Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 11 of 45
Found at i:2136160 original size:19 final size:19
Alignment explanation
Indices: 2136136--2136177 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2136126 GCTCAATCTC
2136136 AAATAATAT-TTTTATATTA
1 AAATAATATATTTT-TATTA
*
2136155 AAATAATATATTTTTATTT
1 AAATAATATATTTTTATTA
2136174 AAAT
1 AAAT
2136178 TTAATTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATAATATATTTTTATTA
Found at i:2136249 original size:22 final size:23
Alignment explanation
Indices: 2136202--2136243 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2136192 TATACATATT
*
2136202 AATATAATAATAATTTTTAATAA
1 AATATAATAATAATTTTAAATAA
2136225 AATA-AATAATAA-TTTAAAT
1 AATATAATAATAATTTTAAAT
2136244 TTAAATGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AATATAATAATAATTTTAAATAA
Found at i:2145452 original size:11 final size:12
Alignment explanation
Indices: 2145430--2145502 Score: 52
Period size: 12 Copynumber: 6.6 Consensus size: 12
2145420 TAAAAATATT
2145430 AAATATATAATA
1 AAATATATAATA
2145442 AAATATA-AAT-
1 AAATATATAATA
*
2145452 AAATAT-T--TT
1 AAATATATAATA
*
2145461 AAAT-T-TTATA
1 AAATATATAATA
*
2145471 TAATATATAATA
1 AAATATATAATA
2145483 AAATATATAAATA
1 AAATATAT-AATA
*
2145496 TAATATA
1 AAATATA
2145503 AAAATATAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 10 0.20
11 4 0.08
12 18 0.37
13 10 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATATATAATA
Found at i:2145463 original size:31 final size:31
Alignment explanation
Indices: 2145422--2145511 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 31
2145412 TCGTACATTA
2145422 AAAATA-TTAAATATATAATAAAATATAAAT
1 AAAATATTTAAATATATAATAAAATATAAAT
* *
2145452 -AAATATTTTAAAT-T-TTATATAATATATAAT
1 AAAATA-TTTAAATATATAATAAAATATA-AAT
*
2145482 AAAATATATAAATATA-ATATAAAAATATAA
1 AAAATATTTAAATATATA-AT-AAAATATAA
2145512 TAATTATACC
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
29 15 0.32
30 10 0.21
31 12 0.26
32 3 0.06
33 7 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (31 bp):
AAAATATTTAAATATATAATAAAATATAAAT
Found at i:2145500 original size:13 final size:13
Alignment explanation
Indices: 2145468--2145513 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
2145458 TTTAAATTTT
2145468 ATATAATATAT-A
1 ATATAATATATAA
*
2145480 ATAAAATATATAA
1 ATATAATATATAA
*
2145493 ATATAATATAAAA
1 ATATAATATATAA
2145506 ATATAATA
1 ATATAATA
2145514 ATTATACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAATATATAA
Found at i:2145509 original size:19 final size:19
Alignment explanation
Indices: 2145468--2145513 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
2145458 TTTAAATTTT
*
2145468 ATATAATATATAATAAAAT
1 ATATAATATATAATAAAAA
2145487 ATATAA-ATATAATATAAAA
1 ATATAATATATAATA-AAAA
2145506 ATATAATA
1 ATATAATA
2145514 ATTATACCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 8 0.33
19 15 0.62
20 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATATAATATATAATAAAAA
Found at i:2145512 original size:31 final size:29
Alignment explanation
Indices: 2145422--2145514 Score: 91
Period size: 31 Copynumber: 3.1 Consensus size: 29
2145412 TCGTACATTA
2145422 AAAATATTAAATATATA-ATAAAATATAAAT
1 AAAATATTAAATATATATA-AAAATAT-AAT
* * *
2145452 AAATATTTTAAAT-TTTATATAATATATAAT
1 AAA-ATATTAAATATATATA-AAAATATAAT
2145482 AAAATATATAAATATAATATAAAAATATAAT
1 AAAATAT-TAAATAT-ATATAAAAATATAAT
2145513 AA
1 AA
2145515 TTATACCAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
29 3 0.06
30 17 0.33
31 28 0.54
32 4 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAATATTAAATATATATAAAAATATAAT
Found at i:2145515 original size:41 final size:39
Alignment explanation
Indices: 2145418--2145519 Score: 102
Period size: 41 Copynumber: 2.6 Consensus size: 39
2145408 AATGTCGTAC
*
2145418 ATTAAAAATATTA-AATATATAATAAAATATAAATAAAT
1 ATTAAAAATATAATAATATATAATAAAATATAAATAAAT
* * *
2145456 ATTTTAAATTTTATATAATATATAATAAAATATATAAATATAAT
1 A-TTAAAAATATA-ATAATATATAAT-AAA-ATATAAATA-AAT
2145500 A-TAAAAATATAATAAT-TATA
1 ATTAAAAATATAATAATATATA
2145520 CCAAGTCAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
38 1 0.02
39 7 0.14
40 5 0.10
41 15 0.29
42 10 0.20
43 9 0.18
44 4 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (39 bp):
ATTAAAAATATAATAATATATAATAAAATATAAATAAAT
Found at i:2145715 original size:12 final size:11
Alignment explanation
Indices: 2145698--2145781 Score: 64
Period size: 12 Copynumber: 7.4 Consensus size: 11
2145688 AATTTGTAAT
*
2145698 ATAAAAAGTATG
1 ATAAAAA-TATA
2145710 ATAAAAATATA
1 ATAAAAATATA
2145721 ATATAAAATATA
1 ATA-AAAATATA
2145733 ATAAAAA-ATAA
1 ATAAAAATAT-A
2145744 ATATAATAATATA
1 ATA-AA-AATATA
* **
2145757 ATCAATTTAT-
1 ATAAAAATATA
*
2145767 ATAAATATATA
1 ATAAAAATATA
2145778 ATAA
1 ATAA
2145782 TTTTAAAATA
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
10 10 0.17
11 21 0.35
12 22 0.37
13 5 0.08
14 2 0.03
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.32
Consensus pattern (11 bp):
ATAAAAATATA
Found at i:2145746 original size:23 final size:23
Alignment explanation
Indices: 2145694--2145758 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 23
2145684 ATCAAATTTG
*
2145694 TAATATAAAAAGTATGATAAAAATA
1 TAATAT-AAAA-TATAATAAAAATA
2145719 TAATATAAAATATAATAAAAA-A
1 TAATATAAAATATAATAAAAATA
2145741 TAAATATAATAATATAAT
1 T-AATATAA-AATATAAT
2145759 CAATTTATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 2 0.05
23 17 0.46
24 12 0.32
25 6 0.16
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (23 bp):
TAATATAAAATATAATAAAAATA
Found at i:2145768 original size:21 final size:20
Alignment explanation
Indices: 2145752--2145793 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 20
2145742 AAATATAATA
2145752 ATATAATCAATTTATATAAAT
1 ATATAAT-AATTTATATAAAT
2145773 ATATAATAATTT-TA-AAAT
1 ATATAATAATTTATATAAAT
2145791 ATA
1 ATA
2145794 ATATGATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
19 2 0.10
20 5 0.24
21 7 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATAATAATTTATATAAAT
Found at i:2145797 original size:21 final size:22
Alignment explanation
Indices: 2145748--2145797 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
2145738 AAATAAATAT
*
2145748 AATAATATAATCAATTTATATA
1 AATAATATAATCAATTTATAAA
2145770 AAT-ATATAAT-AATTT-TAAA
1 AATAATATAATCAATTTATAAA
2145789 ATATAATAT
1 A-ATAATAT
2145798 GATGAAGCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.16
20 7 0.28
21 11 0.44
22 3 0.12
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AATAATATAATCAATTTATAAA
Found at i:2147592 original size:2 final size:2
Alignment explanation
Indices: 2147585--2147621 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2147575 AATCCCAATC
* *
2147585 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TC TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2147622 GGAAGAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2158986 original size:19 final size:20
Alignment explanation
Indices: 2158959--2158996 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2158949 CTCTTCCCTC
2158959 AAAACAGAAAAA-AAAAAAA
1 AAAACAGAAAAAGAAAAAAA
*
2158978 AAAAGAGAAAAAGAAAAAA
1 AAAACAGAAAAAGAAAAAA
2158997 TAACTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.87, C:0.03, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAACAGAAAAAGAAAAAAA
Found at i:2160086 original size:23 final size:24
Alignment explanation
Indices: 2160057--2160101 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2160047 TATATTAAAT
2160057 TTTATTTAATTTTGA-ATTTTTTA
1 TTTATTTAATTTTGATATTTTTTA
* *
2160080 TTTATTTTATTTTTATATTTTT
1 TTTATTTAATTTTGATATTTTT
2160102 AATAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (24 bp):
TTTATTTAATTTTGATATTTTTTA
Found at i:2160999 original size:13 final size:12
Alignment explanation
