Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007958.1 Hibiscus syriacus cultivar Beakdansim tig00110385_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: 62617
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:3678 original size:41 final size:42
Alignment explanation
Indices: 3546--3664 Score: 152
Period size: 41 Copynumber: 2.9 Consensus size: 42
3536 GATTTGTATG
* * *
3546 TCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAA
1 TCCTTCGGGTCATATGTAAGTCTTTCGAGCATGATGCTTAAA
* *
3588 TTCTTCGGGTCATCA-GTAAGTC-TTCGAGTATGATGCTTAAA
1 TCCTTCGGGTCAT-ATGTAAGTCTTTCGAGCATGATGCTTAAA
* *
3629 TCCTTCGGGTCATATGTAAGCCTTTCGAGCAAGATG
1 TCCTTCGGGTCATATGTAAGTCTTTCGAGCATGATG
3665 ATAAGACCTT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
40 1 0.02
41 35 0.54
42 29 0.45
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (42 bp):
TCCTTCGGGTCATATGTAAGTCTTTCGAGCATGATGCTTAAA
Found at i:3866 original size:41 final size:41
Alignment explanation
Indices: 3809--3930 Score: 131
Period size: 41 Copynumber: 3.0 Consensus size: 41
3799 AAGATTAAAG
* *
3809 TAAATCCTTCAGGTCATCAATAAGTCTTTCGAGCATGATGC
1 TAAATCCTTCAGGTCATCAATAAGCCTTTCGAGCAAGATGC
** *
3850 TAAATCCTTCAGGTCATCTGTAAGCCTTTCGAGCAAGATGA
1 TAAATCCTTCAGGTCATCAATAAGCCTTTCGAGCAAGATGC
* * * *
3891 TAAGAT-CTTCGGGCCATCCATAAGACC-TTCGGGCAAGATG
1 TAA-ATCCTTCAGGTCATCAATAAG-CCTTTCGAGCAAGATG
3931 TTTTCAAATG
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 65 0.94
42 4 0.06
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (41 bp):
TAAATCCTTCAGGTCATCAATAAGCCTTTCGAGCAAGATGC
Found at i:4783 original size:119 final size:118
Alignment explanation
Indices: 4577--4852 Score: 349
Period size: 119 Copynumber: 2.3 Consensus size: 118
4567 TTCCAGAAAA
* * * *
4577 AGTTCATAATAATAAGAACTCGTCTGAAGAGGAAGAATAAATTAATAATAAGAAGAGTTGTTCAA
1 AGTTCATAATAAGAAGAACTCATCTGAAGAGAAAGAATAAATTAATAATAAGAAGAGTTGCTCAA
* * * *
4642 CCTTTTGATAGATTCCATCACAGAAGGAGATGAATCGTCATT-CCAGTGGAAG
66 CCTTTTGATAAATTCCATCACAGAAGGAGATGAATCATCATTCCCAATAGAAG
* * *
4694 AGTTCATAATAAGAAGAATTCATCTAGAAGAGAAAGAA-AAAGTTCATAATAATAAGAGCTTGCT
1 AGTTCATAATAAGAAGAACTCATCT-GAAGAGAAAGAATAAA-TTAATAATAAGAAGAG-TTGCT
* *
4758 CAACCTTTTGCTAAATTCCATCACAGAAGGAGATGGATCATCATTCCCAATAGAAG
63 CAACCTTTTGATAAATTCCATCACAGAAGGAGATGAATCATCATTCCCAATAGAAG
* * * * *
4814 AGTTCATAATAATAAAAACTCGTCCGAAGAGGAAGAATA
1 AGTTCATAATAAGAAGAACTCATCTGAAGAGAAAGAATA
4853 GTTCATAATG
Statistics
Matches: 135, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
117 25 0.19
118 25 0.19
119 56 0.41
120 29 0.21
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (118 bp):
AGTTCATAATAAGAAGAACTCATCTGAAGAGAAAGAATAAATTAATAATAAGAAGAGTTGCTCAA
CCTTTTGATAAATTCCATCACAGAAGGAGATGAATCATCATTCCCAATAGAAG
Found at i:5016 original size:3 final size:3
Alignment explanation
Indices: 5008--5063 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
4998 GTCTATTCTT
* * *
5008 TTA TTA TTA TTA ATA TTA ATA TTA TTA TTA ATA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5055 ATA TTA TTA
1 TTA TTA TTA
5064 AATGATAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:10353 original size:23 final size:23
Alignment explanation
Indices: 10322--10366 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
10312 AACGAGGTGC
* *
10322 TAGGGTTAGAGTAGATCTAATGT
1 TAGGATTAGAATAGATCTAATGT
*
10345 TAGGATTAGAATAGCTCTAATG
1 TAGGATTAGAATAGATCTAATG
10367 GTTTTCTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (23 bp):
TAGGATTAGAATAGATCTAATGT
Found at i:11854 original size:17 final size:17
Alignment explanation
