Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 83 of 216
Found at i:25492736 original size:16 final size:16
Alignment explanation
Indices: 25492715--25492767 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
25492705 AGAAATACCT
25492715 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
25492731 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
*
25492747 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
25492763 ATTAC
1 ATTAC
25492768 AGCGAACCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.25, C:0.34, G:0.04, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:25493981 original size:19 final size:20
Alignment explanation
Indices: 25493946--25493986 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
25493936 ACATACGTAT
25493946 AATAAATAACAAGT-AAATG
1 AATAAATAACAAGTAAAATG
*
25493965 AATAAATAA-TAGATAAAATG
1 AATAAATAACAAG-TAAAATG
25493985 AA
1 AA
25493987 ATAATAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 2 0.11
19 10 0.53
20 7 0.37
ACGTcount: A:0.66, C:0.02, G:0.10, T:0.22
Consensus pattern (20 bp):
AATAAATAACAAGTAAAATG
Found at i:25498026 original size:25 final size:26
Alignment explanation
Indices: 25497991--25498040 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
25497981 AATACACGGG
25497991 ATATAAATTGCTCACACAAGCTGTGA
1 ATATAAATTGCTCACACAAGCTGTGA
**
25498017 ATAT-AATTGCTCACATGAGCTGTG
1 ATATAAATTGCTCACACAAGCTGTG
25498041 GGTCAGGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (26 bp):
ATATAAATTGCTCACACAAGCTGTGA
Found at i:25500023 original size:17 final size:17
Alignment explanation
Indices: 25500003--25500047 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
25499993 AGATTAGTGG
*
25500003 CATTGTAAGAACATTTA
1 CATTGTGAGAACATTTA
**
25500020 CATTGTGAGAATGTTTA
1 CATTGTGAGAACATTTA
25500037 CATTGTGAGAA
1 CATTGTGAGAA
25500048 AGACAACTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (17 bp):
CATTGTGAGAACATTTA
Found at i:25501565 original size:37 final size:39
Alignment explanation
Indices: 25501524--25501630 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 39
25501514 CAAAAAATAT
25501524 ATTATTTTAATAGTTTAATATTAAATTTAAT-TT-AA-TG
1 ATTATTTTAATAGTTTAATATT-AATTTAATATTAAAGTG
* *
25501561 ATTATCTTAATAGTATT-TTATTAATTTAATATTAAAGTG
1 ATTATTTTAATAGT-TTAATATTAATTTAATATTAAAGTG
*
25501600 ATTGTTTTAATA-TTTAAT-TTAATTTAATATT
1 ATTATTTTAATAGTTTAATATTAATTTAATATT
25501631 TATCTTGTAG
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
36 8 0.13
37 34 0.57
38 6 0.10
39 12 0.20
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (39 bp):
ATTATTTTAATAGTTTAATATTAATTTAATATTAAAGTG
Found at i:25501693 original size:12 final size:12
Alignment explanation
Indices: 25501661--25501694 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
25501651 TATTATTTTA
25501661 ATAATATTTAAT
1 ATAATATTTAAT
25501673 ATTAA-ATTTAAT
1 A-TAATATTTAAT
25501685 ATAATATTTA
1 ATAATATTTA
25501695 TCTTGATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.15
12 14 0.70
13 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATAATATTTAAT
Found at i:25507053 original size:67 final size:67
Alignment explanation
Indices: 25506976--25507103 Score: 195
Period size: 67 Copynumber: 1.9 Consensus size: 67
25506966 CTATTTGCCA
** *
25506976 AGTAGTCATCCTAG-AATGGTGAGCTTACAAGTGACCTCCCTCCTTGCTGGTGGTAGGCTTACTA
1 AGTAGTCATCC-AGAAATGGTGAGCTTACAAGTGACCTCCCAACTTGCTAGTGGTAGGCTTACTA
25507040 TTT
65 TTT
* *
25507043 AGTAGTCATCCCGAAATGGTGAGCTTACAGGTGACCTCCCAACTTGCTAGTGGTAGGCTTA
1 AGTAGTCATCCAGAAATGGTGAGCTTACAAGTGACCTCCCAACTTGCTAGTGGTAGGCTTA
25507104 TTGTTCAAGC
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 1 0.02
67 54 0.98
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (67 bp):
AGTAGTCATCCAGAAATGGTGAGCTTACAAGTGACCTCCCAACTTGCTAGTGGTAGGCTTACTAT
TT
Found at i:25507424 original size:7 final size:7
Alignment explanation
Indices: 25507412--25507438 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
25507402 AGGAATATCA
25507412 TTTATTG
1 TTTATTG
25507419 TTTATTG
1 TTTATTG
25507426 TTTATTG
1 TTTATTG
25507433 TTTATT
1 TTTATT
25507439 TCTTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.11, T:0.74
Consensus pattern (7 bp):
TTTATTG
Found at i:25510204 original size:58 final size:58
Alignment explanation
Indices: 25510116--25510262 Score: 244
Period size: 58 Copynumber: 2.6 Consensus size: 58
25510106 ACCTATGTTC
*
25510116 TGATAAAATCTCAC--TGTCTACTCAATTCATTCAAAATGGAACAACTTAATTACAAT
1 TGATAAAATCTGACTTTGTCTACTCAATTCATTCAAAATGGAACAACTTAATTACAAT
* *
25510172 TGATAAAATCTGACTTTGTCTACTCAATTCATTCAAAATGGAACAACTTACTTACTAT
1 TGATAAAATCTGACTTTGTCTACTCAATTCATTCAAAATGGAACAACTTAATTACAAT
*
25510230 TGATAAAATCAGACTTTGTCTACTCAATTCATT
1 TGATAAAATCTGACTTTGTCTACTCAATTCATT
25510263 GAAGATCCAA
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
56 13 0.15
58 72 0.85
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.35
Consensus pattern (58 bp):
TGATAAAATCTGACTTTGTCTACTCAATTCATTCAAAATGGAACAACTTAATTACAAT
Found at i:25513754 original size:24 final size:24
Alignment explanation
Indices: 25513720--25513778 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
25513710 CTAGAACTAG
*
25513720 TGAAACA--CAAAGGTTTAGCGCT
1 TGAAACATTCAAAGCTTTAGCGCT
* *
25513742 T-AGAACATTCAAAGCTTTGGGGCT
1 TGA-AACATTCAAAGCTTTAGCGCT
25513766 TGAAACATTCAAA
1 TGAAACATTCAAA
25513779 ACTCTCGGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 1 0.03
22 5 0.17
24 23 0.77
25 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (24 bp):
TGAAACATTCAAAGCTTTAGCGCT
Found at i:25513788 original size:24 final size:24
Alignment explanation
Indices: 25513745--25513790 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25513735 TAGCGCTTAG
* * *
25513745 AACATTCAAAGCTTTGGGGCTTGA
1 AACATTCAAAACTCTCGGGCTTGA
25513769 AACATTCAAAACTCTCGGGCTT
1 AACATTCAAAACTCTCGGGCTT
25513791 TCAGCATTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (24 bp):
AACATTCAAAACTCTCGGGCTTGA
Found at i:25514959 original size:19 final size:19
Alignment explanation
Indices: 25514934--25514987 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
25514924 TTTTAATTTA
25514934 AAATTTTCAAAAATATATAT
1 AAATTTT-AAAAATATATAT
*
25514954 AATTTTTTAAAAA-ATATAT
1 AA-ATTTTAAAAATATATAT
*
25514973 AAATATTAAAAATAT
1 AAATTTTAAAAATAT
25514988 TAAAATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 8 0.28
19 10 0.34
20 7 0.24
21 4 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATTTTAAAAATATATAT
Found at i:25514983 original size:17 final size:17
Alignment explanation
Indices: 25514963--25514996 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
25514953 TAATTTTTTA
25514963 AAAAATA-TATAAATATT
1 AAAAATATTA-AAATATT
25514980 AAAAATATTAAAATATT
1 AAAAATATTAAAATATT
25514997 TTTAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAAATATTAAAATATT
Found at i:25515779 original size:26 final size:26
Alignment explanation
Indices: 25515749--25515838 Score: 110
Period size: 27 Copynumber: 3.4 Consensus size: 26
25515739 GATACTCGTA
25515749 TTTAGTGTCCTGGA-AACTACCCCGTG
1 TTTAGTGTCCT-GACAACTACCCCGTG
*
25515775 TTTAGTGTCCCGACGAACTACCCCGTG
1 TTTAGTGTCCTGAC-AACTACCCCGTG
* *
25515802 TTTATTGTCCTAACAGACTACCCCGTG
1 TTTAGTGTCCTGACA-ACTACCCCGTG
*
25515829 TTTACTGTCC
1 TTTAGTGTCC
25515839 CGATGGACTA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.04
26 11 0.20
27 43 0.77
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.32
Consensus pattern (26 bp):
TTTAGTGTCCTGACAACTACCCCGTG
Found at i:25515824 original size:54 final size:54
Alignment explanation
Indices: 25515764--25515928 Score: 179
Period size: 54 Copynumber: 3.1 Consensus size: 54
25515754 TGTCCTGGAA
* * * *
25515764 ACTACCCCGTGTTTAGTGTCCCGACGAACTACCCCGTGTTTATTGTCCTAACAG
1 ACTACCCCGTGTTTAATGTCCCGATGGACTACCCCGTGTTTAATGTCCTAACAG
* * * *
25515818 ACTACCCCGTGTTTACTGTCCCGATGGACTACCTCGTGTTTAATGT-CTCGACGG
1 ACTACCCCGTGTTTAATGTCCCGATGGACTACCCCGTGTTTAATGTCCT-AACAG
* * *** * *
25515872 ACTACCCCATGTATAATGTCTTTATGGACTACCCTGTGTTTAGTGTCCTAACAG
1 ACTACCCCGTGTTTAATGTCCCGATGGACTACCCCGTGTTTAATGTCCTAACAG
25515926 ACT
1 ACT
25515929 CTGTTGGTTT
Statistics
Matches: 91, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
53 2 0.02
54 87 0.96
55 2 0.02
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (54 bp):
ACTACCCCGTGTTTAATGTCCCGATGGACTACCCCGTGTTTAATGTCCTAACAG
Found at i:25515892 original size:27 final size:27
Alignment explanation
Indices: 25515764--25515919 Score: 150
Period size: 27 Copynumber: 5.8 Consensus size: 27
25515754 TGTCCTGGAA
* *
25515764 ACTACCCCGTGTTTAGTGTCCCGACGA
1 ACTACCCCGTGTTTAATGTCCCGACGG
* ** *
25515791 ACTACCCCGTGTTTATTGTCCTAACAG
1 ACTACCCCGTGTTTAATGTCCCGACGG
* *
25515818 ACTACCCCGTGTTTACTGTCCCGATGG
1 ACTACCCCGTGTTTAATGTCCCGACGG
* *
25515845 ACTACCTCGTGTTTAATGTCTCGACGG
1 ACTACCCCGTGTTTAATGTCCCGACGG
* * *** *
25515872 ACTACCCCATGTATAATGTCTTTATGG
1 ACTACCCCGTGTTTAATGTCCCGACGG
* *
25515899 ACTACCCTGTGTTTAGTGTCC
1 ACTACCCCGTGTTTAATGTCC
25515920 TAACAGACTC
Statistics
Matches: 104, Mismatches: 25, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 104 1.00
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (27 bp):
ACTACCCCGTGTTTAATGTCCCGACGG
Found at i:25515902 original size:81 final size:81
Alignment explanation
Indices: 25515764--25515919 Score: 195
Period size: 81 Copynumber: 1.9 Consensus size: 81
25515754 TGTCCTGGAA
* * * *
25515764 ACTACCCCGTGTTTAGTGTCCCGACGAACTACCCCGTGTTTATTGTCCTAACAGACTACCCCGTG
1 ACTACCCCGTGTTTAATGTCCCGACGAACTACCCCATGTATAATGTCCTAACAGACTACCCCGTG
25515829 TTTACTGTCCCGATGG
66 TTTACTGTCCCGATGG
* * * * * ** *
25515845 ACTACCTCGTGTTTAATGTCTCGACGGACTACCCCATGTATAATGTCTTTATGGACTACCCTGTG
1 ACTACCCCGTGTTTAATGTCCCGACGAACTACCCCATGTATAATGTCCTAACAGACTACCCCGTG
*
25515910 TTTAGTGTCC
66 TTTACTGTCC
25515920 TAACAGACTC
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
81 62 1.00
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (81 bp):
ACTACCCCGTGTTTAATGTCCCGACGAACTACCCCATGTATAATGTCCTAACAGACTACCCCGTG
TTTACTGTCCCGATGG
Found at i:25518378 original size:41 final size:40
Alignment explanation
Indices: 25518333--25518416 Score: 91
Period size: 40 Copynumber: 2.1 Consensus size: 40
25518323 AGCGGCGTTT
25518333 TTAGCAGCG-TTTGGACAAAAAACGCCACTAGAA-ATCGAGCA
1 TTAGCAGCGCTTT--ACAAAAAACGCCACTA-AAGATCGAGCA
* ** *
25518374 TTAGCGGCGCTTTACGTAAAACGCCGCTAAAGATCGAGCA
