Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008560.1 Hibiscus syriacus cultivar Beakdansim tig00111467_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: 753118
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:182272 original size:111 final size:111
Alignment explanation
Indices: 182092--182560 Score: 665
Period size: 111 Copynumber: 4.2 Consensus size: 111
182082 GTATCAATAC
* * * *
182092 TTTATAAAAATGTATCGATATTTTACAATATAACAGGT-AAAATATGACAAAACCAATTTTATTA
1 TTTATAAAAA-GGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTA
* * * *
182156 TGACAAAAACGGTAAAATTTACCTGATATATTAAAAGTA-ATTATCTT
65 TGACAAAAACGGTAAAATTTACCTGATATGTTGAAAGTATA-GATCCT
*
182203 TTTATAAAAAGGATCGACACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTAT
1 TTTATAAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTAT
*
182268 GACAAAAA-GGATAAAATTTACCTGATATGTTGAAAGTATCGATCCT
66 GACAAAAACGG-TAAAATTTACCTGATATGTTGAAAGTATAGATCCT
* * *
182314 TTTATAAAAAAGATCGATACTTTACAATATAACATGTATAAATATGACAAAACCAGTTTCATTAT
1 TTTATAAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTAT
* *
182379 GACAAAATCGGTAAAATTTACCTGATATGTTGAAAGTATATATCCT
66 GACAAAAACGGTAAAATTTACCTGATATGTTGAAAGTATAGATCCT
* * *
182425 TTTATAAAAAGGATAGATATTTTACAATATAATAGGTAAAAATATGACAAAACCAGTTTCATTAT
1 TTTATAAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTAT
* * * *
182490 GACAAAATCGATAAAATTTACCTAATATGTTGAAAGTATAGATACTT
66 GACAAAAACGGTAAAATTTACCTGATATGTTGAAAGTATAGAT-CCT
*
182537 TTTATAAAAAATGATCGATACTTT
1 TTTAT-AAAAAGGATCGATACTTT
182561 TTTGAAAGTT
Statistics
Matches: 322, Mismatches: 30, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
110 26 0.08
111 272 0.84
112 9 0.03
113 15 0.05
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (111 bp):
TTTATAAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTAT
GACAAAAACGGTAAAATTTACCTGATATGTTGAAAGTATAGATCCT
Found at i:183078 original size:73 final size:73
Alignment explanation
Indices: 182976--183116 Score: 246
Period size: 73 Copynumber: 1.9 Consensus size: 73
182966 GTATCGATAT
* *
182976 TTTACAATATAACATGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAAGGGTAAAATTTA
1 TTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAAATTTA
183041 CCTAATAC
66 CCTAATAC
* *
183049 TTTACAATATAACAGGTAAAAATATGACAAAATCAGTTTTATTATGACAAAAACGGTAAAATTTA
1 TTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAAATTTA
183114 CCT
66 CCT
183117 GTTATATTGT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.30
Consensus pattern (73 bp):
TTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAAATTTA
CCTAATAC
Found at i:183431 original size:223 final size:222
Alignment explanation
Indices: 183147--183687 Score: 845
Period size: 223 Copynumber: 2.4 Consensus size: 222
183137 TCATTTTTAT
* * *
183147 AAATATGACGAAACAAATTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTAT
1 AAATATGACAAAACAAGTTTCATTATGACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTAT
*
183212 AGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGACAAAACCTA-T
66 AGATCATTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGACAAAACC-AGT
* * *
183276 TTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTATAGATCCTTTTTATAAAAA
130 TTCATTATGACAAAACCGGTAAAATCTACCTAATATGTTGAAAGTATAGAT-CATTTTATAAAAA
*
183341 AGATAAATACTTTATAATATAACATGTAA
194 AGATAAATACTTTACAATATAACATGTAA
* *
183370 AAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAATATGTTGAAAGTAT
1 AAATATGACAAAACAAGTTTCATTATGACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTAT
* * *
183435 AGATCATTTTATAAAAATGATAGATACTTTACAATATAACATGTAAAAATATGACAAAATCAGTT
66 AGATCATTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTT
* **
183500 TCATTATGACAAAATCGGTAAAATCTACCTAATATGTTGAAAGTATAGATCATTTTATAAAAGGG
131 TCATTATGACAAAACCGGTAAAATCTACCTAATATGTTGAAAGTATAGATCATTTTATAAAAAAG
*
183565 ATAGATACTTTACAATATAACATGTAA
196 ATAAATACTTTACAATATAACATGTAA
*
183592 AAATATGACAAAA-ATAGTTTCATTATGACAAAACCGATAAAATTTACCTAATATGTTGAAAGTA
1 AAATATGACAAAACA-AGTTTCATTATGACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTA
*
183656 TAGATACTTTTTATAAAAAGGATCA-ATACTTT
65 TAGAT-CATTTTATAAAAAGGAT-AGATACTTT
183688 TTTGAAGTTA
Statistics
Matches: 292, Mismatches: 22, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
222 103 0.35
223 188 0.64
224 1 0.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (222 bp):
AAATATGACAAAACAAGTTTCATTATGACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTAT
AGATCATTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTT
TCATTATGACAAAACCGGTAAAATCTACCTAATATGTTGAAAGTATAGATCATTTTATAAAAAAG
ATAAATACTTTACAATATAACATGTAA
Found at i:183499 original size:111 final size:111
Alignment explanation
Indices: 183147--183687 Score: 843
Period size: 111 Copynumber: 4.9 Consensus size: 111
183137 TCATTTTTAT
* * * *
183147 AAATATGACGAAACAAATTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTAT
1 AAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTAT
* *
183212 AGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAA
66 AGATCATTTTATAAAAAGGATAGATACTTTACAATATAACATGTAA
*
183258 AAATATGACAAAACCTA-TTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTGAAAGTA
1 AAATATGACAAAACC-AGTTTCATTATGACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTA
* * * *
183322 TAGATCCTTTTTATAAAAAAGATAAATACTTTATAATATAACATGTAA
65 TAGAT-CATTTTATAAAAAGGATAGATACTTTACAATATAACATGTAA
*
183370 AAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAATATGTTGAAAGTAT
1 AAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTAT
*
183435 AGATCATTTTATAAAAATGATAGATACTTTACAATATAACATGTAA
66 AGATCATTTTATAAAAAGGATAGATACTTTACAATATAACATGTAA
* * *
183481 AAATATGACAAAATCAGTTTCATTATGACAAAATCGGTAAAATCTACCTAATATGTTGAAAGTAT
1 AAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTAT
*
183546 AGATCATTTTATAAAAGGGATAGATACTTTACAATATAACATGTAA
66 AGATCATTTTATAAAAAGGATAGATACTTTACAATATAACATGTAA
** *
183592 AAATATGACAAAAATAGTTTCATTATGACAAAACCGATAAAATTTACCTAATATGTTGAAAGTAT
1 AAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTAT
*
183657 AGATACTTTTTATAAAAAGGATCA-ATACTTT
66 AGAT-CATTTTATAAAAAGGAT-AGATACTTT
183688 TTTGAAGTTA
Statistics
Matches: 400, Mismatches: 25, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
111 274 0.69
112 125 0.31
113 1 0.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (111 bp):
AAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTACCTAATATGTTGAAAGTAT
AGATCATTTTATAAAAAGGATAGATACTTTACAATATAACATGTAA
Found at i:184159 original size:2 final size:2
Alignment explanation
Indices: 184152--184202 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
184142 ATATTAACCG
184152 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
184194 TA TA TA TA T
1 TA TA TA TA T
184203 TTAATTACAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:187116 original size:17 final size:18
Alignment explanation
Indices: 187084--187119 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
187074 ATACCTCAAT
187084 TTATTGTTTTAATTAAAA
1 TTATTGTTTTAATTAAAA
*
187102 TTATT-TTTTATTTAAAA
1 TTATTGTTTTAATTAAAA
187119 T
1 T
187120 GACAAAACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TTATTGTTTTAATTAAAA
Found at i:191860 original size:99 final size:99
Alignment explanation
Indices: 191741--191952 Score: 297
Period size: 99 Copynumber: 2.2 Consensus size: 99
191731 CCATAATGTA
* * *
191741 ATTAT-ATATGTATACAATAAAGCTTGAGTTGTCCCTCTAGAGA-AATTGGTTAAACGCCCC-AG
1 ATTATAATATATATACAATAAAGCTTGAGTTATACCTCTAGA-ACAATTGGTTAAACGCCCCGA-
* *
191803 CTTTATGGATAAGATTCAGCTAGCCAAAT-AAAGATG
64 CTTTATGGATAAGATTCAACTAGCCAAATAAAAG-TC
*
191839 ATTATAATATATATACAATAAAGCTTGAGTTATACCTCTAGAACAATTGGTTAAATGCCCCGACT
1 ATTATAATATATATACAATAAAGCTTGAGTTATACCTCTAGAACAATTGGTTAAACGCCCCGACT
**
191904 TTATGGATAAGATTCAACTAGCCTGATAAAAGTC
66 TTATGGATAAGATTCAACTAGCCAAATAAAAGTC
191938 ATTATAATATATATA
1 ATTATAATATATATA
191953 TATATACACA
Statistics
Matches: 102, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
98 6 0.06
99 91 0.89
100 5 0.05
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (99 bp):
ATTATAATATATATACAATAAAGCTTGAGTTATACCTCTAGAACAATTGGTTAAACGCCCCGACT
TTATGGATAAGATTCAACTAGCCAAATAAAAGTC
Found at i:197303 original size:428 final size:427
Alignment explanation
Indices: 196478--197333 Score: 1521
Period size: 427 Copynumber: 2.0 Consensus size: 427
196468 TGATTAGGCC
196478 AATTTTAAAAAAACTCCATATGAAATTTTCAAAAATAAAAAGCCTAACATTAGCTATTTTCATCC
1 AATTTTAAAAAAACTCCATATGAAATTTTCAAAAATAAAAAGCCTAACATTAGCTATTTTCATCC
*
196543 TTTTGGATGTAAATGTTTTGTTTTAAAAACGTTAAAGAAAACCTTGGCAAATTTGATGCTAAAAG
66 TTTTGGATGTAAATGTTTTGTTTTAAAAACGGTAAAGAAAACCTTGGCAAATTTGATGCTAAAAG
196608 TGATGAAGGAATTTTTCTGGGTTATTCCTTAAATTCTAAAGCTTATCGAGTATTTAATAAAAGAA
131 TGATGAAGGAATTTTTCTGGGTTATTCCTTAAATTCTAAAGCTTATCGAGTATTTAATAAAAGAA
*
196673 CTTTAGTTGTAGAAGAGTCTATACATGTTTTCGATGATAATCTCCTTCGAGGAAGGATTCTGTGT
196 CTTTAGTTGTAGAAGAGTCTACACATGTTTTCGATGATAATCTCCTTCGAGGAAGGATTCTGTGT
196738 TAATGATGATGTAGGTATTAAAATACAAATGCGTTAGACATGACGTTGGAGAATCATCATCAAAG
261 TAATGATGATGTAGGTATTAAAATACAAATGCGTTAGACATGACGTTGGAGAATCATCATCAAAG
196803 GAAGAAACGAAAGAGAGGAAACTCATGATCCTCTCGAGAATCCAACCATTGAAGAAAGGGAAGTA
326 GAAGAAACGAAAGAGAGGAAACTCATGATCCTCTCGAGAATCCAACCATTGAAGAAAGGGAAGTA
196868 TCTTATCCAAGAGAGTACAACTATATCAAGGATGGTGAG
391 TCTTATCC-A-AGAGTACAACTATATCAAGGATGGTGAG
*
196907 AATTTTAAGAAAACTCCATATGAAATTTTC-AAAATAAAAAGCCTAAC-TTAGCTATTTTCATCC
1 AATTTTAAAAAAACTCCATATGAAATTTTCAAAAATAAAAAGCCTAACATTAGCTATTTTCATCC
196970 TTTTGGATGT-AATGTTTTGTTTTAAACAACGGT-AA-AAAA-CTTGGCAAATTTGATGCTAAAA
66 TTTTGGATGTAAATGTTTTGTTTTAAA-AACGGTAAAGAAAACCTTGGCAAATTTGATGCTAAAA
197031 GTGATGAAGGAA-TTTTCTGGGTTATTCCTTAAATTCTAAAGCTTATCGAGTATTTAATAAAAGA
130 GTGATGAAGGAATTTTTCTGGGTTATTCCTTAAATTCTAAAGCTTATCGAGTATTTAATAAAAGA
** *
197095 ACTTTAGTTGTAGAAGAGTCTACATGTTGTTTTCGATGATAATCTCTTTCCGAGGAA-GATTCTT
195 ACTTTAGTTGTAGAAGAGTCTACA-CATGTTTTCGATGATAATCTCCTT-CGAGGAAGGATTC-T
197159 GTGTTAATGATGATGTAGGTATTATAAATACAAATGACGTTAGACATGACGTTGGAGAATCATCA
257 GTGTTAATGATGATGTAGGTATTA-AAATACAAATG-CGTTAGACATGACGTTGGAGAATCATCA
197224 TCAAAGGAAGAAACGAAAGATGAGGAAACTCATGATCCTCTCGAGAATCCAACCATTGAAGAAAG
320 TCAAAGGAAGAAACGAAAGA-GAGGAAACTCATGATCCTCTCGAGAATCCAACCATTGAAGAAAG
197289 GGAAGTATCTTATCCAAGAGTACAACTATATCAAGGATGGTGAG
384 GGAAGTATCTTATCCAAGAGTACAACTATATCAAGGATGGTGAG
197333 A
1 A
197334 TTATAGGTGA
Statistics
Matches: 414, Mismatches: 6, Indels: 17
0.95 0.01 0.04
Matches are distributed among these distances:
423 75 0.18
424 60 0.14
425 36 0.09
426 58 0.14
427 80 0.19
428 76 0.18
429 29 0.07
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (427 bp):
AATTTTAAAAAAACTCCATATGAAATTTTCAAAAATAAAAAGCCTAACATTAGCTATTTTCATCC
TTTTGGATGTAAATGTTTTGTTTTAAAAACGGTAAAGAAAACCTTGGCAAATTTGATGCTAAAAG
TGATGAAGGAATTTTTCTGGGTTATTCCTTAAATTCTAAAGCTTATCGAGTATTTAATAAAAGAA
CTTTAGTTGTAGAAGAGTCTACACATGTTTTCGATGATAATCTCCTTCGAGGAAGGATTCTGTGT
TAATGATGATGTAGGTATTAAAATACAAATGCGTTAGACATGACGTTGGAGAATCATCATCAAAG
GAAGAAACGAAAGAGAGGAAACTCATGATCCTCTCGAGAATCCAACCATTGAAGAAAGGGAAGTA
TCTTATCCAAGAGTACAACTATATCAAGGATGGTGAG
Found at i:199196 original size:19 final size:19
