Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008793.1 Hibiscus syriacus cultivar Beakdansim tig00111937_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: 720278
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:171932 original size:20 final size:20
Alignment explanation
Indices: 171878--171974 Score: 61
Period size: 20 Copynumber: 4.8 Consensus size: 20
171868 CGCAATTCGA
*
171878 TTTCGAATTCGCAACACGAA-
1 TTTCAAATTCGCAACAC-AAT
** **
171898 AGTCAAATTAACAACACAAT
1 TTTCAAATTCGCAACACAAT
* *
171918 TTTCGAATTCGCAACAAGAAT
1 TTTCAAATTCGCAAC-ACAAT
* * *
171939 TTATCAATTTCGCAACTCAGT
1 TT-TCAAATTCGCAACACAAT
*
171960 TTTCAAATTTGCAAC
1 TTTCAAATTCGCAAC
171975 TCGAATTCGG
Statistics
Matches: 56, Mismatches: 18, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
19 2 0.04
20 33 0.59
21 10 0.18
22 11 0.20
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (20 bp):
TTTCAAATTCGCAACACAAT
Found at i:172913 original size:19 final size:19
Alignment explanation
Indices: 172889--172937 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
172879 TCGGACCGGG
* *
172889 TATATATATTTAAATTAAA
1 TATATAAATATAAATTAAA
172908 TATATAAATATAAATTAAA
1 TATATAAATATAAATTAAA
* *
172927 TTTATTAATAT
1 TATATAAATAT
172938 TATATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATAAATATAAATTAAA
Found at i:175756 original size:28 final size:28
Alignment explanation
Indices: 175720--175787 Score: 136
Period size: 28 Copynumber: 2.4 Consensus size: 28
175710 TATAAAATAT
175720 AAGACTTATGACTCAATAGAAAGGTATA
1 AAGACTTATGACTCAATAGAAAGGTATA
175748 AAGACTTATGACTCAATAGAAAGGTATA
1 AAGACTTATGACTCAATAGAAAGGTATA
175776 AAGACTTATGAC
1 AAGACTTATGAC
175788 CAAAGGATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.25
Consensus pattern (28 bp):
AAGACTTATGACTCAATAGAAAGGTATA
Found at i:182886 original size:27 final size:27
Alignment explanation
Indices: 182848--182900 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
182838 GGTCACTCAA
182848 TTATATTTTTCAAAATCATAATTAACG
1 TTATATTTTTCAAAATCATAATTAACG
182875 TTATATTTTTCAAAATCATAATTAAC
1 TTATATTTTTCAAAATCATAATTAAC
182901 AGAACTATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (27 bp):
TTATATTTTTCAAAATCATAATTAACG
Found at i:183290 original size:18 final size:18
Alignment explanation
Indices: 183267--183314 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
183257 AAATTGTCCT
*
183267 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
183285 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
183302 TATTTATATATTT
1 TA-TTATATATTT
183315 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:183389 original size:22 final size:22
Alignment explanation
Indices: 183366--183407 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
183356 TACAAAATTA
*
183366 AAAAT-ATAAAAAATATTTAAT
1 AAAATGATAAAAAAAATTTAAT
*
183387 AAAATGGTAAAAAAAATTTAA
1 AAAATGATAAAAAAAATTTAA
183408 CCCCTGAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (22 bp):
AAAATGATAAAAAAAATTTAAT
Found at i:185416 original size:87 final size:84
Alignment explanation
Indices: 185298--185559 Score: 346
Period size: 87 Copynumber: 3.0 Consensus size: 84
185288 TTTACTAATT
* *
185298 TATTATCTGTTCAGCATTTAAAGATCATATTCAATATTGAAGTATAAAGACTCAATCTTATACAG
1 TATTATCTGTTCAGCATATAAAGATTATATTCAATATTGAAGTATAAAGACTCAATCTTATACA-
185363 GGGTAGATGTACATGGCTCCA
65 GGGTAGATGTACA-GGCTCCA
* * *
185384 TATTATCTGTTTCAACATATAAAGGTTATATTCAATATTGAAGTATAAAGACTCAGTCTTATACA
1 TATTATCTG-TTCAGCATATAAAGATTATATTCAATATTGAAGTATAAAGACTCAATCTTATACA
*
185449 TGGGT-GTATGTATAGGACTCCA
65 -GGGTAG-ATGTACAGG-CTCCA
* * *
185471 TATTATCTGAGTCAGCATATAAAGATTATATTCAATATTGAAGTATAAAGACTCAACCTTATGCA
1 TATTATCTG-TTCAGCATATAAAGATTATATTCAATATTGAAGTATAAAGACTCAATCTTATACA
*
185536 GGGAAGGATGTACAGGGCTCCA
65 GGGTA-GATGTACA-GGCTCCA
185558 TA
1 TA
185560 GGAGAGTCAT
Statistics
Matches: 154, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
86 15 0.10
87 136 0.88
88 3 0.02
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (84 bp):
TATTATCTGTTCAGCATATAAAGATTATATTCAATATTGAAGTATAAAGACTCAATCTTATACAG
GGTAGATGTACAGGCTCCA
Found at i:186295 original size:22 final size:23
Alignment explanation
Indices: 186251--186296 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
186241 AAAATAATAA
*
186251 TAAAATTTTCTATTCCTTATTTT
1 TAAAATTTTATATTCCTTATTTT
*
186274 TAAAATTTTAT-TTCTTTATTTT
1 TAAAATTTTATATTCCTTATTTT
186296 T
1 T
186297 GTATATATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (23 bp):
TAAAATTTTATATTCCTTATTTT
Found at i:195138 original size:6 final size:6
Alignment explanation
Indices: 195127--195151 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
195117 CAAAACGAAG
195127 GGCAAA GGCAAA GGCAAA GGCAAA G
1 GGCAAA GGCAAA GGCAAA GGCAAA G
195152 TACCTGAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.36, T:0.00
Consensus pattern (6 bp):
GGCAAA
Found at i:195348 original size:54 final size:54
Alignment explanation
Indices: 195286--195838 Score: 803
Period size: 54 Copynumber: 10.3 Consensus size: 54
195276 TTACCAAATA
195286 GGCACTAAGTGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * * *
195340 GGTACTAAGTGTGC-AATTCATGGAA-T--TCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAAAGT-ACGAAATTCATCATATGTTGATGAATAACCGTTTC
* *
195391 GGCACTAAGTGTGCAAAGCACGAAATTCATCATATGTTGATTAATAACCGTTTC
1 GGCACTAAGTGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
* *
195445 GGCACTAAGTGTGCAAAGTACGGAATTCATCATATGTTGATGAATAACTGTTTC
1 GGCACTAAGTGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
* *
195499 GACACTAAGTATGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
* *
195553 GACACTAAGTGTGCAAAGTACGAAATTCATCATATGTCGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
* **
195607 GGTACTAAGTGTGCAAAGTAAAAAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * *
195661 AGCACTAAGTGTG-ACAAGCACGGAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCA-AAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * *
195715 GGTACTAAGTGTGCAAAGCACGAAATTCATCATATGTTGATGAATAACTGTTTC
1 GGCACTAAGTGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * * *
195769 GACACTAAGTGTGC-TATTAACAAAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAAAGT-ACGAAATTCATCATATGTTGATGAATAACCGTTTC
*
195823 GGCACTATGTGTGCAA
1 GGCACTAAGTGTGCAA
195839 CTCACAGAAT
Statistics
Matches: 445, Mismatches: 45, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
51 42 0.09
52 3 0.01
53 6 0.01
54 393 0.88
55 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.31
Consensus pattern (54 bp):
GGCACTAAGTGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTC
Found at i:202541 original size:54 final size:54
Alignment explanation
Indices: 202469--202956 Score: 592
Period size: 54 Copynumber: 9.1 Consensus size: 54
202459 TAGGCAGAAA
* ** * *
202469 TGTGCAAAGTACATAATTCATCATATGTTGATGAATAACTGTTTCGGCACTAAC
1 TGTGCAAAGCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAG
* ** * *
202523 TATGCAATTCACGGAATTCATCATATGTTGATGAATAACTGTTTCGACACTAAG
1 TGTGCAAAGCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAG
* ** *
202577 TGTACAAAGCACAAAATTCAGT-ATATGTTGATGAATAACTGTTTCGGCACTAAG
1 TGTGCAAAGCACGGAATTCA-TCATATGTTGATGAATAACCGTTTCGGCACTAAG
* * *
202631 TGTGCAAAGTACGGAATTCATCATATGTTGATGAATAACCGTTGCGGCATTAAG
1 TGTGCAAAGCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAG
* * *
202685 TGTGCAAAGTACGGAATTCATCATATGTTGATGATTAACCGTTTCGACACTAAG
1 TGTGCAAAGCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAG
** *
202739 TGTGCAAAGCACATAATTCATCATATATTGATGAATAACCGTTTCGGCACTAAG
1 TGTGCAAAGCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAG
* * * * *
202793 TGTGCAAAGTACGAAATTCATAATATATTGATGAATAACCGTTTCAGCACTAAG
1 TGTGCAAAGCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAG
* ** * *
202847 TGTGCAAAGAACAAAATTCATCATA-----ATGAATAACCTTTTCGACACTAAG
1 TGTGCAAAGCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAG
* * * *
202896 TGTGCAAAGCCCGGAATTCATCATATGTTGATGAATAACCATTTCAGCACTATG
1 TGTGCAAAGCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAG
202950 TGTGCAA
1 TGTGCAA
202957 CCCACAAATT
Statistics
Matches: 376, Mismatches: 51, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
49 42 0.11
53 1 0.00
54 332 0.88
55 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (54 bp):
TGTGCAAAGCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAG
Found at i:202736 original size:162 final size:162
Alignment explanation
Indices: 202469--202956 Score: 659
Period size: 162 Copynumber: 3.0 Consensus size: 162
202459 TAGGCAGAAA
* * * *
202469 TGTGCAAAGTAC-ATAATTCATCATATGTTGATGAATAACTGTTTCGGCACTAACTATGC-AATT
1 TGTGCAAAGTACGA-AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGT
* *
202532 CACGGAATTCATCATATGTTGATGAATAACTGTTTCGACACTAAGTGTACAAAGCACAAAATTCA
65 -ACGGAATTCATCATATGTTGATGAATAACCGTTTCGACACTAAGTGTGCAAAGCACAAAATTCA
*
202597 GT-ATATGTTGATGAATAACTGTTTCGGCACTAAG
129 -TCATATGTTGATGAATAACCGTTTCGGCACTAAG
* * *
202631 TGTGCAAAGTACGGAATTCATCATATGTTGATGAATAACCGTTGCGGCATTAAGTGTGCAAAGTA
1 TGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTA
* *
202696 CGGAATTCATCATATGTTGATGATTAACCGTTTCGACACTAAGTGTGCAAAGCACATAATTCATC
66 CGGAATTCATCATATGTTGATGAATAACCGTTTCGACACTAAGTGTGCAAAGCACAAAATTCATC
*
202761 ATATATTGATGAATAACCGTTTCGGCACTAAG
131 ATATGTTGATGAATAACCGTTTCGGCACTAAG
* * * *
202793 TGTGCAAAGTACGAAATTCATAATATATTGATGAATAACCGTTTCAGCACTAAGTGTGCAAAGAA
1 TGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTA
** * * **
202858 CAAAATTCATCATA-----ATGAATAACCTTTTCGACACTAAGTGTGCAAAGCCCGGAATTCATC
66 CGGAATTCATCATATGTTGATGAATAACCGTTTCGACACTAAGTGTGCAAAGCACAAAATTCATC
* * *
202918 ATATGTTGATGAATAACCATTTCAGCACTATG
131 ATATGTTGATGAATAACCGTTTCGGCACTAAG
202950 TGTGCAA
1 TGTGCAA
202957 CCCACAAATT
Statistics
Matches: 292, Mismatches: 31, Indels: 11
0.87 0.09 0.03
Matches are distributed among these distances:
157 76 0.26
161 1 0.00
162 212 0.73
163 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (162 bp):
TGTGCAAAGTACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTA
CGGAATTCATCATATGTTGATGAATAACCGTTTCGACACTAAGTGTGCAAAGCACAAAATTCATC
ATATGTTGATGAATAACCGTTTCGGCACTAAG
Found at i:204674 original size:18 final size:17
Alignment explanation
Indices: 204647--204685 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
204637 CCAAAAAAAT
204647 AAAAAATAAAAGAAGAA
1 AAAAAATAAAAGAAGAA
*
204664 GAAAAAGTAAAAGAAGAA
1 -AAAAAATAAAAGAAGAA
204682 AAAA
1 AAAA
204686 GAAAGAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (17 bp):
AAAAAATAAAAGAAGAA
Found at i:208744 original size:19 final size:19
Alignment explanation
Indices: 208720--208767 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
208710 AATTTGATTC
*
208720 TCAAAATCAACTTTTGCTT
1 TCAAAACCAACTTTTGCTT
208739 TCAAAACCAACTTTTGCTT
1 TCAAAACCAACTTTTGCTT
208758 TCAAAACCAA
1 TCAAAACCAA
208768 ATCATTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33
Consensus pattern (19 bp):
TCAAAACCAACTTTTGCTT
Found at i:209578 original size:20 final size:21
Alignment explanation
Indices: 209553--209591 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
209543 GTGACTCTTT
*
209553 ACCGGTTTTGTCAT-TTTTAG
1 ACCGGTTTTATCATATTTTAG
209573 ACCGGTTTTATCATATTTT
1 ACCGGTTTTATCATATTTT
209592 TACCTGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.51
Consensus pattern (21 bp):
ACCGGTTTTATCATATTTTAG
Found at i:209893 original size:180 final size:182
Alignment explanation
Indices: 209431--209987 Score: 913
Period size: 182 Copynumber: 3.1 Consensus size: 182
209421 AACCCAAGTG
* * *
209431 TCGATACATTTTTATAAAGTATCGACACTTTATAGGTGTTATTACGGCTTCTCTTTTAAATTCCA
1 TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCA
* *
209496 AAATTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGACTCTTTACCGGTTT
66 AAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGCTCTTTACCGGTTT
*
209561 TGTCATTTTTAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
131 TGTCATTTTCAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
209613 TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCA
1 TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCA
*
209678 AAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCTGGTGGCTCTTTACCGGTTT
66 AAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGCTCTTTACCGGTTT
* *
209743 TGTCATTTTCAGACCGGTTTTATTATA-TTTTACCTGTTATATTGTTATAGA
131 TGTCATTTTCAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
** *
209794 TCGATACATTTTT-TAAAGTATCGACACTTTATAAACGCTATTACTGCTTGTCTTTTAAATTCCA
1 TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCA
* * *
209858 AAAGTGTCGATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGG-TT
66 AAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGCTCTTTACCGGTTT
* * **
209922 TGATCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTAATATGGA
131 TG-TCATTTTCAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
209975 TCGATACATTTTT
1 TCGATACATTTTT
209988 TATTTGTATC
Statistics
Matches: 351, Mismatches: 22, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
179 4 0.01
180 128 0.36
181 70 0.20
182 149 0.42
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCA
AAAGTGTCGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGCTCTTTACCGGTTT
TGTCATTTTCAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
Found at i:214763 original size:17 final size:17
Alignment explanation
Indices: 214741--214788 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
214731 TCTTTTTAGT
*
214741 AAAATATTTAAAATGAC
1 AAAATATTTAAAATAAC
* *
214758 AAAATATTATAATATAAT
1 AAAATATT-TAAAATAAC
214776 AAATATATTTAAA
1 AAA-ATATTTAAA
214789 TTATAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 8 0.32
18 12 0.48
19 5 0.20
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (17 bp):
AAAATATTTAAAATAAC
Found at i:214839 original size:19 final size:18
Alignment explanation
Indices: 214815--214864 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
214805 TAAATTTATT
*
214815 TAAAAAAATATTGAAAATA
1 TAAAAAAATATT-AAAAAA
* *
214834 TAAAAATAGATTAAAAAA
1 TAAAAAAATATTAAAAAA
*
214852 TAAAAAATTATTA
1 TAAAAAAATATTA
214865 CGGTTTTGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (18 bp):
TAAAAAAATATTAAAAAA
Found at i:215765 original size:169 final size:165
Alignment explanation
Indices: 215481--215820 Score: 448
Period size: 169 Copynumber: 2.0 Consensus size: 165
215471 ATAATAATAC
215481 CAAACAGTTAAATTTTAAATTACATTTTTAAACAACACTTTTAAAAAAAATTATAGCATTTTTAA
1 CAAACAGTTAAATTTTAAATTACATTTTTAAACAACACTTTTAAAAAAAATTATAGCATTTTTAA
* * * *
215546 GTCACTTTTCAAAAGCAATGTCAAACTGACCTTGAATAAACTCGAATAAAATGTAGCTATGAATA
66 GTCACTTTTCAAAAGCAATGCCAAACTGACCCTGAATAAACTCAAATAAAAGGTAGCTATGAATA
* * **
215611 GATCTGATGAGATCAAACTATTGATAGAGTACCGA
131 GATCTGAGGAGATCAAACTATTGACAGACCACCGA
* ** **** *
215646 CAAACTGTTAAATTTTAAATTTTATTTTTAAACAACACTTTTAAAAGTTCGTTTCTA-CATCACT
1 CAAACAGTTAAATTTTAAATTACATTTTTAAACAACACTTTTAAAA--AAAATTATAGCAT---T
* *
215710 TTTAAGTCATTTTTCAAAAGCAATGCCAAACTGACCCTGAATAAACTCAAATAAAAGGTAGTTAT
61 TTTAAGTCACTTTTCAAAAGCAATGCCAAACTGACCCTGAATAAACTCAAATAAAAGGTAGCTAT
* *
215775 GAATATATCTGAGGAGATCAAGCTATTGACAGACCACCGA
126 GAATAGATCTGAGGAGATCAAACTATTGACAGACCACCGA
215815 CAAACA
1 CAAACA
215821 ATAAATCAGA
Statistics
Matches: 149, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
165 43 0.29
166 3 0.02
167 4 0.03
169 99 0.66
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (165 bp):
CAAACAGTTAAATTTTAAATTACATTTTTAAACAACACTTTTAAAAAAAATTATAGCATTTTTAA
GTCACTTTTCAAAAGCAATGCCAAACTGACCCTGAATAAACTCAAATAAAAGGTAGCTATGAATA
GATCTGAGGAGATCAAACTATTGACAGACCACCGA
Found at i:215959 original size:25 final size:27
Alignment explanation
Indices: 215918--215968 Score: 79
Period size: 25 Copynumber: 1.9 Consensus size: 27
215908 TTTTAAATTG
215918 CATTTCTAAACAACACTTTT-AAAAGTT
1 CATTTCT-AACAACACTTTTCAAAAGTT
215945 CATTTCT-ACAACACTTTTCAAAAG
1 CATTTCTAACAACACTTTTCAAAAG
215969 CAATGCCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 11 0.48
26 5 0.22
27 7 0.30
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (27 bp):
CATTTCTAACAACACTTTTCAAAAGTT
Found at i:216261 original size:262 final size:261
Alignment explanation
Indices: 215787--216422 Score: 965
Period size: 262 Copynumber: 2.4 Consensus size: 261
215777 ATATATCTGA
* *
215787 GGAGATCAAGCTATTGACAGACCACCGACAAACAATAAATCAGA---ATCGATGTGAGAAACTAT
1 GGAGATCAAGCTATTGACAGACCACCGACAAACCATAAATCAAATCGATCGATGTGAGAAACTAT
* * * * *
215849 CTATGAATACAAATTGTGCGTCCAAATCCAAATCTAATCCGATGGTCAAAACAGTTAAATTTTAA
66 CCATGAATACAAA---T-CGTGC--ATTCAAATCTAATCCGAGGGTCCAAACAGTTAAATTTTAA
215914 ATTGCATTTCTAAACAACACTTTTAAAAGTTCATTTCTACAACACTTTTCAAAAGCAATGCCAAA
125 ATTGCATTTCTAAACAACACTTTTAAAAGTTCATTTCTACAACACTTTTCAAAAGCAATGCCAAA
* *
215979 CTGCCCCTGAATAAACTCGAATAAAAAGTAGCTATGAATAGATCTGACCACATAGAAAATTAAAT
190 CTGCCCCTGAAAAAACTCGAATAAAAAGTAGCTATAAATAGATCTGACCACATAGAAAATTAAAT
216044 ACAAAAG
255 ACAAAAG
* *
216051 GGAGATAAAGCTATTGACAGACCACTGACAAACCATAAATCATAATCGATCGATGTGAGAAACTA
1 GGAGATCAAGCTATTGACAGACCACCGACAAACCATAAATCA-AATCGATCGATGTGAGAAACTA
*
216116 TCCATGAATACAAATCGTGCATTCAAATCCAATCCGAGGGTCCAAACAGTTAAATTTTAAATTGC
65 TCCATGAATACAAATCGTGCATTCAAATCTAATCCGAGGGTCCAAACAGTTAAATTTTAAATTGC
* * *
216181 ATTTTTAAACAACACTTTTAAAAGTTCGTTTCTACAACACTTTTCAAAAGCAATGCCAAACTGGC
130 ATTTCTAAACAACACTTTTAAAAGTTCATTTCTACAACACTTTTCAAAAGCAATGCCAAACTGCC
* * * *
216246 CCTGAAAAAACTCGAATGAAAGGTAGCTATAAATAGATTTGACCACATCGAAAATTAAATACAAA
195 CCTGAAAAAACTCGAATAAAAAGTAGCTATAAATAGATCTGACCACATAGAAAATTAAATACAAA
216311 AG
260 AG
* *
216313 GGAGATCAAGCTATTGATAGACCACCGACAAACCATAAACCAGAATCGATCGATGTGAGAAAACT
1 GGAGATCAAGCTATTGACAGACCACCGACAAACCATAAATCA-AATCGATCGATGTGAG-AAACT
216378 ATCCATGAATACAAATCGTGCA-TCTAAATCTAATCCGAGGGTCCA
64 ATCCATGAATACAAATCGTGCATTC-AAATCTAATCCGAGGGTCCA
216423 GAGTAGGGAA
Statistics
Matches: 341, Mismatches: 25, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
262 220 0.65
263 46 0.13
264 43 0.13
265 2 0.01
268 30 0.09
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (261 bp):
GGAGATCAAGCTATTGACAGACCACCGACAAACCATAAATCAAATCGATCGATGTGAGAAACTAT
CCATGAATACAAATCGTGCATTCAAATCTAATCCGAGGGTCCAAACAGTTAAATTTTAAATTGCA
TTTCTAAACAACACTTTTAAAAGTTCATTTCTACAACACTTTTCAAAAGCAATGCCAAACTGCCC
CTGAAAAAACTCGAATAAAAAGTAGCTATAAATAGATCTGACCACATAGAAAATTAAATACAAAA
G
Found at i:219983 original size:2 final size:2
Alignment explanation
Indices: 219978--220011 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
219968 GAGAAGGGGG
219978 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
220012 AATGGAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:224288 original size:17 final size:17
Alignment explanation
Indices: 224266--224335 Score: 79
Period size: 18 Copynumber: 4.0 Consensus size: 17
224256 ATATAAAGAG
224266 CTAGTTTAATTAATGAA
1 CTAGTTTAATTAATGAA
*
224283 CTAGTTTAAGTGAATGAA
1 CTAGTTTAA-TTAATGAA
* *
224301 CTAGTTTAATTAGTCAA
1 CTAGTTTAATTAATGAA
224318 CTAGCTTT-ATTGAATGAA
1 CTAG-TTTAATT-AATGAA
224336 AGAGGATACT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
17 21 0.48
18 23 0.52
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (17 bp):
CTAGTTTAATTAATGAA
Found at i:224312 original size:35 final size:35
Alignment explanation
Indices: 224266--224335 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
224256 ATATAAAGAG
*
224266 CTAGTTTAATTAATGAACTAG-TTTAAGTGAATGAA
1 CTAGTTTAATTAATCAACTAGCTTT-AGTGAATGAA
* *
224301 CTAGTTTAATTAGTCAACTAGCTTTATTGAATGAA
1 CTAGTTTAATTAATCAACTAGCTTTAGTGAATGAA
224336 AGAGGATACT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 28 0.90
36 3 0.10
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (35 bp):
CTAGTTTAATTAATCAACTAGCTTTAGTGAATGAA
Found at i:224473 original size:20 final size:20
Alignment explanation
Indices: 224435--224473 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
224425 CAACTTAATG
* *
224435 TCATGCAAATTTATTAACAC
1 TCATGCAAATTCATGAACAC
224455 TCATGCAAATTCATGAACA
1 TCATGCAAATTCATGAACA
