Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000163.1 Hibiscus syriacus cultivar Beakdansim tig00000287_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 301105
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:180145 original size:13 final size:13
Alignment explanation
Indices: 180110--180152 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
180100 ATTTTACTTA
180110 TTTATTTATCTA-T
1 TTTATTT-TCTATT
*
180123 TTT-CTTTCTATT
1 TTTATTTTCTATT
180135 TTTATTTTCTATT
1 TTTATTTTCTATT
180148 TTTAT
1 TTTAT
180153 CTTTTTATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 4 0.15
12 6 0.23
13 16 0.62
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTATTTTCTATT
Found at i:180157 original size:21 final size:21
Alignment explanation
Indices: 180092--180160 Score: 59
Period size: 24 Copynumber: 3.0 Consensus size: 21
180082 ATACTTTCAC
*
180092 TTTTTTATATTTTA-CTTATTTA
1 TTTTCTAT-TTTTATCTT-TTTA
*
180114 TTTATCTATTTTCTTTCTATTTTTA
1 TTT-TCTATTTT-TATC--TTTTTA
180139 TTTTCTATTTTTATCTTTTTA
1 TTTTCTATTTTTATCTTTTTA
180160 T
1 T
180161 CTTCCTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
21 7 0.18
22 6 0.15
23 8 0.21
24 9 0.23
25 7 0.18
26 2 0.05
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTCTATTTTTATCTTTTTA
Found at i:180189 original size:17 final size:17
Alignment explanation
Indices: 180166--180207 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
180156 TTTATCTTCC
*
180166 TTTTATTTGCTTTATTCA
1 TTTTATTTGCATTA-TCA
180184 -TTTATTTGCATTATCA
1 TTTTATTTGCATTATCA
180200 TTTTATTT
1 TTTTATTT
180208 TTATTTGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.19, C:0.10, G:0.05, T:0.67
Consensus pattern (17 bp):
TTTTATTTGCATTATCA
Found at i:180274 original size:17 final size:15
Alignment explanation
Indices: 180252--180300 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 15
180242 ATTATTCTTC
180252 ATTTTATTTATTTATGT
1 ATTTTATTTATTT-T-T
*
180269 ATTTTATTCATTTTT
1 ATTTTATTTATTTTT
180284 ATATTTACTTTATTTTT
1 AT-TTTA-TTTATTTTT
180301 TTATCACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 3 0.11
16 5 0.18
17 20 0.71
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (15 bp):
ATTTTATTTATTTTT
Found at i:180280 original size:26 final size:26
Alignment explanation
Indices: 180249--180299 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
180239 GCTATTATTC
*
180249 TTCATTTTATTTATTTA-TGTATTTTA
1 TTCATTTT-TATATTTACTGTATTTTA
*
180275 TTCATTTTTATATTTACTTTATTTT
1 TTCATTTTTATATTTACTGTATTTT
180300 TTTATCACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.71
Consensus pattern (26 bp):
TTCATTTTTATATTTACTGTATTTTA
Found at i:180314 original size:20 final size:19
Alignment explanation
Indices: 180279--180318 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
180269 ATTTTATTCA
180279 TTTTTATATTTACTTTATT
1 TTTTTATATTTACTTTATT
180298 TTTTTATCACTTT-CTTTATT
1 TTTTTAT-A-TTTACTTTATT
180318 T
1 T
180319 CATTTGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 9 0.47
21 3 0.16
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTATATTTACTTTATT
Found at i:180317 original size:29 final size:28
Alignment explanation
Indices: 180253--180323 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 28
180243 TTATTCTTCA
180253 TTTTATTTATTTATGTATTTTATTCATT
1 TTTTATTTATTTATGTATTTTATTCATT
*
180281 TTTATATTTACTTTAT-TTTTTTA-TCACTT
1 TTT-TATTTA-TTTATGTATTTTATTCA-TT
180310 TCTTTATTTCATTT
1 T-TTTATTT-ATTT
180324 GTTTTACTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
28 6 0.16
29 23 0.62
30 8 0.22
ACGTcount: A:0.20, C:0.08, G:0.01, T:0.70
Consensus pattern (28 bp):
TTTTATTTATTTATGTATTTTATTCATT
Found at i:181287 original size:4 final size:4
Alignment explanation
Indices: 181280--181321 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
181270 TCGTCATTTC
181280 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
181322 TTATTTTACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:183283 original size:22 final size:22
Alignment explanation
Indices: 183257--183337 Score: 79
Period size: 21 Copynumber: 4.0 Consensus size: 22
183247 TTCAAGATTG
183257 CCCAGGGGGTACAGATTCCCCC
1 CCCAGGGGGTACAGATTCCCCC
*
183279 CCCAGGGGGTACAGA-T---AC
1 CCCAGGGGGTACAGATTCCCCC
*
183297 CCC---GGGTACAGATACCCCC
1 CCCAGGGGGTACAGATTCCCCC
*
183316 -CCAGGGGGTACCGATTCCCCC
1 CCCAGGGGGTACAGATTCCCCC
183337 C
1 C
183338 TGTCTAAAGC
Statistics
Matches: 46, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
15 9 0.20
18 6 0.13
19 1 0.02
21 15 0.33
22 15 0.33
ACGTcount: A:0.20, C:0.41, G:0.27, T:0.12
Consensus pattern (22 bp):
CCCAGGGGGTACAGATTCCCCC
Found at i:183305 original size:15 final size:15
Alignment explanation
Indices: 183285--183314 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
183275 CCCCCCCAGG
183285 GGGTACAGATACCCC
1 GGGTACAGATACCCC
183300 GGGTACAGATACCCC
1 GGGTACAGATACCCC
183315 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:183322 original size:36 final size:37
Alignment explanation
Indices: 183263--183335 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 37
183253 ATTGCCCAGG
*
