Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010103.1 Kokia drynarioides strain JFW-HI SEQ_124887, 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: 50895
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 101 characters in sequence are not A, C, G, or T
Found at i:1412 original size:15 final size:15
Alignment explanation
Indices: 1394--1464 Score: 97
Period size: 15 Copynumber: 4.7 Consensus size: 15
1384 TTTTGGGTAG
1394 TTTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
*
1409 TTTGTATTTGGGCCA
1 TTTGTAATTGGGCCA
* *
1424 TCTGTAACTGGGCCA
1 TTTGTAATTGGGCCA
* *
1439 TTTGTTATTGGTCCA
1 TTTGTAATTGGGCCA
1454 TTTGTAATTGG
1 TTTGTAATTGG
1465 ACTTTGTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.17, C:0.14, G:0.25, T:0.44
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:1534 original size:34 final size:33
Alignment explanation
Indices: 1496--1574 Score: 113
Period size: 34 Copynumber: 2.4 Consensus size: 33
1486 TTGGACTTTC
* *
1496 TAAATTTAATTTTATAATAAATTTAAATTTCAAA
1 TAAATTTAATTTTAAAATAAACTTAAATTT-AAA
*
1530 TAAATTTAAATTTAAAATAAACTTAAATTTAAA
1 TAAATTTAATTTTAAAATAAACTTAAATTTAAA
*
1563 TAAATTCAATTT
1 TAAATTTAATTT
1575 CCAATAAGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 13 0.32
34 27 0.68
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (33 bp):
TAAATTTAATTTTAAAATAAACTTAAATTTAAA
Found at i:1547 original size:7 final size:6
Alignment explanation
Indices: 1496--1563 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
1486 TTGGACTTTC
*
1496 TAAATT TAATTT TATAA-- TAAATT TAAATT TCAAA-- TAAATT TAAATT
1 TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT TAAATT
* *
1542 TAAA-A TAAACT TAAATT TAAAT
1 TAAATT TAAATT TAAATT TAAAT
1564 AAATTCAATT
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
4 5 0.10
5 7 0.14
6 34 0.68
7 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:1580 original size:16 final size:17
Alignment explanation
Indices: 1496--1581 Score: 97
Period size: 17 Copynumber: 5.2 Consensus size: 17
1486 TTGGACTTTC
*
1496 TAAATTT-AATTTTATAA
1 TAAATTTAAATTTCA-AA
1513 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
*
1530 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTCAAA
*
1547 TAAACTTAAATTT-AAA
1 TAAATTTAAATTTCAAA
* *
1563 TAAA-TTCAATTTCCAA
1 TAAATTTAAATTTCAAA
1579 TAA
1 TAA
1582 GTCCAGACAA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
15 7 0.11
16 12 0.19
17 37 0.60
18 6 0.10
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:2860 original size:241 final size:238
Alignment explanation
Indices: 2440--2918 Score: 744
Period size: 241 Copynumber: 2.0 Consensus size: 238
2430 ACAATCATAA
*
2440 TAATGATAAAAGATTGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
1 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
* *
2505 TTAGGCTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAATGTATTTTACTAGAATT
66 TTAGGCTTTTTTTACGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAGAATT
2570 ATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATATCTAATTTAAGTTTTAAATTAGATA
131 ATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATATCTAATTTAAGTTTTAAATTAGATA
* * * *
2635 AGTTTGATGAACACGTTTTAGTTAAGTTACAAGTAAATCGGAG
196 AATTTGATGAACACGTCTTAGTCAAATTACAAGTAAATCGGAG
* *
2678 TAATGATAAAATATCGAATAATTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTATTTT
1 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTA----
** * *
2743 TTTTTTAGG-TTTTTTTCCGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTAGTAG
62 ACTTTTAGGCTTTTTTTACGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAG
* * * *
2807 AATTATTTAGGTGTCCTTTAGGGTTCTTTTTAGGAGTAAAAATCTTTAATTTAAGTTTTAAATTA
