Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002185.1 Hibiscus syriacus cultivar Beakdansim tig00004452_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: 60586
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:1486 original size:19 final size:18
Alignment explanation
Indices: 1462--1506 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
1452 GTAGGGTTAA
1462 TTTTGTATA-GATTTATAAT
1 TTTTGTATACGA-TTAT-AT
1481 TTTTGTATACGATTATAT
1 TTTTGTATACGATTATAT
*
1499 TTTCGTAT
1 TTTTGTAT
1507 GTGAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 9 0.38
19 13 0.54
20 2 0.08
ACGTcount: A:0.27, C:0.04, G:0.11, T:0.58
Consensus pattern (18 bp):
TTTTGTATACGATTATAT
Found at i:2204 original size:195 final size:197
Alignment explanation
Indices: 1628--2697 Score: 1900
Period size: 195 Copynumber: 5.5 Consensus size: 197
1618 GGCCAAAAGG
1628 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1693 TGTCGACACTAATATAGTTTGTGTCGATATTT-TTTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
1757 TAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
1821 AT
196 AT
1823 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTTATGTGAGAATATGTCTAAATAAT
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTTATGTGAGAATATGTCTAAATAAT
1888 GTGTCGACACTAATATAGTTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCAC
65 GTGTCGACACTAATATAG-TTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA-
1953 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
128 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
2018 GTAAT
193 GTAAT
2023 ATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
2087 TGTCGACACTAATATAG-TTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
*
2151 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAATTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
2216 AT
196 AT
2218 ATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
* * *
2282 TGTCGACACTAAT-TAGTTTGTGTCGATACTAATTT--AAATATGAATGG-AAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGA-ATGAATGGAAAACAGGGTGCACC
*
2343 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAACATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
2408 AAT
195 AAT
2411 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
* * *
2476 TGTCGACACTAATATAGTTTGTGTCGATACTAATTT--AAATATGAATGGAAAACA-GGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGA-ATGAATGGAAAACAGGGTGCACC
*
2538 ATAAAGTGTCGATCCGTATAT-AAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTAT-ATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
2600 AAT
195 AAT
2603 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
2668 TGTCGACACTAATATAGTTTTGTGTCGATA
66 TGTCGACACTAATATAG-TTTGTGTCGATA
2698 CTAATTTAAA
Statistics
Matches: 856, Mismatches: 8, Indels: 24
0.96 0.01 0.03
Matches are distributed among these distances:
192 89 0.10
193 107 0.12
194 111 0.13
195 261 0.30
196 94 0.11
197 15 0.02
198 74 0.09
199 52 0.06
200 53 0.06
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (197 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
AT
Found at i:2550 original size:388 final size:393
Alignment explanation
Indices: 1628--2710 Score: 1915
Period size: 394 Copynumber: 2.8 Consensus size: 393
1618 GGCCAAAAGG
1628 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
1693 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCAGAATGAATGGAAAACAGGGTGCACCAT
66 TGTCGACACTAATATAGTTTGTGTCGATATTATTT-CAGAATGAATGGAAAACAGGGTGCACCAT
1758 AAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
130 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
1822 TATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTTATGTGAGAATATGTCTAAATAA
195 TATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTTATGTGAGAATATGTCTAAATAA
* * *
1887 TGTGTCGACACTAATATAGTTTTGTGTCGATATTTATTTCCAGA-ATGAATGGAAAACAGGGTGC
259 TGTGTCGACACTAATATAGTTTTGTGTCGATACTAATTT--AAATATGAATGGAAAACAGGGTGC
1951 ACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
322 ACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
2016 ATGTAAT
387 ATGTAAT
2023 ATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