183263 GGGTACAGATTCCCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATTACCCCCCCAGGGGGTACAGATACCCC
* *
183300 GGGTACAGA-TACCCCCCCAGGGGGTACCGATTCCCC
1 GGGTACAGATTACCCCCCCAGGGGGTACAGATACCCC
183336 CCTGTCTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 24 0.73
37 9 0.27
ACGTcount: A:0.21, C:0.38, G:0.27, T:0.14
Consensus pattern (37 bp):
GGGTACAGATTACCCCCCCAGGGGGTACAGATACCCC
Found at i:183402 original size:19 final size:20
Alignment explanation
Indices: 183363--183404 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
183353 AACAGAATGT
183363 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACCGATTCCCC
183383 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACCGATTCCCC
183403 CC
1 CC
183405 TGTTCAACAG
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:0.14, C:0.43, G:0.29, T:0.14
Consensus pattern (20 bp):
CCAGGGGGTACCGATTCCCC
Found at i:183466 original size:21 final size:21
Alignment explanation
Indices: 183440--183481 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
183430 ATTTGAATAT
*
183440 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
183461 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
183482 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:183548 original size:20 final size:22
Alignment explanation
Indices: 183510--183549 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
183500 TTTGAGTATA
183510 AAAATCATCCCCAAACGGCTCT
1 AAAATCATCCCCAAACGGCTCT
183532 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
183550 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCT
Found at i:183809 original size:34 final size:32
Alignment explanation
Indices: 183764--183833 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
183754 TTTTGTAAAG
* *
183764 GGGAAAGGTTCTAGCTTAGCCCGTATAAAAGCTA
1 GGGAAAGGTTCTAGCTTAACCCGGA-AAAA-CTA
* *
183798 GGGAAATGTTCTAGTTTAACCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAACCCGGAAAAACTA
183830 GGGA
1 GGGA
183834 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 4 0.12
34 21 0.66
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAACCCGGAAAAACTA
Found at i:186799 original size:15 final size:15
Alignment explanation
Indices: 186779--186808 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
186769 ATTGCCCAGG
186779 GGGTACAGATACCCC
1 GGGTACAGATACCCC
186794 GGGTACAGATACCCC
1 GGGTACAGATACCCC
186809 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:186897 original size:20 final size:21
Alignment explanation
Indices: 186857--186898 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
186847 AACAGAATGT
186857 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
*
186878 CCAGGGGGTACTGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
186899 TGTTCAACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.40, G:0.29, T:0.17
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:186960 original size:21 final size:21
Alignment explanation
Indices: 186934--186975 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
186924 ATTTGAATAT
*
186934 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
186955 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
186976 CCCATTATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:187042 original size:20 final size:22
Alignment explanation
Indices: 187004--187043 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
186994 TTTGAGTATA
187004 AAAATCATCCCCAAACGGCTCT
1 AAAATCATCCCCAAACGGCTCT
187026 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
187044 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCT
Found at i:187301 original size:34 final size:32
Alignment explanation
Indices: 187258--187327 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
187248 TTTTGTAAAG
* *
187258 GGGAAAGGTTCTAGCTTAGCCCGTATAAAAGCTA
1 GGGAAAGGTTCTAGCTTAACCCGGA-AAAA-CTA
*
187292 GGGAAAGGTTCTAGTTTAACCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAACCCGGAAAAACTA
187324 GGGA
1 GGGA
187328 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 4 0.12
34 22 0.67
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAACCCGGAAAAACTA
Found at i:188105 original size:25 final size:27
Alignment explanation
Indices: 188077--188127 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
188067 ACATTACATA
188077 TTTTGCATTTTATA-TTT-CATGTTTG
1 TTTTGCATTTTATATTTTCCATGTTTG
**
188102 TTTTTTATTTTATATTTTCCATGTTT
1 TTTTGCATTTTATATTTTCCATGTTT
188128 TTACATTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.55
26 3 0.14
27 7 0.32
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.69
Consensus pattern (27 bp):
TTTTGCATTTTATATTTTCCATGTTTG
Found at i:198599 original size:2 final size:2
Alignment explanation
Indices: 198592--198681 Score: 127
Period size: 2 Copynumber: 46.5 Consensus size: 2
198582 TTTTATTAAT
198592 TA TA TA TA TA TA TA TA T- TA TCA T- TA GTA T- TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA -TA TA TA TA TA TA TA TA
198632 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
198674 TA T- TA TA T
1 TA TA TA TA T
198682 TTCCTAATTT
Statistics
Matches: 81, Mismatches: 0, Indels: 14
0.85 0.00 0.15
