Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004586.1 Hibiscus syriacus cultivar Beakdansim tig00010242_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: 50326
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:424 original size:20 final size:20
Alignment explanation
Indices: 395--434 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
385 AGCAACAGAA
*
395 TAAAACTGATTATATCTAAT
1 TAAAACTGATCATATCTAAT
* *
415 TAAAATTGATCCTATCTAAT
1 TAAAACTGATCATATCTAAT
435 AACTAATAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.40
Consensus pattern (20 bp):
TAAAACTGATCATATCTAAT
Found at i:464 original size:53 final size:53
Alignment explanation
Indices: 396--503 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
386 GCAACAGAAT
* *
396 AAAACTGATTATATCTAATTAAAATTGATCCTATCTAATAACTAATAGAATAA
1 AAAACTAATTATATCTAATTAAAACTGATCCTATCTAATAACTAATAGAATAA
*
449 AAAACTAATTCTATCTAATTAAAACTGATCCTATCTAATAACTAATAGAATAA
1 AAAACTAATTATATCTAATTAAAACTGATCCTATCTAATAACTAATAGAATAA
502 AA
1 AA
504 TATCTAGTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.32
Consensus pattern (53 bp):
AAAACTAATTATATCTAATTAAAACTGATCCTATCTAATAACTAATAGAATAA
Found at i:474 original size:20 final size:20
Alignment explanation
Indices: 449--487 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
439 AATAGAATAA
*
449 AAAACTAATTCTATCTAATT
1 AAAACTAATCCTATCTAATT
*
469 AAAACTGATCCTATCTAAT
1 AAAACTAATCCTATCTAAT
488 AACTAATAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.36
Consensus pattern (20 bp):
AAAACTAATCCTATCTAATT
Found at i:7927 original size:2 final size:2
Alignment explanation
Indices: 7920--7966 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
7910 ACATATTATT
7920 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7962 TA TA T
1 TA TA T
7967 GTATCAGATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11787 original size:31 final size:31
Alignment explanation
Indices: 11706--11791 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
11696 TAAGGCGACC
* *
11706 CTTGGGTAGGCTCTAAAGCCCCAAGAACTTT
1 CTTGGGTAGGCTCTCAGGCCCCAAGAACTTT
* * **
11737 CTTGTGTAGGC-CACGAGGCCCTGAGAACTTT
1 CTTGGGTAGGCTCTC-AGGCCCCAAGAACTTT
11768 CTTGGGTAGGCTCTCAGGCCCCAA
1 CTTGGGTAGGCTCTCAGGCCCCAA
11792 TATGCTCCCT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
30 1 0.02
31 40 0.93
32 2 0.05
ACGTcount: A:0.21, C:0.28, G:0.27, T:0.24
Consensus pattern (31 bp):
CTTGGGTAGGCTCTCAGGCCCCAAGAACTTT
Found at i:15167 original size:25 final size:25
Alignment explanation
Indices: 15133--15218 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
15123 GATGTAGGGT
*
15133 TTAGGG-TTTTTATGTTATAA-T-TA
1 TTAGGGTTTTTTATGTTA-AAGTGCA
* *
15156 TTGAGGGTTTTTTAGGTTAAAGTGCC
1 TT-AGGGTTTTTTATGTTAAAGTGCA
*
15182 TTAGGGTTTTTTATGTTAAAGTAGTA
1 TTAGGGTTTTTTATGTTAAAGT-GCA
15208 -TAGGGTTTTTT
1 TTAGGGTTTTTT
15219 GTTTAAATGT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
23 2 0.04
24 6 0.12
25 41 0.79
26 3 0.06
ACGTcount: A:0.22, C:0.02, G:0.24, T:0.51
Consensus pattern (25 bp):
TTAGGGTTTTTTATGTTAAAGTGCA
Found at i:17653 original size:14 final size:14
