Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013666.1 Kokia drynarioides strain JFW-HI SEQ_128694, 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: 56137
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 93 characters in sequence are not A, C, G, or T
Found at i:666 original size:17 final size:17
Alignment explanation
Indices: 646--709 Score: 83
Period size: 17 Copynumber: 3.8 Consensus size: 17
636 AAATAAATTT
*
646 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* *
663 TAAATTTAAATTCAGAA
1 TAAATTTAAATTTAAAA
* *
680 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
697 TAAATTTAAATTT
1 TAAATTTAAATTT
710 TTTGGGCCCG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:1396 original size:205 final size:205
Alignment explanation
Indices: 1037--1432 Score: 596
Period size: 205 Copynumber: 1.9 Consensus size: 205
1027 TCTTGGGCTC
*
1037 CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTATTGCTTTAACATGCTTCTCGGTGTCTCATTA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTATTGCTTTAACATGCTTCTCGGTGTCTCATCA
* * * *
1102 GGAAGTTGGGATTTGAAGATTTACTTACATCGAGCGTGGGTTTGATATGGTCTTCTTCTCGGTGT
66 GGAAGCTGGGATTGGAAGATTTACTTACATCGAGCGTGGGTTTGATATGGTCTTCTTCTCAGTAT
* * *
1167 CTTATCAGGAAGATGACTGCATCGTTTGTTTCAATCTGCTTCTCTGTATCTCATCAGGAAGACGA
131 CTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGA
1232 ATTTGGTACA
196 ATTTGGTACA
* * * * * *
1242 CTTCTCAGTATTTTATCAGGAAGCTGACCTTTTATTG-TTTCGACTTGCTTCTCGGTGTCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTATTGCTTT-AACATGCTTCTCGGTGTCTCATC
* * * * * *
1306 GGGAAGCTGGGGTTGGAAGATTTTCTTGCATCGAGCGTGGGTTTGATTTGGTCTTCTTCTTAGTA
65 AGGAAGCTGGGATTGGAAGATTTACTTACATCGAGCGTGGGTTTGATATGGTCTTCTTCTCAGTA
1371 TCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAG
130 TCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAG
1433 CTAACCGTTT
Statistics
Matches: 170, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
204 3 0.02
205 167 0.98
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (205 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTATTGCTTTAACATGCTTCTCGGTGTCTCATCA
GGAAGCTGGGATTGGAAGATTTACTTACATCGAGCGTGGGTTTGATATGGTCTTCTTCTCAGTAT
CTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGA
ATTTGGTACA
Found at i:1545 original size:168 final size:168
Alignment explanation
Indices: 1242--1600 Score: 540
Period size: 168 Copynumber: 2.1 Consensus size: 168
1232 ATTTGGTACA
* * * * * *
1242 CTTCTCAGTATTTTATCAGGAAGCTGACCTTTTATTGTTTCGACTTGCTTCTCGGTGTCTCATCG
1 CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTATTGTTTCAACTTGCTTCTCGGTGTCTCATCA
* * * * * * *
1307 GGAAGCTGGGGTTGGAAGATTTTCTTGCATCGAGCGTGGGTTTGATTTGGTCTTCTTCTTAGTAT
66 GAAAGCTGGGATTGGAAGATTTGCTTACATCGAGCATGGGTTTGATCTGGTCTTCTTCTCAGTAT
1372 CTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCG
131 CTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCG
*
1410 CTTCTCTGTATCTCATCAGGAAGCTAACCGTTTATTGCTTT-AACTTGCTTCTCGGTGTCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTATTG-TTTCAACTTGCTTCTCGGTGTCTCATC
* * *
1474 AGAAAGCTGGGATTTGAAGATTTGCTTACATCGAGCATGGGTTTGATCTGGTCTTCTTCTCGGTG
