Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001081.1 Hibiscus syriacus cultivar Beakdansim tig00002140_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: 73439
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:1446 original size:42 final size:42
Alignment explanation
Indices: 1376--1570 Score: 129
Period size: 42 Copynumber: 4.8 Consensus size: 42
1366 AGCTAGAGTT
*
1376 CGTGTAATTAGCGGCATTTTTGCATAAAACGCCACTAAAGAA
1 CGTGTAATTAGCGGCATTTGTGCATAAAACGCCACTAAAGAA
* * * *
1418 CGTGTAATTAGCGGCGTTTGTGCTTAAAATGCCACTAAAGTA
1 CGTGTAATTAGCGGCATTTGTGCATAAAACGCCACTAAAGAA
* * * * * * * **
1460 C-AGTATTTATC-GC-GTTAT--ATAAAAACGCCATTATAGTG
1 CGTGTAATTAGCGGCATTTGTGCAT-AAAACGCCACTAAAGAA
* * * * * *
1498 GGTGTAATTCGCGG--TTTGTACATAAAATGCCACGT-ATGTA
1 CGTGTAATTAGCGGCATTTGTGCATAAAACGCCAC-TAAAGAA
1538 CGTGTAATTAGCGG-ATTTGTGCATAAAACGCCA
1 CGTGTAATTAGCGGCATTTGTGCATAAAACGCCA
1571 TGTATATAGT
Statistics
Matches: 115, Mismatches: 31, Indels: 15
0.71 0.19 0.09
Matches are distributed among these distances:
37 1 0.01
38 13 0.11
39 12 0.10
40 25 0.22
41 26 0.23
42 38 0.33
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (42 bp):
CGTGTAATTAGCGGCATTTGTGCATAAAACGCCACTAAAGAA
Found at i:1523 original size:41 final size:39
Alignment explanation
Indices: 1481--1592 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 39
1471 GCGTTATATA
* *
1481 AAAACGCCATTATAGTGGGTGTAATTCGCGGTTTGTACAT
1 AAAACGCCATTATAGT-AGTGTAATTAGCGGTTTGTACAT
* * *
1521 AAAATGCCACGTAT-GTACGTGTAATTAGCGGATTTGTGCAT
1 AAAACGCCA-TTATAGTA-GTGTAATTAGCGG-TTTGTACAT
1562 AAAACGCCATGTATA-TAGTGTAATTAGCGGT
1 AAAACGCCAT-TATAGTAGTGTAATTAGCGGT
1593 GTTTGTGCTT
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
39 1 0.02
40 35 0.58
41 24 0.40
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (39 bp):
AAAACGCCATTATAGTAGTGTAATTAGCGGTTTGTACAT
Found at i:1544 original size:40 final size:39
Alignment explanation
Indices: 1499--1592 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 39
1489 ATTATAGTGG
* * *
1499 GTGTAATTCGCGGTTTGTACATAAAATGCCACGTATGTA
1 GTGTAATTAGCGGTTTGTACATAAAACGCCACGTATATA
* *
1538 CGTGTAATTAGCGGATTTGTGCATAAAACGCCATGTATATA
1 -GTGTAATTAGCGG-TTTGTACATAAAACGCCACGTATATA
1579 GTGTAATTAGCGGT
1 GTGTAATTAGCGGT
1593 GTTTGTGCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.02
40 25 0.52
41 22 0.46
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (39 bp):
GTGTAATTAGCGGTTTGTACATAAAACGCCACGTATATA
Found at i:1598 original size:41 final size:40
Alignment explanation
Indices: 1481--1606 Score: 130
Period size: 41 Copynumber: 3.1 Consensus size: 40
1471 GCGTTATATA
* * *
1481 AAAACGCCAT-TATAGTGGGTGTAATTCGC-GGTTTGTACAT
1 AAAACGCCATGTATA-T-AGTGTAATTAGCGGGTTTGTGCAT
* * * *
1521 AAAATGCCACGTATGTACGTGTAATTAGCGGATTTGTGCAT
1 AAAACGCCATGTATATA-GTGTAATTAGCGGGTTTGTGCAT
*
1562 AAAACGCCATGTATATAGTGTAATTAGCGGTGTTTGTGCTT
1 AAAACGCCATGTATATAGTGTAATTAGCGG-GTTTGTGCAT
1603 AAAA
1 AAAA
1607 ACGGCACATA
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
40 32 0.46
41 38 0.54
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (40 bp):
AAAACGCCATGTATATAGTGTAATTAGCGGGTTTGTGCAT
Found at i:1763 original size:40 final size:41
Alignment explanation
Indices: 1700--1776 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 41
1690 ATGTGCGTGT
*
1700 AATTAGCGGCGTTTATACGTTAAACGCCACTGAAGTATGGG
1 AATTAGCGGCGTTTATACGTTAAACGCCACTAAAGTATGGG
* * *
1741 AATTAGCGGCGTTTGTGC-TTAAATGCCACTAAAGTA
1 AATTAGCGGCGTTTATACGTTAAACGCCACTAAAGTA
1777 CGACCTTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 16 0.50
41 16 0.50
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (41 bp):
AATTAGCGGCGTTTATACGTTAAACGCCACTAAAGTATGGG
Found at i:1831 original size:36 final size:39
Alignment explanation
Indices: 1782--1854 Score: 89
Period size: 40 Copynumber: 1.9 Consensus size: 39
1772 AAGTACGACC
*
1782 TTTAGCGGCG-TTT-TAAAAACACC-CTAAAGTATAGAA
1 TTTAACGGCGTTTTATAAAAACACCACTAAAGTATAGAA
* *
1818 TTTAACGGTGTTTTTATAAAAACGCCACTAAAGTATA
1 TTTAACGGCG-TTTTATAAAAACACCACTAAAGTATA
1855 CTTATTTTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
36 8 0.27
38 3 0.10
39 9 0.30
40 10 0.33
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (39 bp):
TTTAACGGCGTTTTATAAAAACACCACTAAAGTATAGAA
Found at i:2377 original size:14 final size:14
Alignment explanation
Indices: 2362--2414 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
2352 ATTTAAAGTT
*
2362 AATAAAAATAAATT
1 AATAAAAATAAATA
*
2376 AAT-AAAATAACTA
1 AATAAAAATAAATA
*
