Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014705.1 Kokia drynarioides strain JFW-HI SEQ_129744, whole genome shotgun sequence
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: 370394
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1264 original size:86 final size:85
Alignment explanation
Indices: 1120--1432 Score: 344
Period size: 86 Copynumber: 3.7 Consensus size: 85
1110 CGTTTCTACG
*** * *
1120 GATCATGTTCTTTAGCGGCGTTGCGA-GAAAAGCGCCACTAAAGAACATGTTTTTTAGTGGCGTT
1 GATCATGTTCTTTAGCGGCGTTTTTAGGAAAAGCGCCACTAAAGACCATGTTCTTTAGTGGCGTT
* *
1184 TGTATGAAAAGCTCCACTAAA
66 TGT-TGAAAAGCGCCGCTAAA
* * *
1205 GATCATGTTCTTTAGCGGCATTTTTAGGAAAAGCGCCGCTAAAGACCATGTTCTATAGTGGCGTT
1 GATCATGTTCTTTAGCGGCGTTTTTAGGAAAAGCGCCACTAAAGACCATGTTCTTTAGTGGCGTT
* *
1270 TGTTAGGAAAGCGCTGCTAAA
66 TGTT-GAAAAGCGCCGCTAAA
* * * * * *
1291 GACCATGTTCTTTAGTGGCGTTTGTGGGAAAAGCGCCACTAAAGACCATGTTCTTTGGCGGCGTT
1 GATCATGTTCTTTAGCGGCGTTTTTAGGAAAAGCGCCACTAAAGACCATGTTCTTTAGTGGCGTT
*
1356 TGTGTGAAAGGCGCCGCT-AA
66 TGT-TGAAAAGCGCCGCTAAA
* * * * * * *
1376 GATCATGTTTTTTAGCAGCGTTTTTGGGAAAAGC-ACGCTAAAGATCGTGTTCTTTAG
1 GATCATGTTCTTTAGCGGCGTTTTTAGGAAAAGCGCCACTAAAGACCATGTTCTTTAG
1433 CGGTGTTTTT
Statistics
Matches: 191, Mismatches: 34, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
84 18 0.09
85 54 0.28
86 118 0.62
87 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (85 bp):
GATCATGTTCTTTAGCGGCGTTTTTAGGAAAAGCGCCACTAAAGACCATGTTCTTTAGTGGCGTT
TGTTGAAAAGCGCCGCTAAA
Found at i:1441 original size:42 final size:43
Alignment explanation
Indices: 1123--1443 Score: 308
Period size: 43 Copynumber: 7.5 Consensus size: 43
1113 TTCTACGGAT
** * * *
1123 CATGTTCTTTAGCGGCG-TTGCGAGAAAAGCGCCACTAAAGAA
1 CATGTTCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGAC
* * * ** * * *
1165 CATGTTTTTTAGTGGCGTTTGTATGAAAAGCTCCACTAAAGAT
1 CATGTTCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGAC
* *
1208 CATGTTCTTTAGCGGCATTTTTAGGAAAAGCGCCGCTAAAGAC
1 CATGTTCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGAC
* * * *
1251 CATGTTCTATAGTGGCGTTTGTTAGG-AAAGCGCTGCTAAAGAC
1 CATGTTCTTTAGCGGCGTTT-TTGGGAAAAGCGCCGCTAAAGAC
* * *
1294 CATGTTCTTTAGTGGCGTTTGTGGGAAAAGCGCCACTAAAGAC
1 CATGTTCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGAC
* * * * *
1337 CATGTTCTTTGGCGGCGTTTGTGTGAAAGGCGCCGCT-AAGAT
1 CATGTTCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGAC
* * * *
1379 CATGTTTTTTAGCAGCGTTTTTGGGAAAAGC-ACGCTAAAGAT
1 CATGTTCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGAC
* *
1421 CGTGTTCTTTAGCGGTGTTTTTG
1 CATGTTCTTTAGCGGCGTTTTTG
1444 TGACGCCGCG
Statistics
Matches: 234, Mismatches: 41, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
41 4 0.02
42 71 0.30
43 154 0.66
44 5 0.02
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (43 bp):
CATGTTCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGAC
Found at i:1780 original size:7 final size:7
Alignment explanation
Indices: 1744--1796 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
1734 ACAGAACCGA
*
1744 TGACTGT
1 TGACTAT
1751 TGACT-T
1 TGACTAT
*
1757 TGACCAT
1 TGACTAT
* *
1764 TGATTGT
1 TGACTAT
1771 TGACTAT
1 TGACTAT
1778 TGACTAT
1 TGACTAT
*
1785 TGACTGT
1 TGACTAT
1792 TGACT
1 TGACT
1797 TTTTCTTACC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
6 5 0.13
7 33 0.87
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.43
Consensus pattern (7 bp):
TGACTAT
Found at i:1786 original size:21 final size:20
Alignment explanation
Indices: 1744--1798 Score: 83
Period size: 21 Copynumber: 2.7 Consensus size: 20
1734 ACAGAACCGA
1744 TGACTGTTGACTTTGACCAT
1 TGACTGTTGACTTTGACCAT
* *
1764 TGATTGTTGACTATTGACTAT
1 TGACTGTTGACT-TTGACCAT
1785 TGACTGTTGACTTT
1 TGACTGTTGACTTT
1799 TTCTTACCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (20 bp):
TGACTGTTGACTTTGACCAT
Found at i:2352 original size:83 final size:83
Alignment explanation
Indices: 2209--2371 Score: 299
Period size: 83 Copynumber: 2.0 Consensus size: 83
2199 ATTCCTCTTA
2209 AAATGAGGTACGTAAAATACATTCTTTAAAACAATCTTCCTAATATTATCAAAGTGTAAAATAAC
1 AAATGAGGTACGTAAAATACATTCTTTAAAACAATCTTCCTAATATTATCAAAGTGTAAAATAAC
*
2274 TTCTCCCATTGCTTTTGT
66 TTCTCCCATTACTTTTGT
* *
2292 AAATGAGGTACGTAAAATACATTCTTTAAAACAATCTTTCTAATATTATCAAAGTTTAAAATAAC
1 AAATGAGGTACGTAAAATACATTCTTTAAAACAATCTTCCTAATATTATCAAAGTGTAAAATAAC
2357 TTCTCCCATTACTTT
66 TTCTCCCATTACTTT
2372 AGTTGAAACA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.37
Consensus pattern (83 bp):
AAATGAGGTACGTAAAATACATTCTTTAAAACAATCTTCCTAATATTATCAAAGTGTAAAATAAC
TTCTCCCATTACTTTTGT
Found at i:4857 original size:21 final size:21
Alignment explanation
Indices: 4831--4922 Score: 105
Period size: 21 Copynumber: 4.4 Consensus size: 21
4821 AATAGTGCAG
4831 ACTTCTACCGATACAAGTGAT-
1 ACTTCTACCGATACAAGTG-TC
*
4852 AGTTCTACCGATACAAGTGTC
1 ACTTCTACCGATACAAGTGTC
*
4873 TCTTCTACCGATACAAGTGTC
1 ACTTCTACCGATACAAGTGTC
* * * * *
4894 TCTTCTACTGAAACAAGTCTA
1 ACTTCTACCGATACAAGTGTC
4915 ACTTCTAC
1 ACTTCTAC
4923 TGCACTAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 1 0.02
21 61 0.98
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGTC
Found at i:5297 original size:18 final size:18
Alignment explanation
Indices: 5274--5313 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
5264 ATGCTTTACT
5274 ACATTCAACATTCCATAA
1 ACATTCAACATTCCATAA
5292 ACATTCAACATTCCATAA
1 ACATTCAACATTCCATAA
5310 ACAT
1 ACAT
5314 AACAAGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (18 bp):
ACATTCAACATTCCATAA
Found at i:9749 original size:17 final size:17
Alignment explanation
Indices: 9729--9761 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9719 TTTAAGGACT
9729 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
9746 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
9762 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:10070 original size:50 final size:52
Alignment explanation
Indices: 10016--10112 Score: 128
Period size: 52 Copynumber: 1.9 Consensus size: 52
10006 AGCAACTTAA
* * *
10016 ATGTTAGTTAAA-TATGCATCA-TAAATCCTA-TCATGCATTTTGTAACTCCC
1 ATGTTAGTTAAAGTATGAATCATTAAAT-CAAGTCATGCATTTAGTAACTCCC
*
10066 ATGTTAGTTAAAGTTTGAATCATTAAATCAAGTCATGCATTTAGTAA
1 ATGTTAGTTAAAGTATGAATCATTAAATCAAGTCATGCATTTAGTAA
10113 TTCATTAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
50 12 0.30
51 9 0.22
52 19 0.47
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (52 bp):
ATGTTAGTTAAAGTATGAATCATTAAATCAAGTCATGCATTTAGTAACTCCC
Found at i:12280 original size:18 final size:17
Alignment explanation
Indices: 12259--12292 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12249 TCACAATTTC
12259 TTTCAATCTCTCTTTCTT
1 TTTCAATCTCT-TTTCTT
*
12277 TTTCATTCTCTTTTCT
1 TTTCAATCTCTTTTCT
12293 CACACACTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCAATCTCTTTTCTT
Found at i:13317 original size:28 final size:27
Alignment explanation
Indices: 13275--13346 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
13265 TTTAATTCAA
13275 ATTTTTCTTCTTTTTTTCCAA-ACTTCG
1 ATTTTT-TTCTTTTTTTCCAATACTTCG
* * *
13302 AATTTTTTTTTATTTTTTTCAATATTTCG
1 -ATTTTTTTCT-TTTTTTCCAATACTTCG
13331 ATTTTTTTCTTTTTTT
1 ATTTTTTTCTTTTTTT
13347 AAATTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
27 9 0.24
28 24 0.63
29 5 0.13
ACGTcount: A:0.15, C:0.12, G:0.03, T:0.69
Consensus pattern (27 bp):
ATTTTTTTCTTTTTTTCCAATACTTCG
Found at i:13993 original size:50 final size:50
Alignment explanation
Indices: 13906--14036 Score: 147
Period size: 50 Copynumber: 2.6 Consensus size: 50
13896 TGCATGACTT
*
13906 GATTTAATGATGCAAACTTTAACTAACATGGGAGTTACATAATGCATGAT-AG
1 GATTT-ATGATGCAAA-TTTAACTAACATGGAAGTTACATAATGCATG-TCAG
* * * * *
13958 GATTTATGATGCATATTTAACTAAGATGTAAGTTACTTAATGCATGTCAT
1 GATTTATGATGCAAATTTAACTAACATGGAAGTTACATAATGCATGTCAG
* *
14008 TATTTATGATGCAAACTTAACTAATCATG
1 GATTTATGATGCAAATTTAACTAA-CATG
14037 AGAGTTAATG
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
49 1 0.01
50 49 0.73
51 12 0.18
52 5 0.07
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (50 bp):
GATTTATGATGCAAATTTAACTAACATGGAAGTTACATAATGCATGTCAG
Found at i:14129 original size:33 final size:34
Alignment explanation
Indices: 14078--14142 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
14068 ACTTTATTAA
* *
14078 ATGTAGATCACATAATGCATGTCATATTTAAAAG
1 ATGTAGATCACATAATGCATGACATAATTAAAAG
*
14112 ATGTAGATTA-ATAATGCATGACATAATTAAA
1 ATGTAGATCACATAATGCATGACATAATTAAA
14143 TCACAATCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 19 0.68
34 9 0.32
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (34 bp):
ATGTAGATCACATAATGCATGACATAATTAAAAG
Found at i:14270 original size:17 final size:17
Alignment explanation
Indices: 14239--14271 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
14229 CAAACACTTA
14239 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
14256 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
14272 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:19746 original size:8 final size:7
Alignment explanation
Indices: 19719--19766 Score: 51
Period size: 7 Copynumber: 6.4 Consensus size: 7
19709 TATGTGAGGA
19719 TTTTTAT
1 TTTTTAT
19726 TTTTTAT
1 TTTTTAT
*
19733 ATTTTAT
1 TTTTTAT
19740 TTATTTAT
1 TT-TTTAT
*
19748 TTATTAT
1 TTTTTAT
19755 TATTATTAT
1 T-TT-TTAT
19764 TTT
1 TTT
19767 ATGAAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
7 19 0.56
8 10 0.29
9 5 0.15
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAT
Found at i:23561 original size:20 final size:21
Alignment explanation
Indices: 23524--23564 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
23514 TTTAAAAGTA
*
23524 AAAAATATGACATAAATAAAT
1 AAAAATATCACATAAATAAAT
*
23545 AAAAATATCA-ATGAATAAAT
1 AAAAATATCACATAAATAAAT
23565 GAAGACAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (21 bp):
AAAAATATCACATAAATAAAT
Found at i:23625 original size:21 final size:20
Alignment explanation
Indices: 23593--23632 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
23583 AGCATGAAAA
23593 ATAAAAAATAAATAAAATTC
1 ATAAAAAATAAATAAAATTC
23613 ATAAAACAATAAATAAAATT
1 ATAAAA-AATAAATAAAATT
23633 AAATAAAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (20 bp):
ATAAAAAATAAATAAAATTC
Found at i:23996 original size:15 final size:14
Alignment explanation
Indices: 23976--24042 Score: 57
Period size: 15 Copynumber: 4.4 Consensus size: 14
23966 TTAGGCATGA
23976 AAATAAATCACAAAT
1 AAATAAATCA-AAAT
23991 AAATAAAT-AATCAAT
1 AAATAAATCAA--AAT
24006 AAATTAAATGTCAAAAT
1 AAA-TAAA--TCAAAAT
24023 AAATAAAT-AAATAT
1 AAATAAATCAAA-AT
24037 AAATAA
1 AAATAA
24043 TAATAAAAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
13 4 0.09
14 10 0.22
15 14 0.31
16 8 0.18
17 6 0.13
18 1 0.02
19 2 0.04
ACGTcount: A:0.67, C:0.06, G:0.01, T:0.25
Consensus pattern (14 bp):
AAATAAATCAAAAT
Found at i:24044 original size:21 final size:21
Alignment explanation
Indices: 23993--24049 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
23983 TCACAAATAA
23993 ATAAATAATCAATAAATTAAAT
1 ATAAATAAT-AATAAATTAAAT
* *
24015 GTCAA-AATAAATAAA-TAAAT
1 ATAAATAAT-AATAAATTAAAT
24035 ATAAATAATAATAAA
1 ATAAATAATAATAAA
24050 AACGAACTCC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 14 0.48
21 12 0.41
22 3 0.10
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (21 bp):
ATAAATAATAATAAATTAAAT
Found at i:24700 original size:20 final size:19
Alignment explanation
Indices: 24653--24707 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
24643 TCAAATCTCG
24653 TTAA-ATTTTTAATATCTT
1 TTAATATTTTTAATATCTT
* * *
24671 TTATTGTTTTTATTTATCTT
1 TTAATATTTTTA-ATATCTT
24691 TTAATATTTTGTAATAT
1 TTAATATTTT-TAATAT
24708 ACAACTGTAG
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
18 3 0.11
19 6 0.21
20 17 0.61
21 2 0.07
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (19 bp):
TTAATATTTTTAATATCTT
Found at i:25890 original size:15 final size:15
Alignment explanation
Indices: 25858--25903 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
25848 AAGTCAAATC
*
25858 ATTTTTAATGAA-AAT
1 ATTTTTAAT-AATATT
25873 ATTTATTAA-AATATT
1 ATTT-TTAATAATATT
25888 ATTTTTAATAATATT
1 ATTTTTAATAATATT
25903 A
1 A
25904 GCATGACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 17 0.63
16 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTTTAATAATATT
Found at i:26309 original size:22 final size:20
Alignment explanation
Indices: 26274--26325 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
26264 TATTATGTTT
26274 TAATTTTTTTTAATATTTATA
1 TAATTTTTTTTAATATTTA-A
*
26295 TTATTTTATTTTAATATTTAA
1 TAATTTT-TTTTAATATTTAA
26316 TAATTTTTTT
1 TAATTTTTTT
26326 ACATTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 3 0.11
21 13 0.46
22 12 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TAATTTTTTTTAATATTTAA
Found at i:26325 original size:24 final size:24
Alignment explanation
Indices: 26277--26352 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
26267 TATGTTTTAA
*
26277 TTTT-TTTTAATATTT-AT-ATTA
1 TTTTATTTTAATATTTAATAATTT
26298 TTTTATTTTAATATTTAATAATTT
1 TTTTATTTTAATATTTAATAATTT
*
26322 TTTTACATTTT--TATTTATTGAATTT
1 TTTT--ATTTTAATATTTAAT-AATTT
26347 TTTTAT
1 TTTTAT
26353 ATAATCATGC
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
21 4 0.09
22 11 0.23
23 4 0.09
24 14 0.30
25 9 0.19
26 5 0.11
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (24 bp):
TTTTATTTTAATATTTAATAATTT
Found at i:27790 original size:13 final size:13
Alignment explanation
Indices: 27759--27792 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
27749 TGTTCAGATC
27759 TTATATTTTATAT
1 TTATATTTTATAT
**
27772 AAATATTTTATAT
1 TTATATTTTATAT
27785 TTATATTT
1 TTATATTT
27793 GTTCGCTAAC
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATATTTTATAT
Found at i:28097 original size:14 final size:14
Alignment explanation
Indices: 28078--28106 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28068 ATCAAGCAGC
28078 TTATGTTCCTATAG
1 TTATGTTCCTATAG
28092 TTATGTTCCTATAG
1 TTATGTTCCTATAG
28106 T
1 T
28107 CCTGCATGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.52
Consensus pattern (14 bp):
TTATGTTCCTATAG
Found at i:28450 original size:164 final size:161
Alignment explanation
Indices: 28246--28599 Score: 430
Period size: 164 Copynumber: 2.2 Consensus size: 161
28236 TAAAAATTAA
* * * *
28246 AATTGAATAAATCTGTTTC-GAGATTTATTCTCGCCGTTCAACAAATTTTATTTTATTTTGATTT
1 AATTGAATAATTTTGTTTCAG-GATTTATTCCCGCCGTTCAACAAATTTTATTCTATTTTGATTT
* * * * * *
28310 TGTTTCCAAATAAGAATTAATTGAATAATTCTGTTT-TGAGA-TTTATTTCC-GCCGTTCAATAG
65 TGTTCCCAAACAAGAATTAATTAAATAATTCTGTTTCAG-GATTTTATTTCCTACCGTTCAACAG
*
28372 ATTTTATACT-ATTTTAATTTTGTTTCCAAATAAGAATT
129 A----AT--TGATTTTAATTTTGTTTCCAAACAAGAATT
*
28410 AATTGAATAATTTTGTTTCAGGATTTATTCCCTCCGTTCAACAAATTTTATTCTATTTTGATTTT
1 AATTGAATAATTTTGTTTCAGGATTTATTCCCGCCGTTCAACAAATTTTATTCTATTTTGATTTT
* *
28475 GTTCCCAAACAATAATTAATTAAATAATTCTGTTTCAGGATTTTTTTTCCTACCGTTCAACAGAA
66 GTTCCCAAACAAGAATTAATTAAATAATTCTGTTTCAGGATTTTATTTCCTACCGTTCAACAGAA
* *
28540 TTGATTTTGATTTTGTTTTCAAACAAGAATT
131 TTGATTTTAATTTTGTTTCCAAACAAGAATT
* * *
28571 AATTAAACAATTTTGATTCAGGATTTATT
1 AATTGAATAATTTTGTTTCAGGATTTATT
28600 TCTACCGTTC
Statistics
Matches: 166, Mismatches: 19, Indels: 13
0.84 0.10 0.07
Matches are distributed among these distances:
160 1 0.01
161 51 0.31
162 2 0.01
164 91 0.55
165 10 0.06
166 11 0.07
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.46
Consensus pattern (161 bp):
AATTGAATAATTTTGTTTCAGGATTTATTCCCGCCGTTCAACAAATTTTATTCTATTTTGATTTT
GTTCCCAAACAAGAATTAATTAAATAATTCTGTTTCAGGATTTTATTTCCTACCGTTCAACAGAA
TTGATTTTAATTTTGTTTCCAAACAAGAATT
Found at i:28510 original size:82 final size:82
Alignment explanation
Indices: 28246--28599 Score: 389
Period size: 82 Copynumber: 4.4 Consensus size: 82
28236 TAAAAATTAA
* * *
28246 AATTGAATAAATCTGTTTC-GAGATTTATTCTCGCCGTTCAACAAATTTTATTTTATTTTGATTT
1 AATTGAATAATTCTGTTTCAG-GATTTATTCCCGCCGTTCAACAAATTTTATTCTATTTTGATTT
*
28310 TGTTTCCAAATAAGAATT
65 TGTTTCCAAACAAGAATT
* * * * * *
28328 AATTGAATAATTCTGTTT-TGAGATTTATTTCCGCCGTTCAATAGATTTTATACTATTTTAATTT
1 AATTGAATAATTCTGTTTCAG-GATTTATTCCCGCCGTTCAACAAATTTTATTCTATTTTGATTT
*
28392 TGTTTCCAAATAAGAATT
65 TGTTTCCAAACAAGAATT
* *
28410 AATTGAATAATTTTGTTTCAGGATTTATTCCCTCCGTTCAACAAATTTTATTCTATTTTGATTTT
1 AATTGAATAATTCTGTTTCAGGATTTATTCCCGCCGTTCAACAAATTTTATTCTATTTTGATTTT
* *
28475 GTTCCCAAACAATAATT
66 GTTTCCAAACAAGAATT
* * ** * *
28492 AATTAAATAATTCTGTTTCAGGATTTTTTTTCCTACCGTTCAACAGA----ATT-GATTTTGATT
1 AATTGAATAATTCTGTTTCAGGA--TTTATTCCCGCCGTTCAACAAATTTTATTCTATTTTGATT
*
28552 TTGTTTTCAAACAAGAATT
64 TTGTTTCCAAACAAGAATT
* * * *
28571 AATTAAACAATTTTGATTCAGGATTTATT
1 AATTGAATAATTCTGTTTCAGGATTTATT
28600 TCTACCGTTC
Statistics
Matches: 235, Mismatches: 33, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
77 5 0.02
79 45 0.19
80 3 0.01
82 163 0.69
83 1 0.00
84 18 0.08
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.46
Consensus pattern (82 bp):
AATTGAATAATTCTGTTTCAGGATTTATTCCCGCCGTTCAACAAATTTTATTCTATTTTGATTTT
GTTTCCAAACAAGAATT
Found at i:28963 original size:6 final size:6
Alignment explanation
Indices: 28954--29023 Score: 74
Period size: 6 Copynumber: 12.0 Consensus size: 6
28944 GATTTATTTC
* **
28954 TTAAAT TTAAAT TT-ACT TTAAAT TTAAAT TTAAAT TT-GTT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
29000 TTAAAT TT-AGT TTAAAT TTGAAAT
1 TTAAAT TTAAAT TTAAAT TT-AAAT
29024 AATTTTACAC
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
5 11 0.21
6 37 0.71
7 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:28975 original size:11 final size:11
Alignment explanation
Indices: 28957--29008 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
28947 TTATTTCTTA
28957 AATTTAAATTT
1 AATTTAAATTT
*
28968 ACTTTAAATTT
1 AATTTAAATTT
28979 AAATTTAAATTT
1 -AATTTAAATTT
**
28991 GTTTTAAATTT
1 AATTTAAATTT
29002 AAATTTA
1 -AATTTA
29009 GTTTAAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 19 0.58
12 14 0.42
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:28981 original size:23 final size:23
Alignment explanation
Indices: 28954--29008 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
28944 GATTTATTTC
28954 TTAAATTTAAATTTACTTTAAAT
1 TTAAATTTAAATTTACTTTAAAT
**
28977 TTAAATTTAAATTTGTTTTAAAT
1 TTAAATTTAAATTTACTTTAAAT
29000 TTAAATTTA
1 TTAAATTTA
29009 GTTTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
TTAAATTTAAATTTACTTTAAAT
Found at i:28996 original size:17 final size:17
Alignment explanation
Indices: 28976--29023 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
28966 TTACTTTAAA
28976 TTTAAATTTAAATTT-G
1 TTTAAATTTAAATTTAG
28992 TTTTAAATTTAAATTTAG
1 -TTTAAATTTAAATTTAG
29010 TTTAAATTTGAAAT
1 TTTAAATTT-AAAT
29024 AATTTTACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 24 0.83
18 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAG
Found at i:29030 original size:17 final size:17
Alignment explanation
Indices: 28954--29030 Score: 66
Period size: 17 Copynumber: 4.5 Consensus size: 17
