Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold830
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: 58117
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:4458 original size:19 final size:19
Alignment explanation
Indices: 4434--4471 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
4424 TAAGCATGTG
4434 TGGA-CTTCTTGATTGGGCT
1 TGGACCTTCTT-ATTGGGCT
4453 TGGACTCTTCTTATTGGGC
1 TGGAC-CTTCTTATTGGGC
4472 CTTGCCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 7 0.41
21 6 0.35
ACGTcount: A:0.11, C:0.18, G:0.29, T:0.42
Consensus pattern (19 bp):
TGGACCTTCTTATTGGGCT
Found at i:8151 original size:20 final size:20
Alignment explanation
Indices: 8128--8181 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
8118 AGTTTTTCCC
*
8128 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
8148 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
8168 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
8182 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:8163 original size:30 final size:30
Alignment explanation
Indices: 8128--8201 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
8118 AGTTTTTCCC
8128 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
8158 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
8188 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
8202 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:8191 original size:20 final size:20
Alignment explanation
Indices: 8128--8192 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
8118 AGTTTTTCCC
* * * *
8128 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
8148 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
8167 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
8188 AGCTC
1 AGCTC
8193 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:16229 original size:23 final size:22
Alignment explanation
Indices: 16178--16229 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
16168 CCTTGTCTTT
*
16178 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
16200 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
16223 TTCTTTT
1 TTCTTTT
16230 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:21145 original size:20 final size:20
Alignment explanation
Indices: 21098--21145 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
21088 AGTAAGCTCG
21098 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
21118 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
21138 GTTGAGCT
1 GTTGAGCT
21146 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:24225 original size:30 final size:30
Alignment explanation
Indices: 24191--24287 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
24181 TAAACTAAAA
24191 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
24221 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
24251 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
24280 ATGAGCTA
1 -TGAGCTA
24288 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:26481 original size:12 final size:12
Alignment explanation
Indices: 26466--26496 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
26456 TTCTTTTTGC
26466 TTTTCAAAGGCT
1 TTTTCAAAGGCT
26478 TTTTCAAAGGCT
1 TTTTCAAAGGCT
26490 TTTTCAA
1 TTTTCAA
26497 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:26566 original size:6 final size:5
Alignment explanation
Indices: 26544--26585 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
26534 CTCTTGCCTC
26544 TCTTT TCTTT T-TATT TCATTT TCTTTT TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TCTTT TCTTT TCTTT
26586 GTTTTCTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
4 1 0.03
5 22 0.67
6 9 0.27
7 1 0.03
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:26595 original size:16 final size:16
Alignment explanation
Indices: 26542--26596 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
26532 GCCTCTTGCC
26542 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTAT
*
26558 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTAT
*
26574 TTTCTTTTCTTTGTT-T
1 TCTCTTTTCTTT-TTAT
26590 TCTCTTT