Indices: 11791--11855 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 17
11781 TCAACTTTAT
* *
11791 TTAAAATTATATTTTCT
1 TTAAAATTATATTATCA
*
11808 TTAAAATTAAATTAT-A
1 TTAAAATTATATTATCA
*
11824 ATAAAA--AT-TTATCA
1 TTAAAATTATATTATCA
11838 TTAAAATTATATTATCA
1 TTAAAATTATATTATCA
11855 T
1 T
11856 AAATTTAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
13 4 0.11
14 7 0.18
16 7 0.18
17 20 0.53
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAAAATTATATTATCA
Found at i:11918 original size:2 final size:2
Alignment explanation
Indices: 11911--11973 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
11901 TAGTTATTAA
11911 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11953 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
11974 CATTACCCTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12607 original size:35 final size:35
Alignment explanation
Indices: 12568--12635 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
12558 TTTAATTTAA
12568 GGTTTAGAATATAATTAAAGTATTTTGGAATTTGG
1 GGTTTAGAATATAATTAAAGTATTTTGGAATTTGG
* * *
12603 GGTTTAGAATGTAATTGAAGTGTTTTGGAATTT
1 GGTTTAGAATATAATTAAAGTATTTTGGAATTT
12636 TGAACATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (35 bp):
GGTTTAGAATATAATTAAAGTATTTTGGAATTTGG
Found at i:35358 original size:131 final size:132
Alignment explanation
Indices: 35115--35385 Score: 517
Period size: 131 Copynumber: 2.1 Consensus size: 132
35105 TAAACAAAGG
*
35115 AGTTGCTAGGAACCCTTGTTCCATGTTCAATTGAGGTATTGTGTTCCTATTTTTAGAGTTCTGGA
1 AGTTGCTAGGAACCCTTGTTCCATGTTCAATTGAGGTATTGTGTTCCTATTTTTAGAGTTCTGAA
*
35180 AAATAGAGTTGGCATGTAACGAATATCTTCTTGTGTCACTTTCACCTGAAACTGATTGTCATTTG
66 AAATAGAGTTGGCATGTAACGAATATCTTCTTGTGTCACTTTCACCTGAAACTGATTATCATTTG
35245 TC
131 TC
35247 AGTTGCTA-GAACCCTTGTTCCATGTTCAATTGAGGTATTGTGTTCCTATTTTTAGAGTTCTGAA
1 AGTTGCTAGGAACCCTTGTTCCATGTTCAATTGAGGTATTGTGTTCCTATTTTTAGAGTTCTGAA
35311 AAATAGAGTTGGCATGTAACGAATATCTTCTTGTGTCACTTTCACCTGAAACTGATTATCATTTG
66 AAATAGAGTTGGCATGTAACGAATATCTTCTTGTGTCACTTTCACCTGAAACTGATTATCATTTG
35376 TC
131 TC
35378 AGTTGCTA
1 AGTTGCTA
35386 TTTATGTTGA
Statistics
Matches: 137, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
131 129 0.94
132 8 0.06
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (132 bp):
AGTTGCTAGGAACCCTTGTTCCATGTTCAATTGAGGTATTGTGTTCCTATTTTTAGAGTTCTGAA
AAATAGAGTTGGCATGTAACGAATATCTTCTTGTGTCACTTTCACCTGAAACTGATTATCATTTG
TC
Found at i:45808 original size:14 final size:15
Alignment explanation
Indices: 45766--45810 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
45756 TAAAAATATT
45766 TAAAAATATAAACAAG
1 TAAAAATA-AAACAAG
*
45782 TAAAATTAAAACAA-
1 TAAAAATAAAACAAG
*
45796 TAAAAATACAACAAG
1 TAAAAATAAAACAAG
45811 AACGATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
16 7 0.28
ACGTcount: A:0.69, C:0.09, G:0.04, T:0.18
Consensus pattern (15 bp):
TAAAAATAAAACAAG
Found at i:47192 original size:3 final size:3
Alignment explanation
Indices: 47184--47266 Score: 114
Period size: 3 Copynumber: 27.7 Consensus size: 3
47174 AATATATATT
*
47184 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
47231 TAG TAAA TAA TAA TTA TAA TAA CAA TAA TAA TAA TA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
47267 TTTATAATAT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.03
3 66 0.94
4 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:47944 original size:113 final size:113
Alignment explanation
Indices: 47592--48497 Score: 1257
Period size: 113 Copynumber: 8.0 Consensus size: 113
47582 ATAGAATTAT
* * *
47592 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* ** *
