Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005907.1 Hibiscus syriacus cultivar Beakdansim tig00013876_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: 64288
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:3306 original size:2 final size:2
Alignment explanation
Indices: 3299--3329 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3289 AACGACCGAC
3299 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3330 GCATTTCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18835 original size:94 final size:93
Alignment explanation
Indices: 18729--18905 Score: 284
Period size: 94 Copynumber: 1.9 Consensus size: 93
18719 GCGACATCAT
* * *
18729 ATATTTTATTTTGAAAATTAAGATATTTATTT-TAATGATTTGAAACTCGTTATAATATATTTTT
1 ATATTTTATTTTGAAAATTAAGATATTT-TTTATAATGATTTAAAACTCGTTACAATAT-GTTTT
18793 TATTAAAATTTATTATTTCGGTGAAACAAG
64 TATTAAAATTTATTATTTCGGTGAAACAAG
*
18823 ATATTTTATTTTGAAAATTACGATATTTTTTATAATGATTTAAAACTCGTTACAATATGTTTTTA
1 ATATTTTATTTTGAAAATTAAGATATTTTTTATAATGATTTAAAACTCGTTACAATATGTTTTTA
*
18888 TTGAAATTTATTATTTCG
66 TTAAAATTTATTATTTCG
18906 ATAAAATAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
93 26 0.34
94 51 0.66
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (93 bp):
ATATTTTATTTTGAAAATTAAGATATTTTTTATAATGATTTAAAACTCGTTACAATATGTTTTTA
TTAAAATTTATTATTTCGGTGAAACAAG
Found at i:26417 original size:67 final size:67
Alignment explanation
Indices: 26309--26440 Score: 228
Period size: 67 Copynumber: 2.0 Consensus size: 67
26299 AGTATTTTTT
*
26309 CTAACACATGTATGTTGCAATAATAGGAGAATGATCATGCAACACAACATGTAAAAGGTCCAACA
1 CTAACACATGTATGTTGCAATAATAGGAGAATGATCATGCAACACAACATGTAAAAGCTCCAACA
26374 TA
66 TA
* * *
26376 CTAACACATGTATGTTGCAGTAGTAGGAGAATGATCATGCAACATAACATGTAAAAGCTCCAACA
1 CTAACACATGTATGTTGCAATAATAGGAGAATGATCATGCAACACAACATGTAAAAGCTCCAACA
26441 CAACAATTGT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (67 bp):
CTAACACATGTATGTTGCAATAATAGGAGAATGATCATGCAACACAACATGTAAAAGCTCCAACA
TA
Found at i:28375 original size:32 final size:31
Alignment explanation
Indices: 28339--28414 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
28329 GGGGCCGTGA
*
28339 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** ** *
28371 GGCCTACCCGAGAATGATCTCAGGGCCGCAT
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
28402 AGCCTACCTAAGA
1 GGCCTACCTAAGA
28415 GTCACATTAG
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.28, C:0.32, G:0.25, T:0.16
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:28397 original size:63 final size:62
Alignment explanation
Indices: 28291--28414 Score: 146
Period size: 63 Copynumber: 2.0 Consensus size: 62
28281 CCCTAAGGGA
* *
28291 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGAT-A-GCCTACCTAAGAAC
* *
28354 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCATAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCG-ATAGCCTACCTAAGA
28415 GTCACATTAG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
62 2 0.04
63 49 0.92
64 1 0.02
65 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.18
Consensus pattern (62 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGATAGCCTACCTAAGAAC
Found at i:29296 original size:7 final size:7
Alignment explanation
Indices: 29284--29317 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
29274 GTCAAAGAAA
29284 GTCAACG
1 GTCAACG
29291 GTCAACG
1 GTCAACG
29298 GTCAACG
1 GTCAACG
*
29305 GTCAACA
1 GTCAACG
29312 GTCAAC
1 GTCAAC
29318 AGTCGGGTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:29318 original size:7 final size:7
Alignment explanation
Indices: 29283--29321 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
29273 GGTCAAAGAA
29283 AGTCAAC
1 AGTCAAC
*
29290 GGTCAAC
1 AGTCAAC
*
29297 GGTCAAC
1 AGTCAAC
*
29304 GGTCAAC
1 AGTCAAC
29311 AGTCAAC
1 AGTCAAC
29318 AGTC
1 AGTC
29322 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.15
Consensus pattern (7 bp):
AGTCAAC
