Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008856.1 Hibiscus syriacus cultivar Beakdansim tig00112075_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: 559779
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:393252 original size:3 final size:3
Alignment explanation
Indices: 393246--393337 Score: 94
Period size: 3 Copynumber: 29.7 Consensus size: 3
393236 TTATTTAAAT
** * * *
393246 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA GTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
393294 TTA TTTA TTA TTTA TTA TTA ATA TTA ATA TATA TTA TTA TTA TT
1 TTA -TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT
393338 TAATAAATAT
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
3 63 0.88
4 9 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:401830 original size:114 final size:114
Alignment explanation
Indices: 401630--401851 Score: 408
Period size: 114 Copynumber: 1.9 Consensus size: 114
401620 CACGTTCTCG
*
401630 TAGTAGAAATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
*
401695 GGTATAAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTATAAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
401744 TAGTAGAAATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
* *
401809 GGTATGAACCCTAAAACCAATCATTGGAATTGAAAGATGAATT
66 GGTATAAACCCCAAAACCAATCATTGGAATTGAAAGATGAATT
401852 GCATGATCGT
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 104 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.32
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
GGTATAAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
Found at i:402749 original size:35 final size:34
Alignment explanation
Indices: 402704--402769 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
402694 TTCAACCAGA
402704 AATATAATATTGGGGCATTTTGAAGGCTCATAAC
1 AATATAATATTGGGGCATTTTGAAGGCTCATAAC
* *
402738 AATATGAATATTTGGGCATTTTGAAGGTTCAT
1 AATAT-AATATTGGGGCATTTTGAAGGCTCAT
402770 CTAAAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 5 0.17
35 24 0.83
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (34 bp):
AATATAATATTGGGGCATTTTGAAGGCTCATAAC
Found at i:403919 original size:50 final size:50
Alignment explanation
Indices: 403858--403952 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
403848 AGAAACCTTG
* *
403858 GCAGAAGCCACATGAAAGGATA-AATGTGTTTTCAAATGTTTTACATCTGA
1 GCAGAAACCACATGAAAGGA-AGAATGTGTTGTCAAATGTTTTACATCTGA
* *
403908 GCAGAAACCACATGAGATGAAGAATGTGTTGTCAAATGTTTTACA
1 GCAGAAACCACATGAAAGGAAGAATGTGTTGTCAAATGTTTTACA
403953 AACCAGTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 1 0.03
50 39 0.98
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (50 bp):
GCAGAAACCACATGAAAGGAAGAATGTGTTGTCAAATGTTTTACATCTGA
Found at i:404348 original size:22 final size:21
Alignment explanation
Indices: 404322--404398 Score: 86
Period size: 22 Copynumber: 3.7 Consensus size: 21
404312 TATATCTACA
404322 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATT-T
*
404344 CTCTTCAAAGGTGATAGATTT
1 CTCTTCAAAGATGATAGATTT
* *
404365 -T-TTTAAAGATGACAGATTTT
1 CTCTTCAAAGATGATAGA-TTT
*
404385 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
404399 AAGCTTTATC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
19 12 0.26
20 4 0.09
21 2 0.04
22 29 0.62
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (21 bp):
CTCTTCAAAGATGATAGATTT
Found at i:405223 original size:166 final size:167
Alignment explanation
Indices: 404914--405243 Score: 493
Period size: 166 Copynumber: 2.0 Consensus size: 167
404904 AAAATGAGCA
*
404914 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGATGTTTCCAAAAAAAAACATAATGAGAA
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGATATTT----AAAAAAACATAATGAGAA
* **
404979 AACGATTTTCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACAA
62 AACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACAA
* *
405044 TTTTCTTAGTTTTTTTACTTAGTAAACTATTTCCAACAACC
127 TTTCCTTAGTTTTTTTACTTAATAAACTATTTCCAACAACC
* * ** *
405085 TTATCTTGAGATTGGGGCATGTTACTCAATCAACATGTTATTT-TGAAAA-ATAATGAGAAAATG
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGATATTTAAAAAAACATAATGAGAAAACG
*
405148 ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
66 ATTTCCATAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACAATTT
405213 CCTTAGTTTTTTTACTTAATAAACTATTTCC
130 CCTTAGTTTTTTTACTTAATAAACTATTTCC
405244 CACATCTGTA
Statistics
Matches: 146, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
165 40 0.27
166 66 0.45
171 40 0.27
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (167 bp):
TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGATATTTAAAAAAACATAATGAGAAAACG
ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACAATTTC
CTTAGTTTTTTTACTTAATAAACTATTTCCAACAACC
Found at i:405345 original size:76 final size:76
Alignment explanation
Indices: 405246--405883 Score: 1161
Period size: 76 Copynumber: 8.4 Consensus size: 76
405236 CTATTTCCCA
405246 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
405311 AGCCTTAGGGT
66 AGCCTTAGGGT
405322 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
405387 AGCCTTAGGGT
66 AGCCTTAGGGT
*
405398 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
405463 AACCTTAGGAT
66 AGCCTTAGGGT
*
405474 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
405539 AGCCTTAGGGT
66 AGCCTTAGGGT
*
405550 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
405615 AGCCTTAGGGT
66 AGCCTTAGGGT
405626 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
405691 AGCCTTAGGGT
66 AGCCTTAGGGT
405702 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
405767 A-CCTTCGGGT
66 AGCCTTAGGGT
* *
405777 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT-CA
* *
405842 AAACCTTCGGGT
65 AAGCCTTAGGGT
*
405854 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
405884 TCAACATTTC
Statistics
Matches: 545, Mismatches: 15, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
75 69 0.13
76 439 0.81
77 37 0.07
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:406020 original size:3 final size:3
Alignment explanation
Indices: 406014--406104 Score: 92
Period size: 3 Copynumber: 29.7 Consensus size: 3
406004 TTATTTAAAT
** * *
406014 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
406062 TAA TTA TTA TTTA TTA TTA ATA TTA ATA CATA TTA TTA TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TT
406105 TAATAAATAT
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
3 66 0.92
4 6 0.08
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:406109 original size:20 final size:22
Alignment explanation
Indices: 406072--406116 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
406062 TAATTATTAT
*
406072 TTATTATTAATATTAATACATA
1 TTATTATTAATATTAATAAATA
406094 TTATTATT-AT-TTAATAAATA
1 TTATTATTAATATTAATAAATA
406114 TTA
1 TTA
406117 CAAACCCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.55
21 2 0.09
22 8 0.36
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTATTATTAATATTAATAAATA
Found at i:407445 original size:3 final size:3
Alignment explanation
Indices: 407427--407489 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
407417 TATTTTAATC
*
407427 ATT ATTT ATT -TT ATT ATT ATT ATT -TT -TT ATT GTT -TT AATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
*
407470 ATT -TC ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
407490 TATAAAAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
2 9 0.18
3 37 0.73
4 5 0.10
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:414602 original size:18 final size:17
Alignment explanation
Indices: 414579--414623 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
414569 ACACTTTACT
414579 TTTTCTTCAAT-CTGTACC
1 TTTTCTTCAATCCTG-A-C
*
414597 TTTTCTTCATTCCTGAC
1 TTTTCTTCAATCCTGAC
414614 TTTTCTTCAA
1 TTTTCTTCAA
414624 CCCTAGACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 10 0.42
18 11 0.46
19 3 0.12
ACGTcount: A:0.16, C:0.27, G:0.04, T:0.53
Consensus pattern (17 bp):
TTTTCTTCAATCCTGAC
Found at i:415491 original size:31 final size:31
Alignment explanation
Indices: 415456--415520 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
415446 GATTTTTAAA
*
415456 AAAATTGAAAGTTTAGATACTAAAACGGATC
1 AAAATTAAAAGTTTAGATACTAAAACGGATC
*
415487 AAAATTAAAAGTTTAGATATTAAAACGGATC
1 AAAATTAAAAGTTTAGATACTAAAACGGATC
415518 AAA
1 AAA
415521 TCTGATAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.26
Consensus pattern (31 bp):
AAAATTAAAAGTTTAGATACTAAAACGGATC
Found at i:416040 original size:24 final size:24
Alignment explanation
Indices: 416012--416066 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
416002 CCAAGAAGAG
416012 ATCAACAAGCTCCTCAACTTGATC
1 ATCAACAAGCTCCTCAACTTGATC
*
416036 ATCAACCAGCTCCTCAACTTGATC
1 ATCAACAAGCTCCTCAACTTGATC
416060 ATCAACA
1 ATCAACA
416067 CTTTCTACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.35, C:0.35, G:0.07, T:0.24
Consensus pattern (24 bp):
ATCAACAAGCTCCTCAACTTGATC
Found at i:418546 original size:58 final size:58
Alignment explanation
Indices: 418449--418605 Score: 226
Period size: 58 Copynumber: 2.7 Consensus size: 58
418439 ATCGTTAACC
* * * * * *
418449 GGGTGGTATTTTGGTAATTATTTTGAAAATGGTGATATTTTGGTAATTATTTCTAAAA
1 GGGTGCTATTTTCGTAATTATTTTTAAAAAGGTGCTATTTTAGTAATTATTTCTAAAA
*
418507 GGGTGCTATTTTTGTAATT-TTTATTAAAAAGGTGCTATTTTAGTAATTATTTCTAAAA
1 GGGTGCTATTTTCGTAATTATTT-TTAAAAAGGTGCTATTTTAGTAATTATTTCTAAAA
*
418565 GGGTGCTATTTTCGTAATTATTTTTAAAAGGGTGCTATTTT
1 GGGTGCTATTTTCGTAATTATTTTTAAAAAGGTGCTATTTT
418606 CATAAAATTG
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
57 3 0.03
58 83 0.93
59 3 0.03
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (58 bp):
GGGTGCTATTTTCGTAATTATTTTTAAAAAGGTGCTATTTTAGTAATTATTTCTAAAA
Found at i:418606 original size:29 final size:29
