Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga09g00833.P4
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: 21249
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:1951 original size:20 final size:20
Alignment explanation
Indices: 1890--1955 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
1880 CCAAAAAAAG
*
1890 AAAAAAGAAAAACCTAACCC
1 AAAAAAAAAAAACCTAACCC
** *
1910 AAAAAAAAAAAGA-AGAA--G
1 AAAAAAAAAAA-ACCTAACCC
1928 AAAAAAAAAAAACCTAACCC
1 AAAAAAAAAAAACCTAACCC
1948 AAAAAAAA
1 AAAAAAAA
1956 TAATAAAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
17 1 0.03
18 13 0.37
20 20 0.57
21 1 0.03
ACGTcount: A:0.76, C:0.15, G:0.06, T:0.03
Consensus pattern (20 bp):
AAAAAAAAAAAACCTAACCC
Found at i:2572 original size:23 final size:23
Alignment explanation
Indices: 2535--2666 Score: 63
Period size: 25 Copynumber: 5.5 Consensus size: 23
2525 CCTTTTTTGT
2535 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATATTA
* *
2558 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATATTA
** *
2580 TATTAGGTATATT-TTAAATTTTA
1 TATTATATATATTCTT-AATATTA
* * *
2603 TATTACGTATATATATATTTTATACTA
1 TATTA--TATATAT-T-CTTAATATTA
* *
2630 TTTTATGTATATATCTTTAATATTA
1 TATTATATATAT-TC-TTAATATTA
* *
2655 TATGATTTATAT
1 TATTATATATAT
2667 ATATATATAT
Statistics
Matches: 80, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
21 2 0.03
22 15 0.19
23 19 0.24
24 4 0.05
25 29 0.36
26 1 0.01
27 8 0.10
28 2 0.03
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (23 bp):
TATTATATATATTCTTAATATTA
Found at i:2617 original size:2 final size:2
Alignment explanation
Indices: 2610--2686 Score: 54
Period size: 2 Copynumber: 39.5 Consensus size: 2
2600 TTATATTACG
* * * * *
2610 TA TA TA TA TA T- TT TA TA CTA T- TT TA TG TA TA TA TC TT TA -A
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
*
2650 TA T- TA TA TGA TT TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
2687 TTTTTTTACA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
1 4 0.07
2 52 0.87
3 4 0.07
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (2 bp):
TA
Found at i:2640 original size:25 final size:25
Alignment explanation
Indices: 2612--2670 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
2602 ATATTACGTA
* * *
2612 TATATATATTTTATACTATTTTATG
1 TATATATATTTAATACTATATGATG
* * *
2637 TATATATCTTTAATATTATATGATT
1 TATATATATTTAATACTATATGATG
2662 TATATATAT
1 TATATATAT
2671 ATATATATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (25 bp):
TATATATATTTAATACTATATGATG
Found at i:2732 original size:22 final size:24
Alignment explanation
Indices: 2704--2762 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
2694 ACATGTTATC
2704 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
2726 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
2751 TTATGTACATAT
1 TTATGTATATAT
2763 TTTTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 2 0.07
25 15 0.50
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATGTATATATCTTAACACTATA
Found at i:2752 original size:25 final size:25
Alignment explanation
Indices: 2720--2768 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2710 ATATATCTTA
**
2720 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
2745 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
2769 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:2947 original size:16 final size:15
Alignment explanation
Indices: 2923--2970 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
2913 TAATTATTAT
*
2923 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
2939 TATTTTAATATTTTA
1 TATTTTAATATTTTA
2954 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
2970 T
1 T
2971 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:2958 original size:7 final size:8
Alignment explanation
Indices: 2923--2974 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
2913 TAATTATTAT
*
2923 TATTCTAA
1 TATTTTAA
*
2931 TATTTTGA
1 TATTTTAA
2939 TATTTTAA
1 TATTTTAA
2947 TATTTT-A
1 TATTTTAA
2954 TATTTTATA
1 TATTTTA-A
*
2963 TATTTTAT
1 TATTTTAA
2971 TATT
1 TATT
2975 CACATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:9851 original size:70 final size:71
Alignment explanation
Indices: 9777--9918 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 71
