Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008044.1 Hibiscus syriacus cultivar Beakdansim tig00110532_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: 979496
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:940171 original size:179 final size:177
Alignment explanation
Indices: 939866--940235 Score: 501
Period size: 179 Copynumber: 2.1 Consensus size: 177
939856 ATTTGTACAT
* *** * *
939866 GTATCGATACTTTTAGTCCAGTATGCTTCTCAACAATTTGCATGGACAAAGTTTCGATACATGTA
1 GTATCGATACTTTTAGTCCAGTATGCTTCTCAACAATTTACACCCACAAAGTATCGATACACGTA
** *
939931 TAACAAGTATCAATACTTATAATTTTGAAACGATTACTTTAAAGTTATAGGTAAATTTACAATGT
66 TAACAAGTATCAATACTTATAATTTCAAAACGATTACTTTAAAGTAATAGGTAAATTTACAATGT
* * * ** *
939996 CAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAATGTATA
131 AAACGGTAAAAATCTACCGATTTAATGATAATAGGCGTAAACATAAA
* *
940043 GTATCGCTACTTTTAGTCCAGTATGCTT-TGCAAACAATTTACACCCAGAAAGTATCGATACACG
1 GTATCGATACTTTTAGTCCAGTATGCTTCT-C-AACAATTTACACCCACAAAGTATCGATACACG
* * * *
940107 TATCATAAGTATCGATACTGT-TAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTTACA
64 TATAACAAGTATCAATACT-TATAATTTCAAAA-CGATTACTTTAAAGTAATAGGTAAATTTACA
940171 ATGTAAACGGTAAAAATCTACCGATTTAATGATAATAGGCGTAAACATAAA
127 ATGTAAACGGTAAAAATCTACCGATTTAATGATAATAGGCGTAAACATAAA
940222 GTATCGATACTTTT
1 GTATCGATACTTTT
940236 TGTATAGATA
Statistics
Matches: 167, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
176 1 0.01
177 28 0.17
178 50 0.30
179 88 0.53
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (177 bp):
GTATCGATACTTTTAGTCCAGTATGCTTCTCAACAATTTACACCCACAAAGTATCGATACACGTA
TAACAAGTATCAATACTTATAATTTCAAAACGATTACTTTAAAGTAATAGGTAAATTTACAATGT
AAACGGTAAAAATCTACCGATTTAATGATAATAGGCGTAAACATAAA
Found at i:940792 original size:18 final size:18
Alignment explanation
Indices: 940771--940808 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
940761 GGTTCTTGTG
940771 AACCAAAAC-CTTCTTCTC
1 AACC-AAACTCTTCTTCTC
*
940789 AACCAAGCTCTTCTTCTC
1 AACCAAACTCTTCTTCTC
940807 AA
1 AA
940809 GTAAGGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.32, C:0.37, G:0.03, T:0.29
Consensus pattern (18 bp):
AACCAAACTCTTCTTCTC
Found at i:942867 original size:2 final size:2
Alignment explanation
Indices: 942860--942886 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
942850 TAATTTCAAT
942860 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
942887 GTCCTCAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:945121 original size:198 final size:197
Alignment explanation
Indices: 944781--946297 Score: 1587
Period size: 198 Copynumber: 7.6 Consensus size: 197
944771 TGCGTGCAAA
* * * * **
944781 AAAGTATCGATA-CATGTACAACAAGTATCAATATTTATAATTTTGAAACAAATTACTTTAAAGT
1 AAAGTATCGATACCATGTA-TA-AAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGT
** * * * *
944845 TATAGGTACTTTAACAATGTCAACGGCAAAAGTTTACCGG-TTAATGATAATAGGTGTAAACATA
