Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000821.1 Hibiscus syriacus cultivar Beakdansim tig00001588_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: 78671
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:17674 original size:64 final size:63
Alignment explanation
Indices: 17586--17704 Score: 193
Period size: 64 Copynumber: 1.9 Consensus size: 63
17576 ATCAACCTGG
*
17586 GGTTAAAACCTGGGGTACGCCTTTTTAAATAAAAATTTAAAAAGACGGGATTTGGATTAGGTA
1 GGTTAAAACCTGGGGTACGCCTTTTTAAATAAAAATTTAAAAAGACAGGATTTGGATTAGGTA
* * *
17649 GGTTGAAAACCTGGGGTGCGTCTTTTTAAATAAAAATTTAAAAAGACATGATTTGG
1 GGTT-AAAACCTGGGGTACGCCTTTTTAAATAAAAATTTAAAAAGACAGGATTTGG
17705 TATGCGATTC
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
63 4 0.08
64 47 0.92
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (63 bp):
GGTTAAAACCTGGGGTACGCCTTTTTAAATAAAAATTTAAAAAGACAGGATTTGGATTAGGTA
Found at i:21152 original size:20 final size:22
Alignment explanation
Indices: 21127--21184 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
21117 TTCCCCTTGA
21127 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
*
21147 AGTGCATCGATGTATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
21170 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
21185 CTACTCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:24499 original size:29 final size:30
Alignment explanation
Indices: 24452--24523 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
24442 CCCGAAGGAC
*
24452 CTATCCAGAGGTCACAAAG-ACCCCGTCAA
1 CTATCCAGAGGTCACAAAGAACCCCGGCAA
** *
24481 CTATCCAGAGGTCGTAAAGAACCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCCCGGCAA
* *
24511 CTGTCCATAGGTC
1 CTATCCAGAGGTC
24524 CTGAAGAACC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.18
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCCCGGCAA
Found at i:24523 original size:30 final size:31
Alignment explanation
Indices: 24478--24550 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
24468 AAGACCCCGT
* * *
24478 CAACTATCCAGAGGTCGTAAAGAACCT-CGG
1 CAACTGTCCATAGGTCCTAAAGAACCTACGG
* *
24508 CAACTGTCCATAGGTCCTGAAGAACCTACGT
1 CAACTGTCCATAGGTCCTAAAGAACCTACGG
*
24539 AAACTGTCCATA
1 CAACTGTCCATA
24551 TGTCTCGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 23 0.64
31 13 0.36
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (31 bp):
CAACTGTCCATAGGTCCTAAAGAACCTACGG
Found at i:25229 original size:24 final size:20
Alignment explanation
Indices: 25174--25211 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
25164 TTCCCCTTGA
25174 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
25194 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
25212 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:25309 original size:45 final size:45
Alignment explanation
Indices: 25238--25341 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 45
25228 TGTACTACTC
* * *
25238 ATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGGG
1 ATGCATCGATGCACAAATTACATTCGATGTTTT-ATCTTTAAAGAG
* * *
25283 ATGCATCGATGCACCAATTGCATTCGATGTTTTTTCTTTAAAGAG
1 ATGCATCGATGCACAAATTACATTCGATGTTTTATCTTTAAAGAG
25328 -TGCATCGATGCACA
1 ATGCATCGATGCACA
25342 TTCAATATGC
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 14 0.27
45 37 0.73
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (45 bp):
ATGCATCGATGCACAAATTACATTCGATGTTTTATCTTTAAAGAG
Found at i:28895 original size:16 final size:16
Alignment explanation
Indices: 28874--28908 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
28864 AAATTGAAAT
28874 TAATTCGAACCAAAAA
1 TAATTCGAACCAAAAA
28890 TAATTCGAACCAAAAA
1 TAATTCGAACCAAAAA
28906 TAA
1 TAA
28909 CCTAAACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.17, G:0.06, T:0.20
Consensus pattern (16 bp):
TAATTCGAACCAAAAA
Found at i:29121 original size:18 final size:18
Alignment explanation
