Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014942.1 Kokia drynarioides strain JFW-HI SEQ_129985, 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: 71876
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 116 characters in sequence are not A, C, G, or T
Found at i:15052 original size:25 final size:27
Alignment explanation
Indices: 15014--15075 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 27
15004 TATTTTTTAG
* * *
15014 AATTTTTAACTTTTTTTAAA-A-TATA
1 AATTTTAAAATTTTTATAAATATTATA
*
15039 AATTTTAAAATTTTTATAAATATTTTA
1 AATTTTAAAATTTTTATAAATATTATA
15066 AATTTTAAAA
1 AATTTTAAAA
15076 ATTATTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 17 0.55
26 1 0.03
27 13 0.42
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
AATTTTAAAATTTTTATAAATATTATA
Found at i:15072 original size:18 final size:19
Alignment explanation
Indices: 15035--15071 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
15025 TTTTTTAAAA
*
15035 TATAAAT-TTTAAAATTTT
1 TATAAATATTTTAAATTTT
15053 TATAAATATTTTAAATTTT
1 TATAAATATTTTAAATTTT
15072 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:15081 original size:19 final size:20
Alignment explanation
Indices: 15026--15083 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 20
15016 TTTTTAACTT
15026 TTTTTAAAATATAAATTTTAAAA
1 TTTTTAAAA-AT--ATTTTAAAA
*
15049 TTTTTATAAATATTTT-AAA
1 TTTTTAAAAATATTTTAAAA
15068 -TTTTAAAAATTATTTT
1 TTTTTAAAAA-TATTTT
15084 GAGTTTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 8 0.25
19 9 0.28
20 5 0.16
22 2 0.06
23 8 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTTAAAAATATTTTAAAA
Found at i:21997 original size:15 final size:15
Alignment explanation
Indices: 21977--22015 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
21967 TTAATTATTA
21977 TTATTAATAAAGCAT
1 TTATTAATAAAGCAT
* * *
21992 TTATTATTAATGCCT
1 TTATTAATAAAGCAT
22007 TTATTAATA
1 TTATTAATA
22016 GTAATAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (15 bp):
TTATTAATAAAGCAT
Found at i:22788 original size:24 final size:23
Alignment explanation
Indices: 22755--22799 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
22745 GTATTTGGAC
22755 ATTTAAAATAAATTTTAAATTTAA
1 ATTTAAAATAAA-TTTAAATTTAA
*
22779 ATTTATAATAAATTTAAATTT
1 ATTTAAAATAAATTTAAATTT
22800 CAACCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTAAAATAAATTTAAATTTAA
Found at i:22790 original size:17 final size:16
Alignment explanation
Indices: 22770--22846 Score: 73
Period size: 17 Copynumber: 4.6 Consensus size: 16
22760 AAATAAATTT
22770 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
*
22787 TAAATTTAAATTTCAAC
1 TAAATTTAAATTT-AAA
*
22804 CAAATTTAAATTTAGAA
1 TAAATTTAAATTTA-AA
* *
22821 TAAACTTAATTTTAAAA
1 TAAATTTAAATTT-AAA
*
22838 TAGATTTAA
1 TAAATTTAA
22847 GTTGATTGGG
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
16 1 0.02
17 46 0.94
18 2 0.04
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:22845 original size:34 final size:34
Alignment explanation
Indices: 22771--22846 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
22761 AATAAATTTT
* * * *
22771 AAATTTAAATTTATAATAAATTTAAATTTCAACC
1 AAATTTAAATTTAGAATAAACTTAAATTTAAAAC
* *
22805 AAATTTAAATTTAGAATAAACTTAATTTTAAAAT
1 AAATTTAAATTTAGAATAAACTTAAATTTAAAAC
*
22839 AGATTTAA
1 AAATTTAA
22847 GTTGATTGGG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (34 bp):
AAATTTAAATTTAGAATAAACTTAAATTTAAAAC
Found at i:23940 original size:204 final size:204
Alignment explanation
Indices: 23336--24520 Score: 1454
Period size: 204 Copynumber: 5.8 Consensus size: 204
23326 GGTCTTCTTT
* * * * * *
23336 TCAGTATTTTCATCAGGAAGATGA-CTTTTATTGCTCCGATCTGCTTCTCCA-TGTCTCAT-TAG
1 TCAGTA-TCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCT-CAGTGTCTCATCAAG
