Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 3 of 182
Found at i:800987 original size:11 final size:11
Alignment explanation
Indices: 800934--800987 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 11
800924 TATTTTTACA
800934 TAAAAATAAATT
1 TAAAAATAAA-T
*
800946 TAAAAAAATAAT
1 TAAAAATA-AAT
800958 ATAACAAATAAAT
1 -TAA-AAATAAAT
*
800971 TGAAAATAAAT
1 TAAAAATAAAT
800982 TAAAAA
1 TAAAAA
800988 ATCTTTATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
11 13 0.37
12 10 0.29
13 8 0.23
14 4 0.11
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (11 bp):
TAAAAATAAAT
Found at i:801857 original size:36 final size:36
Alignment explanation
Indices: 801806--801875 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
801796 AAAACAACTT
*
801806 ACTTACACCGGTGTAAGTATGATTGCTTTAATCATA
1 ACTTACACCGATGTAAGTATGATTGCTTTAATCATA
801842 ACTTACACCGATGTAAGTATGATTGCTTTAATCA
1 ACTTACACCGATGTAAGTATGATTGCTTTAATCA
801876 AGTTTGGGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (36 bp):
ACTTACACCGATGTAAGTATGATTGCTTTAATCATA
Found at i:807943 original size:15 final size:14
Alignment explanation
Indices: 807906--807944 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
807896 CATATAATTT
807906 TTTAAATTAATATA
1 TTTAAATTAATATA
**
807920 TTTTTATTATATATA
1 TTTAAATTA-ATATA
807935 TTTAAATTAA
1 TTTAAATTAA
807945 ATTAAAAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTAAATTAATATA
Found at i:810906 original size:45 final size:45
Alignment explanation
Indices: 810855--810947 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
810845 AAAATAATAG
810855 AAATTTGATTTAATCCTTTAAGAAATTATAAAGATATAGACTATT
1 AAATTTGATTTAATCCTTTAAGAAATTATAAAGATATAGACTATT
810900 AAATTTGATTTAATCCTTTAAGAAATTATAAAGATATAGACTATT
1 AAATTTGATTTAATCCTTTAAGAAATTATAAAGATATAGACTATT
810945 AAA
1 AAA
810948 ATAATAAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (45 bp):
AAATTTGATTTAATCCTTTAAGAAATTATAAAGATATAGACTATT
Found at i:810980 original size:23 final size:24
Alignment explanation
Indices: 810953--811053 Score: 63
Period size: 24 Copynumber: 4.2 Consensus size: 24
810943 TTAAAATAAT
810953 AAAATTATATTTTTTATA-TCGTA
1 AAAATTATATTTTTTATACTCGTA
* * *
810976 AAAATATACAATTTAATTT-TGACTCCTT
1 AAAAT-TA-TATTT--TTTAT-ACTCGTA
811004 AAAA-TAT-TTTTTTA-ACTC-TAA
1 AAAATTATATTTTTTATACTCGT-A
811025 TAAAATTATATTTTTTATA-TCGTA
1 -AAAATTATATTTTTTATACTCGTA
811049 AAAAT
1 AAAAT
811054 ATACAATTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 26
0.66 0.05 0.29
Matches are distributed among these distances:
20 1 0.02
21 4 0.07
22 7 0.12
23 13 0.22
24 15 0.25
25 6 0.10
26 3 0.05
27 4 0.07
28 7 0.12
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.48
Consensus pattern (24 bp):
AAAATTATATTTTTTATACTCGTA
Found at i:810983 original size:22 final size:23
Alignment explanation
Indices: 810952--811056 Score: 60
Period size: 22 Copynumber: 4.4 Consensus size: 23
810942 ATTAAAATAA
*
810952 TAAAATTATATTTTTTATA-TCG
1 TAAAAATATATTTTTTATACTCG
*
810974 TAAAAATATACAATTTAATTT-TGACTCC
1 TAAAAATAT---ATTT--TTTAT-ACTCG
*
811002 TTAAAATAT-TTTTTTA-ACTC-
1 TAAAAATATATTTTTTATACTCG
811022 TAATAAAATTATATTTTTTATA-TCG
1 T-A-AAAA-TATATTTTTTATACTCG
811047 TAAAAATATA
1 TAAAAATATA
811057 CAATTTAATT
Statistics
Matches: 65, Mismatches: 4, Indels: 28
0.67 0.04 0.29
Matches are distributed among these distances:
20 1 0.02
21 4 0.06
22 19 0.29
23 7 0.11
24 13 0.20
25 6 0.09
26 1 0.02
27 4 0.06
28 10 0.15
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.48
Consensus pattern (23 bp):
TAAAAATATATTTTTTATACTCG
Found at i:811029 original size:73 final size:73
Alignment explanation
Indices: 810949--811096 Score: 296
Period size: 73 Copynumber: 2.0 Consensus size: 73
810939 ACTATTAAAA
810949 TAATAAAATTATATTTTTTATATCGTAAAAATATACAATTTAATTTTGACTCCTTAAAATATTTT
1 TAATAAAATTATATTTTTTATATCGTAAAAATATACAATTTAATTTTGACTCCTTAAAATATTTT
811014 TTTAACTC
66 TTTAACTC
811022 TAATAAAATTATATTTTTTATATCGTAAAAATATACAATTTAATTTTGACTCCTTAAAATATTTT
1 TAATAAAATTATATTTTTTATATCGTAAAAATATACAATTTAATTTTGACTCCTTAAAATATTTT
811087 TTTAACTC
66 TTTAACTC
811095 TA
1 TA
811097 CCACTGGCCT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.48
Consensus pattern (73 bp):
TAATAAAATTATATTTTTTATATCGTAAAAATATACAATTTAATTTTGACTCCTTAAAATATTTT
TTTAACTC
Found at i:811252 original size:47 final size:47
Alignment explanation
Indices: 811198--811291 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
811188 ACAAAGGGAG
811198 CATCGGCAACGTACGAACGACCCTCCATATCATGGCCGCCACTTGGA
1 CATCGGCAACGTACGAACGACCCTCCATATCATGGCCGCCACTTGGA
811245 CATCGGCAACGTACGAACGACCCTCCATATCATGGCCGCCACTTGGA
1 CATCGGCAACGTACGAACGACCCTCCATATCATGGCCGCCACTTGGA
811292 GTTCGAATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.26, C:0.36, G:0.21, T:0.17
Consensus pattern (47 bp):
CATCGGCAACGTACGAACGACCCTCCATATCATGGCCGCCACTTGGA
Found at i:817207 original size:19 final size:19
Alignment explanation
Indices: 817183--817257 Score: 89
Period size: 19 Copynumber: 3.8 Consensus size: 19
817173 ATTTTTCAGA
* *
817183 AAAAGTCAATGGTCAATGC
1 AAAAGTCAACGGTCAACGC
817202 AAAAGTCAACGGTCAACGC
1 AAAAGTCAACGGTCAACGC
*
817221 AAAAGTCAGCGGTCAACAGTC
1 AAAAGTCAACGGTCAAC-G-C
817242 AACAA-TCAACGGTCAA
1 AA-AAGTCAACGGTCAA
817258 TGGTCGGTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 33 0.67
20 1 0.02
21 13 0.27
22 2 0.04
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.15
Consensus pattern (19 bp):
AAAAGTCAACGGTCAACGC
Found at i:817322 original size:20 final size:21
Alignment explanation
Indices: 817299--817347 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
817289 GTCGGTCCGA
*
817299 TTGGGTTTGGTTCACTTG-GT
1 TTGGGTTTGGTTCAATTGTGT
817319 TTGGGTTTGGTTCAATTGTGT
1 TTGGGTTTGGTTCAATTGTGT
817340 TTGAGGTT
1 TTG-GGTT
817348 ATTGGGTCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 17 0.65
21 5 0.19
22 4 0.15
ACGTcount: A:0.08, C:0.06, G:0.35, T:0.51
Consensus pattern (21 bp):
TTGGGTTTGGTTCAATTGTGT
Found at i:818155 original size:20 final size:20
Alignment explanation
Indices: 818130--818167 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
818120 TAGCTATAAA
*
818130 AATTAATTGTTAATTTTATC
1 AATTAATTATTAATTTTATC
818150 AATTAATTATTAATTTTA
1 AATTAATTATTAATTTTA
818168 ATTAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
AATTAATTATTAATTTTATC
Found at i:827323 original size:172 final size:172
Alignment explanation
Indices: 827029--827798 Score: 699
Period size: 172 Copynumber: 4.5 Consensus size: 172
827019 GATTTGGTTT
827029 TTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAACGAGCGAAGGCTTTGCC
1 TTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAACGAGCGAAGGCTTTGCC
* * * * * * *
827094 TTGGCTATGATTTCAATATGACCACTAATGAGCTGCAGTAATATTTCTTACGATGTTTTTCCGAC
66 TTGGCTATGATTACAATATAATCTCTAATGAGCTGCCGT-GTATTTTTTACGATGTTTTTCCGAC
* * *
827159 CGAAAGGTCACA-ATTTTTAAATGAATTTTTGGTTTTTGGGTG
130 CGAAAGGTCACAGATTTTTAAATAAATGTTTGGTTTTTGAGTG
* * * ** *
827201 TTGTTTTGTTGCAAGTGCCGCGATGATTAAAATGAGGTTTAGGGTTGGCGAG-GTCAGGCTTTGC
1 TTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAACGAGCG-AAGGCTTTGC
* * * * **
827265 CTTGGCTATGATTACAATGTAATTTCTAATGAGCCGCCGTTGGT-TTTTTTATGATGTTTTAGCG
65 CTTGGCTATGATTACAATATAATCTCTAATGAGCTGCCG-T-GTATTTTTTACGATGTTTTTCCG
* * *
827329 ACCGAATGG-CTA-AGATTTTTAAACAAATGTTT-GTCTTTCGAGTG
128 ACCGAAAGGTC-ACAGATTTTTAAATAAATGTTTGGT-TTTTGAGTG
* * ** *
827373 TTGTTTTGTAGTAATTGCAGCGATGATT-AAATAAGGTTTAGGGTTAACGAGCTCAGGTTTTGCC
1 TTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAACGAGCGAAGGCTTTGCC
* * * * *
827437 TTGGCTGTGATTACAATATAATCTCAAATGAGTTGCTGCTGT-TTTTTTAAG-TCGTTTTTCCGA
66 TTGGCTATGATTACAATATAATCTCTAATGAGCTGCCG-TGTATTTTTTACGAT-GTTTTTCCGA
* * * * * *
827500 CCG-AATGTTAGAGA--TTTAAATAAATGTTTGTTTTTTTATTG
129 CCGAAAGGTCACAGATTTTTAAATAAATGTTTGGTTTTTGAGTG
* *
827541 TTGTTTTGTAGTAAGTGCAGCGATGATTATAAAAGTAAGGTTTAGGGTTAATAACGAGCGAAGGG
1 TTGTTTTGTAGTAAGTGCAGCGATGA-T-TAAAA-TGAGGTTTAGGG-T--TAACGAGCGAAGGC
* ** * * * *
827606 TTTCTCCTAAGCTATGATTACAATGTAATCTCTAATGAGCTGTCGTCGTCTTTTTTACGACGTTT
60 TTT-GCCTTGGCTATGATTACAATATAATCTCTAATGAGCTGCCGT-GTATTTTTTACGATGTTT
* * ** * **
827671 TTCCAACCGAAAGTTC-CGAGATTTTCGAA-CAATGTAAGGTTTTTGAGTG
123 TTCCGACCGAAAGGTCAC-AGATTTTTAAATAAATGTTTGGTTTTTGAGTG
* * * *
827720 TTGTTTTGTAGT-AGTCGCAGCGATGATTAAAATGAGGTTTAGGGTTAATGAGTGAAGTC-TTGT
1 TTGTTTTGTAGTAAGT-GCAGCGATGATTAAAATGAGGTTTAGGGTTAACGAGCGAAGGCTTTGC
* *
827783 CTTTGCTTTGATTACA
65 CTTGGCTATGATTACA
827799 TTTTGATCTC
Statistics
Matches: 480, Mismatches: 92, Indels: 53
0.77 0.15 0.08
Matches are distributed among these distances:
168 45 0.09
169 6 0.01
170 25 0.05
171 83 0.17
172 172 0.36
173 13 0.03
175 16 0.03
176 45 0.09
177 25 0.05
178 10 0.02
179 36 0.08
180 4 0.01
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (172 bp):
TTGTTTTGTAGTAAGTGCAGCGATGATTAAAATGAGGTTTAGGGTTAACGAGCGAAGGCTTTGCC