Alignment explanation
Indices: 418449--418606 Score: 201
Period size: 29 Copynumber: 5.4 Consensus size: 29
418439 ATCGTTAACC
* * *
418449 GGGTGGTATTTTGGTAATTATTTTGAAAA
1 GGGTGCTATTTTCGTAATTATTTTTAAAA
* * * *
418478 TGGTGATATTTTGGTAATTATTTCTAAAA
1 GGGTGCTATTTTCGTAATTATTTTTAAAA
*
418507 GGGTGCTATTTTTGTAATT-TTTATTAAAA
1 GGGTGCTATTTTCGTAATTATTT-TTAAAA
* * *
418536 AGGTGCTATTTTAGTAATTATTTCTAAAA
1 GGGTGCTATTTTCGTAATTATTTTTAAAA
418565 GGGTGCTATTTTCGTAATTATTTTTAAAA
1 GGGTGCTATTTTCGTAATTATTTTTAAAA
418594 GGGTGCTATTTTC
1 GGGTGCTATTTTC
418607 ATAAAATTGT
Statistics
Matches: 113, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
28 3 0.03
29 107 0.95
30 3 0.03
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.47
Consensus pattern (29 bp):
GGGTGCTATTTTCGTAATTATTTTTAAAA
Found at i:419346 original size:24 final size:24
Alignment explanation
Indices: 419311--419383 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
419301 ATTTTTGACG
419311 GGATTTTGATATGATACTTGACCT
1 GGATTTTGATATGATACTTGACCT
* * *
419335 GGATTTTTATATGATACATGACAT
1 GGATTTTGATATGATACTTGACCT
* * *
419359 GGATTCTGATATGCTAATTGACCT
1 GGATTTTGATATGATACTTGACCT
419383 G
1 G
419384 AATTAAGTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (24 bp):
GGATTTTGATATGATACTTGACCT
Found at i:420072 original size:15 final size:15
Alignment explanation
Indices: 420052--420081 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
420042 TGTAATATAA
420052 GTTGGATGTTAACAT
1 GTTGGATGTTAACAT
420067 GTTGGATGTTAACAT
1 GTTGGATGTTAACAT
420082 TGATTGAGAG
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:0.27, C:0.07, G:0.27, T:0.40
Consensus pattern (15 bp):
GTTGGATGTTAACAT
Found at i:423644 original size:10 final size:10
Alignment explanation
Indices: 423629--423653 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
423619 TATGTCCTAA
423629 ATGCAACTAT
1 ATGCAACTAT
423639 ATGCAACTAT
1 ATGCAACTAT
423649 ATGCA
1 ATGCA
423654 GCTAAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (10 bp):
ATGCAACTAT
Found at i:427118 original size:10 final size:10
Alignment explanation
Indices: 427111--427147 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
427101 AAATAAATCC
427111 ATAAAAATAA
1 ATAAAAATAA
427121 ATAAAAATACA
1 ATAAAAATA-A
427132 ATAATAAATAA
1 ATAA-AAATAA
427143 ATAAA
1 ATAAA
427148 TAAGATAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.40
11 10 0.40
12 5 0.20
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (10 bp):
ATAAAAATAA
Found at i:427122 original size:18 final size:20
Alignment explanation
Indices: 427101--427149 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
427091 AAAAAATAGC
*
427101 AAATAAAT-CCATAA-AAAT
1 AAATAAATACAATAATAAAT
427119 AAATAAAAATACAATAATAAAT
1 AAAT--AAATACAATAATAAAT
427141 AAATAAATA
1 AAATAAATA
427150 AGATAATGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.15
20 9 0.35
21 5 0.19
22 8 0.31
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.22
Consensus pattern (20 bp):
AAATAAATACAATAATAAAT
Found at i:432847 original size:18 final size:18
Alignment explanation
Indices: 432824--432862 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
432814 ATGATCATTA
*
432824 AATGTGATAATAATTGTT
1 AATGTGATAATAATTATT
*
432842 AATGTGTTAATAATTATT
1 AATGTGATAATAATTATT
432860 AAT
1 AAT
432863 TATGTAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (18 bp):
AATGTGATAATAATTATT
Found at i:433218 original size:16 final size:16
Alignment explanation
Indices: 433197--433267 Score: 124
Period size: 16 Copynumber: 4.4 Consensus size: 16
433187 GGTATTACCC
433197 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
433213 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
433229 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
433245 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
433261 GACCTGT
1 GACCTGT
433268 AAATGATCCA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.18, C:0.28, G:0.14, T:0.39
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:433238 original size:32 final size:32
Alignment explanation
Indices: 433197--433267 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
433187 GGTATTACCC
433197 GACCTGTTTTCAACCTGACCTGTTTTTAACCT
1 GACCTGTTTTCAACCTGACCTGTTTTTAACCT
433229 GACCTGTTTTCAACCTGACCTGTTTTTAACCT
1 GACCTGTTTTCAACCTGACCTGTTTTTAACCT
433261 GACCTGT
1 GACCTGT
433268 AAATGATCCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.18, C:0.28, G:0.14, T:0.39
Consensus pattern (32 bp):
GACCTGTTTTCAACCTGACCTGTTTTTAACCT
Found at i:433747 original size:14 final size:14
Alignment explanation
Indices: 433725--433795 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 14
433715 TCCATTTAAA
433725 TTAGGGTTTATGGT
1 TTAGGGTTTATGGT
*
433739 TTAGTGTTTATGGT
1 TTAGGGTTTATGGT
** **
433753 TTAAAGTTTA-GAA
1 TTAGGGTTTATGGT
*
433766 TTAGGGTTTATGAT
1 TTAGGGTTTATGGT
* *
433780 TTAGGATTTAGGGT
1 TTAGGGTTTATGGT
433794 TT
1 TT
433796 CTATAAACTG
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
13 9 0.20
14 36 0.80
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:433795 original size:41 final size:40
Alignment explanation
Indices: 433719--433795 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 40
433709 TGCTAGTCCA
* *
433719 TTTAAATTAGGGTTTATGGTTTAGTGTTTATGGTTTAAAG
1 TTTAAATTAGGGTTTATGATTTAGTGTTTAGGGTTTAAAG
433759 TTTAGAATTAGGGTTTATGATTTAG-GATTTAGGGTTT
1 TTTA-AATTAGGGTTTATGATTTAGTG-TTTAGGGTTT
433796 CTATAAACTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 5 0.15
41 28 0.85
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (40 bp):
TTTAAATTAGGGTTTATGATTTAGTGTTTAGGGTTTAAAG
Found at i:433888 original size:13 final size:13
Alignment explanation
Indices: 433870--433899 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
433860 TAATTTACTT
433870 TATATAGTTTATA
1 TATATAGTTTATA
433883 TATATAGTTTATA
1 TATATAGTTTATA
433896 TATA
1 TATA
433900 CTATACATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:433904 original size:20 final size:21
Alignment explanation
Indices: 433880--433930 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
433870 TATATAGTTT
*
433880 ATATATATAGTTTATATATAC
1 ATATATATAGTTTATACATAC
* *
433901 -TATACATGGTTTATACATAC
1 ATATATATAGTTTATACATAC
433921 ATATTATATA
1 ATA-TATATA
433931 AAATTATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 17 0.74
21 2 0.09
22 4 0.17
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (21 bp):
ATATATATAGTTTATACATAC
Found at i:434416 original size:546 final size:549
Alignment explanation
Indices: 433647--435898 Score: 3820
Period size: 546 Copynumber: 4.1 Consensus size: 549
433637 TTTTGGCAAT
* *
433647 ACATTAGTTTACAAAGG-CCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTG
1 ACATTAGTTTACATAGGCCCAATGC--AAGCCCACTCTTTTATTACAAATATATATGCATTAGTG
* *
433711 CTAGTCCATTTAAATTAGGGTTTATGGTTTAGTGTTTATGGTTTAAAGTTTAGAATTAGGGTTTA
64 CTAGTCCATTTAAATTAGGGTTTATGGTTTAATGTTTATAGTTTAAAGTTTAGAATTAGGGTTTA
*
433776 TGATTTAGGATTTAGGGTTTCTATAAACTGTATATTTTATTACTTTATATAGTTTATGCATAGTG
129 TGATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTG
433841 TTTCTATAAACTATATAAGTAATTTACTTTATATAG-T-T-TATATATATAGTTTATATATACTA
194 TTTCTATAAACTATATAAGTAATTTACTTTATATAGTTATATATATATATAGTTTATATATACTA
433903 TACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGT
259 TACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGT
433968 AAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGG
324 AAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGG
434033 TTCATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTA
389 TTCATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTA
434098 GGTTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAA
454 GGTTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAA
434163 TAAGTCCATTTGCAATAGTGCTAGTCCATTA
519 TAAGTCCATTTGCAATAGTGCTAGTCCATTA
*
434194 ACATTAGTTTACATAGGCCCAATGCAAGTCCACTCTTTTATTACAAATATATATGCATTAGTGCT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
* *
434259 AGTCTATTTAAATTAGGGTTTATGGTTTAATGTTTATAGTTTAAAGCTTAGAATTAGGGTTTATG
66 AGTCCATTTAAATTAGGGTTTATGGTTTAATGTTTATAGTTTAAAGTTTAGAATTAGGGTTTATG
434324 ATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTT
131 ATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTT
434389 TCTATAAACTATATAAGTAATTTACTTTATATAG-T-T-TATATATATAGTTTATATATACTATA
196 TCTATAAACTATATAAGTAATTTACTTTATATAGTTATATATATATATAGTTTATATATACTATA
434451 CATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAA
261 CATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAA
*
434516 ATTATATAAATCATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTT
326 ATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTT
434581 CATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGG
391 CATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGG
*
434646 TTAATTGA-ATTTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAAT
456 TTAATTCACA-TTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAAT
434710 AAGTCCATTTGCAATAGTGCTAGTCCATTA
520 AAGTCCATTTGCAATAGTGCTAGTCCATTA
434740 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
434805 AGTCCATTTAAATTA--G-----GGTTT-ATG------GTTTAAAGTTTAGAATTAGGGTTTATG
66 AGTCCATTTAAATTAGGGTTTATGGTTTAATGTTTATAGTTTAAAGTTTAGAATTAGGGTTTATG
*
434856 ATTTAGGGTTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTT
131 ATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTT
*
434921 TCTATAAACTATATAAGTAGTTTACTTTATATAGTTTATATATATATATAGTTTATATATACTAT
196 TCTATAAACTATATAAGTAATTTACTTTATATAG-TTATATATATATATAGTTTATATATACTAT
434986 ACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTA
260 ACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTA
*
435051 AATTATAT-AAACATGATTAATTAGGTGTTAAATAATTAGTATGTCATATTGCATA-T-TATGGT
