Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014251.1 Kokia drynarioides strain JFW-HI SEQ_129284, 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: 30107
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Warning! 52 characters in sequence are not A, C, G, or T
Found at i:66 original size:12 final size:11
Alignment explanation
Indices: 32--71 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
22 ATCTTTTTTA
32 TTTAAA-TAAT
1 TTTAAATTAAT
42 TTTAAATTAAT
1 TTTAAATTAAT
53 TTTAAATGTAA-
1 TTTAAAT-TAAT
64 TTTAAATT
1 TTTAAATT
72 TCAACTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.25
11 18 0.64
12 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TTTAAATTAAT
Found at i:199 original size:16 final size:16
Alignment explanation
Indices: 162--197 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
152 CATTAATTTC
*
162 TAAATTAATTTTAACT
1 TAAATTAATTTTAAAT
178 TAAATTAATTTTCAAAT
1 TAAATTAATTTT-AAAT
195 TAA
1 TAA
198 TTTTTACACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATTAATTTTAAAT
Found at i:210 original size:28 final size:28
Alignment explanation
Indices: 153--210 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
143 AAACATGTTC
**
153 ATTAATTTCTAAATTAATTTTAACTTAA
1 ATTAATTTCTAAATTAATTTTAACACAA
*
181 ATTAATTT-TCAAATTAATTTTTACACAA
1 ATTAATTTCT-AAATTAATTTTAACACAA
209 AT
1 AT
211 ATTCTTCGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTAATTTCTAAATTAATTTTAACACAA
Found at i:11887 original size:15 final size:15
Alignment explanation
Indices: 11863--11896 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11853 AATTCATTTT
11863 CTATAAAGTAAATTA
1 CTATAAAGTAAATTA
*
11878 CTATAGAGTAAATTA
1 CTATAAAGTAAATTA
11893 -TATA
1 CTATA
11897 TTTTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (15 bp):
CTATAAAGTAAATTA
Found at i:15266 original size:29 final size:29
Alignment explanation
Indices: 15237--15407 Score: 118
Period size: 29 Copynumber: 5.8 Consensus size: 29
15227 CATTCGAGGG
* *
15237 TAAAAGGGTAATTTTTGAAAGTTTTTGGGT
1 TAAAATGGTAA-TTTTGAAAGTTTTGGGGT
* *
15267 TAAAAATGG-AATTTTGGAAG-TTTGGGGG
1 T-AAAATGGTAATTTTGAAAGTTTTGGGGT
*
15295 TAAAATAGTAAATTTTGAAAGTTTTGGGGT
1 TAAAATGGT-AATTTTGAAAGTTTTGGGGT
* * * *
15325 TAAAAATGG-AATTTT-AGAGGTTCGGGGG
1 T-AAAATGGTAATTTTGAAAGTTTTGGGGT
* * *
15353 TAAAATGGTAATTTTTGGAAGTTTCGAGGT
1 TAAAATGGTAA-TTTTGAAAGTTTTGGGGT
*
15383 CAAAAGTGG-AATTTTAGAGAAGTTT
1 TAAAA-TGGTAATTTT-GA-AAGTTT
15408 AGAGATCAAA
Statistics
Matches: 111, Mismatches: 19, Indels: 21
0.74 0.13 0.14
Matches are distributed among these distances:
27 13 0.12
28 19 0.17
29 32 0.29
30 26 0.23
31 21 0.19
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.36
Consensus pattern (29 bp):
TAAAATGGTAATTTTGAAAGTTTTGGGGT
Found at i:15298 original size:58 final size:58
Alignment explanation
Indices: 15234--15407 Score: 215
Period size: 58 Copynumber: 3.0 Consensus size: 58
