Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007711.1 Hibiscus syriacus cultivar Beakdansim tig00109926_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: 1768490
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 3 of 8
Found at i:413049 original size:21 final size:21
Alignment explanation
Indices: 413025--413064 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
413015 TTTATTTTAT
413025 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
413046 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
413065 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:413112 original size:33 final size:33
Alignment explanation
Indices: 413059--413157 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
413049 TTTGTTTCAA
413059 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
413091 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
413124 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
413157 T
1 T
413158 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:413186 original size:13 final size:13
Alignment explanation
Indices: 413143--413197 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
413133 TTGGAAGTAT
413143 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
413156 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
413170 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
413183 TTAAGTATTTGAA
1 TTAAGTATTTCAA
413196 TT
1 TT
413198 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:413419 original size:21 final size:21
Alignment explanation
Indices: 413393--413449 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
413383 TAGAGCGTGG
*
413393 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
413414 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
413435 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
413450 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:425684 original size:3 final size:3
Alignment explanation
Indices: 425676--425716 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
425666 ATTTTTTATT
*
425676 TAA TAA TAA TAA T-A TAA TAA -AT TAA TAA TTAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
425717 AATGAACTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 3 0.09
3 27 0.82
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:425968 original size:76 final size:76
Alignment explanation
Indices: 425842--426328 Score: 929
Period size: 76 Copynumber: 6.4 Consensus size: 76
425832 GAAATGTTGA
425842 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
425907 AGGCTTTTTGG
66 AGGCTTTTTGG
425918 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
425983 AGGCTTTTTGG
66 AGGCTTTTTGG
425994 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
426059 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
426070 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAGAACATCAAAAAGCTCTCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
426135 AGGCTTTTTGG
66 AGGCTTTTTGG
426146 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
426211 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
426222 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAGAACATCAAAAAGCTCTCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
426287 AGGCTTTTTGG
66 AGGCTTTTTGG
*
426298 AAACATCATGCACTGAAGGACTTATAGATGA
1 AAACATCATGCACTGAAGGACTTACAGATGA
426329 GGGAAATAGT
Statistics
Matches: 404, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 404 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:426994 original size:113 final size:113
Alignment explanation
Indices: 426719--427706 Score: 1423
Period size: 113 Copynumber: 8.8 Consensus size: 113
426709 ATCTCCTTCT
* * * *
426719 GTGATAGAATTA-TGCAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTTTTCCTTCTTCA
1 GTGAT-GAATTAGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* * **
426783 GATGAATTCTTCTCATTATGAA-CTTCTCTGG-AAAAGCTGCTCCATCAA
65 GATGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAA-ATAATCCATCAA
* * *
426831 GTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAG
1 GTGATGAATTAGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
426896 ATGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAA
66 ATGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAA
426944 GTGATGAATTCAGA-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
1 GTGATGAATT-AGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* * *
427008 GATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAATGATGATCCATCAA
65 GATGAGTTCTTCTCATTATGAACCTTCTCTGGCAAA-AATAATCCATCAA
* * * *
427057 ATAAT-AGATTCA-AGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTTC
1 GTGATGA-ATT-AGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* *
427120 AGATAAGTTCTTCTCATTATGAACTTTCTCTGGCAAAAATAATCCATC-A
64 AGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAA
* * *
427169 GATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
1 G-TGATGAATTAGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
427234 GATGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAA
65 GATGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAA
427283 GTGATGAATTCAGA-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
1 GTGATGAATT-AGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* * *
427347 GATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAATGATGATCCATCAA
65 GATGAGTTCTTCTCATTATGAACCTTCTCTGGCAAA-AATAATCCATCAA
* * * *
427396 ATAAT-AGATTCA-AGTAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTC
1 GTGATGA-ATT-AGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
427459 AGATGAGTTCTTCTCATTATGAA-CTTCTCTGGCAAAAATAATCCATC-A
64 AGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAA
* * *
427507 GATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
1 G-TGATGAATTAGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
427572 GATGAGTTCTTCTCATTATGAA-CTTCTCTGGCAAAAATAATCCATC-A
65 GATGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAA
* * *
427619 GATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
1 G-TGATGAATTAGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
427684 GATGAGTTCTTCTCATTATGAAC
65 GATGAGTTCTTCTCATTATGAAC
427707 TCGACCTGGA
Statistics
Matches: 806, Mismatches: 49, Indels: 41
0.90 0.05 0.05
Matches are distributed among these distances:
111 5 0.01
112 294 0.36
113 494 0.61
114 13 0.02
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (113 bp):
GTGATGAATTAGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAA
Found at i:427214 original size:339 final size:338
Alignment explanation
Indices: 426734--427707 Score: 1726
Period size: 339 Copynumber: 2.9 Consensus size: 338
426724 AGAATTATGC
* * *
426734 AAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTTTTCCTTCTTCAGATGAA-TTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-AAGTTCTTCTCA
* **
426798 TTATGAACTTCTCTGG-AAAAGCTGCTCCATCA-AGTGATGGATTTGAGCAAAAGGTTGAACAAA
65 TTATGAACTTCTCTGGCAAAA-ATAATCCATCAGA-TGATGGATTTGAGCAAAAGGTTGAACAAA
* *
426861 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
128 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
426926 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
193 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
426991 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCA
258 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCA
427056 AATAATAGATTCAAGT
323 AATAATAGATTCAAGT
*
427072 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATAAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
427137 TATGAACTTTCTCTGGCAAAAATAATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAATT
66 TATGAAC-TTCTCTGGCAAAAATAATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAATT
427202 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGC
130 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGC
427267 AAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
195 AAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
427332 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAA
260 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAA
427397 TAATAGATTCAAGT
325 TAATAGATTCAAGT
* *
427411 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
427476 TATGAACTTCTCTGGCAAAAATAATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAATTC
66 TATGAACTTCTCTGGCAAAAATAATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAATTC
427541 TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTCTCTGGCA
131 TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCA
* * *
427605 AAAATAATCCATC-AGATGATGGATT-TGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATT
196 AAAATAATCCATCAAG-TGATGAATTCAGA-CAAAAGGTTGAACAAATTCTTCTCATTATGAACT
427668 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
259 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
427708 CGACCTGGAA
Statistics
Matches: 615, Mismatches: 15, Indels: 13
0.96 0.02 0.02
Matches are distributed among these distances:
336 4 0.01
337 107 0.17
338 176 0.29
339 323 0.53
340 5 0.01
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (338 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
TATGAACTTCTCTGGCAAAAATAATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAATTC
TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCA
AAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAAT
AATAGATTCAAGT
Found at i:428169 original size:22 final size:22
Alignment explanation
Indices: 428144--428198 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
428134 GATAAAGCTT
*
428144 TCATCTTTGAAAAGGGAATCTG
1 TCATCTTTGAAAAGGGAATCTA
*
428166 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGGGAATCTA
428188 TCATCTTTGAA
1 TCATCTTTGAA
428199 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGGGAATCTA
Found at i:430887 original size:103 final size:107
Alignment explanation
Indices: 430762--431046 Score: 384
Period size: 103 Copynumber: 2.6 Consensus size: 107
430752 CCTACCGAAT
*
430762 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAG
430827 CAAATTCATCTTTCAAATCCAATGA-TT-GG-T-TACCAAAC
66 CAAATTCATCTTTCAAATCCAATGATTTGGGTTATACCAAAC
* *
430865 CAGATCAGATAACTCAAAGAACAC-TCTAAGAAGATGCTA-TGGAGTCTTCTTCTTTCTACTATG
1 CAGATCAGATAACTCAAAGAACACTTC-CAGAAGATGCTATTGG-GTCTTCTTATTTCTACTATG
*
430928 AGCAAATTCATCTTTCAAATCTAATGATTGGTTTTTGGGGTTTATACCAAAC
64 AGCAAATTCATCTTTCAAATCCAATGA------TTT-GGG-TTATACCAAAC
* *
430980 CAGATCAGATAACTCAAAGAACACTTCCAGAATATGCTATTGAGTCTTCTTATTTCTACTATGAG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAG
431045 CA
66 CA
431047 CATGGCACTT
Statistics
Matches: 158, Mismatches: 8, Indels: 20
0.85 0.04 0.11
Matches are distributed among these distances:
102 5 0.03
103 79 0.50
110 2 0.01
112 2 0.01
114 1 0.01
115 65 0.41
116 4 0.03
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.32
Consensus pattern (107 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAG
CAAATTCATCTTTCAAATCCAATGATTTGGGTTATACCAAAC
Found at i:433299 original size:6 final size:6
Alignment explanation
Indices: 433285--433329 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
433275 CTTGATTCGA
* *
433285 TTTTCC TTTTTC TTTTT- TTTTTC TTTTTC TTCTTC TTCTTTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC TTT
433330 GCTGGATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 5 0.15
6 24 0.71
7 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:433310 original size:17 final size:19
Alignment explanation
Indices: 433285--433329 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
433275 CTTGATTCGA
*
433285 TTTTCCTTTTTCTT-TT-T
1 TTTTTCTTTTTCTTCTTCT
433302 TTTTTCTTTTTCTTCTTCT
1 TTTTTCTTTTTCTTCTTCT
*
433321 TCTTTCTTT
1 TTTTTCTTT
433330 GCTGGATGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 13 0.54
18 2 0.08
19 9 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTTCTTCTTCT
Found at i:439640 original size:3 final size:3
Alignment explanation
Indices: 439632--439672 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
439622 ATTTTTTATT
*
439632 TAA TAA TAA TAA T-A TAA TAA -AT TAA TAA TTAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
439673 AATGAACTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 3 0.09
3 27 0.82
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:443620 original size:90 final size:90
Alignment explanation
Indices: 443467--443848 Score: 524
Period size: 90 Copynumber: 4.3 Consensus size: 90
443457 TTTACTCACG
* * *
443467 GCATTATGCCAATTGTTGTAGGCTCTTTGCTGTCCAGTTTTTGTTGTCGAGCCGAATGTTTAGAC
1 GCATTATACCAATTGTTATAGGCCCTTTGCTGTCCAGTTTTTGTTGTCGAGCCGAATGTTTAGAC
* *
443532 CAATTTCTTTCATCCATTAATTACT
66 CAATTTCATTCATCCATTAATTACA
* *
443557 GCATTATACCAATTGTTATAGGCCCTTTGCTGTCCGGTTTTTGTCGTCGAGCCGAATGTTTAGAC
1 GCATTATACCAATTGTTATAGGCCCTTTGCTGTCCAGTTTTTGTTGTCGAGCCGAATGTTTAGAC
*
443622 CAATTTCATTCATCCATTACTTACA
66 CAATTTCATTCATCCATTAATTACA
* * * * *
443647 GCATCATACCAATTGTTATAGGCCCTTTTCTGTCCAGTTTTTGGTGTCAAGTCGAATGTTTAGAC
1 GCATTATACCAATTGTTATAGGCCCTTTGCTGTCCAGTTTTTGTTGTCGAGCCGAATGTTTAGAC
*
443712 CAATTTCATTCATCC----ATTACT
66 CAATTTCATTCATCCATTAATTACA
* * ** *
443733 GCATTATACCAATTGTTATAGACCCTTTGCTGTCCAG-TTTTGTTGTCGAGAC-AATGGCTAGAT
1 GCATTATACCAATTGTTATAGGCCCTTTGCTGTCCAGTTTTTGTTGTCGAGCCGAATGTTTAGAC
* *
443796 CATTTTCATTCATCCATTACTTACA
66 CAATTTCATTCATCCATTAATTACA
*
443821 GCATTATACCAGTTGTTATAGGCCCTTT
1 GCATTATACCAATTGTTATAGGCCCTTT
443849 TTTGTGCTTC
Statistics
Matches: 257, Mismatches: 31, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
84 22 0.09
85 12 0.05
86 38 0.15
88 30 0.12
90 155 0.60
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.40
Consensus pattern (90 bp):
GCATTATACCAATTGTTATAGGCCCTTTGCTGTCCAGTTTTTGTTGTCGAGCCGAATGTTTAGAC
CAATTTCATTCATCCATTAATTACA
Found at i:445941 original size:16 final size:16
Alignment explanation
Indices: 445917--445948 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
445907 AGCATTATTT
445917 ACTTCAAAATAATATG
1 ACTTCAAAATAATATG
*
445933 ACTTGAAAATAATATG
1 ACTTCAAAATAATATG
445949 TGATAGTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.31
Consensus pattern (16 bp):
ACTTCAAAATAATATG
Found at i:446903 original size:2 final size:2
Alignment explanation
Indices: 446896--446926 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
446886 CATAAACAAT
*
446896 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
446927 GTTAAACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:448934 original size:23 final size:23
Alignment explanation
Indices: 448908--448953 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
448898 TTTAGGGATG
*
448908 AAAATCATTAGTTAATAAATGCT
1 AAAATCATTAGATAATAAATGCT
* * *
448931 AAAATTATTTGATATTAAATGCT
1 AAAATCATTAGATAATAAATGCT
448954 CACACCCTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.39
Consensus pattern (23 bp):
AAAATCATTAGATAATAAATGCT
Found at i:450839 original size:29 final size:29
Alignment explanation
Indices: 450779--450839 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
450769 TTCCCTTACA
* *
450779 ATTAAAAATTACAAAATAGTCACATGAGT
1 ATTAAAAATTACAAAATAGTCACACGACT
* *
450808 ATTAAAAGTTACAAAATGGTCATC-CGACT
1 ATTAAAAATTACAAAATAGTCA-CACGACT
450837 ATT
1 ATT
450840 CATATGTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (29 bp):
ATTAAAAATTACAAAATAGTCACACGACT
Found at i:451579 original size:15 final size:16
Alignment explanation
Indices: 451543--451586 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
451533 AAGTTATATT
*
451543 TATTAAAGTGGAGAAG
1 TATTAAAGTAGAGAAG
*
451559 -AATAAAGTAGA-AAG
1 TATTAAAGTAGAGAAG
451573 TATTAAAGTAGAGA
1 TATTAAAGTAGAGA
451587 GAGAAATAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 3 0.13
15 19 0.83
16 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.25, T:0.23
Consensus pattern (16 bp):
TATTAAAGTAGAGAAG
Found at i:452555 original size:17 final size:18
Alignment explanation
Indices: 452533--452571 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
452523 TGTAGTTTTA
452533 TTTTAA-AAATCATTATT
1 TTTTAATAAATCATTATT
*
452550 TTTTAATTAAATCCTTATT
1 TTTTAA-TAAATCATTATT
452569 TTT
1 TTT
452572 ATTGGGTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTAATAAATCATTATT
Found at i:455087 original size:17 final size:18
Alignment explanation
Indices: 455065--455099 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
455055 GCATATAAAA
455065 TTTAAAAATTATT-TTAT
1 TTTAAAAATTATTATTAT
455082 TTTAAAAATTATTATTAT
1 TTTAAAAATTATTATTAT
455100 AATTAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAAAAATTATTATTAT
Found at i:460489 original size:49 final size:49
Alignment explanation
Indices: 460436--460533 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
460426 AAAAGAATAT
460436 CATAGCCCGAGTTCAAACACTAATAGGTGTATGAACATTCATTTTCAAA
1 CATAGCCCGAGTTCAAACACTAATAGGTGTATGAACATTCATTTTCAAA
*
460485 CATAGCCCGAGTTCAATCACTAATAGGTGTATGAACATTCATTTTCAAA
1 CATAGCCCGAGTTCAAACACTAATAGGTGTATGAACATTCATTTTCAAA
460534 TGGTTGAGAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (49 bp):
CATAGCCCGAGTTCAAACACTAATAGGTGTATGAACATTCATTTTCAAA
Found at i:469321 original size:2 final size:2
Alignment explanation
Indices: 469314--469351 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
469304 TGTGTTGATA
469314 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
469352 CTATCCTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:484880 original size:30 final size:30
Alignment explanation
Indices: 484844--484913 Score: 115
Period size: 30 Copynumber: 2.3 Consensus size: 30
484834 AGCTGAGATG
484844 TGCAGTTTTTGCTCAT-TATATATCATTCGA
1 TGCAGTTTTTGCTCATGTA-ATATCATTCGA
*
484874 TGCAGTTTTTGCTCATGTAATGTCATTCGA
1 TGCAGTTTTTGCTCATGTAATATCATTCGA
484904 TGCAGTTTTT
1 TGCAGTTTTT
484914 ACCACAAGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
30 36 0.95
31 2 0.05
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.47
Consensus pattern (30 bp):
TGCAGTTTTTGCTCATGTAATATCATTCGA
Found at i:495036 original size:15 final size:16
Alignment explanation
Indices: 495004--495039 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
494994 TAAATCAAAC
495004 ATAATTTAACTCTAAA
1 ATAATTTAACTCTAAA
*
495020 ATAATTTGACT-TAAA
1 ATAATTTAACTCTAAA
495035 ATAAT
1 ATAAT
495040 CCGACTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (16 bp):
ATAATTTAACTCTAAA
Found at i:497750 original size:14 final size:15
Alignment explanation
Indices: 497710--497751 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
497700 TCGATTAAAT
497710 GAATTTAAGGGATTGA
1 GAATTT-AGGGATTGA
*
497726 GTATTTA-GGATTGA
1 GAATTTAGGGATTGA
497740 -AATTTAGGGATT
1 GAATTTAGGGATT
497752 TAAAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 5 0.22
14 12 0.52
15 1 0.04
