Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 53 of 73
Found at i:12629574 original size:9 final size:9
Alignment explanation
Indices: 12629553--12629586 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
12629543 CTTTAGGAAT
12629553 TGAAAAGAAA
1 TGAAAA-AAA
12629563 TGAAAAAAA
1 TGAAAAAAA
12629572 TGAAAAAAA
1 TGAAAAAAA
12629581 TGAAAA
1 TGAAAA
12629587 CGTATCGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (9 bp):
TGAAAAAAA
Found at i:12632796 original size:18 final size:17
Alignment explanation
Indices: 12632775--12632810 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
12632765 GATGTAAGCC
*
12632775 AAATTTTGTATGTGAATG
1 AAATTATGTATGT-AATG
12632793 AAATTATGTATGTAATG
1 AAATTATGTATGTAATG
12632810 A
1 A
12632811 GCAAAGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (17 bp):
AAATTATGTATGTAATG
Found at i:12636201 original size:199 final size:199
Alignment explanation
Indices: 12635617--12636443 Score: 1046
Period size: 200 Copynumber: 4.1 Consensus size: 199
12635607 TACAATTTCA
* * *
12635617 ATACTTTTATATAAGTATC-ACTACTTTTATTCCAGTGTGCATCTGAAACAATTTTCACGCAAAA
1 ATACTTTTATAT-AGTATCGA-TACTTTTATTCCAGTATGCATCTCAAACAATTTGCACGCAAAA
* * * * * * * *
12635681 AAGTATCGATACACGTCTA-ACAAGTATCAACACTTATAATTTCGAAACCTATTACTGTAAAGTA
64 AAGTATCGATACACATGTATA-AAGTATCGATACGTAGAATTTCGAAACCTATTACTTTAAAGTT
* *
12635745 ATAGGTAATTTTACAATGTAAACGGTAAAAATCTATCGGTTTAATGATAATAGGCATAAACATAA
128 ATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGCATAAACATAA
*
12635810 ACTATCG
193 AGTATCG
* ** * *
12635817 ATACTTAATATATAGTATTAATACTTTTATTCCAGTATGCATGTCAAACAATTTGCGCGCAAAAA
1 ATACTT-TTATATAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAATTTGCACGCAAAAA
** * * *
12635882 AGTATCGATACACATGTATAAAGTATCGATACGCGGCATTTCGAAACCGATTAGTTTAAAGTTAT
65 AGTATCGATACACATGTATAAAGTATCGATACGTAGAATTTCGAAACCTATTACTTTAAAGTTAT
* *
12635947 AGGTAAATTTACAATTTAAACGGTAAAAATCTATCGGTTTAATGATAATAGGCATAAACATAAAG
130 AGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGCATAAACATAAAG
*
12636012 TATTG
195 TATCG
* *
12636017 ATACTTATTATATATTATCGATACTTTTATTCCAGTATGCATCTCCAACAATTTGCACGCAAAAA
1 ATACTT-TTATATAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAATTTGCACGCAAAAA
*
12636082 A-TATCGATACACATGTATAAAGTATCGATACGTGGAATTTCGAAACCTATTACTTTAAAGTTAT
65 AGTATCGATACACATGTATAAAGTATCGATACGTAGAATTTCGAAACCTATTACTTTAAAGTTAT
* * *
12636146 AGGTAAATTTACAATGTAAATGGTAAAAGTCTACCGGTTTAATGATAATAGGCATAAACATCAAG
130 AGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGCATAAACATAAAG
12636211 TATCG
195 TATCG
* * * * *
12636216 ATACGTTTTGTATAGGTACCGATACTTTTAGTCCAATATG-ATTCTC-AACAATTTGCACGC-AC
1 ATAC-TTTTATATA-GTATCGATACTTTTATTCCAGTATGCA-TCTCAAACAATTTGCACGCAAA
* *
12636278 ATAGTATCGATACACATGTATAAAG-ATCGATAC-TCAGAGTTTCGAAACCTATTACTTTAAAGT
63 AAAGTATCGATACACATGTATAAAGTATCGATACGT-AGAATTTCGAAACCTATTACTTTAAAGT
* * * * **
12636341 TATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACCGGTATATTAATAATAGGTGT-AA-ATA
127 TATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGCATAAACATA
12636404 CAAGTATCG
192 -AAGTATCG
12636413 ATA-TTGTCTATATAGGTATCGATACTTTTAT
1 ATACTT-T-TATATA-GTATCGATACTTTTAT
12636444 ACGGGTAAAG
Statistics
Matches: 556, Mismatches: 60, Indels: 25
0.87 0.09 0.04
Matches are distributed among these distances:
195 2 0.00
196 3 0.01
197 34 0.06
198 89 0.16
199 169 0.30
200 252 0.45
201 7 0.01
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (199 bp):
ATACTTTTATATAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAATTTGCACGCAAAAAA
GTATCGATACACATGTATAAAGTATCGATACGTAGAATTTCGAAACCTATTACTTTAAAGTTATA
GGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGCATAAACATAAAGT
ATCG
Found at i:12639767 original size:18 final size:18
Alignment explanation
Indices: 12639736--12639770 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12639726 GCGTAGAATT
*
12639736 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
12639754 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
12639771 CCTTAAGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:12641808 original size:2 final size:2
Alignment explanation
Indices: 12641801--12641829 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12641791 ATGTATCGAT
12641801 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
12641830 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12641834 original size:2 final size:2
Alignment explanation
Indices: 12641829--12641865 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
12641819 ACACACACAC
*
12641829 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12641866 CTTATAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12642558 original size:225 final size:224
Alignment explanation
Indices: 12642167--12642806 Score: 901
Period size: 225 Copynumber: 2.8 Consensus size: 224
12642157 ATGTACATGG
* * * **
12642167 TAATATGTTGATAATACTGAAAACAAATCAAGTAATTAACGTATTTTGTTATCGTGTGAATTCTA
1 TAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGAATTC-A
* * * * * * *
12642232 ATGTCCTATCAGCTTTAAACAGGTGC-ACCTATTACATTAAATAAGTGATACTTGTTCTGTTATT
65 AAGGCCCATCATCTTTAAACAGGCGCTACCTATTACATTAAATAAG-CATACTTGTTATGTTATT
*
12642296 ATGGTTGATAATGTGT-CAAGTAATTAACCTATTTTGTTATGGTTGGATTTCTAAGGCTCCATCA
129 ATGGTTGATAATGTGTCCAA-TAATTAACCTATTTTGTTATGGTCGGATTTCTAAGGCTCCATCA
12642360 GCTTAAACTTTGGTAACATTTTAGGCGCTACC
193 GCTTAAACTTTGGTAACATTTTAGGCGCTACC
*
12642392 TAATATGTTGATAATACTGATAACAAATTAAGTAATTAACTTATTTTGTTATCGTCAGAATTCAA
1 TAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGAATTCAA
* *
12642457 AGGCCCATCATCTTTAAACAAGCGCTACCTATTACACTAAATAAGCATTACTTGTTATGTTATTA
66 AGGCCCATCATCTTTAAACAGGCGCTACCTATTACATTAAATAAGCA-TACTTGTTATGTTATTA
*
12642522 TGGTTGATAATGTGTCCATTAATTAACCTATTTTGTTATGGTCGGATTTCTAAGGCTCCATCAGC
130 TGGTTGATAATGTGTCCAATAATTAACCTATTTTGTTATGGTCGGATTTCTAAGGCTCCATCAGC
12642587 TTAAACTTTGGTAACATTTTAGGCGCTACC
195 TTAAACTTTGGTAACATTTTAGGCGCTACC
* * * *
12642617 TAATATGTTGATAATACTGATAACAAATTAAGTAAATAACCTATTTTGTAATCGTCGGAATTCTA
1 TAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGAATTCAA
* * * *
12642682 AGGCCCTATTAGT-TTTAAACGGGCGCTATCTATTACATTAAATAAACGC-TACTTATTATGTTA
66 AGGCCC-ATCA-TCTTTAAACAGGCGCTACCTATTACATTAAAT-AA-GCATACTTGTTATGTTA
* * * * * *
12642745 TTATGGTTGATAATGTTTACAACAATTAACATATTTTGTTATCGTCAGATTTCTAAGGCTCC
127 TTATGGTTGATAATGTGTCCAATAATTAACCTATTTTGTTATGGTCGGATTTCTAAGGCTCC
12642807 TGTAATATCC
Statistics
Matches: 374, Mismatches: 34, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
224 22 0.06
225 248 0.66
226 99 0.26
227 3 0.01
228 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (224 bp):
TAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGAATTCAA
AGGCCCATCATCTTTAAACAGGCGCTACCTATTACATTAAATAAGCATACTTGTTATGTTATTAT
GGTTGATAATGTGTCCAATAATTAACCTATTTTGTTATGGTCGGATTTCTAAGGCTCCATCAGCT
TAAACTTTGGTAACATTTTAGGCGCTACC
Found at i:12644385 original size:23 final size:24
Alignment explanation
Indices: 12644342--12644386 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
12644332 ACAAACATAT
**
12644342 AATATAAGTTATATGCTAAAGATC
1 AATATAAGTTATATGAAAAAGATC
12644366 AATAT-AGTTATATGAAAAAGA
1 AATATAAGTTATATGAAAAAGA
12644387 GTACATGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.31
Consensus pattern (24 bp):
AATATAAGTTATATGAAAAAGATC
Found at i:12645517 original size:2 final size:2
Alignment explanation
Indices: 12645510--12645544 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12645500 ACAAATACCT
12645510 TA TA TA TA 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 TA TA TA TA T
12645545 GCTTATTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12662195 original size:24 final size:20
Alignment explanation
Indices: 12662161--12662219 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
12662151 ATACACAGGC
*
12662161 AGTGTACCGATACCTCAGTTAAG
1 AGTGTATCGATACCTCA--T-AG
*
12662184 AGATGTATCGATACCTTATAG
1 AG-TGTATCGATACCTCATAG
12662205 AGTGTATCGATACCT
1 AGTGTATCGATACCT
12662220 ACGTTAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 13 0.39
21 4 0.12
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (20 bp):
AGTGTATCGATACCTCATAG
Found at i:12666993 original size:18 final size:18
Alignment explanation
Indices: 12666966--12667028 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
12666956 TTTTCATATA
*
12666966 TTTTTCAACAATTGGTAT
1 TTTTTTAACAATTGGTAT
*
12666984 TTTTTTAACAATTGATATCT
1 TTTTTTAACAATTGGTA--T
12667004 TTTTGTTAACAATTGGTAT
1 TTTT-TTAACAATTGGTAT
12667023 CTTTTT
1 -TTTTT
12667029 CATTAAACAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 15 0.39
19 2 0.05
20 9 0.24
21 12 0.32
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.56
Consensus pattern (18 bp):
TTTTTTAACAATTGGTAT
Found at i:12667012 original size:21 final size:20
Alignment explanation
Indices: 12666966--12667028 Score: 76
Period size: 21 Copynumber: 3.2 Consensus size: 20
12666956 TTTTCATATA
* *
12666966 TTTTTCAACAATTGGTA--T
1 TTTTTTAACAATTGATATCT
12666984 TTTTTTAACAATTGATATCT
1 TTTTTTAACAATTGATATCT
*
12667004 TTTTGTTAACAATTGGTATCT
1 TTTT-TTAACAATTGATATCT
12667025 TTTT
1 TTTT
12667029 CATTAAACAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
18 15 0.38
20 5 0.13
21 19 0.49
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.56
Consensus pattern (20 bp):
TTTTTTAACAATTGATATCT
Found at i:12667264 original size:19 final size:20
Alignment explanation
Indices: 12667240--12667278 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
12667230 AAATATTTTA
*
12667240 ATGAATAGT-ACTATACTGT
1 ATGAATAGTAACGATACTGT
12667259 ATGAATAGTAACGATACTGT
1 ATGAATAGTAACGATACTGT
12667279 GTAAACAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (20 bp):
ATGAATAGTAACGATACTGT
Found at i:12668261 original size:20 final size:20
Alignment explanation
Indices: 12668238--12668291 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
12668228 GGGTCTACGC
*
12668238 GGTCCTTCGAGATATACAGA
1 GGTCCTTCGAGACATACAGA
* * *
12668258 GGTCCTTTGGGACATACATA
1 GGTCCTTCGAGACATACAGA
*
12668278 GGTCCTTCGGGACA
1 GGTCCTTCGAGACA
12668292 ATTTCGCATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (20 bp):
GGTCCTTCGAGACATACAGA
Found at i:12669456 original size:16 final size:16
Alignment explanation
Indices: 12669422--12669457 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12669412 TTTTAATCGG
* *
12669422 TCACCTATTTAATAGA
1 TCACCTATTTAACAAA
12669438 TCACCTATTTAACAAA
1 TCACCTATTTAACAAA
12669454 TCAC
1 TCAC
12669458 ATTATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (16 bp):
TCACCTATTTAACAAA
Found at i:12669735 original size:29 final size:31
Alignment explanation
Indices: 12669702--12669764 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
12669692 TCAAAAAATA
12669702 TAAGAT-ATGATAACTTTCG-TTTT-TTTAAT
1 TAAGATGATG-TAACTTTCGTTTTTATTTAAT
* *
12669731 TAAGATGTTGTCACTTTCGTTTTTATTTAAT
1 TAAGATGATGTAACTTTCGTTTTTATTTAAT
12669762 TAA
1 TAA
12669765 AACATGGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 14 0.48
