Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 22 of 182
Found at i:9015357 original size:2 final size:2
Alignment explanation
Indices: 9015352--9015411 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
9015342 ATGCTTTTTG
9015352 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
9015394 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
9015412 TTGTATTATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9022783 original size:23 final size:23
Alignment explanation
Indices: 9022756--9022800 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9022746 TATAACTATT
*
9022756 AATATAATATAAATTATAATAAA
1 AATATAACATAAATTATAATAAA
* *
9022779 AATATAACATATATTATTATAA
1 AATATAACATAAATTATAATAA
9022801 TGTTTAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AATATAACATAAATTATAATAAA
Found at i:9030312 original size:42 final size:42
Alignment explanation
Indices: 9030253--9030336 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
9030243 CAAATATTTT
* *
9030253 TAAACTCAAATATAATTTCATTCTTAAAAAACACTCGTAAAC
1 TAAACTCAAATATAATTTCATTCCTAAAAAACACTCATAAAC
* * *
9030295 TAAACTCAAATATAATTTTATTCCTAAATAGCACTCATAAAC
1 TAAACTCAAATATAATTTCATTCCTAAAAAACACTCATAAAC
9030337 AACTCATTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.32
Consensus pattern (42 bp):
TAAACTCAAATATAATTTCATTCCTAAAAAACACTCATAAAC
Found at i:9039404 original size:33 final size:34
Alignment explanation
Indices: 9039328--9039404 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 34
9039318 CCTATTTACT
* * **
9039328 TAAAATAAATAATTTTAATCAAAATGAAATTAGA
1 TAAAATAAACAAATTTAATCAAAACAAAATTAGA
*
9039362 -AAAAT-AACAAATTTAATGAAAACAAAATTA-A
1 TAAAATAAACAAATTTAATCAAAACAAAATTAGA
9039393 TAAAATAAACAA
1 TAAAATAAACAA
9039405 CTTTGACTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
31 1 0.03
32 25 0.69
33 10 0.28
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.26
Consensus pattern (34 bp):
TAAAATAAACAAATTTAATCAAAACAAAATTAGA
Found at i:9043678 original size:90 final size:90
Alignment explanation
Indices: 9043485--9043656 Score: 226
Period size: 90 Copynumber: 1.9 Consensus size: 90
9043475 TTCAAACTTT
* * * * *
9043485 AAAAAAAAACAATTAAATG-CC-TA-TTTTTTTTATATTCAATTGGATATTTGAATTATCAAAAT
1 AAAAAAAAACAATTAAGTGCCCATACATTTTTTTACATTCAATTGAATACTTGAATTATCAAAAT
** * *
9043547 GTGTCAAAAATATCCTCAAATTAAA
66 GCATCAAAAAGACCCTCAAATTAAA
9043572 AAAAAAAAACAATTAAGTGCCCATACATTTTTTTACATTCAATTGAATACTTGAACTT-TCAAAA
1 AAAAAAAAACAATTAAGTGCCCATACATTTTTTTACATTCAATTGAATACTTGAA-TTATCAAAA
9043636 TGCATCAAAAAGACCCTCAAA
65 TGCATCAAAAAGACCCTCAAA
9043657 CTTTTCAATA
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
87 18 0.25
88 2 0.03
89 2 0.03
90 48 0.67
91 2 0.03
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.33
Consensus pattern (90 bp):
AAAAAAAAACAATTAAGTGCCCATACATTTTTTTACATTCAATTGAATACTTGAATTATCAAAAT
GCATCAAAAAGACCCTCAAATTAAA
Found at i:9043804 original size:8 final size:9
Alignment explanation
Indices: 9043776--9043812 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
9043766 CACGTGGCAA
*
9043776 AAAAATGAT
1 AAAAATTAT
9043785 AAAAA--AT
1 AAAAATTAT
9043792 AAAAATTAT
1 AAAAATTAT
9043801 AAAAATTAT
1 AAAAATTAT
9043810 AAA
1 AAA
9043813 GCTATTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 7 0.27
9 19 0.73
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (9 bp):
AAAAATTAT
Found at i:9043892 original size:23 final size:22
Alignment explanation
Indices: 9043839--9043895 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
9043829 TAAAAATTAG
*
9043839 AAAAAA-ATATAAAATTCATAA
1 AAAAAATATATAAAATACATAA
9043860 AAAAAATATATAGAAATACA-AA
1 AAAAAATATATA-AAATACATAA
9043882 AAAAAAT-TATAAAA
1 AAAAAATATATAAAA
9043896 CTTTATAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 3 0.09
21 10 0.30
22 14 0.42
23 6 0.18
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAAAATATATAAAATACATAA
Found at i:9043954 original size:11 final size:10
Alignment explanation
Indices: 9043882--9043968 Score: 60
Period size: 10 Copynumber: 9.0 Consensus size: 10
9043872 GAAATACAAA
9043882 AAAAAATTAT
1 AAAAAATTAT
*
9043892 -AAAACTT-T
1 AAAAAATTAT
* * *
9043900 ATAAAGTTGT
1 AAAAAATTAT
9043910 AAGAAAATTAT
1 AA-AAAATTAT
*
9043921 AGAAAA-TAT
1 AAAAAATTAT
9043930 AAAGAAA-TAT
1 AAA-AAATTAT
9043940 --AAAATTCAT
1 AAAAAATT-AT
9043949 AAAAAATTAT
1 AAAAAATTAT
9043959 AAAAAATTAT
1 AAAAAATTAT
9043969 TGTATTAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
7 3 0.05
8 3 0.05
9 18 0.30
10 24 0.39
11 13 0.21
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:9044010 original size:18 final size:18
Alignment explanation
Indices: 9043987--9044023 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
9043977 AAGAAGCATT
9043987 ATAAAAATTATTGTACTA
1 ATAAAAATTATTGTACTA
9044005 ATAAAAATTATTGTACTA
1 ATAAAAATTATTGTACTA
9044023 A
1 A
9044024 AAGAAGCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (18 bp):
ATAAAAATTATTGTACTA
Found at i:9045699 original size:17 final size:18
Alignment explanation
Indices: 9045673--9045711 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
9045663 TTATTTGATG
9045673 AAAAAATATTGA-TTTTT
1 AAAAAATATTGATTTTTT
* *
9045690 AAAAAGTATTTATTTTTT
1 AAAAAATATTGATTTTTT
9045708 AAAA
1 AAAA
9045712 TTTTAATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
AAAAAATATTGATTTTTT
Found at i:9046819 original size:15 final size:17
Alignment explanation
Indices: 9046782--9046820 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
9046772 TTAGTGAAAT
*
9046782 TGAATAAAAAATATTAT
1 TGAATAAAAAATATTAA
9046799 TGAATAAAAAAT-TTAA
1 TGAATAAAAAATATTAA
9046815 T-AATAA
1 TGAATAA
9046821 TTATTCAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.24
16 4 0.19
17 12 0.57
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
TGAATAAAAAATATTAA
Found at i:9047039 original size:23 final size:23
Alignment explanation
Indices: 9046995--9047039 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
9046985 TAGGTTCATT
* *
9046995 TTTATTTTTATACTTTATTTTGG
1 TTTATTTTAATACTTTAATTTGG
9047018 TTTATTTTAATA-TTTGAATTTG
1 TTTATTTTAATACTTT-AATTTG
9047040 TCATTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.22, C:0.02, G:0.09, T:0.67
Consensus pattern (23 bp):
TTTATTTTAATACTTTAATTTGG
Found at i:9050542 original size:3 final size:3
Alignment explanation
Indices: 9050534--9050558 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9050524 CTAGACGGCA
9050534 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
9050559 AGAGGAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:9058580 original size:23 final size:24
Alignment explanation
Indices: 9058554--9058606 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
9058544 TTAACTTAAT
*
9058554 CGAACAT-TAAACGAATATGTTCA
1 CGAACATATAAACGAACATGTTCA
**
9058577 CGAACATATAATTGAACATGTTCA
1 CGAACATATAAACGAACATGTTCA
9058601 CGAACA
1 CGAACA
9058607 ATACTAATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (24 bp):
CGAACATATAAACGAACATGTTCA
Found at i:9059123 original size:12 final size:12
Alignment explanation
Indices: 9059106--9059139 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9059096 ACAGTAAAAC
*
9059106 AACAAAAATAGT
1 AACAAAAATAGA
*
9059118 AACAAAAACAGA
1 AACAAAAATAGA
9059130 AACAAAAATA
1 AACAAAAATA
9059140 ACATCAAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.74, C:0.12, G:0.06, T:0.09
Consensus pattern (12 bp):
AACAAAAATAGA
Found at i:9059164 original size:29 final size:27
Alignment explanation
Indices: 9059131--9059195 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
9059121 AAAAACAGAA
