Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000717.1 Kokia drynarioides strain JFW-HI SEQ_111732, 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: 125265
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 28 characters in sequence are not A, C, G, or T
Found at i:1391 original size:27 final size:28
Alignment explanation
Indices: 1352--1404 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
1342 AGATTGTATC
1352 TATTTTTCCATTTT-AGTATTTAAATTTT
1 TATTTTTCCATTTTGA-TATTTAAATTTT
1380 TATTTTT-CATTTTGATATTTAAATT
1 TATTTTTCCATTTTGATATTTAAATT
1405 ATTCTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (28 bp):
TATTTTTCCATTTTGATATTTAAATTTT
Found at i:1817 original size:28 final size:32
Alignment explanation
Indices: 1786--1850 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 32
1776 TACTATTCTA
1786 TATTTTATATAA-TTAT-T-TTATAA-TGTTT
1 TATTTTATATAATTTATATATTATAATTGTTT
* *
1814 TATTTTGTATAATTTATATATTATAATTTTTT
1 TATTTTATATAATTTATATATTATAATTGTTT
1846 TATTT
1 TATTT
1851 AATTTTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 11 0.35
29 4 0.13
30 1 0.03
31 6 0.19
32 9 0.29
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (32 bp):
TATTTTATATAATTTATATATTATAATTGTTT
Found at i:1855 original size:13 final size:14
Alignment explanation
Indices: 1821--1859 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1811 TTTTATTTTG
* *
1821 TATAATTTATATAT
1 TATAATTTTTTTAT
1835 TATAATTTTTTTAT
1 TATAATTTTTTTAT
1849 T-TAATTTTTTT
1 TATAATTTTTTT
1860 GTTTTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TATAATTTTTTTAT
Found at i:3989 original size:17 final size:18
Alignment explanation
Indices: 3950--3994 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
3940 TTAGATGGGT
* *
3950 TTTAGATTTATTTCTAAA
1 TTTAAATTTACTTCTAAA
*
3968 ATTAAATTTACTT-TAAA
1 TTTAAATTTACTTCTAAA
3985 TTTAAATTTA
1 TTTAAATTTA
3995 AATTCATTTT
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:4808 original size:21 final size:20
Alignment explanation
Indices: 4784--4839 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
4774 ATGACATCAT
* *
4784 TAATAATAATAAATGTTTTGA
1 TAATAATAATAAAT-TATTAA
*
4805 TAATACTAATAAAATTATTAA
1 TAATAATAAT-AAATTATTAA
4826 TAATAATTAATAAA
1 TAATAA-TAATAAA
4840 AAAAGGAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (20 bp):
TAATAATAATAAATTATTAA
Found at i:5839 original size:29 final size:29
Alignment explanation
Indices: 5798--6280 Score: 454
Period size: 29 Copynumber: 16.5 Consensus size: 29
5788 TAAACTATCA
* *
5798 AAAAATTCCATTTTCACCCTCGAACTTCC
1 AAAAATCCCATTTTTACCCTCGAACTTCC
** **
5827 AAAAATCCCATTTTTAACCCTAAAAAGTCC
1 AAAAATCCCATTTTT-ACCCTCGAACTTCC
*
5857 AAAAATTCCATTTTTACCC-CTGAACTTCC
1 AAAAATCCCATTTTTACCCTC-GAACTTCC
* *
5886 AAAAATCCCATTTTTGA-ACTCGAAACTTTC
1 AAAAATCCCATTTTT-ACCCTCG-AACTTCC
*
5916 AAAAATCCCATTTTTACCCCCGAACTTCC
1 AAAAATCCCATTTTTACCCTCGAACTTCC
* **
5945 AAAAATTCCATTTTTAGCCC-CGAACTTTA
1 AAAAATCCCATTTTTA-CCCTCGAACTTCC
*
5974 AAAAATCCCAATTTTGA-CCTCGAAACTTCC
1 AAAAATCCC-ATTTTTACCCTCG-AACTTCC
**
6004 AAAAATTTCATTTTTACCC-CGAACTTCC
1 AAAAATCCCATTTTTACCCTCGAACTTCC
6032 AAAAATCCCATTTTTGACCC-CGAAACTTCC
1 AAAAATCCCATTTTT-ACCCTCG-AACTTCC
*
6062 AAAAATTCCATTTTTACTCC-CGAACTTCC
1 AAAAATCCCATTTTTAC-CCTCGAACTTCC
*
6091 AAAAATCTCATTTTTAACCC-CGAAACTT-C
1 AAAAATCCCATTTTT-ACCCTCG-AACTTCC
* * ** * *
6120 TAAATTTTCATTTTCACCCTCGAGCTTCC
1 AAAAATCCCATTTTTACCCTCGAACTTCC
6149 AAAAATCCCATTTTTAACCCT-GAAACTTCC
1 AAAAATCCCATTTTT-ACCCTCG-AACTTCC
*
6179 AAAAATTCCATTTTTACCCTCGAACTTCC
1 AAAAATCCCATTTTTACCCTCGAACTTCC
*
6208 AAAAATCCCATTTTTGACCC-CAAAACTTCC
1 AAAAATCCCATTTTT-ACCCTC-GAACTTCC
*
6238 AAAAATTACCA-TTTTACCCTCGAA-TGTCC
1 AAAAA-TCCCATTTTTACCCTCGAACT-TCC
6267 AAAAA-CTCCATTTT
1 AAAAATC-CCATTTT
6281 CAACCTTGAA
Statistics
Matches: 377, Mismatches: 49, Indels: 56
0.78 0.10 0.12
Matches are distributed among these distances:
28 34 0.09
29 187 0.50
30 152 0.40
31 4 0.01
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.32
Consensus pattern (29 bp):
AAAAATCCCATTTTTACCCTCGAACTTCC
Found at i:6077 original size:117 final size:116
Alignment explanation
Indices: 5798--6280 Score: 536
Period size: 117 Copynumber: 4.1 Consensus size: 116
5788 TAAACTATCA
* * * ** **
5798 AAAAATTCCATTTTCACCCTCG-AACTTCCAAAAATCCCATTTTTAACCCTAAAAAGTCCAAAAA
1 AAAAATCCCATTTTTACCC-CGAAACTTCCAAAAATTCCATTTTT-ACCC-CGAACTTCCAAAAA
* * * *
5862 TTCCATTTTT-ACCCCTG-AACTTCCAAAAATCCCATTTTTGA-ACTCGAAACTTTC
63 TCCCATTTTTGACCCC-GAAACTTCCAAAAATTCCATTTTT-ACCCTCG-AACTTCC
**
5916 AAAAATCCCATTTTTACCCCCG-AACTTCCAAAAATTCCATTTTTAGCCCCGAACTTTAAAAAAT
1 AAAAATCCCATTTTTA-CCCCGAAACTTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAAT
* * *
5980 CCCAATTTTGACCTCGAAACTTCCAAAAATTTCATTTTTACCC-CGAACTTCC
64 CCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCC
6032 AAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACTCCCGAACTTCCAAAAAT
1 AAAAATCCCATTTTT-ACCCCGAAACTTCCAAAAATTCCATTTTTAC-CCCGAACTTCCAAAAAT
* * * * * * *
6097 CTCATTTTTAACCCCGAAACTT-CTAAATTTTCATTTTCACCCTCGAGCTTCC
64 CCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCC
*
6149 AAAAATCCCATTTTTAACCCTGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAAT
1 AAAAATCCCATTTTT-ACCCCGAAACTTCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAAT
*
6214 CCCATTTTTGACCCCAAAACTTCCAAAAATTACCA-TTTTACCCTCGAA-TGTCC
64 CCCATTTTTGACCCCGAAACTTCCAAAAATT-CCATTTTTACCCTCGAACT-TCC
6267 AAAAA-CTCCATTTT
1 AAAAATC-CCATTTT
6281 CAACCTTGAA
Statistics
Matches: 315, Mismatches: 36, Indels: 28
0.83 0.09 0.07
Matches are distributed among these distances:
116 46 0.15
117 167 0.53
118 97 0.31
119 5 0.02
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.32
Consensus pattern (116 bp):
AAAAATCCCATTTTTACCCCGAAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATCC
CATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCC
Found at i:6253 original size:59 final size:59
Alignment explanation
Indices: 5798--6280 Score: 535
Period size: 59 Copynumber: 8.2 Consensus size: 59
5788 TAAACTATCA
