Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 90 of 214
Found at i:25727285 original size:37 final size:37
Alignment explanation
Indices: 25727242--25727312 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
25727232 CTTGCCTCTC
25727242 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
25727279 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
25727313 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:25727313 original size:16 final size:16
Alignment explanation
Indices: 25727238--25727298 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
25727228 GCCTCTTGCC
*
25727238 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
25727254 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
25727270 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
25727286 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
25727299 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:25729500 original size:6 final size:6
Alignment explanation
Indices: 25729480--25729529 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
25729470 AAGAGAAAAC
*
25729480 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
25729529 A
1 A
25729530 TAAAAAGTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:25729833 original size:11 final size:12
Alignment explanation
Indices: 25729801--25729831 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
25729791 TTGAGAGAAC
25729801 TTGAAAAAGCCT
1 TTGAAAAAGCCT
25729813 TTGAAAAAGCCT
1 TTGAAAAAGCCT
25729825 TTGAAAA
1 TTGAAAA
25729832 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:25732045 original size:30 final size:30
Alignment explanation
Indices: 25732011--25732107 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
25732001 AGCTCACTCC
25732011 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
25732041 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
25732071 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
25732101 TAGCTCA
1 TAGCTCA
25732108 TTTTCTCTCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:25732164 original size:6 final size:6
Alignment explanation
Indices: 25732148--25732197 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
25732138 TTTCTTTTTA
*
25732148 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
25732197 T
1 T
25732198 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:25732180 original size:37 final size:37
Alignment explanation
Indices: 25732137--25732207 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
25732127 CTTGCCTCTC
25732137 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
25732174 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
25732208 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:25732208 original size:16 final size:16
Alignment explanation
Indices: 25732133--25732193 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
25732123 GCCTCTTGCC
*
25732133 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
25732149 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
25732165 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
25732181 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
25732194 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:25735429 original size:5 final size:5
Alignment explanation
Indices: 25735419--25735480 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
25735409 AAGAGAAAAC
* *
25735419 AAAGA AAAGA AAAGA AAAGA AAA-A GCAAGA GAAGAA AAAGA AAATGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA -AAAGA AAAG-A AAAGA AAA-GA
25735466 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
25735481 GAGGCAAGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
4 2 0.04
5 36 0.75
6 9 0.19
7 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:25735459 original size:36 final size:37
Alignment explanation
Indices: 25735409--25735478 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 37
25735399 CATTCTTGTA
25735409 AAGAGAAAACAAAGAAAA-GAAA-AGAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATGAAATA-AAAAGAAAAAGC
25735445 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAATAAAAAGAAAA
25735479 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
36 15 0.48
37 15 0.48
38 1 0.03
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAATAAAAAGAAAAAGC
Found at i:25735602 original size:30 final size:29
Alignment explanation
Indices: 25735508--25735604 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
25735498 AGAGAGAAAA
* *
25735508 TGAGCTAAGTTTTAGCTCGTGAGGTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
* * * * * * *
25735538 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCT-AAAT
25735568 TGAGCTAAGGTTTAGCTCGTGAGCTAAAT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAT
25735597 ATGAGCTA
1 -TGAGCTA
25735605 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 16, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
29 3 0.06
30 44 0.90
31 2 0.04
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (29 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAT
Found at i:25736114 original size:10 final size:10
Alignment explanation
Indices: 25736099--25736155 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
25736089 AACTCCGACC
25736099 AGCTCAATTG
1 AGCTCAATTG
* *
25736109 AGCTCATTTT
1 AGCTCAATTG
*
25736119 AGCTCAATCG
1 AGCTCAATTG
*
25736129 AGCTCAATTT
1 AGCTCAATTG
*
25736139 AGCTACAATTC
1 AGCT-CAATTG
25736150 AGCTCA
1 AGCTCA
25736156 TTTATTTTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
10 29 0.76
11 9 0.24
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (10 bp):
AGCTCAATTG
Found at i:25736122 original size:20 final size:20
Alignment explanation
Indices: 25736099--25736158 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
25736089 AACTCCGACC
25736099 AGCTCAATTGAGCTCATTTT
1 AGCTCAATTGAGCTCATTTT
* *
25736119 AGCTCAATCGAGCTCAATTT
1 AGCTCAATTGAGCTCATTTT
*
25736139 AGCTACAATTCAGCTCATTT
1 AGCT-CAATTGAGCTCATTT
25736159 ATTTTATTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (20 bp):
AGCTCAATTGAGCTCATTTT
Found at i:25738920 original size:24 final size:23
Alignment explanation
Indices: 25738866--25738943 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
25738856 GGATAATTAA
**
25738866 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
25738889 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
25738913 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
25738934 GAAATAGTAT
1 GAAATGGTAT
25738944 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:25738928 original size:21 final size:21
Alignment explanation
Indices: 25738902--25738968 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
25738892 TTGGTATTTG
25738902 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
25738923 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
25738944 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
25738967 GG
1 GG
25738969 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:25743236 original size:17 final size:17
Alignment explanation
Indices: 25743211--25743266 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
25743201 TCTCTTTTCA
*
25743211 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
