Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1056
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: 43567
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1050 original size:75 final size:74
Alignment explanation
Indices: 932--1129 Score: 200
Period size: 75 Copynumber: 2.6 Consensus size: 74
922 TAGGAGTCAT
* * *
932 GTAGAACTTTCATGTCACACATATACTTTAA-AGCATTTTAGTCATTTCACTTTAAACTGGAGTC
1 GTAGAACTTTCATGT--CACATATAC-TTAAGGGCATTTTAGTCATTTCACCTTAAAATGGAGTC
996 TTGTAGGGTCACC
63 TTGTAGGGTC-CC
* * * * ** * *
1009 TTAGAACTTTCACGTCACATGTACTTAAGGGCATTTTAGTCATTTTACCTTAAAATTTAGTTTTT
1 GTAGAACTTTCATGTCACATATACTTAAGGGCATTTTAGTCATTTCACCTTAAAATGGAGTCTTG
*
1074 TAGGGTCGC
66 TAGGGTCCC
* * *
1083 GTATGAACTTTCATTTCACATATACCTTAAGGGAATGTTAGTCATTT
1 GTA-GAACTTTCATGTCACATATA-CTTAAGGGCATTTTAGTCATTT
1130 TCGAGTCTCT
Statistics
Matches: 100, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
74 7 0.07
75 60 0.60
76 20 0.20
77 13 0.13
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (74 bp):
GTAGAACTTTCATGTCACATATACTTAAGGGCATTTTAGTCATTTCACCTTAAAATGGAGTCTTG
TAGGGTCCC
Found at i:1597 original size:19 final size:19
Alignment explanation
Indices: 1573--1625 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
1563 ATCAATACAA
*
1573 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTAAT
* *
1592 TGTATCGATATATACTTAAT
1 TGTATCGATACAT-GTTAAT
1612 TGTATCGATACATG
1 TGTATCGATACATG
1626 AAAGTGGCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATGTTAAT
Found at i:3417 original size:165 final size:160
Alignment explanation
Indices: 3232--3741 Score: 532
Period size: 165 Copynumber: 3.1 Consensus size: 160
3222 TTTGAACATC
* * *
3232 AAAATTCTTTAAATATCATCATTTAATTACCATTAAACTAGTTTTAAAAAATTCCTTTTA-TTTC
1 AAAATTCATCAAATATCATCATTTAATTA-CATTAAATTAGTTTT-AAAAATT--TTTTATTTTC
* * * *
3296 ATGAA-TTTTTCGTTTTTCCTTAAAATTATCCTGTTTTTGAAATACGGAGTTTGCTACTCCGTAA
62 AT-AAGTTTTTCTTTTTTCTTTGAAATT-TCCTGTTTTCGAAATACGGAGTTTGCTACTCCGTAA
*
3360 ATGTTTTCGAGGGGATTTTTCTTATTTTATAAATTTT
125 ATGTTTTC-AGGGGATTTTTCTTAGTTTATAAATTTT
* * *
3397 AAAATTCATCAAATATCATCATTTAATTTATAGTGAATTAGTTTTGAAAAATTTATTTATTTTCA
1 AAAATTCATCAAATATCATCATTTAA-TTACATTAAATTAGTTTT-AAAAATTT-TTTATTTTCA
** * * *
3462 TAAGTTTTTCCTTTTTTCTTTGAAATCCCCCTATTTCCGAAATACGGAGTTTGCTACTTCGTAAA
63 TAAGTTTTT-CTTTTTTCTTTGAAAT-TTCCTGTTTTCGAAATACGGAGTTTGCTACTCCGTAAA
*
3527 TGTTTTCAGGGGGATTTTT-TT-GTTTATAATTTTT
126 TGTTTTCA-GGGGATTTTTCTTAGTTTATAAATTTT
*
3561 AAAATTCATCAAATA--ATCATTTAATT-CATAGTAAATTAGTTTTGAAAATTTAATTTATTTTC
1 AAAATTCATCAAATATCATCATTTAATTACAT--TAAATTAGTTTTAAAAATTT--TTTATTTTC
** *
3623 ATAAGTTTTTCATTTTTTTCTTTGAAATTTCCTTGTTTTCGAAATATTGAGTTTTCTACTCCGTA
62 ATAAGTTTTTC--TTTTTTCTTTGAAATTTCC-TGTTTTCGAAATACGGAGTTTGCTACTCCGTA
* * *
3688 AATATTTTTAGAGGGATTTTTCTCAGTTTA-AAATTTTT
124 AATGTTTTCAG-GGGATTTTTCTTAGTTTATAAA-TTTT
* *
3726 AAAATCCATCTAATAT
1 AAAATTCATCAAATAT
3742 TCTCATTAGA
Statistics
Matches: 291, Mismatches: 36, Indels: 35
0.80 0.10 0.10
Matches are distributed among these distances:
160 1 0.00
161 10 0.03
162 43 0.15
163 59 0.20
164 35 0.12
165 78 0.27
166 65 0.22
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (160 bp):
AAAATTCATCAAATATCATCATTTAATTACATTAAATTAGTTTTAAAAATTTTTTATTTTCATAA
GTTTTTCTTTTTTCTTTGAAATTTCCTGTTTTCGAAATACGGAGTTTGCTACTCCGTAAATGTTT
TCAGGGGATTTTTCTTAGTTTATAAATTTT
Found at i:4331 original size:22 final size:21
Alignment explanation
Indices: 4292--4336 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4282 TAGCAAGTAG
*
4292 AAGAAAAGAGAAAAAAAAAAGA
1 AAGAAAAAAG-AAAAAAAAAGA
* *
4314 AAGAAAAAAGAGAGAAAAAGA
1 AAGAAAAAAGAAAAAAAAAGA
4335 AA
1 AA
4337 AATTAAGCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAGAAAAAAGAAAAAAAAAGA
Found at i:4333 original size:10 final size:11
Alignment explanation
Indices: 4292--4336 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
4282 TAGCAAGTAG
*
4292 AAGAAAAGAGA
1 AAGAAAAAAGA
*
4303 AAAAAAAAAGA
1 AAGAAAAAAGA
4314 AAGAAAAAAGA
1 AAGAAAAAAGA
*
4325 GAG-AAAAAGA
1 AAGAAAAAAGA
4335 AA
1 AA
4337 AATTAAGCCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAGA
Found at i:4337 original size:15 final size:13
Alignment explanation
Indices: 4295--4338 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
4285 CAAGTAGAAG
4295 AAAAGAGAAAAAA
1 AAAAGAGAAAAAA
4308 AAAAGA-AAGAAAA
1 AAAAGAGAA-AAAA
*
4321 AAGAGAGAAAAAGA
1 AAAAGAGAAAAA-A
4335 AAAA
1 AAAA
4339 TTAAGCCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 2 0.08
13 18 0.69
14 6 0.23
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAAAAA
Found at i:4406 original size:12 final size:12
Alignment explanation
Indices: 4389--4425 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
4379 TCTTCTTATT
4389 TTGCTTTCTTTC
1 TTGCTTTCTTTC
4401 TTGCTTTCTTTC
1 TTGCTTTCTTTC
*
4413 TTG-TTTATTTC
1 TTGCTTTCTTTC
4424 TT
1 TT
4426 CATGATGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.03, C:0.19, G:0.08, T:0.70
Consensus pattern (12 bp):
TTGCTTTCTTTC
Found at i:11866 original size:13 final size:13
Alignment explanation
Indices: 11848--11873 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11838 ACACCAAAGT
11848 ATGTATCGATACA
1 ATGTATCGATACA
11861 ATGTATCGATACA
1 ATGTATCGATACA
11874 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:11871 original size:33 final size:33
Alignment explanation
Indices: 11829--11893 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
11819 TAGCCAAACT
* *
11829 TGTATCGATACAC-CAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
11862 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
11894 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:22889 original size:52 final size:51
Alignment explanation
Indices: 22811--22927 Score: 198
Period size: 52 Copynumber: 2.3 Consensus size: 51
22801 AAGTTGCTTG
*
22811 CATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTA
1 CATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA-TTGCCTA
* *
22863 CATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTGCCTG
1 CATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTGCCTA
22914 CATGTATCGATACA
1 CATGTATCGATACA
22928 AAGATCAGTG
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
51 20 0.32
52 42 0.68
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (51 bp):
CATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTGCCTA
Found at i:22954 original size:13 final size:13
Alignment explanation
Indices: 22936--22960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22926 CAAAGATCAG
22936 TGTATCGATACAA
1 TGTATCGATACAA
22949 TGTATCGATACA
1 TGTATCGATACA
22961 TTTGAGTAAC
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:23038 original size:33 final size:33
Alignment explanation
Indices: 23001--23067 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
22991 AGTAGCTTAA
23001 ATTGTATCGATACAAAAAATTATGTATCGATAC
1 ATTGTATCGATACAAAAAATTATGTATCGATAC
* **
23034 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAATTATGTATCGATAC
23067 A
1 A
23068 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAATTATGTATCGATAC
Found at i:23041 original size:13 final size:13
Alignment explanation
Indices: 23023--23047 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23013 CAAAAAATTA
23023 TGTATCGATACAT
1 TGTATCGATACAT
23036 TGTATCGATACA
1 TGTATCGATACA
23048 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:25314 original size:28 final size:28
Alignment explanation
Indices: 25273--25341 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