2389 AATAAATATTAAATA
1 AATAAA-AATAAATA
*
2404 AATAATAATAA
1 AATAAAAATAA
2415 TGAGAAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
13 11 0.35
14 9 0.29
15 11 0.35
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAAAAATAAATA
Found at i:4532 original size:26 final size:27
Alignment explanation
Indices: 4481--4534 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
4471 AAAATACTTG
*
4481 ATGTACCTAAAAATATATAAATAAAAT
1 ATGTACCTAAAAAAATATAAATAAAAT
4508 ATGTACC-AAAAAAAT-TAAATCAAAAT
1 ATGTACCTAAAAAAATATAAAT-AAAAT
4534 A
1 A
4535 ATAATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 5 0.20
26 13 0.52
27 7 0.28
ACGTcount: A:0.61, C:0.09, G:0.04, T:0.26
Consensus pattern (27 bp):
ATGTACCTAAAAAAATATAAATAAAAT
Found at i:7294 original size:12 final size:13
Alignment explanation
Indices: 7277--7309 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
7267 CATAATTCTC
7277 AAATAAATAAA-T
1 AAATAAATAAAGT
7289 AAATAAATAAAGT
1 AAATAAATAAAGT
7302 AATATAAA
1 AA-ATAAA
7310 GAAGTATAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 3 0.16
14 5 0.26
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
AAATAAATAAAGT
Found at i:7416 original size:13 final size:13
Alignment explanation
Indices: 7408--7448 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
7398 TAAAATTATG
7408 AAAATAAATGAAT
1 AAAATAAATGAAT
*
7421 AAAATAAATAAAT
1 AAAATAAATGAAT
*
7434 -AAAT-ATTGAAT
1 AAAATAAATGAAT
7445 AAAA
1 AAAA
7449 AATAATAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
11 5 0.21
12 7 0.29
13 12 0.50
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (13 bp):
AAAATAAATGAAT
Found at i:7479 original size:17 final size:15
Alignment explanation
Indices: 7446--7493 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 15
7436 ATATTGAATA
*
7446 AAAAATAATAATGAG
1 AAAAATAATAAAGAG
7461 AAAAATAAATAAAGTAG
1 AAAAAT-AATAAAG-AG
7478 AAAAATTTAATAAAGA
1 AAAAA--TAATAAAGA
7494 TGATATAGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 6 0.21
16 6 0.21
17 8 0.29
18 7 0.25
19 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (15 bp):
AAAAATAATAAAGAG
Found at i:7492 original size:18 final size:17
Alignment explanation
Indices: 7446--7483 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
7436 ATATTGAATA
*
7446 AAAAAT-AATAATG-AG
1 AAAAATAAATAAAGTAG
7461 AAAAATAAATAAAGTAG
1 AAAAATAAATAAAGTAG
7478 AAAAAT
1 AAAAAT
7484 TTAATAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 6 0.30
17 8 0.40
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (17 bp):
AAAAATAAATAAAGTAG
Found at i:10381 original size:29 final size:28
Alignment explanation
Indices: 10319--10382 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
10309 TTTTCATTCC
* *
10319 CTAAAATTTTATAAATTCAAGTTCATCT
1 CTAAAATGTTATAAATTCAAATTCATCT
* *
10347 CTTAAAATGTTATAAATTTAAATTCGTTCT
1 C-TAAAATGTTATAAATTCAAATTC-ATCT
10377 CTAAAA
1 CTAAAA
10383 GAAAATCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.03
29 25 0.83
30 4 0.13
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.42
Consensus pattern (28 bp):
CTAAAATGTTATAAATTCAAATTCATCT
Found at i:10446 original size:26 final size:25
Alignment explanation
Indices: 10409--10460 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
10399 AGGGCGGTGT
*
10409 GTATAAATGACTAAGGAGACTAAAG
1 GTATAAATGACTAAGAAGACTAAAG
10434 GTATAACATGACTAAGAAGACTAAAG
1 GTATAA-ATGACTAAGAAGACTAAAG
10460 G
1 G
10461 GATTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.48, C:0.10, G:0.23, T:0.19
Consensus pattern (25 bp):
GTATAAATGACTAAGAAGACTAAAG
Found at i:13174 original size:2 final size:2
Alignment explanation
Indices: 13167--13207 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
13157 GCTTATTTAG
13167 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13206 TA
1 TA
13208 GTTTTTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:13307 original size:41 final size:39
Alignment explanation
Indices: 13244--13514 Score: 156
Period size: 40 Copynumber: 7.0 Consensus size: 39
13234 TAAATTTTAG
*
13244 AAAACAGTTTTTGAAAGCATATAATATATAGTTTTTAAAA
1 AAAACAGTTTTTGAAAACATATAATATATAGTTTTT-AAA
* * * *
13284 AAAACCAGATTTTGAAAATATAT-ATA-ATATGGTTTTGAA
1 AAAA-CAGTTTTTGAAAACATATAATATATA-GTTTTTAAA
* * *
13323 AACAC-GTTTTTGAAAACGTATAATATATAG-TTTT--G
1 AAAACAGTTTTTGAAAACATATAATATATAGTTTTTAAA
* * *
13358 AAAGCA-ATTTTGAAAACATATATAATATATAGTTTTT--T
1 AAAACAGTTTTTGAAAAC--ATATAATATATAGTTTTTAAA
* * *
13396 AAAATA-TTTTTGAAAACGTAT-ATAATATAGTTTTTGAA
1 AAAACAGTTTTTGAAAACATATAAT-ATATAGTTTTTAAA
