Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold468
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: 1127621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:890371 original size:14 final size:14
Alignment explanation
Indices: 890343--890381 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
890333 AAAATATTTA
890343 TTTATTATT-TTAT
1 TTTATTATTATTAT
890356 TTTATTATTATTAT
1 TTTATTATTATTAT
*
890370 TTTCTTATTATT
1 TTTATTATTATT
890382 GAAAATTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTATTATTAT
Found at i:892142 original size:166 final size:166
Alignment explanation
Indices: 891919--892537 Score: 827
Period size: 167 Copynumber: 3.7 Consensus size: 166
891909 TTTTTCAGAA
* * * * *
891919 AAAAACTCATGAAAATGAATGAAATTTT-AAAAATTGATTTAAAATTAAATAAATAATAATATTT
1 AAAAACCCATGAAAATGAATGAATTTTTGAAAAA-TAATTTAATATAAAATAAATAATAATATTT
* * *
891983 TATGGATTCTAAAAATTAAAAACTAAGAAAAATCCTCTCAAAAAAATTTACGGAGTAAAAAACTC
65 TATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCTCAAAAAAATTTACGGAGTAAAAAACTC
* *
892048 TATTTTTTAAAAACAAGGGAATGTCAAG-AAAAAATTC
130 TATTTTTTGAAAA-AAGGGAATTTCAAGAAAAAAATTC
* * *
892085 AAAAACCCATGAAAATAAATGAATTTTTGAAAAATAATTTATTATAAAATCAATAATAATATTTT
1 AAAAACCCATGAAAATGAATGAATTTTTGAAAAATAATTTAATATAAAATAAATAATAATATTTT
*
892150 ATGAATTTTAAAAATTAAAAACCAAGAAAAATCC-CTCCAAAAAAATTTACGGAGTAGAAAACTC
66 ATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCT-CAAAAAAATTTACGGAGTAAAAAACTC
* * *
892214 TATTTTTTGGAAATAGGGAAATTTCATGAAAAAAATTC
130 TATTTTTTGAAAAAAGGG-AATTTCAAGAAAAAAATTC
* *
892252 AAAAACCTATGAAAATGAATGAATTTTTGAAAAATAATTT-ATCATGAAATAAATAATAATATTT
1 AAAAACCCATGAAAATGAATGAATTTTTGAAAAATAATTTAAT-ATAAAATAAATAATAATATTT
* * *
892316 TAAGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCTCAAAAAAATTTACGGACTAGAAAAA-T
65 TATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCTCAAAAAAATTTACGGAGTA-AAAAACT
* *
892380 CTATTTTTCGAAAATAAGAGAATTTCAAGAAAAAAATTC
129 CTATTTTTTGAAAA-AAGGGAATTTCAAGAAAAAAATTC
* * * * *
892419 AAAAACCCATGAAAATGAATGAATTTTTGAAAACTGATTTAATATCAATTAAATAGTAATATTTT
1 AAAAACCCATGAAAATGAATGAATTTTTGAAAAATAATTTAATATAAAATAAATAATAATATTTT
* * * *
892484 ATGAATTTTAAAAATTTTAAACCCATG-AAAATCTTCTCAAAAAAATTTACGGAG
66 ATGAATTTTAAAAA-TTAAAAACCAAGAAAAATCCTCTCAAAAAAATTTACGGAG
892538 AAGAGAACTC
Statistics
Matches: 400, Mismatches: 43, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
165 6 0.01
166 127 0.32
167 247 0.62
168 20 0.05
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (166 bp):
AAAAACCCATGAAAATGAATGAATTTTTGAAAAATAATTTAATATAAAATAAATAATAATATTTT
ATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCTCAAAAAAATTTACGGAGTAAAAAACTCT
ATTTTTTGAAAAAAGGGAATTTCAAGAAAAAAATTC
Found at i:892625 original size:333 final size:332
Alignment explanation
Indices: 891930--892648 Score: 837
Period size: 333 Copynumber: 2.2 Consensus size: 332
891920 AAAACTCATG
* * * * * *
891930 AAAATGAATGAAATTTT-AAAAATTGATTTAA-AATTAAATAAATAATAATATTTTATGGATTCT
1 AAAATAAAAGAAATTTTCAAAAA-TAATTTAACAA-GAAATAAATAATAATATTTTAAGAATTCT
* * * *
891993 AAAAATTAAAAACTAAGAAAAATCCTCTCAAAAAAATTTACGGAGTAAAAAACTCTATTTTTTAA
64 AAAAATTAAAAACCAAGAAAAATCCCCTCAAAAAAATTTACGGACTAAAAAACTCTATTTTTCAA
*
892058 AAACAAGGGAATGTCAAGAAAAAATTCAAAAACCCATGAAAATAAATGAATTTTTGAAAAATAAT
129 AAACAAGAGAATGTCAAGAAAAAATTCAAAAACCCATGAAAATAAATGAATTTTTGAAAAATAAT
* *
892123 TTATTATAAAATCAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCC
194 TTAATATAAAATAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCC
* * ** * *
892188 AAAAAAATTTACGGAGTAGAAAACTCTATTTTTTGGAAATAGGGAAATTTCATGAAAAAAATTCA
259 AAAAAAATTTACGGAGAAGAAAACTCCATAATTTGAAAATAGGGAAATTCCA-GAAAAAAATTCA
*
892253 AAAACCTATG
323 AAAACCTATA
* * * * * * *
892263 AAAATGAATGAATTTTTGAAAAATAATTTATCATGAAATAAATAATAATATTTTAAGAATTTTAA
1 AAAATAAAAGAAATTTTCAAAAATAATTTAACAAGAAATAAATAATAATATTTTAAGAATTCTAA
*
892328 AAATTAAAAACCAAGAAAAATCCCCTCAAAAAAATTTACGGACTAGAAAAA-TCTATTTTTCGAA
66 AAATTAAAAACCAAGAAAAATCCCCTCAAAAAAATTTACGGACTA-AAAAACTCTATTTTTCAAA
* * * * *
892392 AATAAGAGAATTTCAAGAAAAAAATTCAAAAACCCATGAAAATGAATGAATTTTTGAAAACTGAT
130 AACAAGAGAATGTCAAG-AAAAAATTCAAAAACCCATGAAAATAAATGAATTTTTGAAAAATAAT
* * * * * * *
892457 TTAATATCAATTAAATAGTAATATTTTATGAATTTTAAAAATTTTAAACCCATG-AAAAT-CTTC
194 TTAATATAAAATAAATAATAATATTTTATGAATTTTAAAAA-TTAAAAACCAAGAAAAATCCCTC
* *
892520 TCAAAAAAATTTACGGAGAAGAGAACTCCGTAATTTGAAAATATGAGG-AATTCCA-AAAGAAAA
258 -CAAAAAAATTTACGGAGAAGAAAACTCCATAATTTGAAAATA-G-GGAAATTCCAGAAA-AAAA
*
892583 -TCAATAA-CTCA-A
319 TTCAAAAACCT-ATA
* ** *
892595 AAAATAAAAGAAAATTTTCAAAACTAATTTAACAAGATTTAAATTATAATATTT
1 AAAATAAAAG-AAATTTTCAAAAATAATTTAACAAGAAATAAATAATAATATTT
892649 GAAAACTTTT
Statistics
Matches: 327, Mismatches: 48, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
332 10 0.03
333 164 0.50
334 135 0.41
335 16 0.05
336 2 0.01
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (332 bp):
AAAATAAAAGAAATTTTCAAAAATAATTTAACAAGAAATAAATAATAATATTTTAAGAATTCTAA
AAATTAAAAACCAAGAAAAATCCCCTCAAAAAAATTTACGGACTAAAAAACTCTATTTTTCAAAA
ACAAGAGAATGTCAAGAAAAAATTCAAAAACCCATGAAAATAAATGAATTTTTGAAAAATAATTT
AATATAAAATAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCCAA
AAAAATTTACGGAGAAGAAAACTCCATAATTTGAAAATAGGGAAATTCCAGAAAAAAATTCAAAA
ACCTATA
Found at i:894211 original size:19 final size:18
Alignment explanation
Indices: 894186--894250 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
894176 ATTTCAACAA
894186 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
894204 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
894220 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
894236 TTTTGTATCGATACA
1 -TTTGTATCGATACA
894251 ATGTATCGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:894225 original size:13 final size:13
Alignment explanation
Indices: 894207--894231 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
894197 ACATAAGTGT
894207 TGTATCGATACAA
1 TGTATCGATACAA
894220 TGTATCGATACA
1 TGTATCGATACA
894232 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:894225 original size:32 final size:32
Alignment explanation
Indices: 894188--894258 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
894178 TTCAACAATT
894188 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
894220 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
894252 TGTATCG
1 TGTATCG
894259 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:898958 original size:20 final size:20
Alignment explanation
Indices: 898933--898984 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
898923 TTACCCAGAT
898933 GTATCGATACATTATTCAAG
1 GTATCGATACATTATTCAAG
* *
898953 GTATCGATATATTATTCAAT
1 GTATCGATACATTATTCAAG
*
898973 GTATTGATACAT
1 GTATCGATACAT
898985 GCAGGCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (20 bp):
GTATCGATACATTATTCAAG
Found at i:899923 original size:20 final size:20
Alignment explanation
Indices: 899879--899923 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
899869 GTTAACAGCC
899879 CATG-TTCATGCATTTTGAG
1 CATGTTTCATGCATTTTGAG
899898 CTATGTTTCATGCATTTAT-AG
1 C-ATGTTTCATGCATTT-TGAG
899919 CATGT
1 CATGT
899924 CCGGCACCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.04
20 7 0.30
21 14 0.61
22 1 0.04
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (20 bp):
CATGTTTCATGCATTTTGAG
Found at i:905075 original size:25 final size:24
Alignment explanation
Indices: 905023--905075 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 24
905013 ACTATTTTGA
*
905023 TTTCGAGGATACTCCAACCTCGCTC
1 TTTCGAGGATACTCCAACCTC-CAC
905048 TTTCGAGGGAATACTCCAACCT-CAC
1 TTTCGA-GG-ATACTCCAACCTCCAC
905073 TTT
1 TTT
905076 TCTTCAAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 11 0.44
26 2 0.08
27 12 0.48
ACGTcount: A:0.23, C:0.32, G:0.15, T:0.30
Consensus pattern (24 bp):
TTTCGAGGATACTCCAACCTCCAC
Found at i:910323 original size:86 final size:86
Alignment explanation
Indices: 910173--910332 Score: 214
Period size: 86 Copynumber: 1.9 Consensus size: 86
910163 TCCCTCGGAG
* * **** * *
910173 GAATGGGGTTGGAGTATCCCTGATGATTTTGATTCAGACAAAGATAAGAATCAAATCTTGACAAG
1 GAATAGGGTTGGAGTATCCCTAATGATAACAATTCAGACAAAAATAAGAATCAAATCATGACAAG
910238 TTTAAAAATATCCTCTTAGAA
66 TTTAAAAATATCCTCTTAGAA
* *
910259 GAATAGGGTTGGAGTATCCCTAATGATAACAATTCA-AGCAAAAATAAGATTTAAATCATGACAA
1 GAATAGGGTTGGAGTATCCCTAATGATAACAATTCAGA-CAAAAATAAGAATCAAATCATGACAA
910323 GTTTAAAAAT
65 GTTTAAAAAT
910333 GGGGTTGGAG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
85 1 0.02
86 62 0.98
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (86 bp):