9767 TTTTTCAGAA
* *
9777 TCAACTCATATTGCTAGAGGT-AGTTGAGCCTC-GGGCACGCTGAGGTATTTTCAATTTTTGTGT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGT-T
*
9840 TTTAATT
65 TTCAATT
*
9847 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTTT
9912 TCAATT
66 TCAATT
9918 T
1 T
9919 ACGTTGTTCA
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
70 20 0.30
71 19 0.29
72 27 0.41
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.39
Consensus pattern (71 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTTT
TCAATT
Found at i:10018 original size:140 final size:140
Alignment explanation
Indices: 9851--10338 Score: 888
Period size: 140 Copynumber: 3.5 Consensus size: 140
9841 TTAATTTCAA
9851 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
9916 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
9981 TCAAAATCAG
131 TCAAAATCAG
* *
9991 CTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
10056 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
10121 TCAAAATCAG
131 TCAAAATCAG
10131 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
* *
10196 TTTATGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
10261 TCAAAATCAG
131 TCAAAATCAG
*
10271 CTAATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATTTCTGTCTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCAC--GCTGAGGTATTTTCAATTTCTGT-TT
10335 TCAA
62 TCAA
10339 AAAAAAAATT
Statistics
Matches: 337, Mismatches: 7, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
139 2 0.01
140 306 0.91
142 23 0.07
143 6 0.02
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (140 bp):
CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
TCAAAATCAG
Found at i:10194 original size:13 final size:13
Alignment explanation
Indices: 10176--10209 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
10166 CGCTGAGGTA
*
10176 TTTTCAATTTCTG
1 TTTTCAATTTATG
10189 TTTTCAATTTATG
1 TTTTCAATTTATG
10202 TTGTTCAA
1 TT-TTCAA
10210 GAATCAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTTCAATTTATG
Found at i:10377 original size:81 final size:72
Alignment explanation
Indices: 10258--10483 Score: 258
Period size: 72 Copynumber: 3.0 Consensus size: 72
10248 AATTTCTACT
* * ** * * *
10258 TTTTCAAAA-TCAGCTAATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTT
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG---ACACGCTGAGGTAATT
10321 TCAATTTCTG
63 TCAATTTCTG
*
10331 TCTTTCAAAAAAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT
1 T-TTTC------AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGT
10396 AATTTCAATTTCTG
59 AATTTCAATTTCTG
* *
10410 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCA
10475 ATTTCTG
66 ATTTCTG
10482 TT
1 TT
10484 CAAAATGAGT
Statistics
Matches: 135, Mismatches: 9, Indels: 19
0.83 0.06 0.12
Matches are distributed among these distances:
72 68 0.50
73 1 0.01
74 4 0.03
78 4 0.03
79 24 0.18
80 4 0.03
81 29 0.21
82 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (72 bp):
TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCA
ATTTCTG
Found at i:10456 original size:72 final size:72
Alignment explanation
Indices: 10343--10483 Score: 273
Period size: 72 Copynumber: 2.0 Consensus size: 72
10333 TTTCAAAAAA
*
10343 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
10408 TGTTTTC
66 TGTTTTC
10415 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
10480 TGTT
66 TGTT
10484 CAAAATGAGT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (72 bp):
AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
TGTTTTC
Found at i:10552 original size:14 final size:14
Alignment explanation
Indices: 10521--10554 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
10511 GCCGAGGTAT
*
10521 TTTCAATTTCTATT
1 TTTCAATTTCTATC
*
10535 TTTCAATTTCTGTC
1 TTTCAATTTCTATC
10549 TTTCAA
1 TTTCAA
10555 AAAAAAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.03, T:0.59
Consensus pattern (14 bp):
TTTCAATTTCTATC
Found at i:10729 original size:151 final size:149
Alignment explanation
Indices: 10557--10909 Score: 496
Period size: 151 Copynumber: 2.3 Consensus size: 149
10547 TCTTTCAAAA
* * *
10557 AAAAAAACATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTT
1 AAAAAAA-ATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAG-TCACACACTGAGGTA--TTG
