Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009611.1 Hibiscus syriacus cultivar Beakdansim tig00116997_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: 6671611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 27
Found at i:5101761 original size:17 final size:17
Alignment explanation
Indices: 5101739--5101772 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5101729 TTTTTGGGTA
5101739 CAAAAGAATGGAAAAAC
1 CAAAAGAATGGAAAAAC
5101756 CAAAAGAATGGAAAAAC
1 CAAAAGAATGGAAAAAC
5101773 GAAGTGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.12, G:0.18, T:0.06
Consensus pattern (17 bp):
CAAAAGAATGGAAAAAC
Found at i:5114979 original size:43 final size:43
Alignment explanation
Indices: 5114918--5115004 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
5114908 GTGTTGAGTC
5114918 GGTTATATTGATTTTTATCCAAATATATAACATGCATATATAT
1 GGTTATATTGATTTTTATCCAAATATATAACATGCATATATAT
5114961 GGTTATATTGATTTTTATCCAAATATATAACATGCATATATAT
1 GGTTATATTGATTTTTATCCAAATATATAACATGCATATATAT
5115004 G
1 G
5115005 CGCATATGCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (43 bp):
GGTTATATTGATTTTTATCCAAATATATAACATGCATATATAT
Found at i:5116504 original size:38 final size:40
Alignment explanation
Indices: 5116453--5116538 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
5116443 TAATTTTTCC
*
5116453 TAATATTTTCGGTTTG-A-TCAAAAATATTGT-ATTCTTCA
1 TAATATTTTCGGTTGGCACTCAAAAATATT-TCATTCTTCA
*
5116491 TAATATTTTCGGTTGGCACTCGAAAATATTTCATTCTTCA
1 TAATATTTTCGGTTGGCACTCAAAAATATTTCATTCTTCA
5116531 TAATATTT
1 TAATATTT
5116539 ATTGGTGAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
38 15 0.35
39 2 0.05
40 26 0.60
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (40 bp):
TAATATTTTCGGTTGGCACTCAAAAATATTTCATTCTTCA
Found at i:5121292 original size:30 final size:30
Alignment explanation
Indices: 5121256--5121321 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
5121246 AGAAGGGGCA
5121256 GAAGATATAGTGCATTTGGTTCACGCAATG
1 GAAGATATAGTGCATTTGGTTCACGCAATG
*
5121286 GAAGATATAGTGTATTTGGTTCACGCAATG
1 GAAGATATAGTGCATTTGGTTCACGCAATG
*
5121316 AAAGAT
1 GAAGAT
5121322 TATTAGTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (30 bp):
GAAGATATAGTGCATTTGGTTCACGCAATG
Found at i:5122661 original size:12 final size:12
Alignment explanation
Indices: 5122644--5122683 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
5122634 ACAGCAGTCC
5122644 CCCCCTTAGCAG
1 CCCCCTTAGCAG
5122656 CCCCCTTAGCAG
1 CCCCCTTAGCAG
5122668 CCCCCCTTAGCAG
1 -CCCCCTTAGCAG
5122681 CCC
1 CCC
5122684 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.15, C:0.55, G:0.15, T:0.15
Consensus pattern (12 bp):
CCCCCTTAGCAG
Found at i:5122672 original size:13 final size:13
Alignment explanation
Indices: 5122643--5122683 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
5122633 TACAGCAGTC
5122643 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
5122656 -CCCCCTTAGCAG
1 CCCCCCTTAGCAG
5122668 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
5122681 CCC
1 CCC
5122684 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.15, C:0.56, G:0.15, T:0.15
Consensus pattern (13 bp):
CCCCCCTTAGCAG
Found at i:5125973 original size:15 final size:16
Alignment explanation
Indices: 5125945--5125976 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
5125935 AAAATCTTTC
5125945 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
5125961 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
5125976 T
1 T
5125977 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:5126751 original size:16 final size:16
Alignment explanation
Indices: 5126727--5126760 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5126717 TATCGCCGAC
*
5126727 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
5126743 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
5126759 CG
1 CG
5126761 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:5127181 original size:12 final size:13
Alignment explanation
Indices: 5127154--5127199 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
5127144 AAAAAATTAC
*
5127154 AGCAGCCCCCCCT
1 AGCAGCCCCCCTT
5127167 AGCAG-CCCCCTT
1 AGCAGCCCCCCTT
5127179 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
5127192 AGCAGCCC
1 AGCAGCCC
5127200 ATGTGTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.35
13 20 0.65
ACGTcount: A:0.17, C:0.54, G:0.17, T:0.11
Consensus pattern (13 bp):
AGCAGCCCCCCTT
Found at i:5127266 original size:13 final size:12
Alignment explanation
Indices: 5127241--5127279 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
5127231 AACTAATCTT
*
5127241 TTTAAAAACAAA
1 TTTAAAAAAAAA
5127253 TTTAAAAATAAAA
1 TTTAAAAA-AAAA
5127266 TTTAGAAAAAAAA
1 TTTA-AAAAAAAA
5127279 T
1 T
5127280 AGAATTTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 8 0.33
13 12 0.50
14 4 0.17
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (12 bp):
TTTAAAAAAAAA
Found at i:5137277 original size:226 final size:225
Alignment explanation
Indices: 5136931--5137550 Score: 782
Period size: 226 Copynumber: 2.7 Consensus size: 225
5136921 ATATTAACTT
* * * * * * ** ** * *
5136931 TAACATAATCGATTAATTATTGGAAACATTATCAACTATAATAACAT-ATAGGTAGTGTTTATGT
1 TAACAAAATAGATTAATTACTAGAAACATTATCAACCATAATAACATAACAAATAACGCTTATTT
* ** * * * *
5136995 AACGTAATAGGTAGC-GTTATTTTAAAGCTGATGGAACTTTAAAAATCTGACGATAACAAAATAT
66 AATGTAATAGGTAGCACCT-GTTTAAAGCTGATGGGACCTTAGAAAT-TGACGATAACAAAATAT
* *
5137059 GTTAATTACTTGATTTGTTATCAATATTATCGACATATTAGGTAGGGCATAAAATGTTACCAAAG
129 GTTAATTACTTGATTTGTTATCAATATTATCAACATATTAGGTAGCGCATAAAATGTTACCAAAG
* *
5137124 TTTAAGCTGAT-AGAGCCTTAGAAA-TCTGACGA
194 TTTAAGCTAATGA-AACCTTAGAAATTC-GACGA
* *
5137156 TAACAAAATAGATTAATTACTAGAAACATTATCAATCATAATAACATAACAAGTAACGCTTATTT
1 TAACAAAATAGATTAATTACTAGAAACATTATCAACCATAATAACATAACAAATAACGCTTATTT
*
5137221 AATGTAATAGGTATCACCTGTTTAAAGCTGATGGGACCTTAGAAATTGGACGATAACAAAATATG
66 AATGTAATAGGTAGCACCTGTTTAAAGCTGATGGGACCTTAGAAATT-GACGATAACAAAATATG
*
5137286 TTAATTACTTGATTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGT
130 TTAATTACTTGATTTGTTATCAATATTATCAACATATTAGGTAGCGCATAAAATGTTACCAAAGT
*
5137351 TTAAGCTAATGAAACCTTATAAATTCGACGA
195 TTAAGCTAATGAAACCTTAGAAATTCGACGA
* * * * *
5137382 TAACAAAATAGTTTAATTACTGGAAGCATTATTAACCATAATAACATAACAAATAGCGCTTATTT
1 TAACAAAATAGATTAATTACTAGAAACATTATCAACCATAATAACATAACAAATAACGCTTATTT
* * * * * *
5137447 AATGTAATAGGTAGCGCTTGTTTAAAGCTGGT-GGAGCCTTAGAAATCAGATGATAACAAAATAA
66 AATGTAATAGGTAGCACCTGTTTAAAGCTGATGGGA-CCTTAGAAAT-TGACGATAACAAAATAT
*
5137511 GTTAATTACTTAATTTGTTATCAATATTATCAACATATTA
129 GTTAATTACTTGATTTGTTATCAATATTATCAACATATTA
5137551 CCGTGTATAT
Statistics
Matches: 347, Mismatches: 41, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
225 45 0.13
226 298 0.86
227 4 0.01
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (225 bp):
TAACAAAATAGATTAATTACTAGAAACATTATCAACCATAATAACATAACAAATAACGCTTATTT
AATGTAATAGGTAGCACCTGTTTAAAGCTGATGGGACCTTAGAAATTGACGATAACAAAATATGT
TAATTACTTGATTTGTTATCAATATTATCAACATATTAGGTAGCGCATAAAATGTTACCAAAGTT
TAAGCTAATGAAACCTTAGAAATTCGACGA
Found at i:5137793 original size:130 final size:125
Alignment explanation
Indices: 5137548--5137860 Score: 297
Period size: 130 Copynumber: 2.4 Consensus size: 125
5137538 TATCAACATA
* * * *
5137548 TTACCGTGTATATTATTAATTTACATATTACTTTAAAGTAATATGTTTCGAATTTATAAGAATTG
1 TTACCGTGTA-ATTGTTAATTAACATATTACTTTAAAGTAATA-GTTTCGAAATTACAAGAATTG
* * * *
5137613 ATACTTATATGTAAGTATAAATCCTTGTACATTTACACCTATTTTTATTATACCGGTAGAAAAGT
64 ATACTTATATGT-AGTATAAATACTTGTACATTTACACCTATTATCATTATACCGATAG--AAGT
* * * *
5137678 TTACTGTGTACATTGTTAATTAACATATTACTTTAAAGTAATACGTTTCGAAATTCCACGTATTG
1 TTACCGTGTA-ATTGTTAATTAACATATTACTTTAAAGTAATA-GTTTCGAAATTACAAGAATTG
* * ** * * **
5137743 ATACTTTATACATGT-GTATCAATATTTG-ATGTTTACGCCTATTATCATTATACCGATTGATTT
64 ATAC-TTAT--ATGTAGTATAAATACTTGTACATTTACACCTATTATCATTATACCGATAGAAGT
* * * *
5137806 TTACCGTTTTAATTGTAAATTAACCTATTACTTTAAAGTAATAGGTTCGAAATTA
1 TTACCG-TGTAATTGTTAATTAACATATTACTTTAAAGTAATAGTTTCGAAATTA
5137861 TAAGTATCGA
Statistics
Matches: 151, Mismatches: 28, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
127 10 0.07
128 37 0.25
129 3 0.02
130 83 0.55
131 14 0.09
133 4 0.03
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (125 bp):
TTACCGTGTAATTGTTAATTAACATATTACTTTAAAGTAATAGTTTCGAAATTACAAGAATTGAT
ACTTATATGTAGTATAAATACTTGTACATTTACACCTATTATCATTATACCGATAGAAGT
Found at i:5138314 original size:202 final size:203
Alignment explanation
Indices: 5137776--5138436 Score: 724
Period size: 201 Copynumber: 3.3 Consensus size: 203
5137766 ATTTGATGTT
* * *
5137776 TACGCCTATTATCATTATACCGATTGATTTTTACCGTTTTA-ATTGTAAATTAACCTATTACTTT
1 TACG-CTATTATCATTATACCGATAGACTTTTACCG-TTTACATTGTAAATTTACCTATTACTTT
*
5137840 AAAGTAATAGG-TTCGAAATTATAAG--TATCGA-AGATTTATATATGTGTATCGATACATTTTG
64 AAAGTAATAGGTTTCGAAATTATAAGTATATCGATA-ATTTATATATGTGTATCGATACTTTTTG
* * * * *
5137901 CGTGCAAATTGTTTAAGATGCATATTGGAATAAAATTATCGATA--TAT-ATATAAAGTATCGAT
128 CGTGCAAATTGTTTGAGATGCATACTGGAATAAAAATATCGATACCTATAAAAAAAAGTATCGAT
* *
5137963 ACGTGGTA-TA
193 ACATTGTATTA
** * * * * * *
5137973 TACGCTATGGTCATTATACCGGTAAACTTTTACCCTTTACATTGTTAATTTACCTATTATTTTAT
1 TACGCTATTATCATTATACCGATAGACTTTTACCGTTTACATTGTAAATTTACCTATTACTTTAA
* * * * * *
5138038 AGTAATAGGTTTCGGAATTAAAAGTAT-T-GATACTTTGTACATGTGAATCGATACTTTTTGCGT
66 AGTAATAGGTTTCGAAATTATAAGTATATCGATAATTTATATATGTGTATCGATACTTTTTGCGT