* * * ** **
5798 AAAAATTCCA-TTTTCACCCTCG-AACTTCCAAAAATCCCATTTTTAACCCTAAAAAGTCC
1 AAAAATCCCATTTTTGACCC-CGAAACTTCCAAAAATTCCATTTTT-ACCCTCGAACTTCC
* * * *
5857 AAAAATTCCATTTTT-ACCCCTG-AACTTCCAAAAATCCCATTTTTGA-ACTCGAAACTTTC
1 AAAAATCCCATTTTTGACCCC-GAAACTTCCAAAAATTCCATTTTT-ACCCTCG-AACTTCC
**
5916 AAAAATCCCATTTTT-ACCCCCG-AACTTCCAAAAATTCCATTTTTAGCCC-CGAACTTTA
1 AAAAATCCCATTTTTGA-CCCCGAAACTTCCAAAAATTCCATTTTTA-CCCTCGAACTTCC
* * *
5974 AAAAATCCCAATTTTGACCTCGAAACTTCCAAAAATTTCATTTTTACCC-CGAACTTCC
1 AAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCC
6032 AAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACTCC-CGAACTTCC
1 AAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTAC-CCTCGAACTTCC
* * * * * * *
6091 AAAAATCTCATTTTTAACCCCGAAACTT-CTAAATTTTCATTTTCACCCTCGAGCTTCC
1 AAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCC
* *
6149 AAAAATCCCATTTTTAACCCTGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCC
1 AAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCC
*
6208 AAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACCA-TTTTACCCTCGAA-TGTCC
1 AAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATT-CCATTTTTACCCTCGAACT-TCC
6267 AAAAA-CTCCATTTT
1 AAAAATC-CCATTTT
6281 CAACCTTGAA
Statistics
Matches: 374, Mismatches: 36, Indels: 28
0.85 0.08 0.06
Matches are distributed among these distances:
57 2 0.01
58 132 0.35
59 228 0.61
60 12 0.03
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.32
Consensus pattern (59 bp):
AAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCC
Found at i:6257 original size:88 final size:87
Alignment explanation
Indices: 5789--6280 Score: 449
Period size: 88 Copynumber: 5.6 Consensus size: 87
5779 GGAGGTCCTT
* * * **
5789 AAACTATCAAAAAATT-CCA-TTTTCACCCTCGAACTTCCAAAAATCCCATTTTTAACCCTAAAA
1 AAACT-TCCAAAAATTCCCATTTTTGACCCTCGAACTTCCAAAAATTCCATTTTT-ACCC-CGAA
**
5852 AGTCCAAAAATTCCATTTTTACCCC
63 CTTCCAAAAATTCCATTTTTACCCC
* * * *
5877 TGAACTTCCAAAAA-TCCCATTTTTGA-ACTCGAAACTTTCAAAAATCCCATTTTTACCCCCGAA
1 -AAACTTCCAAAAATTCCCATTTTTGACCCTCG-AACTTCCAAAAATTCCATTTTTA-CCCCGAA
5940 CTTCCAAAAATTCCATTTTTAGCCCC
63 CTTCCAAAAATTCCATTTTTA-CCCC
* * * * *
5966 GAACTT-TAAAAAATCCCAATTTTGA-CCTCGAAACTTCCAAAAATTTCATTTTTACCCCGAACT
1 AAACTTCCAAAAATTCCCATTTTTGACCCTCG-AACTTCCAAAAATTCCATTTTTACCCCGAACT
*
6029 TCCAAAAATCCCATTTTTGACCCC
65 TCCAAAAATTCCATTTTT-ACCCC
6053 GAAACTTCCAAAAATT-CCATTTTT-ACTCC-CGAACTTCCAAAAA-TCTCATTTTTAACCCCGA
1 -AAACTTCCAAAAATTCCCATTTTTGAC-CCTCGAACTTCCAAAAATTC-CATTTTT-ACCCCG-
* * * *
6114 AACTT-CTAAATTTTCATTTTCACCCTC
61 AACTTCCAAAAATTCCATTTTTACCC-C
* * *
6141 GAGCTTCCAAAAA-TCCCATTTTTAACCCT-GAAACTTCCAAAAATTCCATTTTTACCCTCGAAC
1 AAACTTCCAAAAATTCCCATTTTTGACCCTCG-AACTTCCAAAAATTCCATTTTTACCC-CGAAC
*
6204 TTCCAAAAATCCCATTTTTGACCCC
64 TTCCAAAAATTCCATTTTT-ACCCC
* *
6229 AAAACTTCCAAAAATTACCA-TTTT-ACCCTCGAA-TGTCCAAAAACTCCATTTT
1 -AAACTTCCAAAAATTCCCATTTTTGACCCTCGAACT-TCCAAAAATTCCATTTT
6281 CAACCTTGAA
Statistics
Matches: 339, Mismatches: 37, Indels: 55
0.79 0.09 0.13
Matches are distributed among these distances:
86 2 0.01
87 92 0.27
88 169 0.50
89 72 0.21
90 4 0.01
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (87 bp):
AAACTTCCAAAAATTCCCATTTTTGACCCTCGAACTTCCAAAAATTCCATTTTTACCCCGAACTT
CCAAAAATTCCATTTTTACCCC
Found at i:6311 original size:117 final size:115
Alignment explanation
Indices: 5798--6402 Score: 487
Period size: 117 Copynumber: 5.2 Consensus size: 115
5788 TAAACTATCA
* * ** **
5798 AAAAATTCCATTTTC-ACCCTCG-AACTTCCAAAAATCCCATTTTTAACCCTAAAAAGTCCAAAA
1 AAAAATCCCATTTTCAACCCT-GAAACTTCCAAAAATTCCATTTTT-ACCC-CGAACTTCCAAAA
* ** * * *
5861 ATTCCATTTTT-ACCCCTGAACTTCCAAAAATCCCATTTTTGA-ACTCGAAACTTTC
63 ATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCA-TTTT-ACCCTCG-AA-TTCC
* * * **
5916 AAAAATCCCATTTTTACCCCCG-AACTTCCAAAAATTCCATTTTTAGCCCCGAACTTTAAAAAAT
1 AAAAATCCCATTTTCAACCCTGAAACTTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAAT
* * * * *
5980 CCCAATTTTGACCTCGAAACTTCCAAAAATTTCATTTTTACCC-CGAACTTCC
65 CCCATTTTTAACCCCAAAACTTCCAAAAATTCCA-TTTTACCCTCGAA-TTCC
** *
6032 AAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACTCCCGAACTTCCAAAAAT
1 AAAAATCCCATTTTCAACCCTGAAACTTCCAAAAATTCCATTTTTAC-CCCGAACTTCCAAAAAT
* * * * * *
6097 CTCATTTTTAACCCCGAAACTT-CTAAATTTTCATTTTCACCCTCGAGCTTCC
65 CCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTT-ACCCTCGA-ATTCC
*
6149 AAAAATCCCATTTTTAACCCTGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAAT
1 AAAAATCCCATTTTCAACCCTGAAACTTCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAAT
*
6214 CCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCTCGAATGTCC
65 CCCATTTTTAACCCCAAAACTTCCAAAAATT-CCATTTTACCCTCGAAT-TCC
* * * *
6267 AAAAA-CTCCATTTTCAACCTTGAAAC-TCTC-AAAATAACC-CTTTTACCCCTGAA-TGTCTAA
1 AAAAATC-CCATTTTCAACCCTGAAACTTC-CAAAAAT-TCCATTTTTACCCC-GAACT-TCCAA
* * * ** * * *
6327 AGATCCCATTCTTAACCCTAAAGTTTCCCAAAATTCTCATTTTACCCCCGAGTATCC
61 AAATCCCATTTTTAACCCCAAAACTTCCAAAAATTC-CATTTTACCCTCGAAT-TCC
* *
6384 GAAAAGTCTCATTTTCAAC
1 -AAAAATCCCATTTTCAAC
6403 TCCGATTGTA
Statistics
Matches: 409, Mismatches: 57, Indels: 42
0.81 0.11 0.08
Matches are distributed among these distances:
115 4 0.01
116 45 0.11
117 231 0.56
118 119 0.29
119 10 0.02
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (115 bp):
AAAAATCCCATTTTCAACCCTGAAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATC
CCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTACCCTCGAATTCC
Found at i:18388 original size:11 final size:12
Alignment explanation
Indices: 18367--18475 Score: 50
Period size: 11 Copynumber: 9.3 Consensus size: 12
18357 GATTTATTTC
*
18367 TAAAATTAAATT
1 TAAATTTAAATT
*
18379 T-ACTTTAAATT
1 TAAATTTAAATT
18390 TAAATTTAAATT
1 TAAATTTAAATT
***
18402 CTTTTTTTAAATT
1 -TAAATTTAAATT
* ***
18415 T-ATTTTTTTTT
1 TAAATTTAAATT
18426 TAAATTTAAATT
1 TAAATTTAAATT
*
18438 T-AGTTTAAATT
1 TAAATTTAAATT
18449 TGAAA--T-AATT
1 T-AAATTTAAATT
*
18459 ATAAACTTAAATT
1 -TAAATTTAAATT
18472 TAAA
1 TAAA
18476 ATCAATTACA
Statistics