224474 AGTAAAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (20 bp):
TCATGCAAATTCATGAACAC
Found at i:239990 original size:3 final size:3
Alignment explanation
Indices: 239984--240038 Score: 62
Period size: 3 Copynumber: 18.3 Consensus size: 3
239974 ATTCTTGTCT
239984 TTA TTA TTA TT- TATA TTA TTA TTA TT- TATA TTA TTA TTA -TA TATA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-TA
240029 TTA TTA TTA T
1 TTA TTA TTA T
240039 ATATATTACT
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
2 4 0.09
3 37 0.80
4 5 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:240000 original size:12 final size:11
Alignment explanation
Indices: 239985--240046 Score: 69
Period size: 12 Copynumber: 5.7 Consensus size: 11
239975 TTCTTGTCTT
239985 TATTATTATTTA
1 TATTATTA-TTA
239997 TATTATTATTA
1 TATTATTATTA
240008 T-TTA-TA-T-
1 TATTATTATTA
240015 TATTATTATATA
1 TATTATTAT-TA
240027 TATTATTATTA
1 TATTATTATTA
240038 TATATATTA
1 TAT-TATTA
240047 CTAACCAAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
7 1 0.02
8 4 0.09
9 4 0.09
10 3 0.07
11 10 0.23
12 22 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTATTATTA
Found at i:240002 original size:15 final size:15
Alignment explanation
Indices: 239984--240046 Score: 108
Period size: 15 Copynumber: 4.2 Consensus size: 15
239974 ATTCTTGTCT
*
239984 TTATTATTATTTATA
1 TTATTATTATATATA
*
239999 TTATTATTATTTATA
1 TTATTATTATATATA
240014 TTATTATTATATATA
1 TTATTATTATATATA
240029 TTATTATTATATATA
1 TTATTATTATATATA
240044 TTA
1 TTA
240047 CTAACCAAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTATTATATATA
Found at i:240309 original size:2 final size:2
Alignment explanation
Indices: 240302--240329 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
240292 ATCCCCTATT
240302 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
240330 ATTATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:250943 original size:10 final size:10
Alignment explanation
Indices: 250928--250961 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
250918 GTCCTAAGTT
250928 GAAAAAAAAA
1 GAAAAAAAAA
250938 GAAAAAAAAAA
1 G-AAAAAAAAA
*
250949 GAAAAAAAGA
1 GAAAAAAAAA
250959 GAA
1 GAA
250962 GAACGTTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:250945 original size:11 final size:11
Alignment explanation
Indices: 250929--250956 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
250919 TCCTAAGTTG
250929 AAAAAAAAAGA
1 AAAAAAAAAGA
250940 AAAAAAAAAGA
1 AAAAAAAAAGA
250951 AAAAAA
1 AAAAAA
250957 GAGAAGAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:251973 original size:105 final size:105
Alignment explanation
Indices: 251791--252566 Score: 1268
Period size: 105 Copynumber: 7.4 Consensus size: 105
251781 AGGTTTTACC
*
251791 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
251856 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
251896 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTAAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
251961 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
252001 CAGGGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* **
252066 ACAAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGTTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* * * *
252106 CAGAGCTAATTTCAACTTCACAACGAAGGATATTGGATTCCAGACAACGCAAGAGT-AACATCAC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG-TTCAACTTCAC
*
252170 GACGAAGGGACCGCTGGTTGTTAACAAACATTTCTCAAATT
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
252211 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
252276 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
252316 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAATTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
252381 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* * * *
252421 CAGAGACAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACACAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
252486 ACGAAGGGACGGCTGGTTGTCAACAAACAATTT-TCCAGTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
* ** *
252526 CCAGAACCAATTTCAACTTCACGGCGGAGGATATTGGACTC
1 -CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
252567 GGAACAATAC
Statistics
Matches: 627, Mismatches: 40, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
104 1 0.00
105 586 0.93
106 40 0.06
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:254196 original size:2 final size:2
Alignment explanation
Indices: 254189--254226 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
254179 CCTATTATTA
*
254189 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
254227 TTAATATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:254434 original size:12 final size:12
Alignment explanation
Indices: 254419--254464 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
254409 TTCTTGTCTT
254419 TATTATTATTTA
1 TATTATTATTTA
254431 TATTATTATATATA
1 TATTATTAT-T-TA
254445 TATTATTA-TTA
1 TATTATTATTTA
254456 TATATATTA
1 TAT-TATTA
254465 CTAACCAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 5 0.16
12 15 0.48
13 1 0.03
14 10 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATTATTTA
Found at i:254453 original size:17 final size:16
Alignment explanation
Indices: 254418--254462 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
254408 ATTCTTGTCT
*
254418 TTATTAT-TATTTATA
1 TTATTATATATATATA
254433 TTATTATATATATATTA
1 TTATTATATATATA-TA
254450 TTATTATATATAT
1 TTATTATATATAT
254463 TACTAACCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 7 0.26
16 5 0.19
17 15 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATTATATATATATA
Found at i:254720 original size:2 final size:2
Alignment explanation
Indices: 254713--254774 Score: 83
Period size: 2 Copynumber: 32.0 Consensus size: 2
254703 TTTTATCCCC
* *
254713 TA TA TA TA TA TA TA TA TA TA TA T- TA TT TT 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
*
254754 TA TA TT TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
254775 CTACTTTTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:254749 original size:23 final size:21
Alignment explanation
Indices: 254713--254774 Score: 94
Period size: 19 Copynumber: 3.1 Consensus size: 21
254703 TTTTATCCCC
*
254713 TATATATATA-TATATATATA
1 TATATATTTATTATATATATA
254733 TAT-TATTT-TTATATATATA
1 TATATATTTATTATATATATA
254752 TATATATTTATTATATATATA
1 TATATATTTATTATATATATA
254773 TA
1 TA
254775 CTACTTTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
19 17 0.45
20 8 0.21
21 13 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATATTTATTATATATATA
Found at i:254976 original size:16 final size:15
Alignment explanation
Indices: 254911--254965 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
254901 TACTTAATCC
254911 TTTTTATTTTCTTTA
1 TTTTTATTTTCTTTA
* * *
254926 TCTTT-TTATCTCT-
1 TTTTTATTTTCTTTA
* *
254939 GTATTATTTTCTTTA
1 TTTTTATTTTCTTTA
254954 TTTTTATTTTCT
1 TTTTTATTTTCT
254966 CATTTTTTTA
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
13 2 0.07
14 12 0.43
15 14 0.50
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTTTATTTTCTTTA
Found at i:258411 original size:17 final size:17
Alignment explanation
Indices: 258363--258412 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
258353 TAAGAGTTAT
*
258363 TTTAATAAACGAACTAG
1 TTTAATAAATGAACTAG
* * *
258380 TTTGATGAATAAACTAG
1 TTTAATAAATGAACTAG
*
258397 TTTAATTAATGAACTA
1 TTTAATAAATGAACTA
258413 CTTCCCTAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (17 bp):
TTTAATAAATGAACTAG
Found at i:262980 original size:15 final size:16
Alignment explanation
Indices: 262955--262988 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
262945 ATTAGTAATA
*
262955 AAAAAATAACCTTACC
1 AAAAAATAACCTCACC
262971 AAAAAA-AACCTCACC
1 AAAAAATAACCTCACC
262986 AAA
1 AAA
262989 CACTCCAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.62, C:0.26, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAAATAACCTCACC
Found at i:264571 original size:17 final size:17
Alignment explanation
Indices: 264542--264591 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
264532 TAAGAGTTAT
* *
264542 TTTAATAAATGAATTAG
1 TTTAATGAATGAACTAG
*
264559 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
*
264576 TTTAATTAATGAACTA
1 TTTAATGAATGAACTA
264592 CTTCCCTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.40
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:269771 original size:51 final size:50
Alignment explanation
Indices: 269663--269821 Score: 132
Period size: 51 Copynumber: 3.1 Consensus size: 50
269653 ATTTTATAAA
*
269663 TTAATA-TTAATAAAATATTTTAATATCATTTTAATAA-A-AATATTA-ATT
1 TTAATATTTAATAAAATA-TTT-ATATTATTTTAATAATATAATATTATATT
269711 ATTAAAATATTTAA-AAAATATTTATTATTATTTCTAATAATATAATATTATATT
1 -TT--AATATTTAATAAAATATTTA-TATTATTT-TAATAATATAATATTATATT
* * *
269765 TTAATATTACAATAAAATACTCA-ATTATATTATAATAATATAAGATATTATATT
1 TTAATATT-TAATAAAATATTTATATTAT-TT-TAATAATAT-A-ATATTATATT
269819 TTA
1 TTA
269822 TTGTAATAAT
Statistics
Matches: 92, Mismatches: 5, Indels: 21
0.78 0.04 0.18
Matches are distributed among these distances:
49 3 0.03
50 10 0.11
51 27 0.29
52 18 0.20
53 18 0.20
54 16 0.17
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (50 bp):
TTAATATTTAATAAAATATTTATATTATTTTAATAATATAATATTATATT
Found at i:269778 original size:21 final size:23
Alignment explanation
Indices: 269733--269778 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
269723 AAAAAATATT
*
269733 TATTATTATTTCTAATAATATAA
1 TATTATTATTTCTAATAATACAA
*
269756 TATTA-TATTT-TAATATTACAA
1 TATTATTATTTCTAATAATACAA
269777 TA
1 TA
269779 AAATACTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 5 0.24
23 5 0.24
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTATTATTTCTAATAATACAA
Found at i:269959 original size:24 final size:25
Alignment explanation
Indices: 269926--269993 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
269916 TTAACAGAGA
*
269926 TTTTTGAAATAT-AT-TAATTAATAT