47657 ATTATGAAC-TTCTCTGGAAAAGCTGCCCCATCAAGTGATAGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATAGATTTGA
*
47704 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
* * * * **
47769 CTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGAT-GAATTCAA
63 CTCATTATGAACT-TTCTCTGGAAAAGATGATCCATCAAATGATAG-ATTTGA
* * *
47820 ACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
47885 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATAGATTTGA
*
47933 GCAAAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * **
47998 ATTATGAACTTTCTCTGGAAAAGATAATTCATCAATTGAT-GAATTCAA
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATAG-ATTTGA
* * *
48046 ACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
48111 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATAGATTTGA
* * *
48159 GTAAAAGGTTGAACAAATTCTTCCCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
48224 ATTATGAACTTTCTCTGGAAAAGATAATCCATCAATTGAT-GAATTCA
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATAGATTTGA
* *
48271 GGTAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 -GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * **
48336 CATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAA
65 CATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATAGATTTGA
* *
48385 GTAAAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
48450 ATTATGAACTTTCTCTGGAAATG-TCAATCCATCAAATGATAGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGAT-GATCCATCAAATGATAGATTTGA
48498 ATCTTTGCTA
Statistics
Matches: 707, Mismatches: 74, Indels: 25
0.88 0.09 0.03
Matches are distributed among these distances:
112 59 0.08
113 545 0.77
114 6 0.01
115 21 0.03
116 74 0.10
117 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATAGATTTGA
Found at i:48098 original size:226 final size:226
Alignment explanation
Indices: 47593--48489 Score: 1449
Period size: 226 Copynumber: 4.0 Consensus size: 226
47583 TAGAATTATG
*
47593 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** *
47658 TTATGAAC-TTCTCTGGAAAAGCTGCCCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAAT
* * *
47722 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-
131 TCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCT
* * * * *
47786 CTGGCAATGTTGATCCATCAAATGATGAATTCAAA
192 CTGGAAAAGATAATCCATCAATTGATGAATTCAAA
47821 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
47886 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAAT
47951 TCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
*
48016 AAAAGATAATTCATCAATTGATGAATTCAAA
196 AAAAGATAATCCATCAATTGATGAATTCAAA
48047 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
48112 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGAGTAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAAT
*
48177 TCTTCCCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
**
48242 AAAAGATAATCCATCAATTGATGAATTCAGG
196 AAAAGATAATCCATCAATTGATGAATTCAAA
* * * *
48273 TAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * ** *
48338 TTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAAT
48403 TCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* *
48468 AAATG-TCAATCCATCAAATGAT
196 AAAAGAT-AATCCATCAATTGAT
48490 AGATTTGAAT
Statistics
Matches: 634, Mismatches: 32, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
225 3 0.00
226 472 0.74
228 72 0.11
229 87 0.14
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (226 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGAGCAAAAGGTTGAACAAAT
TCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAAAGATAATCCATCAATTGATGAATTCAAA
