Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold325
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: 15272
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:728 original size:41 final size:41
Alignment explanation
Indices: 605--1043 Score: 524
Period size: 41 Copynumber: 10.9 Consensus size: 41
595 GTTTACAAAC
* *
605 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAG-
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
* *
645 AAAAACGCCGCTAAA-ATCATGTTC-TTAGCGGCGCTTAAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
*
684 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
*
725 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTGTAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG--A
* * *
767 AAAAATGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
808 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGG-GCTT---
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
845 AAAAACGCCGCTAAAG-ACATGTTCTTTAGCGGCGCTTAG-
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
*
884 GAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-A
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
* * ***
924 GAAAAACGCCGCTAAA-ATCATGTTCTTTAGCGGCGTTTTTT
1 -AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
** * * ** ***
965 CTAATCGCCGCTAAAGAACATGTTCTTTAGTGGCATTTTTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
* * *
1006 ACAAACGCCGCAAAAGAACATGTTCTTTAGTGGCGCTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTT
1044 TTATACAAAA
Statistics
Matches: 354, Mismatches: 31, Indels: 27
0.86 0.08 0.07
Matches are distributed among these distances:
36 16 0.05
37 20 0.06
38 13 0.04
39 38 0.11
40 84 0.24
41 147 0.42
42 33 0.09
43 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
Found at i:1402 original size:20 final size:21
Alignment explanation
Indices: 1368--1422 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1358 TTGCTCTGCT
* *
1368 CTGCTTCTCTTGCTGCAG-C-
1 CTGCTTCCCTCGCTGCAGTCG
1387 CTCGCTTCCCTCGCTGCAGTCG
1 CT-GCTTCCCTCGCTGCAGTCG
1409 CTGCTTCCCTCGCT
1 CTGCTTCCCTCGCT
1423 TCCGCCTCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 14 0.45
21 13 0.42
22 2 0.06
ACGTcount: A:0.04, C:0.44, G:0.20, T:0.33
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCAGTCG
Found at i:1433 original size:21 final size:21
Alignment explanation
Indices: 1366--1435 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
1356 TTTTGCTCTG
* *
1366 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
1387 CTC-GCTTCCCTCGCTGCAGT
1 CTCTGCTTCCCTCGCTGCAGC
* * *
1407 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTGCAGC
1428 CTCTGCTT
1 CTCTGCTT
1436 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.03, C:0.44, G:0.19, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:6931 original size:11 final size:9
Alignment explanation
Indices: 6883--7173 Score: 87
Period size: 7 Copynumber: 34.0 Consensus size: 9
6873 AATTGCAATG
6883 GTAAGTTAT
1 GTAAGTTAT
6892 GTAAGTTAT
1 GTAAGTTAT
6901 GTAAGTTAAAT
1 GTAAGTT--AT
6912 GT-A-TTAT
1 GTAAGTTAT
6919 GTAAGTTAAAT
1 GTAAGTT--AT
6930 GTAAG-T-T
1 GTAAGTTAT
6937 GTAAGTTAT
1 GTAAGTTAT
*
6946 -TATGTATTAT
1 GTAAG--TTAT
6956 GTAAG-T-T
1 GTAAGTTAT
6963 GTAAGTTAAAT
1 GTAAGTT--AT
*
6974 GT-A-TTGT
1 GTAAGTTAT
6981 GTAAG-T-T
1 GTAAGTTAT
6988 GTAAGTTAAAT
1 GTAAGTT--AT
6999 GT-A-TTAT
1 GTAAGTTAT
7006 GTAAG-T-T
1 GTAAGTTAT
7013 GTAAGTTAT
1 GTAAGTTAT
*
7022 -TATGTATTAT
1 GTAAG--TTAT
7032 GTAAG-T-T
1 GTAAGTTAT
7039 GTAAGTTAT
1 GTAAGTTAT
* *
7048 -TATGTATTGT
1 GTAAG--TTAT
7058 GTAAG-T-T
1 GTAAGTTAT
7065 GTAAGTTAAAT
1 GTAAGTT--AT
7076 GT-A-TTAT
1 GTAAGTTAT
7083 GTAAG-T-T
1 GTAAGTTAT
7090 GTAAGTTAAT
1 GTAAGTT-AT
7100 GT-A-TTAT
1 GTAAGTTAT
7107 GTAAG-T-T
1 GTAAGTTAT
7114 GTAAGTTAAAT
1 GTAAGTT--AT
7125 GT-A-TTAT
1 GTAAGTTAT
7132 GTAAG-T-T
1 GTAAGTTAT
7139 GTAAGTTAT
1 GTAAGTTAT
*
7148 -TATGTATTAT
1 GTAAG--TTAT
7158 GTAAG-T-T
1 GTAAGTTAT
7165 GTAAGTTAT
1 GTAAGTTAT
7174 TATGTATTGT
Statistics
Matches: 215, Mismatches: 10, Indels: 114