1 TTTTTAAAATATAATATAA-TAATAT
269950 TTTTTAAAATATAATATAATAATAT
1 TTTTTAAAATATAATATAATAATAT
*
269975 TACTTTAATAAT-TAATATA
1 T-TTTTAA-AATATAATATA
269994 TTTATAATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
24 11 0.29
25 9 0.24
26 15 0.39
27 3 0.08
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (25 bp):
TTTTTAAAATATAATATAATAATAT
Found at i:269961 original size:22 final size:23
Alignment explanation
Indices: 269925--269970 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
269915 TTTAACAGAG
269925 ATTTTTGAAATATATTAAT-TAAT
1 ATTTTTGAAATATA-TAATATAAT
*
269948 ATTTTTTAAA-ATATAATATAAT
1 ATTTTTGAAATATATAATATAAT
269970 A
1 A
269971 ATATTACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 8 0.38
23 9 0.43
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTTTTGAAATATATAATATAAT
Found at i:270680 original size:7 final size:7
Alignment explanation
Indices: 270668--270710 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
270658 TCATTAATTG
270668 CTTCAAA
1 CTTCAAA
270675 CTTCAAA
1 CTTCAAA
270682 CTTCAAA
1 CTTCAAA
270689 CTTCAAA
1 CTTCAAA
270696 CTTCAAA
1 CTTCAAA
270703 CTTCAAA
1 CTTCAAA
270710 C
1 C
270711 CCCACCCTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (7 bp):
CTTCAAA
Found at i:271433 original size:13 final size:12
Alignment explanation
Indices: 271415--271471 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 12
271405 AAAATAGAAT
271415 GAATAAAAAACAA
1 GAATAAAAAA-AA
271428 GAAT-AAAAAAA
1 GAATAAAAAAAA
*
271439 GAAT--AAATAA
1 GAATAAAAAAAA
271449 -AATAAAATAAAA
1 GAATAAAA-AAAA
271461 GAAATAAAAAA
1 G-AATAAAAAA
271472 TATATAGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 3 0.08
10 5 0.14
11 8 0.22
12 8 0.22
13 6 0.16
14 7 0.19
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (12 bp):
GAATAAAAAAAA
Found at i:272778 original size:37 final size:37
Alignment explanation
Indices: 272732--273163 Score: 322
Period size: 37 Copynumber: 10.9 Consensus size: 37
272722 CATGAAAATG
* *
272732 TTTTAAAAATATTTTCAAAAATTATATATTATATATA
1 TTTTCAAAATATTTTCAAAAACTATATATTATATATA
*
272769 TTTTCAAAATGTTTTCAAAAACTA-A-ATTATATATA
1 TTTTCAAAATATTTTCAAAAACTATATATTATATATA
*
272804 TATATTCAAAATATTTTCAAAAAATATTATATATATATATA
1 T-T-TTCAAAATATTTTCAAAAACTA-TATAT-TATATATA
*
272845 TATATT---TATATTTTCAAAAAACTATATATTATATATA
1 T-T-TTCAAAATATTTTC-AAAAACTATATATTATATATA
* * *
272882 TTTTAAAAACATTTTTAAAAACTATATA-TATATATA
1 TTTTCAAAATATTTTCAAAAACTATATATTATATATA
272918 TTATAT-ATATATATATGTTTTTAAAATGTTTTCAAAAACTATATATTATATATA
1 TT-T-TCA-A-A-ATA----TTT---------TCAAAAACTATATATTATATATA
*
272972 TTTTCAAAATATTTTCAAAGACTATATATTATATATATATA
1 TTTTCAAAATATTTTCAAAAAC--TATA-TAT-TATATATA
* *
273013 TTTTTAAAATGTTTTCAAAAACTATATATTATATATA
1 TTTTCAAAATATTTTCAAAAACTATATATTATATATA
* * *
273050 TTTTCAAAATTTTTTTAAAAACTCTATATTATATATA
1 TTTTCAAAATATTTTCAAAAACTATATATTATATATA
* *
273087 TGTTTTCAAAACGTTTTTTAAAAAACTATATATTATATATA
1 --TTTTCAAAA--TATTTTCAAAAACTATATATTATATATA
* *
273128 TGTTTTCAAAAT-TTTATAAAAAACTATATACTATAT
1 --TTTTCAAAATATTT-TCAAAAACTATATATTATAT
273164 CTTATATATA
Statistics
Matches: 333, Mismatches: 23, Indels: 76
0.77 0.05 0.18
Matches are distributed among these distances:
35 13 0.04
36 13 0.04
37 112 0.34
38 27 0.08
39 46 0.14
40 7 0.02
41 78 0.23
44 3 0.01
46 3 0.01
50 3 0.01
51 1 0.00
52 2 0.01
53 15 0.05
54 10 0.03
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (37 bp):
TTTTCAAAATATTTTCAAAAACTATATATTATATATA
Found at i:272885 original size:27 final size:27
Alignment explanation
Indices: 272839--272890 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
272829 ATTATATATA
*
272839 TATATATATATTTATATTTTCAAAAAAC
1 TATATATATATATATATTTT-AAAAAAC
272867 TATATAT-TATATATATTTTAAAAA
1 TATATATATATATATATTTTAAAAA
272891 CATTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 5 0.22
27 11 0.48
28 7 0.30
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (27 bp):
TATATATATATATATATTTTAAAAAAC
Found at i:272911 original size:2 final size:2
Alignment explanation
Indices: 272904--272933 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
272894 TTTTAAAAAC
272904 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
272934 GTTTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:272924 original size:13 final size:13
Alignment explanation
Indices: 272906--272931 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
272896 TTAAAAACTA
272906 TATATATATATAT
1 TATATATATATAT
272919 TATATATATATAT
1 TATATATATATAT
272932 ATGTTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:272924 original size:15 final size:15
Alignment explanation
Indices: 272904--272933 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
272894 TTTTAAAAAC
272904 TATATATATATATAT
1 TATATATATATATAT
272919 TATATATATATATAT
1 TATATATATATATAT
272934 GTTTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:273021 original size:78 final size:76
Alignment explanation
Indices: 272919--273172 Score: 321
Period size: 78 Copynumber: 3.2 Consensus size: 76
272909 ATATATATAT
*
272919 TATATATATATATATGTTTTTAAAATGTTTTCAAAAACTATATATTATATATATTTTCAAAATAT
1 TATATATATATATATATTTTTAAAATGTTTTCAAAAACTATATATTATATATATTTTCAAAAT-T
* *
272984 TTTCAAAGACTA
65 TTTAAAAAACTA
272996 TATATTATATATATATATTTTTAAAATGTTTTCAAAAACTATATATTATATATATTTTCAAAATT
1 TATA-TATATATATATATTTTTAAAATGTTTTCAAAAACTATATATTATATATATTTTCAAAA-T
* *
273061 TTTTTAAAAACTC
64 TTTTAAAAAACTA
* * * *
273074 TATAT-TATATATATGTTTTCAAAACGTTTTTTAAAAAACTATATATTATATATATGTTTTCAAA
1 TATATATATATATATATTTTTAAAA--TGTTTTCAAAAACTATATATTATATATA--TTTTCAAA
273138 ATTTTATAAAAAACTA
62 ATTTT-TAAAAAACTA
*
273154 TATACTATATCTTATATAT
1 TATA-TATAT-ATATATAT
273173 ATATATATAC
Statistics
Matches: 155, Mismatches: 12, Indels: 14
0.86 0.07 0.08
Matches are distributed among these distances:
76 17 0.11
77 5 0.03
78 97 0.63
79 5 0.03
80 21 0.14
81 1 0.01
82 3 0.02
83 6 0.04
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.48
Consensus pattern (76 bp):
TATATATATATATATATTTTTAAAATGTTTTCAAAAACTATATATTATATATATTTTCAAAATTT
TTAAAAAACTA
Found at i:282079 original size:23 final size:23
Alignment explanation
Indices: 282036--282080 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
282026 ACCTAGGCAG
*
282036 TGTACCGATACCTCATTAAGGGA
1 TGTACCGATACCTCATAAAGGGA
*
282059 TGTACTGATACC-CTATAAAGGG
1 TGTACCGATACCTC-ATAAAGGG
282081 TATCGATACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (23 bp):
TGTACCGATACCTCATAAAGGGA
Found at i:282935 original size:28 final size:27
Alignment explanation
Indices: 282875--282936 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
282865 AAGAGTCGAG
*
282875 GGTTCTACGTGGTCCTTCGAGACATAT
1 GGTTCTACGTGGTCCTTCGAGAAATAT
* *
282902 GTGTTCTATGTGGTCCTTCGGGAAATAGT
1 G-GTTCTACGTGGTCCTTCGAGAAATA-T
282931 GGTTCT
1 GGTTCT
282937 TCGGGACTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 1 0.03
28 27 0.90
29 2 0.07
ACGTcount: A:0.16, C:0.18, G:0.29, T:0.37
Consensus pattern (27 bp):
GGTTCTACGTGGTCCTTCGAGAAATAT
Found at i:282948 original size:18 final size:18
Alignment explanation
Indices: 282911--282954 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
282901 TGTGTTCTAT
282911 GTGGTCCTTCGGGAAATA
1 GTGGTCCTTCGGGAAATA
* **
282929 GTGGTTCTTCGGGACTTA
1 GTGGTCCTTCGGGAAATA
282947 GTGGTCCT
1 GTGGTCCT
282955 ATGGGACAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.34, T:0.34
Consensus pattern (18 bp):
GTGGTCCTTCGGGAAATA
Found at i:291212 original size:18 final size:18
Alignment explanation
Indices: 291189--291232 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
291179 TGTGTTCTAT
291189 GTGGTCCTTCGGGAAATA
1 GTGGTCCTTCGGGAAATA
**
291207 GTGGTCCTTCGGGACGTA
1 GTGGTCCTTCGGGAAATA
291225 GTGGTCCT
1 GTGGTCCT
291233 ACGGAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.14, C:0.20, G:0.36, T:0.30
Consensus pattern (18 bp):
GTGGTCCTTCGGGAAATA
Found at i:293803 original size:9 final size:9
Alignment explanation
Indices: 293782--293821 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
293772 TATTTGGACC
293782 AAAATAAAA-
1 AAAA-AAAAT
293791 AAAAAAAAT
1 AAAAAAAAT
293800 AAAAAAAAT
1 AAAAAAAAT
293809 -AAAAAAAT
1 AAAAAAAAT
293817 AAAAA
1 AAAAA
293822 TTAATATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 12 0.41
9 17 0.59
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:293812 original size:17 final size:16
Alignment explanation
Indices: 293787--293821 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
293777 GGACCAAAAT
293787 AAAAAAAAAAAATAAA
1 AAAAAAAAAAAATAAA
293803 AAAAATAAAAAAATAAA
1 AAAAA-AAAAAAATAAA
293820 AA
1 AA
293822 TTAATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (16 bp):
AAAAAAAAAAAATAAA
Found at i:293847 original size:10 final size:9
Alignment explanation
Indices: 293784--293849 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 9
293774 TTTGGACCAA
293784 AATAAAAA-
1 AATAAAAAT
293792 AA-AAAAAT
1 AATAAAAAT
*
293800 AAAAAAAAT
1 AATAAAAAT
293809 AA-AAAAAT
1 AATAAAAAT
293817 AA-AAATTAAT
1 AATAAA--AAT
293827 -ATAATAAAT
1 AATAA-AAAT
293836 AATAAAACAT
1 AATAAAA-AT
293846 AATA
1 AATA
293850 CATGAAAATG
Statistics
Matches: 50, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
7 5 0.10
8 15 0.30
9 14 0.28
10 15 0.30
11 1 0.02
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.20
Consensus pattern (9 bp):
AATAAAAAT
Found at i:293849 original size:22 final size:20
Alignment explanation
Indices: 293792--293842 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 20
293782 AAAATAAAAA
293792 AAAAAAATAAAAA--AA-AT
1 AAAAAAATAAAAATTAATAT
293809 AAAAAAATAAAAATTAATAT
1 AAAAAAATAAAAATTAATAT
293829 AATAAATAATAAAA
1 AA-AAA-AATAAAA
293843 CATAATACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 13 0.45
19 2 0.07
20 4 0.14
21 3 0.10
22 7 0.24
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAAAAATAAAAATTAATAT
Found at i:293874 original size:11 final size:11
Alignment explanation
Indices: 293854--293946 Score: 51