TTGGCTATGATTACAATATAATCTCTAATGAGCTGCCGTGTATTTTTTACGATGTTTTTCCGACC
GAAAGGTCACAGATTTTTAAATAAATGTTTGGTTTTTGAGTG
Found at i:835756 original size:23 final size:21
Alignment explanation
Indices: 835721--835774 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
835711 TTTTAAAAAA
835721 ATATTTTTA-TATTAACATTTAT
1 ATATTTTTATTATTAA-ATTT-T
835743 ATATTTTTATTATTAAATTTT
1 ATATTTTTATTATTAAATTTT
*
835764 AAATTTTTATT
1 ATATTTTTATT
835775 TTTTTATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 6 0.20
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
ATATTTTTATTATTAAATTTT
Found at i:842276 original size:5 final size:5
Alignment explanation
Indices: 842268--842293 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
842258 GAGATAGAAT
842268 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
842294 ATATTTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:849436 original size:72 final size:72
Alignment explanation
Indices: 849319--849462 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
849309 TATGTTCTAT
849319 GCTCATATTAAAGTAATGAATACAGCCTGCAGATATGCCAGACGGTTAAATATAATCAAGATAAT
1 GCTCATATTAAAGTAATGAATACAGCCTGCAGATATGCCAGACGGTTAAATATAATCAAGATAAT
849384 AAATGCC
66 AAATGCC
849391 GCTCATATTAAAGTAATGAATACAGCCTGCAGATATGCCAGACGGTTAAATATAATCAAGATAAT
1 GCTCATATTAAAGTAATGAATACAGCCTGCAGATATGCCAGACGGTTAAATATAATCAAGATAAT
849456 AAATGCC
66 AAATGCC
849463 TCGAGGACCA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (72 bp):
GCTCATATTAAAGTAATGAATACAGCCTGCAGATATGCCAGACGGTTAAATATAATCAAGATAAT
AAATGCC
Found at i:854168 original size:13 final size:13
Alignment explanation
Indices: 854150--854178 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
854140 CCTTGTTGCT
854150 ATAGCTACGATGG
1 ATAGCTACGATGG
854163 ATAGCTACGATGG
1 ATAGCTACGATGG
854176 ATA
1 ATA
854179 TCTAAAGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (13 bp):
ATAGCTACGATGG
Found at i:866614 original size:19 final size:20
Alignment explanation
Indices: 866573--866617 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
866563 TAACAAAATT
*
866573 AAAAAAAAAACTATATTTGA
1 AAAAAAAAAACTATATTTAA
* *
866593 AAAAAAAAAAC-CTGTTTAA
1 AAAAAAAAAACTATATTTAA
866612 AAAAAA
1 AAAAAA
866618 TAGCCGTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.69, C:0.07, G:0.04, T:0.20
Consensus pattern (20 bp):
AAAAAAAAAACTATATTTAA
Found at i:867680 original size:37 final size:37
Alignment explanation
Indices: 867630--867703 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
867620 TAGCTCAGAA
867630 AATTCTGGTTCAACAGACTCTAATATGATGCGATTTT
1 AATTCTGGTTCAACAGACTCTAATATGATGCGATTTT
867667 AATTCTGGTTCAACAGACTCTAATATGATGCGATTTT
1 AATTCTGGTTCAACAGACTCTAATATGATGCGATTTT
867704 CTATTCTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (37 bp):
AATTCTGGTTCAACAGACTCTAATATGATGCGATTTT
Found at i:878920 original size:11 final size:11
Alignment explanation
Indices: 878900--878968 Score: 52
Period size: 11 Copynumber: 6.1 Consensus size: 11
878890 ATTCAAAAAA
*
878900 TTAAATTAATT
1 TTAAAATAATT
878911 TTAAAATAATT
1 TTAAAATAATT
*
878922 TAAAAAATTATATT
1 T-TAAAA-TA-ATT
*
878936 TAAAAAATAATT
1 T-TAAAATAATT
878948 TT--AATAATT
1 TTAAAATAATT
*
878957 TTTAAATAATT
1 TTAAAATAATT
878968 T
1 T
878969 GCTGACGTGA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
9 9 0.18
11 19 0.38
12 8 0.16
13 4 0.08
14 10 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAAAATAATT
Found at i:878928 original size:12 final size:12
Alignment explanation
Indices: 878913--878948 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 12
878903 AATTAATTTT
878913 AAAATAATTTAA
1 AAAATAATTTAA
878925 AAAATTATATTTAA
1 AAAA-TA-ATTTAA
878939 AAAATAATTT
1 AAAATAATTT
878949 TAATAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.36
13 4 0.18
14 10 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AAAATAATTTAA
Found at i:879626 original size:48 final size:46
Alignment explanation
Indices: 879551--879718 Score: 153
Period size: 48 Copynumber: 3.6 Consensus size: 46
879541 CCGTAGAGCA
* *
879551 CTCTCCGTTTAGCACGTT-TTGTGCTCTCCATTATTAGCACTTCGTGTG
1 CTCTCCGTTTAGCAC-TTCGTGTACTCTCC-TTATTAGCACTT-GTGTG
* * * *
879599 CTCTTCGATTAGCACTTCGTGTACTCTCC-GATTAGCACTTTGTGTA
1 CTCTCCGTTTAGCACTTCGTGTACTCTCCTTATTAGCAC-TTGTGTG
* * ** *
879645 CTCTCCGTTTAGCACTTAGTGTGCTCTCCGTTACCCAGCACTTTTGTG
1 CTCTCCGTTTAGCACTTCGTGTACTCTCC-TTA-TTAGCACTTGTGTG
*
879693 CTCTCCGTTTAGTACTTCG-GTACTCT
1 CTCTCCGTTTAGCACTTCGTGTACTCT
879719 TCGTTTTTGT
Statistics
Matches: 97, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
46 37 0.38
47 10 0.10
48 45 0.46
49 5 0.05
ACGTcount: A:0.14, C:0.29, G:0.18, T:0.40
Consensus pattern (46 bp):
CTCTCCGTTTAGCACTTCGTGTACTCTCCTTATTAGCACTTGTGTG
Found at i:879675 original size:23 final size:22
Alignment explanation
Indices: 879551--879709 Score: 138
Period size: 23 Copynumber: 6.8 Consensus size: 22
879541 CCGTAGAGCA
*
879551 CTCTCCGTTTAGCACGTTTTGTG
1 CTCTCCGTTTAGCAC-TTGTGTG
*
879574 CTCTCCATTATTAGCACTTCGTGTG
1 CTCTCC-GT-TTAGCACTT-GTGTG
* * *
879599 CTCTTCGATTAGCACTTCGTGTA
1 CTCTCCGTTTAGCACTT-GTGTG
* *
879622 CTCTCCGATTAGCACTTTGTGTA
1 CTCTCCGTTTAGCAC-TTGTGTG
879645 CTCTCCGTTTAGCACTTAGTGTG
1 CTCTCCGTTTAGCACTT-GTGTG
* *
879668 CTCTCCGTTACCCAGCACTTTTGTG
1 CTCTCCGTT---TAGCACTTGTGTG
*
879693 CTCTCCGTTTAGTACTT
1 CTCTCCGTTTAGCACTT
879710 CGGTACTCTT
Statistics
Matches: 115, Mismatches: 13, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
22 8 0.07
23 66 0.57
24 5 0.04
25 29 0.25
26 7 0.06
ACGTcount: A:0.14, C:0.28, G:0.18, T:0.40
Consensus pattern (22 bp):
CTCTCCGTTTAGCACTTGTGTG
Found at i:880629 original size:92 final size:89
Alignment explanation
Indices: 880418--880643 Score: 203
Period size: 92 Copynumber: 2.5 Consensus size: 89
880408 TTTGAGATGG
** * *
880418 TATCGATACTCAATTGACAGAATGCCCTCTTGGTCTCGATTTTTAAGTGAAGTACCGATATTTTA
1 TATCGATAC-CAATTGACAGAATGCTTTTTTGGTCTCGATTTTAAAGTG-AGTACCGATATTTTA
* ** * *
880483 GCAAAAATATCGATACCTTTGAGAAGG
64 -CAAAAATATCAATACCTTACAAAAGA
*
880510 TATCGATACCAGAGTT--CTAGAGA-GCTTTTTTGGCCTCGATTTTGAAAGTTG-GTACCGATAT
1 TATCGATACCA-A-TTGAC-AGA-ATGCTTTTTTGGTCTCGATTTT-AAAG-TGAGTACCGATAT
880571 TTT-CATAAAATTATCAATACCTTACAAAAGA
60 TTTACA-AAAA-TATCAATACCTTACAAAAGA
880602 TATCGATACCAATTTGACAGAATGCTTTATTT-GTCTCGATTT
1 TATCGATACCAA-TTGACAGAATGCTTT-TTTGGTCTCGATTT
880644 CTACTTTTGG
Statistics
Matches: 110, Mismatches: 12, Indels: 24
0.75 0.08 0.16
Matches are distributed among these distances:
90 2 0.02
91 11 0.10
92 85 0.77
93 10 0.09
94 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (89 bp):
TATCGATACCAATTGACAGAATGCTTTTTTGGTCTCGATTTTAAAGTGAGTACCGATATTTTACA
AAAATATCAATACCTTACAAAAGA
Found at i:886368 original size:6 final size:6
Alignment explanation
Indices: 886317--886355 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
886307 GCATGTTCTT
886317 GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGA
1 GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGA
886356 ACGGAGGGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (6 bp):
GGAGAA
Found at i:895771 original size:24 final size:25
Alignment explanation
Indices: 895721--895776 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
895711 ACCATAACCC
* *
895721 GATAGAGCTCCGTATGAAGCCGGTG
1 GATAGAGCTCCATATGAAGCCGATG
* *
895746 GATAG-GCTCCATATGGAGTCGATG
1 GATAGAGCTCCATATGAAGCCGATG
895770 GAT-GAGC
1 GATAGAGC
895777 CCCGTAAGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 1 0.04
24 20 0.77
25 5 0.19
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (25 bp):
GATAGAGCTCCATATGAAGCCGATG
Found at i:897496 original size:24 final size:24
Alignment explanation
Indices: 897469--897514 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
897459 CTGAACTTGA
897469 TGGAGAAGCCCCAT-CTGGTGCCGG
1 TGGAGAAGCCCCATAC-GGTGCCGG
*
897493 TGGAGCAGCCCCATACGGTGCC
1 TGGAGAAGCCCCATACGGTGCC
897515 AATGAAGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.17, C:0.33, G:0.35, T:0.15
Consensus pattern (24 bp):
TGGAGAAGCCCCATACGGTGCCGG
Found at i:900384 original size:186 final size:187
Alignment explanation
Indices: 900067--900427 Score: 571
Period size: 186 Copynumber: 1.9 Consensus size: 187
900057 TTGGTTTTGG
*
900067 TTGCCTTCCTAGTATGTGCATATGATGAACTCAACTCGGATTCCCCTTCAAGACTTCATGGGTGA
1 TTGCCTTCCTAGTATATGCATATGATGAACTCAACTCGGATTCCCCTTCAAGACTTCATGGGTGA
* * * *
900132 TGCTAGCTCGAGTTTTTGATGCAAACATCAAGTGATCAATTTTACGTAGTTCACAAATTTGGTTT
66 TGCTAACTCGAGTTTCTGATGCAAACATCAAGTGATCAATTTTACATAGTTCACAAATTCGGTTT
* * * **
900197 GTATGAAAGT-ATAAGAAATGTGTTTTTTTTTTCTTTCTTCAATTCGGTATGTTAAT
131 GTATGAAAGTAAAAAAAAATGTGTTTCTTCATTCTTTCTTCAATTCGGTATGTTAAT
* *
900253 TTGCCTTCCTATTATATGCATATGATGAACTCTACTCGGATTCCCCTTCAAGACTTCATGGGTGA
1 TTGCCTTCCTAGTATATGCATATGATGAACTCAACTCGGATTCCCCTTCAAGACTTCATGGGTGA
* * *
900318 TGCTAACTCGAGTTTCTGATGCAAACGTTAAGTGATCAATTTTACATGGTTCACAAATTCGGTTT
