Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 37 of 120
Found at i:9589986 original size:16 final size:16
Alignment explanation
Indices: 9589954--9589983 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9589944 TCACCTATCT
9589954 TTTTTTTGAATATTTA
1 TTTTTTTGAATATTTA
9589970 TTTTTTT-AATATTT
1 TTTTTTTGAATATTT
9589984 TATCAAACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
TTTTTTTGAATATTTA
Found at i:9590293 original size:11 final size:10
Alignment explanation
Indices: 9590272--9590308 Score: 56
Period size: 11 Copynumber: 3.5 Consensus size: 10
9590262 AATGAAAGAA
9590272 ATAAAAATAT
1 ATAAAAATAT
9590282 ATAAAAATTAT
1 ATAAAAA-TAT
9590293 ATATAAAATAT
1 ATA-AAAATAT
9590304 ATAAA
1 ATAAA
9590309 GTTCAAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.36
11 12 0.48
12 4 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:9591984 original size:22 final size:22
Alignment explanation
Indices: 9591959--9592023 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
9591949 TAAAAATGAT
* **
9591959 AAAATTTTAATTTAATTTTTTA
1 AAAATTATAATTTAATTTCGTA
* *
9591981 AAAATTATATTTTTATTATCGTA
1 AAAATTATAATTTAATT-TCGTA
9592004 AAAATTATAATTTAATTTCG
1 AAAATTATAATTTAATTTCG
9592024 ACCCCTAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (22 bp):
AAAATTATAATTTAATTTCGTA
Found at i:9592190 original size:32 final size:31
Alignment explanation
Indices: 9592117--9592192 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 31
9592107 AGTCCAATTT
* * *
9592117 GATACTCAAACTTGACACTTTTTTCTAATTT
1 GATACTTAAACTTGACACTTTTTTCTAAGTG
* * * *
9592148 AATACCTAAACTTGACACTTTTTTTTTAGGTG
1 GATACTTAAACTTGACAC-TTTTTTCTAAGTG
9592180 GATACTTAAACTT
1 GATACTTAAACTT
9592193 TTTGGGGTCC
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 15 0.43
32 20 0.57
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (31 bp):
GATACTTAAACTTGACACTTTTTTCTAAGTG
Found at i:9601698 original size:16 final size:16
Alignment explanation
Indices: 9601679--9601721 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
9601669 GATTACAGTT
*
9601679 CTATTCAATTACAACC
1 CTATTCTATTACAACC
*
9601695 CTATTCTATTACAACT
1 CTATTCTATTACAACC
9601711 CTATTCTATTA
1 CTATTCTATTA
9601722 TAGCCTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.42
Consensus pattern (16 bp):
CTATTCTATTACAACC
Found at i:9601707 original size:32 final size:32
Alignment explanation
Indices: 9601670--9601741 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
9601660 TAAATTACTG
*
9601670 ATTACAGTTCTATTCAATTACAACCCTATTCT
1 ATTACAGTTCTATTCAATTACAACCCTATTCC
** * * * *
9601702 ATTACAACTCTATTCTATTATAGCCTTATTCC
1 ATTACAGTTCTATTCAATTACAACCCTATTCC
9601734 ATTACAGT
1 ATTACAGT
9601742 GAATCAAACG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.42
Consensus pattern (32 bp):
ATTACAGTTCTATTCAATTACAACCCTATTCC
Found at i:9604384 original size:31 final size:30
Alignment explanation
Indices: 9604348--9604423 Score: 102
Period size: 28 Copynumber: 2.6 Consensus size: 30
9604338 ATTTAAAGGT
*
9604348 TTATTTTCCAAATAAATACTCCAAATTTCCA
1 TTATTTTACAAATAAATA-TCCAAATTTCCA
*
9604379 TTATTTTAC-AATTAA-ATCCAAATTTCCA
1 TTATTTTACAAATAAATATCCAAATTTCCA
*
9604407 TTATTTTACAATTAAAT
1 TTATTTTACAAATAAAT
9604424 CCAATTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
28 21 0.54
29 5 0.13
30 5 0.13
31 8 0.21
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.43
Consensus pattern (30 bp):
TTATTTTACAAATAAATATCCAAATTTCCA
Found at i:9604406 original size:28 final size:28
Alignment explanation
Indices: 9604367--9604427 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
9604357 AAATAAATAC
9604367 TCCAAATTTCCATTATTTTACAATTAAA
1 TCCAAATTTCCATTATTTTACAATTAAA
9604395 TCCAAATTTCCATTATTTTACAATTAAA
1 TCCAAATTTCCATTATTTTACAATTAAA
9604423 TCCAA
1 TCCAA
9604428 TTTAATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (28 bp):
TCCAAATTTCCATTATTTTACAATTAAA
Found at i:9606570 original size:29 final size:29
Alignment explanation
Indices: 9606528--9606587 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
9606518 CCTTATTAAT
9606528 TGTTTGGGCTGAGTTAGATATAGATGGCA
1 TGTTTGGGCTGAGTTAGATATAGATGGCA
9606557 TGTTTGGGCTGAGTTAGATATAGATGGCA
1 TGTTTGGGCTGAGTTAGATATAGATGGCA
9606586 TG
1 TG
9606588 CGATAGGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.07, G:0.35, T:0.35
Consensus pattern (29 bp):
TGTTTGGGCTGAGTTAGATATAGATGGCA
Found at i:9607893 original size:18 final size:17
Alignment explanation
Indices: 9607866--9607899 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9607856 TTAGGTCTTT
9607866 ATAAAAAATAAAAAATA
1 ATAAAAAATAAAAAATA
*
9607883 ATAATAAAATATAAAAT
1 ATAA-AAAATAAAAAAT
9607900 TCTTAGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAAAAAATAAAAAATA
Found at i:9616348 original size:29 final size:29
Alignment explanation
Indices: 9616273--9616349 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
9616263 AAAACACTGG
* * * * *
9616273 GAAAAGAACGCCTTTGTAGTGAAACTTTG
1 GAAAGGAAAGCCTTTGTGGTGAAACTCTA
9616302 GAAAGGAAAGCCTTTGTGGTGAAACTCTA
1 GAAAGGAAAGCCTTTGTGGTGAAACTCTA
9616331 GAAAGGAAAGCCTTTGTGG
1 GAAAGGAAAGCCTTTGTGG
9616350 CAATCTCGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.25
Consensus pattern (29 bp):
GAAAGGAAAGCCTTTGTGGTGAAACTCTA
Found at i:9616438 original size:28 final size:29
Alignment explanation
Indices: 9616382--9616461 Score: 73
Period size: 28 Copynumber: 2.8 Consensus size: 29
9616372 TATGGCGACT
9616382 TCTATTAAAGGAAGCCTAT-GTTG--TGATC
1 TCTATTAAAGGAAGCCT-TCG-TGACTGATC
9616410 TCTATTAAAGGAAGCCTTCGTGACT-ATC
1 TCTATTAAAGGAAGCCTTCGTGACTGATC
*
9616438 TCTGA--AAAGGAATGCCTTCATGAC
1 TCT-ATTAAAGGAA-GCCTTCGTGAC
9616462 GTAATCTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
27 10 0.22
28 34 0.74
29 2 0.04
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (29 bp):
TCTATTAAAGGAAGCCTTCGTGACTGATC
Found at i:9619282 original size:21 final size:21
Alignment explanation
Indices: 9619247--9619294 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
9619237 AATAAGAGTC
9619247 ATAAAAGGTAAATAAGTGA-AAA
1 ATAAAAGGTAAATAA-T-ATAAA
9619269 ATAAAAGG-AAATAATATAAA
1 ATAAAAGGTAAATAATATAAA
9619289 ATAAAA
1 ATAAAA
9619295 TAAATGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.04
20 10 0.40
21 6 0.24
22 8 0.32
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (21 bp):
ATAAAAGGTAAATAATATAAA
Found at i:9630248 original size:7 final size:6
Alignment explanation
Indices: 9630232--9630265 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
9630222 TAATTATTAA
9630232 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG AAA
9630266 GAACATCGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:9632088 original size:19 final size:19
Alignment explanation
Indices: 9632052--9632102 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
9632042 ACTACATTAA
* *
9632052 AAATGTTAATATAAATTATTG
1 AAATATTAAT-TAAATTA-TC
*
9632073 AAAT-TTAATTAGATTATC
1 AAATATTAATTAAATTATC
9632091 AAATATTAATTA
1 AAATATTAATTA
9632103 TACTTATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 5 0.19
19 13 0.48
20 5 0.19
21 4 0.15
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (19 bp):
AAATATTAATTAAATTATC
Found at i:9633340 original size:28 final size:28
Alignment explanation
Indices: 9633287--9633340 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
9633277 CAACAATATA
* **
9633287 AAAATAAATAAAATATTAATTGAATTTC
1 AAAATAAATAAAATAGTAATAAAATTTC
9633315 AAAATAAATAATAA-AGTAATAAAATT
1 AAAATAAATAA-AATAGTAATAAAATT
9633341 AAATAAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 20 0.91
29 2 0.09
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (28 bp):
AAAATAAATAAAATAGTAATAAAATTTC
Found at i:9635296 original size:114 final size:114
Alignment explanation
Indices: 9635070--9635397 Score: 370
Period size: 114 Copynumber: 2.9 Consensus size: 114
9635060 TCACTATTTG
* * * *
9635070 TTTTAACCCACTTCTCTGTACCTTACCAGAAAGATGAGATTTGAAGCCTCACTCCACTCCACTGT
1 TTTTAACCCACTTCTTTGTACCTCACCAGGAAGATGAGATTTGAAGTCTCACTCCACTCCACTGT
* * **
9635135 AACCTTAGGGACATTGAGCTCTGCTTCGTTATTTTAATCCAACACACTA
66 AACCTCAGGGACGTTGAGCTCAACTTCGTTATTTTAATCCAACACACTA
* * * * * * *
9635184 TTTTGACCCACTTCTTTGTACCTCACTAGGAAGATGGGAGTTGAAGTTTCATTCCACTCTACTGT
1 TTTTAACCCACTTCTTTGTACCTCACCAGGAAGATGAGATTTGAAGTCTCACTCCACTCCACTGT
* * * * * * *
9635249 ATCCTCAGGGATGTTGAGCTCAACTTTGTTGTTTTTAT-TAACAACACTG
66 AACCTCAGGGACGTTGAGCTCAACTTCGTTATTTTAATCCAAC-ACACTA
* * * *
9635298 TTTTAACCCATTTCTTTGTACCTCGCCAAGAAGATGAGATTTGAAGTCTCACTCCACTCCACTAT
1 TTTTAACCCACTTCTTTGTACCTCACCAGGAAGATGAGATTTGAAGTCTCACTCCACTCCACTGT
* ** *
9635363 AACCTCAAGGACGTTGAGCTCTGCTTCATTATTTT
66 AACCTCAGGGACGTTGAGCTCAACTTCGTTATTTT
9635398 GACGTACTTC
Statistics
Matches: 172, Mismatches: 41, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
113 3 0.02
114 169 0.98
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (114 bp):
TTTTAACCCACTTCTTTGTACCTCACCAGGAAGATGAGATTTGAAGTCTCACTCCACTCCACTGT
AACCTCAGGGACGTTGAGCTCAACTTCGTTATTTTAATCCAACACACTA
Found at i:9635837 original size:49 final size:49
Alignment explanation
Indices: 9635792--9635942 Score: 205
Period size: 49 Copynumber: 3.1 Consensus size: 49
