Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 273 of 311
Found at i:90115392 original size:15 final size:14
Alignment explanation
Indices: 90115356--90115388 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
90115346 CGCTGAGGTA
90115356 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
*
90115370 TTTTCAAATTTTGT
1 TTTTCAAATTCTGT
90115384 TTTTC
1 TTTTC
90115389 CAAAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (14 bp):
TTTTCAAATTCTGT
Found at i:90115502 original size:90 final size:90
Alignment explanation
Indices: 90115190--90115744 Score: 416
Period size: 87 Copynumber: 6.0 Consensus size: 90
90115180 CGTTGAGGTA
* * *
90115190 TTTTCAATTTCTGTCTTTCAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCA--AG
1 TTTTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCAC
* *
90115253 ACGCTGAGGTGTTTTCCATTTCTAT
66 ACGCTGAGGTATTTTCAATTTCTAT
* * ** * * *
90115278 TCTTCAATTTCTGTGTTTCAAAAAAAATCAGTTCATATTGCGAGTGGTGAGTTGAGCCTTGACTC
1 TTTTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCA-GC
* *
90115343 ACACGCTGAGGTATTTTCAAATTCTGT
64 ACACGCTGAGGTATTTTCAATTTCTAT
* * * *
90115370 TTTTCAAATTT-TGTTTTTC-CAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGGA
1 TTTTC-AATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCA
* *
90115433 CACGCTGAGATATTTTCAATTTCCTTT
65 CACGCTGAGGTATTTTCAATTT-CTAT
*
90115460 TTTTCAATTTATGT-TTGTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAT
1 TTTTCAATTTCTGTCTT-TCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--
* *
90115523 CACACGCCGAGGTATTTTCAATTGATTTTTAT
63 CACACGCTGAGGTATTTTC-A---ATTTCTAT
* * * *** *
90115555 TTTT-ATTTTTTTTTCAATTTATGCTTTGCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGC
1 TTTTCA-ATTTCTGTC---TT-T-C--AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* ** * **
90115619 CTCGGGTCACATACCGAGGTATTTTCAAAATCTAT
58 CTC-AG-CACACGCTGAGGTATTTTCAATTTCTAT
* * ** *
90115654 TTTACAAATTT-TGT-TTT----AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCT
1 TTTTC-AATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCA
* *
90115713 CACGTGCTGAGCTATTTTCAATTTCTGT
65 CAC--GCTGAGGTATTTTCAATTTCTAT
90115741 TTTT
1 TTTT
90115745 AATGTTTAGT
Statistics
Matches: 380, Mismatches: 59, Indels: 57
0.77 0.12 0.11
Matches are distributed among these distances:
85 3 0.01
86 2 0.01
87 55 0.14
88 53 0.14
89 30 0.08
90 55 0.14
91 33 0.09
92 49 0.13
93 6 0.02
94 2 0.01
95 13 0.03
96 4 0.01
99 13 0.03
100 4 0.01
101 1 0.00
102 1 0.00
103 55 0.14
104 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (90 bp):
TTTTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCAC
ACGCTGAGGTATTTTCAATTTCTAT
Found at i:90115512 original size:181 final size:179
Alignment explanation
Indices: 90115211--90115543 Score: 465
Period size: 181 Copynumber: 1.8 Consensus size: 179
90115201 TGTCTTTCAA
* * * * * *
90115211 AAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTGTTTTCCATTTCT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTCAACCTCAACACGCTGAGATATTTTCAATTTCT
* ** * *
90115276 ATTCTTCAATTTCTGTGTTTCAAAAAAAATCAGTTCATATTGCGAGTGGTGAGTTGAGCCT-TGA
66 ATTCTTCAATTTATGTGTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA
*
90115340 CTCACACGCTGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCC
131 -TCACACGCCGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCC
*
90115390 AAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGGACACGCTGAGATATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTCAACCTCA--ACACGCTGAGATATTTTCAATTT
* *
90115455 CCTTTTTTTCAATTTATGT-TTGTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
64 -CTATTCTTCAATTTATGTGTT-TCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
90115518 CAGATCACACGCCGAGGTATTTTCAA
127 CAGATCACACGCCGAGGTATTTTCAA
90115544 TTGATTTTTA
Statistics
Matches: 134, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
179 37 0.28
181 78 0.58
182 19 0.14
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (179 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTCAACCTCAACACGCTGAGATATTTTCAATTTCT
ATTCTTCAATTTATGTGTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA
TCACACGCCGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCC
Found at i:90115629 original size:103 final size:104
Alignment explanation
Indices: 90115457--90115646 Score: 303
Period size: 103 Copynumber: 1.8 Consensus size: 104
90115447 TTCAATTTCC
*
90115457 TTTTTTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA
1 TTTTTTTCAATTTATGTTTGTC-AAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGA
*
90115522 TCACACGCCGAGGTATTTTCAATTGATTTTTATTTTTATT
65 TCACACACCGAGGTATTTTCAATTGATTTTTATTTTTATT
* *
90115562 TTTTTTTCAATTTATGCTTTG-C-AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGG
1 TTTTTTTCAATTTATG-TTTGTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGA
*
90115625 TCACATACCGAGGTATTTTCAA
65 TCACACACCGAGGTATTTTCAA
90115647 AATCTATTTT
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
103 58 0.73
105 17 0.22
106 4 0.05
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (104 bp):
TTTTTTTCAATTTATGTTTGTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGAT
CACACACCGAGGTATTTTCAATTGATTTTTATTTTTATT
Found at i:90115730 original size:87 final size:87
Alignment explanation
Indices: 90115584--90115811 Score: 237
Period size: 87 Copynumber: 2.6 Consensus size: 87
90115574 TATGCTTTGC
* * * *
90115584 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATACCGAGGTATTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAA
90115649 TCTATTTTACAAAT-TTT-GTTTT
66 TCTATTTT--AAATGTTTAGTTTT
* * * * **
90115671 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAA
* *
90115736 TCTGTTTTTAATGTTTAGTTTT
66 TCTATTTTAAATGTTTAGTTTT
* * * * * *
90115758 AAAGAGTCAATTCATATTGCGAGAAATGAGTTAAG-CTCAGGATCACATGCCGAG
1 AAA-AATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGCTCACATACCGAG
90115812 TAAAGAATAA
Statistics
Matches: 117, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
85 3 0.03
86 3 0.03
87 72 0.62
88 39 0.33
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (87 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAA
TCTATTTTAAATGTTTAGTTTT
Found at i:90116462 original size:30 final size:30
Alignment explanation
Indices: 90116426--90116554 Score: 231
Period size: 30 Copynumber: 4.3 Consensus size: 30
90116416 CTAGCCTTTG
90116426 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
90116456 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
90116486 CCACCACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
90116516 CCACCACCTACTCCATTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
90116546 CCACCACCA
1 CCACCACCA
90116555 CTTGTACCTA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 96 1.00
ACGTcount: A:0.26, C:0.50, G:0.06, T:0.18
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:90117123 original size:25 final size:24
Alignment explanation
Indices: 90117095--90117146 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
90117085 CTATATTACG
*
90117095 TATATATA-TT-ATACTATTTTAT
1 TATATATATTTAATACTATGTTAT
*
90117117 GTATATATCTTTAATACTATGTTAT
1 -TATATATATTTAATACTATGTTAT
90117142 TATAT
1 TATAT
90117147 TTTTTTCTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.28
24 7 0.28
25 11 0.44
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.56
Consensus pattern (24 bp):
TATATATATTTAATACTATGTTAT
Found at i:90117216 original size:25 final size:24
Alignment explanation
Indices: 90117166--90117229 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 24
90117156 CATGTTATCT
*
90117166 TATGTATATATTTTAATTATATTATG
1 TATGTAT-T-TTTTAAGTATATTATG
90117192 TATGTATTTTTTACAGTATATTATG
1 TATGTATTTTTTA-AGTATATTATG
**
90117217 TACATATTTTTTA
1 TATGTATTTTTTA
90117230 TATCTATTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.15
25 22 0.65
26 7 0.21
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (24 bp):
TATGTATTTTTTAAGTATATTATG
Found at i:90117373 original size:38 final size:34
Alignment explanation
Indices: 90117314--90117405 Score: 111
Period size: 32 Copynumber: 2.8 Consensus size: 34
90117304 TTCAAACACT
* *
90117314 ATATATAGTATATTTCTATACTATTACTATTTATAA
1 ATATATA-TATATTACGATACTA-TACTATTTATAA
*
90117350 ATATATATATTTTACG-TAC-ATACTATTTATAA
1 ATATATATATATTACGATACTATACTATTTATAA
90117382 ATATATATATATTACG-TAC-ATACT
1 ATATATATATATTACGATACTATACT
90117406 CTTAATATCT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
32 35 0.67
33 1 0.02
34 3 0.06
35 6 0.12
36 7 0.13
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (34 bp):
ATATATATATATTACGATACTATACTATTTATAA
Found at i:90117376 original size:32 final size:32
Alignment explanation
Indices: 90117338--90117405 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
90117328 TCTATACTAT
*
90117338 TACTATTTATAAATATATATATTTTACGTACA
1 TACTATTTATAAATATATATATATTACGTACA
90117370 TACTATTTATAAATATATATATATTACGTACA
1 TACTATTTATAAATATATATATATTACGTACA
90117402 TACT
1 TACT
90117406 CTTAATATCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (32 bp):
TACTATTTATAAATATATATATATTACGTACA
Found at i:90126380 original size:3 final size:3
Alignment explanation
Indices: 90126301--90126402 Score: 62
Period size: 3 Copynumber: 33.3 Consensus size: 3
90126291 TTTTTGTTGT
* * * * *
