Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008938.1 Hibiscus syriacus cultivar Beakdansim tig00112256_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: 61815
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:913 original size:29 final size:29
Alignment explanation
Indices: 870--931 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
860 AAGATTCACT
870 TAGCATTGCACTTTTTTGACTGCTGCTGG
1 TAGCATTGCACTTTTTTGACTGCTGCTGG
*
899 TAGCATTGCATTTTTTTGACTGCTGCTGG
1 TAGCATTGCACTTTTTTGACTGCTGCTGG
928 TAGC
1 TAGC
932 GAACCAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (29 bp):
TAGCATTGCACTTTTTTGACTGCTGCTGG
Found at i:4396 original size:73 final size:72
Alignment explanation
Indices: 4300--4451 Score: 261
Period size: 73 Copynumber: 2.1 Consensus size: 72
4290 GAGCACACTG
*
4300 TAATATCTTATGATTTAGGGATTTAATTTGATGC-ATATCACTGTATATTACGGTTGGATATTAT
1 TAATGTCTTATGATTTAGGGATTTAATTTGATGCAATATCACTGTATATTACGGTTGGATA-TA-
4364 TTTTTGTTT
64 TTTTTGTTT
4373 TAATGTCTTATGATTTAGGGATTTAATTTGATGCATATATCACTGTATATTACGGTTGGATATAT
1 TAATGTCTTATGATTTAGGGATTTAATTTGATGCA-ATATCACTGTATATTACGGTTGGATATAT
4438 TTTTGTTT
65 TTTTGTTT
4446 TAATGT
1 TAATGT
4452 GTTAACTCCT
Statistics
Matches: 76, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
73 48 0.63
74 2 0.03
75 26 0.34
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.50
Consensus pattern (72 bp):
TAATGTCTTATGATTTAGGGATTTAATTTGATGCAATATCACTGTATATTACGGTTGGATATATT
TTTGTTT
Found at i:7789 original size:21 final size:22
Alignment explanation
Indices: 7748--7789 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
7738 CATGTCAAAC
*
7748 TAATTTTAATAATTTCTTGTAA
1 TAATTTTAATAATTTCATGTAA
7770 TAATTTTAAT-ATTTCATGTA
1 TAATTTTAATAATTTCATGTA
7790 TTCGTTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (22 bp):
TAATTTTAATAATTTCATGTAA
Found at i:10007 original size:35 final size:37
Alignment explanation
Indices: 9944--10018 Score: 109
Period size: 35 Copynumber: 2.1 Consensus size: 37
9934 TTTCGTCTTA
9944 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
* * *
9981 CTAGGATTC-AATTC-CTAAAATAGGATAGAATTTTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
10016 CTA
1 CTA
10019 TGTTTTAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 22 0.63
36 4 0.11
37 9 0.26
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
Found at i:10729 original size:24 final size:24
Alignment explanation
Indices: 10701--10746 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
10691 TGTTTTCATG
*
10701 TATTTATA-TATATTACATTATTAT
1 TATTT-TACTATATTAAATTATTAT
*
10725 TATTTTACTTTATTAAATTATT
1 TATTTTACTATATTAAATTATT
10747 TTTTTCGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTTTACTATATTAAATTATTAT
Found at i:14107 original size:22 final size:20
Alignment explanation
Indices: 14074--14132 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
14064 AACAAAAAGG
14074 GCAAAAAAAAAAGAA-AAGAA
1 GCAAAAAAAAAA-AACAAGAA
14094 GCAAAAAAGGAAAAAACAAGAA
1 GCAAAAAA--AAAAAACAAGAA
14116 -CAAAAATAAAAAAACAA
1 GCAAAAA-AAAAAAACAA
14133 AAATAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
20 17 0.49
21 8 0.23
22 10 0.29
ACGTcount: A:0.78, C:0.08, G:0.12, T:0.02
Consensus pattern (20 bp):
GCAAAAAAAAAAAACAAGAA
Found at i:14131 original size:14 final size:14
Alignment explanation
Indices: 14114--14143 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
14104 AAAAAACAAG
14114 AACAAAAATAAAAA
1 AACAAAAATAAAAA
14128 AACAAAAATAAAAA
1 AACAAAAATAAAAA
14142 AA
1 AA
14144 GGGACAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.87, C:0.07, G:0.00, T:0.07
Consensus pattern (14 bp):
AACAAAAATAAAAA
Found at i:14140 original size:20 final size:20
Alignment explanation
Indices: 14104--14141 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
14094 GCAAAAAAGG
*
14104 AAAAAACAAGAACAAAAATA
1 AAAAAACAAAAACAAAAATA
*
14124 AAAAAACAAAAATAAAAA
1 AAAAAACAAAAACAAAAA
14142 AAGGGACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.84, C:0.08, G:0.03, T:0.05
Consensus pattern (20 bp):
AAAAAACAAAAACAAAAATA
Found at i:14779 original size:22 final size:22
Alignment explanation
