Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009703.1 Kokia drynarioides strain JFW-HI SEQ_124422, 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: 70564
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2632 original size:26 final size:26
Alignment explanation
Indices: 2577--2632 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
2567 GCTAAACCTC
**
2577 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
2603 ATTAAATAAATTCAAATTTAAACAGA
1 ATTAAATAAATTCAAACATAAAAAGA
2629 ATTA
1 ATTA
2633 CTTCCAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:12071 original size:17 final size:17
Alignment explanation
Indices: 12046--12108 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
12036 CCAACAGAAT
12046 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
12063 TTAAGTTTATTTTAAAT
1 TTAAATTTATTTTAAAA
** *
12080 TTAAATTTATTGGAAAT
1 TTAAATTTATTTTAAAA
12097 TTAAATTTATTT
1 TTAAATTTATTT
12109 AAATAATGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:12086 original size:34 final size:33
Alignment explanation
Indices: 12043--12112 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 33
12033 GGCCCAACAG
** *
12043 AATTTAAATTTATTTTAAAATTAAGTTTATTTTA
1 AATTTAAATTTATTGGAAAATTAAATTTA-TTTA
*
12077 AATTTAAATTTATTGGAAATTTAAATTTATTTA
1 AATTTAAATTTATTGGAAAATTAAATTTATTTA
12110 AAT
1 AAT
12113 AATGTTCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 7 0.22
34 25 0.78
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (33 bp):
AATTTAAATTTATTGGAAAATTAAATTTATTTA
Found at i:12793 original size:3 final size:3
Alignment explanation
Indices: 12785--12811 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12775 TTAACGGCAT
12785 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
12812 AGAGAGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:13968 original size:29 final size:29
Alignment explanation
Indices: 13883--14151 Score: 171
Period size: 29 Copynumber: 9.3 Consensus size: 29
13873 GTCCCTGAAC
**
13883 TTTCCAAAATTCCA-TTTTGACCCTGAA-
1 TTTCCAAAATTCCATTTTTGACCCCAAAT
* * ** *
13910 GTTCCAAAATTACATTTTT-ACAGTCGAAT
1 TTTCCAAAATTCCATTTTTGAC-CCCAAAT
*
13939 TTTTCAAAATTCCATTTTTGACCCCAAA-
1 TTTCCAAAATTCCATTTTTGACCCCAAAT
* *
13967 TTTCCAAAAATTACATTTTT-ACCCTCAAAG
1 TTTCC-AAAATTCCATTTTTGACCC-CAAAT
* * * *
13997 TTCCCAAAATTCCATTTTTAATCCTAAAT
1 TTTCCAAAATTCCATTTTTGACCCCAAAT
* *
14026 TTTCCTAAAATTTACA--TTTAACCCCTAAAT
1 TTTCC-AAAA-TTCCATTTTTGACCCC-AAAT
* * **
14056 TTTCCAAAATTCTA-TTTTGACCCTAACG
1 TTTCCAAAATTCCATTTTTGACCCCAAAT
*
14084 TTTCCAAAATTACC-TTTTT-ACCACTCGAAT
1 TTTCCAAAATT-CCATTTTTGACC-C-CAAAT
** *
14114 TTTCCAAAATTATATTTTTGACCCCAAAG
1 TTTCCAAAATTCCATTTTTGACCCCAAAT
14143 TTTCCAAAA
1 TTTCCAAAA
14152 AATTTATATT
Statistics
Matches: 187, Mismatches: 37, Indels: 34
0.72 0.14 0.13
