Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2292
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: 48291
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Found at i:1436 original size:50 final size:50
Alignment explanation
Indices: 1312--1560 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
1302 GATAATAACA
* * ** * *
1312 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
1363 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
1413 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
1463 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
1518 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
1561 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:1490 original size:100 final size:104
Alignment explanation
Indices: 1311--1560 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
1301 TGATAATAAC
**
1311 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
1376 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
1413 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
1476 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
1518 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1561 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:1676 original size:13 final size:13
Alignment explanation
Indices: 1655--1686 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1645 GCTTGGATCA
*
1655 TCATCAAATAAAT
1 TCATAAAATAAAT
1668 TCATAAAATAAAT
1 TCATAAAATAAAT
1681 TCATAA
1 TCATAA
1687 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:1933 original size:30 final size:30
Alignment explanation
Indices: 1898--1955 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1888 CCTCGACTCT
*
1898 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
1928 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
1956 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:9003 original size:50 final size:50
Alignment explanation
Indices: 8879--9127 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
8869 GATAATAACA
* * ** * *
8879 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
8930 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
8980 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
9030 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
9085 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
9128 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:9057 original size:100 final size:104
Alignment explanation
Indices: 8878--9127 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
8868 TGATAATAAC
**
8878 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
8943 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
8980 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
9043 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
9085 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
9128 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:9243 original size:13 final size:13
Alignment explanation
Indices: 9222--9253 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
9212 GCTTGGATCA
*
9222 TCATCAAATAAAT
1 TCATAAAATAAAT
9235 TCATAAAATAAAT
1 TCATAAAATAAAT
9248 TCATAA
1 TCATAA
9254 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:9500 original size:30 final size:30
Alignment explanation
Indices: 9465--9522 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
9455 CCTCGACTCT
*
9465 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
9495 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
9523 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:11375 original size:6 final size:6
Alignment explanation
Indices: 11360--11393 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
11350 GGCCTCTCCA
11360 TTTTTC -TTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
11394 ATCACTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:16410 original size:19 final size:19
Alignment explanation
Indices: 16386--16460 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
16376 AATCACATCT
16386 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
*
16405 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
16426 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