Indices: 14751--14801 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
14741 CCCCATCAAT
14751 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
14773 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
14795 CCTTTGA
1 CCTTTGA
14802 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:15757 original size:37 final size:37
Alignment explanation
Indices: 15668--15777 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
15658 GTGCTCACCA
15668 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
15704 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* *
15741 TTTTCTCTCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
15778 ATTGAAAACA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 31 0.46
37 34 0.50
38 3 0.04
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:15862 original size:102 final size:101
Alignment explanation
Indices: 15686--16041 Score: 586
Period size: 102 Copynumber: 3.5 Consensus size: 101
15676 CTTGAGACAG
** * * *
15686 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCTCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC-CT
15751 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* **
15788 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC-T
*
15853 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
15890 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCT-CCT
15955 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
15992 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
16042 TAAACATTGA
Statistics
Matches: 237, Mismatches: 15, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
101 1 0.00
102 234 0.99
103 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (101 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCTT
GAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:15863 original size:37 final size:37
Alignment explanation
Indices: 15804--15976 Score: 129
Period size: 37 Copynumber: 4.9 Consensus size: 37
15794 TTGAAATGAG
*
15804 TTTTGTCTCTC-TTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
** *
15841 TTCCGTCTCCATTGAGACAGTTTCTCTTGAAACATAAA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA-AAA
* **
15879 ---------CATTGGAAACA-TTTCCCTTGAAA-TGAA
1 TTTTGTCTCCATT-GAGACAGTTTCCCTTGAAACAAAA
*
15906 TTTTGTCTCTC-TTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
* *
15943 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA
15977 TAAACATTGA
Statistics
Matches: 106, Mismatches: 14, Indels: 32
0.70 0.09 0.21
Matches are distributed among these distances:
27 2 0.02
29 15 0.14
30 5 0.05
35 4 0.04
36 16 0.15
37 61 0.58
38 3 0.03
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (37 bp):
TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACAAAA
Found at i:16031 original size:65 final size:65
Alignment explanation
Indices: 15926--16106 Score: 308
Period size: 65 Copynumber: 2.8 Consensus size: 65
15916 CTTGAGATAG
** * *
15926 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAA-TGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
15991 A
65 A
*
15992 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACA
1 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
16057 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACA
16107 AAATTTTGTC
Statistics
Matches: 109, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
65 97 0.89
66 12 0.11
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (65 bp):
TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:16033 original size:167 final size:169
Alignment explanation
Indices: 15824--16141 Score: 534
Period size: 167 Copynumber: 1.9 Consensus size: 169
15814 CTTGAGATAG
*
15824 TTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACATTGGAAAC
1 TTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* *
15889 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCC
66 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCC
15954 TTGAGACAG-TTTCTCTTGAAACATAAACATTGAAAACA
131 TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACA
** * *
15992 TTTCCCTTGAAA-TGAATTTCGTCTCTC-TTGAGATAGTTTCTCTTGAAACATAAACATTGAAAA
