Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001331.1 Hibiscus syriacus cultivar Beakdansim tig00002599_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: 45014
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Found at i:3370 original size:2 final size:2
Alignment explanation
Indices: 3365--3398 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3355 AAAAAACAAT
3365 TA TA TA -A 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
3399 TAAAAAAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18468 original size:161 final size:161
Alignment explanation
Indices: 18166--18476 Score: 464
Period size: 161 Copynumber: 1.9 Consensus size: 161
18156 GTAAAACTAT
* *
18166 GATACATTTAAAGTGTCAGTACTTTAATATAAGGATCGACACTTCGTGAATTTAAAAGAGAAGCA
1 GATACATTGAAAGTGTCAGTACTTTAATATAAGGATCGACACTTAGTGAATTTAAAAGAGAAGCA
* * * *
18231 GTTTTAAATCATATAAAGTGTCGATACTTTTAAAAACGTATCGATCCAAAACAATATACCAGGTA
66 GTTTTAAAGCATATAAAGTGTCGATACTTTAAAAAACATATCGATCCAAAACAATATAACAGGTA
18296 AAAATATGATAAAACCGGTAAAACGTTACCG
131 AAAATATGATAAAACCGGTAAAACGTTACCG
*
18327 GATATATTGAAAGTGTC-GATACTTT-ATATAAGGATCGACACTTAGTGAATTTAAAAGAGAAGC
1 GATACATTGAAAGTGTCAG-TACTTTAATATAAGGATCGACACTTAGTGAATTTAAAAGAGAAGC
** * * * * *
18390 AGTTTTAGCGCCTATAATGTGTCGATACTTTAAAAAAATATATCGATCCACAACGATATAACAGG
65 AGTTTTAAAGCATATAAAGTGTCGATACTTT-AAAAAACATATCGATCCAAAACAATATAACAGG
18455 TAAAAATATGATAAAACCGGTA
129 TAAAAATATGATAAAACCGGTA
18477 TCAAAATGAT
Statistics
Matches: 134, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
160 64 0.48
161 70 0.52
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (161 bp):
GATACATTGAAAGTGTCAGTACTTTAATATAAGGATCGACACTTAGTGAATTTAAAAGAGAAGCA
GTTTTAAAGCATATAAAGTGTCGATACTTTAAAAAACATATCGATCCAAAACAATATAACAGGTA
AAAATATGATAAAACCGGTAAAACGTTACCG
Found at i:18476 original size:20 final size:19
Alignment explanation
Indices: 18453--18499 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
18443 CGATATAACA
18453 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
18473 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
18493 GGTAAAA
1 GGTAAAA
18500 CGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:18504 original size:17 final size:19
Alignment explanation
Indices: 18464--18504 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
18454 GTAAAAATAT
*
18464 GATAAAACCGGTATCAAAAT
1 GATAAAACCGG-ATCAAAAC
18484 GATAAAACCGG-T-AAAAC
1 GATAAAACCGGATCAAAAC
18501 GATA
1 GATA
18505 CCGGATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
20 11 0.55
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (19 bp):
GATAAAACCGGATCAAAAC
Found at i:20746 original size:21 final size:21
Alignment explanation
Indices: 20720--20784 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
20710 AAGACAATCA
*
20720 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
20741 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
20762 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
20783 AG
1 AG
20785 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:20860 original size:33 final size:33
Alignment explanation
Indices: 20818--20883 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
20808 AAATAGATGG
*
20818 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
20851 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
20884 TATTAAGATG
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:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:21704 original size:23 final size:23
Alignment explanation
Indices: 21673--21745 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
