Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011500.1 Kokia drynarioides strain JFW-HI SEQ_126485, 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: 32122
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:1257 original size:29 final size:29
Alignment explanation
Indices: 1201--1257 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
1191 TGTAAATAAA
* * * * *
1201 AAGGGAAATATAAAAAAGATTTTTAAAAG
1 AAGGAAAATACAAAAAAAATCTTCAAAAG
1230 AAGGAAAATACAAAAAAAATCTTCAAAA
1 AAGGAAAATACAAAAAAAATCTTCAAAA
1258 CATTTTTCCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.19
Consensus pattern (29 bp):
AAGGAAAATACAAAAAAAATCTTCAAAAG
Found at i:2047 original size:30 final size:30
Alignment explanation
Indices: 2013--2199 Score: 107
Period size: 30 Copynumber: 6.3 Consensus size: 30
2003 TAAAACTTCG
2013 ATTTTAACCCTCAAACTTTCAAAAAATTAT
1 ATTTTAACCCTCAAACTTTCAAAAAATTAT
* * ** *
2043 ATTTTGACCTTTGAACTTTCCAAAAATTAT
1 ATTTTAACCCTCAAACTTTCAAAAAATTAT
** *
2073 ATTTTAACCC-CTAAACTTTCCAAAACCTCA-
1 ATTTTAACCCTC-AAACTTT-CAAAAAATTAT
* * * * *
2103 ATTTTGACCCTTAAAC-TTCTTAAAAATCAC
1 ATTTTAACCCTCAAACTTTC-AAAAAATTAT
* *** *
2133 ATTTTGACCCTCAAA-TTTTTGAAAATTAC
1 ATTTTAACCCTCAAACTTTCAAAAAATTAT
* *
2162 ATTTTAACCC-CTAAACTTTC-CAAATTTAT
1 ATTTTAACCCTC-AAACTTTCAAAAAATTAT
*
2191 GTTTTAACC
1 ATTTTAACC
2200 TTTTTTTTTT
Statistics
Matches: 121, Mismatches: 28, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
28 2 0.02
29 42 0.35
30 71 0.59
31 6 0.05
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (30 bp):
ATTTTAACCCTCAAACTTTCAAAAAATTAT
Found at i:2098 original size:90 final size:89
Alignment explanation
Indices: 1992--2185 Score: 219
Period size: 90 Copynumber: 2.2 Consensus size: 89
1982 TGTTTAAACA
* * * * * * * *
1992 CCTAAACTCTCTAAAACTTCGATTTTAACCCTCAAACTT-TCAAAAAATTATATTTTGACCTTTG
1 CCTAAACTTTCCAAAACCTCAATTTTAACCCTCAAACTTCT-AAAAAATCACATTTTGACC-CTC
* *
2056 AACTTTCCAAAAATTATATTTTAACC
64 AAATTTCCAAAAATTACATTTTAACC
* * *
2082 CCTAAACTTTCCAAAACCTCAATTTTGACCCTTAAACTTCTTAAAAATCACATTTTGACCCTCAA
1 CCTAAACTTTCCAAAACCTCAATTTTAACCCTCAAACTTCTAAAAAATCACATTTTGACCCTCAA
***
2147 ATTTTTGAAAATTACATTTTAACC
66 ATTTCCAAAAATTACATTTTAACC
2171 CCTAAACTTTCCAAA
1 CCTAAACTTTCCAAA
2186 TTTATGTTTT
Statistics
Matches: 87, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
89 37 0.43
90 49 0.56
91 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (89 bp):
CCTAAACTTTCCAAAACCTCAATTTTAACCCTCAAACTTCTAAAAAATCACATTTTGACCCTCAA
ATTTCCAAAAATTACATTTTAACC
Found at i:2128 original size:60 final size:60
Alignment explanation
Indices: 2013--2199 Score: 150
Period size: 60 Copynumber: 3.1 Consensus size: 60
2003 TAAAACTTCG
* * *
2013 ATTTTAACCCTCAAACTTTCAAAAAATTATATTTTGACCTTTGAACTTTCCAAAAATTAT
1 ATTTTAACCCTCAAACTTTCAAAAAATCATATTTTGACCCTTAAACTTTCCAAAAATTAT
** * * *
2073 ATTTTAACCC-CTAAACTTTCCAAAACCTCA-ATTTTGACCCTTAAAC-TTCTTAAAAATCAC
1 ATTTTAACCCTC-AAACTTT-CAAAAAATCATATTTTGACCCTTAAACTTTC-CAAAAATTAT
* *** * * * * *
2133 ATTTTGACCCTCAAA-TTTTTGAAAATTACATTTTAACCCCTAAACTTTCC-AAATTTAT
1 ATTTTAACCCTCAAACTTTCAAAAAATCATATTTTGACCCTTAAACTTTCCAAAAATTAT
*
2191 GTTTTAACC
1 ATTTTAACC
2200 TTTTTTTTTT
Statistics
Matches: 98, Mismatches: 23, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
58 16 0.16
59 21 0.21
60 53 0.54
61 8 0.08
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (60 bp):
ATTTTAACCCTCAAACTTTCAAAAAATCATATTTTGACCCTTAAACTTTCCAAAAATTAT
Found at i:2165 original size:29 final size:30
Alignment explanation
Indices: 2103--2179 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
2093 CAAAACCTCA
*
2103 ATTTTGACCCTTAAACTTCTTAAAAATCAC
1 ATTTTGACCCTCAAACTTCTTAAAAATCAC
* * *
2133 ATTTTGACCCTCAAA-TTTTTGAAAATTAC
1 ATTTTGACCCTCAAACTTCTTAAAAATCAC
*
2162 ATTTTAACCC-CTAAACTT
