Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007910.1 Hibiscus syriacus cultivar Beakdansim tig00110306_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: 704475
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:667358 original size:21 final size:21
Alignment explanation
Indices: 667334--667373 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
667324 TTTCCTCTGG
*
667334 TTTTATAAAAGTTTTCTTTTC
1 TTTTACAAAAGTTTTCTTTTC
*
667355 TTTTCCAAAAGTTTTCTTT
1 TTTTACAAAAGTTTTCTTT
667374 GTTGTACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTTACAAAAGTTTTCTTTTC
Found at i:673795 original size:40 final size:37
Alignment explanation
Indices: 673758--673858 Score: 102
Period size: 37 Copynumber: 2.7 Consensus size: 37
673748 TTTTATTATC
673758 AAAATAATAAATTTTATCAATTATATTAATTAATAT-T
1 AAAATAATAAATTTTAT-AATTATATTAATTAATATAT
* *
673795 AAAATAATAATATTATTATAA-TATTATAAATTAAAATATT
1 AAAATAATAA-ATT-TTATAATTA-TATTAATTAATATA-T
*
673835 AAAATAA-AAATATTAT-ATTATATT
1 AAAATAATAAATTTTATAATTATATT
673859 TTAAAAATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
36 4 0.07
37 18 0.33
38 18 0.33
39 6 0.11
40 8 0.15
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (37 bp):
AAAATAATAAATTTTATAATTATATTAATTAATATAT
Found at i:673807 original size:14 final size:14
Alignment explanation
Indices: 673788--673849 Score: 65
Period size: 14 Copynumber: 4.6 Consensus size: 14
673778 TTATATTAAT
673788 TAATATTAAAATAA
1 TAATATTAAAATAA
**
673802 TAATATTATTATAA
1 TAATATTAAAATAA
* *
673816 TATTA-TAAATTAA
1 TAATATTAAAATAA
673829 -AATATTAAAATAA
1 TAATATTAAAATAA
*
673842 AAATATTA
1 TAATATTA
673850 TATTATATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
12 3 0.08
13 12 0.32
14 23 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATATTAAAATAA
Found at i:673820 original size:65 final size:65
Alignment explanation
Indices: 673688--673830 Score: 146
Period size: 65 Copynumber: 2.2 Consensus size: 65
673678 CTAGATCATT
* ** * * **
673688 TTATTAAAATAAAAAATATTATTTATTATACTAATTATTTATTAAGACAAAAATATTATATTTTA
1 TTATCAAAATAAAAAATATTATCAATTATACTAATTATATATTAAAACAAAAATATTATATAATA
* * * * *
673753 TTATCAAAATAATAAATTTTATCAATTATATTAATTA-ATATTAAAATAATAATATTATTATAAT
1 TTATCAAAATAAAAAATATTATCAATTATACTAATTATATATTAAAACAAAAATATTA-TATAAT
673817 A
65 A
*
673818 TTAT-AAATTAAAA
1 TTATCAAAATAAAA
673831 TATTAAAATA
Statistics
Matches: 63, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
64 23 0.37
65 40 0.63
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.45
Consensus pattern (65 bp):
TTATCAAAATAAAAAATATTATCAATTATACTAATTATATATTAAAACAAAAATATTATATAATA
Found at i:675233 original size:18 final size:17
Alignment explanation
Indices: 675210--675261 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
675200 AAATGCGTAG
675210 TTTATCAATAATATTGAT
1 TTTATCAATAATATT-AT
675228 TTTATCAATAAT-TTAT
1 TTTATCAATAATATTAT
*
675244 TATATCATATAATATTAT
1 TTTATCA-ATAATATTAT
675262 ATATTATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 8 0.26
17 7 0.23
18 16 0.52
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTATCAATAATATTAT
Found at i:675258 original size:5 final size:5
Alignment explanation
Indices: 675245--675307 Score: 53
Period size: 5 Copynumber: 13.2 Consensus size: 5
675235 ATAATTTATT
* * * *