Alignment explanation
Indices: 17634--17680 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
17624 TTTGAAAAGA
17634 TGATATAATCTATG
1 TGATATAATCTATG
**
17648 TGATATGGTCTATG
1 TGATATAATCTATG
*
17662 TGACATAAAT-TATG
1 TGATAT-AATCTATG
17676 TGATA
1 TGATA
17681 CGTAAATAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 25 0.96
15 1 0.04
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.40
Consensus pattern (14 bp):
TGATATAATCTATG
Found at i:17957 original size:21 final size:21
Alignment explanation
Indices: 17933--17977 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
17923 ATGATCTATG
*
17933 TAAA-TACATGAACATAATATA
1 TAAACTACATGAA-ATAAGATA
*
17954 TAAACTATATGAAATAAGATA
1 TAAACTACATGAAATAAGATA
17975 TAA
1 TAA
17978 TAAATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.29
Consensus pattern (21 bp):
TAAACTACATGAAATAAGATA
Found at i:18095 original size:21 final size:20
Alignment explanation
Indices: 18071--18130 Score: 57
Period size: 23 Copynumber: 2.8 Consensus size: 20
18061 CGGTCCTTCA
18071 GGATATATATGTGGTCTTTTG
1 GGATATATATGTGGTC-TTTG
* *
18092 GGATAATTCTATGAGGTACTTTG
1 GGAT-A-TATATGTGGT-CTTTG
*
18115 GGACATATATGTGGTC
1 GGATATATATGTGGTC
18131 CTTCAGGACA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
20 1 0.03
21 12 0.39
22 2 0.06
23 15 0.48
24 1 0.03
ACGTcount: A:0.23, C:0.08, G:0.28, T:0.40
Consensus pattern (20 bp):
GGATATATATGTGGTCTTTG
Found at i:19022 original size:4 final size:4
Alignment explanation
Indices: 19013--19037 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
19003 AGTGTGAAGT
19013 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
19038 ATGAAAATGA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:19087 original size:30 final size:30
Alignment explanation
Indices: 19053--19112 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
19043 AATGATTGAG
19053 AAATGAAATTGAAAAAATTAACATACACAT
1 AAATGAAATTGAAAAAATTAACATACACAT
19083 AAATGAAATTGAAAAAATTAACATACACAT
1 AAATGAAATTGAAAAAATTAACATACACAT
19113 GTGCACGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.23
Consensus pattern (30 bp):
AAATGAAATTGAAAAAATTAACATACACAT
Found at i:19878 original size:9 final size:9
Alignment explanation
Indices: 19864--19888 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19854 AGTTCCCATA
19864 TATTCTTCT
1 TATTCTTCT
19873 TATTCTTCT
1 TATTCTTCT
19882 TATTCTT
1 TATTCTT
19889 TGATACATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (9 bp):
TATTCTTCT
Found at i:20511 original size:102 final size:102
Alignment explanation
Indices: 20367--20578 Score: 255
Period size: 102 Copynumber: 2.1 Consensus size: 102
20357 ATGTGGTTCA
* * **
20367 CTTGAACTTGAAGGTATTGTGTCATATGGGTTTTTAATAGACTGTTATGTCGAAGGCATTTCCAT
1 CTTGAACTTGAAGGTATAGTGTCATATGGGTTATTAATAGACTGTTATGTCGAAGAAATTTCCAT
* ** *
20432 GTTGAGATCGAAGAAGTTGGTAGATGAATGACTTCCC
66 ATTGAGATCGAAGAAGTTGACAGATGAATCACTTCCC
* * * * *
20469 CTTGAACTTGAAGGTATAGTGTCATATGGG-TATTGATCAGACTTTTGTGTCGATGAAATTTCTA
1 CTTGAACTTGAAGGTATAGTGTCATATGGGTTATTAAT-AGACTGTTATGTCGAAGAAATTTCCA
* * *
20533 TATTGAGGTTGAAGAAGTTGACAGATGAATCTCTTCCC