9059131 ACAAAAATAACATCAAAACAGTAAAAAA-
1 ACAAAAATAAC--CAAAACAGTAAAAAAC
9059159 ACCAAAACAATAACCAAAACAGTAAAAAAC
1 A-C-AAA-AATAACCAAAACAGTAAAAAAC
9059189 ACAAAAA
1 ACAAAAA
9059196 CAGTAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
27 2 0.06
28 4 0.12
29 17 0.52
30 4 0.12
31 6 0.18
ACGTcount: A:0.71, C:0.18, G:0.03, T:0.08
Consensus pattern (27 bp):
ACAAAAATAACCAAAACAGTAAAAAAC
Found at i:9059206 original size:29 final size:29
Alignment explanation
Indices: 9059106--9059209 Score: 91
Period size: 30 Copynumber: 3.3 Consensus size: 29
9059096 ACAGTAAAAC
* *
9059106 AACAAAAATAGTAACAAAAACAGAAACAAAAAT
1 AACAAAAACAGTAA-AAAAAC--AAA-AACAAT
*
9059139 AACATCAAAACAGTAAAAAAACCAAAACAAT
1 AACA--AAAACAGTAAAAAAACAAAAACAAT
* *
9059170 AACCAAAACAGTAAAAAACACAAAAACAGT
1 AACAAAAACAGTAAAAAA-ACAAAAACAAT
*
9059200 AAAAAAAACA
1 AACAAAAACA
9059210 ATACCAAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
29 14 0.23
30 17 0.28
31 8 0.13
32 2 0.03
33 4 0.07
34 6 0.10
35 9 0.15
ACGTcount: A:0.71, C:0.16, G:0.05, T:0.08
Consensus pattern (29 bp):
AACAAAAACAGTAAAAAAACAAAAACAAT
Found at i:9059228 original size:42 final size:42
Alignment explanation
Indices: 9059162--9059249 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
9059152 TAAAAAAACC
*
9059162 AAAACAATAACCAAAACAGTAAAAAAC-ACAAAAACAGTAAAA
1 AAAACAATAACCAAAAAAGTAAAAAACAAC-AAAACAGTAAAA
*
9059204 AAAACAAT-ACCAAAAAAGTAAAAAACAATCAAAATAGTAAAA
1 AAAACAATAACCAAAAAAGTAAAAAACAA-CAAAACAGTAAAA
9059246 AAAA
1 AAAA
9059250 ACACCAAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 17 0.40
42 24 0.57
43 1 0.02
ACGTcount: A:0.73, C:0.14, G:0.05, T:0.09
Consensus pattern (42 bp):
AAAACAATAACCAAAAAAGTAAAAAACAACAAAACAGTAAAA
Found at i:9063981 original size:17 final size:17
Alignment explanation
Indices: 9063935--9063983 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
9063925 TTTAAATTAG
* *
9063935 ATTTATTTTGAATTTAA
1 ATTTATTATAAATTTAA
*
9063952 ATTTA-CATAAAATTTAA
1 ATTTATTAT-AAATTTAA
9063969 ATTTATTATAAATTT
1 ATTTATTATAAATTT
9063984 GCATTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 1 0.04
17 23 0.88
18 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTATTATAAATTTAA
Found at i:9064755 original size:19 final size:18
Alignment explanation
Indices: 9064733--9064781 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
9064723 TAAATATTTT
9064733 TAATAATAATAAACATTAA
1 TAATAATAATAAA-ATTAA
**
9064752 TAATAATGTTTAAAATTAA
1 TAATAAT-AATAAAATTAA
9064771 TAATAATAATA
1 TAATAATAATA
9064782 TAAAAAAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 2 0.08
19 19 0.76
20 4 0.16
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
TAATAATAATAAAATTAA
Found at i:9064763 original size:29 final size:29
Alignment explanation
Indices: 9064706--9064773 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
9064696 GATGACCGTT
** *
9064706 ATAATAATAAATGTTAATAAATATTTTTA
1 ATAATAATAAACATTAATAAATATGTTTA
9064735 ATAATAATAAACATTAAT-AATAATGTTTA
1 ATAATAATAAACATTAATAAAT-ATGTTTA
9064764 A-AATTAATAA
1 ATAA-TAATAA
9064774 TAATAATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.15
29 29 0.85
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (29 bp):
ATAATAATAAACATTAATAAATATGTTTA
Found at i:9065564 original size:30 final size:29
Alignment explanation
Indices: 9065473--9065565 Score: 98
Period size: 29 Copynumber: 3.1 Consensus size: 29
9065463 TAAACTGTTC
* * * *
9065473 AAAAATTATATTTGTGATCCCAAAACTTCA
1 AAAAATTACATTT-TGACCCCCAAACTTCT
*
9065503 AAAAATTACATTTTGACCCCGAAACTTCT
1 AAAAATTACATTTTGACCCCCAAACTTCT
*
9065532 AAAAATTACCGTTTT-ACCCCCAAACTTCCT
1 AAAAATTA-CATTTTGACCCCCAAACTT-CT
9065562 AAAA
1 AAAA
9065566 TTCTATTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
29 32 0.58
30 23 0.42
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (29 bp):
AAAAATTACATTTTGACCCCCAAACTTCT
Found at i:9065621 original size:29 final size:28
Alignment explanation
Indices: 9065495--9065632 Score: 95
Period size: 29 Copynumber: 4.8 Consensus size: 28
9065485 TGTGATCCCA
* *
9065495 AAACTTCAAAAAATTAC-ATTTTGACCCCG
1 AAACTTC-CAAAATTACTATTTT-ACCCCC
* **
9065524 AAACTTCTAAAAATTACCGTTTTACCCCC
1 AAACTTC-CAAAATTACTATTTTACCCCC
* *
9065553 AAACTTCCTAAAATT-CTATTTTAACCTC
1 AAACTTCC-AAAATTACTATTTTACCCCC
* *
9065581 -GATTTCACCCAAAATTACTATTTTACCCCC
1 AAACTT---CCAAAATTACTATTTTACCCCC
9065611 AAACTTTCCAAAATT-CTATTTT
1 AAAC-TTCCAAAATTACTATTTT
9065633 TAACCCTAAA
Statistics
Matches: 87, Mismatches: 14, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
27 3 0.03
28 16 0.18
29 48 0.55
30 17 0.20
31 1 0.01
32 2 0.02
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.35
Consensus pattern (28 bp):
AAACTTCCAAAATTACTATTTTACCCCC
Found at i:9065634 original size:29 final size:28
Alignment explanation
Indices: 9065543--9065632 Score: 87
Period size: 28 Copynumber: 3.1 Consensus size: 28
9065533 AAAATTACCG
9065543 TTTTACCCCCAAAC-TTCCTAAAATTCTA
1 TTTTACCCCCAAACTTTCC-AAAATTCTA
* * *
9065571 TTTTAACCTC-GA-TTTCACCCAAAATTACTA
1 TTTTACCCCCAAACTTT---CCAAAATT-CTA
9065601 TTTTACCCCCAAACTTTCCAAAATTCTA
1 TTTTACCCCCAAACTTTCCAAAATTCTA
9065629 TTTT
1 TTTT
9065633 TAACCCTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
27 3 0.06
28 15 0.31
29 14 0.29
30 13 0.27
31 1 0.02
32 3 0.06
ACGTcount: A:0.31, C:0.29, G:0.01, T:0.39
Consensus pattern (28 bp):
TTTTACCCCCAAACTTTCCAAAATTCTA
Found at i:9065647 original size:29 final size:29
Alignment explanation
Indices: 9065504--9065662 Score: 91
Period size: 29 Copynumber: 5.5 Consensus size: 29
9065494 AAAACTTCAA
* *
9065504 AAAATTAC-ATTTTGACCCCGAAAC-TTCTA
1 AAAATTACTATTTTAACCCC-AAACTTTC-C
** *
9065533 AAAATTACCGTTTTACCCCCAAAC-TTCC
1 AAAATTACTATTTTAACCCCAAACTTTCC
* *
9065561 TAAAATT-CTATTTTAACCTC-GA-TTTCACCC
1 -AAAATTACTATTTTAACCCCAAACTTT---CC
*
9065591 AAAATTACTATTTTACCCCCAAACTTTCC
1 AAAATTACTATTTTAACCCCAAACTTTCC
* *
9065620 AAAATT-CTATTTTTAACCCTAAATTTTCTC
1 AAAATTACTA-TTTTAACCCCAAACTTTC-C
*
9065650 GAAATTAC-ATTTT
1 AAAATTACTATTTT
9065663 TGCCATCGAG
Statistics
Matches: 102, Mismatches: 16, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
27 3 0.03
28 12 0.12
29 54 0.53
30 28 0.27
31 2 0.02
32 3 0.03
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAATTACTATTTTAACCCCAAACTTTCC
Found at i:9065662 original size:58 final size:57
Alignment explanation
Indices: 9065533--9065662 Score: 147
Period size: 58 Copynumber: 2.2 Consensus size: 57
9065523 GAAACTTCTA
* **
9065533 AAAATTACCGTTTTACCCCCAAACTTCCTAAAATTCTATTTTAACCTCGATTTCACCC
1 AAAATTA-CATTTTACCCCCAAACTTCCTAAAATTCTATTTTAACCTAAATTTCACCC
* *
9065591 AAAATTACTATTTTACCCCCAAACTTTCC-AAAATTCTATTTTTAACCCTAAATTT-TCTC
1 AAAATTAC-ATTTTACCCCCAAAC-TTCCTAAAATTCTA-TTTTAA-CCTAAATTTCACCC
*
9065650 GAAATTACATTTT
1 AAAATTACATTTT
9065663 TGCCATCGAG
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
57 1 0.02
58 35 0.56
59 19 0.31
60 7 0.11
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.38
Consensus pattern (57 bp):
AAAATTACATTTTACCCCCAAACTTCCTAAAATTCTATTTTAACCTAAATTTCACCC
Found at i:9070340 original size:22 final size:24
Alignment explanation
Indices: 9070290--9070340 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 24
9070280 AAAATAACTT
9070290 TTAAAATATACTTATTTTGATACA
1 TTAAAATATACTTATTTTGATACA
* *
9070314 -T-AAATA-A-TTATTTTGTTATA
1 TTAAAATATACTTATTTTGATACA
9070334 TTAAAAT
1 TTAAAAT
9070341 TAAAAACTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
20 11 0.48
21 2 0.09
22 9 0.39
23 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
TTAAAATATACTTATTTTGATACA
Found at i:9080039 original size:14 final size:14
