Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3709
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: 38999
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Found at i:668 original size:48 final size:47
Alignment explanation
Indices: 479--884 Score: 534
Period size: 46 Copynumber: 8.5 Consensus size: 47
469 TCTGGACTTC
* * * * * * *
479 ATCACATTTATACCACTTTCACATCCATCACGTTGGCCAGTCGGCCCTG
1 ATCACATATATA-CACTTTCACATTCATCACATCGGCCATTAGG-CCTT
* *
528 CTCAACATATATACACTTTCACA-TCATCACATCAGCCATTAGGCCTT
1 ATC-ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
575 ATCACATATATACACTTTCA-ATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
* *
621 ATCACATATATACACTATCACATTCATCACATCGACCATTTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGCCTT
* * *
669 ATCACATATATACACTATCGCATATCATCACAATCGGTCA-TAGGCCTT
1 ATCACATATATACACTTTCACAT-TCATCAC-ATCGGCCATTAGGCCTT
* *
717 ATCACATATATACACTATCACATTTCATCACA-CGGCCATTCGGCCTT
1 ATCACATATATACACTTTCACA-TTCATCACATCGGCCATTAGGCCTT
764 AAGGTTCACATATATACACTTTCACATTCATCACAT-GGCCATTAGGCCTT
1 -A---TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
814 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
861 ATCACATATATACACTTTCACATT
1 ATCACATATATACACTTTCACATT
885 ACCAACCCTT
Statistics
Matches: 322, Mismatches: 21, Indels: 30
0.86 0.06 0.08
Matches are distributed among these distances:
45 1 0.00
46 95 0.30
47 67 0.21
48 82 0.25
49 21 0.07
50 36 0.11
51 20 0.06
ACGTcount: A:0.31, C:0.30, G:0.09, T:0.31
Consensus pattern (47 bp):
ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
Found at i:806 original size:193 final size:187
Alignment explanation
Indices: 532--876 Score: 559
Period size: 193 Copynumber: 1.8 Consensus size: 187
522 GCCCTGCTCA
*
532 ACATATATACACTTTCACATCATCACATCAGCCATTAGGCCTTATCACATATATACACTTTCAAT
1 ACATATATACACTATCACATCATCACATCAGCCATTAGGCCTTATCACATATATACACTTTCAAT
597 TCATCACATCGGCCATTAGGCCTTATCACATATATACACTATCACATTCATCACATCGACCATTT
66 TCATCACATCGGCCATTAGGCCTTATCACATATATACACTATCACATTCATCACATCGACCA-TT
662 AGGCCTTATCACATATATACACTATCGCATATCATCACAATCGGTCATAGGCCTTATC
130 AGGCCTTATCACATATATACACTATCGCATATCATCACAATCGGTCATAGGCCTTATC
* *
720 ACATATATACACTATCACATTTCATCACA-CGGCCATTCGGCCTTAAGGTTCACATATATACACT
1 ACATATATACACTATCACA--TCATCACATCAGCCATTAGGCCTT-A---TCACATATATACACT
*
784 TTCACATTCATCACAT-GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
60 TTCA-ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTATCACATTCATCACATCG
*
848 GCCATTAGGCCTTATCACATATATACACT
124 ACCATTAGGCCTTATCACATATATACACT
877 TTCACATTAC
Statistics
Matches: 145, Mismatches: 5, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
188 18 0.12
189 13 0.09
190 9 0.06
192 25 0.17
193 69 0.48
194 11 0.08
ACGTcount: A:0.32, C:0.29, G:0.08, T:0.31
Consensus pattern (187 bp):
ACATATATACACTATCACATCATCACATCAGCCATTAGGCCTTATCACATATATACACTTTCAAT
TCATCACATCGGCCATTAGGCCTTATCACATATATACACTATCACATTCATCACATCGACCATTA
GGCCTTATCACATATATACACTATCGCATATCATCACAATCGGTCATAGGCCTTATC
Found at i:5264 original size:40 final size:40
Alignment explanation
Indices: 5219--5458 Score: 363
Period size: 40 Copynumber: 6.0 Consensus size: 40
5209 GGATAACACC
* * **
5219 AGCACGAATGCTCTTCGGAACTTAGTCCGGATACCTCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
* * *
5259 AGCACGAATGCTCTTCGGAACTTAGCCCAGATACATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
* *
5299 AGCATGAATGCTCTTCGGGACTTAGCCCGGTTATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
* *
5339 AGCACGAATGCTCTTTGGGGCTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
* *
5379 AGCACGAATGCTCCTCGGGGCTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
5419 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
5459 CTCAATTCTC
Statistics
Matches: 184, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 184 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
Found at i:7509 original size:47 final size:47
