Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003429.1 Hibiscus syriacus cultivar Beakdansim tig00007227_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: 60560
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:3524 original size:30 final size:30
Alignment explanation
Indices: 3483--3540 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
3473 CAATTTTAAG
*
3483 TTAACCTTCCTCAATCTCTATCATCAACAC
1 TTAAACTTCCTCAATCTCTATCATCAACAC
3513 TTAAACTTCCTCAATCTCTATCATCAAC
1 TTAAACTTCCTCAATCTCTATCATCAAC
3541 TCCCGGCACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (30 bp):
TTAAACTTCCTCAATCTCTATCATCAACAC
Found at i:3655 original size:4 final size:4
Alignment explanation
Indices: 3646--3670 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3636 GATTTATCAT
3646 TTCA TTCA TTCA TTCA TTCA TTCA T
1 TTCA TTCA TTCA TTCA TTCA TTCA T
3671 GTCGGGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TTCA
Found at i:7663 original size:31 final size:31
Alignment explanation
Indices: 7583--7678 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 31
7573 AAGAGTCGAG
*
7583 GGTTACCTATG-TCTTTCGAGATATA-GGAACA
1 GGTTACCTATGTTC-TTCGGGATATATGG-ACA
* * *
7614 GTTTACCTATGTCCTTCGGGACATATGGACA
1 GGTTACCTATGTTCTTCGGGATATATGGACA
* *
7645 GGTTACCTATGTTCTTCGGAATATATGGATA
1 GGTTACCTATGTTCTTCGGGATATATGGACA
7676 GGT
1 GGT
7679 CCTTTGGGAC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
31 51 0.94
32 3 0.06
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (31 bp):
GGTTACCTATGTTCTTCGGGATATATGGACA
Found at i:12092 original size:31 final size:30
Alignment explanation
Indices: 12038--12124 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 30
12028 AGAGTCGATG
* *
12038 GTTACTTATGTCTTTCGAGACATATAGACAA
1 GTTACCTATGTCCTTCG-GACATATAGACAA
* * *
12069 TTTACCTATGTCCTTCGGTACATATGGACAG
1 GTTACCTATGTCCTTCGG-ACATATAGACAA
* *
12100 GTTATCTATGTTCTTCGGAACATAT
1 GTTACCTATGTCCTTCGG-ACATAT
12125 GGATAGTTCC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
30 1 0.02
31 45 0.98
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.38
Consensus pattern (30 bp):
GTTACCTATGTCCTTCGGACATATAGACAA
Found at i:12488 original size:18 final size:18
Alignment explanation
Indices: 12465--12499 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12455 TGATGGCATG
12465 TATGTATGTACGTGTGTA
1 TATGTATGTACGTGTGTA
*
12483 TATGTATGTATGTGTGT
1 TATGTATGTACGTGTGT
12500 GTGTGTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.29, T:0.49
Consensus pattern (18 bp):
TATGTATGTACGTGTGTA
Found at i:13504 original size:21 final size:20
Alignment explanation
Indices: 13480--13518 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13470 TAACTCGGAC
*
13480 TAATTCAATAAATTTAATCCA
1 TAATTCAA-AAAATTAATCCA
*
13501 TAATTTAAAAAATTAATC
1 TAATTCAAAAAATTAATC
13519 AATTTAGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
TAATTCAAAAAATTAATCCA
Found at i:14493 original size:20 final size:22
Alignment explanation
Indices: 14468--14513 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
14458 GAAAACAACA
*
14468 GTCAAACGACCG-A-AAAACGT
1 GTCAAAAGACCGAAGAAAACGT
*
14488 GTCAAAAGATCGAAGAAAACGT
1 GTCAAAAGACCGAAGAAAACGT
14510 GTCA
1 GTCA
14514 TAAAAGCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 1 0.05
22 11 0.50
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (22 bp):
GTCAAAAGACCGAAGAAAACGT
Found at i:14838 original size:20 final size:20
Alignment explanation
Indices: 14784--14839 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
14774 CAACACGAAC
* *
14784 TCCAATTTCGCAACACAGTT
1 TCCAAATTCGCAACTCAGTT
*
14804 TCCAAATTCGTAACTCAGTT
1 TCCAAATTCGCAACTCAGTT
*
14824 TTCAAATTCGCAACTC
1 TCCAAATTCGCAACTC
14840 GAATTTCTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (20 bp):
TCCAAATTCGCAACTCAGTT
Found at i:14846 original size:20 final size:20
Alignment explanation
Indices: 14747--14877 Score: 74
Period size: 20 Copynumber: 6.6 Consensus size: 20
