Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1657
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: 128431
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:743 original size:15 final size:14
Alignment explanation
Indices: 725--776 Score: 77
Period size: 15 Copynumber: 3.6 Consensus size: 14
715 GAATTTTCAA
725 AAAAAAAATTTCGTG
1 AAAAAAAA-TTCGTG
740 AAAAAAAATTCGTG
1 AAAAAAAATTCGTG
*
754 AAAAAAAAATCGTTG
1 AAAAAAAATTCG-TG
769 AAAAAAAA
1 AAAAAAAA
777 AAAAGAAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
14 17 0.49
15 18 0.51
ACGTcount: A:0.63, C:0.06, G:0.12, T:0.19
Consensus pattern (14 bp):
AAAAAAAATTCGTG
Found at i:777 original size:15 final size:14
Alignment explanation
Indices: 724--777 Score: 72
Period size: 14 Copynumber: 3.6 Consensus size: 14
714 AGAATTTTCA
724 AAAAAAAAATTTCGTG
1 AAAAAAAAA--TCGTG
*
740 AAAAAAAATTCGTG
1 AAAAAAAAATCGTG
754 AAAAAAAAATCGTTG
1 AAAAAAAAATCG-TG
769 AAAAAAAAA
1 AAAAAAAAA
778 AAAGAAGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
14 16 0.46
15 11 0.31
16 8 0.23
ACGTcount: A:0.65, C:0.06, G:0.11, T:0.19
Consensus pattern (14 bp):
AAAAAAAAATCGTG
Found at i:3352 original size:18 final size:18
Alignment explanation
Indices: 3329--3394 Score: 53
Period size: 18 Copynumber: 3.5 Consensus size: 18
3319 AACAAGTGAG
3329 GAAAAAGAAAAAGAGAAT
1 GAAAAAGAAAAAGAGAAT
*
3347 GAAAAAGAGCAAAAAGAGATT
1 G-AAAA-AG-AAAAAGAGAAT
* **
3368 GAGAGTGAAAAAGA-AAT
1 GAAAAAGAAAAAGAGAAT
3385 GAAGAAAGAA
1 GAA-AAAGAA
3395 GAGAAAAATG
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
17 4 0.11
18 12 0.33
19 5 0.14
20 4 0.11
21 11 0.31
ACGTcount: A:0.65, C:0.02, G:0.26, T:0.08
Consensus pattern (18 bp):
GAAAAAGAAAAAGAGAAT
Found at i:3361 original size:27 final size:27
Alignment explanation
Indices: 3330--3381 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3320 ACAAGTGAGG
3330 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
3357 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
3382 AATGAAGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:12895 original size:25 final size:25
Alignment explanation
Indices: 12867--12914 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12857 CGTATGCAAT
*
12867 TTTTTTTTCTTTTCAATTTTTTTGA
1 TTTTTTTTATTTTCAATTTTTTTGA
* *
12892 TTTTTTTTATTTTGATTTTTTTT
1 TTTTTTTTATTTTCAATTTTTTT
12915 CGAACTCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.10, C:0.04, G:0.04, T:0.81
Consensus pattern (25 bp):
TTTTTTTTATTTTCAATTTTTTTGA
Found at i:12904 original size:16 final size:15
Alignment explanation
Indices: 12886--12914 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12876 TTTTCAATTT
12886 TTTTGATTTTTTTTA
1 TTTTGATTTTTTTTA
12901 TTTTGATTTTTTTT
1 TTTTGATTTTTTTT
12915 CGAACTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (15 bp):
TTTTGATTTTTTTTA
Found at i:13253 original size:21 final size:21
Alignment explanation
Indices: 13227--13289 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
13217 TTGGTATTTG
13227 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
13248 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
13269 GGTATTTGGTAC-AAATTGGTA
1 GG-AATTGGTACGAAA-TGGTA
13290 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:13258 original size:11 final size:11
Alignment explanation
Indices: 13238--13270 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
13228 GAATTGGTAC
13238 GAAATGGTATG
1 GAAATGGTATG
*
13249 GAATTGGTAT-
1 GAAATGGTATG
13259 GAAATGGTATG
1 GAAATGGTATG
13270 G
1 G
13271 TATTTGGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (11 bp):
GAAATGGTATG
Found at i:15184 original size:12 final size:12
Alignment explanation
Indices: 15167--15239 Score: 56
Period size: 12 Copynumber: 5.8 Consensus size: 12
15157 TTGGAGTAAC
15167 AAAAAAATCAAA
1 AAAAAAATCAAA
*
15179 AAAAAATTCGAAA
1 AAAAAAATC-AAA
* *
15192 AAAAATTGATTGAAA
1 AAAAA---AATCAAA
15207 AAAAAAATCAAA
1 AAAAAAATCAAA
* **
15219 AAAAAAGTGGAA
1 AAAAAAATCAAA
15231 AAAAAAATC
1 AAAAAAATC
15240 GAGCAAAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
12 29 0.60
13 8 0.17
15 8 0.17
16 3 0.06
ACGTcount: A:0.73, C:0.05, G:0.08, T:0.14
Consensus pattern (12 bp):