Alignment explanation
Indices: 9080020--9080059 Score: 50
Period size: 12 Copynumber: 3.1 Consensus size: 14
9080010 TATGAAAAAT
9080020 ATTATATTATATTA
1 ATTATATTATATTA
*
9080034 ATTATA-TATATTT
1 ATTATATTATATTA
9080047 A-TAT-TTATATTA
1 ATTATATTATATTA
9080059 A
1 A
9080060 ATCACTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 10 0.43
13 7 0.30
14 6 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTATATTATATTA
Found at i:9080247 original size:40 final size:38
Alignment explanation
Indices: 9080156--9080236 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
9080146 AAAAAATATA
* * *
9080156 TTTAATACAATAAAATATTTATTATATTTATTTGTGTT
1 TTTAATATAATAAAACATTTATTATATTTATTAGTGTT
9080194 TTTAATATAATAAAACATTTATTATATTTATGATAGTGTT
1 TTTAATATAATAAAACATTTATTATATTTAT--TAGTGTT
9080234 TTT
1 TTT
9080237 TTTAATATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 29 0.76
40 9 0.24
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.54
Consensus pattern (38 bp):
TTTAATATAATAAAACATTTATTATATTTATTAGTGTT
Found at i:9081046 original size:44 final size:44
Alignment explanation
Indices: 9080968--9081095 Score: 141
Period size: 44 Copynumber: 2.8 Consensus size: 44
9080958 TTTTTTACTG
* *
9080968 TTTTGGTTGTTATTTTCGTGTTGTTTTTAGTATTATTTTTGTTGCTA
1 TTTTGGTTGTTATTTAC--GTTGTTTTGA-TATTATTTTTGTTGCTA
* *
9081015 TTTTTGTTGTT-TTTAACGTTGTTTTGATATTATTTTTGTTGCTG
1 TTTTGGTTGTTATTT-ACGTTGTTTTGATATTATTTTTGTTGCTA
** * *
9081059 TTTTGGTTGTTATTTTTGTTGTTTGGATGTTATTTTT
1 TTTTGGTTGTTATTTACGTTGTTTTGATATTATTTTT
9081096 ATGCATTTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
44 44 0.63
45 12 0.17
46 3 0.04
47 11 0.16
ACGTcount: A:0.10, C:0.03, G:0.20, T:0.67
Consensus pattern (44 bp):
TTTTGGTTGTTATTTACGTTGTTTTGATATTATTTTTGTTGCTA
Found at i:9081055 original size:20 final size:20
Alignment explanation
Indices: 9081032--9081095 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
9081022 TGTTTTTAAC
*
9081032 GTTGTTTTGATATTATTTTT
1 GTTGTTTTGATGTTATTTTT
*
9081052 GTTGCTGTTTTGGTTGTTATTTTT
1 G-T--TGTTTT-GATGTTATTTTT
*
9081076 GTTGTTTGGATGTTATTTTT
1 GTTGTTTTGATGTTATTTTT
9081096 ATGCATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
20 12 0.33
21 6 0.17
23 7 0.19
24 11 0.31
ACGTcount: A:0.09, C:0.02, G:0.22, T:0.67
Consensus pattern (20 bp):
GTTGTTTTGATGTTATTTTT
Found at i:9081060 original size:23 final size:24
Alignment explanation
Indices: 9081034--9081079 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
9081024 TTTTTAACGT
9081034 TGTTTT-GATATTATTTTTGTTGC
1 TGTTTTGGATATTATTTTTGTTGC
* *
9081057 TGTTTTGGTTGTTATTTTTGTTG
1 TGTTTTGGATATTATTTTTGTTG
9081080 TTTGGATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.09, C:0.02, G:0.22, T:0.67
Consensus pattern (24 bp):
TGTTTTGGATATTATTTTTGTTGC
Found at i:9081080 original size:12 final size:12
Alignment explanation
Indices: 9080968--9081081 Score: 53
Period size: 12 Copynumber: 9.9 Consensus size: 12
9080958 TTTTTTACTG
*
9080968 TTTTGGTTGTTA
1 TTTTTGTTGTTA
* *
9080980 TTTTCG-TGTTG
1 TTTTTGTTGTTA
*
9080991 TTTTTAG-TATTA
1 TTTTT-GTTGTTA
*
9081003 TTTTTGTTGCTA
1 TTTTTGTTGTTA
9081015 TTTTTGTTGTT-
1 TTTTTGTTGTTA
**
9081026 TTTAACGTTG---
1 TTT-TTGTTGTTA
* *
9081036 -TTTTGATATTA
1 TTTTTGTTGTTA
* *
9081047 TTTTTGTTGCTG
1 TTTTTGTTGTTA
*
9081059 TTTTGGTTGTTA
1 TTTTTGTTGTTA
9081071 TTTTTGTTGTT
1 TTTTTGTTGTT
9081082 TGGATGTTAT
Statistics
Matches: 73, Mismatches: 22, Indels: 14
0.67 0.20 0.13
Matches are distributed among these distances:
8 2 0.03
9 2 0.03
11 12 0.16
12 57 0.78
ACGTcount: A:0.10, C:0.04, G:0.19, T:0.68
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:9088228 original size:2 final size:2
Alignment explanation
Indices: 9088221--9088260 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9088211 AAACACCTTA
9088221 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
9088261 GGTTTATGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:9097461 original size:2 final size:2
Alignment explanation
Indices: 9097454--9097492 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
9097444 AATAGCCACT
*
9097454 GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
9097493 TGATTGGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9097607 original size:11 final size:11
Alignment explanation
Indices: 9097591--9097615 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9097581 ATCCATATCT
9097591 TAACTTATTTA
1 TAACTTATTTA
9097602 TAACTTATTTA
1 TAACTTATTTA
9097613 TAA
1 TAA
9097616 GGGCAGGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
TAACTTATTTA
Found at i:9111779 original size:16 final size:16
Alignment explanation
Indices: 9111748--9111781 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9111738 TCATTAACCT
**
9111748 TTATTTTTTTTTCAAA
1 TTATTTTTTTAACAAA
9111764 TTATTTTTTTAACAAA
1 TTATTTTTTTAACAAA
9111780 TT
1 TT
9111782 TGATAAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTTTTTTAACAAA
Found at i:9124199 original size:18 final size:17
Alignment explanation
Indices: 9124166--9124198 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9124156 TTCAGTTCTT
9124166 ATTTTTTTTATGTTTTG
1 ATTTTTTTTATGTTTTG
9124183 ATTTTCTTTTA-GTTTT
1 ATTTT-TTTTATGTTTT
9124199 TCTCTGTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.76
Consensus pattern (17 bp):
ATTTTTTTTATGTTTTG
Found at i:9128713 original size:2 final size:2
Alignment explanation
Indices: 9128706--9128748 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
9128696 AGGCTACTTT
9128706 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9128748 T
1 T
9128749 TTGATTTGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9133935 original size:16 final size:17
Alignment explanation
Indices: 9133911--9133948 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
9133901 TTTAGAAATT
* *
9133911 TAATAGTAAATATTA-A
1 TAATTGTAAAAATTATA
9133927 TAATTGTAAAAATTATA
1 TAATTGTAAAAATTATA
9133944 TAATT
1 TAATT
9133949 AATAAACAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
TAATTGTAAAAATTATA
Found at i:9135037 original size:34 final size:32
Alignment explanation
Indices: 9134954--9135055 Score: 111
Period size: 30 Copynumber: 3.1 Consensus size: 32
9134944 ATTAATTTTT
*
9134954 TTTAAATATGATTTATCATTATA-TT-AAATA
1 TTTAAATATGATTTATTATTATATTTAAAATA
*
9134984 TTTAAATATAATTTATTATTATATTTAAAAT-
1 TTTAAATATGATTTATTATTATATTTAAAATA
*
9135015 TTTAAAATATTTGATTTATTATTAAATTTACAAATAA
1 TTT-AAATA--TGATTTATTATTATATTTA-AAAT-A
9135052 TTTA
1 TTTA
9135056 TTAATTATTG
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
30 21 0.35
31 5 0.08
32 9 0.15
34 17 0.28
35 4 0.07
36 1 0.02
37 3 0.05
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (32 bp):
TTTAAATATGATTTATTATTATATTTAAAATA
Found at i:9135131 original size:17 final size:17
Alignment explanation
Indices: 9135109--9135153 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
9135099 TTATATTAAA
9135109 AAATTTAAATATTTTTT
1 AAATTTAAATATTTTTT
**
9135126 AAATTTATTTA-TTTTT
1 AAATTTAAATATTTTTT
*
9135142 AAATTTTAATAT
1 AAATTTAAATAT
9135154 AAAATCTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATTTAAATATTTTTT
Found at i:9144433 original size:19 final size:20
Alignment explanation
Indices: 9144406--9144443 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
9144396 TGTTATTTTT
* *
9144406 AAATGTACTTTTATATTCTA
1 AAATGTACTATTACATTCTA
9144426 AAAT-TACTATTACATTCT
1 AAATGTACTATTACATTCT
9144444 TAATAAAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (20 bp):
AAATGTACTATTACATTCTA
Found at i:9169075 original size:3 final size:3
Alignment explanation
