Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007879.1 Hibiscus syriacus cultivar Beakdansim tig00110257_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: 1117421
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:363440 original size:21 final size:21
Alignment explanation
Indices: 363414--363530 Score: 103
Period size: 21 Copynumber: 5.6 Consensus size: 21
363404 CTAATCTGTC
*
363414 ATCGTTCAAGAGGCCTCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
*
363435 ATCGTTCAAGAGGCCCCT-AT
1 ATCGTTCAAGAGGCCCCTCCT
** * *
363455 CATCCCTCAAGAGTCCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
* *
363477 ATCGTTCAAGATGCCCCT-GT
1 ATCGTTCAAGAGGCCCCTCCT
* * *
363497 CATCGTTGAAGAGGTCTCTCCT
1 -ATCGTTCAAGAGGCCCCTCCT
363519 ATCGTTCAAGAG
1 ATCGTTCAAGAG
363531 CCCGATTCAC
Statistics
Matches: 73, Mismatches: 19, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
20 1 0.01
21 71 0.97
22 1 0.01
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.26
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:363481 original size:42 final size:42
Alignment explanation
Indices: 363419--363530 Score: 125
Period size: 42 Copynumber: 2.7 Consensus size: 42
363409 CTGTCATCGT
* *
363419 TCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTATCATCCC
1 TCAAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTATCATCCC
* * * **
363461 TCAAGAGTCCCCTCCCATCGTTCAAGATGCCCCTGTCATCGT
1 TCAAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTATCATCCC
* * * *
363503 TGAAGAGGTCTCTCCTATCGTTCAAGAG
1 TCAAGAGGCCCCTCCCATCGTTCAAGAG
363531 CCCGATTCAC
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (42 bp):
TCAAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTATCATCCC
Found at i:365137 original size:19 final size:20
Alignment explanation
Indices: 365048--365125 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
365038 AGGTACACTT
* * *
365048 TCGCAACGCTAAACTCAAAA
1 TCGCAATGCGAAAGTCAAAA
*
365068 TTGCAATGCGAAAGTCAAAA
1 TCGCAATGCGAAAGTCAAAA
365088 TCGCAATGCGAAAGTCAAAA
1 TCGCAATGCGAAAGTCAAAA
365108 TCGCAATGCGAAAGTCAA
1 TCGCAATGCGAAAGTCAA
365126 TTCGCATTGC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAAAGTCAAAA
Found at i:365185 original size:20 final size:20
Alignment explanation
Indices: 365164--365314 Score: 188
Period size: 20 Copynumber: 7.8 Consensus size: 20
365154 ACGATTTTCT
*
365164 CGTTGCGATAGTCAAATTCT
1 CGTTGCGATAGTCAAATTCG
* *
365184 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
365204 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
365224 CGTTGTGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
365238 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
365258 CGTTGCGATATTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
365278 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
365298 CGTTGCAATATTCAAAT
1 CGTTGCGATAGTCAAAT
365315 GAATGTGTAA
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
14 11 0.10
16 1 0.01
18 1 0.01
20 100 0.88
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:365219 original size:40 final size:40
Alignment explanation
Indices: 365164--365314 Score: 215
Period size: 40 Copynumber: 3.9 Consensus size: 40
365154 ACGATTTTCT
* * *
365164 CGTTGCGATAGTCAAATTCTCGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAATTCG
*
365204 CGTTGCGATAGTCAAATTCGCGTTGTGAT-TT----TT-G
1 CGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAATTCG
365238 CGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAATTCG
*
365278 CGTTGCGATAGTCAAATTCGCGTTGCAATATTCAAAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAAT
365315 GAATGTGTAA
Statistics
Matches: 99, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
34 28 0.28
35 4 0.04
39 3 0.03
40 64 0.65
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (40 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAATTCG
Found at i:365234 original size:74 final size:74
Alignment explanation
Indices: 365156--365302 Score: 251
Period size: 74 Copynumber: 2.0 Consensus size: 74
365146 TACGATTTAC
*
365156 GATTTTCT-CGTTGCGATAGTCAAATTCTCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAA
1 GATTTT-TGCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAA
365220 TTCGCGTTGT
65 TTCGCGTTGT
* *
365230 GATTTTTGCGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAATTCGCGTTGCGATAGTCAAAT
1 GATTTTTGCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAAT
365295 TCGCGTTG
66 TCGCGTTG
365303 CAATATTCAA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
73 1 0.01
74 68 0.99
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.36
Consensus pattern (74 bp):
GATTTTTGCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAAT
TCGCGTTGT
Found at i:365515 original size:129 final size:129
Alignment explanation
Indices: 365285--365528 Score: 454
Period size: 129 Copynumber: 1.9 Consensus size: 129
365275 TCGCGTTGCG
365285 ATAGTCAAATTCGCGTTGCAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
365350 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
* *
365414 ATAGTCAAATTCGCGTTGCGATATTCAAAT-AATTGTGTAATAAGTGATAACAACTGAACATATC
1 ATAGTCAAATTCGCGTTGCAATATTCAAATGAA-TGTGTAATAAGTGATAACAACTGAACAGATC
365478 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTA
65 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTA
365529 CATAAAATAC
Statistics
Matches: 112, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
128 2 0.02
129 110 0.98
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (129 bp):
ATAGTCAAATTCGCGTTGCAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
Found at i:365633 original size:18 final size:17
Alignment explanation
Indices: 365604--365637 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
365594 AAGCCGGTTG
365604 TGATTGGATTTTGATTT
1 TGATTGGATTTTGATTT
365621 TGATTGCGATTTTGATT
1 TGATTG-GATTTTGATT
365638 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.18, C:0.03, G:0.24, T:0.56
Consensus pattern (17 bp):
TGATTGGATTTTGATTT
Found at i:367919 original size:24 final size:24
Alignment explanation
Indices: 367885--367938 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
367875 CTGAAACATC
367885 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
367909 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
367933 ATCAAA
1 ATCAAA
367939 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:367952 original size:24 final size:24
Alignment explanation
Indices: 367885--367952 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
367875 CTGAAACATC
* * *
367885 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
367909 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
367933 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
367953 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:368784 original size:20 final size:20
Alignment explanation
Indices: 368759--368882 Score: 155
Period size: 20 Copynumber: 6.3 Consensus size: 20
368749 TTGAAATTCA
* *
368759 GCGTTGCGACAGTTAGAATC
1 GCGTTGCGATAGTCAGAATC
368779 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
*
368799 GAGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
* * *
368819 CCGTTGCGAT--T-ATGTATT
1 GCGTTGCGATAGTCA-GAATC
*
368837 GCGTTGAGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
368857 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
368877 GCGTTG
1 GCGTTG
368883 TGATTTACAT
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
17 1 0.01
18 12 0.14
20 74 0.84
21 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:368996 original size:19 final size:19
Alignment explanation
Indices: 368972--369008 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
368962 TGCGATACTG
*
368972 GAGATCGCGTTACGATTTA
1 GAGATCGCATTACGATTTA
*
368991 GAGATCGCATTGCGATTT
1 GAGATCGCATTACGATTT
369009 TGTTGGTCAT
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:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:373235 original size:182 final size:182
