Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009036.1 Hibiscus syriacus cultivar Beakdansim tig00112443_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: 1934717
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1844304 original size:3 final size:3
Alignment explanation
Indices: 1844296--1844350 Score: 83
Period size: 3 Copynumber: 18.0 Consensus size: 3
1844286 GATTCATTTG
* *
1844296 ATT ATT ATT ATT ATT ATT ATT ATT ATT AAT ATT AAT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
1844342 ATT ATT ATT
1 ATT ATT ATT
1844351 TAATAAATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1856556 original size:31 final size:32
Alignment explanation
Indices: 1856521--1856607 Score: 115
Period size: 31 Copynumber: 2.8 Consensus size: 32
1856511 TAAATTTTTC
*
1856521 AAATTTAATGGTTATTTTATAATA-ATTTGAT
1 AAATTTAATGGTTATTTTATAATATATTTGAG
* *
1856552 AAATTTAATGATTAATTTATAA-ATATTTGAG
1 AAATTTAATGGTTATTTTATAATATATTTGAG
* *
1856583 AAGTTTAATGGTTATTATATAATAT
1 AAATTTAATGGTTATTTTATAATAT
1856608 TTTATTTATA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
30 1 0.02
31 44 0.94
32 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (32 bp):
AAATTTAATGGTTATTTTATAATATATTTGAG
Found at i:1860141 original size:18 final size:19
Alignment explanation
Indices: 1860101--1860145 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
1860091 TTTGGTTCTC
*
1860101 GGAATATAAGATTATCAGTG
1 GGAATAAAAGATTATCAG-G
*
1860121 GGAATAAAAGATTATTA-G
1 GGAATAAAAGATTATCAGG
1860139 GGAATAA
1 GGAATAA
1860146 GATTACTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.47, C:0.02, G:0.24, T:0.27
Consensus pattern (19 bp):
GGAATAAAAGATTATCAGG
Found at i:1863303 original size:16 final size:16
Alignment explanation
Indices: 1863273--1863318 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1863263 TTTTAGTAAT
1863273 TTATTTAATTATTTTAA
1 TTATTTAA-TATTTTAA
*
1863290 TTATTTAATATTTTAT
1 TTATTTAATATTTTAA
*
1863306 TTAATTAAT-TTTT
1 TTATTTAATATTTT
1863319 TTCAGATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTAATATTTTAA
Found at i:1865576 original size:13 final size:13
Alignment explanation
Indices: 1865534--1865578 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
1865524 TATTTAGTAC
*
1865534 TTTTTTATTGTAG
1 TTTTTTATTGTAA
* * *
1865547 TTGTTTATTGGAC
1 TTTTTTATTGTAA
1865560 TTTTTTATTGTAA
1 TTTTTTATTGTAA
1865573 TTTTTT
1 TTTTTT
1865579 TATTATTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.16, C:0.02, G:0.13, T:0.69
Consensus pattern (13 bp):
TTTTTTATTGTAA
Found at i:1870596 original size:20 final size:20
Alignment explanation
Indices: 1870562--1870612 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1870552 TTCAACTCAA
*
1870562 ATATAAAAA-AATAAA-TTC
1 ATATAAAAATATTAAATTTC
1870580 ATGATAAAAATATTAAATTTC
1 AT-ATAAAAATATTAAATTTC
*
1870601 ATCTAAAAATAT
1 ATATAAAAATAT
1870613 AAAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 2 0.07
19 7 0.25
20 14 0.50
21 5 0.18
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (20 bp):
ATATAAAAATATTAAATTTC
Found at i:1870615 original size:19 final size:19
Alignment explanation
Indices: 1870564--1870615 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1870554 CAACTCAAAT
*
1870564 ATAAAAAAATAAATTCATG
1 ATAAAAATATAAATTCATG
1870583 ATAAAAATATTAAATTTCAT-
1 ATAAAAATA-TAAA-TTCATG
*
1870603 CTAAAAATATAAA
1 ATAAAAATATAAA
1870616 AAAAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 12 0.41
20 12 0.41
21 5 0.17
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (19 bp):
ATAAAAATATAAATTCATG
Found at i:1870656 original size:20 final size:19
Alignment explanation