30 6 0.21
31 9 0.31
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.52
Consensus pattern (31 bp):
TAAGATGATGTAACTTTCGTTTTTATTTAAT
Found at i:12669942 original size:27 final size:30
Alignment explanation
Indices: 12669880--12669950 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
12669870 TTTAGTCATC
** *
12669880 ATTTTAAATAAATTTTAAAATAAAATATAT
1 ATTTTAAATAAAAATAAAAATAAAATATAT
12669910 ATTTTTAAATAAAAATAAAAAT-AAA-ATA-
1 A-TTTTAAATAAAAATAAAAATAAAATATAT
12669938 ATTTTAAATAAAA
1 ATTTTAAATAAAA
12669951 TATTCTCCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 12 0.32
28 1 0.03
29 3 0.08
30 4 0.11
31 17 0.46
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
ATTTTAAATAAAAATAAAAATAAAATATAT
Found at i:12671081 original size:9 final size:10
Alignment explanation
Indices: 12671060--12671090 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
12671050 GGACCGGCTG
*
12671060 AAAACCGGAA
1 AAAACCAGAA
12671070 AAAACCAGAA
1 AAAACCAGAA
12671080 AAAACCAGAA
1 AAAACCAGAA
12671090 A
1 A
12671091 TTTTGTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.68, C:0.19, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAACCAGAA
Found at i:12681624 original size:215 final size:207
Alignment explanation
Indices: 12681362--12681846 Score: 756
Period size: 215 Copynumber: 2.3 Consensus size: 207
12681352 ATTTAAGAAT
12681362 TAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAA-TAAAATTTAAATAAATTAAACAACACACATTGATGAG
* *
12681427 GGATCAAATCGAAATAATTTTAAATTGTG-TGGTTGAAATTAATACAAAAAGTACTAAATTATAC
65 GGATCAAATCGAAATAATTTTAAATTGTGAT-ATTGAAATTAATACAAAAAATACTAAATTATAC
* *
12681491 CCATTTAAAAAGTTATGGGCCAATTTAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAGA
129 CCATTTAAAAAGTTATGGACCAA-TT---AA-A-AAAT-AGTAATAAGTATGAGTCAATTTCAGA
*
12681556 TGCAAATATAATTTGGAGGAC
187 TGCAAATATAATTTGAAGGAC
* *
12681577 TAATTTGATCAAATATGAAATTACAAATAAAATTTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAA-TTTAAATAAATTAAACAACACACATTGATGAG
*
12681642 GGATCAAATCGAAATAATTTTAAATTGTGATATTTAAATTAATACAAAAAATACTAAATTATACC
65 GGATCAAATCGAAATAATTTTAAATTGTGATATTGAAATTAATACAAAAAATACTAAATTATACC
**
12681707 CATTTAAAAAGTTATGGACCAATTAAAAAATAGTAATAAGTATGAGTCAATTTCTTATGCAAATA
130 CATTTAAAAAGTTATGGACCAATTAAAAAATAGTAATAAGTATGAGTCAATTTCAGATGCAAATA
12681772 TAATTTGAAGGAC
195 TAATTTGAAGGAC
* *
12681785 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAACTAAATTAAACAACACACGTTGAT
1 TAAATTGAACAAATATGAAATTACAAAT-AAAATTTAAATAAATTAAACAACACACATTGAT
12681847 TGTAAAATAA
Statistics
Matches: 253, Mismatches: 14, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
208 96 0.38
209 8 0.03
210 1 0.00
211 2 0.01
214 7 0.03
215 138 0.55
216 1 0.00
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (207 bp):
TAAATTGAACAAATATGAAATTACAAATAAAATTTAAATAAATTAAACAACACACATTGATGAGG
GATCAAATCGAAATAATTTTAAATTGTGATATTGAAATTAATACAAAAAATACTAAATTATACCC
ATTTAAAAAGTTATGGACCAATTAAAAAATAGTAATAAGTATGAGTCAATTTCAGATGCAAATAT
AATTTGAAGGAC
Found at i:12682122 original size:2 final size:2
Alignment explanation
Indices: 12682111--12682260 Score: 89
Period size: 2 Copynumber: 75.0 Consensus size: 2
12682101 TTGAAACAAC
*
12682111 TA TA -A TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA AA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * * *
12682152 GA GTT TA TA TA TA AA GTA TA TG TA T- TA TA TA TA TA AA CTC TA
1 TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
12682194 TA T- TT TA TA TT TA TA T- TA T- TA TA TA CTA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
12682233 TA TA TA TA CTC TA TA TA AA CTA TA TA TA
1 TA TA TA TA -TA TA TA TA TA -TA TA TA TA
12682261 CCATGTAAAA
Statistics
Matches: 113, Mismatches: 21, Indels: 28
0.70 0.13 0.17
Matches are distributed among these distances:
1 7 0.06
2 100 0.88
3 6 0.05
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12682141 original size:11 final size:11
Alignment explanation
Indices: 12682111--12682260 Score: 83
Period size: 11 Copynumber: 13.2 Consensus size: 11
12682101 TTGAAACAAC
12682111 TATAATATATA
1 TATAATATATA
12682122 TATATATATATA
1 TATA-ATATATA
12682134 TATAATATATAAA
1 TATAATATAT--A
*
12682147 CTATAGAGTTTATA
1 -TATA-A-TATATA
12682161 TATAA-AGTATA
1 TATAATA-TATA
* *
12682172 TGTATTATATA
1 TATAATATATA
*
12682183 TATAA-ACTCTA
1 TATAATA-TATA
** *
12682194 TATTTTATATT
1 TATAATATATA
*
12682205 TATATTAT-TA
1 TATAATATATA
*
12682215 TATACTATATA
1 TATAATATATA
*
12682226 TATTATATATA
1 TATAATATATA
* *
12682237 TATACTCTATA
1 TATAATATATA
12682248 TA-AACTATATA
1 TATAA-TATATA
12682259 TA
1 TA
12682261 CCATGTAAAA
Statistics
Matches: 106, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
10 10 0.09
11 67 0.63
12 14 0.13
13 5 0.05
14 5 0.05
15 1 0.01
16 4 0.04
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (11 bp):
TATAATATATA
Found at i:12682247 original size:13 final size:13
Alignment explanation
Indices: 12682109--12682260 Score: 70
Period size: 13 Copynumber: 11.8 Consensus size: 13
12682099 AATTGAAACA
12682109 ACTATA-ATATAT
1 ACTATATATATAT
12682121 A-TATATATATAT
1 ACTATATATATAT
*
12682133 A-TATAATATATAA
1 ACTAT-ATATATAT
*
12682146 ACTATAGAGTTTATAT
1 ACTAT--A-TATATAT
* *
12682162 A-TAAAGTATATGT
1 ACTATA-TATATAT
* *
12682175 ATTATATATATAA
1 ACTATATATATAT
* *
12682188 ACTCTATAT-TTT
1 ACTATATATATAT
*
12682200 A-TATTTATATTATT
1 ACTATATATA-TA-T
12682214 A-TATACTATATAT
1 ACTATA-TATATAT
*
12682227 ATTATATATATAT
1 ACTATATATATAT
*
12682240 ACTCTATATA-A-
1 ACTATATATATAT
12682251 ACTATATATA
1 ACTATATATA
12682261 CCATGTAAAA
Statistics
Matches: 108, Mismatches: 21, Indels: 23
0.71 0.14 0.15
Matches are distributed among these distances:
11 18 0.17
12 14 0.13
13 46 0.43
14 17 0.16
15 7 0.06
16 6 0.06
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (13 bp):
ACTATATATATAT
Found at i:12682341 original size:22 final size:22
Alignment explanation
Indices: 12682315--12682473 Score: 86
Period size: 22 Copynumber: 7.4 Consensus size: 22
12682305 TAGAAACTAC
12682315 ATAGTTTATTAATATAAATTAT
1 ATAGTTTATTAATATAAATTAT
12682337 ATAGTTTA-T-ATATAAATTAT
1 ATAGTTTATTAATATAAATTAT
** *
12682357 ATA-TGAAATATATATAAATTAT
1 ATAGTTTATTA-ATATAAATTAT
* * * *
12682379 ACAATTTA-TATTTATATATTAT
1 ATAGTTTATTA-ATATAAATTAT
*
12682401 GTA--TTATGTATAGTTATAAA-TA-
1 ATAGTTTAT-TA-A--TATAAATTAT
* *
12682423 ATA-TATATT-GTATAAATTAT
1 ATAGTTTATTAATATAAATTAT
* *
12682443 TTAGTTTATTAATATAAACTAT
1 ATAGTTTATTAATATAAATTAT
12682465 ATAGTTTAT
1 ATAGTTTAT
12682474 ATATATATCT
Statistics
Matches: 105, Mismatches: 19, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
18 6 0.06
19 4 0.04
20 20 0.19
21 6 0.06
22 57 0.54
23 7 0.07
24 5 0.05
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (22 bp):
ATAGTTTATTAATATAAATTAT
Found at i:12682350 original size:11 final size:11
Alignment explanation
Indices: 12682322--12682379 Score: 63
Period size: 11 Copynumber: 5.5 Consensus size: 11
12682312 TACATAGTTT
12682322 ATTA-ATATAA
1 ATTATATATAA
12682332 ATTATATAGT--
1 ATTATATA-TAA
12682342 -TTATATATAA
1 ATTATATATAA
12682352 ATTATATATGAA
1 ATTATATAT-AA
12682364 A-TATATATAA
1 ATTATATATAA
12682374 ATTATA
1 ATTATA
12682380 CAATTTATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
8 1 0.02
9 7 0.17
10 7 0.17
11 22 0.54
12 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (11 bp):
ATTATATATAA
Found at i:12682387 original size:64 final size:64
Alignment explanation
Indices: 12682289--12682478 Score: 174
Period size: 64 Copynumber: 3.0 Consensus size: 64
12682279 ACTATATAGT
* * * *
12682289 TTATATATGAACTATATAGAAACTACATAGTTTATTAATATAAATTATATAGTTTATATATAAA
1 TTATATATGAAATATATATAAATTATATAGTTTATTAATATAAATTATATAGTTTATATATAAA
* * * * * *
12682353 TTATATATGAAATATATATAAATTATACAATTTA-TATTTATATATTATGTATTATGTATAGTTA
1 TTATATATGAAATATATATAAATTATATAGTTTATTA-ATATAAATTATATAGT-T-TATA--TA
12682417 TAAA
61 TAAA
* * * *
12682421 -TA-ATAT-ATAT-TGTATAAATTATTTAGTTTATTAATATAAACTATATAGTTTATATATA
1 TTATATATGAAATATATATAAATTATATAGTTTATTAATATAAATTATATAGTTTATATATA
12682479 TATCTGGTTT
Statistics
Matches: 100, Mismatches: 20, Indels: 16
0.74 0.15 0.12
Matches are distributed among these distances:
60 4 0.04
62 4 0.04
63 3 0.03
64 67 0.67
65 6 0.06
66 8 0.08
67 2 0.02
68 6 0.06
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (64 bp):
TTATATATGAAATATATATAAATTATATAGTTTATTAATATAAATTATATAGTTTATATATAAA
Found at i:12682628 original size:13 final size:13
Alignment explanation
Indices: 12682610--12682634 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12682600 ATAGTTTACA
12682610 TATGAACTATATG
1 TATGAACTATATG
12682623 TATGAACTATAT
1 TATGAACTATAT
12682635 AACTATATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
TATGAACTATATG
Found at i:12682640 original size:21 final size:22
Alignment explanation
Indices: 12682609--12682665 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
12682599 TATAGTTTAC
* * *
12682609 ATATGAACTATATGTATGAACT
1 ATATAAACTATATATATAAACT
12682631 ATAT-AACTATATATATAAACT
1 ATATAAACTATATATATAAACT
*
12682652 ATGTAAACTATATA
1 ATATAAACTATATA
12682666 GTTTACATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (22 bp):
ATATAAACTATATATATAAACT
Found at i:12682706 original size:24 final size:24
Alignment explanation
Indices: 12682660--12682709 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
12682650 CTATGTAAAC
*
12682660 TATATAGTTTACATATGACCTATA
1 TATATAGTTTACATATGAACTATA
*
12682684 TATATAGTTTA-TTAGTGAACTATA
1 TATATAGTTTACATA-TGAACTATA
12682708 TA
1 TA
12682710 AACTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (24 bp):
TATATAGTTTACATATGAACTATA
Found at i:12682747 original size:18 final size:18
Alignment explanation
Indices: 12682705--12682741 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12682695 TTAGTGAACT
* *
12682705 ATATAAACTATTTATATA
1 ATATATACTATATATATA
12682723 ATATATACTATATATATA
1 ATATATACTATATATATA
12682741 A
1 A
12682742 ATTATAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATATACTATATATATA
Found at i:12683061 original size:16 final size:16
Alignment explanation
Indices: 12683001--12683064 Score: 56
Period size: 16 Copynumber: 3.7 Consensus size: 16
12682991 AAACAATAGT
*
12683001 TAATATATGTAACCTA
1 TAATATATGTAACTTA
*
12683017 TAGTATATGTATACATGTA
1 TAATATATGTA-AC-T-TA
*
12683036 AACTATATATGTAACTTA
1 TA--ATATATGTAACTTA
12683054 TAATATATGTA
1 TAATATATGTA
12683065 TGTACAAACT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
16 19 0.50
17 2 0.05
18 3 0.08
19 4 0.11
20 2 0.05
21 8 0.21
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (16 bp):
TAATATATGTAACTTA
Found at i:12683074 original size:35 final size:36
Alignment explanation
Indices: 12683003--12683076 Score: 87
Period size: 37 Copynumber: 2.1 Consensus size: 36
12682993 ACAATAGTTA
* **
12683003 ATATATGTAACCTATAGTATATGTATACATGTAAACT
1 ATATATGTAACCTATAATATATGTATA-ATACAAACT
* *
12683040 ATATATGTAACTTATAATATATGTAT-GTACAAACT
1 ATATATGTAACCTATAATATATGTATAATACAAACT
12683075 AT
1 AT