Found at i:29338 original size:22 final size:22
Alignment explanation
Indices: 29312--29353 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
29302 ACGGTCAACA
29312 GTCAACAGTCGGGTCGGGTCGG
1 GTCAACAGTCGGGTCGGGTCGG
*
29334 GTCAACGGTCGGGTCGGGTC
1 GTCAACAGTCGGGTCGGGTC
29354 ATACCGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.24, G:0.45, T:0.19
Consensus pattern (22 bp):
GTCAACAGTCGGGTCGGGTCGG
Found at i:29368 original size:9 final size:9
Alignment explanation
Indices: 29350--29448 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
29340 GGTCGGGTCG
*
29350 GGTCATACC
1 GGTCAAACC
29359 GGTCAAACC
1 GGTCAAACC
* *
29368 GATTCAGACC
1 G-GTCAAACC
29378 GGTCAAACC
1 GGTCAAACC
*
29387 GGTTCGAACC
1 GG-TCAAACC
*
29397 GGTTGAAACC
1 GG-TCAAACC
29407 GGTCAAACC
1 GGTCAAACC
29416 GGTCAGAACC
1 GGTCA-AACC
*
29426 GGTTGAAAACC
1 GG-T-CAAACC
29437 GGTCAAACC
1 GGTCAAACC
29446 GGT
1 GGT
29449 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:29378 original size:19 final size:19
Alignment explanation
Indices: 29356--29449 Score: 109
Period size: 19 Copynumber: 4.8 Consensus size: 19
29346 GTCGGGTCAT
* *
29356 ACCGGTCAAACCGATTCAG
1 ACCGGTCAAACCGGTTCAA
*
29375 ACCGGTCAAACCGGTTCGA
1 ACCGGTCAAACCGGTTCAA
*
29394 ACCGGTTGAAACCGG-TCAA
1 ACCGG-TCAAACCGGTTCAA
*
29413 ACCGGTCAGAACCGGTTGAAA
1 ACCGGTCA-AACCGGTT-CAA
29434 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
29450 TCCAGCAGCC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
18 2 0.03
19 35 0.55
20 17 0.27
21 10 0.16
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAA
Found at i:29407 original size:29 final size:31
Alignment explanation
Indices: 29375--29449 Score: 129
Period size: 29 Copynumber: 2.5 Consensus size: 31
29365 ACCGATTCAG
29375 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
29404 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
29434 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
29450 TCCAGCAGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.56
30 16 0.37
31 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:35713 original size:32 final size:31
Alignment explanation
Indices: 35677--35751 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
35667 GGGCCGTGAG
*
35677 GCCTACCTAAGAACACATCTTAAGGCCGCAGA
1 GCCTACCTAAGAA-ACATCTCAAGGCCGCAGA
** ** *
35709 GCCTACCCGAGAATGATCTCAGGGCCGCAGA
1 GCCTACCTAAGAAACATCTCAAGGCCGCAGA
35740 GCCTACCTAAGA
1 GCCTACCTAAGA
35752 GTCACATTAG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.69
32 11 0.31
ACGTcount: A:0.31, C:0.32, G:0.23, T:0.15
Consensus pattern (31 bp):
GCCTACCTAAGAAACATCTCAAGGCCGCAGA
Found at i:35734 original size:63 final size:63
Alignment explanation
Indices: 35628--35751 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
35618 CCCTAAGGGA
* * * *
35628 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAAGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
*
35691 ACATCTTAAGGCC-GCAGAGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAAGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
35752 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 2 0.04
63 49 0.92
64 2 0.04
ACGTcount: A:0.28, C:0.29, G:0.26, T:0.17
Consensus pattern (63 bp):
ACATCTTAAGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:36633 original size:7 final size:7
Alignment explanation
Indices: 36621--36658 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
36611 GTCAAAGAAA
36621 GTCAACG
1 GTCAACG
36628 GTCAACG
1 GTCAACG
36635 GTCAACG
1 GTCAACG
36642 GTCAACG
1 GTCAACG
36649 GTCAACG
1 GTCAACG
36656 GTC
1 GTC
36659 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:36676 original size:22 final size:22
Alignment explanation
Indices: 36648--36690 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
36638 AACGGTCAAC
36648 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
36670 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