Alignment explanation
Indices: 372926--373289 Score: 701
Period size: 182 Copynumber: 2.0 Consensus size: 182
372916 AAGTATAATA
372926 GCTTGGACAGTCTGATAACCCCTTGTTTCAATCACCTGAGCATTGTTATCGTCAAAAGAGACCAA
1 GCTTGGACAGTCTGATAACCCCTTGTTTCAATCACCTGAGCATTGTTATCGTCAAAAGAGACCAA
*
372991 TTGCTCGTTTACATGCTCGATAACGTCAAACTTTTGGAAGCAAATGGAGTGCCTGGTGACATTTA
66 TTGCTCGTTTACATGCTCGATAACGTCAAACTTTTGGAAGCAAATGGAGTGCCTGATGACATTTA
373056 ATGACAACCCCACCTGTTTTTACTAGGCTGCGGCATCATTTCAAGTACACTG
131 ATGACAACCCCACCTGTTTTTACTAGGCTGCGGCATCATTTCAAGTACACTG
373108 GCTTGGACAGTCTGATAACCCCTTGTTTCAATCACCTGAGCATTGTTATCGTCAAAAGAGACCAA
1 GCTTGGACAGTCTGATAACCCCTTGTTTCAATCACCTGAGCATTGTTATCGTCAAAAGAGACCAA
* *
373173 TTGCTCGTTTACATGCTCGATAACTTCAAACTTTTGGGAGCAAATGGAGTGCCTGATGACATTTA
66 TTGCTCGTTTACATGCTCGATAACGTCAAACTTTTGGAAGCAAATGGAGTGCCTGATGACATTTA
373238 ATGACAACCCCACCTGTTTTTACTAGGCTGCGGCATCATTTCAAGTACACTG
131 ATGACAACCCCACCTGTTTTTACTAGGCTGCGGCATCATTTCAAGTACACTG
373290 CCGGGCAAGG
Statistics
Matches: 179, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
182 179 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (182 bp):
GCTTGGACAGTCTGATAACCCCTTGTTTCAATCACCTGAGCATTGTTATCGTCAAAAGAGACCAA
TTGCTCGTTTACATGCTCGATAACGTCAAACTTTTGGAAGCAAATGGAGTGCCTGATGACATTTA
ATGACAACCCCACCTGTTTTTACTAGGCTGCGGCATCATTTCAAGTACACTG
Found at i:385786 original size:16 final size:17
Alignment explanation
Indices: 385747--385786 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
385737 CTTTCAATCT
* *
385747 TTATTAATTAAAATTTA
1 TTATTAATAAAAATATA
385764 TTATTAATAAAAATATA
1 TTATTAATAAAAATATA
385781 TT-TTAA
1 TTATTAA
385787 AAATCTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATTAATAAAAATATA
Found at i:385824 original size:14 final size:14
Alignment explanation
Indices: 385805--385837 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
385795 AATCAAAATA
385805 ATTTTAGAATATAT
1 ATTTTAGAATATAT
*
385819 ATTTTAGAATATTT
1 ATTTTAGAATATAT
385833 ATTTT
1 ATTTT
385838 TTAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (14 bp):
ATTTTAGAATATAT
Found at i:386198 original size:18 final size:18
Alignment explanation
Indices: 386165--386199 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
386155 GATTAAATTT
**
386165 ATTTTTTTAATTTAATAG
1 ATTTTTTTAAAATAATAG
386183 ATTTTTTTAAAATAATA
1 ATTTTTTTAAAATAATA
386200 CTATCTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATTTTTTTAAAATAATAG
Found at i:390245 original size:52 final size:53
Alignment explanation
Indices: 390167--390302 Score: 229
Period size: 52 Copynumber: 2.6 Consensus size: 53
390157 CGACTCTAGG
*
390167 TATTTTTTGGCCCGGGGTAAAATAAAAGAAATGGATTTCTATTTATGTTC-TT
1 TATTTTTTGGCCCGGGGTAAAATAAAAGAAATGAATTTCTATTTATGTTCTTT
* *
390219 TATTTTTTGGCCTGGGGTAAAATAAAAGAAATGAATTTCTATTTATTTTCTTT
1 TATTTTTTGGCCCGGGGTAAAATAAAAGAAATGAATTTCTATTTATGTTCTTT
*
390272 TATTTTTTGGCCCGGGGCAAAATAAAAGAAA
1 TATTTTTTGGCCCGGGGTAAAATAAAAGAAA
390303 CCTAGTTATG
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
52 47 0.60
53 31 0.40
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (53 bp):
TATTTTTTGGCCCGGGGTAAAATAAAAGAAATGAATTTCTATTTATGTTCTTT
Found at i:395368 original size:40 final size:42
Alignment explanation
Indices: 395309--395391 Score: 109
Period size: 40 Copynumber: 2.0 Consensus size: 42
395299 ATATGGTATG
* *
395309 TTTAATATATTTTTATTATTCTA-AAGTAAATATATT-TTTTA
1 TTTAATATATTTATATTATTCTACAA-AAAATATATTATTTTA
*
395350 TTTAATA-ATTTATATTATTTTACAAAAAATATATTATTTTA
1 TTTAATATATTTATATTATTCTACAAAAAATATATTATTTTA
395391 T
1 T
395392 ATTCACCTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 22 0.59
41 15 0.41
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (42 bp):
TTTAATATATTTATATTATTCTACAAAAAATATATTATTTTA
Found at i:396010 original size:2 final size:2
Alignment explanation
Indices: 396003--396035 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
395993 TGATAAAGAA
396003 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
396036 TTTAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:397203 original size:24 final size:24
Alignment explanation
Indices: 397171--397222 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
397161 ACGCATAATT
397171 TTATGCTAGGGGGCGAACATGAAC
1 TTATGCTAGGGGGCGAACATGAAC
397195 TTATGCTAGGGGGCGAACATGAAC
1 TTATGCTAGGGGGCGAACATGAAC
397219 TTAT
1 TTAT
397223 AAAATTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (24 bp):
TTATGCTAGGGGGCGAACATGAAC
Found at i:399818 original size:14 final size:15
Alignment explanation
Indices: 399801--399833 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
399791 TACTGGGGAA
399801 GGTTTAATG-TTTAG
1 GGTTTAATGTTTTAG
*
399815 GGTTTACTGTTTTAG
1 GGTTTAATGTTTTAG
399830 GGTT
1 GGTT
399834 ACAGACAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.15, C:0.03, G:0.30, T:0.52
Consensus pattern (15 bp):
GGTTTAATGTTTTAG
Found at i:401961 original size:17 final size:17
Alignment explanation
Indices: 401919--401961 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
401909 TTATTATTTT
401919 ATTATTGTTTATTTTAAA
1 ATTATTG-TTATTTTAAA
*
401937 A-TAATGTTATTTTAAA
1 ATTATTGTTATTTTAAA
401953 ATTATTGTT
1 ATTATTGTT
401962 TAATATCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 11 0.50
17 10 0.45
18 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (17 bp):
ATTATTGTTATTTTAAA
Found at i:402966 original size:2 final size:2
Alignment explanation
Indices: 402959--402996 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
402949 AAATTAGGTT
402959 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
402997 GAGAGAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:403001 original size:2 final size:2
Alignment explanation
Indices: 402996--403020 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
402986 ATATATATAT
402996 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
403021 AGTAATAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:404192 original size:21 final size:20
Alignment explanation
Indices: 404157--404196 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
404147 TTTATCGATG
404157 AAATTTTAAAATTTTTAAAA
1 AAATTTTAAAATTTTTAAAA
*
404177 AAATTATTAAACTTTTTAAA
1 AAATT-TTAAAATTTTTAAA
404197 TATTTACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTTTAAAATTTTTAAAA
Found at i:408083 original size:20 final size:20
Alignment explanation
Indices: 408054--408093 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
408044 TTTGGGAAAA
* *
408054 ATCGGTTTTTTTTTAACCGG
1 ATCGGATTTTTTTAAACCGG
408074 ATCGGATTTTTTTAAACCGG
1 ATCGGATTTTTTTAAACCGG
408094 TTATTTTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (20 bp):
ATCGGATTTTTTTAAACCGG
Found at i:408152 original size:12 final size:12
Alignment explanation
Indices: 408137--408183 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
408127 CCGGTTTTTT
*
408137 AACCGGATAAAA
1 AACCGGTTAAAA
408149 AACCGGTTTGAAAAA
1 AACCGG-TT--AAAA
408164 AACCGGTTAAAA
1 AACCGGTTAAAA
408176 AACCGGTT
1 AACCGGTT
408184 TTTATCCGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 18 0.58
13 1 0.03
14 2 0.06
15 10 0.32
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (12 bp):
AACCGGTTAAAA
Found at i:410501 original size:21 final size:21
Alignment explanation
Indices: 410477--410516 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
410467 TTTATTTTAT
410477 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
410498 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
410517 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:410564 original size:33 final size:33
Alignment explanation
Indices: 410511--410609 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
410501 TTTGTTTCAA
410511 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
410543 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
410576 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
410609 T
1 T
410610 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:410638 original size:13 final size:13
