Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011799.1 Kokia drynarioides strain JFW-HI SEQ_126794, 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: 25797
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Found at i:7723 original size:49 final size:50
Alignment explanation
Indices: 7659--7758 Score: 157
Period size: 49 Copynumber: 2.0 Consensus size: 50
7649 TCCGTATAGA
* * *
7659 ACTATACTTCTTCTATTTGACATGGATTAGAATAAGGTTTTTCAA-CTTT
1 ACTACACTACTTCTATTTGACATGGATTAGAATAAGGCTTTTCAATCTTT
*
7708 ACTACACTACTTCTATTTGACATTGATTAGAATAAGGCTTTTCAATCTTT
1 ACTACACTACTTCTATTTGACATGGATTAGAATAAGGCTTTTCAATCTTT
7758 A
1 A
7759 AATAGATGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 41 0.89
50 5 0.11
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (50 bp):
ACTACACTACTTCTATTTGACATGGATTAGAATAAGGCTTTTCAATCTTT
Found at i:8841 original size:285 final size:285
Alignment explanation
Indices: 8326--8857 Score: 827
Period size: 285 Copynumber: 1.9 Consensus size: 285
8316 TTTTTTAAAT
* *
8326 GTTTCGAAAATTATTTTAAATTTGAAAAAATGGGAGTCGCCACCAATCCTTTATTTGGTGTGATT
1 GTTTCGAAAATTACTTTAAATTTGAAAAAATGGGAGTCGCCACCAATCCTTTATTCGGTGTGATT
** * * * *
8391 GGATAACCACAAAACGTTTAAAATTCATTTTGAAAAATATTTTGGTCTTCGCAATCCAGAAAACA
66 GGATAACCACAAAACGTTTAAAAACCATTTTGAAAAACATGTAGGTCTTCGAAATCCAGAAAACA
* * *
8456 AGTTCGGGAGTTGGTTACGCATGAGGAAGGGTTAGCACCCTCATACGCCCAAAATTAGTACCACA
131 AGTTCGGGAGTCGGTTACGCAGGAGGAAGGATTAGCACCCTCATACGCCCAAAATTAGTACCACA
*
8521 TTGATTACTTTCGGGTCTTGATTTGTAAAATTTAAAAACTCGAATAAAGTTTTGTCGAAACCATC
196 TTGATTACTTTCGGGTCTTAATTTGTAAAATTTAAAAACTCGAATAAAGTTTTGTCGAAACCATC
8586 CGTTTTTATTTTTGCAAAACGACGA
261 CGTTTTTATTTTTGCAAAACGACGA
*
8611 GTTTCGAAAATTACTTT-AATGTTG-GAAAATGGGAGTCGCCACCAATCCTTTATTCGGTGTGAT
1 GTTTCGAAAATTACTTTAAAT-TTGAAAAAATGGGAGTCGCCACCAATCCTTTATTCGGTGTGAT
*
8674 TGGATCACCACAAAACGTTTTAAAAACCATTTTG-AAAACATGTAGGTCTTCGAAATCCAGAAAA
65 TGGATAACCACAAAACG-TTTAAAAACCATTTTGAAAAACATGTAGGTCTTCGAAATCCAG-AAA
* *
8738 ACAGGTTCGGGAGTCGGTTACGCAGGAGGAAGGATTAGCACCCTCATACGCCCAAAATTGGTACC
128 ACAAGTTCGGGAGTCGGTTACGCAGGAGGAAGGATTAGCACCCTCATACGCCCAAAATTAGTACC
** * * *
8803 GTATTGATTATTTTCGGGTCTTAATTTGTAACATTTAAAAGCTCGAATAAAGTTT
193 ACATTGATTACTTTCGGGTCTTAATTTGTAAAATTTAAAAACTCGAATAAAGTTT
8858 AAAATACGAT
Statistics
Matches: 223, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
284 78 0.35
285 145 0.65
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (285 bp):
GTTTCGAAAATTACTTTAAATTTGAAAAAATGGGAGTCGCCACCAATCCTTTATTCGGTGTGATT
GGATAACCACAAAACGTTTAAAAACCATTTTGAAAAACATGTAGGTCTTCGAAATCCAGAAAACA
AGTTCGGGAGTCGGTTACGCAGGAGGAAGGATTAGCACCCTCATACGCCCAAAATTAGTACCACA
TTGATTACTTTCGGGTCTTAATTTGTAAAATTTAAAAACTCGAATAAAGTTTTGTCGAAACCATC
CGTTTTTATTTTTGCAAAACGACGA
Found at i:9213 original size:96 final size:96
Alignment explanation
Indices: 9042--9223 Score: 244
Period size: 96 Copynumber: 1.9 Consensus size: 96
9032 AAGGATGTTT
* ** * *