65 AGAAAGCTGGGATTGGAAGATTTGCTTACATCGAGCATGGGTTTGATCTGGTCTTCTTCTCAGTA
1539 TCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCG
130 TCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCG
*
1578 CTTCTCCGTATCTCATCAGGAAG
1 CTTCTCAGTATCTCATCAGGAAG
1601 ACAAATTTGG
Statistics
Matches: 172, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
168 169 0.98
169 3 0.02
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (168 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTATTGTTTCAACTTGCTTCTCGGTGTCTCATCA
GAAAGCTGGGATTGGAAGATTTGCTTACATCGAGCATGGGTTTGATCTGGTCTTCTTCTCAGTAT
CTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCG
Found at i:1729 original size:373 final size:373
Alignment explanation
Indices: 1037--1790 Score: 1283
Period size: 373 Copynumber: 2.0 Consensus size: 373
1027 TCTTGGGCTC
* *
1037 CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTATTGCTTTAACATGCTTCTCGGTGTCTCATTA
1 CTTCTCTGTATCTCATCAGGAAGCTAACCGTTTATTGCTTTAACATGCTTCTCGGTGTCTCATCA
* * *
1102 GGAAGTTGGGATTTGAAGATTTACTTACATCGAGCGTGGGTTTGATATGGTCTTCTTCTCGGTGT
66 GAAAGCTGGGATTTGAAGATTTACTTACATCGAGCATGGGTTTGATATGGTCTTCTTCTCGGTGT
* * * * *
1167 CTTATCAGGAAGATGACTGCATCGTTTGTTTCAATCTGCTTCTCTGTATCTCATCAGGAAGACGA
131 CTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTCTCCGTATCTCATCAGGAAGACAA
* *
1232 ATTTGGTACACTTCTCAGTATTTTATCAGGAAGCTGACCTTTTATTGTTTCGACTTGCTTCTCGG
196 ATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTGACCTTTTATTGTTTCGACTTGCTTCTCGG
* * **
1297 TGTCTCATCGGGAAGCTGGGGTTGGAAGATTTTCTTGCATCGAGCGTGGGTTTGATTTGGTCTTC
261 TGTCTCATCGGGAAGCTAGGGTTGAAAGATTCGCTTGCATCGAGCGTGGGTTTGATTTGGTCTTC
*
1362 TTCTTAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCG
326 TTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCG
*
1410 CTTCTCTGTATCTCATCAGGAAGCTAACCGTTTATTGCTTTAACTTGCTTCTCGGTGTCTCATCA
1 CTTCTCTGTATCTCATCAGGAAGCTAACCGTTTATTGCTTTAACATGCTTCTCGGTGTCTCATCA
* *
1475 GAAAGCTGGGATTTGAAGATTTGCTTACATCGAGCATGGGTTTGATCTGGTCTTCTTCTCGGTGT
66 GAAAGCTGGGATTTGAAGATTTACTTACATCGAGCATGGGTTTGATATGGTCTTCTTCTCGGTGT
1540 CTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTCTCCGTATCTCATCAGGAAGACAA
131 CTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTCTCCGTATCTCATCAGGAAGACAA
1605 ATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTGACCTTTTATTGTTTCGACTTGCTTCTCGG
196 ATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTGACCTTTTATTGTTTCGACTTGCTTCTCGG
* *
1670 TGTCTCATCGGGAAGCTAGGGTTGAAAGGTTCGCTTGCATCGAGTGTGGGTTTGATTTGGTCTTC
261 TGTCTCATCGGGAAGCTAGGGTTGAAAGATTCGCTTGCATCGAGCGTGGGTTTGATTTGGTCTTC
* *
1735 TTCTCAGTATCTTATCAGGAAGATGACCGCATCGTTTGTTTCAATTCG
326 TTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCG
*
1783 TTTCTCTG
1 CTTCTCTG
1791 GCTCGTAATC
Statistics
Matches: 356, Mismatches: 25, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
373 356 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (373 bp):
CTTCTCTGTATCTCATCAGGAAGCTAACCGTTTATTGCTTTAACATGCTTCTCGGTGTCTCATCA
GAAAGCTGGGATTTGAAGATTTACTTACATCGAGCATGGGTTTGATATGGTCTTCTTCTCGGTGT
CTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTCTCCGTATCTCATCAGGAAGACAA
ATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTGACCTTTTATTGTTTCGACTTGCTTCTCGG
TGTCTCATCGGGAAGCTAGGGTTGAAAGATTCGCTTGCATCGAGCGTGGGTTTGATTTGGTCTTC
TTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCG
Found at i:1769 original size:205 final size:204
Alignment explanation
Indices: 1410--1788 Score: 555
Period size: 205 Copynumber: 1.8 Consensus size: 204
1400 TTTCAATCCG
*
1410 CTTCTCTGTATCTCATCAGGAAGCTAACCGTTTATTGCTTTAACTTGCTTCTCGGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTATTGCTTTAACTTGCTTCTCGGTGTCTCATCA
* * *
1475 GAAAGCTGGGATTTGAAGATTTGCTTACATCGAGCATGGGTTTGATCTGGTCTTCTTCTCGGTGT
66 GAAAGCTGGGA-TTGAAGATTCGCTTACATCGAGCATGGGTTTGATCTGGTCTTCTTCTCAGTAT
1540 CTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTCTCCGTATCTCATCAGGAAGACAA
130 CTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTCTCCGTATCTCATCAGGAAGACAA
1605 ATTTGGTACA
195 ATTTGGTACA
* * *
1615 CTTCTCAGTATCTCATCAGGAAGCTGACCTTTTATTG-TTTCGACTTGCTTCTCGGTGTCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTATTGCTTT-AACTTGCTTCTCGGTGTCTCATC
* * * * ** *
1679 GGGAAGCTAGGG-TTGAAAGGTTCGCTTGCATCGAGTGTGGGTTTGATTTGGTCTTCTTCTCAGT
65 AGAAAGCT-GGGATTG-AAGATTCGCTTACATCGAGCATGGGTTTGATCTGGTCTTCTTCTCAGT
* * *
1743 ATCTTATCAGGAAGATGACCGCATCGTTTGTTTCAATTCGTTTCTC
128 ATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTCTC
1789 TGGCTCGTAA
Statistics
Matches: 154, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
204 6 0.04
205 145 0.94
206 3 0.02
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (204 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTATTGCTTTAACTTGCTTCTCGGTGTCTCATCA
GAAAGCTGGGATTGAAGATTCGCTTACATCGAGCATGGGTTTGATCTGGTCTTCTTCTCAGTATC
TCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTCTCCGTATCTCATCAGGAAGACAAA
TTTGGTACA
Found at i:13206 original size:59 final size:59
Alignment explanation
Indices: 13143--13522 Score: 421
Period size: 59 Copynumber: 6.4 Consensus size: 59
13133 ACATCCGGGA
* * * * * *
13143 GTAAAATAGTATTTTTTGGATGTTTCGGGGCCAAAAATGGGATTTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATAGGATTTTTGGAAGTTTGGGG
* * * * *
13202 GTAAAATGATAA-TTTTAGAAGTTTTGGGGTCAAAAATAGGATTTTTTAGG-TGTTTAGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATAGGA-TTTTT-GGAAGTTTGGGG
* *
13261 GTAAAATGGTAATTTTTAGAAGTTTCGAGGG-CAAAAATATGATTTTT-GAGAGTTTGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCG-GGGTCAAAAATAGGATTTTTGGA-AGTTTGGGG
* * *
13320 GTAAAATGGTAATTTTTAGAAGGTTT-GGGGTCAAAAATAGAATTTTTGGAAGTTTGAGG
1 GTAAAATGGTAATTTTTGGAA-GTTTCGGGGTCAAAAATAGGATTTTTGGAAGTTTGGGG
* * ** * *
13379 GTAAAATGGTAATTTTAGAAAGTTTTAGGGTTAAAAAT-GAGATTTTTGGAAGTTTAGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATAG-GATTTTTGGAAGTTTGGGG
* * *
13438 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTTAAAAATATGATTTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATAGGATTTTTGGAAGTTTGGGG
*
13497 GTATAATGGTAATTTTTGGACAGTTT
1 GTAAAATGGTAATTTTTGGA-AGTTT
13523 AGGGACCTCC
Statistics
Matches: 273, Mismatches: 35, Indels: 25
0.82 0.11 0.08
Matches are distributed among these distances:
57 1 0.00