* * * *
23398 AAAGCTGGGGTTCGAAGATTTTGCTTGTTTCGAGCCTTGTTTGGATCTTCATCTCAGTGTCTCAT
64 -AAGCTGGGGTTCGAAGATTTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCAT
* * *
23463 CAGGAAGATAATCACGTCGTTGTTTGTTCCAATTCGCTCGTCTGCTCCTCATCAGGAAGACGAAT
128 CAGGAAGATGATCACGTCGCTGTTTGTTCCAATTCGCTCCTCTGCTCCTCATCAGGAAGACGAAT
*
23528 TTGGTTCACTCC
193 TTGGTTCACTTC
* *
23540 TCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAA
1 TCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAAGAA
*
23605 GCTGGGGTTCGAAGATTTTTGCTTGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCA
66 GCTGGGGTTCGAAGA-TTTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCA
*
23670 GGAAGATGATCACGTCGCTGTTTGTTCCAATTTGCTCCTCTGCAT-CTCATCAGGAAGACGAATT
130 GGAAGATGATCACGTCGCTGTTTGTTCCAATTCGCTCCTCTGC-TCCTCATCAGGAAGACGAATT
*
23734 TGATTCACTTC
194 TGGTTCACTTC
*
23745 TCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTTGACCTGCTTCTCAGTGTCTCATCAAGAA
1 TCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAAGAA
* *
23810 GCTGGGGTTCGAAGATTTTGCTCATTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATTAG
66 GCTGGGGTTCGAAGATTTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAG
* * * *
23875 GAAGATGATCACCTCGCTGTTTGTTCCAATTTGCTCCTCTGCTCCTCATTAGGAAGACAAATTTG
131 GAAGATGATCACGTCGCTGTTTGTTCCAATTCGCTCCTCTGCTCCTCATCAGGAAGACGAATTTG
*
23940 ATTCACTTC
196 GTTCACTTC
* * * * * *
23949 TCAGTATCTTATCAGGAAGCTAACCTCTTATTGCTTCGACTTGCATCTTAGTGTCTCCTCAAGAA
1 TCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAAGAA
* * *
24014 GTTGAGGTTCGAAGATTTTTACTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCA
66 GCTGGGGTTCGAAGA-TTTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCA
* *
24079 GGAAGATGATCACGTCGCTGTTTGTTCCAATTCGCTCCTCTGCACCTCATCAGGAAGATG-ATTT
130 GGAAGATGATCACGTCGCTGTTTGTTCCAATTCGCTCCTCTGCTCCTCATCAGGAAGACGAATTT
24143 GGTTCACTTC
195 GGTTCACTTC
* * * *
24153 TCAGTATCTCATCAAGAAGCTAACATTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAAGAA
1 TCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAAGAA
24218 GCTGGGGTTCGAAGATTTTGCTCGTTTCGAGCCTCGTTTGGGTTTGATTTGGTCTTCTTCTCAGT
66 GCTGGGGTTCGAAGATTTTGCTCGTTTCGAGCCTC------GTTTG----GGTCTTCTTCTCAGT
* * * * ** * * * *
24283 ATCTCGTCAAGAAGATGA-C-CG-C-ATCGTTTGTTTTAATTCGCTTCTCCG-TATCTCATCGGG
121 GTCTCATCAGGAAGATGATCACGTCGCT-GTTTGTTCCAATTCGCTCCTCTGCT-CCTCATCAGG
*
24343 AAGACGAATTTGGTACACTTC
184 AAGACGAATTTGGTTCACTTC
* ** * * **
24364 TCAGTATCTCATCAGGAAGCTGACCTTTTATTATTTCGACCTGCTTTTCGGTGTCTCATCGGGAA
1 TCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAAGAA
* * * * * * * * * *
24429 GCTGAGATTGGAAGATTCGCTTGCATCATTTTGAGCATCGTTTGGATTTTCTTCTTAGTGTCGCA
66 GCTGGGGTTCGAAGATT---TTGC-TCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCA
* *
24494 TCAGGAAGATGATCACATCGTTGTTTG
127 TCAGGAAGATGATCACGTCGCTGTTTG
24521 GATAATCATA
Statistics
Matches: 858, Mismatches: 95, Indels: 52
0.85 0.09 0.05
Matches are distributed among these distances:
203 36 0.04
204 322 0.38
205 317 0.37
206 2 0.00
207 1 0.00
208 6 0.01
209 12 0.01
210 33 0.04
211 83 0.10
212 1 0.00
213 30 0.03
214 4 0.00
215 11 0.01
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.37
Consensus pattern (204 bp):
TCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAAGAA
GCTGGGGTTCGAAGATTTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAG
GAAGATGATCACGTCGCTGTTTGTTCCAATTCGCTCCTCTGCTCCTCATCAGGAAGACGAATTTG
GTTCACTTC
Found at i:24095 original size:409 final size:408
Alignment explanation
Indices: 23336--24260 Score: 1415
Period size: 409 Copynumber: 2.3 Consensus size: 408
23326 GGTCTTCTTT
* * * * * *
23336 TCAGTATTTTCATCAGGAAGATGA-CTTTTATTGCTCCGATCTGCTTCTCCA-TGTCTCAT-TAG