Matches are distributed among these distances:
27 14 0.07
28 34 0.18
29 92 0.49
30 40 0.21
31 7 0.04
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.39
Consensus pattern (29 bp):
TTTCCAAAATTCCATTTTTGACCCCAAAT
Found at i:14005 original size:58 final size:58
Alignment explanation
Indices: 13883--14182 Score: 272
Period size: 58 Copynumber: 5.2 Consensus size: 58
13873 GTCCCTGAAC
* * ** *
13883 TTTCCAAAATTCCA-TTTTGACCCTGAAGTTCC-AAAATTACATTTTTACAGTCGAAT
1 TTTCCAAAATTCCATTTTTGACCCTAAATTTCCAAAAATTACATTTTTACCCTCAAAT
* * *
13939 TTTTCAAAATTCCATTTTTGACCCCAAATTTCCAAAAATTACATTTTTACCCTCAAAG
1 TTTCCAAAATTCCATTTTTGACCCTAAATTTCCAAAAATTACATTTTTACCCTCAAAT
* * * * *
13997 TTCCCAAAATTCCATTTTTAATCCTAAATTTTCCTAAAATTTACA-TTTAACCC-CTAAAT
1 TTTCCAAAATTCCATTTTTGACCCTAAA-TTTCC-AAAAATTACATTTTTACCCTC-AAAT
* * * *
14056 TTTCCAAAATTCTA-TTTTGACCCTAACGTTTCC-AAAATTACCTTTTTACCACTCGAAT
1 TTTCCAAAATTCCATTTTTGACCCTAA-ATTTCCAAAAATTACATTTTTACC-CTCAAAT
** * * * *
14114 TTTCCAAAATTATATTTTTGACCCCAAAGTTTCCAAAAAATT-TATATTTTAACCTCAAAC
1 TTTCCAAAATTCCATTTTTGACCCTAAA-TTTCC-AAAAATTACAT-TTTTACCCTCAAAT
14174 TTTCCAAAA
1 TTTCCAAAA
14183 ATTATATTTT
Statistics
Matches: 197, Mismatches: 33, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
56 20 0.10
57 21 0.11
58 76 0.39
59 44 0.22
60 24 0.12
61 12 0.06
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (58 bp):
TTTCCAAAATTCCATTTTTGACCCTAAATTTCCAAAAATTACATTTTTACCCTCAAAT
Found at i:14027 original size:87 final size:84
Alignment explanation
Indices: 13883--14151 Score: 255
Period size: 87 Copynumber: 3.1 Consensus size: 84
13873 GTCCCTGAAC
* * *
13883 TTTCCAAAATTCCATTTTGACCCTGAAGTTCCAAAATTACATTTTTACAGT-C-GAATTTTTCAA
1 TTTCCAAAATT-CATTTTGACCCTAAAGTTCCAAAATTCCATTTTTA-A-TCCTGAATTTTCCAA
*
13946 AATTCCATTTTTGACCCCAAA-
63 AATTACATTTTTGACCCCAAAG
* *
13967 TTTCCAAAAATTACATTTTTACCCTCAAAGTTCCCAAAATTCCATTTTTAATCCTAAATTTTCCT
1 TTTCC-AAAATT-CATTTTGACCCT-AAAGTT-CCAAAATTCCATTTTTAATCCTGAATTTTCC-
* *
14032 AAAATTTACA--TTTAACCCCTAAAT
61 AAAA-TTACATTTTTGACCCC-AAAG
* *
14056 TTTCCAAAATTCTATTTTGACCCTAACGTTTCCAAAATTACC-TTTTT-ACCACTCGAATTTTCC
1 TTTCCAAAATTC-ATTTTGACCCTAAAG-TTCCAAAATT-CCATTTTTAATC-CT-GAATTTTCC
*
14119 AAAATTATATTTTTGACCCCAAAG
61 AAAATTACATTTTTGACCCCAAAG
14143 TTTCCAAAA
1 TTTCCAAAA
14152 AATTTATATT
Statistics
Matches: 154, Mismatches: 15, Indels: 29
0.78 0.08 0.15
Matches are distributed among these distances:
84 5 0.03
85 18 0.12
86 13 0.08
87 66 0.43
88 43 0.28
89 9 0.06
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.39
Consensus pattern (84 bp):
TTTCCAAAATTCATTTTGACCCTAAAGTTCCAAAATTCCATTTTTAATCCTGAATTTTCCAAAAT
TACATTTTTGACCCCAAAG
Found at i:14189 original size:29 final size:28
Alignment explanation
Indices: 13954--14202 Score: 146
Period size: 29 Copynumber: 8.5 Consensus size: 28
13944 AAAATTCCAT
* *