1 TTAGCAGCGCTTTACAAAAAACGCCACTAAAGATCGAGCA
25518414 TTA
1 TTA
25518417 ACGGCGCATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
39 2 0.05
40 24 0.65
41 8 0.22
42 3 0.08
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (40 bp):
TTAGCAGCGCTTTACAAAAAACGCCACTAAAGATCGAGCA
Found at i:25518435 original size:40 final size:37
Alignment explanation
Indices: 25518349--25518445 Score: 104
Period size: 40 Copynumber: 2.5 Consensus size: 37
25518339 GCGTTTGGAC
* *
25518349 AAAAAACGCCACTAGAAATCGAGCATTAGCGGCGCTTT
1 AAAAAACGCCGCTA-AAATCGAGCATTAACGGCGCTTT
*
25518387 ACGTAAAACGCCGCTAAAGATCGAGCATTAACGGCGCATTTT
1 A--AAAAACGCCGCTAAA-ATCGAGCATTAACGGCGC--TTT
*
25518429 AAAAAACACCGCTAAAA
1 AAAAAACGCCGCTAAAA
25518446 ATAAGTATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
38 1 0.02
39 3 0.06
40 41 0.84
42 4 0.08
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.18
Consensus pattern (37 bp):
AAAAAACGCCGCTAAAATCGAGCATTAACGGCGCTTT
Found at i:25518578 original size:40 final size:41
Alignment explanation
Indices: 25518523--25518756 Score: 278
Period size: 41 Copynumber: 5.8 Consensus size: 41
25518513 TTTTGAGGCA
* * **
25518523 TTTAGCGGCGCTTTTGATAAAGCGCCGCTAATGCTCAAG-C
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTGCC
* *
25518563 TTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGCTCGTGCC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTGCC
* * * *
25518604 TTTAGCGGCATTTTTGAAAAAACGCCGCTAATGCTTGGGCC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTGCC
* * *
25518645 TTTACCGGCGTTTTTAAAAAAGCGGCGCTAATGCTCGTGCC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTGCC
* *
25518686 TTTAGCAGCGTTTTTGATAAAGCGCCGCTAATGCT-G-GCC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTGCC
* *
25518725 TTTAGCGGCGCTTTATCAAAAA-CGCCGCTAAT
1 TTTAGCGGCG-TTTTTGAAAAAGCGCCGCTAAT
25518757 AATAAAATCT
Statistics
Matches: 166, Mismatches: 26, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
39 22 0.13
40 42 0.25
41 102 0.61
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGTGCC
Found at i:25520293 original size:20 final size:20
Alignment explanation
Indices: 25520271--25520333 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
25520261 TTCGTGATTT
25520271 AAAATTTTAAAATGAATTTTA
1 AAAATTTTAAAATG-ATTTTA
**
25520292 AAAGATTTT-AAATTTTTTTA
1 AAA-ATTTTAAAATGATTTTA
*
25520312 AAAATTTTAAAAAGATTTTA
1 AAAATTTTAAAATGATTTTA
25520332 AA
1 AA
25520334 CTTTTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.14
20 18 0.51
21 7 0.20
22 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
AAAATTTTAAAATGATTTTA
Found at i:25520301 original size:10 final size:10
Alignment explanation
Indices: 25520274--25520333 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
25520264 GTGATTTAAA
25520274 ATTTTAAAATG
1 ATTTTAAAA-G
25520285 AATTTTAAAAG
1 -ATTTTAAAAG
**
25520296 ATTTTAAATT
1 ATTTTAAAAG
*
25520306 TTTTTAAAA-
1 ATTTTAAAAG
25520315 ATTTTAAAAAG
1 ATTTT-AAAAG
25520326 ATTTTAAA
1 ATTTTAAA
25520334 CTTTTATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
9 4 0.10
10 22 0.54
11 6 0.15
12 9 0.22
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (10 bp):
ATTTTAAAAG
Found at i:25525657 original size:43 final size:43
Alignment explanation
Indices: 25525604--25525829 Score: 236
Period size: 43 Copynumber: 5.3 Consensus size: 43
25525594 GTTATGTTTT
* * *
25525604 TAGCGGCGTTTTTGCGAGAAGCGCCGCTAAAGGTCGCGGTCTA
1 TAGCGGCGTTTCTGGGAAAAGCGCCGCTAAAGGTCGCGGTCTA
* *
25525647 TAGTGGCGTTTCTGTGAAAAGCGCCGCTAAAGGTCGCGGTCTA
1 TAGCGGCGTTTCTGGGAAAAGCGCCGCTAAAGGTCGCGGTCTA
** ***
25525690 TAGCGGCGTTTCTGGGAAAAGCGCCTTTAAAGGTTATGGTCTA
1 TAGCGGCGTTTCTGGGAAAAGCGCCGCTAAAGGTCGCGGTCTA
** * * ** *
25525733 TAGTAGCGTTTGTGGGAAAAGCGCCGTTAAAGGTCTTGGTCTT
1 TAGCGGCGTTTCTGGGAAAAGCGCCGCTAAAGGTCGCGGTCTA
* * * ** *
25525776 TAGCGGCGTTTGTAGGAAAAACGCCGCTAAAGGTCTTGGTCTT
1 TAGCGGCGTTTCTGGGAAAAGCGCCGCTAAAGGTCGCGGTCTA
*
25525819 TAGCGGTGTTT
1 TAGCGGCGTTT
25525830 TTAGAGAAAA
Statistics
Matches: 159, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 159 1.00
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (43 bp):
TAGCGGCGTTTCTGGGAAAAGCGCCGCTAAAGGTCGCGGTCTA
Found at i:25525950 original size:22 final size:22
Alignment explanation
Indices: 25525923--25525966 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
25525913 TAGCGGTGTT
*
25525923 AAAAAGCGCCACTAAAGGCCTA
1 AAAAAGCGCCACTAAAAGCCTA
*
25525945 AAAAAGCGCCGCTAAAAGCCTA
1 AAAAAGCGCCACTAAAAGCCTA
25525967 TTTTGGTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.27, G:0.18, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCACTAAAAGCCTA
Found at i:25535619 original size:21 final size:21
Alignment explanation
Indices: 25535578--25535619 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
25535568 CATATAGATT
* *
25535578 ATAAAAAAAAATTACATATAA
1 ATAAAAAAAAATTAAAAATAA
25535599 ATAAAAATAAAA-TAAAAATAA
1 ATAAAAA-AAAATTAAAAATAA
25535620 TTATATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (21 bp):
ATAAAAAAAAATTAAAAATAA
Found at i:25535747 original size:22 final size:21
Alignment explanation
Indices: 25535678--25535749 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 21
25535668 TATATTTTTT
*
25535678 AAAAAATAATAATTAAATATGA
1 AAAAAATAATAATTAAAAAT-A
* *
25535700 AAAAGA-AATAA-TAATAATA
1 AAAAAATAATAATTAAAAATA
25535719 AAAAAATAATTAATTAAAAATA
1 AAAAAATAA-TAATTAAAAATA
25535741 AAAAAATAA
1 AAAAAATAA
25535750 AAAAAAGCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
19 6 0.14
20 7 0.17
21 8 0.19
22 21 0.50
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (21 bp):
AAAAAATAATAATTAAAAATA
Found at i:25536295 original size:19 final size:19
Alignment explanation
Indices: 25536271--25536345 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
25536261 AATCACATCT
25536271 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
*
25536290 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
25536311 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
25536330 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
25536346 CTCGAAGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 33 0.65
21 18 0.35
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:25536308 original size:21 final size:21
Alignment explanation
Indices: 25536282--25536344 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
25536272 CTAAGATTAC
25536282 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
25536303 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
25536322 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
25536343 AT
1 AT
25536345 CCTCGAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.47
21 21 0.52
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:25536355 original size:17 final size:18
Alignment explanation
Indices: 25536274--25536355 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 18
25536264 CACATCTTCT
* *
25536274 AAGATTACATATCATATCT
1 AAGATTGCATATCA-ATCG
*
25536293 AAGATTGCATATATCATATCT
1 AAGATTGC--ATATCA-ATCG
*
25536314 AAGATTGCATATCATATCT
1 AAGATTGCATATCA-ATCG
*
25536333 AAGATTGCATATC-CTCG
1 AAGATTGCATATCAATCG
25536350 AAGATT
1 AAGATT
25536356 ATGTTTCCAT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.14
19 31 0.53
21 19 0.33
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (18 bp):
AAGATTGCATATCAATCG
Found at i:25536809 original size:128 final size:129
Alignment explanation
Indices: 25536628--25536879 Score: 305
Period size: 128 Copynumber: 2.0 Consensus size: 129
25536618 AGATGAATTT
* * * *
25536628 GATGCGATCTGCTCTACTGTAATTTCAGAGAGATAAGATCCATCATTCTAATCCACTCCGCTACA
1 GATGCGATCTGCTCTAATGCAATTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
* * *
25536693 ACTTTAGGGAGATAGGATT-T-GTTTATTTAGTCTGCTCCACTACAACTTCAGAGAGATAAGACT
66 ACTTCAGGGAGATAGGATTATCG--GATTTAATCTGCTCCACTACAACTTCAGAGAGATAAGACT
25536756 A
129 A
* * * * * *
25536757 GATGCGTTCTGCTC-AATGCAACTTT-AGAGAGATAAGATCCAAGATTTTAATCCGCTTCACTGC
1 GATGCGATCTGCTCTAATGCAA-TTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTAC
* * *
25536820 AACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
65 AACTTCAGGGAGATAGGATTATCGGATTTAATCTGCTCCACTACAACTTCAGAGAGATAA
25536880 AATTTTCCAT
Statistics
Matches: 104, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
128 86 0.83
129 17 0.16
130 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (129 bp):
GATGCGATCTGCTCTAATGCAATTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
ACTTCAGGGAGATAGGATTATCGGATTTAATCTGCTCCACTACAACTTCAGAGAGATAAGACTA
Found at i:25537230 original size:44 final size:44
Alignment explanation
Indices: 25537163--25537800 Score: 569
Period size: 44 Copynumber: 14.5 Consensus size: 44
25537153 GTCGGTGCAC
* * * * * *
25537163 GAAGGCAAGACCTGCTATTTTCGATCTACTTCACGCCAATAAAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATATAG
* * * * *
25537207 AAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATATAG
*
25537252 GAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATATAG
* * * * * * *
25537295 GAAGACAGGACCTGCTATTTTCGATCTACCTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATATAG
* * *
25537339 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCA-CACCAATATAG
* * *
25537384 GAAGATAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATTG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATATAG
* * * *
25537427 GAAGACAAGA-CTTGCTATCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATC-TGCTATCTTCGATCTACTTCACACCAATATAG
** * * *
25537471 GAAGTTAAGATCTGCTTTCTTCGATCTACTTTGC-CACCAGTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTAC-TT-CACACCAATATAG
* *
25537516 GAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATATAG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATATAG
* * * *
25537560 GAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAC
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATATAG
* *
25537604 GAAGACAAGATCTGC-ATCTTTGATCCACTTC-CTACCAATATAG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATATAG
* * * * * *
25537647 GAAGACAGGACCTGCTATCTTCAATCTACTTCACGCCAATAAAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATATAG
* * * * *
25537691 GAAGACAAGATCTGATTTCTTCGATCTACTCCACCACTAATATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCA-CACCAATATAG
* * *
25537736 GAAGACAATATCTGC-ATCTTTGATCCACTTC-CTACCAATATAG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATATAG
* * *
25537779 GAAGACAGGACCTGTTATCTTC
1 GAAGACAAGATCTGCTATCTTC
25537801 ACTGATCTGC
Statistics
Matches: 468, Mismatches: 105, Indels: 42
0.76 0.17 0.07
Matches are distributed among these distances:
42 6 0.01
43 97 0.21
44 264 0.56
45 100 0.21
46 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATATAG
Found at i:25537408 original size:132 final size:132
Alignment explanation
Indices: 25537171--25537678 Score: 752
Period size: 132 Copynumber: 3.8 Consensus size: 132
25537161 ACGAAGGCAA
* *
25537171 GACCTGCTATTTTCGATCTACTTCACGCCAATAAATAAAGACAAGATCTGCTTTCTTCGATCTAC
1 GACCTGCTATTTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTAC
25537236 TTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGAC
66 TTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGAC
25537301 AG
131 AG
*
25537303 GACCTGCTATTTTCGATCTACCTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTAC
1 GACCTGCTATTTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTAC
* * *
25537368 TTCACCACCAGTATGGGAAGATAAGATCTGCATCTTCGATCCACTTCCTACCAATATTGGAAGAC
66 TTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGAC
*
25537433 AA
131 AG
* **
25537435 GACTTGCTATCTTT-GATCTACTTCACGCCAATACATGAAGTTAAGATCTGCTTTCTTCGATCTA
1 GACCTGCTAT-TTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTA
*
25537499 CTTTGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAG
65 CTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTC-CTACCAATATAGGAAG
25537564 ACAG
129 ACAG
* * * * * *
25537568 GATCTGCTATCTTCGATCTACTTCACGCCAATACACGAAGACAAGATCTGC-ATCTTTGATCCAC
1 GACCTGCTATTTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTAC
* * * * * * *
25537632 TTC-CTACCAATATAGGAAGACAGGACCTGCTATCTTCAATCTACTTC
66 TTCGCCACCAGTATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC
25537679 ACGCCAATAA
Statistics
Matches: 339, Mismatches: 33, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
131 22 0.06
132 254 0.75
133 63 0.19
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (132 bp):
GACCTGCTATTTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTAC
TTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGAC
AG
Found at i:25537540 original size:220 final size:219
Alignment explanation
Indices: 25537252--25537800 Score: 656
Period size: 220 Copynumber: 2.5 Consensus size: 219
25537242 ACCAGTATGG
* * * * * *
25537252 GAAGACAAGATCTGC-ATCTTCGATCCAC-TTCCTACCAATATAGGAAGACAGGACCTGCTATTT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTTCC-ACCAATATGGGAAGACAAGATCTGC-ATCT
* * * * *
25537315 TCGATCTACCTCAC-GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAG
64 TCGATCCACCTCACTACCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA-CACCAA
*** * * *
25537379 TATGGGAAGATAAGATCTGCATCTTCGATCCACTTCCTACCAATATTGGAAGACAAGACTTGCTA
128 TACACGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAAGACCTGCTA
** *
25537444 TCTTTGATCTACTTCACGCCAATACAT
193 TCTTCAATCTACTTCACGCCAATAAAT
** *
25537471 GAAGTTAAGATCTGCTTTCTTCGATCTACTTTGCCACCAGTATGGGAAGACAAGATCTGCATCTT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTT-CCACCAATATGGGAAGACAAGATCTGCATCTT
* * * * *
25537536 CGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATA
65 CGATCCACCTCACTACCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATA
* *
25537601 CACGAAGACAAGATCTGCATCTTTGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATC
130 CACGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAAGACCTGCTATC
25537666 TTCAATCTACTTCACGCCAATAAAT
195 TTCAATCTACTTCACGCCAATAAAT
* ** * *
25537691 GAAGACAAGATCTGATTTCTTCGATCTACTCCACCACTAATATGGGAAGACAATATCTGCATCTT
1 GAAGACAAGATCTGCTTTCTTCGATCTACT-TTCCACCAATATGGGAAGACAAGATCTGCATCTT
* * * * * *
25537756 TGATCCACTTC-CTACCAATATAGGAAGACAGGACCTGTTATCTTC
65 CGATCCACCTCACTACCAATACAGGAAGACAAGATCTGCTATCTTC
25537801 ACTGATCTGC
Statistics
Matches: 284, Mismatches: 41, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
219 45 0.16
220 176 0.62
221 61 0.21
222 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (219 bp):
GAAGACAAGATCTGCTTTCTTCGATCTACTTTCCACCAATATGGGAAGACAAGATCTGCATCTTC
GATCCACCTCACTACCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAC
ACGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAAGACCTGCTATCT
TCAATCTACTTCACGCCAATAAAT
Found at i:25543563 original size:26 final size:25
Alignment explanation
Indices: 25543520--25543568 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
25543510 ATATGTATAC
*
25543520 ATACATATATATACTAAAATAAATAT
1 ATACATATAGATACTAAAA-AAATAT
25543546 ATACATATAGATTA-TAAAAAAAT
1 ATACATATAGA-TACTAAAAAAAT
25543569 TACATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 15 0.71
27 2 0.10
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (25 bp):
ATACATATAGATACTAAAAAAATAT
Found at i:25543589 original size:22 final size:23
Alignment explanation
Indices: 25543520--25543591 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 23
25543510 ATATGTATAC
*
25543520 ATACATATATATACTAAAATAAATAT
1 ATACATATAAATA--AAAATAAA-AT
* *
25543546 ATACATATAGATTATAAA-AAAAT
1 ATACATATA-AATAAAAATAAAAT
25543569 -TACATATAAATAAAAATAAAAT
1 ATACATATAAATAAAAATAAAAT
25543591 A
1 A
25543592 AAAATAATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
21 6 0.16
22 13 0.34
23 2 0.05
24 3 0.08
25 3 0.08
26 9 0.24
27 2 0.05
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (23 bp):
ATACATATAAATAAAAATAAAAT
Found at i:25543704 original size:23 final size:22
Alignment explanation
Indices: 25543657--25543734 Score: 93
Period size: 23 Copynumber: 3.4 Consensus size: 22
25543647 TATATTTTTT
*
25543657 AAAAAATAATAATTAAATATGAA
1 AAAAAATAATAATTAAAAAT-AA
*
25543680 AAAGAAATAATAATAAAAAATAA
1 AAA-AAATAATAATTAAAAATAA
*
25543703 AAAAACTAATTAATTAAAAATAA
1 AAAAAATAA-TAATTAAAAATAA
*
25543726 AGAAAATAA
1 AAAAAATAA
25543735 AAAAAGCTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.11
23 27 0.57
24 15 0.32
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (22 bp):
AAAAAATAATAATTAAAAATAA
Found at i:25544252 original size:19 final size:19
Alignment explanation
Indices: 25544228--25544302 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
25544218 AATCACATTT
25544228 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
*
25544247 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
25544268 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
25544287 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
25544303 CTCGAAGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 33 0.65
21 18 0.35
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:25544265 original size:21 final size:21
Alignment explanation
Indices: 25544239--25544301 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
25544229 CTAAGATTAC
25544239 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
25544260 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
25544279 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
25544300 AT
1 AT
25544302 CCTCGAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.47
21 21 0.52
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:25544312 original size:17 final size:18
Alignment explanation
Indices: 25544231--25544312 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 18
25544221 CACATTTTCT
* *
25544231 AAGATTACATATCATATCT
1 AAGATTGCATATCA-ATCG
*
25544250 AAGATTGCATATATCATATCT
1 AAGATTGC--ATATCA-ATCG
*
25544271 AAGATTGCATATCATATCT
1 AAGATTGCATATCA-ATCG
*
25544290 AAGATTGCATATC-CTCG
1 AAGATTGCATATCAATCG
25544307 AAGATT
1 AAGATT
25544313 ATGTTTCCAT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.14
19 31 0.53
21 19 0.33
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (18 bp):
AAGATTGCATATCAATCG
Found at i:25545800 original size:9 final size:9
Alignment explanation
Indices: 25545786--25545870 Score: 100
Period size: 9 Copynumber: 9.4 Consensus size: 9
25545776 TTTTGGTTAA
25545786 AATTAACCG
1 AATTAACCG
*
25545795 AATTAAACG
1 AATTAACCG
*
25545804 AATTAACCT
1 AATTAACCG
25545813 AATT-ACTCG
1 AATTAAC-CG
*
25545822 AATTAATCG
1 AATTAACCG
*
25545831 AATTATCCG
1 AATTAACCG
25545840 AATTAACCG
1 AATTAACCG
* *
25545849 AATTACCCA
1 AATTAACCG
25545858 AATTAACCG
1 AATTAACCG
25545867 AATT
1 AATT
25545871 GAATCACTAC
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
8 2 0.03
9 59 0.95
10 1 0.02
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:25556712 original size:25 final size:25
Alignment explanation
Indices: 25556684--25556732 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
25556674 TTCAAGTGAG
25556684 CTATATCAGGAAGCTCACAAAGAGC
1 CTATATCAGGAAGCTCACAAAGAGC
* *
25556709 CTATATCAGGACGCTCATAAAGAG
1 CTATATCAGGAAGCTCACAAAGAG
25556733 TTGTGGTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.18
Consensus pattern (25 bp):
CTATATCAGGAAGCTCACAAAGAGC
Found at i:25561188 original size:22 final size:22
Alignment explanation
Indices: 25561137--25561188 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
25561127 TAACAACCTT
*
25561137 TAAACATGTTCAAAACATCCCA
1 TAAACATGTTCAAAACATACCA
25561159 -AAACCATG-TCAAAACATACCA
1 TAAA-CATGTTCAAAACATACCA
25561180 TAAATCATG
1 TAAA-CATG
25561189 ATCCCAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.48, C:0.25, G:0.06, T:0.21
Consensus pattern (22 bp):
TAAACATGTTCAAAACATACCA
Found at i:25564647 original size:14 final size:15
Alignment explanation
Indices: 25564630--25564662 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
25564620 TCTAAGTTCA
*
25564630 TTTTAAA-TGTAAAT
1 TTTTAAATTATAAAT
25564644 TTTTAAATTATAAAT
1 TTTTAAATTATAAAT
25564659 TTTT
1 TTTT
25564663 TATAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTTAAATTATAAAT
Found at i:25565291 original size:18 final size:19
Alignment explanation
Indices: 25565247--25565291 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
25565237 TATTTTGTTC
*
25565247 AATTATTTATTATTTTAATA
1 AATT-TTTAATATTTTAATA
*
25565267 TATTTTTAATATTTT-ATA
1 AATTTTTAATATTTTAATA
25565285 AATTTTT
1 AATTTTT
25565292 TGAGTTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 9 0.41
19 10 0.45
20 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTTTTAATATTTTAATA
Found at i:25566443 original size:21 final size:22
Alignment explanation
Indices: 25566419--25566470 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
25566409 TGGCCAGTAC
*
25566419 AAATAACAA-AAACAATAGC-AA
