Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3020
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: 39943
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1830 original size:20 final size:21
Alignment explanation
Indices: 1793--1831 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1783 GACTTATCCA
1793 AAGAATCCAAGCGTACTTTTC
1 AAGAATCCAAGCGTACTTTTC
*
1814 AAGAATGCAAG-GTACTTT
1 AAGAATCCAAGCGTACTTT
1832 AAGCGTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (21 bp):
AAGAATCCAAGCGTACTTTTC
Found at i:2118 original size:11 final size:10
Alignment explanation
Indices: 2093--2118 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2083 TACAATTTTG
2093 ATTTTTAAAT
1 ATTTTTAAAT
2103 ATTTTTAAAT
1 ATTTTTAAAT
2113 ATTTTT
1 ATTTTT
2119 CACACATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTAAAT
Found at i:5799 original size:79 final size:81
Alignment explanation
Indices: 5663--5847 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
5653 TTGAATGATG
*
5663 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
5727 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
5742 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
5804 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
5822 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
5848 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:5861 original size:40 final size:40
Alignment explanation
Indices: 5664--5847 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
5654 TGAATGATGT
* * * *
5664 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
5704 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
5744 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
5782 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
5823 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
5848 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:5869 original size:79 final size:79
Alignment explanation
Indices: 5716--5880 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
5706 GGACTAAGAT
* **
5716 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
5781 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
5795 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
5858 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
5874 CCGAAGG
1 CCGAAGG
5881 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:13839 original size:79 final size:80
Alignment explanation
Indices: 13704--13887 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 80
13694 TTGAATGATG
* *
13704 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
13768 GTGCGAGATAC-TAA
66 GTGCGAGATACGTAA
* * * **
13782 TTCCGGGCTAAGCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
*
13845 TTGTGCGAGTTACTGTAA
64 TTGTGCGAGATAC-GTAA
*
13863 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAG-CCCGAAGGCATTTG
13888 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 1 0.01
79 66 0.73
80 21 0.23
81 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACGTAA
Found at i:13894 original size:40 final size:40
Alignment explanation
Indices: 13704--13887 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
13694 TTGAATGATG
* * * *
13704 TCCGGGCTAAGT-CCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
13743 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
13783 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
13822 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTGTAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAA
*
13863 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
13888 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
39 45 0.36
40 72 0.57