127 AATTATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATATCTAATTTAAGTTTTAAATTA
* *
2872 GATAAATTTGGTGAACACGTCTTAGTCAAATTACAAGTAAATTGGAG
192 GATAAATTTGATGAACACGTCTTAGTCAAATTACAAGTAAATCGGAG
2919 ACATTTTTTA
Statistics
Matches: 218, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
238 58 0.27
241 153 0.70
242 7 0.03
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.43
Consensus pattern (238 bp):
TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
TTAGGCTTTTTTTACGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAGAATT
ATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATATCTAATTTAAGTTTTAAATTAGATA
AATTTGATGAACACGTCTTAGTCAAATTACAAGTAAATCGGAG
Found at i:6231 original size:4 final size:4
Alignment explanation
Indices: 6222--6256 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
6212 GTGCCCCAAT
* *
6222 TTCA TTCA TTCA CTCA TTTA TTCA TTCA TTCA TTC
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTC
6257 GCTCATTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (4 bp):
TTCA
Found at i:6244 original size:12 final size:12
Alignment explanation
Indices: 6223--6263 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
6213 TGCCCCAATT
6223 TCATTCATTCAC
1 TCATTCATTCAC
* *
6235 TCATTTATTCAT
1 TCATTCATTCAC
*
6247 TCATTCATTCGC
1 TCATTCATTCAC
6259 TCATT
1 TCATT
6264 TGTTTATTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.22, C:0.27, G:0.02, T:0.49
Consensus pattern (12 bp):
TCATTCATTCAC
Found at i:11440 original size:25 final size:23
Alignment explanation
Indices: 11399--11444 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
11389 TCAATTAGGG
11399 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
11422 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
11445 TGGATCCAAC
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:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:15956 original size:1 final size:1
Alignment explanation
Indices: 15950--16010 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
15940 TTAAATCAAG
* * * * * * * *
15950 AAAAAAAATAAAAAAAAAGAAAAAGAAAAGAGAAGAAAAAAAAATAAAAAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16011 TGGAAAGAGA
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.87, C:0.00, G:0.08, T:0.05
Consensus pattern (1 bp):
A
Found at i:15996 original size:36 final size:38
Alignment explanation
Indices: 15950--16020 Score: 110
Period size: 36 Copynumber: 1.9 Consensus size: 38
15940 TTAAATCAAG
*
15950 AAAAAAAATAAAAAAAA-AGAAAAA-GAAAAGAGAAGA
1 AAAAAAAATAAAAAAAATAAAAAAATGAAAAGAGAAGA
*
15986 AAAAAAAATAAAAAAAATAAAAAAATGGAAAGAGA
1 AAAAAAAATAAAAAAAATAAAAAAATGAAAAGAGA
16021 GAGCAAGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 17 0.55
37 6 0.19
38 8 0.26
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.06
Consensus pattern (38 bp):
AAAAAAAATAAAAAAAATAAAAAAATGAAAAGAGAAGA
Found at i:16483 original size:42 final size:42
Alignment explanation
Indices: 16418--17667 Score: 1074
Period size: 42 Copynumber: 29.5 Consensus size: 42
16408 AAAGAAAGCA
* **
16418 TTCATTGCATTTAAAGGCTTAGGTGTAGG-GGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGT-GGAGGTCCATTTACTT
* *
16460 TTCATTGCATTCAGAGGCCTAGGTGTGGAGG-CCAATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCC-ATTTACTT
* * * * *
16502 TTCATCGCATTTAGAGGCCCAAGAGTGAAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
16544 TTCATTACATTTAGAGGCCCATGTGTGAAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
16586 TTCCTTGCATTTAGAGGCCTAGGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
16628 TTCATTGCATTCAGAGGCCTAAGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
