Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006049.1 Hibiscus syriacus cultivar Beakdansim tig00014306_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: 112188
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:20997 original size:29 final size:29
Alignment explanation
Indices: 20964--21077 Score: 183
Period size: 29 Copynumber: 3.9 Consensus size: 29
20954 TCCTAACACA
* * *
20964 TAGGTCGTCATGCCCTCCGGGCGACCTTT
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
* *
20993 TAGGTCGCCATGCCCTCCGGGTGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
21022 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
21051 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
21078 ACCCTCGCTC
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 80 1.00
ACGTcount: A:0.12, C:0.35, G:0.30, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:21122 original size:33 final size:33
Alignment explanation
Indices: 21081--21168 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 33
21071 GCGACCTACC
* *
21081 CTCGCTCGGCTT-CCCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTCGGATGCCCTCACATAG
21114 CTCGCTCGGTTGCCCTCGGATGCCCTCACATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCACATAG
* * * *
21147 CTCGTTCAGATGGCCTCGGATG
1 CTCGCTCGGTTGCCCTCGGATG
21169 GGCTCGGTCG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
32 2 0.04
33 46 0.96
ACGTcount: A:0.11, C:0.38, G:0.25, T:0.26
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCACATAG
Found at i:21182 original size:24 final size:24
Alignment explanation
Indices: 21146--21191 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
21136 CCCTCACATA
*
21146 GCTCGTTCAGATGGCCTCGGATGG
1 GCTCGGTCAGATGGCCTCGGATGG
*
21170 GCTCGGTCGGATGGCCTCGGAT
1 GCTCGGTCAGATGGCCTCGGAT
21192 TCCCAGCGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.26, G:0.39, T:0.24
Consensus pattern (24 bp):
GCTCGGTCAGATGGCCTCGGATGG
Found at i:21615 original size:24 final size:24
Alignment explanation
Indices: 21588--21638 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
21578 TCATAATTTC
*
21588 AAATTAAAAAATAATAGAGAACAA
1 AAATTAAAAAAGAATAGAGAACAA
21612 AAA-TAAAAAAGAATAGAGAACAA
1 AAATTAAAAAAGAATAGAGAACAA
21635 AAAT
1 AAAT
21639 CATTAATGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.73, C:0.04, G:0.10, T:0.14
Consensus pattern (24 bp):
AAATTAAAAAAGAATAGAGAACAA
Found at i:23223 original size:15 final size:15
Alignment explanation
Indices: 23203--23238 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
23193 ATATTTAGCT
* *
23203 GGGCGGGCCGATGTG
1 GGGCGGGCAGATGCG
23218 GGGCGGGCAGATGCG
1 GGGCGGGCAGATGCG
23233 GGGCGG
1 GGGCGG
23239 ATGTGGGGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.08, C:0.19, G:0.64, T:0.08
Consensus pattern (15 bp):
GGGCGGGCAGATGCG
Found at i:23772 original size:19 final size:19
Alignment explanation
Indices: 23734--23773 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
23724 TACATAAACA
*
23734 TATTTTTAAGTATTTATAT
1 TATTTTTAAATATTTATAT
23753 TATTATTTAAATATTT-TAT
1 TATT-TTTAAATATTTATAT
23772 TA
1 TA
23774 AGTTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TATTTTTAAATATTTATAT
Found at i:23948 original size:2 final size:2
Alignment explanation
Indices: 23941--23976 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
23931 CTTTTTAATA
23941 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23977 GAAAACCGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25337 original size:2 final size:2
Alignment explanation
Indices: 25330--25360 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25320 AAAATTTTAA
25330 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25361 ATAGGTAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28563 original size:29 final size:29
Alignment explanation
Indices: 28531--28716 Score: 144
Period size: 29 Copynumber: 6.3 Consensus size: 29
28521 AAATTTCTAA
* *
28531 AATGTCATCTTTTTTAAAATAATTCTCAG
1 AATGTCATCTTTTTCAAAATAATTCCCAG
* * * * *
28560 AATGTCACCTTTTTCAAAACATTTTCTAG
1 AATGTCATCTTTTTCAAAATAATTCCCAG
* * *
28589 AATGTCAACTTTTTTTTCAAAATATTTCCCCG
1 AATGTC-A--TCTTTTTCAAAATAATTCCCAG
* * *
28621 AATGTTACCCTTTTTCAAAATATTTCCCAG
1 AATGTCA-TCTTTTTCAAAATAATTCCCAG
* * *
28651 AATATCA-CATTTTTCAAAATATTTCCTAG
1 AATGTCATC-TTTTTCAAAATAATTCCCAG
28680 AATGTCA-CATTTTTCACAAA-AATTCCCAG
1 AATGTCATC-TTTTTCA-AAATAATTCCCAG
28709 AATGTCAT
1 AATGTCAT
28717 TGGGTCGGGT
Statistics
Matches: 127, Mismatches: 24, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
28 1 0.01
29 76 0.60
30 28 0.22
31 1 0.01
32 21 0.17
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.40
Consensus pattern (29 bp):
AATGTCATCTTTTTCAAAATAATTCCCAG
Found at i:36073 original size:28 final size:28
Alignment explanation
Indices: 36042--36130 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
36032 TGTCACTTTT
* *
36042 TTTTCAAAATAATTCTCAAAATGTCATCT
1 TTTTCAAAATATTTCTCAAAATGTCA-CA
