Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2114
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: 19704
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Found at i:174 original size:29 final size:29
Alignment explanation
Indices: 91--284 Score: 123
Period size: 29 Copynumber: 6.7 Consensus size: 29
81 AATGCTATTA
* * *
91 ACTTATGGGCTTT-AAAAGAG-TGCCGCTG
1 ACTTATGAGCTTTGAAAAGGGATG-CACTG
*
119 ACTTATG-GCTTTG-AAAGGAATGCCACTG
1 ACTTATGAGCTTTGAAAAGGGATG-CACTG
*
147 ATTTATGAGCTTTGAAAAGGGATGCACTG
1 ACTTATGAGCTTTGAAAAGGGATGCACTG
* *
176 ACTTGTGAGCTTTGAAAAGGGATGCCATTG
1 ACTTATGAGCTTTGAAAAGGGATG-CACTG
* * * * *
206 ACTTGT-AGGTTT-CAAAGGGGTGCCACTT
1 ACTTATGAGCTTTGAAAAGGGATG-CACTG
* * **
234 ACTTGTGTGCTTTGAAAAAAAGATGCCACTG
1 ACTTATGAGCTTTG-AAAAGGGATG-CACTG
* *
265 ACTTGTGGGCTTT-AAAAGGG
1 ACTTATGAGCTTTGAAAAGGG
285 TGCCACGGAG
Statistics
Matches: 135, Mismatches: 23, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
27 9 0.07
28 38 0.28
29 47 0.35
30 18 0.13
31 23 0.17
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (29 bp):
ACTTATGAGCTTTGAAAAGGGATGCACTG
Found at i:286 original size:59 final size:57
Alignment explanation
Indices: 1--290 Score: 236
Period size: 56 Copynumber: 5.1 Consensus size: 57
* * *
1 CCACTGACTTTGTGGACTTTG--AAAGGATGCCA-TGACTTGTGGGCTTTAAATGGATG
1 CCACTGAC-TTGTGG-CTTTGAAAAAAGATGCCACTGACTTGTGGGCTTTAAAAGGGTG
* * * * * * *
57 CTATTGACTTGTGGGCTTT-AAAAAA-ATGCTATTAACTTATGGGCTTTAAAAGAGTG
1 CCACTGACTTGT-GGCTTTGAAAAAAGATGCCACTGACTTGTGGGCTTTAAAAGGGTG
* * ** * * *
113 CCGCTGACTTATGGCTTTGAAAGGA-ATGCCACTGATTTATGAGCTTTGAAAAGGGATG
1 CCACTGACTTGTGGCTTTGAAAAAAGATGCCACTGACTTGTGGGCTTT-AAAAGGG-TG
** * * *
171 -CACTGACTTGTGAGCTTTGAAAAGGGATGCCATTGACTTGTAGG-TTTCAAAGGGGTG
1 CCACTGACTTGTG-GCTTTGAAAAAAGATGCCACTGACTTGTGGGCTTT-AAAAGGGTG
*
228 CCACTTACTTGTGTGCTTTGAAAAAAAGATGCCACTGACTTGTGGGCTTTAAAAGGGTG
1 CCACTGACTTGTG-GCTTTG-AAAAAAGATGCCACTGACTTGTGGGCTTTAAAAGGGTG
287 CCAC
1 CCAC
291 GGAGTTACGA
Statistics
Matches: 183, Mismatches: 39, Indels: 21
0.75 0.16 0.09
Matches are distributed among these distances:
55 19 0.10
56 59 0.32
57 18 0.10
58 38 0.21
59 46 0.25
60 3 0.02
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (57 bp):
CCACTGACTTGTGGCTTTGAAAAAAGATGCCACTGACTTGTGGGCTTTAAAAGGGTG
Found at i:290 original size:28 final size:28
Alignment explanation
Indices: 1--378 Score: 194
Period size: 28 Copynumber: 13.1 Consensus size: 28
* * *
1 CCACTGACTTTGTGGACTTTGAAAGGATG
1 CCACTGAC-TTGTGGGCTTTAAAAGGGTG
* *
30 CCA-TGACTTGTGGGCTTTAAATGGATG
1 CCACTGACTTGTGGGCTTTAAAAGGGTG
* * ***
57 CTATTGACTTGTGGGCTTTAAAAAAATG
1 CCACTGACTTGTGGGCTTTAAAAGGGTG
* * * * *
85 CTATTAACTTATGGGCTTTAAAAGAGTG
1 CCACTGACTTGTGGGCTTTAAAAGGGTG
* * * *
113 CCGCTGACTTAT-GGCTTTGAAAGGAATG
1 CCACTGACTTGTGGGCTTTAAAAGG-GTG
* * *
141 CCACTGATTTATGAGCTTTGAAAAGGGATG