Period size: 11 Copynumber: 7.9 Consensus size: 11
293844 ATAATACATG
*
293854 AAAATGTTTTA
1 AAAATATTTTA
293865 AAAATATTTTCA
1 AAAATATTTT-A
293877 AAAATTATATATTA
1 AAAA-TAT-T-TTA
* * *
293891 TATATATTTTC
1 AAAATATTTTA
*
293902 TAAATATTTTCA
1 AAAATATTTT-A
*
293914 AAAACTATATTA
1 AAAA-TATTTTA
* * *
293926 TATATATTTTC
1 AAAATATTTTA
293937 AAAATATTTT
1 AAAATATTTT
293947 TTAAAAACTA
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
11 33 0.53
12 12 0.19
13 11 0.18
14 4 0.06
15 2 0.03
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.48
Consensus pattern (11 bp):
AAAATATTTTA
Found at i:293930 original size:35 final size:35
Alignment explanation
Indices: 293860--293963 Score: 138
Period size: 35 Copynumber: 2.9 Consensus size: 35
293850 CATGAAAATG
* *
293860 TTTTAAAAATATTTTCAAAAATTATATATTATATATA
1 TTTTCAAAATATTTTCAAAAA--CTATATTATATATA
*
293897 TTTTCTAAATATTTTCAAAAACTATATTATATATA
1 TTTTCAAAATATTTTCAAAAACTATATTATATATA
*
293932 TTTTCAAAATATTTTTTAAAAACTATA-TATAT
1 TTTTCAAAATA-TTTTCAAAAACTATATTATAT
293964 GTTTTCGAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
35 28 0.46
36 14 0.23
37 19 0.31
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (35 bp):
TTTTCAAAATATTTTCAAAAACTATATTATATATA
Found at i:303308 original size:31 final size:31
Alignment explanation
Indices: 303258--303359 Score: 127
Period size: 31 Copynumber: 3.3 Consensus size: 31
303248 GTTCTTCGGA
*
303258 ACATAGGT-AACTGTTCATATATCCCGAAGG
1 ACATAGGTAAACTGTACATATATCCCGAAGG
*
303288 ACATAGGTAAACTGTACATATGTCCCGAAGG
1 ACATAGGTAAACTGTACATATATCCCGAAGG
* * * *
303319 ACATAGGTAAACTATCCA-ATATCTCGAAAAG
1 ACATAGGTAAACTGTACATATATCCCG-AAGG
303350 ACATAGGTAA
1 ACATAGGTAA
303360 CCCTCTACTC
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
30 14 0.22
31 49 0.78
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (31 bp):
ACATAGGTAAACTGTACATATATCCCGAAGG
Found at i:308590 original size:194 final size:194
Alignment explanation
Indices: 308261--308644 Score: 669
Period size: 194 Copynumber: 2.0 Consensus size: 194
308251 ATCAAGCAAG
* * *
308261 TTAGGATGATATAAGATTGGCCTTTGTATGACGCTCGGGAAACGGTTAGGACACCCGAGTTACTA
1 TTAGGATGATATAAGATTGGCCTTTGTATGACGCTCAGGAAACGATTAAGACACCCGAGTTACTA
* **
308326 TAACATTATGATAATTGTCCTTTATATGAAATATCCAGATATTGTTTGACCATGTACGCATCTGA
66 TAACATTATGATAATTGTCCTTTATATGAAATATCCAAATATTGTTTGACCAAATACGCATCTGA
*
308391 TGCACGTAAAATTCTGGATCGTACCCAACACTCGAGAGCCTATATGTTGGTTCGAGATGTAAGC
131 TGCACGTAAAATTCTGGATCGTACCCAACACTCGAGAGCCTATATGTGGGTTCGAGATGTAAGC
308455 TTAGGATGATATAAGATTGGCCTTTGTATGACGCTCAGGAAACGATTAAGACACCCGAGTTACTA
1 TTAGGATGATATAAGATTGGCCTTTGTATGACGCTCAGGAAACGATTAAGACACCCGAGTTACTA
*
308520 TAACATTATGATAATTGTCCTTTATATGAAATATCCAAATATTGTTTGACCAAATACGCATCTTA
66 TAACATTATGATAATTGTCCTTTATATGAAATATCCAAATATTGTTTGACCAAATACGCATCTGA
* * *
308585 TGCACGTAAAATTTTGGATCGTACCCAACACTCGAGAGCCTATTTGTGGGTTCGGGATGT
131 TGCACGTAAAATTCTGGATCGTACCCAACACTCGAGAGCCTATATGTGGGTTCGAGATGT
308645 GAACTTCCGA
Statistics
Matches: 179, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
194 179 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (194 bp):
TTAGGATGATATAAGATTGGCCTTTGTATGACGCTCAGGAAACGATTAAGACACCCGAGTTACTA
TAACATTATGATAATTGTCCTTTATATGAAATATCCAAATATTGTTTGACCAAATACGCATCTGA
TGCACGTAAAATTCTGGATCGTACCCAACACTCGAGAGCCTATATGTGGGTTCGAGATGTAAGC
Found at i:311185 original size:18 final size:19
Alignment explanation
Indices: 311164--311205 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
311154 AAATAGTGAG
311164 TTATTAT-ATAATATATTT
1 TTATTATAATAATATATTT
*
311182 TTATTATAATTATATATTT
1 TTATTATAATAATATATTT
311201 TTATT
1 TTATT
311206 TTTTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTATAATAATATATTT
Found at i:313498 original size:36 final size:36
Alignment explanation
Indices: 313456--313549 Score: 161
Period size: 36 Copynumber: 2.6 Consensus size: 36
313446 CAGAGGGCTC
* *
313456 GTTCGTTCATTTACGTTTGTGAACGTTCGGTAATAT
1 GTTCGTTCATTTACGTTCGTGAACGTTCGATAATAT
*
313492 GTTCGTTCATTTACGTTCGTGAATGTTCGATAATAT
1 GTTCGTTCATTTACGTTCGTGAACGTTCGATAATAT
313528 GTTCGTTCATTTACGTTCGTGA
1 GTTCGTTCATTTACGTTCGTGA
313550 GTTTATATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.45
Consensus pattern (36 bp):
GTTCGTTCATTTACGTTCGTGAACGTTCGATAATAT
Found at i:313564 original size:24 final size:24
Alignment explanation
Indices: 313536--313588 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
313526 ATGTTCGTTC
*
313536 ATTTACGTTCGTGAGTTTATATTT
1 ATTTACGTTCGTGAGTTTATAATT
** **
313560 ATTTATTTTCGTTCGTTTATAATT
1 ATTTACGTTCGTGAGTTTATAATT
313584 ATTTA
1 ATTTA
313589 TTTTCGTTCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.23, C:0.08, G:0.11, T:0.58
Consensus pattern (24 bp):
ATTTACGTTCGTGAGTTTATAATT
Found at i:313612 original size:24 final size:24
Alignment explanation
Indices: 313550--313613 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
313540 ACGTTCGTGA
313550 GTTTATATTTATTTATTTTCGTTC
1 GTTTATATTTATTTATTTTCGTTC
*
313574 GTTTATAATTATTTATTTTCGTTC
1 GTTTATATTTATTTATTTTCGTTC
* *
313598 GTTTATGTTTGTTTAT
1 GTTTATATTTATTTAT
313614 GTTCATTCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.66
Consensus pattern (24 bp):
GTTTATATTTATTTATTTTCGTTC
Found at i:313994 original size:23 final size:23
Alignment explanation
Indices: 313947--314008 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
313937 TTTATGTTCA
* *
313947 TTTATCGTGTTCGTTTACATTCG
1 TTTATTGTGTTCGTTTACATCCG
313970 TTTATTGTGTTCGTTTACATCCG
1 TTTATTGTGTTCGTTTACATCCG
* *
313993 TTCATTTATGTTCGTT
1 TTTA-TTGTGTTCGTT
314009 CATTTGTGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 24 0.71
24 10 0.29
ACGTcount: A:0.13, C:0.16, G:0.16, T:0.55
Consensus pattern (23 bp):
TTTATTGTGTTCGTTTACATCCG
Found at i:318321 original size:31 final size:31
Alignment explanation
Indices: 318233--318323 Score: 128
Period size: 31 Copynumber: 2.9 Consensus size: 31
318223 AAGAGTCAAT
* * * *
318233 GGTTACCTATATCCTTCAGGACATATAGACA
1 GGTTACCTATGTTCTTCAGAACATATGGACA
* *
318264 GTTTACCTATGTTCTTCGGAACATATGGACA
1 GGTTACCTATGTTCTTCAGAACATATGGACA
318295 GGTTACCTATGTTCTTCAGAACATATGGA
1 GGTTACCTATGTTCTTCAGAACATATGGA
318324 TAGGCCATTC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (31 bp):
GGTTACCTATGTTCTTCAGAACATATGGACA
Found at i:336971 original size:118 final size:117
Alignment explanation
Indices: 336763--336996 Score: 425
Period size: 118 Copynumber: 2.0 Consensus size: 117
336753 TTTATTTTAT
336763 TTTATTCACTTACATCGGTGAAGTATGTGTAAAGTGCTACACTTTTTTATAGTATGAATTATGAT
1 TTTATTCACTTACATCGGTGAAGTATGTGTAAAGTGCTACACTTTTTTATAGTATGAATTATGAT
*
336828 TTTTTTGATAAATAATTCTAATAGGTTATCCGTAGGTTAACATGTAACCGAGC
66 TTTTTTGACAAATAATTCTAATAGGTTAT-CGTAGGTTAACATGTAACCGAGC
336881 TTTATTCACTTACATCGGTGTAAGTATGTGTAAAGTGCTACACTTTTTTATAGTATGAATTATG-
1 TTTATTCACTTACATCGGTG-AAGTATGTGTAAAGTGCTACACTTTTTTATAGTATGAATTATGA
*
336945 TTTTTTTGACAAATAATTCTAATAGGTTATCGTAGGTTAACATGTAATCGAG
65 TTTTTTTGACAAATAATTCTAATAGGTTATCGTAGGTTAACATGTAACCGAG
336997 ATGTCAATAA
Statistics
Matches: 113, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
117 21 0.19
118 49 0.43
119 43 0.38
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (117 bp):
TTTATTCACTTACATCGGTGAAGTATGTGTAAAGTGCTACACTTTTTTATAGTATGAATTATGAT
TTTTTTGACAAATAATTCTAATAGGTTATCGTAGGTTAACATGTAACCGAGC
Found at i:337507 original size:31 final size:31
Alignment explanation
Indices: 337472--337581 Score: 148
Period size: 31 Copynumber: 3.5 Consensus size: 31
337462 TCGATAAATA
* * *
337472 TAAGTTTTGGTCACTTACATTATTATTTCAT
1 TAAGTTTTGGTCACTTACGTTATTGTTTTAT
*
337503 TAAGTTTTGGTCACTTACGTTATCGTTTTAT
1 TAAGTTTTGGTCACTTACGTTATTGTTTTAT
* * * *
337534 TAACTGTTGATCACTTATGTTATTGTTTTAT
1 TAAGTTTTGGTCACTTACGTTATTGTTTTAT
337565 TAAGTTTTGGTCACTTA
1 TAAGTTTTGGTCACTTA
337582 AACATTGAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.52
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACGTTATTGTTTTAT
Found at i:345476 original size:57 final size:59
Alignment explanation
Indices: 345412--345534 Score: 169
Period size: 60 Copynumber: 2.1 Consensus size: 59
345402 AAATTACACT
* * * *
345412 CGCAACATAAAAATATA-T-TTTTTAGGAAATAAATCACTTCTTAACGTTTGTAGCGTC
1 CGCAACATAAAAATATAGTATTTTTAGGAAATAAATCACTTCGTAACGTCTGTAACATC
* *
345469 CGCAACATAAAAATATAGTTATTTTTAGGAGATAAATCATTTCGTAACGTCTGTAACATC
1 CGCAACATAAAAATATAG-TATTTTTAGGAAATAAATCACTTCGTAACGTCTGTAACATC
345529 CGCAAC
1 CGCAAC
345535 TGTGACACTG
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 17 0.30
59 1 0.02
60 39 0.68
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (59 bp):
CGCAACATAAAAATATAGTATTTTTAGGAAATAAATCACTTCGTAACGTCTGTAACATC
Found at i:348064 original size:65 final size:66
Alignment explanation
Indices: 347995--348159 Score: 162
Period size: 65 Copynumber: 2.5 Consensus size: 66
347985 CATCGATAAC
*
347995 ATATATAGTAAAT-ACATTTTAATATAACATAAATTTTTATATATAACATGA-TATAAT-TTTTA
1 ATATA-AGTAAATAACATTTTAATATAACATAAATTTATATATATAACA-GATTATAATCTTTTA
348057 ATA
64 ATA
* * * * * *
348060 ATATAA-TAAATAAAATTTTAATATAATATTAACTATATATATATAAGAGATTATAATCTTTTCA
1 ATATAAGTAAATAACATTTTAATATAACA-TAAATTTATATATATAACAGATTATAATCTTTTAA
348124 TA
65 TA
* * *
348126 ATAAAAGT-AATGAC-TTTTAACATAACATGAAATT
1 ATATAAGTAAATAACATTTTAATATAACAT-AAATT
348160 GTTTCTTTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
63 5 0.06
64 18 0.22
65 40 0.50
66 16 0.20
67 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.41
Consensus pattern (66 bp):
ATATAAGTAAATAACATTTTAATATAACATAAATTTATATATATAACAGATTATAATCTTTTAAT
A
Found at i:348711 original size:24 final size:24
Alignment explanation
Indices: 348684--348730 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
348674 AAGAACGTAA
*
348684 CACAAGAGCAGAGAAAAAGCGTGC
1 CACAAGAGCACAGAAAAAGCGTGC
*
348708 CACAAGAGTACAGAAAAAGCGTG
1 CACAAGAGCACAGAAAAAGCGTG
348731 TCCCAATGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.19, G:0.28, T:0.06
Consensus pattern (24 bp):
CACAAGAGCACAGAAAAAGCGTGC
Found at i:348849 original size:3 final size:3