12683077 GTATAGTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 8 0.25
37 24 0.75
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (36 bp):
ATATATGTAACCTATAATATATGTATAATACAAACT
Found at i:12683102 original size:58 final size:56
Alignment explanation
Indices: 12683034--12683168 Score: 159
Period size: 56 Copynumber: 2.4 Consensus size: 56
12683024 TGTATACATG
* *
12683034 TAAACTATATATGTAACTTATAATATATG-TATGTACAAACTATGTATA-G-TATA
1 TAAACTATATATGTAACCTATAATATATGATATATACAAACTATGTATATGTTATA
* * * *
12683087 TATAACTACATATATATAACCTATAGTATATGTATATATACAATCTATTTATATGTTATA
1 TA-AACT--ATATATGTAACCTATAATATATG-ATATATACAAACTATGTATATGTTATA
12683147 TAAACTATATATGTAACCTATA
1 TAAACTATATATGTAACCTATA
12683169 GTTTATAAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
53 2 0.03
54 4 0.06
56 20 0.29
57 15 0.22
58 16 0.24
59 5 0.07
60 6 0.09
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.41
Consensus pattern (56 bp):
TAAACTATATATGTAACCTATAATATATGATATATACAAACTATGTATATGTTATA
Found at i:12683154 original size:20 final size:22
Alignment explanation
Indices: 12683097--12683155 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
12683087 TATAACTACA
*
12683097 TATATATAACCTATAGTATATG
1 TATATATAAACTATAGTATATG
*
12683119 TATATATACAATCTAT-TTATATG
1 TATATATA-AA-CTATAGTATATG
12683142 T-TATATAAACTATA
1 TATATATAAACTATA
12683156 TATGTAACCT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 4 0.12
21 2 0.06
22 14 0.44
23 8 0.25
24 4 0.12
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (22 bp):
TATATATAAACTATAGTATATG
Found at i:12683368 original size:43 final size:40
Alignment explanation
Indices: 12683294--12683384 Score: 119
Period size: 43 Copynumber: 2.2 Consensus size: 40
12683284 AATTATCTTA
* *
12683294 ACTATAATTTATATTAATATAGTATATAGTTTATATACTAT
1 ACTAT-ATTAATATTAATATAGTATATAGTTTATAAACTAT
*
12683335 ACTATATTAATATTAATTATATTAACTATAGTTTATAAACTAT
1 ACTATATTAATATTAA-TATAGT-A-TATAGTTTATAAACTAT
12683378 ACTATAT
1 ACTATAT
12683385 AGTTTATAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 10 0.23
41 10 0.23
42 1 0.02
43 23 0.52
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (40 bp):
ACTATATTAATATTAATATAGTATATAGTTTATAAACTAT
Found at i:12683406 original size:21 final size:21
Alignment explanation
Indices: 12683311--12683393 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 21
12683301 TTTATATTAA
* *
12683311 TATAGTATATAGTTTATATAC
1 TATACTATATAGTTTATAAAC
* * *
12683332 TATACTATAT--TAATATTAAT
1 TATACTATATAGT-TTATAAAC
*
12683352 TATATTAACTATAGTTTATAAAC
1 TATACT-A-TATAGTTTATAAAC
12683375 TATACTATATAGTTTATAA
1 TATACTATATAGTTTATAA
12683394 CATATAGTTT
Statistics
Matches: 47, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
19 1 0.02
20 9 0.19
21 22 0.47
22 4 0.09
23 10 0.21
24 1 0.02
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (21 bp):
TATACTATATAGTTTATAAAC
Found at i:12683436 original size:31 final size:30
Alignment explanation
Indices: 12683265--12683449 Score: 137
Period size: 31 Copynumber: 5.8 Consensus size: 30
12683255 TAATGTACTA
*
12683265 TATAGTTTATATTAATGTTAATTATCT-TAAC
1 TATAGTTTATATTAATATTAATT-T-TATAAC
*
12683296 TATAATTTATATTAATATAGTATATAGTTTATATAC
1 TATAGTTTATATTAATAT--TA-AT--TTTATA-AC
* *
12683332 TATA--CTATATTAATATTAATTATATTAAC
1 TATAGTTTATATTAATATTAATTTTA-TAAC
12683361 TATAGTTTATA--AACTATACTATATAGTTTATAAC
1 TATAGTTTATATTAA-TAT--TA-AT--TTTATAAC
12683395 ATATAGTTTATATTAATATTAATTTTATAGAC
1 -TATAGTTTATATTAATATTAATTTTATA-AC
*
12683427 TATATTTTATATTAATATTAATT
1 TATAGTTTATATTAATATTAATT
12683450 ATATTAATAT
Statistics
Matches: 127, Mismatches: 7, Indels: 40
0.73 0.04 0.23
Matches are distributed among these distances:
29 11 0.09
30 5 0.04
31 50 0.39
32 6 0.05
33 6 0.05
34 20 0.16
35 17 0.13
36 10 0.08
37 2 0.02
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (30 bp):
TATAGTTTATATTAATATTAATTTTATAAC
Found at i:12683476 original size:28 final size:27
Alignment explanation
Indices: 12683439--12683496 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 27
12683429 TATTTTATAT
12683439 TAATATTAATTATATTAATATTAATTA
1 TAATATTAATTATATTAATATTAATTA
*
12683466 TAATATATAATTATTTTAATATTAATTA
1 TAATAT-TAATTATATTAATATTAATTA
12683494 TAA
1 TAA
12683497 ATAGTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 6 0.21
28 23 0.79
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TAATATTAATTATATTAATATTAATTA
Found at i:12683488 original size:131 final size:131
Alignment explanation
Indices: 12683229--12683496 Score: 291
Period size: 131 Copynumber: 2.0 Consensus size: 131
12683219 ACCTATTGTA
* * * *
12683229 TATAATTTATAAACTATAGTTTATATTAATGTACTATATAGTTTATATTAATGTTAATTATCTTA
1 TATAATTTATAAACTATACTATATATTAATGAACTATATAGTTTATATTAATATTAATTATCTTA
* * *
12683294 ACTATAATTTATATTAATATAGTATATAGTTTATATACTATACTATATTAATATTAATTATATTA
66 ACTATAATTTATATTAATATAATATATAGTTAATATACTATAATATATTAATATT-ATTATATTA
12683359 AC
130 AC
* *
12683361 TATAGTTTATAAACTATACTATATAGTTTAT-AAC-ATATAGTTTATATTAATATTAATT-T-TA
1 TATAATTTATAAACTATACTATATA-TTAATGAACTATATAGTTTATATTAATATTAATTATCT-
* *
12683422 TAGACTATATTTTATATTAATATTAAT-TATA-TTAATATTAATTATAATATA-TAATTATT-TT
64 TA-ACTATAATTTATATTAATA-TAATATATAGTTAATA-T-ACTATAATATATTAA-TATTATT
*
12683483 AATATTAAT
124 -ATATTAAC
12683492 TATAA
1 TATAA
12683497 ATAGTTTATT
Statistics
Matches: 115, Mismatches: 13, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
129 1 0.01
130 10 0.09
131 60 0.52
132 40 0.35
133 4 0.03
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (131 bp):
TATAATTTATAAACTATACTATATATTAATGAACTATATAGTTTATATTAATATTAATTATCTTA
ACTATAATTTATATTAATATAATATATAGTTAATATACTATAATATATTAATATTATTATATTAA
C
Found at i:12683493 original size:15 final size:15
Alignment explanation
Indices: 12683402--12683495 Score: 97
Period size: 15 Copynumber: 6.3 Consensus size: 15
12683392 AACATATAGT
12683402 TTATATTAATATTAA
1 TTATATTAATATTAA
* *
12683417 TTTTA-TAGACTA-TATT
1 TTATATTA-A-TATTA-A
12683433 TTATATTAATATTAA
1 TTATATTAATATTAA
12683448 TTATATTAATATTAA
1 TTATATTAATATTAA
*
12683463 TTATAAT-ATA-TAA
1 TTATATTAATATTAA
*
12683476 TTATTTTAATATTAA
1 TTATATTAATATTAA
12683491 TTATA
1 TTATA
12683496 AATAGTTTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
13 8 0.12
14 8 0.12
15 37 0.58
16 9 0.14
17 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (15 bp):
TTATATTAATATTAA
Found at i:12685952 original size:23 final size:23
Alignment explanation
Indices: 12685919--12685977 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
12685909 TTCTTAATGC
* *
12685919 ATGATACTTGCTGAATTGATGCA
1 ATGATGCTTGCTGAATTGATACA
* * *
12685942 ATGCTGCTTGCCGAATTGGTACA
1 ATGATGCTTGCTGAATTGATACA
*
12685965 TTGATGCTTGCTG
1 ATGATGCTTGCTG
12685978 GTTACTGCTG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (23 bp):
ATGATGCTTGCTGAATTGATACA
Found at i:12686568 original size:13 final size:13
Alignment explanation
Indices: 12686549--12686586 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
12686539 TAATTTAGTG
12686549 ATTATAAATAA-A
1 ATTATAAATAAGA
12686561 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
12686576 ATTATAAATAA
1 ATTATAAATAA
12686587 TATAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:12686596 original size:19 final size:19
Alignment explanation
Indices: 12686565--12686611 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
12686555 AATAAAATTT
*
12686565 ATAATAT-AAGAATTATAA
1 ATAATATAAAGAATTAGAA
*
12686583 ATAATATAAAGAATTGGAA
1 ATAATATAAAGAATTAGAA
*
12686602 TTAATATAAA
1 ATAATATAAA
12686612 AATCAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.32
Consensus pattern (19 bp):
ATAATATAAAGAATTAGAA
Found at i:12695566 original size:29 final size:28
Alignment explanation
Indices: 12695514--12695682 Score: 146
Period size: 29 Copynumber: 5.7 Consensus size: 28
12695504 TGATCTCCAT
*
12695514 TAAAGTAAAA-ATATTTTTAAAAGTTAA-A
1 TAAAATAAAATATATTTTT--AAGTTAAGA
*
12695542 TTAAAATAAAATATATTAATTAAGTTAAGA
1 -TAAAATAAAATATATT-TTTAAGTTAAGA
*
12695572 TACGATATGATTAAAATATATTTTTAAGTTAAAA
1 TA--A-A--A-TAAAATATATTTTTAAGTTAAGA
*
12695606 TAAGAATAATATA-ATTTTTAAGTTAAAGA
1 TAA-AATAAAATATATTTTTAAGTT-AAGA
* *
12695635 TAAAAATAAAATATAATTTTAATTTAAGA
1 T-AAAATAAAATATATTTTTAAGTTAAGA
12695664 TAAAATAAAATATATTTTT
1 TAAAATAAAATATATTTTT
12695683 TTAAAGTTGA
Statistics
Matches: 117, Mismatches: 11, Indels: 25
0.76 0.07 0.16
Matches are distributed among these distances:
28 28 0.24
29 41 0.35
30 18 0.15
31 3 0.03
32 3 0.03
34 13 0.11
35 11 0.09
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.39
Consensus pattern (28 bp):
TAAAATAAAATATATTTTTAAGTTAAGA
Found at i:12695628 original size:28 final size:27
Alignment explanation
Indices: 12695586--12695682 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 27
12695576 ATATGATTAA
12695586 AATAT-ATTTTTAAGTTAAAATAAGAAT
1 AATATAATTTTTAAGTTAAAATAA-AAT
12695613 AATATAATTTTTAAGTTAAAGATAAAAAT
1 AATATAATTTTTAAGTTAAA-AT-AAAAT
* *
12695642 AAAATATAA-TTTTAATTTAAGATAAAAT
1 --AATATAATTTTTAAGTTAAAATAAAAT
*
12695670 AAAATATATTTTT
1 AATATA-ATTTTT
12695683 TTAAAGTTGA
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
26 5 0.08
27 6 0.10
28 23 0.38
29 7 0.12
30 12 0.20
31 7 0.12
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (27 bp):
AATATAATTTTTAAGTTAAAATAAAAT
Found at i:12696377 original size:186 final size:185
Alignment explanation
Indices: 12696043--12696547 Score: 723
Period size: 186 Copynumber: 2.7 Consensus size: 185
12696033 TACTTTCTAA
*
12696043 TTTATTATAATAAAAATATTAACA-TTCAAGATCGCAACCTACTTTCTTAGT-GAATTATAATA-
1 TTTATTATAA-AGAAA-ATTAACATTTC-AGATCGCAACCTACTTTCTTAGTGGAA-TATAATAT
* *
12696105 TTTTTGGACGCAACCAGATTTTTTTTTATAGATATTCATAACATTTTCAGCTTTTAACTTATTTT
62 TTTTTGG-CGCAA-CAGA---TTTCTTATAGATATTCATAACATTTTCAACTTTTAACTTATTTT
*
12696170 GTTATCGTAAGAATGTCTAAGGTCCATTGGCTTAAACTTTGGTAACATTTT-AGACGTAACCGAT
122 GTTATCGTAAGAATGTCTAAGGTCCATTAGCTTAAACTTTGGTAACATTTTAAG-CGTAACCGAT
*
12696234 TTTATTATAAAGAAAATTAACATTTCAGATCGCAACCTACTTTCTTAGTGGACTATAATATTTTT
1 TTTATTATAAAGAAAATTAACATTTCAGATCGCAACCTACTTTCTTAGTGGAATATAATATTTTT
*
12696299 TGGCGCAATCAGATTTCTTATAGATATTCATAACATTTTTAACTTTTAACTTATTTTGTTATCGT
66 TGGCGCAA-CAGATTTCTTATAGATATTCATAACATTTTCAACTTTTAACTTATTTTGTTATCGT
*
12696364 AAGAATGTCTAAGGTCCATTAGCTTAAACTTTGGTAACATTTTAAGCGTAAGCGAT
130 AAGAATGTCTAAGGTCCATTAGCTTAAACTTTGGTAACATTTTAAGCGTAACCGAT
* ** * *
12696420 TTTATTATAAAGAAAATTAACATTTCATATTACAACTTACTTTCTTAGT-GAATCATAACATTTT
1 TTTATTATAAAGAAAATTAACATTTCAGATCGCAACCTACTTTCTTAGTGGAAT-ATAATATTTT
* * *
12696484 TTGGCGCAACCGAATTTCTTATGGATATTCATAACATTTTCAACTTTTAACTTATTTTATTATC
65 TTGGCGCAACAG-ATTTCTTATAGATATTCATAACATTTTCAACTTTTAACTTATTTTGTTATC
12696548 ATTGGAATGT
Statistics
Matches: 290, Mismatches: 18, Indels: 17
0.89 0.06 0.05
Matches are distributed among these distances:
185 5 0.02
186 211 0.73
187 2 0.01
189 46 0.16
190 16 0.06
191 10 0.03
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (185 bp):
TTTATTATAAAGAAAATTAACATTTCAGATCGCAACCTACTTTCTTAGTGGAATATAATATTTTT