9635782 CTCATCTTTG
9635792 GGGTATAAGATTCACCGTTACGGCTTCAATCTTTCCCTTCACATCTCTA
1 GGGTATAAGATTCACCGTTACGGCTTCAATCTTTCCCTTCACATCTCTA
* * ** * * *
9635841 AGGTATAAGGTTTGCCATTGCGGCTTCAACCTTTCCC-TCTACATCTCTA
1 GGGTATAAGATTCACCGTTACGGCTTCAATCTTTCCCTTC-ACATCTCTA
* *
9635890 GGGTATAAGATTCACCGTTATGGCTTCAATCTTTCCCTTCATATCTCTA
1 GGGTATAAGATTCACCGTTACGGCTTCAATCTTTCCCTTCACATCTCTA
9635939 GGGT
1 GGGT
9635943 TTTCATCTCG
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
48 2 0.02
49 80 0.95
50 2 0.02
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (49 bp):
GGGTATAAGATTCACCGTTACGGCTTCAATCTTTCCCTTCACATCTCTA
Found at i:9638232 original size:44 final size:44
Alignment explanation
Indices: 9638169--9638257 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
9638159 GTGATGCTTA
*
9638169 TAAATGCATGTATGCATAAGAAAGGTATTGACTCGTAGTTCAAT
1 TAAATGCATGTATGCATAAGAAAGGTATTGACTCATAGTTCAAT
9638213 TAAATGCATGTATGCATAAGAAAGGTATTGACTCATAGTTCAAT
1 TAAATGCATGTATGCATAAGAAAGGTATTGACTCATAGTTCAAT
9638257 T
1 T
9638258 CTATTAGACA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (44 bp):
TAAATGCATGTATGCATAAGAAAGGTATTGACTCATAGTTCAAT
Found at i:9640196 original size:18 final size:17
Alignment explanation
Indices: 9640173--9640215 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
9640163 GAGCAAAAAT
9640173 AAAAAATA-AAAATATCAA
1 AAAAAATATAAAA-AT-AA
9640191 AAAAAATATAAAAATAA
1 AAAAAATATAAAAATAA
*
9640208 ATAAAATA
1 AAAAAATA
9640216 CTAATTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 9 0.39
18 10 0.43
19 4 0.17
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAAAATATAAAAATAA
Found at i:9640196 original size:20 final size:21
Alignment explanation
Indices: 9640168--9640206 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
9640158 ATAAGGAGCA
9640168 AAAATAAAAAATAAAAATATC
1 AAAATAAAAAATAAAAATATC
*
9640189 AAAA-AAAATATAAAAATA
1 AAAATAAAAAATAAAAATA
9640207 AATAAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (21 bp):
AAAATAAAAAATAAAAATATC
Found at i:9641895 original size:51 final size:51
Alignment explanation
Indices: 9641818--9642005 Score: 281
Period size: 51 Copynumber: 3.7 Consensus size: 51
9641808 AAATGAACGA
*
9641818 GTCCGATGACTAAGTGTCATCTTGAGTAAATGAATTCC-TTACGGATTAAAG
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCATTACGGATTAAAG
* *
9641869 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATTAAAG
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATTACGGATTAAAG
* * *
9641920 GTCCGATGACTAAGTGTCATCGTCAGTAAATGAATCCATGACGAATTAAAG
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATTACGGATTAAAG
*
9641971 GTCCGATGACTCAA-TGTCATCGTGAGTATATGAAT
1 GTCCGATGACT-AAGTGTCATCGTGAGTAAATGAAT
9642006 TCCTATACGG
Statistics
Matches: 126, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
50 3 0.02
51 121 0.96
52 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.29
Consensus pattern (51 bp):
GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATTACGGATTAAAG
Found at i:9649271 original size:53 final size:50
Alignment explanation
Indices: 9649144--9649281 Score: 141
Period size: 51 Copynumber: 2.6 Consensus size: 50
9649134 GCTATAAATG
* * * **
9649144 AAAGAGTCCGATGATTAAGTGTCATCTTGAGTAAATGAATTCCTTACGGATT
1 AAAG-GTCCGATGACTAA-TGTCATCGTGAGTATATGAATTCCTTACGGAAC
* * *
9649196 AAAGGTCCAATGACTCAGTGTCATCGTGAGTATATGAATTCCTATATGGAAC
1 AAAGGTCCGATGACT-AATGTCATCGTGAGTATATGAATTCCT-TACGGAAC
*
9649248 AAGGGGTCCGATGACTATATGTCATCGTGAGTAT
1 AA-AGGTCCGATGACTA-ATGTCATCGTGAGTAT
9649282 TAAATGAAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
51 32 0.45
52 13 0.18
53 26 0.37
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.30
Consensus pattern (50 bp):
AAAGGTCCGATGACTAATGTCATCGTGAGTATATGAATTCCTTACGGAAC
Found at i:9659585 original size:25 final size:25
Alignment explanation
Indices: 9659543--9659593 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
9659533 GATGATGGCA
*
9659543 AAAATAATATAAATACAT-AGATAAT
1 AAAATAAAATAAATACATCA-ATAAT
9659568 AAAATAAAAT-AATAACATCAATAAT
1 AAAATAAAATAAAT-ACATCAATAAT
9659593 A
1 A
9659594 GTACAATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 3 0.13
25 19 0.83
26 1 0.04
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (25 bp):
AAAATAAAATAAATACATCAATAAT
Found at i:9659743 original size:27 final size:27
Alignment explanation
Indices: 9659705--9659762 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 27
9659695 AATGCTAAAA
9659705 ATAACAATAAAAATAATTACAATC-AGG
1 ATAACAATAAAAATAATTA-AATCAAGG
9659732 ATAA-AATAAAAAATAATTAAATCAAGG
1 ATAACAAT-AAAAATAATTAAATCAAGG
9659759 ATAA
1 ATAA
9659763 TAAAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.22
Consensus pattern (27 bp):
ATAACAATAAAAATAATTAAATCAAGG
Found at i:9660114 original size:21 final size:21
Alignment explanation
Indices: 9660088--9660144 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
9660078 AATTAAAAGG
*
9660088 AATAAAAGAAATAAATGATTA
1 AATAAAAGAAATAAAGGATTA
9660109 AATAAAAGAAATAAAGGATTA
1 AATAAAAGAAATAAAGGATTA
9660130 AATAAAAGAAATAAA
1 AATAAAAGAAATAAA
9660145 AAAGGAGTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (21 bp):
AATAAAAGAAATAAAGGATTA
Found at i:9661994 original size:101 final size:101
Alignment explanation
Indices: 9661834--9662363 Score: 509
Period size: 101 Copynumber: 5.2 Consensus size: 101
9661824 GTTTGAGTCC
** *
9661834 GATCCACTACAACTTCAGGGATATATGATTTGGTGTTGT-AGTTTCA-T-C-TTGCTCTACTACA
1 GATCCACTGTAACTTCAGGGATATATGATTTGGTGTTGTGA-CTTCACTCCATT-C-C-ACTACA
* * * * * *
9661895 ACTTTAGAGAGATAAATATTTGCTA-TCGTCA-TTCTAATAT
62 ACTTTAGAGAGATAGAGATCTACTACT-GT-AGTTTTAATCT
* *
9661935 GATCCACGGTAACTTCAGGGATATACGATTTGGTGTTGTGACTTCACTCCATTCCACTACAACTT
1 GATCCACTGTAACTTCAGGGATATATGATTTGGTGTTGTGACTTCACTCCATTCCACTACAACTT
*
9662000 TATG-GAGATTGAGATCTACTACTGTAGTTTTAATCT
66 TA-GAGAGATAGAGATCTACTACTGTAGTTTTAATCT
* ** * * * *
9662036 GATCCAGTACAAATTCAAGGATATATGATTTGGTGTTGTGGCTTCACTCCATTCCACTGCAACTT
1 GATCCACTGTAACTTCAGGGATATATGATTTGGTGTTGTGACTTCACTCCATTCCACTACAACTT
* * * ** *
9662101 CAGGGAGATTGAGATCTTTTACTGTAGTTTTAATCC
66 TAGAGAGATAGAGATCTACTACTGTAGTTTTAATCT
* * * * * *
9662137 AATCCACTGCAACTTCAGGGATATAGGATTTGATGTTGTGGCTTCACTCCATTCTACTACAACTT
1 GATCCACTGTAACTTCAGGGATATATGATTTGGTGTTGTGACTTCACTCCATTCCACTACAACTT
* * *
9662202 TA-AGGAGATTGAGATCTACTATTGTAGTTTTATTCT
66 TAGA-GAGATAGAGATCTACTACTGTAGTTTTAATCT
* * * * * * * *
9662238 GATCCACTGTAACTTTAGGGATATAAGATTTGGTATTGTAACTTTACTCCTTTCCATTGCAACTT
1 GATCCACTGTAACTTCAGGGATATATGATTTGGTGTTGTGACTTCACTCCATTCCACTACAACTT
* * * *
9662303 TAGGGAGATTGAGATCTGCTACTGTAGTTTTAATCC
66 TAGAGAGATAGAGATCTACTACTGTAGTTTTAATCT
*
9662339 GATCCACTGTAACTTTAGGGATATA
1 GATCCACTGTAACTTCAGGGATATA
9662364 GGGTTTGCTG
Statistics
Matches: 360, Mismatches: 59, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
100 2 0.01
101 349 0.97
102 5 0.01
103 2 0.01
104 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (101 bp):
GATCCACTGTAACTTCAGGGATATATGATTTGGTGTTGTGACTTCACTCCATTCCACTACAACTT
TAGAGAGATAGAGATCTACTACTGTAGTTTTAATCT
Found at i:9662277 original size:50 final size:50
Alignment explanation
Indices: 9662213--9662363 Score: 151
Period size: 51 Copynumber: 3.0 Consensus size: 50
9662203 AAGGAGATTG
*
9662213 AGATCTACTATTGTAGTTTTATTCTGATCCACTGTAACTTTAGGGATATA
1 AGATCTGCTATTGTAGTTTTATTCTGATCCACTGTAACTTTAGGGATATA
* * ** * * * * * *
9662263 AGATTTGGTATTGTAACTTTACTCCT-TTCCATTGCAACTTTAGGGAGATTG
1 AGATCTGCTATTGTAGTTTTA-TTCTGATCCACTGTAACTTTAGGGATA-TA
* * *
9662314 AGATCTGCTACTGTAGTTTTAATCCGATCCACTGTAACTTTAGGGATATA
1 AGATCTGCTATTGTAGTTTTATTCTGATCCACTGTAACTTTAGGGATATA
9662364 GGGTTTGCTG
Statistics
Matches: 74, Mismatches: 24, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
50 36 0.49
51 38 0.51
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (50 bp):
AGATCTGCTATTGTAGTTTTATTCTGATCCACTGTAACTTTAGGGATATA
Found at i:9662364 original size:202 final size:202
Alignment explanation
Indices: 9661935--9662370 Score: 620
Period size: 202 Copynumber: 2.2 Consensus size: 202
9661925 ATTCTAATAT
* * *
9661935 GATCCACGGTAACTTCAGGGATATACGATTTGGTGTTGTGACTTCACTCCATTCCACTACAACTT
1 GATCCACTGTAACTTCAGGGATATAGGATTTGATGTTGTGACTTCACTCCATTCCACTACAACTT
* * *
9662000 TATGGAGATTGAGATCTACTACTGTAGTTTTAATCTGATCCAGTACAAATTCAAGGATATATGAT
66 TAAGGAGATTGAGATCTACTACTGTAGTTTTAATCTGATCCACTACAAATTCAAGGATATAAGAT
* ** **
9662065 TTGGTGTTGTGGCTTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCTTTTACTGTAGTT
131 TTGGTATTGTAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCTGCTACTGTAGTT
9662130 TTAATCC
196 TTAATCC
* * * *
9662137 AATCCACTGCAACTTCAGGGATATAGGATTTGATGTTGTGGCTTCACTCCATTCTACTACAACTT
1 GATCCACTGTAACTTCAGGGATATAGGATTTGATGTTGTGACTTCACTCCATTCCACTACAACTT
* * ** * * *
9662202 TAAGGAGATTGAGATCTACTATTGTAGTTTTATTCTGATCCACTGTAACTTTAGGGATATAAGAT
66 TAAGGAGATTGAGATCTACTACTGTAGTTTTAATCTGATCCACTACAAATTCAAGGATATAAGAT
* * * *
9662267 TTGGTATTGTAACTTTACTCCTTTCCATTGCAACTTTAGGGAGATTGAGATCTGCTACTGTAGTT
131 TTGGTATTGTAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCTGCTACTGTAGTT
9662332 TTAATCC
196 TTAATCC
* *
9662339 GATCCACTGTAACTTTAGGGATATAGGGTTTG
1 GATCCACTGTAACTTCAGGGATATAGGATTTG
9662371 CTGCTTCACT
Statistics
