Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006084.1 Hibiscus syriacus cultivar Beakdansim tig00014420_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: 72987
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:821 original size:59 final size:59
Alignment explanation
Indices: 715--842 Score: 139
Period size: 59 Copynumber: 2.2 Consensus size: 59
705 ACTGTGTTAA
* * * ** *
715 CCCGATTATGACACATAAGGTCATGTCCACTATCTGTACTAGGTATACTTAAGTGCAGT
1 CCCGAATATGACACATAAGGTCATGTCCACCATATACACTAAGTATACTTAAGTGCAGT
* ** * * * *
774 CTCGAATATGACACATAAGGTTGTGTCCACCATATACACTAATTATACTTTAGTGTATT
1 CCCGAATATGACACATAAGGTCATGTCCACCATATACACTAAGTATACTTAAGTGCAGT
833 CCCGAATATG
1 CCCGAATATG
843 CGGCCTGCTG
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.32
Consensus pattern (59 bp):
CCCGAATATGACACATAAGGTCATGTCCACCATATACACTAAGTATACTTAAGTGCAGT
Found at i:7840 original size:24 final size:24
Alignment explanation
Indices: 7808--7856 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
7798 AGTCTTCCCG
*
7808 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATATATGTAC
*
7832 ATGATGTATTAAACATATATGTAC
1 ATGATGTATAAAACATATATGTAC
7856 A
1 A
7857 ATGTCATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (24 bp):
ATGATGTATAAAACATATATGTAC
Found at i:8753 original size:30 final size:31
Alignment explanation
Indices: 8713--8770 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
8703 AATCAACATT
8713 AAACCAAGACACCT-AAACTTATCATCTTCC
1 AAACCAAGACACCTCAAACTTATCATCTTCC
* *
8743 AAACTAAGACACCTCAACCTTATCATCT
1 AAACCAAGACACCTCAAACTTATCATCT
8771 CCCATAAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.40, C:0.33, G:0.03, T:0.24
Consensus pattern (31 bp):
AAACCAAGACACCTCAAACTTATCATCTTCC
Found at i:10606 original size:72 final size:69
Alignment explanation
Indices: 10483--10675 Score: 176
Period size: 72 Copynumber: 2.7 Consensus size: 69
10473 GTGTGTCGTA
* * * * ** * *
10483 TCACATGGATTTCCCGTGAAGGGGACTCATCCAAAGAATCGTGACTAACTTAAACCGTGAAGG-G
1 TCACCTGGCTTTCCCGAGAAGGGTA-TCATCCAAAGAATCAAGAC-GACTTAAA-AGTGAAGGTG
10547 AATCCATC
63 AAT-CATC
10555 TCACCTGGCTTTCCCGAGAAGGGTAGTCATCCAAAGAATCAAGATCGACTTAAAAGTGAAGGTGA
1 TCACCTGGCTTTCCCGAGAAGGGTA-TCATCCAAAGAATCAAGA-CGACTTAAAAGTGAAGGTGA
*
10620 GTCATC
64 ATCATC
* * *
10626 TTACCTGGCTTTTCC-ATGAA-GGTATACATCCAAAGAAACAAGACCGACTT
1 TCACCTGGCTTTCCCGA-GAAGGGTAT-CATCCAAAGAATCAAGA-CGACTT
10676 CAATAAAAAA
Statistics
Matches: 103, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
69 1 0.01
70 27 0.26
71 27 0.26
72 47 0.46
73 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (69 bp):
TCACCTGGCTTTCCCGAGAAGGGTATCATCCAAAGAATCAAGACGACTTAAAAGTGAAGGTGAAT
CATC
Found at i:15351 original size:23 final size:23
Alignment explanation
Indices: 15325--15371 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
15315 AATACCCAAG
15325 ATAAA-TATAAATCAACCATTAAA
1 ATAAAGTATAAA-CAACCATTAAA
*
15348 ATAAAGTTTAAACAACCATTAAA
1 ATAAAGTATAAACAACCATTAAA
15371 A
1 A
15372 CAACCCCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.26
Consensus pattern (23 bp):
ATAAAGTATAAACAACCATTAAA
Found at i:19093 original size:27 final size:27
Alignment explanation
Indices: 19063--19116 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
19053 GCTTCCCGTA
19063 TAGTTGATGGACTTTTGATTGTTCGGG
1 TAGTTGATGGACTTTTGATTGTTCGGG
19090 TAGTTGATGGACTTTTGATTGTTCGGG
1 TAGTTGATGGACTTTTGATTGTTCGGG
19117 CATTCACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.07, G:0.33, T:0.44
Consensus pattern (27 bp):
TAGTTGATGGACTTTTGATTGTTCGGG
Found at i:22571 original size:70 final size:70
Alignment explanation
Indices: 22457--22588 Score: 183
Period size: 70 Copynumber: 1.9 Consensus size: 70
22447 TGTATATCTG
* * * * *
22457 GTTTAGAACTATAATGTATAGAAATGACACTTAGTGCAGATGGTGGGCACGACCTTATGTGTCAT
1 GTTTAGAACTATAATGTATAGAAACGAAACCTAATGCAGATGGTGGACACGACCTTATGTGTCAT
22522 ATTCA
66 ATTCA
* * * *
22527 GTTTAGCACTATAGTGTATATAAACGAAACCTAATGCATATGGTGGACACGACCTTATGTGT
1 GTTTAGAACTATAATGTATAGAAACGAAACCTAATGCAGATGGTGGACACGACCTTATGTGT
22589 ATTGAAACTT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
70 53 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (70 bp):
GTTTAGAACTATAATGTATAGAAACGAAACCTAATGCAGATGGTGGACACGACCTTATGTGTCAT
