Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006251.1 Hibiscus syriacus cultivar Beakdansim tig00014898_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: 53319
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3669 original size:19 final size:19
Alignment explanation
Indices: 3645--3702 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 19
3635 TATGGATTAG
*
3645 GCTATGAATTTGAAAATAA
1 GCTATGAATATGAAAATAA
*
3664 GCTATGAATATGACAATAA
1 GCTATGAATATGAAAATAA
* * *
3683 GATATGAGTCTGAAAATAA
1 GCTATGAATATGAAAATAA
3702 G
1 G
3703 TCATGAGTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.28
Consensus pattern (19 bp):
GCTATGAATATGAAAATAA
Found at i:3727 original size:19 final size:19
Alignment explanation
Indices: 3655--3727 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
3645 GCTATGAATT
* * *
3655 TGAAAATAAGCTATGAATA
1 TGAAAATAAGTTATGAGTC
* *
3674 TGACAATAAGATATGAGTC
1 TGAAAATAAGTTATGAGTC
*
3693 TGAAAATAAGTCATGAGTC
1 TGAAAATAAGTTATGAGTC
*
3712 TGGAAAA-ACGTTATGA
1 T-GAAAATAAGTTATGA
3728 TTTAAAAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 39 0.89
20 5 0.11
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.26
Consensus pattern (19 bp):
TGAAAATAAGTTATGAGTC
Found at i:11026 original size:44 final size:44
Alignment explanation
Indices: 10963--11052 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
10953 GAAAGTGTCG
10963 ATACTTTAATATAATTATCGACACTTTTAGAATGAGAAAATAAC
1 ATACTTTAATATAATTATCGACACTTTTAGAATGAGAAAATAAC
11007 ATACTTTAATATAATTATCGACACTTTTAGAATGAGAAAATAAC
1 ATACTTTAATATAATTATCGACACTTTTAGAATGAGAAAATAAC
11051 AT
1 AT
11053 CAGTGACCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (44 bp):
ATACTTTAATATAATTATCGACACTTTTAGAATGAGAAAATAAC
Found at i:11314 original size:41 final size:41
Alignment explanation
Indices: 11269--11361 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 41
11259 AATAAGTAAA
*
11269 TCGCAATGCGATACTGAC-TA-TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGAT--TGACGTATTCGCAATGCAATTTTCATAAT
* * ** *
11310 TCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTGACGTATTCGCAATGCAATTTTCATAAT
11351 TCGCAATGCGA
1 TCGCAATGCGA
11362 ATACGTAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 3 0.07
40 2 0.05
41 38 0.88
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (41 bp):
TCGCAATGCGATTGACGTATTCGCAATGCAATTTTCATAAT
Found at i:11323 original size:21 final size:21
Alignment explanation
Indices: 11207--11361 Score: 79
Period size: 21 Copynumber: 7.5 Consensus size: 21
11197 ATTATGACTA
*
11207 TCGCAATGCGATTTTCCA-ATT
1 TCGCAATGCGATTTT-CATAAT
** **
11228 TCGCGTTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCATAAT
* * *
11249 TCGCAATGCGA--ATAAGTAAA
1 TCGCAATGCGATTTTCA-TAAT
** *
11269 TCGCAATGCGATACTGACT-A-
1 TCGCAATGCGATTTTCA-TAAT
* *
11289 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
11310 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
11330 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
11351 TCGCAATGCGA
1 TCGCAATGCGA
11362 ATACGTAAAT
Statistics
Matches: 99, Mismatches: 28, Indels: 14
0.70 0.20 0.10
Matches are distributed among these distances:
19 2 0.02
20 44 0.44
21 50 0.51
22 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:11376 original size:20 final size:20
Alignment explanation
Indices: 11351--11455 Score: 100
Period size: 20 Copynumber: 5.5 Consensus size: 20
11341 TTTTCATAAT
11351 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
11371 T--C---GC-AATA-GTAAA
1 TCGCAATGCGAATACGTAAA
* *
11384 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
11405 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
11425 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
