Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 51
Found at i:4142135 original size:13 final size:14
Alignment explanation
Indices: 4142117--4142146 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4142107 GCCCAATGCA
4142117 CTAAA-CCTAGTCT
1 CTAAACCCTAGTCT
4142130 CTAAACCCTAGTCT
1 CTAAACCCTAGTCT
4142144 CTA
1 CTA
4142147 CCAGCCGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (14 bp):
CTAAACCCTAGTCT
Found at i:4145394 original size:3 final size:3
Alignment explanation
Indices: 4145360--4145411 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
4145350 ATAAAGGCCT
* *
4145360 ATA AAA ATA A-A ATA A-A ATA A-A ATA ATA GTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4145405 ATA ATA A
1 ATA ATA A
4145412 ACCCCAAACA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 6 0.14
3 36 0.86
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:4145708 original size:41 final size:41
Alignment explanation
Indices: 4145663--4145743 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
4145653 CGCATCAACG
* * * *
4145663 CATCTTGCTCGAAGGTCTTATAGATGGCCCGAAGGACTTAT
1 CATCTTGCTCGAAAGACTAACAGATGGCCCGAAGGACTTAT
* *
4145704 CATCTTGCTCGAAAGACTAACAGATGGTCCGAATGACTTA
1 CATCTTGCTCGAAAGACTAACAGATGGCCCGAAGGACTTA
4145744 CTAATTTTGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (41 bp):
CATCTTGCTCGAAAGACTAACAGATGGCCCGAAGGACTTAT
Found at i:4146127 original size:41 final size:40
Alignment explanation
Indices: 4146077--4146191 Score: 122
Period size: 42 Copynumber: 2.8 Consensus size: 40
4146067 ATCATGCCTG
*
4146077 AAGGCCTTATGGATGGCCTGAAGGACTTATCATCTTGCTCGA
1 AAGG-CTTAT-GATGGCCTGAAGGACTTATCATCATGCTCGA
* * * *
4146119 AAGGCTTATAGATGACATGAAGGATTTAATCATCATGCTTGA
1 AAGGCTTAT-GATGGCCTGAAGGACTT-ATCATCATGCTCGA
* *
4146161 AAGACTTACTGATGGCCCGAAGGACTTATCA
1 AAGGCTTA-TGATGGCCTGAAGGACTTATCA
4146192 ATTTGGGAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
41 23 0.38
42 36 0.60
43 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (40 bp):
AAGGCTTATGATGGCCTGAAGGACTTATCATCATGCTCGA
Found at i:4146159 original size:196 final size:197
Alignment explanation
Indices: 4145823--4146251 Score: 612
Period size: 196 Copynumber: 2.2 Consensus size: 197
4145813 TTTTCAGATG
* * * *
4145823 AGAAACTTTGGAAATAGTTTTCTCATTTTTCGAAAAATATGTGAAAATATCCTGCCTAAAGGTCT
1 AGAAACTTTGGAAATAGTTTTCTCATTTTTCGAAAAACATGTGAAAACATCATGCCTAAAGGCCT
* *
4145888 TATGGATTGCCCGAAGGACTTATCATATTGCTTGAAAGGATTATAGACGACATGAAGGATTTAAT
66 TATGGATGGCCCGAAGGACTTATCATATTGCTCGAAAGGATTATAGACGACATGAAGGATTTAAT
** *
4145953 CATCATGCTTGAAAGACTTACTAATGGCTTGAAAAACTTACCAATTTTGGAAATAGTTTACTAGG
131 CATCATGCTTGAAAGACTTACTAATGGCCCGAAAAACTTACCAATTTGGGAAATAGTTTACTAGG
4146018 TA
196 TA
* * *
4146020 GGAAACTTTGGAAATTGTTTTCTCATTTTTCG-AAAACATGTGAAAACATCATGCCTGAAGGCCT
1 AGAAACTTTGGAAATAGTTTTCTCATTTTTCGAAAAACATGTGAAAACATCATGCCTAAAGGCCT
* * * *
4146084 TATGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACATGAAGGATTTAAT
66 TATGGATGGCCCGAAGGACTTATCATATTGCTCGAAAGGATTATAGACGACATGAAGGATTTAAT
* ** * *
4146149 CATCATGCTTGAAAGACTTACTGATGGCCCGAAGGACTTATCAATTTGGGAAATAGTTTACTATG
131 CATCATGCTTGAAAGACTTACTAATGGCCCGAAAAACTTACCAATTTGGGAAATAGTTTACTAGG
4146214 TA
196 TA
* * *
4146216 AGAAACTTTGAAAATCA-TTTTCTTACTTTTC-AAAAA
1 AGAAACTTTGGAAAT-AGTTTTCTCATTTTTCGAAAAA
4146252 TTCCAATTTT
Statistics
Matches: 204, Mismatches: 26, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
196 174 0.85
197 30 0.15
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (197 bp):
AGAAACTTTGGAAATAGTTTTCTCATTTTTCGAAAAACATGTGAAAACATCATGCCTAAAGGCCT
TATGGATGGCCCGAAGGACTTATCATATTGCTCGAAAGGATTATAGACGACATGAAGGATTTAAT
CATCATGCTTGAAAGACTTACTAATGGCCCGAAAAACTTACCAATTTGGGAAATAGTTTACTAGG
TA
Found at i:4146419 original size:42 final size:41
Alignment explanation
Indices: 4146322--4146424 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 41
4146312 ATTGTGAAAA
* * * * *
4146322 CATCATGCTTGAAGGCCTTATGGATGGCCCAAAGGACTTAT
1 CATCATGCTCGAAAGACTTATAGATGACCCAAAGGACTTAT
* * *
4146363 CATCTTACTCGAAAGACTTATAGATGACCCAAAGGATTTAAT
1 CATCATGCTCGAAAGACTTATAGATGACCCAAAGGACTT-AT
4146405 CATCATGCTCGAAAGACTTA
1 CATCATGCTCGAAAGACTTA
4146425 CTAATGGCCC
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 31 0.61
42 20 0.39
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (41 bp):
CATCATGCTCGAAAGACTTATAGATGACCCAAAGGACTTAT
Found at i:4146689 original size:255 final size:255
Alignment explanation
Indices: 4146021--4146955 Score: 1407
Period size: 255 Copynumber: 3.7 Consensus size: 255
4146011 TACTAGGTAG
*
4146021 GAAACTTTGGAAATTGTTTTCTCATTTTTCG-AAAACATGTGAAAACATCATGCCTGAAGGCCTT
1 GAAACTTTGGAAATCGTTTTCTCATTTTTCGAAAAACATGTGAAAACATCATGCCTGAAGGCCTT
**
4146085 ATGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACATGAAGGATTTAATC
66 ATGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCCGAAGGATTTAATC
* * * *
4146150 ATCATGCTTGAAAGACTTACTGATGGCCCGAAGGACTTATCAATTTGGGAAATAGTTTACTATGT
131 ATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTATGT
* *
4146215 AAGAAACTTTGAAAATCATTTTCTTAC-TTTTCAAAAATTCCAATTTTCAGATTTAAATGA
196 AAGAAACTTTG-AAATCATTTTCTTACTTTTTCAAAAATTTCAATTTTCAGATCTAAATGA
* *
4146275 GAAACTTTGGAAATCGTTTTCTCATTTTTTGAAAAACATTGTGAAAACATCATGCTTGAAGGCCT
1 GAAACTTTGGAAATCGTTTTCTCATTTTTCGAAAAACA-TGTGAAAACATCATGCCTGAAGGCCT
** * * *
4146340 TATGGATGGCCCAAAGGACTTATCATCTTACTCGAAAGACTTATAGATGACCCAAAGGATTTAAT
65 TATGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCCGAAGGATTTAAT
* *
4146405 CATCATGCTCGAAAGACTTACTAATGGCCCGAAGGTCTTACCAATTTTGGAAATAGTTTACTAGG
130 CATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTATG
* * *
4146470 TAAGAAACTTTAGAAATCGTTTCCTTACTTTTTCAAAAATTTCAATTTTCAAATCTAAATGA
195 TAAGAAACTTT-GAAATCATTTTCTTACTTTTTCAAAAATTTCAATTTTCAGATCTAAATGA
* * *
4146532 GAAACTTTGGAAA-CTGTTTTCTTATTTTTCGAAAAACATGTGAAAACATCCTGCCTGAA-CCCT
1 GAAACTTTGGAAATC-GTTTTCTCATTTTTCGAAAAACATGTGAAAACATCATGCCTGAAGGCCT
* * * *
4146595 TATGTATGGTCC-GAAGGACTTATCATCTTGCTCAAAAGGCTTATAGATGACTCGAAGGATTTGA
65 TATGGATGG-CCTGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCCGAAGGATTTAA
* *
4146659 TCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA-CAATTTTAGAAATAGTTTACTAT
129 TCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAT
4146723 GTAAGAAACTTTGGAAATCATTTTCTTACTTTTTCAAAAATTTCAATTTTCAGATCTAAATGA
194 GTAAGAAACTTT-GAAATCATTTTCTTACTTTTTCAAAAATTTCAATTTTCAGATCTAAATGA
* * * *
4146786 GAAACTTTGTAAATCATTTTCTCATTTTTC-AAAAAGCATGTGAAAACATCCTGCCCGAAGGCCT
1 GAAACTTTGGAAATCGTTTTCTCATTTTTCGAAAAA-CATGTGAAAACATCATGCCTGAAGGCCT
* *
4146850 TATGGATGGCCTGAAGGACTTATCACCTTGCTCGAAAGGCTTATAGATGACCCGAAAGATTTAAT
65 TATGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCCGAAGGATTTAAT
* * *
4146915 CATCATTCTTGAAAGATTTACTAATGGCCCGAAGGACTTAC
130 CATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTAC
4146956 TAAGTAAGGA
Statistics
Matches: 613, Mismatches: 57, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
253 5 0.01
254 158 0.26
255 197 0.32
256 188 0.31
257 65 0.11
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (255 bp):
GAAACTTTGGAAATCGTTTTCTCATTTTTCGAAAAACATGTGAAAACATCATGCCTGAAGGCCTT
ATGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCCGAAGGATTTAATC
ATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTATGT
AAGAAACTTTGAAATCATTTTCTTACTTTTTCAAAAATTTCAATTTTCAGATCTAAATGA
Found at i:4146693 original size:42 final size:41
Alignment explanation
Indices: 4146600--4146699 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
4146590 ACCCTTATGT
* * *
4146600 ATGGTCCGAAGGACTTATCATCTTGCTCAAAAGGCTTATAG
1 ATGGCCCGAAGGACTTATCATCATGCTCAAAAGACTTATAG
* * * *
4146641 ATGACTCGAAGGATTTGATCATCATGCTCGAAAGACTTACT-G
1 ATGGCCCGAAGGACTT-ATCATCATGCTCAAAAGACTTA-TAG
4146683 ATGGCCCGAAGGACTTA
1 ATGGCCCGAAGGACTTA
4146700 CAATTTTAGA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
41 13 0.28
42 33 0.70
43 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (41 bp):
ATGGCCCGAAGGACTTATCATCATGCTCAAAAGACTTATAG
Found at i:4151485 original size:16 final size:15
Alignment explanation
Indices: 4151464--4151497 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
4151454 TATGTTGTGA
4151464 GTTCTAGAATAGTGTT
1 GTTCTAGAATAGT-TT
4151480 GTTCTAGAATAGTTT
1 GTTCTAGAATAGTTT
4151495 GTT
1 GTT
4151498 AGCTTGTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (15 bp):
GTTCTAGAATAGTTT
Found at i:4151671 original size:11 final size:11
Alignment explanation
Indices: 4151655--4151684 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4151645 AGAGTAATTC
4151655 AGTTTCTTTCT
1 AGTTTCTTTCT
4151666 AGTTTCTTTCT
1 AGTTTCTTTCT
*
4151677 TGTTTCTT
1 AGTTTCTT
4151685 AGATAGCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.17, G:0.10, T:0.67
Consensus pattern (11 bp):
AGTTTCTTTCT
Found at i:4153836 original size:11 final size:11
Alignment explanation
Indices: 4153820--4153850 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4153810 CAGAGTAATT
4153820 TAGTTTCTTTC
1 TAGTTTCTTTC
4153831 TAGTTTCTTTC
1 TAGTTTCTTTC
*
4153842 TTGTTTCTT
1 TAGTTTCTT
4153851 AGATAGCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.06, C:0.16, G:0.10, T:0.68
Consensus pattern (11 bp):
TAGTTTCTTTC
Found at i:4155819 original size:16 final size:15
Alignment explanation
Indices: 4155798--4155831 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
4155788 TATATTGTGA
4155798 GTTCTAGAATAGTGTT
1 GTTCTAGAATAGT-TT
4155814 GTTCTAGAATAGTTT
1 GTTCTAGAATAGTTT
4155829 GTT
1 GTT
4155832 AGCTTGTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (15 bp):
GTTCTAGAATAGTTT
Found at i:4156005 original size:11 final size:11
Alignment explanation
Indices: 4155989--4156018 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4155979 AGAGTAATTC
4155989 AGTTTCTTTCT
1 AGTTTCTTTCT
4156000 AGTTTCTTTCT
1 AGTTTCTTTCT
*
4156011 TGTTTCTT
1 AGTTTCTT
4156019 AGATAGCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.17, G:0.10, T:0.67
Consensus pattern (11 bp):
AGTTTCTTTCT
Found at i:4157986 original size:16 final size:15
Alignment explanation
Indices: 4157965--4157998 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
4157955 TATGTTGTGA
4157965 GTTCTAGAATAGTGTT
1 GTTCTAGAATAGT-TT
4157981 GTTCTAGAATAGTTT
1 GTTCTAGAATAGTTT
4157996 GTT
1 GTT
4157999 AGCTTGTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (15 bp):
GTTCTAGAATAGTTT
Found at i:4158172 original size:11 final size:11
Alignment explanation
Indices: 4158156--4158185 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4158146 AGAGTAATTC
4158156 AGTTTCTTTCT
1 AGTTTCTTTCT
4158167 AGTTTCTTTCT
1 AGTTTCTTTCT
*
4158178 TGTTTCTT
1 AGTTTCTT
4158186 AGATAGCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.17, G:0.10, T:0.67
Consensus pattern (11 bp):
AGTTTCTTTCT
Found at i:4164644 original size:16 final size:15
Alignment explanation
Indices: 4164623--4164656 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
4164613 TATGTTGTGA
4164623 GTTCTAGAATAGTGTT
1 GTTCTAGAATAGT-TT
4164639 GTTCTAGAATAGTTT
1 GTTCTAGAATAGTTT
4164654 GTT
1 GTT
4164657 AGCTTGTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (15 bp):