Matches: 204, Mismatches: 30, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
202 204 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (202 bp):
GATCCACTGTAACTTCAGGGATATAGGATTTGATGTTGTGACTTCACTCCATTCCACTACAACTT
TAAGGAGATTGAGATCTACTACTGTAGTTTTAATCTGATCCACTACAAATTCAAGGATATAAGAT
TTGGTATTGTAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCTGCTACTGTAGTT
TTAATCC
Found at i:9669550 original size:15 final size:14
Alignment explanation
Indices: 9669524--9669562 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
9669514 ACAAAGAAAT
* *
9669524 TAAAACAAAACAAG
1 TAAAAGAAAACAAA
9669538 TAAAAGTAAAACAAA
1 TAAAAG-AAAACAAA
9669553 TAAAAGAAAA
1 TAAAAGAAAA
9669563 ATTGAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.74, C:0.08, G:0.08, T:0.10
Consensus pattern (14 bp):
TAAAAGAAAACAAA
Found at i:9669562 original size:20 final size:20
Alignment explanation
Indices: 9669524--9669562 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9669514 ACAAAGAAAT
*
9669524 TAAAACAAAACAAGTAAAAG
1 TAAAACAAAAAAAGTAAAAG
9669544 TAAAACAAATAAAAG-AAAA
1 TAAAACAAA-AAAAGTAAAA
9669563 ATTGAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.74, C:0.08, G:0.08, T:0.10
Consensus pattern (20 bp):
TAAAACAAAAAAAGTAAAAG
Found at i:9680114 original size:26 final size:27
Alignment explanation
Indices: 9680078--9680128 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
9680068 AATGCTAAAA
9680078 ATAACAATAAAA-ATAATTACAATCATG
1 ATAACAATAAAACATAATTA-AATCATG
9680105 ATAA-AATAAAACATAATTAAATCA
1 ATAACAATAAAACATAATTAAATCA
9680129 AGGATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (27 bp):
ATAACAATAAAACATAATTAAATCATG
Found at i:9680134 original size:27 final size:27
Alignment explanation
Indices: 9680078--9680135 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
9680068 AATGCTAAAA
*
9680078 ATAACAATAAAAATAATTACAATCATG
1 ATAACAATAAAAATAATTACAATCAGG
9680105 ATAA-AATAAAACATAATTA-AATCAAGG
1 ATAACAATAAAA-ATAATTACAATC-AGG
9680132 ATAA
1 ATAA
9680136 TAAAACTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.62, C:0.09, G:0.05, T:0.24
Consensus pattern (27 bp):
ATAACAATAAAAATAATTACAATCAGG
Found at i:9680252 original size:10 final size:10
Alignment explanation
Indices: 9680225--9680255 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
9680215 AAAATAATAT
9680225 TAAAGCAAAA
1 TAAAGCAAAA
9680235 TGAAAGCAAAA
1 T-AAAGCAAAA
9680246 TAAAGCAAAA
1 TAAAGCAAAA
9680256 CAAATAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.68, C:0.10, G:0.13, T:0.10
Consensus pattern (10 bp):
TAAAGCAAAA
Found at i:9681609 original size:23 final size:23
Alignment explanation
Indices: 9681582--9681627 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
9681572 TAGGGTTTGT
9681582 GGGCTTGTTTTAGGTTTGCGTTA
1 GGGCTTGTTTTAGGTTTGCGTTA
9681605 GGGCTTGTTTTAGGTTTGCGTTA
1 GGGCTTGTTTTAGGTTTGCGTTA
9681628 TTGGGTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.09, G:0.35, T:0.48
Consensus pattern (23 bp):
GGGCTTGTTTTAGGTTTGCGTTA
Found at i:9682204 original size:19 final size:19
Alignment explanation
Indices: 9682180--9682216 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9682170 CACAAAACTA
* *
9682180 AAAATTTAGCTTAATTAAG
1 AAAATTAAGATTAATTAAG
9682199 AAAATTAAGATTAATTAA
1 AAAATTAAGATTAATTAA
9682217 AACTAAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (19 bp):
AAAATTAAGATTAATTAAG
Found at i:9682574 original size:21 final size:18
Alignment explanation
Indices: 9682542--9682591 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
9682532 CAAATGATAT
9682542 TTTTAATAA-TAATAATA
1 TTTTAATAAGTAATAATA
*
9682559 TTATAATAAGTAATAATA
1 TTTTAATAAGTAATAATA
*
9682577 TTTTATTAAGTAATA
1 TTTTAATAAGTAATA
9682592 TTATAAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 8 0.28
18 21 0.72
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (18 bp):
TTTTAATAAGTAATAATA
Found at i:9692385 original size:16 final size:17
Alignment explanation
Indices: 9692356--9692396 Score: 66
Period size: 16 Copynumber: 2.4 Consensus size: 17
9692346 GTTATTTTTA
9692356 AAAAAATGAAAAAAATTC
1 AAAAAATG-AAAAAATTC
9692374 AAAAAATG-AAAAATTC
1 AAAAAATGAAAAAATTC
9692390 AAAAAAT
1 AAAAAAT
9692397 TAGTACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 15 0.65
18 8 0.35
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (17 bp):
AAAAAATGAAAAAATTC
Found at i:9692423 original size:5 final size:6
Alignment explanation
Indices: 9692404--9692563 Score: 76
Period size: 6 Copynumber: 26.3 Consensus size: 6
9692394 AATTAGTACA
* * * * **
9692404 TTTATT TTTATT TTTATT TTCATT ATTT-TC ATTATT TTAATT TCCATT
1 TTTATT TTTATT TTTATT TTTATT -TTTATT TTTATT TTTATT TTTATT
* * * *
9692452 TTCATTT TTTATT TTTCATT TTTATTT TTTACTT TTT-CT TTTACT TTTACT
1 TTTA-TT TTTATT TTT-ATT TTTA-TT TTTA-TT TTTATT TTTATT TTTATT
* * ** * ** *
9692503 TTTACT TTTATT TGTATT TGCATT TGTATT CGTATT TTTA-G TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
9692550 TTT-TAT TTTATT TT
1 TTTAT-T TTTATT TT
9692564 ATTATGCACT
Statistics
Matches: 123, Mismatches: 22, Indels: 18
0.75 0.13 0.11
Matches are distributed among these distances:
5 11 0.09
6 87 0.71
7 25 0.20
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.72
Consensus pattern (6 bp):
TTTATT
Found at i:9692431 original size:9 final size:9
Alignment explanation
Indices: 9692417--9692441 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
9692407 ATTTTTATTT
9692417 TTATTTTCA
1 TTATTTTCA
9692426 TTATTTTCA
1 TTATTTTCA
9692435 TTATTTT
1 TTATTTT
9692442 AATTTCCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (9 bp):
TTATTTTCA
Found at i:9692452 original size:21 final size:20
Alignment explanation
Indices: 9692428--9692482 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
9692418 TATTTTCATT
9692428 ATTTTCATTATTTTAATTTCC
1 ATTTTCATT-TTTTAATTTCC
* *
9692449 ATTTTCATTTTTTATTTTTC
1 ATTTTCATTTTTTAATTTCC
*
9692469 ATTTTTATTTTTTA
1 ATTTTCATTTTTTA
9692483 CTTTTTCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 22 0.71
21 9 0.29
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTTCATTTTTTAATTTCC
Found at i:9692481 original size:14 final size:14
Alignment explanation
Indices: 9692404--9692480 Score: 56
Period size: 13 Copynumber: 5.6 Consensus size: 14
9692394 AATTAGTACA
9692404 TTTATTTTT-A-TT
1 TTTATTTTTCATTT
9692416 TTTA-TTTTCATTAT
1 TTTATTTTTCATT-T
* *
9692430 TTTCATTATTTTAATT
1 TTT-ATT-TTTCATTT
**
9692446 TCCA-TTTTCATTT
1 TTTATTTTTCATTT
9692459 TTTATTTTTCA-TT
1 TTTATTTTTCATTT
9692472 TTTATTTTT
1 TTTATTTTT
9692481 TACTTTTTCT
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
11 4 0.08
12 5 0.10
13 20 0.40
14 11 0.22
15 2 0.04
16 3 0.06
17 5 0.10
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTTTCATTT
Found at i:9693486 original size:22 final size:19
Alignment explanation
Indices: 9693458--9693515 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 19
9693448 TTATTGATTA
9693458 AAAAGAAGAAGAAAAAAAGTAG
1 AAAAGAA-AAGAAAAAAA--AG
9693480 AAAAGAAAAATTGAAAAAAAAG
1 AAAAG-AAAA--GAAAAAAAAG
9693502 AAAAGAAAAGAAAA
1 AAAAGAAAAGAAAA
9693516 GTATTTGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 5 0.15
21 4 0.12
22 14 0.42
23 2 0.06
24 8 0.24
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (19 bp):
AAAAGAAAAGAAAAAAAAG
Found at i:9697275 original size:18 final size:17
Alignment explanation
Indices: 9697227--9697276 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
9697217 CAAATGATAT
9697227 TTTTATTAATAATAATA
1 TTTTATTAATAATAATA
* *
9697244 TTATAATAAGTAATAATA
1 TTTTATTAA-TAATAATA
9697262 TTTTATTAATTAATA
1 TTTTATTAA-TAATA
9697277 TTATAAAGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TTTTATTAATAATAATA
Found at i:9699153 original size:16 final size:16
Alignment explanation
Indices: 9699132--9699164 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
9699122 TAAATGAAGC
*
9699132 GTAATGTAATAGAGCT
1 GTAATGAAATAGAGCT
9699148 GTAATGAAATAGAGCT
1 GTAATGAAATAGAGCT
9699164 G
1 G
9699165 AAATTAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.27, T:0.27
Consensus pattern (16 bp):
GTAATGAAATAGAGCT
Found at i:9700994 original size:24 final size:24
Alignment explanation
Indices: 9700967--9701018 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
9700957 ATATGTATTT
*
9700967 AATAATAAAAATTTCATAATATGA
1 AATAATAAAAATTTAATAATATGA
* * * *
9700991 AATACTAATATTTTAATATTATGA
1 AATAATAAAAATTTAATAATATGA
9701015 AATA
1 AATA
9701019 TTATTAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (24 bp):
AATAATAAAAATTTAATAATATGA
Found at i:9701020 original size:10 final size:10
Alignment explanation
Indices: 9700997--9701042 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
9700987 ATGAAATACT
9700997 AATATT-TT-
1 AATATTATTA
*
9701005 AATATTATGA
1 AATATTATTA
9701015 AATATTATTA
1 AATATTATTA
*
9701025 AATTTTATTA
1 AATATTATTA
9701035 TAATATTA
1 -AATATTA
9701043 GTATTTAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
8 6 0.19
9 1 0.03
10 18 0.58
11 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (10 bp):
AATATTATTA
Found at i:9701062 original size:21 final size:21
Alignment explanation