GAATAGGGTTGGAGTATCCCTAATGATAACAATTCAGACAAAAATAAGAATCAAATCATGACAAG
TTTAAAAATATCCTCTTAGAA
Found at i:913838 original size:33 final size:33
Alignment explanation
Indices: 913801--913867 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
913791 AGTAACTTAA
913801 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
913834 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
913867 A
1 A
913868 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:913841 original size:13 final size:13
Alignment explanation
Indices: 913823--913847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
913813 CAAAAAAATA
913823 TGTATCGATACAT
1 TGTATCGATACAT
913836 TGTATCGATACA
1 TGTATCGATACA
913848 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:915846 original size:13 final size:13
Alignment explanation
Indices: 915830--915854 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
915820 CTTGCTGGCA
915830 AAGGTGGCTGAGT
1 AAGGTGGCTGAGT
915843 AAGGTGGCTGAG
1 AAGGTGGCTGAG
915855 AATAAATGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.48, T:0.20
Consensus pattern (13 bp):
AAGGTGGCTGAGT
Found at i:916299 original size:20 final size:20
Alignment explanation
Indices: 916274--916320 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
916264 CATTTTAGAC
916274 ATGTATCAATACATTCAATT
1 ATGTATCAATACATTCAATT
* *
916294 ATGTATCGATACATTCACTT
1 ATGTATCAATACATTCAATT
916314 ATTGTAT
1 A-TGTAT
916321 AGATAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (20 bp):
ATGTATCAATACATTCAATT
Found at i:916325 original size:21 final size:20
Alignment explanation
Indices: 916282--916325 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
916272 ACATGTATCA
*
916282 ATACATTCAATTATGTATCG
1 ATACATTCAATTATGTATAG
*
916302 ATACATTCACTTATTGTATAG
1 ATACATTCAATTA-TGTATAG
916323 ATA
1 ATA
916326 AAAATTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (20 bp):
ATACATTCAATTATGTATAG
Found at i:918977 original size:27 final size:27
Alignment explanation
Indices: 918938--918990 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
918928 ATTAAAAAAG
* *
918938 AGTCCAACTTAAAAAATCAAAGTCAAA
1 AGTCAAACATAAAAAATCAAAGTCAAA
**
918965 AGTCAAACATAAAAGGTCAAAGTCAA
1 AGTCAAACATAAAAAATCAAAGTCAA
918991 CAAAGAGTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.55, C:0.17, G:0.11, T:0.17
Consensus pattern (27 bp):
AGTCAAACATAAAAAATCAAAGTCAAA
Found at i:920773 original size:20 final size:20
Alignment explanation
Indices: 920748--920787 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
920738 TAACTAAGAT
920748 AATTCGGGATATGTCTCGAA
1 AATTCGGGATATGTCTCGAA
920768 AATTCGGGATATGTCTCGAA
1 AATTCGGGATATGTCTCGAA
920788 TTGTCATTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (20 bp):
AATTCGGGATATGTCTCGAA
Found at i:929435 original size:23 final size:23
Alignment explanation
Indices: 929407--929464 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
929397 CATCAATCGA
** *
929407 TTTTTCCAAATTTTTAAAATATT
1 TTTTTCCAAAAGTTTAAAATATC
* *
929430 TTTTTCAAAAAGTTTACAATATC
1 TTTTTCCAAAAGTTTAAAATATC
*
929453 TCTTTCCAAAAG
1 TTTTTCCAAAAG
929465 GGAATGGTGC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (23 bp):
TTTTTCCAAAAGTTTAAAATATC
Found at i:930178 original size:87 final size:86
Alignment explanation
Indices: 930026--930251 Score: 215
Period size: 87 Copynumber: 2.6 Consensus size: 86
930016 TTCGTATTAC
* * * * *
930026 TTTATCCTTAGGGAAACTCCATCCCTACTCCTCTGAAGAAACACTCCAACCCCACTCTTCAAAAA
1 TTTATCCTTGGGGAAACTCCATCCCTACTCTTC-GAAGAGATACTCCAACCCCACTCTAC-AAAA
**
930091 AATTCAAATTTT-TTTGTACAAT
64 AATTCAAATTTTCTTCATACAAT
* * ** *
930113 TTTATCCTTGGGGAAACTCCATCCCTACTGTTCCAAGGAGATACTCCAACCTTATTCTA-ACAAA
1 TTTATCCTTGGGGAAACTCCATCCCTACTCTTCGAA-GAGATACTCCAACCCCACTCTACA-AAA
* *
930177 AATTTAAATTTTCCTTCATATAAT
64 AATTCAAATTTT-CTTCATACAAT
* * * *
930201 TTTATCATCGGGAAAACTCTATCCCTACTACTTCGAAG-GATACTCCAACCC
1 TTTATCCTTGGGGAAACTCCATCCCTACT-CTTCGAAGAGATACTCCAACCC
930252 TTTTTTCCTT
Statistics
Matches: 113, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
85 1 0.01
86 16 0.14
87 58 0.51
88 33 0.29
89 5 0.04
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.32
Consensus pattern (86 bp):
TTTATCCTTGGGGAAACTCCATCCCTACTCTTCGAAGAGATACTCCAACCCCACTCTACAAAAAA
TTCAAATTTTCTTCATACAAT
Found at i:931135 original size:13 final size:13
Alignment explanation
Indices: 931117--931141 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
931107 GTTTTGAGTT
931117 TCCTGAGGCATTA
1 TCCTGAGGCATTA
931130 TCCTGAGGCATT
1 TCCTGAGGCATT
931142 CGAAACCTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (13 bp):
TCCTGAGGCATTA
Found at i:935466 original size:13 final size:13
Alignment explanation
Indices: 935438--935493 Score: 64
Period size: 13 Copynumber: 4.4 Consensus size: 13
935428 TGCTTGGAAT
935438 TTTCTTTTTTT-C
1 TTTCTTTTTTTCC
935450 --TCTTTTTTTCC
1 TTTCTTTTTTTCC
*
935461 TTTCTTTTTTTCT
1 TTTCTTTTTTTCC
935474 TTTCTTTTTTGTCAC
1 TTTCTTTTTT-TC-C
935489 TTTCT
1 TTTCT
935494 GCCAACCTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 20 0.54
14 2 0.05
15 5 0.14
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTCTTTTTTTCC
Found at i:935468 original size:23 final size:24
Alignment explanation
Indices: 935438--935482 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
935428 TGCTTGGAAT
935438 TTTCTTTTTTTCTCTT-TTTTTCC
1 TTTCTTTTTTTCTCTTCTTTTTCC
*
935461 TTTCTTTTTTTCTTTTCTTTTT
1 TTTCTTTTTTTCTCTTCTTTTT
935483 TGTCACTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTCTTTTTTTCTCTTCTTTTTCC
Found at i:935477 original size:28 final size:28
Alignment explanation
Indices: 935437--935493 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
935427 ATGCTTGGAA
*
935437 TTTTCTTTTTTTCTCTTTTTTTC-CTTTC
1 TTTTCTTTTTTTCT-TTTTTGTCACTTTC
935465 TTTT-TTTCTTTTCTTTTTTGTCACTTTC
1 TTTTCTTT-TTTTCTTTTTTGTCACTTTC
935493 T
1 T
935494 GCCAACCTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (28 bp):
TTTTCTTTTTTTCTTTTTTGTCACTTTC
Found at i:939991 original size:51 final size:52
Alignment explanation
Indices: 939843--939970 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
939833 TGAAATATGA
*
939843 AAATTTGTCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
* *
939895 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
*
939947 AAATTTG-CTGTATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
939971 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
51 16 0.22
52 56 0.78
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:940068 original size:32 final size:32
Alignment explanation
Indices: 940029--940158 Score: 215
Period size: 32 Copynumber: 4.0 Consensus size: 32
940019 AGTAGCTTAT
*
940029 ATTGTTTCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
*
940061 ATTGTTTCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
*
940093 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
*
940125 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAC-TTATGTATCGATAC
940158 A
1 A
940159 AATCGTTAAA
Statistics
Matches: 95, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
32 80 0.84
33 15 0.16
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (32 bp):
ATTGTATCGATACAAAACTTATGTATCGATAC
Found at i:940100 original size:13 final size:13
Alignment explanation
Indices: 940082--940138 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
940072 ACAAAACTTA
940082 TGTATCGATACAT
1 TGTATCGATACAT
940095 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
940113 ATGTATCGATACAT
1 -TGTATCGATACAT
940127 TGTATCGATACA
1 TGTATCGATACA
940139 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:946668 original size:42 final size:42
Alignment explanation
Indices: 946613--946731 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
946603 TTCTTCTCTC
* * *
946613 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCATGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCATATCT
* *
946655 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCATATCT
* *
946697 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
946732 TTGAGGGCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCATATCT
Found at i:946674 original size:12 final size:11
Alignment explanation
Indices: 946652--946721 Score: 58
Period size: 12 Copynumber: 6.4 Consensus size: 11
946642 ATCTCTCATG
946652 TCTCTCCTCCTA
1 TCTC-CCTCCTA
946664 TCATCCCTCCTA
1 TC-TCCCTCCTA
*
946676 TCT--CTACTA
1 TCTCCCTCCTA
946685 TCT--CTCCTA
1 TCTCCCTCCTA
946694 TCTCTCCTCCTA
1 TCTC-CCTCCTA
*
946706 TCATCCCTCCTC
1 TC-TCCCTCCTA
946718 TCTC
1 TCTC
946722 TTCTTTCTCT