* *
5138101 GCAAATTGTTTGAGAAGCTTACTGGAATAAAAATATCGATACCTATAAAAAAAAGTATCGATACA
131 GCAAATTGTTTGAGATGCATACTGGAATAAAAATATCGATACCTATAAAAAAAAGTATCGATACA
*
5138166 TTATATTTA
196 TTGTA-TTA
* * *
5138175 TAC-CTATTATCATTAAACC-AGTAGATTTTTACCGTTTACATTATAAATTTACCTATTACTTTA
1 TACGCTATTATCATTATACCGA-TAGACTTTTACCGTTTACATTGTAAATTTACCTATTACTTTA
* * * *
5138238 AAGT-ATAGGTTTCAAAATTCTGAGTATATCGATATTTTATATATGTGTATCGATACTTTTTGCG
65 AAGTAATAGGTTTCGAAATTATAAGTATATCGATAATTTATATATGTGTATCGATACTTTTTGCG
* * * * * * * *
5138302 TCCAAATTGTTTGAGATGCATACTGGAATTAAAGTATCGACACCGATATAACAAAGTATTGATAC
130 TGCAAATTGTTTGAGATGCATACTGGAATAAAAATATCGATACCTATAAAAAAAAGTATCGATAC
*
5138367 GA-TGTGTT-
195 -ATTGTATTA
* * * *
5138375 TACGTTATTATCATTATACCGATATACTTTTATCGTTTACATTGTAAATTTACATATTACTT
1 TACGCTATTATCATTATACCGATAGACTTTTACCGTTTACATTGTAAATTTACCTATTACTT
5138437 CTACAATGCA
Statistics
Matches: 381, Mismatches: 67, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
195 4 0.01
196 54 0.14
197 80 0.21
198 2 0.01
199 4 0.01
200 39 0.10
201 104 0.27
202 93 0.24
203 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.40
Consensus pattern (203 bp):
TACGCTATTATCATTATACCGATAGACTTTTACCGTTTACATTGTAAATTTACCTATTACTTTAA
AGTAATAGGTTTCGAAATTATAAGTATATCGATAATTTATATATGTGTATCGATACTTTTTGCGT
GCAAATTGTTTGAGATGCATACTGGAATAAAAATATCGATACCTATAAAAAAAAGTATCGATACA
TTGTATTA
Found at i:5141802 original size:20 final size:20
Alignment explanation
Indices: 5141774--5141866 Score: 82
Period size: 20 Copynumber: 4.6 Consensus size: 20
5141764 TCTTTATCGA
* *
5141774 TTTTATCAAATTGAAATTGG
1 TTTTGTCAAATTCAAATTGG
5141794 TTTTGTCAAATATCAACA--GG
1 TTTTGTCAAAT-TCAA-ATTGG
* **
5141814 TTTTGTCAAATTCACTACCGG
1 TTTTGTCAAATTCA-AATTGG
*
5141835 TTTTGTCAAATTGAAATTGG
1 TTTTGTCAAATTCAAATTGG
*
5141855 ATTTGTCAAATT
1 TTTTGTCAAATT
5141867 TCAACATGTA
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
19 4 0.07
20 37 0.62
21 18 0.30
22 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (20 bp):
TTTTGTCAAATTCAAATTGG
Found at i:5141838 original size:21 final size:19
Alignment explanation
Indices: 5141792--5141846 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 19
5141782 AATTGAAATT
5141792 GGTTTTGTCAAATATCAACA
1 GGTTTTGTCAAAT-TCAACA
*
5141812 GGTTTTGTCAAATTCACTACC
1 GGTTTTGTCAAATTCA--ACA
5141833 GGTTTTGTCAAATT
1 GGTTTTGTCAAATT
5141847 GAAATTGGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 3 0.09
20 13 0.41
21 16 0.50
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (19 bp):
GGTTTTGTCAAATTCAACA
Found at i:5141965 original size:115 final size:115
Alignment explanation
Indices: 5141763--5141983 Score: 336
Period size: 115 Copynumber: 1.9 Consensus size: 115
5141753 ATTCCAGTAG
* *
5141763 CTCTTTATCGATTTTATCAAATTGAAATTGGTTTTGTCAAATATCAACAGGTTTTGTCAAATTCA
1 CTCTTTACCGATTTTATCAAATTGAAATTGGTTTTGTCAAATATCAACAGGGTTTGTCAAATTCA
* * *
5141828 CTACCGGTTTTGTCAAATTGAAATTGGATTTGTCAAATTTCAACATGTAA
66 CTACAGGTTTTGTCAAAATGAAATCGGATTTGTCAAATTTCAACATGTAA
* * * *
5141878 CTCTTTACCGGTTTTCTCAAATTGAAATTGGTTTTGTCAAATATCAACCGGGTTTGTCAAATTTG
1 CTCTTTACCGATTTTATCAAATTGAAATTGGTTTTGTCAAATATCAACAGGGTTTGTCAAA-TTC
*
5141943 A-TACATGTTTTGTCAAAATGAAATCGGATTTGTCAAATTTC
65 ACTACAGGTTTTGTCAAAATGAAATCGGATTTGTCAAATTTC
5141984 GACCTATTAT
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
115 92 0.97
116 3 0.03
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (115 bp):
CTCTTTACCGATTTTATCAAATTGAAATTGGTTTTGTCAAATATCAACAGGGTTTGTCAAATTCA
CTACAGGTTTTGTCAAAATGAAATCGGATTTGTCAAATTTCAACATGTAA
Found at i:5142515 original size:11 final size:11
Alignment explanation
Indices: 5142499--5142562 Score: 51
Period size: 11 Copynumber: 5.6 Consensus size: 11
5142489 TCGAGACTCG
5142499 AGCTCGATTGA
1 AGCTCGATTGA
5142510 AGCTCGATTTTG-
1 AGCTCGA--TTGA
* *
5142522 AGCTCGGTTCA
1 AGCTCGATTGA
5142533 AGCTCGATTTTG-
1 AGCTCGA--TTGA
*
5142545 AGCTCGATTCA
1 AGCTCGATTGA
5142556 AGCTCGA
1 AGCTCGA
5142563 CAGGTAAGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
10 4 0.10
11 20 0.48
12 13 0.31
13 5 0.12
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:5142527 original size:12 final size:12
Alignment explanation
Indices: 5142498--5142553 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
5142488 CTCGAGACTC
5142498 GAGCTCGA--TT
1 GAGCTCGATTTT
5142508 GAAGCTCGATTTT
1 G-AGCTCGATTTT
* *
5142521 GAGCTCG-GTTC
1 GAGCTCGATTTT
*
5142532 AAGCTCGATTTT
1 GAGCTCGATTTT
5142544 GAGCTCGATT
1 GAGCTCGATT
5142554 CAAGCTCGAC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
10 1 0.03
11 15 0.42
12 17 0.47
13 3 0.08
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (12 bp):
GAGCTCGATTTT
Found at i:5142527 original size:23 final size:23
Alignment explanation
Indices: 5142498--5142562 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
5142488 CTCGAGACTC
*
5142498 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTCAAGCTCGATTTT
*
5142521 GAGCTCGGTTCAAGCTCGATTTT
1 GAGCTCGATTCAAGCTCGATTTT
5142544 GAGCTCGATTCAAGCTCGA
1 GAGCTCGATTCAAGCTCGA
5142563 CAGGTAAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (23 bp):
GAGCTCGATTCAAGCTCGATTTT
Found at i:5143970 original size:7 final size:7
Alignment explanation
Indices: 5143951--5144002 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
5143941 TCGAATTAAT
*
5143951 GGTTTAA
1 GGTTTAG
5143958 GGTTTAG
1 GGTTTAG
*
5143965 GATTTAG
1 GGTTTAG
*
5143972 TGTTTAG
1 GGTTTAG
*
5143979 GGCTTAG
1 GGTTTAG
*
5143986 GTTTTAG
1 GGTTTAG
5143993 GGTTTAG
1 GGTTTAG
5144000 GGT
1 GGT
5144003 GTAATTTAAC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.17, C:0.02, G:0.37, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:5144048 original size:13 final size:13
Alignment explanation
Indices: 5144017--5144052 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
5144007 TTTAACATGT
*
5144017 GTTTAGGGCTTAG
1 GTTTAGGGTTTAG
5144030 GTTTTAGGGTTTAG
1 G-TTTAGGGTTTAG
5144044 GTTTAGGGT
1 GTTTAGGGT
5144053 GTAATCTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.14, C:0.03, G:0.39, T:0.44
Consensus pattern (13 bp):
GTTTAGGGTTTAG
Found at i:5144227 original size:13 final size:13
Alignment explanation
Indices: 5144204--5144237 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5144194 AATTTTATAA
5144204 TTATCAATAATTTT
1 TTAT-AATAATTTT
*
5144218 TTTTAATAATTTT
1 TTATAATAATTTT
5144231 TTATAAT
1 TTATAAT
5144238 GTAATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATAATAATTTT
Found at i:5144953 original size:22 final size:21
Alignment explanation
Indices: 5144926--5144971 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
5144916 TTTTAAAATA
5144926 AATA-TTTAAATTATTATTTTAT
1 AATATTTTAAA-TATTATTTT-T
*
5144948 AATATTTTAAATATTGTTTTT
1 AATATTTTAAATATTATTTTT
5144969 AAT
1 AAT
5144972 TAAAATCCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
22 12 0.55
23 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
AATATTTTAAATATTATTTTT
Found at i:5145247 original size:43 final size:43
Alignment explanation
Indices: 5145194--5145381 Score: 164
Period size: 43 Copynumber: 4.4 Consensus size: 43
5145184 TTTTCACAAA
* * * *
5145194 AAACGTCGCAATATGTATTGATATTTAGCAAATTTTGTGTGAC
1 AAACGCCGCAATAGGTATTGATATTTAGCAAAGTTTGTATGAC
* * * * * *
5145237 AAACGCCGCAATAGGTGTTGATATTTAGCGACGTTTCTTTCAC
1 AAACGCCGCAATAGGTATTGATATTTAGCAAAGTTTGTATGAC
* * ** *
5145280 AAACGACGCAGTAGGTATTGATATTTAGCGGAGTTTGTCAT-AA
1 AAACGCCGCAATAGGTATTGATATTTAGCAAAGTTTGT-ATGAC
* * ** *
5145323 AAACGCCGCAATAGGTGTTAATATTTAGCAGCGTTTTTCA-GAC
1 AAACGCCGCAATAGGTATTGATATTTAGCAAAGTTTGT-ATGAC
5145366 AAACGCCGCAATAGGT
1 AAACGCCGCAATAGGT
5145382 TATGATGTTT
Statistics
Matches: 118, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
43 117 0.99
44 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (43 bp):
AAACGCCGCAATAGGTATTGATATTTAGCAAAGTTTGTATGAC
Found at i:5145393 original size:43 final size:43
Alignment explanation
Indices: 5145234--5145404 Score: 186
Period size: 43 Copynumber: 4.0 Consensus size: 43
5145224 AATTTTGTGT
*
5145234 GACAAACGCCGCAATAGGTGTTGATATTTAGCGACGTTTCTTTC-
1 GACAAACGCCGCAATAGGTGTTGATATTTAGCGGCG-TT-TTTCA
* * * * *
5145278 -ACAAACGACGCAGTAGGTATTGATATTTAGCGGAGTTTGTCA
1 GACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCA
* * * *
5145320 TAAAAACGCCGCAATAGGTGTTAATATTTAGCAGCGTTTTTCA
1 GACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCA
* *
5145363 GACAAACGCCGCAATAGGT-TATGATGTTTAGTGGCGTTTTTC
1 GACAAACGCCGCAATAGGTGT-TGATATTTAGCGGCGTTTTTC
5145405 GCTAAAACGT
Statistics
Matches: 104, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
41 3 0.03
42 3 0.03
43 98 0.94
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (43 bp):
GACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCA
Found at i:5145413 original size:86 final size:86
Alignment explanation
Indices: 5145194--5145381 Score: 222
Period size: 86 Copynumber: 2.2 Consensus size: 86
5145184 TTTTCACAAA
* * ** * * * *
5145194 AAACGTCGCAATATGTATTGATATTTAGCAAATTTTGT-GTGACAAACGCCGCAATAGGTGTTGA
1 AAACGACGCAATAGGTATTGATATTTAGCGGAGTTTGTCAT-AAAAACGCCGCAATAGGTGTTAA
5145258 TATTTAGCGACGTTTCTTTCAC
65 TATTTAGCGACGTTTCTTTCAC
*
5145280 AAACGACGCAGTAGGTATTGATATTTAGCGGAGTTTGTCATAAAAACGCCGCAATAGGTGTTAAT
1 AAACGACGCAATAGGTATTGATATTTAGCGGAGTTTGTCATAAAAACGCCGCAATAGGTGTTAAT
5145345 ATTTAGC-AGCG-TT-TTTCAGAC
66 ATTTAGCGA-CGTTTCTTTC--AC
*
5145366 AAACGCCGCAATAGGT
