Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1966
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: 403291
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 3
Found at i:142169 original size:49 final size:49
Alignment explanation
Indices: 142094--142282 Score: 246
Period size: 49 Copynumber: 3.9 Consensus size: 49
142084 CTTTTCTCAT
* *
142094 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
142143 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
142191 ---C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCAC
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
142235 CTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 C--TT-CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
142283 ACATCCTTTT
Statistics
Matches: 121, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
43 39 0.32
45 1 0.01
49 45 0.37
50 1 0.01
52 35 0.29
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (49 bp):
CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:142179 original size:116 final size:119
Alignment explanation
Indices: 141975--142196 Score: 279
Period size: 116 Copynumber: 1.9 Consensus size: 119
141965 GCACCTTTTC
* *
141975 CATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAG
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCC---TTCTCATCTTTAAG
* * * *
142040 CCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTT
63 CCCAATATAGCTGGCCGTGAATCAACACATTGGCACCTTTATCACTTTTCTCATCTT
* * * *
142097 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CC-T-TCATCTTTAAGTCC
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTCTCATCTTTAAGCCC
* * *
142159 AATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTA
66 AATATAGCTGGCCGTGAATCAACACATTGGCACCTTTA
142197 AGTCCAATAT
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
116 44 0.51
117 1 0.01
121 2 0.02
122 40 0.46
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (119 bp):
CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTCTCATCTTTAAGCCC
AATATAGCTGGCCGTGAATCAACACATTGGCACCTTTATCACTTTTCTCATCTT
Found at i:142210 original size:43 final size:43
Alignment explanation
Indices: 142100--142238 Score: 170
Period size: 43 Copynumber: 3.1 Consensus size: 43
142090 TCATCTTCAT
* * *
142100 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGGCA----C
* *
142147 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGGCAC
*
142192 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGGCAC
142235 CTTT
1 CTTT
142239 TCCATCTTTA
Statistics
Matches: 84, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
43 44 0.52
45 1 0.01
49 39 0.46
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGGCAC
Found at i:143146 original size:19 final size:18
Alignment explanation
Indices: 143085--143180 Score: 77
Period size: 13 Copynumber: 5.7 Consensus size: 18
143075 ATTTCAACGA
143085 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
143104 TATTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
*
143120 --TATATCGATACATAAG
1 TTTGTATCGATACATAAG
143136 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
143152 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
143168 TTTTGTATCGATA
1 -TTTGTATCGATA
143181 AGCTACTGCC
Statistics
Matches: 62, Mismatches: 2, Indels: 26
0.69 0.02 0.29
Matches are distributed among these distances:
13 21 0.34
15 4 0.06
17 4 0.06
19 21 0.34
20 12 0.19
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:143147 original size:32 final size:32
Alignment explanation
Indices: 143089--143180 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 32
143079 CAACGATTTG
143089 TATCGATACATAAAGTATTGTATCGATACAATA
1 TATCGATACAT-AAGTATTGTATCGATACAATA
* *
143122 TATCGATACATAAGTGTTGTATCGATACAATG
1 TATCGATACATAAGTATTGTATCGATACAATA
*
143154 TATCGATACATAAGTTTTGTATCGATA
1 TATCGATACATAAGTATTGTATCGATA
143181 AGCTACTGCC
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 45 0.80
33 11 0.20
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (32 bp):
TATCGATACATAAGTATTGTATCGATACAATA
Found at i:143215 original size:13 final size:13
Alignment explanation
Indices: 143197--143221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
143187 TGCCAAAAAA
143197 TGTATCGATACAT
1 TGTATCGATACAT
143210 TGTATCGATACA
1 TGTATCGATACA
143222 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:143292 original size:52 final size:52
Alignment explanation
Indices: 143230--143354 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
143220 CACTGATCTT
*
143230 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
143282 TGTATAGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
143334 TGTATCGATACATGCAGGCAA
1 TGTATCGATACATGCAGGCAA
143355 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:146923 original size:2 final size:2
Alignment explanation
Indices: 146911--146940 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
146901 CTTAAGGTAA
*
146911 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
146941 TGTAAACAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:147651 original size:20 final size:20
Alignment explanation
Indices: 147601--147653 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
147591 TTCTATTAAA
*
147601 TTTAATGATGTAAGCTTCAT
1 TTTAATGATGTAAACTTCAT
** * *
147621 TTTTCTAATGTAAACTTTAT
1 TTTAATGATGTAAACTTCAT
147641 TTTAATGATGTAA
1 TTTAATGATGTAA
147654 TAATCACTAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (20 bp):
TTTAATGATGTAAACTTCAT
Found at i:152092 original size:51 final size:52
Alignment explanation
Indices: 152018--152142 Score: 225
Period size: 51 Copynumber: 2.4 Consensus size: 52
152008 AATATGAAAT
*
152018 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC-AA
1 TTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAA
152069 TTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAA
*
152121 TTTGCCTACATGTATCGATACA
1 TTTGCCTGCATGTATCGATACA
152143 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
51 48 0.68
52 23 0.32
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAA
Found at i:152169 original size:13 final size:13
Alignment explanation
Indices: 152151--152175 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
152141 CAAAGATCAG
152151 TGTATCGATACAA
1 TGTATCGATACAA
152164 TGTATCGATACA
1 TGTATCGATACA
152176 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:152266 original size:32 final size:32
Alignment explanation
Indices: 152223--152288 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
152213 TTCGTAATTG
*
152223 TACATTTTATCGATACAAAACTTACGTATCGA
1 TACATTGTATCGATACAAAACTTACGTATCGA
* *
152255 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTACGTATCGA
152287 TA
1 TA
152289 TAAATCATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAAAACTTACGTATCGA
Found at i:154816 original size:48 final size:48
Alignment explanation
Indices: 154764--154867 Score: 208
Period size: 48 Copynumber: 2.2 Consensus size: 48
154754 AATCAAAGAT
154764 AAGCATAATCACTCTCGATTATGAAATGTTCAAGATGAAATTAGAGAA
1 AAGCATAATCACTCTCGATTATGAAATGTTCAAGATGAAATTAGAGAA
154812 AAGCATAATCACTCTCGATTATGAAATGTTCAAGATGAAATTAGAGAA
1 AAGCATAATCACTCTCGATTATGAAATGTTCAAGATGAAATTAGAGAA
154860 AAGCATAA
1 AAGCATAA
154868 AAAAGATGTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.26
Consensus pattern (48 bp):
AAGCATAATCACTCTCGATTATGAAATGTTCAAGATGAAATTAGAGAA
Found at i:168357 original size:2 final size:2
Alignment explanation
Indices: 168350--168380 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
168340 ATAGAGTTCA
168350 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
168381 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:168385 original size:2 final size:2
Alignment explanation
Indices: 168380--168408 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
168370 TCTCTCTCTC
168380 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
168409 TCCTGAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:170703 original size:16 final size:18
Alignment explanation
Indices: 170682--170714 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
170672 ATGTGGTTAG
170682 TTTT-AAAT-TATTATAA
1 TTTTAAAATATATTATAA
170698 TTTTAAAATATATTATA
1 TTTTAAAATATATTATA
170715 TTAGTCGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTAAAATATATTATAA
Found at i:170800 original size:17 final size:18
Alignment explanation
Indices: 170768--170802 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
170758 ATTTATCATC
*
170768 TTTTTACTTTTGTTTAAT
1 TTTTTAATTTTGTTTAAT
170786 TTTTTAATTTT-TTTAAT
1 TTTTTAATTTTGTTTAAT
170803 ATATCTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTTAATTTTGTTTAAT
Found at i:172654 original size:2 final size:2
Alignment explanation
Indices: 172647--172693 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
172637 TATGCAACAT
* * *
172647 TA TA TA TA TA TA TA TA TA TA TA TA CA CA TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
172689 TA TA T
1 TA TA T
172694 TTTCTTTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:173447 original size:13 final size:13
Alignment explanation
Indices: 173429--173455 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
173419 CCTTGACAAT
173429 ATTACTCTTAGAC
1 ATTACTCTTAGAC
173442 ATTACTCTTAGAC
1 ATTACTCTTAGAC
173455 A
1 A
173456 GCAGTGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (13 bp):
ATTACTCTTAGAC
Found at i:175286 original size:13 final size:13
Alignment explanation
Indices: 175268--175293 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
175258 AATTTTTTTG
175268 TGTATCGATACAT
1 TGTATCGATACAT
175281 TGTATCGATACAT
1 TGTATCGATACAT
175294 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:176318 original size:13 final size:13
Alignment explanation
Indices: 176300--176325 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
176290 TACACAAAGT
176300 ATGTATCGATACA
