Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004474.1 Kokia drynarioides strain JFW-HI SEQ_117894, 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: 56376
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:827 original size:110 final size:110
Alignment explanation
Indices: 683--900 Score: 366
Period size: 110 Copynumber: 2.0 Consensus size: 110
673 CATAATAGTC
*
683 ATTACAAACAATGAATTGCATAACTATCTCAAAAAACTAATTTATCTAGTAGACAAAATATAAAA
1 ATTACAAACAATGAATTGAATAACTATCTCAAAAAACTAATTTATCTAGTAGACAAAATATAAAA
* *
748 TTATTTATATTCAATGTTAG-GTTTACATAGATCGGTTATTTAAAA
66 TTATTTATACTCAATGTT-GCGTTTACATAAATCGGTTATTTAAAA
* * *
793 ATTACAAACAATGAATTGAATAATTATCTCAAAAAATTAATTTATCTAGTAGACAAAGTATAAAA
1 ATTACAAACAATGAATTGAATAACTATCTCAAAAAACTAATTTATCTAGTAGACAAAATATAAAA
858 TTATTTATACTCAATGTTGCGTTTACATAAATCGGTTATTTAA
66 TTATTTATACTCAATGTTGCGTTTACATAAATCGGTTATTTAA
901 CTAGTAGATA
Statistics
Matches: 101, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
109 1 0.01
110 100 0.99
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (110 bp):
ATTACAAACAATGAATTGAATAACTATCTCAAAAAACTAATTTATCTAGTAGACAAAATATAAAA
TTATTTATACTCAATGTTGCGTTTACATAAATCGGTTATTTAAAA
Found at i:4392 original size:25 final size:24
Alignment explanation
Indices: 4360--4406 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
4350 TTTAAATTTT
4360 ATATTAATATTAAATAAATATAATC
1 ATATTAATATTAAATAAA-ATAATC
4385 ATATTAATATTAAATAAAATAA
1 ATATTAATATTAAATAAAATAA
4407 AAATCCTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATTAATATTAAATAAAATAATC
Found at i:8651 original size:23 final size:23
Alignment explanation
Indices: 8619--8672 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
8609 TCTTTACACA
* *
8619 TTTATGTAATTGGACTTTTATTTT
1 TTTAT-TAATTGGACTTTCAATTT
*
8643 TTTATTAATTTGACTTTCAATTT
1 TTTATTAATTGGACTTTCAATTT
8666 TTTATTA
1 TTTATTA
8673 TCAACATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.24, C:0.06, G:0.07, T:0.63
Consensus pattern (23 bp):
TTTATTAATTGGACTTTCAATTT
Found at i:9783 original size:10 final size:10
Alignment explanation
Indices: 9770--9833 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
9760 TAACAGATAT
9770 TAAAAAATTA
1 TAAAAAATTA
*
9780 TAAAAACTTA
1 TAAAAAATTA
*
9790 T-AAATATTA
1 TAAAAAATTA
* *
9799 TAAAAACTCA
1 TAAAAAATTA
9809 T-AAAAATCTA
1 TAAAAAAT-TA
9819 -ATAAAAATTA
1 TA-AAAAATTA
9829 TAAAA
1 TAAAA
9834 TATGATTTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
9 12 0.29
10 22 0.54
11 7 0.17
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:9799 original size:9 final size:9
Alignment explanation
Indices: 9768--9833 Score: 71
Period size: 9 Copynumber: 7.0 Consensus size: 9
9758 TTTAACAGAT
9768 ATTA-AAAA
1 ATTATAAAA
9776 ATTATAAAA
1 ATTATAAAA
*
9785 ACTTATAAAT