* * **
13434 AAAA-TGTATTTTTGAAAACATATAATATATA-TATATATATTT
1 AAAACAG--TTTTTGAAAACATATAATATATAGT-T-TTTA-AA
* * *
13476 TAAATA-TTTTTGAAAACATATAGTATATAGTTTTTAAA
1 AAAACAGTTTTTGAAAACATATAATATATAGTTTTTAAA
13514 A
1 A
13515 TGGTTTTTGA
Statistics
Matches: 178, Mismatches: 33, Indels: 42
0.70 0.13 0.17
Matches are distributed among these distances:
35 15 0.08
36 14 0.08
37 29 0.16
38 27 0.15
39 15 0.08
40 55 0.31
41 20 0.11
42 3 0.02
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (39 bp):
AAAACAGTTTTTGAAAACATATAATATATAGTTTTTAAA
Found at i:13334 original size:37 final size:35
Alignment explanation
Indices: 13292--13435 Score: 121
Period size: 37 Copynumber: 3.9 Consensus size: 35
13282 AAAAAACCAG
*
13292 ATTTTGAAAATATATATAATATGGTTTTGAAAACA
1 ATTTTGAAAATATATATAATATAGTTTTGAAAACA
* *
13327 CGTTTTTGAAAACGTATA-AT-ATATAGTTTTGAAAGCA
1 --ATTTTGAAAA--TATATATAATATAGTTTTGAAAACA
* * *
13364 ATTTTGAAAACATATATAATATATAGTTTTTTAAAATA
1 ATTTTGAAAATATATAT-A-ATATAG-TTTTGAAAACA
* **
13402 TTTTTGAAAACGTATATAATATAGTTTTTGAAAA
1 ATTTTGAAAATATATATAATATAG-TTTTGAAAA
13436 AATGTATTTT
Statistics
Matches: 89, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
33 3 0.03
34 2 0.02
35 9 0.10
36 15 0.17
37 31 0.35
38 25 0.28
39 4 0.04
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42
Consensus pattern (35 bp):
ATTTTGAAAATATATATAATATAGTTTTGAAAACA
Found at i:13418 original size:38 final size:38
Alignment explanation
Indices: 13329--13536 Score: 166
Period size: 38 Copynumber: 5.5 Consensus size: 38
13319 TGAAAACACG
* * **
13329 TTTTTGAAAAC--GTATAATATATAG-TTTTGAAAGCA
1 TTTTTGAAAACATATATAATATATAGTTTTTTAAAATA
*
13364 ATTTTGAAAACATATATAATATATAGTTTTTTAAAATA
1 TTTTTGAAAACATATATAATATATAGTTTTTTAAAATA
* *
13402 TTTTTGAAAACGTATAT-A-ATATAGTTTTTGAAAAAATGTA
1 TTTTTGAAAACATATATAATATATAGTTTTT--TAAAA--TA
13442 TTTTTGAAAACATATAATATATATATA-TATATTTT-AAATA
1 TTTTTGAAAACATAT-ATA-ATATATAGT-T-TTTTAAAATA
* *
13482 TTTTTGAAAAC--ATATAGTATATAG-TTTTTAAAATGG
1 TTTTTGAAAACATATATAATATATAGTTTTTTAAAAT-A
*
13518 TTTTTGAAAATATAATATA
1 TTTTTGAAAACAT-ATATA
13537 TGTTTTATAG
Statistics
Matches: 141, Mismatches: 13, Indels: 34
0.75 0.07 0.18
Matches are distributed among these distances:
34 4 0.03
35 15 0.11
36 27 0.19
37 16 0.11
38 29 0.21
39 5 0.04
40 29 0.21
41 2 0.01
42 3 0.02
43 2 0.01
44 6 0.04
45 3 0.02
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (38 bp):
TTTTTGAAAACATATATAATATATAGTTTTTTAAAATA
Found at i:13511 original size:34 final size:33
Alignment explanation
Indices: 13460--13542 Score: 84
Period size: 34 Copynumber: 2.5 Consensus size: 33
13450 AACATATAAT
13460 ATATATATATA-TATTTT-AAAT-ATTTTTGAAAA
1 ATATATATATAGT-TTTTAAAATGATTTTTG-AAA
*
13492 CATATAGTATATAGTTTTTAAAATGGTTTTTGAAA
1 -ATATA-TATATAGTTTTTAAAATGATTTTTGAAA
13527 ATATA-ATATATGTTTT
1 ATATATATATA-GTTTT
13543 ATAGTTTTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
32 5 0.11
33 10 0.23
34 15 0.34
35 8 0.18
36 6 0.14
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.49
Consensus pattern (33 bp):
ATATATATATAGTTTTTAAAATGATTTTTGAAA
Found at i:13562 original size:80 final size:78
Alignment explanation
Indices: 13365--13537 Score: 220
Period size: 80 Copynumber: 2.3 Consensus size: 78
13355 TTGAAAGCAA
*
13365 TTTTGAAAACATAT-ATA-ATATATAGT-T-TTTTAAAATATTTTTGAAAACGTATATAATATAG
1 TTTTGAAAACATATAATATATATATA-TATATTTT-AAATATTTTTGAAAACATATATAATATAG
13426 TTTTTGAAAAAATGTAT
64 TTTTT--AAAAATGTAT
13443 TTTTGAAAACATATAATATATATATATATATTTTAAATATTTTTGAAAACATATAGT-ATATAGT
1 TTTTGAAAACATATAATATATATATATATATTTTAAATATTTTTGAAAACATATA-TAATATAGT
*
13507 TTTT-AAAATG-GT
65 TTTTAAAAATGTAT
13519 TTTTG-AAA-ATATAATATAT
1 TTTTGAAAACATATAATATAT
13538 GTTTTATAGT
Statistics
Matches: 88, Mismatches: 2, Indels: 14
0.85 0.02 0.13
Matches are distributed among these distances:
74 11 0.12
75 3 0.03
76 6 0.07
77 6 0.07
78 14 0.16
79 4 0.05
80 39 0.44
81 5 0.06
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (78 bp):
TTTTGAAAACATATAATATATATATATATATTTTAAATATTTTTGAAAACATATATAATATAGTT
TTTAAAAATGTAT
Found at i:13572 original size:27 final size:29
Alignment explanation
Indices: 13517--13572 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
13507 TTTTAAAATG
*
13517 GTTTTTGAAAATATAATATATGTTTTATA
1 GTTTTTGAAAATATAATATATGTTATATA
13546 GTTTTT-AAAATA-AATATA-GTATATATA
1 GTTTTTGAAAATATAATATATGT-TATATA
13573 TTATTTATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 2 0.08
27 11 0.44
28 6 0.24
29 6 0.24
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (29 bp):