AAAAAAATCAAA
Found at i:15248 original size:40 final size:39
Alignment explanation
Indices: 15167--15252 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 39
15157 TTGGAGTAAC
* *
15167 AAAAAAATCAAAAAAAAATTCGAAAAAAAATTGATTGAAA
1 AAAAAAATCAAAAAAAAAGTCGAAAAAAAATCGA-TGAAA
* *
15207 AAAAAAATCAAAAAAAAAGTGGAAAAAAAAATCGA-GCAA
1 AAAAAAATCAAAAAAAAAGTCG-AAAAAAAATCGATGAAA
15246 AAAAAAA
1 AAAAAAA
15253 GAAAAGAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
39 10 0.24
40 20 0.49
41 11 0.27
ACGTcount: A:0.73, C:0.06, G:0.09, T:0.12
Consensus pattern (39 bp):
AAAAAAATCAAAAAAAAAGTCGAAAAAAAATCGATGAAA
Found at i:20268 original size:20 final size:20
Alignment explanation
Indices: 20245--20298 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
20235 AGTTTTTCCC
*
20245 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
20265 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
20285 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
20299 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:20280 original size:30 final size:30
Alignment explanation
Indices: 20245--20318 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
20235 AGTTTTTCCC
20245 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
20275 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
20305 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
20319 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:20308 original size:20 final size:20
Alignment explanation
Indices: 20245--20309 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
20235 AGTTTTTCCC
* * * *
20245 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
20265 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
20284 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
20305 AGCTC
1 AGCTC
20310 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:21919 original size:12 final size:12
Alignment explanation
Indices: 21902--21934 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
21892 TTGGAGTAAC
21902 AAAAAAAAATCG
1 AAAAAAAAATCG
*
21914 AAAAAAAATTCG
1 AAAAAAAAATCG
21926 AAAAAAAAA
1 AAAAAAAAA
21935 ATTAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.79, C:0.06, G:0.06, T:0.09
Consensus pattern (12 bp):
AAAAAAAAATCG
Found at i:21941 original size:12 final size:13
Alignment explanation
Indices: 21902--21947 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
21892 TTGGAGTAAC
21902 AAAAAAAAA-TC-
1 AAAAAAAAATTCA
*
21913 GAAAAAAAATTCGA
1 AAAAAAAAATTC-A
21927 AAAAAAAAATT-A
1 AAAAAAAAATTCA
21939 AAAAAAAAA
1 AAAAAAAAA
21948 GAAGTGACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 8 0.27
12 12 0.40
14 10 0.33
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.11
Consensus pattern (13 bp):
AAAAAAAAATTCA
Found at i:24242 original size:14 final size:12
Alignment explanation
Indices: 24223--24256 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
24213 TTGTAGATTC
24223 AAAAAAAAATTG
1 AAAAAAAAATTG
24235 AAAAAAAAATTG
1 AAAAAAAAATTG
24247 AGAAAAAAAA
1 A-AAAAAAAA
24257 ATTGCATACG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:24257 original size:14 final size:13
Alignment explanation
Indices: 24223--24260 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
24213 TTGTAGATTC
24223 AAAAAAAAATT-G
1 AAAAAAAAATTGG
24235 AAAAAAAAATTGAG
1 AAAAAAAAATTG-G
24249 AAAAAAAAATTG
1 AAAAAAAAATTG
24261 CATACGGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.46
14 13 0.54
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTGG
Found at i:26509 original size:23 final size:24
Alignment explanation
Indices: 26483--26527 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
26473 GAAAAGAAGA
*
26483 AAAACAAAAAGAGA-GAGTGATTC
1 AAAACAAAAAGAAATGAGTGATTC
*
26506 AAAAGAAAAAGAAATGAGTGAT
1 AAAACAAAAAGAAATGAGTGAT
26528 GAGATTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.60, C:0.04, G:0.22, T:0.13
Consensus pattern (24 bp):
AAAACAAAAAGAAATGAGTGATTC
Found at i:29144 original size:20 final size:20
Alignment explanation
Indices: 29119--29162 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
29109 GGGTTAAGAT
*
29119 TGAGTTGAATTGAGCTTGAG
1 TGAGTTGAATTGAGCTCGAG
*
29139 TGAGTTGACTTGAGCTCGAG