90126301 TTA TTC TTA TT- TTC TTA TTAA ATA TTC TTA TTA TTTA TATA ATA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA -TTA T-TA TTA TTA
* * * * * * *
90126348 GTA CTA TTA CTA TTA CTA TTG TTC TTA TTA TTA TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
90126396 TTA TTA T
1 TTA TTA T
90126403 GTTTTAGTTT
Statistics
Matches: 74, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
2 2 0.03
3 65 0.88
4 7 0.09
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:90139574 original size:71 final size:71
Alignment explanation
Indices: 90139446--90139584 Score: 206
Period size: 71 Copynumber: 2.0 Consensus size: 71
90139436 AATTTTTACT
* * *
90139446 TTTCTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAATACACGTTAAGGTAATTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTAATTTCAA
90139511 TTTATG
66 TTTATG
** * * *
90139517 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTAATTTCAA
90139582 TTT
66 TTT
90139585 CTACTTTCCA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (71 bp):
TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTAATTTCAA
TTTATG
Found at i:90139746 original size:54 final size:54
Alignment explanation
Indices: 90139594--90139809 Score: 308
Period size: 54 Copynumber: 4.0 Consensus size: 54
90139584 TCTACTTTCC
* * *
90139594 AATTCCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTTTC
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
* * *
90139648 AATTTATATTTTTCAAAAAAATCAACTCATATTGCGACAGGTGAGTTGAGCCTTTT
1 AATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
*
90139704 AATTTCTGTTTTTCAAAAAGCAACTCATATTGCGAGAGGTGAGTTGTA-CCTTTT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG-AGCCTTTT
* * *
90139758 AATTTTTGTTTTTCAAAAATCAACCCATATTGCGAGAAGTGAGTTGAGCCTT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
90139810 AGGTCATATG
Statistics
Matches: 144, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
53 1 0.01
54 93 0.65
55 1 0.01
56 49 0.34
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (54 bp):
AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
Found at i:90139940 original size:13 final size:13
Alignment explanation
Indices: 90139914--90139947 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
90139904 CGTGCTGAGT
*
90139914 TTTTTCAATTTCTG
1 TTTTT-AATGTCTG
90139928 TTTTTAATGTCTG
1 TTTTTAATGTCTG
90139941 TTTTTAA
1 TTTTTAA
90139948 AGAGTCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.65
Consensus pattern (13 bp):
TTTTTAATGTCTG
Found at i:90141768 original size:3 final size:3
Alignment explanation
Indices: 90141697--90141801 Score: 79
Period size: 3 Copynumber: 34.0 Consensus size: 3
90141687 TTTTTGTTGT
* * * * *
90141697 TTA TTC TTA TT- TTC TTA TTAA ATA TTC TTA TTA TTTA TATA ATA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA -TTA T-TA TTA TTA
* * *
90141744 GTA CTA TTA CTT- TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
90141789 TTA TTA TGTA TTA
1 TTA TTA T-TA TTA
90141802 GTTTATGTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
2 4 0.05
3 65 0.80
4 12 0.15
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:90142034 original size:15 final size:15
Alignment explanation
Indices: 90142001--90142039 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
90141991 TTTAATGTCG
*
90142001 TATTATTATGTTTTAA
1 TATTA-TATATTTTAA
*
90142017 TATTATATATTTTCA
1 TATTATATATTTTAA
90142032 TATTATAT
1 TATTATAT
90142040 TATATACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTATATATTTTAA
Found at i:90145941 original size:16 final size:15
Alignment explanation
Indices: 90145915--90145949 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
90145905 TGATGTGAAT
90145915 AATATAAAATATTAA
1 AATATAAAATATTAA
*
90145930 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
90145946 AATA
1 AATA
90145950 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:90146132 original size:24 final size:24
Alignment explanation
Indices: 90146105--90146198 Score: 104
Period size: 24 Copynumber: 4.0 Consensus size: 24
90146095 GTGATAATAT
* *
90146105 TAAAAATATGTACATAATATAGTG
1 TAAAAATATATACATAATATAATG
*
90146129 TAAAAATACATACATAATATAAT-
1 TAAAAATATATACATAATATAATG
*
90146152 T-AAAATATATACATAAGATAACATG
1 TAAAAATATATACATAATAT-A-ATG
*
90146177 TAAAAATATATATATAA-ATAAT
1 TAAAAATATATACATAATATAAT
90146199 ATAGTATTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
22 16 0.27
23 4 0.07
24 23 0.38
25 3 0.05
26 14 0.23
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (24 bp):
TAAAAATATATACATAATATAATG
Found at i:90146214 original size:25 final size:24
Alignment explanation
Indices: 90146186--90146315 Score: 108
Period size: 23 Copynumber: 5.6 Consensus size: 24
90146176 GTAAAAATAT
*
90146186 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATT-AAG
* *
90146211 ATATATACATAAAATAGTA-TAAT
1 ATATATACATAATATAGTATTAAG
* * *
90146234 ATATATACGTAATATAGAATTTAG
1 ATATATACATAATATAGTATTAAG
* * *
90146258 A-ATATACCTAATATATTA-AAAG
1 ATATATACATAATATAGTATTAAG
* *
90146280 A-ATATATATAATATAATATTAAG
1 ATATATACATAATATAGTATTAAG
*
90146303 AAATATA-ATAATA
1 ATATATACATAATA
90146316 ACAAAAAAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
22 17 0.20
23 42 0.49
24 9 0.11
25 17 0.20
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (24 bp):
ATATATACATAATATAGTATTAAG
Found at i:90146834 original size:30 final size:30
Alignment explanation
Indices: 90146795--90146893 Score: 162
Period size: 30 Copynumber: 3.3 Consensus size: 30
90146785 TAGGTACAAG
*
90146795 AGGTGGTGGAGCAAGTGTAGCTAGTGGAGT
1 AGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
*
90146825 AGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
1 AGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
*
90146855 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 AGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
*
90146885 TGGTGGTGG
1 AGGTGGTGG
90146894 CAAAGGCTAG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.19, C:0.06, G:0.49, T:0.25
Consensus pattern (30 bp):
AGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:90146851 original size:18 final size:18
Alignment explanation
Indices: 90146828--90146883 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
90146818 GTGGAGTAGG
90146828 TAGTGGAGCAAGTGTGGC
1 TAGTGGAGCAAGTGTGGC
90146846 TAGT-G-G--AGT-TGG-
1 TAGTGGAGCAAGTGTGGC
*
90146858 TGGTGGAGCAAGTGTGGC
1 TAGTGGAGCAAGTGTGGC
90146876 TAGTGGAG
1 TAGTGGAG
90146884 TTGGTGGTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
12 3 0.10
13 4 0.13
14 4 0.13
16 4 0.13
17 4 0.13
18 11 0.37
ACGTcount: A:0.20, C:0.07, G:0.48, T:0.25
Consensus pattern (18 bp):
TAGTGGAGCAAGTGTGGC
Found at i:90149001 original size:23 final size:24
Alignment explanation
Indices: 90148975--90149025 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
90148965 AAAAGGTATC
* *
90148975 GTTTTTACAATAA-TAGTTATAAT
1 GTTTTGACAATAATTAGCTATAAT
*
90148998 GTTTTGAGAATAATTAGCTATAAT
1 GTTTTGACAATAATTAGCTATAAT
90149022 GTTT
1 GTTT
90149026 CTAAAAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (24 bp):
GTTTTGACAATAATTAGCTATAAT
Found at i:90152057 original size:16 final size:16
Alignment explanation
Indices: 90152038--90152071 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
90152028 AGTAAAAAAT
90152038 AATATAAAATTTATAA
1 AATATAAAATTTATAA
**
90152054 AATATAACCTTTATAA
1 AATATAAAATTTATAA
90152070 AA
1 AA
90152072 AAAAGTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
AATATAAAATTTATAA
Found at i:90153609 original size:14 final size:14
Alignment explanation
Indices: 90153590--90153628 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
90153580 CTGTTTGATT
90153590 GAAAATGATTTTCA
1 GAAAATGATTTTCA
* *
90153604 GAAAATAATTTTTA
1 GAAAATGATTTTCA
*
90153618 GAAATTGATTT
1 GAAAATGATTT
90153629 ACTTTTTTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (14 bp):
GAAAATGATTTTCA
Found at i:90153714 original size:33 final size:33
Alignment explanation
Indices: 90153646--90153714 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
90153636 TGAAAAAATT
* * *
90153646 AATATTTTTTGGTGTTTGGATGAATTTGTGCAA
1 AATATTTTTTGGTATTTGGATAAATTTGTGAAA
* *
90153679 AATATTTTTTGTTATTT-GATAAATTTCTTGAAA
1 AATATTTTTTGGTATTTGGATAAATTT-GTGAAA
90153712 AAT
1 AAT
90153715 TTCATAAAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 8 0.27
33 22 0.73
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (33 bp):
AATATTTTTTGGTATTTGGATAAATTTGTGAAA
Found at i:90155234 original size:18 final size:17
Alignment explanation
Indices: 90155193--90155235 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
90155183 TTGGAATGGT
*
90155193 TTGAAATTGTATATTGA
1 TTGAAATTGAATATTGA
*
90155210 TTGGAAATTGAATTATTTA
1 TT-GAAATTGAA-TATTGA
90155229 TTGAAAT
1 TTGAAAT
90155236 ACCCTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 13 0.59
19 7 0.32
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (17 bp):
TTGAAATTGAATATTGA
Found at i:90183346 original size:13 final size:13
Alignment explanation
Indices: 90183328--90183354 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
90183318 TAGAACTCAT
90183328 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
90183341 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
90183354 A
1 A
90183355 GTCATCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:90193855 original size:17 final size:17