Indices: 1870610--1870656 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1870600 CATCTAAAAA
*
1870610 TATAAAAAAAAATATTTTT
1 TATACAAAAAAATATTTTT
*
1870629 TTTGACAAAAAAATATATTTT
1 TAT-ACAAAAAAATAT-TTTT
1870650 TATACAA
1 TATACAA
1870657 GAATATGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 15 0.65
21 6 0.26
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (19 bp):
TATACAAAAAAATATTTTT
Found at i:1873384 original size:18 final size:19
Alignment explanation
Indices: 1873349--1873385 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1873339 CACGGAATGT
1873349 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1873369 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1873386 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1873828 original size:27 final size:28
Alignment explanation
Indices: 1873768--1873828 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
1873758 CTAAGATATA
1873768 ATATTTATTATATTTTCTATATATAATT
1 ATATTTATTATATTTTCTATATATAATT
* *
1873796 -TATTTATT-TATTTATCT-TTTATATTT
1 ATATTTATTATATTT-TCTATATATAATT
1873822 ATATTTA
1 ATATTTA
1873829 ATTCTACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (28 bp):
ATATTTATTATATTTTCTATATATAATT
Found at i:1879367 original size:7 final size:7
Alignment explanation
Indices: 1879357--1879382 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1879347 TATTTTGAAC
1879357 TTTTAAA
1 TTTTAAA
1879364 TTTTAAA
1 TTTTAAA
1879371 TTTTAAA
1 TTTTAAA
1879378 TTTTA
1 TTTTA
1879383 TGTTCGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTAAA
Found at i:1879508 original size:15 final size:15
Alignment explanation
Indices: 1879487--1879543 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
1879477 AACCGGGTAT
1879487 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
* **
1879502 TGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
1879519 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
1879534 CGGGTACCCG
1 CGGGTACCCG
1879544 TAACATCCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.21, C:0.33, G:0.28, T:0.18
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:1880745 original size:3 final size:3
Alignment explanation
Indices: 1880737--1880765 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1880727 GAAACAAACA
1880737 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1880766 ACAGAGATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1888674 original size:30 final size:30
Alignment explanation
Indices: 1888638--1888697 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1888628 ATGCCTTGAC
1888638 TTATCATGTTGATTTCTGGGTTGGTTAGAA
1 TTATCATGTTGATTTCTGGGTTGGTTAGAA
1888668 TTATCATGTTGATTTCTGGGTTGGTTAGAA
1 TTATCATGTTGATTTCTGGGTTGGTTAGAA
1888698 CCGTTTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.07, G:0.27, T:0.47
Consensus pattern (30 bp):
TTATCATGTTGATTTCTGGGTTGGTTAGAA
Found at i:1890326 original size:2 final size:2
Alignment explanation
Indices: 1890164--1890316 Score: 103
Period size: 2 Copynumber: 79.5 Consensus size: 2
1890154 AATTGAAAAA
* *
1890164 AT AT A- AT AT AT AT A- AT AT A- AT AT A- AGT TT AT AT AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT
* * * *
1890204 AT AT AT AA AT -T AT AT TT AT AA ACT AT AT A- AT -T AT -T AT AA
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * *
1890243 AT -T AT AT AT AT AA AT -T AT GT TT AT AT GA- ACT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT
1890284 AT AT AT AT 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 A
1890317 AGCTATATAT
Statistics
Matches: 118, Mismatches: 17, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
