Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007132.1 Hibiscus syriacus cultivar Beakdansim tig00018636_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: 149719
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4536 original size:13 final size:13
Alignment explanation
Indices: 4518--4548 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4508 TTTTTTAAAA
*
4518 TAAAATATTTATT
1 TAAAATATATATT
4531 TAAAATATATATT
1 TAAAATATATATT
4544 TAAAA
1 TAAAA
4549 AAATGAACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAAATATATATT
Found at i:12996 original size:19 final size:19
Alignment explanation
Indices: 12972--13022 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
12962 ACCAACTAAA
12972 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
12991 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
*
13010 TCGCAACGCGATC
1 TCGCAATGCGATC
13023 TCCAGTATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (19 bp):
TCGCAATGCGATCGATAAT
Found at i:13099 original size:21 final size:22
Alignment explanation
Indices: 13070--13112 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
13060 ATTCTGACTA
13070 TCGCATTGCGATTTTCC-AAAT
1 TCGCATTGCGATTTTCCTAAAT
*
13091 TCGCGTTGCGATTTTCCTAAAT
1 TCGCATTGCGATTTTCCTAAAT
13113 CAAAAATGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCTAAAT
Found at i:13185 original size:20 final size:20
Alignment explanation
Indices: 13117--13178 Score: 115
Period size: 20 Copynumber: 3.1 Consensus size: 20
13107 CTAAATCAAA
13117 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
13137 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
*
13157 AATGCGAATATGTAAATCGC
1 AATGCGAATACGTAAATCGC
13177 AA
1 AA
13179 CGTGAATCTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (20 bp):
AATGCGAATACGTAAATCGC
Found at i:13402 original size:22 final size:22
Alignment explanation
Indices: 13377--13439 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
13367 CGACATCCGT
13377 CCCATCTCCGACGAAATCAATC
1 CCCATCTCCGACGAAATCAATC
* *
13399 CCCATCTCCGACGATATCAGTC
1 CCCATCTCCGACGAAATCAATC
* *
13421 TCCATCTCCGGCGAAATCA
1 CCCATCTCCGACGAAATCA
13440 TTCACGGTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.27, C:0.40, G:0.13, T:0.21
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCAATC
Found at i:13907 original size:20 final size:19
Alignment explanation
Indices: 13776--13914 Score: 90
Period size: 20 Copynumber: 7.4 Consensus size: 19
13766 GCGATTCTGT
**
13776 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
13795 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTC-ATTTCG
13815 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
* * **
13835 TGTTACGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
13854 CATTACGAT--TC--TT-G
1 CGTTGCGATAGTCATTTCG
*
13868 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-ATTTCG
*
13888 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
13908 TGTTGCG
1 CGTTGCG
13915 GTTTTCATTT
Statistics
Matches: 94, Mismatches: 17, Indels: 17
0.73 0.13 0.13
Matches are distributed among these distances:
14 8 0.09
15 2 0.02
16 2 0.02
17 2 0.02
19 27 0.29
20 53 0.56
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:13922 original size:20 final size:20
Alignment explanation
Indices: 13884--13939 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
13874 GATAGTCAAA
* **
13884 TTCGCGTTGCGATAATCATT
1 TTCGTGTTGCGATTTTCATT
*
13904 TTCGTGTTGCGGTTTTCATT
1 TTCGTGTTGCGATTTTCATT
13924 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
13940 AAGTTTCAGA
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:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:13946 original size:20 final size:20
Alignment explanation
Indices: 13903--13946 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
13893 CGATAATCAT
* * *
13903 TTTCGTGTTGCGGTTTTCAT
1 TTTCGTGTTGCGATTTTAAG
13923 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
13943 TTTC
1 TTTC
13947 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.14, G:0.23, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:15842 original size:20 final size:20
Alignment explanation
Indices: 15817--15973 Score: 135
Period size: 20 Copynumber: 8.5 Consensus size: 20
15807 GAATTAGTTT
15817 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
15837 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
15857 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
15873 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
15890 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
15906 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
15924 ACTATCGCAATGTGAAAATG
1 ACTATCGCAATGCGAAAATG
**
15944 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
15964 ACTATCGCAA
1 ACTATCGCAA
15974 CGAAAGAATC
Statistics
Matches: 115, Mismatches: 8, Indels: 28
0.76 0.05 0.19