Matches: 72, Mismatches: 16, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
10 7 0.10
11 28 0.39
12 23 0.32
13 14 0.19
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (12 bp):
TAAATTTAAATT
Found at i:18391 original size:6 final size:6
Alignment explanation
Indices: 18367--18475 Score: 50
Period size: 6 Copynumber: 18.7 Consensus size: 6
18357 GATTTATTTC
* * ***
18367 TAAAAT TAAATT T-ACTT TAAATT TAAATT TAAATT CTTTTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT
* *** *
18415 T-ATTT TTTTTT TAAATT TAAATT T-AGTT TAAATT TGAAA-- T-AATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT
*
18459 ATAAACT TAAATT TAAA
1 -TAAATT TAAATT TAAA
18476 ATCAATTACA
Statistics
Matches: 76, Mismatches: 18, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
3 2 0.03
5 13 0.17
6 52 0.68
7 9 0.12
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (6 bp):
TAAATT
Found at i:18392 original size:17 final size:18
Alignment explanation
Indices: 18353--18397 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
18343 TTAGATGGGT
* *
18353 TTTAGATTTATTTCTAAA
1 TTTAAATTTACTTCTAAA
*
18371 ATTAAATTTACTT-TAAA
1 TTTAAATTTACTTCTAAA
18388 TTTAAATTTA
1 TTTAAATTTA
18398 AATTCTTTTT
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:18425 original size:17 final size:17
Alignment explanation
Indices: 18388--18433 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
18378 TTACTTTAAA
18388 TTTAAATTTAAATTCTTTT
1 TTTAAATTT--ATTCTTTT
*
18407 TTTAAATTTATTTTTTT
1 TTTAAATTTATTCTTTT
18424 TTTAAATTTA
1 TTTAAATTTA
18434 AATTTAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 17 0.65
19 9 0.35
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTAAATTTATTCTTTT
Found at i:19270 original size:21 final size:20
Alignment explanation
Indices: 19244--19299 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
19234 TAATAATCAT
* *
19244 TAATAATAATAAATGTTTTGA
1 TAATAATAATAAAT-TATTAA
19265 TAATAATAATAATATTATTAA
1 TAATAATAATAA-ATTATTAA
19286 TAATAATTAATAAA
1 TAATAA-TAATAAA
19300 AAAAAGGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 23 0.74
22 8 0.26
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (20 bp):
TAATAATAATAAATTATTAA
Found at i:20308 original size:29 final size:28
Alignment explanation
Indices: 20261--20635 Score: 319
Period size: 29 Copynumber: 12.8 Consensus size: 28
20251 AATGTCCCTA
* *
20261 AACTATCCAAAAATTTCATTTTCACTCCCG
1 AACT-TCCAAAAATCTCATTTTTAC-CCCG
20291 AACTTCCAAAAATCTCATTTTTAACCCCG
1 AACTTCCAAAAATCTCATTTTT-ACCCCG
* * *
20320 AAACATCCAAAAAT-TCCATTTTCACTCCCT
1 -AACTTCCAAAAATCT-CATTTTTAC-CCCG
* *
20350 AACTTCCAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATCTCATTTTT-ACCCC-G
*
20380 AACTTCCAAAAATCCCATTTTTACCCCCG
1 AACTTCCAAAAATCTCATTTTTA-CCCCG
*
20409 AACTTCCAAAAAT-TCCATTTTTACCCTCA
1 AACTTCCAAAAATCT-CATTTTTACCC-CG
*
20438 AACTTCCAAAAATCCCATTTTTGACCCCG
1 AACTTCCAAAAATCTCATTTTT-ACCCCG
*
20467 AAACTTCCAAAAATATCATTTTTACCCTCG
1 -AACTTCCAAAAATCTCATTTTTACCC-CG
* * *
20497 AACTTTCAAAAATCCCATTTTTAAACCCG
1 AACTTCCAAAAATCTCATTTTT-ACCCCG
* * *
20526 AAACTTCCAAAACT-TCCGTTTTTACTCTCG
1 -AACTTCCAAAAATCT-CATTTTTAC-CCCG
*
20556 AACTTCCAAAAATCCCATTTTTAACCCCG
1 AACTTCCAAAAATCTCATTTTT-ACCCCG
* *
20585 AAACTTCCAAAAATTTCGA--TTCACCCCCG
1 -AACTTCCAAAAATCTC-ATTTTTA-CCCCG
* *
20614 AGCTTCTAAAAATCTCATTTTT
1 AACTTCCAAAAATCTCATTTTT
20636 GACTCCAAAG
Statistics
Matches: 283, Mismatches: 37, Indels: 51
0.76 0.10 0.14
Matches are distributed among these distances:
27 1 0.00
28 17 0.06
29 144 0.51
30 120 0.42
31 1 0.00
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.31
Consensus pattern (28 bp):
AACTTCCAAAAATCTCATTTTTACCCCG
Found at i:20357 original size:59 final size:59
Alignment explanation
Indices: 20260--20598 Score: 354
Period size: 59 Copynumber: 5.7 Consensus size: 59
20250 AAATGTCCCT
**
20260 AAACTATCCAAAAATTTCATTTTCACTCCCGAACTTCCAAAAATCTCATTTTTAACCC-CG
1 AAACT-TCCAAAAATCCCATTTTCACTCCCGAACTTCCAAAAATCTCATTTTT-ACCCTCG
* * * * *
20320 AAACATCCAAAAATTCCATTTTCACTCCCTAACTTCCAAAAATCCCATTTTTAACCC-CA
1 AAACTTCCAAAAATCCCATTTTCACTCCCGAACTTCCAAAAATCTCATTTTT-ACCCTCG
* *
20379 AAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCAAAAAT-TCCATTTTTACCCTC-
1 AAACTTCCAAAAATCCCATTTTCACTCCCGAACTTCCAAAAATCT-CATTTTTACCCTCG
* *
20437 AAACTTCCAAAAATCCCATTTTTGAC-CCCGAAACTTCCAAAAATATCATTTTTACCCTCG
1 AAACTTCCAAAAATCCCA-TTTTCACTCCCG-AACTTCCAAAAATCTCATTTTTACCCTCG
* * ** * * *
20497 -AACTTTCAAAAATCCCATTTTTAAACCCGAAACTTCCAAAACT-TCCGTTTTTACTCTCG
1 AAACTTCCAAAAATCCCATTTTCACTCCCG-AACTTCCAAAAATCT-CATTTTTACCCTCG
*
20556 -AACTTCCAAAAATCCCATTTTTAAC-CCCGAAACTTCCAAAAAT
1 AAACTTCCAAAAATCCCA-TTTTCACTCCCG-AACTTCCAAAAAT
20599 TTCGATTCAC
Statistics
Matches: 248, Mismatches: 22, Indels: 19
0.86 0.08 0.07
Matches are distributed among these distances:
58 32 0.13
59 206 0.83
60 10 0.04
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.30
Consensus pattern (59 bp):
AAACTTCCAAAAATCCCATTTTCACTCCCGAACTTCCAAAAATCTCATTTTTACCCTCG
Found at i:20421 original size:88 final size:88
Alignment explanation
Indices: 20291--20665 Score: 377
Period size: 88 Copynumber: 4.2 Consensus size: 88
20281 TTCACTCCCG
* * *
20291 AACTTCCAAAAATCTCATTTTTAACCCCGAAACATCCAAAAATTCCATTTTCACTCCCTAACTTC
1 AACTTCCAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTCAC-CCCAAACTTC
*
20356 CAAAAATCCCATTTTTAACCCCAA
65 CAAAAATCCCATTTTTGACCCCAA
* *
20380 AACTTCCAAAAATCCCATTTTTACCCCCG-AACTTCCAAAAATTCCATTTTTACCCTCAAACTTC
1 AACTTCCAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTCACCC-CAAACTTC
*
20444 CAAAAATCCCATTTTTGACCCCGA
65 CAAAAATCCCATTTTTGACCCCAA
** * * * *
20468 AACTTCCAAAAATATCATTTTT-ACCCTCG-AACTTTCAAAAATCCCATTTTTAAACCCGAAACT
1 AACTTCCAAAAATCCCATTTTTAACCC-CGAAACTTCCAAAAATTCCA-TTTT-CACCCCAAACT
* * * * *
20531 TCCAAAACTTCCGTTTTT-ACTCTC-G
63 TCCAAAAATCCCATTTTTGAC-CCCAA
* * *
20556 AACTTCCAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAATTTCGA--TTCACCCCCGAGCTT
1 AACTTCCAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAA-TTCCATTTTCA-CCCCAAACTT
* * *
20619 CTAAAAATCTCATTTTTGACTCCAA