1 TGAGTTGAATTGAGCTCGAG
29159 TGAG
1 TGAG
29163 CTGGAAACGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.36, T:0.32
Consensus pattern (20 bp):
TGAGTTGAATTGAGCTCGAG
Found at i:30889 original size:48 final size:48
Alignment explanation
Indices: 30834--30939 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
30824 TTGTCTTTTC
*
30834 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
30882 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
30930 TTTCTTTTTC
1 TTTCTTTTTC
30940 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:35752 original size:18 final size:18
Alignment explanation
Indices: 35726--35847 Score: 102
Period size: 18 Copynumber: 6.6 Consensus size: 18
35716 AAATTGAAAG
* *
35726 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAATGA
* *
35744 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAATGA
* *
35762 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAATGA
35780 AAAAGAAAAAG-AAATCGA
1 AAAAGAAAAAGAAAAT-GA
** * *
35798 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAATGA
*
35816 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-TGA
35837 AAAAGAAAAAG
1 AAAAGAAAAAG
35848 CGAAAAAAGA
Statistics
Matches: 83, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
17 3 0.04
18 58 0.70
19 8 0.10
20 8 0.10
21 6 0.07
ACGTcount: A:0.70, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:35788 original size:5 final size:6
Alignment explanation
Indices: 35722--35847 Score: 83
Period size: 6 Copynumber: 20.7 Consensus size: 6
35712 AAAGAAATTG
* * ** *
35722 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** * ** ** *
35769 AAAGAA ATTGCA AAAGAA AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* *
35817 AATGAAGA AAAGAA AATTGAA AAAGAA AAAG
1 AAAG-A-A AAAGAA AA-AGAA AAAGAA AAAG
35848 CGAAAAAAGA
Statistics
Matches: 87, Mismatches: 30, Indels: 7
0.70 0.24 0.06
Matches are distributed among these distances:
5 3 0.03
6 73 0.84
7 7 0.08
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:35829 original size:14 final size:13
Alignment explanation
Indices: 35808--35845 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
35798 AAAAGTGAGA
35808 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
35820 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
35835 GAAAAAGAAAA
1 GAAAAAGAAAA
35846 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:35859 original size:21 final size:21
Alignment explanation
Indices: 35809--35859 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
35799 AAAGTGAGAG
*
35809 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
35830 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
35851 AAAAAGAAA
1 AAAAAGAAA
35860 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:35899 original size:33 final size:33
Alignment explanation
Indices: 35862--35924 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
35852 AAAAGAAATT
35862 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
35895 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
35925 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:37722 original size:20 final size:20
Alignment explanation
Indices: 37699--37752 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
37689 AGTTTTTCCC
*
37699 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
37719 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
37739 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
37753 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:37734 original size:30 final size:30
Alignment explanation
Indices: 37699--37772 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
37689 AGTTTTTCCC
37699 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
37729 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
37759 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
37773 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:37762 original size:20 final size:20
Alignment explanation
Indices: 37699--37763 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
37689 AGTTTTTCCC
* * * *
37699 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
37719 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