* * *
36071 TTTTTAAAACATTTC-CTAGAATGTCACA
1 TTTTCAAAATATTTCTC-AAAATGTCACA
**
36099 TTTTCAAAATATTTCTCAGGATGTCACA
1 TTTTCAAAATATTTCTCAAAATGTCACA
36127 TTTT
1 TTTT
36131 TCACAAAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
28 29 0.58
29 21 0.42
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.43
Consensus pattern (28 bp):
TTTTCAAAATATTTCTCAAAATGTCACA
Found at i:36123 original size:57 final size:57
Alignment explanation
Indices: 36042--36154 Score: 140
Period size: 57 Copynumber: 2.0 Consensus size: 57
36032 TGTCACTTTT
* * *
36042 TTTTCAAAATAATTCTCAAAATGTCATC-TTTTTTA-AAACATTTCCTAGAATGTCACA
1 TTTTCAAAATAATTCTCAAAATGTCA-CATTTTTCACAAA-AATTCCCAGAATGTCACA
* **
36099 TTTTCAAAATATTTCTCAGGATGTCACATTTTTCACAAAAATTCCCAGAATGTCAC
1 TTTTCAAAATAATTCTCAAAATGTCACATTTTTCACAAAAATTCCCAGAATGTCAC
36155 TGGGTCGGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
56 1 0.02
57 44 0.92
58 3 0.06
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.38
Consensus pattern (57 bp):
TTTTCAAAATAATTCTCAAAATGTCACATTTTTCACAAAAATTCCCAGAATGTCACA
Found at i:36151 original size:29 final size:29
Alignment explanation
Indices: 36041--36154 Score: 108
Period size: 29 Copynumber: 4.0 Consensus size: 29
36031 ATGTCACTTT
* *
36041 TTTTTCAAAATAATTCTCAAAATGTCATC-
1 TTTTTCAAAATAATTCCCAGAATGTCA-CA
* * * *
36070 TTTTTTAAAACATTTCCTAGAATGTCACA
1 TTTTTCAAAATAATTCCCAGAATGTCACA
* * *
36099 -TTTTCAAAATATTTCTCAGGATGTCACA
1 TTTTTCAAAATAATTCCCAGAATGTCACA
36127 TTTTTCACAAA-AATTCCCAGAATGTCAC
1 TTTTTCA-AAATAATTCCCAGAATGTCAC
36155 TGGGTCGGGT
Statistics
Matches: 68, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
28 24 0.35
29 41 0.60
30 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (29 bp):
TTTTTCAAAATAATTCCCAGAATGTCACA
Found at i:36232 original size:19 final size:19
Alignment explanation
Indices: 36186--36233 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
36176 ACAGGTCAGG
*
36186 TCAGACCGATCAAACCGAT
1 TCAGACCGGTCAAACCGAT
*
36205 TCAGACCGGTCAAACTGAT
1 TCAGACCGGTCAAACCGAT
36224 TCAGACCGGT
1 TCAGACCGGT
36234 TTGGACCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGAT
Found at i:48485 original size:30 final size:30
Alignment explanation
Indices: 48444--48632 Score: 164
Period size: 30 Copynumber: 6.3 Consensus size: 30
48434 CATACACTTG
*
48444 AGGACCAAAATAGCAAAAATAGAAACTTAA
1 AGGACTAAAATAGCAAAAATAGAAACTTAA
* *
48474 ATGACTAAAATAGCAAAAATAAAAACTTAA
1 AGGACTAAAATAGCAAAAATAGAAACTTAA
* *
48504 AGGATTAAAATAGCAAAAA-AAAAACTTAA
1 AGGACTAAAATAGCAAAAATAGAAACTTAA
* * * * * * * *
48533 GGGACTAAAACAACAAATACATATATTTAA
1 AGGACTAAAATAGCAAAAATAGAAACTTAA
** * *
48563 ATAACTAAAATAGAAAAAAAAAGAAACTTAA
1 AGGACTAAAATAG-CAAAAATAGAAACTTAA
* * * *
48594 GGGACTAAAACATCAAAAATAGAAATTTAA
1 AGGACTAAAATAGCAAAAATAGAAACTTAA
*
48624 AAGACTAAA
1 AGGACTAAA
48633 CTGGTATTAA
Statistics
Matches: 123, Mismatches: 34, Indels: 4
0.76 0.21 0.02
Matches are distributed among these distances:
29 24 0.20
30 80 0.65
31 19 0.15
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.18
Consensus pattern (30 bp):
AGGACTAAAATAGCAAAAATAGAAACTTAA
Found at i:48563 original size:59 final size:59
Alignment explanation
Indices: 48450--48612 Score: 164
Period size: 59 Copynumber: 2.7 Consensus size: 59
48440 CTTGAGGACC
* ** * * * * *
48450 AAAATAGCAAAAATAGAAACTTAAATGACTAAAATAGCAAAAATAAAAACTTAAAGGATT
1 AAAATAGCAAAAA-AAAAACTTAAGGGACTAAAACAACAAAAACAAAAACTTAAAGAACT
* * * * *
48510 AAAATAGCAAAAAAAAAACTTAAGGGACTAAAACAACAAATACATATATTTAAATAACT
1 AAAATAGCAAAAAAAAAACTTAAGGGACTAAAACAACAAAAACAAAAACTTAAAGAACT
* *
48569 AAAATAGAAAAAAAAAGAAACTTAAGGGACTAAAACATCAAAAA
1 AAAATAG-CAAAAAAA-AAACTTAAGGGACTAAAACAACAAAAA
48613 TAGAAATTTA
Statistics
Matches: 85, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
59 40 0.47
60 20 0.24
61 25 0.29
ACGTcount: A:0.63, C:0.10, G:0.09, T:0.18
Consensus pattern (59 bp):
AAAATAGCAAAAAAAAAACTTAAGGGACTAAAACAACAAAAACAAAAACTTAAAGAACT
Found at i:48622 original size:61 final size:59
Alignment explanation
Indices: 48450--48632 Score: 188
Period size: 61 Copynumber: 3.1 Consensus size: 59
48440 CTTGAGGACC
* ** * * * * *
48450 AAAATAGCAAAAATAGAAACTTAAATGACTAAAATAGCAAAAATAAAAACTTAAAGGATT
1 AAAATAGCAAAAAAAGAAACTTAAGGGACTAAAACAACAAAAATAAAAATTTAAA-AACT
* * * *
48510 AAAATAGCAAAAAAA-AAACTTAAGGGACTAAAACAACAAATACATATATTTAAATAACT
1 AAAATAGCAAAAAAAGAAACTTAAGGGACTAAAACAACAAAAATAAAAATTTAAA-AACT
* * *
48569 AAAATAGAAAAAAAAAGAAACTTAAGGGACTAAAACATCAAAAATAGAAATTTAAAAGACT
1 AAAATAG-CAAAAAAAGAAACTTAAGGGACTAAAACAACAAAAATAAAAATTTAAAA-ACT
48630 AAA
1 AAA
48633 CTGGTATTAA
Statistics
Matches: 101, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
59 39 0.39
60 22 0.22
61 40 0.40
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.19
Consensus pattern (59 bp):
AAAATAGCAAAAAAAGAAACTTAAGGGACTAAAACAACAAAAATAAAAATTTAAAAACT
Found at i:53033 original size:18 final size:18
Alignment explanation