16 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.29, T:0.38
Consensus pattern (15 bp):
GAATTTAGGGATTGA
Found at i:501847 original size:14 final size:15
Alignment explanation
Indices: 501825--501857 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
501815 ATTTAATTAG
501825 TTTTAATTAAATAAA
1 TTTTAATTAAATAAA
501840 TTTT-ATTAAATAAA
1 TTTTAATTAAATAAA
501854 TTTT
1 TTTT
501858 CTCACCAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTAATTAAATAAA
Found at i:502193 original size:11 final size:11
Alignment explanation
Indices: 502169--502198 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
502159 AATATTTTTA
502169 TTTAAATTATT
1 TTTAAATTATT
502180 TTTATAATTATT
1 TTTA-AATTATT
502192 TTTAAAT
1 TTTAAAT
502199 AATAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTAAATTATT
Found at i:502231 original size:26 final size:28
Alignment explanation
Indices: 502195--502252 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 28
502185 AATTATTTTT
*
502195 AAATAATAATATA-T-AAATTATATTA-A
1 AAATAAAAATATATTAAAATTAT-TTAGA
502221 AAATAAAAATATATTAAAATTATTTAGA
1 AAATAAAAATATATTAAAATTATTTAGA
502249 AAAT
1 AAAT
502253 TCAAATCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 12 0.43
27 4 0.14
28 12 0.43
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (28 bp):
AAATAAAAATATATTAAAATTATTTAGA
Found at i:502341 original size:2 final size:2
Alignment explanation
Indices: 502334--502410 Score: 51
Period size: 2 Copynumber: 42.0 Consensus size: 2
502324 ACTATAGTTA
* *
502334 AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT AT TT AT -T AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
502373 AT TT GT -T TT A- AT A- AT TT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
502411 GTGTCAAATA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
1 7 0.12
2 52 0.88
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:508827 original size:31 final size:30
Alignment explanation
Indices: 508792--508857 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
508782 TATTTACGGA
*
508792 TTGTTA-GAGTTTGTTA-TGGTTTGTTATTAG
1 TTGTTATGAG-TTGTTATTAGTTTGTTA-TAG
*
508822 CTTGTTATTAGTTGTTATTAGTTTGTTATAG
1 -TTGTTATGAGTTGTTATTAGTTTGTTATAG
508853 TTGTT
1 TTGTT
508858 GGTTACTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 5 0.16
31 15 0.48
32 11 0.35
ACGTcount: A:0.17, C:0.02, G:0.23, T:0.59
Consensus pattern (30 bp):
TTGTTATGAGTTGTTATTAGTTTGTTATAG
Found at i:508828 original size:11 final size:10
Alignment explanation
Indices: 508812--508857 Score: 67
Period size: 11 Copynumber: 4.5 Consensus size: 10
508802 TTGTTATGGT
508812 TTGTTATTAG
1 TTGTTATTAG
508822 CTTGTTATTAG
1 -TTGTTATTAG
508833 TTGTTATTAG
1 TTGTTATTAG
508843 TTTGTTA-TAG
1 -TTGTTATTAG
508853 TTGTT
1 TTGTT
508858 GGTTACTTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.15
10 13 0.38
11 16 0.47
ACGTcount: A:0.17, C:0.02, G:0.20, T:0.61
Consensus pattern (10 bp):
TTGTTATTAG
Found at i:508828 original size:21 final size:20
Alignment explanation
Indices: 508802--508857 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
508792 TTGTTAGAGT
*
508802 TTGTTATGGTTTGTTATTAGC
1 TTGTTATAG-TTGTTATTAGC
*
508823 TTGTTATTAGTTGTTATTAGT
1 TTGTTA-TAGTTGTTATTAGC
508844 TTGTTATAGTTGTT
1 TTGTTATAGTTGTT
508858 GGTTACTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 8 0.25
21 22 0.69
22 2 0.06
ACGTcount: A:0.16, C:0.02, G:0.21, T:0.61
Consensus pattern (20 bp):
TTGTTATAGTTGTTATTAGC
Found at i:508853 original size:10 final size:11
Alignment explanation
Indices: 508799--508854 Score: 73
Period size: 10 Copynumber: 5.4 Consensus size: 11
508789 GGATTGTTAG
508799 AGTTTGTTA-T
1 AGTTTGTTATT
*
508809 GGTTTGTTATT
1 AGTTTGTTATT
*
508820 AGCTTGTTATT
1 AGTTTGTTATT
508831 AG-TTGTTATT
1 AGTTTGTTATT
508841 AGTTTGTTA-T
1 AGTTTGTTATT
508851 AGTT
1 AGTT
508855 GTTGGTTACT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
10 23 0.56
11 18 0.44
ACGTcount: A:0.18, C:0.02, G:0.21, T:0.59
Consensus pattern (11 bp):
AGTTTGTTATT
Found at i:510468 original size:21 final size:20
Alignment explanation
Indices: 510443--510498 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
510433 ATGTTAGAGT
*
510443 TTGTTATGGTTTGTTATTAGC
1 TTGTTATAG-TTGTTATTAGC
*
510464 TTGTTATTAGTTGTTATTAGT
1 TTGTTA-TAGTTGTTATTAGC
510485 TTGTTATAGTTGTT
1 TTGTTATAGTTGTT
510499 GGTTACTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 8 0.25
21 22 0.69
22 2 0.06
ACGTcount: A:0.16, C:0.02, G:0.21, T:0.61
Consensus pattern (20 bp):
TTGTTATAGTTGTTATTAGC
Found at i:510469 original size:11 final size:10
Alignment explanation
Indices: 510453--510498 Score: 67
Period size: 11 Copynumber: 4.5 Consensus size: 10
510443 TTGTTATGGT
510453 TTGTTATTAG
1 TTGTTATTAG
510463 CTTGTTATTAG
1 -TTGTTATTAG
510474 TTGTTATTAG
1 TTGTTATTAG
510484 TTTGTTA-TAG
1 -TTGTTATTAG
510494 TTGTT
1 TTGTT
510499 GGTTACTTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.15
10 13 0.38
11 16 0.47
ACGTcount: A:0.17, C:0.02, G:0.20, T:0.61
Consensus pattern (10 bp):
TTGTTATTAG
Found at i:510494 original size:10 final size:11
Alignment explanation
Indices: 510440--510495 Score: 73
Period size: 10 Copynumber: 5.4 Consensus size: 11
510430 TGAATGTTAG
510440 AGTTTGTTA-T
1 AGTTTGTTATT
*
510450 GGTTTGTTATT
1 AGTTTGTTATT
*
510461 AGCTTGTTATT
1 AGTTTGTTATT
510472 AG-TTGTTATT
1 AGTTTGTTATT
510482 AGTTTGTTA-T
1 AGTTTGTTATT
510492 AGTT
1 AGTT
510496 GTTGGTTACT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
10 23 0.56
11 18 0.44
ACGTcount: A:0.18, C:0.02, G:0.21, T:0.59
Consensus pattern (11 bp):
AGTTTGTTATT
Found at i:511356 original size:21 final size:21
Alignment explanation
Indices: 511330--511389 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
511320 GATGGACTGC
* *
511330 CACGTCAGCATCGTAGACCGT
1 CACGTCAGCACCGTAGACCAT
511351 CACGTCAGCACCGTAGACCAT
1 CACGTCAGCACCGTAGACCAT
*
511372 CACGTTAGCACCGTAGAC
1 CACGTCAGCACCGTAGAC
511390 TAGGGCTGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.27, C:0.35, G:0.22, T:0.17
Consensus pattern (21 bp):
CACGTCAGCACCGTAGACCAT
Found at i:511947 original size:31 final size:31
Alignment explanation
Indices: 511912--511991 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 31
511902 AAAAACATAG
* *
511912 GTTAAAGGGTCACATTGGACTTATTTTGTGA
1 GTTAAAGGGTCACATTGAACTTATTTTCTGA
**
511943 GTTAAAAAGTCACATTGAACTTATTTTCTGA
1 GTTAAAGGGTCACATTGAACTTATTTTCTGA
** *
511974 GTTGGAGGATCACATTGA
1 GTTAAAGGGTCACATTGA
511992 GAGAAACAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (31 bp):
GTTAAAGGGTCACATTGAACTTATTTTCTGA
Found at i:519070 original size:26 final size:27
Alignment explanation
Indices: 519034--519087 Score: 101
Period size: 26 Copynumber: 2.0 Consensus size: 27
519024 TGGTGGCTTG
519034 TGCTGGAAAATATAATAG-TTTTCTTT
1 TGCTGGAAAATATAATAGTTTTTCTTT
519060 TGCTGGAAAATATAATAGTTTTTCTTT
1 TGCTGGAAAATATAATAGTTTTTCTTT
519087 T
1 T
519088 TTAAGTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (27 bp):
TGCTGGAAAATATAATAGTTTTTCTTT
Found at i:525754 original size:28 final size:29
Alignment explanation
Indices: 525712--525766 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
525702 GTATATAGAA
* *
525712 GTAATTGATTCTTTTAG-AAATTTGTGAC
1 GTAATTGAATATTTTAGAAAATTTGTGAC
525740 GTAATTGAATATTTTAGAAAATTTGTG
1 GTAATTGAATATTTTAGAAAATTTGTG
525767 GGTCTAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (29 bp):
GTAATTGAATATTTTAGAAAATTTGTGAC
Found at i:525840 original size:22 final size:21
Alignment explanation
Indices: 525806--525850 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
525796 GTATTTATTT
*
525806 TTTAAATAAAAATAATTTTAA
1 TTTAAATAAAAATAATTTAAA
* *
525827 TTTAACATATAAATTATTTAAA
1 TTTAA-ATAAAAATAATTTAAA
525849 TT
1 TT
525851 CTACAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTAAATAAAAATAATTTAAA
Found at i:526561 original size:167 final size:166
Alignment explanation
Indices: 526267--526593 Score: 421
Period size: 167 Copynumber: 2.0 Consensus size: 166
526257 ATAAATTTTT
* * *
526267 AAAAGAAATGACGAGTTTGAAACAATGAATAGTTGAGTGATCATTTTATAACTTTTAATAGTCAG
1 AAAAGAAAGGACGAGTTTGAAACAATGAATAATGGAGTGATCATTTTATAACTTTTAATAGTCAG
* * *
526332 AGACTTAAAAAAGCAACATCCTATATCGGGACCATTTTGTAACTTTTAATAGTCAGAGGACTT-A
66 AGACTT-AAAAA-CAACATCCTATATCGGAACCATTTTATAACTTTTAATAGTCAAAGGACTTAA
*
526396 TAAAATAATATTCTATAGTCGAGGGACCATCATATTTA
129 TAAAATAATACTCTATAGTCGAGGGACCATCATATTTA
* *
526434 AAAAGAAAGGACGAGTTTGGAACATAATGAATAATCGGA-TGATCATTTTGTAACTTTTAATAGT
1 AAAAGAAAGGACGAGTTT-GAA-ACAATGAATAAT-GGAGTGATCATTTTATAACTTTTAATAGT
* * *
526498 CAG-GACTT-AAAA-AACATTCTATAGTCGAAGAATCATTTTATAACTTTTAATAGTTAAAGGAC
63 CAGAGACTTAAAAACAACATCCTATA-TCG--GAACCATTTTATAACTTTTAATAGTCAAAGGAC
* *
526560 TTAATAAAGTAATACTCTATAGTTGAGGGACCAT
125 TTAATAAAATAATACTCTATAGTCGAGGGACCAT
526594 TTGCATATTT
Statistics
Matches: 139, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
164 10 0.07
165 3 0.02
166 4 0.03
167 47 0.34
168 36 0.26
169 37 0.27
170 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.32
Consensus pattern (166 bp):
AAAAGAAAGGACGAGTTTGAAACAATGAATAATGGAGTGATCATTTTATAACTTTTAATAGTCAG
AGACTTAAAAACAACATCCTATATCGGAACCATTTTATAACTTTTAATAGTCAAAGGACTTAATA
AAATAATACTCTATAGTCGAGGGACCATCATATTTA
Found at i:528975 original size:205 final size:204
Alignment explanation
Indices: 528622--529037 Score: 782
Period size: 205 Copynumber: 2.0 Consensus size: 204