58 32 0.12
59 201 0.74
60 36 0.13
61 3 0.01
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.37
Consensus pattern (59 bp):
GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATAGGATTTTTGGAAGTTTGGGG
Found at i:13207 original size:29 final size:28
Alignment explanation
Indices: 13176--13522 Score: 213
Period size: 29 Copynumber: 11.8 Consensus size: 28
13166 TTCGGGGCCA
* *
13176 AAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGAATTTTTGGAAGTTTGGGGGT
* * *
13204 AAAAT-GATAATTTTAGAAGTTTTGGGGT
1 AAAATGGA-ATTTTTGGAAGTTTGGGGGT
* * *
13232 CAAAAATAGGATTTTTTAGG-TGTTTAGGGGT
1 --AAAAT-GGAATTTTT-GGAAGTTTGGGGGT
* **
13263 AAAATGGTAATTTTTAGAAGTTTCGAGGGCA
1 AAAATGG-AATTTTTGGAAGTTT-G-GGGGT
*
13294 AAAATATG-ATTTTT-GAGAGTTTGGGGGT
1 AAAAT-GGAATTTTTGGA-AGTTTGGGGGT
*
13322 AAAATGGTAATTTTTAGAAGGTTT-GGGGT
1 AAAATGG-AATTTTTGGAA-GTTTGGGGGT
* *
13351 CAAAAATAGAATTTTTGGAAGTTTGAGGGT
1 --AAAATGGAATTTTTGGAAGTTTGGGGGT
* * * *
13381 AAAATGGTAATTTTAGAAAGTTTTAGGGTT
1 AAAATGG-AATTTTTGGAAG-TTTGGGGGT
*
13411 AAAAAT-GAGATTTTTGGAAGTTTAGGGGT
1 -AAAATGGA-ATTTTTGGAAGTTTGGGGGT
*
13440 AAAATGGTAATTTTTGGAAGTTTCGGGGTT
1 AAAATGG-AATTTTTGGAAGTTT-GGGGGT
* *
13470 AAAAATATG-ATTTTTGGAAGTTCGGGGGT
1 -AAAAT-GGAATTTTTGGAAGTTTGGGGGT
*
13499 ATAATGGTAATTTTTGGACAGTTT
1 AAAATGG-AATTTTTGGA-AGTTT
13523 AGGGACCTCC
Statistics
Matches: 248, Mismatches: 40, Indels: 60
0.71 0.11 0.17
Matches are distributed among these distances:
27 3 0.01
28 47 0.19
29 82 0.33
30 74 0.30
31 37 0.15
32 5 0.02
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.37
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTGGGGGT
Found at i:13306 original size:30 final size:29
Alignment explanation
Indices: 13272--13491 Score: 114
Period size: 30 Copynumber: 7.4 Consensus size: 29
13262 TAAAATGGTA
*
13272 ATTTTTAGAAGTTTCGAGGGCAAAAATATG
1 ATTTTTGGAAGTTT-GAGGGCAAAAATATG
** * *
13302 ATTTTT-GAGAGTTTG-GGGGTAAAATGGTA
1 ATTTTTGGA-AGTTTGAGGGCAAAAAT-ATG
*
13331 ATTTTTAGAAGGTTTG-GGGTCAAAAATA-G
1 ATTTTTGGAA-GTTTGAGGG-CAAAAATATG
* * *
13360 AATTTTTGGAAGTTTGAGGG-TAAAATGGTA
1 -ATTTTTGGAAGTTTGAGGGCAAAAAT-ATG
* * * *
13390 ATTTTAGAAAGTTTTAGGGTTAAAAATGA-G
1 ATTTTTGGAAGTTTGAGGG-CAAAAAT-ATG
** * *
13420 ATTTTTGGAAGTTT-AGGGGTAAAATGGTA
1 ATTTTTGGAAGTTTGAGGGCAAAAAT-ATG
*
13449 ATTTTTGGAAGTTTCG-GGGTTAAAAATATG
1 ATTTTTGGAAGTTT-GAGGG-CAAAAATATG
13479 ATTTTTGGAAGTT
1 ATTTTTGGAAGTT
13492 CGGGGGTATA
Statistics
Matches: 147, Mismatches: 28, Indels: 30
0.72 0.14 0.15
Matches are distributed among these distances:
28 19 0.13
29 50 0.34
30 62 0.42
31 16 0.11
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.38
Consensus pattern (29 bp):
ATTTTTGGAAGTTTGAGGGCAAAAATATG
Found at i:14611 original size:18 final size:17
Alignment explanation
Indices: 14588--14627 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
14578 CGATTTTTTT
14588 TATTTTAATTAATAATAA
1 TATTTTAA-TAATAATAA
14606 TATTTTTAATAATAATAA
1 TA-TTTTAATAATAATAA
14624 -ATTT
1 TATTT
14628 CATTTAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.14
17 1 0.05
18 11 0.52
19 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTTTAATAATAATAA
Found at i:15292 original size:17 final size:16
Alignment explanation
Indices: 15270--15357 Score: 86
Period size: 17 Copynumber: 5.2 Consensus size: 16
15260 TCTGGACATT
15270 ATTTAAATAAATTTTAA
1 ATTTAAATAAA-TTTAA
** *
15287 ATTTAAATTTATAATAA
1 ATTTAAATAAAT-TTAA
15304 ATTTAAATAAATTTAA
1 ATTTAAATAAATTTAA
* *
15320 ATTCAGAATAAACTTAA
1 ATTTA-AATAAATTTAA
*
15337 TTTTAAAATAAATTTAA
1 ATTT-AAATAAATTTAA
15354 ATTT
1 ATTT
15358 TTTGGGTCCG
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
16 8 0.14
17 47 0.84
18 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (16 bp):
ATTTAAATAAATTTAA
Found at i:15293 original size:6 final size:6
Alignment explanation
Indices: 15277--15357 Score: 50
Period size: 6 Copynumber: 14.2 Consensus size: 6
15267 ATTATTTAAA
15277 TAAATTT TAAATT TAAATT TATAA-- TAAATT TAAA-- TAAATT TAAATT
1 TAAA-TT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT
* * * *
15323 CAGAA-- TAAACT TAATTT TAAA-A TAAATT TAAATT T
1 TA-AATT TAAATT TAAATT TAAATT TAAATT TAAATT T
15358 TTTGGGTCCG
Statistics
Matches: 58, Mismatches: 7, Indels: 19
0.69 0.08 0.23
Matches are distributed among these distances:
4 8 0.14
5 7 0.12
6 35 0.60
7 8 0.14
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:15314 original size:10 final size:10
Alignment explanation
Indices: 15270--15321 Score: 68
Period size: 10 Copynumber: 4.8 Consensus size: 10
15260 TCTGGACATT
15270 ATTTAAATAA
1 ATTTAAATAA
15280 ATTTTAAATTTAA
1 A-TTTAAA--TAA
15293 ATTTATAATAA
1 ATTTA-AATAA
15304 ATTTAAATAA
1 ATTTAAATAA
15314 ATTTAAAT
1 ATTTAAAT
15322 TCAGAATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 14 0.37
11 14 0.37
12 4 0.11
13 6 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
ATTTAAATAA
Found at i:17512 original size:28 final size:27
Alignment explanation
Indices: 17461--17522 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
17451 ATATTATATT
**
17461 TATAAAATAAATCAATATTTATTAATAA
1 TATAAAATAAATCAATATAAATTAA-AA
17489 TATAAAATATAA-CAATATAAATTAAAA
1 TATAAAATA-AATCAATATAAATTAAAA
17516 TAATAAA
1 T-ATAAA
17523 TTATCTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 3 0.10
28 25 0.83
29 2 0.07
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (27 bp):
TATAAAATAAATCAATATAAATTAAAA
Found at i:18623 original size:6 final size:6
Alignment explanation
Indices: 18612--18641 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
18602 GATGGGAGGT
18612 GGATGG GGATGG GGATGG GGATGG GGATGG
1 GGATGG GGATGG GGATGG GGATGG GGATGG
18642 ATACTTTAAT
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:0.17, C:0.00, G:0.67, T:0.17
Consensus pattern (6 bp):
GGATGG
Found at i:19457 original size:12 final size:12
Alignment explanation
Indices: 19363--19493 Score: 74
Period size: 12 Copynumber: 11.3 Consensus size: 12
19353 CTAAATAACC
*
19363 AAAATAACAACC
1 AAAATAACAACA
* * *
19375 AAAACAGCAGCA
1 AAAATAACAACA
* *
19387 AAAATAATAGC-
1 AAAATAACAACA
*
19398 AAAATAACAATA
1 AAAATAACAACA
19410 AAAAT---AACA
1 AAAATAACAACA
* *
19419 AAATTAGCAACA
1 AAAATAACAACA
* *
19431 AAAACAACAATA
1 AAAATAACAACA
*
19443 AAAATAACAGCA
1 AAAATAACAACA
*