25743228 TTCTTTTTTTTT-ATCATTT
1 TTCTTTTTTTTTGA--A-TT
* *
25743247 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
25743264 TTC
1 TTC
25743267 GCTCTTTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.03
17 16 0.50
18 2 0.06
19 13 0.41
ACGTcount: A:0.09, C:0.12, G:0.04, T:0.75
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:25745494 original size:13 final size:13
Alignment explanation
Indices: 25745476--25745527 Score: 79
Period size: 13 Copynumber: 3.9 Consensus size: 13
25745466 AAACCGTATG
25745476 CAATTTTTTTTTT
1 CAATTTTTTTTTT
25745489 CAA-TTTTTTTTT
1 CAATTTTTTTTTT
25745501 CAATTTTTTTTTT
1 CAATTTTTTTTTT
25745514 CGAACTTTTTTTTT
1 C-AA-TTTTTTTTT
25745528 ACGCACCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.33
13 13 0.36
14 2 0.06
15 9 0.25
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (13 bp):
CAATTTTTTTTTT
Found at i:25745497 original size:12 final size:13
Alignment explanation
Indices: 25745480--25745527 Score: 71
Period size: 12 Copynumber: 3.7 Consensus size: 13
25745470 CGTATGCAAT
25745480 TTTTTTTTTCAA-
1 TTTTTTTTTCAAC
*
25745492 TTTTTTTTTCAAT
1 TTTTTTTTTCAAC
25745505 TTTTTTTTTCGAAC
1 TTTTTTTTTC-AAC
25745519 TTTTTTTTT
1 TTTTTTTTT
25745528 ACGCACCTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
12 12 0.36
13 10 0.30
14 11 0.33
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTCAAC
Found at i:25745844 original size:24 final size:23
Alignment explanation
Indices: 25745790--25745867 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
25745780 GGATAATTAA
**
25745790 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
25745813 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
25745837 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
25745858 GAAATAGTAT
1 GAAATGGTAT
25745868 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:25745852 original size:21 final size:21
Alignment explanation
Indices: 25745826--25745892 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
25745816 TTGGTATTTG
25745826 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
25745847 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
25745868 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
25745891 GG
1 GG
25745893 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:25747440 original size:5 final size:6
Alignment explanation
Indices: 25747424--25747449 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
25747414 AGCATCATGT
25747424 GAAAAA GAAAAA GAAAAA GAAAAA GA
1 GAAAAA GAAAAA GAAAAA GAAAAA GA
25747450 GTGTGAGCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:25747480 original size:18 final size:19
Alignment explanation
Indices: 25747459--25747497 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
25747449 AGTGTGAGCG
*
25747459 AGAAAATGAAA-AAGAAGA
1 AGAAAATGAAAGAAAAAGA
25747477 AG-AAATGAAAGAAAAAGA
1 AGAAAATGAAAGAAAAAGA
25747495 AGA
1 AGA
25747498 TGAGTGTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (19 bp):
AGAAAATGAAAGAAAAAGA
Found at i:25766701 original size:19 final size:18
Alignment explanation
Indices: 25766665--25766704 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25766655 GTTCCACTCA
*
25766665 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
25766683 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
25766702 TTT
1 TTT
25766705 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:25768066 original size:20 final size:20
Alignment explanation
Indices: 25768020--25768066 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
25768010 AGCTTGTTTC
*
25768020 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
25768040 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
25768060 CAGCTCA
1 CAGCTCA
25768067 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:25772005 original size:11 final size:12
Alignment explanation
Indices: 25771988--25772033 Score: 56
Period size: 13 Copynumber: 3.6 Consensus size: 12
25771978 TAGCTCTCTT
25771988 TTTTTTTCACAA
1 TTTTTTTCACAA
25772000 TTTTTTTTCACAA
1 -TTTTTTTCACAA
*
25772013 TTTTTTTTTCAAAA
1 --TTTTTTTCACAA
25772027 TTTTTTT
1 TTTTTTT
25772034 TTCACAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
12 7 0.23
13 12 0.39
14 12 0.39
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTTTTCACAA
Found at i:25772005 original size:14 final size:14
Alignment explanation
Indices: 25771986--25772040 Score: 94
Period size: 14 Copynumber: 4.0 Consensus size: 14
25771976 ACTAGCTCTC
25771986 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
25772000 -TTTTTTTTCACAA
1 TTTTTTTTTCACAA
*
25772013 TTTTTTTTTCAAAA
1 TTTTTTTTTCACAA
25772027 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
25772041 CTTGATATCC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.34
14 25 0.66
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTTTTTCACAA
Found at i:25774658 original size:12 final size:12
Alignment explanation
Indices: 25774604--25774662 Score: 57
Period size: 12 Copynumber: 4.6 Consensus size: 12
25774594 TTGGAGTAAC
25774604 AAAAAAAA-TCA
1 AAAAAAAATTCA
25774615 AAAAAAAATTCGAA
1 AAAAAAAATTC--A
*
25774629 AAAAAAATTGATTGA
1 AAAAAAA---ATTCA
25774644 AAAAAAAATTCA
1 AAAAAAAATTCA
25774656 AAAAAAA
1 AAAAAAA
25774663 GTGAAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
11 8 0.20
12 13 0.32
14 8 0.20
15 8 0.20
17 3 0.08
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:25775614 original size:18 final size:18
Alignment explanation
Indices: 25775593--25775627 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25775583 AGAAAAGAAA
25775593 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
25775611 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
25775628 AAAAGAAAAA
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:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:25779139 original size:4 final size:4
Alignment explanation
Indices: 25779123--25779153 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
25779113 TAAAAATTTA
*
25779123 AAAT AAGT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
25779154 AATAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:25780566 original size:23 final size:22
Alignment explanation
Indices: 25780514--25780566 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
25780504 TCCACGTCTT
*
25780514 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
25780536 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
25780559 TTTCTTTT
1 TTTCTTTT
25780567 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:25796682 original size:27 final size:26
Alignment explanation
Indices: 25796644--25796704 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 26
25796634 ACTGTTTTAG
25796644 GTTGCTGGAATTTTTGGGAAAAATCAA
1 GTTGCTGGAATTTTTGGGAAAAA-CAA
25796671 GTTGCTGGAATTTTTGGGAAAAACAA
1 GTTGCTGGAATTTTTGGGAAAAACAA
25796697 GTTGCTGG
1 GTTGCTGG
25796705 CTTTATTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 11 0.32
27 23 0.68
ACGTcount: A:0.30, C:0.08, G:0.30, T:0.33
Consensus pattern (26 bp):
GTTGCTGGAATTTTTGGGAAAAACAA
Found at i:25797987 original size:23 final size:22
Alignment explanation
Indices: 25797935--25797987 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