Matches are distributed among these distances:
1 5 0.06
2 72 0.89
3 4 0.05
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (2 bp):
TA
Found at i:198831 original size:13 final size:13
Alignment explanation
Indices: 198796--198836 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
198786 ATTTTACTTA
198796 TTTATTTATCTA-T
1 TTTATTT-TCTATT
*
198809 TTT-CTTTCTATT
1 TTTATTTTCTATT
198821 TTTATTTTCTATT
1 TTTATTTTCTATT
198834 TTT
1 TTT
198837 CTATTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 4 0.17
12 6 0.25
13 14 0.58
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTCTATT
Found at i:198873 original size:17 final size:17
Alignment explanation
Indices: 198852--198893 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
198842 TTTATCTTCC
*
198852 TTTTATTTGCTTTATTCA
1 TTTTATTTGCATTA-TCA
198870 -TTTATTTGCATTATCA
1 TTTTATTTGCATTATCA
198886 TTTTATTT
1 TTTTATTT
198894 TTATTTGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.19, C:0.10, G:0.05, T:0.67
Consensus pattern (17 bp):
TTTTATTTGCATTATCA
Found at i:210688 original size:6 final size:6
Alignment explanation
Indices: 210677--210702 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
210667 TAGATAAAAG
210677 ATTAAA ATTAAA ATTAAA ATTAAA AT
1 ATTAAA ATTAAA ATTAAA ATTAAA AT
210703 GAAATATTTA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATTAAA
Found at i:211234 original size:22 final size:22
Alignment explanation
Indices: 211206--211260 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
211196 TACATTACAC
211206 AATTCAAAGCAGAAAGCTGATG
1 AATTCAAAGCAGAAAGCTGATG
211228 AATTCAAAGCAGAAAGCTGATG
1 AATTCAAAGCAGAAAGCTGATG
*
211250 AATCCAAAGCA
1 AATTCAAAGCA
211261 TTATACTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.16
Consensus pattern (22 bp):
AATTCAAAGCAGAAAGCTGATG
Found at i:214593 original size:4 final size:4
Alignment explanation
Indices: 214586--215097 Score: 452
Period size: 4 Copynumber: 127.8 Consensus size: 4
214576 TAGATAGATA
214586 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * *
214634 GATG GATG GATG GATG GATG GATG GATG GACG GATG GACG GACG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * *
214682 GATG GACG GACG GATG GATG GACG GACG GATG GATG GACG GACG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * * * *
214730 GACG GATG GATG GATG GACG GATG GATA GACG GACG GATA GACG GACG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * * * * *
214778 GACG GACG GATG GATG GACG GACG GACG GATA GACG GATG GACG GATA
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * *
214826 GACG GATG GATA GACG GATG GATG GACG GATG GATG GATG GATG GACG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * * *
214874 GATG GACG GATG GACG TATG GACG GATG GACG GATG GGTG GATG GATAG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GAT-G
* * * * *
214923 G-TAG G-TG GGTG GGTG GATG GATG GATG GATG GGTG GGTG GGTG GATG
1 GAT-G GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
*
214970 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATAG GATG GATA
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GAT-G GATG GATG
* * * * * * * * * * *
215019 GATA GATA GATA GATG GATA GATA GATA GATA GATA GATA GATA GATA
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
* * * * *
215067 GATA GATG GATA GATA GATA GATA GATG GAT
1 GATG GATG GATG GATG GATG GATG GATG GAT
215098 AGATAGATAG
Statistics
Matches: 442, Mismatches: 63, Indels: 6
0.86 0.12 0.01
Matches are distributed among these distances:
3 2 0.00
4 434 0.98
5 6 0.01
ACGTcount: A:0.28, C:0.06, G:0.46, T:0.19
Consensus pattern (4 bp):
GATG
Found at i:215102 original size:4 final size:4
Alignment explanation
Indices: 215015--219327 Score: 8263
Period size: 4 Copynumber: 1090.2 Consensus size: 4
215005 GGATAGGATG
*
215015 GATA GATA GATA GATA GATG GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
* *
215063 GATA GATA GATG GATA GATA GATA GATA GATG GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215111 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215159 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215207 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215255 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GAT-
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215302 -ATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215349 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215397 GATA GATA GATA GATA GATA GATA GAT- -ATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215443 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215491 GATA GATA GATA GATA GAT- -ATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215537 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215585 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA G--A GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215631 GATA GATA GATA GATA GATA GATA GATA GATA G--A GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215677 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215725 GATA GATA GATA GATA GATA GATA GATA GATA GATA GAT- -ATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215771 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215819 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215867 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215915 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
