Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010792.1 Kokia drynarioides strain JFW-HI SEQ_125759, 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: 152671
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 218 characters in sequence are not A, C, G, or T
Found at i:261 original size:111 final size:110
Alignment explanation
Indices: 95--312 Score: 418
Period size: 111 Copynumber: 2.0 Consensus size: 110
85 TCTTAAAAGA
95 TTTGAAATTTTTCATTTTTCTTAGATCTTCAAACTTTAGAAAATAAAAATTAAAAAAAAAAAATT
1 TTTGAAATTTTTCATTTTTCTTAGATCTTCAAACTTTAGAAAATAAAAATTAAAAAAAAAAAATT
160 AGATCCGTTTCACCCTTTTTTGTTACAAAATATTCTGTAATTNAGG
66 AGATCCGTTTCACCCTTTTTTGTTACAAAATATTCTGTAATT-AGG
*
206 TTTGAAATTTTTCATTTTTCTTAGATCTTCAAACTTTAGAAAATAAAAATTAAAAAAAAAAACTT
1 TTTGAAATTTTTCATTTTTCTTAGATCTTCAAACTTTAGAAAATAAAAATTAAAAAAAAAAAATT
271 AGATCCGTTTCACCCTTTTTTGTTACAAAATATTCTGTAATT
66 AGATCCGTTTCACCCTTTTTTGTTACAAAATATTCTGTAATT
313 TTTAAAACGC
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (110 bp):
TTTGAAATTTTTCATTTTTCTTAGATCTTCAAACTTTAGAAAATAAAAATTAAAAAAAAAAAATT
AGATCCGTTTCACCCTTTTTTGTTACAAAATATTCTGTAATTAGG
Found at i:1275 original size:17 final size:17
Alignment explanation
Indices: 1237--1343 Score: 92
Period size: 17 Copynumber: 6.1 Consensus size: 17
1227 TGTTTTGGAC
*
1237 TTTT-AATATAATATTAAG
1 TTTTAAATA-AAT-TTAAA
*
1255 TTTTAAATCAATTTAAA
1 TTTTAAATAAATTTAAA
*
1272 TTTTAATTAAATTTAAA
1 TTTTAAATAAATTTAAA
*
1289 -TTTAAAGCAAATTTAAA
1 TTTTAAA-TAAATTTAAA
*
1306 TTTAAAAGATAAATTTAAA
1 TTT-TAA-ATAAATTTAAA
*
1325 TTTAAAACTAAATTTAAA
1 TTTTAAA-TAAATTTAAA
1343 T
1 T
1344 CAATTTAAAC
Statistics
Matches: 75, Mismatches: 8, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
16 5 0.07
17 29 0.39
18 23 0.31
19 17 0.23
20 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTTAAATAAATTTAAA
Found at i:1279 original size:6 final size:6
Alignment explanation
Indices: 1264--1343 Score: 74
Period size: 6 Copynumber: 13.5 Consensus size: 6
1254 GTTTTAAATC
* **
1264 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-GCA AATTTA AATTTAA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A
** **
1311 AAGATA AATTTA AATTTA AAACTA AATTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AAT
1344 CAATTTAAAC
Statistics
Matches: 57, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
5 7 0.12
6 46 0.81
7 4 0.07
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (6 bp):
AATTTA
Found at i:1350 original size:10 final size:11
Alignment explanation
Indices: 1323--1364 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
1313 GATAAATTTA
*
1323 AATTTAAAACTA
1 AATTT-AAACTC
1335 AATTTAAA-TC
1 AATTTAAACTC
1345 AATTTAAACTC
1 AATTTAAACTC
1356 AATCTTAAA
1 AAT-TTAAA
1365 ATAGAAGGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 9 0.33
11 8 0.30
12 10 0.37
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTTAAACTC
Found at i:2078 original size:206 final size:206
Alignment explanation
Indices: 1714--2162 Score: 648
Period size: 206 Copynumber: 2.2 Consensus size: 206
1704 TCTGGTTTCA
* * ** *
1714 TTGACTTGGCCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCACGT
* * * * * * *
1779 CTCTGTGTTTCATCAGTAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAAACTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAACTAACCAT
** * *
1844 TTTATTACTTTGACTTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACAT
131 TTTATTACTTCAACCTGCATCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACAT
1909 CGAGCGTGGGT
196 CGAGCGTGGGT
* * * **
1920 TTGATTTGGTCTTCTTCTCTA-TGTCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCACG
1 TTGATTTGGTCTTCTTCTC-AGTATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCACG
* * *
1984 TCTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAATAAGCTAACCA
65 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAACTAACCA
* *
2049 TTTTATTGCTTCAACCTGCATCTCAGTATCTCATCAAGAAGTTGGGGTTCGAAGATTTGCTCACA
130 TTTTATTACTTCAACCTGCATCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACA
2114 TCGAGCGTGGGT
195 TCGAGCGTGGGT
2126 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGA
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGA
2163 CGAATTTGGT
Statistics
Matches: 213, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
205 1 0.00
206 211 0.99
207 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCACGT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAACTAACCAT
TTTATTACTTCAACCTGCATCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACAT
CGAGCGTGGGT
Found at i:2180 original size:37 final size:37
Alignment explanation
Indices: 2129--2199 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
2119 CGTGGGTTTG
** *
2129 ATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGACGA
1 ATTTGGTCCACTTCTCAATATCTCATCAAGAAGACGA
*
2166 ATTTGGTCCACTTCTCAATATCTCATCAGGAAGA
1 ATTTGGTCCACTTCTCAATATCTCATCAAGAAGA
2200 TGACCGCGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (37 bp):
ATTTGGTCCACTTCTCAATATCTCATCAAGAAGACGA
Found at i:2238 original size:243 final size:243
Alignment explanation
Indices: 1923--2404 Score: 748
Period size: 243 Copynumber: 2.0 Consensus size: 243
1913 CGTGGGTTTG
** * *
1923 ATTTGGTCTTCTTCTCTATGTCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCACGTCTC
1 ATTTGGTCCACTTCTCAATATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCACGTCTC
* * * *
1988 TGTATCTCATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAATAAGCTAACCATTTT
66 AGTATCTCATCAGGAAAACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTT
* *
2053 ATTGCTTCAACCTGCATCTCAGTATCTCATCAAGAAGTTGGGGTTCGAAGATTTGCTCACATCGA
131 ATTGCTTCAACCTGCATCTCAGTATCTCATCAAGAAGCTGGGGTTCGAACATTTGCTCACATCGA
*
2118 GCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGACGA
196 GCGTGGATTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGACGA
* *
2166 ATTTGGTCCACTTCTCAATATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTC
1 ATTTGGTCCACTTCTCAATATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCACGTCTC
* * * * *
2231 AGTATCTCATTAGGAAAACGAATTTGGTCTACTTCTCAGTATCTCATTAGGAAGCTAACCTTTTT
66 AGTATCTCATCAGGAAAACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTT
** * * *
2296 ATTGCTTCGCCCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAACATTTGCTCGCATTGA
131 ATTGCTTCAACCTGCATCTCAGTATCTCATCAAGAAGCTGGGGTTCGAACATTTGCTCACATCGA
*
2361 GCGTGGATTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAG
196 GCGTGGATTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAG
2405 GTAATCGCAT
Statistics
Matches: 215, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
243 215 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (243 bp):
ATTTGGTCCACTTCTCAATATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCACGTCTC
AGTATCTCATCAGGAAAACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTT
ATTGCTTCAACCTGCATCTCAGTATCTCATCAAGAAGCTGGGGTTCGAACATTTGCTCACATCGA
GCGTGGATTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGACGA
Found at i:2436 original size:206 final size:204
Alignment explanation
Indices: 2166--2824 Score: 752
Period size: 206 Copynumber: 3.3 Consensus size: 204
2156 AAGAAGACGA
* * * * *
2166 ATTTGGTCCACTTCTCAATATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTC
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATAACCGCATCGCTTGTTTCAATCCGCTTCTC
* * *
2231 AGTATCTCATTAGGAAAACGAATTTGGTCTACTTCTCAGTATCTCATTAGGAAGCTAACCTTTTT
66 -GTATCTCATCAGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTT
*
2296 ATTGCTTCGCCCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAACATTTGCTCGCATTGA
129 ATTGCTTCGCCCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCGCATTGA
*
2361 GCGTGGATTTG
194 GCCTGGATTTG
* * * *
2372 ATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGGTAATCGCATCGCTTGTTTCAATCTGCTTCTC
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATAACCGCATCGCTTGTTTCAATCCGCTTCTC
* *
2437 TGTATCTCATCAGGAAGATGAATTTGGT-TCACTTCTCAGTATCTCATCAGGAAGATAACCATTT
66 -GTATCTCATCAGGAAGACGAATTTGGTCT-ACTTCTCAGTATCTCATCAGGAAGCTAACC-TTT
* * * *
2501 TATTGCTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCGCATTG
128 TATTGCTTCGCCCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCGCATTG
*
2566 AGCCTCGA---G
193 AGCCTGGATTTG
* * * * * * ** *
2575 --TTGGTATCCTTCTCTGTATCTCATTAGGAAGATGACCGCCTTACTTGTTTCAATCCGGTTCT-
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATAACCGCATCGCTTGTTTCAATCCGCTTCTC
* * *
2637 GTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAA-C--A--TTTTAT
66 GTATCTCATCAGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTAT
* ** * *
2697 TACTTCGCTTTGCTTCTCAGTATCTCATTAAGAAGCTGGGGTTCGAAGATTTGCTCGCTTTGAGC
131 TGCTTCGCCCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGC
**
2762 CTCGTTTCATTG
196 CT-GGAT--TTG
** *
2774 ATTTGGTCTACTTCTTGGTATCTCATCAGAAAGATGAA-CGCATCGC-TGTTT