Indices: 53010--53055 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
53000 AGCTCCACTG
*
53010 AAGAGACATGCAAAAGGA
1 AAGAGAAATGCAAAAGGA
53028 AAGAGAAATGCAAAAGGA
1 AAGAGAAATGCAAAAGGA
53046 AAGAGAAATG
1 AAGAGAAATG
53056 GAACATATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.59, C:0.07, G:0.28, T:0.07
Consensus pattern (18 bp):
AAGAGAAATGCAAAAGGA
Found at i:61572 original size:23 final size:24
Alignment explanation
Indices: 61543--61590 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
61533 ATAATATCTC
61543 TATATATTA-TTTTTTCAATTAAA
1 TATATATTATTTTTTTCAATTAAA
61566 TATATATTATTTTTTTCAATTAAA
1 TATATATTATTTTTTTCAATTAAA
61590 T
1 T
61591 CACTGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATATTATTTTTTTCAATTAAA
Found at i:62938 original size:24 final size:24
Alignment explanation
Indices: 62911--62962 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
62901 CCGATTGAAC
62911 CGCTATTAGTGAACCGGCCGGAAT
1 CGCTATTAGTGAACCGGCCGGAAT
62935 CGCTATTAGTGAACCGGCCGGAAT
1 CGCTATTAGTGAACCGGCCGGAAT
62959 CGCT
1 CGCT
62963 GAACCGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.23, C:0.27, G:0.29, T:0.21
Consensus pattern (24 bp):
CGCTATTAGTGAACCGGCCGGAAT
Found at i:73706 original size:86 final size:86
Alignment explanation
Indices: 73561--73733 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
73551 TATCTGTGTT
73561 GTGTTGTAGGATATTGAGGTTTCCCAGATTGTCTTTAGATTTCATGTCATCATATCTTATTGTTA
1 GTGTTGTAGGATATTGAGGTTTCCCAGATTGTCTTTAGATTTCATGTCATCATATCTTATTGTTA
73626 ACCTTTAACAATCAACAGATA
66 ACCTTTAACAATCAACAGATA
73647 GTGTTGTAGGATATTGAGGTTTCCCAGATTGTCTTTAGATTTCATGTCATCATATCTTATTGTTA
1 GTGTTGTAGGATATTGAGGTTTCCCAGATTGTCTTTAGATTTCATGTCATCATATCTTATTGTTA
73712 ACCTTTAACAATCAACAGATA
66 ACCTTTAACAATCAACAGATA
73733 G
1 G
73734 AAAATGTTAG
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (86 bp):
GTGTTGTAGGATATTGAGGTTTCCCAGATTGTCTTTAGATTTCATGTCATCATATCTTATTGTTA
ACCTTTAACAATCAACAGATA
Found at i:79308 original size:15 final size:15
Alignment explanation
Indices: 79288--79323 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
79278 GATATTCTTT
79288 TATTAAG-CATTTAAC
1 TATTAAGTC-TTTAAC
79303 TATTAAGTCTTTAAC
1 TATTAAGTCTTTAAC
79318 TATTAA
1 TATTAA
79324 AAGTTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (15 bp):
TATTAAGTCTTTAAC
Found at i:79829 original size:15 final size:15
Alignment explanation
Indices: 79809--79844 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
79799 GATATTCTTT
79809 TATTAAG-CATTTAAC
1 TATTAAGTC-TTTAAC
79824 TATTAAGTCTTTAAC
1 TATTAAGTCTTTAAC
79839 TATTAA
1 TATTAA
79845 AAGTTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (15 bp):
TATTAAGTCTTTAAC
Found at i:80351 original size:15 final size:15
Alignment explanation
Indices: 80331--80366 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
80321 GATATTCTTT
80331 TATTAAG-CATTTAAC
1 TATTAAGTC-TTTAAC
80346 TATTAAGTCTTTAAC
1 TATTAAGTCTTTAAC
80361 TATTAA
1 TATTAA
80367 AAGTTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (15 bp):
TATTAAGTCTTTAAC
Found at i:80442 original size:522 final size:522
Alignment explanation
Indices: 78726--80807 Score: 3846
Period size: 522 Copynumber: 4.0 Consensus size: 522
78716 TATTATATTG
* * * * * *
78726 CAGGTAAAGTATACAAATGATCCCGATCATAATATATTCTTTTACTAAACATTTAACTATTAAGT
1 CAGGTAAACTACACAAATGATCTCGATCATAAGATATTCTTTTATTAAGCATTTAACTATTAAGT
* *
78791 CTTTAATTATTAAAAGTTATAAAATGGTTCTTTAATTATAGAATATTGTTTTATTAAGTACTTCA
66 CTTTAACTATTAAAAGTTATAAAATGGTTCTTTAATTATAGAGTATTGTTTTATTAAGTACTTCA
78856 ATTATTAGAAGTTACAAAATGATCATTTGTTATTCATTATGTTTTAACTCGTCATTTTCTATTAA
131 ATTATTAGAAGTTACAAAATGATCATTTGTTATTCATTATGTTTTAACTCGTCATTTTCTATTAA
*
78921 AAAATTGGTTATTGTTTAAGATGGAAATTAACATGATGACTGAGATATAATAGTCATTTATAATT
196 AAAATTGGTTATTGTTTAAGATGGAAATTAACATGATGACTGGGATATAATAGTCATTTATAATT
* * * *
78986 TTGAGATCAGATTTTATTATATTACAGTCAACATGTTAACGTTCAGCTCATAATTTTGTCA--TT
261 TTGAGATCGGATTTTATTATATTACAGTCAACATGTTAACGTTCGGCTCATAATATCGTCATTTT
*
79049 TTTAACGGAAAATGACGAGTTTAGAATATAATAAATAGTCGGGTGACTATTTTGTAACTTTTAAT
326 TTTAACGGAAAATGACGAGTTTAGAATATAATAAATAGTCAGGTGACTATTTTGTAACTTTTAAT
79114 AGTCGAGAGATTTAACAAAGTAATATTTTATAATCTAAGGATCATTTTGTAACTTTTAATAATTA
391 AGTCGAGAGATTTAACAAAGTAATATTTTATAATCTAAGGATCATTTTGTAACTTTTAATAATTA
79179 ACTTAATATAACAATATTCTATAACTATAATCGGACCGTTTATATACTTTACCCTATAGTGTATT
456 ACTTAATATAACAATATTCTATAACTATAATCGGACCGTTTATATACTTTACCCTATAGTGTATT
79244 TC
521 TC
79246 CAGGTAAACTACACAAATGATCTCGATCATAAGATATTCTTTTATTAAGCATTTAACTATTAAGT
1 CAGGTAAACTACACAAATGATCTCGATCATAAGATATTCTTTTATTAAGCATTTAACTATTAAGT
79311 CTTTAACTATTAAAAGTTATAAAATGGTTCTTTAATTATAGAGTATTGTTTTATTAAGTACTTCA
66 CTTTAACTATTAAAAGTTATAAAATGGTTCTTTAATTATAGAGTATTGTTTTATTAAGTACTTCA
* *
79376 ATTATTAGAAGTTACAAAATGATCAGTTGTTATTCATTATGTTTTAACTTGTCATTTTCTATTAA
131 ATTATTAGAAGTTACAAAATGATCATTTGTTATTCATTATGTTTTAACTCGTCATTTTCTATTAA
79441 AAAATTGGTTATTGTTTAAGATGGAAATTAACATGATGACTGGGATATAATAGTCATTTATAATT