ATTCA
Found at i:26502 original size:19 final size:19
Alignment explanation
Indices: 26478--26514 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
26468 AATTTTTTGG
26478 TTTATGAACATGTT-ATGGC
1 TTTATGAA-ATGTTGATGGC
26497 TTTATGAAATGTTGATGG
1 TTTATGAAATGTTGATGG
26515 ATTTCGAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.27, C:0.05, G:0.24, T:0.43
Consensus pattern (19 bp):
TTTATGAAATGTTGATGGC
Found at i:28260 original size:26 final size:26
Alignment explanation
Indices: 28231--28346 Score: 151
Period size: 26 Copynumber: 4.5 Consensus size: 26
28221 AGTCTTTGGT
* ***
28231 ATAAATAACACTTTCAAGTGTTAGTG
1 ATAAATAGCACTTTCAAGTACGAGTG
28257 ATAAATAGCACTTTCAAGTACGAGTG
1 ATAAATAGCACTTTCAAGTACGAGTG
28283 ATAAATAGCACTTTCAAGTACGAGTG
1 ATAAATAGCACTTTCAAGTACGAGTG
* * * *
28309 ATAAATAGCATTTTCGAGTGCAAGTG
1 ATAAATAGCACTTTCAAGTACGAGTG
*
28335 ATAAATGGCACT
1 ATAAATAGCACT
28347 ATGTGTGCAA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (26 bp):
ATAAATAGCACTTTCAAGTACGAGTG
Found at i:30433 original size:16 final size:15
Alignment explanation
Indices: 30412--30445 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
30402 TTGTTATAGC
30412 ATTATCTTATTTCTTT
1 ATTATCTTATTT-TTT
30428 ATTATCTTATTTTTT
1 ATTATCTTATTTTTT
30443 ATT
1 ATT
30446 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTATCTTATTTTTT
Found at i:35033 original size:3 final size:3
Alignment explanation
Indices: 35025--35062 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
35015 ATAAATATAG
35025 TAA TAA TAA TAA TAA TAA TAA TAA TAA GT-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TA
35063 TTTTTGGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 31 0.94
4 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:37373 original size:40 final size:40
Alignment explanation
Indices: 37318--37439 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
37308 ACCGTAGTGC
37318 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
*
37358 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
*
37398 TACACATAAGGTCGTGCCCACCATATACGCCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
37438 TA
1 TA
37440 TAAACCTGCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:41132 original size:6 final size:6
Alignment explanation
Indices: 41116--41214 Score: 55
Period size: 6 Copynumber: 16.8 Consensus size: 6
41106 TCTCTCATTT
* * * *
41116 TTTTCTC TTTTTC -TTTTC TTTCTC GTTTTC -ATTT- TTTTTC TTCTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* * * * *
41162 GTTTTC ATTTTC ATTTTC TATAT- TTTTTC TATTTT- TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC
41209 TGTTTT
1 T-TTTT
41215 TTTCCTTCTT
Statistics
Matches: 71, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
5 18 0.25
6 41 0.58
7 12 0.17
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:41149 original size:34 final size:33
Alignment explanation
Indices: 41110--41206 Score: 108
Period size: 34 Copynumber: 2.8 Consensus size: 33
41100 TTTTCATCTC
41110 TCATTTTTTTCTCTTTTTCTTTTCTTTCTCGTTT
1 TCATTTTTTTCTCTTTTTCTTTTCTTT-TCGTTT
* *
41144 TCATTTTTTT-TCTTCTTCGTTTTCATTTTCATTT
1 TCATTTTTTTCTCTTTTTC-TTTTC-TTTTCGTTT
*
41178 TCTATATTTTTTCTATTTTT-TTTTCTTTT
1 TC-AT-TTTTTTCTCTTTTTCTTTTCTTTT
41207 TCTGTTTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
33 7 0.13
34 26 0.48
35 10 0.19
36 6 0.11
37 5 0.09
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.74
Consensus pattern (33 bp):
TCATTTTTTTCTCTTTTTCTTTTCTTTTCGTTT
Found at i:41154 original size:28 final size:28
Alignment explanation
Indices: 41123--41178 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
41113 TTTTTTTCTC
*
41123 TTTTTCTT-TTC-TTTCTCGTTTTCATTT
1 TTTTTCTTCTTCGTTT-TCATTTTCATTT
41150 TTTTTCTTCTTCGTTTTCATTTTCATTT
1 TTTTTCTTCTTCGTTTTCATTTTCATTT
41178 T
1 T
41179 CTATATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 8 0.31
28 15 0.58
29 3 0.12
ACGTcount: A:0.05, C:0.18, G:0.04, T:0.73
Consensus pattern (28 bp):
TTTTTCTTCTTCGTTTTCATTTTCATTT
Found at i:41157 original size:22 final size:23
Alignment explanation
Indices: 41124--41214 Score: 82
Period size: 22 Copynumber: 3.9 Consensus size: 23
41114 TTTTTTCTCT
41124 TTTTCTTTTCTT-TCTCGTTTTCA