Alignment explanation
Indices: 410595--410649 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
410585 TTGGAAGTAT
410595 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
410608 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
410622 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
410635 TTAAGTATTTGAA
1 TTAAGTATTTCAA
410648 TT
1 TT
410650 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:410973 original size:19 final size:20
Alignment explanation
Indices: 410915--410972 Score: 89
Period size: 20 Copynumber: 2.8 Consensus size: 20
410905 CCGTTGAATA
*
410915 GGGGAGAATCGGTACCCCCTAT
1 GGGG-GAATCGGT-TCCCCTAT
410937 GGGGGAATCGGTTCCCCTAT
1 GGGGGAATCGGTTCCCCTAT
410957 GGGGGAATCGGTTCCC
1 GGGGGAATCGGTTCCC
410973 TCCGAGCATT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 23 0.66
21 8 0.23
22 4 0.11
ACGTcount: A:0.17, C:0.26, G:0.36, T:0.21
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCCTAT
Found at i:411239 original size:15 final size:17
Alignment explanation
Indices: 411213--411244 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
411203 TTCTATGGGA
411213 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
411229 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
411245 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:419282 original size:4 final size:4
Alignment explanation
Indices: 419273--419299 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
419263 CTCAACTATG
419273 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
419300 ACATGCATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:420803 original size:15 final size:15
Alignment explanation
Indices: 420783--420835 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
420773 AGAAGAGGTG
420783 GCGAAGGAGGAGTAT
1 GCGAAGGAGGAGTAT
* *
420798 GCGAAGAAGAAGAGGT-G
1 GCGAAG--GAGGA-GTAT
420815 GCGAAGGAGGAGTAT
1 GCGAAGGAGGAGTAT
420830 GCGAAG
1 GCGAAG
420836 AAGAAGAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 2 0.07
15 16 0.53
17 10 0.33
18 2 0.07
ACGTcount: A:0.36, C:0.08, G:0.47, T:0.09
Consensus pattern (15 bp):
GCGAAGGAGGAGTAT
Found at i:420806 original size:32 final size:32
Alignment explanation
Indices: 420770--420939 Score: 247
Period size: 32 Copynumber: 5.3 Consensus size: 32
420760 GAGCAGCAGG
420770 AGAAGAAGAGGTGGCGAAGGAGGAGTATGCGA
1 AGAAGAAGAGGTGGCGAAGGAGGAGTATGCGA
420802 AGAAGAAGAGGTGGCGAAGGAGGAGTATGCGA
1 AGAAGAAGAGGTGGCGAAGGAGGAGTATGCGA
*
420834 AGAAGAAGAGGTGGCG-A--AGGAGTATGTGA
1 AGAAGAAGAGGTGGCGAAGGAGGAGTATGCGA
*
420863 AGAAGAAGAGAGTGGCGAAGGAGGAGTATGGGA
1 AGAAGAAGAG-GTGGCGAAGGAGGAGTATGCGA
* * * *
420896 AGAAGAAGATGCTGGCGGAGGAGGAGTATGTGG
1 AGAAGAAGA-GGTGGCGAAGGAGGAGTATGCGA
420929 AGAAGAAGAGG
1 AGAAGAAGAGG
420940 CGGTGCGCGA
Statistics
Matches: 126, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
29 21 0.17
30 6 0.05
31 2 0.02
32 49 0.39
33 47 0.37
34 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.47, T:0.11
Consensus pattern (32 bp):
AGAAGAAGAGGTGGCGAAGGAGGAGTATGCGA
Found at i:420954 original size:33 final size:32
Alignment explanation
Indices: 420768--420969 Score: 133
Period size: 33 Copynumber: 6.3 Consensus size: 32
420758 AGGAGCAGCA
*
420768 GGAGAAGAAGA--GGTGGCGAAGGAGGAGTATGC
1 GGAGAAGAAGAGCGGTGGCG-A-GAGGAGTATGT
* *
420800 GAAGAAGAAGA--GGTGGCGAAGGAGGAGTATGC
1 GGAGAAGAAGAGCGGTGGCG-A-GAGGAGTATGT
*
420832 GAAGAAGAAGA--GGTGGCGA-AGGAGTATGT
1 GGAGAAGAAGAGCGGTGGCGAGAGGAGTATGT
* *
420861 GAAGAAGAAGAG-AGTGGCGAAGGAGGAGTATG-
1 GGAGAAGAAGAGCGGTGGCG-A-GAGGAGTATGT
420893 GGAAGAAGAAGATGC--TGGCGGAGGAGGAGTATGT
1 GG-AGAAGAAGA-GCGGTGGC-GA-GAGGAGTATGT
*
420927 GGAGAAGAAGAGGCGGTGCGCGA-AGGAGCA-GT
1 GGAGAAGAAGA-GCGGTG-GCGAGAGGAGTATGT
420959 AGGAGAAGAAG
1 -GGAGAAGAAG
420970 CTGTTGGAAA
Statistics
Matches: 151, Mismatches: 6, Indels: 25
0.83 0.03 0.14
Matches are distributed among these distances:
29 20 0.13
30 6 0.04
31 2 0.01
32 52 0.34
33 61 0.40
34 4 0.03
35 4 0.03
36 2 0.01
ACGTcount: A:0.37, C:0.06, G:0.48, T:0.10
Consensus pattern (32 bp):
GGAGAAGAAGAGCGGTGGCGAGAGGAGTATGT
Found at i:420969 original size:36 final size:32
Alignment explanation
Indices: 420770--420969 Score: 198
Period size: 32 Copynumber: 6.2 Consensus size: 32
420760 GAGCAGCAGG
*
420770 AGAAGAAGAG-GTGGCGAAGGAGGAGTATGCGA
1 AGAAGAAGAGCGTGGCGAAGGAGGAGTA-GGGA
*
420802 AGAAGAAGAG-GTGGCGAAGGAGGAGTATGCGA
1 AGAAGAAGAGCGTGGCGAAGGAGGAGTA-GGGA
* *
420834 AGAAGAAGAG-GTGGCGAAGGAGTA-T-GTGA
1 AGAAGAAGAGCGTGGCGAAGGAGGAGTAGGGA
*
420863 AGAAGAAGAGAGTGGCGAAGGAGGAGTATGGGA
1 AGAAGAAGAGCGTGGCGAAGGAGGAGTA-GGGA
*
420896 AGAAGAAGATGC-TGGCGGAGGAGGAGTATGTGG-
1 AGAAGAAGA-GCGTGGCGAAGGAGGAGTA-G-GGA
*
420929 AGAAGAAGAGGCGGTGCGCGAAGGAGCAGTAGGAGA
1 AGAAGAAGA-GC-GTG-GCGAAGGAGGAGTAGG-GA
420965 AGAAG
1 AGAAG
420970 CTGTTGGAAA
Statistics
Matches: 148, Mismatches: 9, Indels: 18
0.85 0.05 0.10
Matches are distributed among these distances:
29 13 0.09
30 13 0.09
31 2 0.01
32 55 0.37
33 40 0.27
34 4 0.03
35 4 0.03
36 17 0.11
ACGTcount: A:0.37, C:0.06, G:0.47, T:0.10
Consensus pattern (32 bp):
AGAAGAAGAGCGTGGCGAAGGAGGAGTAGGGA
Found at i:424802 original size:23 final size:23
Alignment explanation
Indices: 424775--424839 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
424765 CCATTGATCA
424775 GGGGGAATCGGTACCCTCTTGGG
1 GGGGGAATCGGTACCCTCTTGGG
424798 GGGGGAATCGGTACCC-CATTGGG
1 GGGGGAATCGGTACCCTC-TTGGG
* * *
424821 GGGAGAATCGATTCCCTCT
1 GGGGGAATCGGTACCCTCT
424840 GAGCAATCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.17, C:0.23, G:0.38, T:0.22
Consensus pattern (23 bp):
GGGGGAATCGGTACCCTCTTGGG
Found at i:425832 original size:18 final size:18
Alignment explanation
Indices: 425809--425849 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
425799 AGGCATTGGA
*
425809 TCCTCTGGTCGTGCTTGT
1 TCCTCTGGTCGAGCTTGT
*
425827 TCCTCTGGTGGAGCTTGT
1 TCCTCTGGTCGAGCTTGT
425845 TCCTC
1 TCCTC
425850 ATGTTGTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.02, C:0.29, G:0.27, T:0.41
Consensus pattern (18 bp):
TCCTCTGGTCGAGCTTGT
Found at i:427365 original size:22 final size:23
Alignment explanation
Indices: 427338--427399 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
427328 ATTCCTCTAC
*
427338 AGGGGGAATTGATTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTCAA
*
427361 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGATTCCCCTTCAA
* *
427383 AGGGGGTATCAATTCCC
1 AGGGGGAATCGATTCCC
427400 TCTGCACCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (23 bp):
AGGGGGAATCGATTCCCCTTCAA
Found at i:427400 original size:21 final size:22
Alignment explanation
Indices: 427318--427399 Score: 76
Period size: 22 Copynumber: 3.7 Consensus size: 22
427308 CAGAACCCCA
* *
427318 GGGGATATCAATTCCTCTAC-AG
1 GGGGA-ATCAATTCCCCTTCAAG
**
427340 GGGGAATTGATTCCCCTTCAAAG
1 GGGGAATCAATTCCCCTTC-AAG
**
427363 GGGGAATCGGTTCCCCTTCAAG
1 GGGGAATCAATTCCCCTTCAAG
*
427385 GGGGTATCAATTCCC
1 GGGGAATCAATTCCC
427400 TCTGCACCAA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
21 10 0.20
22 20 0.41
23 19 0.39
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (22 bp):
GGGGAATCAATTCCCCTTCAAG
Found at i:446635 original size:20 final size:20
Alignment explanation
Indices: 446580--446633 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
446570 TATTTTTCGT
446580 TAATTAATTATTAAATATAA
1 TAATTAATTATTAAATATAA
446600 TAATTAATTATTAAATATAA
1 TAATTAATTATTAAATATAA
446620 TAATTAA-TATTAAA
1 TAATTAATTATTAAA
446634 ATTGTTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 7 0.21
20 27 0.79
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATTAATTATTAAATATAA
Found at i:446811 original size:14 final size:14
Alignment explanation
Indices: 446794--446832 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
446784 AGTTAGTTTT
*
446794 TTTAATAAATTTAA
1 TTTAATTAATTTAA
*
446808 TTTAATTTATTTAA
1 TTTAATTAATTTAA
446822 -TTAATTAATTT
1 TTTAATTAATTT
446833 TTATAATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAATTAATTTAA
Found at i:446820 original size:23 final size:23
Alignment explanation
Indices: 446778--446832 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
446768 TTAATATTAG
* * *
446778 AATTTAAGTTAGTTTTTTTAATA
1 AATTTAATTTAATTTATTTAATA
*
446801 AATTTAATTTAATTTATTTAATT
1 AATTTAATTTAATTTATTTAATA
446824 AA-TTAATTT
1 AATTTAATTT
446833 TTATAATCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (23 bp):
AATTTAATTTAATTTATTTAATA
Found at i:451064 original size:17 final size:17
Alignment explanation
Indices: 451042--451095 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
451032 ACTTAATTAA
451042 ATATTTAATAAATTTTT
1 ATATTTAATAAATTTTT
** **
451059 ATATTTTTTAAATTTAA
1 ATATTTAATAAATTTTT
451076 ATATTTAAT-AATTGTTT
1 ATATTTAATAAATT-TTT
451093 ATA
1 ATA
451096 CTTTTTAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 4 0.14
17 24 0.86
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
ATATTTAATAAATTTTT
Found at i:451081 original size:34 final size:34
Alignment explanation
Indices: 451038--451116 Score: 133
Period size: 34 Copynumber: 2.3 Consensus size: 34
451028 CGCTACTTAA
*
451038 TTAAATATTTAATAAATT-TTTATATTTTTTAAAT
1 TTAAATATTTAAT-AATTGTTTATACTTTTTAAAT
451072 TTAAATATTTAATAATTGTTTATACTTTTTAAAT
1 TTAAATATTTAATAATTGTTTATACTTTTTAAAT
451106 TTAAATATTTA
1 TTAAATATTTA
451117 TTTTTACATA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
33 4 0.09
34 39 0.91
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (34 bp):
TTAAATATTTAATAATTGTTTATACTTTTTAAAT
Found at i:458753 original size:14 final size:14
Alignment explanation
Indices: 458734--458766 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
458724 TGGGGAGTAA
*
458734 TCCCTGTAAATAAT
1 TCCCTGCAAATAAT
458748 TCCCTGCAAATAAT
1 TCCCTGCAAATAAT
458762 TCCCT
1 TCCCT
458767 ACATAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (14 bp):
TCCCTGCAAATAAT
Found at i:464366 original size:2 final size:2
Alignment explanation
Indices: 464359--464388 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
464349 CCCGGTTAGT
464359 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
464389 ATCCAATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:465597 original size:60 final size:59
Alignment explanation
Indices: 465533--465652 Score: 213
Period size: 60 Copynumber: 2.0 Consensus size: 59
465523 TCAAAACTTC
* *
465533 AAATATATTTTGATAACCACTAAATAAAGTAGCATTTTTTTTCTTTTTGAATATAAATTA
1 AAATATATTTTGATAACCACTAAACAAAGTAGCA-TTTTTTTCTTTATGAATATAAATTA
465593 AAATATATTTTGATAACCACTAAACAAAGTAGCATTTTTTTCTTTATGAATATAAATTA
1 AAATATATTTTGATAACCACTAAACAAAGTAGCATTTTTTTCTTTATGAATATAAATTA
465652 A
1 A
465653 TATTGATAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 25 0.43
60 33 0.57
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (59 bp):
AAATATATTTTGATAACCACTAAACAAAGTAGCATTTTTTTCTTTATGAATATAAATTA
Found at i:466362 original size:96 final size:96
Alignment explanation
Indices: 466248--466461 Score: 329
Period size: 96 Copynumber: 2.2 Consensus size: 96
466238 GGTTTCTTTG
* *
466248 AAATCCTGAGGAAGTTCAGATTGTGAAAGCAACGAAGATTCTTCAGGATTTGACTGAGGAAAATA
1 AAATCCTGAGGAAATTCAGATTGTGAAAGCAACGAAGATTCTTCAGAATTTGACTGAGGAAAATA
* * *
466313 TTGGGGTTCAGAAGAAAATTTGGAAGCTTCA
66 TTGGGATTCAGAAGAAAACTTGGAAGCATCA
* * * **
466344 AAATCCTGGGGAAATTCAGATTGTGAAAGCAACGATGGTTCTTCAGAATTTGTTTGAGGAAAATA
1 AAATCCTGAGGAAATTCAGATTGTGAAAGCAACGAAGATTCTTCAGAATTTGACTGAGGAAAATA
466409 TTGGGATTCAGAAGAAAACTTGGAAGCATCA
66 TTGGGATTCAGAAGAAAACTTGGAAGCATCA
*
466440 AAATCCAGAGGAAATTCAGATT
1 AAATCCTGAGGAAATTCAGATT
466462 CGAAATCAAA
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 106 1.00
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (96 bp):
AAATCCTGAGGAAATTCAGATTGTGAAAGCAACGAAGATTCTTCAGAATTTGACTGAGGAAAATA
TTGGGATTCAGAAGAAAACTTGGAAGCATCA
Found at i:472630 original size:25 final size:25
Alignment explanation
Indices: 472594--472660 Score: 125
Period size: 25 Copynumber: 2.7 Consensus size: 25
472584 CCCCCGTCCT
472594 CGTCCCCGTTTAAAAAACCGGTACC
1 CGTCCCCGTTTAAAAAACCGGTACC
*
472619 CGTCCCCATTTAAAAAACCGGTACC
1 CGTCCCCGTTTAAAAAACCGGTACC
472644 CGTCCCCGTTTAAAAAA
1 CGTCCCCGTTTAAAAAA
472661 TCGCGGGGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.31, C:0.34, G:0.13, T:0.21
Consensus pattern (25 bp):
CGTCCCCGTTTAAAAAACCGGTACC
Found at i:472767 original size:12 final size:12
Alignment explanation
Indices: 472752--472806 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
472742 GTTATTTAAA
472752 CGGGTATTGGGC
1 CGGGTATTGGGC
*
472764 CGGGTATTGGGT
1 CGGGTATTGGGC
*
472776 CGGGTATTGGGT
1 CGGGTATTGGGC
* * *
472788 CGAGAATCGGGC
1 CGGGTATTGGGC
472800 CGGGTAT
1 CGGGTAT
472807 ATATATATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.13, C:0.15, G:0.47, T:0.25
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:472811 original size:2 final size:2
Alignment explanation
Indices: 472804--472903 Score: 68
Period size: 2 Copynumber: 53.0 Consensus size: 2
472794 TCGGGCCGGG
* * * *
472804 TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
472844 TT TT TA TT TA AA T- TA AA TT TA T- TA -A TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
472882 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
472904 ATTATTTTTA
Statistics
Matches: 75, Mismatches: 17, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
1 6 0.08
2 69 0.92
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:472950 original size:13 final size:12
Alignment explanation
Indices: 472919--472955 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
472909 TTTTAATATT
*
472919 TATCGGGTCGGG
1 TATCGGGGCGGG
472931 TATCGGGGCGGG
1 TATCGGGGCGGG
472943 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
472956 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:482584 original size:31 final size:30
Alignment explanation
Indices: 482501--482609 Score: 98
Period size: 28 Copynumber: 3.6 Consensus size: 30
482491 TAATATTTTT
* * *
482501 AAAATATTAATATAATTTA-TTTATT-ATT
1 AAAATATTAATATTATATATTTTATTAATA
** *
482529 AAAATATTGTTTTTATA-ATTTTATTAATA
1 AAAATATTAATATTATATATTTTATTAATA
482558 AAAATATTAATATTAGTATATTTTATTGAAATA
1 AAAATATTAATATTA-TATATTTTATT--AATA
*
482591 AAAATATTATAAATTATAT
1 AAAATATTA-ATATTATAT
482610 TAATTATTTG
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
27 1 0.02
28 18 0.28
29 14 0.22
30 2 0.03
31 8 0.12
33 16 0.25
34 5 0.08
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.50
Consensus pattern (30 bp):
AAAATATTAATATTATATATTTTATTAATA
Found at i:482610 original size:31 final size:31
Alignment explanation
Indices: 482501--482610 Score: 92
Period size: 31 Copynumber: 3.7 Consensus size: 31
482491 TAATATTTTT
*
482501 AAAATATTAATATAATT-TA-TTTATT-ATT
1 AAAATATTAATATAATTATATTTTATTAATA
* *
482529 AAAATATT-GT-T-TTTATAATTTTATTAATA
1 AAAATATTAATATAATTAT-ATTTTATTAATA
* *
482558 AAAATATTAATATTAGTATATTTTATTGAAATA
1 AAAATATTAATATAATTATATTTTATT--AATA
482591 AAAATATT-ATA-AATTATATT
1 AAAATATTAATATAATTATATT
482611 AATTATTTGT
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
25 2 0.03
26 2 0.03
27 2 0.03
28 14 0.22
29 10 0.15
30 1 0.02
31 16 0.25
32 6 0.09
33 12 0.18
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (31 bp):
AAAATATTAATATAATTATATTTTATTAATA
Found at i:482668 original size:23 final size:23
Alignment explanation
Indices: 482640--482712 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
482630 AGTGTTATAT
482640 TATATTTTTAAAATATTAATTAA
1 TATATTTTTAAAATATTAATTAA
* *
482663 TATA-TTTTAAATATCTTTATTAA
1 TATATTTTTAAA-ATATTAATTAA
* * * *
482686 AATATTATTATATTATTATATTAA
1 TATATTTTTAAAATATTA-ATTAA
482710 TAT
1 TAT
482713 TAAATATATA
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
22 7 0.18
23 19 0.50
24 12 0.32
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (23 bp):
TATATTTTTAAAATATTAATTAA
Found at i:482880 original size:55 final size:52
Alignment explanation
Indices: 482790--482899 Score: 134
Period size: 55 Copynumber: 2.1 Consensus size: 52