36691 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:36705 original size:9 final size:9
Alignment explanation
Indices: 36687--36785 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
36677 GGTCGGGTCG
*
36687 GGTCAGACC
1 GGTCAAACC
36696 GGTCAAACC
1 GGTCAAACC
* *
36705 GATTCAGACC
1 G-GTCAAACC
36715 GGTCAAACC
1 GGTCAAACC
*
36724 GGTTCGAACC
1 GG-TCAAACC
* *
36734 GATTGAAACC
1 G-GTCAAACC
36744 GGTCAAACC
1 GGTCAAACC
36753 GGTCAGAACC
1 GGTCA-AACC
*
36763 GGTTGAAAACC
1 GG-T-CAAACC
36774 GGTCAAACC
1 GGTCAAACC
36783 GGT
1 GGT
36786 TTCCAGCAGC
Statistics
Matches: 71, Mismatches: 13, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
9 36 0.51
10 27 0.38
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:36734 original size:19 final size:19
Alignment explanation
Indices: 36693--36786 Score: 86
Period size: 19 Copynumber: 4.8 Consensus size: 19
36683 GTCGGGTCAG
*
36693 ACCGGTCAAACCGATTC-A
1 ACCGGTCAAACCGGTTCGA
36711 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
* * *
36731 ACCGATTGAAACCGG-TCAA
1 ACCG-GTCAAACCGGTTCGA
36750 ACCGGTCAGAACCGGTT-GAAA
1 ACCGGTCA-AACCGGTTCG--A
36771 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
36787 TCCAGCAGCC
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.03
19 33 0.53
20 18 0.29
21 9 0.15
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:38091 original size:17 final size:16
Alignment explanation
Indices: 38069--38100 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
38059 TTCATTTTTA
38069 CTAATTAAAATAAATAC
1 CTAATTAAAA-AAATAC
38086 CTAATTAAAAAAATA
1 CTAATTAAAAAAATA
38101 TAAAGAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (16 bp):
CTAATTAAAAAAATAC
Found at i:42023 original size:16 final size:15
Alignment explanation
Indices: 41980--42023 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 15
41970 CGGTATCAGC
41980 TTCTCCTCAACTAAA
1 TTCTCCTCAACTAAA
*
41995 TT-TCATC-ACTAAA
1 TTCTCCTCAACTAAA
42008 TTTCTCCTCAACTAAA
1 -TTCTCCTCAACTAAA
42024 GATTAAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 6 0.25
14 6 0.25
15 6 0.25
16 6 0.25
ACGTcount: A:0.34, C:0.30, G:0.00, T:0.36
Consensus pattern (15 bp):
TTCTCCTCAACTAAA
Found at i:43282 original size:19 final size:20
Alignment explanation
Indices: 43253--43299 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
43243 TTTATAATTA
*
43253 ATATT-TTAATA-ATTTTTT
1 ATATTATTAATATATTATTT
43271 ATATTATTAATATATTATTT
1 ATATTATTAATATATTATTT
43291 A-ATTATTAA
1 ATATTATTAA
43300 AAATATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 5 0.19
19 14 0.54
20 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTATTAATATATTATTT
Found at i:43311 original size:29 final size:31
Alignment explanation
Indices: 43279--43377 Score: 116
Period size: 32 Copynumber: 3.3 Consensus size: 31
43269 TTATATTATT
43279 AATATATTA-TTTAATTA-TTAAAAATATAA
1 AATATATTATTTTAATTATTTAAAAATATAA
* *
43308 AATATATTATTTTAA-CAGTTTAAATATAATAA
1 AATATATTATTTTAATTA-TTTAAAAAT-ATAA
* *
43340 AATATATTATTTTAATTATTTTAAAATAT-T
1 AATATATTATTTTAATTATTTAAAAATATAA
43370 AATATATT
1 AATATATT
43378 CAGATTGGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
29 10 0.17
30 13 0.22
31 9 0.15
32 26 0.44
33 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (31 bp):
AATATATTATTTTAATTATTTAAAAATATAA
Found at i:44112 original size:14 final size:14
Alignment explanation
Indices: 44093--44119 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44083 ATTAAAAATT
44093 TATATTTTAGAAAA
1 TATATTTTAGAAAA
44107 TATATTTTAGAAA
1 TATATTTTAGAAA
44120 TCTTTAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
TATATTTTAGAAAA
Found at i:44171 original size:14 final size:16
Alignment explanation
Indices: 44135--44175 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
44125 AATCAATTAG
44135 TTTTAAAATATATATT
1 TTTTAAAATATATATT
**
44151 TAATAAAAT-T-TATT
1 TTTTAAAATATATATT
44165 TTTTAAAATAT
1 TTTTAAAATAT
44176 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 11 0.55