325 AATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGT
*
435113 TCATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTTTATTTTAGTTGCATGTTAG
390 TCATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAG
435178 GTTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAAT
455 GTTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAAT
*
435243 AAGTCCATTTGTAATAGTGCTAGTCCATTA
520 AAGTCCATTTGCAATAGTGCTAGTCCATTA
* * *
435273 ACATTAGTTTACATAGGCCCAGTGCAAGCCCACTATTTTATTATAAATATATATGCATTAGTGCT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
* * * * * *** *
435338 AGTCTATTTATATTAGGGTTTATGATTTAGTATTTAGT-GTTTGTGGTTTA-AAGTTTAGTGTTT
66 AGTCCATTTAAATTAGGGTTTATGGTTTAATGTTTA-TAGTTTAAAGTTTAGAA--TTAGGGTTT
* * * * *
435401 ATGGTTTATGATTTAAGGTTTCTATAAACTATATATTTTACTACTTTATATAGTTTATGTATAGT
128 ATGATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGT
435466 GTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATATAGTTTATATATAC
193 GTTTCTATAAACTATATAAGTAATTTACTTTATATAG-TTATATATATATATAGTTTATATATAC
435531 TATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAAT
257 TATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAAT
* *
435596 GTAAACTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTCCATATTATAT
322 GTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATAT
* * * *
435661 GGTTCATAAATAATAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGT
387 GGTTCATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGT
* * *
435726 TAGGTTAATTCACATTAATAGCCCATTTATTTTGTTATTATGAATAAGTAATAATAAAACCCAAA
452 TAGGTTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAA
* *
435791 ATTAAGTCCATTTGTAATAGTGCTAGTCCATTA
517 AATAAGTCCATTTGCAATAGTGCTAGTCCATTA
* * * *
435824 ACATTAATTTAGATAGGCCCAATGCAATCCCACTCTTTTATTACAAATATATATGCATTAGTGAT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
435889 AGTCCATTTA
66 AGTCCATTTA
435899 CATTTTAAAT
Statistics
Matches: 1620, Mismatches: 59, Indels: 48
0.94 0.03 0.03
Matches are distributed among these distances:
532 123 0.08
533 236 0.15
534 3 0.00
535 47 0.03
536 98 0.06
538 3 0.00
539 5 0.00
540 4 0.00
541 1 0.00
544 1 0.00
545 1 0.00
546 591 0.36
547 25 0.02
548 212 0.13
549 45 0.03
550 1 0.00
551 224 0.14
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (549 bp):
ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
AGTCCATTTAAATTAGGGTTTATGGTTTAATGTTTATAGTTTAAAGTTTAGAATTAGGGTTTATG
ATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTT
TCTATAAACTATATAAGTAATTTACTTTATATAGTTATATATATATATAGTTTATATATACTATA
CATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAA
ATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTT
CATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGG
TTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATA
AGTCCATTTGCAATAGTGCTAGTCCATTA
Found at i:434434 original size:13 final size:13
Alignment explanation
Indices: 434416--434445 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
434406 TAATTTACTT
434416 TATATAGTTTATA
1 TATATAGTTTATA
434429 TATATAGTTTATA
1 TATATAGTTTATA
434442 TATA
1 TATA
434446 CTATACATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:434450 original size:20 final size:21
Alignment explanation
Indices: 434426--434476 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
434416 TATATAGTTT
*
434426 ATATATATAGTTTATATATAC
1 ATATATATAGTTTATACATAC
* *
434447 -TATACATGGTTTATACATAC
1 ATATATATAGTTTATACATAC
434467 ATATTATATA
1 ATA-TATATA
434477 AAATTATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 17 0.74
21 2 0.09
22 4 0.17
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (21 bp):
ATATATATAGTTTATACATAC
Found at i:434863 original size:14 final size:14
Alignment explanation
Indices: 434817--434867 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
434807 TCCATTTAAA
*
434817 TTAGGGTTTATGGT
1 TTAGGGTTTATGAT
** *
434831 TTAAAGTTTA-GAA
1 TTAGGGTTTATGAT
434844 TTAGGGTTTATGAT
1 TTAGGGTTTATGAT
434858 TTAGGGTTTA
1 TTAGGGTTTA
434868 GGGTTTCTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
13 9 0.31
14 20 0.69
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.47
Consensus pattern (14 bp):
TTAGGGTTTATGAT
Found at i:434960 original size:9 final size:9
Alignment explanation
Indices: 434946--434979 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
434936 AGTAGTTTAC
434946 TTTATATAG
1 TTTATATAG
434955 TTTATATA-
1 TTTATATAG
*
434963 TATATATAG
1 TTTATATAG
434972 TTTATATA
1 TTTATATA
434980 TACTATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (9 bp):
TTTATATAG
Found at i:434997 original size:20 final size:18
Alignment explanation
Indices: 434948--434986 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
434938 TAGTTTACTT
434948 TATATAGTTTATATATA-
1 TATATAGTTTATATATAC
434965 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
434983 TATA
1 TATA
434987 CATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:435379 original size:21 final size:20
Alignment explanation
Indices: 435343--435415 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
435333 GTGCTAGTCT
*
435343 ATTTATA-TTAGGGTTTATG
1 ATTTATATTTAGTGTTTATG
*
435362 ATTTAGTATTTAGTGTTTGTG
1 ATTTA-TATTTAGTGTTTATG
* *
435383 GTTTAAAGTTTAGTGTTTATG
1 ATTTATA-TTTAGTGTTTATG
*
435404 GTTTATGATTTA
1 ATTTAT-ATTTA
435416 AGGTTTCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 5 0.11
20 3 0.07
21 35 0.80
22 1 0.02
ACGTcount: A:0.23, C:0.00, G:0.22, T:0.55
Consensus pattern (20 bp):
ATTTATATTTAGTGTTTATG
Found at i:435472 original size:48 final size:49
Alignment explanation
Indices: 435418--435512 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 49
435408 ATGATTTAAG
** * *
435418 GTTTCTATAAACTATATATTTTA-CTACTTTATATAGTTTATGTATAGT
1 GTTTCTATAAACTATATAAGTAATCTACTTTATATAGTTTATATATAGT
*
435466 GTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATA
1 GTTTCTATAAACTATATAAGTAATCTACTTTATATAGTTTATATATA
435513 TATATAGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 20 0.49
49 21 0.51
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (49 bp):
GTTTCTATAAACTATATAAGTAATCTACTTTATATAGTTTATATATAGT
Found at i:435508 original size:9 final size:9
Alignment explanation
Indices: 435494--435527 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
435484 AGTAATTTAC
435494 TTTATATAG
1 TTTATATAG
435503 TTTATATA-
1 TTTATATAG
*
435511 TATATATAG
1 TTTATATAG
435520 TTTATATA
1 TTTATATA
435528 TACTATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (9 bp):
TTTATATAG
Found at i:435545 original size:20 final size:18
Alignment explanation
Indices: 435496--435534 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
435486 TAATTTACTT
435496 TATATAGTTTATATATA-
1 TATATAGTTTATATATAC
435513 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
435531 TATA
1 TATA
435535 CATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:435763 original size:548 final size:548
Alignment explanation
Indices: 434844--435898 Score: 1799
Period size: 551 Copynumber: 1.9 Consensus size: 548
434834 AAGTTTAGAA
* * *
434844 TTAGGGTTTATGATTTAGGGTTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTT
1 TTAGGGTTTATGATTTAGGATTTAAGGTTTCTATAAACTATATATTTTACTACTTTATATAGTTT
*
434909 ATGCATAGTGTTTCTATAAACTATATAAGTAGTTTACTTTATATAGTTTATATATATATATAGTT
66 ATGCATAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATATAGTT
434974 TATATATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAAT
131 TATATATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAAT
* * *
435039 TATTTAAATGTAAATTATATAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCATATTGCA
196 TATTTAAATGTAAACTATATAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTCCA
* **
435104 TATTATGGTTCATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTTTATTTTAGTT
261 TATTATGGTTCATAAATAATAGTACATGTCATATTAATTTAAATTGCATAATTAGTATTTTAGTT
* *
435169 GCATGTTAGGTTAATTCACATTAATGGCTCATTTATTTTGTTG-TTATGAATAAGTAATAATAAA
326 GCATGTTAGGTTAATTCACATTAATAGCCCATTTA-TTTGTTGTTTATGAATAAGTAATAATAAA
* *
435233 ACCCAAAAATAAGTCCATTTGTAATAGTGCTAGTCCATTAACATTAGTTTACATAGGCCCAGTGC
390 ACCCAAAAATAAGTCCATTTGTAATAGTGCTAGTCCATTAACATTAATTTACATAGGCCCAATGC
* * *
435298 AAGCCCACTATTTTATTATAAATATATATGCATTAGTGCTAGTCTATTTATATTAGGGTTTATGA
455 AAGCCCACTATTTTATTACAAATATATATGCATTAGTGATAGTCCATTTATATTAGGGTTTATGA
435363 TTTAGTATTTAGTGTTTGTGGTTTAAAGT
520 TTTAGTATTTAGTGTTTGTGGTTTAAAGT
* * *
435392 TTAGTGTTTATGGTTTATGATTTAAGGTTTCTATAAACTATATATTTTACTACTTTATATAGTTT
1 TTAGGGTTTATGATTTAGGATTTAAGGTTTCTATAAACTATATATTTTACTACTTTATATAGTTT
*
435457 ATGTATAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATATAGTT
66 ATGCATAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATATAGTT
435522 TATATATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAAT
131 TATATATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAAT
435587 TATTTAAATGTAAACTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTCC
196 TATTTAAATGTAAACTATAT-AAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTCC
* *
435652 ATATTATATGGTTCATAAATAATAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTA
260 ATA-T-TATGGTTCATAAATAATAGTACATGTCATATTAATTTAAATTGCATAATTAGTATTTTA
*
435717 GTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTT-ATTATGAATAAGTAATAAT
323 GTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTA-TTTGTTGTTTATGAATAAGTAATAAT
* *
435781 AAAACCCAAAATTAAGTCCATTTGTAATAGTGCTAGTCCATTAACATTAATTTAGATAGGCCCAA
387 AAAACCCAAAAATAAGTCCATTTGTAATAGTGCTAGTCCATTAACATTAATTTACATAGGCCCAA
* *
435846 TGCAATCCCACTCTTTTATTACAAATATATATGCATTAGTGATAGTCCATTTA
452 TGCAAGCCCACTATTTTATTACAAATATATATGCATTAGTGATAGTCCATTTA
435899 CATTTTAAAT
Statistics
Matches: 476, Mismatches: 27, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
548 206 0.43
549 45 0.09
550 1 0.00