1 TCAGTA-TCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCT-CAGTGTCTCATCAAG
* * *
23398 AAAGCTGGGGTTCGAAGATTTTGCTTGTTTCGAGCCTTGTTTGGATCTTCATCTCAGTGTCTCAT
64 -AAGCTGGGGTTCGAAGATTTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCATCTCAGTGTCTCAT
* * * *
23463 CAGGAAGATAATCACGTCGTTGTTTGTTCCAATTCGCTCGTCTGCTCCTCATCAGGAAGACGAAT
128 CAGGAAGATAATCACCTCGCTGTTTGTTCCAATTCGCTCCTCTGCTCCTCATCAGGAAGACAAAT
* * *
23528 TTGGTTCACTCCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTA
193 TTGATTCACTCCTCAGTATCTCATCAGGAAGCTAACCTCTTATTGCTTCGACCTGCATCTCAGTA
* * * *
23593 TCTCATCAGGAAGCTGGGGTTCGAAGATTTTTGCTTGTTTCGAGCCTCGTTTGGGTCTTCTTCTC
258 TCTCATCAAGAAGCTGAGGTTCGAAGATTTTTACTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTC
* *
23658 AGTGTCTCATCAGGAAGATGATCACGTCGCTGTTTGTTCCAATTTGCTCCTCTGCATCTCATCAG
323 AGTGTCTCATCAGGAAGATGATCACGTCGCTGTTTGTTCCAATTCGCTCCTCTGCACCTCATCAG
23723 GAAGACGAATTTGATTCACTTC
388 GAAGACG-ATTTGATTCACTTC
*
23745 TCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTTGACCTGCTTCTCAGTGTCTCATCAAGAA
1 TCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAAGAA
* * *
23810 GCTGGGGTTCGAAGATTTTGCTCATTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATTAG
66 GCTGGGGTTCGAAGATTTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCATCTCAGTGTCTCATCAG
* * *
23875 GAAGATGATCACCTCGCTGTTTGTTCCAATTTGCTCCTCTGCTCCTCATTAGGAAGACAAATTTG
131 GAAGATAATCACCTCGCTGTTTGTTCCAATTCGCTCCTCTGCTCCTCATCAGGAAGACAAATTTG
* * * * *
23940 ATTCACTTCTCAGTATCTTATCAGGAAGCTAACCTCTTATTGCTTCGACTTGCATCTTAGTGTCT
196 ATTCACTCCTCAGTATCTCATCAGGAAGCTAACCTCTTATTGCTTCGACCTGCATCTCAGTATCT
* *
24005 CCTCAAGAAGTTGAGGTTCGAAGATTTTTACTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGT
261 CATCAAGAAGCTGAGGTTCGAAGATTTTTACTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGT
24070 GTCTCATCAGGAAGATGATCACGTCGCTGTTTGTTCCAATTCGCTCCTCTGCACCTCATCAGGAA
326 GTCTCATCAGGAAGATGATCACGTCGCTGTTTGTTCCAATTCGCTCCTCTGCACCTCATCAGGAA
* *
24135 GATGATTTGGTTCACTTC
391 GACGATTTGATTCACTTC
* * * *
24153 TCAGTATCTCATCAAGAAGCTAACATTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAAGAA
1 TCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAAGAA
24218 GCTGGGGTTCGAAGATTTTGCTCGTTTCGAGCCTCGTTTGGGT
66 GCTGGGGTTCGAAGATTTTGCTCGTTTCGAGCCTCGTTTGGGT
24261 TTGATTTGGT
Statistics
Matches: 469, Mismatches: 44, Indels: 7
0.90 0.08 0.01
Matches are distributed among these distances:
408 131 0.28
409 336 0.72
410 2 0.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (408 bp):
TCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAAGAA
GCTGGGGTTCGAAGATTTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCATCTCAGTGTCTCATCAG
GAAGATAATCACCTCGCTGTTTGTTCCAATTCGCTCCTCTGCTCCTCATCAGGAAGACAAATTTG
ATTCACTCCTCAGTATCTCATCAGGAAGCTAACCTCTTATTGCTTCGACCTGCATCTCAGTATCT
CATCAAGAAGCTGAGGTTCGAAGATTTTTACTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGT
GTCTCATCAGGAAGATGATCACGTCGCTGTTTGTTCCAATTCGCTCCTCTGCACCTCATCAGGAA
GACGATTTGATTCACTTC
Found at i:24445 original size:211 final size:213
Alignment explanation
Indices: 24055--24445 Score: 495
Period size: 211 Copynumber: 1.8 Consensus size: 213
24045 GCCTCGTTTG
* * *
24055 GGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACGTCGCTGTTTGTTCCAATTCGCTCCTCT
1 GGTCTTCTTCTCAGTATCTCATCAAGAAGATGATCACGTCGCTGTTTGTTCCAATTCGCTCCTCC
* *
24120 GCACCTCATCAGGAAGATGATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACATTTTATT
66 GCACCTCATCAGGAAGACGATTTGGTACACTTCTCAGTATCTCATCAAGAAGCTAACATTTTATT
* * *
24185 GCTTCGACCTGCTTCTTAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTTGCTCGTTTCGAGC
131 ACTTCGACCTGCTTCTTAGTATCTCATCAAGAAGCTGAGATTCGAAGATTTTGCTCGTTTCGAGC
24250 CTCGTTTGGGTTTGATTT
196 CTCGTTTGGGTTTGATTT
* * ** *