Indices: 29098--29137 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
29088 CAACTATGGT
29098 AATAGTGTAATGAATATC
1 AATAGTGTAATGAATATC
29116 AATAGTGTAATGAATATC
1 AATAGTGTAATGAATATC
29134 AATA
1 AATA
29138 TCATTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.33
Consensus pattern (18 bp):
AATAGTGTAATGAATATC
Found at i:30062 original size:32 final size:30
Alignment explanation
Indices: 30027--30177 Score: 142
Period size: 32 Copynumber: 4.7 Consensus size: 30
30017 ACCCAAACTG
* *
30027 AAAATCAATCGATCTGATATTGACCCAATCCG
1 AAAATCAATCGAT-TGATATTGACCCGA-CCC
30059 AAAATCAATCGATTCGATATTGACCCGACCC
1 AAAATCAATCGATT-GATATTGACCCGACCC
*
30090 AAAATCTAATCGATTCGATATTGACCTGACCC
1 AAAATC-AATCGATT-GATATTGACCCGACCC
* * * *
30122 AAAATCTAATTGATTTGATATTGACTCGGTCCA
1 AAAATC-AATCGA-TTGATATTGAC-CCGACCC
30155 AAAATCAA-CTGATATGATATTGA
1 AAAATCAATC-GAT-TGATATTGA
30178 TCTGAACTGA
Statistics
Matches: 105, Mismatches: 8, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
31 10 0.10
32 83 0.79
33 12 0.11
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (30 bp):
AAAATCAATCGATTGATATTGACCCGACCC
Found at i:32419 original size:183 final size:184
Alignment explanation
Indices: 32111--32497 Score: 665
Period size: 183 Copynumber: 2.1 Consensus size: 184
32101 TTTTCTAATT
* * * *
32111 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
*
32175 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
*
32240 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
131 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGG-TTAAGCCCATATGTTA
32294 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAAATAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAAATAATTTAAATAATATATAA
*
32358 TTATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 TTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
32422 TGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTAAGCCCATATGTTA
130 TGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTAAGCCCATATGTTA
32477 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
32498 AAAATTTAAT
Statistics
Matches: 194, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
182 2 0.01
183 127 0.65
184 65 0.34
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTAAGCCCATATGTTA
Found at i:32616 original size:72 final size:72
Alignment explanation
Indices: 32537--32693 Score: 296
Period size: 72 Copynumber: 2.2 Consensus size: 72
32527 TAACCGAATT
*
32537 CGAACCGAATTAACCGTTAACCAAATTTTAAAAATTTTCTTAACCGTTAACCGACCGAACTAATT
1 CGAACCGAATTAACCGTTAACCAAATTCTAAAAATTTTCTTAACCGTTAACCGACCGAACTAATT
32602 CGATAAC
66 CGATAAC
32609 CGAACCGAATTAACCGTTAACCAAATTCTAAAAATTTTCTTAACCGTTAACCGACCGAACTAATT
1 CGAACCGAATTAACCGTTAACCAAATTCTAAAAATTTTCTTAACCGTTAACCGACCGAACTAATT
32674 CGATAAC
66 CGATAAC
*
32681 CGAATCGAATTAA
1 CGAACCGAATTAA
32694 TCAAACTAAT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 83 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (72 bp):
CGAACCGAATTAACCGTTAACCAAATTCTAAAAATTTTCTTAACCGTTAACCGACCGAACTAATT
CGATAAC
Found at i:32629 original size:21 final size:20
Alignment explanation
Indices: 32576--32630 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
32566 AAAAATTTTC
32576 TTAACCGTTAACCGACCGAA
1 TTAACCGTTAACCGACCGAA
* * *
32596 CTAATTCGATAACCGAACCGAA
1 TTAA-CCGTTAACCG-ACCGAA
32618 TTAACCGTTAACC
1 TTAACCGTTAACC
32631 AAATTCTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 3 0.11
21 15 0.56
22 9 0.33
ACGTcount: A:0.36, C:0.29, G:0.13, T:0.22
Consensus pattern (20 bp):
TTAACCGTTAACCGACCGAA
Found at i:33373 original size:211 final size:210
Alignment explanation
Indices: 33009--33426 Score: 818
Period size: 211 Copynumber: 2.0 Consensus size: 210
32999 TCAATCTTAA
33009 AAATATTATATTCTCTATTATTTCAAGAAACTCCACTTATAGGATTTCATATTAAATTGATTCTT
1 AAATATTATATTCTCTATTATTTCAAGAAACTCCACTTATAGGATTTCATATTAAATTGATTCTT
33074 TTATCTACTTTTTCAAATACTACGTGAAAACTAACATTGCAATTAAAAAGTATTTGGAGCAACAT