551 224 0.47
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (548 bp):
TTAGGGTTTATGATTTAGGATTTAAGGTTTCTATAAACTATATATTTTACTACTTTATATAGTTT
ATGCATAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATATAGTT
TATATATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAAT
TATTTAAATGTAAACTATATAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTCCA
TATTATGGTTCATAAATAATAGTACATGTCATATTAATTTAAATTGCATAATTAGTATTTTAGTT
GCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTGTTGTTTATGAATAAGTAATAATAAAA
CCCAAAAATAAGTCCATTTGTAATAGTGCTAGTCCATTAACATTAATTTACATAGGCCCAATGCA
AGCCCACTATTTTATTACAAATATATATGCATTAGTGATAGTCCATTTATATTAGGGTTTATGAT
TTAGTATTTAGTGTTTGTGGTTTAAAGT
Found at i:439811 original size:120 final size:120
Alignment explanation
Indices: 439597--439818 Score: 327
Period size: 120 Copynumber: 1.9 Consensus size: 120
439587 ATACTTAAAT
* * * * *
439597 TATCAGTTTTGGTTCGTTTTAATACCTAATTTTTAATTTTTTCAAAACTATACATATCGTTTAGT
1 TATCAGTTTTGCTTCGTTTTAATACATAAATTTTAATTTTTTCAAAACTATACATAACGTTTAAT
* *
439662 TTTTGTTTCATTTTAGTACTCACTGTTAAAAACTTAATGCTTTTAGTACCTAGAC
66 TTTTGTTTCATTTTAGTACCCACTATTAAAAACTTAATGCTTTTAGTACCTAGAC
* * * * **
439717 TATCAGTTTTGCTTCTTTTTAGTACATAAATTTTATTTTTTTTAAAACTATATTTAACGTTTAAT
1 TATCAGTTTTGCTTCGTTTTAATACATAAATTTTAATTTTTTCAAAACTATACATAACGTTTAAT
439782 TTTTGTTTCATTTTAGTACCCACTATTAAAAACTTAA
66 TTTTGTTTCATTTTAGTACCCACTATTAAAAACTTAA
439819 CGTGTTTAGT
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
120 89 1.00
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (120 bp):
TATCAGTTTTGCTTCGTTTTAATACATAAATTTTAATTTTTTCAAAACTATACATAACGTTTAAT
TTTTGTTTCATTTTAGTACCCACTATTAAAAACTTAATGCTTTTAGTACCTAGAC
Found at i:439857 original size:120 final size:120
Alignment explanation
Indices: 439583--439860 Score: 326
Period size: 120 Copynumber: 2.3 Consensus size: 120
439573 GAAATAAGTA
* * * * * * *
439583 TTTAATACTTAAATTATCAGTTTTGGTTCGTTTTAATACCTAATTTTTAATTTTTTCAAAACTAT
1 TTTAGTACATAAACTATCAGTTTTGGCTCGTTTTAGTACATAAATTTTAATTTTTTCAAAACTAT
* * * * *
439648 ACATATCGTTTAGTTTTTGTTTCATTTTAGTACTCACTGTTAAAAACTTAATGCT
66 ACATAACGTTTAATTTTTGTTTCATTTTAGTACCCACTATTAAAAACTTAACGCT
* * * * *
439703 TTTAGTACCTAGACTATCAGTTTT-GCTTCTTTTTAGTACATAAATTTTATTTTTTTTAAAACTA
1 TTTAGTACATAAACTATCAGTTTTGGC-TCGTTTTAGTACATAAATTTTAATTTTTTCAAAACTA
**
439767 TATTTAACGTTTAATTTTTGTTTCATTTTAGTACCCACTATTAAAAACTTAACG-T
65 TACATAACGTTTAATTTTTGTTTCATTTTAGTACCCACTATTAAAAACTTAACGCT
* * *
439822 GTTTAGTATATAAACTATAAGTTTTGGCTAGTTTTAGTA
1 -TTTAGTACATAAACTATCAGTTTTGGCTCGTTTTAGTA
439861 TCTAATTTCA
Statistics
Matches: 131, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
119 2 0.02
120 127 0.97
121 2 0.02
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.49
Consensus pattern (120 bp):
TTTAGTACATAAACTATCAGTTTTGGCTCGTTTTAGTACATAAATTTTAATTTTTTCAAAACTAT
ACATAACGTTTAATTTTTGTTTCATTTTAGTACCCACTATTAAAAACTTAACGCT
Found at i:440804 original size:21 final size:22
Alignment explanation
Indices: 440768--440809 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
440758 CAAGGAAGCA
440768 AACTTCTAACATTTTAGAGGGGC
1 AACTTCTAACATTTTA-AGGGGC
440791 AACTTC-AA-ATTTTAAGGGG
1 AACTTCTAACATTTTAAGGGG
440810 ACAAAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 2 0.11
23 6 0.32
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.31
Consensus pattern (22 bp):
AACTTCTAACATTTTAAGGGGC
Found at i:442665 original size:18 final size:18
Alignment explanation
Indices: 442642--442680 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
442632 TTATACTATG
442642 ATGTCTTCTTTTGGGGAA
1 ATGTCTTCTTTTGGGGAA
442660 ATGTCTTCTTTTGGGGAA
1 ATGTCTTCTTTTGGGGAA
442678 ATG
1 ATG
442681 ATCACGTGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.10, G:0.28, T:0.44
Consensus pattern (18 bp):
ATGTCTTCTTTTGGGGAA
Found at i:444570 original size:27 final size:28
Alignment explanation
Indices: 444537--444604 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
444527 TCAAAAGAAG
* *
444537 AACAAATTAAAAATTTAATTAAT-AAAT
1 AACAAATTAAAAATATAATAAATAAAAT
444564 AACAAATTTAAAAATATAATAAATAAAAT
1 AACAAA-TTAAAAATATAATAAATAAAAT
* *
444593 AAGAGATTAAAA
1 AACAAATTAAAA
444605 TTCAACAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 6 0.17
28 21 0.60
29 8 0.23
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (28 bp):
AACAAATTAAAAATATAATAAATAAAAT
Found at i:444584 original size:20 final size:20
Alignment explanation
Indices: 444547--444585 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
444537 AACAAATTAA
*
444547 AAATTTAATTAATAAATAAC
1 AAATTTAATAAATAAATAAC
444567 AAATTTAA-AAATATAATAA
1 AAATTTAATAAATA-AATAA
444586 ATAAAATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATTTAATAAATAAATAAC
Found at i:445030 original size:34 final size:34
Alignment explanation
Indices: 444987--445052 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
444977 TCATTGTAGT
444987 TTTTTTTTGTCGAAAGCTATGATATCATCAAAAG
1 TTTTTTTTGTCGAAAGCTATGATATCATCAAAAG
445021 TTTTTTTTGTCGAAAGCTATGATATCATCAAA
1 TTTTTTTTGTCGAAAGCTATGATATCATCAAA
445053 CTGTAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (34 bp):
TTTTTTTTGTCGAAAGCTATGATATCATCAAAAG
Found at i:449443 original size:18 final size:18
Alignment explanation
Indices: 449402--449445 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
449392 CTTGGTCCAA
449402 CGTTGACCGTTAACCGAC
1 CGTTGACCGTTAACCGAC
*
449420 CATTGACCGTTAACC-ACC
1 CGTTGACCGTTAACCGA-C
449438 CGTTGACC
1 CGTTGACC
449446 AAAAAGTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (18 bp):
CGTTGACCGTTAACCGAC
Found at i:456558 original size:18 final size:17
Alignment explanation
Indices: 456535--456586 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
456525 CCCGGTCCAA
456535 CGTTGACCGTTGACCACC
1 CGTTGACCGTTGACCA-C
**
456553 CGTTGACTATTGACCGAC
1 CGTTGACCGTTGACC-AC
*
456571 CGTAGACCGTTGACCA
1 CGTTGACCGTTGACCA
456587 AAAAGTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 1 0.04
18 26 0.93
19 1 0.04
ACGTcount: A:0.21, C:0.33, G:0.23, T:0.23
Consensus pattern (17 bp):
CGTTGACCGTTGACCAC
Found at i:457922 original size:29 final size:29
Alignment explanation
Indices: 457880--457951 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
457870 TCTACTATGG
457880 TTTTGAAAATATCTTTTAAATAGTTGCTA
1 TTTTGAAAATATCTTTTAAATAGTTGCTA
457909 TTTTGAAAATATCTTTTAAATAGTTGCTA
1 TTTTGAAAATATCTTTTAAATAGTTGCTA
*
457938 TTTTGAAAAGATCT
1 TTTTGAAAATATCT
457952 ATATATTTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.47
Consensus pattern (29 bp):
TTTTGAAAATATCTTTTAAATAGTTGCTA
Found at i:460179 original size:14 final size:14
Alignment explanation
Indices: 460125--460176 Score: 79
Period size: 14 Copynumber: 3.7 Consensus size: 14
460115 GTTAATAGAA
460125 TGAGTCAACTCGCC
1 TGAGTCAACTCGCC
460139 TGAGTCAACTCGCC
1 TGAGTCAACTCGCC
*
460153 TGAGTCAACTTGTCC
1 TGAGTCAACTCG-CC
460168 -GAGTCAACT
1 TGAGTCAACT
460177 TGTTTGATTC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
14 34 0.94
15 2 0.06
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (14 bp):
TGAGTCAACTCGCC
Found at i:465013 original size:101 final size:100
Alignment explanation
Indices: 464835--465036 Score: 296
Period size: 101 Copynumber: 2.0 Consensus size: 100
464825 ACTTCAACTC
* * **
464835 TTTTTTTAGCATACTTTAAAGGGAGTCATCTCATCACACTATGATCCCACACTCTAAGTGAAAGG
1 TTTTTTAAGCATACTTTAAAGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAGG
* *
464900 GAGCATAACTTCCACCCTCGAGCTAGTCAAGTAGAG
66 GAACATAACTTCCACCC-CAAGCTAGTCAAGTAGAG
* * *
464936 TTTTTTAAGCGTACTTTAAGGGGAGTCAGCTCATCACACTACCATCCCGCACTCTAAGTGAAAGG
1 TTTTTTAAGCATACTTTAAAGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAGG
* *
465001 GAACATACCTTCCACCCCAAGCTAGTCAGGTAGAG
66 GAACATAACTTCCACCCCAAGCTAGTCAAGTAGAG
465036 T
1 T
465037 CATACCGTGA
Statistics
Matches: 90, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
100 17 0.19
101 73 0.81
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (100 bp):
TTTTTTAAGCATACTTTAAAGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAGG
GAACATAACTTCCACCCCAAGCTAGTCAAGTAGAG
Found at i:470050 original size:102 final size:102
Alignment explanation
Indices: 469874--470074 Score: 339
Period size: 102 Copynumber: 2.0 Consensus size: 102
469864 ACATCAACTC
* * *
469874 TTTTTTTAGCATACTTTAAAGGGAGTCATCTCATCACACTACGATCCCACACTCTAAGTGAAAGG
1 TTTTTTAAGCATACTTTAAAGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAGG
*
469939 GAGAATACCTTCCACTCCCGAGCTAGTCAAGTAGGTG
66 GAGAATACCTTCCACCCCCGAGCTAGTCAAGTAGGTG
*
469976 TTTTTTAAGCATACTTTAAGGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAGG
1 TTTTTTAAGCATACTTTAAAGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAGG
* *
470041 GAGCATACCTTCCACCCCCGAGCTAGTCAGGTAG
66 GAGAATACCTTCCACCCCCGAGCTAGTCAAGTAG
470075 AGTCATCCCG
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 92 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (102 bp):
TTTTTTAAGCATACTTTAAAGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAGG
GAGAATACCTTCCACCCCCGAGCTAGTCAAGTAGGTG
Found at i:477996 original size:21 final size:22
Alignment explanation
Indices: 477961--478003 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
477951 TGAACAAGGG
477961 ATCGAGGAAGATCGATCCTTTTC
1 ATCGAGG-AGATCGATCCTTTTC
477984 ATCGAGG-GATCGATCCTTTT
1 ATCGAGGAGATCGATCCTTTT
478004 TGTAAAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 13 0.65
23 7 0.35
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (22 bp):
ATCGAGGAGATCGATCCTTTTC
Found at i:480258 original size:5 final size:5
Alignment explanation
Indices: 480248--480272 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
480238 GTGTGGGCAT
480248 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
480273 TAGTATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:480398 original size:23 final size:23