24268 GGTCTTCTTCTCAGTATCTCGTCAAGAAGATGA-C-CG-C-ATCGTTTGTTTTAATTCGCTTCTC
1 GGTCTTCTTCTCAGTATCTCATCAAGAAGATGATCACGTCGCT-GTTTGTTCCAATTCGCTCCTC
* * * * * *
24329 CGTATCTCATCGGGAAGACGAATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTGACCTTTTA
65 CGCACCTCATCAGGAAGACG-ATTTGGTACACTTCTCAGTATCTCATCAAGAAGCTAACATTTTA
* * * ** *
24394 TTATTTCGACCTGCTT-TTCGGTGTCTCATCGGGAAGCTGAGATTGGAAGATT
129 TTACTTCGACCTGCTTCTT-AGTATCTCATCAAGAAGCTGAGATTCGAAGATT
24446 CGCTTGCATC
Statistics
Matches: 150, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
209 1 0.01
210 36 0.24
211 82 0.55
212 1 0.01
213 30 0.20
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (213 bp):
GGTCTTCTTCTCAGTATCTCATCAAGAAGATGATCACGTCGCTGTTTGTTCCAATTCGCTCCTCC
GCACCTCATCAGGAAGACGATTTGGTACACTTCTCAGTATCTCATCAAGAAGCTAACATTTTATT
ACTTCGACCTGCTTCTTAGTATCTCATCAAGAAGCTGAGATTCGAAGATTTTGCTCGTTTCGAGC
CTCGTTTGGGTTTGATTT
Found at i:24976 original size:23 final size:23
Alignment explanation
Indices: 24946--24990 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
24936 GAATTCTATT
* *
24946 AAAGAGGATCAATGGAAACAATA
1 AAAGAGGATCAAAGAAAACAATA
24969 AAAGAGGATCAAAGAAAACAAT
1 AAAGAGGATCAAAGAAAACAAT
24991 CACTAGTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.09, G:0.20, T:0.11
Consensus pattern (23 bp):
AAAGAGGATCAAAGAAAACAATA
Found at i:33138 original size:41 final size:41
Alignment explanation
Indices: 33081--33158 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
33071 AACATCAACG
*
33081 TCCAATCCTAAAAGCACCTTCTCTTCCTCCAGTTTTTTTAA
1 TCCAATCCTAAAAGCACCTTCTCTTCATCCAGTTTTTTTAA
33122 TCCAATCCTAAAAGCACCTTCTCTTCATCCAGTTTTT
1 TCCAATCCTAAAAGCACCTTCTCTTCATCCAGTTTTT
33159 CTATCACTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.24, C:0.32, G:0.05, T:0.38
Consensus pattern (41 bp):
TCCAATCCTAAAAGCACCTTCTCTTCATCCAGTTTTTTTAA
Found at i:36190 original size:29 final size:29
Alignment explanation
Indices: 36130--36387 Score: 215
Period size: 30 Copynumber: 8.7 Consensus size: 29
36120 CGAACATCTA
* *
36130 GGGGCAAAAATGGTAATTTTTGGAAGTTTC
1 GGGGTAAAAATGG-GATTTTTGGAAGTTTC
*
36160 GGGGTCAAAAATGGGATTTTTGGGAG-TTC
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTC
* *
36189 GGAGGT-AAAATGGTAATTTTTAGAAG-TTC
1 GG-GGTAAAAATGG-GATTTTTGGAAGTTTC
* *
36218 GGGGGT-AAAATGGTAATTTTGGAAGTTTC
1 -GGGGTAAAAATGGGATTTTTGGAAGTTTC
* *
36247 GAGGTAAAAAATGGGATGTTTGGAAG-TTC
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTC
* *
36276 GGGTGT-ATAATGGTATTTTTTTTGGAAGTTTC
1 GGG-GTAAAAATGGGA---TTTTTGGAAGTTTC
* * *
36308 GGGGTTAAAAATGTGATTTTTAGAAGTTTG
1 GGGG-TAAAAATGGGATTTTTGGAAGTTTC
*
36338 GGGGT-AAAATGGTAATTTTTGGAAGTTTC
1 GGGGTAAAAATGG-GATTTTTGGAAGTTTC
36367 GGGGTAAAAAATGGGATTTTT
1 GGGGT-AAAAATGGGATTTTT
36388 TTAAATTCGA
Statistics
Matches: 184, Mismatches: 27, Indels: 34
0.75 0.11 0.14
Matches are distributed among these distances:
28 33 0.18
29 54 0.29
30 59 0.32
31 25 0.14
32 7 0.04
33 6 0.03
ACGTcount: A:0.29, C:0.03, G:0.32, T:0.36
Consensus pattern (29 bp):
GGGGTAAAAATGGGATTTTTGGAAGTTTC
Found at i:36200 original size:59 final size:57
Alignment explanation
Indices: 36136--36415 Score: 203
Period size: 59 Copynumber: 4.8 Consensus size: 57
36126 TCTAGGGGCA
* * *
36136 AAAATGGTAATTTTTGGAAGTTTC-GGGGTCAAAAATGGGATTTTTGGGAG-TTCGGAGGT
1 AAAATGGTAATTTTTAGAAG-TTCGGGGGT--AAAATGGGAATTTTGGAAGTTTC-GAGGT
*
36195 AAAATGGTAATTTTTAGAAGTTCGGGGGTAAAATGGTAATTTTGGAAGTTTCGAGGT
1 AAAATGGTAATTTTTAGAAGTTCGGGGGTAAAATGGGAATTTTGGAAGTTTCGAGGT
* * * * * * * *
36252 AAAAAATGG-GATGTTTGGAAGTTCGGGTGTATAATGGTATTTTTTTTGGAAGTTTCGGGGTT
1 --AAAATGGTAATTTTTAGAAGTTCGGGGGTAAAATGGGA---ATTTTGGAAGTTTCGAGG-T
* * * *
36314 AAAAAT-GTGATTTTTAGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGT
1 -AAAATGGTAATTTTTAGAAGTTCGGGGGTAAAATGGGAA-TTTTGGAAGTTTCGAGGT
* * * *
36372 AAAAAATGGGATTTTTTTA-AA-TTCGAGGGTAAAATGGTAATTTT
1 --AAAATGGTA-ATTTTTAGAAGTTCGGGGGTAAAATGGGAATTTT
36416 TGAACAATTT
Statistics
Matches: 186, Mismatches: 22, Indels: 27
0.79 0.09 0.11
Matches are distributed among these distances:
57 21 0.11
58 36 0.19
59 71 0.38
60 4 0.02
61 53 0.28
62 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.37
Consensus pattern (57 bp):
AAAATGGTAATTTTTAGAAGTTCGGGGGTAAAATGGGAATTTTGGAAGTTTCGAGGT
Found at i:36208 original size:28 final size:30
Alignment explanation
Indices: 36136--36417 Score: 209
Period size: 29 Copynumber: 9.5 Consensus size: 30
36126 TCTAGGGGCA
36136 AAAATGGTAATTTTTGGAAGTTTCGG-GGT
1 AAAATGGTAATTTTTGGAAGTTTCGGAGGT
* *
36165 CAAAAATGG-GATTTTTGGGAG-TTCGGAGGT
1 --AAAATGGTAATTTTTGGAAGTTTCGGAGGT
* *
36195 AAAATGGTAATTTTTAGAAG-TTCGGGGGT
1 AAAATGGTAATTTTTGGAAGTTTCGGAGGT
36224 AAAATGGTAA-TTTTGGAAGTTTC-GAGGT
1 AAAATGGTAATTTTTGGAAGTTTCGGAGGT
* *
36252 AAAAAATGG-GATGTTTGGAAG-TTCGG-GTGT
1 --AAAATGGTAATTTTTGGAAGTTTCGGAG-GT
* *
36282 ATAATGGTATTTTTTTTGGAAGTTTCGG-GGTT
1 AAAATGGTA--ATTTTTGGAAGTTTCGGAGG-T
* * *
36314 AAAAAT-GTGATTTTTAGAAGTTT-GGGGGT
1 -AAAATGGTAATTTTTGGAAGTTTCGGAGGT
36343 AAAATGGTAATTTTTGGAAGTTTCGG-GGT
1 AAAATGGTAATTTTTGGAAGTTTCGGAGGT
* ** *
36372 AAAAAATGG-GATTTTTTTAA-ATTC-GAGGGT
1 --AAAATGGTAATTTTTGGAAGTTTCGGA-GGT
36402 AAAATGGTAATTTTTG
1 AAAATGGTAATTTTTG
36418 AACAATTTAG
Statistics
Matches: 203, Mismatches: 26, Indels: 46
0.74 0.09 0.17
Matches are distributed among these distances:
28 38 0.19
29 70 0.34
30 58 0.29
31 24 0.12
32 9 0.04
33 4 0.02
ACGTcount: A:0.29, C:0.03, G:0.30, T:0.37
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAGTTTCGGAGGT
Found at i:36318 original size:61 final size:59
Alignment explanation
Indices: 36207--36417 Score: 271
Period size: 59 Copynumber: 3.6 Consensus size: 59
36197 AATGGTAATT
*
36207 TTTAGAAGTTCGGGGGTAAAATGGTAA-TTTTGGAAGTTTCGAGGTAAAAAATGGGATG
1 TTTAGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTAAAAAATGGGATG
* * * * * * *
36265 TTTGGAAGTTCGGGTGTATAATGGTATTTTTTTTGGAAGTTTCGGGGTTAAAAATGTGATT
1 TTTAGAAGTTCGGGGGTAAAATGGTA--ATTTTTGGAAGTTTCGGGGTAAAAAATGGGATG
* *
36326 TTTAGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTAAAAAATGGGATT
1 TTTAGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTAAAAAATGGGATG
** * *
36385 TTTTTAAATTCGAGGGTAAAATGGTAATTTTTG
1 TTTAGAAGTTCGGGGGTAAAATGGTAATTTTTG
36418 AACAATTTAG
Statistics
Matches: 130, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
58 23 0.18
59 58 0.45
61 49 0.38
ACGTcount: A:0.29, C:0.03, G:0.30, T:0.38
Consensus pattern (59 bp):
TTTAGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTAAAAAATGGGATG
Found at i:36416 original size:59 final size:59
Alignment explanation
Indices: 36167--36417 Score: 260
Period size: 59 Copynumber: 4.3 Consensus size: 59
36157 TTCGGGGTCA
* * * * *
36167 AAAATGG-GATTTTTGGGAG-TTCGGAGGT--AAAATGGTAATTTTTAGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGTTTCGG-GGTAAAAAATGG-GATTTTTTGAAATTCGGGGGT
* * * * *
36224 AAAATGGTAA-TTTTGGAAGTTTCGAGGTAAAAAATGGGATGTTTGGAAGTTCGGGTGT
1 AAAATGGTAATTTTTGGAAGTTTCGGGGTAAAAAATGGGATTTTTTGAAATTCGGGGGT
* * * * * * *
36282 ATAATGGTATTTTTTTTGGAAGTTTCGGGGTTAAAAATGTGATTTTTAGAAGTTTGGGGGT
1 AAAATGGTA--ATTTTTGGAAGTTTCGGGGTAAAAAATGGGATTTTTTGAAATTCGGGGGT
* *
36343 AAAATGGTAATTTTTGGAAGTTTCGGGGTAAAAAATGGGATTTTTTTAAATTCGAGGGT
1 AAAATGGTAATTTTTGGAAGTTTCGGGGTAAAAAATGGGATTTTTTGAAATTCGGGGGT
36402 AAAATGGTAATTTTTG
1 AAAATGGTAATTTTTG
36418 AACAATTTAG
Statistics
Matches: 162, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
57 18 0.11
58 30 0.19
59 65 0.40
61 49 0.30
ACGTcount: A:0.29, C:0.03, G:0.30, T:0.37