1 TTTTCTTTTCTTCT-TCGTTTTCA
41147 TTTT-TTTTCTTCTTCGTTTTCA
1 TTTTCTTTTCTTCTTCGTTTTCA
*
41169 TTTTCATTTTCTATATT--TTTTCTA
1 TTTTC-TTTTCT-TCTTCGTTTTC-A
* *
41193 TTTTTTTTTCTTTTTCTGTTTT
1 TTTTCTTTTCTTCTTC-GTTTT
41215 TTTCCTTCTT
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
22 23 0.40
23 16 0.28
24 11 0.19
25 7 0.12
ACGTcount: A:0.07, C:0.15, G:0.03, T:0.75
Consensus pattern (23 bp):
TTTTCTTTTCTTCTTCGTTTTCA
Found at i:41208 original size:35 final size:33
Alignment explanation
Indices: 41095--41208 Score: 97
Period size: 35 Copynumber: 3.3 Consensus size: 33
41085 AAGTGAAATA
*
41095 TTTT-TTTTTCATCTCTCAT-TTTTTTCTCTTTTT
1 TTTTCTTTTTCAT-TTTCATATTTTTTCT-TTTTT
* * * **
41128 CTTTTCTTTCTCGTTTTCATTTTTTTTCTTCTTCG
1 -TTTTCTTTTTCATTTTCATATTTTTTCTT-TTTT
*
41163 TTTTCATTTTCATTTTCTATATTTTTTCTATTTTT
1 TTTTCTTTTTCATTTTC-ATATTTTTTCT-TTTTT
41198 TTTTCTTTTTC
1 TTTTCTTTTTC
41209 TGTTTTTTTC
Statistics
Matches: 63, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
34 24 0.38
35 38 0.60
36 1 0.02
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.74
Consensus pattern (33 bp):
TTTTCTTTTTCATTTTCATATTTTTTCTTTTTT
Found at i:43545 original size:18 final size:19
Alignment explanation
Indices: 43504--43551 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
43494 AGTAAATGAT
*
43504 ATTATAAAAATATCATATC
1 ATTATAAAATTATCATATC
*
43523 A-TATAAAATTA-CATTTC
1 ATTATAAAATTATCATATC
43540 ATTATAATAATT
1 ATTATAA-AATT
43552 TAATTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 6 0.24
18 14 0.56
19 5 0.20
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTATAAAATTATCATATC
Found at i:44207 original size:46 final size:47
Alignment explanation
Indices: 44098--44214 Score: 139
Period size: 46 Copynumber: 2.5 Consensus size: 47
44088 ACCTTTTATC
44098 CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTAACATTTAAATT
1 CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTAACATTT-AATT
* ** * **
44146 CCATAAGCTCGTAAGCTTATTATTTTTCAATATACTTGCCA-TT-ATT
1 CCATAAGCTCATAAGCTTATT-TTTACCAAAATACTTAACATTTAATT
*
44192 CCGTAAGCTCATAAGCTTATTTT
1 CCATAAGCTCATAAGCTTATTTT
44215 CATGGTTACC
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
45 2 0.03
46 22 0.37
48 22 0.37
49 14 0.23
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (47 bp):
CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTAACATTTAATT
Found at i:44375 original size:40 final size:40
Alignment explanation
Indices: 44318--44439 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
44308 ACCGTAGTGC
*
44318 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
44358 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
44398 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
44438 TA
1 TA
44440 TAAACCTGCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:46263 original size:22 final size:21
Alignment explanation
Indices: 46234--46295 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
46224 CGGTAACATA
46234 ATAGAGTATC-AGTACCATGGT
1 ATAGAGTATCGA-TACCATGGT
46255 ATAGTAGTATCGATACCATGGT
1 ATAG-AGTATCGATACCATGGT
* *
46277 A-GGGGTATCGATACTCATG
1 ATAGAGTATCGATAC-CATG
46296 AGCCAACAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 16 0.44
23 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.29
Consensus pattern (21 bp):
ATAGAGTATCGATACCATGGT
Found at i:46703 original size:56 final size:56
Alignment explanation
Indices: 46625--46832 Score: 310
Period size: 56 Copynumber: 3.6 Consensus size: 56
46615 CTATGTGTAC
46625 AAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCTTATGGGCACTTTGTGTGCA
1 AAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCTTATGGGCACTTTGTGTGCA
* *
46681 AAAGTTAAGAAATTCATAATAAGTTTATGAATTT-ATGTATGGGCATTTTGTGTGCA
1 AAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCT-TATGGGCACTTTGTGTGCA
* * *
46737 AAAGTAAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTGTGTGCA
1 AAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCTTATGGGCACTTTGTGTGCA
46793 AAAGTTAAGATAATAAATTCATAATAAGTTTATGAATTTC
1 AAAGTTAAG-----AAATTCATAATAAGTTTATGAATTTC
46833 GGTATTGGTA
Statistics
Matches: 137, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
55 1 0.01
56 111 0.81
61 25 0.18