482780 AATATAAATT
* *
482790 TTATTAATAATTTATTATATATTATTAAAAATAAAAATATAATATCTTATATTA
1 TTATTAATAATTGATTATATATTATTAAAAATAAAAATATAAT-GC-TATATTA
*
482844 TTATTATATAATTGATTAT-T-TTATTATAATATTAAAAATATAATGCTATATTA
1 TTATTA-ATAATTGATTATATATTATTA-AA-AATAAAAATATAATGCTATATTA
482897 TTA
1 TTA
482900 GAAACATTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
53 16 0.32
54 10 0.20
55 24 0.48
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (52 bp):
TTATTAATAATTGATTATATATTATTAAAAATAAAAATATAATGCTATATTA
Found at i:482958 original size:24 final size:23
Alignment explanation
Indices: 482931--482976 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
482921 TTAAATATTT
482931 TAATAATT-AATATTTTGATTAAAA
1 TAAT-ATTAAATATTTT-ATTAAAA
482955 TAATATTAAAATATTTTATTAA
1 TAATATT-AAATATTTTATTAA
482977 TATTAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 3 0.15
24 9 0.45
25 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TAATATTAAATATTTTATTAAAA
Found at i:486809 original size:26 final size:26
Alignment explanation
Indices: 486762--486815 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
486752 CAATAATGAG
* * *
486762 TAATATTTATTTAAATACATCATTAA
1 TAATATATATTGAAATACATCACTAA
* *
486788 TAATATATATTGAAGTATATCACTAA
1 TAATATATATTGAAATACATCACTAA
486814 TA
1 TA
486816 TAAAATAAGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (26 bp):
TAATATATATTGAAATACATCACTAA
Found at i:487509 original size:26 final size:26
Alignment explanation
Indices: 487473--487523 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
487463 AGAAGAGTCT
* *
487473 ACATTTATTGAAATGCATCACTAATG
1 ACATGTATTGAAATACATCACTAATG
*
487499 ACATGTATTGAAATACATTACTAAT
1 ACATGTATTGAAATACATCACTAAT
487524 ATAAATAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (26 bp):
ACATGTATTGAAATACATCACTAATG
Found at i:490162 original size:41 final size:40
Alignment explanation
Indices: 490067--490158 Score: 100
Period size: 41 Copynumber: 2.4 Consensus size: 40
490057 ATCGGGCCAG
490067 ATATA-TA-TATTTAAATTAAATATATAAATATTATATAA
1 ATATATTATTATTTAAATTAAATATATAAATATTATATAA
* * * * *
490105 ATATTTTTTTAATTTAAATTAAATCTATTAATATTATATAT
1 ATATATTATT-ATTTAAATTAAATATATAAATATTATATAA
*
490146 ATA-ATAATTATTT
1 ATATATTATTATTT
490159 TTAATATTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
38 4 0.09
39 5 0.12
40 4 0.09
41 30 0.70
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (40 bp):
ATATATTATTATTTAAATTAAATATATAAATATTATATAA
Found at i:490558 original size:15 final size:16
Alignment explanation
Indices: 490531--490565 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
490521 AATTATTTTA
490531 AAATTATTAAAATGAT
1 AAATTATTAAAATGAT
*
490547 AAATTA-TAAAATTAT
1 AAATTATTAAAATGAT
490562 AAAT
1 AAAT
490566 AATAGCATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
AAATTATTAAAATGAT
Found at i:495483 original size:21 final size:21
Alignment explanation
Indices: 495457--495498 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
495447 ATTTGAATAT
495457 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
495478 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
495499 CCCATTATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTATCGATTCCC
Found at i:496752 original size:20 final size:19
Alignment explanation
Indices: 496710--496758 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
496700 AAACGATTTT
*
496710 ATTTTGAAAACAAAAATAG
1 ATTTTGAAAACAAAAATAA
* *
496729 ATTTTGAAAGCCAAAATTAA
1 ATTTTGAAA-ACAAAAATAA
496749 ATTTTGAAAA
1 ATTTTGAAAA
496759 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.31
Consensus pattern (19 bp):
ATTTTGAAAACAAAAATAA
Found at i:498398 original size:21 final size:21
Alignment explanation
Indices: 498372--498413 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
498362 ATTTGAATAT
*
498372 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
498393 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
498414 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:500504 original size:2 final size:2
Alignment explanation
Indices: 500497--500588 Score: 184
Period size: 2 Copynumber: 46.0 Consensus size: 2
500487 TATAATTAAT
500497 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
500539 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
500581 TA TA TA TA
1 TA TA TA TA
500589 CAATCTGATT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 90 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:503497 original size:17 final size:17
Alignment explanation
Indices: 503475--503524 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
503465 GTGTTTAATG
503475 GGTTTTTGTTTCACTGT
1 GGTTTTTGTTTCACTGT
503492 GG-TTTTG----A-TG-
1 GGTTTTTGTTTCACTGT
503502 GGTTTTTGTTTCACTGT
1 GGTTTTTGTTTCACTGT
503519 GGTTTT
1 GGTTTT
503525 GATGATGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 14
0.65 0.00 0.35
Matches are distributed among these distances:
10 2 0.08
11 7 0.27
12 1 0.04
15 1 0.04
16 7 0.27
17 8 0.31
ACGTcount: A:0.06, C:0.08, G:0.28, T:0.58
Consensus pattern (17 bp):
GGTTTTTGTTTCACTGT
Found at i:503502 original size:27 final size:27
Alignment explanation
Indices: 503451--503528 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 27
503441 GTTGTTTTCC
* *
503451 TTTTGGTTTCGACTGT-G-TTTAATGGG
1 TTTTTGTTTC-ACTGTGGTTTTGATGGG
503477 TTTTTGTTTCACTGTGGTTTTGATGGG
1 TTTTTGTTTCACTGTGGTTTTGATGGG
503504 TTTTTGTTTCACTGTGGTTTTGATG
1 TTTTTGTTTCACTGTGGTTTTGATG
503529 ATGATTATGT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
25 5 0.10
26 10 0.21
27 33 0.69
ACGTcount: A:0.09, C:0.08, G:0.28, T:0.55
Consensus pattern (27 bp):
TTTTTGTTTCACTGTGGTTTTGATGGG
Found at i:504093 original size:4 final size:4
Alignment explanation
Indices: 504086--504155 Score: 97
Period size: 4 Copynumber: 17.0 Consensus size: 4
504076 AACAACAATA
504086 AAAT AAAT AAAT AAAT -AAT AAAT GAAAT AAAAT AAAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT -AAAT AAAT AAAT AAAT
*
504136 AAAT AGAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT
504156 TAAAAACATT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
3 3 0.05
4 45 0.74
5 13 0.21
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:504125 original size:34 final size:33
Alignment explanation
Indices: 504082--504159 Score: 113
Period size: 34 Copynumber: 2.3 Consensus size: 33
504072 AACAAACAAC
504082 AATAAAATAAATAAATAAAT-AATAAATGAAATAA
1 AATAAAATAAATAAATAAATAAATAAAT-AAAT-A
*
504116 AATAAAATAAATAAATAAATAAATAGATAAATA
1 AATAAAATAAATAAATAAATAAATAAATAAATA
*
504149 AATAAATTAAA
1 AATAAAATAAA
504160 AACATTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
33 11 0.27
34 24 0.59
35 6 0.15
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (33 bp):
AATAAAATAAATAAATAAATAAATAAATAAATA
Found at i:504137 original size:38 final size:38
Alignment explanation
Indices: 504086--504160 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
504076 AACAACAATA
504086 AAATAAATAAATAAATA-ATAAATGAAATAAAATAAAAT
1 AAATAAATAAATAAATAGATAAAT-AAATAAAATAAAAT
*
504124 AAATAAATAAATAAATAGATAAATAAATAAATTAAAA
1 AAATAAATAAATAAATAGATAAATAAATAAAATAAAA
504161 ACATTTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 29 0.83
39 6 0.17
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (38 bp):
AAATAAATAAATAAATAGATAAATAAATAAAATAAAAT
Found at i:504231 original size:38 final size:38
Alignment explanation
Indices: 504180--504407 Score: 165
Period size: 38 Copynumber: 6.2 Consensus size: 38
504170 AAACTATACA
*
504180 ATATATGTTTTAAAAAATAATTTTCAAAACCATATAAT
1 ATATATATTTTAAAAAATAATTTTCAAAACCATATAAT
* * *
504218 ATATATATTTTAAAAACTAATTTTC-AAACTATATGAT
1 ATATATATTTTAAAAAATAATTTTCAAAACCATATAAT
* * * * *
504255 ATATATTTTTTTCAAAAAT-GTTTTTAAAACTATATATTAT
1 ATATA-TATTTTAAAAAATAATTTTCAAAACCATATA--AT
* * *
504295 ATATATTTTTTAAAAAA-AGTTTTCAAAACGATAT-A-
1 ATATATATTTTAAAAAATAATTTTCAAAACCATATAAT
* * ** *
504330 ATATATATTTT-CAAAA-CATTTAAAAAACCCATATATT