41 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:13909 original size:79 final size:78
Alignment explanation
Indices: 13756--13920 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 78
13746 GGACTAAGAT
**
13756 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAA-TCCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
13821 ATCCGGGTTAAGTC
65 ATCCGGGTTAAATC
* *
13835 CCGAAGGCATTTGTGCGAGTTACTGTAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATAC--TAATCCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
13898 TATATCC-GGTTAAATT
62 TAAATCCGGGTTAAATC
13914 CCGAAGG
1 CCGAAGG
13921 TACGTGATTT
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
79 47 0.63
80 25 0.33
81 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGATACTAATCCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA
TCCGGGTTAAATC
Found at i:20258 original size:20 final size:20
Alignment explanation
Indices: 20214--20258 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
20204 TATATTTTTT
*
20214 AATTTAAAATTTATCATTAA
1 AATTTAAAATTTATCATCAA
* * *
20234 TATTTAATATTTTTCATCAA
1 AATTTAAAATTTATCATCAA
20254 AATTT
1 AATTT
20259 GTGAATTAAG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTAAAATTTATCATCAA
Found at i:20443 original size:29 final size:28
Alignment explanation
Indices: 20397--20452 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
20387 TTCAATTAAA
*
20397 AAATAATAAAACTTAATTTAAAAATTTAG
1 AAATAATAAAACTAAATTT-AAAATTTAG
*
20426 AAAT-ATAAAACCTAAATTTTAAATTTA
1 AAATAATAAAA-CTAAATTTAAAATTTA
20453 TTAAAACACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (28 bp):
AAATAATAAAACTAAATTTAAAATTTAG
Found at i:20851 original size:22 final size:22
Alignment explanation
Indices: 20808--20851 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20798 ATTTACAAAT
* *
20808 TTTAAAAATTCTTTAAATTTTA
1 TTTAAAAATTCATAAAATTTTA
20830 TTTAAAAA-TCATAAAATCTTTA
1 TTTAAAAATTCATAAAAT-TTTA
20852 AACAATAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAAAAATTCATAAAATTTTA
Found at i:20961 original size:39 final size:39
Alignment explanation
Indices: 20898--20972 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
20888 TTATAGACAT
* *
20898 TATAAAAAATACAAATTATTATAAAATTATTAAAAATTC
1 TATAAAAAATACAAATAATTATAAAATTATAAAAAATTC
*
20937 TATATAAAGATACAAA-AATTATAAAATTATAAAAAA
1 TATA-AAAAATACAAATAATTATAAAATTATAAAAAA
20973 CACTTACAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 22 0.69
40 10 0.31
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (39 bp):
TATAAAAAATACAAATAATTATAAAATTATAAAAAATTC
Found at i:21159 original size:18 final size:16
Alignment explanation
Indices: 21138--21172 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
21128 ATACATTTTA
21138 TAATTGTTTTAAAAGTTT
1 TAATT-TTTTAAAA-TTT
21156 TAATTTTTTAAAATTT
1 TAATTTTTTAAAATTT
21172 T
1 T
21173 TTAAAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 8 0.47
18 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
TAATTTTTTAAAATTT
Found at i:21165 original size:28 final size:29
Alignment explanation
Indices: 21133--21193 Score: 90
Period size: 28 Copynumber: 2.1 Consensus size: 29
21123 TTTAAATACA
*
21133 TTTTATAATTGTTTTAAAAG-TTTTAATT-
1 TTTTAAAATT-TTTTAAAAGTTTTTAATTG
21161 TTTTAAAATTTTTTAAAAGTTTTTAATTG
1 TTTTAAAATTTTTTAAAAGTTTTTAATTG
21190 TTTT
1 TTTT
21194 TGTTAGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 9 0.30
28 17 0.57
29 4 0.13
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (29 bp):
TTTTAAAATTTTTTAAAAGTTTTTAATTG
Found at i:21174 original size:18 final size:19
Alignment explanation
Indices: 21132--21176 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