66 TTATCTACTTTTTCAAATACTACGTGAAAACTAACATTGCAATTAAAAAGTATTTGGAGCAACAT
33139 TTATAGAACAAACTTTTTAAATTTATAAATTTTAATGTAATATATATGTATATATTAATAATGTT
131 TTATAGAACAAACTTTTTAAATTTATAAATTTTAATGTAATATATATGTATATATTAATAATG-T
33204 TTTTTGTTTTAATTAT
195 TTTTTGTTTTAATTAT
33220 AAATATTATATTCTCTATTATTTCAAGAAACTCCACTTATAGGATTTCATATTAAATTGATTCTT
1 AAATATTATATTCTCTATTATTTCAAGAAACTCCACTTATAGGATTTCATATTAAATTGATTCTT
*
33285 TTATCTCCTTTTTCAAATACTACGTGAAAACTAACATTGCAATTAAAAAGTATTTGGAGCAACAT
66 TTATCTACTTTTTCAAATACTACGTGAAAACTAACATTGCAATTAAAAAGTATTTGGAGCAACAT
33350 TTATAGAACAAACTTTTTAAATTTATAAATTTTAATGTAATATATATGTATATATTAATAATGTT
131 TTATAGAACAAACTTTTTAAATTTATAAATTTTAATGTAATATATATGTATATATTAATAATGTT
33415 TTTTGTTTTAAT
196 TTTTGTTTTAAT
33427 AATTGGTTAT
Statistics
Matches: 206, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
210 14 0.07
211 192 0.93
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (210 bp):
AAATATTATATTCTCTATTATTTCAAGAAACTCCACTTATAGGATTTCATATTAAATTGATTCTT
TTATCTACTTTTTCAAATACTACGTGAAAACTAACATTGCAATTAAAAAGTATTTGGAGCAACAT
TTATAGAACAAACTTTTTAAATTTATAAATTTTAATGTAATATATATGTATATATTAATAATGTT
TTTTGTTTTAATTAT
Found at i:37024 original size:17 final size:17
Alignment explanation
Indices: 36999--37048 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
36989 AAAATATGTA
36999 AAAAT-ATAATATTAAT
1 AAAATAATAATATTAAT
*
37015 AAAATAATAATATAAAT
1 AAAATAATAATATTAAT
37032 ATAAA-AATAATAATTAA
1 A-AAATAATAAT-ATTAA
37049 AATAGCGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 5 0.17
17 17 0.59
18 7 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATAATAATATTAAT
Found at i:37383 original size:91 final size:92
Alignment explanation
Indices: 37230--37429 Score: 260
Period size: 91 Copynumber: 2.2 Consensus size: 92
37220 GACGACACTA
* * ** *
37230 CTCATACGTGATGAAGAGGTCTGGTCGTCTAAGGGTGGATGATAACTCGGTTCCTACGTGATGAG
1 CTCATACGTGATGAAGAGGTCTGGCCATCTAAGGAAGGATGATAACACGGTTCCTACGTGATGAG
* *
37295 GACGACTGGTT-GGT-GGATGACATGG
66 GACGACTGGTTAGCTAGGATGACACGG
* * *
37320 CTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGTGATGA
1 CTCATACGTGATGAAGAGGTCTGGCCATC-TAAGGAAGGATGATAACACGGTTCCTACGTGATGA
* * *
37385 GGACGGCTGGTTATCTAGGGTGACACGG
65 GGACGACTGGTTAGCTAGGATGACACGG
37413 CTCATACGTGATGAAGA
1 CTCATACGTGATGAAGA
37430 TCTGGTCGGG
Statistics
Matches: 94, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
90 26 0.28
91 41 0.44
92 1 0.01
93 26 0.28
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (92 bp):
CTCATACGTGATGAAGAGGTCTGGCCATCTAAGGAAGGATGATAACACGGTTCCTACGTGATGAG
GACGACTGGTTAGCTAGGATGACACGG
Found at i:37579 original size:28 final size:28
Alignment explanation
Indices: 37559--37620 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
37549 AAACCAAATT
37559 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
37587 AAAGATTTGTTTCAAGAA-AAATAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
37615 AAAGAT
1 AAAGAT
37621 GATATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:38610 original size:66 final size:66
Alignment explanation
Indices: 38540--38665 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 66
38530 AAACGGTCTC
* * *
38540 AAGAGATACAAAATTCAT-TTT-AAGAGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTAT
1 AAGAGAGACAAAATT-ATGTTTCAA-AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTAT
38603 CTT
64 CTT
*
38606 AAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
1 AAGAGAGACAAAATTATGTTT-CAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
38666 CAATCTCAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
65 1 0.02
66 17 0.32
67 33 0.62
68 2 0.04
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (66 bp):
AAGAGAGACAAAATTATGTTTCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCT
T
Found at i:38653 original size:30 final size:30
Alignment explanation
Indices: 38619--38682 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