14737 AAATAACCAA
14747 CAAATTCGCAA-TGCG-ATTT
1 CAAATTCGCAACT-CGAATTT
* * *
14766 CAAATTCGCAACACGAACTC
1 CAAATTCGCAACTCGAATTT
* * *
14786 CAATTTCGCAACAC-AGTTT
1 CAAATTCGCAACTCGAATTT
* *
14805 CCAAATTCGTAACTC-AGTTTT
1 -CAAATTCGCAACTCGA-ATTT
14826 CAAATTCGCAACTCGAATTT
1 CAAATTCGCAACTCGAATTT
*** *
14846 CTTTTTCGCAA-TGCGATTTT
1 CAAATTCGCAACT-CGAATTT
*
14866 TAAATTCGCAAC
1 CAAATTCGCAAC
14878 ACAATAGTCC
Statistics
Matches: 84, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
19 16 0.19
20 64 0.76
21 4 0.05
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.32
Consensus pattern (20 bp):
CAAATTCGCAACTCGAATTT
Found at i:15450 original size:20 final size:20
Alignment explanation
Indices: 15427--15486 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 20
15417 AAACTTAAAA
15427 TCGCAACACGAAAATGAAAT
1 TCGCAACACGAAAATGAAAT
*
15447 TCGCATCAC----A--AAAT
1 TCGCAACACGAAAATGAAAT
15461 T-GCAACACGAAAATGAAAT
1 TCGCAACACGAAAATGAAAT
*
15480 TTGCAAC
1 TCGCAAC
15487 GCGATTTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
13 6 0.19
14 5 0.16
16 1 0.03
17 1 0.03
19 5 0.16
20 13 0.42
ACGTcount: A:0.47, C:0.22, G:0.13, T:0.18
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAT
Found at i:15520 original size:20 final size:20
Alignment explanation
Indices: 15490--15542 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
15480 TTGCAACGCG
15490 ATTTTAGTTTTCGCGCTGCGA
1 ATTTTA-TTTTCGCGCTGCGA
* *
15511 ATTTTATTTTCGTGTTGCGA
1 ATTTTATTTTCGCGCTGCGA
*
15531 ATTTCATTTTCG
1 ATTTTATTTTCG
15543 AGTTGTGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 23 0.79
21 6 0.21
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.51
Consensus pattern (20 bp):
ATTTTATTTTCGCGCTGCGA
Found at i:15547 original size:20 final size:20
Alignment explanation
Indices: 15506--15547 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
15496 GTTTTCGCGC
* *
15506 TGCGAATTTTATTTTCGTGT
1 TGCGAATTTCATTTTCGAGT
15526 TGCGAATTTCATTTTCGAGT
1 TGCGAATTTCATTTTCGAGT
15546 TG
1 TG
15548 TGGTTTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.12, G:0.21, T:0.50
Consensus pattern (20 bp):
TGCGAATTTCATTTTCGAGT
Found at i:17196 original size:41 final size:40
Alignment explanation
Indices: 17098--17241 Score: 148
Period size: 41 Copynumber: 3.5 Consensus size: 40
17088 TTTTTAGTTT
* * * * *
17098 GACACCGAGATTCATCACCTCATAGAGTCGATTCTCCACTTC
1 GACACCGAGATCCATCACCT-AT-GAGCCAATTCTACACCTC
17140 GACACCGAGATCCATCACCTGATGAGCCAATTCTACACCTC
1 GACACCGAGATCCATCACCT-ATGAGCCAATTCTACACCTC
* * * * *
17181 GATACTGAGAGCCATCACCTCT-AGCCGACTT-TACACCTC
1 GACACCGAGATCCATCACCTATGAGCC-AATTCTACACCTC
17220 GACACCGAGATCCATCACCTAT
1 GACACCGAGATCCATCACCTAT
17242 TCCATCATAT
Statistics
Matches: 86, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
39 30 0.35
40 4 0.05
41 31 0.36
42 21 0.24
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.22
Consensus pattern (40 bp):
GACACCGAGATCCATCACCTATGAGCCAATTCTACACCTC
Found at i:17398 original size:21 final size:20
Alignment explanation
Indices: 17348--17527 Score: 92
Period size: 21 Copynumber: 8.6 Consensus size: 20
17338 GGATGAGTTA
*
17348 GGTGCTTTACGTGGTGAGGT
1 GGTGCTTTACGTGATGAGGT
*
17368 GAGTGTTTTACGTGATGAGGT
1 G-GTGCTTTACGTGATGAGGT
* **
17389 CGGTGCTTTATGTGATGACAAT
1 -GGTGCTTTACGTGATGA-GGT
* **
17411 GGTGCATGGCGTGATGAGGT
1 GGTGCTTTACGTGATGAGGT
* *
17431 AGG-GTCTTTATGTGGTGAGGT
1 -GGTG-CTTTACGTGATGAGGT
* * **
17452 AGTTGTTTTACGTGATGACAAT
1 -GGTGCTTTACGTGATGA-GGT
* *
17474 GGTGCTTTACGTGGTGAGGCA
1 GGTGCTTTACGTGATGAGG-T
* * *
17495 GCTACTTTACATGATGAGGT
1 GGTGCTTTACGTGATGAGGT
*
17515 CGGTGCTCTACGT
1 -GGTGCTTTACGT
17528 AAGATTGTTT
Statistics
Matches: 113, Mismatches: 38, Indels: 17
0.67 0.23 0.10
Matches are distributed among these distances:
20 3 0.03
21 106 0.94
22 4 0.04
ACGTcount: A:0.18, C:0.12, G:0.36, T:0.34
Consensus pattern (20 bp):
GGTGCTTTACGTGATGAGGT
Found at i:17398 original size:42 final size:43