GTTCTAGAATAGTTT
Found at i:4166373 original size:2 final size:2
Alignment explanation
Indices: 4166366--4166421 Score: 52
Period size: 2 Copynumber: 31.0 Consensus size: 2
4166356 TTGTTTGTAT
* *
4166366 TA TA TA TA -A T- TA -A TA TA -A AA TA TA TA -A AA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4166402 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
4166422 ATCGGGGCGG
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
1 6 0.13
2 40 0.87
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:4166418 original size:16 final size:15
Alignment explanation
Indices: 4166366--4166423 Score: 61
Period size: 14 Copynumber: 4.1 Consensus size: 15
4166356 TTGTTTGTAT
4166366 TATATATA-AT-TAA
1 TATATATATATATAA
*
4166379 TATA-AAATATATAA
1 TATATATATATATAA
*
4166393 AATAT-TATATATATA
1 TATATATATATATA-A
4166408 TATATATATATATAA
1 TATATATATATATAA
4166423 T
1 T
4166424 CGGGGCGGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 13 0.36
15 7 0.19
16 8 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:4166724 original size:82 final size:82
Alignment explanation
Indices: 4166606--4167802 Score: 978
Period size: 82 Copynumber: 14.5 Consensus size: 82
4166596 AATATGTACA
* * *
4166606 TCTCTTTCGGGTAGACAAATCAATGTTGGAAGACGTGTCTGCTCCACTATACATTCAGGGGAAAT
1 TCTCTTTTGGGTAGACAAATCAATGTTGGAAGACGTGTCTGCTCCACCATTCATTCAGGGGAAAT
* *
4166671 CA-AGCTGGATCTGTACC
66 CAGA-CTGGATTTGTGCC
* * * * * *
4166688 TCTCTTTTGGGTAGACAAATCAATGTTGGAATACGTGTTTGCTTCACCATGCATTAAGAGGAAAT
1 TCTCTTTTGGGTAGACAAATCAATGTTGGAAGACGTGTCTGCTCCACCATTCATTCAGGGGAAAT
*
4166753 CAGACAGGATTTGTGCC
66 CAGACTGGATTTGTGCC
* * * ** * * * ** *
4166770 TCT-TTTCGGGTAGAAAAATCCATGTCAGAATACGTGTCTACTCCACTATGAATTTAGGGGAAAT
1 TCTCTTTTGGGTAGACAAATCAATGTTGGAAGACGTGTCTGCTCCACCATTCATTCAGGGGAAAT
* * * *
4166834 TAGACTAGATCTATGCC
66 CAGACTGGATTTGTGCC
* * * * * * * *
4166851 TCTTTTTTTGGGTAGACTAATCCATGTCGGAATATGTGTTTGCTCCACCATGT-ATTCATGGGAA
1 TC-TCTTTTGGGTAGACAAATCAATGTTGGAAGACGTGTCTGCTCCACCAT-TCATTCAGGGGAA
* * *
4166915 ATCAGACTTGATATATGCC
64 ATCAGACTGGATTTGTGCC
* * *
4166934 TCTCTTTTGGGTAGACAAATCAATATTGGAAGACGTGTCTGCTCTACCATGCATTCAGGGGAAAT
1 TCTCTTTTGGGTAGACAAATCAATGTTGGAAGACGTGTCTGCTCCACCATTCATTCAGGGGAAAT
* *
4166999 CTGACTTGATTTGTGCC
66 CAGACTGGATTTGTGCC
* * * * * * * *
4167016 TCT-TTTTCAGGTAAACAAATCCATGTT-GCAGTACGTGTTTGTTCCACCATGCATTCAAGGGAA
1 TCTCTTTT-GGGTAGACAAATCAATGTTGGAAG-ACGTGTCTGCTCCACCATTCATTCAGGGGAA
*
4167079 ATCAGACTTGATTTGTGCC
64 ATCAGACTGGATTTGTGCC
* * * * * * *
4167098 TCTCTTTTGGGTTGACAGATCTATTTTGTAAGACGTGTCTGCTTCACCATTCATTCAGGAGAAAT
1 TCTCTTTTGGGTAGACAAATCAATGTTGGAAGACGTGTCTGCTCCACCATTCATTCAGGGGAAAT
* *
4167163 CAGAATGGATTTGTACC
66 CAGACTGGATTTGTGCC
* * * * * * ** *
4167180 TCTCCTTCGAGTAGACATATCAACT-TTGAAAGACGTGTATATTCCACTATTCATTCAGGGGAAA
1 TCTCTTTTGGGTAGACAAATCAA-TGTTGGAAGACGTGTCTGCTCCACCATTCATTCAGGGGAAA
* *
4167244 TCTGATTGGATTTGTGCC
65 TCAGACTGGATTTGTGCC
* * * * * *
4167262 TCTCTTTTCAGGTAGACAAATCCATGTTGG-AGTACGTGTCTGCTCTAACATGCATTCAAGGGAA
1 TCTCTTTT-GGGTAGACAAATCAATGTTGGAAG-ACGTGTCTGCTCCACCATTCATTCAGGGGAA
* * *
4167326 ATCAAACTTGATATGTGCC
64 ATCAGACTGGATTTGTGCC
* * ** * * * * * *
4167345 TCTCTTTCGGGTAGACATATTTATTTTGTAAGACGTGTCTGCTTCAACATTCATTCAGAGAAAAT
1 TCTCTTTTGGGTAGACAAATCAATGTTGGAAGACGTGTCTGCTCCACCATTCATTCAGGGGAAAT
* * *
4167410 CAAACTAGATCTGTGCC
66 CAGACTGGATTTGTGCC
* * * *
4167427 TCT-TCTTTGGGTAGACAGATCAACT-TTGGAAGACGTGTATGTTCCACCATTCATTCAGGAGAA
1 TCTCT-TTTGGGTAGACAAATCAA-TGTTGGAAGACGTGTCTGCTCCACCATTCATTCAGGGGAA
* *
4167490 ATCAGATTGGATATGTGCC
64 ATCAGACTGGATTTGTGCC
* * * * * *
4167509 TCTTTTTTGGGTAGACAGATTAATATTGGAAGACGTGTATGTTCCACCATTCATTCAGGGGAAAT
1 TCTCTTTTGGGTAGACAAATCAATGTTGGAAGACGTGTCTGCTCCACCATTCATTCAGGGGAAAT
4167574 CAGACTGGATTTGTGCC
66 CAGACTGGATTTGTGCC
* * * ** *
4167591 TCT-TTTTCGGGTAGACAAATCAATGTTGAAAGACGTGATTTGCTCCGCTTTTCTTTCAGGGGAA
1 TCTCTTTT-GGGTAGACAAATCAATGTTGGAAGACGTG-TCTGCTCCACCATTCATTCAGGGGAA
*
4167655 ATCAGACTTGGTTTTGTGCC
64 ATCAGAC-TGGATTTGTGCC
* * * * * * * * ** * *
4167675 TCT-TTTTCGGGTAGACAGATCAATTTTGAAAGATGTGATTTGTTTCTCTTTTCTTTTAGGGGAA
1 TCTCTTTT-GGGTAGACAAATCAATGTTGGAAGACGTG-TCTGCTCCACCATTCATTCAGGGGAA
*
4167739 ATCAGACTTGATTTGTGCC
64 ATCAGACTGGATTTGTGCC
* * * * * *
4167758 T-TATTTTCGGGTAGATAGATCAATTTTGGAATACGGGTCTGCTCC
1 TCTCTTTT-GGGTAGACAAATCAATGTTGGAAGACGTGTCTGCTCC
4167803 GCTTTTCTTT
Statistics
Matches: 911, Mismatches: 182, Indels: 44
0.80 0.16 0.04
Matches are distributed among these distances:
81 76 0.08
82 558 0.61
83 202 0.22
84 75 0.08
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (82 bp):
TCTCTTTTGGGTAGACAAATCAATGTTGGAAGACGTGTCTGCTCCACCATTCATTCAGGGGAAAT
CAGACTGGATTTGTGCC
Found at i:4167381 original size:411 final size:409
Alignment explanation
Indices: 4166608--4167691 Score: 1152
Period size: 411 Copynumber: 2.6 Consensus size: 409
4166598 TATGTACATC
* * * *
4166608 TCTTTCGGGTAGACAAATCAATGTTGGAAGACGTGTCTGCTCCACTATACATTCAGGGGAAATCA
1 TCTTTCGGGTAGACAAATCAATGTTGGAAGACGTGTATGTTCCACCATACATTCAAGGGAAATCA
* * * * * * * *
4166673 -AGCTGGATCTGTACCTCTCTTTTGGGTAGACAAATCAATGTTGGAATACGTGTTTGCTTCACCA
66 GA-CTTGATATGTGCCTCTCTTTTGGGTAGACAGATCTATATTGGAAGACGTGTATGCTTCACCA
* * * * * *
4166737 TGCATT-AAGAGGAAATCAGACA-GGATTTGTGCCTCTTTTCGGGTAGAAAAATCCATGTCAGAA
130 TTCATTCAGGA-GAAATCAGA-ATGGATTTGTGCCTCTTTTCGGGTAGACAAATCAATTTGA-AA
* * * ** * * * * * *
4166800 TACGTGTCTACTCCACTATGAATTTAGGGGAAAT-TAGACTAGATCTATGCCTCTTTTTTTGGGT
192 GACGTGTATATTCCACTATTCATTCAGGGGAAATCT-GATTGGATTTGTGCCTC-TTTTTCGGGT
* * * * * * *
4166864 AGACTAATCCATGTCGGAATATGTGTTTGCTCCACCATGTATTCATGGGAAATCAGACTTGATAT
255 AGACAAATCCATGTCGGAATACGTGTCTGCTCCAACATGCATTCAAGGGAAATCAAACTTGATAT
* * *
4166929 ATGCCTCTCTTTTGGGTAGACAAATCAATATTGGAAGACGTGTCTGC-TCTACCATGCATTCAGG
320 ATGCCTCTCTTTCGGGTAGACAAATCAATATTGGAAGACGTGTCTGCTTC-AACATGCATTCAGA
* ** * *
4166993 GGAAATCTGACTTGATTTGTGCCTCT
384 GAAAATCAAACTAGATCTGTGCCTCT
* * * * * *
4167019 T-TTTCAGGTAAACAAATCCATGTT-GCAGTACGTGTTTGTTCCACCATGCATTCAAGGGAAATC
1 TCTTTCGGGTAGACAAATCAATGTTGGAAG-ACGTGTATGTTCCACCATACATTCAAGGGAAATC
* * * * *
4167082 AGACTTGATTTGTGCCTCTCTTTTGGGTTGACAGATCTATTTTGTAAGACGTGTCTGCTTCACCA
65 AGACTTGATATGTGCCTCTCTTTTGGGTAGACAGATCTATATTGGAAGACGTGTATGCTTCACCA
* * * *
4167147 TTCATTCAGGAGAAATCAGAATGGATTTGTACCTCTCCTTCGAGTAGACATATCAACTTTGAAAG
130 TTCATTCAGGAGAAATCAGAATGGATTTGTGCCTCT-TTTCGGGTAGACAAATCAA-TTTGAAAG
*
4167212 ACGTGTATATTCCACTATTCATTCAGGGGAAATCTGATTGGATTTGTGCCTCTCTTTTCAGGTAG
193 ACGTGTATATTCCACTATTCATTCAGGGGAAATCTGATTGGATTTGTGCCTCT-TTTTCGGGTAG
* * * *
4167277 ACAAATCCATGTTGGAGTACGTGTCTGCTCTAACATGCATTCAAGGGAAATCAAACTTGATATGT
257 ACAAATCCATGTCGGAATACGTGTCTGCTCCAACATGCATTCAAGGGAAATCAAACTTGATATAT
* ** * * *
4167342 GCCTCTCTTTCGGGTAGACATATTTATTTTGTAAGACGTGTCTGCTTCAACATTCATTCAGAGAA
322 GCCTCTCTTTCGGGTAGACAAATCAATATTGGAAGACGTGTCTGCTTCAACATGCATTCAGAGAA
4167407 AATCAAACTAGATCTGTGCCTCT
387 AATCAAACTAGATCTGTGCCTCT
* *
4167430 TCTTT-GGGTAGACAGATCAACT-TTGGAAGACGTGTATGTTCCACCATTCATTC-AGGAGAAAT
1 TCTTTCGGGTAGACAAATCAA-TGTTGGAAGACGTGTATGTTCCACCATACATTCAAGG-GAAAT
*
4167492 CAGA-TTGGATATGTGCCTCTTTTTTGGGTAGACAGAT-TAATATTGGAAGACGTGTATG-TTCC
64 CAGACTT-GATATGTGCCTCTCTTTTGGGTAGACAGATCT-ATATTGGAAGACGTGTATGCTT-C
* *
4167554 ACCATTCATTCAGGGGAAATCAGACTGGATTTGTGCCTCTTTTTCGGGTAGACAAATCAATGTTG
126 ACCATTCATTCAGGAGAAATCAGAATGGATTTGTGCCTC-TTTTCGGGTAGACAAATCAAT-TTG
* * * * * *
4167619 AAAGACGTG-ATTTGCTCCGCTTTTCTTTCAGGGGAAATCAGACTTGGTTTTGTGCCTCTTTTTC
189 AAAGACGTGTATAT--TCCACTATTCATTCAGGGGAAATCTGA-TTGGATTTGTGCCTCTTTTTC
4167683 GGGTAGACA
251 GGGTAGACA
4167692 GATCAATTTT
Statistics
Matches: 560, Mismatches: 92, Indels: 41
0.81 0.13 0.06
Matches are distributed among these distances:
409 4 0.01
410 142 0.25
411 349 0.62
412 50 0.09
413 15 0.03
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (409 bp):
TCTTTCGGGTAGACAAATCAATGTTGGAAGACGTGTATGTTCCACCATACATTCAAGGGAAATCA
GACTTGATATGTGCCTCTCTTTTGGGTAGACAGATCTATATTGGAAGACGTGTATGCTTCACCAT
TCATTCAGGAGAAATCAGAATGGATTTGTGCCTCTTTTCGGGTAGACAAATCAATTTGAAAGACG
TGTATATTCCACTATTCATTCAGGGGAAATCTGATTGGATTTGTGCCTCTTTTTCGGGTAGACAA
ATCCATGTCGGAATACGTGTCTGCTCCAACATGCATTCAAGGGAAATCAAACTTGATATATGCCT
CTCTTTCGGGTAGACAAATCAATATTGGAAGACGTGTCTGCTTCAACATGCATTCAGAGAAAATC
AAACTAGATCTGTGCCTCT
Found at i:4167427 original size:329 final size:329
Alignment explanation
Indices: 4166894--4167627 Score: 896
Period size: 329 Copynumber: 2.2 Consensus size: 329
4166884 ATGTGTTTGC
* * *
4166894 TCCACCATGT-ATTCATGGGAAATCAGACTT-GATATATGCCTCTCTTTT-GGGTAGACAAATCA
1 TCCACCAT-TCATTCAGGGGAAATCAGA-TTGGATTTGTGCCTCTCTTTTCGGGTAGACAAATCA
* * * ** * *
4166956 ATATTGGAAGACGTGTCTGCTCTACCATGCATTCAGGGGAAATCTGACTTGATTTGTGCCTCTTT
64 ATGTTGGAAGACGTGTCTGCTCTAACATGCATTCAAGGGAAATCAAACTTGATATGTGCCTCTCT
* * * * *
4167021 TTCAGGTAAACAAATCCATGTTGCAGTACGTGTTTGTTCCACCATGCATTCAAGGGAAATCAGAC
129 TTCAGGTAAACAAATCCATGTTGAAGTACGTGTCTGTTCCAACATGCATTCAAGGAAAATCAAAC
* * * * * * *
4167086 TTGATTTGTGCCTC-TCTTTTGGGTTGACAGATCTATTTTGTAAGACGTGTCTGCTT-CACCATT
194 TAGATCTGTGCCTCTTC-TTTGGGTAGACAGATCAACTTTGGAAGACGTGTATG-TTCCACCATT
* *
4167149 CATTCAGGAGAAATCAGAATGGATTTGTACCTCTCCTTCGAGTAGACATATCAACT-TTGAAAGA
257 CATTCAGGAGAAATCAGAATGGATATGTACCTCTCCTTCGAGTAGACAGATCAA-TATTGAAAGA
4167213 CGTGTATAT
321 CGTGTATAT
* * * *
4167222 TCCACTATTCATTCAGGGGAAATCTGATTGGATTTGTGCCTCTCTTTTCAGGTAGACAAATCCAT
1 TCCACCATTCATTCAGGGGAAATCAGATTGGATTTGTGCCTCTCTTTTCGGGTAGACAAATCAAT
4167287 GTTGG-AGTACGTGTCTGCTCTAACATGCATTCAAGGGAAATCAAACTTGATATGTGCCTCTCTT
66 GTTGGAAG-ACGTGTCTGCTCTAACATGCATTCAAGGGAAATCAAACTTGATATGTGCCTCTCTT
* * * ** * *
4167351 TCGGGTAGACATATTTATTTTGTAAG-ACGTGTCTGCTT-CAACATTCATTC-AGAGAAAATCAA
130 TCAGGTAAACAAATCCATGTTG-AAGTACGTGTCTG-TTCCAACATGCATTCAAG-GAAAATCAA
4167413 ACTAGATCTGTGCCTCTTCTTTGGGTAGACAGATCAACTTTGGAAGACGTGTATGTTCCACCATT
192 ACTAGATCTGTGCCTCTTCTTTGGGTAGACAGATCAACTTTGGAAGACGTGTATGTTCCACCATT
* * ** * * * *
4167478 CATTCAGGAGAAATCAGATTGGATATGTGCCTCTTTTTTGGGTAGACAGATTAATATTGGAAGAC
257 CATTCAGGAGAAATCAGAATGGATATGTACCTCTCCTTCGAGTAGACAGATCAATATTGAAAGAC
*
4167543 GTGTATGT
322 GTGTATAT
*
4167551 TCCACCATTCATTCAGGGGAAATCAGACTGGATTTGTGCCTCT-TTTTCGGGTAGACAAATCAAT
1 TCCACCATTCATTCAGGGGAAATCAGATTGGATTTGTGCCTCTCTTTTCGGGTAGACAAATCAAT
*
4167615 GTTGAAAGACGTG
66 GTTGGAAGACGTG
4167628 ATTTGCTCCG
Statistics
Matches: 345, Mismatches: 50, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
327 3 0.01
328 73 0.21
329 263 0.76
330 6 0.02
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (329 bp):
TCCACCATTCATTCAGGGGAAATCAGATTGGATTTGTGCCTCTCTTTTCGGGTAGACAAATCAAT
GTTGGAAGACGTGTCTGCTCTAACATGCATTCAAGGGAAATCAAACTTGATATGTGCCTCTCTTT
CAGGTAAACAAATCCATGTTGAAGTACGTGTCTGTTCCAACATGCATTCAAGGAAAATCAAACTA
GATCTGTGCCTCTTCTTTGGGTAGACAGATCAACTTTGGAAGACGTGTATGTTCCACCATTCATT
CAGGAGAAATCAGAATGGATATGTACCTCTCCTTCGAGTAGACAGATCAATATTGAAAGACGTGT
ATAT
Found at i:4168845 original size:65 final size:63
Alignment explanation
Indices: 4168647--4168846 Score: 203
Period size: 65 Copynumber: 3.1 Consensus size: 63
4168637 GAGTGTATCG
* *
4168647 ATGCATGAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGACTGGTGCATCA
1 ATGCATGAAATGCATTCGATGTTTCAAAATATCCAG-GTGCATCGATGCATGATTGGTGCATCA