1 TTTCCCTTGAAACAAAATTCCGTCTC-CATTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
*
16055 CATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCC
65 CATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCC
16120 CTTGAGACAGTTTTCTCTTGAA
130 CTTGAGACAGTTTTCTCTTGAA
16142 GCATCATCTT
Statistics
Matches: 140, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
167 116 0.83
168 24 0.17
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (169 bp):
TTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCC
TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:16114 original size:204 final size:199
Alignment explanation
Indices: 15670--16141 Score: 576
Period size: 204 Copynumber: 2.3 Consensus size: 199
15660 GCTCACCATT
*
15670 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* *
15735 AAAATTTTTTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
66 AAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
* * *
15800 TGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTC
131 TGAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA--------CCATTGAAACAGTTTC
* *
15865 TCTTGAAACATA
188 CCTTGAAAAATA
** * * * ** *
15877 AAC-AT-TGGAAACA-TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
15939 AAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
66 AAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
*
16004 TGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAA-CATTGAAAACA-TTTCCCTTGA
131 TGAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAACCATTG-AAACAGTTTCCCTTGA
*
16067 AATGAATTTC
194 AA--AA--TA
* * *
16077 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTTCTCTTGAA
1 GTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAA
16142 GCATCATCTT
Statistics
Matches: 225, Mismatches: 29, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
196 16 0.07
197 4 0.02
198 1 0.00
200 2 0.01
201 1 0.00
202 6 0.03
203 11 0.05
204 163 0.72
205 19 0.08
206 1 0.00
207 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (199 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
TGAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAACCATTGAAACAGTTTCCCTTGAAA
AATA
Found at i:16284 original size:37 final size:37
Alignment explanation
Indices: 16214--16285 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
16204 TGGAACTAAG
* * **
16214 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
* *
16251 TTTTGTCTCCCTTAAGACCGTTTCCCTTGAAACAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAA
16286 CAAATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
Found at i:16872 original size:160 final size:160
Alignment explanation
Indices: 16608--16944 Score: 611
Period size: 160 Copynumber: 2.1 Consensus size: 160
16598 CAACACAAGT
*
16608 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
1 TCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
*
16673 ACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCT
66 ACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGACT
*
16738 GACTGTCGACAAACAATTGCGGAGCCAATC
131 GACTGTCGACAAACAATTGCGGAGCCAAAC
16768 TCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
1 TCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
*
16833 ACTTCACATCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGACT
66 ACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGACT
* *
16898 GACTGTCGACAAGCAATTTCGGAGCCAAAC
131 GACTGTCGACAAACAATTGCGGAGCCAAAC
*
16928 TCAACTTCACAGCGAAG
1 TCAACTTCACAACGAAG
16945 GATATTGGAC
Statistics
Matches: 170, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
160 170 1.00
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (160 bp):
TCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
ACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGACT
GACTGTCGACAAACAATTGCGGAGCCAAAC
Found at i:17327 original size:106 final size:105
Alignment explanation
Indices: 16768--17487 Score: 653
Period size: 109 Copynumber: 6.9 Consensus size: 105
16758 GGAGCCAATC
* * * * * *
16768 TCAACTTCACAACGAAGAGACGGCTGGTTGTCAAC-AATAATTTCCCAGTTTCAGGGCCAATTTT
1 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-TCAATTTCAGAGCCAATTTC
* * * * *