0.63 0.03 0.34
Matches are distributed among these distances:
7 83 0.39
8 39 0.18
9 34 0.16
10 24 0.11
11 35 0.16
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:6962 original size:26 final size:25
Alignment explanation
Indices: 6928--7321 Score: 561
Period size: 26 Copynumber: 15.8 Consensus size: 25
6918 TGTAAGTTAA
6928 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
*
6954 ATGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
* *
6979 GTGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
7004 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
7030 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
* *
7056 GTGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
7081 ATGTAAGTTGTAAGTTA-ATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
*
7105 ATGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
7130 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
7156 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
*
7182 GTGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
7208 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-TATGTATT
* *
7234 GTGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
*
7259 ATGTCAG-T-T-A---A-ATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
*
7277 ATGTAAGTTGTAAGTTAAATGTATT
1 ATGTAAGTTGTAAGTTATATGTATT
*
7302 ATGTAAGTTGTAAGTAATAT
1 ATGTAAGTTGTAAGTTATAT
7322 AATTATTAAT
Statistics
Matches: 341, Mismatches: 17, Indels: 21
0.90 0.04 0.06
Matches are distributed among these distances:
18 13 0.04
19 2 0.01
20 1 0.00
21 1 0.00
22 1 0.00
23 1 0.00
24 26 0.08
25 131 0.38
26 165 0.48
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (25 bp):
ATGTAAGTTGTAAGTTATATGTATT
Found at i:7310 original size:18 final size:18
Alignment explanation
Indices: 7242--7285 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
7232 TTGTGTAAGT
7242 TGTAAGTTAAATGTATTA
1 TGTAAGTTAAATGTATTA
*
7260 TGTCAGTTAAATGTATTA
1 TGTAAGTTAAATGTATTA
7278 TGTAAGTT
1 TGTAAGTT
7286 GTAAGTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.45
Consensus pattern (18 bp):
TGTAAGTTAAATGTATTA
Found at i:7438 original size:73 final size:73
Alignment explanation
Indices: 7319--7614 Score: 583
Period size: 73 Copynumber: 4.1 Consensus size: 73
7309 TTGTAAGTAA
7319 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
7384 TATTTTTT
66 TATTTTTT
7392 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
7457 TATTTTTT
66 TATTTTTT
7465 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
7530 TATTTTTT
66 TATTTTTT
*
7538 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAGTATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
7603 TATTTTTT
66 TATTTTTT
7611 TATA
1 TATA
7615 TTTTATTTTA
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 222 1.00
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.51
Consensus pattern (73 bp):
TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
TATTTTTT
Found at i:7779 original size:13 final size:13
Alignment explanation
Indices: 7761--7831 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
7751 ATTTATAATT
7761 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
7774 ATTTAAGTAACAT
1 ATTTAAGTAATAA
7787 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
7800 ATTTAAGTAACAT
1 ATTTAAGTAATAA
7813 ATTTAAGTAATAA
1 ATTTAAGTAATAA
7826 ATTTAA
1 ATTTAA
7832 ACAAATTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAAGTAATAA
Found at i:7790 original size:26 final size:26
Alignment explanation
Indices: 7760--7831 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
7750 TATTTATAAT
7760 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
7786 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
7812 TATTTAAGTAATAAATTTAA
1 TATTTAAGTAATAAATTTAA
7832 ACAAATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (26 bp):
TATTTAAGTAATAAATTTAAGTAACA
Found at i:7858 original size:17 final size:17
Alignment explanation
Indices: 7836--7993 Score: 149
Period size: 17 Copynumber: 8.6 Consensus size: 17