GTTTTTGAAAATATAATATATGTTATATA
Found at i:13605 original size:14 final size:14
Alignment explanation
Indices: 13567--13614 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
13557 AAATATAGTA
*
13567 TATATATTATTTATAG
1 TATAT-TTA-TTATAT
*
13583 TATTATTTATTATTT
1 TA-TATTTATTATAT
13598 TATATTTATTATAT
1 TATATTTATTATAT
13612 TAT
1 TAT
13615 TACTAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 14 0.50
15 6 0.21
16 5 0.18
17 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
TATATTTATTATAT
Found at i:13611 original size:9 final size:8
Alignment explanation
Indices: 13569--13626 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
13559 ATATAGTATA
13569 TATATTATT
1 TATATTA-T
*
13578 TATAGTAT
1 TATATTAT
13586 TAT-TTAT
1 TATATTAT
*
13593 TATTTTA-
1 TATATTAT
13600 TAT-TTAT
1 TATATTAT
13607 TATATTAT
1 TATATTAT
*
13615 TACTAATAT
1 TA-TATTAT
13624 TAT
1 TAT
13627 TTTTTGATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
6 3 0.07
7 12 0.29
8 14 0.33
9 13 0.31
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:16518 original size:23 final size:23
Alignment explanation
Indices: 16484--16529 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
16474 CATTGTGAAA
*
16484 GAATCAATATAGATCGGGTCTAC
1 GAATCAAAATAGATCGGGTCTAC
16507 GAATCAAAATAGATCGGGTCTAC
1 GAATCAAAATAGATCGGGTCTAC
16530 ACCAAGTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (23 bp):
GAATCAAAATAGATCGGGTCTAC
Found at i:21831 original size:26 final size:26
Alignment explanation
Indices: 21800--21851 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
21790 TTATTGGGTC
21800 CCTCCTAAAGCATGAGTTTATTGTTA
1 CCTCCTAAAGCATGAGTTTATTGTTA
*
21826 CCTCCTGAAGCATGAGTTTATTGTTA
1 CCTCCTAAAGCATGAGTTTATTGTTA
21852 TACTTAAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (26 bp):
CCTCCTAAAGCATGAGTTTATTGTTA
Found at i:23509 original size:202 final size:200
Alignment explanation
Indices: 23066--23513 Score: 508
Period size: 201 Copynumber: 2.2 Consensus size: 200
23056 TAGAGGAACC
23066 ATTTACAGCATAGCTCAAG--GAGAGAAAGACTATATGTCAAACAAAACTTTCGAGTTCGATTCC
1 ATTTACAGCATAGCTCAAGTCGAGA-AAAG-CTATATGTC-AACAAAACTTTCGAGTTCGATTCC
** * * * **
23129 ATTCAGCTCGAGGGCATATCAACCACATGGTAGCAGTGATGAATTACTTTCTGGTTGAAGTTTAA
63 ATTCAGCTCGAGGGCATATCAACCACATGGTAGCAGCAAGGAACTACTTACCAGTTGAAGTTTAA
** * * *
23194 GATGAGGTCTTTAAGTAAAAAAGAAGACCTATGTTGATTGCGATTTAGCAACAAAAAACTATCTC
128 GATGAAATCTTTAAGCAAAAAAGAAGACCTATGTTGATTGCAATTTAGCAACAAAAAACTACCTC
23259 CTAACCAA
193 CTAACCAA
* ** * *
23267 ATTTACAACATAGCTCAAGTCGAGAAGGGTTATTTGTCAACGAAAACTTTCGAGTTCGATTCCAT
1 ATTTACAGCATAGCTCAAGTCGAGAAAAGCTATATGTCAAC-AAAACTTTCGAGTTCGATTCCAT
* * * * *
23332 TTAGCTCGATGGCATATCAACCGCTTGGTAGCAGCAAGGAACTACTTACCAGTTGAATTTTAA-A
65 TCAGCTCGAGGGCATATCAACCACATGGTAGCAGCAAGGAACTACTTACCAGTTGAAGTTTAAGA
* * * **
23396 TAGAAATCTTTTAAGCCAATAAGAAGACCTATGTTGGTTGCAATTTAGCAACAAGGAACTACCT-
130 T-GAAATC-TTTAAGCAAAAAAGAAGACCTATGTTGATTGCAATTTAGCAACAAAAAACTACCTC
* *
23460 CTCAGCCTA
193 CT-AACCAA
* * * *
23469 ATTTACAGCATAACTTAAGTCGAGAAAAGCTGTCTGTCAACAAAA
1 ATTTACAGCATAGCTCAAGTCGAGAAAAGCTATATGTCAACAAAA
23514 AACTTTCCAG
Statistics
Matches: 204, Mismatches: 37, Indels: 12
0.81 0.15 0.05
Matches are distributed among these distances:
200 5 0.02
201 109 0.53
202 86 0.42
203 4 0.02
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (200 bp):
ATTTACAGCATAGCTCAAGTCGAGAAAAGCTATATGTCAACAAAACTTTCGAGTTCGATTCCATT
CAGCTCGAGGGCATATCAACCACATGGTAGCAGCAAGGAACTACTTACCAGTTGAAGTTTAAGAT
GAAATCTTTAAGCAAAAAAGAAGACCTATGTTGATTGCAATTTAGCAACAAAAAACTACCTCCTA
ACCAA
Found at i:24048 original size:60 final size:59
Alignment explanation
Indices: 23968--24086 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 59
23958 AAAAAATCAA
* *
23968 AAAATATATAATATGATTTTGAAAACACGTTTTTGAAAAC-ATATAATATATAGTTTTG
1 AAAACATATAATATGATTTTGAAAACACATTTTTGAAAACAATATAATATATAGTTTTG
* *
24026 AAAACATATAATATATAGTTTTGAAAATACATTTTTGAAAACATATATAATATATAGTTTT
1 AAAACATATAATAT-GA-TTTTGAAAACACATTTTTGAAAACA-ATATAATATATAGTTTT
24087 TTAAAATATT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
58 13 0.25
59 1 0.02
60 22 0.42
62 17 0.32
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.40
Consensus pattern (59 bp):
AAAACATATAATATGATTTTGAAAACACATTTTTGAAAACAATATAATATATAGTTTTG
Found at i:24057 original size:25 final size:23
Alignment explanation
Indices: 23998--24052 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
23988 GAAAACACGT
23998 TTTTGAAAACATATAATATATAG