675245 ATATC ATATA ATATT ATATA TTATTA AAATA A-A-A ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATA-TA ATATA ATATA ATATA ATATA ATATA
675294 ATAT- -TATA ATATA A
1 ATATA ATATA ATATA A
675308 CTAAGCATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
3 5 0.11
4 2 0.04
5 37 0.79
6 3 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:675294 original size:18 final size:18
Alignment explanation
Indices: 675273--675307 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
675263 TATTATTAAA
675273 ATAAAAATATAATATAAT
1 ATAAAAATATAATATAAT
* *
675291 ATAATATTATAATATAA
1 ATAAAAATATAATATAA
675308 CTAAGCATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAAAATATAATATAAT
Found at i:675294 original size:39 final size:40
Alignment explanation
Indices: 675245--675353 Score: 107
Period size: 39 Copynumber: 2.8 Consensus size: 40
675235 ATAATTTATT
*
675245 ATATCATATAATATTATATATTATTAAAATAAAAATA-TA
1 ATATAATATAATATTATATATTATTAAAATAAAAATACTA
* * * *
675284 ATATAATATAATATTATAATATAACTAAGCATATAAATACTA
1 ATATAATATAATATTAT-ATATTATTAA-AATAAAAATACTA
* * *
675326 AAAAAATATTATA-T-TATATTATTAAAAT
1 ATATAATATAATATTATATATTATTAAAAT
675354 TATGGGTAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.04
39 24 0.43
40 9 0.16
41 9 0.16
42 12 0.21
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (40 bp):
ATATAATATAATATTATATATTATTAAAATAAAAATACTA
Found at i:676268 original size:6 final size:6
Alignment explanation
Indices: 676257--676471 Score: 261
Period size: 6 Copynumber: 33.7 Consensus size: 6
676247 TGAGTGGTTT
676257 AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG
1 AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG
676305 AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG
1 AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG
* *
676353 AAGAAG AAGAAG AAGAAG AAGAAG AGAGAGAG GAGAGAG AGAGAGAG AGGAGAG
1 AAGAAG AAGAAG AAGAAG AAGAAG A-AGA-AG AAGA-AG A-AGA-AG AAGA-AG
* *
676407 AGAGAGAG AGAGAGG AGAGAGAG AGAGGAG AGAGAAG AAGAAG AGAGAAG
1 A-AGA-AG A-AGAAG A-AGA-AG A-AGAAG A-AGAAG AAGAAG A-AGAAG
676457 -AGAAG AAGAAG AAGA
1 AAGAAG AAGAAG AAGA
676472 CCAAAATCAC
Statistics
Matches: 194, Mismatches: 8, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
5 5 0.03
6 130 0.67
7 35 0.18
8 24 0.12
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (6 bp):
AAGAAG
Found at i:676271 original size:9 final size:9
Alignment explanation
Indices: 676257--676471 Score: 261
Period size: 9 Copynumber: 22.4 Consensus size: 9
676247 TGAGTGGTTT
676257 AAGAAGAAG
1 AAGAAGAAG
676266 AAGAAGAAG
1 AAGAAGAAG
676275 AAGAAGAAG
1 AAGAAGAAG
676284 AAGAAGAAG
1 AAGAAGAAG
676293 AAGAAGAAG
1 AAGAAGAAG
676302 AAGAAGAAG
1 AAGAAGAAG
676311 AAGAAGAAG
1 AAGAAGAAG
676320 AAGAAGAAG
1 AAGAAGAAG
676329 AAGAAGAAG
1 AAGAAGAAG
676338 AAGAAGAAG
1 AAGAAGAAG
676347 AAGAAGAAG
1 AAGAAGAAG
676356 AAGAAGAAG
1 AAGAAGAAG
676365 AAGAAGAAG
1 AAGAAGAAG
676374 AAGAGAGAGAG
1 AAGA-AGA-AG
*
676385 GAGAGAGAGAG
1 AAGA-AGA-AG
*
676396 AGAGAGGAGAG
1 A-AGAAGA-AG
676407 AGAGAGAGAGAG
1 A-AGA-AGA-AG
*
676419 AGGAGAGAGAG
1 AAGA-AGA-AG
*
676430 AGAGGAGAGAG
1 A-AGAAGA-AG
676441 AAGAAGAAG
1 AAGAAGAAG
676450 AGAGAAG-AG
1 A-AGAAGAAG
676459 AAGAAGAAG
1 AAGAAGAAG
676468 AAGA
1 AAGA
676472 CCAAAATCAC
Statistics
Matches: 191, Mismatches: 8, Indels: 14
0.90 0.04 0.07