37738 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
37759 AGCTC
1 AGCTC
37764 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:42486 original size:21 final size:21
Alignment explanation
Indices: 42460--42522 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
42450 TTGGTATTTG
42460 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
42481 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
42502 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
42523 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:43813 original size:14 final size:13
Alignment explanation
Indices: 43794--43845 Score: 77
Period size: 14 Copynumber: 3.8 Consensus size: 13
43784 ACTAGCTCTC
43794 TTTTTTTTCAAATT
1 TTTTTTTTCAAA-T
43808 TTTTTTTTCACAAT
1 TTTTTTTTCA-AAT
43822 TTTTTTTTCAAAAT
1 TTTTTTTTC-AAAT
43836 TTTTTTTTCA
1 TTTTTTTTCA
43846 CAACTTGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.03
14 32 0.89
15 3 0.08
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTTTCAAAT
Found at i:43838 original size:28 final size:28
Alignment explanation
Indices: 43794--43848 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
43784 ACTAGCTCTC
*
43794 TTTTTTTTCAAATTTTTTTTTTCACAAT
1 TTTTTTTTCAAAATTTTTTTTTCACAAT
43822 TTTTTTTTCAAAATTTTTTTTTCACAA
1 TTTTTTTTCAAAATTTTTTTTTCACAA
43849 CTTGATATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTTTTTTCAAAATTTTTTTTTCACAAT
Found at i:43904 original size:11 final size:11
Alignment explanation
Indices: 43888--43921 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
43878 GAAACTAGTT
43888 TTTTTTTTGAA
1 TTTTTTTTGAA
*
43899 TTTTTTTTCAAA
1 TTTTTTTT-GAA
43911 TTTTTTTTGAA
1 TTTTTTTTGAA
43922 GAAACTACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.71
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:48240 original size:21 final size:23
Alignment explanation
Indices: 48195--48241 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
48185 TCACCTGCAA
* *
48195 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
48218 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
48239 TAA
1 TAA
48242 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:49587 original size:4 final size:4
Alignment explanation
Indices: 49580--49606 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
49570 CTAAGTAAGA
49580 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
49607 AATAAAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:55040 original size:30 final size:30
Alignment explanation
Indices: 55004--55080 Score: 145
Period size: 30 Copynumber: 2.6 Consensus size: 30
54994 AATTAAGAAC
55004 AACACTTATTAAATAAAGTTCAGCAAAAAA
1 AACACTTATTAAATAAAGTTCAGCAAAAAA
55034 AACACTTATTAAATAAAGTTCAGCAAAAAA
1 AACACTTATTAAATAAAGTTCAGCAAAAAA
*
55064 AACACTTATTAATTAAA
1 AACACTTATTAAATAAA
55081 ACTAAGATGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (30 bp):
AACACTTATTAAATAAAGTTCAGCAAAAAA
Found at i:57286 original size:24 final size:25
Alignment explanation
Indices: 57230--57287 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
57220 GGGTCACACG
* *
57230 GCCATGTCACATGCCCGTGTGCCAG
1 GCCATGTGACATGCCCGTGTGCCAA
*
57255 GCCGTGTGACA-GCCCGTGT-CTCAA
1 GCCATGTGACATGCCCGTGTGC-CAA
57279 GCCATGTGA
1 GCCATGTGA
57288 ACTCAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.04
24 18 0.64
25 9 0.32
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.21
Consensus pattern (25 bp):
GCCATGTGACATGCCCGTGTGCCAA
Found at i:60515 original size:10 final size:10
Alignment explanation
Indices: 60500--60524 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
60490 TTAGTTAAGT
60500 GCTGAATTGA
1 GCTGAATTGA
60510 GCTGAATTGA
1 GCTGAATTGA
60520 GCTGA
1 GCTGA
60525 TACGAGCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.28
Consensus pattern (10 bp):
GCTGAATTGA
Found at i:63504 original size:23 final size:23
Alignment explanation
Indices: 63477--63527 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
63467 AAAAACACTC
63477 GTTTTTT-TATTTTCAT-ACTCTT
1 GTTTTTTGTATTTT-ATCACTCTT
* *
63499 GTTTTTTGTCTTTTGTCACTCTT
1 GTTTTTTGTATTTTATCACTCTT
63522 GTTTTT
1 GTTTTT