1 ATGTATCGATACA
176313 ATGTATCGATACA
1 ATGTATCGATACA
176326 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:176323 original size:32 final size:33
Alignment explanation
Indices: 176282--176345 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
176272 TAGCCAAACT
**
176282 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
176314 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
176346 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:178275 original size:23 final size:23
Alignment explanation
Indices: 178249--178303 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
178239 TAAAAATTAT
178249 TTAATAATAACATGA-ATAATTTA
1 TTAATAATAACAT-ACATAATTTA
* * *
178272 TTAAAAATTATATACATAATTTA
1 TTAATAATAACATACATAATTTA
178295 TTAAATAAT
1 TT-AATAAT
178304 TATAAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.04
23 20 0.77
24 5 0.19
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (23 bp):
TTAATAATAACATACATAATTTA
Found at i:178302 original size:12 final size:12
Alignment explanation
Indices: 178263--178304 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
178253 TAATAACATG
178263 AATAATTTATTA
1 AATAATTTATTA
178275 AA-AA-TTATATA
1 AATAATTTAT-TA
*
178286 CATAATTTATTA
1 AATAATTTATTA
178298 AATAATT
1 AATAATT
178305 ATAAATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 4 0.16
11 5 0.20
12 12 0.48
13 4 0.16
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (12 bp):
AATAATTTATTA
Found at i:178313 original size:19 final size:18
Alignment explanation
Indices: 178266--178328 Score: 54
Period size: 23 Copynumber: 3.2 Consensus size: 18
178256 TAACATGAAT
178266 AATTTATTAAAAATTATATACA
1 AATTTATTAAAAA-T-TAT--A
178288 TAATTTATTAAATAATTATA
1 -AATTTATTAAA-AATTATA
* *
178308 AATTTATTTAAAATTTTA
1 AATTTATTAAAAATTATA
178326 AAT
1 AAT
178329 ATAAAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
18 9 0.24
19 10 0.27
20 1 0.03
22 3 0.08
23 12 0.32
24 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTTATTAAAAATTATA
Found at i:178688 original size:2 final size:2
Alignment explanation
Indices: 178681--178712 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
178671 TTTTAAGAAA
*
178681 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
178713 GTACTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:179499 original size:21 final size:21
Alignment explanation
Indices: 179473--179515 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
179463 TTTAATCATA
*
179473 ATTCAATATGTTTACATTTTC
1 ATTCAATATGTTGACATTTTC
*
179494 ATTCAATATGTTGATATTTTC
1 ATTCAATATGTTGACATTTTC
179515 A
1 A
179516 CATTTTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (21 bp):
ATTCAATATGTTGACATTTTC
Found at i:181865 original size:12 final size:13
Alignment explanation
Indices: 181837--181896 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 13
181827 AGATGAAAAA
*
181837 AAAAACAAAG-AG
1 AAAAAGAAAGAAG
181849 TAAAAAGAAAGCAA-
1 -AAAAAGAAAG-AAG
181863 AAAAAG-AAGAAG
1 AAAAAGAAAGAAG
181875 AAAAAGAAAG-AG
1 AAAAAGAAAGAAG
*
181887 AGAAAGAAAG
1 AAAAAGAAAG
181897 TTTAATAGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
11 2 0.05
12 20 0.49
13 18 0.44
15 1 0.02
ACGTcount: A:0.73, C:0.03, G:0.22, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAGAAG
Found at i:181872 original size:25 final size:26
Alignment explanation
Indices: 181835--181884 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
181825 TTAGATGAAA
181835 AAAAAAACAAAG-AGTAAAAAGAAAGC
1 AAAAAAACAAAGAAG-AAAAAGAAAGC
*
181861 AAAAAAA-GAAGAAGAAAAAGAAAG
1 AAAAAAACAAAGAAGAAAAAGAAAG
181885 AGAGAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (26 bp):
AAAAAAACAAAGAAGAAAAAGAAAGC
Found at i:182674 original size:58 final size:58
Alignment explanation
Indices: 182546--182878 Score: 248
Period size: 58 Copynumber: 5.6 Consensus size: 58
182536 TTGCAATTCC
* * * * *
182546 CATGCA-TTTTAGGT-AATTTTAGTCATTTTCCATGACTTAGGGATTTTTATGACTTTT
1 CATGCATTTTTATGTCAA-TTTAGTAATTTTTCATGACTTAAGGATTTTTATGACATTT
*
182603 CATGCA-TTTTATGTCAATTTAGTAATTTTTCATGACTTAAGGATTTTTATGATATTT
1 CATGCATTTTTATGTCAATTTAGTAATTTTTCATGACTTAAGGATTTTTATGACATTT
* * * ** * * *
182660 CATGCATTTTTATGTCATTTTAGTCATTTTGCATGACCCAAGGATCTTTATAAAATTT
1 CATGCATTTTTATGTCAATTTAGTAATTTTTCATGACTTAAGGATTTTTATGACATTT
* * * *
182718 TATGCGTTTTTATGTCATTTTAATTATTTTAGTCAATTTTT-ATAACTTAGGGATTTTTATGACA
1 CATGCATTTTTATGTC------A--A-TTTAGT-AATTTTTCATGACTTAAGGATTTTTATGACA
182782 TTT
56 TTT
* * * * * *
182785 CATTCATTTTTGTGTTATTTTTAGTCAATTTTT-ATGA-TCGAAGGA-GTTTAGTGACATTT
1 CATGCATTTTTATGTCA-ATTTAGT-AATTTTTCATGACT-TAAGGATTTTTA-TGACATTT
* *
182844 CATGGATTTTTATGTCATTTTAGTAATTTTTCATG
1 CATGCATTTTTATGTCAATTTAGTAATTTTTCATG
182879 GCAGGGGGAT
Statistics
Matches: 221, Mismatches: 40, Indels: 29
0.76 0.14 0.10
Matches are distributed among these distances:
57 61 0.28
58 74 0.33
59 42 0.19
60 1 0.00
61 1 0.00
64 1 0.00
67 36 0.16
68 5 0.02
ACGTcount: A:0.25, C:0.10, G:0.14, T:0.51
Consensus pattern (58 bp):
CATGCATTTTTATGTCAATTTAGTAATTTTTCATGACTTAAGGATTTTTATGACATTT
Found at i:182863 original size:126 final size:125
Alignment explanation
Indices: 182620--182865 Score: 302
Period size: 126 Copynumber: 2.0 Consensus size: 125
182610 TTTATGTCAA
* *
182620 TTTAGTAATTTTTCATGACTTAAGGATTTTTATGATATTTCATGCATTTTTATGTCATTTTAGTC
1 TTTAGTAATTTTTCATAACTTAAGGATTTTTATGACATTTCATGCATTTTTATGTCATTTTAGTC
*
182685 ATTTTGCATGACCCAAGGATCTTTATAAAATTTTATGCGTTTTTATGTCATTTTAATTAT
66 ATTTTGCATGACCCAAGGATCTTTATAAAATTTCATGCGTTTTTATGTCATTTTAATTAT
* * * *
182745 TTTAGTCAATTTTT-ATAACTTAGGGATTTTTATGACATTTCATTCATTTTTGTGTTATTTTTAG
1 TTTAGT-AATTTTTCATAACTTAAGGATTTTTATGACATTTCATGCATTTTTATGTCA-TTTTAG
* * * * * *
182809 TCAATTTT-TATGATCGAAGGA-GTTTAGTGACATTTCATG-GATTTTTATGTCATTTTA
64 TC-ATTTTGCATGACCCAAGGATCTTTA-TAAAATTTCATGCG-TTTTTATGTCATTTTA
182866 GTAATTTTTC
Statistics
Matches: 103, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
125 48 0.47
126 50 0.49
127 5 0.05
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.52
Consensus pattern (125 bp):
TTTAGTAATTTTTCATAACTTAAGGATTTTTATGACATTTCATGCATTTTTATGTCATTTTAGTC
ATTTTGCATGACCCAAGGATCTTTATAAAATTTCATGCGTTTTTATGTCATTTTAATTAT
Found at i:182873 original size:126 final size:125
Alignment explanation
Indices: 182599--182873 Score: 301
Period size: 126 Copynumber: 2.2 Consensus size: 125
182589 TTTTTATGAC
* * *
182599 TTTTCATG-CATTTTATGTCAA-TTTAGTAATTTTTCATGACTTAAGGATTTTTATGATATTTCA
1 TTTTTATGTCATTTTA-GT-AATTTTAGTAATTTTTCATAACTTAAGGATTTTTATGACATTTCA
*
182662 TGCATTTTTATGTCATTTTAGTCATTTTGCATGACCCAAGGATCTTTATAAAATTTTATGCG
64 TGCATTTTTATGTCATTTTAGTCATTTTGCATGACCCAAGGATCTTTATAAAATTTCATGCG
* * *
182724 TTTTTATGTCATTTTAATTATTTTAGTCAATTTTT-ATAACTTAGGGATTTTTATGACATTTCAT
1 TTTTTATGTCATTTTAGTAATTTTAGT-AATTTTTCATAACTTAAGGATTTTTATGACATTTCAT
* * * * * * * * *
182788 TCATTTTTGTGTTATTTTTAGTCAATTTT-TATGATCGAAGGA-GTTTAGTGACATTTCATG-G
65 GCATTTTTATGTCA-TTTTAGTC-ATTTTGCATGACCCAAGGATCTTTA-TAAAATTTCATGCG
182849 ATTTTTATGTCATTTTAGTAATTTT
1 -TTTTTATGTCATTTTAGTAATTTT
182874 TCATGGCAGG
Statistics
Matches: 125, Mismatches: 18, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
124 1 0.01
125 56 0.45
126 63 0.50
127 5 0.04
ACGTcount: A:0.25, C:0.09, G:0.13, T:0.52
Consensus pattern (125 bp):
TTTTTATGTCATTTTAGTAATTTTAGTAATTTTTCATAACTTAAGGATTTTTATGACATTTCATG
CATTTTTATGTCATTTTAGTCATTTTGCATGACCCAAGGATCTTTATAAAATTTCATGCG
Found at i:182931 original size:29 final size:29
Alignment explanation
Indices: 182899--182959 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
182889 TTTTTTATGC
* *
182899 CATTTCATGTATTTTGATGTCATATAGGT
1 CATTTCATGTATGTTGAGGTCATATAGGT
* * *
182928 CATTTTATGTATGTTGGGGTCATTTAGGT
1 CATTTCATGTATGTTGAGGTCATATAGGT
182957 CAT
1 CAT
182960 ATTTCATGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.48
Consensus pattern (29 bp):
CATTTCATGTATGTTGAGGTCATATAGGT
Found at i:182999 original size:58 final size:57
Alignment explanation
Indices: 182929--183150 Score: 212
Period size: 58 Copynumber: 3.7 Consensus size: 57
182919 CATATAGGTC
* * * *
182929 ATTTTATGTATGTTGGGGTCATTTAGGTCATATTTCATGATCTAAGAACTTTCATACA
1 ATTTTATATATGTTAGGGTCATTTAGGTCATTTTTCATGATCTAAGAACTTT-ATGCA
*
182987 ATTTTATATATGTTAGGGTAATTTAGGTCATTTTTCATGATCTATGATCTAGGAACGTTTATGCA
1 ATTTTATATATGTTAGGGTCATTTAGGTCATTTTTCATGATC--T-A---A-GAAC-TTTATGCA
* * * * * * *
183052 ATTTTATGTATGTTGGGGTTATTTAAGTCA-TTTTCTATAATCTAAGGACTTTTATGTA
1 ATTTTATATATGTTAGGGTCATTTAGGTCATTTTTC-ATGATCTAAGAAC-TTTATGCA
* *
183110 ATTTTATAAATGTTAGGGCCATTTAGGTCATTTTTCATGAT
1 ATTTTATATATGTTAGGGTCATTTAGGTCATTTTTCATGAT
183151 TTAGGGATTT
Statistics
Matches: 134, Mismatches: 20, Indels: 20
0.77 0.11 0.11
Matches are distributed among these distances:
58 76 0.57
59 6 0.04
60 1 0.01
61 1 0.01
62 1 0.01
63 1 0.01
64 6 0.04
65 39 0.29
66 3 0.02
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.46
Consensus pattern (57 bp):
ATTTTATATATGTTAGGGTCATTTAGGTCATTTTTCATGATCTAAGAACTTTATGCA
Found at i:183054 original size:65 final size:63
Alignment explanation
Indices: 182965--183151 Score: 190
Period size: 65 Copynumber: 3.0 Consensus size: 63
182955 GTCATATTTC
* *
182965 ATGATCTAAGAACTTTCATACAATTTTATATATGTTAGGGTAATTTAGGTCATTTTTCATGATCT
1 ATGATCTAGGAACTTT-ATGCAATTTTATATATGTTAGGGTAATTTAGGTCATTTTTCATGAT-T
* * * *
183030 ATGATCTAGGAACGTTTATGCAATTTTATGTATGTTGGGGTTATTTAAGTCA-TTTTC-T-A-T
1 ATGATCTAGGAAC-TTTATGCAATTTTATATATGTTAGGGTAATTTAGGTCATTTTTCATGATT
* * **
183090 A--ATCTAAGG-ACTTTTATGTAATTTTATAAATGTTAGGGCCATTTAGGTCATTTTTCATGATT
1 ATGATCT-AGGAAC-TTTATGCAATTTTATATATGTTAGGGTAATTTAGGTCATTTTTCATGATT
183152 TAGGGATTTT
Statistics
Matches: 102, Mismatches: 14, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
58 37 0.36
59 8 0.08
60 3 0.03
61 1 0.01
62 2 0.02
63 1 0.01
64 5 0.05
65 42 0.41
66 3 0.03