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
9 16 0.32
11 3 0.06
12 27 0.54
13 4 0.08
ACGTcount: A:0.11, C:0.49, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTCCCTCCTA
Found at i:946699 original size:9 final size:9
Alignment explanation
Indices: 946670--946701 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
946660 CCTATCATCC
946670 CTCCTATCT
1 CTCCTATCT
*
946679 CTACTATCT
1 CTCCTATCT
946688 CTCCTATCT
1 CTCCTATCT
946697 CTCCT
1 CTCCT
946702 CCTATCATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.12, C:0.44, G:0.00, T:0.44
Consensus pattern (9 bp):
CTCCTATCT
Found at i:949473 original size:19 final size:18
Alignment explanation
Indices: 949449--949543 Score: 84
Period size: 19 Copynumber: 5.7 Consensus size: 18
949439 AGTGATACAT
949449 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
949468 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
949481 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
949500 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
949513 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
949532 TGTATAGATACA
1 TGTATCGATACA
949544 GTTACGGTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 22 0.35
14 2 0.03
16 4 0.06
18 2 0.03
19 33 0.52
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:949483 original size:32 final size:32
Alignment explanation
Indices: 949442--949543 Score: 186
Period size: 32 Copynumber: 3.2 Consensus size: 32
949432 GCTTCGTAGT
949442 GATACATTGTATCGATACAAAACTTATGTATC
1 GATACATTGTATCGATACAAAACTTATGTATC
949474 GATACATTGTATCGATACAAAACTTATGTATC
1 GATACATTGTATCGATACAAAACTTATGTATC
* *
949506 GATACATTGTATCGATACAACACTTATGTATA
1 GATACATTGTATCGATACAAAACTTATGTATC
949538 GATACA
1 GATACA
949544 GTTACGGTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 68 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (32 bp):
GATACATTGTATCGATACAAAACTTATGTATC
Found at i:949486 original size:13 final size:13
Alignment explanation
Indices: 949468--949524 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
949458 ACAAAACTTA
949468 TGTATCGATACAT
1 TGTATCGATACAT
949481 TGTATCGATACAAAACTT
1 TGTATCGATAC---A--T
949499 ATGTATCGATACAT
1 -TGTATCGATACAT
949513 TGTATCGATACA
1 TGTATCGATACA
949525 ACACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:950435 original size:165 final size:165
Alignment explanation
Indices: 950254--950635 Score: 429
Period size: 165 Copynumber: 2.3 Consensus size: 165
950244 CCCCGGAAAT
* * * *
950254 ATTTATGGAATAGAAAACTTAGT-TTTTAGGGAAAATGAGG-ATTTCAAAGAAAAATCCAAAACT
1 ATTTACGGAGTAGAAAACTTAGTATTTT--GAAAAAAGAGGAATTTCAAAGAAAAATCCAAAACT
* *
950317 CATGAAAATGAATGAATT-TTCAAAAAATAATTTAATATGAAATAAATAATAATATTTTAT-AGA
64 CATGAAAATGAATGAATTCTTCAAAAAAGAA-TTAATATGAAATAAATAATAATATTCTATGA-A
**
950380 TTTTAAAAATTAAAAACCAA-GAAAAATTCC-CTTGAAAAA
127 TTTTAAAAATTAAAAA-CAATGAAAAA-TCCTCGCGAAAAA
* * * * * *
950419 ATTTACGGAGTAGAAAACTTCGTATTTTGAAAAAAGGGGAATTTCAAGGAAAAATTCAAAATTTA
1 ATTTACGGAGTAGAAAACTTAGTATTTTGAAAAAAGAGGAATTTCAAAGAAAAATCCAAAACTCA
** * * *
950484 TGGGAATGAATGAATTCTTGAAAACAGAATTAATTTGAAATAAATAATAATATTCTATGAATTTT
66 TGAAAATGAATGAATTCTTCAAAAAAGAATTAATATGAAATAAATAATAATATTCTATGAATTTT
950549 AAAAATTAAAAACAATGAAAAATCCTCGCGAAAAA
131 AAAAATTAAAAACAATGAAAAATCCTCGCGAAAAA
* ** * * *
950584 ATTTACGTAGTAGAAAACTCCGTATTTCGAAAAAA-AGAAATTT-TAAGAAAAA
1 ATTTACGGAGTAGAAAACTTAGTATTTTGAAAAAAGAGGAATTTCAAAGAAAAA
950636 AATTTGAAAA
Statistics
Matches: 185, Mismatches: 26, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
163 7 0.04
164 20 0.11
165 144 0.78
166 14 0.08
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (165 bp):
ATTTACGGAGTAGAAAACTTAGTATTTTGAAAAAAGAGGAATTTCAAAGAAAAATCCAAAACTCA
TGAAAATGAATGAATTCTTCAAAAAAGAATTAATATGAAATAAATAATAATATTCTATGAATTTT
AAAAATTAAAAACAATGAAAAATCCTCGCGAAAAA
Found at i:950639 original size:165 final size:165
Alignment explanation
Indices: 950323--950636 Score: 431
Period size: 165 Copynumber: 1.9 Consensus size: 165
950313 AACTCATGAA
* *
950323 AATGAATGAATTTTCAAAAAATAATTTAATATGAAATAAATAATAATATTTTATAGATTTTAAAA
1 AATGAATGAATTTTCAAAAAAGAATTTAATATGAAATAAATAATAATATTCTATAGATTTTAAAA
** * *
950388 ATTAAAAACCAAGAAAAATTCCCTTGAAAAAATTTACGGAGTAGAAAACTTCGTATTTTGAAAAA
66 ATTAAAAACCAAGAAAAATTCCCGCGAAAAAATTTACGGAGTAGAAAACTCCGTATTTCGAAAAA
* * *
950453 AGGGGAATTTCAAGGAAAAATTCAAAATTTATGGG
131 AGAGAAATTTCAAGAAAAAATTCAAAATTTATGGG
* * *
950488 AATGAATGAATTCTTGAAAACAGAA-TTAATTTGAAATAAATAATAATATTCTAT-GAATTTTAA
1 AATGAATGAATT-TTCAAAAAAGAATTTAATATGAAATAAATAATAATATTCTATAG-ATTTTAA
*
950551 AAATTAAAAA-CAATGAAAAA-TCCTCGCGAAAAAATTTACGTAGTAGAAAACTCCGTATTTCGA
64 AAATTAAAAACCAA-GAAAAATTCC-CGCGAAAAAATTTACGGAGTAGAAAACTCCGTATTTCGA
*
950614 AAAAA-AGAAATTTTAAGAAAAAA
127 AAAAAGAGAAATTTCAAGAAAAAA
950637 ATTTGAAAAA
Statistics
Matches: 131, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
164 21 0.16
165 101 0.77
166 9 0.07
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.30
Consensus pattern (165 bp):
AATGAATGAATTTTCAAAAAAGAATTTAATATGAAATAAATAATAATATTCTATAGATTTTAAAA
ATTAAAAACCAAGAAAAATTCCCGCGAAAAAATTTACGGAGTAGAAAACTCCGTATTTCGAAAAA
AGAGAAATTTCAAGAAAAAATTCAAAATTTATGGG
Found at i:952862 original size:13 final size:13
Alignment explanation
Indices: 952844--952869 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
952834 CAATTTTTTG
952844 TGTATCGATACAT
1 TGTATCGATACAT
952857 TGTATCGATACAT
1 TGTATCGATACAT
952870 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:955437 original size:13 final size:13
Alignment explanation
Indices: 955419--955443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
955409 TCACCCTGTA
955419 GTATCGATACAAT
1 GTATCGATACAAT
955432 GTATCGATACAA
1 GTATCGATACAA
955444 AGAAAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:959379 original size:21 final size:21
Alignment explanation
Indices: 959350--959394 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
959340 AAGTTTTCAT
*
959350 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
959370 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
959392 TTT
1 TTT
959395 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:961633 original size:13 final size:13
Alignment explanation
Indices: 961615--961640 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
961605 CAATTTTTTG
961615 TGTATCGATACAT
1 TGTATCGATACAT
961628 TGTATCGATACAT
1 TGTATCGATACAT
961641 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:961763 original size:41 final size:39
Alignment explanation
Indices: 961673--961764 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 39
961663 ACTGCCAAGA
961673 ATGTATCGATACATCTTTTCATGTATCGATACATGCAAC
1 ATGTATCGATACATCTTTTCATGTATCGATACATGCAAC
961712 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATC-TTTTCATGTATCGATACA-TGCAAC
961753 ATGTATCGATAC
1 ATGTATCGATAC
961765 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
39 15 0.29
40 18 0.35
41 18 0.35
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (39 bp):
ATGTATCGATACATCTTTTCATGTATCGATACATGCAAC
Found at i:961784 original size:40 final size:40
Alignment explanation
Indices: 961673--961764 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 40
961663 ACTGCCAAGA
961673 ATGTATCGATACATCTT-TTCATGTATCGATACATGCAAC
1 ATGTATCGATACATCTTATTCATGTATCGATACATGCAAC
*
961712 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTATTCATGTATCGATACA-TGCAAC
961753 ATGTATCGATAC
1 ATGTATCGATAC
961765 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
39 17 0.33
40 16 0.31
41 18 0.35
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (40 bp):
ATGTATCGATACATCTTATTCATGTATCGATACATGCAAC
Found at i:962373 original size:79 final size:78
Alignment explanation
Indices: 962129--962374 Score: 249
Period size: 79 Copynumber: 3.1 Consensus size: 78
962119 AAAAGCATCG
* * * * ** * **
962129 AATTTTTCGCCATTGGGGATACTCCAATCCCATCATTTTTGAAAAGATACTCTAACCCCATTTTT
1 AATTTTTCACCATTAGGGATACTCCAACCCCATCA-TTTTCAAGGGATACTCCAACCCTGTTTTT
*
962194 ACTTCTAAAAGCATT
65 ACTTCTAAAA-TATT
* * * * * * * *
962209 GAATTTTTCATCGTCAGGGATACTTCAACCCTATTATTTCCAAGAGGATACTCCAACCTTGTTTT
1 -AATTTTTCACCATTAGGGATACTCCAACCCCATCATTTTCAAG-GGATACTCCAACCCTGTTTT
* *
962274 TATTTCTAAAATATC
64 TACTTCTAAAATATT
*
962289 GATTTTTCACCATTAGGGATACTCCAACCCCATCATTTTCAAGGTGATACTCCAACCCTGTTTTT
1 AATTTTTCACCATTAGGGATACTCCAACCCCATCATTTTCAAGG-GATACTCCAACCCTGTTTTT
*
962354 ACTTCCAAAATATT
65 ACTTCTAAAATATT
962368 AATTTTT
1 AATTTTT
962375 TTCATCCCAG
Statistics
Matches: 130, Mismatches: 33, Indels: 6
0.77 0.20 0.04
Matches are distributed among these distances:
78 1 0.01
79 71 0.55
80 7 0.05
81 51 0.39
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (78 bp):
AATTTTTCACCATTAGGGATACTCCAACCCCATCATTTTCAAGGGATACTCCAACCCTGTTTTTA
CTTCTAAAATATT
Found at i:966145 original size:51 final size:51
Alignment explanation
Indices: 966067--966196 Score: 188
Period size: 51 Copynumber: 2.5 Consensus size: 51
966057 GCATATATTG
* * * *
966067 ATACATTGAAGAATATATCGATACATTTAGGTCAAAACCCAGAATGTATCA
1 ATACAATGAAAAATGTATCGATACATTTAGGTCAAAACCCAAAATGTATCA
***
966118 ATTTGATGAAAAATGTATCGATACATTTAGGTCAAAACCCAAAATGTATCA
1 ATACAATGAAAAATGTATCGATACATTTAGGTCAAAACCCAAAATGTATCA
*
966169 ATACAATGAAAATTGTATCGATACATTT
1 ATACAATGAAAAATGTATCGATACATTT
966197 TCTTTCCATA
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (51 bp):
ATACAATGAAAAATGTATCGATACATTTAGGTCAAAACCCAAAATGTATCA
Found at i:970074 original size:2 final size:2
Alignment explanation
Indices: 970069--970098 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
970059 TATTATTCAT
970069 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
970099 AGAATGATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:970996 original size:2 final size:2
Alignment explanation
Indices: 970989--971055 Score: 89
Period size: 2 Copynumber: 33.5 Consensus size: 2
970979 CATTGTTCAT
* * *
970989 TA TA TA TA TA TA TA TA TG TA TA TA TA TG TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
971031 TA TA TG TA TG TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
971056 GTGTGTGCGT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
TA
Found at i:971014 original size:20 final size:20
Alignment explanation
Indices: 970989--971057 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
970979 CATTGTTCAT
* * *
970989 TATATATATATATATATGTA
1 TATATATGTATGTATATATA
971009 TATATATGTATGTATATATA
1 TATATATGTATGTATATATA
971029 TATATATGTATGTATATATA
1 TATATATGTATGTATATATA
971049 TATATATGT
1 TATATATGT
971058 GTGTGCGTGC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.51
Consensus pattern (20 bp):
TATATATGTATGTATATATA
Found at i:971781 original size:106 final size:106
Alignment explanation
Indices: 971580--971789 Score: 278
Period size: 106 Copynumber: 2.0 Consensus size: 106
971570 TAAAAAAATA
* ** *
971580 CCATAAACTTAAACTAAATAATCATCCAAGCAACTATTATTTTATTGTAATCAATTGAGCCATCA
1 CCATAAACTCAAACTAAATAATCATCCAAGCAACTATTATTTTATTACAATCAATTAAGCCATCA
*
971645 AACATTTATTTTCGCCCAATTAAGCCTTTGATTAGACAAAG
66 AACATTTATTTTCACCCAATTAAGCCTTTGATTAGACAAAG
* * *
971686 CCATTAACTCAAACTAAATAATCATCCAAGTC-ATTATTATTTTATTACAATCAATTAAGTCATC
1 CCATAAACTCAAACTAAATAATCATCCAAG-CAACTATTATTTTATTACAATCAATTAAGCCATC
* ** * * *
971750 AAATATTTATTTTCATTCAATTACGCTTTTGATTGGACAA
65 AAACATTTATTTTCACCCAATTAAGCCTTTGATTAGACAA
971790 TATTTTGTTA
Statistics
Matches: 89, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
106 88 0.99
107 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (106 bp):
CCATAAACTCAAACTAAATAATCATCCAAGCAACTATTATTTTATTACAATCAATTAAGCCATCA
AACATTTATTTTCACCCAATTAAGCCTTTGATTAGACAAAG
Found at i:971915 original size:29 final size:29
Alignment explanation
Indices: 971881--971939 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
971871 ATGAAAGTAG
971881 ATGTTTAAGGGTTCAAATAAATAAAATAA
1 ATGTTTAAGGGTTCAAATAAATAAAATAA
* * * * *
971910 ATGTTTGAGTGTTCAATTAATTGAAATAA
1 ATGTTTAAGGGTTCAAATAAATAAAATAA
971939 A
1 A
971940 ATGATAGAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (29 bp):
ATGTTTAAGGGTTCAAATAAATAAAATAA
Found at i:980143 original size:13 final size:13
Alignment explanation
Indices: 980125--980150 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
980115 ATTTTTTTGG
980125 TGTATCGATACAT
1 TGTATCGATACAT
980138 TGTATCGATACAT
1 TGTATCGATACAT
980151 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:982571 original size:18 final size:19
Alignment explanation
Indices: 982530--982571 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
982520 ACAAATCATT
982530 TTTTTCTTCATCAACATCA
1 TTTTTCTTCATCAACATCA
*
982549 TTTTTCTTCCTC-ACAATCA
1 TTTTTCTTCATCAAC-ATCA
982568 TTTT
1 TTTT
982572 AAAACACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTTCTTCATCAACATCA
Found at i:984895 original size:14 final size:14
Alignment explanation
Indices: 984876--984921 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
984866 CATTACTATT
*
984876 TATCACTATTCATG
1 TATCACTGTTCATG
*
984890 TATCACTGTTCATA
1 TATCACTGTTCATG
*
984904 TATCACTGTTTATG
1 TATCACTGTTCATG
984918 TATC
1 TATC
984922 GATACATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.46
Consensus pattern (14 bp):
TATCACTGTTCATG
Found at i:984934 original size:13 final size:13
Alignment explanation
Indices: 984916--984954 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
984906 TCACTGTTTA
984916 TGTATCGATACAT
1 TGTATCGATACAT
* * *
984929 TGTATCAATATAG
1 TGTATCGATACAT
984942 TGTATCGATACAT
1 TGTATCGATACAT
984955 GTGAATAGTA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:986298 original size:37 final size:37
Alignment explanation
Indices: 986248--986319 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
986238 ATATGAAGGG
986248 ATGAATTAAGTCAAGGAGTCGAAGATAAGTATGCTTA
1 ATGAATTAAGTCAAGGAGTCGAAGATAAGTATGCTTA
986285 ATGAATTAAGTCAAGGAGTCGAAGATAAGTATGCT
1 ATGAATTAAGTCAAGGAGTCGAAGATAAGTATGCT
986320 GATCGTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.40, C:0.08, G:0.25, T:0.26
Consensus pattern (37 bp):
ATGAATTAAGTCAAGGAGTCGAAGATAAGTATGCTTA
Found at i:987127 original size:21 final size:21
Alignment explanation
Indices: 987101--987141 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
987091 AATATTCTTG
* *
987101 AAAAGAAATTAAGTGAATTAA
1 AAAAGAAAATAAATGAATTAA
987122 AAAAGAAAATAAATGAATTA
1 AAAAGAAAATAAATGAATTA
987142 TAGGAGAAAA
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:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (21 bp):
AAAAGAAAATAAATGAATTAA
Found at i:990687 original size:14 final size:14
Alignment explanation
Indices: 990663--990717 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 14
990653 ATTACTGTTC
*
990663 ATCACTATTCATGT
1 ATCACTGTTCATGT
*
990677 ATCATTGTTC----
1 ATCACTGTTCATGT
990687 ATCACTGTTCATGT
1 ATCACTGTTCATGT
*
990701 ATCACTGTTCTTGT
1 ATCACTGTTCATGT
990715 ATC
1 ATC
990718 TATAAACTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
10 9 0.27
14 24 0.73
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (14 bp):
ATCACTGTTCATGT
Found at i:990687 original size:24 final size:24
Alignment explanation
Indices: 990656--990710 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
990646 TTGATACATT
990656 ACTGTTCATCACTATTCATGTATC
1 ACTGTTCATCACTATTCATGTATC
* *
990680 ATTGTTCATCACTGTTCATGTATC
1 ACTGTTCATCACTATTCATGTATC
990704 ACTGTTC
1 ACTGTTC
990711 TTGTATCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.44
Consensus pattern (24 bp):
ACTGTTCATCACTATTCATGTATC
Found at i:991316 original size:13 final size:13
Alignment explanation
Indices: 991280--991318 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
991270 CACACCCAAA
*
991280 TGTATCGATACAT
1 TGTATCGATATAT
*
991293 AGTATCGATATAT
1 TGTATCGATATAT
991306 TGTATCGATATAT
1 TGTATCGATATAT
991319 GTTCTTGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATATAT
Found at i:991412 original size:743 final size:743
Alignment explanation
Indices: 989987--991446 Score: 2586
Period size: 743 Copynumber: 2.0 Consensus size: 743
989977 TCGAGTTATA
989987 TAATTAAAAATTGGTATTAAGAAACATTTCGAGACTTTATTGAATATCTATGAACTTTTCTAATA
1 TAATTAAAAATTGGTATTAAGAAACATTTCGAGACTTTATTGAATATCTATGAACTTTTCTAATA
* * *
990052 ATTTTTGTGAGTTGCGAATGTCAAATTACAGATTACGATCTTTGATGAAATGGAGAGTATGATTG
66 ATTTTTGTAAGTTGCGAATGTCAAATTACAGATTACGATCTTTGATGAAACGGAGAGTACGATTG
990117 TTCAACGACCTTGAAATTATTGGTAAGGTTATATACATTTTCGAAAATGCATCTTTGAAATTCCT
131 TTCAACGACCTTGAAATTATTGGTAAGGTTATATACATTTTCGAAAATGCATCTTTGAAATTCCT
*
990182 TATAGCATGTAAAGTGAGTAAGTCAACCAAATTTATTTTAAAGTTTTGTTATATCAGAAAAGGGG
196 TATAGCATGTAAAGTGAGTAAGTCAACCAAATTTATTTTAAAGTTTTGTTATATCAGAAAAGGAG
* *
990247 AGATTGTTGGATCTTGGTTTTTATATAACAAAGTATGAATAAAATCGAAAAATACTTTGAAAAAT
261 AGATTGTTGGATCTTGGTTTTCATATAACAAAGTATAAATAAAATCGAAAAATACTTTGAAAAAT
* * *
990312 CGTAACAAGTTTTATTCACTTAAAAACTCTCTAAATTTTGCTCAAAATGATCCTCAATATCAAAG
326 CATAACAAGTTTTATTCACTCAAAAACTCTCTAAATCTTGCTCAAAATGATCCTCAATATCAAAG
* *
990377 ATATTTTAGAGTTAAGTATAAATGTTTTTCAAGCAGTAAATCATATGTTTTTAAGTAAAAATAAT
391 ATATTTTAGAGTTAAGTATAAATGTTTTTCAAGCAATAAATCATATGTTTTCAAGTAAAAATAAT
*
990442 CCAAAGTATCGATACATATGTATTTGTAATGATACATAAAGGTTAACTTAAGCTACAAAGGTCAA