21663 ATAGGTAAAA
*
21673 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
21696 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
21719 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
21742 ATAT
1 ATAT
21746 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:22193 original size:23 final size:23
Alignment explanation
Indices: 22162--22234 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
22152 ATAGGTAAAA
*
22162 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
22185 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
22208 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
22231 ATAT
1 ATAT
22235 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:22342 original size:489 final size:490
Alignment explanation
Indices: 21416--23123 Score: 3167
Period size: 489 Copynumber: 3.5 Consensus size: 490
21406 ATATAATAGG
* *
21416 TAAAAATAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTATTAAATTTAAA
1 TAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAA
* * *
21481 TACTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTA
66 TTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTA
21546 AATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAAC
131 AATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAAC
21611 TTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATA
196 TTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATA
21676 TGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCT
261 TGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCT
21741 TATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTA
326 TATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTA
21806 ATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATT
391 ATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATT
21871 TATTTTTTACGTTACGATATATATTATTATTAAAT
456 TATTTTTTACGTTACGATATATATTATTATTAAAT
*
21906 TAAAAACAATAAACATATATATTATATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAA
1 TAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAA
21971 TTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTA
66 TTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTA
22036 AATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAAC
131 AATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAAC
22100 TTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATA
196 TTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATA
22165 TGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCT
261 TGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCT
*
22230 TATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTA
326 TATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTA
*
22295 ATTTAAAGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATT
391 ATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATT
22360 TATTTTTTACGTTACGATATATATTATTATTAAAT
456 TATTTTTTACGTTACGATATATATTATTATTAAAT
22395 TAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAA
1 TAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAA
*
22460 TTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATATTTTGTGCAAATGAAATTATTA
66 TTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTA
22525 AATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAAC
131 AATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAAC
*
22590 TTTAAAAAAAATATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATA
196 TTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATA
*
22655 TGATGTAATAGGTAGCACTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCT
261 TGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCT
*
22720 TATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATTA
326 TATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTA
* * **
22785 ATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATATGTATCTAATGATT
391 ATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATT
* * *
22850 TATTTTTTATGTTACGGTATATATTATCATTAAAT
456 TATTTTTTACGTTACGATATATATTATTATTAAAT
22885 T-AAAACAATAAAC--ATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAA
1 TAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAA
22947 TTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTA
66 TTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTA
23012 AATTAATATTGTAGGTGGAAAACATGAAACACTATT--AAAAAATTGAAACATAAATTACATAAC
131 AATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAAC
* * *
23075 TTTAAAAAAAGTATCGATCTTTTTTATAAAAAAATATAGACACTTTCAA
196 TTTAAAAAAAGTATCGATCCTTTTTAT-AAAAAGTATGGACACTTTCAA
23124 CATATTATAA
Statistics
Matches: 1189, Mismatches: 27, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
485 52 0.04
486 19 0.02
487 149 0.13
489 497 0.42
490 472 0.40
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (490 bp):
TAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAA
TTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTA
AATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAAC
TTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATA
TGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCT
TATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTA
ATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATT
TATTTTTTACGTTACGATATATATTATTATTAAAT
Found at i:22683 original size:23 final size:23
Alignment explanation
Indices: 22652--22724 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
22642 ATAGGTAAAA
* *
22652 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCGCTT
*
22675 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
22698 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
22721 ATAT
1 ATAT
22725 TGTAAAGTAT
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:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:23871 original size:183 final size:182
Alignment explanation
Indices: 23559--24227 Score: 826
Period size: 183 Copynumber: 3.7 Consensus size: 182
23549 TTGTCTGTAC
* * * * * * *
23559 GTATCGATACAATTA-AAATATATATAGATACATAACAATATATCAGGTAAAAATATGAGAAAAC
1 GTATCGATAC-TTTATAAACATGTATTGATACACAACAATATAACAGGTAAAAATATGACAAAAC
* * * * ** * *
23623 CGGGTTCAATATAACAAAACCGGTAAAACGCTATTGGATATGTTGAAAGTATCGATTCTATTTAA
65 CGGTTTCAA-ATGACAAAAACAGTAAAACGCTACAGAATATGTTGAAAGTATCGATTCCATTTAA
* ** * *
23688 AAAAGTATCGACACTTTTGGGGTTTAAAAGAAAAATATTAATAGCGCCTAAAAA
129 ATAAGTATCGACACTTTTGGAATTTAAAAGAAAAACAGTAATAGCGCCTAAAAA
* * *
23742 GTATCGATAATTTATAAACATGTATTGATATACAACAATATAACAGGTAAAAATATGATAAAACC
1 GTATCGATACTTTATAAACATGTATTGATACACAACAATATAACAGGTAAAAATATGACAAAACC
* * *
23807 GGTTTCATAATGATAAAAACAGTAAAATGCTACAGGATATGTTGAAAGTATCGATTCCATTTAAA
66 GGTTTCA-AATGACAAAAACAGTAAAACGCTACAGAATATGTTGAAAGTATCGATTCCATTTAAA
*
23872 TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAGTAATAGCGCCTAAAAA
130 TAAGTATCGACACTTTTGGAATTTAAAAGAAAAACAGTAATAGCGCCTAAAAA
*
23925 GTATCGATACTTTATAAACATGTATCT-ATACACATCAATATAACAGGTAAAAATATGACAAAAC
1 GTATCGATACTTTATAAACATGTAT-TGATACACAACAATATAACAGGTAAAAATATGACAAAAC
* * * * * *
23989 CAGTTTCATTATGACAAAACCAGTAAAGAC-ATACCGAATATGTTGAAAGTATCGATTCCATTGA
65 CGGTTTCA-AATGACAAAAACAGTAAA-ACGCTACAGAATATGTTGAAAGTATCGATTCCATTTA
* *