Alignment explanation
Indices: 199166--199223 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
199156 TTATAGGGCA
199166 GAGGGAATCGATACCCCCT
1 GAGGGAATCGATACCCCCT
*
199185 GAGGGGAA-CGATTCCCCCAT
1 GA-GGGAATCGATACCCCC-T
199205 -AGGGAATCGATACCCCCT
1 GAGGGAATCGATACCCCCT
199223 G
1 G
199224 GGTTCTGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 6 0.18
19 21 0.64
20 6 0.18
ACGTcount: A:0.26, C:0.31, G:0.28, T:0.16
Consensus pattern (19 bp):
GAGGGAATCGATACCCCCT
Found at i:203642 original size:37 final size:37
Alignment explanation
Indices: 203583--203708 Score: 144
Period size: 37 Copynumber: 3.4 Consensus size: 37
203573 TTTGACCTTC
* *
203583 GAAGAAAATCAATCTTAAGCCTTCACGGAAGAGTAGT
1 GAAGCAAATAAATCTTAAGCCTTCACGGAAGAGTAGT
* * * *
203620 GAAGCAAGTAAATCTTAAGCCTTTACGGAAAATTAGT
1 GAAGCAAATAAATCTTAAGCCTTCACGGAAGAGTAGT
* * * * *
203657 GAACCAAATCATTCTTAAGCTTTCATGGAAGAGTAGT
1 GAAGCAAATAAATCTTAAGCCTTCACGGAAGAGTAGT
*
203694 GAAGCAAATCAATCT
1 GAAGCAAATAAATCT
203709 CGAGTCTGAT
Statistics
Matches: 72, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (37 bp):
GAAGCAAATAAATCTTAAGCCTTCACGGAAGAGTAGT
Found at i:203918 original size:111 final size:110
Alignment explanation
Indices: 203760--204292 Score: 529
Period size: 111 Copynumber: 4.8 Consensus size: 110
203750 TTCTAAAGAA
* * * ** *** * * **
203760 TTTTCAAGTCCTATACTCTCTGAAAGAAGATGAAGCATACTTGTCTTCCGAATATTTTTTTAGTC
1 TTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATCTTCTGAAGATTTTTCAAGTC
203825 TTATCTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATTAAGTT
66 TTATCTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATTAAGTT
* * * * *
203870 TTTCCCAAGTCCAATACTCTCTGAAAGAAGAGGGAGCGGGCCCATCTTCTGAAGATTTTTCGAGT
1 TTT-TCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATCTTCTGAAGATTTTTCAAGT
* * * *
203935 TTTATCTCCCTGAAAGAAGAGTGGAGCA-ACCCGTCTTATCAAGTAT
65 CTTATCTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATTAAGT-T
* * * * *
203981 TTTTCAAGTTCTATACTCCCTGAAAGAAGATGGAGCAGACCCATTTTCTGAAGATTTTTTAAGTC
1 TTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATCTTCTGAAGATTTTTCAAGTC
* * * *
204046 CTATACTCCCTGAAAGAAGAG-GGAGC-GAACCCGT-TT-TTCGAAGAT
66 TTAT-CTCCCTGAAAGAATAGTGGAGCAG-ACCCATCTTATT--AAGTT
* * ***
204091 TTTTCAAGTCCTATACTCTCTGAAAGAAGAGGGAACGGACATGTCTTCTGAAGATTTTTCAAGTC
1 TTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATCTTCTGAAGATTTTTCAAGTC
* *
204156 TTATCTCCCTGAAAGAATAGTGGAGCATACCCATCTTATGAAGTT
66 TTATCTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATTAAGTT
* * * ** * * *
204201 TTTCTCAAGTCCTACACTCCCTAAAAGAAGAGGGAGCGGGCCCGCCTTCCGAAGATATTTCGAGT
1 TTT-TCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATCTTCTGAAGATTTTTCAAGT
*
204266 C-TATTTTACCCTGAAAGAATAGTGGAG
65 CTTA-TCT-CCCTGAAAGAATAGTGGAG
204293 TATACTCATC
Statistics
Matches: 349, Mismatches: 60, Indels: 26
0.80 0.14 0.06
Matches are distributed among these distances:
109 16 0.05
110 156 0.45
111 157 0.45
112 20 0.06
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (110 bp):
TTTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATCTTCTGAAGATTTTTCAAGTC
TTATCTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATTAAGTT
Found at i:203984 original size:55 final size:55
Alignment explanation
Indices: 203755--204237 Score: 403
Period size: 55 Copynumber: 8.8 Consensus size: 55
203745 TCGTTTTCTA
* * * *** **
203755 AAGAATTTTCAAGTCCTATACTCTCTGAAAGAAGA-TGAAGCATACTTGTCTTCCG
1 AAGATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGTGGAGCA-ACCCATCTTATG
* ** * * *
203810 AATATTTTTTTAGTCTTAT-CTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATT
1 AAGATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGTGGAGCA-ACCCATCTTATG
* * ** *
203865 AAG-TTTTTCCCAAGTCCAATACTCTCTGAAAGAAGAG-GGAGCGGGCCCATCTTCTG
1 AAGATTTTT--CAAGTCCTATACTCCCTGAAAGAAGAGTGGAGC-AACCCATCTTATG
* ** * *
203921 AAGATTTTTCGAGTTTTAT-CTCCCTGAAAGAAGAGTGGAGCAACCCGTCTTATC
1 AAGATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGTGGAGCAACCCATCTTATG
* * *
203975 AAGTATTTTTCAAGTTCTATACTCCCTGAAAGAAGA-TGGAGCAGACCCATTTTCTG
1 AAG-ATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGTGGAGCA-ACCCATCTTATG
* * *
204031 AAGATTTTTTAAGTCCTATACTCCCTGAAAGAAGAG-GGAGCGAACCCGT-TTTTCG
1 AAGATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGTGGAGC-AACCCATCTTAT-G
* * * *** *
204086 AAGATTTTTCAAGTCCTATACTCTCTGAAAGAAGAG-GGAACGGACATGTCTTCTG
1 AAGATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGTGGAGC-AACCCATCTTATG
* *
204141 AAGATTTTTCAAGTCTTAT-CTCCCTGAAAGAATAGTGGAGCATACCCATCTTATG
1 AAGATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGTGGAGCA-ACCCATCTTATG
* * *
204196 AAGTTTTTCTCAAGTCCTACACTCCCTAAAAGAAGAG-GGAGC
1 AAGATTTT-TCAAGTCCTATACTCCCTGAAAGAAGAGTGGAGC
204238 GGGCCCGCCT
Statistics
Matches: 343, Mismatches: 67, Indels: 35
0.77 0.15 0.08
Matches are distributed among these distances:
54 61 0.18
55 182 0.53
56 67 0.20
57 33 0.10
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (55 bp):
AAGATTTTTCAAGTCCTATACTCCCTGAAAGAAGAGTGGAGCAACCCATCTTATG
Found at i:204016 original size:110 final size:111
Alignment explanation
Indices: 203708--204292 Score: 560
Period size: 110 Copynumber: 5.3 Consensus size: 111
203698 CAAATCAATC
* * * * * * *
203708 TCGAGTCTGATCTCCCCTGAAAGAAGAG-GGACCAGACTCGTTTTCTAAAG-AATTTTCAAGTCC
1 TCGAGTCTTATCT-CCCTGAAAGAAGAGTGGAGCAGACCCGTCTTATCAAGTATTTTTCAAGTCC
* * ** ** * *
203771 TATACTCTCTGAAAGAAGATGAAGCATACTTGTCTTCCGAATATTTT
65 TATACTCTCTGAAAGAAGAGGGAGCGGACCCGTCTTCTGAAGATTTT
** * * * *
203818 TTTAGTCTTATCTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATTAAGT-TTTTCCCAAGTCC
1 TCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTATCAAGTATTTT-TCAAGTCC
* * *
203882 AATACTCTCTGAAAGAAGAGGGAGCGGGCCCATCTTCTGAAGATTTT
65 TATACTCTCTGAAAGAAGAGGGAGCGGACCCGTCTTCTGAAGATTTT
* *
203929 TCGAGTTTTATCTCCCTGAAAGAAGAGTGGAGCA-ACCCGTCTTATCAAGTATTTTTCAAGTTCT
1 TCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTATCAAGTATTTTTCAAGTCCT
* * * * *
203993 ATACTCCCTGAAAGAAGATGGAGCAGACCCATTTTCTGAAGATTTT
66 ATACTCTCTGAAAGAAGAGGGAGCGGACCCGTCTTCTGAAGATTTT
** * *
204039 TTAAGTCCTATACTCCCTGAAAGAAGAG-GGAGC-GAACCCGT-TTTTCGAAG-ATTTTTCAAGT
1 TCGAGTCTTAT-CTCCCTGAAAGAAGAGTGGAGCAG-ACCCGTCTTATC-AAGTATTTTTCAAGT
* **
204100 CCTATACTCTCTGAAAGAAGAGGGAACGGACATGTCTTCTGAAGATTTT
63 CCTATACTCTCTGAAAGAAGAGGGAGCGGACCCGTCTTCTGAAGATTTT
* * * * *
204149 TCAAGTCTTATCTCCCTGAAAGAATAGTGGAGCATACCCATCTTATGAAGT-TTTTCTCAAGTCC
1 TCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTATCAAGTATTTT-TCAAGTCC
* * * * * * *
204213 TACACTCCCTAAAAGAAGAGGGAGCGGGCCCGCCTTCCGAAGATATT
65 TATACTCTCTGAAAGAAGAGGGAGCGGACCCGTCTTCTGAAGATTTT
* *
204260 TCGAGTC-TATTTTACCCTGAAAGAATAGTGGAG
1 TCGAGTCTTA-TCT-CCCTGAAAGAAGAGTGGAG
204293 TATACTCATC
Statistics
Matches: 390, Mismatches: 70, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
109 28 0.07
110 185 0.47
111 158 0.41
112 19 0.05
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (111 bp):
TCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCGTCTTATCAAGTATTTTTCAAGTCCT
ATACTCTCTGAAAGAAGAGGGAGCGGACCCGTCTTCTGAAGATTTT
Found at i:204017 original size:166 final size:165
Alignment explanation
Indices: 203821--204292 Score: 537
Period size: 166 Copynumber: 2.8 Consensus size: 165
203811 ATATTTTTTT
* *
203821 AGTCTTATCTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATTAAGTTTTTCCCAAGTCCAATA
1 AGTCTTATCTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATGAAGTTTTT-CCAAGTCCTATA
* *
203886 CTCTCTGAAAGAAGAGGGAGCGGGCCCATCTTCTGAAGATTTTTCGAGTTTTATCTCCCTGAAAG
65 CTCCCTGAAAGAAGAGGGAGCGGGCCCGTCTTCTGAAGATTTTTCGAGTTTTATCTCCCTGAAAG
*
203951 AAGAGTGGAGC-AACCCGTCTTATCAAGTATTTTTCA
130 AAGAGTGGAGCGAACACGTCTTATCAAG-ATTTTTCA
* * * *
203987 AGT-TCTATACTCCCTGAAAGAAGA-TGGAGCAGACCCATTTTCTGAAGATTTTT-TAAGTCCTA
1 AGTCT-TAT-CTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATGAAG-TTTTTCCAAGTCCTA
** * * ** *
204049 TACTCCCTGAAAGAAGAGGGAGCGAACCCGT-TTTTCGAAGATTTTTCAAGTCCTATACTCTCTG
63 TACTCCCTGAAAGAAGAGGGAGCGGGCCCGTCTTCT-GAAGATTTTTCGAGTTTTAT-CTCCCTG
* * * * *
204113 AAAGAAGAG-GGAACGGACATGTCTTCTGAAGATTTTTCA
126 AAAGAAGAGTGGAGCGAACACGTCTTATCAAGATTTTTCA
* *
204152 AGTCTTATCTCCCTGAAAGAATAGTGGAGCATACCCATCTTATGAAGTTTTTCTCAAGTCCTACA
1 AGTCTTATCTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATGAAGTTTTTC-CAAGTCCTATA
* * * *
204217 CTCCCTAAAAGAAGAGGGAGCGGGCCCGCCTTCCGAAGATATTTCGAGTCTATT-T-TACCCTGA
65 CTCCCTGAAAGAAGAGGGAGCGGGCCCGTCTTCTGAAGATTTTTCGAGT-T-TTATCT-CCCTGA
*
204280 AAGAATAGTGGAG
127 AAGAAGAGTGGAG
204293 TATACTCATC
Statistics
Matches: 251, Mismatches: 40, Indels: 29
0.78 0.12 0.09
Matches are distributed among these distances:
164 22 0.09
165 91 0.36
166 112 0.45
167 25 0.10
168 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (165 bp):
AGTCTTATCTCCCTGAAAGAATAGTGGAGCAGACCCATCTTATGAAGTTTTTCCAAGTCCTATAC
TCCCTGAAAGAAGAGGGAGCGGGCCCGTCTTCTGAAGATTTTTCGAGTTTTATCTCCCTGAAAGA
AGAGTGGAGCGAACACGTCTTATCAAGATTTTTCA
Found at i:205621 original size:2 final size:2
Alignment explanation
Indices: 205614--205712 Score: 175
Period size: 2 Copynumber: 50.5 Consensus size: 2
205604 GATAATCTAC
205614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
205656 AT AT A- AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
205696 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
205713 GTAAAGTTTA
Statistics
Matches: 93, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
1 2 0.02
2 91 0.98
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:206190 original size:23 final size:23
Alignment explanation
Indices: 206164--206221 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
206154 GCTCGTATAA
*
206164 TGCATCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
206187 TGCACCGGAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
206210 TGCACCGTAGTG
1 TGCACCGAAGTG
206222 TCATATAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:212166 original size:2 final size:2
Alignment explanation
Indices: 212159--212193 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
212149 ACGATAATCT
212159 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
212194 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:212198 original size:2 final size:2
Alignment explanation
Indices: 212193--212221 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
212183 ACACACACAC
212193 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
212222 AGTTTATACA
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:212694 original size:23 final size:23
Alignment explanation
Indices: 212668--212759 Score: 132
Period size: 23 Copynumber: 4.0 Consensus size: 23
212658 CACCACAGCT
*
212668 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
212691 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
212714 CGTAGAATTGCACC-AGAGTGCCG
1 CGTAGAATTGCACCGA-AGTGCCA
*
212737 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
212760 TATAATAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:213382 original size:20 final size:20
Alignment explanation
