Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga09g00833.P6
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: 14142
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:2747 original size:70 final size:71
Alignment explanation
Indices: 2673--2814 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 71
2663 TTTTTCAGAA
* *
2673 TCAACTCATATTGCTAGAGGT-AGTTGAGCCTC-GGGCACGCTGAGGTATTTTCAATTTTTGTGT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGT-T
*
2736 TTTAATT
65 TTCAATT
*
2743 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTTT
2808 TCAATT
66 TCAATT
2814 T
1 T
2815 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:2914 original size:140 final size:140
Alignment explanation
Indices: 2747--3234 Score: 888
Period size: 140 Copynumber: 3.5 Consensus size: 140
2737 TTAATTTCAA
2747 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
2812 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
2877 TCAAAATCAG
131 TCAAAATCAG
* *
2887 CTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
2952 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
3017 TCAAAATCAG
131 TCAAAATCAG
3027 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
* *
3092 TTTATGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
3157 TCAAAATCAG
131 TCAAAATCAG
*
3167 CTAATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATTTCTGTCTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCAC--GCTGAGGTATTTTCAATTTCTGT-TT
3231 TCAA
62 TCAA
3235 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:3090 original size:13 final size:13
Alignment explanation
Indices: 3072--3105 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3062 CGCTGAGGTA
*
3072 TTTTCAATTTCTG
1 TTTTCAATTTATG
3085 TTTTCAATTTATG
1 TTTTCAATTTATG
3098 TTGTTCAA
1 TT-TTCAA
3106 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:3273 original size:81 final size:72
Alignment explanation
Indices: 3154--3379 Score: 258
Period size: 72 Copynumber: 3.0 Consensus size: 72
3144 AATTTCTACT
* * ** * * *
3154 TTTTCAAAA-TCAGCTAATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTT
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG---ACACGCTGAGGTAATT
3217 TCAATTTCTG
63 TCAATTTCTG
*
3227 TCTTTCAAAAAAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT
1 T-TTTC------AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGT
3292 AATTTCAATTTCTG
59 AATTTCAATTTCTG
* *
3306 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCA
3371 ATTTCTG
66 ATTTCTG
3378 TT
1 TT
3380 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:3352 original size:72 final size:72
Alignment explanation
Indices: 3239--3379 Score: 273
Period size: 72 Copynumber: 2.0 Consensus size: 72
3229 TTTCAAAAAA
*
3239 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
3304 TGTTTTC
66 TGTTTTC
3311 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
3376 TGTT
66 TGTT
3380 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:3448 original size:14 final size:14
Alignment explanation
Indices: 3417--3450 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3407 GCCGAGGTAT
*
3417 TTTCAATTTCTATT
1 TTTCAATTTCTATC
*
3431 TTTCAATTTCTGTC
1 TTTCAATTTCTATC
3445 TTTCAA
1 TTTCAA
3451 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:3625 original size:151 final size:149
Alignment explanation
Indices: 3453--3805 Score: 496
Period size: 151 Copynumber: 2.3 Consensus size: 149
3443 TCTTTCAAAA
* * *
3453 AAAAAAACATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTT
1 AAAAAAA-ATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAG-TCACACACTGAGGTA--TTG
* *
3518 TCAA-TT-TATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCAGGACACGC
62 TCAATTTCTATGTTTC-AAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
3581 TGAGGTATTTTCAATTTCTGTTGT
126 TGAGGTATTTTCAATTTCTGTTGT
* ** *
3605 CAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTC-GGGACACGCTGAGGTATTGTCAA
1 AAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGTCACACACTGAGGTATTGTCAA
*
3669 TTTTTCGTATGTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
66 --TTTC-TATGTTTCAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
*
3734 AGGTATTTTTAATTTCTGTTGT
128 AGGTATTTTCAATTTCTGTTGT
*
3756 AAAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACAC
1 AAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCA-GTCACAC
3806 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:3626 original size:74 final size:74
Alignment explanation