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (63 bp):
ATGATCTAGGAACTTTATGCAATTTTATATATGTTAGGGTAATTTAGGTCATTTTTCATGATT
Found at i:183067 original size:123 final size:123
Alignment explanation
Indices: 182929--183150 Score: 338
Period size: 123 Copynumber: 1.8 Consensus size: 123
182919 CATATAGGTC
* *
182929 ATTTTATGTATGTTGGGGTCATTTAGGTCATATTTC-ATGATCTAAGAACTTTCATACAATTTTA
1 ATTTTATGTATGTTGGGGTCATTTAAGTCAT-TTTCTATAATCTAAGAACTTTCATACAATTTTA
* *
182993 TATATGTTAGGGTAATTTAGGTCATTTTTCATGATCTATGATCTAGGAACGTTTATGCA
65 TAAATGTTAGGGCAATTTAGGTCATTTTTCATGATCTATGATCTAGGAACGTTTATGCA
* * * **
183052 ATTTTATGTATGTTGGGGTTATTTAAGTCATTTTCTATAATCTAAGGACTTTTATGTAATTTTAT
1 ATTTTATGTATGTTGGGGTCATTTAAGTCATTTTCTATAATCTAAGAACTTTCATACAATTTTAT
*
183117 AAATGTTAGGGCCATTTAGGTCATTTTTCATGAT
66 AAATGTTAGGGCAATTTAGGTCATTTTTCATGAT
183151 TTAGGGATTT
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
122 4 0.05
123 84 0.95
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.46
Consensus pattern (123 bp):
ATTTTATGTATGTTGGGGTCATTTAAGTCATTTTCTATAATCTAAGAACTTTCATACAATTTTAT
AAATGTTAGGGCAATTTAGGTCATTTTTCATGATCTATGATCTAGGAACGTTTATGCA
Found at i:185242 original size:20 final size:19
Alignment explanation
Indices: 185217--185271 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
185207 TTTTACCCAG
*
185217 ATGTATCGATACATTTTGCA
1 ATGTATCGATACATTATG-A
185237 ATGTATCGATACATGTATGA
1 ATGTATCGATACAT-TATGA
*
185257 ATGCATCGATACATT
1 ATGTATCGATACATT
185272 GTCTTTTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 1 0.03
20 28 0.88
21 3 0.09
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGTATCGATACATTATGA
Found at i:187119 original size:20 final size:20
Alignment explanation
Indices: 187094--187135 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
187084 CTCTGCGAGC
187094 AGCGCAATTCACCCAATTTT
1 AGCGCAATTCACCCAATTTT
187114 AGCGCAATTCACCCAATTTT
1 AGCGCAATTCACCCAATTTT
187134 AG
1 AG
187136 GAATTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (20 bp):
AGCGCAATTCACCCAATTTT
Found at i:190022 original size:28 final size:28
Alignment explanation
Indices: 189936--190609 Score: 482
Period size: 28 Copynumber: 23.9 Consensus size: 28
189926 AGTTCACGAT
* * *
189936 TCAGTGGCATTTCTTTCCAAAGTCTACAAC
1 TCAGTGGCA-TCCTTT-TAAAGTCCACAAC
*
189966 TCCGTGGCATCCTTTT-AAGTCCACAAC
1 TCAGTGGCATCCTTTTAAAGTCCACAAC
*
189993 TCCGTGGCATCCTTTTAAAGTCCACAAC
1 TCAGTGGCATCCTTTTAAAGTCCACAAC
* * **
190021 TCCGTGGCACCCTTTTAAAGTTTACAAC
1 TCAGTGGCATCCTTTTAAAGTCCACAAC
*
190049 TCCGTGGCATCCTTTT-AAGTCCACAAC
1 TCAGTGGCATCCTTTTAAAGTCCACAAC
* * *
190076 TCTGTGGCA-CCCTTTAAAGTCCATAAC
1 TCAGTGGCATCCTTTTAAAGTCCACAAC
* *
190103 TCTGTGGCACCCTTTTAAAGTCCACAAC
1 TCAGTGGCATCCTTTTAAAGTCCACAAC
* * *
190131 ACCGTGGCACCCTTTT-AAGTCCACAAC
1 TCAGTGGCATCCTTTTAAAGTCCACAAC
* * *
190158 TCTGTGACACCCTTTT-AAGTCCACAAC
1 TCAGTGGCATCCTTTTAAAGTCCACAAC
* * * *
190185 TCTGTGACA-CCTTTTTAAGTCCACTAC
1 TCAGTGGCATCCTTTTAAAGTCCACAAC
* * *
190212 TCCA-TGGCACCCTTTTAAAGCCCACAAG
1 T-CAGTGGCATCCTTTTAAAGTCCACAAC
* * *
190240 TTAGTGGCATCCTTTTAAAGCCCACAAG
1 TCAGTGGCATCCTTTTAAAGTCCACAAC
* *
190268 TCAGTGGCATCCTTTCAAAGCCCACAAC
1 TCAGTGGCATCCTTTTAAAGTCCACAAC
* ** * *
190296 TTAGTGGCATCTCTTCAAAAGACCACAAG
1 TCAGTGGCATC-CTTTTAAAGTCCACAAC
* * * *
190325 TCAGTGGCATCCTTTCAAAGCCCGCAAG
1 TCAGTGGCATCCTTTTAAAGTCCACAAC
* * * *
190353 TTAGTGGCATCCTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTTAAAGTCCACAAC
** * *
190381 TCAGTGGCATCTCTTCAAAAGACCACAAA
1 TCAGTGGCATC-CTTTTAAAGTCCACAAC
* * *
190410 TCAGTGGCACCCTTTAAAAGTCCACAAG
1 TCAGTGGCATCCTTTTAAAGTCCACAAC
* * * * * *
190438 TCAATGGCACCCTTTCAAAGCCCATAAA
1 TCAGTGGCATCCTTTTAAAGTCCACAAC
* * * *
190466 TCAGTGGCACCCTTTAAAAGCCCACATAAA
1 TCAGTGGCATCCTTTTAAAGTCCAC--AAC
* ** * *
190496 TCAGTGGCACCCTTCCAAAGCCCACAAG
1 TCAGTGGCATCCTTTTAAAGTCCACAAC
* * * *
190524 TCAGTGCCACCCTTTCAAAG-CCTACAAG
1 TCAGTGGCATCCTTTTAAAGTCC-ACAAC
* * * *
190552 TCAATGGCACCCTTTCAAAGTCCACACAAG
1 TCAGTGGCATCCTTTTAAAGT-C-CACAAC
* *
190582 TCAGTGGCAACTCCTTTCAAAGCCCACA
1 TCAGTGGC-A-TCCTTTTAAAGTCCACA
190610 CAAGTTAATG
Statistics
Matches: 556, Mismatches: 71, Indels: 34
0.84 0.11 0.05
Matches are distributed among these distances:
26 11 0.02
27 124 0.22
28 306 0.55
29 51 0.09
30 51 0.09
31 3 0.01
32 10 0.02
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (28 bp):
TCAGTGGCATCCTTTTAAAGTCCACAAC
Found at i:190331 original size:85 final size:84
Alignment explanation
Indices: 189986--190609 Score: 452
Period size: 85 Copynumber: 7.4 Consensus size: 84
189976 CCTTTTAAGT
* * * * * * * *** *
189986 CCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTTTACAACTC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTC
* * ** *
190051 CGTGGCATCCTT-TTAAGT
66 AGTGGCACCCTTCAAAAGC
* * * * * * * * * **
190069 CCACAACTCTGTGGCACCCTTT-AAAGTCCATAACTCTGTGGCACCCTTTTAAAGTCCACAACAC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTC
* ** *
190133 CGTGGCACCCTT-TTAAGT
66 AGTGGCACCCTTCAAAAGC
* * * * * * * * * ** * * *
190151 CCACAACTCTGTGACACCCTTT-TAAGTCCACAACTCTGTGACA-CCTTTTTAAGTCCACTACTC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGT-
**
190214 CA-TGGCACCCTTTTAAAGC
65 CAGTGGCACCCTTCAAAAGC
* * * * *
190233 CCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAACTT
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTC
* *
190298 AGTGGCATCTCTTCAAAAGA
66 AGTGGCA-CCCTTCAAAAGC
* * *
190318 CCACAAGTCAGTGGCATCCTTTCAAAGCCCGCAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTC
* *
190383 AGTGGCATCTCTTCAAAAGA
66 AGTGGCA-CCCTTCAAAAGC
* * * * * * *
190403 CCACAAATCAGTGGCACCCTTTAAAAGTCCACAAGTCAATGGCACCCTTTCAAAGCCCATAAATC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTC
*
190468 AGTGGCACCCTTTAAAAGC
66 AGTGGCACCCTTCAAAAGC
* * * * *
190487 CCACATAAATCAGTGGCACCCTTCCAAAGCCCACAAGTCAGTGCCACCCTTTCAAAGCCTACAAG
1 CCAC--AAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
*
190552 TCAATGGCACCCTTTC-AAAGTC
64 TCAGTGGCACCC-TTCAAAAG-C
190574 CACACAAGTCAGTGGCAACTCCTTTCAAAGCCCACA
1 C-CACAAGTCAGTGGC-A-TCCTTTCAAAGCCCACA
190610 CAAGTTAATG
Statistics
Matches: 459, Mismatches: 69, Indels: 21
0.84 0.13 0.04
Matches are distributed among these distances:
81 26 0.06
82 115 0.25
83 37 0.08
84 33 0.07
85 149 0.32
86 76 0.17
87 5 0.01
88 18 0.04
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.24
Consensus pattern (84 bp):
CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTC
AGTGGCACCCTTCAAAAGC
Found at i:190347 original size:113 final size:111
Alignment explanation
Indices: 190215--190609 Score: 470
Period size: 113 Copynumber: 3.5 Consensus size: 111
190205 CCACTACTCC
* * *
190215 ATGGCACCCTTTTAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCC
1 ATGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
190280 TTTCAAAGCCCACAACTTAGTGGCATCTCTTCAAAAGACCACAAGTCA
66 TTTCAAAGCCCACAAATCAGTGGCA-CCCTTCAAAAG-CCACAAGTCA
* * * *
190328 GTGGCATCCTTTCAAAGCCCGCAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAT-C
1 ATGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
* *
190392 TCTTCAAAAGACCACAAATCAGTGGCACCCTTTAAAAGTCCACAAGTCA
66 T-TTC-AAAGCCCACAAATCAGTGGCACCCTTCAAAAG-CCACAAGTCA
* * * * * *
190441 ATGGCACCCTTTCAAAGCCCATAAATCAGTGGCACCCTTTAAAAGCCCACATAAATCAGTGGCAC
1 ATGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCAC--AAGTCAGTGGCAT
* * *
190506 CCTTCCAAAGCCCACAAGTCAGTGCCACCCTTTC-AAAGCCTACAAGTCA
64 CCTTTCAAAGCCCACAAATCAGTGGCACCC-TTCAAAAGCC-ACAAGTCA
190555 ATGGCACCCTTTCAAAGTCCACACAAGTCAGTGGCAACTCCTTTCAAAGCCCACA
1 ATGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGC-A-TCCTTTCAAAGCCCACA
190610 CAAGTTAATG
Statistics
Matches: 241, Mismatches: 30, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
112 2 0.01
113 124 0.51
114 68 0.28
115 17 0.07
116 15 0.06
117 1 0.00
118 14 0.06
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (111 bp):
ATGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
TTTCAAAGCCCACAAATCAGTGGCACCCTTCAAAAGCCACAAGTCA
Found at i:190776 original size:45 final size:46
Alignment explanation
Indices: 190709--190828 Score: 127
Period size: 49 Copynumber: 2.6 Consensus size: 46
190699 TCCGATATCG
* * *
190709 TTGGCATTGAATCAGCATATTGGCACCTTT-ATTAGCCCAATGTCA
1 TTGGCCTTGAATTAGCACATTGGCACCTTTCATTAGCCCAATGTCA
* * *
190754 TTGGCCTTGAATTAGCACATTGGTCTACTTTTCCCTTAGCCCAATGTCG
1 TTGGCCTTGAATTAGCACATTGG-C-ACCTTT-CATTAGCCCAATGTCA
*
190803 CTGGCCTTGAATT-GCCACATTGGCAC
1 TTGGCCTTGAATTAG-CACATTGGCAC
190829 TCCTCTCATC
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
45 20 0.32
46 1 0.02
47 7 0.11
48 2 0.03
49 33 0.52
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (46 bp):
TTGGCCTTGAATTAGCACATTGGCACCTTTCATTAGCCCAATGTCA
Found at i:193804 original size:97 final size:97
Alignment explanation
Indices: 193642--193878 Score: 296
Period size: 97 Copynumber: 2.4 Consensus size: 97
193632 TTATTTATCA
* * * * * * * *
193642 GGGATACTCCAACCCTATTCTTCCGAGGGGATACTCTAACCCTGCTTTTGAACACATCAAAGTTT
1 GGGACACTCCAACCCCATTCCTCTGAGGAGATACTCCAACCCCGCTTTTAAACACATCAAAGTTT
* *
193707 AAATCTTATTCTCACTTAAGTTGTCATTATCG
66 AAATCTTATTCTCACTTAAATTGTCATCATCG
* * ** *
193739 GGGACACTTCAACCCCATTTCTCTGAGGAGATACTCCAACCCCGCTTTTAAATGCATCAATGTTT
1 GGGACACTCCAACCCCATTCCTCTGAGGAGATACTCCAACCCCGCTTTTAAACACATCAAAGTTT
* *
193804 AAATTTTATTCTCACTTAAATTGTTATCATCG
66 AAATCTTATTCTCACTTAAATTGTCATCATCG
*
193836 GGGACACTCCAACCCCATTCCTCTGA-GAGAATATTCCAACCCC
1 GGGACACTCCAACCCCATTCCTCTGAGGAG-ATACTCCAACCCC
193879 ATTTTTCAAT
Statistics
Matches: 119, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
96 3 0.03
97 116 0.97
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (97 bp):
GGGACACTCCAACCCCATTCCTCTGAGGAGATACTCCAACCCCGCTTTTAAACACATCAAAGTTT
AAATCTTATTCTCACTTAAATTGTCATCATCG
Found at i:198741 original size:13 final size:13
Alignment explanation
Indices: 198723--198747 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