1 11 0.09
2 103 0.87
3 4 0.03
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1890523 original size:19 final size:19
Alignment explanation
Indices: 1890501--1890572 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
1890491 GAGAATATAT
1890501 GGAAATTGAGAATTTAGAG
1 GGAAATTGAGAATTTAGAG
1890520 GGAAATTGAGAAATTTAGAG
1 GGAAATTGAG-AATTTAGAG
** * *
1890540 GG-AATAAAAAATTTTGAAG
1 GGAAATTGAGAATTTAG-AG
1890559 GGAAATTGAGAATT
1 GGAAATTGAGAATT
1890573 GAGATTTTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
18 6 0.14
19 18 0.42
20 19 0.44
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.26
Consensus pattern (19 bp):
GGAAATTGAGAATTTAGAG
Found at i:1890536 original size:20 final size:20
Alignment explanation
Indices: 1890501--1890570 Score: 83
Period size: 19 Copynumber: 3.6 Consensus size: 20
1890491 GAGAATATAT
1890501 GGAAATTGAG-AATTTAGAG
1 GGAAATTGAGAAATTTAGAG
1890520 GGAAATTGAGAAATTTAGAG
1 GGAAATTGAGAAATTTAGAG
* * *
1890540 GG-AA-TAAAAAATTTTGAAG
1 GGAAATTGAGAAATTTAG-AG
1890559 GGAAATTGAGAA
1 GGAAATTGAGAA
1890571 TTGAGATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
18 9 0.21
19 16 0.38
20 13 0.31
21 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAAATTGAGAAATTTAGAG
Found at i:1890854 original size:10 final size:9
Alignment explanation
Indices: 1890836--1890944 Score: 74
Period size: 8 Copynumber: 12.6 Consensus size: 9
1890826 ATTTATATTA
1890836 ATATAGTAT
1 ATATAGTAT
1890845 ATATATGTAT
1 ATATA-GTAT
* *
1890855 GTATAACTA-
1 ATAT-AGTAT
1890864 ATATAAGTAAT
1 ATAT-AGT-AT
*
1890875 CTATAG-ATT
1 ATATAGTA-T
*
1890884 TTATA-TAT
1 ATATAGTAT
1890892 ATATA-TAT
1 ATATAGTAT
1890900 ATATA-TAT
1 ATATAGTAT
1890908 ATATA-TAT
1 ATATAGTAT
1890916 ATATA-TAT
1 ATATAGTAT
1890924 ATATA-TAT
1 ATATAGTAT
1890932 ATATA-TAT
1 ATATAGTAT
1890940 ATATA
1 ATATA
1890945 TTAGAAACAC
Statistics
Matches: 87, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
8 54 0.62
9 17 0.20
10 12 0.14
11 4 0.05
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (9 bp):
ATATAGTAT
Found at i:1890892 original size:2 final size:2
Alignment explanation
Indices: 1890885--1890945 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1890875 CTATAGATTT
1890885 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
1890927 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1890946 TAGAAACACT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1900672 original size:14 final size:14
Alignment explanation
Indices: 1900634--1900672 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1900624 CTAGATCGTG
*
1900634 AACCCTAAACCTTT
1 AACCCTAAACCTTC
* *
1900648 AACCTTCAACCTTC
1 AACCCTAAACCTTC
1900662 AACCCTAAACC
1 AACCCTAAACC
1900673 ATAAACTATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.41, G:0.00, T:0.23
Consensus pattern (14 bp):
AACCCTAAACCTTC
Found at i:1900747 original size:19 final size:20
Alignment explanation
Indices: 1900702--1900763 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
1900692 TATAGTACAT
* * *
1900702 GTATGTATAAACCATGTATA
1 GTATATATAAACTATATATA
1900722 GTATATATAAACTATATATA
1 GTATATATAAACTATATATA
* *
1900742 -TATATATAAACTTTATAAA
1 GTATATATAAACTATATATA
1900761 GTA
1 GTA
1900764 AATTACTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
19 17 0.47
20 19 0.53
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (20 bp):
GTATATATAAACTATATATA
Found at i:1900850 original size:49 final size:49
Alignment explanation
Indices: 1900747--1900850 Score: 120
Period size: 48 Copynumber: 2.1 Consensus size: 49
1900737 ATATATATAT
* * ** **
1900747 ATAAACTTTATAAAGTAAATTACTTATATAGTTTATAGAAACACTATGC