* *
4168711 ATGCATCAAATGAATTCGATGTTTTCATAAA-ACTCTCA-GTGCATCGATGCAT-AGTAT-GTGC
1 ATGCATGAAATGCATTCGATG-TTTCA-AAATA-TC-CAGGTGCATCGATGCATGA-T-TGGTGC
4168772 ATCA
60 ATCA
* * *
4168776 ATGCATGAAATGCATACGATG-TTCAAAATATTCCATGGTGCATCTATGCATGGATTGGTGGATC
1 ATGCATGAAATGCATTCGATGTTTCAAAATA-TCCA-GGTGCATCGATGCAT-GATTGGTGCATC
*
4168840 G
63 A
4168841 ATGCAT
1 ATGCAT
4168847 CACTTTGAAA
Statistics
Matches: 113, Mismatches: 11, Indels: 23
0.77 0.07 0.16
Matches are distributed among these distances:
62 5 0.04
63 7 0.06
64 34 0.30
65 59 0.52
66 6 0.05
67 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (63 bp):
ATGCATGAAATGCATTCGATGTTTCAAAATATCCAGGTGCATCGATGCATGATTGGTGCATCA
Found at i:4169931 original size:21 final size:21
Alignment explanation
Indices: 4169907--4169950 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
4169897 GTGCCGGAGG
* *
4169907 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAACT
* *
4169928 AGGAGCAGCTCGTGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
4169949 AG
1 AG
4169951 CTCTCGGGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:4171524 original size:23 final size:22
Alignment explanation
Indices: 4171494--4171575 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
4171484 GCATGGCCTT
4171494 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * * *
4171516 TGTGTATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
4171538 GTGTATCAATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
4171561 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
4171576 TGTTAAGTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 18 0.39
24 11 0.24
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:4171550 original size:21 final size:21
Alignment explanation
Indices: 4171502--4171556 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
4171492 TTGTGCATCG
* *
4171502 ATGCACATTCAAGGTGTGTATCG
1 ATGCACATTC-ATG-GTGTATCA
* *
4171525 GTGCACCTTCATGGTGTATCA
1 ATGCACATTCATGGTGTATCA
4171546 ATGCACATTCA
1 ATGCACATTCA
4171557 AAGGGATGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 16 0.62
22 2 0.08
23 8 0.31
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (21 bp):
ATGCACATTCATGGTGTATCA
Found at i:4178876 original size:24 final size:23
Alignment explanation
Indices: 4178849--4178900 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
4178839 TTTTTTGAAA
* *
4178849 TTTTGGCTTTTTTGTTTTGTTTTT
1 TTTTGGCCTTTTTGCTTT-TTTTT
*
4178873 TTTTTGCCTTTTTGCTTTTTTTT
1 TTTTGGCCTTTTTGCTTTTTTTT
4178896 TTTTG
1 TTTTG
4178901 AAAAAAATAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.00, C:0.08, G:0.13, T:0.79
Consensus pattern (23 bp):
TTTTGGCCTTTTTGCTTTTTTTT
Found at i:4182889 original size:28 final size:28
Alignment explanation
Indices: 4182857--4182919 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
4182847 TCAAATACAT
* *
4182857 TCGATGTTTTCATAAAACTATGAGTGCA
1 TCGATGCTTTCATAAAACTATAAGTGCA
*
4182885 TCGATGCTTTCATAAAACTCTAAGTGCA
1 TCGATGCTTTCATAAAACTATAAGTGCA
4182913 TCGATGC
1 TCGATGC
4182920 ATAGTATGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (28 bp):
TCGATGCTTTCATAAAACTATAAGTGCA
Found at i:4183756 original size:51 final size:51
Alignment explanation
Indices: 4183639--4183774 Score: 139
Period size: 51 Copynumber: 2.7 Consensus size: 51
4183629 CATTACAGAC
* * * * * * *
4183639 AAGTTGACTTCTTTACACTAGAAAGTCAAGTTGAGAAATGATACTACTGAA
1 AAGTTGACATCTCTCCACGAGAAAGTCAAGTTGAAAAAGGATACTACTAAA
* * *
4183690 AAGTTGTCATCTCTCCACGAGAAAGTCGAGTTGAAAAAGGATATTACTAAA
1 AAGTTGACATCTCTCCACGAGAAAGTCAAGTTGAAAAAGGATACTACTAAA
* * *
4183741 AAGTTGACTAT-TCTCCGCGAGGAAGTCAAATTGA
1 AAGTTGAC-ATCTCTCCACGAGAAAGTCAAGTTGA
4183775 GAATGGCATC
Statistics
Matches: 69, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
51 67 0.97
52 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (51 bp):
AAGTTGACATCTCTCCACGAGAAAGTCAAGTTGAAAAAGGATACTACTAAA
Found at i:4183859 original size:45 final size:45
Alignment explanation
Indices: 4183784--4183889 Score: 115
Period size: 45 Copynumber: 2.4 Consensus size: 45
4183774 AGAATGGCAT
* * * *
4183784 CACTAAAAGTTTGACTTCCCTTTCATAGAAAGTTAAGAATCACAA
1 CACTAAAAGATTGACTTCCCTTTCAGAGAAAGTCAAAAATCACAA
* * *
4183829 CACTGAAAGATTGACTTCTCTTT-ACGAGAAAGTCAAAAATGACAA
1 CACTAAAAGATTGACTTCCCTTTCA-GAGAAAGTCAAAAATCACAA
* *
4183874 TACTAAAAGATCGACT
1 CACTAAAAGATTGACT
4183890 CTTCTTTCCA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 1 0.02
45 49 0.98
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (45 bp):
CACTAAAAGATTGACTTCCCTTTCAGAGAAAGTCAAAAATCACAA
Found at i:4183896 original size:45 final size:45
Alignment explanation
Indices: 4183784--4183981 Score: 107
Period size: 45 Copynumber: 4.4 Consensus size: 45
4183774 AGAATGGCAT
* * * * * *
4183784 CACTAAAAGTTTGACTTCCCTTT-CATAGAAAGTTAAGAATCACAA
1 CACTAAAAGATCGACTTCTCTTTAC-GAGAAAGTCAAAAATCACAA
* * *
4183829 CACTGAAAGATTGACTTCTCTTTACGAGAAAGTCAAAAATGACAA
1 CACTAAAAGATCGACTTCTCTTTACGAGAAAGTCAAAAATCACAA
* * * * *
4183874 TACTAAAAGATCGAC-TCTTCTTTCCATGAGAAATTCAAGAAT-AAAA
1 CACTAAAAGATCGACTTC-TCTTT--ACGAGAAAGTCAAAAATCACAA
* * * * * * * *
4183920 CCACTAAAAGGTTGATTTCTCTTCATGAGAGAGTCAAGTAA-GACAA
1 -CACTAAAAGATCGACTTCTCTTTACGAGAAAGTCAA-AAATCACAA
*
4183966 CACTAAATGATCGACT
1 CACTAAAAGATCGACT
4183982 CTTCTACGAG
Statistics
Matches: 118, Mismatches: 27, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
44 2 0.02
45 76 0.64
46 9 0.08
47 29 0.25
48 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (45 bp):
CACTAAAAGATCGACTTCTCTTTACGAGAAAGTCAAAAATCACAA
Found at i:4183906 original size:47 final size:47
Alignment explanation
Indices: 4183805--4183986 Score: 137
Period size: 45 Copynumber: 4.0 Consensus size: 47
4183795 TGACTTCCCT
* * * * *
4183805 TTCAT-AGAAAGTTAAGAATCACAACACTGAAAGATTGA--CTTCTC
1 TTCATGAGAAAGTCAAAAATGACAACACTAAAAGATCGACTCTTCTC
* * *
4183849 TTTACGAGAAAGTCAAAAATGACAATACTAAAAGATCGACTCTTCT-
1 TTCATGAGAAAGTCAAAAATGACAACACTAAAAGATCGACTCTTCTC
* * * * *
4183895 TTCCATGAGAAATTCAAGAAT-AAAACCACTAAAAGGTTGA-T-TTCTC
1 TT-CATGAGAAAGTCAAAAATGACAA-CACTAAAAGATCGACTCTTCTC
* * *
4183941 TTCATGAGAGAGTCAAGTAA-GACAACACTAAATGATCGACTCTTCT
1 TTCATGAGAAAGTCAA-AAATGACAACACTAAAAGATCGACTCTTCT
4183987 ACGAGAGAAA
Statistics
Matches: 105, Mismatches: 23, Indels: 17
0.72 0.16 0.12
Matches are distributed among these distances:
44 3 0.03
45 54 0.51
46 14 0.13
47 34 0.32
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (47 bp):
TTCATGAGAAAGTCAAAAATGACAACACTAAAAGATCGACTCTTCTC
Found at i:4184009 original size:92 final size:92
Alignment explanation
Indices: 4183829--4183998 Score: 211
Period size: 92 Copynumber: 1.9 Consensus size: 92
4183819 AGAATCACAA
* * *
4183829 CACTGAAAGATTGACTTCTCTTTACGAGAAAGTCAAAAATGACAATACTAAAAGATCGACTCTTC
1 CACTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAAAATGACAACACTAAAAGATCGACTCTTC
*
4183894 TTTCCATGAGAAATTCAAGAATAAAAC
66 TTACCATGAGAAATTCAAGAATAAAAC
* * * * * *
4183921 CACTAAAAGGTTGATTTCTCTTCATGAGAGAGTCAAGTAA-GACAACACTAAATGATCGACTCTT
1 CACTAAAAGATTGACTTCTCTTCACGAGAAAGTCAA-AAATGACAACACTAAAAGATCGACTCTT
*
4183985 C-TACGA-GAGAAATT
65 CTTACCATGAGAAATT
4183999 AAACAAAATA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
90 8 0.12
91 3 0.05
92 53 0.80
93 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.26
Consensus pattern (92 bp):
CACTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAAAATGACAACACTAAAAGATCGACTCTTC
TTACCATGAGAAATTCAAGAATAAAAC
Found at i:4185604 original size:20 final size:20
Alignment explanation
Indices: 4185579--4185622 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
4185569 GATGATTTTC
4185579 GGGCTTAAAATGCAAATTCT
1 GGGCTTAAAATGCAAATTCT
4185599 GGGCTTAAAATGCAAATTCT
1 GGGCTTAAAATGCAAATTCT
4185619 GGGC
1 GGGC
4185623 AAGGTGTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (20 bp):
GGGCTTAAAATGCAAATTCT
Found at i:4185820 original size:20 final size:22
Alignment explanation
Indices: 4185775--4185832 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
4185765 GCATGGGTAG
4185775 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
4185799 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
4185819 TGCATCGATGCACT
1 TGCATCGATGCACT
4185833 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:4188386 original size:99 final size:98
Alignment explanation
Indices: 4188210--4188402 Score: 298
Period size: 99 Copynumber: 2.0 Consensus size: 98
4188200 GTATTTTGCA
* * * *
4188210 TTTATCAGGCTAGCTGAATCTTATCCATAAAGTTAGGGTGTTTAACCAATTGCTCTAGAGGGGCA
1 TTTATCAGGCTAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAATTACTCTAGAGGGACA
*
4188275 GTTCAAGCTTTATTGTATATATATTATAATCACC
66 GTTCAAGCTTTATTGTATACATA-TATAATCACC
*
4188309 TTTATCAGGCTAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAATTACTCTAGATGGACA
1 TTTATCAGGCTAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAATTACTCTAGAGGGACA
*
4188374 -TCTCAAGTTTTATTGTATACATATATAAT
66 GT-TCAAGCTTTATTGTATACATATATAAT
4188403 TTCATTCTGG
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
98 7 0.08
99 79 0.92
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (98 bp):
TTTATCAGGCTAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAATTACTCTAGAGGGACA
GTTCAAGCTTTATTGTATACATATATAATCACC
Found at i:4193256 original size:12 final size:12
Alignment explanation
Indices: 4193239--4193269 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
4193229 ATTAAAATCA
4193239 TTAAAATCTATT
1 TTAAAATCTATT
4193251 TTAAAATCTATT
1 TTAAAATCTATT
4193263 TTAAAAT
1 TTAAAAT
4193270 ATGGATTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (12 bp):
TTAAAATCTATT
Found at i:4193287 original size:22 final size:22
Alignment explanation
Indices: 4193259--4193729 Score: 719
Period size: 22 Copynumber: 21.5 Consensus size: 22
4193249 TTTTAAAATC
4193259 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
4193281 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
4193303 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
*
4193325 TATTTTAAAATATGAATTGATT
1 TATTTTAAAATATGGATTGATT
*** *
4193347 TATTTTAAAATAT-GAAAAAAT
1 TATTTTAAAATATGGATTGATT
*
4193368 TATTTTAAAATATGAATTGATT
1 TATTTTAAAATATGGATTGATT
***
4193390 TATTTTAAAATATGGAAAAATT
1 TATTTTAAAATATGGATTGATT
4193412 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
*
4193434 TATTTTAAAATATAGATTGATT
1 TATTTTAAAATATGGATTGATT
4193456 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
*
4193478 TATTTTAAAATATGGATTAATT
1 TATTTTAAAATATGGATTGATT
*
4193500 TATTTTAAAATATGGATGGATT
1 TATTTTAAAATATGGATTGATT
* *
4193522 TATTTTAAAATATGAATGGATT
1 TATTTTAAAATATGGATTGATT
***
4193544 TATTTTAAAATATGGAAAAATT
1 TATTTTAAAATATGGATTGATT
4193566 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
* ***
4193588 TATTTTAAAATATGAAAAAATT
1 TATTTTAAAATATGGATTGATT
4193610 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
4193632 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
*
4193654 TATTTTATAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
*
4193676 TATTTTAAAATATGAATTGATT
1 TATTTTAAAATATGGATTGATT
*
4193698 TATTTTAAAATATGAATTGATT