15 2 0.10
16 7 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTTAAAATATATATT
Found at i:44423 original size:2 final size:2
Alignment explanation
Indices: 44418--44462 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
44408 AAGGATAGAA
*
44418 AT AT AT -T AT -T A- AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44457 AT AT AT
1 AT AT AT
44463 CTAAATTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:46109 original size:8 final size:8
Alignment explanation
Indices: 46074--46111 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
46064 TTATTTCACT
46074 TATATGT-
1 TATATGTA
46081 TATAT-TA
1 TATATGTA
*
46088 TATATATA
1 TATATGTA
46096 TATATGTA
1 TATATGTA
46104 TATATGTA
1 TATATGTA
46112 CACATTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (8 bp):
TATATGTA
Found at i:46221 original size:13 final size:14
Alignment explanation
Indices: 46203--46234 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
46193 TATATATATA
46203 TATTTTC-TTATTT
1 TATTTTCATTATTT
46216 TATTTTCATTATTT
1 TATTTTCATTATTT
46230 T-TTTT
1 TATTTT
46235 TATTTTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (14 bp):
TATTTTCATTATTT
Found at i:57735 original size:105 final size:105
Alignment explanation
Indices: 57553--58221 Score: 1214
Period size: 105 Copynumber: 6.4 Consensus size: 105
57543 AGGTTTTACC
*
57553 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACT
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
57618 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
*
57658 CAGAGCCAATTCCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
57723 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
57763 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
57828 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
*
57868 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCACACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
57933 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
* *
57973 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACTACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
58038 ACGAAGGGACCGCTGGTTGTC-ACGAGCATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
** * * *
58077 CAGAGCCAATTTCTGCTTCCCAACGAGGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
58142 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
58182 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
58222 GAAACGATGC
Statistics
Matches: 542, Mismatches: 21, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
104 97 0.18
105 445 0.82
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
Found at i:59786 original size:16 final size:16
Alignment explanation
Indices: 59692--59790 Score: 51
Period size: 16 Copynumber: 5.8 Consensus size: 16
59682 TATTTTACCC
* * *
59692 TATTTCTTTACTTCTT
1 TATTTTTTTATTTCAT
59708 TATTATTATTTATTTACAT
1 TATT-TT-TTTATTT-CAT
*
59727 TATTTTTTT-TCTCTAT
1 TATTTTTTTATTTC-AT
*
59743 TATTGTTATATATATAT-AT
1 TATT-TT-T-T-TATTTCAT
59762 T-TTTATTTTATTTCAT
1 TATTT-TTTTATTTCAT
59778 TATTTTTTTATTT
1 TATTTTTTTATTT
59791 TACATGTACA
Statistics
Matches: 65, Mismatches: 6, Indels: 24
0.68 0.06 0.25
Matches are distributed among these distances:
15 5 0.08
16 24 0.37
17 11 0.17
18 12 0.18
19 10 0.15
20 1 0.02
21 2 0.03
ACGTcount: A:0.22, C:0.07, G:0.01, T:0.70
Consensus pattern (16 bp):
TATTTTTTTATTTCAT
Found at i:62168 original size:20 final size:19
Alignment explanation
Indices: 62126--62186 Score: 88
Period size: 19 Copynumber: 3.2 Consensus size: 19
62116 TGGTTTACGT
62126 AATATAAGATTACCAGTGG
1 AATATAAGATTACCAGTGG
62145 AATATAAGATTACCAGTGGG
1 AATATAAGATTACCAGT-GG
* *
62165 AATAAAAGATTGCCAG-GG
1 AATATAAGATTACCAGTGG
62183 AATA
1 AATA
62187 GGATTACTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
18 6 0.15
19 17 0.44
20 16 0.41
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.23
Consensus pattern (19 bp):
AATATAAGATTACCAGTGG
Done.