38609 AGAGACAAAA
*
38619 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
*
38649 TTTTGTTTCAAAAGAAACAATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
38679 TTTT
1 TTTT
38683 TCACAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:38744 original size:52 final size:53
Alignment explanation
Indices: 38670--38772 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 53
38660 AAGAAACAAT
* *
38670 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAACACTTTGTTTCAGA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGAAAAAACTTTGTTTCAGA
* *
38723 CTCAAAGA-TTTTTCACGAAATTGTCTTAAGAGAGAAAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGAAAAAACTTTGTTTCA
38773 AAATAAATAG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 38 0.83
53 8 0.17
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.33
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGAAAAAACTTTGTTTCAGA
Found at i:38829 original size:28 final size:29
Alignment explanation
Indices: 38769--38892 Score: 132
Period size: 29 Copynumber: 4.4 Consensus size: 29
38759 AAAACTTTGT
* *
38769 TTCAAAATAAATAGACTCAAAGAT-TTT-
1 TTCAAAAGAAACAGACTCAAAGATATTTA
38796 TTCAAAAGAAACA-ACTCAAAGATATTTA
1 TTCAAAAGAAACAGACTCAAAGATATTTA
* * * *
38824 TTCAAAAGGAACAAACTCCAAGATTTTTA
1 TTCAAAAGAAACAGACTCAAAGATATTTA
*
38853 TTCAAAAGGAACAGACTCAAAG--ATTTA
1 TTCAAAAGAAACAGACTCAAAGATATTTA
*
38880 TCTCAAGAGAAAC
1 T-TCAAAAGAAAC
38893 TGTCTCCAGA
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
26 10 0.12
27 19 0.23
28 21 0.25
29 33 0.40
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.26
Consensus pattern (29 bp):
TTCAAAAGAAACAGACTCAAAGATATTTA
Found at i:38852 original size:29 final size:29
Alignment explanation
Indices: 38783--38878 Score: 135
Period size: 29 Copynumber: 3.4 Consensus size: 29
38773 AAATAAATAG
*
38783 ACTCAAAGA-TTTT-TTCAAAAGAAAC-A
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
38809 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
* *
38838 ACTCCAAGATTTTTATTCAAAAGGAACAG
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
38867 ACTCAAAGATTT
1 ACTCAAAGATTT
38879 ATCTCAAGAG
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
26 9 0.15
27 3 0.05
28 11 0.18
29 38 0.62
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (29 bp):
ACTCAAAGATTTTTATTCAAAAGGAACAA
Found at i:38900 original size:57 final size:54
Alignment explanation
Indices: 38769--38892 Score: 133
Period size: 57 Copynumber: 2.2 Consensus size: 54
38759 AAAACTTTGT
* * * *
38769 TTCAAAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCCAAGATTTTTTCAAAAGAAACAACTCAAAGA-ATTTA
* *
38824 TTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAAGGAACAGACTCAAAG-ATTTA
1 TTCAAAAGAAACAAACTCCAAGA-TTTT-TTCAAAAGAAACA-ACTCAAAGAATTTA
*
38880 TCTCAAGAGAAAC
1 T-TCAAAAGAAAC
38893 TGTCTCCAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
55 18 0.32
56 10 0.18
57 21 0.37
58 8 0.14
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.26
Consensus pattern (54 bp):
TTCAAAAGAAACAAACTCCAAGATTTTTTCAAAAGAAACAACTCAAAGAATTTA
Found at i:39221 original size:36 final size:35
Alignment explanation
Indices: 39137--39234 Score: 117
Period size: 36 Copynumber: 2.8 Consensus size: 35
39127 GAGAAAATGA
* * *
39137 TGTCTCAAGCGAGACGAAATTTG-CTTTAAGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
* **
39171 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTA-AGAAAT
*
39207 TGTCTCAAGCGAGACAAAGTTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT
39235 GAGGAAACGA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 19 0.37
35 4 0.08
36 29 0.56
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
Found at i:39249 original size:36 final size:36
Alignment explanation
Indices: 39138--39256 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
39128 AGAAAATGAT
* * * *
