Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007495.1 Hibiscus syriacus cultivar Beakdansim tig00020730_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: 426237
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:329689 original size:19 final size:21
Alignment explanation
Indices: 329665--329716 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
329655 TGGCCAAGAG
*
329665 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
329684 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
329705 CATGTATTTTCA
1 CATGTATTTTCA
329717 AAGGGGTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:330418 original size:12 final size:11
Alignment explanation
Indices: 330401--330472 Score: 58
Period size: 12 Copynumber: 6.4 Consensus size: 11
330391 GTGCAAAAAG
330401 AAAGAAAAGACA
1 AAAGAAAAGA-A
*
330413 AAAGAAGAGAA
1 AAAGAAAAGAA
330424 AAA-AAAAGAA
1 AAAGAAAAGAA
*
330434 TAA-AAAAGAAGA
1 AAAGAAAAG-A-A
*
330446 AAATAAAAGAA
1 AAAGAAAAGAA
*
330457 AAAGAGAAAGAG
1 AAAGA-AAAGAA
330469 AAAG
1 AAAG
330473 CAAGCCAAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
10 13 0.26
11 10 0.20
12 22 0.44
13 5 0.10
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.03
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:330433 original size:10 final size:10
Alignment explanation
Indices: 330395--330459 Score: 51
Period size: 11 Copynumber: 6.1 Consensus size: 10
330385 ATTGGAGTGC
330395 AAAAAG-AAA
1 AAAAAGAAAA
*
330404 GAAAAGACAAA
1 AAAAAGA-AAA
*
330415 AGAAGAGAAAA
1 A-AAAAGAAAA
330426 AAAAAGAATAAA
1 AAAAAG-A-AAA
330438 AAAGAAGAAAA
1 AAA-AAGAAAA
*
330449 TAAAAGAAAA
1 AAAAAGAAAA
330459 A
1 A
330460 GAGAAAGAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
9 5 0.11
10 11 0.25
11 13 0.30
12 12 0.27
13 3 0.07
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.03
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:330446 original size:23 final size:23
Alignment explanation
Indices: 330412--330471 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
330402 AAGAAAAGAC
330412 AAAAGAAGAGAAAAAAAAAGAAT
1 AAAAGAAGAGAAAAAAAAAGAAT
*
330435 AAAA-AAGAAGAAAATAAAAGAA-
1 AAAAGAAG-AGAAAAAAAAAGAAT
330457 AAAGAGAAAGAGAAA
1 AAA-AG-AAGAGAAA
330472 GCAAGCCAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
22 6 0.19
23 18 0.56
24 5 0.16
25 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.03
Consensus pattern (23 bp):
AAAAGAAGAGAAAAAAAAAGAAT
Found at i:333000 original size:17 final size:18
Alignment explanation
Indices: 332978--333015 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
332968 ACCTATAGTT
332978 CACATC-TATATAATATG
1 CACATCATATATAATATG
*
332995 CACATCATTATATTATATG
1 CACATCA-TATATAATATG
333014 CA
1 CA
333016 TTATATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.37
Consensus pattern (18 bp):
CACATCATATATAATATG
Found at i:333846 original size:19 final size:21
Alignment explanation
Indices: 333822--333873 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
333812 CGGCCAAGAG
*
333822 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
333841 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
333862 CATGTATTTTCA
1 CATGTATTTTCA
333874 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:334602 original size:16 final size:15
Alignment explanation
Indices: 334552--334615 Score: 60
Period size: 15 Copynumber: 4.2 Consensus size: 15
334542 ATTGGAGTGC
334552 AAAAAGAAAGAAAA-A
1 AAAAAG-AAGAAAATA
*
334567 GACAAAAGAAGAGAA-A
1 -A-AAAAGAAGAAAATA
**
334583 AAAAATCAGAAAATA
1 AAAAAGAAGAAAATA
334598 AAAAAGAAGAAAATA
1 AAAAAGAAGAAAATA
334613 AAA
1 AAA
334616 GAAAAAGAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
14 9 0.22
15 18 0.45
16 8 0.20
17 5 0.12
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.05