25797925 TCCACATCTT
*
25797935 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
25797957 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
25797980 TTTCTTTT
1 TTTCTTTT
25797988 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:25801328 original size:14 final size:14
Alignment explanation
Indices: 25801311--25801343 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
25801301 AAAAAAACTC
25801311 AAAAAAAATTCAAA
1 AAAAAAAATTCAAA
25801325 AAAAAAAATTCAAA
1 AAAAAAAATTCAAA
25801339 AAAAA
1 AAAAA
25801344 TTTTTTTGGT
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:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAAAATTCAAA
Found at i:25801339 original size:11 final size:11
Alignment explanation
Indices: 25801300--25801345 Score: 56
Period size: 11 Copynumber: 3.9 Consensus size: 11
25801290 TAGTTTCTCG
*
25801300 AAAAAAAACTC
1 AAAAAAAATTC
25801311 AAAAAAAATTC
1 AAAAAAAATTC
25801322 AAAAAAAAAAATTC
1 ---AAAAAAAATTC
25801336 AAAAAAAATT
1 AAAAAAAATT
25801346 TTTTTGGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 20 0.65
14 11 0.35
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:25801405 original size:14 final size:14
Alignment explanation
Indices: 25801386--25801427 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
25801376 GGATATCAAG
25801386 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
25801400 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
25801414 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
25801428 GAGAGCTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:25807091 original size:20 final size:20
Alignment explanation
Indices: 25807066--25807149 Score: 105
Period size: 20 Copynumber: 4.2 Consensus size: 20
25807056 GAGCTCAATA
* *
25807066 AGCTGAATTGAGCTCGTGGG
1 AGCTGAATTGAGCTCGAGTG
* *
25807086 AGCTGACTTGAGCTCGAATG
1 AGCTGAATTGAGCTCGAGTG
*
25807106 AGCTGACTTGAGCTCGAGTG
1 AGCTGAATTGAGCTCGAGTG
**
25807126 AGCTGAATTGAGCTTAAGTG
1 AGCTGAATTGAGCTCGAGTG
25807146 AGCT
1 AGCT
25807150 AAACCGCATG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (20 bp):
AGCTGAATTGAGCTCGAGTG
Found at i:25807149 original size:40 final size:40
Alignment explanation
Indices: 25807056--25807139 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
25807046 AGCTAATAAC
* * *
25807056 GAGCTC-AATAAGCTGAATTGAGCTCGTGGGAGCTGACTT
1 GAGCTCGAATGAGCTGAATTGAGCTCGAGGGAGCTGAATT
* *
25807095 GAGCTCGAATGAGCTGACTTGAGCTCGAGTGAGCTGAATT
1 GAGCTCGAATGAGCTGAATTGAGCTCGAGGGAGCTGAATT
25807135 GAGCT
1 GAGCT
25807140 TAAGTGAGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 6 0.15
40 33 0.85
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (40 bp):
GAGCTCGAATGAGCTGAATTGAGCTCGAGGGAGCTGAATT
Found at i:25807606 original size:18 final size:18
Alignment explanation
Indices: 25807580--25807621 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
25807570 AGTGTGAGTG
* *
25807580 AAGAGATTGAGATTGAAA
1 AAGAAATTGAAATTGAAA
25807598 AAGAAATTGAAATTGAAA
1 AAGAAATTGAAATTGAAA
25807616 AAGAAA
1 AAGAAA
25807622 GTAAGCAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.21, T:0.19
Consensus pattern (18 bp):
AAGAAATTGAAATTGAAA
Found at i:25813922 original size:30 final size:30
Alignment explanation
Indices: 25813888--25813984 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
25813878 TAAACTAAAA
*
25813888 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
25813918 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
25813948 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
25813977 ATGAGCTA
1 -TGAGCTA
25813985 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:25816181 original size:12 final size:12
Alignment explanation
Indices: 25816166--25816196 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
25816156 TTCTTTTTGC
25816166 TTTTCAAAGGCT
1 TTTTCAAAGGCT
25816178 TTTTCAAAGGCT
1 TTTTCAAAGGCT
25816190 TTTTCAA
1 TTTTCAA
25816197 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:25816273 original size:6 final size:6
Alignment explanation
Indices: 25816257--25816306 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
25816247 TTTCTTTTTA
*
25816257 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
25816306 T
1 T
25816307 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:25816289 original size:37 final size:37
Alignment explanation
Indices: 25816246--25816316 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
25816236 CTTGCCTCTC
25816246 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
25816283 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
25816317 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:25816317 original size:16 final size:16
Alignment explanation
Indices: 25816242--25816302 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
25816232 GCCTCTTGCC
*
25816242 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
25816258 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
25816274 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
25816290 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
25816303 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:25817249 original size:12 final size:11
Alignment explanation
Indices: 25817233--25817284 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 11
25817223 TTTTAACTCG
25817233 ATTTTTTTGTC
1 ATTTTTTTGTC
25817244 ACTTTTTTT-TC
1 A-TTTTTTTGTC
*
25817255 ATTTTTTTTTC
1 ATTTTTTTGTC
*
25817266 GATTTTTTTG-A
1 -ATTTTTTTGTC
25817277 ATTTTTTT
1 ATTTTTTT
25817285 TCTGAATTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
10 15 0.42
11 6 0.17
12 15 0.42
ACGTcount: A:0.12, C:0.08, G:0.06, T:0.75
Consensus pattern (11 bp):
ATTTTTTTGTC
Found at i:25817262 original size:11 final size:11
Alignment explanation
Indices: 25817233--25817274 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
25817223 TTTTAACTCG
*
25817233 ATTTTTTTGTC
1 ATTTTTTTTTC
*
25817244 ACTTTTTTTTC
1 ATTTTTTTTTC
25817255 ATTTTTTTTTC
1 ATTTTTTTTTC
25817266 GATTTTTTT
1 -ATTTTTTT
25817275 GAATTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 19 0.70
12 8 0.30
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.76
Consensus pattern (11 bp):
ATTTTTTTTTC
Found at i:25817285 original size:22 final size:22
Alignment explanation
Indices: 25817233--25817285 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
25817223 TTTTAACTCG
* **
25817233 ATTTTTTTGTCACTTTTTTTTC
1 ATTTTTTTTTCACTTTTTTTGA
25817255 ATTTTTTTTTCGA-TTTTTTTGA
1 ATTTTTTTTTC-ACTTTTTTTGA
25817277 ATTTTTTTT
1 ATTTTTTTT
25817286 CTGAATTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.11, C:0.08, G:0.06, T:0.75
Consensus pattern (22 bp):
ATTTTTTTTTCACTTTTTTTGA
Found at i:25819054 original size:30 final size:30
Alignment explanation
Indices: 25819020--25819116 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
25819010 TAAACTAAAA
*
25819020 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
25819050 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
25819080 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
25819109 ATGAGCTA
1 -TGAGCTA
25819117 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:25823457 original size:13 final size:13
Alignment explanation