2087 TGTCGACACTAATATAG-TTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTATTT-CAGAATGAATGGAAAACAGGGTGCACCA
*
2151 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAATTATAATGTA
129 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
2216 ATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAA
194 ATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAA
2280 TGTGTCGACACTAAT-TAG-TTTGTGTCGATACTAATTTAAATATGAATGG-AAACAGGGTGCA-
259 TGTGTCGACACTAATATAGTTTTGTGTCGATACTAATTTAAATATGAATGGAAAACAGGGTGCAC
*
2341 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAACATCATCGAACCCAAAAGTATAAT
324 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
2406 GTAAT
389 GTAAT
2411 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
* *
2476 TGTCGACACTAATATAGTTTGTGTCGATACTAATTT-AAATATGAATGGAAAACA-GGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTATTTCAGA-ATGAATGGAAAACAGGGTGCACCA
*
2539 TAAAGTGTCGATCCGTATAT-AAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTAT-ATGTA
129 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
2601 ATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAA
194 ATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAA
2666 TGTGTCGACACTAATATAGTTTTGTGTCGATACTAATTTAAATAT
259 TGTGTCGACACTAATATAGTTTTGTGTCGATACTAATTTAAATAT
2711 CAAGTGTTTT
Statistics
Matches: 668, Mismatches: 11, Indels: 25
0.95 0.02 0.04
Matches are distributed among these distances:
385 13 0.02
386 77 0.12
387 33 0.05
388 130 0.19
389 103 0.15
390 24 0.04
391 17 0.03
392 3 0.00
393 52 0.08
394 158 0.24
395 58 0.09
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (393 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTGTGTCGATATTATTTCAGAATGAATGGAAAACAGGGTGCACCATA
AAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAAT
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTTGTGTCGATACTAATTTAAATATGAATGGAAAACAGGGTGCACCC
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AAT
Found at i:4178 original size:18 final size:18
Alignment explanation
Indices: 4157--4218 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
4147 AGCGGTCGCA
4157 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
4175 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
4193 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
4211 GAAGATGA
1 GAAGATGA
4219 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:4181 original size:6 final size:6
Alignment explanation
Indices: 4157--4242 Score: 64
Period size: 6 Copynumber: 14.3 Consensus size: 6
4147 AGCGGTCGCA
* * * * * *
4157 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * *
4205 GGCGAT GAAGAT GATGAC GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
4243 TGATCCAAAC
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:4192 original size:3 final size:3
Alignment explanation
Indices: 4172--4246 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
4162 TGAAGCTGAC
* * * * * ** *
4172 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
4220 GAC GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
4247 CCAAACAAGT
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:4211 original size:36 final size:36
Alignment explanation
Indices: 4160--4238 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
4150 GGTCGCAGAA
*
4160 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * *
4196 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
4232 GATGAAG
1 GATGAAG
4239 ATGATGATCC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.20
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:4246 original size:12 final size:12
Alignment explanation
Indices: 4160--4242 Score: 94
Period size: 12 Copynumber: 6.9 Consensus size: 12
4150 GGTCGCAGAA
*
4160 GATGAAGCTGAC
1 GATGAAGATGAC
4172 GATGAAGATGAC
1 GATGAAGATGAC
*
4184 GATGATGATGAC
1 GATGAAGATGAC
* *
4196 GATGAAGCTGGC
1 GATGAAGATGAC
*
4208 GATGAAGATGAT
1 GATGAAGATGAC
* * *
4220 GACGATGATGAT
1 GATGAAGATGAC
4232 GATGAAGATGA
1 GATGAAGATGA
4243 TGATCCAAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.20
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:5387 original size:19 final size:19
