Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005506.1 Hibiscus syriacus cultivar Beakdansim tig00012696_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: 200244
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:128820 original size:16 final size:17
Alignment explanation
Indices: 128780--128822 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
128770 AAGGGGAACG
128780 AATGAAAGAAATGTAAA
1 AATGAAAGAAATGTAAA
128797 AAT-AAAGAAATGT-AA
1 AATGAAAGAAATGTAAA
*
128812 AATGTAAGAAA
1 AATGAAAGAAA
128823 AATGATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 16 0.67
17 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (17 bp):
AATGAAAGAAATGTAAA
Found at i:137870 original size:11 final size:11
Alignment explanation
Indices: 137854--137886 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
137844 TCTTAGCCAT
137854 TAGATCCAATA
1 TAGATCCAATA
*
137865 TAGATCCAATC
1 TAGATCCAATA
137876 TAGATCCAATA
1 TAGATCCAATA
137887 ATTGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (11 bp):
TAGATCCAATA
Found at i:138226 original size:14 final size:14
Alignment explanation
Indices: 138207--138235 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
138197 GGGTTTTTTG
138207 TTTTATTTATTTAT
1 TTTTATTTATTTAT
138221 TTTTATTTATTTAT
1 TTTTATTTATTTAT
138235 T
1 T
138236 AATGCATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTATTTATTTAT
Found at i:138420 original size:17 final size:18
Alignment explanation
Indices: 138383--138420 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
138373 TAATATCTAA
138383 TATAATATACAATACTATT
1 TATAATATACAATA-TATT
*
138402 TATAATATGCAAT-TATT
1 TATAATATACAATATATT
138419 TA
1 TA
138421 ATATGAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (18 bp):
TATAATATACAATATATT
Found at i:139468 original size:21 final size:21
Alignment explanation
Indices: 139439--139486 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
139429 GAAAAGAAAC
*
139439 AAATGAGAATATCATCAAAAT
1 AAATAAGAATATCATCAAAAT
*
139460 AAATAAGAATATCATTAAAAT
1 AAATAAGAATATCATCAAAAT
*
139481 AGATAA
1 AAATAA
139487 CAACAAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.25
Consensus pattern (21 bp):
AAATAAGAATATCATCAAAAT
Found at i:140050 original size:254 final size:255
Alignment explanation
Indices: 139563--140075 Score: 737
Period size: 254 Copynumber: 2.0 Consensus size: 255
139553 TTTCATGGAT
* *
139563 GTAGCATTTTTGCAGTAAATCTAACTCTTTGGTCTATTCGATATTGTTTATCTGATGATGTGTGA
1 GTAGCATTTTTGCAGTAAATCTAACTCTTTGGTCTATTCGAGATTATTTATCTGATGATGTGTGA
* * * * * *
139628 ATGATCCATAAATTAGATTGGTATTGTGTTATTTCTCTCTTTCTGGTGGTAATATGTCATATGGG
66 AGGAGCCATAAATTAGATTGGTATGGTGTTATTTCCCTCTTTCTGGTGGTAATATGTAAGATGGG
* * *
139693 TTACCTAACACTTCTTGAAAATCCTGTAAGAGATAAATAAACATAATAGGAGAGCCGTGTTATTA
131 TTACCTAACACTTCTTGAAAATCATGTAAGAGAAAAATAAACATAATAGGAGAGCCATGTTATTA
* * *
139758 TTAGAAATCAAAACAAGTGGTTTCCTATGGTAGACAATAATGCAAGGC-TTTTTTGTGAA
196 TCAGAAATCAAAACAAGTGGTTTCCTAAGGTAGACAATAATACAAGGCTTTTTTTGTGAA
* * *
139817 GTAGCCTTTTTGCAGTAAATCTAACTCTTTGGTCTCTTTGAGATTATTT-TCCTGATGATGTGTG
1 GTAGCATTTTTGCAGTAAATCTAACTCTTTGGTCTATTCGAGATTATTTAT-CTGATGATGTGTG
* * * *
139881 AAGGAGCCTTGAATTAGATTGGTATGGTGTTCTTTCCCTCTTTCTGGTGGTAATATGTAAGGTGG
65 AAGGAGCCATAAATTAGATTGGTATGGTGTTATTTCCCTCTTTCTGGTGGTAATATGTAAGATGG
* *
139946 GTTACCTAACACTTCTTGAAAATCATGTAAGAGAAAAATAATCATATTAGGAGAGCCAATGTTAT
130 GTTACCTAACACTTCTTGAAAATCATGTAAGAGAAAAATAAACATAATAGGAGAGCC-ATGTTAT
* *
140011 TATCAGAAATCGAAACAAGTGGTTT-CTAAGGCT-GACAATAATACATGGCTTTTTTTTGTGAA
194 TATCAGAAATCAAAACAAGTGGTTTCCTAAGG-TAGACAATAATACAAGGC-TTTTTTTGTGAA
140073 GTA
1 GTA
140076 TGTTCTCTCT
Statistics
Matches: 229, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
253 1 0.00
254 184 0.80
255 30 0.13
256 14 0.06
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.37
Consensus pattern (255 bp):
GTAGCATTTTTGCAGTAAATCTAACTCTTTGGTCTATTCGAGATTATTTATCTGATGATGTGTGA
AGGAGCCATAAATTAGATTGGTATGGTGTTATTTCCCTCTTTCTGGTGGTAATATGTAAGATGGG
TTACCTAACACTTCTTGAAAATCATGTAAGAGAAAAATAAACATAATAGGAGAGCCATGTTATTA
TCAGAAATCAAAACAAGTGGTTTCCTAAGGTAGACAATAATACAAGGCTTTTTTTGTGAA
Found at i:142907 original size:28 final size:29
Alignment explanation
Indices: 142859--142914 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
142849 AGTCAAATGA
*
142859 AAATAAACAAATACTATAAAAT-AAAAAT
1 AAATAAACAAATACTACAAAATGAAAAAT
* *
142887 AAATAAATAAATACTGCAAAATGAAAAA
1 AAATAAACAAATACTACAAAATGAAAAA
142915 GGCCAATGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.20
Consensus pattern (29 bp):
AAATAAACAAATACTACAAAATGAAAAAT
Found at i:143640 original size:24 final size:24
Alignment explanation