Alignment explanation
Indices: 348835--348883 Score: 82
Period size: 3 Copynumber: 16.3 Consensus size: 3
348825 AATATTATAA
348835 ATT ATAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
348880 ATT A
1 ATT A
348884 ACATACAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:350419 original size:30 final size:30
Alignment explanation
Indices: 350385--350475 Score: 105
Period size: 30 Copynumber: 3.0 Consensus size: 30
350375 ACTGTTCAAC
*
350385 CCTTTAACTATCTATTTTT-TCTATTTTAGT
1 CCTTTAACTATCTATTTTTAT-TATTTTAAT
*
350415 CCTTTAACTTTCTATTTTTATTATTTTAAT
1 CCTTTAACTATCTATTTTTATTATTTTAAT
* * *
350445 CCTTTAAGT-TCATGTTTTTGTTATTTTAAT
1 CCTTTAACTATC-TATTTTTATTATTTTAAT
350475 C
1 C
350476 TTGTAAATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
29 2 0.04
30 51 0.94
31 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.04, T:0.60
Consensus pattern (30 bp):
CCTTTAACTATCTATTTTTATTATTTTAAT
Found at i:350490 original size:30 final size:30
Alignment explanation
Indices: 350406--350500 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
350396 CTATTTTTTC
* * * *
350406 TATTTTAGTCCTTTAACTTTC-TATTTTTAT
1 TATTTTAATCCTTTAA-ATTCATGTTTTTGT
*
350436 TATTTTAATCCTTTAAGTTCATGTTTTTGT
1 TATTTTAATCCTTTAAATTCATGTTTTTGT
*
350466 TATTTTAAT-CTTGTAAATTTATGTTTTTGT
1 TATTTTAATCCTT-TAAATTCATGTTTTTGT
350496 TATTT
1 TATTT
350501 AGTCTTTTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
29 6 0.11
30 51 0.89
ACGTcount: A:0.21, C:0.08, G:0.07, T:0.63
Consensus pattern (30 bp):
TATTTTAATCCTTTAAATTCATGTTTTTGT
Found at i:350808 original size:15 final size:16
Alignment explanation
Indices: 350782--350815 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
350772 TTTTATCGTT
350782 TTTCACTTTTATTTCA
1 TTTCACTTTTATTTCA
*
350798 TTTCA-TTTTATTTTA
1 TTTCACTTTTATTTCA
350813 TTT
1 TTT
350816 TATCTTTGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCACTTTTATTTCA
Found at i:354139 original size:14 final size:13
Alignment explanation
Indices: 354103--354216 Score: 91
Period size: 12 Copynumber: 9.2 Consensus size: 13
354093 AGATCAAATC
354103 AAAACAAAGAG-A
1 AAAACAAAGAGAA
*
354115 AAAGCAAAGA-AA
1 AAAACAAAGAGAA
*
354127 GAAACAAAGAGAA
1 AAAACAAAGAGAA
* *
354140 AATAAGAAAAAGAA
1 AA-AACAAAGAGAA
354154 AAAACAAAGAG--
1 AAAACAAAGAGAA
* *
354165 CAAA-GAAGA-AA
1 AAAACAAAGAGAA
354176 AAAATCAAAGA-AA
1 AAAA-CAAAGAGAA
354189 AAAACAAAGA-AA
1 AAAACAAAGAGAA
*
354201 AAAACAAAAAGAA
1 AAAACAAAGAGAA
354214 AAA
1 AAA
354217 GAGAAGAAAC
Statistics
Matches: 81, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
10 4 0.05
11 6 0.07
12 35 0.43
13 25 0.31
14 11 0.14
ACGTcount: A:0.77, C:0.07, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAACAAAGAGAA
Found at i:354170 original size:34 final size:35
Alignment explanation
Indices: 354131--354198 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
354121 AAGAAAGAAA
354131 CAAAG-AGAAAATAAGA-AAAAG-AAAAAACAAAGAG
1 CAAAGAAGAAAA-AA-ATAAAAGAAAAAAACAAAGAG
*
354165 CAAAGAAGAAAAAAATCAAAGAAAAAAACAAAGA
1 CAAAGAAGAAAAAAATAAAAGAAAAAAACAAAGA
354199 AAAAAACAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 1 0.03
34 11 0.37
35 18 0.60
ACGTcount: A:0.75, C:0.07, G:0.15, T:0.03
Consensus pattern (35 bp):
CAAAGAAGAAAAAAATAAAAGAAAAAAACAAAGAG
Found at i:354173 original size:27 final size:28
Alignment explanation
Indices: 354120--354177 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
354110 AGAGAAAAGC
*
354120 AAAGAAAGAAACAAAGAGAAAATAAGAA
1 AAAGAAAGAAACAAAGAGAAAAGAAGAA
*
354148 AAAGAAA-AAACAAAGAGCAAAGAAGAA
1 AAAGAAAGAAACAAAGAGAAAAGAAGAA
354175 AAA
1 AAA
354178 AATCAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (28 bp):
AAAGAAAGAAACAAAGAGAAAAGAAGAA
Found at i:354216 original size:24 final size:24
Alignment explanation
Indices: 354103--354225 Score: 106
Period size: 24 Copynumber: 5.0 Consensus size: 24
354093 AGATCAAATC
*
354103 AAAACAAAGAGAAAAGCAAAGAAA
1 AAAACAAAGAGAAAAACAAAGAAA
* * *
354127 GAAACAAAGAGAAAATAAGAAAAAGAA
1 AAAACAAAGAG-AAA-AACAAAGA-AA
* *
354154 AAAACAAAGAG-CAAA-GAAGAAA
1 AAAACAAAGAGAAAAACAAAGAAA
*
354176 AAAATCAAAGAAAAAAACAAAGAAA
1 AAAA-CAAAGAGAAAAACAAAGAAA
* *
354201 AAAACAAAAAGAAAAAGAGAAGAAA
1 AAAACAAAGAGAAAAACA-AAGAAA
354226 CACATACAAA
Statistics
Matches: 78, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
22 6 0.08
23 9 0.12
24 26 0.33
25 20 0.26
26 5 0.06
27 12 0.15
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.02
Consensus pattern (24 bp):
AAAACAAAGAGAAAAACAAAGAAA
Found at i:355326 original size:32 final size:32
Alignment explanation
Indices: 355267--355329 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
355257 AGAAACGATG
*
355267 AATGATGGGGCATCTTTAGAGAGTCAACATCA
1 AATGATGGGACATCTTTAGAGAGTCAACATCA
* * * *
355299 AATGTTGGGACATCTTTGGGGATTCAACATC
1 AATGATGGGACATCTTTAGAGAGTCAACATC
355330 TTGATGTGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (32 bp):
AATGATGGGACATCTTTAGAGAGTCAACATCA
Found at i:355652 original size:66 final size:62
Alignment explanation
Indices: 355474--355661 Score: 193
Period size: 66 Copynumber: 2.9 Consensus size: 62
355464 TCTTTGAGTC
* * * *
355474 TGTCTCTCTTGAGACAGTTTTTTTGAAAAA-ATCTTTGAGATTGTTT-CATTTGAAACATATCT
1 TGTCTCCCTTGAGACAGTTTCTTTGAAAAATATCTTTGAG-TTGTTTCCA-TTGAAACAAAGCT
* * *
355536 TATCTCACCTTGAGACAGTTTCTCATGAAACACATATCTTTGAGTCGTTTCCATTGAAACAAAGC
1 TGTCTC-CCTTGAGACAGTTTCT-TTGAAA-A-ATATCTTTGAGTTGTTTCCATTGAAACAAAGC
355601 TT
62 -T
355603 TGTCTCCCTTGAGACAGTTTCTTTGGAAAAATCATCTTTGAGTTGGTTTCTC-TTGAAAC
1 TGTCTCCCTTGAGACAGTTTCTTT-GAAAAAT-ATCTTTGAGTT-GTTTC-CATTGAAAC
355662 CAAAATCCCT
Statistics
Matches: 105, Mismatches: 10, Indels: 18
0.79 0.08 0.14
Matches are distributed among these distances:
62 5 0.05
63 14 0.13
64 7 0.07
65 13 0.12
66 48 0.46
67 18 0.17
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (62 bp):
TGTCTCCCTTGAGACAGTTTCTTTGAAAAATATCTTTGAGTTGTTTCCATTGAAACAAAGCT
Found at i:355978 original size:131 final size:131
Alignment explanation
Indices: 355817--356165 Score: 420
Period size: 131 Copynumber: 2.6 Consensus size: 131
355807 TGGTATGTCA
* * *
355817 TCCTCATCACGTAGGAAC-CGTGTCATCCCTAGATAACCAACCGTCCTCATCACGTAGGAACCGA
1 TCCTCATCACGTAGG-ACTCGTATCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGA
* * *
355881 GTTATCATTTCTAAAGATGGCCTACCGTCCTCATCACGTAGG-A-GTTGTATCATCCCCCGACCA
65 GTTATCATTCCTAAAGATGGCCTACCATCCTCATCACGTAGGAACCTTG--TCATCCCCCGACCA
355944 GACC
128 GACC
* * *
355948 TCCTCATCATGTAGGACTCATATCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTG
1 TCCTCATCACGTAGGACTCGTATCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAG
* * *
356013 TTACCA-TCGCTAAAGATGGCCTACCATCCTCATCACGTAGGAACCTTGTCATCCCTCGACTAGA
66 TTATCATTC-CTAAAGATGGCCTACCATCCTCATCACGTAGGAACCTTGTCATCCCCCGACCAGA
356077 CC
130 CC
* * ** * *
356079 TCCTCATCACGTAGGAGCAGT-GTCTCACCCCTAGATAATCAGCCGTCCTCATTGCGTAGAAACT
1 TCCTCATCACGTAGGA-C--TCGTATCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACC
356143 GAGTTATCACATTCCTAAAGATG
63 GAGTTAT--CATTCCTAAAGATG
356166 ACCAGAACTC
Statistics
Matches: 186, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
130 3 0.02
131 123 0.66
132 2 0.01
133 44 0.24
134 1 0.01
135 11 0.06
136 2 0.01
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.24
Consensus pattern (131 bp):
TCCTCATCACGTAGGACTCGTATCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAG
TTATCATTCCTAAAGATGGCCTACCATCCTCATCACGTAGGAACCTTGTCATCCCCCGACCAGAC
C
Found at i:357940 original size:30 final size:30
Alignment explanation
Indices: 357904--358018 Score: 144
Period size: 30 Copynumber: 3.9 Consensus size: 30
357894 ACTGTTCAAC
*
357904 CCTTTAACTATT-TGTTTTTGTTATTTTAGT
1 CCTTTAACT-TTATGTTTTTGTTATTTTAAT
* *
357934 CCTTTAACTTTCT-TTTTTATTATTTTAAT
1 CCTTTAACTTTATGTTTTTGTTATTTTAAT
* * *
357963 CCTTTAAGTTTTTGTTTTTGTTGTTTTAAT
1 CCTTTAACTTTATGTTTTTGTTATTTTAAT
*
357993 CCTTTAAATTTATGTTTTTGTTATTT
1 CCTTTAACTTTATGTTTTTGTTATTT
358019 AGTCTTTTAT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
29 27 0.36
30 47 0.64
ACGTcount: A:0.17, C:0.10, G:0.08, T:0.65
Consensus pattern (30 bp):
CCTTTAACTTTATGTTTTTGTTATTTTAAT
Found at i:357979 original size:59 final size:60
Alignment explanation
Indices: 357904--358018 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 60
357894 ACTGTTCAAC
* * *
357904 CCTTTAACTATTTGTTTTTGTTATTTTAGTCCTTTAACTTTCT-TTTTTATTATTTTAAT
1 CCTTTAACTATTTGTTTTTGTTATTTTAATCCTTTAAATTTATGTTTTTATTATTTTAAT
* * * *
357963 CCTTTAAGTTTTTGTTTTTGTTGTTTTAATCCTTTAAATTTATGTTTTTGTTATTT
1 CCTTTAACTATTTGTTTTTGTTATTTTAATCCTTTAAATTTATGTTTTTATTATTT
358019 AGTCTTTTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 37 0.77
60 11 0.23
ACGTcount: A:0.17, C:0.10, G:0.08, T:0.65
Consensus pattern (60 bp):
CCTTTAACTATTTGTTTTTGTTATTTTAATCCTTTAAATTTATGTTTTTATTATTTTAAT
Found at i:358764 original size:21 final size:21
Alignment explanation
Indices: 358740--358779 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
358730 GTCATAACTG
* *
358740 TTTTTA-AAATAATATTTATT
1 TTTTTATAAAAAATAGTTATT
358760 TTTTTATAAAAAATAGTTAT
1 TTTTTATAAAAAATAGTTAT
358780 GACAATATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
TTTTTATAAAAAATAGTTATT
Found at i:365735 original size:32 final size:33
Alignment explanation
Indices: 365681--365745 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
365671 TTGTAACAAA
* *
365681 CTCTAACGACCCAAACTAACCGACTCAACGCAT
1 CTCTAACAACCCAAACTAACCGACCCAACGCAT
*
365714 CTCTAACAACCC-AACTAACCGACCCAATGCAT
1 CTCTAACAACCCAAACTAACCGACCCAACGCAT
365746 ATTAGAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.37, C:0.40, G:0.08, T:0.15
Consensus pattern (33 bp):
CTCTAACAACCCAAACTAACCGACCCAACGCAT
Found at i:369305 original size:3 final size:3
Alignment explanation
Indices: 369292--369348 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
369282 TCTATAAAAA
369292 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
369338 TAT TAT TAT TA
1 TAT TAT TAT TA