39138 GTCTCAAGCGAGACGAAATTTG-CTTTA-AGATATA
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
** *
39172 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
*
39208 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGGAAA-C
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGA-GAAATC
*
39243 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
39257 TCAACTTTGT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
34 19 0.27
35 7 0.10
36 44 0.63
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
Found at i:39395 original size:105 final size:105
Alignment explanation
Indices: 39211--39448 Score: 283
Period size: 105 Copynumber: 2.3 Consensus size: 105
39201 AGAAATTGTC
* * *
39211 TCAAGCGAGAC-AAAGTTTGTTTT-TGAG-GA-AACGATCTCAA-GTGAGATCAACTTTGTTTAA
1 TCAAGCGAGACGAAA-TTTGTTTTAAGAGAAACAACAATCT-AAGGTGAGATCAACTTTGTTTAA
* *
39271 TGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAGGTA
64 TGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAGGTA
* *
39313 TCAAGCGAGACGAAATTTGTTTTGAA-AGAAACAACAATCTAAGGTGAGATTAATTTTGTTTTAA
1 TCAAGCGAGACGAAATTTGTTTT-AAGAGAAACAACAATCTAAGGTGAGATCAACTTTG-TTTAA
* * * *
39377 -GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAATGTC
64 TGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAGGTA
*
39418 TCAAGCGAGACGAAGTTTGTTTTAAGAGAAA
1 TCAAGCGAGACGAAATTTGTTTTAAGAGAAA
39449 ATTGTCTCAA
Statistics
Matches: 116, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
102 19 0.16
103 5 0.04
104 5 0.04
105 82 0.71
106 5 0.04
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (105 bp):
TCAAGCGAGACGAAATTTGTTTTAAGAGAAACAACAATCTAAGGTGAGATCAACTTTGTTTAATG
TGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAGGTA
Found at i:39449 original size:37 final size:36
Alignment explanation
Indices: 39389--39552 Score: 181
Period size: 37 Copynumber: 4.4 Consensus size: 36
39379 GAATCAAATT
* *
39389 CAAAATTTGTATCTCAAAGGAAAAATGTCTCAAGCGAGA
1 CAAAATTTGT-T-TTAAA-GAAAATTGTCTCAAGCGAGA
* *
39428 CGAAGTTTGTTTTAAGAGAAAATTGTCTCAAGCGAGA
1 CAAAATTTGTTTTAA-AGAAAATTGTCTCAAGCGAGA
* **
39465 CAAAATTTGTTTT-TAGAAAGCTGTCTCAAGCGAGA
1 CAAAATTTGTTTTAAAGAAAATTGTCTCAAGCGAGA
39500 CAAAATTT-TCTTTGAAAG-AAATTGTCTCAAGCGAGA
1 CAAAATTTGT-TTT-AAAGAAAATTGTCTCAAGCGAGA
39536 CAAAAATTTGTTTTAAA
1 C-AAAATTTGTTTTAAA
39553 ATTCTCAAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
34 1 0.01
35 30 0.28
36 20 0.19
37 45 0.42
38 3 0.03
39 8 0.07
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (36 bp):
CAAAATTTGTTTTAAAGAAAATTGTCTCAAGCGAGA
Found at i:39499 original size:72 final size:72
Alignment explanation
Indices: 39414--39549 Score: 206
Period size: 72 Copynumber: 1.9 Consensus size: 72
39404 AAAGGAAAAA
* *
39414 TGTCTCAAGCGAGACGAAGTTTGT-TTT-AAGAGAAAATTGTCTCAAGCGAGAC-AAAATTTGTT
1 TGTCTCAAGCGAGACAAAATTT-TCTTTGAA-AG-AAATTGTCTCAAGCGAGACAAAAATTTGTT
39476 TTTAGAAAGC
63 TTTAGAAAGC
39486 TGTCTCAAGCGAGACAAAATTTTCTTTGAAAGAAATTGTCTCAAGCGAGACAAAAATTTGTTTT
1 TGTCTCAAGCGAGACAAAATTTTCTTTGAAAGAAATTGTCTCAAGCGAGACAAAAATTTGTTTT
39550 AAAATTCTCA
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
71 20 0.34
72 37 0.63
73 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (72 bp):
TGTCTCAAGCGAGACAAAATTTTCTTTGAAAGAAATTGTCTCAAGCGAGACAAAAATTTGTTTTT
AGAAAGC
Found at i:41880 original size:26 final size:26
Alignment explanation
Indices: 41802--41883 Score: 86
Period size: 26 Copynumber: 3.4 Consensus size: 26
41792 TTTCAAGGTG
41802 GAAAGAATGTTTCAAGGTCTCAAAGA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
**
41828 GAGGGAATGTTTCAAGG-C-C---GA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
*
41849 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
*
41874 GATAGAATGT
1 GAAAGAATGT
41884 CAAAAATTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
20 13 0.30
21 3 0.07
22 1 0.02
24 1 0.02
25 3 0.07
26 22 0.51
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23