65 TATTGAGATCGAAGAAGTTGACAGATGAATCACTTCCC
*
20571 CGTGAACT
1 CTTGAACT
20579 GTAAGAGATG
Statistics
Matches: 92, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
101 5 0.05
102 87 0.95
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (102 bp):
CTTGAACTTGAAGGTATAGTGTCATATGGGTTATTAATAGACTGTTATGTCGAAGAAATTTCCAT
ATTGAGATCGAAGAAGTTGACAGATGAATCACTTCCC
Found at i:21533 original size:169 final size:170
Alignment explanation
Indices: 21200--21828 Score: 619
Period size: 169 Copynumber: 3.7 Consensus size: 170
21190 CCTCTATAAC
* *
21200 TAATATGTAGATATGATGTTCCCATTTCGGGAACTATTTACAT-T-AACCCCTCATTTGTTTGAT
1 TAATATGCAGATATGATGTTCCCATTTGGGGAACTA-TT-CATGTCAACCCCTCATTTGTTTGAT
* *
21263 GGGATGAGACAATATGACATGGCAGAGATTCTCTGAAAAAGGTG--AAAGCGTATATTATGGGAC
64 GGGATAAGACAATATGACATGGCAGAGATTCTCTGAAAAAGGTGAAAAAGC-T-TCTTATGGGAC
* * *
21326 ACGTCTTCCCTTTTTGTCAGAGTTTCTCTACA-TTTTCAGTAAA
127 ACGCCTTCCCTTTTTTTCAAAGTTTCTCTACATTTTTCAGTAAA
* * * * *
21369 TGATATGTAGATATGATATTCCCATTTGGGGAACTATTCATGTCAACCCCTAATATGTTTGATGG
1 TAATATGCAGATATGATGTTCCCATTTGGGGAACTATTCATGTCAACCCCTCATTTGTTTGATGG
* * * * * * * *
21434 GATAAGA-AATATGACATAGTAGATATTCTTTTAAAAAGATGAAAAAGCTTCTTGTGGGATACGC
66 GATAAGACAATATGACATGGCAGAGATTCTCTGAAAAAGGTGAAAAAGCTTCTTATGGGACACGC
*
21498 CTTCCCTTTTTTTCAAAGTTTCTCTATATTTTTCAGTAAA
131 CTTCCCTTTTTTTCAAAGTTTCTCTACATTTTTCAGTAAA
* * ** * * *
21538 TAATATACATATATGATGTTCCCATTCAGGGAACTATTAATGTCAACACCTCATCTGTTTGATGG
1 TAATATGCAGATATGATGTTCCCATTTGGGGAACTATTCATGTCAACCCCTCATTTGTTTGATGG
* * * * * ** * * *
21603 GATAAGACAGTATAACATGACAGAGATACTCTGGAAAAGGTGAAAGCGCTTCTTTTGGGACGCAC
66 GATAAGACAATATGACATGGCAGAGATTCTCTGAAAAAGGTGAAAAAGCTTCTTATGGGACACGC
* * * *
21668 CTTCCCTTTTTGTT-AAATTTTCTCAACATATTT-AGTCAA
131 CTTCCCTTTTT-TTCAAAGTTTCTCTACATTTTTCAGTAAA
* * ** * *** *
21707 TTATATGCATATATGATGTTTTCAGTTGGGGAACTATTCACACCAACCCCTTATTTGTTTGATGG
1 TAATATGCAGATATGATGTTCCCATTTGGGGAACTATTCATGTCAACCCCTCATTTGTTTGATGG
* * * * * * **
21772 GATAAAATAATATGGCATGGTAGAGATTCTCT-TAAAAGGTTAAAGTGCTTCTTATGG
66 GATAAGACAATATGACATGGCAGAGATTCTCTGAAAAAGGTGAAAAAGCTTCTTATGG
21829 AACGAACATT
Statistics
Matches: 375, Mismatches: 78, Indels: 15
0.80 0.17 0.03
Matches are distributed among these distances:
167 3 0.01
168 88 0.23
169 211 0.56
170 71 0.19
171 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (170 bp):
TAATATGCAGATATGATGTTCCCATTTGGGGAACTATTCATGTCAACCCCTCATTTGTTTGATGG
GATAAGACAATATGACATGGCAGAGATTCTCTGAAAAAGGTGAAAAAGCTTCTTATGGGACACGC
CTTCCCTTTTTTTCAAAGTTTCTCTACATTTTTCAGTAAA
Found at i:22666 original size:35 final size:35
Alignment explanation
Indices: 22593--22666 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
22583 CGTCAAGTCC
* **
22593 AGTAAGGCCCTGAGCACACAGCCAAGGAGCCGGTA
1 AGTAAGGCCCTGAGCACACAGCCAAGGAACCGCCA
*
22628 AGTAAGGCCCTGAGCACACAGCCAAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCAAGGAACCGCCA
22663 AGTA
1 AGTA
22667 TATTTCCTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.30, G:0.27, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCAAGGAACCGCCA
Found at i:22753 original size:24 final size:24