1 TATTTTAAAATATGGATTGATT
4193720 TATTTTAAAA
1 TATTTTAAAA
4193730 AATTTATTAT
Statistics
Matches: 406, Mismatches: 42, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
21 16 0.04
22 390 0.96
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
TATTTTAAAATATGGATTGATT
Found at i:4193810 original size:31 final size:31
Alignment explanation
Indices: 4193753--4193811 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
4193743 AGTTGTATGG
*
4193753 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
4193784 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
4193812 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:4196111 original size:42 final size:42
Alignment explanation
Indices: 4195922--4196835 Score: 1042
Period size: 42 Copynumber: 21.6 Consensus size: 42
4195912 GAGCATGCAA
* * * * *
4195922 AAACGGTAAGGACTTACCCTTGCATATAGCAAA-AAAGCCTGGG
1 AAACTGTAAGG-CTTACCCTTGCACACAACAAAGGAA-CCTGGG
* * * * * *
4195965 AAACGGTAAGGTCTTACCTTTGCAAATAGCAAA-TAAGCCTGGGG
1 AAACTGTAAGG-CTTACCCTTGCACACAACAAAGGAA-CCT-GGG
*
4196009 AAACTGTAAGGCTTACCTTTGCACACAACAAAGGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
4196051 AAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
1 -AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* * ** * *
4196094 AAACTGTAAAGCTTACCCTTGCACATAGTACAGGAACATGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* * * * * * *
4196136 GAACTCTAAGGCTTACCCATGCACACAGCAAAGAAACTTAGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
*
4196178 AAACTGTAAGGCTTACCCTTGCATACAACAAAGGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* * *
4196220 AAACTATAAGGCTTACCCTTGCAAACAGCAAAGGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* * *
4196262 AAACTGTAAGGCTTACCCTTGCACACAGCAAATGAATCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* * *
4196304 AAACTGTAAGGCTTACCCATGCACACATCAAATGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* * **
4196346 GAATTGTAACACTTACCCTTGCACACAACAAAGGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* * * *
4196388 AAACTATAAGGTTTACCCTTGCACAAAACAAATGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* *
4196430 AAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAA-CTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* *
4196471 GAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* *
4196513 AAACTGTAAGGATTACCCTTGCACACAACAAAAGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* *
4196555 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACTTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* * * * *
4196597 AAATTGTAAGGCTTCCCCTTGCAAACAACAAATGAACATGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* * * * **
4196639 GAACTGTAAGGTCTTATCCTTACACACAATAAAGGAACCTGTA
1 AAACTGTAAGG-CTTACCCTTGCACACAACAAAGGAACCTGGG
* * *
4196682 AAACTATAAGCCTTACCCTTGCACACTACAAAGGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* **
4196724 AAACTGTAAGGCTTCCCCTTGCACACAGTAAAGGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* * *
4196766 GAACTGTAAGGTCTTACCCTTGCACACAGCAAAGGAGCCTGCGG
1 AAACTGTAAGG-CTTACCCTTGCACACAACAAAGGAACCTG-GG
* * * *
4196810 TAACGGTAAAGACTTACCCTTTCACA
1 AAACTGT-AAGGCTTACCCTTGCACA
4196836 TATCAGAGGA
Statistics
Matches: 747, Mismatches: 116, Indels: 15
0.85 0.13 0.02
Matches are distributed among these distances:
41 37 0.05
42 518 0.69
43 154 0.21
44 35 0.05
45 3 0.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (42 bp):
AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
Found at i:4197662 original size:56 final size:55
Alignment explanation
Indices: 4197567--4197696 Score: 199
Period size: 56 Copynumber: 2.3 Consensus size: 55
4197557 TATGTTACCC
4197567 AACAATCA-GGGTATTCAGGAGTATGTATTGAATTAACATGATTTTAGTCCAATTG
1 AACAA-CATGGGTATTCAGGAGTATGTATTGAATTAACATGATTTTAGTCCAATTG
* * *
4197622 AACCACATGTGGTATTCAGGGGTGTGTATTGAATTAACATGATTTTAGTCCAATTG
1 AACAACATG-GGTATTCAGGAGTATGTATTGAATTAACATGATTTTAGTCCAATTG
4197678 AACAACATGGAGTATTCAG
1 AACAACATGG-GTATTCAG
4197697 AATCCTTTGC
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
54 2 0.03
55 6 0.09
56 60 0.88
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (55 bp):
AACAACATGGGTATTCAGGAGTATGTATTGAATTAACATGATTTTAGTCCAATTG
Found at i:4199026 original size:18 final size:17
Alignment explanation
Indices: 4198984--4199025 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
4198974 ACGTAAAATA
4198984 TGACTTTTCAAAAATTT
1 TGACTTTTCAAAAATTT
*
4199001 TGACTTTTCGAAAATTT
1 TGACTTTTCAAAAATTT
4199018 TGACTTTT
1 TGACTTTT
4199026 TGGTCAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.50
Consensus pattern (17 bp):
TGACTTTTCAAAAATTT
Found at i:4201272 original size:42 final size:42
Alignment explanation
Indices: 4201086--4201872 Score: 959
Period size: 42 Copynumber: 18.6 Consensus size: 42
4201076 GAGCATCCAA
* * * *
4201086 AAACGGTAAGGTCTTACCCTTGCACATAGCAAAAGG-GCCTGGG
1 AAACTGTAAGG-CTTACCCTTGCACACAAC-AAAGGAACCTGGG
* * * * *
4201129 GAACAGTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTGAGG
1 AAACTGTAAGG-CTTACCCTTGCACACAACAAAGGAACCTG-GG
* * * *
4201173 AAATTGTAAGGCTTACCTTTGCACACATCAAAGGAACATGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCT-GGG
*
4201216 AAACTGTAAGGCTTACCCTTGCACACAACAAACGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
*
4201258 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* *
4201300 GAACTGTAAGGCTTACCCTTGCACATAACAAAGGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* *
4201342 AAACTGTAAGGCTTACCCTTACACACAACAAAGGAACCTGGA
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* *
4201384 AAACTATAAGGCTTACCCTTACACACAACAAAGGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* * *
4201426 AAACTGTAAGGCATACCCTTGCACACAACAAAGAAACCTGAG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* *
4201468 AAACTGTAAGGCTTACCCTTGCATATAACAAAGGAACCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* * *
4201510 GAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTCGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
*
4201552 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACTTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* *
4201594 AAACTGTAAGGCTTACCCTTGGACACAACAAAGGAATCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* * * **
4201636 GAACTGTAAGGCTTACCCTTCCACACAACAAAGAAACCTCAG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* * **
4201678 AAATTGTAAGGCTTACCCTTAG-ACACAATAAAGGAACCTTAG
1 AAACTGTAAGGCTTACCCTT-GCACACAACAAAGGAACCTGGG
* * * **
4201720 AAACTATAAGGCTTACCCTTGCACACAGCAAAGGACCCTAAG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* * *
4201762 AAACTGTAAGGCTTACCCTTGTACATAGCAAAGGAACCT-GG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
*** * * * *
4201803 AAACAACAAGGGTTACCCTTACACACATCAAAGGATCCTGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
* * *
4201845 GAACTGTAAGGTCTTACCTTTGTACACA
1 AAACTGTAAGG-CTTACCCTTGCACACA
4201873 GTAACGGAGC
Statistics
Matches: 648, Mismatches: 89, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
41 32 0.05
42 501 0.77
43 104 0.16
44 11 0.02
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.19
Consensus pattern (42 bp):
AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG
Found at i:4202719 original size:56 final size:56
Alignment explanation
Indices: 4202652--4202773 Score: 174
Period size: 56 Copynumber: 2.2 Consensus size: 56
4202642 CCAACAATCA
* * *
4202652 GGGGTATTCAGGAGTTTGTATTGAATTAACAGGATTTCAGTCCTATT-AAGCCACAT
1 GGGGTATTCAGGAGTATGTATTGAATTAACAAGATTTCAGTCCAATTGAA-CCACAT
* * *
4202708 GGGGTATTCAGGGGTATGTATTGAATTAACAAGATTTTAGTCCAATTGAACTACAT
1 GGGGTATTCAGGAGTATGTATTGAATTAACAAGATTTCAGTCCAATTGAACCACAT
4202764 GGGGTATTCA
1 GGGGTATTCA
4202774 AAATCCTTTG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
56 57 0.97
57 2 0.03
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.34
Consensus pattern (56 bp):
GGGGTATTCAGGAGTATGTATTGAATTAACAAGATTTCAGTCCAATTGAACCACAT
Found at i:4210770 original size:19 final size:19
Alignment explanation
Indices: 4210746--4210797 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
4210736 AATGTAATTA
*
4210746 GTGTACCGATACACCTAGT
1 GTGTACCGGTACACCTAGT
4210765 GTGTACCGGTACACCTAGT
1 GTGTACCGGTACACCTAGT
4210784 GTGTACCGGTACAC
1 GTGTACCGGTACAC
4210798 TCGGTCATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (19 bp):
GTGTACCGGTACACCTAGT
Found at i:4213687 original size:20 final size:20
Alignment explanation
Indices: 4213662--4213711 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
4213652 GAAAAAGGTG
4213662 ACTTACAACCCAAGAACAAT
1 ACTTACAACCCAAGAACAAT
4213682 ACTTACAACCCAAGAACAAT
1 ACTTACAACCCAAGAACAAT
4213702 ACTTACAACC
1 ACTTACAACC
4213712 TTTCCTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.48, C:0.32, G:0.04, T:0.16
Consensus pattern (20 bp):
ACTTACAACCCAAGAACAAT
Found at i:4213868 original size:15 final size:16
Alignment explanation
Indices: 4213828--4213871 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
4213818 TTGTTGGAAA
4213828 TTTCTTTCTTTTTGCCT
1 TTTC-TTCTTTTTGCCT
4213845 TTTCTTCTTTTGTG-CT
1 TTTCTTCTTTT-TGCCT
4213861 TTTC-TCTTTTT
1 TTTCTTCTTTTT
4213872 TTTTAAACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.04
15 6 0.23
16 13 0.50
17 6 0.23
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.73
Consensus pattern (16 bp):
TTTCTTCTTTTTGCCT
Found at i:4224815 original size:14 final size:14
Alignment explanation
Indices: 4224796--4224876 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
4224786 GGTCAAGTCA
4224796 CCGAGTCAACTCGT
1 CCGAGTCAACTCGT
* *
4224810 CCGAGTTAACCCGT
1 CCGAGTCAACTCGT
* *
4224824 CTGAGTCAATTCAGT
1 CCGAGTCAACTC-GT
** *
4224839 TTGAGTCAACCCGT
1 CCGAGTCAACTCGT
*
4224853 CAGAGTCAACTCGT
1 CCGAGTCAACTCGT
4224867 CCGAGTCAAC
1 CCGAGTCAAC
4224877 CCTTTGACTT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
14 42 0.79
15 11 0.21
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (14 bp):
CCGAGTCAACTCGT
Found at i:4224849 original size:29 final size:28
Alignment explanation
Indices: 4224798--4224878 Score: 108
Period size: 29 Copynumber: 2.9 Consensus size: 28
4224788 TCAAGTCACC
* *
4224798 GAGTCAACTCGTCCGAGTTAACCCGTCT
1 GAGTCAACTCGTCCGAGTCAACCCGTCA
* **
4224826 GAGTCAATTCAGTTTGAGTCAACCCGTCA
1 GAGTCAACTC-GTCCGAGTCAACCCGTCA
4224855 GAGTCAACTCGTCCGAGTCAACCC
1 GAGTCAACTCGTCCGAGTCAACCC
4224879 TTTGACTTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 21 0.48
29 23 0.52
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (28 bp):
GAGTCAACTCGTCCGAGTCAACCCGTCA
Found at i:4224898 original size:13 final size:13
Alignment explanation
Indices: 4224880--4224927 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
4224870 AGTCAACCCT
* *
4224880 TTGACTTTGATCG
1 TTGACTTTAAACG
* *
4224893 TTGACTTTAAGCA
1 TTGACTTTAAACG
4224906 TTGACTTTAACACG
1 TTGACTTTAA-ACG
4224920 TTGACTTT
1 TTGACTTT
4224928 GACCATTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 20 0.69
14 9 0.31
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.44
Consensus pattern (13 bp):
TTGACTTTAAACG
Found at i:4224925 original size:14 final size:15
Alignment explanation