1 A-TTATAAAA
9795 ATTATAAAA
1 ATTATAAAA
*
9804 ACTCATAAAA
1 A-TTATAAAA
9814 ATCTAATAAAA
1 AT-T-ATAAAA
9825 ATTATAAAA
1 ATTATAAAA
9834 TATGATTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
8 4 0.08
9 20 0.41
10 17 0.35
11 8 0.16
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (9 bp):
ATTATAAAA
Found at i:9800 original size:19 final size:19
Alignment explanation
Indices: 9772--9833 Score: 81
Period size: 19 Copynumber: 3.2 Consensus size: 19
9762 ACAGATATTA
9772 AAAAATTATAAAAACTTAT
1 AAAAATTATAAAAACTTAT
* *
9791 AAATATTATAAAAACTCAT
1 AAAAATTATAAAAACTTAT
9810 AAAAATCTAATAAAAA-TTAT
1 AAAAAT-T-ATAAAAACTTAT
9830 AAAA
1 AAAA
9834 TATGATTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 22 0.59
20 8 0.22
21 7 0.19
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATTATAAAAACTTAT
Found at i:10636 original size:24 final size:23
Alignment explanation
Indices: 10598--10647 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
10588 TTAATATATG
* *
10598 AAATATTAATTTTAAATATTTTT
1 AAATATTAATATTAAATATTTAT
*
10621 AAATAATTAATATTAATTATTTAT
1 AAAT-ATTAATATTAAATATTTAT
10645 AAA
1 AAA
10648 ATCTAATTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATATTAATATTAAATATTTAT
Found at i:16513 original size:19 final size:19
Alignment explanation
Indices: 16491--16527 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16481 GTAACCATTG
*
16491 TTATCAATTGTAATCAAAT
1 TTATCAATCGTAATCAAAT
*
16510 TTATCTATCGTAATCAAA
1 TTATCAATCGTAATCAAA
16528 ATTGTTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (19 bp):
TTATCAATCGTAATCAAAT
Found at i:17293 original size:30 final size:28
Alignment explanation
Indices: 17259--17318 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 28
17249 TGAGAGGGGA
17259 GTAAAAAATTTAAGAGAAAAGTGGAAAAAG
1 GTAAAAAATTTAAGAGAAAAGT--AAAAAG
** *
17289 GTAAAAGTTTTGAGAGAAAAGTAAAAAG
1 GTAAAAAATTTAAGAGAAAAGTAAAAAG
17317 GT
1 GT
17319 TTTGAGTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 8 0.30
30 19 0.70
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.20
Consensus pattern (28 bp):
GTAAAAAATTTAAGAGAAAAGTAAAAAG
Found at i:17300 original size:169 final size:176
Alignment explanation
Indices: 16982--17324 Score: 463
Period size: 169 Copynumber: 2.0 Consensus size: 176
16972 GGGAGTAAAA
*
16982 TTTTGAGGGAAAGTAAATAGGAGAGTAAAATTTTGGAGGGAAAATATTTAAAAAAAATTAAGAGG
1 TTTTGAGGGAAAATAAATAGGAGAGTAAAATTTTGGAGGGAAAATATTTAAAAAAAATT-AGAGG
* * * ** * *
17047 GGGGAATGGATTTGGGATAGATGGAGGGTTGGATGGGAGGAGAGTAAAAGTTTTAGGAGGAAAGT
65 GGGAAATGAATTTGGGATAGATGGAGGGTTGGATGAGAGGAGAGTAAAAAATTTAAGAGAAAAGT
* * *
17112 GAGAATAAGTAAAAGTTTTGGGAGAAAA-TAAAGA-GTTTTGAGGGT
130 GAGAAAAAGTAAAAGTTTTGAGAGAAAAGTAAAAAGGTTTTGAGGGT
*
17157 TTTTG-GGGAAAATAAATAGGAGAGTAAAATTTTGGAGGGGAAATA-TT-AAAAAAATT-G-GGG