Alignment explanation
Indices: 22726--22849 Score: 81
Period size: 24 Copynumber: 5.2 Consensus size: 24
22716 TATATCAAAA
22726 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* * *
22750 ATCATATCAAATTCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
22774 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
22798 ATCAGATCAGAATCCATGTC-AGAT
1 ATCAAAACAAAATCCAGGTCAAG-T
* * * *
22822 ATCAGATCAGAATCCATGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
22846 ATCA
1 ATCA
22850 GATCAGAATT
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
23 5 0.06
24 82 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:22850 original size:24 final size:24
Alignment explanation
Indices: 22743--22858 Score: 173
Period size: 24 Copynumber: 4.8 Consensus size: 24
22733 CATAAATCAG
* *
22743 GTCAAGTATCATATCA-AATTCCAG
1 GTCAAGTATCAGATCAGAA-TCCAT
*
22767 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
22791 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
22815 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
22839 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
22859 TCAAATCGAA
Statistics
Matches: 86, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
23 2 0.02
24 80 0.93
25 4 0.05
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:22874 original size:48 final size:48
Alignment explanation
Indices: 22774--22876 Score: 145
Period size: 48 Copynumber: 2.1 Consensus size: 48
22764 CAGGTCAAGT
** *
22774 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCATGTCAGAT
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAA
* *
22822 ATCAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATC-GAAA
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAG-AA
22870 ATCAGAT
1 ATCAGAT
22877 AAAATATTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
47 1 0.02
48 48 0.98
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (48 bp):
ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAA
Found at i:27802 original size:19 final size:21
Alignment explanation
Indices: 27778--27826 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
27768 CAAATATTTT
27778 TATGAATAGTAT-C-ATACTG
1 TATGAATAGTATGCAATACTG
*
27797 TATGAATA-T-TGCAATATTG
1 TATGAATAGTATGCAATACTG
27816 TATGAATAGTA
1 TATGAATAGTA
27827 CCGATAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 1 0.04
18 2 0.08
19 21 0.84
20 1 0.04
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (21 bp):
TATGAATAGTATGCAATACTG
Found at i:27863 original size:21 final size:21
Alignment explanation
Indices: 27837--27897 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
27827 CCGATAATGT
27837 GTGAACAGTAGTATCGATACC
1 GTGAACAGTAGTATCGATACC
*
27858 GTGAACAGTAGTACCGATACC
1 GTGAACAGTAGTATCGATACC
*
27879 ATGAACAGTAGTATCGATA
1 GTGAACAGTAGTATCGATA
27898 TTATAAACAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (21 bp):
GTGAACAGTAGTATCGATACC
Found at i:29483 original size:13 final size:13
Alignment explanation
Indices: 29465--29505 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
29455 TTAAAATTTG
29465 AAATAATATTAAA
1 AAATAATATTAAA