456 CCAAAGTATCGATACATAGGTATTTGTAATGATACATAAAGGTTAACTTAAGCTACAAAGGTCAA
* * *
990507 AATTCTAGAAAGTATCGATACACACCCAGATGCATCGATATATAGTATCGACACATTGTATCGAT
521 AATCCTAGAAAGTATCGATACACACCCAAATGCATCGATACATAGTATCGACACATTGTATCGAT
* * *
990572 ATATGTTCTTGGTATCGATACATCATAAATTGTTTCAATATATAAAACTGACAGTAGCTAAATCT
586 ATATGTTCTTGGTATCGATACATCATAAATTGTATCAATACATAAAACTGACAATAGCTAAATCT
*
990637 CAGTTTTAATTGATACATTACTGTTCATCACTATTCATGTATCATTGTTCATCACTGTTCATGTA
651 CACTTTTAATTGATACATTACTGTTCATCACTATTCATGTATCATTGTTCATCACTGTTCATGTA
990702 TCACTGTTCTTGTATCTATAAACTTTTC
716 TCACTGTTCTTGTATCTATAAACTTTTC
990730 TAATTAAAAATTGGTATTAAGAAACATTTCGAGACTTTATTGAATATCTATGAACTTTTCTAATA
1 TAATTAAAAATTGGTATTAAGAAACATTTCGAGACTTTATTGAATATCTATGAACTTTTCTAATA
*
990795 ATTTTTGTAAGTTGCGAATGTCAAATTACAGGTTACGATCTTTGATGAAACGGAGAGTACGATTG
66 ATTTTTGTAAGTTGCGAATGTCAAATTACAGATTACGATCTTTGATGAAACGGAGAGTACGATTG
990860 TTCAACGACCTTGAAATTATTGGTAAGGTTATATACATTTTCGAAAATGCATCTTTGAAATTCCT
131 TTCAACGACCTTGAAATTATTGGTAAGGTTATATACATTTTCGAAAATGCATCTTTGAAATTCCT
990925 TATAGCATGTAAAGTGAGTAAGTCAACCAAATTTATTTTAAAGTTTTGTTATATCAGAAAAGGAG
196 TATAGCATGTAAAGTGAGTAAGTCAACCAAATTTATTTTAAAGTTTTGTTATATCAGAAAAGGAG
*
990990 AGATTGTTAGGATCTTGGTTTTCATATAATAAAGTATAAATAAAATCGAAAAATACTTTGAAAAA
261 AGATTGTT-GGATCTTGGTTTTCATATAACAAAGTATAAATAAAATCGAAAAATACTTTGAAAAA
991055 TCATAACAAGTTTTATTCACTCAAAAACTCTCTAAAGTCTTGCTCAAAATGATCCTCAATATCAA
325 TCATAACAAGTTTTATTCACTCAAAAACTCTCTAAA-TCTTGCTCAAAATGATCCTCAATATCAA
*
991120 AGATGTTTTAGAGTTAAGT-TAAATGTTTTTCAAGCAATAAATCATATGTTTTCAAGT-AAAATA
389 AGATATTTTAGAGTTAAGTATAAATGTTTTTCAAGCAATAAATCATATGTTTTCAAGTAAAAATA
* *
991183 ATCCAAAGTATTGATACATAGGTATTTGT-ATCGATACATAAAGGTTAATTTAAGCTACAAAGGT
454 ATCCAAAGTATCGATACATAGGTATTTGTAAT-GATACATAAAGGTTAACTTAAGCTACAAAGGT
* * * *
991247 CAAAA-CCATAGGAAGTATCGATACACACCCAAATGTATCGATACATAGTATCGATATATTGTAT
518 CAAAATCC-TAGAAAGTATCGATACACACCCAAATGCATCGATACATAGTATCGACACATTGTAT
* *
991311 CGATATATGTTCTTGGTATCGATACATCATAAATTGTATCAATACATAGAACTGGCAATAGCTAA
582 CGATATATGTTCTTGGTATCGATACATCATAAATTGTATCAATACATAAAACTGACAATAGCTAA
991376 ATCTCACTTTTAATTGATACATTACTGTTCATCACTATTCATGTATCATTGTTCATCACTGTTCA
647 ATCTCACTTTTAATTGATACATTACTGTTCATCACTATTCATGTATCATTGTTCATCACTGTTCA
991441 TGTATC
712 TGTATC
991447 GACGCAATGT
Statistics
Matches: 683, Mismatches: 30, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
742 3 0.00
743 512 0.75
744 123 0.18
745 45 0.07
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (743 bp):
TAATTAAAAATTGGTATTAAGAAACATTTCGAGACTTTATTGAATATCTATGAACTTTTCTAATA
ATTTTTGTAAGTTGCGAATGTCAAATTACAGATTACGATCTTTGATGAAACGGAGAGTACGATTG
TTCAACGACCTTGAAATTATTGGTAAGGTTATATACATTTTCGAAAATGCATCTTTGAAATTCCT
TATAGCATGTAAAGTGAGTAAGTCAACCAAATTTATTTTAAAGTTTTGTTATATCAGAAAAGGAG
AGATTGTTGGATCTTGGTTTTCATATAACAAAGTATAAATAAAATCGAAAAATACTTTGAAAAAT
CATAACAAGTTTTATTCACTCAAAAACTCTCTAAATCTTGCTCAAAATGATCCTCAATATCAAAG
ATATTTTAGAGTTAAGTATAAATGTTTTTCAAGCAATAAATCATATGTTTTCAAGTAAAAATAAT
CCAAAGTATCGATACATAGGTATTTGTAATGATACATAAAGGTTAACTTAAGCTACAAAGGTCAA
AATCCTAGAAAGTATCGATACACACCCAAATGCATCGATACATAGTATCGACACATTGTATCGAT
ATATGTTCTTGGTATCGATACATCATAAATTGTATCAATACATAAAACTGACAATAGCTAAATCT
CACTTTTAATTGATACATTACTGTTCATCACTATTCATGTATCATTGTTCATCACTGTTCATGTA
TCACTGTTCTTGTATCTATAAACTTTTC
Found at i:991430 original size:24 final size:24
Alignment explanation
Indices: 991401--991446 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
991391 GATACATTAC
991401 TGTTCATCACTATTCATGTATCAT
1 TGTTCATCACTATTCATGTATCAT
*
991425 TGTTCATCACTGTTCATGTATC
1 TGTTCATCACTATTCATGTATC
991447 GACGCAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.46
Consensus pattern (24 bp):
TGTTCATCACTATTCATGTATCAT
Found at i:994427 original size:11 final size:11
Alignment explanation
Indices: 994411--994462 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
994401 TAGAGAAGGA
994411 AAAAAAGAAAG
1 AAAAAAGAAAG
**
994422 AAAAAAGAGGG
1 AAAAAAGAAAG
994433 AAAAAAGTAAA-
1 AAAAAAG-AAAG
994444 AAAAAA-AAAGG
1 AAAAAAGAAA-G
994455 AAAAAAGA
1 AAAAAAGA
994463 GCCCATCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
9 3 0.09
11 28 0.85
12 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:994434 original size:23 final size:23
Alignment explanation
Indices: 994406--994460 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
994396 GCAACTAGAG
*
994406 AAGGAAAAAAAG-AAAGAAAAAA
1 AAGGAAAAAAAGTAAAAAAAAAA
* *
994428 GAGGGAAAAAAGTAAAAAAAAAA
1 AAGGAAAAAAAGTAAAAAAAAAA
994451 AAGGAAAAAA
1 AAGGAAAAAA
994461 GAGCCCATCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (23 bp):
AAGGAAAAAAAGTAAAAAAAAAA
Found at i:994439 original size:22 final size:21
Alignment explanation
Indices: 994406--994462 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
994396 GCAACTAGAG
*
994406 AAGGAAAAAAAGAAAGAAAAAAG
1 AAGG-AAAAAAGAAA-AAAAAAA
*
994429 AGGGAAAAAAGTAAAAAAAAAA
1 AAGGAAAAAAG-AAAAAAAAAA
994451 AAGGAAAAAAGA
1 AAGGAAAAAAGA
994463 GCCCATCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.03
22 23 0.77
23 6 0.20
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (21 bp):
AAGGAAAAAAGAAAAAAAAAA
Found at i:995184 original size:29 final size:28
Alignment explanation
Indices: 995102--995184 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 28
995092 TTTCATACAT
* *
995102 TTTAGGGTTATTTAGTTTATTTTATGTAA
1 TTTAGGGCTATTTAG-TTATTTTATGTCA
* *
995131 TTTAGGGACCATTTAGTAATATTTATG-CA
1 TTTAGGG-CTATTTAGTTAT-TTTATGTCA
995160 TTTGAGGGCTATTTAAGTTATTTTA
1 TTT-AGGGCTATTT-AGTTATTTTA
995185 CATAATCTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
29 23 0.52
30 21 0.48
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.51
Consensus pattern (28 bp):
TTTAGGGCTATTTAGTTATTTTATGTCA
Found at i:995498 original size:77 final size:77
Alignment explanation
Indices: 995371--995572 Score: 262
Period size: 77 Copynumber: 2.6 Consensus size: 77
995361 GTTATATGGA
* * * * *
995371 AACTTTCATGTCAATACAGGTTTATTAAGGTCATTTAAGTAATAGTACCTTAAAACCAAGTTTCT
1 AACTTTCATGTCAATACAAGTCTATTAAGGTCATTTAGGTAATAGTACCTTAAAACCAAATCTCT
* *
995436 TAGTCATGTGCG
66 TAGTCACGTGAG
* * *
995448 AACTTTCATGTCAATATAAGTCTGTTAGGGTCATTTAGGTAATAGTACCTTAAAACCAAATCTCT
1 AACTTTCATGTCAATACAAGTCTATTAAGGTCATTTAGGTAATAGTACCTTAAAACCAAATCTCT
995513 TAGTCACGTGAG
66 TAGTCACGTGAG
* * *
995525 AAATTTCATGTCGATACATA-TCAATTAAGGTCATTTTAGGTAATAGTA
1 AACTTTCATGTCAATACA-AGTCTATTAAGGTCA-TTTAGGTAATAGTA
995573 ATTTATCAAA
Statistics
Matches: 107, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
77 92 0.86
78 15 0.14
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (77 bp):
AACTTTCATGTCAATACAAGTCTATTAAGGTCATTTAGGTAATAGTACCTTAAAACCAAATCTCT
TAGTCACGTGAG
Found at i:997081 original size:18 final size:19
Alignment explanation
Indices: 997060--997101 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
997050 ACTCTTTAAT
* *
997060 AAATTCA-ACTTTCTCGTC
1 AAATTCACACCTTCTAGTC
997078 AAATTCACACCTTCTAGTC
1 AAATTCACACCTTCTAGTC
997097 AAATT
1 AAATT
997102 AATTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (19 bp):
AAATTCACACCTTCTAGTC
Found at i:997669 original size:3 final size:3
Alignment explanation
Indices: 997661--997687 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
997651 GTGAAAGCAA
997661 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
997688 CAGCAAGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:997987 original size:24 final size:24
Alignment explanation
Indices: 997941--997987 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
997931 GAGGGGAAGA
* * *
997941 AAAATGAAAAGAAAAATGTAAAAT
1 AAAAGGAAAAGAAAAAGGAAAAAT
*
997965 AAAAGGAAAAGGAAAAGGAAAAA
1 AAAAGGAAAAGAAAAAGGAAAAA
997988 AAGGAACATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (24 bp):
AAAAGGAAAAGAAAAAGGAAAAAT
Found at i:999531 original size:37 final size:36
Alignment explanation
Indices: 999481--999558 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 36
999471 GTTATATATA
999481 TATATATATATATATAAAATTATTGATAAATGACTGT
1 TATATATATATATATAAAATTATTGATAAATG-CTGT
* *
999518 TATATATATATATATATAATTATTGATAAATGTTGT
1 TATATATATATATATAAAATTATTGATAAATGCTGT
999554 TATAT
1 TATAT
999559 TAACAACAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 8 0.21
37 31 0.79
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (36 bp):
TATATATATATATATAAAATTATTGATAAATGCTGT
Found at i:1002302 original size:24 final size:24
Alignment explanation
Indices: 1002251--1002302 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
1002241 TTTATTATTG
*
1002251 ATATTTATTATAATTAATCATTATA
1 ATATTTATTATAATTAA-CATTACA
*