198713 ATGTTGCACA
198723 GTATCGATACATT
1 GTATCGATACATT
198736 GTATCGATACAT
1 GTATCGATACAT
198748 GATCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:198765 original size:33 final size:33
Alignment explanation
Indices: 198700--198765 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
198690 TACACATTTA
* *
198700 ATTGTATCGATACATGTTGCACAGTATCGATAC
1 ATTGTATCGATACATGATGCAAAGTATCGATAC
*
198733 ATTGTATCGATACATGAT-CAAATGTATTGATAC
1 ATTGTATCGATACATGATGCAAA-GTATCGATAC
198766 TTGAAAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACATGATGCAAAGTATCGATAC
Found at i:198857 original size:13 final size:13
Alignment explanation
Indices: 198839--198863 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
198829 ACACACAGTA
198839 TGTATCGATACAT
1 TGTATCGATACAT
198852 TGTATCGATACA
1 TGTATCGATACA
198864 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:198860 original size:32 final size:33
Alignment explanation
Indices: 198819--198886 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
198809 GTAGCCAAAC
**
198819 TTGTATCGATACA-CACAGTATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
*
198851 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
198884 TTG
1 TTG
198887 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:200477 original size:9 final size:9
Alignment explanation
Indices: 200463--200493 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
200453 CATCAAGGAC
200463 GATGAAGAT
1 GATGAAGAT
200472 GATGAAGAT
1 GATGAAGAT
*
200481 GATGATGAT
1 GATGAAGAT
200490 GATG
1 GATG
200494 CTGACTCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.35, T:0.26
Consensus pattern (9 bp):
GATGAAGAT
Found at i:205057 original size:13 final size:13
Alignment explanation
Indices: 205038--205076 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
205028 ACAGCATTCT
205038 CTGTATCGATACA
1 CTGTATCGATACA
*
205051 TTGTATCGATACA
1 CTGTATCGATACA
205064 CTGTATCGATACA
1 CTGTATCGATACA
205077 AGGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:205251 original size:22 final size:21
Alignment explanation
Indices: 205208--205248 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
205198 CAAAATTCTT
205208 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAATACATC
205230 GTTTTTCA-TCAAAAT-CATC
1 GTTTTTCACTCAAAATACATC
205249 ATCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (21 bp):
GTTTTTCACTCAAAATACATC
Found at i:207498 original size:20 final size:21
Alignment explanation
Indices: 207473--207523 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
207463 ATTGATACAT
**
207473 TGTATCGATACATGACCAA-A
1 TGTATCGATACATGAAAAAGA
*
207493 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
207514 TGTATCGATA
1 TGTATCGATA
207524 TAGGTCATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:207503 original size:33 final size:33
Alignment explanation
Indices: 207438--207503 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
207428 TACACATTTA
** * *
207438 ATTGTATCGATACATGTTGCACAGTATTGATAC
1 ATTGTATCGATACATGTACCAAAGTATCGATAC
207471 ATTGTATCGATACATG-ACCAAATGTATCGATAC
1 ATTGTATCGATACATGTACCAAA-GTATCGATAC
207504 TTGAAAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACATGTACCAAAGTATCGATAC
Found at i:209927 original size:30 final size:31
Alignment explanation
Indices: 209891--209948 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
209881 AACCTTCATA
209891 AATAGTGC-ACTTGGCATAGCATTCCTTAGC
1 AATAGTGCTACTTGGCATAGCATTCCTTAGC
209921 AATAGTGCTACTTGGCATAGCATTCCTT
1 AATAGTGCTACTTGGCATAGCATTCCTT
209949 GGCAGCAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (31 bp):
AATAGTGCTACTTGGCATAGCATTCCTTAGC
Found at i:209949 original size:15 final size:15
Alignment explanation
Indices: 209900--209952 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
209890 AAATAGTGCA
209900 CTTGGCATAGCATTC
1 CTTGGCATAGCATTC
* *** *
209915 CTTAGCAATAGTGCTA
1 CTTGGC-ATAGCATTC
209931 CTTGGCATAGCATTC
1 CTTGGCATAGCATTC
209946 CTTGGCA
1 CTTGGCA
209953 GCAACACTAC
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
15 17 0.63
16 10 0.37
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (15 bp):
CTTGGCATAGCATTC
Found at i:215593 original size:25 final size:25
Alignment explanation
Indices: 215560--215617 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
215550 CTATATTAAA
*
215560 ATTA-TAAAGAGTTAA-GAAAAAAT
1 ATTATTAAAGAGTTAATAAAAAAAT
*
215583 ATTAATTAAAGATTTAATAAAAAAAT
1 ATT-ATTAAAGAGTTAATAAAAAAAT
215609 ATTATTAAA
1 ATTATTAAA
215618 ATTTGAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 3 0.10
24 1 0.03
25 16 0.53
26 10 0.33
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (25 bp):
ATTATTAAAGAGTTAATAAAAAAAT
Found at i:216714 original size:6 final size:6
Alignment explanation
Indices: 216703--216728 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
216693 GTAGATCATA
216703 AAGATG AAGATG AAGATG AAGATG AA
1 AAGATG AAGATG AAGATG AAGATG AA
216729 TGTTTCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.31, T:0.15
Consensus pattern (6 bp):
AAGATG
Found at i:217065 original size:2 final size:2
Alignment explanation
Indices: 217058--217091 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
217048 ATTTGCAGTC
*
217058 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
217092 CACCAATAAT
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:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:220522 original size:35 final size:35
Alignment explanation
Indices: 220455--220569 Score: 117
Period size: 36 Copynumber: 3.3 Consensus size: 35
220445 TGGAAGTTTG
* * *
220455 TGAAACATCCTCAAAAGAGGCTTTAAAAGTTTTTAA
1 TGAAACATCCT-TAAAGAAGCTTTGAAAGTTTTTAA
* **
220491 TGAAACATCCTTAAAGAAGCTTTG-AAGGTTTTGC
1 TGAAACATCCTTAAAGAAGCTTTGAAAGTTTTTAA
*
220525 TGAAATATCCTTAAGAGAAGGC-TTGAAAGTTTTTAA
1 TGAAACATCCTTAA-AGAA-GCTTTGAAAGTTTTTAA
*
220561 TAAAACATC
1 TGAAACATC
220570 TTCTAGAGGA
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
34 20 0.31
35 17 0.27
36 27 0.42
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (35 bp):
TGAAACATCCTTAAAGAAGCTTTGAAAGTTTTTAA
Found at i:220535 original size:34 final size:35
Alignment explanation
Indices: 220451--220557 Score: 96
Period size: 35 Copynumber: 3.1 Consensus size: 35
220441 TCTTTGGAAG
* * *
220451 TTTG-TGAAACATCCTCAAAAG-AGGCTTTAAAAGTT
1 TTTGCTGAAACATCCTTAAGAGAAGGC-TTGAAAG-T
** *
220486 TTTAATGAAACATCCTTAA-AGAA-GCTTTGAAGGT
1 TTTGCTGAAACATCCTTAAGAGAAGGC-TTGAAAGT
*
220520 TTTGCTGAAATATCCTTAAGAGAAGGCTTGAAAGT
1 TTTGCTGAAACATCCTTAAGAGAAGGCTTGAAAGT
220555 TTT
1 TTT
220558 TAATAAAACA
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
34 17 0.28
35 27 0.45
36 16 0.27
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.34
Consensus pattern (35 bp):
TTTGCTGAAACATCCTTAAGAGAAGGCTTGAAAGT
Found at i:220972 original size:16 final size:16
Alignment explanation
Indices: 220953--220988 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
220943 GGATGTAGAA
220953 GAGTGCAATTGCACGT
1 GAGTGCAATTGCACGT
220969 GAGTGCAATTGCACGT
1 GAGTGCAATTGCACGT
220985 GAGT
1 GAGT
220989 ACAAATGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (16 bp):
GAGTGCAATTGCACGT
Found at i:221207 original size:16 final size:16
Alignment explanation
Indices: 221188--221236 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
221178 AAAGCACATA
221188 AATGAGAATGCACGTG
1 AATGAGAATGCACGTG
*
221204 AATGTA-AATGCTCGTG
1 AATG-AGAATGCACGTG
*
221220 AATGAGAAAGCACGTG
1 AATGAGAATGCACGTG
221236 A
1 A
221237 GTGCCAATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 1 0.04
16 26 0.93
17 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.29, T:0.20
Consensus pattern (16 bp):
AATGAGAATGCACGTG
Found at i:222692 original size:14 final size:15
Alignment explanation
Indices: 222669--222713 Score: 74
Period size: 14 Copynumber: 3.1 Consensus size: 15
222659 TTTTTATTGA
*
222669 TTTTGCTTTTGCTTT
1 TTTTTCTTTTGCTTT
222684 TTTTT-TTTTGCTTT
1 TTTTTCTTTTGCTTT
222698 TTTTTCTTTTGCTTT
1 TTTTTCTTTTGCTTT
222713 T
1 T
222714 GATTTTTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 14 0.50
15 14 0.50
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.80
Consensus pattern (15 bp):
TTTTTCTTTTGCTTT
Found at i:224553 original size:79 final size:79
Alignment explanation
Indices: 224338--224561 Score: 229
Period size: 80 Copynumber: 2.8 Consensus size: 79
224328 GTGAAAATTT
* * * * * * *
224338 GATATTTTTAAAATAGAACCGCGATTGGAGTATCCTCTCAGAAATAACGT-GGTTGAAGTATCTC
1 GATATTTTAAAAATAAAACCGAGGTTGGAGTATCCCCTCAGAAATAAC-TAGGTTGGAGTATCCC
*
224402 CGATGATGAAAAATC
65 CGATGATAAAAAATC
* * * * * *
224417 AATATTTTAAAAAAGAAAACC-AGGGTTGGAATATTCCCTCAAAAATAACGAGGTTGGAGTATCC
1 GATATTTT-AAAAATAAAACCGA-GGTTGGAGTATCCCCTCAGAAATAACTAGGTTGGAGTATCC
*
224481 CCGATGGTAAAAAATC
64 CCGATGATAAAAAATC
* * *
224497 GATATTTTGAAAATAAAACCGAGGTTGGAGTATCCCCTTAGAAATAA-TAGGATTGGAGTACCCC
1 GATATTTTAAAAATAAAACCGAGGTTGGAGTATCCCCTCAGAAATAACTAGG-TTGGAGTATCCC
224561 C
65 C
224562 TCGAAAATAA
Statistics
Matches: 116, Mismatches: 24, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
78 3 0.03
79 50 0.43
80 63 0.54
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (79 bp):
GATATTTTAAAAATAAAACCGAGGTTGGAGTATCCCCTCAGAAATAACTAGGTTGGAGTATCCCC
GATGATAAAAAATC
Found at i:224554 original size:28 final size:29
Alignment explanation
Indices: 224521--224589 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
224511 AAAACCGAGG
* *
224521 TTGGAGTATCCCCTTAG-AAATAATAGGA
1 TTGGAGTATCCCCCTAGAAAATAACAGGA
* *
224549 TTGGAGTA-CCCCCTCGAAAATAACAGGG
1 TTGGAGTATCCCCCTAGAAAATAACAGGA
*
224577 TTGGAGTGTCCCC
1 TTGGAGTATCCCC
224590 GATAGTGAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 6 0.18
28 24 0.71
29 4 0.12
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (29 bp):
TTGGAGTATCCCCCTAGAAAATAACAGGA