Matches are distributed among these distances:
14 14 0.12
16 10 0.09
17 8 0.07
18 5 0.04
19 7 0.06
20 71 0.62
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:15886 original size:34 final size:34
Alignment explanation
Indices: 15840--15994 Score: 152
Period size: 34 Copynumber: 4.4 Consensus size: 34
15830 GAAAATGACT
* *
15840 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
** *
15874 ATCGCAATGCG-AAATGAAAATCGCAAC-AACAAA
1 ATCGCAATGCGAAAATGACTATCGCAACGAA-AGA
* *
15907 ATCGCAACGCGAAAATGACTATCGCAATGTGAAAATGA
1 ATCGCAATGCGAAAATGACTATCGCAA--CG-AAA-GA
**
15945 CTATCGCAATGCGAATTTGACTATCGCAACGAAAGA
1 --ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
15981 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
15995 TGAAAATCGC
Statistics
Matches: 97, Mismatches: 15, Indels: 18
0.75 0.12 0.14
Matches are distributed among these distances:
32 1 0.01
33 26 0.27
34 36 0.37
36 2 0.02
37 4 0.04
38 4 0.04
40 24 0.25
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.16
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
Found at i:16057 original size:19 final size:20
Alignment explanation
Indices: 16018--16061 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
16008 GTGATTCTCT
16018 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
16038 CGTTGCGATAGTCA-TTTCG
1 CGTTGCGATAGTCATTTTCG
16057 CGTTG
1 CGTTG
16062 TGATTTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.14, C:0.20, G:0.27, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:18046 original size:14 final size:14
Alignment explanation
Indices: 18027--18062 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
18017 ATTGTTTAAT
18027 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
18041 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
18055 TGATTTGT
1 TGATTTGT
18063 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:18295 original size:20 final size:20
Alignment explanation
Indices: 18270--18338 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
18260 GCGATTCTCT
18270 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
18290 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTTCG
*
18310 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATTTTCG
18330 CGTTGCGAT
1 CGTTGCGAT
18339 TTTCCGCGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:18350 original size:35 final size:35
Alignment explanation
Indices: 18252--18358 Score: 126
Period size: 40 Copynumber: 2.9 Consensus size: 35
18242 CGATTTTTAT
* * * *
18252 TTCGCATTGCGATTCT-CTCGTTGCGATAGTCATT
1 TTCGCGTTGCGATTTTCCGCGTTGCGATAGTCATA
18286 TTCGCGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATA
1 TTCGCGTTGCG--A-T--TTTCCGCGTTGCGATAGTCATA
18326 TTCGCGTTGCGATTTTCCGCGTTGCGATAGTCA
1 TTCGCGTTGCGATTTTCCGCGTTGCGATAGTCA
18359 AATGAATGTC
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
34 10 0.16
35 20 0.32
36 1 0.02
37 2 0.03
38 1 0.02
39 2 0.03
40 27 0.43
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.37
Consensus pattern (35 bp):
TTCGCGTTGCGATTTTCCGCGTTGCGATAGTCATA
Found at i:20830 original size:24 final size:24
Alignment explanation
Indices: 20779--20830 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
20769 ATCCAAGTAT
** *
20779 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
20803 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
20827 TGAC
1 TGAC
20831 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:21665 original size:20 final size:20
Alignment explanation
Indices: 21641--21787 Score: 186
Period size: 20 Copynumber: 7.3 Consensus size: 20
21631 AAATTCAGTA
* * *
21641 TTGCGATAATAAGAATCGCA
1 TTGCGATAGTCAGAATCGCG
*
21661 TTGCGATAGTCAAAATCGCG
1 TTGCGATAGTCAGAATCGCG
* *
21681 TTGTGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
21701 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
21721 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
* * *
21741 TTGTGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCG
*
21761 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
21781 TTGCGAT
1 TTGCGAT
21788 TTACGTATTC
Statistics
Matches: 111, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 111 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:21716 original size:60 final size:60
Alignment explanation
Indices: 21640--21787 Score: 206
Period size: 60 Copynumber: 2.5 Consensus size: 60
21630 AAAATTCAGT
* * * *
21640 ATTGCGATAATAAGAATCGCATTGCGATAGTCAAAATCGCGTTGTGATAGTCAGAATCTC
1 ATTGCGATAGTCAGAATCGCGTTGCGATAGTCAAAATCGCGTTGTGATAGTCAGAATCGC
* * * * *
21700 GTTGCGATAGTCAGAATCTCGTTGCGATAGTCAGAATCTCGTTGTGATAGTCATAATCGC
1 ATTGCGATAGTCAGAATCGCGTTGCGATAGTCAAAATCGCGTTGTGATAGTCAGAATCGC
*
21760 ATTGCGATAGTCAGATTCGCGTTGCGAT
1 ATTGCGATAGTCAGAATCGCGTTGCGAT
21788 TTACGTATTC
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 76 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (60 bp):