11445 TCGCAATGCGA
1 TCGCAATGCGA
11456 TTTACATAGC
Statistics
Matches: 71, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
13 6 0.08
14 4 0.06
15 3 0.04
18 3 0.04
19 5 0.07
20 34 0.48
21 16 0.23
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:11384 original size:13 final size:14
Alignment explanation
Indices: 11361--11390 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
11351 TCGCAATGCG
11361 AATACGTAAATCGC
1 AATACGTAAATCGC
11375 AATA-GTAAATCGC
1 AATACGTAAATCGC
11388 AAT
1 AAT
11391 GCGAATTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (14 bp):
AATACGTAAATCGC
Found at i:11719 original size:27 final size:27
Alignment explanation
Indices: 11662--11714 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
11652 CATCGCCGGC
* *
11662 GAAATCCCTCACAACCATTCACAGTCA
1 GAAATCCCTCACAACCATTCAAAATCA
*
11689 GAAATCCCTCACAATCATTCAGAAAT
1 GAAATCCCTCACAACCATTCA-AAAT
11715 GGAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.40, C:0.32, G:0.08, T:0.21
Consensus pattern (27 bp):
GAAATCCCTCACAACCATTCAAAATCA
Found at i:12027 original size:19 final size:19
Alignment explanation
Indices: 11963--12066 Score: 112
Period size: 19 Copynumber: 5.7 Consensus size: 19
11953 TAGTTTCGAG
11963 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
*
11983 AAT-AACTATCGCAA--CG-
1 AATGAA-AATCGCAACGCGA
*
11999 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
12016 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
12035 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
**
12054 AACCAAAATCGCA
1 AATGAAAATCGCA
12067 TTGCGATTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
14 7 0.10
15 2 0.03
16 2 0.03
17 1 0.01
18 2 0.03
19 47 0.66
20 10 0.14
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:12084 original size:19 final size:19
Alignment explanation
Indices: 12062--12193 Score: 121
Period size: 19 Copynumber: 7.1 Consensus size: 19
12052 GAAACCAAAA
*
12062 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
12081 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
12100 TCGCGTTGCGATTCTC--T
1 TCGCGTTGCGATTTTCATT
**
12117 T---GTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
12133 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* * *
12152 TCCGTGTTACGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
12172 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
12192 TC
1 TC
12194 AACCAAAAGA
Statistics
Matches: 94, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
14 10 0.11
16 2 0.02
17 2 0.02
19 51 0.54
20 28 0.30
21 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:12151 original size:52 final size:53
Alignment explanation
Indices: 12067--12168 Score: 143
Period size: 52 Copynumber: 1.9 Consensus size: 53
12057 CAAAATCGCA
** ** *
12067 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTT-CGCGTTGCGATTCTCTTG
1 TTGCGATAGTCATTTCGCGTTGCGATAGTCATTTCCGCGTTACGATTCTCTTG
*
12119 TTGCGATAGTCATTTCGCGTTGCGATAGTCATTTCCGTGTTACGATTCTC
1 TTGCGATAGTCATTTCGCGTTGCGATAGTCATTTCCGCGTTACGATTCTC
12169 ATTATCTCGT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 30 0.70
53 13 0.30
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (53 bp):
TTGCGATAGTCATTTCGCGTTGCGATAGTCATTTCCGCGTTACGATTCTCTTG
Found at i:14362 original size:21 final size:21
Alignment explanation
Indices: 14338--14404 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
14328 TCATTCCTCG
14338 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
14359 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
14380 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
14401 AGAG
1 AGAG
14405 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:14362 original size:42 final size:42