Indices: 9701038--9701077 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9701028 TTTATTATAA
*
9701038 TATTAGTA-TTTAGATATTTAC
1 TATTAATATTTTA-ATATTTAC
9701059 TATTAATATTTTAATATTT
1 TATTAATATTTTAATATTT
9701078 TTTACCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (21 bp):
TATTAATATTTTAATATTTAC
Found at i:9701675 original size:15 final size:15
Alignment explanation
Indices: 9701655--9701687 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
9701645 GCTTTTAAAA
9701655 GTTAAGTTAAAATCT
1 GTTAAGTTAAAATCT
9701670 GTTAAGTTAAAATCT
1 GTTAAGTTAAAATCT
9701685 GTT
1 GTT
9701688 TCCGTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.42
Consensus pattern (15 bp):
GTTAAGTTAAAATCT
Found at i:9714622 original size:12 final size:12
Alignment explanation
Indices: 9714607--9714643 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
9714597 GTAGGAGCAA
9714607 AGGAAGGAAAAG
1 AGGAAGGAAAAG
9714619 AGGAA-GAAAGAG
1 AGGAAGGAAA-AG
9714631 AGGAAGGAAAAG
1 AGGAAGGAAAAG
9714643 A
1 A
9714644 AGTCAAGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.17
12 15 0.65
13 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (12 bp):
AGGAAGGAAAAG
Found at i:9715126 original size:47 final size:47
Alignment explanation
Indices: 9715063--9715160 Score: 196
Period size: 47 Copynumber: 2.1 Consensus size: 47
9715053 AGTTTTTAGT
9715063 TTGTTAGAAATCATTGCCATCACATTCTCATTGTCATTACATTTTAA
1 TTGTTAGAAATCATTGCCATCACATTCTCATTGTCATTACATTTTAA
9715110 TTGTTAGAAATCATTGCCATCACATTCTCATTGTCATTACATTTTAA
1 TTGTTAGAAATCATTGCCATCACATTCTCATTGTCATTACATTTTAA
9715157 TTGT
1 TTGT
9715161 CACTTCATTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (47 bp):
TTGTTAGAAATCATTGCCATCACATTCTCATTGTCATTACATTTTAA
Found at i:9716628 original size:24 final size:24
Alignment explanation
Indices: 9716595--9716649 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
9716585 GTTAAGAGTA
*
9716595 AAAATTGTCAGTGTAAATGTAATAC
1 AAAA-TGTCAGTGCAAATGTAATAC
* *
9716620 AAAATGTCAGTGCAACTGTAATAT
1 AAAATGTCAGTGCAAATGTAATAC
9716644 AAAATG
1 AAAATG
9716650 AATTGAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.29
Consensus pattern (24 bp):
AAAATGTCAGTGCAAATGTAATAC
Found at i:9719297 original size:12 final size:12
Alignment explanation
Indices: 9719280--9719322 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
9719270 TGGGGTAACA
9719280 TCTTCTTCTTT-T
1 TCTTCTT-TTTCT
*
9719292 TCTTCTTTCTCT
1 TCTTCTTTTTCT
*
9719304 TCTTCTTTTCCT
1 TCTTCTTTTTCT
9719316 TCTTCTT
1 TCTTCTT
9719323 CCTTTACCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 2 0.07
12 25 0.93
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
TCTTCTTTTTCT
Found at i:9719306 original size:21 final size:21
Alignment explanation
Indices: 9719280--9719319 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
9719270 TGGGGTAACA
*
9719280 TCTTCTTCTTTTTCTTCTTTC
1 TCTTCTTCTTTTCCTTCTTTC
9719301 TCTTCTTCTTTTCCTTCTT
1 TCTTCTTCTTTTCCTTCTT
9719320 CTTCCTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (21 bp):
TCTTCTTCTTTTCCTTCTTTC
Found at i:9737198 original size:3 final size:3
Alignment explanation
Indices: 9737190--9737256 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
9737180 TTCGAAACAA
* *
9737190 CTT CTT CTT CTT ATT CTT TTT CCTT C-T CTT CTT -TT CCTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT -CTT CTT CTT CTT CTT -CTT CTT CTT
*
9737235 -TT CTT -TT CTT -TT CTT CTA CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
9737257 AATACCTACA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
2 10 0.20
3 37 0.73
4 4 0.08
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:9737237 original size:12 final size:11
Alignment explanation
Indices: 9737191--9737251 Score: 65
Period size: 12 Copynumber: 5.6 Consensus size: 11
9737181 TCGAAACAAC
9737191 TTCTTCTTCTT
1 TTCTTCTTCTT
* *
9737202 ATTCTTTTTC-C
1 -TTCTTCTTCTT
9737213 TTC-TCTTCTT
1 TTCTTCTTCTT
9737223 TTCCTTCTTCTT
1 TT-CTTCTTCTT
9737235 TTCTT-TTCTT
1 TTCTTCTTCTT
9737245 TTCTTCT
1 TTCTTCT
9737252 ACTTCAATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
9 4 0.10
10 15 0.37
11 5 0.12
12 17 0.41
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (11 bp):
TTCTTCTTCTT
Found at i:9750546 original size:21 final size:21
Alignment explanation
Indices: 9750522--9750583 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
9750512 AATACCTGAT
* *
9750522 AAAATGTATCGATACTTTTTC
1 AAAAGGTATAGATACTTTTTC
* *
9750543 AAAAGGTATTGATACTTTTTG
1 AAAAGGTATAGATACTTTTTC
*
9750564 AAAAGGTATAAATACTTTTT
1 AAAAGGTATAGATACTTTTT
9750584 TTCATTATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (21 bp):
AAAAGGTATAGATACTTTTTC
Found at i:9751009 original size:15 final size:15
Alignment explanation
Indices: 9750991--9751019 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9750981 AATTTAAGGT
9750991 ATAAAGATTTGAAAC
1 ATAAAGATTTGAAAC
9751006 ATAAAGATTTGAAA
1 ATAAAGATTTGAAA
9751020 TATGCTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.14, T:0.28
Consensus pattern (15 bp):
ATAAAGATTTGAAAC
Found at i:9764474 original size:17 final size:17
Alignment explanation
Indices: 9764452--9764517 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 17
9764442 CTGTAGCATA
9764452 ATTGTCCTTGCATTTTT
1 ATTGTCCTTGCATTTTT
*
9764469 ATTGTCAC-TGTATTTTT
1 ATTGTC-CTTGCATTTTT
* **
9764486 ATTGTCGTTGCATTTAC
1 ATTGTCCTTGCATTTTT
*
9764503 ATTGTCATTGCATTT
1 ATTGTCCTTGCATTT
9764518 ACATATATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
17 40 0.98
18 1 0.02
ACGTcount: A:0.17, C:0.15, G:0.14, T:0.55
Consensus pattern (17 bp):
ATTGTCCTTGCATTTTT
Found at i:9771238 original size:4 final size:4
Alignment explanation
Indices: 9771229--9771306 Score: 79
Period size: 4 Copynumber: 18.8 Consensus size: 4
9771219 GCAACTCAAT
*
9771229 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TATT- TATA TTTA TTTA TTTTCA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA -TTT-A
*
9771279 TTTC TATT- TTTA TTTA TTTTA TTTA TTT
1 TTTA T-TTA TTTA TTTA -TTTA TTTA TTT
9771307 TCATTTTATG
Statistics
Matches: 64, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
3 3 0.05
4 46 0.72
5 14 0.22
6 1 0.02
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:9771312 original size:6 final size:5
Alignment explanation
Indices: 9771227--9771315 Score: 61
Period size: 4 Copynumber: 18.4 Consensus size: 5
9771217 AGGCAACTCA
9771227 ATTTT A-TTT A-TTT A-TTT A-TTT A-TTT A-TTT ATATTT ATATTT A-TTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT-TTT AT-TTT ATTTT
9771272 ATTTT CATTTCT ATTTT -TATTT ATTTT A-TTT ATTTT CATTTT AT
1 ATTTT -ATTT-T ATTTT AT-TTT ATTTT ATTTT ATTTT -ATTTT AT
9771316 GTCCAGGAAA
Statistics
Matches: 75, Mismatches: 0, Indels: 18
0.81 0.00 0.19
Matches are distributed among these distances:
4 33 0.44
5 17 0.23
6 24 0.32
7 1 0.01
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (5 bp):
ATTTT
Found at i:9773451 original size:108 final size:108
Alignment explanation
Indices: 9773262--9773468 Score: 310
Period size: 108 Copynumber: 1.9 Consensus size: 108
9773252 AAAATAAAAA
*
9773262 AATAAATTAGGAGTGTGTTGGACTGAGTAACCGGGATAGAGGGCTTGGGCTGTCATTCCATTTCG
1 AATAAATTAGGAGTGTGTTGGACTGAGTAACCGGGATAGAGGGCTTGGACTGTCATTCCATTTCG
* *
9773327 CATCAAAAGGGTCAATACATTCTTAAGTAAAAAAAATAATGAT
66 CATCAAAAGGGCCAATACATTCTTAAGCAAAAAAAATAATGAT
* * *
9773370 AATAAATTGGGAGTGTGTTAGG-CTGAGTAACCGGGAT-GGGGTGCTTGGATTGTCATTCCATTT
1 AATAAATTAGGAGTGTGTT-GGACTGAGTAACCGGGATAGAGG-GCTTGGACTGTCATTCCATTT
* *
9773433 TGCATCAAAAGGGCCAATATATTCTTAAGCAAAAAA
64 CGCATCAAAAGGGCCAATACATTCTTAAGCAAAAAA
9773469 GAAGAAAAGA
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 3 0.03
108 84 0.94
109 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (108 bp):
AATAAATTAGGAGTGTGTTGGACTGAGTAACCGGGATAGAGGGCTTGGACTGTCATTCCATTTCG
CATCAAAAGGGCCAATACATTCTTAAGCAAAAAAAATAATGAT
Found at i:9773977 original size:8 final size:8
Alignment explanation
Indices: 9773956--9773986 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
9773946 ATATGGAAGA
9773956 GAAAGTGTT
1 GAAAGTG-T
9773965 GAAAGTGT
1 GAAAGTGT
9773973 GAAAGTGT
1 GAAAGTGT
9773981 GAAAGT
1 GAAAGT
9773987 ATGGAAGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.68
9 7 0.32
ACGTcount: A:0.39, C:0.00, G:0.35, T:0.26
Consensus pattern (8 bp):
GAAAGTGT
Found at i:9795640 original size:123 final size:123
Alignment explanation
Indices: 9795493--9795846 Score: 538
Period size: 123 Copynumber: 2.9 Consensus size: 123
9795483 AATAATTTTG
*
9795493 TTAAATATT-AAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTT
1 TTAAATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTC
* * * * *
9795557 CATGTATTTCTTTAAAGGAACATTTCCATTTTAATATTAGATATTATACAAAAGGAAA
66 CATATATTTCTTTAAAGAAATATTTCCATTTTAATATGAGATATTATACAAAAAGAAA
*
9795615 TTGAATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTC
1 TTAAATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTC
* * *
9795680 CATATATTTTTTTAAAGAAATATTTCCATTTTAATATGATATATTATATAAAAAGAAA
66 CATATATTTCTTTAAAGAAATATTTCCATTTTAATATGAGATATTATACAAAAAGAAA
* *
9795738 TTAAATATTAAAAAC----AAGCTAATATCCTTTTGGAAAGGGTATAATGTTTTAATAAACCTTC
1 TTAAATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTC
*