Indices: 143608--143654 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
143598 TTAATTTTAT
143608 TATAATATAATATAAT-TAATGATA
1 TATAATAT-ATATAATATAATGATA
*
143632 TATAATATATATTATATAATGAT
1 TATAATATATATAATATAATGAT
143655 GTAATCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (24 bp):
TATAATATATATAATATAATGATA
Found at i:146307 original size:21 final size:21
Alignment explanation
Indices: 146256--146308 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
146246 ATTATGACTA
146256 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
146277 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
146298 TCGCAATGCGA
1 TCGCAATGCGA
146309 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:146323 original size:20 final size:21
Alignment explanation
Indices: 146298--146349 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
146288 TTTTCCCAAT
*
146298 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
146318 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
146339 TCGCAATGCGA
1 TCGCAATGCGA
146350 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:146328 original size:41 final size:41
Alignment explanation
Indices: 146283--146514 Score: 105
Period size: 41 Copynumber: 5.7 Consensus size: 41
146273 AATTTCGCGT
*
146283 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * * *
146324 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCGA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * * **
146365 TGCAATTTTCCTAATTCGCATTGAGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAATCGCAA
* * *
146406 TGCGATTTTCATAATTTGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * * *
146447 CGCGA-TTAAGTAAATCGCAATGCGAATTAGGAAAATTGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TAAGTAAATCGCAA
* * * *
146488 TGCGA-ATACGTAAATCGCAATGCGAAT
1 TGCGATTTTCCTAATTCGCAATGCGAAT
146515 CTTACTATCG
Statistics
Matches: 141, Mismatches: 43, Indels: 15
0.71 0.22 0.08
Matches are distributed among these distances:
39 2 0.01
40 25 0.18
41 112 0.79
43 1 0.01
44 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:146393 original size:21 final size:21
Alignment explanation
Indices: 146369--146421 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
146359 TCGCGATGCA
*
146369 ATTTTCCTAATTCGCATTGAG
1 ATTTTCATAATTCGCATTGAG
* * * *
146390 ATTTACGT-ATTCGCGTTGCG
1 ATTTTCATAATTCGCATTGAG
146410 ATTTTCATAATT
1 ATTTTCATAATT
146422 TGCAATGCGA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (21 bp):
ATTTTCATAATTCGCATTGAG
Found at i:146451 original size:20 final size:20
Alignment explanation
Indices: 146423--146532 Score: 123
Period size: 20 Copynumber: 5.5 Consensus size: 20
146413 TTCATAATTT
146423 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
* * *
146443 GCAACGCGATTAAGTAAATC
1 GCAATGCGAATACGTAAATC
* * *
146463 GCAATGCGAATTAGGAAAATT
1 GCAATGCGAA-TACGTAAATC
146484 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
* *
146504 GCAATGCGAAT-CTTACTATC
1 GCAATGCGAATACGTA-AATC
146524 GCAATGCGA
1 GCAATGCGA
146533 TTTACATAGC
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.04
20 55 0.73
21 17 0.23
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (20 bp):
GCAATGCGAATACGTAAATC
Found at i:148955 original size:20 final size:20
Alignment explanation
Indices: 148932--149001 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
148922 TATTATCTGG
* *
148932 TTGCGATAGTCAAAATCTCA
1 TTGCGAAAGTCAAAATCGCA
* *
148952 TTGCGAAAGTCAGAATCGCG
1 TTGCGAAAGTCAAAATCGCA
** *
148972 TTGCGAAAGTCAGTATCGCG
1 TTGCGAAAGTCAAAATCGCA
148992 TTGCGAAAGT
1 TTGCGAAAGT
149002 AAGTATCGCG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (20 bp):
TTGCGAAAGTCAAAATCGCA
Found at i:149006 original size:20 final size:20
Alignment explanation
Indices: 148952--149017 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
148942 CAAAATCTCA
*
148952 TTGCGAAAGTCAGAATCGCG
1 TTGCGAAAGTCAGTATCGCG
148972 TTGCGAAAGTCAGTATCGCG
1 TTGCGAAAGTCAGTATCGCG
*
148992 TTGCGAAAGTAAGTATCGCG
1 TTGCGAAAGTCAGTATCGCG
149012 TTGCGA
1 TTGCGA
149018 TTTTCCAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (20 bp):
TTGCGAAAGTCAGTATCGCG
Found at i:149048 original size:21 final size:20
Alignment explanation
Indices: 149028--149079 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
149018 TTTTCCAAAT
*
149028 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
**
149048 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATAAGG-AAA
149069 TCGCAATGCGA
1 TCGCAATGCGA
149080 TAATGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:149053 original size:20 final size:21
Alignment explanation
Indices: 149028--149079 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