66 TGCTAACTCGAGTTTCTGATGCAAACATCAAGTGATCAATTTTACATAGTTCACAAATTCGGTTT
900383 GTATGAAAGTACAAAAAAAATGTGTTTCTTCATTCTTTCTTCAAT
131 GTATGAAAGTA-AAAAAAAATGTGTTTCTTCATTCTTTCTTCAAT
900428 CCTCTAATAA
Statistics
Matches: 158, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
186 130 0.82
188 28 0.18
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (187 bp):
TTGCCTTCCTAGTATATGCATATGATGAACTCAACTCGGATTCCCCTTCAAGACTTCATGGGTGA
TGCTAACTCGAGTTTCTGATGCAAACATCAAGTGATCAATTTTACATAGTTCACAAATTCGGTTT
GTATGAAAGTAAAAAAAAATGTGTTTCTTCATTCTTTCTTCAATTCGGTATGTTAAT
Found at i:903628 original size:18 final size:18
Alignment explanation
Indices: 903605--903640 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
903595 CTCCCAACTT
903605 TTTTAT-TATTTAAAAATA
1 TTTTATATA-TTAAAAATA
903623 TTTTATATATTAAAAATA
1 TTTTATATATTAAAAATA
903641 AATTAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTATATATTAAAAATA
Found at i:903695 original size:2 final size:2
Alignment explanation
Indices: 903688--903737 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
903678 TGAGTCTTGA
*
903688 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
903730 AT AT AT AT
1 AT AT AT AT
903738 TAAAAAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:907227 original size:23 final size:23
Alignment explanation
Indices: 907179--907227 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
907169 TGATCTAAGG
* *
907179 AAAAATAAAAGAAACTGAATTAA
1 AAAAATAAAAGAAAATGAACTAA
907202 AAAAATAAAAGAAAATAGAACTAA
1 AAAAATAAAAGAAAAT-GAACTAA
907226 AA
1 AA
907228 GAAGTAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.14
Consensus pattern (23 bp):
AAAAATAAAAGAAAATGAACTAA
Found at i:908302 original size:103 final size:103
Alignment explanation
Indices: 908091--908324 Score: 260
Period size: 103 Copynumber: 2.2 Consensus size: 103
908081 TTTATTTTGT
* * * * *
908091 GAATTTTTTCCTTT-TTTTTTCTTTAAGAATACATTGGATCTTTTGACGCGAAATGAAATGACAC
1 GAATTTTTTTCTTTCTTTTTT-TTT-AGAATACATTAGACCTTTTAACGCGAAATGAAATGACAA
* *
908155 CCAAGCACTCCATCCCGGTTACTCAGCCCAACATGATCTC
64 CCAAGCACTCCACCCCGGTTACTCAGCCCAACATCATCTC
* * *
908195 -AATTTTTTTCTTCTCTTTTTTTTTAGAATGCATTAGCCCTTTTAACGCGAAGTGAAATGACAAC
1 GAATTTTTTTCTT-TCTTTTTTTTTAGAATACATTAGACCTTTTAACGCGAAATGAAATGACAAC
* *
908259 CAAGCACTCCACCCCGGTTACTCAGTCTAACA-CAT-TCC
65 CAAGCACTCCACCCCGGTTACTCAGCCCAACATCATCT-C
*
908297 GAATTTATTTATTATTTCTTTTTTTTTA
1 GAA-TT-TTT-TTCTTTCTTTTTTTTTA
908325 TTCGGGTTAG
Statistics
Matches: 110, Mismatches: 13, Indels: 13
0.81 0.10 0.10
Matches are distributed among these distances:
101 1 0.01
102 3 0.03
103 75 0.68
104 6 0.05
105 21 0.19
106 4 0.04
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (103 bp):
GAATTTTTTTCTTTCTTTTTTTTTAGAATACATTAGACCTTTTAACGCGAAATGAAATGACAACC
AAGCACTCCACCCCGGTTACTCAGCCCAACATCATCTC
Found at i:908980 original size:4 final size:4
Alignment explanation
Indices: 908971--909022 Score: 54
Period size: 4 Copynumber: 12.8 Consensus size: 4
908961 TCCTGGACAA
*
908971 AAAT AAAT AAAT AAAT AAAAT AAGAT AGAA- AAAT AAAA AAAT AAA- AAAT
1 AAAT AAAT AAAT AAAT -AAAT AA-AT A-AAT AAAT AAAT AAAT AAAT AAAT
909020 AAA
1 AAA
909023 AATAACTGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
3 5 0.12
4 27 0.66
5 8 0.20
6 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:914679 original size:23 final size:23
Alignment explanation
Indices: 914631--914679 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
914621 TGATCTAAGG
* *
914631 AAAAATAAAAGAAACTGAATTAA
1 AAAAATAAAAGAAAATGAACTAA
914654 AAAAATAAAAGAAAATAGAACTAA
1 AAAAATAAAAGAAAAT-GAACTAA
914678 AA
1 AA
914680 GAAGTAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.14
Consensus pattern (23 bp):
AAAAATAAAAGAAAATGAACTAA
Found at i:916968 original size:12 final size:12
Alignment explanation
Indices: 916950--916982 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
916940 TGCGAACAAG
916950 CTCGTTTATTGA
1 CTCGTTTATTGA
*
916962 TTCGTTTA-TGA
1 CTCGTTTATTGA
916973 CTCGTTTATT
1 CTCGTTTATT
916983 TATTAATGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (12 bp):
CTCGTTTATTGA
Found at i:919163 original size:16 final size:16
Alignment explanation
Indices: 919138--919178 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
919128 ACACTTTTAT
*
919138 AAAATTTATA-ACTA-
1 AAAATTTTTATACTAC
*
919152 AAAATTTTTATATTAC
1 AAAATTTTTATACTAC
919168 AAAATTTTTAT
1 AAAATTTTTAT
919179 TTCGTCAGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 9 0.39
15 3 0.13
16 11 0.48
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (16 bp):
AAAATTTTTATACTAC
Found at i:921771 original size:2 final size:2
Alignment explanation
Indices: 921764--921809 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
921754 TTATTATTTG
921764 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
921806 AT AT
1 AT AT
921810 TTAATTTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:922387 original size:11 final size:11
Alignment explanation
Indices: 922366--922426 Score: 61
Period size: 11 Copynumber: 5.4 Consensus size: 11
922356 TTTTTCATTA
922366 TTTTGGTTGTTG
1 TTTT-GTTGTTG
922378 TTTTAG-TGTTG
1 TTTT-GTTGTTG
*
922389 TTTTGTTGTTAT
1 TTTTGTTGTT-G
922401 TTTTGTTGTTG
1 TTTTGTTGTTG
* *
922412 TTTTGATGTTA
1 TTTTGTTGTTG
922423 TTTT
1 TTTT
922427 TGCTGCTGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
10 1 0.02
11 26 0.62
12 15 0.36
ACGTcount: A:0.07, C:0.00, G:0.23, T:0.70
Consensus pattern (11 bp):
TTTTGTTGTTG
Found at i:922392 original size:23 final size:23
Alignment explanation
Indices: 922366--922451 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
922356 TTTTTCATTA
* *
922366 TTTTGGTTGTTGTTTTAG-TGTTG
1 TTTT-GTTGTTATTTTTGCTGTTG
*
922389 TTTTGTTGTTATTTTTGTTGTTG
1 TTTTGTTGTTATTTTTGCTGTTG
* *
922412 TTTTGATGTTATTTTTGCTGCTG
1 TTTTGTTGTTATTTTTGCTGTTG
*
922435 TTTTGGTTATTATTTTT
1 TTTT-GTTGTTATTTTT
922452 ATTGTTTGGA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 11 0.20
23 33 0.61
24 10 0.19
ACGTcount: A:0.07, C:0.02, G:0.22, T:0.69
Consensus pattern (23 bp):
TTTTGTTGTTATTTTTGCTGTTG
Found at i:922427 original size:12 final size:12
Alignment explanation
Indices: 922363--922457 Score: 61
Period size: 12 Copynumber: 8.2 Consensus size: 12
922353 TTTTTTTTCA
*
922363 TTATTTTGGTTG
1 TTATTTTTGTTG
* *
922375 TTGTTTTAG-TG
1 TTATTTTTGTTG
*
922386 TT-GTTTTGTTG
1 TTATTTTTGTTG
922397 TTATTTTTGTTG
1 TTATTTTTGTTG
* *
922409 TT-GTTTTGATG
1 TTATTTTTGTTG
*
922420 TTATTTTTGCTG
1 TTATTTTTGTTG
* * * *
922432 CTGTTTTGGTTA
1 TTATTTTTGTTG
*
922444 TTATTTTTATTG
1 TTATTTTTGTTG
922456 TT
1 TT
922458 TGGATGTTAT
Statistics
Matches: 61, Mismatches: 19, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
10 4 0.07
11 17 0.28
12 40 0.66
ACGTcount: A:0.08, C:0.02, G:0.21, T:0.68
Consensus pattern (12 bp):
TTATTTTTGTTG
Found at i:940283 original size:13 final size:14
Alignment explanation
Indices: 940260--940288 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
940250 AAGTAACATG
940260 GAGGCCCTATATTA
1 GAGGCCCTATATTA
940274 GAGG-CCTATATTA
1 GAGGCCCTATATTA
940287 GA
1 GA
940289 AGTCAGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (14 bp):
GAGGCCCTATATTA
Found at i:944330 original size:35 final size:33
Alignment explanation
Indices: 944257--944331 Score: 78
Period size: 35 Copynumber: 2.2 Consensus size: 33
944247 ATCTATTTTT
* * **
944257 AATAAAAAAATTAATTTACTTTTTAATATAATG
1 AATAAAAAAATTAATTAACTTTTTAATAAAAAA
* *
944290 TATAAAAATTAATTTATTAACTTTTTAATAAAAAA
1 AATAAAAA--AATTAATTAACTTTTTAATAAAAAA
944325 AATAAAA
1 AATAAAA
944332 TACAATTTGA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
33 7 0.21
35 26 0.79
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (33 bp):
AATAAAAAAATTAATTAACTTTTTAATAAAAAA
Found at i:949562 original size:13 final size:12
Alignment explanation
Indices: 949538--949579 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
949528 TTTAAATTCA
949538 ATTTTATTATTT
1 ATTTTATTATTT
949550 ATTTT-TTAAATTT
1 ATTTTATT--ATTT
949563 -TTTTATTATTT
1 ATTTTATTATTT
949574 ATTTTA
1 ATTTTA
949580 AATTTAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 6 0.23
12 14 0.54
13 6 0.23
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTTATTATTT
Found at i:949562 original size:21 final size:22
Alignment explanation
Indices: 949537--949584 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
949527 TTTTAAATTC
949537 AATTTTATTATT-TATT-TTTTA
1 AATTTTATTATTAT-TTATTTTA
*
949558 AATTTTTTTATTATTTATTTTA
1 AATTTTATTATTATTTATTTTA
949580 AATTT
1 AATTT
949585 AATAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
AATTTTATTATTATTTATTTTA
Found at i:959419 original size:23 final size:23
Alignment explanation
Indices: 959314--959463 Score: 128
Period size: 23 Copynumber: 6.4 Consensus size: 23
959304 CGAAGTACTT
959314 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
*
959340 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * * *
959362 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
*
959384 AATCAGTAGGCACACAAAGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
*
959408 AACATTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
* *
959431 AACAGTAAGCACGCACAGTGCTG-
1 AACAGTAAGCACACAAAGTGC-GA
959454 AACAGTAAGC
1 AACAGTAAGC
959464 GCGCTAGCGT
Statistics
Matches: 105, Mismatches: 15, Indels: 11
0.80 0.11 0.08
Matches are distributed among these distances:
22 19 0.18
23 63 0.60
24 4 0.04
26 14 0.13
27 5 0.05
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.12
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:959918 original size:11 final size:11
Alignment explanation
Indices: 959893--959921 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
959883 AGACTCTAAT
959893 AATTTTTCTAC
1 AATTTTTCTAC
959904 -ATTTTTCTAC
1 AATTTTTCTAC
959914 AATTTTTC
1 AATTTTTC
959922 AAAGTCAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (11 bp):
AATTTTTCTAC
Found at i:960370 original size:33 final size:36
Alignment explanation
Indices: 960313--960378 Score: 102
Period size: 33 Copynumber: 1.9 Consensus size: 36
960303 CTCTTTTACC
*
960313 CCTTGCTCTACTCTTTTCCTTTCTCTTCAATTTGAT
1 CCTTGCTCTACTCTTCTCCTTTCTCTTCAATTTGAT
960349 CCTTGC-CT-CTCTTCT-CTTTCTCTTCAATTT
1 CCTTGCTCTACTCTTCTCCTTTCTCTTCAATTT
960379 CACATAAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 15 0.52
34 6 0.21
35 2 0.07
36 6 0.21
ACGTcount: A:0.09, C:0.33, G:0.05, T:0.53
Consensus pattern (36 bp):
CCTTGCTCTACTCTTCTCCTTTCTCTTCAATTTGAT
Found at i:965715 original size:42 final size:42
Alignment explanation
Indices: 965668--965751 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
965658 GCAAACCAGT
965668 TCAAGCTCTAGAAGAATCACGTCTCAATAAATTTTGAATATA
1 TCAAGCTCTAGAAGAATCACGTCTCAATAAATTTTGAATATA
965710 TCAAGCTCTAGAAGAATCACGTCTCAATAAATTTTGAATATA
1 TCAAGCTCTAGAAGAATCACGTCTCAATAAATTTTGAATATA
965752 GGTGAATAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (42 bp):
TCAAGCTCTAGAAGAATCACGTCTCAATAAATTTTGAATATA
Found at i:990268 original size:28 final size:28
Alignment explanation
Indices: 990237--990290 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
990227 TTTTATAATA
* *
990237 TTTTAGGATTTAAATTGATTATTCTTCT
1 TTTTAGAAGTTAAATTGATTATTCTTCT
*
990265 TTTTAGAAGTTAAATTGATTGTTCTT
1 TTTTAGAAGTTAAATTGATTATTCTT
990291 AAATATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.56
Consensus pattern (28 bp):
TTTTAGAAGTTAAATTGATTATTCTTCT
Found at i:992358 original size:23 final size:22
Alignment explanation
Indices: 992332--992405 Score: 85
Period size: 23 Copynumber: 3.3 Consensus size: 22
992322 TAATTTGATC
* *
992332 AAAATTTTTAAATTTGAAATAT
1 AAAAATTTTAAATTTTAAATAT
* *
992354 AAAAATATTAAATTTCTAAAAAT
1 AAAAATTTTAAATTT-TAAATAT
*
992377 AAAAATTTTAAATTTTAAATGT
1 AAAAATTTTAAATTTTAAATAT
992399 ATAAAAT
1 A-AAAAT
992406 ACTGACATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
22 19 0.44
23 24 0.56
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (22 bp):
AAAAATTTTAAATTTTAAATAT
Found at i:995532 original size:16 final size:18
Alignment explanation
Indices: 995513--995545 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
995503 AATTTAGTAA
995513 AAATT-TAA-ATTATAAT
1 AAATTCTAATATTATAAT
995529 AAATTCTAATATTATAA
1 AAATTCTAATATTATAA
995546 AATCTGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 3 0.20
18 7 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTCTAATATTATAAT
Found at i:997922 original size:13 final size:15
Alignment explanation
Indices: 997904--997936 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
997894 AACAAAGTAA
997904 TAAAAAAA-T-ATTT
1 TAAAAAAATTAATTT
997917 TAAAAAAATTAATTT
1 TAAAAAAATTAATTT
997932 TAAAA
1 TAAAA
997937 TTTTCGAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 1 0.06
15 9 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAAAAATTAATTT
Found at i:998526 original size:19 final size:19
Alignment explanation
Indices: 998457--998556 Score: 93
Period size: 19 Copynumber: 5.4 Consensus size: 19
998447 TAAATTTTAA
998457 TAAAAA-TTATTAAAAATTAG
1 TAAAAATTTA-TAAAAA-TAG
*
998477 -AAAAA-ATATAAAAATAG
1 TAAAAATTTATAAAAATAG
* *
998494 TAAAAATATA-AAAAATTG
1 TAAAAATTTATAAAAATAG
* *
998512 TAAAATTTTATAAAAATCG
1 TAAAAATTTATAAAAATAG
998531 TAAAAATTTATAAAAAATA-
1 TAAAAATTTAT-AAAAATAG
998550 TAAAAAT
1 TAAAAAT
998557 ATAAAATTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
17 3 0.04
18 26 0.38
19 34 0.49
20 6 0.09
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (19 bp):
TAAAAATTTATAAAAATAG
Found at i:998535 original size:46 final size:44
Alignment explanation
Indices: 998485--998612 Score: 152
Period size: 46 Copynumber: 2.8 Consensus size: 44
998475 AGAAAAAATA
*
998485 TAAAAA-TAGTAAAAATATAAAAAATTGTAAAATTTTATAAAAATCG
1 TAAAAATTA-TAAAAATATAAAAAA-TATAAAATTTTAT-AAAATCG
998531 TAAAAATTTATAAAAA-ATATAAAAATATAAAATTTTATAAAATCG
1 TAAAAA-TTATAAAAATATA-AAAAATATAAAATTTTATAAAATCG
998576 TATGAAAATTATACAAAATATAAAGAAATATAAAATT
1 TA--AAAATTATA-AAAATATAAA-AAATATAAAATT
998613 GGTAAAAAAA
Statistics
Matches: 73, Mismatches: 1, Indels: 14
0.83 0.01 0.16
Matches are distributed among these distances:
45 9 0.12
46 26 0.36
47 21 0.29
48 17 0.23
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (44 bp):
TAAAAATTATAAAAATATAAAAAATATAAAATTTTATAAAATCG
Found at i:998563 original size:7 final size:8
Alignment explanation
Indices: 998478--998562 Score: 62
Period size: 9 Copynumber: 9.5 Consensus size: 8
998468 AAAAATTAGA
998478 AAAAATAT
1 AAAAATAT
998486 AAAAATAGT
1 AAAAATA-T
998495 AAAAATAT
1 AAAAATAT
*
998503 AAAAAATTGT
1 -AAAAA-TAT
*
998513 AAAATTTTAT
1 AAAA--ATAT
*
998523 AAAAATCGT
1 AAAAAT-AT
998532 AAAAATTTAT
1 AAAAA--TAT
998542 AAAAAATAT
1 -AAAAATAT
998551 AAAAATAT
1 AAAAATAT
998559 AAAA
1 AAAA
998563 TTTTATAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
8 21 0.34
9 26 0.42
10 9 0.15
11 6 0.10
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (8 bp):
AAAAATAT
Found at i:998584 original size:56 final size:55
Alignment explanation
Indices: 998479--998610 Score: 142
Period size: 56 Copynumber: 2.4 Consensus size: 55
998469 AAAATTAGAA
* ** *
998479 AAAATAT-AAAAATAGTAAAAATATAAAAAATTGTAAAATTTTATAAAAATCGTA-
1 AAAATATAAAAAATA-TAAAAATATAAAAAATTATAAAATCGTATAAAAATCATAC
** * *
998533 AAAATTTATAAAAAATATAAAAATATAAAATTTTATAAAATCGTATGAAAATTATAC
1 AAAA--TATAAAAAATATAAAAATATAAAAAATTATAAAATCGTATAAAAATCATAC
998590 AAAATATAAAGAAATATAAAA
1 AAAATATAAA-AAATATAAAA
998611 TTGGTAAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
54 4 0.06
55 6 0.09
56 44 0.68
57 11 0.17
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (55 bp):
AAAATATAAAAAATATAAAAATATAAAAAATTATAAAATCGTATAAAAATCATAC
Found at i:998948 original size:28 final size:28
Alignment explanation
Indices: 998891--998949 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
998881 TAAAAAAAAG
* **
998891 TTTAAATTTTTAATAAATTTTAATTTTT
1 TTTAAATTTTTAATAAAATTTAATAATT
* *
998919 TTTATATTTTTATTAAAATTTAATAATT
1 TTTAAATTTTTAATAAAATTTAATAATT
998947 TTT
1 TTT
998950 CTAAAATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTAAATTTTTAATAAAATTTAATAATT
Found at i:999158 original size:91 final size:88
Alignment explanation
Indices: 999000--999195 Score: 250
Period size: 90 Copynumber: 2.2 Consensus size: 88
998990 AGAGCAAGTG
* *
999000 CTTAATTGGTTTTTTTTGAAAATTTTTGAGATATTTTTTATGCATTTTGAAAGTTCAAGTACCCA
1 CTTAATT-GCTTTTTTTGAAAATGTTTGAGATATTTTTTATGCATTTTGAAAGTTCAAGTACCCA
** * **
999065 ATTGAGTGTGAGAAAAAAGCAGAGA
65 ATTGAGT-AAAAAAAAAAAAAGAGA
* * *
999090 CTTAATTGCTTTTTTTGAAGAA-GTTTGAGGGTATTTTTTTATGCATTTTGAAAGTTCAAGTGCT
1 CTTAATTGCTTTTTTTGAA-AATGTTTGA-GATA-TTTTTTATGCATTTTGAAAGTTCAAGTACC
999154 CAATTGAGTAAAAAAAAAAAAAGAGA
63 CAATTGAGTAAAAAAAAAAAAAGAGA
999180 CTTAATTGCTTTTTTT
1 CTTAATTGCTTTTTTT
999196 TTTAAAATTT
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
89 16 0.17
90 40 0.43
91 37 0.40
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (88 bp):
CTTAATTGCTTTTTTTGAAAATGTTTGAGATATTTTTTATGCATTTTGAAAGTTCAAGTACCCAA
TTGAGTAAAAAAAAAAAAAGAGA
Found at i:999210 original size:91 final size:90
Alignment explanation
Indices: 999000--999211 Score: 268
Period size: 91 Copynumber: 2.3 Consensus size: 90
998990 AGAGCAAGTG
* *
999000 CTTAATTGGTTTTTTTTGAAAATTTTTGA-GATATTTTTTATGCATTTTGAAAGTTCAAGTACCC
1 CTTAATTGCTTTTTTTTGAAAA-TTTTGAGGGTATTTTTTATGCATTTTGAAAGTTCAAGTACCC
** * **
999064 AATTGAGTGTGAGAAAAAAGCAGAGA
65 AATTGAGTGAAAAAAAAAAAAAGAGA
* * *
999090 CTTAATTGC-TTTTTTTGAAGAAGTTTGAGGGTATTTTTTTATGCATTTTGAAAGTTCAAGTGCT
1 CTTAATTGCTTTTTTTTGAA-AATTTTGAGGGTA-TTTTTTATGCATTTTGAAAGTTCAAGTACC
999154 CAATTGAGT-AAAAAAAAAAAAAGAGA
64 CAATTGAGTGAAAAAAAAAAAAAGAGA
*
999180 CTTAATTGCTTTTTTTTTTAAAATTTTGAGGG
1 CTTAATTGC-TTTTTTTTGAAAATTTTGAGGG
999212 CTTTTTACAC
Statistics
Matches: 105, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
89 15 0.14