TGGCGCAACAGATTTCTTATAGATATTCATAACATTTTCAACTTTTAACTTATTTTGTTATCGTA
AGAATGTCTAAGGTCCATTAGCTTAAACTTTGGTAACATTTTAAGCGTAACCGAT
Found at i:12696630 original size:186 final size:186
Alignment explanation
Indices: 12696045--12696609 Score: 586
Period size: 186 Copynumber: 3.0 Consensus size: 186
12696035 CTTTCTAATT
* * * *
12696045 TATTATAATAAAAATATTAACA-TTCAAGATCGCAACCTACTTTCTTAGTGAATTATAATA-TTT
1 TATTATAA-AGAAA-ATTAACATTTC-AGATCACAACCTACTTTCTTAGTGAACTATAACATTTT
* * *
12696108 TTGGACGCAACCAGATTTTTTTTTATAGATATTCATAACATTTTCAGCTTTTAACTTATTTTGTT
63 TTGG-CGCAACCAGA---TTTCTTATAGATATTCATAACATTTTCAACTTTTAACTTATTTTATT
* * ** * ***
12696173 ATCGTAAGAATGTCTAAGGTCCATTGGCTTAAACTTTGGTAACATTTT-AG-ACGTAACCGATTT
124 ATCATAAGAATGTCTAAAGTCCATCAGCTTAAACTTTGATAACATTTTAAGCAC--AACCGAAAA
* * *
12696236 TATTATAAAGAAAATTAACATTTCAGATCGCAACCTACTTTCTTAGTGGACTATAATATTTTTTG
1 TATTATAAAGAAAATTAACATTTCAGATCACAACCTACTTTCTTAGTGAACTATAACATTTTTTG
* * * *
12696301 GCGCAATCAGATTTCTTATAGATATTCATAACATTTTTAACTTTTAACTTATTTTGTTATCGTAA
66 GCGCAACCAGATTTCTTATAGATATTCATAACATTTTCAACTTTTAACTTATTTTATTATCATAA
* * * ** * ***
12696366 GAATGTCTAAGGTCCATTAGCTTAAACTTTGGTAACATTTTAAGCGTAAGCGATTT
131 GAATGTCTAAAGTCCATCAGCTTAAACTTTGATAACATTTTAAGCACAACCGAAAA
* * *
12696422 TATTATAAAGAAAATTAACATTTCATATTACAACTTACTTTCTTAGTGAA-TCATAACATTTTTT
1 TATTATAAAGAAAATTAACATTTCAGATCACAACCTACTTTCTTAGTGAACT-ATAACATTTTTT
*
12696486 GGCGCAACC-GAATTTCTTATGGATATTCATAACATTTTCAACTTTTAACTTATTTTATTATCAT
65 GGCGCAACCAG-ATTTCTTATAGATATTCATAACATTTTCAACTTTTAACTTATTTTATTATCAT
** * * * * *
12696550 TGGAATGTTTAAAGTCACATCATCTTAAACTATT-ATGACATTTTAGGCACAACCTAAAA
129 AAGAATGTCTAAAGTC-CATCAGCTTAAACT-TTGATAACATTTTAAGCACAACCGAAAA
12696609 T
1 T
12696610 GTTAAAATAT
Statistics
Matches: 328, Mismatches: 38, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
185 2 0.01
186 224 0.68
187 30 0.09
188 2 0.01
189 48 0.15
190 14 0.04
191 8 0.02
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (186 bp):
TATTATAAAGAAAATTAACATTTCAGATCACAACCTACTTTCTTAGTGAACTATAACATTTTTTG
GCGCAACCAGATTTCTTATAGATATTCATAACATTTTCAACTTTTAACTTATTTTATTATCATAA
GAATGTCTAAAGTCCATCAGCTTAAACTTTGATAACATTTTAAGCACAACCGAAAA
Found at i:12699141 original size:20 final size:20
Alignment explanation
Indices: 12699118--12699160 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
12699108 AAAATATTTT
*
12699118 ATTATTTTATATAATAAAAC
1 ATTACTTTATATAATAAAAC
*
12699138 ATTACTTTATATAATATAAC
1 ATTACTTTATATAATAAAAC
12699158 ATT
1 ATT
12699161 TAGTGTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTACTTTATATAATAAAAC
Found at i:12700168 original size:15 final size:16
Alignment explanation
Indices: 12700136--12700190 Score: 76
Period size: 15 Copynumber: 3.4 Consensus size: 16
12700126 GAAATCGTCG
*
12700136 ACCCGGAAGTTCCGGGT
1 ACCCGGAA-ATCCGGGT
12700153 ACCCGGAAAT-CGGGT
1 ACCCGGAAATCCGGGT
*
12700168 ACCCGAAAATCCGGGT
1 ACCCGGAAATCCGGGT
12700184 ACCCGGA
1 ACCCGGA
12700191 TTTGCACACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.41
16 12 0.35
17 8 0.24
ACGTcount: A:0.25, C:0.31, G:0.31, T:0.13
Consensus pattern (16 bp):
ACCCGGAAATCCGGGT
Found at i:12701597 original size:16 final size:16
Alignment explanation
Indices: 12701576--12701611 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12701566 TTCATGAAAC
* *
12701576 TGTTCTACGTGAAAAG
1 TGTTCTACCTGAAAAA
12701592 TGTTCTACCTGAAAAA
1 TGTTCTACCTGAAAAA
12701608 TGTT
1 TGTT
12701612 ATATATGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (16 bp):
TGTTCTACCTGAAAAA
Found at i:12701654 original size:28 final size:29
Alignment explanation
Indices: 12701621--12701679 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
12701611 TATATATGAT
*
12701621 AATGTGCTAAGTGAAAAGA-TTCTACATG
1 AATGTGCTAAGTGAAAAAAGTTCTACATG
*
12701649 AATGTGCTAAGTGAAAAAAGTTCTACGTG
1 AATGTGCTAAGTGAAAAAAGTTCTACATG
12701678 AA
1 AA
12701680 GATACCCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (29 bp):
AATGTGCTAAGTGAAAAAAGTTCTACATG
Found at i:12701885 original size:47 final size:46
Alignment explanation
Indices: 12701811--12701908 Score: 142
Period size: 47 Copynumber: 2.1 Consensus size: 46
12701801 GAGTCAAGGG
* *
12701811 TTCTATGCGGTCATTTGGGATAATTCTAGGTGGTCATTCGGGACAT
1 TTCTATGCGGTCATTCGGGACAATTCTAGGTGGTCATTCGGGACAT
* * *
12701857 ATTCTATGCGGTCATTCGGGACATTTCTATGTGGTCCTTCGGGACAT
1 -TTCTATGCGGTCATTCGGGACAATTCTAGGTGGTCATTCGGGACAT
12701904 TTCTA
1 TTCTA
12701909 CGTGGCACTT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
46 5 0.11
47 41 0.89
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (46 bp):
TTCTATGCGGTCATTCGGGACAATTCTAGGTGGTCATTCGGGACAT
Found at i:12701913 original size:23 final size:23
Alignment explanation
Indices: 12701811--12701913 Score: 125
Period size: 23 Copynumber: 4.4 Consensus size: 23
12701801 GAGTCAAGGG
* * * *
12701811 TTCTATGCGGTCATTTGGGATAA
1 TTCTATGTGGTCATTCGGGACAT
*
12701834 TTCTAGGTGGTCATTCGGGACAT
1 TTCTATGTGGTCATTCGGGACAT
*
12701857 ATTCTATGCGGTCATTCGGGACAT
1 -TTCTATGTGGTCATTCGGGACAT
*
12701881 TTCTATGTGGTCCTTCGGGACAT
1 TTCTATGTGGTCATTCGGGACAT
*
12701904 TTCTACGTGG
1 TTCTATGTGG
12701914 CACTTCAGTG
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
23 48 0.70
24 21 0.30
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.37
Consensus pattern (23 bp):
TTCTATGTGGTCATTCGGGACAT
Found at i:12701919 original size:23 final size:25
Alignment explanation
Indices: 12701833--12701942 Score: 101
Period size: 24 Copynumber: 4.7 Consensus size: 25
12701823 ATTTGGGATA
*
12701833 ATTCTAGGTGGTCA-TTCGGGACAT
1 ATTCTACGTGGTCACTTCGGGACAT
* *
12701857 ATTCTATGCGGTCA-TTCGGGACAT
1 ATTCTACGTGGTCACTTCGGGACAT
*
12701881 -TTCTATGTGGTC-CTTCGGGACAT
1 ATTCTACGTGGTCACTTCGGGACAT
*
12701904 -TTCTACGTGG-CACTTCAGTG-CAT
1 ATTCTACGTGGTCACTTC-GGGACAT
*
12701927 ATTCTACGCGG-CACTT
1 ATTCTACGTGGTCACTT
12701943 TGGTGCAATT
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
22 1 0.01
23 37 0.49
24 38 0.50
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.35
Consensus pattern (25 bp):
ATTCTACGTGGTCACTTCGGGACAT
Found at i:12701939 original size:24 final size:23
Alignment explanation
Indices: 12701904--12701955 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
12701894 TTCGGGACAT
*
12701904 TTCTACGTGGCACTTCAGTGCATA
1 TTCTACGCGGCACTTCAGTGCA-A
**
12701928 TTCTACGCGGCACTTTGGTGCAA
1 TTCTACGCGGCACTTCAGTGCAA
12701951 TTCTA
1 TTCTA
12701956 TGTGGTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (23 bp):
TTCTACGCGGCACTTCAGTGCAA
Found at i:12706283 original size:16 final size:16
Alignment explanation
Indices: 12706262--12706301 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
12706252 ATTTTTCAAG
12706262 AGTCAATGATTTGTAA
1 AGTCAATGATTTGTAA
12706278 AGTCAATGATTTGTAA
1 AGTCAATGATTTGTAA
*
12706294 AGTTAATG
1 AGTCAATG
12706302 TGACACCTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (16 bp):
AGTCAATGATTTGTAA
Found at i:12707243 original size:29 final size:28
Alignment explanation
Indices: 12707203--12707294 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
12707193 TATTAGATTA
* * *
12707203 TTTACATATAGGTTCTTATACTTTATATT
1 TTTACAT-TAGGTCCCTAAACTTTATATT
*
12707232 TTTACACTTAGGTCCCTAAATTTTATATT
1 TTTACA-TTAGGTCCCTAAACTTTATATT
12707261 TTTACAATTAGGTCCCTAAACTTTAGT-TT
1 TTTAC-ATTAGGTCCCTAAACTTTA-TATT
12707290 TTTAC
1 TTTAC
12707295 TTTTTAGTCC
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
29 52 0.95
30 3 0.05
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (28 bp):
TTTACATTAGGTCCCTAAACTTTATATT
Found at i:12711680 original size:36 final size:36
Alignment explanation
Indices: 12711603--12711801 Score: 242
Period size: 36 Copynumber: 5.5 Consensus size: 36
12711593 ACGCAATAAT
12711603 ATCTCACTCGAGATTGTTTTT-TTAAAACATAT-TAC
1 ATCTCACTCGAGATTGTTTTTCTTAAAACATATAT-C
* *
12711638 ATCTCACTCGAGATTATTTTTCTTAAAACAAATATC
1 ATCTCACTCGAGATTGTTTTTCTTAAAACATATATC
* *
12711674 ACCTCACTCGAGATTGTTTTTCTTAAAACATACATC
1 ATCTCACTCGAGATTGTTTTTCTTAAAACATATATC
* * * *
12711710 TTCTCACTCGAGATTGGTTTTT-TTTAAACATACAAC
1 ATCTCACTCGAGATT-GTTTTTCTTAAAACATATATC
* * *
12711746 ATCTCACTCGAGATTGTTTTTCTTAAAAACAAATTTT
1 ATCTCACTCGAGATTGTTTTTCTT-AAAACATATATC
*
12711783 ATCTCACTTGAGATTGTTT
1 ATCTCACTCGAGATTGTTT
12711802 AAGAAAACTA
Statistics
Matches: 141, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
35 26 0.18
36 84 0.60
37 31 0.22
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (36 bp):
ATCTCACTCGAGATTGTTTTTCTTAAAACATATATC
Found at i:12711754 original size:108 final size:108
Alignment explanation
Indices: 12711604--12711801 Score: 308
Period size: 108 Copynumber: 1.8 Consensus size: 108
12711594 CGCAATAATA
**
12711604 TCTCACTCGAGATTGTTTTTTTAAAACATATTACATCTCACTCGAGATTATTTTTCTT-AAAACA
1 TCTCACTCGAGATTGTTTTTTTAAAACATACAACATCTCACTCGAGATTATTTTTCTTAAAAACA
12711668 AATATCACCTCACTCGAGATTGTTTTTCTTAAAACATACATCT
66 AATATCACCTCACTCGAGATTGTTTTTCTTAAAACATACATCT
* *
12711711 TCTCACTCGAGATTGGTTTTTTTTAAACATACAACATCTCACTCGAGATTGTTTTTCTTAAAAAC
1 TCTCACTCGAGATT-GTTTTTTTAAAACATACAACATCTCACTCGAGATTATTTTTCTTAAAAAC
* * * *
12711776 AAATTTTATCTCACTTGAGATTGTTT
65 AAATATCACCTCACTCGAGATTGTTT
12711802 AAGAAAACTA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
107 14 0.17
108 40 0.49
109 27 0.33
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.41
Consensus pattern (108 bp):
TCTCACTCGAGATTGTTTTTTTAAAACATACAACATCTCACTCGAGATTATTTTTCTTAAAAACA
AATATCACCTCACTCGAGATTGTTTTTCTTAAAACATACATCT
Found at i:12712017 original size:16 final size:16
Alignment explanation
Indices: 12711982--12712031 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
12711972 ATGATGTTCA
*
12711982 AAAAATGGAAAAAGGA-
1 AAAAATGGAAAAA-TAT
12711998 AAAAATGGAAAAATAT
1 AAAAATGGAAAAATAT
12712014 AAAAAT-GAAAAAT-T
1 AAAAATGGAAAAATAT
12712028 AAAA
1 AAAA
12712032 TGAAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 19 0.59
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (16 bp):
AAAAATGGAAAAATAT
Found at i:12712033 original size:13 final size:15
Alignment explanation
Indices: 12711998--12712038 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
12711988 GGAAAAAGGA
12711998 AAAAATGGAAAAATAT
1 AAAAAT-GAAAAATAT
12712014 AAAAATGAAAAAT-T
1 AAAAATGAAAAATAT
12712028 -AAAATGAAAAA
1 AAAAATGAAAAA
12712039 AAAACAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 11 0.44
14 1 0.04
15 7 0.28
16 6 0.24
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (15 bp):
AAAAATGAAAAATAT
Found at i:12712674 original size:116 final size:115
Alignment explanation
Indices: 12712347--12712690 Score: 384
Period size: 116 Copynumber: 2.9 Consensus size: 115
12712337 GTTCCTAGAG
* * * *
12712347 GAAGGGTTCTTAATGATAAGAACTCGTTTAATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
1 GAAGGGTTCGTAATGAAAAGAACTCGTTCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* *
12712412 TTCAGAACTAGACACATGTCCGTCG-CAAGATAATATAGATCAACATTTCAGAA
66 TTCAGAACTAGACACA--TCCGTCGACAAG-GAA-ATGGATCAACATTTCAGAA
* * * *