Alignment explanation
Indices: 14286--14404 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
14276 GACTCGCCTG
* * * * * * *
14286 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
14328 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
14370 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
14405 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:15777 original size:14 final size:14
Alignment explanation
Indices: 15758--15793 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
15748 ATTGTTTAAT
15758 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
15772 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
15786 TGATTTGT
1 TGATTTGT
15794 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:15924 original size:19 final size:19
Alignment explanation
Indices: 15900--15982 Score: 88
Period size: 19 Copynumber: 4.6 Consensus size: 19
15890 AAAAAGTACT
*
15900 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
15919 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
15933 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
15952 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
15971 ATCGCAACGCGA
1 ATCGCAACGCGA
15983 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 38 0.69
20 1 0.02
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:16023 original size:33 final size:33
Alignment explanation
Indices: 15979--16098 Score: 154
Period size: 33 Copynumber: 3.6 Consensus size: 33
15969 AAATCGCAAC
15979 GCGATTTTCATTTCGCATTGCGATTCCCTCGTT
1 GCGATTTTCATTTCGCATTGCGATTCCCTCGTT
** *
16012 TTGATTTTCATTTCGCATTGCGAAATT-CGT-GTT
1 GCGATTTTCATTTCGCATTGCG--ATTCCCTCGTT
* *
16045 GCGATTTTCATTTTTGCATTGCGATTCTCTCGTT
1 GCGATTTTCA-TTTCGCATTGCGATTCCCTCGTT
16079 GCGATTTTCATTTCGCATTG
1 GCGATTTTCATTTCGCATTG
16099 TGATAGTAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
32 3 0.04
33 41 0.56
34 26 0.36
35 3 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
GCGATTTTCATTTCGCATTGCGATTCCCTCGTT
Found at i:18359 original size:12 final size:12
Alignment explanation
Indices: 18341--18377 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
18331 TCTTCGGGGA
18341 CTTTTTCTTCTT
1 CTTTTTCTTCTT
*
18353 TTTTTTCTTCTT
1 CTTTTTCTTCTT
18365 CTTTTTCTTCTT
1 CTTTTTCTTCTT
18377 C
1 C
18378 AGGATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:18363 original size:15 final size:15
Alignment explanation
Indices: 18345--18377 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
18335 CGGGGACTTT
*
18345 TTCTTCTTTTTTTTC
1 TTCTTCTTTTTCTTC
18360 TTCTTCTTTTTCTTC
1 TTCTTCTTTTTCTTC
18375 TTC
1 TTC
18378 AGGATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTTCTTTTTCTTC
Found at i:18586 original size:24 final size:24
Alignment explanation
Indices: 18552--18605 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
18542 CTGAAACATC
*
18552 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
18576 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
18600 ATCAAA
1 ATCAAA
18606 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:19462 original size:20 final size:20
Alignment explanation
Indices: 19429--19507 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
19419 AATTTGGAAA
* *
19429 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
19449 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
19470 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
19490 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
19508 AAATCACAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:19845 original size:19 final size:18
Alignment explanation
Indices: 19823--19890 Score: 81
Period size: 19 Copynumber: 3.9 Consensus size: 18