369349 CATATATTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.08
3 48 0.92
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:369325 original size:26 final size:26
Alignment explanation
Indices: 369292--369348 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
369282 TCTATAAAAA
369292 TATTATATTATTATTATTATTATTAT
1 TATTATATTATTATTATTATTATTAT
369318 TATTATATTATTATTATTATTATTAT
1 TATTATATTATTATTATTATTATTAT
369344 TATTA
1 TATTA
369349 CATATATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TATTATATTATTATTATTATTATTAT
Found at i:370008 original size:5 final size:5
Alignment explanation
Indices: 370000--370025 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
369990 TTTTTTTATT
370000 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
370026 TTCTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:371386 original size:30 final size:30
Alignment explanation
Indices: 371311--371470 Score: 134
Period size: 30 Copynumber: 5.4 Consensus size: 30
371301 TTTTATTTGG
*
371311 TATTTTAGTCCTTTAAATGTTTGTATTTG--C
1 TATTTTAGTCCTTT-AA-GTTTCTATTTGTAC
* *
371341 TA-TTTAGTCCCTTAAGTTTCTATTTTTAC
1 TATTTTAGTCCTTTAAGTTTCTATTTGTAC
371370 TATTTTAG-CCATTTAAGTTTCTATTTGT-C
1 TATTTTAGTCC-TTTAAGTTTCTATTTGTAC
* * *
371399 -ATTTTAGTCCTATAAATTCCTATTTGTAC
1 TATTTTAGTCCTTTAAGTTTCTATTTGTAC
* * * * * *
371428 TATTTTGGTCCTTTGAGTTTATGTTTTTGC
1 TATTTTAGTCCTTTAAGTTTCTATTTGTAC
*
371458 TATTTTGGTCCTT
1 TATTTTAGTCCTT
371471 GTAATTTTTA
Statistics
Matches: 106, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
27 9 0.08
28 23 0.22
29 19 0.18
30 55 0.52
ACGTcount: A:0.19, C:0.14, G:0.12, T:0.56
Consensus pattern (30 bp):
TATTTTAGTCCTTTAAGTTTCTATTTGTAC
Found at i:372416 original size:26 final size:26
Alignment explanation
Indices: 372386--372435 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
372376 TTACGATCAA
*
372386 TTTATTTATTTTTGAGTTTCAACACT
1 TTTATTTATTTTCGAGTTTCAACACT
372412 TTTATTTATTTTCGAGTTTCAACA
1 TTTATTTATTTTCGAGTTTCAACA
372436 TATTATGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (26 bp):
TTTATTTATTTTCGAGTTTCAACACT
Found at i:372441 original size:25 final size:26
Alignment explanation
Indices: 372387--372441 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
372377 TACGATCAAT
* *
372387 TTATTTATTTTTGAGTTTCAACACTT
1 TTATTTATTTTCGAGTTTCAACACTA
372413 TTATTTATTTTCGAGTTTCAACA-TA
1 TTATTTATTTTCGAGTTTCAACACTA
372438 TTAT
1 TTAT
372442 GCATTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.25, C:0.11, G:0.07, T:0.56
Consensus pattern (26 bp):
TTATTTATTTTCGAGTTTCAACACTA
Found at i:372449 original size:26 final size:26
Alignment explanation
Indices: 372393--372449 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
372383 CAATTTATTT
* **
372393 ATTTTTGAGTTTCAACACTTTTATTT
1 ATTTTTGAGTTTCAACACTATTATGC
*
372419 ATTTTCGAGTTTCAACA-TATTATGC
1 ATTTTTGAGTTTCAACACTATTATGC
372444 ATTTTT
1 ATTTTT
372450 TAACTAATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.54
Consensus pattern (26 bp):
ATTTTTGAGTTTCAACACTATTATGC
Found at i:376285 original size:22 final size:22
Alignment explanation
Indices: 376257--376315 Score: 118
Period size: 22 Copynumber: 2.7 Consensus size: 22
376247 CAAGGAGACA
376257 ATATTTTTCAAAATTCCTTTCG
1 ATATTTTTCAAAATTCCTTTCG
376279 ATATTTTTCAAAATTCCTTTCG
1 ATATTTTTCAAAATTCCTTTCG
376301 ATATTTTTCAAAATT
1 ATATTTTTCAAAATT
376316 TTGAAAATCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.51
Consensus pattern (22 bp):
ATATTTTTCAAAATTCCTTTCG
Found at i:376611 original size:14 final size:15
Alignment explanation
Indices: 376592--376626 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
376582 ACATACATCA
376592 ACACATACAGACA-G
1 ACACATACAGACATG
*
376606 ACACATACATACATG
1 ACACATACAGACATG
376621 ACACAT
1 ACACAT
376627 GAAATTTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.49, C:0.29, G:0.09, T:0.14
Consensus pattern (15 bp):
ACACATACAGACATG
Found at i:377140 original size:88 final size:90
Alignment explanation
Indices: 376980--377142 Score: 224
Period size: 88 Copynumber: 1.8 Consensus size: 90
376970 GAGAAAGTTT
* * ****
376980 TTTTAAAAACAAATTTTGTCTCACTTGAGACAACTTTCTCTTTTAAAAAATTATGTCTCGCTTGA
1 TTTTAAAAACAAAATTTGTATCACTTGAGACAACTTTCTCACAAAAAAAATTATGTCTCGCTTGA
*
377045 GATATTTTTCCACAAATTTTGAGAA
66 GACATTTTTCCACAAATTTTGAGAA
*
377070 TTTTAAAAA-AAAATTTGTATCGCTTGAGACAA-TTTCTCACAAAACAAAATT-TGTCTCGCTTG
1 TTTTAAAAACAAAATTTGTATCACTTGAGACAACTTTCTCACAAAA-AAAATTATGTCTCGCTTG
377132 AGACATTTTTC
65 AGACATTTTTC
377143 TCTGAGATAC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
88 29 0.45
89 26 0.41
90 9 0.14
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.39
Consensus pattern (90 bp):
TTTTAAAAACAAAATTTGTATCACTTGAGACAACTTTCTCACAAAAAAAATTATGTCTCGCTTGA
GACATTTTTCCACAAATTTTGAGAA
Found at i:377455 original size:30 final size:28
Alignment explanation
Indices: 377389--377482 Score: 111
Period size: 28 Copynumber: 3.3 Consensus size: 28
377379 CTCTTGAAAC
377389 AAATCTTTGAGTCTG-TTCATTTAAAAAA
1 AAATCTTTGAGTCTGTTTC-TTTAAAAAA
377417 AAATCTTTGAGTCTGTTTCTCTTAACAAAA
1 AAATCTTTGAGTCTGTTTCT-TTAA-AAAA
** * *
377447 TCATCTTTGAGTCTATTTCTTTAAAAAC
1 AAATCTTTGAGTCTGTTTCTTTAAAAAA
377475 AAAT-TTTG
1 AAATCTTTG
377483 TATCTATTGA
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
27 4 0.07
28 21 0.37
29 11 0.19
30 21 0.37
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.43
Consensus pattern (28 bp):
AAATCTTTGAGTCTGTTTCTTTAAAAAA
Found at i:377841 original size:66 final size:64
Alignment explanation
Indices: 377704--377883 Score: 191
Period size: 67 Copynumber: 2.8 Consensus size: 64
377694 ACAAAACAAA
* *
377704 CATCTTTGAGATCATTTCCCTTTAAACGAATTTTATCTCATTCGAGACAGTTTCCCATGAAACAC
1 CATCTTTGAGATCATTTCCCTTAAAACGAATTTTATCTCATT-GAGACAATTTCCCATGAAACAC
* * * * *
377769 CGATCTTTGAGAACATTTCCCTTAAAAACAAATTTTATCTCGCTTGAGACAATTTCCCTTTAAAC
1 C-ATCTTTGAGATCATTTCCCTT-AAAACGAATTTTATCTC-ATTGAGACAATTTCCCATGAAAC
**
377834 GT
63 AC
* * * *
377836 CATCTTTTAG-TCGTTTCCCTTGAAACGAATTTTATCTCTTTTGAGACA
1 CATCTTTGAGATCATTTCCCTTAAAACGAATTTTATCTC-ATTGAGACA
377884 GTTGCATTTG
Statistics
Matches: 96, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
64 23 0.24
65 10 0.10
66 28 0.29
67 33 0.34
68 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (64 bp):
CATCTTTGAGATCATTTCCCTTAAAACGAATTTTATCTCATTGAGACAATTTCCCATGAAACAC
Found at i:377943 original size:28 final size:28
Alignment explanation
Indices: 377910--377983 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
377900 ATCATCTTTG
*
377910 AGTTTGTTTTTCTTGAAAGAAATATTTA
1 AGTTTGTTTTTCTTGAAAAAAATATTTA
*
377938 AGTTTGTTTCTT-TTGAAAAAAATATTTG
1 AGTTTGTTT-TTCTTGAAAAAAATATTTA
** *
377966 AGTCGGTTTCTCTTGAAA
1 AGTTTGTTTTTCTTGAAA
377984 TCATAATCCC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
27 1 0.03
28 36 0.92
29 2 0.05
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (28 bp):
AGTTTGTTTTTCTTGAAAAAAATATTTA
Found at i:378329 original size:131 final size:130
Alignment explanation
Indices: 378010--378431 Score: 468
Period size: 130 Copynumber: 3.2 Consensus size: 130
378000 TGGCATGTCA
* *** * * * *
378010 TCCTCATCACGTAGGAGTCACATCAACCTTAGATAACCAACCGTCCTCATCACGTAGGAACCGTG
1 TCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCATG
* * * **
378075 TTATCATTCCTAAAGATGGCTTGCTGTCCTCATCACATAGGAACCATGTCATCCCCGACCAAACC
66 TTATCATCCCTAAAGATGGCCTACCATCCTCATCACATAGGAACCATGTCATCCCCGACCAAACC
* * ** *
378140 ACCTCATCACGTAGGAGCCGTGTCACCCCTAGATAATCAGCCGTCCTTGTCACGTAGGAATCATG
1 TCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCATG
* * *
378205 TTATCATCCCTAAAGATGGCCTACCATCCTCATCATATAGGAACCGTGTCATCCCTTGACCAAAC
66 TTATCATCCCTAAAGATGGCCTACCATCCTCATCACATAGGAACCATGTCATCCC-CGACCAAAC
378270 C
130 C
* *
378271 TCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCATAGGAACCATG
1 TCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCATG
** * * ** *
378336 TTATCACCCTCCCTAAAGATGGCC-AGAACTCTTCATCACATATGAGTCGTGTCATCCACCGACC
66 TTATCA---TCCCTAAAGATGGCCTACCA-TCCTCATCACATAGGAACCATGTCATCC-CCGACC
* *
378400 AGATC
126 AAACC
* * *
378405 TCGTCATCACGTAGGAGTCATGTCACC
1 TCCTCATCACGTAGGAGCCGTGTCACC
378432 TTAGACGACC
Statistics
Matches: 245, Mismatches: 41, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
130 100 0.41
131 73 0.30
133 2 0.01
134 69 0.28
135 1 0.00
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.24
Consensus pattern (130 bp):
TCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCATG
TTATCATCCCTAAAGATGGCCTACCATCCTCATCACATAGGAACCATGTCATCCCCGACCAAACC
Found at i:380291 original size:30 final size:30
Alignment explanation
Indices: 380207--380364 Score: 112
Period size: 30 Copynumber: 5.3 Consensus size: 30
380197 TTATTTGTTG
* * *
380207 TTTTAGTCCTTTAAATGTCTGTATTTT-CTA
1 TTTTAGTCCTTTAAGTTTATGT-TTTTACTA
* *
380237 -TTTAGT-CTCTTAAGTTTCTATTTTTACTA
1 TTTTAGTCCT-TTAAGTTTATGTTTTTACTA
*
380266 TTTTAG-CCATTTAAGTTTATGTTTTT-GTCA
1 TTTTAGTCC-TTTAAGTTTATGTTTTTACT-A
* **
380296 TTTTAGTCCTTTAAATTCCT-TTTTGTACTA
1 TTTTAGTCCTTTAAGTTTATGTTTT-TACTA
* * *
380326 TTTTGGTCCTTTGAGTTTATGTTTTTGCTA
1 TTTTAGTCCTTTAAGTTTATGTTTTTACTA
*
380356 TTTTGGTCC
1 TTTTAGTCC
380365 ATTTTCTTTG
Statistics
Matches: 102, Mismatches: 16, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
28 6 0.06
29 23 0.23
30 65 0.64
31 8 0.08
ACGTcount: A:0.17, C:0.13, G:0.12, T:0.58
Consensus pattern (30 bp):
TTTTAGTCCTTTAAGTTTATGTTTTTACTA
Found at i:380811 original size:16 final size:16
Alignment explanation
Indices: 380787--380832 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
380777 ATTCGACTTG
380787 TGCTCGTTAAGCTCGT
1 TGCTCGTTAAGCTCGT
* *
380803 TGCTAGTTAAGCCCGT
1 TGCTCGTTAAGCTCGT
380819 TGCTCGTTAAGCTC
1 TGCTCGTTAAGCTC
380833 ACTAAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.15, C:0.26, G:0.24, T:0.35
Consensus pattern (16 bp):
TGCTCGTTAAGCTCGT
Found at i:381197 original size:16 final size:16
Alignment explanation
Indices: 381176--381208 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