Alignment explanation
Indices: 90193830--90193863 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
90193820 TCAGACTAAA
90193830 TTTTCAAAAAAGATTAT
1 TTTTCAAAAAAGATTAT
* *
90193847 TTTTTAAAAAATATTAT
1 TTTTCAAAAAAGATTAT
90193864 AAAAATAGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTTCAAAAAAGATTAT
Found at i:90194878 original size:16 final size:15
Alignment explanation
Indices: 90194846--90194875 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
90194836 ACTATTAGTA
90194846 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
*
90194861 ATTTTTTTAATATTT
1 ATTTTTTAAATATTT
90194876 TATCATACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTTTAAATATTT
Found at i:90202742 original size:15 final size:16
Alignment explanation
Indices: 90202724--90202757 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
90202714 TTTTCTCCTT
90202724 GTTC-TTTTTATTTTG
1 GTTCTTTTTTATTTTG
*
90202739 GTTCTTTTTTCTTTTG
1 GTTCTTTTTTATTTTG
90202755 GTT
1 GTT
90202758 AATCTACCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.03, C:0.09, G:0.15, T:0.74
Consensus pattern (16 bp):
GTTCTTTTTTATTTTG
Found at i:90204933 original size:30 final size:31
Alignment explanation
Indices: 90204899--90204978 Score: 119
Period size: 30 Copynumber: 2.6 Consensus size: 31
90204889 GGTGGAGATC
90204899 GTGATGGTGGTGGCGTTGAAAGGGG-AGGTT
1 GTGATGGTGGTGGCGTTGAAAGGGGAAGGTT
90204929 GTGATGGTGGTGGCGTTG-AAGGGGAAGGTT
1 GTGATGGTGGTGGCGTTGAAAGGGGAAGGTT
* * *
90204959 GTGATGATGGAGGCGGTGAA
1 GTGATGGTGGTGGCGTTGAA
90204979 CTAACAGGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.13
30 38 0.84
31 1 0.02
ACGTcount: A:0.19, C:0.04, G:0.53, T:0.25
Consensus pattern (31 bp):
GTGATGGTGGTGGCGTTGAAAGGGGAAGGTT
Found at i:90210035 original size:13 final size:14
Alignment explanation
Indices: 90210009--90210037 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
90209999 TAACATAATC
90210009 ATAATCTCTAAAAA
1 ATAATCTCTAAAAA
90210023 ATAATCT-TAAAAA
1 ATAATCTCTAAAAA
90210036 AT
1 AT
90210038 TTGAAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (14 bp):
ATAATCTCTAAAAA
Found at i:90211550 original size:12 final size:12
Alignment explanation
Indices: 90211533--90211562 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
90211523 TCAAGTAGTT
90211533 ACACGGCCTAGC
1 ACACGGCCTAGC
*
90211545 ACACGGCCTGGC
1 ACACGGCCTAGC
90211557 ACACGG
1 ACACGG
90211563 GCGTGAGGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:90211813 original size:11 final size:11
Alignment explanation
Indices: 90211786--90211816 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
90211776 AGTCTCAATT
*
90211786 TGTTTATAAAG
1 TGTTTCTAAAG
90211797 TGTTTCTAAAG
1 TGTTTCTAAAG
90211808 TGTTTCTAA
1 TGTTTCTAA
90211817 GGCCTCGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.48
Consensus pattern (11 bp):
TGTTTCTAAAG
Found at i:90213422 original size:24 final size:21
Alignment explanation
Indices: 90213389--90213433 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
90213379 GATAAGGAAT
90213389 GAAATATGTACAAATAATGAATAA
1 GAAATATGT--AAAT-ATGAATAA
*
90213413 GAAATGTGTAAATATGAATAA
1 GAAATATGTAAATATGAATAA
90213434 AATAGACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 4 0.20
24 8 0.40
ACGTcount: A:0.56, C:0.02, G:0.16, T:0.27
Consensus pattern (21 bp):
GAAATATGTAAATATGAATAA
Found at i:90216880 original size:46 final size:46
Alignment explanation
Indices: 90216828--90217131 Score: 466
Period size: 46 Copynumber: 6.6 Consensus size: 46
90216818 GCTTTCTGAA
90216828 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
90216874 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
90216920 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
90216966 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
90217012 ATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAACGTG-T
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * * * *
90217057 CATGAAATGAATAAGACTATGGTTGAAATATACCAAGGCAACATGAC
1 -ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * *
90217104 AAAAAATGAGTAAGACCATAGTTGAAAG
1 ATGAAATGTGTAAGACCATGGTTGAAAG
90217132 GCACTATGGC
Statistics
Matches: 236, Mismatches: 20, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
45 1 0.00
46 235 1.00
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.23
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:90216899 original size:21 final size:21
Alignment explanation
Indices: 90216875--90216946 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
90216865 CAACATGATA
90216875 TGAAATGTGTAAGACCATGGT
1 TGAAATGTGTAAGACCATGGT
* *
90216896 TGAAA-G-ATACCATGACAACATGAT
1 TGAAATGTGTA--A-GAC--CATGGT
90216920 ATGAAATGTGTAAGACCATGGT
1 -TGAAATGTGTAAGACCATGGT
90216942 TGAAA
1 TGAAA
90216947 GATACCATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 11 0.28
22 8 0.21
24 8 0.21
25 6 0.15
26 1 0.03
27 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (21 bp):
TGAAATGTGTAAGACCATGGT
Found at i:90220219 original size:50 final size:50
Alignment explanation
Indices: 90220095--90220343 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
90220085 GATAATAACA
* * ** * *
90220095 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
90220146 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
90220196 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
90220246 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
90220301 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
90220344 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:90220273 original size:100 final size:104
Alignment explanation
Indices: 90220094--90220343 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
90220084 TGATAATAAC
**
90220094 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
90220159 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
90220196 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
90220259 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
90220301 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
90220344 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:90220459 original size:13 final size:13
Alignment explanation
Indices: 90220438--90220469 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
90220428 GCTTGGATCA
*
90220438 TCATCAAATAAAT
1 TCATAAAATAAAT
90220451 TCATAAAATAAAT
1 TCATAAAATAAAT
90220464 TCATAA
1 TCATAA
90220470 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:90220716 original size:30 final size:30
Alignment explanation
Indices: 90220681--90220738 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
90220671 CCTCGACTCT
*
90220681 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
90220711 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
90220739 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:90227795 original size:45 final size:49
Alignment explanation
Indices: 90227744--90227833 Score: 143
Period size: 45 Copynumber: 1.9 Consensus size: 49
90227734 AAATGTAGTA
*
90227744 GACCATGGTTG-AAAGA-ACCATGGCA-ACATGAT-ATGAAATGTTAAG
1 GACCATGGTTGAAAAGATACCATGACAGACATGATAATGAAATGTTAAG
90227789 GACCATGGTTGAAAAGATACCATGACAGACATGATAATGAAATGT
1 GACCATGGTTGAAAAGATACCATGACAGACATGATAATGAAATGT
90227834 GTGAACCATG
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
45 11 0.28
46 5 0.12
47 8 0.20
48 7 0.17
49 9 0.22
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.22
Consensus pattern (49 bp):
GACCATGGTTGAAAAGATACCATGACAGACATGATAATGAAATGTTAAG
Found at i:90227843 original size:48 final size:45
Alignment explanation
Indices: 90227730--90227850 Score: 126
Period size: 45 Copynumber: 2.6 Consensus size: 45
90227720 GTGCTTCTGA
*
90227730 AATGAAATGTAGT-AGACCATGGTTGAAAGAACCATGGCAACATGAT
1 AATGAAATGT-GTGA-ACCATGGTTGAAAGAACCATGACAACATGAT
*
90227776 -ATGAAATGT-TAAGGACCATGGTTGAAAAGATACCATGACAGACATGAT
1 AATGAAATGTGT--GAACCATGGTTG-AAAGA-ACCATGACA-ACATGAT
90227824 AATGAAATGTGTGAACCAT-G-TGAAAGA
1 AATGAAATGTGTGAACCATGGTTGAAAGA
90227851 TACATCAACT
Statistics
Matches: 64, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
43 1 0.02
45 24 0.38
46 7 0.11
47 9 0.14
48 13 0.20
49 9 0.14
50 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (45 bp):
AATGAAATGTGTGAACCATGGTTGAAAGAACCATGACAACATGAT
Found at i:90245562 original size:5 final size:5
Alignment explanation
Indices: 90245549--90245593 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
90245539 CCGACCCTAT
* * *
90245549 TCTCA TCTCG TCTCA TCTCG TCTCC TCTCG TCATCG TCTCG TCTC
1 TCTCG TCTCG TCTCG TCTCG TCTCG TCTCG TC-TCG TCTCG TCTC
90245594 CCCTTGTCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.07, C:0.42, G:0.11, T:0.40
Consensus pattern (5 bp):
TCTCG
Found at i:90245564 original size:10 final size:10
Alignment explanation
Indices: 90245549--90245593 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
90245539 CCGACCCTAT
90245549 TCTCATCTCG
1 TCTCATCTCG
90245559 TCTCATCTCG
1 TCTCATCTCG
*
90245569 TCTCCTCTCG
1 TCTCATCTCG
*
90245579 TCATCGTCTCG
1 TC-TCATCTCG
90245590 TCTC
1 TCTC
90245594 CCCTTGTCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 23 0.72
11 9 0.28
ACGTcount: A:0.07, C:0.42, G:0.11, T:0.40
Consensus pattern (10 bp):
TCTCATCTCG
Found at i:90251330 original size:93 final size:93
Alignment explanation
