Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5040.1
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: 35443
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.28
Warning! 4998 characters in sequence are not A, C, G, or T
Found at i:1477 original size:39 final size:39
Alignment explanation
Indices: 1415--1515 Score: 157
Period size: 39 Copynumber: 2.6 Consensus size: 39
1405 ATCGTGATCT
** * * *
1415 GAAGCCCGAAATCTAGCTAAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAATGCTAAACG
1454 GAAGCCCGAAGGCTAACTGAAGCACATAAATGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAATGCTAAACG
1493 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
1516 TCATCAGAGT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.13
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAATGCTAAACG
Found at i:1497 original size:21 final size:21
Alignment explanation
Indices: 1434--1497 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
1424 AATCTAGCTA
*
1434 AAGCACATAAGTGCTAAACGG
1 AAGCACATAAATGCTAAACGG
** * *
1455 AAGC-C-CGAAGGCT-AACTG
1 AAGCACATAAATGCTAAACGG
1473 AAGCACATAAATGCTAAACGG
1 AAGCACATAAATGCTAAACGG
1494 AAGC
1 AAGC
1498 CCGAAGGCTA
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
18 8 0.26
19 5 0.16
20 6 0.19
21 12 0.39
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.12
Consensus pattern (21 bp):
AAGCACATAAATGCTAAACGG
Found at i:8148 original size:20 final size:21
Alignment explanation
Indices: 8113--8151 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
8103 CTTAATTGAC
*
8113 TAACTGACATTAACTAACTTT
1 TAACTGACAATAACTAACTTT
8134 TAACT-ACAATAACTAACT
1 TAACTGACAATAACTAACT
8152 ACATTGCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.33
Consensus pattern (21 bp):
TAACTGACAATAACTAACTTT
Found at i:9866 original size:28 final size:28
Alignment explanation
Indices: 9826--9883 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
9816 TAAATTAAAT
9826 AATTAATCCTATAAATCAACTCAATTCA
1 AATTAATCCTATAAATCAACTCAATTCA
* * *
9854 AATTAATTCTATAAATTAATTCAATTCA
1 AATTAATCCTATAAATCAACTCAATTCA
9882 AA
1 AA
9884 AAAACACTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (28 bp):
AATTAATCCTATAAATCAACTCAATTCA
Found at i:9893 original size:28 final size:28
Alignment explanation
Indices: 9834--9893 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
9824 ATAATTAATC
** **
9834 CTATAAATCAACTCAATTCAAATTAATT
1 CTATAAATCAACTCAATTCAAAAAAACA
* *
9862 CTATAAATTAATTCAATTCAAAAAAACA
1 CTATAAATCAACTCAATTCAAAAAAACA
9890 CTAT
1 CTAT
9894 GATTTTGGGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (28 bp):
CTATAAATCAACTCAATTCAAAAAAACA
Found at i:11260 original size:21 final size:21
Alignment explanation
Indices: 11234--11275 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11224 CTTTATATTA
* *
11234 ATTTTTGTTTGGGATGGGTTT
1 ATTTTTATTTAGGATGGGTTT
*
11255 ATTTTTATTTAGGTTGGGTTT
1 ATTTTTATTTAGGATGGGTTT
11276 TGATTAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.29, T:0.60
Consensus pattern (21 bp):
ATTTTTATTTAGGATGGGTTT
Found at i:20637 original size:14 final size:13
Alignment explanation