Consensus pattern (15 bp):
AAAAAGAAGAAAATA
Found at i:337161 original size:17 final size:18
Alignment explanation
Indices: 337139--337176 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
337129 ACCTATAGTT
337139 CACATC-TATATAATATG
1 CACATCATATATAATATG
*
337156 CACATCATTATATTATATG
1 CACATCA-TATATAATATG
337175 CA
1 CA
337177 TTATATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.37
Consensus pattern (18 bp):
CACATCATATATAATATG
Found at i:338007 original size:19 final size:21
Alignment explanation
Indices: 337983--338034 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
337973 CGGCCAAGAG
* *
337983 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAA
338002 CATGTATTTTCATTTAAAAAA
1 CATGTATTTTCATTTAAAAAA
338023 CATGTATTTTCA
1 CATGTATTTTCA
338035 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 16 0.55
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAA
Found at i:339739 original size:17 final size:17
Alignment explanation
Indices: 339717--339776 Score: 102
Period size: 17 Copynumber: 3.5 Consensus size: 17
339707 TAATTTAATA
339717 AATGAACTAGTTTGATG
1 AATGAACTAGTTTGATG
339734 AATGAACTAGTTTGATG
1 AATGAACTAGTTTGATG
* *
339751 AATGAACTAGTTTAATT
1 AATGAACTAGTTTGATG
339768 AATGAACTA
1 AATGAACTA
339777 CTTCCCTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (17 bp):
AATGAACTAGTTTGATG
Found at i:339789 original size:34 final size:34
Alignment explanation
Indices: 339714--339794 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
339704 AGTTAATTTA
* * **
339714 ATAAATGAACTAGTTTGATGAATGAACTAGTTTG
1 ATAAATGAACTAGTTTAATGAATGAACTACTTCC
* *
339748 ATGAATGAACTAGTTTAATTAATGAACTACTTCC
1 ATAAATGAACTAGTTTAATGAATGAACTACTTCC
*
339782 CTAAATGAACTAG
1 ATAAATGAACTAG
339795 ATGATTTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (34 bp):
ATAAATGAACTAGTTTAATGAATGAACTACTTCC
Found at i:349357 original size:23 final size:23
Alignment explanation
Indices: 349307--349376 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 23
349297 ACACATGCCT
* *
349307 TACATCAAGTGGCATCATA-AGCCT
1 TACATCAAGTGGTAT-A-AGAGCCA
349331 TACATCAAGTGGTATAAGAGCCA
1 TACATCAAGTGGTATAAGAGCCA
* *
349354 TACATCAAGCGGTAATCAGAGCC
1 TACATCAAGTGGT-ATAAGAGCC
349377 TTGGTAGAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 17 0.43
24 22 0.55
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (23 bp):
TACATCAAGTGGTATAAGAGCCA
Found at i:350816 original size:24 final size:25
Alignment explanation
Indices: 350770--350824 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
350760 ACAGTTATGC
*
350770 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
350794 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
350819 CA-TTGA
1 CACTTGA
350825 GGCTCTAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:357003 original size:19 final size:21
Alignment explanation
Indices: 356979--357030 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
356969 CGGCCAAGAG
*
356979 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
*
356998 CATGTATTTTAATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
357019 CATGTATTTTCA
1 CATGTATTTTCA
357031 AAGGGTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 2 0.07
21 16 0.57
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:357782 original size:18 final size:18
Alignment explanation
Indices: 357753--357806 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
357743 AGAAAAAGAC
357753 AAAAGAAGAGAAA-AAATTAG
1 AAAAGAAGA-AAAGAAA--AG
357773 AAAAGAAGAAAAGAAAAG
1 AAAAGAAGAAAAGAAAAG
357791 AAAAGAA-AAAGAGAAA
1 AAAAGAAGAAA-AGAAA
357807 GCAAGCCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.09
18 14 0.44
19 3 0.09
20 12 0.38
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (18 bp):