**
16670 TTCATCACATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
16712 TTCATTGCATTTAGAGGCCCAGGTATAGG-GGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGT-GGAGGTCCATTTACTT
* * *
16754 TTCATCGCATTCAGAGGCCCAGGTGTGGAGGTCCATTTAATT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
16796 TTCATCGCATTCAGAGGCCCAGGAGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
16838 TTCGTCGCATTCAGAGGCCCAGGTGTGGAGGTCCATTTAATT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
16880 TTCATCGCATTCAGAGGCCCAGGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
16922 TTCATCGCATTCAGAGGCCCAGGTGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
16964 TTCATCGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTAC-T
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *************
17005 TTAATCGCATTTAGAGGCCCAGGTGTGGANNNNNNNNNNNNNNNNNNNNNNNN
1 TTCATTGCATTTAGAGGCCCAGGTGTGGA-----------GGTCCATTTACTT
************************** * ** ** *
17058 NNNNNNNNNNNNNNNNNNNNNNNNNNGG-TGTAGAGGTCCATT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTAC-TT
* * *
17100 TACTTTTCATTGCATTCAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCA-T---TT-AGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
17147 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
17189 TTCATTGCATTCAGAGGCCTAAGTGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
17231 TTTATTGCATTTAGAGGCCTATGTGTAGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
17273 TTCATTGCA-TTAGAGGCCTAAGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
17314 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
17356 TTCATTGCATTCAGAGGCCTAAGTTTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
17398 TTCATTGCATTCAGAGGCCCAGGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
17440 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTAC-T
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
17481 TTCATCGCATTTAGAGGCCCAGGTGAGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * **
17523 TTCATTGCATTTAGAGGCCTAAGTGTGAAGACCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
17565 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCTATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
** *
17607 TTCATTGCATTCGGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
17649 TTTATTGCAATTAGAGGCC
1 TTCATTGCATTTAGAGGCC
17668 TAAGCATAGA
Statistics
Matches: 977, Mismatches: 205, Indels: 52
0.79 0.17 0.04
Matches are distributed among these distances:
41 109 0.11
42 845 0.86
43 6 0.01
46 1 0.00
47 9 0.01
48 5 0.01
53 2 0.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.33
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:17362 original size:167 final size:168
Alignment explanation
Indices: 17084--17667 Score: 902
Period size: 167 Copynumber: 3.5 Consensus size: 168
17074 NNNNNNNNNN
*
17084 GGTGTAGAGGTCCATTTACTTTTCATTGCATTCAGAGGCCCAGGTGTGGAGGTCCATTTACTTTT
1 GGTGTAGAGGTCCATTTACTTTTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTTTT
*
17149 CATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTCAGAGGCCTAAGTG
66 CATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTCAGAGGCCTAAGTG
* *
17214 TGGAGGTCCATTTATTTTTTATTGCATTTAGAGGCCTA
131 TGGAGGTCCATTTATTTTTCATTGCATTTAGAGGCCCA
* * * *
17252 TGTGTAGAGGTCTATTTACTTTTCATTGCATT-AGAGGCCTAAGTGTGGAGGCCCATTTACTTTT
1 GGTGTAGAGGTCCATTTACTTTTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTTTT
* *
17316 CATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTCAGAGGCCTAAGTT
66 CATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTCAGAGGCCTAAGTG
*
17381 TGGAGGTCCATTTATTTTTCATTGCATTCAGAGGCCCA