90 34 0.32
91 47 0.45
92 9 0.09
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (90 bp):
CTTAATTGCTTTTTTTTGAAAATTTTGAGGGTATTTTTTATGCATTTTGAAAGTTCAAGTACCCA
ATTGAGTGAAAAAAAAAAAAAGAGA
Found at i:999806 original size:161 final size:162
Alignment explanation
Indices: 999630--999944 Score: 596
Period size: 162 Copynumber: 2.0 Consensus size: 162
999620 ACTTATACTA
999630 AATATATAATACTAATCTAATGTCCACTAAAAAAATGTTAAGATAACTATA-AAACATTTTCAAT
1 AATATATAATACTAATCTAATGTCCACTAAAAAAATGTTAAGATAACTATATAAACATTTTCAAT
999694 AAATAATTTTTTATAAAATTATTAAATATTAGAATAATATAATATAAATATTTTTTAAAATTAAA
66 AAATAATTTTTTATAAAATTATTAAATATTAGAATAATATAATATAAATATTTTTTAAAATTAAA
999759 AACTAATATAGACATGCCTAAAATTAAAAACT
131 AACTAATATAGACATGCCTAAAATTAAAAACT
* * *
999791 AATATATAATACTAATTTAATGTCCATTAAAAAAATGTTAAGATGACTATATAAACATTTTCAAT
1 AATATATAATACTAATCTAATGTCCACTAAAAAAATGTTAAGATAACTATATAAACATTTTCAAT
999856 AAATAATTTTTTATAAAATTATTAAATATTAGAATAATATAATATAAATATTTTTTAAAATTAAA
66 AAATAATTTTTTATAAAATTATTAAATATTAGAATAATATAATATAAATATTTTTTAAAATTAAA
999921 AACTAATATAGACATGCCTAAAAT
131 AACTAATATAGACATGCCTAAAAT
999945 GGGTTTGGGT
Statistics
Matches: 150, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
161 48 0.32
162 102 0.68
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.37
Consensus pattern (162 bp):
AATATATAATACTAATCTAATGTCCACTAAAAAAATGTTAAGATAACTATATAAACATTTTCAAT
AAATAATTTTTTATAAAATTATTAAATATTAGAATAATATAATATAAATATTTTTTAAAATTAAA
AACTAATATAGACATGCCTAAAATTAAAAACT
Found at i:1010741 original size:12 final size:13
Alignment explanation
Indices: 1010718--1010746 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1010708 ATCTAACTAG
1010718 AAATTAAAAATTA
1 AAATTAAAAATTA
1010731 AAATT-AAAATTA
1 AAATTAAAAATTA
1010743 AAAT
1 AAAT
1010747 AATTACTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATTAAAAATTA
Found at i:1010824 original size:22 final size:20
Alignment explanation
Indices: 1010783--1010827 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1010773 AGACAAAACA
* *
1010783 AAAATTATAAAAAATGAATT
1 AAAATTAAAAAAAAAGAATT
1010803 AAAATTAAAAACAAAAGAAATT
1 AAAATTAAAAA-AAAAG-AATT
1010825 AAA
1 AAA
1010828 GAAGTGGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 4 0.19
22 7 0.33
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (20 bp):
AAAATTAAAAAAAAAGAATT
Found at i:1013464 original size:141 final size:141
Alignment explanation
Indices: 1013210--1013494 Score: 570
Period size: 141 Copynumber: 2.0 Consensus size: 141
1013200 TTGTAAATTG
1013210 GTTATGCTATTGATGAATCGGTTAATCAAGGCATATTTTCAGTTCAACAGGTGTCTTTAACGAAG
1 GTTATGCTATTGATGAATCGGTTAATCAAGGCATATTTTCAGTTCAACAGGTGTCTTTAACGAAG
1013275 TTTTTAAATAGAATGAGTGGAATTTCGTAGCCTAAGCCTAAACCGTGCCTCGTGGGTTAGGATCA
66 TTTTTAAATAGAATGAGTGGAATTTCGTAGCCTAAGCCTAAACCGTGCCTCGTGGGTTAGGATCA
1013340 TTCTTGGATAT
131 TTCTTGGATAT
1013351 GTTATGCTATTGATGAATCGGTTAATCAAGGCATATTTTCAGTTCAACAGGTGTCTTTAACGAAG
1 GTTATGCTATTGATGAATCGGTTAATCAAGGCATATTTTCAGTTCAACAGGTGTCTTTAACGAAG
1013416 TTTTTAAATAGAATGAGTGGAATTTCGTAGCCTAAGCCTAAACCGTGCCTCGTGGGTTAGGATCA
66 TTTTTAAATAGAATGAGTGGAATTTCGTAGCCTAAGCCTAAACCGTGCCTCGTGGGTTAGGATCA
1013481 TTCTTGGATAT
131 TTCTTGGATAT
1013492 GTT
1 GTT
1013495 TCACATCCTT
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 144 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (141 bp):
GTTATGCTATTGATGAATCGGTTAATCAAGGCATATTTTCAGTTCAACAGGTGTCTTTAACGAAG
TTTTTAAATAGAATGAGTGGAATTTCGTAGCCTAAGCCTAAACCGTGCCTCGTGGGTTAGGATCA
TTCTTGGATAT
Found at i:1014506 original size:26 final size:26
Alignment explanation
Indices: 1014477--1014547 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 26
1014467 CCATAAAATA
1014477 ATTTTTTTTTAAAGTTAAATTTGATC
1 ATTTTTTTTTAAAGTTAAATTTGATC
*
1014503 A--TTTTTTTGAAGTGTCAAATTTGATC
1 ATTTTTTTTTAAAGT-T-AAATTTGATC
*
1014529 ATTAATTTTTTAAA-TTAAA
1 ATT-TTTTTTTAAAGTTAAA
1014548 ATATTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
24 11 0.30
25 1 0.03
26 15 0.41
27 1 0.03
28 1 0.03
29 8 0.22
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.54
Consensus pattern (26 bp):
ATTTTTTTTTAAAGTTAAATTTGATC
Found at i:1014515 original size:24 final size:26
Alignment explanation
Indices: 1014480--1014531 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
1014470 TAAAATAATT
1014480 TTTTTTTAAAGT-T-AAATTTGATCA
1 TTTTTTTAAAGTGTCAAATTTGATCA
*
1014504 TTTTTTTGAAGTGTCAAATTTGATCA
1 TTTTTTTAAAGTGTCAAATTTGATCA
1014530 TT
1 TT
1014532 AATTTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 11 0.44
25 1 0.04
26 13 0.52
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.54
Consensus pattern (26 bp):
TTTTTTTAAAGTGTCAAATTTGATCA
Found at i:1014567 original size:19 final size:20
Alignment explanation
Indices: 1014533--1014571 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1014523 TTGATCATTA
*
1014533 ATTTTTTAAATTAAAATATT
1 ATTTTTTAAATGAAAATATT
1014553 ATTTTTT-AATGAAAATATT
1 ATTTTTTAAATGAAAATATT
1014572 TTTGAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
ATTTTTTAAATGAAAATATT
Found at i:1014751 original size:29 final size:29
Alignment explanation
Indices: 1014675--1014756 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 29
1014665 ATAAATCTCT
* *
1014675 ATTTTTTTTTTTGTAAA-TTT-GAAATTTA
1 ATTTTTATTTTT-TAAATTTTAGAAATGTA
* **
1014703 ATTTTTATACTTTT-GTTTTTAGAAATGTA
1 ATTTTTAT-TTTTTAAATTTTAGAAATGTA
1014732 ATTTTTATTTTTTAAATTTTA-AAAT
1 ATTTTTATTTTTTAAATTTTAGAAAT
1014757 TTAAGTCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
28 19 0.45
29 23 0.55
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.62
Consensus pattern (29 bp):
ATTTTTATTTTTTAAATTTTAGAAATGTA
Found at i:1023690 original size:271 final size:271
Alignment explanation
Indices: 1023207--1023752 Score: 1092
Period size: 271 Copynumber: 2.0 Consensus size: 271
1023197 TAGCTTGAGT
1023207 TAGTGATCCTTGGTTTGAACCAAAAGACAAATCCTTGAAAGGCTAATGAGTAAAGAGTTCCCATA
1 TAGTGATCCTTGGTTTGAACCAAAAGACAAATCCTTGAAAGGCTAATGAGTAAAGAGTTCCCATA
1023272 TGTTGTTCCAAATATGATACATTTCTAGTGCTCAAAAACTGACATAAAATAAGGGGTAAAAGTAC
66 TGTTGTTCCAAATATGATACATTTCTAGTGCTCAAAAACTGACATAAAATAAGGGGTAAAAGTAC
1023337 CATGTTTGTTCCCTCTACTTAAAAAATAGACAAATTAGTCCATATAAATTAGATCAAAAACAAAT
131 CATGTTTGTTCCCTCTACTTAAAAAATAGACAAATTAGTCCATATAAATTAGATCAAAAACAAAT
1023402 TTGCTCTTTGGTCTAATATATAAGAACTAATTTTCTCCCATTTTTTGAGTAGAGGAGGCAAAATG
196 TTGCTCTTTGGTCTAATATATAAGAACTAATTTTCTCCCATTTTTTGAGTAGAGGAGGCAAAATG
1023467 CAATAAATTTC
261 CAATAAATTTC
1023478 TAGTGATCCTTGGTTTGAACCAAAAGACAAATCCTTGAAAGGCTAATGAGTAAAGAGTTCCCATA
1 TAGTGATCCTTGGTTTGAACCAAAAGACAAATCCTTGAAAGGCTAATGAGTAAAGAGTTCCCATA
1023543 TGTTGTTCCAAATATGATACATTTCTAGTGCTCAAAAACTGACATAAAATAAGGGGTAAAAGTAC
66 TGTTGTTCCAAATATGATACATTTCTAGTGCTCAAAAACTGACATAAAATAAGGGGTAAAAGTAC
1023608 CATGTTTGTTCCCTCTACTTAAAAAATAGACAAATTAGTCCATATAAATTAGATCAAAAACAAAT
131 CATGTTTGTTCCCTCTACTTAAAAAATAGACAAATTAGTCCATATAAATTAGATCAAAAACAAAT
1023673 TTGCTCTTTGGTCTAATATATAAGAACTAATTTTCTCCCATTTTTTGAGTAGAGGAGGCAAAATG
196 TTGCTCTTTGGTCTAATATATAAGAACTAATTTTCTCCCATTTTTTGAGTAGAGGAGGCAAAATG
1023738 CAATAAATTTC
261 CAATAAATTTC
1023749 TAGT
1 TAGT
1023753 ACAAAAACAT
Statistics
Matches: 275, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
271 275 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (271 bp):
TAGTGATCCTTGGTTTGAACCAAAAGACAAATCCTTGAAAGGCTAATGAGTAAAGAGTTCCCATA
TGTTGTTCCAAATATGATACATTTCTAGTGCTCAAAAACTGACATAAAATAAGGGGTAAAAGTAC
CATGTTTGTTCCCTCTACTTAAAAAATAGACAAATTAGTCCATATAAATTAGATCAAAAACAAAT
TTGCTCTTTGGTCTAATATATAAGAACTAATTTTCTCCCATTTTTTGAGTAGAGGAGGCAAAATG
CAATAAATTTC
Found at i:1031997 original size:31 final size:31
Alignment explanation
Indices: 1031962--1032020 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1031952 TTATCCATAT
*
1031962 ATTTTATT-CATGAGAATAATTATCAAATTTA
1 ATTTT-TTACATGAAAATAATTATCAAATTTA
* *
1031993 ATTTTTTATATGAAAATATTTATCAAAT
1 ATTTTTTACATGAAAATAATTATCAAAT
1032021 AATTTATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 22 0.92
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (31 bp):
ATTTTTTACATGAAAATAATTATCAAATTTA
Found at i:1043134 original size:5 final size:5
Alignment explanation
Indices: 1043124--1043148 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1043114 GTAATTTATG
1043124 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
1043149 TTTCATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1043193 original size:29 final size:30
Alignment explanation
Indices: 1043156--1043213 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
1043146 AATTTTCATA
*
1043156 TATAAAATTACATA-AAATCAATATTTACG
1 TATAAAATTACATATAAATCAAAATTTACG
1043185 TATAAAATTACATATTAAATCAAAATTTA
1 TATAAAATTACATA-TAAATCAAAATTTA
1043214 TATATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 14 0.54
31 12 0.46
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (30 bp):
TATAAAATTACATATAAATCAAAATTTACG
Found at i:1043217 original size:29 final size:27