9795799 CATATATTTCTCTAAAGAAATATATTTCCATTTTAATATGAGATATTA
66 CATATATTTCTTTAAAG-AA-ATATTTCCATTTTAATATGAGATATTA
9795847 AAATAAAAAG
Statistics
Matches: 213, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
119 59 0.28
120 2 0.01
121 26 0.12
122 8 0.04
123 118 0.55
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (123 bp):
TTAAATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTC
CATATATTTCTTTAAAGAAATATTTCCATTTTAATATGAGATATTATACAAAAAGAAA
Found at i:9800595 original size:21 final size:21
Alignment explanation
Indices: 9800571--9800611 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
9800561 AAATACCTAA
*
9800571 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATAGATACTTTTTG
9800592 AAAAGGTATAGATACTTTTT
1 AAAAGGTATAGATACTTTTT
9800612 TTCATTGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (21 bp):
AAAAGGTATAGATACTTTTTG
Found at i:9803710 original size:21 final size:21
Alignment explanation
Indices: 9803681--9803722 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9803671 GATACTTGAT
**
9803681 AAAAAGTATCGATACTTTTTG
1 AAAAAGTATAAATACTTTTTG
*
9803702 AAAAGGTATAAATACTTTTTG
1 AAAAAGTATAAATACTTTTTG
9803723 TCATTGTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (21 bp):
AAAAAGTATAAATACTTTTTG
Found at i:9804106 original size:33 final size:34
Alignment explanation
Indices: 9804061--9804128 Score: 120
Period size: 33 Copynumber: 2.0 Consensus size: 34
9804051 TGAATAAATT
*
9804061 GCTCTCCCTTATATAAAAATCATTTTTAATTTAA
1 GCTCTCCCTTATATAAAAATCATTTTCAATTTAA
9804095 GCTCT-CCTTATATAAAAATCATTTTCAATTTAA
1 GCTCTCCCTTATATAAAAATCATTTTCAATTTAA
9804128 G
1 G
9804129 GTATAAAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 28 0.85
34 5 0.15
ACGTcount: A:0.35, C:0.18, G:0.04, T:0.43
Consensus pattern (34 bp):
GCTCTCCCTTATATAAAAATCATTTTCAATTTAA
Found at i:9814730 original size:85 final size:85
Alignment explanation
Indices: 9814625--9814788 Score: 251
Period size: 85 Copynumber: 1.9 Consensus size: 85
9814615 CAAACCCCAT
*
9814625 CTTCCTGATGAGATACAGAGAAGTGGGTTAAAGT-AATAAAGCGACT-ATCTTCCTAATGAGATA
1 CTTCCTGATGAGATACAGAGAAGTGGATTAAA-TCAATAAAGCG-CTCATCTTCCTAATGAGATA
*
9814688 CAGAGAAGTGGACCAAATCCGC
64 CAGAGAAGTAGACCAAATCCGC
* * *
9814710 CTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCATCTTCCTGATGAGATACA
1 CTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATAAAGCGCTCATCTTCCTAATGAGATACA
9814775 GAGAAGTAGACCAA
66 GAGAAGTAGACCAA
9814789 TTCAATGAAG
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
84 2 0.03
85 70 0.97
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.23
Consensus pattern (85 bp):
CTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATAAAGCGCTCATCTTCCTAATGAGATACA
GAGAAGTAGACCAAATCCGC
Found at i:9814903 original size:209 final size:208
Alignment explanation
Indices: 9814543--9815122 Score: 786
Period size: 209 Copynumber: 2.8 Consensus size: 208
9814533 AACTTTAAAA
* * * *
9814543 GGTCATCTTTCTGATAAGATATAGAGAAGTAGACCAATTCAATGAAGCGAAGCTCAATGTGAGTG
1 GGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAATTCAATGAAGCGAAGCTCAATATGAGTG
** * *
9814608 AAACTTCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTTAAAGTAATAAAGCGACTAT
66 AAACTTCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCGAAGTAATAAAGGGTC-AT
* * *
9814673 CTTCCTAATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATGAGATACAGAGAAGTGGAT
130 CTTCTTGATGAGATACAGAGAAGTGGACCAAATCCACCTTCCTGATGAGATACAGAGAAGTGGAT
*
9814738 TAAATCAATGAAGC
195 TAAAACAATGAAGC
9814752 GGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAATTCAATGAAGCGAAGCTCAATATGAGTG
1 GGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAATTCAATGAAGCGAAGCTCAATATGAGTG
*
9814817 AAACTTCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGTGGTCAT
66 AAACTTCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCGAAGTAATAAAG-GGTCAT
* * * * * *
9814882 CTTCTTGACGAGATGCAGAGAAGTGAACCAAATCCATCTTTCTGATGAGATATAGAGAAGTGGAT
130 CTTCTTGATGAGATACAGAGAAGTGGACCAAATCCACCTTCCTGATGAGATACAGAGAAGTGGAT
9814947 TAAAACAATGAAGC
195 TAAAACAATGAAGC
* * * * * * * * ** *
9814961 AGACATCTTCTTAATGAGATACAAAGAAGTAGACCAAATT-GATGAAGCGGAGCTTAATACAAAT
1 GGTCATCTTCCTGATGAGATACAGAGAAGTAGACC-AATTCAATGAAGCGAAGCTCAATATGAGT
* * * * *
9815025 GAGACGT-CAAACCCCTATCTTCCTGATGAGATACAGAGAAGTGGGTCGATGTAATAAAACGATC
65 GAAACTTCCAAACCCC-ATCTTCCTGATGAGATACAGAGAAGTGGGTCGAAGTAAT-AAAGGGTC
9815089 ATCTTCTTGATGAGATACAGAGAAGTGGACCAAA
128 ATCTTCTTGATGAGATACAGAGAAGTGGACCAAA
9815123 AGATGAAGTT
Statistics
Matches: 328, Mismatches: 39, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
208 8 0.02
209 311 0.95
210 9 0.03
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (208 bp):
GGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAATTCAATGAAGCGAAGCTCAATATGAGTG
AAACTTCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCGAAGTAATAAAGGGTCATC
TTCTTGATGAGATACAGAGAAGTGGACCAAATCCACCTTCCTGATGAGATACAGAGAAGTGGATT
AAAACAATGAAGC
Found at i:9814980 original size:85 final size:85
Alignment explanation
Indices: 9814830--9814999 Score: 198
Period size: 85 Copynumber: 2.0 Consensus size: 85
9814820 CTTCCAAACC
* * * ** * *
9814830 CCATCTTCCTGATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGTGGTCATCTTCTTGACGAGA
1 CCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCAGACATCTTCTTAACGAGA
* *
9814895 TGCAGAGAAGT-GAACCAAAT
66 TACAAAGAAGTAG-ACCAAAT
* * * * *
9814915 CCATCTTTCTGATGAGATATAGAGAAGTGGATTAAAACAATGAAGCAGACATCTTCTTAATGAGA
1 CCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCAGACATCTTCTTAACGAGA
9814980 TACAAAGAAGTAGACCAAAT
66 TACAAAGAAGTAGACCAAAT
9815000 TGATGAAGCG
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
85 69 0.99
86 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (85 bp):
CCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCAGACATCTTCTTAACGAGA
TACAAAGAAGTAGACCAAAT
Found at i:9817075 original size:59 final size:59
Alignment explanation
Indices: 9817007--9817333 Score: 386
Period size: 60 Copynumber: 5.5 Consensus size: 59
9816997 CCCAAGAGGT
* * * * * * *
9817007 CCCTAAACTTTACAAAAATCATATTTTAACCCT-AAATTTTTCTAAGATTATATTTTCA
1 CCCTAAACTTTTCAAAAATCACATTTTAACCCTAAAACTTTCCCAAAATCATATTTTCA
* * * * * * *
9817065 CCCCTAAACTTTTCAAAAATCATATTTTGATCCTAAAACTTTTCTAAAATTACATTTTCA
1 -CCCTAAACTTTTCAAAAATCACATTTTAACCCTAAAACTTTCCCAAAATCATATTTTCA
* *
9817125 CCCTTAAACTTTTCCAAAATCACATTTTAACCCTAAAATTTTCCCAAAATCATATTTTCA
1 CCC-TAAACTTTTCAAAAATCACATTTTAACCCTAAAACTTTCCCAAAATCATATTTTCA
* *
9817185 CCCTCAAACTTTTCCAAAATCACATTTTAACCCTAAAACTTTCCCAAAATCATATTTTTA
1 CCCT-AAACTTTTCAAAAATCACATTTTAACCCTAAAACTTTCCCAAAATCATATTTTCA
* * * *
9817245 CCCTAAACTTTTCAAAAATCACAATTTAACCCTTAAACTTTCCTAAAATCATATTTTAA
1 CCCTAAACTTTTCAAAAATCACATTTTAACCCTAAAACTTTCCCAAAATCATATTTTCA
* * * *
9817304 CCCTAAAATTTCCCAAAATCATATTTTAAC
1 CCCTAAACTTTTCAAAAATCACATTTTAAC
9817334 TTCAAATTTT
Statistics
Matches: 238, Mismatches: 27, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
59 109 0.46
60 129 0.54
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (59 bp):
CCCTAAACTTTTCAAAAATCACATTTTAACCCTAAAACTTTCCCAAAATCATATTTTCA
Found at i:9817385 original size:28 final size:29
Alignment explanation
Indices: 9817309--9817387 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 29
9817299 TTTAACCCTA
* *
9817309 AAATTTC-CCAAAATCATATTTTAACTTC
1 AAATTTCTCCAAAATTACATTTTAACTTC
*
9817337 AAATTTTTCCAAAATTACATTTTAACCTT-
1 AAATTTCTCCAAAATTACATTTTAA-CTTC
9817366 AAA-TTCTCCAAAACTT-CATTTT
1 AAATTTCTCCAAAA-TTACATTTT
9817388 TTGACCCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
28 21 0.48
29 20 0.45
30 3 0.07
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (29 bp):
AAATTTCTCCAAAATTACATTTTAACTTC
Found at i:9817388 original size:29 final size:29
Alignment explanation
Indices: 9817010--9817378 Score: 293
Period size: 30 Copynumber: 12.5 Consensus size: 29
9817000 AAGAGGTCCC
*
9817010 TAAACTTTACAAAAATCATATTTTAACCC-
1 TAAACTTT-CCAAAATCATATTTTAACCCT
* * * * * *
9817039 TAAATTTTTCTAAGATTATATTTTCACCCC
1 TAAA-CTTTCCAAAATCATATTTTAACCCT
* * *
9817069 TAAACTTTTCAAAAATCATATTTTGATCCT
1 TAAAC-TTTCCAAAATCATATTTTAACCCT
* * * * *
9817099 AAAACTTTTCTAAAATTACATTTTCACCCT
1 TAAAC-TTTCCAAAATCATATTTTAACCCT
*
9817129 TAAACTTTTCCAAAATCACATTTTAACCCT
1 TAAAC-TTTCCAAAATCATATTTTAACCCT
* * *
9817159 AAAATTTTCCCAAAATCATATTTTCACCCT
1 TAAACTTT-CCAAAATCATATTTTAACCCT
* *
9817189 CAAACTTTTCCAAAATCACATTTTAACCCT
1 TAAAC-TTTCCAAAATCATATTTTAACCCT
* *
9817219 AAAACTTTCCCAAAATCATATTTTTACCC-
1 TAAACTTT-CCAAAATCATATTTTAACCCT
* * *
9817248 TAAACTTTTCAAAAATCACAATTTAACCCT
1 TAAAC-TTTCCAAAATCATATTTTAACCCT
9817278 TAAACTTTCCTAAAATCATATTTTAACCC-
1 TAAACTTTCC-AAAATCATATTTTAACCCT
*
9817307 TAAAATTTCCCAAAATCATATTTTAA--CT
1 TAAACTTT-CCAAAATCATATTTTAACCCT
* * *
9817335 TCAAATTTTTCCAAAATTACATTTTAA-CCT
1 T-AAA-CTTTCCAAAATCATATTTTAACCCT
9817365 TAAA-TTCTCCAAAA
1 TAAACTT-TCCAAAA
9817379 CTTCATTTTT
Statistics
Matches: 280, Mismatches: 45, Indels: 31
0.79 0.13 0.09
Matches are distributed among these distances:
27 3 0.01
28 8 0.03
29 93 0.33
30 173 0.62
31 3 0.01
ACGTcount: A:0.38, C:0.23, G:0.01, T:0.38
Consensus pattern (29 bp):
TAAACTTTCCAAAATCATATTTTAACCCT