29478 AAATAA-ATTAATA
1 AAATAATATTAA-A
29491 AAAT-AT-TTAAA
1 AAATAATATTAAA
29502 AAAT
1 AAAT
29506 TAAATAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.19
12 10 0.38
13 11 0.42
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATAATATTAAA
Found at i:29500 original size:24 final size:23
Alignment explanation
Indices: 29469--29558 Score: 83
Period size: 24 Copynumber: 3.6 Consensus size: 23
29459 AATTTGAAAT
29469 AATATTAAAAAATAAATTAATAA
1 AATATTAAAAAATAAATTAATAA
*
29492 AATATTTAAAAAATTAAATAACATAA
1 AATA-TTAAAAAA-TAAATTA-ATAA
29518 TTTAATATT-AAAAATAACAATTAATAA
1 ---AATATTAAAAAAT-A-AATTAATAA
29545 AATATTCAAAAAAT
1 AATATT-AAAAAAT
29559 TAAAATAACA
Statistics
Matches: 55, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
23 4 0.07
24 14 0.25
25 6 0.11
26 11 0.20
27 10 0.18
28 6 0.11
29 4 0.07
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (23 bp):
AATATTAAAAAATAAATTAATAA
Found at i:29511 original size:21 final size:21
Alignment explanation
Indices: 29482--29522 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29472 ATTAAAAAAT
29482 AAATTAATAAAAT-ATTTAAA
1 AAATTAATAAAATAATTTAAA
*
29502 AAATTAAATAACATAATTTAA
1 AAATT-AATAAAATAATTTAA
29523 TATTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATTAATAAAATAATTTAAA
Found at i:29547 original size:53 final size:53
Alignment explanation
Indices: 29468--29577 Score: 179
Period size: 53 Copynumber: 2.1 Consensus size: 53
29458 AAATTTGAAA
*
29468 TAATATTAAAAAATAAATTAATAAAATATTTAAAAAATT-AAATAACATAATT
1 TAATATTAAAAAATAAATTAATAAAATATTCAAAAAATTAAAATAACATAATT
29520 TAATATT-AAAAATAACAATTAATAAAATATTCAAAAAATTAAAATAACATAATT
1 TAATATTAAAAAAT-A-AATTAATAAAATATTCAAAAAATTAAAATAACATAATT
29574 TAAT
1 TAAT
29578 TTTTTTTACC
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
51 6 0.11
52 8 0.15
53 23 0.43
54 17 0.31
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.34
Consensus pattern (53 bp):
TAATATTAAAAAATAAATTAATAAAATATTCAAAAAATTAAAATAACATAATT
Found at i:32082 original size:21 final size:21
Alignment explanation
Indices: 32056--32105 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
32046 GATTTCTATT
32056 AAATAAAAGTCATTTTGACTA
1 AAATAAAAGTCATTTTGACTA
32077 AAATAAAAGTCATTTTGACTA
1 AAATAAAAGTCATTTTGACTA
32098 AAATAAAA
1 AAATAAAA
32106 ATATTGAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (21 bp):
AAATAAAAGTCATTTTGACTA
Found at i:35577 original size:17 final size:18
Alignment explanation
Indices: 35555--35589 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
35545 CATCAATTTG
35555 ATAAATATTTA-ATATGT
1 ATAAATATTTACATATGT
*
35572 ATAAATTTTTACATATGT
1 ATAAATATTTACATATGT
35590 CACATCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (18 bp):
ATAAATATTTACATATGT
Found at i:35593 original size:47 final size:47
Alignment explanation
Indices: 35533--35629 Score: 140
Period size: 47 Copynumber: 2.1 Consensus size: 47
35523 GTAATATAAG
* * * *
35533 TTACATATATCACATCAATTTGATAAATATTTAATATGTATAAATTT
1 TTACATATATCACATCAATTAGATAAACATTTAATATGAATAAATAT
* *
35580 TTACATATGTCACATCAATTAGATAAACATTTACTATGAATAAATAT