Alignment explanation
Indices: 7431--7924 Score: 814
Period size: 47 Copynumber: 10.6 Consensus size: 47
7421 CCCTTCGGGA
* * * * * *
7431 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCAGTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7478 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7525 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7572 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7619 CTTATCACATATATACAC-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7665 CTTATCAC--ATATACACTATCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7710 CTTATCACATATATACACTATCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
7757 CTTATCACATATATACACTTTCACATTCATCACATTGGTCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7804 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7851 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7898 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
7925 ACCAACCCAT
Statistics
Matches: 424, Mismatches: 20, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
44 8 0.02
45 34 0.08
46 36 0.08
47 346 0.82
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:8248 original size:40 final size:40
Alignment explanation
Indices: 8149--8251 Score: 120
Period size: 40 Copynumber: 2.6 Consensus size: 40
8139 GCTACTCGTT
* * *
8149 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
* * *
8189 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TAGCA
8230 CAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
8252 AGACATCATT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
39 3 0.06
40 39 0.74
41 11 0.21
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
Found at i:13521 original size:46 final size:46
Alignment explanation
Indices: 13454--13628 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
13444 TGTAACCCGC
*
13454 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* * *
13500 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * *
13550 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
13593 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG
13629 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 60 0.57
47 26 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:13569 original size:93 final size:93
Alignment explanation
Indices: 13461--13632 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
13451 CGCCCATAAG
* * *
13461 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
13526 ATGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
13554 CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
13619 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
13633 TCAACCATCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:13648 original size:46 final size:46
Alignment explanation
Indices: 13457--13648 Score: 137
Period size: 46 Copynumber: 4.2 Consensus size: 46
13447 AACCCGCCCA
* * ** * *
13457 TAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC--GCATCC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-C
*
13502 ATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGC-CTAGTTA-CATC
1 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC
* * * * * *
13551 TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCA--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-G-GATGCTCAACCATC
13596 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
*
13642 TTAGTGA
1 TAAGTGA
13649 CATGTCACTT
Statistics
Matches: 114, Mismatches: 19, Indels: 26
0.72 0.12 0.16
Matches are distributed among these distances:
44 8 0.07
45 4 0.04
46 63 0.55
47 27 0.24
48 3 0.03
49 5 0.04
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
Found at i:14094 original size:30 final size:31
Alignment explanation
Indices: 14051--14108 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
14041 TTAACTCAAA
14051 TTTTGGCAAATTTACAATTTTACCCCTAAAC
1 TTTTGGCAAATTTACAATTTTACCCCTAAAC
