Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga09g00833.P3
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: 21287
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:1989 original size:20 final size:20
Alignment explanation
Indices: 1928--1993 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
1918 CCAAAAAAAG
*
1928 AAAAAAGAAAAACCTAACCC
1 AAAAAAAAAAAACCTAACCC
** *
1948 AAAAAAAAAAAGA-AGAA--G
1 AAAAAAAAAAA-ACCTAACCC
1966 AAAAAAAAAAAACCTAACCC
1 AAAAAAAAAAAACCTAACCC
1986 AAAAAAAA
1 AAAAAAAA
1994 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:2610 original size:23 final size:23
Alignment explanation
Indices: 2573--2704 Score: 63
Period size: 25 Copynumber: 5.5 Consensus size: 23
2563 CCTTTTTTGT
2573 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATATTA
* *
2596 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATATTA
** *
2618 TATTAGGTATATT-TTAAATTTTA
1 TATTATATATATTCTT-AATATTA
* * *
2641 TATTACGTATATATATATTTTATACTA
1 TATTA--TATATAT-T-CTTAATATTA
* *
2668 TTTTATGTATATATCTTTAATATTA
1 TATTATATATAT-TC-TTAATATTA
* *
2693 TATGATTTATAT
1 TATTATATATAT
2705 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:2655 original size:2 final size:2
Alignment explanation
Indices: 2648--2724 Score: 54
Period size: 2 Copynumber: 39.5 Consensus size: 2
2638 TTATATTACG
* * * * *
2648 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
*
2688 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
2725 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:2678 original size:25 final size:25
Alignment explanation
Indices: 2650--2708 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
2640 ATATTACGTA
* * *
2650 TATATATATTTTATACTATTTTATG
1 TATATATATTTAATACTATATGATG
* * *
2675 TATATATCTTTAATATTATATGATT
1 TATATATATTTAATACTATATGATG
2700 TATATATAT
1 TATATATAT
2709 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:2770 original size:22 final size:24
Alignment explanation
Indices: 2742--2800 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
2732 ACATGTTATC
2742 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
2764 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
2789 TTATGTACATAT
1 TTATGTATATAT
2801 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:2790 original size:25 final size:25
Alignment explanation
Indices: 2758--2806 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2748 ATATATCTTA
**
2758 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
2783 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
2807 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:2985 original size:16 final size:15
Alignment explanation
Indices: 2961--3008 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
2951 TAATTATTAT
*
2961 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
2977 TATTTTAATATTTTA
1 TATTTTAATATTTTA
2992 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
3008 T
1 T
3009 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:2996 original size:7 final size:8
Alignment explanation
Indices: 2961--3012 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
2951 TAATTATTAT
*
2961 TATTCTAA
1 TATTTTAA
*
2969 TATTTTGA
1 TATTTTAA
2977 TATTTTAA
1 TATTTTAA
2985 TATTTT-A
1 TATTTTAA
2992 TATTTTATA
1 TATTTTA-A
*
3001 TATTTTAT
1 TATTTTAA
3009 TATT
1 TATT
3013 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:9889 original size:70 final size:71
Alignment explanation
Indices: 9815--9956 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 71
9805 TTTTTCAGAA
* *
9815 TCAACTCATATTGCTAGAGGT-AGTTGAGCCTC-GGGCACGCTGAGGTATTTTCAATTTTTGTGT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGT-T
*
9878 TTTAATT
65 TTCAATT
*
9885 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTTT
9950 TCAATT
66 TCAATT
9956 T
1 T
9957 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:10056 original size:140 final size:140
Alignment explanation
Indices: 9889--10376 Score: 888
Period size: 140 Copynumber: 3.5 Consensus size: 140
9879 TTAATTTCAA
9889 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
9954 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
10019 TCAAAATCAG
131 TCAAAATCAG
* *