Matches are distributed among these distances:
8 5 0.03
9 124 0.65
10 13 0.07
11 39 0.20
12 10 0.05
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (9 bp):
AAGAAGAAG
Found at i:676277 original size:15 final size:15
Alignment explanation
Indices: 676257--676471 Score: 261
Period size: 15 Copynumber: 13.5 Consensus size: 15
676247 TGAGTGGTTT
676257 AAGAAGAAGAAGAAG
1 AAGAAGAAGAAGAAG
676272 AAGAAGAAGAAGAAG
1 AAGAAGAAGAAGAAG
676287 AAGAAGAAGAAGAAG
1 AAGAAGAAGAAGAAG
676302 AAGAAGAAGAAGAAG
1 AAGAAGAAGAAGAAG
676317 AAGAAGAAGAAGAAG
1 AAGAAGAAGAAGAAG
676332 AAGAAGAAGAAGAAG
1 AAGAAGAAGAAGAAG
676347 AAGAAGAAGAAGAAG
1 AAGAAGAAGAAGAAG
676362 AAGAAGAAGAAGAAG
1 AAGAAGAAGAAGAAG
*
676377 AGAGAGAGGAGAGAGAGAG
1 A-AGA-AGAAGA-AGA-AG
*
676396 AGAGAGGAGAGAGAGAGAG
1 A-AGAAGA-AGA-AGA-AG
*
676415 AGAGAGGAGAGAGAGAGAG
1 A-AGAAGA-AGA-AGA-AG
*
676434 GAGAGAGAAGAAGAAG
1 AAGA-AGAAGAAGAAG
676450 AGAGAAG-AGAAGAAG
1 A-AGAAGAAGAAGAAG
676465 AAGAAGA
1 AAGAAGA
676472 CCAAAATCAC
Statistics
Matches: 186, Mismatches: 6, Indels: 16
0.89 0.03 0.08
Matches are distributed among these distances:
14 5 0.03
15 115 0.62
16 7 0.04
17 11 0.06
18 10 0.05
19 38 0.20
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (15 bp):
AAGAAGAAGAAGAAG
Found at i:676382 original size:2 final size:2
Alignment explanation
Indices: 676375--676459 Score: 114
Period size: 2 Copynumber: 46.5 Consensus size: 2
676365 AAGAAGAAGA
676375 AG AG AG AG AG -G AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
676415 AG AG AG -G AG AG AG AG AG AG -G AG AG AG A- AG A- AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
676452 AG A- AG AG A
1 AG AG AG AG A
676460 AGAAGAAGAA
Statistics
Matches: 75, Mismatches: 0, Indels: 16
0.82 0.00 0.18
Matches are distributed among these distances:
1 8 0.11
2 67 0.89
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:676393 original size:13 final size:13
Alignment explanation
Indices: 676375--676454 Score: 116
Period size: 13 Copynumber: 6.5 Consensus size: 13
676365 AAGAAGAAGA
676375 AGAGAGAGAGGAG
1 AGAGAGAGAGGAG
676388 AGAGAGAGA-GAG
1 AGAGAGAGAGGAG
676400 AG-GAGAGA-GAG
1 AGAGAGAGAGGAG
676411 AGAGAGAGAGGAG
1 AGAGAGAGAGGAG
676424 AGAGAGAGAGGAG
1 AGAGAGAGAGGAG
*
676437 AGAGA-AGAAGA-
1 AGAGAGAGAGGAG
676448 AGAGAGA
1 AGAGAGA
676455 AGAGAAGAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
11 16 0.25
12 17 0.27
13 30 0.48
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (13 bp):
AGAGAGAGAGGAG
Found at i:677157 original size:13 final size:15
Alignment explanation
Indices: 677139--677170 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
677129 CTTTGACTTA
677139 GGAATAT-TT-TAAT
1 GGAATATATTGTAAT
677152 GGAATATATTGTAAT
1 GGAATATATTGTAAT
677167 GGAA
1 GGAA
677171 ATTGGTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (15 bp):
GGAATATATTGTAAT
Found at i:678506 original size:15 final size:17
Alignment explanation
Indices: 678476--678513 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
678466 GGCGGTACGA
678476 TTTAGTTTCATATCG-AT
1 TTTA-TTTCATATCGAAT
678493 TTTATTTC-TATCGAAT
1 TTTATTTCATATCGAAT
678509 TTTAT
1 TTTAT
678514 ATTTACGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 5 0.25
16 11 0.55
17 4 0.20
ACGTcount: A:0.24, C:0.11, G:0.08, T:0.58
Consensus pattern (17 bp):