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (56 bp):
AAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCTTATGGGCACTTTGTGTGCA
Found at i:46869 original size:112 final size:109
Alignment explanation
Indices: 46618--46854 Score: 294
Period size: 112 Copynumber: 2.1 Consensus size: 109
46608 AATGACACTA
* * *
46618 TGTGTACAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCTTATGGGCACTTTGTGTGCAAA
1 TGTGTGCAAAGTAAAGAAA-T-ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAA
* * *
46683 AGTTAAGAAATTCATAATAAGTTTATGAATTTATGTATGGGCATTT
64 AGTTAAGAAATTCATAATAAGTTTATGAATTTAGGTATGGGCAATG
*
46729 TGTGTGCAAAAGTAAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTGTGTGCAA
1 TGTGTGC-AAAGTAAAGAAA-T-ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAA
* * *
46794 AAGTTAAGATAATAAATTCATAATAAGTTTATGAATTTCGGTATTGGTAATG
63 AAGTTAAG-----AAATTCATAATAAGTTTATGAATTTAGGTATGGGCAATG
46846 TGTGTGCAA
1 TGTGTGCAA
46855 TTTACGTAAA
Statistics
Matches: 110, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
111 6 0.05
112 62 0.56
116 2 0.02
117 40 0.36
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (109 bp):
TGTGTGCAAAGTAAAGAAATATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAG
TTAAGAAATTCATAATAAGTTTATGAATTTAGGTATGGGCAATG
Found at i:47206 original size:81 final size:80
Alignment explanation
Indices: 46984--47543 Score: 614
Period size: 81 Copynumber: 7.1 Consensus size: 80
46974 ACTATTTCAA
* * *
46984 AGTAAAAGATTAATGGCCTAGCTGTGTATTTGGAAGAAATGTGTCAATTATGCCAATTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGCAA-AAATGTGTCAATTATGCCAGTTAGATGAA
*
47049 AGGTTAAATATCTTTG
65 AGGTTAAATACCTTTG
* * *
47065 AGTAAAAGATTAAT-GACTAGCTGTGCATTTGGC-AAAATAGTGCCAATTATGCCAGTTAGATGT
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTT-GCAAAAAT-GTGTCAATTATGCCAGTTAGATGA
47128 AAGGTTAAATACCTTTG
64 AAGGTTAAATACCTTTG
*
47145 AGTAAAAGATTAATGGCCTAGTTGTGCATTTCGCAAAAATGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTT-GCAAAAATGTGTCAATTATGCCAGTTAGATGAA
47210 AGGTTAAATACCTTTG
65 AGGTTAAATACCTTTG
* * * * *
47226 AGTAAAAGATTAATGGCCTAGCTGTGCTTTTGGCAAAAAGGTGTCAATTATGACAATTCGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTT-GCAAAAATGTGTCAATTATGCCAGTTAGATGAA
*
47291 AGGTTAAATTCCTTTG
65 AGGTTAAATACCTTTG
*
47307 AGTAAAAGATTAACGGCCTAGCTGTGCA--T-------T-TGTCAATTATGCCAGTTAGATGAAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGCAAAAATGTGTCAATTATGCCAGTTAGATGAAA
*
47362 GGTTAAATACATTTG
66 GGTTAAATACCTTTG
* * * * * * *
47377 AGTAAAATATTAACGG-C---CTGTGCATTTGACAGAAAGGTGTCAGTTATGCTAGTAAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTG-CAAAAATGTGTCAATTATGCCAGTTAGATGAA
47438 AGGTTAAATACCTTTG
65 AGGTTAAATACCTTTG
* * * * * * * *
47454 ACTAAAATATTAACGCCCTAGCTGTACATTTGACAGGAAA-GTGTCAATCATGCAAGTTAGATGA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTG-CA-AAAATGTGTCAATTATGCCAGTTAGATGA
* * **
47518 AAGGCTATATGTCTTTG
64 AAGGTTAAATACCTTTG
47535 AGTAAAAGA
1 AGTAAAAGA
47544 CTAAATGCTT
Statistics
Matches: 412, Mismatches: 47, Indels: 40
0.83 0.09 0.08
Matches are distributed among these distances:
66 7 0.02
68 1 0.00
69 1 0.00
70 50 0.12
77 50 0.12
78 1 0.00
79 5 0.01
80 66 0.16
81 222 0.54
82 9 0.02
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (80 bp):
AGTAAAAGATTAATGGCCTAGCTGTGCATTTGCAAAAATGTGTCAATTATGCCAGTTAGATGAAA
GGTTAAATACCTTTG
Found at i:47380 original size:70 final size:70
Alignment explanation
Indices: 47267--47485 Score: 231
Period size: 70 Copynumber: 3.0 Consensus size: 70
47257 GGCAAAAAGG
* * * * *
47267 TGTCAATTATGACAATTCGATGAAAGGTTAAATTCCTTTGAGTAAAAGATTAACGGCCTAGCTGT
1 TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAATATTAACGGCCTAGCTGT
47332 GCATT
66 GCATT
* *
47337 TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAATATTAACGGCCTGTGCAT
1 TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAATATTAACGGCCT-AGC-T
* **
47402 TTGACAGAAAGG
64 GTG-C----ATT
* * * * *
47414 TGTCAGTTATGCTAGTAAGATGAAAGGTTAAATACCTTTGACTAAAATATTAACGCCCTAGCTGT
1 TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAATATTAACGGCCTAGCTGT
*
47479 ACATT
66 GCATT
47484 TG
1 TG
47486 ACAGGAAAGT
Statistics
Matches: 121, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