7826 ATTTAAACAA
7836 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
7853 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
7870 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
7887 AAACAAATTTTAGTAAGTAATGT
1 ------ATTTTAGTAAGTAATGT
7910 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
7927 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
*
7944 AAACAAATTTTAGTAAGTAATTT
1 ------ATTTTAGTAAGTAATGT
7967 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
7984 ATTTTAGTAA
1 ATTTTAGTAA
7994 TAAATTTAAC
Statistics
Matches: 121, Mismatches: 4, Indels: 32
0.77 0.03 0.20
Matches are distributed among these distances:
16 2 0.02
17 88 0.73
23 29 0.24
24 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.46
Consensus pattern (17 bp):
ATTTTAGTAAGTAATGT
Found at i:7882 original size:57 final size:57
Alignment explanation
Indices: 7803--8002 Score: 364
Period size: 57 Copynumber: 3.5 Consensus size: 57
7793 GTAATAAATT
** *
7803 TAAGTAACATATTTAAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
7860 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
*
7917 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATTTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
7974 TAAGTAATGTATTTTAGTAATAAATTTAA
1 TAAGTAATGTATTTTAGTAATAAATTTAA
8003 CATTCAATCG
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 139 1.00
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (57 bp):
TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
Found at i:9351 original size:11 final size:11
Alignment explanation
Indices: 9335--9374 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
9325 GATGATAATA
9335 CATTAGTTACC
1 CATTAGTTACC
9346 CATTAGTTACC
1 CATTAGTTACC
*
9357 CACTAGTTACC
1 CATTAGTTACC
9368 CA-TAGTT
1 CATTAGTT
9375 TGAGATATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 5 0.18
11 23 0.82
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.35
Consensus pattern (11 bp):
CATTAGTTACC
Found at i:10465 original size:84 final size:83
Alignment explanation
Indices: 10358--10558 Score: 330
Period size: 84 Copynumber: 2.4 Consensus size: 83
10348 ATTAACACCG
10358 TTTTGTGGCGTTTTTGGTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACAACACCGTTT
1 TTTTGTGGCGTTTTT-G-AAAAACGCCACTAAATATTACAGCTGTGAACAGAAACAACACCGTTT
10423 TCGTGGTCTGGAATTGCATT
64 TCGTGGTCTGGAATTGCATT
*
10443 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTT
1 TTTTGTGGCGTTTTT-GAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACAACACCGTTTT
10508 CGTGGTCTGGAATTGCATT
65 CGTGGTCTGGAATTGCATT
* * *
10527 ATTTGTGGCATTTTCTTAAAAACGCCACTAAA
1 TTTTGTGGCGTTTT-TGAAAAACGCCACTAAA
10559 AGTTTAACTA
Statistics
Matches: 110, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
84 93 0.85
85 17 0.15
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (83 bp):
TTTTGTGGCGTTTTTGAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACAACACCGTTTTC
GTGGTCTGGAATTGCATT
Found at i:10961 original size:12 final size:12
Alignment explanation
Indices: 10944--10969 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10934 TTAAAATAGC
10944 ACGACCTCTTTT
1 ACGACCTCTTTT
10956 ACGACCTCTTTT
1 ACGACCTCTTTT
10968 AC
1 AC
10970 AGTTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.35, G:0.08, T:0.38
Consensus pattern (12 bp):
ACGACCTCTTTT
Found at i:11827 original size:111 final size:112
Alignment explanation
Indices: 11582--12169 Score: 975
Period size: 112 Copynumber: 5.3 Consensus size: 112
11572 AACACCTAGA
* * *
11582 TTAGCGGCGCTTTACAAAAAACGCCACTAA-TGCCCCCCAAAGGACACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
* * * * * ** *
11646 GAGTATTATTTGCGGCATTTTTTTATAAGCGCTGCTAATGTTCACTCT
66 GTGTATTATTTGCGGC-GTTATCTATAAACGCCACTAATGCTCACTCT
11694 TTAGCGGCGCTTTACAATAAACGCCACTAAGT-CCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
11758 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
66 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
**
11805 TTAGCGGCGCTTCGCAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