1 TTTTGAAAACATATAATATATAG
24021 TTTTGAAAACATATAATATATAG
1 TTTTGAAAACATATAATATATAG
24044 TTTTGAAAA
1 TTTTGAAAA
24053 TACATTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (23 bp):
TTTTGAAAACATATAATATATAG
Found at i:24111 original size:38 final size:38
Alignment explanation
Indices: 24021--24131 Score: 149
Period size: 38 Copynumber: 2.9 Consensus size: 38
24011 TAATATATAG
24021 TTTTGAAAAC-ATATAATATATAG-TTTTGAAAATACAT
1 TTTTGAAAACTATATAATATATAGTTTTTGAAAATA-AT
*
24058 TTTTGAAAACATATATAATATATAGTTTTTTAAAAT-AT
1 TTTTGAAAAC-TATATAATATATAGTTTTTGAAAATAAT
24096 TTTTGAAAACGTATAT-ATAATATAGTTTTTGAAAAT
1 TTTTGAAAAC-TATATAAT-ATATAGTTTTTGAAAAT
24132 GTATAATATA
Statistics
Matches: 67, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
37 12 0.18
38 33 0.49
39 13 0.19
40 9 0.13
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (38 bp):
TTTTGAAAACTATATAATATATAGTTTTTGAAAATAAT
Found at i:24142 original size:24 final size:26
Alignment explanation
Indices: 24094--24149 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
24084 TTTTTAAAAT
24094 ATTTTTGAAAACGTATATATAATATA
1 ATTTTTGAAAACGTATATATAATATA
* *
24120 GTTTTTGAAAATGTATA-AT-ATATA
1 ATTTTTGAAAACGTATATATAATATA
24144 ATTTTT
1 ATTTTT
24150 TTAAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 10 0.37
25 2 0.07
26 15 0.56
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (26 bp):
ATTTTTGAAAACGTATATATAATATA
Found at i:24163 original size:36 final size:36
Alignment explanation
Indices: 24121--24204 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 36
24111 TATAATATAG
** *
24121 TTTTTGAAAATGTATAATATATAATTTTTTTAAAT-A
1 TTTTTGAAAATACATAATATAT-AGTTTTTTAAATGA
* * *
24157 TTTTTGAAAACACATAGTATATAGTTTTTTAAATGG
1 TTTTTGAAAATACATAATATATAGTTTTTTAAATGA
24193 TTTTTGAAAATA
1 TTTTTGAAAATA
24205 TAATGTATGT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 11 0.28
36 29 0.73
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (36 bp):
TTTTTGAAAATACATAATATATAGTTTTTTAAATGA
Found at i:24198 original size:98 final size:96
Alignment explanation
Indices: 23996--24202 Score: 249
Period size: 98 Copynumber: 2.1 Consensus size: 96
23986 TTGAAAACAC
23996 GTTTTTGAAAACATATAATATATAGTTTTGAAAACATATAATATATAGTTTTGAAAATACATTTT
1 GTTTTTGAAAACATATAATATATAGTTTTGAAAACATATAATATATAGTTTTGAAAATA-ATTTT
*
24061 TGAAAACATATATAATATATAGTTTTTTAAAAT
65 TGAAAACA-ACATAATATATAGTTTTTTAAAAT
* * ** * **
24094 ATTTTTGAAAACGTATATATAATATAGTTTTTGAAAATGTATAATATATAATTTTTTTAAAT-AT
1 GTTTTTGAAAACATATA-AT-ATATAG-TTTTGAAAACATATAATATAT-AGTTTTGAAAATAAT
*
24158 TTTTGAAAAC-ACATAGTATATAGTTTTTT-AAAT
62 TTTTGAAAACAACATAATATATAGTTTTTTAAAAT
24191 GGTTTTTGAAAA
1 -GTTTTTGAAAA
24203 TATAATGTAT
Statistics
Matches: 94, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
97 4 0.04
98 42 0.45
99 2 0.02
100 18 0.19
101 19 0.20
102 9 0.10
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (96 bp):
GTTTTTGAAAACATATAATATATAGTTTTGAAAACATATAATATATAGTTTTGAAAATAATTTTT
GAAAACAACATAATATATAGTTTTTTAAAAT
Found at i:29781 original size:3 final size:3
Alignment explanation
Indices: 29775--29848 Score: 78
Period size: 3 Copynumber: 24.7 Consensus size: 3
29765 TAATTTTTTT
** **
29775 TTA TTA TTA TTA TTA AAA TTA AAA TTA TTA TTA TTA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* *
29821 ATA TTA TTA TTA -TA TTA TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29849 TACAAACAGT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
2 2 0.04
3 53 0.93
4 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:29807 original size:24 final size:25
Alignment explanation
Indices: 29775--29843 Score: 106
Period size: 24 Copynumber: 2.8 Consensus size: 25
29765 TAATTTTTTT
*
29775 TTATTATTATTATTAAAATTAAA-A
1 TTATTATTATTATTATAATTAAATA
*
29799 TTATTATTATTATTATTATTAAATA
1 TTATTATTATTATTATAATTAAATA
29824 TTATTATTA-TATTATAATTA
1 TTATTATTATTATTATAATTA
29844 TTATTTACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 31 0.76
25 10 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTATTATTATTATTATAATTAAATA
Found at i:29811 original size:30 final size:30
Alignment explanation
Indices: 29775--29848 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
29765 TAATTTTTTT
29775 TTATTATTATTATTAAA-ATTAAAATTATTA
1 TTATTATTATTATTAAATATTAAAATTA-TA
**
29805 TTATTATTATTATTAAATATTATTATTATA
1 TTATTATTATTATTAAATATTAAAATTATA
*
29835 TTATAATTATTATT
1 TTATTATTATTATT
29849 TACAAACAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 32 0.80
31 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TTATTATTATTATTAAATATTAAAATTATA