AAAAGAAGAAAAGAAAAG
Found at i:364110 original size:20 final size:20
Alignment explanation
Indices: 364087--364130 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
364077 TAAGCACTCA
*
364087 AAAAAAAAAAAAAAAGAGAG
1 AAAAAAAAAAAAAAAGAAAG
* *
364107 AAAAAGAAAAGAAAAGAAAG
1 AAAAAAAAAAAAAAAGAAAG
364127 AAAA
1 AAAA
364131 GTTGAAGCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAGAAAG
Found at i:391880 original size:17 final size:19
Alignment explanation
Indices: 391844--391881 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
391834 AACTATATAA
391844 TGCATATAATATAATGATG
1 TGCATATAATATAATGATG
*
391863 TGCATATTATA-AAT-ATG
1 TGCATATAATATAATGATG
391880 TG
1 TG
391882 AACTATAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 3 0.17
19 10 0.56
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (19 bp):
TGCATATAATATAATGATG
Found at i:394675 original size:20 final size:20
Alignment explanation
Indices: 394625--394676 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
394615 TTAATAAAGG
394625 ATAATAATATAAGTAATGAAA
1 ATAATAA-ATAAGTAATGAAA
394646 ATAA-ATAATAAG-AATGAAA
1 ATAATA-AATAAGTAATGAAA
*
394665 TGTAATAAATAA
1 -ATAATAAATAA
394677 AAAGATAGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 7 0.26
20 14 0.52
21 6 0.22
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (20 bp):
ATAATAAATAAGTAATGAAA
Found at i:395936 original size:17 final size:19
Alignment explanation
Indices: 395900--395937 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
395890 AACTATATAA
395900 TGCATATAATATAATGATG
1 TGCATATAATATAATGATG
*
395919 TGCATATTATA-AAT-ATG
1 TGCATATAATATAATGATG
395936 TG
1 TG
395938 AACTATAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 3 0.17
19 10 0.56
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (19 bp):
TGCATATAATATAATGATG
Found at i:398274 original size:15 final size:15
Alignment explanation
Indices: 398254--398356 Score: 165
Period size: 15 Copynumber: 7.0 Consensus size: 15
398244 TAATAAGGTT
398254 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
398269 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
398284 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
398299 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
*
398313 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
398328 A-TTATTTTAAAATA
1 ATTTATTTTAAAATA
*
398342 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
398357 TGGATTGATT
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
14 26 0.32
15 55 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:398321 original size:29 final size:30
Alignment explanation
Indices: 398254--398356 Score: 183
Period size: 29 Copynumber: 3.5 Consensus size: 30
398244 TAATAAGGTT
*
398254 ATTTATTTTAAAATAATTTATTTTAAAATA
1 ATTTATTATAAAATAATTTATTTTAAAATA
398284 ATTTATTATAAAATAATTTATTTT-AAATA
1 ATTTATTATAAAATAATTTATTTTAAAATA
398313 ATTTATTATAAAATAA-TTATTTTAAAATA
1 ATTTATTATAAAATAATTTATTTTAAAATA
398342 ATTTATTATAAAATA
1 ATTTATTATAAAATA
398357 TGGATTGATT
Statistics
Matches: 71, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
28 7 0.10
29 41 0.58
30 23 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTTATTATAAAATAATTTATTTTAAAATA
Found at i:398396 original size:32 final size:31
Alignment explanation
Indices: 398269--398811 Score: 202
Period size: 32 Copynumber: 18.4 Consensus size: 31
398259 TTTTAAAATA
* * *
398269 ATTTATTTTAAAATAATTTATTATA--AAATA
1 ATTTATTTT-AAATAATTTATTATATGGATTG
* *
398299 ATTTATTTTAAATAATTTATTATA--AAAT-
1 ATTTATTTTAAATAATTTATTATATGGATTG
*
398327 AATTATTTTAAAATAATTTATTATAAAATATGGATTG
1 ATTTATTTT-AAATAATTTA-T-T---ATATGGATTG
398364 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
398396 ATTTATTTT--A-AA---A-TATA--GATTG