Found at i:9820643 original size:25 final size:23
Alignment explanation
Indices: 9820614--9820660 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
9820604 TCGATAGTTA
9820614 CATAATAAGTATCGATAGTTCTGTT
1 CATAA-AAGTATCGATAG-TCTGTT
* *
9820639 CATAAGAGTATCGGTAGTCTGT
1 CATAAAAGTATCGATAGTCTGT
9820661 GTACTTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (23 bp):
CATAAAAGTATCGATAGTCTGTT
Found at i:9825929 original size:15 final size:15
Alignment explanation
Indices: 9825909--9825968 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
9825899 ATTTGAAAAA
9825909 TATTTTAATATAAAT
1 TATTTTAATATAAAT
*
9825924 TATTTTATTATAAAAT
1 TATTTTAATAT-AAAT
* * *
9825940 GTAATTTAAAATAAAA
1 -TATTTTAATATAAAT
*
9825956 TATTTTTATATAA
1 TATTTTAATATAA
9825969 TTTAATATAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
15 20 0.57
16 7 0.20
17 8 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TATTTTAATATAAAT
Found at i:9825991 original size:32 final size:32
Alignment explanation
Indices: 9825921--9825991 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 32
9825911 TTTTAATATA
*
9825921 AATTAT-TTTATTATAAAATGTAATTTAAAAT
1 AATTATATTTATTATAAAATGTAATTAAAAAT
* * *
9825952 AA-AATATTT-TTATATAATTTAATATAAAAAT
1 AATTATATTTATTATAAAATGTAAT-TAAAAAT
9825983 AATTATATT
1 AATTATATT
9825992 AAGAATGTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
30 14 0.44
31 13 0.41
32 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (32 bp):
AATTATATTTATTATAAAATGTAATTAAAAAT
Found at i:9826033 original size:14 final size:16
Alignment explanation
Indices: 9826016--9826053 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
9826006 ATTATATATT
*
9826016 ATTA-ATTTTATAA-A
1 ATTATATTTAATAATA
9826030 ATTATATTTAATAATA
1 ATTATATTTAATAATA
9826046 ATTATATT
1 ATTATATT
9826054 AAAATATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 8 0.38
16 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTATATTTAATAATA
Found at i:9826050 original size:24 final size:23
Alignment explanation
Indices: 9825983--9826051 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 23
9825973 ATATAAAAAT
* * *
9825983 AATTATA-TTAAGAATGTTATTA
1 AATTATATTTAATAATATTATAA
* *
9826005 AATTATATATTATTAATTTTATAA
1 AATTATAT-TTAATAATATTATAA
9826029 AATTATATTTAATAATAATTATA
1 AATTATATTTAATAAT-ATTATA
9826052 TTAAAATATG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 7 0.18
23 7 0.18
24 24 0.63
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (23 bp):
AATTATATTTAATAATATTATAA
Found at i:9826093 original size:61 final size:62
Alignment explanation
Indices: 9825957--9826109 Score: 184
Period size: 61 Copynumber: 2.5 Consensus size: 62
9825947 AAAATAAAAT
* * * * * * *
9825957 ATTTTTATATAATTTA-ATATAAAAATAATTATATTAAGAATGTTATTAAATTATATATTATT
1 ATTTTTAT-TAAATTATATTTAATAATAATTATATTAAGAATATGATTAAAATATATATTATC
* * *
9826019 AATTTTATAAAATTATATTTAATAATAATTATATTAA-AATATGATTAAAATATTTATTATC
1 ATTTTTATTAAATTATATTTAATAATAATTATATTAAGAATATGATTAAAATATATATTATC
*
9826080 ATTTTTATTAAATTATACTTAATAATAATT
1 ATTTTTATTAAATTATATTTAATAATAATT
9826110 TTGTTATATT
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
61 51 0.66
62 26 0.34
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (62 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAGAATATGATTAAAATATATATTATC
Found at i:9826266 original size:44 final size:46
Alignment explanation
Indices: 9826216--9826304 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 46
9826206 ATCTATTATA
*
9826216 TCAACCAAACACA-AGAA-TA-TTATTACAA-TTCTATTCCATTACAT
1 TCAACCAAACA-ATAGAATTACTGATTACAACTT-TATTCCATTACAT
*
9826260 TCAACCAAACAATTGAATTACTGATTACAACTTTATTCCATTACA
1 TCAACCAAACAATAGAATTACTGATTACAACTTTATTCCATTACA
9826305 ACCCTATTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
43 1 0.03
44 14 0.36
45 2 0.05
46 20 0.51
47 2 0.05
ACGTcount: A:0.42, C:0.22, G:0.03, T:0.33
Consensus pattern (46 bp):
TCAACCAAACAATAGAATTACTGATTACAACTTTATTCCATTACAT
Found at i:9826845 original size:23 final size:23
Alignment explanation
Indices: 9826811--9826865 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
9826801 AACTTAAGGG
*
9826811 TTGACACTTATCATTCTGTTATA
1 TTGACACTTATCATTCTCTTATA
9826834 TTGACA-TCTATCATTCTCTTATA
1 TTGACACT-TATCATTCTCTTATA
*
9826857 TGGACACTT
1 TTGACACTT
9826866 GTCAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 1 0.04
23 26 0.93
24 1 0.04
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.45
Consensus pattern (23 bp):
TTGACACTTATCATTCTCTTATA
Found at i:9831637 original size:29 final size:27
Alignment explanation
Indices: 9831570--9831647 Score: 66
Period size: 29 Copynumber: 2.7 Consensus size: 27
9831560 AAACAAAACA
* *
9831570 GAGGGATAAAACGCAATTTTTGGATACTC
1 GAGGG-TAAAACGTAA-TTTTGGACACTC
* *
9831599 GGGGGCAAAACGGTAATTTTGGACACTTC
1 GAGGGTAAAAC-GTAATTTTGGACAC-TC
*
9831628 GAGGGTAAAATAGTAATTTT
1 GAGGGTAAAA-CGTAATTTT
9831648 AAAGGTTAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
28 14 0.36
29 25 0.64
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (27 bp):
GAGGGTAAAACGTAATTTTGGACACTC
Found at i:9831694 original size:28 final size:29
Alignment explanation
Indices: 9831663--9831723 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
9831653 TTAAGAGTCA
*
9831663 AAAATGG-AATTTT-TGGAAATTTGAGGGT
1 AAAATGGTAATTTTGT-GAAATTTAAGGGT
*
9831691 AAAATGGTAATTTTGTGAAGTTTAAGGGT
1 AAAATGGTAATTTTGTGAAATTTAAGGGT
9831720 AAAA
1 AAAA
9831724 ATATGATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.24
29 21 0.72
30 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTGTGAAATTTAAGGGT
Found at i:9831694 original size:29 final size:30
Alignment explanation
Indices: 9831653--9831725 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
9831643 ATTTTAAAGG
*
9831653 TTAAGAGTCAAAAATGG-AATTTT-TGGAAAT
1 TTAAGGGT-AAAAATGGTAATTTTGT-GAAAT
* *
9831683 TTGAGGGT-AAAATGGTAATTTTGTGAAGT
1 TTAAGGGTAAAAATGGTAATTTTGTGAAAT
9831712 TTAAGGGTAAAAAT
1 TTAAGGGTAAAAAT
9831726 ATGATTTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 7 0.19
29 17 0.47
30 12 0.33
ACGTcount: A:0.40, C:0.01, G:0.25, T:0.34
Consensus pattern (30 bp):
TTAAGGGTAAAAATGGTAATTTTGTGAAAT
Found at i:9832653 original size:20 final size:22
Alignment explanation
Indices: 9832614--9832653 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
9832604 ATCTTATTGC
*
9832614 TTGGAAGAATCCTCAGATCTAT
1 TTGGAAGAACCCTCAGATCTAT
9832636 TTGGAA-AACCCT-AGATCT
1 TTGGAAGAACCCTCAGATCT
9832654 GGGTTCGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 5 0.29
22 6 0.35
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (22 bp):
TTGGAAGAACCCTCAGATCTAT
Found at i:9832869 original size:7 final size:7
Alignment explanation
Indices: 9832854--9832894 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
9832844 TCCCTTTTTC
9832854 TTTATTA
1 TTTATTA
*
9832861 TTTAATA
1 TTTATTA
9832868 TTTATTA
1 TTTATTA
9832875 -TTATTA
1 TTTATTA
9832881 -TTATATA
1 TTTAT-TA
9832888 TTTATTA
1 TTTATTA
9832895 CTATATTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 10 0.33
7 16 0.53
8 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (7 bp):
TTTATTA
Found at i:9832880 original size:20 final size:21
Alignment explanation
Indices: 9832855--9832903 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
9832845 CCCTTTTTCT
9832855 TTATTATTTA-ATATTTATTA
1 TTATTATTTATATATTTATTA
9832875 TTATTA-TTATATATTTATTA
1 TTATTATTTATATATTTATTA
*
9832895 CTA-TATTTA
1 TTATTATTTA
9832904 CTAAATGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATTATTTATATATTTATTA
Found at i:9833524 original size:6 final size:6
Alignment explanation
Indices: 9833503--9833645 Score: 100
Period size: 6 Copynumber: 24.0 Consensus size: 6
9833493 TTTTTAGACT
* *
9833503 TTTAAA -TTAAA TTTAAA ATTAAA TTTAAAACCA TTTCAAA TTTAAA -CTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT--AA--A TTT-AAA TTTAAA TTTAAA
** **
9833554 TTTAAA TTTAAA -ACAAA TTTAAA TTTAAA AATAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** * *
9833601 TTTAAA -ATAAA TTTAAA ACT-AA TTTAAA CTT-AA TATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
9833646 ATCAAAAGTT
Statistics
Matches: 104, Mismatches: 23, Indels: 20
0.71 0.16 0.14
Matches are distributed among these distances:
5 22 0.21
6 70 0.67
7 4 0.04
8 2 0.02
9 2 0.02
10 4 0.04
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:9833618 original size:11 final size:11
Alignment explanation
Indices: 9833573--9833628 Score: 69
Period size: 11 Copynumber: 4.9 Consensus size: 11
9833563 AAAACAAATT
9833573 TAAATTTAAAAA
1 TAAATTT-AAAA
*
9833585 TAAATTTAAATT
1 TAAATTTAAA-A
9833597 TAAATTTAAAA
1 TAAATTTAAAA
9833608 TAAATTTAAAA
1 TAAATTTAAAA
9833619 CT-AATTTAAA
1 -TAAATTTAAA
9833629 CTTAATATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
11 22 0.55
12 18 0.45
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:9833634 original size:11 final size:11
Alignment explanation
Indices: 9833541--9833644 Score: 64
Period size: 11 Copynumber: 9.2 Consensus size: 11
9833531 AACCATTTCA
* *
9833541 AATTTAAACTA
1 AATTTAAATTT
9833552 AATTTAAATTT
1 AATTTAAATTT
***
9833563 AAAACAAATTT
1 AATTTAAATTT
* *
9833574 AAATTTAAAAATA
1 -AATTT-AAATTT