Indices: 25823439--25823463 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25823429 AGACCGTATG
25823439 CAATTTTTTTTCT
1 CAATTTTTTTTCT
25823452 CAATTTTTTTTC
1 CAATTTTTTTTC
25823464 GATTTCTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (13 bp):
CAATTTTTTTTCT
Found at i:25828130 original size:20 final size:19
Alignment explanation
Indices: 25828107--25828171 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
25828097 AAGCTCAAAC
25828107 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
25828127 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
25828147 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
25828167 GAGCT
1 GAGCT
25828172 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:25829988 original size:33 final size:33
Alignment explanation
Indices: 25829950--25830012 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
25829940 GATTACTCAC
25829950 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
25829983 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
25830013 AATTTCTTTT
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:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:25830039 original size:21 final size:21
Alignment explanation
Indices: 25830010--25830065 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
25830000 CAAGCTCTCT
*
25830010 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
25830031 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
25830052 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
25830066 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:25830058 original size:14 final size:14
Alignment explanation
Indices: 25830009--25830065 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
25829999 TCAAGCTCTC
25830009 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
25830022 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
25830036 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
25830050 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
25830064 TT
1 TT
25830066 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:25830093 original size:18 final size:18
Alignment explanation
Indices: 25830072--25830130 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
25830062 TTTTCTCTCA
25830072 CTTTTTTGATTTCTTTTT
1 CTTTTTTGATTTCTTTTT
* *
25830090 CTTTTGTAATTTCTTTTT
1 CTTTTTTGATTTCTTTTT
* * *
25830108 CTTCTTCGTTTTCTTTTT
1 CTTTTTTGATTTCTTTTT
*
25830126 GTTTT
1 CTTTT
25830131 CTTTCAATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.05, C:0.14, G:0.07, T:0.75
Consensus pattern (18 bp):
CTTTTTTGATTTCTTTTT
Found at i:25830147 original size:6 final size:6
Alignment explanation
Indices: 25830027--25830134 Score: 51
Period size: 6 Copynumber: 17.7 Consensus size: 6
25830017 TCTTTTTTCG
* * * **
25830027 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* ** * *
25830078 -TGATTT CTTTTT CTTTTGT -AATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CT-TTTT CTTTTT CTTTT-T CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
25830126 -GTTTT CTTT
1 CTTTTT CTTT
25830135 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 23, Indels: 14
0.66 0.21 0.13
Matches are distributed among these distances:
5 6 0.08
6 52 0.72
7 11 0.15
8 3 0.04
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:25832530 original size:13 final size:13
Alignment explanation
Indices: 25832514--25832590 Score: 52
Period size: 12 Copynumber: 5.6 Consensus size: 13
25832504 AAAAAAAATC
25832514 AAAAAAAATTCGAA
1 AAAAAAAATTCG-A
*
25832528 AAAAAAAATTGATTGAA
1 AAAAAAAA-T--TCG-A
25832545 AAAAAAAATTC-A
1 AAAAAAAATTCGA
*
25832557 AAAAAAAAGT-GA
1 AAAAAAAATTCGA
25832569 AAAAAAAA-TCGA
1 AAAAAAAATTCGA
25832581 GCAAAAAAAA
1 --AAAAAAAA
25832591 AAGGTGAGCA
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
11 1 0.02
12 21 0.40
14 17 0.32
15 1 0.02
16 1 0.02
17 12 0.23
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.13
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:25832531 original size:14 final size:14
Alignment explanation
Indices: 25832514--25832576 Score: 60
Period size: 17 Copynumber: 4.5 Consensus size: 14
25832504 AAAAAAAATC
25832514 AAAAAAAATTCGAA
1 AAAAAAAATTCGAA
*
25832528 AAAAAAAATTGATTGAA
1 AAAAAAAA-T--TCGAA
25832545 AAAAAAAATTC--A
1 AAAAAAAATTCGAA
*
25832557 AAAAAAAAGT-GAA
1 AAAAAAAATTCGAA
25832570 AAAAAAA
1 AAAAAAA
25832577 TCGAGCAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
12 10 0.24
13 8 0.20
14 9 0.22
15 1 0.02
16 1 0.02
17 12 0.29
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (14 bp):
AAAAAAAATTCGAA
Found at i:25832588 original size:17 final size:17
Alignment explanation
Indices: 25832568--25832608 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
25832558 AAAAAAAGTG
25832568 AAAAAAAA-ATCGAGCAA
1 AAAAAAAAGAT-GAGCAA
*
25832585 AAAAAAAAGGTGAGCAA
1 AAAAAAAAGATGAGCAA
25832602 AAAAAAA
1 AAAAAAA
25832609 TCAAGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 21 0.95
18 1 0.05
ACGTcount: A:0.73, C:0.07, G:0.15, T:0.05
Consensus pattern (17 bp):
AAAAAAAAGATGAGCAA
Found at i:25839353 original size:20 final size:19
Alignment explanation
Indices: 25839330--25839394 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
25839320 AAGCTCAAAC
25839330 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
25839350 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
25839370 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
25839390 GAGCT
1 GAGCT
25839395 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:25842265 original size:23 final size:22
Alignment explanation
Indices: 25842213--25842265 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
25842203 TCCACGTCTT
*
25842213 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
25842235 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
25842258 TTTCTTTT
1 TTTCTTTT
25842266 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:25847085 original size:14 final size:14
Alignment explanation
Indices: 25847066--25847104 Score: 71
Period size: 13 Copynumber: 2.9 Consensus size: 14
25847056 TAGCTCTCTC
25847066 TTTTTTTCACAATT
1 TTTTTTTCACAATT
25847080 TTTTTTTCA-AATT
1 TTTTTTTCACAATT
25847093 TTTTTTTCACAA
1 TTTTTTTCACAA
25847105 CTTGATATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTTTCACAATT
Found at i:25847160 original size:11 final size:10
Alignment explanation
Indices: 25847142--25847171 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
25847132 TGGAAACCAA
25847142 AATTTTTTTT
1 AATTTTTTTT
25847152 AATTTTTTTT
1 AATTTTTTTT
25847162 AATTTTTTTT
1 AATTTTTTTT
25847172 CGAGTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
AATTTTTTTT
Found at i:25847180 original size:13 final size:13
Alignment explanation
Indices: 25847164--25847188 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25847154 TTTTTTTTAA
25847164 TTTTTTTTCGAGT
1 TTTTTTTTCGAGT
25847177 TTTTTTTTCGAG
1 TTTTTTTTCGAG
25847189 AAACTATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.08, G:0.16, T:0.68
Consensus pattern (13 bp):
TTTTTTTTCGAGT
Found at i:25854938 original size:22 final size:21
Alignment explanation
Indices: 25854907--25854957 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
25854897 ACCTCTTTGA