1 AAACGACGCAATAGGT
5145382 TATGATGTTT
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
84 4 0.05
85 3 0.03
86 79 0.91
87 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (86 bp):
AAACGACGCAATAGGTATTGATATTTAGCGGAGTTTGTCATAAAAACGCCGCAATAGGTGTTAAT
ATTTAGCGACGTTTCTTTCAC
Found at i:5145940 original size:21 final size:21
Alignment explanation
Indices: 5145861--5145941 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 21
5145851 GTTGATATGA
* * *
5145861 TGCTTCTCTCTGTGCTGCCGC
1 TGCTTCTCTCTCTGCTTCTGC
*
5145882 TGCTTCTTTCTCTGCTT-TCGC
1 TGCTTCTCTCTCTGCTTCT-GC
* *
5145903 TGCTGCTCTAGT-TGCTTCTGC
1 TGCTTCTCT-CTCTGCTTCTGC
*
5145924 TACTTCTCTCTCTGCTTC
1 TGCTTCTCTCTCTGCTTC
5145942 CCTTGCTTTA
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
20 1 0.02
21 43 0.93
22 2 0.04
ACGTcount: A:0.02, C:0.35, G:0.17, T:0.46
Consensus pattern (21 bp):
TGCTTCTCTCTCTGCTTCTGC
Found at i:5153479 original size:16 final size:16
Alignment explanation
Indices: 5153445--5153479 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5153435 CCAAACAAAT
*
5153445 AAATTGAAACACCATA
1 AAATTGAAACACCACA
*
5153461 AAATTGAAACACCGCA
1 AAATTGAAACACCACA
5153477 AAA
1 AAA
5153480 GTAGGTAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.20, G:0.09, T:0.14
Consensus pattern (16 bp):
AAATTGAAACACCACA
Found at i:5154735 original size:41 final size:42
Alignment explanation
Indices: 5154655--5154748 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 42
5154645 TAAATTATTA
* *
5154655 CGGCGTTTATTACGAAAATACCACTAACGGAGAAAACAATTG
1 CGGCGTTTATTACGAAAATACCACTAAAGAAGAAAACAATTG
*
5154697 CGGCGTTTATTAC-AAAA-AGCCACTAAAGAAGAATACAATTG
1 CGGCGTTTATTACGAAAATA-CCACTAAAGAAGAAAACAATTG
*
5154738 CGGCATTTATT
1 CGGCGTTTATT
5154749 TAAAAACGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
40 1 0.02
41 33 0.70
42 13 0.28
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (42 bp):
CGGCGTTTATTACGAAAATACCACTAAAGAAGAAAACAATTG
Found at i:5154817 original size:41 final size:41
Alignment explanation
Indices: 5154693--5154970 Score: 211
Period size: 41 Copynumber: 6.8 Consensus size: 41
5154683 GGAGAAAACA
* * * *
5154693 ATTGCGGCGTTTAT-TACAAAAAGCCACTAAAG-AAGAATACA
1 ATTGCGGCGTTTATATA-AAAACGCCACTAAAGTACGAGT-CT
* * * * ** *
5154734 ATTGCGGCATTTATTTAAAAACGCCGC-AAAATATTATATCT
1 ATTGCGGCGTTTATATAAAAACGCCACTAAAGTACGA-GTCT
*
5154775 ATTGCGGCGTTTATCTAAAAACGCCACTAAAGTACGAGTCT
1 ATTGCGGCGTTTATATAAAAACGCCACTAAAGTACGAGTCT
* * * *
5154816 ATAGCGACGTTTGTATAAAAACGCCACTAAAGTACTAGTCT
1 ATTGCGGCGTTTATATAAAAACGCCACTAAAGTACGAGTCT
* ** *
5154857 ATTGCGGCGTTTATATAAAAATGCTGCTAAAGTACGAGTTT
1 ATTGCGGCGTTTATATAAAAACGCCACTAAAGTACGAGTCT
* * * * * * * *
5154898 ATAGTGGCTTTTAGATTCAAAATGCCACTAAAGTATGAGTAT
1 ATTGCGGCGTTTATA-TAAAAACGCCACTAAAGTACGAGTCT
* * * *
5154940 ATAGCGGCATTTGTATAGAAACGCCACTAAA
1 ATTGCGGCGTTTATATAAAAACGCCACTAAA
5154971 CGTTTGTATA
Statistics
Matches: 189, Mismatches: 43, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
40 3 0.02
41 144 0.76
42 42 0.22
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (41 bp):
ATTGCGGCGTTTATATAAAAACGCCACTAAAGTACGAGTCT
Found at i:5154970 original size:83 final size:82
Alignment explanation
Indices: 5154778--5154970 Score: 201
Period size: 83 Copynumber: 2.3 Consensus size: 82
5154768 TATATCTATT
* *
5154778 GCGGCGTTTATCTAAAAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCAC
1 GCGGCATTTATATAAAAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCAC
* *
5154843 TAAAGTACTAGTCTATT
66 TAAAGTACTAGTATATA
* * ** * * * * * *
5154860 GCGGCGTTTATATAAAAATGCTGCTAAAGTACGAGTTTATAGTGGCTTTTAG-ATTCAAAATGCC
1 GCGGCATTTATATAAAAACGCCACTAAAGTACGAGTCTATAGCGACGTTT-GTA-TAAAAACGCC
5154924 ACTAAAGTA-TGAGTATATA
64 ACTAAAGTACT-AGTATATA
* *
5154943 GCGGCATTTGTATAGAAACGCCACTAAA
1 GCGGCATTTATATAAAAACGCCACTAAA
5154971 CGTTTGTATA
Statistics
Matches: 90, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
82 44 0.49
83 46 0.51
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (82 bp):
GCGGCATTTATATAAAAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCAC
TAAAGTACTAGTATATA
Found at i:5155047 original size:40 final size:41
Alignment explanation
Indices: 5154971--5155056 Score: 113
Period size: 40 Copynumber: 2.1 Consensus size: 41
5154961 CGCCACTAAA
* *
5154971 CGTTTGTATAAAAACGCCACTAATGTACGATTCTATAGCAG
1 CGTTTGTATAAAAACGCCACTAAAGTACGATCCTATAGCAG
* *
5155012 CGTTTGTATAAAAATG-CACTAAAGTACG-TACCTATAGCGG
1 CGTTTGTATAAAAACGCCACTAAAGTACGAT-CCTATAGCAG
5155052 CGTTT
1 CGTTT
5155057 ATTGGAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
39 1 0.03
40 24 0.60
41 15 0.38
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (41 bp):
CGTTTGTATAAAAACGCCACTAAAGTACGATCCTATAGCAG
Found at i:5156529 original size:41 final size:40
Alignment explanation
Indices: 5156462--5156613 Score: 182
Period size: 41 Copynumber: 3.8 Consensus size: 40
5156452 GTTTATACAA
5156462 AAAAAACACCACTATTGATT-ACACTATTGTGGCGTTTGTT
1 AAAAAACACCACTATTGATTAACACTATTGTGGCGTTT-TT
*
5156502 AAAAAACACCACTATTGATTAAAACTATTGTGGCGTTTTT
1 AAAAAACACCACTATTGATTAACACTATTGTGGCGTTTTT
* * **
5156542 CTAAAAACGCCACTATTGATTAACACTATTACGGCGTTTATCT
1 -AAAAAACACCACTATTGATTAACACTATTGTGGCGTTT-T-T
* * *
5156585 -AAAAACGCCACTATTTATTATCACTATTG
1 AAAAAACACCACTATTGATTAACACTATTG
5156614 CGATGTTTTA
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
40 22 0.22
41 75 0.76
42 1 0.01
43 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (40 bp):
AAAAAACACCACTATTGATTAACACTATTGTGGCGTTTTT
Found at i:5156589 original size:82 final size:81
Alignment explanation
Indices: 5156463--5156613 Score: 205
Period size: 82 Copynumber: 1.9 Consensus size: 81
5156453 TTTATACAAA
** *
5156463 AAAAACACCACTATTGATTACACTATTGTGGCGTTTGTTAAAAAACACCACTATTGATTAAAACT
1 AAAAACACCACTATTGATTACACTATTACGGCGTTTATTAAAAAACACCACTATTGATTAAAACT
5156528 ATTGTGGCGTTTTTCT
66 ATTGTGGCGTTTTTCT
* * * **
5156544 AAAAACGCCACTATTGATTAACACTATTACGGCGTTTATCT-AAAAACGCCACTATTTATTATCA
1 AAAAACACCACTATTGATT-ACACTATTACGGCGTTTAT-TAAAAAACACCACTATTGATTAAAA
5156608 CTATTG
64 CTATTG
5156614 CGATGTTTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
81 18 0.30
82 41 0.68
83 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (81 bp):
AAAAACACCACTATTGATTACACTATTACGGCGTTTATTAAAAAACACCACTATTGATTAAAACT
ATTGTGGCGTTTTTCT
Found at i:5156743 original size:40 final size:41
Alignment explanation
Indices: 5156627--5156758 Score: 155
Period size: 42 Copynumber: 3.2 Consensus size: 41
5156617 TGTTTTAAGA
* * *
5156627 ATAAATGCCACTATATGTGTAATCTATTACGGCGTTTGTTGT
1 ATAAACGCCACTATATGT-TAATCTATTGCGGCGTTTGTGGT
*
5156669 ATAAACGCCACTA-AT-TTACCGATCTATTGTGGCGTTT-TGGCT
1 ATAAACGCCACTATATGTTA---ATCTATTGCGGCGTTTGTGG-T
5156711 A-AAACGCCACTATATGTTAATCTATTGCGGCGTTTGTGGT
1 ATAAACGCCACTATATGTTAATCTATTGCGGCGTTTGTGGT
5156751 ATAAACGC
1 ATAAACGC
5156759 TGTTAATTTA
Statistics
Matches: 77, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
39 2 0.03
40 18 0.23
41 24 0.31
42 30 0.39
43 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (41 bp):
ATAAACGCCACTATATGTTAATCTATTGCGGCGTTTGTGGT
Found at i:5156779 original size:42 final size:41
Alignment explanation
Indices: 5156648--5156789 Score: 157
Period size: 42 Copynumber: 3.4 Consensus size: 41
5156638 TATATGTGTA
* *
5156648 ATCTATTACGGCGTTTGTTGTATAAACGCCACTAATTTACC
1 ATCTATTGCGGCGTTTGTGGTATAAACGCCACTAATTTACC
*
5156689 GATCTATTGTGGCGTTT-TGGCTA-AAACGCCACTATATGTTA--
1 -ATCTATTGCGGCGTTTGTGG-TATAAACGCCACTA-AT-TTACC
***
5156730 ATCTATTGCGGCGTTTGTGGTATAAACGCTGTTAATTTACC
1 ATCTATTGCGGCGTTTGTGGTATAAACGCCACTAATTTACC
5156771 ACTCTATTGCGGCGTTTGT
1 A-TCTATTGCGGCGTTTGT
5156790 TAAAAAACGT
Statistics
Matches: 85, Mismatches: 7, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
39 3 0.04
40 19 0.22
41 25 0.29
42 35 0.41
43 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (41 bp):
ATCTATTGCGGCGTTTGTGGTATAAACGCCACTAATTTACC
Found at i:5156798 original size:82 final size:83
Alignment explanation
Indices: 5156633--5156787 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 83
5156623 AAGAATAAAT
*
5156633 GCCACTATATGTGTAATCTATTACGGCGTTTGTTGTATAAACGCCACTAATTTACCGATCTATTG
1 GCCACTATATGTGTAATCTATTACGGCGTTTGTGGTATAAACGCCACTAATTTACCGATCTATTG
*
5156698 TGGCGTTTTGGCTAAAAC
66 CGGCGTTTTGGCTAAAAC
* ***
5156716 GCCACTATATGT-TAATCTATTGCGGCGTTTGTGGTATAAACGCTGTTAATTTACC-ACTCTATT
1 GCCACTATATGTGTAATCTATTACGGCGTTTGTGGTATAAACGCCACTAATTTACCGA-TCTATT
5156779 GCGGCGTTT
65 GCGGCGTTT
5156788 GTTAAAAAAC
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 1 0.02
82 52 0.80
83 12 0.18
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.37
Consensus pattern (83 bp):
GCCACTATATGTGTAATCTATTACGGCGTTTGTGGTATAAACGCCACTAATTTACCGATCTATTG
CGGCGTTTTGGCTAAAAC
Found at i:5158834 original size:18 final size:18
Alignment explanation
Indices: 5158803--5158837 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5158793 GGGGCACAGA
5158803 ATAACACATACAACAACC
1 ATAACACATACAACAACC
5158821 ATAAGCACAT-CAACAAC
1 ATAA-CACATACAACAAC
5158838 AAATACATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.54, C:0.31, G:0.03, T:0.11
Consensus pattern (18 bp):
ATAACACATACAACAACC
Found at i:5160143 original size:2 final size:2
Alignment explanation
Indices: 5160136--5160162 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5160126 TTATATTACG