Found at i:243041 original size:29 final size:29
Alignment explanation
Indices: 243022--243089 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
243012 TTTTGGAAGT
243022 TAAGGGGCTAA-AATGCAATTTTAAAAAGC
1 TAAGGGGCTAACAA-GCAATTTTAAAAAGC
* * *
243051 TAAGGGGCTAACAAGCAATTCTGAAAAGT
1 TAAGGGGCTAACAAGCAATTTTAAAAAGC
*
243080 TAAGAGGCTA
1 TAAGGGGCTA
243090 TACTGTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 32 0.94
30 2 0.06
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.22
Consensus pattern (29 bp):
TAAGGGGCTAACAAGCAATTTTAAAAAGC
Found at i:245985 original size:14 final size:12
Alignment explanation
Indices: 245960--245999 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
245950 TTTCTCATTC
245960 ATCATAAATATT
1 ATCATAAATATT
245972 AATCATACAATATT
1 -ATCATA-AATATT
*
245986 ATCATATATATT
1 ATCATAAATATT
245998 AT
1 AT
246000 ATCTACTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 7 0.28
13 12 0.48
14 6 0.24
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (12 bp):
ATCATAAATATT
Found at i:246541 original size:2 final size:2
Alignment explanation
Indices: 246534--246566 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
246524 CATTGTTAGC
246534 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
246567 TCGTATAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:247127 original size:165 final size:164
Alignment explanation
Indices: 246850--247180 Score: 554
Period size: 165 Copynumber: 2.0 Consensus size: 164
246840 TGGATTTGAC
*
246850 TAAAAACCAACGAAGAGATGACGTGGACTAATCCCTCGCCAGAGCATAAGCATGACACTTTTGGT
1 TAAAAACCAACGAAGAGATGACGTGGACTAATCCCTCCCCAGAGCATAAGCATGACACTTTTGGT
*
246915 AACTCCATGCTGGTAACAACTCCATTTTACGGATCTAACTTGCCACGTTGCCCACCCAAACTACA
66 AACTCCATGCTCGTAACAACTCCATTTTACGGATCTAACTTGCCACGTTGCCCACCCAAACTACA
246980 CATTAGCCACACATTTCAAAGGCATAACTCTATT
131 CATTAGCCACACATTTCAAAGGCATAACTCTATT
*
247014 TAAAAGACCAACGAAGAGATGACGTGGACTAATCCCTCCCCAGAGCATAAGTATGACACTTTTGG
1 TAAAA-ACCAACGAAGAGATGACGTGGACTAATCCCTCCCCAGAGCATAAGCATGACACTTTTGG
* * * *
247079 TAACTTCATGCTCGTAACAACTCCATTTTACGGATCTCACTTGCCACGTTGCCCACCCAGAGTAC
65 TAACTCCATGCTCGTAACAACTCCATTTTACGGATCTAACTTGCCACGTTGCCCACCCAAACTAC
* * * *
247144 ACATTAGCCACACGTTTCACAGGTATAAGTCTATT
130 ACATTAGCCACACATTTCAAAGGCATAACTCTATT
247179 TA
1 TA
247181 TTCTATTTAA
Statistics
Matches: 155, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
164 5 0.03
165 150 0.97
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (164 bp):
TAAAAACCAACGAAGAGATGACGTGGACTAATCCCTCCCCAGAGCATAAGCATGACACTTTTGGT
AACTCCATGCTCGTAACAACTCCATTTTACGGATCTAACTTGCCACGTTGCCCACCCAAACTACA
CATTAGCCACACATTTCAAAGGCATAACTCTATT
Found at i:253306 original size:14 final size:15
Alignment explanation
Indices: 253282--253321 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
253272 ATAATTTATT
*
253282 TAATTATTATTTAAAA
1 TAATTATT-TATAAAA
253298 TAAATTATTTATAAAA
1 T-AATTATTTATAAAA
253314 TAATTATT
1 TAATTATT
253322 GTTTATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 7 0.32
16 8 0.36
17 7 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATTTATAAAA
Found at i:254252 original size:43 final size:45
Alignment explanation
Indices: 254165--254252 Score: 103
Period size: 43 Copynumber: 2.0 Consensus size: 45
254155 AAAAAAAAAT
* *
254165 TTAAATATAAAATCTTAAATTTATTAGATGTATTTTTTAAATTAA
1 TTAAATATAAAATCTTAAATTTATTAGATATATTTTATAAATTAA
*
254210 TTAAAT-T-AAAT-TTAAATTTATATA-ATAATATTTTATATATTAA
1 TTAAATATAAAATCTTAAATTTAT-TAGAT-ATATTTTATAAATTAA
254253 AAATAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
42 12 0.32
43 19 0.50
44 1 0.03
45 6 0.16
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (45 bp):
TTAAATATAAAATCTTAAATTTATTAGATATATTTTATAAATTAA
Found at i:255121 original size:18 final size:19
Alignment explanation
Indices: 255091--255138 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
255081 TCATTAGATT
255091 ATTC-ATTTGAAAT-TATAA
1 ATTCAATTT-AAATATATAA
*
255109 ATTCAATTTAAATATTTAA
1 ATTCAATTTAAATATATAA
*
255128 ATTGAATTTAA
1 ATTCAATTTAA
255139 GATAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (19 bp):
ATTCAATTTAAATATATAA
Found at i:260195 original size:20 final size:19
Alignment explanation
Indices: 260150--260199 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
260140 CGACAGATAT
*
260150 ATGTTCAATAAATAATTTA
1 ATGTTAAATAAATAATTTA
*
260169 ATATTAAATAAATAATTGTA
1 ATGTTAAATAAATAATT-TA
260189 ATGTTAAATAA
1 ATGTTAAATAA
260200 GTATTAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (19 bp):
ATGTTAAATAAATAATTTA
Found at i:260214 original size:16 final size:16
Alignment explanation
Indices: 260195--260237 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
260185 TGTAATGTTA
*
260195 AATAAGTATTAAATAT
1 AATAAATATTAAATAT
* *
260211 AATAAATATTTAATAAA
1 AATAAATATTAAAT-AT
260228 AATAAATATT
1 AATAAATATT
260238 TAATTAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
AATAAATATTAAATAT
Found at i:260231 original size:17 final size:17
Alignment explanation
Indices: 260156--260241 Score: 66
Period size: 17 Copynumber: 4.8 Consensus size: 17
260146 ATATATGTTC
*
260156 AATAAATAATTTAATATTA
1 AATAAAT-ATTTAATA-AA
**
260175 AATAAATAATTGTAATGTTA
1 AATAAAT-ATT-TAAT-AAA
* * *
260195 AATAAGTATTAAAT-AT
1 AATAAATATTTAATAAA
260211 AATAAATATTTAATAAA
1 AATAAATATTTAATAAA
260228 AATAAATATTTAAT
1 AATAAATATTTAAT
260242 TAAATGATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
16 12 0.21
17 15 0.27
18 3 0.05
19 14 0.25
20 12 0.21
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
AATAAATATTTAATAAA
Found at i:276060 original size:11 final size:11
Alignment explanation
Indices: 276046--276116 Score: 67
Period size: 11 Copynumber: 6.4 Consensus size: 11
276036 AAAAAATTTT
276046 AAAAAAAC--A
1 AAAAAAACAAA
276055 AAAAAAA-AAA
1 AAAAAAACAAA
* *
276065 CAAAAAACCAA
1 AAAAAAACAAA
276076 AAAAAAACAAA
1 AAAAAAACAAA
276087 AAAAAAACCAAGGA
1 AAAAAAA-CAA--A
276101 AAAAATAACAAA
1 AAAAA-AACAAA
276113 AAAA
1 AAAA
276117 TAAAAAAGAG
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
9 7 0.14
10 7 0.14
11 18 0.35
12 8 0.16
14 9 0.18
15 2 0.04
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:276061 original size:12 final size:12
Alignment explanation
Indices: 276047--276121 Score: 62
Period size: 12 Copynumber: 5.9 Consensus size: 12
276037 AAAAATTTTA
*
276047 AAAAAACAAAAAA
1 AAAAAA-AAAAAC
276060 AAAAACAAAAAAC
1 AAAAA-AAAAAAC
*
276073 -CAAAAAAAAAC
1 AAAAAAAAAAAC
*
276084 AAAAAAAAAACC
1 AAAAAAAAAAAC
*
276096 AAGGAAAAAATAAC
1 AA--AAAAAAAAAC
276110 AAAAAAATAAAA
1 AAAAAAA-AAAA
276122 AAGAGTCCAG
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
11 7 0.14
12 19 0.38
13 13 0.26
14 11 0.22
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.03
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:276105 original size:1 final size:1
Alignment explanation
Indices: 276046--276093 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
276036 AAAAAATTTT
* * ** *
276046 AAAAAAACAAAAAAAAAAACAAAAAACCAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
276094 CCAAGGAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:276119 original size:11 final size:10
Alignment explanation
Indices: 276046--276092 Score: 69
Period size: 10 Copynumber: 4.7 Consensus size: 10
276036 AAAAAATTTT
276046 AAAAAAACAA
1 AAAAAAACAA
276056 AAAAAAA-AA
1 AAAAAAACAA
*
276065 CAAAAAACCAA
1 -AAAAAAACAA
276076 AAAAAAACAA
1 AAAAAAACAA
276086 AAAAAAA
1 AAAAAAA
276093 ACCAAGGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 2 0.06
10 29 0.88
11 2 0.06
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:277404 original size:28 final size:28
Alignment explanation
Indices: 277331--278138 Score: 819
Period size: 28 Copynumber: 28.0 Consensus size: 28
277321 CTAGAACGTT
277331 CATCTCTTT-AAAGCCCACAAGTCAGTGG
1 CATCT-TTTCAAAGCCCACAAGTCAGTGG
* *
277359 CACTATTTTCAAAGCCCATAAGTCAGTGG
1 CA-TCTTTTCAAAGCCCACAAGTCAGTGG
* *
277388 CATCTTTTCAAAGCCCATAAGTTAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* * *
277416 CAACCTTTCAAAGCCCACAAGTCAATGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* * *
277444 TACCATTTTCAAAACCCACAAGTCAGTGG
1 CATC-TTTTCAAAGCCCACAAGTCAGTGG
* * *
277473 CATCCTTTCAAAGCCCACGAGTCGGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
277501 CAACTCTTTTCAAAGCCCACAAGTCAGTGG
1 C-A-TCTTTTCAAAGCCCACAAGTCAGTGG
* * * * *
277531 CACCCTTTCAAAGCCCATAAGTTAATGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* * * *
277559 TACCCTTTCAAAGCTCACAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
*
277587 CAACTCTTTTTAAAGCCCACAAGTCAGTGG
1 C-A-TCTTTTCAAAGCCCACAAGTCAGTGG
* *
277617 CACCCTTTTCAAAGCCCATAAGTCAGTGG
1 CA-TCTTTTCAAAGCCCACAAGTCAGTGG
* *
277646 CATCCTTTCAAAGCCCATAAGTC-GATGG
1 CATCTTTTCAAAGCCCACAAGTCAG-TGG
* * * * *
277674 AAACTTTTTTCAAAGCTCACAAGTCATTGT
1 -CA-TCTTTTCAAAGCCCACAAGTCAGTGG
*
277704 CATCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* *
277732 CACCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
*
277760 CACTCTTTTCAAAGCCCACACGAGTCAATGG
1 CA-TCTTTTCAAAGCCCACA--AGTCAGTGG
*
277791 CAACTATTTTCAAAGCCCACAAGTCAGTGG
1 C-A-TCTTTTCAAAGCCCACAAGTCAGTGG
* *
277821 CATCCTTTCAAAGCCCCCAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* * * *
277849 TACCTTTTCAAAGCCCACAAGTTAATGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* *
277877 CACCATTTTCAAAGCCCACAAGTCAATGG
1 CATC-TTTTCAAAGCCCACAAGTCAGTGG
* * *
277906 CATCCTTTCAAAGCCCACGAGTCGGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
277934 CAACTCTTTTCAAAGCCCACAAGTCAGTGG
1 C-A-TCTTTTCAAAGCCCACAAGTCAGTGG
* * * *
277964 CATCCTTTCAAAGCCTACAAGTTAATGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* * *
277992 CACCCTTTCAAAGCCCACAAGTTAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* * *
278020 CACCCTTTCAAAGCCCACAAGTCAGTAG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* *