Alignment explanation
Indices: 1043154--1043222 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 27
1043144 AAAATTTTCA
*
1043154 TATATAAAATTACATAAAATCAATATT
1 TATATAAAATTACATAAAATCAAAATT
1043181 TACGTATAAAATTACATATTAAATCAAAATT
1 TA--TATAAAATTACATA--AAATCAAAATT
*
1043212 TATATATAATT
1 TATATAAAATT
1043223 TTAATATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 2 0.06
29 22 0.61
31 12 0.33
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.39
Consensus pattern (27 bp):
TATATAAAATTACATAAAATCAAAATT
Found at i:1043220 original size:31 final size:29
Alignment explanation
Indices: 1043127--1043220 Score: 100
Period size: 31 Copynumber: 3.1 Consensus size: 29
1043117 ATTTATGAAA
* *
1043127 ATAAAATAAAATAAAAT-AAAATTTTCATAT
1 ATAAAATTACATAAAATCAAAA-TTT-ATAT
* **
1043157 ATAAAATTACATAAAATCAATATTTACGT
1 ATAAAATTACATAAAATCAAAATTTATAT
1043186 ATAAAATTACATATTAAATCAAAATTTATAT
1 ATAAAATTACATA--AAATCAAAATTTATAT
1043217 ATAA
1 ATAA
1043221 TTTTAATATT
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
29 15 0.28
30 18 0.34
31 20 0.38
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.35
Consensus pattern (29 bp):
ATAAAATTACATAAAATCAAAATTTATAT
Found at i:1046916 original size:21 final size:22
Alignment explanation
Indices: 1046887--1046928 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1046877 AAAAAAAACT
*
1046887 GTTGCTTTTTGTTGTTGTTTTC
1 GTTGCTTTTTGTTGTTATTTTC
1046909 GTTG-TTTTTGTTGTTATTTT
1 GTTGCTTTTTGTTGTTATTTT
1046929 GTCACTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.02, C:0.05, G:0.21, T:0.71
Consensus pattern (22 bp):
GTTGCTTTTTGTTGTTATTTTC
Found at i:1047495 original size:7 final size:7
Alignment explanation
Indices: 1047483--1047511 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1047473 ACTGAAAGAG
1047483 AGTGCCA
1 AGTGCCA
1047490 AGTGCCA
1 AGTGCCA
1047497 AGTGCCA
1 AGTGCCA
1047504 AGTGCCA
1 AGTGCCA
1047511 A
1 A
1047512 CTCATACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.14
Consensus pattern (7 bp):
AGTGCCA
Found at i:1048960 original size:60 final size:59
Alignment explanation
Indices: 1048880--1049025 Score: 184
Period size: 60 Copynumber: 2.4 Consensus size: 59
1048870 AAATTTGATA
* ** *
1048880 TTTTTCTTAAATTGGTACCTAAATTTTTTTTTATCCAATTTGATACTTGAACTTGACATT
1 TTTTTCTTAATTTGGTACCTAAATTTTTTTGGACCCAATTTGATACTTGAACTTGACA-T
* * * *
1048940 TTTTTCTTAATTTGGCACCTAAACTTTTTTTGGACCCAATTTGGTACTTGAATTTGGCAT
1 TTTTTCTTAATTTGGTACCTAAA-TTTTTTTGGACCCAATTTGATACTTGAACTTGACAT
* *
1049000 CTTTTCCTAATTTGGTACCTAAATTT
1 TTTTTCTTAATTTGGTACCTAAATTT
1049026 ATTAAATATT
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
59 3 0.04
60 42 0.57
61 29 0.39
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (59 bp):
TTTTTCTTAATTTGGTACCTAAATTTTTTTGGACCCAATTTGATACTTGAACTTGACAT
Found at i:1049311 original size:33 final size:31
Alignment explanation
Indices: 1049243--1049336 Score: 101
Period size: 31 Copynumber: 3.1 Consensus size: 31
1049233 CTAACTTAAA
*
1049243 AAAAAAGTGACAAGTTTATGTACCAGATTAG
1 AAAAAAGTGACAAGTTTATGTACCAAATTAG
*
1049274 AAAAAAGTGTCAAGTTTGA-GTACCAAATTAG
1 AAAAAAGTGACAAGTTT-ATGTACCAAATTAG
1049305 ACAAAAA---A-AA-TTTATGTACCAAATTAAG
1 A-AAAAAGTGACAAGTTTATGTACCAAATT-AG
1049333 AAAA
1 AAAA
1049337 GTATCAAGTT
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
26 1 0.02
27 16 0.29
28 5 0.09
31 28 0.50
32 6 0.11
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.24
Consensus pattern (31 bp):
AAAAAAGTGACAAGTTTATGTACCAAATTAG
Found at i:1049903 original size:18 final size:18
Alignment explanation
Indices: 1049870--1049904 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1049860 ATAACTTTTA
*
1049870 AAAGTAAAAATTAAAAAT
1 AAAGTAAAAATGAAAAAT
*
1049888 AAAGTAAAACTGAAAAA
1 AAAGTAAAAATGAAAAA
1049905 AAAAAAAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (18 bp):
AAAGTAAAAATGAAAAAT
Found at i:1051543 original size:10 final size:10
Alignment explanation
Indices: 1051528--1051554 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1051518 TCACACCTTC
1051528 ATATATGTAT
1 ATATATGTAT
1051538 ATATATGTAT
1 ATATATGTAT
1051548 ATATATG
1 ATATATG
1051555 ATGTCTTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (10 bp):
ATATATGTAT
Found at i:1053576 original size:31 final size:31
Alignment explanation
Indices: 1053539--1053605 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
1053529 GTTATAAGAT
* *
1053539 GGTCATTAAATTAATCAAAAGTTTTTATTTA
1 GGTCATTAAACTAATCAAAAGTTTTTAATTA
*
1053570 GGTCATTAAACTATTCAAAAGTTTTTAATTA
1 GGTCATTAAACTAATCAAAAGTTTTTAATTA
*
1053601 AGTCA
1 GGTCA
1053606 CTGAATTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (31 bp):
GGTCATTAAACTAATCAAAAGTTTTTAATTA
Found at i:1082671 original size:3 final size:3
Alignment explanation
Indices: 1082663--1082693 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1082653 GACCGGTTTT
1082663 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1082694 GGATGAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1083205 original size:43 final size:42
Alignment explanation
Indices: 1083092--1083232 Score: 165
Period size: 43 Copynumber: 3.3 Consensus size: 42
1083082 TTATGAGTAA
* * * * * *
1083092 AAACGCCGCTATAGAACATGATCTTTAACGACGCTTTCCCCAC
1 AAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTT-TCCAC
* *
1083135 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTTAC
1 AAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTC-CAC
* *
1083178 AAACACCGCTAAATAACATGGTCTTTAGTGGCGCTTTTCCAC
1 AAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCAC
*
1083220 AAACACCACTAAA
1 AAACACCGCTAAA
1083233 ATTAACAGAT
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
42 15 0.17
43 71 0.83
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (42 bp):
AAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCAC
Found at i:1083843 original size:26 final size:26
Alignment explanation
Indices: 1083785--1083843 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
1083775 GGTGGTAGCT
* *
1083785 AAATAAATCATGGTTAAATAGCATGC
1 AAATAAACCATGGTTAAATAGAATGC
*
1083811 AACTAAACCATGGTTAAATAGAAAT-C
1 AAATAAACCATGGTTAAATAG-AATGC
1083837 AAATAAA
1 AAATAAA
1083844 TAAATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (26 bp):
AAATAAACCATGGTTAAATAGAATGC
Found at i:1085488 original size:2 final size:2
Alignment explanation
Indices: 1085481--1085519 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1085471 GAGTGAGTGA
1085481 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1085520 AAGGAGGTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:1087184 original size:41 final size:41
Alignment explanation
Indices: 1087092--1087305 Score: 130
Period size: 41 Copynumber: 5.2 Consensus size: 41
1087082 AAACATCGCT
* * * *
1087092 ACCGCTATTGCTTAACCATTAGCGACGCTTTTCTCATAAAC
1 ACCGCTAATGCTTAACCTTTAGCAACACTTTTCTCATAAAC
** * *
1087133 GTCACTAATGCTGTAACCTTTAGCAACACTTTT-TGATAAAC
1 ACCGCTAATGCT-TAACCTTTAGCAACACTTTTCTCATAAAC
* ** * *
1087174 ACCGCTAATGCTCTGACCTTTAGCGGCGC-TTTCTCATAAAT
1 ACCGCTAATGCT-TAACCTTTAGCAACACTTTTCTCATAAAC
* * * ** *
1087215 GCTGCTAATGCTATGACCTTTAGCGGCGC-TTTCTCATAAAC
1 ACCGCTAATGCT-TAACCTTTAGCAACACTTTTCTCATAAAC
* * * ** *
1087256 GCCGCTAATGCTCTGACCTTCAGCGGCGC-TTTCTCATAAAC
1 ACCGCTAATGCT-TAACCTTTAGCAACACTTTTCTCATAAAC
*
1087297 GCCGCTAAT
1 ACCGCTAAT
1087306 ACTCTTTTCC
Statistics
Matches: 146, Mismatches: 25, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
40 3 0.02
41 126 0.86
42 17 0.12
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (41 bp):
ACCGCTAATGCTTAACCTTTAGCAACACTTTTCTCATAAAC
Found at i:1087304 original size:82 final size:82
Alignment explanation
Indices: 1087112--1087305 Score: 253
Period size: 82 Copynumber: 2.4 Consensus size: 82
1087102 CTTAACCATT
* * * * * *
1087112 AGCGACGCTTTTCTCATAAACGTCACTAATGCTGTAACCTTTAGCAACACTTTTTGATAAACACC
1 AGCGGCGC-TTTCTCATAAACGCCGCTAATGCTATAACCTTTAGCAACACTTTCTCATAAACACC
*
1087177 GCTAATGCTCTGACCTTT
65 GCTAATGCTCTGACCTTC
* * * ** * *
1087195 AGCGGCGCTTTCTCATAAATGCTGCTAATGCTATGACCTTTAGCGGCGCTTTCTCATAAACGCCG
1 AGCGGCGCTTTCTCATAAACGCCGCTAATGCTATAACCTTTAGCAACACTTTCTCATAAACACCG
1087260 CTAATGCTCTGACCTTC
66 CTAATGCTCTGACCTTC
1087277 AGCGGCGCTTTCTCATAAACGCCGCTAAT
1 AGCGGCGCTTTCTCATAAACGCCGCTAAT
1087306 ACTCTTTTCC
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
82 88 0.93
83 7 0.07
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.30
Consensus pattern (82 bp):
AGCGGCGCTTTCTCATAAACGCCGCTAATGCTATAACCTTTAGCAACACTTTCTCATAAACACCG
CTAATGCTCTGACCTTC
Found at i:1088589 original size:2 final size:2
Alignment explanation
Indices: 1088582--1088607 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1088572 TATTACATTA
1088582 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1088608 TAGTATAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1089519 original size:41 final size:41