25263 ATAAAGCCAG
** *
25273 GGTTGGAGTATCCCCTCGGAAGTAACG-
1 GGTTGGAGTATCCCCGAGGAAATAACGA
*
25300 GAGTTGGAGTATCCCCGATGAAATAACGA
1 G-GTTGGAGTATCCCCGAGGAAATAACGA
25329 GGTTGGAGTATCC
1 GGTTGGAGTATCC
25342 TCGATTGTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 1 0.03
28 34 0.94
29 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGAGGAAATAACGA
Found at i:25402 original size:55 final size:51
Alignment explanation
Indices: 25334--25461 Score: 132
Period size: 51 Copynumber: 2.4 Consensus size: 51
25324 AACGAGGTTG
* * *
25334 GAGTATCCTCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCACGATTGTG-AGAAATTAGTG---TTTTGAAAATAAAATCGGAGTTA
* * *
25389 GAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCACGATTGTGAG-AAATTAGTGTTTTGAAAATAAAATCGGAGTTA
*
25440 GAATATCCACGATTGTGGAGAA
1 GAGTATCCACGATTGT-GAGAA
25462 TTGAGAAACT
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
51 34 0.55
52 2 0.03
53 4 0.06
54 8 0.13
55 14 0.23
ACGTcount: A:0.34, C:0.09, G:0.24, T:0.32
Consensus pattern (51 bp):
GAGTATCCACGATTGTGAGAAATTAGTGTTTTGAAAATAAAATCGGAGTTA
Found at i:27840 original size:13 final size:13
Alignment explanation
Indices: 27822--27847 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27812 ACAAAGATCC
27822 ATGTATCGATACA
1 ATGTATCGATACA
27835 ATGTATCGATACA
1 ATGTATCGATACA
27848 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:27843 original size:33 final size:33
Alignment explanation
Indices: 27801--27867 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
27791 AAAATTTCCA
***
27801 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
27834 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
27867 A
1 A
27868 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:27911 original size:19 final size:18
Alignment explanation
Indices: 27887--27954 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
27877 CAGTAGCTAA
27887 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
27906 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
*
27921 -T-TGTATTGATACAAAAC
1 TTATGTATCGATAC-AAAC
27938 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
27955 TTGCTGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 10 0.24
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.59
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:27932 original size:32 final size:32
Alignment explanation
Indices: 27890--27952 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
27880 TAGCTAATTA
*
27890 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
*
27922 TGTATTGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
27953 AATTGCTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:28458 original size:20 final size:21
Alignment explanation
Indices: 28424--28462 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
28414 CTATATTTTC
28424 AAATATGTATCGATACATTAA
1 AAATATGTATCGATACATTAA
*
28445 AAAT-TGTATTGATACATT
1 AAATATGTATCGATACATT
28463 TACACGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (21 bp):
AAATATGTATCGATACATTAA
Found at i:28620 original size:59 final size:59
Alignment explanation
Indices: 28528--28822 Score: 456
Period size: 59 Copynumber: 5.1 Consensus size: 59
28518 CACTTGTAGA
28528 CACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGG
1 CACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGG
28587 CACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGG
1 CACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGG
* * * *
28646 CACTTTCAGTCCTCAAAGAGCGGGACACCTTTTCTTTTAAAGCCCACCCGAGTTGGTGG
1 CACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGG
* * *
28705 CACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGG
* *