24053 AATAAGTATCGACACTTTTGAAATTTAAAAGAAAAACAGTAATAGCGCCTATAAA
128 AATAAGTATCGACACTTTTGGAATTTAAAAGAAAAACAGTAATAGCGCCTAAAAA
* * * * *
24108 GTATCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATC
1 GTATCGATACTTTATAAACATGTATTGATACACAACAATATAACAGGTAAAAATATGACAAAACC
* * *
24173 GGTCTCGAAATGAC-AAAACAGGTAAAGCGCTACCA-AATATGTTGAATGTATCGAT
66 GGTTTC-AAATGACAAAAACA-GTAAAACGCTA-CAGAATATGTTGAAAGTATCGAT
24228 ACTTTTATAA
Statistics
Matches: 423, Mismatches: 54, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
182 9 0.02
183 409 0.97
184 5 0.01
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (182 bp):
GTATCGATACTTTATAAACATGTATTGATACACAACAATATAACAGGTAAAAATATGACAAAACC
GGTTTCAAATGACAAAAACAGTAAAACGCTACAGAATATGTTGAAAGTATCGATTCCATTTAAAT
AAGTATCGACACTTTTGGAATTTAAAAGAAAAACAGTAATAGCGCCTAAAAA
Found at i:24876 original size:200 final size:199
Alignment explanation
Indices: 24532--25333 Score: 1090
Period size: 200 Copynumber: 4.0 Consensus size: 199
24522 TTTTAAAATT
* ** * *
24532 GTATCGATCCAAAAAATATCGAAATTGATAATTATAAAGTAATAGGTAAATTTACAAAGTAACCG
1 GTATCGATCC-AAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * * * * *
24597 GTAAGAATATATCAATTTAATTAGAAAATAGGTAAACATAATGTATTGATACTTTTTTATATTGT
65 GTAAGAATATACCGATTTTATGAGAGAATAGGTCAACATAATGTATCGATACTTTTTTATATTGT
* * * * * * *
24662 GTC-AGTATTTTTTGTCCAAAATGAATGTCTAACGAGGTGTACACATAAAATGTCGATTCATTCA
130 GTCGA-TACTTTTTGTCCAAAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTCA
24726 TAATAA
194 TAATAA
*
24732 GTATCGATTCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCT
1 GTATCGA-TCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * *
24797 GTAAGAATATACCGGTTTTATGAGAGAATAGGCCAACATAATGTATCGATACTATTTTACATTGT
65 GTAAGAATATACCGATTTTATGAGAGAATAGGTCAACATAATGTATCGATACTTTTTTATATTGT
** * * *
24862 GTTTATACTTTTTGTCCAAAATGAATGCCCAATGAGGTGCACGTATAAAGTGTCGATACATTTAT
130 GTCGATACTTTTTGTCCAAAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTCAT
24927 AATAA
195 AATAA
* * *
24932 GTATCGATCTCAAAAACATCGAAACCGATAATTATAATGTATTAGGTAAATTTACAATGTAATCA
1 GTATCGATC-CAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * *
24997 GTAAGAATATACCGGTTTCATGAGAGAATATGTCAACTTAATGTATCGATA-TTGTTTTATATTG
65 GTAAGAATATACCGATTTTATGAGAGAATAGGTCAACATAATGTATCGATACTT-TTTTATATTG
* * *
25061 TGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATATATTTA
129 TGTCGATACTTTTTGTCCAAAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTCA
25126 TAATAA
194 TAATAA
* *
25132 GTATCGATCCCAAAAATATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATATAACCG
1 GTATCGAT-CCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * *
25197 GTCA-AA-ATACCGATTTTATGAGAGAATATGTCAACATATTGTATCGATACTTTTTTAAATTGT
65 GTAAGAATATACCGATTTTATGAGAGAATAGGTCAACATAATGTATCGATACTTTTTTATATTGT
* **
25260 GTCGATACTTTTTGTTCAAGCTGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTCAT
130 GTCGATACTTTTTGTCCAAAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTCAT
25325 AATAA
195 AATAA
25330 GTAT
1 GTAT
25334 TGATATTTTA
Statistics
Matches: 536, Mismatches: 60, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
198 117 0.22
199 7 0.01
200 407 0.76
201 5 0.01
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (199 bp):
GTATCGATCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGG
TAAGAATATACCGATTTTATGAGAGAATAGGTCAACATAATGTATCGATACTTTTTTATATTGTG
TCGATACTTTTTGTCCAAAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTCATA
ATAA
Found at i:25834 original size:21 final size:22
Alignment explanation
Indices: 25810--25856 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