Indices: 9169069--9169098 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
9169059 AATAATAATA
9169069 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9169099 CTTAAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:9169431 original size:19 final size:20
Alignment explanation
Indices: 9169395--9169432 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9169385 ACTTAATAAT
* *
9169395 ATTTTTAATTAATTATTTAC
1 ATTTTAAATTAATAATTTAC
9169415 ATTTTAAATTAA-AATTTA
1 ATTTTAAATTAATAATTTA
9169433 TTGAAGATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTTAAATTAATAATTTAC
Found at i:9172718 original size:32 final size:29
Alignment explanation
Indices: 9172669--9172727 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 29
9172659 TTTTATAATT
9172669 AAATTTTTTATTATTTTTAAGAGTTAAAATA
1 AAATTTTTTATTATTTTTAA-A-TTAAAATA
*
9172700 AAATTTTATTTTTATTTTTAAATTAAAA
1 AAATTTT-TTATTATTTTTAAATTAAAA
9172728 ATTTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 6 0.23
31 8 0.31
32 12 0.46
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (29 bp):
AAATTTTTTATTATTTTTAAATTAAAATA
Found at i:9173007 original size:17 final size:17
Alignment explanation
Indices: 9172987--9173024 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
9172977 ATAAATTTAT
9172987 TAAATA-TTAAAATAAAA
1 TAAATATTTAAAA-AAAA
9173004 TAAATATTTAAAAAAAA
1 TAAATATTTAAAAAAAA
9173021 TAAA
1 TAAA
9173025 AATAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAATATTTAAAAAAAA
Found at i:9175255 original size:9 final size:9
Alignment explanation
Indices: 9175219--9175302 Score: 57
Period size: 9 Copynumber: 9.2 Consensus size: 9
9175209 ACATGTGACA
9175219 AAAAATTAT
1 AAAAATTAT
*
9175228 AAAAA-AAT
1 AAAAATTAT
*
9175236 -AAAATAAAT
1 AAAAAT-TAT
9175245 AAAAATTAT
1 AAAAATTAT
9175254 AAAAATTAT
1 AAAAATTAT
* *
9175263 -TAAATTTT
1 AAAAATTAT
9175271 AAAAAATATAT
1 -AAAAAT-TAT
* *
9175282 ATAATTTATT
1 AAAAATTA-T
9175292 AAAAATTAT
1 AAAAATTAT
9175301 AA
1 AA
9175303 TTTTTTATAA
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
7 4 0.07
8 8 0.14
9 24 0.41
10 20 0.34
11 2 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAAATTAT
Found at i:9175266 original size:19 final size:19
Alignment explanation
Indices: 9175243--9175302 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
9175233 AATAAAATAA
9175243 ATAAAAATTA-TAAAAATT
1 ATAAAAATTATTAAAAATT
*
9175261 AT-TAAATT-TTAAAAAATAT
1 ATAAAAATTATT-AAAAAT-T
* *
9175280 ATATAATTTATTAAAAATT
1 ATAAAAATTATTAAAAATT
9175299 ATAA
1 ATAA
9175303 TTTTTTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
17 6 0.18
18 8 0.24
19 7 0.21
20 11 0.32
21 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAAAATTATTAAAAATT
Found at i:9175313 original size:19 final size:19
Alignment explanation
Indices: 9175250--9175313 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
9175240 TAAATAAAAA
9175250 TTATAAAAATTATTAA-ATT
1 TTATAAAAATTA-TAATATT
*
9175269 TTA-AAAAA-TATATATAAT
1 TTATAAAAATTATA-ATATT
*
9175287 TTATTAAAAATTATAATTTT
1 TTA-TAAAAATTATAATATT
9175307 TTATAAA
1 TTATAAA
9175314 TATCGTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
16 2 0.05
17 3 0.08
18 10 0.27
19 7 0.19
20 11 0.30
21 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTATAAAAATTATAATATT
Found at i:9175511 original size:13 final size:12
Alignment explanation
Indices: 9175472--9175522 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
9175462 GACATGTGGC
*
9175472 AAAAAATGATAA
1 AAAAAATTATAA
**
9175484 AAAATAAAAATAA
1 AAAA-AATTATAA
*
9175497 AAAAATTTATAA
1 AAAAAATTATAA
9175509 AAAAAATTATAA
1 AAAAAATTATAA
9175521 AA
1 AA
9175523 TACTTCTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 22 0.69
13 10 0.31
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (12 bp):
AAAAAATTATAA
Found at i:9175624 original size:10 final size:10
Alignment explanation
Indices: 9175611--9175746 Score: 50
Period size: 10 Copynumber: 13.6 Consensus size: 10
9175601 CTATATAAAA
9175611 TTTTATAATT
1 TTTTATAATT
*
9175621 TTTTCTATATT
1 TTTTATA-ATT
*
9175632 TTTT-T-ATG
1 TTTTATAATT
* *
9175640 TTGTATAGTT
1 TTTTATAATT
*
9175650 TTTT-TACAAT
1 TTTTATA-ATT
9175660 TTTTATAATT
1 TTTTATAATT
* *
9175670 TTATCTAATT
1 TTTTATAATT
* *
9175680 TTTAATAA-A
1 TTTTATAATT
*
9175689 GTTTA-AATAT
1 TTTTATAAT-T
*
9175699 TTTTATAGCTT
1 TTTTATA-ATT
**
9175710 TTTTATTAAAG
1 TTTTA-TAATT
*
9175721 TTTAATAA-T
1 TTTTATAATT
9175730 TTTTATATATT
1 TTTTATA-ATT
9175741 TTTTAT
1 TTTTAT
9175747 TTTTTAACTT
Statistics
Matches: 88, Mismatches: 26, Indels: 23
0.64 0.19 0.17
Matches are distributed among these distances:
8 7 0.08
9 12 0.14
10 39 0.44
11 27 0.31
12 3 0.03
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.63
Consensus pattern (10 bp):
TTTTATAATT
Found at i:9175713 original size:31 final size:31
Alignment explanation
Indices: 9175678--9175745 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
9175668 TTTTATCTAA
*
9175678 TTTTTAATAAAGTTTAA-ATATTTTTATAGCT
1 TTTTTAATAAAGTTTAATA-ATTTTTATAGAT
* *
9175709 TTTTTATTAAAGTTTAATAATTTTTATATAT
1 TTTTTAATAAAGTTTAATAATTTTTATAGAT
9175740 TTTTTA
1 TTTTTA
9175746 TTTTTTAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (31 bp):
TTTTTAATAAAGTTTAATAATTTTTATAGAT
Found at i:9177656 original size:3 final size:3
Alignment explanation
Indices: 9177650--9177675 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9177640 CCTTCCCCCT
9177650 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
9177676 TTCCCCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:9179628 original size:6 final size:6
Alignment explanation
Indices: 9179617--9179664 Score: 87
Period size: 6 Copynumber: 8.0 Consensus size: 6
9179607 AATACAAGTG
*
9179617 CTCATC CTCATC CTCATC CTCAGC CTCATC CTCATC CTCATC CTCATC
1 CTCATC CTCATC CTCATC CTCATC CTCATC CTCATC CTCATC CTCATC
9179665 ATTATTATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.17, C:0.50, G:0.02, T:0.31
Consensus pattern (6 bp):
CTCATC
Found at i:9188408 original size:21 final size:22
Alignment explanation
Indices: 9188368--9188413 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
9188358 TATAAAACAT
9188368 TATTTATATTATTTAATTAAGAA
1 TATTTATATTATTT-ATTAAGAA
* *
9188391 TATTTATTTTATTT-TTAATAA
1 TATTTATATTATTTATTAAGAA
9188412 TA
1 TA
9188414 GATTAGTGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
23 13 0.62
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TATTTATATTATTTATTAAGAA
Found at i:9194365 original size:16 final size:18
Alignment explanation
Indices: 9194326--9194359 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9194316 TAAGTTTATA
9194326 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
9194343 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
9194360 AATTTAGAAC
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:9195916 original size:3 final size:3
Alignment explanation
Indices: 9195910--9195934 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9195900 ACAACATCAG
9195910 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
9195935 AAGGTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:9197731 original size:19 final size:18
Alignment explanation
Indices: 9197692--9197732 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
9197682 TTTGATTTTT
* *
9197692 TCAAAAATGCTTTTGACA
1 TCAAAAATGCTTTAGAAA
9197710 TCAAAAATGCTTTAGAAAA
1 TCAAAAATGCTTTAG-AAA
9197729 TCAA
1 TCAA
9197733 TTTTTTGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (18 bp):
TCAAAAATGCTTTAGAAA
Found at i:9207278 original size:20 final size:20
Alignment explanation