Found at i:29905 original size:26 final size:26
Alignment explanation
Indices: 29855--29909 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
29845 TATTTACAAA
* *
29855 CAGTTACAAACAAAACTGGACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
* *
29881 CAGTTACAAACAAACCAGAATCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
29907 CAG
1 CAG
29910 ACCAACCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.31, G:0.18, T:0.11
Consensus pattern (26 bp):
CAGTTACAAACAAAACAGAACCGGCC
Found at i:38859 original size:114 final size:113
Alignment explanation
Indices: 38689--39228 Score: 864
Period size: 114 Copynumber: 4.7 Consensus size: 113
38679 GTAGAAGACT
* *
38689 CAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCTAAAATCA
1 CAATAGCATCTTCTGGAGGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCC-AAAATCA
*
38754 ATCATTGGATTTAAAAGATCCATGTGCTCATAGTAGAAATAAGGAGGCC
65 ATCATTGGATTTGAAAGATCCATGTGCTCATAGTAGAAATAAGGAGGCC
38803 CAATAGCATCTTCTGGAGGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAAAATCA
1 CAATAGCATCTTCTGGAGGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAA-CCCAAAATCA
* * *
38868 ATCATTAGATTTGAAAGATCCATGTGCTCATAGTAAAAATAAGGAAGCC
65 ATCATTGGATTTGAAAGATCCATGTGCTCATAGTAGAAATAAGGAGGCC
38917 CAATAGCATCTTCTGGAGGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCCAAAATCA
1 CAATAGCATCTTCTGGAGGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAA-CCCAAAATCA
38982 ATCATTGGATTTGAAAGATCCATGTGCTCATAGTAGAAATAAGGAGGCC
65 ATCATTGGATTTGAAAGATCCATGTGCTCATAGTAGAAATAAGGAGGCC
*
39031 CAATAGCATCTTCTGGAGGTGTTCTTTGAGTTATCTGATCTGTTTTGGTATGAAACCCAAAATCA
1 CAATAGCATCTTCTGGAGGTGTTCTTTGAGTTATCTGATCTGATTTGGTATG-AACCCAAAATCA
** * *
39096 ATCATTGGATTTGAAAGATGAATGTGCTCATAGTAGAAATAAGAAGACC
65 ATCATTGGATTTGAAAGATCCATGTGCTCATAGTAGAAATAAGGAGGCC
* * * * * *
39145 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCACAGAACCA
1 CAATAGCATCTTCTGGAGGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACC-CAAAATCA
* *
39210 ATCATTGGAATTAAAAGAT
65 ATCATTGGATTTGAAAGAT
39229 GAACTGCATG
Statistics
Matches: 401, Mismatches: 22, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
113 4 0.01
114 392 0.98
115 5 0.01
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (113 bp):
CAATAGCATCTTCTGGAGGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACCCAAAATCAA
TCATTGGATTTGAAAGATCCATGTGCTCATAGTAGAAATAAGGAGGCC
Found at i:41450 original size:55 final size:54
Alignment explanation
Indices: 41384--41500 Score: 173
Period size: 55 Copynumber: 2.1 Consensus size: 54
41374 ACTTCAATGA
* *
41384 TTACGAACATCTGAGCAGAAGCCA-AAAAAAAGGATGAATGTATTGTCAAAATGTT
1 TTACGAACATCTGAGCAGAAGCCACAAAAAAA-GATGAATGCACTGTC-AAATGTT
**
41439 TTACGAACATCTGAGCAGAAGCCACAGGAAAAGATGAATGCACTGTCAAATGTT
1 TTACGAACATCTGAGCAGAAGCCACAAAAAAAGATGAATGCACTGTCAAATGTT
41493 TTACGAAC
1 TTACGAAC
41501 CTGTTATTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
54 15 0.26
55 37 0.65
56 5 0.09
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (54 bp):
TTACGAACATCTGAGCAGAAGCCACAAAAAAAGATGAATGCACTGTCAAATGTT
Found at i:41895 original size:22 final size:22
Alignment explanation
Indices: 41867--41923 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
41857 ATCTACATTC
*
41867 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGAAAGATTCTCTT
*
41889 TTTAAAGATGAAAGATTCTCTT
1 TTCAAAGATGAAAGATTCTCTT
41911 TTCAAAGATGAAA
1 TTCAAAGATGAAA
41924 ACTTTATGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.37
Consensus pattern (22 bp):
TTCAAAGATGAAAGATTCTCTT
Found at i:42698 original size:76 final size:76
Alignment explanation
Indices: 42598--43160 Score: 1038
Period size: 76 Copynumber: 7.4 Consensus size: 76
42588 ACTATTTCCC
*
42598 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
42663 AAGCCTTCGGG
66 AAGCCTTCGGG
*
42674 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
42739 AAGCCTTCGGG
66 AAGCCTTCGGG
42750 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
42815 AAGCCTTCGGG
66 AAGCCTTCGGG
*
42826 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
42891 AAGCCTTCGGG
66 AAGCCTTCGGG
42902 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
42967 AAGCCTTCGGG
66 AAGCCTTCGGG
*
42978 TCATCTGTAAGTCCTTAAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
43043 AAGCCTTCGGG
66 AAGCCTTCGGG
*
43054 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
43119 AAACCTT-GGG
66 AAGCCTTCGGG
* *
43129 ATCATCTGTAAGTCATGCAGTGCATGATGTTT