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGAT-AACCGCATCGCTTGTTT
2825 GTGGATAATC
Statistics
Matches: 380, Mismatches: 62, Indels: 28
0.81 0.13 0.06
Matches are distributed among these distances:
193 64 0.17
196 1 0.00
199 48 0.13
200 5 0.01
201 82 0.22
202 1 0.00
203 1 0.00
205 1 0.00
206 177 0.47
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (204 bp):
ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATAACCGCATCGCTTGTTTCAATCCGCTTCTC
GTATCTCATCAGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTAT
TGCTTCGCCCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGC
CTGGATTTG
Found at i:14177 original size:96 final size:96
Alignment explanation
Indices: 14000--14180 Score: 240
Period size: 96 Copynumber: 1.9 Consensus size: 96
13990 ATGATGTTCG
** *
14000 ATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATCGAAGAT
1 ATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAAAATCGAAGAT
* *
14065 AAGGAAACATTGCCTCGATTAAGGGTATTTA
66 AAAGAAACATTACCTCGATTAAGGGTATTTA
* * * *
14096 ATTATTTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTTGAAACTCGAA-A
1 ATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAA-TTTTCAAAATCGAAGA
*
14160 TAAA-AGAATATTACCTCGATT
65 TAAAGA-AACATTACCTCGATT
14181 TTAAAGTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
95 1 0.01
96 60 0.82
97 12 0.16
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (96 bp):
ATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAAAATCGAAGAT
AAAGAAACATTACCTCGATTAAGGGTATTTA
Found at i:14479 original size:59 final size:58
Alignment explanation
Indices: 14410--14929 Score: 275
Period size: 59 Copynumber: 8.8 Consensus size: 58
14400 TTGGATACCC
* *
14410 AGGGTAAAATGGTAATTATGGGAAAGTTCGGGGTTAAAAATGAATTTTTTAGACATTCG
1 AGGGTAAAATGGTAATTTTGGGAAAGTTCGGGGTTAAAAATGAA-TTTTTGGACATTCG
* * ** ** * * *
14469 GGGGTAAAATGGTAACTTT-AAAAAAATCGGGATCGAAAACA-GAATTTTTGGACA-TCT
1 AGGGTAAAATGGTAATTTTGGGAAAGTTCGGGGT-TAAAA-ATGAATTTTTGGACATTCG
* * * * *
14526 AGGGGTAAAATGGTAATTTTTAGGTAAA--TCAGGATCAAAAAAGGAATTTTTGGACATTCG
1 A-GGGTAAAATGGTAA-TTTT-GGGAAAGTTCGGGGT-TAAAAATGAATTTTTGGACATTCG
* * * *
14586 AGGGTAAAACGATAATTTTTGG-AAGTTTCGGGGTTAAAAATGGAATTTTTGGACA-TCTA
1 AGGGTAAAATGGTAATTTTGGGAAAG-TTCGGGGTTAAAAAT-GAATTTTTGGACATTC-G
* * *
14645 AGGGCAAAATGGTAATTTTTGG-AAGTTTCGGGGTCAAAAATGGAATTTTTGGACATTCG
1 AGGGTAAAATGGTAATTTTGGGAAAG-TTCGGGGTTAAAAAT-GAATTTTTGGACATTCG
* * * * * *
14704 AGGGTAAAACGGTAATTTT-TGAAAGTTTTGAGATCAAAAATGGAATTTTTGGA-AGTTCG
1 AGGGTAAAATGGTAATTTTGGGAAAG-TTCGGGGTTAAAAAT-GAATTTTTGGACA-TTCG
* * ** * *
14763 GGGGTAAAAAT-ATAATTTTTAG-AAGTTTTGGGGTT-AAAATGTAATTTTTGGA-AGTTCA
1 AGGGT-AAAATGGTAATTTTGGGAAAG-TTCGGGGTTAAAAATG-AATTTTTGGACA-TTCG
* ** *
14821 AGGGTAAAAAT-ATAATTTTTTG-AAGTGTCGAGGTTAAAAATAGAATTTTTGGA-AGTTCG
1 AGGGT-AAAATGGTAATTTTGGGAAAGT-TCGGGGTTAAAAAT-GAATTTTTGGACA-TTCG
* ** ** * *
14880 GGGGTAAAATTATAATTTT-CAAAAGTTTCGAGGTCAAAAATGGAATTTTT
1 AGGGTAAAATGGTAATTTTGGGAAAG-TTCGGGGTTAAAAAT-GAATTTTT
14930 TGGAAGGTTT
Statistics
Matches: 380, Mismatches: 56, Indels: 50
0.78 0.12 0.10
Matches are distributed among these distances:
56 2 0.01
57 5 0.01
58 100 0.26
59 257 0.68
60 13 0.03
61 3 0.01
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (58 bp):
AGGGTAAAATGGTAATTTTGGGAAAGTTCGGGGTTAAAAATGAATTTTTGGACATTCG
Found at i:14594 original size:29 final size:29
Alignment explanation
Indices: 14510--14888 Score: 161
Period size: 29 Copynumber: 12.9 Consensus size: 29
14500 ATCGAAAACA
*
14510 GAATTTTTGGACA-TCTAGGGGT-AAAATG
1 GAATTTTTGGACATTCGA-GGGTAAAAATG
* * *
14538 GTAATTTTTAGGTA-AATC-AGGATCAAAAAAG
1 G-AATTTTT-GG-ACATTCGAGGGT-AAAAATG
14569 GAATTTTTGGACATTCGAGGGTAAAACGAT-
1 GAATTTTTGGACATTCGAGGGTAAAA--ATG
14599 -AATTTTTGGA-AGTTTCG-GGGTTAAAAATG
1 GAATTTTTGGACA--TTCGAGGG-TAAAAATG
* *
14628 GAATTTTTGGACA-TCTAAGGG-CAAAATG
1 GAATTTTTGGACATTC-GAGGGTAAAAATG
14656 GTAATTTTTGGA-AGTTTCG-GGGTCAAAAATG
1 G-AATTTTTGGACA--TTCGAGGGT-AAAAATG
*
14687 GAATTTTTGGACATTCGAGGGT-AAAACG
1 GAATTTTTGGACATTCGAGGGTAAAAATG
* * *
14715 GTAATTTTT-GAAAGTTTTGA-GATCAAAAATG
1 G-AATTTTTGGACA--TTCGAGGGT-AAAAATG
* *
14746 GAATTTTTGGA-AGTTCGGGGGTAAAAATA
1 GAATTTTTGGACA-TTCGAGGGTAAAAATG
* * * *
14775 TAATTTTTAGA-AGTTTTG-GGGTTAAAATG
1 GAATTTTTGGACA--TTCGAGGGTAAAAATG
* * *
14804 TAATTTTTGGA-AGTTCAAGGGTAAAAATA
1 GAATTTTTGGACA-TTCGAGGGTAAAAATG
* * * *
14833 TAATTTTTTGA-AGTGTCGAGGTTAAAAATA
1 GAATTTTTGGACA-T-TCGAGGGTAAAAATG
*
14863 GAATTTTTGGA-AGTTCGGGGGTAAAA