64 CCAAAAATCCCATTTTTGACCCCAA
* * *
20644 AGCTTCCCAAAATTACCATTTT
1 AACTT-CCAAAAATCCCATTTT
20666 GCCCTCGGAT
Statistics
Matches: 235, Mismatches: 39, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
86 1 0.00
87 27 0.11
88 118 0.50
89 82 0.35
90 7 0.03
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (88 bp):
AACTTCCAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTCACCCCAAACTTCC
AAAAATCCCATTTTTGACCCCAA
Found at i:20713 original size:117 final size:117
Alignment explanation
Indices: 20442--20815 Score: 284
Period size: 117 Copynumber: 3.2 Consensus size: 117
20432 CCCTCAAACT
** * * * * *
20442 TCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATATCATTTTTACCCTCGAACTTTC-AA
1 TCCAAAAATCCCATTTTCAACCCCGAAACTTCCAAAATTATCA-ATTCACCCCCGAA-TGTCTAA
* * * * * *
20506 AAATCCCATTTTTAAACCCGAAAC-TT-CCAAAACTT-CCGTTTTTACTCTCGAACT-
64 AAATCCCATTCTT-AACCCTAAACTTTCCCAAAA-TTACC-ATTTTGCCCTCGGA-TG
* * *
20560 TCCAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAATT-TCGATTCACCCCCGAGCT-TCTAA
1 TCCAAAAATCCCATTTTCAACCCCGAAACTTCC-AAAATTATCAATTCACCCCCGA-ATGTCTAA
* * *
20623 AAATCTCATTTTTGACTCC-AAAGC-TTCCCAAAATTACCATTTTGCCCTCGGATG
64 AAATCCCATTCTTAAC-CCTAAA-CTTTCCCAAAATTACCATTTTGCCCTCGGATG
* * * *
20677 TCCAAAAA-CTCCATTTTCGACCTCGAAAC-TCTCAAAATTATCAATTTACCCCTGAATGTCTAA
1 TCCAAAAATC-CCATTTTCAACCCCGAAACTTC-CAAAATTATCAATTCACCCCCGAATGTCTAA
* * * * *
20740 AGATCCCATTCTTAACCCTAAACTTTCCCAAAATTCCCATTTTGCCCCCGGGTA
64 AAATCCCATTCTTAACCCTAAACTTTCCCAAAATTACCATTTTGCCCTCGGATG
* *
20794 TCCGAAAAGTCTCATTTTCAAC
1 TCC-AAAAATCCCATTTTCAAC
20816 TTCGATTTTA
Statistics
Matches: 209, Mismatches: 31, Indels: 32
0.77 0.11 0.12
Matches are distributed among these distances:
116 21 0.10
117 127 0.61
118 55 0.26
119 6 0.03
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.31
Consensus pattern (117 bp):
TCCAAAAATCCCATTTTCAACCCCGAAACTTCCAAAATTATCAATTCACCCCCGAATGTCTAAAA
ATCCCATTCTTAACCCTAAACTTTCCCAAAATTACCATTTTGCCCTCGGATG
Found at i:27459 original size:9 final size:9
Alignment explanation
Indices: 27445--27493 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
27435 ATAAATGATT
27445 TTAAAATTA
1 TTAAAATTA
27454 TTAAAATTA
1 TTAAAATTA
*
27463 TTTTTAAAAATA
1 ---TTAAAATTA
27475 -TAAAATTA
1 TTAAAATTA
27483 TTAAAATTA
1 TTAAAATTA
27492 TT
1 TT
27494 TTTTTTTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
8 7 0.21
9 19 0.56
12 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TTAAAATTA
Found at i:27465 original size:20 final size:20
Alignment explanation
Indices: 27437--27493 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
27427 CCTCGTCAAT
*
27437 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
*
27457 AAATTATTTTTAAAAATA-TA
1 AAATTA-TTTTAAAATTATTA
27477 AAATTA--TTAAAATTATT
1 AAATTATTTTAAAATTATT
27494 TTTTTTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 8 0.25
18 1 0.03
20 13 0.41
21 10 0.31
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:27786 original size:17 final size:17
Alignment explanation
Indices: 27766--27801 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
27756 AAAAAACATT
*
27766 AAGAGCCAAAATGACCC
1 AAGAACCAAAATGACCC
*
27783 AAGAACCAAAGTGACCC
1 AAGAACCAAAATGACCC
27800 AA
1 AA
27802 CACCCAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.28, G:0.17, T:0.06
Consensus pattern (17 bp):
AAGAACCAAAATGACCC
Found at i:27808 original size:17 final size:17
Alignment explanation
Indices: 27771--27809 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
27761 ACATTAAGAG
*
27771 CCAAAATGACCCAAGAA
1 CCAAAATGACCCAACAA
* *
27788 CCAAAGTGACCCAACAC
1 CCAAAATGACCCAACAA
27805 CCAAA
1 CCAAA
27810 CATTAGGGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.36, G:0.10, T:0.05
Consensus pattern (17 bp):
CCAAAATGACCCAACAA
Found at i:31366 original size:129 final size:129
Alignment explanation
Indices: 31136--31395 Score: 511
Period size: 129 Copynumber: 2.0 Consensus size: 129
31126 GCCAGGTTCT
31136 AGAGATGATGTGAATTTGTGCTTCCCTTTATCTGAAAGCTTCATTTCCCATTAAGGCCATGGCTT
1 AGAGATGATGTGAATTTGTGCTTCCCTTTATCTGAAAGCTTCATTTCCCATTAAGGCCATGGCTT
*
31201 TAACATCCATGACTTGGGTGGGGGATTATATTGGGATTGCCTTACAATCGGCGATTATTGATTC
66 TAACATCCATGACTTGGGTGGGGGATTATATTGGGATTGCCTTACAATCGGCAATTATTGATTC
31265 AGAGATGATGTGAATTTGTGCTTCCCTTTATCTGAAAGCTTCATTTCCCATTAAGGCCATGGCTT
1 AGAGATGATGTGAATTTGTGCTTCCCTTTATCTGAAAGCTTCATTTCCCATTAAGGCCATGGCTT
31330 TAACATCCATGACTTGGGTGGGGGATTATATTGGGATTGCCTTACAATCGGCAATTATTGATTC
66 TAACATCCATGACTTGGGTGGGGGATTATATTGGGATTGCCTTACAATCGGCAATTATTGATTC
31394 AG
1 AG
31396 GGTGGGTTTG
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 130 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (129 bp):
AGAGATGATGTGAATTTGTGCTTCCCTTTATCTGAAAGCTTCATTTCCCATTAAGGCCATGGCTT
TAACATCCATGACTTGGGTGGGGGATTATATTGGGATTGCCTTACAATCGGCAATTATTGATTC
Found at i:33021 original size:20 final size:20
Alignment explanation
Indices: 33009--33064 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
32999 AGAAGTATAC
*
33009 TTGTATCGGTAGAACTGAAG
1 TTGTATCGGTAGAAGTGAAG
*
33029 TTGTATCGGTAGAAATGAAG
1 TTGTATCGGTAGAAGTGAAG
*
33049 TTCTATCGGTAGAAGT
1 TTGTATCGGTAGAAGT
33065 CCTAAGGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.09, G:0.29, T:0.32
Consensus pattern (20 bp):
TTGTATCGGTAGAAGTGAAG
Found at i:35125 original size:60 final size:57
Alignment explanation
Indices: 35056--35205 Score: 167
Period size: 60 Copynumber: 2.5 Consensus size: 57
35046 ATACACCATA
* *
35056 TTTTTTATCTGATAAAAAATAATTTTTTTTAGTATTGACCATGTATTGGCCGACACTACC
1 TTTTTTATCTGATAAAAAATAATTTTTTTTAGTA--GACAATG-ATTGGCCGACACCACC
* * * *
35116 TTTTTTATCTGATAAAAAA-ATATTTTTTTGTGGTAGTCAATGCTTGGTCGACACCACC
1 TTTTTTATCTGATAAAAAATA-ATTTTTTT-TAGTAGACAATGATTGGCCGACACCACC
*
35174 TTTTTTATCAGATAAAAAAATAAATTTTTTTT
1 TTTTTTATCTGAT-AAAAAAT-AATTTTTTTT
35206 GTGTTGGCCA
Statistics
Matches: 78, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
58 25 0.32
59 13 0.17
60 35 0.45
61 5 0.06
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (57 bp):
