Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006263.1 Hibiscus syriacus cultivar Beakdansim tig00014939_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: 95497
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:2533 original size:4 final size:4
Alignment explanation
Indices: 2524--2561 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
2514 GAAGACCAAG
*
2524 ATAA ATAA ATAA ATAA AT-- ATAA ATAA ATAA ATAT ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
2562 TGTGACGGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.07
4 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAA
Found at i:2547 original size:14 final size:14
Alignment explanation
Indices: 2528--2558 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2518 ACCAAGATAA
2528 ATAAATAAATAAAT
1 ATAAATAAATAAAT
2542 ATAAATAAATAAAT
1 ATAAATAAATAAAT
2556 ATA
1 ATA
2559 TAATGTGACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
ATAAATAAATAAAT
Found at i:8126 original size:3 final size:3
Alignment explanation
Indices: 8118--8143 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
8108 TTATAATTCA
8118 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
8144 ATGCAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:8835 original size:31 final size:31
Alignment explanation
Indices: 8798--8867 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
8788 TTGAAGTCGA
*
8798 TCCTCCATTTTCCATTCAAATCTCTGATTAC
1 TCCTCCACTTTCCATTCAAATCTCTGATTAC
8829 TCCTCCACTTTCCATTCAAATCTCTGATTAC
1 TCCTCCACTTTCCATTCAAATCTCTGATTAC
8860 TCCTCCAC
1 TCCTCCAC
8868 ATGCTGCTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.21, C:0.37, G:0.03, T:0.39
Consensus pattern (31 bp):
TCCTCCACTTTCCATTCAAATCTCTGATTAC
Found at i:15214 original size:23 final size:23
Alignment explanation
Indices: 15188--15235 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
15178 ATAAAGTACA
*
15188 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
15211 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
15234 AT
1 AT
15236 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:15738 original size:23 final size:23
Alignment explanation
Indices: 15711--15783 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
15701 ATACTTTATA
*
15711 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
15734 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
15757 ATATAAGTGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
15780 ATAT
1 ATAT
15784 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:16178 original size:23 final size:23
Alignment explanation
Indices: 16148--16197 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
16138 ATACTTTACA
* *
16148 ATATAAGCACTACTTATTACATT
1 ATATAAGCACTACCTATTACATC
**
16171 ATATAAGCGTTACCTATTACATC
1 ATATAAGCACTACCTATTACATC
16194 ATAT
1 ATAT
16198 TTTTACCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATC
Found at i:16589 original size:23 final size:23
Alignment explanation
Indices: 16563--16612 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
16553 ATATTTTACA
*
16563 ATATAAACACTACCTATTACATT
1 ATATAAACACTACCTATTACATC
* *
16586 ATATAAGCGCTACCTATTACATC
1 ATATAAACACTACCTATTACATC
16609 ATAT
1 ATAT
16613 TTTTACCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAAACACTACCTATTACATC
Found at i:16702 original size:414 final size:415
Alignment explanation
Indices: 15734--16874 Score: 2124
Period size: 415 Copynumber: 2.8 Consensus size: 415
15724 CTATTACATT
* *
15734 ATATAAACGCTACCTATTACATTATATAAGTGCTACCTATTACATCATATTTTTACCTATTATAT
1 ATATAAACACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATAT
*
15799 TGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATCTTT
66 TGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
*
15864 CAATTTTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTGCAC
131 CAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
15929 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
196 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
15994 AACCAAAGATAATAAT-AATATGTAATATATATGTTTATTGTTTTTAATTTACTAAATTAATATC
261 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTACTAAATTAATATC
*
16058 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTT
326 TTAAAACTCACTCAAAAGATAACCATAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTT
*
16123 TTATAAAAAGAATAGATACTTTACA
391 TTATAAAAAGAATAAATACTTTACA
* * *
16148 ATATAAGCACTACTTATTACATTATATAAGCGTTACCTATTACATCATATTTTTACCTATTATAT
1 ATATAAACACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATAT
*
16213 TGAAAGTGTCCATACTTTTTATAAAAATGATTGATACTTTTTTTAAAGTTATGTAATTTATGTTT
66 TGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
16278 CAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
131 CAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
16343 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
196 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
*
16408 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTATTAAATTAATATC
261 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTACTAAATTAATATC
*
16473 TTAAAACTCACTCAAAAGATAACCATAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
326 TTAAAACTCACTCAAAAGATAACCATAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTT
*
16538 TTATAAAAATG-ATAAATATTTTACA
391 TTATAAAAA-GAATAAATACTTTACA
16563 ATATAAACACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATAT
1 ATATAAACACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATAT
* *
16628 TGAAAGTGTTCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
66 TGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
16693 CAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
131 CAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
16758 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
196 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
16823 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTA
261 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTA
16875 ATAATAATAT
Statistics
Matches: 706, Mismatches: 19, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
414 268 0.38
415 437 0.62
416 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (415 bp):
ATATAAACACTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATAT
TGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTT
CAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTACTAAATTAATATC
TTAAAACTCACTCAAAAGATAACCATAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTT
TTATAAAAAGAATAAATACTTTACA
Found at i:19714 original size:183 final size:183
Alignment explanation
Indices: 19406--20165 Score: 1414
Period size: 183 Copynumber: 4.2 Consensus size: 183
19396 ACTCCTATTG
*
19406 TAAAGTACGGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
1 TAAAGTACAGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
* *
19471 GTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTA
66 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
*
19536 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACA
131 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACA
*
19589 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
1 TAAAGTACAGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
* *
19654 GTATATTTATACCAGTTATATTAAAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
66 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
19719 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACA
131 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACA
*
19772 TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
1 TAAAGTACAGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
* *
19837 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGTGTTCCAATGTGTA
66 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
19902 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACA
131 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACA
*
19955 TAAAGTACAAACACAATA-TAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
1 TAAAGTACAGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
20019 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
66 GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
20084 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACA
131 AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACA
20137 TAAAGTACAGACACAATATTAAAAAGTGT
1 TAAAGTACAGACACAATATTAAAAAGTGT
20166 GAAAACTTTG
Statistics
Matches: 561, Mismatches: 15, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
182 179 0.32
183 382 0.68
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (183 bp):
TAAAGTACAGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCG
GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA
AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACA
Found at i:22951 original size:200 final size:200
Alignment explanation
Indices: 22603--25364 Score: 4695
Period size: 200 Copynumber: 13.9 Consensus size: 200
22593 TTTAAATTAG
*
22603 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
22668 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* * * *
22733 TCGACACTTTTTATATATGGATCGACACTTTACGGTTGCACCTTGTTTGCCATTAATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
22798 AAAAA
196 AAAAA
* *
22803 TATCAACACAAACTAAAAAAGTGTCGACACATTATTTAGATATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
22868 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
22933 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGAGC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
22998 AAAAA
196 AAAAA
*
23003 TATCAACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
23068 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
23133 TCGACACTTTTTATATATGGATCGACATTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
23198 AAAAA
196 AAAAA
23203 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
23268 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
23333 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTTATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
23398 AAAAA
196 AAAAA
*