Alignment explanation
Indices: 5363--5399 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5353 TAATATATTG
*
5363 TAAAGTATCTATCCTTTTA
1 TAAAGTATCTATACTTTTA
*
5382 TAAAGTGTCTATACTTTT
1 TAAAGTATCTATACTTTT
5400 TCCACTGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.49
Consensus pattern (19 bp):
TAAAGTATCTATACTTTTA
Found at i:6398 original size:183 final size:183
Alignment explanation
Indices: 5703--6509 Score: 1476
Period size: 182 Copynumber: 4.4 Consensus size: 183
5693 CTTTCAACAT
** * * * * * *
5703 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
5768 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
5833 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
5886 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
5951 GGTCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
6015 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
6068 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTAT-AATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
*
6132 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTTCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
6197 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
6250 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
6315 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
6380 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* * *
6433 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAA-ATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
*
6497 TGTCTACAACCTA
66 GGTCTACAACCTA
6510 AAATGTGTCG
Statistics
Matches: 608, Mismatches: 14, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
181 47 0.08
182 299 0.49
183 262 0.43
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:9044 original size:28 final size:23
Alignment explanation
Indices: 8988--9041 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
8978 TAACTACAAG
*
8988 TATATAATGTAATAGGTATCGTT
1 TATATAATGTAATAGGTAGCGTT
*
9011 TATATAATGTAATAGGTAGCGCT
1 TATATAATGTAATAGGTAGCGTT
9034 TATATAAT
1 TATATAAT
9042 ATATTGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.41
Consensus pattern (23 bp):
TATATAATGTAATAGGTAGCGTT
Found at i:9490 original size:18 final size:18
Alignment explanation
Indices: 9469--9505 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9459 GTAATTGGAG
9469 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
9487 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
9505 T
1 T
9506 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:9513 original size:24 final size:24
Alignment explanation
Indices: 9461--9507 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
9451 TTTCATATGT
* *
9461 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
9485 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
9508 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:9804 original size:39 final size:39
Alignment explanation
Indices: 9761--9847 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
9751 TCCGATGCTC
*
9761 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
9800 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
9839 ATCAAAATC
1 ATCAAAATC
9848 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:10340 original size:3 final size:3
Alignment explanation
Indices: 10325--10367 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
10315 AGTTAAAAAA
* *
10325 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
10368 AGTGTGTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:11266 original size:43 final size:44
Alignment explanation
Indices: 11181--11272 Score: 170
Period size: 44 Copynumber: 2.1 Consensus size: 44
11171 AGGTGCAGCC
11181 GAAGG-GGTTATGAAGGAAGGTTGAAGGAAAAGAGAGAAAGAGT
1 GAAGGAGGTTATGAAGGAAGGTTGAAGGAAAAGAGAGAAAGAGT
11224 GAAGGAGGTTATGAAGGAAGGTTGAAGGAAAAGAGAG-AAGAGT
1 GAAGGAGGTTATGAAGGAAGGTTGAAGGAAAAGAGAGAAAGAGT
11267 GAAGGA
1 GAAGGA
11273 AGAGAAGTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 17 0.35
44 31 0.65
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.13
Consensus pattern (44 bp):
GAAGGAGGTTATGAAGGAAGGTTGAAGGAAAAGAGAGAAAGAGT