* * *
14082 TTTT-GCATATTTACATTTTTGCCCCTA
1 TTTTGGCAAATTTACAATTTTACCCCTA
14109 GGCTCGGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.45
Consensus pattern (31 bp):
TTTTGGCAAATTTACAATTTTACCCCTAAAC
Found at i:15519 original size:64 final size:64
Alignment explanation
Indices: 15444--15635 Score: 323
Period size: 64 Copynumber: 3.0 Consensus size: 64
15434 TCATTCATAA
* **
15444 CACATCCAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCAT
*
15508 CACATCTAGTTAGGTGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCAT
*
15572 CACATCTAGTTAGGAGCATTTGATTCATTTTGATCATAACATCCTAATTATTTGGA-ATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTTGATCATAGCATCCTAATTATTT-GACATAAGCAT
15636 GATACATGAA
Statistics
Matches: 121, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
64 119 0.98
65 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCAT
Found at i:16107 original size:177 final size:177
Alignment explanation
Indices: 15811--16646 Score: 565
Period size: 177 Copynumber: 4.7 Consensus size: 177
15801 CAGATCATAA
* * *
15811 CAAGTCTTATCTCCTTGAGGTTGCAGTGGAGTAGACTAAAGATT-ACAGGTCTTATTTCCCTAAG
1 CAAGTCTTATCTCCCTGAGGTTGCAGTGGAGTAGACTGAAGATTGA-AGATCTTATTTCCCTAAG
* * * * * * * *
15875 CAGTAGTGGAACAGACCAAAGACGACGAGTCTTATCTTCATGTACCGGCAATGGAGCAGATTTAA
65 CAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTAA
* * * *
15940 GTCACCAG-CCTTATCTCCCCGAAGTTGC-AGTGGAACAGGCT-CAATATG
130 GCCA-CAGACCTTATCTCCCCGAAGTAGCAAG-AGAACAAGCTGCAAT-TG
* * *
15988 CAAGTCTTATCTCCCTAAGGTTGCAGTGGAGTAGACTGAAGATTGAAGATCTTATCTCCCTAAGA
1 CAAGTCTTATCTCCCTGAGGTTGCAGTGGAGTAGACTGAAGATTGAAGATCTTATTTCCCTAAGC
** * *
16053 AGTAGCAGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCAGCAATGGAGCAGATTTTAG
66 AGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTAAG
* *** ** * * *
16118 CCACTGACCTTATCTCTTTGTGGTAGCAAGAGAGCAAGTTGGCGATTG
131 CCACAGACCTTATCTCCCCGAAGTAGCAAGAGAACAAGCT-GCAATTG
* * * * *
16166 -TAGTCTTATCTTCCTGAGGTAGCAAG-GAAGCAGACTGAAGATTGAAGATC-TATTTCCCTAAG
1 CAAGTCTTATCTCCCTGAGGTTGC-AGTGGAGTAGACTGAAGATTGAAGATCTTATTTCCCTAAG
* * * * *
16228 CAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCCCCATGTATTGGCAATGGAGCATATTTTA
65 CAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTAA
* *** * * ** * * *
16293 -CCACTAG-TCTTATCTCTTTGAGGTAGCAAGAGAGCCGGTTGAAGAATG
130 GCCAC-AGACCTTATCTCCCCGAAGTAGCAAGAGAACAAGCTGCA-ATTG
* * * * * * * * *
16341 --AGTCTTATATTCCTGAGGTAGCAAG-GAAGCAGACTGAAAATTGAAGATTTTATATCTCTAAG
1 CAAGTCTTATCTCCCTGAGGTTGC-AGTGGAGTAGACTGAAGATTGAAGATCTTATTTCCCTAAG
* * * * * *
16403 CAGTAGGGGATCAAATCGAAGATGGTGAATTTTATCTCCATGTATCGGCAATGGAGCAGATTTTA
65 CAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTAA
*** ** * * *
16468 -CCACTAG-CCTTATCT-CTTTAAGGTAGCAAGAGAGTAGGTTGGCGATTG
130 GCCAC-AGACCTTATCTCCCCGAA-GTAGCAAGAGAACAAGCT-GCAATTG
* ** ** **** * * * * *
16516 -TAGTCTTATCTTTCTGAGGCAGCAAAAAAGCAGGCTAAAGATTGAAGATCTTATCTCCCTAAAC
1 CAAGTCTTATCTCCCTGAGGTTGCAGTGGAGTAGACTGAAGATTGAAGATCTTATTTCCCTAAGC
* * * * * *
16580 AG-AATCAGAGTAGATTGAAAGA-GGTGAATCTTATCTCCTTGTATCGGCAATGGAGCAGATTTA
66 AGTAGT-GGAGCAGATCG-AAGATGGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTA
16643 AGCC
129 AGCC
16647 CCAAGATTTA
Statistics
Matches: 546, Mismatches: 97, Indels: 32
0.81 0.14 0.05
Matches are distributed among these distances:
174 50 0.09
175 139 0.25
176 168 0.31
177 179 0.33
178 7 0.01
179 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (177 bp):
CAAGTCTTATCTCCCTGAGGTTGCAGTGGAGTAGACTGAAGATTGAAGATCTTATTTCCCTAAGC
AGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTAAG
CCACAGACCTTATCTCCCCGAAGTAGCAAGAGAACAAGCTGCAATTG
Found at i:16425 original size:175 final size:176
Alignment explanation
Indices: 16020--16641 Score: 804
Period size: 176 Copynumber: 3.5 Consensus size: 176
16010 GCAGTGGAGT
* * * * *
16020 AGACTGAAGATTGAAGATCTTATCTCCCTAAGAAGTAGCAGAGCAGATCGAAGATGGCGAATCTT
