Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008066.1 Hibiscus syriacus cultivar Beakdansim tig00110564_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 100046
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1376 original size:18 final size:18
Alignment explanation
Indices: 1353--1407 Score: 110
Period size: 18 Copynumber: 3.1 Consensus size: 18
1343 CGAGGGTTAT
1353 ATAGTGGTCCTTCGGGAC
1 ATAGTGGTCCTTCGGGAC
1371 ATAGTGGTCCTTCGGGAC
1 ATAGTGGTCCTTCGGGAC
1389 ATAGTGGTCCTTCGGGAC
1 ATAGTGGTCCTTCGGGAC
1407 A
1 A
1408 AATATTCTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.18, C:0.22, G:0.33, T:0.27
Consensus pattern (18 bp):
ATAGTGGTCCTTCGGGAC
Found at i:2029 original size:21 final size:21
Alignment explanation
Indices: 2003--2043 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1993 GATATTTTTG
2003 TGCATCGATGCACTGTAGCAA
1 TGCATCGATGCACTGTAGCAA
2024 TGCATCGATGCACTGTAGCA
1 TGCATCGATGCACTGTAGCA
2044 CTGTTCACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
TGCATCGATGCACTGTAGCAA
Found at i:6266 original size:230 final size:230
Alignment explanation
Indices: 5863--6316 Score: 881
Period size: 230 Copynumber: 2.0 Consensus size: 230
5853 TGATCATTTT
5863 TATTTTTATTTAATTAAGATAGGTTACTAAGGGTTAATAGTCAGACTTTTAACGGATTATTGACG
1 TATTTTTATTTAATTAAGATAGGTTACTAAGGGTTAATAGTCAGACTTTTAACGGATTATTGACG
*
5928 TAGCACAATGAATATATAAAATTGAAAAAAGTGAACTACATAAATGGTCATTAATATTTGAGTAA
66 TAGCACAATGAATATATAAAATTGAAAAAAGTGAACTACATAAATAGTCATTAATATTTGAGTAA
5993 GTTTTCGTTTTCCCAGTAAAATTTCAAAAGTAATAAATTGGTTGAGATAATTTTACAATATATAT
131 GTTTTCGTTTTCCCAGTAAAATTTCAAAAGTAATAAATTGGTTGAGATAATTTTACAATATATAT
6058 CCGATAATGATCCTAACCGATACAAAAATAAACCA
196 CCGATAATGATCCTAACCGATACAAAAATAAACCA
6093 TATTTTTATTTAATTAAGATAGGTTACTAAGGGTTAATAGTCAGACTTTTAACGGATTATTGACG
1 TATTTTTATTTAATTAAGATAGGTTACTAAGGGTTAATAGTCAGACTTTTAACGGATTATTGACG
*
6158 TAGCACAATGAATATATAAAATTGAAAAGAGTGAACTACATAAATAGTCATTAATATTTGAGTAA
66 TAGCACAATGAATATATAAAATTGAAAAAAGTGAACTACATAAATAGTCATTAATATTTGAGTAA
*
6223 GTTTTCGTTTTCCCAGTAAAATTTTAAAAGTAATAAATTGGTTGAGATAATTTTACAATATATAT
131 GTTTTCGTTTTCCCAGTAAAATTTCAAAAGTAATAAATTGGTTGAGATAATTTTACAATATATAT
6288 CCGATAATGATCCTAACCGATACAAAAAT
196 CCGATAATGATCCTAACCGATACAAAAAT
6317 CCACCATGAA
Statistics
Matches: 221, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
230 221 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (230 bp):
TATTTTTATTTAATTAAGATAGGTTACTAAGGGTTAATAGTCAGACTTTTAACGGATTATTGACG
TAGCACAATGAATATATAAAATTGAAAAAAGTGAACTACATAAATAGTCATTAATATTTGAGTAA
GTTTTCGTTTTCCCAGTAAAATTTCAAAAGTAATAAATTGGTTGAGATAATTTTACAATATATAT
CCGATAATGATCCTAACCGATACAAAAATAAACCA
Found at i:7763 original size:70 final size:70
Alignment explanation
Indices: 7616--7773 Score: 172
Period size: 70 Copynumber: 2.3 Consensus size: 70
7606 ACAATGCTAA
* * * *** *
7616 ACGAACACTAAATGAACGGTAAACGAACATGTTCATGAACACGTTCGTAAATGTATAAACAAATA
1 ACGAACATTAAATGAACGCTAAACGAACATGTTCATGAACAAGTTCGTAAACACATAAACAAACA
7681 CGTTC
66 CGTTC
*** * ** * *
7686 GTAAACATTAAACGAACGCTAAACGAATGTGTTCATGAACAAGTTCGTGAACACATAAACGAACA
1 ACGAACATTAAATGAACGCTAAACGAACATGTTCATGAACAAGTTCGTAAACACATAAACAAACA
*
7751 TGTTC
66 CGTTC
7756 ACGAACATTAAATGAACG
1 ACGAACATTAAATGAACG
7774 AACATGAATA
Statistics
Matches: 68, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.22
Consensus pattern (70 bp):
ACGAACATTAAATGAACGCTAAACGAACATGTTCATGAACAAGTTCGTAAACACATAAACAAACA
CGTTC
Found at i:8863 original size:24 final size:24
Alignment explanation
Indices: 8835--8889 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
8825 TTAAGGATAT
8835 ATTAATCTTGTATATATATTTTTA
1 ATTAATCTTGTATATATATTTTTA
8859 ATTAATCTTGTATATATATTTTTA
1 ATTAATCTTGTATATATATTTTTA
8883 ATTAATC
1 ATTAATC
8890 ACTAATATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (24 bp):
ATTAATCTTGTATATATATTTTTA
Found at i:8897 original size:24 final size:24
Alignment explanation
Indices: 8835--8897 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
8825 TTAAGGATAT
* *
8835 ATTAATCTTGTATATATATTTTTA
1 ATTAATCCTGAATATATATTTTTA
* *
8859 ATTAATCTTGTATATATATTTTTA
1 ATTAATCCTGAATATATATTTTTA
8883 ATTAATCACT-AATAT
1 ATTAATC-CTGAATAT
8898 CTAATCTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 35 0.97
25 1 0.03
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (24 bp):
ATTAATCCTGAATATATATTTTTA
Found at i:20343 original size:24 final size:25
Alignment explanation
Indices: 20316--20364 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
20306 ATTTTATGTT
20316 AAGAG-AT-AATTTATAAAAATTTAA
1 AAGAGAATAAATTTAT-AAAATTTAA
20340 AAGAGAATAAATTTATAAAATTTAA
1 AAGAGAATAAATTTATAAAATTTAA
20365 GGGCGAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.22
25 11 0.48
26 7 0.30
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (25 bp):
AAGAGAATAAATTTATAAAATTTAA
Found at i:20631 original size:28 final size:25
Alignment explanation
Indices: 20581--20631 Score: 66