Found at i:24439 original size:24 final size:24
Alignment explanation
Indices: 24412--24513 Score: 76
Period size: 24 Copynumber: 4.5 Consensus size: 24
24402 CTTGAAGAAA
*
24412 AAAAAGGGAACAAAT-AAAAAGATG
1 AAAAA-GGAAAAAATGAAAAAGATG
* **
24436 AAAAATGAAAAAATGAAAAAGAAA
1 AAAAAGGAAAAAATGAAAAAGATG
*
24460 AAAAATG-AAAAATG-AAAA-ATG
1 AAAAAGGAAAAAATGAAAAAGATG
*
24481 AAAAA--AAGAAATGAAAAA-AT-
1 AAAAAGGAAAAAATGAAAAAGATG
24501 AAAAAGAGAAAAA
1 AAAAAG-GAAAAA
24514 TGAGGGTTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
20 11 0.17
21 12 0.19
22 4 0.06
23 18 0.28
24 19 0.30
ACGTcount: A:0.75, C:0.01, G:0.15, T:0.09
Consensus pattern (24 bp):
AAAAAGGAAAAAATGAAAAAGATG
Found at i:24441 original size:15 final size:14
Alignment explanation
Indices: 24423--24514 Score: 89
Period size: 14 Copynumber: 6.3 Consensus size: 14
24413 AAAAGGGAAC
24423 AAATAAAAAGATGAA
1 AAATAAAAA-ATGAA
24438 AAATGAAAAAATGAAA
1 AAAT-AAAAAATG-AA
*
24454 AAGAAAAAAAATGAA
1 AA-ATAAAAAATGAA
*
24469 AAATGAAAAATGAA
1 AAATAAAAAATGAA
*
24483 AAA-AAGAAATGAAA
1 AAATAAAAAATG-AA
24497 AAATAAAAAGA-GAA
1 AAATAAAAA-ATGAA
24511 AAAT
1 AAAT
24515 GAGGGTTTGA
Statistics
Matches: 65, Mismatches: 6, Indels: 13
0.77 0.07 0.15
Matches are distributed among these distances:
13 6 0.09
14 24 0.37
15 16 0.25
16 18 0.28
17 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (14 bp):
AAATAAAAAATGAA
Found at i:24445 original size:7 final size:7
Alignment explanation
Indices: 24423--24516 Score: 70
Period size: 7 Copynumber: 12.9 Consensus size: 7
24413 AAAAGGGAAC
*
24423 AAATAAA
1 AAATGAA
24430 AAGATGAA
1 AA-ATGAA
24438 AAATGAAA
1 AAATG-AA
24446 AAATGAA
1 AAATGAA
24453 AAA-GAAAAA
1 AAATG---AA
24462 AAATGAA
1 AAATGAA
24469 AAATGAA
1 AAATGAA
24476 AAATGAA
1 AAATGAA
24483 AAA--AA
1 AAATGAA
24488 GAAATGAAA
1 -AAATG-AA
24497 AAAT-AA
1 AAATGAA
*
24503 AAAGAGAA
1 AAA-TGAA
24511 AAATGA
1 AAATGA
24517 GGGTTTGAGA
Statistics
Matches: 72, Mismatches: 3, Indels: 24
0.73 0.03 0.24
Matches are distributed among these distances:
5 2 0.03
6 9 0.12
7 31 0.43
8 22 0.31
9 7 0.10
10 1 0.01
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.11
Consensus pattern (7 bp):
AAATGAA
Found at i:24462 original size:31 final size:30
Alignment explanation
Indices: 24427--24485 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 30
24417 GGGAACAAAT
*
24427 AAAAAGATGAAAAATGAAAAAATGAAAAAGA
1 AAAAAAATGAAAAATG-AAAAATGAAAAAGA
24458 AAAAAAATGAAAAATGAAAAATGAAAAA
1 AAAAAAATGAAAAATGAAAAATGAAAAA
24486 AAGAAATGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (30 bp):
AAAAAAATGAAAAATGAAAAATGAAAAAGA
Found at i:24480 original size:38 final size:38
Alignment explanation
Indices: 24423--24516 Score: 124
Period size: 35 Copynumber: 2.6 Consensus size: 38
24413 AAAAGGGAAC
*
24423 AAATAAAAAGATGAAAAATGAAAAAATGAAAAAGAAAAA
1 AAATAAAAAGATGAAAAATGAAAAAAAG-AAAAGAAAAA
* *
24462 AAATGAAAA-ATGAAAAATGAAAAAAAGAAATG--AAA
1 AAATAAAAAGATGAAAAATGAAAAAAAGAAAAGAAAAA
24497 AAATAAAAAGA-GAAAAATGA
1 AAATAAAAAGATGAAAAATGA
24517 GGGTTTGAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
35 20 0.40
36 1 0.02
37 4 0.08
38 17 0.34
39 8 0.16
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.11
Consensus pattern (38 bp):
AAATAAAAAGATGAAAAATGAAAAAAAGAAAAGAAAAA
Found at i:24486 original size:31 final size:32
Alignment explanation
Indices: 24427--24516 Score: 98
Period size: 31 Copynumber: 2.8 Consensus size: 32
24417 GGGAACAAAT
*
24427 AAAAAGATGAAAAATGAAAAAATG-AAAAAGA
1 AAAAAAATGAAAAATGAAAAAATGAAAAAAGA
24458 AAAAAAATGAAAAATG-AAAAATGAAAAAAAGAA
1 AAAAAAATGAAAAATGAAAAAATG-AAAAAAG-A
24491 ATGAAAAAAT-AAAAA-GAGAAAAATGA
1 A--AAAAAATGAAAAATGA-AAAAATGA
24517 GGGTTTGAGA
Statistics
Matches: 51, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
30 7 0.14
31 15 0.29
32 6 0.12
33 3 0.06
34 6 0.12
35 14 0.27
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (32 bp):
AAAAAAATGAAAAATGAAAAAATGAAAAAAGA
Found at i:25876 original size:105 final size:105
Alignment explanation
Indices: 25656--25910 Score: 314
Period size: 105 Copynumber: 2.4 Consensus size: 105
25646 CTCGCTTGAG
*
25656 GGATCGACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