1 CCACTGACTTGTGGGCTTT-AAAAGGG-TG
*
171 -CACTGACTTGTGAGCTTTGAAAAGGGATG
1 CCACTGACTTGTGGGCTTT-AAAAGGG-TG
* * *
200 CCATTGACTTGTAGG-TTTCAAAGGGGTG
1 CCACTGACTTGTGGGCTTT-AAAAGGGTG
* * * *
228 CCACTTACTTGTGTGCTTTGAAAAAAAGATG
1 CCACTGACTTGTGGGCTTT---AAAAGGGTG
259 CCACTGACTTGTGGGCTTTAAAAGGGTG
1 CCACTGACTTGTGGGCTTTAAAAGGGTG
* * ** **
287 CCACGGAGTTACGACCTTTAAAAACGGGTG
1 CCACTGACTTGTGGGCTTT-AAAA-GGGTG
* *
317 CCA-TGGAGTTGTGGACTTTAAAAGGGGTG
1 CCACT-GACTTGTGGGCTTTAAAA-GGGTG
* *
346 CCA-TGGAGTTGT-GGATTTAAAAAGAGGTG
1 CCACT-GACTTGTGGGCTTT-AAAAG-GGTG
375 CCAC
1 CCAC
379 GAAGTTGTAG
Statistics
Matches: 278, Mismatches: 56, Indels: 29
0.77 0.15 0.08
Matches are distributed among these distances:
27 29 0.10
28 107 0.38
29 83 0.30
30 36 0.13
31 23 0.08
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (28 bp):
CCACTGACTTGTGGGCTTTAAAAGGGTG
Found at i:349 original size:29 final size:29
Alignment explanation
Indices: 257--1140 Score: 657
Period size: 29 Copynumber: 29.9 Consensus size: 29
247 GAAAAAAAGA
* * *
257 TGCCACTGACTTGTGGGCTTT-AAAAGGG
1 TGCCACGGAGTTGTGGACTTTAAAAAGGG
**
285 TGCCACGGAGTT-ACGACCTTTAAAAACGGG
1 TGCCACGGAGTTGTGGA-CTTTAAAAA-GGG
* *
315 TGCCATGGAGTTGTGGACTTTAAAAGGGG
1 TGCCACGGAGTTGTGGACTTTAAAAAGGG
*
344 TGCCATGGAGTTGTGGA-TTTAAAAAGAGG
1 TGCCACGGAGTTGTGGACTTTAAAAAG-GG
* * *
373 TGCCACGAAGTTGTAGAC-TTAAAAAGGCA
1 TGCCACGGAGTTGTGGACTTTAAAAAGG-G
** * * *
402 TGCCATAGAGTTATGGAATTTAAAAAGGA
1 TGCCACGGAGTTGTGGACTTTAAAAAGGG
* *
431 TGCCACAGTGTTGTGGACTTTTAAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTTAAAAAGGG
* * *
461 TTCCACGGAGTTGTGGACTTTTGAAAAGGT
1 TGCCACGGAGTTGTGGAC-TTTAAAAAGGG
** * *
491 TGCCATAGAGTTATGGACTTTTGAAAA-GG
1 TGCCACGGAGTTGTGGAC-TTTAAAAAGGG
* *
520 TGCCACAGAGTTGTGGACTTAAAAAAGAGGG
1 TGCCACGGAGTTGTGGACTT-TAAAA-AGGG
* * *
551 TGCCACGTAGTTATGGACTTTAAAAAGGA
1 TGCCACGGAGTTGTGGACTTTAAAAAGGG
* * *
580 TGCCATGGAGTTGTGGGCTTTTAAAAAAGG
1 TGCCACGGAGTTGTGGAC-TTTAAAAAGGG
*
610 TGTCACGGAGTTGTGGACTTTTAAAAA-GG
1 TGCCACGGAGTTGTGGAC-TTTAAAAAGGG
* * * *
639 TACCATGAAGTTGTGGACTTAAAAAGAGGG
1 TGCCACGGAGTTGTGGACTTTAAAA-AGGG
* *
669 TGCCACAGAGTTGTGAACTTT-AAAAGGG
1 TGCCACGGAGTTGTGGACTTTAAAAAGGG
* *
697 GGCCACGGATTTGTGGAC-TTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTTAAAAAGGG
** *
725 -GTCCACAAAGTTGTCGACTTTTTAAAAAGGG
1 TG-CCACGGAGTTGTGGAC--TTTAAAAAGGG
*
756 TGCCACAGAGTTGTGGACTTTTAAAAA-GG
1 TGCCACGGAGTTGTGGAC-TTTAAAAAGGG
* * **
785 TGCCACAGAGTTATGGACATAAAAACAAAGGG
1 TGCCACGGAGTTGTGGAC-T-TTAA-AAAGGG
*
817 -GCCATGGAGTTGTGGACTTTAAAAA-GG
1 TGCCACGGAGTTGTGGACTTTAAAAAGGG
* * *
844 TACCACGAAGTTGTGGACTTTTAAAAATGG
1 TGCCACGGAGTTGTGGAC-TTTAAAAAGGG
*
874 TGCCACGGACTTGTGGACTTTTAAAAA-GG
1 TGCCACGGAGTTGTGGAC-TTTAAAAAGGG
* *
903 TGCCATGGAGTTGTGGACTTAAAAAAGAGGG
1 TGCCACGGAGTTGTGGACTT-TAAAA-AGGG
* ** * * *
934 TTCCACAAAGTTATAGACTTTAAAAGGGG