25854907 ACCATTACCAATTCATACCAAAT
1 ACCA-TACCAATTCATACC-AAT
* *
25854930 ACCATACCATTTCGTACCAAT
1 ACCATACCAATTCATACCAAT
*
25854951 TCCATAC
1 ACCATAC
25854958 TATCTCGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.36
22 12 0.48
23 4 0.16
ACGTcount: A:0.37, C:0.33, G:0.02, T:0.27
Consensus pattern (21 bp):
ACCATACCAATTCATACCAAT
Found at i:25854957 original size:21 final size:21
Alignment explanation
Indices: 25854912--25854974 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
25854902 TTTGAACCAT
* * *
25854912 TACCAATTCATACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
25854934 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* * *
25854955 TACTATCTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
25854975 CAAATACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 23 0.66
22 12 0.34
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.29
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:25856880 original size:11 final size:11
Alignment explanation
Indices: 25856864--25856906 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
25856854 CGTATACAAT
25856864 TTTTTTTTCAA
1 TTTTTTTTCAA
* *
25856875 TTTTTTTTGAT
1 TTTTTTTTCAA
25856886 TTTTTTTTCAA
1 TTTTTTTTCAA
25856897 TTTTTTTTCA
1 TTTTTTTTCA
25856907 CGAATCTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:25856890 original size:22 final size:22
Alignment explanation
Indices: 25856862--25856904 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
25856852 ACCGTATACA
25856862 ATTTTTTTTTCAATTTTTTTTG
1 ATTTTTTTTTCAATTTTTTTTG
25856884 ATTTTTTTTTCAATTTTTTTT
1 ATTTTTTTTTCAATTTTTTTT
25856905 CACGAATCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (22 bp):
ATTTTTTTTTCAATTTTTTTTG
Found at i:25857113 original size:57 final size:57
Alignment explanation
Indices: 25857025--25857138 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
25857015 TGCCCGATCG
25857025 TTAAAACAGGGAAGAATCATGATACGACCATGCCTCAAGTCCTACCTAGCTCGAACA
1 TTAAAACAGGGAAGAATCATGATACGACCATGCCTCAAGTCCTACCTAGCTCGAACA
25857082 TTAAAACAGGGAAGAATCATGATACGACCATGCCTCAAGTCCTACCTAGCTCGAACA
1 TTAAAACAGGGAAGAATCATGATACGACCATGCCTCAAGTCCTACCTAGCTCGAACA
25857139 AGGAGCCGTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (57 bp):
TTAAAACAGGGAAGAATCATGATACGACCATGCCTCAAGTCCTACCTAGCTCGAACA
Found at i:25858405 original size:4 final size:4
Alignment explanation
Indices: 25858396--25858422 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
25858386 AAACTAAGTA
25858396 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
25858423 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:25869995 original size:20 final size:20
Alignment explanation
Indices: 25869972--25870025 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
25869962 AGTTTTTCCC
*
25869972 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
25869992 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
25870012 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
25870026 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:25870007 original size:30 final size:30
Alignment explanation
Indices: 25869972--25870045 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
25869962 AGTTTTTCCC
25869972 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
25870002 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
25870032 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
25870046 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:25870035 original size:20 final size:20
Alignment explanation
Indices: 25869972--25870036 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
25869962 AGTTTTTCCC
* * * *
25869972 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
25869992 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
25870011 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
25870032 AGCTC
1 AGCTC
25870037 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:25872173 original size:14 final size:13
Alignment explanation
Indices: 25872154--25872189 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
25872144 AAAGAGTTCG
25872154 AAAAAAAAATTGA
1 AAAAAAAAATTGA
25872167 AAAAAAAAATTGA
1 AAAAAAAAATTGA
25872180 AAAGAAAAAA
1 AAA-AAAAAA
25872190 AAATTGCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:25878585 original size:18 final size:18
Alignment explanation
Indices: 25878559--25878599 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
25878549 AAATTGAAAG
*
25878559 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
*
25878577 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
25878595 AAAAG
1 AAAAG
25878600 TGAGAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:25878587 original size:6 final size:6
Alignment explanation
Indices: 25878555--25878670 Score: 51
Period size: 6 Copynumber: 19.7 Consensus size: 6
25878545 AAAGAAATTG
* * ** **
25878555 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATCGAA AAAGTG
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* * * * ** * *
25878602 AGAGAA AAA-AT GAAG-A AAAGAA AATTGAA AAAGAA ATTGAG AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AA-AGAA AAAGAA AAAGAA AAAGAA
*
25878649 AAA-AA AATTGAA AAAGAA AAAG
1 AAAGAA AA-AGAA AAAGAA AAAG
25878671 CGAAAAAAGA
Statistics
Matches: 77, Mismatches: 28, Indels: 11
0.66 0.24 0.09
Matches are distributed among these distances:
5 13 0.17
6 55 0.71
7 9 0.12
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.09
Consensus pattern (6 bp):
AAAGAA
Found at i:25878648 original size:18 final size:18
Alignment explanation
Indices: 25878621--25878670 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
25878611 ATGAAGAAAA
25878621 GAAAATTGAAAAAGAAATT
1 GAAAA-TGAAAAAGAAATT
* *
25878640 GAGAATGAAAAAAAAATT
1 GAAAATGAAAAAGAAATT
*
25878658 GAAAAAGAAAAAG
1 GAAAATGAAAAAG
25878671 CGAAAAAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.14
Consensus pattern (18 bp):
GAAAATGAAAAAGAAATT
Found at i:25880805 original size:19 final size:19
Alignment explanation
Indices: 25880781--25880819 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
25880771 ATGGCTTAGA
25880781 CAATGACTCTTGAGTTGTC
1 CAATGACTCTTGAGTTGTC
25880800 CAATGACTCTTGAGTTGTC
1 CAATGACTCTTGAGTTGTC
25880819 C
1 C
25880820 TTGGCTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (19 bp):
CAATGACTCTTGAGTTGTC
Found at i:25882532 original size:77 final size:77
Alignment explanation
Indices: 25882439--25882592 Score: 299
Period size: 77 Copynumber: 2.0 Consensus size: 77
25882429 CAACATATTG
25882439 ATTCAAAATACAATTTTGATACTCACCTTCGCTTGACGTCAACTTAGGAATACAGGCTCCGGGTT
1 ATTCAAAATACAATTTTGATACTCACCTTCGCTTGACGTCAACTTAGGAATACAGGCTCCGGGTT
25882504 TAAAAACATGGT
66 TAAAAACATGGT
*
25882516 ATTCAAAATACAATTTTGATACTCACCTTCGCTTGACGTCAACTTATGAATACAGGCTCCGGGTT
1 ATTCAAAATACAATTTTGATACTCACCTTCGCTTGACGTCAACTTAGGAATACAGGCTCCGGGTT
25882581 TAAAAACATGGT
66 TAAAAACATGGT
25882593 TTTGATCGGT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (77 bp):
ATTCAAAATACAATTTTGATACTCACCTTCGCTTGACGTCAACTTAGGAATACAGGCTCCGGGTT
TAAAAACATGGT
Found at i:25883381 original size:19 final size:21
Alignment explanation
Indices: 25883340--25883382 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