* *
10622 TCAA-TT-TATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCAGGACACGC
62 TCAATTTCTATGTTTC-AAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
10685 TGAGGTATTTTCAATTTCTGTTGT
126 TGAGGTATTTTCAATTTCTGTTGT
* ** *
10709 CAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTC-GGGACACGCTGAGGTATTGTCAA
1 AAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGTCACACACTGAGGTATTGTCAA
*
10773 TTTTTCGTATGTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
66 --TTTC-TATGTTTCAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
*
10838 AGGTATTTTTAATTTCTGTTGT
128 AGGTATTTTCAATTTCTGTTGT
*
10860 AAAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACAC
1 AAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCA-GTCACAC
10910 GTCAAGTGAG
Statistics
Matches: 179, Mismatches: 15, Indels: 13
0.86 0.07 0.06
Matches are distributed among these distances:
147 6 0.03
149 12 0.07
150 3 0.02
151 140 0.78
152 13 0.07
153 5 0.03
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (149 bp):
AAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGTCACACACTGAGGTATTGTCAA
TTTCTATGTTTCAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
TATTTTCAATTTCTGTTGT
Found at i:10730 original size:74 final size:74
Alignment explanation
Indices: 10558--10903 Score: 462
Period size: 74 Copynumber: 4.6 Consensus size: 74
10548 CTTTCAAAAA
* * *
10558 AAAAAACATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTT
1 AAAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--GACACGCTGAGGTA--TTTT
* *
10623 CAATTTAT-TTTTC
61 CAATTTCTGTTGTC
* *
10636 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
10701 TCTGTTGTC
66 TCTGTTGTC
* * *
10710 AAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTGTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
*
10775 TTTCGTATGTTTC
66 TCT-GT-TG--TC
*
10788 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
*
10852 TCTGTTGTA
66 TCTGTTGTC
* *
10861 AAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGG
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
10904 TCACACGTCA
Statistics
Matches: 241, Mismatches: 21, Indels: 16
0.87 0.08 0.06
Matches are distributed among these distances:
73 12 0.05
74 106 0.44
75 16 0.07
76 4 0.02
77 95 0.39
78 8 0.03
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (74 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
TCTGTTGTC
Found at i:11591 original size:31 final size:34
Alignment explanation
Indices: 11556--11629 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 34
11546 TAAGCCCCCC
11556 AAAAAA-AAGAAAAAAGAAAAACCTAACCCAAAAAA
1 AAAAAAGAAGAAAAAA-AAAAACCTAACCC-AAAAA
11591 AAAAGAAGAAGAAAAAAAAAAACCTAACCCAAAAA
1 AAAA-AAGAAGAAAAAAAAAAACCTAACCCAAAAA
11626 AAAA
1 AAAA
11630 TAATAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
35 13 0.35
36 15 0.41
37 9 0.24
ACGTcount: A:0.77, C:0.14, G:0.07, T:0.03
Consensus pattern (34 bp):
AAAAAAGAAGAAAAAAAAAAACCTAACCCAAAAA
Found at i:11594 original size:19 final size:19
Alignment explanation
Indices: 11565--11629 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
11555 CAAAAAAAAG
11565 AAAAAAGAAAAACCTAACCC
1 AAAAAA-AAAAACCTAACCC
** *
11585 AAAAAAAAAAGA-AGAA--G
1 AAAAAAAAAA-ACCTAACCC
11602 AAAAAAAAAAACCTAACCC
1 AAAAAAAAAAACCTAACCC
11621 AAAAAAAAA
1 AAAAAAAAA
11630 TAATAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
16 1 0.03
17 12 0.34
19 15 0.43
20 7 0.20
ACGTcount: A:0.75, C:0.15, G:0.06, T:0.03
Consensus pattern (19 bp):
AAAAAAAAAAACCTAACCC
Found at i:12246 original size:23 final size:23
Alignment explanation
Indices: 12209--12340 Score: 63
Period size: 25 Copynumber: 5.5 Consensus size: 23
12199 CCTTTTTTGT
12209 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATATTA
* *
12232 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATATTA
** *
12254 TATTAGGTATATT-TTAAATTTTA
1 TATTATATATATTCTT-AATATTA
* * *
12277 TATTACGTATATATATATTTTATACTA
1 TATTA--TATATAT-T-CTTAATATTA
* *
12304 TTTTATGTATATATCTTTAATATTA
1 TATTATATATAT-TC-TTAATATTA
* *
12329 TATGATTTATAT
1 TATTATATATAT
12341 ATATATATAT
Statistics
Matches: 80, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
21 2 0.03
22 15 0.19
23 19 0.24
24 4 0.05
25 29 0.36
26 1 0.01