70 56 0.46
71 2 0.02
72 3 0.02
73 1 0.01
74 1 0.01
75 2 0.02
76 2 0.02
77 54 0.45
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (70 bp):
TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAATATTAACGGCCTAGCTGT
GCATT
Found at i:47464 original size:77 final size:80
Alignment explanation
Indices: 47337--47521 Score: 252
Period size: 77 Copynumber: 2.3 Consensus size: 80
47327 GCTGTGCATT
* * *
47337 TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAATATTAACGGCCT-G-TG-
1 TGTCAATTATGCAAGTTAGATGAAAGGTTAAATACATTTGACTAAAATATTAACGCCCTAGCTGA
47399 CATTTGACA-GAAAGG
66 CATTTGACAGGAAA-G
* * * *
47414 TGTCAGTTATGCTAGTAAGATGAAAGGTTAAATACCTTTGACTAAAATATTAACGCCCTAGCTGT
1 TGTCAATTATGCAAGTTAGATGAAAGGTTAAATACATTTGACTAAAATATTAACGCCCTAGCTG-
47479 ACATTTGACAGGAAAG
65 ACATTTGACAGGAAAG
*
47495 TGTCAATCATGCAAGTTAGATGAAAGG
1 TGTCAATTATGCAAGTTAGATGAAAGG
47522 CTATATGTCT
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
77 53 0.57
78 1 0.01
79 2 0.02
81 33 0.35
82 4 0.04
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (80 bp):
TGTCAATTATGCAAGTTAGATGAAAGGTTAAATACATTTGACTAAAATATTAACGCCCTAGCTGA
CATTTGACAGGAAAG
Found at i:47474 original size:147 final size:149
Alignment explanation
Indices: 47186--47485 Score: 417
Period size: 147 Copynumber: 2.0 Consensus size: 149
47176 CGCAAAAATG
* *
47186 TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGT
1 TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAACGGCC-A-CTGT
* * ** * *
47251 GCTTTTGGCAAAAAGGTGTCAATTATGACAATTCGATGAAAGGTTAAATTCCTTTGAGTAAAAGA
64 GCATTTGACAAAAAGGTGTCAATTATGACAATAAGATGAAAGGTTAAATACCTTTGACTAAAAGA
* *
47316 TTAACGGCCTAGCTGTGCATT
129 TTAACGCCCTAGCTGTACATT
*
47337 TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAATATTAACGG-C-CTGTGC
1 TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAACGGCCACTGTGC
* * * *
47400 ATTTGACAGAAAGGTGTCAGTTATG-CTAGTAAGATGAAAGGTTAAATACCTTTGACTAAAATAT
66 ATTTGACAAAAAGGTGTCAATTATGAC-AATAAGATGAAAGGTTAAATACCTTTGACTAAAAGAT
47464 TAACGCCCTAGCTGTACATT
130 TAACGCCCTAGCTGTACATT
47484 TG
1 TG
47486 ACAGGAAAGT
Statistics
Matches: 133, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
146 1 0.01
147 78 0.59
150 1 0.01
151 53 0.40
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (149 bp):
TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAACGGCCACTGTGC
ATTTGACAAAAAGGTGTCAATTATGACAATAAGATGAAAGGTTAAATACCTTTGACTAAAAGATT
AACGCCCTAGCTGTACATT
Found at i:47519 original size:228 final size:229
Alignment explanation
Indices: 46986--47543 Score: 599
Period size: 228 Copynumber: 2.4 Consensus size: 229
46976 TATTTCAAAG
* * ** * * * *
46986 TAAAAGATTAATGGCCTAGCTGTGTATTTGGA-AGAAATGTGTCAATTATGCCAATTAGATGAAA
1 TAAAAGATTAACGCCCTAGCTGTACATTT-GACAAAAAGGTGTCAATCATGACAATTAGATGAAA
* * * *
47050 GGTTAAATATCTTTGAGTAAAAGATTAA-TGACTAGCTGTGCATTTGGCAAAATAGTGCCAATTA
65 GGCTAAATGTCTTTGAGTAAAAGATTAACGGCCTAGCTGTGCA-TT-------T-GT--CAATTA
* * *
47114 TGCCAGTTAGATGTAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTCGC
119 TGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAACGGCC---TTGTGCATTTCGC
* * *
47179 AAAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAG
181 AAAAAGGTGTCAATTATGCCAGTAAGATGAAAGGTTAAATACCTTTGAC
* * * * * * *
47228 TAAAAGATTAATGGCCTAGCTGTGCTTTTGGCAAAAAGGTGTCAATTATGACAATTCGATGAAAG
1 TAAAAGATTAACGCCCTAGCTGTACATTTGACAAAAAGGTGTCAATCATGACAATTAGATGAAAG
*
47293 GTTAAAT-TCCTTTGAGTAAAAGATTAACGGCCTAGCTGTGCATTTGTCAATTATGCCAGTTAGA
66 GCTAAATGT-CTTTGAGTAAAAGATTAACGGCCTAGCTGTGCATTTGTCAATTATGCCAGTTAGA
* * *
47357 TGAAAGGTTAAATACATTTGAGTAAAATATTAACGGCC-TGTGCATTT-GACAGAAAGGTGTCAG
130 TGAAAGGTTAAATACATTTGAGTAAAAGATTAACGGCCTTGTGCATTTCG-CAAAAAGGTGTCAA
*
47420 TTATGCTAGTAAGATGAAAGGTTAAATACCTTTGAC
194 TTATGCCAGTAAGATGAAAGGTTAAATACCTTTGAC
* *
47456 TAAAATATTAACGCCCTAGCTGTACATTTGACAGGAAA-GTGTCAATCATG-CAAGTTAGATGAA
1 TAAAAGATTAACGCCCTAGCTGTACATTTGACA-AAAAGGTGTCAATCATGACAA-TTAGATGAA
*
47519 AGGCTATATGTCTTTGAGTAAAAGA
64 AGGCTAAATGTCTTTGAGTAAAAGA
47544 CTAAATGCTT
Statistics
Matches: 279, Mismatches: 30, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
227 4 0.01
228 120 0.43
229 4 0.01
232 51 0.18
234 2 0.01
235 1 0.00
241 2 0.01
242 83 0.30
243 12 0.04