28944 GATTTATTTC
* **
28954 TTAAATTTAAATTTACT
1 TTAATTTTAAATTTAAA
*
28971 TTAAATTTAAATTTAAA
1 TTAATTTTAAATTTAAA
**
28988 TTTGTTTTAAATTTAAA
1 TTAATTTTAAATTTAAA
* *
29005 TTTAGTTTAAATTTGAAA
1 TTAATTTTAAATTT-AAA
29023 -TAATTTTA
1 TTAATTTTA
29031 CACTTAAAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
17 47 0.94
18 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (17 bp):
TTAATTTTAAATTTAAA
Found at i:29752 original size:3 final size:3
Alignment explanation
Indices: 29733--29845 Score: 57
Period size: 3 Copynumber: 35.7 Consensus size: 3
29723 TAAGAATCAT
* * * *
29733 TAA TAA TTAA TAT TAA TAA TAA TAA TAA TAA TAAA TAA CAA -AT TTA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* * * * * * *
29779 TAA TAA TGA TAT TAA TAA GTAT TAA TAA CAG TAA TTAA TAA TACC TAT
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA -TAA TAA TA-A TAA
29827 TAA TAA TTAA TAA TTAA TA
1 TAA TAA -TAA TAA -TAA TA
29846 TTTAGTAATA
Statistics
Matches: 82, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
2 1 0.01
3 62 0.76
4 19 0.23
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:29854 original size:14 final size:14
Alignment explanation
Indices: 29718--29845 Score: 61
Period size: 13 Copynumber: 9.0 Consensus size: 14
29708 TTCAAAACGT
* *
29718 ATTAATAA-GAATC
1 ATTAATAATTAATA
29731 ATTAATAATTAAT-
1 ATTAATAATTAATA
29744 ATTAATAA-TAATA
1 ATTAATAATTAATA
* *
29757 ATAATAATAAATAACAA
1 AT--TAATAATTAA-TA
*
29774 ATTTATAA-TAATGA
1 ATTAATAATTAAT-A
* *
29788 TATTAATAAGTATTA
1 -ATTAATAATTAATA
*
29803 ATAACAGTAATTAATA
1 ATTA-A-TAATTAATA
*
29819 A-TACCT-ATTAATA
1 ATTA-ATAATTAATA
29832 ATTAATAATTAATA
1 ATTAATAATTAATA
29846 TTTAGTAATA
Statistics
Matches: 90, Mismatches: 12, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
12 4 0.04
13 27 0.30
14 20 0.22
15 22 0.24
16 14 0.16
17 3 0.03
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (14 bp):
ATTAATAATTAATA
Found at i:31050 original size:29 final size:29
Alignment explanation
Indices: 30998--31084 Score: 131
Period size: 30 Copynumber: 2.9 Consensus size: 29
30988 GGAGGTCTCT
30998 AAACTGTCCAAAAATTCCATTTTTGACCCCA
1 AAACT-TCCAAAAATTCCATTTTT-ACCCCA
*
31029 AAACTTCCAAAAATTCCTTTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
31059 AAACTTCC-AAAATTCCATTTTTACCC
1 AAACTTCCAAAAATTCCATTTTTACCC
31085 TCGAACCTCC
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
28 4 0.08
29 13 0.25
30 31 0.58
31 5 0.09
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCA
Found at i:31230 original size:59 final size:59
Alignment explanation
Indices: 31115--31247 Score: 135
Period size: 58 Copynumber: 2.3 Consensus size: 59
31105 CCAAAACTCT
* * * *
31115 TAAAAATTACCATTTTACCCTCGAATGACCAAAAATTCTATTTTTAATCTCGATTTTTC
1 TAAAAATTACCATTTTACCCTCAAATGACCAAAAATTCCATTTTAAATCTCAATTTTTC
* * * * *
31174 TAAAAATTATCGTTTTACCCTCAAATG-TCTAAAATTCCATTTTAAA-CTCCAAATTTTC
1 TAAAAATTACCATTTTACCCTCAAATGACCAAAAATTCCATTTTAAATCT-CAATTTTTC
***
31232 CCGAAATTACCATTTT
1 TAAAAATTACCATTTT
31248 GCCCCCGAGA
Statistics
Matches: 59, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
57 2 0.03
58 33 0.56
59 24 0.41
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.40
Consensus pattern (59 bp):
TAAAAATTACCATTTTACCCTCAAATGACCAAAAATTCCATTTTAAATCTCAATTTTTC
Found at i:31269 original size:28 final size:28
Alignment explanation
Indices: 31235--31293 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
31225 AATTTTCCCG
* *
31235 AAATTACCATTTTGCCCCCGAGAATCCA
1 AAATTACCATTTTACCCCCAAGAATCCA
* *
31263 AAATTACCATTTTACCCTCAAGTATCCA
1 AAATTACCATTTTACCCCCAAGAATCCA
31291 AAA
1 AAA
31294 AAGTCTCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (28 bp):
AAATTACCATTTTACCCCCAAGAATCCA
Found at i:43125 original size:115 final size:114
Alignment explanation
Indices: 42957--43163 Score: 342
Period size: 115 Copynumber: 1.8 Consensus size: 114
42947 GGCTCAAAGC
* *
42957 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGAAGGTCAAAGTAATAAAATGG
1 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGAAGGGCAAAGCAATAAAA-GG
43022 CTAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGTTCGATAT
65 CTAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGTTCGATAT
* * * *
43072 GAGCAAATCTTTGAATCCCAGCTTCCTGATGAGATACTGAGAAGTAGGGCAAAGCAATAAAAGGT
1 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGAAGGGCAAAGCAATAAAAGGC
*
43137 TAGCTTCCTGATGAGATACTGAGAAGT
66 TAGCTTCCTGATGAGATACAGAGAAGT
43164 GGACCAAATT
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
114 28 0.33
115 57 0.67
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (114 bp):
GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGAAGGGCAAAGCAATAAAAGGC
TAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGTTCGATAT
Found at i:43558 original size:206 final size:203
Alignment explanation
Indices: 43026--43661 Score: 756
Period size: 206 Copynumber: 3.2 Consensus size: 203
43016 AAATGGCTAG
* * * ** * * * *
43026 CTTCCTGATGAGATACAGAGAAGTATACCAACTC--AGGGTTCGATATGAGCAAATCTTTGAATC
1 CTTCCTGATGAGATACTGAGAAGAAGACCAACTCAAAACGCTCGATGTGAGCAAATCTTCGAACC
* * *
43089 CCAGCTTCCTGATGAGATACTGAGAAGTAGGGCAAAGCAATAAAA-GGTTAGCTTCCTGATGAGA
66 CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGA
* * *
43153 TACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTAC-------CGGATTGAAACAAGTAAG
131 TACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAT
*
43211 GCGGTCAT
196 ACGGTCAT
* * * ** *
43219 CTTCCTGATGATATACAGAGAAGAATACCAACTC--AGGGCTCAATGTGAGCAAATCTTCGAACC
1 CTTCCTGATGAGATACTGAGAAGAAGACCAACTCAAAACGCTCGATGTGAGCAAATCTTCGAACC
* * *
43282 CCAGATTCCTGATGAGATACTGAGAAGCATGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGA
66 CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGA
* *
43347 TACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGGTTGAAACAAGCGAT
131 TACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAT
43412 ACGGTCAT
196 ACGGTCAT
* * *
43420 CTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCAA
1 CTTCCTGATGAGATACTGAGAAGAAGACCAACTCAAA---ACGCTCGATGTGAGCAAATCTTCGA
* * *
43485 ACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTTGAAGCAATAAAATGGTTAGCTTCCTGTTG
63 ACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATG
* * * * * * **
43550 AAATACTGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACACAGAGAAGTGGATCAAAACAAGT
128 AGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGT
* *
43615 GATATGGTCGT
193 GATACGGTCAT
* *
43626 CTTCCTGATGAGATACTAAGAAGAAGGCCAACTCAA
1 CTTCCTGATGAGATACTGAGAAGAAGACCAACTCAA
43662 TGAAACCAGA
Statistics
Matches: 380, Mismatches: 50, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
193 96 0.25
194 57 0.15
201 50 0.13
203 1 0.00
206 176 0.46
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (203 bp):
CTTCCTGATGAGATACTGAGAAGAAGACCAACTCAAAACGCTCGATGTGAGCAAATCTTCGAACC
CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGA
TACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAT
ACGGTCAT
Found at i:44062 original size:17 final size:18
Alignment explanation
Indices: 44022--44066 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
44012 TAGATTAATT
* *
44022 TTTAGATTTATTTCTAAA
1 TTTAAATTTACTTCTAAA
*
44040 TATAAATTTACTT-TAAA
1 TTTAAATTTACTTCTAAA
44057 TTTAAATTTA
1 TTTAAATTTA
44067 AGTTCATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTAAATTTACTTCTAAA
Found at i:44062 original size:23 final size:23
Alignment explanation
Indices: 44036--44086 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
44026 GATTTATTTC
*
44036 TAAATATAAATTTACTTTAAATT
1 TAAATATAAATTCACTTTAAATT
* * *
44059 TAAATTTAAGTTCATTTTAAATT
1 TAAATATAAATTCACTTTAAATT
44082 TAAAT
1 TAAAT
44087 TTGAAATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAATATAAATTCACTTTAAATT
Found at i:44098 original size:23 final size:23
Alignment explanation
Indices: 44051--44108 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
44041 ATAAATTTAC
* *
44051 TTTAAATTTAAATTTAAGTTCAT
1 TTTAAATTTAAATTTAAGATAAT
44074 TTTAAATTTAAATTTGAA-ATAAT
1 TTTAAATTTAAATTT-AAGATAAT
*
44097 TTTAAACTTAAA
1 TTTAAATTTAAA
44109 ACTTTAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 29 0.94
24 2 0.06
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (23 bp):
TTTAAATTTAAATTTAAGATAAT
Found at i:44830 original size:3 final size:3
Alignment explanation
Indices: 44817--44938 Score: 102
Period size: 3 Copynumber: 38.7 Consensus size: 3
44807 TAAGTATCGT
44817 TAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
* * * * * *
44864 CAA -AT TTA TAA TAA TGA TAT TAA TAA GTAT TAA TAA TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA -TAA
* *
44910 TAA TACC TAT TAA TAA TTAA TAA TTAA TA
1 TAA TA-A TAA TAA TAA -TAA TAA -TAA TA
44939 TTTAGTAATA
Statistics
Matches: 97, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
2 1 0.01
3 77 0.79
4 19 0.20
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:44830 original size:10 final size:9
Alignment explanation
Indices: 44817--44938 Score: 102
Period size: 10 Copynumber: 12.9 Consensus size: 9
44807 TAAGTATCGT
44817 TAATAATTAA
1 TAATAA-TAA
44827 TAATAATAA
1 TAATAATAA
44836 TAATAATAA
1 TAATAATAA
44845 TAATAATAA
1 TAATAATAA
44854 TAATAAATAA
1 TAAT-AATAA
* * *
44864 CAA-ATTTA
1 TAATAATAA
*
44872 TAATAATGA
1 TAATAATAA
*
44881 TATTAATAA
1 TAATAATAA
*
44890 GTATTAATAA
1 -TAATAATAA
44900 TAATAATTAA
1 TAATAA-TAA
* *
44910 TAATACCTAT
1 TAATA-ATAA
44920 TAATAATTAA
1 TAATAA-TAA
44930 TAATTAATA
1 TAA-TAATA