Period size: 28 Copynumber: 1.9 Consensus size: 25
20571 TAGATTTTTA
*
20581 AAAATTTTATTTTTTGAAAAAATTC
1 AAAATTTTATTTTTTAAAAAAATTC
20606 AAAATTATTATTATTTTCAAAAAAAT
1 AAAATT-TTATT-TTTT-AAAAAAAT
20632 CTAATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 5 0.23
27 4 0.18
28 7 0.32
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (25 bp):
AAAATTTTATTTTTTAAAAAAATTC
Found at i:28110 original size:31 final size:31
Alignment explanation
Indices: 28043--28102 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
28033 CAATTTAAGG
*
28043 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
28074 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
28103 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:29037 original size:14 final size:16
Alignment explanation
Indices: 29018--29059 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
29008 CTTTATCCTT
29018 TTGTTTTG-CTT-ATC
1 TTGTTTTGTCTTAATC
29032 TTGTTTTGTCTTAATC
1 TTGTTTTGTCTTAATC
*
29048 TTCTATTTGTCT
1 TTGT-TTTGTCT
29060 CAATTTCCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 8 0.33
15 3 0.12
16 6 0.25
17 7 0.29
ACGTcount: A:0.10, C:0.14, G:0.12, T:0.64
Consensus pattern (16 bp):
TTGTTTTGTCTTAATC
Found at i:31303 original size:12 final size:13
Alignment explanation
Indices: 31267--31310 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
31257 GCCCCGATTA
31267 CCCGATTACCCGC
1 CCCGATTACCCGC
31280 CCCGATTACCCGC
1 CCCGATTACCCGC
*
31293 CCCGA-TACCCGA
1 CCCGATTACCCGC
31305 CCCGAT
1 CCCGAT
31311 AAATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.18, C:0.52, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:31391 original size:27 final size:27
Alignment explanation
Indices: 31359--31411 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
31349 AATAAATTTA
*
31359 ATTTAAATAAAAAATATATATTTATAT
1 ATTTAAATAAAAAATATATATATATAT
* * *
31386 ATTTAATTTAAATATATATATATATA
1 ATTTAAATAAAAAATATATATATATA
31412 CCCGACCCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTTAAATAAAAAATATATATATATAT
Found at i:31436 original size:24 final size:24
Alignment explanation
Indices: 31409--31463 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
31399 ATATATATAT
* * * *
31409 ATACCCGACCCGATTCTCGGCTCA
1 ATACCCGACCCAATACCCGGCCCA
31433 ATACCCGACCCAATACCCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
31457 ATACCCG
1 ATACCCG
31464 TTTATGCTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.45, G:0.15, T:0.15
Consensus pattern (24 bp):
ATACCCGACCCAATACCCGGCCCA
Found at i:31448 original size:12 final size:12
Alignment explanation
Indices: 31431--31463 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
31421 ATTCTCGGCT
31431 CAATACCCGACC
1 CAATACCCGACC
*
31443 CAATACCCGGCC
1 CAATACCCGACC
31455 CAATACCCG
1 CAATACCCG
31464 TTTATGCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.30, C:0.48, G:0.12, T:0.09
Consensus pattern (12 bp):
CAATACCCGACC
Found at i:33043 original size:18 final size:20
Alignment explanation
Indices: 33022--33073 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
33012 ATATATGAAA
33022 ATTTAAAATT-TAAAAT-TT
1 ATTTAAAATTATAAAATATT
33040 ATTTAAAATTATAAAATATT
1 ATTTAAAATTATAAAATATT
33060 -TTATAAAATTATAA
1 ATT-TAAAATTATAA
33074 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.32
19 8 0.26
20 13 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTTAAAATTATAAAATATT
Found at i:33078 original size:17 final size:17
Alignment explanation
Indices: 33025--33085 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
33015 TATGAAAATT
*
33025 TAAAATTTAAAATTTATT-
1 TAAAA-TTATAATTT-TTA
33043 TAAAATTATAAAATATTTTA
1 TAAAATTAT--AAT-TTTTA
33063 TAAAATTATAATTTTTA
1 TAAAATTATAATTTTTA
*
33080 AAAAAT
1 TAAAAT
33086 CTTTTACAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 13 0.35
18 8 0.22
19 5 0.14
20 11 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAATTATAATTTTTA
Found at i:33302 original size:26 final size:25
Alignment explanation
Indices: 33263--33326 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 25
33253 TTAAGACTAA
* *
33263 TTTA-TTTTACAAAATATTTTTTATT
1 TTTATTTTTA-AAAATATATTTAATT
33288 TTTATTATTTAAAAATATATTTAATT
1 TTTATT-TTTAAAAATATATTTAATT
33314 TTTATTTTTAAAA
1 TTTATTTTTAAAA
33327 TTTAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 11 0.31
26 20 0.57
27 4 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTATTTTTAAAAATATATTTAATT
Found at i:34762 original size:15 final size:15
Alignment explanation
Indices: 34744--34793 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
34734 AAATTTATAA
34744 ATTAAAAATATAAAG
1 ATTAAAAATATAAAG
* *
34759 ATTAAATATTGTAAA-
1 ATTAAA-AATATAAAG
34774 ATT-AAAATATAAAG
1 ATTAAAAATATAAAG
*
34788 ACTAAA
1 ATTAAA
34794 TTTAAATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
13 6 0.22
14 4 0.15
15 11 0.41
16 6 0.22
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (15 bp):
ATTAAAAATATAAAG
Found at i:35044 original size:20 final size:20