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (229 bp):
TAAAAGATTAACGCCCTAGCTGTACATTTGACAAAAAGGTGTCAATCATGACAATTAGATGAAAG
GCTAAATGTCTTTGAGTAAAAGATTAACGGCCTAGCTGTGCATTTGTCAATTATGCCAGTTAGAT
GAAAGGTTAAATACATTTGAGTAAAAGATTAACGGCCTTGTGCATTTCGCAAAAAGGTGTCAATT
ATGCCAGTAAGATGAAAGGTTAAATACCTTTGAC
Found at i:49816 original size:12 final size:12
Alignment explanation
Indices: 49799--49832 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
49789 CCCCCTATTA
49799 CATTCTCTTCTT
1 CATTCTCTTCTT
49811 CATTCTCTTCTT
1 CATTCTCTTCTT
49823 CATTCTCTTC
1 CATTCTCTTC
49833 CTCCTCCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.09, C:0.35, G:0.00, T:0.56
Consensus pattern (12 bp):
CATTCTCTTCTT
Found at i:49849 original size:24 final size:24
Alignment explanation
Indices: 49799--49850 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
49789 CCCCCTATTA
* * * *
49799 CATTCTCTTCTTCATTCTCTTCTT
1 CATTCTCTTCCTCATCCTCTACCT
*
49823 CATTCTCTTCCTCCTCCTCTACCT
1 CATTCTCTTCCTCATCCTCTACCT
49847 CATT
1 CATT
49851 ATCAATAACC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.10, C:0.40, G:0.00, T:0.50
Consensus pattern (24 bp):
CATTCTCTTCCTCATCCTCTACCT
Found at i:51979 original size:15 final size:15
Alignment explanation
Indices: 51959--52047 Score: 55
Period size: 15 Copynumber: 6.1 Consensus size: 15
51949 TAGCAAAAAG
51959 AAGAGAAAACATAAA-
1 AAGAGAAAA-ATAAAT
51974 AAGAGAGAAAATAAAT
1 AAGAGA-AAAATAAAT
* *
51990 AA-AGAAAAAAAAAG
1 AAGAGAAAAATAAAT
*
52004 AA-AGAAAAA-AGA-
1 AAGAGAAAAATAAAT
*
52016 GAGAG-AAAATAAAGT
1 AAGAGAAAAATAAA-T
* *
52031 AAAAGAGAAATAAAT
1 AAGAGAAAAATAAAT
52046 AA
1 AA
52048 AAAAAGATCA
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
12 5 0.08
13 6 0.10
14 16 0.27
15 20 0.34
16 12 0.20
ACGTcount: A:0.74, C:0.01, G:0.17, T:0.08
Consensus pattern (15 bp):
AAGAGAAAAATAAAT
Found at i:52006 original size:40 final size:42
Alignment explanation
Indices: 51953--52033 Score: 107
Period size: 40 Copynumber: 2.0 Consensus size: 42
51943 AATATATAGC
*
51953 AAAAAGAAGAGAAA-ACATAAAA-AGAGAGAAAATAAA-TAAAG
1 AAAAAGAAAAGAAAGA-A-AAAAGAGAGAGAAAATAAAGTAAAG
51994 AAAAA-AAAAGAAAGAAAAAAGAGAGAGAAAATAAAGTAAA
1 AAAAAGAAAAGAAAGAAAAAAGAGAGAGAAAATAAAGTAAA
52034 AGAGAAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
39 4 0.11
40 22 0.61
41 10 0.28
ACGTcount: A:0.75, C:0.01, G:0.17, T:0.06
Consensus pattern (42 bp):
AAAAAGAAAAGAAAGAAAAAAGAGAGAGAAAATAAAGTAAAG
Found at i:52013 original size:11 final size:11
Alignment explanation
Indices: 51990--52054 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
51980 GAAAATAAAT
51990 AAAGAAA-AAA
1 AAAGAAAGAAA
52000 AAAGAAAGAAA
1 AAAGAAAGAAA
* *
52011 AAAGAGAGAGA
1 AAAGAAAGAAA
*
52022 AAATAAAGTAAA
1 AAAGAAAG-AAA
* *
52034 AGAGAAATAAA
1 AAAGAAAGAAA
*
52045 TAAAAAAAGA
1 -AAAGAAAGA
52055 TCAAATCCTT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
10 7 0.17
11 21 0.51
12 13 0.32
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (11 bp):
AAAGAAAGAAA
Found at i:52048 original size:15 final size:17
Alignment explanation
Indices: 52017--52049 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
52007 GAAAAAAGAG
52017 AGAGAAAATAAAGTAAA
1 AGAGAAAATAAAGTAAA
52034 AGAG-AAATAAA-TAAA
1 AGAGAAAATAAAGTAAA
52049 A
1 A
52050 AAAGATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (17 bp):
AGAGAAAATAAAGTAAA
Found at i:52051 original size:17 final size:16
Alignment explanation
Indices: 51954--52051 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 16
51944 ATATATAGCA
*
51954 AAAAGAAGAGAAAACAT
1 AAAA-AAGAGAAAAAAT
51971 AAAAAGAGAGAAAATAAAT
1 AAAAA-AGAG-AAA-AAAT
* * *
51990 AAAGAAAAAAAAAGAAAG
1 AAA-AAAGAGAAA-AAAT
52008 AAAAAAGAGAGAGAAAAT
1 AAAAAAGAGA-A-AAAAT
52026 AAAGTAAAAGAGAAATAAAT
1 -AA--AAAAGAGAAA-AAAT
52046 AAAAAA
1 AAAAAA
52052 AGATCAAATC
Statistics
Matches: 63, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
16 1 0.02
17 17 0.27
18 16 0.25
19 14 0.22
20 7 0.11
21 8 0.13
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.07
Consensus pattern (16 bp):
AAAAAAGAGAAAAAAT
Found at i:52831 original size:28 final size:28
Alignment explanation
Indices: 52784--52851 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 28
52774 CAAAGAAGCC
*