44939 TTTAGTAATA
Statistics
Matches: 92, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
8 5 0.05
9 40 0.43
10 44 0.48
11 3 0.03
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (9 bp):
TAATAATAA
Found at i:44947 original size:14 final size:14
Alignment explanation
Indices: 44816--44938 Score: 84
Period size: 13 Copynumber: 8.9 Consensus size: 14
44806 ATAAGTATCG
44816 TTAATAATTAATAA
1 TTAATAATTAATAA
44830 -TAATAA-TAATAA
1 TTAATAATTAATAA
44842 -TAATAA-TAATAA
1 TTAATAATTAATAA
* *
44854 -TAATAAATAACAAA
1 TTAATAATTAA-TAA
*
44868 TTTATAA-TAATGATA
1 TTAATAATTAAT-A-A
44883 TTAATAAGTATTAATAA
1 TTAAT-A--ATTAATAA
44900 -TAATAATTAATAA
1 TTAATAATTAATAA
*
44913 -TACCT-ATTAATAA
1 TTA-ATAATTAATAA
44926 TTAATAATTAATA
1 TTAATAATTAATA
44939 TTTAGTAATA
Statistics
Matches: 91, Mismatches: 6, Indels: 24
0.75 0.05 0.20
Matches are distributed among these distances:
12 24 0.26
13 28 0.31
14 16 0.18
15 11 0.12
16 5 0.05
17 1 0.01
18 2 0.02
19 4 0.04
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (14 bp):
TTAATAATTAATAA
Found at i:46088 original size:30 final size:29
Alignment explanation
Indices: 46043--46213 Score: 109
Period size: 30 Copynumber: 5.8 Consensus size: 29
46033 GGAGGTCCCA
* *
46043 AAACTATCAAAAAATTCCATTTTCGACCTCG
1 AAACTTTC-AAAAATTACATTTT-GACCTCG
* *
46074 AAACTTTCAAAAATTATATTTTTACCCTCG
1 AAACTTTCAAAAATTACATTTTGA-CCTCG
* * * *
46104 -AACTTCCAAAAATTTCATTTTTGACCCCA
1 AAACTTTCAAAAATTACA-TTTTGACCTCG
*
46133 AAACTTTCAAAAATTAC-TTTTTACCCTCG
1 AAACTTTCAAAAATTACATTTTGA-CCTCG
* *
46162 -AAC-TTCAAAAAATTTCATTTTTGATCC-CA
1 AAACTTTC-AAAAATTACA-TTTTGA-CCTCG
* *
46191 AAATTTTGAAAAATTACCATTTT
1 AAACTTTCAAAAATTA-CATTTT
46214 ACCCCTGAAT
Statistics
Matches: 108, Mismatches: 22, Indels: 21
0.72 0.15 0.14
Matches are distributed among these distances:
27 3 0.03
28 16 0.15
29 22 0.20
30 56 0.52
31 11 0.10
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (29 bp):
AAACTTTCAAAAATTACATTTTGACCTCG
Found at i:46108 original size:29 final size:29
Alignment explanation
Indices: 46069--46172 Score: 117
Period size: 29 Copynumber: 3.6 Consensus size: 29
46059 CCATTTTCGA
46069 CCTCGAAACTTTCAAAAATTATATTTTTAC
1 CCTCG-AACTTTCAAAAATTATATTTTTAC
*
46099 CCTCGAACTTCCAAAAATT-TCATTTTTGAC
1 CCTCGAACTTTCAAAAATTAT-ATTTTT-AC
* *
46129 CC-CAAAACTTTCAAAAATTA-CTTTTTAC
1 CCTC-GAACTTTCAAAAATTATATTTTTAC
46157 CCTCGAAC-TTCAAAAA
1 CCTCGAACTTTCAAAAA
46173 ATTTCATTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
27 8 0.12
28 8 0.12
29 26 0.41
30 22 0.34
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.35
Consensus pattern (29 bp):
CCTCGAACTTTCAAAAATTATATTTTTAC
Found at i:46176 original size:58 final size:59
Alignment explanation
Indices: 46044--46217 Score: 233
Period size: 58 Copynumber: 2.9 Consensus size: 59
46034 GAGGTCCCAA
* * * * **
46044 AACTATCAAAAAATTCCATTTTCGACCTCGAAACTTTCAAAAATTATATTTTTACCCTCG
1 AACT-TCAAAAAATTTCATTTTTGACCCCAAAACTTTCAAAAATTACCTTTTTACCCTCG
*
46104 AACTTCCAAAAATTTCATTTTTGACCCCAAAACTTTCAAAAATTA-CTTTTTACCCTCG
1 AACTTCAAAAAATTTCATTTTTGACCCCAAAACTTTCAAAAATTACCTTTTTACCCTCG
* * * *
46162 AACTTCAAAAAATTTCATTTTTGATCCCAAAATTTTGAAAAATTACCATTTTACCC
1 AACTTCAAAAAATTTCATTTTTGACCCCAAAACTTTCAAAAATTACCTTTTTACCC
46218 CTGAATGTCC
Statistics
Matches: 102, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
58 53 0.52
59 45 0.44
60 4 0.04
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (59 bp):
AACTTCAAAAAATTTCATTTTTGACCCCAAAACTTTCAAAAATTACCTTTTTACCCTCG
Found at i:46234 original size:29 final size:28
Alignment explanation
Indices: 46199--46376 Score: 96
Period size: 29 Copynumber: 6.2 Consensus size: 28
46189 CAAAATTTTG
46199 AAAAATTACCATTTTACCCCTGAATGTCC
1 AAAAATTACCATTTTACCCC-GAATGTCC
* * * * * *
46228 AAAAATT-CTATTTTTTATCTCGATTTTCT
1 AAAAATTACCA--TTTTACCCCGAATGTCC
*
46257 AAAAATTACCGTTTTACCCTCGAATGT-C
1 AAAAATTACCATTTTACCC-CGAATGTCC
* * *
46285 TAAAATT-CCATTTTAAACCCCAAATTTTCC
1 AAAAATTACCATTTT--ACCCCGAA-TGTCC
* *
46315 CAAAATTACCATTTTACCCCCAA-GAATCC
1 AAAAATTACCATTTTACCCCGAATG--TCC
* * *
46344 -AAAATTACCATTTTGCCCCCAAGTATCC
1 AAAAATTACCATTTTACCCCGAA-TGTCC
46372 AAAAA
1 AAAAA
46377 AGTCTCATTT
Statistics
Matches: 113, Mismatches: 22, Indels: 28
0.69 0.13 0.17
Matches are distributed among these distances:
27 6 0.05
28 41 0.36
29 44 0.39
30 15 0.13
31 7 0.06
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (28 bp):
AAAAATTACCATTTTACCCCGAATGTCC
Found at i:46312 original size:58 final size:58
Alignment explanation
Indices: 46052--46333 Score: 227
Period size: 58 Copynumber: 4.8 Consensus size: 58
46042 AAAACTATCA
** * * *
46052 AAAAATTCCATTTTCGACCTCGAAACTTTCAAAAATTA-TATTTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTTAACC-CCAAATTTTCAAAAATTACCA-TTTTACCCTCGAACTTCC
* * * * *
46111 AAAAATTTCATTTTTGACCCCAAAACTTTCAAAAATTA-CTTTTTACCCTCGAACTTCA
1 AAAAATTCCATTTTTAACCCC-AAATTTTCAAAAATTACCATTTTACCCTCGAACTTCC
* * * *
46169 AAAAATTTCATTTTTGATCCCAAAATTTTGAAAAATTACCATTTTACCC-CTGAA-TGTCC
1 AAAAATTCCATTTTT-AACCCCAAATTTTCAAAAATTACCATTTTACCCTC-GAACT-TCC
* * * * * *
46228 AAAAATTCTATTTTTTATCTC-GATTTTCTAAAAATTACCGTTTTACCCTCGAA-TGT-C
1 AAAAATTCCATTTTTAACCCCAAATTTTC-AAAAATTACCATTTTACCCTCGAACT-TCC
* * *
46285 TAAAATTCCATTTTAAACCCCAAATTTTCCCAAAATTACCATTTTACCC
1 AAAAATTCCATTTTTAACCCCAAATTTT-CAAAAATTACCATTTTACCC
46334 CCAAGAATCC
Statistics
Matches: 182, Mismatches: 32, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
57 21 0.12
58 96 0.53
59 65 0.36
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (58 bp):
AAAAATTCCATTTTTAACCCCAAATTTTCAAAAATTACCATTTTACCCTCGAACTTCC
Found at i:46351 original size:28 final size:28
Alignment explanation
Indices: 46314--46375 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
46304 CCAAATTTTC
46314 CCAAAATTACCATTTTACCCCCAAGAAT
1 CCAAAATTACCATTTTACCCCCAAGAAT
* *
46342 CCAAAATTACCATTTTGCCCCCAAGTAT
1 CCAAAATTACCATTTTACCCCCAAGAAT
46370 CCAAAA
1 CCAAAA
46376 AAGTCTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.39, C:0.32, G:0.05, T:0.24
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCCCAAGAAT
Found at i:49723 original size:19 final size:20
Alignment explanation
Indices: 49692--49744 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
49682 CAAATGCTAG
49692 AATAAATAAAATGCAAGGAC
1 AATAAATAAAATGCAAGGAC
*
49712 AATAAA-AAAATGCAATGAC
1 AATAAATAAAATGCAAGGAC
*
49731 AATGAAATGAAATG
1 AAT-AAATAAAATG
49745 TATGCAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 15 0.52
20 9 0.31
21 5 0.17
ACGTcount: A:0.60, C:0.08, G:0.15, T:0.17
Consensus pattern (20 bp):
AATAAATAAAATGCAAGGAC
Found at i:50172 original size:17 final size:17
Alignment explanation
Indices: 50144--50186 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
50134 CCTCTTCTTC
*
50144 TCTTTCCTTCTTTTCCTG
1 TCTTT-CTTCTTCTCCTG
50162 TCTTTCTTCTTCTCCTG
1 TCTTTCTTCTTCTCCTG
50179 -C-TTCTTCT
1 TCTTTCTTCT
50187 CTTACTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 1 0.04
17 11 0.46
18 5 0.21
ACGTcount: A:0.00, C:0.35, G:0.05, T:0.60
Consensus pattern (17 bp):
TCTTTCTTCTTCTCCTG
Found at i:62215 original size:25 final size:25
Alignment explanation
Indices: 62187--62236 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
62177 CGAATTTTAG
62187 TGGGGAGTATTTATTATAACTTGTT
1 TGGGGAGTATTTATTATAACTTGTT
62212 TGGGGAGTATTTATTATAACTTGTT
1 TGGGGAGTATTTATTATAACTTGTT
62237 GGCCTGAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (25 bp):
TGGGGAGTATTTATTATAACTTGTT
Found at i:67040 original size:30 final size:29
Alignment explanation
Indices: 66997--67119 Score: 99
Period size: 29 Copynumber: 4.3 Consensus size: 29
66987 TCAATATAAT
* *
66997 ATTTAGTACCTAAACTTGACTTTTTTTTTT
1 ATTTGGTACCTAAACTTGA-TTTTTTTTTA
* * *
67027 ATTTGGTATCTAAA-TT-ATTTTTGTTCA
1 ATTTGGTACCTAAACTTGATTTTTTTTTA
* *
67054 ATTTGGTA-TTAAAACTAGATTTTTTTTTA
1 ATTTGGTACCT-AAACTTGATTTTTTTTTA
* * * *
67083 ATTTGATACCTAAGCTTGACTATTTTTTA
1 ATTTGGTACCTAAACTTGATTTTTTTTTA
*
67112 AGTTGGTA
1 ATTTGGTA
67120 TTTAAATTTT
Statistics
Matches: 72, Mismatches: 17, Indels: 9
0.73 0.17 0.09
Matches are distributed among these distances:
26 1 0.01
27 18 0.25
28 2 0.03
29 38 0.53
30 13 0.18
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.53
Consensus pattern (29 bp):
ATTTGGTACCTAAACTTGATTTTTTTTTA
Found at i:67436 original size:61 final size:59
Alignment explanation
Indices: 67330--67501 Score: 206
Period size: 61 Copynumber: 2.9 Consensus size: 59
67320 ATTTAATAAA
* * * *
67330 TTTAGGTACCAAATTGAATCTAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCAAG
1 TTTAGGTATCAAATTGGATCCAAAAAAAGTTTA-GTACCAAATTAAGAAAAAATATCAAG
* *
67390 TTTAGGTATCAAATTGGGTCCAAAAAAAGGTTTAGCTACCAAATTAAGAAAAATTATCAAG
1 TTTAGGTATCAAATTGGATCCAAAAAAA-GTTTAG-TACCAAATTAAGAAAAAATATCAAG
* *
67451 TTCAGATATCAAATTGGAT-CAAAAAATA-TTTAAGTACCAAATTAA-AAAAAA
1 TTTAGGTATCAAATTGGATCCAAAAAA-AGTTT-AGTACCAAATTAAGAAAAAA
67502 CGTATTAATT
Statistics
Matches: 98, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
58 5 0.05
59 14 0.14
60 34 0.35
61 45 0.46
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.27
Consensus pattern (59 bp):
TTTAGGTATCAAATTGGATCCAAAAAAAGTTTAGTACCAAATTAAGAAAAAATATCAAG
Found at i:67514 original size:59 final size:57
Alignment explanation
Indices: 67328--67523 Score: 164
Period size: 60 Copynumber: 3.3 Consensus size: 57
67318 ACATTTAATA
* * * *
67328 AATTTAGGTACCAAATTGAATCTAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCA-
1 AATTCAGGTATCAAATTGGATC-AAAAAAAGTTTAAGTACCAAATTAA-AAAAAA-GT-AT