28765 CACCTTTCAGTCCTCAAAGAGCAGGACGCC-TTTC----AAAGCCCACACGAGTTGGTGG
1 CACC-TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGG
28820 CAC
1 CAC
28823 TTTTTACTCC
Statistics
Matches: 220, Mismatches: 14, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
55 23 0.10
59 147 0.67
60 27 0.12
61 23 0.10
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (59 bp):
CACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:29460 original size:13 final size:13
Alignment explanation
Indices: 29442--29466 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29432 AGAGCGTTTG
29442 AAAAAAAAATTAA
1 AAAAAAAAATTAA
29455 AAAAAAAAATTA
1 AAAAAAAAATTA
29467 TCCAAATGTA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTAA
Found at i:29497 original size:21 final size:21
Alignment explanation
Indices: 29471--29569 Score: 189
Period size: 21 Copynumber: 4.7 Consensus size: 21
29461 AAATTATCCA
29471 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTGG
*
29492 AATGTATCGATACATTTATGG
1 AATGTATCGATACATTTGTGG
29513 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTGG
29534 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTGG
29555 AATGTATCGATACAT
1 AATGTATCGATACAT
29570 CCTACAAATG
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTGG
Found at i:29580 original size:42 final size:42
Alignment explanation
Indices: 29471--29589 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
29461 AAATTATCCA
* ***
29471 AATGTATCGATACATTTGTGGAATGTATCGATACATTTATGG
1 AATGTATCGATACATCTGACAAATGTATCGATACATTTATGG
* *** *
29513 AATGTATCGATACATTTGTGGAATGTATCGATACATTTGTGG
1 AATGTATCGATACATCTGACAAATGTATCGATACATTTATGG
29555 AATGTATCGATACATCCT-ACAAATGTATCGATACA
1 AATGTATCGATACAT-CTGACAAATGTATCGATACA
29590 GGGTCCCAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
42 70 0.99
43 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (42 bp):
AATGTATCGATACATCTGACAAATGTATCGATACATTTATGG
Found at i:29580 original size:63 final size:63
Alignment explanation
Indices: 29471--29589 Score: 195
Period size: 63 Copynumber: 1.9 Consensus size: 63
29461 AAATTATCCA
* **
29471 AATGTATCGATACATTTGTGGAATGTATCGATACATTTATGGAATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTGGAATGTATCGATACATCTATCAAATGTATCGATACATTTGTGG
29534 AATGTATCGATACATTTGTGGAATGTATCGATACATCCTA-CAAATGTATCGATACA
1 AATGTATCGATACATTTGTGGAATGTATCGATACAT-CTATCAAATGTATCGATACA
29590 GGGTCCCAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
63 50 0.96
64 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (63 bp):
AATGTATCGATACATTTGTGGAATGTATCGATACATCTATCAAATGTATCGATACATTTGTGG
Found at i:29718 original size:13 final size:13
Alignment explanation
Indices: 29700--29725 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29690 CATTTTTCTG
29700 TGTATCGATACAT
1 TGTATCGATACAT
29713 TGTATCGATACAT
1 TGTATCGATACAT
29726 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:29722 original size:33 final size:33
Alignment explanation
Indices: 29680--29746 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
29670 GCCAAGGAAA
***
29680 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
29713 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
29746 T
1 T
29747 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:32182 original size:28 final size:28
Alignment explanation
Indices: 32146--32222 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
32136 TTTTTTCACA
* *
32146 ATCGAGGATACTCCAACCTCGTTA-TCTC
1 ATCGGGGATACTCCAACCCCGTTACT-TC
32174 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
*
32202 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
32223 GCTTTATTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 1 0.02
28 42 0.95
29 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Done.