Indices: 20607--20687 Score: 53
Period size: 13 Copynumber: 6.3 Consensus size: 13
20597 TAATATTGAA
* *
20607 AATATATGTATAT
1 AATATATATAAAT
20620 AATATATATAACAT
1 AATATATATAA-AT
20634 AATAT-TA-AAAT
1 AATATATATAAAT
20645 ACATATATAT-AAT
1 A-ATATATATAAAT
* *
20658 -ATATAAAAAAAT
1 AATATATATAAAT
* *
20670 TACATATATAATAT
1 AATATATATAA-AT
20684 AATA
1 AATA
20688 CATAAGTATA
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
11 9 0.17
12 9 0.17
13 23 0.44
14 11 0.21
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (13 bp):
AATATATATAAAT
Found at i:20650 original size:26 final size:26
Alignment explanation
Indices: 20621--20679 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
20611 TATGTATATA
**
20621 ATATATATAACATAATATTAAAA-TAC
1 ATATATATAACAT-ATAAAAAAATTAC
*
20647 ATATATATAATATATAAAAAAATTAC
1 ATATATATAACATATAAAAAAATTAC
20673 ATATATA
1 ATATATA
20680 ATATAATACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 7 0.24
26 22 0.76
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATATATAACATATAAAAAAATTAC
Found at i:20768 original size:9 final size:9
Alignment explanation
Indices: 20738--20770 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
20728 ACACTAAGAC
20738 ATATAATAA
1 ATATAATAA
*
20747 ATACAATAA
1 ATATAATAA
20756 ATATAATAA
1 ATATAATAA
20765 ATATAA
1 ATATAA
20771 ATATTATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (9 bp):
ATATAATAA
Found at i:20770 original size:15 final size:16
Alignment explanation
Indices: 20738--20789 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
20728 ACACTAAGAC
20738 ATATAATAAATACAATAA
1 ATATAATAAAT--AATAA
20756 ATATAATAAAT-ATAA
1 ATATAATAAATAATAA
* *
20771 ATATTATAATTAATAA
1 ATATAATAAATAATAA
20787 ATA
1 ATA
20790 ACAGAAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 13 0.42
16 7 0.23
18 11 0.35
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATAATAAATAATAA
Found at i:20778 original size:18 final size:18
Alignment explanation
Indices: 20738--20787 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
20728 ACACTAAGAC
*
20738 ATATAATAAATACAATAA
1 ATATAATAAATAAAATAA
20756 ATATAATAAATATAAAT-A
1 ATATAATAAATA-AAATAA
* *
20774 TTATAATTAATAAA
1 ATATAATAAATAAA
20788 TAACAGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 2 0.07
18 23 0.82
19 3 0.11
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATAATAAATAAAATAA
Found at i:22655 original size:90 final size:86
Alignment explanation
Indices: 22540--23516 Score: 823
Period size: 87 Copynumber: 11.0 Consensus size: 86
22530 AACATATACT
* * *
22540 AAAAACAGAAATTGAAAATAGCTCAGCGCATGTGCCAAGGCTCAACTTACTTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCG--TGT-CCAAGGCTCAACTCACCTCTCGCAATATGAG
* *
22605 TTGA-TTCTTGACCAACAGAAATTTG
63 TTGATTTTTTGA-AAACAGAAA-TTG
* * * *
22630 AAAAGCAGAAACTGAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC--GTG-TCCAAGGCTCAACTCACCTCTCGCAATATGAG
* * *
22695 TTGATTTTTTTGAAAA-ATACAAATA
63 TTGA-TTTTTTGAAAACAGA-AATTG
* *
22720 AAAAACA-AAATTTGAAAATATCTCAGCGTGAACCAAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAAACAGAAA-TTGAAAATACCTCAGCGTG-TCCAAGGCTCAACTCACCTCTCGCAATATGAGT