215963 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216011 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216059 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216107 GATA GATA GATA GAT- -ATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216153 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216201 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216249 GATA GATA GATA GAT- -ATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216295 GATA GATA GATA GATA GATA GAT- -ATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216341 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216389 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216437 GATA GATA GATA GATA G--A GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216483 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216531 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216579 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216627 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216675 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216723 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216771 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216819 GATA GATA GATA GATA GATA GATA GATA GATA GATA GAT- -ATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216865 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216913 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
216961 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217009 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217057 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217105 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217153 GATA GATA GATA GAT- -ATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217199 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217247 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA G--A
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217293 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217341 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217389 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217437 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217485 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217533 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217581 GATA GATA GATA GAT- -ATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217627 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217675 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217723 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217771 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217819 GAT- -ATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217865 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217913 GATA GATA GATA GATA GATA GATA GAT- -ATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
217959 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218007 GATA GATA GATA GATA GATA GATA GATA GATA G--A GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218053 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218101 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218149 GATA GATA GATA GATA GAT- -ATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218195 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218243 GATA GATA GATA GATA GATA G--A GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218289 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218337 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218385 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218433 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218481 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218529 G--A GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218575 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218623 GATA GATA GATA GAT- -ATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218669 GATA G--A GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218715 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218763 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218811 GATA GATA GATA GAT- -ATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218857 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218905 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
218953 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
219001 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
219049 GATA GAT- -ATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
219095 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
219143 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
219191 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
219239 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
219287 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA G