9833587 AATTTAAATTT
1 AATTTAAATTT
* *
9833598 AAATTTAAAATA
1 -AATTTAAATTT
**
9833610 AATTTAAAACT
1 AATTTAAATTT
*
9833621 AATTTAAACTT
1 AATTTAAATTT
*
9833632 AATATAAATTT
1 AATTTAAATTT
9833643 AA
1 AA
9833645 AATCAAAAGT
Statistics
Matches: 70, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
11 50 0.71
12 16 0.23
13 4 0.06
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:9833642 original size:17 final size:17
Alignment explanation
Indices: 9833503--9833645 Score: 123
Period size: 17 Copynumber: 8.4 Consensus size: 17
9833493 TTTTTAGACT
*
9833503 TTTAAA-TTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
* **
9833520 ATTAAATTTAAAA-CCA
1 TTTAAATTTAAAATAAA
*
9833536 TTTCAAATTTAAACTAAA
1 TTT-AAATTTAAAATAAA
*
9833554 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
9833571 TTTAAATTTAAAAATAAA
1 TTTAAATTT-AAAATAAA
*
9833589 TTTAAATTTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
*
9833607 -ATAAATTTAAAACT-AA
1 TTTAAATTTAAAA-TAAA
* *
9833623 TTTAAACTTAATATAAA
1 TTTAAATTTAAAATAAA
9833640 TTTAAA
1 TTTAAA
9833646 ATCAAAAGTT
Statistics
Matches: 101, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
16 6 0.06
17 66 0.65
18 29 0.29
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:9834406 original size:209 final size:209
Alignment explanation
Indices: 9834034--9834826 Score: 1066
Period size: 209 Copynumber: 3.8 Consensus size: 209
9834024 CTTTACTAGA
* * * * * * * *
9834034 AAGACGAATTTGGTTCACTTCTCTGTGTCTCGTCAGGAAGATGACCATTTTATTATTTCAACCTG
1 AAGACGGATCTGGTTCACTTCTCTATATCTCATCAGGAAGATAACCATTTTATTACTTCGACCTG
* * * *
9834099 CTTCTCCGTACCTCATCAGGAAGCTGGGGTCCGAAGATTTGCTCACTTTGAGCCTGGTTTCGTTG
66 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTGGTTTCATTG
* * *
9834164 ATTTGGTCTACTTCTCGGTATCTCATTAGGAAGACGACCGCATCACTTGTTTTGATCCACTTCTC
131 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTC
9834229 TGTGTCTCATCAGG
196 TGTGTCTCATCAGG
* * * ** *
9834243 AAGATGGATCTGGTTCACTTATCTATATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTG
1 AAGACGGATCTGGTTCACTTCTCTATATCTCATCAGGAAGATAACCATTTTATTACTTCGACCTG
* * * * *
9834308 CTTCTTAGTATCTAATTAGGAAGCTGGGGTTCGAAAATTTGCTCACTTTGAGCCTGGTTTCGTTG
66 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTGGTTTCATTG
9834373 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTC
131 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTC
9834438 TGTGTCTCATCAGG
196 TGTGTCTCATCAGG
* * * * ** *
9834452 AAGACGGATCTGGTTCACTTCTCTGTATCTCATTAAGAAGTTAACCGGTTTATTGCTTCGACCTG
1 AAGACGGATCTGGTTCACTTCTCTATATCTCATCAGGAAGATAACCATTTTATTACTTCGACCTG
* * * *
9834517 CTTCTTAGTATCTCATTAGGAAGTTGGGGTTCGAAGATTTGCTCACTTTGAGTCTGGTTTCATTG
66 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTGGTTTCATTG
* * * ** **
9834582 ATTTGGTCTACTTCTCAATACCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCTGCTTCTC
131 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTC
*
9834647 TGTATCTCATCAGG
196 TGTGTCTCATCAGG
* * * * *
9834661 AAGACGAATTTGGTCCACTTCTC-AGTATCTCATCAGAAAGCTAACCATTTTATTACTTCGACCT
1 AAGACGGATCTGGTTCACTTCTCTA-TATCTCATCAGGAAGATAACCATTTTATTACTTCGACCT
**
9834725 GCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTTGAGCCTTATTTCAT
65 GCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAC-TTTGAGCCTGGTTTCAT
* **
9834790 TGATTTGGTATACTTCTTTGTATCTCATCAGGAAGAT
129 TGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGAT
9834827 AATCGCCTCG
Statistics
Matches: 515, Mismatches: 67, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
209 470 0.91
210 45 0.09
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (209 bp):
AAGACGGATCTGGTTCACTTCTCTATATCTCATCAGGAAGATAACCATTTTATTACTTCGACCTG
CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTGGTTTCATTG
ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTC
TGTGTCTCATCAGG
Found at i:9846713 original size:29 final size:28
Alignment explanation
Indices: 9846665--9846843 Score: 159
Period size: 29 Copynumber: 6.2 Consensus size: 28
9846655 AGGTTCAGGT
*
9846665 TAAAATGGAATTTTTAGAAATTTAGGGG
1 TAAAATGGAATTTTTGGAAATTTAGGGG
*
9846693 TAAAATGGTAAGTTTTGGAAAGTTT-GGGG
1 TAAAATGG-AATTTTTGGAAA-TTTAGGGG
* *
9846722 TTTAAAAATAGAATTTTTGGAAATTTAGAGG
1 --T-AAAATGGAATTTTTGGAAATTTAGGGG
*
9846753 TAAAATGGTAA-TTTTGGAAAGTTTAGGGT
1 TAAAATGG-AATTTTTGGAAA-TTTAGGGG
*
9846782 TAAAATGGAATTTTTGGAAA-TTCGAGGG
1 TAAAATGGAATTTTTGGAAATTTAG-GGG
* * *
9846810 CAAAATGTAATTTTTGTGAAGTTT-GAGGG
1 TAAAATGGAATTTTTG-GAAATTTAG-GGG
9846839 TAAAA
1 TAAAA
9846844 ATATGATTTC
Statistics
Matches: 125, Mismatches: 14, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
27 3 0.02
28 41 0.33
29 52 0.42
30 8 0.06
31 15 0.12
32 6 0.05
ACGTcount: A:0.37, C:0.01, G:0.26, T:0.36
Consensus pattern (28 bp):
TAAAATGGAATTTTTGGAAATTTAGGGG
Found at i:9846736 original size:60 final size:57
Alignment explanation
Indices: 9846662--9846845 Score: 221
Period size: 57 Copynumber: 3.2 Consensus size: 57
9846652 TAGAGGTTCA
* * *
9846662 GGTTAAAATGGAATTTTTAGAAATTTAGGGGTAAAATGGTAAGTTTTGGAAAGTTTGG
1 GGTTAAAATGGAATTTTTGGAAATTTAGAGGTAAAATGGTAA-TTTTGGAAAGTTTAG
*
9846720 GGTTTAAAAATAGAATTTTTGGAAATTTAGAGGTAAAATGGTAATTTTGGAAAGTTTAG
1 GG-TT-AAAATGGAATTTTTGGAAATTTAGAGGTAAAATGGTAATTTTGGAAAGTTTAG
* *
9846779 GGTTAAAATGGAATTTTTGGAAA-TTCGAGGGCAAAAT-GTAATTTTTGTG-AAGTTTGAG
1 GGTTAAAATGGAATTTTTGGAAATTTAGA-GGTAAAATGGTAA-TTTTG-GAAAGTTT-AG
*
9846837 GGTAAAAAT
1 GGTTAAAAT
9846846 ATGATTTCTA
Statistics
Matches: 112, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
56 8 0.07
57 36 0.32
58 15 0.13
59 18 0.16
60 35 0.31
ACGTcount: A:0.36, C:0.01, G:0.27, T:0.36
Consensus pattern (57 bp):
GGTTAAAATGGAATTTTTGGAAATTTAGAGGTAAAATGGTAATTTTGGAAAGTTTAG
Found at i:9847986 original size:6 final size:7
Alignment explanation
Indices: 9847964--9848000 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
9847954 TCTTCCCTTT
9847964 TTATTTA
1 TTATTTA
9847971 TTATTTA
1 TTATTTA
9847978 TTA-TTA
1 TTATTTA
9847984 TTA-TTA
1 TTATTTA
9847990 TATATTTA
1 T-TATTTA
9847998 TTA
1 TTA
9848001 CTATATTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 10 0.36
7 14 0.50
8 4 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TTATTTA
Found at i:9848654 original size:17 final size:17
Alignment explanation
Indices: 9848611--9848700 Score: 77
Period size: 17 Copynumber: 5.6 Consensus size: 17
9848601 TTTGGACTTT
9848611 TAAA-TTAAATTTAAAA
1 TAAATTTAAATTTAAAA
**
9848627 -CCATTTCAAATTTAAAA
1 TAAATTT-AAATTTAAAA
9848644 TAAATTTAAATTT-AAA
1 TAAATTTAAATTTAAAA
9848660 -AAA--TAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
9848674 CT-AATTTAAACTTAATA
1 -TAAATTTAAATTTAAAA
9848691 TAAATTTAAA
1 TAAATTTAAA
9848701 ATCAAAAGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
13 7 0.12
14 3 0.05
15 6 0.10
16 6 0.10
17 33 0.56
18 4 0.07
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:9848842 original size:61 final size:61
Alignment explanation
Indices: 9848774--9848901 Score: 170
Period size: 61 Copynumber: 2.1 Consensus size: 61
9848764 TAACCCTAAA
* * * * *
9848774 AATAATTATATTAAGAAT-GTTATTAAATTATATATTTTTA-TTTTATTAAATTATATTTAAT
1 AATAATTATATTAA-AATAG-GACTAAATTATATATTATAATTTTTATTAAATTATATTTAAC
*
9848835 AATAATTATATTAAAATAGGACTAAATTATTTATTATAATTTTTATTAAATTATATTTAAC
1 AATAATTATATTAAAATAGGACTAAATTATATATTATAATTTTTATTAAATTATATTTAAC
9848896 AATAAT
1 AATAAT
9848902 CCTGTTATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
60 18 0.31
61 41 0.69
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (61 bp):
AATAATTATATTAAAATAGGACTAAATTATATATTATAATTTTTATTAAATTATATTTAAC
Found at i:9848925 original size:6 final size:6
Alignment explanation
Indices: 9848916--9848942 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
9848906 TTATATTTAT
9848916 TAACAA TAACAA TAACAA TAACAA TAA
1 TAACAA TAACAA TAACAA TAACAA TAA
9848943 TCATCTACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.19
Consensus pattern (6 bp):
TAACAA
Found at i:9849074 original size:44 final size:44
Alignment explanation
Indices: 9849019--9849121 Score: 197
Period size: 44 Copynumber: 2.3 Consensus size: 44
9849009 AATATTTATC
9849019 ACATTCAACCAAACATAAATATACTATTATAGTTCTATTCCATT
1 ACATTCAACCAAACATAAATATACTATTATAGTTCTATTCCATT
*
9849063 ACATTCTACCAAACATAAATATACTATTATAGTTCTATTCCATT
1 ACATTCAACCAAACATAAATATACTATTATAGTTCTATTCCATT
9849107 ACATTCAACCAAACA
1 ACATTCAACCAAACA
9849122 ATTGAATTAC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.42, C:0.22, G:0.02, T:0.34
Consensus pattern (44 bp):
ACATTCAACCAAACATAAATATACTATTATAGTTCTATTCCATT
Found at i:9849177 original size:16 final size:16
Alignment explanation
Indices: 9849152--9849196 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
9849142 TTTATTTCAC
*
9849152 TACAGTCCTATTCCAT
1 TACAGCCCTATTCCAT
*
9849168 TATAGCCCTATTCCAT
1 TACAGCCCTATTCCAT
*
9849184 TACAGCCTTATTC
1 TACAGCCCTATTC
9849197 AATTCTAGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.24, C:0.31, G:0.07, T:0.38
Consensus pattern (16 bp):
TACAGCCCTATTCCAT
Found at i:9850394 original size:29 final size:28
Alignment explanation
Indices: 9850337--9850403 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
9850327 TAAATTTTAA
* *