10029 CTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
10094 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
10159 TCAAAATCAG
131 TCAAAATCAG
10169 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
* *
10234 TTTATGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
10299 TCAAAATCAG
131 TCAAAATCAG
*
10309 CTAATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATTTCTGTCTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCAC--GCTGAGGTATTTTCAATTTCTGT-TT
10373 TCAA
62 TCAA
10377 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:10232 original size:13 final size:13
Alignment explanation
Indices: 10214--10247 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
10204 CGCTGAGGTA
*
10214 TTTTCAATTTCTG
1 TTTTCAATTTATG
10227 TTTTCAATTTATG
1 TTTTCAATTTATG
10240 TTGTTCAA
1 TT-TTCAA
10248 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:10415 original size:81 final size:72
Alignment explanation
Indices: 10296--10521 Score: 258
Period size: 72 Copynumber: 3.0 Consensus size: 72
10286 AATTTCTACT
* * ** * * *
10296 TTTTCAAAA-TCAGCTAATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTT
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG---ACACGCTGAGGTAATT
10359 TCAATTTCTG
63 TCAATTTCTG
*
10369 TCTTTCAAAAAAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT
1 T-TTTC------AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGT
10434 AATTTCAATTTCTG
59 AATTTCAATTTCTG
* *
10448 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCA
10513 ATTTCTG
66 ATTTCTG
10520 TT
1 TT
10522 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:10494 original size:72 final size:72
Alignment explanation
Indices: 10381--10521 Score: 273
Period size: 72 Copynumber: 2.0 Consensus size: 72
10371 TTTCAAAAAA
*
10381 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
10446 TGTTTTC
66 TGTTTTC
10453 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
10518 TGTT
66 TGTT
10522 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:10590 original size:14 final size:14
Alignment explanation
Indices: 10559--10592 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
10549 GCCGAGGTAT
*
10559 TTTCAATTTCTATT
1 TTTCAATTTCTATC
*
10573 TTTCAATTTCTGTC
1 TTTCAATTTCTATC
10587 TTTCAA
1 TTTCAA
10593 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:10767 original size:151 final size:149
Alignment explanation
Indices: 10595--10947 Score: 496
Period size: 151 Copynumber: 2.3 Consensus size: 149
10585 TCTTTCAAAA
* * *
10595 AAAAAAACATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTT
1 AAAAAAA-ATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAG-TCACACACTGAGGTA--TTG
* *
10660 TCAA-TT-TATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCAGGACACGC
62 TCAATTTCTATGTTTC-AAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
10723 TGAGGTATTTTCAATTTCTGTTGT
126 TGAGGTATTTTCAATTTCTGTTGT
* ** *
10747 CAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTC-GGGACACGCTGAGGTATTGTCAA
1 AAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGTCACACACTGAGGTATTGTCAA
*
10811 TTTTTCGTATGTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
66 --TTTC-TATGTTTCAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
*
10876 AGGTATTTTTAATTTCTGTTGT
128 AGGTATTTTCAATTTCTGTTGT
*
10898 AAAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACAC
1 AAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCA-GTCACAC
10948 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:10768 original size:74 final size:74
Alignment explanation
Indices: 10596--10941 Score: 462
Period size: 74 Copynumber: 4.6 Consensus size: 74
10586 CTTTCAAAAA
* * *
10596 AAAAAACATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTT
1 AAAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--GACACGCTGAGGTA--TTTT
* *
10661 CAATTTAT-TTTTC
61 CAATTTCTGTTGTC
* *
10674 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
10739 TCTGTTGTC
66 TCTGTTGTC
* * *
10748 AAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTGTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
*
10813 TTTCGTATGTTTC
66 TCT-GT-TG--TC
*
10826 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
*
10890 TCTGTTGTA