19455 AAAATAGCAAC-
1 AAAATAACAACA
* * *
19466 AAAACAGCAATA
1 AAAATAACAACA
*
19478 AAAATAACAGCA
1 AAAATAACAACA
19490 AAAA
1 AAAA
19494 AGCACCAAAA
Statistics
Matches: 87, Mismatches: 27, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
9 7 0.08
11 17 0.20
12 63 0.72
ACGTcount: A:0.68, C:0.16, G:0.06, T:0.10
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:19477 original size:35 final size:35
Alignment explanation
Indices: 19382--19525 Score: 154
Period size: 33 Copynumber: 4.2 Consensus size: 35
19372 ACCAAAACAG
** * *
19382 CAGCAAAAATAATAGCAAAATAACAATAAAAAT-A
1 CAGCAAAAATAGCAACAAAACAACAATAAAAATAA
*
19416 -A-CAAAATTAGCAACAAAAACAACAATAAAAATAA
1 CAGCAAAAATAGCAAC-AAAACAACAATAAAAATAA
*
19450 CAGCAAAAATAGCAACAAAACAGCAATAAAAATAA
1 CAGCAAAAATAGCAACAAAACAACAATAAAAATAA
* * *
19485 CAGCAAAAA-AGCACCAAAACAATAA-AAAAACAA
1 CAGCAAAAATAGCAACAAAACAACAATAAAAATAA
*
19518 CACCAAAA
1 CAGCAAAA
19526 TAACAACCTA
Statistics
Matches: 94, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
32 9 0.10
33 31 0.33
34 14 0.15
35 28 0.30
36 12 0.13
ACGTcount: A:0.68, C:0.17, G:0.06, T:0.09
Consensus pattern (35 bp):
CAGCAAAAATAGCAACAAAACAACAATAAAAATAA
Found at i:19480 original size:23 final size:23
Alignment explanation
Indices: 19363--19497 Score: 78
Period size: 23 Copynumber: 5.9 Consensus size: 23
19353 CTAAATAACC
* **
19363 AAAATAACAACCAAAACAGCAGCA
1 AAAATAACAA-CAAAAAAGCAATA
* *
19387 AAAATAATAGCAAAATAA-CAATA
1 AAAATAACAACAAAA-AAGCAATA
** *
19410 AAAATAAC-A-AAATTAGCAACA
1 AAAATAACAACAAAAAAGCAATA
* * * **
19431 AAAACAACAATAAAAATAACAGCA
1 AAAATAACAACAAAAA-AGCAATA
* *
19455 AAAATAGCAACAAAACAGCAATA
1 AAAATAACAACAAAAAAGCAATA
*
19478 AAAATAACAGCAAAAAAGCA
1 AAAATAACAACAAAAAAGCA
19498 CCAAAACAAT
Statistics
Matches: 81, Mismatches: 25, Indels: 11
0.69 0.21 0.09
Matches are distributed among these distances:
20 1 0.01
21 14 0.17
22 1 0.01
23 39 0.48
24 26 0.32
ACGTcount: A:0.67, C:0.16, G:0.07, T:0.10
Consensus pattern (23 bp):
AAAATAACAACAAAAAAGCAATA
Found at i:19514 original size:68 final size:68
Alignment explanation
Indices: 19375--19532 Score: 169
Period size: 68 Copynumber: 2.3 Consensus size: 68
19365 AATAACAACC
* * * * **
19375 AAAACAGCAGCAAAAATAATAGCAAAATAACAATAAAAATAACAAAATTAGCAACAAAAACAACA
1 AAAACAACAGCAAAAATAACAACAAAACAACAATAAAAATAACAAAAAAAGCAACAAAAACAACA
19440 ATA
66 ATA
* * * *
19443 AAAATAACAGCAAAAATAGCAACAAAACAGCAATAAAAATAACAGCAAAAAAGC-ACCAAAACAA
1 AAAACAACAGCAAAAATAACAACAAAACAACAATAAAAATAACA--AAAAAAGCAACAAAAACAA
*
19507 TAA-A
64 CAATA
*
19511 AAAACAACA-CCAAAATAACAAC
1 AAAACAACAGCAAAAATAACAAC
19533 CTAAATAGTA
Statistics
Matches: 74, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
67 11 0.15
68 46 0.62
69 11 0.15
70 6 0.08
ACGTcount: A:0.68, C:0.18, G:0.06, T:0.09
Consensus pattern (68 bp):
AAAACAACAGCAAAAATAACAACAAAACAACAATAAAAATAACAAAAAAAGCAACAAAAACAACA
ATA
Found at i:26764 original size:21 final size:21
Alignment explanation
Indices: 26740--26781 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
26730 TATATTTAAA
*
26740 AAGTGCAAGGAGTGTAGAATT
1 AAGTGCAAGGAATGTAGAATT
*
26761 AAGTGTAAGGAATGTAGAATT