TTTTTTATCTGATAAAAAATAATTTTTTTTAGTAGACAATGATTGGCCGACACCACC
Found at i:35176 original size:58 final size:60
Alignment explanation
Indices: 35056--35205 Score: 182
Period size: 58 Copynumber: 2.5 Consensus size: 60
35046 ATACACCATA
* *
35056 TTTTTTATCTGAT-AAAAAATAATTTTTTTTAGTATTGACCATGTATTGGCCGACACTACC
1 TTTTTTATCTGATAAAAAAATAATTTTTTTTAGTA-TGACAATGTATTGGCCGACACCACC
* * * *
35116 TTTTTTATCTGATAAAAAAAT-ATTTTTTTGTGGTA-GTCAATG-CTTGGTCGACACCACC
1 TTTTTTATCTGATAAAAAAATAATTTTTTT-TAGTATGACAATGTATTGGCCGACACCACC
*
35174 TTTTTTATCAGATAAAAAAATAAATTTTTTTT
1 TTTTTTATCTGATAAAAAAAT-AATTTTTTTT
35206 GTGTTGGCCA
Statistics
Matches: 79, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
58 33 0.42
59 6 0.08
60 29 0.37
61 11 0.14
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (60 bp):
TTTTTTATCTGATAAAAAAATAATTTTTTTTAGTATGACAATGTATTGGCCGACACCACC
Found at i:36015 original size:47 final size:47
Alignment explanation
Indices: 35961--36119 Score: 149
Period size: 47 Copynumber: 3.2 Consensus size: 47
35951 AGAATGTTTG
35961 TATTTTATTGTATTAATATAATTTCGATTTATAAAAAAATTATTAAA
1 TATTTTATTGTATTAATATAATTTCGATTTATAAAAAAATTATTAAA
* * * ** * ** * *
36008 TATTTTATTGTGTAAATGTTAAGAAAT-AATTATTATCGACAAATTAAATATATA
1 TATTTTATTGTATTAAT-AT-A-ATTTCGA-T-TTATAAAAAAATT--AT-TAAA
36062 TATTTTATTGTATTAATATAATTTCGATTTATAAAAAAATTATTAAA
1 TATTTTATTGTATTAATATAATTTCGATTTATAAAAAAATTATTAAA
36109 TATTTTATTGT
1 TATTTTATTGT
36120 GTAAATGTTA
Statistics
Matches: 83, Mismatches: 20, Indels: 18
0.69 0.17 0.15
Matches are distributed among these distances:
47 29 0.35
48 3 0.04
49 2 0.02
50 13 0.16
51 13 0.16
52 2 0.02
53 3 0.04
54 18 0.22
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (47 bp):
TATTTTATTGTATTAATATAATTTCGATTTATAAAAAAATTATTAAA
Found at i:36070 original size:101 final size:101
Alignment explanation
Indices: 35961--36163 Score: 406
Period size: 101 Copynumber: 2.0 Consensus size: 101
35951 AGAATGTTTG
35961 TATTTTATTGTATTAATATAATTTCGATTTATAAAAAAATTATTAAATATTTTATTGTGTAAATG
1 TATTTTATTGTATTAATATAATTTCGATTTATAAAAAAATTATTAAATATTTTATTGTGTAAATG
36026 TTAAGAAATAATTATTATCGACAAATTAAATATATA
66 TTAAGAAATAATTATTATCGACAAATTAAATATATA
36062 TATTTTATTGTATTAATATAATTTCGATTTATAAAAAAATTATTAAATATTTTATTGTGTAAATG
1 TATTTTATTGTATTAATATAATTTCGATTTATAAAAAAATTATTAAATATTTTATTGTGTAAATG
36127 TTAAGAAATAATTATTATCGACAAATTAAATATATA
66 TTAAGAAATAATTATTATCGACAAATTAAATATATA
36163 T
1 T
36164 TGAAAAAAAA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (101 bp):
TATTTTATTGTATTAATATAATTTCGATTTATAAAAAAATTATTAAATATTTTATTGTGTAAATG
TTAAGAAATAATTATTATCGACAAATTAAATATATA
Found at i:36159 original size:48 final size:48
Alignment explanation
Indices: 36002--36159 Score: 144
Period size: 48 Copynumber: 3.2 Consensus size: 48
35992 TAAAAAAATT
36002 ATTAAATATTTTATTGTGTAAATGTTAAGAAATAATTATTATCGACAA
1 ATTAAATATTTTATTGTGTAAATGTTAAGAAATAATTATTATCGACAA
* * * * ** *
36050 ATTAAATATATATATT-T-T-ATTGTATTA-ATATAATTTCGATTTATAAAAAAA
1 ATTAAATAT-TTTATTGTGTAAATGT-TAAGAAATAA-TT--A-TTAT-CGACAA
36101 TTATTAAATATTTTATTGTGTAAATGTTAAGAAATAATTATTATCGACAA
1 --ATTAAATATTTTATTGTGTAAATGTTAAGAAATAATTATTATCGACAA
36151 ATTAAATAT
1 ATTAAATAT
36160 ATATTGAAAA
Statistics
Matches: 83, Mismatches: 14, Indels: 26
0.67 0.11 0.21
Matches are distributed among these distances:
46 9 0.11
47 5 0.06
48 19 0.23
49 6 0.07
50 7 0.08
51 7 0.08
52 6 0.07
53 10 0.12
54 5 0.06
55 9 0.11
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (48 bp):
ATTAAATATTTTATTGTGTAAATGTTAAGAAATAATTATTATCGACAA
Found at i:37827 original size:21 final size:22
Alignment explanation
Indices: 37801--37845 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
37791 GGTGACTCAA
**
37801 TAAATTGATTTTATA-TATTTT
1 TAAATTGATTAAATATTATTTT
*
37822 TAAATTTATTAAATATTATTTT
1 TAAATTGATTAAATATTATTTT
37844 TA
1 TA
37846 TTCTAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TAAATTGATTAAATATTATTTT
Found at i:37994 original size:21 final size:20
Alignment explanation
Indices: 37970--38016 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
37960 ATATTTTCGA
* *
37970 ATTTTTAAAATATTTTTTTCT
1 ATTTTTAAAAT-GTTTTTTAT
*
37991 ATTTTCAAAATGTTTTTTAT
1 ATTTTTAAAATGTTTTTTAT
38011 ATTTTT
1 ATTTTT
38017 GAATTTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (20 bp):
ATTTTTAAAATGTTTTTTAT
Found at i:38084 original size:18 final size:18
Alignment explanation
Indices: 38061--38102 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
38051 TTTGCATATA
*
38061 TTTTTATATTTTCGAATT
1 TTTTTAGATTTTCGAATT
* *
38079 TTTTTAGCTTTTTGAATT
1 TTTTTAGATTTTCGAATT
38097 TTTTTA
1 TTTTTA
38103 AAATTATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.07, T:0.69
Consensus pattern (18 bp):
TTTTTAGATTTTCGAATT
Found at i:38136 original size:36 final size:36
Alignment explanation
Indices: 38091--38163 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
38081 TTTAGCTTTT
*
38091 TGAATTTTTTTAAA-ATTATTTTTTATATCTTCAAAA
1 TGAAATTTTTTAAATA-TATTTTTTATATCTTCAAAA
* * *
38127 TGAAATTTTTTACATATATTTTTTATATTTTCGAAA
1 TGAAATTTTTTAAATATATTTTTTATATCTTCAAAA
38163 T
1 T
38164 ATTAAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.56
Consensus pattern (36 bp):
TGAAATTTTTTAAATATATTTTTTATATCTTCAAAA
Found at i:39305 original size:30 final size:30
Alignment explanation
Indices: 39269--39389 Score: 181
Period size: 30 Copynumber: 4.1 Consensus size: 30
39259 TTTTGAATTT
* *
39269 TTTCATTTATTTTTTAAATTTAATTTGTAA
1 TTTCATTTATATTTTAAATTTAATTTCTAA
39299 TTTCATTTATATTTT-AATTTAATTTCTAA
1 TTTCATTTATATTTTAAATTTAATTTCTAA
**
39328 TTTTGTTTATATTTTAAATTTAATTTCTAA
1 TTTCATTTATATTTTAAATTTAATTTCTAA
* *
39358 TTTCGTTTATATTTTAAATTTCATTTCTAA
1 TTTCATTTATATTTTAAATTTAATTTCTAA
39388 TT
1 TT
39390 ATTATTTTTT
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
29 26 0.31
30 58 0.69
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (30 bp):
TTTCATTTATATTTTAAATTTAATTTCTAA
Found at i:39347 original size:59 final size:60
Alignment explanation
Indices: 39274--39389 Score: 189
Period size: 59 Copynumber: 1.9 Consensus size: 60