Alignment explanation
Indices: 35021--35060 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
35011 TCGAGAAAGA
*
35021 GGAAAAGAATGTAATATGGT
1 GGAAAAGAATATAATATGGT
35041 GGAAAAGAATATAATATGGT
1 GGAAAAGAATATAATATGGT
35061 TATTTACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.25
Consensus pattern (20 bp):
GGAAAAGAATATAATATGGT
Found at i:37294 original size:21 final size:21
Alignment explanation
Indices: 37270--37335 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
37260 GGGGCATATT
37270 GATATTGCTACCCGGAGTATC
1 GATATTGCTACCCGGAGTATC
* * * *
37291 GATACTGCGA---GGATAATATT
1 GATATTGCTACCCGG--AGTATC
37311 GATATTGCTACCCGGAGTATC
1 GATATTGCTACCCGGAGTATC
37332 GATA
1 GATA
37336 CTGCGAGGAT
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
18 2 0.06
20 12 0.38
21 16 0.50
23 2 0.06
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (21 bp):
GATATTGCTACCCGGAGTATC
Found at i:37322 original size:41 final size:41
Alignment explanation
Indices: 37265--37378 Score: 201
Period size: 41 Copynumber: 2.8 Consensus size: 41
37255 AAAATGGGGC
37265 ATATTGATATTGCTACCCGGAGTATCGATACTGCGAGGATA
1 ATATTGATATTGCTACCCGGAGTATCGATACTGCGAGGATA
37306 ATATTGATATTGCTACCCGGAGTATCGATACTGCGAGGATA
1 ATATTGATATTGCTACCCGGAGTATCGATACTGCGAGGATA
* * *
37347 ATATTGATACTGCTACCCTGAGTATCAATACT
1 ATATTGATATTGCTACCCGGAGTATCGATACT
37379 TCACTCTGAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (41 bp):
ATATTGATATTGCTACCCGGAGTATCGATACTGCGAGGATA
Found at i:37357 original size:20 final size:20
Alignment explanation
Indices: 37291--37359 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
37281 CCGGAGTATC
37291 GATACTGCGAGGATAATATT
1 GATACTGCGAGGATAATATT
* * * *
37311 GATATTGCTACCCGG--AGTATC
1 GATACTGCGA---GGATAATATT
37332 GATACTGCGAGGATAATATT
1 GATACTGCGAGGATAATATT
37352 GATACTGC
1 GATACTGC
37360 TACCCTGAGT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
18 2 0.06
20 20 0.56
21 12 0.33
23 2 0.06
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (20 bp):
GATACTGCGAGGATAATATT
Found at i:38166 original size:17 final size:18
Alignment explanation
Indices: 38144--38181 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
38134 AGGGTGTTGT
*
38144 ATATTTAAA-ATTTAAAA
1 ATATTTAAACAGTTAAAA
38161 ATATTTAAACAGTTAAAA
1 ATATTTAAACAGTTAAAA
38179 ATA
1 ATA
38182 AATATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (18 bp):
ATATTTAAACAGTTAAAA
Found at i:38242 original size:8 final size:7
Alignment explanation
Indices: 38221--38264 Score: 79
Period size: 7 Copynumber: 6.1 Consensus size: 7
38211 TATATGAAAT
38221 ATTAAAA
1 ATTAAAA
38228 ATTAAAA
1 ATTAAAA
38235 ATTAAAA
1 ATTAAAA
38242 ATTAAAA
1 ATTAAAA
38249 ATTAAAA
1 ATTAAAA
38256 ATATAAAA
1 AT-TAAAA
38264 A
1 A
38265 AATATAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 30 0.83
8 6 0.17
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
ATTAAAA
Found at i:38247 original size:21 final size:22
Alignment explanation
Indices: 38206--38264 Score: 84
Period size: 21 Copynumber: 2.6 Consensus size: 22
38196 TTTTGAAAGA
38206 AAAAATATATGAAATATTAAAAATT
1 AAAAATATA--AAA-ATTAAAAATT
38231 AAAAAT-TAAAAATTAAAAATT
1 AAAAATATAAAAATTAAAAATT
38252 AAAAATATAAAAA
1 AAAAATATAAAAA
38265 AATATAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
21 16 0.48
22 9 0.27
24 2 0.06
25 6 0.18
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAATATAAAAATTAAAAATT
Found at i:38273 original size:8 final size:8
Alignment explanation
Indices: 38206--38280 Score: 68
Period size: 7 Copynumber: 9.4 Consensus size: 8
38196 TTTTGAAAGA
38206 AAAAATAT
1 AAAAATAT
*
38214 ATGAAATATT
1 A-AAAATA-T
38224 AAAAAT-T
1 AAAAATAT
38231 AAAAAT-T
1 AAAAATAT
38238 AAAAAT-T
1 AAAAATAT
38245 AAAAAT-T
1 AAAAATAT
38252 AAAAATAT
1 AAAAATAT
*
38260 AAAAAAAT
1 AAAAATAT
38268 ATAAAATGAT
1 A-AAAAT-AT
38278 AAA
1 AAA
38281 GTATAAATTA
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
7 28 0.48
8 10 0.17
9 15 0.26
10 5 0.09
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.27
Consensus pattern (8 bp):
AAAAATAT
Found at i:38324 original size:32 final size:30
Alignment explanation
Indices: 38228--38320 Score: 89
Period size: 32 Copynumber: 3.0 Consensus size: 30
38218 AATATTAAAA
* * *
38228 ATTAAAAATTAAAAATTA-AAAATTAAAAAT
1 ATTAAAAAATAAAAAATATAAAA-TAAAATT
* * *
38258 ATAAAAAAATATAAAATGATAAAGTATAAATT
1 ATTAAAAAATAAAAAAT-ATAAAATA-AAATT
38290 ATTAAAAAATAAAAAATACTAAAATAAAATT
1 ATTAAAAAATAAAAAATA-TAAAATAAAATT
38321 TATTTGTACA
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
30 13 0.26
31 9 0.18
32 28 0.56
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (30 bp):
ATTAAAAAATAAAAAATATAAAATAAAATT
Found at i:41816 original size:6 final size:6
Alignment explanation
Indices: 41807--41862 Score: 60
Period size: 6 Copynumber: 9.3 Consensus size: 6
41797 TCCTCATTAG
* * *
41807 CATCAT CATCAT CATCAT CATCAT CAAT-AT CATTAT CAACAT CATTAT