16832 AACTTCACATCGAAGGATATTGGACCCAAGACAGCACAAGC
65 AACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* * * ** * * * **
16873 TCAACTTCACAGCGAAGGGGCGACTGACTGT---C-GACAA---GCAATTTCGGAGCCAAACTCA
1 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCAATTTCAGAGCCAATTTCA
16931 ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
66 ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* * * * *
16971 TCAACTTCACAGCGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTCCAGAGCCGATTTC
1 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-TCAATTTCAGAGCCAATTTC
* * * *
17036 AACTCCAC-GACGGAGGATATCGTGCTACCCGAGACAACACAAGT
65 AACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGT
* * * ** *
17080 TCAACTTCATAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCA-TTCGCGATTT
1 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTTCAATTTCAGAGC-CAATTT
* * *
17144 CAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACACAAGT
64 CAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGT
*
17189 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCAATTTC
1 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTC-AATTTCAGAGCCAATTTC
*
17254 AACTTCGCAGCGAAGGATATTGGACTCGAGACAACACAAGT
65 AACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* * * * * *
17295 TCAACTTCATAATGAAGGGACGGCTGATTGTCAAC-AA-GA-TTTC--GTTCAGAGTCAATTTCA
1 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCAATTTCAGAGCCAATTTCA
* * * * *
17355 TCTTCACAACGAAGGATATTAGACTCGAGACAGCACAAGC
66 ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* * ** * * * *
17395 TCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTTTAGAACCAATTTC
1 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-TCAATTTCAGAGCCAATTTC
*
17460 AACTTCACAGCGGAGGATATTGGACTCG
65 AACTTCACAGCGAAGGATATTGGACTCG
17488 GAACAATATT
Statistics
Matches: 506, Mismatches: 86, Indels: 45
0.79 0.14 0.07
Matches are distributed among these distances:
98 76 0.15
100 79 0.16
101 3 0.01
102 8 0.02
103 6 0.01
104 1 0.00
105 28 0.06
106 116 0.23
107 2 0.00
108 8 0.02
109 174 0.34
110 5 0.01
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (105 bp):
TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCAATTTCAGAGCCAATTTCA
ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
Found at i:18011 original size:35 final size:35
Alignment explanation
Indices: 17948--18047 Score: 119
Period size: 35 Copynumber: 2.7 Consensus size: 35
17938 TTTCGTCCTA
*
17948 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
17985 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
18020 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
18048 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:18498 original size:2 final size:2
Alignment explanation
Indices: 18493--18526 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
18483 TTAAAGTTAT
*
18493 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18527 ACTATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:18744 original size:16 final size:16
Alignment explanation
Indices: 18725--18758 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18715 CATGTATTTA
18725 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
18741 TATTATTTTACTTTAT
1 TATTATATTACATTAT
18757 TA
1 TA
18759 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:18804 original size:17 final size:16
Alignment explanation
Indices: 18775--18816 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
18765 TTTTTTTCGT
*
18775 TATAATATTTATTATA
1 TATAATATATATTATA
18791 TATATATATATATTATA
1 TATA-ATATATATTATA
18808 TCATAATAT
1 T-ATAATAT
18817 TTTTTGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 16 0.70
18 3 0.13
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TATAATATATATTATA
Found at i:22376 original size:19 final size:20
Alignment explanation
Indices: 22340--22382 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
22330 TTCTTTTTTA
22340 ATGACTGATACTCAGTAAT-
1 ATGACTGATACTCAGTAATG
*
22359 ATGACTGTATATTC-GTAATG
1 ATGACTG-ATACTCAGTAATG
22379 ATGA
1 ATGA
22383 TGTTTTCTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (20 bp):
ATGACTGATACTCAGTAATG