5160136 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5160163 TAGAGATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5168665 original size:21 final size:21
Alignment explanation
Indices: 5168640--5168687 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
5168630 TCATCTATAT
*
5168640 TTTAATAATATATAA-AAATTA
1 TTTAATAATA-AAAATAAATTA
5168661 TTTAATAATAAAAATAAATTA
1 TTTAATAATAAAAATAAATTA
5168682 -TTAATA
1 TTTAATA
5168688 TGATTGATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTAATAATAAAAATAAATTA
Found at i:5168686 original size:17 final size:17
Alignment explanation
Indices: 5168645--5168687 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5168635 TATATTTTAA
* *
5168645 TAATATATAAAAATTATT
1 TAATA-ATAAAAATAAAT
5168663 TAATAATAAAAATAAAT
1 TAATAATAAAAATAAAT
*
5168680 TATTAATA
1 TAATAATA
5168688 TGATTGATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAATAATAAAAATAAAT
Found at i:5168743 original size:21 final size:21
Alignment explanation
Indices: 5168694--5168749 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
5168684 AATATGATTG
5168694 ATACTACTTATTATTT--TATT
1 ATACTA-TTATTATTTAATATT
*
5168714 A-A-AATTATTATTTAATATT
1 ATACTATTATTATTTAATATT
5168733 ATACTATTATTATTTAA
1 ATACTATTATTATTTAA
5168750 CCTTTTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 9 0.30
18 1 0.03
19 6 0.20
20 2 0.07
21 12 0.40
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
ATACTATTATTATTTAATATT
Found at i:5169391 original size:63 final size:63
Alignment explanation
Indices: 5169292--5169417 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
5169282 CCCATCAGAA
5169292 ATGGAGGACTTGAGGAACTGTATGACAAGTCTGGGATTAGTGGATCACCCCTTCTTTGGGCAT
1 ATGGAGGACTTGAGGAACTGTATGACAAGTCTGGGATTAGTGGATCACCCCTTCTTTGGGCAT
5169355 ATGGAGGACTTGAGGAACTGTATGACAAGTCTGGGATTAGTGGATCACCCCTTCTTTGGGCAT
1 ATGGAGGACTTGAGGAACTGTATGACAAGTCTGGGATTAGTGGATCACCCCTTCTTTGGGCAT
5169418 GTTTTCACTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (63 bp):
ATGGAGGACTTGAGGAACTGTATGACAAGTCTGGGATTAGTGGATCACCCCTTCTTTGGGCAT
Found at i:5171880 original size:21 final size:21
Alignment explanation
Indices: 5171824--5171882 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
5171814 AGGGTGTCAA
* *
5171824 AGTGCATTCATGCACCCCTGC
1 AGTGCATCCATGCATCCCTGC
5171845 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
5171866 AGTGTATCCATGCATCC
1 AGTGCATCCATGCATCC
5171883 ATACACCTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.20, C:0.36, G:0.19, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:5171975 original size:20 final size:20
Alignment explanation
Indices: 5171950--5172006 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
5171940 AAATGCAATT
5171950 AGTGCATCGATGCATCATTC
1 AGTGCATCGATGCATCATTC
*
5171970 AGTGCATCGATGCATCCTTC
1 AGTGCATCGATGCATCATTC
*
5171990 TGTGCATCGATGCATCA
1 AGTGCATCGATGCATCA
5172007 AGGCTGTGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (20 bp):
AGTGCATCGATGCATCATTC
Found at i:5172035 original size:41 final size:41
Alignment explanation
Indices: 5171951--5172053 Score: 113
Period size: 41 Copynumber: 2.5 Consensus size: 41
5171941 AATGCAATTA
** * *
5171951 GTGCATCGATGCATC-ATTCAGTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCAAGGCTGTGCATCGATGCATCCTTAT
*
5171991 GTGCATCGATGCATCAAGGCTGTGTATCGATGCAT-CTTGAT
1 GTGCATCGATGCATCAAGGCTGTGCATCGATGCATCCTT-AT
*
5172032 GTGCATCCATGCA-CGAAGGCTG
1 GTGCATCGATGCATC-AAGGCTG
5172054 CAACGGCTAG
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
40 19 0.35
41 35 0.65
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.29
Consensus pattern (41 bp):
GTGCATCGATGCATCAAGGCTGTGCATCGATGCATCCTTAT
Found at i:5172043 original size:20 final size:21
Alignment explanation
Indices: 5171951--5172044 Score: 95
Period size: 20 Copynumber: 4.6 Consensus size: 21
5171941 AATGCAATTA
*
5171951 GTGCATCGATGCATCATTCA-
1 GTGCATCGATGCATCATTGAT
* *
5171971 GTGCATCGATGCATCCTT-CT
1 GTGCATCGATGCATCATTGAT
** *
5171991 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCATTGAT
*
5172012 GTGTATCGATGCATC-TTGAT
1 GTGCATCGATGCATCATTGAT
*
5172032 GTGCATCCATGCA
1 GTGCATCGATGCA
5172045 CGAAGGCTGC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
20 45 0.74
21 16 0.26
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.31
Consensus pattern (21 bp):
GTGCATCGATGCATCATTGAT
Found at i:5172451 original size:34 final size:32
Alignment explanation
Indices: 5172412--5172481 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
5172402 TTTTGTAAAG
* *
5172412 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
5172446 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
5172478 GGGA
1 GGGA
5172482 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:5176413 original size:3 final size:3
Alignment explanation
Indices: 5176405--5176458 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
5176395 ACTTAAAAAG
* *
5176405 ATT ATT ATT ATT ATT ATA ATA ATT ATT ATT ATT A-T ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5176452 ATT ATT A
1 ATT ATT A
5176459 AATAATAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:5176477 original size:20 final size:20
Alignment explanation
Indices: 5176405--5176471 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
5176395 ACTTAAAAAG
*
5176405 ATTATTATTATTATTATAATA
1 ATTATTATTATTA-AATAATA
* * *
5176426 ATTATTATTATTATATTATT
1 ATTATTATTATTAAATAATA
5176446 ATTATTATTATTAAATAATA
1 ATTATTATTATTAAATAATA
5176466 ATTATT
1 ATTATT
5176472 TATATTGCAG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 28 0.68
21 13 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTATTATTATTAAATAATA
Found at i:5178640 original size:14 final size:15
Alignment explanation
Indices: 5178610--5178642 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5178600 TTTGTCTTAA
5178610 AAAATGATTTTTCTT
1 AAAATGATTTTTCTT
*
5178625 AAAATTATTTTT-TT
1 AAAATGATTTTTCTT
5178639 AAAA
1 AAAA
5178643 GACATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (15 bp):
AAAATGATTTTTCTT
Found at i:5186196 original size:27 final size:28
Alignment explanation
Indices: 5186155--5186209 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
5186145 ATGCTAAAAA
5186155 GAAGGCTTTGCCGCTAAGTTTTAGCATG
1 GAAGGCTTTGCCGCTAAGTTTTAGCATG
5186183 GAAGGC-TTGCCGCTAAGTTTTAGCATG
1 GAAGGCTTTGCCGCTAAGTTTTAGCATG
5186210 CTCACACCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (28 bp):
GAAGGCTTTGCCGCTAAGTTTTAGCATG
Found at i:5186767 original size:13 final size:13
Alignment explanation
Indices: 5186739--5186790 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
5186729 TTCATTTGTA
*
5186739 TTAAACCCTAAACC
1 TTAAA-CCTAAGCC
5186753 TTAAACCTAAGCC
1 TTAAACCTAAGCC
*
5186766 TTAAACATCAAGCC
1 TTAAACCT-AAGCC
*
5186780 CTAAACTCTAA
1 TTAAAC-CTAA
5186791 ATCATAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 14 0.44
14 17 0.53
15 1 0.03
ACGTcount: A:0.42, C:0.31, G:0.04, T:0.23
Consensus pattern (13 bp):
TTAAACCTAAGCC
Found at i:5189583 original size:17 final size:17
Alignment explanation
Indices: 5189561--5189624 Score: 110
Period size: 17 Copynumber: 3.8 Consensus size: 17
5189551 AAATTCGAGT
5189561 TCGAGTTCGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
*
5189578 TCGAGTTCGAGTTTGAA
1 TCGAGTTCGAGCTTGAA
*
5189595 TCGAGTTCTAGCTTGAA
1 TCGAGTTCGAGCTTGAA
5189612 TCGAGTTCGAGCT
1 TCGAGTTCGAGCT
5189625 CAAAATCGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (17 bp):
TCGAGTTCGAGCTTGAA
Found at i:5189644 original size:23 final size:23
Alignment explanation
Indices: 5189618--5189671 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
5189608 TGAATCGAGT
5189618 TCGAGCTC-AAAATCGAGCTTCAA
1 TCGAGCTCGAAAATCGAGCTTC-A
***
5189641 TCGAGCTCGAGTCTCGAGCTTCA
1 TCGAGCTCGAAAATCGAGCTTCA
5189664 TCGAGCTC
1 TCGAGCTC
5189672 CTGAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (23 bp):
TCGAGCTCGAAAATCGAGCTTCA
Found at i:5189880 original size:173 final size:173
Alignment explanation
Indices: 5189679--5190021 Score: 537
Period size: 173 Copynumber: 2.0 Consensus size: 173
5189669 CTCCTGAATT
* * *
5189679 TTTTTTGAGTTCGAGCCTTTTCGAGTTCGAGTCCAGTTTCAATATTATCTTTCGAGTTTGAGTCG
1 TTTTTTAAGTTCGAGCCTTTTCGAGTTCGAGTCCAGTTTCAATATTATCTTTCAAGTTCGAGTCG
*
5189744 AGCTTGAAAATTTTAAGCTCGCGAGTTTTCGAGTCGA-T-CTACATTTAAAGTTTTCGAGTTCGA
66 AGCTTGAAAATTTTAAGCT--CGAGTTTTCGAGTCGAGTCCTACATTTAAAATTTTCGAGTTCGA
*
5189807 GTCGAGCTTGGCAATACTCGAGCTCGACTCGGCTCGTTCCTCTGA
129 GTCGAGCTTGACAATACTCGAGCTCGACTCGGCTCGTTCCTCTGA
* *
5189852 TTTTTTAAGTTCGAGCCTTTTTGAGTTCGAGTCGAGTTTCAATATTATCTTTCAAGTTCGAGTCG
1 TTTTTTAAGTTCGAGCCTTTTCGAGTTCGAGTCCAGTTTCAATATTATCTTTCAAGTTCGAGTCG
*
5189917 AGCTTGAAAATTTTAAGCTCGTGTTTTCGAGTCGAGTCGAGCCTACATTTAAAATTTTCGAGTTC
66 AGCTTGAAAATTTTAAGCTCGAGTTTTCGAGTCGAGT----CCTACATTTAAAATTTTCGAGTTC
*
5189982 GAGTCGAGCTTGATAATACTCGAGCTCGACTCGGCTCGTT
127 GAGTCGAGCTTGACAATACTCGAGCTCGACTCGGCTCGTT
5190022 TACACCATAG
Statistics
Matches: 155, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
171 15 0.10
172 1 0.01
173 79 0.51
177 60 0.39
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (173 bp):
TTTTTTAAGTTCGAGCCTTTTCGAGTTCGAGTCCAGTTTCAATATTATCTTTCAAGTTCGAGTCG
AGCTTGAAAATTTTAAGCTCGAGTTTTCGAGTCGAGTCCTACATTTAAAATTTTCGAGTTCGAGT
CGAGCTTGACAATACTCGAGCTCGACTCGGCTCGTTCCTCTGA
Found at i:5190365 original size:23 final size:23
Alignment explanation
Indices: 5190338--5190403 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