1 ATTTATTTTAAATAATTTATTATATGGATTG
*
398418 ATTTATTTTATATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
398450 ATTTA-TTT---TAA---A--ATATGGATTG
1 ATTTATTTTAAATAATTTATTATATGGATTG
*
398472 ATTTATTTTAAATAATTTATTAGTATGGGTTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
* *
398504 ATTTATTTTAAAATATGGATTGATT-TAT-TATTG
1 ATTTATTTT-AAATA---ATTTATTATATGGATTG
* * * ** * * * *
398537 TAGTTGTATGGATTAATTTATTTTAAAT-AATTT
1 -ATTTATTTTAAATAATTTA--TTATATGGATTG
* ** * ** *
398570 ATTAGTATGGATTGATTTATTTTAAAATATGAATTG
1 ATT--TAT---TTTAAATAATTTATTATATGGATTG
398606 ATTTA-TTT---TAA---A--ATATGGATTG
1 ATTTATTTTAAATAATTTATTATATGGATTG
* *
398628 ATTTATTTTAAATAATTTATTATTATAGATTA
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
*
398660 ATTCATTTT--A-AA---A-TATA--GATTG
1 ATTTATTTTAAATAATTTATTATATGGATTG
398682 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
398714 ATTTA-TTT--A-AA---A--ATATGGATTG
1 ATTTATTTTAAATAATTTATTATATGGATTG
*
398736 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
*
398768 ATTTATTTTAAATATTTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
398800 ATTTATTTTAAA
1 ATTTATTTTAAA
398812 ATATGGATTG
Statistics
Matches: 400, Mismatches: 39, Indels: 146
0.68 0.07 0.25
Matches are distributed among these distances:
22 68 0.17
23 11 0.03
24 7 0.02
25 11 0.03
26 10 0.03
27 2 0.00
28 15 0.04
29 41 0.10
30 22 0.05
31 11 0.03
32 124 0.31
33 16 0.04
34 16 0.04
35 4 0.01
36 25 0.06
37 17 0.04
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (31 bp):
ATTTATTTTAAATAATTTATTATATGGATTG
Found at i:398401 original size:18 final size:18
Alignment explanation
Indices: 398378--398456 Score: 58
Period size: 22 Copynumber: 4.4 Consensus size: 18
398368 ATTTTAAATA
398378 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
* *
398396 ATTTATTTTAAAATATAGATTG
1 ATTTA--TT--AGTATGGATTG
* *
398418 ATTTATT-TTAT--A-TA
1 ATTTATTAGTATGGATTG
398432 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
398450 ATTTATT
1 ATTTATT
398457 TTAAAATATG
Statistics
Matches: 47, Mismatches: 6, Indels: 16
0.68 0.09 0.23
Matches are distributed among these distances:
14 8 0.17
15 4 0.09
17 4 0.09
18 13 0.28
20 4 0.09
22 14 0.30
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGGATTG
Found at i:398416 original size:22 final size:22
Alignment explanation
Indices: 398391--398483 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
398381 TATTAGTATG
398391 GATTGATTTATTTTAAAATATA
1 GATTGATTTATTTTAAAATATA
398413 GATTGATTTATTTTATATAATTTATTA
1 GATTGATTTATTTTA-A-AA--TA-TA
* *
398440 GTATGGATTGATTTATTTTAAAATATG
1 G-ATTGA-T---TTATTTTAAAATATA
398467 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
398484 TAATTTATTA
Statistics
Matches: 58, Mismatches: 3, Indels: 20
0.72 0.04 0.25
Matches are distributed among these distances:
22 25 0.43
23 1 0.02
24 2 0.03
25 1 0.02
26 6 0.10
27 5 0.09
28 6 0.10
29 1 0.02
30 2 0.03
31 1 0.02
32 8 0.14
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATA
Found at i:398417 original size:54 final size:54
Alignment explanation
Indices: 398342--398923 Score: 623
Period size: 54 Copynumber: 10.8 Consensus size: 54
398332 TTTTAAAATA
*
398342 ATTTATTATAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
* *
398396 ATTTATTTTAAAATATAGATTGATTTATTTTATATAATTTATTAGTATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
*
398450 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGGTTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
* *
398504 ATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTG
** ** * ** * * * *
398552 ATTTATTTT-AAATAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGAATTG
1 ATTTATTTTAAAAT-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTG
* * *