ATTGCGATAGTCAGAATCGCGTTGCGATAGTCAAAATCGCGTTGTGATAGTCAGAATCGC
Found at i:21848 original size:21 final size:21
Alignment explanation
Indices: 21796--21848 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
21786 ATTTACGTAT
*
21796 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* *
21817 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTAGGAAAA
*
21838 TCGTAATGCGA
1 TCGCAATGCGA
21849 TAGTCAGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:22418 original size:75 final size:75
Alignment explanation
Indices: 22287--22598 Score: 383
Period size: 75 Copynumber: 4.2 Consensus size: 75
22277 CTTAACATGT
* * ** * * * *
22287 TAAAATAAAATAGGTC-CTACCTATTATGTTAAATTATTTACTGGTTTGCTTGAAGGTTACTTAT
1 TAAAATAAAATAGG-CACTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAAT
* *
22351 AATGTAAACGG
65 AATGTAAAAGA
** * *
22362 TAAAATAAAATAGGCGTTACCTATTACGTTAAAATACCTACCGATTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAGGCACTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
*
22427 ATGTAAACGA
66 ATGTAAAAGA
*
22437 TAAAATAAAATAGACACTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAGGCACTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
22502 ATGTAAAAGA
66 ATGTAAAAGA
* * * * ** * *
22512 TAAAATAAAATAGGCACTACTTTTTACGTGAAACTAACTACTTGTTTGTTTAAAAGTTAATAATA
1 TAAAATAAAATAGGCACTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
*
22577 ATGTAAAAAA
66 ATGTAAAAGA
22587 TAAAATAAAATA
1 TAAAATAAAATA
22599 AGTGTTTCTA
Statistics
Matches: 209, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
74 1 0.00
75 208 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (75 bp):
TAAAATAAAATAGGCACTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
ATGTAAAAGA
Found at i:22663 original size:23 final size:23
Alignment explanation
Indices: 22606--22664 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
22596 ATAAGTGTTT
** *
22606 CTATTATGTTAAATATGTTCTAT
1 CTATTATGTTAAATAAATTCTAC
**
22629 CTATTACATTAAATAAATAT-TAC
1 CTATTATGTTAAATAAAT-TCTAC
22652 CTATTATGTTAAA
1 CTATTATGTTAAA
22665 CTAACTACTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (23 bp):
CTATTATGTTAAATAAATTCTAC
Found at i:23381 original size:108 final size:106
Alignment explanation
Indices: 23204--23424 Score: 300
Period size: 108 Copynumber: 2.1 Consensus size: 106
23194 GAAGGCCTCT
* * *
23204 TCAGTTTAAACTTTGATAATATTATAGGCGCTATATATGTTGATAATATTAATAACAAAATAAGT
1 TCAGCTTAAACTTTGATAATATTATAGACGCTATATATGTTGATAATATTAATAACAAAATAAGC
* * * *
23269 AATTAACCTATTTTTTTATTGTCAGATTT-TTAAGGTCCCA
66 AATTAACATATTTTGTTATCGTCAGATTTCTTAAAGTCCCA
* * *
23309 TCAGCTTAAACTTTGATAATATTTTAGACGCTACCTAATATGTTGATAATATTGATAACAAATTA
1 TCAGCTTAAACTTTGATAATATTATAGACGCTA--T-ATATGTTGATAATATTAATAACAAAATA
* *
23374 AGCAATTAATATATTTTGTTATCGTCGGATTTCTTAAAGTCCCA
63 AGCAATTAACATATTTTGTTATCGTCAGATTTCTTAAAGTCCCA
23418 TCAGCTT
1 TCAGCTT
23425 TAAAAAGACG
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
105 30 0.30
107 1 0.01
108 52 0.52
109 17 0.17
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (106 bp):
TCAGCTTAAACTTTGATAATATTATAGACGCTATATATGTTGATAATATTAATAACAAAATAAGC
AATTAACATATTTTGTTATCGTCAGATTTCTTAAAGTCCCA
Found at i:23735 original size:224 final size:226
Alignment explanation
Indices: 23313--23737 Score: 551
Period size: 224 Copynumber: 1.9 Consensus size: 226
23303 GTCCCATCAG
* * * * ** *
23313 CTTAAACTTTGATAATATTTTAGACGCTACCTAATATGTTGATAATATTGATAACAAATTAAGCA
1 CTTAAACTTTAATAACATTTTAGACGCTACCTAATATGTTAATAATATCGATAACAAACCAAACA
* *
23378 ATTAATATATTTTGTTATCGTCGGATTTCTTAAAGTCCCATCAGCTTTAAAAAGACGCTACCTAT
66 ATTAATATATTTTGTTATCGTCGGA-TTCTTAAAGCCCCACCAGCTTTAAAAAGACGCTACCTAT
* *
23443 TACATTAAATAAGCACTACTTGTTATGTTATTATGGTTAATAATGTTTCCAGTAATTAACTGGTT
130 TACATTAAATAAGCACTACTTGTTATGTTATTATGATTAATAATGTTTCCAGTAATTAACTAGTT
23508 ATGTTATCGTCGAATTTCTAAAACTCCATTAA
195 ATGTTATCGTCGAATTTCTAAAACTCCATTAA
*
23540 CTTAAACTTTAATAACATTTTA-A-GCATTATCTAATATGTTAATAATATCGATAACAAACCAAA
1 CTTAAACTTTAATAACATTTTAGACGC--TACCTAATATGTTAATAATATCGATAACAAACCAAA
* *
23603 TAATTAACT-TATTTTGTTATCGTCGGA-T-TT-AAGACCCCACCAGTTTTAAAAAGACGCTACC
64 CAATTAA-TATATTTTGTTATCGTCGGATTCTTAAAG-CCCCACCAGCTTTAAAAAGACGCTACC
* * * * * *
23664 TATTACGTTACAA-AAGTATTA-TCTGTTATGTTATTATGATTGATAATGTTTCTAGTAATTAAT
127 TATTACATTA-AATAAGCACTACT-TGTTATGTTATTATGATTAATAATGTTTCCAGTAATTAAC
23727 TAGTTATGTTA
190 TAGTTATGTTA
23738 AAGTCAATAT
Statistics
Matches: 172, Mismatches: 20, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
223 4 0.02
224 87 0.51
225 5 0.03
226 1 0.01
227 74 0.43
228 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (226 bp):
CTTAAACTTTAATAACATTTTAGACGCTACCTAATATGTTAATAATATCGATAACAAACCAAACA
ATTAATATATTTTGTTATCGTCGGATTCTTAAAGCCCCACCAGCTTTAAAAAGACGCTACCTATT
ACATTAAATAAGCACTACTTGTTATGTTATTATGATTAATAATGTTTCCAGTAATTAACTAGTTA
TGTTATCGTCGAATTTCTAAAACTCCATTAA