9850337 AATTATATATGAACTTTAATTTAATGTGC
1 AATTATATATAAACTTTAATTT-AGGTGC
9850366 AATTATATATAAAGACTTTAATTT-GGTGC
1 AATTATATAT-AA-ACTTTAATTTAGGTGC
9850395 AATTATATA
1 AATTATATA
9850404 CGTGAAACTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 23 0.68
30 1 0.03
31 10 0.29
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.43
Consensus pattern (28 bp):
AATTATATATAAACTTTAATTTAGGTGC
Found at i:9851562 original size:18 final size:20
Alignment explanation
Indices: 9851541--9851586 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
9851531 TTTAATTTTG
9851541 TTTTTAAT-TTTTTAAA-TA
1 TTTTTAATATTTTTAAATTA
9851559 -TTTTAATATTTTTAAATTA
1 TTTTTAATATTTTTAAATTA
9851578 TTTGTTAAT
1 TTT-TTAAT
9851587 GTGTTATGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 7 0.29
18 8 0.33
19 2 0.08
20 2 0.08
21 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTAATATTTTTAAATTA
Found at i:9853522 original size:19 final size:19
Alignment explanation
Indices: 9853488--9853533 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
9853478 TTTTTAAAAA
*
9853488 TTAAAAATCATGAAAATTAT
1 TTAAAAATCATAAAAATT-T
9853508 TTAAAAAT-ATAAAAATTT
1 TTAAAAATCATAAAAATTT
*
9853526 TAAAAAAT
1 TTAAAAAT
9853534 TAATTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 8 0.33
20 8 0.33
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
TTAAAAATCATAAAAATTT
Found at i:9853664 original size:15 final size:15
Alignment explanation
Indices: 9853633--9853664 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
9853623 TTAAAAAAAC
9853633 AAAAATTAAAAACTA
1 AAAAATTAAAAACTA
*
9853648 AAAAATTAAAAATTA
1 AAAAATTAAAAACTA
9853663 AA
1 AA
9853665 TGAAGGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAAATTAAAAACTA
Found at i:9854958 original size:32 final size:32
Alignment explanation
Indices: 9854903--9854967 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
9854893 ATTTGATTTT
9854903 AAATATTATAATAATTAAGAATAT-TAAAATC
1 AAATATTATAATAATTAAGAATATATAAAATC
* * *
9854934 AAATTTTATAATTAATTTATAATATATAAAATC
1 AAATATTATAA-TAATTAAGAATATATAAAATC
9854967 A
1 A
9854968 CGAGTTTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 10 0.34
32 11 0.38
33 8 0.28
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (32 bp):
AAATATTATAATAATTAAGAATATATAAAATC
Found at i:9862686 original size:6 final size:6
Alignment explanation
Indices: 9862675--9862728 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
9862665 TTTTTAATGT
* * *
9862675 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAATCA AATTAA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
9862723 AATTTA
1 AATTTA
9862729 TTATTAATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:9865988 original size:8 final size:8
Alignment explanation
Indices: 9865977--9866004 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
9865967 TTTTATAAGT
9865977 TTTTGAAA
1 TTTTGAAA
9865985 TTTTGAAA
1 TTTTGAAA
9865993 TTTTGAAA
1 TTTTGAAA
9866001 TTTT
1 TTTT
9866005 AAAAAGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (8 bp):
TTTTGAAA
Found at i:9870497 original size:14 final size:14
Alignment explanation
Indices: 9870478--9870506 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9870468 TTCTAATTTA
9870478 TCCCCTGAAAACGG
1 TCCCCTGAAAACGG
9870492 TCCCCTGAAAACGG
1 TCCCCTGAAAACGG
9870506 T
1 T
9870507 GCCACATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.34, G:0.21, T:0.17
Consensus pattern (14 bp):
TCCCCTGAAAACGG
Found at i:9874172 original size:25 final size:25
Alignment explanation
Indices: 9874144--9874249 Score: 158
Period size: 25 Copynumber: 4.2 Consensus size: 25
9874134 CTAGCTCTGT
*
9874144 AGAGCGATATTCTGTCTGGCTCGTA
1 AGAGCAATATTCTGTCTGGCTCGTA
9874169 AGAGCAATATTCTGTCTGGCTCGTA
1 AGAGCAATATTCTGTCTGGCTCGTA
* *
9874194 AGAGCAATGTTCTGACTGGCTCGTA
1 AGAGCAATATTCTGTCTGGCTCGTA
* *
9874219 AGAGCGATATTTTGTCTAGGCTCGTA
1 AGAGCAATATTCTGTCT-GGCTCGTA
9874245 AGAGC
1 AGAGC
9874250 TAAATTTTTG
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
25 60 0.82
26 13 0.18
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (25 bp):
AGAGCAATATTCTGTCTGGCTCGTA
Found at i:9876255 original size:15 final size:15
Alignment explanation
Indices: 9876235--9876265 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9876225 AACCTTTTCC
9876235 TATGTTTTTTGATTG
1 TATGTTTTTTGATTG
*
9876250 TATGTTTTTTGGTTG
1 TATGTTTTTTGATTG
9876265 T
1 T
9876266 CATGCAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.00, G:0.23, T:0.68
Consensus pattern (15 bp):
TATGTTTTTTGATTG
Found at i:9876982 original size:20 final size:19
Alignment explanation
Indices: 9876957--9876995 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
9876947 TAGTGCTTAT
9876957 AAAATAA-ATAATAAAGAAAA
1 AAAATAAGA-AAT-AAGAAAA
9876977 AAAATAAGAAATAAGAAAA
1 AAAATAAGAAATAAGAAAA
9876996 GTTCATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 10 0.56
21 1 0.06
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (19 bp):
AAAATAAGAAATAAGAAAA
Found at i:9877376 original size:19 final size:18
Alignment explanation
Indices: 9877323--9877380 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
9877313 AAAATATAGA
9877323 TTATTAAAAAT-TAAAAT
1 TTATTAAAAATATAAAAT
*
9877340 TTATAAAAGGAAT-TAAAAT
1 TTATTAAA--AATATAAAAT
*
9877359 TTATTAAAAATATAAAAA
1 TTATTAAAAATATAAAAT
9877377 TTAT
1 TTAT
9877381 ATGTTCTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 10 0.29
18 9 0.26
19 16 0.46
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TTATTAAAAATATAAAAT
Found at i:9877550 original size:11 final size:11
Alignment explanation
Indices: 9877518--9877567 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
9877508 GAGCTTCTTA
9877518 AAATAATTTTT
1 AAATAATTTTT
*
9877529 --ATAA-ATTT
1 AAATAATTTTT
*
9877537 AAATACTTTTT
1 AAATAATTTTT
9877548 AAATAATTTTT
1 AAATAATTTTT
*
9877559 AAAGAATTT
1 AAATAATTT
9877568 AAAGGAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
8 3 0.10
9 4 0.13
10 3 0.10
11 21 0.68
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (11 bp):
AAATAATTTTT
Found at i:9879024 original size:16 final size:17
Alignment explanation
Indices: 9878985--9879017 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9878975 GACCAAAATT
9878985 TAAT-AAATATATAATGG
1 TAATAAAATATATAAT-G
9879002 TAATAAAATATATAAT
1 TAATAAAATATATAAT
9879018 TATTAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
TAATAAAATATATAATG
Found at i:9879063 original size:18 final size:17
Alignment explanation
Indices: 9879032--9879065 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9879022 AAATTAAATA
9879032 TTAAAAAAACAATATAT
1 TTAAAAAAACAATATAT
*
9879049 TTAAAAATAATAATATA
1 TTAAAAA-AACAATATA
9879066 AGGAGTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAAAAAAACAATATAT
Found at i:9886894 original size:19 final size:19
Alignment explanation
Indices: 9886866--9886904 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
9886856 TTTATGGTTT
9886866 TAAATAATTTTTGGGTAAAA
1 TAAATAA-TTTTGGGTAAAA
*
9886886 TAAAT-ATTTTGGGTTAAA
1 TAAATAATTTTGGGTAAAA
9886904 T
1 T
9886905 TGGAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 1 0.06
20 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (19 bp):
TAAATAATTTTGGGTAAAA
Found at i:9890855 original size:14 final size:15
Alignment explanation
Indices: 9890836--9890864 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9890826 TCAGAAAAAC
9890836 CTTTTATT-TATTTT
1 CTTTTATTATATTTT
9890850 CTTTTATTATATTTT
1 CTTTTATTATATTTT
9890865 ATTAAATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTTTATTATATTTT
Found at i:9911226 original size:12 final size:12
Alignment explanation
Indices: 9911195--9911237 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
9911185 CAATACTTTC
9911195 TTCTTCTTCCTT
1 TTCTTCTTCCTT
* *
9911207 CTCCTCTTCCTT
1 TTCTTCTTCCTT
* *
9911219 TTCTTCTTTCTC
1 TTCTTCTTCCTT
9911231 TTCTTCT
1 TTCTTCT
9911238 CTTACTCCTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (12 bp):
TTCTTCTTCCTT
Found at i:9916602 original size:14 final size:14
Alignment explanation
Indices: 9916583--9916613 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
9916573 GTTGAGAAAA
9916583 CAGTAGATAGATCT
1 CAGTAGATAGATCT
9916597 CAGTAGATAGATCT
1 CAGTAGATAGATCT
9916611 CAG
1 CAG
9916614 CAGCCGCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (14 bp):
CAGTAGATAGATCT
Found at i:9918737 original size:80 final size:81
Alignment explanation
Indices: 9918592--9918750 Score: 230
Period size: 80 Copynumber: 2.0 Consensus size: 81
9918582 AGCCAAATGG
* ** * *
9918592 AACCAATCATTTTATTATTCATCAATTATCACAAAAACTATTGTTCTAGTGATAGAAAGCAAAGC
1 AACCAATCATTTTATTATTCATCAATTATCACAAAAACAATCATTCTACTGATAGAAAACAAAGC
9918657 AGAGTCAAGATCCAAC
66 AGAGTCAAGATCCAAC
* * * *
9918673 AACCATTCATTTTATTATTCGTCCATTATCA-GAAAACAATCATTCTACTGATAGAAAACAAAGC
1 AACCAATCATTTTATTATTCATCAATTATCACAAAAACAATCATTCTACTGATAGAAAACAAAGC
9918737 AGAGTCAAGATCCA
66 AGAGTCAAGATCCA
9918751 GCACCTTGCA
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
80 41 0.59
81 28 0.41
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (81 bp):
AACCAATCATTTTATTATTCATCAATTATCACAAAAACAATCATTCTACTGATAGAAAACAAAGC
AGAGTCAAGATCCAAC
Done.