Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003555.1 Hibiscus syriacus cultivar Beakdansim tig00007501_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: 51605
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1098 original size:21 final size:20
Alignment explanation
Indices: 1070--1133 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 20
1060 AAGACAATCA
*
1070 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGA-AAACTTGAG
* *
1091 ATAGTCGAAGATAACTTGAG
1 AGAGTCGAAGAAAACTTGAG
*
1111 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGA-AAACTTGAG
1132 AG
1 AG
1134 GATAAGGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.41, C:0.11, G:0.28, T:0.20
Consensus pattern (20 bp):
AGAGTCGAAGAAAACTTGAG
Found at i:1108 original size:20 final size:20
Alignment explanation
Indices: 1070--1133 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
1060 AAGACAATCA
* *
1070 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGA-TAACTTGAG
*
1091 ATAGTCGAAGATAACTTGAG
1 AGAGTCGAAGATAACTTGAG
1111 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGATA-ACTTGAG
1132 AG
1 AG
1134 GATAAGGGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 19 0.50
21 19 0.50
ACGTcount: A:0.41, C:0.11, G:0.28, T:0.20
Consensus pattern (20 bp):
AGAGTCGAAGATAACTTGAG
Found at i:3010 original size:19 final size:19
Alignment explanation
Indices: 2986--3034 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
2976 AATGTAGGGT
2986 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
3005 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
3024 TAATTTTGTAT
1 TAATTTTGTAT
3035 GTGAATATAA
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:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:3744 original size:200 final size:199
Alignment explanation
Indices: 3264--4048 Score: 1293
Period size: 197 Copynumber: 4.0 Consensus size: 199
3254 AATTTACAAT
* *
3264 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAGAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
3329 CG-AACCCA-AAGTATAATGTAATA--TAATTTTTCAATCTAATCGGTACAAGTATACCGG-TTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
3389 ATGAGAGAATATGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTGGTCCAGA
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTGGTCCAGA
3454 ATGA
196 ATGA
* *
3458 ATGGCAAAC-GGATGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGAT-CGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
3521 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCAAAACCGGTACAAGTATATCGGTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATC-TAACCGGTACAAGTATACCGGTTT
3586 TATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
130 TATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATA-TTTTGGTCCA
*
3651 GAATAA
194 GAATGA
* *
3657 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATGTATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
3722 CGAAA-CCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTAT--TGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
3784 ATGAGAGAATAGGTCTAAATAATGTTTCGACACTTTTTTAGTCTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATA-TTTTGGTCCAG
3849 AATGA
195 AATGA
* * *
3854 ATGGCAAATAGGGTGCAACAATAAAGTATCGATCCATATATAAAAAGTGTTGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
3919 CGAAACCCATAAGTATAATGTAATAGGTACTTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
3984 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTGGTCCAGA
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTGGTCCAGA
4049 TTTAAATATC
Statistics
Matches: 552, Mismatches: 27, Indels: 19
0.92 0.05 0.03
Matches are distributed among these distances:
192 11 0.02
193 47 0.09
194 24 0.04
196 13 0.02
197 155 0.28
198 104 0.19
199 51 0.09
200 132 0.24
201 15 0.03
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (199 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTGGTCCAGA
ATGA
Found at i:3993 original size:397 final size:391
Alignment explanation
Indices: 3264--4048 Score: 1295
Period size: 397 Copynumber: 2.0 Consensus size: 391
3254 AATTTACAAT
* *
3264 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAGAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
3329 CGAACCCAAAGTATAATGTAATATAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTATGAG
66 CGAAACCAAAGTATAATGTAATATAATTTTTCAATCTAACCGGTACAAGTATA-CGGTTTATGAG
* *
3394 AGAATATGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTGGTCCAGAATGAA
130 AGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTCTGTGTCGATATTTTGGTCCAGAATGAA
* * *
3459 TGGCAAACGGATGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCGATAAACATCGA
195 TGGCAAAAGGATGCAACAATAAAGTATCGATCCATATATAAAAAGTGTCGATCCATAAACATCGA
*
3524 AACCCATAAGTATAATGTAATAGGTAATTTTTCAATCAAAACCGGTACAAGTATATCGGTTTTAT