Found at i:25933 original size:4 final size:4
Alignment explanation
Indices: 25924--25971 Score: 73
Period size: 4 Copynumber: 12.5 Consensus size: 4
25914 TGTATATGTT
*
25924 TATG TATG TATG TATG TATG TATG TATG TA-- TATA TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
25970 TA
1 TA
25972 GGCTAAACTC
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
2 2 0.05
4 39 0.95
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:30305 original size:26 final size:24
Alignment explanation
Indices: 30243--30305 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
30233 CATTTTAATC
30243 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
30267 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
30290 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
30306 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:30420 original size:18 final size:20
Alignment explanation
Indices: 30399--30439 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
30389 TAATAAAATT
30399 ATAAAAAAT-AA-TATTTTA
1 ATAAAAAATAAATTATTTTA
*
30417 ATAATAAATAAATTATTTTA
1 ATAAAAAATAAATTATTTTA
30437 ATA
1 ATA
30440 TTTAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 2 0.10
20 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAAAAAATAAATTATTTTA
Found at i:36525 original size:31 final size:31
Alignment explanation
Indices: 36487--36652 Score: 201
Period size: 31 Copynumber: 5.4 Consensus size: 31
36477 CTAATGTGAC
* *
36487 TCTTGGGTAGGCTCTACGGCCCTGAGATCAT
1 TCTTGGGTAGGCCCTACGGCCCTGAGATCTT
* *
36518 TCTTGGGTAGGCCCTACAGCCCTGAGATTTT
1 TCTTGGGTAGGCCCTACGGCCCTGAGATCTT
* * *
36549 TCTTAGGTAGGCCCCATGGCCCTGAGATCTT
1 TCTTGGGTAGGCCCTACGGCCCTGAGATCTT
*
36580 TCTTCGGTAGGCCCTACGGCCCTGAGATCTT
1 TCTTGGGTAGGCCCTACGGCCCTGAGATCTT
* * * *
36611 TCTTAGATAGGCCC--CGTGGCCTGAAATCTT
1 TCTTGGGTAGGCCCTACG-GCCCTGAGATCTT
36641 TCTTGGGTAGGC
1 TCTTGGGTAGGC
36653 TCTCAAGCCC
Statistics
Matches: 116, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
29 2 0.02
30 21 0.18
31 93 0.80
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (31 bp):
TCTTGGGTAGGCCCTACGGCCCTGAGATCTT
Found at i:36570 original size:62 final size:62
Alignment explanation
Indices: 36504--36652 Score: 228
Period size: 62 Copynumber: 2.4 Consensus size: 62
36494 TAGGCTCTAC
* * *
36504 GGCCCTGAGATCATTCTTGGGTAGGCCCTACAGCCCTGAGATTTTTCTTAGGTAGGCCCCAT
1 GGCCCTGAGATCTTTCTTGGGTAGGCCCTACAGCCCTGAGATCTTTCTTAGATAGGCCCCAT
* * *
36566 GGCCCTGAGATCTTTCTTCGGTAGGCCCTACGGCCCTGAGATCTTTCTTAGATAGGCCCCGT
1 GGCCCTGAGATCTTTCTTGGGTAGGCCCTACAGCCCTGAGATCTTTCTTAGATAGGCCCCAT
*
36628 GG-CCTGAAATCTTTCTTGGGTAGGC
1 GGCCCTGAGATCTTTCTTGGGTAGGC
36653 TCTCAAGCCC
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
61 21 0.27
62 58 0.73
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.30
Consensus pattern (62 bp):
GGCCCTGAGATCTTTCTTGGGTAGGCCCTACAGCCCTGAGATCTTTCTTAGATAGGCCCCAT
Found at i:49631 original size:23 final size:23
Alignment explanation
Indices: 49605--49656 Score: 95
Period size: 23 Copynumber: 2.2 Consensus size: 23
49595 TTTGATCAAT
49605 TATATAATGTGATATATAAATTG
1 TATATAATGTGATATATAAATTG
49628 TATATAATGTGATATATAAATTG
1 TATATAATGTGATATATAAATTG
49651 TGATAT
1 T-ATAT
49657 GATTTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 24 0.86
24 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (23 bp):
TATATAATGTGATATATAAATTG
Found at i:49652 original size:14 final size:13
Alignment explanation
Indices: 49605--49656 Score: 67
Period size: 12 Copynumber: 4.2 Consensus size: 13
49595 TTTGATCAAT
49605 TATAT-AATGTGA
1 TATATAAATGTGA
49617 TATATAAAT-TG-
1 TATATAAATGTGA
49628 TATAT-AATGTGA
1 TATATAAATGTGA
49640 TATATAAATTGTGA
1 TATATAAA-TGTGA
49654 TAT
1 TAT
49657 GATTTAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 3 0.09
11 7 0.20
12 12 0.34
13 5 0.14
14 8 0.23
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (13 bp):
TATATAAATGTGA
Found at i:49668 original size:23 final size:23
Alignment explanation
Indices: 49605--49670 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
49595 TTTGATCAAT
*
49605 TATATAATGTGATATATAAATTG
1 TATATAATGTAATATATAAATTG
*
49628 TATATAATGTGATATATAAATTG
1 TATATAATGTAATATATAAATTG
* *
49651 TGATATGATTTAATTATATA
1 T-ATATAATGTAA-TATATA
49671 CATAAAACTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 24 0.63
24 8 0.21
25 6 0.16
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (23 bp):
TATATAATGTAATATATAAATTG
Found at i:52102 original size:6 final size:6
Alignment explanation
Indices: 52080--52121 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
52070 GTAAAAATGT
*
52080 AATTAA TAATAAA AATTAA AATT-- AATTAA AATTAA AATTAA A
1 AATTAA -AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA A
52122 GGGCCTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
4 4 0.13
6 22 0.71