Indices: 90251222--90251487 Score: 451
Period size: 93 Copynumber: 2.9 Consensus size: 93
90251212 CACCCATAAG
* * *
90251222 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTAAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
90251287 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
* * *
90251315 CGAACTCGGACTCAACTCAATGAGTTCGGCCGTTCGCATCCATAAGTGAACTCATACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
90251380 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
*
90251408 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
* *
90251473 ACGAGTTCGAATGCC
66 ACGAGCTCGGATGCC
90251488 CAAATATCCG
Statistics
Matches: 162, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 162 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:90251421 original size:47 final size:47
Alignment explanation
Indices: 90251270--90251437 Score: 184
Period size: 47 Copynumber: 3.6 Consensus size: 47
90251260 TCCATAAGTA
90251270 AACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCACG
1 AACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCACG
* * * * * *
90251317 AACTCGGACTCAACTCAATGAGTTC-G--GCC--GTTCGCATCCATAAGTG
1 AACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT-C-TCA-CG
*
90251363 AACTCATACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCACG
1 AACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCACG
* *
90251410 AACTCGGACTCAACTCAACGAGTTCGGA
1 AACTCAGACTCAACTCAACGAGCTCGGA
90251438 CGTTCGCATC
Statistics
Matches: 96, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 4 0.04
45 2 0.02
46 23 0.24
47 49 0.51
48 2 0.02
49 4 0.04
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.22
Consensus pattern (47 bp):
AACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCACG
Found at i:90251481 original size:46 final size:46
Alignment explanation
Indices: 90251215--90251477 Score: 236
Period size: 46 Copynumber: 5.7 Consensus size: 46
90251205 TGCAACCCAC
*
90251215 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
** * *
90251261 CCATAAGTAAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C--GTTCGCAT
* * * *
90251311 -C-TCA-CGAACTCGGACTCAACTCAATGAGTTCGGCCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* ** *
90251354 CCATAAGTGAACTCATACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C--GTTCGCAT
* *
90251404 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
*
90251447 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGCGAACTCGGACTCAACTCAACGAG
90251478 TTCGAATGCC
Statistics
Matches: 170, Mismatches: 29, Indels: 36
0.72 0.12 0.15
Matches are distributed among these distances:
42 6 0.04
43 6 0.04
44 4 0.02
45 4 0.02
46 80 0.47
47 50 0.29
48 4 0.02
49 4 0.02
50 6 0.04
51 6 0.04
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:90257186 original size:35 final size:35
Alignment explanation
Indices: 90257140--90257210 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
90257130 AATCAATGCA
90257140 AGCATGTTTGACATGTTAAAAACAAGTTTTAAAAC
1 AGCATGTTTGACATGTTAAAAACAAGTTTTAAAAC
90257175 AGCATGTTTGACATGTTAAAAACAAGTTTTAAAAC
1 AGCATGTTTGACATGTTAAAAACAAGTTTTAAAAC
90257210 A
1 A
90257211 TGAATAGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (35 bp):
AGCATGTTTGACATGTTAAAAACAAGTTTTAAAAC
Found at i:90264040 original size:16 final size:17
Alignment explanation
Indices: 90264003--90264043 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
90263993 TTTCCATTTA
*
90264003 TCTATTTTTTCATCCCT
1 TCTAATTTTTCATCCCT
*
90264020 T-TAATTTTTCAT-CTT
1 TCTAATTTTTCATCCCT
90264035 TCTAATTTT
1 TCTAATTTT
90264044 CTTTACAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 3 0.14
16 17 0.81
17 1 0.05
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.63
Consensus pattern (17 bp):
TCTAATTTTTCATCCCT
Found at i:90269213 original size:36 final size:37
Alignment explanation
Indices: 90269173--90269250 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 37
90269163 AAATTAAATT
*
90269173 TCACATTTTATCTTTAAGATAATTTTT-ATTTAAAAA
1 TCACATTTTATATTTAAGATAATTTTTAATTTAAAAA
* * * *
90269209 TCACATTTTTTATTTAATATATTTTTTAATTTCAAAA
1 TCACATTTTATATTTAAGATAATTTTTAATTTAAAAA
90269246 T-ACAT
1 TCACAT
90269251 AATGACAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
36 27 0.75
37 9 0.25
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (37 bp):
TCACATTTTATATTTAAGATAATTTTTAATTTAAAAA
Found at i:90269821 original size:3 final size:3
Alignment explanation
Indices: 90269813--90269866 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
90269803 TGTATTAACA
90269813 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
90269861 AAT AAT
1 AAT AAT
90269867 CCATTGAGGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:90275596 original size:22 final size:22
Alignment explanation
Indices: 90275568--90275610 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
90275558 ATATAAAAAT
90275568 AAAAATACCTTCAAAATAATAG
1 AAAAATACCTTCAAAATAATAG
** *
90275590 AAAAATATTTTTAAAATAATA
1 AAAAATACCTTCAAAATAATA
90275611 TTTGTTACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAAATACCTTCAAAATAATAG
Found at i:90288873 original size:17 final size:16
Alignment explanation
Indices: 90288853--90288892 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
90288843 ATAACTTTTT
*
90288853 ATTTTTATATATTTTAA
1 ATTTTTA-AGATTTTAA
90288870 ATTTGTTAAGATTTTAA
1 ATTT-TTAAGATTTTAA
90288887 ATTTTT
1 ATTTTT
90288893 TGAATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 16 0.76
18 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
ATTTTTAAGATTTTAA
Found at i:90293855 original size:21 final size:21
Alignment explanation
Indices: 90293829--90293869 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
90293819 ATCTGCTCAA
* *
90293829 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
90293850 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
90293870 TCGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:90311911 original size:39 final size:39
Alignment explanation
Indices: 90311852--90311930 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
90311842 AAGTAGATTC
*
90311852 CATAGCTATCCACCTATTACTCTACCATGTTCAGAAACA
1 CATAACTATCCACCTATTACTCTACCATGTTCAGAAACA
90311891 CATAACTATCCACCTATTACTCTACCATGTTCAGAAACA
1 CATAACTATCCACCTATTACTCTACCATGTTCAGAAACA
90311930 C
1 C
90311931 TTAGCACTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.34, C:0.32, G:0.06, T:0.28
Consensus pattern (39 bp):
CATAACTATCCACCTATTACTCTACCATGTTCAGAAACA
Found at i:90313317 original size:18 final size:19
Alignment explanation
Indices: 90313276--90313318 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
90313266 TCAGTTTTAA
*
90313276 TATTATGTACTTTTAGTTT
1 TATTATATACTTTTAGTTT
* *
90313295 AATTATATA-TTTTATTTT
1 TATTATATACTTTTAGTTT
90313313 TATTAT
1 TATTAT
90313319 TAATTCCAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (19 bp):
TATTATATACTTTTAGTTT
Found at i:90314010 original size:18 final size:19
Alignment explanation
Indices: 90313964--90314010 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
90313954 ATATTATAAA
* *
90313964 AAACTCAAATTCAAGTTTG
1 AAACTCAATTTAAAGTTTG
* *
90313983 AAATTAAATTTAAAG-TTG
1 AAACTCAATTTAAAGTTTG
90314001 AAACTCAATT
1 AAACTCAATT
90314011 CCACAATTGT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.34
Consensus pattern (19 bp):
AAACTCAATTTAAAGTTTG
Found at i:90320500 original size:12 final size:12
Alignment explanation
Indices: 90320483--90320515 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
90320473 TAGTTAGAAA
90320483 AAGAAATTGTTG
1 AAGAAATTGTTG
90320495 AAGAAATTGTTG
1 AAGAAATTGTTG
90320507 AAGAAATTG
1 AAGAAATTG
90320516 GGTAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.30
Consensus pattern (12 bp):
AAGAAATTGTTG
Found at i:90328792 original size:17 final size:18
Alignment explanation
Indices: 90328763--90328798 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
90328753 TTAGGGGTGT
*
90328763 TAAAATATTTATAGCAAA
1 TAAAATATTTATACCAAA
90328781 TAAAAT-TTTATACCAAA
1 TAAAATATTTATACCAAA
90328798 T
1 T
90328799 TACCATACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (18 bp):
TAAAATATTTATACCAAA
Found at i:90331432 original size:6 final size:6
Alignment explanation
Indices: 90331421--90331445 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
90331411 ATAAAAAGCT
90331421 GTAGAG GTAGAG GTAGAG GTAGAG G
1 GTAGAG GTAGAG GTAGAG GTAGAG G
90331446 GAAAAGGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.52, T:0.16
Consensus pattern (6 bp):
GTAGAG
Found at i:90343455 original size:27 final size:27
Alignment explanation
Indices: 90343417--90343471 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
90343407 TTGTGGGGTG
90343417 TATGTGTTTTTTATATCTTCATAGAAT
1 TATGTGTTTTTTATATCTTCATAGAAT
90343444 TATGTGTTTTTTATATCTTCATAGAAT
1 TATGTGTTTTTTATATCTTCATAGAAT
90343471 T
1 T
90343472 TGACTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.56
Consensus pattern (27 bp):
TATGTGTTTTTTATATCTTCATAGAAT
Found at i:90343481 original size:27 final size:27
Alignment explanation
Indices: 90343423--90343482 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
90343413 GGTGTATGTG
**
90343423 TTTTTTATATCTTCATAGAATTATGTG
1 TTTTTTATATCTTCATAGAATTATGAC
90343450 TTTTTTATATCTTCATAGAATT-TGAC
1 TTTTTTATATCTTCATAGAATTATGAC
90343476 TCTTTTT