64 TATAGGTAAATTAA-AATATCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACATA
* * * * *
944909 GAA-TATCAATACTTTTTGTATATGTATTGATACTTTTAGTCCAATATGCTTATCTACAATTTGC
128 -AAGTATCTATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGC
944973 ACGCAC
192 ACGCAC
* ** * *
944979 AAAGTATTGATACTCATGTATAAAGTATCGATACACATAATTTCAAAACCGATTACTTTAAAGTT
1 AAAGTATCGATAC-CATGTATAAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTT
** *
945044 ATAACTAAATTAAAATATCAACGGTAAAAGTCTACGGGTTTAATGATAATAGGCGTAAACATAAA
65 ATAGGTAAATTAAAATATCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACATAAA
* * * * *
945109 GTATCTATACTTTTTGTATAGGTATCAATACTTTTCGTTCAATATGCTTTTCAACAATTTGCACA
130 GTATCTATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCACG
945174 CAC
195 CAC
* *
945177 AAAGTATCGATA-CATGTATAACAAGTATCAATACTTATAATTTCGAAACCAATTAC--T----T
1 AAAGTATCGATACCATGTAT-A-AAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGT
* *
945235 TATAGGTAAATTCACAATGTCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACATA
64 TATAGGTAAATT-AAAATATCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACATA
* * * *
945300 TAA-TATCGATAGTTTTTGTATAGGTATTGATACTTTTAGTCCAGTATGCTTCTCAACAATTTGC
128 -AAGTATCTATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGC
* *
945364 ATG-AA
192 ACGCAC
* * *
945369 AAATGTATCGATACACGTGTATAAAGTATAGATACTTATAATTT-GAAACCTATTACTCTAAAGT
1 AAA-GTATCGATAC-CATGTATAAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGT
* * *
945433 TATAGGTAAATTAAAATATCAGCGGTAAAAGTCTACCGGTTTAATGATAATATGCGTAAACAAAA
64 TATAGGTAAATTAAAATATCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACATAA
* * * * * *
945498 ATTATATATACTTTTTGTATATGTATC-ACTACTTTTCGTCCAGTGTGCTTCTCAACAATTTGCA
129 AGTATCTATACTTTTTGTATAGGTATCGA-TACTTTTAGTCCAATATGCTTCTCAACAATTTGCA
*
945562 TGCAC
193 CGCAC
* * *
945567 AAAGTATCGATA-CATGTATAACAAGTATTGATACTTATAATTTCAAAACCAATTACTTTAAAGT
1 AAAGTATCGATACCATGTAT-A-AAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGT
* * * ** *
945631 TATAGGTAAATTCACAATGTCAACGGTAAAAGTGTACATGTTTAATGATAATAAGCGTAAACATA
64 TATAGGTAAATT-AAAATATCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACATA
* ** * * *
945696 TAGTAT-TGATACTTTTTGTATATATATCGGTACTTTTAGTCCATTATGCTTCTCAACAATTTAC
128 AAGTATCT-ATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGC
945760 ACGCA-
192 ACGCAC
* *
945765 AAATGTATCGATACACATGTATAAAGTATATG-TACTTATAATTTCGAAACTTATTACTTTAAAG
1 AAA-GTATCGATAC-CATGTATAAAGTAT-CGATACTTATAATTTCGAAACCTATTACTTTAAAG
** * * *
945829 TTATATTTACATGAAAATATCAACGGTAGAAA-TCTACCGGTTTAATGATAATAGGCATAAACAT
63 TTATAGGTAAATTAAAATATCAACGGTA-AAAGTCTACCGGTTTAATGATAATAGGCGTAAACAT
* * * *
945893 AAAGTATCGATACGTATCTATACCTTTTGTATAGGTATCGATATTTTTCGTCTAATATGCTTTTC
127 AAAGTATC--TA--TA-C--T---TTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTTCTC
945958 AACAATTTGCACGCAC
182 AACAATTTGCACGCAC
*