528612 TTTTATACAA
528622 CGAACAAAGACAATTAACCTATGGTGCCAATGGGAGCACAGTGGTAAGTTTTATGTTGCCGATAT
1 CGAACAAAGACAATTAACCTATGGTGCCAATGGGAGCACAGTGGTAAGTTTTATGTTGCCGATAT
528687 CTATATTGGGTAGAACATTTTAATCGTTACATCTATGGATGTTCAACAATTTTTCTTTTCTTTTC
66 CTATATTGGGTAGAACATTTTAATCGTTACATCTATGGATGTTCAACAATTTTTCTTTTCTTTTC
528752 TCTCCTTTCAAACCCTATCTATGAAGGGAAAAGTGGTGGAC-GGGAATCTACAGGGCTTTCAGTT
131 TCTCCTTTCAAACCCTATCTATGAAGGG-AAAGTGGT-GACGGGGAATCTACA-GGCTTTCAGTT
528816 TCATAGCAATTT
193 TCATAGCAATTT
528828 CGAACAAAGACAATTAACCTATGGTGCCAATGGGAGCACAGTGGTAAG-TTTATGTTGCCGATAT
1 CGAACAAAGACAATTAACCTATGGTGCCAATGGGAGCACAGTGGTAAGTTTTATGTTGCCGATAT
528892 CTATATTGGGTAGAACATTTTAATCGTTACATCTATGGATGTTCAACAATTTTTCTTTTCTTTTC
66 CTATATTGGGTAGAACATTTTAATCGTTACATCTATGGATGTTCAACAATTTTTCTTTTCTTTTC
528957 TCTCCTTTCAAACCCTATCTATGAAGGGAAAGTGGTGACGGGGAATCTACAGGCTTTCAGTTTCA
131 TCTCCTTTCAAACCCTATCTATGAAGGGAAAGTGGTGACGGGGAATCTACAGGCTTTCAGTTTCA
529022 TAGCAATTT
196 TAGCAATTT
*
529031 AGAACAA
1 CGAACAA
529038 GATCTGCCAG
Statistics
Matches: 208, Mismatches: 1, Indels: 5
0.97 0.00 0.02
Matches are distributed among these distances:
203 32 0.15
204 19 0.09
205 109 0.52
206 48 0.23
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (204 bp):
CGAACAAAGACAATTAACCTATGGTGCCAATGGGAGCACAGTGGTAAGTTTTATGTTGCCGATAT
CTATATTGGGTAGAACATTTTAATCGTTACATCTATGGATGTTCAACAATTTTTCTTTTCTTTTC
TCTCCTTTCAAACCCTATCTATGAAGGGAAAGTGGTGACGGGGAATCTACAGGCTTTCAGTTTCA
TAGCAATTT
Found at i:539553 original size:2 final size:2
Alignment explanation
Indices: 539548--539596 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
539538 AAAAATAAAA
*
539548 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
539590 AT AT AT A
1 AT AT AT A
539597 ATCTTAGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:540077 original size:60 final size:60
Alignment explanation
Indices: 540007--540127 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
539997 TAAAGAATAG
* ** *
540007 TCGGGTGATCATTTTGTAACTTTTAATAGTC-AGGAGA-TTAAACAAAGTAACATCATATAA
1 TCGGGAGATCATTTTGTAACTTTTAATAGTCGAGG-GACTT-AACAAAACAACAACATATAA
540067 TCGGGAGATCATTTTGTAACTTTTAATAGTCGAGGGACTTAACAAAACAACAACATATAA
1 TCGGGAGATCATTTTGTAACTTTTAATAGTCGAGGGACTTAACAAAACAACAACATATAA
540127 T
1 T
540128 TAGAGGATCA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
60 50 0.91
61 5 0.09
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (60 bp):
TCGGGAGATCATTTTGTAACTTTTAATAGTCGAGGGACTTAACAAAACAACAACATATAA
Found at i:540137 original size:60 final size:60
Alignment explanation
Indices: 540013--540148 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
540003 ATAGTCGGGT
** * * *
540013 GATCATTTTGTAACTTTTAATAGTCAGGAGATTAAACAAAGTAACATCATATAATCGGGA
1 GATCATTTTGTAACTTTTAATAGTCAGGAGATTAAACAAAACAACAACATATAATAGAGA
540073 GATCATTTTGTAACTTTTAATAGTCGAGG-GACTT-AACAAAACAACAACATATAATTAGAG-
1 GATCATTTTGTAACTTTTAATAGTC-AGGAGA-TTAAACAAAACAACAACATATAA-TAGAGA
540133 GATCA-TTTGTATACTT
1 GATCATTTTGTA-ACTT
540149 AGCCTAATTG
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
59 6 0.09
60 53 0.79
61 8 0.12
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (60 bp):
GATCATTTTGTAACTTTTAATAGTCAGGAGATTAAACAAAACAACAACATATAATAGAGA
Found at i:543839 original size:13 final size:13
Alignment explanation
Indices: 543821--543849 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
543811 CCACCGTATT
543821 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
543834 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
543847 CCG
1 CCG
543850 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:544567 original size:3 final size:3
Alignment explanation
Indices: 544550--544659 Score: 120
Period size: 3 Copynumber: 36.7 Consensus size: 3
544540 TTATTTATTA
544550 AAT AAT -AT AAT -AT AAT AAT AAT AAT ATAT AATT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA-T AAT AAT AAT AAT
* * *
544595 AAT AAT AAT TAT AAT TAT AAT AAAT AAT -AT ACT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
*
544640 AAT AAT -TT CAAT AAT AAT AA
1 AAT AAT AAT -AAT AAT AAT AA
544660 ATTTAAATGA
Statistics
Matches: 91, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
2 7 0.08
3 74 0.81
4 10 0.11
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:544914 original size:76 final size:76
Alignment explanation
Indices: 544783--545957 Score: 2004
Period size: 76 Copynumber: 15.5 Consensus size: 76
544773 GATGGAAATG
*
544783 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
544848 CCTGAAGGCTT
66 CCTGAAGGCTT
* *
544859 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
*
544924 -CTCGAAGGTTT
66 CCT-GAAGGCTT
*
544935 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
*
545000 CCCGAAGGCTT
66 CCTGAAGGCTT
* *
545011 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
* *
545076 CCCGAAGGATT
66 CCTGAAGGCTT
* * *
545087 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCTGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
545152 -CTCGAAGGCTT
66 CCT-GAAGGCTT
*
545163 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCTGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
545228 CCTGAAGGCTT
66 CCTGAAGGCTT
* *
545239 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
545304 -CTCGAAGGCTT
66 CCT-GAAGGCTT
545315 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
545380 CC-GAAGGCTT
66 CCTGAAGGCTT
*
545390 TTTGGGAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
* *
545455 CCCGAAGGATT
66 CCTGAAGGCTT
* * *
545466 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCTGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
545531 -CTCGAAGGCTT
66 CCT-GAAGGCTT
545542 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
545607 -CTCGAAGGCTT
66 CCT-GAAGGCTT
545618 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
*
545683 CCCGAAGGCTT
66 CCTGAAGGCTT
*
545694 TTTGGGAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
*
545759 CCCGAAGGCTT
66 CCTGAAGGCTT
545770 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
545835 -CTCGAAGGCTT
66 CCT-GAAGGCTT
545846 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
*
545911 CCCGAAGGCTTT
66 CCTGAAGGC-TT
545923 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
545958 TGAGAAATAG
Statistics
Matches: 1052, Mismatches: 35, Indels: 23
0.95 0.03 0.02
Matches are distributed among these distances:
75 81 0.08
76 928 0.88
77 43 0.04
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
CCTGAAGGCTT
Found at i:549071 original size:115 final size:115
Alignment explanation
Indices: 548871--549211 Score: 560
Period size: 115 Copynumber: 3.0 Consensus size: 115
548861 GATCATGCAG
* * * * * * *
548871 TTCATCTTTCAATTCCAATGATCGG--TTCTGGGTTCCTACCGAATCAGATCAGATAACTCAAAG
1 TTCATCTTTAAAATCCAATGATTGGTTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* * *
548934 AACACTTTCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
*
548984 TTCATCTTTTAAATCCAATGATTGGTTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTAAAATCCAATGATTGGTTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAG
549049 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
549099 TTCATCTTTAAAATCCAATGATTGGTTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTAAAATCCAATGATTGGTTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
549164 AACACTTCCAGAAGATGCTATTAAGTCTTCTTATTTCTACTATGAGCA
66 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
549212 CATGGAACTT
Statistics
Matches: 214, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
113 22 0.10
115 192 0.90
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.34
Consensus pattern (115 bp):
TTCATCTTTAAAATCCAATGATTGGTTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
Found at i:558133 original size:3 final size:3
Alignment explanation
Indices: 558125--558249 Score: 162
Period size: 3 Copynumber: 40.7 Consensus size: 3
558115 TATTTATTAA
*
558125 AAT AAT AAT AAT ATAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* * *
558172 AAT AAT AAT AAT AAAT AAT TAT AAT TAT AAT AAT AAT AAT AAT ACT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
558218 AAT AAT AAT AAT AAT AAT -TT CAAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AA
558250 ATTTAAATGA
Statistics
Matches: 107, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
2 1 0.01
3 96 0.90
4 10 0.09
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:571305 original size:23 final size:22
Alignment explanation
Indices: 571270--571313 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
571260 CCATAAAAAT
*
571270 AGAGATAAACGTGTCATGAAAGC
1 AGAGATAAACGTGCCAT-AAAGC
571293 AGAGA-AAATCGTGCCATAAAG
1 AGAGATAAA-CGTGCCATAAAG
571314 ATAAAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.45, C:0.14, G:0.25, T:0.16
Consensus pattern (22 bp):
AGAGATAAACGTGCCATAAAGC
Found at i:576852 original size:2 final size:2
Alignment explanation
Indices: 576845--576878 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
576835 ACCCACCCAC
576845 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
576879 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:577873 original size:29 final size:30
Alignment explanation
Indices: 577836--577894 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
577826 TGAATGATGC
* *
577836 ATGCGAAAATGCTTAAAT-AAATGCAATGG
1 ATGCAAAAATGCATAAATCAAATGCAATGG
*
577865 ATGCAAAAATGCATATATGCAAATGCAATG
