Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 34 of 226
Found at i:14777694 original size:59 final size:59
Alignment explanation
Indices: 14777572--14777725 Score: 159
Period size: 59 Copynumber: 2.6 Consensus size: 59
14777562 AACAATTCAA
* *** *
14777572 TATAATTGGATGACTAAAAAAGAAAAAATTTGAATAGTTAAGTGATCGTTTTGCAACCTTT
1 TATAGTTGGATGACTAAAAAAGAAAAAA--ACCATAGTTAAGTGATCATTTTGCAACCTTT
* **
14777633 TATAGTTGGATGACTAAAAAAGAAAAAAACCATAGTTAAGTGA-CTATTTTGTAATTTTT
1 TATAGTTGGATGACTAAAAAAGAAAAAAACCATAGTTAAGTGATC-ATTTTGCAACCTTT
* * *
14777692 TATAGTT-AAGTGACAAAAAAAGAAAATAACCATA
1 TATAGTTGGA-TGACTAAAAAAGAAAAAAACCATA
14777726 ATTGGGTAAG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
58 2 0.03
59 51 0.64
61 27 0.34
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (59 bp):
TATAGTTGGATGACTAAAAAAGAAAAAAACCATAGTTAAGTGATCATTTTGCAACCTTT
Found at i:14790628 original size:2 final size:2
Alignment explanation
Indices: 14790621--14790647 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14790611 TGGTGTCATT
14790621 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
14790648 TAATTAGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14797002 original size:17 final size:17
Alignment explanation
Indices: 14796967--14797012 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
14796957 AGAAAGATAC
*
14796967 TTTTAATTT-ATTTTTA
1 TTTTAATTTAATTTTAA
14796983 -TTTAATATTAATTTTAA
1 TTTTAAT-TTAATTTTAA
14797000 TTTTAATTTAATT
1 TTTTAATTTAATT
14797013 CTTTTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 6 0.23
16 2 0.08
17 12 0.46
18 6 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTAATTTAATTTTAA
Found at i:14797008 original size:23 final size:21
Alignment explanation
Indices: 14796969--14797011 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
14796959 AAAGATACTT
*
14796969 TTAATTTATTTTTATTTAATA
1 TTAATTTATTTTAATTTAATA
14796990 TTAATTTTAATTTTAATTTAAT
1 TTAA-TTT-ATTTTAATTTAAT
14797012 TCTTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 3 0.16
23 12 0.63
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTAATTTATTTTAATTTAATA
Found at i:14797012 original size:11 final size:11
Alignment explanation
Indices: 14796967--14797012 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
14796957 AGAAAGATAC
14796967 TTTTAATTT-A
1 TTTTAATTTAA
*
14796977 TTTTTATTTAA
1 TTTTAATTTAA
*
14796988 TATTAATTTTAA
1 TTTTAA-TTTAA
14797000 TTTTAATTTAA
1 TTTTAATTTAA
14797011 TT
1 TT
14797013 CTTTTATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 8 0.27
11 12 0.40
12 10 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTAATTTAA
Found at i:14810445 original size:36 final size:36
Alignment explanation
Indices: 14810405--14810474 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
14810395 AACACAATTC
14810405 AATTTCATATTGAATATTTCAATATTTACTCAATAT
1 AATTTCATATTGAATATTTCAATATTTACTCAATAT
14810441 AATTTCATATTGAATATTTCAATATTTACTCAAT
1 AATTTCATATTGAATATTTCAATATTTACTCAAT
14810475 CTTTGTCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (36 bp):
AATTTCATATTGAATATTTCAATATTTACTCAATAT
Found at i:14810908 original size:15 final size:14
Alignment explanation
Indices: 14810888--14810939 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
14810878 TCCTTTTTCC
14810888 TTCTTTCTTTCCTTT
1 TTCTTTCTTT-CTTT
14810903 TTCTTTCTGTTTCTTT
1 TTCTTTC--TTTCTTT
* *
14810919 TCACTTTGTTTCTTT
1 T-TCTTTCTTTCTTT
14810934 TTCTTT
1 TTCTTT
14810940 TTCTATTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 4 0.13
15 15 0.48
16 5 0.16
17 7 0.23
ACGTcount: A:0.02, C:0.21, G:0.04, T:0.73
Consensus pattern (14 bp):
TTCTTTCTTTCTTT
Found at i:14810938 original size:6 final size:6
Alignment explanation
Indices: 14810880--14810970 Score: 53
Period size: 6 Copynumber: 14.8 Consensus size: 6
14810870 TGGCTTTCTC
* * *
14810880 CTTTTT CCTTCTTT C-TTTC CTTTTT C--TTT CTGTTT CTTTTCA CTTTGTTT
1 CTTTTT -CTT-TTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT-T C-TT-TTT
* * * *
14810930 CTTTTT CTTTTT CTATTT CTATTT CTATTT CTATTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT
14810971 ATTTTGTTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.06
5 3 0.04
6 48 0.69
7 7 0.10
8 6 0.09
9 2 0.03
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:14810948 original size:12 final size:12
Alignment explanation
Indices: 14810927--14810967 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
14810917 TTTCACTTTG
* *
14810927 TTTCTTTTTCTT
1 TTTCTATTTCTA
14810939 TTTCTATTTCTA
1 TTTCTATTTCTA
14810951 TTTCTATTTCTA
1 TTTCTATTTCTA
14810963 TTTCT
1 TTTCT
14810968 TTTATTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTCTATTTCTA
Found at i:14810954 original size:18 final size:18
Alignment explanation
Indices: 14810927--14810970 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
14810917 TTTCACTTTG
*
14810927 TTTCTTTTTCTTTTTCTA
1 TTTCTTTTTCTATTTCTA
*
14810945 TTTCTATTTCTATTTCTA
1 TTTCTTTTTCTATTTCTA
14810963 TTTCTTTT
1 TTTCTTTT
14810971 ATTTTGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTCTTTTTCTATTTCTA
Found at i:14811608 original size:75 final size:75
Alignment explanation
Indices: 14811479--14811622 Score: 175
Period size: 75 Copynumber: 1.9 Consensus size: 75
14811469 GCAATCACCA
* * *
14811479 TTGGTTGATCCAACTGGAGCTGGGCTCACAATTATTATCGTCGGTATACCCGACTAGCACTGGGT
1 TTGGTTGATCCAACTAGAGCTGGGCTCACAATTATTACCGTCGGTATACCCGACTAGCACTGGGC
14811544 GCAAATATTG
66 GCAAATATTG
* * * ** *
14811554 TTGGTTTATCCAACTAGAGCTGGGCTCAC-CTTCATTACCGTCAGT-TAATTCGACTAGCGCTGG
1 TTGGTTGATCCAACTAGAGCTGGGCTCACAATT-ATTACCGTCGGTAT-ACCCGACTAGCACTGG
14811617 GCGCAA
64 GCGCAA
14811623 CCTTTTCTGC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
74 3 0.05
75 55 0.95
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (75 bp):
TTGGTTGATCCAACTAGAGCTGGGCTCACAATTATTACCGTCGGTATACCCGACTAGCACTGGGC
GCAAATATTG
Found at i:14812373 original size:30 final size:30
Alignment explanation
Indices: 14812339--14812435 Score: 151
Period size: 30 Copynumber: 3.2 Consensus size: 30
14812329 GTATCTCAGC
*
14812339 CGTGTGTGACACACAGCCAGGTAACACGGT
1 CGTGTGTGACACACGGCCAGGTAACACGGT
14812369 CGTGTGTGACACACGGCCAGGTAACACGGT
1 CGTGTGTGACACACGGCCAGGTAACACGGT
* *
14812399 CGTGTGTGACACATGGTCAGGTAACACGG-
1 CGTGTGTGACACACGGCCAGGTAACACGGT
14812428 CTGTGTGT
1 C-GTGTGT
14812436 CCCCTGTAAC
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
29 1 0.02
30 62 0.98
ACGTcount: A:0.23, C:0.24, G:0.33, T:0.21
Consensus pattern (30 bp):
CGTGTGTGACACACGGCCAGGTAACACGGT
Found at i:14812384 original size:17 final size:17
Alignment explanation
Indices: 14812362--14812416 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
14812352 CAGCCAGGTA
14812362 ACACGGTCGTGTGTGAC
1 ACACGGTCGTGTGTGAC
**
14812379 ACACGG-CCAG-GT-A-
1 ACACGGTCGTGTGTGAC
14812392 ACACGGTCGTGTGTGAC
1 ACACGGTCGTGTGTGAC
*
14812409 ACATGGTC
1 ACACGGTC
14812417 AGGTAACACG
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
13 6 0.21
14 3 0.10
15 4 0.14
16 3 0.10
17 13 0.45
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.20
Consensus pattern (17 bp):
ACACGGTCGTGTGTGAC
Found at i:14813360 original size:15 final size:15
Alignment explanation
Indices: 14813323--14813368 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
14813313 TTATTGTATA
*
14813323 TTATTTTTAAATAT-
1 TTATTTTTAAATTTG
14813337 TTATATTTTAAATTTG
1 TTAT-TTTTAAATTTG
*
14813353 TTATTTTTATATTTG
1 TTATTTTTAAATTTG
14813368 T
1 T
14813369 ACATGTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 4 0.14
15 20 0.71
16 4 0.14
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (15 bp):
TTATTTTTAAATTTG
Found at i:14814383 original size:15 final size:17
Alignment explanation
Indices: 14814358--14814389 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
14814348 TAATTCATCT
14814358 TTTTAATTAAT-ATATC
1 TTTTAATTAATAATATC
14814374 TTTT-ATTAATAATATC
1 TTTTAATTAATAATATC
14814390 AAATTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAATTAATAATATC
Found at i:14814876 original size:17 final size:17
Alignment explanation
Indices: 14814854--14814909 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