1 ATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAACACTAACC
*
1900796 ATAAACTATATAAAGT-AATAAAATATATAGTTTATAGAAACCCTAAACC
1 ATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAACACT-AACC
*
1900845 CTAAAC
1 ATAAAC
1900851 CAAAAATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 24 0.52
49 22 0.48
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (49 bp):
ATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAACACTAACC
Found at i:1901277 original size:2 final size:2
Alignment explanation
Indices: 1901265--1901332 Score: 86
Period size: 2 Copynumber: 34.0 Consensus size: 2
1901255 ATAAACCAAG
* *
1901265 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA TA -A CA 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
1901308 TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1901333 AAGTAAATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
1 2 0.03
2 54 0.92
3 3 0.05
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1901277 original size:20 final size:20
Alignment explanation
Indices: 1901245--1901334 Score: 70
Period size: 19 Copynumber: 4.8 Consensus size: 20
1901235 AATTTATATA
*
1901245 ATAT-GTATGTATAAACCA-
1 ATATAGTATATATAAACCAT
*
1901263 AGTATAGTATATATAAACTAT
1 A-TATAGTATATATAAACCAT
1901284 ATATA-TATATAT-AA-CAT
1 ATATAGTATATATAAACCAT
* *
1901301 ATATA-TATATATATA-TAT
1 ATATAGTATATATAAACCAT
1901319 ATATA-TAATATATAAA
1 ATATAGT-ATATATAAA
1901335 GTAAATAAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
17 14 0.23
18 12 0.20
19 18 0.30
20 16 0.26
21 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (20 bp):
ATATAGTATATATAAACCAT
Found at i:1901294 original size:19 final size:19
Alignment explanation
Indices: 1901265--1901334 Score: 92
Period size: 19 Copynumber: 3.7 Consensus size: 19
1901255 ATAAACCAAG
1901265 TATAGTATATATAAACTATA
1 TATA-TATATATAAACTATA
1901285 TATATATATAT-AAC-ATA
1 TATATATATATAAACTATA
*
1901302 TATATATATATATA-TATA
1 TATATATATATAAACTATA
1901320 TATATAATATATAAA
1 TATAT-ATATATAAA
1901335 GTAAATAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
17 14 0.31
18 12 0.27
19 15 0.33
20 4 0.09
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (19 bp):
TATATATATATAAACTATA
Found at i:1901426 original size:7 final size:7
Alignment explanation
Indices: 1901416--1901480 Score: 58
Period size: 7 Copynumber: 9.3 Consensus size: 7
1901406 TAGTTTATAG
1901416 AAACCCT
1 AAACCCT
1901423 AAACCCT
1 AAACCCT
1901430 AAACCCT
1 AAACCCT
**
1901437 AAACTTT
1 AAACCCT
*
1901444 AAACCTT
1 AAACCCT
**
1901451 AAATACT
1 AAACCCT
*
1901458 AACCCCT
1 AAACCCT
*
1901465 AAACCAT
1 AAACCCT
*
1901472 AAACTCT
1 AAACCCT
1901479 AA
1 AA
1901481 TATAAATGGA
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (7 bp):
AAACCCT
Found at i:1901843 original size:15 final size:15
Alignment explanation
Indices: 1901825--1901860 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
1901815 ATAAACCATG
1901825 TATAGTATATAT-AAC
1 TATA-TATATATAAAC
1901840 TATATATATATAAAC
1 TATATATATATAAAC
1901855 TATATA
1 TATATA
1901861 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:1902275 original size:15 final size:15
Alignment explanation
Indices: 1902252--1902285 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1902242 ACCTAATTAA
* *
1902252 TTATGTTTATATAAT
1 TTATATTTAAATAAT
1902267 TTATATTTAAATAAT
1 TTATATTTAAATAAT
1902282 TTAT
1 TTAT
1902286 TAAATAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
TTATATTTAAATAAT
Found at i:1902383 original size:2 final size:2
Alignment explanation
Indices: 1902338--1902374 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1902328 ATATGTAAAC