1 ATATATATTTTAAAAAATAATTTTCAAAA-CCATATAAT
**
504367 ATATA-ATTTTTCAAAATAA-TTTC-AAA-C-TATAAT
1 ATATATATTTTAAAAAATAATTTTCAAAACCATATAAT
504400 ATATATAT
1 ATATATAT
504408 ATATATATAT
Statistics
Matches: 154, Mismatches: 25, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
33 10 0.06
34 14 0.09
35 15 0.10
36 9 0.06
37 31 0.20
38 43 0.28
39 25 0.16
40 7 0.05
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (38 bp):
ATATATATTTTAAAAAATAATTTTCAAAACCATATAAT
Found at i:504257 original size:37 final size:35
Alignment explanation
Indices: 504155--504409 Score: 162
Period size: 38 Copynumber: 7.0 Consensus size: 35
504145 AATAAATAAA
* * * * *
504155 TTAAAAACATTTTTAAAACTATACA-ATATATGTT
1 TTAAAAATAATTTTCAAACTATATATATATATATT
*
504189 TTAAAAAATAATTTTCAAAACCATATAATATATATATT
1 TT-AAAAATAATTTTC-AAACTATAT-ATATATATATT
*
504227 TTAAAAACTAATTTTCAAACTATATGATATATATTTTT
1 TTAAAAA-TAATTTTCAAACTATAT-ATATATA-TATT
** *
504265 TTCAAAAATGTTTTTAAAACTATATATTATATATATTTT
1 TT-AAAAATAATTTTCAAACTATATA-TATATATA--TT
*
504304 TTAAAAA-AAGTTTTCAAAACGATATA-ATATATATT
1 TTAAAAATAA-TTTTC-AAACTATATATATATATATT
* * ** *
504339 TTCAAAA-CATTTAAAAAACCCATATAT-TATATAATTT
1 TTAAAAATAATTT-TCAAA-CTATATATATATAT-A-TT
*
504376 TTCAAAATAA-TTTCAAACTATAATATATATATAT
1 TTAAAAATAATTTTCAAACTAT-ATATATATATAT
504410 ATATATATAT
Statistics
Matches: 175, Mismatches: 26, Indels: 39
0.73 0.11 0.16
Matches are distributed among these distances:
34 8 0.05
35 34 0.19
36 16 0.09
37 46 0.26
38 53 0.30
39 18 0.10
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.42
Consensus pattern (35 bp):
TTAAAAATAATTTTCAAACTATATATATATATATT
Found at i:504405 original size:2 final size:2
Alignment explanation
Indices: 504394--504426 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
504384 AATTTCAAAC
504394 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
504427 AATAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:504728 original size:22 final size:22
Alignment explanation
Indices: 504695--504740 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
504685 TTTTGTGCAC
**
504695 ATAACATTATATGTTTATTTTT
1 ATAACATTATATAATTATTTTT
504717 ATAA-ATTCATATAATTATTTTT
1 ATAACATT-ATATAATTATTTTT
504739 AT
1 AT
504741 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (22 bp):
ATAACATTATATAATTATTTTT
Found at i:505767 original size:42 final size:41
Alignment explanation
Indices: 505720--505831 Score: 125
Period size: 32 Copynumber: 2.9 Consensus size: 41
505710 TTCGCATTGT
*
505720 GATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGC
1 GATAGT-CAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
*
505762 G--A-T--AG-T--CG-AGCGATTTATTCCAAATTCGTTGC
1 GATAGTCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
505794 GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 GATAGTC-AAGTTCGCGTTGCGATTTATTCCAAATTCG
505832 CGTCGCAACG
Statistics
Matches: 57, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
32 23 0.40
33 2 0.04
34 1 0.02
35 2 0.04
36 2 0.04
38 2 0.04
39 2 0.04
40 1 0.02
41 2 0.04
42 20 0.35
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (41 bp):
GATAGTCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
Found at i:506428 original size:6 final size:6
Alignment explanation
Indices: 506402--506460 Score: 70
Period size: 6 Copynumber: 10.3 Consensus size: 6
506392 CGCCGTCCGT
* * *
506402 GTCG-G GTCG-G GTCG-G GTCGTT GTCGTT GTCGTT GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
506447 GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GT
506461 AATACGTGTC
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
5 14 0.27
6 37 0.73
ACGTcount: A:0.00, C:0.17, G:0.47, T:0.36
Consensus pattern (6 bp):
GTCGTG
Found at i:506752 original size:2 final size:2
Alignment explanation
Indices: 506742--506779 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
506732 CTATTAAAAA
*
506742 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
506780 TAATATTAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:509630 original size:4 final size:4
Alignment explanation
Indices: 509621--509650 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
509611 CACCCATTTC
509621 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
509651 TGAAATCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:511945 original size:43 final size:43
Alignment explanation
Indices: 511897--511984 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
511887 CACTAAACTG
* *
511897 TATTCAAATGATTATTTTAATTATTAAATTAATCAAATTCTTA
1 TATTCAAATAATTATTTTAATTATTAAATTAATCAAATTCATA
511940 TATTCAAATAATTATTTTAATTATTAAATTAATCAAATTCATA
1 TATTCAAATAATTATTTTAATTATTAAATTAATCAAATTCATA
511983 TA
1 TA
511985 AAGCAATCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.48
Consensus pattern (43 bp):
TATTCAAATAATTATTTTAATTATTAAATTAATCAAATTCATA
Found at i:513633 original size:21 final size:21
Alignment explanation
Indices: 513609--513648 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
513599 ACCGATTTTG
513609 CCGGTTTTCAGCCGGTTCACC
1 CCGGTTTTCAGCCGGTTCACC
*
513630 CCGGTTTTCAGTCGGTTCA
1 CCGGTTTTCAGCCGGTTCA
513649 TTGCCAGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.33, G:0.25, T:0.33
Consensus pattern (21 bp):
CCGGTTTTCAGCCGGTTCACC
Found at i:514876 original size:27 final size:27
Alignment explanation
Indices: 514831--514889 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
514821 TTAATTTAGG
*
514831 TTTAGGGTTTAGGTCTTATAAGA-TAGA
1 TTTAGGGTTTAAGTCTTATAA-ACTAGA
514858 TTTAGGGTTTATAGT-TTATAAACTAGA
1 TTTAGGGTTTA-AGTCTTATAAACTAGA
514885 TTTAG
1 TTTAG
514890 ATGTGTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 1 0.03
27 26 0.90
28 2 0.07
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.44
Consensus pattern (27 bp):
TTTAGGGTTTAAGTCTTATAAACTAGA
Found at i:526101 original size:3 final size:3
Alignment explanation
Indices: 526095--526119 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
526085 ATAATTTTTA
526095 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
526120 ATTTTGAATT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:528077 original size:21 final size:21
Alignment explanation
Indices: 528052--528096 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
528042 ATAGAATATA
528052 AAATTGAGGGACTAAATTGAT
1 AAATTGAGGGACTAAATTGAT
528073 AAATTGAGGGACTAAATTGAT
1 AAATTGAGGGACTAAATTGAT
528094 AAA
1 AAA
528097 AAAATATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.27
Consensus pattern (21 bp):
AAATTGAGGGACTAAATTGAT
Found at i:528490 original size:46 final size:45
Alignment explanation
Indices: 528418--528504 Score: 147
Period size: 46 Copynumber: 1.9 Consensus size: 45
528408 ATGAATATTT
*
528418 CCGATATTAACATTTCCGGTAGAAAAAATAACATTTTTGGTAGAGC
1 CCGATATTAACATTTCCGGTA-AAAAAATAACATTTTAGGTAGAGC
*
528464 CCGATATTAATATTTCCGGTAAAAAAATAACATTTTAGGTA
1 CCGATATTAACATTTCCGGTAAAAAAATAACATTTTAGGTA
528505 ACGATCTACC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 19 0.49
46 20 0.51
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (45 bp):
CCGATATTAACATTTCCGGTAAAAAAATAACATTTTAGGTAGAGC
Found at i:540829 original size:2 final size:2
Alignment explanation
Indices: 540824--540864 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
540814 ACATACACAC
540824 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
540865 AAGTGATAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:545312 original size:34 final size:31
Alignment explanation
Indices: 545272--545336 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
545262 TTTTCACATG
545272 TTTTTTTCCCAAAATACAATAAATAATGGAATAT
1 TTTTTTTCCCAAAAT--AA-AAATAATGGAATAT
***
545306 TTTTTTTTTGAAAATAAAAATAATGGAATAT
1 TTTTTTTCCCAAAATAAAAATAATGGAATAT
545337 AATTACGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 14 0.50
32 2 0.07
34 12 0.43
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.42
Consensus pattern (31 bp):
TTTTTTTCCCAAAATAAAAATAATGGAATAT
Found at i:555618 original size:23 final size:24