5190328 GAAATTCTTC
*
5190338 ATTAAAATAAAGT-TAAAATCAAA
1 ATTAAAATAAA-TATAAAATAAAA
* *
5190361 TTTAAAATTAATATAAAATAAAA
1 ATTAAAATAAATATAAAATAAAA
*
5190384 ATAAAAATAAA-A-AAAATAAA
1 ATTAAAATAAATATAAAATAAA
5190404 TTTAATTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 8 0.22
22 2 0.06
23 26 0.72
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (23 bp):
ATTAAAATAAATATAAAATAAAA
Found at i:5190856 original size:19 final size:20
Alignment explanation
Indices: 5190834--5190871 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5190824 AGTTTTCAAA
5190834 TTCGC-ACGCGAATTTCGTT
1 TTCGCAACGCGAATTTCGTT
*
5190853 TTCGCAACTCGAATTTCGT
1 TTCGCAACGCGAATTTCGT
5190872 AACGCTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.37
Consensus pattern (20 bp):
TTCGCAACGCGAATTTCGTT
Found at i:5191100 original size:20 final size:20
Alignment explanation
Indices: 5191077--5191137 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
5191067 AAATTCGCAA
*
5191077 TACGAATTTGAAAACCACGT
1 TACGAATTTAAAAACCACGT
5191097 TACGAATTTAAAAAACCACGT
1 TACGAATTT-AAAAACCACGT
*
5191118 T-CGAATTTAAAAACCGCGT
1 TACGAATTTAAAAACCACGT
5191137 T
1 T
5191138 GCGATTTTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 11 0.29
20 16 0.42
21 11 0.29
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (20 bp):
TACGAATTTAAAAACCACGT
Found at i:5191146 original size:20 final size:19
Alignment explanation
Indices: 5191087--5191146 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
5191077 TACGAATTTG
*
5191087 AAAACCACGTTACGAATTTAA
1 AAAACCACGTT-CG-ATTTTA
*
5191108 AAAACCACGTTCGAATTTA
1 AAAACCACGTTCGATTTTA
*
5191127 AAAACCGCGTTGCGATTTTA
1 AAAACCACGTT-CGATTTTA
5191147 GAGAATCGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 14 0.41
20 9 0.26
21 11 0.32
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (19 bp):
AAAACCACGTTCGATTTTA
Found at i:5191265 original size:68 final size:70
Alignment explanation
Indices: 5191183--5191317 Score: 256
Period size: 69 Copynumber: 2.0 Consensus size: 70
5191173 TTATTTTTTC
5191183 AAATAAAAAAATGATT-AAAATTACATATTATAAGACATTTTCGATCACTGAAATTATTCTCAAA
1 AAATAAAAAAATGATTAAAAATTACATATTATAAGACATTTTCGATCACTGAAATTATTCTCAAA
5191247 AAATA
66 AAATA
5191252 AAAT-AAAAAATGATTAAAAATTACATATTATAAGACATTTTCGATCACTGAAATTATTCTCAAA
1 AAATAAAAAAATGATTAAAAATTACATATTATAAGACATTTTCGATCACTGAAATTATTCTCAAA
5191316 AA
66 AA
5191318 TAATCAGCAG
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
68 11 0.17
69 54 0.83
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (70 bp):
AAATAAAAAAATGATTAAAAATTACATATTATAAGACATTTTCGATCACTGAAATTATTCTCAAA
AAATA
Found at i:5196703 original size:24 final size:25
Alignment explanation
Indices: 5196671--5196717 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
5196661 TTATTCTTTC
5196671 ACTTCAATCAAGC-TCGAATTTTAG
1 ACTTCAATCAAGCTTCGAATTTTAG
* * *
5196695 ACTTTAATCGAGCTTCTAATTTT
1 ACTTCAATCAAGCTTCGAATTTT
5196718 TTTTGAGTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (25 bp):
ACTTCAATCAAGCTTCGAATTTTAG
Found at i:5200105 original size:2 final size:2
Alignment explanation
Indices: 5200098--5200131 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
5200088 TATTTTTAAC
* *
5200098 AT AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5200132 GAAGTGTTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:5204744 original size:14 final size:14
Alignment explanation
Indices: 5204727--5204778 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
5204717 ATTTATATTT
5204727 GTTTATGTTTGTTC
1 GTTTATGTTTGTTC
5204741 GTTTATG-TTGATTC
1 GTTTATGTTTG-TTC
***
5204755 GTTTATGTGCATTC
1 GTTTATGTTTGTTC
5204769 GTTTATGTTT
1 GTTTATGTTT
5204779 AGCCCAATCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 3 0.10
14 28 0.90
ACGTcount: A:0.12, C:0.08, G:0.21, T:0.60
Consensus pattern (14 bp):
GTTTATGTTTGTTC
Found at i:5206417 original size:60 final size:59
Alignment explanation
Indices: 5206310--5206432 Score: 151
Period size: 60 Copynumber: 2.1 Consensus size: 59
5206300 AGGTGATCAC
* *
5206310 TTTGTAATTTTTAATAGTCATGTGACTCAACAAAGCATTACTCTATAGTCAATGGACCAT
1 TTTGTAACTTTTAATAGTCATGTGACTCAAAAAAGCA-TACTCTATAGTCAATGGACCAT
* * *
5206370 TTTGTAACTTTTAATAGTCATAG-GACTCAAAAAAGCA-ACATGTTATAGTCAGTGGACTAT
1 TTTGTAACTTTTAATAGTCAT-GTGACTCAAAAAAGCATAC-T-CTATAGTCAATGGACCAT
5206430 TTT
1 TTT
5206433 TGTACATTAC
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
58 2 0.04
59 1 0.02
60 51 0.93
61 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (59 bp):
TTTGTAACTTTTAATAGTCATGTGACTCAAAAAAGCATACTCTATAGTCAATGGACCAT
Found at i:5206903 original size:12 final size:12
Alignment explanation
Indices: 5206872--5206911 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5206862 AACGAGTTTA
5206872 TTAAAAATATTT
1 TTAAAAATATTT
*
5206884 ATAAAAATATTT
1 TTAAAAATATTT
* *
5206896 TTATAAATTTTT
1 TTAAAAATATTT
5206908 TTAA
1 TTAA
5206912 TGGTACTCGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAAAATATTT
Found at i:5206927 original size:2 final size:2
Alignment explanation
Indices: 5206922--5206949 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5206912 TGGTACTCGG
5206922 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5206950 TATTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5210130 original size:50 final size:50
Alignment explanation
Indices: 5210057--5210152 Score: 183
Period size: 50 Copynumber: 1.9 Consensus size: 50
5210047 ACTAAGCTCA
*
5210057 CACCTAGGTCTCAGTGGAGTGTCATGACTTTCAGTAGCAAGGATGGACCT
1 CACCTAGGTCTCAGTGGAGTGTCATGACTTCCAGTAGCAAGGATGGACCT
5210107 CACCTAGGTCTCAGTGGAGTGTCATGACTTCCAGTAGCAAGGATGG
1 CACCTAGGTCTCAGTGGAGTGTCATGACTTCCAGTAGCAAGGATGG
5210153 TCCGGGTGGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (50 bp):
CACCTAGGTCTCAGTGGAGTGTCATGACTTCCAGTAGCAAGGATGGACCT
Found at i:5210980 original size:64 final size:63
Alignment explanation
Indices: 5210912--5211091 Score: 206
Period size: 65 Copynumber: 2.8 Consensus size: 63
5210902 TTGGACCCTT
*
5210912 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAAC-CAG
1 AGTGCATCGATGCACT-AGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAA-AACTCAG
* * *
5210976 AGTGCATCGATACATGGCT-G-GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACTC
1 AGTGCATCGATGCA---CTAGAGTGCATCGATGCATGAAATGCATTCGATG-TTTCAAAAAACTC
*
5211039 TG
62 AG
*
5211041 AGTGCATCGATGCA-TAGTATGTGCATCGATACATGAAATGCATTCGATGTT
1 AGTGCATCGATGCACTAG-A-GTGCATCGATGCATGAAATGCATTCGATGTT
5211092 CAATTTATTC
Statistics
Matches: 99, Mismatches: 8, Indels: 18
0.79 0.06 0.14
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
64 45 0.45
65 50 0.51
67 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (63 bp):
AGTGCATCGATGCACTAGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAAAACTCAG
Found at i:5211065 original size:65 final size:65
Alignment explanation
Indices: 5210932--5211091 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
5210922 TGCACTAAGA
*
5210932 GTGCATCGATGCATGAAATGCATTCGATG-TTTCAAAATAACCAGAGTGCATCGATACATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAACCAGAGTGCATCGATACATAGCTG
* * * *
5210996 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAA-AACTCTGAGTGCATCGATGCATAG-T
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAAC-CAGAGTGCATCGATACATAGCT
*
5211059 AT
65 -G
*
5211061 GTGCATCGATACATGAAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
5211092 CAATTTATTC
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 32 0.38
65 53 0.62
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAACCAGAGTGCATCGATACATAGCTG
Found at i:5211130 original size:65 final size:64
Alignment explanation
Indices: 5210932--5211132 Score: 216
Period size: 65 Copynumber: 3.1 Consensus size: 64
5210922 TGCACTAAGA
* * *
5210932 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAACCA-GAGTGCATCGATACATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTC-AATTAACCATGAGTGCATCGATGCATGGTTG
* * *
5210996 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAACTC-TGAGTGCATCGATGCATAGT
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCAAT-TAAC-CATGAGTGCATCGATGCATGGT
5211059 AT-
63 -TG
* *
5211061 GTGCATCGATACATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA-TTA-ACCATGAGTGCATCGATGCATGG-T
5211124 TG
63 TG
5211126 GTGCATC
1 GTGCATC
5211133 ACTTTGAAAA
Statistics
Matches: 115, Mismatches: 11, Indels: 21
0.78 0.07 0.14
Matches are distributed among these distances:
63 4 0.03
64 50 0.43
65 60 0.52
66 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAACCATGAGTGCATCGATGCATGGTTG
Found at i:5212674 original size:53 final size:53
Alignment explanation
Indices: 5212599--5212700 Score: 195
Period size: 53 Copynumber: 1.9 Consensus size: 53
5212589 ACTAAGCTCA
*
5212599 CACCTAGGTCTCAGTGGAGTGTCATGACTTTCAGTAGCAAGGATGGTCCACCT
1 CACCTAGGTCTCAGTGGAGTGTCATGACTTCCAGTAGCAAGGATGGTCCACCT
5212652 CACCTAGGTCTCAGTGGAGTGTCATGACTTCCAGTAGCAAGGATGGTCC
1 CACCTAGGTCTCAGTGGAGTGTCATGACTTCCAGTAGCAAGGATGGTCC
5212701 GGGTGGATGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (53 bp):
CACCTAGGTCTCAGTGGAGTGTCATGACTTCCAGTAGCAAGGATGGTCCACCT
Found at i:5214077 original size:19 final size:20
Alignment explanation
Indices: 5214041--5214078 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
5214031 AAAAAAAAAA
* *
5214041 GTATGAAATTGAGTGATTTT
1 GTATGAAATTAAGCGATTTT