Indices: 4224891--4224927 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
4224881 TGACTTTGAT
4224891 CGTTGACTTTAAGCA
1 CGTTGACTTTAAGCA
4224906 --TTGACTTTAA-CA
1 CGTTGACTTTAAGCA
4224918 CGTTGACTTT
1 CGTTGACTTT
4224928 GACCATTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 2 0.10
13 10 0.50
14 8 0.40
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (15 bp):
CGTTGACTTTAAGCA
Found at i:4228593 original size:20 final size:19
Alignment explanation
Indices: 4228568--4228608 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
4228558 TTTATGTAAG
*
4228568 TATATATTTATATATCATAT
1 TATATATGTATATATC-TAT
4228588 TATATATGTATATATCTAT
1 TATATATGTATATATCTAT
4228607 TA
1 TA
4228609 AATGTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (19 bp):
TATATATGTATATATCTAT
Found at i:4235076 original size:36 final size:35
Alignment explanation
Indices: 4234963--4235281 Score: 166
Period size: 36 Copynumber: 9.7 Consensus size: 35
4234953 ACAATCATCT
* * *
4234963 TTGAGATTGTTTCCCTTGAAACGAATTTTGTCTCCC
1 TTGAGATAGTTTCCCTTGAAACAAATTTTGTAT-CC
* * **
4234999 TTGAGACAGTTTCTCTTGAAAC--A--TCATAT--
1 TTGAGATAGTTTCCCTTGAAACAAATTTTGTATCC
* *
4235028 TTGAGATCGTTTCCCTTGAAACAAATTTTGTTTACC
1 TTGAGATAGTTTCCCTTGAAACAAATTTTGTAT-CC
* * *
4235064 TTGAGATAGTTTCTCTTG----AAA-TAT-TATCT
1 TTGAGATAGTTTCCCTTGAAACAAATTTTGTATCC
* * *
4235093 TTGAGATCGGTTCCCTTGAAACAAATTTTGTCTCCC
1 TTGAGATAGTTTCCCTTGAAACAAATTTTGTAT-CC
* * **
4235129 TTGAGACAGTTTCTCTTGAAAC--A--TCATAT--
1 TTGAGATAGTTTCCCTTGAAACAAATTTTGTATCC
* * *
4235158 TTAAGATCGTTTCCCTTGAAACAAATTTTGTTTCCC
1 TTGAGATAGTTTCCCTTGAAACAAATTTTGTAT-CC
* * *
4235194 TTGAGACAGTTTCTCTTGAAAC--A---T-TATCT
1 TTGAGATAGTTTCCCTTGAAACAAATTTTGTATCC
*
4235223 TTGAGATCA-TTTCCCTTGAAACAAATTTTGTCTCCC
1 TTGAGAT-AGTTTCCCTTGAAACAAATTTTGTAT-CC
*
4235259 TTGAGATAGTTTCACTTGAAACA
1 TTGAGATAGTTTCCCTTGAAACA
4235282 TTATCCCTAA
Statistics
Matches: 205, Mismatches: 48, Indels: 60
0.65 0.15 0.19
Matches are distributed among these distances:
29 72 0.35
30 5 0.02
31 6 0.03
32 9 0.04
33 9 0.04
34 6 0.03
35 5 0.02
36 93 0.45
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (35 bp):
TTGAGATAGTTTCCCTTGAAACAAATTTTGTATCC
Found at i:4235286 original size:65 final size:65
Alignment explanation
Indices: 4234746--4235282 Score: 698
Period size: 65 Copynumber: 8.2 Consensus size: 65
4234736 TTGGAAATTA
* * * * **
4234746 TTTCTCTTGAAACATTATCTTTGAGAACGTCTCCCTTGAAACAAATTTTGTCTCTCTTGAGGTAG
1 TTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
* * * * * * *
4234811 TTTCTCTTAAAACATCAT-TTGTAAGATTGCTTCTCATGAAACAAGTTTTGTCTCCCTTGAGACA
1 TTTCTCTTGAAACATCATCTT-TGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
4234875 G
65 G
* ** * * ** *
4234876 TTTCTCTTGAAACAATCATCATTGAGATTATTTCCTTTAAAATGAATTTTGTCTCCCTTGAGAGA
1 TTTCTCTTGAAAC-ATCATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
*
4234941 A
65 G
* *
4234942 TTTCTCTTGAAACAATCATCTTTGAGATTGTTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACA
1 TTTCTCTTGAAAC-ATCATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
4235007 G
65 G
* * * *
4235008 TTTCTCTTGAAACATCATATTTGAGATCGTTTCCCTTGAAACAAATTTTGTTTACCTTGAGATAG
1 TTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
* * *
4235073 TTTCTCTTGAAATATTATCTTTGAGATCGGTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
* * *
4235138 TTTCTCTTGAAACATCATATTTAAGATCGTTTCCCTTGAAACAAATTTTGTTTCCCTTGAGACAG
1 TTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
* * *
4235203 TTTCTCTTGAAACATTATCTTTGAGATCATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAG
1 TTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
4235268 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
4235283 TATCCCTAAA
Statistics
Matches: 409, Mismatches: 60, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
64 2 0.00
65 297 0.73
66 109 0.27
67 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (65 bp):
TTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
Found at i:4235618 original size:134 final size:130
Alignment explanation
Indices: 4235281--4235644 Score: 388
Period size: 131 Copynumber: 2.8 Consensus size: 130
4235271 CACTTGAAAC
* * * * * *
4235281 ATTATCCCTAAAGATGGCTAGCAGTCCTCATCGTGTAGAAACCATGTCATCCACCGACCAGATCT
1 ATTATCCCTAAAGATGGCCAGCCGTCCTCATCGCGTAGGAACCGTGTCATCCACCGACAAGATCT
* * * * * ** *
4235346 TCTCATCACGTAGGAGACACTTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCATGT
66 CCTCATCACGTAGGAG-CGCGTCACCCTTAGATAACCAGCCATCCTCATCACACACGAACCATGT
4235411 T
130 T
* ** * *
4235412 ATTATCCCTAAAGATGGCCAGCCATCCTCATTACGTAGGAACCGTGTCATCCCCCAACCAA-ATC
1 ATTATCCCTAAAGATGGCCAGCCGTCCTCATCGCGTAGGAACCGTGTCATCCACCGA-CAAGATC
* * * *
4235476 TCCTCATCACGTAAGAGTCGCGTCAACCTTAGATAACCAGTCATCCTCATCGCACACGAACCATG
65 TCCTCATCACGTAGGAG-CGCGTCACCCTTAGATAACCAGCCATCCTCATCACACACGAACCATG
4235541 TT
129 TT
* * * * *
4235543 ATCATCATCCTTAAAGATGGCCAACCGTCCTTATCGCGTAGGAACTGTGTCATCCACTGACAAGA
1 AT--T-ATCCCTAAAGATGGCCAGCCGTCCTCATCGCGTAGGAACCGTGTCATCCACCGACAAGA
* *
4235608 TCTCCTCATCAAGTAGGAGCTGTGTCACCCTTAGATA
63 TCTCCTCATCACGTAGGAGC-GCGTCACCCTTAGATA
4235645 GCCATACTTC
Statistics
Matches: 189, Mismatches: 38, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
131 106 0.56
132 2 0.01
133 5 0.03
134 76 0.40
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.24
Consensus pattern (130 bp):
ATTATCCCTAAAGATGGCCAGCCGTCCTCATCGCGTAGGAACCGTGTCATCCACCGACAAGATCT
CCTCATCACGTAGGAGCGCGTCACCCTTAGATAACCAGCCATCCTCATCACACACGAACCATGTT
Found at i:4237423 original size:20 final size:19
Alignment explanation
Indices: 4237398--4237438 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
4237388 TTTATGTAAA
*
4237398 TATATATTTATATATCATAT
1 TATATATGTATATATC-TAT
4237418 TATATATGTATATATCTAT
1 TATATATGTATATATCTAT
4237437 TA
1 TA
4237439 AATGTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (19 bp):
TATATATGTATATATCTAT
Found at i:4238072 original size:43 final size:43
Alignment explanation
Indices: 4238011--4238096 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
4238001 CGACAACGAG
4238011 TAAGCGATTAAGTACCAATTTTGGGCGCTGTGGGGTTTTTAAT
1 TAAGCGATTAAGTACCAATTTTGGGCGCTGTGGGGTTTTTAAT
4238054 TAAGCGATTAAGTACCAATTTTGGGCGCTGTGGGGTTTTTAAT
1 TAAGCGATTAAGTACCAATTTTGGGCGCTGTGGGGTTTTTAAT
4238097 CCTTCCCTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (43 bp):
TAAGCGATTAAGTACCAATTTTGGGCGCTGTGGGGTTTTTAAT
Found at i:4239909 original size:14 final size:14
Alignment explanation
Indices: 4239890--4239920 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4239880 ACTTGATCTA
*
4239890 AGTCAACCTGTTCG
1 AGTCAACCCGTTCG
4239904 AGTCAACCCGTTCG
1 AGTCAACCCGTTCG
4239918 AGT
1 AGT
4239921 TAACTCATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (14 bp):
AGTCAACCCGTTCG
Found at i:4244314 original size:29 final size:29
Alignment explanation
Indices: 4244279--4244337 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
4244269 CCAAAATTTT
*
4244279 ATTTGAAAATTATTAACCAAACTGAATTA
1 ATTTGAAAATTATTAACCAAACCGAATTA
*
4244308 ATTTGAAAATTATTAACTAAACCGAATTA
1 ATTTGAAAATTATTAACCAAACCGAATTA
4244337 A
1 A
4244338 CTGATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (29 bp):
ATTTGAAAATTATTAACCAAACCGAATTA
Found at i:4244455 original size:30 final size:30
Alignment explanation
Indices: 4244403--4244466 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
4244393 TTCGGTTCTG
* *
4244403 TTAAACGAACCAAATTTTATTTGAAAATTA
1 TTAAACGAACCAAAATTAATTTGAAAATTA
* *
4244433 TTAACCGAACTAAAATTAATTTGAAAATTA
1 TTAAACGAACCAAAATTAATTTGAAAATTA
4244463 TTAA
1 TTAA
4244467 GCAAACCGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (30 bp):
TTAAACGAACCAAAATTAATTTGAAAATTA
Found at i:4244456 original size:143 final size:140
Alignment explanation
Indices: 4244259--4244695 Score: 558
Period size: 142 Copynumber: 3.1 Consensus size: 140
4244249 AAAAAATTCG
*
4244259 GTTAATCGAACCAAAATTTTATTTGAAAATTATTAACCAAACTGAATTAATTTGAAAATTATTAA
1 GTTAATCGAACC-AAATTTTATTTGAAAATTATTAACCGAACTGAATTAATTTGAAAATTATTAA
* * *
4244324 CTAAACCGAATTAACTGATTTTTTTTTAAATATTATTAACCAAATTAATCAAAACAAAATTTTGG
65 C-AAACCGAATTAACCGATTTTTTTTTAAA-ATTATTAACCAAATTAATCAAAACAAAAATTCGG
4244389 TTAATTCGGTTCT
128 TTAATTCGGTTCT
* *
4244402 GTTAAACGAACCAAATTTTATTTGAAAATTATTAACCGAACTAAAATTAATTTGAAAATTATTAA
1 GTTAATCGAACCAAATTTTATTTGAAAATTATTAACCGAACT-GAATTAATTTGAAAATTATTAA
* * * * **
4244467 GCAAACCGAAATAACCGATTTTTTTTTTAAATTATTAACCCAATTAATCGATGCAAAAATTCGGT
65 -CAAACCGAATTAACCGATTTTTTTTTAAAATTATTAACCAAATTAATCAAAACAAAAATTCGGT
*
4244532 TAATTTGGTTCT
129 TAATTCGGTTCT
* *
4244544 GTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGATCTGAATTAATTTGAAAATTATTAAC
1 GTTAATCGAACCAAATTTTATTTGAAAATTATTAACCGAACTGAATTAATTTGAAAATTATTAA-
* * * * * * **
4244609 CGAACCAAATTAACCGA---ATTTTTAAAATTATTAA-CGAATTAGTCAAAGCAAAAATTCTATT
65 CAAACCGAATTAACCGATTTTTTTTTAAAATTATTAACCAAATTAATCAAAACAAAAATTCGGTT
* *
4244670 AATTCAGTTCA
130 AATTCGGTTCT
*
4244681 GTTAATCAAACCAAA
1 GTTAATCGAACCAAA
4244696 ATTCTGTTAA
Statistics
Matches: 259, Mismatches: 33, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
137 43 0.17
138 15 0.06
141 35 0.14
142 108 0.42
143 57 0.22
144 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.36
Consensus pattern (140 bp):
GTTAATCGAACCAAATTTTATTTGAAAATTATTAACCGAACTGAATTAATTTGAAAATTATTAAC
AAACCGAATTAACCGATTTTTTTTTAAAATTATTAACCAAATTAATCAAAACAAAAATTCGGTTA
ATTCGGTTCT
Found at i:4244619 original size:29 final size:29
Alignment explanation
Indices: 4244545--4244621 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
4244535 TTTGGTTCTG
* *
4244545 TTAATCGAACCAAAATTTATTTGAAAATTA
1 TTAACCGAACC-AAATTAATTTGAAAATTA
* **
4244575 TTAACCGATCTGAATTAATTTGAAAATTA
1 TTAACCGAACCAAATTAATTTGAAAATTA
4244604 TTAACCGAACCAAATTAA
1 TTAACCGAACCAAATTAA
4244622 CCGAATTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 31 0.79
30 8 0.21
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34
Consensus pattern (29 bp):
TTAACCGAACCAAATTAATTTGAAAATTA
Found at i:4244919 original size:30 final size:29
Alignment explanation
Indices: 4244884--4244949 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
4244874 ATTAATGGCC
*
4244884 GGTGGTTTGATTGAATCAATTAAATAGTTG
1 GGTGGTCTGATTGAATCAATTAAA-AGTTG
* * *
4244914 GGTGGTCTGATTGATTCAATTGAAAGTTT
1 GGTGGTCTGATTGAATCAATTAAAAGTTG
4244943 GGTGGTC
1 GGTGGTC
4244950 ACATTGCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 11 0.34
30 21 0.66
ACGTcount: A:0.24, C:0.06, G:0.30, T:0.39
Consensus pattern (29 bp):
GGTGGTCTGATTGAATCAATTAAAAGTTG
Found at i:4244955 original size:29 final size:30
Alignment explanation
Indices: 4244893--4244955 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
4244883 CGGTGGTTTG
**
4244893 ATTGAATCAATTAAATAGTTGGGTGGTCTG
1 ATTGAATCAATTAAATAGTTGGGTGGTCAC
* * *
4244923 ATTGATTCAATTGAA-AGTTTGGTGGTCAC
1 ATTGAATCAATTAAATAGTTGGGTGGTCAC
4244952 ATTG
1 ATTG
4244956 CTTTTTTACC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.29, C:0.08, G:0.25, T:0.38
Consensus pattern (30 bp):
ATTGAATCAATTAAATAGTTGGGTGGTCAC
Found at i:4248928 original size:20 final size:19
Alignment explanation
Indices: 4248884--4248930 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