19813 GAAATGAAAA
19823 TTGCATTGCGATTTTC--
1 TTGCATTGCGATTTTCAT
*
19839 -T-CGTTGCGATTTTCAT
1 TTGCATTGCGATTTTCAT
19855 TTCGCATTGCGATTTTCAT
1 TT-GCATTGCGATTTTCAT
19874 TTCGCATTGCGATTTTC
1 TT-GCATTGCGATTTTC
19891 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 12 0.27
15 1 0.02
17 1 0.02
19 31 0.69
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (18 bp):
TTGCATTGCGATTTTCAT
Found at i:19847 original size:14 final size:16
Alignment explanation
Indices: 19827--19900 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
19817 TGAAAATTGC
19827 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
19842 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
19859 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
19878 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
19894 -TTGCGAT
1 ATTGCGAT
19901 AGTCAGTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:21533 original size:42 final size:41
Alignment explanation
Indices: 21443--21533 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 41
21433 CTCTTCAACG
* *
21443 ATGACAGTGGCCTCTTGAACGGTGGGGGGAACTCTTGAGGG
1 ATGACAGGGGCCTCTTGAACGGTGGGGGGAACTCTTGAGGA
* *
21484 ATAACAGGGGCCTCTTGAACGATTGGAGGGG-ACTCTTGAGGA
1 ATGACAGGGGCCTCTTGAACG-GTGG-GGGGAACTCTTGAGGA
21526 ATGACAGG
1 ATGACAGG
21534 TGAGTCGGGC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 19 0.44
42 20 0.47
43 4 0.09
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.21
Consensus pattern (41 bp):
ATGACAGGGGCCTCTTGAACGGTGGGGGGAACTCTTGAGGA
Found at i:21947 original size:20 final size:20
Alignment explanation
Indices: 21922--21967 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
21912 TCACTTTGCA
21922 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* *
21942 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCGCG
21962 TTGCGA
1 TTGCGA
21968 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:22525 original size:18 final size:18
Alignment explanation
Indices: 22502--22549 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
22492 CGGGTCGATC
22502 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
22520 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
22538 AGGTGATGGCTC
1 AGGTGATGGCTC
22550 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:23916 original size:20 final size:20
Alignment explanation
Indices: 23868--23926 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
23858 AATAGTTTCT
* *
23868 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
23888 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
23908 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
23927 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:24207 original size:22 final size:22
Alignment explanation
Indices: 24180--24223 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
24170 GATGGAGATA
24180 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
24202 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
24224 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:24503 original size:20 final size:20
Alignment explanation
Indices: 24410--24502 Score: 114
Period size: 20 Copynumber: 4.7 Consensus size: 20
24400 GATTATGTAT
*
24410 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
24430 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
24450 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
24470 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
24490 TACCGCGTTGCGA
1 TATCGCGTTGCGA
24503 TTTTCCAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:24523 original size:21 final size:21
Alignment explanation
Indices: 24497--24544 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