Indices: 2160962--2161000 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
2160952 ATTTTAGAAA
2160962 TATAATAATTAT
1 TATAATAATTAT
2160974 TATAATAATTTAT
1 TATAATAA-TTAT
*
2160987 TATTAATAGTTAT
1 TA-TAATAATTAT
2161000 T
1 T
2161001 TAAAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 8 0.33
13 11 0.46
14 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (12 bp):
TATAATAATTAT
Found at i:2161015 original size:26 final size:26
Alignment explanation
Indices: 2160964--2161016 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
2160954 TTTAGAAATA
*
2160964 TAATAATTATTATAATAATTTATTAT
1 TAATAATTATTATAAAAATTTATTAT
* *
2160990 TAATAGTTATT-TAAAAATATTTTTAT
1 TAATAATTATTATAAAAAT-TTATTAT
2161016 T
1 T
2161017 CATGCATTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
TAATAATTATTATAAAAATTTATTAT
Found at i:2161670 original size:2 final size:2
Alignment explanation
Indices: 2161663--2161688 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2161653 TGCTTCCCCT
2161663 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
2161689 ATTTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2161985 original size:18 final size:17
Alignment explanation
Indices: 2161938--2161988 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
2161928 AATTAATTAG
2161938 TTTAAATATTAAATTTTT
1 TTTAAATA-TAAATTTTT
2161956 TTT-AATA-AAATTATTT
1 TTTAAATATAAATT-TTT
*
2161972 TTTAAATATCAATTTTT
1 TTTAAATATAAATTTTT
2161989 AAAAATAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 5 0.17
16 6 0.21
17 11 0.38
18 7 0.24
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTAAATATAAATTTTT
Found at i:2162773 original size:15 final size:15
Alignment explanation
Indices: 2162741--2162779 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2162731 ATGATATAAA
2162741 TTATATTATTTAAATT
1 TTATATT-TTTAAATT
* *
2162757 TTTTATTTTTAATTT
1 TTATATTTTTAAATT
2162772 TTATATTT
1 TTATATTT
2162780 GATATTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATATTTTTAAATT
Found at i:2166448 original size:34 final size:35
Alignment explanation
Indices: 2166408--2166494 Score: 99
Period size: 34 Copynumber: 2.5 Consensus size: 35
2166398 TTAAAATTTA
**
2166408 TTTTATTATTAATAA-TAATATTAAAAT-ATTATAT
1 TTTTATTATTAATAATTAA-ATTAAAATAAAAATAT
* *
2166442 TTTTATT-TTTATAATTAAATTTAAATAAAAATAT
1 TTTTATTATTAATAATTAAATTAAAATAAAAATAT
2166476 TTTTATTATTAATATATTA
1 TTTTATTATTAATA-ATTA
2166495 TTTCAAGTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
33 13 0.30
34 22 0.50
35 5 0.11
36 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (35 bp):
TTTTATTATTAATAATTAAATTAAAATAAAAATAT
Found at i:2167764 original size:72 final size:72
Alignment explanation
Indices: 2167647--2167785 Score: 242
Period size: 72 Copynumber: 1.9 Consensus size: 72
2167637 CAGCCATTGT
*
2167647 ATATAATGTCATGGAAATAAAGAACTAACTGTTTAAATGGATTCTTCTGATATATGGATAGCCGG
1 ATATAATGTCATGGAAATAAAGAACTAACTGCTTAAATGGATTCTTCTGATATATGGATAGCCGG
2167712 GTCGAGG
66 GTCGAGG
* * *
2167719 ATATAATGTCGTGGAAATAAAGAACTAACTGCTTACATGGATTCTTCTGATATATGGATAGCTGG
1 ATATAATGTCATGGAAATAAAGAACTAACTGCTTAAATGGATTCTTCTGATATATGGATAGCCGG
2167784 GT
66 GT
2167786 TTGGGGATAC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (72 bp):
ATATAATGTCATGGAAATAAAGAACTAACTGCTTAAATGGATTCTTCTGATATATGGATAGCCGG
GTCGAGG
Found at i:2170690 original size:16 final size:16
Alignment explanation
Indices: 2170655--2170744 Score: 60
Period size: 18 Copynumber: 5.4 Consensus size: 16
2170645 TATGTCCTTA
*
2170655 TATTATATCTATGTATTT
1 TATTATAT-TAT-AATTT
2170673 TATTATATTATAATTT
1 TATTATATTATAATTT
**
2170689 TATT-TAAAAT-ATTT
1 TATTATATTATAATTT
*
2170703 TA-TATTTATATTAATTT
1 TATTATAT-TA-TAATTT
*
2170720 TAATATATTAATAATTT
1 TATTATATT-ATAATTT
2170737 ATATTATA
1 -TATTATA
2170745 AAAATTTTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
13 1 0.02
14 7 0.12
15 5 0.09
16 9 0.16
17 16 0.28
18 19 0.33
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (16 bp):
TATTATATTATAATTT
Found at i:2170721 original size:27 final size:27
Alignment explanation
Indices: 2170691--2170742 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2170681 TATAATTTTA
*
2170691 TTTAAAATATT-TTATATTTATATTAAT
1 TTTAAAATATTAATA-ATTTATATTAAT
*
2170718 TTTAATATATTAATAATTTATATTA
1 TTTAAAATATTAATAATTTATATTA
2170743 TAAAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTAAAATATTAATAATTTATATTAAT
Found at i:2170751 original size:32 final size:33
Alignment explanation
Indices: 2170696--2170759 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
2170686 TTTTATTTAA
* ** *
2170696 AATATTTTATATTTATATTAATTTTAATATATT
1 AATAATTTATATTTATAAAAATTTTAAAATATT
2170729 AATAATTTATA-TTATAAAAATTTTAAAATAT
1 AATAATTTATATTTATAAAAATTTTAAAATAT
2170760 ATATTTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
AATAATTTATATTTATAAAAATTTTAAAATATT
Found at i:2171861 original size:13 final size:13
Alignment explanation
Indices: 2171843--2171869 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2171833 TCTCTCTCTA
2171843 TAATTAAAAAAAG
1 TAATTAAAAAAAG
2171856 TAATTAAAAAAAG
1 TAATTAAAAAAAG
2171869 T
1 T
2171870 TGGCACATGT
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:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (13 bp):
TAATTAAAAAAAG
Found at i:2172542 original size:19 final size:20
Alignment explanation
Indices: 2172520--2172558 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2172510 TATAAAAAAT
2172520 ATTTATAA-ATATTATATAA
1 ATTTATAATATATTATATAA
*
2172539 ATTTATAATATTTTATATAA
1 ATTTATAATATATTATATAA
2172559 CAAAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTATAATATATTATATAA
Found at i:2172616 original size:20 final size:19
Alignment explanation
Indices: 2172591--2172637 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
2172581 TTTTTTCTCC
2172591 TTTCTTCTCTTCTTCTTTCT
1 TTTCTTCTCTTC-TCTTTCT
*
2172611 TTTCTTTTTCTTCTCTTTCT
1 TTTC-TTCTCTTCTCTTTCT
2172631 TTCTCTT
1 TT-TCTT
2172638 TGCCGGCTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTCTTCTCTTCTCTTTCT
Found at i:2172632 original size:15 final size:15
Alignment explanation
Indices: 2172593--2172637 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
2172583 TTTTCTCCTT
2172593 TCTTCTC-TTC-TTC
1 TCTTCTCTTTCTTTC
*
2172606 T-TTCT-TTTCTTTT
1 TCTTCTCTTTCTTTC
2172619 TCTTCTCTTTCTTTC
1 TCTTCTCTTTCTTTC
2172634 TCTT
1 TCTT
2172638 TGCCGGCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 7 0.27
13 4 0.15
14 4 0.15
15 11 0.42
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
TCTTCTCTTTCTTTC
Found at i:2172743 original size:21 final size:23
Alignment explanation
Indices: 2172719--2172760 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2172709 AGATAGATAG
*
2172719 ATAT-AAAAA-AATTTAAATACA
1 ATATGAAAAATAATATAAATACA
2172740 ATATGAAAAATAATATAAATA
1 ATATGAAAAATAATATAAATA
2172761 TGATACGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 5 0.28
23 9 0.50
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (23 bp):
ATATGAAAAATAATATAAATACA
Found at i:2176061 original size:12 final size:12
Alignment explanation
Indices: 2176033--2176078 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
2176023 GATTTTTTAT
*
2176033 TATTTTAAAAT-
1 TATTTTAATATA
*
2176044 TATTTTAATGTA
1 TATTTTAATATA
2176056 TATTTTAATATA
1 TATTTTAATATA
2176068 T-TTTTAA-ATA
1 TATTTTAATATA
2176078 T
1 T
2176079 TGATATGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 4 0.13
11 15 0.48
12 12 0.39
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
TATTTTAATATA
Found at i:2180244 original size:2 final size:2
Alignment explanation
Indices: 2180237--2180261 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2180227 TCTTGCCTCA
2180237 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