278048 CACCTTTTCAAAGCCCACAAGTTAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
278076 CACTCTTTTCAAAGCCCACACGAGTCAGTGG
1 CA-TCTTTTCAAAGCCCACA--AGTCAGTGG
*
278107 CAACTCTTTTCAAAGCCCGCACAAGTTAGTGG
1 C-A-TCTTTTCAAAG-CC-CACAAGTCAGTGG
278139 TACCTTTTTT
Statistics
Matches: 660, Mismatches: 96, Indels: 44
0.82 0.12 0.05
Matches are distributed among these distances:
27 1 0.00
28 360 0.55
29 137 0.21
30 99 0.15
31 18 0.03
32 39 0.06
33 2 0.00
34 4 0.01
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (28 bp):
CATCTTTTCAAAGCCCACAAGTCAGTGG
Found at i:277529 original size:143 final size:141
Alignment explanation
Indices: 277331--278138 Score: 942
Period size: 143 Copynumber: 5.6 Consensus size: 141
277321 CTAGAACGTT
* * *
277331 CATCTCTTT-AAAGCCCACAAGTCAGTGGCACTATTTTCAAAGCCCATAAGTCAGTGGCATCTTT
1 CATC-CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTT
* * * *
277395 TCAAAGCCCATAAGTTAGTGGCAACCTTTCAAAGCCCACAAGTCAATGGTACCATTTTCAAAACC
65 TCAAAGCCCACAAGTTAGTGGCAACCTTTCAAAGCCCACAAGTCAGTGGCACC-TTTTCAAAGCC
277460 CACAAGTCAGTGG
129 CACAAGTCAGTGG
* * *
277473 CATCCTTTCAAAGCCCACGAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTT
1 CATCCTTTCAAAGCCCACAAGTCAGTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTT
* * * * * *
277538 TCAAAGCCCATAAGTTAATGGTACCCTTTCAAAGCTCACAAGTCAGTGGCAACTCTTTTTAAAGC
65 TCAAAGCCCACAAGTTAGTGGCAACCTTTCAAAGCCCACAAGTCAGTGGC-AC-CTTTTCAAAGC
277603 CCACAAGTCAGTGG
128 CCACAAGTCAGTGG
* * * * * *
277617 CACCCTTTTCAAAGCCCATAAGTCAGTGGCA-TCCTTTCAAAGCCCATAAGTC-GATGGAAACTT
1 CATCC-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAG-TGG-CA-TC
* * * * * * *
277680 TTTTCAAAGCTCACAAGTCATTGTCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
62 CTTTCAAAGCCCACAAGTTAGTGGCAACCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAG
277745 CCCACAAGTCAGTGG
127 CCCACAAGTCAGTGG
* * *
277760 CACTCTTTTCAAAGCCCACACGAGTCAATGGCAACTATTTTCAAAGCCCACAAGTCAGTGGCATC
1 CA-TCCTTTCAAAGCCCACA--AGTCAGTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCATC
* * * * *
277825 CTTTCAAAGCCCCCAAGTCAGTGG-TACCTTTTCAAAGCCCACAAGTTAATGGCACCATTTTCAA
62 CTTTCAAAGCCCACAAGTTAGTGGCAACC-TTTCAAAGCCCACAAGTCAGTGGCACC-TTTTCAA
*
277889 AGCCCACAAGTCAATGG
125 AGCCCACAAGTCAGTGG
* *
277906 CATCCTTTCAAAGCCCACGAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTT
1 CATCCTTTCAAAGCCCACAAGTCAGTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTT
* * * * *
277971 TCAAAGCCTACAAGTTAATGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCC
65 TCAAAGCCCACAAGTTAGTGGCAACCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCC
*
278036 ACAAGTCAGTAG
130 ACAAGTCAGTGG
*
278048 CA-CCTTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACACGAGTCAGTGGCAACT
1 CATCC-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA--AGTCAGTGGC-A-T
*
278112 CTTTTCAAAGCCCGCACAAGTTAGTGG
61 CCTTTCAAAG-CC-CACAAGTTAGTGG
278139 TACCTTTTTT
Statistics
Matches: 567, Mismatches: 75, Indels: 43
0.83 0.11 0.06
Matches are distributed among these distances:
141 25 0.04
142 67 0.12
143 231 0.41
144 38 0.07
145 145 0.26
146 28 0.05
147 32 0.06
148 1 0.00
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (141 bp):
CATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTT
CAAAGCCCACAAGTTAGTGGCAACCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCA
CAAGTCAGTGG
Found at i:279101 original size:20 final size:20
Alignment explanation
Indices: 279044--279101 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
279034 TGAATTTTTC
*
279044 AATGTATCGATACATGT-ATG
1 AATGTATCGATACAT-TCTTG
*
279064 AATGTATCGATACATTCTTT
1 AATGTATCGATACATTCTTG
279084 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
279102 GTCTTTTTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 1 0.03
20 34 0.97
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTCTTG
Found at i:282515 original size:13 final size:13
Alignment explanation
Indices: 282497--282521 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
282487 CACTTAAAAT
282497 TTAATTTAATTAA
1 TTAATTTAATTAA
282510 TTAATTTAATTA
1 TTAATTTAATTA
282522 TTTTTATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATTTAATTAA
Found at i:283666 original size:15 final size:16
Alignment explanation
Indices: 283618--283667 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
283608 TAAAATTTTG
*
283618 AATATAACATTTACATT
1 AATATAAAATTTA-ATT
283635 AATATAAAATATATAATT
1 AATATAAAAT-T-TAATT
283653 -ATATAAAATTTAATT
1 AATATAAAATTTAATT
283668 TTTAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 5 0.17
16 1 0.03
17 18 0.60
18 4 0.13
19 2 0.07
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
AATATAAAATTTAATT
Found at i:283679 original size:34 final size:37
Alignment explanation
Indices: 283641--283719 Score: 96
Period size: 34 Copynumber: 2.3 Consensus size: 37
283631 CATTAATATA
*
283641 AAATATATAATT-ATA-TAAAATTTAATT-TTTAAAT
1 AAATATATAATTAAAATTAAAATTTAATTATTTAAAT
*
283675 AAATA-AT-TTTAAAATTAAAATTTAATTATTTAAAT
1 AAATATATAATTAAAATTAAAATTTAATTATTTAAAT
*
283710 AATTATATAA
1 AAATATATAA
283720 AATAAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
32 2 0.06
33 4 0.11
34 17 0.47
35 11 0.31
36 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (37 bp):
AAATATATAATTAAAATTAAAATTTAATTATTTAAAT
Found at i:283725 original size:17 final size:17
Alignment explanation
Indices: 283636--283742 Score: 59
Period size: 17 Copynumber: 6.7 Consensus size: 17
283626 ATTTACATTA
*
283636 ATATAAAATATATAATT
1 ATATAAAATAAATAATT
*
283653 ATATAAAAT--TTAATT
1 ATATAAAATAAATAATT
*
283668 -T-TTAAATAAATAATT
1 ATATAAAATAAATAATT
*
283683 -T-TAAAATTAA-AATT
1 ATATAAAATAAATAATT
* **
283697 -TAATTATTTAAATAATT
1 AT-ATAAAATAAATAATT
**
283714 ATATAAAATAAATAAAA
1 ATATAAAATAAATAATT
*
283731 ATATAATATAAA
1 ATATAAAATAAA
283743 AATAACATAA
Statistics
Matches: 69, Mismatches: 15, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
13 5 0.07
14 6 0.09
15 18 0.26
16 5 0.07
17 34 0.49
18 1 0.01
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAAAATAAATAATT
Found at i:283747 original size:11 final size:11
Alignment explanation
Indices: 283706--283764 Score: 59
Period size: 11 Copynumber: 5.2 Consensus size: 11
283696 TTAATTATTT
283706 AAATAATTATATA
1 AAATAA-TATA-A
283719 AAATAA-ATAAA
1 AAATAATAT-AA
283730 AATATAATATAA
1 AA-ATAATATAA
*
283742 AAATAACATAA
1 AAATAATATAA
283753 AAATAAT-TAA
1 AAATAATATAA
283763 AA
1 AA
283765 TATGTTACGA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
10 5 0.12
11 19 0.46
12 9 0.22
13 8 0.20
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATAATATAA
Found at i:283752 original size:24 final size:25
Alignment explanation
Indices: 283708--283757 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
283698 AATTATTTAA
283708 ATAATTATATAAAATAAATAAAAAT
1 ATAATTATATAAAATAAATAAAAAT
283733 ATAA-TATA-AAAATAACATAAAAAT
1 ATAATTATATAAAATAA-ATAAAAAT
283757 A
1 A
283758 ATTAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 7 0.29
24 13 0.54
25 4 0.17
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (25 bp):
ATAATTATATAAAATAAATAAAAAT
Found at i:283758 original size:22 final size:22
Alignment explanation
Indices: 283706--283764 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
283696 TTAATTATTT
283706 AAATAATTATATAAAATAAATAAA
1 AAATAA-TATA-AAAATAAATAAA
283730 AATATAATATAAAAATAACAT-AA
1 AA-ATAATATAAAAATAA-ATAAA
283753 AAATAAT-TAAAA
1 AAATAATATAAAA
283765 TATGTTACGA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
21 5 0.15
22 5 0.15
23 11 0.33
24 8 0.24
25 4 0.12
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATAATATAAAAATAAATAAA
Found at i:283805 original size:27 final size:28
Alignment explanation
Indices: 283747--283805 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
283737 TATAAAAATA
*
283747 ACAT-AAAAATAATTAAAATATGTTACG
1 ACATAAAAAATAATAAAAATATGTTACG
*
283774 A-ATAAAAAATAATAAAAATATTTTAC-
1 ACATAAAAAATAATAAAAATATGTTACG
283800 ACATAA
1 ACATAA
283806 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.29
Consensus pattern (28 bp):
ACATAAAAAATAATAAAAATATGTTACG
Found at i:285316 original size:24 final size:24
Alignment explanation
Indices: 285267--285315 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
285257 GTATTTATAC
*
285267 ATATAAAAAAATTATAATTTAAAA
1 ATATAAAAAAATTAAAATTTAAAA
285291 ATATAAAAAAATTAAAATATTAAAA
1 ATATAAAAAAATTAAAAT-TTAAAA
285316 TTCAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (24 bp):
ATATAAAAAAATTAAAATTTAAAA
Found at i:285944 original size:14 final size:13
Alignment explanation
Indices: 285921--285967 Score: 53
Period size: 12 Copynumber: 3.6 Consensus size: 13
285911 TAAATTTTTT
*
285921 TATTTCTTAATATA
1 TATTTTTTAA-ATA
285935 TATTTTTTAAA-A
1 TATTTTTTAAATA
285947 TATTTTTTAAA-A
1 TATTTTTTAAATA
285959 TATGTTTTT
1 TAT-TTTTT
285968 CTTACAATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
12 16 0.52
13 6 0.19
14 9 0.29
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (13 bp):
TATTTTTTAAATA
Found at i:285951 original size:12 final size:12
Alignment explanation
Indices: 285934--285967 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
285924 TTCTTAATAT
285934 ATATTTTTTAAA
1 ATATTTTTTAAA
285946 ATATTTTTTAAA
1 ATATTTTTTAAA
285958 ATATGTTTTT
1 ATAT-TTTTT
285968 CTTACAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (12 bp):
ATATTTTTTAAA
Found at i:286805 original size:91 final size:92
Alignment explanation
Indices: 286647--286838 Score: 242
Period size: 91 Copynumber: 2.1 Consensus size: 92
286637 CTATTGCATG
* ** * * * *
286647 GATTGTAAATATCAAAATACAAATATTAGACTAATGCATGGATTGTATTTGAGAATCAAATTTCT
1 GATTGTAAATATCAAAATACAAAGATTAGACTAATGCATAAACTCTATTTGAAAATCAAATTCCT
286712 TTTGGTA-GAAAAAAAAAAAGTTGATT
66 TTTGGTAGGAAAAAAAAAAAGTTGATT
* * * * * *