1 TTTTGAGGGAAAATAAATAGGAGAGTAAAATTTTGGAGGGAAAATATTTAAAAAAAATTAGAGGG
*
17217 GGAAAATGAATTTGGGATAGATGG-GGG-TGAGATGAGAGGGGAGTAAAAAATTTAAGAGAAAAG
66 GG-AAATGAATTTGGGATAGATGGAGGGTTG-GATGAGAGGAGAGTAAAAAATTTAAGAGAAAAG
17280 TG-GAAAAAGGTAAAAGTTTTGAGAGAAAAGTAAAAAGGTTTTGAG
129 TGAGAAAAA-GTAAAAGTTTTGAGAGAAAAGTAAAAAGGTTTTGAG
17325 TTTGGGATAA
Statistics
Matches: 150, Mismatches: 13, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
168 7 0.05
169 56 0.37
170 25 0.17
171 8 0.05
172 9 0.06
173 2 0.01
174 38 0.25
175 5 0.03
ACGTcount: A:0.42, C:0.00, G:0.34, T:0.24
Consensus pattern (176 bp):
TTTTGAGGGAAAATAAATAGGAGAGTAAAATTTTGGAGGGAAAATATTTAAAAAAAATTAGAGGG
GGAAATGAATTTGGGATAGATGGAGGGTTGGATGAGAGGAGAGTAAAAAATTTAAGAGAAAAGTG
AGAAAAAGTAAAAGTTTTGAGAGAAAAGTAAAAAGGTTTTGAGGGT
Found at i:20906 original size:20 final size:19
Alignment explanation
Indices: 20883--20947 Score: 53
Period size: 21 Copynumber: 3.3 Consensus size: 19
20873 ATTTATTAGT
20883 TTTTAAGATTTTTTAATATA
1 TTTTAA-ATTTTTTAATATA
*
20903 TTTTTTTAAA-CTTTTAATATA
1 ---TTTTAAATTTTTTAATATA
*
20924 TTTTATAAATTTTTAATAT-
1 TTTTA-AATTTTTTAATATA
20943 TTTTA
1 TTTTA
20948 TGATTTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 5 0.13
19 7 0.18
20 9 0.24
21 10 0.26
22 1 0.03
23 6 0.16
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTAAATTTTTTAATATA
Found at i:20953 original size:18 final size:20
Alignment explanation
Indices: 20892--20948 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
20882 TTTTTAAGAT
*
20892 TTTTTAATATATTTTTTTAAA
1 TTTTTAATATA-TTTTATAAA
*
20913 CTTTTAATATATTTTATAAA
1 TTTTTAATATATTTTATAAA
20933 TTTTTAATAT-TTTTAT
1 TTTTTAATATATTTTAT
20949 GATTTATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 6 0.18
20 17 0.52
21 10 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTAATATATTTTATAAA
Found at i:21375 original size:84 final size:84
Alignment explanation
Indices: 21276--21528 Score: 463
Period size: 84 Copynumber: 3.0 Consensus size: 84
21266 ATTGGTAAAA
21276 AATTTTCTCTTTTTTCATTTTCACTTACTTAGGATTCTATTTATAAATAATTGACATTCAATGCA
1 AATTTTCTCTTTTTTCATTTTCACTTACTTAGGATTCTATTTATAAATAATTGACATTCAATGCA
21341 ACATAAATAAATGAAGCTT
66 ACATAAATAAATGAAGCTT
*
21360 AATTTTCTCTTTTTTCATTTTCACTTACGTAGGATTCTATTTATAAATAATTGACATTCAATGCA
1 AATTTTCTCTTTTTTCATTTTCACTTACTTAGGATTCTATTTATAAATAATTGACATTCAATGCA
21425 ACATAAATAAATGAAGCTT
66 ACATAAATAAATGAAGCTT
* *
21444 AATTTTCTCTTTTTTCATTTTCACTTA-TGTAGGATTCTATTTATAAGTAATTGACATTCAAAGC
1 AATTTTCTCTTTTTTCATTTTCACTTACT-TAGGATTCTATTTATAAATAATTGACATTCAATGC
21508 AACATAAATAAATGAAGCTT
65 AACATAAATAAATGAAGCTT
21528 A
1 A
21529 CTTATGTGCT
Statistics
Matches: 164, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
84 164 1.00