1 TCTCTTT
26597 ACAAGAATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.06
16 28 0.82
17 4 0.12
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (16 bp):
TCTCTTTTCTTTTTAT
Found at i:27553 original size:14 final size:14
Alignment explanation
Indices: 27534--27562 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
27524 TTATTTTCGA
27534 TTTTTTTT-TGAAT
1 TTTTTTTTCTGAAT
27547 TTTTTTTTCTGAAT
1 TTTTTTTTCTGAAT
27561 TT
1 TT
27563 CTTCTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.76
Consensus pattern (14 bp):
TTTTTTTTCTGAAT
Found at i:29315 original size:30 final size:30
Alignment explanation
Indices: 29281--29377 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
29271 TAAACTAAAA
*
29281 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
29311 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
29341 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
29370 ATGAGCTA
1 -TGAGCTA
29378 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:29712 original size:11 final size:12
Alignment explanation
Indices: 29682--29713 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
29672 TTTCACTCTT
29682 CTCTTTTTCAAA
1 CTCTTTTTCAAA
29694 CTCTTTTTCAAA
1 CTCTTTTTCAAA
*
29706 TTCTTTTT
1 CTCTTTTT
29714 TCGCTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:29725 original size:27 final size:27
Alignment explanation
Indices: 29695--29756 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
29685 TTTTTCAAAC
*
29695 TCTTTTTCAAATTCTT-TTTTC-GCTTTT
1 TCTTTTTC-AATT-TTCTTTTCTGCATTT
*
29722 TCTTTTTCAATTTTCTTTTCTTCATTT
1 TCTTTTTCAATTTTCTTTTCTGCATTT
29749 TCTTTTTC
1 TCTTTTTC
29757 TCTCACTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 9 0.29
27 20 0.65
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (27 bp):
TCTTTTTCAATTTTCTTTTCTGCATTT
Found at i:29735 original size:13 final size:12
Alignment explanation
Indices: 29719--29837 Score: 54
Period size: 11 Copynumber: 10.0 Consensus size: 12
29709 TTTTTTCGCT
29719 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
29732 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
29746 TTTTCTTTTTC-
1 TTTTCTTTTTCA
** *
29757 TCTCACTTTTTTGA
1 T-TTTC-TTTTTCA
29771 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
29781 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
*
29794 TTTTCTTTTT-G
1 TTTTCTTTTTCA
*
29805 TTTTCTTTTT-G
1 TTTTCTTTTTCA
29816 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
29826 ATTTCTTTTTCA
1 TTTTCTTTTTCA
29838 ATCTCTTTCT
Statistics
Matches: 82, Mismatches: 13, Indels: 23
0.69 0.11 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 25 0.30
12 21 0.26
13 17 0.21
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:29748 original size:14 final size:14
Alignment explanation
Indices: 29697--29755 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
29687 TTTCAAACTC
*
29697 TTTTTCAA-ATTCT
1 TTTTTCAATTTTCT
**
29710 TTTTTCGCTTTT-T
1 TTTTTCAATTTTCT
29723 CTTTTTCAATTTTCT
1 -TTTTTCAATTTTCT
29738 TTTCTTC-ATTTTCT
1 TTT-TTCAATTTTCT
29752 TTTT
1 TTTT
29756 CTCTCACTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 8 0.22
14 25 0.68
15 4 0.11
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTCAATTTTCT
Found at i:29783 original size:18 final size:18
Alignment explanation
Indices: 29762--29819 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
29752 TTTTCTCTCA
29762 CTTTTTTGATTTCTTTTT
1 CTTTTTTGATTTCTTTTT
***
29780 CTTTTGCAATTTCTTTTT
1 CTTTTTTGATTTCTTTTT
*
29798 C-TTTTTGTTTTCTTTTT
1 CTTTTTTGATTTCTTTTT
*
29815 GTTTT
1 CTTTT
29820 CTTTCAATTT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.76
Consensus pattern (18 bp):
CTTTTTTGATTTCTTTTT
Found at i:29810 original size:11 final size:11
Alignment explanation
Indices: 29794--29823 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
29784 TGCAATTTCT
29794 TTTTCTTTTTG
1 TTTTCTTTTTG
29805 TTTTCTTTTTG
1 TTTTCTTTTTG
29816 TTTTCTTT
1 TTTTCTTT
29824 CAATTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTG
Found at i:29836 original size:6 final size:6
Alignment explanation