1 CATCAT CATCAT CATCAT CATCAT C-ATCAT CATCAT CATCAT CATCAT
*
41855 CATTAT CA
1 CATCAT CA
41863 CTATAATTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
5 2 0.05
6 40 0.91
7 2 0.05
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.36
Consensus pattern (6 bp):
CATCAT
Found at i:41828 original size:18 final size:17
Alignment explanation
Indices: 41800--41862 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 17
41790 ATATATATCC
*
41800 TCATTAGCATCATCATCA
1 TCATTATCATCATCAT-A
*
41818 TCATCATCATCATCAATA
1 TCATTATCATCATC-ATA
*
41836 TCATTATCAACATCATTA
1 TCATTATCATCATCA-TA
41854 TCATTATCA
1 TCATTATCA
41863 CTATAATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 1 0.03
18 36 0.92
19 2 0.05
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (17 bp):
TCATTATCATCATCATA
Found at i:41871 original size:18 final size:17
Alignment explanation
Indices: 41834--41882 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
41824 TCATCATCAA
*
41834 TATCATTATCAACATCAT
1 TATCATTATC-ACATAAT
41852 TATCATTATCACTATAAT
1 TATCATTATCAC-ATAAT
*
41870 TATTATTATCACA
1 TATCATTATCACA
41883 ATTCATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.11
18 25 0.89
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (17 bp):
TATCATTATCACATAAT
Found at i:42058 original size:46 final size:46
Alignment explanation
Indices: 42008--42104 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 46
41998 AAGTGCCACT
* *
42008 TAGAAATGTCCCGAAGGACCACATAGTATTGTCCCGAAGGACCGTG
1 TAGAAATGTCCCGAAGGACCACATAGAATTGTCCCGAAGGACCGCG
* * ** *
42054 TAGAAATGTCCCGAATGACTATGTAGAATTGTCCCGAAGGACTGCG
1 TAGAAATGTCCCGAAGGACCACATAGAATTGTCCCGAAGGACCGCG
42100 TAGAA
1 TAGAA
42105 CCCTCGACTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.22
Consensus pattern (46 bp):
TAGAAATGTCCCGAAGGACCACATAGAATTGTCCCGAAGGACCGCG
Found at i:42096 original size:23 final size:23
Alignment explanation
Indices: 42008--42095 Score: 104
Period size: 23 Copynumber: 3.8 Consensus size: 23
41998 AAGTGCCACT
**
42008 TAGAAATGTCCCGAAGGACCACA
1 TAGAAATGTCCCGAAGGACCATG
* * *
42031 TAGTATTGTCCCGAAGGACCGTG
1 TAGAAATGTCCCGAAGGACCATG
* *
42054 TAGAAATGTCCCGAATGACTATG
1 TAGAAATGTCCCGAAGGACCATG
*
42077 TAGAATTGTCCCGAAGGAC
1 TAGAAATGTCCCGAAGGAC
42096 TGCGTAGAAC
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (23 bp):
TAGAAATGTCCCGAAGGACCATG
Found at i:42102 original size:23 final size:23
Alignment explanation
Indices: 41995--42104 Score: 96
Period size: 23 Copynumber: 4.8 Consensus size: 23
41985 ATAAATTGCA
*
41995 CCGAAGTG-CCACTTAGAAATGTC
1 CCGAAG-GACCACGTAGAAATGTC
* * *
42018 CCGAAGGACCACATAGTATTGTC
1 CCGAAGGACCACGTAGAAATGTC
**
42041 CCGAAGGACCGTGTAGAAATGTC
1 CCGAAGGACCACGTAGAAATGTC
* * * *
42064 CCGAATGACTATGTAGAATTGTC
1 CCGAAGGACCACGTAGAAATGTC
**
42087 CCGAAGGACTGCGTAGAA
1 CCGAAGGACCACGTAGAA
42105 CCCTCGACTC
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
22 1 0.01
23 70 0.99
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (23 bp):
CCGAAGGACCACGTAGAAATGTC
Found at i:42272 original size:14 final size:13
Alignment explanation
Indices: 42240--42315 Score: 55
Period size: 14 Copynumber: 5.2 Consensus size: 13
42230 TTTCAAATAT
42240 TCACATAGTTCAGTA
1 TCACATAGTT-A-TA
42255 TCACATAGCTTATA
1 TCACATAG-TTATA
42269 TCACAT-GTTCACATAA
1 TCACATAGTT---AT-A
*
42285 TCACATAGATCATA
1 TCACATAG-TTATA
42299 TCACATAGCTTATA
1 TCACATAG-TTATA
42313 TCA
1 TCA
42316 AATGTTCACA
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
12 2 0.04
13 1 0.02
14 24 0.47
15 13 0.25
16 9 0.18
17 1 0.02
18 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (13 bp):
TCACATAGTTATA
Found at i:42283 original size:22 final size:22
Alignment explanation
Indices: 42255--42327 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
42245 TAGTTCAGTA
42255 TCACATAGCTTATATCACATGT
1 TCACATAGCTTATATCACATGT
* * * * *
42277 TCACATA-ATCACATAGATCAT-A
1 TCACATAGCTTATAT-CA-CATGT
*
42299 TCACATAGCTTATATCAAATGT
1 TCACATAGCTTATATCACATGT
42321 TCACATA
1 TCACATA
42328 ATCACATAGA
Statistics
Matches: 36, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
21 6 0.17
22 23 0.64
23 7 0.19
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (22 bp):
TCACATAGCTTATATCACATGT
Found at i:42310 original size:44 final size:44
Alignment explanation
Indices: 42206--42431 Score: 220
Period size: 44 Copynumber: 5.0 Consensus size: 44
42196 ACATAAACAT
* * * * * *
42206 ATATCCACATAGATCATTTCACATTTTCAAATATTCACATAGTTC
1 ATAT-CACATAGCTTATATCACATTTTCACATAATCACATAGATC
*
42251 AGTATCACATAGCTTATATCACATGTTCACATAATCACATAGATC
1 A-TATCACATAGCTTATATCACATTTTCACATAATCACATAGATC
* *
42296 ATATCACATAGCTTATATCAAATGTTCACATAATCACATAGATC
1 ATATCACATAGCTTATATCACATTTTCACATAATCACATAGATC
* * * ** ** * *
42340 ATATCATATAACTTATATCACATTTTCATATGTTCATGTAGTTT
1 ATATCACATAGCTTATATCACATTTTCACATAATCACATAGATC
* *
42384 AGTATCACATAGCTTATATCA-TTTTTCTCATATATCCACATAGATC
1 A-TATCACATAGCTTATATCACATTTTCACATA-AT-CACATAGATC
42430 AT