TTTATTTCATATCGAAT
Found at i:679575 original size:20 final size:20
Alignment explanation
Indices: 679550--679622 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
679540 GCAGCCTTCG
679550 TGCATCGATGCATAACAGGA
1 TGCATCGATGCATAACAGGA
* **
679570 TGCATCGATGCAAAACCTTGA
1 TGCATCGATGCATAA-CAGGA
679591 TGCATCGATGCATAGA-AGGA
1 TGCATCGATGCATA-ACAGGA
679611 TGCATCGATGCA
1 TGCATCGATGCA
679623 CTAATTGTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 28 0.62
21 16 0.36
22 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.22
Consensus pattern (20 bp):
TGCATCGATGCATAACAGGA
Found at i:679701 original size:19 final size:20
Alignment explanation
Indices: 679677--679730 Score: 92
Period size: 19 Copynumber: 2.7 Consensus size: 20
679667 CACTAGTGCA
679677 TGCATGGATGCACTGCA-GG
1 TGCATGGATGCACTGCAGGG
679696 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCA-GGG
679717 TGCATGGATGCACT
1 TGCATGGATGCACT
679731 TTGACACCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.20, C:0.20, G:0.37, T:0.22
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGG
Found at i:679878 original size:34 final size:29
Alignment explanation
Indices: 679810--679869 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
679800 AAACTTTGAA
*
679810 TAAATTCAATTAATTCCAAAAACATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
*
679839 TAAATTCAATTCAAGTCCAAATACCATTTTG
1 TAAATTCAATT-AAGTCCAAA-AACATTTTG
679870 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 8 0.30
31 8 0.30
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.37
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:681130 original size:19 final size:20
Alignment explanation
Indices: 681087--681134 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
681077 TCTAAATCCT
*
681087 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
681107 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
681126 TTTTCAAAA
1 TTTTCAAAA
681135 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:681808 original size:23 final size:23
Alignment explanation
Indices: 681778--681831 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
681768 TTCGATAACC
681778 GAACGGTTTGTAAATAGGGGTCG
1 GAACGGTTTGTAAATAGGGGTCG
681801 GAACGGTTTGTAAATAGGGGTCG
1 GAACGGTTTGTAAATAGGGGTCG
*
681824 GAATGGTT
1 GAACGGTT
681832 ATGAGTTTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.26, C:0.07, G:0.39, T:0.28
Consensus pattern (23 bp):
GAACGGTTTGTAAATAGGGGTCG
Found at i:682064 original size:32 final size:33
Alignment explanation
Indices: 682003--682071 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
681993 ACCTTACAAC
* * *
682003 TCCCTAGTTTTTCCGGGCTAAAACTAGAACCTT
1 TCCCTAGCTTTTACGGGATAAAACTAGAACCTT
*
682036 TCCCTAGCTTTTACGGGAT-AAGCTAGAACCTT
1 TCCCTAGCTTTTACGGGATAAAACTAGAACCTT
682068 TCCC
1 TCCC
682072 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 16 0.50
33 16 0.50
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (33 bp):
TCCCTAGCTTTTACGGGATAAAACTAGAACCTT
Found at i:682471 original size:21 final size:20
Alignment explanation
Indices: 682427--682500 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
682417 GCAGCCTTTG
*
682427 TGCATAGATGCACAACAGGA
1 TGCATCGATGCACAACAGGA
**
682447 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCACAA-CAGGA