1 GAATTTTTGGACA-TTCGAGGGTAAAA
14889 TTATAATTTT
Statistics
Matches: 277, Mismatches: 38, Indels: 71
0.72 0.10 0.18
Matches are distributed among these distances:
28 26 0.09
29 129 0.47
30 93 0.34
31 29 0.10
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.34
Consensus pattern (29 bp):
GAATTTTTGGACATTCGAGGGTAAAAATG
Found at i:14656 original size:118 final size:117
Alignment explanation
Indices: 14510--14756 Score: 352
Period size: 118 Copynumber: 2.1 Consensus size: 117
14500 ATCGAAAACA
* *
14510 GAATTTTTGGACATCTAGGGGTAAAATGGTAATTTTTAGGTAA-ATCAGGATCAAAAAAGGAATT
1 GAATTTTTGGACATCTAAGGGCAAAATGGTAATTTTT-GG-AAGATCAGGATCAAAAAAGGAATT
* * * *
14574 TTTGGACATTCGAGGGTAAAACGATAATTTTTGGAAGTTTCGGGGTTAAAAATG
64 TTTGGACATTCGAGGGTAAAACGATAATTTTTGAAAGTTTCGAGATCAAAAATG
* * * *
14628 GAATTTTTGGACATCTAAGGGCAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTT
1 GAATTTTTGGACATCTAAGGGCAAAATGGTAATTTTTGGAAG-ATCAGGATCAAAAAAGGAATTT
* *
14693 TTGGACATTCGAGGGTAAAACGGTAATTTTTGAAAGTTTTGAGATCAAAAATG
65 TTGGACATTCGAGGGTAAAACGATAATTTTTGAAAGTTTCGAGATCAAAAATG
14746 GAATTTTTGGA
1 GAATTTTTGGA
14757 AGTTCGGGGG
Statistics
Matches: 115, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
116 2 0.02
117 2 0.02
118 111 0.97
ACGTcount: A:0.34, C:0.07, G:0.26, T:0.33
Consensus pattern (117 bp):
GAATTTTTGGACATCTAAGGGCAAAATGGTAATTTTTGGAAGATCAGGATCAAAAAAGGAATTTT
TGGACATTCGAGGGTAAAACGATAATTTTTGAAAGTTTCGAGATCAAAAATG
Found at i:14812 original size:88 final size:87
Alignment explanation
Indices: 14560--14935 Score: 302
Period size: 88 Copynumber: 4.3 Consensus size: 87
14550 TAAATCAGGA
* ** *
14560 TCAAAAAAGGAATTTTTGGACA-TTCGAGGGTAAAACGATAATTTTTGGAAGTTTCGGGGTTAAA
1 TCAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAATAGAATTTTTGGAAG-TTCGGGGTTAAA
* * *
14624 AATGGAATTTTTGGACA--TCTAAGG
64 ACTGTAATTTTT-GAAAGTTC-AAGG
* *
14648 GC-AAAATGGTAATTTTTGGAAGTTTCG-GGGTCAAAAATGGAATTTTTGGACA-TTCGAGGG-T
1 TCAAAAATGG-AATTTTTGGAAG-TTCGAGGGT-AAAAATAGAATTTTTGGA-AGTTCG-GGGTT
* ** *
14709 AAAACGGTAATTTTTGAAAGTTTTGAGA
61 AAAACTGTAATTTTTGAAAG-TTCAAGG
* * * *
14737 TCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATATAATTTTTAGAAGTTTTGGGGTTAAAA
1 TCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATAGAATTTTTGGAAG-TTCGGGGTTAAAA
*
14802 -TGTAATTTTTGGAAGTTCAAGGG
65 CTGTAATTTTTGAAAGTTCAA-GG
** * * *
14825 T-AAAAATATAATTTTTTGAAGTGTCGAGGTTAAAAATAGAATTTTTGGAAGTTCGGGGGTAAAA
1 TCAAAAATGGAATTTTTGGAAGT-TCGAGGGTAAAAATAGAATTTTTGGAAGTTCGGGGTTAAAA
* * ** *
14889 TTATAATTTTCAAAAGTTTCGAGG
65 CTGTAATTTTTGAAAG-TTCAAGG
14913 TCAAAAATGGAATTTTTTGGAAG
1 TCAAAAATGGAA-TTTTTGGAAG
14936 GTTTAGGGAC
Statistics
Matches: 228, Mismatches: 40, Indels: 38
0.75 0.13 0.12
Matches are distributed among these distances:
87 43 0.19
88 107 0.47
89 60 0.26
90 18 0.08
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.35
Consensus pattern (87 bp):
TCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATAGAATTTTTGGAAGTTCGGGGTTAAAAC
TGTAATTTTTGAAAGTTCAAGG
Found at i:14896 original size:29 final size:29
Alignment explanation
Indices: 14570--14898 Score: 224
Period size: 29 Copynumber: 11.2 Consensus size: 29
14560 TCAAAAAAGG
* *
14570 AATTTTTGGACA-TTCGAGGGT-AAAACGAT
1 AATTTTTGGA-AGTTCGGGGGTAAAAATG-T
* *
14599 AATTTTTGGAAGTTTCGGGGTTAAAAATGG
1 AATTTTTGGAAG-TTCGGGGGTAAAAATGT
** *
14629 AATTTTTGGACA--TCTAAGGG-CAAAATGGT
1 AATTTTTGGA-AGTTC-GGGGGTAAAAAT-GT
*
14658 AATTTTTGGAAGTTTC-GGGGTCAAAAATGG
1 AATTTTTGGAAG-TTCGGGGGT-AAAAATGT
* **
14688 AATTTTTGGACA-TTCGAGGGTAAAACGGT
1 AATTTTTGGA-AGTTCGGGGGTAAAAATGT
* ** * * *
14717 AATTTTTGAAAGTTTTGAGATCAAAAATGG
1 AATTTTTGGAAGTTCGGGGGT-AAAAATGT
*
14747 AATTTTTGGAAGTTCGGGGGTAAAAATAT
1 AATTTTTGGAAGTTCGGGGGTAAAAATGT
* ** *
14776 AATTTTTAGAAGTTTTGGGGTTAAAATGT
1 AATTTTTGGAAGTTCGGGGGTAAAAATGT
** *
14805 AATTTTTGGAAGTTCAAGGGTAAAAATAT
1 AATTTTTGGAAGTTCGGGGGTAAAAATGT
* * *
14834 AATTTTTTGAAGTGTCGAGGTTAAAAATAG-
1 AATTTTTGGAAGT-TCGGGGGTAAAAAT-GT
* *
14864 AATTTTTGGAAGTTCGGGGGTAAAATTAT
1 AATTTTTGGAAGTTCGGGGGTAAAAATGT
14893 AATTTT
1 AATTTT
14899 CAAAAGTTTC
Statistics
Matches: 230, Mismatches: 52, Indels: 36
0.72 0.16 0.11
Matches are distributed among these distances:
28 10 0.04
29 129 0.56
30 77 0.33
31 14 0.06
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (29 bp):
AATTTTTGGAAGTTCGGGGGTAAAAATGT
Found at i:16794 original size:17 final size:17
Alignment explanation