1 ATGCAAAAATGCATAAAT-CAAATGCAATG
577895 CAATTTGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.60
31 10 0.40
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.24
Consensus pattern (30 bp):
ATGCAAAAATGCATAAATCAAATGCAATGG
Found at i:579579 original size:17 final size:16
Alignment explanation
Indices: 579542--579583 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
579532 AAATGTCCTT
579542 AAAAATAATTTTAAAG
1 AAAAATAATTTTAAAG
*
579558 AAAAATCATTTTAAAG
1 AAAAATAATTTTAAAG
579574 ACAAAA-AATT
1 A-AAAATAATT
579584 GTTTTTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (16 bp):
AAAAATAATTTTAAAG
Found at i:580194 original size:2 final size:2
Alignment explanation
Indices: 580183--580216 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
580173 CTAAATAAAC
580183 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
580217 TAAAAAGAAC
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:585038 original size:2 final size:2
Alignment explanation
Indices: 585033--585059 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
585023 ATATATTTTG
585033 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 A
585060 ATTCTTTCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:585446 original size:15 final size:16
Alignment explanation
Indices: 585407--585447 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
585397 TATATTTTTA
585407 TAATTATTTTATTCAT
1 TAATTATTTTATTCAT
585423 TCAA-T-TTTTATTC-T
1 T-AATTATTTTATTCAT
585437 TAATTATTTTA
1 TAATTATTTTA
585448 AAAAGAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.09
14 3 0.14
15 13 0.59
16 2 0.09
17 2 0.09
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTATTTTATTCAT
Found at i:586173 original size:59 final size:59
Alignment explanation
Indices: 586080--586213 Score: 187
Period size: 59 Copynumber: 2.3 Consensus size: 59
586070 GATAATAATT
* ** *
586080 AAATAGTTAGGTGTTCTAATTGGTAAAATTGAGAGATCAATGAAAAAACTAAAAGGCTT
1 AAATAGTTAGGTGGTCTAATTGACAAAATTGAGAGATCAATGAAAAAACTAAAAGGCTC
* * * *
586139 TAATAGTTAGGTGGTCTAATTGACAAAATTGAGAGATCAATGACAAAAGTAAAAGGGTC
1 AAATAGTTAGGTGGTCTAATTGACAAAATTGAGAGATCAATGAAAAAACTAAAAGGCTC
*
586198 AAATAATTAGGTGGTC
1 AAATAGTTAGGTGGTC
586214 AAAGATATAA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (59 bp):
AAATAGTTAGGTGGTCTAATTGACAAAATTGAGAGATCAATGAAAAAACTAAAAGGCTC
Found at i:587850 original size:27 final size:29
Alignment explanation
Indices: 587786--587843 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 29
587776 TGACTACATC
*
587786 TTAATTAAATAAAAACGAAAGTGATCAAA
1 TTAATTAAATAAAAACGAAAGTGACCAAA
587815 TCTTAATTAAATAAAAACGAAAGTGACCA
1 --TTAATTAAATAAAAACGAAAGTGACCA
587844 GATATTATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.24
Consensus pattern (29 bp):
TTAATTAAATAAAAACGAAAGTGACCAAA
Found at i:588108 original size:3 final size:3
Alignment explanation
Indices: 588100--588172 Score: 137
Period size: 3 Copynumber: 24.3 Consensus size: 3
588090 GATCCATCGG
*
588100 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
588148 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
588173 GTATCACAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:589809 original size:17 final size:17
Alignment explanation
Indices: 589787--589825 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
589777 ATCATCAACA
*
589787 TTTTTATTGT-TTTCTAT
1 TTTTTATCGTATTT-TAT
589804 TTTTTATCGTATTTTAT
1 TTTTTATCGTATTTTAT
589821 TTTTT
1 TTTTT
589826 GTTTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.77
Consensus pattern (17 bp):
TTTTTATCGTATTTTAT
Found at i:589897 original size:23 final size:23
Alignment explanation
Indices: 589845--589890 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
589835 TTTTAATAAT
* *
589845 TATGTCTTTATGACACGTTTTCA
1 TATGTTTTTATGACACATTTTCA
*
589868 TATGTTTTTATGTCACATTTTCA
1 TATGTTTTTATGACACATTTTCA
589891 ATCGTTTGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (23 bp):
TATGTTTTTATGACACATTTTCA
Found at i:591878 original size:20 final size:20
Alignment explanation
Indices: 591835--591878 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
591825 TACCAGAGAG
* *
591835 TCAACGATCAACAACGACAG
1 TCAACGATCAACAACAACAA
* *
591855 TCAACGATTAACACCAACAA
1 TCAACGATCAACAACAACAA
591875 TCAA
1 TCAA
591879 TAAATTAGGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.30, G:0.09, T:0.14
Consensus pattern (20 bp):
TCAACGATCAACAACAACAA
Found at i:593549 original size:29 final size:29
Alignment explanation
Indices: 593483--593550 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
593473 TATATCTTTA
*
593483 TCCTAATTCTGCATGGGATTATATCCCAG
1 TCCTAATTCTACATGGGATTATATCCCAG
* * * *
593512 TCTTGATTCTACATGGGATTGTATCCCCG
1 TCCTAATTCTACATGGGATTATATCCCAG
593541 TCCTAATTCT
1 TCCTAATTCT
593551 GTTTGAGATC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (29 bp):
TCCTAATTCTACATGGGATTATATCCCAG
Found at i:593746 original size:12 final size:12
Alignment explanation
Indices: 593731--593755 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
593721 TATTTGTGTT
593731 TTTATATATATA
1 TTTATATATATA
593743 TTTATATATATA
1 TTTATATATATA
593755 T
1 T
593756 GTTTACTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTATATATATA
Found at i:601313 original size:29 final size:29
Alignment explanation
Indices: 601278--601359 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
601268 AAACTAAATT
*
601278 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
601307 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
601336 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
601360 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:606077 original size:29 final size:29
Alignment explanation
Indices: 606042--606123 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
606032 AAACTAAATT
*
606042 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
606071 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
606100 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
606124 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:607761 original size:22 final size:23
Alignment explanation
Indices: 607736--607778 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
607726 GTAAACACAA
607736 ATAAATA-TTTTTAAGTGAATCC
1 ATAAATATTTTTTAAGTGAATCC
607758 ATAAATATTTTTTAAGTGAAT
1 ATAAATATTTTTTAAGTGAAT
607779 TGATGTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (23 bp):
ATAAATATTTTTTAAGTGAATCC
Found at i:609233 original size:36 final size:36
Alignment explanation
Indices: 609162--609281 Score: 163
Period size: 35 Copynumber: 3.3 Consensus size: 36
609152 ATCCCGTTAT
* * *
609162 CATTTTTC-AACAAACATCTACCAAACTTTAAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTT-GAAAAC
* *
609198 TATTTTTCAAAGAAACATTTACAAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
609234 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
609269 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
609282 TTGGTTACCA
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
35 34 0.46
36 13 0.18
37 27 0.36
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:609237 original size:21 final size:20
Alignment explanation
Indices: 609213--609273 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
609203 TTCAAAGAAA
609213 CATTTACAAAACTTTGAAAAC
1 CATTTAC-AAACTTTGAAAAC
*
609234 CATTTTCAAA----G-AAA-
1 CATTTACAAACTTTGAAAAC
609248 CATTTACCAAACTTTGAAAAC
1 CATTTA-CAAACTTTGAAAAC
609269 CATTT
1 CATTT
609274 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 6 0.19
21 11 0.35
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (20 bp):
CATTTACAAACTTTGAAAAC
Found at i:613848 original size:37 final size:36
Alignment explanation
Indices: 613785--613903 Score: 152
Period size: 35 Copynumber: 3.3 Consensus size: 36
613775 ATCCCATTAT
* * *
613785 CATTTTTC-AACAAGCATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAA
*
613820 CTATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAAAAACATTTACCAAACTTTGAAAAA
* *
613857 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAT
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAA
613892 CATTTTTTCAAA
1 CA-TTTTTCAAA
613904 GTTGGTTACC
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
35 34 0.46
36 8 0.11
37 32 0.43
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAA
Found at i:613860 original size:21 final size:20
Alignment explanation
Indices: 613832--613896 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
613822 ATTTTTCAAA
613832 AAAACATTTACCAAACTTTG
1 AAAACATTTACCAAACTTTG
*
613852 AAAACCATTT-TCAAA----G
1 AAAA-CATTTACCAAACTTTG
613868 -AAACATTTACCAAACTTTG
1 AAAACATTTACCAAACTTTG
613887 AAAATCATTT
1 AAAA-CATTT
613897 TTTCAAAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.14
15 7 0.20
16 1 0.03
19 1 0.03
20 11 0.31
21 10 0.29
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.31
Consensus pattern (20 bp):
AAAACATTTACCAAACTTTG
Found at i:615587 original size:19 final size:20
Alignment explanation
Indices: 615551--615589 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
615541 CTCCCAGACA
615551 GATACCGAACGAAGAAATGG
1 GATACCGAACGAAGAAATGG
*
615571 GATACCGAA-GGAGAAATGG
1 GATACCGAACGAAGAAATGG
615590 CCATGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.44, C:0.13, G:0.33, T:0.10
Consensus pattern (20 bp):
GATACCGAACGAAGAAATGG