14814844 TTTTATGAAT
14814854 AAAAGATTTATTAATTA
1 AAAAGATTTATTAATTA
** *
14814871 AAAAGATGAATTAA-AA
1 AAAAGATTTATTAATTA
*
14814887 ATAATATATTTATTAATTA
1 A-AA-AGATTTATTAATTA
14814906 AAAA
1 AAAA
14814910 ACATGAATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
16 2 0.07
17 15 0.52
18 10 0.34
19 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (17 bp):
AAAAGATTTATTAATTA
Found at i:14825079 original size:2 final size:2
Alignment explanation
Indices: 14825072--14825105 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
14825062 ATTGTAGAAC
14825072 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
14825106 GTGCATGGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14832476 original size:6 final size:6
Alignment explanation
Indices: 14832465--14832508 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
14832455 GGGTACTGGA
14832465 TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TT
1 TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TT
14832509 TGAAAGGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (6 bp):
TTGGGG
Found at i:14833730 original size:16 final size:16
Alignment explanation
Indices: 14833706--14833739 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
14833696 ATTAAGTACA
14833706 AATAAATAATATTTAT
1 AATAAATAATATTTAT
*
14833722 AATATATAATATTTAT
1 AATAAATAATATTTAT
14833738 AA
1 AA
14833740 ATAAGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAATAATATTTAT
Found at i:14840492 original size:19 final size:18
Alignment explanation
Indices: 14840458--14840493 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
14840448 AAATTTAAAT
*
14840458 TTTGAGTTATTTGAATTG
1 TTTGAGTTAGTTGAATTG
14840476 TTTGAGTTGAGTTGAATT
1 TTTGAGTT-AGTTGAATT
14840494 TTATAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (18 bp):
TTTGAGTTAGTTGAATTG
Found at i:14840638 original size:19 final size:18
Alignment explanation
Indices: 14840614--14840660 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
14840604 TAAAAATATT
*
14840614 TTTTTAAAAATTGAAATAA
1 TTTTTAAAAATTAAAAT-A
*
14840633 TTTTTAAAATTTAAAATA
1 TTTTTAAAAATTAAAATA
*
14840651 TTTATAAAAA
1 TTTTTAAAAA
14840661 AATCAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TTTTTAAAAATTAAAATA
Found at i:14840653 original size:18 final size:18
Alignment explanation
Indices: 14840600--14840659 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
14840590 TTATAAATGG
14840600 AATTTAAAAATATTTTTTTAA
1 AATTT-AAAATA--TTTTTAA
* *
14840621 AAATTGAAATAATTTTTAA
1 AATTTAAAAT-ATTTTTAA
*
14840640 AATTTAAAATATTTATAA
1 AATTTAAAATATTTTTAA
14840658 AA
1 AA
14840660 AAATCAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
18 9 0.27
19 15 0.45
20 4 0.12
21 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
AATTTAAAATATTTTTAA
Found at i:14840955 original size:22 final size:21
Alignment explanation
Indices: 14840926--14840974 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
14840916 TTCATTCAAT
14840926 TTAAAAAAAAACTAAATTAAA
1 TTAAAAAAAAACTAAATTAAA
* *
14840947 TTAATAAAATAACTAAATTAAT
1 TTAA-AAAAAAACTAAATTAAA
14840969 TTAAAA
1 TTAAAA
14840975 TTTTTTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (21 bp):
TTAAAAAAAAACTAAATTAAA
Found at i:14862124 original size:2 final size:2
Alignment explanation
Indices: 14862117--14862141 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14862107 TGGTATTTTC
14862117 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
14862142 ATTTATCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14884040 original size:51 final size:51
Alignment explanation
Indices: 14883943--14884046 Score: 122
Period size: 51 Copynumber: 2.0 Consensus size: 51
14883933 TTATAAAACT
* *
14883943 TATATATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATA
1 TATACATATAAAATACATAATGCATTTATCAAAACAAGGAAAATATAAATA
* * * *
14883994 TATACATATAAAATATATTCATGCATTTA-CAAAA-AATGAAATATATAAGTA
1 TATACATATAAAATACA-TAATGCATTTATCAAAACAAGGAAA-ATATAAATA
14884045 TA
1 TA
14884047 ATATAAAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
50 6 0.13
51 29 0.64
52 10 0.22
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (51 bp):
TATACATATAAAATACATAATGCATTTATCAAAACAAGGAAAATATAAATA
Found at i:14884745 original size:30 final size:31
Alignment explanation
Indices: 14884711--14884777 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
14884701 AATAAATACC
*
14884711 AAAAATTTATTTTAAAAAT-TAAAAAAATTA
1 AAAAATGTATTTTAAAAATATAAAAAAATTA
* ***
14884741 AAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATGTATTTTAAAAATATAAAAAAATTA
14884772 AAAAAT
1 AAAAAT
14884778 AAAAAATAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (31 bp):
AAAAATGTATTTTAAAAATATAAAAAAATTA
Found at i:14885039 original size:19 final size:21
Alignment explanation
Indices: 14885001--14885039 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
14884991 CTTTTTTTAA
*
14885001 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
14885022 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
14885040 ACAATAAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:14890008 original size:13 final size:14
Alignment explanation
Indices: 14889990--14890019 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
14889980 ACTGTAATAA
14889990 TTTTTTAGATTA-T
1 TTTTTTAGATTACT
14890003 TTTTTTAGATTACT
1 TTTTTTAGATTACT
14890017 TTT
1 TTT
14890020 AACTTAACAT
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:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (14 bp):
TTTTTTAGATTACT
Found at i:14891562 original size:16 final size:19
Alignment explanation
Indices: 14891531--14891570 Score: 59
Period size: 16 Copynumber: 2.3 Consensus size: 19
14891521 TTACGAGTAG
14891531 GTTTTTGTATGTTATTT-T
1 GTTTTTGTATGTTATTTCT
14891549 GTTTTTG-A-GTTATTTCT
1 GTTTTTGTATGTTATTTCT
14891566 GTTTT
1 GTTTT
14891571 AGAAATAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 7 0.33
18 7 0.33
ACGTcount: A:0.10, C:0.03, G:0.17, T:0.70
Consensus pattern (19 bp):
GTTTTTGTATGTTATTTCT
Found at i:14894748 original size:51 final size:51
Alignment explanation
Indices: 14894688--14894789 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
14894678 GATTCAGGTG
14894688 CACCTGTTGTGCCTCAAATTATGGGCTCTACATCAGCGGTTCCAATAGCTT
1 CACCTGTTGTGCCTCAAATTATGGGCTCTACATCAGCGGTTCCAATAGCTT
14894739 CACCTGTTGTGCCTCAAATTATGGGCTCTACATCAGCGGTTCCAATAGCTT
1 CACCTGTTGTGCCTCAAATTATGGGCTCTACATCAGCGGTTCCAATAGCTT
14894790 ACTCTCAGGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (51 bp):
CACCTGTTGTGCCTCAAATTATGGGCTCTACATCAGCGGTTCCAATAGCTT
Found at i:14902066 original size:68 final size:69
Alignment explanation
Indices: 14901974--14902110 Score: 231
Period size: 68 Copynumber: 2.0 Consensus size: 69
14901964 TTAAACAGTG
*
14901974 TATAAATTTTCGTTTTCATCCTTTAGTTAAAAATTCATAAATTTCATTTAAATCACTGAATTATT
1 TATAAATTTTCGTTTTCATCCTTTAATTAAAAATTCATAAATTTCATTTAAATCACTGAATTATT
14902039 CAAA
66 CAAA
* * *
14902043 TATAAATTTT-GTTTTCATTCTTTAATTAAAAATTCATAATTTTCATTTAAATTACTGAATTATT
1 TATAAATTTTCGTTTTCATCCTTTAATTAAAAATTCATAAATTTCATTTAAATCACTGAATTATT
14902107 CAAA
66 CAAA
14902111 AGTTTTTATT
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
68 54 0.84
69 10 0.16
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (69 bp):
TATAAATTTTCGTTTTCATCCTTTAATTAAAAATTCATAAATTTCATTTAAATCACTGAATTATT
CAAA
Found at i:14902140 original size:68 final size:66
Alignment explanation
Indices: 14902000--14902132 Score: 153
Period size: 68 Copynumber: 2.0 Consensus size: 66
14901990 CATCCTTTAG
* ** *
14902000 TTAAAAATTCATAAATTTCATTTAAATCACTGAATTATTCAAATATAAATTTTGTTTTCATTCTT
1 TTAAAAATTCATAAATTTCATTTAAATCACTGAATTATTCAAATAT--ATTTTATTTAAATTCTA
*
14902065 TAA
64 GAA
* *
14902068 TTAAAAATTCATAATTTTCATTTAAATTACTGAATTATTCAAA-AGT-TTTTATTTAAATTACTA
1 TTAAAAATTCATAAATTTCATTTAAATCACTGAATTATTCAAATA-TATTTTATTTAAATT-CTA
14902131 GA
64 GA
14902133 CTCTTAAATC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
65 10 0.18
66 3 0.05
67 1 0.02
68 42 0.75
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.47
Consensus pattern (66 bp):
TTAAAAATTCATAAATTTCATTTAAATCACTGAATTATTCAAATATATTTTATTTAAATTCTAGA