Consensus pattern (26 bp):
GAAAGAATGTTTCAAGGTCTCAAAGA
Found at i:41882 original size:46 final size:45
Alignment explanation
Indices: 41790--41883 Score: 134
Period size: 46 Copynumber: 2.1 Consensus size: 45
41780 ATAAATACAG
* * * *
41790 TGTTTCAAGGTGGAAAGAATGTTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGCGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
*
41835 TGTTTCAAGGCCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGG-CGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
41881 TGT
1 TGT
41884 CAAAAATTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 10 0.23
46 33 0.77
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.26
Consensus pattern (45 bp):
TGTTTCAAGGCGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:46088 original size:10 final size:11
Alignment explanation
Indices: 46073--46111 Score: 55
Period size: 10 Copynumber: 3.7 Consensus size: 11
46063 GATCATAGCA
46073 AATAAT-AAAT
1 AATAATAAAAT
46083 AATAATAAAAT
1 AATAATAAAAT
*
46094 AA-AGTAAAAT
1 AATAATAAAAT
46104 AATAATAA
1 AATAATAA
46112 TATATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:48176 original size:106 final size:106
Alignment explanation
Indices: 47992--49192 Score: 2032
Period size: 106 Copynumber: 11.4 Consensus size: 106
47982 GCATTGTTCC
* * * * * *
47992 GAGTCCAATACCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * * * *
48057 CCACCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** * *
48098 GAGTCCAATATCCTTTGCAGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
48163 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
48204 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
48268 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
48309 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
48374 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
48415 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
48479 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
48520 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
48585 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
48626 GAGTCCAATATCCTTCGTTGTGAAGCTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
48690 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
48731 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
48796 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
48837 GAGTCCAATATACTTCGTTGTGAAGCTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
48901 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
48942 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
49007 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
49048 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* *
49113 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
49154 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
49193 AAAGGCTGTA
Statistics
Matches: 1040, Mismatches: 51, Indels: 8
0.95 0.05 0.01
Matches are distributed among these distances:
105 404 0.39
106 636 0.61
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:48291 original size:211 final size:211
Alignment explanation
Indices: 47992--49192 Score: 2069
Period size: 211 Copynumber: 5.7 Consensus size: 211
47982 GCATTGTTCC
* * * * * *
47992 GAGTCCAATACCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
* * * * * * **
48057 CCACCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTTGCAGTGAA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * *
48122 GTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
130 GTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
48187 TGAACTTGCGTTGTCTT
195 TGAACTTGCGTTGTCTG
48204 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
48269 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* *
48334 TTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
48399 GAACTTGCGTTGTCTG
196 GAACTTGCGTTGTCTG