7 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATTAA
Found at i:52110 original size:16 final size:16
Alignment explanation
Indices: 52086--52120 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
52076 ATGTAATTAA
52086 TAATAAAAATTAAAAT
1 TAATAAAAATTAAAAT
*
52102 TAATTAAAATTAAAAT
1 TAATAAAAATTAAAAT
52118 TAA
1 TAA
52121 AGGGCCTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATAAAAATTAAAAT
Found at i:52282 original size:2 final size:2
Alignment explanation
Indices: 52275--52310 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
52265 CGTTTGATTC
52275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52311 TATTAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52659 original size:50 final size:50
Alignment explanation
Indices: 52584--52683 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 50
52574 TAATTCGTGC
* * *
52584 TCGGAAATATAATGCATGATTAATAAATTATACGTGCTTGATATGATATT
1 TCGGAAATACAATGCATGATTAATAAAATATACGTGCTTGATAAGATATT
*
52634 TCGGAAATACAATGTATGATTAATAAAATATACGTGCTTGATAAGATATT
1 TCGGAAATACAATGCATGATTAATAAAATATACGTGCTTGATAAGATATT
52684 CTTATTTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (50 bp):
TCGGAAATACAATGCATGATTAATAAAATATACGTGCTTGATAAGATATT
Found at i:57707 original size:12 final size:12
Alignment explanation
Indices: 57690--57714 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57680 AGTAAAACGG
57690 TTCAGTTCGGTT
1 TTCAGTTCGGTT
57702 TTCAGTTCGGTT
1 TTCAGTTCGGTT
57714 T
1 T
57715 AAAGTCTTTA
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:0.08, C:0.16, G:0.24, T:0.52
Consensus pattern (12 bp):
TTCAGTTCGGTT
Found at i:61049 original size:21 final size:20
Alignment explanation
Indices: 61006--61070 Score: 80
Period size: 21 Copynumber: 3.3 Consensus size: 20
60996 TATGGTATGT
* *
61006 TTAAAAAAAGATTAAA-A-A
1 TTAAAAAATGAATAAATATA
61024 TTAAAAAATGAATAAATATTA
1 TTAAAAAATGAATAAATA-TA
*
61045 TTAAAATATGAATAAATATA
1 TTAAAAAATGAATAAATATA
61065 TTAAAA
1 TTAAAA
61071 TTATTAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
18 14 0.34
19 1 0.02
20 8 0.20
21 18 0.44
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
TTAAAAAATGAATAAATATA
Found at i:61082 original size:21 final size:21
Alignment explanation
Indices: 61023--61082 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
61013 AAGATTAAAA
* *
61023 ATTAAAAAATGAATAAATATT
1 ATTAAAATATGAAAAAATATT
*
61044 ATTAAAATATGAATAAATA-T
1 ATTAAAATATGAAAAAATATT
*
61064 ATTAAAATTATTAAAAAAT
1 ATTAAAA-TATGAAAAAAT
61083 TAAAAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 8 0.23
21 27 0.77
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
ATTAAAATATGAAAAAATATT
Found at i:61088 original size:18 final size:17
Alignment explanation
Indices: 61064--61138 Score: 60
Period size: 18 Copynumber: 4.2 Consensus size: 17
61054 GAATAAATAT
*
61064 ATTAAAATTATTAAAAA
1 ATTAAAAATATTAAAAA
* **
61081 ATTAAAAATTATGAACATT
1 ATTAAAAA-TATTAA-AAA
*
61100 ATTAAAAATGTTAAAAA
1 ATTAAAAATATTAAAAA
* *
61117 CAGTAAAAAGATTAAAAA
1 -ATTAAAAATATTAAAAA
61135 ATTA
1 ATTA
61139 TTAAAATTAC
Statistics
Matches: 43, Mismatches: 12, Indels: 6
0.70 0.20 0.10
Matches are distributed among these distances:
17 11 0.26
18 23 0.53
19 9 0.21
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (17 bp):
ATTAAAAATATTAAAAA
Found at i:61106 original size:27 final size:28
Alignment explanation
Indices: 61019--61116 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 28
61009 AAAAAAGATT
61019 AAAAATTAAAAA-ATGAAT-AAATATTATTA
1 AAAAATTAAAAATAT--ATGAAA-ATTATTA
* * *
61048 AAATATGAATAAATATATTAAAATTATTA
1 AAAAATTAA-AAATATATGAAAATTATTA
*
61077 AAAAATTAAAAAT-TATGAACATTATTA
1 AAAAATTAAAAATATATGAAAATTATTA
*
61104 AAAATGTTAAAAA
1 AAAA-ATTAAAAA
61117 CAGTAAAAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
27 16 0.28
28 11 0.19
29 23 0.40
30 6 0.10
31 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (28 bp):
AAAAATTAAAAATATATGAAAATTATTA
Found at i:64708 original size:5 final size:5
Alignment explanation
Indices: 64698--64732 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
64688 CTTGACATCC
64698 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
64733 AGTGGCTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
TTTTG
Found at i:69770 original size:25 final size:26
Alignment explanation
Indices: 69740--69789 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
69730 ATTTGAGGAC
* *
69740 TTATTTA-ATTTAAAAAATTAAATAT
1 TTATTTAGATTAAAAAAATAAAATAT
69765 TTATTTAGATTAAAAAAATAAAATA
1 TTATTTAGATTAAAAAAATAAAATA
69790 CAAACATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
TTATTTAGATTAAAAAAATAAAATAT
Found at i:85691 original size:171 final size:172
Alignment explanation
Indices: 85404--85743 Score: 533
Period size: 171 Copynumber: 2.0 Consensus size: 172
85394 GTTCGACTCG
***** *
85404 AACTTGAAATCCTGAACTGAAGCTCATGAGCAGCTAGAAAAGGCTCGAAATGAATTTTTTTTTCT