1 AGACTGAAAATTGAAGATCTTATATCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGTGAATCTT
* *
16085 ATCTCCATGTATCAGCAATGGAGCAGATTTTAGCCACT-GACCTTATCTCTTTGTGGTAGCAAGA
66 ATCTCCATGTATCGGCAATGGAGCAGATTTTA-CCACTAG-CCTTATCTCTTTGAGGTAGCAAGA
*
16149 GAGCAAGTTGGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGC
129 GAGCAGGTTGGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGC
* * *
16197 AGACTGAAGATTGAAGATC-TATTTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTT
1 AGACTGAAAATTGAAGATCTTATATCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGTGAATCTT
* * * *
16261 ATCCCCATGTATTGGCAATGGAGCATATTTTACCACTAGTCTTATCTCTTTGAGGTAGCAAGAGA
66 ATCTCCATGTATCGGCAATGGAGCAGATTTTACCACTAGCCTTATCTCTTTGAGGTAGCAAGAGA
* ** * *
16326 GCCGGTTGAAGAATG-AGTCTTATATTCCTGAGGTAGCAAGGAAGC
131 GCAGGTTGGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGC
* * * * * *
16371 AGACTGAAAATTGAAGATTTTATATCTCTAAGCAGTAGGGGATCAAATCGAAGATGGTGAATTTT
1 AGACTGAAAATTGAAGATCTTATATCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGTGAATCTT
*
16436 ATCTCCATGTATCGGCAATGGAGCAGATTTTACCACTAGCCTTATCTCTTTAAGGTAGCAAGAGA
66 ATCTCCATGTATCGGCAATGGAGCAGATTTTACCACTAGCCTTATCTCTTTGAGGTAGCAAGAGA
* * * **
16501 GTAGGTTGGCGATTGTAGTCTTATCTTTCTGAGGCAGCAAAAAAGC
131 GCAGGTTGGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGC
* * * * * * * *
16547 AGGCT-AAAGATTGAAGATCTTATCTCCCTAAACAGAATCAGAGTAGATTGAAAGA-GGTGAATC
1 AGACTGAAA-ATTGAAGATCTTATATCCCTAAGCAGTAGCGGAGCAGATCG-AAGATGGTGAATC
*
16610 TTATCTCCTTGTATCGGCAATGGAGCAGATTT
64 TTATCTCCATGTATCGGCAATGGAGCAGATTT
16642 AAGCCCCAAG
Statistics
Matches: 385, Mismatches: 55, Indels: 11
0.85 0.12 0.02
Matches are distributed among these distances:
174 46 0.12
175 151 0.39
176 165 0.43
177 23 0.06
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (176 bp):
AGACTGAAAATTGAAGATCTTATATCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGTGAATCTT
ATCTCCATGTATCGGCAATGGAGCAGATTTTACCACTAGCCTTATCTCTTTGAGGTAGCAAGAGA
GCAGGTTGGCGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGC
Found at i:16906 original size:266 final size:265
Alignment explanation
Indices: 16422--16910 Score: 583
Period size: 266 Copynumber: 1.8 Consensus size: 265
16412 ATCAAATCGA
* * * * *
16422 AGATGGTGAATTTTATCTCCATGTATCGGCAATGGAGCAGATTTTACCACTAGCCTTATCTCTTT
1 AGATAGTGAATCTTATCTCCATGTATCGGCAATGGAACAGATTTGACCACTAGCCTTATCTCTCT
* * *** * * *
16487 AAGGTAGCAAGAGAGTAGGTTGGCGATTGTAGTCTTATCTTTCTGAGGCAGCAAAAAAGCAGGCT
66 AAGGTAGCAAGAGAGCAGGCTAAAGATTGTAGTCTTATCTTTCTAAAGCAGCAAAAAAGCAGACT
* **
16552 AAAGATTGAAGATCTTATCTCCCTAAACAGAATCAGAGTAGATTGAAAGAGGTGAATCTTATCTC
131 AAAGATTGAAGATCTTATCTCCCTAAACAGAATCAGAGCAGATTGAAAGAGACGAATCTTATCTC
* *
16617 CTTGTATCGGCAATGGAGCAGATTTAAGCCCCAAGATTTATTTCCCTGAAGTTGCAGTAGAGCAA
196 CATGTATCGGAAATGGAGCAGATTTAAGCCCCAAGATTTATTTCCCTGAAGTTGCAGTAGAGCAA
16682 ATTGC
261 ATTGC
* *
16687 AGATAGTGAATCTTATCTCCATGTATTGTCAATGGAACAGATTTAGACCA-TCAGCCTTATCTCT
1 AGATAGTGAATCTTATCTCCATGTATCGGCAATGGAACAGATTT-GACCACT-AGCCTTATCTCT
* * ** ***
16751 CTGAGGTAGCAAGAGAGCAGGCTAAAGATTG-GGTCTTAT-TTTCCTAAAGTGGCAGGGAAGCAG
64 CTAAGGTAGCAAGAGAGCAGGCTAAAGATTGTAGTCTTATCTTT-CTAAAGCAGCAAAAAAGCAG
* * * * * *
16814 ACTGAAGATTGAAGATCTTATTTCCCTAGAGCAG-TTGCGGAGCAGATTG-AGGATGACGAATCT
128 ACTAAAGATTGAAGATCTTATCTCCCTA-AACAGAAT-CAGAGCAGATTGAAAGA-GACGAATCT
*
16877 TATCTCCATGTATTGGAAATGGAGCAGATTTAAG
190 TATCTCCATGTATCGGAAATGGAGCAGATTTAAG
16911 TCACCAAGCC
Statistics
Matches: 184, Mismatches: 34, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
264 3 0.02
265 89 0.48
266 92 0.50
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (265 bp):
AGATAGTGAATCTTATCTCCATGTATCGGCAATGGAACAGATTTGACCACTAGCCTTATCTCTCT
AAGGTAGCAAGAGAGCAGGCTAAAGATTGTAGTCTTATCTTTCTAAAGCAGCAAAAAAGCAGACT
AAAGATTGAAGATCTTATCTCCCTAAACAGAATCAGAGCAGATTGAAAGAGACGAATCTTATCTC
CATGTATCGGAAATGGAGCAGATTTAAGCCCCAAGATTTATTTCCCTGAAGTTGCAGTAGAGCAA
ATTGC