24487 CAGTACCGCG
24497 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
24518 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
24539 TTGCGA
1 TTGCGA
24545 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCA
Found at i:24558 original size:21 final size:20
Alignment explanation
Indices: 24534--24586 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
24524 TTTTCCAAAT
24534 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
**
24555 TCGCAACGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
*
24576 TCACATTGCGA
1 TCGCATTGCGA
24587 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.04
21 21 0.81
22 4 0.15
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:25324 original size:182 final size:182
Alignment explanation
Indices: 24753--25402 Score: 876
Period size: 183 Copynumber: 3.6 Consensus size: 182
24743 TATTTTCTCT
* * * * * *
24753 TTTA-GAATTTAAAAGAAAATAAGTTATAGCGCTTATAAAGTGTCGATACTTTAAAAAAATATAT
1 TTTATGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTT-AAAAAATGTAT
* *
24817 CGATCCATAATAATATAACAGGTAAAAAAAGGACAAAACAAGTCTAAAAAATGACAAAACTGGTA
65 CGATCCATAACAATATAACAGGTAAAAAAAGGACAAAACAGGTCTAAAAAATGACAAAACTGGTA
* *
24882 AAACGATACCGGATATATTGAAAGTGTCGATAATTTAATATAAATATCGACAA
130 AAACGATACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACAC
* *
24935 TTTATGAATTTAAAAGAGAAGAAATTATAGCGCCTAAAACGTGTCGACACTTTAAAAAGATGTAT
1 TTTATGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAAAAA-ATGTAT
* *
25000 CGATCCATAACAATATAACAGGTAAAAAAAGGACAAAACATGTCTAAAAAATGACAAAACCGGTA
65 CGATCCATAACAATATAACAGGTAAAAAAAGGACAAAACAGGTCTAAAAAATGACAAAACTGGTA
25065 AAACGATACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACAC
130 AAACGATACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACAC
* * *
25118 TTTCTGAATTTAAAAGATAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTTAAAAAATGTAT
1 TTTATGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACAC-TTTAAAAAATGTAT
** * * * * *
25183 TAATCCATAACAATATAACAAGTAAAAATATGACAAAA-ACGGTCT-CAAAATGACAAAACTAGT
65 CGATCCATAACAATATAACAGGTAAAAAAAGGACAAAACA-GGTCTAAAAAATGACAAAACTGGT
* *** * *
25246 AAAAGGATACTAAATATATTGAAATTGTCAATAATTTAATATAAGTATCGACAC
129 AAAACGATACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACAC
* * * *
25300 TTTATGAATTTAAAAGAGAAGAAG-TATAACGCCTACAAAGTGACGACACTTTAGGAAAATGTAT
1 TTTATGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTA-AAAAATGTAT
* * * * *
25364 CGATCTATAACAATATAATATGTAAAAATATGACAAAAC
65 CGATCCATAACAATATAACAGGTAAAAAAAGGACAAAAC
25403 CGGTAAAACG
Statistics
Matches: 417, Mismatches: 45, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
180 4 0.01
181 63 0.15
182 95 0.23
183 247 0.59
184 8 0.02
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (182 bp):
TTTATGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAAAAAATGTATC
GATCCATAACAATATAACAGGTAAAAAAAGGACAAAACAGGTCTAAAAAATGACAAAACTGGTAA
AACGATACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACAC
Found at i:25435 original size:161 final size:162
Alignment explanation
Indices: 25232--25568 Score: 428
Period size: 161 Copynumber: 2.1 Consensus size: 162
25222 CGGTCTCAAA
** * *
25232 ATGACAAAACTAGTAAAAGGATACTAAATATATTGAAATTGTCAATAATTTAATATAAGTATCGA
1 ATGACAAAACCGGTAAAACGATACTAAATATATTGAAATTGTCAATAATTTAATATAAATATCGA
* *
25297 CACTTTATGAATTTAAAAGAGAAG-AAGTATAACGCCTACAAAGTGACGACAC-TTTAGGAAAAT
66 CACTTTATGAATTTAAAAGAGAAGAAAGTATAACGCCTAAAAAGTGACGACACTTTTA-AAAAAT
* * *
25360 GTATCGATCTATAACAATATAATATGTAAAAAT
130 ATATCGATCTATAACAATATAACAGGTAAAAAT
* * * *
25393 ATGACAAAACCGGTAAAACGTTAC-AAGATATGTTGCAATTGTCGATAATTTAATATAAATATCG
1 ATGACAAAACCGGTAAAACGATACTAA-ATATATTGAAATTGTCAATAATTTAATATAAATATCG