13954 TTTTGACCCCAAA-TTTCCAAAAATTACA
1 TTTTAACCCCAAACTTTCC-AAAATTATA
* * *
13982 TTTTTACCCTCAAAGTTCCCAAAATTCCAT-
1 TTTTAACCC-CAAACTTTCCAAAATT--ATA
* * *
14012 TTTTAATCCTAAATTTTCCTAAAATT-TA
1 TTTTAACCCCAAACTTTCC-AAAATTATA
* * *
14040 CATTTAACCCCTAAATTTTCCAAAATTCTA
1 -TTTTAACCCC-AAACTTTCCAAAATTATA
* * **
14070 TTTTGA-CCCTAACGTTTCCAAAATTACC
1 TTTTAACCCCAAAC-TTTCCAAAATTATA
* * *
14098 TTTTTACCACTCGAATTTTCCAAAATTATA
1 TTTTAACC-C-CAAACTTTCCAAAATTATA
* *
14128 TTTTTGACCCCAAAGTTTCCAAAAAATTTATA
1 -TTTTAACCCCAAACTTTCC--AAAA-TTATA
*
14160 TTTTAACCTCAAACTTTCCAAAAATTATA
1 TTTTAACCCCAAACTTTCC-AAAATTATA
14189 TTTTAACCCCAAAC
1 TTTTAACCCCAAAC
14203 CTTTTGAAAA
Statistics
Matches: 174, Mismatches: 30, Indels: 33
0.73 0.13 0.14
Matches are distributed among these distances:
27 3 0.02
28 27 0.16
29 61 0.35
30 47 0.27
31 31 0.18
32 5 0.03
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (28 bp):
TTTTAACCCCAAACTTTCCAAAATTATA
Found at i:16873 original size:6 final size:6
Alignment explanation
Indices: 16862--16890 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
16852 GGAAAGATAT
16862 ATGGAA ATGGAA ATGGAA ATGGAA ATGGA
1 ATGGAA ATGGAA ATGGAA ATGGAA ATGGA
16891 TTCCGTACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.34, T:0.17
Consensus pattern (6 bp):
ATGGAA
Found at i:18999 original size:29 final size:29
Alignment explanation
Indices: 18955--19118 Score: 165
Period size: 30 Copynumber: 5.6 Consensus size: 29
18945 CATTCGGGGG
18955 TAAAATGGTAATTTTTGGAAGGTTCGAGGT
1 TAAAATGG-AATTTTTGGAAGGTTCGAGGT
* * * *
18985 TAAAAATAGAATTTTTAGACA--TCCGAGGG
1 T-AAAATGGAATTTTTGGA-AGGTTCGAGGT
19014 TAAAATGGTAATTTTTGGAAGGTTCGAGGT
1 TAAAATGG-AATTTTTGGAAGGTTCGAGGT
* *
19044 TAAAATGGAATTTTTAGACA--TTCGAGGG
1 TAAAATGGAATTTTTGGA-AGGTTCGAGGT
*
19072 TAAAATGGTAATTTTTGGAAGGTTCGGGGT
1 TAAAATGG-AATTTTTGGAAGGTTCGAGGT
*
19102 CAAAAATGGAATTTTTG
1 -TAAAATGGAATTTTTG
19119 AAAACTTCAA
Statistics
Matches: 110, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
28 23 0.21
29 34 0.31
30 39 0.35
31 14 0.13
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (29 bp):
TAAAATGGAATTTTTGGAAGGTTCGAGGT
Found at i:19015 original size:59 final size:59
Alignment explanation
Indices: 18943--19117 Score: 298
Period size: 59 Copynumber: 3.0 Consensus size: 59
18933 GGTAACTTTG
* *
18943 GACATTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATAGAATTTTTA
1 GACATTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTTA
*
19002 GACATCCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTT-AAAATGGAATTTTTA
1 GACATTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTTA
* *
19060 GACATTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGAATTTTT
1 GACATTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTT
19118 GAAAACTTCA
Statistics