945974 AAAGTATCGATA-CATGTATAACAAGTATCGATAC-TATAAATTT-GAAA-TTGATTACTTTAAA
1 AAAGTATCGATACCATGTAT-A-AAGTATCGATACTTAT-AATTTCGAAACCT-ATTACTTTAAA
* * *
946035 GTTATAGGTAAATTCACAATATCAACGATAAAAGTCTACCGGTTTATTGATAATAGGCGTAAACA
62 GTTATAGGTAAATT-AAAATATCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACA
* * * *
946100 TATAGTAT-TGATACTTTTTGCATAGGTATCGATACTTTTAGTCCAATATGATTCTCTACAATTT
126 TAAAGTATCT-ATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTT
*
946164 GCAAGCA-
190 GCACGCAC
* * * * *
946171 AAATGTATCGATACACA--TATAAAGTATCAACACTTATAATTTTGAAACCTATTACTGTAAGGT
1 AAA-GTATCGATAC-CATGTATAAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGT
* * * * * *
946234 AATAGGTTAATTTACAATGA-AAACGGTAAAAGCCTACCGGTATAATGATAATAGGCGTAAACAT
64 TATAGG-TAAATTAAAAT-ATCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACAT
946298 CAATTATTGA
Statistics
Matches: 1117, Mismatches: 143, Indels: 119
0.81 0.10 0.09
Matches are distributed among these distances:
192 26 0.02
193 131 0.12
194 4 0.00
195 12 0.01
196 27 0.02
197 226 0.20
198 339 0.30
199 158 0.14
200 12 0.01
201 9 0.01
202 2 0.00
203 2 0.00
204 2 0.00
205 2 0.00
206 10 0.01
207 33 0.03
208 119 0.11
209 3 0.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (197 bp):
AAAGTATCGATACCATGTATAAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTTA
TAGGTAAATTAAAATATCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACATAAAG
TATCTATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCACGC
AC
Found at i:945510 original size:390 final size:393
Alignment explanation
Indices: 944781--946296 Score: 1818
Period size: 390 Copynumber: 3.8 Consensus size: 393
944771 TGCGTGCAAA
* * * *
944781 AAAGTATCGATACATGTACAACAAGTATCAATATTTATAATTTTGAAACAAATTACTTTAAAGTT
1 AAAGTATCGATACATGTATAACAAGTATCAATACTTATAATTTCGAAACCAATTAC-TT--A-TT
** * * * * *
944846 ATAGGTACTTTAACAATGTCAACGGCAAAAGTTTACCGG-TTAATGATAATAGGTGTAAACATAG
62 ATAGGTAAATTCACAATGTCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACATAT
* * * * *
944910 AATATCAATACTTTTTGTATATGTATTGATACTTTTAGTCCAATATGCTTATCTACAATTTGCAC
127 AATATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCAC
* * * * ** * *
944975 GCACAAA-GTATTGATACTCATGTATAAAGTATCGATACACATAATTTCAAAACCGATTACTTTA
192 G-AAAAATGTATCGATACACATGTATAAAGTATAGATACTTATAATTTCGAAACCTATTACTTTA
** *
945039 AAGTTATAACTAAATTAAAATATCAACGGTAAAAGTCTACGGGTTTAATGATAATAGGCGTAAAC
256 AAGTTATAGGTAAATTAAAATATCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAAC
* * *
945104 ATAAAGTATCTATACTTTTTGTATAGGTATCAATACTTTTCGTTCAATATGCTTTTCAACAATTT
321 AAAAATTATATATACTTTTTGTATAGGTATCAATACTTTTCGTTCAATATGCTTTTCAACAATTT
*
945169 GCACACAC
386 GCACGCAC
945177 AAAGTATCGATACATGTATAACAAGTATCAATACTTATAATTTCGAAACCAATTAC-T-TTATAG
1 AAAGTATCGATACATGTATAACAAGTATCAATACTTATAATTTCGAAACCAATTACTTATTATAG
945240 GTAAATTCACAATGTCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACATATAATA
66 GTAAATTCACAATGTCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACATATAATA
* * * *
945305 TCGATAGTTTTTGTATAGGTATTGATACTTTTAGTCCAGTATGCTTCTCAACAATTTGCATGAAA
131 TCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCACGAAA
* *
945370 AATGTATCGATACACGTGTATAAAGTATAGATACTTATAATTT-GAAACCTATTACTCTAAAGTT
196 AATGTATCGATACACATGTATAAAGTATAGATACTTATAATTTCGAAACCTATTACTTTAAAGTT
* *
945434 ATAGGTAAATTAAAATATCAGCGGTAAAAGTCTACCGGTTTAATGATAATATGCGTAAACAAAAA
261 ATAGGTAAATTAAAATATCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACAAAAA
* * * * * * *
945499 TTATATATACTTTTTGTATATGTATCACTACTTTTCGTCCAGTGTGCTTCTCAACAATTTGCATG
326 TTATATATACTTTTTGTATAGGTATCAATACTTTTCGTTCAATATGCTTTTCAACAATTTGCACG
945564 CAC
391 CAC
** *
945567 AAAGTATCGATACATGTATAACAAGTATTGATACTTATAATTTCAAAACCAATTACTTTAAAGTT
1 AAAGTATCGATACATGTATAACAAGTATCAATACTTATAATTTCGAAACCAATTAC-TT--A-TT
* ** *
945632 ATAGGTAAATTCACAATGTCAACGGTAAAAGTGTACATGTTTAATGATAATAAGCGTAAACATAT
62 ATAGGTAAATTCACAATGTCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACATAT
* * ** * * *
945697 AGTATTGATACTTTTTGTATATATATCGGTACTTTTAGTCCATTATGCTTCTCAACAATTTACAC
127 AATATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCAC
* *
945762 GCAAAATGTATCGATACACATGTATAAAGTATATG-TACTTATAATTTCGAAACTTATTACTTTA
192 GAAAAATGTATCGATACACATGTATAAAGTATA-GATACTTATAATTTCGAAACCTATTACTTTA
** * * *
945826 AAGTTATATTTACATGAAAATATCAACGGTAGAAA-TCTACCGGTTTAATGATAATAGGCATAAA
256 AAGTTATAGGTAAATTAAAATATCAACGGTA-AAAGTCTACCGGTTTAATGATAATAGGCGTAAA
* * *
945890 CATAAAGTATCGATACGTATCTATACCTTTTGTATAGGTATCGATATTTTTCG-TCTAATATGCT
320 CA-AAA--AT---TA--TA--TATACTTTTTGTATAGGTATCAATACTTTTCGTTC-AATATGCT
945954 TTTCAACAATTTGCACGCAC
374 TTTCAACAATTTGCACGCAC
* ***
945974 AAAGTATCGATACATGTATAACAAGTATCGATAC-TATAAATTT-GAAATTGATTACTTTAAAGT
1 AAAGTATCGATACATGTATAACAAGTATCAATACTTAT-AATTTCGAAACCAATTAC-TT--A-T
* * *
946037 TATAGGTAAATTCACAATATCAACGATAAAAGTCTACCGGTTTATTGATAATAGGCGTAAACATA
61 TATAGGTAAATTCACAATGTCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACATA
* * * * *
946102 TAGTATTGATACTTTTTGCATAGGTATCGATACTTTTAGTCCAATATGATTCTCTACAATTTGCA
126 TAATATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCA
* * * * *
946167 AGCAAAATGTATCGATACACA--TATAAAGTATCA-ACACTTATAATTTTGAAACCTATTACTGT
191 CGAAAAATGTATCGATACACATGTATAAAGTAT-AGATACTTATAATTTCGAAACCTATTACTTT
* * * * * * *
946229 AAGGTAATAGGTTAATTTACAATGA-AAACGGTAAAAGCCTACCGGTATAATGATAATAGGCGTA
255 AAAGTTATAGG-TAAATTAAAAT-ATCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTA
946293 AACA
318 AACA
946297 TCAATTATTG
Statistics
Matches: 973, Mismatches: 119, Indels: 47
0.85 0.10 0.04
Matches are distributed among these distances:
390 228 0.23
391 116 0.12
392 1 0.00
394 1 0.00
396 213 0.22
397 70 0.07
398 6 0.01
400 2 0.00
403 2 0.00
404 44 0.05
405 45 0.05
406 156 0.16
407 89 0.09
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (393 bp):