25883330 ACAACACTTG
* *
25883340 TTTCTCTCACTCTTTCTTTTC
1 TTTCTCTCAATCTTTCTTCTC
25883361 TTTCTC-CAATCTTT-TTCTC
1 TTTCTCTCAATCTTTCTTCTC
25883380 TTT
1 TTT
25883383 TTCAATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 7 0.35
21 6 0.30
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTCTCTCAATCTTTCTTCTC
Found at i:25884366 original size:17 final size:17
Alignment explanation
Indices: 25884344--25884401 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
25884334 CTTATTCTTC
*
25884344 TTTTTTTCATGAAAATT
1 TTTTTTTCACGAAAATT
25884361 TTTTTTTCACG--AATT
1 TTTTTTTCACGAAAATT
*
25884376 TTTTTTTCACGAAATTT
1 TTTTTTTCACGAAAATT
25884393 TTTTTTTCA
1 TTTTTTTCA
25884402 ACTTGATATC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
15 15 0.41
17 22 0.59
ACGTcount: A:0.22, C:0.10, G:0.05, T:0.62
Consensus pattern (17 bp):
TTTTTTTCACGAAAATT
Found at i:25884398 original size:16 final size:16
Alignment explanation
Indices: 25884344--25884398 Score: 85
Period size: 15 Copynumber: 3.4 Consensus size: 16
25884334 CTTATTCTTC
*
25884344 TTTTTTTCATGAAAATT
1 TTTTTTTCACG-AAATT
25884361 TTTTTTTCACG-AATT
1 TTTTTTTCACGAAATT
25884376 TTTTTTTCACGAAATT
1 TTTTTTTCACGAAATT
25884392 TTTTTTT
1 TTTTTTT
25884399 TCAACTTGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
15 15 0.42
16 11 0.31
17 10 0.28
ACGTcount: A:0.22, C:0.09, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTTTTTCACGAAATT
Found at i:25884455 original size:11 final size:11
Alignment explanation
Indices: 25884439--25884495 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
25884429 ATGGAAACCA
25884439 AATTTTTTTTC
1 AATTTTTTTTC
*
25884450 AATTTTTTTCC
1 AATTTTTTTTC
*
25884461 AATTTTTTTTTTG
1 AA--TTTTTTTTC
*
25884474 AATTTTTTTTTG
1 AA-TTTTTTTTC
25884486 AATTTTTTTT
1 AATTTTTTTT
25884496 TGAAGAAACT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
11 20 0.49
12 12 0.29
13 9 0.22
ACGTcount: A:0.18, C:0.05, G:0.04, T:0.74
Consensus pattern (11 bp):
AATTTTTTTTC
Found at i:25884497 original size:12 final size:12
Alignment explanation
Indices: 25884441--25884499 Score: 75
Period size: 12 Copynumber: 4.9 Consensus size: 12
25884431 GGAAACCAAA
*
25884441 TTTTTTTTCAA-
1 TTTTTTTTGAAT
**
25884452 TTTTTTTCCAATT
1 TTTTTTTTGAA-T
25884465 TTTTTTTTGAAT
1 TTTTTTTTGAAT
25884477 TTTTTTTTGAAT
1 TTTTTTTTGAAT
25884489 TTTTTTTTGAA
1 TTTTTTTTGAA
25884500 GAAACTACTA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
11 10 0.23
12 24 0.56
13 9 0.21
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:25884499 original size:24 final size:24
Alignment explanation
Indices: 25884441--25884496 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
25884431 GGAAACCAAA
*
25884441 TTTTTTTTCAATTTTTTTCCAATT
1 TTTTTTTTGAATTTTTTTCCAATT
**
25884465 TTTTTTTTGAATTTTTTTTTGAATT
1 TTTTTTTTGAA-TTTTTTTCCAATT
25884490 TTTTTTT
1 TTTTTTT
25884497 GAAGAAACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.14, C:0.05, G:0.04, T:0.77
Consensus pattern (24 bp):
TTTTTTTTGAATTTTTTTCCAATT
Found at i:25885210 original size:19 final size:19
Alignment explanation
Indices: 25885186--25885223 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
25885176 TGGCTTAGAA
25885186 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
25885205 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
25885224 TTGGCTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
AATGACTCTTGAGTTGTCC
Found at i:25886491 original size:20 final size:20
Alignment explanation
Indices: 25886468--25886521 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
25886458 AGTTTTTCCC
*
25886468 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
25886488 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
25886508 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
25886522 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:25886512 original size:30 final size:30
Alignment explanation
Indices: 25886468--25886541 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
25886458 AGTTTTTCCC
25886468 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
25886498 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
25886528 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
25886542 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:25886531 original size:20 final size:20
Alignment explanation
Indices: 25886468--25886532 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
25886458 AGTTTTTCCC
* * * *
25886468 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
25886488 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
25886507 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
25886528 AGCTC
1 AGCTC
25886533 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:25888046 original size:15 final size:15
Alignment explanation
Indices: 25887999--25888038 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
25887989 TATAAGCAAC
25887999 AAAACATAGTAATTA
1 AAAACATAGTAATTA
* *
25888014 AAAAAATAATTAATTA
1 AAAACAT-AGTAATTA
25888030 AAAACATAG
1 AAAACATAG
25888039 CTATTAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (15 bp):
AAAACATAGTAATTA
Found at i:25903253 original size:29 final size:30
Alignment explanation
Indices: 25903173--25903254 Score: 75
Period size: 29 Copynumber: 2.8 Consensus size: 30
25903163 AAAGTCATGC
25903173 ATTATGTAACTTTCATGTTAGTTAAGTTTGCA
1 ATTATGTAACTTTCATGTTAGTT-AGTTT-CA
* * *
25903205 A-TAT-TAA-ATT-AAGTCAAGTTAGTTT-A
1 ATTATGTAACTTTCATGT-TAGTTAGTTTCA
25903231 ATTATGTAACTTTCATGTTAGTTA
1 ATTATGTAACTTTCATGTTAGTTA
25903255 AATTTGCATT
Statistics
Matches: 39, Mismatches: 6, Indels: 13
0.67 0.10 0.22
Matches are distributed among these distances:
26 2 0.05
27 3 0.08
28 11 0.28
29 13 0.33
30 6 0.15
31 3 0.08
32 1 0.03
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.46
Consensus pattern (30 bp):
ATTATGTAACTTTCATGTTAGTTAGTTTCA
Found at i:25904479 original size:13 final size:13
Alignment explanation
Indices: 25904461--25904510 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
25904451 TATCAAGTTG
25904461 TGAAAAAAAATTT
1 TGAAAAAAAATTT
*
25904474 TGAAAAAAAATTA
1 TGAAAAAAAATTT
*
25904487 TGAAAAAAAAAATT
1 TG-AAAAAAAATTT
25904501 TGAAAAAAAA
1 TGAAAAAAAA
25904511 AGAGAGCTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
13 22 0.67
14 11 0.33
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (13 bp):
TGAAAAAAAATTT
Found at i:25904482 original size:14 final size:14
Alignment explanation
Indices: 25904463--25904511 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
25904453 TCAAGTTGTG
25904463 AAAAAAAATTTTG-
1 AAAAAAAATTTTGA
*
25904476 AAAAAAAATTATGA
1 AAAAAAAATTTTGA
*
25904490 AAAAAAAAATTTGA
1 AAAAAAAATTTTGA
25904504 AAAAAAAA
1 AAAAAAAA
25904512 GAGAGCTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
13 12 0.38
14 20 0.62
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.20
Consensus pattern (14 bp):
AAAAAAAATTTTGA
Found at i:25906382 original size:13 final size:13
Alignment explanation
Indices: 25906361--25906397 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
25906351 ATTTTTTTTT
25906361 TGAAAAAAACATTG
1 TGAAAAAAA-ATTG
25906375 TGAAAAAAAATTG
1 TGAAAAAAAATTG
25906388 TGAAAAAAAA
1 TGAAAAAAAA