Indices: 16769--16827 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
16759 TAATTTAATA
*
16769 TTAAGTTTTAAATCAAT
1 TTAAATTTTAAATCAAT
* *
16786 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATCAAT
*
16803 TTAAA-TTTAAAGCAAAT
1 TTAAATTTTAAATC-AAT
16820 TTAAATTT
1 TTAAATTT
16828 AAAAATAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 5 0.15
17 27 0.79
18 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TTAAATTTTAAATCAAT
Found at i:16798 original size:6 final size:6
Alignment explanation
Indices: 16783--16830 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
16773 GTTTTAAATC
* **
16783 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-GCA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
16829 AA
1 AA
16831 AATAAATTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.21
6 27 0.79
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:16828 original size:17 final size:17
Alignment explanation
Indices: 16783--16830 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
16773 GTTTTAAATC
* **
16783 AATTTAAATTTTAATTA
1 AATTTAAATTTAAAGCA
16800 AATTTAAATTTAAAGCA
1 AATTTAAATTTAAAGCA
16817 AATTTAAATTTAAA
1 AATTTAAATTTAAA
16831 AATAAATTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
AATTTAAATTTAAAGCA
Found at i:17785 original size:21 final size:22
Alignment explanation
Indices: 17750--17792 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
17740 ACTATTATTT
*
17750 ATTAATTAATTTAATTAGATAA
1 ATTAATTAATTTAATTAAATAA
*
17772 ATTAATT-TTTTAATTAAATAA
1 ATTAATTAATTTAATTAAATAA
17793 TTTTTTCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATTAATTAATTTAATTAAATAA
Found at i:20359 original size:9 final size:9
Alignment explanation
Indices: 20342--20406 Score: 55
Period size: 9 Copynumber: 7.3 Consensus size: 9
20332 ACTTTGTAAT
*
20342 ATATTAAAA
1 ATATAAAAA
20351 ATAT-AAAA
1 ATATAAAAA
*
20359 ATATAAAAC
1 ATATAAAAA
*
20368 ATATAAGAA
1 ATATAAAAA
*
20377 TTAT-AAAA
1 ATATAAAAA
20385 ATA-AAAAA
1 ATATAAAAA
20393 GTATATAAAAA
1 --ATATAAAAA
20404 ATA
1 ATA
20407 AATAACAAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
8 17 0.38
9 20 0.44
10 3 0.07
11 5 0.11
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (9 bp):
ATATAAAAA
Found at i:20484 original size:22 final size:22
Alignment explanation
Indices: 20459--20501 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
20449 AACTATCCCA
* *
20459 AATTTTCTCATGAACCAAACAC
1 AATTCTCTCATCAACCAAACAC
*
20481 AATTCTCTCATCAATCAAACA
1 AATTCTCTCATCAACCAAACA
20502 ATAGACAAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.28, G:0.02, T:0.28
Consensus pattern (22 bp):
AATTCTCTCATCAACCAAACAC
Found at i:41985 original size:21 final size:21
Alignment explanation
Indices: 41958--42012 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
41948 TACTTTAGCC
* *
41958 ATTTTTTTATTTTTT-GTTTT
1 ATTTTTTTATTTTTTAATTTA
41978 ATTTTTTTCATTTTTTAATTTA
1 ATTTTTTT-ATTTTTTAATTTA
*
42000 ATTTTTATATTTT
1 ATTTTTTTATTTT
42013 AATTTTATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.27
21 12 0.40
22 10 0.33
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (21 bp):
ATTTTTTTATTTTTTAATTTA
Found at i:44718 original size:21 final size:21
Alignment explanation
Indices: 44692--44737 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
44682 ATGTTATTTT
44692 AAAAAAAAATAAAAAAATTCA
1 AAAAAAAAATAAAAAAATTCA
** * *
44713 AAAAAAAGTTGAAAAAATTGA
1 AAAAAAAAATAAAAAAATTCA
44734 AAAA
1 AAAA
44738 TTCAAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (21 bp):
AAAAAAAAATAAAAAAATTCA
Found at i:44854 original size:6 final size:6
Alignment explanation
Indices: 44757--44838 Score: 103
Period size: 6 Copynumber: 13.0 Consensus size: 6
44747 AATTAGTACA
*
44757 TTTATT TTT-TT TTCATTT TTTCATT TTTCATT TTTCATT TTTCATT TTTATT
1 TTTATT TTTATT TTTA-TT TTT-ATT TTT-ATT TTT-ATT TTT-ATT TTTATT
44809 TTTATT TTTATT TTTATT TTTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT
44839 ATGCACTATT
Statistics
Matches: 71, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
5 4 0.06
6 36 0.51
7 30 0.42
8 1 0.01
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:49863 original size:61 final size:61
Alignment explanation
Indices: 49793--49915 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
49783 ACTGAAACTT
*
49793 GTCTATTTCTATCAGTAGAAGTGGACAAGTATCGGTAGATTCGGGCATATATATACCCCAA
1 GTCTATTTCTATCAGTAGAAGTGGACAAGTATCGATAGATTCGGGCATATATATACCCCAA