2180262 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2180266 original size:2 final size:2
Alignment explanation
Indices: 2180261--2180294 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2180251 ACACACACAC
2180261 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
2180295 GAAACCGCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2181133 original size:44 final size:45
Alignment explanation
Indices: 2181084--2181183 Score: 134
Period size: 44 Copynumber: 2.2 Consensus size: 45
2181074 ATGATTTGAT
2181084 AAATTTAATTTAAATTAA-ATTAATTAAATATAAATAT-TTTTATT-
1 AAATTTAATTT-AATTAATATTAATTAAATA-AAATATATTTTATTA
* * *
2181128 TAATTTAATTTAATTAATATTTATTTAATAAAATATATTTTATTA
1 AAATTTAATTTAATTAATATTAATTAAATAAAATATATTTTATTA
2181173 AAATTTAATTT
1 AAATTTAATTT
2181184 TAAAAATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
43 12 0.24
44 27 0.55
45 10 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (45 bp):
AAATTTAATTTAATTAATATTAATTAAATAAAATATATTTTATTA
Found at i:2181156 original size:15 final size:15
Alignment explanation
Indices: 2181129--2181179 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
2181119 ATTTTTATTT
2181129 AATTTAATTTAATTAA
1 AATTT-ATTTAATTAA
*
2181145 TATTTATTTAA-TAA
1 AATTTATTTAATTAA
* *
2181159 AATATATTTTATTAA
1 AATTTATTTAATTAA
2181174 AATTTA
1 AATTTA
2181180 ATTTTAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 11 0.38
15 14 0.48
16 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTTATTTAATTAA
Found at i:2181167 original size:29 final size:29
Alignment explanation
Indices: 2181135--2181194 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
2181125 ATTTAATTTA
*
2181135 ATTTAATTAATATTT-ATTTAATAAAATAT
1 ATTTAATTAAAATTTAATTTAA-AAAATAT
* *
2181164 ATTTTATTAAAATTTAATTTTAAAAATAT
1 ATTTAATTAAAATTTAATTTAAAAAATAT
2181193 AT
1 AT
2181195 AAATATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
ATTTAATTAAAATTTAATTTAAAAAATAT
Found at i:2181185 original size:16 final size:15
Alignment explanation
Indices: 2181129--2181185 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
2181119 ATTTTTATTT
*
2181129 AATTTAATTTAATTAA
1 AATTT-ATTTTATTAA
* *
2181145 TATTTA-TTTAATAA
1 AATTTATTTTATTAA
*
2181159 AATATATTTTATTAA
1 AATTTATTTTATTAA
2181174 AATTTAATTTTA
1 AATTT-ATTTTA
2181186 AAAATATATA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
14 10 0.31
15 12 0.38
16 10 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTTATTTTATTAA
Found at i:2184207 original size:21 final size:23
Alignment explanation
Indices: 2184170--2184217 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
2184160 TGATTTGGAG
2184170 TTTTGGATATAATTTTGTGATTA
1 TTTTGGATATAATTTTGTGATTA
*
2184193 TTTT-GATAT-ATTTTGTGTTTA
1 TTTTGGATATAATTTTGTGATTA
2184214 TTTT
1 TTTT
2184218 CATGTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 15 0.62
22 5 0.21
23 4 0.17
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.65
Consensus pattern (23 bp):
TTTTGGATATAATTTTGTGATTA
Found at i:2184494 original size:23 final size:23
Alignment explanation
Indices: 2184451--2184494 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2184441 TTAGAATTTA
*
2184451 AAAAAATGATAAATAATTATTCC
1 AAAAAATGATAAATAACTATTCC
*
2184474 AAAAAATAGTTAAA-AACTATT
1 AAAAAAT-GATAAATAACTATT
2184495 TATTTTGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (23 bp):
AAAAAATGATAAATAACTATTCC
Found at i:2184767 original size:29 final size:29
Alignment explanation
Indices: 2184735--2184920 Score: 116
Period size: 29 Copynumber: 6.5 Consensus size: 29
2184725 GATCAACATG
*
2184735 TAATTTTAAAAAGTTAAGGAGTTAAAATA
1 TAATTTTAAAAAGTTAAGGAGTCAAAATA
* **
2184764 TAATTTTAAAAAGTTTAAAGA-TCAAAACG
1 TAATTTTAAAAAG-TTAAGGAGTCAAAATA
* * * * *
2184793 TAATTTTGATAAGTTTAAGG-GTTAATATG
1 TAATTTTAAAAAG-TTAAGGAGTCAAAATA
* * **
2184822 TAATTTTAAAAA-ATAAGAAGTCAAAGCA
1 TAATTTTAAAAAGTTAAGGAGTCAAAATA
* * ** *
2184850 TAATTTTAAAAAGTTTAGGGGT-AATGTG
1 TAATTTTAAAAAGTTAAGGAGTCAAAATA
*
2184878 TAATTTTAAAAAATTTAA-GA-TCAAAATGA
1 TAATTTT-AAAAAGTTAAGGAGTCAAAAT-A
2184907 -AATTTTAAAAAGTT
1 TAATTTTAAAAAGTT
2184921 TAAAAATTTA
Statistics
Matches: 117, Mismatches: 33, Indels: 16
0.70 0.20 0.10
Matches are distributed among these distances:
27 12 0.10
28 36 0.31
29 63 0.54
30 6 0.05
ACGTcount: A:0.48, C:0.03, G:0.14, T:0.35
Consensus pattern (29 bp):
TAATTTTAAAAAGTTAAGGAGTCAAAATA
Found at i:2184911 original size:56 final size:56
Alignment explanation
Indices: 2184724--2184922 Score: 199
Period size: 56 Copynumber: 3.5 Consensus size: 56
2184714 GGCCATTTTG
* * * * * *
2184724 AGATCAACATGTAATTTTAAAAAGTTAAGGAGTTAAAATATAATTTTAAAAAGTTTAA
1 AGATCAAAATGAAATTTTAAAAAGTTTAGG-GTTAATATGTAATTTTAAAAAATTT-A
* * * *
2184782 AGATCAAAACGTAATTTTGATAAGTTTAAGGGTTAATATGTAATTTTAAAAAA--TA
1 AGATCAAAATGAAATTTTAAAAAGTTT-AGGGTTAATATGTAATTTTAAAAAATTTA
* *
2184837 AGAAGTC-AAA-GCATAATTTTAAAAAGTTTAGGGGTAATGTGTAATTTTAAAAAATTTA
1 AG-A-TCAAAATG-A-AATTTTAAAAAGTTTAGGGTTAATATGTAATTTTAAAAAATTTA
2184895 AGATCAAAATGAAATTTTAAAAAGTTTA
1 AGATCAAAATGAAATTTTAAAAAGTTTA
2184923 AAAATTTAAT
Statistics
Matches: 119, Mismatches: 13, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
55 4 0.03
56 46 0.39
57 20 0.17
58 46 0.39
59 3 0.03
ACGTcount: A:0.48, C:0.04, G:0.14, T:0.35
Consensus pattern (56 bp):
AGATCAAAATGAAATTTTAAAAAGTTTAGGGTTAATATGTAATTTTAAAAAATTTA
Found at i:2187457 original size:18 final size:19
Alignment explanation
Indices: 2187430--2187470 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
2187420 TAAATGTAAT
2187430 ATTTTGATT-ATAAT-TATA
1 ATTTTGATTAAT-ATGTATA
*
2187448 ATTTTTATTAATATGTATA
1 ATTTTGATTAATATGTATA
2187467 ATTT
1 ATTT
2187471 CATAAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
ATTTTGATTAATATGTATA
Found at i:2188168 original size:2 final size:2
Alignment explanation
Indices: 2188161--2188205 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2188151 GAGAAGGGTT
2188161 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
2188203 TA T
1 TA T
2188206 GTATGTATCG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2188627 original size:2 final size:2
Alignment explanation
Indices: 2188620--2188651 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2188610 AATCTTTCAA
2188620 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
2188652 CATGTTCCCC
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:2189057 original size:2 final size:2
Alignment explanation
Indices: 2189050--2189100 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
2189040 ATTATTTTGT
* *
2189050 TA TA TA TA TA TA TA -A CA AA TA -A 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
2189090 TA TA TA TA TA T
1 TA TA TA TA TA T
2189101 GAATGATTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2195576 original size:2 final size:2
Alignment explanation
Indices: 2195569--2195620 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
2195559 TGGATTCCTT
* *
2195569 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA CA 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
*
2195611 -A TT TA TA TA T
1 TA TA TA TA TA T
2195621 TAGCATTAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2196357 original size:21 final size:22
Alignment explanation
Indices: 2196315--2196369 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
2196305 CTCATTTTTC
2196315 AAAATGCATTCATTTTAGATAA
1 AAAATGCATTCATTTTAGATAA
* *
2196337 AAAATGCTTTCATTTT-TATAA
1 AAAATGCATTCATTTTAGATAA
2196358 ATCAAATGCATT
1 A--AAATGCATT
2196370 TCCAATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.18
22 15 0.54
23 8 0.29
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (22 bp):
AAAATGCATTCATTTTAGATAA
Found at i:2196424 original size:34 final size:34
Alignment explanation
Indices: 2196376--2196441 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
2196366 CATTTCCAAT
*