Indices: 213357--213394 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
213347 CTCTTTTTTA
213357 TGGGGGAATCGATTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
213377 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
213395 TTTAGCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.32, G:0.32, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:216017 original size:21 final size:20
Alignment explanation
Indices: 215992--216046 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
215982 TATGGGCAAG
215992 GGGTACCGATACCTTATGAAT
1 GGGTACCGATACC-TATGAAT
*
216013 GGGTACTGATACACTATGAAT
1 GGGTACCGATAC-CTATGAAT
*
216034 GGGTATCGATACC
1 GGGTACCGATACC
216047 CTAAGACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (20 bp):
GGGTACCGATACCTATGAAT
Found at i:222593 original size:15 final size:15
Alignment explanation
Indices: 222573--222639 Score: 82
Period size: 15 Copynumber: 4.5 Consensus size: 15
222563 TTCCGGAAAA
*
222573 TGAATTACTAGAATT
1 TGAATTACTGGAATT
**
222588 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
222603 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
222618 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
222632 TGAATTAC
1 TGAATTAC
222640 ATTTCTGGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
14 12 0.27
15 32 0.73
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.34
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:222637 original size:29 final size:30
Alignment explanation
Indices: 222567--222639 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
222557 TTGGTTTTCC
222567 GGAAAATGAATTACTAGAATTTGAATTACT
1 GGAAAATGAATTACTAGAATTTGAATTACT
*
222597 GGAAAATGAATTACTGGAATTTGAATT-CT
1 GGAAAATGAATTACTAGAATTTGAATTACT
222626 GGAAAATGAATTAC
1 GGAAAATGAATTAC
222640 ATTTCTGGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (30 bp):
GGAAAATGAATTACTAGAATTTGAATTACT
Found at i:222827 original size:15 final size:16
Alignment explanation
Indices: 222807--222836 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
222797 AATACAATAA
222807 ATAAAA-TTATTTATC
1 ATAAAACTTATTTATC
222822 ATAAAACTTATTTAT
1 ATAAAACTTATTTAT
222837 TACTAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAAACTTATTTATC
Found at i:222851 original size:17 final size:16
Alignment explanation
Indices: 222809--222854 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
222799 TACAATAAAT
*
222809 AAAATTATTTATCATA
1 AAAATTATTTATTATA
*
222825 AAACTTATTTATTACTA
1 AAAATTATTTATTA-TA
*
222842 AAAATAATTTATT
1 AAAATTATTTATT
222855 TATTATTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (16 bp):
AAAATTATTTATTATA
Found at i:223022 original size:23 final size:23
Alignment explanation
Indices: 222973--223035 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
222963 GTATTATATT
* **
222973 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
222996 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
223019 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
223036 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:223063 original size:19 final size:20
Alignment explanation
Indices: 223011--223122 Score: 63
Period size: 20 Copynumber: 5.6 Consensus size: 20
223001 TTAAATATCT
223011 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
223030 ATATATAAATAATATT-TTTCA
1 TTAT-TAAAT-ATATTATTTAA
* **
223051 TTATTAAATATATAATTTTT
1 TTATTAAATATATTATTTAA
*
223071 TTATT--ATATATTATTAAA
1 TTATTAAATATATTATTTAA
* * *
223089 ATA-AAAATATAATATCTTATA
1 TTATTAAATATATTAT-TTA-A
223110 TTATTATAATATA
1 TTATTA-AATATA
223123 ATTCATTATT
Statistics
Matches: 67, Mismatches: 16, Indels: 16
0.68 0.16 0.16
Matches are distributed among these distances:
18 11 0.16
19 15 0.22
20 19 0.28
21 10 0.15
22 6 0.09
23 6 0.09
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:223082 original size:59 final size:60
Alignment explanation
Indices: 223010--223152 Score: 143
Period size: 59 Copynumber: 2.4 Consensus size: 60
223000 TTTAAATATC
* * *
223010 TTTATTAAAATATTATTTAAATATATAA-ATAATAT-TTTTCATTATTAAATATATAATT-TT
1 TTTATT-ATATATTATTTAAATATAAAATATAATATCTTAT-ATTATTAAA-ATATAATTATT
* *
223070 TTTATTATATATTATTAAAATA-AAAATATAATATCTTATATTATTATAATATAATTCATT
1 TTTATTATATATTATTTAAATATAAAATATAATATCTTATATTATTAAAATATAATT-ATT
* *
223130 ATT-TTATATAATATTATAAATAT
1 TTTATTATATATTATT-TAAATAT
223153 TATATTATAT
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
58 11 0.16
59 40 0.58
60 18 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (60 bp):
TTTATTATATATTATTTAAATATAAAATATAATATCTTATATTATTAAAATATAATTATT
Found at i:223124 original size:23 final size:22
Alignment explanation
Indices: 223094--223143 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
223084 TTAAAATAAA
223094 AATATAATATC-TTATATTATTAT
1 AATATAAT-TCATTATATTA-TAT
*
223117 AATATAATTCATTATTTTATAT
1 AATATAATTCATTATATTATAT
223139 AATAT
1 AATAT
223144 TATAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATAATTCATTATATTATAT
Found at i:223145 original size:15 final size:16
Alignment explanation
Indices: 223107--223160 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 16
223097 ATAATATCTT
223107 ATATTATTATAATATA
1 ATATTATTATAATATA
*
223123 ATTCATTATT-TTATATA
1 A-T-ATTATTATAATATA
*
223140 ATATTA-TA-AATATT
1 ATATTATTATAATATA
223154 ATATTAT
1 ATATTAT
223161 ATTATTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
14 11 0.35
15 4 0.13
16 2 0.06
17 8 0.26
18 6 0.19
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATTATTATAATATA
Found at i:223157 original size:19 final size:20
Alignment explanation
Indices: 223133--223180 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
223123 ATTCATTATT
223133 TTATATAA-TATTATAAATA
1 TTATATAATTATTATAAATA
223152 TTATATTATATTATTATAAATA
1 TTATA-TA-ATTATTATAAATA
223174 TTA-ATAA
1 TTATATAA
223181 ATAAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 6 0.23
20 4 0.15
21 2 0.08
22 14 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATATAATTATTATAAATA
Found at i:223432 original size:42 final size:42
Alignment explanation
Indices: 223370--223489 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
223360 ATGAATTACG
* *
223370 TTCCGGAAAACCAATTACGTGAAACAAACACTGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
223412 TTTCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
223454 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
223490 TTCGGGGAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:224045 original size:22 final size:22
Alignment explanation
Indices: 224017--224069 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
224007 GAGTCGAGGG
*
224017 TATTCATAGGTCCTTCGGGACA
1 TATTCATAGGTCCTTAGGGACA
224039 TATTCATAGGTCCTTAGGGACA
1 TATTCATAGGTCCTTAGGGACA
*
224061 AATTTCATA
1 TA-TTCATA
224070 TGCCACTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (22 bp):
TATTCATAGGTCCTTAGGGACA
Found at i:226782 original size:31 final size:31
Alignment explanation
Indices: 226747--226816 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
226737 GTAATTTTTA
* *
226747 ATAGTCGGAGAACTCAACAAAATAGTATCAT
1 ATAGTCGGAAAACTCAACAAAATAATATCAT
* * *
226778 ATAGTCAGAAAACTTAACAAAATAATATCTT
1 ATAGTCGGAAAACTCAACAAAATAATATCAT
226809 ATAGTCGG
1 ATAGTCGG
226817 GAATCATTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (31 bp):
ATAGTCGGAAAACTCAACAAAATAATATCAT
Found at i:227416 original size:20 final size:21
Alignment explanation
Indices: 227391--227442 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
227381 TTTTCCCAAT
*
227391 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
227411 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
227432 TCGCAATGCGA
1 TCGCAATGCGA
227443 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:227456 original size:20 final size:20
Alignment explanation
Indices: 227431--227544 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
227421 AATTGGGAAA
*
227431 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
227451 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
227471 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
227492 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
227512 TTTGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
227532 TTCGCAACGCGAT
1 ATCGCAACGCGAT
227545 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.78
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:227475 original size:61 final size:61
Alignment explanation
Indices: 227428--227544 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
227418 GCGAATTGGG
* * * * *
227428 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
227489 AAAATCGCAACGAGATACTGACTTTTGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
227545 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:228141 original size:19 final size:19
Alignment explanation
Indices: 228119--228303 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
228109 GAAACCAAAA
*
228119 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
228138 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
228157 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
228176 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
228196 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
228212 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
228229 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
228243 TCTCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
228263 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
228282 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
228302 TC
1 TC
228304 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 61 0.44
20 49 0.36
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:228196 original size:39 final size:38
Alignment explanation
Indices: 228119--228303 Score: 174
Period size: 33 Copynumber: 5.1 Consensus size: 38
228109 GAAACCAAAA
*
228119 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
228157 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
228196 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
228229 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCA-TT
* *
228263 TCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
228302 TC
1 TC
228304 AACCAAAAGA
Statistics
Matches: 124, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
31 3 0.02
33 35 0.28
34 13 0.10
35 1 0.01
36 3 0.02
38 21 0.17
39 33 0.27
40 15 0.12
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:230343 original size:42 final size:42
Alignment explanation
Indices: 230283--230405 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
230273 GCCCGACTCG
* * *
230283 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
230325 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
230367 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
230406 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:230363 original size:21 final size:21
Alignment explanation
Indices: 230339--230405 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
230329 TCATTCCTCG
230339 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
230360 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