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAGTTTCGGGGTAAAAAATGGGATTTTTTGAAATTCGGGGGT
Found at i:37437 original size:15 final size:15
Alignment explanation
Indices: 37417--37455 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
37407 TTAATTATTA
37417 TTATTAATAAAGCAT
1 TTATTAATAAAGCAT
* * *
37432 TTATTATTAATGCCT
1 TTATTAATAAAGCAT
37447 TTATTAATA
1 TTATTAATA
37456 GTAATAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (15 bp):
TTATTAATAAAGCAT
Found at i:38217 original size:24 final size:23
Alignment explanation
Indices: 38184--38228 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
38174 GTATTTGGAC
38184 ATTTAAAATAAATTTTAAATTTAA
1 ATTTAAAATAAA-TTTAAATTTAA
*
38208 ATTTATAATAAATTTAAATTT
1 ATTTAAAATAAATTTAAATTT
38229 CAACCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTAAAATAAATTTAAATTTAA
Found at i:38219 original size:17 final size:16
Alignment explanation
Indices: 38199--38275 Score: 73
Period size: 17 Copynumber: 4.6 Consensus size: 16
38189 AAATAAATTT
38199 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
*
38216 TAAATTTAAATTTCAAC
1 TAAATTTAAATTT-AAA
*
38233 CAAATTTAAATTTAGAA
1 TAAATTTAAATTTA-AA
* *
38250 TAAACTTAATTTTAAAA
1 TAAATTTAAATTT-AAA
*
38267 TAGATTTAA
1 TAAATTTAA
38276 GTTGATTGGA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
16 1 0.02
17 46 0.94
18 2 0.04
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:38274 original size:34 final size:34
Alignment explanation
Indices: 38200--38275 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
38190 AATAAATTTT
* * * *
38200 AAATTTAAATTTATAATAAATTTAAATTTCAACC
1 AAATTTAAATTTAGAATAAACTTAAATTTAAAAC
* *
38234 AAATTTAAATTTAGAATAAACTTAATTTTAAAAT
1 AAATTTAAATTTAGAATAAACTTAAATTTAAAAC
*
38268 AGATTTAA
1 AAATTTAA
38276 GTTGATTGGA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (34 bp):
AAATTTAAATTTAGAATAAACTTAAATTTAAAAC
Found at i:38992 original size:13 final size:14
Alignment explanation
Indices: 38964--38996 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
38954 ATAAACATTT
*
38964 AATTAATTTTTTAA
1 AATTAATTTTTAAA
38978 AATTAA-TTTTAAA
1 AATTAATTTTTAAA
38991 AATTAA
1 AATTAA
38997 AAATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTAATTTTTAAA
Found at i:39019 original size:20 final size:20
Alignment explanation
Indices: 38972--39019 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
38962 TTAATTAATT
38972 TTTTAAAATTAATTTTAAAA
1 TTTTAAAATTAATTTTAAAA
* * * *
38992 ATTAAAAATTATTTTTTAAA
1 TTTTAAAATTAATTTTAAAA
39012 TTTTAAAA
1 TTTTAAAA
39020 AAATTAATTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTAAAATTAATTTTAAAA
Found at i:42067 original size:11 final size:10
Alignment explanation
Indices: 42049--42079 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
42039 TTTAAAATTT
42049 TAATTTTTTA
1 TAATTTTTTA
42059 TATATTTTTTA
1 TA-ATTTTTTA
42070 TAATTTTTTA
1 TAATTTTTTA
42080 AAAAATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:42077 original size:9 final size:11
Alignment explanation
Indices: 42051--42079 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
42041 TAAAATTTTA
42051 ATTTTTTATAT
1 ATTTTTTATAT
42062 ATTTTTTATA-
1 ATTTTTTATAT
42072 ATTTTTTA
1 ATTTTTTA
42080 AAAAATACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTTTATAT
Found at i:42140 original size:20 final size:19
Alignment explanation
Indices: 42090--42154 Score: 78
Period size: 20 Copynumber: 3.4 Consensus size: 19
42080 AAAAATACAA
*
42090 ATTTTAGAATTTTATAAA-T
1 ATTTT-GAATTTTAAAAATT
42109 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAATT
* *
42128 ATTTTTAATTTTTGAAAATT
1 ATTTTGAA-TTTTAAAAATT
42148 ATTTTGA
1 ATTTTGA
42155 TAATTTTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 11 0.28
19 13 0.32
20 16 0.40
