Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1498
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: 33068
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Found at i:386 original size:18 final size:17
Alignment explanation
Indices: 352--395 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
342 TTTATTTATG
352 TATTATAAAATTAATAT
1 TATTATAAAATTAATAT
369 TATTATTAAAA-TACATAT
1 TATTA-TAAAATTA-ATAT
*
387 TAGTATAAA
1 TATTATAAA
396 TAAAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TATTATAAAATTAATAT
Found at i:1102 original size:30 final size:30
Alignment explanation
Indices: 1068--1126 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
1058 ACTAGTTATC
*
1068 TTTAATATATATTCAAAAAAATTTTTAACT
1 TTTAATATATATACAAAAAAATTTTTAACT
* *
1098 TTTAATTTATATACAAATAAATTTTTAAC
1 TTTAATATATATACAAAAAAATTTTTAAC
1127 ATAAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (30 bp):
TTTAATATATATACAAAAAAATTTTTAACT
Found at i:1533 original size:14 final size:14
Alignment explanation
Indices: 1514--1549 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1504 AAATATAAAA
*
1514 AATATTTTTATATT
1 AATATTTATATATT
1528 AATATTTATATATT
1 AATATTTATATATT
*
1542 TATATTTA
1 AATATTTA
1550 ATTTAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
AATATTTATATATT
Found at i:1923 original size:20 final size:20
Alignment explanation
Indices: 1885--1929 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1875 ATACTCAAAA
*
1885 ATAAAATAAAAAATAAATTT
1 ATAAAAAAAAAAATAAATTT
*
1905 TTAAAAAAAATAAAT-AATTT
1 ATAAAAAAAA-AAATAAATTT
1925 ATAAA
1 ATAAA
1930 TATATATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAAAAAAAAAAATAAATTT
Found at i:2480 original size:55 final size:56
Alignment explanation
Indices: 2408--2517 Score: 188
Period size: 55 Copynumber: 2.0 Consensus size: 56
2398 CAACACTTTT
*
2408 ATTTTCTTTTTTCTTTCATTCAAATTTGGAGGATTTGTTTTTA-TAACAAGTAAGC
1 ATTTTCTTTTCTCTTTCATTCAAATTTGGAGGATTTGTTTTTATTAACAAGTAAGC
2463 ATTTTCTTTATCT-TTTCATTCAAATTTGGAGGATTTGTTTTTATTAACAAGTAAG
1 ATTTTCTTT-TCTCTTTCATTCAAATTTGGAGGATTTGTTTTTATTAACAAGTAAG
2518 AAAAATGATA
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
55 39 0.75
56 13 0.25
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (56 bp):
ATTTTCTTTTCTCTTTCATTCAAATTTGGAGGATTTGTTTTTATTAACAAGTAAGC
Found at i:2912 original size:10 final size:10
Alignment explanation
Indices: 2884--2913 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2874 TCTCTCTCTC
*
2884 TATATATATA
1 TATATATAAA
2894 TATATATAAA
1 TATATATAAA
2904 TATATATAAA
1 TATATATAAA
2914 GTAGTTAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TATATATAAA
Found at i:5575 original size:17 final size:17
Alignment explanation
Indices: 5555--5596 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
5545 TAGTAATATT
5555 TATTAAATATTTAAATA
1 TATTAAATATTTAAATA
*
5572 TATTAAATATTTAAATT
1 TATTAAATATTTAAATA
5589 TATTAAAT
1 TATTAAAT
5597 CAATTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTAAATATTTAAATA
Found at i:5579 original size:9 final size:9
Alignment explanation
Indices: 5555--5596 Score: 61
Period size: 8 Copynumber: 4.9 Consensus size: 9
5545 TAGTAATATT
5555 TATTAAATA
1 TATTAAATA
5564 T-TTAAATA
1 TATTAAATA
5572 TATTAAATA
1 TATTAAATA
*
5581 T-TTAAATT
1 TATTAAATA
5589 TATTAAAT
1 TATTAAAT
5597 CAATTTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 15 0.50