Alignment explanation
Indices: 555600--555645 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
555590 TATGTTCGAG
*
555600 AATAT-TAAACAAATGTGTTCACA
1 AATATATAAACAAATATGTTCACA
555623 AATATATAAACAAATATGTTCAC
1 AATATATAAACAAATATGTTCAC
555646 GAACGTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (24 bp):
AATATATAAACAAATATGTTCACA
Found at i:555637 original size:24 final size:23
Alignment explanation
Indices: 555600--555668 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
555590 TATGTTCGAG
*
555600 AATATTAAACAAATGTGTTCACA
1 AATATTAAACAAATATGTTCACA
*
555623 AATATATAAACAAATATGTTCACG
1 AATAT-TAAACAAATATGTTCACA
** * *
555647 AACGTTAAACGAATTTGTTCAC
1 AATATTAAACAAATATGTTCAC
555669 GAATGGTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.30
Consensus pattern (23 bp):
AATATTAAACAAATATGTTCACA
Found at i:555678 original size:23 final size:23
Alignment explanation
Indices: 555629--555678 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
555619 CACAAATATA
*
555629 TAAACAAATATGTTCACGAACGT
1 TAAACAAATATGTTCACGAACGG
* * *
555652 TAAACGAATTTGTTCACGAATGG
1 TAAACAAATATGTTCACGAACGG
555675 TAAA
1 TAAA
555679 TGAAACAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (23 bp):
TAAACAAATATGTTCACGAACGG
Found at i:559705 original size:29 final size:29
Alignment explanation
Indices: 559672--559739 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
559662 CCCAGAATCA
559672 GATAATTCATGAATTTTGGGTTAGGGTTT
1 GATAATTCATGAATTTTGGGTTAGGGTTT
559701 GATAATTCATGAATTTTGGGTTAGGGTTT
1 GATAATTCATGAATTTTGGGTTAGGGTTT
*
559730 GATCATTCAT
1 GATAATTCAT
559740 CTCCTTTTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (29 bp):
GATAATTCATGAATTTTGGGTTAGGGTTT
Found at i:563545 original size:12 final size:12
Alignment explanation
Indices: 563528--563555 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
563518 GGGTTAATAT
563528 GAAAAATGCTCA
1 GAAAAATGCTCA
563540 GAAAAATGCTCA
1 GAAAAATGCTCA
563552 GAAA
1 GAAA
563556 GCTTCATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.14, G:0.18, T:0.14
Consensus pattern (12 bp):
GAAAAATGCTCA
Found at i:570501 original size:2 final size:2
Alignment explanation
Indices: 570490--570523 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
570480 GCCTGAATTT
570490 TA TA -A 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
570524 TGCAGAGCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:574305 original size:183 final size:183
Alignment explanation
Indices: 573997--574362 Score: 732
Period size: 183 Copynumber: 2.0 Consensus size: 183
573987 GACTATGATG
573997 CTATTGCCATCACACTCGGTTATCGGAGAGGTATACGAGTAAGGGTTCGGTTGGATGTTCGTAGG
1 CTATTGCCATCACACTCGGTTATCGGAGAGGTATACGAGTAAGGGTTCGGTTGGATGTTCGTAGG
574062 GCGTTAAAACGCAAAAAAAGCTTACGCTGAAAAATGGGACAATCATGTATGCGCTATTCCAATAC
66 GCGTTAAAACGCAAAAAAAGCTTACGCTGAAAAATGGGACAATCATGTATGCGCTATTCCAATAC
574127 GAGAAGCTTAGACTTTTCTGCTTTATCTACGGTAAATTAGGACATTGTGAGAA
131 GAGAAGCTTAGACTTTTCTGCTTTATCTACGGTAAATTAGGACATTGTGAGAA
574180 CTATTGCCATCACACTCGGTTATCGGAGAGGTATACGAGTAAGGGTTCGGTTGGATGTTCGTAGG
1 CTATTGCCATCACACTCGGTTATCGGAGAGGTATACGAGTAAGGGTTCGGTTGGATGTTCGTAGG
574245 GCGTTAAAACGCAAAAAAAGCTTACGCTGAAAAATGGGACAATCATGTATGCGCTATTCCAATAC
66 GCGTTAAAACGCAAAAAAAGCTTACGCTGAAAAATGGGACAATCATGTATGCGCTATTCCAATAC
574310 GAGAAGCTTAGACTTTTCTGCTTTATCTACGGTAAATTAGGACATTGTGAGAA
131 GAGAAGCTTAGACTTTTCTGCTTTATCTACGGTAAATTAGGACATTGTGAGAA
574363 GTTCTGCCCT
Statistics
Matches: 183, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
183 183 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (183 bp):
CTATTGCCATCACACTCGGTTATCGGAGAGGTATACGAGTAAGGGTTCGGTTGGATGTTCGTAGG
GCGTTAAAACGCAAAAAAAGCTTACGCTGAAAAATGGGACAATCATGTATGCGCTATTCCAATAC
GAGAAGCTTAGACTTTTCTGCTTTATCTACGGTAAATTAGGACATTGTGAGAA
Found at i:575100 original size:20 final size:20
Alignment explanation
Indices: 575063--575101 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
575053 AGCTCTACAC
*
575063 TCTTCCACTCCTTTCCATAT
1 TCTTCCACTACTTTCCATAT
575083 TCTTCCA-TACTTTACCATA
1 TCTTCCACTACTTT-CCATA
575102 AGGTTCCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.44
Consensus pattern (20 bp):
TCTTCCACTACTTTCCATAT
Found at i:576561 original size:89 final size:89
Alignment explanation
Indices: 576456--576633 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
576446 TCGAATTTTA
576456 CGAGGAATTAAATGTTAGGAAAATAAACCGAGTACAAGTAATTTCCCTATAACCAGATTAGTGAG
1 CGAGGAATTAAATGTTAGGAAAATAAACCGAGTACAAGTAATTTCCCTATAACCAGATTAGTGAG
576521 AATGCGAAATAAAAGCGGAAAAAT
66 AATGCGAAATAAAAGCGGAAAAAT
576545 CGAGGAATTAAATGTTAGGAAAATAAACCGAGTACAAGTAATTTCCCTATAACCAGATTAGTGAG
1 CGAGGAATTAAATGTTAGGAAAATAAACCGAGTACAAGTAATTTCCCTATAACCAGATTAGTGAG
576610 AATGCGAAATAAAAGCGGAAAAAT
66 AATGCGAAATAAAAGCGGAAAAAT
576634 AATACCCGAA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.21
Consensus pattern (89 bp):
CGAGGAATTAAATGTTAGGAAAATAAACCGAGTACAAGTAATTTCCCTATAACCAGATTAGTGAG
AATGCGAAATAAAAGCGGAAAAAT
Found at i:580981 original size:16 final size:17
Alignment explanation
Indices: 580960--580993 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
580950 CCGACCGAAT
580960 TTCACTATTCACG-GAA
1 TTCACTATTCACGTGAA
580976 TTCACTATTCACGTGAA
1 TTCACTATTCACGTGAA
580993 T
1 T
580994 AGTAATGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (17 bp):
TTCACTATTCACGTGAA
Found at i:592827 original size:37 final size:37
Alignment explanation
Indices: 592754--592828 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
592744 GTTGAAAAAT
* *
592754 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
592791 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
592828 A
1 A
592829 AGATTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:593740 original size:22 final size:20
Alignment explanation
Indices: 593715--593842 Score: 71
Period size: 20 Copynumber: 6.0 Consensus size: 20
593705 GGCATTTTAT
593715 TTTATATTATTAAAATATATTA
1 TTTA-ATTATTAAAA-ATATTA
*
593737 TTTAATTATTAAAAATATCA
1 TTTAATTATTAAAAATATTA
** * *
593757 AATAATTATAAAAACATACTA
1 TTTAATTATTAAAA-ATATTA
* *
593778 TTTTAACCGT-TTAAAATATAATA
1 -TTTAA--TTATTAAAA-ATATTA
**
593801 AATAATTA-TAAAATATATTA
1 TTTAATTATTAAAA-ATATTA
593821 TTTTAATTATTTAAAAATATTA
1 -TTTAATTA-TTAAAAATATTA
593843 ATATATTCAT
Statistics
Matches: 80, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
20 28 0.35
21 20 0.25
22 16 0.20
23 15 0.19
24 1 0.01
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.45
Consensus pattern (20 bp):
TTTAATTATTAAAAATATTA
Found at i:593838 original size:44 final size:44
Alignment explanation
Indices: 593720--593845 Score: 136
Period size: 43 Copynumber: 2.9 Consensus size: 44
593710 TTTATTTTAT
*
593720 ATTATTAAAATATATTA-TTTAATTA-TTAAAAATAT--CAAATA
1 ATTA-TAAAATATATTATTTTAATTATTTAAAAATATAATAAATA
* * ***
593761 ATTATAAAAACATACTATTTTAACCGTTT-AAAATATAATAAATA
1 ATTAT-AAAATATATTATTTTAATTATTTAAAAATATAATAAATA
593805 ATTATAAAATATATTATTTTAATTATTTAAAAATATTAATA
1 ATTATAAAATATATTATTTTAATTATTTAAAAATA-TAATA
593846 TATTCATATT
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
40 1 0.01
41 13 0.19
42 12 0.18
43 20 0.30
44 16 0.24
45 5 0.07
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (44 bp):
ATTATAAAATATATTATTTTAATTATTTAAAAATATAATAAATA
Found at i:597148 original size:27 final size:27
Alignment explanation
Indices: 597075--597156 Score: 92
Period size: 27 Copynumber: 2.9 Consensus size: 27
597065 ACTTAAAAAA
597075 TATTTTTATTTTAATTTAGTAAATATATTT
1 TATTTTTATTTTAATTT--TAAA-ATATTT
* **
597105 TATTATTAAATTAATTTTAAAATATTT
1 TATTTTTATTTTAATTTTAAAATATTT
* *
597132 TATTTTTATTTTCATTTAAAAATAT
1 TATTTTTATTTTAATTTTAAAATAT
597157 ATATTTTATG
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
27 26 0.59
28 4 0.09
30 14 0.32
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (27 bp):
TATTTTTATTTTAATTTTAAAATATTT
Found at i:597149 original size:57 final size:58
Alignment explanation
Indices: 597075--597187 Score: 149