Alignment explanation
Indices: 480368--480411 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
480358 TGTGATAGTA
*
480368 CATATTAAGTAATAGTTGCATTG
1 CATATTAAATAATAGTTGCATTG
480391 CATATTAAATAATAGTTGCAT
1 CATATTAAATAATAGTTGCAT
480412 ATTATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (23 bp):
CATATTAAATAATAGTTGCATTG
Found at i:480411 original size:18 final size:18
Alignment explanation
Indices: 480387--480434 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
480377 TAATAGTTGC
480387 ATTGCATATTAAATAATAG
1 ATTGCATATTAAA-AATAG
*
480406 -TTGCATATTATAAATAG
1 ATTGCATATTAAAAATAG
480423 TATTGCATATTA
1 -ATTGCATATTA
480435 TATTCGATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 11 0.42
19 10 0.38
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (18 bp):
ATTGCATATTAAAAATAG
Found at i:480430 original size:19 final size:19
Alignment explanation
Indices: 480387--480436 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
480377 TAATAGTTGC
480387 ATTGCATA-T-TAAATAAT
1 ATTGCATATTATAAATAAT
*
480404 AGTTGCATATTATAAATAGT
1 A-TTGCATATTATAAATAAT
480424 ATTGCATATTATA
1 ATTGCATATTATA
480437 TTCGATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 1 0.03
18 7 0.24
19 13 0.45
20 8 0.28
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (19 bp):
ATTGCATATTATAAATAAT
Found at i:488485 original size:11 final size:11
Alignment explanation
Indices: 488471--488506 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
488461 TCTTTTTCCC
488471 TTTTTTTCTTT
1 TTTTTTTCTTT
*
488482 TTTTTTTCTTA
1 TTTTTTTCTTT
488493 TTTTTTTCTTT
1 TTTTTTTCTTT
488504 TTT
1 TTT
488507 CTTCAGGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:488488 original size:22 final size:22
Alignment explanation
Indices: 488458--488506 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
488448 TTTTACTCTA
* *
488458 TTTTCTTTTTC-CCTTTTTTTC
1 TTTTTTTTTTCTCATTTTTTTC
*
488479 TTTTTTTTTTCTTATTTTTTTC
1 TTTTTTTTTTCTCATTTTTTTC
488501 TTTTTT
1 TTTTTT
488507 CTTCAGGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (22 bp):
TTTTTTTTTTCTCATTTTTTTC
Found at i:509482 original size:2 final size:2
Alignment explanation
Indices: 509471--509542 Score: 50
Period size: 2 Copynumber: 38.5 Consensus size: 2
509461 CATTTAATAA
* * *
509471 AT AT -T AT AT AT AT AT AT AT AT TT A- AT AT -T AT -T TT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
509509 AT AT ACT CA- AT AT A- AT AT A- AT AT AT AT AT AT AT A
1 AT AT A-T -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
509543 ATAGAAAACG
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
1 7 0.12
2 47 0.84
3 1 0.02
4 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:509535 original size:23 final size:23
Alignment explanation
Indices: 509470--509536 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
509460 ACATTTAATA
* *
509470 AATATTATATATATATATATATTT
1 AATATTATATA-ATATATATACTC
* * *
509494 AATATTATTTTATAAATATACTC
1 AATATTATATAATATATATACTC
*
509517 AATATAATATAATATATATA
1 AATATTATATAATATATATA
509537 TATATAATAG
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
23 25 0.74
24 9 0.26
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (23 bp):
AATATTATATAATATATATACTC
Found at i:509781 original size:28 final size:29
Alignment explanation
Indices: 509745--509800 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
509735 GTTAATCCAT
*
509745 ATAATTAATAATAATATA-ACATATATAA
1 ATAACTAATAATAATATATACATATATAA
* *
509773 ATAACTAATTATAATATATAGATATATA
1 ATAACTAATAATAATATATACATATATA
509801 TAACCCAGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (29 bp):
ATAACTAATAATAATATATACATATATAA
Found at i:512561 original size:13 final size:14
Alignment explanation
Indices: 512543--512581 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
512533 TTTTCCCCTA
512543 AAAATAAATAAAT-
1 AAAATAAATAAATG
512556 AAAAT-AATAAATG
1 AAAATAAATAAATG
512569 AAAATAAAATAAA
1 AAAAT-AAATAAA
512582 ATTTCTTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.30
13 10 0.43
15 6 0.26
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AAAATAAATAAATG
Found at i:514665 original size:29 final size:29
Alignment explanation
Indices: 514606--514667 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
514596 TAAAGTGTAG
* *
514606 TAAAATAAAATTTAGTAGTTAATATGTAA
1 TAAAATAAAATTTAGTAGTTAAAATGAAA
514635 TAAAAT-AAATGTTAGTAGTTAGAAAT-AAA
1 TAAAATAAAAT-TTAGTAGTTA-AAATGAAA
514664 TAAA
1 TAAA
514668 GTACATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 4 0.14
29 22 0.76
30 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (29 bp):
TAAAATAAAATTTAGTAGTTAAAATGAAA
Found at i:515811 original size:116 final size:115
Alignment explanation
Indices: 515611--515836 Score: 301
Period size: 116 Copynumber: 2.0 Consensus size: 115
515601 TCACTCCACT
* * * * * *
515611 TCCTTTTGTGATGGAATCACCAATTTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCGT
1 TCCTTCTGTGATGGAATAACCAATGTTGAACAAGTTCTTCTCATTATGAACTTACTCTCCCTCAT
** * * *
515676 TGGATGAGTTCTTCTCATTATGAACTCTCCACTATAAATATTGATTCATC
66 CAGACGAGTTCTTCCCATTATGAACTCTCCACTAGAAATATTGATTCATC
*
515726 TCCTTCTGTGATGGAATTGAACCAA-GTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTC
1 TCCTTCTGTGATGGAA-T-AACCAATGTTGAACAAGTTCTTCTCATTATGAACTTACTCTCCCTC
* *
515790 ATCAGACGAGTTCTTCCCATTATGAACTCTCTACTAGAAATGTTGAT
64 ATCAGACGAGTTCTTCCCATTATGAACTCTCCACTAGAAATATTGAT
515837 GCAAGGTTGA
Statistics
Matches: 95, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
115 15 0.16
116 75 0.79
117 5 0.05
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (115 bp):
TCCTTCTGTGATGGAATAACCAATGTTGAACAAGTTCTTCTCATTATGAACTTACTCTCCCTCAT
CAGACGAGTTCTTCCCATTATGAACTCTCCACTAGAAATATTGATTCATC
Found at i:515906 original size:91 final size:91
Alignment explanation
Indices: 515741--516003 Score: 361
Period size: 91 Copynumber: 2.9 Consensus size: 91
515731 CTGTGATGGA
* * * * *
515741 ATTGAACCAA-GTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCAGACGAGTTCTT
1 ATTGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTAGATGAGTTCTT
*
515805 CCCATTATGAACTCTCTACTAGAAAT
66 CCCATTATGAACTCTCCACTAGAAAT
* * *
515831 GTTGATG-CAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCT
1 ATTGA-GCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTAGATGAGTTCT
* *
515895 TCGCATTATGAACTCTCCACTGGAAAT
65 TCCCATTATGAACTCTCCACTAGAAAT
*
515922 ATTGAGCCAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTAGATGAGTT-TT
1 ATTGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTAGATGAGTTCTT
** *
515986 TTCATTATGAACACTCCA
66 CCCATTATGAACTCTCCA
516004 TGTTAATCCC
Statistics
Matches: 152, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
90 25 0.16
91 127 0.84
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.37
Consensus pattern (91 bp):
ATTGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTAGATGAGTTCTT
CCCATTATGAACTCTCCACTAGAAAT
Found at i:517370 original size:20 final size:20
Alignment explanation
Indices: 517345--517417 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
517335 TCATCTTACT
517345 CGAAAGACTTATAGATGGCC
1 CGAAAGACTTATAGATGGCC
* * *
517365 CGAAAGACTTA-CGCATCATGCT
1 CGAAAGACTTATAG-AT--GGCC
*
517387 CGAGAGACTTATAGATGGCC
1 CGAAAGACTTATAGATGGCC
*
517407 CGAAGGACTTA
1 CGAAAGACTTA
517418 CTCGTCAAGA
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
19 1 0.03
20 24 0.60
22 14 0.35
23 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.21
Consensus pattern (20 bp):
CGAAAGACTTATAGATGGCC
Found at i:517594 original size:52 final size:52
Alignment explanation
Indices: 517499--517602 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 52
517489 CTTCCTTTTA
* * *
517499 AAAAATTCATTGAAAATCATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCT
1 AAAAACTCATTGAAAATCATCAAGAAACCCATAAAAATCAGGCTTAGCTTCT
* * *
517551 AAAAACTCATTTGAAAA-CATCAAGAAACCCATGAAGATTAGGCTTAGCTTCT
1 AAAAACTCA-TTGAAAATCATCAAGAAACCCATAAAAATCAGGCTTAGCTTCT
517603 TTTAAAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
52 38 0.84
53 7 0.16
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (52 bp):
AAAAACTCATTGAAAATCATCAAGAAACCCATAAAAATCAGGCTTAGCTTCT
Found at i:519551 original size:9 final size:9
Alignment explanation
Indices: 519533--519666 Score: 67
Period size: 9 Copynumber: 13.8 Consensus size: 9
519523 AAGTGTTTGA
519533 TCTTCTTTTT
1 TCTT-TTTTT
*
519543 T-TTTCTTT
1 TCTTTTTTT
*
519551 TCTTTTTTA
1 TCTTTTTTT
*
519560 TCTATATTTT
1 TCT-TTTTTT
519570 TCATTCTTTTT
1 TC-TT-TTTTT
*
519581 T-TCCTTTTT
1 TCT-TTTTTT
*
519590 TCTCTTTTT
1 TCTTTTTTT
519599 T-TTTTTTT
1 TCTTTTTTT
*
519607 TCTCTTTTT
1 TCTTTTTTT
*
519616 CCTGGTTTTTCT
1 TCT--TTTTT-T
519628 TCTTTTTTT
1 TCTTTTTTT
519637 TCTTTTCTATCTT
1 TC-TTT-T-T-TT
519650 TCTTTCTTTT
1 TCTTT-TTTT
519660 TCTTTTT
1 TCTTTTT
519667 GCTTTTTCGT
Statistics
Matches: 98, Mismatches: 12, Indels: 29
0.71 0.09 0.21
Matches are distributed among these distances:
8 12 0.12
9 37 0.38
10 24 0.24
11 12 0.12
12 9 0.09
13 4 0.04
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.78
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:519603 original size:33 final size:35
Alignment explanation
Indices: 519566--519637 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 35
519556 TTTATCTATA
*
519566 TTTTTCATTCTTTTTTTCCT-TTTTTC-TCTTTTT
1 TTTTTCATTCTCTTTTTCCTGTTTTTCTTCTTTTT
**
519599 TTTTTTTTTCTCTTTTTCCTGGTTTTTCTTCTTTTT
1 TTTTTCATTCTCTTTTTCCT-GTTTTTCTTCTTTTT
519635 TTT
1 TTT
519638 CTTTTCTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 17 0.52
35 6 0.18
36 10 0.30
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.79
Consensus pattern (35 bp):
TTTTTCATTCTCTTTTTCCTGTTTTTCTTCTTTTT
Found at i:519605 original size:35 final size:35