AAAGTATCGATACATGTATAACAAGTATCAATACTTATAATTTCGAAACCAATTACTTATTATAG
GTAAATTCACAATGTCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACATATAATA
TCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCACGAAA
AATGTATCGATACACATGTATAAAGTATAGATACTTATAATTTCGAAACCTATTACTTTAAAGTT
ATAGGTAAATTAAAATATCAACGGTAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACAAAAA
TTATATATACTTTTTGTATAGGTATCAATACTTTTCGTTCAATATGCTTTTCAACAATTTGCACG
CAC
Found at i:946711 original size:118 final size:118
Alignment explanation
Indices: 946548--946939 Score: 393
Period size: 118 Copynumber: 3.4 Consensus size: 118
946538 TAACAAACCA
*
946548 AATAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAACAGACGCTACC
1 AATAATTAACCTATTTTGTTATCGTCGAATTTCTAAGGCCCCATCAGCTTTAAACAGACGCTACC
* * *
946613 TATTACATTAAATAAACGCTACTTGTTATGTTATTATGGTTGATAATCTGTCC
66 TATTACATTAAATAAGCGTTACTTGTTATGTTATTATGGTTGATAATCTATCC
** * ***
946666 AATAATTAACCTATTTTGTTATCGTCGAATTTCTAAGGCTTCATCAGC-TT--A-A-AC-TTTGG
1 AATAATTAACCTATTTTGTTATCGTCGAATTTCTAAGGCCCCATCAGCTTTAAACAGACGCTACC
* * * ** * * * *
946725 TA--ACATT--TTAGGCGTTACCTAATATATTGATAAT-ATTGATAA-CAAAT-C
66 TATTACATTAAATAAGCGTTACTTGTTATGTT-ATTATGGTTGATAATC-TATCC
* * *
946773 AAGTAAATAACCTATTTTGTTATCGTCGGATTTC--AGGCCCCATCAGCTTTAAACATG-TGCTA
1 AA-TAATTAACCTATTTTGTTATCGTCGAATTTCTAAGGCCCCATCAGCTTTAAACA-GACGCTA
* * *
946835 CCTATTACATTAAATAAGCATTACTTGTTATGTTATTATGGTTGATAATGTTTCC
64 CCTATTACATTAAATAAGCGTTACTTGTTATGTTATTATGGTTGATAATCTATCC
* *
946890 AATAATTAACCTATTTTGTTATCGTCAAATTTCTAAGGCTCCATCAGCTT
1 AATAATTAACCTATTTTGTTATCGTCGAATTTCTAAGGCCCCATCAGCTT
946940 AAAATTTGGT
Statistics
Matches: 211, Mismatches: 44, Indels: 38
0.72 0.15 0.13
Matches are distributed among these distances:
106 11 0.05
107 6 0.03
108 50 0.24
109 5 0.02
110 6 0.03
112 6 0.03
113 2 0.01
114 6 0.03
115 5 0.02
116 50 0.24
117 5 0.02
118 59 0.28
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39
Consensus pattern (118 bp):
AATAATTAACCTATTTTGTTATCGTCGAATTTCTAAGGCCCCATCAGCTTTAAACAGACGCTACC
TATTACATTAAATAAGCGTTACTTGTTATGTTATTATGGTTGATAATCTATCC
Found at i:946923 original size:224 final size:225
Alignment explanation
Indices: 946518--947079 Score: 876
Period size: 224 Copynumber: 2.5 Consensus size: 225
946508 ATGTACACGG
* *
946518 TAATATGTTGATAATATTGATAACAAACCAAATAATTAACCTATTTTGTTATCGTCGGATTTCTA
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTC-A
* *
946583 AGGCCCCATCAGCTTTAAACA-GACGCTACCTATTACATTAAATAAACGCTACTTGTTATGTTAT
65 AGGCCCCATCAGCTTTAAACATG-CGCTACCTATTACATTAAATAAGCACTACTTGTTATGTTAT
* *
946647 TATGGTTGATAATCTGTCCAATAATTAACCTATTTTGTTATCGTCGAATTTCTAAGGCTTCATCA
129 TATGGTTGATAATCTGTCCAATAATTAACCTATTTTGTTATCGTCAAATTTCTAAGGCTCCATCA
* ** *
946712 GCTTAAACTTTGGTAACATTTTAGGCGTTACC
194 GCTTAAAATTTGGTAACATTTTAGGCACTACA
* *
946744 TAATATATTGATAATATTGATAACAAATCAAGTAAATAACCTATTTTGTTATCGTCGGATTTC-A