196 AAAATTGGTTATTGTTTAAGATGGAAATTAACATGATGACTGGGATATAATAGTCATTTATAATT
*
79506 TTGAGATCGGATTTTATTATATTACAGTCAACATGTTAACGTTCGGCTCATAATATTGTCATTTT
261 TTGAGATCGGATTTTATTATATTACAGTCAACATGTTAACGTTCGGCTCATAATATCGTCATTTT
* * *
79571 TTTAATGGAAAATGACGAGTTTA-AATATAATAAATAGTCGGGTGATTATTTTGTAACTTTTAAT
326 TTTAACGGAAAATGACGAGTTTAGAATATAATAAATAGTCAGGTGACTATTTTGTAACTTTTAAT
*
79635 AGTCGAGAGATTTAACAAAGTAATATTTTATAATCTAATGATCATTTTGTAACTTTTAATAATTA
391 AGTCGAGAGATTTAACAAAGTAATATTTTATAATCTAAGGATCATTTTGTAACTTTTAATAATTA
*
79700 ACTTAATATAACAATATTCTATAATTATAATCGGACCGTTTATATACTTTACCCTATAGTGTATT
456 ACTTAATATAACAATATTCTATAACTATAATCGGACCGTTTATATACTTTACCCTATAGTGTATT
79765 TC
521 TC
79767 CAGGTAAACTACACAAATGATCTCGATCATAAGATATTCTTTTATTAAGCATTTAACTATTAAGT
1 CAGGTAAACTACACAAATGATCTCGATCATAAGATATTCTTTTATTAAGCATTTAACTATTAAGT
79832 CTTTAACTATTAAAAGTTATAAAATGGTTCTTTAATTATAGAGTATTGTTTTATTAAGTACTTCA
66 CTTTAACTATTAAAAGTTATAAAATGGTTCTTTAATTATAGAGTATTGTTTTATTAAGTACTTCA
79897 ATTATTAGAAGTTACAAAATGATCATTTGTTATTCATTATGTTTTAACTCGTCATTTTCTATTAA
131 ATTATTAGAAGTTACAAAATGATCATTTGTTATTCATTATGTTTTAACTCGTCATTTTCTATTAA
79962 AAAATTGGTTATTGTTTAAGATGGAAATTAACATGATGACTGGGATATAATAGTCATTTATAATT
196 AAAATTGGTTATTGTTTAAGATGGAAATTAACATGATGACTGGGATATAATAGTCATTTATAATT
* *
80027 TTGAGATCGGATTTTATTATATTACAGTTAACAAGTTAACGTTCGGCTCATAATATCGTCATTTT
261 TTGAGATCGGATTTTATTATATTACAGTCAACATGTTAACGTTCGGCTCATAATATCGTCATTTT
* *
80092 TTTAACGAAAAATGACGAGTTTAGAATATAATAAATAGTTAGGTGACTATTTTGTAACTTTTAAT
326 TTTAACGGAAAATGACGAGTTTAGAATATAATAAATAGTCAGGTGACTATTTTGTAACTTTTAAT
80157 AGTCGAGAGATTTAACAAAGTAATATTTTATAATCTAAGGATCATTTTGTAACTTTTAATAATTA
391 AGTCGAGAGATTTAACAAAGTAATATTTTATAATCTAAGGATCATTTTGTAACTTTTAATAATTA
*
80222 ACTTAATATAACAATATTCTATAATTATAATCGGACCGTTTATATACTTTACCCTATAGTGTATT
456 ACTTAATATAACAATATTCTATAACTATAATCGGACCGTTTATATACTTTACCCTATAGTGTATT
80287 TC
521 TC
80289 CAGGTAAACTACACAAATGATCTCGATCATAAGATATTCTTTTATTAAGCATTTAACTATTAAGT
1 CAGGTAAACTACACAAATGATCTCGATCATAAGATATTCTTTTATTAAGCATTTAACTATTAAGT
80354 CTTTAACTATTAAAAGTTATAAAATGGTTCTTTAATTATAGAGTATTGTTTTATTAAGTACTTCA
66 CTTTAACTATTAAAAGTTATAAAATGGTTCTTTAATTATAGAGTATTGTTTTATTAAGTACTTCA
*
80419 ATTATTAGAGGTTACAAAATGATCATTTGTTATTCATTATGTTTTAACTCGTCATTTTCTATTAA
131 ATTATTAGAAGTTACAAAATGATCATTTGTTATTCATTATGTTTTAACTCGTCATTTTCTATTAA
*
80484 AAAATTGGTTATTGTTTAAGATGGAAATTAACATGATAACTGGGATATAATAGTCATTTATAATT
196 AAAATTGGTTATTGTTTAAGATGGAAATTAACATGATGACTGGGATATAATAGTCATTTATAATT
*
80549 TTGAGATCGGATTTTATTATATTACAGTCAACATTTTAACGTTCGGCTCATAATATCGTCATTTT
261 TTGAGATCGGATTTTATTATATTACAGTCAACATGTTAACGTTCGGCTCATAATATCGTCATTTT
*
80614 TTTAACGGAAAATGACGAGTTTAGAATATAATAAATAATCAGGTGACTATTTTGTAACTTTTAAT
326 TTTAACGGAAAATGACGAGTTTAGAATATAATAAATAGTCAGGTGACTATTTTGTAACTTTTAAT
*
80679 AGTCGAGAGATTTAACAAAGTAATATTTTATAATCTAAAGATCATTTTGTAACTTTTAATAATTA
391 AGTCGAGAGATTTAACAAAGTAATATTTTATAATCTAAGGATCATTTTGTAACTTTTAATAATTA
*
80744 ACTTAATATAACAATATTCTATAACTATAATCGGATCGTTTATATACTTTACCCTATAGTGTAT
456 ACTTAATATAACAATATTCTATAACTATAATCGGACCGTTTATATACTTTACCCTATAGTGTAT
80808 CCCCCCCCCC
Statistics
Matches: 1519, Mismatches: 40, Indels: 4
0.97 0.03 0.00
Matches are distributed among these distances:
520 307 0.20
521 511 0.34
522 701 0.46
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.41
Consensus pattern (522 bp):
CAGGTAAACTACACAAATGATCTCGATCATAAGATATTCTTTTATTAAGCATTTAACTATTAAGT
CTTTAACTATTAAAAGTTATAAAATGGTTCTTTAATTATAGAGTATTGTTTTATTAAGTACTTCA
ATTATTAGAAGTTACAAAATGATCATTTGTTATTCATTATGTTTTAACTCGTCATTTTCTATTAA
AAAATTGGTTATTGTTTAAGATGGAAATTAACATGATGACTGGGATATAATAGTCATTTATAATT
TTGAGATCGGATTTTATTATATTACAGTCAACATGTTAACGTTCGGCTCATAATATCGTCATTTT
TTTAACGGAAAATGACGAGTTTAGAATATAATAAATAGTCAGGTGACTATTTTGTAACTTTTAAT
AGTCGAGAGATTTAACAAAGTAATATTTTATAATCTAAGGATCATTTTGTAACTTTTAATAATTA
ACTTAATATAACAATATTCTATAACTATAATCGGACCGTTTATATACTTTACCCTATAGTGTATT
TC
Found at i:81948 original size:20 final size:20
Alignment explanation
Indices: 81918--82093 Score: 113
Period size: 20 Copynumber: 8.7 Consensus size: 20
81908 GTTTCCAGAT
*
81918 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* * * *
81938 TCGCATTGCGATTTTTTA-AA
1 TCGCAATGCGA-TTCTGACTA
** *
81958 TTCGCGTTGCGATTTTCCGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * *
81981 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
*
82001 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTCTGACTA
* *
82021 TCGCAACGCGATTATGACTA
1 TCGCAATGCGATTCTGACTA
* * *
82041 TCGCAACGAGATTCTTACTA
1 TCGCAATGCGATTCTGACTA
** *
82061 TTACAATGCGATGCTGACTA
1 TCGCAATGCGATTCTGACTA
82081 TCGCAATGCGATT
1 TCGCAATGCGATT
82094 TTTAAAACGC
Statistics
Matches: 119, Mismatches: 31, Indels: 12
0.73 0.19 0.07
Matches are distributed among these distances:
19 1 0.01
20 89 0.75
21 15 0.13
22 13 0.11
23 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:81991 original size:43 final size:40
Alignment explanation
Indices: 81918--82036 Score: 121
Period size: 43 Copynumber: 2.9 Consensus size: 40