Alignment explanation
Indices: 17339--17527 Score: 122
Period size: 42 Copynumber: 4.5 Consensus size: 43
17329 ACCTCCACGG
* *
17339 GATGAGTTAGGTGCTTTACGTGGTGAGGTGAG-TGTTTTACGT
1 GATGAGGTAGGTGCTTTACGTGGTGAGGTGAGCTGCTTTACGT
* * * ** * **
17381 GATGAGGTCGGTGCTTTATGTGATGACAATG-G-TGCATGGCGT
1 GATGAGGTAGGTGCTTTACGTGGTGA-GGTGAGCTGCTTTACGT
* * *
17423 GATGAGGTAGG-GTCTTTATGTGGTGAGGT-AGTTGTTTTACGT
1 GATGAGGTAGGTG-CTTTACGTGGTGAGGTGAGCTGCTTTACGT
** * * *
17465 GATGA-CAATGGTGCTTTACGTGGTGAGG-CAGCTACTTTACAT
1 GATGAGGTA-GGTGCTTTACGTGGTGAGGTGAGCTGCTTTACGT
* *
17507 GATGAGGTCGGTGCTCTACGT
1 GATGAGGTAGGTGCTTTACGT
17528 AAGATTGTTT
Statistics
Matches: 110, Mismatches: 29, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
41 4 0.04
42 103 0.94
43 3 0.03
ACGTcount: A:0.19, C:0.11, G:0.36, T:0.34
Consensus pattern (43 bp):
GATGAGGTAGGTGCTTTACGTGGTGAGGTGAGCTGCTTTACGT
Found at i:17492 original size:63 final size:63
Alignment explanation
Indices: 17348--17492 Score: 175
Period size: 63 Copynumber: 2.3 Consensus size: 63
17338 GGATGAGTTA
* * *
17348 GGTGCTTTACGTGGTGAGGTGAGTGTTTTACGTGATGAGGTCGGTGCTTTATGTGATGACAAT
1 GGTGCTTTACGTGGTGAGGTGAGGGTTTTACGTGATGAGGTAGGTGCTTTACGTGATGACAAT
* ** * * * * *
17411 GGTGCATGGCGTGATGAGGT-AGGGTCTTTATGTGGTGAGGTAGTTGTTTTACGTGATGACAAT
1 GGTGCTTTACGTGGTGAGGTGAGGGT-TTTACGTGATGAGGTAGGTGCTTTACGTGATGACAAT
17474 GGTGCTTTACGTGGTGAGG
1 GGTGCTTTACGTGGTGAGG
17493 CAGCTACTTT
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
62 4 0.06
63 62 0.94
ACGTcount: A:0.17, C:0.09, G:0.39, T:0.35
Consensus pattern (63 bp):
GGTGCTTTACGTGGTGAGGTGAGGGTTTTACGTGATGAGGTAGGTGCTTTACGTGATGACAAT
Found at i:17503 original size:63 final size:61
Alignment explanation
Indices: 17348--17527 Score: 162
Period size: 63 Copynumber: 2.9 Consensus size: 61
17338 GGATGAGTTA
* * * *
17348 GGTGCTTTACGTGGTGAGGTGAGTGTTTTACGTGATGAGGTCGGTGCTTTATGTGATGACAAT
1 GGTGCTTTACGTGGTGAGG-CAGT-CTTTACGTGATGAGGTAGGTGCTTTACGTGATGACAAT
* ** * * * * * *
17411 GGTGCATGGCGTGATGAGGTAGGGTCTTTATGTGGTGAGGTAGTTGTTTTACGTGATGACAAT
1 GGTGCTTTACGTGGTGAGGCA--GTCTTTACGTGATGAGGTAGGTGCTTTACGTGATGACAAT
* * *
17474 GGTGCTTTACGTGGTGAGGCAGCTACTTTACATGATGAGGTCGGTGCTCTACGT
1 GGTGCTTTACGTGGTGAGGCAG-T-CTTTACGTGATGAGGTAGGTGCTTTACGT
17528 AAGATTGTTT
Statistics
Matches: 89, Mismatches: 24, Indels: 8
0.74 0.20 0.07
Matches are distributed among these distances:
61 1 0.01
62 2 0.02
63 84 0.94
64 2 0.02
ACGTcount: A:0.18, C:0.12, G:0.36, T:0.34
Consensus pattern (61 bp):
GGTGCTTTACGTGGTGAGGCAGTCTTTACGTGATGAGGTAGGTGCTTTACGTGATGACAAT
Found at i:17905 original size:21 final size:20
Alignment explanation
Indices: 17866--17952 Score: 86
Period size: 21 Copynumber: 4.2 Consensus size: 20
17856 ACCTCTCATA
17866 GTTCAAGAGGCCC-CCCATC
1 GTTCAAGAGGCCCTCCCATC
17885 GTTCAAGAGGCCTCTCCCATC
1 GTTCAAGAGGCC-CTCCCATC
* *
17906 ATTCAAGAAGCCCCTCCCATC
1 GTTCAAG-AGGCCCTCCCATC
* * **
17927 GATCAGGATCCACCTCCCATC
1 GTTCAAGAGGC-CCTCCCATC
17948 GTTCA
1 GTTCA
17953 GAATCCACAT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
19 12 0.21
20 4 0.07
21 37 0.65
22 4 0.07
ACGTcount: A:0.23, C:0.40, G:0.16, T:0.21
Consensus pattern (20 bp):
GTTCAAGAGGCCCTCCCATC
Found at i:17953 original size:21 final size:21
Alignment explanation
Indices: 17828--17960 Score: 76
Period size: 21 Copynumber: 6.4 Consensus size: 21
17818 ACAACCATTT
**
17828 AGGATCCACCTCCCATTATTC
1 AGGATCCACCTCCCATCGTTC
* * *
17849 AGGATTCACCTCTCATAGTTC
1 AGGATCCACCTCCCATCGTTC
* **
17870 AAGAGGC-CC-CCCATCGTTC
1 AGGATCCACCTCCCATCGTTC
* * * *
17889 AAGAGGCC-TCTCCCATCATTC
1 AGGA-TCCACCTCCCATCGTTC
* * *
17910 AAGAAGCC-CCTCCCATCGATC
1 -AGGATCCACCTCCCATCGTTC
17931 AGGATCCACCTCCCATCGTTC
1 AGGATCCACCTCCCATCGTTC
*
17952 AGAATCCAC
1 AGGATCCAC
17961 ATTCTATACT
Statistics
Matches: 87, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
19 12 0.14
20 10 0.11
21 63 0.72
22 2 0.02
ACGTcount: A:0.25, C:0.38, G:0.14, T:0.23