9 15 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TATTAAATA
Found at i:6343 original size:13 final size:13
Alignment explanation
Indices: 6325--6397 Score: 57
Period size: 13 Copynumber: 5.8 Consensus size: 13
6315 TAATAATTTT
*
6325 AAATATGATATAA
1 AAATATAATATAA
6338 AAATATAATATAA
1 AAATATAATATAA
* **
6351 ATAAAAT-ATATTT
1 A-AATATAATATAA
6364 AAA-ATAA-AT-A
1 AAATATAATATAA
6374 AAA-ATAATATAA
1 AAATATAATATAA
6386 TAAATATAATAT
1 -AAATATAATAT
6398 TATATATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
10 7 0.14
11 6 0.12
12 4 0.08
13 21 0.43
14 11 0.22
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:6353 original size:24 final size:24
Alignment explanation
Indices: 6324--6397 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 24
6314 TTAATAATTT
*
6324 TAAATATGATATAAAAATATAATA
1 TAAATATAATATAAAAATATAATA
*
6348 TAAATAAAATATATTTAAAATA-AATA
1 TAAATATAATATA---AAAATATAATA
6374 -AAA-ATAATATAATAAATATAATA
1 TAAATATAATATAA-AAATATAATA
6397 T
1 T
6398 TATATATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
21 1 0.02
22 5 0.12
23 4 0.10
24 18 0.44
25 3 0.07
26 4 0.10
27 6 0.15
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (24 bp):
TAAATATAATATAAAAATATAATA
Found at i:6494 original size:15 final size:15
Alignment explanation
Indices: 6474--6503 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6464 ATATTTAATA
*
6474 ATTTATATTATTTAT
1 ATTTATATAATTTAT
6489 ATTTATATAATTTAT
1 ATTTATATAATTTAT
6504 TCAAAGAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTATATAATTTAT
Found at i:6835 original size:22 final size:23
Alignment explanation
Indices: 6810--6868 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 23
6800 ATTTAAAAAG
* *
6810 TATTAAAATACTTTTAT-ATTAA
1 TATTTAAATATTTTTATAATTAA
*
6832 TATTTATATATTTTTATAATTAA
1 TATTTAAATATTTTTATAATTAA
6855 -ATTTAAATATTTTT
1 TATTTAAATATTTTT
6869 TAAATAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 27 0.84
23 5 0.16
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TATTTAAATATTTTTATAATTAA
Found at i:6876 original size:21 final size:22
Alignment explanation
Indices: 6815--6876 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
6805 AAAAGTATTA
* *
6815 AAATACTTTTAT-ATTAATATTT
1 AAATATTTTTATAAATAA-ATTT
* *
6837 ATATATTTTTATAATTAAATTT
1 AAATATTTTTATAAATAAATTT
6859 AAATATTTTT-TAAATAAA
1 AAATATTTTTATAAATAAA
6877 AAATTATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.20
22 23 0.66
23 5 0.14
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
AAATATTTTTATAAATAAATTT
Found at i:7571 original size:26 final size:26
Alignment explanation
Indices: 7549--7600 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
7539 GAGTAAATTT
*
7549 AATA-ATTTTAAATATAATATAAATAA
1 AATATATTTAAAAT-TAATATAAATAA
*
7575 AATATATTTAAAATTAATAAAAATAA
1 AATATATTTAAAATTAATATAAATAA
7601 CATCATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
AATATATTTAAAATTAATATAAATAA
Found at i:7702 original size:14 final size:15
Alignment explanation
Indices: 7685--7717 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
7675 CAAATTTTAA
7685 TATATTTA-ATAATT
1 TATATTTATATAATT
7699 TATATTTATATAATT
1 TATATTTATATAATT
7714 TATA
1 TATA
7718 AAAAAAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATATTTATATAATT
Found at i:10144 original size:31 final size:31
Alignment explanation
Indices: 10106--10227 Score: 147
Period size: 31 Copynumber: 4.0 Consensus size: 31