48415 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
48480 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* *
48545 TTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
48610 GAACTTGCGTTGTCTG
196 GAACTTGCGTTGTCTG
*
48626 GAGTCCAATATCCTTCGTTGTGAAGCTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
48691 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
*
48756 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
*
48821 GAACTTACGTTGTCTG
196 GAACTTGCGTTGTCTG
* *
48837 GAGTCCAATATACTTCGTTGTGAAGCTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
48902 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
*
48967 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
*
49032 GAACTTACGTTGTCTG
196 GAACTTGCGTTGTCTG
* *
49048 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAA
* *
49113 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTATCTGGAGTCCAATATCCTTCGTTGTGAA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
49178 GTTGAAATTGGCTCT
130 GTTGAAATTGGCTCT
49193 AAAGGCTGTA
Statistics
Matches: 954, Mismatches: 34, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
211 820 0.86
212 134 0.14
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (211 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
TTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
GAACTTGCGTTGTCTG
Found at i:52859 original size:10 final size:11
Alignment explanation
Indices: 52844--52882 Score: 55
Period size: 10 Copynumber: 3.7 Consensus size: 11
52834 GATCATAGCA
52844 AATAAT-AAAT
1 AATAATAAAAT
52854 AATAATAAAAT
1 AATAATAAAAT
*
52865 AA-AGTAAAAT
1 AATAATAAAAT
52875 AATAATAA
1 AATAATAA
52883 TATATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:55398 original size:17 final size:17
Alignment explanation
Indices: 55373--55422 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
55363 AAAATATGTA
55373 AAAAT-ATAATATTAAT
1 AAAATAATAATATTAAT
*
55389 AAAATAATAATATAAAT
1 AAAATAATAATATTAAT
55406 ATAAA-AATAATAATTAA
1 A-AAATAATAAT-ATTAA
55423 AATAGCGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 5 0.17
17 17 0.59
18 7 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATAATAATATTAAT
Found at i:56480 original size:19 final size:19
Alignment explanation
Indices: 56456--56512 Score: 114
Period size: 19 Copynumber: 3.0 Consensus size: 19
56446 AAGAACAACA
56456 CTTAATGGCATGTAACCCT
1 CTTAATGGCATGTAACCCT
56475 CTTAATGGCATGTAACCCT
1 CTTAATGGCATGTAACCCT
56494 CTTAATGGCATGTAACCCT
1 CTTAATGGCATGTAACCCT
56513 GTCGTCGTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (19 bp):
CTTAATGGCATGTAACCCT
Found at i:57893 original size:29 final size:29
Alignment explanation
Indices: 57850--57932 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
57840 CTCACCTAAC
*
57850 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
57880 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
* *
57909 TAAATGATGCAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
57933 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:62659 original size:29 final size:29
Alignment explanation
Indices: 62613--62695 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
62603 CTCACCTAAC
*
62613 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
* *
62643 TAAATGATGTAAACAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
62672 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
62696 ATTTAGTTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 43 0.91
30 4 0.09
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:64290 original size:10 final size:10
Alignment explanation
Indices: 64275--64305 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
64265 TAAATTCTAG
64275 TGAACAATGT
1 TGAACAATGT
64285 TGAACAATGT
1 TGAACAATGT
*
64295 TGAACTATGT
1 TGAACAATGT
64305 T
1 T
64306 ACATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (10 bp):
TGAACAATGT