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCAA
* *
946808 GGCCCCATCAGCTTTAAACATGTGCTACCTATTACATTAAATAAGCATTACTTGTTATGTTATTA
66 GGCCCCATCAGCTTTAAACATGCGCTACCTATTACATTAAATAAGCACTACTTGTTATGTTATTA
* *
946873 TGGTTGATAATGTTTCCAATAATTAACCTATTTTGTTATCGTCAAATTTCTAAGGCTCCATCAGC
131 TGGTTGATAATCTGTCCAATAATTAACCTATTTTGTTATCGTCAAATTTCTAAGGCTCCATCAGC
946938 TTAAAATTTGGTAACATTTTAGGCACTACA
196 TTAAAATTTGGTAACATTTTAGGCACTACA
* * *
946968 TAATATGCTGATAATATTGATAACAAATCAAGTACTTAACCTATTTTGTTATCGTCGAATTTCTA
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTC-A
* * * *
947033 AGGCCCCATCAGCTTTAAAAATACGCTACCTATTACGTTACATAAGC
65 AGGCCCCATCAGCTTTAAACATGCGCTACCTATTACATTAAATAAGC
947080 GGTACCTATT
Statistics
Matches: 307, Mismatches: 26, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
224 205 0.67
225 1 0.00
226 101 0.33
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (225 bp):
TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCAA
GGCCCCATCAGCTTTAAACATGCGCTACCTATTACATTAAATAAGCACTACTTGTTATGTTATTA
TGGTTGATAATCTGTCCAATAATTAACCTATTTTGTTATCGTCAAATTTCTAAGGCTCCATCAGC
TTAAAATTTGGTAACATTTTAGGCACTACA
Found at i:947089 original size:23 final size:23
Alignment explanation
Indices: 947056--947109 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
947046 TTTAAAAATA
947056 CGCTACCTATTACGTTACATAAG
1 CGCTACCTATTACGTTACATAAG
*
947079 CGGTACCTATTACGTTACATAAG
1 CGCTACCTATTACGTTACATAAG
947102 CGCTACCT
1 CGCTACCT
947110 GTTTGTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (23 bp):
CGCTACCTATTACGTTACATAAG
Found at i:950540 original size:54 final size:54
Alignment explanation
Indices: 950476--950646 Score: 229
Period size: 54 Copynumber: 3.2 Consensus size: 54
950466 ACCAAATGGC
** *
950476 ACTATGTGTGCAACTCAC-GAAATTCATCATATGTTGATGAACAACTGTTTCGGT
1 ACTATGTGTGCAACTCACAG-AATTCATCATATGTTGATGAACAACCATTTCGGA
*
950530 TCTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTCGGA
1 ACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTCGGA
* * * * *
950584 ACTATGTGTACAACTCACAGAATTCATCATAAGTTGATGAAGAATCGTTTC-GA
1 ACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTCGGA
950637 CACTATGTGT
1 -ACTATGTGT
950647 CTGTTGAGTT
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
53 2 0.02
54 102 0.97
55 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (54 bp):
ACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTCGGA
Found at i:963634 original size:23 final size:23
Alignment explanation
Indices: 963607--963659 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
963597 TCCCAAAGAA
**
963607 CCACATAGGTTTGCGTAGAAGTG
1 CCACATAGGTTTGCACAGAAGTG
*
963630 CCACATAGGTTTGCACCGAAGTG
1 CCACATAGGTTTGCACAGAAGTG
963653 CCACATA
1 CCACATA
963660 TTTTTCCCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (23 bp):
CCACATAGGTTTGCACAGAAGTG
Found at i:965288 original size:26 final size:26