230381 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
230402 AGAG
1 AGAG
230406 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:231781 original size:14 final size:14
Alignment explanation
Indices: 231762--231797 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
231752 ATTGTTTAAT
231762 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
231776 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
231790 TGATTTGT
1 TGATTTGT
231798 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:232022 original size:33 final size:32
Alignment explanation
Indices: 231980--232106 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
231970 ATTAAATTTG
231980 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
232013 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
232046 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
232079 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
232107 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:232069 original size:66 final size:66
Alignment explanation
Indices: 231973--232105 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
231963 ACGCGAAATT
*
231973 AAATTTGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
232038 G
66 G
*
232039 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
232104 G
66 G
232105 A
1 A
232106 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:234415 original size:12 final size:12
Alignment explanation
Indices: 234398--234422 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
234388 TCTTCGGGGA
234398 CTTTTTCTTCTT
1 CTTTTTCTTCTT
234410 CTTTTTCTTCTT
1 CTTTTTCTTCTT
234422 C
1 C
234423 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:234631 original size:24 final size:24
Alignment explanation
Indices: 234597--234650 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
234587 CTGAAACATC
* *
234597 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
234621 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
234645 ATCAAA
1 ATCAAA
234651 TTTCGAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:234661 original size:24 final size:24
Alignment explanation
Indices: 234610--234664 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
234600 AAAATCCGTG
* **
234610 TATTGACCAATATCAAAGTCCGGG
1 TATTGACCAAGATCAAAGTCCGAA
* *
234634 TATTGACCAAGATCAAATTTCGAA
1 TATTGACCAAGATCAAAGTCCGAA
234658 TATTGAC
1 TATTGAC
234665 TAGTACTCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (24 bp):
TATTGACCAAGATCAAAGTCCGAA
Found at i:235728 original size:20 final size:20
Alignment explanation
Indices: 235703--235760 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
235693 ATTCATTTGA
235703 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
235723 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
235743 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
235761 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:235803 original size:14 final size:14
Alignment explanation
Indices: 235784--235837 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
235774 GAAAATCGCA
235784 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
235798 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
235815 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
235831 TTGCGAT
1 TTGCGAT
235838 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:235803 original size:33 final size:33
Alignment explanation
Indices: 235766--235836 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
235756 AAAATCGCAA
235766 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
235799 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
235832 TGCGA
1 TGCGA
235837 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:235845 original size:33 final size:33
Alignment explanation
Indices: 235779--235856 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
235769 GAAATGAAAA
***
235779 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
235812 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
**
235845 TCGTGTTGCGAT
1 TCGCATTGCGAT
235857 AGTCTGTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:235963 original size:14 final size:14
Alignment explanation
Indices: 235944--235980 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
235934 CATCAATTAA
235944 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
235958 ACAAATCATCTTTT
1 ACAAATCAACATTT
235972 ACAAATCAA
1 ACAAATCAA
235981 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:237870 original size:19 final size:19
Alignment explanation
Indices: 237846--237912 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
237836 GAAACTTAAA
237846 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
* *
237865 ATCGCAACACGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
237885 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
237904 ATCGCAACG
1 ATCGCAACG
237913 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:237881 original size:20 final size:19
Alignment explanation
Indices: 237827--237911 Score: 71
Period size: 20 Copynumber: 4.4 Consensus size: 19
237817 TAGTTTACTT
* **
237827 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAA-TGACTA
*
237847 TCGCAACGCGAAATGACTA
1 TCGCAACACGAAATGACTA
*
237866 TCGCAACACGGAAATGGCTA
1 TCGCAACAC-GAAATGACTA
** **
237886 TCGCAATGCGAAATGAAAA
1 TCGCAACACGAAATGACTA
237905 TCGCAAC
1 TCGCAAC
237912 GACAAAATCG
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
19 24 0.46
20 28 0.54
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.15
Consensus pattern (19 bp):
TCGCAACACGAAATGACTA
Found at i:237920 original size:14 final size:14
Alignment explanation
Indices: 237901--237958 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
237891 ATGCGAAATG
*
237901 AAAATCGCAACGAC
1 AAAATCGCAACGAA
237915 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAA
237931 ATGAAATCGCAACGAA
1 A--AAATCGCAACGAA
237947 AAAATCGCAACG
1 AAAATCGCAACG
237959 CGAAACACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 21 0.54
16 9 0.23
18 9 0.23
ACGTcount: A:0.50, C:0.24, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:237943 original size:32 final size:33
Alignment explanation
Indices: 237885--237963 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
237875 GGAAATGGCT
* *
237885 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
237918 ATCGCAACGCGAAATG-AAATCGCAACGAAAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
237950 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
237964 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
Found at i:237970 original size:19 final size:17
Alignment explanation
Indices: 237885--237974 Score: 66
Period size: 14 Copynumber: 5.4 Consensus size: 17
237875 GGAAATGGCT
*
237885 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAA--AAA
*
237904 ATCGCAA--CG-ACAAA
1 ATCGCAACGCGAAAAAA
*
237918 ATCGCAACGCGAAATGAA
1 ATCGCAACGCGAAA-AAA
237936 ATCGCAA--CG-AAAAA
1 ATCGCAACGCGAAAAAA
237950 ATCGCAACGCGAAACACAA
1 ATCGCAACGCGAAA-A-AA
237969 ATCGCA
1 ATCGCA
237975 TTGCGATTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
14 19 0.33
15 2 0.03
16 7 0.12
17 5 0.09
18 10 0.17
19 15 0.26
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (17 bp):
ATCGCAACGCGAAAAAA
Found at i:237992 original size:19 final size:19
Alignment explanation
Indices: 237970--238051 Score: 104
Period size: 18 Copynumber: 4.6 Consensus size: 19
237960 GAAACACAAA
237970 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
237989 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
238007 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
238023 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
238040 TCGCATTGCGAT
1 TCGCATTGCGAT
238052 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.11
15 3 0.06
16 4 0.07
17 4 0.07
18 20 0.37
19 17 0.31
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:238079 original size:39 final size:34
Alignment explanation
Indices: 237970--238071 Score: 102
Period size: 33 Copynumber: 2.8 Consensus size: 34
237960 GAAACACAAA
237970 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTCATT
1 TCGCATTGCGA---TCATTTCGCGTTGCGATTTCATT
238007 TCGCATTGCGAT--TTT-GTCGTTGCGATTTTCATT
1 TCGCATTGCGATCATTTCG-CGTTGCGA-TTTCATT
238040 TCGCATTGCGATAGCCATTTCCGCGTTGCGAT
1 TCGCATTGCGAT---CATTT-CGCGTTGCGAT
238072 AGTCATTTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 17
0.77 0.00 0.23
Matches are distributed among these distances:
31 1 0.02
32 11 0.20
33 19 0.34
34 1 0.02
37 11 0.20
38 4 0.07
39 8 0.14
40 1 0.02
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.42
Consensus pattern (34 bp):
TCGCATTGCGATCATTTCGCGTTGCGATTTCATT
Found at i:238087 original size:20 final size:20
Alignment explanation
Indices: 238036--238079 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
238026 TTGCGATTTT
*
238036 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
238055 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
238075 CATTT
1 CATTT
238080 TCGTGTTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:238598 original size:18 final size:18
Alignment explanation
Indices: 238572--238616 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
238562 GTCGATCAGA
*
238572 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
238590 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
238608 TGATGGCTC
1 TGATGGCTC
238617 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:239959 original size:20 final size:20
Alignment explanation
Indices: 239934--239971 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
239924 AATAGTTTCT
239934 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
239954 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
239972 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:240253 original size:20 final size:21
Alignment explanation
Indices: 240228--240276 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
240218 TCTGAGAGAT
240228 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
240248 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
*
240270 GAAGATG
1 GGAGATG
240277 GGTGAGAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 1 0.04
22 17 0.71
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:240262 original size:22 final size:22
Alignment explanation
Indices: 240235--240278 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
240225 GATGGAGATA
*
240235 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGAAGATGGG
*
240257 GACGGATTTCGTCGAAGATGGG
1 GACGGATTTCGCCGAAGATGGG
240279 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGAAGATGGG
Found at i:240552 original size:20 final size:20
Alignment explanation
Indices: 240446--240560 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
240436 CGCTTTGAAA
*
240446 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
240467 ATCGCGTTGCAAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
240487 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
240507 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
240528 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