260 AACCCATAAGTATAATGTAATAGGTAATTTTTCAATCAAAACCGGTACAAGTATACCGGTTTTAT
3589 GAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAA
325 GAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATA-TTTTGGTCCAGAA
3654 TAA
389 TAA
* *
3657 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATGTATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
3722 CGAAACCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTAT-TGGTTTTAT
66 CGAAACCA-AAGTATAATGTAATA--TAATTTTTCAATCTAACCGGTACAAGTATACGG-TTTAT
* *
3786 GAGAGAATAGGTCTAAATAATGTTTCGACACTTTTTTAGTCTGTGTCGATATTTTTGGTCCAGAA
127 GAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTCTGTGTCGATA-TTTTGGTCCAGAA
* *
3851 TGAATGGCAAATAGGGTGCAACAATAAAGTATCGATCCATATATAAAAAGTGTTGATCCCATAAA
191 TGAATGGCAAA-AGGATGCAACAATAAAGTATCGATCCATATATAAAAAGTGTCGAT-CCATAAA
* *
3916 CATCGAAACCCATAAGTATAATGTAATAGGTACTTTTTCAATC-TAACCGGTACAAGTATACCGG
254 CATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCAAAACCGGTACAAGTATACCGG
*
3980 TTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTGGTC
319 TTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTGGTC
4045 CAGA
384 CAGA
4049 TTTAAATATC
Statistics
Matches: 365, Mismatches: 20, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
393 68 0.19
394 17 0.05
395 52 0.14
396 64 0.18
397 116 0.32
398 48 0.13
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (391 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCAAAGTATAATGTAATATAATTTTTCAATCTAACCGGTACAAGTATACGGTTTATGAGA
GAATAGGTCTAAATAATGTATCGACACTTTTGTAGTCTGTGTCGATATTTTGGTCCAGAATGAAT
GGCAAAAGGATGCAACAATAAAGTATCGATCCATATATAAAAAGTGTCGATCCATAAACATCGAA
ACCCATAAGTATAATGTAATAGGTAATTTTTCAATCAAAACCGGTACAAGTATACCGGTTTTATG
AGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTGGTCCAGAATA
A
Found at i:5529 original size:12 final size:12
Alignment explanation
Indices: 5507--5543 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
5497 CAAGCAGTCA
*
5507 ATGAAGATGAAG
1 ATGACGATGAAG
*
5519 CTGACGATGAAG
1 ATGACGATGAAG
5531 ATGACGATGAAG
1 ATGACGATGAAG
5543 A
1 A
5544 AGATGATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.43, C:0.08, G:0.32, T:0.16
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:5551 original size:3 final size:3
Alignment explanation
Indices: 5524--5574 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
5514 TGAAGCTGAC
* * * * *
5524 GAT GAA GAT GAC GAT GAA GAA GAT GAT GAT GAT AAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
5572 GAT
1 GAT
5575 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.41, C:0.02, G:0.31, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:7103 original size:118 final size:119
Alignment explanation
Indices: 6866--7105 Score: 403
Period size: 118 Copynumber: 2.0 Consensus size: 119
6856 CGGAACCCAT
*
6866 AATTATAATGTAATAGATAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
*
6931 AGGTCTACAACCTATATCGACACTTTTAATTTTGTGTCGGTACTTTATGTCCAG
66 AGGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCAG
* * *
6985 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACC-GTTTTATTAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
*
7049 A-GTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAG
66 AGGTCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCAG
7103 AAT
1 AAT
7106 GGAAGAAAAA
Statistics
Matches: 114, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
117 20 0.18
118 48 0.42
119 46 0.40
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (119 bp):
AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
AGGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCAG
Found at i:7315 original size:117 final size:120
Alignment explanation
Indices: 7163--7401 Score: 405
Period size: 117 Copynumber: 2.0 Consensus size: 120
7153 ATCGGAACCC
7163 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAGTATACC-GTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATGAGCGAATA
7227 -GTCTACAACCTATAT-GACACTTTTTAAT-TTTGTGTCGGTACTTTATATCCAGA
66 GGTCTACAACCTATATCGACACTTTTTAATATTT-TGTCGGTACTTTATATCCAGA
* *
7280 ATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATGAGCGAATA
* *
7345 GGTCTACAACCTATGTCGACACTTTTTAATATTTTGTCGGTACTTTATGTCCAGA
66 GGTCTACAACCTATATCGACACTTTTTAATATTTTGTCGGTACTTTATATCCAGA
7400 AT
1 AT
7402 GGAAGAAAAA
Statistics
Matches: 114, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
117 47 0.41
118 15 0.13
119 14 0.12
120 35 0.31
121 3 0.03
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.39
Consensus pattern (120 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTTTGTCGGTACTTTATATCCAGA
Found at i:7394 original size:296 final size:298
Alignment explanation
Indices: 6796--7566 Score: 1363
Period size: 296 Copynumber: 2.6 Consensus size: 298
6786 TTTAGTATTG
*
6796 TGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTATCGACATTTACACATCGGAA
1 TGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAA
*
6861 CCCATAATTATAATGTAATAGATAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAG
66 CCC--AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAG
*
6926 CGAATAGGTCTACAACCTATATCGACAC-TTTTAATTTTGTGTCGGTACTTTATGTCCAGAATTA
129 CGAATAGGTCTACAACCTATAT-GACACTTTTTAATTTTGTGTCGGTACTTTATATCCAGAATTA
6990 TAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGTTTTATTAGCGAATAGTCTA
193 TAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGTTTTATTAGCGAATAGTCTA
7055 CAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTA
258 CAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTA
*
7096 TGTCCAGAATGGAAGAAAAATGTATCGATA-CTTGTCAAAAAGTGTCGACATTTACACATCGGAA
1 TGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAA
*
7160 CCC-ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAGTATACC-GTTTTATGAGCG
66 CCCAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCG
7223 AATA-GTCTACAACCTATATGACACTTTTTAATTTTGTGTCGGTACTTTATATCCAGAATTATAA
131 AATAGGTCTACAACCTATATGACACTTTTTAATTTTGTGTCGGTACTTTATATCCAGAATTATAA
7287 TGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTCTAC
196 TGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACC-GTTTTATTAGCGAATA-GTCTAC
*
7352 AACCTATGTCGACACTTTTTAATATTTTGTCGGTACTTTA
259 AACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTA
*
7392 TGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTTAAAAAGTGTCGACATTTACACATCGGAA
1 TGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAA
7457 CCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAG
66 CCC--AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAG
*
7522 CGAATAGGTCTACAACCTATATTGACACTTTTTAATATTGTGTCG
129 CGAATAGGTCTACAACCTATA-TGACACTTTTTAATTTTGTGTCG
7567 CTAATTTTAA
Statistics
Matches: 451, Mismatches: 10, Indels: 17
0.94 0.02 0.04
Matches are distributed among these distances:
293 5 0.01
294 94 0.21
295 32 0.07
296 120 0.27
297 36 0.08
299 36 0.08
300 76 0.17
301 16 0.04
302 14 0.03
303 22 0.05
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (298 bp):
TGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAA
CCCAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCG
AATAGGTCTACAACCTATATGACACTTTTTAATTTTGTGTCGGTACTTTATATCCAGAATTATAA
TGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGTTTTATTAGCGAATAGTCTACAA
CCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTA
Found at i:10315 original size:23 final size:23
Alignment explanation
Indices: 10289--10353 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
10279 AAATATGATG
10289 TAATAGGTAGCGCTTATATAATA
1 TAATAGGTAGCGCTTATATAATA
* *
10312 TAATAGGTAGCGTTTATATAATG
1 TAATAGGTAGCGCTTATATAATA
*
10335 TAATAGGTAGTGCTTATAT
1 TAATAGGTAGCGCTTATAT
10354 TGTAAAGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
TAATAGGTAGCGCTTATATAATA
Found at i:10357 original size:21 final size:22
Alignment explanation
Indices: 10281--10358 Score: 95
Period size: 23 Copynumber: 3.5 Consensus size: 22
10271 ATAGGTAAAA
10281 ATATGATGTAATAGGTAGCGCTT
1 ATAT-ATGTAATAGGTAGCGCTT
* *
10304 ATATAATATAATAGGTAGCGTTT
1 ATAT-ATGTAATAGGTAGCGCTT
*
10327 ATATAATGTAATAGGTAGTGCTT
1 ATAT-ATGTAATAGGTAGCGCTT
10350 ATAT-TGTAA
1 ATATATGTAA
10359 AGTATTTATC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
21 5 0.10
23 44 0.90
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (22 bp):
ATATATGTAATAGGTAGCGCTT
Found at i:23713 original size:34 final size:32
Alignment explanation
Indices: 23633--23721 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 32
23623 TTAGTATTTT
* * *
23633 TTTAAATAGTTATTATTTTTTATATTAATATA
1 TTTATATAATTATTATTTTTTATATAAATATA
* *
23665 TTTATGTAAATATTATTTTATTAT-TAAAATAATA
1 TTTATATAATTATTATTTT-TTATAT-AAAT-ATA
23699 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTT-TTTA
23722 GAATTATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
32 16 0.35
33 7 0.15
34 22 0.48
35 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (32 bp):
TTTATATAATTATTATTTTTTATATAAATATA
Found at i:25473 original size:21 final size:21
Alignment explanation
Indices: 25443--25490 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
25433 GCAGGGGTAC
* *
25443 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
25464 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
25485 ATGCCA
1 ATGCCA
25491 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:25520 original size:21 final size:21
Alignment explanation
Indices: 25494--25587 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
25484 TATGCCATCT
* *
25494 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
25515 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
25536 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
25557 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