10096 AGTTTCAAAT
* * *
10106 CGTGCCACTGGTTAAGAATAGTGATTTTTGC
1 CGTGCCACCGGATAAGAATAGTGGTTTTTGC
* *
10137 CGTGCCACCAGATAAGAATAGCGGTTTTTGC
1 CGTGCCACCGGATAAGAATAGTGGTTTTTGC
* * *
10168 CGTGTCACC-GAAAAAAATAGTGGTTTTTGC
1 CGTGCCACCGGATAAGAATAGTGGTTTTTGC
* *
10198 CGTTCCACCGAATAAGAATAGTGGTTTTTG
1 CGTGCCACCGGATAAGAATAGTGGTTTTTG
10228 TTCCAACCCG
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
30 25 0.33
31 51 0.67
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (31 bp):
CGTGCCACCGGATAAGAATAGTGGTTTTTGC
Found at i:11618 original size:12 final size:12
Alignment explanation
Indices: 11601--11627 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11591 TAAAAATTAA
11601 AAATTCAAATTC
1 AAATTCAAATTC
11613 AAATTCAAATTC
1 AAATTCAAATTC
11625 AAA
1 AAA
11628 AAAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTCAAATTC
Found at i:11817 original size:50 final size:49
Alignment explanation
Indices: 11755--11917 Score: 272
Period size: 50 Copynumber: 3.3 Consensus size: 49
11745 AATAGAAAAT
11755 GCATGCATGGGAAAGCATAAAGATTGCAATTGGAGACAAAACATGCAGAG
1 GCATGCATGGGAAAGCATAAA-ATTGCAATTGGAGACAAAACATGCAGAG
* * *
11805 GCATGCATGGGAAAACACAAAATTGCAATTGGAGACAAAACATGCGGAG
1 GCATGCATGGGAAAGCATAAAATTGCAATTGGAGACAAAACATGCAGAG
11854 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
1 GCATGCATGGGAAAGCAT-AAAATTGCAATTGGAGACAAAACATGCAGAG
*
11904 ACATGCATGGGAAA
1 GCATGCATGGGAAA
11918 TGAAAAAAGC
Statistics
Matches: 105, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
49 43 0.41
50 62 0.59
ACGTcount: A:0.43, C:0.15, G:0.27, T:0.15
Consensus pattern (49 bp):
GCATGCATGGGAAAGCATAAAATTGCAATTGGAGACAAAACATGCAGAG
Found at i:13738 original size:79 final size:79
Alignment explanation
Indices: 13521--13815 Score: 466
Period size: 79 Copynumber: 3.7 Consensus size: 79
13511 TTTAATCGAA
* * * *
13521 GGGATACTCCAACTCCGGTTTTATTTCTAAAATATTAATTTTTCACAATCGGGGGTACTCCAACC
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACC
*
13586 CCGTTATTTTCGAG
66 CCGTTATTTCCGAG
* * * *
13600 GGGATACTCCAA-CCCGGTTCTATCTCTAAAATATTAATTTTTCACAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACC
13664 CCGTTATTTCCGAG
66 CCGTTATTTCCGAG
* *
13678 GGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACC
13743 CCGTTATTTCCGAG
66 CCGTTATTTCCGAG
* *
13757 GGGATACTCCAACCTCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACT
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACT
13816 TTAATCCCGA
Statistics
Matches: 202, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
78 73 0.36
79 129 0.64
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (79 bp):
GGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACC
CCGTTATTTCCGAG
Found at i:15794 original size:299 final size:298
Alignment explanation
Indices: 15258--15901 Score: 975
Period size: 299 Copynumber: 2.2 Consensus size: 298
15248 AAGTTGAGGA
* * *
15258 AAATTTTTTCTTAGTCTTTTTATAGATAAA-GAAAACTCGTATTTAAGTCATTATCGAAAAATGA
1 AAATTTTTTCTTAGTCATTTTATAGATAAAGGAAAACTCGTATTTAAGACATTACCGAAAAATGA
* * * * * * * *
15322 AATGTGTGCTTCTTTAAATTCAAAATAAGTCATTATGGAAAAAAGTAATTTATTGTTGACGAACA
66 AATGCGTACGTCTATAAATCCAAAATAAATCATTATCGAAAAAAATAATTTATTGTTGACGAACA
* * *
15387 TAAATTTAAGTTCTATTAATTATAAAATAAAGACATGTACAATATTAATTAATTTTAATAAAAAT
131 TAAATTTAAATTCTATCAATTATAAAAAAAAGACATGTACAATATTAATTAATTTTAATAAAAAT
*
15452 AAATTTATATAATTTACAAATAAATTAAAAATAATTTATAAATAAAAAATAATAATGCATGCACA
