Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021415.1 Corchorus olitorius cultivar O-4 contig21448, 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: 120126
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1166 original size:11 final size:12
Alignment explanation
Indices: 1150--1178 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1140 TTTAAAATGC
1150 AAAAAAGAAAA-
1 AAAAAAGAAAAG
1161 AAAAAAGAAAAG
1 AAAAAAGAAAAG
1173 AAAAAA
1 AAAAAA
1179 AAATCACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:11254 original size:10 final size:10
Alignment explanation
Indices: 11239--11273 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
11229 TTTTGTATTT
11239 AAAAAAAACA
1 AAAAAAAACA
11249 AAAAAAAACCAA
1 AAAAAAAA-C-A
11261 AAAAAAAACA
1 AAAAAAAACA
11271 AAA
1 AAA
11274 CACAAACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 12 0.52
11 2 0.09
12 9 0.39
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:11255 original size:11 final size:11
Alignment explanation
Indices: 11239--11273 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
11229 TTTTGTATTT
11239 AAAAAAAACAA
1 AAAAAAAACAA
*
11250 AAAAAAACCAA
1 AAAAAAAACAA
11261 AAAAAAAACAA
1 AAAAAAAACAA
11272 AA
1 AA
11274 CACAAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:17699 original size:21 final size:21
Alignment explanation
Indices: 17673--17714 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
17663 CTGCTTTTGG
17673 TAGATATGCTCATGGTCAAGC
1 TAGATATGCTCATGGTCAAGC
* *
17694 TAGATATGTTTATGGTCAAGC
1 TAGATATGCTCATGGTCAAGC
17715 CTAATCGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (21 bp):
TAGATATGCTCATGGTCAAGC
Found at i:26278 original size:48 final size:48
Alignment explanation
Indices: 26207--26305 Score: 144
Period size: 48 Copynumber: 2.1 Consensus size: 48
26197 CAGGATGATA
* *
26207 CTTGACCTTTGCGGTAGAATTGTGGTTGGCTTCTACCGTAAAATGGTG
1 CTTGACCTTTGCGGTAAAATTGTGATTGGCTTCTACCGTAAAATGGTG
* * * *
26255 CTTGACTTTTTCGGTAAAATTGTGATTGGCTTCTGCCGTAGAATGGTG
1 CTTGACCTTTGCGGTAAAATTGTGATTGGCTTCTACCGTAAAATGGTG
26303 CTT
1 CTT
26306 AAGATTGGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.38
Consensus pattern (48 bp):
CTTGACCTTTGCGGTAAAATTGTGATTGGCTTCTACCGTAAAATGGTG
Found at i:26695 original size:35 final size:35
Alignment explanation
Indices: 26654--26728 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
26644 AGTTCGTTTA
*
26654 TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGGCTCATTTATTGTTCATTTAAG
*
26689 TGTTCACGAACATGCTCATTTATTGTTCATTTAAG
1 TGTTCACGAACAGGCTCATTTATTGTTCATTTAAG
26724 TGTTC
1 TGTTC
26729 GTTTATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (35 bp):
TGTTCACGAACAGGCTCATTTATTGTTCATTTAAG
Found at i:26791 original size:16 final size:16
Alignment explanation
Indices: 26770--26822 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
26760 TATAATTATT
26770 TATATATTAATAATAA
1 TATATATTAATAATAA
*
26786 TATATATTATTAATAAA
1 TATATATTAATAAT-AA
* *
26803 AATTATATAAATAATAA
1 TA-TATATTAATAATAA
26820 TAT
1 TAT
26823 TCTATTATCA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 14 0.47
17 6 0.20
18 10 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:26957 original size:18 final size:18
Alignment explanation
Indices: 26930--26964 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
26920 AATTTTTACA
26930 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
26948 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
26965 CAATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:29616 original size:2 final size:2
Alignment explanation
Indices: 29600--29635 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
29590 CAAAAATAAC
29600 TA TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29636 CTCAATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45168 original size:21 final size:21
Alignment explanation