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (84 bp):
AATTTTCTCTTTTTTCATTTTCACTTACTTAGGATTCTATTTATAAATAATTGACATTCAATGCA
ACATAAATAAATGAAGCTT
Found at i:22869 original size:18 final size:18
Alignment explanation
Indices: 22843--22881 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
22833 CTCGAGAAAC
*
22843 TTTATATCCTTCAGGGAT
1 TTTAAATCCTTCAGGGAT
*
22861 TTTAAATCCTTCTGGGAT
1 TTTAAATCCTTCAGGGAT
22879 TTT
1 TTT
22882 CATATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (18 bp):
TTTAAATCCTTCAGGGAT
Found at i:24939 original size:29 final size:29
Alignment explanation
Indices: 24907--25141 Score: 227
Period size: 29 Copynumber: 8.1 Consensus size: 29
24897 GAAATCATAC
* *
24907 TTTAACCCTCGAACTCTCCAAAATTACAT
1 TTTAACCCTCAAACTTTCCAAAATTACAT
* *
24936 TTTAACCCTTAAACTTTCTAAAAATTACAT
1 TTTAACCCTCAAACTTTC-CAAAATTACAT
* *
24966 TTTAACCC-CTTAACTTTCAAAAATTACAT
1 TTTAACCCTC-AAACTTTCCAAAATTACAT
*
24995 CTTT-ACCCTTAAAC-TTCCAAAAATTACAT
1 -TTTAACCCTCAAACTTTCC-AAAATTACAT
* *
25024 TTTACCCCT-AAACTTTCTAAAATTACATT
1 TTTAACCCTCAAACTTTCCAAAATTACA-T
25053 TTTAA-CCT-AAACTTTCCAAAATTACATT
1 TTTAACCCTCAAACTTTCCAAAATTACA-T
*
25081 TTTGACCCT-AAACTTTCCAAACATTACAT
1 TTTAACCCTCAAACTTTCCAAA-ATTACAT
*
25110 TTTAA-CCTCGAAC-TTCCAAAAATTACTAT
1 TTTAACCCTCAAACTTTCC-AAAATTAC-AT
25139 TTT
1 TTT
25142 GCCCCTCGAG
Statistics
Matches: 177, Mismatches: 16, Indels: 26
0.81 0.07 0.12
Matches are distributed among these distances:
28 57 0.32
29 86 0.49
30 34 0.19
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.37
Consensus pattern (29 bp):
TTTAACCCTCAAACTTTCCAAAATTACAT
Found at i:25050 original size:57 final size:58
Alignment explanation
Indices: 24926--25141 Score: 264
Period size: 57 Copynumber: 3.7 Consensus size: 58
24916 CGAACTCTCC
* *
24926 AAAATTACATTTTAACCCTTAAACTTTCTAAAAATTACATTTTAACCCCTTAACTTTCA
1 AAAATTACATTTTAA-CCTTAAACTTTCCAAAAATTACATTTTAACCCCTAAACTTTCA
* *
24985 AAAATTACATCTTTACCCTTAAAC-TTCCAAAAATTACATTTT-ACCCCTAAACTTTCT
1 AAAATTACAT-TTTAACCTTAAACTTTCCAAAAATTACATTTTAACCCCTAAACTTTCA
*
25042 AAAATTACATTTTTAACC-TAAACTTTCC-AAAATTACATTTTTGA-CCCTAAACTTTCCA
1 AAAATTACA-TTTTAACCTTAAACTTTCCAAAAATTACA-TTTTAACCCCTAAACTTT-CA
* **
25100 AACATTACATTTTAACCTCGAAC-TTCCAAAAATTACTATTTT
1 AAAATTACATTTTAACCTTAAACTTTCCAAAAATTAC-ATTTT
25142 GCCCCTCGAG
Statistics
Matches: 139, Mismatches: 9, Indels: 19
0.83 0.05 0.11
Matches are distributed among these distances:
56 14 0.10
57 59 0.42
58 43 0.31
59 19 0.14
60 4 0.03
ACGTcount: A:0.38, C:0.23, G:0.01, T:0.38
Consensus pattern (58 bp):
AAAATTACATTTTAACCTTAAACTTTCCAAAAATTACATTTTAACCCCTAAACTTTCA
Found at i:25218 original size:29 final size:29
Alignment explanation
Indices: 25097--25264 Score: 121
Period size: 29 Copynumber: 5.8 Consensus size: 29