1 AACTTGAAATCCTGAACTGAAGCTCAT-AGCAGCTAGAAAAGGCTCGAAATGAAAAAAATATTCT
*
85469 TAAACTTAACTCGATTGAAGCCTCAAACTCTAACCTGAACCTTAAATACATGAAAATCTTACTGT
65 TAAACTTAACTCGATTGAAGCCTCAAACTCGAACCTGAACCTTAAATACATGAAAATCTTACTGT
*
85534 ATT-TTTAAAAAAAATCAATACATAAATGTTTATATTATTCTTA
130 ATTATTT-AAAAAAATCAATACAAAAATGTTTATATTATTCTTA
*
85577 AACTTGAAATCCTGAACTGAAGCTCAT-G-AGCTCGAAAAGGCTCGAAATGAAAAAAAATATTCT
1 AACTTGAAATCCTGAACTGAAGCTCATAGCAGCTAGAAAAGGCTCGAAATG-AAAAAAATATTCT
*
85640 TAAACTTAACTCGATTGAAGCCTCAAACTCGAACCTGAACTTTAAATACATGAAAATCTTACTGT
65 TAAACTTAACTCGATTGAAGCCTCAAACTCGAACCTGAACCTTAAATACATGAAAATCTTACTGT
*
85705 ATTATTTTAAAAAATCAATACAAAAATGTTTATATTATT
130 ATTATTTAAAAAAATCAATACAAAAATGTTTATATTATT
85744 AATAATTTTT
Statistics
Matches: 154, Mismatches: 11, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
170 20 0.13
171 104 0.68
172 3 0.02
173 27 0.18
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (172 bp):
AACTTGAAATCCTGAACTGAAGCTCATAGCAGCTAGAAAAGGCTCGAAATGAAAAAAATATTCTT
AAACTTAACTCGATTGAAGCCTCAAACTCGAACCTGAACCTTAAATACATGAAAATCTTACTGTA
TTATTTAAAAAAATCAATACAAAAATGTTTATATTATTCTTA
Found at i:88548 original size:142 final size:142
Alignment explanation
Indices: 88292--88575 Score: 559
Period size: 142 Copynumber: 2.0 Consensus size: 142
88282 AGCAGCAACA
*
88292 GGATACAGATTCAATCCCTTTACCCTTAGGATTTGAAATCTTTATGTAAACTCCAATTGGTTGTG
1 GGATACAGATTCAATCCCTTTACCCTTAAGATTTGAAATCTTTATGTAAACTCCAATTGGTTGTG
88357 AGATTTGGTTGATTTCGTTTCTGAAATCATGTGTACTGAATTGTTGAATTTATCTTGTTTTGGTC
66 AGATTTGGTTGATTTCGTTTCTGAAATCATGTGTACTGAATTGTTGAATTTATCTTGTTTTGGTC
88422 TCATTTTGTTTC
131 TCATTTTGTTTC
88434 GGATACAGATTCAATCCCTTTACCCTTAAGATTTGAAATCTTTATGTAAACTCCAATTGGTTGTG
1 GGATACAGATTCAATCCCTTTACCCTTAAGATTTGAAATCTTTATGTAAACTCCAATTGGTTGTG
88499 AGATTTGGTTGATTTCGTTTCTGAAATCATGTGTACTGAATTGTTGAATTTATCTTGTTTTGGTC
66 AGATTTGGTTGATTTCGTTTCTGAAATCATGTGTACTGAATTGTTGAATTTATCTTGTTTTGGTC
88564 TCATTTTGTTTC
131 TCATTTTGTTTC
88576 AAGTGGGATG
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 141 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (142 bp):
GGATACAGATTCAATCCCTTTACCCTTAAGATTTGAAATCTTTATGTAAACTCCAATTGGTTGTG
AGATTTGGTTGATTTCGTTTCTGAAATCATGTGTACTGAATTGTTGAATTTATCTTGTTTTGGTC
TCATTTTGTTTC
Found at i:90677 original size:26 final size:26
Alignment explanation
Indices: 90639--90704 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 26
90629 CATCCACCTG
90639 ATCAGACCAGACCCAAAAATTTTACATC
1 ATCA-ACC-GACCCAAAAATTTTACATC
**
90667 ATCAACCGACCTTAAAATTTTACATC
1 ATCAACCGACCCAAAAATTTTACATC
*
90693 CTCAACCCGACC
1 ATCAA-CCGACC
90705 TAAACCCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 21 0.62
27 9 0.26
28 4 0.12
ACGTcount: A:0.38, C:0.33, G:0.06, T:0.23
Consensus pattern (26 bp):
ATCAACCGACCCAAAAATTTTACATC
Found at i:90708 original size:26 final size:26
Alignment explanation
Indices: 90654--90705 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
90644 ACCAGACCCA
90654 AAAATTTTACATCATCAACCGACCTT
1 AAAATTTTACATCATCAACCGACCTT
*
90680 AAAATTTTACATCCTCAACCCGACCT
1 AAAATTTTACATCATCAA-CCGACCT
90706 AAACCCAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.37, C:0.31, G:0.04, T:0.29
Consensus pattern (26 bp):
AAAATTTTACATCATCAACCGACCTT
Found at i:90786 original size:19 final size:20
Alignment explanation
Indices: 90754--90798 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
90744 ATCCCACCTG
*
90754 AAATAATATATTTATT-AAA
1 AAATATTATATTTATTCAAA
* *
90773 AAATATTATTTTTATTCAAT
1 AAATATTATATTTATTCAAA
90793 AAATAT
1 AAATAT
90799 AAGGATTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATATTATATTTATTCAAA
Found at i:92596 original size:6 final size:6
Alignment explanation
Indices: 92579--92612 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
92569 ATAAGTCATA
* *
92579 ATATAC ACATAC ATATAC ATGTAC ATATAC ATAT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATAT
92613 GAGTTGAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (6 bp):
ATATAC
Found at i:94078 original size:3 final size:3
Alignment explanation
Indices: 94066--94100 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
94056 GCCAAAAAAA
*
94066 AAG AATG AAG AAG AAG AAG AAG ATG AAG AAG AAG A
1 AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG A
94101 CTTACGCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.31, T:0.06
Consensus pattern (3 bp):
AAG
Found at i:94949 original size:21 final size:21
Alignment explanation
Indices: 94923--94964 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
94913 CTTATTAGGG
94923 TTGATTTGAAATGTATAAAAT
1 TTGATTTGAAATGTATAAAAT
94944 TTGATTTGAAATGTATAAAAT
1 TTGATTTGAAATGTATAAAAT
94965 CTTCTTTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (21 bp):
TTGATTTGAAATGTATAAAAT
Found at i:95760 original size:110 final size:111
Alignment explanation
Indices: 95547--95768 Score: 410