1 GGATCAACATTTCC--TGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
* * * * **
25721 TGAGAAGAACTTGTTCCTTTCAAATTCACCACAGATGGAGGT
64 TGAGAAAAACATGTTCCTTTCAAATCCACCACAAAAAGAGGT
* * * * *
25763 GAACCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCGTCCTAAATGAGAAAGTTCATAATG
1 GGATCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATG
* * **
25828 AGAAAAACATGTT-CTTTCTAAGTCCACCGCAAAAAGATTT
66 AGAAAAACATGTTCCTTTC-AAATCCACCACAAAAAGAGGT
**
25868 GGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATC
1 GGATCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCATC
25911 CACGTGAAAA
Statistics
Matches: 126, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
104 5 0.04
105 110 0.87
107 11 0.09
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (105 bp):
GGATCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATG
AGAAAAACATGTTCCTTTCAAATCCACCACAAAAAGAGGT
Found at i:26089 original size:3 final size:3
Alignment explanation
Indices: 26074--26119 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
26064 AGTTAAAAAA
* *
26074 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
26120 AGTGTGTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 1 0.03
3 37 0.97
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:26984 original size:44 final size:44
Alignment explanation
Indices: 26931--27023 Score: 179
Period size: 44 Copynumber: 2.1 Consensus size: 44
26921 AGGTGCAGCC
26931 GAAGG-GGTTATGAAGGAAGGTTGAAGGAAAAGAGAGAAAGAGT
1 GAAGGAGGTTATGAAGGAAGGTTGAAGGAAAAGAGAGAAAGAGT
26974 GAAGGAGGTTATGAAGGAAGGTTGAAGGAAAAGAGAGAAAGAGT
1 GAAGGAGGTTATGAAGGAAGGTTGAAGGAAAAGAGAGAAAGAGT
27018 GAAGGA
1 GAAGGA
27024 AGAGAAGTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 5 0.10
44 44 0.90
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.13
Consensus pattern (44 bp):
GAAGGAGGTTATGAAGGAAGGTTGAAGGAAAAGAGAGAAAGAGT
Found at i:29301 original size:23 final size:23
Alignment explanation
Indices: 29252--29303 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
29242 GTTACGACAC
*
29252 TTATATAATGTAATAGGTATCGT
1 TTATATAATGTAATAGGTATCGG
29275 TTATATAATGTAATAGGTAGT-GG
1 TTATATAATGTAATAGGTA-TCGG
29298 TTATAT
1 TTATAT
29304 TGTAAAGTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (23 bp):
TTATATAATGTAATAGGTATCGG
Found at i:29696 original size:23 final size:23
Alignment explanation
Indices: 29665--29737 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
29655 ATAGGTAAAA
*
29665 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
29688 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
29711 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
29734 ATAT
1 ATAT
29738 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:30097 original size:434 final size:432
Alignment explanation
Indices: 29251--30081 Score: 1525
Period size: 425 Copynumber: 1.9 Consensus size: 432
29241 GGTTACGACA
29251 CTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCT
1 CTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCT
29316 ATCATTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTT
66 ATCATTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTT
29381 GAGTGAGTTTTAAGATTTTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGA
131 GAGTGAGTTTTAAGATTTTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGA
*
29446 TATATATTTAATGTTGCTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
196 TATATA-TTAATGAT-CTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
29511 TAATATTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
259 TAATATTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
*
29576 AAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGG
324 AAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGG
29641 ACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCG
389 ACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCG
29685 CTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCT
1 CTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCT
* *
29750 ATCCTTTTTATAAAAGTGTCCATAC-TTTTTCACTGTTGAAAACATTAATTTAAGGTTATCTTTT
66 ATCATTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTT
29814 GAGTGAGTTTTAAGA-TTTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGA
131 GAGTGAGTTTTAAGATTTTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGA
*
29878 TATATA-T-AT-AT-TAAATTAAAAATTCTAAAT-ATATTTTATAAAATATCAAATAATCAAATA
196 TATATATTAATGATCTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATA
* *
29938 ATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-CAA
261 ATATTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
30002 AAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGAC
326 AAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGAC
30067 ACTTTCAATATAATA
391 ACTTTCAATATAATA
30082 TAATGTAATA
Statistics
Matches: 390, Mismatches: 7, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
424 81 0.21
425 89 0.23
426 19 0.05
428 1 0.00
429 2 0.01
430 1 0.00
432 55 0.14
433 53 0.14
434 89 0.23
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.40
Consensus pattern (432 bp):
CTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCT
ATCATTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTT
GAGTGAGTTTTAAGATTTTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGA
TATATATTAATGATCTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATA
ATATTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
AAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGAC
ACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCG
Found at i:30728 original size:5 final size:5
Alignment explanation
Indices: 30718--30790 Score: 76
Period size: 5 Copynumber: 14.8 Consensus size: 5
30708 AGGGTTTGAT
* * * * *
30718 TTTTA TTTTA TTTTA TTTTA TATAA TTTTA TTTTA TTTTA TATAA TTGTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* *
30768 TTTTA TTCTA TCTT- TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTT
30791 GTTGCAAGAA
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
4 3 0.06
5 50 0.94
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:30747 original size:20 final size:20
Alignment explanation
Indices: 30722--30774 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
30712 TTTGATTTTT
30722 ATTTTATTTTATTTTATATA
1 ATTTTATTTTATTTTATATA
30742 ATTTTATTTTATTTTATATA
1 ATTTTATTTTATTTTATATA
*
30762 ATTGTATTTTATT
1 ATTTTATTTTATT
30775 CTATCTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (20 bp):
ATTTTATTTTATTTTATATA
Found at i:34043 original size:13 final size:13
Alignment explanation
Indices: 33981--34043 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 13
33971 GAAATAAATA
33981 AAAAATACTTTAAT
1 AAAAA-ACTTTAAT
*
33995 ATAAAACTTTAAT
1 AAAAAACTTTAAT
*
34008 AATGAAAACACCTTAAT
1 -A--AAAA-ACTTTAAT
34025 AAAAAACTTTAAT
1 AAAAAACTTTAAT
34038 AAAAAA
1 AAAAAA
34044 TAAAAAGCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
13 21 0.51
14 9 0.22
16 4 0.10
17 7 0.17
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (13 bp):
AAAAAACTTTAAT
Found at i:37707 original size:122 final size:121
Alignment explanation
Indices: 37564--37784 Score: 390
Period size: 122 Copynumber: 1.8 Consensus size: 121
37554 TTTTAACACA
*
37564 TTTTTATTTTTATAAAAATAATTTTTGTATAATATAAATACTTATATAAAAAACTTTTATTTTAT
1 TTTTTATTTTTATAAAAATAATTTTTGTATAATATAAATAC-T-TATAAAAAACTTTTAATTTAT
37629 A-ATTTTTTATTATGATTGGGAATATAGACATAAGTGGTAAATTTTTTCTAATACATT
64 ATATTTTTTATTATGATTGGGAATATAGACATAAGTGGTAAATTTTTTCTAATACATT
*
37686 TTTTTATTTTTATAAAAATAATTTTTGTATAATATAAATACTTATAACAAACTTTTAATTTATAT
1 TTTTTATTTTTATAAAAATAATTTTTGTATAATATAAATACTTATAAAAAACTTTTAATTTATAT
*
37751 ATTTTTTATTATGATTGGGAATATATACATAAGT
66 ATTTTTTATTATGATTGGGAATATAGACATAAGT
37785 AGTGCACATT
Statistics
Matches: 95, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
120 20 0.21
121 34 0.36
122 41 0.43
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (121 bp):
TTTTTATTTTTATAAAAATAATTTTTGTATAATATAAATACTTATAAAAAACTTTTAATTTATAT
ATTTTTTATTATGATTGGGAATATAGACATAAGTGGTAAATTTTTTCTAATACATT
Found at i:40186 original size:22 final size:22
Alignment explanation
Indices: 40155--40226 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
40145 CTGAGTGGCA
40155 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