12712465 GAAGGGTTTGTAATGAAAAAAACTCATTCGATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 GAAGGGTTCGTAATGAAAAGAACTCGTTCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* ** * * **
12712530 TTCAGAACTTGACACATCTATAGCACAAGGAGATGGATCAACATTTTTGAA
66 TTCAGAACTAGACACATCCGTCG-ACAAGGAAATGGATCAACATTTCAGAA
* * * * * *
12712581 GAAGTGTTCGTAATGAGAAGAACTCGTTCAACGAGGAAGAAGAAGTTCACAGTGAGAAGAACTCG
1 GAAGGGTTCGTAATGAAAAGAACTCGTTCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * *
12712646 TTCGGAACTCGACACATCCGTCGTACAAGGAAATGAATCGACATT
66 TTCAGAACTAGACACATCCGTCG-ACAAGGAAATGGATCAACATT
12712691 GCTGAGAAAA
Statistics
Matches: 188, Mismatches: 36, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
116 111 0.59
117 1 0.01
118 76 0.40
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.24
Consensus pattern (115 bp):
GAAGGGTTCGTAATGAAAAGAACTCGTTCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
TTCAGAACTAGACACATCCGTCGACAAGGAAATGGATCAACATTTCAGAA
Found at i:12712711 original size:116 final size:113
Alignment explanation
Indices: 12712352--12712765 Score: 330
Period size: 116 Copynumber: 3.6 Consensus size: 113
12712342 TAGAGGAAGG
* * * * * *
12712352 GTTCTTAATGATAAGAACTCGTTTAATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAG
1 GTTCGTAATGAGAAGAACTCGTTCAACGAGGAAGAAGAAGTTCACAATGAGAAGAACTTGTTCAG
* * *
12712417 AACTAGACACATGTCCGTCG-CAA-GATAATATAGATCAACATTTCAGAAGAAGG
66 AACTAGACACA--TCCGTCGACAAGGA-AAT-GA-ATCAACATTTGAGAA-AA-A
* * * * * * *
12712470 GTTTGTAATGAAAAAAACTCATTCGATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAG
1 GTTCGTAATGAGAAGAACTCGTTCAACGAGGAAGAAGAAGTTCACAATGAGAAGAACTTGTTCAG
* ** * * * ** *
12712535 AACTTGACACATCTATAGCACAAGGAGATGGATCAACATTTTTGAAGAAGT
66 AACTAGACACATCCGTCG-ACAAGGAAATGAATCAACATTTGAGAA-AA-A
* * *
12712586 GTTCGTAATGAGAAGAACTCGTTCAACGAGGAAGAAGAAGTTCACAGTGAGAAGAACTCGTTCGG
1 GTTCGTAATGAGAAGAACTCGTTCAACGAGGAAGAAGAAGTTCACAATGAGAAGAACTTGTTCAG
* *
12712651 AACTCGACACATCCGTCGTACAAGGAAATGAATCGACATTGCTGAGAAAAA
66 AACTAGACACATCCGTCG-ACAAGGAAATGAATCAACATT--TGAGAAAAA
* * * * * * * * *
12712702 GTTCATAATGAGAATAATTC-ATCTGACGAGGAAGAAAAAGTTCGCAATGAGAAGAGCTTATTCA
1 GTTCGTAATGAGAAGAACTCGTTC-AACGAGGAAGAAGAAGTTCACAATGAGAAGAACTTGTTCA
12712766 ACTTGGGATC
Statistics
Matches: 239, Mismatches: 51, Indels: 14
0.79 0.17 0.05
Matches are distributed among these distances:
115 2 0.01
116 157 0.66
117 2 0.01
118 76 0.32
119 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (113 bp):
GTTCGTAATGAGAAGAACTCGTTCAACGAGGAAGAAGAAGTTCACAATGAGAAGAACTTGTTCAG
AACTAGACACATCCGTCGACAAGGAAATGAATCAACATTTGAGAAAAA
Found at i:12714322 original size:15 final size:15
Alignment explanation
Indices: 12714304--12714346 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12714294 AGACTTTATA
*
12714304 TTTTTACACTTAGCT
1 TTTTTACACTTAGAT
*
12714319 TTTTGGACA-TTAGAT
1 TTTT-TACACTTAGAT
12714334 TTTTTACACTTAG
1 TTTTTACACTTAG
12714347 GTCCCTAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 3 0.13
15 17 0.74
16 3 0.13
ACGTcount: A:0.23, C:0.14, G:0.12, T:0.51
Consensus pattern (15 bp):
TTTTTACACTTAGAT
Found at i:12714367 original size:30 final size:29
Alignment explanation
Indices: 12714328--12714396 Score: 120
Period size: 29 Copynumber: 2.3 Consensus size: 29
12714318 TTTTTGGACA
*
12714328 TTAGATTTTTTACACTTAGGTCCCTAAACT
1 TTAG-TTTTTTACACTTAAGTCCCTAAACT
12714358 TTAGTTTTTTACACTTAAGTCCCTAAACT
1 TTAGTTTTTTACACTTAAGTCCCTAAACT
12714387 TTAGTTTTTT
1 TTAGTTTTTT
12714397 TTTACATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 34 0.89
30 4 0.11
ACGTcount: A:0.25, C:0.17, G:0.09, T:0.49
Consensus pattern (29 bp):
TTAGTTTTTTACACTTAAGTCCCTAAACT
Found at i:12716423 original size:2 final size:2
Alignment explanation
Indices: 12716416--12716470 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
12716406 CAAACTACCC
*
12716416 AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12716457 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
12716471 TCTTTCCAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12718004 original size:21 final size:22
Alignment explanation
Indices: 12717944--12718008 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
12717934 ATTGTCATAG
12717944 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGATTCCCCTGCTACA
*
12717966 GGGAATCGATTCCCCTGCTACA
1 GGGAACCGATTCCCCTGCTACA
*
12717988 GGGAACCGA-TACCCTGCTACA
1 GGGAACCGATTCCCCTGCTACA
12718009 ATACTGCTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 11 0.28
22 29 0.73
ACGTcount: A:0.25, C:0.34, G:0.23, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCTGCTACA
Found at i:12719312 original size:2 final size:2
Alignment explanation
Indices: 12719305--12719348 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
12719295 TTATGTCATC
12719305 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12719347 AT
1 AT
12719349 CATCTATGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12722646 original size:988 final size:987
Alignment explanation
Indices: 12720726--12722664 Score: 3833
Period size: 988 Copynumber: 2.0 Consensus size: 987
12720716 TTACAGACCC
12720726 TTAAACTCGATATTTTTGTAAAATAAAATATATTATTAAATATACCTGATTTTTATGGTGTTCCA
1 TTAAACTCGATATTTTTGTAAAATAAAATATATTATTAAATATACCTGATTTTTATGGTGTTCCA
12720791 ATCGCACCTTAAAATGGTTGGTGGCGACTTCTAAATTTTTTATTCAAATCGATTTTGAAAACATT
66 ATCGCACCTTAAAATGGTTGGTGGCGACTTCTAAATTTTTTATTCAAATCGATTTTGAAAACATT
12720856 ATTAACCCTTGAAAGTCATGTCGTACATGATCATTTTCAATCGCTCATCCAAAAAATGGTGACGA
131 ATTAACCCTTGAAAGTCATGTCGTACATGATCATTTTCAATCGCTCATCCAAAAAATGGTGACGA
12720921 CATATATTTTCACCACTCTCTATCATAAGAAAACATCGATAAGTAACTCCTGAGCCTTTGAATTT
196 CATATATTTTCACCACTCTCTATCATAAGAAAACATCGATAAGTAACTCCTGAGCCTTTGAATTT
12720986 CATTTTTGGAGATTTTGGTGAAATTTCGATAGTCTTGCCTGCCACGCACTCCTTATGTATTGCTC
261 CATTTTTGGAGATTTTGGTGAAATTTCGATAGTCTTGCCTGCCACGCACTCCTTATGTATTGCTC
12721051 ACTGCGCGTGGGCGTTGTTCTTATCCAATGGAGTTTCTAGAAATCAATATGAACCAACTTGAATC
326 ACTGCGCGTGGGCGTTGTTCTTATCCAATGGAGTTTCTAGAAATCAATATGAACCAACTTGAATC
12721116 GGTCTAGATCAATTCGAGTTGAGCCATCTCAGTCGAGACATTTGAGTCGAGCCGTTCAAGACAAG
391 GGTCTAGATCAATTCGAGTTGAGCCATCTCAGTCGAGACATTTGAGTCGAGCCGTTCAAGACAAG
*
12721181 CTGTCCAAGCCAAGTCGAGTTGTAAGCAAAGTCGAGCCAAGCTAAGTCGAACCATAATCGATCAT
456 CTGTCCAAGCCAAGTCGAGTTGTAAGCAAAGTCGAGCCAAGCTAAGTCGAACCATAATCGACCAT
12721246 TGATCGACCCTTGATTGAACGTTAACTAACAATTGACTTTTTCTAAGAACACTTATCCAGACATT
521 TGATCGACCCTTGATTGAACGTTAACTAACAATTGACTTTTTCTAAGAACACTTATCCAGACATT
12721311 TTTAGGTTCGTTTTTTCCAAAATAAAACTCGGTAAATTATTTTCAACATTTTACCTTTCAATTTT
586 TTTAGGTTCGTTTTTTCCAAAATAAAACTCGGTAAATTATTTTCAACATTTTACCTTTCAATTTT
12721376 CGTAATTAAATTTTGTTTATGATGTAATTTATTTTGTAATATATCTGATATATTATTGGATGTCG
651 CGTAATTAAATTTTGTTTATGATGTAATTTATTTTGTAATATATCTGATATATTATTGGATGTCG
12721441 AATTAAAGTTTTAAGGCAATCGATTGAAGTTTCAATGGCTGAATGATGTATATCATAAATCAAGG
716 AATTAAAGTTTTAAGGCAATCGATTGAAGTTTCAATGGCTGAATGATGTATATCATAAATCAAGG
12721506 TAATACTTTACTACCCTATGCATGCTTTATGGTATATGTTGGTAATTGGTTGATGAATGGTTGAA
781 TAATACTTTACTACCCTATGCATGCTTTATGGTATATGTTGGTAATTGGTTGATGAATGGTTGAA
12721571 ATGATTGGTCATGTAAATCCTGAGGATTATTCTTAAATTCAAATTGAATATGCTAATAGAATATT
846 ATGATTGGTCATGTAAATCCTGAGGATTATTCTTAAATTCAAATTGAATATGCTAATAGAATATT
12721636 AAATTGATTAAGACTCAATTAAATCATATAATAAATGAGAATATTAAATTGAATATGCTAATAGA
911 AAATTGATTAAGACTCAATTAAATCATATAATAAATGAGAATATTAAATTGAATATGCTAATAGA
12721701 ATAAAAAATTGA
976 ATAAAAAATTGA
*
12721713 TTAAGACTCGATATTTTTGTAAAATAAAATATTTTATTAAATATACCTGATTTTTATGGTGTTCC
1 TTAA-ACTCGATATTTTTGTAAAATAAAATATATTATTAAATATACCTGATTTTTATGGTGTTCC
12721778 AATCGCACCTTAAAATGGTTGGTGGCGACTTCTAAATTTTTTATTCAAATCGATTTTGAAAACAT
65 AATCGCACCTTAAAATGGTTGGTGGCGACTTCTAAATTTTTTATTCAAATCGATTTTGAAAACAT
*
12721843 TATTAACCCTTGAAAGTCATGTCGTACATGATCATTTTCAATTGCTCATCCAAAAAATGGTGACG
130 TATTAACCCTTGAAAGTCATGTCGTACATGATCATTTTCAATCGCTCATCCAAAAAATGGTGACG
12721908 ACATATATTTTCACCACTCTCTATCATAAGAAAACATCGATAAGTAACTCCTGAGCCTTTGAATT
195 ACATATATTTTCACCACTCTCTATCATAAGAAAACATCGATAAGTAACTCCTGAGCCTTTGAATT
12721973 TCATTTTTGGAGATTTTGGTGAAATTTCGATAGTCTTGCCTGCCACGCACTCCTTATGTATTGCT
260 TCATTTTTGGAGATTTTGGTGAAATTTCGATAGTCTTGCCTGCCACGCACTCCTTATGTATTGCT
12722038 CACTGCGCGTGGGCGTTGTTCTTATCCAATGGAGTTTCTAGAAATCAATATGAACCAACTTGAAT
325 CACTGCGCGTGGGCGTTGTTCTTATCCAATGGAGTTTCTAGAAATCAATATGAACCAACTTGAAT
12722103 CGGTCTAGATCAATTCGAGTTGAGCCATCTCAGTCGAGACATTTGAGTCGAGCCGTTCAAGACAA
390 CGGTCTAGATCAATTCGAGTTGAGCCATCTCAGTCGAGACATTTGAGTCGAGCCGTTCAAGACAA
12722168 GCTGTCCAAGCCAAGTCGAGTTGTAAGCAAAGTCGAGCCAAGCTAAGTCGAACCATAATCGACCA
455 GCTGTCCAAGCCAAGTCGAGTTGTAAGCAAAGTCGAGCCAAGCTAAGTCGAACCATAATCGACCA
12722233 TTGATCGACCCTTGATTGAACGTTAACTAACAATTGACTTTTTCTAAGAACACTTATCCAGACAT
520 TTGATCGACCCTTGATTGAACGTTAACTAACAATTGACTTTTTCTAAGAACACTTATCCAGACAT
*
12722298 TTTTAGGTTCGTTTTTTCCAAAATCAAACTCGGTAAATTATTTTCAACATTTTACCTTTCAATTT
585 TTTTAGGTTCGTTTTTTCCAAAATAAAACTCGGTAAATTATTTTCAACATTTTACCTTTCAATTT
12722363 TCGTAATTAAATTTTGTTTATGATGTAATTTATTTTGTAATATATCTGATATATTATTGGATGTC
650 TCGTAATTAAATTTTGTTTATGATGTAATTTATTTTGTAATATATCTGATATATTATTGGATGTC
12722428 GAATTAAAGTTTTAAGGCAATCGATTGAAGTTTCAATGGCTGAATGATGTATATCATAAATCAAG
715 GAATTAAAGTTTTAAGGCAATCGATTGAAGTTTCAATGGCTGAATGATGTATATCATAAATCAAG
12722493 GTAATACTTTACTACCCTATGCATGCTTTATGGTATATGTTGGTAATTGGTTGATGAATGGTTGA
780 GTAATACTTTACTACCCTATGCATGCTTTATGGTATATGTTGGTAATTGGTTGATGAATGGTTGA
12722558 AATGATTGGTCATGTAAATCCTGAGGATTATTCTTAAATTCAAATTGAATATGCTAATAGAATAT
845 AATGATTGGTCATGTAAATCCTGAGGATTATTCTTAAATTCAAATTGAATATGCTAATAGAATAT
12722623 TAAATTGATTAAGACTCAATTAAATCATATAATAAATGAGAA
910 TAAATTGATTAAGACTCAATTAAATCATATAATAAATGAGAA
12722665 GATTGATCAA
Statistics
Matches: 947, Mismatches: 4, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
987 4 0.00
988 943 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (987 bp):
TTAAACTCGATATTTTTGTAAAATAAAATATATTATTAAATATACCTGATTTTTATGGTGTTCCA
ATCGCACCTTAAAATGGTTGGTGGCGACTTCTAAATTTTTTATTCAAATCGATTTTGAAAACATT
ATTAACCCTTGAAAGTCATGTCGTACATGATCATTTTCAATCGCTCATCCAAAAAATGGTGACGA
CATATATTTTCACCACTCTCTATCATAAGAAAACATCGATAAGTAACTCCTGAGCCTTTGAATTT
CATTTTTGGAGATTTTGGTGAAATTTCGATAGTCTTGCCTGCCACGCACTCCTTATGTATTGCTC
ACTGCGCGTGGGCGTTGTTCTTATCCAATGGAGTTTCTAGAAATCAATATGAACCAACTTGAATC
GGTCTAGATCAATTCGAGTTGAGCCATCTCAGTCGAGACATTTGAGTCGAGCCGTTCAAGACAAG
CTGTCCAAGCCAAGTCGAGTTGTAAGCAAAGTCGAGCCAAGCTAAGTCGAACCATAATCGACCAT
TGATCGACCCTTGATTGAACGTTAACTAACAATTGACTTTTTCTAAGAACACTTATCCAGACATT
TTTAGGTTCGTTTTTTCCAAAATAAAACTCGGTAAATTATTTTCAACATTTTACCTTTCAATTTT
CGTAATTAAATTTTGTTTATGATGTAATTTATTTTGTAATATATCTGATATATTATTGGATGTCG
AATTAAAGTTTTAAGGCAATCGATTGAAGTTTCAATGGCTGAATGATGTATATCATAAATCAAGG
TAATACTTTACTACCCTATGCATGCTTTATGGTATATGTTGGTAATTGGTTGATGAATGGTTGAA
ATGATTGGTCATGTAAATCCTGAGGATTATTCTTAAATTCAAATTGAATATGCTAATAGAATATT
AAATTGATTAAGACTCAATTAAATCATATAATAAATGAGAATATTAAATTGAATATGCTAATAGA
ATAAAAAATTGA
Found at i:12725476 original size:28 final size:27
Alignment explanation
Indices: 12725439--12725492 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