* * * * * * *
25457 ATACTTTCTGAATTTAAAAGAGAAGAAATTATAGCGTCTAAAAAGTGTCGATACTTTTAAAAAAT
65 ACACTTTATGAATTTAAAAGAGAAGAAAGTATAACGCCTAAAAAGTGACGACACTTTTAAAAAAT
* *
25522 ATATCGATTTATAATAATATAACAGGTAAAAAT
130 ATATCGATCTATAACAATATAACAGGTAAAAAT
*
25555 ATGACAAAATCGGT
1 ATGACAAAACCGGT
25569 CTCAAAATAA
Statistics
Matches: 150, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
160 2 0.01
161 76 0.51
162 68 0.45
163 4 0.03
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.30
Consensus pattern (162 bp):
ATGACAAAACCGGTAAAACGATACTAAATATATTGAAATTGTCAATAATTTAATATAAATATCGA
CACTTTATGAATTTAAAAGAGAAGAAAGTATAACGCCTAAAAAGTGACGACACTTTTAAAAAATA
TATCGATCTATAACAATATAACAGGTAAAAAT
Found at i:26636 original size:36 final size:36
Alignment explanation
Indices: 26582--26717 Score: 211
Period size: 36 Copynumber: 3.8 Consensus size: 36
26572 GCTGCTGTTG
* *
26582 GCGTTTCCCAA-CGAGAGGCTGCTGCAGTTGCGGTCA
1 GCGTCTCCCAACCG-GAGGCTGCTGCAGTTGCGGTTA
*
26618 GCGTCTCCCAACCGGAGGCTGCTGCAGTTGAGGTTA
1 GCGTCTCCCAACCGGAGGCTGCTGCAGTTGCGGTTA
* *
26654 TCGTCTCCCAACTGGAGGCTGCTGCAGTTGCGGTTA
1 GCGTCTCCCAACCGGAGGCTGCTGCAGTTGCGGTTA
26690 GCGTCTCCCAACCGGAGGCTGCTGCAGT
1 GCGTCTCCCAACCGGAGGCTGCTGCAGT
26718 GGGCGTTCGG
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
36 89 0.98
37 2 0.02
ACGTcount: A:0.15, C:0.29, G:0.32, T:0.23
Consensus pattern (36 bp):
GCGTCTCCCAACCGGAGGCTGCTGCAGTTGCGGTTA
Found at i:32262 original size:162 final size:160
Alignment explanation
Indices: 31991--32312 Score: 554
Period size: 162 Copynumber: 2.0 Consensus size: 160
31981 ATACTCAAAT
* *
31991 GTCAAATTAAGTCGAATCCAAGTCAAAAACAAATACCCATTTACAATTATTTACCCATTACCACA
1 GTCAAATTAAGTAGAATCCAAGTCAAAAACAAATACCCATTTACAACTATTTACCCATTACCACA
*
32056 ACCCATATGCATTACATCCAATACTTTACATGTCACCAATGACCAAATGACCCAAACCATCTTAC
66 ACCCATATACATTACATCCAATACTTTACATGTCACCAATGACCAAATGACCC-AACCATCTTAC
*
32121 AAAGTCAAACTTATAGCCCATTTTTAACCCAA
130 AAAGTC-AACTCATAGCCCATTTTTAACCCAA
*
32153 GTCAAATTAAGTAGAATCCAAGTCAAAAACAAATACCCATTTGCAACTATTTACCCATTACCACA
1 GTCAAATTAAGTAGAATCCAAGTCAAAAACAAATACCCATTTACAACTATTTACCCATTACCACA
* * *
32218 ACCCATATACATTACATCCGATACTTTACATGTCACCCATGACCAAATGACTCAACCATCTTACA
66 ACCCATATACATTACATCCAATACTTTACATGTCACCAATGACCAAATGACCCAACCATCTTACA
32283 AAGTCAACTCATAGCCCATTTTTAACCCAA
131 AAGTCAACTCATAGCCCATTTTTAACCCAA
32313 TTAAACCCAT
Statistics
Matches: 152, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
160 24 0.16
161 17 0.11
162 111 0.73
ACGTcount: A:0.39, C:0.28, G:0.07, T:0.26
Consensus pattern (160 bp):
GTCAAATTAAGTAGAATCCAAGTCAAAAACAAATACCCATTTACAACTATTTACCCATTACCACA
ACCCATATACATTACATCCAATACTTTACATGTCACCAATGACCAAATGACCCAACCATCTTACA
AAGTCAACTCATAGCCCATTTTTAACCCAA
Found at i:32724 original size:14 final size:15
Alignment explanation
Indices: 32705--32740 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
32695 ATTAAATTTT
*
32705 AAAAAATGTT-ATAG
1 AAAAAATGTTAAAAG
32719 AAAAAATGTTAAAAG
1 AAAAAATGTTAAAAG
32734 AAAAAAT
1 AAAAAAT
32741 AAAATAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (15 bp):
AAAAAATGTTAAAAG
Found at i:33061 original size:18 final size:18
Alignment explanation
Indices: 33039--33081 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
33029 GTTATTTTTA
*
33039 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
* *
33057 GAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
33075 AAATAAA
1 AAATAAA
33082 TAATCTAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:35239 original size:18 final size:18
Alignment explanation
Indices: 35218--35256 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
35208 GCATTTGATA
*
35218 CTCTGGACGAGGTTGTTC
1 CTCTGGACGAGCTTGTTC
* *
35236 CTCTGGAGGTGCTTGTTC
1 CTCTGGACGAGCTTGTTC