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA G
219328 TTCAATAGGT
Statistics
Matches: 4255, Mismatches: 6, Indels: 96
0.98 0.00 0.02
Matches are distributed among these distances:
2 48 0.01
4 4207 0.99
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
GATA
Found at i:229400 original size:29 final size:28
Alignment explanation
Indices: 229358--229414 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
229348 TTTATGTTTG
* **
229358 CATTATGTTGTTGAGTCAATACTTGAAAA
1 CATTATATTGTTGAACCAATACTT-AAAA
229387 CATTATATTGTTGAACCAATACTTAAAA
1 CATTATATTGTTGAACCAATACTTAAAA
229415 GCAACTGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (28 bp):
CATTATATTGTTGAACCAATACTTAAAA
Found at i:229606 original size:19 final size:20
Alignment explanation
Indices: 229574--229613 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
229564 TAAAAAACTC
229574 AAAAAAATAATATTATATAAT
1 AAAAAAAT-ATATTATATAAT
*
229595 AAAAAAAT-TATTTTATAAT
1 AAAAAAATATATTATATAAT
229614 TTTTAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAAAATATATTATATAAT
Found at i:236137 original size:28 final size:29
Alignment explanation
Indices: 236082--236137 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
236072 ATTATTAACA
* *
236082 AAAAATATTACGAAGAAGATAATATTTTT
1 AAAAATATTACGAAAAAGATAACATTTTT
* *
236111 AAAAATATTA-GAAAAATATCACATTTT
1 AAAAATATTACGAAAAAGATAACATTTT
236138 ATATTGCATC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (29 bp):
AAAAATATTACGAAAAAGATAACATTTTT
Found at i:236555 original size:20 final size:20
Alignment explanation
Indices: 236530--236568 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
236520 TCACCACACC
236530 AAATCCT-TTCAAATTCTCTT
1 AAATCCTCTT-AAATTCTCTT
236550 AAATCCTCTTAAATTCTCT
1 AAATCCTCTTAAATTCTCT
236569 CACATCTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATCCTCTTAAATTCTCTT
Found at i:236660 original size:29 final size:31
Alignment explanation
Indices: 236609--236670 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 31
236599 TATTTTATTC
*
236609 TATTTAATATTTTGTTAGTATTTTATTTAAT
1 TATTTAATATCTTGTTAGTATTTTATTTAAT
236640 TATTTAA-ATCTT-TTAGTATTTTATTTAAT
1 TATTTAATATCTTGTTAGTATTTTATTTAAT
236669 TA
1 TA
236671 ATTTTTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 19 0.63
30 4 0.13
31 7 0.23
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.63
Consensus pattern (31 bp):
TATTTAATATCTTGTTAGTATTTTATTTAAT
Found at i:242491 original size:30 final size:30
Alignment explanation
Indices: 242455--242522 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
242445 ATCAAAGATA
242455 AGAGGATTATCGGGTGATATTTACAGGTTG
1 AGAGGATTATCGGGTGATATTTACAGGTTG
* * * * * *
242485 AGAGGATTGTTGTGTGATGTTTTCGGGTTG
1 AGAGGATTATCGGGTGATATTTACAGGTTG
242515 AGAGGATT
1 AGAGGATT
242523 GTTGTGTGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.22, C:0.04, G:0.37, T:0.37
Consensus pattern (30 bp):
AGAGGATTATCGGGTGATATTTACAGGTTG
Found at i:242548 original size:31 final size:30
Alignment explanation
Indices: 242468--242549 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
242458 GGATTATCGG
* *
242468 GTGATATTTACAGGTTGAGAGGATTGTTGT
1 GTGATGTTTACGGGTTGAGAGGATTGTTGT
*
242498 GTGATGTTTTCGGGTTGAGAGGATTGTTGT
1 GTGATGTTTACGGGTTGAGAGGATTGTTGT
*
242528 GTGAATGTTTACGGGGTGAGAG
1 GTG-ATGTTTACGGGTTGAGAG
242550 CGTTTCATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 30 0.65
31 16 0.35
ACGTcount: A:0.20, C:0.04, G:0.39, T:0.38
Consensus pattern (30 bp):
GTGATGTTTACGGGTTGAGAGGATTGTTGT
Found at i:245897 original size:19 final size:19
Alignment explanation
Indices: 245873--245977 Score: 111
Period size: 19 Copynumber: 5.2 Consensus size: 19
245863 CGATTTTTGA
245873 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
245892 AAAATGTATTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
245911 AAAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
*
245931 GAAAAACGTGTTGTTGCGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
* *
245955 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTT
245974 AAAA
1 AAAA
245978 ATCCAAAATA
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
19 50 0.68
20 3 0.04
22 8 0.11
24 3 0.04
25 10 0.14
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:246416 original size:25 final size:25
Alignment explanation
Indices: 246382--246431 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
246372 AATTTGTATT
246382 ATCGCGTTGCGATAGTCAGAATCGC
1 ATCGCGTTGCGATAGTCAGAATCGC
246407 ATCGCGTTGCGATAGTCAGAATCGC
1 ATCGCGTTGCGATAGTCAGAATCGC
246432 GTTGCGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (25 bp):
ATCGCGTTGCGATAGTCAGAATCGC
Found at i:246599 original size:20 final size:20
Alignment explanation
Indices: 246576--246662 Score: 81
Period size: 20 Copynumber: 4.3 Consensus size: 20
246566 GGAAACTGAT
246576 TTGCGATACTGGAGATCGCG
1 TTGCGATACTGGAGATCGCG
* *
246596 TTGCGATAGT-CAGAATCGCG
1 TTGCGATACTGGAG-ATCGCG
* **
246616 TTGCGA-ATCTGGA-AACTGAT
1 TTGCGATA-CTGGAGATC-GCG
246636 TTGCGATACTGGAGATCGCG
1 TTGCGATACTGGAGATCGCG
246656 TTGCGAT
1 TTGCGAT
246663 TTAGAGATCG