Found at i:21737 original size:46 final size:46
Alignment explanation
Indices: 21685--21944 Score: 200
Period size: 46 Copynumber: 5.7 Consensus size: 46
21675 ATTTGGGCAT
* *
21685 CCGAACTCATTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
* *** *
21731 CCGAACTCGTTGAGTTGAGTCCGAATTC-GGGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--GC
* * * * *
21776 ATCCAAACTCGTTGAGTTGAGTCCAATTTCACTTATGGATGCGAACGT
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
* * * *
21824 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAG-
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T-GC
* *
21867 --GTACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
* *
21911 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTAT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAT
21945 AGGCGGTTAC
Statistics
Matches: 163, Mismatches: 33, Indels: 36
0.70 0.14 0.16
Matches are distributed among these distances:
41 25 0.15
42 6 0.04
43 9 0.06
44 4 0.02
45 7 0.04
46 79 0.48
47 25 0.15
48 2 0.01
50 4 0.02
51 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
Found at i:21839 original size:93 final size:92
Alignment explanation
Indices: 21680--21939 Score: 377
Period size: 93 Copynumber: 2.9 Consensus size: 92
21670 AGGATATTTG
* * *
21680 GGCATCCGAACTCATTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAG
1 GGCATCC-AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
* *
21745 TTGAGTCCGAATTCGGGAGATGTAACTA
65 TTGAGTCCGAGTTCGGGAAATGTAACTA
* * *
21773 GGCATCCAAACTCGTTGAGTTGAGTCCAATTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCC-AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
21838 TTGAGTCCGAGTTCGTGAAATGTAACTA
65 TTGAGTCCGAGTTCGGGAAATGTAACTA
*
21866 GG--T---ACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GGCATCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
21926 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
21940 CTTATAGGCG
Statistics
Matches: 153, Mismatches: 14, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
87 67 0.44
91 1 0.01
93 85 0.56
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (92 bp):
GGCATCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGGGAAATGTAACTA
Found at i:28686 original size:42 final size:42
Alignment explanation
Indices: 28639--28741 Score: 145
Period size: 42 Copynumber: 2.5 Consensus size: 42
28629 ACCGAAACTA
* *
28639 CGTGTAAGACTATATCTGAGA-TATGGCATCATTATGAGACTT
1 CGTGTAAGACCATATCTG-GATTATGGCATCAATATGAGACTT
* *
28681 CGTGTAAGACCCTATCTGGATTATGGCATCAATATGAGATTT
1 CGTGTAAGACCATATCTGGATTATGGCATCAATATGAGACTT
*
28723 CGTGTAAGACCATAGCTGG
1 CGTGTAAGACCATATCTGG
28742 GCTATTGGCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 2 0.04
42 52 0.96
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (42 bp):
CGTGTAAGACCATATCTGGATTATGGCATCAATATGAGACTT
Found at i:31083 original size:79 final size:81
Alignment explanation
Indices: 30974--31156 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
30964 TACTCGTTCA
* *
30974 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
31037 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
31054 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
31117 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
31133 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
31157 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:31156 original size:40 final size:40
Alignment explanation
Indices: 30953--31156 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
30943 CGGAATTTAA
** *
30953 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
30993 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
31033 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
31072 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
31112 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
31152 CCGGA
1 CCGGA
31157 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.