1 T-TTTTT
90343483 TTTCTGGTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.10
27 27 0.90
ACGTcount: A:0.23, C:0.10, G:0.08, T:0.58
Consensus pattern (27 bp):
TTTTTTATATCTTCATAGAATTATGAC
Found at i:90347487 original size:14 final size:14
Alignment explanation
Indices: 90347468--90347494 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
90347458 CAAAATTTCA
90347468 AAAAATAAAAATTT
1 AAAAATAAAAATTT
90347482 AAAAATAAAAATT
1 AAAAATAAAAATT
90347495 GCATTTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATAAAAATTT
Found at i:90347524 original size:30 final size:31
Alignment explanation
Indices: 90347490--90347591 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
90347480 TTAAAAATAA
*
90347490 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
90347520 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
90347550 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
90347580 AAATTTCATTTT
1 AAATTTCATTTT
90347592 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:90347955 original size:3 final size:3
Alignment explanation
Indices: 90347949--90348020 Score: 62
Period size: 3 Copynumber: 24.0 Consensus size: 3
90347939 GCTAGACTTT
*
90347949 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA G-AA
*
90347996 GAAA GAA -AA -AA GAA AAA GAA -AA GAA
1 G-AA GAA GAA GAA GAA GAA GAA GAA GAA
90348021 ATAATAAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 8 0.14
3 38 0.64
4 13 0.22
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:90347967 original size:10 final size:10
Alignment explanation
Indices: 90347952--90347980 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
90347942 AGACTTTGAA
90347952 GAAGAAGAAG
1 GAAGAAGAAG
90347962 GAAGAAGAAG
1 GAAGAAGAAG
90347972 GAAGAAGAA
1 GAAGAAGAA
90347981 AAGAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:90347967 original size:13 final size:13
Alignment explanation
Indices: 90347949--90347994 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
90347939 GCTAGACTTT
90347949 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
90347962 GAAGAAGAAGGAA-
1 GAAGAAGAA-GAAG
90347975 GAAGAA-AAG-AG
1 GAAGAAGAAGAAG
90347986 GAAGAAGAA
1 GAAGAAGAA
90347995 AGAAAGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 7 0.23
12 4 0.13
13 15 0.50
14 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:90348120 original size:21 final size:21
Alignment explanation
Indices: 90348094--90348137 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
90348084 CCAGCAGCCC
90348094 AAGAAA-AAACAACAAAAAAAA
1 AAGAAACAAAC-ACAAAAAAAA
* *
90348115 AAGAAACAAGCCCAAAAAAAA
1 AAGAAACAAACACAAAAAAAA
90348136 AA
1 AA
90348138 CCAAAGCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.80, C:0.14, G:0.07, T:0.00
Consensus pattern (21 bp):
AAGAAACAAACACAAAAAAAA
Found at i:90348189 original size:23 final size:24
Alignment explanation
Indices: 90348152--90348205 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
90348142 AGCAAAAAAA
90348152 AAGCAGCAAAAAAGAAGAAGAAAG
1 AAGCAGCAAAAAAGAAGAAGAAAG
90348176 AAGCAG-AAAAAAGAAGAAGAAAG
1 AAGCAGCAAAAAAGAAGAAGAAAG
90348199 AAGCAGC
1 AAGCAGC
90348206 CCAAATGCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.65, C:0.09, G:0.26, T:0.00
Consensus pattern (24 bp):
AAGCAGCAAAAAAGAAGAAGAAAG
Found at i:90348347 original size:17 final size:17
Alignment explanation
Indices: 90348322--90348381 Score: 81
Period size: 16 Copynumber: 3.6 Consensus size: 17
90348312 CCAGCCCAGC
90348322 AAAAA-AAAAAGAGAAA
1 AAAAAGAAAAAGAGAAA
*
90348338 AAAAAGAAAAAGAG-AG
1 AAAAAGAAAAAGAGAAA
90348354 AAAAAGAAAAA-AGAAA
1 AAAAAGAAAAAGAGAAA
90348370 AAACAAGAAAAA
1 AAA-AAGAAAAA
90348382 AGAGGTTCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
15 2 0.05
16 21 0.54
17 16 0.41
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAGAGAAA
Found at i:90348364 original size:34 final size:31
Alignment explanation
Indices: 90348322--90348385 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 31
90348312 CCAGCCCAGC
90348322 AAAAAAAAAAGAGAAAAAAAAGAAAAAGAGAGA
1 AAAAAAAAAAGA-AAAAAAAAGAAAAA-AGAGA
*
90348355 AAAAGAAAAAAGAAAAAACAAGAAAAAAGAG
1 AAAA-AAAAAAGAAAAAAAAAGAAAAAAGAG
90348386 GTTCAATTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 4 0.14
33 17 0.59
34 8 0.28
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (31 bp):
AAAAAAAAAAGAAAAAAAAAGAAAAAAGAGA
Found at i:90348369 original size:32 final size:32
Alignment explanation
Indices: 90348322--90348385 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
90348312 CCAGCCCAGC
90348322 AAAAAAAAAAGAGAAAAAA-AAGAAAAAGAGAG
1 AAAAAAAAAAGAGAAAAAACAAGAAAAA-AGAG
90348354 AAAAAGAAAAA-AGAAAAAACAAGAAAAAAGAG
1 AAAAA-AAAAAGAGAAAAAACAAGAAAAAAGAG
90348386 GTTCAATTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (32 bp):
AAAAAAAAAAGAGAAAAAACAAGAAAAAAGAG
Found at i:90348377 original size:10 final size:10
Alignment explanation
Indices: 90348323--90348382 Score: 59
Period size: 10 Copynumber: 5.6 Consensus size: 10
90348313 CAGCCCAGCA
90348323 AAAAAAAAAG
1 AAAAAAAAAG
90348333 AGAAAAAAAAG
1 A-AAAAAAAAG
90348344 AAAAAGAGAGAA-
1 AAAAA-A-A-AAG
90348356 AAAGAAAAAAG
1 AAA-AAAAAAG
*
90348367 AAAAAACAAG
1 AAAAAAAAAG
90348377 AAAAAA
1 AAAAAA
90348383 GAGGTTCAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
10 19 0.44
11 15 0.35
12 5 0.12
13 4 0.09
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:90348378 original size:23 final size:23
Alignment explanation
Indices: 90348337--90348381 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
90348327 AAAAAGAGAA
*
90348337 AAAAAAGAAAAAGAGAGAAAAAG
1 AAAAAAGAAAAAGAAAGAAAAAG
90348360 AAAAAAGAAAAA-ACAAGAAAAA
1 AAAAAAGAAAAAGA-AAGAAAAA
90348382 AGAGGTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAAAAGAAAGAAAAAG
Found at i:90348382 original size:17 final size:17
Alignment explanation
Indices: 90348322--90348385 Score: 80
Period size: 17 Copynumber: 3.8 Consensus size: 17
90348312 CCAGCCCAGC
90348322 AAAA-AAAAAAGAGAAA
1 AAAAGAAAAAAGAGAAA
*
90348338 AAAA-AGAAAAAGAGAGA
1 AAAAGA-AAAAAGAGAAA
90348355 AAAAGAAAAAAGA-AAA
1 AAAAGAAAAAAGAGAAA
90348371 AACAAGAAAAAAGAG
1 AA-AAGAAAAAAGAG
90348386 GTTCAATTCG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
16 9 0.21
17 32 0.76
18 1 0.02
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAGAGAAA
Found at i:90348384 original size:7 final size:7
Alignment explanation
Indices: 90348337--90348372 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
90348327 AAAAAGAGAA
90348337 AAAAAAG
1 AAAAAAG
90348344 AAAAAGAG
1 AAAAA-AG
90348352 AGAAAAAG
1 A-AAAAAG
90348360 AAAAAAG
1 AAAAAAG
90348367 AAAAAA
1 AAAAAA
90348373 CAAGAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 17 0.63
8 6 0.22
9 4 0.15
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:90348550 original size:16 final size:17
Alignment explanation
Indices: 90348524--90348561 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
90348514 TTATATTTAT
90348524 ATTTTTAATTTAATTTG
1 ATTTTTAATTTAATTTG
* *
90348541 ATTTTT-ATTTTATTTT
1 ATTTTTAATTTAATTTG
90348557 ATTTT
1 ATTTT
90348562 AAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTTTAATTTAATTTG
Found at i:90348757 original size:18 final size:18
Alignment explanation
Indices: 90348713--90349233 Score: 256
Period size: 17 Copynumber: 29.8 Consensus size: 18
90348703 TTAATAATCA
*
90348713 TCGTGCTTTT-AAAAATTC
1 TCGTG-TTTTCAAAAATTT
* *
90348731 TCATG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
*
90348748 TCGTGTTTTC-AAAATTC
1 TCGTGTTTTCAAAAATTT
*
90348765 TAGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
90348782 TCTTGTTTTCAGAAAAAATTT
1 TCGTGTTTTC---AAAAATTT
* *
90348803 TCATGTTTT-ATAAATTT
1 TCGTGTTTTCAAAAATTT
* * **
90348820 CCGTATTTTCAAAAA-AA
1 TCGTGTTTTCAAAAATTT
*
90348837 TCATGTCTTTCAAAAATTT
1 TCGTGT-TTTCAAAAATTT
***
90348856 TCGTGTTTTCAAAAAAAAAGA
1 TCGTGTTTTC---AAAAATTT
*
90348877 CCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
* *** *
90348894 CCGTGTTAAAAAAAAATCT
1 TCGTGTT-TTCAAAAATTT
* *
90348913 TCGTATTTTCAAAAAAATT
1 TCGTGTTTTC-AAAAATTT
*
90348932 TCGTG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
90348949 TCGTGTTTTCAAAAA-TT
1 TCGTGTTTTCAAAAATTT
*
90348966 TCG-GTGTTTCAAAGATTT
1 TCGTGT-TTTCAAAAATTT
*
90348984 TCGTGTTTTCAAAAA-CT
1 TCGTGTTTTCAAAAATTT
* * ***
90349001 CCGGTGATTTTAAAAAAAAA
1 TC-GTG-TTTTCAAAAATTT
*
90349021 TCGT-TTTCTAAAAAATTT
1 TCGTGTTT-TCAAAAATTT
*
90349039 CCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
90349056 TCGTGTTTT-AAAAATTT
1 TCGTGTTTTCAAAAATTT
*
90349073 TCGTGTTTT-AAAAATTC
1 TCGTGTTTTCAAAAATTT
*
90349090 TCGTATTTT---AAATTT
1 TCGTGTTTTCAAAAATTT
*** **
90349105 T--T-TTAAGAAAAAAAT
1 TCGTGTTTTCAAAAATTT
* *
90349120 T-GTG-TTTCAAAAAATG
1 TCGTGTTTTCAAAAATTT
* *
90349136 TCTTGTTTT-AAAAATTC
1 TCGTGTTTTCAAAAATTT
* *
90349153 TCGTG-TTTCAAAAAATG
1 TCGTGTTTTCAAAAATTT
90349170 TCGTGTTTT-AAAAATTT
1 TCGTGTTTTCAAAAATTT
*
90349187 TCGTG-TTTCATAAATTT
1 TCGTGTTTTCAAAAATTT
* *
90349204 CCGTG-TTT-AAAAATTC
1 TCGTGTTTTCAAAAATTT
90349220 TCGTGTTTT-AAAAA
1 TCGTGTTTTCAAAAA
90349234 AAAACTTTCA
Statistics
Matches: 381, Mismatches: 85, Indels: 75
0.70 0.16 0.14
Matches are distributed among these distances:
12 2 0.01
13 1 0.00
15 11 0.03
16 34 0.09
17 183 0.48
18 80 0.21
19 40 0.10
20 5 0.01
21 25 0.07