Indices: 9207241--9207279 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9207231 ATTCTAACAC
*
9207241 TACAGTGTAATTTATTTTAG
1 TACAGTGTAATTCATTTTAG
*
9207261 TACAGTGTAATTCGTTTTA
1 TACAGTGTAATTCATTTTA
9207280 ACACTTCGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (20 bp):
TACAGTGTAATTCATTTTAG
Found at i:9207498 original size:25 final size:23
Alignment explanation
Indices: 9207440--9207498 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 23
9207430 ATTTAATATG
9207440 TCATTTTGATTCTGAAAATAATA
1 TCATTTTGATTCTGAAAATAATA
*
9207463 TTATATCTTGATTCATTGATAAA-AATA
1 TCAT-T-TTGATTC--TGA-AAATAATA
9207490 TCATTTTGA
1 TCATTTTGA
9207499 ATTTGATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
23 3 0.10
24 1 0.03
25 11 0.38
26 1 0.03
27 10 0.34
28 3 0.10
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.46
Consensus pattern (23 bp):
TCATTTTGATTCTGAAAATAATA
Found at i:9216665 original size:26 final size:28
Alignment explanation
Indices: 9216636--9216698 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
9216626 AAATATAAAA
*
9216636 TTTTAAAAAGTA-TTTAAATTTCAAT-T
1 TTTTAAAAAGTACTTGAAATTTCAATAT
** * *
9216662 TTTTATCAATTACTTGAAATTTCAGTAT
1 TTTTAAAAAGTACTTGAAATTTCAATAT
9216690 TTTTAAAAA
1 TTTTAAAAA
9216699 AAATTTATAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
26 9 0.32
27 11 0.39
28 8 0.29
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (28 bp):
TTTTAAAAAGTACTTGAAATTTCAATAT
Found at i:9216988 original size:28 final size:25
Alignment explanation
Indices: 9216955--9217017 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 25
9216945 ATGTTTTTAA
* *
9216955 TATTTTAATATTCAATATTATTATTTTT
1 TATTTTAAT-TTAAAT-TTAATA-TTTT
9216983 TATTTTTTAATTTAAATTTAATATTTT
1 TA-TT-TTAATTTAAATTTAATATTTT
9217010 TATTTTAA
1 TATTTTAA
9217018 ATGAACTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
25 4 0.13
26 2 0.06
27 6 0.19
28 7 0.23
29 7 0.23
30 5 0.16
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTTTAATTTAAATTTAATATTTT
Found at i:9222370 original size:51 final size:52
Alignment explanation
Indices: 9222294--9222395 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 52
9222284 ATAAGAGAAG
** * *
9222294 TAAATAGGGTCAAATTTATTTTTTTTATTTTATTA-TTTTTATTCAATATAA
1 TAAATAGGGTCAAACCTATCTTTTTTACTTTATTATTTTTTATTCAATATAA
*
9222345 TAAATAGGGTCAAACCTATCTTTTTTACTTTGTTATTTTTTATTCAATATA
1 TAAATAGGGTCAAACCTATCTTTTTTACTTTATTATTTTTTATTCAATATA
9222396 TCCAATTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 30 0.67
52 15 0.33
ACGTcount: A:0.31, C:0.08, G:0.07, T:0.54
Consensus pattern (52 bp):
TAAATAGGGTCAAACCTATCTTTTTTACTTTATTATTTTTTATTCAATATAA
Found at i:9225113 original size:31 final size:31
Alignment explanation
Indices: 9225065--9225137 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
9225055 AAAAAAAACT
* *
9225065 AATAGCTCAATGACTTAAATAAAGACTTTC-
1 AATAGTTCAATGACTTAAATAAAAACTTTCG
* *
9225095 AGATAGTTCAGTGACTTAAATAAAAATTTTCG
1 A-ATAGTTCAATGACTTAAATAAAAACTTTCG
9225127 AATAGTTCAAT
1 AATAGTTCAAT
9225138 AATAATTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 1 0.03
31 34 0.94
32 1 0.03
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (31 bp):
AATAGTTCAATGACTTAAATAAAAACTTTCG
Found at i:9225632 original size:14 final size:15
Alignment explanation
Indices: 9225615--9225643 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9225605 TTTTATGTTT
9225615 TTTA-GAAAATTTTA
1 TTTATGAAAATTTTA
9225629 TTTATGAAAATTTTA
1 TTTATGAAAATTTTA
9225644 AATGATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (15 bp):
TTTATGAAAATTTTA
Found at i:9226958 original size:3 final size:3
Alignment explanation
Indices: 9226950--9227024 Score: 87
Period size: 3 Copynumber: 25.0 Consensus size: 3
9226940 CTAAAAGAAG
* * * * * * *
9226950 TAT TAT TAT TAT TAT TAT CAT TAT CAT CAT CAT CAT CAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9226998 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
9227025 CGACTCGTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:9227436 original size:2 final size:2
Alignment explanation
Indices: 9227429--9227474 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
9227419 CGATACAATA
9227429 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
9227471 AT AT
1 AT AT
9227475 TCTATTTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9246135 original size:29 final size:29
Alignment explanation
Indices: 9246094--9246156 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
9246084 TTAATAGTGT
9246094 TAAAATTACATTTTAA-CTCTT-AAAAATGA
1 TAAAATTACA-TTTAATCTCTTAAAAAAT-A
** *
9246123 TAAAATTTGATTTAATCTTTTAAAAAATA
1 TAAAATTACATTTAATCTCTTAAAAAATA
9246152 TAAAA
1 TAAAA
9246157 ATATAAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 5 0.17
29 18 0.62
30 6 0.21
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (29 bp):
TAAAATTACATTTAATCTCTTAAAAAATA
Found at i:9248428 original size:17 final size:17
Alignment explanation
Indices: 9248408--9248446 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
9248398 ATTATTCTAT
9248408 ATTTTATAAAT-TTCTTA
1 ATTTT-TAAATGTTCTTA
*
9248425 ATTTTTAAATGTTTTTA
1 ATTTTTAAATGTTCTTA
9248442 ATTTT
1 ATTTT
9248447 CTTTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (17 bp):
ATTTTTAAATGTTCTTA
Found at i:9251808 original size:21 final size:20
Alignment explanation
Indices: 9251762--9251808 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
9251752 ACGTATTATG
*
9251762 TAATAATTAATTTAAATATA
1 TAATAATTAATTTAAAAATA
*
9251782 TAAATAATTTATTTAAAAATAA
1 T-AATAATTAATTTAAAAAT-A
9251804 TAATA
1 TAATA
9251809 TTTCAACATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 20 0.87
22 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAATAATTAATTTAAAAATA
Found at i:9254857 original size:21 final size:21
Alignment explanation
Indices: 9254809--9254857 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
9254799 ATTTAAGGAT
9254809 TGATA-ATAAAAGAAATAAAA
1 TGATATATAAAAGAAATAAAA
* *
9254829 TAAAATAT-AAAGAAATAAAAA
1 TGATATATAAAAGAAAT-AAAA
9254850 TGATATAT
1 TGATATAT
9254858 TAAGTGATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (21 bp):
TGATATATAAAAGAAATAAAA
Found at i:9255366 original size:25 final size:25
Alignment explanation
Indices: 9255315--9255366 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
9255305 TTAATTTTCA
***
9255315 ATCAATTTATTTTTTCTAACTGTTT
1 ATCAATTTATTTTTTCTAACAAATT
9255340 ATCAATTTGATTTTTTC-AACAAATT
1 ATCAATTT-ATTTTTTCTAACAAATT
9255365 AT
1 AT
9255367 TTTCAAACGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.54
Consensus pattern (25 bp):
ATCAATTTATTTTTTCTAACAAATT
Found at i:9256107 original size:20 final size:18
Alignment explanation
Indices: 9256064--9256108 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
9256054 TTACAAAATA
*
9256064 TATTTTTTTTCTTCATTT
1 TATTTTTTTTCTTCAGTT
9256082 TCATTTTTTTTCTCTCTAGTT
1 T-ATTTTTTTTCT-TC-AGTT
9256103 TATTTT
1 TATTTT
9256109 ATCTAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 1 0.04
19 11 0.48
20 7 0.30
21 4 0.17
ACGTcount: A:0.11, C:0.13, G:0.02, T:0.73
Consensus pattern (18 bp):
TATTTTTTTTCTTCAGTT
Found at i:9260950 original size:15 final size:16
Alignment explanation
Indices: 9260909--9260950 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
9260899 ACTTGTACTA
*
9260909 AAATTATTTTATTCTT
1 AAATTATTTTATCCTT
**
9260925 AAATTCGTTTATCCTT
1 AAATTATTTTATCCTT
9260941 -AATTATTTTA
1 AAATTATTTTA
9260951 ATCTCTCTCT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57
Consensus pattern (16 bp):
AAATTATTTTATCCTT
Found at i:9261017 original size:13 final size:13
Alignment explanation