1 ATTTTGACCCTC-AAACTT
2180 TCCAAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 1 0.03
29 23 0.57
30 16 0.40
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (30 bp):
ATTTTGACCCTCAAACTTCTTAAAAATCAC
Found at i:5497 original size:2 final size:2
Alignment explanation
Indices: 5490--5517 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5480 CATGATTATC
5490 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
5518 TGCCTCAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6208 original size:7 final size:7
Alignment explanation
Indices: 6186--6296 Score: 73
Period size: 7 Copynumber: 16.0 Consensus size: 7
6176 GGAAAATATG
6186 AACGGTC
1 AACGGTC
*
6193 AA-AGTC
1 AACGGTC
6199 AACGGTC
1 AACGGTC
*
6206 AACGGTT
1 AACGGTC
*
6213 AACAGTC
1 AACGGTC
6220 AACGGTC
1 AACGGTC
6227 AACAGGT-
1 AAC-GGTC
** *
6234 AACAATT
1 AACGGTC
*
6241 AACAGTC
1 AACGGTC
*
6248 AATGGTC
1 AACGGTC
**
6255 AACAATC
1 AACGGTC
*
6262 AACAGTC
1 AACGGTC
6269 AACGGTC
1 AACGGTC
*
6276 AACAGTC
1 AACGGTC
**
6283 AACGACC
1 AACGGTC
6290 AACGGTC
1 AACGGTC
6297 GTTCAACGAT
Statistics
Matches: 78, Mismatches: 23, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
6 6 0.08
7 69 0.88
8 3 0.04
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (7 bp):
AACGGTC
Found at i:6221 original size:21 final size:21
Alignment explanation
Indices: 6186--6296 Score: 118
Period size: 21 Copynumber: 5.3 Consensus size: 21
6176 GGAAAATATG
6186 AACGGTCAA-AGTCAACGGTC
1 AACGGTCAACAGTCAACGGTC
*
6206 AACGGTTAACAGTCAACGGTC
1 AACGGTCAACAGTCAACGGTC
* * *
6227 AACAGGT-AACAATTAACAGTC
1 AAC-GGTCAACAGTCAACGGTC
* * *
6248 AATGGTCAACAATCAACAGTC
1 AACGGTCAACAGTCAACGGTC
**
6269 AACGGTCAACAGTCAACGACC
1 AACGGTCAACAGTCAACGGTC
6290 AACGGTC
1 AACGGTC
6297 GTTCAACGAT
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
20 11 0.14
21 63 0.82
22 3 0.04
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (21 bp):
AACGGTCAACAGTCAACGGTC
Found at i:6421 original size:22 final size:22
Alignment explanation
Indices: 6371--6423 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
6361 CTTGGTTCAA
*
6371 TTGGGTTATTGGGTCAAATGGGT
1 TTGGGTTATTGGGTCAAAT-GAT
*
6394 TT-GGTTATTGGGTTTAAAT-AT
1 TTGGGTTATTGGG-TCAAATGAT
6415 TTGGGTTAT
1 TTGGGTTAT
6424 GTTAGCTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 3 0.12
22 16 0.62
23 7 0.27
ACGTcount: A:0.19, C:0.02, G:0.32, T:0.47
Consensus pattern (22 bp):
TTGGGTTATTGGGTCAAATGAT
Found at i:17725 original size:112 final size:111
Alignment explanation
Indices: 17507--17822 Score: 421
Period size: 112 Copynumber: 2.9 Consensus size: 111
17497 CATTTTTAAT
*
17507 TTCATACGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA------CAAGCATTTT
1 TTCATACGAGTTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAACCTGTTCAAGCATTTT
* * *
17566 TGCATCGAAATAACGGTTACTGGACCAATGATTCGTAATCTTTTCA
66 TACATTGAAATAACGGTTAGTGGACCAATGATTCGTAATCTTTTCA
* *
17612 TTCATACGAGTTTTGTCTCCAATAAAATTCAATTTTATCCACCTTACAACCTTGTTCAAGCCTTT
1 TTCATACGAGTTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAACC-TGTTCAAGCATTT
* *
17677 TTACATTGAAATAACGGTTAGTGGACCAATGACTT-TTATTCTTTTCA
65 TTACATTGAAATAACGGTTAGTGGACCAATGA-TTCGTAATCTTTTCA
** *
17724 TTCACGCGAGTTTTGCCTCCAATAAAATTCAATTTTATCCATCTTACAACCCTGTTCAAGCATTT
1 TTCATACGAGTTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA-CCTGTTCAAGCATTT
* * *
17789 TTAGCATTGAAATGACGGTTAGTGGTCTAATGAT
65 TTA-CATTGAAATAACGGTTAGTGGACCAATGAT
17823 ATAAGAAATA
Statistics
Matches: 185, Mismatches: 16, Indels: 13
0.86 0.07 0.06
Matches are distributed among these distances:
105 47 0.25
112 108 0.58
113 30 0.16
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (111 bp):
TTCATACGAGTTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAACCTGTTCAAGCATTTT
TACATTGAAATAACGGTTAGTGGACCAATGATTCGTAATCTTTTCA
Found at i:18588 original size:49 final size:50
Alignment explanation
Indices: 18350--18594 Score: 221
Period size: 49 Copynumber: 5.0 Consensus size: 50
18340 GGCGGATCTA
* *
18350 GTACCATAG-AGATATAAAGGGAAAGGTTGAGG-TCGCAATGGCGAACCCG
1 GTACCATAGAAGATATGAAGGGAAAGGTTGAGGCT-GCAACGGCGAACCCG
* * * ** * **
18399 GTACCTTAGAAGATATGATGGGAAAGATTGAGGCTATAACGACGAATTCG
1 GTACCATAGAAGATATGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCCG
* * * *
18449 ATACCAT-GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCG
1 GTACCATAGAAGATATGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCCG
* * * * ***
18498 GTACCTTAGAAGACATGATGGG-AAGGATTGAGGCTACAACGGCGAATATG
1 GTACCATAGAAGATATGAAGGGAAAGG-TTGAGGCTGCAACGGCGAACCCG
* * *
18548 GTATCAT-GAAGATATGAAGGGAAAGGTTGAGGTTGTAACGGCGAACC
1 GTACCATAGAAGATATGAAGGGAAAGGTTGAGGCTGCAACGGCGAACC
18595 TTGTACCTTA
Statistics
Matches: 151, Mismatches: 40, Indels: 10
0.75 0.20 0.05
Matches are distributed among these distances:
49 79 0.52
50 71 0.47
51 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.32, T:0.19
Consensus pattern (50 bp):
GTACCATAGAAGATATGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCCG
Found at i:18619 original size:49 final size:50
Alignment explanation
Indices: 18336--18914 Score: 211
Period size: 49 Copynumber: 11.8 Consensus size: 50
18326 ATCGAGATTA
* * * * * *
18336 CAACGGCGGATCTAGTACCATAG-AGATATAAAGGGAAAGGTTGAGG-TCG
1 CAACGGCGAACCTGGTACCTTAGAAGATATGATGGGAAAGGTTGAGGCT-G
* * * *
18385 CAATGGCGAACCCGGTACCTTAGAAGATATGATGGGAAAGATTGAGGCTA
1 CAACGGCGAACCTGGTACCTTAGAAGATATGATGGGAAAGGTTGAGGCTG
* * * * * * * *
18435 TAACGACGAA-TTCGATACCAT-GAAGATGTGAAGGGAAAGGTTGAGGCCG
1 CAACGGCGAACCT-GGTACCTTAGAAGATATGATGGGAAAGGTTGAGGCTG
* * * *
18484 CAACGACGAACCCGGTACCTTAGAAGACATGATGGG-AAGGATTGAGGCTA
1 CAACGGCGAACCTGGTACCTTAGAAGATATGATGGGAAAGG-TTGAGGCTG
** * * * *
18534 CAACGGCGAATATGGTATCAT-GAAGATATGAAGGGAAAGGTTGAGGTTG
1 CAACGGCGAACCTGGTACCTTAGAAGATATGATGGGAAAGGTTGAGGCTG
* * * * * *
18583 TAACGGCGAACCTTGTACCTTAG-AGACT-TGATGGGAACGATTGAAGCCG
1 CAACGGCGAACCTGGTACCTTAGAAGA-TATGATGGGAAAGGTTGAGGCTG
* *** * ** * * * * * **
18632 TAATTACGAATCTTATACCAT-GGAGATGTGAAGGGAAAGGTTGAAGCCA
1 CAACGGCGAACCTGGTACCTTAGAAGATATGATGGGAAAGGTTGAGGCTG
* * * ** ** * *
18681 CAACGACGAACCTTGTATCTTAGAA-ACGTGATGGGAAAGAATGAAGCCG
1 CAACGGCGAACCTGGTACCTTAGAAGATATGATGGGAAAGGTTGAGGCTG
* * * ** * * *
18730 TAACGGTGAATCTTATACCAT-GAAGATATGGA-GGGAAAGGTTGAAGCCG
1 CAACGGCGAACCTGGTACCTTAGAAGATAT-GATGGGAAAGGTTGAGGCTG
* * * * ** * *
18779 TAATGGCGAACCTTGTACCTTAG-AGATGTGATGGGAAATATTGAAGCCG
1 CAACGGCGAACCTGGTACCTTAGAAGATATGATGGGAAAGGTTGAGGCTG
* * * * * * * *
18828 CAACGACGAATCTTGTACCGT-GGAGATATAGA-GGGAAATGTTGAAGCCG
1 CAACGGCGAACCTGGTACCTTAGAAGATAT-GATGGGAAAGGTTGAGGCTG
** ** *
18877 CAACGATGAACCTTATACCTTA-AAGATGTGAT-GGAAAG
1 CAACGGCGAACCTGGTACCTTAGAAGATATGATGGGAAAG
18915 ATTAAAGCCG
Statistics
Matches: 400, Mismatches: 110, Indels: 41
0.73 0.20 0.07
Matches are distributed among these distances:
48 15 0.04
49 305 0.76
50 79 0.20
51 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (50 bp):
CAACGGCGAACCTGGTACCTTAGAAGATATGATGGGAAAGGTTGAGGCTG
Found at i:18673 original size:98 final size:98
Alignment explanation
Indices: 18351--18943 Score: 525
Period size: 98 Copynumber: 6.0 Consensus size: 98
18341 GCGGATCTAG
* * * **
18351 TACCAT-AGAGATATAAAGGGAAAGGTTGAGGTCGCAATGGCGAACCCGGTACCTTAGAAGA-TA
1 TACCATGA-AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTTGTACCTTAG-AGACT-
* ** *
18414 TGATGGGAAAGATTGAGGCTATAACGACGAAT-TCGA
63 TGATGGGAAAGATTGAAGCCGTAACGACGAATCT-TA
* * ** *
18450 TACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCTTAGAAGACATG
1 TACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTTGTACCTTAG-AGACTTG