63528 ATCTCACTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.08, C:0.14, G:0.10, T:0.69
Consensus pattern (23 bp):
GTTTTTTGTATTTTATCACTCTT
Found at i:63595 original size:14 final size:14
Alignment explanation
Indices: 63553--63596 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
63543 TTCGTTTCTT
63553 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTC
*
63567 ACTCTTTT-TTTTTC
1 TCT-TTTTCTTTTTC
63581 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTC
63595 TC
1 TC
63597 ACTTAATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 4 0.15
14 18 0.69
15 4 0.15
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (14 bp):
TCTTTTTCTTTTTC
Found at i:65596 original size:13 final size:13
Alignment explanation
Indices: 65576--65626 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
65566 TAAATTGTAG
65576 ATTCAAAAAAAAA
1 ATTCAAAAAAAAA
*
65589 AATC-AAAAAAAA
1 ATTCAAAAAAAAA
*
65601 ATTGAAAAAAAAA
1 ATTCAAAAAAAAA
*
65614 ATTGAAAAAAAAA
1 ATTCAAAAAAAAA
65627 TTGCATACGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 10 0.29
13 24 0.71
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (13 bp):
ATTCAAAAAAAAA
Found at i:65614 original size:25 final size:25
Alignment explanation
Indices: 65580--65629 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
65570 TTGTAGATTC
65580 AAAAAAAAAAATCAAAAAAAAATTG
1 AAAAAAAAAAATCAAAAAAAAATTG
* *
65605 AAAAAAAAAATTGAAAAAAAAATTG
1 AAAAAAAAAAATCAAAAAAAAATTG
65630 CATACGGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (25 bp):
AAAAAAAAAAATCAAAAAAAAATTG
Found at i:65628 original size:12 final size:12
Alignment explanation
Indices: 65581--65629 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
65571 TGTAGATTCA
* *
65581 AAAAAAAAAATC
1 AAAAAAAAATTG
65593 AAAAAAAAATTG
1 AAAAAAAAATTG
65605 AAAAAAAAAATTG
1 -AAAAAAAAATTG
65618 AAAAAAAAATTG
1 AAAAAAAAATTG
65630 CATACGGTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
12 22 0.65
13 12 0.35
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:73605 original size:12 final size:12
Alignment explanation
Indices: 73588--73612 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
73578 AAAAGAGAAG
73588 AAATTCAAAAAA
1 AAATTCAAAAAA
73600 AAATTCAAAAAA
1 AAATTCAAAAAA
73612 A
1 A
73613 TTGAAAAAAA
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:74728 original size:6 final size:6
Alignment explanation
Indices: 74695--74808 Score: 61
Period size: 6 Copynumber: 18.5 Consensus size: 6
74685 AAAGAAATTG
* * * ** *
74695 AAAG-A AAACAA AAAGAA AACGAA GAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
74742 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
74793 AAAGAA AAAGCAA AAA
1 AAAGAA AAAG-AA AAA
74809 AAGAAATTGA
Statistics
Matches: 78, Mismatches: 24, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
5 4 0.05
6 57 0.73
7 13 0.17
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:74782 original size:14 final size:15
Alignment explanation
Indices: 74684--74824 Score: 60
Period size: 15 Copynumber: 9.2 Consensus size: 15
74674 AAGAGATTGA
*
74684 AAAAGAAATTGAAAG
1 AAAAGAAAATGAAAG
* *
74699 AAAACAAAAAGAAAACG
1 AAAAGAAAATG-AAA-G
*
74716 AAGAAGAAAAAGAAATTG
1 AA-AAGAAAATGAAA--G
* *
74734 CAAAAGAAAAAGAAAT
1 -AAAAGAAAATGAAAG
* * *
74750 CAAA-AAAGTGAGAG
1 AAAAGAAAATGAAAG
74764 AAAAAGAAAATG-AAG
1 -AAAAGAAAATGAAAG
74779 AAAAGAAAATTG--A-
1 AAAAGAAAA-TGAAAG
*
74792 AAAAGAAAAAGCAAA-
1 AAAAGAAAATG-AAAG
*
74807 AAAAGAAATTGAAAG
1 AAAAGAAAATGAAAG
74822 AAA
1 AAA
74825 GCTTGAAAAG
Statistics
Matches: 97, Mismatches: 17, Indels: 24
0.70 0.12 0.17
Matches are distributed among these distances:
12 1 0.01
13 9 0.09
14 19 0.20
15 31 0.32
16 8 0.08
17 6 0.06
18 21 0.22
19 2 0.02
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.08
Consensus pattern (15 bp):
AAAAGAAAATGAAAG
Found at i:74808 original size:13 final size:12
Alignment explanation
Indices: 74681--74800 Score: 54
Period size: 12 Copynumber: 10.0 Consensus size: 12
74671 AGAAAGAGAT
*
74681 TGAAAAAGAAAT
1 TGAAAAAGAAAA
74693 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
74703 -CAAAAAGAAAA
1 TGAAAAAGAAAA
* *
74714 CGAAGAAGAAAA
1 TGAAAAAGAAAA
* **
74726 AGAAATTGCAAAA
1 TGAAAAAG-AAAA