1 TGCCACGGAGTTGTGGACTTTAAAAAGGG
* *
963 TGTCACGGAGTTGTGGACTTTTTAAAAAAGG
1 TGCCACGGAGTTGTGGAC--TTTAAAAAGGG
* *
994 TGCCACGAAGTTATGGACTTTTGAAAAA--G
1 TGCCACGGAGTTGTGGAC-TTT-AAAAAGGG
* ** *
1023 TGTCACATAGTTGTGGACTTAAAAAAAAGGG
1 TGCCACGGAGTTGTGGACTT--TAAAAAGGG
* *
1054 TGCCATGGTGTTGTGGACTTT-AAAAGGG
1 TGCCACGGAGTTGTGGACTTTAAAAAGGG
* *
1082 TGCCACAGAGTTGTGGACTTTAAGAAAAAGGT
1 TGCCACGGAGTTGTGGACTTT---AAAAAGGG
* * * *
1114 TGCCACTGAGTCGTGGGCTTTGAAAAG
1 TGCCACGGAGTTGTGGACTTTAAAAAG
1141 TTACTTTACT
Statistics
Matches: 685, Mismatches: 130, Indels: 81
0.76 0.15 0.09
Matches are distributed among these distances:
27 6 0.01
28 114 0.17
29 224 0.33
30 191 0.28
31 123 0.18
32 27 0.04
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (29 bp):
TGCCACGGAGTTGTGGACTTTAAAAAGGG
Found at i:495 original size:60 final size:58
Alignment explanation
Indices: 250--1140 Score: 666
Period size: 60 Copynumber: 15.1 Consensus size: 58
240 GTGCTTTGAA
* * * * **
250 AAAAAGATGCCACTGACTTGTGGGC-TTT-AAAAGGGTGCCACGGAGTT-ACGACCTTT
1 AAAAAGGTGCCACAGAGTTGTGGACTTTTAAAAAGGGTGCCACGGAGTTGTGGA-CTTT
** * *
306 AAAAACGGGTGCCATGGAGTTGTGGAC-TTTAAAAGGGGTGCCATGGAGTTGTGGA-TTT
1 AAAAA--GGTGCCACAGAGTTGTGGACTTTTAAAAAGGGTGCCACGGAGTTGTGGACTTT
* * ** * *
364 AAAAAGAGGTGCCAC-GAAGTTGTAGAC--TTAAAAAGGCATGCCATAGAGTTATGGAATTT
1 -AAAA-AGGTGCCACAG-AGTTGTGGACTTTTAAAAAGG-GTGCCACGGAGTTGTGGACTTT
* *
423 AAAAAGGATGCCACAGTGTTGTGGACTTTTAAAAAGGGTTCCACGGAGTTGTGGACTTTT
1 AAAAAGG-TGCCACAGAGTTGTGGACTTTTAAAAAGGGTGCCACGGAGTTGTGGAC-TTT
* * * * * *
483 GAAAAGGTTGCCATAGAGTTATGGACTTTTGAAAA-GGTGCCACAGAGTTGTGGACTTAA
1 AAAAAGG-TGCCACAGAGTTGTGGACTTTTAAAAAGGGTGCCACGGAGTTGTGGACTT-T
* * * *
542 AAAAGAGGGTGCCAC-GTAGTTATGGAC-TTTAAAAAGGATGCCATGGAGTTGTGGGCTTTT
1 AAAA-A-GGTGCCACAG-AGTTGTGGACTTTTAAAAAGGGTGCCACGGAGTTGTGGAC-TTT
* * * * * *
602 AAAAAAGGTGTCACGGAGTTGTGGACTTTTAAAAA-GGTACCATGAAGTTGTGGACTTA
1 -AAAAAGGTGCCACAGAGTTGTGGACTTTTAAAAAGGGTGCCACGGAGTTGTGGACTTT
* * *
660 AAAAGAGGGTGCCACAGAGTTGTGAAC-TTT-AAAAGGGGGCCACGGATTTGTGGAC-TT
1 AAAA-A-GGTGCCACAGAGTTGTGGACTTTTAAAAAGGGTGCCACGGAGTTGTGGACTTT
* * * *
717 AAAAAGGGGTCCACAAAGTTGTCGACTTTTTAAAAAGGGTGCCACAGAGTTGTGGACTTTT
1 AAAAAGGTG-CCACAGAGTTGTGGAC-TTTTAAAAAGGGTGCCACGGAGTTGTGGAC-TTT
* *** *
778 AAAAAGGTGCCACAGAGTTATGGACATAAAAACAAAGGG-GCCATGGAGTTGTGGACTTT
1 AAAAAGGTGCCACAGAGTTGTGGAC-TTTTAA-AAAGGGTGCCACGGAGTTGTGGACTTT
* * *
837 AAAAAGGTACCAC-GAAGTTGTGGACTTTTAAAAATGGTGCCACGGACTTGTGGACTTTT
1 AAAAAGGTGCCACAG-AGTTGTGGACTTTTAAAAAGGGTGCCACGGAGTTGTGGAC-TTT
** ** * ** * *
896 AAAAAGGTGCCATGGAGTTGTGGACTTAAAAAAGAGGGTTCCACAAAGTTATAGACTTT
1 AAAAAGGTGCCACAGAGTTGTGGACTTTTAAAA-AGGGTGCCACGGAGTTGTGGACTTT
* * * * * *
955 AAAAGGGGTGTCACGGAGTTGTGGACTTTTTAAAAAAGGTGCCACGAAGTTATGGACTTTT
1 AAAA-AGGTGCCACAGAGTTGTGGAC-TTTTAAAAAGGGTGCCACGGAGTTGTGGAC-TTT
* * ** * *