66 TCTGTTGTC
* *
10899 AAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGG
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
10942 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:11629 original size:31 final size:34
Alignment explanation
Indices: 11594--11667 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 34
11584 TAAGCCCCCC
11594 AAAAAA-AAGAAAAAAGAAAAACCTAACCCAAAAAA
1 AAAAAAGAAGAAAAAA-AAAAACCTAACCC-AAAAA
11629 AAAAGAAGAAGAAAAAAAAAAACCTAACCCAAAAA
1 AAAA-AAGAAGAAAAAAAAAAACCTAACCCAAAAA
11664 AAAA
1 AAAA
11668 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:11632 original size:19 final size:19
Alignment explanation
Indices: 11603--11667 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
11593 CAAAAAAAAG
11603 AAAAAAGAAAAACCTAACCC
1 AAAAAA-AAAAACCTAACCC
** *
11623 AAAAAAAAAAGA-AGAA--G
1 AAAAAAAAAA-ACCTAACCC
11640 AAAAAAAAAAACCTAACCC
1 AAAAAAAAAAACCTAACCC
11659 AAAAAAAAA
1 AAAAAAAAA
11668 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:12284 original size:23 final size:23
Alignment explanation
Indices: 12247--12378 Score: 63
Period size: 25 Copynumber: 5.5 Consensus size: 23
12237 CCTTTTTTGT
12247 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATATTA
* *
12270 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATATTA
** *
12292 TATTAGGTATATT-TTAAATTTTA
1 TATTATATATATTCTT-AATATTA
* * *
12315 TATTACGTATATATATATTTTATACTA
1 TATTA--TATATAT-T-CTTAATATTA
* *
12342 TTTTATGTATATATCTTTAATATTA
1 TATTATATATAT-TC-TTAATATTA
* *
12367 TATGATTTATAT
1 TATTATATATAT
12379 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:12352 original size:25 final size:25
Alignment explanation
Indices: 12324--12382 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
12314 ATATTACGTA
* * *
12324 TATATATATTTTATACTATTTTATG
1 TATATATATTTAATACTATATGATG
* * *
12349 TATATATCTTTAATATTATATGATT
1 TATATATATTTAATACTATATGATG
12374 TATATATAT
1 TATATATAT
12383 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:12442 original size:22 final size:24
Alignment explanation
Indices: 12414--12472 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
12404 ACATGTTATC
12414 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
12436 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
12461 TTATGTACATAT
1 TTATGTATATAT
12473 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:12462 original size:25 final size:25
Alignment explanation
Indices: 12430--12478 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
12420 ATATATCTTA
**
12430 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
12455 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
12479 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:12657 original size:16 final size:15
Alignment explanation
Indices: 12633--12680 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
12623 TAATTATTAT
*
12633 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
12649 TATTTTAATATTTTA
1 TATTTTAATATTTTA
12664 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
12680 T
1 T
12681 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:12668 original size:7 final size:8
Alignment explanation
Indices: 12633--12684 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
12623 TAATTATTAT
*
12633 TATTCTAA
1 TATTTTAA
*
12641 TATTTTGA
1 TATTTTAA
12649 TATTTTAA
1 TATTTTAA
12657 TATTTT-A
1 TATTTTAA
12664 TATTTTATA
1 TATTTTA-A
*
12673 TATTTTAT
1 TATTTTAA
12681 TATT
1 TATT
12685 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:19566 original size:72 final size:71
Alignment explanation
Indices: 19490--19633 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 71
19480 TTTTTCAGAA
* * *
19490 TCAACTCATATTGCTAGAGGTAAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT
1 TCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGT-T
*
19555 TTTAATT
65 TTCAATT
* *
19562 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTTT
19627 TCAATT
66 TCAATT
19633 T
1 T
19634 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:19738 original size:140 final size:140
Alignment explanation
Indices: 19566--20053 Score: 870
Period size: 140 Copynumber: 3.5 Consensus size: 140
19556 TTAATTTCAA
