGCATGAAAGCA
TGAATTAAGGCATGAAAGGATGCCATATATATGAAAATGCATAAATGGATGCCATAATTGAAAAT
GC
Found at i:35703 original size:25 final size:25
Alignment explanation
Indices: 35673--35723 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
35663 GTACATTCAT
35673 AGGGCACCTAT-GGTGCAATTGATTC
1 AGGGCA-CTATAGGTGCAATTGATTC
* *
35698 AGGGCACTATATGTGCAATTTATTC
1 AGGGCACTATAGGTGCAATTGATTC
35723 A
1 A
35724 TATGCAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (25 bp):
AGGGCACTATAGGTGCAATTGATTC
Found at i:43850 original size:71 final size:70
Alignment explanation
Indices: 43729--43866 Score: 231
Period size: 71 Copynumber: 2.0 Consensus size: 70
43719 ATATCCCATA
* * *
43729 GTCAAAGATGAACCAAATTGAAGTTGATTTTCTACTTTAACCACACAATTTTTAAAAATTGTAAT
1 GTCAAAGACGAACCAAATTGAAGTTAACTTTCTACTTTAACCACACAATTTTT-AAAATTGTAAT
43794 TTATTC
65 TTATTC
*
43800 GTCAAAGACGAACCAAATTGAAGTTAACTTTCTACTTTAACCACATAATTTTTAAAATTGTAATT
1 GTCAAAGACGAACCAAATTGAAGTTAACTTTCTACTTTAACCACACAATTTTTAAAATTGTAATT
43865 TA
66 TA
43867 GTCAATATAT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 14 0.22
71 49 0.78
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.37
Consensus pattern (70 bp):
GTCAAAGACGAACCAAATTGAAGTTAACTTTCTACTTTAACCACACAATTTTTAAAATTGTAATT
TATTC
Found at i:59239 original size:18 final size:19
Alignment explanation
Indices: 59211--59249 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
59201 CTCTTATATT
*
59211 TTTACTTTAATTGCTTTTA
1 TTTACTTTAATCGCTTTTA
*
59230 TTTA-TTTAATCGTTTTTA
1 TTTACTTTAATCGCTTTTA
59248 TT
1 TT
59250 ACTACTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTACTTTAATCGCTTTTA
Found at i:65844 original size:81 final size:81
Alignment explanation
Indices: 65709--65871 Score: 317
Period size: 81 Copynumber: 2.0 Consensus size: 81
65699 TAGATGTTTC
65709 TTTTCAACCATAATTTTCTTCAGGAGGTCACAATAATCCATCAACCAGCTCATCCAATAAGGTTT
1 TTTTCAACCATAATTTTCTTCAGGAGGTCACAATAATCCATCAACCAGCTCATCCAATAAGGTTT
65774 CATGTCCACTCCTTCT
66 CATGTCCACTCCTTCT
*
65790 TTTTCAACCATAATTTTCTTCAGGAGGTCACAATAATCCATCAACTAGCTCATCCAATAAGGTTT
1 TTTTCAACCATAATTTTCTTCAGGAGGTCACAATAATCCATCAACCAGCTCATCCAATAAGGTTT
65855 CATGTCCACTCCTTCT
66 CATGTCCACTCCTTCT
65871 T
1 T
65872 GTCTGACTGA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (81 bp):
TTTTCAACCATAATTTTCTTCAGGAGGTCACAATAATCCATCAACCAGCTCATCCAATAAGGTTT
CATGTCCACTCCTTCT
Found at i:67074 original size:6 final size:6
Alignment explanation
Indices: 67063--67099 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
67053 ACTAGACCCG
67063 TTGACT TTGACT TTGACT TTGAC- TTGACT TTGACT TT
1 TTGACT TTGACT TTGACT TTGACT TTGACT TTGACT TT
67100 AACCCGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (6 bp):
TTGACT
Found at i:67091 original size:11 final size:11
Alignment explanation
Indices: 67063--67098 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
67053 ACTAGACCCG
67063 TTGACTTTGAC
1 TTGACTTTGAC
67074 TTTGACTTTGAC
1 -TTGACTTTGAC
67086 TTGACTTTGAC
1 TTGACTTTGAC
67097 TT
1 TT
67099 TAACCCGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (11 bp):
TTGACTTTGAC
Found at i:67091 original size:17 final size:18
Alignment explanation
Indices: 67063--67099 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
67053 ACTAGACCCG
67063 TTGACTTTGACTTTGACT
1 TTGACTTTGACTTTGACT
67081 TTGAC-TTGACTTTGACT
1 TTGACTTTGACTTTGACT
67098 TT
1 TT
67100 AACCCGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (18 bp):
TTGACTTTGACTTTGACT
Done.