Consensus pattern (21 bp):
AGGATCCACCTCCCATCGTTC
Found at i:19484 original size:20 final size:20
Alignment explanation
Indices: 19456--19535 Score: 88
Period size: 20 Copynumber: 4.0 Consensus size: 20
19446 TCGATATTCA
* *
19456 AATTTGCAATACGAAAATCG
1 AATTCGCAACACGAAAATCG
*
19476 AATTCGCAACACGAAAATTG
1 AATTCGCAACACGAAAATCG
** ** *
19496 GTTTCGCAATTCGAAAATCA
1 AATTCGCAACACGAAAATCG
19516 AATTCGCAACACGAAAATCG
1 AATTCGCAACACGAAAATCG
19536 CGTTGCGAAT
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (20 bp):
AATTCGCAACACGAAAATCG
Found at i:19560 original size:20 final size:20
Alignment explanation
Indices: 19532--19581 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
19522 CAACACGAAA
*
19532 ATCGCGTTGCGAATTTTAAT
1 ATCGAGTTGCGAATTTTAAT
19552 ATCGAGTTGCGAATTTTAAT
1 ATCGAGTTGCGAATTTTAAT
19572 ATCGAGTTGC
1 ATCGAGTTGC
19582 AGTTTTCATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (20 bp):
ATCGAGTTGCGAATTTTAAT
Found at i:22119 original size:24 final size:24
Alignment explanation
Indices: 22085--22138 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
22075 CTGAAACATC
22085 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
22109 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
22133 ATCAAA
1 ATCAAA
22139 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:22912 original size:14 final size:15
Alignment explanation
Indices: 22876--22913 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
22866 GAAATCATTG
22876 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
22891 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
22906 AAAAATTA
1 AAAAATTA
22914 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:22950 original size:22 final size:21
Alignment explanation
Indices: 22921--22964 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
22911 TTAGAGATGG
*
22921 GGAAGGATGTCGTCGGATATA
1 GGAAGGATGTCGTCGGAGATA
22942 GGAACGGATGTCGTCGGAGATA
1 GGAA-GGATGTCGTCGGAGATA
22964 G
1 G
22965 TGAGAGATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.27, C:0.11, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAAGGATGTCGTCGGAGATA
Found at i:23085 original size:20 final size:20
Alignment explanation
Indices: 23048--23224 Score: 132
Period size: 20 Copynumber: 8.8 Consensus size: 20
23038 ATATATCTAA
*
23048 AAAATTTGTGTTGTGAAAAAG
1 AAAA-TTGTGTTGCGAAAAAG
*
23069 AAAATTGAGTTGCGAAAAAG
1 AAAATTGTGTTGCGAAAAAG
23089 -AAATTCGTGTTGCG-AAAAG
1 AAAATT-GTGTTGCGAAAAAG
* *
23108 AAAATCT-AGTTGCGAAGAAG
1 AAAAT-TGTGTTGCGAAAAAG
*
23128 AAATTTGTGTTGCGAAAAAG
1 AAAATTGTGTTGCGAAAAAG
* **
23148 AAATTTGTGTTGCGAATTCA-
1 AAAATTGTGTTGCGAA-AAAG
* * * *
23168 AAAATCGAGTTGTGAAATTA-
1 AAAATTGTGTTGCGAAA-AAG
* *
23188 AAAATCGTATTGCGAAAAAG
1 AAAATTGTGTTGCGAAAAAG
23208 -AAATTCGTGTTGCGAAA
1 AAAATT-GTGTTGCGAAA
23225 TTGTCAAAAT
Statistics
Matches: 125, Mismatches: 22, Indels: 19
0.75 0.13 0.11
Matches are distributed among these distances:
19 22 0.18
20 97 0.78
21 6 0.05
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.28
Consensus pattern (20 bp):
AAAATTGTGTTGCGAAAAAG
Found at i:23140 original size:59 final size:57
Alignment explanation
Indices: 23057--23224 Score: 194
Period size: 60 Copynumber: 2.8 Consensus size: 57
23047 AAAAATTTGT
* *
23057 GTTGTGAAAAAGAAAATTGAGTTGCGAAAAAGAAATTCGTGTTGCGAAAAGAAAATCTA
1 GTTGTG-AAAAGAAAATTGTGTTGCGAAAAAGAAATTCGTGTTGCGAAAA-AAAATCGA
* * * *
23116 GTTGCGAAGAAGAAATTTGTGTTGCGAAAAAGAAATTTGTGTTGCGAATTCAAAAATCGA
1 GTTGTGAA-AAGAAAATTGTGTTGCGAAAAAGAAATTCGTGTTGCGAA--AAAAAATCGA
* *
23176 GTTGTGAAATTA-AAAATCGTATTGCGAAAAAGAAATTCGTGTTGCGAAA
1 GTTGTGAAA--AGAAAATTGTGTTGCGAAAAAGAAATTCGTGTTGCGAAA
23225 TTGTCAAAAT
Statistics
Matches: 92, Mismatches: 12, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
58 2 0.02
59 42 0.46
60 46 0.50
61 2 0.02
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.27
Consensus pattern (57 bp):
GTTGTGAAAAGAAAATTGTGTTGCGAAAAAGAAATTCGTGTTGCGAAAAAAAATCGA