49854 GTCTATTTCTATCAGTAGAAGTGGACAAGTATCGATAGATTCGGGCATATATATACCCCAA
1 GTCTATTTCTATCAGTAGAAGTGGACAAGTATCGATAGATTCGGGCATATATATACCCCAA
49915 G
1 G
49916 AAACGTGTTT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (61 bp):
GTCTATTTCTATCAGTAGAAGTGGACAAGTATCGATAGATTCGGGCATATATATACCCCAA
Found at i:50247 original size:2 final size:2
Alignment explanation
Indices: 50242--50300 Score: 61
Period size: 2 Copynumber: 31.0 Consensus size: 2
50232 TAAAAAAAAT
*
50242 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TG T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
50282 AA T- TT TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
50301 GTTTTTTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
1 3 0.06
2 45 0.94
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:55665 original size:58 final size:58
Alignment explanation
Indices: 55592--55738 Score: 190
Period size: 58 Copynumber: 2.5 Consensus size: 58
55582 GATTTTTGCT
* *
55592 AATTCATATTTTAATAATAATTATATTAAAAATGTTATTAAATTATATATTA-TTTTATTA
1 AATT-ATA-TTTAATAATAATTATATTAAAAA-ATAATTAAATTATATATTATTTTTATTA
* * * *
55652 AATTGTATTTAATAATTATTATGTTAAAAAATAATTAAATTATTTATTATTTTTATTA
1 AATTATATTTAATAATAATTATATTAAAAAATAATTAAATTATATATTATTTTTATTA
55710 AATTATATTTAATAATAATCT-TATTAAAA
1 AATTATATTTAATAATAAT-TATATTAAAA
55739 TTTAATAACA
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
57 16 0.21
58 53 0.70
59 3 0.04
60 4 0.05
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (58 bp):
AATTATATTTAATAATAATTATATTAAAAAATAATTAAATTATATATTATTTTTATTA
Found at i:55898 original size:44 final size:45
Alignment explanation
Indices: 55824--55917 Score: 140
Period size: 44 Copynumber: 2.1 Consensus size: 45
55814 TATTACAACA
*
55824 CCATTCCATTCAACCAAACACAATAATACT-ATTACAGCTCTATT
1 CCATTCCATTCAACCAAACACAATAATACTAATTACAGCCCTATT
55868 CCATTCCATTCAACCAAA-A-AATTAATTACTAATTACAGCCCTATT
1 CCATTCCATTCAACCAAACACAA-TAA-TACTAATTACAGCCCTATT
55913 CCATT
1 CCATT
55918 ACAGCACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
42 2 0.04
43 4 0.09
44 22 0.48
45 18 0.39
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.31
Consensus pattern (45 bp):
CCATTCCATTCAACCAAACACAATAATACTAATTACAGCCCTATT
Found at i:55920 original size:16 final size:16
Alignment explanation
Indices: 55899--55954 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
55889 TTAATTACTA
*
55899 ATTACAGCCCTATTCC
1 ATTACAGCACTATTCC
55915 ATTACAGCACTATTCC
1 ATTACAGCACTATTCC
* *
55931 ATTACAACTCTATTCC
1 ATTACAGCACTATTCC
55947 ATTACAGC
1 ATTACAGC
55955 GAACCAAACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.30, C:0.32, G:0.05, T:0.32
Consensus pattern (16 bp):
ATTACAGCACTATTCC
Found at i:61642 original size:17 final size:16
Alignment explanation
Indices: 61604--61647 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
61594 ATTAAATTAG
61604 CACTTAA-TTTTCAAA
1 CACTTAATTTTTCAAA
* *
61619 CATTTAATTTTTCTTAA
1 CACTTAATTTTTC-AAA
61636 CACTTAATTTTT
1 CACTTAATTTTT
61648 TAATTTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 6 0.25
16 5 0.21
17 13 0.54
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (16 bp):
CACTTAATTTTTCAAA
Found at i:61850 original size:100 final size:100
Alignment explanation
Indices: 61677--61877 Score: 366
Period size: 100 Copynumber: 2.0 Consensus size: 100
61667 TTAAAGTTAA
*
61677 TAAATCAAAATAATTGGTCCAACTATGTGGATTTTATTATTTTGGTTAGGTTACAACAATGGTAG
1 TAAATCAAAATAATTGATCCAACTATGTGGATTTTATTATTTTGGTTAGGTTACAACAATGGTAG
61742 CCGATAATCAATTATATTTTATTAAGGGTCAATAT
66 CCGATAATCAATTATATTTTATTAAGGGTCAATAT
* *
61777 TAAATCAAAATAATTGATCCAACTGTGTGGATTTTATTATTTTGGTTAGGTTACAACAATGGTGG
1 TAAATCAAAATAATTGATCCAACTATGTGGATTTTATTATTTTGGTTAGGTTACAACAATGGTAG
*
61842 CCGATAATCAGTTATATTTTATTAAGGGTCAATAT
66 CCGATAATCAATTATATTTTATTAAGGGTCAATAT
61877 T
1 T
61878 CAACTTTCAG
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (100 bp):
TAAATCAAAATAATTGATCCAACTATGTGGATTTTATTATTTTGGTTAGGTTACAACAATGGTAG
CCGATAATCAATTATATTTTATTAAGGGTCAATAT
Found at i:88931 original size:14 final size:15
Alignment explanation
Indices: 88912--88942 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
88902 GGATCTCCCA
88912 ATCTTCATAG-TATC
1 ATCTTCATAGATATC
88926 ATCTTCATAGATATC
1 ATCTTCATAGATATC
88941 AT
1 AT
88943 TATCAGAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (15 bp):
ATCTTCATAGATATC
Found at i:93073 original size:25 final size:26
Alignment explanation