149018 TTTTCCAAAT
*
149028 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
149048 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
149069 TCGCAATGCGA
1 TCGCAATGCGA
149080 TAATGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:149093 original size:20 final size:20
Alignment explanation
Indices: 149068--149177 Score: 96
Period size: 20 Copynumber: 5.5 Consensus size: 20
149058 AATTTGGAAA
*
149068 ATCGCAATGCGATAATGACT
1 ATCGCAACGCGATAATGACT
*
149088 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATAATGAC--T
*
149109 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATAATGACT
* **
149129 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATGACT
* * **
149149 TTCACAACGCGATTCTGACT
1 ATCGCAACGCGATAATGACT
*
149169 TTCGCAACG
1 ATCGCAACG
149178 AGATTCTGAA
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.03
20 60 0.76
21 15 0.19
22 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATAATGACT
Found at i:149195 original size:20 final size:20
Alignment explanation
Indices: 149110--149186 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
149100 TAATACAAAA
*
149110 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
149130 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
149150 TCACAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
149170 TCGCAACGAGATTCTGA
1 TCGCAACGCGATTCTGA
149187 AAATCGCAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:149434 original size:20 final size:20
Alignment explanation
Indices: 149409--149462 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
149399 CTACGGGGAA
149409 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* *
149429 ATCGCAACGCGAAAATGGCT
1 ATCGCAATGCGAAAATGACT
149449 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
149463 TGAAAATCGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:149471 original size:19 final size:20
Alignment explanation
Indices: 149407--149479 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
149397 CGCTACGGGG
149407 AAATCGCAATGCGAAAATGA
1 AAATCGCAATGCGAAAATGA
** * *
149427 CTATCGCAACGCGAAAATGG
1 AAATCGCAATGCGAAAATGA
**
149447 CTATCGCAATGCG-AAATGA
1 AAATCGCAATGCGAAAATGA
*
149466 AAATCGCATTGCGA
1 AAATCGCAATGCGA
149480 TTTTATCGTT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
19 15 0.35
20 28 0.65
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.18
Consensus pattern (20 bp):
AAATCGCAATGCGAAAATGA
Found at i:149512 original size:19 final size:19
Alignment explanation
Indices: 149488--149532 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
149478 GATTTTATCG
149488 TTGCGATAGCCATTTCACA
1 TTGCGATAGCCATTTCACA
*** *
149507 TTGCGATTTTCATTTCGCA
1 TTGCGATAGCCATTTCACA
149526 TTGCGAT
1 TTGCGAT
149533 TTTCTCGTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (19 bp):
TTGCGATAGCCATTTCACA
Found at i:149533 original size:19 final size:19
Alignment explanation
Indices: 149498--149536 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
149488 TTGCGATAGC
149498 CATTTCACATTGCGATTTT
1 CATTTCACATTGCGATTTT
*
149517 CATTTCGCATTGCGATTTT
1 CATTTCACATTGCGATTTT
149536 C
1 C
149537 TCGTTGCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.18, C:0.23, G:0.13, T:0.46
Consensus pattern (19 bp):
CATTTCACATTGCGATTTT
Found at i:151147 original size:41 final size:42
Alignment explanation
Indices: 151101--151188 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
151091 CCTCTTCAAC
* *
151101 GATGATAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGATAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
*
151142 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGATAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
151184 GATGA
1 GATGA
151189 CAGGTGAGTC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
41 21 0.49
42 22 0.51
ACGTcount: A:0.20, C:0.14, G:0.42, T:0.24
Consensus pattern (42 bp):
GATGATAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:151157 original size:21 final size:21
Alignment explanation
Indices: 151128--151188 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
151118 GAACGGTGGG
*
151128 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
151149 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
151170 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
151189 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:151556 original size:20 final size:20
Alignment explanation
Indices: 151531--151569 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
151521 GAAGAATAGT
151531 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAC
*
151551 TTACTTTCGCAACGCGAAA
1 TTACTTTCGCAACACGAAA
151570 ATGACTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAC
Found at i:151580 original size:20 final size:20
Alignment explanation
Indices: 151537--151624 Score: 95
Period size: 20 Copynumber: 4.4 Consensus size: 20
151527 TAGTTTACTT
* * * *
151537 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
151557 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* * *
151577 TCGCAATGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* *
151597 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
151617 TCGCAACG
1 TCGCAACG
151625 ACAAAATCGC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:151631 original size:20 final size:20
Alignment explanation
Indices: 151557--151624 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
151547 AAACTTACTT
*
151557 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGGCTA
* *
151577 TCGCAATGCGGAAATGGCTA
1 TCGCAACGCGAAAATGGCTA
*
151597 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGGCTA
151617 TCGCAACG
1 TCGCAACG
151625 ACAAAATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGAAAATGGCTA
Found at i:151684 original size:33 final size:33
Alignment explanation
Indices: 151620--151684 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
151610 ATGGCTATCG
* *
151620 CAACGACAAAATCGCAATGCGAAATGAAAATCA
1 CAACGACAAAATCGCAACGCGAAATCAAAATCA
151653 CAACGACAAAATCGCAACGCGAAA-CACAAATC
1 CAACGACAAAATCGCAACGCGAAATCA-AAATC
151685 GCATTACGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 28 0.97
ACGTcount: A:0.51, C:0.26, G:0.14, T:0.09
Consensus pattern (33 bp):
CAACGACAAAATCGCAACGCGAAATCAAAATCA
Found at i:151745 original size:19 final size:19
Alignment explanation
Indices: 151683--151746 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
151673 GAAACACAAA
*
151683 TCGCATTACGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
151702 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
151718 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
151735 TCGCATTGCGAT
1 TCGCATTGCGAT
151747 AGCCATTTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 6 0.17
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 16 0.44
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:151765 original size:20 final size:19
Alignment explanation
Indices: 151731--151785 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
151721 TTGCGATTTT
*
151731 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
151750 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
151770 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
151786 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:153723 original size:20 final size:20
Alignment explanation
Indices: 153675--153733 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
153665 AATATTTTCT
* *
153675 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
153695 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
153715 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
153734 AGAGAATAAA
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:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:154325 original size:41 final size:41
Alignment explanation
Indices: 154206--154343 Score: 188
Period size: 41 Copynumber: 3.4 Consensus size: 41
154196 CGCTTTGAAA
* * *
154206 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** * *
154247 ATTGCGTTGCGAAATT-AAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
154287 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
154328 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
154344 CCAAATTCGC
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 34 0.41
41 48 0.59
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:154340 original size:20 final size:20
Alignment explanation
Indices: 154226--154339 Score: 131
Period size: 20 Copynumber: 5.7 Consensus size: 20
154216 GATTATGTAT
*
154226 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * *
154246 TATTGCGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
154266 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
154286 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
154307 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
154327 TATCGCGTTGCGA
1 TATCGCGTTGCGA
154340 TTTTCCAAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 60 0.76
21 14 0.18
22 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:154358 original size:21 final size:20
Alignment explanation
Indices: 154329--154380 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
154319 ATAGTCAGTA
* *
154329 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
**
154350 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACAAAT
154370 TCGCATTGCGA