* * *** * * **
18515 ATGGGAAGGATTGAGGCTACAACGGCGAATATGG
65 ATGGGAAAGATTGAAGCCGTAACGACGAATCTTA
* ** *
18549 TATCATGAAGATATGAAGGGAAAGGTTGAGGTTGTAACGGCGAACCTTGTACCTTAGAGACTTGA
1 TACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTTGTACCTTAGAGACTTGA
* **
18614 TGGGAACGATTGAAGCCGTAATTACGAATCTTA
66 TGGGAAAGATTGAAGCCGTAACGACGAATCTTA
* * * * * * * *
18647 TACCATGGAGATGTGAAGGGAAAGGTTGAAGCCACAACGACGAACCTTGTATCTTAGAAACGTGA
1 TACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTTGTACCTTAGAGACTTGA
* **
18712 TGGGAAAGAATGAAGCCGTAACGGTGAATCTTA
66 TGGGAAAGATTGAAGCCGTAACGACGAATCTTA
* * * *
18745 TACCATGAAGATATGGAGGGAAAGGTTGAAGCCGTAATGGCGAACCTTGTACCTTAGAGA-TGTG
1 TACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTTGTACCTTAGAGACT-TG
* * *
18809 ATGGGAAATATTGAAGCCGCAACGACGAATCTTG
65 ATGGGAAAGATTGAAGCCGTAACGACGAATCTTA
* * * * ** * *
18843 TACCGTGGAGATAT-AGAGGGAAATGTTGAAGCCGCAACGATGAACCTTATACCTTAAAGA-TGT
1 TACCATGAAGATATGA-AGGGAAAGGTTGAGGCCGCAACGGCGAACCTTGTACCTTAGAGACT-T
* * **
18906 GAT-GGAAAGATTAAAGCCGCAACGGTGAATCTTA
64 GATGGGAAAGATTGAAGCCGTAACGACGAATCTTA
18940 TACC
1 TACC
18944 CTAAGGATAA
Statistics
Matches: 410, Mismatches: 79, Indels: 12
0.82 0.16 0.02
Matches are distributed among these distances:
97 30 0.07
98 245 0.60
99 133 0.32
100 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.21
Consensus pattern (98 bp):
TACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTTGTACCTTAGAGACTTGA
TGGGAAAGATTGAAGCCGTAACGACGAATCTTA
Found at i:18813 original size:196 final size:196
Alignment explanation
Indices: 18351--18943 Score: 685
Period size: 196 Copynumber: 3.0 Consensus size: 196
18341 GCGGATCTAG
* * **
18351 TACCAT-AGAGATATAAAGGGAAAGGTTGAGGTCGCAATGGCGAACCCGGTACCTTAGAAGATAT
1 TACCATGA-AGATATGAAGGGAAAGGTTGAGGTCGTAATGGCGAACCTTGTACCTTAG-AGAT-T
* ** * *
18415 GATGGGAAAGATTGAGGCTATAACGACGAAT-TCGATACCATGAAGATGTGAAGGGAAAGGTTGA
63 GATGGGAAAGATTGAAGCCGTAACGACGAATCT-TATACCATGGAGATGTGAAGGGAAAGGTTGA
* ** * * * ** *
18479 GGCCGCAACGACGAACCCGGTACCTTAGAAGACATGATGGGAAGGATTGAGGCTACAACGGCGAA
127 AGCCGCAACGACGAACCTTGTACCTTAGAAGACGTGATGGGAAAGATTGAAGCCGCAACGGTGAA
* **
18544 TATGG
192 TCTTA
* * *
18549 TATCATGAAGATATGAAGGGAAAGGTTGAGGTTGTAACGGCGAACCTTGTACCTTAGAGACTTGA
1 TACCATGAAGATATGAAGGGAAAGGTTGAGGTCGTAATGGCGAACCTTGTACCTTAGAGA-TTGA
* **
18614 TGGGAACGATTGAAGCCGTAATTACGAATCTTATACCATGGAGATGTGAAGGGAAAGGTTGAAGC
65 TGGGAAAGATTGAAGCCGTAACGACGAATCTTATACCATGGAGATGTGAAGGGAAAGGTTGAAGC
* * * *
18679 CACAACGACGAACCTTGTATCTTAGAA-ACGTGATGGGAAAGAATGAAGCCGTAACGGTGAATCT
130 CGCAACGACGAACCTTGTACCTTAGAAGACGTGATGGGAAAGATTGAAGCCGCAACGGTGAATCT
18743 TA
195 TA
* * *
18745 TACCATGAAGATATGGAGGGAAAGGTTGAAGCCGTAATGGCGAACCTTGTACCTTAGAGATGTGA
1 TACCATGAAGATATGAAGGGAAAGGTTGAGGTCGTAATGGCGAACCTTGTACCTTAGAGAT-TGA
* * * * * *
18810 TGGGAAATATTGAAGCCGCAACGACGAATCTTGTACCGTGGAGATAT-AGAGGGAAATGTTGAAG
65 TGGGAAAGATTGAAGCCGTAACGACGAATCTTATACCATGGAGATGTGA-AGGGAAAGGTTGAAG
* * * *
18874 CCGCAACGATGAACCTTATACCTTA-AAGATGTGAT-GGAAAGATTAAAGCCGCAACGGTGAATC
129 CCGCAACGACGAACCTTGTACCTTAGAAGACGTGATGGGAAAGATTGAAGCCGCAACGGTGAATC
18937 TTA
194 TTA
18940 TACC
1 TACC
18944 CTAAGGATAA
Statistics
Matches: 335, Mismatches: 54, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
195 36 0.11
196 165 0.49
197 83 0.25
198 50 0.15
199 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.21
Consensus pattern (196 bp):
TACCATGAAGATATGAAGGGAAAGGTTGAGGTCGTAATGGCGAACCTTGTACCTTAGAGATTGAT
GGGAAAGATTGAAGCCGTAACGACGAATCTTATACCATGGAGATGTGAAGGGAAAGGTTGAAGCC
GCAACGACGAACCTTGTACCTTAGAAGACGTGATGGGAAAGATTGAAGCCGCAACGGTGAATCTT
A
Found at i:18864 original size:147 final size:147
Alignment explanation
Indices: 18623--18895 Score: 325
Period size: 147 Copynumber: 1.9 Consensus size: 147