74739 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* * *
74749 TCAAAAAAGTGAGA
1 T-GAAAAAG-AAAA
74763 -GAAAAAGAAAA
1 TGAAAAAGAAAA
74774 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
74788 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
74801 AGCAAAAAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 23
0.68 0.13 0.19
Matches are distributed among these distances:
10 10 0.12
11 10 0.12
12 33 0.41
13 14 0.17
14 12 0.15
15 2 0.02
ACGTcount: A:0.70, C:0.03, G:0.18, T:0.08
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:75959 original size:20 final size:20
Alignment explanation
Indices: 75913--75959 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
75903 AGCTCGTTTC
*
75913 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
75933 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
75953 CAGCTCA
1 CAGCTCA
75960 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:85432 original size:56 final size:56
Alignment explanation
Indices: 85327--85433 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
85317 ATTAATGCCG
* * * * *
85327 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATTCCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATTCCGT
85383 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
85434 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.41
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATTCCGT
Found at i:86082 original size:20 final size:20
Alignment explanation
Indices: 86057--86111 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
86047 ACGAGTTAAA
* *
86057 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
86077 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
86097 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
86112 TTGAATCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:87558 original size:21 final size:23
Alignment explanation
Indices: 87513--87559 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
87503 TCACCTGCAA
* *
87513 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
87536 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
87557 TAA
1 TAA
87560 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:92231 original size:10 final size:11
Alignment explanation
Indices: 92209--92233 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
92199 AAAAAAATCG
92209 AAATTCAAAAA
1 AAATTCAAAAA
92220 AAATTCAAAAA
1 AAATTCAAAAA
92231 AAA
1 AAA
92234 GTGAAAAAAT
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:92255 original size:26 final size:25
Alignment explanation
Indices: 92226--92283 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
92216 AAAAAAATTC
*
92226 AAAAAAAAGTGAAAAAA-TCGAGCAAA
1 AAAAAAAAG-AAAAAAAGT-GAGCAAA
92252 AAAAAGAAAGAAAAAAAGTGAGCAAA
1 AAAAA-AAAGAAAAAAAGTGAGCAAA
92278 AAAAAA
1 AAAAAA
92284 TCAAGTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 1 0.03
26 23 0.79
27 5 0.17
ACGTcount: A:0.74, C:0.05, G:0.16, T:0.05
Consensus pattern (25 bp):
AAAAAAAAGAAAAAAAGTGAGCAAA
Found at i:93333 original size:11 final size:11
Alignment explanation
Indices: 93317--93346 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
93307 AAAGAAATTG
93317 AAAGAAAACAA
1 AAAGAAAACAA
*
93328 AAAGAAAAGAA
1 AAAGAAAACAA
93339 AAAGAAAA
1 AAAGAAAA
93347 AGAAATTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAGAAAACAA
Found at i:93341 original size:6 final size:6
Alignment explanation
Indices: 93317--93423 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
93307 AAAGAAATTG
* ** *
93317 AAAG-A AAACAA AAAG-A AAAGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
93363 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
93414 AAAGAA AAAG
1 AAAGAA AAAG
93424 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 22, Indels: 9
0.71 0.21 0.08
Matches are distributed among these distances:
5 8 0.11
6 56 0.75
7 7 0.09
8 4 0.05
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:93377 original size:18 final size:18
Alignment explanation
Indices: 93321--93423 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
93311 AAATTGAAAG
*
93321 AAAACAAAAAGAAA-AGA
1 AAAAGAAAAAGAAATAGA
* *
93338 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATAGA
*
93356 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATAGA
** * *
93374 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAATAGA
* *
93392 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAG-AAATAGA
93413 AAAAGAAAAAG
1 AAAAGAAAAAG
93424 CGAAAAAAGA
Statistics
Matches: 65, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
17 13 0.20
18 34 0.52
19 5 0.08
20 4 0.06
21 9 0.14
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATAGA
Found at i:93405 original size:14 final size:13
Alignment explanation
Indices: 93384--93421 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
93374 AAAAGTGAGA
93384 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
93396 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
93411 GAAAAAGAAAA
1 GAAAAAGAAAA
93422 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:93435 original size:21 final size:21
Alignment explanation
Indices: 93329--93435 Score: 51
Period size: 24 Copynumber: 4.9 Consensus size: 21
93319 AGAAAACAAA
93329 AAGAAAAG-AAAAAGAAAAAG
1 AAGAAAAGAAAAAAGAAAAAG
**
93349 AAATTGCAAAAG-AAAAAGAAATCG
1 -AA--G-AAAAGAAAAAAGAAAAAG
*
93373 AA-AAAGTGAGAGAAAAAGAAAATG
1 AAGAAA---AGA-AAAAAGAAAAAG
**
93397 AAGAAAAGAAAATTGAAAAAG
1 AAGAAAAGAAAAAAGAAAAAG
*
93418 AA-AAAGCGAAAAAAGAAA
1 AAGAAA-AGAAAAAAGAAA
93436 TTGAAAGAGA
Statistics
Matches: 66, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
19 3 0.05
20 3 0.05
21 22 0.33
22 5 0.08
23 3 0.05
24 27 0.41
25 3 0.05
ACGTcount: A:0.71, C:0.03, G:0.20, T:0.07
Consensus pattern (21 bp):
AAGAAAAGAAAAAAGAAAAAG
Found at i:93475 original size:33 final size:33
Alignment explanation
Indices: 93438--93500 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
93428 AAAAGAAATT
93438 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
93471 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
93501 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:99663 original size:17 final size:18
Alignment explanation
Indices: 99626--99663 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
99616 GATTGAGAGT
* *
99626 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
99644 GAAAAGAAAT-TGAAAAA
1 GAAAAGAAATGTGAAAAA
99661 GAA
1 GAA
99664 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:103591 original size:20 final size:19
Alignment explanation
Indices: 103568--103632 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
103558 AAGCTCAAAC
103568 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
103588 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
103608 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
103628 GAGCT
1 GAGCT
103633 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:105137 original size:15 final size:15
Alignment explanation
Indices: 105117--105157 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
105107 TAGCTTCTTC
105117 TTTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
105132 TTTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
105147 TTTTTTTTTCA
1 TTTTTTTTTCA
105158 ACTTGATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.66
Consensus pattern (15 bp):
TTTTTTTTTCACGAA
Found at i:106256 original size:21 final size:23
Alignment explanation
Indices: 106211--106257 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
106201 TCACCTGCAA
* *
106211 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
106234 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
106255 TAA
1 TAA
106258 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:122044 original size:18 final size:18
Alignment explanation
Indices: 122023--122057 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
122013 TTTTTCTTTT
122023 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
122041 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
122058 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:128250 original size:1 final size:1
Alignment explanation
Indices: 128177--128234 Score: 116
Period size: 1 Copynumber: 58.0 Consensus size: 1
128167 CATTTTGTTC
128177 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
128235 GACAACAGTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.