1 TCGCATTGCGA
154381 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:154361 original size:41 final size:40
Alignment explanation
Indices: 154226--154360 Score: 155
Period size: 41 Copynumber: 3.3 Consensus size: 40
154216 GATTATGTAT
* * ** *
154226 TATCTCGTTGCGAAAGTCAGTATTGCGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTAAA
* *
154266 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTT-AAA
*
154307 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAA
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTT--AAA
*
154349 T-TCGCATTGCGA
1 TATCGCGTTGCGA
154361 TTTACTTATT
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
40 33 0.40
41 47 0.57
42 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (40 bp):
TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTAAA
Found at i:154422 original size:21 final size:22
Alignment explanation
Indices: 154370--154422 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
154360 ATTTACTTAT
154370 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
154391 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
154412 TCGCATTGCGA
1 TCGCATTGCGA
154423 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:156120 original size:52 final size:50
Alignment explanation
Indices: 156063--156181 Score: 132
Period size: 52 Copynumber: 2.3 Consensus size: 50
156053 AGATTTATTA
* * * * *
156063 AAAATATTTTATTAGAT-TTTTACAATAATTGTGTAATATTTTTATAATTTCT
1 AAAATATTTTA-TA-ATACTTTAAAATAATTATGTAACATTTTTATAACTT-T
156115 AAAATAATTTTATAATACTTTAAAATAATTATGTAACATTTTTATAACTTT
1 AAAAT-ATTTTATAATACTTTAAAATAATTATGTAACATTTTTATAACTTT
*
156166 AATATATTTTTATAAT
1 AAAATA-TTTTATAAT
156182 TTATCATTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
50 1 0.02
51 16 0.28
52 35 0.60
53 6 0.10
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.51
Consensus pattern (50 bp):
AAAATATTTTATAATACTTTAAAATAATTATGTAACATTTTTATAACTTT
Found at i:156125 original size:20 final size:20
Alignment explanation
Indices: 156097--156144 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
156087 ATAATTGTGT
*
156097 AATATTTTTATAAT-TTCTAA
1 AATAATTTTATAATATT-TAA
156117 AATAATTTTATAATACTTTAA
1 AATAATTTTATAATA-TTTAA
156138 AATAATT
1 AATAATT
156145 ATGTAACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 13 0.52
21 10 0.40
22 2 0.08
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
AATAATTTTATAATATTTAA
Found at i:163769 original size:123 final size:124
Alignment explanation
Indices: 163627--163874 Score: 435
Period size: 124 Copynumber: 2.0 Consensus size: 124
163617 TTGAAATTGT
*
163627 TTATAAGTAATATTTTTCATTTTTCTCCCCCTTT-GAAAAAGAATTTAAAAATATATGATTAAAA
1 TTATAAGTAATATTTTTCATTTTTCTCCCCCTTTAAAAAAAGAATTTAAAAATATATGATTAAAA
*
163691 AACATGCAAAGATAAAAAGTTTCATAAAACAAAATTTTACTAGAATTTTCTCCCCTTTC
66 AACATGCAAAGATAAAAAGTTTCACAAAACAAAATTTTACTAGAATTTTCTCCCCTTTC
*
163750 TTATAAGTGATATTTTTCATTTTTCTCCCCCTTTAAAAAAAGAATTTAAAAATATATGATTAAAA
1 TTATAAGTAATATTTTTCATTTTTCTCCCCCTTTAAAAAAAGAATTTAAAAATATATGATTAAAA
* * *
163815 AACATGCAAAGATGAAAAGTTTGACAAAACAAAATTTTACTAGAATTTTCTCCCTTTTC
66 AACATGCAAAGATAAAAAGTTTCACAAAACAAAATTTTACTAGAATTTTCTCCCCTTTC
163874 T
1 T
163875 ATTAGATAAA
Statistics
Matches: 118, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
123 33 0.28
124 85 0.72
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (124 bp):
TTATAAGTAATATTTTTCATTTTTCTCCCCCTTTAAAAAAAGAATTTAAAAATATATGATTAAAA
AACATGCAAAGATAAAAAGTTTCACAAAACAAAATTTTACTAGAATTTTCTCCCCTTTC
Found at i:166525 original size:30 final size:30
Alignment explanation
Indices: 166450--166595 Score: 114
Period size: 30 Copynumber: 4.7 Consensus size: 30
166440 ATGTACATTG
* * * * * *
166450 AGTGCCCTTACACACCACAATGTTGCACTG
1 AGTGTCCTTACACACTATAGTGATGCACTA
* * *
166480 AGTGTCCATACACACTACAGTGATGTACTA
1 AGTGTCCTTACACACTATAGTGATGCACTA
* *
166510 AGTGTCCTTACACACTGTAGT-ACTGTACTA
1 AGTGTCCTTACACACTATAGTGA-TGCACTA
* * *
166540 AGTGTCCTTATACACCATAGTACCATATGCACTA
1 AGTGTCCTTACACACTATAGT----GATGCACTA
166574 AGTGTCCTTACACACTATAGTG
1 AGTGTCCTTACACACTATAGTG
166596 CTAATTCGAT
Statistics
Matches: 93, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
29 1 0.01
30 66 0.71
34 25 0.27
35 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (30 bp):
AGTGTCCTTACACACTATAGTGATGCACTA
Found at i:168496 original size:17 final size:17
Alignment explanation
Indices: 168458--168497 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
168448 AAATTTCATC
168458 CCATTTGCCACGACATTT
1 CCATTTGCCAC-ACATTT
168476 CCATTTGCCAC-CATATT
1 CCATTTGCCACACAT-TT
168493 CCATT
1 CCATT
168498 ACACCATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.14
17 7 0.33
18 11 0.52