1016 GAAAAA-GTGTCACATAGTTGTGGACTTAAAAAAAAGGGTGCCATGGTGTTGTGGACTTT
1 -AAAAAGGTGCCACAGAGTTGTGGACTT-TTAAAAAGGGTGCCACGGAGTTGTGGACTTT
* * * * * *
1075 AAAAGGGTGCCACAGAGTTGTGGACTTTAAGAAAAAGGTTGCCACTGAGTCGTGGGCTTT
1 AAAAAGGTGCCACAGAGTTGTGGACTTT--TAAAAAGGGTGCCACGGAGTTGTGGACTTT
*
1135 GAAAAG
1 AAAAAG
1141 TTACTTTACT
Statistics
Matches: 665, Mismatches: 124, Indels: 88
0.76 0.14 0.10
Matches are distributed among these distances:
55 3 0.00
56 19 0.03
57 30 0.05
58 119 0.18
59 223 0.34
60 234 0.35
61 33 0.05
62 4 0.01
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (58 bp):
AAAAAGGTGCCACAGAGTTGTGGACTTTTAAAAAGGGTGCCACGGAGTTGTGGACTTT
Found at i:578 original size:59 final size:58
Alignment explanation
Indices: 257--1140 Score: 639
Period size: 59 Copynumber: 15.0 Consensus size: 58
247 GAAAAAAAGA
* * * * **
257 TGCCACTGACTTGTGGGC-TTTAAAAGGGTGCCACGGAGTT-ACGACCTTTAAAAACGGG
1 TGCCACGGAGTTGTGGACTTTTAAAAAGGTGCCACGGAGTTGTGGA-CTTTAAAAA-GGG
* * *
315 TGCCATGGAGTTGTGGAC-TTTAAAAGGGGTGCCATGGAGTTGTGGA-TTTAAAAAGAGG
1 TGCCACGGAGTTGTGGACTTTTAAAA-AGGTGCCACGGAGTTGTGGACTTTAAAAAG-GG
* * ** * * *
373 TGCCACGAAGTTGTAGAC--TTAAAAAGGCATGCCATAGAGTTATGGAATTTAAAAAGGA
1 TGCCACGGAGTTGTGGACTTTTAAAAAGG--TGCCACGGAGTTGTGGACTTTAAAAAGGG
* * * * *
431 TGCCACAGTGTTGTGGACTTTTAAAAAGGGTTCCACGGAGTTGTGGACTTTTGAAAAGGT
1 TGCCACGGAGTTGTGGACTTTTAAAAA-GGTGCCACGGAGTTGTGGAC-TTTAAAAAGGG
** * * * *
491 TGCCATAGAGTTATGGACTTTTGAAAAGGTGCCACAGAGTTGTGGACTTAAAAAAGAGGG
1 TGCCACGGAGTTGTGGACTTTTAAAAAGGTGCCACGGAGTTGTGGACTT-TAAAA-AGGG
* * * * *
551 TGCCACGTAGTTATGGAC-TTTAAAAAGGATGCCATGGAGTTGTGGGCTTTTAAAAAAGG
1 TGCCACGGAGTTGTGGACTTTTAAAAAGG-TGCCACGGAGTTGTGGAC-TTTAAAAAGGG
* * * * *
610 TGTCACGGAGTTGTGGACTTTTAAAAAGGTACCATGAAGTTGTGGACTTAAAAAGAGGG
1 TGCCACGGAGTTGTGGACTTTTAAAAAGGTGCCACGGAGTTGTGGACTTTAAAA-AGGG
* * * * *
669 TGCCACAGAGTTGTGAAC-TTTAAAAGGGGGCCACGGATTTGTGGAC-TTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTTTAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAAGGG
** * *
725 -GTCCACAAAGTTGTCGACTTTTTAAAAAGGGTGCCACAGAGTTGTGGACTTTTAAAAA-GG
1 TG-CCACGGAGTTGTGGAC-TTTTAAAAA-GGTGCCACGGAGTTGTGGAC-TTTAAAAAGGG
* * *** * *
785 TGCCACAGAGTTATGGACATAAAAACAAAGGGGCCATGGAGTTGTGGACTTTAAAAA-GG
1 TGCCACGGAGTTGTGGAC-TTTTAA-AAAGGTGCCACGGAGTTGTGGACTTTAAAAAGGG
* * *
844 TACCACGAAGTTGTGGACTTTTAAAAATGGTGCCACGGACTTGTGGACTTTTAAAAA-GG
1 TGCCACGGAGTTGTGGACTTTTAAAAA-GGTGCCACGGAGTTGTGGAC-TTTAAAAAGGG
* ** * ** * * *
903 TGCCATGGAGTTGTGGACTTAAAAAAGAGGGTTCCACAAAGTTATAGACTTTAAAAGGGG
1 TGCCACGGAGTTGTGGACTTTTAAAA-A-GGTGCCACGGAGTTGTGGACTTTAAAAAGGG
* * *
963 TGTCACGGAGTTGTGGACTTTTTAAAAAAGGTGCCACGAAGTTATGGACTTTTGAAAAA--G
1 TGCCACGGAGTTGTGGAC-TTTT-AAAAAGGTGCCACGGAGTTGTGGAC-TTT-AAAAAGGG
* ** ** * *
1023 TGTCACATAGTTGTGGACTTAAAAAAAAGGGTGCCATGGTGTTGTGGACTTT-AAAAGGG
1 TGCCACGGAGTTGTGGACTT-TTAAAAA-GGTGCCACGGAGTTGTGGACTTTAAAAAGGG
* * * * * *