Period size: 58 Copynumber: 2.0 Consensus size: 58
597065 ACTTAAAAAA
** * *
597075 TATTTTTATTTTAATTTAGTAA-ATATATTTTAT-TATTAAATTAATTTTAAAATATTT
1 TATTTTTATTTTAATTTAAAAATATATATTTTATGT-TAAAATTAATTTAAAAATATTT
* *
597132 TATTTTTATTTTCATTTAAAAATATATATTTTATGTTAAAATTTATTTAAAAATAT
1 TATTTTTATTTTAATTTAAAAATATATATTTTATGTTAAAATTAATTTAAAAATAT
597188 GACTAAATTG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 19 0.40
58 28 0.58
59 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.58
Consensus pattern (58 bp):
TATTTTTATTTTAATTTAAAAATATATATTTTATGTTAAAATTAATTTAAAAATATTT
Found at i:597359 original size:31 final size:31
Alignment explanation
Indices: 597296--597363 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
597286 TAATGACAGC
** *
597296 ATCTTAATTAAATAAAAATGAAATTGAACAT
1 ATCTTAATTAAATAAAAACAAAAGTGAACAT
**
597327 ATCTTAATTAAATAAAAACAAAAGTGGTCAT
1 ATCTTAATTAAATAAAAACAAAAGTGAACAT
597358 ATCTTA
1 ATCTTA
597364 TGTTTTTTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.32
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAGTGAACAT
Found at i:599803 original size:15 final size:15
Alignment explanation
Indices: 599785--599815 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
599775 GTATGATTAT
599785 AAGTGAAAAAATGAA
1 AAGTGAAAAAATGAA
599800 AAGTGAAAAAATGAA
1 AAGTGAAAAAATGAA
599815 A
1 A
599816 TTTAATGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.13
Consensus pattern (15 bp):
AAGTGAAAAAATGAA
Found at i:611717 original size:33 final size:35
Alignment explanation
Indices: 611652--611717 Score: 84
Period size: 33 Copynumber: 1.9 Consensus size: 35
611642 TTTTTAATCT
* *
611652 TTATATATCTTTCCATTGATCGTTTTATTTATTCA
1 TTATATATCTTTCAATTGATCGTTTTAATTATTCA
611687 TTATATAT-TTTCAATT-ATC-TTTCTAATTATT
1 TTATATATCTTTCAATTGATCGTTT-TAATTATT
611718 ATATTCTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 3 0.11
33 10 0.36
34 7 0.25
35 8 0.29
ACGTcount: A:0.26, C:0.12, G:0.03, T:0.59
Consensus pattern (35 bp):
TTATATATCTTTCAATTGATCGTTTTAATTATTCA
Found at i:612469 original size:2 final size:2
Alignment explanation
Indices: 612464--612507 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
612454 AATCACCAAT
612464 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
612506 TA
1 TA
612508 ATAGTGGACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:613454 original size:2 final size:2
Alignment explanation
Indices: 613447--613475 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
613437 GGTAGGTATT
613447 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 T
613476 TGAGCTGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:614261 original size:28 final size:28
Alignment explanation
Indices: 614225--614288 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
614215 ATAAGAACAG
*
614225 TTTAGTCAAATATACATTCTAATAATCT
1 TTTATTCAAATATACATTCTAATAATCT
*
614253 TTTATTCAAATATACATTTTAATAATCT
1 TTTATTCAAATATACATTCTAATAATCT
614281 TTTATTCA
1 TTTATTCA
614289 TTTAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (28 bp):
TTTATTCAAATATACATTCTAATAATCT
Found at i:627578 original size:32 final size:32
Alignment explanation
Indices: 627493--627579 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
627483 TGATCATTAT
*
627493 AATT-TTATAAAGGGGTCATTAAA-TTTATCA
1 AATTATTATAAAAGGGTCATTAAATTTTATCA
* * * *
627523 AAATATTACAAAATGGTTATTAAATTTTATCA
1 AATTATTATAAAAGGGTCATTAAATTTTATCA
*
627555 AATTATTATAAAAGGGTCCTTAAAT
1 AATTATTATAAAAGGGTCATTAAAT
627580 GATTGAATTT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
30 3 0.07
31 15 0.33
32 27 0.60
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (32 bp):
AATTATTATAAAAGGGTCATTAAATTTTATCA
Found at i:628232 original size:21 final size:21
Alignment explanation
Indices: 628192--628232 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
628182 AGTAACACCC
***
628192 AATAATAATATTTTCGGTAAA
1 AATAATAATATTTAAAGTAAA
628213 AATAATAATATTTAAAGTAA
1 AATAATAATATTTAAAGTAA
628233 CATTTTACTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (21 bp):
AATAATAATATTTAAAGTAAA
Found at i:629811 original size:30 final size:30
Alignment explanation
Indices: 629755--629811 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
629745 ATAAACATTA
* *
629755 AAAAAATTAGATCTCTAATAAAAAATACAG
1 AAAAAATTAGAACTCTAACAAAAAATACAG
*
629785 AAAAAATTA-AACTCATAACAATAAATA
1 AAAAAATTAGAACTC-TAACAAAAAATA
629812 AATATTAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 4 0.17
30 19 0.83
ACGTcount: A:0.63, C:0.11, G:0.04, T:0.23
Consensus pattern (30 bp):
AAAAAATTAGAACTCTAACAAAAAATACAG
Found at i:630282 original size:29 final size:29
Alignment explanation
Indices: 630224--630313 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
630214 TTGTATTATT
* *
630224 TTAAATTTTCA-TTTATAAATCA-ATAGATA
1 TTAAATTTT-ATTTTATATAT-ATATATATA
*
630253 TTAAATTTTTTTTTATATATATATATATA
1 TTAAATTTTATTTTATATATATATATATA
** *
630282 TTTGATTTTAATTTTAT-TAGATAT-TATA
1 TTAAATTTT-ATTTTATATATATATATATA
630310 TTAA
1 TTAA
630314 TAATATGAAC
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
28 7 0.14
29 36 0.73
30 6 0.12
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (29 bp):
TTAAATTTTATTTTATATATATATATATA
Found at i:636405 original size:15 final size:15
Alignment explanation
Indices: 636385--636414 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
636375 CTCTAATTCA
636385 ATACAAATTTTCACT
1 ATACAAATTTTCACT
636400 ATACAAATTTTCACT
1 ATACAAATTTTCACT
636415 TTAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (15 bp):
ATACAAATTTTCACT
Found at i:636422 original size:15 final size:15
Alignment explanation
Indices: 636389--636422 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
636379 AATTCAATAC
*
636389 AAATTTTCACTATAC
1 AAATTTTCACTATAA
*
636404 AAATTTTCACTTTAA
1 AAATTTTCACTATAA
636419 AAAT
1 AAAT
636423 ATAATTGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTTTCACTATAA
Found at i:638581 original size:12 final size:11
Alignment explanation
Indices: 638560--638596 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
638550 AAGATGATGA
638560 AGAAAAGAAGG
1 AGAAAAGAAGG
638571 AGAAGAAGAAGG
1 AGAA-AAGAAGG
638583 AAGAAAAGAAGG
1 -AGAAAAGAAGG
638595 AG
1 AG
638597 GTAGGCATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.25
12 14 0.58
13 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (11 bp):
AGAAAAGAAGG
Found at i:638872 original size:21 final size:21
Alignment explanation
Indices: 638846--638887 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
638836 GAAGAAAAAG
638846 ATGAAGTAGCCAACCTATGCC
1 ATGAAGTAGCCAACCTATGCC
*
638867 ATGAAGTAGTCAACCTATGCC
1 ATGAAGTAGCCAACCTATGCC
638888 TCATGACCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
ATGAAGTAGCCAACCTATGCC
Found at i:639120 original size:20 final size:20
Alignment explanation
Indices: 639056--639109 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
639046 AATGATTTGG
639056 TTTTGA-AATCAAAAGTTAA
1 TTTTGAGAATCAAAAGTTAA
639075 TTTTGAGAATCAAAAGTTAA
1 TTTTGAGAATCAAAAGTTAA
639095 TTTTGAGAATCAAAA
1 TTTTGAGAATCAAAA
639110 TGAAATTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 6 0.18
20 28 0.82
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (20 bp):
TTTTGAGAATCAAAAGTTAA
Found at i:643938 original size:2 final size:2
Alignment explanation
Indices: 643931--643961 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
643921 GACTTACTGT
643931 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
643962 TTTCTTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:652894 original size:27 final size:27
Alignment explanation
Indices: 652864--652916 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
652854 TTCATGAAGA
652864 TGTAGATTCAGTATGATGTATGATATG
1 TGTAGATTCAGTATGATGTATGATATG
652891 TGTAGATTCAGTATGATGTATGATAT
1 TGTAGATTCAGTATGATGTATGATAT
652917 TTAACCACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.04, G:0.25, T:0.42
Consensus pattern (27 bp):
TGTAGATTCAGTATGATGTATGATATG
Done.