25800 AATAGGTAAA
*
25810 TAAAATATATCGATA-GTTTTT
1 TAAAATATATCGATACATTTTT
* *
25831 TAAATTGTATCGATACATTTTT
1 TAAAATATATCGATACATTTTT
25853 TAAA
1 TAAA
25857 TTACGCCTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (22 bp):
TAAAATATATCGATACATTTTT
Found at i:25854 original size:22 final size:21
Alignment explanation
Indices: 25817--25858 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
25807 AAATAAAATA
*
25817 TATCGATAGTTTTTTAAATTG
1 TATCGATAATTTTTTAAATTG
25838 TATCGATACATTTTTTAAATT
1 TATCGATA-ATTTTTTAAATT
25859 ACGCCTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (21 bp):
TATCGATAATTTTTTAAATTG
Found at i:28692 original size:64 final size:62
Alignment explanation
Indices: 28614--28747 Score: 166
Period size: 64 Copynumber: 2.1 Consensus size: 62
28604 CAATGTGTAC
* *
28614 CGATGCACTCTT-AAATA-AGGAACATCGAATGTCATTAATGCATCGATGCATAAGG-AGTGCAT
1 CGATGCACTCTTAAAATACA--AACATCGAATGGCATTAATGCATCGATACAT-AGGTAGTGCAT
* *
28676 CGATGCACTCGTTTAAAATACAAACATCGAATGGGATTTATGCATCGATACATAGGTAGTGCAT
1 CGATGCACTC--TTAAAATACAAACATCGAATGGCATTAATGCATCGATACATAGGTAGTGCAT
28740 CGATGCAC
1 CGATGCAC
28748 CTGTTAAGGG
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
62 10 0.16
63 3 0.05
64 44 0.70
65 5 0.08
66 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (62 bp):
CGATGCACTCTTAAAATACAAACATCGAATGGCATTAATGCATCGATACATAGGTAGTGCAT
Found at i:29353 original size:20 final size:19
Alignment explanation
Indices: 29304--29359 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
29294 AGGGATTATC
29304 AGTGGTCCTTCGGGAC-AT
1 AGTGGTCCTTCGGGACAAT
** *
29322 AGTGGTTATTCGGAACAATT
1 AGTGGTCCTTCGGGACAA-T
29342 AGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACAA
29360 ATATTCAGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 13 0.43
19 1 0.03
20 16 0.53
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (19 bp):
AGTGGTCCTTCGGGACAAT
Found at i:36160 original size:20 final size:19
Alignment explanation
Indices: 36111--36166 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
36101 AGGGATTATC
36111 AGTGGTCCTTCGGGAC-AT
1 AGTGGTCCTTCGGGACAAT
** *
36129 AGTGGTTATTCGGAACAATT
1 AGTGGTCCTTCGGGACAA-T
36149 AGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACAA
36167 ATATTCAGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 13 0.43
19 1 0.03
20 16 0.53
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (19 bp):
AGTGGTCCTTCGGGACAAT
Found at i:37684 original size:24 final size:23
Alignment explanation
Indices: 37653--37697 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
37643 TTCATTTCAT
*
37653 ATTTAATTGGAGTTTGAATTTAA
1 ATTTAATTGAAGTTTGAATTTAA
*
37676 ATTTCAATTTAAGTTTGAATTT
1 ATTT-AATTGAAGTTTGAATTT
37698 CAATATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.51
Consensus pattern (23 bp):
ATTTAATTGAAGTTTGAATTTAA
Found at i:37708 original size:24 final size:24
Alignment explanation
Indices: 37663--37709 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
37653 ATTTAATTGG
* *
37663 AGTTTGAATTTAAATTTCAATTTA
1 AGTTTGAATTTAAATATAAATTTA
*
37687 AGTTTGAATTTCAATATAAATTT
1 AGTTTGAATTTAAATATAAATTT
37710 CGGCTCCACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (24 bp):
AGTTTGAATTTAAATATAAATTTA
Found at i:39025 original size:270 final size:272
Alignment explanation
Indices: 38526--39068 Score: 1020
Period size: 270 Copynumber: 2.0 Consensus size: 272
38516 TCCTAAATGC
38526 TTCTGATGCTTTAAATGTTTGAGAACCAAATGGATTGCCTTCGAGATTTTAAATATGCAGCTGCT
1 TTCTGATGCTTTAAATGTTTGAGAACCAAATGGATTGCCTTCGAGATTTTAAATATGCAGCTGCT