25087 CCTAAACTTT
*
25097 CCAAACATTA-CATTTTAACCTCGAACT-TC
1 CCAAA-ATTACCATTTTACCCTCGAA-TGTC
* * * *
25126 CAAAAATTACTATTTTGCCCCTCGAGTGAT-
1 CCAAAATTACCATTTT-ACCCTCGAATG-TC
* **
25156 -AAAAATTACCATTTTACCCTCGAACATC
1 CCAAAATTACCATTTTACCCTCGAATGTC
** *
25184 TAAAAATTACCATTTTACCCTCGGATGTC
1 CCAAAATTACCATTTTACCCTCGAATGTC
* *
25213 CCAAAATTACTATTTTACCC-CTAATTGTC
1 CCAAAATTACCATTTTACCCTCGAA-TGTC
* *
25242 CCAAAATTATCATTTTGCCCTCG
1 CCAAAATTACCATTTTACCCTCG
25265 GGTACCCAAA
Statistics
Matches: 109, Mismatches: 22, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
27 1 0.01
28 13 0.12
29 87 0.80
30 7 0.06
31 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.33
Consensus pattern (29 bp):
CCAAAATTACCATTTTACCCTCGAATGTC
Found at i:25219 original size:58 final size:59
Alignment explanation
Indices: 25096--25232 Score: 149
Period size: 58 Copynumber: 2.4 Consensus size: 59
25086 CCCTAAACTT
* * * *
25096 TCCAAACATTA-CATTTTAACCTCGAACTTCCAAAAATTACTATTTTGCCCCTCGAGTGA
1 TCCAAA-ATTACCATTTTACCCTCGAACATCCAAAAATTACCATTTTGACCCTCGAGTGA
* *
25155 T-AAAAATTACCATTTTACCCTCGAACATCTAAAAATTACCATTTT-ACCCTCG-GATG-
1 TCCAAAATTACCATTTTACCCTCGAACATCCAAAAATTACCATTTTGACCCTCGAG-TGA
*
25211 TCCCAAAATTACTATTTTACCC
1 T-CCAAAATTACCATTTTACCC
25233 CTAATTGTCC
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
56 2 0.03
57 12 0.18
58 51 0.77
59 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.33
Consensus pattern (59 bp):
TCCAAAATTACCATTTTACCCTCGAACATCCAAAAATTACCATTTTGACCCTCGAGTGA
Found at i:31576 original size:5 final size:5
Alignment explanation
Indices: 31566--31594 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
31556 TTCAATTTTC
31566 AATAT AATAT AATAT AATAT AATAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATA
31595 ATAAACAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:31955 original size:22 final size:22
Alignment explanation
Indices: 31930--31987 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
31920 TTACATTTAT
31930 TAATTTAAAATTTTAAAAAATA
1 TAATTTAAAATTTTAAAAAATA
31952 TAATTTAAAATTTTAAAAAATA
1 TAATTTAAAATTTTAAAAAATA
31974 TAATTTAAAATTTT
1 TAATTTAAAATTTT
31988 TATCTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATTTAAAATTTTAAAAAATA
Found at i:32014 original size:29 final size:29
Alignment explanation
Indices: 31982--32094 Score: 97
Period size: 28 Copynumber: 3.6 Consensus size: 29
31972 TATAATTTAA
*
31982 AATTTTTATC-TTTTTTAAGGGTAAAATAT
1 AATTTTTA-CATTTATTAAGGGTAAAATAT
32011 AA-TTTTACATTTATTAAGGGTAAAATAT
1 AATTTTTACATTTATTAAGGGTAAAATAT
32039 AATTATATTTTACATTTATCTTTTTTAAGGGTAAAATAT
1 -A--AT-TTTTACATTTA------TTAAGGGTAAAATAT
32078 AA-TTTTACATTTATTAA
1 AATTTTTACATTTATTAA
32095 TTTAAAATTT
Statistics
Matches: 71, Mismatches: 1, Indels: 25
0.73 0.01 0.26