16445 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
16461 CTCAAAGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 33 0.65
21 18 0.35
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:16423 original size:21 final size:21
Alignment explanation
Indices: 16397--16459 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
16387 CTAAGATTAC
16397 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
16418 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
16437 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
16458 AT
1 AT
16460 CCTCAAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.47
21 21 0.52
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:16470 original size:17 final size:18
Alignment explanation
Indices: 16389--16470 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 18
16379 CACATCTTCT
* *
16389 AAGATTACATATCATATCT
1 AAGATTGCATATCA-ATCA
*
16408 AAGATTGCATATATCATATCT
1 AAGATTGC--ATATCA-ATCA
*
16429 AAGATTGCATATCATATCT
1 AAGATTGCATATCA-ATCA
*
16448 AAGATTGCATATC-CTCA
1 AAGATTGCATATCAATCA
16465 AAGATT
1 AAGATT
16471 ATGTTTCCAT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.14
19 31 0.53
21 19 0.33
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (18 bp):
AAGATTGCATATCAATCA
Found at i:16562 original size:16 final size:17
Alignment explanation
Indices: 16531--16565 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
16521 AAAAATAATT
*
16531 CAATTATCATATTTACA
1 CAATTATCACATTTACA
16548 CAATT-TCACATTTACA
1 CAATTATCACATTTACA
16564 CA
1 CA
16566 CATATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (17 bp):
CAATTATCACATTTACA
Found at i:19370 original size:20 final size:19
Alignment explanation
Indices: 19354--19472 Score: 75
Period size: 19 Copynumber: 6.3 Consensus size: 19
19344 ATTTTATATT
19354 TTTTTTACTATTTTTATCAA
1 TTTTTTA-TATTTTTATCAA
*
19374 TTTTTTATATTTTTTTTCTAA
1 TTTTTTATA-TTTTTATC-AA
* * ** *
19395 GTTTTAATAAATTTA-AAA
1 TTTTTTATATTTTTATCAA
*
19413 TATTTTTATATTTTTATTAA
1 T-TTTTTATATTTTTATCAA
** *
19433 AATTTTATA-TTTTAT-AT
1 TTTTTTATATTTTTATCAA
*
19450 TTTTTTATTTTTTTATC-A
1 TTTTTTATATTTTTATCAA
19468 TTTTT
1 TTTTT
19473 GCCACATGTC
Statistics
Matches: 74, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
17 7 0.09
18 19 0.26
19 20 0.27
20 19 0.26
21 9 0.12
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (19 bp):
TTTTTTATATTTTTATCAA
Found at i:19425 original size:8 final size:8
Alignment explanation
Indices: 19412--19472 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 8
19402 TAAATTTAAA
19412 ATATTTTT
1 ATATTTTT
19420 ATATTTTT
1 ATATTTTT
*
19428 ATTAAAATTTT
1 A-T--ATTTTT
19439 ATATTTTAT
1 ATATTTT-T
*
19448 ATTTTTTT
1 ATATTTTT
*
19456 ATTTTTTT
1 ATATTTTT
19464 ATCATTTTT
1 AT-ATTTTT
19473 GCCACATGTC
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
8 24 0.55
9 13 0.30
10 1 0.02
11 6 0.14
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (8 bp):
ATATTTTT
Found at i:19428 original size:28 final size:26
Alignment explanation
Indices: 19396--19453 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
19386 TTTTTCTAAG
19396 TTTTAAT-AAATTTAAAATATTTTTATAT
1 TTTTAATAAAATTT--AATA-TTTTATAT
* *
19424 TTTTATTAAAATTTTATATTTTATAT
1 TTTTAATAAAATTTAATATTTTATAT
19450 TTTT
1 TTTT
19454 TTATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 12 0.44
27 3 0.11
28 6 0.22
29 6 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTTAATAAAATTTAATATTTTATAT
Found at i:19457 original size:17 final size:19
Alignment explanation
Indices: 19435--19472 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
19425 TTTATTAAAA
19435 TTTTA-TATTTTAT-ATTT
1 TTTTATTATTTTATCATTT
*
19452 TTTTATTTTTTTATCATTT
1 TTTTATTATTTTATCATTT
19471 TT
1 TT
19473 GCCACATGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 7 0.39
19 6 0.33
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTATTATTTTATCATTT
Found at i:20132 original size:86 final size:86
Alignment explanation
Indices: 19964--20221 Score: 392
Period size: 86 Copynumber: 3.0 Consensus size: 86
19954 TTTTTTGAAA
* * ** * * * * *
19964 AAAAAGTTTGAG-GACCTTTTTGATACATTTTGGCAGTTCAAATACACAAGTAAGAGAAAAAAAA