A
Found at i:14904094 original size:15 final size:15
Alignment explanation
Indices: 14904065--14904102 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
14904055 CTGTAGCAGC
*
14904065 TTTTGT-TGTTTCTG
1 TTTTGTATGGTTCTG
14904079 TTTTGTATGGTTCTG
1 TTTTGTATGGTTCTG
14904094 TTTTGTATG
1 TTTTGTATG
14904103 TTTGTATTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.05, C:0.05, G:0.24, T:0.66
Consensus pattern (15 bp):
TTTTGTATGGTTCTG
Found at i:14925690 original size:23 final size:23
Alignment explanation
Indices: 14925664--14925739 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
14925654 AGTGTTATTG
14925664 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
14925687 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
14925710 TTCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
14925733 ATCAGTG
1 ATCAGTG
14925740 TGACACTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:14930109 original size:15 final size:15
Alignment explanation
Indices: 14930089--14930118 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
14930079 ATCATATCGT
14930089 TTATAAAATTCATAA
1 TTATAAAATTCATAA
14930104 TTATAAAATTCATAA
1 TTATAAAATTCATAA
14930119 AATTCATTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
TTATAAAATTCATAA
Found at i:14930399 original size:27 final size:27
Alignment explanation
Indices: 14930369--14930428 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
14930359 GTAACACAAT
** *
14930369 AGATGGTCGAGTCGACGGTGATGCAGC
1 AGATGGTCGAGTCGACGGCAATGCAAC
* * *
14930396 AGATAGTCGGGTTGACGGCAATGCAAC
1 AGATGGTCGAGTCGACGGCAATGCAAC
14930423 AGATGG
1 AGATGG
14930429 GTTGGGATTT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.27, C:0.17, G:0.38, T:0.18
Consensus pattern (27 bp):
AGATGGTCGAGTCGACGGCAATGCAAC
Found at i:14931378 original size:28 final size:27
Alignment explanation
Indices: 14931341--14931475 Score: 94
Period size: 28 Copynumber: 4.8 Consensus size: 27
14931331 TATCAAAATC
*
14931341 CCTAAACCCTAAAACATAAACAATGAAT
1 CCTAAACCCTAAAACATAAACAAT-AAA
*
14931369 CCTAAACCCTAAAATCCTAAA-ACATAAA
1 CCTAAACCCTAAAA-CATAAACA-ATAAA
* **
14931397 CCTTAAACCAT-AAACATTAAACACCAAA
1 CC-TAAACCCTAAAACA-TAAACAATAAA
* * * *
14931425 CACCAAACACTAAAACATAAACACTAATC
1 C-CTAAACCCTAAAACATAAACAATAA-A
*
14931454 CCTAAACCCAAAAACACTAAAC
1 CCTAAACCCTAAAACA-TAAAC
14931476 CATGAACATT
Statistics
Matches: 84, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
27 1 0.01
28 56 0.67
29 27 0.32
ACGTcount: A:0.54, C:0.30, G:0.01, T:0.16
Consensus pattern (27 bp):
CCTAAACCCTAAAACATAAACAATAAA
Found at i:14931742 original size:7 final size:7
Alignment explanation
Indices: 14931726--14931770 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
14931716 TAACACATTA
*
14931726 AAACCCT
1 AAACCTT
14931733 AAACCTT
1 AAACCTT
*
14931740 AAACATT
1 AAACCTT
*
14931747 AAATCTT
1 AAACCTT
14931754 AAACCTT
1 AAACCTT
*
14931761 AAACCCT
1 AAACCTT
14931768 AAA
1 AAA
14931771 ATAAAATGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (7 bp):
AAACCTT
Found at i:14931758 original size:21 final size:22
Alignment explanation
Indices: 14931714--14931764 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
14931704 GAGTCAGTTG
14931714 CTTAACACATTAAAACCCTAAAC
1 CTTAA-ACATTAAAACCCTAAAC
* *
14931737 CTTAAACATT-AAATCTTAAAC
1 CTTAAACATTAAAACCCTAAAC
14931758 CTTAAAC
1 CTTAAAC
14931765 CCTAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 16 0.62
22 5 0.19
23 5 0.19
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.27
Consensus pattern (22 bp):
CTTAAACATTAAAACCCTAAAC
Found at i:14932591 original size:41 final size:41
Alignment explanation
Indices: 14932526--14932630 Score: 147
Period size: 41 Copynumber: 2.6 Consensus size: 41
14932516 TTTTTTACGA
* *
14932526 CGTTTTTCTCATAAATGCCTCTACTGCTTGACCTTTTGCGG
1 CGTTTTTCTCATAAACGCCGCTACTGCTTGACCTTTTGCGG
* * * *
14932567 TGTTTTTCTCACAAACACCGCTACTGCTTGACCTTTTGGGG
1 CGTTTTTCTCATAAACGCCGCTACTGCTTGACCTTTTGCGG
*
14932608 CGTTTTTCTAATAAACGCCGCTA
1 CGTTTTTCTCATAAACGCCGCTA
14932631 TAGCTCTAAC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (41 bp):
CGTTTTTCTCATAAACGCCGCTACTGCTTGACCTTTTGCGG
Found at i:14942659 original size:19 final size:19
Alignment explanation
Indices: 14942631--14942669 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
14942621 TAACAAGATA
* *
14942631 GTAAAGATACCATTGTGAT
1 GTAAACATACCATTATGAT
14942650 GTAAACATACCATTATGAT
1 GTAAACATACCATTATGAT
14942669 G
1 G
14942670 GTGGCATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (19 bp):
GTAAACATACCATTATGAT
Found at i:14947975 original size:7 final size:8
Alignment explanation
Indices: 14947950--14947979 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
14947940 TAGTATTTAA
14947950 TTAATATTT
1 TTAA-ATTT
14947959 TTAAATTT
1 TTAAATTT
14947967 TTAAATTT
1 TTAAATTT
14947975 TTAAA
1 TTAAA
14947980 AAAATTATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TTAAATTT
Found at i:14955746 original size:21 final size:21
Alignment explanation
Indices: 14955720--14955765 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
14955710 ACTTAACAAG
14955720 CAAATGCCTCTAAAATAATAA
1 CAAATGCCTCTAAAATAATAA
*
14955741 CAAATGCCTTTAAAATAATAA
1 CAAATGCCTCTAAAATAATAA
14955762 CAAA
1 CAAA
14955766 ATTAACAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.54, C:0.17, G:0.04, T:0.24
Consensus pattern (21 bp):
CAAATGCCTCTAAAATAATAA
Found at i:14957086 original size:10 final size:10
Alignment explanation
Indices: 14957071--14957095 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
14957061 CTTTTTTGGC
14957071 CCCGACCCGG
1 CCCGACCCGG
14957081 CCCGACCCGG
1 CCCGACCCGG
14957091 CCCGA
1 CCCGA
14957096 ATATAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.60, G:0.28, T:0.00
Consensus pattern (10 bp):
CCCGACCCGG
Found at i:14957195 original size:26 final size:27
Alignment explanation
Indices: 14957144--14957205 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
14957134 TTTAAAATAC
* *
14957144 TTTTAAAATTATTTTTTATTTTTTTAT
1 TTTTAAAATTATTTTTTATATGTTTAT
14957171 TTTTAAAA-TATTTTTT-TAATGTTTAT
1 TTTTAAAATTATTTTTTAT-ATGTTTAT
*
14957197 TTTAAAAAT
1 TTTTAAAAT
14957206 GGGCCGGGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 1 0.03
26 21 0.70
27 8 0.27
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (27 bp):
TTTTAAAATTATTTTTTATATGTTTAT
Found at i:14964040 original size:2 final size:2
Alignment explanation
Indices: 14964033--14964071 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
14964023 ATTTAACGTA
14964033 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14964072 CTTTTTGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14964387 original size:39 final size:39
Alignment explanation
Indices: 14964333--14964411 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
14964323 TTATACTGGT
14964333 AAGGTACATTGTCCTGACATGAAGAGGACTTAAATTTAA
1 AAGGTACATTGTCCTGACATGAAGAGGACTTAAATTTAA
14964372 AAGGTACATTGTCCTGACATGAAGAGGACTTAAATTTAA
1 AAGGTACATTGTCCTGACATGAAGAGGACTTAAATTTAA
14964411 A
1 A
14964412 CCTTAGAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (39 bp):
AAGGTACATTGTCCTGACATGAAGAGGACTTAAATTTAA
Found at i:14964796 original size:21 final size:21
Alignment explanation
Indices: 14964770--14964818 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
14964760 GCTGTTTTTG
14964770 TTGTTTTTCCA-TGTTTTG-CTA
1 TTGTTTTTCCACT-TTTTGTC-A
14964791 TTGTTTTTCCACTTTTTGTCA
1 TTGTTTTTCCACTTTTTGTCA
14964812 TTGTTTT
1 TTGTTTT
14964819 GCTACCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.08, C:0.14, G:0.12, T:0.65
Consensus pattern (21 bp):
TTGTTTTTCCACTTTTTGTCA
Found at i:14966425 original size:9 final size:9
Alignment explanation
Indices: 14966411--14966442 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
14966401 GTTTAAAAAT
14966411 AATTTTTTA
1 AATTTTTTA
14966420 AATTTTTTA
1 AATTTTTTA
14966429 AATTTTTTA
1 AATTTTTTA
14966438 AATTT
1 AATTT
14966443 AAAAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
AATTTTTTA
Found at i:14967037 original size:7 final size:7
Alignment explanation
Indices: 14967025--14967067 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