Indices: 29717--29823 Score: 58
Period size: 6 Copynumber: 17.7 Consensus size: 6
29707 TCTTTTTTCG
* * * **
29717 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * ** *
29768 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT -GTTTT CTTTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
29815 -GTTTT CTTT
1 CTTTTT CTTT
29824 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 23, Indels: 12
0.67 0.21 0.11
Matches are distributed among these distances:
5 9 0.12
6 50 0.69
7 10 0.14
8 3 0.04
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:30911 original size:20 final size:20
Alignment explanation
Indices: 30886--30943 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
30876 TTGTCACTTC
30886 TTTTTTTTCTTTTTTTTCG-A
1 TTTTTTTTCTTTTTTTT-GAA
**
30906 TTTTTTTGAATTTTTTTTGAA
1 TTTTTTT-TCTTTTTTTTGAA
* *
30927 TTTCTTCTCTTTTTTTT
1 TTTTTTTTCTTTTTTTT
30944 AAAATCCAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.09, C:0.09, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTTTTTTCTTTTTTTTGAA
Found at i:36987 original size:19 final size:18
Alignment explanation
Indices: 36951--36990 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
36941 TTTCCACTCG
*
36951 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
36969 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
36988 TTT
1 TTT
36991 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:38094 original size:12 final size:13
Alignment explanation
Indices: 38045--38091 Score: 85
Period size: 13 Copynumber: 3.5 Consensus size: 13
38035 AACTAGCTTC
38045 TTTTTTTTCAAAT
1 TTTTTTTTCAAAT
38058 TTTTTTTTCACAAT
1 TTTTTTTTCA-AAT
38072 TTTTTTTTCAAAT
1 TTTTTTTTCAAAT
38085 TTTTTTT
1 TTTTTTT
38092 CAACTTGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 20 0.61
14 13 0.39
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTTTCAAAT
Found at i:38149 original size:12 final size:12
Alignment explanation
Indices: 38132--38163 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
38122 TGGAAACTAG
38132 TTTTTTTTTGAA
1 TTTTTTTTTGAA
38144 TTTTTTTTTGAA
1 TTTTTTTTTGAA
38156 TTTTTTTT
1 TTTTTTTT
38164 CGAGAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:39198 original size:21 final size:23
Alignment explanation
Indices: 39153--39199 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39143 TCACCTGCAA
* *
39153 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
39176 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
39197 TAA
1 TAA
39200 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:44557 original size:16 final size:15
Alignment explanation
Indices: 44536--44590 Score: 101
Period size: 15 Copynumber: 3.6 Consensus size: 15
44526 TAGCTTCTTC
44536 TTTTTTTCACGAAATT
1 TTTTTTTCACG-AATT
44552 TTTTTTTCACGAATT
1 TTTTTTTCACGAATT
44567 TTTTTTTCACGAATT
1 TTTTTTTCACGAATT
44582 TTTTTTTCA
1 TTTTTTTCA
44591 ACTTGATATC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
15 28 0.72
16 11 0.28
ACGTcount: A:0.20, C:0.13, G:0.05, T:0.62
Consensus pattern (15 bp):
TTTTTTTCACGAATT
Found at i:44664 original size:11 final size:12
Alignment explanation
Indices: 44628--44661 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
44618 ATGGAAACCA
44628 AATTTTTTTTTG
1 AATTTTTTTTTG
44640 AATTTTTTTTTG
1 AATTTTTTTTTG
44652 AATTTTTTTT
1 AATTTTTTTT
44662 GAAGAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:45699 original size:21 final size:23
Alignment explanation
Indices: 45654--45700 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
45644 TCACCTGCAA
* *
45654 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
45677 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
45698 TAA
1 TAA
45701 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:53432 original size:21 final size:20
Alignment explanation
Indices: 53383--53438 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
53373 GACCTCTTTG
*
53383 AACCATTACCAATTCGTACCA
1 AACCA-TACCATTTCGTACCA
53404 AACCATACCATTTCGTACCA
1 AACCATACCATTTCGTACCA
*
53424 ATTCCATACCATTTC
1 A-ACCATACCATTTC
53439 AAGCCAATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.29