25578 CCGCAGGGTT
1 CCGCAGGGTT
25588 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:26169 original size:33 final size:34
Alignment explanation
Indices: 26110--26206 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
26100 AAATGTTTTT
*
26110 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
26144 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
26177 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
26207 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:26213 original size:34 final size:33
Alignment explanation
Indices: 26108--26213 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
26098 ATAAATGTTT
*
26108 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
26142 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
26174 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
26209 TTAAA
1 TTAAA
26214 TTTAAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:26727 original size:126 final size:126
Alignment explanation
Indices: 26502--27105 Score: 1145
Period size: 126 Copynumber: 4.8 Consensus size: 126
26492 TTAAGTTATT
*
26502 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
1 CCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
*
26567 CGTCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGA
66 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGA
26628 CCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
1 CCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
*
26693 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTATTGATATATCTAGTGA
66 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGA
26754 CCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
1 CCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
* *
26819 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTGT
66 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGA
26880 CCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
1 CCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
* *
26945 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTATTGATATATCTAGTGT
66 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGA
27006 CCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
1 CCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
27071 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
27106 CCGATTATAG
Statistics
Matches: 470, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 470 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (126 bp):
CCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGA
Found at i:30218 original size:13 final size:12
Alignment explanation
Indices: 30199--30234 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
30189 ATACATAAAT
30199 ATATTTAATATA
1 ATATTTAATATA
*
30211 TTTATTTAATATA
1 -ATATTTAATATA
30224 ATATTTAATAT
1 ATATTTAATAT
30235 TATAGTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTTAATATA
Found at i:30230 original size:12 final size:13
Alignment explanation
Indices: 30197--30238 Score: 61
Period size: 12 Copynumber: 3.4 Consensus size: 13
30187 AAATACATAA
30197 ATATATTTAATAT
1 ATATATTTAATAT
*
30210 ATTTATTTAATAT
1 ATATATTTAATAT
30223 A-ATATTTAATAT
1 ATATATTTAATAT
30235 -TATA
1 ATATA
30239 GTTATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 13 0.50
13 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:30285 original size:23 final size:23
Alignment explanation
Indices: 30247--30303 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
30237 TAGTTATAAT
30247 TTTTACAT--TATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
30268 TTTTACATAATATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
30291 TTTTACATAATAT
1 TTTTACATAATAT
30304 TATTAATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 8 0.24
23 26 0.76
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (23 bp):
TTTTACATAATATAATCGAAACA
Found at i:30741 original size:19 final size:20
Alignment explanation
Indices: 30697--30733 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
30687 AAAACAAGTG
30697 TTTAAATTATGTATTTTTAT
1 TTTAAATTATGTATTTTTAT
*
30717 TTTAAA-TATTTATTTTT
1 TTTAAATTATGTATTTTT
30734 TTATTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTAAATTATGTATTTTTAT
Found at i:30743 original size:20 final size:20
Alignment explanation
Indices: 30697--30745 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
30687 AAAACAAGTG
*
30697 TTTAAATTATGTATTTTTAT
1 TTTAAAATATGTATTTTTAT
*
30717 TTT-AAATATTTATTTTT-T
1 TTTAAAATATGTATTTTTAT
30735 TATTAAAATAT
1 T-TTAAAATAT
30746 ACGTAATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 2 0.08
19 14 0.56
20 9 0.36
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTAAAATATGTATTTTTAT
Found at i:30801 original size:22 final size:23
Alignment explanation
Indices: 30776--30831 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