23403 TATCGACACAAACTAAAAAAGTGTCGACATATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
23468 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* * *
23533 TCGACACTTTTTATATATGGATCGACACTTTACGGTTGCACCCTGTTTGCCATTAATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
23598 AAAAA
196 AAAAA
* *
23603 TATCAACACAAACTAAAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
23668 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* * *
23733 TCGACACTTTTTATATATGGATCGACACTTTACGGTTGCACCCTGTTTGCCATTCATTCTGGAGC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
23798 AAAAA
196 AAAAA
*
23803 TATCAACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
23868 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
23933 TCGACACTTTTTATATATGGATCGACATTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
23998 AAAAA
196 AAAAA
24003 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
24068 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
24133 TCGACACTTTTTATATATGGATCGACATTTTATGGTTGCACCCTGTTGGCCATTCATTCTTGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
24198 AAAAA
196 AAAAA
*
24203 TATCGACACAAACTAAAAAAGTGTCGCCACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
24268 CTTGTACCGGTTAGATTGAAAAATTACATAATACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
24333 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
24398 AAAAA
196 AAAAA
** * * * * * * * *
24403 TATCGACACATTATTTAGACATA-T-TC-TCTCA-TA---AAACCGGTATACT-T-GT---ACCG
1 TATCGACACA--AACTA-AAAAAGTGTCGACACATTATTTAGA-C-ATATTCTCTCATAAAACCG
* * * * * * ** * *
24456 GT-TAGATTG-A-----AAAATT-ACATATTACAT-TATAC-TTTTGGTTTTCG--AT--AT-TT
61 GTATA-CTTGTACCGGTTAGATTGAAAAATTACATAT-TACATTATACTTTTGGTTTTCGATGTT
* * *
24506 TTGGGATCGA-C-AC-TTTTTA-TATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTC
124 TTTGG---GATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTC
24567 ATTCTGGACCAAAAA
186 ATTCTGGACCAAAAA
24582 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
24647 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
24712 TCGACACTTTTTATATATGGATCGACACTATATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
24777 AAAAA
196 AAAAA
*
24782 TATCGACACAAACTAAAAAAGTGTCGACATATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
24847 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
24912 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTTATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
24977 AAAAA
196 AAAAA
*
24982 TATCGACACAAACTAAAAAAGTGTCGACATATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
25047 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
25112 TCGACACGTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
25177 AAAAA
196 AAAAA
25182 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
25247 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
25312 TCGACACTTTTTATATATGGATCGGCACTTTATGGTTGCACCCTGTTGGCCAT
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCAT
25365 ATTGTAAATT
Statistics
Matches: 2428, Mismatches: 93, Indels: 82
0.93 0.04 0.03
Matches are distributed among these distances:
176 3 0.00
177 4 0.00
178 2 0.00
179 70 0.03
180 12 0.00
181 9 0.00
182 3 0.00
183 6 0.00
185 8 0.00
186 21 0.01
187 7 0.00
192 7 0.00
193 21 0.01
194 9 0.00
196 6 0.00
197 3 0.00
198 9 0.00
199 12 0.00
200 2207 0.91
201 2 0.00
202 4 0.00
203 3 0.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
AAAAA
Found at i:25488 original size:18 final size:18
Alignment explanation
Indices: 25465--25525 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
25455 TCTCATTCAT
*
25465 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
25483 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
25502 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
25521 AATTA
1 AATTA
25526 ACCCTATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:25501 original size:19 final size:19
Alignment explanation
Indices: 25477--25525 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
25467 TTATATTCAC
25477 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
25496 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
25515 ATACAAAATTA
1 ATACAAAATTA
25526 ACCCTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:26113 original size:4 final size:4
Alignment explanation
Indices: 26104--26128 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
26094 AATGTCCTTT
26104 CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA C
26129 CAATCTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:27362 original size:33 final size:33
Alignment explanation
Indices: 27325--27390 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
27315 CATCTTAATA
*
27325 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
27358 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
27391 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:27449 original size:21 final size:21
Alignment explanation
Indices: 27424--27488 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
27414 CCCCTTATGC