Found at i:23204 original size:60 final size:60
Alignment explanation
Indices: 23078--23245 Score: 175
Period size: 60 Copynumber: 2.8 Consensus size: 60
23068 GAAAATTGAG
* * * * *
23078 TTGCGAAAAAGAAATTCGTGTTGCGAA--AAGAAAATCTAGTTGCGAAGAAGAAATTTGTG
1 TTGCGAAAAAGAAATTCGTGTTGCGAATTCA-AAAATCGAGTTGCGAAGAAGAAAATCGTA
* *
23137 TTGCGAAAAAGAAATTTGTGTTGCGAATTCAAAAATCGAGTTGTGAA-ATTA-AAAATCGTA
1 TTGCGAAAAAGAAATTCGTGTTGCGAATTCAAAAATCGAGTTGCGAAGA--AGAAAATCGTA
*
23197 TTGCGAAAAAGAAATTCGTGTTGCGAAATTGTC-AAAATCGAGTTACGAA
1 TTGCGAAAAAGAAATTCGTGTTGCG-AA-T-TCAAAAATCGAGTTGCGAA
23246 TTTGACTTAT
Statistics
Matches: 92, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
59 27 0.29
60 44 0.48
61 4 0.04
62 15 0.16
63 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (60 bp):
TTGCGAAAAAGAAATTCGTGTTGCGAATTCAAAAATCGAGTTGCGAAGAAGAAAATCGTA
Found at i:23293 original size:20 final size:20
Alignment explanation
Indices: 23270--23325 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
23260 TGCGAATTCC
*
23270 AAATTCGCGTTGCGAAAAAG
1 AAATTCGAGTTGCGAAAAAG
* *
23290 AAATTTGAGTTGCGAAAAAAA
1 AAATTCGAGTTGCG-AAAAAG
23311 AAATT-GAGTTGCGAA
1 AAATTCGAGTTGCGAA
23326 TTCGGAAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.06
20 20 0.62
21 10 0.31
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (20 bp):
AAATTCGAGTTGCGAAAAAG
Found at i:23322 original size:40 final size:40
Alignment explanation
Indices: 23049--23325 Score: 174
Period size: 40 Copynumber: 6.9 Consensus size: 40
23039 TATATCTAAA
*
23049 AAATTTGTGTTGTGAAAAAGAAAATTGAGTTGCGAAAAAG
1 AAATTTGTGTTGCGAAAAAGAAAATTGAGTTGCGAAAAAG
* *
23089 AAATTCGTGTTGCG-AAAAGAAAATCT-AGTTGCGAAGAAG
1 AAATTTGTGTTGCGAAAAAGAAAAT-TGAGTTGCGAAAAAG
* * *
23128 AAATTTGTGTTGCGAAAAAGAAATTTGTGTTGCGAATTCAA-
1 AAATTTGTGTTGCGAAAAAGAAAATTGAGTTGCGAA--AAAG
* * * * *
23169 AAA-TCGAGTTGTGAAATTA-AAAATCGTA-TTGCGAAAAAG
1 AAATTTGTGTTGCGAAA-AAGAAAATTG-AGTTGCGAAAAAG
* ** * * ***
23208 AAATTCGTGTTGCGAAATTGTCAAAATCGAGTTACGAATTTG
1 AAATTTGTGTTGCGAAAAAG--AAAATTGAGTTGCGAAAAAG
* **** *
23250 -ACTTATGTGTTGCG-AATTCCAAATTCGCGTTGCGAAAAAG
1 AAATT-TGTGTTGCGAAAAAGAAAATT-GAGTTGCGAAAAAG
* *
23290 AAATTTGAGTTGCGAAAAAAAAAATTGAGTTGCGAA
1 AAATTTGTGTTGCGAAAAAGAAAATTGAGTTGCGAA
23326 TTCGGAAACT
Statistics
Matches: 181, Mismatches: 39, Indels: 34
0.71 0.15 0.13
Matches are distributed among these distances:
38 2 0.01
39 44 0.24
40 89 0.49
41 22 0.12
42 24 0.13
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (40 bp):
AAATTTGTGTTGCGAAAAAGAAAATTGAGTTGCGAAAAAG
Found at i:23323 original size:122 final size:119
Alignment explanation
Indices: 23045--23325 Score: 282
Period size: 122 Copynumber: 2.3 Consensus size: 119
23035 TTTATATATC
* *
23045 TAAAAAATTTGTGTTGTGAAAAAGAAAATTGAGTTGCGAAAAAGAAATTCGTGTTGCGAAAAGAA
1 TAAAAAATTTGAGTTGTGAAAAAAAAAATTGAGTTGCGAAAAAGAAATTCGTGTTGCGAAAAGAA
* * * * *
23110 AATCTAGTTGCGAAGAAGAAATTTGTGTTGCGAAAAAGAAATTTGTGTTGCGAA
66 AATCGAGTTACGAAGAAGAAATTTGTGTTGCGAAAAACAAATTCGCGTTGCGAA
* * ** * *
23164 TTCAAAAA-TCGAGTTGTGAAATTAAAAATCGTA-TTGCGAAAAAGAAATTCGTGTTGCGAAATT
1 -TAAAAAATTTGAGTTGTGAAAAAAAAAATTG-AGTTGCGAAAAAGAAATTCGTGTTGCGAAA-A
*** * ***
23227 GTCAAAATCGAGTTACGAATTTG-ACTTATGTGTTGCGAATTCCAAATTCGCGTTGCGAA
63 G--AAAATCGAGTTACGAAGAAGAAATT-TGTGTTGCGAAAAACAAATTCGCGTTGCGAA
*
23286 -AAAGAAATTTGAGTTGCGAAAAAAAAAATTGAGTTGCGAA
1 TAAA-AAATTTGAGTTGTGAAAAAAAAAATTGAGTTGCGAA
23326 TTCGGAAACT
Statistics
Matches: 127, Mismatches: 26, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
119 45 0.35
120 10 0.08
121 7 0.06
122 65 0.51
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.28
Consensus pattern (119 bp):
TAAAAAATTTGAGTTGTGAAAAAAAAAATTGAGTTGCGAAAAAGAAATTCGTGTTGCGAAAAGAA
AATCGAGTTACGAAGAAGAAATTTGTGTTGCGAAAAACAAATTCGCGTTGCGAA
Found at i:35207 original size:111 final size:113
Alignment explanation
Indices: 34990--35215 Score: 321
Period size: 111 Copynumber: 2.0 Consensus size: 113
34980 ATTTGTTGGG
* * * *