30766 TTTAAGATTC
*
30776 ATTTAATTTATTTGTTAAAAA-T
1 ATTTAATTTATTCGTTAAAAATT
*
30798 ATTTATTTTATTCGTTAAAAATT
1 ATTTAATTTATTCGTTAAAAATT
30821 ATTT-ATTTATT
1 ATTTAATTTATT
30832 ATTGATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 25 0.83
23 5 0.17
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (23 bp):
ATTTAATTTATTCGTTAAAAATT
Found at i:32428 original size:2 final size:2
Alignment explanation
Indices: 32421--32447 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
32411 CTCATATCCC
32421 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
32448 GCGGACGCTC
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:32689 original size:44 final size:41
Alignment explanation
Indices: 32611--32692 Score: 112
Period size: 44 Copynumber: 1.9 Consensus size: 41
32601 GCAACGCGAT
*
32611 TTTGAAAAATGTGTTGCGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGATAGTAAAAATGTGTTGCGAGAG
32652 TTTGAAAAACGTGTTGTTGCGATAGTGAAAAAT-TGTTGCGA
1 TTTGAAAAA--TG-TGTTGCGATAGT-AAAAATGTGTTGCGA
32693 TAGTGAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
41 9 0.25
43 2 0.06
44 20 0.56
45 5 0.14
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAGTAAAAATGTGTTGCGAGAG
Found at i:32702 original size:19 final size:20
Alignment explanation
Indices: 32613--32703 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
32603 AACGCGATTT
32613 TGAAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
* *
32633 T-TAAAATGTGTTGCGAGAG
1 TGAAAAATGTGTTGCGATAG
32652 TTTGAAAAACGTGTTGTTGCGATAG
1 --TGAAAAA--TG-TGTTGCGATAG
32677 TGAAAAAT-TGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
32696 TGAAAAAT
1 TGAAAAAT
32704 CCAAAATAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
19 35 0.57
20 1 0.02
21 2 0.03
22 4 0.07
23 7 0.11
24 2 0.03
25 10 0.16
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.32
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:33101 original size:19 final size:19
Alignment explanation
Indices: 33077--33113 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
33067 TGCGATACTG
*
33077 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
*
33096 GAGATCGCATTGTGATTT
1 GAGATCGCATTGCGATTT
33114 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:34417 original size:15 final size:15
Alignment explanation
Indices: 34397--34427 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
34387 CAACGGCCAG
34397 AGAGCAAAGTACGGC
1 AGAGCAAAGTACGGC
34412 AGAGCAAAGTACGGC
1 AGAGCAAAGTACGGC
34427 A
1 A
34428 TTCCTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.32, T:0.06
Consensus pattern (15 bp):
AGAGCAAAGTACGGC
Found at i:40226 original size:26 final size:26
Alignment explanation
Indices: 40204--40254 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
40194 TTTTAAATAT
40204 TTTTATATTTAAAATTTTATAAATTC
1 TTTTATATTTAAAATTTTATAAATTC
*
40230 TTTTTTATTTAAAATTTTATAAATT
1 TTTTATATTTAAAATTTTATAAATT
40255 TACCCATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTATATTTAAAATTTTATAAATTC
Found at i:41941 original size:31 final size:29
Alignment explanation
Indices: 41890--41947 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
41880 ATCGCATTGG
41890 ATACTTTTTCAAAGCACAAGTACCACATA
1 ATACTTTTTCAAAGCACAAGTACCACATA
*
41919 ATACATTTTTACAAAGTC-CAAGTATCACA
1 ATAC-TTTTT-CAAAG-CACAAGTACCACA
41948 GATATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 4 0.16
30 5 0.20
31 15 0.60
32 1 0.04
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.29
Consensus pattern (29 bp):
ATACTTTTTCAAAGCACAAGTACCACATA
Found at i:46127 original size:2 final size:2
Alignment explanation
Indices: 46114--46146 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
46104 ACTTTTACAC
46114 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46147 CTTTTTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46832 original size:2 final size:2
Alignment explanation
Indices: 46827--46860 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
46817 AAAAACACAC
46827 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
46861 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:46865 original size:2 final size:2
Alignment explanation
Indices: 46860--46924 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
46850 TCTCTCTCTC
46860 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46902 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
46925 CAAGCGTATT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47427 original size:13 final size:13
Alignment explanation
Indices: 47409--47437 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
47399 TTGGGATTGC
47409 GATGAAACTCAAA
1 GATGAAACTCAAA
47422 GATGAAACTCAAA
1 GATGAAACTCAAA
47435 GAT
1 GAT
47438 CAATCGATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.17
Consensus pattern (13 bp):
GATGAAACTCAAA
Done.