27 8 0.10
28 2 0.03
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (23 bp):
TATTATATATATTCTTAATATTA
Found at i:12314 original size:25 final size:25
Alignment explanation
Indices: 12286--12344 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
12276 ATATTACGTA
* * *
12286 TATATATATTTTATACTATTTTATG
1 TATATATATTTAATACTATATGATG
* * *
12311 TATATATCTTTAATATTATATGATT
1 TATATATATTTAATACTATATGATG
12336 TATATATAT
1 TATATATAT
12345 ATATATATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (25 bp):
TATATATATTTAATACTATATGATG
Found at i:12404 original size:22 final size:24
Alignment explanation
Indices: 12376--12434 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
12366 ACATGTTATC
12376 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
12398 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
12423 TTATGTACATAT
1 TTATGTATATAT
12435 TTTTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 2 0.07
25 15 0.50
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATGTATATATCTTAACACTATA
Found at i:12424 original size:25 final size:25
Alignment explanation
Indices: 12392--12440 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
12382 ATATATCTTA
**
12392 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
12417 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
12441 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:12619 original size:16 final size:15
Alignment explanation
Indices: 12595--12642 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
12585 TAATTATTAT
*
12595 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
12611 TATTTTAATATTTTA
1 TATTTTAATATTTTA
12626 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
12642 T
1 T
12643 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:12630 original size:7 final size:8
Alignment explanation
Indices: 12595--12646 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
12585 TAATTATTAT
*
12595 TATTCTAA
1 TATTTTAA
*
12603 TATTTTGA
1 TATTTTAA
12611 TATTTTAA
1 TATTTTAA
12619 TATTTT-A
1 TATTTTAA
12626 TATTTTATA
1 TATTTTA-A
*
12635 TATTTTAT
1 TATTTTAA
12643 TATT
1 TATT
12647 CACATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:19528 original size:72 final size:71
Alignment explanation
Indices: 19452--19595 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 71
19442 TTTTTCAGAA
* * *
19452 TCAACTCATATTGCTAGAGGTAAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT
1 TCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGT-T
*
19517 TTTAATT
65 TTCAATT
* *
19524 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTTT
19589 TCAATT
66 TCAATT
19595 T
1 T
19596 ACGTTGTTCA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
71 8 0.12
72 58 0.88
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (71 bp):
TCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTTT
TCAATT
Found at i:19700 original size:140 final size:140
Alignment explanation
Indices: 19528--20015 Score: 870
Period size: 140 Copynumber: 3.5 Consensus size: 140
19518 TTAATTTCAA
19528 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
19593 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
19658 TCAAAATCAG
131 TCAAAATCAG
* *
19668 CTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
19733 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
19798 TCAAAATCAG
131 TCAAAATCAG
19808 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
* *
19873 TTTATGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
*
19938 TCAAAATTAG
131 TCAAAATCAG
* *
19948 CTAATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAGTTTCTGTCTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCAC--GCTGAGGTATTTTCAATTTCTGT-TT
20012 TCAA
62 TCAA
20016 AAAAAAAAAT
Statistics
Matches: 335, Mismatches: 9, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
139 2 0.01
140 305 0.91
142 22 0.07
143 6 0.02
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (140 bp):
CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
TCAAAATCAG
Found at i:19871 original size:13 final size:13
Alignment explanation
Indices: 19853--19886 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
19843 CGCTGAGGTA
*
19853 TTTTCAATTTCTG
1 TTTTCAATTTATG
19866 TTTTCAATTTATG
1 TTTTCAATTTATG