21122 ATTTAAATAC
*
21132 ATTTTATAATTGTTTTAAA
1 ATTTTTTAATTGTTTTAAA
*
21151 A-GTTTTAATT-TTTTAAA
1 ATTTTTTAATTGTTTTAAA
21168 ATTTTTTAA
1 ATTTTTTAA
21177 AAGTTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 8 0.36
18 13 0.59
19 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (19 bp):
ATTTTTTAATTGTTTTAAA
Found at i:21183 original size:11 final size:10
Alignment explanation
Indices: 21157--21186 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
21147 TAAAAGTTTT
21157 AATTTTTTAA
1 AATTTTTTAA
21167 AATTTTTTAA
1 AATTTTTTAA
*
21177 AAGTTTTTAA
1 AATTTTTTAA
21187 TTGTTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:21971 original size:3 final size:3
Alignment explanation
Indices: 21963--21991 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
21953 TTTGAAATCG
21963 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
21992 AATTCAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:22294 original size:9 final size:9
Alignment explanation
Indices: 22282--22350 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
22272 GTATTTAATT
22282 AATTTTAAA
1 AATTTTAAA
22291 AATTTTAAAA
1 AATTTT-AAA
*
22301 ATATTTTTATA
1 A-A-TTTTAAA
* *
22312 ATTTTTAAT
1 AATTTTAAA
22321 AATTTTAATA
1 AATTTTAA-A
22331 AATTTT-AA
1 AATTTTAAA
*
22339 AATTGTAAA
1 AATTTTAAA
22348 AAT
1 AAT
22351 AGTTTTTATA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
8 6 0.12
9 24 0.50
10 10 0.21
11 4 0.08
12 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (9 bp):
AATTTTAAA
Found at i:22301 original size:10 final size:10
Alignment explanation
Indices: 22282--22340 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
22272 GTATTTAATT
22282 AATTTT-AAA
1 AATTTTAAAA
22291 AATTTTAAAA
1 AATTTTAAAA
* *
22301 ATATTTT-TAT
1 A-ATTTTAAAA
* *
22311 AATTTTTAAT
1 AATTTTAAAA
*
22321 AATTTTAATA
1 AATTTTAAAA
22331 AATTTTAAAA
1 AATTTTAAAA
22341 TTGTAAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
9 11 0.28
10 24 0.60
11 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
AATTTTAAAA
Found at i:22375 original size:48 final size:49
Alignment explanation
Indices: 22275--22386 Score: 146
Period size: 49 Copynumber: 2.4 Consensus size: 49
22265 CACATAAGTA
* *
22275 TTTAATTAATTTTAAAAATTTTAAAAATATTTTTATAATTTTTAATAAT
1 TTTAATAAATTTTAAAAATTGTAAAAATATTTTTATAATTTTTAATAAT
22324 TTTAATAAATTTT-AAAATTGTAAAAATAGTTTTTATATATTTTT-AT--T
1 TTTAATAAATTTTAAAAATTGTAAAAATA-TTTTTATA-ATTTTTAATAAT
22371 TTT--TAAATTTTAAAAA
1 TTTAATAAATTTTAAAAA
22387 ATTAATTAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
45 8 0.14
46 4 0.07
47 4 0.07
48 14 0.24
49 22 0.38
50 6 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (49 bp):
TTTAATAAATTTTAAAAATTGTAAAAATATTTTTATAATTTTTAATAAT
Found at i:24472 original size:4 final size:4
Alignment explanation
Indices: 24463--24493 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
24453 TAAATTTTAA
24463 AATT AATT AATTT AATT AATT AATT AATT AA
1 AATT AATT AA-TT AATT AATT AATT AATT AA
24494 ATTCAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:26192 original size:13 final size:13
Alignment explanation
Indices: 26174--26239 Score: 80
Period size: 13 Copynumber: 5.1 Consensus size: 13
26164 AGTTTGGCAA
26174 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
26187 TGCTTTTCAAAAG
1 TGCTTTTGAAAAG
*
26200 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
**
26213 TGCTTTTGGTAAG
1 TGCTTTTGAAAAG
26226 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
26239 T
1 T
26240 TTGGTTTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
12 2 0.05
13 38 0.88
14 3 0.07
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:26237 original size:26 final size:26