1082 TGCCACAGAGTTGTGGACTTTAAGAAAAAGGTTGCCACTGAGTCGTGGGCTTTGAAAAG
1 TGCCACGGAGTTGTGGACTTT--TAAAAAGG-TGCCACGGAGTTGTGGACTTTAAAAAG
1141 TTACTTTACT
Statistics
Matches: 660, Mismatches: 126, Indels: 77
0.76 0.15 0.09
Matches are distributed among these distances:
55 1 0.00
56 19 0.03
57 19 0.03
58 133 0.20
59 227 0.34
60 227 0.34
61 26 0.04
62 8 0.01
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (58 bp):
TGCCACGGAGTTGTGGACTTTTAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAAGGG
Found at i:3831 original size:19 final size:19
Alignment explanation
Indices: 3807--3874 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
3797 AATTCAACGA
3807 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3826 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3841 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
**
3858 AGTGTATCGATACATAA
1 TTTGTATCGATACATAA
3875 TTAGGTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3845 original size:32 final size:32
Alignment explanation
Indices: 3809--3871 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
3799 TTCAACGATT
**
3809 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTAGTGTATCGATACAA
3841 TGTATCGATACATAAGTAGTGTATCGATACA
1 TGTATCGATACATAAGTAGTGTATCGATACA
3872 TAATTAGGTA
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:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTAGTGTATCGATACAA
Found at i:3846 original size:13 final size:13
Alignment explanation
Indices: 3828--3852 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3818 ACATAAGTTT
3828 TGTATCGATACAA
1 TGTATCGATACAA
3841 TGTATCGATACA
1 TGTATCGATACA
3853 TAAGTAGTGT
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:3932 original size:13 final size:13
Alignment explanation
Indices: 3914--3939 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3904 CATTTTTCTG
3914 TGTATCGATACAT
1 TGTATCGATACAT
3927 TGTATCGATACAT
1 TGTATCGATACAT
3940 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:3936 original size:33 final size:33
Alignment explanation
Indices: 3894--3960 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3884 GCCAAGGAAA
***
3894 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
3927 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
3960 T
1 T
3961 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:3985 original size:31 final size:31
Alignment explanation
Indices: 3947--4023 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
3937 CATGGATCTT
3947 TGTATCGATACATTT-GGAAATTTTACCCAGA
1 TGTATCGATACATTTGGGAAATTTTA-CCAGA
*
3978 TGTATCGATACATTTGGGAAATTTTACCATA
1 TGTATCGATACATTTGGGAAATTTTACCAGA
4009 TGTATCGATACATTT
1 TGTATCGATACATTT
4024 TACAATGTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 34 0.77
32 10 0.23
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (31 bp):