Found at i:49423 original size:83 final size:83
Alignment explanation
Indices: 49282--49649 Score: 605
Period size: 83 Copynumber: 4.4 Consensus size: 83
49272 CTTATTTCTA
* * *
49282 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAATTCAAA
1 CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
* * *
49347 GACCACTTTCAGAAAATG
66 GAACACTTCCAGAAGATG
* * *
49365 CTATGAACACA-TTATTCTTCTC-AATTCAATGATTGGTTTTATCAAACCAGATCGGATAACTCA
1 CTATGAGCACATTTA-TCTTC-CAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCA
49428 AAGAACACTTCCAGAAGATG
64 AAGAACACTTCCAGAAGATG
49448 CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
*
49513 GAACATTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
49531 CTATGAGCACATTTATCTTCCCAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
49596 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
49614 CTATGAGCACATTTATCTTCCAAATTCAATGATTGG
1 CTATGAGCACATTTATCTTCCAAATTCAATGATTGG
49650 ACTAGGATAT
Statistics
Matches: 265, Mismatches: 16, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
82 3 0.01
83 258 0.97
84 4 0.02
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (83 bp):
CTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:50428 original size:16 final size:18
Alignment explanation
Indices: 50387--50434 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
50377 ATTCAATAGA
*
50387 AAAATAAATTGAATTTCC
1 AAAATAAATTGAATCTCC
50405 AAAAATAAATTGAATCT-C
1 -AAAATAAATTGAATCTCC
50423 -AAATAAATTGAA
1 AAAATAAATTGAA
50435 CTTGAAATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 12 0.43
18 1 0.04
19 15 0.54
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.29
Consensus pattern (18 bp):
AAAATAAATTGAATCTCC
Found at i:50801 original size:25 final size:25
Alignment explanation
Indices: 50766--50831 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
50756 GACCCCCCTT
50766 TTTTTTCTTTTTTCTCTTT-TTTTTTC
1 TTTTTT-TTTTTTCT-TTTCTTTTTTC
50792 TTTTTTTTTTTTCTTTTCTTTTTTC
1 TTTTTTTTTTTTCTTTTCTTTTTTC
* **
50817 CTTCATTTTTTTCTT
1 TTTTTTTTTTTTCTT
50832 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.08
25 27 0.75
26 6 0.17
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (25 bp):
TTTTTTTTTTTTCTTTTCTTTTTTC
Found at i:50815 original size:12 final size:12
Alignment explanation
Indices: 50764--50816 Score: 65
Period size: 12 Copynumber: 4.4 Consensus size: 12
50754 TTGACCCCCC
50764 TTTT-TTTTCTT
1 TTTTCTTTTCTT
50775 TTTTCTCTTT-TT
1 TTTTCT-TTTCTT
*
50787 TTTTCTTTTTTTT
1 TTTTC-TTTTCTT
50800 TTTTCTTTTCTT
1 TTTTCTTTTCTT
50812 TTTTC
1 TTTTC
50817 CTTCATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
11 4 0.11
12 22 0.59
13 11 0.30
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTCTTTTCTT
Found at i:50828 original size:1 final size:1
Alignment explanation
Indices: 50764--50815 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
50754 TTGACCCCCC
* * * * * *
50764 TTTTTTTTCTTTTTTCTCTTTTTTTTTCTTTTTTTTTTTTCTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
50816 CCTTCATTTT
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:61420 original size:16 final size:16
Alignment explanation
Indices: 61386--61434 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
61376 ATGAAACATT
61386 AATAAA-ATATAT-AA
1 AATAAATATATATAAA
*
61400 TATAAATA-ATATGAAA
1 AATAAATATATAT-AAA
*
61416 AATAAGTATATATAAA
1 AATAAATATATATAAA
61432 AAT
1 AAT
61435 TTGAAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 9 0.32
15 1 0.04
16 14 0.50
17 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (16 bp):
AATAAATATATATAAA
Done.