34990 AAGTTAATCTCCTCAAGCATTCATTCATGGGTTCGTCCTGTCTGGAGCTGAAGGTTTTTGGAGAG
1 AAGTTAATATCCTCAAGCATTCATTCATCGGTTCATCCTGTCTGGAGCTGAAGGTTGTTGGAGAG
* *
35055 TTTCAATATGGTGCCAGAAACAGGAGATGCCCTTAATAACATTACAGC
66 TTTCAATATGGTCCCAGAAACAGGAGATACCCTTAATAACATTACAGC
* * * *
35103 AAGTTAATATTCT-AAGCATTCATTCATCGGTTCATTCTGTTTGGAGCTGAAGG-TGTTGTAGAG
1 AAGTTAATATCCTCAAGCATTCATTCATCGGTTCATCCTGTCTGGAGCTGAAGGTTGTTGGAGAG
* * *
35166 TTTCAATGTGGTCCCAGAAACAGGTGATACCTTTAATAACATTACAGC
66 TTTCAATATGGTCCCAGAAACAGGAGATACCCTTAATAACATTACAGC
35214 AA
1 AA
35216 CCCCATAGCT
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
111 53 0.53
112 36 0.36
113 11 0.11
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (113 bp):
AAGTTAATATCCTCAAGCATTCATTCATCGGTTCATCCTGTCTGGAGCTGAAGGTTGTTGGAGAG
TTTCAATATGGTCCCAGAAACAGGAGATACCCTTAATAACATTACAGC
Found at i:37945 original size:60 final size:60
Alignment explanation
Indices: 37781--37950 Score: 171
Period size: 60 Copynumber: 2.8 Consensus size: 60
37771 CTATGACTGT
* * * * *
37781 CATTTTAAATTAATCCCTAAACTTTTGATTATTTCAATTTCATCATCAAACTATGATCTC
1 CATTTTAAATTAGTCCCTAAACTTTTGAATATTACAATTTCATCCTCAAACTATGACCTC
* * ** * * * *
37841 CATTCTAAATTAGTCCTTAAACTTTTGAGCATCATAATTTCATCCTTAAACTATGGCC-C
1 CATTTTAAATTAGTCCCTAAACTTTTGAATATTACAATTTCATCCTCAAACTATGACCTC
* * * *
37900 TCTTTTTAAATTGGTCCCCAAACTTTTGAATATTACAATTTCATCCCCAAA
1 -CATTTTAAATTAGTCCCTAAACTTTTGAATATTACAATTTCATCCTCAAA
37951 TTCATCCAAA
Statistics
Matches: 86, Mismatches: 23, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
59 1 0.01
60 85 0.99
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (60 bp):
CATTTTAAATTAGTCCCTAAACTTTTGAATATTACAATTTCATCCTCAAACTATGACCTC
Found at i:38655 original size:15 final size:15
Alignment explanation
Indices: 38635--38671 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
38625 TGAGACATTA
*
38635 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
38650 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
38665 CCCGCCC
1 CCCGCCC
38672 AGCTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.70, G:0.16, T:0.05
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:38981 original size:69 final size:69
Alignment explanation
Indices: 38868--39003 Score: 209
Period size: 69 Copynumber: 2.0 Consensus size: 69
38858 ACCACGTCAC
* *
38868 TTTCCATGTTCTTTAGCCCATCTAAACACAAATTAGCCGTACTATAAGCATTAACATCAAAAGCA
1 TTTCCATGTTCTTTAGCCCATCAAAACACAAATTAGCCGCACTATAAGCATTAACATCAAAAGCA
38933 ACAG
66 ACAG
* * * * *
38937 TTTCCATGTTCTTTAGCCCCTCAAAACCCATATTAGGCGCACTATAAGCATTAACATCGAAAGCA
1 TTTCCATGTTCTTTAGCCCATCAAAACACAAATTAGCCGCACTATAAGCATTAACATCAAAAGCA
39002 AC
66 AC
39004 TCAACAATCC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.27
Consensus pattern (69 bp):
TTTCCATGTTCTTTAGCCCATCAAAACACAAATTAGCCGCACTATAAGCATTAACATCAAAAGCA
ACAG
Found at i:43775 original size:12 final size:12
Alignment explanation
Indices: 43758--43782 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43748 TAACTGAAAC
43758 TCTTCCAGATGT
1 TCTTCCAGATGT
43770 TCTTCCAGATGT
1 TCTTCCAGATGT
43782 T
1 T
43783 GGATTCTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (12 bp):
TCTTCCAGATGT
Found at i:46912 original size:41 final size:41
Alignment explanation
Indices: 46858--47085 Score: 260
Period size: 41 Copynumber: 5.4 Consensus size: 41
46848 ATTCACGTTG
* * *
46858 CATTTCGCATTGCGATAGTTGAAAATCGTGTTGCGTTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
46899 CATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* * **
46940 CATTTCGCGTTGCGATAGTTGAAATCACAACGCGATCT-CCATCATC
1 CATTTCGCGTTGCGATAGTTG-AA--A-ATCGCG-T-TGCGATTTTC
* * *
46986 GCAAATTCGCGTTGCGATAGTTGAAAATCGCGTTGTGGTTTTC
1 -C-ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
47029 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
47070 CATTTCACGTTGCGAT
1 CATTTCGCGTTGCGAT
47086 TTTCCATTTC
Statistics
Matches: 156, Mismatches: 22, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