* *
11870 GTGTATTATTTGCGGCGTTATTTATAAACGCCGCTAATGCTCACTCT
66 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
*
11917 TTAGCGGCGCTTTACAATAAATGCCACTAAGT-CCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
11981 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
66 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
12028 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
12093 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
66 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
* **
12140 TTAGCGGCGCTTTTCCTTAAACGCCACTAA
1 TTAGCGGCGCTTTACAATAAACGCCACTAA
12170 TGCTCACTCT
Statistics
Matches: 450, Mismatches: 23, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
111 162 0.36
112 287 0.64
113 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (112 bp):
TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
Found at i:11931 original size:223 final size:223
Alignment explanation
Indices: 11582--12169 Score: 1007
Period size: 223 Copynumber: 2.6 Consensus size: 223
11572 AACACCTAGA
* * *
11582 TTAGCGGCGCTTTACAAAAAACGCCACTAA-TGCCCCCCAAAGGACACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
* * * * * *
11646 GAGTATTATTTGCGGCATTTTTTTATAAGCGCTGCTAATGTTCACTCTTTAGCGGCGCTTTACAA
66 GTGTATTATTTGCGGC-GTTATTTATAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTACAA
11711 TAAACGCCACTAAGTCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATTATTTGCGGCGT
130 TAAACGCCACTAAGTCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATTATTTGCGGCGT
11776 TATCTATAAACGCCACTAATGCTCACTCT
195 TATCTATAAACGCCACTAATGCTCACTCT
**
11805 TTAGCGGCGCTTCGCAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
11870 GTGTATTATTTGCGGCGTTATTTATAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTACAAT
66 GTGTATTATTTGCGGCGTTATTTATAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTACAAT
*
11935 AAATGCCACTAAGTCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATTATTTGCGGCGTT
131 AAACGCCACTAAGTCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATTATTTGCGGCGTT
12000 ATCTATAAACGCCACTAATGCTCACTCT
196 ATCTATAAACGCCACTAATGCTCACTCT
12028 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
* * * **
12093 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTCCTT
66 GTGTATTATTTGCGGCGTTATTTATAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTACAAT
12158 AAACGCCACTAA
131 AAACGCCACTAA
12170 TGCTCACTCT
Statistics
Matches: 344, Mismatches: 20, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
223 297 0.86
224 47 0.14
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (223 bp):
TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
GTGTATTATTTGCGGCGTTATTTATAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTACAAT
AAACGCCACTAAGTCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATTATTTGCGGCGTT
ATCTATAAACGCCACTAATGCTCACTCT
Found at i:12162 original size:40 final size:40
Alignment explanation
Indices: 12117--12233 Score: 198
Period size: 40 Copynumber: 2.9 Consensus size: 40
12107 GCGTTATCTA
**
12117 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTCCT
1 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTAAT
12157 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTAAT
1 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTAAT
* *
12197 TAAACGCCGCTATTGCTCACTCTTTAGCGGCGCTTTT
1 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTT
12234 GCTCCAAACG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (40 bp):
TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTAAT
Found at i:13843 original size:21 final size:21
Alignment explanation
Indices: 13796--13845 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
13786 CATACGGGTG
* **
13796 GCCACACGGGCGTGTGCCTTG
1 GCCACACGGGCGTGTCCCTCA
* *
13817 GACACACGGTCGTGTCCCTCA
1 GCCACACGGGCGTGTCCCTCA
13838 GCCACACG
1 GCCACACG
13846 AGCATATGAG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.16, C:0.38, G:0.30, T:0.16
Consensus pattern (21 bp):
GCCACACGGGCGTGTCCCTCA
Done.