25906398 AGAGCTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.65, C:0.03, G:0.14, T:0.19
Consensus pattern (13 bp):
TGAAAAAAAATTG
Found at i:25907340 original size:18 final size:17
Alignment explanation
Indices: 25907319--25907363 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
25907309 GAGTGACGAG
25907319 AGAAAAAGAAACTGAAAA
1 AGAAAAA-AAACTGAAAA
*
25907337 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAACTGAAAA
25907355 AGATAAAAA
1 AGA-AAAAA
25907364 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.13, T:0.09
Consensus pattern (17 bp):
AGAAAAAAAACTGAAAA
Found at i:25907393 original size:21 final size:19
Alignment explanation
Indices: 25907353--25907395 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
25907343 AAAAATTGAA
* *
25907353 AAAGATAAAAAGATTGGAG
1 AAAGAAAAAAAGAGTGGAG
25907372 AAAGAAAAGAAAGAGTGCGAG
1 AAAGAAAA-AAAGAGTG-GAG
25907393 AAA
1 AAA
25907396 CAAGTGTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 7 0.35
21 6 0.30
ACGTcount: A:0.60, C:0.02, G:0.28, T:0.09
Consensus pattern (19 bp):
AAAGAAAAAAAGAGTGGAG
Found at i:25913299 original size:15 final size:15
Alignment explanation
Indices: 25913278--25913335 Score: 98
Period size: 15 Copynumber: 3.7 Consensus size: 15
25913268 TAGCTTCTTC
25913278 TTTTTTTTTCACGAAA
1 TTTTTTTTTCACG-AA
25913294 TTTTTTTTTTCACGAA
1 -TTTTTTTTTCACGAA
25913310 TTTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
25913325 TTTTTTTTTCA
1 TTTTTTTTTCA
25913336 ACTTGATATC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 26 0.63
16 2 0.05
17 13 0.32
ACGTcount: A:0.19, C:0.12, G:0.05, T:0.64
Consensus pattern (15 bp):
TTTTTTTTTCACGAA
Found at i:25913390 original size:12 final size:12
Alignment explanation
Indices: 25913373--25913430 Score: 91
Period size: 12 Copynumber: 4.9 Consensus size: 12
25913363 ATGGAAACCA
25913373 AATTTTTTTTTG
1 AATTTTTTTTTG
25913385 AA-TTTTTTTTG
1 AATTTTTTTTTG
25913396 AATTTTTTTTTG
1 AATTTTTTTTTG
*
25913408 AATTTTTTTTCG
1 AATTTTTTTTTG
*
25913420 AGTTTTTTTTT
1 AATTTTTTTTT
25913431 CGAGAAACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
11 11 0.26
12 31 0.74
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.74
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:25913399 original size:23 final size:24
Alignment explanation
Indices: 25913373--25913430 Score: 100
Period size: 23 Copynumber: 2.5 Consensus size: 24
25913363 ATGGAAACCA
25913373 AATTTTTTTTTGAATTTTTTTT-G
1 AATTTTTTTTTGAATTTTTTTTCG
25913396 AATTTTTTTTTGAATTTTTTTTCG
1 AATTTTTTTTTGAATTTTTTTTCG
*
25913420 AGTTTTTTTTT
1 AATTTTTTTTT
25913431 CGAGAAACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 22 0.67
24 11 0.33
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.74
Consensus pattern (24 bp):
AATTTTTTTTTGAATTTTTTTTCG
Found at i:25914464 original size:21 final size:23
Alignment explanation
Indices: 25914419--25914465 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
25914409 TCACCTGCAA
* *
25914419 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
25914442 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
25914463 TAA
1 TAA
25914466 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:25922507 original size:33 final size:33
Alignment explanation
Indices: 25922469--25922531 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
25922459 GATTACTCAC
25922469 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
25922502 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
25922532 AATTTCTTTT
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:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:25922558 original size:21 final size:21
Alignment explanation
Indices: 25922529--25922584 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
25922519 CAAGCTCTCT
*
25922529 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
25922550 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
25922571 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
25922585 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:25922577 original size:14 final size:14
Alignment explanation
Indices: 25922528--25922584 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
25922518 TCAAGCTCTC
25922528 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
25922541 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
25922555 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
25922569 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
25922583 TT
1 TT
25922585 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:25922644 original size:18 final size:18
Alignment explanation
Indices: 25922546--25922649 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
25922536 TCTTTTTTCG
25922546 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
25922565 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
25922585 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
25922603 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
25922621 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
25922639 CTTTTTGTTTT
1 CTTTTTCTTTT
25922650 CTTTCAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
17 1 0.02
18 46 0.70
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:25922666 original size:6 final size:6
Alignment explanation
Indices: 25922546--25922653 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
25922536 TCTTTTTTCG
* * * **
25922546 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
25922597 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
25922645 -GTTTT CTTT
1 CTTTTT CTTT
25922654 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:25923725 original size:10 final size:10
Alignment explanation
Indices: 25923710--25923742 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
25923700 TTTTTGTCAC
25923710 TTCTTTTTTT
1 TTCTTTTTTT
25923720 TTCTTTTTTT
1 TTCTTTTTTT
25923730 TTCTATTTTTT
1 TTCT-TTTTTT
25923741 TT
1 TT
25923743 TGAATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:25923728 original size:12 final size:12
Alignment explanation
Indices: 25923713--25923755 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
25923703 TTGTCACTTC
25923713 TTTTTTTTTC--
1 TTTTTTTTTCTA
25923723 TTTTTTTTTCTA
1 TTTTTTTTTCTA
**
25923735 TTTTTTTTTGAA
1 TTTTTTTTTCTA
25923747 TTTTTTTTT
1 TTTTTTTTT
25923756 GAATTTCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 10 0.34
12 19 0.66
ACGTcount: A:0.07, C:0.05, G:0.02, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTCTA
Found at i:25923756 original size:12 final size:12
Alignment explanation
Indices: 25923723--25923761 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
25923713 TTTTTTTTTC
**
25923723 TTTTTTTTTCTA
1 TTTTTTTTTGAA
25923735 TTTTTTTTTGAA
1 TTTTTTTTTGAA
25923747 TTTTTTTTTGAA
1 TTTTTTTTTGAA
25923759 TTT
1 TTT
25923762 CTTCTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.13, C:0.03, G:0.05, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:25925963 original size:40 final size:40
Alignment explanation
Indices: 25925863--25926034 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
25925853 GCTCCTCGTT
* * *
25925863 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