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:90348775 original size:16 final size:16
Alignment explanation
Indices: 90348724--90348777 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
90348714 CGTGCTTTTA
90348724 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* *
90348740 AAAAATCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
90348758 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
90348774 AAAA
1 AAAA
90348778 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:90348884 original size:74 final size:75
Alignment explanation
Indices: 90348770--90348945 Score: 178
Period size: 74 Copynumber: 2.4 Consensus size: 75
90348760 AATTCTAGTG
* * **** * * * **
90348770 TTTCAAAAATTTTCTTGTTTTCAGAAAAAATTTTCATGTTTTATAAATTTCCGTATTTTCAAAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAAAGACCATGTTTCAAAAATTTCCGT-GTTAAAAAAA
90348835 AATCAT-GT-C
65 AATCATCGTAC
*
90348844 TTTCAAAAATTTTCGTGTTTTCAAAAAAAAAGACCGTGTTTCAAAAATTTCCGTGTTAAAAAAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAAAGACCATGTTTCAAAAATTTCCGTGTTAAAAAAAA
* *
90348909 ATCTTCGTAT
66 ATCATCGTAC
*
90348919 TTTCAAAAAAATTTCGTG-TTTCAAAAA
1 TTTC-AAAAATTTTCGTGTTTTCAAAAA
90348946 TCTTCGTGTT
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
73 12 0.14
74 47 0.56
75 13 0.15
76 12 0.14
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (75 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAAAAAGACCATGTTTCAAAAATTTCCGTGTTAAAAAAAA
ATCATCGTAC
Found at i:90348886 original size:38 final size:37
Alignment explanation
Indices: 90348734--90349086 Score: 124
Period size: 36 Copynumber: 9.8 Consensus size: 37
90348724 AAAATTCTCA
*
90348734 TGTTTCAAAAATCTT-CGTGTTTTC---AAAATTCTA-G
1 TGTTTCAAAAAT-TTCCGTGTTTTCAAAAAAAATC-ACG
* * * ** *
90348768 TGTTTCAAAAATTTTCTTGTTTTCAGAAAAAATTTTCA
1 TGTTTCAAAAATTTCCGTGTTTTCA-AAAAAAATCACG
* * * *
90348806 TGTTTTATAAATTTCCGTATTTTC-AAAAAAATCATG
1 TGTTTCAAAAATTTCCGTGTTTTCAAAAAAAATCACG
* * **
90348842 TCTTTCAAAAATTTTCGTGTTTTCAAAAAAAAAGACCG
1 TGTTTCAAAAATTTCCGTGTTTTCAAAAAAAATCA-CG
* *
90348880 TGTTTCAAAAATTTCCGTG--TTAAAAAAAAATCTTCG
1 TGTTTCAAAAATTTCCGTGTTTTCAAAAAAAATC-ACG
* *
90348916 TATTTTCAAAAAAATTT-CGTG-TTTC---AAAAATCTTCG
1 T-GTTTC--AAAAATTTCCGTGTTTTCAAAAAAAATC-ACG
* * * **
90348952 TGTTTTCAAAAATTTCGGTG-TTTC--AAAGATTTTCG
1 TG-TTTCAAAAATTTCCGTGTTTTCAAAAAAAATCACG
* *
90348987 TGTTTTCAAAAA-CTCCGGTGATTTTAAAAAAAAAT--CG
1 TG-TTTCAAAAATTTCC-GTG-TTTTCAAAAAAAATCACG
* **
90349024 T-TTTCTAAAAAATTTCCGTG-TTTC--AAAAATTTTCG
1 TGTTTC--AAAAATTTCCGTGTTTTCAAAAAAAATCACG
* *
90349059 TGTTTTAAAAATTTTCGTGTTTT-AAAAA
1 TGTTTCAAAAATTTCCGTGTTTTCAAAAA
90349087 TTCTCGTATT
Statistics
Matches: 244, Mismatches: 45, Indels: 58
0.70 0.13 0.17
Matches are distributed among these distances:
33 8 0.03
34 42 0.17
35 38 0.16
36 65 0.27
37 26 0.11
38 50 0.20
39 15 0.06
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (37 bp):
TGTTTCAAAAATTTCCGTGTTTTCAAAAAAAATCACG
Found at i:90348929 original size:55 final size:56
Alignment explanation
Indices: 90348848--90348955 Score: 139
Period size: 55 Copynumber: 1.9 Consensus size: 56
90348838 CATGTCTTTC
* *
90348848 AAAAATTTTCGTGTTTTCAAAAAAAAAGACCGTGTTTCAAAAAT-TTCCGTGTTAAAA
1 AAAAATCTTCGTATTTTC-AAAAAAAAGACCGTGTTTCAAAAATCTT-CGTGTTAAAA
***
90348905 AAAAATCTTCGTATTTTC-AAAAAAATTTCGTGTTTCAAAAATCTTCGTGTT
1 AAAAATCTTCGTATTTTCAAAAAAAAGACCGTGTTTCAAAAATCTTCGTGTT
90348956 TTCAAAAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
55 27 0.60
56 2 0.04
57 16 0.36
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (56 bp):
AAAAATCTTCGTATTTTCAAAAAAAAGACCGTGTTTCAAAAATCTTCGTGTTAAAA
Found at i:90349132 original size:97 final size:95
Alignment explanation
Indices: 90349008--90349190 Score: 249
Period size: 97 Copynumber: 1.9 Consensus size: 95
90348998 ACTCCGGTGA
* * * * *
90349008 TTTTAAAAAAAAATCGTTTTCTAAAAAATTTCCGTGTTTCAAAAATTTTCGTGTTTTAAAAATTT
1 TTTTAAAAAAAAATCGTTTTC-AAAAAATGT-CGTGTTTCAAAAATTCTCGTGTTTCAAAAAATG
90349073 TCGTGTTTTAAAAATTCTCGTATTTTAAATTT
64 TCGTGTTTTAAAAATTCTCGTATTTTAAATTT
* * *
90349105 TTTTAAGAAAAAAATTGTGTTTCAAAAAATGTCTTGTTTTAAAAATTCTCGTGTTTCAAAAAATG
1 TTTTAA-AAAAAAATCGT-TTTCAAAAAATGTCGTGTTTCAAAAATTCTCGTGTTTCAAAAAATG
*
90349170 TCGTGTTTTAAAAATTTTCGT
64 TCGTGTTTTAAAAATTCTCGT
90349191 GTTTCATAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
97 53 0.71
98 18 0.24
99 4 0.05
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (95 bp):
TTTTAAAAAAAAATCGTTTTCAAAAAATGTCGTGTTTCAAAAATTCTCGTGTTTCAAAAAATGTC
GTGTTTTAAAAATTCTCGTATTTTAAATTT
Found at i:90349272 original size:17 final size:17
Alignment explanation
Indices: 90349252--90349289 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
90349242 CATTTTTTAA
*
90349252 AAAAATTTTCGTG-CTT
1 AAAAATTCTCGTGTCTT
*
90349268 CAAAATTCTCGTGTCTT
1 AAAAATTCTCGTGTCTT
90349285 AAAAA
1 AAAAA
90349290 AAGTTTTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (17 bp):
AAAAATTCTCGTGTCTT
Found at i:90351721 original size:50 final size:50
Alignment explanation
Indices: 90351663--90351764 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
90351653 CATCTCTATC
90351663 TATACTATATTTAAATCTGATTAAATTAGAATTAAGAGTCAATAAAAAAT
1 TATACTATATTTAAATCTGATTAAATTAGAATTAAGAGTCAATAAAAAAT
90351713 TATACTATATTTAAATCTGATTAAATTAGAATTAAGAGTCAATAAAAAAT
1 TATACTATATTTAAATCTGATTAAATTAGAATTAAGAGTCAATAAAAAAT
90351763 TA
1 TA
90351765 ACTCAATTGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (50 bp):
TATACTATATTTAAATCTGATTAAATTAGAATTAAGAGTCAATAAAAAAT
Found at i:90359886 original size:47 final size:47
Alignment explanation
Indices: 90359792--90360025 Score: 220
Period size: 47 Copynumber: 4.9 Consensus size: 47
90359782 ATACACCGAA
* ** * *
90359792 GCCATAGCCCAGCCATGGTCTTACACGG-ATCACATATCACACTGAT
1 GCCATATCCCAGATATGGTCTTATACGGAAGCACATATCACACTGAT
* * ** *
90359838 GCCATATCCCAAATATGGTCTTACATAGAAGCACATATCACATTGAT
1 GCCATATCCCAGATATGGTCTTATACGGAAGCACATATCACACTGAT
* *
90359885 GCTATATCCCAGATATGGTATTATACGGAAGCACATAATCACATCACACTGAT
1 GCCATATCCCAGATATGGTCTTATACGGAAGCAC---AT---ATCACACTGAT
*
90359938 GCCATAGT-CCAGTTATGGTCTTATACGGAAGCACATATCACACTGAT
1 GCCATA-TCCCAGATATGGTCTTATACGGAAGCACATATCACACTGAT
* * * * *
90359985 GCCATAGCTCAGCTATGATCTTATACGGAAATCACATATCA
1 GCCATATCCCAGATATGGTCTTATACGG-AAGCACATATCA
90360026 TATGTTGCAA
Statistics
Matches: 155, Mismatches: 23, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
46 22 0.14
47 78 0.50
48 11 0.07
50 4 0.03
53 39 0.25
54 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (47 bp):
GCCATATCCCAGATATGGTCTTATACGGAAGCACATATCACACTGAT
Found at i:90359955 original size:53 final size:52
Alignment explanation
Indices: 90359827--90359979 Score: 174
Period size: 53 Copynumber: 3.0 Consensus size: 52
90359817 CGGATCACAT
* * * **
90359827 ATCACACTGATGCCATATCCCAAATATGGTCTTACATAGAAGCACATATCAC
1 ATCACACTGATGCCATATCCCAGATATGGTATTATACGGAAGCACATATCAC
*
90359879 AT-----TGATGCTATATCCCAGATATGGTATTATACGGAAGCACATAATCAC
1 ATCACACTGATGCCATATCCCAGATATGGTATTATACGGAAGCACAT-ATCAC
* *
90359927 ATCACACTGATGCCATAGT-CCAGTTATGGTCTTATACGGAAGCACATATCAC
1 ATCACACTGATGCCATA-TCCCAGATATGGTATTATACGGAAGCACATATCAC
90359979 A
1 A
90359980 CTGATGCCAT
Statistics
Matches: 85, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
47 34 0.40
48 7 0.08
52 8 0.09
53 35 0.41
54 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.27
Consensus pattern (52 bp):
ATCACACTGATGCCATATCCCAGATATGGTATTATACGGAAGCACATATCAC
Found at i:90359955 original size:100 final size:100
Alignment explanation
Indices: 90359827--90360014 Score: 252
Period size: 100 Copynumber: 1.9 Consensus size: 100
90359817 CGGATCACAT
* * * *
90359827 ATCACACTGATGCCATATCCCAAATATGGTCTTACATAGAAGCACATATCACATTGATGCTATAT
1 ATCACACTGATGCCATATCCCAAATATGGTCTTACACAGAAGCACATATCACACTGATGCCATAG
*
90359892 CCCAGATATGGTATTATACGGAAGCACATAATCAC
66 CCCAGATATGATATTATACGGAAGCACATAATCAC
** * *
90359927 ATCACACTGATGCCATAGT-CCAGTTATGGTCTTATACGGAAGCACATATCACACTGATGCCATA
1 ATCACACTGATGCCATA-TCCCAAATATGGTCTTACACAGAAGCACATATCACACTGATGCCATA
* * *
90359991 GCTCAGCTATGATCTTATACGGAA
65 GCCCAGATATGATATTATACGGAA
90360015 ATCACATATC
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
100 74 0.99
101 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (100 bp):
ATCACACTGATGCCATATCCCAAATATGGTCTTACACAGAAGCACATATCACACTGATGCCATAG
CCCAGATATGATATTATACGGAAGCACATAATCAC
Found at i:90360628 original size:16 final size:15
Alignment explanation
Indices: 90360585--90360634 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 15
90360575 AATTAGGTCC
* *
90360585 TAAAATCATTTTTAT
1 TAAAATCATCTTTAA
90360600 TAAAATCA-C-TTAA
1 TAAAATCATCTTTAA
90360613 TAAAATCATCATTTAA
1 TAAAATCATC-TTTAA
*
90360629 TGAAAT
1 TAAAAT
90360635 TAAAGCTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 11 0.38
14 1 0.03
15 8 0.28
16 9 0.31
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (15 bp):
TAAAATCATCTTTAA
Found at i:90361963 original size:25 final size:24
Alignment explanation
Indices: 90361931--90361997 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 24
90361921 GAGTGGTTTC
90361931 AAGAGTTTTTCAATGTTTCTTTCCT
1 AAGAGTTTTTCAATGTTT-TTTCCT
* *
90361956 AAGTGTTTGT-AA-GCTACTTTTTCCT
1 AAGAGTTTTTCAATG-T--TTTTTCCT
90361981 AAGAGTTTTTCAATGTT
1 AAGAGTTTTTCAATGTT