Found at i:617078 original size:42 final size:42
Alignment explanation
Indices: 617023--617110 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
617013 ATTCGCATTG
* * *
617023 CGATAGTCCAAGTTCGCGTTGCGATTTATT-TCAAATTCGTTA
1 CGATAGTCCAAGTTCACATTACGATTTATTCT-AAATTCGTTA
* *
617065 CGATAGTCGAAGTTCATATTACGATTTATTCTAAATTCGTTA
1 CGATAGTCCAAGTTCACATTACGATTTATTCTAAATTCGTTA
617107 CGAT
1 CGAT
617111 TTATTCCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 39 0.98
43 1 0.03
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (42 bp):
CGATAGTCCAAGTTCACATTACGATTTATTCTAAATTCGTTA
Found at i:617107 original size:21 final size:21
Alignment explanation
Indices: 617039--617127 Score: 83
Period size: 21 Copynumber: 4.2 Consensus size: 21
617029 TCCAAGTTCG
* *
617039 CGTTGCGATTTATTTCAAATT
1 CGTTACGATTTATTCCAAATT
* * *
617060 CGTTACGA--TAGTCGAAGTT
1 CGTTACGATTTATTCCAAATT
* *
617079 CATATTACGATTTATTCTAAATT
1 C--GTTACGATTTATTCCAAATT
617102 CGTTACGATTTATTCCAAATT
1 CGTTACGATTTATTCCAAATT
617123 CGTTA
1 CGTTA
617128 GGTTTGATTT
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
19 8 0.15
21 36 0.68
23 9 0.17
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (21 bp):
CGTTACGATTTATTCCAAATT
Found at i:618710 original size:18 final size:18
Alignment explanation
Indices: 618687--618730 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
618677 TTATCTTATA
* *
618687 ATTTAATAAATATTTAAT
1 ATTTAATAAAAATTAAAT
*
618705 ATTTAAAAAAAATTAAAT
1 ATTTAATAAAAATTAAAT
*
618723 ATTGAATA
1 ATTTAATA
618731 TTTACCGATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
ATTTAATAAAAATTAAAT
Found at i:622674 original size:23 final size:23
Alignment explanation
Indices: 622648--622706 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
622638 ATATTCGATA
*
622648 ATTCGTTCGTTTATGTTATTTAT
1 ATTCATTCGTTTATGTTATTTAT
*
622671 ATTCATTCGTTTATGTTGTTTAT
1 ATTCATTCGTTTATGTTATTTAT
*
622694 ATTCATTTGTTTA
1 ATTCATTCGTTTA
622707 AATTTATTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.19, C:0.08, G:0.12, T:0.61
Consensus pattern (23 bp):
ATTCATTCGTTTATGTTATTTAT
Found at i:628681 original size:22 final size:21
Alignment explanation
Indices: 628642--628682 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
628632 TACTTTACCC
* *
628642 TTAAATATATAGCTAAATCTA
1 TTAAATATATACCCAAATCTA
628663 TTAAATGATATACCCAAATC
1 TTAAAT-ATATACCCAAATC
628683 CAATACGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (21 bp):
TTAAATATATACCCAAATCTA
Found at i:630821 original size:18 final size:18
Alignment explanation
Indices: 630798--630833 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
630788 GTGTGAGAAA
*
630798 ACCTAACGAAAATAAAAT
1 ACCTAAAGAAAATAAAAT
630816 ACCTAAAGAAAATAAAAT
1 ACCTAAAGAAAATAAAAT
630834 CCTTGGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.14, G:0.06, T:0.17
Consensus pattern (18 bp):
ACCTAAAGAAAATAAAAT
Found at i:632349 original size:2 final size:2
Alignment explanation
Indices: 632342--632382 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
632332 TAGACTATTA
632342 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
632383 CTTAAACGAT
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:636075 original size:26 final size:26
Alignment explanation
Indices: 636039--636089 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
636029 AAAGTATGTC
636039 CCTGCATTTGCCACTCTACTTTATTG
1 CCTGCATTTGCCACTCTACTTTATTG
636065 CCTGCATTTGCCACTCTACTTTATT
1 CCTGCATTTGCCACTCTACTTTATT
636090 TCATCTAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.16, C:0.31, G:0.10, T:0.43
Consensus pattern (26 bp):
CCTGCATTTGCCACTCTACTTTATTG
Found at i:642045 original size:2 final size:2
Alignment explanation
Indices: 642038--642079 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
642028 AATAATAATA
642038 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
642080 TATGTTTGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:643592 original size:60 final size:61
Alignment explanation
Indices: 643495--643647 Score: 177
Period size: 60 Copynumber: 2.5 Consensus size: 61
643485 TATATACATG
* * * *
643495 TAGTTTGA-GATAAAATTGGAATGTTAAAAAATTTTGAGGATCAATTTAGAATGA-AGGTCA
1 TAGTTTGAGGATGAAATTGAAATGTTAAAAAATGTTGAGGATCAATTTAAAATGATA-GTCA
* **
643555 TAGTTTGAGGATGAAATTGAAATGTT-CAAAATGTTGAGGATTGATTTAAAATGATAGTCA
1 TAGTTTGAGGATGAAATTGAAATGTTAAAAAATGTTGAGGATCAATTTAAAATGATAGTCA
* * * *
643615 TAGTTTAAGGATGAAATTGGAATATTTAAAAAT
1 TAGTTTGAGGATGAAATTGAAATGTTAAAAAAT
643648 TTAGGGCTTA
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
60 58 0.73
61 21 0.27
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.35
Consensus pattern (61 bp):
TAGTTTGAGGATGAAATTGAAATGTTAAAAAATGTTGAGGATCAATTTAAAATGATAGTCA
Found at i:643662 original size:60 final size:60
Alignment explanation
Indices: 643507--643666 Score: 175
Period size: 60 Copynumber: 2.6 Consensus size: 60
643497 GTTTGAGATA
* * * * *
643507 AAATTGGAATGTTAAAAAATTTTGAGGATCAATTTAGAATGAAGGTCATAGTTTGAGGATG
1 AAATTGGAATATTTAAAAA-TTTGAGGATTAATTTAAAATGAAGGTCATAGTTTAAGGATG
* *
643568 AAATT-GAA-ATGTTCAAAATGTTGAGGATTGATTTAAAATGATA-GTCATAGTTTAAGGATG
1 AAATTGGAATAT-TTAAAAAT-TTGAGGATTAATTTAAAATGA-AGGTCATAGTTTAAGGATG
*
643628 AAATTGGAATATTTAAAAATTT-AGGGCTTAATTTAAAAT
1 AAATTGGAATATTTAAAAATTTGA-GGATTAATTTAAAAT
643667 CATACTTTAA
Statistics
Matches: 83, Mismatches: 10, Indels: 13
0.78 0.09 0.12
Matches are distributed among these distances:
59 3 0.04
60 62 0.75
61 16 0.19
62 2 0.02
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (60 bp):
AAATTGGAATATTTAAAAATTTGAGGATTAATTTAAAATGAAGGTCATAGTTTAAGGATG
Found at i:647484 original size:37 final size:37
Alignment explanation
Indices: 647434--647509 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
647424 ATTGCAAATA
647434 ATGCAATGCTTTGTTAACAGTAAAACTTTATTTAACC
1 ATGCAATGCTTTGTTAACAGTAAAACTTTATTTAACC
647471 ATGCAATGCTTTGTTAACAGTAAAACTTTATTTAACC
1 ATGCAATGCTTTGTTAACAGTAAAACTTTATTTAACC
647508 AT
1 AT
647510 TCTAAAACCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (37 bp):
ATGCAATGCTTTGTTAACAGTAAAACTTTATTTAACC
Found at i:653747 original size:31 final size:31
Alignment explanation
Indices: 653709--653768 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
653699 AACCAGAATG
* ** *
653709 TCATAACTCGAAAATGTAAGTGATCAAAATA
1 TCATAACTAGAAAACATAAGCGATCAAAATA
653740 TCATAACTAGAAAACATAAGCGATCAAAA
1 TCATAACTAGAAAACATAAGCGATCAAAA
653769 CCAATATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.22
Consensus pattern (31 bp):
TCATAACTAGAAAACATAAGCGATCAAAATA
Found at i:655533 original size:3 final size:3
Alignment explanation
Indices: 655525--655590 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
655515 TTGAGGAAAT
* *
655525 TGA TGA TGA T-A TTGA T-A TTGA AGA TGA AGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA -TGA TGA -TGA TGA TGA TGA TGA TGA TGA TGA TGA
* *
655570 TGA TGA TGA AGA TTA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA
655591 GGTTTGAACT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 2 0.04
3 47 0.92
4 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:657599 original size:70 final size:72
Alignment explanation
Indices: 657485--657631 Score: 280
Period size: 70 Copynumber: 2.1 Consensus size: 72
657475 ACGAAACTCT
657485 AGAATCGAGTTAGAGAAAAAAGCCATTGTTTTAATTATTTCTAGGTTTCCATATGCTCATTTG-T
1 AGAATCGAGTTAGAGAAAAAAGCCATTGTTTTAATTATTTCTAGGTTTCCATATGCTCATTTGTT
657549 TTGATTA
66 TTGATTA
657556 AGAATCGAGTTAGAG-AAAAAGCCATTGTTTTAATTATTTCTAGGTTTCCATATGCTCATTTGTT
1 AGAATCGAGTTAGAGAAAAAAGCCATTGTTTTAATTATTTCTAGGTTTCCATATGCTCATTTGTT
657620 TTGATTA
66 TTGATTA
657627 AGAAT
1 AGAAT
657632 GTAAGGATGT
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
70 47 0.63
71 28 0.37
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (72 bp):
AGAATCGAGTTAGAGAAAAAAGCCATTGTTTTAATTATTTCTAGGTTTCCATATGCTCATTTGTT
TTGATTA
Found at i:658260 original size:17 final size:16
Alignment explanation
Indices: 658223--658257 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
658213 GGTGACTAAA
658223 TTTAGTAAGGACTTGT
1 TTTAGTAAGGACTTGT
658239 TTTAGTAATGGA-TTGT
1 TTTAGTAA-GGACTTGT
658255 TTT
1 TTT
658258 TAGGTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.51
Consensus pattern (16 bp):
TTTAGTAAGGACTTGT
Found at i:675829 original size:20 final size:20
Alignment explanation
Indices: 675800--675837 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
675790 ACTGAAAAAA
*
675800 CTAACTTAAAATCATAAATC
1 CTAACCTAAAATCATAAATC
*
675820 CTAACCTAAAATCCTAAA
1 CTAACCTAAAATCATAAA
675838 CCCCTAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (20 bp):
CTAACCTAAAATCATAAATC
Found at i:675846 original size:14 final size:14
Alignment explanation
Indices: 675836--675872 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
675826 TAAAATCCTA
675836 AACCCCTAATCTCT
1 AACCCCTAATCTCT
*
675850 AACCCCTAAACTCT
1 AACCCCTAATCTCT
*
675864 TACCCCTAA
1 AACCCCTAA
675873 CCCCTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.32, C:0.43, G:0.00, T:0.24
Consensus pattern (14 bp):
AACCCCTAATCTCT
Found at i:694739 original size:61 final size:61
Alignment explanation
Indices: 694655--694835 Score: 183
Period size: 59 Copynumber: 3.0 Consensus size: 61
694645 TCATATGCCT
*
694655 CTAAACTAT-ACTCTCATTTTAAATTGATCCTTAAACTTTTAAATATTCTAATTTCATCCC
1 CTAAACTATGACTCTCATTCTAAATTGATCCTTAAACTTTTAAATATTCTAATTTCATCCC