* * * * *
67388 AGTTTAGGTATCAAATTGGGTCCAAAAAAAGGTTT-AGCTACCAAATTAAGAAAAATTAT
1 AATTCAGGTATCAAATTGGAT-CAAAAAAA-GTTTAAG-TACCAAATTAAAAAAAAGTAT
*
67447 CAAGTTCAGATATCAAATTGGATCAAAAAATA-TTTAAGTACCAAATTAAAAAAAACGTATT
1 -AA-TTCAGGTATCAAATTGGATCAAAAAA-AGTTTAAGTACCAAATTAAAAAAAA-GTA-T
*
67508 AATTCAGGTACCAAAT
1 AATTCAGGTATCAAAT
67524 ATTATATTAA
Statistics
Matches: 111, Mismatches: 15, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
58 1 0.01
59 32 0.29
60 44 0.40
61 34 0.31
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (57 bp):
AATTCAGGTATCAAATTGGATCAAAAAAAGTTTAAGTACCAAATTAAAAAAAAGTAT
Found at i:79300 original size:13 final size:13
Alignment explanation
Indices: 79282--79306 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
79272 AATATCAGAA
79282 AAAAAGGGAGGAT
1 AAAAAGGGAGGAT
79295 AAAAAGGGAGGA
1 AAAAAGGGAGGA
79307 AATTTCTTTT
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:0.56, C:0.00, G:0.40, T:0.04
Consensus pattern (13 bp):
AAAAAGGGAGGAT
Found at i:79767 original size:20 final size:21
Alignment explanation
Indices: 79742--79782 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
79732 GCAAGTATGA
*
79742 TTTTTTATTTTATC-TGAGTT
1 TTTTTTATGTTATCTTGAGTT
79762 TTTTTTATGTTATCTTGAGTT
1 TTTTTTATGTTATCTTGAGTT
79783 ATGGAATGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.15, C:0.05, G:0.12, T:0.68
Consensus pattern (21 bp):
TTTTTTATGTTATCTTGAGTT
Found at i:85318 original size:23 final size:25
Alignment explanation
Indices: 85259--85318 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
85249 AGATTTGGAG
85259 ACCTTATCTTTATGGGGAGAAGTGC
1 ACCTTATCTTTATGGGGAGAAGTGC
85284 ACCTTATCTTTATGGGGAGAAGTGC
1 ACCTTATCTTTATGGGGAGAAGTGC
85309 A-C-TATCTTTA
1 ACCTTATCTTTA
85319 CTAACCATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 8 0.23
24 1 0.03
25 26 0.74
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (25 bp):
ACCTTATCTTTATGGGGAGAAGTGC
Found at i:90620 original size:20 final size:20
Alignment explanation
Indices: 90593--90648 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
90583 GGGGCACCAA
90593 AGTGCATTCAGGGGCATGAG
1 AGTGCATTCAGGGGCATGAG
* * *
90613 TGTTCATTCA-GGGCATTAG
1 AGTGCATTCAGGGGCATGAG
*
90632 AGTGCATTCAGAGGCAT
1 AGTGCATTCAGGGGCAT
90649 CGAAGTGTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.27
Consensus pattern (20 bp):
AGTGCATTCAGGGGCATGAG
Found at i:90655 original size:20 final size:18
Alignment explanation
Indices: 90592--90655 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 18
90582 TGGGGCACCA
90592 AAGTGCATTCAGGGGCATG
1 AAGTGCATTCA-GGGCATG
*
90611 -AGTGTTCATTCAGGGCATT
1 AAGTG--CATTCAGGGCATG
90630 AGAGTGCATTCAGAGGCATCG
1 A-AGTGCATTCAG-GGCAT-G
90651 AAGTG
1 AAGTG
90656 TAATCAGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
18 4 0.11
19 13 0.35
20 15 0.41
21 5 0.14
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.25
Consensus pattern (18 bp):
AAGTGCATTCAGGGCATG
Found at i:93125 original size:19 final size:20
Alignment explanation
Indices: 93101--93149 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
93091 TTATTCCAAA
*
93101 AAAATAATTTTAAT-TTTTT
1 AAAATAATTTTAATAATTTT
93120 AAAATAATTTTAATAATTTT
1 AAAATAATTTTAATAATTTT
*
93140 AAAATCATTT
1 AAAATAATTT
93150 GCTGAAGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAATAATTTTAATAATTTT
Found at i:93787 original size:18 final size:18
Alignment explanation
Indices: 93766--93833 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
93756 TACTTTTATT
93766 TATATTAATTATTTAAAA
1 TATATTAATTATTTAAAA
*
93784 TATATTTAAATATTTAGATTAATTTA
1 TATA-TTAATTATTT--A--AA---A
93810 TATATTAATTATTTAAAA
1 TATATTAATTATTTAAAA
93828 TATATT
1 TATATT
93834 TAAAAATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
18 11 0.28
19 9 0.22
21 3 0.08
23 3 0.08
25 9 0.22
26 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (18 bp):
TATATTAATTATTTAAAA
Found at i:93805 original size:24 final size:23
Alignment explanation
Indices: 93778--93858 Score: 62
Period size: 24 Copynumber: 3.6 Consensus size: 23
93768 TATTAATTAT
93778 TTAAAATATATTTAAATATTTAGA
1 TTAAAATATATTTAAA-ATTTAGA
** *
93802 TTAATTTATATATT--AA-TTA-T
1 TTAAAATATAT-TTAAAATTTAGA
93822 TTAAAATATATTTAAAAATTTAGA
1 TTAAAATATATTT-AAAATTTAGA
**
93846 TTAATTTATATTT
1 TTAAAATATATTT
93859 CATATCATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
19 2 0.05
20 9 0.21
21 3 0.07
22 3 0.07
23 4 0.09
24 20 0.47
25 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAAAATATATTTAAAATTTAGA
Found at i:93817 original size:44 final size:44
Alignment explanation
Indices: 93766--93856 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
93756 TACTTTTATT
*
93766 TATATTAATTATTTAAAATATATTTAAATATTTAGATTAATTTA
1 TATATTAATTATTTAAAATATATTTAAAAATTTAGATTAATTTA
93810 TATATTAATTATTTAAAATATATTTAAAAATTTAGATTAATTTA
1 TATATTAATTATTTAAAATATATTTAAAAATTTAGATTAATTTA
93854 TAT
1 TAT
93857 TTCATATCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (44 bp):
TATATTAATTATTTAAAATATATTTAAAAATTTAGATTAATTTA
Found at i:95185 original size:27 final size:26
Alignment explanation
Indices: 95156--95205 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
95146 GTGAAAGTGT
* *
95156 TTTTTACATAGTTGTCAAGAAAGCAC
1 TTTTTACATAGTTGCCAAAAAAGCAC
*
95182 TTTTTGCATAGTTGCCAAAAAAGC
1 TTTTTACATAGTTGCCAAAAAAGC
95206 GCCTCTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (26 bp):
TTTTTACATAGTTGCCAAAAAAGCAC
Found at i:96695 original size:22 final size:20
Alignment explanation
Indices: 96646--96702 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 20
96636 ATGATTATTG
96646 ATAATTATTTTATTTAATTT
1 ATAATTATTTTATTTAATTT
*
96666 AAAGATTATTATGT-TTTAATTT
1 ATA-ATTATT-T-TATTTAATTT
*
96688 CATAATTATATTATT
1 -ATAATTATTTTATT
96703 AGTGAATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
20 3 0.10
21 9 0.31
22 14 0.48
23 3 0.10
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (20 bp):
ATAATTATTTTATTTAATTT
Found at i:104257 original size:16 final size:16
Alignment explanation
Indices: 104236--104266 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
104226 ATTGCATATG
104236 TCTAATCGATCCCTTC
1 TCTAATCGATCCCTTC
*
104252 TCTAATCGGTCCCTT
1 TCTAATCGATCCCTT
104267 TGCTAGCTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.35, G:0.10, T:0.39
Consensus pattern (16 bp):
TCTAATCGATCCCTTC
Found at i:104417 original size:56 final size:56
Alignment explanation
Indices: 104351--104462 Score: 154
Period size: 56 Copynumber: 2.0 Consensus size: 56
104341 AAGAAAAAAG
*
104351 AATCAATTGGAAATGATTAAGGTTTT-TCCAAAATGAAAATGAAAATGGAGAAATGA
1 AATCAATTGGAAATGAATAAGGTTTTCTCCAAAATGAAAATGAAAATGGA-AAATGA
* ** * *
104407 AATCATTTGGAAATGAATGTGGTTTTCTCCTAAATGAAAATGAAAATTGAAAATGA
1 AATCAATTGGAAATGAATAAGGTTTTCTCCAAAATGAAAATGAAAATGGAAAATGA
104463 CCTTAAAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
56 28 0.57
57 21 0.43
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.29
Consensus pattern (56 bp):
AATCAATTGGAAATGAATAAGGTTTTCTCCAAAATGAAAATGAAAATGGAAAATGA
Found at i:105071 original size:20 final size:17
Alignment explanation
Indices: 105036--105077 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 17
105026 TCAAAATAAT
105036 TATTAAATTAATATTAA
1 TATTAAATTAATATTAA
105053 TATTAAATTTAATAAATTAA
1 TATTAAA-TTAAT--ATTAA
105073 TATTA
1 TATTA
105078 TTTTTGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.32
18 5 0.23
20 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTAAATTAATATTAA
Found at i:106842 original size:25 final size:26
Alignment explanation
Indices: 106803--106851 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
106793 GGTTTAAAGT
* *
106803 ATTTAAATTAACCCACTTAATTAACA
1 ATTTAAATAAACCCAATTAATTAACA
*
106829 ATTT-AATAAACCCAATTTATTAA
1 ATTTAAATAAACCCAATTAATTAA
106852 TGAAATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (26 bp):
ATTTAAATAAACCCAATTAATTAACA
Found at i:108199 original size:15 final size:15
Alignment explanation
Indices: 108179--108208 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
108169 AATCATCATT
108179 ATGCTTGCATTCAAA
1 ATGCTTGCATTCAAA
108194 ATGCTTGCATTCAAA
1 ATGCTTGCATTCAAA
108209 CTAACTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (15 bp):
ATGCTTGCATTCAAA
Found at i:118393 original size:21 final size:21
Alignment explanation
Indices: 118369--118421 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
118359 GTTATGGAGG
118369 TTCTACCGATACAAGTACA-AC
1 TTCTACCGATACAA-TACATAC
* * *
118390 TTCTATCGAAACAATTCATAC
1 TTCTACCGATACAATACATAC
*
118411 TACTACCGATA
1 TTCTACCGATA
118422 TAACAAACAC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.38, C:0.26, G:0.08, T:0.28
Consensus pattern (21 bp):
TTCTACCGATACAATACATAC
Found at i:119141 original size:25 final size:25
Alignment explanation
Indices: 119105--119156 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
119095 TTCCAGAAAT
* *
119105 TTAGCTCATATGAGCCTATATAGAG
1 TTAGCTCATATGAGCCCAGATAGAG
*
119130 TTAGCTCTTATGAGCCCAGATAGAG
1 TTAGCTCATATGAGCCCAGATAGAG
119155 TT
1 TT
119157 TAACCAGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (25 bp):
TTAGCTCATATGAGCCCAGATAGAG
Found at i:132341 original size:7 final size:7
Alignment explanation
Indices: 132325--132386 Score: 56
Period size: 7 Copynumber: 9.1 Consensus size: 7
132315 TTAACCCGAC
132325 CCATTGA
1 CCATTGA
*
132332 CCATTAA
1 CCATTGA
132339 CCATTGA
1 CCATTGA
*
132346 CCATTGT
1 CCATTGA
132353 CCATTGA
1 CCATTGA
*
132360 TCATT-A
1 CCATTGA
*
132366 CTATTGA