39264 AATTTTTTCA
* *
39274 TTTATTTTTTAAATTTAATTTGTAATTTCATTTATATTTT-AATTTAATTTCTAATTTTG
1 TTTATATTTTAAATTTAATTTCTAATTTCATTTATATTTTAAATTTAATTTCTAATTTTG
* *
39333 TTTATATTTTAAATTTAATTTCTAATTTCGTTTATATTTTAAATTTCATTTCTAATT
1 TTTATATTTTAAATTTAATTTCTAATTTCATTTATATTTTAAATTTAATTTCTAATT
39390 ATTATTTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
59 37 0.71
60 15 0.29
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (60 bp):
TTTATATTTTAAATTTAATTTCTAATTTCATTTATATTTTAAATTTAATTTCTAATTTTG
Found at i:39406 original size:59 final size:55
Alignment explanation
Indices: 39274--39408 Score: 162
Period size: 59 Copynumber: 2.3 Consensus size: 55
39264 AATTTTTTCA
*
39274 TTTATTTTTTAAATTTAATTTGTAATTTCATTTATATTTTAATTTAATTTCTAATTTT
1 TTTATTTTTTAAATTTAATTTCTAATTTCATTTATATTTTAATTTAATTTCTAA---T
* * *
39332 GTTTATATTTTAAATTTAATTTCTAATTTCGTTTATATTTTAAATTTCATTTCTAAT
1 -TTTATTTTTTAAATTTAATTTCTAATTTCATTTATATTTT-AATTTAATTTCTAAT
39389 TATTATTTTTTCAAAATTTA
1 T-TTATTTTTT--AAATTTA
39409 TATAATCTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
56 1 0.01
57 9 0.13
59 44 0.66
60 13 0.19
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.62
Consensus pattern (55 bp):
TTTATTTTTTAAATTTAATTTCTAATTTCATTTATATTTTAATTTAATTTCTAAT
Found at i:40353 original size:55 final size:55
Alignment explanation
Indices: 40246--40358 Score: 122
Period size: 55 Copynumber: 2.1 Consensus size: 55
40236 CATGACTAAC
* * * **
40246 AAAAAAATTTTATTAGATAAAAAAAATGATGTCGACCAAGCATTGGTGAACACCA
1 AAAAAAAATTTATTAGATAAAAAAAATGATATCGACCAAGCATTAGCCAACACCA
* * *
40301 AAAAAAAATTTATCT-GATAAAAAAATTGGTATCGACCAATGCA-TAGCCAACACTA
1 AAAAAAAATTTAT-TAGATAAAAAAAATGATATCGACCAA-GCATTAGCCAACACCA
40356 AAA
1 AAA
40359 TTTTTTTTGA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
55 44 0.92
56 4 0.08
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.23
Consensus pattern (55 bp):
AAAAAAAATTTATTAGATAAAAAAAATGATATCGACCAAGCATTAGCCAACACCA
Found at i:40396 original size:56 final size:54
Alignment explanation
Indices: 40309--40482 Score: 163
Period size: 59 Copynumber: 3.1 Consensus size: 54
40299 CAAAAAAAAA
* * * *
40309 TTTATCTGATAAAAAAAT-TGGTATCGACCAATGCATAGCCAACACTAAAATTTTT
1 TTTATCAGAT-AAAAAATGTGGTATCGGCCAATGAATGGCCAACAC-AAAATTTTT
* * *
40364 TTTGATCAGATAAAAAATGTGGTGTCGGCCAATAAATGGCCACCACCAAAAAAATATTTT
1 TTT-ATCAGATAAAAAATGTGGTATCGGCCAATGAATGGCCA--A-C-ACAAAAT-TTTT
* * *
40424 TTTATCAGATAAAAAA-GATTGTATCTGCCAATGGATGGCCAACACAAAATTTTT
1 TTTATCAGATAAAAAATG-TGGTATCGGCCAATGAATGGCCAACACAAAATTTTT
40478 TTTAT
1 TTTAT
40483 TTTTTTATCA
Statistics
Matches: 98, Mismatches: 13, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
54 9 0.09
55 16 0.16
56 25 0.26
57 1 0.01
58 2 0.02
59 37 0.38
60 8 0.08
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (54 bp):
TTTATCAGATAAAAAATGTGGTATCGGCCAATGAATGGCCAACACAAAATTTTT
Found at i:40431 original size:59 final size:57
Alignment explanation
Indices: 40355--40567 Score: 180
Period size: 59 Copynumber: 3.6 Consensus size: 57
40345 AGCCAACACT
* *
40355 AAAAT-TTTTTTTGATCAGATAAAAAATGTGGTGTCGGCCAATAAATGGCCACCACCAAA
1 AAAATATTTTTTT-ATCAGAT-AAAAAGGTGGTGTCGGCCAAT-AATGGCCAACACCAAA
* * * * *
40414 AAAATATTTTTTTATCAGATAAAAAAGATTGTATCTGCCAATGGATGGCCAACA-CAAA
1 AAAATATTTTTTTATCAGAT-AAAAAGGTGGTGTCGGCCAAT-AATGGCCAACACCAAA
*** * * *
40472 ATTTTTTTTATTTTTTTATCAGATAAAAAGGTAGTGTCGGTCAAGTATTGGCCAACACCAAA
1 A----AAATATTTTTTTATCAGATAAAAAGGTGGTGTCGGCCAA-TAATGGCCAACACCAAA
*
40534 AAGAATA-TTTTTTATCCGATAAAAAGGTGGTGTC
1 AA-AATATTTTTTTATCAGATAAAAAGGTGGTGTC
40568 AACTAATGCA
Statistics
Matches: 123, Mismatches: 23, Indels: 17
0.75 0.14 0.10
Matches are distributed among these distances:
58 30 0.24
59 40 0.33
60 7 0.06
61 24 0.20
62 22 0.18
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (57 bp):
AAAATATTTTTTTATCAGATAAAAAGGTGGTGTCGGCCAATAATGGCCAACACCAAA
Found at i:40527 original size:61 final size:63
Alignment explanation
Indices: 40418--40534 Score: 150
Period size: 61 Copynumber: 1.9 Consensus size: 63
40408 ACCAAAAAAA
* *
40418 TATTTTTTTATCAGATAAAAAAGATTGTATCTGCCAATGGATGGCCAACA-CAAAATTTTTTT
1 TATTTTTTTATCAGATAAAAAAGATAGTATCGGCCAATGGATGGCCAACACCAAAATTTTTTT
* * * *
40480 TATTTTTTTATCAGAT-AAAAAGGTAGTGTCGGTCAA-GTATTGGCCAACACCAAAA
1 TATTTTTTTATCAGATAAAAAAGATAGTATCGGCCAATGGA-TGGCCAACACCAAAA
40535 AGAATATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 2 0.04
61 24 0.51
62 21 0.45
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (63 bp):
TATTTTTTTATCAGATAAAAAAGATAGTATCGGCCAATGGATGGCCAACACCAAAATTTTTTT
Found at i:40588 original size:120 final size:122
Alignment explanation
Indices: 40360--40602 Score: 280
Period size: 120 Copynumber: 2.0 Consensus size: 122
40350 ACACTAAAAT
* * *
40360 TTTTTTTGATCAGATAAAAAATGTGGTGTCGGCCAATAAATGGCCACCACCAAAAAAATATTTTT
1 TTTTTTTGATCAGATAAAAAAGGTAGTGTCGGCCAATAAATGGCCAACACCAAAAAAATATTTTT
* ** * * *
40425 TTATCAGATAAAAAAGATTGTATCTGCCAATGGATGGCCAACACAAAATTTTTTTTA
66 TTATCAGATAAAAAAGATGGTATCAACCAATGCACGGCAAACACAAAATTTTTTTTA
* *
40482 TTTTTTT-ATCAGAT-AAAAAGGTAGTGTCGGTCAAGT-ATTGGCCAACACCAAAAAGAATA-TT
1 TTTTTTTGATCAGATAAAAAAGGTAGTGTCGGCCAA-TAAATGGCCAACACCAAAAA-AATATTT
* * * * *
40543 TTTTATCCGAT-AAAAAGGTGGTGTCAACTAATGCACGGTCAAACACCAAATTTTTTTTA
64 TTTTATCAGATAAAAAAGATGGTATCAACCAATGCACGG-CAAACACAAAATTTTTTTTA
40602 T
1 T
40603 CTGATAAAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
119 19 0.19
120 64 0.63
121 12 0.12
122 7 0.07
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (122 bp):
TTTTTTTGATCAGATAAAAAAGGTAGTGTCGGCCAATAAATGGCCAACACCAAAAAAATATTTTT
TTATCAGATAAAAAAGATGGTATCAACCAATGCACGGCAAACACAAAATTTTTTTTA
Found at i:40722 original size:55 final size:54
Alignment explanation
Indices: 40584--40790 Score: 171
Period size: 55 Copynumber: 3.9 Consensus size: 54
40574 TGCACGGTCA
* *
40584 AACACCAAATT-TTTTTTATCTGATAAAAAAGATGGTGTCGGCCAATGTATGACC
1 AACA-CAAATTATTTTTTATCTGATAAAAAACATGGTGTCGGCCAATGCATGACC
* ** *
40638 AACACAAA-AAAATTTTATCTGATAAAAAAACACTGGTGTCGGTCAATGCATGACC
1 AACACAAATTATTTTTTATCTGAT-AAAAAACA-TGGTGTCGGCCAATGCATGACC