4248874 TAAATTAGAA
4248884 TTAAATAATTTCATAATAT
1 TTAAATAATTTCATAATAT
*
4248903 TATAAATATTTATCATTAA-AT
1 T-TAAATAATT-TCA-TAATAT
4248924 TTAAATA
1 TTAAATA
4248931 GAAACTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 14 0.58
21 6 0.25
22 3 0.12
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAATAATTTCATAATAT
Found at i:4249149 original size:3 final size:3
Alignment explanation
Indices: 4249141--4249212 Score: 110
Period size: 3 Copynumber: 24.3 Consensus size: 3
4249131 CAATCTACCC
*
4249141 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
4249189 TAT TA- TAT TAT AAA TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
4249213 TACAAACCAA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
2 2 0.03
3 60 0.97
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:4249285 original size:24 final size:25
Alignment explanation
Indices: 4249257--4249314 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
4249247 GAAATAACGA
*
4249257 AAAACCCAG-GCCCCTTTACAAAGT
1 AAAACCCAGAGCCCCTTTACAAAAT
* *
4249281 GAAACCC-GAGCCCCTTTATAAAAT
1 AAAACCCAGAGCCCCTTTACAAAAT
4249305 AAAACCCAGA
1 AAAACCCAGA
4249315 CTCGGAGCCC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.04
24 25 0.89
25 2 0.07
ACGTcount: A:0.41, C:0.31, G:0.12, T:0.16
Consensus pattern (25 bp):
AAAACCCAGAGCCCCTTTACAAAAT
Found at i:4253135 original size:62 final size:62
Alignment explanation
Indices: 4253059--4253186 Score: 256
Period size: 62 Copynumber: 2.1 Consensus size: 62
4253049 TAAATAGTGA
4253059 AAATGGTAAAATTTCAAGTAAAGATGGATGAAGATAAGCCACATGATCATTTCAAAAGGGGT
1 AAATGGTAAAATTTCAAGTAAAGATGGATGAAGATAAGCCACATGATCATTTCAAAAGGGGT
4253121 AAATGGTAAAATTTCAAGTAAAGATGGATGAAGATAAGCCACATGATCATTTCAAAAGGGGT
1 AAATGGTAAAATTTCAAGTAAAGATGGATGAAGATAAGCCACATGATCATTTCAAAAGGGGT
4253183 AAAT
1 AAAT
4253187 TCGTGTTCCT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.24
Consensus pattern (62 bp):
AAATGGTAAAATTTCAAGTAAAGATGGATGAAGATAAGCCACATGATCATTTCAAAAGGGGT
Found at i:4259243 original size:50 final size:50
Alignment explanation
Indices: 4259165--4259272 Score: 198
Period size: 50 Copynumber: 2.2 Consensus size: 50
4259155 TGATGAACCC
*
4259165 TTCAGCTAGCCCGATAAAGGCGATTATAATATATATACAATAAAGCTGAA
1 TTCAGCTAGCCCGATAAAGGCAATTATAATATATATACAATAAAGCTGAA
*
4259215 TTTAGCTAGCCCGATAAAGGCAATTATAATATATATACAATAAAGCTGAA
1 TTCAGCTAGCCCGATAAAGGCAATTATAATATATATACAATAAAGCTGAA
4259265 TTCAGCTA
1 TTCAGCTA
4259273 ACCAAACAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.28
Consensus pattern (50 bp):
TTCAGCTAGCCCGATAAAGGCAATTATAATATATATACAATAAAGCTGAA
Found at i:4259287 original size:50 final size:51
Alignment explanation
Indices: 4259187--4259295 Score: 150
Period size: 50 Copynumber: 2.2 Consensus size: 51
4259177 GATAAAGGCG
* * ** *
4259187 ATTATAATATATATACAATAAAGCTGAATTTAGCTAGCCCGATAAAGGC-A
1 ATTATAATATATATACAATAAAGCTGAATTCAGCTAACCAAACAAAGGCAA
*
4259237 ATTATAATATATATACAATAAAGCTGAATTCAGCTAACCAAACAATGGCAA
1 ATTATAATATATATACAATAAAGCTGAATTCAGCTAACCAAACAAAGGCAA
4259288 ATTA-AATA
1 ATTATAATA
4259296 AAATTTATGT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 47 0.90
51 5 0.10
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.28
Consensus pattern (51 bp):
ATTATAATATATATACAATAAAGCTGAATTCAGCTAACCAAACAAAGGCAA
Found at i:4261097 original size:42 final size:42
Alignment explanation
Indices: 4261008--4261097 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
4260998 AGTTCTTTGA
* * *
4261008 GCCATAAGTAAGTCTTTTGAGCATGATGTTTAAGTCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAGTCCTTCGG
*
4261050 GCCATCAGTAGGTCTTTCGAGCATGATGCTTAAGTCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAGTCCTTCGG
4261092 GCCATC
1 GCCATC
4261098 CATAAGCCCT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.32
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAGTCCTTCGG
Found at i:4261404 original size:239 final size:240
Alignment explanation
Indices: 4261016--4261488 Score: 756
Period size: 239 Copynumber: 2.0 Consensus size: 240
4261006 GAGCCATAAG
* * *
4261016 TAAGTCTTTTGAGCATGATGTTTAAGTCCTTCGGGCCATCAGTAGGTCTTTCGAGCATGATGCTT
1 TAAGTCATTTGAGCATGATGTTTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTT
** * *
4261081 AAGTCCTTCGGGCCATCCATAAGCCCTTCGGCTAGGATGTTTTCACATGATTTTTGGAAATGAGA
66 AAGTCCTTAAGGCCATCCATAAGCCCTTCGGCTAGGATGTTATCACATGATTTTTGAAAATGAGA
*
4261146 AAACAATTTTAATGTTTCTCATTTAAATCTTTTCTGAAAATTGA-TTTTT-TTGAAAAGTAAGAA
131 AAACAATTTTAAAGTTTCTCATTTAAATCTTTTCTGAAAATT-ATTTTTTCTTGAAAAGTAAGAA
4261209 AATGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGGCTATTTA
195 AATGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGGCTATTTA
* *
4261255 TAAGTCATTTGAGCATGATGTTTAAGTCATTTGGGCCATCAGTAAGTCTTTCGAGCATGGTGCTT
1 TAAGTCATTTGAGCATGATGTTTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTT
* * *
4261320 AAGTTCTTAAGGCTATCCATAAGGCCTTCGGGC-AGGATGTTATCACATGA-TTTTGAAAATGAG
66 AAGTCCTTAAGGCCATCCATAAGCCCTTC-GGCTAGGATGTTATCACATGATTTTTGAAAATGAG
* *
4261383 AAAGCGATTTTCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTATTTTTTCTTGAAAAGTAAGA
130 AAAACAATTTT-AAAGTTTCTCATTTAAATCTTTTCTGAAAATTATTTTTTCTTGAAAAGTAAGA
4261448 AAATGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGGC
194 AAATGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGGC
4261489 CATCAGTAAG
Statistics
Matches: 215, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
238 22 0.10
239 136 0.63
240 57 0.27
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (240 bp):
TAAGTCATTTGAGCATGATGTTTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTT
AAGTCCTTAAGGCCATCCATAAGCCCTTCGGCTAGGATGTTATCACATGATTTTTGAAAATGAGA
AAACAATTTTAAAGTTTCTCATTTAAATCTTTTCTGAAAATTATTTTTTCTTGAAAAGTAAGAAA
ATGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGGCTATTTA
Found at i:4261657 original size:58 final size:60
Alignment explanation
Indices: 4261570--4261693 Score: 175
Period size: 58 Copynumber: 2.1 Consensus size: 60
4261560 CGCAGGGCCC
* *
4261570 AAAATATAGGGCCCCCGAAATCTAGTATATCTATCAATTGTTGCCATTAA-AATGCCCCAA
1 AAAATATAGGGCCCCCGAAATCTAGTATATCTATCAATTATTGCCATTAAGAA-GCCCAAA
*
4261630 AAAATAT-GGG-CCCCGAAAT-TGAGTATATCTATCAGTTATTGCCATTAAGAAGCCCAAA
1 AAAATATAGGGCCCCCGAAATCT-AGTATATCTATCAATTATTGCCATTAAGAAGCCCAAA
4261688 AAAATA
1 AAAATA
4261694 GAGGCCCTAA
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
57 1 0.02
58 46 0.78
59 5 0.08
60 7 0.12
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.26
Consensus pattern (60 bp):
AAAATATAGGGCCCCCGAAATCTAGTATATCTATCAATTATTGCCATTAAGAAGCCCAAA
Found at i:4262490 original size:23 final size:23
Alignment explanation
Indices: 4262450--4262493 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
4262440 CAATATACCC
* *
4262450 TTATATTATTATTATTATTATAT
1 TTATATTATAAATATTATTATAT
*
4262473 TTATATTATAAATCTTATTAT
1 TTATATTATAAATATTATTAT
4262494 TTATAAACCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TTATATTATAAATATTATTATAT
Found at i:4265285 original size:17 final size:17
Alignment explanation
Indices: 4265263--4265295 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4265253 AGTTTTGGTA
*
4265263 AAAATATATTAAATAAT
1 AAAATAGATTAAATAAT
4265280 AAAATAGATTAAATAA
1 AAAATAGATTAAATAA
4265296 AAGTCAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
AAAATAGATTAAATAAT
Found at i:4269657 original size:19 final size:21
Alignment explanation
Indices: 4269614--4269665 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
4269604 GAAACCCCTT
*
4269614 TGAAAATAAATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
4269635 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
4269654 TGAAGATACATG
1 TGAAAATACATG
4269666 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:4272649 original size:8 final size:8
Alignment explanation
Indices: 4272638--4272735 Score: 139
Period size: 8 Copynumber: 12.1 Consensus size: 8
4272628 TCTTTTTCTT
4272638 TTCTTTTC
1 TTCTTTTC
4272646 TTCTTTTC
1 TTCTTTTC
4272654 TT-TTTTC
1 TTCTTTTC
4272661 TTCTTTTC
1 TTCTTTTC
4272669 TTCTTTTC
1 TTCTTTTC
4272677 TTC-TTTC
1 TTCTTTTC
4272684 TTC-TTTC
1 TTCTTTTC
4272691 TTCTTTTC
1 TTCTTTTC
4272699 TTTCTTCTTC
1 -TTCTT-TTC
4272709 TTTTCTTTTC
1 --TTCTTTTC
4272719 TTCTTTTC
1 TTCTTTTC
4272727 TTCTTTTC
1 TTCTTTTC
4272735 T
1 T
4272736 GATTTTTTTA
Statistics
Matches: 85, Mismatches: 0, Indels: 10
0.89 0.00 0.11
Matches are distributed among these distances:
7 21 0.25
8 47 0.55
9 5 0.06
10 6 0.07
11 6 0.07
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:4272661 original size:15 final size:15
Alignment explanation
Indices: 4272633--4272735 Score: 135
Period size: 15 Copynumber: 7.1 Consensus size: 15
4272623 CTTTCTCTTT
4272633 TTCTTTTC--TTTTC
1 TTCTTTTCTTTTTTC
4272646 TTCTTTTCTTTTTTC
1 TTCTTTTCTTTTTTC
4272661 TTCTTTTCTTCTTTTC
1 TTCTTTTCTT-TTTTC
*
4272677 TTC-TTTCTTCTTTC
1 TTCTTTTCTTTTTTC
*
4272691 TTCTTTTCTTTCTTC
1 TTCTTTTCTTTTTTC
4272706 TTCTTTTC--TTTTC
1 TTCTTTTCTTTTTTC
4272719 TTCTTTTCTTCTTTTC
1 TTCTTTTCTT-TTTTC
4272735 T
1 T
4272736 GATTTTTTTA
Statistics
Matches: 79, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
13 20 0.25
14 7 0.09
15 38 0.48
16 14 0.18
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTTTTCTTTTTTC
Found at i:4272664 original size:23 final size:23
Alignment explanation
Indices: 4272623--4272735 Score: 144
Period size: 23 Copynumber: 5.0 Consensus size: 23
4272613 ACTTGGCTTG
*
4272623 CTTTCTCTTTTTCTTTTCTTTTCTT
1 CTTT-TCTTTTT-TCTTCTTTTCTT
4272648 CTTTTCTTTTTTCTTCTTTTCTT
1 CTTTTCTTTTTTCTTCTTTTCTT
*
4272671 CTTTTCTTCTTTCTTC-TTTCTT
1 CTTTTCTTTTTTCTTCTTTTCTT
*
4272693 CTTTTCTTTCTTCTTC--TT-TT
1 CTTTTCTTTTTTCTTCTTTTCTT
4272713 CTTTTCTTCTTTTCTTCTTTTCT
1 CTTTTCTT-TTTTCTTCTTTTCT
4272736 GATTTTTTTA
Statistics
Matches: 79, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.13
21 9 0.11
22 20 0.25
23 28 0.35
24 8 0.10
25 4 0.05
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (23 bp):
CTTTTCTTTTTTCTTCTTTTCTT
Found at i:4272682 original size:50 final size:49
Alignment explanation
Indices: 4272624--4272733 Score: 147
Period size: 50 Copynumber: 2.2 Consensus size: 49
4272614 CTTGGCTTGC
4272624 TTTC-TCTTTTTCTTTTCTT-TTCTTCTTTTCTT-TT-TTCTTCTTTTCTTCT
1 TTTCTTCTTTTTC-TTTCTTCTT-TTC-TTTCTTCTTCTT-TTCTTTTCTTCT
4272673 TTTCTTCTTTCTTCTTTCTTCTTTTCTTTCTTCTTCTTTTCTTTTCTTCT
1 TTTCTTCTTT-TTCTTTCTTCTTTTCTTTCTTCTTCTTTTCTTTTCTTCT
4272723 TTTCTTCTTTT
1 TTTCTTCTTTT
4272734 CTGATTTTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
49 11 0.20
50 38 0.68
51 7 0.12
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (49 bp):
TTTCTTCTTTTTCTTTCTTCTTTTCTTTCTTCTTCTTTTCTTTTCTTCT
Found at i:4272752 original size:45 final size:42
Alignment explanation
Indices: 4272638--4272771 Score: 127
Period size: 45 Copynumber: 3.2 Consensus size: 42
4272628 TCTTTTTCTT
*
4272638 TTCTTTTCTTCTTTTCTTTTTTCTTCTT-TTC-T-TCTTTTC
1 TTCTTTTCTTCTTTTCTTTTTTTTTCTTCTTCTTCTCTTTTC
*
4272677 TTC-TTTCTTC-TTTCTTCTTTTCTTTCTTCTTCTTTTCTTTTC
1 TTCTTTTCTTCTTTTCTT-TTTT-TTTCTTCTTCTTCTCTTTTC
* *
4272719 TTCTTTTCTTCTTTTCTGATTTTTTTATATTCTT-TTGTCTTTTTC