18613 ATGGGAACGA
* * * *
18623 TTGAAGCCGTAATTACGAATCTTATACCATGGAGATGTGAAGGGAAAGGTTGAAGCCACAACGAC
1 TTGAAGCCGTAATGACGAACCTTATACCATAGAGATGTGAAGGGAAAGATTGAAGCCACAACGAC
* * * * * *
18688 GAACCTTGTATCTTAGAAACGTGATGGGAAA-GAATGAAGCCGTAACGGTGAATCTTATACCATG
66 GAACCTTGTACCGTAGAAACATGATGGGAAATG-ATGAAGCCGCAACGATGAACCTTATACCATG
18752 AAGATATGGAGGGAAAGG
130 AAGATATGGAGGGAAAGG
* * * * * *
18770 TTGAAGCCGTAATGGCGAACCTTGTACCTTAGAGATGTGATGGGAAATATTGAAGCCGCAACGAC
1 TTGAAGCCGTAATGACGAACCTTATACCATAGAGATGTGAAGGGAAAGATTGAAGCCACAACGAC
* * * * *
18835 GAATCTTGTACCGTGGAGATATAGA-GGGAAATGTTGAAGCCGCAACGATGAACCTTATACC
66 GAACCTTGTACCGTAGAAACAT-GATGGGAAATGATGAAGCCGCAACGATGAACCTTATACC
18896 TTAAAGATGT
Statistics
Matches: 103, Mismatches: 21, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
147 100 0.97
148 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.22
Consensus pattern (147 bp):
TTGAAGCCGTAATGACGAACCTTATACCATAGAGATGTGAAGGGAAAGATTGAAGCCACAACGAC
GAACCTTGTACCGTAGAAACATGATGGGAAATGATGAAGCCGCAACGATGAACCTTATACCATGA
AGATATGGAGGGAAAGG
Found at i:19219 original size:36 final size:37
Alignment explanation
Indices: 19168--19268 Score: 107
Period size: 38 Copynumber: 2.7 Consensus size: 37
19158 GCGAAGCTAT
*
19168 CATCCAAT-TTCTTACCCCGATC-GGGGTAGATTGAAG
1 CATCCAATATT-TTACCCCGATCAGAGGTAGATTGAAG
* * * *
19204 CATTCAATCTTTTACCTCGATCATGAGGTAGATTTAAG
1 CATCCAATATTTTACCCCGATCA-GAGGTAGATTGAAG
**
19242 CATCCAATATTTTACCCTAATCAGAGG
1 CATCCAATATTTTACCCCGATCAGAGG
19269 GCAAATTGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
36 17 0.32
37 6 0.11
38 30 0.57
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (37 bp):
CATCCAATATTTTACCCCGATCAGAGGTAGATTGAAG
Found at i:19314 original size:78 final size:78
Alignment explanation
Indices: 19208--19369 Score: 189
Period size: 78 Copynumber: 2.1 Consensus size: 78
19198 TTGAAGCATT
* ** * * * * *
19208 CAATCTTTTACCTCGATCATGAGGTAGATTTAAGCATCCAATATTTTACCCTAATCAGAGGGCAA
1 CAATCTTTTACCTCAATCAAAAGATAGATTGAAGCATACAATATATTACCCTAATCAGAGGACAA
19273 ATTGAAGACACAC
66 ATTGAAGACACAC
* * * * * * *
19286 CAATCTTTTACCTTAATCAAAAGATAGATTGAAGCATATAATCTATTACCTTAATTAGAGGATAG
1 CAATCTTTTACCTCAATCAAAAGATAGATTGAAGCATACAATATATTACCCTAATCAGAGGACAA
19351 ATTGAAGACACAC
66 ATTGAAGACACAC
19364 CAATCT
1 CAATCT
19370 CTTATCTTGA
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.30
Consensus pattern (78 bp):
CAATCTTTTACCTCAATCAAAAGATAGATTGAAGCATACAATATATTACCCTAATCAGAGGACAA
ATTGAAGACACAC
Found at i:19496 original size:75 final size:78
Alignment explanation
Indices: 19400--20016 Score: 407
Period size: 78 Copynumber: 7.8 Consensus size: 78
19390 GATTGAGGAC
*
19400 CATCAAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCATACAATCTCTTACCCCAATCA
1 CATC-AATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCATACAATCTCTTACCCCGATCA
* *
19465 TGGGTGAA-ACAGT
65 TGGGTAAATAAAGT
* * *
19478 C-T-AATCTCTTACCCCGATCATGGGGCAAATTAAAGACATCAT-CAATCTCTTACCCCGATCAT
1 CATCAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCATACAATCTCTTACCCCGATCAT
19540 GAGGTAAATTAAAGT
66 G-GGTAAA-TAAAGT
* *
19555 CATCCAATCTCTTACCTCGATCATGGGGCAGATTGAAG---TCGTACAATCTCTTACCCTGATCA
1 CAT-CAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCATACAATCTCTTACCCCGATCA
* *
19617 TGGGGCAAATTGAAG-
65 T-GGGTAAA-TAAAGT
* * ** *
19632 CATCCAGTCTCTTACCT-TAGTCA-GAGGGCAGATTGAAGACA-C-GCCAATCTCTTACGCCGAT
1 CAT-CAATCTCTTACCTCGA-TCATG-GGGCAGATTGAAGACATCATACAATCTCTTACCCCGAT
* *
19693 CATGAGGCAGATTAAAGACAT
63 CATG-GGTA-AATAAAG---T
* * **
19714 CATCCAATCTCTTACC-CAGATCATGGGGCAAATTGAAG-CATC-T--AGTCTCTTA-CCTTAGT
1 CAT-CAATCTCTTACCTC-GATCATGGGGCAGATTGAAGACATCATACAATCTCTTACCCCGA-T
* * * * *
19773 CAGAGGGCATATTGAAGC
63 CA-TGGGTA-AATAAAGT
* * *
19791 CATCCAATCTCTTACCCCGATCAT-GGGCAGATTGAAGACA-CACA-AATCTCTTACCTCGATCA