398606 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTATTATAGATTA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
* *
398660 ATTCATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
* *
398714 ATTTATTTAAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
** ** * ** * * *
398768 ATTTATTTT-AAATATTTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTG
1 ATTTATTTTAAAATA-TGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTG
*** * *
398822 ATTTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATGTATTG
1 ATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
398880 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
398924 TCATAGTTGT
Statistics
Matches: 433, Mismatches: 72, Indels: 46
0.79 0.13 0.08
Matches are distributed among these distances:
47 4 0.01
48 25 0.06
49 3 0.01
50 5 0.01
51 1 0.00
52 5 0.01
53 16 0.04
54 312 0.72
55 20 0.05
56 10 0.02
57 12 0.03
58 18 0.04
59 2 0.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (54 bp):
ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:398521 original size:76 final size:76
Alignment explanation
Indices: 398441--398693 Score: 371
Period size: 76 Copynumber: 3.3 Consensus size: 76
398431 AATTTATTAG
*
398441 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGGTTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
398506 TTATTTTAAAA
66 TTATTTTAAAA
*** *
398517 TATGGATTGATTTATTATTGTAGTTGTATGGATTAATTTATTTTAAATAATTTATTAGTATGGAT
1 TATGGATTGATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGAT
398582 TGATTTATTTTAAAA
62 TGATTTATTTTAAAA
* * * *
398597 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTATTATAGATTAAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
*
398662 TCATTTTAAAA
66 TTATTTTAAAA
*
398673 TATAGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
398694 TAATTTATTA
Statistics
Matches: 157, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
76 82 0.52
77 3 0.02
78 4 0.03
79 3 0.02
80 65 0.41
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (76 bp):
TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
TTATTTTAAAA
Found at i:398591 original size:22 final size:22
Alignment explanation
Indices: 398575--398639 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
398565 AATTTATTAG
398575 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
398597 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
398619 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
398640 TAATTTATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:398676 original size:22 final size:22
Alignment explanation
Indices: 398651--398693 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
398641 AATTTATTAT
398651 TATAGATTAATTCATTTTAAAA
1 TATAGATTAATTCATTTTAAAA
* *
398673 TATAGATTGATTTATTTTAAA
1 TATAGATTAATTCATTTTAAA
398694 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (22 bp):
TATAGATTAATTCATTTTAAAA
Found at i:398850 original size:264 final size:268
Alignment explanation
Indices: 398342--398929 Score: 786
Period size: 264 Copynumber: 2.2 Consensus size: 268
398332 TTTTAAAATA
* * * * *
398342 ATTTATTATAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTATTATAGATTAATTCATTTTAA
* *
398407 AATATAGATTGATTTATTTTATATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
66 AATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTAAAAATATGGATTG
** * *
398472 ATTTATTTTAAATAATTTATTAGTATGGGTTGATTTATTTTAAAATATGGATTGATTTATTATTG
131 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATGGATTGATTATTG
*** * *
398537 TAGTTGTATGGATTAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA-TA
196 TAGAAATATGGATTAATTTA-TTT-AAT-ATGTATTAGTATGAATTGATTTATTTTAAATAATTA
398599 -T-G-A-ATTG
258 TTAGTATATTG