1 AAATAACAACAAA-AACAGCAAA
25566440 AAATAACAACAAAAACAGCAGAA
1 AAATAACAACAAAAACAGCA-AA
25566463 AAATAACA
1 AAATAACA
25566471 GCACCAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 14 0.52
22 3 0.11
23 10 0.37
ACGTcount: A:0.71, C:0.15, G:0.06, T:0.08
Consensus pattern (22 bp):
AAATAACAACAAAAACAGCAAA
Found at i:25566464 original size:23 final size:24
Alignment explanation
Indices: 25566423--25566470 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
25566413 CAGTACAAAT
*
25566423 AACAAAAACAATAGCAAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
*
25566447 AACAAAAACAGCAG-AAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
25566470 A
1 A
25566471 GCACCAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.71, C:0.17, G:0.06, T:0.06
Consensus pattern (24 bp):
AACAAAAACAACAGCAAAAATAAC
Found at i:25567025 original size:27 final size:25
Alignment explanation
Indices: 25566977--25567026 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
25566967 TTTGATTCTA
*
25566977 ATTTTTTTTAAATTTCTCTCAATTT
1 ATTTTTTTTAAATTTATCTCAATTT
*
25567002 ATTTATTTTTAACTTTATCGTCAAT
1 ATTT-TTTTTAAATTTATC-TCAAT
25567027 ATGCTTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 12 0.57
27 5 0.24
ACGTcount: A:0.26, C:0.12, G:0.02, T:0.60
Consensus pattern (25 bp):
ATTTTTTTTAAATTTATCTCAATTT
Found at i:25567121 original size:11 final size:11
Alignment explanation
Indices: 25567101--25567138 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
25567091 CTTAACACCA
25567101 AAATTGAGAGG
1 AAATTGAGAGG
*
25567112 AAATTTAGAGG
1 AAATTGAGAGG
25567123 AAATTGAGAGG
1 AAATTGAGAGG
25567134 AAATT
1 AAATT
25567139 TTAAAGAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (11 bp):
AAATTGAGAGG
Found at i:25573196 original size:31 final size:32
Alignment explanation
Indices: 25573146--25573205 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
25573136 TTGCTTGGCA
* *
25573146 AAGTGGAATGAAAATTAGAAAGATGGAAATTG
1 AAGTGGAATGAAAAATAGAAAGATAGAAATTG
* *
25573178 AAGTGGTA-GAAAAATAGAAGGATAGAAA
1 AAGTGGAATGAAAAATAGAAAGATAGAAA
25573206 ATATAATTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 17 0.71
32 7 0.29
ACGTcount: A:0.53, C:0.00, G:0.28, T:0.18
Consensus pattern (32 bp):
AAGTGGAATGAAAAATAGAAAGATAGAAATTG
Found at i:25575141 original size:13 final size:13
Alignment explanation
Indices: 25575123--25575149 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25575113 TCAAGATAAA
25575123 TTTTGATGTAATT
1 TTTTGATGTAATT
25575136 TTTTGATGTAATT
1 TTTTGATGTAATT
25575149 T
1 T
25575150 AAATTCTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (13 bp):
TTTTGATGTAATT
Found at i:25577291 original size:19 final size:20
Alignment explanation
Indices: 25577250--25577291 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
25577240 ATTTCTATGC
* *
25577250 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
25577270 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
25577289 CAT
1 CAT
25577292 CACATCAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:25581000 original size:24 final size:24
Alignment explanation
Indices: 25580973--25581018 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25580963 AGAACAGTCC
* *
25580973 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGAAAATGAAGGAGCAGCTT
*
25580997 CAAAAGAAAATGAATGAGCAGC
1 CAAAAGAAAATGAAGGAGCAGC
25581019 AAAAAATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (24 bp):
CAAAAGAAAATGAAGGAGCAGCTT
Found at i:25589224 original size:44 final size:45
Alignment explanation
Indices: 25589155--25589272 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 45
25589145 GATCGCATCT
*
25589155 AGTCTTATC-TCCTTGAAGTTGCAGTGGAGTAGACT-AAG-TAAGCA
1 AGTCCTATCTTCC-TGAAGTTGCAGTGGAGTAGACTGAAGAT-AGCA
* *
25589199 AGTCCTATCTTCCTGAAGTTACAGT-GAGGTAGACTGAAGATGGCA
1 AGTCCTATCTTCCTGAAGTTGCAGTGGA-GTAGACTGAAGATAGCA
* *
25589244 A-ACCTTATCTCCCTGAAGTTGCAGTGGAG
1 AGTCC-TATCTTCCTGAAGTTGCAGTGGAG
25589273 CAGGTTAAAG
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
43 2 0.03
44 28 0.45
45 29 0.47
46 3 0.05
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (45 bp):
AGTCCTATCTTCCTGAAGTTGCAGTGGAGTAGACTGAAGATAGCA
Found at i:25589262 original size:45 final size:45
Alignment explanation
Indices: 25589158--25589715 Score: 146
Period size: 44 Copynumber: 12.8 Consensus size: 45
25589148 CGCATCTAGT
* *
25589158 CTTATCTCCTTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAGTC
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAGAC
* * *
25589203 C-TATCTTCCTGAAGTTACAGT-GAGGTAGACTGAAG-ATGGCAA-AC
1 CTTATCTCCCTGAAGTTGCAGTGGA-GTAGACT-AAGTA-AGCAAGAC
* ** *
25589247 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGT-CG-ATA-ATC
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACT-AAGTAAGCA-AGA-C
* ** * * ** *
25589292 C-TATCTCCCTAAAGTTGTC-GTGGAGCGGATTAA--AATCTTGGAT
1 CTTATCTCCCTGAAGTTG-CAGTGGAGTAGACTAAGTAAGC-AAGAC
* * * * * * * *
25589335 CTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CG-CATCTAG-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAGAC
* * * *
25589375 CTTGTCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAAG-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAGAC
* * *
25589419 CTTATC-CTCCTAAAGTTGCAGTGGGGTAGACTGAAG-ATGGCAA-AC
1 CTTATCTC-CCTGAAGTTGCAGTGGAGTAGACT-AAGTA-AGCAAGAC
* * * *
25589464 CTTATCTCCCTAAAGTTGCAGTGGAGCAG-GTTA--AAGCCGATA-ATC
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAG-C-A-AGA-C
* * * * * * *
25589509 C-TATCTCCCTAAAGTTGTAGTGGAGCAGATTAA--AA-TATTGGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCA--AGAC
* * * * * * * * *
25589552 CTTATCTCTCTGAAGTTGTAG-AGAGCAGA-T-CG-CATCTA-AT
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAGAC
* *
25589592 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAG-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAGAC
* * *
25589636 CTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAG-ATGGCAA-AC
1 CTTATCTC-CCTGAAGTTGCAGTGGAGTAGACT-AAGTA-AGCAAGAC
* *
25589681 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAG
25589716 GCCAATAATC
Statistics
Matches: 395, Mismatches: 73, Indels: 91
0.71 0.13 0.16
Matches are distributed among these distances:
40 41 0.10
41 16 0.04
42 11 0.03
43 28 0.07
44 186 0.47
45 109 0.28
46 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAGAC
Found at i:25589307 original size:44 final size:44
Alignment explanation
Indices: 25589249--25589759 Score: 195
Period size: 44 Copynumber: 11.8 Consensus size: 44
25589239 TGGCAAACCT
* *
25589249 TATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGTCGATAATCC
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGTCGATAATCC
* * * * *
25589293 TATCTCCCTAAAGTTGTC-GTGGAGCGGATTAAAATC-TTGGATCT
1 TATCTCCCTAAAGTTG-CAGTGGAGCAGATTAAAGTCGAT-AATCC
* * * *** * *
25589337 TATCTCTCTGAAGTTGCAG-AGAGCAGATCGCA-TC--TAGTCT
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGTCGATAATCC
* * * * * * *
25589377 TGTCTCCCTGAAGTTGCAGTGGAGCAAACT-AAGTAAGCA-AGTCT
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGT-CG-ATAATCC
* * * * *
25589421 TATC-CTCCTAAAGTTGCAGTGGGGTAGACTGAAGATGGCA-AA-CC
1 TATCTC-CCTAAAGTTGCAGTGGAGCAGATTAAAG-TCG-ATAATCC
* *
25589465 TTATCTCCCTAAAGTTGCAGTGGAGCAGGTTAAAGCCGATAATCC
1 -TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGTCGATAATCC
* * * *
25589510 TATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAAT--ATTGGATCT
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGTCGA-T-AATCC
* * * * *** *
25589554 TATCTCTCTGAAGTTGTAG-AGAGCAGATCGCA-TC--TAATCT
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGTCGATAATCC
* * * * *
25589594 TATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCA-AGTCT
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGT-CG-ATAATCC
* * * * *
25589638 TATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCA-AA-CC
1 TATCTC-CCTAAAGTTGCAGTGGAGCAGATTAAAG-TCG-ATAATCC
* * * *
25589682 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGGCCAATAAT-C
1 -TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGTCGATAATCC
* *
25589726 TCATCTCCCTAAAGTTGCAGCGGAGCGGATTAAA
1 T-ATCTCCCTAAAGTTGCAGTGGAGCAGATTAAA
25589760 ATCACAGATC
Statistics
Matches: 359, Mismatches: 75, Indels: 66
0.72 0.15 0.13
Matches are distributed among these distances:
40 43 0.12
41 17 0.05
42 4 0.01
43 25 0.07
44 194 0.54
45 72 0.20
46 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGTCGATAATCC
Found at i:25589449 original size:217 final size:217
Alignment explanation
Indices: 25589062--25589839 Score: 1188
Period size: 217 Copynumber: 3.6 Consensus size: 217
25589052 GAATAGATCG
* * * * * *
25589062 AAAGCCAATGATCCTATCTCTCTGAAGTTGCACTGGAGCGGATTAAAACCACAGATCTTATCTCT
1 AAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCT
* * *
25589127 CTGAAGTTACAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGTAGACTAA
66 CTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
* * * *
25589192 GTAAGCAAGTCCTATCTTCCTGAAGTTACAGTGAGGTAGACTGAAGATGGCAAACCTTATCTCCC
131 GTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGGGGTAGACTGAAGATGGCAAACCTTATCTCCC
25589257 TGAAGTTGCAGTGGAGCAGGTT
196 TGAAGTTGCAGTGGAGCAGGTT
* ***
25589279 AAAGTCGATAATCCTATCTCCCTAAAGTTGTC-GTGGAGCGGATTAAAATCTTGGATCTTATCTC
1 AAAGCCGATAATCCTATCTCCCTAAAGTTG-CAGTGGAGCGGATTAAAATCACAGATCTTATCTC
* *
25589343 TCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTGTCTCCCTGAAGTTGCAGTGGAGCAAACTA
65 TCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTA
*
25589408 AGTAAGCAAGTCTTATCCTCCTAAAGTTGCAGTGGGGTAGACTGAAGATGGCAAACCTTATCTCC
130 AGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGGGGTAGACTGAAGATGGCAAACCTTATCTCC
*
25589473 CTAAAGTTGCAGTGGAGCAGGTT
195 CTGAAGTTGCAGTGGAGCAGGTT
* * **
25589496 AAAGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAAT-ATTGGATCTTATCTC
1 AAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCA-CAGATCTTATCTC
* *
25589560 TCTGAAGTTGTAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTA
65 TCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTA
*
25589625 AGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCC
130 AGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGGGGTAGACTGAAGATGGCAAACCTTATCTCC
*
25589690 CTGAAGTTGCAGTGGAGCAGATT
195 CTGAAGTTGCAGTGGAGCAGGTT
* * *
25589713 AAGGCCAATAAT-CTCATCTCCCTAAAGTTGCAGCGGAGCGGATTAAAATCACAGATCTTATCTC