Indices: 93044--93101 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
93034 ATTCTTTTCT
93044 AATTTTTAATTGA-TTTAAATTGTTA
1 AATTTTTAATTGATTTTAAATTGTTA
*
93069 AATTTTTAATTTATTTTAAATTGTTA
1 AATTTTTAATTGATTTTAAATTGTTA
93095 ATATTTT
1 A-ATTTT
93102 AGACTAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 12 0.40
26 13 0.43
27 5 0.17
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (26 bp):
AATTTTTAATTGATTTTAAATTGTTA
Found at i:95884 original size:8 final size:10
Alignment explanation
Indices: 95858--95886 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
95848 ACATTCTCTT
95858 TTTTCTCTCA
1 TTTTCTCTCA
95868 TTTTCTCTCA
1 TTTTCTCTCA
95878 TTTTCTCTC
1 TTTTCTCTC
95887 TAGCTTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.07, C:0.31, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTTCTCTCA
Found at i:112231 original size:23 final size:24
Alignment explanation
Indices: 112205--112269 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 24
112195 TTAACTTAAT
*
112205 CGAACATGTTCACGAATA-ATAAA
1 CGAACATGTTCACGAACATATAAA
* *
112228 CGAACATGTTCATGAACATATAAT
1 CGAACATGTTCACGAACATATAAA
* *
112252 TGAACACGTTCACGAACA
1 CGAACATGTTCACGAACA
112270 ATGTTAATGA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
23 16 0.46
24 19 0.54
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (24 bp):
CGAACATGTTCACGAACATATAAA
Found at i:112256 original size:24 final size:23
Alignment explanation
Indices: 112201--112271 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
112191 TTATTTAACT
*
112201 TAATCGAACATGTTCACGAATAA
1 TAATCGAACATGTTCACGAACAA
* *
112224 TAAACGAACATGTTCATGAACATA
1 TAATCGAACATGTTCACGAACA-A
* *
112248 TAATTGAACACGTTCACGAACAA
1 TAATCGAACATGTTCACGAACAA
112271 T
1 T
112272 GTTAATGAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 21 0.52
24 19 0.47
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (23 bp):
TAATCGAACATGTTCACGAACAA
Found at i:113273 original size:21 final size:20
Alignment explanation
Indices: 113249--113306 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
113239 TAGAAGCATG
*
113249 ACTTGTTTCAGTAGAAATCTC
1 ACTTGTATC-GTAGAAATCTC
*
113270 ACTTGTATCGATAGAAGTCTC
1 ACTTGTATCG-TAGAAATCTC
113291 ACTTGTATCGGTAGAA
1 ACTTGTATC-GTAGAA
113307 CTGTCTTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (20 bp):
ACTTGTATCGTAGAAATCTC
Found at i:121348 original size:58 final size:58
Alignment explanation
Indices: 121234--121348 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
121224 TTCACTCTAA
*
121234 ACACATCAATTGCATAAACAAAAAAATCAACCACTTCACTAGAATAACATTTACATAG
1 ACACATCAATTGCATAAACAAAAAAATCAACCACTTCACTAGAATAACATTCACATAG
* *
121292 ACACATCAATTGCATAAACAAAAAAATCAACCACTTTACTTGAATAACCA-TCACATA
1 ACACATCAATTGCATAAACAAAAAAATCAACCACTTCACTAGAATAA-CATTCACATA
121349 ATAACATTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
58 51 0.96
59 2 0.04
ACGTcount: A:0.50, C:0.23, G:0.04, T:0.23
Consensus pattern (58 bp):
ACACATCAATTGCATAAACAAAAAAATCAACCACTTCACTAGAATAACATTCACATAG
Found at i:122454 original size:14 final size:14
Alignment explanation
Indices: 122435--122461 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
122425 CAAATTTTCC
122435 AATTTAATTTCTTG
1 AATTTAATTTCTTG
122449 AATTTAATTTCTT
1 AATTTAATTTCTT
122462 AGTGAGTCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (14 bp):
AATTTAATTTCTTG
Found at i:133807 original size:23 final size:23
Alignment explanation
Indices: 133770--133836 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
133760 TTATTATTTA
*
133770 GAAAAAGAAAAAAAATAAACAAATT
1 GAAAAA-AAAAAAAAGAAA-AAATT
133795 GAAAAAAAAAAAAAGAAAAAATT
1 GAAAAAAAAAAAAAGAAAAAATT
* * *
133818 GGAAAAAAGAAGAAGAAAA
1 GAAAAAAAAAAAAAGAAAA
133837 GATAAAAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
23 21 0.55
24 11 0.29
25 6 0.16
ACGTcount: A:0.78, C:0.01, G:0.13, T:0.07
Consensus pattern (23 bp):
GAAAAAAAAAAAAAGAAAAAATT
Found at i:134885 original size:23 final size:25
Alignment explanation
Indices: 134858--134903 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
134848 CTAATTAGGG
134858 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
134881 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
134904 TGGATTTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:136298 original size:8 final size:8
Alignment explanation
Indices: 136282--136311 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
136272 GTTAAACACA