Period size: 110 Copynumber: 2.0 Consensus size: 111
95537 GGCTGTTCTG
95547 CAATTGCAGATTTCAGAAGCATTATAATATACATAATAATGTTGATAAACGCGTGCATATGCATC
1 CAATTGCAGATTTCAGAAGCATTATAATATACATAATAATGTTGATAAAC-CGTGCATATGCATC
*
95612 TACTAGATATGCTTGCCTACCAAAATCTATGCTGCAAATCTCATAAT
65 TACTACATATGCTTGCCTACCAAAATCTATGCTGCAAATCTCATAAT
95659 CAATTGCAGATTTCAGAAGCATTATAATATACATAATAATGTTGATAAA-CGTGCATATGCATCT
1 CAATTGCAGATTTCAGAAGCATTATAATATACATAATAATGTTGATAAACCGTGCATATGCATCT
*
95723 ACTACATATGTTTGCCTACCAAAATCTATGCTGCAAATCTCATAAT
66 ACTACATATGCTTGCCTACCAAAATCTATGCTGCAAATCTCATAAT
95769 TTTCAAACAA
Statistics
Matches: 108, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
110 59 0.55
112 49 0.45
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (111 bp):
CAATTGCAGATTTCAGAAGCATTATAATATACATAATAATGTTGATAAACCGTGCATATGCATCT
ACTACATATGCTTGCCTACCAAAATCTATGCTGCAAATCTCATAAT
Found at i:100826 original size:14 final size:14
Alignment explanation
Indices: 100807--100836 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
100797 AGCGTTTCTA
100807 AAGTCTGATACATC
1 AAGTCTGATACATC
*
100821 AAGTCTGATAGATC
1 AAGTCTGATACATC
100835 AA
1 AA
100837 TATGAACAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (14 bp):
AAGTCTGATACATC
Found at i:118469 original size:12 final size:12
Alignment explanation
Indices: 118452--118482 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
118442 ATTGAATTTA
118452 CTTCTTTTAAAT
1 CTTCTTTTAAAT
*
118464 CTTCTTCTAAAT
1 CTTCTTTTAAAT
118476 CTTCTTT
1 CTTCTTT
118483 ACTTTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (12 bp):
CTTCTTTTAAAT
Found at i:118519 original size:5 final size:5
Alignment explanation
Indices: 118509--118533 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
118499 ATTTTCTTGT
118509 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
118534 CTCTCTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:119127 original size:156 final size:156
Alignment explanation
Indices: 118826--119137 Score: 608
Period size: 156 Copynumber: 2.0 Consensus size: 156
118816 GTTAAGACGA
118826 GTTAGTGAATTTAATTTCATGTGGCCCTGGAATTCTGTCCCATCATTAATTCTGTACTATTTCGA
1 GTTAGTGAATTTAATTTCATGTGGCCCTGGAATTCTGTCCCATCATTAATTCTGTACTATTTCGA
118891 AACGAGTTGGTACTTTGTTTGATTCATCAAAACACCAATTAATCAAGAAGATGCGATGGTTTTGT
66 AACGAGTTGGTACTTTGTTTGATTCATCAAAACACCAATTAATCAAGAAGATGCGATGGTTTTGT
118956 ATGTTCAAAATAAAAGGATAATCAAT
131 ATGTTCAAAATAAAAGGATAATCAAT
118982 GTTAGTGAATTTAATTTCATGTGGCCCTGGAATTCTGTCCCATCATTAATTCTGTACTATTTCGA
1 GTTAGTGAATTTAATTTCATGTGGCCCTGGAATTCTGTCCCATCATTAATTCTGTACTATTTCGA
119047 AACGAGTTGGTACTTTGTTTGATTCATCAAAACACCAATTAATCAAGAAGATGCGAT-GTTTTGT
66 AACGAGTTGGTACTTTGTTTGATTCATCAAAACACCAATTAATCAAGAAGATGCGATGGTTTTGT
119111 ATGTTCAAAATAAAAAGGATAATCAAT
131 ATGTTCAAAAT-AAAAGGATAATCAAT
119138 ATTTTTTTTG
Statistics
Matches: 155, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
155 18 0.12
156 137 0.88
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (156 bp):
GTTAGTGAATTTAATTTCATGTGGCCCTGGAATTCTGTCCCATCATTAATTCTGTACTATTTCGA
AACGAGTTGGTACTTTGTTTGATTCATCAAAACACCAATTAATCAAGAAGATGCGATGGTTTTGT
ATGTTCAAAATAAAAGGATAATCAAT
Found at i:120707 original size:24 final size:24
Alignment explanation
Indices: 120680--120728 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
120670 TGTGATCTTA
120680 ATGGTGATAATGGTGGGGCC-GTTG
1 ATGGTGATAATGGT-GGGCCAGTTG
*
120704 ATGGTGATGATGGTGGGCCAGTTG
1 ATGGTGATAATGGTGGGCCAGTTG
120728 A
1 A
120729 AAGTATGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.18, C:0.08, G:0.45, T:0.29
Consensus pattern (24 bp):
ATGGTGATAATGGTGGGCCAGTTG
Found at i:120808 original size:39 final size:39
Alignment explanation
Indices: 120691--120813 Score: 129
Period size: 39 Copynumber: 3.2 Consensus size: 39
120681 TGGTGATAAT
* *
120691 GGTGGGGCCGTTGATGGTGATGATGGTGGGCCAGTTGAA
1 GGTGGGGCAGTTGATGGTGATAATGGTGGGCCAGTTGAA
* ** * * * * * *
120730 AGTATGACACTTGATGGTGATTATGGTAGTCTAGTTGAA
1 GGTGGGGCAGTTGATGGTGATAATGGTGGGCCAGTTGAA
* *
120769 GGTGGGGCGGTTGATGGTGATAAAGGTGGGCCAGTTGAA
1 GGTGGGGCAGTTGATGGTGATAATGGTGGGCCAGTTGAA
120808 GGTGGG
1 GGTGGG
120814 CTGATTGATG
Statistics
Matches: 63, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.20, C:0.08, G:0.44, T:0.28
Consensus pattern (39 bp):
GGTGGGGCAGTTGATGGTGATAATGGTGGGCCAGTTGAA
Found at i:122171 original size:21 final size:21
Alignment explanation
Indices: 122116--122174 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
122106 CAGCAGCATG
122116 CAACAACTTCATCTCAGACTA
1 CAACAACTTCATCTCAGACTA
** * *
122137 CAACAGTTTAATCTCAGTCTA
1 CAACAACTTCATCTCAGACTA
122158 CAACAACTTCATCTCAG
1 CAACAACTTCATCTCAG
122175 CCAGTAACAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.36, C:0.31, G:0.07, T:0.27
Consensus pattern (21 bp):
CAACAACTTCATCTCAGACTA
Found at i:122189 original size:42 final size:42