1 CCATTGA
*
132373 -CTTTGA
1 CCATTGA
*
132379 TCATTGA
1 CCATTGA
132386 C
1 C
132387 TTTTTTCGAG
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
6 8 0.19
7 34 0.81
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.37
Consensus pattern (7 bp):
CCATTGA
Found at i:143013 original size:277 final size:281
Alignment explanation
Indices: 142473--143027 Score: 875
Period size: 277 Copynumber: 2.0 Consensus size: 281
142463 TTAAACTCGA
** * *
142473 CAATTATGAGGATAAGGTATGGTTTGATGTTGTCCCCATGCATTCCATGCATTTACTTCTTGGAA
1 CAATTATGAGGATAAGGTATGGTTCAATGTTGTCCCCATGCATGCCACGCATTTACTTCTTGGAA
* *
142538 GGCCATGAAAATTTGATCATGATGTCATACACAATGGCAAACAAAATCGATATTCCCTTATCTTT
66 GGCCATGAAAATTTGATCATGATGTCATACACAATGGCAAACAAAATCGATATT-CCTAATCATT
*
142603 AAAGGGACGAAATTTACTCTAGCCCCTTTGAATCCCAATGACGTGTATAAAGATTAATTAAAAAT
130 AAAGGGAAGAAATTTACTCTAGCCCCTTTGAATCCCAATGACGTGTATAAAGATTAATTAAAAAT
* *** *
142668 GATGAAATTTTGTGAGAAGGTTAAAGGGAAAGGAAAAATAAAAAAGACTGCGAGAAAAGTGGCCA
195 GATGAAATTCTGTGAGAAGGTTAAAGGGAAAGGAAAAATAAAAAAGACTAAAAGAAAAGTGACCA
142733 TTAGTACTAAAAGTCAAATTGG
260 TTAGTACTAAAAGTCAAATTGG
*
142755 CAATTATGAGGATGAGGTATGGTTCAATGTTGTCCCCATGCATGCCACGCATTTACTTCTTGGAA
1 CAATTATGAGGATAAGGTATGGTTCAATGTTGTCCCCATGCATGCCACGCATTTACTTCTTGGAA
* *
142820 GGCCATGAAAGTTTGATCATGATGTCATACACCATGGCAAACAAAATCGATA-T-C-AAT-ATTA
66 GGCCATGAAAATTTGATCATGATGTCATACACAATGGCAAACAAAATCGATATTCCTAATCATTA
* * *
142881 AAGGGAATAAATTTACTCTAGCCCCTTTGAATCCTAATGACGTGTATAAAGATTAATTAACAATG
131 AAGGGAAGAAATTTACTCTAGCCCCTTTGAATCCCAATGACGTGTATAAAGATTAATTAAAAATG
* * * *
142946 ATGAAATTCTGTGAGGAGGTTAAAGGGAATGGACAAATAAAAAAGGCTAAAAGAAAAGTGACCAT
196 ATGAAATTCTGTGAGAAGGTTAAAGGGAAAGGAAAAATAAAAAAGACTAAAAGAAAAGTGACCAT
143011 TAGTACTAAAAGTCAAA
261 TAGTACTAAAAGTCAAA
143028 ATTCAAATGG
Statistics
Matches: 251, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
277 137 0.55
278 2 0.01
279 1 0.00
281 1 0.00
282 110 0.44
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (281 bp):
CAATTATGAGGATAAGGTATGGTTCAATGTTGTCCCCATGCATGCCACGCATTTACTTCTTGGAA
GGCCATGAAAATTTGATCATGATGTCATACACAATGGCAAACAAAATCGATATTCCTAATCATTA
AAGGGAAGAAATTTACTCTAGCCCCTTTGAATCCCAATGACGTGTATAAAGATTAATTAAAAATG
ATGAAATTCTGTGAGAAGGTTAAAGGGAAAGGAAAAATAAAAAAGACTAAAAGAAAAGTGACCAT
TAGTACTAAAAGTCAAATTGG
Found at i:146686 original size:24 final size:21
Alignment explanation
Indices: 146639--146693 Score: 56
Period size: 24 Copynumber: 2.5 Consensus size: 21
146629 ACATAATTTG
* *
146639 TTTCTTCTTTTTCTTCTCTCT
1 TTTCTTTTTTTTCTTATCTCT
146660 TTTCTTTTTCTTTCTTTATCTCAT
1 TTTCTTTTT-TTTC-TTATCTC-T
*
146684 TTTCCTTTTT
1 TTTCTTTTTT
146694 ACGTGACTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 8 0.29
22 4 0.14
23 7 0.25
24 9 0.32
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTCTTTTTTTTCTTATCTCT
Found at i:162119 original size:17 final size:18
Alignment explanation
Indices: 162082--162121 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
162072 AACAAAAATG
162082 ATGCAATGACAAAATAAA
1 ATGCAATGACAAAATAAA
* *
162100 ATGCAATGATAATA-AAA
1 ATGCAATGACAAAATAAA
162117 ATGCA
1 ATGCA
162122 TTAAAACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.20
Consensus pattern (18 bp):
ATGCAATGACAAAATAAA
Found at i:170950 original size:80 final size:80
Alignment explanation
Indices: 170759--171101 Score: 372
Period size: 80 Copynumber: 4.3 Consensus size: 80
170749 ATGATTCTAG
* * ** * * * *
170759 CACCCAATGCCTAGCGGATAAATAGCAAAAGTAAGGCC-AGCTCTAATTGGATTAACTAACAAAT
1 CACCCAGTGCCTAGCAGATAAACCGCAAAAGTGAGCCCTAGCTCTAGTTGGATTAACCAACAAAT
170823 ATCCGTCAAATCCTA
66 ATCCGTCAAATCCTA
* * * *
170838 CACCTAGTGCCTAGCAAATAAACCGCAGAAGTGAGCCCTA-CTCTAGTTGGATTAACCAATAAAT
1 CACCCAGTGCCTAGCAGATAAACCGCAAAAGTGAGCCCTAGCTCTAGTTGGATTAACCAACAAAT
* *
170902 GTCCGTTAAATCCTGA
66 ATCCGTCAAATCCT-A
** * * *
170918 CACCCAGTGCCTAGTTGATAAACCGCAAAAGTGAGCTC-AACTCTAGTTGGATTAACCAATAAAT
1 CACCCAGTGCCTAGCAGATAAACCGCAAAAGTGAGCCCTAGCTCTAGTTGGATTAACCAACAAAT
*
170982 ATCTGTCAAATCCTA
66 ATCCGTCAAATCCTA
* * * *
170997 GCACCCAATGCCTAGCAGATAAACCACAAAAGTGAG-CTTAGCTCTAGTTGGATTAAGCAACAAA
1 -CACCCAGTGCCTAGCAGATAAACCGCAAAAGTGAGCCCTAGCTCTAGTTGGATTAACCAACAAA
*
171061 TATCCGTCAAATCCTGG
65 TATCCGTCAAATCCT-A
* *
171078 TACTCAGTGCCTAGC-GAATAAACC
1 CACCCAGTGCCTAGCAG-ATAAACC
171102 ACAATTGTGT
Statistics
Matches: 220, Mismatches: 37, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
79 65 0.30
80 155 0.70
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.23
Consensus pattern (80 bp):
CACCCAGTGCCTAGCAGATAAACCGCAAAAGTGAGCCCTAGCTCTAGTTGGATTAACCAACAAAT
ATCCGTCAAATCCTA
Found at i:171101 original size:160 final size:158
Alignment explanation
Indices: 170759--171101 Score: 411
Period size: 160 Copynumber: 2.1 Consensus size: 158
170749 ATGATTCTAG
* ** * *
170759 CACCCAATGCCTAGCGGATAAATAGCAAAAGTAAGGCCAGCTCTAATTGGATTAACTAACAAATA
1 CACCCAGTGCCTAGC-GATAAACCGCAAAAGTAAGGCCAACTCTAATTGGATTAACCAACAAATA
* * * *
170824 TCCGTCAAATCCTACACCTAGTGCCTAGCAAATAAACCGCAGAAGTGAGCCCTACTCTAGTTGGA
65 TCCGTCAAATCCTACACCCAATGCCTAGCAAATAAACCACAAAAGTGAGCCCTACTCTAGTTGGA
* * *
170889 TTAACCAATAAATGTCCGTTAAATCCTGA
130 TTAACCAACAAATATCCGTCAAATCCTGA
* * * *
170918 CACCCAGTGCCTAGTTGATAAACCGCAAAAGTGA-GCTCAACTCTAGTTGGATTAACCAATAAAT
1 CACCCAGTGCCTAG-CGATAAACCGCAAAAGTAAGGC-CAACTCTAATTGGATTAACCAACAAAT
* * *
170982 ATCTGTCAAATCCTAGCACCCAATGCCTAGCAGATAAACCACAAAAGTGAG-CTTAGCTCTAGTT
64 ATCCGTCAAATCCTA-CACCCAATGCCTAGCAAATAAACCACAAAAGTGAGCCCTA-CTCTAGTT
* *
171046 GGATTAAGCAACAAATATCCGTCAAATCCTGG
127 GGATTAACCAACAAATATCCGTCAAATCCTGA
* *
171078 TACTCAGTGCCTAGCGAATAAACC
1 CACCCAGTGCCTAGCG-ATAAACC
171102 ACAATTGTGT
Statistics
Matches: 155, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
158 2 0.01
159 69 0.45
160 84 0.54
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.23
Consensus pattern (158 bp):
CACCCAGTGCCTAGCGATAAACCGCAAAAGTAAGGCCAACTCTAATTGGATTAACCAACAAATAT
CCGTCAAATCCTACACCCAATGCCTAGCAAATAAACCACAAAAGTGAGCCCTACTCTAGTTGGAT
TAACCAACAAATATCCGTCAAATCCTGA
Found at i:171561 original size:2 final size:2
Alignment explanation
Indices: 171556--171611 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
171546 AAAAAAAAAA
* ** * *
171556 AT AT AT AT AT AT AT AT AT GT AT AT GC AT AT AC AT AT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
171598 AT AT CT AT AT AT AT
1 AT AT AT AT AT AT AT
171612 TGGAAAAAAT
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:174154 original size:40 final size:40
Alignment explanation
Indices: 174109--174216 Score: 121
Period size: 40 Copynumber: 2.7 Consensus size: 40
174099 GACCATAAGG
* *
174109 CAGATTGAAGACCATCCAATCTTTTACCCTAATCA-GAGGG
1 CAGATTGAAGACCATCCAATCTTTTACCCTAACCATG-GGA
* * * * *
174149 TAGATTAAAGATCATTCAATCTTTTACCCTGACCATGGGA
1 CAGATTGAAGACCATCCAATCTTTTACCCTAACCATGGGA
*
174189 CAGATTGAAG-CAATCCAATCTTTTACCC
1 CAGATTGAAGACCATCCAATCTTTTACCC
174217 CTAAAGCTAT
Statistics
Matches: 55, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
39 15 0.27
40 39 0.71
41 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (40 bp):
CAGATTGAAGACCATCCAATCTTTTACCCTAACCATGGGA
Found at i:174967 original size:13 final size:13
Alignment explanation
Indices: 174934--174968 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
174924 AAAACCTAAT
174934 TTTATTTATTTTA
1 TTTATTTATTTTA
174947 TATT-TTTATTTTA
1 T-TTATTTATTTTA
174960 TTTATTTAT
1 TTTATTTAT
174969 CATTTTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.10
13 16 0.80
14 2 0.10
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:174976 original size:21 final size:22
Alignment explanation
Indices: 174932--174974 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
174922 ACAAAACCTA
174932 ATTTTATTTATTTTATATTTTT
1 ATTTTATTTATTTTATATTTTT
174954 ATTTTATTTA-TTTATCATTTT
1 ATTTTATTTATTTTAT-ATTTT
174975 ATAAATGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
ATTTTATTTATTTTATATTTTT
Found at i:175107 original size:10 final size:10
Alignment explanation
Indices: 175092--175134 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
175082 TTTTATTTTT
175092 ATAAATATAA
1 ATAAATATAA
*
175102 ATAAATACAA
1 ATAAATATAA
*
175112 ATGAAAAATAA
1 AT-AAATATAA
175123 ATAAATAATAA
1 ATAAAT-ATAA
175134 A
1 A
175135 ATTAAACAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 14 0.52
11 13 0.48
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (10 bp):
ATAAATATAA
Found at i:175135 original size:17 final size:17
Alignment explanation
Indices: 175095--175146 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
175085 TATTTTTATA
* *
175095 AATATAAATAAATACA-
1 AATAAAAATAAATAAAT
175111 AATGAAAAATAAATAAAT
1 AAT-AAAAATAAATAAAT
* *
175129 AATAAAATTAAACAAAT
1 AATAAAAATAAATAAAT
175146 A
1 A
175147 CATATACCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 3 0.10
17 24 0.80
18 3 0.10
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (17 bp):
AATAAAAATAAATAAAT
Found at i:176167 original size:30 final size:30
Alignment explanation
Indices: 176107--176321 Score: 202
Period size: 30 Copynumber: 7.2 Consensus size: 30
176097 AATTATGTTG
*
176107 TGACCCCCAAA-TTATCCAAAAATTC-AATT
1 TGACCCTCAAACTT-TCCAAAAATTCAAATT
* *
176136 TGATCCTCAAACTTTCCAAAAATTCCAATT
1 TGACCCTCAAACTTTCCAAAAATTCAAATT
* * **
176166 TGACCCTTAAACTTTTCAAAAATTTGAATT
1 TGACCCTCAAACTTTCCAAAAATTCAAATT
* * * **
176196 TGGCCCTCGAACTTTCCAAAATTTTTAATT
1 TGACCCTCAAACTTTCCAAAAATTCAAATT
* * *
176226 AGACCC-CAAACTTTCCAATAATTCTAATT
1 TGACCCTCAAACTTTCCAAAAATTCAAATT