90361998 GGACCACTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 11
0.69 0.08 0.23
Matches are distributed among these distances:
23 1 0.03
24 4 0.12
25 22 0.67
26 5 0.15
27 1 0.03
ACGTcount: A:0.22, C:0.13, G:0.15, T:0.49
Consensus pattern (24 bp):
AAGAGTTTTTCAATGTTTTTTCCT
Found at i:90366906 original size:37 final size:37
Alignment explanation
Indices: 90366855--90366953 Score: 162
Period size: 37 Copynumber: 2.6 Consensus size: 37
90366845 CAGCGCTATA
90366855 TAAATTTGACACCCAGTGTCTCATCGGTTAAACCGAAG
1 TAAA-TTGACACCCAGTGTCTCATCGGTTAAACCGAAG
*
90366893 TAAATTGACACCCACTGTCTCATCGGTTAAACCGAAG
1 TAAATTGACACCCAGTGTCTCATCGGTTAAACCGAAG
**
90366930 TAAATTGACACTTAGTGTCTCATC
1 TAAATTGACACCCAGTGTCTCATC
90366954 CACTTGAGGT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
37 53 0.93
38 4 0.07
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (37 bp):
TAAATTGACACCCAGTGTCTCATCGGTTAAACCGAAG
Found at i:90371888 original size:30 final size:30
Alignment explanation
Indices: 90371837--90371893 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
90371827 AAGTTTTCAG
*
90371837 GATCCACACGGACTGAGCACATGCCCAAGT
1 GATCCACACGGACAGAGCACATGCCCAAGT
*
90371867 GATCCACACGGGCAG-GCCACATGCCCA
1 GATCCACACGGACAGAG-CACATGCCCA
90371894 TGTGCCAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.28, C:0.37, G:0.25, T:0.11
Consensus pattern (30 bp):
GATCCACACGGACAGAGCACATGCCCAAGT
Found at i:90378369 original size:33 final size:32
Alignment explanation
Indices: 90378326--90378433 Score: 93
Period size: 33 Copynumber: 3.4 Consensus size: 32
90378316 TGTCTTTATA
*
90378326 ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
1 ATTATGTTAAAATTAATTT-TTAGTAATTTAGG
**
90378359 ATTATGTTAAAATT--TTTTGGGT--TTGTA--
1 ATTATGTTAAAATTAATTTTTAGTAATT-TAGG
*
90378386 ATTATTTTAAAATTAATTTATTAGTAATTTAGG
1 ATTATGTTAAAATTAATTT-TTAGTAATTTAGG
*
90378419 ATTAAGTTATAAATT
1 ATTATGTTA-AAATT
90378434 GTTGTGTTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
27 13 0.22
28 2 0.03
29 5 0.09
30 6 0.10
31 5 0.09
32 2 0.03
33 20 0.34
34 5 0.09
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (32 bp):
ATTATGTTAAAATTAATTTTTAGTAATTTAGG
Found at i:90378765 original size:27 final size:27
Alignment explanation
Indices: 90378724--90378792 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
90378714 CACCATTTGT
90378724 GCCTCTGAGATAGGCACAATTAGTCGC
1 GCCTCTGAGATAGGCACAATTAGTCGC
* *
90378751 GCCTCTGAGAAAGGCTCAATTAGTCGC
1 GCCTCTGAGATAGGCACAATTAGTCGC
*
90378778 GCCTCAGAGATAGGC
1 GCCTCTGAGATAGGC
90378793 GCAACCTGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (27 bp):
GCCTCTGAGATAGGCACAATTAGTCGC
Found at i:90378877 original size:27 final size:27
Alignment explanation
Indices: 90378819--90378878 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
90378809 TCTATAATCT
* **
90378819 AAAAACAAAAAATAATATTTTATTTTA
1 AAAAACAAAAAAAAATATTTTATAATA
90378846 AAAAACAAAAAAAAATATATTT-TAATA
1 AAAAACAAAAAAAAATAT-TTTATAATA
90378873 TAAAAA
1 -AAAAA
90378879 AAAGAATCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAAACAAAAAAAAATATTTTATAATA
Found at i:90383147 original size:24 final size:27
Alignment explanation
Indices: 90383094--90383156 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
90383084 CTACATATAA
* *
90383094 ATATACATGATAATAGTATTAAAAACT
1 ATATACATAATAATAATATTAAAAACT
90383121 ATATACATAAT-ATAATATTAAAATA-T
1 ATATACATAATAATAATATTAAAA-ACT
90383147 ATATACATAA
1 ATATACATAA
90383157 AAGGGTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 22 0.67
27 11 0.33
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (27 bp):
ATATACATAATAATAATATTAAAAACT
Found at i:90383271 original size:18 final size:19
Alignment explanation
Indices: 90383248--90383288 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
90383238 AATAAGGTAT
*
90383248 ATAAAATAATTTAAAATA-
1 ATAAAACAATTTAAAATAG
*
90383266 ATAAAACAATTTTAAATAG
1 ATAAAACAATTTAAAATAG
90383285 ATAA
1 ATAA
90383289 TACATGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
ATAAAACAATTTAAAATAG
Found at i:90387495 original size:52 final size:51
Alignment explanation
Indices: 90387424--90387632 Score: 275
Period size: 52 Copynumber: 4.1 Consensus size: 51
90387414 ATCAAGTGAT
* * *
90387424 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGT-G
* *
90387476 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
* *
90387527 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC-----
1 -AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
*
90387574 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC-AAGTG
90387626 ATAAGTG
1 A-AAGTG
90387633 GCTACACTTA
Statistics
Matches: 141, Mismatches: 8, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
46 43 0.30
51 1 0.01
52 92 0.65
53 5 0.04
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
Found at i:90387546 original size:98 final size:97
Alignment explanation
Indices: 90387410--90387632 Score: 231
Period size: 98 Copynumber: 2.3 Consensus size: 97
90387400 TTTGAGTACT
* * *
90387410 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTAC-ACT-TATCTGATCAAGTGA-CAA
1 TCTGATCAAGTGA-CAAGTGATAAGTGATAGCTATAGCTACGACTATA-CTGATC---TGATCAA
* * *
90387472 GTG-GAAAGTGATAAGTGATAGCTTCGGCTACACTTA
61 GAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * * *
90387508 TCTGATCAAGTGACAAGTGAAAAGTGATAAG-TGATAGCTTCGGCTATACTTATCTGATCAAGAG
1 TCTGATCAAGTGACAAGTGATAAGTGAT-AGCT-ATAGCTACGACTATACTGATCTGATCAAGAG
*
90387572 ACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
64 ACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
90387606 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGAC-AAGTGATAAGTG
90387633 GCTACACTTA
Statistics
Matches: 105, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
96 3 0.03
97 18 0.17
98 64 0.61
99 18 0.17
100 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (97 bp):
TCTGATCAAGTGACAAGTGATAAGTGATAGCTATAGCTACGACTATACTGATCTGATCAAGAGAC
AAAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:90387605 original size:46 final size:44
Alignment explanation
Indices: 90387528--90387743 Score: 199
Period size: 37 Copynumber: 5.3 Consensus size: 44
90387518 TGACAAGTGA
*
90387528 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTT--GCTACACTTATCTGATCAAGAGAC
90387574 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGC-TT-GCTACACTTATCTGATCAAGAGAC
*
90387620 AAAGTGATAA--G-T-G---GCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
*
90387657 AAAGTGATAA--G-T-G---GCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
*
90387694 AAAGTGAT-AG-G-T-G---GCTACACTTATCTGATC-AGGGAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
90387730 -AAGTGATAAGTGAT
1 AAAGTGATAAGTGAT
90387744 CATACGTAAG
Statistics
Matches: 160, Mismatches: 5, Indels: 18
0.87 0.03 0.10
Matches are distributed among these distances:
35 7 0.04
36 7 0.04
37 89 0.56
38 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 51 0.32
47 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (44 bp):
AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
Found at i:90387640 original size:37 final size:37
Alignment explanation
Indices: 90387596--90387741 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
90387586 GATAGCTTTA
*
90387596 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
90387633 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
90387670 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
90387707 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
90387742 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:90389570 original size:13 final size:14
Alignment explanation
Indices: 90389554--90389589 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
90389544 CAATCTCATA
90389554 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
90389567 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
90389580 TCTC-ATTTCA
1 TCTCAATTTCA
90389590 TTCCAATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:90389579 original size:18 final size:19
Alignment explanation
Indices: 90389541--90389581 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
90389531 TGGTTCATGT
90389541 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
90389560 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
90389578 TTTC
1 TTTC
90389582 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:90389811 original size:23 final size:23
Alignment explanation
Indices: 90389757--90389817 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 23
90389747 GACATATAAA
90389757 GTGCCT-AAA-ACGACACACGAG
1 GTGCCTGAAATACGACACACGAG
*
90389778 GTGCTTG--ATACGACACACGAG
1 GTGCCTGAAATACGACACACGAG
90389799 GTGCCTGAAATACGACACA
1 GTGCCTGAAATACGACACA
90389818 TAAAGTGCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 23 0.68
23 10 0.29
ACGTcount: A:0.34, C:0.26, G:0.25, T:0.15
Consensus pattern (23 bp):
GTGCCTGAAATACGACACACGAG
Found at i:90389825 original size:23 final size:23
Alignment explanation
Indices: 90389743--90389827 Score: 70
Period size: 21 Copynumber: 3.9 Consensus size: 23
90389733 CCTGATCAGT
* *
90389743 ATACGACATATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* * *
90389765 A-ACGACACACGAGGTGCTTG--
1 ATACGACACACAAAGTGCCTGAA
* *
90389785 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
90389808 ATACGACACATAAAGTGCCT
1 ATACGACACACAAAGTGCCT