81908 GTTTCCAGAT
* * * * *
81918 TCGCAACGCGATTCTGACTATCGCATTGCGATTTTTTAAA
1 TCGCAATGCGATTATGACTATCGCAATGCGATTATGTAAA
** * *
81958 TTCGCGTTGCGATTTTCCGACTATCGCAATGCGAATATGTAAA
1 -TCGCAATGCGATTAT--GACTATCGCAATGCGATTATGTAAA
*
82001 TCGCAATGCGATTATGACTATCGCAACGCGATTATG
1 TCGCAATGCGATTATGACTATCGCAATGCGATTATG
82037 ACTATCGCAA
Statistics
Matches: 63, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
40 19 0.30
41 11 0.17
42 12 0.19
43 21 0.33
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (40 bp):
TCGCAATGCGATTATGACTATCGCAATGCGATTATGTAAA
Found at i:82322 original size:20 final size:21
Alignment explanation
Indices: 82276--82322 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
82266 TCCGTCCCCG
*
82276 TCTCTGACGAAATCAGTCTCCA
1 TCTCCGACGAAATCAGTCT-CA
*
82298 TCTCCGACGAAATCCGTCT-A
1 TCTCCGACGAAATCAGTCTCA
82318 TCTCC
1 TCTCC
82323 ATCTCTCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
22 17 0.74
ACGTcount: A:0.23, C:0.36, G:0.13, T:0.28
Consensus pattern (21 bp):
TCTCCGACGAAATCAGTCTCA
Found at i:82772 original size:20 final size:20
Alignment explanation
Indices: 82708--82799 Score: 89
Period size: 19 Copynumber: 4.7 Consensus size: 20
82698 GCGATTTTAG
* **
82708 TTTCGCGTTGTGATTTTC-A
1 TTTCGCGTTGCGATAGTCAA
**
82727 TTTCGCGTTGCGATTTTC-A
1 TTTCGCGTTGCGATAGTCAA
82746 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAA
* * *
82766 ATTCGCGTTGCAATAGTCAT
1 TTTCGCGTTGCGATAGTCAA
*
82786 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
82800 TTTCATTTTC
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
19 34 0.54
20 29 0.46
ACGTcount: A:0.15, C:0.18, G:0.23, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAA
Found at i:82805 original size:20 final size:19
Alignment explanation
Indices: 82697--82822 Score: 119
Period size: 20 Copynumber: 6.5 Consensus size: 19
82687 ATAATCGCAA
82697 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCA-TTTCGCGT
*
82716 TGTGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
82735 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
** *
82754 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTC-ATTTCGCGT
* ** *
82774 TGCAATAGTCATTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
**
82794 TGCGATTTTCATTTTCGTAT
1 TGCGATTTTCA-TTTCGCGT
82814 TGCGATTTT
1 TGCGATTTT
82823 AAGTTTCAGA
Statistics
Matches: 92, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
19 43 0.47
20 49 0.53
ACGTcount: A:0.15, C:0.17, G:0.21, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:82829 original size:20 final size:20
Alignment explanation
Indices: 82786--82829 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
82776 CAATAGTCAT
* * *
82786 TTTCGTGTTGCGATTTTCAT
1 TTTCGTATTGCGATTTTAAG
82806 TTTCGTATTGCGATTTTAAG
1 TTTCGTATTGCGATTTTAAG
82826 TTTC
1 TTTC
82830 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTATTGCGATTTTAAG
Found at i:84830 original size:20 final size:20
Alignment explanation
Indices: 84803--84890 Score: 140
Period size: 20 Copynumber: 4.4 Consensus size: 20
84793 GCGATTCTCA
**
84803 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
84823 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
84843 CGGTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
84863 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
84883 CGTTGCGA
1 CGTTGCGA
84891 AAGTAAACTA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:85161 original size:20 final size:20
Alignment explanation
Indices: 85132--85180 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
85122 GCGATTCTCT
*
85132 CGTTGTGATAGTCAAATCCG
1 CGTTGCGATAGTCAAATCCG
** *
85152 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATCCG
85172 CGTTGCGAT
1 CGTTGCGAT
85181 GATCATTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATCCG
Found at i:85186 original size:20 final size:20
Alignment explanation
Indices: 85150--85219 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
85140 TAGTCAAATC
85150 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGATAGTCATTTT
85170 CGCGTTGCGAT-GATCATTTT
1 CGCGTTGCGATAG-TCATTTT
*
85190 CACGTTGCGATAGTCATTTT
1 CGCGTTGCGATAGTCATTTT
85210 CGCGTTGCGA
1 CGCGTTGCGA
85220 AAGTAAACTA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.02
20 44 0.96
21 1 0.02
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATAGTCATTTT
Found at i:85395 original size:329 final size:329
Alignment explanation
Indices: 84792--85437 Score: 1177
Period size: 329 Copynumber: 2.0 Consensus size: 329
84782 AAAATCACAT
*
84792 TGCGATTCTCACGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCGGTGCGATAGTCA
1 TGCGATTCTCACGTTGCGATAGTCAAATCCGCATTGCGATAGTCATTTTCGCGGTGCGATAGTCA
*
84857 TTTTCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTAATCTTCTTCTGCAAATTGAAA
66 TTTTCACGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTAATCTTCTTCTGCAAATTGAAA
84922 CTTGAATGGATTGCTTAGTAAATTCATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTA
131 CTTGAATGGATTGCTTAGTAAATTCATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTA
* *
84987 ACCCTGTGAAGTTAATATTTGTTTTTGGTTGTCTTTTGGTTGAAGTAATGCAATCCATTCAAGTT
196 ACACTGTAAAGTTAATATTTGTTTTTGGTTGTCTTTTGGTTGAAGTAATGCAATCCATTCAAGTT
85052 TCAATTTACAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTATCGCAACGAAAGAATC
261 TCAATTTACAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTATCGCAACGAAAGAATC
85117 GCAA
326 GCAA
* * * *
85121 TGCGATTCTCTCGTTGTGATAGTCAAATCCGCGTTGCGATAGTCATTTTCGCGTTGCGAT-GATC
1 TGCGATTCTCACGTTGCGATAGTCAAATCCGCATTGCGATAGTCATTTTCGCGGTGCGATAG-TC
85185 ATTTTCACGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTAATCTTCTTCTGCAAATTGAA
65 ATTTTCACGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTAATCTTCTTCTGCAAATTGAA
85250 ACTTGAATGGATTGCTTAGTAAATTCATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTT
130 ACTTGAATGGATTGCTTAGTAAATTCATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTT
* *
85315 AACACTGTAAAGTTAGTATTTGTTTTTGGTTGTCTTTTGGTTGAAGTAATGCAATTCATTCAAGT
195 AACACTGTAAAGTTAATATTTGTTTTTGGTTGTCTTTTGGTTGAAGTAATGCAATCCATTCAAGT
*
85380 TTCAATTTGCAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTATCGCAACG
260 TTCAATTTACAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTATCGCAACG
85438 CGAATTTTAC
Statistics
Matches: 305, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
328 1 0.00
329 304 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (329 bp):
TGCGATTCTCACGTTGCGATAGTCAAATCCGCATTGCGATAGTCATTTTCGCGGTGCGATAGTCA
TTTTCACGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTAATCTTCTTCTGCAAATTGAAA
CTTGAATGGATTGCTTAGTAAATTCATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTA
ACACTGTAAAGTTAATATTTGTTTTTGGTTGTCTTTTGGTTGAAGTAATGCAATCCATTCAAGTT
TCAATTTACAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTATCGCAACGAAAGAATC
GCAA
Found at i:85435 original size:20 final size:20
Alignment explanation
Indices: 85410--85457 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
85400 TAGTTTACTT
85410 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
** *
85430 TCGCAACGCGAATTTTACTA
1 TCGCAACGCGAAAATGACTA
85450 TCGCAACG
1 TCGCAACG
85458 AAATAATCGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:85527 original size:20 final size:20
Alignment explanation
Indices: 85500--85576 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
85490 GCGATTCTCT
**
85500 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
85520 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
85540 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
85560 CGTTGCGATAGTCATTT
1 CGTTGCGATAGTCATTT
85577 AAGTTGAATG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:86113 original size:18 final size:19
Alignment explanation
Indices: 86075--86114 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
86065 CCTGTCATCG
86075 TTCAAGAGGCCTCCCCTATCA
1 TTCAAGAGGCCT--CCTATCA
86096 TTCAAGAGGCCT-CTATCA
1 TTCAAGAGGCCTCCTATCA
86114 T
1 T
86115 CCCTCAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
21 12 0.63
ACGTcount: A:0.25, C:0.33, G:0.15, T:0.28
Consensus pattern (19 bp):
TTCAAGAGGCCTCCTATCA
Found at i:87750 original size:20 final size:20
Alignment explanation
Indices: 87725--87782 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
87715 AGGTACACTT
*
87725 TCGCAAAGCTAAACTCAAAA
1 TCGCAAAGCGAAACTCAAAA
* *
87745 TCGCAATGCGAAAGTCAAAA
1 TCGCAAAGCGAAACTCAAAA
* *
87765 TCGCAACGCGAAAGTCAA
1 TCGCAAAGCGAAACTCAA
87783 TTCGCGTTGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.45, C:0.24, G:0.17, T:0.14
Consensus pattern (20 bp):
TCGCAAAGCGAAACTCAAAA
Found at i:87830 original size:34 final size:34
Alignment explanation
Indices: 87787--87923 Score: 148
Period size: 34 Copynumber: 3.9 Consensus size: 34
87777 AGTCAATTCG
* * *
87787 CGTTGCGATAGTCTAATACGCTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACCCGTTGCGATTTTCT
* * *
87821 CGTTGCGATAGTAAAATACCCATTGCGATAATAAAATTCG
1 CGTTGCGATAGTCAAATACCCGTTGCGAT--T----TTCT
* *
87861 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACCCGTTGCGATTTTCT
87895 CGTTGCGATAGTCAAATACCCGTTGCGAT
1 CGTTGCGATAGTCAAATACCCGTTGCGAT
87924 AATCAAATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
34 55 0.65
36 1 0.01
38 1 0.01
40 28 0.33
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATACCCGTTGCGATTTTCT
Found at i:87871 original size:74 final size:74
Alignment explanation
Indices: 87781--87963 Score: 285
Period size: 74 Copynumber: 2.5 Consensus size: 74
87771 CGCGAAAGTC
* *
87781 AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTAAAATACCCATTG
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCGTTGCGATAGTAAAATACCCATTG
87846 CGATAATAA
66 CGATAATAA
* * *
87855 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCGTTGCGATAGTAAAATACCCATTG
*
87920 CGATAATCA
66 CGATAATAA
** *
87929 AATTCGCGTTGCGATAGAAAAATTCGCGTTGCGAT