5214061 GTAT-AAATTAAGCGATTT
1 GTATGAAATTAAGCGATTT
5214079 ATGATTGATC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.34, C:0.03, G:0.21, T:0.42
Consensus pattern (20 bp):
GTATGAAATTAAGCGATTTT
Found at i:5221834 original size:21 final size:20
Alignment explanation
Indices: 5221806--5221849 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
5221796 TATATATATC
*
5221806 TAATAGCACTATAGATAAAA
1 TAATAGCACTATAAATAAAA
5221826 TAATAAGCACTATAAATAAAA
1 TAAT-AGCACTATAAATAAAA
5221847 TAA
1 TAA
5221850 GGGTAAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.25
Consensus pattern (20 bp):
TAATAGCACTATAAATAAAA
Found at i:5222256 original size:16 final size:16
Alignment explanation
Indices: 5222237--5222270 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5222227 CAATATACGA
5222237 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
5222253 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
5222269 AT
1 AT
5222271 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:5222344 original size:16 final size:18
Alignment explanation
Indices: 5222312--5222345 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
5222302 TATTAATGTA
5222312 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
5222330 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
5222346 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:5223020 original size:130 final size:130
Alignment explanation
Indices: 5222816--5223063 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
5222806 AATTTTCTTC
* *
5222816 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAAAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAAAT
** * *
5222881 CCTGGTTAAATGATTAATTTATTTAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTATATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
5222946 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAAAT
5223011 CCTAATTAAATGATTAATTTATTAAATTATATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTATATTTAATTTAGGACCAAATTGAT
5223064 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAAAT
CCTAATTAAATGATTAATTTATTAAATTATATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:5225016 original size:16 final size:17
Alignment explanation
Indices: 5224982--5225021 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
5224972 TTATATGAAA
*
5224982 TGATATGTGCTTATATG
1 TGATATGTGATTATATG
*
5224999 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
5225015 TGATATG
1 TGATATG
5225022 CCATATGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:5225619 original size:23 final size:23
Alignment explanation
Indices: 5225585--5225671 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
5225575 ACATATTATA
5225585 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
5225608 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
5225631 CGGTC-CTTCGG-GACAAAATTCTACG
1 TGG-CACTACGGTG-C--AATTCTACG
5225656 TGGCACTACGGTGCAA
1 TGGCACTACGGTGCAA
5225672 ATTTATATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
22 1 0.02
23 32 0.62
24 2 0.04
25 16 0.31
26 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:5227137 original size:30 final size:29
Alignment explanation
Indices: 5227073--5227188 Score: 151
Period size: 29 Copynumber: 4.0 Consensus size: 29
5227063 TTTCGGTTAT
*
5227073 GGTGTTATTTTCGTAATTATTTTTAAAAG
1 GGTGTTATTTTTGTAATTATTTTTAAAAG
* *
5227102 TGTGTTATTTTTGTATTTATTTTTAAAAAG
1 GGTGTTATTTTTGTAATTATTTTT-AAAAG
* *
5227132 GGTGTTATTTTTGTAATTAATTTTAAAAC
1 GGTGTTATTTTTGTAATTATTTTTAAAAG
* * *
5227161 GGTGCTATTTTGGTAATTATTGTTAAAA
1 GGTGTTATTTTTGTAATTATTTTTAAAA
5227189 AACAGTGATA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
29 49 0.65
30 26 0.35
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.53
Consensus pattern (29 bp):
GGTGTTATTTTTGTAATTATTTTTAAAAG
Found at i:5227141 original size:59 final size:59
Alignment explanation
Indices: 5227073--5227189 Score: 164
Period size: 59 Copynumber: 2.0 Consensus size: 59
5227063 TTTCGGTTAT
* * * * *
5227073 GGTGTTATTTTCGTAATTATTTTTAAAA-GTGTGTTATTTTTGTATTTATTTTTAAAAAG
1 GGTGTTATTTTCGTAATTAATTTTAAAACG-GTGCTATTTTGGTAATTATTGTTAAAAAG
*
5227132 GGTGTTATTTTTGTAATTAATTTTAAAACGGTGCTATTTTGGTAATTATTGTTAAAAA
1 GGTGTTATTTTCGTAATTAATTTTAAAACGGTGCTATTTTGGTAATTATTGTTAAAAA
5227190 ACAGTGATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
59 50 0.98
60 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (59 bp):
GGTGTTATTTTCGTAATTAATTTTAAAACGGTGCTATTTTGGTAATTATTGTTAAAAAG
Found at i:5227203 original size:59 final size:59
Alignment explanation
Indices: 5227078--5227209 Score: 149
Period size: 59 Copynumber: 2.2 Consensus size: 59
5227068 GTTATGGTGT
* * * * * ** *
5227078 TATTTTCGTAATTATTTTTAAAAGTGTGTTATTTTTGTATTTATTTTTAAAAAGGGTGT
1 TATTTTCGTAATTAATTTTAAAAGTGTGCTATTTTGGTAATTATTTTAAAAAACAGTGA
*
5227137 TATTTTTGTAATTAATTTTAAAACG-GTGCTATTTTGGTAATTATTGTTAAAAAACAGTGA
1 TATTTTCGTAATTAATTTTAAAA-GTGTGCTATTTTGGTAATTATT-TTAAAAAACAGTGA
*
5227197 TATTTTGGTAATT
1 TATTTTCGTAATT
5227210 GTTTAAAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 38 0.62
60 23 0.38
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (59 bp):
TATTTTCGTAATTAATTTTAAAAGTGTGCTATTTTGGTAATTATTTTAAAAAACAGTGA
Found at i:5227215 original size:29 final size:31
Alignment explanation
Indices: 5227156--5227219 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
5227146 AATTAATTTT
* * *
5227156 AAAACGGTGCTATTTTGGTAATTATTGTTAA
1 AAAACAGTGATATTTTGGTAATTAGTGTTAA
5227187 AAAACAGTGATATTTTGGTAATT-GT-TTAA
1 AAAACAGTGATATTTTGGTAATTAGTGTTAA
5227216 AAAA
1 AAAA
5227220 TGATATTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 8 0.27
30 1 0.03
31 21 0.70
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (31 bp):
AAAACAGTGATATTTTGGTAATTAGTGTTAA
Found at i:5233867 original size:21 final size:20
Alignment explanation
Indices: 5233839--5233923 Score: 109
Period size: 21 Copynumber: 4.2 Consensus size: 20
5233829 TATATATATC
*
5233839 TAATAGCACTATAGATAAAA
1 TAATAGCACTATAAATAAAA
5233859 TAATAAGCACTATAAATAAAA
1 TAAT-AGCACTATAAATAAAA
**
5233880 TAATAAGCACTATAAATATTA
1 TAAT-AGCACTATAAATAAAA
5233901 TAATAGCACTA-AGAATAAAA
1 TAATAGCACTATA-AATAAAA
5233921 TAA
1 TAA
5233924 AATGAAGTGA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
19 1 0.02
20 19 0.33
21 38 0.66
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (20 bp):
TAATAGCACTATAAATAAAA
Found at i:5233909 original size:41 final size:41
Alignment explanation
Indices: 5233839--5233923 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
5233829 TATATATATC
*
5233839 TAATAGCACTATAGATAAAATAATAAGCACTATA-AATAAAA
1 TAATAGCACTATAAATAAAATAATAAGCACTA-AGAATAAAA
**
5233880 TAATAAGCACTATAAATATTATAAT-AGCACTAAGAATAAAA
1 TAAT-AGCACTATAAATAAAATAATAAGCACTAAGAATAAAA
5233921 TAA
1 TAA
5233924 AATGAAGTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 1 0.03
41 21 0.54
42 17 0.44
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (41 bp):
TAATAGCACTATAAATAAAATAATAAGCACTAAGAATAAAA
Found at i:5234473 original size:29 final size:29
Alignment explanation
Indices: 5234441--5234575 Score: 146
Period size: 29 Copynumber: 4.6 Consensus size: 29
5234431 TTCGGTTATG
5234441 GTGTTATTTTCGTAATTATTTTTAAAAGT
1 GTGTTATTTTCGTAATTATTTTTAAAAGT
* * *
5234470 GTGTTATTTTTGTATTTATTTTTAAAAAGG
1 GTGTTATTTTCGTAATTATTTTT-AAAAGT
* *
5234500 GTGTTATTTTCGTAATTAATTTTAAAACT
1 GTGTTATTTTCGTAATTATTTTTAAAAGT
* * *
5234529 GT-TCTATTTTGGTAATTATTGTTAAAAAT
1 GTGT-TATTTTCGTAATTATTTTTAAAAGT
* *
5234558 AGTGATATTTTGGTAATT
1 -GTGTTATTTTCGTAATT
5234576 GTTTAAAAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.01
29 48 0.54
30 40 0.45
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (29 bp):
GTGTTATTTTCGTAATTATTTTTAAAAGT
Found at i:5234504 original size:30 final size:30
Alignment explanation
Indices: 5234440--5234575 Score: 134
Period size: 30 Copynumber: 4.6 Consensus size: 30
5234430 TTTCGGTTAT
5234440 GGTGTTATTTTCGTAATTATTTTT-AAAAG
1 GGTGTTATTTTCGTAATTATTTTTAAAAAG
* * *
5234469 TGTGTTATTTTTGTATTTATTTTTAAAAAG
1 GGTGTTATTTTCGTAATTATTTTTAAAAAG
* *
5234499 GGTGTTATTTTCGTAATTAATTTT-AAAAC
1 GGTGTTATTTTCGTAATTATTTTTAAAAAG
* * * *
5234528 TGT-TCTATTTTGGTAATTATTGTTAAAAAT
1 GGTGT-TATTTTCGTAATTATTTTTAAAAAG
* * *
5234558 AGTGATATTTTGGTAATT
1 GGTGTTATTTTCGTAATT
5234576 GTTTAAAAAA
Statistics
Matches: 88, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
28 1 0.01
29 43 0.49
30 44 0.50
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (30 bp):
GGTGTTATTTTCGTAATTATTTTTAAAAAG
Found at i:5234508 original size:59 final size:59
Alignment explanation
Indices: 5234440--5234575 Score: 175
Period size: 59 Copynumber: 2.3 Consensus size: 59
5234430 TTTCGGTTAT
* * * * *
5234440 GGTGTTATTTTCGTAATTATTTTTAAAAGTGTGT-TATTTTTGTATTTATTTTTAAAAAG
1 GGTGTTATTTTCGTAATTAATTTTAAAACTGT-TCTATTTTGGTAATTATTGTTAAAAAG
*
5234499 GGTGTTATTTTCGTAATTAATTTTAAAACTGTTCTATTTTGGTAATTATTGTTAAAAAT
1 GGTGTTATTTTCGTAATTAATTTTAAAACTGTTCTATTTTGGTAATTATTGTTAAAAAG
* * *
5234558 AGTGATATTTTGGTAATT
1 GGTGTTATTTTCGTAATT
5234576 GTTTAAAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
58 1 0.01
59 66 0.99
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (59 bp):
GGTGTTATTTTCGTAATTAATTTTAAAACTGTTCTATTTTGGTAATTATTGTTAAAAAG
Found at i:5234586 original size:30 final size:28
Alignment explanation
Indices: 5234533--5234595 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 28