* *
22784 TGATTTTTTGAAAAATATAAATTG
64 TGATTTTTTG-AAAACAGAAATTG
**
22808 AAAGAACAGAAATTGAAAAATACCTCAGCACGTCCTAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAA-AACAGAAATTG-AAAATACCTCAGCGTGTCC-AAGGCTCAACTCACCTCTCGCAATATGAG
*
22873 TTGA--TTTTGAAAAGCAGAAATTA
63 TTGATTTTTTGAAAA-CAGAAATTG
* ** * *
22896 AAAAATAGATTTTGAAAATACCTCAGCGTGTCCTAGGGCTCAACTCACCTCTAGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTCC-AAGGCTCAACTCACCTCTCGCAATATGAGTT
22961 GATTTTTTTGAAAAGCAGAAATTG
65 GA-TTTTTTGAAAA-CAGAAATTG
* * ** *
22985 AAAACCAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAATT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTC-CAAGGCTCAACTCACCTCTCGCAATATGAGTT
* *
23050 GA-TTTTGGAAAAATAGAAATTG
65 GATTTTTTG-AAAACAGAAATTG
* ** * *** * * *
23072 -AAAACAGAATTTGAACAATAGAATTTGAAAATACCTCGGCATATGACTCGAGGCTCAACTCACT
1 AAAAACAGAAATTGAA-AAT---ACCTCAGCGT--GTC--CA-A-G---G----CTCAACTCACC
*
23136 TCTCGCAATATGAGTTGA-TTTTTGAAAA-ATACATATT-
49 TCTCGCAATATGAGTTGATTTTTTGAAAACAGA-A-ATTG
* * *
23173 AAAAACAGAATTTGAAAAAACCTCAGC-TGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTCC-AAGGCTCAACTCACCTCTCGCAATATGAGTT
23237 GA-TTTTTGAAAACATG-AATT-
65 GATTTTTTGAAAACA-GAAATTG
*
23257 AAAAACAGAAATTGAAAATACCTCGGCATGCGAG-CCAAGGCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGAAATTGAAAATACCT---CA-GCGTGTCCAAGGCTCAACTCACCTCTCGCAATATGA
23321 GTTGA-TTTTTGAAAACATG-AATT-
62 GTTGATTTTTTGAAAACA-GAAATTG
*
23344 AAAAACAGAAATTGAAAATACCTCGGCATGCGAG-CCAAGGCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGAAATTGAAAATACCT---CA-GCGTGTCCAAGGCTCAACTCACCTCTCGCAATATGA
23408 GTTGA-TTTTTGAAAACATG-AATT-
62 GTTGATTTTTTGAAAACA-GAAATTG
*
23431 AAAAACAGAAATTGAAAATACCTCGGCATGCGAG-CCAAGGCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGAAATTGAAAATACCT---CA-GCGTGTCCAAGGCTCAACTCACCTCTCGCAATATGA
* *
23495 GTTGA-TTTCTGAAAGCAGAAAT
62 GTTGATTTTTTGAAAACAGAAAT
23517 AAAACATCAA
Statistics
Matches: 759, Mismatches: 81, Indels: 97
0.81 0.09 0.10
Matches are distributed among these distances:
84 24 0.03
85 39 0.05
86 64 0.08
87 255 0.34
88 70 0.09
89 90 0.12
90 134 0.18
91 4 0.01
92 10 0.01
93 2 0.00
94 1 0.00
95 3 0.00
97 1 0.00
98 3 0.00
100 2 0.00
101 7 0.01
102 50 0.07
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (86 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTTGAAAACAGAAATTG
Found at i:22810 original size:14 final size:14
Alignment explanation
Indices: 22791--22829 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
22781 AGTTGATTTT
*
22791 TTGAAAAATATAAA
1 TTGAAAAATAGAAA
*
22805 TTGAAAGAACAGAAA
1 TTGAAA-AATAGAAA
22820 TTGAAAAATA
1 TTGAAAAATA
22830 CCTCAGCACG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.62, C:0.03, G:0.13, T:0.23
Consensus pattern (14 bp):
TTGAAAAATAGAAA
Found at i:22987 original size:14 final size:14
Alignment explanation
Indices: 22968--23001 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
22958 GTTGATTTTT
*
22968 TTGAAAAGCAGAAA
1 TTGAAAACCAGAAA
22982 TTGAAAACCAGAAA
1 TTGAAAACCAGAAA
22996 TTGAAA
1 TTGAAA
23002 TTACCTCAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.56, C:0.09, G:0.18, T:0.18