19879 TTGTTCAA
1 TT-TTCAA
19887 GAATCAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTTCAATTTATG
Found at i:20138 original size:72 final size:72
Alignment explanation
Indices: 20021--20161 Score: 273
Period size: 72 Copynumber: 2.0 Consensus size: 72
20011 TTCAAAAAAA
*
20021 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
20086 TGTTTTC
66 TGTTTTC
20093 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
20158 TGTT
66 TGTT
20162 CAAAATGAGT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (72 bp):
AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
TGTTTTC
Found at i:20172 original size:49 final size:50
Alignment explanation
Indices: 20115--20211 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 50
20105 ATATTGCGAG
**
20115 AAATGAGTTGAACCTCAAG-ACACGTTGAGGTAATTTCAATTTCTGTTCA
1 AAATGAGTTGAACCTCAAGCACACGCCGAGGTAATTTCAATTTCTGTTCA
* * *
20164 AAATGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCTGT
1 AAATGAGTTGAACCTCAAG-CACACGCCGAGGTAATTTCAATTTCTGT
20212 CTTTCAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
49 17 0.41
51 24 0.59
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (50 bp):
AAATGAGTTGAACCTCAAGCACACGCCGAGGTAATTTCAATTTCTGTTCA
Found at i:20396 original size:74 final size:74
Alignment explanation
Indices: 20167--20568 Score: 466
Period size: 77 Copynumber: 5.2 Consensus size: 74
20157 CTGTTCAAAA
* *
20167 TGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAAAAACATC
1 TGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATTTCTGT-TGTC-----AAAAAA-ATC
20232 AACTCATATTGCGAGAGG
57 AACTCATATTGCGAGAGG
* * * * * *
20250 TGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACT
1 TGAGTTGAGCCTCAG--GACACGCTGAGGTA--TTTTCAATTTCT-GTTGTCAAAAAAATCAACT
* *
20315 CACATTGCGAGATG
61 CATATTGCGAGAGG
*
20329 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCATAT
20394 TGCGAGAGG
66 TGCGAGAGG
* * * *
20403 TGAGTTGAGCCTCGGGACACACTGAGGTATTGTCAATTTTTCGTATGTTTC-AAAAAATCAACTC
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT-GT-TG--TCAAAAAAATCAACTC
20467 ATATTGCGAGAGG
62 ATATTGCGAGAGG
* *
20480 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATTTCTGTTGT-AAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCATAT
20544 TGCGAGAGG
66 TGCGAGAGG
*
20553 CGAGTTGAGCCTCAGG
1 TGAGTTGAGCCTCAGG
20569 TCACACGTCA
Statistics
Matches: 280, Mismatches: 29, Indels: 30
0.83 0.09 0.09
Matches are distributed among these distances:
73 41 0.15
74 65 0.23
75 15 0.05
76 4 0.01
77 73 0.26
78 2 0.01
79 33 0.12
80 6 0.02
83 25 0.09
85 15 0.05
86 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (74 bp):
TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCATAT
TGCGAGAGG
Found at i:20499 original size:151 final size:150
Alignment explanation
Indices: 20167--20574 Score: 525
Period size: 151 Copynumber: 2.6 Consensus size: 150
20157 CTGTTCAAAA
* *
20167 TGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAAAAACATC
1 TGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATTTCTGT-TGTC-----AAAAAA-ATC
* * ** *
20232 AACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTCAATTTATAT
57 AACTCGTATTGCGAGAGGTGAGTTGAGCCTC-G-GGACACACTGAGGTA-TTTGTCAATTTATAT
* *
20297 TTTTCAAAAAAATCAACTCACATTGCGAGATG
119 GTTTCAAAAAAATCAACTCACATTGCGAGAGG
20329 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
*
20394 TGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTA-TTGTCAATTTTTCGTATGTTTC-AAA
66 TGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTTGTCAA--TTT-ATATGTTTCAAAA
*
20457 AAATCAACTCATATTGCGAGAGG
128 AAATCAACTCACATTGCGAGAGG
*
20480 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATTTCTGTTGT-AAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
* * *
20544 TGCGAGAGGCGAGTTGAGCCTCAGGTCACAC
66 TGCGAGAGGTGAGTTGAGCCTCGGGACACAC
20575 GTCAAGTGAG
Statistics
Matches: 228, Mismatches: 15, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
149 6 0.03
150 46 0.20
151 85 0.37
152 8 0.04
153 32 0.14
154 6 0.03
159 3 0.01
160 26 0.11
162 16 0.07
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (150 bp):
TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
TGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTTGTCAATTTATATGTTTCAAAAAAA
TCAACTCACATTGCGAGAGG
Done.