14967015 TGCTGTAATT
14967025 ATTTTTA
1 ATTTTTA
14967032 ATTTTTA
1 ATTTTTA
14967039 TATGTTTTA
1 -AT-TTTTA
14967048 TATTTTTA
1 -ATTTTTA
*
14967056 AATTTTA
1 ATTTTTA
14967063 ATTTT
1 ATTTT
14967068 CACGAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 17 0.53
8 7 0.22
9 8 0.25
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (7 bp):
ATTTTTA
Found at i:14967048 original size:9 final size:8
Alignment explanation
Indices: 14967024--14967061 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
14967014 TTGCTGTAAT
14967024 TATTTTTA
1 TATTTTTA
14967032 -ATTTTTA
1 TATTTTTA
14967039 TATGTTTTA
1 TAT-TTTTA
14967048 TATTTTTA
1 TATTTTTA
*
14967056 AATTTT
1 TATTTT
14967062 AATTTTCACG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
7 7 0.26
8 12 0.44
9 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (8 bp):
TATTTTTA
Found at i:14969042 original size:16 final size:15
Alignment explanation
Indices: 14969021--14969050 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
14969011 AGTTAACTCC
14969021 TCTTTTTTTATTTTTT
1 TCTTTTTTT-TTTTTT
14969037 TCTTTTTTTTTTTT
1 TCTTTTTTTTTTTT
14969051 AACTTTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (15 bp):
TCTTTTTTTTTTTTT
Found at i:14978771 original size:20 final size:18
Alignment explanation
Indices: 14978740--14978796 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 18
14978730 TCATTTTTCA
14978740 ATAAATTCAATTTCAATAATT
1 ATAAA-TCAATTT-AAT-ATT
14978761 -TAATATCAATTTAATATT
1 ATAA-ATCAATTTAATATT
14978779 ATAAATCAATTATAATAT
1 ATAAATCAATT-TAATAT
14978797 AGTCTGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 10 0.30
19 12 0.36
20 10 0.30
21 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAATCAATTTAATATT
Found at i:14980436 original size:37 final size:37
Alignment explanation
Indices: 14980333--14980552 Score: 383
Period size: 37 Copynumber: 6.0 Consensus size: 37
14980323 TACGTATGAT
*
14980333 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
14980368 CACTTATCACTTTGTCTC-TGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
* *
14980404 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
14980441 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
14980478 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
14980515 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
14980552 C
1 C
14980553 GAAGCTATCA
Statistics
Matches: 176, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
35 10 0.06
36 39 0.22
37 127 0.72
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:14980581 original size:45 final size:46
Alignment explanation
Indices: 14980515--14980632 Score: 195
Period size: 45 Copynumber: 2.6 Consensus size: 46
14980505 TAAGTGTAGC
*
14980515 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
14980561 CACTT-TCCAC-TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTAT-CACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
14980606 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
14980633 AGTACTCAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
45 42 0.63
46 25 0.37
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:15012329 original size:17 final size:16
Alignment explanation
Indices: 15012302--15012349 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
15012292 TGATAGTATA
15012302 ATTAT-ATTATTTAAT
1 ATTATAATTATTTAAT
15012317 ATTATGAATTATTT--T
1 ATTAT-AATTATTTAAT
*
15012332 ATTATAATT-GTTAAT
1 ATTATAATTATTTAAT
15012347 ATT
1 ATT
15012350 TTATTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
13 2 0.07
14 4 0.14
15 15 0.54
17 7 0.25
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
ATTATAATTATTTAAT
Found at i:15019480 original size:2 final size:2
Alignment explanation
Indices: 15019475--15019502 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15019465 TCAAACTGTT
15019475 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
15019503 GTAGGTATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15023979 original size:18 final size:18
Alignment explanation
Indices: 15023956--15023994 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
15023946 ATAACTGCCA
15023956 CTTAAATTTGCCTGGTAC
1 CTTAAATTTGCCTGGTAC
15023974 CTTAAATTTGCCTGGTAC
1 CTTAAATTTGCCTGGTAC
15023992 CTT
1 CTT
15023995 GTATTATACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (18 bp):
CTTAAATTTGCCTGGTAC
Found at i:15034268 original size:9 final size:9
Alignment explanation
Indices: 15034254--15034278 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
15034244 CCTCCACCAC
15034254 CAACGACAA
1 CAACGACAA
15034263 CAACGACAA
1 CAACGACAA
15034272 CAACGAC
1 CAACGAC
15034279 GAAGATGTTC
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:0.52, C:0.36, G:0.12, T:0.00
Consensus pattern (9 bp):
CAACGACAA
Found at i:15043070 original size:29 final size:29
Alignment explanation
Indices: 15043016--15043071 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
15043006 CAACGGTGCC
* *
15043016 TTCGAACCAATAACTCAGATATCACTTGG
1 TTCGAACCAACAACTCAGATACCACTTGG
*
15043045 TTCGAACCAACAGCTCTA-ATACCACTT
1 TTCGAACCAACAACTC-AGATACCACTT
15043072 ATCATGGGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 22 0.96
30 1 0.04
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.27
Consensus pattern (29 bp):
TTCGAACCAACAACTCAGATACCACTTGG
Found at i:15044658 original size:45 final size:46
Alignment explanation
Indices: 15044591--15044714 Score: 191
Period size: 46 Copynumber: 2.8 Consensus size: 46
15044581 CATATGACCT
*
15044591 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
* *
15044634 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTATCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
15044680 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
15044715 CACTTATCAC
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.29
46 40 0.55
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:15044699 original size:46 final size:45
Alignment explanation
Indices: 15044591--15044788 Score: 198
Period size: 37 Copynumber: 4.8 Consensus size: 45
15044581 CATATGACCT
*
15044591 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
* *
15044634 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTATCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
15044680 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
15044717 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
15044754 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
15044789 CACTTATCAC
Statistics
Matches: 138, Mismatches: 9, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
37 63 0.46
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.07
44 6 0.04
45 21 0.15
46 33 0.24
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:15044721 original size:37 final size:37
Alignment explanation
Indices: 15044678--15044815 Score: 231
Period size: 37 Copynumber: 3.7 Consensus size: 37
15044668 CTGAAGCTAT
*
15044678 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
* *
15044715 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
**
15044752 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
15044789 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
15044816 AGTACTCAAA
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 94 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
Found at i:15053660 original size:21 final size:21
Alignment explanation
Indices: 15053634--15053674 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
15053624 AAATGAAACT
15053634 TGTTCTAATGGTCTCGAGACA
1 TGTTCTAATGGTCTCGAGACA
** *
15053655 TGTTCTTTTTGTCTCGAGAC
1 TGTTCTAATGGTCTCGAGAC
15053675 TAAATGGTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (21 bp):
TGTTCTAATGGTCTCGAGACA
Found at i:15054956 original size:2 final size:2
Alignment explanation
Indices: 15054951--15054980 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15054941 TCATACACAC
15054951 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
15054981 CATGACTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15056003 original size:23 final size:23
Alignment explanation