Alignment explanation
Indices: 1089472--1089617 Score: 152
Period size: 40 Copynumber: 3.6 Consensus size: 41
1089462 AACAAACGCT
* *
1089472 GCTAATGCTCTGACCTTTAGTGGCGTTTATGAGGAAGCACC
1 GCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAGCACC
* * * *
1089513 GTTAATGCTC-GACCTTTAACGGCGTTTATTAGAAAGCGCC
1 GCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAGCACC
* * * * * **
1089553 GCTAATGCTCTAAACTATAGCGGCGTTTATTAGAAAACGTC
1 GCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAGCACC
*
1089594 GCTAATGCT-AGACCTTTAGCGGCG
1 GCTAATGCTCTGACCTTTAGCGGCG
1089618 CTTTCTTATT
Statistics
Matches: 87, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
40 45 0.52
41 42 0.48
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (41 bp):
GCTAATGCTCTGACCTTTAGCGGCGTTTATGAGAAAGCACC
Found at i:1089678 original size:41 final size:42
Alignment explanation
Indices: 1089604--1089712 Score: 114
Period size: 41 Copynumber: 2.6 Consensus size: 42
1089594 GCTAATGCTA
* * * **
1089604 GACCTTTAGCGGCGCTTT-CTTATTAACGACGTTAATGCTCT
1 GACCTTTAGCGACGCTTTCCCTATAAACGACGTTAATAATCT
** * *
1089645 GATTTTTAGTGACG-TTTCCCTATAAACGCCGTTAATAATCT
1 GACCTTTAGCGACGCTTTCCCTATAAACGACGTTAATAATCT
*
1089686 GACCTTTAGCGACGCTTTTCCTATAAA
1 GACCTTTAGCGACGCTTTCCCTATAAA
1089713 TACCGCTATT
Statistics
Matches: 53, Mismatches: 13, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
40 3 0.06
41 39 0.74
42 11 0.21
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.37
Consensus pattern (42 bp):
GACCTTTAGCGACGCTTTCCCTATAAACGACGTTAATAATCT
Found at i:1096612 original size:29 final size:30
Alignment explanation
Indices: 1096545--1096614 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 30
1096535 TTACAAAATG
* * *
1096545 ATTATTAAACTATTTAAAAGTTTTTTTTAA
1 ATTATTGAACTATTCAAAAGTTTTTTATAA
* * *
1096575 GTCACTGAACTATTCAAAA-TTTTTTATAA
1 ATTATTGAACTATTCAAAAGTTTTTTATAA
1096604 ATTATTGAACT
1 ATTATTGAACT
1096615 GTTAAGTTTT
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
29 17 0.55
30 14 0.45
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.47
Consensus pattern (30 bp):
ATTATTGAACTATTCAAAAGTTTTTTATAA
Found at i:1097385 original size:6 final size:6
Alignment explanation
Indices: 1097376--1097413 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
1097366 ATTCTCTTAA
* *
1097376 CCGCCT CCGCCT CCGCGT CCGCCT CCGCGT CCGCCT CC
1 CCGCCT CCGCCT CCGCCT CCGCCT CCGCCT CCGCCT CC
1097414 ACCCTCCTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.63, G:0.21, T:0.16
Consensus pattern (6 bp):
CCGCCT
Found at i:1097396 original size:12 final size:12
Alignment explanation
Indices: 1097376--1097413 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
1097366 ATTCTCTTAA
*
1097376 CCGCCTCCGCCT
1 CCGCGTCCGCCT
1097388 CCGCGTCCGCCT
1 CCGCGTCCGCCT
1097400 CCGCGTCCGCCT
1 CCGCGTCCGCCT
1097412 CC
1 CC
1097414 ACCCTCCTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.63, G:0.21, T:0.16
Consensus pattern (12 bp):
CCGCGTCCGCCT
Found at i:1100570 original size:18 final size:18
Alignment explanation
Indices: 1100549--1100589 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1100539 TGAGCGTGAT
1100549 CGTGACCATGATAGAGAA
1 CGTGACCATGATAGAGAA
* * *
1100567 CGTGATCGTGATAGAGAC
1 CGTGACCATGATAGAGAA
1100585 CGTGA
1 CGTGA
1100590 GCGTTATAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.17, G:0.32, T:0.20
Consensus pattern (18 bp):
CGTGACCATGATAGAGAA
Found at i:1100598 original size:18 final size:18
Alignment explanation
Indices: 1100557--1100598 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1100547 ATCGTGACCA
*
1100557 TGATAGAGAACGTGATCG
1 TGATAGAGAACGTGAGCG
*
1100575 TGATAGAGACCGTGAGCG
1 TGATAGAGAACGTGAGCG
*
1100593 TTATAG
1 TGATAG
1100599 GGAGCGGGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.12, G:0.33, T:0.24
Consensus pattern (18 bp):
TGATAGAGAACGTGAGCG
Found at i:1104744 original size:29 final size:30
Alignment explanation
Indices: 1104707--1104788 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 30
1104697 TTAATAATTG
* *
1104707 GATTGAATTT-GAATTTTGAAAAGTA-AAAA
1 GATTAAATTTAGAATTTT-AAAAATATAAAA
*
1104736 GATTAAATTTATAATTTTAAAAATATAAAA
1 GATTAAATTTAGAATTTTAAAAATATAAAA
**
1104766 -ATTAAATTTTTAATTTTTAAAAA
1 GATTAAATTTAGAA-TTTTAAAAA
1104789 ATACAGGGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 27 0.59
30 19 0.41
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (30 bp):
GATTAAATTTAGAATTTTAAAAATATAAAA
Found at i:1104756 original size:23 final size:22
Alignment explanation
Indices: 1104730--1104775 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1104720 TTTTGAAAAG
* *
1104730 TAAAAAGATTAAATTTATAATTT
1 TAAAAAGATAAAAATTA-AATTT
*
1104753 TAAAAATATAAAAATTAAATTT
1 TAAAAAGATAAAAATTAAATTT
1104775 T
1 T
1104776 TAATTTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TAAAAAGATAAAAATTAAATTT
Found at i:1104786 original size:30 final size:30
Alignment explanation
Indices: 1104718--1104788 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
1104708 ATTGAATTTG
* *
1104718 AATTTTGAAAAGTAAAAAGATTAAATTTAT
1 AATTTTTAAAAATAAAAAGATTAAATTTAT
*
1104748 AA-TTTTAAAAATATAAAA-ATTAAATTTTT
1 AATTTTTAAAAATA-AAAAGATTAAATTTAT
1104777 AATTTTTAAAAA
1 AATTTTTAAAAA
1104789 ATACAGGGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (30 bp):
AATTTTTAAAAATAAAAAGATTAAATTTAT
Found at i:1109219 original size:18 final size:18
Alignment explanation
Indices: 1109178--1109213 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1109168 AACGCGACCA
* *
1109178 TGATAGAGAGCGTGATCG
1 TGATAGAGACCGTGAGCG
1109196 TGATAGAGACCGTGAGCG
1 TGATAGAGACCGTGAGCG
1109214 CTATAGGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.39, T:0.19
Consensus pattern (18 bp):
TGATAGAGACCGTGAGCG
Found at i:1114112 original size:53 final size:53
Alignment explanation
Indices: 1114050--1114157 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
1114040 GGTTGCGGCC
1114050 ATATGATTCCAAAAGGCAAGGCATATCCCCCACTAATAAATGACTTCATTTAT
1 ATATGATTCCAAAAGGCAAGGCATATCCCCCACTAATAAATGACTTCATTTAT
1114103 ATATGATTCCAAAAGGCAAGGCATATCCCCCACTAATAAATGACTTCATTTAT
1 ATATGATTCCAAAAGGCAAGGCATATCCCCCACTAATAAATGACTTCATTTAT
1114156 AT
1 AT
1114158 CAAACTGTTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (53 bp):
ATATGATTCCAAAAGGCAAGGCATATCCCCCACTAATAAATGACTTCATTTAT
Found at i:1116717 original size:1 final size:1
Alignment explanation
Indices: 1116711--1116739 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
1116701 GAGAGAATTT
1116711 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1116740 TTGAATTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1117728 original size:16 final size:16
Alignment explanation
Indices: 1117709--1117743 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1117699 AGGTGTATTT
* *
1117709 TTAAATTTTTATTTTA
1 TTAAAATTTTATTTAA
1117725 TTAAAATTTTATTTAA
1 TTAAAATTTTATTTAA
1117741 TTA
1 TTA
1117744 TTAGCAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTAAAATTTTATTTAA
Found at i:1118135 original size:24 final size:24
Alignment explanation
Indices: 1118103--1118152 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1118093 TGATGTGGAA
1118103 CCAGTAGAAAATGAAGATCCAACT
1 CCAGTAGAAAATGAAGATCCAACT
*
1118127 CCAGTAGAAAATGAATATCCAACT
1 CCAGTAGAAAATGAAGATCCAACT
1118151 CC
1 CC
1118153 GTGTATGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.24, G:0.14, T:0.18
Consensus pattern (24 bp):
CCAGTAGAAAATGAAGATCCAACT
Found at i:1120371 original size:13 final size:12
Alignment explanation
Indices: 1120338--1120371 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1120328 CCAGTATCAG
1120338 GTATTTTTTTTC
1 GTATTTTTTTTC
*
1120350 GTATATTTTCTTC
1 GTAT-TTTTTTTC
1120363 GTATTTTTT
1 GTATTTTTT
1120372 GTCCCTTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.71
Consensus pattern (12 bp):
GTATTTTTTTTC
Found at i:1123529 original size:11 final size:10
Alignment explanation
Indices: 1123498--1123554 Score: 53
Period size: 10 Copynumber: 5.3 Consensus size: 10
1123488 TCTAAACTTT
1123498 TTTAAA-AAA
1 TTTAAATAAA
1123507 TATATAAATAAA
1 T-T-TAAATAAA
1123519 TTTAAATTAAA
1 TTTAAA-TAAA
*
1123530 TTTTAGATTAAA
1 -TTTA-AATAAA
1123542 TTTAAATAAA
1 TTTAAATAAA
1123552 TTT
1 TTT
1123555 TTTTAGTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
9 1 0.03
10 13 0.32
11 13 0.32
12 12 0.30
13 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (10 bp):
TTTAAATAAA
Found at i:1128245 original size:20 final size:19
Alignment explanation
Indices: 1128216--1128258 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1128206 TTCGAGATAA
* *
1128216 AAAATTTTATCAAAATTATT
1 AAAATATTAT-AAAATAATT
*
1128236 AAAATATTATTAAATAATT
1 AAAATATTATAAAATAATT
1128255 AAAA
1 AAAA
1128259 AAAATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATATTATAAAATAATT
Found at i:1128520 original size:19 final size:19