Alignment explanation
Indices: 26166--26239 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
26156 TAAGGGCTAG
*
26166 TTTGGCAA-TGCTTTTGAAAAGTGCT
1 TTTGGAAAGTGCTTTTGAAAAGTGCT
** *
26191 TTTCAAAAGTGC-TGTGAAAAAGTGCT
1 TTTGGAAAGTGCTTTTG-AAAAGTGCT
*
26217 TTTGGTAAGTGCTTTTGAAAAGT
1 TTTGGAAAGTGCTTTTGAAAAGT
26240 TTGGTTTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
25 8 0.21
26 27 0.71
27 3 0.08
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.38
Consensus pattern (26 bp):
TTTGGAAAGTGCTTTTGAAAAGTGCT
Found at i:30447 original size:56 final size:56
Alignment explanation
Indices: 30350--30458 Score: 148
Period size: 56 Copynumber: 1.9 Consensus size: 56
30340 GACCATAAAT
* * *
30350 CGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACTC
1 CGATATATGTGTGCGAGTAAGACCACGTCTGAGACGTTGGCATCGATATGTGACTC
** *
30406 CGATATATGTGTGCGAGTAAGACCTTGTCTGGGACAG-TGGCATCGATATGTGA
1 CGATATATGTGTGCGAGTAAGACCACGTCTGAGAC-GTTGGCATCGATATGTGA
30459 TTACATGTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
56 45 0.98
57 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (56 bp):
CGATATATGTGTGCGAGTAAGACCACGTCTGAGACGTTGGCATCGATATGTGACTC
Found at i:36483 original size:18 final size:18
Alignment explanation
Indices: 36460--36538 Score: 131
Period size: 18 Copynumber: 4.4 Consensus size: 18
36450 TGAAAACCCG
*
36460 CAAAGGGTACTTTGAGAC
1 CAAAGGGCACTTTGAGAC
*
36478 CAAAGGGCACTTTGGGAC
1 CAAAGGGCACTTTGAGAC
*
36496 CAAAGGGCGCTTTGAGAC
1 CAAAGGGCACTTTGAGAC
36514 CAAAGGGCACTTTGAGAC
1 CAAAGGGCACTTTGAGAC
36532 CAAAGGG
1 CAAAGGG
36539 GTTTTGAATT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 56 1.00
ACGTcount: A:0.32, C:0.20, G:0.32, T:0.16
Consensus pattern (18 bp):
CAAAGGGCACTTTGAGAC
Found at i:37387 original size:46 final size:46
Alignment explanation
Indices: 37311--37543 Score: 286
Period size: 46 Copynumber: 5.1 Consensus size: 46
37301 CAAATCAATT
** * * *
37311 GATTAAAGAAGCCACAAATCCTATATCCCTGAGTTGTAGTAGGATG
1 GATTAAAGAAGATACAAATCCTATACCCCTGAGTTGCAGTGGGATG
* * * * *
37357 GATTGAAGAAGATACAAATCCCATACCCCTGAATTACAGTGGGATA
1 GATTAAAGAAGATACAAATCCTATACCCCTGAGTTGCAGTGGGATG
* * * *
37403 GATTAAAGATGATACAAATCCCATACCCCTGATTTGCAATGGGATG
1 GATTAAAGAAGATACAAATCCTATACCCCTGAGTTGCAGTGGGATG
* * *
37449 GATTAAAGAAGATACAAATCCTATTCCCCTGAGCTGTAGTGGGATG
1 GATTAAAGAAGATACAAATCCTATACCCCTGAGTTGCAGTGGGATG
* * *
37495 GATTGAAGATGGTACAAATCCTATACCCCTGAGTTGCAGTGGGATG
1 GATTAAAGAAGATACAAATCCTATACCCCTGAGTTGCAGTGGGATG
37541 GAT
1 GAT
37544 GAAAAAAACC
Statistics
Matches: 158, Mismatches: 29, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 158 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (46 bp):
GATTAAAGAAGATACAAATCCTATACCCCTGAGTTGCAGTGGGATG
Found at i:37572 original size:138 final size:138
Alignment explanation
Indices: 37311--37559 Score: 340
Period size: 138 Copynumber: 1.8 Consensus size: 138
37301 CAAATCAATT
* *
37311 GATTAAAGAAGCCACAAATCCTATATCCCTGAGTTGTAGTAGGATGGATTGAAGAAGATACAAAT
1 GATTAAAGAAGACACAAATCCTATATCCCTGAGCTGTAGTAGGATGGATTGAAGAAGATACAAAT
* ** *
37376 CCCATACCCCTGAATTACAGTGGGATAGATTAAAGATGATACAAATCCCATACCCCTGATTTGCA
66 CCCATACCCCTGAATTACAGTGGGATAGATGAAAGAAAACACAAATCCCATACCCCTGATTTGCA
37441 ATGGGATG
131 ATGGGATG
* * * *
37449 GATTAAAGAAGATACAAATCCTAT-TCCCCTGAGCTGTAGTGGGATGGATTGAAGATGGTACAAA
1 GATTAAAGAAGACACAAATCCTATAT-CCCTGAGCTGTAGTAGGATGGATTGAAGAAGATACAAA
* * * *
37513 TCCTATACCCCTGAGTTGCAGTGGGATGGATGAAA-AAAACCACAAAT
65 TCCCATACCCCTGAATTACAGTGGGATAGATGAAAGAAAA-CACAAAT
37560 TTTATCACCC
Statistics
Matches: 95, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
137 3 0.03
138 92 0.97
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (138 bp):