196 AAATTTATATAATTTACAAATAAATTAAAAATAATTTATAAATAAAAAATAATAATACATGCACA
*
15517 ATATCAATTAATTTTAATAAAAATAATAAATATACAAT
261 ATATCAATTAATTTTAATAAAAATAATAAATATAAAAT
* *
15555 AAATTTTTTCTTAGTCATTTTATAGATAAAGGAAAGCTTGTATTTAAGACATTACCGAAAAATGA
1 AAATTTTTTCTTAGTCATTTTATAGATAAAGGAAAACTCGTATTTAAGACATTACCGAAAAATGA
* * * *
15620 AATGCGTACGTCTATAAATCCGAAATAAATCGTTATCGAAAAAAATAATTTATTGTTGGCTAACA
66 AATGCGTACGTCTATAAATCCAAAATAAATCATTATCGAAAAAAATAATTTATTGTTGACGAACA
* *
15685 TAAATTTAAATTGTATCAATTATAAAAAATAATACATGTACAATATTAATTAATTTTAATAAAAA
131 TAAATTTAAATTCTATCAATTATAAAAAA-AAGACATGTACAATATTAATTAATTTTAATAAAAA
* * *
15750 TAAATTTGTATAATTTATAAATAAATTAAAATTAATTTATAAATAAAAAATAATAATACATGCAC
195 TAAATTTATATAATTTACAAATAAATTAAAAATAATTTATAAATAAAAAATAATAATACATGCAC
* * *
15815 AATATTAATTAATTTTAATAAAAATAATACATGTAAAAT
260 AATATCAATTAATTTTAATAAAAATAATAAATATAAAAT
* * *
15854 AAATTTTTTCTTAGTCATTTTACATATAAAGAAAAACTCGTATTTAAG
1 AAATTTTTTCTTAGTCATTTTATAGATAAAGGAAAACTCGTATTTAAG
15902 TTGTTATCGA
Statistics
Matches: 310, Mismatches: 35, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
297 29 0.09
298 108 0.35
299 173 0.56
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.37
Consensus pattern (298 bp):
AAATTTTTTCTTAGTCATTTTATAGATAAAGGAAAACTCGTATTTAAGACATTACCGAAAAATGA
AATGCGTACGTCTATAAATCCAAAATAAATCATTATCGAAAAAAATAATTTATTGTTGACGAACA
TAAATTTAAATTCTATCAATTATAAAAAAAAGACATGTACAATATTAATTAATTTTAATAAAAAT
AAATTTATATAATTTACAAATAAATTAAAAATAATTTATAAATAAAAAATAATAATACATGCACA
ATATCAATTAATTTTAATAAAAATAATAAATATAAAAT
Found at i:16100 original size:32 final size:37
Alignment explanation
Indices: 16061--16141 Score: 98
Period size: 34 Copynumber: 2.3 Consensus size: 37
16051 ATCATACCTT
* *
16061 ATTTTTTAAAAA-AATTTATTAA-ATATTATTT-TT-A
1 ATTTTATAAAAATAA-TAATTAATATATTATTTATTAA
16095 ATTTTATAAAAATAATAATTAATATATTATTTATTAA
1 ATTTTATAAAAATAATAATTAATATATTATTTATTAA
*
16132 ATTTTTTAAA
1 ATTTTATAAA
16142 TTTAATTAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
34 17 0.43
35 11 0.28
36 2 0.05
37 10 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (37 bp):
ATTTTATAAAAATAATAATTAATATATTATTTATTAA
Found at i:16587 original size:24 final size:25
Alignment explanation
Indices: 16560--16625 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
16550 ATTTTTATTG
*
16560 AATTTAAATATATTTAAATTAT-AT
1 AATTTAAATATATTTAAAATATAAT
* *
16584 AATTTCTTAATATATATAAAATATAAT
1 AA-TT-TAAATATATTTAAAATATAAT
* *
16611 AAATAAAATATATTT
1 AATTTAAATATATTT
16626 TCATCGTCTC
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
24 2 0.06
25 10 0.31
26 16 0.50
27 4 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
AATTTAAATATATTTAAAATATAAT
Found at i:23200 original size:52 final size:52
Alignment explanation
Indices: 23052--23180 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
23042 CAAAATATGA
23052 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
* **
23104 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
*
23156 AAATTTACCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
23181 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
Found at i:23207 original size:13 final size:13
Alignment explanation
Indices: 23189--23213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23179 CAAAGATCAG
23189 TGTATCGATACAA
1 TGTATCGATACAA
23202 TGTATCGATACA
1 TGTATCGATACA
23214 TTTGAGTAAT
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:23292 original size:19 final size:19