38591 TTTACATCAGCTATGTTTCTCTCAGATGATTTCAGTTTACGGTTTTCCTATCTTCATGAGCTTGA
66 TTTACATCAGCTATGTTTCTCTCAGATGATTTCAGTTTACGGTTTTCCTATCTTCATGAGCTTGA
38656 TGAAATGGATAATATCCGGAAGGCATTCTTCGCATCTCCAATCATCCTGCTTGTTAATCAAAATT
131 TGAAATGGATAATATCCGGAAGGCATTCTTCGCATCTCCAATCATCCTGCTTGTTAATCAAAATT
*
38721 ATGATGGTCGGGATTTCCCTTGGGTTCATTTAGGTTGATTGCTCCGAATATATAACGACATTTGA
196 ATGATGGTCGGGATTTCCCTCGGGTTCATTTAGGTTGATTGCTCCGAATATATAACGACATTTGA
38786 TCTCCGAATCGT
261 TCTCCGAATCGT
*
38798 TTCTGATGCTTTAAATGTTTGAGAACCAAATGGATTGCCTTCGAGATTTTAAATATGTAGCTGCT
1 TTCTGATGCTTTAAATGTTTGAGAACCAAATGGATTGCCTTCGAGATTTTAAATATGCAGCTGCT
* *
38863 TTTACATCAGCTATGTTTCTCTCAGATGGTTTCGGTTTACGG-TTTCCTATC-TCATGAGCTTGA
66 TTTACATCAGCTATGTTTCTCTCAGATGATTTCAGTTTACGGTTTTCCTATCTTCATGAGCTTGA
38926 TGAAATGGATAATATCCGGAAGGCATTCTTCGCATCTCCAATCATCCTGCTTGTTAATCAAAATT
131 TGAAATGGATAATATCCGGAAGGCATTCTTCGCATCTCCAATCATCCTGCTTGTTAATCAAAATT
38991 ATGATGGTCGGGA-TTCCCTCGGGTTTCATTTAGGTTGATTGCTCCGAATATATAACGACATTTG
196 ATGATGGTCGGGATTTCCCTCGGG-TTCATTTAGGTTGATTGCTCCGAATATATAACGACATTTG
39055 ATCTCCGAATCGT
260 ATCTCCGAATCGT
39068 T
1 T
39069 GTTGGTTGAT
Statistics
Matches: 266, Mismatches: 4, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
269 9 0.03
270 144 0.54
271 9 0.03
272 104 0.39
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (272 bp):
TTCTGATGCTTTAAATGTTTGAGAACCAAATGGATTGCCTTCGAGATTTTAAATATGCAGCTGCT
TTTACATCAGCTATGTTTCTCTCAGATGATTTCAGTTTACGGTTTTCCTATCTTCATGAGCTTGA
TGAAATGGATAATATCCGGAAGGCATTCTTCGCATCTCCAATCATCCTGCTTGTTAATCAAAATT
ATGATGGTCGGGATTTCCCTCGGGTTCATTTAGGTTGATTGCTCCGAATATATAACGACATTTGA
TCTCCGAATCGT
Found at i:40275 original size:199 final size:199
Alignment explanation
Indices: 39693--40493 Score: 1160
Period size: 199 Copynumber: 4.0 Consensus size: 199
39683 TTTTAAATTT
39693 GTATCGATCCC-AAAACA-CGAAACCGAT-A--ATAAAGTAATAGGTAAATTTACAA--TAACCG
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCG
39751 ATAAGAATATACCGGTTTTATGACAGAATAGGTCAACATAATGTATCGATACTTTTTTAAATTGT
66 ATAAGAATATACCGGTTTTATGACAGAATAGGTCAACATAATGTATCGATAC-TTTTTAAATTGT
* * * *
39816 GTCAATACTTTTTGTCCA-CATGAATTTTGGTCCCAATGAGGTGCACACATAAAGTGTCGATACA
130 GTCGATACTTTTGGTCCAGAATGAA---T-G-CCCAACGAGGTGCACACATAAAGTGTCGATACA
39880 TTTATTGTAA
190 TTTATTGTAA
* *
39890 GTATCGATCCCAAAAATATCGAAACCGATAATTAT-AAGTAATAGGTAAATTTACAATGCAACCG
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCG
* * *
39954 GTAAGAATAT--CGGTTTTATAACAGAGTAGGTCAACATAATGTATCGATACTTTTTTTTAAATT
66 ATAAGAATATACCGGTTTTATGACAGAATAGGTCAACATAATGTATCGATAC---TTTTTAAATT
* *
40017 GTGTCGATACTTTTTGTCCAGAATGAATGTCCAACGA-GTGCACACATAAAGTGTCGATACATTT
128 GTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACATTT
40081 ATTGTAA
193 ATTGTAA
* *
40088 GTATCGATCCCAAAAACACCGAAACCGATAATTATAAAGTAATAGGTAAATTTACCATGTAACCG
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCG
* * * * *
40153 GTAAGAATATACCGATTTTATGGCAGAATAGGTCAACATAATGTATCGATAC-CTTTACATTTGT
66 ATAAGAATATACCGGTTTTATGACAGAATAGGTCAACATAATGTATCGATACTTTTTA-AATTGT
* *
40217 GTCGATACTTTTGGTTCAGAATGAATGCCCAATGAGGTGCACACATAAAGTGTCGATACATTTAT
130 GTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACATTTAT
40282 TGTAA
195 TGTAA
* *
40287 GAATCGATCCCAAAAACATCAAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCG
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCG
* * * * *
40352 ATAAAAATATACTGGTTTTATGACAGAGTAGGTCAACATAATGTATCGATACTTTTTAATTTATG
66 ATAAGAATATACCGGTTTTATGACAGAATAGGTCAACATAATGTATCGATACTTTTTAAATTGTG
* *
40417 TCGATACTTTTGGTCCAGAATGAATGCCTAACGAGGTGCACGCATAAAGTGTCGATACATTTATT