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGAT
87964 AGACAAATTC
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 101 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (74 bp):
AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCGTTGCGATAGTAAAATACCCATTG
CGATAATAA
Found at i:87878 original size:20 final size:20
Alignment explanation
Indices: 87772--88079 Score: 189
Period size: 20 Copynumber: 16.6 Consensus size: 20
87762 AAATCGCAAC
*
87772 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
87791 GCGATAGTCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTT
*
87811 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
* * * *
87825 GCGATAGTAAAATACCCATT
1 GCGATAGTCAAATTCGCGTT
* *
87845 GCGATAATAAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
87865 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
87885 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
* *
87899 GCGATAGTCAAATACCCGTT
1 GCGATAGTCAAATTCGCGTT
*
87919 GCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
**
87939 GCGATAGAAAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
87959 GCGATAGACAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
87979 GCGAT--T----TTTGTGTT
1 GCGATAGTCAAATTCGCGTT
* *
87993 GCGATAGTCATATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
** *
88013 ATGATAGTCAAATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
* *
88033 GCGAT--T----TTTGAGTT
1 GCGATAGTCAAATTCGCGTT
88047 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
88067 GCGATATTCAAAT
1 GCGATAGTCAAAT
88080 GAATGTGTAA
Statistics
Matches: 225, Mismatches: 39, Indels: 49
0.72 0.12 0.16
Matches are distributed among these distances:
14 44 0.20
16 4 0.02
18 3 0.01
19 8 0.04
20 166 0.74
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:87919 original size:94 final size:94
Alignment explanation
Indices: 87821--88002 Score: 269
Period size: 94 Copynumber: 1.9 Consensus size: 94
87811 GCGATTTTCT
* *
87821 CGTTGCGATAGTAAAATACCCATTGCGATA-ATAAAATTCGCGTTGCGATAGTCAAATTCGCGTT
1 CGTTGCGATAATAAAATACCCATTGCGATAGA-AAAATTCGCGTTGCGATAGACAAATTCGCGTT
87885 GCGATTTTCT-CGTTGCGATAGTCAAATACC
65 GCGATTTT-TGCGTTGCGATAGTCAAATACC
* * * *
87915 CGTTGCGATAATCAAATTCGCGTTGCGATAGAAAAATTCGCGTTGCGATAGACAAATTCGCGTTG
1 CGTTGCGATAATAAAATACCCATTGCGATAGAAAAATTCGCGTTGCGATAGACAAATTCGCGTTG
*
87980 CGATTTTTGTGTTGCGATAGTCA
66 CGATTTTTGCGTTGCGATAGTCA
88003 TATTCGTGTT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
93 1 0.01
94 77 0.97
95 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (94 bp):
CGTTGCGATAATAAAATACCCATTGCGATAGAAAAATTCGCGTTGCGATAGACAAATTCGCGTTG
CGATTTTTGCGTTGCGATAGTCAAATACC
Found at i:88024 original size:94 final size:94
Alignment explanation
Indices: 87843--88037 Score: 268
Period size: 94 Copynumber: 2.1 Consensus size: 94
87833 AAAATACCCA
*
87843 TTGCGATAATAAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTC
1 TTGCGATAATAAAATTCGCGTTGCGATAGACAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTC
*
87908 AAATACCCGTTGCGATAATCAAATTCGCG
66 AAATACCCGTTACGATAATCAAATTCGCG
*
87937 TTGCGATAGA-AAAATTCGCGTTGCGATAGACAAATTCGCGTTGCGATTTT-TGTGTTGCGATAG
1 TTGCGATA-ATAAAATTCGCGTTGCGATAGACAAATTCGCGTTGCGATTTTCT-CGTTGCGATAG
* * ** * * *
88000 TCATATTCGTGTTATGATAGTCAAATTCGTG
64 TCAAATACCCGTTACGATAATCAAATTCGCG
88031 TTGCGAT
1 TTGCGAT
88038 TTTTGAGTTG
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
93 1 0.01
94 87 0.98
95 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (94 bp):
TTGCGATAATAAAATTCGCGTTGCGATAGACAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTC
AAATACCCGTTACGATAATCAAATTCGCG
Found at i:88078 original size:54 final size:54
Alignment explanation
Indices: 87772--88079 Score: 201
Period size: 54 Copynumber: 5.6 Consensus size: 54
87762 AAATCGCAAC
* * * * *
87772 GCGAAAGTC-AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCT-CGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGAGTT
* * * * * * ** ** *
87825 GCGATAGTAAAATACCCATTGCGATAATAAAATTCGCGTTGCGATAGTCAAATT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTT
* ** * * * * *
87879 CGCG-TTG-CGATTTTCTCGTTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCGCGTT
1 -GCGATAGTC-AAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTTGAGTT
** * *
87939 GCGATAGAAAAATTCGCGTTGCGATAGACAAATTCGCGTTGCGATTTTTGTGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTT
* * ** *
87993 GCGATAGTCATATTCGTGTTATGATAGTCAAATTCGTGTTGCGATTTTTGAGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTT
*
88047 GCGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
88080 GAATGTGTAA
Statistics
Matches: 188, Mismatches: 55, Indels: 23
0.71 0.21 0.09
Matches are distributed among these distances:
53 7 0.04
54 138 0.73
55 3 0.02
58 1 0.01
59 3 0.02
60 36 0.19
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (54 bp):
GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTT
Found at i:88302 original size:140 final size:140