2196376 AAAATATAAAATGAAAACCGTTTTTAAGAAAATA
1 AAAATATAAAATGAAAACCATTTTTAAGAAAATA
* *
2196410 AAAATA-AAATATGAAAACTATTTTTTAGAAAA
1 AAAATATAAA-ATGAAAACCATTTTTAAGAAAA
2196442 ACCAAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 3 0.11
34 25 0.89
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.29
Consensus pattern (34 bp):
AAAATATAAAATGAAAACCATTTTTAAGAAAATA
Found at i:2197111 original size:2 final size:2
Alignment explanation
Indices: 2197071--2197098 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2197061 ACAAAAATAA
2197071 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
2197099 TGATTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2197811 original size:2 final size:2
Alignment explanation
Indices: 2197806--2197830 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2197796 AAATAATGAT
2197806 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2197831 TTTGACCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2198806 original size:14 final size:14
Alignment explanation
Indices: 2198787--2198817 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2198777 GAATACTTAA
*
2198787 ATATATATGTGTAT
1 ATATATATATGTAT
2198801 ATATATATATGTAT
1 ATATATATATGTAT
2198815 ATA
1 ATA
2198818 AATACAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (14 bp):
ATATATATATGTAT
Found at i:2198808 original size:16 final size:16
Alignment explanation
Indices: 2198787--2198817 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2198777 GAATACTTAA
*
2198787 ATATATATGTGTATAT
1 ATATATATGTATATAT
2198803 ATATATATGTATATA
1 ATATATATGTATATA
2198818 AATACAATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (16 bp):
ATATATATGTATATAT
Found at i:2199739 original size:5 final size:5
Alignment explanation
Indices: 2199729--2199757 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2199719 TTAGAGGTGA
2199729 TATAT TATAT TATAT TATAT TAT-T TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
2199758 ATGGCTGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:2200914 original size:19 final size:20
Alignment explanation
Indices: 2200890--2200938 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
2200880 TTTATTTTGA
*
2200890 TTTAATTTAAAATAGTAT-T
1 TTTAATTTAAAATAATATAT
2200909 TTTAA-TTAAAATAATATAT
1 TTTAATTTAAAATAATATAT
*
2200928 TTTTATTTAAA
1 TTTAATTTAAA
2200939 TTTTATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 10 0.38
20 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTAATTTAAAATAATATAT
Found at i:2200939 original size:19 final size:21
Alignment explanation
Indices: 2200900--2200938 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2200890 TTTAATTTAA
2200900 AATAGTATTTTTAATTAAAAT
1 AATAGTATTTTTAATTAAAAT
*
2200921 AATA-TATTTTTATTTAAA
1 AATAGTATTTTTAATTAAA
2200939 TTTTATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
AATAGTATTTTTAATTAAAAT
Found at i:2201994 original size:2 final size:2
Alignment explanation
Indices: 2201987--2202029 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2201977 TTTATGGCAA
2201987 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
2202029 A
1 A
2202030 AGTCAATAGT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2208513 original size:26 final size:29
Alignment explanation
Indices: 2208451--2208523 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 29
2208441 TATTGCTTTG
2208451 AAATTAATTTTTAAATTTTAATTTTCATCCT
1 AAATT-ATTTTT-AATTTTAATTTTCATCCT
2208482 -AA--ATTTTTAATTTTAA-TTT-AT-CT
1 AAATTATTTTTAATTTTAATTTTCATCCT
*
2208505 AAATTATTTTTATTTTTAA
1 AAATTATTTTTAATTTTAA
2208524 GAAATATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
23 2 0.05
24 4 0.11
25 3 0.08
26 21 0.55
27 6 0.16
30 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (29 bp):
AAATTATTTTTAATTTTAATTTTCATCCT
Found at i:2208663 original size:19 final size:21
Alignment explanation
Indices: 2208639--2208687 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
2208629 AAAATTATTT
2208639 AAATATAAATTAAA-A-ACTA
1 AAATATAAATTAAATATACTA
* *
2208658 AAATATTATTTAAATATACTA
1 AAATATAAATTAAATATACTA
2208679 AAATATAAA
1 AAATATAAA
2208688 AATTTACCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 12 0.50
20 1 0.04
21 11 0.46
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATATAAATTAAATATACTA
Found at i:2208687 original size:28 final size:28
Alignment explanation
Indices: 2208623--2208689 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 28
2208613 TTTCGTTTGG
*
2208623 AAATAAAAAATTATTTAAATATAAATTAA
1 AAATAAAAAATTATTTAAATAT-AACTAA
*
2208652 AAACTAAAATATTATTTAAATAT-ACTAA
1 AAA-TAAAAAATTATTTAAATATAACTAA
2208680 AATATAAAAA
1 AA-ATAAAAA
2208690 TTTACCTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 11 0.33
29 4 0.12
30 18 0.55
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (28 bp):
AAATAAAAAATTATTTAAATATAACTAA
Found at i:2209560 original size:2 final size:2
Alignment explanation
Indices: 2209555--2209597 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2209545 TGATATATAT
*
2209555 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AT AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2209597 A
1 A
2209598 AATATATTGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.47, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:2211754 original size:13 final size:13
Alignment explanation
Indices: 2211738--2211789 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
2211728 TTATTTAAAA
2211738 AATAATAAAATAT
1 AATAATAAAATAT
*
2211751 AATAATTAAATAT
1 AATAATAAAATAT
* *
2211764 AAAAATAATATA-
1 AATAATAAAATAT
2211776 AAT-ATATAAATAT
1 AATAATA-AAATAT
2211789 A
1 A
2211790 TCAAAATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 3 0.10
12 6 0.19
13 22 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAATAAAATAT
Found at i:2211796 original size:10 final size:8
Alignment explanation
Indices: 2211737--2211836 Score: 66
Period size: 8 Copynumber: 12.2 Consensus size: 8
2211727 ATTATTTAAA
2211737 AAATA-AT
1 AAATATAT
2211744 AAA-ATAT
1 AAATATAT
2211751 -AATA-ATT
1 AAATATA-T
*
2211758 AAATATAA
1 AAATATAT
2211766 AAATAATAT
1 AAAT-ATAT
2211775 AAATATAT
1 AAATATAT
2211783 AAATATAT
1 AAATATAT
*
2211791 CAAAATTTAT
1 --AAATATAT
*
2211801 AAATTTATT
1 AAATATA-T
2211810 AAATAT-T
1 AAATATAT
*
2211817 AAATTTATTT
1 AAA--TATAT
2211827 AAATATAT
1 AAATATAT
2211835 AA
1 AA
2211837 CCTTTTGTTC
Statistics
Matches: 76, Mismatches: 5, Indels: 23
0.73 0.05 0.22
Matches are distributed among these distances:
6 4 0.05
7 11 0.14
8 33 0.43
9 17 0.22
10 11 0.14
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (8 bp):
AAATATAT
Found at i:2213070 original size:2 final size:2
Alignment explanation
Indices: 2213057--2213086 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2213047 AGGAACAAGA
*
2213057 AT AT AC 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
2213087 GCACACACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2213120 original size:12 final size:12
Alignment explanation
Indices: 2213105--2213129 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2213095 TAATAGTAAC
2213105 ACTCAAATTGCG
1 ACTCAAATTGCG
2213117 ACTCAAATTGCG
1 ACTCAAATTGCG
2213129 A
1 A
2213130 TATTTTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (12 bp):
ACTCAAATTGCG
Found at i:2213668 original size:13 final size:13
Alignment explanation
Indices: 2213650--2213697 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
2213640 AACATTTTAT
2213650 ATAATATAAATAA
1 ATAATATAAATAA
2213663 ATAATATAAA-AA
1 ATAATATAAATAA
2213675 ATTAA-ATAAATATA
1 A-TAATATAAATA-A
2213689 ATATATATA
1 ATA-ATATA
2213698 TTAAAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 8 0.27
13 16 0.53
14 3 0.10
15 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
ATAATATAAATAA
Found at i:2213671 original size:9 final size:9