Matches: 109, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
58 54 0.50
59 55 0.50
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (59 bp):
GACATTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTTA
Found at i:20476 original size:58 final size:58
Alignment explanation
Indices: 20403--20517 Score: 185
Period size: 58 Copynumber: 2.0 Consensus size: 58
20393 AATTGGTTTA
* *
20403 TATTCTGGCTTTATAGTCATGTTTACAATTATTCTCTCTTGTTTCTTTCAATTTAATC
1 TATTCTGGCTTTATAGCCATGTTTACAATGATTCTCTCTTGTTTCTTTCAATTTAATC
* * *
20461 TATTTTGGCTTTATAGCCATGTTTACAATGATTCTTTGTTGTTTCTTTCAATTTAAT
1 TATTCTGGCTTTATAGCCATGTTTACAATGATTCTCTCTTGTTTCTTTCAATTTAAT
20518 GTCTGTCTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.21, C:0.15, G:0.10, T:0.54
Consensus pattern (58 bp):
TATTCTGGCTTTATAGCCATGTTTACAATGATTCTCTCTTGTTTCTTTCAATTTAATC
Found at i:21576 original size:209 final size:206
Alignment explanation
Indices: 21090--21624 Score: 612
Period size: 208 Copynumber: 2.6 Consensus size: 206
21080 GGTAATCGCA
* * * *
21090 TTATTGCTTCGACTTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTTGAAGATTTGCTTACTTT
1 TTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCT-GGATTCGAAG-TTTGCTCACTTT
*** * * *
21155 GAGCTTGGTTTCATTGATTTGGCCTTCTTCTTAGTGTCTCATCAGGAAGATGACTGCATCACTTG
64 GAGCTTAACTTCATTGATTTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGACTACATCACTTG
* * * * * * * *
21220 TTTCAATCTTCTTTTGAATCTCATCAGAAAGGCGAATTTTGGTTCACTTCTTAGTATTTTATCAG
129 TTTCAATATGCTTTTGAATCTCATCAGAAAGACGAATTTTGGTCCACTTCTCAGTATCTCACCAG
21285 GAAGCTAACCATT
194 GAAGCTAACCATT
* * * *
21298 TTATTGCTTCGTCCTGCTTCTCAGTATCTCATCAGGAAGTTGGAGTTCAAAGTTTTGCTCACTTT
1 TTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGA-TTCGAAG-TTTGCTCACTTT
* * * *
21363 GAGCTTAACTTCATTGATTTGGTCTTCTTCTCAGTATTTCATTAGGAAGATGACTATATCACTTG
64 GAGCTTAACTTCATTGATTTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGACTACATCACTTG
* *
21428 TTTCAATATGCTTCTCTGTATCTCATCAGGAAGACGAA-TTTGGTCCACTTCTCAGTATCTCACC
129 TTTCAATATGCTT-T-TGAATCTCATCAGAAAGACGAATTTTGGTCCACTTCTCAGTATCTCACC
21492 AGGAAGCTAACCATT
192 AGGAAGCTAACCATT
** * *
21507 TTATTGCTTTAACCTGCTTCTTAGTATCTCATCAGGAAGCTGAGATTCGAAGTTTCGCTCGCATT
1 TTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTG-GATTCGAAGTTT-GCTCACTTT
* * *
21572 GAGCTCT--GTTCCATTGAGTT-G-ATTCCCTTCTCAGTATCTCATCAGGAAGATGA
64 GAGCT-TAACTT-CATTGATTTGGCCTT--CTTCTCAGTATCTCATCAGGAAGATGA
21625 TCGCGTCACT
Statistics
Matches: 276, Mismatches: 42, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
207 4 0.01
208 125 0.45
209 125 0.45
210 22 0.08
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (206 bp):
TTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGATTCGAAGTTTGCTCACTTTGA
GCTTAACTTCATTGATTTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGACTACATCACTTGTT
TCAATATGCTTTTGAATCTCATCAGAAAGACGAATTTTGGTCCACTTCTCAGTATCTCACCAGGA
AGCTAACCATT
Found at i:33722 original size:29 final size:30
Alignment explanation
Indices: 33644--33822 Score: 83
Period size: 29 Copynumber: 6.1 Consensus size: 30
33634 AAACGGTAAC
* *
33644 TTTAGACATTCAGGGGC-AAAATGGTAATT
1 TTTAGACATTCGGGGGCAAAAATGGAAATT
* * *
33673 TTTGGA-AGGTTCGGAGTCAAAAAT-GAAATT
1 TTTAGACA--TTCGGGGGCAAAAATGGAAATT
*
33703 TTTAGACATTCGGGGGC-AAAATGGTAA-T
1 TTTAGACATTCGGGGGCAAAAATGGAAATT
* * **
33731 TTTGGA-AGGTTC-GAGGTTAAAATGG-AATT
1 TTTAGACA--TTCGGGGGCAAAAATGGAAATT
* * *
33760 TTTAGACATTCGAGGG-TAAAATGGTAATT
1 TTTAGACATTCGGGGGCAAAAATGGAAATT
* * *
33789 TTTGGA-AGGTTCGGGGTCAAAAATAG-AATT
1 TTTAGACA--TTCGGGGGCAAAAATGGAAATT
33819 TTTA
1 TTTA
33823 AAAACTTCAG
Statistics
Matches: 114, Mismatches: 21, Indels: 29
0.70 0.13 0.18
Matches are distributed among these distances:
27 1 0.01
28 29 0.25
29 42 0.37
30 30 0.26
31 12 0.11
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (30 bp):
TTTAGACATTCGGGGGCAAAAATGGAAATT
Found at i:33733 original size:28 final size:29
Alignment explanation
Indices: 33625--33791 Score: 121
Period size: 28 Copynumber: 5.8 Consensus size: 29
33615 TTTTGGATGC
* * *
33625 TCGGGGGTAAAACGGTAA-CTTTAGACAT
1 TCGGGGGCAAAATGGTAATTTTTAGACAT
* *
33653 TCAGGGGCAAAATGGTAATTTTTGGA-AGGT
1 TCGGGGGCAAAATGGTAATTTTTAGACA--T
* * *
33683 TCGGAGTCAAAAAT-GAAATTTTTAGACAT
1 TCGGGGGC-AAAATGGTAATTTTTAGACAT
*
33712 TCGGGGGCAAAATGGTAA-TTTTGGA-AGGT
1 TCGGGGGCAAAATGGTAATTTTTAGACA--T
* **
33741 TCGAGGTTAAAATGG-AATTTTTAGACAT
1 TCGGGGGCAAAATGGTAATTTTTAGACAT
* *
33769 TCGAGGGTAAAATGGTAATTTTT
1 TCGGGGGCAAAATGGTAATTTTT
33792 GGAAGGTTCG
Statistics
Matches: 109, Mismatches: 19, Indels: 21
0.73 0.13 0.14
Matches are distributed among these distances:
27 1 0.01
28 44 0.40
29 41 0.38
30 17 0.16
31 6 0.06
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.31
Consensus pattern (29 bp):
TCGGGGGCAAAATGGTAATTTTTAGACAT
Found at i:33792 original size:58 final size:58
Alignment explanation
Indices: 33644--33822 Score: 256
Period size: 59 Copynumber: 3.1 Consensus size: 58
33634 AAACGGTAAC
*
33644 TTTAGACATTC-AGGGGCAAAATGGTAATTTTTGGAAGGTTCGGAGTCAAAAATGAAATT
1 TTTAGACATTCGA-GGGCAAAATGGTAATTTTTGGAAGGTTCGG-GTCAAAAATGGAATT
* *
33703 TTTAGACATTCGGGGGCAAAATGGTAA-TTTTGGAAGGTTCGAGGT-TAAAATGGAATT
1 TTTAGACATTCGAGGGCAAAATGGTAATTTTTGGAAGGTTCG-GGTCAAAAATGGAATT
* *
33760 TTTAGACATTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATAGAATT
1 TTTAGACATTCGAGGGCAAAATGGTAATTTTTGGAAGGTTC-GGGTCAAAAATGGAATT
33819 TTTA
1 TTTA
33823 AAAACTTCAG
Statistics
Matches: 108, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
57 35 0.32
58 32 0.30
59 41 0.38
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (58 bp):
TTTAGACATTCGAGGGCAAAATGGTAATTTTTGGAAGGTTCGGGTCAAAAATGGAATT