** ** *
176255 TGATGCTTGAACTTTCTAAAAATTCAAATT
1 TGACCCTCAAACTTTCCAAAAATTCAAATT
*
176285 TGACCCTCGAACTTTCCAAAAATTCAAAATT
1 TGACCCTCAAACTTTCCAAAAATTC-AAATT
176316 TGACCC
1 TGACCC
176322 AATTTTATTT
Statistics
Matches: 151, Mismatches: 31, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
29 42 0.28
30 98 0.65
31 11 0.07
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.34
Consensus pattern (30 bp):
TGACCCTCAAACTTTCCAAAAATTCAAATT
Found at i:176309 original size:60 final size:60
Alignment explanation
Indices: 176107--176318 Score: 216
Period size: 59 Copynumber: 3.5 Consensus size: 60
176097 AATTATGTTG
* * *
176107 TGACCCCCAAA-TTATCCAAAAATTC-AATTTGATCCTCAAACTTTCCAAAAATTCCAATT
1 TGACCCTCAAACTT-TCCAAAAATTCTAATTTGATCCTCGAACTTTCCAAAAATTCAAATT
* * ** * **
176166 TGACCCTTAAACTTTTCAAAAATT-TGAATTTGGCCCTCGAACTTTCCAAAATTTTTAATT
1 TGACCCTCAAACTTTCCAAAAATTCT-AATTTGATCCTCGAACTTTCCAAAAATTCAAATT
* * * * *
176226 AGACCC-CAAACTTTCCAATAATTCTAATTTGATGCTTGAACTTTCTAAAAATTCAAATT
1 TGACCCTCAAACTTTCCAAAAATTCTAATTTGATCCTCGAACTTTCCAAAAATTCAAATT
* *
176285 TGACCCTCGAACTTTCCAAAAATTCAAAATTTGA
1 TGACCCTCAAACTTTCCAAAAATTC-TAATTTGA
176319 CCCAATTTTA
Statistics
Matches: 122, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
59 63 0.52
60 52 0.43
61 7 0.06
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (60 bp):
TGACCCTCAAACTTTCCAAAAATTCTAATTTGATCCTCGAACTTTCCAAAAATTCAAATT
Found at i:176323 original size:89 final size:88
Alignment explanation
Indices: 176121--176321 Score: 242
Period size: 89 Copynumber: 2.2 Consensus size: 88
176111 CCCCAAATTA
*
176121 TCCAAAAATTCAATTTGATCCTCAAACTTTCCAAAAATTCCAATTTGACCCTTAAACTTTTCAAA
1 TCCAAAAATTCAATTTGA-CCCCAAACTTTCCAAAAATTCCAATTTGACCCTTAAACTTTTCAAA
** *
176186 AATTTGAATTTGGCCCTCGAACTT
65 AATTCAAATTTGACCCTCGAACTT
* * * * * ** *
176210 TCCAAAATTTTTAATTAGACCCCAAACTTTCCAATAATTCTAATTTGATGCTTGAAC-TTTCTAA
1 TCCAAAA-ATTCAATTTGACCCCAAACTTTCCAAAAATTCCAATTTGACCCTTAAACTTTTC-AA
176274 AAATTCAAATTTGACCCTCGAACTT
64 AAATTCAAATTTGACCCTCGAACTT
176299 TCCAAAAATTCAAAATTTGACCC
1 TCCAAAAATTC--AATTTGACCC
176322 AATTTTATTT
Statistics
Matches: 93, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
88 6 0.06
89 70 0.75
90 17 0.18
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.35
Consensus pattern (88 bp):
TCCAAAAATTCAATTTGACCCCAAACTTTCCAAAAATTCCAATTTGACCCTTAAACTTTTCAAAA
ATTCAAATTTGACCCTCGAACTT
Found at i:176534 original size:18 final size:19
Alignment explanation
Indices: 176487--176540 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
176477 ATCTACTTAA
176487 TTTATTATTT-TATTGTAT
1 TTTATTATTTATATTGTAT
176505 TTTATGTA--TATATTGT-T
1 TTTAT-TATTTATATTGTAT
176522 TTTATTATTTATACTTGTA
1 TTTATTATTTATA-TTGTA
176541 AATCATGTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
16 2 0.07
17 7 0.23
18 15 0.50
19 6 0.20
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTATTATTTATATTGTAT
Found at i:177703 original size:19 final size:19
Alignment explanation
Indices: 177679--177723 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
177669 TTAGAGAATA
177679 TTGTTATTT-GTGAAATATT
1 TTGTTATTTAG-GAAATATT
*
177698 TTGTTATTTAGGAGATATT
1 TTGTTATTTAGGAAATATT
177717 TTGTTAT
1 TTGTTAT
177724 GTGTCATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (19 bp):
TTGTTATTTAGGAAATATT
Found at i:178725 original size:19 final size:19
Alignment explanation
Indices: 178685--178731 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
178675 AACCGATCGA
*
178685 TTAATCGAATTAATTCAGT
1 TTAATCGAATTAATTAAGT
*
178704 TTAATCG-ATTAATTTAATT
1 TTAATCGAATTAA-TTAAGT
*
178723 TTAACCGAA
1 TTAATCGAA
178732 ATTTAAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.43
Consensus pattern (19 bp):
TTAATCGAATTAATTAAGT
Found at i:184711 original size:24 final size:24
Alignment explanation
Indices: 184683--184793 Score: 132
Period size: 24 Copynumber: 4.6 Consensus size: 24
184673 TAGACTAATA
* *
184683 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAT
* * *
184707 AGAGTTTAATTGAAACAAGTAAAC
1 AGAGTTTAACTGAAACAAATAAAT
*
184731 CGAGTTTAACTGAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAT
* * **
184755 AGAGTTTAATTGAAACAATTAAGC
1 AGAGTTTAACTGAAACAAATAAAT
184779 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
184794 GATTATTTCT
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAT
Found at i:184747 original size:48 final size:48
Alignment explanation
Indices: 184683--184793 Score: 177
Period size: 48 Copynumber: 2.3 Consensus size: 48
184673 TAGACTAATA
* *
184683 AGAGTTTGACTCAAACAAATAAATAGAGTTTAATTGAAACAAGTAAAC
1 AGAGTTTAACTGAAACAAATAAATAGAGTTTAATTGAAACAAGTAAAC
* * *
184731 CGAGTTTAACTGAAACAAATAAATAGAGTTTAATTGAAACAATTAAGC
1 AGAGTTTAACTGAAACAAATAAATAGAGTTTAATTGAAACAAGTAAAC
184779 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
184794 GATTATTTCT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (48 bp):
AGAGTTTAACTGAAACAAATAAATAGAGTTTAATTGAAACAAGTAAAC
Found at i:188054 original size:100 final size:100
Alignment explanation
Indices: 187875--188056 Score: 253
Period size: 100 Copynumber: 1.8 Consensus size: 100
187865 ACTTCAGTAA
*
187875 AACTTTAGGAAGATAAGATTTGCTTTCATAACTTCAATCCGGCCCACTACAACTTCGAGGGTATA
1 AACTTTAGGAAGATAAGATTTGCTTTCATAACTTCAATCCGACCCACTACAACTTCGAGGGTATA
187940 GGATTTGATGTCGTAGCCTCATCTTACTCTATTGC
66 GGATTTGATGTCGTAGCCTCATCTTACTCTATTGC
* * **
187975 AACTTTA-GAGAGATAAGATTTG-TTTCTATAACTTCAATCTGATCCACTGTAACTTC-AGGGAT
1 AACTTTAGGA-AGATAAGATTTGCTTTC-ATAACTTCAATCCGACCCACTACAACTTCGAGGG-T
* *
188037 ATAGGATTTGGTTTCGTAGC
63 ATAGGATTTGATGTCGTAGC
188057 TTCAGTGCAC
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
99 10 0.14
100 62 0.86
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (100 bp):
AACTTTAGGAAGATAAGATTTGCTTTCATAACTTCAATCCGACCCACTACAACTTCGAGGGTATA
GGATTTGATGTCGTAGCCTCATCTTACTCTATTGC
Found at i:188722 original size:20 final size:20
Alignment explanation
Indices: 188706--188743 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
188696 CAGAAATTGT
188706 AAACATTGGTAAAAAATGGA
1 AAACATTGGTAAAAAATGGA
*
188726 AAACGTTGGTAAAAAATG
1 AAACATTGGTAAAAAATG
188744 CTAAACACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (20 bp):
AAACATTGGTAAAAAATGGA
Found at i:188749 original size:20 final size:20
Alignment explanation
Indices: 188705--188750 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
188695 TCAGAAATTG
*
188705 TAAACATTGGTAAAAAATGG
1 TAAACATTGGTAAAAAATGC
* *
188725 AAAACGTTGGTAAAAAATGC
1 TAAACATTGGTAAAAAATGC
188745 TAAACA
1 TAAACA
188751 CAAGGTGGGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.22
Consensus pattern (20 bp):
TAAACATTGGTAAAAAATGC
Found at i:189214 original size:44 final size:47
Alignment explanation
Indices: 189148--189247 Score: 134
Period size: 45 Copynumber: 2.2 Consensus size: 47
189138 TTCTTTTTTT
* *
189148 TTTTTTTTAGATTTCAATATGCCCTTT-ACAGGTTTTCATCTCGA-C
1 TTTTTTTTACATTTCAAGATGCCCTTTCACAGGTTTTCATCTCGACC
* *
189193 TTTTTTTT-CATTTCAAGATGCCCTTTCGCAGGTTTTCATCTTGACC
1 TTTTTTTTACATTTCAAGATGCCCTTTCACAGGTTTTCATCTCGACC
189239 TTTATTTTT
1 TTT-TTTTT
189248 TGGAAAAAGC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
44 16 0.33
45 23 0.48
46 4 0.08
47 5 0.10
ACGTcount: A:0.17, C:0.20, G:0.11, T:0.52
Consensus pattern (47 bp):
TTTTTTTTACATTTCAAGATGCCCTTTCACAGGTTTTCATCTCGACC
Found at i:190845 original size:15 final size:15
Alignment explanation
Indices: 190827--190875 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
190817 TTGAAACATT
190827 AGTGTTTGTAATGTG
1 AGTGTTTGTAATGTG
* * *
190842 AGTGTTCGTAATATC
1 AGTGTTTGTAATGTG
*
190857 AGTGTTTGCAATGTG
1 AGTGTTTGTAATGTG
190872 AGTG
1 AGTG
190876 CTCACAACAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.22, C:0.06, G:0.31, T:0.41
Consensus pattern (15 bp):
AGTGTTTGTAATGTG
Found at i:190847 original size:30 final size:30
Alignment explanation
Indices: 190811--190875 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
190801 CTCACAACGC
* * *
190811 GAGTGTTTGAAACATTAGTGTTTGTAATGT
1 GAGTGTTCGAAACATCAGTGTTTGCAATGT
* *
190841 GAGTGTTCGTAATATCAGTGTTTGCAATGT
1 GAGTGTTCGAAACATCAGTGTTTGCAATGT
190871 GAGTG
1 GAGTG
190876 CTCACAACAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.06, G:0.29, T:0.40
Consensus pattern (30 bp):
GAGTGTTCGAAACATCAGTGTTTGCAATGT
Found at i:190892 original size:30 final size:30
Alignment explanation
Indices: 190821--190892 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
190811 GAGTGTTTGA
* * * **
190821 AACATTAGTGTTTGTAATGTGAGTGTTCGT
1 AACATTCGTGTTTGCAATGTGAGTGCTCAC
*
190851 AATA-TCAGTGTTTGCAATGTGAGTGCTCAC
1 AACATTC-GTGTTTGCAATGTGAGTGCTCAC
190881 AACATTCGTGTT
1 AACATTCGTGTT
190893 CGCAGCATAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
29 1 0.03
30 30 0.91
31 2 0.06
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (30 bp):
AACATTCGTGTTTGCAATGTGAGTGCTCAC
Found at i:192496 original size:17 final size:17
Alignment explanation
Indices: 192474--192508 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
192464 TATCAAAGCA
192474 GCACAAAAGGATAAAAT
1 GCACAAAAGGATAAAAT
192491 GCACAAAAGGATAAAAT
1 GCACAAAAGGATAAAAT
192508 G
1 G
192509 TAAAGGATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.11, G:0.20, T:0.11
Consensus pattern (17 bp):
GCACAAAAGGATAAAAT
Found at i:193368 original size:23 final size:22
Alignment explanation
Indices: 193319--193394 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
193309 GATGTTGACA
* *
193319 AAATAAAAATACAT-ACATGAAT
1 AAAT-AAAATAAATAACATAAAT