1002276 ATATTTATTATATTTGAA-ATTACA
1 ATATTTATTATAATT-AACATTACA
1002300 ATA
1 ATA
1002303 AATATGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 14 0.58
26 2 0.08
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
ATATTTATTATAATTAACATTACA
Found at i:1004503 original size:14 final size:15
Alignment explanation
Indices: 1004478--1004506 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1004468 TTCATTTATT
1004478 TATAATTATAATAAA
1 TATAATTATAATAAA
1004493 TATAA-TATAATAAA
1 TATAATTATAATAAA
1004507 AAATATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TATAATTATAATAAA
Found at i:1004998 original size:2 final size:2
Alignment explanation
Indices: 1004991--1005018 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1004981 TAGAATTTCT
1004991 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1005019 GAACATTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1007734 original size:27 final size:27
Alignment explanation
Indices: 1007690--1007975 Score: 177
Period size: 27 Copynumber: 10.7 Consensus size: 27
1007680 TATTATGATT
* ** *
1007690 TTAGACTTTATATTTATGGATTTTTAT
1 TTAGACTTTTTACATATGGATTTTTAA
*
1007717 TTAGACTTTTTACATATGAATTTTTAA
1 TTAGACTTTTTACATATGGATTTTTAA
* * * *
1007744 TTGGACTTCTTGCACAT-GA-TTTT-A
1 TTAGACTTTTTACATATGGATTTTTAA
1007768 TT---C-TTTTACATAT-GATTTTTTAA
1 TTAGACTTTTTACATATGGA-TTTTTAA
* *
1007791 TTAGACATTTTGCATGAT-GATTTTTTAA
1 TTAGACTTTTTACAT-ATGGA-TTTTTAA
* * *
1007819 TTGGACTTTCTACATATGAATTTTTAA
1 TTAGACTTTTTACATATGGATTTTTAA
*
1007846 TTAGACTTTTTACATGT-GATTTTTAA
1 TTAGACTTTTTACATATGGATTTTTAA
1007872 -TAGACTTTTT--ATATGTGATTTTTAA
1 TTAGACTTTTTACATATG-GATTTTTAA
* * *
1007897 TTATAC-TTTTAGAAATGGAATTTTTAA
1 TTAGACTTTTTACATATGG-ATTTTTAA
* ** *
1007924 TTAAACTTTTGGTTTTATATAGAATTTTTAA
1 TTAGAC-TTT--TTACATAT-GGATTTTTAA
*
1007955 TTAGACATTATTACATATGGA
1 TTAGAC-TTTTTACATATGGA
1007976 AATTTAAGTT
Statistics
Matches: 202, Mismatches: 37, Indels: 39
0.73 0.13 0.14
Matches are distributed among these distances:
20 9 0.04
21 1 0.00
22 4 0.02
23 6 0.03
24 3 0.01
25 27 0.13
26 15 0.07
27 82 0.41
28 26 0.13
29 8 0.04
31 20 0.10
32 1 0.00
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (27 bp):
TTAGACTTTTTACATATGGATTTTTAA
Found at i:1007843 original size:55 final size:51
Alignment explanation
Indices: 1007708--1007907 Score: 162
Period size: 55 Copynumber: 3.9 Consensus size: 51
1007698 TATATTTATG
* * * **
1007708 GATTTTTATTTAGACTTTTTACATATGAATTTTTAATTGGAC-TTCTTGCACAT
1 GATTTTTA-ATAGAC-TTTTACATATGAATTTTTAATTAGACATT-TTACATGT
* * *
1007761 GA-TTTT-AT--TCTTTTACATATGATTTTTTAATTAGACATTTTGCATGAT
1 GATTTTTAATAGACTTTTACATATGAATTTTTAATTAGACATTTTACATG-T
* *
1007809 GATTTTTTAATTGGACTTTCTACATATGAATTTTTAATTAGACTTTTTACATGT
1 GA-TTTTTAA-TAGACTTT-TACATATGAATTTTTAATTAGACATTTTACATGT
* * *
1007863 GATTTTTAATAGACTTTT-TATATGTGATTTTTAATTATAC-TTTTA
1 GATTTTTAATAGACTTTTACATATG-AATTTTTAATTAGACATTTTA
1007908 GAAATGGAAT
Statistics
Matches: 123, Mismatches: 14, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
47 29 0.24
48 6 0.05
50 15 0.12
51 15 0.12
52 12 0.10
53 9 0.07
54 7 0.06
55 30 0.24
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.54
Consensus pattern (51 bp):
GATTTTTAATAGACTTTTACATATGAATTTTTAATTAGACATTTTACATGT
Found at i:1007857 original size:13 final size:13
Alignment explanation
Indices: 1007784--1007906 Score: 60
Period size: 13 Copynumber: 9.3 Consensus size: 13
1007774 TACATATGAT
1007784 TTTTTAATTAGAC
1 TTTTTAATTAGAC
** * *
1007797 ATTTTGCATGATGAT
1 -TTTTTAATTA-GAC
*
1007812 TTTTTAATTGGAC
1 TTTTTAATTAGAC
* *
1007825 TTTCTACA-TATGAA
1 TTTTTA-ATTA-GAC
1007839 TTTTTAATTAGAC
1 TTTTTAATTAGAC
1007852 TTTTTACATGT-GA-
1 TTTTTA-AT-TAGAC
1007865 TTTTTAA-TAGAC
1 TTTTTAATTAGAC
1007877 TTTTTATATGT-GA-
1 TTTTTA-AT-TAGAC
*
1007890 TTTTTAATTATAC
1 TTTTTAATTAGAC
1007903 TTTT
1 TTTT
1007907 AGAAATGGAA
Statistics
Matches: 81, Mismatches: 15, Indels: 27
0.66 0.12 0.22
Matches are distributed among these distances:
10 1 0.01
11 3 0.04
12 10 0.12
13 34 0.42
14 29 0.36
15 4 0.05
ACGTcount: A:0.28, C:0.07, G:0.11, T:0.54
Consensus pattern (13 bp):
TTTTTAATTAGAC
Found at i:1008168 original size:3 final size:3
Alignment explanation
Indices: 1008160--1008198 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1008150 TAATTGGATT
1008160 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1008199 AACTTTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1009394 original size:33 final size:33
Alignment explanation
Indices: 1009354--1009422 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1009344 CCGTTACAAG
* *
1009354 CAATGTATCGATACAAT-TCATCATTTATCGATA
1 CAATGTATCGATACAATGT-ACCATGTATCGATA
1009387 CAATGTATCGATACAATGTACCATGTATCGATA
1 CAATGTATCGATACAATGTACCATGTATCGATA
1009420 CAA
1 CAA
1009423 ATAGTAGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATGTACCATGTATCGATA
Found at i:1009397 original size:13 final size:13
Alignment explanation
Indices: 1009379--1009406 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1009369 ATTCATCATT
1009379 TATCGATACAATG
1 TATCGATACAATG
1009392 TATCGATACAATG
1 TATCGATACAATG
1009405 TA
1 TA
1009407 CCATGTATCG
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:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:1010805 original size:10 final size:10
Alignment explanation
Indices: 1010790--1010824 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
1010780 TTTGAAAATA
1010790 TAGCCGTTAC
1 TAGCCGTTAC
1010800 TAGCCGTTAC
1 TAGCCGTTAC
1010810 TAGCCGTTAC
1 TAGCCGTTAC
*
1010820 AAGCC
1 TAGCC
1010825 AATGTATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (10 bp):
TAGCCGTTAC
Found at i:1010864 original size:13 final size:13
Alignment explanation
Indices: 1010846--1010871 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1010836 ACATTTTGGG
1010846 ATGTATCGATACA
1 ATGTATCGATACA
1010859 ATGTATCGATACA
1 ATGTATCGATACA
1010872 TATTGTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1010890 original size:32 final size:33
Alignment explanation
Indices: 1010824--1010891 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
1010814 CGTTACAAGC
*
1010824 CAATGTATCAATACATTTTGGGATGTATCGATA
1 CAATGTATCAATACATATTGGGATGTATCGATA
* * *
1010857 CAATGTATCGATACATATTGTG-TTTATCGATA
1 CAATGTATCAATACATATTGGGATGTATCGATA
1010889 CAA
1 CAA
1010892 ATTTGGCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (33 bp):
CAATGTATCAATACATATTGGGATGTATCGATA
Found at i:1010970 original size:20 final size:21
Alignment explanation
Indices: 1010923--1010975 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1010913 TGCAATGACC
**
1010923 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
1010944 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
1010964 TGTATCGATACA
1 TGTATCGATACA
1010976 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:1010981 original size:13 final size:13
Alignment explanation
Indices: 1010963--1010987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1010953 ACATTTGGTC
1010963 ATGTATCGATACA
1 ATGTATCGATACA
1010976 ATGTATCGATAC
1 ATGTATCGATAC
1010988 TGTGCAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1012998 original size:20 final size:20
Alignment explanation
Indices: 1012969--1013022 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1012959 GCCCGGTTGT
* *
1012969 GACCTAGGGGTGCCAGTCGC
1 GACCTGGGGGTGCCAGTCAC
* *
1012989 GACCTGGGGGTGTCGGTCAC
1 GACCTGGGGGTGCCAGTCAC
1013009 GACCTGGTGGGTGC
1 GACCTGG-GGGTGC
1013023 TGCCTAAGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.11, C:0.26, G:0.44, T:0.19
Consensus pattern (20 bp):
GACCTGGGGGTGCCAGTCAC
Found at i:1019664 original size:32 final size:33
Alignment explanation
Indices: 1019601--1019664 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
1019591 GTTACAAGCC
* *
1019601 AATGTATTGATACATTTTGGGATGTATCGATAT
1 AATGTATGGATACATATTGGGATGTATCGATAT
*
1019634 AATGTATGGATACATATTGTG-TGTATCGATA
1 AATGTATGGATACATATTGGGATGTATCGATA
1019665 CAAATTTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 10 0.36
33 18 0.64
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41
Consensus pattern (33 bp):
AATGTATGGATACATATTGGGATGTATCGATAT
Found at i:1019736 original size:20 final size:21
Alignment explanation
Indices: 1019689--1019741 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1019679 GCCAATGACC
**
1019689 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
1019710 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
1019730 TGTATCGATACA
1 TGTATCGATACA