9042 GATTATCTCGATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGCGTAAATTTTCAGAATCGAAGA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAAA
*
9107 TAAGGAAATATTGCCTCGATTAAGGGTATTC
66 TAAAGAAATATTGCCTCGATTAAGGGTATTC
* *
9138 GATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTT-TGAAACTC-AA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAG-AA-TCGAA
9201 AATAAA-AGAATATTGCCTCGATT
64 AATAAAGA-AATATTGCCTCGATT
9224 TTAAAGTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
95 2 0.03
96 71 0.95
97 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAAA
TAAAGAAATATTGCCTCGATTAAGGGTATTC
Found at i:9593 original size:30 final size:30
Alignment explanation
Indices: 9559--9768 Score: 234
Period size: 30 Copynumber: 7.1 Consensus size: 30
9549 TAATTTCGAG
* *
9559 AGTTTCAAGGTCAAAAATGGAGTTTTTGGA
1 AGTTTCAGGGTCAAAAATGGAATTTTTGGA
**
9589 AGTTTTGGGGTCAAAAATGGAATTTTTGGA
1 AGTTTCAGGGTCAAAAATGGAATTTTTGGA
* * *
9619 AGTTTGAGGGTAAAAACAT--AACTTTTGGA
1 AGTTTCAGGGTCAAAA-ATGGAATTTTTGGA
* * * *
9648 AGTTTTAGGATAAAAAATGGAATTTTTAGA
1 AGTTTCAGGGTCAAAAATGGAATTTTTGGA
*
9678 AGTTTGAGGGT-AAAAATGGAATTTTTGGA
1 AGTTTCAGGGTCAAAAATGGAATTTTTGGA
*
9707 AGTTTCGGGGTCAAAAATGGAATTTTTGGA
1 AGTTTCAGGGTCAAAAATGGAATTTTTGGA
*
9737 AG-TTC-GTGAT-AAAAATGGAATTTTTGGA
1 AGTTTCAG-GGTCAAAAATGGAATTTTTGGA
9765 AGTT
1 AGTT
9769 CGTGATAAAA
Statistics
Matches: 156, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.15
29 55 0.35
30 76 0.49
31 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (30 bp):
AGTTTCAGGGTCAAAAATGGAATTTTTGGA
Found at i:9624 original size:29 final size:29
Alignment explanation
Indices: 9571--9808 Score: 243
Period size: 29 Copynumber: 8.1 Consensus size: 29
9561 TTTCAAGGTC
* *
9571 AAAAATGGAGTTTTTGGAAGTTTTGGGGTC
1 AAAAATGGAATTTTTGGAAG-TTTGGGGTA
9601 AAAAATGGAATTTTTGGAAGTTTGAGGGTA
1 AAAAATGGAATTTTTGGAAGTTTG-GGGTA
* * *
9631 AAAACAT--AACTTTTGGAAGTTTTAGGATA
1 AAAA-ATGGAATTTTTGGAAG-TTTGGGGTA
*
9660 AAAAATGGAATTTTTAGAAGTTTGAGGGT-
1 AAAAATGGAATTTTTGGAAGTTTG-GGGTA
*
9689 AAAAATGGAATTTTTGGAAGTTTCGGGGTC
1 AAAAATGGAATTTTTGGAAGTTT-GGGGTA
* * *
9719 AAAAATGGAATTTTTGGAAGTTCGTGAT-
1 AAAAATGGAATTTTTGGAAGTTTGGGGTA
* * *
9747 AAAAATGGAATTTTTGGAAGTTCGTGATA
1 AAAAATGGAATTTTTGGAAGTTTGGGGTA
*
9776 AAAAATATG-ATTTTTGGAAGTTTGGGGGTA
1 AAAAAT-GGAATTTTTGGAAGTTT-GGGGTA
9806 AAA
1 AAA
9809 TTTTAATTTT
Statistics
Matches: 180, Mismatches: 17, Indels: 22
0.82 0.08 0.10
Matches are distributed among these distances:
28 30 0.17
29 74 0.41
30 74 0.41
31 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTGGGGTA
Found at i:9634 original size:59 final size:59
Alignment explanation
Indices: 9571--9808 Score: 275
Period size: 59 Copynumber: 4.1 Consensus size: 59
9561 TTTCAAGGTC
* * * *
9571 AAAAATGGAGTTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGGGATAAAAAATGGAATTTTTGGAAGTTTGAGGGT
*** * ** *
9630 AAAAACATAACTTTTGGAAGTTTTAGGATAAAAAATGGAATTTTTAGAAGTTTGAGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGGGATAAAAAATGGAATTTTTGGAAGTTTGAGGGT