682468 TGCATCGATGCACATA-AGGA
1 TGCATCGATGCACA-ACAGGA
*
682488 TGCATTGATGCAC
1 TGCATCGATGCAC
682501 TAATTGCATT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 28 0.61
21 17 0.37
22 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (20 bp):
TGCATCGATGCACAACAGGA
Found at i:682546 original size:20 final size:19
Alignment explanation
Indices: 682521--682577 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 19
682511 CGGTGTTTGA
682521 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCA-G
*
682541 GTGCATCGATGCACTAGTGCAG
1 GTGCATGGATGCAC---TGCAG
682563 GTGCATGGATGCACT
1 GTGCATGGATGCACT
682578 TTGACACCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 1 0.03
20 13 0.41
22 14 0.44
23 4 0.12
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.25
Consensus pattern (19 bp):
GTGCATGGATGCACTGCAG
Found at i:682568 original size:22 final size:23
Alignment explanation
Indices: 682535--682577 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
682525 ATGGATGCAC
682535 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
682558 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
682578 TTGACACCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:682687 original size:29 final size:31
Alignment explanation
Indices: 682655--682714 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
682645 AAACTTTGAA
*
682655 TAAATTAAATT-AATTCCAAA-AACATTTTG
1 TAAATTAAATTCAAGTCCAAACAACATTTTG
* *
682684 TAAATTCAATTCAAGTCCAAACACCATTTTG
1 TAAATTAAATTCAAGTCCAAACAACATTTTG
682715 CCTTAAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 10 0.38
30 8 0.31
31 8 0.31
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.35
Consensus pattern (31 bp):
TAAATTAAATTCAAGTCCAAACAACATTTTG
Found at i:683785 original size:7 final size:7
Alignment explanation
Indices: 683773--683797 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
683763 TTAGAAAAAA
683773 AAAACTC
1 AAAACTC
683780 AAAACTC
1 AAAACTC
683787 AAAACTC
1 AAAACTC
683794 AAAA
1 AAAA
683798 GAAAACTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.24, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAACTC
Found at i:685395 original size:30 final size:32
Alignment explanation
Indices: 685334--685395 Score: 92
Period size: 30 Copynumber: 2.0 Consensus size: 32
685324 ATTTTATTCG
*
685334 AATTCCTTAAATTATTTCATCATAACGTTCTA
1 AATTCCTTAAATTATTTCATCATAACATTCTA
*
685366 AATT-CTTAAATTA-TTCATCCTAACATTCTA
1 AATTCCTTAAATTATTTCATCATAACATTCTA
685396 CATTATTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 15 0.54
31 9 0.32
32 4 0.14
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (32 bp):
AATTCCTTAAATTATTTCATCATAACATTCTA
Found at i:686955 original size:17 final size:18
Alignment explanation
Indices: 686921--686957 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
686911 TTTAAGATTT
686921 TATATTCGATTCAAAATTA
1 TATATTCGATTC-AAATTA
686940 TATATTCGATTC-AATTA
1 TATATTCGATTCAAATTA
686957 T
1 T
686958 TCAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATTCGATTCAAATTA
Found at i:687258 original size:18 final size:18
Alignment explanation
Indices: 687232--687297 Score: 123
Period size: 18 Copynumber: 3.7 Consensus size: 18
687222 AAGCAAAATG
*
687232 GGTACCGATACCATGACA
1 GGTATCGATACCATGACA
687250 GGTATCGATACCATGACA
1 GGTATCGATACCATGACA