1 AT
42432 GTAACACATA
Statistics
Matches: 147, Mismatches: 30, Indels: 8
0.79 0.16 0.04
Matches are distributed among these distances:
44 83 0.56
45 54 0.37
46 10 0.07
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.38
Consensus pattern (44 bp):
ATATCACATAGCTTATATCACATTTTCACATAATCACATAGATC
Found at i:49064 original size:15 final size:15
Alignment explanation
Indices: 49040--49071 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
49030 GGATTAAGCT
*
49040 TGCAAGATGAGGTCA
1 TGCAAAATGAGGTCA
49055 TGCAAAATGAGGTCA
1 TGCAAAATGAGGTCA
49070 TG
1 TG
49072 AAATCCATGG
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:0.34, C:0.12, G:0.31, T:0.22
Consensus pattern (15 bp):
TGCAAAATGAGGTCA
Found at i:49105 original size:29 final size:29
Alignment explanation
Indices: 49063--49129 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
49053 CATGCAAAAT
49063 GAGGTCATGAAATCCATGGTTGATTCTTA
1 GAGGTCATGAAATCCATGGTTGATTCTTA
49092 GAGGTCATGAAATCCATGGTTGATTCTTA
1 GAGGTCATGAAATCCATGGTTGATTCTTA
*
49121 AAGGTCATG
1 GAGGTCATG
49130 CAAAATGAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.33
Consensus pattern (29 bp):
GAGGTCATGAAATCCATGGTTGATTCTTA
Found at i:54374 original size:2 final size:2
Alignment explanation
Indices: 54367--54445 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
54357 AATAATTTGG
54367 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
54409 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54446 TTATGTGATA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54500 original size:19 final size:19
Alignment explanation
Indices: 54472--54509 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
54462 TCATCTTATT
*
54472 AAATAATTTAAAAACTATA
1 AAATAATTTAAAAAATATA
*
54491 AAATATTTTAAAAAATATA
1 AAATAATTTAAAAAATATA
54510 TTTAGATCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATAATTTAAAAAATATA
Found at i:57272 original size:12 final size:13
Alignment explanation
Indices: 57255--57288 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
57245 ATATTTTATT
57255 ATGATTT-GTTAA
1 ATGATTTCGTTAA
*
57267 ATGATTTCTTTAA
1 ATGATTTCGTTAA
57280 ATGATTTCG
1 ATGATTTCG
57289 GGTATGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.50
Consensus pattern (13 bp):
ATGATTTCGTTAA
Found at i:57678 original size:23 final size:23
Alignment explanation
Indices: 57644--57746 Score: 107
Period size: 23 Copynumber: 4.4 Consensus size: 23
57634 GAGTCGAAAG
* *
57644 TTCTACGCGGTCCTTCGGGGCAA
1 TTCTACGTGGTCCTTCGGGACAA
* *
57667 TTCTATGTGGTCCTTCAGGACAAA
1 TTCTACGTGGTCCTTCGGGAC-AA
* *
57691 TTCTACGTTGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
* * * *
57714 TTCTACGTGGTTCTTTGGAACAT
1 TTCTACGTGGTCCTTCGGGACAA
57737 TTCTACGTGG
1 TTCTACGTGG
57747 CACTTAAGTG
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
23 47 0.70
24 20 0.30
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:63246 original size:18 final size:18
Alignment explanation
Indices: 63223--63257 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
63213 ATCATTAACT
* *
63223 AAATATGAATAATAAAAC
1 AAATATAAAAAATAAAAC
63241 AAATATAAAAAATAAAA
1 AAATATAAAAAATAAAA
63258 ATGAAGTGAT
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:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (18 bp):
AAATATAAAAAATAAAAC
Found at i:63524 original size:19 final size:20
Alignment explanation
Indices: 63492--63530 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
63482 TCTTTTCTTT
63492 AAAAAAATCAATATAAAATAC
1 AAAAAAAT-AATATAAAATAC
63513 AAAAAAAT-ATATAAAATA
1 AAAAAAATAATATAAAATA
63531 TATGAGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAAAATAATATAAAATAC
Found at i:69829 original size:29 final size:29
Alignment explanation
Indices: 69796--69973 Score: 83
Period size: 30 Copynumber: 6.0 Consensus size: 29
69786 TTGTAATTAC
69796 TGTTTTAGCCCTTTAAGTTTCTATATTTG
1 TGTTTTAGCCCTTTAAGTTTCTATATTTG
* * * *
69825 TGTTTTAGTCCTTTAAATTTTTGT-TATTG
1 TGTTTTAGCCCTTTAAGTTTCTATAT-TTG
* * * * * *
69854 TTGTTTAATCCCTTAAAGTTTATATTTTTAC
1 -TGTTTTAGCCCTTTAAGTTTCTATATTT-G
* * **
69885 TG-TTTAGTCCTTTAAGTGTT-TGTAATTAC
1 TGTTTTAGCCCTTTAAGT-TTCTAT-ATTTG
* * *
69914 TGTTTTAGGCTTTTAAGTTTCTATTTTTTG
1 TGTTTTAGCCCTTTAAGTTTCTA-TATTTG
* * * *
69944 ATATTTTAACCCCTTCAGTTTCTATATTTG
1 -TGTTTTAGCCCTTTAAGTTTCTATATTTG
69974 CTATTTAGTC
Statistics
Matches: 107, Mismatches: 32, Indels: 19
0.68 0.20 0.12
Matches are distributed among these distances:
28 1 0.01
29 41 0.38
30 46 0.43
31 19 0.18
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.56
Consensus pattern (29 bp):
TGTTTTAGCCCTTTAAGTTTCTATATTTG
Found at i:69939 original size:59 final size:59
Alignment explanation
Indices: 69785--69941 Score: 181
Period size: 59 Copynumber: 2.7 Consensus size: 59
69775 CTCTGTTTTA
* * *
69785 TTTGTAATTACTGTTTTAGCCCTTTAAGTTTCTATATTTGTGTTTTAGTCCTTTAAATT
1 TTTGTAATTACTGTTTTAGCCCTTTAAGTTTCTATTTTTCTGTTTTAGTCCTTTAAATG
* ** * * * * *