Indices: 15055977--15056098 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
15055967 ATAAGTGCCA
15055977 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
15056000 CACTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
15056023 CACTGAAATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
15056046 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
15056069 CACTAAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
15056092 CATTGAT
1 CACTGAT
15056099 CAGTAACACT
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 86 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:15061993 original size:12 final size:12
Alignment explanation
Indices: 15061976--15062000 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15061966 GGTGTTCATT
15061976 CGGTTAACCGAC
1 CGGTTAACCGAC
15061988 CGGTTAACCGAC
1 CGGTTAACCGAC
15062000 C
1 C
15062001 CGAAATTACT
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:15062175 original size:9 final size:9
Alignment explanation
Indices: 15062161--15062273 Score: 174
Period size: 9 Copynumber: 12.4 Consensus size: 9
15062151 TTTGGTTAAA
15062161 AATTACCCG
1 AATTACCCG
15062170 AATTACCCG
1 AATTACCCG
15062179 AATTACCCG
1 AATTACCCG
15062188 AATTACCCG
1 AATTACCCG
15062197 AATTACCCG
1 AATTACCCG
15062206 AATTACCCG
1 AATTACCCG
*
15062215 AATTAACCG
1 AATTACCCG
15062224 AATTACCCG
1 AATTACCCG
*
15062233 AATTAACCG
1 AATTACCCG
15062242 AATTA-CCG
1 AATTACCCG
*
15062250 AAAAATACCCG
1 --AATTACCCG
15062261 AATTACCCG
1 AATTACCCG
15062270 AATT
1 AATT
15062274 TTTTTATTTT
Statistics
Matches: 96, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
8 3 0.03
9 86 0.90
10 4 0.04
11 3 0.03
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:15064971 original size:18 final size:17
Alignment explanation
Indices: 15064948--15064981 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
15064938 TAAATTTGAT
*
15064948 TGAAAATATATAAAAAAA
1 TGAAAACAT-TAAAAAAA
15064966 TGAAAACATTAAAAAA
1 TGAAAACATTAAAAAA
15064982 TCTAAGATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (17 bp):
TGAAAACATTAAAAAAA
Found at i:15082814 original size:22 final size:20
Alignment explanation
Indices: 15082773--15082815 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
15082763 CCAATATATA
*
15082773 TATTTTAAATTTTTTTAATT
1 TATTTTAAATTTTTTGAATT
*
15082793 TATTATTATATTTGTTTGAATT
1 TATT-TTAAATTT-TTTGAATT
15082815 T
1 T
15082816 TTAGAATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 7 0.37
22 8 0.42
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
TATTTTAAATTTTTTGAATT
Found at i:15110157 original size:126 final size:127
Alignment explanation
Indices: 15109921--15110263 Score: 526
Period size: 126 Copynumber: 2.7 Consensus size: 127
15109911 GAGAGGTCTG
* * *
15109921 TTTTAGGTCAGATGCACTGTTGTCAATCGGAGGTTGCTCCAAATCATCCATTAATGAAGAGGAAG
1 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATT-A-GAAGAGGAAG
* * *
15109986 TTGGCTGGCATGCCTCAAACTTAAAGTCGGCTGCATCGTAGGTAATCAGATTCTCCTCACCCTC
64 TTGGCTGGCATGCCTCGAACTTAAAGTCAGCTGCATAGTAGGTAATCAGATTCTCCTCACCCTC
* * *
15110050 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTTCTCCAAATGATCCATTA-AAGAGGATGTT
1 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTAGAAGAGGAAGTT
* *
15110114 GGCTGGCATGCCTCGAACTTAAAGTCAGTTGCATAGTAGGTAATCAGATTCTCTTCACCCTC
66 GGCTGGCATGCCTCGAACTTAAAGTCAGCTGCATAGTAGGTAATCAGATTCTCCTCACCCTC
*
15110176 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTACTGTAGAGGAAG
1 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTA--GAAGAGGAAG
*
15110241 TTGTCTGGCATGCCTCGAACTTA
64 TTGGCTGGCATGCCTCGAACTTA
15110264 GAGTTGGCTG
Statistics
Matches: 195, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
126 118 0.61
128 1 0.01
129 76 0.39
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (127 bp):
TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTAGAAGAGGAAGTT
GGCTGGCATGCCTCGAACTTAAAGTCAGCTGCATAGTAGGTAATCAGATTCTCCTCACCCTC
Found at i:15112451 original size:15 final size:14
Alignment explanation
Indices: 15112428--15112462 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
15112418 TGCATATGTG
15112428 AAAAAAGAACAGTT
1 AAAAAAGAACAGTT
*
15112442 AAAAAGAGAATAGTT
1 AAAAA-AGAACAGTT
15112457 AAAAAA
1 AAAAAA
15112463 AAAAAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.69, C:0.03, G:0.14, T:0.14
Consensus pattern (14 bp):
AAAAAAGAACAGTT
Found at i:15116469 original size:31 final size:30
Alignment explanation
Indices: 15116397--15116469 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
15116387 AATTAAATTA
*
15116397 AAATTAAAATTTTATATATTTATATCAACC
1 AAATTAAAATTTTATATATTTATAGCAACC
* *
15116427 ACAATTTAAATTTTATATGTATTAGT-GCAACC
1 A-AATTAAAATTTTATATAT-TTA-TAGCAACC
15116459 AAATTAAAATT
1 AAATTAAAATT
15116470 CATTCATCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 1 0.03
31 25 0.69
32 9 0.25
33 1 0.03
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (30 bp):
AAATTAAAATTTTATATATTTATAGCAACC
Found at i:15117112 original size:18 final size:18
Alignment explanation
Indices: 15117091--15117144 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
15117081 TTTTTGTTCA
*
15117091 AAAATACTTTTTAACCCG
1 AAAATACTTTTTAGCCCG
* *
15117109 AAAATA--TTTT-GCTCA
1 AAAATACTTTTTAGCCCG
15117124 AAAATACTTTTTAGCCCG
1 AAAATACTTTTTAGCCCG
15117142 AAA
1 AAA
15117145 GCATTTTTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 8 0.29
16 4 0.14
17 4 0.14
18 12 0.43
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (18 bp):
AAAATACTTTTTAGCCCG
Found at i:15117119 original size:33 final size:33
Alignment explanation
Indices: 15117082--15117144 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
15117072 AAATTTTAAT
*
15117082 TTTTGTTCAAAAATACTTTTTAACCCGAAAATA
1 TTTTGCTCAAAAATACTTTTTAACCCGAAAATA
*
15117115 TTTTGCTCAAAAATACTTTTTAGCCCGAAA
1 TTTTGCTCAAAAATACTTTTTAACCCGAAA
15117145 GCATTTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (33 bp):
TTTTGCTCAAAAATACTTTTTAACCCGAAAATA
Found at i:15117135 original size:17 final size:17
Alignment explanation
Indices: 15117081--15117135 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
15117071 AAAATTTTAA
*
15117081 TTTTTGTTCAAAAATAC
1 TTTTTGCTCAAAAATAC
* * *
15117098 TTTTTAACCCGAAAATA-
1 TTTTT-GCTCAAAAATAC
15117115 -TTTTGCTCAAAAATAC
1 TTTTTGCTCAAAAATAC
15117131 TTTTT
1 TTTTT
15117136 AGCCCGAAAG
Statistics
Matches: 28, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
15 8 0.29
16 4 0.14
17 9 0.32
18 7 0.25
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (17 bp):
TTTTTGCTCAAAAATAC
Found at i:15120970 original size:43 final size:43
Alignment explanation
Indices: 15120904--15121050 Score: 174
Period size: 43 Copynumber: 3.4 Consensus size: 43
15120894 TCCCAAACGT
* *
15120904 GGTCTTACATGTAATCAAATAACGATGCCACTGTCCTAGACAG
1 GGTCTTACACGTAATCAAATAACGATGCCACTGTCCCAGACAG
* *
15120947 GGTCTTACACGTAATTAAGTAACGATGCCACTGTCCCAGACAG
1 GGTCTTACACGTAATCAAATAACGATGCCACTGTCCCAGACAG
* *
15120990 GGTCTTACACGTAAATCTCAAAT--TGATGCCAAC-GTCCCAGACAT
1 GGTCTTACACGT-AA--TCAAATAACGATGCC-ACTGTCCCAGACAG
*
15121034 GGTCTTACACGAAATCA
1 GGTCTTACACGTAATCA
15121051 CATTTCAGCA
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
41 3 0.03
43 53 0.58
44 29 0.32
45 2 0.02
46 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (43 bp):
GGTCTTACACGTAATCAAATAACGATGCCACTGTCCCAGACAG
Found at i:15143213 original size:18 final size:19
Alignment explanation
Indices: 15143168--15143215 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
15143158 TTTTATGTTC
*
15143168 AAAATTTTAA-TATATTTT
1 AAAATTTTAAGTATATTTA
* *
15143186 AATATATTAAGTATA-TTA
1 AAAATTTTAAGTATATTTA
15143204 AAAATTTTAAGT
1 AAAATTTTAAGT
15143216 TAGTTATACT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (19 bp):
AAAATTTTAAGTATATTTA
Found at i:15143422 original size:21 final size:20
Alignment explanation
Indices: 15143393--15143431 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
15143383 TAAAATTGGG
15143393 TATACTTTAACCATTTTTTTAA
1 TATACTTTAA--ATTTTTTTAA
15143415 TATA-TTTAAATTTTTTT
1 TATACTTTAAATTTTTTT
15143432 TAGATTTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (20 bp):