*
1902338 TA TA TA TA -A AA 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
1902375 AACTATATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1902468 original size:7 final size:7
Alignment explanation
Indices: 1902458--1902518 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
1902448 TAGTTTATAG
1902458 AAACCTT
1 AAACCTT
1902465 AAACCTT
1 AAACCTT
*
1902472 AAACCCT
1 AAACCTT
* *
1902479 AAATCAT
1 AAACCTT
*
1902486 AAACCCT
1 AAACCTT
1902493 AAATCC-T
1 AAA-CCTT
*
1902500 AAACTTT
1 AAACCTT
*
1902507 AAACCAT
1 AAACCTT
1902514 AAACC
1 AAACC
1902519 ATAATGTAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
6 1 0.02
7 41 0.93
8 2 0.05
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23
Consensus pattern (7 bp):
AAACCTT
Found at i:1902481 original size:14 final size:14
Alignment explanation
Indices: 1902458--1902518 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
1902448 TAGTTTATAG
* *
1902458 AAACCTTAAACCTT
1 AAACCCTAAACCAT
*
1902472 AAACCCTAAATCAT
1 AAACCCTAAACCAT
1902486 AAACCCTAAATCC-T
1 AAACCCTAAA-CCAT
**
1902500 AAACTTTAAACCAT
1 AAACCCTAAACCAT
1902514 AAACC
1 AAACC
1902519 ATAATGTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
13 2 0.05
14 35 0.92
15 1 0.03
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
AAACCCTAAACCAT
Found at i:1902509 original size:21 final size:20
Alignment explanation
Indices: 1902462--1902518 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
1902452 TTATAGAAAC
*
1902462 CTTAAACCTTAAACCCTAAA
1 CTTAAACCATAAACCCTAAA
* * *
1902482 TCATAAACCCTAAATCCTAAA
1 -CTTAAACCATAAACCCTAAA
1902503 CTTTAAACCATAAACC
1 C-TTAAACCATAAACC
1902519 ATAATGTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (20 bp):
CTTAAACCATAAACCCTAAA
Found at i:1902705 original size:14 final size:14
Alignment explanation
Indices: 1902686--1902732 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1902676 ATTTTTTCTT
1902686 TATATAAATTAAAC
1 TATATAAATTAAAC
1902700 TATAT-AATT----
1 TATATAAATTAAAC
1902709 TATATAAATTAAAC
1 TATATAAATTAAAC
*
1902723 TATATTAATT
1 TATATAAATT
1902733 TTCCATTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:1902711 original size:23 final size:24
Alignment explanation
Indices: 1902684--1902733 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
1902674 TTATTTTTTC
1902684 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
1902707 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
1902731 TTT
1 TTT
1902734 TCCATTACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:1908054 original size:66 final size:67
Alignment explanation
Indices: 1907955--1908088 Score: 243
Period size: 66 Copynumber: 2.0 Consensus size: 67
1907945 AAGATGGATC
*
1907955 GTTTTACATGCTGAGAGGAAACAATCAGAGAGAACCACTTATCGGAGAAGATATTGGTG-TTACT
1 GTTTTACATGCTGAAAGGAAACAATCAGAGAGAACCACTTATCGGAGAAGATATTGGTGTTTACT
1908019 AT
66 AT
*
1908021 GTTTTACATGCTGAAAGGAAACAATCAGAGAGAACCACTTATCGGAGAAGATGTTGGTGTTTACT
1 GTTTTACATGCTGAAAGGAAACAATCAGAGAGAACCACTTATCGGAGAAGATATTGGTGTTTACT
1908086 AT
66 AT
1908088 G
1 G
1908089 CAGATTATTA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
66 57 0.88
67 8 0.12
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (67 bp):
GTTTTACATGCTGAAAGGAAACAATCAGAGAGAACCACTTATCGGAGAAGATATTGGTGTTTACT
AT
Found at i:1909238 original size:41 final size:42
Alignment explanation
Indices: 1909187--1909281 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
1909177 TTTTTTACTG
* * **
1909187 AAACATCACTAAAGGTCAT-GATATAGTGGCGTTTTACACGT
1 AAACACCACTAAAAGTCATAGATATAGTGGCGTTTTACACAC
* * *
1909228 AAACGCCACTAAAAGTCATATATATAGTGGCGTTTTTCACAC