687268 GGTATCGATACCATGACA
1 GGTATCGATACCATGACA
687286 GGTATCGATACC
1 GGTATCGATACC
687298 TATTTACATA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (18 bp):
GGTATCGATACCATGACA
Found at i:695365 original size:14 final size:13
Alignment explanation
Indices: 695337--695363 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
695327 TATAATGGGG
695337 AGTAATTTTTCAA
1 AGTAATTTTTCAA
695350 AGTAATTTTTCAA
1 AGTAATTTTTCAA
695363 A
1 A
695364 AGACAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
AGTAATTTTTCAA
Found at i:695472 original size:13 final size:13
Alignment explanation
Indices: 695454--695480 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
695444 AAATGTTTAA
695454 TGAATTTTAAGAT
1 TGAATTTTAAGAT
695467 TGAATTTTAAGAT
1 TGAATTTTAAGAT
695480 T
1 T
695481 TTATATTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TGAATTTTAAGAT
Found at i:695516 original size:15 final size:16
Alignment explanation
Indices: 695481--695516 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
695471 TTTTAAGATT
695481 TTATATTCGATTCAAAA
1 TTATATTCGATTC-AAA
695498 TTATATTCGATTC-AA
1 TTATATTCGATTCAAA
695513 TTAT
1 TTAT
695517 TCGAATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
17 13 0.68
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (16 bp):
TTATATTCGATTCAAA
Found at i:696858 original size:175 final size:176
Alignment explanation
Indices: 696562--696933 Score: 649
Period size: 175 Copynumber: 2.1 Consensus size: 176
696552 CAATAAATGA
*
696562 ACATAAACGAACATAAATGAATTTTAGGATTATATTTTATTTAATTGTTTTGATCTTTTTTATTT
1 ACATAAATGAACATAAATGAATTTTAGGATTATATTTTATTTAATTGTTTTGATCTTTTTTATTT
* * * *
696627 GTATTTAAAATTAATTGAGTTTTAAAATATTTATGGGTATCAGATTAAATTTTATTGGGCTTTAA
66 GAATTTAAAATTAATTGAATTGTAAAATATTTATGGGTATCAGATTAAAATTTATTGGGCTTTAA
696692 TATTTTAAA-GGGTCTAGAGAGATTGGTCTAAACATAAATGAACGC
131 TATTTTAAATGGGTCTAGAGAGATTGGTCTAAACATAAATGAACGC
696737 ACATAAATGAACATAAATGAATTTTAGGATTATATTTTATTTAATTGTTTTGATCTTTTTTATTT
1 ACATAAATGAACATAAATGAATTTTAGGATTATATTTTATTTAATTGTTTTGATCTTTTTTATTT
*
696802 GAATTTAAAATTAATTGAATTGTAAAATATTTATGGGTATCATATTAAAATTTATTGGGCTTTAA
66 GAATTTAAAATTAATTGAATTGTAAAATATTTATGGGTATCAGATTAAAATTTATTGGGCTTTAA
*
696867 TATTTTAAATGGGTCTAGAGAGATTGGTCTACACATAAATGAACGC
131 TATTTTAAATGGGTCTAGAGAGATTGGTCTAAACATAAATGAACGC
*
696913 ATATAAACT-AACATAAATGAA
1 ACATAAA-TGAACATAAATGAA
696934 CATAAACAAA
Statistics
Matches: 187, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
175 133 0.71
176 53 0.28
177 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.42
Consensus pattern (176 bp):
ACATAAATGAACATAAATGAATTTTAGGATTATATTTTATTTAATTGTTTTGATCTTTTTTATTT
GAATTTAAAATTAATTGAATTGTAAAATATTTATGGGTATCAGATTAAAATTTATTGGGCTTTAA
TATTTTAAATGGGTCTAGAGAGATTGGTCTAAACATAAATGAACGC
Found at i:696931 original size:24 final size:24
Alignment explanation
Indices: 696899--697013 Score: 126
Period size: 24 Copynumber: 4.8 Consensus size: 24
696889 ATTGGTCTAC
* *
696899 ACATAAATGAACGCATATAAACT-A
1 ACATAAATGAACGAACATAAA-TGA
* * *
696923 ACATAAATGAAC-ATAAACAAACGA
1 ACATAAATGAACGA-ACATAAATGA
**
696947 ACATAAACAAACGAACATAAATGA
1 ACATAAATGAACGAACATAAATGA
*
696971 ACATAAATGAACGAACGTAAATGA
1 ACATAAATGAACGAACATAAATGA
696995 ACATAAATGAACGAACATA
1 ACATAAATGAACGAACATA
697014 GTACCGAACA
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