TATACTTTAAATTTTTTTAA
Found at i:15149653 original size:21 final size:20
Alignment explanation
Indices: 15149623--15149662 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
15149613 CCGCCACTCT
15149623 TTCTCCCCCTTAC-CCTCCCC
1 TTCTCCCCCTT-CTCCTCCCC
15149643 TTCTCGCCCCTTCTCCTCCC
1 TTCTC-CCCCTTCTCCTCCC
15149663 GAACGCCACG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.03, C:0.62, G:0.03, T:0.33
Consensus pattern (20 bp):
TTCTCCCCCTTCTCCTCCCC
Found at i:15162031 original size:26 final size:26
Alignment explanation
Indices: 15161995--15162047 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
15161985 ATCGAGGTTC
15161995 AACATTTGTTGCGAACTTTCGTGTTT
1 AACATTTGTTGCGAACTTTCGTGTTT
15162021 AACATTTGTTGCGAACTTTCGTGTTT
1 AACATTTGTTGCGAACTTTCGTGTTT
15162047 A
1 A
15162048 CTTTCCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (26 bp):
AACATTTGTTGCGAACTTTCGTGTTT
Found at i:15162109 original size:21 final size:21
Alignment explanation
Indices: 15162085--15162161 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
15162075 GTTGAACTCA
*
15162085 TATGAGTTTCTGTTTAACCCT
1 TATGAGTTTCTGTTCAACCCT
* * *
15162106 TATGGGTTTCCGTTCAGCTCC-
1 TATGAGTTTCTGTTCAAC-CCT
* *
15162127 TATGAGCTTCCGTTCAACCCT
1 TATGAGTTTCTGTTCAACCCT
15162148 TAT-AGGTTTCTGTT
1 TATGA-GTTTCTGTT
15162162 TAGCACTTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 3 0.07
21 39 0.89
22 2 0.05
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (21 bp):
TATGAGTTTCTGTTCAACCCT
Found at i:15164714 original size:51 final size:51
Alignment explanation
Indices: 15164635--15164889 Score: 321
Period size: 51 Copynumber: 5.2 Consensus size: 51
15164625 TTCTGATCAA
* *
15164635 TGACAAGTGATAATTAGTAGCTTCAGCTACACTTATCTGATCAATGACAAG
1 TGACAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAATGACAAG
* * *
15164686 TGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGAT-AAGTGAAAAG
1 TGACAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAA-TGACAAG
* *
15164737 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTAT-T--T-GAT--C-AG
1 TGACAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAATGACAAG
* *
15164781 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
1 TGACAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAATGACAAG
* **
15164832 TGGCAAGTGATAAGTGGTAGC-TCAGCTACACTTATCTGATCAGGGACAAG
1 TGACAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAATGACAAG
*
15164882 TGATAAGT
1 TGACAAGT
15164890 AATCATACGT
Statistics
Matches: 179, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
44 38 0.21
45 1 0.01
47 2 0.01
48 3 0.02
50 37 0.21
51 98 0.55
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (51 bp):
TGACAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAATGACAAG
Found at i:15164809 original size:95 final size:94
Alignment explanation
Indices: 15164635--15164889 Score: 330
Period size: 95 Copynumber: 2.6 Consensus size: 94
15164625 TTCTGATCAA
* * *
15164635 TGACAAGTGATAATTAGTAGCTTCAGCTACACTTATCTGATCAATGACAAGTGGCAAGTGATAAG
1 TGACAAGTGATAAGTGGTAGC-TCAGCTACACTTATCTG----AT--C-AGTGACAAGTGATAAG
15164700 TGATAGCTTCAGCTACACTTATCTGATAAGTGAAAAG
58 TGATAGCTTCAGCTACACTTATCTGATAAGTGAAAAG
* * *
15164737 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATTTGATCAGTGACAAGTGATAAGTGGTAGC
1 TGACAAGTGATAAGTGGTAGC-TCAGCTACACTTATCTGATCAGTGACAAGTGATAAGTGATAGC
* * *
15164802 TTTAGCTACACTTATCTGATCAGTGACAAG
65 TTCAGCTACACTTATCTGATAAGTGAAAAG
* *
15164832 TGGCAAGTGATAAGTGGTAGCTCAGCTACACTTATCTGATCAGGGACAAGTGATAAGT
1 TGACAAGTGATAAGTGGTAGCTCAGCTACACTTATCTGATCAGTGACAAGTGATAAGT
15164890 AATCATACGT
Statistics
Matches: 140, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
94 34 0.24
95 68 0.49
96 1 0.01
98 2 0.01
102 35 0.25
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (94 bp):
TGACAAGTGATAAGTGGTAGCTCAGCTACACTTATCTGATCAGTGACAAGTGATAAGTGATAGCT
TCAGCTACACTTATCTGATAAGTGAAAAG
Found at i:15170473 original size:25 final size:26
Alignment explanation
Indices: 15170418--15170553 Score: 82
Period size: 24 Copynumber: 5.7 Consensus size: 26
15170408 GTCGTAATCA
*
15170418 GGAAGCTCAT-GCA-AGCCAA-TATTG
1 GGAAGCTCATAG-AGAGCCAATTATCG
15170442 GGAAGCTC-TAGAGAGCCAATTATCG
1 GGAAGCTCATAGAGAGCCAATTATCG
* * *
15170467 GGAAGCTCATA-TGAGCC-ATAAACG
1 GGAAGCTCATAGAGAGCCAATTATCG
* * *
15170491 GAAAGCTCA-ATAGAGTC-ATTAATCG
1 GGAAGCTCATAGAGAGCCAATT-ATCG
*
15170516 GGAAGCTCGT-GAGAGCC-A-TA-CG
1 GGAAGCTCATAGAGAGCCAATTATCG
*
15170538 GGATGCTCATA-AGAGC
1 GGAAGCTCATAGAGAGC
15170554 TAAATAATGG
Statistics
Matches: 89, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
22 15 0.17
23 4 0.04
24 35 0.39
25 33 0.37
26 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.19
Consensus pattern (26 bp):
GGAAGCTCATAGAGAGCCAATTATCG
Found at i:15172876 original size:22 final size:21
Alignment explanation
Indices: 15172843--15172885 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
15172833 TTACATGTAG
*
15172843 TTATTAAGTAAATTATATTAT
1 TTATTAAGTAAATAATATTAT
*
15172864 TTATGTAATTAAATAATATTAT
1 TTAT-TAAGTAAATAATATTAT
15172886 ACTTCGTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
TTATTAAGTAAATAATATTAT
Found at i:15179656 original size:6 final size:5
Alignment explanation
Indices: 15179651--15179731 Score: 54
Period size: 6 Copynumber: 14.4 Consensus size: 5
15179641 GGGTATGGAT
* *
15179651 GGGGA TGGGGT GGAGGA GGTGGG GGGGA GGAGGA GGGGA GGGGA GGGGA
1 GGGGA -GGGGA GG-GGA GG-GGA GGGGA GG-GGA GGGGA GGGGA GGGGA
*
15179700 GGAGGTG GGGGA TGGGGA TGGGGA GGAGGA GG
1 GG-GG-A GGGGA -GGGGA -GGGGA GG-GGA GG
15179732 TGGTGGTTGG
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
5 23 0.37
6 37 0.60
7 2 0.03
ACGTcount: A:0.19, C:0.00, G:0.74, T:0.07
Consensus pattern (5 bp):
GGGGA
Found at i:15179677 original size:17 final size:17
Alignment explanation
Indices: 15179657--15179710 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
15179647 GGATGGGGAT
*
15179657 GGGGTGGAGGAGGTGGG
1 GGGGAGGAGGAGGTGGG
15179674 GGGGAGGAGGAGG-GGAG
1 GGGGAGGAGGAGGTGG-G
*
15179691 GGGAGGGGAGGAGGTGGG
1 GGG-GAGGAGGAGGTGGG
15179709 GG
1 GG
15179711 ATGGGGATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 2 0.06
17 16 0.50
18 12 0.38
19 2 0.06
ACGTcount: A:0.17, C:0.00, G:0.78, T:0.06
Consensus pattern (17 bp):
GGGGAGGAGGAGGTGGG
Found at i:15179711 original size:17 final size:17
Alignment explanation
Indices: 15179662--15179717 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
15179652 GGGATGGGGT
15179662 GGAGGAGGTGGGGG-GG
1 GGAGGAGGTGGGGGAGG
*
15179678 AGGAGGAGGGGAGGGGAGG
1 -GGAGGAGGTG-GGGGAGG
15179697 GGAGGAGGTGGGGGATGG
1 GGAGGAGGTGGGGGA-GG
15179715 GGA
1 GGA
15179718 TGGGGAGGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 14 0.41
18 18 0.53
19 2 0.06
ACGTcount: A:0.20, C:0.00, G:0.75, T:0.05
Consensus pattern (17 bp):
GGAGGAGGTGGGGGAGG
Found at i:15179731 original size:35 final size:34
Alignment explanation
Indices: 15179662--15179731 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 34
15179652 GGGATGGGGT
15179662 GGAGGAGGTGGGGGGGAGGAGGAGGGGAGGGGAGG
1 GGAGGAGGT-GGGGGGAGGAGGAGGGGAGGGGAGG
15179697 GGAGGAGGT-GGGGGATGG-GGATGGGGAGGAGGAGG
1 GGAGGAGGTGGGGGGA-GGAGGA-GGGGAGG-GGAGG
15179732 TGGTGGTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
33 9 0.28
34 9 0.28
35 14 0.44
ACGTcount: A:0.20, C:0.00, G:0.74, T:0.06
Consensus pattern (34 bp):
GGAGGAGGTGGGGGGAGGAGGAGGGGAGGGGAGG
Found at i:15188801 original size:17 final size:17
Alignment explanation
Indices: 15188770--15188808 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
15188760 TTTTATATTG
15188770 AATTGAATGTATGTGA-
1 AATTGAATGTATGTGAT
*
15188786 AATTGAGATTTATGTGAT
1 AATTGA-ATGTATGTGAT
15188804 AATTG
1 AATTG
15188809 TGGCATTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (17 bp):
AATTGAATGTATGTGAT
Found at i:15191256 original size:74 final size:75
Alignment explanation
Indices: 15191024--15191291 Score: 242
Period size: 74 Copynumber: 3.6 Consensus size: 75
15191014 AGCATGTAAA
* * * * *
15191024 CAGGAAGCTCTTCCAAGCCATATAATGGGAAGCTCATGTGAGCCATGTAA-CGGGAAGCTCATAA
1 CAGGAAGCTCATACGAGCCATATAATGGGAAGCTCATGAGAGCCAT-TAATCGGGAAGCTCATGA
* *