25925903 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
25925942 CGAATGCCTTCGGGGCTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
25925982 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
25926022 CAAATGCCTTCGG
1 CAAATGCCTTCGG
25926035 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:25926047 original size:80 final size:78
Alignment explanation
Indices: 25925863--25926087 Score: 220
Period size: 80 Copynumber: 2.8 Consensus size: 78
25925853 GCTCCTCGTT
* * * * *
25925863 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
25925927 ATTTAATAACTCGCA
64 ATTTAATAACTCGCA
* * * *
25925942 CGAATGCCTTCGGGGCTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
25926007 AATTT-GTATCTCGCA
63 AATTTAATAACTCGCA
* * * * *
25926022 CAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCGG
25926087 A
63 A
25926088 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
78 1 0.01
79 37 0.31
80 69 0.57
81 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAAT
TTAATAACTCGCA
Found at i:25926096 original size:41 final size:41
Alignment explanation
Indices: 25926019--25926096 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
25926009 TTTGTATCTC
* * *
25926019 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
25926060 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
25926097 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:25932282 original size:40 final size:40
Alignment explanation
Indices: 25932182--25932352 Score: 211
Period size: 40 Copynumber: 4.3 Consensus size: 40
25932172 GCTCCTCGTT
* * *
25932182 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
25932222 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
25932261 CGAATGCCTTCGGGACTTAACCCAGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
25932301 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
25932341 CAAATGCCTTCG
1 CAAATGCCTTCG
25932353 AATCTTAGTC
Statistics
Matches: 116, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 35 0.30
40 77 0.66
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:25935160 original size:18 final size:18
Alignment explanation
Indices: 25935122--25935163 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
25935112 AAATCGAAAG
* **
25935122 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCCA
25935140 AAAAGAAAAAGAAATCCA
1 AAAAGAAAAAGAAATCCA
25935158 AAAAGA
1 AAAAGA
25935164 GAGTGAGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCCA
Found at i:25943009 original size:28 final size:28
Alignment explanation
Indices: 25942978--25943044 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
25942968 CAGCTATGAC
*
25942978 TTAGACATCATTAA-AGCATGTAATAAAA
1 TTAGACA-CATTAATAACATGTAATAAAA
25943006 TTAGACACATTAATAACATGTAATAAAA
1 TTAGACACATTAATAACATGTAATAAAA
* *
25943034 TAAAACACATT
1 TTAGACACATT
25943045 TATCACAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 6 0.17
28 29 0.83
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.28
Consensus pattern (28 bp):
TTAGACACATTAATAACATGTAATAAAA
Found at i:25943605 original size:25 final size:25
Alignment explanation
Indices: 25943561--25943613 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
25943551 TTCTTGTTCT
25943561 AAGTTTTCATTTTAATTCCAAATACC
1 AAGTTTTCATTTTAATTCCAAA-ACC
* * *
25943587 AAGTTTTCTTTTTCA-TCCACAACC
1 AAGTTTTCATTTTAATTCCAAAACC
25943611 AAG
1 AAG
25943614 CCTTAATCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.25
25 5 0.21
26 13 0.54
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.40
Consensus pattern (25 bp):
AAGTTTTCATTTTAATTCCAAAACC
Found at i:25945722 original size:20 final size:20
Alignment explanation
Indices: 25945697--25945755 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
25945687 TAAACACAAA
*
25945697 TGAGCTTAAAA-TGAGCTGAT
1 TGAGC-TAAAAGTGAGCTGAG
25945717 TGAGCTAAAAGTGAGCTCG-G
1 TGAGCTAAAAGTGAGCT-GAG
*
25945737 TGAGCTAAAATTGAGCTGA
1 TGAGCTAAAAGTGAGCTGA
25945756 ATGAACTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 6 0.18
20 27 0.79
21 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (20 bp):
TGAGCTAAAAGTGAGCTGAG
Found at i:25948739 original size:24 final size:23
Alignment explanation
Indices: 25948686--25948762 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 23
25948676 ATTAATTAGA
**
25948686 AAATGGTATTTGGTTTTGGTACG
1 AAATGGTATTTGGAATTGGTACG
** *
25948709 ATTTGGTATTTGGGAATTGGTACT
1 AAATGGTATTT-GGAATTGGTACG
** *
25948733 AAATGGTA-AAGGATTTGGTACG
1 AAATGGTATTTGGAATTGGTACG
25948755 AAATGGTA
1 AAATGGTA
25948763 ATGGTTCAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
22 18 0.43
23 9 0.21
24 15 0.36
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.38
Consensus pattern (23 bp):
AAATGGTATTTGGAATTGGTACG
Found at i:25955243 original size:11 final size:11
Alignment explanation
Indices: 25955222--25955252 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
25955212 TGCAATTTTT
25955222 TTTTCTTTTCAA
1 TTTT-TTTTCAA
25955234 TTTTTTTTCAA
1 TTTTTTTTCAA
25955245 TTTTTTTT
1 TTTTTTTT
25955253 TCGAACTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:25955586 original size:24 final size:23
Alignment explanation
Indices: 25955533--25955609 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 23
25955523 ATTAATTAGA
**
25955533 AAATGGTATTTGGTTTTGGTACG
1 AAATGGTATTTGGAATTGGTACG
** *
25955556 ATTTGGTATTTGGGAATTGGTACT
1 AAATGGTATTT-GGAATTGGTACG
** *
25955580 AAATGGTA-AAGGATTTGGTACG
1 AAATGGTATTTGGAATTGGTACG
25955602 AAATGGTA
1 AAATGGTA
25955610 ATGGTTCAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
22 18 0.43
23 9 0.21
24 15 0.36
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.38
Consensus pattern (23 bp):
AAATGGTATTTGGAATTGGTACG
Found at i:25959566 original size:12 final size:12
Alignment explanation
Indices: 25959549--25959591 Score: 63
Period size: 11 Copynumber: 3.8 Consensus size: 12
25959539 AGACCGTATA
25959549 CAATTTTTTTTT
1 CAATTTTTTTTT
25959561 CAA-TTTTTTTT
1 CAATTTTTTTTT
*
25959572 -GATTTTTTTTT
1 CAATTTTTTTTT
25959583 CAATTTTTT
1 CAATTTTTT
25959592 ACGAACCTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 1 0.04
11 16 0.59
12 10 0.37
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.74
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:25960965 original size:20 final size:20
Alignment explanation
Indices: 25960940--25960998 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
25960930 TAAACGCAAA
*
25960940 TGAGCTTAAAA-TGAGCTGAT
1 TGAGC-TAAAAGTGAGCTGAG
25960960 TGAGCTAAAAGTGAGCTCG-G
1 TGAGCTAAAAGTGAGCT-GAG
*
25960980 TGAGCTAAAATTGAGCTGA
1 TGAGCTAAAAGTGAGCTGA
25960999 ATGAACTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 6 0.18
20 27 0.79
21 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (20 bp):
TGAGCTAAAAGTGAGCTGAG
Found at i:25962969 original size:10 final size:10
Alignment explanation
Indices: 25962954--25963015 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
25962944 TTTGAACCAT
*
25962954 TACCAATTCG
1 TACCAATTCA
*
25962964 TACCAAATACCA
1 TACC-AAT-TCA
*
25962976 TACCATTTCA
1 TACCAATTCA
25962986 TACCAATTCCA
1 TACCAATT-CA
* *
25962997 TACCATTTCG
1 TACCAATTCA
25963007 TACCAATTC
1 TACCAATTC
25963016 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Done.