1 TTACATATATCACATCAATTAGATAAACATTTAATATGAATAAATAT
35627 TTA
1 TTA
35630 AAATATCGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.41
Consensus pattern (47 bp):
TTACATATATCACATCAATTAGATAAACATTTAATATGAATAAATAT
Found at i:37304 original size:13 final size:13
Alignment explanation
Indices: 37286--37310 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37276 AAACAAAGAT
37286 AATAAAGAATAAG
1 AATAAAGAATAAG
37299 AATAAAGAATAA
1 AATAAAGAATAA
37311 AATGAAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (13 bp):
AATAAAGAATAAG
Found at i:37558 original size:37 final size:35
Alignment explanation
Indices: 37339--37570 Score: 186
Period size: 35 Copynumber: 6.4 Consensus size: 35
37329 AATATGATGT
37339 AACTATATAATATA--TTTTCAAAAATATGTTTTCGAA
1 AACTATATAATATACGTTTTCAAAAATA--TTTTC-AA
* * *
37375 AA-T-TATATTACACG-TTTCAAAAATAATTTTTTAAAA
1 AACTATATAATATACGTTTTCAAAAAT-A--TTTT-CAA
* * *
37411 AACTATATATTATACGTTTTCAAAAGTATTTTTTAAA
1 AACTATATAATATACGTTTTCAAAA--ATATTTTCAA
*
37448 AACTATATATTATATACGTTTTCAGAAAATGTTTTCAA
1 AACTATATA--ATATACGTTTTCA-AAAATATTTTCAA
* * *
37486 AACCATATATTATACATTTTCAAAAATATTTTCAA
1 AACTATATAATATACGTTTTCAAAAATATTTTCAA
* *
37521 AACTATATAATATATGTTTTTTAAAACATATTTTCAA
1 AACTATATAATATACG-TTTTCAAAA-ATATTTTCAA
*
37558 AACTATATTATAT
1 AACTATATAATAT
37571 TTTTTTCAAA
Statistics
Matches: 163, Mismatches: 19, Indels: 27
0.78 0.09 0.13
Matches are distributed among these distances:
34 7 0.04
35 35 0.21
36 31 0.19
37 35 0.21
38 30 0.18
39 20 0.12
40 3 0.02
41 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (35 bp):
AACTATATAATATACGTTTTCAAAAATATTTTCAA
Found at i:42854 original size:12 final size:13
Alignment explanation
Indices: 42837--42866 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
42827 AAGGATCGAG
42837 AATTT-AAATTAA
1 AATTTAAAATTAA
42849 AATTTAAAATTAA
1 AATTTAAAATTAA
42862 AATTT
1 AATTT
42867 TTGCTTAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AATTTAAAATTAA
Found at i:44395 original size:18 final size:18
Alignment explanation
Indices: 44374--44409 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
44364 AAAAAAGAAT
44374 AAATA-ATAAAATGAAATA
1 AAATATATAAAAT-AAATA
44392 AAATATATAAAATAAATA
1 AAATATATAAAATAAATA
44410 TGATGTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (18 bp):
AAATATATAAAATAAATA
Found at i:44532 original size:40 final size:36
Alignment explanation
Indices: 44416--44609 Score: 156
Period size: 35 Copynumber: 5.4 Consensus size: 36
44406 AATATGATGT
* *
44416 AACTATATAATATA--TTTTCAAAAATATTTTTTCGAA
1 AACTATATATTATACGTTTTC-AAAATATTTTTT-AAA
* *
44452 AA-T-TATATTACATG-TTTCAAAAATCATTTTTT--A
1 AACTATATATTATACGTTTTC-AAAAT-ATTTTTTAAA
44485 AACTATATATTATACGTTTTCAAAAGTATTTTTTAAAA
1 AACTATATATTATACGTTTTCAAAA-TATTTTTT-AAA
* *
44523 AACTATATATTATATACGTTTTCAGAAA-ATGTTTTCAA
1 AACTATATA-T-TATACGTTTTCA-AAATATTTTTTAAA
* *
44561 AACCATATATTATACGTTTTCGAAAATA--TTTTCAA
1 AACTATATATTATACGTTTTC-AAAATATTTTTTAAA
44596 AACTATATATTATA
1 AACTATATATTATA
44610 TTCGTTTTTA
Statistics
Matches: 135, Mismatches: 8, Indels: 31
0.78 0.05 0.18
Matches are distributed among these distances:
33 3 0.02
34 8 0.06
35 51 0.38
36 28 0.21
37 3 0.02
38 20 0.15
39 7 0.05
40 12 0.09
41 3 0.02
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.44
Consensus pattern (36 bp):
AACTATATATTATACGTTTTCAAAATATTTTTTAAA
Found at i:44617 original size:25 final size:25
Alignment explanation
Indices: 44588--44648 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
44578 TTTCGAAAAT
* *
44588 ATTTTCAAAACTATATATTATATTC
1 ATTTTTAAAACTATATATTATAATC
* *
44613 GTTTTTAAAACTGTATATTATAATC
1 ATTTTTAAAACTATATATTATAATC
44638 ATTTTTAAAAC
1 ATTTTTAAAAC
44649 ATTTTCAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (25 bp):
ATTTTTAAAACTATATATTATAATC
Found at i:44667 original size:36 final size:34
Alignment explanation
Indices: 44626--44741 Score: 94
Period size: 38 Copynumber: 3.3 Consensus size: 34
44616 TTTAAAACTG
44626 TATATTATAATCATTTTTAAAACATTTTCAAAAAC
1 TATATTATAATCATTTTTAAAACATTTTC-AAAAC
* *
44661 ATATATTAT-A-CATTTTCAAAA-ATGTTTTTAAAAC
1 -TATATTATAATCATTTTTAAAACA--TTTTCAAAAC
* **
44695 TATATAATATATGTTTTTTAAAACATATTTTTCAAAAC
1 TATATTATA-ATCATTTTTAAAAC--A-TTTTCAAAAC
44733 TATATTATA
1 TATATTATA
44742 TATTTTGAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
33 8 0.13
34 15 0.24
35 6 0.10
36 16 0.25
38 17 0.27
39 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.46
Consensus pattern (34 bp):
TATATTATAATCATTTTTAAAACATTTTCAAAAC
Found at i:44737 original size:71 final size:71
Alignment explanation
Indices: 44613--44753 Score: 180
Period size: 71 Copynumber: 2.0 Consensus size: 71
44603 TATTATATTC
* *
44613 GTTTTTAAAACTGTATATTATAATCATTTTTAAAACATTTTCAAAAACATATATTATACATTTTC
1 GTTTTTAAAACTATATAATATAATCATTTTTAAAACATTTTCAAAAACATATATTATACATTTTC
44678 AAAAAT
66 AAAAAT
** *
44684 GTTTTTAAAACTATATAATAT-ATGTTTTTTAAAACATATTTTTC-AAAAC-TATATTATATATT
1 GTTTTTAAAACTATATAATATAATCATTTTTAAAAC--A-TTTTCAAAAACATATATTATACATT
*
44746 TTGAAAAA
63 TTCAAAAA
44754 ACCGATTTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
70 12 0.20
71 38 0.62
72 6 0.10
73 5 0.08
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (71 bp):
GTTTTTAAAACTATATAATATAATCATTTTTAAAACATTTTCAAAAACATATATTATACATTTTC
AAAAAT
Found at i:46644 original size:17 final size:18
Alignment explanation
Indices: 46602--46664 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 18
46592 TTTGTGTCTG
* * *
46602 ATAATTGTAAAACATCTA
1 ATAACTGTAAATCATCAA
* **
46620 ATATCTGTAAAT-ATCTT
1 ATAACTGTAAATCATCAA
46637 ATAACTGT-AATCATCAA
1 ATAACTGTAAATCATCAA
46654 ATAACTGTAAA
1 ATAACTGTAAA
46665 CATTTAGAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
16 3 0.08
17 22 0.61
18 11 0.31
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (18 bp):
ATAACTGTAAATCATCAA
Found at i:48281 original size:21 final size:22
Alignment explanation
Indices: 48250--48290 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
48240 TCCAAATTTA
48250 AATTCCAACATGTAATCATTAT
1 AATTCCAACATGTAATCATTAT
* *
48272 AATT-CAACATTTTATCATT
1 AATTCCAACATGTAATCATT
48291 CAAACCATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.41
Consensus pattern (22 bp):
AATTCCAACATGTAATCATTAT
Done.