1 -TCATCTGTAAGTCCTTCAGTGCATGATGTTT
43161 TTAAGACCTC
Statistics
Matches: 477, Mismatches: 9, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
75 3 0.01
76 474 0.99
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTCGGG
Found at i:43311 original size:3 final size:3
Alignment explanation
Indices: 43305--43369 Score: 60
Period size: 3 Copynumber: 21.7 Consensus size: 3
43295 ACTATTTTTT
** ** *
43305 TTA TTA TTA TTA AAA TTA AAA TTA TTA TTA TTA TTA TTAA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
43351 TTA -TA TTA TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
43370 TACAAACAGT
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
2 2 0.04
3 44 0.92
4 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:43331 original size:21 final size:22
Alignment explanation
Indices: 43305--43364 Score: 88
Period size: 21 Copynumber: 2.8 Consensus size: 22
43295 ACTATTTTTT
*
43305 TTATTATTATTAAAATTAAA-A
1 TTATTATTATTATAATTAAATA
*
43326 TTATTATTATTATTATTAAATA
1 TTATTATTATTATAATTAAATA
43348 TTATTA-TATTATAATTA
1 TTATTATTATTATAATTA
43365 TTATTTACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 28 0.80
22 7 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATTATTATTATAATTAAATA
Found at i:43343 original size:27 final size:27
Alignment explanation
Indices: 43305--43369 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
43295 ACTATTTTTT
43305 TTATTATTATTAAA-ATTAAAATTATTA
1 TTATTATTATTAAATATTAAAA-TATTA
**
43332 TTATTATTATTAAATATTATTATATTA
1 TTATTATTATTAAATATTAAAATATTA
*
43359 TAATTATTATT
1 TTATTATTATT
43370 TACAAACAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTATTATTATTAAATATTAAAATATTA
Found at i:43412 original size:26 final size:26
Alignment explanation
Indices: 43376--43430 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
43366 TATTTACAAA
* *
43376 CAGTTACAAACAAAACTGGACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
*
43402 CAGTTACAAACAAACCAGAACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
43428 CAG
1 CAG
43431 ACCAACCAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.33, G:0.18, T:0.09
Consensus pattern (26 bp):
CAGTTACAAACAAAACAGAACCGGCC
Found at i:46897 original size:12 final size:12
Alignment explanation
Indices: 46865--46904 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
46855 TCAAAGAACA
46865 TTAAAA-TTA-T
1 TTAAAATTTATT
*
46875 TT-AAATCTATT
1 TTAAAATTTATT
46886 TTAAAATTTATT
1 TTAAAATTTATT
46898 TTAAAAT
1 TTAAAAT
46905 ATGAATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 3 0.12
10 4 0.16
11 3 0.12
12 15 0.60
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:46916 original size:22 final size:22
Alignment explanation
Indices: 46891--47299 Score: 481
Period size: 22 Copynumber: 18.6 Consensus size: 22
46881 CTATTTTAAA
46891 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGAATTG
46913 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGAATTG
46935 ATTTATTTTAAAATAT-AGATTG
1 ATTTATTTTAAAATATGA-ATTG
* *
46957 ATTTATTTTAAAATAGGAAGTG
1 ATTTATTTTAAAATATGAATTG
***
46979 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGAATTG
* * *
47001 AATTATTTTAAAATAAGGATTG
1 ATTTATTTTAAAATATGAATTG
47023 ATTTATTTTAAAAATAT-AGATTG
1 ATTTATTTT-AAAATATGA-ATTG
**
47046 ATTTATTTTAAAATATGAA-AA
1 ATTTATTTTAAAATATGAATTG
* *
47067 ATTTATTTTTAAATCTTG-ATTG
1 ATTTATTTTAAAAT-ATGAATTG
47089 ATTTATTTTAAAATATTG-ATTG
1 ATTTATTTTAAAATA-TGAATTG
**
47111 ATTTATTTTAAAATATGGTTTG
1 ATTTATTTTAAAATATGAATTG
***
47133 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGAATTG
* * *
47155 AATTATTTTAAAATTTGGATTG
1 ATTTATTTTAAAATATGAATTG
* * *
47177 ATTTATTTTAAAACATGGATTT
1 ATTTATTTTAAAATATGAATTG
*
47199 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGAATTG
47221 ATTTATTTTAAAATAT-AGATTG
1 ATTTATTTTAAAATATGA-ATTG
47243 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGAATTG
*
47265 ATTTATTTTAAAAT-TTAGATTG
1 ATTTATTTTAAAATATGA-ATTG
47287 ATTTATTTTAAAA
1 ATTTATTTTAAAA
47300 AATTTATTAT
Statistics
Matches: 332, Mismatches: 43, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
21 19 0.06
22 291 0.88
23 22 0.07
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATGAATTG
Found at i:47380 original size:31 final size:31
Alignment explanation
Indices: 47323--47381 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
47313 AGTTGCGTAG
*
47323 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
* * *
47354 ATTATTTCAATTTTAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