Alignment explanation
Indices: 965252--965332 Score: 162
Period size: 26 Copynumber: 3.1 Consensus size: 26
965242 AGAAGAACAT
965252 GATGCTTATCTTCGAGTGGTTCTTCA
1 GATGCTTATCTTCGAGTGGTTCTTCA
965278 GATGCTTATCTTCGAGTGGTTCTTCA
1 GATGCTTATCTTCGAGTGGTTCTTCA
965304 GATGCTTATCTTCGAGTGGTTCTTCA
1 GATGCTTATCTTCGAGTGGTTCTTCA
965330 GAT
1 GAT
965333 ACTTTGTGAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (26 bp):
GATGCTTATCTTCGAGTGGTTCTTCA
Found at i:967120 original size:18 final size:18
Alignment explanation
Indices: 967097--967143 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
967087 GCTGATTGAA
*
967097 GAAGAATGTATCACCCTG
1 GAAGAAGGTATCACCCTG
*
967115 GAAGAAGGTATCGCCCTG
1 GAAGAAGGTATCACCCTG
967133 GAAGAAGGTAT
1 GAAGAAGGTAT
967144 TAGGTTTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (18 bp):
GAAGAAGGTATCACCCTG
Found at i:968218 original size:54 final size:54
Alignment explanation
Indices: 967982--968218 Score: 214
Period size: 54 Copynumber: 4.4 Consensus size: 54
967972 ACCAAATGGT
* **
967982 ACTATGTGTACAACTCAC-AGAATTCATCATATGTTGATGAACAACTGTTTC-AGC
1 ACTATGTGTGCAACTCACGA-AATTCATCATATGTTGATGAACAACCATTTCGA-C
* * * * * * * *
968036 ACTATGCGTGTAACTCACGGAGTTCATCATATGTTGATGAAGAACCGTTTTGGC
1 ACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCATTTCGAC
* ** * * * *
968090 ACTTTGTGTGCTTCTAAGGAAATTCATGATATG-T--TGAACAACCATTTCAAC
1 ACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCATTTCGAC
* * *
968141 ACTATGTGTGCAACTTAGGAAATTCATCATATGTTGATGAACAATCATTTCGAC
1 ACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCATTTCGAC
* *
968195 ACTATGTGTGCAACCCACAAAATT
1 ACTATGTGTGCAACTCACGAAATT
968219 TATAATATAT
Statistics
Matches: 143, Mismatches: 35, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
51 40 0.28
52 1 0.01
53 1 0.01
54 101 0.71
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (54 bp):
ACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCATTTCGAC
Found at i:968218 original size:105 final size:107
Alignment explanation
Indices: 967982--968218 Score: 237
Period size: 105 Copynumber: 2.2 Consensus size: 107
967972 ACCAAATGGT
* * ** * *
967982 ACTATGTGTACAACTCACAGAATTCATCATATGTTGATGAACAACTGTTTCAGCACTATGCGTGT
1 ACTATGTGTGCAACTCACAAAATTCATCATATGTT-ATGAACAACCATTTCAACACTATGCGTGC
* * * * *
968047 AACTCACGGAGTTCATCATATGTTGATGAAGAACCGTTTTGGC
65 AACTCACGGAATTCATCATATGTTGATGAACAACCATTTCGAC
* ** * ** * *
968090 ACTTTGTGTGCTTCTAAGGAAATTCATGATATG-T-TGAACAACCATTTCAACACTATGTGTGCA
1 ACTATGTGTGCAACTCACAAAATTCATCATATGTTATGAACAACCATTTCAACACTATGCGTGCA
* *
968153 ACTTA-GGAAATTCATCATATGTTGATGAACAATCATTTCGAC
66 ACTCACGG-AATTCATCATATGTTGATGAACAACCATTTCGAC
*
968195 ACTATGTGTGCAACCCACAAAATT
1 ACTATGTGTGCAACTCACAAAATT
968219 TATAATATAT
Statistics
Matches: 100, Mismatches: 28, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
104 2 0.02
105 73 0.73
107 1 0.01
108 24 0.24