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATT
Found at i:45669 original size:17 final size:17
Alignment explanation
Indices: 45647--45688 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
45637 AGAGGTCTTT
45647 ACAAGGTTGTAATGGGG
1 ACAAGGTTGTAATGGGG
45664 ACAAGGTTGTAATGGGG
1 ACAAGGTTGTAATGGGG
*
45681 CCAAGGTT
1 ACAAGGTT
45689 AAGGGTATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.38, T:0.24
Consensus pattern (17 bp):
ACAAGGTTGTAATGGGG
Found at i:46872 original size:12 final size:12
Alignment explanation
Indices: 46851--46904 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
46841 AATAGTACAT
46851 AATT-AAAATAA
1 AATTAAAAATAA
46862 AATTAAAAATAA
1 AATTAAAAATAA
*
46874 AA-TAAAACTAA
1 AATTAAAAATAA
46885 AATTAAAAATAA
1 AATTAAAAATAA
*
46897 AATGAAAA
1 AATTAAAA
46905 TGAAAAATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
11 14 0.37
12 24 0.63
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (12 bp):
AATTAAAAATAA
Found at i:46874 original size:6 final size:6
Alignment explanation
Indices: 46855--46921 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
46845 GTACATAATT
* * * *
46855 AAAATA AAATTA AAAAT- AAAATA AAACTA AAATTA AAAAT- AAAATG
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
46901 AAAATGA AAAATG AAAATA AA
1 AAAAT-A AAAATA AAAATA AA
46922 TATACTAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
5 10 0.20
6 35 0.70
7 5 0.10
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:46886 original size:23 final size:22
Alignment explanation
Indices: 46854--46921 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 22
46844 AGTACATAAT
46854 TAAAATAAAATTAAAAATAAAA
1 TAAAATAAAATTAAAAATAAAA
46876 TAAAACTAAAATTAAAAATAAAA
1 TAAAA-TAAAATTAAAAATAAAA
* *
46899 TGAAAATGAAAAATGAAAATAAA
1 T-AAAAT-AAAATTAAAAATAAA
46922 TATACTAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.12
23 19 0.46
24 17 0.41
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (22 bp):
TAAAATAAAATTAAAAATAAAA
Found at i:46957 original size:12 final size:12
Alignment explanation
Indices: 46940--46965 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
46930 TTTTTTTGAA
46940 TTTTTCATTTTT
1 TTTTTCATTTTT
46952 TTTTTCATTTTT
1 TTTTTCATTTTT
46964 TT
1 TT
46966 AAAAAACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTCATTTTT
Found at i:48994 original size:20 final size:21
Alignment explanation
Indices: 48971--49020 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
48961 AATAAAAAAT
48971 AAATGTAAAAAT-T-AAATTAA
1 AAAT-TAAAAATATGAAATTAA
48991 AAA-TAAAAATATGAAATTAA
1 AAATTAAAAATATGAAATTAA
*
49011 AAATAAAAAA
1 AAATTAAAAA
49021 GGCTAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.27
19 1 0.04
20 13 0.50
21 5 0.19
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (21 bp):
AAATTAAAAATATGAAATTAA
Found at i:48997 original size:6 final size:6
Alignment explanation
Indices: 48954--49019 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
48944 AAGAACCTAT
** * *
48954 AAAAT- AAAATAA AAAATA AATGTA AAAATT AAATTA AAAATA AAAATA
1 AAAATA AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
49002 TGAAATTA AAAATA AAAA
1 --AAAATA AAAATA AAAA
49020 AGGCTAAATT
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
5 5 0.11
6 32 0.68
7 5 0.11
8 5 0.11
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (6 bp):
AAAATA
Found at i:50571 original size:23 final size:24
Alignment explanation
Indices: 50538--50617 Score: 85
Period size: 23 Copynumber: 3.4 Consensus size: 24
50528 AATATTCACA
* *
50538 AACATGTTCATTTAAC-TTAATCG
1 AACATGTTCATTGAACATTAAACG
*
50561 AATATGTTCA-TGAACATTAAACG
1 AACATGTTCATTGAACATTAAACG
**
50584 AACATGTTCA-TGAACATATAATTG
1 AACATGTTCATTGAACAT-TAAACG
50608 AACATGTTCA