136282 ACAATCAC
1 ACAATCAC
*
136290 ACTATCAC
1 ACAATCAC
136298 ACAATCAC
1 ACAATCAC
136306 ACAATC
1 ACAATC
136312 GTAGTACTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (8 bp):
ACAATCAC
Found at i:147812 original size:24 final size:24
Alignment explanation
Indices: 147779--147854 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
147769 AGACATAAGC
* *
147779 TCTTCTATTAAAGAAATCACCAAG
1 TCTTCCATTAAAGATATCACCAAG
* *
147803 TCTTCCATTAAAGATACCATTC-AG
1 TCTTCCATTAAAGATATCA-CCAAG
* *
147827 TCCTCCATTAAAGATATCACTAAG
1 TCTTCCATTAAAGATATCACCAAG
147851 TCTT
1 TCTT
147855 TCATATCATA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
24 40 0.98
25 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.33
Consensus pattern (24 bp):
TCTTCCATTAAAGATATCACCAAG
Found at i:152490 original size:17 final size:17
Alignment explanation
Indices: 152468--152572 Score: 111
Period size: 17 Copynumber: 6.1 Consensus size: 17
152458 CAAACTCCTT
152468 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
152485 TTAAATTTGTTTAAAAA
1 TTAAATTTATTTTAAAA
* *
152502 TTTAAATTTATTTTCAAT
1 -TTAAATTTATTTTAAAA
*
152520 TTAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAA
* **
152537 TTAAATTTAATTTAAGT
1 TTAAATTTATTTTAAAA
* *
152554 TTAAAATTATTTTCAAA
1 TTAAATTTATTTTAAAA
152571 TT
1 TT
152573 TAAAATTATC
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
17 60 0.82
18 13 0.18
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:152506 original size:35 final size:34
Alignment explanation
Indices: 152467--152581 Score: 122
Period size: 35 Copynumber: 3.3 Consensus size: 34
152457 CCAAACTCCT
*
152467 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAAATTAAATTTATTT-AAAA
* * *
152502 TTTAAATTTATTTTCAATTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAAATTAAATTTATTTAAAA
* ** * *
152536 TTTAAATTTAATTTAAGTTTAAAATTATTTTCAAA
1 TTTAAATTTATTTTAAAATTAAATTTA-TTTAAAA
*
152571 TTTAAAATTAT
1 TTTAAATTTAT
152582 CATAAGTTTA
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
34 26 0.38
35 42 0.62
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (34 bp):
TTTAAATTTATTTTAAAATTAAATTTATTTAAAA
Found at i:152508 original size:6 final size:6
Alignment explanation
Indices: 152499--152576 Score: 65
Period size: 6 Copynumber: 13.5 Consensus size: 6
152489 ATTTGTTTAA
* * *
152499 AAATTT AAATTT -ATTTT CAATTT AAATTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * *
152545 -AATTT AAGTTT AAAATT -ATTTT CAAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAA
152577 ATTATCATAA
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
5 16 0.29
6 36 0.64
7 4 0.07
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:152528 original size:52 final size:52
Alignment explanation
Indices: 152467--152581 Score: 153
Period size: 52 Copynumber: 2.2 Consensus size: 52
152457 CCAAACTCCT
* *
152467 TTTAAATTTATTTTAAAATTAAATTT-GTTTAAAAATTTAAATTTATTTTC-AA
1 TTTAAATTTATTTTAAAATTAAATTTAATTT--AAATTTAAAATTATTTTCAAA
* *
152519 TTTAAATTTATTTTAAATTTAAATTTAATTTAAGTTTAAAATTATTTTCAAA
1 TTTAAATTTATTTTAAAATTAAATTTAATTTAAATTTAAAATTATTTTCAAA
*
152571 TTTAAAATTAT
1 TTTAAATTTAT
152582 CATAAGTTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
51 16 0.29
52 37 0.66
53 3 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (52 bp):
TTTAAATTTATTTTAAAATTAAATTTAATTTAAATTTAAAATTATTTTCAAA
Found at i:152533 original size:11 final size:11
Alignment explanation
Indices: 152519--152574 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
152509 TTATTTTCAA
152519 TTTAAATTTAT
1 TTTAAATTTAT
*
152530 TTTAAATTTAAA
1 TTTAAATTT-AT
*
152542 TTT-AATTTAAG
1 TTTAAATTT-AT
*
152553 TTTAAAATTAT
1 TTTAAATTTAT
152564 TTTCAAATTTA
1 TTT-AAATTTA
152575 AAATTATCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 23 0.62
12 14 0.38
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:152588 original size:35 final size:34
Alignment explanation
Indices: 152519--152595 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 34
152509 TTATTTTCAA
* * *
152519 TTTAAATTTATTTTAAATTTAAATTTAATTTAAG
1 TTTAAAATTATTTTAAATTTAAAATTAATATAAG
152553 TTTAAAATTATTTTCAAATTTAAAATT-ATCATAAG
1 TTTAAAATTATTTT-AAATTTAAAATTAAT-ATAAG
152588 TTTAAAAT
1 TTTAAAAT
152596 AAATAAAGCC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
34 15 0.39
35 23 0.61
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (34 bp):
TTTAAAATTATTTTAAATTTAAAATTAATATAAG
Done.