69844 TTTGTTATTGTTGTTTAATCCCTTAAAGTTTATATTTTTACTG-TTTAGTCCTTTAAGTG
1 TTTGTAATTACTGTTTTAGCCCTTTAAGTTTCTATTTTT-CTGTTTTAGTCCTTTAAATG
* *
69903 TTTGTAATTACTGTTTTAGGCTTTTAAGTTTCTATTTTT
1 TTTGTAATTACTGTTTTAGCCCTTTAAGTTTCTATTTTT
69942 TGATATTTTA
Statistics
Matches: 77, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
59 75 0.97
60 2 0.03
ACGTcount: A:0.20, C:0.10, G:0.13, T:0.57
Consensus pattern (59 bp):
TTTGTAATTACTGTTTTAGCCCTTTAAGTTTCTATTTTTCTGTTTTAGTCCTTTAAATG
Found at i:82660 original size:16 final size:17
Alignment explanation
Indices: 82610--82661 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
82600 ATAAAAAATA
82610 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
82627 TA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
82642 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
82658 AATT
1 AATT
82662 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:84210 original size:35 final size:34
Alignment explanation
Indices: 84171--84282 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 34
84161 AAAATAGTCC
*
84171 TCAATTTCATTCTAAACCTCAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
*
84206 TCAATTTCACTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
** * *
84241 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAA-CCCAAATTCCAAAATAAT
84276 TCAATTT
1 TCAATTT
84283 AAGGTTTAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
34 1 0.01
35 63 0.94
36 3 0.04
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:85943 original size:35 final size:34
Alignment explanation
Indices: 85897--86005 Score: 128
Period size: 35 Copynumber: 3.1 Consensus size: 34
85887 AAGAAAGTAT
* **
85897 TTGAAGTATTTTAGAATTTGGGGTTTAGAATTTAA
1 TTGAA-TATTTTGGAATTTGGGGTTTAGAATGAAA
* *
85932 TTGAATTATTTTGGAATTTAGGGTTTAGAGTGAAA
1 TTGAA-TATTTTGGAATTTGGGGTTTAGAATGAAA
* *
85967 TTGACATACTTTGGAATTTGAGGTTTAGAATGAAA
1 TTGA-ATATTTTGGAATTTGGGGTTTAGAATGAAA
86002 TTGA
1 TTGA
86006 GGACTGTTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 62 0.98
36 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.24, T:0.42
Consensus pattern (34 bp):
TTGAATATTTTGGAATTTGGGGTTTAGAATGAAA
Found at i:86195 original size:29 final size:29
Alignment explanation
Indices: 86136--86198 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
86126 GCAAACGAAA
* * *
86136 TAAATGTTGAGGGACTACATTGCAAGTTT
1 TAAAAGTTGAGGGACTACAATGCAAGCTT
*
86165 TAAAAGTTGAGGGACCTA-AATGTAAGCTT
1 TAAAAGTTGAGGGA-CTACAATGCAAGCTT
86194 TAAAA
1 TAAAA
86199 ATGTTCAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 26 0.90
30 3 0.10
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (29 bp):
TAAAAGTTGAGGGACTACAATGCAAGCTT
Found at i:86884 original size:30 final size:29
Alignment explanation
Indices: 86850--87091 Score: 181
Period size: 30 Copynumber: 8.1 Consensus size: 29
86840 ATTAAAAAAG
*
86850 TAAGATAACAATAACATATATTTTTTAAAT
1 TAAGATAAAAATAA-ATATATTTTTTAAAT
** *
86880 TAAGATAAAAAT--ATATATTTAATAATT
1 TAAGATAAAAATAAATATATTTTTTAAAT
*
86907 TAAGATAAAAATAAA-ATATATTTTAAATT
1 TAAGATAAAAATAAATATATTTTTTAAA-T
* * *
86936 TGAGATCTATTAAAATAAAGAATTTTTTTTAAAAGT
1 TAAGA--TA--AAAATAAA-TATATTTTTT-AAA-T
* *
86972 TAAGATAAAAATAAAATATATTATTTAAGT
1 TAAGATAAAAAT-AAATATATTTTTTAAAT
* *
87002 TAAGATAAAACTAAAATATATTTTTTAAGT
1 TAAGATAAAAAT-AAATATATTTTTTAAAT
* * *
87032 TAAAATAAAAAT-AATATA-TATTTAAGT
1 TAAGATAAAAATAAATATATTTTTTAAAT
*
87059 TAAAGATAAATAT-AATATATTTTTTAAAAT
1 T-AAGATAAAAATAAATATATTTTTT-AAAT
87089 TAA
1 TAA
87092 TAAGTGAAAT
Statistics
Matches: 172, Mismatches: 26, Indels: 29
0.76 0.11 0.13
Matches are distributed among these distances:
27 33 0.19
28 29 0.17
29 12 0.07
30 54 0.31
31 4 0.02
32 12 0.07
33 11 0.06
34 2 0.01
35 7 0.04
36 8 0.05
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (29 bp):
TAAGATAAAAATAAATATATTTTTTAAAT
Found at i:86893 original size:25 final size:27
Alignment explanation
Indices: 86865--86919 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
86855 TAACAATAAC
**
86865 ATATATTTTTTAAATTAAGATAAAAAT
1 ATATATTTAATAAATTAAGATAAAAAT
*
86892 ATATATTTAATAATTTAAGATAAAAAT
1 ATATATTTAATAAATTAAGATAAAAAT
86919 A
1 A
86920 AAATATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (27 bp):
ATATATTTAATAAATTAAGATAAAAAT
Found at i:87768 original size:17 final size:16
Alignment explanation
Indices: 87728--87760 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
87718 AATATTTTTC
87728 AAAAATTAAATATAAA
1 AAAAATTAAATATAAA
87744 AAAAATTAAA-ATAAA
1 AAAAATTAAATATAAA
87759 AA
1 AA
87761 TTAAATTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATTAAATATAAA
Found at i:91882 original size:18 final size:19
Alignment explanation
Indices: 91851--91890 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
91841 GTGTATCTTT
91851 AAAAGATGGCTTAATATAA
1 AAAAGATGGCTTAATATAA
* *
91870 AAAAG-TGGTTTAATGTAA
1 AAAAGATGGCTTAATATAA
91888 AAA
1 AAA
91891 CAGGTGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.28