1 AAAGCCGATAATCCT-ATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTC
*
25589777 TCTGAAGTTGCAGAG-GCAGATCGCATCTAGTCTTATCTCCCTGACA-TTGCAGTGGAGTAGACT
65 TCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGA-AGTTGCAGTGGAGCAGACT
25589840 GCAGCACTAG
Statistics
Matches: 512, Mismatches: 43, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
216 46 0.09
217 464 0.91
218 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (217 bp):
AAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCT
CTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
GTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGGGGTAGACTGAAGATGGCAAACCTTATCTCCC
TGAAGTTGCAGTGGAGCAGGTT
Found at i:25590124 original size:15 final size:15
Alignment explanation
Indices: 25590104--25590142 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
25590094 AACAAAGCGG
25590104 TGGCCCAAATTACAA
1 TGGCCCAAATTACAA
25590119 TGGCCCAAATTACAA
1 TGGCCCAAATTACAA
25590134 TGGCCCAAA
1 TGGCCCAAA
25590143 ACAGATGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.18
Consensus pattern (15 bp):
TGGCCCAAATTACAA
Found at i:25592935 original size:24 final size:25
Alignment explanation
Indices: 25592908--25592959 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
25592898 ATTAGAATAT
*
25592908 ATATATT-TTTAA-AAATTATTAAAA
1 ATATATTATTTAATAAATT-TAAAAA
25592932 ATATATTATTTAATAAATTTAAAAA
1 ATATATTATTTAATAAATTTAAAAA
25592957 ATA
1 ATA
25592960 AACACATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 7 0.28
25 13 0.52
26 5 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATATATTATTTAATAAATTTAAAAA
Found at i:25596688 original size:31 final size:32
Alignment explanation
Indices: 25596653--25596713 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
25596643 ATAAATTGCT
*
25596653 CTCCCTTA-ATAAAATTCATTTTCAATTTAAG
1 CTCCCCTATATAAAATTCATTTTCAATTTAAG
25596684 CTCCCCTATATAAAATTCATTTTCAATTTA
1 CTCCCCTATATAAAATTCATTTTCAATTTA
25596714 GGGCTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 7 0.25
32 21 0.75
ACGTcount: A:0.34, C:0.21, G:0.02, T:0.43
Consensus pattern (32 bp):
CTCCCCTATATAAAATTCATTTTCAATTTAAG
Found at i:25599154 original size:41 final size:41
Alignment explanation
Indices: 25599108--25599232 Score: 189
Period size: 41 Copynumber: 3.0 Consensus size: 41
25599098 AGAATAATGA
* *
25599108 TGAATTGCACATACGTGCCCTTGTTTGTACTTCGGTACCCT
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCT
*
25599149 TGAATTGCACATACGTGCCCCTATTTGTACTTCAGTAACCC-
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGGT-ACCCT
* *
25599190 TGTATTGCACAGACGTGCCCCTATTTGTACTTCGGTACCCT
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCT
25599231 TG
1 TG
25599233 GATGTACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
40 4 0.05
41 68 0.89
42 4 0.05
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.34
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCT
Found at i:25601045 original size:51 final size:50
Alignment explanation
Indices: 25600880--25601066 Score: 179
Period size: 51 Copynumber: 3.7 Consensus size: 50
25600870 AGTGAAAGTG
* ***
25600880 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATG--
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTATATATG-ATGCA
* * *
25600929 ATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTAT-TGGATAGTTTCA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTA--CGTATAT--AT-GATGCA
*
25600984 A---TCACTTGTGTAGTACTATGTGCAGGCTACTACGTATATATGATGGCA
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTATATATGAT-GCA
*
25601032 ATGGTCACATGTGTAGTACTATGTGCAAGCTACTA
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
25601067 TGTGAACTAA
Statistics
Matches: 112, Mismatches: 13, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
47 2 0.02
48 5 0.04
49 7 0.06
50 33 0.29
51 58 0.52
52 4 0.04
53 1 0.01
54 1 0.01
55 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTATATATGATGCA
Found at i:25606648 original size:51 final size:50
Alignment explanation
Indices: 25606481--25606648 Score: 151
Period size: 51 Copynumber: 3.3 Consensus size: 50
25606471 AGTGAAAGTG
* * * * *
25606481 ATGGTCACGTGTGTAGTAC-ATATGCAAGCTTCTACGTGTACCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAATGGT
* * * * *
25606531 A-GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATGGT
* * * * * *
25606580 TTCGATCACGTGAGTAGTACTGTGTGCAGGCTACTACGTGTATCGAATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATGGT
25606631 AATGGTCACATGTGTAGT
1 -ATGGTCACATGTGTAGT
25606649 GTGAACCAAA
Statistics
Matches: 89, Mismatches: 25, Indels: 7
0.74 0.21 0.06
Matches are distributed among these distances:
49 19 0.21
50 19 0.21
51 50 0.56
52 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATGGT
Found at i:25606708 original size:45 final size:45
Alignment explanation
Indices: 25606658--25606746 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
25606648 TGTGAACCAA
* * *
25606658 ACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGATGAATCCACCGG
*
25606703 ACATCATTGATTAATAAGGTGGTTGTTATGTGATGAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGATGAATCCACCG
25606747 AGTATTTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.35
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGATGAATCCACCGG
Found at i:25625310 original size:39 final size:39
Alignment explanation
Indices: 25625254--25625508 Score: 308
Period size: 39 Copynumber: 6.5 Consensus size: 39
25625244 AGATGTTTTG
* *
25625254 AGTATTGTGATATATGCTTAAGTATTATGAGATTATATGT
1 AGTATTGTGATATATGCTTAA-TGTTATGTGATTATATGT
* *
25625294 A-TATTGTGATATATGCTTAAATATTATGTGATTATACG-
1 AGTATTGTGATATATGCTT-AATGTTATGTGATTATATGT
*
25625332 AGTATTGTGATATATGCTTACATGTTATGAGATTATATGT
1 AGTATTGTGATATATGCTTA-ATGTTATGTGATTATATGT
* *
25625372 A-TATTATGATATATGCTTGAATGTTATGTGATTATA-CT
1 AGTATTGTGATATATGCTT-AATGTTATGTGATTATATGT
25625410 AGTATTGTGATATATGCTTAAATGTTATGTGATTATATG-
1 AGTATTGTGATATATGCTT-AATGTTATGTGATTATATGT
* *
25625449 AGTATTGTGATATATGCTTGGATGTTAGGTGATTATATGT
1 AGTATTGTGATATATGCTT-AATGTTATGTGATTATATGT
*
25625489 -GTAATAG-GATATATGCTTAA
1 AGT-ATTGTGATATATGCTTAA
25625509 AAGTGAATAT
Statistics
Matches: 190, Mismatches: 16, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
38 5 0.03
39 177 0.93
40 8 0.04
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (39 bp):
AGTATTGTGATATATGCTTAATGTTATGTGATTATATGT
Found at i:25625467 original size:117 final size:117
Alignment explanation
Indices: 25625256--25625508 Score: 357
Period size: 117 Copynumber: 2.2 Consensus size: 117
25625246 ATGTTTTGAG
* *
25625256 TATTGTGATATATGCTTAAGTATTATGAGATTATATGTATATTGTGATATATGCTTAAATATTAT
1 TATTATGATATATGCTTAAGTATTATGAGATTATATCTATATTGTGATATATGCTTAAATATTAT
*
25625321 GTGATTATACGAGTATTGTGATATATGCTTACATGTTATGAGATTATATGTA
66 GTGATTATACGAGTATTGTGATATATGCTTACATGTTAGGAGATTATATGTA
* * *
25625373 TATTATGATATATGCTTGAA-TGTTATGTGATTATA-CTAGTATTGTGATATATGCTTAAATGTT
1 TATTATGATATATGCTT-AAGTATTATGAGATTATATCTA-TATTGTGATATATGCTTAAATATT
* ** * *
25625436 ATGTGATTATATGAGTATTGTGATATATGCTTGGATGTTAGGTGATTATATGTG
64 ATGTGATTATACGAGTATTGTGATATATGCTTACATGTTAGGAGATTATATGTA
* *
25625490 TAATAGGATATATGCTTAA
1 TATTATGATATATGCTTAA
25625509 AAGTGAATAT
Statistics
Matches: 121, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
116 4 0.03
117 115 0.95
118 2 0.02
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (117 bp):
TATTATGATATATGCTTAAGTATTATGAGATTATATCTATATTGTGATATATGCTTAAATATTAT
GTGATTATACGAGTATTGTGATATATGCTTACATGTTAGGAGATTATATGTA
Found at i:25625509 original size:78 final size:78
Alignment explanation
Indices: 25625252--25625509 Score: 360
Period size: 78 Copynumber: 3.3 Consensus size: 78
25625242 AAAGATGTTT
* * * *
25625252 TGAGTATTGTGATATATGCTTAAGTATTATGAGATTATATGTATATTGTGATATATGCTTAAATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGAGATTATATGTATATTGTGATATATGCTTGAATG
25625317 TTATGTGATTATA
66 TTATGTGATTATA
* * *
25625330 CGAGTATTGTGATATATGCTTACATGTTATGAGATTATATGTATATTATGATATATGCTTGAATG
1 TGAGTATTGTGATATATGCTTAAATGTTATGAGATTATATGTATATTGTGATATATGCTTGAATG
25625395 TTATGTGATTATA
66 TTATGTGATTATA
* *
25625408 CT-AGTATTGTGATATATGCTTAAATGTTATGTGATTATATG-AGTATTGTGATATATGCTTGGA
1 -TGAGTATTGTGATATATGCTTAAATGTTATGAGATTATATGTA-TATTGTGATATATGCTTGAA
*
25625471 TGTTAGGTGATTATA
64 TGTTATGTGATTATA
* *
25625486 TGTGTAATAG-GATATATGCTTAAA
1 TGAGT-ATTGTGATATATGCTTAAA
25625510 AGTGAATATA
Statistics
Matches: 161, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
77 2 0.01
78 156 0.97
79 3 0.02
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (78 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGAGATTATATGTATATTGTGATATATGCTTGAATG
TTATGTGATTATA
Found at i:25636236 original size:29 final size:29
Alignment explanation
Indices: 25636182--25636522 Score: 342
Period size: 29 Copynumber: 11.7 Consensus size: 29
25636172 TATCGACAAT
* * ***
25636182 CATCAATCAATGAAAAAGGATGGTTTTGAC
1 CATCAA-CTATGAAAAGGGATGGTGACGAC
* * * **
25636212 CATCGATTATGAAAAGGGATAGTTTCGAC
1 CATCAACTATGAAAAGGGATGGTGACGAC
* * *
25636241 TATCGACTATGAAAAGGGATGGTCACGAC
1 CATCAACTATGAAAAGGGATGGTGACGAC
* *
25636270 CATCAACTATAAAAAGGGATGGTCACGAC
1 CATCAACTATGAAAAGGGATGGTGACGAC
25636299 CATCAACTATGAAAAGGGATGGTGACGAC
1 CATCAACTATGAAAAGGGATGGTGACGAC
* *
25636328 TATAAACTATGAAAAGGGATGGTGACGAC
1 CATCAACTATGAAAAGGGATGGTGACGAC
* * ***
25636357 CATCGTA-TATGAAAAGGGATAGTTTTGAC
1 CATC-AACTATGAAAAGGGATGGTGACGAC
* *
25636386 TATCGACTATGAAAAGGGATGGTGACGAC
1 CATCAACTATGAAAAGGGATGGTGACGAC
25636415 CATCAACTATGAAAAGGGATGGTGACGAC
1 CATCAACTATGAAAAGGGATGGTGACGAC
* * *
25636444 CATCTACTATGAAAAAGGATGGTGACAAC
1 CATCAACTATGAAAAGGGATGGTGACGAC
* * * *
25636473 CATCGATTAATGAAAAAGGATGATGACGAC
1 CATCAACT-ATGAAAAGGGATGGTGACGAC
** *
25636503 CATCAAAAATGAAAGGGGAT
1 CATCAACTATGAAAAGGGAT
25636523 AGTTATGATC
Statistics
Matches: 263, Mismatches: 45, Indels: 7
0.83 0.14 0.02
Matches are distributed among these distances:
28 1 0.00
29 232 0.88
30 30 0.11
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (29 bp):
CATCAACTATGAAAAGGGATGGTGACGAC
Found at i:25645201 original size:25 final size:25
Alignment explanation
Indices: 25645163--25645220 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
25645153 TTAATTAGTA
* *
25645163 TAAATATT-AATAATTCAAT-AAAT
1 TAAAAATTAAATAATTAAATAAAAT
25645186 TGAAAAATTAAATAATTAAATAAAAT
1 T-AAAAATTAAATAATTAAATAAAAT
25645212 TAAAAATTA