TGTATCGATACATTTGGGAAATTTTACCAGA
Found at i:4033 original size:20 final size:22
Alignment explanation
Indices: 3998--4042 Score: 76
Period size: 20 Copynumber: 2.1 Consensus size: 22
3988 CATTTGGGAA
3998 ATTTTACCATATGTATCGATAC
1 ATTTTACCATATGTATCGATAC
4020 ATTTTA-CA-ATGTATCGATAC
1 ATTTTACCATATGTATCGATAC
4040 ATT
1 ATT
4043 CAGGCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 15 0.65
21 2 0.09
22 6 0.26
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (22 bp):
ATTTTACCATATGTATCGATAC
Found at i:6504 original size:28 final size:27
Alignment explanation
Indices: 6438--6505 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
6428 TTCACAATCA
*
6438 GGGATACTCCAACCCCGTTAATCATCG
1 GGGATACTCCAACCCCGTTAATCATAG
* **
6465 GGGATACTCCAACCCCGTTATTTTTGAG
1 GGGATACTCCAACCCCGTTAATCAT-AG
6493 GGGATACTCCAAC
1 GGGATACTCCAAC
6506 TCCGGTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (27 bp):
GGGATACTCCAACCCCGTTAATCATAG
Found at i:6649 original size:52 final size:51
Alignment explanation
Indices: 6492--6662 Score: 170
Period size: 52 Copynumber: 3.3 Consensus size: 51
6482 TTATTTTTGA
* * *
6492 GGGGATACTCCAACTCCGGTTTT-TATCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTATTTC-C-AAAACACCAAATTTT-CACAATC
* *
6545 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCC-AATTTTC-CTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATTTCCAAAACACCAAATTTTCAC---AATC
* *
6597 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAAATTTTCACAATC
1 GGGGATACTCCAACTCCGGTTTTATTTCC-AAAACACCAAATTTTCACAATC
*
6649 GAGGATACTCCAAC
1 GGGGATACTCCAAC
6663 CTCGTTATTT
Statistics
Matches: 99, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
49 1 0.01
50 1 0.01
51 5 0.05
52 53 0.54
53 29 0.29
54 9 0.09
55 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGGTTTTATTTCCAAAACACCAAATTTTCACAATC
Found at i:6682 original size:28 final size:28
Alignment explanation
Indices: 6646--6722 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
6636 AATTTTCACA
* * *
6646 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
6674 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
6702 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
6723 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:6695 original size:213 final size:212
Alignment explanation
Indices: 6324--6723 Score: 592
Period size: 213 Copynumber: 1.9 Consensus size: 212
6314 TTATCAATTC
* *
6324 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTCAAAACACTAATTTTCTATAATCGGGGAT
1 TCCACAATCGAGGATACTCCAACTCCGATTTTATTTCAAAACACCAATTTTCTATAATCGGGGAT
* *
6389 ACTCTAACTCCGATTTTATTTCCAAAAAGCACCAATTTCTTCACAATCAGGGATACTCCAACCCC
66 ACTCCAACTCCGATTTTATTTCCAAAAAGCACCAAATTCTTCACAATCAGGGATACTCCAACCCC
* ** *
6454 GTTAATCATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACTCCGGTTTTTATC
131 GTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGTTTTTATC
6519 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * * *
6536 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAACTCC-GATTTTA-TTTCAAAACACCAATTTT-CTATAATCGGG
*
6600 GATACTCCAACTCCGATTTTATTTCCAAAAA-TACCAAATT-TTCACAATC-GAGGATACTCCAA
63 GATACTCCAACTCCGATTTTATTTCCAAAAAGCACCAAATTCTTCACAATCAG-GGATACTCCAA
* *
6662 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGG
127 CCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGG
6724 CTTTATTCCC
Statistics
Matches: 168, Mismatches: 15, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
211 4 0.02
212 53 0.32
213 71 0.42
214 40 0.24
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (212 bp):
TCCACAATCGAGGATACTCCAACTCCGATTTTATTTCAAAACACCAATTTTCTATAATCGGGGAT
ACTCCAACTCCGATTTTATTTCCAAAAAGCACCAAATTCTTCACAATCAGGGATACTCCAACCCC
GTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGTTTTTATC
GCTAAAACACTAATTTT
Found at i:6729 original size:108 final size:106
Alignment explanation
Indices: 6383--6737 Score: 307
Period size: 108 Copynumber: 3.3 Consensus size: 106
6373 TTCTATAATC
*
6383 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAGCACCAATTTCTTCACAATC-AGGGATACTC
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAA-CACCAATTT-TTCACAATCGA-GGATACTC
* * *
6447 CAACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTATTTTTGA
63 CAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTA--TTCGA
* * * * *
6492 GGGGATACTCCAACTCCGGTTTT-TATCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAATTTTT-CACAATCGAGGATACTCC
* * * * ** * *
6556 AATCCTGGTTTTATTT--TC---AAAACGCCAATTTTCCTTTAATC--
64 AA-CCTCG--TTATTTCATCGGGGATACTCCAA--CCCCGTTATTCGA
* *
6597 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAAATTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAA
6662 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTA-TT-CGA
* ** *
6705 GGGGATACTCCAACCCCGGCTTTATTCCCAAAA
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAA
6738 TATTGATTTC
Statistics
Matches: 191, Mismatches: 36, Indels: 39
0.72 0.14 0.15
Matches are distributed among these distances:
101 6 0.03
103 6 0.03
104 24 0.13
105 36 0.19
106 11 0.06
107 10 0.05
108 58 0.30
109 34 0.18
110 2 0.01
111 3 0.02
112 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (106 bp):
GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAA
CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTATTCGA
Found at i:19299 original size:1 final size:1
Alignment explanation
Indices: 19293--19349 Score: 105
Period size: 1 Copynumber: 57.0 Consensus size: 1
19283 CCTTCTCTTC
*
19293 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19350 CCTACTTAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.98, C:0.00, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Done.