Consensus pattern (14 bp):
TTGAAAACCAGAAA
Found at i:23094 original size:14 final size:13
Alignment explanation
Indices: 23059--23104 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
23049 TGATTTTGGA
*
23059 AAAATAGAAATTG
1 AAAATAGAATTTG
*
23072 AAAACAGAATTTG
1 AAAATAGAATTTG
23085 AACAATAGAATTTG
1 AA-AATAGAATTTG
23099 AAAATA
1 AAAATA
23105 CCTCGGCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.59, C:0.04, G:0.13, T:0.24
Consensus pattern (13 bp):
AAAATAGAATTTG
Found at i:23439 original size:174 final size:174
Alignment explanation
Indices: 22539--23508 Score: 932
Period size: 174 Copynumber: 5.5 Consensus size: 174
22529 TAACATATAC
* * * *
22539 TAAAAACAGAAATTGAAAATAGCTCAGCGCAT--GTGCCAAGGCTCAACTTACTTCTCGCAATAT
1 TAAAAACAGAAATTGAAAATACCTC-G-GCATGCGAGCCAAGGCTCAACTCACCTCTCGCAATAT
* * * * *
22602 GAGTTGATTCTTGACCAACA-GAAATTTGAAAAGCAGAAACTGAAAATACCTCAGCATGTGAGCC
64 GAGTTGATTTTTGA-AAACATG-AA-TTGAAAAACAGAAATTGAAAATACCTCAGCATGCG-GCC
* *
22666 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAA-ATACAAAT
125 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAACAT--GAAT
* * * * *
22719 AAAAAACA-AAATTTGAAAATATCTCAGC--GTGAACCAAGGCTCAACTCACCTCTCGCAATATG
1 TAAAAACAGAAA-TTGAAAATACCTCGGCATGCGAGCCAAGGCTCAACTCACCTCTCGCAATATG
* * *
22781 AGTTGATTTTTTGAAAAATATAAATTGAAAGAACAGAAATTGAAAAATACCTCAGCA--CGTCCT
65 AGTTGA-TTTTTG-AAAACATGAATTGAAA-AACAGAAATTG-AAAATACCTCAGCATGCGGCC-
22844 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAAGCA-GAAAT
125 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-CATG-AAT
* ** * * *
22894 TAAAAAATAGATTTTGAAAATACCT---CA-GCGTGTCCTAGGGCTCAACTCACCTCTAGCAATA
1 T-AAAAACAGAAATTGAAAATACCTCGGCATGCGAG-CC-AAGGCTCAACTCACCTCTCGCAATA
* * * *
22955 TGAGTTGATTTTTTTGAAAAGCA-GAAATTGAAAACCAGAAATTGAAATTACCTCAGCGTGTCTT
63 TGAGTTGA--TTTTTGAAAA-CATG-AATTGAAAAACAGAAATTGAAAATACCTCAGCATG-C-G
* *
23019 G---AGGCTCAACTCACCTCTCGCAATATGAATTGATTTTGGAAAA-ATAGAAAT
122 GCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAT-G-AAT
* ** *
23070 TGAAAACAGAATTTGAACAATAGAATTTGAAAATACCTCGGCATATGA-CTCGAGGCTCAACTCA
1 T------A-AA----AAC---AGAAATTGAAAATACCTCGGCATGCGAGC-CAAGGCTCAACTCA
* * * *
23134 CTTCTCGCAATATGAGTTGATTTTTGAAAA-AT-ACATATTAAAAACAGAATTTGAAAAAACCTC
51 CCTCTCGCAATATGAGTTGATTTTTGAAAACATGA-AT-TGAAAAACAGAAATTGAAAATACCTC
**
23197 AGC-TGTC--CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAAT
114 AGCATG-CGGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAAT
23256 TAAAAACAGAAATTGAAAATACCTCGGCATGCGAGCCAAGGCTCAACTCACCTCTCGCAATATGA
1 TAAAAACAGAAATTGAAAATACCTCGGCATGCGAGCCAAGGCTCAACTCACCTCTCGCAATATGA
*
23321 GTTGATTTTTGAAAACATGAATT-AAAAACAGAAATTGAAAATACCTCGGCATGCGAGCCAAGGC
66 GTTGATTTTTGAAAACATGAATTGAAAAACAGAAATTGAAAATACCTCAGCATGCG-GCCAAGGC
23385 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAAT
130 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAAT
23430 TAAAAACAGAAATTGAAAATACCTCGGCATGCGAGCCAAGGCTCAACTCACCTCTCGCAATATGA
1 TAAAAACAGAAATTGAAAATACCTCGGCATGCGAGCCAAGGCTCAACTCACCTCTCGCAATATGA
*
23495 GTTGATTTCTGAAA
66 GTTGATTTTTGAAA
23509 GCAGAAATAA