1 TAAAAATTA
25645221 GGAGAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 1 0.03
24 6 0.20
25 18 0.60
26 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (25 bp):
TAAAAATTAAATAATTAAATAAAAT
Found at i:25646076 original size:16 final size:15
Alignment explanation
Indices: 25646051--25646084 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
25646041 AAGTTTGATA
*
25646051 ATAATTAATATATATT
1 ATAATCAATATA-ATT
25646067 ATAATCAATATAATT
1 ATAATCAATATAATT
25646082 ATA
1 ATA
25646085 CACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATCAATATAATT
Found at i:25661545 original size:19 final size:20
Alignment explanation
Indices: 25661521--25661560 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
25661511 TTCTATCCAT
25661521 AAAATA-CTAAACCATAATC
1 AAAATACCTAAACCATAATC
25661540 AAAATATGCCTAAACCATAAT
1 AAAATA--CCTAAACCATAAT
25661561 TCACTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
22 12 0.67
ACGTcount: A:0.55, C:0.20, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAATACCTAAACCATAATC
Found at i:25662324 original size:43 final size:43
Alignment explanation
Indices: 25662277--25662376 Score: 173
Period size: 43 Copynumber: 2.3 Consensus size: 43
25662267 TCCCGGATAG
*
25662277 GGTCTTACACGAAAACACAAGTCAATTCCAACGTCCCAGACGT
1 GGTCTTACACGAAAACACAAGTCAATTCCAACATCCCAGACGT
*
25662320 GGTCTTACACGAAAACACAAGTCAATTCTAACATCCCAGACGT
1 GGTCTTACACGAAAACACAAGTCAATTCCAACATCCCAGACGT
*
25662363 GGTCTTACATGAAA
1 GGTCTTACACGAAA
25662377 TCACTTATCA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (43 bp):
GGTCTTACACGAAAACACAAGTCAATTCCAACATCCCAGACGT
Found at i:25670526 original size:43 final size:43
Alignment explanation
Indices: 25670453--25670606 Score: 168
Period size: 43 Copynumber: 3.6 Consensus size: 43
25670443 CAACGCCAAC
* * * * * *
25670453 GTCCCAGA-AGTGGTCTTACATGTAATCACAAATCGATGTCGCT
1 GTCCCAGACA-TGGTCTTACACGAAAACACAAGTCGATGCCACT
* * *
25670496 GTCCCAGACAAGGTCTTACACGAAAACACAAGTCAATACCAAC-
1 GTCCCAGACATGGTCTTACACGAAAACACAAGTCGATGCC-ACT
* * *
25670539 GTCTCAGACGTGGTCTTACACGAAAACACAAGTCGATGCCAAT
1 GTCCCAGACATGGTCTTACACGAAAACACAAGTCGATGCCACT
25670582 GTCCCAGACATGGTCTTACACGAAA
1 GTCCCAGACATGGTCTTACACGAAA
25670607 TCACTTATCA
Statistics
Matches: 91, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
42 1 0.01
43 88 0.97
44 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.21
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGAAAACACAAGTCGATGCCACT
Found at i:25670597 original size:86 final size:86
Alignment explanation
Indices: 25670448--25670606 Score: 228
Period size: 86 Copynumber: 1.8 Consensus size: 86
25670438 TTGTACAACG
* * * * **
25670448 CCAACGTCCCAGAAGTGGTCTTACATGTAATCACAAATCGATGTCGCTGTCCCAGACAAGGTCTT
1 CCAACGTCCCAGAAGTGGTCTTACACGAAAACACAAATCGATGCCAATGTCCCAGACAAGGTCTT
25670513 ACACGAAAACACAAGTCAATA
66 ACACGAAAACACAAGTCAATA
* * * *
25670534 CCAACGTCTCAGACGTGGTCTTACACGAAAACACAAGTCGATGCCAATGTCCCAGACATGGTCTT
1 CCAACGTCCCAGAAGTGGTCTTACACGAAAACACAAATCGATGCCAATGTCCCAGACAAGGTCTT
25670599 ACACGAAA
66 ACACGAAA
25670607 TCACTTATCA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 63 1.00
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (86 bp):
CCAACGTCCCAGAAGTGGTCTTACACGAAAACACAAATCGATGCCAATGTCCCAGACAAGGTCTT
ACACGAAAACACAAGTCAATA
Found at i:25675530 original size:30 final size:30
Alignment explanation
Indices: 25675484--25675544 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
25675474 CGTAGTCTGG
* *
25675484 CACATGGCCATGTGTCCA-CCAGGTGTGGCT
1 CACACGGCCATGTGTCCAGCC-CGTGTGGCT
*
25675514 CACACGGCCGTGTGTCCAGCCCGTGTGGCT
1 CACACGGCCATGTGTCCAGCCCGTGTGGCT
25675544 C
1 C
25675545 TTAAAAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.13, C:0.34, G:0.31, T:0.21
Consensus pattern (30 bp):
CACACGGCCATGTGTCCAGCCCGTGTGGCT
Found at i:25682487 original size:12 final size:13
Alignment explanation
Indices: 25682454--25682484 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
25682444 ATATGGTTCA
25682454 TAAAAACATAGCT
1 TAAAAACATAGCT
*
25682467 TAAAAACATATCT
1 TAAAAACATAGCT
25682480 TAAAA
1 TAAAA
25682485 CATTTAAAAT
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:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (13 bp):
TAAAAACATAGCT
Found at i:25685469 original size:4 final size:4
Alignment explanation
Indices: 25685460--25685518 Score: 118
Period size: 4 Copynumber: 14.8 Consensus size: 4
25685450 TTAGTTTATG
25685460 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25685508 CATA CATA CAT
1 CATA CATA CAT
25685519 GGCTTTTCAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:25699041 original size:22 final size:22
Alignment explanation
Indices: 25699016--25699065 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
25699006 TTTTTTTCCT
*
25699016 TATTTTCATTGATTTTCTAATC
1 TATTTTCATTGATTTACTAATC
**
25699038 TATTTTTGTTGATTTACTAATC
1 TATTTTCATTGATTTACTAATC
*
25699060 TGTTTT
1 TATTTT
25699066 GGTCTCTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.10, G:0.08, T:0.62
Consensus pattern (22 bp):
TATTTTCATTGATTTACTAATC
Found at i:25702973 original size:28 final size:28
Alignment explanation
Indices: 25702942--25702995 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
25702932 AAAATTCTAA
*
25702942 AAAATATAAATAT-AAACTTTAAAAATTC
1 AAAATA-AAATATAAAAATTTAAAAATTC
*
25702970 AAAATAATATATAAAAATTTAAAAAT
1 AAAATAAAATATAAAAATTTAAAAAT
25702996 ATATTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (28 bp):
AAAATAAAATATAAAAATTTAAAAATTC
Found at i:25702986 original size:21 final size:20
Alignment explanation
Indices: 25702962--25703004 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
25702952 TATAAACTTT
*
25702962 AAAAATTCAAAATAATATATA
1 AAAAATTAAAAAT-ATATATA
* *
25702983 AAAATTTAAAAATATATTTA
1 AAAAATTAAAAATATATATA
25703003 AA
1 AA
25703005 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTAAAAATATATATA
Found at i:25702998 original size:18 final size:18
Alignment explanation
Indices: 25702961--25703020 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
25702951 ATATAAACTT
*
25702961 TAAAAATTCAAAATAATATA
1 TAAAAATT-TAAA-AATATA
25702981 TAAAAATTTAAAAATATA
1 TAAAAATTTAAAAATATA
**
25702999 TTTAAATTTAAAAA-AT-
1 TAAAAATTTAAAAATATA
25703015 TAAAAA
1 TAAAAA
25703021 ACATAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 4 0.11
17 2 0.06
18 18 0.51
19 3 0.09
20 8 0.23
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAATTTAAAAATATA
Found at i:25704604 original size:43 final size:43
Alignment explanation
Indices: 25704522--25704681 Score: 243
Period size: 42 Copynumber: 3.8 Consensus size: 43
25704512 GTTTATAAGA
* *
25704522 AAAAACGCCGCTAAAGAACATGACATTTAGC-GCACTTTGCCC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCCC
* *
25704564 AAAAACGCCGCTAAAGAATATGACCTTTAACGGCGCTTTG-CC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCCC
* *
25704606 ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCCC
*
25704649 ATAAACGCCGCTAAAGAACATGACCTTTAGCGG
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGG
25704682 TTCTTTAGCG
Statistics
Matches: 107, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
42 66 0.62
43 41 0.38
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCCC
Found at i:25705725 original size:40 final size:40
Alignment explanation
Indices: 25705662--25705746 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
25705652 TAGCTTGAAT
* * *
25705662 ATCAACACTTCAATATTTAATATGCAAGGAATTATCAAAA
1 ATCAACACTTCAATAATTAATATGCAAGAAATTAACAAAA
*
25705702 ATCAACATTTCAATAAATT-ATATGCAAGAAATTAACAAAA
1 ATCAACACTTCAAT-AATTAATATGCAAGAAATTAACAAAA
25705742 ATCAA
1 ATCAA
25705747 TCTTACAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 37 0.93
41 3 0.08
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.28
Consensus pattern (40 bp):
ATCAACACTTCAATAATTAATATGCAAGAAATTAACAAAA
Found at i:25705857 original size:86 final size:85
Alignment explanation
Indices: 25705753--25706098 Score: 270
Period size: 86 Copynumber: 4.0 Consensus size: 85
25705743 TCAATCTTAC
* * * * ***
25705753 AACAGTTTATGTGAAACAAATTAGCAAAATCAA-GTATTCATAGTTCATATATTTATCGGTAAT-
1 AACAATTTATATGCAACAAATTAGCAAAATCAATG-ATTCA-AGTTCATATATTTACCAAAAATC
*
25705816 AGGGCTAAATCTTCAAT-TTCTAT
64 A-GACTAAATCTTCAATATT-TAT
* * *
25705839 AACGATTTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTCATGTATTTACCAAAAATCA
1 AACAATTTATATGCAACAAATTAGC-AAAATCAATGATTCAAGTTCATATATTTACCAAAAATCA
* *
25705904 GACTAATTTTTCAATATTTAT
65 GACTAAATCTTCAATATTTAT
* * * * ** * **
25705925 AACAACTTATATGCAACAAATTAGCAAAAATAAATGGTTTAAGTTCATGCATTTACCAACAGCCA
1 AACAATTTATATGCAACAAATTAGC-AAAATCAATGATTCAAGTTCATATATTTACCAAAAATCA
* *
25705990 GACTAAATTTTCAATTTTTAT
65 GACTAAATCTTCAATATTTAT
* * * ** * * *
25706011 AACAACTTATGTGCAACAAATTAGAAAAAATCAACTG-TTCAAGTTCATGCATTCACCAACAACC
1 AACAATTTATATGCAACAAATTAG-CAAAATCAA-TGATTCAAGTTCATATATTTACCAAAAATC
* *
25706075 AGACCAAATTTTCAACT-TTTAT
64 AGACTAAATCTTCAA-TATTTAT
25706097 AA
1 AA
25706099 AGTAGAAGGA
Statistics
Matches: 223, Mismatches: 30, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
86 204 0.91
87 18 0.08
88 1 0.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (85 bp):
AACAATTTATATGCAACAAATTAGCAAAATCAATGATTCAAGTTCATATATTTACCAAAAATCAG
ACTAAATCTTCAATATTTAT
Found at i:25709863 original size:11 final size:11
Alignment explanation
Indices: 25709849--25709930 Score: 93
Period size: 10 Copynumber: 7.7 Consensus size: 11
25709839 AAAATAAAAG
*
25709849 TTTAAAATCTT
1 TTTAAAATCAT
*
25709860 TTTAAAAT-TT
1 TTTAAAATCAT
25709870 TTTAAAA--AT
1 TTTAAAATCAT
25709879 TTTAAAATC-T
1 TTTAAAATCAT
25709889 TTTAAAATTCAT
1 TTTAAAA-TCAT
25709901 TTTAAAATC-T
1 TTTAAAATCAT
25709911 TTTAAAATTCAT
1 TTTAAAA-TCAT
25709923 TTTAAAAT
1 TTTAAAAT
25709931 TTTAAATCAT
Statistics
Matches: 64, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
9 8 0.12
10 25 0.39
11 15 0.23
12 16 0.25
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTAAAATCAT
Found at i:25709905 original size:22 final size:21
Alignment explanation
Indices: 25709849--25709941 Score: 115
Period size: 22 Copynumber: 4.6 Consensus size: 21
25709839 AAAATAAAAG
* *
25709849 TTTAAAATCTTTTTAAAATTT
1 TTTAAAATCATTTTAAAATCT
25709870 TTTAAAA--ATTTTAAAATCT
1 TTTAAAATCATTTTAAAATCT
25709889 TTTAAAATTCATTTTAAAATCT
1 TTTAAAA-TCATTTTAAAATCT
25709911 TTTAAAATTCATTTTAAAA--T
1 TTTAAAA-TCATTTTAAAATCT