240548 ATCGCATTGCGAT
1 ATCGCATTGCGAT
240561 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 49 0.66
21 23 0.31
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:240578 original size:21 final size:21
Alignment explanation
Indices: 240549--240641 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
240539 ATAGTCAGTA
240549 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
240570 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
240590 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
240611 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
240631 TCGCATTGCGA
1 TCGCATTGCGA
240642 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:240579 original size:41 final size:41
Alignment explanation
Indices: 240488--240622 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
240478 AAAGTCAGTA
* * * ** *
240488 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
240528 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
240570 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
240611 TCGCGTTGCGAT
1 TCGCGTTGCGAT
240623 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:240623 original size:41 final size:41
Alignment explanation
Indices: 240549--240641 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
240539 ATAGTCAGTA
240549 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
240590 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
240631 TCGCATTGCGA
1 TCGCATTGCGA
240642 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:248008 original size:12 final size:13
Alignment explanation
Indices: 247982--248010 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
247972 CGGCGATGGA
247982 AAAAGATGAGATG
1 AAAAGATGAGATG
247995 AAAAGATG-GATG
1 AAAAGATGAGATG
248007 AAAA
1 AAAA
248011 ATAAAAGACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.14
Consensus pattern (13 bp):
AAAAGATGAGATG
Found at i:248011 original size:13 final size:14
Alignment explanation
Indices: 247980--248011 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
247970 AGCGGCGATG
247980 GAAAAAGATGAGAT
1 GAAAAAGATGAGAT
247994 G-AAAAGATG-GAT
1 GAAAAAGATGAGAT
248006 GAAAAA
1 GAAAAA
248012 TAAAAGACGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 12 0.71
14 1 0.06
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.12
Consensus pattern (14 bp):
GAAAAAGATGAGAT
Found at i:248931 original size:95 final size:95
Alignment explanation
Indices: 248805--248985 Score: 258
Period size: 95 Copynumber: 1.9 Consensus size: 95
248795 TGTCCTTTTT
* * * * * * *
248805 CCATCGTCCCTCATCCTCGGTGAACATGAAACACAACCAAACCGATCCATT-CCTTGAGCGTCAT
1 CCATCGACCCTCACCCCCAGTGAACATGAAACACAACCAAACCGAACC-TTCCCTTGAACCTCAT
*
248869 CTCGATTGGCCCTAACTGACTCCTCCGTTTA
65 CTCGATCGGCCCTAACTGACTCCTCCGTTTA
248900 CCATCGACCCTCACCCCCAGTGAAC-TCGAAACACAACCAAACCGAACCTTCCCTTGAACCTCAT
1 CCATCGACCCTCACCCCCAGTGAACAT-GAAACACAACCAAACCGAACCTTCCCTTGAACCTCAT
248964 CTCGATCGGCCCTAACTGACTC
65 CTCGATCGGCCCTAACTGACTC
248986 GTATTTCGAC
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
94 3 0.04
95 73 0.96
ACGTcount: A:0.26, C:0.39, G:0.13, T:0.22
Consensus pattern (95 bp):
CCATCGACCCTCACCCCCAGTGAACATGAAACACAACCAAACCGAACCTTCCCTTGAACCTCATC
TCGATCGGCCCTAACTGACTCCTCCGTTTA
Found at i:258231 original size:14 final size:14
Alignment explanation
Indices: 258212--258241 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
258202 ACAAGGTAGT
258212 CTATTCAAAGATAA
1 CTATTCAAAGATAA
258226 CTATTCAAAGATAA
1 CTATTCAAAGATAA
258240 CT
1 CT
258242 TTTAATCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.30
Consensus pattern (14 bp):
CTATTCAAAGATAA
Found at i:259705 original size:74 final size:74
Alignment explanation
Indices: 259572--259842 Score: 382
Period size: 75 Copynumber: 3.6 Consensus size: 74
259562 CTTAACATGT
* * * **
259572 TAAAATAAAATAGGTGATACCTATTATGTTAAACTACCTACTGGTTTGTTTGAGTGTTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGGTTTGTTAAAG-GTTACTAATA
*
259637 ATGTAAATGG
65 ATGTAAACGG
* * *
259647 TAAAA-AAGATAGGCGCTACCTATTACGTTAAAATACTTACTGGTTTGATTAAAGGTTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGGTTTG-TTAAAGGTTACTAATA
259711 ATGTAAACGG
65 ATGTAAACGG
* * *
259721 TAAAATAAAATAGGCACTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAATGTTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGGTTTG-TTAAAGGTTACTAATA
259786 ATGTAAACGG
65 ATGTAAACGG
* *
259796 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTAGCTACCGGTTT
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGGTTT
259843 TTTAGATACA
Statistics
Matches: 176, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
74 60 0.34
75 116 0.66
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (74 bp):
TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGGTTTGTTAAAGGTTACTAATAA
TGTAAACGG
Found at i:262790 original size:3 final size:3
Alignment explanation
Indices: 262777--262832 Score: 96
Period size: 3 Copynumber: 18.7 Consensus size: 3
262767 AATAAATGTA
262777 AAT ATAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
262822 AAT AAT AAT AA
1 AAT AAT AAT AA
262833 ATAACGTAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:263391 original size:134 final size:134
Alignment explanation
Indices: 263025--263423 Score: 491
Period size: 134 Copynumber: 3.0 Consensus size: 134
263015 TATATTTGGA
* ** *
263025 GATAACACGATTCCTACGTGATGAGGA-AATCTGGTTATCTAAGGGTGACACTGCTCCTAAATGA
1 GATAACACGATTCCTACGTGATGAGGACGA-CTGGTTATCTAAGGGTGACACAACTCCTAAGTGA
* * * * *
263089 TGAGGAGATCTGGTCGGTGGATGACACGGTTCATACGTGACGAGGATGGTTGGCCAACTTTAGGG
65 TGAGGAGATCTGGTAGGTGGATGACACGGTTCCTACGTGATGAGGATGGATGGCCATCTTTAGGG
263154 ATGAT
130 ATGAT
* * * * * *
263159 GATAACATGATTCGTACATGATGAGGACGACTGGTTATCTAAGGGTGACACGACTCTTACGTGAT
1 GATAACACGATTCCTACGTGATGAGGACGACTGGTTATCTAAGGGTGACACAACTCCTAAGTGAT
* * *
263224 GAGGAGATCTGATCA-GTGGATGACACGGTTCCTACATGTTGAGGATGGATGGCCATCTTTAGGG
66 GAGGAGATCTGGT-AGGTGGATGACACGGTTCCTACGTGATGAGGATGGATGGCCATCTTTAGGG
263288 ATGAT
130 ATGAT
* * *
263293 GATAACAC-AGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGTTGACGCAACTCCTAAGTGA
1 GATAACACGA-TTCCTACGTGATGAGGACGACTGGTTATCTAAGGGTGACACAACTCCTAAGTGA
* ** * * *
263357 TGAGGAGATATGGTAGGTGGATGACACGACTCCTACGCGATGAGGA-CGACTGGACATCTTTAGG
65 TGAGGAGATCTGGTAGGTGGATGACACGGTTCCTACGTGATGAGGATGGA-TGGCCATCTTTAGG
263421 GAT
129 GAT
263424 AATTTGTTTC
Statistics
Matches: 225, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
133 4 0.02
134 220 0.98
135 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (134 bp):
GATAACACGATTCCTACGTGATGAGGACGACTGGTTATCTAAGGGTGACACAACTCCTAAGTGAT
GAGGAGATCTGGTAGGTGGATGACACGGTTCCTACGTGATGAGGATGGATGGCCATCTTTAGGGA
TGAT
Found at i:263646 original size:71 final size:71
Alignment explanation
Indices: 263426--263773 Score: 480
Period size: 71 Copynumber: 5.0 Consensus size: 71
263416 TTAGGGATAA
* * *
263426 TTTGTTTC-A-AGAAACTGTCTTAAGAGAGACAACACATT-TTTCAAGGGAAACAAACTCAAAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA
263488 ----TT
66 TTTTTT
* *
263490 TTTGTTCCAAGAGAAACTGTATCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA
263555 TTTTTTTT
66 --TTTTTT
* * * *
263563 TTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAACATTGTTTCAATGGAAACAGACTCAAAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA
263628 TTTTTT
66 TTTTTT
* *
263634 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAATAGACTC-AAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA
*
263698 -TTTGT
66 TTTTTT
* * *
263703 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTAAGAGAAACAATCTCAAAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA
263768 TTTTTT
66 TTTTTT
263774 AGGAAAAACT
Statistics
Matches: 251, Mismatches: 22, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
64 7 0.03
65 1 0.00
66 25 0.10
67 24 0.10
69 59 0.24
70 8 0.03
71 66 0.26
73 61 0.24
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (71 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA
TTTTTT
Found at i:263734 original size:140 final size:140
Alignment explanation
Indices: 263426--263773 Score: 471
Period size: 140 Copynumber: 2.5 Consensus size: 140
263416 TTAGGGATAA
* *
263426 TTTGTTTC-A-AGAAACTGTCTTAAGAGAGACAACACATT-TTTCAAGGGAAACAAACTCAAAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACATTGTTTCAA-GGAAAC-AACTCAAAGA
263488 ----TTTTTGTTCCAAGAGAAACTGTATCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACT
64 TTTTTTTTTGTTCCAAGAGAAACTGTATCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACT
*
263549 CAAAGATTTTTTTT
129 CAAAGA--TTTTGT
*
263563 TTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAACATTGTTTCAATGGAAACAGACTCAAAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACATTGTTTCAA-GGAAACA-ACTCAAAGA
* * * *
263628 TTTTTTTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAATAGACT
64 TTTTTTTTTGTTCCAAGAGAAACTGTATCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACT
263693 C-AAGA-TTTGT
129 CAAAGATTTTGT
* *
263703 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTAAGAGAAACAATCTCAAAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACATTGTTTCAAG-GAAACAA-CTCAAAGA
263768 TTTTTT
64 TTTTTT
263774 AGGAAAAACT
Statistics
Matches: 189, Mismatches: 12, Indels: 17
0.87 0.06 0.08
Matches are distributed among these distances:
137 8 0.04
138 1 0.01
139 29 0.15
140 89 0.47
143 4 0.02
144 58 0.31
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (140 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACATTGTTTCAAGGAAACAACTCAAAGATT
TTTTTTTGTTCCAAGAGAAACTGTATCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCA
AAGATTTTGT
Found at i:264148 original size:37 final size:37
Alignment explanation
Indices: 264046--264270 Score: 267
Period size: 36 Copynumber: 6.1 Consensus size: 37
264036 CATCTCAAAG
* * *
264046 GAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAGA
1 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
* * *
264083 G-AAATTGTATCAAGCGAGTCAAAATTTGTTTTTAGA
1 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
* * * *
264119 GAAAACTGTTTCAAGTGAGACGAAGTTTGTTTTTA-A
1 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
* *
264155 AAAAACTGTCTCAAGTGAGACAAAATTTGTTTTTAGA
1 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
* * *
264192 GAAAACTGTCTCAAAGCAAGACAAAATTTATTTTTGGA
1 GAAAACTGTCTC-AAGCGAGACAAAATTTGTTTTTAGA
* *
264230 GAAAATTGTCTCAAGCGAGACAAAATTGGTTTTTA-A
1 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
264266 GAAAA
1 GAAAA
264271 TTTATCTCTA
Statistics
Matches: 160, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
36 69 0.43
37 59 0.37
38 32 0.20
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (37 bp):
GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
Found at i:264148 original size:73 final size:73
Alignment explanation
Indices: 264046--264270 Score: 274
Period size: 73 Copynumber: 3.1 Consensus size: 73
264036 CATCTCAAAG
* * *
264046 GAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAGAGAAATTGTATCAAGCGAGTCAAAATTTG
1 GAAAACTGTCTCAAGCGAGACGAAATTTGTTTTGAGAGAAATTGTCTCAAGCGAGACAAAATTTG