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.35
Consensus pattern (17 bp):
CCATTTGCCACACATTT
Found at i:168847 original size:25 final size:26
Alignment explanation
Indices: 168808--168862 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 26
168798 CTTTTTCATT
168808 TTTTATATATATAGTTTTACTTGCTA
1 TTTTATATATATAGTTTTACTTGCTA
168834 TTTT-TATATATAGTTTTACTTGCTA
1 TTTTATATATATAGTTTTACTTGCTA
168859 TTTT
1 TTTT
168863 CCTTACTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (26 bp):
TTTTATATATATAGTTTTACTTGCTA
Found at i:171708 original size:14 final size:14
Alignment explanation
Indices: 171686--171751 Score: 95
Period size: 14 Copynumber: 5.0 Consensus size: 14
171676 TCAATTATAT
*
171686 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
171700 GTTCATTTA---T-
1 GTTCATTTATGTTC
171710 GTTCATTTATGTTC
1 GTTCATTTATGTTC
171724 GTTCATTTATGTTC
1 GTTCATTTATGTTC
171738 GTTCATTTATGTTC
1 GTTCATTTATGTTC
171752 TAACAGAGGG
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
10 9 0.19
11 1 0.02
13 1 0.02
14 36 0.77
ACGTcount: A:0.14, C:0.14, G:0.15, T:0.58
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:171751 original size:24 final size:24
Alignment explanation
Indices: 171673--171740 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
171663 CGTTCGTGAA
171673 CGTTCAATTATATGTTCGTTTATGTT
1 CGTTC-ATT-TATGTTCGTTTATGTT
*
171699 CGTTCATTTATGTTCATTTATGTT
1 CGTTCATTTATGTTCGTTTATGTT
171723 CGTTCATTTATGTTCGTT
1 CGTTCATTTATGTTCGTT
171741 CATTTATGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
24 32 0.80
25 3 0.08
26 5 0.12
ACGTcount: A:0.16, C:0.13, G:0.15, T:0.56
Consensus pattern (24 bp):
CGTTCATTTATGTTCGTTTATGTT
Found at i:172049 original size:10 final size:10
Alignment explanation
Indices: 171999--172075 Score: 66
Period size: 10 Copynumber: 7.5 Consensus size: 10
171989 ATAAGTTTTT
*
171999 TTTATGTTTG
1 TTTATGTTCG
172009 TTT-TGTTCG
1 TTTATGTTCG
* *
172018 TTTATATTTG
1 TTTATGTTCG
172028 TTTATTGTGTTCG
1 TTTA---TGTTCG
172041 TTTATGTTCG
1 TTTATGTTCG
** *
172051 TTCGTGTTCA
1 TTTATGTTCG
172061 TTTATGTTCG
1 TTTATGTTCG
172071 TTTAT
1 TTTAT
172076 TATTTAAATG
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
9 8 0.15
10 36 0.69
13 8 0.15
ACGTcount: A:0.10, C:0.08, G:0.18, T:0.64
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:178669 original size:21 final size:20
Alignment explanation
Indices: 178631--178669 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
178621 TAATGGATGG
*
178631 TTGTTTTTATATGTTGTTAT
1 TTGTTTTTATATGATGTTAT
*
178651 TTGTTTTGTTTATGATGTT
1 TTGTTTT-TATATGATGTT
178670 TAATGCCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.13, C:0.00, G:0.18, T:0.69
Consensus pattern (20 bp):
TTGTTTTTATATGATGTTAT
Found at i:180658 original size:20 final size:19
Alignment explanation
Indices: 180615--180659 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
180605 CAAAAAAATC
* *
180615 CAATTTCACATTCTAACAT
1 CAATTTCACACTCAAACAT
180634 CAATTTCAACACTCAAACAT
1 CAATTTC-ACACTCAAACAT
*
180654 TAATTT
1 CAATTT
180660 ACAGTATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (19 bp):
CAATTTCACACTCAAACAT
Found at i:190084 original size:179 final size:181
Alignment explanation
Indices: 189759--190220 Score: 694
Period size: 179 Copynumber: 2.6 Consensus size: 181
189749 TTAAAATGTG
* * *
189759 TCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATAAAACCGGTA
1 TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-TCAAATGATAAAACCGGTA
* * * * *
189824 AAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTCGTGAATTTA
65 AAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTTA
* *
189889 AAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTAAAAAATATA
130 AAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAAAATATA
* *
189941 TCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTATCAAATGATAAAACTGGTAA
1 TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAATGATAAAACCGGTAA
* * *
190006 AATGTTA-CGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTTGTGAATTTAA
66 AACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTTAA
* ** *
190069 AAGAGAAGTAGTTTTAGCGCCTATAATGTGTCGATACTTTAAAAAAATATA
131 AAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAAAATATA
* * *
190120 TCGATCCACAATGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTA
1 TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATC-AAATGATAAAACCGGTA
190185 AAACGATACCGGATATATTGAAAGTGTCGATACTTT
65 AAACGATACCGGATATATTGAAAGTGTCGATACTTT
190221 TGTAAGTACG
Statistics
Matches: 253, Mismatches: 25, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
179 116 0.46
180 46 0.18
181 49 0.19
182 42 0.17