286738 GATTGTAAATGTCACACTGCAAAGATTAGACTAATGCATAAACTCTATTTGAAAATTAGATTCCT
1 GATTGTAAATATCAAAATACAAAGATTAGACTAATGCATAAACTCTATTTGAAAATCAAATTCCT
* *
286803 TTTGGTAGGAAAGAAGAAAAGTTGATT
66 TTTGGTAGGAAAAAAAAAAAGTTGATT
286830 GATTGTAAA
1 GATTGTAAA
286839 ACTCGTACTT
Statistics
Matches: 85, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
91 59 0.69
92 26 0.31
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (92 bp):
GATTGTAAATATCAAAATACAAAGATTAGACTAATGCATAAACTCTATTTGAAAATCAAATTCCT
TTTGGTAGGAAAAAAAAAAAGTTGATT
Found at i:291717 original size:24 final size:20
Alignment explanation
Indices: 291676--291717 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
291666 AAATCCAAAT
291676 ATAAATTATAAAATAATAAA
1 ATAAATTATAAAATAATAAA
* *
291696 ATAAA-TATATAATAATTAA
1 ATAAATTATAAAATAATAAA
291715 ATA
1 ATA
291718 CATCTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATTATAAAATAATAAA
Found at i:291853 original size:31 final size:31
Alignment explanation
Indices: 291818--291908 Score: 131
Period size: 31 Copynumber: 3.1 Consensus size: 31
291808 TGCCTATCAC
291818 TATTATTTATAAAAAAATTAATAAAATTATT
1 TATTATTTATAAAAAAATTAATAAAATTATT
291849 TATTATTTATAAAAAAATTAAT-AAA--A-T
1 TATTATTTATAAAAAAATTAATAAAATTATT
*
291876 T-TTATTTATAAAAAAATTAA-AAATTTATT
1 TATTATTTATAAAAAAATTAATAAAATTATT
291905 TATT
1 TATT
291909 CATTACAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
26 21 0.39
27 2 0.04
28 2 0.04
29 2 0.04
30 5 0.09
31 22 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TATTATTTATAAAAAAATTAATAAAATTATT
Found at i:291868 original size:22 final size:22
Alignment explanation
Indices: 291840--291894 Score: 58
Period size: 26 Copynumber: 2.3 Consensus size: 22
291830 AAAAATTAAT
291840 AAAATTAT-TTATTATTTATAAA
1 AAAATTATATT-TTATTTATAAA
291862 AAAATTAATAAAATTTTATTTATAAA
1 AAAATT-AT---ATTTTATTTATAAA
291888 AAAATTA
1 AAAATTA
291895 AAAATTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
22 6 0.21
23 2 0.07
25 1 0.04
26 17 0.61
27 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAATTATATTTTATTTATAAA
Found at i:291896 original size:23 final size:25
Alignment explanation
Indices: 291851--291907 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
291841 AAATTATTTA
*
291851 TTATTTATAAAAAAATTAATAAAATT
1 TTATTTATAAAAAAATT-ATAAAAAT
291877 TTATTTATAAAAAAA-T-TAAAAAT
1 TTATTTATAAAAAAATTATAAAAAT
291900 TTATTTAT
1 TTATTTAT
291908 TCATTACAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 14 0.47
25 1 0.03
26 15 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TTATTTATAAAAAAATTATAAAAAT
Found at i:293490 original size:16 final size:16
Alignment explanation
Indices: 293450--293492 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
293440 AATTTGACAG
*
293450 GTTCAGATTCGGACTC
1 GTTCAGGTTCGGACTC
* * *
293466 ATTCGGGTTTGGACTC
1 GTTCAGGTTCGGACTC
293482 GTTCAGGTTCG
1 GTTCAGGTTCG
293493 AGTTTTTTTA
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.14, C:0.21, G:0.30, T:0.35
Consensus pattern (16 bp):
GTTCAGGTTCGGACTC
Found at i:293780 original size:18 final size:18
Alignment explanation
Indices: 293741--293780 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
293731 ATATTTATAT
*
293741 ATAAAATTAATTTGTTAT
1 ATAAAATTAATTTGTTAA
293759 ATAAAATTAAATTT-TTAA
1 ATAAAATT-AATTTGTTAA
293777 ATAA
1 ATAA
293781 TTTATTGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
ATAAAATTAATTTGTTAA
Found at i:294966 original size:16 final size:16
Alignment explanation
Indices: 294947--294991 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
294937 TTCTCTCGAA
294947 TTCGAATTCTTTT-AAG
1 TTCGAATT-TTTTCAAG
*
294963 TTCGGATTTTTTCAAG
1 TTCGAATTTTTTCAAG
*
294979 TTCAAATTTTTTC
1 TTCGAATTTTTTC
294992 GAATTCAGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.53
Consensus pattern (16 bp):
TTCGAATTTTTTCAAG
Found at i:296287 original size:20 final size:20
Alignment explanation
Indices: 296259--296301 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
296249 AATTTTAAAT
**
296259 AATTCATGATTATAATTGATA
1 AATTCATGACAATAATT-ATA
296280 AATT-ATGACAATAATTATA
1 AATTCATGACAATAATTATA
296299 AAT
1 AAT
296302 AATATCTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 10 0.50
21 4 0.20
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (20 bp):
AATTCATGACAATAATTATA
Found at i:296620 original size:30 final size:30
Alignment explanation
Indices: 296584--296648 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
296574 CGCGACAGGC
*
296584 AACGCGAGAGGGACCGCGACAGAGACCGAG
1 AACGCGAGAGGGACCGCGACAGAGACAGAG
* * * *
296614 AACGCGAGCGTGACCGCGACCGCGACAGAG
1 AACGCGAGAGGGACCGCGACAGAGACAGAG
296644 AACGC
1 AACGC
296649 AGACGCGACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.31, G:0.37, T:0.02
Consensus pattern (30 bp):
AACGCGAGAGGGACCGCGACAGAGACAGAG
Found at i:296703 original size:6 final size:6
Alignment explanation
Indices: 296692--296722 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
296682 GACCGAGAGC
*
296692 GAGACA GGGACA GAGACA GAGACA GAGACA G
1 GAGACA GAGACA GAGACA GAGACA GAGACA G
296723 GGAACGGACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.45, C:0.16, G:0.39, T:0.00
Consensus pattern (6 bp):
GAGACA
Found at i:296707 original size:12 final size:12
Alignment explanation
Indices: 296692--296725 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
296682 GACCGAGAGC
296692 GAGACAGGGACA
1 GAGACAGGGACA
*
296704 GAGACAGAGACA
1 GAGACAGGGACA
296716 GAGACAGGGA
1 GAGACAGGGA
296726 ACGGACGCGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.41, T:0.00
Consensus pattern (12 bp):
GAGACAGGGACA
Found at i:302307 original size:2 final size:2
Alignment explanation
Indices: 302302--302332 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
302292 CGTGTGTATG
302302 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
302333 TGTTGAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:303491 original size:14 final size:15
Alignment explanation
Indices: 303466--303496 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
303456 AAAAAATTTA
303466 AAAAATACAAAACTT
1 AAAAATACAAAACTT
303481 AAAAATA-AAAACTT
1 AAAAATACAAAACTT
303495 AA
1 AA
303497 GTGGTTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAAATACAAAACTT
Found at i:309118 original size:2 final size:2
Alignment explanation
Indices: 309106--309140 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
309096 CTTTTCTGTC
* *
309106 AT AT GT AT AT AT AT AT AT GT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
309141 GAGTAGGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:309125 original size:14 final size:14
Alignment explanation
Indices: 309106--309137 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
309096 CTTTTCTGTC
309106 ATATGTATATATAT
1 ATATGTATATATAT
309120 ATATGTATATATAT
1 ATATGTATATATAT
309134 ATAT
1 ATAT
309138 ATAGAGTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
ATATGTATATATAT
Found at i:309742 original size:9 final size:9
Alignment explanation
Indices: 309725--309759 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
309715 GGTCAGTTGT
309725 TGCTGGTGG
1 TGCTGGTGG
*
309734 TGGTGGTGG
1 TGCTGGTGG
*
309743 TGCTGCTGG
1 TGCTGGTGG
309752 TGCTGGTG
1 TGCTGGTG
309760 CTGGTAGGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.11, G:0.54, T:0.34
Consensus pattern (9 bp):
TGCTGGTGG
Found at i:311111 original size:25 final size:24
Alignment explanation
Indices: 311067--311114 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
311057 TATTATTAAC
311067 TTTAATTAATTATCAAATATATAT
1 TTTAATTAATTATCAAATATATAT
*
311091 TTTAATTTAATT-T-ATATATATAT
1 TTTAA-TTAATTATCAAATATATAT
311114 T
1 T
311115 GTTTATGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 10 0.45
24 6 0.27
25 6 0.27
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTAATTAATTATCAAATATATAT
Found at i:313597 original size:2 final size:2
Alignment explanation
Indices: 313590--313618 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
313580 GTGGAAAAAG
313590 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
313619 ATGAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:313891 original size:17 final size:17
Alignment explanation
Indices: 313858--313899 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
313848 GTTTATATAT
*
313858 ATTTTAATAATATTTAA
1 ATTTTTATAATATTTAA
313875 ATTTTTAT-ATATATTAA
1 ATTTTTATAATAT-TTAA
313892 ATATTTTA
1 AT-TTTTA
313900 ATTAATTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 13 0.59
18 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTTATAATATTTAA
Found at i:321408 original size:42 final size:42
Alignment explanation
Indices: 321352--321505 Score: 139
Period size: 42 Copynumber: 3.6 Consensus size: 42
321342 GAAAACGAAA
** *
321352 TGCGTCCTACTCTTTGGGGACAAAAGAAAGAGGAAAATAAAG
1 TGCGTCCTGTTCTTTGAGGACAAAAGAAAGAGGAAAATAAAG
* * * ** *
321394 TGCATCCTGTTCTTTGAAGACAAAAGAAAAAATAAGGGAATGAAG
1 TGCGTCCTGTTCTTTGAGGACAAAAGAAAGAGGAA---AATAAAG
* * * *
321439 TGTGTCTTGCTCTTTGAGGACAAAAGAGAGAGGAAAATAAAG
1 TGCGTCCTGTTCTTTGAGGACAAAAGAAAGAGGAAAATAAAG
*
321481 TACGTCCTGCTT-TTTGAGGACAAAA
1 TGCGTCCTG-TTCTTTGAGGACAAAA
321506 AGTGCCACCA
Statistics
Matches: 85, Mismatches: 23, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
42 52 0.61
43 1 0.01
45 32 0.38
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (42 bp):
TGCGTCCTGTTCTTTGAGGACAAAAGAAAGAGGAAAATAAAG
Found at i:321714 original size:62 final size:60
Alignment explanation
Indices: 321483--321741 Score: 311
Period size: 61 Copynumber: 4.3 Consensus size: 60
321473 AAATAAAGTA
*
321483 CGTCCTGCTTTTTGAGGAC-A-AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAAGAAAGG
1 CGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTG-AAAA-AAAGG
* * * *
321543 CGTCCTACTCTTTGATGACT-GGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAA-G