1 AAACACCACTAAAAGTCATAGATATAGTGGCGTTTTACACAC
1909270 AAACACCACTAA
1 AAACACCACTAA
1909282 GTTTAATTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 16 0.36
42 29 0.64
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (42 bp):
AAACACCACTAAAAGTCATAGATATAGTGGCGTTTTACACAC
Found at i:1909260 original size:42 final size:41
Alignment explanation
Indices: 1909152--1909281 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 41
1909142 ACAAATGCTG
* * * *
1909152 CTAAAATTCATTATATATAGTGGCATTTTTTACTGAAACATCA
1 CTAAAAGTCA-TATATATAGTGGCGTTTTTCACT-AAACACCA
* * * *
1909195 CTAAAGGTCAT-GATATAGTGGCGTTTTACACGTAAACGCCA
1 CTAAAAGTCATATATATAGTGGCGTTTTTCAC-TAAACACCA
*
1909236 CTAAAAGTCATATATATAGTGGCGTTTTTCACACAAACACCA
1 CTAAAAGTCATATATATAGTGGCGTTTTTCAC-TAAACACCA
1909278 CTAA
1 CTAA
1909282 GTTTAATTGA
Statistics
Matches: 71, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
41 32 0.45
42 31 0.44
43 8 0.11
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (41 bp):
CTAAAAGTCATATATATAGTGGCGTTTTTCACTAAACACCA
Found at i:1917222 original size:19 final size:19
Alignment explanation
Indices: 1917198--1917235 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1917188 ATACTACTAT
1917198 GTATAGGGGTATCGATACC
1 GTATAGGGGTATCGATACC
1917217 GTATAGGGGTATCGATACC
1 GTATAGGGGTATCGATACC
1917236 ACTTTGGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (19 bp):
GTATAGGGGTATCGATACC
Found at i:1925762 original size:43 final size:42
Alignment explanation
Indices: 1925710--1925812 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 42
1925700 ATCGATACAG
* **
1925710 GACCAAGGGGTATCGGTACTACTTTGTAGTGTAGTATCAATACC
1 GACC-AGGGGTATCGGTACTACTATGTA-AATAGTATCAATACC
* *
1925754 GACCAGGGGTATCGATACTACTATGTAAATAGTATCAATACT
1 GACCAGGGGTATCGGTACTACTATGTAAATAGTATCAATACC
* *
1925796 GATCA-TGGTATCGGTAC
1 GACCAGGGGTATCGGTAC
1925813 CCAAATTGTA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 10 0.20
42 16 0.31
43 21 0.41
44 4 0.08
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (42 bp):
GACCAGGGGTATCGGTACTACTATGTAAATAGTATCAATACC
Found at i:1928716 original size:16 final size:18
Alignment explanation
Indices: 1928696--1928734 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
1928686 AAATTCCAGA
1928696 ATACCGAAAT-GGTATCG
1 ATACCGAAATGGGTATCG
*
1928713 -TACCGAAGTGGGTATCG
1 ATACCGAAATGGGTATCG
1928730 ATACC
1 ATACC
1928735 ATAGAAGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 8 0.42
17 7 0.37
18 4 0.21
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.23
Consensus pattern (18 bp):
ATACCGAAATGGGTATCG
Found at i:1929352 original size:21 final size:22
Alignment explanation
Indices: 1929302--1929353 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
1929292 GTTGAGGGTT
1929302 CTATGTGGTTCTTCGGGACAAA
1 CTATGTGGTTCTTCGGGACAAA
1929324 GCTATGTGG-TCTTTCGGGACAAA
1 -CTATGTGGTTC-TTCGGGACAAA
1929347 -TATGTGG
1 CTATGTGG
1929354 CACTTCGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.25
22 2 0.07
23 19 0.68
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (22 bp):
CTATGTGGTTCTTCGGGACAAA
Found at i:1929360 original size:21 final size:21
Alignment explanation
Indices: 1929302--1929360 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
1929292 GTTGAGGGTT
*
1929302 CTATGTGGTTCTTCGGGACAAA
1 CTATGTGG-CCTTCGGGACAAA
*
1929324 GCTATGTGGTCTTTCGGGACAAA
1 -CTATGTGG-CCTTCGGGACAAA
1929347 -TATGTGGCACTTCG
1 CTATGTGGC-CTTCG
1929361 TTGCAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 1 0.03
21 11 0.34
23 20 0.62
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (21 bp):
CTATGTGGCCTTCGGGACAAA
Done.