Alignment explanation
Indices: 519533--519660 Score: 106
Period size: 39 Copynumber: 3.5 Consensus size: 35
519523 AAGTGTTTGA
519533 TCTTCTTTTTTT--TTCTTTTCTT-TTTTATCTATATTTT
1 TCTTCTTTTTTTCCTT-TTTTCTTCTTTT-T-T-T-TTTT
519570 TCATTCTTTTTTTCCTTTTTTC-TCTTTTTTTTTTT
1 TC-TTCTTTTTTTCCTTTTTTCTTCTTTTTTTTTTT
*
519605 T-TTCTCTTTTTCCTGGTTTTTCTTCTTTTTTTTCTTT
1 TCTTCTTTTTTTCCT--TTTTTCTTCTTTTTTTT-TTT
*
519642 TCTATCTTTCTTT-CTTTTT
1 TCT-TCTTTTTTTCCTTTTT
519661 CTTTTTGCTT
Statistics
Matches: 78, Mismatches: 3, Indels: 21
0.76 0.03 0.21
Matches are distributed among these distances:
33 12 0.15
35 11 0.14
36 15 0.19
37 7 0.09
38 15 0.19
39 16 0.21
40 2 0.03
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (35 bp):
TCTTCTTTTTTTCCTTTTTTCTTCTTTTTTTTTTT
Found at i:519658 original size:45 final size:45
Alignment explanation
Indices: 519533--519661 Score: 127
Period size: 45 Copynumber: 2.8 Consensus size: 45
519523 AAGTGTTTGA
* * *
519533 TCTTCTTTTTTTTTCTTTTCTTTTTTATCTATATTTTTCATTCTTTT
1 TCTTC-TTTTTTTTCTTTTCTTTTTT-TCTTTCTTTTTCATGCTTTT
* * * *
519580 T-TTCCTTTTTTCTCTTTT-TTTTTTTTTTCTCTTTTTCCTGGTTTT
1 TCTT-CTTTTTTTTCTTTTCTTTTTTTCTT-TCTTTTTCATGCTTTT
* *
519625 TCTTCTTTTTTTTCTTTTCTATCTTTCTTTCTTTTTC
1 TCTTCTTTTTTTTCTTTTCTTTTTTTCTTTCTTTTTC
519662 TTTTTGCTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
44 2 0.03
45 40 0.60
46 23 0.34
47 2 0.03
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (45 bp):
TCTTCTTTTTTTTCTTTTCTTTTTTTCTTTCTTTTTCATGCTTTT
Found at i:519661 original size:35 final size:36
Alignment explanation
Indices: 519586--519663 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 36
519576 TTTTTTTCCT
* * * *
519586 TTTTTC-TCTTTTTTTTTTTTTTCTCTTTTTCCTGG
1 TTTTTCTTCTTTTTTTTTCTTTTCTATCTTTCCTGC
* *
519621 TTTTTCTTC-TTTTTTTTCTTTTCTATCTTTCTTTC
1 TTTTTCTTCTTTTTTTTTCTTTTCTATCTTTCCTGC
519656 TTTTTCTT
1 TTTTTCTT
519664 TTTGCTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
35 34 0.94
36 2 0.06
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.78
Consensus pattern (36 bp):
TTTTTCTTCTTTTTTTTTCTTTTCTATCTTTCCTGC
Found at i:519671 original size:17 final size:15
Alignment explanation
Indices: 519535--519671 Score: 56
Period size: 15 Copynumber: 8.8 Consensus size: 15
519525 GTGTTTGATC
*
519535 TTCTTTTTTTTTCTT
1 TTCTTTTTCTTTCTT
*
519550 TTCTTTTT-TATCTAT
1 TTCTTTTTCTTTCT-T
519565 ATT-TTTCATTCTTT-TT
1 -TTCTTT--TTCTTTCTT
*
519581 TTCCTTTTT-TCTCTT
1 TT-CTTTTTCTTTCTT
519596 TT-TTTTT-TTT-TT
1 TTCTTTTTCTTTCTT
* *
519608 CTCTTTTTCCTGGTTTTT
1 TTCTTTTT-CT--TTCTT
519626 CTTCTTTTT-TTTCTT
1 -TTCTTTTTCTTTCTT
519641 TTCTATCTTTCTTTCTTT
1 TTCT-T-TTTCTTTC-TT
519659 TTCTTTTTGCTTT
1 TTCTTTTT-CTTT
519672 TTCGTGTGTG
Statistics
Matches: 95, Mismatches: 7, Indels: 38
0.68 0.05 0.27
Matches are distributed among these distances:
12 3 0.03
13 12 0.13
14 10 0.11
15 26 0.27
16 9 0.09
17 18 0.19
18 10 0.11
19 7 0.07
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (15 bp):
TTCTTTTTCTTTCTT
Found at i:520998 original size:20 final size:20
Alignment explanation
Indices: 520973--521010 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
520963 AATGTATATG
520973 TACAAATGCAAAGATGCACA
1 TACAAATGCAAAGATGCACA
520993 TACAAATGCAAAGATGCA
1 TACAAATGCAAAGATGCA
521011 AATGCAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.18, G:0.16, T:0.16
Consensus pattern (20 bp):
TACAAATGCAAAGATGCACA
Found at i:521175 original size:23 final size:23
Alignment explanation
Indices: 521144--521204 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
521134 AGCATCTGGG
* *
521144 TACTGCATCATCTTCAAAGCTTA
1 TACTTCATCATCTACAAAGCTTA
*
521167 TACTTCATCATCTACAAAGCTTC
1 TACTTCATCATCTACAAAGCTTA
521190 TACTTCATCATCTAC
1 TACTTCATCATCTAC
521205 TTCCAGAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.36
Consensus pattern (23 bp):
TACTTCATCATCTACAAAGCTTA
Found at i:523413 original size:12 final size:12
Alignment explanation
Indices: 523364--523450 Score: 56
Period size: 12 Copynumber: 7.3 Consensus size: 12
523354 ATCATGAAAC
523364 AAAACAATTAATA
1 AAAACAA-TAATA
* *
523377 ACAAAC-TTAATT
1 A-AAACAATAATA
*
523389 AAAATAA-AATA
1 AAAACAATAATA
523400 AAAACAATAATA
1 AAAACAATAATA
*
523412 AAAACAGT-A-A
1 AAAACAATAATA
* * *
523422 AAAATAGTAAAA
1 AAAACAATAATA
523434 AAAACAATAAATA
1 AAAACAAT-AATA
523447 AAAA
1 AAAA
523451 ACTTAAAATA
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
10 8 0.14
11 14 0.25
12 23 0.40
13 8 0.14
14 4 0.07
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.18
Consensus pattern (12 bp):
AAAACAATAATA
Found at i:523424 original size:22 final size:22
Alignment explanation
Indices: 523399--523444 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
523389 AAAATAAAAT
* *
523399 AAAAACAATAATAAAAACAGTA
1 AAAAACAATAAAAAAAACAATA
* *
523421 AAAAATAGTAAAAAAAACAATA
1 AAAAACAATAAAAAAAACAATA
523443 AA
1 AA
523445 TAAAAAACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.76, C:0.07, G:0.04, T:0.13
Consensus pattern (22 bp):
AAAAACAATAAAAAAAACAATA
Found at i:523458 original size:35 final size:33
Alignment explanation
Indices: 523364--523458 Score: 95
Period size: 35 Copynumber: 2.7 Consensus size: 33
523354 ATCATGAAAC
*
523364 AAAACAATTAATAACAAACTTAATTAAAATAAAATA
1 AAAACAA-TAATAAAAAACTTAA--AAAATAAAATA
*
523400 AAAACAATAAT-AAAAACAGTAAAAAATAGTAAA-A
1 AAAACAATAATAAAAAAC-TTAAAAAATA--AAATA
523434 AAAACAATAAATAAAAAACTTAAAA
1 AAAACAAT-AATAAAAAACTTAAAA
523459 TAAACATAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
33 6 0.12
34 14 0.27
35 18 0.35
36 13 0.25
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.19
Consensus pattern (33 bp):
AAAACAATAATAAAAAACTTAAAAAATAAAATA
Found at i:523611 original size:121 final size:120
Alignment explanation
Indices: 523486--523756 Score: 276
Period size: 132 Copynumber: 2.2 Consensus size: 120
523476 TGAATAAAAT
523486 TAAATAACATAAATAAAT-TGCAATAAAATAAAAGTCAGTAATTAGCAGAGTCAAAACCATAATA
1 TAAATAACATAAATAAATATGCAATAAAATAAAAGT-AGTAATTAGCAGAGTCAAAACCATAATA
* * *
523550 ATAAGGATCATACCCCGAATCGGGTCACCATAAGGTCGAATCAAATATTATAAATAA
65 ATAAGGATCATA-CCCGAATCGGGTCACCACAAGGCCGAATCAAATATTAGAAATAA
* * * *
523607 TAAATAAACAAACAAAAAACAAAAGTTAGAATGCAATAAAATAAAAGTAGTAGTTAGCAGAGTCC
1 TAAAT-----AAC-ATAAA-TAAA--T---ATGCAATAAAATAAAAGTAGTAATTAGCAGAGTCA
* ** * *
523672 GAACCATAATAATGCGGATCATACCCGGATCGGGTCACCACAAGGCCGAATCGAATATTAGAAAT
54 AAACCATAATAATAAGGATCATACCCGAATCGGGTCACCACAAGGCCGAATCAAATATTAGAAAT
*
523737 AG
119 AA
*
523739 TCAATAA-ATAAATAAATA
1 TAAATAACATAAATAAATA
523757 AATAAATAAC
Statistics
Matches: 121, Mismatches: 16, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
119 1 0.01
121 5 0.04
122 1 0.01
124 3 0.02
125 4 0.03
126 3 0.02
127 6 0.05
128 3 0.02
130 1 0.01
132 42 0.35
133 35 0.29
134 17 0.14
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.21
Consensus pattern (120 bp):
TAAATAACATAAATAAATATGCAATAAAATAAAAGTAGTAATTAGCAGAGTCAAAACCATAATAA
TAAGGATCATACCCGAATCGGGTCACCACAAGGCCGAATCAAATATTAGAAATAA
Found at i:523745 original size:132 final size:134
Alignment explanation
Indices: 523504--523746 Score: 364
Period size: 132 Copynumber: 1.8 Consensus size: 134
523494 ATAAATAAAT
523504 TGCAATAAAATAAAAGTCAGTAATTAGCAGAGTCAAAACCATAATAATAAGGATCATACCCCGAA
1 TGCAATAAAATAAAAGTCAGTAATTAGCAGAGTCAAAACCATAATAATAAGGATCATACCCCGAA
* * *
523569 TCGGGTCACCATAAGGTCGAATCAAATATTATAAATAATAAATAAACAAACAAAAAACAAAAGTT
66 TCGGGTCACCACAAGGCCGAATCAAATATTAGAAATAATAAATAAACAAACAAAAAACAAAAGTT
523634 AGAA
131 AGAA
* ** ** *
523638 TGCAATAAAATAAAAGT-AGTAGTTAGCAGAGTCCGAACCATAATAATGCGGATCATA-CCCGGA
1 TGCAATAAAATAAAAGTCAGTAATTAGCAGAGTCAAAACCATAATAATAAGGATCATACCCCGAA
* * *
523701 TCGGGTCACCACAAGGCCGAATCGAATATTAGAAATAGTCAATAAA
66 TCGGGTCACCACAAGGCCGAATCAAATATTAGAAATAATAAATAAA
523747 TAAATAAATA
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
132 45 0.46
133 35 0.36
134 17 0.18
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.20
Consensus pattern (134 bp):
TGCAATAAAATAAAAGTCAGTAATTAGCAGAGTCAAAACCATAATAATAAGGATCATACCCCGAA
TCGGGTCACCACAAGGCCGAATCAAATATTAGAAATAATAAATAAACAAACAAAAAACAAAAGTT
AGAA
Found at i:523750 original size:4 final size:4
Alignment explanation
Indices: 523741--523765 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
523731 AGAAATAGTC
523741 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
523766 CAATGATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:523842 original size:29 final size:29
Alignment explanation
Indices: 523783--523846 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
523773 TAAAGTGCAG
* *
523783 TAAAATAAAAGTTAGTAGTTAATATGTAA
1 TAAAATAAAAGTTAGTAGTTAAAATGAAA
523812 TAAAATAAAAGTTAGTAGTTAGAAAT-AAA
1 TAAAATAAAAGTTAGTAGTTA-AAATGAAA
523841 TAAAAT
1 TAAAAT
523847 GCATAAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 29 0.91
30 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (29 bp):
TAAAATAAAAGTTAGTAGTTAAAATGAAA
Found at i:524594 original size:12 final size:12
Alignment explanation
Indices: 524565--524609 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
524555 AAAAATTCAA
524565 GAGCTCGA--TT
1 GAGCTCGATTTT
524575 GAAGCTCGATTTT
1 G-AGCTCGATTTT
524588 GAGCTCGATTTT
1 GAGCTCGATTTT
524600 GAGCTCGATT
1 GAGCTCGATT
524610 CAAGCTCGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 1 0.03
11 7 0.22
12 21 0.66
13 3 0.09
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.36
Consensus pattern (12 bp):
GAGCTCGATTTT
Found at i:524617 original size:11 final size:12
Alignment explanation
Indices: 524566--524618 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
524556 AAAATTCAAG
*
524566 AGCTCGA-TTGA
1 AGCTCGATTTTA
*
524577 AGCTCGATTTTG
1 AGCTCGATTTTA
*
524589 AGCTCGATTTTG
1 AGCTCGATTTTA
*
524601 AGCTCGA-TTCA
1 AGCTCGATTTTA
524612 AGCTCGA