398606 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTATTATAGATTAATTCATTTTAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTATTATAGATTAATTCATTTTAA
398671 AATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTAAAAATATGGATTG
66 AATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTAAAAATATGGATTG
*
398736 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATATTTTATTAGTATGGATTGA
131 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAA-A---TA-T-GGATGGATTGA
* *
398801 TTTATTTTA-AAATATGGATTGATTTA-TT-AT-TGTAGTT-GTATGAATTGATTTATTTTAAAT
190 -TTATTGTAGAAATATGGATTAATTTATTTAATATGTA-TTAGTATGAATTGATTTATTTTAAAT
398861 AATTTATTAGTATGTATTG
253 AA-TTATTAGTA--TATTG
*
398880 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTATCATAG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTATTATAG
398930 TTGTATGGAT
Statistics
Matches: 286, Mismatches: 20, Indels: 26
0.86 0.06 0.08
Matches are distributed among these distances:
264 186 0.65
265 5 0.02
266 4 0.01
268 6 0.02
269 2 0.01
270 22 0.08
271 8 0.03
274 53 0.19
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (268 bp):
ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTATTATAGATTAATTCATTTTAA
AATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTAAAAATATGGATTG
ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATGGATTGATTATTG
TAGAAATATGGATTAATTTATTTAATATGTATTAGTATGAATTGATTTATTTTAAATAATTATTA
GTATATTG
Found at i:398887 original size:22 final size:22
Alignment explanation
Indices: 398871--398913 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
398861 AATTTATTAG
*
398871 TATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
398893 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
398914 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:398973 original size:31 final size:31
Alignment explanation
Indices: 398938--398996 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
398928 AGTTGTATGG
* *
398938 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
398969 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
398997 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:399973 original size:21 final size:23
Alignment explanation
Indices: 399949--399996 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
399939 AAAAAAACTT
399949 TGTTAACCA-A-TCAGAAAACCC
1 TGTTAACCAGAGTCAGAAAACCC
* *
399970 TGTTTACCAGAGTCAGAAAACTC
1 TGTTAACCAGAGTCAGAAAACCC
399993 TGTT
1 TGTT
399997 TTTACATGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 1 0.04
23 14 0.61
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (23 bp):
TGTTAACCAGAGTCAGAAAACCC
Found at i:401798 original size:415 final size:418
Alignment explanation
Indices: 401025--401865 Score: 1424
Period size: 415 Copynumber: 2.0 Consensus size: 418
401015 CCTTATCTTG
*
401025 CAAAATTATTTCCCAAATTATTTATTAATAAAAATCCCGCATCGTTTTCTTGTGACATTTGTTGT
1 CAAAATTATTTCCCAAATTATTTATTAATAAAAATCCCGCATCGTTTTCTTGTGACATTTGTTCT
*
401090 CTTGCAAAACGCATTCAGAGCTCTTATCCTCCTTCTCCCTCCCGCTCAGCTACCTTTTTCCTTAA
66 CTTGCAAAACACATTCAGAGCTCTTATCCTCC-TCT-CCTCCCGCTCAGCTACCTTTTTCCTTAA
* *
401155 TTCATAGTGATATTTGGGGACCTTCACAGGTTACGGGTTTACATGAAATTCGTTGGTTTATTACT
129 TTCATAGTGACATTTGGGGACCTTCACAGGTTACAGGTTTACATGAAATTCGTTGGTTTATTACT
*
401220 TTAATTGATGACCACTCTCGTACCACTTGGACCTTTCTTATGAAGGACAAATCTGAGTCTTGCAT
194 TTAATTGATGACCACTCTCGTACCACTTGGACCTTTCTTATGAAGGACAAATCTGAGTCGTGCAT
401285 CATCTTCAAACAATTCCACAAAATGGTTGAATCACAATTCCAAAGTTCCATTGGCATCCTGAAAT
259 CATCTTCAAACAATTCCACAAAATGGTTGAATCACAATTCCAAAGTTCCATTGGCATCCTGAAAT
* *
401350 CTGATAATGTGGGGAAATACCTCTCTCAGTCGTTAGGATATTTCTTCCAGG-AAA-AGAATAGTT
324 ATGATAATGTGGGGAAATACCTCTCTCAGTCGTTAGGATATTTCTTCCAGGAAAACAGAATAGTC
401413 CATCTCAC-TTCTTGTGTCGACACTCCACAA
389 CATCTCACTTTC-TGTGTCGACACTCCACAA
401443 CAAAATTATTTCCCAAATTATTTATTAATAAAAATCCCGCATCGTTTTCTTGTGACATTTGTTCT