Alignment explanation
Indices: 88050--88319 Score: 531
Period size: 140 Copynumber: 1.9 Consensus size: 140
88040 TTGAGTTGCG
*
88050 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
88115 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
88180 AATACACATA
131 AATACACATA
88190 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
88255 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
88320 TACAACGTTT
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 129 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:90348 original size:17 final size:17
Alignment explanation
Indices: 90321--90359 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
90311 AATTTATAAT
90321 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
90337 TAATTATAAATAATATC
1 TAATTATAAATAATATC
90354 TAATTA
1 TAATTA
90360 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:92136 original size:20 final size:20
Alignment explanation
Indices: 92111--92178 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
92101 GAAATTCAGT
*
92111 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
92131 GTTGCGATAGTCAGAATCTC
1 GTTGCGATAGTCAGAATCGC
92151 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
92171 ATTGCGAT
1 GTTGCGAT
92179 TTACATATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:92190 original size:20 final size:20
Alignment explanation
Indices: 92167--92218 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
92157 ATAGTCAGAA
92167 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
92187 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
92207 TCGCATTGCGAT
1 TCGCATTGCGAT
92219 AGTCGGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:92196 original size:40 final size:40
Alignment explanation
Indices: 92112--92280 Score: 101
Period size: 40 Copynumber: 4.2 Consensus size: 40
92102 AAATTCAGTG
* * * *
92112 TTGCGACAGTCAGAATCGCGTTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCATTGCGATAGTCAGAATCGCA
* * *
92152 TTGCGATAGTCAGAATCGCATTGCGAT-TTACATATTCGCA
1 TTGCGATAGTCAGAATCGCATTGCGATAGT-CAGAATCGCA
* * * *
92192 TTGCGAT-TTACATATTCGCATTGCGATAGTCGGAAAATCGCA
1 TTGCGATAGT-CAGAATCGCATTGCGATAGTC--AGAATCGCA
** * * * * *
92234 ACGCGA-ATTTAAAAAATCGCAATGCGATAGTCAGAATCGCG
1 TTGCGATA-GT-CAGAATCGCATTGCGATAGTCAGAATCGCA
92275 TTGCGA
1 TTGCGA
92281 ATTTGGAAAC
Statistics
Matches: 99, Mismatches: 23, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
39 2 0.02
40 54 0.55
41 12 0.12
42 11 0.11
43 20 0.20
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (40 bp):
TTGCGATAGTCAGAATCGCATTGCGATAGTCAGAATCGCA
Found at i:92239 original size:22 final size:22
Alignment explanation
Indices: 92214--92266 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
92204 TATTCGCATT
**
92214 GCGATAGTCGGAAAATCGCAAC
1 GCGATAGTCAAAAAATCGCAAC
* * *
92236 GCGA-ATTTAAAAAATCGCAAT
1 GCGATAGTCAAAAAATCGCAAC
92257 GCGATAGTCA
1 GCGATAGTCA
92267 GAATCGCGTT
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.19
Consensus pattern (22 bp):
GCGATAGTCAAAAAATCGCAAC
Found at i:98983 original size:25 final size:26
Alignment explanation
Indices: 98931--98983 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
98921 TTCGGTTCGG
* *
98931 TTCGGTTTGGCTTTAAACGATTCGTT
1 TTCGGTTCGGCTTTAAACGATTCATT
* *
98957 TTCGGTTCGG-TTTAAAGGCTTCATT
1 TTCGGTTCGGCTTTAAACGATTCATT
98982 TT
1 TT
98984 TTTGATTCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.47
Consensus pattern (26 bp):
TTCGGTTCGGCTTTAAACGATTCATT
Found at i:101475 original size:40 final size:37
Alignment explanation
Indices: 101431--101515 Score: 125
Period size: 37 Copynumber: 2.2 Consensus size: 37
101421 AATGATCATT
101431 AATTTATTAATTAATATAAAATAATCTTTAAGCTTAGCAA
1 AATTTATT-ATT--TATAAAATAATCTTTAAGCTTAGCAA
* *
101471 AATTTATTCTTTATAAAATAATCTTTAAGCTTAGCAG
1 AATTTATTATTTATAAAATAATCTTTAAGCTTAGCAA
101508 AATTTATT
1 AATTTATT
101516 CTTACTTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
37 33 0.77
39 2 0.05
40 8 0.19
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (37 bp):
AATTTATTATTTATAAAATAATCTTTAAGCTTAGCAA
Found at i:101489 original size:37 final size:37
Alignment explanation
Indices: 101445--101518 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
101435 TATTAATTAA
101445 TATAAAATAATCTTTAAGCTTAGCAAAATTTATTCTT
1 TATAAAATAATCTTTAAGCTTAGCAAAATTTATTCTT
*
101482 TATAAAATAATCTTTAAGCTTAGCAGAATTTATTCTT
1 TATAAAATAATCTTTAAGCTTAGCAAAATTTATTCTT
101519 ACTTTATAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (37 bp):
TATAAAATAATCTTTAAGCTTAGCAAAATTTATTCTT
Found at i:105437 original size:19 final size:20
Alignment explanation
Indices: 105415--105454 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
105405 GGTTAAAATG
105415 TTACAT-TGTACATAAA-AAA
1 TTACATATGTA-ATAAATAAA
105434 TTACATATGTAATAAATAAA
1 TTACATATGTAATAAATAAA
105454 T
1 T
105455 AAAATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (20 bp):
TTACATATGTAATAAATAAA
Done.