1 AGCTCGA
524619 ACTCGATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
11 16 0.43
12 21 0.57
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (12 bp):
AGCTCGATTTTA
Found at i:524942 original size:21 final size:21
Alignment explanation
Indices: 524917--525010 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
524907 TGGCATAACT
524917 TAAACCCTAACACATAAACCC
1 TAAACCCTAACACATAAACCC
*
524938 TAAACCTTAACACATAAACCC
1 TAAACCCTAACACATAAACCC
* * *
524959 TAAACTCTAA-ACTTTAAACCT
1 TAAACCCTAACAC-ATAAACCC
* * *
524980 TAAATCCTATCACATAAACTC
1 TAAACCCTAACACATAAACCC
525001 TAAACCCTAA
1 TAAACCCTAA
525011 ACCCTAAACC
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
20 2 0.03
21 54 0.93
22 2 0.03
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACCCTAACACATAAACCC
Found at i:524943 original size:7 final size:7
Alignment explanation
Indices: 524917--525020 Score: 61
Period size: 7 Copynumber: 14.9 Consensus size: 7
524907 TGGCATAACT
524917 TAAACCC
1 TAAACCC
*
524924 T-AACACA
1 TAAAC-CC
524931 TAAACCC
1 TAAACCC
524938 TAAA-CC
1 TAAACCC
* *
524944 TTAACACA
1 TAAAC-CC
524952 TAAACCC
1 TAAACCC
*
524959 TAAACTC
1 TAAACCC
**
524966 TAAACTT
1 TAAACCC
*
524973 TAAACCT
1 TAAACCC
*
524980 TAAATCC
1 TAAACCC
* *
524987 T-ATCACA
1 TAAAC-CC
*
524994 TAAACTC
1 TAAACCC
525001 TAAACCC
1 TAAACCC
525008 TAAACCC
1 TAAACCC
525015 TAAACC
1 TAAACC
525021 TTATCACATA
Statistics
Matches: 73, Mismatches: 18, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
6 9 0.12
7 54 0.74
8 10 0.14
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:524970 original size:35 final size:34
Alignment explanation
Indices: 524917--525031 Score: 95
Period size: 35 Copynumber: 3.1 Consensus size: 34
524907 TGGCATAACT
*
524917 TAAACCCTAACACATAAACCCTAAACCTTAACACA
1 TAAACCCTAA-ACCTAAACCCTAAACCTTAACACA
**
524952 TAAACCCTAAACTCTAAACTTTAAACCTTAAATCCTATCACA
1 TAAACCCTAAAC-CTAAACCCTAAACCTT--A----A-CACA
* *
524994 TAAACTCTAAACCCTAAACCCTAAACCTTATCACA
1 TAAACCCTAAA-CCTAAACCCTAAACCTTAACACA
525029 TAA
1 TAA
525032 TTAGTTATGA
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
34 2 0.03
35 30 0.47
37 1 0.02
40 1 0.02
41 1 0.02
42 28 0.44
43 1 0.02
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.23
Consensus pattern (34 bp):
TAAACCCTAAACCTAAACCCTAAACCTTAACACA
Found at i:526756 original size:65 final size:65
Alignment explanation
Indices: 526649--527116 Score: 695
Period size: 65 Copynumber: 7.2 Consensus size: 65
526639 AGCTACACCG
* * *
526649 GTACAAATCACTCGTATGACACAT-TACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATT
1 GTACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATT
* * * *
526713 GTACATATCACTCATATGACTCATGTACCTTTGTGGTACATGAGGTGGAATAATAATTGAATATT
1 GTACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATT
* * * * * * *
526778 GGACAGTTCACTCATATCACTCATGTACATTTATGGTGCATGAGATGGAGTGATAATTGAATACT
1 GTACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATT
**
526843 GTACAGATCACTCATATGACTCACCTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATT
1 GTACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATT
*
526908 GTACAGATCACTCATATGACTCATGTAACTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATT
1 GTACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATT
* * *
526973 GTACAGATCACTCATATGACTTAAGTATCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATT
1 GTACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATT
* * **
527038 GTACAGATCACTCATATGACTCAAGTACCTTTGTGGCGCATGAGGAAGAGTGATAATTGAATATT
1 GTACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATT
**
527103 GTATTGATCACTCA
1 GTACAGATCACTCA
527117 CGAGACTTGT
Statistics
Matches: 364, Mismatches: 39, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
64 21 0.06
65 343 0.94
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33
Consensus pattern (65 bp):
GTACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATT
Found at i:540534 original size:20 final size:20
Alignment explanation
Indices: 540509--540547 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
540499 CAATGACTGA
*
540509 AGATTGTCCATGGGTCATTT
1 AGATTGTCCATGGGCCATTT
*
540529 AGATTGTCCTTGGGCCATT
1 AGATTGTCCATGGGCCATT
540548 AGAGAAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (20 bp):
AGATTGTCCATGGGCCATTT
Found at i:540864 original size:51 final size:51
Alignment explanation
Indices: 540788--540884 Score: 185
Period size: 51 Copynumber: 1.9 Consensus size: 51
540778 CCACGCTAAT
540788 GTCTTCATCCAATAATTCAAGATCATCATCATCAAGTGATAAAAGTTTAGC
1 GTCTTCATCCAATAATTCAAGATCATCATCATCAAGTGATAAAAGTTTAGC
*
540839 GTCTTTATCCAATAATTCAAGATCATCATCATCAAGTGATAAAAGT
1 GTCTTCATCCAATAATTCAAGATCATCATCATCAAGTGATAAAAGT
540885 CCATCCAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (51 bp):
GTCTTCATCCAATAATTCAAGATCATCATCATCAAGTGATAAAAGTTTAGC
Found at i:541047 original size:3 final size:3
Alignment explanation
Indices: 541039--541108 Score: 58
Period size: 3 Copynumber: 23.7 Consensus size: 3
541029 CATCCATTTG
*
541039 TTA TTA TTA TTA TT- TTA CTA TTA TTA TT- TTA -TA TT- TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
* *
541081 TTA TTA TTTA TTTA ATA ATA TTA TTA TT
1 TTA TTA -TTA -TTA TTA TTA TTA TTA TT
541109 TACAGACCCA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
2 7 0.12
3 42 0.74
4 8 0.14
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:541076 original size:11 final size:13
Alignment explanation
Indices: 541043--541105 Score: 58
Period size: 14 Copynumber: 4.8 Consensus size: 13
541033 CATTTGTTAT
541043 TATTATTATTTTA
1 TATTATTATTTTA
541056 CTATTATTATTTTA
1 -TATTATTATTTTA
*
541070 TA-T-TTATATTA
1 TATTATTATTTTA
*
541081 TTATTATTTATTTAA
1 -TATTA-TTATTTTA
*
541096 TAATATTATT
1 TATTATTATT
541106 ATTTACAGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
11 7 0.17
12 3 0.07
13 8 0.20
14 17 0.41
15 6 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (13 bp):
TATTATTATTTTA
Found at i:543334 original size:28 final size:27
Alignment explanation
Indices: 543303--543356 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
543293 TAATTCTTTC
543303 TTTTCAAAAT-TTGTATATATACTTATTA
1 TTTTCAAAATATT-TATATATA-TTATTA
*
543331 TTTTCATAATATTTATATATATTATT
1 TTTTCAAAATATTTATATATATTATT
543357 TTATTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.21
28 17 0.71
29 2 0.08
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATATTATTA
Found at i:543361 original size:18 final size:16
Alignment explanation
Indices: 543340--543377 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 16
543330 ATTTTCATAA
543340 TATTTATATATATTATTT
1 TATTTA-ATAT-TTATTT
543358 TA-TTAATATTTATTT
1 TATTTAATATTTATTT
543373 TATTT
1 TATTT
543378 TCAAGTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.42
16 6 0.32
17 3 0.16
18 2 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTAATATTTATTT
Found at i:543372 original size:15 final size:16
Alignment explanation
Indices: 543347--543376 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
543337 TAATATTTAT
543347 ATATATTATTTTATTA
1 ATATATTATTTTATTA
543363 ATAT-TTATTTTATT
1 ATATATTATTTTATT
543377 TTCAAGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATATATTATTTTATTA
Found at i:548610 original size:47 final size:48
Alignment explanation
Indices: 548556--548659 Score: 124
Period size: 47 Copynumber: 2.2 Consensus size: 48
548546 AAATATTTTA
*
548556 TCTGATTTCCGA-CTTGAATTCTGTTCTGATA-CATGACCTGAATT-TGT
1 TCTGATTTCCGATCTAG-ATTCTGTTCTGATATC-TGACCTGAATTCTGT
* **
548603 TCTGATTTCTGATCTAGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCCGATCTAGATTCTGTTCTGATATCTGACCTGAATTCTGT
*
548651 TTTGATTTC
1 TCTGATTTC
548660 TGATATATCC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
47 34 0.69
48 15 0.31
ACGTcount: A:0.18, C:0.17, G:0.16, T:0.48
Consensus pattern (48 bp):
TCTGATTTCCGATCTAGATTCTGTTCTGATATCTGACCTGAATTCTGT
Found at i:548637 original size:12 final size:12
Alignment explanation
Indices: 548600--548661 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
548590 GACCTGAATT
*
548600 TGTTCTGATTTC
1 TGTTCTGATATC
*
548612 TGATCTAGAT-TC
1 TGTTCT-GATATC
548624 TGTTCTGATATC
1 TGTTCTGATATC
548636 TGTTCTGA-ATTC
1 TGTTCTGATA-TC
* *
548648 TGTTTTGATTTC
1 TGTTCTGATATC
548660 TG
1 TG
548662 ATATATCCGT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
11 4 0.10
12 35 0.83
13 3 0.07
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.53
Consensus pattern (12 bp):
TGTTCTGATATC
Found at i:548661 original size:24 final size:24
Alignment explanation
Indices: 548556--548663 Score: 107
Period size: 24 Copynumber: 4.5 Consensus size: 24
548546 AAATATTTTA
*
548556 TCTGATTTCCGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
* *
548580 TCTGA-TACATGACCTGAATT-TGT
1 TCTGATTTC-TGATCTGAATTCTGT
548603 TCTGATTTCTGATCT-AGATTCTGT
1 TCTGATTTCTGATCTGA-ATTCTGT
* *
548627 TCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
548651 TTTGATTTCTGAT
1 TCTGATTTCTGAT
548664 ATATCCGTTT
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
22 1 0.01
23 18 0.26
24 48 0.70
25 2 0.03
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:552140 original size:8 final size:9
Alignment explanation
Indices: 552110--552139 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
552100 AAATGGCAAT
552110 CATTCTTTA
1 CATTCTTTA
552119 CATTCTTTA
1 CATTCTTTA
552128 CATT-TTTA
1 CATTCTTTA
552136 CATT
1 CATT
552140 TATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (9 bp):
CATTCTTTA
Found at i:555674 original size:10 final size:10
Alignment explanation
Indices: 555658--555696 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
555648 CTTAAAGAAG
555658 AAAAAATGAT
1 AAAAAATGAT
*
555668 GAAAAATGA-
1 AAAAAATGAT
*
555677 AAAAAATGAA
1 AAAAAATGAT