264111 TTTTTAGA
66 TTTTTAGA
* * * * * * * *
264119 GAAAACTGTTTCAAGTGAGACGAAGTTTGTTTTTAAAAAAACTGTCTCAAGTGAGACAAAATTTG
1 GAAAACTGTCTCAAGCGAGACGAAATTTGTTTTGAGAGAAATTGTCTCAAGCGAGACAAAATTTG
264184 TTTTTAGA
66 TTTTTAGA
* * *
264192 GAAAACTGTCTCAAAGCAAGACAAAATTTATTTTTG-GAGAAAATTGTCTCAAGCGAGACAAAAT
1 GAAAACTGTCTC-AAGCGAGACGAAATTT-GTTTTGAGAG-AAATTGTCTCAAGCGAGACAAAAT
*
264256 TGGTTTTTA-A
63 TTGTTTTTAGA
264266 GAAAA
1 GAAAA
264271 TTTATCTCTA
Statistics
Matches: 126, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
73 73 0.58
74 19 0.15
75 34 0.27
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (73 bp):
GAAAACTGTCTCAAGCGAGACGAAATTTGTTTTGAGAGAAATTGTCTCAAGCGAGACAAAATTTG
TTTTTAGA
Found at i:264287 original size:37 final size:35
Alignment explanation
Indices: 264046--264287 Score: 162
Period size: 37 Copynumber: 6.6 Consensus size: 35
264036 CATCTCAAAG
* * * *
264046 GAAAAATGTCTCAAGCGAGACGAAATTTG-TTTTGA
1 GAAAATTGTCTC-AGAGAGACAAAATTTGTTTTTAA
* * *
264081 GAGAAATTGTATCAAGCGAGTCAAAATTTGTTTTTAGA
1 GA-AAATTGTCTC-AGAGAGACAAAATTTGTTTTTA-A
* * * * *
264119 GAAAACTGTTTCAAGTGAGACGAAGTTTGTTTTTAA
1 GAAAATTGTCTC-AGAGAGACAAAATTTGTTTTTAA
* * *
264155 AAAAACTGTCTCAAGTGAGACAAAATTTGTTTTTAGA
1 GAAAATTGTCTC-AGAGAGACAAAATTTGTTTTTA-A
* * * *
264192 GAAAACTGTCTCAAAGCAAGACAAAATTTATTTTTGGA
1 GAAAATTGTCTCAGAG--AGACAAAATTTGTTTTT-AA
* *
264230 GAAAATTGTCTCAAGCGAGACAAAATTGGTTTTTAA
1 GAAAATTGTCTC-AGAGAGACAAAATTTGTTTTTAA
*
264266 GAAAATTTATCTCTAGAGAGAC
1 GAAAA-TTGTCTC-AGAGAGAC
264288 GACACTTTGT
Statistics
Matches: 169, Mismatches: 29, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
35 2 0.01
36 63 0.37
37 71 0.42
38 31 0.18
39 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.31
Consensus pattern (35 bp):
GAAAATTGTCTCAGAGAGACAAAATTTGTTTTTAA
Found at i:265541 original size:14 final size:15
Alignment explanation
Indices: 265518--265548 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
265508 TTTCATGTGC
265518 TTCTTGTCTTTTTCT
1 TTCTTGTCTTTTTCT
265533 TTCTT-TCTTTTTCT
1 TTCTTGTCTTTTTCT
265547 TT
1 TT
265549 TTTATTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (15 bp):
TTCTTGTCTTTTTCT
Found at i:265562 original size:13 final size:13
Alignment explanation
Indices: 265546--265576 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
265536 TTTCTTTTTC
265546 TTTTTTATTTGAT
1 TTTTTTATTTGAT
*
265559 TTTTTTCTTTGAT
1 TTTTTTATTTGAT
265572 TTTTT
1 TTTTT
265577 CTTTGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.10, C:0.03, G:0.06, T:0.81
Consensus pattern (13 bp):
TTTTTTATTTGAT
Found at i:265563 original size:12 final size:12
Alignment explanation
Indices: 265546--265591 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
265536 TTTCTTTTTC
*
265546 TTTTTTATTTGA
1 TTTTTTCTTTGA
265558 TTTTTTTCTTTGA
1 -TTTTTTCTTTGA
265571 TTTTTTCTTTG-
1 TTTTTTCTTTGA
265582 TTTTTATCTT
1 TTTTT-TCTT
265592 CGCCTTGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 5 0.16
12 15 0.48
13 11 0.35
ACGTcount: A:0.09, C:0.07, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTTCTTTGA
Found at i:265574 original size:11 final size:11
Alignment explanation
Indices: 265521--265591 Score: 54
Period size: 12 Copynumber: 6.1 Consensus size: 11
265511 CATGTGCTTC
265521 TTGTCTTTTTCT
1 TTGT-TTTTTCT
* *
265533 TTCTTTCTT-T
1 TTGTTTTTTCT
* *
265543 TTCTTTTTTAT
1 TTGTTTTTTCT
265554 TTGATTTTTTTCT
1 TTG--TTTTTTCT
265567 TTGATTTTTTCT
1 TTG-TTTTTTCT
265579 TTGTTTTTATCT
1 TTGTTTTT-TCT
265591 T
1 T
265592 CGCCTTGATT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
10 9 0.18
11 12 0.24
12 18 0.37
13 10 0.20
ACGTcount: A:0.06, C:0.11, G:0.06, T:0.77
Consensus pattern (11 bp):
TTGTTTTTTCT
Found at i:269665 original size:22 final size:22
Alignment explanation
Indices: 269637--269678 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
269627 ATGTGAAATC
269637 TATGTCCCGAAGGACCTATGCA
1 TATGTCCCGAAGGACCTATGCA
* *
269659 TATGTCCTGAAGGCCCTATG
1 TATGTCCCGAAGGACCTATG
269679 TAACCCTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (22 bp):
TATGTCCCGAAGGACCTATGCA
Found at i:273735 original size:3 final size:3
Alignment explanation
Indices: 273727--273781 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
273717 AAATGTAAAT
273727 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
273775 ATA ATA A
1 ATA ATA A
273782 ATGACGAACG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:275729 original size:3 final size:3
Alignment explanation
Indices: 275715--275751 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
275705 TTCGCCCGGG
*
275715 TTA TTA TATA TTA TTA TTA TTA TTA TTA TTA TCA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
275752 ATTAAGTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:277190 original size:37 final size:38
Alignment explanation
Indices: 277109--277192 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 38
277099 TAAACCCGAA
*
277109 CCGACCCAACCCGACCCAAATATCACACTTAAAAAAAC
1 CCGACCCGACCCGACCCAAATATCACACTTAAAAAAAC
* *
277147 CCGACCCGACTCGACCCGAATATCACACTT-AAAAAAC
1 CCGACCCGACCCGACCCAAATATCACACTTAAAAAAAC
277184 CCGACCCGA
1 CCGACCCGA
277193 ACAAAATAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
37 16 0.37
38 27 0.63
ACGTcount: A:0.39, C:0.40, G:0.10, T:0.11
Consensus pattern (38 bp):
CCGACCCGACCCGACCCAAATATCACACTTAAAAAAAC
Found at i:277411 original size:37 final size:38
Alignment explanation
Indices: 277327--277411 Score: 118
Period size: 38 Copynumber: 2.3 Consensus size: 38
277317 CCTAAACTCG
* *
277327 AACCCGACCCGACCCGACCCGAATATCACACTTAAAAA
1 AACCCGACCCAACCCGACCCGAATAGCACACTTAAAAA
* * *
277365 AACCTGACCCAACTCGACCCGAATAGCATACTT-AAAA
1 AACCCGACCCAACCCGACCCGAATAGCACACTTAAAAA
277402 AACCCGACCC
1 AACCCGACCC
277412 GAACAAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
37 13 0.32
38 28 0.68
ACGTcount: A:0.39, C:0.39, G:0.11, T:0.12
Consensus pattern (38 bp):
AACCCGACCCAACCCGACCCGAATAGCACACTTAAAAA
Found at i:287408 original size:244 final size:243
Alignment explanation
Indices: 286979--287850 Score: 1174
Period size: 244 Copynumber: 3.5 Consensus size: 243
286969 TTTAATGCTT
*
286979 TCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCATTAAATTATT
1 TCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAATAAATTATT
* * **
287044 TCCAAAATTTGTAAGTCCTTCGGGCCATCAATAAGTTTTTCGAGCATGATGCTTAAATCCTTCAA
66 TCCAAAATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTTGA
* *
287109 GTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATTTATAAGACCTTTGGGCTG
131 GTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGG-TG
287174 GATGTTTTCACATGATTTTGAAAAATAAGAAAGCGATTTCCAAAGTTTC
195 GATGTTTTCACATGATTTTGAAAAATAAGAAAGCGATTTCCAAAGTTTC
*
287223 TCAGAAAATGAACTTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAATAAATTATT
1 TCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAATAAATTATT
* * *
287288 TCTAAAATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATAATGCTTAAATCCTTTGG
66 TCCAAAATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTTGA
* * * *
287353 GTCGTCTGTAAGTCTTTCGAGCAAGATGATAAGCCCTTCAGACCATCTATAAGACCTTCGGGTTG
131 GTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGG-TG
**
287418 GATGTTTTCACATGATTTTGAAAAA-AGAGAAAATGATTTCCAAAGTTTC
195 GATGTTTTCACATGATTTTGAAAAATA-AGAAAGCGATTTCCAAAGTTTC
* ** * *
287467 TCAGAAAATGAAATTTTTGAAATGTAAGAAAACGATTTCCAATGTTTCTTACCCAGTAAATTATT
1 TCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAATAAATTATT
* *
287532 TCCATAATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAAT-CTTTCG
66 TCCAAAATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTT-G
* * * **
287596 TGTCATTTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCTATCCGTAAGACCTTCGGGTA
130 AGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGT-
* * *
287661 GGATGTTTTCACATGAACTTCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTC
194 GGATGTTTTCACATG-ATTTTGAAAAATAAGAAAGCGATTTCCAAAG-TT-TC
*
287714 ATTTAATGTTTTCAGAAAATGAAATCTTTGAAAAGTAA-AAAGTGATTTCCAAAGTTTCTTACCC
1 -----------TCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCC
** ** * ** * *
287778 AATAAATTATTTCCAAAATTTGTAAGTCCTTCAAGAAATCAGTAACTCTTTTAAGCGTGATGATT
55 AATAAATTATTTCCAAAATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTT
287843 AAATCCTT
120 AAATCCTT
287851 CGGGTTATAT
Statistics
Matches: 552, Mismatches: 57, Indels: 24
0.87 0.09 0.04
Matches are distributed among these distances:
243 6 0.01
244 407 0.74
245 25 0.05
246 2 0.00
247 2 0.00
257 82 0.15
258 28 0.05
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (243 bp):
TCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAATAAATTATT
TCCAAAATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTTGA
GTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGTGG
ATGTTTTCACATGATTTTGAAAAATAAGAAAGCGATTTCCAAAGTTTC
Found at i:287653 original size:488 final size:495
Alignment explanation
Indices: 286725--287828 Score: 1521
Period size: 488 Copynumber: 2.2 Consensus size: 495
286715 TAATGTTTTT
* * **
286725 AGAAAATGAAATTTTTGGAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCGGTAAATTATTTC
1 AGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAATAAATTATTTC
* * *
286790 CAAAATTTGTATGTCCTACAGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCTGGT
66 CAAAATTTGTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATAATGCTTAAATCATTCTGGT
* * *
286855 CATCTGTAAGTCTTCGAGCTAGATGATGAGTCCTTCAGACCATCTATAAAACCTTCGGGATGAAT
131 CATCTGTAAGTCTTCGAGCAAGATGATAAGCCCTTCAGACCATCTATAAAACCTTCGGGATGAAT
* *
286920 GTTTTCACATGATTTTGAAAAATGAGAAAGTGATTTCCAAAGTTTCTTATTTAATGCTTTCAGAA
196 GTTTTCACATGATTTTGAAAAAAGAGAAAATGATTTCCAAAG-------TTT-ATGC-TTCAGAA
** *
286985 AATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCATTAAATTATTTCCAAA
252 AATGAAATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAA
287050 ATTTGTAAGTCCTTCGGGCCATCAATAAGTTTTTCGAGCATGATGCTTAAATCCTTCAAGTCATC
317 ATTTGTAAGTCCTTCGGGCCATCAATAAGTTTTTCGAGCATGATGCTTAAATCCTTCAAGTCATC
** *
287115 TGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATTTATAAGACCTTTGGGCT-GGATGT
382 TGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGG-TAGGATGT
* *
287179 TTTCACATG-ATTTTGAAAAATAAGAAAGCGATTTCCAAAG-TT-TC-TC
446 TTTCACATGAACTTCGAAAAATAAGAAAGCGATTTCCAAAGTTTCTCTTC
*
287225 AGAAAATGAACTTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAATAAATTATTTC
1 AGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAATAAATTATTTC
* * *
287290 TAAAATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATAATGCTTAAATCCTT-TGGG
66 CAAAATTTGTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATAATGCTTAAATCATTCT-GG
* * * *
287354 TCGTCTGTAAGTCTTTCGAGCAAGATGATAAGCCCTTCAGACCATCTATAAGACCTTCGGGTTGG
130 TCATCTGTAAGTC-TTCGAGCAAGATGATAAGCCCTTCAGACCATCTATAAAACCTTCGGGATGA
287419 ATGTTTTCACATGATTTTGAAAAAAGAGAAAATGATTTCCAAAG-TT-T-C-TCAGAAAATGAAA
194 ATGTTTTCACATGATTTTGAAAAAAGAGAAAATGATTTCCAAAGTTTATGCTTCAGAAAATGAAA
* * *
287480 TTTTTGAAATGTAAGAAAACGATTTCCAATGTTTCTTACCCAGTAAATTATTTCCATAATTTGTA
259 TTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTA
* * ** *
287545 AGTCCTTCGGGCCATCAGTAAGTCTTTT-GAGCATGATGCTTAAATCTTTCGTGTCATTTGTAAG