* * ** *
40693 AACACAAATTATTTTTTATCTAATTAAAAAGGTGGTGTCGG----T---TGGCC
1 AACACAAATTATTTTTTATCTGATAAAAAACATGGTGTCGGCCAATGCATGACC
* * * *
40740 AACACCAATTTTTTTTTTATCTGATAAAAAATATTTGTGTCGGCCAATGCA
1 AACA-CAAATTATTTTTTATCTGATAAAAAACA-TGGTGTCGGCCAATGCA
40791 CGGGTGATGG
Statistics
Matches: 119, Mismatches: 21, Indels: 24
0.73 0.13 0.15
Matches are distributed among these distances:
47 8 0.07
48 22 0.18
49 8 0.07
50 1 0.01
53 16 0.13
54 20 0.17
55 33 0.28
56 11 0.09
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (54 bp):
AACACAAATTATTTTTTATCTGATAAAAAACATGGTGTCGGCCAATGCATGACC
Found at i:42005 original size:32 final size:33
Alignment explanation
Indices: 41945--42024 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 33
41935 CTATTCACTT
* * * * *
41945 AAAATAAATAATTTTAGTCAAAATAAAATTAGG
1 AAAATAAACAAATTTAATCAAAACAAAATTAAG
*
41978 AAAAT-AACAAATTTAATCAAAACAAAATTAAT
1 AAAATAAACAAATTTAATCAAAACAAAATTAAG
42010 AAAATAAACAAATTT
1 AAAATAAACAAATTT
42025 GACTAAGCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
32 26 0.65
33 14 0.35
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (33 bp):
AAAATAAACAAATTTAATCAAAACAAAATTAAG
Found at i:46660 original size:18 final size:16
Alignment explanation
Indices: 46629--46671 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
46619 AGGTTTGGGT
*
46629 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
46646 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
46660 TTAAAAATTTAT
1 TTAAAAATTTAT
46672 GCTCATTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 10 0.43
15 3 0.13
16 8 0.35
17 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:47565 original size:19 final size:20
Alignment explanation
Indices: 47541--47583 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
47531 TTCAAAATTC
47541 TAATAAAAGTAAA-AATATA
1 TAATAAAAGTAAACAATATA
* *
47560 TAATAATAGTAAACGATATA
1 TAATAAAAGTAAACAATATA
47580 TAAT
1 TAAT
47584 TAATAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.30
Consensus pattern (20 bp):
TAATAAAAGTAAACAATATA
Found at i:47580 original size:20 final size:19
Alignment explanation
Indices: 47541--47588 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
47531 TTCAAAATTC
*
47541 TAATAAAAGTAAAAATATA
1 TAATAATAGTAAAAATATA
*
47560 TAATAATAGTAAACGATATA
1 TAATAATAGTAAA-AATATA
47580 TAATTAATA
1 TAA-TAATA
47589 AATATCAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.48
20 8 0.32
21 5 0.20
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.31
Consensus pattern (19 bp):
TAATAATAGTAAAAATATA
Found at i:67651 original size:18 final size:18
Alignment explanation
Indices: 67606--67654 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
67596 TTTTTATTAA
* *
67606 TTTATATATTATATATTT
1 TTTATATACTATAGATTT
* *
67624 TTTAAAATACTATAGGTTT
1 TTT-ATATACTATAGATTT
67643 TTTATATACTAT
1 TTTATATACTAT
67655 TAATTGTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (18 bp):
TTTATATACTATAGATTT
Found at i:68657 original size:18 final size:18
Alignment explanation
Indices: 68634--68670 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
68624 TAAACTTAAA
*
68634 AAATTATAAAAAATCTAT
1 AAATTATAAAAAATATAT
68652 AAATTATAAAAAATATAT
1 AAATTATAAAAAATATAT
68670 A
1 A
68671 TAAGATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATTATAAAAAATATAT
Found at i:74002 original size:54 final size:52
Alignment explanation
Indices: 73939--74044 Score: 185
Period size: 54 Copynumber: 2.0 Consensus size: 52
73929 TTTAAAATAT
73939 ATATATAATACACCAAAGACACTAAAAATATTAAAAAAAATATTTTTGAACAAA
1 ATATATAATACACCAAAGACACTAAAAA-ATT-AAAAAAATATTTTTGAACAAA
*
73993 ATATATAATACACCAAAGACACTAAAAAATTAAAATAATATTTTTGAACAAA
1 ATATATAATACACCAAAGACACTAAAAAATTAAAAAAATATTTTTGAACAAA
74045 TTGAAAATAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 20 0.39
53 3 0.06
54 28 0.55
ACGTcount: A:0.58, C:0.11, G:0.04, T:0.26
Consensus pattern (52 bp):
ATATATAATACACCAAAGACACTAAAAAATTAAAAAAATATTTTTGAACAAA
Found at i:83288 original size:31 final size:31
Alignment explanation
Indices: 83250--83308 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
83240 TATTTGAGTT
83250 AATCAAGTTATTCGGATCAACTCGAATAAAA
1 AATCAAGTTATTCGGATCAACTCGAATAAAA
* * *
83281 AATCAAGTTTTTCGGTTTAACTCGAATA
1 AATCAAGTTATTCGGATCAACTCGAATA
83309 TGAATTACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (31 bp):
AATCAAGTTATTCGGATCAACTCGAATAAAA
Found at i:85540 original size:20 final size:20
Alignment explanation
Indices: 85512--85583 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 20
85502 TCTCAACAAA
*
85512 AATTATAAAAATTTAAAATT
1 AATTTTAAAAATTTAAAATT
*
85532 AATTTT-AAAATTCAAAA-T
1 AATTTTAAAAATTTAAAATT
85550 -ATTTATAAAAATTCTAAAATTT
1 AATTT-TAAAAATT-TAAAA-TT
85572 ATATTTTAAAAA
1 A-ATTTTAAAAA
85584 ATCATAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
17 4 0.10
18 2 0.05
19 16 0.38
20 9 0.21
22 1 0.02
23 6 0.14
24 4 0.10
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTTTAAAAATTTAAAATT
Found at i:86374 original size:52 final size:54
Alignment explanation
Indices: 86300--86416 Score: 134
Period size: 52 Copynumber: 2.2 Consensus size: 54
86290 CCCAATTTTT
* * *
86300 TTTTACTTCT-CCAAACCTCTAAAACCT-TTTCCCTTTTTCTTCCT-CTCCAAAC
1 TTTTACTTTTCCCAAACCTCTAAAA-CTGTTTCCCTTTTACTTCCTCCTCAAAAC
* * * *
86352 TTTTATTTTTCCCAAACC-CTAAAACTGTTTTCCTTTTACTTTCTCCTCAAAAT
1 TTTTACTTTTCCCAAACCTCTAAAACTGTTTCCCTTTTACTTCCTCCTCAAAAC
86405 TTTTACTTTTCC
1 TTTTACTTTTCC
86417 GCTTTTATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
51 2 0.04
52 28 0.52
53 24 0.44
ACGTcount: A:0.21, C:0.31, G:0.01, T:0.47
Consensus pattern (54 bp):
TTTTACTTTTCCCAAACCTCTAAAACTGTTTCCCTTTTACTTCCTCCTCAAAAC
Found at i:86423 original size:34 final size:34
Alignment explanation
Indices: 86384--86448 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
86374 AACTGTTTTC
*
86384 CTTTTACTTTCTCCTCAAAATTTTTACTTTTCCG
1 CTTTTACTTTCTCCCCAAAATTTTTACTTTTCCG
* *
86418 CTTTTATTTTCTCCCCAAAATTTTTATTTTT
1 CTTTTACTTTCTCCCCAAAATTTTTACTTTT