1 AAGTGCAAGGAATGTAGAATT
26782 TGAAGTTTTA
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:0.40, C:0.02, G:0.31, T:0.26
Consensus pattern (21 bp):
AAGTGCAAGGAATGTAGAATT
Found at i:33687 original size:14 final size:14
Alignment explanation
Indices: 33668--33696 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
33658 TAACTCTAGG
33668 CTAGGAGTGTAACA
1 CTAGGAGTGTAACA
33682 CTAGGAGTGTAACA
1 CTAGGAGTGTAACA
33696 C
1 C
33697 CCAAAAACCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (14 bp):
CTAGGAGTGTAACA
Found at i:35221 original size:36 final size:36
Alignment explanation
Indices: 35169--35268 Score: 148
Period size: 36 Copynumber: 2.8 Consensus size: 36
35159 TTGATATTTG
*
35169 ATTTACTCCCTATTGACCCAAAAGTCATGATGCTCA
1 ATTTACTCCCTGTTGACCCAAAAGTCATGATGCTCA
* * *
35205 TTTTACTCCTTGTTGACCCAAAGGTCATGATGCTCA
1 ATTTACTCCCTGTTGACCCAAAAGTCATGATGCTCA
*
35241 ATTTACTCCCTGTTGA-CCTAAAGTCATG
1 ATTTACTCCCTGTTGACCCAAAAGTCATG
35269 CCTGTTACCA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 10 0.18
36 46 0.82
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (36 bp):
ATTTACTCCCTGTTGACCCAAAAGTCATGATGCTCA
Found at i:36275 original size:14 final size:15
Alignment explanation
Indices: 36243--36275 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
36233 GTGTTTCCGC
36243 TTGAAGAAGAAGAAA
1 TTGAAGAAGAAGAAA
36258 -TGAAGAA-AAGAAA
1 TTGAAGAAGAAGAAA
36271 TTGAA
1 TTGAA
36276 TTTACAACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (15 bp):
TTGAAGAAGAAGAAA
Found at i:37683 original size:48 final size:48
Alignment explanation
Indices: 37562--37698 Score: 130
Period size: 48 Copynumber: 2.9 Consensus size: 48
37552 TCGACATGAT
* * * * * * *
37562 AAGCATAATCCCAAGCCATCAGGCCAACGATTGCCCCTTCGACATAAC
1 AAGCATAATCCCGAGCCATTAGGTCAACGGTTGCACCTTTGGCATAAC
* * * * ** *
37610 AAGCATAATCTCGGGTCGTTAGGTCAGTGGTTGCACTTTTGGCATAAC
1 AAGCATAATCCCGAGCCATTAGGTCAACGGTTGCACCTTTGGCATAAC
* *
37658 AAGCATGATCCCGAGCCATTGGGTCAACGGTTGCACCTTTG
1 AAGCATAATCCCGAGCCATTAGGTCAACGGTTGCACCTTTG
37699 ATAGAGTTGG
Statistics
Matches: 66, Mismatches: 23, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (48 bp):
AAGCATAATCCCGAGCCATTAGGTCAACGGTTGCACCTTTGGCATAAC
Found at i:46091 original size:22 final size:24
Alignment explanation
Indices: 46052--46106 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
46042 AAGCACTGCC
* *
46052 AAGAAGGGTAAAATAAAATAAAAA
1 AAGAAGGGTAAAAGAAAAGAAAAA
*
46076 AAGAA-GG-AAAAGAAAAGAAAAG
1 AAGAAGGGTAAAAGAAAAGAAAAA
46098 AA-AAGGGTA
1 AAGAAGGGTA
46107 GCTTATCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 2 0.08
22 16 0.62
23 3 0.12
24 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (24 bp):
AAGAAGGGTAAAAGAAAAGAAAAA
Found at i:47293 original size:27 final size:26
Alignment explanation
Indices: 47262--47312 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
47252 TTAGATTATG
47262 TAATATAATTTGAATTAAATATGTTTT
1 TAATATAATTTGAATTAAAT-TGTTTT
* **
47289 TAATATATTTTTTATTAAATTGTT
1 TAATATAATTTGAATTAAATTGTT
47313 CATGTTAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (26 bp):
TAATATAATTTGAATTAAATTGTTTT
Done.