15191088 GAGTCGTA-AT
65 GAGCCATATAT
* * * ** * *
15191098 CAAGAAGCTCATGCAAGCCA-AT-ATCGGGAAGCTCCGGAGAGCCATTAATCAGAAAGCTCATGA
1 CAGGAAGCTCATACGAGCCATATAAT-GGGAAGCTCATGAGAGCCATTAATCGGGAAGCTCATGA
15191161 GAGCCA-ATTAT
65 GAGCCATA-TAT
* * *
15191172 CAGGAGGCTCATACGAGCCATA-AATGGGAAGCTCAAGAGAGCCATTAATCGGGAAGCTCGTGAG
1 CAGGAAGCTCATACGAGCCATATAATGGGAAGCTCATGAGAGCCATTAATCGGGAAGCTCATGAG
*
15191236 AGCCATATAA
66 AGCCATATAT
* * * * * * *
15191246 CGGGATGCTCATAAGAGCTAAATAACGGGAAGCTCGTGAGAGCCAT
1 CAGGAAGCTCATACGAGCCATATAATGGGAAGCTCATGAGAGCCAT
15191292 ATAACATGAT
Statistics
Matches: 157, Mismatches: 29, Indels: 15
0.78 0.14 0.07
Matches are distributed among these distances:
72 6 0.04
73 34 0.22
74 93 0.59
75 24 0.15
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.18
Consensus pattern (75 bp):
CAGGAAGCTCATACGAGCCATATAATGGGAAGCTCATGAGAGCCATTAATCGGGAAGCTCATGAG
AGCCATATAT
Found at i:15191275 original size:50 final size:50
Alignment explanation
Indices: 15191221--15191325 Score: 183
Period size: 50 Copynumber: 2.1 Consensus size: 50
15191211 AGCCATTAAT
*
15191221 CGGGAAGCTCGTGAGAGCCATATAACGGGATGCTCATAAGAGCTAAATAA
1 CGGGAAGCTCGTGAGAGCCATATAACAGGATGCTCATAAGAGCTAAATAA
*
15191271 CGGGAAGCTCGTGAGAGCCATATAACATGATGCTCATAAGAGCTAAATAA
1 CGGGAAGCTCGTGAGAGCCATATAACAGGATGCTCATAAGAGCTAAATAA
*
15191321 TGGGA
1 CGGGA
15191326 CGCTTTTGCA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (50 bp):
CGGGAAGCTCGTGAGAGCCATATAACAGGATGCTCATAAGAGCTAAATAA
Found at i:15191296 original size:25 final size:25
Alignment explanation
Indices: 15191039--15191296 Score: 190
Period size: 25 Copynumber: 10.4 Consensus size: 25
15191029 AGCTCTTCCA
* *
15191039 AGCCATATAATGGGAAGCTCATGTG
1 AGCCATATAACGGGAAGCTCATGAG
* *
15191064 AGCCATGTAACGGGAAGCTCATAAG
1 AGCCATATAACGGGAAGCTCATGAG
* * * **
15191089 AGTCGTA-ATCAAGAAGCTCATGCA-
1 AGCCATATAACGGGAAGCTCATG-AG
* **
15191113 AGCCA-ATATCGGGAAGCTCCGGAG
1 AGCCATATAACGGGAAGCTCATGAG
* *
15191137 AGCCAT-TAATCAGAAAGCTCATGAG
1 AGCCATATAA-CGGGAAGCTCATGAG
* * *
15191162 AGCCA-ATTATCAGGAGGCTCAT-ACG
1 AGCCATA-TAACGGGAAGCTCATGA-G
* *
15191187 AGCCATA-AATGGGAAGCTCAAGAG
1 AGCCATATAACGGGAAGCTCATGAG
*
15191211 AGCCAT-TAATCGGGAAGCTCGTGAG
1 AGCCATATAA-CGGGAAGCTCATGAG
* *
15191236 AGCCATATAACGGGATGCTCATAAG
1 AGCCATATAACGGGAAGCTCATGAG
* * *
15191261 AGCTAAATAACGGGAAGCTCGTGAG
1 AGCCATATAACGGGAAGCTCATGAG
15191286 AGCCATATAAC
1 AGCCATATAAC
15191297 ATGATGCTCA
Statistics
Matches: 177, Mismatches: 43, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
23 2 0.01
24 51 0.29
25 118 0.67
26 6 0.03
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.18
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCATGAG
Found at i:15191312 original size:25 final size:25
Alignment explanation
Indices: 15191178--15191313 Score: 116
Period size: 25 Copynumber: 5.5 Consensus size: 25
15191168 TTATCAGGAG
* * *
15191178 GCTCATACGAGCCATA-AATGGGAA
1 GCTCATAAGAGCCATATAACGGGAT
*
15191202 GCTCA-AGAGAGCCAT-TAATCGGGAA
1 GCTCATA-AGAGCCATATAA-CGGGAT
* *
15191227 GCTCGTGAGAGCCATATAACGGGAT
1 GCTCATAAGAGCCATATAACGGGAT
* * *
15191252 GCTCATAAGAGCTAAATAACGGGAA
1 GCTCATAAGAGCCATATAACGGGAT
* * **
15191277 GCTCGTGAGAGCCATATAACATGAT
1 GCTCATAAGAGCCATATAACGGGAT
15191302 GCTCATAAGAGC
1 GCTCATAAGAGC
15191314 TAAATAATGG
Statistics
Matches: 88, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
23 1 0.01
24 14 0.16
25 70 0.80
26 3 0.03
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.18
Consensus pattern (25 bp):
GCTCATAAGAGCCATATAACGGGAT
Found at i:15194030 original size:37 final size:37
Alignment explanation
Indices: 15193942--15194154 Score: 329
Period size: 37 Copynumber: 5.8 Consensus size: 37
15193932 AGCTAAAGCT
*
15193942 ACCACTTATCACTTTGTCTCTTGATCAGATAAGT-TT
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
* *
15193978 AGCACTTATCACTTTGTCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
*
15194015 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
* *
15194052 ACCACTTATCACTTTGTTTCATGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
*
15194089 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
* * *
15194126 GCCACTTATCACTTTTTCACTTGATCAGA
1 ACCACTTATCACTTTGTCTCTTGATCAGA
15194155 AGTACCCAAA
Statistics
Matches: 164, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
36 32 0.20
37 132 0.80
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
Found at i:15195151 original size:12 final size:12
Alignment explanation
Indices: 15195134--15195166 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
15195124 TCGGTCCTTT
15195134 CTCAATTAACCC
1 CTCAATTAACCC
15195146 CTCAATTAACCC
1 CTCAATTAACCC
15195158 CTCAATTAA
1 CTCAATTAA
15195167 TCTAATTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.27
Consensus pattern (12 bp):
CTCAATTAACCC
Found at i:15202777 original size:29 final size:31
Alignment explanation
Indices: 15202726--15202787 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
15202716 TCATTTCAAC
15202726 TTTATAATTTTTAAAGGATTAAA-TAAAATT
1 TTTATAATTTTTAAAGGATTAAAGTAAAATT
* *
15202756 TTTATCATTTTT-AA-GAGTTAAAGTACAATT
1 TTTATAATTTTTAAAGGA-TTAAAGTAAAATT
15202786 TT
1 TT
15202788 ACTTTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.07
29 7 0.25
30 19 0.68
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.48
Consensus pattern (31 bp):
TTTATAATTTTTAAAGGATTAAAGTAAAATT
Found at i:15212493 original size:12 final size:12
Alignment explanation
Indices: 15212476--15212511 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
15212466 AGGCATTCTT
*
15212476 CTGCTACTGCTA
1 CTGCTACTACTA
15212488 CTGCTACTACTA
1 CTGCTACTACTA
*
15212500 CTACTACTACTA
1 CTGCTACTACTA
15212512 TCTTTTATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.25, C:0.33, G:0.08, T:0.33
Consensus pattern (12 bp):
CTGCTACTACTA
Found at i:15225756 original size:22 final size:23
Alignment explanation
Indices: 15225728--15225781 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
15225718 ATTAATGAAT
*
15225728 AGAGAGCACTA-AAGTGCTATAC
1 AGAGAGCACTAGAAGTGCTAAAC
*
15225750 AGAGAGCAC-AGATGTGCTAAAC
1 AGAGAGCACTAGAAGTGCTAAAC
*
15225772 GGAGAGCACT
1 AGAGAGCACT
15225782 GTCGTGCTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.15
Consensus pattern (23 bp):
AGAGAGCACTAGAAGTGCTAAAC
Found at i:15233798 original size:22 final size:22
Alignment explanation
Indices: 15233773--15233835 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
15233763 TGGTTATAAT
15233773 TAATTAAATAGTTAGTGAATTC
1 TAATTAAATAGTTAGTGAATTC
15233795 TAATCT-AAT-G--A-TG-A-T-
1 TAAT-TAAATAGTTAGTGAATTC
15233810 TAATTAAATAGTTAGTGAATTC
1 TAATTAAATAGTTAGTGAATTC
15233832 TAAT
1 TAAT
15233836 CTAATGGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 18
0.64 0.00 0.36
Matches are distributed among these distances:
14 1 0.03
15 7 0.22
16 2 0.06
17 1 0.03
18 3 0.09
19 3 0.09
20 1 0.03
21 2 0.06
22 11 0.34
23 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (22 bp):
TAATTAAATAGTTAGTGAATTC
Found at i:15233812 original size:37 final size:37
Alignment explanation
Indices: 15233771--15233841 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
15233761 GCTGGTTATA
15233771 ATTAATTAAATAGTTAGTGAATTCTAATCTAATGATG
1 ATTAATTAAATAGTTAGTGAATTCTAATCTAATGATG
15233808 ATTAATTAAATAGTTAGTGAATTCTAATCTAATG
1 ATTAATTAAATAGTTAGTGAATTCTAATCTAATG
15233842 GAAAAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.41
Consensus pattern (37 bp):
ATTAATTAAATAGTTAGTGAATTCTAATCTAATGATG
Found at i:15235429 original size:35 final size:36
Alignment explanation
Indices: 15235385--15235461 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 36
15235375 ATTTGTTAGA
*
15235385 TATTGATTATGTTTTAACCTTA-TTGGATATTGAATT
1 TATTGATTATGTTTTAACC-TAGTTGGATATTGAAAT
*
15235421 TATT-ATTATGTTTTAAGCTAGTTGGATATTGAAAT
1 TATTGATTATGTTTTAACCTAGTTGGATATTGAAAT
15235456 TATTGA
1 TATTGA
15235462 CAATGATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
34 2 0.05
35 30 0.81
36 5 0.14
ACGTcount: A:0.30, C:0.04, G:0.16, T:0.51
Consensus pattern (36 bp):
TATTGATTATGTTTTAACCTAGTTGGATATTGAAAT
Found at i:15236796 original size:14 final size:15
Alignment explanation