Indices: 45116--45168 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
45106 AGGAGGTTCA
* *
45116 GATAAGGAAAATGATGTTGAT
1 GATAAGGAAACTGATGCTGAT
*
45137 GATAAGGAAACTGCTGCTGAT
1 GATAAGGAAACTGATGCTGAT
45158 GATAAGGAAAC
1 GATAAGGAAAC
45169 AGAAGAAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.28, T:0.23
Consensus pattern (21 bp):
GATAAGGAAACTGATGCTGAT
Found at i:51231 original size:13 final size:13
Alignment explanation
Indices: 51206--51232 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
51196 AATATAATTA
51206 AATAATTATATTT
1 AATAATTATATTT
51219 AATAATTATATTT
1 AATAATTATATTT
51232 A
1 A
51233 TACATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATAATTATATTT
Found at i:57363 original size:12 final size:12
Alignment explanation
Indices: 57346--57385 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
57336 TTCGATATCG
57346 TTTCTCTAACAT
1 TTTCTCTAACAT
*
57358 TTTCTCT--C-G
1 TTTCTCTAACAT
57367 TTTCTCTAACAT
1 TTTCTCTAACAT
57379 TTTCTCT
1 TTTCTCT
57386 CACGTACGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
9 7 0.30
10 1 0.04
11 1 0.04
12 14 0.61
ACGTcount: A:0.15, C:0.28, G:0.03, T:0.55
Consensus pattern (12 bp):
TTTCTCTAACAT
Found at i:57367 original size:21 final size:21
Alignment explanation
Indices: 57343--57386 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
57333 TGTTTCGATA
57343 TCGTTTCTCTAACATTTTCTC
1 TCGTTTCTCTAACATTTTCTC
57364 TCGTTTCTCTAACATTTTCTC
1 TCGTTTCTCTAACATTTTCTC
57385 TC
1 TC
57387 ACGTACGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.30, G:0.05, T:0.52
Consensus pattern (21 bp):
TCGTTTCTCTAACATTTTCTC
Found at i:59710 original size:6 final size:6
Alignment explanation
Indices: 59699--59728 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
59689 CATGGTGATT
59699 GGTGAA GGTGAA GGTGAA GGTGAA GGTGAA
1 GGTGAA GGTGAA GGTGAA GGTGAA GGTGAA
59729 CTAGTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.50, T:0.17
Consensus pattern (6 bp):
GGTGAA
Found at i:64059 original size:51 final size:51
Alignment explanation
Indices: 63964--64063 Score: 123
Period size: 51 Copynumber: 2.0 Consensus size: 51
63954 CATATTTTCC
* **
63964 TTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGTTTTTCTT
1 TTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTTTTCTT
* *
64015 TTGTTTCA-ATCTTGTCTCTGGACATACAAACACT-GTACACGTGTTTTTC
1 TTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGTTTTTC
64064 ATTCAGAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 2 0.05
51 39 0.93
52 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43
Consensus pattern (51 bp):
TTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTTTTCTT
Found at i:72052 original size:18 final size:18
Alignment explanation
Indices: 72022--72072 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
72012 AAAAGAATTA
*
72022 TGTT-AAACATGTATCGT
1 TGTTGAAACTTGTATCGT
72039 TGTTGAAACTTGTATCGT
1 TGTTGAAACTTGTATCGT
72057 TGTTGAAACTTGTATC
1 TGTTGAAACTTGTATC
72073 ATCTTTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 4 0.12
18 28 0.88
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (18 bp):
TGTTGAAACTTGTATCGT
Found at i:72243 original size:61 final size:61
Alignment explanation
Indices: 72148--72268 Score: 197
Period size: 61 Copynumber: 2.0 Consensus size: 61
72138 CAGGTGCTCC
* * *
72148 AACAAAACCTGGCCCATTAATTATGACGTACTAACAATTTACATTTAGAGGAATTAAGACT
1 AACAAAACCTGGCCCATTAATCATCACGTACTAACAATTTACATTCAGAGGAATTAAGACT
* *
72209 AACAAAACCTGTCCTATTAATCATCACGTACTAACAATTTACATTCAGAGGAATTAAGAC
1 AACAAAACCTGGCCCATTAATCATCACGTACTAACAATTTACATTCAGAGGAATTAAGAC
72269 AGAAGATCAC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (61 bp):
AACAAAACCTGGCCCATTAATCATCACGTACTAACAATTTACATTCAGAGGAATTAAGACT
Found at i:72894 original size:20 final size:20
Alignment explanation
Indices: 72869--72949 Score: 117