324 AGTCCTTCGGGCCATCAATAAGT-TTTTCGAGCATGATGCTTAAATCCTTCAAGTCATCTGTAAG
* *
287609 TCTTTCGAGCAAGATGATAAGTCCTTCGGGCTATCCGTAAGACCTTCGGGTAGGATGTTTTCACA
388 TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACA
*
287674 TGAACTTCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTC
453 TGAACTTCGAAAAATAAGAAAGCGATTTCCAAAGTTTCTC----------TTC
*
287727 AGAAAATGAAATCTTTGAAAAGTAA-AAAGTGATTTCCAAAGTTTCTTACCCAATAAATTATTTC
1 AGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAATAAATTATTTC
* ** *
287791 CAAAATTTGTAAGTCCTTCAAGAAATCAGTAACTCTTT
66 CAAAATTTGTAAGTCCTTCAGGCCATCAGTAAGTCTTT
287829 TAAGCGTGAT
Statistics
Matches: 539, Mismatches: 47, Indels: 35
0.87 0.08 0.06
Matches are distributed among these distances:
487 1 0.00
488 186 0.35
489 32 0.06
490 3 0.01
491 3 0.01
493 2 0.00
499 1 0.00
500 128 0.24
501 158 0.29
502 25 0.05
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (495 bp):
AGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAATAAATTATTTC
CAAAATTTGTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATAATGCTTAAATCATTCTGGT
CATCTGTAAGTCTTCGAGCAAGATGATAAGCCCTTCAGACCATCTATAAAACCTTCGGGATGAAT
GTTTTCACATGATTTTGAAAAAAGAGAAAATGATTTCCAAAGTTTATGCTTCAGAAAATGAAATT
TTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAG
TCCTTCGGGCCATCAATAAGTTTTTCGAGCATGATGCTTAAATCCTTCAAGTCATCTGTAAGTCT
TTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGA
ACTTCGAAAAATAAGAAAGCGATTTCCAAAGTTTCTCTTC
Found at i:290383 original size:23 final size:23
Alignment explanation
Indices: 290354--290404 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
290344 ATGTAAAATA
** *
290354 AAATAGGTGCTACCTATGATGTT
1 AAATAGGCACTACCTATGACGTT
*
290377 AAATAGGCACTACCTATTACGTT
1 AAATAGGCACTACCTATGACGTT
290400 AAATA
1 AAATA
290405 AGCGCTACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (23 bp):
AAATAGGCACTACCTATGACGTT
Found at i:290412 original size:23 final size:23
Alignment explanation
Indices: 290362--290425 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
290352 TAAAATAGGT
* * *
290362 GCTACCTATGATGTTAAATAGGC
1 GCTACCTATTACGTTAAATAAGC
*
290385 ACTACCTATTACGTTAAATAAGC
1 GCTACCTATTACGTTAAATAAGC
* *
290408 GCTACATATTACATTAAA
1 GCTACCTATTACGTTAAA
290426 CTAGCTATGG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (23 bp):
GCTACCTATTACGTTAAATAAGC
Found at i:290585 original size:98 final size:96
Alignment explanation
Indices: 290377--290669 Score: 406
Period size: 98 Copynumber: 3.0 Consensus size: 96
290367 CTATGATGTT
*
290377 AAATAGGCACTACCTATTACGTTAAATAAGCGCTACATATTACATTAAACTAGCTATGGTTTGTT
1 AAATAGGCACTACCTATTACGTTAAATAAGCGCTAC-TATTACGTTAAACTAGCTATGGTTTGTT
** * *
290442 TAAAGGTTAATAATGCTATAAACGGCAAAATA
65 TAAAGGTTAATAATAATGTAAACGGTAAAATA
* * * ***
290474 AAATAGGCTCTACCTATTACGTTAAATAAACGCTATCTATTATGTTAAACTAGCTACCAATTTGT
1 AAATAGGCACTACCTATTACGTTAAATAAGCGCTA-CTATTACGTTAAACTAGCTA-TGGTTTGT
*
290539 TTAAAGTTTAATAATAATGTAAACGGTAAAATA
64 TTAAAGGTTAATAATAATGTAAACGGTAAAATA
* * *
290572 AAATAGGCGCTACCTATTATGTTAAATAAGCGCTACCTATTACGTTAAACTAGCTAATGGCTTGT
1 AAATAGGCACTACCTATTACGTTAAATAAGCGCTA-CTATTACGTTAAACTAGCT-ATGGTTTGT
290637 TTAAAGGTTAATAATAATGTAAACGGTAAAATA
64 TTAAAGGTTAATAATAATGTAAACGGTAAAATA
290670 TATACAACTT
Statistics
Matches: 171, Mismatches: 22, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
97 50 0.29
98 120 0.70
99 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (96 bp):
AAATAGGCACTACCTATTACGTTAAATAAGCGCTACTATTACGTTAAACTAGCTATGGTTTGTTT
AAAGGTTAATAATAATGTAAACGGTAAAATA
Found at i:290598 original size:23 final size:23
Alignment explanation
Indices: 290572--290620 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
290562 CGGTAAAATA
* *
290572 AAATAGGCGCTACCTATTATGTT
1 AAATAAGCGCTACCTATTACGTT
290595 AAATAAGCGCTACCTATTACGTT
1 AAATAAGCGCTACCTATTACGTT
290618 AAA
1 AAA
290621 CTAGCTAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (23 bp):
AAATAAGCGCTACCTATTACGTT
Found at i:292452 original size:22 final size:22
Alignment explanation
Indices: 292427--292472 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
292417 TATAAAATAT
*
292427 AAAACCCTAAAATCAATTTTAA
1 AAAAACCTAAAATCAATTTTAA
* * *
292449 AAAAACCTTAAATTAGTTTTAA
1 AAAAACCTAAAATCAATTTTAA
292471 AA
1 AA
292473 TATAAATCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAAACCTAAAATCAATTTTAA
Found at i:301971 original size:65 final size:63
Alignment explanation
Indices: 301902--302061 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 63
301892 AATTAAATTG
* *
301902 AACATCGAATGCATTTCATGCATCGATGCACATGCCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-GCCATGCACCGATGCACTCAGGATATTT-TG-
301966 A
63 A
* * * *
301967 AACATCGAATGCATTTGATGCATCGATGCACCAGCTATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAGCCATGCACCGATGCACTCAGGATATTTTGA
* *
302031 AACATCGAATGCACTTGATGCATCTATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
302062 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
63 1 0.01
64 29 0.34
65 50 0.59
66 5 0.06
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAGCCATGCACCGATGCACTCAGGATATTTTGA
Found at i:307894 original size:23 final size:20
Alignment explanation
Indices: 307843--307902 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
307833 TTTGGTGCAG
*
307843 AGGGAATCGATTCCCCCTTT
1 AGGGAACCGATTCCCCCTTT
307863 AGGGAACCGATTCCCCCTTT
1 AGGGAACCGATTCCCCCTTT
307883 GAAGGGGAACCGATTCCCCC
1 --A-GGGAACCGATTCCCCC
307903 ACAAGGGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 19 0.53
22 1 0.03
23 16 0.44
ACGTcount: A:0.22, C:0.33, G:0.23, T:0.22
Consensus pattern (20 bp):
AGGGAACCGATTCCCCCTTT
Found at i:307916 original size:20 final size:20
Alignment explanation
Indices: 307843--307922 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
307833 TTTGGTGCAG
* **
307843 AGGGAATCGATTCCCCCTTT
1 AGGGAACCGATTCCCCCTCA
*
307863 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCCCC--TCA
*
307885 AGGGGAACCGATTCCCCCACA
1 A-GGGAACCGATTCCCCCTCA
* *
307906 AGGGAATCGATACCCCC
1 AGGGAACCGATTCCCCC
307923 CTGGGGTTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 30 0.60
21 2 0.04
22 2 0.04
23 16 0.32
ACGTcount: A:0.25, C:0.34, G:0.23, T:0.19
Consensus pattern (20 bp):
AGGGAACCGATTCCCCCTCA
Found at i:313674 original size:20 final size:21
Alignment explanation
Indices: 313629--313689 Score: 88
Period size: 20 Copynumber: 2.9 Consensus size: 21
313619 TTCCCCTGTG
313629 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
313652 GGGGGAATCGGTTCCCT-AAA
1 GGGGGAATCGGTTCCCTCAAA
*
313672 GGGGGAATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
313690 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 19 0.53
21 1 0.03
22 3 0.08
23 13 0.36
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:323003 original size:2 final size:2
Alignment explanation
Indices: 322996--323037 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
322986 CAGCTTAAGC
322996 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
323038 GATAGATAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:323629 original size:65 final size:63
Alignment explanation
Indices: 323510--323719 Score: 214
Period size: 65 Copynumber: 3.3 Consensus size: 63
323500 TTTTTCAGAG
* *
323510 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATGC
323572 ATT
61 ATT
* * *
323575 TCATGCATCGATGCACATACCATGCA-CTGATGCAGTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACA-ACCATGCATC-GATGCACTCAGGATATTT-TG-AAACATCGAATGCA
323638 TT
62 TT
* * * *
323640 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
323704 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
323720 TCTTAGTGCA
Statistics
Matches: 123, Mismatches: 12, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 45 0.37
65 67 0.54
66 6 0.05
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:329453 original size:75 final size:74
Alignment explanation
Indices: 329372--329552 Score: 240
Period size: 75 Copynumber: 2.4 Consensus size: 74
329362 TTGAAAATGT
* * * *
329372 TTTTTGAAAAAAATATAATATATAATTTTTAGAAAACAATTTTCGAAAATATATATATTATATAG
1 TTTTTGAAAAATATATATTATATAGTTTTT-GAAAAC-ATTTT-GAAAATATATATAATATATAG
329437 -TTTTAAAAACA
63 TTTTTAAAAACA
*
329448 -TTTTGAAAATATATATATTATATAGTTTTTGAAAACATTTTTAAAATATATATAATATATAGTT
1 TTTTTGAAAA-ATATATATTATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTT
*
329512 TTTGAAAACA
65 TTTAAAAACA
*
329522 TTTTTGAAGACATATATATTATATAGTTTTT
1 TTTTTGAA-AAATATATATTATATAGTTTTT
329553 TATTTTACCA
Statistics
Matches: 94, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
73 19 0.20
74 15 0.16
75 42 0.45
76 18 0.19
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (74 bp):
TTTTTGAAAAATATATATTATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTT
TTAAAAACA
Found at i:329483 original size:37 final size:37
Alignment explanation
Indices: 329373--329552 Score: 238
Period size: 37 Copynumber: 4.8 Consensus size: 37
329363 TGAAAATGTT
* * *
329373 TTTTGAAAA-AAATATAATATATAATTTTTAGAAAACAA
1 TTTTGAAAATATATATATTATATAGTTTTT-GAAAAC-A
*
329411 TTTTCGAAAATATATATATTATATAG-TTTTAAAAACA
1 TTTT-GAAAATATATATATTATATAGTTTTTGAAAACA
329448 TTTTGAAAATATATATATTATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATATTATATAGTTTTTGAAAACA
* *
329485 TTTTTAAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATATTATATAGTTTTTGAAAACA
* *
329522 TTTTTGAAGACATATATATTATATAGTTTTT
1 -TTTTGAAAATATATATATTATATAGTTTTT
329553 TATTTTACCA
Statistics
Matches: 127, Mismatches: 11, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
36 21 0.17
37 50 0.39
38 35 0.28
39 9 0.07
40 12 0.09
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTGAAAATATATATATTATATAGTTTTTGAAAACA
Found at i:329599 original size:21 final size:20
Alignment explanation
Indices: 329573--329629 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 20
329563 TTTTATTTAT
329573 TTTGTTTTTTATTATTTTCC
1 TTTGTTTTTTATTATTTTCC
329593 ATTTGTTTTTTTATT-TTTTCC
1 -TTTG-TTTTTTATTATTTTCC
329614 TTTGTTATTTT-TTATT
1 TTTGTT-TTTTATTATT
329630 GTTTTCATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
19 4 0.12
20 10 0.30
21 10 0.30
22 9 0.27
ACGTcount: A:0.11, C:0.07, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTGTTTTTTATTATTTTCC
Found at i:329604 original size:29 final size:31
Alignment explanation
Indices: 329548--329611 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
329538 TATTATATAG
*
329548 TTTTTTATTTTACCATTTTATTTATTTTGTT
1 TTTTTTATTTTACCATTTTATTTATTTTATT
*
329579 TTTTATTATTTT-CCA-TTTGTTT-TTTTATT
1 TTTT-TTATTTTACCATTTTATTTATTTTATT
329608 TTTT
1 TTTT
329612 CCTTTGTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 10 0.33
30 6 0.20
31 7 0.23
32 7 0.23
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (31 bp):
TTTTTTATTTTACCATTTTATTTATTTTATT
Found at i:329610 original size:20 final size:21
Alignment explanation
Indices: 329573--329635 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
329563 TTTTATTTAT
329573 TTTG-TTTTTTATTATTTTCC
1 TTTGTTTTTTTATTATTTTCC
329593 ATTTGTTTTTTTATT-TTTTCC
1 -TTTGTTTTTTTATTATTTTCC
*
329614 TTTGTTATTTTTTATTGTTTTC
1 TTTG-T-TTTTTTATTATTTTC