* * ** * *
694715 CTAAATTATGACTTTCATTCTAAATT-AGTTATTAAACTTTTAAACATT-TCAATTACAT-CC
1 CTAAACTATGACTCTCATTCTAAATTGA-TCCTTAAACTTTTAAATATTCT-AATTTCATCCC
* * ** * * *
694775 AT-AACTATGACTCTCATTCTAAATTGGTCCACAAACTTCTAAATTTTCTAATTTTATCCC
1 CTAAACTATGACTCTCATTCTAAATTGATCCTTAAACTTTTAAATATTCTAATTTCATCCC
694835 C
1 C
694836 AAATTCATCC
Statistics
Matches: 94, Mismatches: 21, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
59 40 0.43
60 16 0.17
61 38 0.40
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (61 bp):
CTAAACTATGACTCTCATTCTAAATTGATCCTTAAACTTTTAAATATTCTAATTTCATCCC
Found at i:696330 original size:9 final size:9
Alignment explanation
Indices: 696316--696348 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
696306 AAACCGCTCT
696316 TCTTCTTCG
1 TCTTCTTCG
696325 TCTTCTTCG
1 TCTTCTTCG
696334 TCTTCTTCG
1 TCTTCTTCG
*
696343 TTTTCT
1 TCTTCT
696349 CAGATTAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.30, G:0.09, T:0.61
Consensus pattern (9 bp):
TCTTCTTCG
Found at i:699829 original size:143 final size:142
Alignment explanation
Indices: 699518--699788 Score: 436
Period size: 143 Copynumber: 1.9 Consensus size: 142
699508 TAGGGGAATA
* * *
699518 ACAATGATAGGAATTATTGAAACATGATAATGGTTAGTTTTTCAGATGAGATGTTTTCTAGGAAC
1 ACAATGATA-GAATAATTGAAA-ATAATAATGGTTAGTTTTTCAGATGAGATGTTTCCTAGGAAC
699583 CGGTCATAATTATACGATCGAAAAGACTGGTTCATACATCAGTTTCGTAGGCATTGAAAGTATGT
64 CGGTCATAATTATACGATCGAAAAGACTGGTTCATACATCAGTTTCGTAGGCATTGAAAGTATGT
**
699648 ACCTTTGGGCGTACAC
129 ACCTAAGGGCG-A-AC
*
699664 ACAATGATAGAATTATTGAAAATAATAATGGTTAGTTTTTCAGATGAGATGTTTCCTAGGAA-CG
1 ACAATGATAGAATAATTGAAAATAATAATGGTTAGTTTTTCAGATGAGATGTTTCCTAGGAACCG
*
699728 GTCATAATTATACGATCGAAAAGACTGGTTCATACATCAGTTTCGTAGGCATTTAAAGTAT
66 GTCATAATTATACGATCGAAAAGACTGGTTCATACATCAGTTTCGTAGGCATTGAAAGTAT
699789 TTACAAGGTT
Statistics
Matches: 122, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
143 62 0.51
144 39 0.32
145 12 0.10
146 9 0.07
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.33
Consensus pattern (142 bp):
ACAATGATAGAATAATTGAAAATAATAATGGTTAGTTTTTCAGATGAGATGTTTCCTAGGAACCG
GTCATAATTATACGATCGAAAAGACTGGTTCATACATCAGTTTCGTAGGCATTGAAAGTATGTAC
CTAAGGGCGAAC
Found at i:706382 original size:98 final size:98
Alignment explanation
Indices: 706216--706523 Score: 469
Period size: 105 Copynumber: 3.1 Consensus size: 98
706206 TACAAAAGGC
* * * *
706216 ATCACAATACATAAG-C-ATAT-ATTCAACCCTTAGATTTGAACGACTTGAAGTCCAATGGATGA
1 ATCACAATACATAAGTCTATATAATTCAATCCTCAGATTTGAACAACTCGAAGTCCAATGGATGA
706278 AATGTGACATACATCATACGATTACCAATTCTT
66 AATGTGACATACATCATACGATTACCAATTCTT
706311 ATCACAATACATAAGTCTATATAATTCAATCCTCAGATTTGAACAACTCGAAGTCCAATGGATGA
1 ATCACAATACATAAGTCTATATAATTCAATCCTCAGATTTGAACAACTCGAAGTCCAATGGATGA
706376 AATGTGACATACATCATACGATTACCAAATACCAATTCTT
66 AATGTGACATACATCATACGA-T------TACCAATTCTT
706416 ATCACAATACATAAGTCTATATAATTCAATCCTCAGATTTGAACAACTCGAAGTCCAATGGATGA
1 ATCACAATACATAAGTCTATATAATTCAATCCTCAGATTTGAACAACTCGAAGTCCAATGGATGA
* *
706481 AATGTGACATACAGCATATGATTACCAATTCTT
66 AATGTGACATACATCATACGATTACCAATTCTT
*
706514 ATCACGATAC
1 ATCACAATAC
706524 GCAAGTAAAT
Statistics
Matches: 196, Mismatches: 7, Indels: 17
0.89 0.03 0.08
Matches are distributed among these distances:
95 15 0.08
96 1 0.01
97 4 0.02
98 79 0.40
99 1 0.01
104 1 0.01
105 95 0.48
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (98 bp):
ATCACAATACATAAGTCTATATAATTCAATCCTCAGATTTGAACAACTCGAAGTCCAATGGATGA
AATGTGACATACATCATACGATTACCAATTCTT
Found at i:710921 original size:13 final size:13
Alignment explanation
Indices: 710882--710923 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
710872 TTTACTCTAA
710882 AAATATATCATTA-
1 AAATATAT-ATTAT
710895 AAATATAATATTAT
1 AAATAT-ATATTAT
*
710909 AAATATATTTTAT
1 AAATATATATTAT
710922 AA
1 AA
710924 TTTTAGATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 18 0.69
14 8 0.31
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATATATATTAT
Found at i:713866 original size:43 final size:43
Alignment explanation
Indices: 713800--713883 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
713790 GATGATAGGC
*
713800 TTCACGCTAATCATGTATAATCCTATTGTAAGTTATGAAGTTG
1 TTCACGCTAATCATGTATAATCCTAGTGTAAGTTATGAAGTTG
* *
713843 TTCATGCTAATTATGTATAATCCTAGTGTAAGTTATGAAGT
1 TTCACGCTAATCATGTATAATCCTAGTGTAAGTTATGAAGT
713884 CGTGATAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (43 bp):
TTCACGCTAATCATGTATAATCCTAGTGTAAGTTATGAAGTTG
Found at i:738536 original size:23 final size:23
Alignment explanation
Indices: 738509--738568 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
738499 ATCAAGCACA
*
738509 ATAATATATTAGGTACCGCTTAT
1 ATAATATAATAGGTACCGCTTAT
* *
738532 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTACCGCTTAT
*
738555 ATAATAAAATAGGT
1 ATAATATAATAGGT
738569 TAATTACTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (23 bp):
ATAATATAATAGGTACCGCTTAT
Found at i:738642 original size:87 final size:87
Alignment explanation
Indices: 738496--738746 Score: 387
Period size: 87 Copynumber: 2.9 Consensus size: 87
738486 AACCGGAACT
* * *
738496 ATTATCAAGCACAATAATATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATA
1 ATTATCAAGCACAATAACATATTAGGTAACGCTTATATAATATAATAGGTAGCGCTTATATAATA
738561 AAATAGGTTAATTACTGGAAAC
66 AAATAGGTTAATTACTGGAAAC
* ** * *
738583 ATTATAAAGCACAATAACATATTAGGTAAAACTTATATAATATAATATGTAGCGTTTATATAATA
1 ATTATCAAGCACAATAACATATTAGGTAACGCTTATATAATATAATAGGTAGCGCTTATATAATA
738648 AAATAGGTTAATTACTGGAAAC
66 AAATAGGTTAATTACTGGAAAC
* *
738670 ATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAA-AGTAATAGGTAGTGCTTATATAAT
1 ATTATCAAGCACAATAACATATTAGGTAACGCTTATATAATA-TAATAGGTAGCGCTTATATAAT
*
738734 AAAATATGTTAAT
65 AAAATAGGTTAAT
738747 AATTTAATTT
Statistics
Matches: 147, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
86 1 0.01
87 146 0.99
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.33
Consensus pattern (87 bp):
ATTATCAAGCACAATAACATATTAGGTAACGCTTATATAATATAATAGGTAGCGCTTATATAATA
AAATAGGTTAATTACTGGAAAC
Found at i:739084 original size:156 final size:156
Alignment explanation
Indices: 738790--739104 Score: 522
Period size: 156 Copynumber: 2.0 Consensus size: 156
738780 CGCCTAAAAT
* *
738790 ATTATCAAGAATAACATAACCGATTATTTACTGAAAACATTATCCAGTATAATAATGTAAACGGT
1 ATTACCAAGAATAACATAACCGATTATTTACTGAAAACATTATCAAGTATAATAATGTAAACGGT
* *
738855 AAAAAAAATAGGCGTTATCTATTACATTAAACTACCTACAAGATATGTTGAAAGTATCGATTCCA
66 AAAAAAAATAGGCGCTACCTATTACATTAAACTACCTACAAGATATGTTGAAAGTATCGATTCCA
*
738920 TTTAAATAAGTATCGACACTTTTGGA
131 TTTAAATAAGTATCGACACTTTTAGA
* * *
738946 ATTACCAAGGATAACATAATCGATTATTTACTGGAAACATTATCAAGTATAATAATGTAAACGGT
1 ATTACCAAGAATAACATAACCGATTATTTACTGAAAACATTATCAAGTATAATAATGTAAACGGT
** * *
739011 AAAAAAAATAGGCGCTACCTATTACATTAAACTACCTACCGGATATGTTGAAAGTGTCGATTCTA
66 AAAAAAAATAGGCGCTACCTATTACATTAAACTACCTACAAGATATGTTGAAAGTATCGATTCCA
739076 TTTAAATAAGTATCGACACTTTTAGA
131 TTTAAATAAGTATCGACACTTTTAGA
739102 ATT
1 ATT
739105 TAAAAAAAAT
Statistics
Matches: 147, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
156 147 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (156 bp):
ATTACCAAGAATAACATAACCGATTATTTACTGAAAACATTATCAAGTATAATAATGTAAACGGT
AAAAAAAATAGGCGCTACCTATTACATTAAACTACCTACAAGATATGTTGAAAGTATCGATTCCA
TTTAAATAAGTATCGACACTTTTAGA
Found at i:739336 original size:23 final size:23
Alignment explanation
Indices: 739278--739339 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
739268 AACTTATTTT
*
739278 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGGTACCTATTAC
739301 ATTATATAAGCGGTACCTATTAC
1 ATTATATAAGCGGTACCTATTAC
739324 ATTATATAAGCGGTAC
1 ATTATATAAGCGGTAC
739340 TTAATATGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (23 bp):
ATTATATAAGCGGTACCTATTAC
Found at i:739414 original size:23 final size:23
Alignment explanation
Indices: 739379--739463 Score: 125
Period size: 23 Copynumber: 3.7 Consensus size: 23
739369 CTAGTAATTA
**
739379 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
739402 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
* *
739425 ACCTATTATATTATATAAGTGCT
1 ACCTATTACATTATATAAGCGCT
*
739448 ACCTATTACATCATAT
1 ACCTATTACATTATAT
739464 TTTTATCTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:739438 original size:110 final size:110
Alignment explanation
Indices: 739243--739443 Score: 350
Period size: 110 Copynumber: 1.8 Consensus size: 110
739233 ATTTGTTGAA
* *
739243 GTGCTTGATAATGTTTACAGTAATTAACTTATTTTATTATATAAGCGCTACCTATTACATTATAT
1 GTGCTTGAAAATGTTTACAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATAT
*
739308 AAGCGGTACCTATTACATTATATAAGCGGTACTTAATATGTTACT
66 AAGCGCTACCTATTACATTATATAAGCGGTACTTAATATGTTACT
739353 GTGCTTGAAAATGTTT-CTAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATA
1 GTGCTTGAAAATGTTTAC-AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATA
*
739417 TAAGCGCTACCTATTATATTATATAAG
65 TAAGCGCTACCTATTACATTATATAAG
739444 TGCTACCTAT
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
109 1 0.01
110 85 0.99
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (110 bp):
GTGCTTGAAAATGTTTACAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATAT
AAGCGCTACCTATTACATTATATAAGCGGTACTTAATATGTTACT
Found at i:741497 original size:21 final size:21
Alignment explanation