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
19 5 0.10
20 42 0.82
21 4 0.08
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (20 bp):
TTGCGATACTGGAGATCGCG
Found at i:246623 original size:60 final size:60
Alignment explanation
Indices: 246537--246662 Score: 234
Period size: 60 Copynumber: 2.1 Consensus size: 60
246527 AAAATCGCAA
246537 TGCGATAGTCAAAATCGCGTTACGAATCTGGAAACTGATTTGCGATACTGGAGATCGCGT
1 TGCGATAGTCAAAATCGCGTTACGAATCTGGAAACTGATTTGCGATACTGGAGATCGCGT
* *
246597 TGCGATAGTCAGAATCGCGTTGCGAATCTGGAAACTGATTTGCGATACTGGAGATCGCGT
1 TGCGATAGTCAAAATCGCGTTACGAATCTGGAAACTGATTTGCGATACTGGAGATCGCGT
246657 TGCGAT
1 TGCGAT
246663 TTAGAGATCG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (60 bp):
TGCGATAGTCAAAATCGCGTTACGAATCTGGAAACTGATTTGCGATACTGGAGATCGCGT
Found at i:246671 original size:19 final size:19
Alignment explanation
Indices: 246647--246683 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
246637 TGCGATACTG
*
246647 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
*
246666 GAGATCGCATTGTGATTT
1 GAGATCGCATTGCGATTT
246684 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:247161 original size:31 final size:30
Alignment explanation
Indices: 247117--247176 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
247107 AGGGTAAACT
247117 ATTTATTTAGTATTTAAATTATCAATTTTA
1 ATTTATTTAGTATTTAAATTATCAATTTTA
* * *
247147 ATTTATTTTTGTATTTAAATTTTTAATTTT
1 ATTTA-TTTAGTATTTAAATTATCAATTTT
247177 TTAAAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (30 bp):
ATTTATTTAGTATTTAAATTATCAATTTTA
Found at i:248528 original size:25 final size:25
Alignment explanation
Indices: 248494--248555 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
248484 AAAGGAATCA
*
248494 ATAGCTCTTTAATGCTTTCAGATTT
1 ATAGCTCTTTAATGCTTTCAGAGTT
248519 ATAGCTCTTTAATGCTTTCAGAGTT
1 ATAGCTCTTTAATGCTTTCAGAGTT
248544 ATAGCTCTTTAA
1 ATAGCTCTTTAA
248556 CAAATGTCCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (25 bp):
ATAGCTCTTTAATGCTTTCAGAGTT
Found at i:249160 original size:95 final size:95
Alignment explanation
Indices: 248989--249187 Score: 305
Period size: 95 Copynumber: 2.1 Consensus size: 95
248979 GGACAACTCA
248989 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTCGAGGCATCTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTCGAGGCATCTAACCAATT
249054 ACTTTAGAGGGACAACTCAAGCTTTATTGT
66 ACTTTAGAGGGACAACTCAAGCTTTATTGT
* *
249084 ATATTA-AATTCACCTTTATCAGGCTAGCTGAATCTTATCCATAAA-TCTGAGGCGTTTAACCAA
1 ATATTATAA-TCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTC-GAGGCATCTAACCAA
** * *
249147 TTGTTTTATAGGGACAGCTCAAGCTTTATTGT
64 TTACTTTAGAGGGACAACTCAAGCTTTATTGT
249179 ATA-TATAAT
1 ATATTATAAT
249188 ATTATAATCT
Statistics
Matches: 95, Mismatches: 6, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
94 7 0.07
95 88 0.93
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (95 bp):
ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTCGAGGCATCTAACCAATT
ACTTTAGAGGGACAACTCAAGCTTTATTGT
Found at i:254001 original size:11 final size:11
Alignment explanation
Indices: 253985--254036 Score: 61
Period size: 11 Copynumber: 4.5 Consensus size: 11
253975 TAATGATATA
253985 TAATAAATTAT
1 TAATAAATTAT
253996 TAATAAATT-T
1 TAATAAATTAT
254006 TATATAAATAATAT
1 TA-ATAAAT--TAT
*
254020 TATTAAATTAT
1 TAATAAATTAT
254031 TAATAA
1 TAATAA
254037 TGCGTAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 3 0.09
11 23 0.66
13 6 0.17
14 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAATAAATTAT
Found at i:255950 original size:55 final size:55
Alignment explanation
Indices: 255874--256025 Score: 187
Period size: 55 Copynumber: 2.8 Consensus size: 55
255864 TCGAGTGATG
* * ** *
255874 ACACTGTTCCTTTTCTTTGAGGACGTCGGGTCAATCTGGAGATAATTTGGTGTTG
1 ACACTGTTCCTTCTCTCTGAGGAAATCGGGTCAATCTGGAGATAATTTGGTGTTA
* * *
255929 AGACTGTTCCTTCTCTCTGAGGAAATCGGGTCAATATGAAGATAATTTGGTGTTA
1 ACACTGTTCCTTCTCTCTGAGGAAATCGGGTCAATCTGGAGATAATTTGGTGTTA
* * * * *
255984 ACATTGTTTCTTCTCTCTAAGAAAATCGGGTCAATCTAGAGA
1 ACACTGTTCCTTCTCTCTGAGGAAATCGGGTCAATCTGGAGA
256026 ATTTGAAGAT
Statistics
Matches: 81, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 81 1.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (55 bp):
ACACTGTTCCTTCTCTCTGAGGAAATCGGGTCAATCTGGAGATAATTTGGTGTTA
Found at i:267355 original size:19 final size:19
Alignment explanation
Indices: 267331--267379 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
267321 AAGCTAGGGA
267331 GGTACCGATACCCTATAGG
1 GGTACCGATACCCTATAGG
*
267350 GGTACCGATACCCTATGGG
1 GGTACCGATACCCTATAGG
267369 GGTACCGATAC
1 GGTACCGATAC
267380 TACTCCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.24, C:0.27, G:0.29, T:0.20
Consensus pattern (19 bp):
GGTACCGATACCCTATAGG
Found at i:272450 original size:24 final size:24
Alignment explanation
Indices: 272422--272467 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
272412 TATAAATTTT
* *
272422 CACCGAAGTGCCGCGTAGAAATTG
1 CACCGAAGTGCCACATAGAAATTG
272446 CACCGAAGTGCCACATAGAAAT
1 CACCGAAGTGCCACATAGAAAT
272468 GTCCCGAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (24 bp):
CACCGAAGTGCCACATAGAAATTG