1 CAT-CAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCATACAATCTCTTACCCCGATCA
* * * *
19853 TGGGGCAGATTGAGGAT
65 T-GGGTA-AATAAAG-T
* * * *
19870 CATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAGACATTATCCAATCTCTTACCCCGATCA
1 CAT-CAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCATACAATCTCTTACCCCGATCA
* * * *
19935 TAAGGTAGATTGAAGC
65 T-GGGTA-AATAAAGT
* * * *
19951 CATCCAATCTTTTACCCCGATCATGAGGCAGATTGAAGACA-C-TAACTAATCTCTTACCCAGAT
1 CAT-CAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCAT-AC-AATCTCTTACCCCGAT
20014 CAT
63 CAT
20017 TGGGCAGATT
Statistics
Matches: 445, Mismatches: 57, Indels: 71
0.78 0.10 0.12
Matches are distributed among these distances:
74 20 0.04
75 42 0.09
76 15 0.03
77 66 0.15
78 80 0.18
79 32 0.07
80 67 0.15
81 62 0.14
82 59 0.13
83 2 0.00
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (78 bp):
CATCAATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCATACAATCTCTTACCCCGATCAT
GGGTAAATAAAGT
Found at i:19576 original size:39 final size:39
Alignment explanation
Indices: 19167--20035 Score: 506
Period size: 40 Copynumber: 22.1 Consensus size: 39
19157 AGCGAAGCTA
* * *
19167 TCATCCAATTTCTTACCCCGATC--GGGGTAGATTGAAG
1 TCATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* * * * *
19204 -CATTCAATCTTTTACCTCGATCATGAGGTAGATTTAAG
1 TCATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* * ** *
19242 -CATCCAATATTTTACCCTAATCA-GAGGGCAAATTGAAG
1 TCATCCAATCTCTTACCCCGATCATGA-GGCAGATTGAAG
* * * *** ** **
19280 ACACACCAATCTTTTACCTTAATCAAAAGATAGATTGAAG
1 TCA-TCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
** * *** * *
19320 -CATATAATCTATTACCTTAATTA-GAGGATAGATTGAAG
1 TCATCCAATCTCTTACCCCGATCATGAGG-CAGATTGAAG
* * * ** * *
19358 ACACACCAATCTCTTATCTTGATCATGGGGCAGATTGAGG
1 TCA-TCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* * * *
19398 ACCATCAAATCTCTTACCTCGATCATGGGGCAGATTGAAG
1 -TCATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* *
19438 ACATCATACAATCTCTTACCCCAATCAT--GG--G--TGAA-
1 ---TCATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* * * * *
19473 ACAGTCTAATCTCTTACCCCGATCATGGGGCAAATTAAAG
1 TCA-TCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* * * *
19513 ACATCATCAATCTCTTACCCCGATCATGAGGTAAATTAAAG
1 TCATC--CAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* *
19554 TCATCCAATCTCTTACCTCGATCATGGGGCAGATTGAAG
1 TCATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* * * * *
19593 TCGTACAATCTCTTACCCTGATCATGGGGCAAATTGAAG
1 TCATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* **
19632 -CATCCAGTCTCTTA-CCTTAGTCA-GAGGGCAGATTGAAG
1 TCATCCAATCTCTTACCCCGA-TCATGA-GGCAGATTGAAG
* * * *
19670 ACACGCCAATCTCTTACGCCGATCATGAGGCAGATTAAAG
1 TCA-TCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* * *
19710 ACATCATCCAATCTCTTACCCAGATCATGGGGCAAATTGAAG
1 ---TCATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* * ** *
19752 -CATCTAGTCTCTTA-CCTTAGTCA-GAGGGCATATTGAAG
1 TCATCCAATCTCTTACCCCGA-TCATGA-GGCAGATTGAAG
*
19790 CCATCCAATCTCTTACCCCGATCATG-GGCAGATTGAAG
1 TCATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* * * *
19828 ACA-CACAAATCTCTTACCTCGATCATGGGGCAGATTGAGG
1 TCATC-C-AATCTCTTACCCCGATCATGAGGCAGATTGAAG
19868 ATCATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
1 -TCATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* * *
19908 ACATTATCCAATCTCTTACCCCGATCATAAGGTAGATTGAAG
1 ---TCATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* *
19950 CCATCCAATCTTTTACCCCGATCATGAGGCAGATTGAAG
1 TCATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* * * *
19989 ACACTAACTAATCTCTTACCCAGATCATTG-GGCAGATTAAAG
1 TCA-T--CCAATCTCTTACCCCGATCA-TGAGGCAGATTGAAG
*
20031 ACATC
1 TCATC
20036 ATCAAATATT
Statistics
Matches: 665, Mismatches: 119, Indels: 94