1 TTCTTTTCTTCTTTTCT--TTTTTTT-TCTTCTTCTTCTC-TTTTC
4272764 TTTCTTTT
1 -TTCTTTT
4272772 TGCACTCCAA
Statistics
Matches: 80, Mismatches: 3, Indels: 17
0.80 0.03 0.17
Matches are distributed among these distances:
37 6 0.08
38 11 0.14
39 8 0.10
40 3 0.04
41 1 0.01
42 10 0.12
43 7 0.09
44 11 0.14
45 15 0.19
46 8 0.10
ACGTcount: A:0.02, C:0.21, G:0.01, T:0.75
Consensus pattern (42 bp):
TTCTTTTCTTCTTTTCTTTTTTTTTCTTCTTCTTCTCTTTTC
Found at i:4272765 original size:42 final size:38
Alignment explanation
Indices: 4272637--4272766 Score: 95
Period size: 43 Copynumber: 3.2 Consensus size: 38
4272627 CTCTTTTTCT
* * *
4272637 TTTCTTTTCTTCTTTTCTTTTTTCTTCTT-TTCTTC-T
1 TTTCTTTTCTTCTTTTCTTTTTTTTTATTCTTTTTCTT
*
4272673 TTTCTTCTTTCTTC-TTTCTTCTTTTCTTTCTTCTTCTTTTCTTT
1 TTTC-T-TTTCTTCTTTTCTT-TTTT-TTTATTC-T-TTTTC-TT
4272717 TCTTCTTTTCTTCTTTTCTGATTTTTTTATATTCTTTTGTCTT
1 T-TTCTTTTCTTCTTTTCT--TTTTTTT-TATTCTTTT-TCTT
4272760 TTTCTTT
1 TTTCTTT
4272767 CTTTTTGCAC
Statistics
Matches: 76, Mismatches: 3, Indels: 24
0.74 0.03 0.23
Matches are distributed among these distances:
36 4 0.05
37 7 0.09
38 11 0.14
39 5 0.07
41 1 0.01
42 10 0.13
43 13 0.17
44 13 0.17
45 11 0.14
46 1 0.01
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (38 bp):
TTTCTTTTCTTCTTTTCTTTTTTTTTATTCTTTTTCTT
Found at i:4273516 original size:19 final size:21
Alignment explanation
Indices: 4273473--4273524 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
4273463 GAAACCCCTT
4273473 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
4273494 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
4273513 TGAAGATACATG
1 TGAAAATACATG
4273525 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:4274567 original size:20 final size:20
Alignment explanation
Indices: 4274542--4274675 Score: 144
Period size: 20 Copynumber: 6.7 Consensus size: 20
4274532 AATTGGGAAA
*
4274542 ATCGCATTGCGATACTGACT
1 ATCGCAATGCGATACTGACT
4274562 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
4274582 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
4274602 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
4274623 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
4274643 TTCGCAATGCGATTCTTACT
1 ATCGCAATGCGATACTGACT
* *
4274663 TTCGCAACGCGAT
1 ATCGCAATGCGAT
4274676 TTTAGCGCCA
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.02
20 80 0.82
21 13 0.13
22 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:4274648 original size:41 final size:40
Alignment explanation
Indices: 4274552--4274655 Score: 129
Period size: 41 Copynumber: 2.6 Consensus size: 40
4274542 ATCGCATTGC
* * * *
4274552 GATACTGACTATCGCAATGCGATACTGACTATCGCAATGC
1 GATACTGACTATCGCAATGCGATAATGACAATCGCAACGA
*
4274592 GATACTTACTATCGCAATGCGATAAT-ACAAAATCGCAACGA
1 GATACTGACTATCGCAATGCGATAATGAC--AATCGCAACGA
*
4274633 GATACTGACTTTCGCAATGCGAT
1 GATACTGACTATCGCAATGCGAT
4274656 TCTTACTTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
39 2 0.04
40 24 0.44
41 29 0.53
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (40 bp):
GATACTGACTATCGCAATGCGATAATGACAATCGCAACGA
Found at i:4275218 original size:19 final size:19
Alignment explanation
Indices: 4275178--4275222 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
4275168 GCAACGAGAG
*
4275178 AATCGCAACGCGAAATACA
1 AATCGCAACGCGAAACACA
4275197 AATCGCAACGCGAAAC-CAA
1 AATCGCAACGCGAAACAC-A
4275216 AATCGCA
1 AATCGCA
4275223 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACACA
Found at i:4275288 original size:52 final size:52
Alignment explanation
Indices: 4275218--4275334 Score: 171
Period size: 52 Copynumber: 2.2 Consensus size: 52
4275208 GAAACCAAAA
* ** **
4275218 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATT
*
4275270 TCGCGTTGCGATAGTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATAGTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATT
4275322 TCCGCGTTGCGAT
1 T-CGCGTTGCGAT
4275335 TCTCATTATC
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
52 47 0.81
53 11 0.19
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.41
Consensus pattern (52 bp):
TCGCGTTGCGATAGTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATT
Found at i:4275310 original size:33 final size:34
Alignment explanation
Indices: 4275273--4275338 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
4275263 TTTCATTTCG
4275273 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
4275306 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
4275339 ATTATCTCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 17 0.53
34 15 0.47
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.38
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:4275340 original size:20 final size:19
Alignment explanation
Indices: 4275218--4275363 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
4275208 GAAACCAAAA
* *
4275218 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
*
4275237 TCGCATTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
*
4275253 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
**
4275270 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
4275289 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
4275305 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
4275322 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTCTCATT
* *
4275342 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTCTCATT
4275362 TC
1 TC
4275364 AACCAAAAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
14 22 0.22
16 2 0.02
17 2 0.02
19 45 0.44
20 30 0.29
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTCTCATT
Found at i:4278629 original size:18 final size:18
Alignment explanation
Indices: 4278608--4278642 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4278598 TTCCATTCGG
*
4278608 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
4278626 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
4278643 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:4283786 original size:18 final size:18
Alignment explanation
Indices: 4283765--4283799 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4283755 TTCCATTCGG
*
4283765 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
4283783 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
4283800 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:4287163 original size:42 final size:41
Alignment explanation
Indices: 4287087--4287289 Score: 183
Period size: 42 Copynumber: 4.8 Consensus size: 41
4287077 AACTCGCCTG
* * * * * *
4287087 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCC-CTCCCACCGTTCAAGAGGCCACTA
*
4287129 TCATTCCTCGAGAGTCTCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTC-CCTCCCACCGTTCAAGAGGCCACTA
* * * * * * *
4287171 TCATCCCTCAAGATTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCC-CTCCCACCGTTCAAGAGGCCACTA
*
4287213 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGT-CCCTCCCACCGTTCAAGAGGCCACTA
* * *
4287255 TCA-TCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCTCCCACCGTTCAAGAG
4287290 CCGATTCACA
Statistics
Matches: 130, Mismatches: 26, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
41 5 0.04
42 120 0.92
43 5 0.04
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (41 bp):
TCATTCCTCGAGAGTCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:4287225 original size:84 final size:84
Alignment explanation
Indices: 4287084--4287259 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
4287074 CCCAACTCGC
*
4287084 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCTCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
4287149 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
*
4287168 CTGTCATCCCTCAAGATTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
4287233 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
4287252 CTGTCATC
1 CTGTCATC
4287260 GTTGAAGAGG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:4287247 original size:21 final size:21
Alignment explanation
Indices: 4287223--4287289 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
4287213 TCATTCCTCG
4287223 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
4287244 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
4287265 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
4287286 AGAG
1 AGAG
4287290 CCGATTCACA
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:4287289 original size:84 final size:84
Alignment explanation
Indices: 4287084--4287289 Score: 279
Period size: 84 Copynumber: 2.5 Consensus size: 84
4287074 CCCAACTCGC
* * * * *
4287084 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCTCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
4287149 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * * *
4287168 CTGTCATCCCTCAAGATTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
4287233 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** *
4287252 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
4287290 CCGATTCACA
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
84 108 0.97
85 3 0.03
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:4288790 original size:19 final size:18
Alignment explanation
Indices: 4288766--4288820 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 18
4288756 AAAAAGTACT
4288766 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
4288785 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
4288799 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
4288818 ATC
1 ATC
4288821 ACAACGAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 10 0.34
15 1 0.03
16 2 0.07
17 2 0.07
18 1 0.03
19 13 0.45
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:4288811 original size:33 final size:33
Alignment explanation
Indices: 4288766--4288855 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
4288756 AAAAAGTACT
*
4288766 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
4288799 ATCGCAACGCGAAATGAAAATCACAACGAGATA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
4288832 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
4288856 GTTGCGATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.44, C:0.21, G:0.20, T:0.14
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:4288894 original size:33 final size:33
Alignment explanation
Indices: 4288848--4288944 Score: 142
Period size: 33 Copynumber: 2.9 Consensus size: 33
4288838 ACGCGAAATT
4288848 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
* *
4288881 AAATTAGCATTGCGATTTTCATTTCGCATTGCG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
* *
4288914 -ATTCTCTCGTTGCGATTTTCATTTCGCATTG
1 AAAT-TCGCGTTGCGATTTTCATTTCGCATTG
4288945 TGATAGTAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (33 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
Found at i:4288911 original size:19 final size:19
Alignment explanation
Indices: 4288851--4288944 Score: 82
Period size: 19 Copynumber: 5.5 Consensus size: 19
4288841 CGAAATTAAA
*
4288851 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
4288870 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
*
4288884 TTAGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