Indices: 9260995--9261028 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
9260985 TTCTTTTTAA
9260995 AATT-TTTATTAC
1 AATTATTTATTAC
*
9261007 AATTATTTATTAT
1 AATTATTTATTAC
9261020 AATTATTTA
1 AATTATTTA
9261029 AGCGTAGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (13 bp):
AATTATTTATTAC
Found at i:9272500 original size:20 final size:20
Alignment explanation
Indices: 9272463--9272500 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9272453 TCAAAATCTA
*
9272463 ATATAAAATAGATTATAAAC
1 ATATAAAATAGATAATAAAC
9272483 ATATAATAATA-ATAATAA
1 ATATAA-AATAGATAATAA
9272501 TAAACCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
ATATAAAATAGATAATAAAC
Found at i:9274426 original size:6 final size:6
Alignment explanation
Indices: 9274417--9274455 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
9274407 TTTGCTTTTG
* * *
9274417 CTGCCT CTGCCT CTGCCT CTGTCT CTGCCC CTGTCT CTG
1 CTGCCT CTGCCT CTGCCT CTGCCT CTGCCT CTGCCT CTG
9274456 AGTCATAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.46, G:0.18, T:0.36
Consensus pattern (6 bp):
CTGCCT
Found at i:9274434 original size:12 final size:12
Alignment explanation
Indices: 9274417--9274455 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
9274407 TTTGCTTTTG
*
9274417 CTGCCTCTGCCT
1 CTGCCTCTGTCT
9274429 CTGCCTCTGTCT
1 CTGCCTCTGTCT
*
9274441 CTGCCCCTGTCT
1 CTGCCTCTGTCT
9274453 CTG
1 CTG
9274456 AGTCATAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.46, G:0.18, T:0.36
Consensus pattern (12 bp):
CTGCCTCTGTCT
Found at i:9275868 original size:2 final size:2
Alignment explanation
Indices: 9275861--9275892 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9275851 GGAAAGACAG
9275861 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
9275893 GGATTGCGTT
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:9282626 original size:5 final size:5
Alignment explanation
Indices: 9282618--9282642 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9282608 TTTTATTATG
9282618 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
9282643 ACCTTCTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:9294328 original size:37 final size:36
Alignment explanation
Indices: 9294287--9294373 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 36
9294277 ATAAAGCATG
9294287 ATTTATATTTTTATTTTTAAAAGTTTTAATATATATT
1 ATTTATATTTTTATTTTTAAAA-TTTTAATATATATT
***
9294324 ATTTATATTTGTAATATTTTTTTTATTTTAATATATATT
1 ATTTATATTT-T--TATTTTTAAAATTTTAATATATATT
9294363 -TTTA-ATTTTTA
1 ATTTATATTTTTA
9294374 GATACCCATA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
34 2 0.05
36 1 0.02
37 14 0.32
38 5 0.11
39 14 0.32
40 8 0.18
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (36 bp):
ATTTATATTTTTATTTTTAAAATTTTAATATATATT
Found at i:9294350 original size:18 final size:17
Alignment explanation
Indices: 9294319--9294363 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
9294309 GTTTTAATAT
9294319 ATATTATTTATATTTGTA
1 ATATTATTTATATTT-TA
* *
9294337 ATATTTTTTTTATTTTA
1 ATATTATTTATATTTTA
9294354 ATATATATTT
1 ATAT-TATTT
9294364 TTAATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
ATATTATTTATATTTTA
Found at i:9294364 original size:20 final size:20
Alignment explanation
Indices: 9294310--9294371 Score: 78
Period size: 19 Copynumber: 3.2 Consensus size: 20
9294300 TTTTTAAAAG
9294310 TTTTAATATATATTATTTATA
1 TTTTAATATATATT-TTTATA
9294331 TTTGTAATAT-T-TTTTT-TA
1 TTT-TAATATATATTTTTATA
9294349 TTTTAATATATATTTTTA-A
1 TTTTAATATATATTTTTATA
9294368 TTTT
1 TTTT
9294372 TAGATACCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
17 6 0.16
18 6 0.16
19 13 0.35
20 2 0.05
21 4 0.11
22 6 0.16
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTAATATATATTTTTATA
Found at i:9294906 original size:9 final size:9
Alignment explanation
Indices: 9294819--9294927 Score: 71
Period size: 9 Copynumber: 11.9 Consensus size: 9
9294809 TTTAAATCTC
9294819 AAAATTACTA
1 AAAATTA-TA
* *
9294829 AAATGTTATG
1 AAA-ATTATA
9294839 AAAATT-TA
1 AAAATTATA
9294847 AAAATTAATA
1 AAAATT-ATA
**
9294857 AAAACAATA
1 AAAATTATA
* *
9294866 ATATATTTTGA
1 A-AAATTAT-A
9294877 AAAA-TATA
1 AAAATTATA
9294885 AAAA-TATA
1 AAAATTATA
* *
9294893 GAAATTATT
1 AAAATTATA
*
9294902 AAAATGATA
1 AAAATTATA
9294911 AAAATTATA
1 AAAATTATA
9294920 AAAATTAT
1 AAAATTAT
9294928 TAAAGATATA
Statistics
Matches: 75, Mismatches: 18, Indels: 13
0.71 0.17 0.12
Matches are distributed among these distances:
8 19 0.25
9 33 0.44
10 18 0.24
11 5 0.07
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:9294924 original size:27 final size:25
Alignment explanation
Indices: 9294877--9294938 Score: 88
Period size: 27 Copynumber: 2.4 Consensus size: 25
9294867 TATATTTTGA
*
9294877 AAAATATAAAAATATAGAAATTATT
1 AAAATATAAAAATATAAAAATTATT
9294902 AAAATGATAAAAATTATAAAAATTATT
1 AAAAT-ATAAAAA-TATAAAAATTATT
9294929 AAAGATATAA
1 AAA-ATATAA
9294939 TTTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 5 0.15
26 7 0.21
27 19 0.58
28 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.31
Consensus pattern (25 bp):
AAAATATAAAAATATAAAAATTATT
Found at i:9295418 original size:21 final size:22
Alignment explanation
Indices: 9295383--9295434 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
9295373 TTTTTTTATG
9295383 TTTTAA-ATATTTTAATAA-AA
1 TTTTAATATATTTTAATAATAA
*
9295403 TTTTAATATTTTTTAATAATAA
1 TTTTAATATATTTTAATAATAA
9295425 -TTTAATATAT
1 TTTTAATATAT
9295435 AATTTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 6 0.21
21 20 0.71
22 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTAATATATTTTAATAATAA
Found at i:9311896 original size:6 final size:6
Alignment explanation
Indices: 9311885--9311911 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
9311875 GTCCTGATGT
9311885 TTCTGA TTCTGA TTCTGA TTCTGA TTC
1 TTCTGA TTCTGA TTCTGA TTCTGA TTC
9311912 AATATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.52
Consensus pattern (6 bp):
TTCTGA
Found at i:9317343 original size:6 final size:6
Alignment explanation
Indices: 9317332--9317356 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9317322 AAAATAAGTA
9317332 TTAATT TTAATT TTAATT TTAATT T
1 TTAATT TTAATT TTAATT TTAATT T
9317357 ATGATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTAATT
Found at i:9319351 original size:18 final size:17
Alignment explanation
Indices: 9319315--9319347 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
9319305 ATTTTTAGAT
9319315 TAATTTTTATTTAAAAA
1 TAATTTTTATTTAAAAA
9319332 TAATTTTT-TTTAAAAA
1 TAATTTTTATTTAAAAA
9319348 AATATAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TAATTTTTATTTAAAAA
Found at i:9341575 original size:218 final size:218
Alignment explanation
Indices: 9341145--9341576 Score: 645
Period size: 217 Copynumber: 2.0 Consensus size: 218
9341135 TTGTATTTTG
* * *
9341145 GTTGTATTTTTCTCGTAACACTTTTTAAAAAAAATATAGAATGCCATGAGTTAACTTGTCAACTT
1 GTTGTATTGTACTCGTAACACTTTTTAAAAAAAATATAGAACGCCATGAGTTAACTTGTCAACTT
* * *
9341210 ACAAATTTTTGCTTAACTTGTTGGTAATATCTGTAAGTTTTGAATTTAGCCCCTTACTTTTATTT
66 ACAAATTTTTGCTTAACTTGCTGGTAATATCTATAAATTTTGAATTTAGCCCCTTACTTTTATTT
* * **
9341275 CAAAAATTTAACACCTCCATTTTTCAAATTTAAATATGTAAGTTCAATTATTAACATTATTTTCT
131 CAAAAATTTAACACATCCATTTTTCAAATTTAAAAATGTAAGTTCAATTATTAACACCATTTTCT
*
9341340 GTTAATTTTAGTTCATTATTTCA
196 GTTAATTTTAATTCATTATTTCA
* * *
9341363 GTTGTATTGTACTCGTAACACTTTTT-TAAAAAATATGGAACGGCATGAGTTAACTTGTCAACTT
1 GTTGTATTGTACTCGTAACACTTTTTAAAAAAAATATAGAACGCCATGAGTTAACTTGTCAACTT
9341427 ACAAATTTTTGCTTAACTTGCTGGTAATATCTATAAATTTTGAATTTAGCCTCC-TACTTTTATT