* * * * *
9689 AAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCG-TGAT
1 AAAAATGGAATTTTTGGAAGTTTCGGGATAAAAAATGGAATTTTTGGAAGTTTGAGGGT
* * *
9747 AAAAATGGAATTTTTGGAAG-TTCGTGATAAAAAATATG-ATTTTTGGAAGTTTGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGGGATAAAAAAT-GGAATTTTTGGAAGTTTGAGGGT
9805 AAAA
1 AAAA
9809 TTTTAATTTT
Statistics
Matches: 149, Mismatches: 28, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
57 26 0.17
58 29 0.19
59 94 0.63
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTTCGGGATAAAAAATGGAATTTTTGGAAGTTTGAGGGT
Found at i:10973 original size:3 final size:3
Alignment explanation
Indices: 10965--11010 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
10955 TTAGTAATAT
* *
10965 TTA TTA TTA TTA TTA TTA TTGA -TA TTA TTG TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
11010 T
1 T
11011 GACTAAAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 35 0.95
4 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:10976 original size:6 final size:6
Alignment explanation
Indices: 10906--11010 Score: 59
Period size: 6 Copynumber: 17.2 Consensus size: 6
10896 TTAATAACAT
* * * * * * * * *
10906 TTATTA ATACTTA TTACTA TTATTA CTGTCA TTAGTA TTACTA ATGTTA
1 TTATTA TTA-TTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
* * * *
10955 TTAGTA ATATTTA TTATTA TTATTA TTATTGA -TATTA TTGTTA TTGTTA
1 TTATTA TTA-TTA TTATTA TTATTA TTATT-A TTATTA TTATTA TTATTA
11004 TTATTA T
1 TTATTA T
11011 GACTAAAGGT
Statistics
Matches: 72, Mismatches: 23, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
5 1 0.01
6 61 0.85
7 10 0.14
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (6 bp):
TTATTA
Found at i:11007 original size:9 final size:9
Alignment explanation
Indices: 10906--11010 Score: 59
Period size: 9 Copynumber: 11.4 Consensus size: 9
10896 TTAATAACAT
*
10906 TTATTAATA
1 TTATTATTA
*
10915 CTTATTACTA
1 -TTATTATTA
* *
10925 TTATTACTG
1 TTATTATTA
* *
10934 TCATTAGTA
1 TTATTATTA
* * *
10943 TTACTAATG
1 TTATTATTA
*
10952 TTATTAGTA
1 TTATTATTA
*
10961 ATATTTATTA
1 TTA-TTATTA
10971 TTATTATTA
1 TTATTATTA
10980 TTATTGA-TA
1 TTATT-ATTA
*
10989 TTATTGTTA
1 TTATTATTA
*
10998 TTGTTATTA
1 TTATTATTA
11007 TTAT
1 TTAT
11011 GACTAAAGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
9 57 0.78
10 16 0.22
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (9 bp):
TTATTATTA
Found at i:11663 original size:206 final size:206
Alignment explanation
Indices: 11287--11684 Score: 557
Period size: 206 Copynumber: 1.9 Consensus size: 206
11277 TCTGGTTTCA
* * **
11287 TTGACTTGGCCTTCTTCTCAGTATCTCATCAGGAAGACGACCATATCACTTGTTTTGATCCACTT
1 TTGACTTGGCCTTCTTCTCAATATCTCATCAGAAAGACGACCATATCACTTGTTTCAATCCACTT
* * * *
11352 CTTTGTGTTTCATCAGGAAGACAGATTTGGTTCACTTCTCAGTATTTCAACAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACAGATTTGGTTCACTTCTCAGTATCTCAACAGGAAGCTAACCAT
* *