12725429 TTTTGTTAGC
*
12725439 ATTTTTTTTAATTATGTTATTATTTTTT
1 ATTTTATTTAATTATGTTATT-TTTTTT
*
12725467 ATTTTATTTAATTATTTTATTTTTTT
1 ATTTTATTTAATTATGTTATTTTTTT
12725493 GCAGTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (27 bp):
ATTTTATTTAATTATGTTATTTTTTTT
Found at i:12725694 original size:20 final size:21
Alignment explanation
Indices: 12725658--12725700 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
12725648 GTGTAACTGC
12725658 AAAAAAATAAAATAATTAAAT
1 AAAAAAATAAAATAATTAAAT
*
12725679 AAAATAATAAAA-AATTAAAT
1 AAAAAAATAAAATAATTAAAT
12725699 AA
1 AA
12725701 TACAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAAATAAAATAATTAAAT
Found at i:12725707 original size:20 final size:21
Alignment explanation
Indices: 12725658--12725708 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
12725648 GTGTAACTGC
*
12725658 AAAAAAATAAAATAATTAAAT
1 AAAACAATAAAATAATTAAAT
*
12725679 AAAATAATAAAA-AATTAAAT
1 AAAACAATAAAATAATTAAAT
*
12725699 AATACAATAA
1 AAAACAATAA
12725709 TTAAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAACAATAAAATAATTAAAT
Found at i:12725714 original size:16 final size:15
Alignment explanation
Indices: 12725675--12725716 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
12725665 TAAAATAATT
*
12725675 AAATAAAATAATAAA
1 AAATTAAATAATAAA
12725690 AAATTAAATAATACAA
1 AAATTAAATAATA-AA
*
12725706 TAATTAAATAA
1 AAATTAAATAA
12725717 AATACTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATTAAATAATAAA
Found at i:12729559 original size:3 final size:3
Alignment explanation
Indices: 12729545--12729590 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
12729535 TACATTAAGG
*
12729545 ATA ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12729591 TCATAATCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:12730243 original size:2 final size:2
Alignment explanation
Indices: 12730194--12730233 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12730184 ATATTGCCCA
12730194 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12730234 TAATTATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12732721 original size:41 final size:42
Alignment explanation
Indices: 12732660--12732738 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
12732650 CGAAGGTCTT
* *
12732660 ACAGATGGACCGAAGAATTT-ATCATCTTGCTCGAAAGACTG
1 ACAGATGGACCGAAGAATTTAATCATCATGCTCAAAAGACTG
*
12732701 ACAGAT-GACCCGAAGGATTTAATCATCATGCTCAAAAG
1 ACAGATGGA-CCGAAGAATTTAATCATCATGCTCAAAAG
12732739 GCTTCCTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 2 0.06
41 16 0.48
42 15 0.45
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (42 bp):
ACAGATGGACCGAAGAATTTAATCATCATGCTCAAAAGACTG
Found at i:12732791 original size:257 final size:258
Alignment explanation
Indices: 12732079--12733019 Score: 1293
Period size: 257 Copynumber: 3.7 Consensus size: 258
12732069 TTATTGGGTA
* * * *
12732079 AGAAACTTTGGAAATCGCTTTCTCATTTTTTGAAAATCATGTGGAAATATCCTGCCCGAAGGTCT
1 AGAAACTTTGGAAATCGCTTTCTCA-TTTTTCAAAATCATGTGAAAACATCCTACCCGAAGGTCT
* * * *
12732144 TATACATGGCCCGAAGGACTTATCATCTTGCTCGAAGGACTGACAGATGACCCGAAAAATTTAAT
65 TACAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGAATTTAAT
*
12732209 CATCATGCTCAAAAGACTTACAT-ATTGCCCAAAAGACTTACAAATTTGGGAAATAGTTTACTGG
130 CATCATGCTCAAAAGACTTAC-TGATGGCCCAAAAGACTTACAAATTTGGGAAATAGTTTACTGG
* * **
12732273 GTAAGAAACCTTGGAAATCGT-TTTCTTACTTTTCAAAAATTTAATTTTCTGAAAATTGTAAATG
194 GTAAGAAACTTTGGAAATCATCTTTCTTACTTTTCAAAAATTTAATTTTCTGAAAATAATAAATG
** * **
12732337 AGAAACTTTGGAAATCATTTTCTCATTTTTCAAAAATCATGTGGAAACATCCTGGCCGAAGGTCT
1 AGAAACTTTGGAAATCGCTTTCTCATTTTTC-AAAATCATGTGAAAACATCCTACCCGAAGGTCT
** *
12732402 TATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCAAAGAATTTAAT
65 TACAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGAATTTAAT
* * * * * * *
12732467 CATCATACTCGAAAGACTTACTGATAGCCCAAAAGACTTACTAATTTTGGAAATAATTTGCTGGG
130 CATCATGCTCAAAAGACTTACTGATGGCCCAAAAGACTTACAAATTTGGGAAATAGTTTACTGGG
*
12732532 TAAGAAACTTTGGAAAT-ATCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATAATAAATG
195 TAAGAAACTTTGGAAATCATCTTTCTTACTTTTCAAAAATTTAATTTTCTGAAAATAATAAATG
* *
12732595 AGAAACTTTGGAAATCGTTTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTT
1 AGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAATCATGTGAAAACATCCTACCCGAAGGTCTT
* * * *
12732660 ACAGATGGACCGAAGAATTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATC
66 ACAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGAATTTAATC
* * * * * *
12732725 ATCATGCTCAAAAGGCTTCCTGATGGCTCGAAAGACTTACCAATTTGGGAAATAGTTTAATGGGT
131 ATCATGCTCAAAAGACTTACTGATGGCCCAAAAGACTTACAAATTTGGGAAATAGTTTACTGGGT
* * * *
12732790 AATAAACTTTGGAAATCA-CTTTCTTACTTTTCAAAAATTTTATTTTCTAAAAATACTAAATG
196 AAGAAACTTTGGAAATCATCTTTCTTACTTTTCAAAAATTTAATTTTCTGAAAATAATAAATG
* ** * * *
12732852 AGAAACTTTGGAAATTGCTTTCTCATTTTTCAATTTTACGTGAAAACATCCTACCCGAAGGTGTT
1 AGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAATCATGTGAAAACATCCTACCCGAAGGTCTT
* *
12732917 ACAGATGG-CCGAAGGACTTATCTTCTTGCTCGAAAAACTGACAGATGACCCGAATG-ATTTAAT
66 ACAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAA-GAATTTAAT
* * *
12732980 CATCATGCTCGAAAGACTTAC-GATGGCCCGAAGGACTTAC
130 CATCATGCTCAAAAGACTTACTGATGGCCCAAAAGACTTAC
12733020 TAAGTAAGAA
Statistics
Matches: 613, Mismatches: 65, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
255 17 0.03
256 67 0.11
257 272 0.44
258 257 0.42
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (258 bp):
AGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAATCATGTGAAAACATCCTACCCGAAGGTCTT
ACAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGAATTTAATC
ATCATGCTCAAAAGACTTACTGATGGCCCAAAAGACTTACAAATTTGGGAAATAGTTTACTGGGT
AAGAAACTTTGGAAATCATCTTTCTTACTTTTCAAAAATTTAATTTTCTGAAAATAATAAATG
Found at i:12734820 original size:27 final size:27
Alignment explanation
Indices: 12734790--12734885 Score: 101
Period size: 26 Copynumber: 3.5 Consensus size: 27
12734780 ATTTGATTTA
12734790 TTTTTTTCTCTTTT-TTTCTTATTATTC
1 TTTTTTTCTCTTTTCTTTCTTATT-TTC
*
12734817 TTTTTTTATCTTTTCTCTT-TTATTTTTC
1 TTTTTTTCTCTTTTCT-TTCTTA-TTTTC
*
12734845 TATTTTTTCACTTTTCTTTC-T-TTTTC
1 T-TTTTTTCTCTTTTCTTTCTTATTTTC
12734871 TTGTTTTTCTCTTTT
1 TT-TTTTTCTCTTTT
12734886 TCTCTTCTCT
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
25 1 0.02
26 17 0.29
27 13 0.22
28 11 0.19
29 17 0.29
ACGTcount: A:0.06, C:0.16, G:0.01, T:0.77
Consensus pattern (27 bp):
TTTTTTTCTCTTTTCTTTCTTATTTTC
Found at i:12734822 original size:19 final size:17
Alignment explanation
Indices: 12734791--12734891 Score: 69
Period size: 17 Copynumber: 5.5 Consensus size: 17
12734781 TTTGATTTAT
*
12734791 TTTTTTCTCTTTTTTTC
1 TTTTTTCTTTTTTTTTC
*
12734808 TTATTATTCTTTTTTTATC
1 TT-TT-TTCTTTTTTTTTC
*
12734827 TTTTCTCTTTTATTTTTC
1 TTTTTTCTTTT-TTTTTC
* *
12734845 TATTTTTTCACTTTTCTTTC
1 --TTTTTTC-TTTTTTTTTC
*
12734865 -TTTTTCTTGTTTTTCTC
1 TTTTTTCTT-TTTTTTTC
12734882 TTTTTCTCTT
1 TTTTT-TCTT
12734892 CTCTATCCTA
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
16 1 0.02
17 20 0.31
18 13 0.20
19 17 0.26
20 11 0.17
21 3 0.05
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.76
Consensus pattern (17 bp):
TTTTTTCTTTTTTTTTC
Found at i:12734825 original size:14 final size:14
Alignment explanation
Indices: 12734802--12734868 Score: 55
Period size: 15 Copynumber: 4.5 Consensus size: 14
12734792 TTTTTCTCTT
*
12734802 TTTTTCTTATTATTC
1 TTTTT-TTATTTTTC
12734817 TTTTTTTATCTTTTC
1 TTTTTTTAT-TTTTC
*
12734832 -TCTTTTATTTTTC
1 TTTTTTTATTTTTC
*
12734845 TATTTTTTCACTTTTC
1 T-TTTTTT-ATTTTTC
12734861 TTTCTTTT
1 TTT-TTTT
12734869 TCTTGTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
13 5 0.12
14 11 0.26
15 16 0.37
16 11 0.26
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTTTATTTTTC
Found at i:12734835 original size:17 final size:17
Alignment explanation
Indices: 12734793--12734886 Score: 51
Period size: 18 Copynumber: 5.7 Consensus size: 17
12734783 TGATTTATTT
12734793 TTTTCTC-TTTTTT-TC
1 TTTTCTCTTTTTTTATC
*
12734808 TTATTATTCTTTTTTTATC
1 TT-TT-CTCTTTTTTTATC
12734827 TTTTCTC---TTTTAT-
1 TTTTCTCTTTTTTTATC
* *
12734840 TTTTCTATTTTTTCA-C
1 TTTTCTCTTTTTTTATC
*
12734856 TTTTCTTTCTTTTTCTTGT-
1 TTTTC--TCTTTTT-TTATC
12734875 TTTTCTCTTTTT
1 TTTTCTCTTTTT
12734887 CTCTTCTCTA
Statistics
Matches: 60, Mismatches: 7, Indels: 22
0.67 0.08 0.25
Matches are distributed among these distances:
13 6 0.10
14 6 0.10
15 2 0.03
16 11 0.18
17 11 0.18
18 14 0.23
19 10 0.17
ACGTcount: A:0.06, C:0.16, G:0.01, T:0.77
Consensus pattern (17 bp):
TTTTCTCTTTTTTTATC
Found at i:12734850 original size:29 final size:28
Alignment explanation
Indices: 12734790--12734866 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 28
12734780 ATTTGATTTA
*
12734790 TTTTTTTCTCTTTT-TTTCTTATTATTC
1 TTTTTTTATCTTTTCTTTCTTATTATTC
*
12734817 TTTTTTTATCTTTTCTCTT-TTATTTTTC
1 TTTTTTTATCTTTTCT-TTCTTATTATTC
12734845 TATTTTTTCA-CTTTTCTTTCTT
1 T-TTTTTT-ATCTTTTCTTTCTT
12734867 TTTCTTGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
27 13 0.30
28 12 0.28
29 17 0.40
30 1 0.02
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTTTTTATCTTTTCTTTCTTATTATTC
Found at i:12734852 original size:22 final size:22
Alignment explanation
Indices: 12734817--12734859 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12734807 CTTATTATTC
* *
12734817 TTTTTTTATCTTTTCTCTTTTA
1 TTTTTCTATCTTTTCACTTTTA
*
12734839 TTTTTCTATTTTTTCACTTTT
1 TTTTTCTATCTTTTCACTTTT
12734860 CTTTCTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTTCTATCTTTTCACTTTTA
Found at i:12735722 original size:31 final size:31
Alignment explanation
Indices: 12735665--12735725 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
12735655 TCTTCCCGGG
**
12735665 AAGGTAAAAGTATGGATTTGGTGTCTCAAAA
1 AAGGTAAAAGTATGGATTTGAAGTCTCAAAA
*
12735696 AAGGTAAAGGTAT-GACTTTGAAGTCTCAAA
1 AAGGTAAAAGTATGGA-TTTGAAGTCTCAAA
12735726 TAAATGTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.28
Consensus pattern (31 bp):
AAGGTAAAAGTATGGATTTGAAGTCTCAAAA
Found at i:12737329 original size:15 final size:15
Alignment explanation
Indices: 12737309--12737340 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12737299 GCTTGAAGAC
12737309 GGTGTAATTCTCAAT
1 GGTGTAATTCTCAAT
12737324 GGTGTAATTCTCAAT
1 GGTGTAATTCTCAAT
12737339 GG
1 GG
12737341 CATGTCTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (15 bp):
GGTGTAATTCTCAAT
Found at i:12737654 original size:20 final size:20
Alignment explanation
Indices: 12737617--12737655 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12737607 CATTGAGCTC
*
12737617 TTTCTTTTCTCTTGCAAAAG
1 TTTCTTTTCTCCTGCAAAAG
12737637 TTTCTTTTC-CCTGCCAAAA
1 TTTCTTTTCTCCTG-CAAAA
12737656 TAGCTAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.21, C:0.26, G:0.08, T:0.46
Consensus pattern (20 bp):
TTTCTTTTCTCCTGCAAAAG
Found at i:12737999 original size:19 final size:19
Alignment explanation
Indices: 12737975--12738014 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