66 ACAAATTTTTGCTTAACTTGCTGGTAATATCTATAAATTTTGAATTTAGCC-CCTTACTTTTATT
* ** *
9341491 TCAAGGAATTTAGTACATCCACTTTTT-AAATTTAAAAATGTAAGTTCAATTGTTAACACCATTT
130 TCAA-AAATTTAACACATCCA-TTTTTCAAATTTAAAAATGTAAGTTCAATTATTAACACCATTT
*
9341555 TTTGTTAATTTTAATTCATTAT
193 TCTGTTAATTTTAATTCATTAT
9341577 GATATTCTTT
Statistics
Matches: 192, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
217 96 0.50
218 91 0.47
219 5 0.03
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (218 bp):
GTTGTATTGTACTCGTAACACTTTTTAAAAAAAATATAGAACGCCATGAGTTAACTTGTCAACTT
ACAAATTTTTGCTTAACTTGCTGGTAATATCTATAAATTTTGAATTTAGCCCCTTACTTTTATTT
CAAAAATTTAACACATCCATTTTTCAAATTTAAAAATGTAAGTTCAATTATTAACACCATTTTCT
GTTAATTTTAATTCATTATTTCA
Found at i:9349014 original size:20 final size:19
Alignment explanation
Indices: 9348984--9349037 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
9348974 TTTTTTTTAT
*
9348984 AATTATAATTTTAAAAATTA
1 AATTATGATTTTAAAAA-TA
* *
9349004 ATTTATGATTTCAAAAATA
1 AATTATGATTTTAAAAATA
9349023 AATTATGAATTTTAA
1 AATTATG-ATTTTAA
9349038 TATTTTAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (19 bp):
AATTATGATTTTAAAAATA
Found at i:9358230 original size:25 final size:26
Alignment explanation
Indices: 9358197--9358260 Score: 103
Period size: 25 Copynumber: 2.5 Consensus size: 26
9358187 AAAATTTAAA
9358197 AAATAAATTTTTTGTTATAAAAA-TT
1 AAATAAATTTTTTGTTATAAAAATTT
9358222 AAATAAATTTTTTGTTATAAAAATTT
1 AAATAAATTTTTTGTTATAAAAATTT
*
9358248 AATATAAAATTTT
1 AA-ATAAATTTTT
9358261 AAATATTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 23 0.64
26 4 0.11
27 9 0.25
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (26 bp):
AAATAAATTTTTTGTTATAAAAATTT
Found at i:9358482 original size:16 final size:16
Alignment explanation
Indices: 9358437--9358486 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
9358427 TAAACCTAAT
*
9358437 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
9358453 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
9358467 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
9358483 TAAT
1 TAAT
9358487 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:9358553 original size:30 final size:30
Alignment explanation
Indices: 9358519--9358611 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 30
9358509 AAATGATACA
*
9358519 AAATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATATATTTTGTACCATTTTAGT
** * * * *
9358549 AAAT-AAT-GGTGTGTGGATACTATTTTAGT
1 AAATAAATATATATTTTG-TACCATTTTAGT
*
9358578 ATATAAATATATATTTTGTACCATTTTAGT
1 AAATAAATATATATTTTGTACCATTTTAGT
9358608 AAAT
1 AAAT
9358612 GGTCCCTCCC
Statistics
Matches: 46, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
28 4 0.09
29 17 0.37
30 21 0.46
31 4 0.09
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (30 bp):
AAATAAATATATATTTTGTACCATTTTAGT
Found at i:9362833 original size:2 final size:2
Alignment explanation
Indices: 9362826--9362865 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9362816 AGTTGTATGC
9362826 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
9362866 TTATGTATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9388584 original size:26 final size:26
Alignment explanation
Indices: 9388545--9388615 Score: 124
Period size: 26 Copynumber: 2.7 Consensus size: 26
9388535 GTGCACTTTA
*
9388545 TTTTTGTAGTTTTTTTTATAATACCC
1 TTTTTGTAGCTTTTTTTATAATACCC
9388571 TTTTTGTAGCTTTTTTTATAATACCC
1 TTTTTGTAGCTTTTTTTATAATACCC
*
9388597 TTTTTGTAGCTTTCTTTAT
1 TTTTTGTAGCTTTTTTTAT
9388616 TAGTAATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.17, C:0.13, G:0.08, T:0.62
Consensus pattern (26 bp):
TTTTTGTAGCTTTTTTTATAATACCC
Found at i:9392506 original size:16 final size:17
Alignment explanation
Indices: 9392466--9392506 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
9392456 TATTTACATG
9392466 TGAATTTTGATTTAATA
1 TGAATTTTGATTTAATA
*
9392483 TGAATTTTGATTTGATA
1 TGAATTTTGATTTAATA
9392500 T-AATTTT
1 TGAATTTT
9392507 ATGATAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (17 bp):
TGAATTTTGATTTAATA
Found at i:9405108 original size:2 final size:2
Alignment explanation
Indices: 9405101--9405144 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
9405091 CTTGCATCTA
9405101 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
9405143 AT
1 AT
9405145 TAAAACATGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9405377 original size:32 final size:32
Alignment explanation
Indices: 9405313--9405383 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 32
9405303 TTTACTTATT
*
9405313 TTTTA-ATGTAAATAATTAAATTAAAATCAAA
1 TTTTATATGTAAATAATTAAATTAAAATAAAA
9405344 TTTTCATATGTAAA-AATTAAA-TAAAATTAAAA
1 TTTT-ATATGTAAATAATTAAATTAAAA-TAAAA
9405376 TTTTATAT
1 TTTTATAT
9405384 ATATAATTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
31 13 0.36
32 16 0.44
33 7 0.19
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (32 bp):
TTTTATATGTAAATAATTAAATTAAAATAAAA
Found at i:9410720 original size:14 final size:15
Alignment explanation
Indices: 9410703--9410749 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
9410693 ATAAATATGG
*
9410703 AAAAA-GTAAGTGTT
1 AAAAATGTAAGTATT
*
9410717 AAAAATTTAAGTATT
1 AAAAATGTAAGTATT
* *
9410732 AAAAATTTAAGTACT
1 AAAAATGTAAGTATT
9410747 AAA
1 AAA
9410750 TTCAAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 5 0.17
15 24 0.83
ACGTcount: A:0.55, C:0.02, G:0.11, T:0.32
Consensus pattern (15 bp):
AAAAATGTAAGTATT
Found at i:9410737 original size:15 final size:15
Alignment explanation
Indices: 9410709--9410749 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
9410699 ATGGAAAAAG
*
9410709 TAAGTGTTAAAAATT
1 TAAGTATTAAAAATT
9410724 TAAGTATTAAAAATT
1 TAAGTATTAAAAATT
*
9410739 TAAGTACTAAA
1 TAAGTATTAAA
9410750 TTCAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (15 bp):
TAAGTATTAAAAATT
Found at i:9425329 original size:3 final size:3
Alignment explanation
Indices: 9425321--9425367 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
9425311 AAATTAAAAG
9425321 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
9425368 TGTACACAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:9426541 original size:23 final size:23
Alignment explanation
Indices: 9426467--9426680 Score: 160
Period size: 23 Copynumber: 9.5 Consensus size: 23
9426457 TAAACGGAAC
* * *
9426467 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
9426489 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
9426511 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
9426537 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
9426557 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
9426576 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
9426599 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
9426622 AATAACAGAGAGCACGA-GATGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
9426647 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
9426670 AATCAGAGAGC
1 AAACAGAGAGC
9426681 GCGCTAGTGT
Statistics
Matches: 153, Mismatches: 23, Indels: 31
0.74 0.11 0.15
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 18 0.12
23 79 0.52
24 2 0.01
25 29 0.19
26 8 0.05
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:9426546 original size:48 final size:44
Alignment explanation
Indices: 9426468--9426680 Score: 168
Period size: 48 Copynumber: 4.8 Consensus size: 44
9426458 AAACGGAACA
* * * * *
9426468 AACAGAGAGTAC-CGAAGTACTGAACAGAGAGCACATAAGTGCT
1 AACAGAGAGCACACAAAGTGCTAAACAGAGAGCACAGAAGTGCT
* * *
9426511 GGGCAACAGAGAGCACACAAAGTGCTAAACAGAGAGTACACAA-AG-T
1 ----AACAGAGAGCACACAAAGTGCTAAACAGAGAGCACAGAAGTGCT
* *