5234523 AAAACTGTTC
*
5234533 TATTTTGGTAATTATTGTTAAAAATAGTGA
1 TATTTTGGTAATTATTG-TAAAAA-AATGA
*
5234563 TATTTTGGTAATTGTT-TAAAAAAAATGA
1 TATTTTGGTAATTATTGT-AAAAAAATGA
5234591 TATTT
1 TATTT
5234596 CTATAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 10 0.33
29 5 0.17
30 15 0.50
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (28 bp):
TATTTTGGTAATTATTGTAAAAAAATGA
Found at i:5234591 original size:28 final size:30
Alignment explanation
Indices: 5234533--5234595 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 30
5234523 AAAACTGTTC
* * *
5234533 TATTTTGGTAATTATTGTTAAAAATAGTGA
1 TATTTTGGTAATTAGTGTTAAAAAAAATGA
5234563 TATTTTGGTAATT-GT-TTAAAAAAAATGA
1 TATTTTGGTAATTAGTGTTAAAAAAAATGA
5234591 TATTT
1 TATTT
5234596 CTATAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 16 0.53
29 1 0.03
30 13 0.43
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (30 bp):
TATTTTGGTAATTAGTGTTAAAAAAAATGA
Found at i:5234602 original size:28 final size:27
Alignment explanation
Indices: 5234546--5234603 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
5234536 TTTGGTAATT
* * *
5234546 ATTGTTAAAAATAGTGATATTTTGGTA
1 ATTGTTAAAAAAAATGATATTTTGATA
5234573 ATTGTTTAAAAAAAATGATATTTCT-ATA
1 ATTG-TTAAAAAAAATGATATTT-TGATA
5234601 ATT
1 ATT
5234604 TTTTTACTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 4 0.15
28 21 0.81
29 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (27 bp):
ATTGTTAAAAAAAATGATATTTTGATA
Found at i:5236464 original size:2 final size:2
Alignment explanation
Indices: 5236457--5236504 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5236447 TTTGAATCTT
5236457 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5236499 TA TA TA
1 TA TA TA
5236505 CATTTATTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5245693 original size:3 final size:3
Alignment explanation
Indices: 5245646--5245678 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
5245636 CCTCAATGTA
*
5245646 ATT A-T ATT ATT ATT ATT ATT AAT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5245679 ATGTTACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:5252925 original size:24 final size:25
Alignment explanation
Indices: 5252898--5252958 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 25
5252888 GAAAGTCAAC
5252898 GGTCAACGGTCAACGG-TCGGGTCG
1 GGTCAACGGTCAACGGCTCGGGTCG
5252922 GGTCAACGGT---CGGCTCGGGTCG
1 GGTCAACGGTCAACGGCTCGGGTCG
5252944 GGTCAGACCGGTCAA
1 GGTCA-A-CGGTCAA
5252959 ACCGGTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
21 3 0.10
22 13 0.42
23 1 0.03
24 14 0.45
ACGTcount: A:0.16, C:0.26, G:0.41, T:0.16
Consensus pattern (25 bp):
GGTCAACGGTCAACGGCTCGGGTCG
Found at i:5252927 original size:17 final size:17
Alignment explanation
Indices: 5252905--5252942 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
5252895 AACGGTCAAC
*
5252905 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGCTCG
5252922 GGTCAACGGTCGGCTCG
1 GGTCAACGGTCGGCTCG
5252939 GGTC
1 GGTC
5252943 GGGTCAGACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.26, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGCTCG
Found at i:5255816 original size:27 final size:28
Alignment explanation
Indices: 5255769--5255831 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
5255759 TAAATTATTT
5255769 AAAATTATGAAAGGATAATTAAATT-TAA
1 AAAATTATGAAAGGATAATT-AATTATAA
*
5255797 AAAATTATCGAAA-TAT-ATTAATTATAA
1 AAAATTAT-GAAAGGATAATTAATTATAA
*
5255824 TAAATTAT
1 AAAATTAT
5255832 AATAATTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 4 0.13
27 13 0.42
28 10 0.32
29 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (28 bp):
AAAATTATGAAAGGATAATTAATTATAA
Found at i:5256613 original size:182 final size:181
Alignment explanation
Indices: 5256320--5256966 Score: 872
Period size: 182 Copynumber: 3.6 Consensus size: 181
5256310 CGATACAAAT
* * * * * *
5256320 TAAAAATATATCGATTCATAGCAATATAACATGTAAAAATATGATAAAACCGGTGTC-ATTATGA
1 TAAAAATATATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGA-AATGA
** *
5256384 TAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTGTCGACACT
65 TAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACT
5256449 TTTATAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGGTGTCGATACTTTA
130 TTTATAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAA-GTGTCGATACTTTA
* * *
5256502 TAAAAATATGTCGATCCATAGCAATATAACATGTAATAATATGACAAAACAGGTCTCGAAATGAT
1 TAAAAATATATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGAT
5256567 AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
66 AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
* * *
5256632 TTTTAATTTAAAAGAGAATAAGTTATAGCGTCTGAAAAGTGTCGATACTTTA
131 TTATAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTGTCGATACTTTA
* * * * * * * *
5256684 TACAAATGTATCGATCCATAGTAATATATCCGGTAATAATATGAC-AAAGAGGTCTCGGAATGAT
1 TAAAAATATATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGAT
*
5256748 AAAACCGGT-AAAAGATACCGGATATATTGAAAGTGTCGATAAATTAATAT-AGTATCGACACTT
66 AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
* *
5256811 TCATAATTTAAAAGAGAAGAAATTATAGCGCCTAAAAAGTGTCGATACTTTA
131 TTATAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTGTCGATACTTTA
* * * * * * **
5256863 -AGAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGATAAAACCGGTATTAAAATGA
1 TA-AAAATATATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGA
* * * *
5256927 CAAAACCGGTAAAACGCTACCGGTTATGTTGAAAGTGTCG
65 TAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCG
5256967 GTACTTTAAT
Statistics
Matches: 412, Mismatches: 48, Indels: 11
0.87 0.10 0.02
Matches are distributed among these distances:
178 1 0.00
179 94 0.23
180 61 0.15
181 51 0.12
182 200 0.49
183 5 0.01
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (181 bp):
TAAAAATATATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGAT
AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
TTATAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGTGTCGATACTTTA
Found at i:5258231 original size:102 final size:103
Alignment explanation
Indices: 5258116--5258302 Score: 243
Period size: 104 Copynumber: 1.8 Consensus size: 103
5258106 AATGACAATG
* * * * * *
5258116 ATATAATGTATAGGTAAATTGACAATGTAACTAGTA-CACTATACC-GTTTATTATAAAACAGGT
1 ATATAATGTATAGGTAAATTGACAATGTAACCAGTAGAAATATACCGGTTCATGAGAAAACAGGT
*
5258179 TAACATAAAGTATCGACACTATTAATTTTGTGTCGATA
66 CAACATAAAGTATCGACACTATTAATTTTGTGTCGATA
** * * *
5258217 ATATAATGTAATAGGTAAATTTTCAATGTAACCGGTAGAAATATACCGGTTCATGAGAGAATAGG
1 ATATAATGT-ATAGGTAAATTGACAATGTAACCAGTAGAAATATACCGGTTCATGAGAAAACAGG
5258282 TCAACATAAAGTATCGACACT
65 TCAACATAAAGTATCGACACT
5258303 TTGTTTAATT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
101 9 0.13
102 23 0.32
103 7 0.10
104 32 0.45
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (103 bp):
ATATAATGTATAGGTAAATTGACAATGTAACCAGTAGAAATATACCGGTTCATGAGAAAACAGGT
CAACATAAAGTATCGACACTATTAATTTTGTGTCGATA
Found at i:5258582 original size:194 final size:195
Alignment explanation
Indices: 5258218--5258681 Score: 471
Period size: 194 Copynumber: 2.4 Consensus size: 195
5258208 GTGTCGATAA
* * *
5258218 TATAATGTAATAGGTAAATTTTCAATGTAACCGGTAGAAATATACCGGTTCATGAGAGAATAGGT
1 TATAATGTAATAGGTAAATTTACAATGTAACCGGT-TAAATATACCGGTTAATGAGAGAATAGGT
* * * *
5258283 CAACATAAAGTATCGACACTTTGTTTAATTTGTGTCGATACATTTTTTCAAAATGAATGGCAAAC
65 CAACATAAAGTATCGACACTCTGTTAAATATGTGTCGATACATTTTTTCAAAATGAATAGCAAAC
* * * *
5258348 GAGGTGTACGCATAAGTGTCGATACATTTTAAAAGTATCGATCCTCG-AAACATCAAAATCGATA
130 GAGGTGCACGCATAAATATCGATACATTTTAAAAGTATCGATCCT-GAAAACATCAAAACCGATA
5258412 -T
194 TT
* * * *
5258413 TAT-TTGTAACAGGTAAATTTACAATGTAACCGGTTAAATATACCGGTTAATTAGCA-AATATGT
1 TATAATGTAATAGGTAAATTTACAATGTAACCGGTTAAATATACCGGTTAATGAG-AGAATAGGT
* * *
5258476 CTACAT-TATTATCGAACACTCT-TTAAATATGTGTCGATAC-TTTTTTCCAAAAT-AA-AGCAC
65 CAACATAAAGTATCG-ACACTCTGTTAAATATGTGTCGATACATTTTTT-CAAAATGAATAGCA-
* * *
5258536 AATCTAGTTGCACGCATAAAATATCGATACA-TTTAAAATTGTATCGATCCTGAAAACATCGAAA
127 AA-CGAGGTGCACGCAT-AAATATCGATACATTTTAAAA--GTATCGATCCTGAAAACATCAAAA
5258600 CCGATATT
188 CCGATATT
* * * * * * * * *
5258608 TATAATGTAATATGTCAATTTATAATGTAACCGATTTAAATTTACCGTTTTTATGAGAAAATATG
1 TATAATGTAATAGGTAAATTTACAATGTAACCG-GTTAAATATACCG-GTTAATGAGAGAATAGG
*
5258673 TCAATATAA
64 TCAACATAA
5258682 GCGCTACCTA
Statistics
Matches: 220, Mismatches: 34, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
190 3 0.01
191 10 0.05
192 46 0.21
193 46 0.21
194 55 0.25
195 7 0.03
196 24 0.11
197 12 0.05
198 17 0.08
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (195 bp):
TATAATGTAATAGGTAAATTTACAATGTAACCGGTTAAATATACCGGTTAATGAGAGAATAGGTC
AACATAAAGTATCGACACTCTGTTAAATATGTGTCGATACATTTTTTCAAAATGAATAGCAAACG
AGGTGCACGCATAAATATCGATACATTTTAAAAGTATCGATCCTGAAAACATCAAAACCGATATT
Found at i:5258787 original size:23 final size:23
Alignment explanation
Indices: 5258737--5258781 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5258727 TGCCTATTTT
*
5258737 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
5258760 ATTATCTAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
5258782 TGTTATTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:5269169 original size:20 final size:20
Alignment explanation
Indices: 5269133--5269170 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5269123 ATCCTATTCC