35254 CTC
1 CTC
35257 GTGCTGCTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.26, G:0.31, T:0.36
Consensus pattern (18 bp):
CTCTGGACGAGCTTGTTC
Found at i:36866 original size:21 final size:21
Alignment explanation
Indices: 36834--36923 Score: 81
Period size: 23 Copynumber: 4.1 Consensus size: 21
36824 ATAGAACCTC
*
36834 CAGGGGGTATCGATTCCCCTA
1 CAGGGGGAATCGATTCCCCTA
* *
36855 CATGGGGAATCGGTTCCCCTTTA
1 CAGGGGGAATCGATTCCCC--TA
* * *
36878 AAGGGGGAATCGATTTCCCTT
1 CAGGGGGAATCGATTCCCCTA
*
36899 CAAGGGGGTATCGATTCCCTCTA
1 C-AGGGGGAATCGATTCCC-CTA
36922 CA
1 CA
36924 CCAAAACTGA
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
21 17 0.32
22 16 0.30
23 20 0.38
ACGTcount: A:0.21, C:0.26, G:0.27, T:0.27
Consensus pattern (21 bp):
CAGGGGGAATCGATTCCCCTA
Found at i:36903 original size:22 final size:22
Alignment explanation
Indices: 36835--36917 Score: 87
Period size: 22 Copynumber: 3.8 Consensus size: 22
36825 TAGAACCTCC
* *
36835 AGGGGGTATCGATTCCCCTAC-
1 AGGGGGAATCGATTCCCCTTCA
* * *
36856 ATGGGGAATCGGTTCCCCTTTAA
1 AGGGGGAATCGATTCCCC-TTCA
*
36879 AGGGGGAATCGATTTCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
*
36901 AGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
36918 TCTACACCAA
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 15 0.31
22 19 0.39
23 15 0.31
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:40620 original size:21 final size:21
Alignment explanation
Indices: 40570--40621 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
40560 GAAGCTTTAA
*
40570 GATCATCAATTTTCTTTTGAT
1 GATCATCATTTTTCTTTTGAT
40591 GATCATCATTTTTCTTTTGAT
1 GATCATCATTTTTCTTTTGAT
40612 GATCATCATT
1 GATCATCATT
40622 GAGCTTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.52
Consensus pattern (21 bp):
GATCATCATTTTTCTTTTGAT
Found at i:40628 original size:21 final size:21
Alignment explanation
Indices: 40583--40628 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
40573 CATCAATTTT
***
40583 CTTTTGATGATCATCATTTTT
1 CTTTTGATGATCATCATTGAG
40604 CTTTTGATGATCATCATTGAG
1 CTTTTGATGATCATCATTGAG
40625 CTTT
1 CTTT
40629 GAAAGTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.15, G:0.13, T:0.52
Consensus pattern (21 bp):
CTTTTGATGATCATCATTGAG
Found at i:44211 original size:270 final size:270
Alignment explanation
Indices: 43799--44367 Score: 869
Period size: 270 Copynumber: 2.1 Consensus size: 270
43789 GAAATTGTGA
*
43799 GTGGCTCATTCGTTGTGAAGTTGAGCTTTGAACTGAAAAATCCTAAGCACGATATCATTCTTCAT
1 GTGGCTCATTCGTTGTGAAGTTGAGCTTTGAACTAAAAAATCCTAAGCACGATATCATTCTTCAT
* * *
43864 GAAGTTGAAATCGGGCTCAAAGCATTGGAAAGTCGCTCCTGGATCGTCTTCTAGCCCAATACACT
66 GAAGTTGAAACCGGGCTCAAAGCATTGGAAAGTCACTCCTGGATCGTATTCTAGCCCAATACACT
* *
43929 TCGTCGTGAAGCTGAAATTTGACCTGAAGACTTTGGTATGAAACT-GGTTTTTCATTGTTGTGTT
131 TCGTCGTGAAGCTGAAATTTAACCTGAAGACCTTGGTATGAAA-TAGGTTTTTCATTGTTGTGTT
* *** *
43993 ACAGATGACTCATTCGTCGTGAAGTTG-GGTAAATCTTTTGG-TATGGTATCCTTCGTTTTGAAG
195 ACAGATGACTCATTCGTCGTGAAG-TGAGCTAAATCTTTTGGTTACAATATCCTTCGTTGTGAAG
44056 TCAAAATCGTAG
259 TCAAAATCGTAG
* *
44068 GTGGCTCATTCATTGTGAAGTTGAGCTTTGAACTAAAAAAATCCTAAGCATGATATTC-TT-TGT
1 GTGGCTCATTCGTTGTGAAGTTGAGCTTTGAACT-AAAAAATCCTAAGCACGATA-TCATTCT-T
*
44131 CATGAAGTTGAAACCGGGCTCAAAGCATTGGAAAGTCACTCCTGGATCGTATTCTAGCCCAATAT
63 CATGAAGTTGAAACCGGGCTCAAAGCATTGGAAAGTCACTCCTGGATCGTATTCTAGCCCAATAC
* * *
44196 ACTTCTTTGTGAAGCTGAACTTTAACCTGAAGACCTTGGTATGAAATAGGTTTTTCATTGTTGTG
128 ACTTCGTCGTGAAGCTGAAATTTAACCTGAAGACCTTGGTATGAAATAGGTTTTTCATTGTTGTG
*
44261 TTACAGATGACTCATTCGTCGTGAAGTGAGCTCAATCTTTTGGTTACAATATCCTTCGTTGTGAA
193 TTACAGATGACTCATTCGTCGTGAAGTGAGCTAAATCTTTTGGTTACAATATCCTTCGTTGTGAA
44326 GTCAAAATCGTAG
258 GTCAAAATCGTAG
* * *