131 TGGAGGTCCATTTATTTTTCATTGCATTTAGAGGCCCA
* *
17419 GGTGTAGAGGTCCATTTACTTTTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTAC-TTT
1 GGTGTAGAGGTCCATTTACTTTTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTTTT
* *
17483 CATCGCATTTAGAGGCCCAGGTGAGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAAGTG
66 CATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTCAGAGGCCTAAGTG
* ** *
17548 TGAAGACCCATTTACTTTTCATTGCATTTAGAGGCCCA
131 TGGAGGTCCATTTATTTTTCATTGCATTTAGAGGCCCA
* * * * * *
17586 GGTGTGGAGGTCTATTTATTTTTCATTGCATTCGGAGGCCTAGGTGTGGAGGTCCATTTACTTTT
1 GGTGTAGAGGTCCATTTACTTTTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTTTT
* * *
17651 TATTGCAATTAGAGGCC
66 CATCGCATTTAGAGGCC
17668 TAAGCATAGA
Statistics
Matches: 378, Mismatches: 36, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
167 305 0.81
168 73 0.19
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (168 bp):
GGTGTAGAGGTCCATTTACTTTTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTTTT
CATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTCAGAGGCCTAAGTG
TGGAGGTCCATTTATTTTTCATTGCATTTAGAGGCCCA
Found at i:17455 original size:209 final size:209
Alignment explanation
Indices: 16447--17671 Score: 1135
Period size: 209 Copynumber: 5.8 Consensus size: 209
16437 TAGGTGTAGG
* * * *
16447 GGTCCATTTACTTTTCATTGCATTCAGAGGCCTAGGTGTGGAGGCCAATTTACTTTTCATCGCAT
1 GGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCAT
* * * * * * *
16512 TTAGAGGCCCAAGAGTGAAGGTCCATTTATTTTTCATTACATTTAGAGGCCCATGTGTGAAGGTC
66 TTAGAGGCCCAAGTGTGGAGGTCCATTTATTTTTCATTGCATTCAGAGGCCTAGGTGTGGAGGTC
* * * *
16577 CATTTA-TTTTTCCTTGCATTTAGAGGCCTAGGTGTAGAGGTCCATTTACTTTTCATTGCATTCA
131 CATTTACTTTTT-ATTGCATTTAGAGGCCTAAGTGTAGAGGTCCATTTAC-TTTCATCGCATTTA
*
16641 GAGGCCTAAGTGTGGA
194 GAGGCCCAAGTGTGGA
* ** *
16657 GGCCCATTTACTTTTCATCACATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCAT
1 GGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCAT
* * * * * *
16722 TTAGAGGCCCAGGTATAGG-GGCCCATTTACTTTTCATCGCATTCAGAGGCCCAGGTGTGGAGGT
66 TTAGAGGCCCAAGTGT-GGAGGTCCATTTATTTTTCATTGCATTCAGAGGCCTAGGTGTGGAGGT
* * * * * * * * *
16786 CCATTTAATTTTCATCGCATTCAGAGGCCCAGGAGTAGAGGTCCATTTACTTTTCGTCGCATTCA
130 CCATTTACTTTTTATTGCATTTAGAGGCCTAAGTGTAGAGGTCCATTTAC-TTTCATCGCATTTA
*
16851 GAGGCCCAGGTGTGGA
194 GAGGCCCAAGTGTGGA
* * * * * *
16867 GGTCCATTTAATTTTCATCGCATTCAGAGGCCCAGGTGTAGAGGTCCATTTACTTTTCATCGCAT
1 GGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCAT
* * * * * * * *
16932 TCAGAGGCCCAGGTGTGGAGGTTCATTTACTTTTCATCGCATTTAGAAGCCCAGGTGTGGAGGTC
66 TTAGAGGCCCAAGTGTGGAGGTCCATTTATTTTTCATTGCATTCAGAGGCCTAGGTGTGGAGGTC
* * * * * **********
16997 CATTTAC-TTTAATCGCATTTAGAGGCCCAGGTGTGGANNNNNNNNNNNNNNNNNNNNNNNNNNN
131 CATTTACTTTTTATTGCATTTAGAGGCCTAAGTGTAGA-----------------GGTCCATTTA
************************ *
17061 NNNNNNNNNNNNNNNNNNNNNNNGGTGTAGA
179 CTTTCATCGCATTTAGAGGCCCAAGTGTGGA
* * *
17092 GGTCCATTTACTTTTCATTGCATTCAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATCGCAT
1 GGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCAT
* *
17157 TTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTCAGAGGCCTAAGTGTGGAGGTC
66 TTAGAGGCCCAAGTGTGGAGGTCCATTTATTTTTCATTGCATTCAGAGGCCTAGGTGTGGAGGTC
* * * *
17222 CATTTATTTTTTATTGCATTTAGAGGCCTATGTGTAGAGGTCTATTTACTTTTCATTGCA-TTAG
131 CATTTACTTTTTATTGCATTTAGAGGCCTAAGTGTAGAGGTCCATTTAC-TTTCATCGCATTTAG
*
17286 AGGCCTAAGTGTGGA
195 AGGCCCAAGTGTGGA
* *
17301 GGCCCATTTACTTTTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCAT
1 GGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCAT
* * * * *
17366 TCAGAGGCCTAAGTTTGGAGGTCCATTTATTTTTCATTGCATTCAGAGGCCCAGGTGTAGAGGTC