12737965 AAGCAAATAA
*
12737975 CAAAATTGATAA-GCTAATG
1 CAAAA-TGATAATGCAAATG
12737994 CAAAATGATAATGCAAATG
1 CAAAATGATAATGCAAATG
12738013 CA
1 CA
12738015 GATGCAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (19 bp):
CAAAATGATAATGCAAATG
Found at i:12739810 original size:20 final size:20
Alignment explanation
Indices: 12739785--12739832 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
12739775 ATTGTTCATC
12739785 ACTGTTCACACAGTATCGAT
1 ACTGTTCACACAGTATCGAT
* *
12739805 ACTGTTCACACATTATCGGT
1 ACTGTTCACACAGTATCGAT
*
12739825 ACTATTCA
1 ACTGTTCA
12739833 TTACTGTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (20 bp):
ACTGTTCACACAGTATCGAT
Found at i:12740113 original size:18 final size:19
Alignment explanation
Indices: 12740060--12740116 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
12740050 ATATTTAATG
*
12740060 AAAAAGATACCAATTTTTA
1 AAAAAGATACCAATTGTTA
***
12740079 ACAAAAGGATTTTAATTGTT-
1 A-AAAA-GATACCAATTGTTA
12740099 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
12740117 GGAAAATATA
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
18 10 0.34
19 5 0.17
20 5 0.17
21 9 0.31
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTA
Found at i:12743286 original size:20 final size:20
Alignment explanation
Indices: 12743261--12743309 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
12743251 TACTGTTCAT
12743261 TATTGTTCACACAATATCGG
1 TATTGTTCACACAATATCGG
*
12743281 TATTGTTCACACATTATCGG
1 TATTGTTCACACAATATCGG
*
12743301 TACTGTTCA
1 TATTGTTCA
12743310 TTATTGTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (20 bp):
TATTGTTCACACAATATCGG
Found at i:12745707 original size:21 final size:22
Alignment explanation
Indices: 12745670--12745722 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
12745660 GATGGGTTTG
*
12745670 TAAAAA-AACAATAATAAA-AA
1 TAAAAATAATAATAATAAATAA
12745690 TTAAAAATAATAAT-ATAAATAA
1 -TAAAAATAATAATAATAAATAA
*
12745712 TAATAATAATA
1 TAAAAATAATA
12745723 TTAAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
TAAAAATAATAATAATAAATAA
Found at i:12745711 original size:12 final size:12
Alignment explanation
Indices: 12745694--12745735 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
12745684 TAAAAATTAA
12745694 AAATAATAATAT
1 AAATAATAATAT
12745706 AAATAATAATA-
1 AAATAATAATAT
*
12745717 ATAATATTAAATAT
1 A-AATAAT-AATAT
12745731 AAATA
1 AAATA
12745736 TAAATATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 1 0.04
12 16 0.62
13 8 0.31
14 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATAATAATAT
Found at i:12745717 original size:31 final size:31
Alignment explanation
Indices: 12745679--12745741 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
12745669 GTAAAAAAAC
12745679 AATAATAA-AA-ATTAAAAATAATAATATAAAT
1 AATAATAATAATATTAAAAAT-A-AATATAAAT
*
12745710 AATAATAATAATATTAAATATAAATATAAAT
1 AATAATAATAATATTAAAAATAAATATAAAT
12745741 A
1 A
12745742 TTCAATAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 18 0.62
32 3 0.10
33 8 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (31 bp):
AATAATAATAATATTAAAAATAAATATAAAT
Found at i:12745735 original size:19 final size:18
Alignment explanation
Indices: 12745693--12745748 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
12745683 ATAAAAATTA
12745693 AAAATAATAATA-TAAAT
1 AAAATAATAATATTAAAT
12745710 AATAATAATAATATTAAAT
1 AA-AATAATAATATTAAAT
*
12745729 ATAAAT-ATAAATATTCAAT
1 A-AAATAAT-AATATTAAAT
12745748 A
1 A
12745749 GTACACTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 2 0.06
18 12 0.35
19 19 0.56
20 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATAATAATATTAAAT
Found at i:12747267 original size:24 final size:24
Alignment explanation
Indices: 12747214--12747268 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
12747204 AAAATAATAT
* *
12747214 ATAA-ATACATATAATATGATATA
1 ATAATATACATATAATAGGATAAA
* * *
12747237 ATTATATATATATAATAGGGTAAA
1 ATAATATACATATAATAGGATAAA
12747261 ATAATATA
1 ATAATATA
12747269 AAGTATAGGG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (24 bp):
ATAATATACATATAATAGGATAAA
Found at i:12748242 original size:2 final size:2
Alignment explanation
Indices: 12748235--12748283 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
12748225 TTTGGCTTAT
12748235 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
12748277 AC AC AC A
1 AC AC AC A
12748284 TATATATATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12748288 original size:2 final size:2
Alignment explanation
Indices: 12748283--12748312 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12748273 ACACACACAC
12748283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12748313 GTTTGGGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12748734 original size:110 final size:110
Alignment explanation
Indices: 12748587--12748785 Score: 301
Period size: 110 Copynumber: 1.8 Consensus size: 110
12748577 CAATTGAAAA
* ** *
12748587 ATGGATAAAAGGTCGAACAAGCTCTCCTATATGAACTTCCTCTTCCTTGGTGGTCGAGTTCTTCA
1 ATGGATAAAAGGTCGAACAAGCTCTCATATACAAACTTCATCTTCCTTGGTGGTCGAGTTCTTCA
* *
12748652 TATTTTGAACTCTT-CATTAGAAATGTCATTCTACCTCATTCTGTG
66 TATTATGAACT-TTCCATCAGAAATGTCATTCTACCTCATTCTGTG
* * *
12748697 ATGGATCAAAGGTCGATCAAGCTCTCATATACAAACTTCATCTTTCTTGGTGGTCGAGTTCTTCA
1 ATGGATAAAAGGTCGAACAAGCTCTCATATACAAACTTCATCTTCCTTGGTGGTCGAGTTCTTCA
12748762 TATTATGAACTTTCCATCAGAAAT
66 TATTATGAACTTTCCATCAGAAAT
12748786 ATCAGTCCAT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
109 2 0.03
110 77 0.97
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (110 bp):
ATGGATAAAAGGTCGAACAAGCTCTCATATACAAACTTCATCTTCCTTGGTGGTCGAGTTCTTCA
TATTATGAACTTTCCATCAGAAATGTCATTCTACCTCATTCTGTG
Found at i:12748804 original size:110 final size:110
Alignment explanation
Indices: 12748587--12748811 Score: 299
Period size: 110 Copynumber: 2.0 Consensus size: 110
12748577 CAATTGAAAA
* ** *
12748587 ATGGATAAAAGGTCGAACAAGCTCTCCTATATGAACTTCCTCTTCCTTGGTGGTCGAGTTCTTCA
1 ATGGATAAAAGGTCGAACAAGCTCTCATATACAAACTTCATCTTCCTTGGTGGTCGAGTTCTTCA
* * * * * *
12748652 TATTTTGAACTCTTCATTAGAAATGTCATTCTACCTCATTCTGTG
66 TATTATGAACTCTTCATCAGAAATATCAGTCCACATCATTCTGTG
* * *
12748697 ATGGATCAAAGGTCGATCAAGCTCTCATATACAAACTTCATCTTTCTTGGTGGTCGAGTTCTTCA
1 ATGGATAAAAGGTCGAACAAGCTCTCATATACAAACTTCATCTTCCTTGGTGGTCGAGTTCTTCA
* *
12748762 TATTATGAACT-TTCCATCAGAAATATCAGTCCATATCCTTCTGTG
66 TATTATGAACTCTT-CATCAGAAATATCAGTCCACATCATTCTGTG
12748807 ATGGA
1 ATGGA
12748812 CGAGCCAAAG
Statistics
Matches: 99, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
109 2 0.02
110 97 0.98
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (110 bp):
ATGGATAAAAGGTCGAACAAGCTCTCATATACAAACTTCATCTTCCTTGGTGGTCGAGTTCTTCA
TATTATGAACTCTTCATCAGAAATATCAGTCCACATCATTCTGTG
Found at i:12757595 original size:20 final size:20
Alignment explanation
Indices: 12757572--12757611 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
12757562 ATTATTACAG
12757572 ATACAATTAAGATATTAGTC
1 ATACAATTAAGATATTAGTC
*
12757592 ATACTATTAAGATATTAGTC
1 ATACAATTAAGATATTAGTC
12757612 TTCTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (20 bp):
ATACAATTAAGATATTAGTC
Found at i:12770125 original size:29 final size:29
Alignment explanation
Indices: 12770091--12770150 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
12770081 CCTAAATTAA
*
12770091 TTTGATGTCATTGTTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
12770120 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
12770149 TT
1 TT
12770151 GGTGAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.23, C:0.12, G:0.13, T:0.52
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:12774812 original size:29 final size:29
Alignment explanation
Indices: 12774778--12774837 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
12774768 CCTAAATTAA
*
12774778 TTTGATGTCATTTCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
12774807 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
12774836 TT
1 TT
12774838 GGTGAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.23, C:0.13, G:0.12, T:0.52
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:12777127 original size:55 final size:53
Alignment explanation
Indices: 12777051--12777239 Score: 220
Period size: 55 Copynumber: 3.5 Consensus size: 53
12777041 TTCCATGGCT
* * * * * * *
12777051 TTGCACACGTAGTTCCGATACGATAGTTCACAAAATCATTATGAATTATGTAGGG
1 TTGCACACATAGTGCCAATACGA-AATTCATAAACTCATTATGAATT-TGTGGGG
* *
12777106 TTGCACACGA-AGTACCAATACGGAAATTTATAAACTCATTATGAATTTCGTGGGG
1 TTGCACAC-ATAGTGCCAATAC-GAAATTCATAAACTCATTATGAATTT-GTGGGG
12777161 TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTTGTGGGG
1 TTGCACACATAGTGCCAATACG-AAATTCATAAACTCATTATGAA-TTTGTGGGG
12777216 TT-CACACATAGTGCCAATACGAAA
1 TTGCACACATAGTGCCAATACGAAA
12777240 ATTGCAACAT
Statistics
Matches: 118, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
53 3 0.03
54 22 0.19
55 88 0.75
56 5 0.04
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (53 bp):
TTGCACACATAGTGCCAATACGAAATTCATAAACTCATTATGAATTTGTGGGG
Found at i:12782706 original size:35 final size:36
Alignment explanation
Indices: 12782650--12782721 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 36
12782640 GACTATGAAA
12782650 ATGTGAAATGTGAATATGTGAATACAAAGATA-TTCG
1 ATGTGAAATGTGAATATGTGAATA-AAAGATACTTCG
** *
12782686 ATGTGAAA-GTGCCTATGTGAATAAAATATACTTCG
1 ATGTGAAATGTGAATATGTGAATAAAAGATACTTCG
12782721 A
1 A
12782722 ATAATGAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 6 0.19
35 18 0.56
36 8 0.25
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (36 bp):
ATGTGAAATGTGAATATGTGAATAAAAGATACTTCG
Found at i:12782852 original size:23 final size:21
Alignment explanation
Indices: 12782812--12782907 Score: 59
Period size: 23 Copynumber: 4.3 Consensus size: 21
12782802 GTCGAGGGTT
* *
12782812 TTATGTGATCCTTCGGGATAAAA
1 TTATGTGGT-CTTTGGGA-AAAA
12782835 TTATGTGGTCTTTTGGGACAAAA
1 TTATGTGGTC-TTTGGGA-AAAA
* * *
12782858 CCTATGTGGTGCTTTGGGACAAT
1 -TTATGTGGT-CTTTGGGAAAAA
* *
12782881 TTATGTGGTCATTCGGG-ACAA
1 TTATGTGGTC-TTTGGGAAAAA
12782902 TTATGT
1 TTATGT
12782908 CGCACTTTGG
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
21 8 0.14
22 14 0.24
23 20 0.34
24 15 0.26
25 1 0.02
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (21 bp):
TTATGTGGTCTTTGGGAAAAA
Found at i:12782888 original size:22 final size:21
Alignment explanation
Indices: 12782860--12782907 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
12782850 GGACAAAACC
*
12782860 TATGTGGTGC-TTTGGGACAATT
1 TATGTGGT-CATTCGGGACAA-T
12782882 TATGTGGTCATTCGGGACAAT
1 TATGTGGTCATTCGGGACAAT
12782903 TATGT
1 TATGT
12782908 CGCACTTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.21, C:0.10, G:0.29, T:0.40
Consensus pattern (21 bp):
TATGTGGTCATTCGGGACAAT
Found at i:12789782 original size:21 final size:22
Alignment explanation
Indices: 12789726--12789776 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
12789716 TTAAGGGTTC
*