**
5269133 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
5269153 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
5269171 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:5269957 original size:21 final size:21
Alignment explanation
Indices: 5269933--5269988 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
5269923 ACTATCGCAA
5269933 TGCGATAGTCCAAATTCGCGT
1 TGCGATAGTCCAAATTCGCGT
* *
5269954 TGCGATCGTCCGAATTCGCGT
1 TGCGATAGTCCAAATTCGCGT
* *
5269975 TGTGATAATCCAAA
1 TGCGATAGTCCAAA
5269989 ATCATTGCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (21 bp):
TGCGATAGTCCAAATTCGCGT
Found at i:5270150 original size:16 final size:17
Alignment explanation
Indices: 5270121--5270172 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
5270111 ATCATAAATA
*
5270121 ATTTAGAATTTATATTT
1 ATTTAAAATTTATATTT
*
5270138 ATTT-AATTTTATA-TT
1 ATTTAAAATTTATATTT
5270153 ATTTAAAATTTATAGTTT
1 ATTTAAAATTTATA-TTT
5270171 AT
1 AT
5270173 CATAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 15 0.52
17 4 0.14
18 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
ATTTAAAATTTATATTT
Found at i:5270547 original size:16 final size:17
Alignment explanation
Indices: 5270518--5270569 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
5270508 ATCATAAATA
*
5270518 ATTTAGAATTTATATTT
1 ATTTAAAATTTATATTT
*
5270535 ATTT-AATTTTATA-TT
1 ATTTAAAATTTATATTT
5270550 ATTTAAAATTTATAGTTT
1 ATTTAAAATTTATA-TTT
5270568 AT
1 AT
5270570 CATAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 15 0.52
17 4 0.14
18 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
ATTTAAAATTTATATTT
Found at i:5270751 original size:21 final size:21
Alignment explanation
Indices: 5270725--5270808 Score: 141
Period size: 21 Copynumber: 4.0 Consensus size: 21
5270715 AATTCACAAT
5270725 GTGAACAGTGCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
*
5270746 GTGAACAGTGATATCGCAACG
1 GTGAACAGTGCTATCGCAACG
*
5270767 GTGAACAGTGCTATTGCAACG
1 GTGAACAGTGCTATCGCAACG
*
5270788 GTGAACAGTACTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
5270809 CGAATTTGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.20
Consensus pattern (21 bp):
GTGAACAGTGCTATCGCAACG
Found at i:5270846 original size:20 final size:20
Alignment explanation
Indices: 5270821--5270873 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
5270811 AATTTGGACT
5270821 ATCGCATTGCGATAGTCAGA
1 ATCGCATTGCGATAGTCAGA
*
5270841 ATCGCATTGCAATAGTCAGA
1 ATCGCATTGCGATAGTCAGA
5270861 ATCGCATTGCGAT
1 ATCGCATTGCGAT
5270874 TTTTCAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGA
Found at i:5271242 original size:21 final size:22
Alignment explanation
Indices: 5271216--5271266 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
5271206 ACGAAATAAT
5271216 AATAAAAATATTA-TTTTATTC
1 AATAAAAATATTATTTTTATTC
5271237 AATAAAAATATTATTTTTATTC
1 AATAAAAATATTATTTTTATTC
5271259 AATAAAAA
1 AATAAAAA
5271267 CAGTGACTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
AATAAAAATATTATTTTTATTC
Found at i:5278267 original size:9 final size:9
Alignment explanation
Indices: 5278237--5278290 Score: 60
Period size: 8 Copynumber: 6.3 Consensus size: 9
5278227 ATCTGCAAAA
5278237 AAATTAAAT
1 AAATTAAAT
*
5278246 -AAGTAAA-
1 AAATTAAAT
*
5278253 ATATTAAAT
1 AAATTAAAT
5278262 AAATTAAAT
1 AAATTAAAT
*
5278271 -ACTTAAAT
1 AAATTAAAT
5278279 AAATTAAAT
1 AAATTAAAT
5278288 AAA
1 AAA
5278291 AAATATAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
8 18 0.50
9 18 0.50
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
AAATTAAAT
Found at i:5278287 original size:17 final size:16
Alignment explanation
Indices: 5278239--5278288 Score: 73
Period size: 17 Copynumber: 3.1 Consensus size: 16
5278229 CTGCAAAAAA
* *
5278239 ATTAAATAAGTAAAAT
1 ATTAAATAAATTAAAT
5278255 ATTAAATAAATTAAAT
1 ATTAAATAAATTAAAT
5278271 ACTTAAATAAATTAAAT
1 A-TTAAATAAATTAAAT
5278288 A
1 A
5278289 AAAAATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 15 0.48
17 16 0.52
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:5278303 original size:21 final size:22
Alignment explanation
Indices: 5278249--5278317 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 22
5278239 ATTAAATAAG
*
5278249 TAAAATATTAAATAAATTAAATAC
1 TAAAAAATTAAATAAA--AAATAC
5278273 TTAAATAAATTAAATAAAAAATA-
1 -TAAA-AAATTAAATAAAAAATAC
*
5278296 TAAAAAA-TATAATAAAATATAC
1 TAAAAAATTA-AATAAAAAATAC
5278318 CTTAGAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 2 0.05
21 13 0.33
22 4 0.10
24 5 0.13
25 4 0.10
26 11 0.28
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAAATTAAATAAAAAATAC
Found at i:5278312 original size:10 final size:9
Alignment explanation
Indices: 5278286--5278316 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
5278276 AATAAATTAA
5278286 ATAAAAAAT
1 ATAAAAAAT
5278295 ATAAAAAAT
1 ATAAAAAAT
5278304 ATAATAAAAT
1 ATAA-AAAAT
5278314 ATA
1 ATA
5278317 CCTTAGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:5278347 original size:10 final size:10
Alignment explanation
Indices: 5278334--5278373 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
5278324 AGAGATTATA
*
5278334 AGAGTATTTG
1 AGAGAATTTG
*
5278344 AGAGAAGTTG
1 AGAGAATTTG
*
5278354 CGAGAATTTG
1 AGAGAATTTG
5278364 AGAGAATTTG
1 AGAGAATTTG
5278374 GTATGATGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.35, C:0.03, G:0.33, T:0.30
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:5278595 original size:14 final size:14
Alignment explanation
Indices: 5278573--5278607 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5278563 GTCAGCATAA
*
5278573 GGCGTGCTTCAGGG
1 GGCGCGCTTCAGGG
5278587 GGCGCGCTTCAGGG
1 GGCGCGCTTCAGGG
*
5278601 AGCGCGC
1 GGCGCGC
5278608 CTTAGCCCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.09, C:0.29, G:0.49, T:0.14
Consensus pattern (14 bp):
GGCGCGCTTCAGGG
Found at i:5281493 original size:6 final size:6
Alignment explanation
Indices: 5281482--5281515 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5281472 CAGAGTACCT
* *
5281482 GTCCTA GTCCTA GTCCTA ATCCTA TTCCTA GTCC
1 GTCCTA GTCCTA GTCCTA GTCCTA GTCCTA GTCC
5281516 CAGAAACTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.35, G:0.12, T:0.35
Consensus pattern (6 bp):
GTCCTA
Found at i:5295431 original size:29 final size:29
Alignment explanation
Indices: 5295399--5295470 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
5295389 GTCACTTGTC
* *
5295399 AACTTGAATTCTTGGTGGTAGCAAAATCA
1 AACTTGAATTCTTAGTGGTAACAAAATCA
* * **
5295428 AACTTGAATTTTTTAGTGGTAACAAATTTG
1 AACTTGAA-TTCTTAGTGGTAACAAAATCA
5295458 AACTTGAATTCTT
1 AACTTGAATTCTT
5295471 TGATGACTAC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
29 12 0.34
30 23 0.66
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (29 bp):
AACTTGAATTCTTAGTGGTAACAAAATCA
Found at i:5311508 original size:8 final size:8
Alignment explanation
Indices: 5311463--5311500 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
5311453 TATTTTTTTC
5311463 AAAAAC-A
1 AAAAACAA
5311470 AAAAACAA
1 AAAAACAA
5311478 AAAAACAA
1 AAAAACAA
5311486 AAAAAGGCAA
1 AAAAA--CAA
5311496 AAAAA
1 AAAAA
5311501 AAACAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 6 0.21
8 14 0.50
10 8 0.29
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (8 bp):
AAAAACAA
Found at i:5316732 original size:31 final size:31
Alignment explanation
Indices: 5316696--5316768 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
5316686 AAATTATAAT
*
5316696 TAAAATTTTATATGAAATTCAGATGTTAAAA
1 TAAAATTTTATATGAAATTCAGAGGTTAAAA
* *
5316727 TAAAATTTTATATGAAGTTCAGGGGTTAAAA
1 TAAAATTTTATATGAAATTCAGAGGTTAAAA
5316758 TAAAATTTTAT
1 TAAAATTTTAT
5316769 CCTTTCATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (31 bp):
TAAAATTTTATATGAAATTCAGAGGTTAAAA
Found at i:5328133 original size:31 final size:31
Alignment explanation
Indices: 5328095--5328312 Score: 366
Period size: 31 Copynumber: 7.0 Consensus size: 31
5328085 CCCGAAGGAC
* * *
5328095 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
5328126 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5328157 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
5328188 CAGTCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
5328219 CAGTCCGTATGTCCCGAAGAATATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5328250 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5328281 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5328312 C
1 C
5328313 CCTCGAACCT
Statistics
Matches: 177, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
31 176 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:5329225 original size:21 final size:21
Alignment explanation
Indices: 5329201--5329245 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5329191 TTTTGTTCGT
* *
5329201 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5329222 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5329243 TTG
1 TTG
5329246 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:5330584 original size:21 final size:21
Alignment explanation
Indices: 5330558--5330601 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5330548 AATATAAATT
5330558 GTGTATTGATACACTACTACA
1 GTGTATTGATACACTACTACA
* *
5330579 GTGTATTGATGCACTGCTACA
1 GTGTATTGATACACTACTACA
5330600 GT
1 GT
5330602 AACTTCAGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (21 bp):
GTGTATTGATACACTACTACA
Done.