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (181 bp):
TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAATGATAAAACCGGTAA
AACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTTAA
AAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAAAATATA
Found at i:190192 original size:17 final size:19
Alignment explanation
Indices: 190152--190192 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
190142 GTAAAAATAT
*
190152 GATAAAACCGGTATCAAAAT
1 GATAAAACCGG-ATCAAAAC
190172 GATAAAACCGG-T-AAAAC
1 GATAAAACCGGATCAAAAC
190189 GATA
1 GATA
190193 CCGGATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
20 11 0.55
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (19 bp):
GATAAAACCGGATCAAAAC
Found at i:192361 original size:21 final size:21
Alignment explanation
Indices: 192311--192375 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
192301 AAGACAATCA
*
192311 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
192332 AGA-TCCGAAGAGAAACTTGAG
1 AGAGT-CGAAGAGAAACTTGAG
* *
192353 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
192374 AG
1 AG
192376 GCATAAGGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
20 1 0.03
21 37 0.95
22 1 0.03
ACGTcount: A:0.42, C:0.12, G:0.29, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:194292 original size:19 final size:19
Alignment explanation
Indices: 194268--194316 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
194258 AATGTAGGGT
194268 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
194287 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
194306 TAATTTTGTAT
1 TAATTTTGTAT
194317 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:194891 original size:200 final size:200
Alignment explanation
Indices: 194548--195504 Score: 1606
Period size: 200 Copynumber: 4.8 Consensus size: 200
194538 AATTTACAAT
* * *
194548 ATGGCAAACAGGGTGCAACCATAAAGTGTCAATCCATATATAAAGAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
194613 CGAAACCCA-AATGTATAATGTAATAGGTAATTTTTCAATCTAATCGTTACAAGTATACCGGTTT
66 CGAAACCCATAA-GTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
* *
194677 TATGAGAGAATAGGTCTAAATAATGTATCAACACTTTTGTAGATTGTGTCGATATTTTTGGTCCA
130 TATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
194742 GAATGA
195 GAATGA
** *
194748 ATGGCAAACAACGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
194813 CAAAATCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
194878 ATGAGAGAATAGGTCT-AA-AATGTATCGATAC-TTT-TAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
194939 AATGA
196 AATGA
*
194944 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
195009 CGAAACCCATAAGTATAATGTAATGGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
195074 ATGAGAGAATAGGTCT--A-AATGTTTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCTAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
195136 AATGA
196 AATGA
195141 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
195206 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
195271 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGCGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
*
195336 ATTGA
196 AATGA
* * * *
195341 ATGGTAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTTGATCCCATAAACGT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
195406 CTAAACCCATAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
195471 ATGAGAGAATAGGTCTAAATAATGTATCGACACT
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACT
195505 GTTTAATGTT
Statistics
Matches: 716, Mismatches: 35, Indels: 12
0.94 0.05 0.02
Matches are distributed among these distances:
195 12 0.02
196 175 0.24
197 178 0.25
198 11 0.02
199 3 0.00
200 335 0.47
201 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:197023 original size:12 final size:12
Alignment explanation
Indices: 197001--197046 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
196991 CAATCGGTCA
*
197001 ATGAAGATGAAG
1 ATGACGATGAAG
*
197013 CTGACGATGAAG
1 ATGACGATGAAG
*
197025 ATGACGATGATG
1 ATGACGATGAAG
*
197037 ATGATGATGA
1 ATGACGATGA
197047 TCCAAACAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.22
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:197039 original size:18 final size:18
Alignment explanation
Indices: 197001--197046 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
196991 CAATCGGTCA
*
197001 ATGAAGATGAAGCTGACG
1 ATGAAGATGAAGATGACG
* *
197019 ATGAAGATGACGATGATG
1 ATGAAGATGAAGATGACG
*
197037 ATGATGATGA
1 ATGAAGATGA
197047 TCCAAACAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.22
Consensus pattern (18 bp):
ATGAAGATGAAGATGACG
Found at i:198528 original size:116 final size:117