*
193341 AAAATAAAATAAAT-AGATACAATT
1 -AAATAAAATAAATAACATA-AA-T
*
193365 AAATAAAATTAATAACATAAAT
1 AAATAAAATAAATAACATAAAT
193387 AAATAAAA
1 AAATAAAA
193395 AATAGTAGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
22 20 0.44
23 20 0.44
24 5 0.11
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (22 bp):
AAATAAAATAAATAACATAAAT
Found at i:193624 original size:14 final size:15
Alignment explanation
Indices: 193552--193636 Score: 61
Period size: 14 Copynumber: 5.7 Consensus size: 15
193542 TAAAAGGCAA
193552 AAAATATAAAT-AAT
1 AAAATATAAATAAAT
* *
193566 ATCAAT-TAAATGGAAT
1 A-AAATATAAAT-AAAT
*
193582 AAAA-ATAAATAAGT
1 AAAATATAAATAAAT
* *
193596 AAGCATGAGAAATAAAT
1 AA-AAT-ATAAATAAAT
193613 AAAA-ATAAATAAAT
1 AAAATATAAATAAAT
193627 AAAATATAAA
1 AAAATATAAA
193637 AATAAAAGGG
Statistics
Matches: 54, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
14 23 0.43
15 16 0.30
16 5 0.09
17 10 0.19
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (15 bp):
AAAATATAAATAAAT
Found at i:193632 original size:13 final size:13
Alignment explanation
Indices: 193605--193643 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
193595 TAAGCATGAG
193605 AAATAAATAAAAAT
1 AAATAAAT-AAAAT
193619 AAATAAATAAAAT
1 AAATAAATAAAAT
193632 ATAA-AAATAAAA
1 A-AATAAATAAAA
193644 GGGGTGCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:193640 original size:31 final size:31
Alignment explanation
Indices: 193579--193642 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
193569 AATTAAATGG
* * *
193579 AATAAAAATAAATAAGTAAGCATGAGAAATA
1 AATAAAAATAAATAAATAAGAATGAAAAATA
*
193610 AATAAAAATAAATAAATAA-AATATAAAAATA
1 AATAAAAATAAATAAATAAGAAT-GAAAAATA
193641 AA
1 AA
193643 AGGGGTGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (31 bp):
AATAAAAATAAATAAATAAGAATGAAAAATA
Found at i:198362 original size:29 final size:29
Alignment explanation
Indices: 198329--198396 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 29
198319 ATAGTTCATT
* *
198329 CGAGCCCAGAAACAGATTAACTCTCTATC
1 CGAGCCCAAAAACAGATTAACGCTCTATC
198358 CGAG-CCAAAAACAGATTAACGCTCTATC
1 CGAGCCCAAAAACAGATTAACGCTCTATC
* *
198386 TGAGCCGAAAA
1 CGAGCCCAAAA
198397 TGGAATGATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 25 0.74
29 9 0.26
ACGTcount: A:0.38, C:0.28, G:0.16, T:0.18
Consensus pattern (29 bp):
CGAGCCCAAAAACAGATTAACGCTCTATC
Found at i:198437 original size:28 final size:28
Alignment explanation
Indices: 198406--198539 Score: 112
Period size: 28 Copynumber: 4.8 Consensus size: 28
198396 ATGGAATGAT
** *
198406 GCTCTACCTTAGCCAGATTCAGAGTAAC
1 GCTCTACCCGAGCAAGATTCAGAGTAAC
* * * *
198434 GCTCTACCCAAG-ATATAATCAGAATAAC
1 GCTCTACCCGAGCA-AGATTCAGAGTAAC
* * * *
198462 GCTCTACCCGAGCCAGAAGT-AGA-AAAT
1 GCTCTACCCGAGCAAG-ATTCAGAGTAAC
*
198489 GCTCTACCCGAGCAAGATTCAAAGTAAC
1 GCTCTACCCGAGCAAGATTCAGAGTAAC
*
198517 GCTCTACCTGAGCAAGATTCAGA
1 GCTCTACCCGAGCAAGATTCAGA
198540 ATATCATTCT
Statistics
Matches: 82, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
26 2 0.02
27 19 0.23
28 59 0.72
29 2 0.02
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (28 bp):
GCTCTACCCGAGCAAGATTCAGAGTAAC
Found at i:199659 original size:4 final size:4
Alignment explanation
Indices: 199650--199704 Score: 64
Period size: 4 Copynumber: 14.8 Consensus size: 4
199640 AAAGTGTTGG
*
199650 AAAT AAAT AAAT AAAT AAAT AAAT -AAT -AAT AAAT -AAT AAA- CAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
199694 AAAT GAAT AAA
1 AAAT AAAT AAA
199705 GGACTAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
3 11 0.25
4 33 0.75
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:199684 original size:7 final size:7
Alignment explanation
Indices: 199650--199704 Score: 58
Period size: 7 Copynumber: 7.4 Consensus size: 7
199640 AAAGTGTTGG
199650 AAATAAAT
1 AAAT-AAT
199658 AAATAAAT
1 AAAT-AAT
199666 AAATAA-
1 AAATAAT
199672 ATAATAAT
1 A-AATAAT
199680 AAATAAT
1 AAATAAT
*
199687 AAACAAT
1 AAATAAT
199694 AAATGAAT
1 AAAT-AAT
199702 AAA
1 AAA
199705 GGACTAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
6 1 0.02
7 22 0.52
8 19 0.45
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (7 bp):
AAATAAT
Found at i:199695 original size:10 final size:10
Alignment explanation
Indices: 199655--199688 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
199645 GTTGGAAATA
199655 AATAAATAAAT
1 AATAAAT-AAT
199666 AAATAAATAAT
1 -AATAAATAAT
199677 AATAAATAAT
1 AATAAATAAT
199687 AA
1 AA
199689 ACAATAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 3 0.14
12 7 0.32
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AATAAATAAT
Found at i:199814 original size:24 final size:23
Alignment explanation
Indices: 199772--199831 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
199762 AAAGTGCAAG
199772 AAAT-AAATAAATAAT-AAAAAT
1 AAATGAAATAAATAATAAAAAAT
199793 AAAATGAAATGAAAT-ATAAAAAAAT
1 -AAATGAAAT-AAATAAT-AAAAAAT
199818 AAATG-AATAAATAA
1 AAATGAAATAAATAA
199832 GCAAAGGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
22 8 0.24
23 10 0.30
24 9 0.27
25 6 0.18
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (23 bp):
AAATGAAATAAATAATAAAAAAT
Found at i:201023 original size:23 final size:23
Alignment explanation
Indices: 200988--201031 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
200978 CTAAGTTACA
200988 AAAAAAAACTTCATGCTACAGAC
1 AAAAAAAACTTCATGCTACAGAC
* *
201011 AAAAGAAATTTCATGCTACAG
1 AAAAAAAACTTCATGCTACAG
201032 CATTGCTAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.20
Consensus pattern (23 bp):
AAAAAAAACTTCATGCTACAGAC
Found at i:209359 original size:82 final size:81
Alignment explanation
Indices: 209220--209486 Score: 392
Period size: 82 Copynumber: 3.3 Consensus size: 81
209210 AGTTTAACTG
* * * *
209220 ACTAGAGCTGGGCTCACTTATTGCGGTTTATCCGCTAAGCATTGGGTCCCAGAAATTGACGGAAT
1 ACTAGAGCTGGGCTCACTTATTGCGGTTTATCCGCTAGGCACT-GGTGCCAGGAATTGACGGAAT
209285 TATTGTTGGTTAATCCA
65 TATTGTTGGTTAATCCA
* *
209302 ACTAGAGCTGAGCTCACTTATTGCGGTTTATCCTCTAGGCACTGGATGCCAGGAATTGACGGAAT
1 ACTAGAGCTGGGCTCACTTATTGCGGTTTATCCGCTAGGCACTGG-TGCCAGGAATTGACGGAAT
209367 TATTGTTGGTTAATCCA
65 TATTGTTGGTTAATCCA
* * * *
209384 ACTAGAGTTTGGCTCACTTATTGCGGTTTATCCGCTAGGCACTAGGTGCTAGGAATTGACGGGAT
1 ACTAGAGCTGGGCTCACTTATTGCGGTTTATCCGCTAGGCACT-GGTGCCAGGAATTGACGGAAT
* *
209449 AATTGTTGCTTAATCCA
65 TATTGTTGGTTAATCCA
209466 ACTAGAGCTGGGCTCA-TTATT
1 ACTAGAGCTGGGCTCACTTATT
209487 AATATCGTCG
Statistics
Matches: 167, Mismatches: 16, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
81 7 0.04
82 158 0.95
83 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (81 bp):
ACTAGAGCTGGGCTCACTTATTGCGGTTTATCCGCTAGGCACTGGTGCCAGGAATTGACGGAATT
ATTGTTGGTTAATCCA
Found at i:217229 original size:20 final size:22
Alignment explanation
Indices: 217185--217231 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
217175 CAAATATTGA
217185 TTAATAAAAGGATTAATTAAGG
1 TTAATAAAAGGATTAATTAAGG
* *
217207 TTAA-AAAATGATTAGTTAA-G
1 TTAATAAAAGGATTAATTAAGG
217227 TTAAT
1 TTAAT
217232 CATGACAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 13 0.59
22 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (22 bp):
TTAATAAAAGGATTAATTAAGG
Found at i:218328 original size:94 final size:94
Alignment explanation
Indices: 218198--218408 Score: 316
Period size: 94 Copynumber: 2.2 Consensus size: 94
218188 GCATACTCTT
* * *
218198 GACAGCTCGTGTGAGCAGCATCGTTAGGAAACAATTTACAATACAGATAGACA-CTGTATCGATG
1 GACAGCTCGTGTGAGCAGCATCGTTAGAAAACAATTTACAATACAAATAGACATC-ATATCGATG
*
218262 GTTGGGGTACCACATAGGTTGCGAGTCCTC
65 GTTGGGGTACCACATAGGTTACGAGTCCTC
* * *
218292 GACAGCTCGTGTGAGCAGCATCGTTAGAAAATAATTTACAGTATAAATAGACATCATATCGATGG
1 GACAGCTCGTGTGAGCAGCATCGTTAGAAAACAATTTACAATACAAATAGACATCATATCGATGG
218357 TTGGGGTACCACATAGGTTACGAGTCCTC
66 TTGGGGTACCACATAGGTTACGAGTCCTC
** *
218386 GACAATTCGTGTGAGCAGTATCG
1 GACAGCTCGTGTGAGCAGCATCG
218409 GGTATTGGTA
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 105 0.99
95 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (94 bp):
GACAGCTCGTGTGAGCAGCATCGTTAGAAAACAATTTACAATACAAATAGACATCATATCGATGG
TTGGGGTACCACATAGGTTACGAGTCCTC
Found at i:219654 original size:2 final size:2
Alignment explanation
Indices: 219647--219672 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
219637 AAATGATGTG
219647 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
219673 GAACTTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:220183 original size:24 final size:24
Alignment explanation
Indices: 220151--220230 Score: 160
Period size: 24 Copynumber: 3.3 Consensus size: 24
220141 TTTTGGGTAT
220151 GAGCACGGCCTGGTACATGGCCAA
1 GAGCACGGCCTGGTACATGGCCAA
220175 GAGCACGGCCTGGTACATGGCCAA
1 GAGCACGGCCTGGTACATGGCCAA
220199 GAGCACGGCCTGGTACATGGCCAA
1 GAGCACGGCCTGGTACATGGCCAA
220223 GAGCACGG
1 GAGCACGG
220231 GCGTGTGGAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.25, C:0.29, G:0.35, T:0.11
Consensus pattern (24 bp):
GAGCACGGCCTGGTACATGGCCAA
Found at i:223565 original size:24 final size:25
Alignment explanation
Indices: 223533--223596 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
223523 CTTTTTCAAA
* *
223533 ATTTGATAAAAAAATTTAAAATTT-
1 ATTTTATAAAAAAATTGAAAATTTC
* *
223557 ATTTTATAAATATAGTTGAAAATTTC
1 ATTTTATAAA-AAAATTGAAAATTTC
*
223583 ATTTTAAAAAAAAA
1 ATTTTATAAAAAAA
223597 ATAGATGTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
24 9 0.29
25 13 0.42
26 9 0.29
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (25 bp):
ATTTTATAAAAAAATTGAAAATTTC
Done.