* *
27424 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
27445 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
27466 CTATCAAGTTTCTCTTCAACT
1 CTCTCAAGTTTCTCTTCGACT
27487 CT
1 CT
27489 TGATTGTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.18, C:0.31, G:0.09, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:29726 original size:17 final size:18
Alignment explanation
Indices: 29704--29746 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
29694 ATATATCTGG
29704 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
29721 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
29741 TATCAT
1 TATCAT
29747 ATTTTTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:29979 original size:180 final size:182
Alignment explanation
Indices: 29676--30147 Score: 680
Period size: 180 Copynumber: 2.6 Consensus size: 182
29666 CGTACTTACG
* * *
29676 AAAGTATCGACACTTTCAATATATCTGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
29741 TATCATATTTTTACTTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACATGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
29806 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
29857 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTA-CGAGTTTTATCATTTTGATACCGG-T
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCG-GTTTTATCATTTTGATACCGGTT
* * *
29920 TTATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTA
65 TTATCATATTTTTACATGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTA
** * *
29985 TAGGATTTAAAACTGCTTTTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 TAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * ** *
30038 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACAGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
30103 TGTCATAGTTTTACATGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACATGTTATATCGTTTTGGATCGATACATTTTT
30148 AATTTGGATC
Statistics
Matches: 260, Mismatches: 27, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
180 108 0.42
181 108 0.42
182 44 0.17
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACATGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:36604 original size:17 final size:17
Alignment explanation
Indices: 36577--36615 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
36567 AATTTACAAT
36577 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
36593 TAATTATAAATAATATC
1 TAATTATAAATAATATC
36610 TAATTA
1 TAATTA
36616 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:39717 original size:19 final size:19
Alignment explanation
Indices: 39693--39736 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
39683 AAAATATTTT
*
39693 TATGAATAGTATTAT-ATCG
1 TATGAATAGTACTATAAT-G
39712 TATGAATAGTACTATAATG
1 TATGAATAGTACTATAATG
39731 TATGAA
1 TATGAA
39737 CAATGCCGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.39
Consensus pattern (19 bp):
TATGAATAGTACTATAATG
Found at i:50425 original size:17 final size:17
Alignment explanation
Indices: 50398--50436 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
50388 AATTTACAAT
50398 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
50414 TAATTATAAATAATATC
1 TAATTATAAATAATATC
50431 TAATTA
1 TAATTA
50437 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:56009 original size:14 final size:14
Alignment explanation
Indices: 55990--56029 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
55980 CATGGGCTAA
55990 TGAACTTAATAATG
1 TGAACTTAATAATG
56004 TGAACTT-ATGAATG
1 TGAACTTAAT-AATG
*
56018 TGAATTTAATAA
1 TGAACTTAATAA
56030 ATCTATGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 2 0.09
14 19 0.83
15 2 0.09
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (14 bp):
TGAACTTAATAATG
Found at i:58832 original size:29 final size:29
Alignment explanation
Indices: 58790--58849 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
58780 TGGTCATTAT
58790 GAATTCATTGTAATGCCCTTCGGAGTAAC
1 GAATTCATTGTAATGCCCTTCGGAGTAAC
58819 GAATTCATTGTAATGCCCTTCGGAGTAAC
1 GAATTCATTGTAATGCCCTTCGGAGTAAC
58848 GA
1 GA
58850 TTGCAGTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (29 bp):
GAATTCATTGTAATGCCCTTCGGAGTAAC
Found at i:61458 original size:30 final size:30
Alignment explanation
Indices: 61424--61492 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
61414 TTATATGAGT
* *
61424 TATGTGATAAATGAATGG-AAATGATATGTC
1 TATGTGATAAAGGAA-GGAAAATAATATGTC
*
61454 TATGTGATAAAGGTAGGAAAATAATATGTC
1 TATGTGATAAAGGAAGGAAAATAATATGTC
*
61484 TACGTGATA
1 TATGTGATA
61493 CAAATTATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 2 0.06
30 32 0.94
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (30 bp):
TATGTGATAAAGGAAGGAAAATAATATGTC
Found at i:67532 original size:12 final size:12
Alignment explanation
Indices: 67511--67543 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
67501 TCCCCCACGC
67511 AAAAAA-AAAGA
1 AAAAAAGAAAGA
67522 AAAAAAGAAAGA
1 AAAAAAGAAAGA
67534 AAAAAAGAAA
1 AAAAAAGAAA
67544 TTTAATGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAGA
Done.