Found at i:22567 original size:3 final size:3
Alignment explanation
Indices: 22552--22613 Score: 88
Period size: 3 Copynumber: 20.0 Consensus size: 3
22542 CTATTTTAAT
* *
22552 TTA TTA CTA TTA TTA TTT TTAA TTA TTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA -TTA TTA TTA TTA TTA
22599 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
22614 ATACAAATGG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
3 48 0.91
4 5 0.09
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:22576 original size:19 final size:18
Alignment explanation
Indices: 22552--22613 Score: 88
Period size: 19 Copynumber: 3.3 Consensus size: 18
22542 CTATTTTAAT
* *
22552 TTATTACTATTATTATTT
1 TTATTATTATTATTATTA
22570 TTAATTATTATTATTTATTA
1 TT-ATTATTATTA-TTATTA
22590 TTATTATTATTATTATTA
1 TTATTATTATTATTATTA
22608 TTATTA
1 TTATTA
22614 ATACAAATGG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.35
19 19 0.47
20 7 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATTATTATTATTATTA
Found at i:28829 original size:30 final size:30
Alignment explanation
Indices: 28772--28839 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
28762 ATGCATAAGT
* **
28772 AAATTCATCATTTATAATGCATCACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
* *
28802 AAATGCATCATTTATAGCACATTACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
*
28832 ATATGCAT
1 AAATGCAT
28840 TCGAATTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (30 bp):
AAATGCATCATTTATAACACATCACCAATA
Found at i:35984 original size:19 final size:17
Alignment explanation
Indices: 35962--36001 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 17
35952 ATATGATGGA
35962 AAAATGAAAAAAGAAAAAG
1 AAAATG-AAAAA-AAAAAG
35981 AAAATGAAAAAAAAAAG
1 AAAATGAAAAAAAAAAG
35998 AAAA
1 AAAA
36002 AAATAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 10 0.48
18 5 0.24
19 6 0.29
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.05
Consensus pattern (17 bp):
AAAATGAAAAAAAAAAG
Found at i:36003 original size:19 final size:19
Alignment explanation
Indices: 35929--36003 Score: 71
Period size: 19 Copynumber: 3.9 Consensus size: 19
35919 TATTACACTT
35929 AAAAAAAAAAGGAAAAAATG
1 AAAAAAAAAA-GAAAAAATG
* ** * *
35949 AAAATATGATGGAAAAATG
1 AAAAAAAAAAGAAAAAATG
*
35968 AAAAAAGAAAA-AGAAAATG
1 AAAAAA-AAAAGAAAAAATG
35987 AAAAAAAAAAGAAAAAA
1 AAAAAAAAAAGAAAAAA
36004 ATAAATAAAG
Statistics
Matches: 41, Mismatches: 12, Indels: 5
0.71 0.21 0.09
Matches are distributed among these distances:
18 4 0.10
19 30 0.73
20 7 0.17
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (19 bp):
AAAAAAAAAAGAAAAAATG
Found at i:37239 original size:39 final size:38
Alignment explanation
Indices: 37169--37243 Score: 87
Period size: 39 Copynumber: 1.9 Consensus size: 38
37159 CTAAAGATGG
* * *
37169 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCGA
1 CCAGAACTCCTCATCACGTAGGAGCCATGTCA-CCCCGA
* * *
37208 CCAGATCTCCTCATCGCGTAGGAGCTATGTCACCCC
1 CCAGAACTCCTCATCACGTAGGAGCCATGTCACCCC
37244 TAGATAACCA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
38 4 0.13
39 26 0.87
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (38 bp):
CCAGAACTCCTCATCACGTAGGAGCCATGTCACCCCGA
Found at i:37248 original size:133 final size:134
Alignment explanation
Indices: 36943--37365 Score: 563
Period size: 133 Copynumber: 3.2 Consensus size: 134
36933 AACATCAGCT
* * * * ** *
36943 GACCAGATCTCCTCATCATGTAGGAGCAACGTCAACATTAGATAACCAGCCGTCCTCATTACGTA
1 GACCAGATCTCCTCATCACGTAGGAGCTATGTCACCCCTAGATAACCAGCCGTCCTCATCACGTA
** * * *
37008 GGAACTATATTATCG--C-T-ATAAA-ATGGCCAAGAACTCTTCATCACGTATGAGTAGTGTCAT
66 GGAACCGTGTTATCGCCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCAT
37068 CCCC
131 CCCC
** * * *
37072 TGATTAGATCTCCTCATCACGTAGGAG-TCGTGTCACCCCTAGATAACCAGACATCCTCATCACG
1 -GACCAGATCTCCTCATCACGTAGGAGCT-ATGTCACCCCTAGATAACCAGCCGTCCTCATCACG
*
37136 TAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCC-AGAACTCTTCATCACGTATGAGCCGTGTC
64 TAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTC
37200 ATCCCC
129 ATCCCC
* *
37206 GACCAGATCTCCTCATCGCGTAGGAGCTATGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTA
1 GACCAGATCTCCTCATCACGTAGGAGCTATGTCACCCCTAGATAACCAGCCGTCCTCATCACGTA
* *
37271 GGAACCGAGTTATCACCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCAT
66 GGAACCGTGTTATCGCCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCAT
37336 CCCTC
131 CCC-C
*
37341 GACCAGATTTCCTCATCACGTAGGA
1 GACCAGATCTCCTCATCACGTAGGA
37366 ACCGTGTCAC
Statistics
Matches: 254, Mismatches: 30, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
130 64 0.25
132 1 0.00
133 88 0.35
134 71 0.28
135 30 0.12
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (134 bp):
GACCAGATCTCCTCATCACGTAGGAGCTATGTCACCCCTAGATAACCAGCCGTCCTCATCACGTA
GGAACCGTGTTATCGCCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCAT
CCCC
Found at i:37416 original size:43 final size:40
Alignment explanation
Indices: 37305--37421 Score: 119
Period size: 43 Copynumber: 2.9 Consensus size: 40
37295 AAGATGGCCA
37305 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
** * * * *
37345 AGATTTCCTCATCACGTAGGAACCGTGTCA-CCCTTAGACGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCC-T---CGACC
* *
37388 CGAACTCTTCATCACGTATGAGCAGTGTCGTCCC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCC
37422 CAACAACTAA
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
39 3 0.05
40 25 0.43
43 27 0.47
44 3 0.05
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (40 bp):
AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
Found at i:37593 original size:3 final size:3
Alignment explanation
Indices: 37578--37630 Score: 70
Period size: 3 Copynumber: 17.0 Consensus size: 3
37568 CTATTTTAAT
* *
37578 TTA TTA CTA TTA TTA TTT TTAA TTA TTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA -TTA TTA TTA TTA TTA
37625 TTA TTA
1 TTA TTA
37631 ATACAAATGG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
3 39 0.89
4 5 0.11
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:37595 original size:16 final size:16
Alignment explanation
Indices: 37576--37630 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
37566 TTCTATTTTA
*
37576 ATTTATTACTATTATT
1 ATTTATTATTATTATT
37592 ATTT-TTAATTATTATT
1 ATTTATT-ATTATTATT
37608 ATTTATTATTATTATT
1 ATTTATTATTATTATT
37624 A-TTATTA
1 ATTTATTA
37631 ATACAAATGG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
15 8 0.22
16 26 0.72
17 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTATTATTATTATT
Found at i:37602 original size:19 final size:18
Alignment explanation
Indices: 37578--37630 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
37568 CTATTTTAAT
* *
37578 TTATTACTATTATTATTT
1 TTATTATTATTATTATTA
37596 TTAATTATTATTATTTATTA
1 TT-ATTATTATTA-TTATTA
37616 TTATTATTATTATTA
1 TTATTATTATTATTA
37631 ATACAAATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.16
19 19 0.61
20 7 0.23
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATTATTATTATTATTA
Found at i:37604 original size:10 final size:10
Alignment explanation
Indices: 37580--37627 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
37570 ATTTTAATTT
*
37580 ATTACTATT-
1 ATTATTATTA
*
37589 ATTATTTTTA
1 ATTATTATTA
37599 ATTATTATTA
1 ATTATTATTA
*
37609 TTTATTATT-
1 ATTATTATTA
37618 ATTATTATTA
1 ATTATTATTA
37628 TTAATACAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
9 15 0.47
10 17 0.53
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTATTATTA
Found at i:43154 original size:18 final size:18
Alignment explanation
Indices: 43131--43166 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
43121 AGGGATTTAC
*
43131 AGTGGTCCGTCGGGACAT
1 AGTGGTCCGTCAGGACAT
*
43149 AGTGGTCCTTCAGGACAT
1 AGTGGTCCGTCAGGACAT
43167 TTCATATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.25
Consensus pattern (18 bp):
AGTGGTCCGTCAGGACAT
Found at i:43206 original size:23 final size:23
Alignment explanation
Indices: 43146--43221 Score: 107
Period size: 23 Copynumber: 3.2 Consensus size: 23
43136 TCCGTCGGGA
*
43146 CATAGTGGTCCTTCAGGACATTT
1 CATAGTGGTCCTTCGGGACATTT
*
43169 CATATTGGTCCTTCGGGACATTT
1 CATAGTGGTCCTTCGGGACATTT
*
43192 CATAGTGGTCCTTCGAGACAAATTT
1 CATAGTGGTCCTTCGGGAC--ATTT
43217 CATAG
1 CATAG
43222 CCCCTAGTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