1 AAAAAGTTTGAGAG-CTTTTTTGATATATTTTGAAAGTTTAAATACCCAATTGAGTG-AAAAAAA
20028 TAGGGGCTTAATTGCTTTTTTTG
64 TAGGGGCTTAATTGCTTTTTTTG
20051 AAAAAGTTTGAGAGCTTTTTTGATATATTTTGAAAGTTTAAATACCCAATTGAGTGAAAAAAATA
1 AAAAAGTTTGAGAGCTTTTTTGATATATTTTGAAAGTTTAAATACCCAATTGAGTGAAAAAAATA
20116 GGGGCTTAATTGCTTTTTTTG
66 GGGGCTTAATTGCTTTTTTTG
20137 AAAAAGTTTGAGAGCTTTTTTGATATATTTTGAAAGTTTAAATACCCAATTGAGTGAAAAAAATA
1 AAAAAGTTTGAGAGCTTTTTTGATATATTTTGAAAGTTTAAATACCCAATTGAGTGAAAAAAATA
* *
20202 GGGGCTTAAATGTTTTTTTT
66 GGGGCTTAATTGCTTTTTTT
20222 AAGGGTTTGA
Statistics
Matches: 159, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
86 113 0.71
87 45 0.28
88 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (86 bp):
AAAAAGTTTGAGAGCTTTTTTGATATATTTTGAAAGTTTAAATACCCAATTGAGTGAAAAAAATA
GGGGCTTAATTGCTTTTTTTG
Found at i:21400 original size:20 final size:20
Alignment explanation
Indices: 21375--21428 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
21365 AAATTAAGTT
*
21375 AAAATGATTTTAACCTAGCC
1 AAAATGATTTTAACCAAGCC
* **
21395 AAAATGATTTCAACCAAGTT
1 AAAATGATTTTAACCAAGCC
*
21415 AAAATAATTTTAAC
1 AAAATGATTTTAAC
21429 ATATCAAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.31
Consensus pattern (20 bp):
AAAATGATTTTAACCAAGCC
Found at i:21446 original size:40 final size:40
Alignment explanation
Indices: 21370--21453 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
21360 TTTTAAAATT
* * *
21370 AAGTTAAAATGATTTTAACCTAGCCAAAATGATTTCAACC
1 AAGTTAAAATAATTTTAACATAGCCAAAATGATTTCAAAC
* *
21410 AAGTTAAAATAATTTTAACATA-TCAAAGTGATTTTCAAAC
1 AAGTTAAAATAATTTTAACATAGCCAAAATGA-TTTCAAAC
21450 AAGT
1 AAGT
21454 CAGAATTGCT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
39 7 0.18
40 31 0.82
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (40 bp):
AAGTTAAAATAATTTTAACATAGCCAAAATGATTTCAAAC
Found at i:24413 original size:39 final size:38
Alignment explanation
Indices: 24359--24432 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 38
24349 ATTCCCCGAT
24359 TATTAATAACATAATTATTTAATTTAATTATTATTTTTAC
1 TATTAATAACATAATTATTT-ATTTAATTA-TATTTTTAC
* *
24399 TATTATTAAC-TAATTATTTATTTTATTATATTTT
1 TATTAATAACATAATTATTTATTTAATTATATTTT
24433 AATTCCTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 6 0.19
38 8 0.25
39 9 0.28
40 9 0.28
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.59
Consensus pattern (38 bp):
TATTAATAACATAATTATTTATTTAATTATATTTTTAC
Found at i:26775 original size:16 final size:16
Alignment explanation
Indices: 26738--26774 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
26728 GGAATTTTGA
*
26738 AAAAATTAAAAAAATT
1 AAAAATTAAAAAAACT
26754 AAAAATTAAAAAAACCT
1 AAAAATTAAAAAAA-CT
26771 AAAA
1 AAAA
26775 TCCCAACTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAAATTAAAAAAACT
Found at i:29151 original size:18 final size:18
Alignment explanation
Indices: 29116--29154 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
29106 CTTGAGAAAC
* **
29116 TTTATATCCTTCTGGGAT
1 TTTAAATCCTTCAAGGAT
29134 TTTAAATCCTTCAAGGAT
1 TTTAAATCCTTCAAGGAT
29152 TTT
1 TTT
29155 CATATAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.49
Consensus pattern (18 bp):
TTTAAATCCTTCAAGGAT
Found at i:38937 original size:11 final size:11
Alignment explanation
Indices: 38920--38949 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
38910 ATAATGCTTA
38920 AGATAATCTAC
1 AGATAATCTAC
*
38931 GGATAATCTAC
1 AGATAATCTAC
38942 AGATAATC
1 AGATAATC
38950 ATGCAATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (11 bp):
AGATAATCTAC
Found at i:43108 original size:40 final size:40
Alignment explanation
Indices: 43071--43256 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
43061 GCTACTCGTT
* *
43071 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
43111 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
43151 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
43191 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
43232 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
43257 CATCATTCAA
Statistics
Matches: 133, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
39 3 0.02
40 117 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Done.