555687 AAAAAATGAT
1 AAAAAATGAT
555697 GATGAAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (10 bp):
AAAAAATGAT
Found at i:555681 original size:9 final size:9
Alignment explanation
Indices: 555658--555691 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
555648 CTTAAAGAAG
555658 AAAAAATGA
1 AAAAAATGA
*
555667 TGAAAAATGA
1 -AAAAAATGA
555677 AAAAAATGA
1 AAAAAATGA
555686 AAAAAA
1 AAAAAA
555692 ATGATGATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (9 bp):
AAAAAATGA
Found at i:555682 original size:19 final size:19
Alignment explanation
Indices: 555658--555695 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
555648 CTTAAAGAAG
**
555658 AAAAAATGATGAAAAATGA
1 AAAAAATGAAAAAAAATGA
555677 AAAAAATGAAAAAAAATGA
1 AAAAAATGAAAAAAAATGA
555696 TGATGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (19 bp):
AAAAAATGAAAAAAAATGA
Found at i:555720 original size:29 final size:28
Alignment explanation
Indices: 555658--555721 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
555648 CTTAAAGAAG
555658 AAAAAATGATGAAAAATGAAAAAAATGAA
1 AAAAAATGATGAAAAATG-AAAAAATGAA
*
555687 AAAAAATGATGATGAAATG-AAAAATGAA
1 AAAAAATGATGA-AAAATGAAAAAATGAA
*
555715 AGAAAAT
1 AAAAAAT
555722 AAGGGTCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 15 0.47
29 12 0.38
30 5 0.16
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (28 bp):
AAAAAATGATGAAAAATGAAAAAATGAA
Found at i:557669 original size:235 final size:230
Alignment explanation
Indices: 557255--557717 Score: 700
Period size: 235 Copynumber: 2.0 Consensus size: 230
557245 TAGCAAAAGA
* *
557255 TTTGAATCCATTACTCAATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTG
1 TTTGAATCCATCACTCAATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTATCTG
* * *
557320 AAGAGGAAGGAGTTCATAATGAAAAGAACTTGTTCAATCTTTTTCTTGATTCTATCACAGAAGGA
66 AAGAGGAAGGAGTTCATAATGAAAAGAACTTGTTCAATCTTTTGCATGACTCTATCACAGAAGGA
*
557385 GATAGATCATCATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
131 GATAGATCAGCATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-A-
557450 AAGAAATTCATAATGAAAAGAATTTGTTCAAACCTTTTG
193 AAGAAATTCATAATGAAAAGAATTTGTTC-AACCTTTTG
* * *
557489 TTTGAATTCATCACTCGATGGATCAATTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTATCTG
1 TTTGAATCCATCACTCAATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTATCTG
* *
557554 AAGAGGAAGAAGAAGTTCATGAT-AAGAAGAGCTTGTTCAA-C-TTTGCATGACTCTATCACAGA
66 AAGAGGAAG--G-AGTTCATAATGAA-AAGAACTTGTTCAATCTTTTGCATGACTCTATCACAGA
557616 AGGAGATAGATCAGCATCAACTTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
127 AGGAGATAGATCAGCATCAACTTTTCCAGAAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAA
* *
557680 GAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
191 GAAAGAAATTCATAATGAAAAGAATTTGTTCAACCTTT
557718 ACATGACTCT
Statistics
Matches: 211, Mismatches: 13, Indels: 13
0.89 0.05 0.05
Matches are distributed among these distances:
231 7 0.03
232 27 0.13
233 1 0.00
234 72 0.34
235 78 0.37
236 4 0.02
237 22 0.10
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (230 bp):
TTTGAATCCATCACTCAATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTATCTG
AAGAGGAAGGAGTTCATAATGAAAAGAACTTGTTCAATCTTTTGCATGACTCTATCACAGAAGGA
GATAGATCAGCATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAG
AAATTCATAATGAAAAGAATTTGTTCAACCTTTTG
Found at i:557800 original size:235 final size:235
Alignment explanation
Indices: 557276--557803 Score: 634
Period size: 235 Copynumber: 2.2 Consensus size: 235
557266 TACTCAATGG
*
557276 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGGAGTTCATAATG
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTG-A-A-GAAGAAGTTCATAATG
* * * *
557341 AAAAGAACTTGTTCAATCTTTTTCTTGATTCTATCACAGAAGGAGATAGATCATCATCAACTTTT
63 AAAAGAACTTGTTCAATCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTT
557406 CCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAAAAGA
128 CCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAAAAGA
*** ** *
557471 ATTTGTTCAAACCTTTTGTTTGAATTCATCACTCGATGGATCA
193 ATTTGTTCAAACCTTTTACATGAATTCATCACGAGATAGATCA
* *
557514 AT----TTTTCCAGAAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATG
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCT------GAAGAAGAAGTTCATA
*
557575 AT-AAGAAGAGCTTGTTCAA-C-TTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATCAAC
60 ATGAA-AAGAACTTGTTCAATCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATCAAC
*
557637 TTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-A-AAGAAGTTCATAATGA
124 TTTTCCAGAAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
* *
557698 GAAGAATTTGTTC-AACC-TTTACATG-ACTCTATCACAGAAAGAGATAGATCA
188 AAAGAATTTGTTCAAACCTTTTACATGAATTC-ATCAC-----GAGATAGATCA
557749 TCATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAG
1 --ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAG
557804 AACTCATCAG
Statistics
Matches: 252, Mismatches: 18, Indels: 43
0.81 0.06 0.14
Matches are distributed among these distances:
229 3 0.01
230 10 0.04
231 4 0.02
232 27 0.11
233 1 0.00
234 39 0.15
235 96 0.38
236 3 0.01
237 28 0.11
238 3 0.01
239 1 0.00
240 1 0.00
241 36 0.14
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (235 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGTTCATAATGAAA
AGAACTTGTTCAATCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCA
GAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAAAAGAATT
TGTTCAAACCTTTTACATGAATTCATCACGAGATAGATCA
Found at i:557804 original size:19 final size:19
Alignment explanation
Indices: 557780--557824 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
557770 GTTCATAATG
* * *
557780 AGAAGAACTTATCTGAAGA
1 AGAAGAACTCATCAGAAAA
557799 AGAAGAACTCATCAGAAAA
1 AGAAGAACTCATCAGAAAA
557818 AGAAGAA
1 AGAAGAA
557825 TTTGTTCAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.56, C:0.11, G:0.20, T:0.13
Consensus pattern (19 bp):
AGAAGAACTCATCAGAAAA
Found at i:557862 original size:121 final size:118
Alignment explanation
Indices: 557276--557838 Score: 582
Period size: 120 Copynumber: 4.7 Consensus size: 118
557266 TACTCAATGG
* * *
557276 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGGAGTTCATAATG
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGTTCAGAAT-
* * * * * *
557341 AA-AAGAACTTGTTCAATCTTTTTCTTGATTCTATCACAGAAGGAGATAGATCATC
65 AAGAAGAATTTGTTCAA-CCTTTGCATGACTCTATCACAGAA-GAGATAGATCAGC
*
557396 ATCAACTTTTCCAGA-AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCA
1 ATCAACTTTTCCAGAGA-AAGTTCATAATGAGAAGAACTTATCTGAAGAA-GAAGAAG---TTCA
* ** * * *
557460 TAATGAA-AAGAATTTGTTCAAACCTTTTGTTTGAAT-TCATCAC--------TCGAT--GG
61 GAAT-AAGAAGAATTTGTTC-AACC-TTTGCATGACTCT-ATCACAGAAGAGATAGATCAGC
* *
557510 ATCAATTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATG
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTG-A-A-GAAGAAGAAGTTCA-G
**
557575 -ATAAGAAGAGCTTGTTCAA-CTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
62 AATAAGAAGAATTTGTTCAACCTTTGCATGACTCTATCACAGAA-GAGATAGATCAGC
* *
557631 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGTTCATAAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAG-AAGAAGTTCAGAAT
* * *
557696 GAGAAGAATTTGTTCAACCTTTACATGACTCTATCACAGAAAGAGATAGATCATC
65 AAGAAGAATTTGTTCAACCTTTGCATGACTCTATCACAG-AAGAGATAGATCAGC
*
557751 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAACTCATCAGAA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGT--TCAGAA
*
557816 AAAGAAGAATTTGTTCAACCTTT
64 TAAGAAGAATTTGTTCAACCTTT
557839 TGCTAGATTA
Statistics
Matches: 376, Mismatches: 35, Indels: 63
0.79 0.07 0.13
Matches are distributed among these distances:
110 13 0.03
111 2 0.01
112 4 0.01
113 16 0.04
114 40 0.11
115 2 0.01
116 12 0.03
117 3 0.01
118 4 0.01
119 38 0.10
120 127 0.34
121 76 0.20
124 24 0.06
125 15 0.04
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (118 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGTTCAGAATA
AGAAGAATTTGTTCAACCTTTGCATGACTCTATCACAGAAGAGATAGATCAGC
Found at i:558067 original size:3 final size:3
Alignment explanation
Indices: 558059--558130 Score: 53
Period size: 3 Copynumber: 24.7 Consensus size: 3
558049 CATCTATTTG
* *
558059 TTA TTA TTA TTA TT- TTC CTA TTA TTA TT- TTA -TA TT- TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
* * *
558101 TTA TTA TTTA TTA ATA ATA ATA TTA TTA TT
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
558131 TACAGACCCA
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
2 7 0.12
3 47 0.81
4 4 0.07
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:558132 original size:22 final size:23
Alignment explanation
Indices: 558077--558132 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
558067 ATTATTTTCC
* * *
558077 TATTATTATTT-TATATTTATAT
1 TATTATTATTTATATAATAATAA
558099 TATTATTATTTAT-TAATAATAA
1 TATTATTATTTATATAATAATAA
558121 TATTATTATTTA
1 TATTATTATTTA
558133 CAGACCCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTATTATTTATATAATAATAA
Found at i:558275 original size:98 final size:98
Alignment explanation
Indices: 558115--558312 Score: 387
Period size: 98 Copynumber: 2.0 Consensus size: 98
558105 TATTTATTAA
*
558115 TAATAATATTATTATTTACAGACCCAAAACTAGACCGGCCCAGTTACAAAAGATCAACCCATACT
1 TAATAATATTATTATTTACAGACCCAAAACTAGACCGACCCAGTTACAAAAGATCAACCCATACT
558180 GACCTAACTATAAACCCTAAACCCATTTAGGGT
66 GACCTAACTATAAACCCTAAACCCATTTAGGGT
558213 TAATAATATTATTATTTACAGACCCAAAACTAGACCGACCCAGTTACAAAAGATCAACCCATACT
1 TAATAATATTATTATTTACAGACCCAAAACTAGACCGACCCAGTTACAAAAGATCAACCCATACT
558278 GACCTAACTATAAACCCTAAACCCATTTAGGGT
66 GACCTAACTATAAACCCTAAACCCATTTAGGGT
558311 TA
1 TA
558313 GTATCAATTT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (98 bp):
TAATAATATTATTATTTACAGACCCAAAACTAGACCGACCCAGTTACAAAAGATCAACCCATACT
GACCTAACTATAAACCCTAAACCCATTTAGGGT
Done.