1019742 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:1019747 original size:13 final size:13
Alignment explanation
Indices: 1019729--1019753 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1019719 ACATTTGGTC
1019729 ATGTATCGATACA
1 ATGTATCGATACA
1019742 ATGTATCGATAC
1 ATGTATCGATAC
1019754 TGTGCAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1020244 original size:81 final size:82
Alignment explanation
Indices: 1020109--1020282 Score: 242
Period size: 81 Copynumber: 2.1 Consensus size: 82
1020099 TTAACGAGAT
** * * * *
1020109 TTTCTCCCCCTAAAAACTTATTTTTGAAACAATATTTCTCCCCCTTTTCAAAGCAAAATTTATTT
1 TTTCTCCCCCTAAAAACTTATTTTCAAAACAACATTTCTCCCCATTTTAAAAGCAAAATTTATTA
1020174 TATTTTCAAAA-AAATA
66 TATTTTCAAAAGAAATA
* * *
1020190 TTTCTCCCCCTGAAAACTTATTTTCAAAAGAACATTTCTCCCTATTTTAAAAGCAAAATTTATTA
1 TTTCTCCCCCTAAAAACTTATTTTCAAAACAACATTTCTCCCCATTTTAAAAGCAAAATTTATTA
*
1020255 TATTTTCAAAAGCAATA
66 TATTTTCAAAAGAAATA
*
1020272 TTTCTCTCCCT
1 TTTCTCCCCCT
1020283 TTTTGTTATA
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
81 67 0.83
82 14 0.17
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.40
Consensus pattern (82 bp):
TTTCTCCCCCTAAAAACTTATTTTCAAAACAACATTTCTCCCCATTTTAAAAGCAAAATTTATTA
TATTTTCAAAAGAAATA
Found at i:1020250 original size:24 final size:25
Alignment explanation
Indices: 1020208--1020277 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 25
1020198 CCTGAAAACT
* *
1020208 TATTTTCAAAAG-AACATTTCTCCC
1 TATTTTCAAAAGCAAAATTTCTCCA
* *
1020232 TATTTT-AAAAGCAAAATTTAT-TA
1 TATTTTCAAAAGCAAAATTTCTCCA
*
1020255 TATTTTCAAAAGCAATATTTCTC
1 TATTTTCAAAAGCAAAATTTCTC
1020278 TCCCTTTTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
23 11 0.30
24 26 0.70
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (25 bp):
TATTTTCAAAAGCAAAATTTCTCCA
Found at i:1022618 original size:81 final size:82
Alignment explanation
Indices: 1022483--1022656 Score: 251
Period size: 81 Copynumber: 2.1 Consensus size: 82
1022473 TTAACGAGAT
** * * * *
1022483 TTTCTCCCCCTAAAAACTTATTTTTGAAACAATATTTCTCCCCCTTTTCAAAGCAAAATTTATTT
1 TTTCTCCCCCTAAAAACTTATTTTCAAAACAACATTTCTCCCCATTTTAAAAGCAAAATTTATTA
1022548 TATTTTCAAAA-CAATA
66 TATTTTCAAAAGCAATA
* * *
1022564 TTTCTCCCCCTGAAAACTTATTTTCAAAAGAACATTTCTCCCTATTTTAAAAGCAAAATTTATTA
1 TTTCTCCCCCTAAAAACTTATTTTCAAAACAACATTTCTCCCCATTTTAAAAGCAAAATTTATTA
1022629 TATTTTCAAAAGCAATA
66 TATTTTCAAAAGCAATA
*
1022646 TTTCTCTCCCT
1 TTTCTCCCCCT
1022657 TTTTGTTATA
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
81 67 0.82
82 15 0.18
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.40
Consensus pattern (82 bp):
TTTCTCCCCCTAAAAACTTATTTTCAAAACAACATTTCTCCCCATTTTAAAAGCAAAATTTATTA
TATTTTCAAAAGCAATA
Found at i:1022624 original size:24 final size:25
Alignment explanation
Indices: 1022582--1022651 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 25
1022572 CCTGAAAACT
* *
1022582 TATTTTCAAAAG-AACATTTCTCCC
1 TATTTTCAAAAGCAAAATTTCTCCA
* *
1022606 TATTTT-AAAAGCAAAATTTAT-TA
1 TATTTTCAAAAGCAAAATTTCTCCA
*
1022629 TATTTTCAAAAGCAATATTTCTC
1 TATTTTCAAAAGCAAAATTTCTC
1022652 TCCCTTTTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
23 11 0.30
24 26 0.70
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (25 bp):
TATTTTCAAAAGCAAAATTTCTCCA
Found at i:1029014 original size:9 final size:9
Alignment explanation
Indices: 1029000--1029033 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1028990 TCCAAGTCAC
*
1029000 CATCATCAT
1 CATCATTAT
1029009 CATCATTAT
1 CATCATTAT
*
1029018 CATCTTTAT
1 CATCATTAT
1029027 CATCATT
1 CATCATT
1029034 GATGGTTGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.44
Consensus pattern (9 bp):
CATCATTAT
Found at i:1030538 original size:13 final size:13
Alignment explanation
Indices: 1030498--1030550 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1030488 CTGTTACAAG
1030498 CAATGTATCGATA
1 CAATGTATCGATA
1030511 CAA--T-TC-AT-
1 CAATGTATCGATA
1030519 C-ATGTATCGATA
1 CAATGTATCGATA
*
1030531 CAATGTATCGATG
1 CAATGTATCGATA
1030544 CAATGTA
1 CAATGTA
1030551 CCATGTATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 20 0.61
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1030538 original size:33 final size:33
Alignment explanation
Indices: 1030498--1030566 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1030488 CTGTTACAAG
* *
1030498 CAATGTATCGATACAAT-TCATCATGTATCGATA
1 CAATGTATCGATACAATGT-ACCATGTATCAATA
*
1030531 CAATGTATCGATGCAATGTACCATGTATCAATA
1 CAATGTATCGATACAATGTACCATGTATCAATA
1030564 CAA
1 CAA
1030567 ACAGTTGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (33 bp):
CAATGTATCGATACAATGTACCATGTATCAATA
Found at i:1030640 original size:19 final size:20
Alignment explanation
Indices: 1030594--1030655 Score: 74
Period size: 19 Copynumber: 3.1 Consensus size: 20
1030584 ACTGCCAGTT
* *
1030594 TCATGTATTGATACAGTTGT-
1 TCATGTATCGATACA-ATGTA
*
1030614 TTATGTATCGATACAATG-A
1 TCATGTATCGATACAATGTA
1030633 TCATGTATCGATACAATGTA
1 TCATGTATCGATACAATGTA
1030653 TCA
1 TCA
1030656 ATAAAAAGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 19 0.53
20 17 0.47
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (20 bp):
TCATGTATCGATACAATGTA
Found at i:1031006 original size:14 final size:15
Alignment explanation
Indices: 1030983--1031023 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1030973 CATCTTTAAG
*
1030983 AGAAAAAAAGAGAA-
1 AGAAAGAAAGAGAAT
1030997 AGAAAGAAAGA-AAT
1 AGAAAGAAAGAGAAT
*
1031011 AAAAAGAAAGAGA
1 AGAAAGAAAGAGA
1031024 GGTTCTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 2 0.09
14 20 0.87
15 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AGAAAGAAAGAGAAT
Found at i:1032619 original size:13 final size:13
Alignment explanation
Indices: 1032601--1032625 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1032591 AGATTGCACA
1032601 GTATCGATACATT
1 GTATCGATACATT
1032614 GTATCGATACAT
1 GTATCGATACAT
1032626 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1032638 original size:20 final size:21
Alignment explanation
Indices: 1032613--1032665 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1032603 ATCGATACAT
**
1032613 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
1032633 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
1032654 TGTATCGATACA
1 TGTATCGATACA
1032666 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:1032744 original size:31 final size:30
Alignment explanation
Indices: 1032690--1032751 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
1032680 GCCAAATTTG
*
1032690 TATCGATACACACAATATGTATCGATACAT
1 TATCGATACACACAAAATGTATCGATACAT
*
1032720 TATCGATACATCCCAAAATGTATCGATACAT
1 TATCGATACA-CACAAAATGTATCGATACAT
1032751 T
1 T
1032752 GGCTTGTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 10 0.34
31 19 0.66
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.31
Consensus pattern (30 bp):
TATCGATACACACAAAATGTATCGATACAT
Found at i:1033771 original size:13 final size:13
Alignment explanation
Indices: 1033753--1033790 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1033743 ACATTTGACC
*
1033753 ATGTATCGATATA
1 ATGTATCGATACA
1033766 ATGTATCGATACA
1 ATGTATCGATACA
*
1033779 CTGTATCGATAC
1 ATGTATCGATAC
1033791 TGAGTAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1033843 original size:20 final size:19
Alignment explanation
Indices: 1033817--1033872 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1033807 CTGCCAATTT
**
1033817 CATGTATCGATACAATTCA
1 CATGTATCGATACAATGAA
*
1033836 CTATGTATCGGTACCAA-GAA
1 C-ATGTATCGATA-CAATGAA
1033856 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1033873 TATCATTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
18 3 0.10
19 12 0.40
20 12 0.40
21 3 0.10
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1033958 original size:19 final size:19
Alignment explanation
Indices: 1033934--1033971 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1033924 TCTAGGTTTT
1033934 GACCTTTATAGCTTTAGTC
1 GACCTTTATAGCTTTAGTC
*
1033953 GACCTTTGTAGCTTTAGTC
1 GACCTTTATAGCTTTAGTC
1033972 AACATTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.42
Consensus pattern (19 bp):
GACCTTTATAGCTTTAGTC
Found at i:1034069 original size:23 final size:22
Alignment explanation
Indices: 1034027--1034069 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
1034017 TTATTTTTAA
*
1034027 CTTGAAAACATTATTTTTTATG
1 CTTGAAAACATTATTATTTATG
1034049 CTTGAAAAACATT-TATATTTA
1 CTTG-AAAACATTAT-TATTTA
1034070 ACTCTAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (22 bp):
CTTGAAAACATTATTATTTATG
Found at i:1036219 original size:27 final size:27