0.76 0.14 0.11
Matches are distributed among these distances:
32 2 0.00
33 19 0.03
35 2 0.00
36 22 0.03
37 14 0.02
38 131 0.20
39 147 0.22
40 155 0.23
41 49 0.07
42 120 0.18
43 4 0.01
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (39 bp):
TCATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
Found at i:19892 original size:198 final size:200
Alignment explanation
Indices: 19363--20058 Score: 715
Period size: 198 Copynumber: 3.5 Consensus size: 200
19353 TGAAGACACA
* * * * *
19363 CCAATCTCTTATCTTGATCATGGGGCAGATTGAGGACCATCAAATCTCTTACCTCGATCATGGGG
1 CCAATCTCTTACCTAGATCATGGGGCAGATTGAAG-CCATCCAATCTCTTACCCCGATCATGGGG
* * * * *
19428 CAGATTGAAGACATCATACAATCTCTTACCCCAATCAT--GG--G--TGAAACAGTCTAATCTCT
65 CAGATTGAAGACATCACA-AATCTCTTACCTCAATCATGGGGCAGATTGAGACACTCCAATCTCT
* * *
19487 TACCCCGATCATGGGGCAAATTAAAGACATCAT-CAATCTCTTACCCCGATCATGAGGTAAATTA
129 TACCCCGATCATGAGGCAGATTAAAGACATCATCCAATCTCTTACCCCGATCATGAGGCAAATTA
19551 AAGTCAT
194 AAGTCAT
* * * * *
19558 CCAATCTCTTACCTCGATCATGGGGCAGATTGAAGTCGTACAATCTCTTACCCTGATCATGGGGC
1 CCAATCTCTTACCTAGATCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCCGATCATGGGGC
* * * * *
19623 AAATTGAAG-CATC-C-AGTCTCTTACCTTAGTCA-GAGGGCAGATTGAAGACACGCCAATCTCT
66 AGATTGAAGACATCACAAATCTCTTACCTCAATCATG-GGGCAGATTG-AGACACTCCAATCTCT
* * * *
19684 TACGCCGATCATGAGGCAGATTAAAGACATCATCCAATCTCTTACCCAGATCATGGGGCAAATTG
129 TACCCCGATCATGAGGCAGATTAAAGACATCATCCAATCTCTTACCCCGATCATGAGGCAAATTA
19749 AAG-CAT
194 AAGTCAT
* * *
19755 CTAGTCTCTTACCTTAG-TCA-GAGGGCATATTGAAGCCATCCAATCTCTTACCCCGATCAT-GG
1 CCAATCTCTTACC-TAGATCATG-GGGCAGATTGAAGCCATCCAATCTCTTACCCCGATCATGGG
*
19817 GCAGATTGAAGACA-CACAAATCTCTTACCTCGATCATGGGGCAGATTGAGGATCA-TCCAATCT
64 GCAGATTGAAGACATCACAAATCTCTTACCTCAATCATGGGGCAGATTGA-GA-CACTCCAATCT
* * * * *
19880 CTTACCCCGATCATGAGGCAGATTGAAGACATTATCCAATCTCTTACCCCGATCATAAGGTAGAT
127 CTTACCCCGATCATGAGGCAGATTAAAGACATCATCCAATCTCTTACCCCGATCATGAGGCAAAT
* *
19945 TGAAGCCAT
192 TAAAGTCAT
* ** * * * * *
19954 CCAATCTTTTACCCCGATCATGAGGCAGATTGAAGACACTAACTAATCTCTTACCCAGATCATTG
1 CCAATCTCTTACCTAGATCATGGGGCAGATTGAAG-C-C-ATCCAATCTCTTACCCCGATCATGG
* * *
20019 GGCAGATTAAAGACATCATCAAATATTTTACCTCGAATCA
63 GGCAGATTGAAGACATCA-CAAATCTCTTACCTC-AATCA
20059 AGAGAGATAG
Statistics
Matches: 412, Mismatches: 62, Indels: 43
0.80 0.12 0.08
Matches are distributed among these distances:
190 14 0.03
192 2 0.00
193 4 0.01
194 33 0.08
195 32 0.08
196 16 0.04
197 96 0.23
198 128 0.31
199 30 0.07
200 2 0.00
201 1 0.00
202 20 0.05
203 15 0.04
204 2 0.00
205 13 0.03
206 4 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (200 bp):
CCAATCTCTTACCTAGATCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCCGATCATGGGGC
AGATTGAAGACATCACAAATCTCTTACCTCAATCATGGGGCAGATTGAGACACTCCAATCTCTTA
CCCCGATCATGAGGCAGATTAAAGACATCATCCAATCTCTTACCCCGATCATGAGGCAAATTAAA
GTCAT
Found at i:20050 original size:42 final size:40
Alignment explanation
Indices: 19480--20038 Score: 447
Period size: 39 Copynumber: 14.0 Consensus size: 40
19470 GAAACAGTCT
* *
19480 AATCTCTTACCCCGATCATGGGGCAAATTAAAGACATCAT-C
1 AATCTCTTACCCCGATCAT-GGGCAGATTGAAGACA-CATCC
* * **
19521 AATCTCTTACCCCGATCATGAGGTAAATT-AA-AGTCATCC
1 AATCTCTTACCCCGATCATG-GGCAGATTGAAGACACATCC
* * * *
19560 AATCTCTTACCTCGATCATGGGGCAGATTGAAG--TCGTAC
1 AATCTCTTACCCCGATCAT-GGGCAGATTGAAGACACATCC
* *
19599 AATCTCTTACCCTGATCATGGGGCAAATTGAAG---CATCC
1 AATCTCTTACCCCGATCAT-GGGCAGATTGAAGACACATCC
* ** * *
19637 AGTCTCTTA-CCTTAGTCAGAGGGCAGATTGAAGACAC-GCC
1 AATCTCTTACCCCGA-TCA-TGGGCAGATTGAAGACACATCC
* *
19677 AATCTCTTACGCCGATCATGAGGCAGATTAAAGACATCATCC
1 AATCTCTTACCCCGATCATG-GGCAGATTGAAGACA-CATCC
* * *
19719 AATCTCTTACCCAGATCATGGGGCAAATTGAAG---CATCT
1 AATCTCTTACCCCGATCAT-GGGCAGATTGAAGACACATCC
* ** * *