Matches are distributed among these distances:
27 1 0.01
28 27 0.38
29 3 0.04
31 1 0.01
33 11 0.15
34 11 0.15
36 1 0.01
38 1 0.01
39 15 0.21
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (29 bp):
AATTTTTACATTTATTAAGGGTAAAATAT
Found at i:32088 original size:34 final size:34
Alignment explanation
Indices: 31968--32091 Score: 125
Period size: 34 Copynumber: 3.6 Consensus size: 34
31958 AAAATTTTAA
* *
31968 AAAATATAATTTAAAATTTTTATCTTTTTTAAGGGT
1 AAAATATAATTTTACA--TTTATCTTTTTTAAGGGT
32004 AAAATATAATTTTACATTTA------TTAAGGGT
1 AAAATATAATTTTACATTTATCTTTTTTAAGGGT
32032 AAAATATAATTATATTTTACATTTATCTTTTTTAAGGGT
1 -AAA-AT-A-TA-ATTTTACATTTATCTTTTTTAAGGGT
32071 AAAATATAATTTTACATTTAT
1 AAAATATAATTTTACATTTAT
32092 TAATTTAAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 24
0.74 0.02 0.24
Matches are distributed among these distances:
28 8 0.11
29 3 0.04
30 2 0.03
31 1 0.01
32 2 0.03
33 12 0.16
34 17 0.23
35 2 0.03
36 15 0.20
37 2 0.03
38 3 0.04
39 8 0.11
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.48
Consensus pattern (34 bp):
AAAATATAATTTTACATTTATCTTTTTTAAGGGT
Found at i:40283 original size:11 final size:11
Alignment explanation
Indices: 40223--40283 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
40213 ACTTTTTCAT
*
40223 TTCACTCACAA
1 TTCACTCTCAA
*
40234 TTCTCTCTCAA
1 TTCACTCTCAA
*
40245 TTCATTCTCAA
1 TTCACTCTCAA
*
40256 -TCATTTCTCAA
1 TTCA-CTCTCAA
40267 TT--CTCTCAA
1 TTCACTCTCAA
40276 TTCACTCT
1 TTCACTCT
40284 TATTTTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 8 0.20
10 3 0.07
11 29 0.71
12 1 0.02
ACGTcount: A:0.25, C:0.33, G:0.00, T:0.43
Consensus pattern (11 bp):
TTCACTCTCAA
Found at i:44909 original size:69 final size:69
Alignment explanation
Indices: 44798--44937 Score: 262
Period size: 69 Copynumber: 2.0 Consensus size: 69
44788 CTAACGAACA
*
44798 ACATCGTTGTTTCTTTTTCTGTTAGTGGTTGTTGCACTTGAGTTGTCACATCTCACCACCTCTGT
1 ACATCGTTGTTTCTTTTTCTGTTAGTGGTTGTTGCACTTGAGTTATCACATCTCACCACCTCTGT
44863 GCGT
66 GCGT
*
44867 ACATCGTTTTTTCTTTTTCTGTTAGTGGTTGTTGCACTTGAGTTATCACATCTCACCACCTCTGT
1 ACATCGTTGTTTCTTTTTCTGTTAGTGGTTGTTGCACTTGAGTTATCACATCTCACCACCTCTGT
44932 GCGT
66 GCGT
44936 AC
1 AC
44938 TGTCTAAAAC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (69 bp):
ACATCGTTGTTTCTTTTTCTGTTAGTGGTTGTTGCACTTGAGTTATCACATCTCACCACCTCTGT
GCGT
Found at i:54416 original size:26 final size:27
Alignment explanation
Indices: 54387--54439 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
54377 AAATAACTTT
*
54387 AGCTTCAATTACCATATAA-GAGAAGA
1 AGCTTCAATTACCATAAAAGGAGAAGA
* *
54413 AGCTTGAATTATCATAAAAGGAGAAGA
1 AGCTTCAATTACCATAAAAGGAGAAGA
54440 TACATCTCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (27 bp):
AGCTTCAATTACCATAAAAGGAGAAGA
Done.