40178 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
* * *
40200 TATG-AGTGGTCCCGAAAGACC
1 TATGAATTTGTCCCGAAGGACC
40221 TATGAA
1 TATGAA
40227 ACCCTCGACT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 18 0.42
22 22 0.51
23 3 0.07
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:40213 original size:21 final size:21
Alignment explanation
Indices: 40165--40225 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
40155 TATGAAATTT
* * *
40165 GTCCCGAAGGACCTGTGAATTT
1 GTCCCGAAGGACCTATG-AGTG
40187 GTCCCGAAGGACCTATGAGTG
1 GTCCCGAAGGACCTATGAGTG
*
40208 GTCCCGAAAGACCTATGA
1 GTCCCGAAGGACCTATGA
40226 AACCCTCGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
21 19 0.54
22 16 0.46
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (21 bp):
GTCCCGAAGGACCTATGAGTG
Found at i:40820 original size:64 final size:63
Alignment explanation
Indices: 40668--40823 Score: 172
Period size: 63 Copynumber: 2.5 Consensus size: 63
40658 TAATGAAGGT
* * * * ***
40668 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGG
1 ATGCATCGATGCATTACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAAG
* * *
40731 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAAAG
1 ATGCATCGATGCATTACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAAG
*
40794 AGTGCATCGATGCATTACAAATGCATCGAT
1 A-TGCATCGATGCATTACTAATGCATCGAT
40824 ACACCTTCAA
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
63 46 0.59
64 32 0.41
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATTACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAAG
Found at i:41876 original size:23 final size:24
Alignment explanation
Indices: 41826--41877 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
41816 TAACCACACG
* *
41826 CCAAAACGGCGTCGTCGCGTTTAGGT
1 CCAAAACGGCGTCGT--CGTTGACGT
41852 CCAAAACGGCGTCGT-GTTGACGT
1 CCAAAACGGCGTCGTCGTTGACGT
41875 CCA
1 CCA
41878 GGAGGGTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.38
26 15 0.62
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (24 bp):
CCAAAACGGCGTCGTCGTTGACGT
Found at i:44772 original size:54 final size:52
Alignment explanation
Indices: 44692--44802 Score: 195
Period size: 54 Copynumber: 2.1 Consensus size: 52
44682 CGTAGATGAT
44692 ATATATATATAGATATAGAGAGAGAAAGAAGTTCTACCGTACGGCGGTCTTA
1 ATATATATATAGATATAGAGAGAGAAAGAAGTTCTACCGTACGGCGGTCTTA
*
44744 ATATATATATAGATATAGAGAGAGAGAAAGAAGTTCTACCGTACTGCGGTCTTA
1 ATATATATATAGATAT--AGAGAGAGAAAGAAGTTCTACCGTACGGCGGTCTTA
44798 ATATA
1 ATATA
44803 CGGTTAAGGA
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 16 0.29
54 40 0.71
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.28
Consensus pattern (52 bp):
ATATATATATAGATATAGAGAGAGAAAGAAGTTCTACCGTACGGCGGTCTTA
Found at i:47499 original size:9 final size:10
Alignment explanation
Indices: 47474--47502 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
47464 TTAAAATATC
47474 AATTATAAAA
1 AATTATAAAA
47484 AATTATAAAA
1 AATTATAAAA
47494 AA-TATAAAA
1 AATTATAAAA
47503 TTTAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AATTATAAAA
Found at i:48217 original size:17 final size:18
Alignment explanation
Indices: 48181--48231 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
48171 ATGAGCTCAC
*
48181 ATATCCAAAATAAAATTATA
1 ATAT-CAAAA-AAAAATATA
48201 AT-TCAAAAAAAAATATA
1 ATATCAAAAAAAAATATA
48218 ATATCAAAAAAAAA
1 ATATCAAAAAAAAA
48232 AAACTCTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 10 0.34
18 16 0.55
19 1 0.03
20 2 0.07
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.24
Consensus pattern (18 bp):
ATATCAAAAAAAAATATA
Found at i:48232 original size:19 final size:19
Alignment explanation
Indices: 48181--48232 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 19
48171 ATGAGCTCAC
* *
48181 ATATCCAAAATAAAATTATA
1 ATAT-CAAAAAAAAAATATA
48201 AT-TC-AAAAAAAAATATA
1 ATATCAAAAAAAAAATATA
48218 ATATCAAAAAAAAAA
1 ATATCAAAAAAAAAA
48233 AACTCTCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 13 0.46
18 3 0.11
19 10 0.36
20 2 0.07
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (19 bp):
ATATCAAAAAAAAAATATA
Found at i:50681 original size:12 final size:12