Consensus pattern (20 bp):
AACCATACCATTTCGTACCA
Found at i:53445 original size:21 final size:21
Alignment explanation
Indices: 53389--53449 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
53379 TTTGAACCAT
* * *
53389 TACCAATTCGTACCAA-ACCA
1 TACCATTTCGAACCAATTCCA
*
53409 TACCATTTCGTACCAATTCCA
1 TACCATTTCGAACCAATTCCA
53430 TACCATTTC-AAGCCAATTCC
1 TACCATTTCGAA-CCAATTCC
53450 CAAATACCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.33, C:0.34, G:0.05, T:0.28
Consensus pattern (21 bp):
TACCATTTCGAACCAATTCCA
Found at i:53828 original size:16 final size:16
Alignment explanation
Indices: 53807--53874 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
53797 TTTGGTTCGC
53807 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
53823 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
53839 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
53855 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
53871 TGTA
1 TGTA
53875 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:54303 original size:117 final size:120
Alignment explanation
Indices: 54096--54529 Score: 787
Period size: 119 Copynumber: 3.7 Consensus size: 120
54086 ATCATATTTA
54096 AACATAATTATTATT-AATATA-TATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
54159 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
54214 AACATAATTATTATTAAATATATTATAATT-AAA-ATATAATTTAATAAAATTCTTAA-AATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
54276 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
54331 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAA-AATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
54395 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* *
54450 AACATAATTATTATTAAATATATTATAACT-AAA-ATATAATTTAATAAAATTATTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
54513 TATTCTTATAT-AATTTA
66 TATTCTTATATGAATTTA
54530 ATAAACAATT
Statistics
Matches: 309, Mismatches: 2, Indels: 11
0.96 0.01 0.03
Matches are distributed among these distances:
117 119 0.39
118 61 0.20
119 122 0.39
120 7 0.02
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:54376 original size:14 final size:15
Alignment explanation
Indices: 54210--54378 Score: 58
Period size: 15 Copynumber: 11.6 Consensus size: 15
54200 ATAAAATATA
54210 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
54225 TATTAAATATATTAT
1 AATTAAATATATTAT
54240 AATTAAAATATAATT-T
1 AATT-AAATAT-ATTAT
* * *
54256 AATAAAAT-TCTTAA
1 AATTAAATATATTAT
*
54270 AATT-AATATTCTTAT
1 AATTAAATA-TATTAT
* * *
54285 -A-TGAATTTACTCA-
1 AATTAAATATA-TTAT
* *
54298 AATCATAATATATGAT
1 AATTA-AATATATTAT
*
54314 ACTATAAA-ATA-TA-
1 AAT-TAAATATATTAT
54327 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
54342 TATTAAATATATTAT
1 AATTAAATATATTAT
54357 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
54370 AATTTAATA
1 AATTAAATA
54379 AAATTCTTAA
Statistics
Matches: 114, Mismatches: 21, Indels: 39
0.66 0.12 0.22
Matches are distributed among these distances:
12 3 0.03
13 20 0.18
14 25 0.22
15 43 0.38
16 19 0.17
17 4 0.04
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:54497 original size:15 final size:16
Alignment explanation
Indices: 54465--54504 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
54455 AATTATTATT
54465 AAATATATTATAACTA
1 AAATATATTATAACTA
54481 AAATATAATT-TAA-TA
1 AAATAT-ATTATAACTA
54496 AAAT-TATTA
1 AAATATATTA
54505 ATAATTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.14
14 1 0.05
15 6 0.27
16 9 0.41
17 3 0.14
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATATTATAACTA
Found at i:58080 original size:13 final size:13
Alignment explanation
Indices: 58045--58086 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
58035 TTCTTTTTCT
*
58045 TTTCTTGCTTTGC
1 TTTCTTCCTTTGC
*
58058 -TTCCTCCTTTGC
1 TTTCTTCCTTTGC
58070 TTTCTTCCTTTGGC
1 TTTCTTCCTTT-GC
58084 TTT
1 TTT
58087 GCTTTCTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.42
13 9 0.38
14 5 0.21
ACGTcount: A:0.00, C:0.29, G:0.12, T:0.60
Consensus pattern (13 bp):
TTTCTTCCTTTGC
Done.