19757 AGTCTCTTA-CCTTAGTCAGAGGGCATATTGAAG-C-CATCC
1 AATCTCTTACCCCGA-TCA-TGGGCAGATTGAAGACACATCC
*
19796 AATCTCTTACCCCGATCATGGGCAGATTGAAGACACA-CA
1 AATCTCTTACCCCGATCATGGGCAGATTGAAGACACATCC
* * *
19835 AATCTCTTACCTCGATCATGGGGCAGATTGAGGA-TCATCC
1 AATCTCTTACCCCGATCAT-GGGCAGATTGAAGACACATCC
*
19875 AATCTCTTACCCCGATCATGAGGCAGATTGAAGACATTATCC
1 AATCTCTTACCCCGATCATG-GGCAGATTGAAGACA-CATCC
* *
19917 AATCTCTTACCCCGATCATAAGGTAGATTGAAG-C-CATCC
1 AATCTCTTACCCCGATCAT-GGGCAGATTGAAGACACATCC
* * *
19956 AATCTTTTACCCCGATCATGAGGCAGATTGAAGACACTAACT
1 AATCTCTTACCCCGATCATG-GGCAGATTGAAGACAC-ATCC
* *
19998 AATCTCTTACCCAGATCATTGGGCAGATTAAAGACATCATC
1 AATCTCTTACCCCGATCA-TGGGCAGATTGAAGACA-CATC
20039 AAATATTTTA
Statistics
Matches: 423, Mismatches: 62, Indels: 65
0.77 0.11 0.12
Matches are distributed among these distances:
37 7 0.02
38 68 0.16
39 132 0.31
40 83 0.20
41 32 0.08
42 97 0.23
43 4 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (40 bp):
AATCTCTTACCCCGATCATGGGCAGATTGAAGACACATCC
Found at i:22075 original size:29 final size:30
Alignment explanation
Indices: 21922--22079 Score: 137
Period size: 30 Copynumber: 5.3 Consensus size: 30
21912 TAAAACTTTG
** *
21922 ATTTTGACCCTCAAACTTTTCAAAAATTAT
1 ATTTTGACCCTTGAACTTTTCAAAAATTAC
*
21952 ATTTTGA-CCTTCGAAC-TTTCAAAAATTAT
1 ATTTTGACCCTT-GAACTTTTCAAAAATTAC
* **
21981 ATTTTAACCCTTGAACTTTTCAAAACCT-C
1 ATTTTGACCCTTGAACTTTTCAAAAATTAC
* * * **
22010 GATTTTAACCCCTAAACTTCTT-AAAAATCGC
1 -ATTTTGACCCTTGAACTT-TTCAAAAATTAC
*
22041 ATTTTGACCCTTGAACTTTTAAAAAATTAC
1 ATTTTGACCCTTGAACTTTTCAAAAATTAC
22071 A-TTTGACCC
1 ATTTTGACCC
22080 CCAAACTTTC
Statistics
Matches: 105, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
29 36 0.34
30 66 0.63
31 3 0.03
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (30 bp):
ATTTTGACCCTTGAACTTTTCAAAAATTAC
Found at i:24481 original size:44 final size:44
Alignment explanation
Indices: 24383--24487 Score: 138
Period size: 44 Copynumber: 2.4 Consensus size: 44
24373 GTCTTTAGTC
* * **
24383 CGCCATTTTAGCTTGCACCCACTCGGGCTTGCATTTAGACTGTT
1 CGCCATTTTGGCTTGCACCCACTCAGGCTTGCATTTAGACCATT
* *
24427 CGCCACTTTGGCTTGCACCCACTCAGGCTTGTATTTAGACCATT
1 CGCCATTTTGGCTTGCACCCACTCAGGCTTGCATTTAGACCATT
**
24471 TTCCATTTTGGCTTGCA
1 CGCCATTTTGGCTTGCA
24488 TTTCGGCAGG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.16, C:0.30, G:0.19, T:0.35
Consensus pattern (44 bp):
CGCCATTTTGGCTTGCACCCACTCAGGCTTGCATTTAGACCATT
Found at i:24646 original size:18 final size:18
Alignment explanation
Indices: 24623--24703 Score: 78
Period size: 18 Copynumber: 4.6 Consensus size: 18
24613 CTTTGATTGA
* *
24623 TCGCACATTTTCCAAAGC
1 TCGCACATTTTGCAGAGC
* *
24641 TCGCACCTTTTGCTGAGC
1 TCGCACATTTTGCAGAGC
*
24659 TCACACATTTTGCAGAGC
1 TCGCACATTTTGCAGAGC
*
24677 TCGCAC-TTTGAGCAGAG-
1 TCGCACATTT-TGCAGAGC
24694 TCGCAC-TTTT
1 TCGCACATTTT
24704 TACTAAGCTC
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
17 12 0.23
18 40 0.77
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.31
Consensus pattern (18 bp):
TCGCACATTTTGCAGAGC
Found at i:24646 original size:33 final size:33
Alignment explanation
Indices: 24564--24687 Score: 97
Period size: 33 Copynumber: 3.7 Consensus size: 33
24554 GGTTCCCACC
* * * *
24564 TTTTACAGAGCTCGCACTTTGATAGCTCGCACC
1 TTTTCCAGAGCTCGCACTTTGATTGATCGCACA
* * * *
24597 TTTTTCTGTGCCCGCACTTTGATTGATCGCACA
1 TTTTCCAGAGCTCGCACTTTGATTGATCGCACA
* * *
24630 TTTTCCAAAGCTCGCACCTTTTG-CTGAGCTCACACA
1 TTTTCCAGAGCTCGCA-C-TTTGATTGA--TCGCACA
*
24666 TTTTGCAGAGCTCGCACTTTGA
1 TTTTCCAGAGCTCGCACTTTGA
24688 GCAGAGTCGC
Statistics
Matches: 70, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
33 37 0.53
34 8 0.11
35 5 0.07
36 20 0.29
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (33 bp):
TTTTCCAGAGCTCGCACTTTGATTGATCGCACA
Done.