66 TTAGAGGCCCAAGTGTGGAGGTCCATTTATTTTTCATTGCATTCAGAGGCCTAGGTGTGGAGGTC
* * * *
17431 CATTTACTTTTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTCATCGCATTTAGA
131 CATTTACTTTTTATTGCATTTAGAGGCCTAAGTGTAGAGGTCCATTTACTTTCATCGCATTTAGA
* *
17496 GGCCCAGGTGAGGA
196 GGCCCAAGTGTGGA
* * * *
17510 GGTCCATTTACTTTTCATTGCATTTAGAGGCCTAAGTGTGAAGACCCATTTACTTTTCATTGCAT
1 GGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCAT
* * *
17575 TTAGAGGCCCAGGTGTGGAGGTCTATTTATTTTTCATTGCATTCGGAGGCCTAGGTGTGGAGGTC
66 TTAGAGGCCCAAGTGTGGAGGTCCATTTATTTTTCATTGCATTCAGAGGCCTAGGTGTGGAGGTC
*
17640 CATTTACTTTTTATTGCAATTAGAGGCCTAAG
131 CATTTACTTTTTATTGCATTTAGAGGCCTAAG
17672 CATAGAGTTC
Statistics
Matches: 820, Mismatches: 172, Indels: 47
0.79 0.17 0.05
Matches are distributed among these distances:
208 9 0.01
209 354 0.43
210 295 0.36
211 5 0.01
225 132 0.16
226 25 0.03
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.33
Consensus pattern (209 bp):
GGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCAT
TTAGAGGCCCAAGTGTGGAGGTCCATTTATTTTTCATTGCATTCAGAGGCCTAGGTGTGGAGGTC
CATTTACTTTTTATTGCATTTAGAGGCCTAAGTGTAGAGGTCCATTTACTTTCATCGCATTTAGA
GGCCCAAGTGTGGA
Found at i:18846 original size:241 final size:238
Alignment explanation
Indices: 18419--18892 Score: 727
Period size: 241 Copynumber: 2.0 Consensus size: 238
18409 ACAATCATAA
* * *
18419 TAATGATAAAATATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGCAACTT
1 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATACTTCTCTTAATTCATTAGAAACTT
* *
18484 TTAGGCTTTTTTTAGGATTTTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTTACTAGAATT
66 TTAGGCTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAGAATT
*
18549 ATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTATGTTTTAAATTAGATA
131 ATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
* * * * *
18614 AGTTTGGTGAACACGTTTTAGTTAAGTTACAAGTAAATCGGAG
196 AGTTAGGTGAACACGTCTTAGTCAAATTACAAATAAATCGGAG
18657 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATACTTCTCTTAATTCATTAGTAAATT
1 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATACTTCTCTTAATTCATTAG-AAA--
* *
18722 TTTTTTAGG-TTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATAT-AAAGTATTTTATTA
63 -CTTTTAGGCTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAAT-TGAAAGTATTTTACTA
* * * *
18785 GAATTATTTAGGTATCTTTTAGGGTTTTTATTAGGAGTAAAAATTTTTAATTTAAGTTTTAAATT
126 GAATTATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATT
*
18850 AGATAAGTTAGGTGAACATGTCTTAGTCAAATTACAAATAAAT
191 AGATAAGTTAGGTGAACACGTCTTAGTCAAATTACAAATAAAT
18893 TGGAAGCATT
Statistics
Matches: 213, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
238 57 0.27
239 2 0.01
241 146 0.69
242 8 0.04
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (238 bp):
TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATACTTCTCTTAATTCATTAGAAACTT
TTAGGCTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAGAATT
ATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
AGTTAGGTGAACACGTCTTAGTCAAATTACAAATAAATCGGAG
Found at i:19687 original size:18 final size:18
Alignment explanation
Indices: 19644--19694 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
19634 GTTTTTATTG
* *
19644 TATTTTTAAGTTTATAGT
1 TATTTTTTATTTTATAGT
*
19662 T-TAATTTTATTTTATAGT
1 TAT-TTTTTATTTTATAGT
*
19680 TATTTTTTTTTTTAT
1 TATTTTTTATTTTAT
19695 CTTTTAAGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 1 0.04
18 24 0.92
19 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (18 bp):
TATTTTTTATTTTATAGT
Found at i:22403 original size:32 final size:34
Alignment explanation