19566 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
19631 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
19696 TCAAAATCAG
131 TCAAAATCAG
* *
19706 CTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
19771 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
19836 TCAAAATCAG
131 TCAAAATCAG
19846 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
* *
19911 TTTATGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
*
19976 TCAAAATTAG
131 TCAAAATCAG
* *
19986 CTAATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAGTTTCTGTCTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCAC--GCTGAGGTATTTTCAATTTCTGT-TT
20050 TCAA
62 TCAA
20054 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:19909 original size:13 final size:13
Alignment explanation
Indices: 19891--19924 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
19881 CGCTGAGGTA
*
19891 TTTTCAATTTCTG
1 TTTTCAATTTATG
19904 TTTTCAATTTATG
1 TTTTCAATTTATG
19917 TTGTTCAA
1 TT-TTCAA
19925 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:20176 original size:72 final size:72
Alignment explanation
Indices: 20059--20199 Score: 273
Period size: 72 Copynumber: 2.0 Consensus size: 72
20049 TTCAAAAAAA
*
20059 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
20124 TGTTTTC
66 TGTTTTC
20131 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
20196 TGTT
66 TGTT
20200 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:20210 original size:49 final size:50
Alignment explanation
Indices: 20153--20249 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 50
20143 ATATTGCGAG
**
20153 AAATGAGTTGAACCTCAAG-ACACGTTGAGGTAATTTCAATTTCTGTTCA
1 AAATGAGTTGAACCTCAAGCACACGCCGAGGTAATTTCAATTTCTGTTCA
* * *
20202 AAATGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCTGT
1 AAATGAGTTGAACCTCAAG-CACACGCCGAGGTAATTTCAATTTCTGT
20250 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:20434 original size:74 final size:74
Alignment explanation
Indices: 20205--20606 Score: 466
Period size: 77 Copynumber: 5.2 Consensus size: 74
20195 CTGTTCAAAA
* *
20205 TGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAAAAACATC
1 TGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATTTCTGT-TGTC-----AAAAAA-ATC
20270 AACTCATATTGCGAGAGG
57 AACTCATATTGCGAGAGG
* * * * * *
20288 TGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACT
1 TGAGTTGAGCCTCAG--GACACGCTGAGGTA--TTTTCAATTTCT-GTTGTCAAAAAAATCAACT
* *
20353 CACATTGCGAGATG
61 CATATTGCGAGAGG
*
20367 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCATAT
20432 TGCGAGAGG
66 TGCGAGAGG
* * * *
20441 TGAGTTGAGCCTCGGGACACACTGAGGTATTGTCAATTTTTCGTATGTTTC-AAAAAATCAACTC
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT-GT-TG--TCAAAAAAATCAACTC
20505 ATATTGCGAGAGG
62 ATATTGCGAGAGG
* *
20518 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATTTCTGTTGT-AAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCATAT
20582 TGCGAGAGG
66 TGCGAGAGG
*
20591 CGAGTTGAGCCTCAGG
1 TGAGTTGAGCCTCAGG
20607 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:20537 original size:151 final size:150
Alignment explanation
Indices: 20205--20612 Score: 525
Period size: 151 Copynumber: 2.6 Consensus size: 150
20195 CTGTTCAAAA
* *
20205 TGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAAAAACATC
1 TGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATTTCTGT-TGTC-----AAAAAA-ATC
* * ** *
20270 AACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTCAATTTATAT
57 AACTCGTATTGCGAGAGGTGAGTTGAGCCTC-G-GGACACACTGAGGTA-TTTGTCAATTTATAT
* *
20335 TTTTCAAAAAAATCAACTCACATTGCGAGATG
119 GTTTCAAAAAAATCAACTCACATTGCGAGAGG
20367 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
*
20432 TGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTA-TTGTCAATTTTTCGTATGTTTC-AAA
66 TGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTTGTCAA--TTT-ATATGTTTCAAAA
*
20495 AAATCAACTCATATTGCGAGAGG
128 AAATCAACTCACATTGCGAGAGG
*
20518 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATTTCTGTTGT-AAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
* * *
20582 TGCGAGAGGCGAGTTGAGCCTCAGGTCACAC
66 TGCGAGAGGTGAGTTGAGCCTCGGGACACAC
20613 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.