Alignment explanation
Indices: 2213648--2213719 Score: 51
Period size: 9 Copynumber: 7.9 Consensus size: 9
2213638 ATAACATTTT
2213648 ATATAATATA
1 ATATAA-ATA
2213658 A-ATAAATA
1 ATATAAATA
*
2213666 ATATAAAAA
1 ATATAAATA
2213675 AT-TAAATAA
1 ATATAAAT-A
2213684 ATATAATATA
1 ATATAA-ATA
*
2213694 TATATTAA-A
1 -ATATAAATA
* *
2213703 ATTTATATA
1 ATATAAATA
2213712 ATATAAAT
1 ATATAAAT
2213720 TATTAATATA
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
8 12 0.25
9 23 0.48
10 6 0.12
11 7 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
ATATAAATA
Found at i:2213702 original size:18 final size:18
Alignment explanation
Indices: 2213681--2213743 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 18
2213671 AAAAATTAAA
*
2213681 TAAATATAATATATATAT
1 TAAATATATTATATATAT
2213699 TAAA-AT-TTATATA-AT
1 TAAATATATTATATATAT
2213714 ATAAAT-TATTA-ATATAT
1 -TAAATATATTATATATAT
2213731 TAAAT-T-TTATATA
1 TAAATATATTATATA
2213744 AATATATACT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
15 5 0.13
16 23 0.59
17 7 0.18
18 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATATATTATATATAT
Found at i:2213704 original size:23 final size:24
Alignment explanation
Indices: 2213663--2213725 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
2213653 ATATAAATAA
**
2213663 ATAATATAAAAAATT-AAATAAAT
1 ATAATATAAATTATTAAAATAAAT
* **
2213686 ATAATATATA-TATTAAAATTTAT
1 ATAATATAAATTATTAAAATAAAT
2213709 ATAATATAAATTATTAA
1 ATAATATAAATTATTAA
2213726 TATATTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 3 0.09
23 24 0.73
24 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATAATATAAATTATTAAAATAAAT
Found at i:2213711 original size:14 final size:14
Alignment explanation
Indices: 2213692--2213743 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
2213682 AAATATAATA
2213692 TATATATTAAAATT
1 TATATATTAAAATT
2213706 TATATAATATAAATTATT
1 TATAT-AT-TAAA--ATT
* *
2213724 AATATATTAAATTT
1 TATATATTAAAATT
2213738 TATATA
1 TATATA
2213744 AATATATACT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 12 0.39
15 2 0.06
16 8 0.26
17 2 0.06
18 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATATTAAAATT
Found at i:2213711 original size:16 final size:16
Alignment explanation
Indices: 2213690--2213743 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
2213680 ATAAATATAA
*
2213690 TATATATATTAAAATT
1 TATATATATTAAATTT
2213706 TATATA-ATATAAATTAT
1 TATATATAT-TAAATT-T
2213723 TA-ATATATTAAATTT
1 TATATATATTAAATTT
2213738 TATATA
1 TATATA
2213744 AATATATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 5 0.15
16 23 0.70
17 5 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATATATTAAATTT
Found at i:2217113 original size:18 final size:18
Alignment explanation
Indices: 2217090--2217124 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2217080 TAAAATAAAT
*
2217090 AAAATTTTAAATATATAA
1 AAAATTTAAAATATATAA
2217108 AAAATTTAAAATATATA
1 AAAATTTAAAATATATA
2217125 TTTATATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATTTAAAATATATAA
Found at i:2217122 original size:16 final size:15
Alignment explanation
Indices: 2217066--2217120 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
2217056 TGAAAATTTA
2217066 TTAAAATAAAAAAA-
1 TTAAAATAAAAAAAT
2217080 -TAAAATAAATAAAATT
1 TTAAAATAAA-AAAA-T
2217096 TTAAATATATAAAAAAT
1 TTAAA-ATA-AAAAAAT
2217113 TTAAAATA
1 TTAAAATA
2217121 TATATTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
13 9 0.26
14 4 0.11
16 3 0.09
17 10 0.29
18 7 0.20
19 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAAATAAAAAAAT
Found at i:2217613 original size:14 final size:14
Alignment explanation
Indices: 2217571--2217622 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
2217561 TCGATTTTGA
*
2217571 TTAAATTAATAAAT
1 TTAAATTAATTAAT
* * *
2217585 TTTATTTTATATAAT
1 TTAAATTAAT-TAAT
2217600 TTAAATTAATTAAT
1 TTAAATTAATTAAT
2217614 TTAAATTAA
1 TTAAATTAA
2217623 ATTATTATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 20 0.67
15 10 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAAATTAATTAAT
Found at i:2231543 original size:2 final size:2
Alignment explanation
Indices: 2231531--2231565 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2231521 ACGAACATAC
*
2231531 AT AT A- AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2231566 CCTAGCTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2235028 original size:19 final size:19
Alignment explanation
Indices: 2235004--2235044 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2234994 ATATCTGATA
2235004 ATTTATATATTCGTATTAT
1 ATTTATATATTCGTATTAT
**
2235023 ATTTATATATTTTTATTAT
1 ATTTATATATTCGTATTAT
2235042 ATT
1 ATT
2235045 ATAATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTATATATTCGTATTAT
Found at i:2236296 original size:86 final size:87
Alignment explanation
Indices: 2236147--2236310 Score: 303
Period size: 86 Copynumber: 1.9 Consensus size: 87
2236137 TTGGTCTGAG
2236147 TGCATAAACACTTATAATTGATTTTTTTTAATTTTTTATATTATTTATTTTTAAGTTACCGTATT
1 TGCATAAACACTTATAATTGATTTTTTTTAATTTTTTATATTATTTATTTTTAAGTTACCGTATT
2236212 TAAAAATTCACATTAGTTTGAA
66 TAAAAATTCACATTAGTTTGAA
*
2236234 TGCATAAACACTTATAATTGATTTTTTTTAA-TTTTTATATTATTTATTTTTAAGTTATCGTATT
1 TGCATAAACACTTATAATTGATTTTTTTTAATTTTTTATATTATTTATTTTTAAGTTACCGTATT
*
2236298 TAAAAATTTACAT
66 TAAAAATTCACAT
2236311 AAAATATGAA
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
86 44 0.59
87 31 0.41
ACGTcount: A:0.34, C:0.07, G:0.06, T:0.53
Consensus pattern (87 bp):
TGCATAAACACTTATAATTGATTTTTTTTAATTTTTTATATTATTTATTTTTAAGTTACCGTATT
TAAAAATTCACATTAGTTTGAA
Found at i:2241559 original size:21 final size:21
Alignment explanation
Indices: 2241521--2241561 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2241511 TTTACAAGAC
*
2241521 ATATTTTAATATTTAAATTAT
1 ATATTTTAATATTCAAATTAT
2241542 ATATTTTAACT-TTCAAATTA
1 ATATTTTAA-TATTCAAATTA
2241562 AAAGTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATTTTAATATTCAAATTAT
Found at i:2244743 original size:26 final size:27
Alignment explanation
Indices: 2244699--2244757 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
2244689 TAAATTAATA
2244699 ATTTATATTATATAAAATT-TTAAATT
1 ATTTATATTATATAAAATTATTAAATT
* ** *
2244725 ATTTTTATTATATTTAATTATTATATT
1 ATTTATATTATATAAAATTATTAAATT
2244752 AATTTA
1 -ATTTA
2244758 ATATATTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 16 0.62
27 6 0.23
28 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
ATTTATATTATATAAAATTATTAAATT
Found at i:2244747 original size:13 final size:12
Alignment explanation
Indices: 2244729--2244767 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
2244719 TAAATTATTT
2244729 TTATTATATTTAA
1 TTATTATA-TTAA
2244742 TTATTATATTAA
1 TTATTATATTAA
*
2244754 TTTAATATATTAA
1 -TTATTATATTAA
2244767 T
1 T
2244768 AGTTTATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 5 0.21
13 19 0.79
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATTATATTAA
Found at i:2244764 original size:18 final size:18
Alignment explanation
Indices: 2244730--2244765 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2244720 AAATTATTTT
2244730 TATTATATTTAATTATTA
1 TATTATATTTAATTATTA
2244748 TATTA-ATTTAATATATTA
1 TATTATATTTAAT-TATTA
2244766 ATAGTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATATTTAATTATTA
Found at i:2244802 original size:70 final size:69
Alignment explanation
Indices: 2244673--2244803 Score: 165
Period size: 70 Copynumber: 1.9 Consensus size: 69
2244663 TATTTTATAT
* * ** *
2244673 TTATTATAAAATTTTATAAATTAATAATTTATATTATATAAAATTTTAAATTATTTTTATTATAT
1 TTATTATAAAATTTAATAAATTAATAATTTATATGATATAAAATTAAAAATAATTTTTATTATAT
2244738 TTAA
66 TTAA
* * *
2244742 TTATTATATTAATTTAATATATTAATAGTTTATATGATAT-AAATTAAAAATAATTGTTTATT