44339 GTGGCTCATTTGTTGTGAAATTAAGCTTT
1 GTGGCTCATTCGTTGTGAAGTTGAGCTTT
44368 AAATTGGATA
Statistics
Matches: 272, Mismatches: 22, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
269 37 0.14
270 178 0.65
271 57 0.21
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (270 bp):
GTGGCTCATTCGTTGTGAAGTTGAGCTTTGAACTAAAAAATCCTAAGCACGATATCATTCTTCAT
GAAGTTGAAACCGGGCTCAAAGCATTGGAAAGTCACTCCTGGATCGTATTCTAGCCCAATACACT
TCGTCGTGAAGCTGAAATTTAACCTGAAGACCTTGGTATGAAATAGGTTTTTCATTGTTGTGTTA
CAGATGACTCATTCGTCGTGAAGTGAGCTAAATCTTTTGGTTACAATATCCTTCGTTGTGAAGTC
AAAATCGTAG
Found at i:44570 original size:123 final size:123
Alignment explanation
Indices: 44340--44581 Score: 306
Period size: 123 Copynumber: 2.0 Consensus size: 123
44330 AAATCGTAGG
* *
44340 TGGCTCATTTGTTGTGAAATTAAGCTTTAAATTGGATATCATTCATTGTGAAGTTGAAATCCAAT
1 TGGCTCATTCGCTGTGAAATTAAGCTTTAAATTGGATATCATTCATTGTGAAGTTGAAATCCAAT
* * * * * *
44405 CTCGTAAATTGAATCGCTTTGAGATTAGTATCTTTTGTTGTGAAGTTGAAATTGTGGA
66 CTCGAAAATTGAATCGCTCTGAGATTAATACCATTTGCTGTGAAGTTGAAATTGTGGA
* * * * *
44463 TGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCCTTCATTGTGAAGTTGAAATCCAAT
1 TGGCTCATTCGCTGTGAAATTAAGCTTTAAATTGGATATCATTCATTGTGAAGTTGAAATCCAAT
* * * * *
44528 CTTGAAAATTGCATTGGCTCT-AGTTTAATACCATTTGCTGTGAAGTTGACATTG
66 CTCGAAAATTG-AATCGCTCTGAGATTAATACCATTTGCTGTGAAGTTGAAATTG
44582 ACTCTAACAA
Statistics
Matches: 100, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
123 94 0.94
124 6 0.06
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.39
Consensus pattern (123 bp):
TGGCTCATTCGCTGTGAAATTAAGCTTTAAATTGGATATCATTCATTGTGAAGTTGAAATCCAAT
CTCGAAAATTGAATCGCTCTGAGATTAATACCATTTGCTGTGAAGTTGAAATTGTGGA
Found at i:45665 original size:25 final size:25
Alignment explanation
Indices: 45581--45671 Score: 62
Period size: 25 Copynumber: 3.6 Consensus size: 25
45571 TTTTCCTTCC
*
45581 ATTTTTTTATTTTTTTCGAAAGAAG-G
1 ATTTTTTT-TTTTTTTCGAAA-CAGTG
*
45607 -TTTTTTTTTCTGTTT-GAAACAGTG
1 ATTTTTTTTT-TTTTTCGAAACAGTG
*****
45631 AACAACTTTTTTTTTCGAAACAGTG
1 ATTTTTTTTTTTTTTCGAAACAGTG
45656 ATTTTTTTTTTCTTTT
1 ATTTTTTTTTT-TTTT
45672 TTTTTTCGTT
Statistics
Matches: 47, Mismatches: 13, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
23 2 0.04
24 11 0.23
25 30 0.64
26 4 0.09
ACGTcount: A:0.22, C:0.09, G:0.12, T:0.57
Consensus pattern (25 bp):
ATTTTTTTTTTTTTTCGAAACAGTG
Found at i:51548 original size:19 final size:19
Alignment explanation
Indices: 51526--51568 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
51516 ATTAAAATTA
*
51526 GAATTTAAATACTCGATTT
1 GAATTTAAATACTCGATTC
51545 GAATTTAAATACTCGATTC
1 GAATTTAAATACTCGATTC
51564 GAATT
1 GAATT
51569 ACTTACCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (19 bp):
GAATTTAAATACTCGATTC
Found at i:51771 original size:14 final size:13
Alignment explanation
Indices: 51754--51819 Score: 55
Period size: 13 Copynumber: 4.9 Consensus size: 13
51744 ATTAAATTTC
51754 ATAAAATAAAAATA
1 ATAAAATAAAAA-A
51768 ATAAAATATAAAAA
1 ATAAAATA-AAAAA
** *
51782 A-AATGTTAAAACA
1 ATAA-AATAAAAAA
51795 A-AAAATAGAAAAA
1 ATAAAATA-AAAAA
51808 ATAAAATAAAAA
1 ATAAAATAAAAA
51820 GTGGGAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
12 2 0.05
13 18 0.43
14 18 0.43
15 4 0.10
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (13 bp):
ATAAAATAAAAAA
Found at i:52035 original size:18 final size:18
Alignment explanation
Indices: 52014--52056 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
52004 GTTGTTTTTA
*
52014 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
* *
52032 AAATTAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
52050 AAATAAA
1 AAATAAA
52057 TAATCTAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Done.