86449 TCCGAATTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.18, C:0.23, G:0.02, T:0.57
Consensus pattern (34 bp):
CTTTTACTTTCTCCCCAAAATTTTTACTTTTCCG
Found at i:89654 original size:6 final size:6
Alignment explanation
Indices: 89643--89671 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
89633 CAATGAGAGC
89643 GGGGTA GGGGTA GGGGTA GGGGTA GGGGT
1 GGGGTA GGGGTA GGGGTA GGGGTA GGGGT
89672 GGGTTATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.69, T:0.17
Consensus pattern (6 bp):
GGGGTA
Found at i:95732 original size:16 final size:16
Alignment explanation
Indices: 95713--95758 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
95703 AATATTTAAA
95713 GAAAAAATTATTTGTT
1 GAAAAAATTATTTGTT
*
95729 GAAATAAAATATTTGTT
1 GAAA-AAATTATTTGTT
95746 -AAAATAATTATTT
1 GAAAA-AATTATTT
95759 TTAAGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 14 0.54
17 11 0.42
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (16 bp):
GAAAAAATTATTTGTT
Found at i:95743 original size:17 final size:17
Alignment explanation
Indices: 95697--95752 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
95687 TACTTTTAAA
***
95697 AAATAAAATATTTAAAG
1 AAATAAAATATTTGTTG
*
95714 AAA-AAATTATTTGTTG
1 AAATAAAATATTTGTTG
*
95730 AAATAAAATATTTGTTA
1 AAATAAAATATTTGTTG
95747 AAATAA
1 AAATAA
95753 TTATTTTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 12 0.38
17 20 0.62
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (17 bp):
AAATAAAATATTTGTTG
Found at i:96332 original size:20 final size:20
Alignment explanation
Indices: 96307--96356 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
96297 AAAAATATAA
*
96307 ATTTTGGAATTTTTATAAA-T
1 ATTTT-GAATTTTTAGAAATT
96327 ATTTTGAATTTTTAGAAATT
1 ATTTTGAATTTTTAGAAATT
96347 ATTTTGAATT
1 ATTTTGAATT
96357 ATTTTGTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (20 bp):
ATTTTGAATTTTTAGAAATT
Found at i:96337 original size:19 final size:19
Alignment explanation
Indices: 96302--96356 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
96292 TTTTAAAAAA
*
96302 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
96320 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
*
96339 TAGAAATTATTTTGAATT
1 TATAAA-TATTTTGAATT
96357 ATTTTGTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.21
19 15 0.45
20 11 0.33
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:108061 original size:21 final size:21
Alignment explanation
Indices: 108022--108061 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
108012 TAAATAACAA
* *
108022 AATATTACTATTTATTATAAT
1 AATATTACTAATTAATATAAT
*
108043 AATATTATTAATTAATATA
1 AATATTACTAATTAATATA
108062 TCTTTTGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATTACTAATTAATATAAT
Found at i:110662 original size:26 final size:27
Alignment explanation
Indices: 110619--110669 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
110609 ATTATAAGTG
110619 TTAAAAAATAAAAGAAATTT-AAAATT
1 TTAAAAAATAAAAGAAATTTCAAAATT
*
110645 TTAAAAAATGATAA-AAATTTCAAAA
1 TTAAAAAAT-AAAAGAAATTTCAAAA
110670 AAAATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (27 bp):
TTAAAAAATAAAAGAAATTTCAAAATT
Found at i:110678 original size:19 final size:19
Alignment explanation
Indices: 110628--110680 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
110618 GTTAAAAAAT
* * *
110628 AAAAGAAATTTAAAATTTT
1 AAAAAAAATTAAAAATTTC
*
110647 AAAAAATGA-TAAAAATTTC
1 AAAAAA-AATTAAAAATTTC
110666 AAAAAAAATTAAAAA
1 AAAAAAAATTAAAAA
110681 AAGAAGAAGC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 1 0.04
19 25 0.93
20 1 0.04
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (19 bp):
AAAAAAAATTAAAAATTTC
Found at i:114157 original size:20 final size:20
Alignment explanation
Indices: 114132--114171 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
114122 CACAAAATTG
114132 TTTGGACAAA-AGAACAGAGC
1 TTTGGA-AAAGAGAACAGAGC
114152 TTTGGAAAAGAGAACAGAGC
1 TTTGGAAAAGAGAACAGAGC
114172 ACCTCCAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.45, C:0.12, G:0.28, T:0.15
Consensus pattern (20 bp):
TTTGGAAAAGAGAACAGAGC
Found at i:118108 original size:11 final size:11
Alignment explanation
Indices: 118087--118116 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
118077 ATAATCATTT
118087 AATTATTTTTAA
1 AATT-TTTTTAA
118099 AATTTTTTTAA
1 AATTTTTTTAA
118110 AATTTTT
1 AATTTTT
118117 AAATTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
AATTTTTTTAA
Found at i:120931 original size:26 final size:26
Alignment explanation
Indices: 120882--120942 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
120872 ATACAGAGAT
120882 TAATTAATTAAATAAAAACATAAAAA
1 TAATTAATTAAATAAAAACATAAAAA
* * ** *
120908 TTATTAATTAAATACAAATTTAAACA
1 TAATTAATTAAATAAAAACATAAAAA
120934 TAATTAATT
1 TAATTAATT
120943 TTAAATTCAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (26 bp):
TAATTAATTAAATAAAAACATAAAAA
Found at i:124840 original size:34 final size:33
Alignment explanation
Indices: 124794--124873 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 33
124784 GGCCCGTTGA
* * *
124794 AAATTGAATTTATTTCAAATTTAAGTTTATTTT
1 AAATTTAATTTATTTCAAATTTAAATTTATTAT
*
124827 AAATTTAAGTTTATTTGAAATTTAAATTTATTAT
1 AAATTTAA-TTTATTTCAAATTTAAATTTATTAT
*
124861 AAAATTAAATTTA
1 -AAATTTAATTTA
124874 GAAAAGTCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
33 7 0.17
34 26 0.65
35 7 0.17
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.51
Consensus pattern (33 bp):
AAATTTAATTTATTTCAAATTTAAATTTATTAT
Found at i:124868 original size:17 final size:17
Alignment explanation
Indices: 124800--124873 Score: 87
Period size: 17 Copynumber: 4.4 Consensus size: 17
124790 TTGAAAATTG
124800 AATTTATTTCAAATTTA
1 AATTTATTTCAAATTTA
* *
124817 AGTTTATTTTAAATTTA
1 AATTTATTTCAAATTTA
* *
124834 AGTTTATTTGAAATTTA
1 AATTTATTTCAAATTTA
*
124851 AATTTATTAT-AAAATTA
1 AATTTATT-TCAAATTTA
124868 AATTTA
1 AATTTA
124874 GAAAAGTCCA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
17 50 0.98
18 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTATTTCAAATTTA
Done.