Alignment explanation
Indices: 50664--50711 Score: 78
Period size: 12 Copynumber: 4.0 Consensus size: 12
50654 ACGGAGATAT
50664 CAGAAATCAGAG
1 CAGAAATCAGAG
*
50676 CAGAAATCAGAA
1 CAGAAATCAGAG
*
50688 CAGAAATCAAAG
1 CAGAAATCAGAG
50700 CAGAAATCAGAG
1 CAGAAATCAGAG
50712 AAAATATCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.54, C:0.17, G:0.21, T:0.08
Consensus pattern (12 bp):
CAGAAATCAGAG
Found at i:54405 original size:12 final size:12
Alignment explanation
Indices: 54388--54444 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
54378 ACGGAGATAT
* *
54388 CAGAAATTAGAG
1 CAGAAATCAGAA
54400 CAGAAATCAGAA
1 CAGAAATCAGAA
* *
54412 CAAAAATCAGAG
1 CAGAAATCAGAA
*
54424 CAAAAATCAGAA
1 CAGAAATCAGAA
54436 CAGAAATCA
1 CAGAAATCA
54445 TATAAAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.11
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:54423 original size:24 final size:24
Alignment explanation
Indices: 54391--54444 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
54381 GAGATATCAG
* *
54391 AAATTAGAGCAGAAATCAGAACAA
1 AAATCAGAGCAAAAATCAGAACAA
*
54415 AAATCAGAGCAAAAATCAGAACAG
1 AAATCAGAGCAAAAATCAGAACAA
54439 AAATCA
1 AAATCA
54445 TATAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.11
Consensus pattern (24 bp):
AAATCAGAGCAAAAATCAGAACAA
Found at i:56025 original size:13 final size:13
Alignment explanation
Indices: 56009--56052 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
55999 CGACGACTCA
56009 GCTCAGTGGCTCG
1 GCTCAGTGGCTCG
*
56022 GCTC-GACGGCTCG
1 GCTCAG-TGGCTCG
*
56035 GCTCAATGGCTCG
1 GCTCAGTGGCTCG
56048 GCTCA
1 GCTCA
56053 CACCCGTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 1 0.04
13 25 0.96
ACGTcount: A:0.11, C:0.34, G:0.34, T:0.20
Consensus pattern (13 bp):
GCTCAGTGGCTCG
Found at i:56029 original size:26 final size:26
Alignment explanation
Indices: 55993--56051 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
55983 AACAGCTCAG
*
55993 TCGGCTCGACGACTCAGCTCAGTGGC
1 TCGGCTCGACGACTCAGCTCAATGGC
* *
56019 TCGGCTCGACGGCTCGGCTCAATGGC
1 TCGGCTCGACGACTCAGCTCAATGGC
56045 TCGGCTC
1 TCGGCTC
56052 ACACCCGTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.12, C:0.36, G:0.32, T:0.20
Consensus pattern (26 bp):
TCGGCTCGACGACTCAGCTCAATGGC
Found at i:59059 original size:36 final size:35
Alignment explanation
Indices: 59019--59217 Score: 197
Period size: 36 Copynumber: 5.6 Consensus size: 35
59009 GTTCACTTCC
* *
59019 GATTCAAGTCGAACGGAAGAAAGCATCGACACTTCT
1 GATTCAAGTCGAACAGAAGGAAGCATCGACACTT-T
* * * * *
59055 GATTCAAGTCGAACAAAAGAAAACACCGATACTTT
1 GATTCAAGTCGAACAGAAGGAAGCATCGACACTTT
* *
59090 CGATTCAAGTCGAACAGAGGGAAGCATCGGCACTTT
1 -GATTCAAGTCGAACAGAAGGAAGCATCGACACTTT
* * * *
59126 CGATTCAAGTCGAACGGATGGGAAGCTTCGACACTTCC
1 -GATTCAAGTCGAACAGA-AGGAAGCATCGACACTT-T
59164 GATT--AGTCGAACAGAAGGAAGCATC-ATCACTTT
1 GATTCAAGTCGAACAGAAGGAAGCATCGA-CACTTT
*
59197 GATTCAAGTCGAACGGAAGGA
1 GATTCAAGTCGAACAGAAGGA
59218 TGTGTGTCTT
Statistics
Matches: 136, Mismatches: 21, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
33 5 0.04
34 13 0.10
35 25 0.18
36 74 0.54
37 19 0.14
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (35 bp):
GATTCAAGTCGAACAGAAGGAAGCATCGACACTTT
Found at i:59135 original size:72 final size:73
Alignment explanation
Indices: 59012--59211 Score: 223
Period size: 72 Copynumber: 2.8 Consensus size: 73
59002 ATCAAAAGTT
* *
59012 CACTTCCGATTCAAGTCGAACGGAAGAAAGCATCGACAC-TTCTGATTCAAGTCGAAC-AAAAGA
1 CACTTCCGATTCAAGTCGAACAGAAGGAAGCATCGACACTTTC-GATTCAAGTCGAACGAAAAGA
59075 AAACACCGA
65 AAACACCGA
* * * * * ** *
59084 TACTTTCGATTCAAGTCGAACAGAGGGAAGCATCGGCACTTTCGATTCAAGTCGAACGGATGGGA
1 CACTTCCGATTCAAGTCGAACAGAAGGAAGCATCGACACTTTCGATTCAAGTCGAACGAAAAGAA
* **
59149 AGCTTCGA
66 AACACCGA
59157 CACTTCCGATT--AGTCGAACAGAAGGAAGCATC-ATCACTTT-GATTCAAGTCGAACG
1 CACTTCCGATTCAAGTCGAACAGAAGGAAGCATCGA-CACTTTCGATTCAAGTCGAACG
59212 GAAGGATGTG
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
70 15 0.14
71 26 0.24
72 47 0.44
73 20 0.19
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (73 bp):
CACTTCCGATTCAAGTCGAACAGAAGGAAGCATCGACACTTTCGATTCAAGTCGAACGAAAAGAA
AACACCGA
Done.