25709931 TTT-AAATCATT
1 TTTAAAATCATT
25709942 AAAAATATAA
Statistics
Matches: 67, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
18 5 0.07
19 20 0.30
20 4 0.06
21 7 0.10
22 31 0.46
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTAAAATCATTTTAAAATCT
Found at i:25710468 original size:14 final size:14
Alignment explanation
Indices: 25710448--25710638 Score: 86
Period size: 14 Copynumber: 13.4 Consensus size: 14
25710438 ACTAGTTAAT
*
25710448 CTAAACCCTAAACC
1 CTAAACCATAAACC
* *
25710462 ATAAACC-TAAGCC
1 CTAAACCATAAACC
25710475 CTAAAACCATAAACC
1 CT-AAACCATAAACC
*
25710490 CTTAACACAT-AACC
1 CTAAAC-CATAAACC
*
25710504 TCTAAACCTTAAACC
1 -CTAAACCATAAACC
* * *
25710519 C-CAGCCTTTAAACC
1 CTAAACC-ATAAACC
* *
25710533 ATAAATCATAAACC
1 CTAAACCATAAACC
* * *
25710547 ATAACCCCTAAACC
1 CTAAACCATAAACC
*
25710561 CATAATCCATAAACC
1 C-TAAACCATAAACC
* *
25710576 TTAAA--ATGGTAACAC
1 CTAAACCAT--AAAC-C
* *
25710591 CTAAACCTTAAACT
1 CTAAACCATAAACC
*
25710605 CTAAACCATATACC
1 CTAAACCATAAACC
*
25710619 CTAAACCAAAAACC
1 CTAAACCATAAACC
*
25710633 TTAAAC
1 CTAAAC
25710639 TATAGTGATA
Statistics
Matches: 131, Mismatches: 33, Indels: 26
0.69 0.17 0.14
Matches are distributed among these distances:
12 2 0.02
13 9 0.07
14 79 0.60
15 40 0.31
17 1 0.01
ACGTcount: A:0.46, C:0.32, G:0.02, T:0.20
Consensus pattern (14 bp):
CTAAACCATAAACC
Found at i:25710483 original size:21 final size:20
Alignment explanation
Indices: 25710448--25710489 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
25710438 ACTAGTTAAT
25710448 CTAAACCCTAAACCATAAAC
1 CTAAACCCTAAACCATAAAC
*
25710468 CTAAGCCCTAAAACCATAAAC
1 CTAAACCCT-AAACCATAAAC
25710489 C
1 C
25710490 CTTAACACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.48, C:0.36, G:0.02, T:0.14
Consensus pattern (20 bp):
CTAAACCCTAAACCATAAAC
Found at i:25710537 original size:7 final size:7
Alignment explanation
Indices: 25710527--25710638 Score: 57
Period size: 7 Copynumber: 15.7 Consensus size: 7
25710517 CCCCAGCCTT
25710527 TAAACCA
1 TAAACCA
*
25710534 TAAATCA
1 TAAACCA
25710541 TAAACCA
1 TAAACCA
* *
25710548 TAACCCC
1 TAAACCA
25710555 TAAACCCA
1 TAAA-CCA
*
25710563 TAATCCA
1 TAAACCA
*
25710570 TAAACCT
1 TAAACCA
***
25710577 TAAAATGG
1 T-AAACCA
25710585 TAACACC-
1 TAA-ACCA
*
25710592 TAAACCT
1 TAAACCA
25710599 TAAACTC-
1 TAAAC-CA
25710606 TAAACCA
1 TAAACCA
* *
25710613 TATACCC
1 TAAACCA
25710620 TAAACCA
1 TAAACCA
* *
25710627 AAAACCT
1 TAAACCA
25710634 TAAAC
1 TAAAC
25710639 TATAGTGATA
Statistics
Matches: 78, Mismatches: 21, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
6 4 0.05
7 63 0.81
8 11 0.14
ACGTcount: A:0.48, C:0.29, G:0.02, T:0.21
Consensus pattern (7 bp):
TAAACCA
Found at i:25710580 original size:22 final size:22
Alignment explanation
Indices: 25710449--25710489 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 22
25710439 CTAGTTAATC
25710449 TAAACCCTAAA-CCATAAACC-
1 TAAACCCTAAACCCATAAACCA
* *
25710469 TAAGCCCTAAAACCATAAACC
1 TAAACCCTAAACCCATAAACC
25710490 CTTAACACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.49, C:0.34, G:0.02, T:0.15
Consensus pattern (22 bp):
TAAACCCTAAACCCATAAACCA
Found at i:25710878 original size:41 final size:40
Alignment explanation
Indices: 25710820--25710984 Score: 258
Period size: 41 Copynumber: 4.0 Consensus size: 40
25710810 ATTTTAAATC
25710820 CCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAG
1 CCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAG
* *
25710860 CACTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAAC
1 C-CTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCT-AAAG
*
25710902 CCTGAGCATTAGCGGCGCTTTCTCAAAAATGCCGCTAAAG
1 CCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAG
* *
25710942 CCTTAAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAG
1 CC-TGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAG
25710983 CC
1 CC
25710985 CCGAAAGCTC
Statistics
Matches: 114, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
40 6 0.05
41 104 0.91
42 4 0.04
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (40 bp):
CCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAG
Found at i:25710956 original size:82 final size:82
Alignment explanation
Indices: 25710814--25710981 Score: 284
Period size: 82 Copynumber: 2.0 Consensus size: 82
25710804 TAAATTATTT
* *
25710814 TAAATCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCACTGAGCATTAGCGGCGC
1 TAAAACCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCACTAAGCATTAGCGGCGC
25710879 TTTCTAAAAAACGCCGC
66 TTTCTAAAAAACGCCGC
*
25710896 TAAAACCCTGAGCATTAGCGGCGCTTTCTCAAAAATGCCGCTAAAGC-CTTAAGCATTAGCGGCG
1 TAAAACCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCAC-TAAGCATTAGCGGCG
*
25710960 CTTTCTTAAAAACGCCGC
65 CTTTCTAAAAAACGCCGC
25710978 TAAA
1 TAAA
25710982 GCCCCGAAAG
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
81 1 0.01
82 80 0.99
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (82 bp):
TAAAACCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCACTAAGCATTAGCGGCGC
TTTCTAAAAAACGCCGC
Found at i:25711809 original size:12 final size:13
Alignment explanation
Indices: 25711782--25711832 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
25711772 TTTTATTATT
25711782 AATTAAAATAAAA
1 AATTAAAATAAAA
*
25711795 AATTAAAA-GAAA
1 AATTAAAATAAAA
25711807 AATTACTAAATAAAA
1 AATTA--AAATAAAA
*
25711822 TATTAAGAATA
1 AATTAA-AATA
25711833 TTAATGGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 8 0.26
13 9 0.29
14 7 0.23
15 7 0.23
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (13 bp):
AATTAAAATAAAA
Found at i:25721452 original size:22 final size:22
Alignment explanation
Indices: 25721422--25721465 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
25721412 AGTTTAAAGG
* *
25721422 TTAAGAGGGTTTTAGGTTTTAA
1 TTAAAAGGGTTTTAGGATTTAA
*
25721444 TTAAAAGGGTTTTGGGATTTAA
1 TTAAAAGGGTTTTAGGATTTAA
25721466 ATAGGGTAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (22 bp):
TTAAAAGGGTTTTAGGATTTAA
Found at i:25721495 original size:23 final size:23
Alignment explanation
Indices: 25721464--25721510 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
25721454 TTTGGGATTT
*
25721464 AAATAGGGTAAGTTAAGGGTTTA
1 AAATAGGGTAAATTAAGGGTTTA
* *
25721487 AAATTGGGTAAATTTAGGGTTTA
1 AAATAGGGTAAATTAAGGGTTTA
25721510 A
1 A
25721511 TTAACTGGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (23 bp):
AAATAGGGTAAATTAAGGGTTTA
Found at i:25722458 original size:5 final size:5
Alignment explanation
Indices: 25722448--25722478 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
25722438 TGAGCATTCG
*
25722448 ATCGA ATCGA ATTGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
25722479 AATTTTCGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (5 bp):
ATCGA
Found at i:25723285 original size:30 final size:31
Alignment explanation
Indices: 25723228--25723287 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
25723218 GGAGGTGGGA
*
25723228 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
*
25723259 TGGGAA-GGAGTAAAAATTTT-GAGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAG-GGGAAAA
25723288 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.04
30 19 0.73
31 6 0.23
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:25723460 original size:30 final size:30
Alignment explanation
Indices: 25723401--25723460 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
25723391 GGGGAGGGGA
* * ***
25723401 GTAAAAGTTTTGGGGGGAAAGTGGGAAGGT
1 GTAAAAGTTTTGAGGGAAAAGTAAAAAGGT
25723431 GTAAAAGTTTTGAGGGAAAAGTAAAAAGGT
1 GTAAAAGTTTTGAGGGAAAAGTAAAAAGGT
25723461 TTGGAAGTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (30 bp):
GTAAAAGTTTTGAGGGAAAAGTAAAAAGGT
Found at i:25725136 original size:18 final size:18
Alignment explanation
Indices: 25725093--25725128 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
25725083 TGAATTTAAT
25725093 AAATAAAACATGAAAGAA
1 AAATAAAACATGAAAGAA
25725111 AAATAAAACATGAAAGAA
1 AAATAAAACATGAAAGAA
25725129 TTATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.72, C:0.06, G:0.11, T:0.11
Consensus pattern (18 bp):
AAATAAAACATGAAAGAA
Found at i:25728401 original size:12 final size:12
Alignment explanation
Indices: 25728381--25728416 Score: 63
Period size: 12 Copynumber: 2.9 Consensus size: 12
25728371 ATGGCCATGT
25728381 CTCAGCCCGTGTC
1 CTCA-CCCGTGTC
25728394 CTCACCCGTGTC
1 CTCACCCGTGTC
25728406 CTCACCCGTGT
1 CTCACCCGTGT
25728417 AACTCTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.08, C:0.47, G:0.19, T:0.25
Consensus pattern (12 bp):
CTCACCCGTGTC
Found at i:25730501 original size:21 final size:22
Alignment explanation
Indices: 25730462--25730502 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
25730452 CTTTATTTAA
* *
25730462 TTATTAAATTACCTTAATAACC
1 TTATTAAATTAACTAAATAACC
25730484 TTATT-AATTAACTAAATAA
1 TTATTAAATTAACTAAATAA
25730503 AACATCTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (22 bp):
TTATTAAATTAACTAAATAACC
Found at i:25735474 original size:13 final size:13
Alignment explanation
Indices: 25735456--25735481 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25735446 TAATGAGAAG
25735456 ATATCATTTACCC
1 ATATCATTTACCC
25735469 ATATCATTTACCC
1 ATATCATTTACCC
25735482 TTTTCTTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATCATTTACCC
Found at i:25742444 original size:115 final size:115
Alignment explanation
Indices: 25742300--25742529 Score: 451
Period size: 115 Copynumber: 2.0 Consensus size: 115
25742290 GTTTCCAGAT
25742300 AAATATGGATTAGAAATTGTGAAATGTGGTACCACACAAGTCGAATCTACAGAATTTTCTGAGTG
1 AAATATGGATTAGAAATTGTGAAATGTGGTACCACACAAGTCGAATCTACAGAATTTTCTGAGTG
25742365 TTTAAAGAGAAGTGTTGGAGTAATCTAATGAGTCAAGTTGTAATGCTCCA
66 TTTAAAGAGAAGTGTTGGAGTAATCTAATGAGTCAAGTTGTAATGCTCCA
*
25742415 AAATATGGATTAGAAATTGTGAAATGTGGTGCCACACAAGTCGAATCTACAGAATTTTCTGAGTG
1 AAATATGGATTAGAAATTGTGAAATGTGGTACCACACAAGTCGAATCTACAGAATTTTCTGAGTG
25742480 TTTAAAGAGAAGTGTTGGAGTAATCTAATGAGTCAAGTTGTAATGCTCCA
66 TTTAAAGAGAAGTGTTGGAGTAATCTAATGAGTCAAGTTGTAATGCTCCA
25742530 TACCCAGTTT
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 114 1.00
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.30
Consensus pattern (115 bp):
AAATATGGATTAGAAATTGTGAAATGTGGTACCACACAAGTCGAATCTACAGAATTTTCTGAGTG
TTTAAAGAGAAGTGTTGGAGTAATCTAATGAGTCAAGTTGTAATGCTCCA