24 74 0.99
25 1 0.01
ACGTcount: A:0.58, C:0.16, G:0.10, T:0.16
Consensus pattern (24 bp):
ACATAAATGAACGAACATAAATGA
Found at i:696950 original size:14 final size:14
Alignment explanation
Indices: 696931--696967 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
696921 TAACATAAAT
696931 GAACATAAACAAAC
1 GAACATAAACAAAC
696945 GAACATAAACAAAC
1 GAACATAAACAAAC
696959 GAACATAAA
1 GAACATAAA
696968 TGAACATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.65, C:0.19, G:0.08, T:0.08
Consensus pattern (14 bp):
GAACATAAACAAAC
Found at i:696972 original size:10 final size:10
Alignment explanation
Indices: 696959--697006 Score: 60
Period size: 10 Copynumber: 4.4 Consensus size: 10
696949 ATAAACAAAC
696959 GAACATAAAT
1 GAACATAAAT
696969 GAACATAAAT
1 GAACATAAAT
696979 GAACGAACGTAAAT
1 GAAC--A--TAAAT
696993 GAACATAAAT
1 GAACATAAAT
697003 GAAC
1 GAAC
697007 GAACATAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 23 0.68
12 2 0.06
14 9 0.26
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.17
Consensus pattern (10 bp):
GAACATAAAT
Found at i:696972 original size:38 final size:38
Alignment explanation
Indices: 696917--696991 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
696907 GAACGCATAT
*
696917 AAACTAACATAAATGAACATAAACAAACGAACATAAAC
1 AAACGAACATAAATGAACATAAACAAACGAACATAAAC
** *
696955 AAACGAACATAAATGAACATAAATGAACGAACGTAAA
1 AAACGAACATAAATGAACATAAACAAACGAACATAAA
696992 TGAACATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.61, C:0.16, G:0.09, T:0.13
Consensus pattern (38 bp):
AAACGAACATAAATGAACATAAACAAACGAACATAAAC
Found at i:696986 original size:14 final size:13
Alignment explanation
Indices: 696931--697013 Score: 61
Period size: 14 Copynumber: 6.5 Consensus size: 13
696921 TAACATAAAT
*
696931 GAACATAAACAAAC
1 GAACATAAA-TAAC
*
696945 GAACATAAACAAAC
1 GAACATAAA-TAAC
696959 GAACATAAAT---
1 GAACATAAATAAC
696969 GAACATAAATGAAC
1 GAACATAAAT-AAC
*
696983 GAACGTAAAT---
1 GAACATAAATAAC
696993 GAACATAAATGAAC
1 GAACATAAAT-AAC
697007 GAACATA
1 GAACATA
697014 GTACCGAACA
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
10 19 0.33
14 39 0.67
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.13
Consensus pattern (13 bp):
GAACATAAATAAC
Found at i:702777 original size:19 final size:18
Alignment explanation
Indices: 702755--702809 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 18
702745 TTCTTTTGAA
702755 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
702773 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
702792 TGTCTTTTTCTTTT-TTTT
1 T-TCTTTTTCTTTTCTTTT
702810 GCACTCCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
18 12 0.36
19 14 0.42
20 7 0.21
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:702797 original size:14 final size:12
Alignment explanation
Indices: 702755--702807 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 12
702745 TTCTTTTGAA
*
702755 TTCTTTT-TCTT
1 TTCTTTTCTTTT
702766 TTCTTTTCTTCTT
1 TTCTTTTCTT-TT
702779 TTCTTCTTCTTTT
1 TTCTT-TTCTTTT
702792 TGTCTTTTTCTTTT
1 T-TC-TTTTCTTTT
702806 TT
1 TT
702808 TTGCACTCCA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
11 7 0.19
12 1 0.03
13 11 0.31
14 15 0.42
15 2 0.06
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (12 bp):
TTCTTTTCTTTT
Done.