Found at i:34545 original size:17 final size:17
Alignment explanation
Indices: 34525--34559 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
34515 TTTTAAAAGA
*
34525 TGTTTTTTATTATTATT
1 TGTTTTCTATTATTATT
*
34542 TGTTTTCTGTTATTATT
1 TGTTTTCTATTATTATT
34559 T
1 T
34560 AAAAAAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (17 bp):
TGTTTTCTATTATTATT
Found at i:35532 original size:17 final size:16
Alignment explanation
Indices: 35511--35589 Score: 68
Period size: 17 Copynumber: 4.7 Consensus size: 16
35501 TAGAATAATT
35511 ATAAATTTAAACTTAA
1 ATAAATTTAAACTTAA
*
35527 ATTAAATTTAAATTTTAA
1 A-TAAATTTAAA-CTTAA
* * *
35545 AAAAAATTAAATTTAAA
1 ATAAATTTAAACTT-AA
* *
35562 ATAAATTCAATCTTGAA
1 ATAAATTTAAACTT-AA
35579 ATAAATTTAAA
1 ATAAATTTAAA
35590 ATGGGTTTAG
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
16 4 0.08
17 40 0.82
18 5 0.10
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (16 bp):
ATAAATTTAAACTTAA
Found at i:35561 original size:16 final size:17
Alignment explanation
Indices: 35534--35568 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
35524 TAAATTAAAT
35534 TTAAATTTTAAAAAAAA
1 TTAAATTTTAAAAAAAA
*
35551 TTAAA-TTTAAAATAAA
1 TTAAATTTTAAAAAAAA
35567 TT
1 TT
35569 CAATCTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAATTTTAAAAAAAA
Found at i:35589 original size:34 final size:34
Alignment explanation
Indices: 35511--35589 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
35501 TAGAATAATT
* *
35511 ATAAATTTAAACTTAAATTAAATTTAAATTTTAA
1 ATAAATTTAAACTTAAAATAAATTTAAATTTGAA
* * * *
35545 AAAAAATTAAATTTAAAATAAA-TTCAATCTTGAA
1 ATAAATTTAAACTTAAAATAAATTTAAAT-TTGAA
35579 ATAAATTTAAA
1 ATAAATTTAAA
35590 ATGGGTTTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
33 5 0.14
34 31 0.86
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (34 bp):
ATAAATTTAAACTTAAAATAAATTTAAATTTGAA
Found at i:36920 original size:3 final size:3
Alignment explanation
Indices: 36912--36936 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
36902 TAAACGATAT
36912 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
36937 ACTAGTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:57417 original size:39 final size:39
Alignment explanation
Indices: 57236--57426 Score: 213
Period size: 39 Copynumber: 4.9 Consensus size: 39
57226 AGTCTGGTAA
* * * * * *
57236 TGTTTACAGTGTGACTACCTA-TTCAATATAGCATTACGG
1 TGTTTACAGTGTCACTGCC-AGTTCAGTATTGCATTGCAG
* * * * *
57275 TGTTTACAGTGTTACCGCCAGTTCAATATGGCAGTGCAG
1 TGTTTACAGTGTCACTGCCAGTTCAGTATTGCATTGCAG
* * *
57314 TGTTTACAGTGTCACTACCAGTTCAGTTTTGCATTGTAG
1 TGTTTACAGTGTCACTGCCAGTTCAGTATTGCATTGCAG
* *
57353 TGTTTATAGTGTCACTGCCAGTTCAGTATTGCATTGTAG
1 TGTTTACAGTGTCACTGCCAGTTCAGTATTGCATTGCAG
*
57392 TGTTTACAGTGTCACTGCCAATTCAGTATTGCATT
1 TGTTTACAGTGTCACTGCCAGTTCAGTATTGCATT