23 38 0.81
25 9 0.19
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (23 bp):
CATAGTGGTCCTTCGGGACATTT
Found at i:59715 original size:34 final size:33
Alignment explanation
Indices: 59635--59715 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 33
59625 GTTAAGGGAC
* * *
59635 AAAATATCAAAATAGAAATTTAAATGACTAAAAT
1 AAAATAAC-AAATATAAACTTAAATGACTAAAAT
*
59669 AAAATAAC----ATAAACTTAAGTGACTAAAAT
1 AAAATAACAAATATAAACTTAAATGACTAAAAT
59698 AAAATAACAGAATATAAA
1 AAAATAACA-AATATAAA
59716 GTGACAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
29 26 0.68
34 12 0.32
ACGTcount: A:0.63, C:0.07, G:0.06, T:0.23
Consensus pattern (33 bp):
AAAATAACAAATATAAACTTAAATGACTAAAAT
Found at i:59717 original size:29 final size:29
Alignment explanation
Indices: 59650--59752 Score: 104
Period size: 29 Copynumber: 3.5 Consensus size: 29
59640 ATCAAAATAG
*
59650 AAATTTAAA-TGACTAAAATAAAATAACA
1 AAATATAAAGTGACTAAAATAAAATAACA
59678 TAAACT-T-AAGTGACTAAAATAAAATAACA
1 -AAA-TATAAAGTGACTAAAATAAAATAACA
* *
59707 GAATATAAAGTGACAAAAATCAGAAATAAACA
1 AAATATAAAGTGACTAAAAT-A-AAAT-AACA
*
59739 AAATAGAAAGTGAC
1 AAATATAAAGTGAC
59753 ATGCTATGAC
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
27 1 0.02
28 5 0.08
29 35 0.56
30 2 0.03
31 4 0.06
32 16 0.25
ACGTcount: A:0.61, C:0.09, G:0.10, T:0.20
Consensus pattern (29 bp):
AAATATAAAGTGACTAAAATAAAATAACA
Found at i:61563 original size:84 final size:83
Alignment explanation
Indices: 61447--61798 Score: 363
Period size: 85 Copynumber: 4.2 Consensus size: 83
61437 TCATCGAGCA
* ** * ** * * *
61447 GAATGAAATCGAACTCGACAACT-TTTATTGACAGATCACTTTTCTCGACTTAAGCTATG-TTTA
1 GAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGAT-ACCCTTCTCGCCTTGAGCTATGCTGTA
61510 AATTTGACT-TGCCCTTTAGCT
64 AATTTGA-TATG-CCTTTAGCT
61531 GAATGTAATCGAACTCGAAGGTCTTTGTTGACA-ATAGCCCTTCTCGCCTTGAGCTATGCTGT-A
1 GAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATA-CCCTTCTCGCCTTGAGCTATGCTGTAA
*
61594 ATTTGATATGCCTTTGACCT
65 ATTTGATATGCCTTT-AGCT
* * * * *
61614 GAATGTTATCGAACTCAAAAGGTCTTTGTTGATAGATAACCCTTCTCGCCGTGAGTTATGCTGTA
1 GAATGTAATCGAACTC-GAAGGTCTTTGTTGACAGAT-ACCCTTCTCGCCTTGAGCTATGCTGTA
* *
61679 AATTTGATACGTCCTTGAGCT
64 AATTTGATATG-CCTTTAGCT
* * * *
61700 GAATGTAATCGAACTCGAAGGACTTTGCTGGCAGATAGCCCTTCTCGCCTTGAGCTATACTGTAA
1 GAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATA-CCCTTCTCGCCTTGAGCTATGCTGTAA
61765 ATTTGATATGCCTTTGAGCT
65 ATTTGATATGCCTTT-AGCT
* *
61785 GAATCTAATTGAAC
1 GAATGTAATCGAAC
61799 AAAAATGTCT
Statistics
Matches: 225, Mismatches: 31, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
82 7 0.03
83 48 0.21
84 48 0.21
85 89 0.40
86 29 0.13
87 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (83 bp):
GAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATACCCTTCTCGCCTTGAGCTATGCTGTAAA
TTTGATATGCCTTTAGCT
Found at i:61726 original size:85 final size:85
Alignment explanation
Indices: 61488--61798 Score: 391
Period size: 85 Copynumber: 3.7 Consensus size: 85
61478 CAGATCACTT
* * *
61488 TTCTCGACTTAAGCTATG-TTTAAATTTGACT-TGCCCTTT-AGCTGAATGTAATCGAACTCGAA
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGA-TATG-CCTTTGAGCTGAATGTAATCGAACTCGAA
61550 GGTCTTTGTTGACA-ATAGCCC
64 GGTCTTTGTTGACAGATAGCCC
* * *
61571 TTCTCGCCTTGAGCTATGCTGT-AATTTGATATGCCTTTGACCTGAATGTTATCGAACTCAAAAG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTC-GAAG
* *
61635 GTCTTTGTTGATAGATAACCC
65 GTCTTTGTTGACAGATAGCCC
* * *
61656 TTCTCGCCGTGAGTTATGCTGTAAATTTGATACGTCC-TTGAGCTGAATGTAATCGAACTCGAAG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATG-CCTTTGAGCTGAATGTAATCGAACTCGAAG
* * *
61720 GACTTTGCTGGCAGATAGCCC
65 GTCTTTGTTGACAGATAGCCC
* * *
61741 TTCTCGCCTTGAGCTATACTGTAAATTTGATATGCCTTTGAGCTGAATCTAATTGAAC
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAAC
61799 AAAAATGTCT
Statistics
Matches: 195, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
82 6 0.03
83 43 0.22
84 19 0.10
85 94 0.48
86 31 0.16
87 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (85 bp):
TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGG
TCTTTGTTGACAGATAGCCC
Done.