Period size: 20 Copynumber: 4.0 Consensus size: 20
72859 CAACAATCAA
*
72869 AAGAAATTTGAGAGAGACAG
1 AAGAAATTCGAGAGAGACAG
*
72889 AAGAAATTCGAGAGAGACAA
1 AAGAAATTCGAGAGAGACAG
* *
72909 AAGAAATTTGAGAGAGACGG
1 AAGAAATTCGAGAGAGACAG
*
72929 AAGAAATTCGAGAAAGACAG
1 AAGAAATTCGAGAGAGACAG
72949 A
1 A
72950 GATCAGAGAG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.52, C:0.07, G:0.28, T:0.12
Consensus pattern (20 bp):
AAGAAATTCGAGAGAGACAG
Found at i:72921 original size:40 final size:40
Alignment explanation
Indices: 72866--72947 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
72856 CTTCAACAAT
*
72866 CAAAAGAAATTTGAGAGAGACAGAAGAAATTCGAGAGAGA
1 CAAAAGAAATTTGAGAGAGACAGAAGAAATTCGAGAAAGA
*
72906 CAAAAGAAATTTGAGAGAGACGGAAGAAATTCGAGAAAGA
1 CAAAAGAAATTTGAGAGAGACAGAAGAAATTCGAGAAAGA
72946 CA
1 CA
72948 GAGATCAGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.52, C:0.09, G:0.27, T:0.12
Consensus pattern (40 bp):
CAAAAGAAATTTGAGAGAGACAGAAGAAATTCGAGAAAGA
Found at i:76755 original size:66 final size:66
Alignment explanation
Indices: 76639--76950 Score: 412
Period size: 66 Copynumber: 4.7 Consensus size: 66
76629 CAGAGATGGT
* *
76639 GATGCCGGAGAAAGACACAATGCATTTGGTGGTTTTGACAAAACCCCAGATTTCAAGGAGTCAGG
1 GATGGCGGAGAAAGACACAATGCATTTGGGGGTTTTGACAAAACCCCAGATTTCAAGGAGTCAGG
76704 G
66 G
* * *
76705 GATGGCGGATAAAGACACAATCCATTTGGGGGTTTTGAGAAAACCCCAGATTTCAAGGAGTCAGG
1 GATGGCGGAGAAAGACACAATGCATTTGGGGGTTTTGACAAAACCCCAGATTTCAAGGAGTCAGG
76770 G
66 G
* * * *
76771 GATGGCGGACAAAGACACAATCCATTTGGGGGTTTTG-CGAAAACCCCAGATTTGAAGGAGTCAC
1 GATGGCGGAGAAAGACACAATGCATTTGGGGGTTTTGAC-AAAACCCCAGATTTCAAGGAGTCAG
76835 GG
65 GG
* * * *** * **
76837 GATGCCGGGGAAAGACAAAATGCATTTGGGGGTTTTGACAAAATGACAGATTTCAAGGGGTCAAA
1 GATGGCGGAGAAAGACACAATGCATTTGGGGGTTTTGACAAAACCCCAGATTTCAAGGAGTCAGG
*
76902 T
66 G
*
76903 GAT-GCTGGAGAAAGACACAATGCATTTGGGAGTTTTGACAAAACCCCA
1 GATGGC-GGAGAAAGACACAATGCATTTGGGGGTTTTGACAAAACCCCA
76951 ACGAAGCAGG
Statistics
Matches: 214, Mismatches: 29, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
65 1 0.00
66 212 0.99
67 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (66 bp):
GATGGCGGAGAAAGACACAATGCATTTGGGGGTTTTGACAAAACCCCAGATTTCAAGGAGTCAGG
G
Found at i:78916 original size:2 final size:2
Alignment explanation
Indices: 78909--78946 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
78899 TGTTTTCATG
*
78909 TA TA TA TA AA TA TA TA TA TA TA TA TA TA T- TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
78947 ATTCATAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:79535 original size:50 final size:51
Alignment explanation
Indices: 79481--79583 Score: 190
Period size: 50 Copynumber: 2.0 Consensus size: 51
79471 TCATGTCTCA
79481 TTAACTTCATTTATTTCCCTCTACAAATCTTTAAATCAACATC-AATTTTT
1 TTAACTTCATTTATTTCCCTCTACAAATCTTTAAATCAACATCAAATTTTT
*
79531 TTAACTTCATTTATTTTCCTCTACAAATCTTTAAATCAACATCAAATTTTT
1 TTAACTTCATTTATTTCCCTCTACAAATCTTTAAATCAACATCAAATTTTT
79582 TT
1 TT
79584 TCTCCTCCAC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 42 0.82
51 9 0.18
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (51 bp):
TTAACTTCATTTATTTCCCTCTACAAATCTTTAAATCAACATCAAATTTTT
Found at i:83189 original size:52 final size:52
Alignment explanation
Indices: 83111--83213 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
83101 CTTATAGCAC
*
83111 TGTTGATTATGATTGCAGATCAATGCTCAATAAATTCCAGCTGAGGGAACTT
1 TGTTGATTATGATTACAGATCAATGCTCAATAAATTCCAGCTGAGGGAACTT
* *
83163 TGTTGTTTATGATTACATATCAATGCTCAATAAATTCCAGCTGAGGGAACT
1 TGTTGATTATGATTACAGATCAATGCTCAATAAATTCCAGCTGAGGGAACT
83214 CTGGAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (52 bp):
TGTTGATTATGATTACAGATCAATGCTCAATAAATTCCAGCTGAGGGAACTT
Found at i:83694 original size:30 final size:30
Alignment explanation
Indices: 83635--83696 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
83625 GTTAATAAGC
* *