11417 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATTAGGAAGCTGAGATTCGAAGATTTGCTCACAT
131 TTTATTGCTTCGACATGCTTCTCAGTATCTCATCAGGAAGCTGAGATTCGAAGATTTGCTCACAT
11482 CAAGCGTGGGT
196 CAAGCGTGGGT
* * * * * * * * *
11493 TTGATTTGGTCTTTTTCTCAATATCTCATTAGAAAGATGCCCGTATCGCTTGTTTCAATCCGCTT
1 TTGACTTGGCCTTCTTCTCAATATCTCATCAGAAAGACGACCATATCACTTGTTTCAATCCACTT
*
11558 CTCTGTATCTCATCAGGAAGA-AGAATTTGG-TCTACTTCTCAGTATCTCATCAGGAAGCTAACC
66 CTCTGTATCTCATCAGGAAGACAG-ATTTGGTTC-ACTTCTCAGTATCTCAACAGGAAGCTAACC
* * *
11621 ATTTTATTGCTTCGACATGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
129 ATTTTATTGCTTCGACATGCTTCTCAGTATCTCATCAGGAAGCTGAGATTCGAAGATTTGCTCA
11685 TATCGAGCCC
Statistics
Matches: 167, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
205 4 0.02
206 163 0.98
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (206 bp):
TTGACTTGGCCTTCTTCTCAATATCTCATCAGAAAGACGACCATATCACTTGTTTCAATCCACTT
CTCTGTATCTCATCAGGAAGACAGATTTGGTTCACTTCTCAGTATCTCAACAGGAAGCTAACCAT
TTTATTGCTTCGACATGCTTCTCAGTATCTCATCAGGAAGCTGAGATTCGAAGATTTGCTCACAT
CAAGCGTGGGT
Found at i:11741 original size:152 final size:152
Alignment explanation
Indices: 11555--12189 Score: 1171
Period size: 152 Copynumber: 4.2 Consensus size: 152
11545 TTTCAATCCG
* *
11555 CTTCTCTGTATCTCATCAGGAAGAAGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAAC
1 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
11620 CATTTTATTGCTTCGACATGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
66 CATTTTATTGCTTCGACATGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
*
11685 TATCGAGCCCTGAGTTGGTATT
131 CATCGAGCCCTGAGTTGGTATT
* * *
11707 CCTCTCTGTATCTCATCAAGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
1 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
*
11772 CATTTTATTGCTTCGACATGCTTCTCGGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCA
66 CATTTTATTGCTTCGACATGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
11837 CATCGAGCCCTGAGTTGGTATT
131 CATCGAGCCCTGAGTTGGTATT
*
11859 TTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
1 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
11924 CATTTTATTGCTTCGACATGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
66 CATTTTATTGCTTCGACATGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
*
11989 CATCGAGCCTTGAGTTGGTATT
131 CATCGAGCCCTGAGTTGGTATT
12011 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
1 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
12076 CATTTTATTGCTTCGACATGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
66 CATTTTATTGCTTCGACATGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
*
12141 CATCTAGCCCTGAGTTGGTATT
131 CATCGAGCCCTGAGTTGGTATT
*
12163 CTTCTTTGTATCTCATCAGGAAGACGA
1 CTTCTCTGTATCTCATCAGGAAGACGA
12190 CCGCCTTATT
Statistics
Matches: 467, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
152 467 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (152 bp):
CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
CATTTTATTGCTTCGACATGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
CATCGAGCCCTGAGTTGGTATT
Found at i:12415 original size:121 final size:121
Alignment explanation
Indices: 12249--12508 Score: 466
Period size: 121 Copynumber: 2.1 Consensus size: 121
12239 TTTGGTCCAC
*
12249 TTCTCATTATCTCATCAGGAAGCCAACCGTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAG
1 TTCTCAGTATCTCATCAGGAAGCCAACCGTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAG
* * *
12314 GAAGCTGGGTTTCGAAGATTTGCTCTCTTTGAGCCTCGTTCATTGATTTAGTCTAT
66 GAAGATGGGGTTCGAAGATTTGCTCTCTTTGAGCCTCATTCATTGATTTAGTCTAT
* *
12370 TTCTCAGTATCTCATCAGGAAGCTAACCGTTTATTACTTTGACCTGCTTCTCAGTATCTCATCAG
1 TTCTCAGTATCTCATCAGGAAGCCAACCGTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAG
12435 GAAGATGGGGTTCGAAGATTTGCTCTCTTTGAGCCTCATTCATTGATTTAGTCTAT
66 GAAGATGGGGTTCGAAGATTTGCTCTCTTTGAGCCTCATTCATTGATTTAGTCTAT
12491 TTCTCAGTATCTCATCAG
1 TTCTCAGTATCTCATCAG
12509 AAAGATGATC
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
121 133 1.00
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (121 bp):
TTCTCAGTATCTCATCAGGAAGCCAACCGTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAG
GAAGATGGGGTTCGAAGATTTGCTCTCTTTGAGCCTCATTCATTGATTTAGTCTAT
Found at i:18347 original size:47 final size:47
Alignment explanation
Indices: 18278--18371 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
18268 ACTATATTCA
18278 CTATACATTAAAAACTTTAAAAACTCCTTTGCCTCATTCTCAGATAC
1 CTATACATTAAAAACTTTAAAAACTCCTTTGCCTCATTCTCAGATAC
18325 CTATACATTAAAAACTTTAAAAACTCCTTTGCCTCATTCTCAGATAC
1 CTATACATTAAAAACTTTAAAAACTCCTTTGCCTCATTCTCAGATAC
18372 AGGCTCGTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (47 bp):
CTATACATTAAAAACTTTAAAAACTCCTTTGCCTCATTCTCAGATAC
Found at i:22948 original size:24 final size:24
Alignment explanation
Indices: 22914--22962 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
22904 CAAGTATAGC
* *
22914 ATAGAACCTAAAAGTTTGTCTTGG
1 ATAGAAACTAAAAGTTTATCTTGG
22938 ATAGAAACTAAAAGTTTATCTTGG
1 ATAGAAACTAAAAGTTTATCTTGG
22962 A
1 A
22963 AGGTTGCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (24 bp):
ATAGAAACTAAAAGTTTATCTTGG
Found at i:24078 original size:96 final size:96
Alignment explanation
Indices: 23894--24085 Score: 219
Period size: 96 Copynumber: 2.0 Consensus size: 96
23884 ATTTTGGGAA
* * * * ** * * **
23894 AAGGATGTTTGATTATCTCGATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTTA
1 AAGGATATTCGATTATCTCGATTTAAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTCGA
*
23959 GAATCGAAGATAAGGAAGCATTGCCTCGATT
66 GAATCGAAGATAAAGAAGCATTGCCTCGATT
*
23990 AAGGATATTCGATTATTTCGATTTAAAGAAAAATTACACCTAGTAAGTTAAGGCACAAAATTTCG
1 AAGGATATTCGATTATCTCGATTTAAAGAAAAATTACACCTAGTAAGTTAAGGCAC-AAATTTCG
*
24055 A-AACTCGAA-ATAAAAGAA-TATTGCCTCGATT
65 AGAA-TCGAAGAT-AAAGAAGCATTGCCTCGATT
24086 TTAAAGTTTT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
96 63 0.79
97 17 0.21