41 109 0.70
42 3 0.02
43 4 0.03
44 5 0.03
45 6 0.04
46 6 0.04
47 4 0.03
48 19 0.12
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:46954 original size:20 final size:20
Alignment explanation
Indices: 46887--46955 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
46877 TGAAAATCGT
*
46887 GTTGCGTTTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
* ** **
46907 GTTGCGATAGTTGGAGATCGC
1 GTTGCGAT-TTTCCATTTCGC
46928 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
46948 GTTGCGAT
1 GTTGCGAT
46956 AGTTGAAATC
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 22 0.59
21 15 0.41
ACGTcount: A:0.12, C:0.20, G:0.28, T:0.41
Consensus pattern (20 bp):
GTTGCGATTTTCCATTTCGC
Found at i:47016 original size:21 final size:21
Alignment explanation
Indices: 46992--47065 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
46982 CATCGCAAAT
46992 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * * ** **
47013 TCGCGTTGTGGT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
47033 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
47054 TCGCGTTGCGAT
1 TCGCGTTGCGAT
47066 TTTCCATTTC
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 13 0.34
21 25 0.66
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:47082 original size:20 final size:20
Alignment explanation
Indices: 47057--47105 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
47047 TTGAAAATCG
47057 CGTTGCGATTTTCCATTTCA
1 CGTTGCGATTTTCCATTTCA
47077 CGTTGCGATTTTCCATTTCA
1 CGTTGCGATTTTCCATTTCA
47097 CGTTGCGAT
1 CGTTGCGAT
47106 AGTCTACAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCA
Found at i:47142 original size:61 final size:60
Alignment explanation
Indices: 47024--47142 Score: 143
Period size: 61 Copynumber: 1.9 Consensus size: 60
47014 CGCGTTGTGG
* *
47024 TTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCACGTTGCGA
1 TTTTCCATTTCACGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATT-ACGTTGCGA
* * *
47085 TTTTCCATTTCACGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT-CGTTG
1 TTTTCCATTTCACGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATTACGTTG
47143 AAAAAAAGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
61 32 0.64
62 15 0.30
63 3 0.06
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (60 bp):
TTTTCCATTTCACGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTACGTTGCGA
Found at i:47232 original size:6 final size:6
Alignment explanation
Indices: 47223--47267 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
47213 TATTACCATT
47223 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
47268 CGAGACGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:47763 original size:5 final size:5
Alignment explanation
Indices: 47749--47799 Score: 95
Period size: 5 Copynumber: 10.4 Consensus size: 5
47739 CCGCCGCCGC
47749 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT
47798 CG
1 CG
47800 GGTCGTGGTC
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.09
5 42 0.91
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.37
Consensus pattern (5 bp):
CGTCT
Found at i:47811 original size:6 final size:6
Alignment explanation
Indices: 47800--47826 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
47790 TCTCGTCTCG
47800 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
47827 TACGTGTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:47986 original size:21 final size:20
Alignment explanation
Indices: 47960--48080 Score: 134
Period size: 21 Copynumber: 5.9 Consensus size: 20
47950 GCAACGAATT
47960 TGGAAAATCGCAAACGCGAAA
1 TGGAAAATCGC-AACGCGAAA
*
47981 TGGAAAATCGCAACGCGAAT
1 TGGAAAATCGCAACGCGAAA
** *
48001 TTCAACTATCGCAACGCGAAA
1 TGGAA-AATCGCAACGCGAAA
**
48022 TGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGCGAAA
** *
48042 TTCAACTATCGCAACGCGAAA
1 TGGAA-AATCGCAACGCGAAA
48063 TGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGCGA
48081 TTTTCAACTA
Statistics