1 CGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTG-AAA-A-AAAGG
* * *
321604 CATCATGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGAAATAGG
1 CGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAA-AAA-AGG
*
321665 CGTCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT----AAAAGG
1 CGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAGG
321721 CGTCCTGCTCTTTGAGGACTA
1 CGTCCTGCTCTTTGAGGACTA
321742 AAGGGCGAAA
Statistics
Matches: 175, Mismatches: 17, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
56 23 0.13
57 3 0.02
59 2 0.01
60 22 0.13
61 94 0.54
62 31 0.18
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (60 bp):
CGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAGG
Found at i:321853 original size:56 final size:55
Alignment explanation
Indices: 321763--322066 Score: 394
Period size: 55 Copynumber: 5.4 Consensus size: 55
321753 GAGAGAGCGC
* * *
321763 CCTGCTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGT
1 CCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGT
* * * *
321818 CCTGTTCTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGTTTTGAAAGACGT
1 CCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGT
*
321874 CCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGACGT
1 CCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTT-----G--AAAGGCGT
321936 CCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGT
1 CCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGT
* * * *
321992 CCTGCTCTTTGAGGACTGAAAGGTGTCACCAACTTGTGTGGGCTTTGAAAGGCAT
1 CCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGT
*
322047 CCTACTCTTTGAGGACTAAA
1 CCTGCTCTTTGAGGACTAAA
322067 GGGTGAAAGG
Statistics
Matches: 223, Mismatches: 16, Indels: 20
0.86 0.06 0.08
Matches are distributed among these distances:
55 91 0.41
56 76 0.34
58 1 0.00
60 1 0.00
62 31 0.14
63 23 0.10
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (55 bp):
CCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGT
Found at i:321886 original size:150 final size:152
Alignment explanation
Indices: 321609--321891 Score: 428
Period size: 150 Copynumber: 1.8 Consensus size: 152
321599 GAAAGCATCA
321609 TGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAATAGGCGTCCTACT
1 TGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT---A-AAATAGGCGTCCTACT
* * *
321674 CTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGA
62 CTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGACGTCCTGCTCTTTGAGGA
321739 CTAAAGGGCGAAAGGAGAGAGCGCCC
127 CTAAAGGGCGAAAGGAGAGAGCGCCC
* **
321765 TGCTCTTTGAGGACT-GAGAAGTGCCACCAACTTGTGTGGGCTTT-AAA-AGGCGTCCTGTTCTT
1 TGCTCTTTGAGGACTGGA-AAATGCCACCAACTTGTGTGGGCTTTAAAATAGGCGTCCTACTCTT
* *
321827 TGAGGACTAAAAAAATGCCACCAACTTGTGTGGGTTTTGAAAGACGTCCTGCTCTTTGAGGACTA
65 TGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGACGTCCTGCTCTTTGAGGACTA
321892 GAAAATGCCA
Statistics
Matches: 118, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
150 73 0.62
151 3 0.03
155 2 0.02
156 40 0.34
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.27
Consensus pattern (152 bp):
TGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAATAGGCGTCCTACTCTTT
GAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGACGTCCTGCTCTTTGAGGACTAA
AGGGCGAAAGGAGAGAGCGCCC
Found at i:321984 original size:118 final size:111
Alignment explanation
Indices: 321763--322066 Score: 423
Period size: 118 Copynumber: 2.7 Consensus size: 111
321753 GAGAGAGCGC
*
321763 CCTGCTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAA-GGCGTCCTGTTCTT
1 CCTGCTCTTTGAGGACTGA-AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGGCGTCCTGCTCTT
*
321827 TGAGGACTAAAAAAATGCCACCAACTTGTGTGGGTTTTGAAAGACGT
65 TGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGACGT
*
321874 CCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGACGTCCT
1 CCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG-----G-CGTCCT
* * *
321939 GCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGT
59 GCTCTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGACGT
* * * *
321992 CCTGCTCTTTGAGGACTGAAAGGTGTCACCAACTTGTGTGGGCTTTGAAA-GGCATCCTACTCTT
1 CCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGGCGTCCTGCTCTT
322056 TGAGGACTAAA
65 TGAGGACTAAA
322067 GGGTGAAAGG
Statistics
Matches: 172, Mismatches: 12, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
111 66 0.38
112 4 0.02
117 6 0.03
118 96 0.56
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (111 bp):
CCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGGCGTCCTGCTCTTT
GAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGACGT
Found at i:321992 original size:268 final size:272
Alignment explanation
Indices: 321486--322014 Score: 757
Period size: 268 Copynumber: 1.9 Consensus size: 272
321476 TAAAGTACGT
*
321486 CCTGCTTTTTGAGGACAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAAGAAAGGCGTCCTAC
1 CCTGCTCTTTGAGGACAAAAAGTGCCACCAACTTGTGTGGGCTTT----AAGAAAGGCGTCCTAC
* ** **
321551 TCTTTGATGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCATGCTCTT
62 TCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTG-AAAGAG-AAGCATCATGCTCTT
* * * *
321616 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAATAGGCGTCCTACTCTTTGAG
125 TGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGACGTCCTACTCTTTGAG
321681 GACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACT-AAAG
190 GACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACTGAAAG
321745 GGCGAAAGGAGAGAGCGC
255 GGCGAAAGGAGAGAGCGC
* * **
321763 CCTGCTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTT-A-AAAGGCGTCCTGTTCT
1 CCTGCTCTTTGAGGAC-AAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGCGTCCTACTCT
* * *
321826 TTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGTTTTG-AA-AG-A-CGTCCTGCTCTTTGAG
65 TTGAGGACT-AAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAGAAGCATCATGCTCTTTGAG
*
321887 GACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGACGTCCTGCTCTTTGAGGAC
129 GACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAAGACGTCCTACTCTTTGAGGAC
*
321952 TAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGG
193 TAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGG
322015 TGTCACCAAC
Statistics
Matches: 229, Mismatches: 19, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
267 49 0.21
268 81 0.35
269 5 0.02
270 2 0.01
271 2 0.01
272 22 0.10
273 26 0.11
277 15 0.07
278 27 0.12
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (272 bp):
CCTGCTCTTTGAGGACAAAAAGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGCGTCCTACTCTT
TGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAGAAGCATCATGCTCTTTGAGGA
CTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGACGTCCTACTCTTTGAGGACTAG
AAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGGCGAA
AGGAGAGAGCGC
Found at i:322061 original size:323 final size:326
Alignment explanation
Indices: 321483--322137 Score: 925
Period size: 323 Copynumber: 2.0 Consensus size: 326
321473 AAATAAAGTA
*
321483 CGTCCTGCTTTTTGAGGACAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAAGAAAGGCGTCC
1 CGTCCTGCTTTTTGAGGACAAAAAATGCCACCAACTTGTGTGGGCTTTG-AAAAG-AA-GCGTCC
* * ** * *
321548 TACTCTTTGATGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCATGCT
63 TACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCATGCT
*
321613 CTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAATAGGCGTCCTACTCTTT
128 CTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT---AGAAATAGGCGTCCTACTCTTT
* *
321678 GAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACTAA
190 GAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTACTCTTTGAGGACTAA
* *
321743 AGGGCGAAAGGAGAGAGCGCCCTGCTCTTTGAGGACTGAGAA-GTGCCACCAACTTGTGTGGGCT
255 AGGGCGAAAGGAGAGAACGCCCTACTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCT
321807 TTAAAAGG
319 TTAAAAGG
*
321815 CGTCCTG-TTCTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGTTTTG-AAAG-A-CGTCC
1 CGTCCTGCTT-TTTGAGGAC--AAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAGCGTCC
* * *
321876 TGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAAGACGTCCTG
63 TACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAA-GAAAAAG-CATCATG
*
321940 CTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT-G-AA-AGGCGTCCTGCTCTTT
126 CTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTAGAAATAGGCGTCCTACTCTTT
* * *
322002 GAGGACT-GAAAGGTGTCACCAACTTGTGTGGGCTTTGAAAGGCATCCTACTCTTTGAGGACTAA
190 GAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTACTCTTTGAGGACTAA
* *
322066 AGGGTGAAAGGAGAGAACGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTT
255 AGGGCGAAAGGAGAGAACGCCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTT
322131 TAAAAGG
320 TAAAAGG
322138 AAAAAGCGTC
Statistics
Matches: 294, Mismatches: 22, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
322 4 0.01
323 115 0.39
324 22 0.07
325 2 0.01
326 1 0.00
327 3 0.01
328 50 0.17
329 23 0.08
330 24 0.08
331 2 0.01
332 20 0.07
334 28 0.10
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (326 bp):
CGTCCTGCTTTTTGAGGACAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAGCGTCCTAC
TCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCATGCTCTT
TGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAGAAATAGGCGTCCTACTCTTTGAGGAC
TAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTACTCTTTGAGGACTAAAGGGCG
AAAGGAGAGAACGCCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
G
Found at i:323175 original size:10 final size:10
Alignment explanation
Indices: 323162--323199 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
323152 TTTTTCCTTT
323162 TTGTTTTTTG
1 TTGTTTTTTG
323172 TTGTTTTTTG
1 TTGTTTTTTG
*
323182 TTG-TTGTTG
1 TTGTTTTTTG
323191 TTGTTTTTT
1 TTGTTTTTT
323200 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (10 bp):
TTGTTTTTTG
Done.