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTAAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTCGA
GAATCGAAGATAAAGAAGCATTGCCTCGATT
Found at i:24360 original size:28 final size:27
Alignment explanation
Indices: 24301--24362 Score: 97
Period size: 28 Copynumber: 2.3 Consensus size: 27
24291 AAATGAGACT
24301 TTTTGGATACCGAAGGCAAAATGGTAA
1 TTTTGGATACCGAAGGCAAAATGGTAA
* *
24328 TTTTGGATTCTCGAGGGCAAAATGGTAA
1 TTTTGGATAC-CGAAGGCAAAATGGTAA
24356 TTTTGGA
1 TTTTGGA
24363 AAATACAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.32
Consensus pattern (27 bp):
TTTTGGATACCGAAGGCAAAATGGTAA
Found at i:24600 original size:59 final size:59
Alignment explanation
Indices: 24433--24661 Score: 264
Period size: 59 Copynumber: 3.9 Consensus size: 59
24423 TTCGGGATCG
* * * * *
24433 AAAATGGAGTTTTTGGAAGTTTC-TGGGTCAAAAATGAAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-AAAAATGAAATTTTTAGAAGTTTCGAGGTCA
* ** * ** *
24493 AAAATTGAATTTTTAAAAGTTTG-GGGTAAAAACAAAATTTTTAGAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTAGAAGTTTCGAGGTCA
* *
24551 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTAGAAGTTTCGAGGTCA
* * *
24610 AAAATGGGATTTTTGGAAGCTCGAGGGTAAAAATGTAATTTTTAGATAGTTT
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTAGA-AGTTT
24662 AGGGACCTCC
Statistics
Matches: 142, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
58 44 0.31
59 78 0.55
60 20 0.14
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.35
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTAGAAGTTTCGAGGTCA
Found at i:24633 original size:29 final size:29
Alignment explanation
Indices: 24433--24652 Score: 205
Period size: 30 Copynumber: 7.5 Consensus size: 29
24423 TTCGGGATCG
* *
24433 AAAATGGAGTTTTTGGAAGTTTC-TGGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
* *
24463 AAAATGAAATTTTTGGAAGTTTTG-GGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
* ** *
24493 AAAATTGAATTTTTAAAAGTTTG-GGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*** * *
24521 AAAACAAAATTTTTAGAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
24551 AAAATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
24580 AAAATGGAATTTTTGGAAGTTTCGA-GGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
* *
24610 AAAATGGGATTTTTGGAAGCTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
24639 AAAATGTAATTTTT
1 AAAATGGAATTTTT
24653 AGATAGTTTA
Statistics
Matches: 162, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
28 16 0.10
29 59 0.36
30 87 0.54
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:25771 original size:18 final size:18
Alignment explanation
Indices: 25745--25792 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
25735 ATTAATACTT
* *
25745 ATTACTATTATTACTGTC
1 ATTAGTATTATTAATGTC
* *
25763 ATTAGTATTACTAATGTT
1 ATTAGTATTATTAATGTC
*
25781 ATTAGTAATATT
1 ATTAGTATTATT
25793 TATTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.50
Consensus pattern (18 bp):
ATTAGTATTATTAATGTC
Done.