1 AACATGTTCA
50618 CAAACAATGT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
22 4 0.08
23 31 0.63
24 14 0.29
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (24 bp):
AACATGTTCATTGAACATTAAACG
Found at i:50764 original size:24 final size:24
Alignment explanation
Indices: 50728--50775 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
50718 TAAATGAGTC
* *
50728 AAACGAGTCAATAAATGAGCTTAT
1 AAACAAGTCAATAAACGAGCTTAT
*
50752 AAACAAGTTAATAAACGAGCTTAT
1 AAACAAGTCAATAAACGAGCTTAT
50776 TCGTGAACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (24 bp):
AAACAAGTCAATAAACGAGCTTAT
Found at i:61560 original size:7 final size:7
Alignment explanation
Indices: 61550--61574 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
61540 TTTTTGTATT
61550 TTTTATA
1 TTTTATA
61557 TTTTATA
1 TTTTATA
61564 TTTTATA
1 TTTTATA
61571 TTTT
1 TTTT
61575 TTTTGGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTATA
Found at i:63788 original size:29 final size:29
Alignment explanation
Indices: 63746--63818 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
63736 CGTATGGTCG
63746 ACACGGTCTGCCACAC-GTCCGTGTGACCC
1 ACACGGTCTGCCACACGGT-CGTGTGACCC
* *
63775 ACACGGTCTACCACACGGTTGTGTGACCC
1 ACACGGTCTGCCACACGGTCGTGTGACCC
*
63804 ACATGGTCTGCCACA
1 ACACGGTCTGCCACA
63819 TGGCATACCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 37 0.95
30 2 0.05
ACGTcount: A:0.21, C:0.37, G:0.23, T:0.19
Consensus pattern (29 bp):
ACACGGTCTGCCACACGGTCGTGTGACCC
Found at i:67104 original size:42 final size:42
Alignment explanation
Indices: 66999--67182 Score: 201
Period size: 42 Copynumber: 4.3 Consensus size: 42
66989 TTGATGTGTA
* **
66999 TTAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGATTATGT
1 TTAAAGGAAGACTCATGACTCGGGAAGAGCATGAGATTATGT
* *
67041 TAAAAAGGAAGACTCATGACTCGGGAAAAGCATGAGATTATGAT
1 T-TAAAGGAAGACTCATGACTCGGGAAGAGCATGAGATTATG-T
* *
67085 TT-AAGGAAGACTCATGACTC-GGAAGGAGTATGAGGTTATGTT
1 TTAAAGGAAGACTCATGACTCGGGAA-GAGCATGAGATTATG-T
* ** * *
67127 TTAAAAGGAAGACTCGTGACTCAAGATGAGCATGAGATTTTGT
1 TT-AAAGGAAGACTCATGACTCGGGAAGAGCATGAGATTATGT
67170 TTAAAGGAAGACT
1 TTAAAGGAAGACT
67183 TACGACTCAA
Statistics
Matches: 120, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
41 4 0.03
42 45 0.38
43 38 0.32
44 31 0.26
45 2 0.02
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (42 bp):
TTAAAGGAAGACTCATGACTCGGGAAGAGCATGAGATTATGT
Found at i:67178 original size:86 final size:86
Alignment explanation
Indices: 66999--67182 Score: 228
Period size: 86 Copynumber: 2.2 Consensus size: 86
66989 TTGATGTGTA
* *** *
66999 TTAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGATTATGTTAAAAAGGAAGACTCATGACTCG
1 TTAAAGGAAGACTCATGACTCGGAAGGAGCATGAGATTATGTTAAAAAGGAAGACTCATGACTCA
*
67064 GGAAAAGCATGAGATTATGAT
66 AGAAAAGCATGAGATTATGAT
* * * *
67085 TT-AAGGAAGACTCATGACTCGGAAGGAGTATGAGGTTATGTTTTAAAAGGAAGACTCGTGACTC
1 TTAAAGGAAGACTCATGACTCGGAAGGAGCATGAGATTATG-TTAAAAAGGAAGACTCATGACTC
** *
67149 AAGATGAGCATGAGATTTTG-T
65 AAGAAAAGCATGAGATTATGAT
67170 TTAAAGGAAGACT
1 TTAAAGGAAGACT
67183 TACGACTCAA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
85 35 0.42
86 48 0.58
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (86 bp):
TTAAAGGAAGACTCATGACTCGGAAGGAGCATGAGATTATGTTAAAAAGGAAGACTCATGACTCA
AGAAAAGCATGAGATTATGAT
Found at i:71252 original size:28 final size:27
Alignment explanation
Indices: 71211--71263 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
71201 TTTTTAACTT
* *
71211 AAATTTAAAGTTATTTTATTGGTATCA
1 AAATTTAAAGTTATTTAATTAGTATCA
*
71238 AAATATTAAATTTATTTAATTAGTAT
1 AAAT-TTAAAGTTATTTAATTAGTAT
71264 AAATTGACCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.49
Consensus pattern (27 bp):
AAATTTAAAGTTATTTAATTAGTATCA
Done.