Indices: 15236774--15236850 Score: 61
Period size: 14 Copynumber: 5.0 Consensus size: 15
15236764 CAATCAAACA
15236774 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
15236788 CCAGGAAATCATTTT
1 CCAGAAAATCATTTT
*
15236803 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
15236823 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
*
15236837 CCGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
15236851 ACTGCCAATC
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 22 0.43
15 15 0.29
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:15241227 original size:23 final size:24
Alignment explanation
Indices: 15241207--15241252 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
15241197 AAATAGGATG
15241207 TGATAGGTG-AAATTTTTAGGAAT
1 TGATAGGTGAAAATTTTTAGGAAT
* *
15241230 TGATGGGTGAAAATTTTTTGGAA
1 TGATAGGTGAAAATTTTTAGGAA
15241253 GAGTGGACGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (24 bp):
TGATAGGTGAAAATTTTTAGGAAT
Found at i:15241637 original size:6 final size:6
Alignment explanation
Indices: 15241622--15241666 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
15241612 GTTTCCCTGC
15241622 AAAAAT -AAAAT AAAAAT AAAAAT -AAAAT AAAATAGT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAA
15241667 TAAATAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 10 0.29
6 18 0.51
7 2 0.06
8 5 0.14
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:15241638 original size:11 final size:11
Alignment explanation
Indices: 15241622--15241655 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
15241612 GTTTCCCTGC
15241622 AAAAATAAAAT
1 AAAAATAAAAT
15241633 AAAAATAAAA-
1 AAAAATAAAAT
15241643 ATAAAATAAAAT
1 A-AAAATAAAAT
15241655 A
1 A
15241656 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 19 0.90
12 1 0.05
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:15241644 original size:17 final size:17
Alignment explanation
Indices: 15241622--15241676 Score: 76
Period size: 17 Copynumber: 3.1 Consensus size: 17
15241612 GTTTCCCTGC
15241622 AAAAATAAAATAAAAAT
1 AAAAATAAAATAAAAAT
15241639 AAAAATAAAATAAAATAGT
1 AAAAATAAAATAAAA-A-T
15241658 AAAAAT-AAATAAATAAT
1 AAAAATAAAATAAA-AAT
15241675 AA
1 AA
15241677 TTATAATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 18 0.51
18 9 0.26
19 8 0.23
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAAATAAAATAAAAAT
Found at i:15245328 original size:18 final size:18
Alignment explanation
Indices: 15245307--15245349 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
15245297 ATGATATCGA
*
15245307 TATTGATGATAGTGACGC
1 TATTGATGATAATGACGC
*
15245325 TATTGATGATAATGACTC
1 TATTGATGATAATGACGC
15245343 TATTGAT
1 TATTGAT
15245350 CGTGACCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (18 bp):
TATTGATGATAATGACGC
Found at i:15248285 original size:43 final size:43
Alignment explanation
Indices: 15248216--15248439 Score: 292
Period size: 43 Copynumber: 5.3 Consensus size: 43
15248206 GATATGATTT
* *
15248216 CGTGTAAGACCACGTCTGGGATGTTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
*
15248259 CGTGTAAGACCACATCTGCGACGTTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
** * * * *
15248302 CGTGTAAGACCATGTTTGAGACGTTGGCACCAACTTGTGTTTA
1 CGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
* *
15248345 CGTGTAAGACCACATCTGGAACATTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
* * *
15248388 CGTGTAAGACCATATCTGGGACATTGGCATCGTA-TT-TGATT-
1 CGTGTAAGACCACATCTGGGACGTTGGCATCG-ACTTGTGTTTA
15248429 CGTGTAAGACC
1 CGTGTAAGACC
15248440 CTGTCTAGGA
Statistics
Matches: 160, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
41 11 0.07
42 4 0.03
43 144 0.90
44 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
Found at i:15252751 original size:13 final size:13
Alignment explanation
Indices: 15252699--15252775 Score: 100
Period size: 13 Copynumber: 5.9 Consensus size: 13
15252689 AGTTCTTCAT
15252699 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
15252712 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
* *
15252725 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
15252738 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
15252751 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
15252764 TGCTTTTGAAAA
1 TGCTTTTGAAAA
15252776 ATTTGAGTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 58 1.00
ACGTcount: A:0.29, C:0.08, G:0.30, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:15253029 original size:19 final size:18
Alignment explanation
Indices: 15253005--15253052 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
15252995 AATTATTTAT
15253005 TAAATTTAATTAGAATATA
1 TAAATTTAATTA-AATATA
* *
15253024 TAAATTATATTTAAATATT
1 TAAATT-TAATTAAATATA
*
15253043 TAAATATAAT
1 TAAATTTAAT
15253053 AATTAAGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.12
19 16 0.67
20 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
TAAATTTAATTAAATATA
Found at i:15262536 original size:46 final size:46
Alignment explanation
Indices: 15262400--15262538 Score: 188
Period size: 46 Copynumber: 3.0 Consensus size: 46
15262390 ACAATGCTAT
* * *
15262400 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCAC
* * *
15262446 AACTTAGTATGGTTTTCGTTACTGAAATACCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCAC
* * * *
15262492 AACTCAGTATGATTTTCTTTACTGAATTACCATACTTGCATTCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCAC
15262538 A
1 A
15262539 CTTTGCCATG
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCAC
Found at i:15269613 original size:2 final size:2
Alignment explanation
Indices: 15269606--15269656 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
15269596 TACATTGATA
15269606 AT AT AT 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 AT AT AT
15269648 AT AT AT AT A
1 AT AT AT AT A
15269657 AACTGATTAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15279256 original size:1 final size:1
Alignment explanation
Indices: 15279252--15279287 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
15279242 ACAAAAACGC
* *
15279252 AAAAAAAAAAAAAAAAAAAAAAAAAACAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15279288 CAAACCCCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:15279288 original size:10 final size:9
Alignment explanation
Indices: 15279237--15279291 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
15279227 ACACTTACAG
15279237 AAACAACAAA
1 AAACAA-AAA
*
15279247 AACGCAAAAA
1 AA-ACAAAAA
*
15279257 AAAAAAAAA
1 AAACAAAAA
*
15279266 AAAAAAAAA
1 AAACAAAAA
15279275 AAACAAAACA
1 AAACAAAA-A
15279285 AAACAAA
1 AAACAAA
15279292 CCCCTTAAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 21 0.54
10 15 0.38
11 3 0.08
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (9 bp):
AAACAAAAA
Found at i:15287183 original size:16 final size:18
Alignment explanation
Indices: 15287144--15287177 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15287134 TAAGTTTATA
15287144 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
15287161 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
15287178 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:15299300 original size:2 final size:2
Alignment explanation
Indices: 15299293--15299326 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
15299283 TTCGAATAAG
15299293 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
15299327 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15299537 original size:2 final size:2
Alignment explanation
Indices: 15299490--15299521 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
15299480 TTAGTTAGAC
15299490 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
15299522 GCATTTCGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15305434 original size:15 final size:15
Alignment explanation
Indices: 15305414--15305444 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
15305404 CAGCTAGTGA
15305414 ACCTCGAATCCATTC
1 ACCTCGAATCCATTC
15305429 ACCTCGAATCCATTC
1 ACCTCGAATCCATTC
15305444 A
1 A
15305445 ACAGACGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.39, G:0.06, T:0.26
Consensus pattern (15 bp):
ACCTCGAATCCATTC
Done.