Alignment explanation
Indices: 198324--198562 Score: 394
Period size: 116 Copynumber: 2.1 Consensus size: 117
198314 ACATCGGAAC
198324 CCAG-ATTATAATGTAATAGATAATTTGTAATAAACCGGTATAAATATACCGGTTTTATGAGCGA
1 CCAGAATTATAATGTAATAGATAATTTGTAATAAACCGGTATAAATATACCGGTTTTATGAGCGA
* *
198388 ATAGGTCTACAACCTATATCGACACTTTTAATTTTGTGTCGGTACTTTATTT
66 ATAGGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGT
* * *
198440 CCAGAATTATAATGTACTAGATAATTTTGTAAT-AACCGGTATAAGTATACC-GTTTTATTAGCG
1 CCAGAATTATAATGTAATAGATAA-TTTGTAATAAACCGGTATAAATATACCGGTTTTATGAGCG
*
198503 AATAGGTCTACAACCTATGTCGACACTTTTAATATTGTGTCGGTACTTTATGT
65 AATAGGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGT
198556 CCAGAAT
1 CCAGAAT
198563 GGAAGAAAAA
Statistics
Matches: 115, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
116 72 0.63
117 35 0.30
118 8 0.07
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (117 bp):
CCAGAATTATAATGTAATAGATAATTTGTAATAAACCGGTATAAATATACCGGTTTTATGAGCGA
ATAGGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGT
Found at i:198819 original size:119 final size:117
Alignment explanation
Indices: 198623--198858 Score: 382
Period size: 119 Copynumber: 2.0 Consensus size: 117
198613 CGGAACCCAG
198623 AATTATAATGTAATAGATAATTTTGTAATATAACCCGTATAAATACCGGTTTTATGAGCGAATAG
1 AATTATAATGTAATAGATAATTTTGTAATATAACCCGTATAAATACCGGTTTTATGAGCGAATAG
* *
198688 GTCTACAACCTATATCGATACTTTTTAATTTTGTGTCGGTACTTTATGTCCA
66 GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
* * * * *
198740 AATTATAATGTACTATATAATTTTGTAATATAATCGGTATAAGTATACCGGTTTTATTAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCCGTATAA--ATACCGGTTTTATGAGCGAAT
*
198805 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
64 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
198859 GAATGGAAGA
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
117 38 0.35
119 71 0.65
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.40
Consensus pattern (117 bp):
AATTATAATGTAATAGATAATTTTGTAATATAACCCGTATAAATACCGGTTTTATGAGCGAATAG
GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
Found at i:198920 original size:300 final size:298
Alignment explanation
Indices: 198261--199026 Score: 1375
Period size: 300 Copynumber: 2.6 Consensus size: 298
198251 TTAATATTGT
198261 TCCAGAATGGAAGAAAAATGTGTCGATACCTTGTC-AAAAGTGTCGACATTTACACATCGGAACC
1 TCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACC
*
198325 CAG-ATTATAATGTAATAGATAA-TTTGTAATA-AACCGGTATAAATATACCGGTTTTATGAGCG
66 CAGAATTATAATGTAATAGATAATTTTGTAATATAACCAGTATAAATATACCGGTTTTATGAGCG
*
198387 AATAGGTCTACAACCTATATCGACACTTTTAATTTTGTGTCGGTACTTTATTTCCAGAATTATAA
131 AATAGGTCTACAACCTATATCGACACTTTTAATTTTGTGTCGGTACTTTATGTCCAGAATTATAA
198452 TGTACTAGATAATTTTGTAATAACCGGTATAAGTATACCGTTTTATTAGCGAATAGGTCTACAAC
196 TGTACTAGATAATTTTGTAATAACCGGTATAAGTATACCGTTTTATTAGCGAATAGGTCTACAAC
198517 CTATGTCGACACTTTTAATATTGTGTCGGTACTTTATG
261 CTATGTCGACACTTTTAATATTGTGTCGGTACTTTATG
198555 TCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACC
1 TCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACC
*
198620 CAGAATTATAATGTAATAGATAATTTTGTAATATAACCCGTAT-AA-ATACCGGTTTTATGAGCG
66 CAGAATTATAATGTAATAGATAATTTTGTAATATAACCAGTATAAATATACCGGTTTTATGAGCG
*
198683 AATAGGTCTACAACCTATATCGATACTTTTTAATTTTGTGTCGGTACTTTATGTCCA-AATTATA
131 AATAGGTCTACAACCTATATCGACAC-TTTTAATTTTGTGTCGGTACTTTATGTCCAGAATTATA
* *
198747 ATGTACTATATAATTTTGTAATATAATCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTCTA
195 ATGTACTAGATAATTTTGT-A-ATAACCGGTATAAGTATACC-GTTTTATTAGCGAATAGGTCTA
198812 CAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATG
257 CAACCTATGTCGACAC-TTTTAATATTGTGTCGGTACTTTATG
198855 TCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACC
1 TCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACC
198920 CAGAATTATAATGTAATAGATAATTTTGTAATATAACCAGTATAAATATACCGGTTTTATGAGCG
66 CAGAATTATAATGTAATAGATAATTTTGTAATATAACCAGTATAAATATACCGGTTTTATGAGCG
*
198985 AATAGGTCTACAACCTATATCGACACTTTTAATATTGTGTCG
131 AATAGGTCTACAACCTATATCGACACTTTTAATTTTGTGTCG
199027 CTAATTTTAA
Statistics
Matches: 453, Mismatches: 8, Indels: 15
0.95 0.02 0.03
Matches are distributed among these distances:
294 35 0.08
295 32 0.07
296 87 0.19
297 41 0.09
298 27 0.06
299 38 0.08
300 133 0.29
301 17 0.04
302 43 0.09
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (298 bp):
TCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACC
CAGAATTATAATGTAATAGATAATTTTGTAATATAACCAGTATAAATATACCGGTTTTATGAGCG
AATAGGTCTACAACCTATATCGACACTTTTAATTTTGTGTCGGTACTTTATGTCCAGAATTATAA
TGTACTAGATAATTTTGTAATAACCGGTATAAGTATACCGTTTTATTAGCGAATAGGTCTACAAC
CTATGTCGACACTTTTAATATTGTGTCGGTACTTTATG
Done.