47382 CTTTTAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:53068 original size:15 final size:16
Alignment explanation
Indices: 53042--53072 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
53032 ATACCCTGCA
53042 TTTTGCATATGCATTT
1 TTTTGCATATGCATTT
53058 TTTTGCA-ATGCATTT
1 TTTTGCATATGCATTT
53073 AAGTTTTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.55
Consensus pattern (16 bp):
TTTTGCATATGCATTT
Found at i:54878 original size:3 final size:3
Alignment explanation
Indices: 54870--54910 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
54860 ATTTGTAATA
*
54870 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
54911 CAAATATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:55766 original size:28 final size:28
Alignment explanation
Indices: 55680--55774 Score: 81
Period size: 28 Copynumber: 3.4 Consensus size: 28
55670 AAATTAAAAA
* *
55680 TTCATATATTTA-ATTTATAATTCATTCTT
1 TTCATATATTTATATATAT-ATT-ATTATT
* *
55709 TTCA-AAATTTTTATATATACTTATTATT
1 TTCATATATTTATATATATA-TTATTATT
*
55737 TTCATAATATTTATATGTATATTATT-TT
1 TTCAT-ATATTTATATATATATTATTATT
55765 TT-ATATATTT
1 TTCATATATTT
55775 TTTATTTTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
26 6 0.11
27 2 0.04
28 19 0.35
29 16 0.29
30 12 0.22
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (28 bp):
TTCATATATTTATATATATATTATTATT
Found at i:55772 original size:26 final size:30
Alignment explanation
Indices: 55680--55774 Score: 80
Period size: 29 Copynumber: 3.4 Consensus size: 30
55670 AAATTAAAAA
* * *
55680 TTCAT-ATATTTA-ATTTATAATTCATTCTT
1 TTCATAATATTTATATATATACTT-ATTATT
*
55709 TTCA-AA-ATTTTTATATATACTTATTATT
1 TTCATAATATTTATATATATACTTATTATT
*
55737 TTCATAATATTTATATGTATA-TTATT-TT
1 TTCATAATATTTATATATATACTTATTATT
55765 TT-AT-ATATTT
1 TTCATAATATTT
55775 TTTATTTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
26 6 0.11
27 2 0.04
28 17 0.30
29 20 0.36
30 11 0.20
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (30 bp):
TTCATAATATTTATATATATACTTATTATT
Found at i:66834 original size:19 final size:19
Alignment explanation
Indices: 66786--66863 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 19
66776 ATTTATTAAT
66786 AAATTCTAAGTTTATTTTCTCT-
1 AAATTC-AA-TTTATTTT-T-TG
66808 AAATTCAATTTATTTTTTG
1 AAATTCAATTTATTTTTTG
*
66827 AGATTCAATTTA-TTTTTG
1 AAATTCAATTTATTTTTTG
66845 AAATTCAATTTATTCTTTT
1 AAATTCAATTTATT-TTTT
66864 ATTTTGTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
18 18 0.35
19 13 0.25
20 12 0.24
21 2 0.04
22 6 0.12
ACGTcount: A:0.29, C:0.09, G:0.05, T:0.56
Consensus pattern (19 bp):
AAATTCAATTTATTTTTTG
Found at i:70098 original size:111 final size:113
Alignment explanation
Indices: 69847--70284 Score: 614
Period size: 111 Copynumber: 4.0 Consensus size: 113
69837 TAGCAAAGAT
* *
69847 TCAAATCCATCAC--AATGGATCAACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
69909 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACC-TTTTC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTTC
* * *
69956 CCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG-
1 TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
70020 A-AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTCCAACCTTTTTC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTTC
* *
70067 TCAAATCCATCACTTGATGGAT-AAGCTTTTCCAGAGAAAGTTCATAATGAGAATAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAA-CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* ** * *
70131 AAGAAGGAAGAAGAAATT-ATAATGAGAAGAATTTATTCAA-CTTTTTGT
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTT-C
** * *
70179 TTGAATTCATCA-TTGATGGATCAACATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
70243 AG-AGGAAGAAGAAGTTCATAATGAG-A-AGCTTGTTCAACCTTT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
70285 ATTTGATTCT
Statistics
Matches: 293, Mismatches: 25, Indels: 21
0.86 0.07 0.06
Matches are distributed among these distances:
109 20 0.07
110 58 0.20
111 144 0.49
112 57 0.19
113 14 0.05
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTTC
Found at i:72347 original size:17 final size:19
Alignment explanation
Indices: 72322--72363 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
72312 ATATTTTTGA
72322 AAATTTAA-TAAT-AG-AC
1 AAATTTAATTAATGAGTAC
72338 AAATTATAATTAATGAGTAC
1 AAATT-TAATTAATGAGTAC
72358 AAATTT
1 AAATTT
72364 TGGTCGTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 3 0.14
18 4 0.18
19 3 0.14
20 7 0.32
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (19 bp):
AAATTTAATTAATGAGTAC
Done.