4288903 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
4288919 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
4288936 TTCGCATTG
1 TTCGCATTG
4288945 TGATAGTAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 18 0.31
16 7 0.12
17 7 0.12
19 26 0.45
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:4291219 original size:12 final size:12
Alignment explanation
Indices: 4291202--4291226 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4291192 TCTTCGGGGA
4291202 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4291214 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4291226 C
1 C
4291227 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:4292221 original size:20 final size:20
Alignment explanation
Indices: 4292196--4292266 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
4292186 TGTATTATCT
4292196 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
4292216 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
* *
4292236 CGTTTCGAAATTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
4292256 TGTTGCGAAAG
1 CGTTGCGAAAG
4292267 GCAATCATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:4292573 original size:19 final size:19
Alignment explanation
Indices: 4292546--4292598 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
4292536 GCATTGCGAT
*
4292546 TTTCTCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
4292565 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
4292584 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
4292599 CTCTCGTTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.49
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:4292585 original size:12 final size:14
Alignment explanation
Indices: 4292537--4292563 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4292527 ATGAAAATCG
4292537 CATTGCGATTTTCT
1 CATTGCGATTTTCT
4292551 CATTGCGATTTTC
1 CATTGCGATTTTC
4292564 ATTTCGCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (14 bp):
CATTGCGATTTTCT
Found at i:4292744 original size:14 final size:14
Alignment explanation
Indices: 4292725--4292761 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4292715 CATCAATTAA
4292725 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
4292739 ACAAATCATCTTTT
1 ACAAATCAACATTT
4292753 ACAAATCAA
1 ACAAATCAA
4292762 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:4294647 original size:20 final size:19
Alignment explanation
Indices: 4294624--4294691 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
4294614 GAAACTTAAA
4294624 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
4294644 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
4294664 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
4294683 ATCGCAACG
1 ATCGCAACG
4294692 ACAAAATTGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:4294703 original size:14 final size:14
Alignment explanation
Indices: 4294680--4294737 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
4294670 ATGCGAAATG
4294680 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
4294694 AAAATTGCAATGCGAAAT
1 AAAATCGCAA--CG--AC
4294712 AAAATCGCAACGAC
1 AAAATCGCAACGAC
4294726 AAAATCGCAACG
1 AAAATCGCAACG
4294738 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:4294721 original size:32 final size:32
Alignment explanation
Indices: 4294664--4294753 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
4294654 GGAAATGGCT
4294664 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAAT-AAAATCGCAACGACAAA
*
4294697 ATTGCAATGCGAAATAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAATCGCAACGACAAA
* *
4294729 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAATGCGAAATA-AAATCGCA
4294754 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 30 0.58
33 22 0.42
ACGTcount: A:0.48, C:0.23, G:0.17, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATAAAATCGCAACGACAAA
Found at i:4294790 original size:14 final size:14
Alignment explanation
Indices: 4294771--4294828 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
4294761 TTTCATTTCG
4294771 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
4294785 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
4294801 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
4294817 CGTTGCGATTTT
1 CGTTGCGATTTT
4294829 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:4294835 original size:33 final size:33
Alignment explanation
Indices: 4294754--4294844 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
4294744 ACAAATCGCA
*
4294754 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
4294787 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
4294819 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
4294845 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:4294851 original size:19 final size:19
Alignment explanation
Indices: 4294829--4294872 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
4294819 TTGCGATTTT
4294829 CATTTCGCA-TTGCGATAGC
1 CATTTC-CACTTGCGATAGC
*
4294848 CATTTCCACGTTGCGATAGT
1 CATTTCCAC-TTGCGATAGC
4294868 CATTT
1 CATTT
4294873 TTGTGTTGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 14 0.64
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (19 bp):
CATTTCCACTTGCGATAGC
Found at i:4295385 original size:18 final size:18
Alignment explanation
Indices: 4295359--4295403 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
4295349 GTCGATCAGA
*
4295359 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
4295377 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
4295395 TGATGGCTC
1 TGATGGCTC
4295404 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:4296558 original size:25 final size:26
Alignment explanation
Indices: 4296529--4296585 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
4296519 TACAAAAACA
*
4296529 AAAAACATACTA-AGT-TAGATATACC
1 AAAAACATAC-ACAGTGAAGATATACC
*
4296554 AAAAAC-TACACTGTGAAGATATACC
1 AAAAACATACACAGTGAAGATATACC
4296579 AAAAACA
1 AAAAACA
4296586 ATAATAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.04
24 5 0.19
25 21 0.78
ACGTcount: A:0.54, C:0.18, G:0.09, T:0.19
Consensus pattern (26 bp):
AAAAACATACACAGTGAAGATATACC
Found at i:4296770 original size:20 final size:20
Alignment explanation
Indices: 4296722--4296780 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
4296712 AATAGTTTCT
** *
4296722 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
4296742 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
4296762 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
4296781 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:4297364 original size:20 final size:20
Alignment explanation
Indices: 4297255--4297389 Score: 94
Period size: 20 Copynumber: 6.7 Consensus size: 20
4297245 AGCTTTGAAA
*
4297255 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTAAGT
* * * *
4297276 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTAAGT
* * *
4297296 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
4297316 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
4297337 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* *
4297357 ATCACATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTAAGT
4297377 ATCGCATTGCGAT
1 ATCGCATTGCGAT
4297390 TTTCCCAATT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.05
20 64 0.68
21 23 0.24
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:4297367 original size:61 final size:61
Alignment explanation
Indices: 4297255--4297392 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
4297245 AGCTTTGAAA
* * * * *
4297255 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCACATTGCGAAAGTCAGT
* * * * *
4297316 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCACATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCACATTGCGAAAGTCAGT
4297377 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
4297393 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCACATTGCGAAAGTCAGT
Found at i:4297422 original size:20 final size:21
Alignment explanation
Indices: 4297378--4297429 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
4297368 ATAGTCAGTA
*
4297378 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
**
4297399 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
4297419 TCGCATTGCGA
1 TCGCATTGCGA
4297430 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:4301616 original size:26 final size:26
Alignment explanation
Indices: 4301575--4301626 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
4301565 CCAGAAGGCG
* *
4301575 CGCTGACTATATCTTCTAGAAACTGC
1 CGCTGACTAGACCTTCTAGAAACTGC
4301601 CGCTGACTAGACCTTCTAGAAACTGC
1 CGCTGACTAGACCTTCTAGAAACTGC
4301627 TATGTCAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (26 bp):
CGCTGACTAGACCTTCTAGAAACTGC
Found at i:4304149 original size:40 final size:40
Alignment explanation
Indices: 4304080--4304167 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 40
4304070 ATTGGAGAGG
* * * * *
4304080 TTCTAGAAAATTCTAGAGCTTTCTGGAGAAGTGTAGAATT
1 TTCTAGAAAATTCCAGAGATCTCTAGAGAAGTGTAGAACT
*
4304120 TTCTAGAACATTCCAGAGATCTCTAGAGAAGTGTAGAACT
1 TTCTAGAAAATTCCAGAGATCTCTAGAGAAGTGTAGAACT
*
4304160 CTCTAGAA
1 TTCTAGAA
4304168 GCTTGTGGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (40 bp):
TTCTAGAAAATTCCAGAGATCTCTAGAGAAGTGTAGAACT
Found at i:4305848 original size:19 final size:20
Alignment explanation
Indices: 4305805--4305848 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
4305795 TTGCTATTTG
*
4305805 AAAAAAAACAAAAAAAAGGC
1 AAAAAAAACAAAAAAAACGC
*
4305825 AAAAAAAA-AATAAAAACGCC
1 AAAAAAAACAAAAAAAACG-C
4305845 AAAA
1 AAAA
4305849 TTTCAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.80, C:0.11, G:0.07, T:0.02
Consensus pattern (20 bp):
AAAAAAAACAAAAAAAACGC
Found at i:4321749 original size:23 final size:22
Alignment explanation
Indices: 4321705--4321749 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4321695 AATGTCATGG
*
4321705 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
4321727 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
4321750 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:4323234 original size:121 final size:121
Alignment explanation
Indices: 4323070--4323433 Score: 613
Period size: 121 Copynumber: 3.0 Consensus size: 121
4323060 CGAGGGTCTA
* *
4323070 TGTGTTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* *
4323135 GATCCCTAGTATATGTATATGATTCTTAAAGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCAGGACAT
* *
4323191 TTTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACAT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* * * *
4323256 GATCCTTGGCATATGTATATGATTCTTAAGGAATGATATGTGGTCTTTCAGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCAGGACAT
*
4323312 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
4323377 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTT-ATGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCA-GGACAT
4323433 T
1 T
4323434 ATTATATGGC
Statistics
Matches: 225, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
120 1 0.00
121 224 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCAGGACAT
Done.