381166 AAAAGCATAC
381176 AGATAGTACAATTGAA
1 AGATAGTACAATTGAA
381192 AGATAGTACAATTGAA
1 AGATAGTACAATTGAA
381208 A
1 A
381209 AGCATGCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.24
Consensus pattern (16 bp):
AGATAGTACAATTGAA
Found at i:381463 original size:99 final size:100
Alignment explanation
Indices: 381291--381491 Score: 395
Period size: 99 Copynumber: 2.0 Consensus size: 100
381281 GGACAGTGAG
381291 ATATATGTTTCTTTACTTTTTTTTTCTTTATTATCTTTCATTTATATATTTTACTTTTTAATTAT
1 ATATATGTTTCTTTACTTTTTTTTTCTTTATTATCTTTCATTTATATATTTTACTTTTTAATTAT
381356 CATCTGATGCAGGCTTTATTTCGTTGTAATTGTTC
66 CATCTGATGCAGGCTTTATTTCGTTGTAATTGTTC
381391 ATATATG-TTCTTTACTTTTTTTTTCTTTATTATCTTTCATTTATATATTTTACTTTTTAATTAT
1 ATATATGTTTCTTTACTTTTTTTTTCTTTATTATCTTTCATTTATATATTTTACTTTTTAATTAT
381455 CATCTGATGCAGGCTTTATTTCGTTGTAATTGTTC
66 CATCTGATGCAGGCTTTATTTCGTTGTAATTGTTC
381490 AT
1 AT
381492 GCTCATGTTT
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
99 94 0.93
100 7 0.07
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.60
Consensus pattern (100 bp):
ATATATGTTTCTTTACTTTTTTTTTCTTTATTATCTTTCATTTATATATTTTACTTTTTAATTAT
CATCTGATGCAGGCTTTATTTCGTTGTAATTGTTC
Found at i:381616 original size:20 final size:21
Alignment explanation
Indices: 381588--381626 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
381578 GGTAAAAAAT
*
381588 TATTTAAAA-ATTATTATTTC
1 TATTGAAAATATTATTATTTC
*
381608 TATTGAAAATGTTATTATT
1 TATTGAAAATATTATTATT
381627 AGATATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (21 bp):
TATTGAAAATATTATTATTTC
Found at i:382356 original size:20 final size:19
Alignment explanation
Indices: 382293--382357 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
382283 ACAAATTTTA
382293 TATTTTTCAATTTAGTCCCTT
1 TATTTTTCAATTTA-T-CCTT
* *
382314 AATTTTTCATAATT-TCC-T
1 TATTTTTCA-ATTTATCCTT
382332 TATTTATTCAATTTATCCTT
1 TATTT-TTCAATTTATCCTT
382352 TATTTT
1 TATTTT
382358 AAGTCTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
18 8 0.22
19 10 0.28
20 7 0.19
21 8 0.22
22 3 0.08
ACGTcount: A:0.23, C:0.15, G:0.02, T:0.60
Consensus pattern (19 bp):
TATTTTTCAATTTATCCTT
Found at i:383486 original size:190 final size:189
Alignment explanation
Indices: 383164--383545 Score: 730
Period size: 190 Copynumber: 2.0 Consensus size: 189
383154 AGTTCGTTTG
383164 ACTTTGGTACATTTAAGCTATTGAACCAATAGTTTTTTTTATTTAATTTTGATAATTGGTGCTCT
1 ACTTTGGTACATTTAAGCTATTGAACCAATAGTTTTTTTTATTTAATTTTGATAATTGGTGCTCT
383229 TTTTTATTTTTGTTTTGGTTGTGGACCTTGTTGAACCAACTTTTGATTTTGATATAACATGATTT
66 TTTTTATTTTTGTTTTGGTTGTGGACCTTGTTGAACCAACTTTTGATTTTGATATAACATGATTT
383294 TTTAAATGTTTTAAGTAT-TTAAAATTTGCAGTTTAAGAGTTTATAAATAATTTGTATAA
131 TTTAAATGTTTTAAGT-TGTTAAAATTTGCAGTTTAAGAGTTTATAAATAATTTGTATAA
383353 ACTTTGGTACATTTAAGCTATTGAACCAATAGTTTTTTTTTATTTAATTTTGATAATTGGTGCTC
1 ACTTTGGTACATTTAAGCTATTGAACCAATAG-TTTTTTTTATTTAATTTTGATAATTGGTGCTC
383418 TTTTTTATTTTTGTTTTGGTTGTGGACCTTGTTGAACCAACTTTTGATTTTGATATAACATGATT
65 TTTTTTATTTTTGTTTTGGTTGTGGACCTTGTTGAACCAACTTTTGATTTTGATATAACATGATT
*
383483 TTTTAAATGTTTTAAGTTGTTAAAATTTGCAGTTTAAGATTTTATAAATAATTTGTATAA
130 TTTTAAATGTTTTAAGTTGTTAAAATTTGCAGTTTAAGAGTTTATAAATAATTTGTATAA
383543 ACT
1 ACT
383546 ATTTTAAAGC
Statistics
Matches: 190, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
189 33 0.17
190 157 0.83
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.51
Consensus pattern (189 bp):
ACTTTGGTACATTTAAGCTATTGAACCAATAGTTTTTTTTATTTAATTTTGATAATTGGTGCTCT
TTTTTATTTTTGTTTTGGTTGTGGACCTTGTTGAACCAACTTTTGATTTTGATATAACATGATTT
TTTAAATGTTTTAAGTTGTTAAAATTTGCAGTTTAAGAGTTTATAAATAATTTGTATAA
Found at i:383686 original size:20 final size:20
Alignment explanation
Indices: 383661--383701 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
383651 AACCCTCGTT
* *
383661 AGTCTCGAGACCAACATTCC
1 AGTCTCAAGACCAAAATTCC
383681 AGTCTCAAGACCAAAATTCC
1 AGTCTCAAGACCAAAATTCC
383701 A
1 A
383702 AAAAGCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.32, G:0.12, T:0.20
Consensus pattern (20 bp):
AGTCTCAAGACCAAAATTCC
Found at i:387735 original size:17 final size:16
Alignment explanation
Indices: 387709--387740 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
387699 TAAAATACAA
387709 ATAAAAAATTTAAAAT
1 ATAAAAAATTTAAAAT
387725 ATAAGAAAATTTAAAA
1 ATAA-AAAATTTAAAA
387741 ATTTTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (16 bp):
ATAAAAAATTTAAAAT
Found at i:391618 original size:44 final size:43
Alignment explanation
Indices: 391550--391749 Score: 141
Period size: 45 Copynumber: 4.5 Consensus size: 43
391540 AGTTTTCACG
*
391550 AACATGATCTTTTAGTGCTT-GTGTTGGTTCGCTTAGCTTTCGCA
1 AACATGATCTTTTAGT-ATTCGTGTTGGTTCG-TTAGCTTTCGCA
* * * * **
391594 AATATGCTCTTTTAGTATTCGTGTTTGGTTCGTTAGTTTTTGTG
1 AACATGATCTTTTAGTATTCGTG-TTGGTTCGTTAGCTTTCGCA
* * * * ***
391638 AACATGATGTTTTAGTATTCGTGTTCAGTTCATTTAACTTTCATG
1 AACATGATCTTTTAGTATTCGTGTT-GGTTC-GTTAGCTTTCGCA
* * * ***
391683 AACATGATGTTTTAGTATTCGTGTTTGGTTCATTTAGATTTCATG
1 AACATGATCTTTTAGTATTCGTG-TTGGTTC-GTTAGCTTTCGCA
*
391728 AACATGATCTTTTAGCATTCGT
1 AACATGATCTTTTAGTATTCGT
391750 CAACATGTTC
Statistics
Matches: 130, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
43 4 0.03
44 49 0.38
45 75 0.58
46 2 0.02
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (43 bp):
AACATGATCTTTTAGTATTCGTGTTGGTTCGTTAGCTTTCGCA
Found at i:391696 original size:45 final size:45
Alignment explanation
Indices: 391603--391749 Score: 181
Period size: 45 Copynumber: 3.3 Consensus size: 45
391593 AAATATGCTC
** * * **
391603 TTTTAGTATTCGTGTTTGGTTC-GTTAGTTTTTGTGAACATGATG
1 TTTTAGTATTCGTGTTCAGTTCATTTAGATTTCATGAACATGATG
391647 TTTTAGTATTCGTGTTCAGTTCATTTA-ACTTTCATGAACATGATG
1 TTTTAGTATTCGTGTTCAGTTCATTTAGA-TTTCATGAACATGATG
** *
391692 TTTTAGTATTCGTGTTTGGTTCATTTAGATTTCATGAACATGATC
1 TTTTAGTATTCGTGTTCAGTTCATTTAGATTTCATGAACATGATG
*
391737 TTTTAGCATTCGT
1 TTTTAGTATTCGT
391750 CAACATGTTC
Statistics
Matches: 90, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
44 20 0.22
45 69 0.77
46 1 0.01
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.50
Consensus pattern (45 bp):
TTTTAGTATTCGTGTTCAGTTCATTTAGATTTCATGAACATGATG
Found at i:403124 original size:27 final size:27
Alignment explanation
Indices: 403085--403298 Score: 206
Period size: 27 Copynumber: 8.1 Consensus size: 27
403075 CTCACAAAAC
* *
403085 TTTTTTACTTTTTCCATTTCTCTTTCA
1 TTTTTAACCTTTTCCATTTCTCTTTCA
403112 TTTTTAACCTTTTCCATTTCTCTTTCA
1 TTTTTAACCTTTTCCATTTCTCTTTCA
403139 TTTTTAACCTTTTCCATTTCTCTTTCA
1 TTTTTAACCTTTTCCATTTCTCTTTCA
* * * * ****
403166 -TTTCACCCATTTCC-CTT-TAAAAC-
1 TTTTTAACCTTTTCCATTTCTCTTTCA
* * *
403189 TTTTTTACTTTTTTCATTTCTCTTTCA
1 TTTTTAACCTTTTCCATTTCTCTTTCA
*
403216 TTTTTAACCTTTTTCATTTCTCTTTCA
1 TTTTTAACCTTTTCCATTTCTCTTTCA
*
403243 TTTCTAA-CTTTTCCCATTTCTCTTTCA
1 TTTTTAACCTTTT-CCATTTCTCTTTCA
* * * *
403270 TTTGTAA-CTTTTTCTTTTCTCTCTCA
1 TTTTTAACCTTTTCCATTTCTCTTTCA
403296 TTT
1 TTT
403299 CTTCATCTTC
Statistics
Matches: 153, Mismatches: 29, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
24 10 0.07
25 4 0.03
26 32 0.21
27 107 0.70
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.60
Consensus pattern (27 bp):
TTTTTAACCTTTTCCATTTCTCTTTCA
Found at i:403189 original size:104 final size:104
Alignment explanation
Indices: 403080--403272 Score: 343
Period size: 104 Copynumber: 1.9 Consensus size: 104
403070 TTTCTCTCAC
*
403080 AAAACTTTTTTACTTTTTCCATTTCTCTTTCATTTTTAACCTTTTCCATTTCTCTTTCATTTTTA
1 AAAACTTTTTTACTTTTTCCATTTCTCTTTCATTTTTAACCTTTTCCATTTCTCTTTCATTTCTA
403145 ACCTTTT-CCATTTCTCTTTCATTTCACCCATTTCCCTTT
66 A-CTTTTCCCATTTCTCTTTCATTTCACCCATTTCCCTTT
* *
403184 AAAACTTTTTTACTTTTTTCATTTCTCTTTCATTTTTAACCTTTTTCATTTCTCTTTCATTTCTA
1 AAAACTTTTTTACTTTTTCCATTTCTCTTTCATTTTTAACCTTTTCCATTTCTCTTTCATTTCTA
403249 ACTTTTCCCATTTCTCTTTCATTT
66 ACTTTTCCCATTTCTCTTTCATTT
403273 GTAACTTTTT
Statistics
Matches: 85, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
103 5 0.06
104 80 0.94
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.59
Consensus pattern (104 bp):
AAAACTTTTTTACTTTTTCCATTTCTCTTTCATTTTTAACCTTTTCCATTTCTCTTTCATTTCTA
ACTTTTCCCATTTCTCTTTCATTTCACCCATTTCCCTTT
Found at i:403891 original size:15 final size:16
Alignment explanation
Indices: 403871--403905 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
403861 GATATTTGAT
403871 CAACCGTGA-CATCTA
1 CAACCGTGAGCATCTA
403886 CAACCGTGAGCATCTA
1 CAACCGTGAGCATCTA
403902 CAAC
1 CAAC
403906 TACGTGCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.17
Consensus pattern (16 bp):
CAACCGTGAGCATCTA
Found at i:415884 original size:37 final size:37
Alignment explanation
Indices: 415841--416111 Score: 166
Period size: 37 Copynumber: 7.8 Consensus size: 37
415831 AAATGTCGTC
415841 TCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTT
1 TCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTT
* ** *
415878 TCACTTGAGACATTTTCCTTCGGAACACAAA-----TT
1 TCACTTGAGACATTTTTC-TCTTAAAACAAATTTTGTT
* *** * * *
415911 TCA---AAGTTGTTTTTCT-TAAAAACAAATTCTGTC
1 TCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTT
* *
415944 TCACTTGAGACATTTTTCTCTTAAAACAAATATCGTT
1 TCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTT
* **
415981 TCACTTGAGTCATTTTTCT-TCGGAAACAAA-----TT
1 TCACTTGAGACATTTTTCTCT-TAAAACAAATTTTGTT
* *** *
416013 TCA---AAGTTGTTTTTCT-TAAAAACAAATTTTGTT
1 TCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTT
416046 TCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTT
1 TCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTT
* * * *
416083 TAACGTGAGATATTTTTCTCTCAAAACAA
1 TCACTTGAGACATTTTTCTCTTAAAACAA
416112 GCATCGTCTC
Statistics
Matches: 175, Mismatches: 39, Indels: 40
0.69 0.15 0.16
Matches are distributed among these distances:
28 14 0.08
29 12 0.07
30 7 0.04
32 5 0.03
33 14 0.08
36 19 0.11
37 95 0.54
38 9 0.05
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.42
Consensus pattern (37 bp):
TCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTT
Done.