Found at i:68022 original size:13 final size:14
Alignment explanation
Indices: 67984--68017 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
67974 TTATTAATAC
67984 ATTTTTTATGC-ATT
1 ATTTTTTAT-CTATT
67998 ATTTTTTATCTATT
1 ATTTTTTATCTATT
68012 ATTTTT
1 ATTTTT
68018 CTCTACATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 1 0.05
14 18 0.95
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (14 bp):
ATTTTTTATCTATT
Found at i:74871 original size:20 final size:20
Alignment explanation
Indices: 74846--74894 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
74836 TGTTCGTTTT
*
74846 TATCGATACT-GACCTTTCAG
1 TATCGATACTAAACCTTT-AG
*
74866 TATCGATACTAAACCTTTGG
1 TATCGATACTAAACCTTTAG
74886 TATCGATAC
1 TATCGATAC
74895 CCACTTACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (20 bp):
TATCGATACTAAACCTTTAG
Found at i:75092 original size:41 final size:41
Alignment explanation
Indices: 75046--75129 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
75036 TTGAAAAAAC
75046 CCCAATATTGATACCCATATGGGGGTTTATCGATACTCCTA
1 CCCAATATTGATACCCATATGGGGGTTTATCGATACTCCTA
*
75087 CCCAATATTGATACCCCTATGGGGGTTTATCGATACTCCTA
1 CCCAATATTGATACCCATATGGGGGTTTATCGATACTCCTA
75128 CC
1 CC
75130 ATGATATAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (41 bp):
CCCAATATTGATACCCATATGGGGGTTTATCGATACTCCTA
Found at i:77982 original size:18 final size:18
Alignment explanation
Indices: 77944--77995 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
77934 TAGAGAAAAT
* *
77944 ATAATAAGAATAAAATAAT
1 ATAATAATAA-AAAATAAG
*
77963 A-AAT-ATAATAAATAAG
1 ATAATAATAAAAAATAAG
77979 ATAATAATAAAAAATAA
1 ATAATAATAAAAAATAA
77996 ATTAAAGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 7 0.26
17 6 0.22
18 13 0.48
19 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (18 bp):
ATAATAATAAAAAATAAG
Found at i:77982 original size:21 final size:23
Alignment explanation
Indices: 77940--77985 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
77930 ATATTAGAGA
77940 AAATATAATAAGAATAAAATAAT
1 AAATATAATAAGAATAAAATAAT
*
77963 AAATATAAT-A-AATAAGATAAT
1 AAATATAATAAGAATAAAATAAT
77984 AA
1 AA
77986 TAAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 1 0.05
23 9 0.41
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (23 bp):
AAATATAATAAGAATAAAATAAT
Found at i:77987 original size:27 final size:28
Alignment explanation
Indices: 77941--77994 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
77931 TATTAGAGAA
*
77941 AATATAATAAGAATAAAATAATAAATAT
1 AATATAATAAGAATAAAATAAAAAATAT
77969 AATA-AATAAG-ATAATAATAAAAAATA
1 AATATAATAAGAATAA-AATAAAAAATA
77995 AATTAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 16 0.67
28 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (28 bp):
AATATAATAAGAATAAAATAAAAAATAT
Found at i:78003 original size:24 final size:22
Alignment explanation
Indices: 77955--78020 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 22
77945 TAATAAGAAT
77955 AAAATAATAAATATAATAAATAAG
1 AAAATAATAAA-A-AATAAATAAG
*
77979 ATAATAATAAAAAATAAATTAAAG
1 AAAATAATAAAAAATAAA-T-AAG
*
78003 AAAATACTAAAAATATAA
1 AAAATAATAAAAA-ATAA
78021 GGAACAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 6 0.17
23 2 0.06
24 24 0.67
25 4 0.11
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (22 bp):
AAAATAATAAAAAATAAATAAG
Found at i:78008 original size:32 final size:33
Alignment explanation
Indices: 77932--78008 Score: 81
Period size: 32 Copynumber: 2.4 Consensus size: 33
77922 TATGTAAAAT
*
77932 ATTAGAGAAAATATAATAAGAATAAAATAATAA
1 ATTAAAGAAAATATAATAAGAATAAAATAATAA
* *
77965 A-TATAA-TAAATA-AGATAATAATAAAA-AATAA
1 ATTA-AAGAAAATATA-ATAAGAATAAAATAATAA
77996 ATTAAAGAAAATA
1 ATTAAAGAAAATA
78009 CTAAAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
31 9 0.25
32 25 0.69
33 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (33 bp):
ATTAAAGAAAATATAATAAGAATAAAATAATAA
Done.