Alignment explanation
Indices: 1036181--1036234 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1036171 TAGGGTGCTT
*
1036181 GGTTCAGGTCTTTTGTCGAACAGGTTA
1 GGTTCAGGTCTTTTGTCAAACAGGTTA
1036208 GGTTCAGGTCTTTTGTCAAACAGGTTA
1 GGTTCAGGTCTTTTGTCAAACAGGTTA
1036235 TGGATACGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.20, C:0.15, G:0.28, T:0.37
Consensus pattern (27 bp):
GGTTCAGGTCTTTTGTCAAACAGGTTA
Found at i:1036247 original size:27 final size:27
Alignment explanation
Indices: 1036190--1036247 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
1036180 TGGTTCAGGT
* * * *
1036190 CTTTTGTCGAACAGGTTAGGTTCAGGT
1 CTTTTGTCAAACAGGTTAGGATCACGA
1036217 CTTTTGTCAAACAGGTTATGGAT-ACGA
1 CTTTTGTCAAACAGGTTA-GGATCACGA
1036244 CTTT
1 CTTT
1036248 GAGACCTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (27 bp):
CTTTTGTCAAACAGGTTAGGATCACGA
Found at i:1036632 original size:13 final size:13
Alignment explanation
Indices: 1036607--1036640 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1036597 AGTGGCCTTA
*
1036607 TATCGAAACAATG
1 TATCGATACAATG
*
1036620 TATTGATACAATG
1 TATCGATACAATG
1036633 TATCGATA
1 TATCGATA
1036641 TTAAGAATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:1039683 original size:78 final size:79
Alignment explanation
Indices: 1039583--1039783 Score: 221
Period size: 79 Copynumber: 2.6 Consensus size: 79
1039573 AATAACAGGG
* * * * * *
1039583 TTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTA
1 TTGGAGTATCCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTA
1039646 GAAAAAAAACCGGGA
65 GAAAAAAAACCGGGA
* *
1039661 TTGGAGTA-CCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTG
1 TTGGAGTATCCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-TTTA
* * ** *
1039725 GGAATAAAGTCGGGG
65 GAAAAAAAACCGGGA
* *
1039740 TTGGAGTATCCCC-TCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1039784 GAAATAACGA
Statistics
Matches: 103, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
77 6 0.06
78 45 0.44
79 48 0.47
80 4 0.04
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (79 bp):
TTGGAGTATCCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAG
AAAAAAAACCGGGA
Found at i:1039769 original size:28 final size:28
Alignment explanation
Indices: 1039735--1039806 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
1039725 GGAATAAAGT
** *
1039735 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1039763 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1039791 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1039807 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1039957 original size:28 final size:28
Alignment explanation
Indices: 1039912--1039993 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 28
1039902 AGTGTTTTAG
* *
1039912 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
*
1039939 TCGA-AAATAATGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
1039966 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
1039994 GATTGTGAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
26 3 0.07
27 23 0.51
28 19 0.42
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:1040080 original size:51 final size:53
Alignment explanation
Indices: 1039984--1040102 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
1039974 AACGGGGTTG
* * *
1039984 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
1040038 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
* *
1040089 GAATATCCTCGATT
1 GAGTATCCCCGATT
1040103 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:1042482 original size:13 final size:13
Alignment explanation
Indices: 1042464--1042489 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1042454 ACATTGATCC
1042464 ATGTATCGATACA
1 ATGTATCGATACA
1042477 ATGTATCGATACA
1 ATGTATCGATACA
1042490 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1042553 original size:19 final size:18
Alignment explanation
Indices: 1042529--1042596 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1042519 CAGTAGCTAA
1042529 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1042548 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1042563 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1042580 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1042597 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1042569 original size:13 final size:13
Alignment explanation
Indices: 1042551--1042575 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1042541 ACAATACTTA
1042551 TGTATCGATACAT
1 TGTATCGATACAT
1042564 TGTATCGATACA
1 TGTATCGATACA
1042576 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1042573 original size:32 final size:32
Alignment explanation
Indices: 1042532--1042594 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1042522 TAGCTAATTA
*
1042532 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1042564 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1042595 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1044921 original size:21 final size:23
Alignment explanation
Indices: 1044875--1044924 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
1044865 TCTTATCCAT
1044875 TAATTC-TTTATTAACTTCTTAC
1 TAATTCATTTATTAACTTCTTAC
*
1044897 -AATTCATTTATTCACTT-TT-C
1 TAATTCATTTATTAACTTCTTAC
1044917 TAATTCAT
1 TAATTCAT
1044925 CTACTTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.04
21 14 0.56
22 10 0.40
ACGTcount: A:0.28, C:0.18, G:0.00, T:0.54
Consensus pattern (23 bp):
TAATTCATTTATTAACTTCTTAC
Found at i:1047995 original size:20 final size:20
Alignment explanation
Indices: 1047952--1048003 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
1047942 TAAGTGAAAT
* **
1047952 GTATCGATACATGGGACATT
1 GTATCGATACATGGGAAAAA
*
1047972 GTATCGATACATGGTAAAAA
1 GTATCGATACATGGGAAAAA
*
1047992 GTATCAATACAT
1 GTATCGATACAT
1048004 TGTGCCCAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (20 bp):
GTATCGATACATGGGAAAAA
Found at i:1048430 original size:23 final size:23
Alignment explanation
Indices: 1048400--1048443 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1048390 GCATTCAACC
1048400 TTAGGGTACAATCTCTT-AAGAAT
1 TTAGGGTACAAT-TCTTGAAGAAT
*
1048423 TTAGGGTATAATTCTTGAAGA
1 TTAGGGTACAATTCTTGAAGA
1048444 GATTGTGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.36
Consensus pattern (23 bp):
TTAGGGTACAATTCTTGAAGAAT
Found at i:1052315 original size:13 final size:13
Alignment explanation
Indices: 1052297--1052322 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1052287 CAATTTTTTG
1052297 TGTATCGATACAT
1 TGTATCGATACAT
1052310 TGTATCGATACAT
1 TGTATCGATACAT
1052323 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1052337 original size:32 final size:33
Alignment explanation
Indices: 1052277--1052340 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1052267 TACAAGCCAA
** *
1052277 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1052310 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1052341 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1053023 original size:39 final size:38
Alignment explanation
Indices: 1052967--1053060 Score: 113
Period size: 36 Copynumber: 2.5 Consensus size: 38
1052957 TTTTCTTTCT
*
1052967 CCCTTAATCAAAATAATTTTAACAG-ATTCGTACATTCTCC
1 CCCTTAAT-AAAGTAATTTTAAC-GCATTC-TACATTCTCC
* *
1053007 CCCTTAATAAAGTAA--TTCACGCATTCTCCATTCTCC
1 CCCTTAATAAAGTAATTTTAACGCATTCTACATTCTCC
1053043 CCCTTAATAAAGTAATTT
1 CCCTTAATAAAGTAATTT
1053061 ACACACACAT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
36 25 0.52
37 8 0.17
38 1 0.02
39 6 0.12
40 8 0.17
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (38 bp):
CCCTTAATAAAGTAATTTTAACGCATTCTACATTCTCC
Found at i:1068737 original size:20 final size:20
Alignment explanation
Indices: 1068712--1068749 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1068702 AATTTTGATA
1068712 TTTGTTATGAT-TGAATTATG
1 TTTGTT-TGATATGAATTATG
1068732 TTTGTTTGATATGAATTA
1 TTTGTTTGATATGAATTA
1068750 GGGTCTATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTGTTTGATATGAATTATG
Found at i:1076687 original size:13 final size:13
Alignment explanation
Indices: 1076669--1076724 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 13
1076659 TTATGCTTTG
1076669 TATCGATACATTC
1 TATCGATACATTC
1076682 TATCGATACATGCTC
1 TATCGATACAT--TC
1076697 ATTATATCGATACATTC
1 ----TATCGATACATTC
1076714 TATCGATACAT
1 TATCGATACAT
1076725 GCTCAATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 22 0.59
15 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (13 bp):
TATCGATACATTC
Done.