Consensus pattern (19 bp):
AAAAGATGGCTTAATATAA
Found at i:93596 original size:19 final size:19
Alignment explanation
Indices: 93572--93609 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
93562 CTAGTCAACG
93572 GGAAGTGTTGAACATTACT
1 GGAAGTGTTGAACATTACT
*
93591 GGAAGTGTTGAGCATTACT
1 GGAAGTGTTGAACATTACT
93610 CAATTAACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.32
Consensus pattern (19 bp):
GGAAGTGTTGAACATTACT
Found at i:94165 original size:20 final size:20
Alignment explanation
Indices: 94071--94439 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
94061 GATTTTCCAT
* ** *
94071 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
94091 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
94111 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
94131 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
94151 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
94171 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
94191 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
94211 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
94231 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
94251 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
94271 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
94291 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
94311 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
94331 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
94351 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
94371 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
94391 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
94411 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
94431 AATCACAAC
1 AATCGCAAC
94440 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:95155 original size:24 final size:23
Alignment explanation
Indices: 95112--95157 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
95102 AAATTTGGTC
*
95112 TTGGTCAATATCGGACTTTGATA
1 TTGGTCAATAACGGACTTTGATA
*
95135 TTGGTCAATACACGGATTTTGAT
1 TTGGTCAATA-ACGGACTTTGAT
95158 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (23 bp):
TTGGTCAATAACGGACTTTGATA
Found at i:97665 original size:19 final size:19
Alignment explanation
Indices: 97643--97947 Score: 340
Period size: 19 Copynumber: 17.4 Consensus size: 19
97633 CGGAAAATAC
*
97643 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
97662 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
97676 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
97696 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
97710 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
97728 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
97747 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
97761 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
97780 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
97799 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
97813 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
97832 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
97851 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
97869 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
97888 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
97902 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
97921 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
97940 AATCGCAA
1 AATCGCAA
97948 CGAGATAATC
Statistics
Matches: 245, Mismatches: 13, Indels: 56
0.78 0.04 0.18
Matches are distributed among these distances:
14 45 0.18
15 4 0.02
16 16 0.07
17 15 0.06
18 40 0.16
19 112 0.46
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:97715 original size:14 final size:15
Alignment explanation
Indices: 97696--97773 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 15
97686 CGGAAATGAA
97696 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
*
97710 AATCGCAATGCGAAATG
1 AATCGCAA-GCGAGA-G
*
97727 AAATCGCAATGCGAAATGAA
1 -AATCGCAA-GCG--A-GAG
97747 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
97761 AATCGCAATGCGA
1 AATCGCAA-GCGA
97774 AATGAAAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.14
17 3 0.06
18 12 0.24
19 8 0.16
20 1 0.02
21 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (15 bp):
AATCGCAAGCGAGAG
Found at i:97768 original size:33 final size:33
Alignment explanation
Indices: 97710--97928 Score: 196
Period size: 33 Copynumber: 6.2 Consensus size: 33
97700 GCAACGAGAG
97710 AATCGCAATGCGAAATGAAATCGCAATGCGAAATGAA
1 AATCGCAA--CGAAA-G-AATCGCAATGCGAAATGAA
*
97747 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAAAGAATCGCAATGCGAAATGAA
**
97780 AATCGCAATGCGAAATGAA----AAT-CGAACCGACA
1 AATCGCAA--CGAAA-GAATCGCAATGCGAAATGA-A
* *
97812 TAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 -AATCGCAA--CG-AA--AGAATCGCAATGCGAAATGAA
97851 AATCGCAATGCGAAATGAAATCGCAATGCGAAATGAA
1 AATCGCAA--CGAAA-G-AATCGCAATGCGAAATGAA