83635 CATTAAAATTTGAGGGTATAAGAGAAAAGT
1 CATTAAAATTAGAGGGTATAAAAGAAAAGT
83665 CATTAAAATTAGAGGGTATAAAA-AGAAAGT
1 CATTAAAATTAGAGGGTATAAAAGA-AAAGT
83695 CA
1 CA
83697 AGATAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (30 bp):
CATTAAAATTAGAGGGTATAAAAGAAAAGT
Found at i:84164 original size:36 final size:36
Alignment explanation
Indices: 84117--84191 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
84107 GTTCTACTAA
84117 TTATACTCATCAGTATTTAATTAAACTCAAAAGCTC
1 TTATACTCATCAGTATTTAATTAAACTCAAAAGCTC
84153 TTATACTCATCAGTATTTAATTAAACTCAAAAGCTC
1 TTATACTCATCAGTATTTAATTAAACTCAAAAGCTC
84189 TTA
1 TTA
84192 GCAAGTGCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (36 bp):
TTATACTCATCAGTATTTAATTAAACTCAAAAGCTC
Found at i:84257 original size:53 final size:53
Alignment explanation
Indices: 84177--84284 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
84167 ATTTAATTAA
*
84177 ACTCAAAAGCTCTTAGCAAGTGCATATATAGTAACTAGAAAAAGCAAAAATTT
1 ACTCAAAAGCTCTTAGCAAGTACATATATAGTAACTAGAAAAAGCAAAAATTT
*
84230 ACTCAAAAGCTCTTAGCAAGTACATATATAGTGACTAGAAAAAGCAAAAATTT
1 ACTCAAAAGCTCTTAGCAAGTACATATATAGTAACTAGAAAAAGCAAAAATTT
84283 AC
1 AC
84285 AATTTATAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (53 bp):
ACTCAAAAGCTCTTAGCAAGTACATATATAGTAACTAGAAAAAGCAAAAATTT
Found at i:86671 original size:3 final size:3
Alignment explanation
Indices: 86663--86694 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
86653 TCCCTTTAGA
86663 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
86695 TTACAGCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:88329 original size:13 final size:13
Alignment explanation
Indices: 88311--88336 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
88301 TACATTCAAA
88311 ATTCATTCATTAC
1 ATTCATTCATTAC
88324 ATTCATTCATTAC
1 ATTCATTCATTAC
88337 TTTCCATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTCATTCATTAC
Found at i:95600 original size:25 final size:24
Alignment explanation
Indices: 95549--95605 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
95539 GTCAGTCTTG
* *
95549 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATATTTAATTATTA
*
95572 AATTTATTTAATATCTTAATTATTC
1 AATTTATTTAATAT-TTAATTATTA
95597 AATTTATTT
1 AATTTATTT
95606 TACAATCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 7 0.24
25 17 0.59
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATATTTAATTATTA
Found at i:109208 original size:27 final size:27
Alignment explanation
Indices: 109178--109231 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
109168 ACAAACAATG
109178 CACTCCATGAGCATCTCAAATCACCAA
1 CACTCCATGAGCATCTCAAATCACCAA
*
109205 CACTCCATGAGCATCTCAAATTACCAA
1 CACTCCATGAGCATCTCAAATCACCAA
109232 TAATATCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.35, G:0.07, T:0.20
Consensus pattern (27 bp):
CACTCCATGAGCATCTCAAATCACCAA
Found at i:109306 original size:33 final size:34
Alignment explanation
Indices: 109269--109338 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
109259 CAAACAACAC
109269 AATTT-GGGGTAATTTCTGCATAAGAATTCAGAA
1 AATTTGGGGGTAATTTCTGCATAAGAATTCAGAA
109302 AATTTGGGGGTAATTTCTGCATAAGAATTCAGAA
1 AATTTGGGGGTAATTTCTGCATAAGAATTCAGAA
109336 AAT
1 AAT
109339 AAGATTGGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 5 0.14
34 31 0.86
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (34 bp):
AATTTGGGGGTAATTTCTGCATAAGAATTCAGAA
Found at i:119556 original size:6 final size:6
Alignment explanation
Indices: 119532--119579 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
119522 CTACAAAATT
*
119532 AACAAA AACACAA AA-AAA AACAAA AACAAA ATACGAAA AATAAA AACA
1 AACAAA AACA-AA AACAAA AACAAA AACAAA A-AC-AAA AACAAA AACA
119580 GAACTAAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
5 4 0.11
6 21 0.58
7 7 0.19
8 4 0.11
ACGTcount: A:0.79, C:0.15, G:0.02, T:0.04
Consensus pattern (6 bp):
AACAAA
Done.