Indices: 22331--22407 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 34
22321 ATTTTAATAA
* * *
22331 GATTTAATATTAAATATAATTTAATATTTATGTT
1 GATTAAATATTAAATATAATTTAATATTAAAGTT
*
22365 GA-TAAATATTATAT-TAATTTAATATTAAAG-T
1 GATTAAATATTAAATATAATTTAATATTAAAGTT
22396 GATTAAAT-TTAA
1 GATTAAATATTAA
22408 TCATAGTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
31 6 0.16
32 19 0.51
33 10 0.27
34 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (34 bp):
GATTAAATATTAAATATAATTTAATATTAAAGTT
Found at i:34690 original size:23 final size:23
Alignment explanation
Indices: 34660--34717 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
34650 TTAGCATCAG
* *
34660 TACGTTTACGCTCGTCAGCATGA
1 TACGTTTACACTCGTCAACATGA
34683 TACGTTTACACTCGTCAACATGA
1 TACGTTTACACTCGTCAACATGA
34706 TACGTTTACACT
1 TACGTTTACACT
34718 TATTTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (23 bp):
TACGTTTACACTCGTCAACATGA
Found at i:37544 original size:16 final size:16
Alignment explanation
Indices: 37523--37553 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37513 ATACTATTTT
*
37523 TATTTAATTTTAAAAA
1 TATTTAATATTAAAAA
37539 TATTTAATATTAAAA
1 TATTTAATATTAAAA
37554 TGATAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTAATATTAAAAA
Found at i:37843 original size:15 final size:16
Alignment explanation
Indices: 37825--37865 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
37815 AAAAAACTAT
*
37825 ATTTTAA-ATTTAATA
1 ATTTTAATATTCAATA
*
37840 A-TTTAATATTCATTA
1 ATTTTAATATTCAATA
37855 ATTTTAATATT
1 ATTTTAATATT
37866 ATAACATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 5 0.23
15 8 0.36
16 9 0.41
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTAATATTCAATA
Found at i:47371 original size:11 final size:11
Alignment explanation
Indices: 47355--47422 Score: 66
Period size: 11 Copynumber: 6.0 Consensus size: 11
47345 AACCAAATTG
*
47355 AATTTATTTTA
1 AATTTAATTTA
47366 AATTTAAATTT-
1 AATTT-AATTTA
*
47377 ATTTTAAGTTTA
1 AATTTAA-TTTA
*
47389 AATTTATTTTA
1 AATTTAATTTA
*
47400 AATTTAAATTA
1 AATTTAATTTA
47411 AATTTAAATTTA
1 AATTT-AATTTA
47423 TCTTAAAGTC
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
10 2 0.04
11 30 0.65
12 14 0.30
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:47400 original size:28 final size:28
Alignment explanation
Indices: 47368--47429 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
47358 TTATTTTAAA
** *
47368 TTTAAATTTATTTTAAGTTTAAATTTAT
1 TTTAAATTTAAATTAAATTTAAATTTAT
47396 TTTAAATTTAAATTAAATTTAAATTTAT
1 TTTAAATTTAAATTAAATTTAAATTTAT
*
47424 CTTAAA
1 TTTAAA
47430 GTCCAAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (28 bp):
TTTAAATTTAAATTAAATTTAAATTTAT
Found at i:47411 original size:5 final size:6
Alignment explanation
Indices: 47362--47422 Score: 74
Period size: 6 Copynumber: 10.7 Consensus size: 6
47352 TTGAATTTAT
* * *
47362 TTTAAA TTTAAA TTT-AT TTTAAG TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
47408 -TTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTA
47423 TCTTAAAGTC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
5 13 0.28
6 34 0.72
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:47429 original size:17 final size:17
Alignment explanation
Indices: 47355--47422 Score: 109
Period size: 17 Copynumber: 4.0 Consensus size: 17
47345 AACCAAATTG
47355 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
47372 AATTTATTTTAAGTTTA
1 AATTTATTTTAAATTTA
47389 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
47406 AATTAAATTTAAATTTA
1 AATTTATTTTAAATTTA
47423 TCTTAAAGTC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 47 1.00
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Done.