131 TCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACATTTATT
40482 GTAA
196 GTAA
40486 GTATCGAT
1 GTATCGAT
40494 ACATAATGAT
Statistics
Matches: 548, Mismatches: 40, Indels: 30
0.89 0.06 0.05
Matches are distributed among these distances:
197 15 0.03
198 108 0.20
199 272 0.50
200 6 0.01
201 96 0.18
202 2 0.00
203 44 0.08
204 5 0.01
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (199 bp):
GTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCG
ATAAGAATATACCGGTTTTATGACAGAATAGGTCAACATAATGTATCGATACTTTTTAAATTGTG
TCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACATTTATT
GTAA
Found at i:42284 original size:20 final size:21
Alignment explanation
Indices: 42268--42307 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
42258 ATAACTTTTA
42268 TATAT-GTATCAATACTTTGT
1 TATATCGTATCAATACTTTGT
*
42288 TATATCGGTCTCAATACTTT
1 TATATC-GTATCAATACTTT
42308 AATTCCCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
22 12 0.71
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (21 bp):
TATATCGTATCAATACTTTGT
Found at i:42871 original size:23 final size:24
Alignment explanation
Indices: 42826--42871 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
42816 ATCAACTTTA
*
42826 ATAATGCGCAACCTATTACGTTAC
1 ATAATGCGCAACCTAATACGTTAC
* *
42850 ATAA-GCGCTACCTAATATGTTA
1 ATAATGCGCAACCTAATACGTTA
42872 TTATGCTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (24 bp):
ATAATGCGCAACCTAATACGTTAC
Found at i:43030 original size:23 final size:23
Alignment explanation
Indices: 42979--43030 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
42969 TAATCAATTT
* *
42979 TATTATATAAGTTCTACCTATTA
1 TATTATATAAGTGCTACCTAATA
**
43002 CGTTATATAAGTGCTACCTAATA
1 TATTATATAAGTGCTACCTAATA
43025 TATTAT
1 TATTAT
43031 TGTGCTTGAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (23 bp):
TATTATATAAGTGCTACCTAATA
Found at i:43117 original size:132 final size:133
Alignment explanation
Indices: 42925--43179 Score: 340
Period size: 132 Copynumber: 1.9 Consensus size: 133
42915 CCTTGGTAAC
* *
42925 ATTTTAGGTGTTACCTAATATGTTGTAATAACAAATTAAGTAATTAATCAATTTTATTATAT-AA
1 ATTTTAGGCGTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCAATTTTATTATATGAA
* * * * *
42989 -GTTCTACCTATTACGTTATATAAGTGCTACCTAATATATTATTGTGCTTGATAATGTTTCTAGT
66 CG--CTACCTACTACATTATAT-AGCGCTACCTAATATATTATTGTACTTGATAATATTTCTAGT
43053 AATTAT
128 AATTAT
*
43059 ATTTTAGGCGTTTACCTAATATG-T-T-ATAACAAATTAAGTAATTAACCTATTTTATTATATGA
1 ATTTTAGGCG-TTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCAATTTTATTATATGA
* * *
43121 ACGCTACTTACTACATTATATAGCGTTACCTAATATGTTATTGTACTTGATAATATTTC
65 ACGCTACCTACTACATTATATAGCGCTACCTAATATATTATTGTACTTGATAATATTTC
43180 CAATTAAATA
Statistics
Matches: 107, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
131 33 0.31
132 48 0.45
133 3 0.03
134 11 0.10
135 12 0.11
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (133 bp):
ATTTTAGGCGTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCAATTTTATTATATGAA
CGCTACCTACTACATTATATAGCGCTACCTAATATATTATTGTACTTGATAATATTTCTAGTAAT
TAT
Found at i:43229 original size:16 final size:16
Alignment explanation
Indices: 43208--43260 Score: 79
Period size: 16 Copynumber: 3.2 Consensus size: 16
43198 ACCGATTTAG
*
43208 ATTTAACCGATCACTT
1 ATTTAACCAATCACTT
*
43224 ATTTAACTAATCACTT
1 ATTTAACCAATCACTT
43240 ATTTAACCAATCACATT
1 ATTTAACCAATCAC-TT
43257 ATTT
1 ATTT
43261 TTTAAAACCG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
16 27 0.82
17 6 0.18
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.42
Consensus pattern (16 bp):
ATTTAACCAATCACTT
Done.