1 TTATTATA-AAATTTAATAAATTAATAATTTATATGATATAAAATTAAAAATAATT-TTTATT
2244804 TTTATTTTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
69 20 0.38
70 32 0.62
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (69 bp):
TTATTATAAAATTTAATAAATTAATAATTTATATGATATAAAATTAAAAATAATTTTTATTATAT
TTAA
Found at i:2250216 original size:17 final size:16
Alignment explanation
Indices: 2250194--2250250 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 16
2250184 TAAAGTCTCA
2250194 TAAATTTAATTTATAAT
1 TAAATTTAATTT-TAAT
*
2250211 TAAATTTTAAATTTAAT
1 TAAA-TTTAATTTTAAT
2250228 ATAAA-TTAA-TTTAAT
1 -TAAATTTAATTTTAAT
2250243 T-AATTTAA
1 TAAATTTAA
2250251 ATATTAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 2 0.06
14 5 0.14
15 6 0.17
16 4 0.11
17 8 0.22
18 11 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAAATTTAATTTTAAT
Found at i:2250245 original size:9 final size:9
Alignment explanation
Indices: 2250231--2250274 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
2250221 ATTTAATATA
2250231 AATTAATTT
1 AATTAATTT
2250240 AATTAATTT
1 AATTAATTT
* *
2250249 AAAT-ATTA
1 AATTAATTT
*
2250257 AATTAATTA
1 AATTAATTT
2250266 AATTAATTT
1 AATTAATTT
2250275 TACATTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 6 0.20
9 24 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
AATTAATTT
Found at i:2250252 original size:30 final size:32
Alignment explanation
Indices: 2250193--2250273 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 32
2250183 TTAAAGTCTC
2250193 ATAAATTTAATTTATAATTAAATTTTAAAT-TTAA
1 ATAAA-TTAA-TT-TAATTAAATTTTAAATATTAA
2250227 TATAAATTAATTTAATT-AA-TTTAAATATTAA
1 -ATAAATTAATTTAATTAAATTTTAAATATTAA
* *
2250258 ATTAATTAAATTAATT
1 ATAAATTAATTTAATT
2250274 TTACATTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
30 21 0.49
31 6 0.14
32 5 0.12
33 2 0.05
34 4 0.09
35 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
ATAAATTAATTTAATTAAATTTTAAATATTAA
Found at i:2250256 original size:21 final size:21
Alignment explanation
Indices: 2250232--2250271 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2250222 TTTAATATAA
* *
2250232 ATTAATTTAATTAATTTAAAT
1 ATTAAATTAATTAAATTAAAT
2250253 ATTAAATTAATTAAATTAA
1 ATTAAATTAATTAAATTAA
2250272 TTTTACATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTAAATTAATTAAATTAAAT
Found at i:2250263 original size:26 final size:24
Alignment explanation
Indices: 2250220--2250274 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 24
2250210 TTAAATTTTA
*
2250220 AATTTAATATAAATTAATTTAATT
1 AATTTAATATAAATTAATTAAATT
2250244 AATTTAAATATTAAATTAATTAAATT
1 AATTT-AATA-TAAATTAATTAAATT
2250270 AATTT
1 AATTT
2250275 TACATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 5 0.18
25 4 0.14
26 19 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTTAATATAAATTAATTAAATT
Found at i:2250283 original size:26 final size:24
Alignment explanation
Indices: 2250196--2250284 Score: 76
Period size: 26 Copynumber: 3.5 Consensus size: 24
2250186 AAGTCTCATA
2250196 AATTTAATTT--A-TAATTAAATTTT
1 AATTTAATTTAAATTAATTAAA--TT
* *
2250219 AAATTTAATATAAATTAATTTAATT
1 -AATTTAATTTAAATTAATTAAATT
2250244 AATTTAAATATTAAATTAATTAAATT
1 AATTT-AAT-TTAAATTAATTAAATT
2250270 AATTTTACATTTAAA
1 AA-TTTA-ATTTAAA
2250285 AATTTTAAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
24 14 0.26
25 5 0.09
26 23 0.43
27 12 0.22
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTTAATTTAAATTAATTAAATT
Found at i:2256426 original size:4 final size:4
Alignment explanation
Indices: 2256417--2256448 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
2256407 TGTTGAATCT
2256417 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
2256449 TTTTAGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:2258793 original size:15 final size:16
Alignment explanation
Indices: 2258736--2258813 Score: 55
Period size: 15 Copynumber: 5.3 Consensus size: 16
2258726 ACATAAATAT
2258736 ATAATAA-TAAT-TAA
1 ATAATAATTAATATAA
* *
2258750 ATTATAATAAAT-TAA
1 ATAATAATTAATATAA
2258765 A-AAT-A-TATATATAA
1 ATAATAATTA-ATATAA
2258779 ATAA-AATTAATAT-A
1 ATAATAATTAATATAA
* *
2258793 ATAATTATTAATATAT
1 ATAATAATTAATATAA
2258809 ATAAT
1 ATAAT
2258814 TTATATAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
12 1 0.02
13 3 0.06
14 17 0.34
15 22 0.44
16 7 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAATAATTAATATAA
Found at i:2258805 original size:24 final size:22
Alignment explanation
Indices: 2258749--2258805 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
2258739 ATAATAATTA
2258749 AATTA-TAAT-AAATTAAAAAT
1 AATTATTAATAAAATTAAAAAT
*
2258769 ATATATATAAATAAAATTAATATAAT
1 A-AT-TATTAATAAAATTAA-A-AAT
2258795 AATTATTAATA
1 AATTATTAATA
2258806 TATATAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
20 1 0.03
21 2 0.07
22 2 0.07
23 3 0.10
24 14 0.48
25 3 0.10
26 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTATTAATAAAATTAAAAAT
Found at i:2258808 original size:17 final size:17
Alignment explanation
Indices: 2258731--2258826 Score: 63
Period size: 18 Copynumber: 5.4 Consensus size: 17
2258721 ATATGACATA
*
2258731 AATATATAATAATAATT
1 AATATATAATAATTATT
**
2258748 AA-ATTATAATAAATTAAA
1 AATA-TATAAT-AATTATT
* *
2258766 AATATATATATAAATA-A
1 AATATATA-ATAATTATT
2258783 AATTAATATAATAATTATT
1 AA-T-ATATAATAATTATT
2258802 AATATAT-ATAATTTATAT
1 AATATATAATAA-TTAT-T
2258820 AATATAT
1 AATATAT
2258827 GAATTTTAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 17
0.74 0.07 0.20
Matches are distributed among these distances:
16 5 0.08
17 19 0.30
18 30 0.47
19 10 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATATAATAATTATT
Found at i:2258814 original size:16 final size:17
Alignment explanation
Indices: 2258784--2258826 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
2258774 TATAAATAAA
2258784 ATTAATATA-ATAA-TT
1 ATTAATATATATAATTT
2258799 ATTAATATATATAATTT
1 ATTAATATATATAATTT
2258816 ATATAATATAT
1 AT-TAATATAT
2258827 GAATTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.36
16 4 0.16
17 4 0.16
18 8 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTAATATATATAATTT
Found at i:2258819 original size:28 final size:28
Alignment explanation
Indices: 2258694--2258823 Score: 80
Period size: 28 Copynumber: 4.9 Consensus size: 28
2258684 CAAAGTAGAG
* *
2258694 TTAATATATTTAA--AATAAAATAA-TA
1 TTAATATATATAATTAATATAATAATTA
* * *
2258719 TT-ATATGACATAAAT-ATATAATAATAA
1 TTAATAT-ATATAATTAATATAATAATTA
* *
2258746 TTAA-AT-TATAATAAAT-TAA-AAATA
1 TTAATATATATAATTAATATAATAATTA
* *
2258770 TATATATAAATAAAATTAATATAATAATTA
1 T-TA-ATATATATAATTAATATAATAATTA
*
2258800 TTAATATATATAATTTATATAATA
1 TTAATATATATAATTAATATAATA
2258824 TATGAATTTT
Statistics
Matches: 77, Mismatches: 16, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
24 8 0.10
25 15 0.19
26 11 0.14
27 6 0.08
28 27 0.35
29 5 0.06
30 5 0.06
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (28 bp):
TTAATATATATAATTAATATAATAATTA
Found at i:2264760 original size:16 final size:15
Alignment explanation
Indices: 2264741--2264791 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
2264731 TATATTTTTT
2264741 TTAAAAAATATAAATA
1 TTAAAAAAT-TAAATA
** *
2264757 TTAAAATTTTAAATT
1 TTAAAAAATTAAATA
2264772 TTAAACAAATTAAATA
1 TTAAA-AAATTAAATA
2264788 TTAA
1 TTAA
2264792 TTTTAATAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAAAAAATTAAATA
Found at i:2266486 original size:21 final size:21
Alignment explanation
Indices: 2266462--2266508 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
2266452 AATATTTTAA
*
2266462 TTAATTCAAGTAAT-ACAAATT
1 TTAATTAAAGTAATCA-AAATT
*
2266483 TTAAATTAAATTAATCAAAATT
1 TT-AATTAAAGTAATCAAAATT
2266505 TTAA
1 TTAA
2266509 CTTCTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 4 0.18
22 17 0.77
23 1 0.05
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAATTAAAGTAATCAAAATT
Found at i:2269203 original size:13 final size:13
Alignment explanation
Indices: 2269186--2269307 Score: 76
Period size: 13 Copynumber: 9.5 Consensus size: 13
2269176 AAAATTTTAA
*
2269186 ATATAAT-TATAT
1 ATATAATATAAAT
2269198 AATATAATATAAAT
1 -ATATAATATAAAT
* * *
2269212 AAATATTATACAT
1 ATATAATATAAAT
2269225 AT-T-ATATAAAT
1 ATATAATATAAAT
* **
2269236 ATATTAAAATTTAT
1 ATA-TAATATAAAT
2269250 ATA-AATATAAAAT
1 ATATAATAT-AAAT
*
2269263 ATTTTAA-ATATAAT
1 A-TATAATATA-AAT
*
2269277 -TATAATATAAAA
1 ATATAATATAAAT
2269289 ATATAATATAAAT
1 ATATAATATAAAT
2269302 ATATAA
1 ATATAA
2269308 AATCATTCAA
Statistics
Matches: 82, Mismatches: 17, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
11 8 0.10
12 11 0.13
13 43 0.52
14 18 0.22
15 2 0.02
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATAATATAAAT
Found at i:2269215 original size:4 final size:5
Alignment explanation
Indices: 2269185--2269307 Score: 66
Period size: 5 Copynumber: 25.4 Consensus size: 5
2269175 AAAAATTTTA
* *
2269185 AATAT AAT-T -ATAT AATAT AATAT AA-AT AA-AT ATTAT ACATAT TATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT A-ATAT AATAT
* * * * * *
2269232 AAATAT ATTAA AAT-T TATAT AAATAT AAAAT ATTTT AAATAT AATTAT
1 -AATAT AATAT AATAT AATAT -AATAT AATAT AATAT -AATAT AA-TAT
2269280 AATAT AA-A- AATAT AATAT AA-AT -ATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AA
2269308 AATCATTCAA
Statistics
Matches: 89, Mismatches: 16, Indels: 26
0.68 0.12 0.20
Matches are distributed among these distances:
3 5 0.06
4 17 0.19
5 48 0.54
6 19 0.21
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.41
Consensus pattern (5 bp):
AATAT
Found at i:2269239 original size:22 final size:22
Alignment explanation
Indices: 2269183--2269310 Score: 86
Period size: 20 Copynumber: 6.2 Consensus size: 22
2269173 TCAAAAATTT
*
2269183 TAAATATAATTATATAATATAATA
1 TAAATAT-ATTATA-AATATTATA
*
2269207 TAAATAAATATTATACATATTATA
1 TAAAT--ATATTATAAATATTATA
2269231 TAAATATATTA-AAAT-TTATA
1 TAAATATATTATAAATATTATA
2269251 T-AA-ATA-TA-AAATATT-T-
1 TAAATATATTATAAATATTATA
2269267 TAAATATAATTAT-AATA-TA-A
1 TAAATAT-ATTATAAATATTATA
*
2269287 -AAATATAATATAAATA-TATA
1 TAAATATATTATAAATATTATA
2269307 -AAAT
1 TAAAT
2269311 CATTCAATGA
Statistics
Matches: 88, Mismatches: 4, Indels: 28
0.73 0.03 0.23
Matches are distributed among these distances:
16 1 0.01
17 9 0.10
18 11 0.12
19 16 0.18
20 17 0.19
21 3 0.03
22 6 0.07
24 17 0.19
25 6 0.07
26 2 0.02
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATATATTATAAATATTATA
Found at i:2269301 original size:11 final size:11
Alignment explanation
Indices: 2269183--2269304 Score: 81
Period size: 11 Copynumber: 10.7 Consensus size: 11
2269173 TCAAAAATTT
2269183 TAAATATAATTA
1 TAAATATAA-TA
2269195 TATAATATAATA
1 TA-AATATAATA
2269207 TAAATA-AATA
1 TAAATATAATA
*
2269217 TTATACATATTATA
1 -TA-A-ATATAATA
*
2269231 TAAATATATTA
1 TAAATATAATA
*
2269242 -AAAT-TTATA
1 TAAATATAATA
*
2269251 TAAATATAAAA
1 TAAATATAATA
* *
2269262 T-ATTTTAAATA
1 TAAATAT-AATA
*
2269273 TAATTATAATA
1 TAAATATAATA
2269284 TAAAAATATAATA
1 T--AAATATAATA
2269297 TAAATATA
1 TAAATATA
2269305 TAAAATCATT
Statistics
Matches: 87, Mismatches: 12, Indels: 23
0.71 0.10 0.19
Matches are distributed among these distances:
9 3 0.03
10 15 0.17
11 32 0.37
12 12 0.14
13 22 0.25
14 3 0.03
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAATATAATA
Found at i:2273162 original size:21 final size:20
Alignment explanation
Indices: 2273101--2273162 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
2273091 ACTATTTAAT
*
2273101 TAAATTTAAATTTAACTTATTAAA
1 TAAA-TTAAATTTAA-ATATT--A
2273125 TAAATTAAATTTAAATATTA
1 TAAATTAAATTTAAATATTA
* *
2273145 TAATATTTAATTTGAATA
1 TAA-ATTAAATTTAAATA
2273163 AGTAATGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 4 0.12
21 12 0.35
22 4 0.12
23 10 0.29
24 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
TAAATTAAATTTAAATATTA
Found at i:2275739 original size:14 final size:14
Alignment explanation
Indices: 2275720--2275749 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2275710 CGTTCATCGG
2275720 TGACAGAATTGATA
1 TGACAGAATTGATA
2275734 TGACAGAATTGATA
1 TGACAGAATTGATA
2275748 TG
1 TG
2275750 GCATATCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (14 bp):
TGACAGAATTGATA
Found at i:2282612 original size:3 final size:3
Alignment explanation
Indices: 2282606--2282639 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2282596 TAATAATAAT
* *
2282606 AAG AAG AAG AAG AAG CAG AAG AAG AAG GAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
2282640 CAACATACCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2283088 original size:21 final size:21
Alignment explanation
Indices: 2283064--2283103 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2283054 CTTTAATAAC
*
2283064 AAAAAAATATATTATTAAATT
1 AAAAAAATATATTAATAAATT
*
2283085 AAAATAATATATTAATAAA
1 AAAAAAATATATTAATAAA
2283104 ATTTATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAAAATATATTAATAAATT
Found at i:2283256 original size:14 final size:14
Alignment explanation
Indices: 2283237--2283289 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
2283227 ATTAAATAAT
*
2283237 TTTTATTTATATTA
1 TTTTATTTTTATTA
*
2283251 TTTTATATTTTATAA
1 TTTTAT-TTTTATTA
*
2283266 TTTTATTTTTATTT
1 TTTTATTTTTATTA
2283280 TTTTATTTTT
1 TTTTATTTTT
2283290 TATTTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTTTTATTA
Found at i:2283278 original size:29 final size:30
Alignment explanation
Indices: 2283232--2283292 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
2283222 GAGTAATTAA
2283232 ATAATTTTTATTTATATTATTTTATATTTT
1 ATAATTTTTATTTATATTATTTTATATTTT
* * *
2283262 ATAA-TTTTATTTTTATTTTTTTATTTTTT
1 ATAATTTTTATTTATATTATTTTATATTTT
2283291 AT
1 AT
2283293 TTAAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (30 bp):
ATAATTTTTATTTATATTATTTTATATTTT
Found at i:2283293 original size:15 final size:14
Alignment explanation
Indices: 2283236--2283294 Score: 64
Period size: 15 Copynumber: 4.1 Consensus size: 14
2283226 AATTAAATAA
*
2283236 TTTTTATTTATATT
1 TTTTTATTTTTATT
* *
2283250 ATTTTATATTTTATA
1 TTTTTAT-TTTTATT
*
2283265 ATTTTATTTTTATT
1 TTTTTATTTTTATT
2283279 TTTTTATTTTTTATT
1 TTTTTA-TTTTTATT
2283294 T
1 T
2283295 AAAAAATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
14 17 0.45
15 21 0.55
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:2283316 original size:130 final size:132
Alignment explanation
Indices: 2283140--2283392 Score: 363
Period size: 132 Copynumber: 1.9 Consensus size: 132
2283130 AAAAAATTAT
* *
2283140 TTTTTACTATTTTTTATTTTTTATTTAAAAACATAAAAATACTTTTTTTACTATTATTTA-TTTT
1 TTTTTACTATTTTTTATTTTTTATTTAAAAACATAAAAATACTTTTTTTACTACTACTTACTTTT
* *
2283204 TTTATTTAAAAAATTTATGAGTAATTAAATAATTTTTAT-TTATATTATTTTATATTTTATAATT
66 TTTATTTAAAAAAATTATGAGTAATTAAATAATTTTTATATTATATAATTTT-TATTTTATAATT
2283268 TTA
130 TTA
*
2283271 TTTTTA-T-TTTTTTATTTTTTATTTAAAAAATATAAAAATTA-TTTTTTTACTACTACTTACTT
1 TTTTTACTATTTTTTATTTTTTATTT-AAAAACATAAAAA-TACTTTTTTTACTACTACTTAC-T
* * *
2283333 TTTTTTATTTAAAAAAATTATGATTAATTAAATATTTTTTATATTTTATAATTTTTATTT
63 TTTTTTATTTAAAAAAATTATGAGTAATTAAATAATTTTTATATTATATAATTTTTATTT
2283393 CACTCATTTC
Statistics
Matches: 109, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
129 17 0.16
130 29 0.27
131 8 0.07
132 45 0.41
133 10 0.09
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (132 bp):
TTTTTACTATTTTTTATTTTTTATTTAAAAACATAAAAATACTTTTTTTACTACTACTTACTTTT
TTTATTTAAAAAAATTATGAGTAATTAAATAATTTTTATATTATATAATTTTTATTTTATAATTT
TA
Found at i:2283440 original size:15 final size:16
Alignment explanation
Indices: 2283420--2283452 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2283410 ATAATTTGAT
2283420 ATAATTAAATAA-AAA
1 ATAATTAAATAATAAA
*