Indices: 741473--741514 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
741463 AAATGTTAAA
*
741473 AAATATTAATGTTTTAAGTAT
1 AAATAATAATGTTTTAAGTAT
*
741494 AAATAATAATGTTTTAGGTAT
1 AAATAATAATGTTTTAAGTAT
741515 TTTTTTACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (21 bp):
AAATAATAATGTTTTAAGTAT
Found at i:750127 original size:377 final size:374
Alignment explanation
Indices: 749385--750134 Score: 1383
Period size: 375 Copynumber: 2.0 Consensus size: 374
749375 AAAAATATTT
749385 TTATTGTCCATATTAGCTTATTTTGGAATATATTTTCCCCTTCTCCCTGAATGGGAGTTTGGGGG
1 TTATTGTCCATATTAGCTTATTTTGGAATATATTTTCCCCTTCTCCCTGAATGGGAGTTTGGGGG
*
749450 GGGGGTTAGACAGCTTTAATCAGAACACTGAAGTTTGCATTACAAAGCAGAAGACCATGTATCCG
66 GGGGGTTAGACAGCTTTAATCAGAACACTGAAGTTTACATTACAAAGCAGAAGACCATGTATCCG
* ** *
749515 AGGCATTGATATAACCTTCGTATTTATATAGAATTACAAGTTTCGGCTTCACGATGCATAAGTGA
131 AGGCATTGATATAACCTTCGTATTTATATAGAACTACAAGTTTCAACTTCACAATGCATAAGTGA
*
749580 AAATACAAAAAAATAAATCAAAGATAAATGGAGTTGGGGTAGCAAAAAAACAAGAATGATTGTTT
196 AAATACAAAAAAATAAATCAAAGATAAATGGAGTTGGAGTAGCAAAAAAACAAGAATGATTGTTT
*
749645 TATTTGTTTGTCACCATTGCCATTTGCTAAAATTATGCATTCACAAATACTAAATCAGCTTTCAA
261 TATTTGTTTGTCACCATTGCCATTTGCTAAAATTATGCATTCACAAAGACTAAATCAGCTTTCAA
749710 ACTATGTAAATCCTGAAGGGAACCAATTACAAATAAGACTTCCATGCAA
326 ACTATGTAAATCCTGAAGGGAACCAATTACAAATAAGACTTCCATGCAA
749759 TTATTGTCCATATTAGCTTATTTTGGAATATATTTTCCCCTTCTCCCTGAATGGGAGTTTGGGGG
1 TTATTGTCCATATTAGCTTATTTTGGAATATATTTTCCCCTTCTCCCTGAATGGGAGTTT-GGGG
*
749824 GGGGGGTTAGACAGCTTTAATCAGAACACTGAAGTTTACATTTCAAAGCAGAAGACCATGTATCC
65 GGGGGGTTAGACAGCTTTAATCAGAACACTGAAGTTTACATTACAAAGCAGAAGACCATGTATCC
749889 GAGGCATTGATATAACCTTCGTATTTATATAGAACTACAAGTTTCAACTTCACAATGCATAAGTG
130 GAGGCATTGATATAACCTTCGTATTTATATAGAACTACAAGTTTCAACTTCACAATGCATAAGTG
*
749954 AAAATACAAAAAAAATAAATCAAATATAAATGGAGTTGGAGTAGCAACAAAAACAAGAATGATTG
195 AAAATAC-AAAAAAATAAATCAAAGATAAATGGAGTTGGAGTAGCAA-AAAAACAAGAATGATTG
750019 TTTTATTTGTTTGTCACCATTGCCATTTGCTAAAATTATGCATTCACAAAGACTAAATCAGCTTT
258 TTTTATTTGTTTGTCACCATTGCCATTTGCTAAAATTATGCATTCACAAAGACTAAATCAGCTTT
*
750084 CAAATTATGTAAATCCTGAAGGGAACCAATTACAAATAAGACTTCCATGCA
323 CAAACTATGTAAATCCTGAAGGGAACCAATTACAAATAAGACTTCCATGCA
750135 TTAACACTTC
Statistics
Matches: 363, Mismatches: 10, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
374 60 0.17
375 135 0.37
376 37 0.10
377 131 0.36
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (374 bp):
TTATTGTCCATATTAGCTTATTTTGGAATATATTTTCCCCTTCTCCCTGAATGGGAGTTTGGGGG
GGGGGTTAGACAGCTTTAATCAGAACACTGAAGTTTACATTACAAAGCAGAAGACCATGTATCCG
AGGCATTGATATAACCTTCGTATTTATATAGAACTACAAGTTTCAACTTCACAATGCATAAGTGA
AAATACAAAAAAATAAATCAAAGATAAATGGAGTTGGAGTAGCAAAAAAACAAGAATGATTGTTT
TATTTGTTTGTCACCATTGCCATTTGCTAAAATTATGCATTCACAAAGACTAAATCAGCTTTCAA
ACTATGTAAATCCTGAAGGGAACCAATTACAAATAAGACTTCCATGCAA
Found at i:751730 original size:17 final size:17
Alignment explanation
Indices: 751705--751737 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
751695 TCAATTTAAT
*
751705 TTATTATAAAAATATAA
1 TTATAATAAAAATATAA
751722 TTATAATAAAAATATA
1 TTATAATAAAAATATA
751738 TTTTATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTATAATAAAAATATAA
Found at i:751747 original size:17 final size:16
Alignment explanation
Indices: 751703--751747 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
751693 TATCAATTTA
751703 ATTTATTATAAAAATAT
1 ATTTA-TATAAAAATAT
*
751720 AATTATAATAAAAATAT
1 ATTTAT-ATAAAAATAT
751737 ATTTTATATAA
1 A-TTTATATAA
751748 GTCACTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 1 0.04
17 19 0.79
18 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTATATAAAAATAT
Found at i:752200 original size:16 final size:17
Alignment explanation
Indices: 752179--752230 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 17
752169 ACCCCAAGGA
752179 TGACACTT-TTGAGGGG
1 TGACACTTGTTGAGGGG
* *
752195 TGACACTTGTATTAAGGG
1 TGACACTTGT-TGAGGGG
*
752213 TGACACTTGTGGAGGGG
1 TGACACTTGTTGAGGGG
752230 T
1 T
752231 TGCTTGGGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 8 0.28
17 6 0.21
18 15 0.52
ACGTcount: A:0.21, C:0.12, G:0.37, T:0.31
Consensus pattern (17 bp):
TGACACTTGTTGAGGGG
Found at i:758637 original size:31 final size:31
Alignment explanation
Indices: 758602--758672 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
758592 GTTTCAAAAA
* * *
758602 TAACAAATTGGTCATTAATGTTATCGATTTG
1 TAACAAAATGATCATTAAGGTTATCGATTTG
*
758633 TAACAAAATGATCTTTAAGGTTATCGATTTG
1 TAACAAAATGATCATTAAGGTTATCGATTTG
758664 TAACAAAAT
1 TAACAAAAT
758673 AGTCACTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (31 bp):
TAACAAAATGATCATTAAGGTTATCGATTTG
Found at i:759408 original size:31 final size:31
Alignment explanation
Indices: 759365--759441 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
759355 GACAGTGGAG
*
759365 TGACCATTTTGTTACAAATAGATAATGTTAA
1 TGACCATTTTGTTACAAATAGACAATGTTAA
* * *
759396 TGACTATTTTGTTATAAATCGACAATGTTAA
1 TGACCATTTTGTTACAAATAGACAATGTTAA
* *
759427 TGACCAATTTATTAC
1 TGACCATTTTGTTAC
759442 TTTTGAAACT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (31 bp):
TGACCATTTTGTTACAAATAGACAATGTTAA
Found at i:760533 original size:21 final size:20
Alignment explanation
Indices: 760504--760545 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
760494 TATTATTGGA
*
760504 TTTTTTACCGGTTTTGTTAT
1 TTTTTTACCGATTTTGTTAT
760524 TTTTTCTACCGATTTTGTTAT
1 TTTTT-TACCGATTTTGTTAT
760545 T
1 T
760546 GTTGGACACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (20 bp):
TTTTTTACCGATTTTGTTAT
Found at i:766454 original size:132 final size:132
Alignment explanation
Indices: 766216--766540 Score: 580
Period size: 132 Copynumber: 2.5 Consensus size: 132
766206 CTTTTTTGGC
* * *
766216 CTTTTCACCTGAGTTCGGCACGAATAGGCCACTCACTAGTCCGGTCTATGTTAAGTCCCCCAACA
1 CTTTTCACCCGAGTTCGGCACGAATGGGCCACTCACTAGTCCGGTCTATGTT-AGCCCCCCAACA
*
766281 CAGTTTGTTTCGGCCGTGACAGGCAGGTGACGACGGTTTAATAGTGGTATAAAGGGAAAACTAAT
65 CAGTTTGTTTCGGCCGTGACAGGCAGGCGACGACGGTTTAATAGTGGTATAAAGGGAAAACTAAT
766346 CA-G
130 -AGG
*
766349 CTTTTCACCCGAGTTCGGCACGAATGGGCCACTCACTAGTCCGATCTATGTTAGCCCCCCAACAC
1 CTTTTCACCCGAGTTCGGCACGAATGGGCCACTCACTAGTCCGGTCTATGTTAGCCCCCCAACAC
766414 AGTTTGTTTCGGCCGTGACAGGCAGGCGACGACGGTTTAATAGTGGTATAAAGGGAAAACTAATA
66 AGTTTGTTTCGGCCGTGACAGGCAGGCGACGACGGTTTAATAGTGGTATAAAGGGAAAACTAATA
766479 GG
131 GG
766481 CTTTTCACCCGAGTTCGGCACGAATGGGCCACTCACTAGTCCGGTCTATGTTAGCCCCCC
1 CTTTTCACCCGAGTTCGGCACGAATGGGCCACTCACTAGTCCGGTCTATGTTAGCCCCCC
766541 CCCCCCCCCC
Statistics
Matches: 185, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
131 1 0.01
132 135 0.73
133 49 0.26
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (132 bp):
CTTTTCACCCGAGTTCGGCACGAATGGGCCACTCACTAGTCCGGTCTATGTTAGCCCCCCAACAC
AGTTTGTTTCGGCCGTGACAGGCAGGCGACGACGGTTTAATAGTGGTATAAAGGGAAAACTAATA
GG
Found at i:768659 original size:35 final size:37
Alignment explanation
Indices: 768620--768694 Score: 91
Period size: 38 Copynumber: 2.1 Consensus size: 37
768610 CTTAATATTA
*
768620 AATTTTGAACG-G-GATACTTAAATAAAACAAAAACT
1 AATTTTGAACGAGTGATACTAAAATAAAACAAAAACT
* * *
768655 AATTTTTAACGACGTGGTACTAAAATGAAACAAAAACT
1 AATTTTGAACGA-GTGATACTAAAATAAAACAAAAACT
768693 AA
1 AA
768695 ACTCTAGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 10 0.30
37 1 0.03
38 22 0.67
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (37 bp):
AATTTTGAACGAGTGATACTAAAATAAAACAAAAACT
Found at i:773710 original size:15 final size:16
Alignment explanation
Indices: 773681--773710 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
773671 ATCATGTATT
773681 TAAAATTTGATTAAAG
1 TAAAATTTGATTAAAG
773697 TAAAATTT-ATTAAA
1 TAAAATTTGATTAAA
773711 TAATTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (16 bp):
TAAAATTTGATTAAAG
Found at i:781630 original size:23 final size:23
Alignment explanation
Indices: 781596--781659 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
781586 CAATGTGTTT
*
781596 GTGAGCGATAAACGAACGTGCTC
1 GTGAGCGTTAAACGAACGTGCTC
** *
781619 GTGAGCGTTAAATTAACGTGTTC
1 GTGAGCGTTAAACGAACGTGCTC
**
781642 GTGAATGTTAAACGAACG
1 GTGAGCGTTAAACGAACG
781660 AACACGAATA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (23 bp):
GTGAGCGTTAAACGAACGTGCTC
Found at i:781783 original size:14 final size:14
Alignment explanation
Indices: 781764--781804 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
781754 CAAACACAAT
781764 CTTATTCGTTTAAA
1 CTTATTCGTTTAAA
781778 CTTATTCGTTTAAA
1 CTTATTCGTTTAAA
*
781792 CTCGATTCGTTTA
1 CT-TATTCGTTTA
781805 CACCCTATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (14 bp):
CTTATTCGTTTAAA
Found at i:783035 original size:4 final size:4
Alignment explanation
Indices: 783026--783056 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
783016 GATAACTGAC
783026 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
783057 AATTAAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:784527 original size:18 final size:17
Alignment explanation
Indices: 784475--784529 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
784465 ATTAAATATT
*
784475 TTATAATTAAAAAATAGA
1 TTATAATTATAAAATA-A
*
784493 TTATAATTAATTTAAATAA
1 TTATAATT-A-TAAAATAA
784512 TATATAATTATAAAATAA
1 T-TATAATTATAAAATAA
784530 AAATTTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 15 0.48
19 4 0.13
20 12 0.39
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TTATAATTATAAAATAA
Done.