Statistics
Matches: 667, Mismatches: 64, Indels: 124
0.78 0.07 0.15
Matches are distributed among these distances:
171 25 0.04
172 69 0.10
173 6 0.01
174 132 0.20
175 60 0.09
176 76 0.11
177 20 0.03
178 76 0.11
179 24 0.04
180 35 0.05
181 1 0.00
182 2 0.00
186 7 0.01
187 48 0.07
188 26 0.04
189 26 0.04
191 30 0.04
192 3 0.00
193 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.26
Consensus pattern (174 bp):
TAAAAACAGAAATTGAAAATACCTCGGCATGCGAGCCAAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTGAAAACATGAATTGAAAAACAGAAATTGAAAATACCTCAGCATGCGGCCAAGGCT
CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAAT
Found at i:24402 original size:25 final size:25
Alignment explanation
Indices: 24330--24402 Score: 59
Period size: 25 Copynumber: 3.1 Consensus size: 25
24320 TGTTAATCAA
* *
24330 GATGCCCTTTTCGGGTTTTCACCCT
1 GATGCCCTTTTCGGGTTTTCATCTT
* *
24355 GAT-CCCTTTT----TTTT-GTTTGT
1 GATGCCCTTTTCGGGTTTTCATCT-T
24375 GATGCCCTTTTCGGGTTTTCATCTT
1 GATGCCCTTTTCGGGTTTTCATCTT
24400 GAT
1 GAT
24403 TTTCTTTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
20 8 0.23
21 7 0.20
24 7 0.20
25 11 0.31
26 2 0.06
ACGTcount: A:0.08, C:0.23, G:0.19, T:0.49
Consensus pattern (25 bp):
GATGCCCTTTTCGGGTTTTCATCTT
Found at i:28316 original size:23 final size:23
Alignment explanation
Indices: 28286--28335 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
28276 ACCCCTTTTA
28286 ATTAACAACAGCGTGTTTCGTAG
1 ATTAACAACAGCGTGTTTCGTAG
*
28309 ATTAACAACAGCTTGTTTCGTAG
1 ATTAACAACAGCGTGTTTCGTAG
28332 ATTA
1 ATTA
28336 TCTTGTCCGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (23 bp):
ATTAACAACAGCGTGTTTCGTAG
Found at i:32270 original size:58 final size:58
Alignment explanation
Indices: 32206--32322 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
32196 TCGTAAGCAC
*
32206 CAATGTCTCTATCATACTGACTATTCTTTTCTTCCAGAGCCTCCAAGAGAGTATCTAG
1 CAATGTCTCTATCATACTGACTATTCTTTTCTTCCAGAGCCTCCAAGAGAGTAACTAG
32264 CAATGTCTCTATCATACTGACTATTCTTTTCTTCCAGAGCCTCCAAGAGAGTAACTAG
1 CAATGTCTCTATCATACTGACTATTCTTTTCTTCCAGAGCCTCCAAGAGAGTAACTAG
32322 C
1 C
32323 TGTTGTTGAC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (58 bp):
CAATGTCTCTATCATACTGACTATTCTTTTCTTCCAGAGCCTCCAAGAGAGTAACTAG
Found at i:35218 original size:111 final size:111
Alignment explanation
Indices: 35047--35268 Score: 399
Period size: 111 Copynumber: 2.0 Consensus size: 111
35037 CGATCCTTTT
35047 TCCTAGGTGTGATCGGACACCTATTAGATTTCCTTTTTTAAAACAAACAGAAGGCCAAGTTTAGG
1 TCCTAGGTGTGATCGGACACCTATTAGATTTCCTTTTTTAAAACAAACAGAAGGCCAAGTTTAGG
*
35112 TCTACGTGAAAGTCCAGAGAAAAATTAGGGTTCGGGAGTCGGTTAC
66 TCTACGTGAAAGTCCAAAGAAAAATTAGGGTTCGGGAGTCGGTTAC
** **
35158 TCCTAGGTGTGATCGGACACCTATTAGATTTCCTTTTTTAAAACAATTAGAAGGTGAAGTTTAGG
1 TCCTAGGTGTGATCGGACACCTATTAGATTTCCTTTTTTAAAACAAACAGAAGGCCAAGTTTAGG
35223 TCTACGTGAAAGTCCAAAGAAAAATTAGGGTTCGGGAGTCGGTTAC
66 TCTACGTGAAAGTCCAAAGAAAAATTAGGGTTCGGGAGTCGGTTAC
35269 GCCCGAGGAA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (111 bp):
TCCTAGGTGTGATCGGACACCTATTAGATTTCCTTTTTTAAAACAAACAGAAGGCCAAGTTTAGG
TCTACGTGAAAGTCCAAAGAAAAATTAGGGTTCGGGAGTCGGTTAC
Done.