Alignment explanation
Indices: 1128498--1128536 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1128488 TATTTGATAT
1128498 TTATAA-AATTATTAAATAA
1 TTATAATAATT-TTAAATAA
*
1128517 TTATAATTATTTTAAATAA
1 TTATAATAATTTTAAATAA
1128536 T
1 T
1128537 AAATTTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATAATAATTTTAAATAA
Found at i:1129662 original size:15 final size:16
Alignment explanation
Indices: 1129642--1129671 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1129632 CTTTTTCAAA
1129642 TTTTAATT-TATTTAC
1 TTTTAATTATATTTAC
1129657 TTTTAATTATATTTA
1 TTTTAATTATATTTA
1129672 TTTGTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTAATTATATTTAC
Found at i:1130961 original size:31 final size:31
Alignment explanation
Indices: 1130918--1130978 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1130908 TACAAAATGG
1130918 TCACGAAACTATTCGAAAGTTTTCATTTAAA
1 TCACGAAACTATTCGAAAGTTTTCATTTAAA
* * *
1130949 TCACTAAACTATTTGAAAGTTTTTATTTAA
1 TCACGAAACTATTCGAAAGTTTTCATTTAA
1130979 CTCGTTTGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (31 bp):
TCACGAAACTATTCGAAAGTTTTCATTTAAA
Found at i:1131952 original size:31 final size:31
Alignment explanation
Indices: 1131914--1131974 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1131904 TATCAAAGTG
*
1131914 AATTTAATTGCCAAGTTCAAGGACTAAAATA
1 AATTTAATTGCCAAGTTCAAGGACAAAAATA
* *
1131945 AATTTAATTGCTAAGTTCAAGTACAAAAAT
1 AATTTAATTGCCAAGTTCAAGGACAAAAAT
1131975 GAAAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (31 bp):
AATTTAATTGCCAAGTTCAAGGACAAAAATA
Found at i:1149853 original size:76 final size:75
Alignment explanation
Indices: 1149727--1149880 Score: 274
Period size: 76 Copynumber: 2.0 Consensus size: 75
1149717 AGCCCATTGA
*
1149727 ATACCAAATTAAAGAATCTCTCTTTTTGTAAAGTAAGTTATATTATTACGAGAATATTTTCTCTT
1 ATACCAAAGTAAAGAATCTCTCTTTTTGTAAAGTAAGTTATATTATTACGAGAATA-TTTCTCTT
1149792 TTTATATTTTT
65 TTTATATTTTT
1149803 ATACCAAAGTAAAGAATC-CTTCTTTTTGTAAAGTAAGTTATATTATTACGAGAATATTTCTCTT
1 ATACCAAAGTAAAGAATCTC-TCTTTTTGTAAAGTAAGTTATATTATTACGAGAATATTTCTCTT
1149867 TTTATATTTTT
65 TTTATATTTTT
1149878 ATA
1 ATA
1149881 ATGGTTAAAG
Statistics
Matches: 76, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
75 23 0.30
76 53 0.70
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.47
Consensus pattern (75 bp):
ATACCAAAGTAAAGAATCTCTCTTTTTGTAAAGTAAGTTATATTATTACGAGAATATTTCTCTTT
TTATATTTTT
Found at i:1150182 original size:23 final size:25
Alignment explanation
Indices: 1150132--1150184 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
1150122 CCATTTATTT
*
1150132 ATTTTTTAATAATAAAAAATAAGTTA
1 ATTTTTTAATAAT-AAAAATAAGATA
*
1150158 ATTTTTTAATAGT-AAAATAA-ATA
1 ATTTTTTAATAATAAAAATAAGATA
1150181 ATTT
1 ATTT
1150185 AAAACTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 7 0.28
26 12 0.48
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (25 bp):
ATTTTTTAATAATAAAAATAAGATA
Found at i:1150747 original size:29 final size:30
Alignment explanation
Indices: 1150682--1150744 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1150672 ATATCCCTGC
1150682 AAAATTTAATAAAATTTGAGAGACTAATTA
1 AAAATTTAATAAAATTTGAGAGACTAATTA
* * *
1150712 AAAATTTAA-AAATTTTGGAGGGCCTAATTA
1 AAAATTTAATAAAATTT-GAGAGACTAATTA
1150742 AAA
1 AAA
1150745 TTTTCTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 6 0.21
30 23 0.79
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.32
Consensus pattern (30 bp):
AAAATTTAATAAAATTTGAGAGACTAATTA
Found at i:1153004 original size:16 final size:16
Alignment explanation
Indices: 1152983--1153014 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1152973 TTCATATCTT
1152983 ATAGTAAACCTATACC
1 ATAGTAAACCTATACC
1152999 ATAGTAAACCTATACC
1 ATAGTAAACCTATACC
1153015 TGAATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (16 bp):
ATAGTAAACCTATACC
Found at i:1156187 original size:12 final size:11
Alignment explanation
Indices: 1156142--1156197 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
1156132 TCACTAATCA
1156142 AAATTTTAT-T
1 AAATTTTATAT
*
1156152 TAATTTTATAT
1 AAATTTTATAT
1156163 AAATTTT-TAAT
1 AAATTTTAT-AT
1156174 AAATTATTATAT
1 AAATT-TTATAT
*
1156186 AACTTTT-TAT
1 AAATTTTATAT
1156196 AA
1 AA
1156198 CATATTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 14 0.36
11 16 0.41
12 8 0.21
13 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
AAATTTTATAT
Found at i:1157039 original size:152 final size:155
Alignment explanation
Indices: 1156851--1157248 Score: 658
Period size: 152 Copynumber: 2.6 Consensus size: 155
1156841 TTTATAATTG
* * * *
1156851 TTTTTCCTTTATTATTTTTCTCAGCAACCAAACAGATTCTGTATACAATTCATTTATAATCCCGA
1 TTTTTCCTTT-TTATTTTTCTCAGAAACCAAACAGATCCTGTATTCAATTCATTTATAATCGCGA
1156916 TTTCTATATTTCTACTAACTACATTTCCACCAGAAAAAAGAAACCATATATTATTCCATAAAAAG
65 TTTCTATATTTCTACTAACTACATTTCCACCAGAAAAAAGAAACCATATATTATTCCATAAAAAG
*
1156981 C-TT-T-TTATAAACTCTATGACCCT
130 CTTTATCTTAGAAACTCTATGACCCT
1157004 TTTTTCCTTTTTATTTTTCTCAGAAACCAAACAGATCCTGTATTCAATTCATTTATAATCGCGAT
1 TTTTTCCTTTTTATTTTTCTCAGAAACCAAACAGATCCTGTATTCAATTCATTTATAATCGCGAT
*
1157069 TTCTATATTTCTACTAACTACATTTCCTCCAGAAAAAAGAAACCATATATTATTCCATAAAAAGC
66 TTCTATATTTCTACTAACTACATTTCCACCAGAAAAAAGAAACCATATATTATTCCATAAAAAGC
1157134 TTTTAAATCCTTAGAAACTCTATGACCCT
131 -TTT--AT-CTTAGAAACTCTATGACCCT
*
1157163 TTTTTCCTTTTTATTTTTCTCAGAAACCAAACAGATCCTGTATTCAATTCATTTATAATCGTGAT
1 TTTTTCCTTTTTATTTTTCTCAGAAACCAAACAGATCCTGTATTCAATTCATTTATAATCGCGAT
*
1157228 TTCTAGATTTCTACTAACTAC
66 TTCTATATTTCTACTAACTAC
1157249 CAAAATAATT
Statistics
Matches: 230, Mismatches: 8, Indels: 8
0.93 0.03 0.03
Matches are distributed among these distances:
152 115 0.50
153 10 0.04
154 2 0.01
157 1 0.00
159 102 0.44
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (155 bp):
TTTTTCCTTTTTATTTTTCTCAGAAACCAAACAGATCCTGTATTCAATTCATTTATAATCGCGAT
TTCTATATTTCTACTAACTACATTTCCACCAGAAAAAAGAAACCATATATTATTCCATAAAAAGC
TTTATCTTAGAAACTCTATGACCCT
Found at i:1158309 original size:15 final size:15
Alignment explanation
Indices: 1158289--1158319 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1158279 GTTTTATTAT
*
1158289 TTATAAATAATAAAA
1 TTATAAAAAATAAAA
1158304 TTATAAAAAATAAAA
1 TTATAAAAAATAAAA
1158319 T
1 T
1158320 AAATATTTTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TTATAAAAAATAAAA
Found at i:1162550 original size:13 final size:13
Alignment explanation
Indices: 1162532--1162608 Score: 52
Period size: 12 Copynumber: 5.9 Consensus size: 13
1162522 CAATACTTAA
1162532 TTTATAAAAATAT
1 TTTATAAAAATAT
1162545 TTTATAAAAAAATAT
1 TTTAT--AAAAATAT
* *
1162560 ATTA-AAGATATAT
1 TTTATAA-AAATAT
**
1162573 TTTAT-AACTTAT
1 TTTATAAAAATAT
* *
1162585 TTTTTAAAACTA-
1 TTTATAAAAATAT
1162597 TTTATAAAAATA
1 TTTATAAAAATA
1162609 GATTTCCTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
12 20 0.41
13 18 0.37
15 11 0.22
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (13 bp):
TTTATAAAAATAT
Found at i:1172477 original size:13 final size:14
Alignment explanation
Indices: 1172448--1172480 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1172438 CCCAAAAAAG
1172448 TAAAAATTGTGTAT
1 TAAAAATTGTGTAT
*
1172462 TAAACATTGT-TAT
1 TAAAAATTGTGTAT
1172475 TAAAAA
1 TAAAAA
1172481 AAAAAAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (14 bp):
TAAAAATTGTGTAT
Found at i:1183761 original size:2 final size:2
Alignment explanation
Indices: 1183754--1183779 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1183744 TGAAACTTCA
1183754 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1183780 CATAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1184312 original size:93 final size:92
Alignment explanation
Indices: 1184159--1184338 Score: 290
Period size: 93 Copynumber: 1.9 Consensus size: 92
1184149 TTCTTAATTT
1184159 TTTATTCAATCAATCATTTAAGAAAAAAATTACCATAAAAATACTAAATCCAATAAATCATATTT
1 TTTATTCAATCAATCATTTAAGAAAAAAATTACCATAAAAATACTAAATCCAATAAATCATATTT
*
1184224 AATAAAGTTACCTGAATTAATTTATTG
66 AATAAAGTTACCTAAATTAATTTATTG
* * *
1184251 TTTATTCAATCAATCATTTAA-AAAAAATATTTACCATAAAAATACTAAATTCGATCAATCATAT
1 TTTATTCAATCAATCATTTAAGAAAAAA-A-TTACCATAAAAATACTAAATCCAATAAATCATAT
*
1184315 TTAATAAAGTTGCCTAAATTAATT
64 TTAATAAAGTTACCTAAATTAATT
1184339 AAATATGATT
Statistics
Matches: 81, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
91 6 0.07
92 22 0.27
93 53 0.65
ACGTcount: A:0.47, C:0.12, G:0.04, T:0.37
Consensus pattern (92 bp):
TTTATTCAATCAATCATTTAAGAAAAAAATTACCATAAAAATACTAAATCCAATAAATCATATTT
AATAAAGTTACCTAAATTAATTTATTG
Found at i:1187476 original size:20 final size:20
Alignment explanation
Indices: 1187448--1187486 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1187438 AATCCACTCT
*
1187448 AAAACTCAA-ATTAAATATCA
1 AAAAATCAACATT-AATATCA
1187468 AAAAATCAACATTAATATC
1 AAAAATCAACATTAATATC
1187487 TTTTTTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAATCAACATTAATATCA
Done.