Alignment explanation
Indices: 23266--23349 Score: 81
Period size: 19 Copynumber: 4.7 Consensus size: 19
23256 AGCAGTACAT
23266 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
23285 TCTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
* *
23298 TGTATCAATACAACACTTA
1 TGTATCGATACAAAACTTA
* *
23317 TGTATCGATACAACACTAA
1 TGTATCGATACAAAACTTA
23336 TGTATCGATACAAA
1 TGTATCGATACAAA
23350 TCGTTGAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
13 9 0.17
14 1 0.02
16 2 0.04
18 1 0.02
19 40 0.75
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:23302 original size:32 final size:32
Alignment explanation
Indices: 23261--23328 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
23251 TTCGTAGCAG
*
23261 TACATTGTATCGATACAAAACTTATCTATCGA
1 TACATTGTATCAATACAAAACTTATCTATCGA
* *
23293 TACATTGTATCAATACAACACTTATGTATCGA
1 TACATTGTATCAATACAAAACTTATCTATCGA
23325 TACA
1 TACA
23329 ACACTAATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (32 bp):
TACATTGTATCAATACAAAACTTATCTATCGA
Found at i:28487 original size:20 final size:20
Alignment explanation
Indices: 28458--28532 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
28448 AAAAAGACAT
*
28458 AATGTATCGATACATTGCAG
1 AATGTATCGATACATTGCAA
*
28478 AATATATCGATACATT-CATA
1 AATGTATCGATACATTGCA-A
* * *
28498 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGCAA
28518 AATGTATCGATACAT
1 AATGTATCGATACAT
28533 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 42 0.93
21 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGCAA
Found at i:28526 original size:40 final size:39
Alignment explanation
Indices: 28455--28532 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
28445 GGTAAAAAGA
* *
28455 CATAATGTATCGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
28494 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
28533 CTGGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:31384 original size:15 final size:15
Alignment explanation
Indices: 31364--31392 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31354 GGAATTTTAT
31364 GGGCCATTAGAACCG
1 GGGCCATTAGAACCG
31379 GGGCCATTAGAACC
1 GGGCCATTAGAACC
31393 ACTTCGCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.31, T:0.14
Consensus pattern (15 bp):
GGGCCATTAGAACCG
Found at i:32176 original size:76 final size:76
Alignment explanation
Indices: 31954--32185 Score: 229
Period size: 76 Copynumber: 3.0 Consensus size: 76
31944 GCAAAGCAAG
* * * * * *
31954 ATGCTTTCCCAAATTCC-TTAACCTTCCCAAAAGCTTCAAATTGATTATCTTGCCTTCTCAAGCT
1 ATGCCTTCCCAAA-ACCTTTAACCTTCCC-AAAGGTTCAAATTGATCATCTTGCATTCTTAAGCT
* *
32018 TGAGAATATTGCT
64 CGAGAATGTTGCT
* * * *
32031 ATGCCTTTCCAAAACCTTAAACCTTCCCAAATGTTCAAATTGATCATC-T-CA-CCTTTACAGGC
1 ATGCCTTCCCAAAACCTTTAACCTTCCCAAAGGTTCAAATTGATCATCTTGCATTC-TTA-A-GC
*
32093 TCAAGAATGTTGCT
63 TCGAGAATGTTGCT
** * *
32107 ATGCCTTCCCAAAGGCTTTAACCTTCCCAAAGGTTCAAATTGATCATCTTGTATTCTTAAACTCG
1 ATGCCTTCCCAAAACCTTTAACCTTCCCAAAGGTTCAAATTGATCATCTTGCATTCTTAAGCTCG
*
32172 AGAATGTTACT
66 AGAATGTTGCT
32183 ATG
1 ATG
32186 TCTTTCCCTA
Statistics
Matches: 125, Mismatches: 23, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
73 1 0.01
74 3 0.02
75 2 0.02
76 91 0.73
77 23 0.18
78 4 0.03
79 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (76 bp):
ATGCCTTCCCAAAACCTTTAACCTTCCCAAAGGTTCAAATTGATCATCTTGCATTCTTAAGCTCG
AGAATGTTGCT
Done.