1 CAAAATTATTTCCCAAATTATTTATTAATAAAAATCCCGCATCGTTTTCTTGTGACATTTGTTCT
*
401508 CTTGCAAAACACATTCAGAGCTCTTATCCT-C-CT-CTCCCGCTCAGCTAAACCTTTTTTCTTAA
66 CTTGCAAAACACATTCAGAGCTCTTATCCTCCTCTCCTCCCGCTCAGCT--ACCTTTTTCCTTAA
* *
401570 TTCATAGTGACATTTGGGGACCTTCACGGGTTACAGGTTTACATGGAATTCGTTGGTTTATTACT
129 TTCATAGTGACATTTGGGGACCTTCACAGGTTACAGGTTTACATGAAATTCGTTGGTTTATTACT
* * *
401635 TTTATTGATGACCACTCTCGTACCACTTGGACTTTTCTTATGAAGGACAAATCTGAGTCGTGTAT
194 TTAATTGATGACCACTCTCGTACCACTTGGACCTTTCTTATGAAGGACAAATCTGAGTCGTGCAT
*
401700 CATCTTCAAACAATTCCACTAAATGGTTGAATCACAATTCCAAAGTTCCATTGGCATCCTGAAAT
259 CATCTTCAAACAATTCCACAAAATGGTTGAATCACAATTCCAAAGTTCCATTGGCATCCTGAAAT
* *
401765 ATGATAATGTGGGGGAATACCTCTCTCAGTCGTTAGGATCTTTCTTCCAGGAAAACAGAATAGTC
324 ATGATAATGTGGGGAAATACCTCTCTCAGTCGTTAGGATATTTCTTCCAGGAAAACAGAATAGTC
* *
401830 CATCTCACTTTCTGTGTTGACACTCTACAA
389 CATCTCACTTTCTGTGTCGACACTCCACAA
*
401860 TAAAAT
1 CAAAAT
401866 GGGGTCACCG
Statistics
Matches: 399, Mismatches: 19, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
413 13 0.03
415 249 0.62
416 3 0.01
417 38 0.10
418 96 0.24
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (418 bp):
CAAAATTATTTCCCAAATTATTTATTAATAAAAATCCCGCATCGTTTTCTTGTGACATTTGTTCT
CTTGCAAAACACATTCAGAGCTCTTATCCTCCTCTCCTCCCGCTCAGCTACCTTTTTCCTTAATT
CATAGTGACATTTGGGGACCTTCACAGGTTACAGGTTTACATGAAATTCGTTGGTTTATTACTTT
AATTGATGACCACTCTCGTACCACTTGGACCTTTCTTATGAAGGACAAATCTGAGTCGTGCATCA
TCTTCAAACAATTCCACAAAATGGTTGAATCACAATTCCAAAGTTCCATTGGCATCCTGAAATAT
GATAATGTGGGGAAATACCTCTCTCAGTCGTTAGGATATTTCTTCCAGGAAAACAGAATAGTCCA
TCTCACTTTCTGTGTCGACACTCCACAA
Found at i:406085 original size:17 final size:16
Alignment explanation
Indices: 406063--406124 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 16
406053 AAATTGGAGT
406063 ACAAAAAGAAAGAAAAG
1 ACAAAAAG-AAGAAAAG
406080 ACAAAAAGAAGAAAA-
1 ACAAAAAGAAGAAAAG
406095 ATTCAGAAAAGAAG-AAA-
1 A--CA-AAAAGAAGAAAAG
*
406112 ATAAAAAGAAGAA
1 ACAAAAAGAAGAA
406125 TTTCAAAAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 8 0.20
15 3 0.08
16 7 0.17
17 14 0.35
18 8 0.20
ACGTcount: A:0.74, C:0.05, G:0.16, T:0.05
Consensus pattern (16 bp):
ACAAAAAGAAGAAAAG
Found at i:406132 original size:14 final size:14
Alignment explanation
Indices: 406082--406124 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 14
406072 AAGAAAAGAC
406082 AAAAAGAAGAAAAATT
1 AAAAAGAAG-AAAA-T
406098 CAGAAAAGAAGAAAAT
1 -A-AAAAGAAGAAAAT
406114 AAAAAGAAGAA
1 AAAAAGAAGAA
406125 TTTCAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 10 0.40
15 1 0.04
16 1 0.04
17 5 0.20
18 8 0.32
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.07
Consensus pattern (14 bp):
AAAAAGAAGAAAAT
Found at i:412671 original size:5 final size:5
Alignment explanation
Indices: 412661--412686 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
412651 CAGCCTCTCA
412661 AGCTC AGCTC AGCTC AGCTC AGCTC A
1 AGCTC AGCTC AGCTC AGCTC AGCTC A
412687 ATTCCATTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.38, G:0.19, T:0.19
Consensus pattern (5 bp):
AGCTC
Found at i:419496 original size:13 final size:13
Alignment explanation
Indices: 419478--419507 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
419468 ATGCGTTTTA
419478 CATAAATGCACGT
1 CATAAATGCACGT
*
419491 CATAAATGCGCGT
1 CATAAATGCACGT
419504 CATA
1 CATA
419508 GATTTATGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (13 bp):
CATAAATGCACGT
Found at i:423685 original size:4 final size:4
Alignment explanation
Indices: 423671--423699 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
423661 CAACTTTTTC
423671 AATA AAT- AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
423700 AGGGTGTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Done.