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (107 bp):
ACTATGTGTGCAACTCACAAAATTCATCATATGTTATGAACAACCATTTCAACACTATGCGTGCA
ACTCACGGAATTCATCATATGTTGATGAACAACCATTTCGAC
Found at i:968235 original size:54 final size:54
Alignment explanation
Indices: 968124--968235 Score: 134
Period size: 54 Copynumber: 2.1 Consensus size: 54
968114 CATGATATGT
** ** * *
968124 TGAACAACCATTTCAACACTATGTGTGCAACTTAGGAAATTCATCATATGTTGA
1 TGAACAACCATTTCAACACTATGTGTGCAACCCACAAAATTCATAATATATTGA
* * * *
968178 TGAACAATCATTTCGACACTATGTGTGCAACCCACAAAATTTATAATATATTTA
1 TGAACAACCATTTCAACACTATGTGTGCAACCCACAAAATTCATAATATATTGA
968232 TGAA
1 TGAA
968236 TGACCGTATA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (54 bp):
TGAACAACCATTTCAACACTATGTGTGCAACCCACAAAATTCATAATATATTGA
Found at i:968983 original size:21 final size:21
Alignment explanation
Indices: 968959--969023 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
968949 ATGCGACTGA
*
968959 GATTTTTTCGGTTTACTGGTT
1 GATTTTTTCGGTTTACTAGTT
*
968980 GATTTTTTTGGTTTACTAGTT
1 GATTTTTTCGGTTTACTAGTT
969001 GATTGATTTT--GTTTACTAGTT
1 GATT--TTTTCGGTTTACTAGTT
969022 GA
1 GA
969024 ATTGGTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
21 36 0.90
23 4 0.10
ACGTcount: A:0.15, C:0.06, G:0.22, T:0.57
Consensus pattern (21 bp):
GATTTTTTCGGTTTACTAGTT
Found at i:969052 original size:2 final size:2
Alignment explanation
Indices: 969045--969071 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
969035 GTTGTTTGAT
969045 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
969072 GTGGTGTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:969710 original size:18 final size:18
Alignment explanation
Indices: 969684--969740 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
969674 TTGAGGACAA
969684 GCCTGCAAATATAGATGG
1 GCCTGCAAATATAGATGG
* *
969702 GCCTACAAATGTAGATGG
1 GCCTGCAAATATAGATGG
* *
969720 GTCTGCTAATATAGATGG
1 GCCTGCAAATATAGATGG
969738 GCC
1 GCC
969741 AACTTTTAGG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.25
Consensus pattern (18 bp):
GCCTGCAAATATAGATGG
Found at i:976350 original size:20 final size:21
Alignment explanation
Indices: 976325--976363 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
976315 TTTTGGTGCA
*
976325 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
976345 GAGGGAACCGATTCCCCCC
1 GAGGGAACCGATTCCCCCC
976364 CACAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.23, C:0.38, G:0.26, T:0.13
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:977096 original size:12 final size:12
Alignment explanation
Indices: 977063--977088 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
977053 TAGTCGTCAA
977063 CCAAATCCTCCT
1 CCAAATCCTCCT
977075 CCAAATCCTCCT
1 CCAAATCCTCCT
977087 CC
1 CC
977089 TATTCCTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.54, G:0.00, T:0.23
Consensus pattern (12 bp):
CCAAATCCTCCT
Done.