Indices: 3454--3799 Score: 462
Period size: 74 Copynumber: 4.6 Consensus size: 74
3444 CTTTCAAAAA
* * *
3454 AAAAAACATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTT
1 AAAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--GACACGCTGAGGTA--TTTT
* *
3519 CAATTTAT-TTTTC
61 CAATTTCTGTTGTC
* *
3532 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
3597 TCTGTTGTC
66 TCTGTTGTC
* * *
3606 AAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTGTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
*
3671 TTTCGTATGTTTC
66 TCT-GT-TG--TC
*
3684 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
*
3748 TCTGTTGTA
66 TCTGTTGTC
* *
3757 AAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGG
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
3800 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:4487 original size:31 final size:34
Alignment explanation
Indices: 4452--4525 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 34
4442 TAAGCCCCCC
4452 AAAAAA-AAGAAAAAAGAAAAACCTAACCCAAAAAA
1 AAAAAAGAAGAAAAAA-AAAAACCTAACCC-AAAAA
4487 AAAAGAAGAAGAAAAAAAAAAACCTAACCCAAAAA
1 AAAA-AAGAAGAAAAAAAAAAACCTAACCCAAAAA
4522 AAAA
1 AAAA
4526 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:4490 original size:19 final size:19
Alignment explanation
Indices: 4461--4525 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
4451 CAAAAAAAAG
4461 AAAAAAGAAAAACCTAACCC
1 AAAAAA-AAAAACCTAACCC
** *
4481 AAAAAAAAAAGA-AGAA--G
1 AAAAAAAAAA-ACCTAACCC
4498 AAAAAAAAAAACCTAACCC
1 AAAAAAAAAAACCTAACCC
4517 AAAAAAAAA
1 AAAAAAAAA
4526 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:5142 original size:23 final size:23
Alignment explanation
Indices: 5105--5236 Score: 63
Period size: 25 Copynumber: 5.5 Consensus size: 23
5095 CCTTTTTTGT
5105 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATATTA
* *
5128 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATATTA
** *
5150 TATTAGGTATATT-TTAAATTTTA
1 TATTATATATATTCTT-AATATTA
* * *
5173 TATTACGTATATATATATTTTATACTA
1 TATTA--TATATAT-T-CTTAATATTA
* *
5200 TTTTATGTATATATCTTTAATATTA
1 TATTATATATAT-TC-TTAATATTA
* *
5225 TATGATTTATAT
1 TATTATATATAT
5237 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:5210 original size:25 final size:25
Alignment explanation
Indices: 5182--5240 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
5172 ATATTACGTA
* * *
5182 TATATATATTTTATACTATTTTATG
1 TATATATATTTAATACTATATGATG
* * *
5207 TATATATCTTTAATATTATATGATT
1 TATATATATTTAATACTATATGATG
5232 TATATATAT
1 TATATATAT
5241 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:5300 original size:22 final size:24
Alignment explanation
Indices: 5272--5330 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
5262 ACATGTTATC
5272 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
5294 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
5319 TTATGTACATAT
1 TTATGTATATAT
5331 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:5320 original size:25 final size:25
Alignment explanation
Indices: 5288--5336 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
5278 ATATATCTTA
**
5288 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
5313 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
5337 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:5515 original size:16 final size:15
Alignment explanation
Indices: 5491--5538 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
5481 TAATTATTAT
*
5491 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
5507 TATTTTAATATTTTA
1 TATTTTAATATTTTA
5522 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
5538 T
1 T
5539 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:5526 original size:7 final size:8
Alignment explanation
Indices: 5491--5542 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
5481 TAATTATTAT
*
5491 TATTCTAA
1 TATTTTAA
*
5499 TATTTTGA
1 TATTTTAA
5507 TATTTTAA
1 TATTTTAA
5515 TATTTT-A
1 TATTTTAA
5522 TATTTTATA
1 TATTTTA-A
*
5531 TATTTTAT
1 TATTTTAA
5539 TATT
1 TATT
5543 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:12424 original size:72 final size:71
Alignment explanation
Indices: 12348--12491 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 71
12338 TTTTTCAGAA
* * *
12348 TCAACTCATATTGCTAGAGGTAAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT
1 TCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGT-T
*
12413 TTTAATT
65 TTCAATT
* *
12420 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTTT
12485 TCAATT
66 TCAATT
12491 T
1 T
12492 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:12596 original size:140 final size:140
Alignment explanation
Indices: 12424--12911 Score: 870
Period size: 140 Copynumber: 3.5 Consensus size: 140
12414 TTAATTTCAA
12424 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
12489 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
12554 TCAAAATCAG
131 TCAAAATCAG
* *
12564 CTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
12629 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
12694 TCAAAATCAG
131 TCAAAATCAG
12704 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
* *
12769 TTTATGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
*
12834 TCAAAATTAG
131 TCAAAATCAG
* *
12844 CTAATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAGTTTCTGTCTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCAC--GCTGAGGTATTTTCAATTTCTGT-TT
12908 TCAA
62 TCAA
12912 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:12767 original size:13 final size:13
Alignment explanation
Indices: 12749--12782 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
12739 CGCTGAGGTA
*
12749 TTTTCAATTTCTG
1 TTTTCAATTTATG
12762 TTTTCAATTTATG
1 TTTTCAATTTATG
12775 TTGTTCAA
1 TT-TTCAA
12783 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:13034 original size:72 final size:72
Alignment explanation
Indices: 12917--13057 Score: 273
Period size: 72 Copynumber: 2.0 Consensus size: 72
12907 TTCAAAAAAA
*
12917 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
12982 TGTTTTC
66 TGTTTTC
12989 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
13054 TGTT
66 TGTT
13058 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:13068 original size:49 final size:50
Alignment explanation
Indices: 13011--13107 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 50
13001 ATATTGCGAG
**
13011 AAATGAGTTGAACCTCAAG-ACACGTTGAGGTAATTTCAATTTCTGTTCA
1 AAATGAGTTGAACCTCAAGCACACGCCGAGGTAATTTCAATTTCTGTTCA
* * *
13060 AAATGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCTGT
1 AAATGAGTTGAACCTCAAG-CACACGCCGAGGTAATTTCAATTTCTGT
13108 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:13292 original size:74 final size:74
Alignment explanation
Indices: 13063--13464 Score: 466
Period size: 77 Copynumber: 5.2 Consensus size: 74
13053 CTGTTCAAAA
* *
13063 TGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAAAAACATC
1 TGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATTTCTGT-TGTC-----AAAAAA-ATC
13128 AACTCATATTGCGAGAGG
57 AACTCATATTGCGAGAGG
* * * * * *
13146 TGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACT
1 TGAGTTGAGCCTCAG--GACACGCTGAGGTA--TTTTCAATTTCT-GTTGTCAAAAAAATCAACT
* *
13211 CACATTGCGAGATG
61 CATATTGCGAGAGG
*
13225 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCATAT
13290 TGCGAGAGG
66 TGCGAGAGG
* * * *
13299 TGAGTTGAGCCTCGGGACACACTGAGGTATTGTCAATTTTTCGTATGTTTC-AAAAAATCAACTC
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT-GT-TG--TCAAAAAAATCAACTC
13363 ATATTGCGAGAGG
62 ATATTGCGAGAGG
* *
13376 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATTTCTGTTGT-AAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCATAT
13440 TGCGAGAGG
66 TGCGAGAGG
*
13449 CGAGTTGAGCCTCAGG
1 TGAGTTGAGCCTCAGG
13465 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:13395 original size:151 final size:150
Alignment explanation
Indices: 13063--13470 Score: 525
Period size: 151 Copynumber: 2.6 Consensus size: 150
13053 CTGTTCAAAA
* *
13063 TGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAAAAACATC
1 TGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATTTCTGT-TGTC-----AAAAAA-ATC
* * ** *
13128 AACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTCAATTTATAT
57 AACTCGTATTGCGAGAGGTGAGTTGAGCCTC-G-GGACACACTGAGGTA-TTTGTCAATTTATAT
* *
13193 TTTTCAAAAAAATCAACTCACATTGCGAGATG
119 GTTTCAAAAAAATCAACTCACATTGCGAGAGG
13225 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
*
13290 TGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTA-TTGTCAATTTTTCGTATGTTTC-AAA
66 TGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTTGTCAA--TTT-ATATGTTTCAAAA
*
13353 AAATCAACTCATATTGCGAGAGG
128 AAATCAACTCACATTGCGAGAGG
*
13376 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATTTCTGTTGT-AAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
* * *
13440 TGCGAGAGGCGAGTTGAGCCTCAGGTCACAC
66 TGCGAGAGGTGAGTTGAGCCTCGGGACACAC
13471 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.