GATTAAAGAAGACACAAATCCTATATCCCTGAGCTGTAGTAGGATGGATTGAAGAAGATACAAAT
CCCATACCCCTGAATTACAGTGGGATAGATGAAAGAAAACACAAATCCCATACCCCTGATTTGCA
ATGGGATG
Found at i:38379 original size:44 final size:45
Alignment explanation
Indices: 38310--38430 Score: 138
Period size: 44 Copynumber: 2.7 Consensus size: 45
38300 AAAATGGGGG
* *
38310 ATCTTATCTTCCTAAAGTTACAGTGGAGCAGA-TCGAAGCCA-CTA
1 ATCTTATCTCCCTAAAGTTACAGTGGAGCAGACT-GAAGACAGCTA
* * **
38354 GTCTTATCTCCCAAAAGTTGTAGTGGAGCAGACTGAAGACAGCTA
1 ATCTTATCTCCCTAAAGTTACAGTGGAGCAGACTGAAGACAGCTA
* * *
38399 ATCTTATTTCCCTAAAGTTACAGCGGAACAGA
1 ATCTTATCTCCCTAAAGTTACAGTGGAGCAGA
38431 TTTAAGCTAC
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
44 33 0.53
45 29 0.47
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (45 bp):
ATCTTATCTCCCTAAAGTTACAGTGGAGCAGACTGAAGACAGCTA
Found at i:38593 original size:44 final size:44
Alignment explanation
Indices: 38519--38686 Score: 187
Period size: 44 Copynumber: 3.8 Consensus size: 44
38509 AAGTTCCAGC
*
38519 GGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATT
1 GGAGTAGATCGAAGCCACAAATCTCTTCTCCCTGAAATTACATT
** * * * *
38563 GGAACAGATCGAAGCCAC-AATC-CTTATCTCCTTAAAGTTCCAGT
1 GGAGTAGATCGAAGCCACAAATCTCTTCTC-CCTGAAA-TTACATT
* *
38607 AGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATT
1 GGAGTAGATCGAAGCCACAAATCTCTTCTCCCTGAAATTACATT
* * * *
38651 GGAGTAAATCAAAGCCACAAGTCTCATCTCCCTGAA
1 GGAGTAGATCGAAGCCACAAATCTCTTCTCCCTGAA
38687 GTTGCAATGG
Statistics
Matches: 99, Mismatches: 21, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
42 5 0.05
43 10 0.10
44 69 0.70
45 10 0.10
46 5 0.05
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.26
Consensus pattern (44 bp):
GGAGTAGATCGAAGCCACAAATCTCTTCTCCCTGAAATTACATT
Found at i:38689 original size:88 final size:88
Alignment explanation
Indices: 38502--38689 Score: 279
Period size: 88 Copynumber: 2.1 Consensus size: 88
38492 CAATTCTTAC
*
38502 CTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTGGAA
1 CTCCTTGAAGTTCCAGCAGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTGGAA
* * *
38567 CAGATCGAAGCCACAATCCTTAT
66 CAAATCAAAGCCACAATCCTCAT
* * *
38590 CTCCTTAAAGTTCCAGTAGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTGGAG
1 CTCCTTGAAGTTCCAGCAGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTGGAA
*
38655 TAAATCAAAGCCACAAGT-CTCAT
66 CAAATCAAAGCCACAA-TCCTCAT
*
38678 CTCCCTGAAGTT
1 CTCCTTGAAGTT
38690 GCAATGGATT
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 88 0.99
89 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (88 bp):
CTCCTTGAAGTTCCAGCAGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTGGAA
CAAATCAAAGCCACAATCCTCAT
Found at i:38712 original size:88 final size:88
Alignment explanation
Indices: 38520--38712 Score: 253
Period size: 88 Copynumber: 2.2 Consensus size: 88
38510 AGTTCCAGCG
* *
38520 GAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTGGAACAGATCGAAGCCACAATC
1 GAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTGGAACAAATCAAAGCCACAATC
* * *
38585 CTTATCTCCTTAAAGTTCCAGTA
66 CTCATCTCCCTAAAGTTCCAATA
**
38608 GAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTGGAGTAAATCAAAGCCACAAGT
1 GAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTGGAACAAATCAAAGCCACAA-T
* * *
38673 -CTCATCTCCCTGAAGTTGCAATG
65 CCTCATCTCCCTAAAGTTCCAATA
* * *
38696 GATTAGAACGAGGCTAC
1 GAGTAGATCGAAGCTAC
38713 TTGAAGAAGA
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
88 90 0.99
89 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (88 bp):
GAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTGGAACAAATCAAAGCCACAATC
CTCATCTCCCTAAAGTTCCAATA
Done.