9426557 -AC--TGAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCT
1 AACAGAGAGCACACAAAGTGCTAAACAGAGAGCACA-GAAGTGCT
* *
9426599 AATCAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGATGTGCT
1 AA-CAGAGAGCACACAAAGTGCT-A-AACAGAGAGCAC-AGAAGTGCT
* *
9426647 AAACAGAGAGCACACACAGTGCTAATCAGAGAGC
1 -AACAGAGAGCACACAAAGTGCTAAACAGAGAGC
9426681 GCGCTAGTGT
Statistics
Matches: 137, Mismatches: 17, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
39 28 0.20
40 2 0.01
41 3 0.02
42 1 0.01
43 1 0.01
44 1 0.01
46 25 0.18
47 14 0.10
48 59 0.43
49 3 0.02
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (44 bp):
AACAGAGAGCACACAAAGTGCTAAACAGAGAGCACAGAAGTGCT
Found at i:9426575 original size:39 final size:39
Alignment explanation
Indices: 9426521--9426595 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
9426511 GGGCAACAGA
*
9426521 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
9426560 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
9426596 GCTAATCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:9432995 original size:23 final size:23
Alignment explanation
Indices: 9432969--9433134 Score: 150
Period size: 23 Copynumber: 7.4 Consensus size: 23
9432959 AGTGCTGGGC
9432969 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
9432992 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
9433011 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
9433031 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
9433054 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* * *
9433078 TAACAGAGAGCACGA-GATGTTCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
*
9433102 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
9433125 ATCAGAGAGC
1 AACAGAGAGC
9433135 GCGCTAGTGT
Statistics
Matches: 114, Mismatches: 18, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 1 0.01
23 78 0.68
24 2 0.02
25 15 0.13
26 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.13
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:9433029 original size:39 final size:39
Alignment explanation
Indices: 9432975--9433049 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
9432965 GGGCAACAGA
*
9432975 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
9433014 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
9433050 GCTAATCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:9433092 original size:46 final size:46
Alignment explanation
Indices: 9433014--9433134 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
9433004 ACAAAGTACT
* * *
9433014 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GATGTGCTAAACAGA
*
9433060 GAGCACACACAGTGCTAATAACAGAGAGCACGAGATGTTCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGATGTGCTAAACAGA
9433108 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
9433135 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.13
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGATGTGCTAAACAGA
Found at i:9439304 original size:16 final size:16
Alignment explanation
Indices: 9439259--9439304 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
9439249 TTTATTCCTT
9439259 TTTAAAATAATA-TAA
1 TTTAAAATAATATTAA
*
9439274 TATTAAAATTATATTAA
1 T-TTAAAATAATATTAA
*
9439291 TTTATAATAATATT
1 TTTAAAATAATATT
9439305 GATATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 1 0.04
16 21 0.81
17 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTAAAATAATATTAA
Found at i:9439674 original size:22 final size:22
Alignment explanation
Indices: 9439647--9439702 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
9439637 TTAACACTAT
9439647 TTTTACTTTTTAAATATTTT-TA
1 TTTTACTTTTTAAA-ATTTTATA
* *
9439669 TTTTACTATTTAAAATTTTATT
1 TTTTACTTTTTAAAATTTTATA
*
9439691 TTTTATTTTTTA
1 TTTTACTTTTTA
9439703 TTTTTTAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 5 0.17
22 24 0.83
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTACTTTTTAAAATTTTATA
Found at i:9439694 original size:7 final size:7
Alignment explanation
Indices: 9439684--9439709 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
9439674 CTATTTAAAA
9439684 TTTTATT
1 TTTTATT
9439691 TTTTATT
1 TTTTATT
9439698 TTTTATT
1 TTTTATT
9439705 TTTTA
1 TTTTA
9439710 AGTATTTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:9440194 original size:14 final size:13
Alignment explanation
Indices: 9440167--9440202 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
9440157 ATTGATTATC
*
9440167 AATTAAATATAAT
1 AATTAAAGATAAT
9440180 AATTATAAGATAAT
1 AATTA-AAGATAAT
9440194 AATTAAAGA
1 AATTAAAGA
9440203 AGTATTCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (13 bp):
AATTAAAGATAAT
Found at i:9440575 original size:21 final size:22
Alignment explanation
Indices: 9440551--9440594 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
9440541 AACTTAATAA
*
9440551 TTTAT-TTTTAAATAGATTATT
1 TTTATATTTTAAATAAATTATT
*
9440572 TTTATGATTTTATATAAATTATT
1 TTTAT-ATTTTAAATAAATTATT
9440595 AAAAGACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (22 bp):
TTTATATTTTAAATAAATTATT
Found at i:9443418 original size:3 final size:3
Alignment explanation
Indices: 9443410--9443435 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9443400 TGGGGATGAA
9443410 AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AG
9443436 ATGAAGTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:9457539 original size:31 final size:31
Alignment explanation
Indices: 9457504--9457572 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
9457494 CTTGATTTTA
9457504 CGTTTGCCAAATAATTTAAATGGTCAAGCTT
1 CGTTTGCCAAATAATTTAAATGGTCAAGCTT
9457535 CGTTTGCCAAATAATTTAAATGGTCAAGCTT
1 CGTTTGCCAAATAATTTAAATGGTCAAGCTT
*
9457566 CTTTTGC
1 CGTTTGC
9457573 GTATGCAGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (31 bp):
CGTTTGCCAAATAATTTAAATGGTCAAGCTT
Found at i:9459434 original size:14 final size:15
Alignment explanation
Indices: 9459417--9459450 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
9459407 AAGAAGTTGT
9459417 TGAAAAG-AAAATAA
1 TGAAAAGTAAAATAA
9459431 TGAAAAGTAAAATAA
1 TGAAAAGTAAAATAA
9459446 T-AAAA
1 TGAAAA
9459451 ATTGGACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (15 bp):
TGAAAAGTAAAATAA
Found at i:9466108 original size:41 final size:41
Alignment explanation
Indices: 9466051--9466136 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
9466041 TTGGGAGCAA
9466051 ACAATTGGTATAAAACTCATGATTTAAAGGGTACAAGTTTC
1 ACAATTGGTATAAAACTCATGATTTAAAGGGTACAAGTTTC
*
9466092 ACAATTGGTATAAAACTCATGATTTAAAGGGTACAAGTTTG
1 ACAATTGGTATAAAACTCATGATTTAAAGGGTACAAGTTTC
9466133 ACAA
1 ACAA
9466137 AAAAGAAAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (41 bp):
ACAATTGGTATAAAACTCATGATTTAAAGGGTACAAGTTTC
Found at i:9475333 original size:25 final size:27
Alignment explanation
Indices: 9475277--9475333 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 27
9475267 GCTTGCACCC
*
9475277 AAATTTTTTAAATCCGTCTTAAAGATAT
1 AAATTTTTTAAATCCG-CTTAAAGATAA
**
9475305 AAATTTTTTAAA-CC-CTTAAATTTAA
1 AAATTTTTTAAATCCGCTTAAAGATAA
9475330 AAAT
1 AAAT
9475334 ATTATAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 12 0.46
27 2 0.08
28 12 0.46
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.42
Consensus pattern (27 bp):
AAATTTTTTAAATCCGCTTAAAGATAA
Found at i:9475477 original size:2 final size:2
Alignment explanation
Indices: 9475470--9475513 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
9475460 AATAAACAAC
9475470 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
9475512 AG
1 AG
9475514 TCTAGGTTCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.