329636 ATATTTATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.11
21 11 0.29
22 18 0.47
23 5 0.13
ACGTcount: A:0.10, C:0.08, G:0.06, T:0.76
Consensus pattern (21 bp):
TTTGTTTTTTTATTATTTTCC
Found at i:329643 original size:22 final size:20
Alignment explanation
Indices: 329571--329643 Score: 58
Period size: 22 Copynumber: 3.4 Consensus size: 20
329561 CATTTTATTT
*
329571 ATTTTGTTTTTTATTATTTTCC
1 ATTTTATTTTTTATT-TTTT-C
329593 ATTTGT-TTTTTTATTTTTTCC
1 ATTT-TATTTTTTATTTTTT-C
*
329614 TTTGTTATTTTTTATTGTTTTC
1 ATT-TTATTTTTTATT-TTTTC
329636 ATATTTAT
1 AT-TTTAT
329644 ACATTTCTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
21 9 0.20
22 29 0.66
23 6 0.14
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.74
Consensus pattern (20 bp):
ATTTTATTTTTTATTTTTTC
Found at i:333547 original size:99 final size:99
Alignment explanation
Indices: 333361--333566 Score: 340
Period size: 99 Copynumber: 2.1 Consensus size: 99
333351 AGATTATAAT
333361 ATTATATATATATACACAATAAAGATTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGC
1 ATTATA-ATATATACACAATAAAGATTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGC
*
333426 TTTATGGATAACATTCAGCTAGCCTGATAAAGGTG
65 TTTATAGATAACATTCAGCTAGCCTGATAAAGGTG
* * * * *
333461 ATTATAATATCTATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGTCTCGGCT
1 ATTATAATATATACACAATAAAGATTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCT
*
333526 TTATAGATAAGATTCAGCTAGCCTGATAAAGGTG
66 TTATAGATAACATTCAGCTAGCCTGATAAAGGTG
333560 ATTATAA
1 ATTATAA
333567 GATTGAGCTG
Statistics
Matches: 99, Mismatches: 7, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
99 93 0.94
100 6 0.06
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (99 bp):
ATTATAATATATACACAATAAAGATTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCT
TTATAGATAACATTCAGCTAGCCTGATAAAGGTG
Found at i:334803 original size:86 final size:86
Alignment explanation
Indices: 334658--334870 Score: 318
Period size: 86 Copynumber: 2.5 Consensus size: 86
334648 GGAGTCACTC
* * * * * *
334658 GAAGAATATCCCACATGGCTTTCCCGTGAAGGGTAGTCATCCAAATATTATCTCACCTGGTTCAG
1 GAAGAATATACCACTTGGCTTTCCCGTGAAGGGGAGTCATTCAAAGATCATCTCACCTGGTTCAG
*
334723 ACCCGCGAAGGGGAACCACCT
66 ACCCGCGAAGGGGAACCACAT
* *
334744 GAAGAACATACCACTTGGCTTTCTCGTGAAGGGGAGTCATTCAAAGATCATCTCACCTGGTTCAG
1 GAAGAATATACCACTTGGCTTTCCCGTGAAGGGGAGTCATTCAAAGATCATCTCACCTGGTTCAG
334809 ACCCGCGAAGGGGAACCACAT
66 ACCCGCGAAGGGGAACCACAT
** *
334830 GAAGAATGCACCACTTAGCTTTCCCGTGAAGGGGAGTCATT
1 GAAGAATATACCACTTGGCTTTCCCGTGAAGGGGAGTCATT
334871 TAGAAAATTA
Statistics
Matches: 113, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 113 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (86 bp):
GAAGAATATACCACTTGGCTTTCCCGTGAAGGGGAGTCATTCAAAGATCATCTCACCTGGTTCAG
ACCCGCGAAGGGGAACCACAT
Found at i:335472 original size:85 final size:85
Alignment explanation
Indices: 334937--335465 Score: 752
Period size: 85 Copynumber: 6.2 Consensus size: 85
334927 ACTATTCGCG
* * * *
334937 GCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGGGTTCGATTCCATTCAGCTC
1 GCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTC
*
335002 AAAGGCATATCAAATTTGCA
66 AAAGGCATATCAAATTTACA
* * ** * * * *
335022 GAATAACTCAAGGCGAGAAGGGTTATCTACCAACAAAGGCCTTCTAGTTCGATTCCATTCAGCTT
1 GCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTC
335087 AAAGGCATATCAAATTTACA
66 AAAGGCATATCAAATTTACA
* * * * *
335107 ACATAACTCAAGGAGAAAAGGGTTATATGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTC
1 GCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTC
335172 AAAGGCATATCAAATTTACA
66 AAAGGCATATCAAATTTACA
* *
335192 ACATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAGCTC
1 GCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTC
*
335257 TAAGGCATATCAAATTTACA
66 AAAGGCATATCAAATTTACA
* * *
335277 GCATAACTCAAGGCGAGAAGGGTTATCTGTCAGCAAAGACCTTCGAGTTCAATTACATTCAGCTC
1 GCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTC
* *
335342 AGAGGCACATCAAATTTACA
66 AAAGGCATATCAAATTTACA
* * **
335362 GCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAATACCTTCGAGTTCGATCCCATTCAGCTC
1 GCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTC
* *
335427 AAAGGCATGTCAGATTTACA
66 AAAGGCATATCAAATTTACA
* *
335447 GCATAGCTTAAGTCGAGAA
1 GCATAGCTCAAGGCGAGAA
335466 AAGCTATATG
Statistics
Matches: 395, Mismatches: 49, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 395 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (85 bp):
GCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTC
AAAGGCATATCAAATTTACA
Found at i:336082 original size:3 final size:3
Alignment explanation
Indices: 336076--336100 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
336066 TTTTTTTTTT
336076 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
336101 GTATATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:336181 original size:33 final size:34
Alignment explanation
Indices: 336108--336187 Score: 83
Period size: 33 Copynumber: 2.3 Consensus size: 34
336098 TATGTATATA
* * **
336108 ATAATATAGTATAATTTTTGAAAATGTTTTTTAAAT
1 ATAAT-TA-TATAATTTTTAAAAAAGTTTTCGAAAT
336144 ATAA-TATATAATTTTTAAAAACAGTTTTCGAAA-
1 ATAATTATATAATTTTTAAAAA-AGTTTTCGAAAT
336177 ATAATTATATA
1 ATAATTATATA
336188 TATTATATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
33 18 0.47
34 16 0.42
36 4 0.11
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (34 bp):
ATAATTATATAATTTTTAAAAAAGTTTTCGAAAT
Found at i:336239 original size:37 final size:37
Alignment explanation
Indices: 336182--336561 Score: 267
Period size: 37 Copynumber: 10.5 Consensus size: 37
336172 CGAAAATAAT
*
336182 TATATATATTATATAG--TTTGAAAACATTTCAAAAA
1 TATATATATTATATAGTTTTTGAAAACATTTTAAAAA
* * *
336217 TATATATATTATATAGTTTTTGAAATCTTTTTTAAAA
1 TATATATATTATATAGTTTTTGAAAACATTTTAAAAA
* *
336254 TATATATAATATATAGTTTTTGAAAACAATTTTGAAAA
1 TATATATATTATATAGTTTTTGAAAAC-ATTTTAAAAA
*
336292 TATATATATTATATAGTTTTT-AAAACATTTTTGAAAA
1 TATATATATTATATAGTTTTTGAAAACA-TTTTAAAAA
* ** *
336329 CATATATATTATATAGTTTTAAAAATATATTTTTGAAAACA
1 TATATATATTATATAGTTTTTGAAA-ACA-TTTT-AAAA-A
* * * *
336370 TATATATAATATATAATTTAT-AAAACATTTT--GAA
1 TATATATATTATATAGTTTTTGAAAACATTTTAAAAA
* * *
336404 TATATATAATATATA-TTTTTTAAAACATTTTGAAAAC
1 TATATATATTATATAGTTTTTGAAAACATTTT-AAAAA
* *** *
336441 T-TATATAGT-T-T--TTTAAAAAAACATTTT--GAA
1 TATATATATTATATAGTTTTTGAAAACATTTTAAAAA
* * *
336471 -A-ATATATTATATGGTTTTTAAAAAACATTTTGAAAAC
1 TATATATATTATATAGTTTTT-GAAAACATTTT-AAAAA
* * *
336508 TATAT-GA-TATATAG-TTTTGAAAACTTTTTAAAAC
1 TATATATATTATATAGTTTTTGAAAACATTTTAAAAA
* *
336542 TATATATAATATATGGTTTT
1 TATATATATTATATAGTTTT
336562 AAAATCTTTT
Statistics
Matches: 279, Mismatches: 40, Indels: 50
0.76 0.11 0.14
Matches are distributed among these distances:
29 6 0.02
30 2 0.01
31 1 0.00
33 20 0.07
34 48 0.17
35 28 0.10
36 18 0.06
37 85 0.30
38 37 0.13
39 11 0.04
40 6 0.02
41 17 0.06
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (37 bp):
TATATATATTATATAGTTTTTGAAAACATTTTAAAAA
Found at i:336407 original size:34 final size:34
Alignment explanation
Indices: 336252--336555 Score: 174
Period size: 34 Copynumber: 8.5 Consensus size: 34
336242 TCTTTTTTAA
336252 AATATATATAATATATAGTTTT-TGAAAACAATTTTG
1 AATATATATAATATATA-TTTTAT-AAAAC-ATTTTG
*
336288 AAAATATATATATTATATAGTTTT-TAAAACATTTTTG
1 --AATATATATAATATATA-TTTTATAAAACA-TTTTG
* * * *
336325 AAAACATATATATTATATAGTTTTAAAAATATATTTTTG
1 --AATATATATAATATATA-TTTTATAAA-ACA-TTTTG
*
336364 AAAACATATATATAATATATAATTTATAAAACATTTTG
1 ---A-ATATATATAATATATATTTTATAAAACATTTTG
*
336402 AATATATATAATATATATTTTTTAAAACATTTTG
1 AATATATATAATATATATTTTATAAAACATTTTG
* *
336436 AA-A-ACT-T-ATATAGTTTTTTAAAAAAACATTTTG
1 AATATA-TATAATATA-TATTTT-ATAAAACATTTTG
* * * *
336469 AAAATATATTATATGGT-TTTTAAAAAACATTTTG
1 AATATATATAATAT-ATATTTTATAAAACATTTTG
* * * * *
336503 AAAACTATATGATATATAGTTTT-GAAAACTTTTTAA
1 AATA-TATATAATATATA-TTTTATAAAACATTTT-G
336539 AACTATATATAATATAT
1 AA-TATATATAATATAT
336556 GGTTTTAAAA
Statistics
Matches: 226, Mismatches: 22, Indels: 38
0.79 0.08 0.13
Matches are distributed among these distances:
31 5 0.02
32 7 0.03
33 15 0.07
34 53 0.23
35 25 0.11
36 23 0.10
37 34 0.15
38 30 0.13
39 10 0.04
40 10 0.04
41 14 0.06
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (34 bp):
AATATATATAATATATATTTTATAAAACATTTTG
Found at i:336587 original size:9 final size:9
Alignment explanation
Indices: 336573--336638 Score: 72
Period size: 9 Copynumber: 7.8 Consensus size: 9
336563 AAATCTTTTG
336573 ATTATTATT
1 ATTATTATT
336582 ATTATTATT
1 ATTATTATT
336591 ATTATTATTT
1 ATTATTA-TT
336601 ATT-TTATT
1 ATTATTATT
336609 -TTATT-TT
1 ATTATTATT
336616 ATT-TTATT
1 ATTATTATT
336624 -TTATTTATT
1 ATTA-TTATT
336633 -TTATTA
1 ATTATTA
336639 ATTGTGGTCC
Statistics
Matches: 51, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
7 8 0.16
8 11 0.22
9 27 0.53
10 5 0.10
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
ATTATTATT
Found at i:336608 original size:5 final size:5
Alignment explanation
Indices: 336577--336637 Score: 81
Period size: 5 Copynumber: 12.0 Consensus size: 5
336567 CTTTTGATTA
336577 TTATT ATTATT ATTATT ATTA-T TTATT TTATT TTATT TTATT TTATT
1 TTATT -TTATT -TTATT -TTATT TTATT TTATT TTATT TTATT TTATT
336624 TTA-T TTATT TTATT
1 TTATT TTATT TTATT
336638 AATTGTGGTC
Statistics
Matches: 53, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
4 7 0.13
5 31 0.58
6 15 0.28
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (5 bp):
TTATT
Found at i:340947 original size:8 final size:8
Alignment explanation
Indices: 340934--340958 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
340924 GAGATGGTAA
340934 AGTGTTAT
1 AGTGTTAT
340942 AGTGTTAT
1 AGTGTTAT
340950 AGTGTTAT
1 AGTGTTAT
340958 A
1 A
340959 AGAAGGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (8 bp):
AGTGTTAT
Found at i:341627 original size:27 final size:27
Alignment explanation
Indices: 341596--341677 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 27
341586 CTAATTGTCG
341596 AATGCATCTTTATGTGTGAACTATGTA
1 AATGCATCTTTATGTGTGAACTATGTA
* *
341623 AATGCA----TATGTCT-AA-T-TGTCG
1 AATGCATCTTTATGTGTGAACTATGT-A
*
341644 AATGCATCTTTATGTGAGAACTATGTA
1 AATGCATCTTTATGTGTGAACTATGTA
341671 AATGCAT
1 AATGCAT
341678 GTACGTATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 16
0.67 0.08 0.25
Matches are distributed among these distances:
20 3 0.07
21 7 0.17
22 2 0.05
23 6 0.14
25 5 0.12
26 2 0.05
27 14 0.33
28 3 0.07
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (27 bp):
AATGCATCTTTATGTGTGAACTATGTA
Found at i:341628 original size:48 final size:48
Alignment explanation
Indices: 341572--341677 Score: 203
Period size: 48 Copynumber: 2.2 Consensus size: 48
341562 TGGTATCTGA
*
341572 GTAAATGCATATGTCTAATTGTCGAATGCATCTTTATGTGTGAACTAT
1 GTAAATGCATATGTCTAATTGTCGAATGCATCTTTATGTGAGAACTAT
341620 GTAAATGCATATGTCTAATTGTCGAATGCATCTTTATGTGAGAACTAT
1 GTAAATGCATATGTCTAATTGTCGAATGCATCTTTATGTGAGAACTAT
341668 GTAAATGCAT
1 GTAAATGCAT
341678 GTACGTATGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (48 bp):
GTAAATGCATATGTCTAATTGTCGAATGCATCTTTATGTGAGAACTAT
Done.