Found at i:25748616 original size:10 final size:10
Alignment explanation
Indices: 25748603--25748652 Score: 66
Period size: 11 Copynumber: 4.9 Consensus size: 10
25748593 TTTAATTTCA
25748603 AATTTTTTTG
1 AATTTTTTTG
*
25748613 AATTTTTTTTCA
1 AA-TTTTTTT-G
25748625 AATTTTTTTG
1 AATTTTTTTG
25748635 AATTTTTTT-
1 AATTTTTTTG
25748644 AATTTTTTT
1 AATTTTTTT
25748653 TCACATACCT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
9 9 0.25
10 11 0.31
11 14 0.39
12 2 0.06
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (10 bp):
AATTTTTTTG
Found at i:25748653 original size:10 final size:10
Alignment explanation
Indices: 25748603--25748653 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
25748593 TTTAATTTCA
*
25748603 AATTTTTTTG
1 AATTTTTTTT
25748613 AATTTTTTTT
1 AATTTTTTTT
*
25748623 CAAATTTTTTTG
1 --AATTTTTTTT
25748635 AA-TTTTTTT
1 AATTTTTTTT
25748644 AATTTTTTTT
1 AATTTTTTTT
25748654 CACATACCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 8 0.23
10 18 0.51
12 9 0.26
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.73
Consensus pattern (10 bp):
AATTTTTTTT
Found at i:25748653 original size:22 final size:22
Alignment explanation
Indices: 25748598--25748643 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
25748588 TTTTTTTTAA
25748598 TTTCAAATTTTTTTGAATTTTT
1 TTTCAAATTTTTTTGAATTTTT
25748620 TTTCAAATTTTTTTGAATTTTT
1 TTTCAAATTTTTTTGAATTTTT
25748642 TT
1 TT
25748644 AATTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTCAAATTTTTTTGAATTTTT
Found at i:25748872 original size:44 final size:43
Alignment explanation
Indices: 25748824--25748964 Score: 115
Period size: 44 Copynumber: 3.2 Consensus size: 43
25748814 GTAGGCTAAA
* * * * *
25748824 TTTGGT-CGAATATGGTTTAGGTTTAGTTAGGGAATGGTATTGGT
1 TTTGGTACGAATAGGGTTT-GGTATAGGTA-CGAATGGTATAGGT
*
25748868 TTTGGTACAAAATAGGGTTTGGTATAGGTACGAATGGTATAGGT
1 TTTGGTAC-GAATAGGGTTTGGTATAGGTACGAATGGTATAGGT
** * * *
25748912 TTTGGTACGAA-ATGAATTTTGGTGTAAGTACGAAAGGGTATAGGT
1 TTTGGTACGAATA-G-GGTTTGGTATAGGTACG-AATGGTATAGGT
25748957 TTTGGTAC
1 TTTGGTAC
25748965 AAAAATGGAT
Statistics
Matches: 80, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
42 1 0.01
43 3 0.04
44 39 0.49
45 28 0.35
46 9 0.11
ACGTcount: A:0.26, C:0.04, G:0.32, T:0.38
Consensus pattern (43 bp):
TTTGGTACGAATAGGGTTTGGTATAGGTACGAATGGTATAGGT
Found at i:25748963 original size:45 final size:44
Alignment explanation
Indices: 25748859--25748968 Score: 132
Period size: 44 Copynumber: 2.5 Consensus size: 44
25748849 GTTAGGGAAT
* * * *
25748859 GGTATTGGTTTTGGTACAAAATAGGGTTTGGTATAGGTACGAAT
1 GGTATAGGTTTTGGTACAAAATAGAGTTTGGTATAAGTACGAAG
* * *
25748903 GGTATAGGTTTTGGTACGAAAT-GAATTTTGGTGTAAGTACGAAAG
1 GGTATAGGTTTTGGTACAAAATAG-AGTTTGGTATAAGTACG-AAG
25748948 GGTATAGGTTTTGGTACAAAA
1 GGTATAGGTTTTGGTACAAAA
25748969 ATGGATCAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
43 1 0.02
44 33 0.59
45 22 0.39
ACGTcount: A:0.30, C:0.05, G:0.31, T:0.35
Consensus pattern (44 bp):
GGTATAGGTTTTGGTACAAAATAGAGTTTGGTATAAGTACGAAG
Found at i:25749871 original size:20 final size:20
Alignment explanation
Indices: 25749846--25749890 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
25749836 TAAATTCACA
25749846 TAATTAAAACT-AGACACAAT
1 TAATT-AAACTAAGACACAAT
**
25749866 TAATTAAGTTAAGACACAAT
1 TAATTAAACTAAGACACAAT
25749886 TAATT
1 TAATT
25749891 CGGTTAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (20 bp):
TAATTAAACTAAGACACAAT
Found at i:25765732 original size:6 final size:6
Alignment explanation
Indices: 25765721--25765753 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
25765711 ACAAAAATGT
*
25765721 AATGAC AATGAC AATGAA AATG-C AATGAC AATG
1 AATGAC AATGAC AATGAC AATGAC AATGAC AATG
25765754 TATACTTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.52, C:0.12, G:0.18, T:0.18
Consensus pattern (6 bp):
AATGAC
Found at i:25777780 original size:40 final size:39
Alignment explanation
Indices: 25777677--25777838 Score: 157
Period size: 40 Copynumber: 4.1 Consensus size: 39
25777667 AACCTATGTT
** * * *
25777677 TTATATTA-CCTGAGAATCCACGACAAGGGTTGGATCTCA
1 TTATATTACCCTGAGAATCTGCAACAA-GGCTAGATCTCA
* *
25777716 TTATATT-GCCTGAGAACCTGCAACAAGGCTAGATCTCA
1 TTATATTACCCTGAGAATCTGCAACAAGGCTAGATCTCA
*
25777754 TTATATTACCCTTGAGAATCTGCAACAAGGCTAGATCTCG
1 TTATATTACCC-TGAGAATCTGCAACAAGGCTAGATCTCA
* ** ** *
25777794 TTGTATTACCCCAAGAATCTGCAACAAAAACTAGATCTTA
1 TTATATTACCCTGAGAATCTGCAAC-AAGGCTAGATCTCA
25777834 TTATA
1 TTATA
25777839 ATCTATAATA
Statistics
Matches: 102, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
38 17 0.17
39 35 0.34
40 50 0.49
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (39 bp):
TTATATTACCCTGAGAATCTGCAACAAGGCTAGATCTCA
Found at i:25779172 original size:21 final size:21
Alignment explanation
Indices: 25779132--25779174 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
25779122 TCAAATTCGT
*
25779132 TATACGTTTTAACTTAATTGA
1 TATACGTTTTAACCTAATTGA
* *
25779153 TATACGTTTTGACCTGATTGA
1 TATACGTTTTAACCTAATTGA
25779174 T
1 T
25779175 GGATCTAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.47
Consensus pattern (21 bp):
TATACGTTTTAACCTAATTGA
Found at i:25782432 original size:27 final size:26
Alignment explanation
Indices: 25782402--25782453 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
25782392 AATGAATTCT
25782402 TTTTGAGTTTTTCTTTT-CAAGAGTTTC
1 TTTTGAG--TTTCTTTTACAAGAGTTTC
25782429 TTTTGAGTTTCTTTTACAAGAGTTT
1 TTTTGAGTTTCTTTTACAAGAGTTT
25782454 TAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 8 0.33
26 9 0.38
27 7 0.29
ACGTcount: A:0.17, C:0.10, G:0.15, T:0.58
Consensus pattern (26 bp):
TTTTGAGTTTCTTTTACAAGAGTTTC
Found at i:25782453 original size:15 final size:14
Alignment explanation
Indices: 25782411--25782453 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 14
25782401 TTTTTGAGTT
25782411 TTTCTTTTCAAGAG
1 TTTCTTTTCAAGAG
25782425 TTTCTTTT---GAG
1 TTTCTTTTCAAGAG
25782436 TTTCTTTTACAAGAG
1 TTTCTTTT-CAAGAG
25782451 TTT
1 TTT
25782454 TAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
11 11 0.44
14 8 0.32
15 6 0.24
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.56
Consensus pattern (14 bp):
TTTCTTTTCAAGAG
Found at i:25786117 original size:27 final size:27
Alignment explanation
Indices: 25786082--25786163 Score: 105
Period size: 27 Copynumber: 3.1 Consensus size: 27
25786072 GTTATGGTAT
* *
25786082 CAAA-GATAGTTCGACGAGATGTTAAA
1 CAAAGGATAGTTCGATGGGATGTTAAA
25786108 CAAAGGATAGTTCGATGGGATGTTAAA
1 CAAAGGATAGTTCGATGGGATGTTAAA
**
25786135 CACGGGATAG-TCTGATGGGATGTTAAA
1 CAAAGGATAGTTC-GATGGGATGTTAAA
25786162 CA
1 CA
25786164 CGAGGTAGTC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 6 0.12
27 44 0.88
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.24
Consensus pattern (27 bp):
CAAAGGATAGTTCGATGGGATGTTAAA
Found at i:25786164 original size:27 final size:28
Alignment explanation
Indices: 25786086--25786173 Score: 103
Period size: 27 Copynumber: 3.2 Consensus size: 28
25786076 TGGTATCAAA
* * **
25786086 GATAGT-TCGACGAGATGTTAAACAAAG
1 GATAGTCTCGATGGGATGTTAAACACGG
25786113 GATAGT-TCGATGGGATGTTAAACACGG
1 GATAGTCTCGATGGGATGTTAAACACGG
25786140 GATAGTCT-GATGGGATGTTAAACACGAG
1 GATAGTCTCGATGGGATGTTAAACACG-G
25786168 G-TAGTC
1 GATAGTC
25786174 CACTAGGACG
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
27 52 0.95
28 3 0.05
ACGTcount: A:0.33, C:0.11, G:0.31, T:0.25
Consensus pattern (28 bp):
GATAGTCTCGATGGGATGTTAAACACGG
Found at i:25798182 original size:69 final size:69
Alignment explanation
Indices: 25798100--25798252 Score: 270
Period size: 69 Copynumber: 2.2 Consensus size: 69
25798090 CAGGACTAAA
* *
25798100 ACCATAGTTGGACTATGGCATCCTAGTACTCTACCAAGAAAATAAACACGGTGAAACATAAGGTG
1 ACCATAGTTGGACTATGCCATCCTAGTACTCTACCAAGAAAATAAACACGATGAAACATAAGGTG
25798165 TAAG
66 TAAG
*
25798169 ACCATAGTTGGACTATGCCATCCTAGTACTCTACCAAGAAAATAAACACGATGAGACATAAGGTG
1 ACCATAGTTGGACTATGCCATCCTAGTACTCTACCAAGAAAATAAACACGATGAAACATAAGGTG
25798234 TAAG
66 TAAG
*
25798238 ACCATAGCTGGACTA
1 ACCATAGTTGGACTA
25798253 AAGCCACTGC
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 80 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (69 bp):
ACCATAGTTGGACTATGCCATCCTAGTACTCTACCAAGAAAATAAACACGATGAAACATAAGGTG
TAAG
Found at i:25798423 original size:27 final size:27
Alignment explanation
Indices: 25798392--25798444 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
25798382 ACGGCAACAA
*
25798392 AGATAGTCTGACGGGACATTAAACATG
1 AGATAGTCTGACGGGACATCAAACATG
*
25798419 AGATAGTTTGACGGGACATCAAACAT
1 AGATAGTCTGACGGGACATCAAACAT
25798445 AGGGTTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (27 bp):
AGATAGTCTGACGGGACATCAAACATG
Found at i:25800916 original size:42 final size:43
Alignment explanation
Indices: 25800830--25800951 Score: 160
Period size: 42 Copynumber: 2.9 Consensus size: 43
25800820 GGCTCGTACA
* * *
25800830 ATGCCAACGTCCCAGACGTGGTATTACATGTAATCACAGATCG
1 ATGCCAACGTCCCAGACGTGGTATTACATGAAAACACAAATCG
*
25800873 ATGCC-ACTGTCCCAGACAG-GGT-TTACACGAAAACACAAATCG
1 ATGCCAAC-GTCCCAGAC-GTGGTATTACATGAAAACACAAATCG
*
25800915 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACAC
1 ATGCCAACGTCCCAGACGTGGTATTACATGAAAACAC
25800952 TTTTCGAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
41 1 0.01
42 35 0.51
43 32 0.46
44 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.20
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTATTACATGAAAACACAAATCG
Found at i:25802908 original size:17 final size:18
Alignment explanation
Indices: 25802866--25802908 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
25802856 AACACAAGAT
*
25802866 TTCGCAAGGTAACTATAG
1 TTCGCAAGATAACTATAG
* *
25802884 TTCACAAGATACCTA-AG
1 TTCGCAAGATAACTATAG
25802901 TTCGCAAG
1 TTCGCAAG
25802909 CTTTAGAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (18 bp):
TTCGCAAGATAACTATAG
Found at i:25804824 original size:27 final size:27
Alignment explanation
Indices: 25804794--25804872 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
25804784 CCCCGGTTCA
* *
25804794 CCAAATAGAATGGTGAACCCCAGCTAG
1 CCAAATAGACTGGCGAACCCCAGCTAG
* * * *
25804821 CCAAATAGACTAGCAAACCCTAGCTTG
1 CCAAATAGACTGGCGAACCCCAGCTAG
25804848 CCAAATAGACTGGCGAACCCCAGCT
1 CCAAATAGACTGGCGAACCCCAGCT
25804873 CATCAGCACG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.15
Consensus pattern (27 bp):
CCAAATAGACTGGCGAACCCCAGCTAG
Done.