Found at i:272546 original size:23 final size:23
Alignment explanation
Indices: 272500--272558 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
272490 TACCCCGAAA
*
272500 GACCACGTAGAAATATCCCGAAG
1 GACCACGTAGAAATATCCCAAAG
* * *
272523 GACCACGTAGAATTGTCCTAAAG
1 GACCACGTAGAAATATCCCAAAG
*
272546 GACCGCGTA-AAAT
1 GACCACGTAGAAAT
272559 CCTCGACTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 3 0.10
23 27 0.90
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (23 bp):
GACCACGTAGAAATATCCCAAAG
Found at i:272714 original size:45 final size:45
Alignment explanation
Indices: 272659--272760 Score: 132
Period size: 45 Copynumber: 2.3 Consensus size: 45
272649 CATAGACATG
* * **
272659 TAATCACATAGGTCATTGTCACATAGCTTATACCACATTTTCATA
1 TAATCACATAGGCCAATACCACATAGCTTATACCACATTTTCATA
* * * *
272704 TAGTCACATAGGCCAATACCACATAGTTTATATCACCTTTTCATA
1 TAATCACATAGGCCAATACCACATAGCTTATACCACATTTTCATA
272749 TAATCACATAGG
1 TAATCACATAGG
272761 ATGAAATATA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.33
Consensus pattern (45 bp):
TAATCACATAGGCCAATACCACATAGCTTATACCACATTTTCATA
Found at i:281277 original size:22 final size:22
Alignment explanation
Indices: 281252--281334 Score: 71
Period size: 23 Copynumber: 3.8 Consensus size: 22
281242 ATATGGCAGA
*
281252 GGGAATTGATACCCCCATGAAG
1 GGGAATCGATACCCCCATGAAG
* * *
281274 GGGAA-CTGATTCCCCCTTTGAAT
1 GGGAATC-GATACCCCC-ATGAAG
* * *
281297 GGGAATCGATTCCCCTAT-TAG
1 GGGAATCGATACCCCCATGAAG
281318 GGGAATCGATACCCCCA
1 GGGAATCGATACCCCCA
281335 AGGGTTCTGG
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
21 16 0.33
22 14 0.29
23 17 0.35
24 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.23
Consensus pattern (22 bp):
GGGAATCGATACCCCCATGAAG
Found at i:287281 original size:64 final size:64
Alignment explanation
Indices: 287180--287304 Score: 214
Period size: 64 Copynumber: 2.0 Consensus size: 64
287170 GCCGTTGCAG
* * *
287180 CCAGGGGGTATGGATACCCCTGGGGGGTATCGGTACCCTATTTGTATTCTGGAATTTTTGCCTT
1 CCAGGGGGTATGGATACCCCTGGAGGGTATCGGTACCCTATTTGCATTCTAGAATTTTTGCCTT
*
287244 CCAGGGGGTATGGATACCCCTGGAGGGTATCGGTACCCTCTTTGCATTCTAGAATTTTTGC
1 CCAGGGGGTATGGATACCCCTGGAGGGTATCGGTACCCTATTTGCATTCTAGAATTTTTGC
287305 TCAAATCCGA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.17, C:0.22, G:0.29, T:0.33
Consensus pattern (64 bp):
CCAGGGGGTATGGATACCCCTGGAGGGTATCGGTACCCTATTTGCATTCTAGAATTTTTGCCTT
Found at i:289845 original size:43 final size:41
Alignment explanation
Indices: 289792--290212 Score: 170
Period size: 43 Copynumber: 9.8 Consensus size: 41
289782 TCTTATTTTT
*
289792 TTTTACCTTTATAATTGAGCTCCTAATTTTATTTAATCTCAC
1 TTTTACCTTTATAATTGAGCTCCTAATTTT-TTTAATCCCAC
* * *
289834 TTTTCATCTTTATAATTGAAG-TCTCTAATTTTTTCAATCCCTC
1 TTTT-ACCTTTATAATTG-AGCTC-CTAATTTTTTTAATCCCAC
* *
289877 TTTTACCTTTACAATTGAGGCCCCTAA-TTTTTTAAT-CC-C
1 TTTTACCTTTATAATTGA-GCTCCTAATTTTTTTAATCCCAC
* *
289916 ----A-CTTTATAATTGAAGC-CCTTAAGTTTTTTCAATCTCAC
1 TTTTACCTTTATAATTG-AGCTCC-TAA-TTTTTTTAATCCCAC
* * * *
289954 TTTCTACCTTTTCTATCTTTACAATTGAGGCCCCTAATTTTTCTGAATCTCAA
1 TTT-TACC--TT-TA----T--AATTGA-GCTCCTAATTTTT-TTAATCCCAC
* *
290007 TTTCTACCTTTATAATTGAAGCCCCTAA-TTTTTTAATCTCAC
1 TTT-TACCTTTATAATTG-AGCTCCTAATTTTTTTAATCCCAC
* * *
290049 TTTCTAACTTTATAATTGAGGC-CCTTAAGTTTTTCAATCCCAC
1 TTT-TACCTTTATAATTGA-GCTCC-TAATTTTTTTAATCCCAC
* * * *
290092 TTTCTACCTTTATAA-CGAGAC-CTCTAAGTTTTTTCAATCTCAAA
1 TTT-TACCTTTATAATTGAG-CTC-CTAA-TTTTTTTAATC-CCAC
* * * *
290136 TTCTACCTTTATAATTTAGGCCCCTAATTTTTTTCAATCTCGA-
1 TTTTACCTTTATAATTGA-GCTCCTAATTTTTTT-AATC-CCAC
* * * *
290179 TTATACCTATATAATTGATACCCCTAATTTTTTT
1 TTTTACCTTTATAATTGA-GCTCCTAATTTTTTT
290213 TCAATCTCAA
Statistics
Matches: 305, Mismatches: 33, Indels: 81
0.73 0.08 0.19
Matches are distributed among these distances:
33 2 0.01
34 15 0.05
35 2 0.01
36 8 0.03
37 1 0.00
38 1 0.00
39 1 0.00
40 2 0.01
41 13 0.04
42 57 0.19
43 115 0.38
44 41 0.13
45 3 0.01
46 3 0.01
47 2 0.01
50 2 0.01
51 3 0.01
52 6 0.02
53 26 0.09
54 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.06, T:0.46
Consensus pattern (41 bp):
TTTTACCTTTATAATTGAGCTCCTAATTTTTTTAATCCCAC
Found at i:289927 original size:34 final size:36
Alignment explanation
Indices: 289883--289956 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 36
289873 CCTCTTTTAC
*
289883 CTTTACAATTGAGGCCCCTAA-TTTTTT-AATCCCA
1 CTTTACAATTGAAGCCCCTAAGTTTTTTCAATCCCA
* * *
289917 CTTTATAATTGAAGCCCTTAAGTTTTTTCAATCTCA
1 CTTTACAATTGAAGCCCCTAAGTTTTTTCAATCCCA
289953 CTTT
1 CTTT
289957 CTACCTTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 18 0.53
35 6 0.18
36 10 0.29
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.43
Consensus pattern (36 bp):
CTTTACAATTGAAGCCCCTAAGTTTTTTCAATCCCA
Found at i:289982 original size:87 final size:91
Alignment explanation
Indices: 289883--290059 Score: 240
Period size: 87 Copynumber: 1.9 Consensus size: 91
289873 CCTCTTTTAC
*
289883 CTTTACAATTGAGGCCCCTAATTTTT-T-AATC-C-C-A-CTTTATAATTGAAGCCCTTAAGTTT
1 CTTTACAATTGAGGCCCCTAATTTTTCTGAATCTCTCTACCTTTATAATTGAAGCCCCTAA-TTT
*
289942 TTTCAATCTCACTTTCTACCTTTTCTAT
65 TTT-AATCTCACTTTCTAACTTTTCTAT