2283435 ATAATTAATTAATAAA
1 ATAATTAAATAATAAA
2283451 AT
1 AT
2283453 TTTAATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAATTAAATAATAAA
Found at i:2283763 original size:20 final size:20
Alignment explanation
Indices: 2283738--2283775 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2283728 AATGTCAATT
2283738 TAATTAATAAAACTAATTAC
1 TAATTAATAAAACTAATTAC
* *
2283758 TAATTACTAATACTAATT
1 TAATTAATAAAACTAATT
2283776 TAATATTACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATTAATAAAACTAATTAC
Found at i:2294545 original size:18 final size:17
Alignment explanation
Indices: 2294506--2294558 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
2294496 ATATGTTTAG
*
2294506 AAATTTTTATAATT-T-
1 AAATTTATATAATTATA
2294521 AAA-TTAT-TAATATATTA
1 AAATTTATATAAT-TA-TA
2294538 AAATTTATATAATTATA
1 AAATTTATATAATTATA
2294555 AAAT
1 AAAT
2294559 ATTTTATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
13 4 0.13
14 4 0.13
15 3 0.10
16 1 0.03
17 9 0.29
18 6 0.19
19 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTTATATAATTATA
Found at i:2297578 original size:14 final size:14
Alignment explanation
Indices: 2297559--2297591 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
2297549 CACCAGAAAG
2297559 AGATTTGGAAGTTC
1 AGATTTGGAAGTTC
2297573 AGATTTGGAAGTTC
1 AGATTTGGAAGTTC
2297587 AGATT
1 AGATT
2297592 GATGGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.36
Consensus pattern (14 bp):
AGATTTGGAAGTTC
Found at i:2299443 original size:19 final size:21
Alignment explanation
Indices: 2299419--2299467 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
2299409 TTATTTAAAA
2299419 ATATTAAAATAT-TAT-TTTT
1 ATATTAAAATATATATATTTT
* *
2299438 ATATTAATATTTATATATTTT
1 ATATTAAAATATATATATTTT
2299459 ATAATTAAA
1 AT-ATTAAA
2299468 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 10 0.42
20 3 0.12
21 6 0.25
22 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATTAAAATATATATATTTT
Found at i:2306477 original size:15 final size:16
Alignment explanation
Indices: 2306459--2306496 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2306449 TGTTTTATTC
2306459 TTTTAATTTTTA-ATT
1 TTTTAATTTTTACATT
*
2306474 TTTTATTTTTTACTATT
1 TTTTAATTTTTAC-ATT
2306491 TTTTAA
1 TTTTAA
2306497 AAAGCGTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 11 0.58
17 8 0.42
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTAATTTTTACATT
Found at i:2308945 original size:27 final size:27
Alignment explanation
Indices: 2308896--2308948 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2308886 AATTCCCCTG
2308896 AAACCCTCAGTTTTCCATATGTATTTC
1 AAACCCTCAGTTTTCCATATGTATTTC
2308923 AAACCCTGCA-TTGTTCCAT-TGTATTT
1 AAACCCT-CAGTT-TTCCATATGTATTT
2308949 TATACTCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.42
Consensus pattern (27 bp):
AAACCCTCAGTTTTCCATATGTATTTC
Found at i:2311555 original size:9 final size:9
Alignment explanation
Indices: 2311527--2311682 Score: 76
Period size: 9 Copynumber: 17.3 Consensus size: 9
2311517 ATTATACGAT
*
2311527 TAAAAAATA
1 TAAAATATA
2311536 TAAAATA-A
1 TAAAATATA
2311544 TAAAATATA
1 TAAAATATA
2311553 TAATATAGATATA
1 T-A-A-A-ATATA
* *
2311566 AAAAATATT
1 TAAAATATA
2311575 TAAAATAT-
1 TAAAATATA
2311583 TATAAA-ATA
1 TA-AAATATA
2311592 T-AAAT-TA
1 TAAAATATA
* *
2311599 T-TAATTTA
1 TAAAATATA
* *
2311607 TTAAATTTA
1 TAAAATATA
*
2311616 TATAA-ATA
1 TAAAATATA
*
2311624 TAAAATATT
1 TAAAATATA
*
2311633 TTAAATATAA
1 TAAAATAT-A
*
2311643 TTAAAATAAA
1 -TAAAATATA
2311653 TAAAATATA
1 TAAAATATA
*
2311662 T-TAATATA
1 TAAAATATA
2311670 TATAAATATA
1 TA-AAATATA
2311680 TAA
1 TAA
2311683 CTTATTAAGT
Statistics
Matches: 114, Mismatches: 18, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
7 9 0.08
8 28 0.25
9 51 0.45
10 11 0.10
11 8 0.07
12 2 0.02
13 5 0.04
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (9 bp):
TAAAATATA
Found at i:2311570 original size:22 final size:22
Alignment explanation
Indices: 2311532--2311669 Score: 67
Period size: 22 Copynumber: 6.3 Consensus size: 22
2311522 ACGATTAAAA
2311532 AATATAAAATAATAAAATATAT
1 AATATAAAATAATAAAATATAT
*
2311554 AATATAGATATAA-AAAATAT-T
1 AATATA-AAATAATAAAATATAT
*
2311575 --TA-AAATATTATAAAATATA-
1 AATATAAA-ATAATAAAATATAT
** * *
2311594 AATTATTAATTTATTAAATTTATAT
1 AA-TA-TAAAATAATAAA-ATATAT
* **
2311619 AAATATAAAATATTTTAA-ATAT
1 -AATATAAAATAATAAAATATAT
2311641 AAT-TAAAATAAATAAAATATATT
1 AATATAAAAT-AATAAAATATA-T
2311664 AATATA
1 AATATA
2311670 TATAAATATA
Statistics
Matches: 84, Mismatches: 16, Indels: 30
0.65 0.12 0.23
Matches are distributed among these distances:
17 1 0.01
18 4 0.05
19 9 0.11
20 6 0.07
21 8 0.10
22 22 0.26
23 14 0.17
24 16 0.19
25 2 0.02
26 2 0.02
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (22 bp):
AATATAAAATAATAAAATATAT
Found at i:2311593 original size:39 final size:36
Alignment explanation
Indices: 2311510--2311594 Score: 91
Period size: 37 Copynumber: 2.2 Consensus size: 36
2311500 TAATAATTTT
*
2311510 AAATATTATTATACGATTAAAAAATATAAAATAATAA
1 AAATA-TAATATACGATTAAAAAATATAAAATAATAA
*
2311547 AATATATAATATA-GATATAAAAAATATTTAAAATATTATA
1 AA-ATATAATATACGAT-TAAAAAATA--TAAAATAATA-A
2311587 AAATATAA
1 AAATATAA
2311595 ATTATTAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
36 3 0.07
37 17 0.41
38 3 0.07
39 15 0.37
40 3 0.07
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (36 bp):
AAATATAATATACGATTAAAAAATATAAAATAATAA
Found at i:2311629 original size:58 final size:54
Alignment explanation
Indices: 2311532--2311679 Score: 151
Period size: 58 Copynumber: 2.7 Consensus size: 54
2311522 ACGATTAAAA
* *
2311532 AATATAAAAT-AATAAAATATA-TAATATAGAT--ATAAAAAATATTTAAAATAT
1 AATA-AAAATAAATAAAATATATTAATATATATAAATATAAAATATTTAAAATAT
* * * * *
2311583 TATAAAATATAAATTATTAATTTATTAAATTTATATAAATATAAAATATTTTAAATAT
1 AATAAAA-ATAAA-TA-AAATATATT-AATATATATAAATATAAAATATTTAAAATAT
*
2311641 AATTAAAATAAATAAAATATATTAATATATATAAATATA
1 AATAAAAATAAATAAAATATATTAATATATATAAATATA
2311680 TAACTTATTA
Statistics
Matches: 77, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
50 3 0.04
51 5 0.06
52 2 0.03
53 2 0.03
54 20 0.26
55 8 0.10
56 9 0.12
57 5 0.06
58 23 0.30
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (54 bp):
AATAAAAATAAATAAAATATATTAATATATATAAATATAAAATATTTAAAATAT
Found at i:2311631 original size:7 final size:8
Alignment explanation
Indices: 2311531--2311682 Score: 66
Period size: 7 Copynumber: 18.2 Consensus size: 8
2311521 TACGATTAAA
2311531 AAATATA-
1 AAATATAT
2311538 AAATA-AT
1 AAATATAT
2311545 AAA-ATAT
1 AAATATAT
*
2311552 ATA-ATAT
1 AAATATAT
* *
2311559 AGATATAAA
1 AAATAT-AT
*
2311568 AAATATTT
1 AAATATAT
2311576 AAAATATTAT
1 -AAATA-TAT
2311586 AAA-ATAT
1 AAATATAT
2311593 AAAT-TAT
1 AAATATAT
* *
2311600 TAATTTATT
1 AAATATA-T
2311609 AAATTTATAT
1 AAA--TATAT
2311619 AAATATA-
1 AAATATAT
*
2311626 AAATATTTT
1 AAATA-TAT
2311635 AAATATAATT
1 AAATAT-A-T
*
2311645 AAAATAAAT
1 -AAATATAT
2311654 AAAATATATT
1 -AAATATA-T
2311664 AATATATAT
1 AA-ATATAT
2311673 AAATATAT
1 AAATATAT
2311681 AA
1 AA
2311683 CTTATTAAGT
Statistics
Matches: 113, Mismatches: 14, Indels: 35
0.70 0.09 0.22
Matches are distributed among these distances:
6 2 0.02
7 35 0.31
8 19 0.17
9 35 0.31
10 14 0.12
11 8 0.07
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.39
Consensus pattern (8 bp):
AAATATAT
Found at i:2311664 original size:19 final size:18
Alignment explanation
Indices: 2311634--2311680 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
2311624 TAAAATATTT
2311634 TAAATATAATTAAAATAAA
1 TAAATAT-ATTAAAATAAA
* *
2311653 TAAAATATATTAATATATA
1 T-AAATATATTAAAATAAA
2311672 TAAATATAT
1 TAAATATAT
2311681 AACTTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.32
19 11 0.44
20 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAATATATTAAAATAAA
Done.