Alignment explanation
Indices: 122116--122195 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
122106 CAGCAGCATG
* *
122116 CAACAACTTCATCTCAGACTACAACAGTTTAATCTCAGTCTA
1 CAACAACTTCATCTCAGACCACAACAATTTAATCTCAGTCTA
*
122158 CAACAACTTCATCTCAG-CCAGTAACAATTTAATCTCAG
1 CAACAACTTCATCTCAGACCA-CAACAATTTAATCTCAG
122196 CCTCTAGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 2 0.06
42 32 0.94
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.28
Consensus pattern (42 bp):
CAACAACTTCATCTCAGACCACAACAATTTAATCTCAGTCTA
Found at i:124747 original size:51 final size:51
Alignment explanation
Indices: 124671--124780 Score: 193
Period size: 51 Copynumber: 2.2 Consensus size: 51
124661 AGGCAAGGGC
*
124671 GACCCTCCCAACCCAATTTACTCCATTTGCAACTATCATGATTTAAACCCT
1 GACCCTGCCAACCCAATTTACTCCATTTGCAACTATCATGATTTAAACCCT
* *
124722 GACCCTGCCAACCCAATTTACTCCATTTGCAACTGTCATGATTTAAATCCT
1 GACCCTGCCAACCCAATTTACTCCATTTGCAACTATCATGATTTAAACCCT
124773 GACCCTGC
1 GACCCTGC
124781 TTAAGGGATA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.27, C:0.35, G:0.09, T:0.29
Consensus pattern (51 bp):
GACCCTGCCAACCCAATTTACTCCATTTGCAACTATCATGATTTAAACCCT
Found at i:125911 original size:2 final size:2
Alignment explanation
Indices: 125904--125954 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
125894 TAAAAATAAT
125904 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
125946 TA TA TA TA T
1 TA TA TA TA T
125955 TAATAAATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:134483 original size:37 final size:36
Alignment explanation
Indices: 134427--134543 Score: 166
Period size: 35 Copynumber: 3.2 Consensus size: 36
134417 CCCATTCCTA
* *
134427 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTAT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAAC-AT
*
134463 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACAT
*
134498 TTTTCAAAGAAACATTTACCAAACTTTGAAAATCATT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACA-T
134535 TTTTCAAAG
1 TTTTCAAAG
134544 TTGGTTACCA
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 34 0.46
36 6 0.08
37 34 0.46
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (36 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAAACAT
Found at i:134499 original size:21 final size:20
Alignment explanation
Indices: 134472--134535 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
134462 TTTTTCAAAG
134472 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
134492 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
134507 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
134527 AAATCATTT
1 AAA-CATTT
134536 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:139114 original size:35 final size:36
Alignment explanation
Indices: 139031--139122 Score: 134
Period size: 35 Copynumber: 2.6 Consensus size: 36
139021 ACCCATTCCT
* * *
139031 ATTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTCAAAGAAACATTTACCAAACTTTGAAAAACC
139066 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACC
1 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAAACC
139102 ATTTTCAAAGAAACATTTACC
1 ATTTTCAAAGAAACATTTACC
139123 TGAAAACCAT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
35 21 0.40
36 11 0.21
37 20 0.38
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (36 bp):
ATTTTCAAAGAAACATTTACCAAACTTTGAAAAACC
Found at i:143186 original size:16 final size:17
Alignment explanation
Indices: 143159--143191 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
143149 GTATTGTCGG
143159 CAAAATTTTACTATTCA
1 CAAAATTTTACTATTCA
143176 CAAAA-TTTACTATTCA
1 CAAAATTTTACTATTCA
143192 TTTGAATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (17 bp):
CAAAATTTTACTATTCA
Found at i:143630 original size:26 final size:27
Alignment explanation
Indices: 143598--143648 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
143588 CCCATTCCTA
*
143598 TTTTC-AACAAACATCTATCAAACTAT
1 TTTTCAAACAAACATCTACCAAACTAT
* *
143624 TTTTCAAAGAAACATTTACCAAACT
1 TTTTCAAACAAACATCTACCAAACT
143649 TTGAAAACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.43, C:0.22, G:0.02, T:0.33
Consensus pattern (27 bp):
TTTTCAAACAAACATCTACCAAACTAT
Found at i:143712 original size:35 final size:35
Alignment explanation
Indices: 143617--143730 Score: 144
Period size: 34 Copynumber: 3.3 Consensus size: 35
143607 AACATCTATC
*
143617 AAACTATTTTTCAAAGAAACATTTACCAAACTTTGA
1 AAACCATTTTTCAAAGAAACA-TTACCAAACTTTGA
143653 AAACCA-TTTTCAAAGAAACATTACCAAACTTTGA
1 AAACCATTTTTCAAAGAAACATTACCAAACTTTGA
****
143687 AAACCAATTTTTCAAAG-TTGGTTACCAAAC-TTGA
1 AAACC-ATTTTTCAAAGAAACATTACCAAACTTTGA
143721 AAACCATTTT
1 AAACCATTTT
143731 AATACTTTCA
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
33 5 0.07
34 28 0.39
35 24 0.34
36 14 0.20
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (35 bp):
AAACCATTTTTCAAAGAAACATTACCAAACTTTGA
Done.