97888 AATCGCAACGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAAAGAATCGCAATGCGAAATGAA
97921 AATCGCAA
1 AATCGCAA
97929 TGCGAAATGA
Statistics
Matches: 158, Mismatches: 9, Indels: 34
0.79 0.04 0.17
Matches are distributed among these distances:
31 6 0.04
32 4 0.03
33 66 0.42
34 4 0.03
35 16 0.10
36 4 0.03
37 36 0.23
38 12 0.08
39 4 0.03
40 6 0.04
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (33 bp):
AATCGCAACGAAAGAATCGCAATGCGAAATGAA
Found at i:97783 original size:52 final size:53
Alignment explanation
Indices: 97671--97947 Score: 356
Period size: 52 Copynumber: 5.2 Consensus size: 53
97661 AAATCCCAAC
97671 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAGAGAATCGCAATGCGAA
97724 ATG-AAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAGAATCGCAATGCGAA
* * *
97775 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAGAATCGCAATGCGAA
* * *
97827 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAGA-G-AATCGCAATGCGAA
*
97883 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAGAATCGCAATGCGAA
97935 ATGAAAATCGCAA
1 ATGAAAATCGCAA
97948 CGAGATAATC
Statistics
Matches: 205, Mismatches: 10, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
51 53 0.26
52 109 0.53
53 7 0.03
54 10 0.05
56 26 0.13
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAGAATCGCAATGCGAA
Found at i:97893 original size:141 final size:136
Alignment explanation
Indices: 97643--97979 Score: 493
Period size: 141 Copynumber: 2.4 Consensus size: 136
97633 CGGAAAATAC
* * * *
97643 AATCGCAACGCGAAATGAAAATCCCAACATGAA-AATCGCAATGCGGAAATGAAAATCGC-AACG
1 AATCGCAATGCGAAATGAAAAT-CGAAC-CGAATAATCGCAATGC-GAAATTAAAATCGCAAACG
* *
97706 AGAGAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATG
63 AGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATG
97771 CGAAATGAA
128 CGAAATGAA
97780 AATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAATCGCAATACGA
1 AATCGCAATGCGAAATGAAAATCGAACCGA-ATAATCGCAATGCGAAATTAAAATCGCAA-ACG-
97845 AATGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA
63 -A-GAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA
97910 TGCGAAATGAA
126 TGCGAAATGAA
97921 AATCGCAATGCGAAATGAAAATCGCAA-CGAGATAATCGCAATGCGAAATTATAAA-CGCA
1 AATCGCAATGCGAAATGAAAATCG-AACCGA-ATAATCGCAATGCGAAATTA-AAATCGCA
97980 TTGCGATTTT
Statistics
Matches: 184, Mismatches: 7, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
135 2 0.01
136 18 0.10
137 33 0.18
138 3 0.02
140 1 0.01
141 122 0.66
142 5 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (136 bp):
AATCGCAATGCGAAATGAAAATCGAACCGAATAATCGCAATGCGAAATTAAAATCGCAAACGAGA
AAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:97985 original size:52 final size:51
Alignment explanation
Indices: 97713--97985 Score: 231
Period size: 52 Copynumber: 5.2 Consensus size: 51
97703 ACGAGAGAAT
* *
97713 CGCAATGCGAAATG-AAATCGCAATGCGAAATGAAAATCGCAA--CGAGA-G-AAT
1 CGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAA
* * *
97764 CGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCG-AA-CCGACAT--AAT
1 CGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAA
* *
97816 CGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAT
1 CGCAATGCGAAATGAAAATCGC-A-ACGAAA-G--AATCGCAATGCGAAATGAAAA
97872 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAA
1 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAA
* * *
97923 TCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTATAAA
1 -CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGA-AAA
*
97976 CGCATTGCGA
1 CGCAATGCGA
97986 TTTTCATTTC
Statistics
Matches: 201, Mismatches: 10, Indels: 21
0.87 0.04 0.09
Matches are distributed among these distances:
51 36 0.18
52 121 0.60
53 7 0.03
54 12 0.06
55 1 0.00
56 24 0.12
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.16
Consensus pattern (51 bp):
CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAA
Found at i:98084 original size:19 final size:19
Alignment explanation
Indices: 97976--98076 Score: 142
Period size: 20 Copynumber: 5.6 Consensus size: 19
97966 AAATTATAAA
97976 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
97995 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
98015 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
98031 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
98048 CGCATTGCGA-TTTCATTT
1 CGCATTGCGATTTTCATTT
98066 CGCATTGCGAT
1 CGCATTGCGAT
98077 AGTCATTTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
18 18 0.25
19 16 0.22
20 19 0.26
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:98199 original size:13 final size:13
Alignment explanation
Indices: 98183--98217 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
98173 CATCAATTAC
98183 ACAAATCAACTTT
1 ACAAATCAACTTT
*
98196 ACAAATCATCTTT
1 ACAAATCAACTTT
98209 ACAAATCAA
1 ACAAATCAA
98218 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.29
Consensus pattern (13 bp):
ACAAATCAACTTT
Done.