289970 CTTTACAATTGAGGCCCCTAATTTTTCTGAATCTCAATTTCTACCTTTATAATTGAAGCCCCTAA
1 CTTTACAATTGAGGCCCCTAATTTTTCTGAATCTC----TCTACCTTTATAATTGAAGCCCCTAA
290035 TTTTTTAATCTCACTTTCTAACTTT
62 TTTTTTAATCTCACTTTCTAACTTT
290060 ATAATTGAGG
Statistics
Matches: 78, Mismatches: 2, Indels: 12
0.85 0.02 0.13
Matches are distributed among these distances:
87 26 0.33
88 1 0.01
89 4 0.05
90 1 0.01
95 19 0.24
96 7 0.09
97 20 0.26
ACGTcount: A:0.25, C:0.24, G:0.07, T:0.45
Consensus pattern (91 bp):
CTTTACAATTGAGGCCCCTAATTTTTCTGAATCTCTCTACCTTTATAATTGAAGCCCCTAATTTT
TTAATCTCACTTTCTAACTTTTCTAT
Found at i:290003 original size:53 final size:53
Alignment explanation
Indices: 289917--290017 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
289907 TTTAATCCCA
* * *
289917 CTTTATAATTGAAGCCCTTAAGTTTTTTCAATCTCACTTTCTACCTTTTCTAT
1 CTTTACAATTGAAGCCCCTAAGTTTTTTCAATCTCAATTTCTACCTTTTCTAT
* *
289970 CTTTACAATTGAGGCCCCTAA-TTTTTCTGAATCTCAATTTCTACCTTT
1 CTTTACAATTGAAGCCCCTAAGTTTTT-TCAATCTCAATTTCTACCTTT
290018 ATAATTGAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 5 0.12
53 37 0.88
ACGTcount: A:0.23, C:0.24, G:0.07, T:0.47
Consensus pattern (53 bp):
CTTTACAATTGAAGCCCCTAAGTTTTTTCAATCTCAATTTCTACCTTTTCTAT
Found at i:290018 original size:131 final size:131
Alignment explanation
Indices: 289833--290102 Score: 332
Period size: 131 Copynumber: 2.0 Consensus size: 131
289823 TTTAATCTCA
* * * ** *
289833 CTTTTCATCTTTATAATTGAAGTCTCTAATTTTTTCAATCCCTCTTTTACCTTTACAATTGAGGC
1 CTTTTCATCTTTACAATTGAAGCCCCTAATTTTTTCAATCCCAATTTTACCTTTACAATTGAAGC
*
289898 CCCTAATTTTTTAA-TC-C-C-ACTTTATAATTGAAGCCCTTAAGTTTTTTCAATCTCACTTTCT
66 CCCTAATTTTTTAACTCACTCAACTTTATAATTGAAGCCCTTAAG-TTTTTCAATCCCACTTTCT
289959 AC
130 AC
* * * *
289961 CTTTTCTATCTTTACAATTGAGGCCCCTAATTTTTCTGAATCTCAATTTCTACCTTTATAATTGA
1 CTTTTC-ATCTTTACAATTGAAGCCCCTAATTTTT-TCAATCCCAATTT-TACCTTTACAATTGA
*
290026 AGCCCCTAATTTTTTAATCTCACTTTCTAACTTTATAATTGAGGCCCTTAAGTTTTTCAATCCCA
63 AGCCCCTAATTTTTTAA-CTCAC--TC-AACTTTATAATTGAAGCCCTTAAGTTTTTCAATCCCA
290091 CTTTCTAC
124 CTTTCTAC
290099 CTTT
1 CTTT
290103 ATAACGAGAC
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
128 6 0.05
129 24 0.20
130 9 0.08
131 30 0.25
133 2 0.02
134 1 0.01
137 1 0.01
138 24 0.20
139 22 0.18
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.46
Consensus pattern (131 bp):
CTTTTCATCTTTACAATTGAAGCCCCTAATTTTTTCAATCCCAATTTTACCTTTACAATTGAAGC
CCCTAATTTTTTAACTCACTCAACTTTATAATTGAAGCCCTTAAGTTTTTCAATCCCACTTTCTA
C
Found at i:290031 original size:44 final size:44
Alignment explanation
Indices: 289963--290239 Score: 266
Period size: 43 Copynumber: 6.4 Consensus size: 44
289953 CTTTCTACCT
* * * *
289963 TTTCTATCTTTACAATTGAGGCCCCTAA-TTTTTCTGAATCTCAA
1 TTTCTACCTTTATAATTGAAGCCCCTAAGTTTTT-TCAATCTCAA
*
290007 TTTCTACCTTTATAATTGAAGCCCCTAA-TTTTTT-AATCTCAC
1 TTTCTACCTTTATAATTGAAGCCCCTAAGTTTTTTCAATCTCAA
* * * * *
290049 TTTCTAACTTTATAATTGAGGCCCTTAAG-TTTTTCAATCCCAC
1 TTTCTACCTTTATAATTGAAGCCCCTAAGTTTTTTCAATCTCAA
* *
290092 TTTCTACCTTTATAA-CG-AGACCTCTAAGTTTTTTCAATCTCAA
1 TTTCTACCTTTATAATTGAAG-CCCCTAAGTTTTTTCAATCTCAA
* * * * *
290135 ATTCTACCTTTATAATTTAGGCCCCTAATTTTTTTCAATCTCGA
1 TTTCTACCTTTATAATTGAAGCCCCTAAGTTTTTTCAATCTCAA
* * *
290179 -TTATACCTATATAATTGATA-CCCCTAATTTTTTTTCAATCTCAA
1 TTTCTACCTTTATAATTGA-AGCCCCTAA-GTTTTTTCAATCTCAA
290223 TTTCTA-CTATTATAATT
1 TTTCTACCT-TTATAATT
290240 AAGGTCTCTA
Statistics
Matches: 194, Mismatches: 29, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
41 1 0.01
42 44 0.23
43 70 0.36
44 67 0.35
45 12 0.06
ACGTcount: A:0.27, C:0.22, G:0.06, T:0.45
Consensus pattern (44 bp):
TTTCTACCTTTATAATTGAAGCCCCTAAGTTTTTTCAATCTCAA
Found at i:290983 original size:20 final size:20
Alignment explanation
Indices: 290947--291006 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
290937 AATATTATAT
*
290947 TTAAAATTAAAT-CAAAATAA
1 TTAAAA-TAAATATAAAATAA
290967 TTAAAATAAATATAAAAT--
1 TTAAAATAAATATAAAATAA
*
290985 TT-TAATAATATATAAAATAA
1 TTAAAATAA-ATATAAAATAA
291005 TT
1 TT
291007 TATATGATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
17 5 0.15
18 11 0.32
19 5 0.15
20 13 0.38
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAAATAAATATAAAATAA
Found at i:291008 original size:20 final size:20
Alignment explanation
Indices: 290960--291021 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
290950 AAATTAAATC
*
290960 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
290980 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
290998 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
291017 AAAAT
1 AAAAT
291022 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:291115 original size:12 final size:12
Alignment explanation
Indices: 291069--291118 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
291059 AATTTATTTA
291069 AAAATTAAA-ATT
1 AAAATTAAATA-T
*
291081 AAAATCAAATAT
1 AAAATTAAATAT
*
291093 AATA-T-AATAT
1 AAAATTAAATAT
291103 AAAATTAAATAT
1 AAAATTAAATAT
291115 AAAA
1 AAAA
291119 CCTCTTTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 8 0.26
11 1 0.03
12 21 0.68
13 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAATTAAATAT
Done.