Matches: 80, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
20 38 0.47
21 42 0.52
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAA
Found at i:48026 original size:41 final size:41
Alignment explanation
Indices: 47966--48102 Score: 256
Period size: 41 Copynumber: 3.3 Consensus size: 41
47956 AATTTGGAAA
*
47966 ATCGCAAACGCGAAATGGAAAATCGCAACGCGAATTTCAACT
1 ATCGC-AACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
48008 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
48049 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
48090 ATCGCAACGCGAA
1 ATCGCAACGCGAA
48103 TTTGCGATAG
Statistics
Matches: 94, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
41 89 0.95
42 5 0.05
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.18
Consensus pattern (41 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
Found at i:48026 original size:62 final size:61
Alignment explanation
Indices: 47919--48039 Score: 151
Period size: 62 Copynumber: 2.0 Consensus size: 61
47909 ACAACGAATT
*
47919 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCAAACGCGAAA
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATATGGAAAATCGC-AACGCGAAA
*
47981 TGGAAAATCGCAACG-CGAA-TTTCA-ACTATCGCAACGCGAA-ATGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGAC-AACTGT-AGACTATCGCAA--CGAATATGGAAAATCGCAACGCGA
48040 TTTTCAACTA
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
61 20 0.38
62 29 0.55
63 4 0.08
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.16
Consensus pattern (61 bp):
TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATATGGAAAATCGCAACGCGAAA
Found at i:48095 original size:21 final size:21
Alignment explanation
Indices: 47987--48105 Score: 134
Period size: 21 Copynumber: 5.8 Consensus size: 21
47977 GAAATGGAAA
47987 ATCGCAACGCGAATTTCAACT
1 ATCGCAACGCGAATTTCAACT
* ** *
48008 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGAATTTCAACT
*
48028 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAATTTCAACT
* ** *
48049 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGAATTTCAACT
*
48069 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAATTTCAACT
48090 ATCGCAACGCGAATTT
1 ATCGCAACGCGAATTT
48106 GCGATAGTGG
Statistics
Matches: 76, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
20 30 0.39
21 46 0.61
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAATTTCAACT
Found at i:51016 original size:134 final size:135
Alignment explanation
Indices: 50730--51141 Score: 503
Period size: 134 Copynumber: 3.1 Consensus size: 135
50720 TTGGGTTGTT
* * ** * * *
50730 TTTAGGAATGATGATAACACAATTCCACTCTTTTGGGGACGAATGGTTATCTGAGGTTGACATGG
1 TTTAGGGATGATGATAACACAGTTCCACTCTGCTGGGGACGACTGGTTATTTGAGGTTGACATGA
* * * * * *
50795 TTCCACTCTGTTGGGGAAATCTGGTCGGGGGATAACACTGCTCATTCGTGATGAAGAGTTATTGG
66 TTCCACTCTGATGAGGAAATCTGGTCGGGGGATGACACTGCTCATACATGATGAAGAGTTCTTGG
*
50860 TCATC
131 CCATC
* ** *
50865 TTTA-GGAAGTATGATAACATGGTTCCACTCTGCTGGGGACGGCTGGTTATTTGAGGTTGACATG
1 TTTAGGGATG-ATGATAACACAGTTCCACTCTGCTGGGGACGACTGGTTATTTGAGGTTGACATG
* * *
50929 ATTCCACTCTGCT-AGGAAAACTGGTCGGGGGATGACACTGCTTATACATGATGAAGAGTTCTTG
65 ATTCCACTCTGATGAGGAAATCTGGTCGGGGGATGACACTGCTCATACATGATGAAGAGTTCTTG
50993 GCCATC
130 GCCATC
* *
50999 TTTAGGGATGATGATAACACAGTTCCACTCTGCTGGGGACGACTGGTTATCTT-AGATTGACACG
1 TTTAGGGATGATGATAACACAGTTCCACTCTGCTGGGGACGACTGGTTAT-TTGAGGTTGACATG
* * * *
51063 ACTCCTAC-GTGATGAGGAGATCTGGTCGGGTGATGACACTGCTCATA-AGTGATGAAGAGTTC-
65 ATTCC-ACTCTGATGAGGAAATCTGGTCGGGGGATGACACTGCTCATACA-TGATGAAGAGTTCT
51125 TGGCCATC
128 TGGCCATC
51133 TTTAGGGAT
1 TTTAGGGAT
51142 AATGGTTTCA
Statistics
Matches: 238, Mismatches: 33, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
134 127 0.53
135 111 0.47
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (135 bp):
TTTAGGGATGATGATAACACAGTTCCACTCTGCTGGGGACGACTGGTTATTTGAGGTTGACATGA
TTCCACTCTGATGAGGAAATCTGGTCGGGGGATGACACTGCTCATACATGATGAAGAGTTCTTGG
CCATC
Done.