12789726 TATGTGGTCTTTCGGGACAAAAT
1 TATGTGGTCCTTCGGGAC-AAAT
12789749 TATGTGGTCCTTCGGGAC-AAT
1 TATGTGGTCCTTCGGGACAAAT
12789770 TATGTGG
1 TATGTGG
12789777 CACTTCAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 10 0.37
23 17 0.63
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.35
Consensus pattern (22 bp):
TATGTGGTCCTTCGGGACAAAT
Found at i:12793236 original size:13 final size:14
Alignment explanation
Indices: 12793218--12793250 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
12793208 TTAAATTAAT
12793218 TTTTTATTT-TTTA
1 TTTTTATTTATTTA
12793231 TTTTTATTTATTTA
1 TTTTTATTTATTTA
*
12793245 CTTTTA
1 TTTTTA
12793251 AAATTGGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTATTTATTTA
Found at i:12794661 original size:10 final size:10
Alignment explanation
Indices: 12794643--12794692 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
12794633 ATTATGTTTG
*
12794643 AAGAGGAAAA
1 AAGAAGAAAA
12794653 AAGAAGAAAA
1 AAGAAGAAAA
*
12794663 AATAA-AAAA
1 AAGAAGAAAA
*
12794672 AA-TAGAAAA
1 AAGAAGAAAA
12794681 AAGAAAGAAAA
1 AAG-AAGAAAA
12794692 A
1 A
12794693 TTAGGGTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
8 1 0.03
9 12 0.36
10 13 0.39
11 7 0.21
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (10 bp):
AAGAAGAAAA
Found at i:12794691 original size:18 final size:18
Alignment explanation
Indices: 12794648--12794693 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
12794638 GTTTGAAGAG
*
12794648 GAAAAAAGA-AGAAAAAA
1 GAAAAAAAATAGAAAAAA
*
12794665 TAAAAAAAATAGAAAAAA
1 GAAAAAAAATAGAAAAAA
12794683 GAAAGAAAAAT
1 GAAA-AAAAAT
12794694 TAGGGTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 7 0.29
18 11 0.46
19 6 0.25
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (18 bp):
GAAAAAAAATAGAAAAAA
Found at i:12795561 original size:12 final size:13
Alignment explanation
Indices: 12795544--12795572 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12795534 CTTTACAATA
12795544 TAAATT-AAGAAT
1 TAAATTAAAGAAT
12795556 TAAATTAAAGAAT
1 TAAATTAAAGAAT
12795569 TAAA
1 TAAA
12795573 AAAGATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (13 bp):
TAAATTAAAGAAT
Found at i:12795571 original size:20 final size:21
Alignment explanation
Indices: 12795546--12795601 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
12795536 TTACAATATA
12795546 AATTAAGAATTAAATT-AAAG
1 AATTAAGAATTAAATTAAAAG
*
12795566 AATTAA-AA--AAGATTAAAAAT
1 AATTAAGAATTAA-ATT-AAAAG
12795586 AATTAAGAATTAAATT
1 AATTAAGAATTAAATT
12795602 CTAAAATGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
17 2 0.07
18 3 0.10
19 2 0.07
20 15 0.52
21 2 0.07
22 3 0.10
23 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
AATTAAGAATTAAATTAAAAG
Found at i:12797385 original size:126 final size:127
Alignment explanation
Indices: 12797159--12797388 Score: 331
Period size: 126 Copynumber: 1.8 Consensus size: 127
12797149 CCTGCTTCTC
* * * *
12797159 TAGCACAATAGTAGTTGGATCAGCGTAATCTTTTTATTCGTCCATCATAAAATGATGTGGATCAA
1 TAGCACAACAGTAGTTGGATCAGCGTAATCTTTTTATTCCTCCATCACAAAATGATGTGGACCAA
*
12797224 CAAGGTGGTTTCACTCGTCCATCAAAGAAAGGGTTGGATCAACGTAGTATTATCTGATCATT
66 CAAGCTGGTTTCACTCGTCCATCAAAGAAAGGGTTGGATCAACGTAGTATTATCTGATCATT
* *
12797286 TAGCACAACAGTAGTTGGATCAGCGTAATCTTTTT-TTCCTCCATCACAAAA-GTATTTGGGCCA
1 TAGCACAACAGTAGTTGGATCAGCGTAATCTTTTTATTCCTCCATCACAAAATG-ATGTGGACCA
* * *
12797349 ACATA-CTGGTTTTACTCGTCCATCGAAGAATGGGTTGGAT
65 ACA-AGCTGGTTTCACTCGTCCATCAAAGAAAGGGTTGGAT
12797389 TATCATAATC
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
125 1 0.01
126 55 0.60
127 35 0.38
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (127 bp):
TAGCACAACAGTAGTTGGATCAGCGTAATCTTTTTATTCCTCCATCACAAAATGATGTGGACCAA
CAAGCTGGTTTCACTCGTCCATCAAAGAAAGGGTTGGATCAACGTAGTATTATCTGATCATT
Found at i:12799304 original size:20 final size:20
Alignment explanation
Indices: 12799279--12799317 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12799269 TGGTTAGGAC
*
12799279 TGTTAGTAGTTTGTAACTGA
1 TGTTAGTAGGTTGTAACTGA
12799299 TGTTAGTAGGTTGTAACTG
1 TGTTAGTAGGTTGTAACTG
12799318 CATGCATGTA
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:0.23, C:0.05, G:0.28, T:0.44
Consensus pattern (20 bp):
TGTTAGTAGGTTGTAACTGA
Found at i:12803292 original size:20 final size:20
Alignment explanation
Indices: 12803269--12803307 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12803259 TGGTTAGGAC
**
12803269 TGTTAGTAGTTTGTAACTGA
1 TGTTAGTAGGCTGTAACTGA
12803289 TGTTAGTAGGCTGTAACTG
1 TGTTAGTAGGCTGTAACTG
12803308 CATGCATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.28, T:0.41
Consensus pattern (20 bp):
TGTTAGTAGGCTGTAACTGA
Found at i:12805475 original size:26 final size:26
Alignment explanation
Indices: 12805427--12805476 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
12805417 TATATATATA
**
12805427 TATATATTATTTTATAATTTTTAATT
1 TATATATTATTTTATAAACTTTAATT
12805453 TATATATCT-TTTTATAAACTTTAA
1 TATATAT-TATTTTATAAACTTTAA
12805477 ATTCATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (26 bp):
TATATATTATTTTATAAACTTTAATT
Found at i:12809750 original size:136 final size:135
Alignment explanation
Indices: 12809569--12810084 Score: 701
Period size: 136 Copynumber: 3.8 Consensus size: 135
12809559 TTACTAATTC
* * *
12809569 GAAATGCTATGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATAAACTTTTTCTCCCTCTG
1 GAAATGTTATGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTG
* * * * *
12809634 TCGGATGAGTTCTTCTCATTAGGAACTCTCTATTGGAAATATCAATACCTCAAGTAAGGTGTTGT
66 TCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCAAGGT-TTGT
12809699 TGATTT
130 TGATTT
* * *
12809705 GAAATGTTGTGAATCGAGCAATAGATCGAACAAGTTCTTCTCATTATGATCTT-TCTCTCCCTCT
1 GAAATGTTATGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCT-TCTCCCTCT
*
12809769 GTCGGATGTGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCAAGGCATTT
65 GTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCAAGG--TTT
12809834 GTTGATTT
128 GTTGATTT
* * ** * * *
12809842 AAAATGTCATGAATTAAGCAGTATGTCGAACAAGTTCCTCTCATTATGAACTTCTTCTCCCTCTG
1 GAAATGTTATGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTG
* * * * *
12809907 TCGGATGAGTTTTTCTCATTATGAACTCTCTATTGGAAATGTCAATCCCTCAAGCGAGGCATTGC
66 TCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCAAGG-TTTGT
*
12809972 TGATTC
130 TGATTT
* * * *
12809978 GAAATGTTGTGAATCGAGTAATAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTCCCTCTG
1 GAAATGTTATGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTG
* *
12810043 TCGGATGAGTTATTCTCTTTATGAACTCTCCATTGGAAATGT
66 TCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGT
12810085 TGATCGGTTT
Statistics
Matches: 333, Mismatches: 43, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
135 1 0.00
136 212 0.64
137 118 0.35
138 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (135 bp):
GAAATGTTATGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTG
TCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCAAGGTTTGTT
GATTT
Found at i:12810080 original size:273 final size:273
Alignment explanation
Indices: 12809593--12810084 Score: 788
Period size: 273 Copynumber: 1.8 Consensus size: 273
12809583 CGAGCAATAG
* *
12809593 GTCGAACAAGTTCTTCTCATTATAAACTTTTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAGGA
1 GTCGAACAAGTTCCTCTCATTATAAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAGGA
* ** * *
12809658 ACTCTCTATTGGAAATATCAATACCTCAAGTAAGGTGTTGTTGATTTGAAATGTTGTGAATCGAG
66 ACTCTCTATTGGAAATATCAATACCTCAAGCAAGGCATTGCTGATTCGAAATGTTGTGAATCGAG
* * *
12809723 CAATAGATCGAACAAGTTCTTCTCATTATGATCTTTCTCTCCCTCTGTCGGATGTGTTCTTCTCA
131 CAATAGATCGAACAAGTTCTTCTCATTATGAACTTTCTCTCCCTCTGTCGGATGAGTTATTCTCA
12809788 TTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCAAGGCATTTGTTGATTTAAAATGTCATG
196 TTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCAAGGCATTTGTTGATTTAAAATGTCATG
12809853 AATTAAGCAGTAT
261 AATTAAGCAGTAT
* * *
12809866 GTCGAACAAGTTCCTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTTTTCTCATTATGA
1 GTCGAACAAGTTCCTCTCATTATAAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAGGA
* * *
12809931 ACTCTCTATTGGAAATGTCAATCCCTCAAGCGAGGCATTGCTGATTCGAAATGTTGTGAATCGAG
66 ACTCTCTATTGGAAATATCAATACCTCAAGCAAGGCATTGCTGATTCGAAATGTTGTGAATCGAG
* * *
12809996 TAATAGGTTGAACAAGTTCTTCTCATTATGAAC-TTCTCCTCCCTCTGTCGGATGAGTTATTCTC
131 CAATAGATCGAACAAGTTCTTCTCATTATGAACTTTCT-CTCCCTCTGTCGGATGAGTTATTCTC
*
12810060 TTTATGAACTCTCCATTGGAAATGT
195 ATTATGAACTCTCCATTGGAAATGT
12810085 TGATCGGTTT
Statistics
Matches: 198, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
272 4 0.02
273 194 0.98
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (273 bp):
GTCGAACAAGTTCCTCTCATTATAAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAGGA
ACTCTCTATTGGAAATATCAATACCTCAAGCAAGGCATTGCTGATTCGAAATGTTGTGAATCGAG
CAATAGATCGAACAAGTTCTTCTCATTATGAACTTTCTCTCCCTCTGTCGGATGAGTTATTCTCA
TTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCAAGGCATTTGTTGATTTAAAATGTCATG
AATTAAGCAGTAT
Found at i:12811113 original size:6 final size:6
Alignment explanation
Indices: 12811098--12811184 Score: 69
Period size: 6 Copynumber: 15.2 Consensus size: 6
12811088 TAACCTCTCA
* **
12811098 TTTT-T TTTTCT TTTTCT TTTTCT TTCTTTT CTTTTCT TTTTC- -TTTAA
1 TTTTCT TTTTCT TTTTCT TTTTCT TT-TTCT -TTTTCT TTTTCT TTTTCT
* *
12811145 TTTTCT TTTT-T ATTTCT TTTTC- -TTTAT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T
12811185 CTCTTTTCTT
Statistics
Matches: 65, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
4 6 0.09
5 8 0.12
6 43 0.66
7 6 0.09
8 2 0.03
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:12811123 original size:10 final size:10
Alignment explanation
Indices: 12811110--12811198 Score: 76
Period size: 10 Copynumber: 8.6 Consensus size: 10
12811100 TTTTTTTCTT
12811110 TTTCTTTTTC
1 TTTCTTTTTC
12811120 TTTC-TTTTC
1 TTTCTTTTTC
12811129 TTTTCTTTTTC
1 -TTTCTTTTTC
**
12811140 TTTAATTTTC
1 TTTCTTTTTC
*
12811150 TTTTTTATTTC
1 TTTCTT-TTTC
12811161 TTTTTCTTTATT-
1 --TTTCTTT-TTC
12811173 TTTCTTTTTC
1 TTTCTTTTTC
12811183 -TTCTCTTTTC
1 TTTCT-TTTTC
12811193 TTTCTT
1 TTTCTT
12811199 AGGCGTAATA
Statistics
Matches: 65, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
9 11 0.17
10 33 0.51
11 13 0.20
12 1 0.02
13 7 0.11
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:12811123 original size:16 final size:16
Alignment explanation
Indices: 12811098--12811195 Score: 96
Period size: 16 Copynumber: 6.2 Consensus size: 16
12811088 TAACCTCTCA
*
12811098 TTTTTTTTTCTTTTTC
1 TTTTTCTTTCTTTTTC
12811114 TTTTTCTTTC-TTTTC
1 TTTTTCTTTCTTTTTC
*
12811129 -TTTTCTTT-TTCTTTA
1 TTTTTCTTTCTT-TTTC
* *
12811144 ATTTTCTTTTTTATTTC
1 TTTTTCTTTCTT-TTTC
*
12811161 TTTTTCTTTATTTTTC
1 TTTTTCTTTCTTTTTC
12811177 TTTTTC-TTCTCTTTTC
1 TTTTTCTTTCT-TTTTC
12811193 TTT
1 TTT
12811196 CTTAGGCGTA
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
14 9 0.13
15 11 0.16
16 35 0.50
17 15 0.21
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTCTTTTTC
Done.