57427 CGACATGGAT
Statistics
Matches: 131, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
38 1 0.01
39 130 0.99
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (39 bp):
TGTTTACAGTGTCACTGCCAGTTCAGTATTGCATTGCAG
Found at i:57888 original size:72 final size:72
Alignment explanation
Indices: 57812--57959 Score: 208
Period size: 72 Copynumber: 2.1 Consensus size: 72
57802 TACGCTAAAT
* * * * *
57812 CACAAAACAGTTTGCATACACGGTCT-AGGACACGCCCATTTGTCCAGCCCGTGTGTCTCAAGTT
1 CACAAAACAGTATGCACACACGGTCTGACG-CACGCCCATGTGTCCAGCCCGTGTGTCTCAAGTC
57876 AGTATACA
65 AGTATACA
* * *
57884 CACAAAACAGTATGCACACACGGTTTGACGCACGTCCATGTGTCCAGCCCTTGTGTCTCAAGTCA
1 CACAAAACAGTATGCACACACGGTCTGACGCACGCCCATGTGTCCAGCCCGTGTGTCTCAAGTCA
57949 GTATACA
66 GTATACA
57956 CACA
1 CACA
57960 CGGTCTAGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
72 65 0.97
73 2 0.03
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (72 bp):
CACAAAACAGTATGCACACACGGTCTGACGCACGCCCATGTGTCCAGCCCGTGTGTCTCAAGTCA
GTATACA
Found at i:59970 original size:21 final size:21
Alignment explanation
Indices: 59944--59996 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
59934 TGCGAGCTAG
59944 TTATATGTTGTGTGAACTCTT
1 TTATATGTTGTGTGAACTCTT
* *
59965 TTATATGCTATGTGAACTCTT
1 TTATATGTTGTGTGAACTCTT
*
59986 TTAGATGTTGT
1 TTATATGTTGT
59997 ACGAACATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (21 bp):
TTATATGTTGTGTGAACTCTT
Found at i:60910 original size:31 final size:29
Alignment explanation
Indices: 60875--60940 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
60865 CATGCATGTG
60875 AACTGTATATATATGTGAACCGTTATATGCA
1 AACTGT-T-TATATGTGAACCGTTATATGCA
* * *
60906 AACTGTTTATGTGTGAACTGTTGTATGCA
1 AACTGTTTATATGTGAACCGTTATATGCA
60935 AACTGT
1 AACTGT
60941 CTAAGTGCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 25 0.78
30 1 0.03
31 6 0.19
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (29 bp):
AACTGTTTATATGTGAACCGTTATATGCA
Found at i:66617 original size:24 final size:24
Alignment explanation
Indices: 66589--66670 Score: 128
Period size: 24 Copynumber: 3.4 Consensus size: 24
66579 GACTAATAAG
* *
66589 AGTTTGATTGAAACAAATAAACAT
1 AGTTTAATTGAAACAAATAAACAA
* *
66613 AGTTTAATTGAAACAAATAAATAG
1 AGTTTAATTGAAACAAATAAACAA
66637 AGTTTAATTGAAACAAATAAACAA
1 AGTTTAATTGAAACAAATAAACAA
66661 AGTTTAATTG
1 AGTTTAATTG
66671 GAAGATTATT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.30
Consensus pattern (24 bp):
AGTTTAATTGAAACAAATAAACAA
Found at i:70279 original size:12 final size:12
Alignment explanation
Indices: 70262--70288 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
70252 AGCATACAGA
70262 TTACTATCATTC
1 TTACTATCATTC
70274 TTACTATCATTC
1 TTACTATCATTC
70286 TTA
1 TTA
70289 GGTAGAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (12 bp):
TTACTATCATTC
Done.