52784 AACCTGAAACACATTGCCTCGCC-AAATT
1 AACCTGAAACACATTACCTC-CCTAAATT
*
52812 AACTTGAAACACATTACCTCCCTAAATT
1 AACCTGAAACACATTACCTCCCTAAATT
52840 AACCTGAAACAC
1 AACCTGAAACAC
52852 TCTACTTTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 2 0.06
28 34 0.94
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (28 bp):
AACCTGAAACACATTACCTCCCTAAATT
Found at i:58799 original size:14 final size:14
Alignment explanation
Indices: 58735--58799 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
58725 CCCATGAGAA
*
58735 ATGATATAAGTTAT
1 ATGATATATGTTAT
58749 ATGATATGAT-TTAT
1 ATGATAT-ATGTTAT
* **
58763 ATGATTACATGCACAT
1 ATGA-TATATG-TTAT
*
58779 GTGATATATGTTAT
1 ATGATATATGTTAT
58793 ATGATAT
1 ATGATAT
58800 GGATCGATGT
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
14 25 0.66
15 8 0.21
16 5 0.13
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (14 bp):
ATGATATATGTTAT
Found at i:60027 original size:23 final size:21
Alignment explanation
Indices: 59980--60027 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
59970 AAAGTACTAT
**
59980 AGCAGGGAATCGGTACCCTGT
1 AGCAGGGAATCGGTACCCTCA
*
60001 AGCAGGGGAATCGGTTCCCCTCA
1 AGCA-GGGAATCGG-TACCCTCA
60024 AGCA
1 AGCA
60028 ATCTGGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 4 0.18
22 9 0.41
23 9 0.41
ACGTcount: A:0.25, C:0.27, G:0.31, T:0.17
Consensus pattern (21 bp):
AGCAGGGAATCGGTACCCTCA
Found at i:63479 original size:104 final size:104
Alignment explanation
Indices: 63274--63479 Score: 290
Period size: 104 Copynumber: 2.0 Consensus size: 104
63264 TCACGGGATG
* *
63274 ACTCTACCTGACTAGCTCGGGGATGGAAGTTATGCTCCCTTTCACTTAGAGTGTGGGATGTTAGG
1 ACTCTACCTGACTAGCTCGGGGATGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGG
* *
63339 TGTGATGGGCTGAATCCCCTCAAAGCAGTGTTAAAAAAA
66 TGTGATGAGATGAATCCCCTCAAAGCAGTGTTAAAAAAA
* * *
63378 ACTCTACTTGACTAGCTTGGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTA-G
1 ACTCTACCTGACTAGCTCGGGGATGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGG
* * * *
63442 TGTGATGAGATTACTCCCCTTAAAGTA-TGCTTAAAAAA
66 TGTGATGAGATGAATCCCCTCAAAGCAGTG-TTAAAAAA
63480 GAGAGTTGAA
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
102 2 0.02
103 30 0.33
104 58 0.64
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (104 bp):
ACTCTACCTGACTAGCTCGGGGATGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGG
TGTGATGAGATGAATCCCCTCAAAGCAGTGTTAAAAAAA
Found at i:65953 original size:44 final size:45
Alignment explanation
Indices: 65821--65954 Score: 209
Period size: 45 Copynumber: 3.0 Consensus size: 45
65811 ATCAATAAAT
* *
65821 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
65866 TTACCATTTAATTCCATAAGCTCGT-AGCTTATTTTGCCAATATAC
1 TTACCATTT-ATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
65911 TTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACTAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
65955 ATGCCATTAA
Statistics
Matches: 82, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
43 15 0.18
44 20 0.24
45 33 0.40
46 14 0.17
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:66115 original size:59 final size:59
Alignment explanation
Indices: 66027--66523 Score: 437
Period size: 58 Copynumber: 8.5 Consensus size: 59
66017 AATTCATGTA
* * * * * * *
66027 ATTTCCTTTTAATATTAGCACTCTCAGTGCTCTATCTGGAAAAT-TATACGCTTAGTATG
1 ATTTCCTTATCATTTTAGCACACTAAGTGCTCTATATGG-AAATCTATACACTTAGTATG
* * * * **
66086 CTTCCCCTT-TCATTTTAGCACACGAAGTGCCCTAT-TAAAAAT-TCATAC-CATTAGTATG
1 ATT-TCCTTATCATTTTAGCACACTAAGTGCTCTATATGGAAATCT-ATACAC-TTAGTATG
** * * * * * *
66144 ATTTTGTTACCATTTTAGCACA-TGAAATGCCCTATGTGAAAATCCATAC-CATTAGTATG
1 ATTTCCTTATCATTTTAGCACACT-AAGTGCTCTATATGGAAATCTATACAC-TTAGTATG
* * * * *
66203 ATTTCCTTATC-TTTGTAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTTAGTATG
1 ATTTCCTTATCATTT-TAGCACACTAAGTGCTCTATATGGAAATCTATACACTTAGTATG
* * * * *
66262 ATTCCCTTA-CATTTTTAGCACA-TAAAATGC-CGTATCTGAAAATCCATACACTTAGTATG
1 ATTTCCTTATCA-TTTTAGCACACT-AAGTGCTC-TATATGGAAATCTATACACTTAGTATG
* * *
66321 ATTTCCTTATCA-TTTAGCACACTCAGTGCTCAATATGGAAATCTATACACTCAGTATG
1 ATTTCCTTATCATTTTAGCACACTAAGTGCTCTATATGGAAATCTATACACTTAGTATG
* * *
66379 ATTTCCTTATCA-TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATG
1 ATTTCCTTATCATTTTAGCACACTAAGTGCTCTATATGGAAATCTATACACTTAGTATG
* * *
66437 ATTTCCTTATCA-TTTAGCATACTCAGTGCTCCATATGGAAATCTATACACTTAGTATG
1 ATTTCCTTATCATTTTAGCACACTAAGTGCTCTATATGGAAATCTATACACTTAGTATG
*
66495 ATTTCCTTATCATTTTAGCACACAAAGTG
1 ATTTCCTTATCATTTTAGCACACTAAGTG
66524 TCATTCGGTA
Statistics
Matches: 371, Mismatches: 49, Indels: 36
0.81 0.11 0.08
Matches are distributed among these distances:
57 8 0.02
58 202 0.54
59 150 0.40
60 11 0.03
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.37
Consensus pattern (59 bp):
ATTTCCTTATCATTTTAGCACACTAAGTGCTCTATATGGAAATCTATACACTTAGTATG
Found at i:66158 original size:58 final size:59
Alignment explanation
Indices: 66096--66206 Score: 179
Period size: 59 Copynumber: 1.9 Consensus size: 59
66086 CTTCCCCTTT
* *
66096 CATTTTAGCACACGAAGTGCCCTAT-TAAAAATTCATACCATTAGTATGATTTTGTTAC
1 CATTTTAGCACACGAAATGCCCTATGTAAAAATCCATACCATTAGTATGATTTTGTTAC
* *
66154 CATTTTAGCACATGAAATGCCCTATGTGAAAATCCATACCATTAGTATGATTT
1 CATTTTAGCACACGAAATGCCCTATGTAAAAATCCATACCATTAGTATGATTT
66207 CCTTATCTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
58 23 0.48
59 25 0.52
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (59 bp):
CATTTTAGCACACGAAATGCCCTATGTAAAAATCCATACCATTAGTATGATTTTGTTAC
Found at i:66339 original size:176 final size:172
Alignment explanation
Indices: 66027--66517 Score: 472
Period size: 176 Copynumber: 2.8 Consensus size: 172
66017 AATTCATGTA
* * * * *
66027 ATTTCCTTTTAATATTAGCACTCTCAGTGCTCTATCTGGAAAAT-TATACGCTTAGTATGCTTCC
1 ATTTCCTTATCAT-TTAGCACACTCAGTGCTCTATCTGG-AAATCTATACACTTAGTATGATT-C
* * * * ** *
66091 CCTTTCATTTTAGCACACGAAGTGCCCTATTAAAAATTCATAC-CATTAGTATGATTTTGTTACC
63 CCTTACATTTTAGCACA-TAAGTG-CCTATTGAAAATCCATACAC-TTAGTATGATTTCCTTATC
* * *
66155 ATTTTAGCACA-TGAAATGCCCTATGTGAAAATCCATAC-CATTAGTATG
125 ATTTTAGCACACT-AAATGCCCAATATGAAAATCCATACAC-TCAGTATG
* * * * *
66203 ATTTCCTTATCTTTGTAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTTAGTATGATTCCC
1 ATTTCCTTATCATT-TAGCACACTCAGTGCTCTATCTGGAAATCTATACACTTAGTATGATTCCC
*
66268 TTACATTTTTAGCACATAAAATGCCGTATCTGAAAATCCATACACTTAGTATGATTTCCTTATCA
65 TTACA-TTTTAGCACAT-AAGTGCC-TAT-TGAAAATCCATACACTTAGTATGATTTCCTTATCA
* * * * *
66333 -TTTAGCACACTCAGTGCTCAATATGGAAATCTATACACTCAGTATG
126 TTTTAGCACACTAAATGCCCAATATGAAAATCCATACACTCAGTATG
* * * *
66379 ATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCCT
1 ATTTCCTTATCATTTAGCACACTCAGTGCTCTATCTGGAAATCTATACACTTAGTATGATTCCCT
* * * * *
66444 TATCA-TTTAGCATACTCAGTGCTCCATATGGAAATCTATACACTTAGTATGATTTCCTTATCAT
66 TA-CATTTTAGCACA-TAAGTGC-CTAT-TGAAAATCCATACACTTAGTATGATTTCCTTATCAT
66508 TTTAGCACAC
127 TTTAGCACAC
66518 AAAGTGTCAT
Statistics
Matches: 261, Mismatches: 41, Indels: 27
0.79 0.12 0.08
Matches are distributed among these distances:
174 47 0.18
175 71 0.27
176 112 0.43
177 30 0.11
178 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (172 bp):
ATTTCCTTATCATTTAGCACACTCAGTGCTCTATCTGGAAATCTATACACTTAGTATGATTCCCT
TACATTTTAGCACATAAGTGCCTATTGAAAATCCATACACTTAGTATGATTTCCTTATCATTTTA
GCACACTAAATGCCCAATATGAAAATCCATACACTCAGTATG
Found at i:66403 original size:30 final size:30
Alignment explanation
Indices: 66367--66463 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 30
66357 GGAAATCTAT
66367 ACACTCAGTATGATTTCCTTATCATTTAGC
1 ACACTCAGTATGATTTCCTTATCATTTAGC
* * * * *
66397 ACACTCAG--TG--CTCCATATGGAAATCTA-T
1 ACACTCAGTATGATTTCCTTAT---CATTTAGC
66425 ACACTCAGTATGATTTCCTTATCATTTAGC
1 ACACTCAGTATGATTTCCTTATCATTTAGC
*
66455 ATACTCAGT
1 ACACTCAGT
66464 GCTCCATATG
Statistics
Matches: 48, Mismatches: 11, Indels: 16
0.64 0.15 0.21
Matches are distributed among these distances:
26 6 0.12
28 10 0.21
29 8 0.17
30 18 0.38
32 6 0.12
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (30 bp):
ACACTCAGTATGATTTCCTTATCATTTAGC
Found at i:67617 original size:25 final size:25
Alignment explanation
Indices: 67589--67639 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
67579 TAAAATTCTT
67589 TTTAGGAAATTATCACTTAATTCCC
1 TTTAGGAAATTATCACTTAATTCCC
67614 TTTAGGAAATTATCACTTAATTCCC
1 TTTAGGAAATTATCACTTAATTCCC
67639 T
1 T
67640 AAACGTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (25 bp):
TTTAGGAAATTATCACTTAATTCCC
Done.