90389828 AATCGGTAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
20 1 0.02
21 31 0.62
22 1 0.02
23 17 0.34
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.18
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:90390225 original size:15 final size:15
Alignment explanation
Indices: 90390200--90390257 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
90390190 TCATATATAT
90390200 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
90390216 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
90390231 AATAATTTCAATCAA
1 TATAAATTCAATCAA
90390246 TATAAATTCAAT
1 TATAAATTCAAT
90390258 AAAACAGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:90390242 original size:30 final size:28
Alignment explanation
Indices: 90390203--90390261 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
90390193 TATATATTAT
90390203 ATAATTCAATCAATATAAATTCAATCAAA
1 ATAATTCAATCAATATAAATTCAAT-AAA
90390232 ATAATTTCAATCAATATAAATTCAATAAA
1 ATAA-TTCAATCAATATAAATTCAATAAA
90390261 A
1 A
90390262 CAGATATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATTCAATCAATATAAATTCAATAAA
Found at i:90391236 original size:13 final size:13
Alignment explanation
Indices: 90391218--90391245 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
90391208 CCTCTTTTTA
90391218 TTCTTTTGTTTCT
1 TTCTTTTGTTTCT
90391231 TTCTTTTGTTTCT
1 TTCTTTTGTTTCT
90391244 TT
1 TT
90391246 TATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (13 bp):
TTCTTTTGTTTCT
Found at i:90393861 original size:33 final size:31
Alignment explanation
Indices: 90393801--90393918 Score: 103
Period size: 33 Copynumber: 3.6 Consensus size: 31
90393791 ATGAACTTGA
* *
90393801 GCCGAGAGGAGTAGAATATGGAGGTGGATATGG
1 GCCG-GAGGAGTAGAGTACGGAGGTGGATA-GG
*
90393834 GCCAGGAGGAGTAGAGTACGGCA-GTGGATACG
1 GCC-GGAGGAGTAGAGTACGG-AGGTGGATAGG
* **
90393866 GCTCTGGAGGAGTTGAGTACATAGGTGGATACGG
1 GC-C-GGAGGAGTAGAGTACGGAGGTGGATA-GG
90393900 GCCGGAAGGAGTAGAGTAC
1 GCCGG-AGGAGTAGAGTAC
90393919 TGAGATAAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
32 6 0.09
33 59 0.84
34 5 0.07
ACGTcount: A:0.28, C:0.12, G:0.43, T:0.17
Consensus pattern (31 bp):
GCCGGAGGAGTAGAGTACGGAGGTGGATAGG
Found at i:90395705 original size:22 final size:22
Alignment explanation
Indices: 90395671--90395734 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
90395661 TCAACATTTT
*
90395671 AATAAATCA-ATAAAAATTATCA
1 AATAAAT-ATATAAAAATTATAA
*
90395693 AATAAATATATAATAA-TATAA
1 AATAAATATATAAAAATTATAA
*
90395714 AATTACATTATATAAAAATTA
1 AA-TA-AATATATAAAAATTA
90395735 CATTAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 15 0.44
23 10 0.29
24 2 0.06
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAAATATATAAAAATTATAA
Found at i:90395728 original size:15 final size:16
Alignment explanation
Indices: 90395708--90395739 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
90395698 ATATATAATA
90395708 ATAT-AAAATTACATT
1 ATATAAAAATTACATT
90395723 ATATAAAAATTACATT
1 ATATAAAAATTACATT
90395739 A
1 A
90395740 AAAAATCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAAAATTACATT
Found at i:90395939 original size:115 final size:113
Alignment explanation
Indices: 90395797--90396240 Score: 671
Period size: 115 Copynumber: 3.9 Consensus size: 113
90395787 ATACTAACAC
* * * *
90395797 AAAATAACTATAAAATTA-TTTTTTAAAATACATTACTAAAAAAAATCACAATACATTAATACAC
1 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACT-AAAAAAATCACAATACACTAAT--AC
90395861 ACTAAACCACTAAACACTAACAA-TATATAACCTAATCTTAAATTACTAAT
63 ACTAAACCACTAAACACTAACAATTATATAACCTAATCTTAAATTACTAAT
90395911 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAAATCACAATACACTAATACAC
1 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACT-AAAAAAATCACAATACACTAATACAC
*
90395976 TAAACCACTAAACACTAATAATTTATATAACCTAATCTTAAATTACTAAT
65 TAAACCACTAAACACTAACAA-TTATATAACCTAATCTTAAATTACTAAT
* * *
90396026 AAAATAGCTATAAAAATATTTTTTTTAAAATATATTACTAAAAAAATTACCATACGCTAAT--AC
1 AAAATAGCTATAAAAATA-TTTTTTTAAAATATATTACTAAAAAAATCACAATACACTAATACAC
90396089 TAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
65 TAAACCACTAAACACTAACAA-TTATATAACCTAATCTTAAATTACTAAT
* *
90396139 AAAATAGCTATAAAATTATTATTTTTAAAATATATTACTAAAACAATCACAATACACTAATACAC
1 AAAATAGCTATAAAAATATT-TTTTTAAAATATATTACTAAAAAAATCACAATACACTAATACAC
* *
90396204 TAAACTACTAAACACTAACAATTTATATAACCAAATC
65 TAAACCACTAAACACTAACAA-TTATATAACCTAATC
90396241 AACTATAAAT
Statistics
Matches: 307, Mismatches: 16, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
112 2 0.01
113 128 0.42
114 16 0.05
115 141 0.46
116 20 0.07
ACGTcount: A:0.52, C:0.16, G:0.01, T:0.32
Consensus pattern (113 bp):
AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATCACAATACACTAATACACT
AAACCACTAAACACTAACAATTATATAACCTAATCTTAAATTACTAAT
Found at i:90396128 original size:228 final size:226
Alignment explanation
Indices: 90395797--90396240 Score: 687
Period size: 228 Copynumber: 1.9 Consensus size: 226
90395787 ATACTAACAC
*
90395797 AAAATAACTATAAAATTATTTTTTAAAATACATTACTAAAAAAAATCACAATACATTAATACACA
1 AAAATAACTATAAAATTATTTTTTAAAATACATTACTAAAAAAAATCACAATACACTAAT--A-A
90395862 CTAAACCACTAAACACTAACAATATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAAA
63 CTAAACCACTAAACACTAACAATATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAAA
90395927 TATT-TTTTTAAAATATATTACTAAAAAAAATCACAATACACTAATACACTAAACCACTAAACAC
128 TATTATTTTTAAAATATATTACT-AAAAAAATCACAATACACTAATACACTAAACCACTAAACAC
* *
90395991 TAATAATTTATATAACCTAATCTTAAATTACTAAT
192 TAACAATTTATATAACCAAATCTTAAATTACTAAT
* * * * * *
90396026 AAAATAGCTATAAAAATATTTTTTTTAAAATATATTACT-AAAAAAATTACCATACGCTAAT-AC
1 AAAATAACTAT-AAAAT-TATTTTTTAAAATACATTACTAAAAAAAATCACAATACACTAATAAC
90396089 TAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAA
64 TAAACCACTAAACACTAACAA--TATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAA
* * *
90396154 TTATTATTTTTAAAATATATTACTAAAACAATCACAATACACTAATACACTAAACTACTAAACAC
127 ATATTATTTTTAAAATATATTACTAAAAAAATCACAATACACTAATACACTAAACCACTAAACAC
90396219 TAACAATTTATATAACCAAATC
192 TAACAATTTATATAACCAAATC
90396241 AACTATAAAT
Statistics
Matches: 198, Mismatches: 12, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
226 23 0.12
228 105 0.53
229 28 0.14
230 23 0.12
231 19 0.10
ACGTcount: A:0.52, C:0.16, G:0.01, T:0.32
Consensus pattern (226 bp):
AAAATAACTATAAAATTATTTTTTAAAATACATTACTAAAAAAAATCACAATACACTAATAACTA
AACCACTAAACACTAACAATATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAAATAT
TATTTTTAAAATATATTACTAAAAAAATCACAATACACTAATACACTAAACCACTAAACACTAAC
AATTTATATAACCAAATCTTAAATTACTAAT
Found at i:90396541 original size:22 final size:22
Alignment explanation
Indices: 90396509--90396551 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
90396499 CCTTTTTCTT
90396509 CTTCTTCTTCTCCTTCACCTTC
1 CTTCTTCTTCTCCTTCACCTTC
* *
90396531 CTTCTTTTTCTCCTTCTCCTT
1 CTTCTTCTTCTCCTTCACCTT
90396552 TCTCTCCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.02, C:0.42, G:0.00, T:0.56
Consensus pattern (22 bp):
CTTCTTCTTCTCCTTCACCTTC
Found at i:90399350 original size:17 final size:16
Alignment explanation
Indices: 90399308--90399356 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
90399298 ATTGATTTAG
90399308 AAAAAAAAATAAGTTAC
1 AAAAAAAAATAA-TTAC
* *
90399325 AAATTAAAAATAATTAT
1 AAA-AAAAAATAATTAC
90399342 AAAAGAAAAATAATT
1 AAAA-AAAAATAATT
90399357 TTATTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (16 bp):
AAAAAAAAATAATTAC
Found at i:90399448 original size:16 final size:16
Alignment explanation
Indices: 90399427--90399492 Score: 73
Period size: 16 Copynumber: 4.2 Consensus size: 16
90399417 TTATAAATAG
90399427 TTTTAATAAAATAAAA
1 TTTTAATAAAATAAAA
90399443 TTTT-A-AAAATAGAAA
1 TTTTAATAAAATA-AAA
* *
90399458 TTATAATTAAATAAAA
1 TTTTAATAAAATAAAA
* *
90399474 TTTTAAAAAAATTAAA
1 TTTTAATAAAATAAAA
90399490 TTT
1 TTT
90399493 CTTGGAATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
14 6 0.15
15 7 0.17
16 23 0.56
17 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
TTTTAATAAAATAAAA
Found at i:90403788 original size:16 final size:16
Alignment explanation
Indices: 90403757--90403793 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
90403747 ATATGAAGAA
90403757 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
90403773 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
90403789 TATTA
1 TATTA
90403794 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:90403832 original size:16 final size:16
Alignment explanation
Indices: 90403813--90403847 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
90403803 TGAAATATTA
*
90403813 AATAATTTATTAAAAT
1 AATAAATTATTAAAAT
*
90403829 AATAAATTATTAATAT
1 AATAAATTATTAAAAT
90403845 AAT
1 AAT
90403848 TTATTATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATAAATTATTAAAAT
Found at i:90403853 original size:16 final size:15
Alignment explanation
Indices: 90403808--90403854 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 15
90403798 AAAATTGAAA
90403808 TATTAAATAATTTAT
1 TATTAAATAATTTAT
**
90403823 TA--AAATAATAAAT
1 TATTAAATAATTTAT
90403836 TATTAATATAATTTAT
1 TATTAA-ATAATTTAT
90403852 TAT
1 TAT
90403855 ATGATTAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
13 11 0.44
15 4 0.16
16 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTAAATAATTTAT
Done.