15224 GGACATTCGA
* *
15234 GGGTAAAAGGGTAATTTTTGAAAGTTTTTGGGTTAAAAATGGAATTTTGGAAGTTTGG
1 GGGTAAAATGGTAATTTTTGAAAGTTTTCGGGTTAAAAATGGAATTTTGGAAGTTTGG
* * * * * *
15292 GGGTAAAATAGTAAATTTTGAAAGTTTTGGGGTTAAAAATGGAATTTTAGAGGTTCGG
1 GGGTAAAATGGTAATTTTTGAAAGTTTTCGGGTTAAAAATGGAATTTTGGAAGTTTGG
* * *
15350 GGGTAAAATGGTAATTTTTGGAAG-TTTCGAGGTCAAAAGTGGAATTTTAGAGAAGTTT
1 GGGTAAAATGGTAATTTTTGAAAGTTTTCG-GGTTAAAAATGGAATTTT-G-GAAGTTT
15408 AGAGATCAAA
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
57 4 0.04
58 88 0.91
60 5 0.05
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.36
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGAAAGTTTTCGGGTTAAAAATGGAATTTTGGAAGTTTGG
Found at i:15396 original size:30 final size:28
Alignment explanation
Indices: 15210--15407 Score: 93
Period size: 29 Copynumber: 6.8 Consensus size: 28
15200 ATCGGGATCA
*
15210 AAAAAGGAATTTTTGGACA--TTCGAGGGT
1 AAAATGGAATTTTTGGA-AGTTTCGA-GGT
* * *
15238 AAAAGGGTAATTTTTGAAAGTTTTTG-GGTT
1 AAAATGG-AATTTTTGGAAG-TTTCGAGG-T
* *
15268 AAAAATGGAA-TTTTGGAAGTTTGGGGGT
1 -AAAATGGAATTTTTGGAAGTTTCGAGGT
* * * * *
15296 AAAATAGTAAATTTTGAAAGTTTTGGGGTT
1 AAAAT-GGAATTTTTGGAAGTTTCGAGG-T
* * *
15326 AAAAATGGAA-TTTTAG-AGGTTCGGGGGT
1 -AAAATGGAATTTTTGGAAGTTTC-GAGGT
15354 AAAATGGTAATTTTTGGAAGTTTCGAGGT
1 AAAATGG-AATTTTTGGAAGTTTCGAGGT
*
15383 CAAAAGTGGAATTTTAGAGAAGTTT
1 -AAAA-TGGAATTTTTG-GAAGTTT
15408 AGAGATCAAA
Statistics
Matches: 134, Mismatches: 18, Indels: 33
0.72 0.10 0.18
Matches are distributed among these distances:
27 12 0.09
28 22 0.16
29 53 0.40
30 23 0.17
31 24 0.18
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.35
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGT
Found at i:15426 original size:30 final size:30
Alignment explanation
Indices: 15361--15427 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
15351 GGTAAAATGG
* * * *
15361 TAATTTTTGGAAGTTTCGAGGTCAAAAGTG
1 TAATTTTAGGAAGTTTAGAGATCAAAAGTA
*
15391 GAATTTTAGAGAAGTTTAGAGATCAAAA-TA
1 TAATTTTAG-GAAGTTTAGAGATCAAAAGTA
15421 TAATTTT
1 TAATTTT
15428 TTGACAGTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.37
Consensus pattern (30 bp):
TAATTTTAGGAAGTTTAGAGATCAAAAGTA
Found at i:16523 original size:12 final size:12
Alignment explanation
Indices: 16506--16530 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16496 ATATTACTAT
16506 TTATTATTAATA
1 TTATTATTAATA
16518 TTATTATTAATA
1 TTATTATTAATA
16530 T
1 T
16531 CAATAAGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:18280 original size:206 final size:205
Alignment explanation
Indices: 18016--18748 Score: 1128
Period size: 206 Copynumber: 3.6 Consensus size: 205
18006 NNNNNNNNNN
* * *
18016 ATTGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGTTGGGATTCGAAGATTTGCTCACATCGA
1 ATTGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGATTCGAAGATTTGCTCACATCGA
* *
18081 GCGTGGGTTTGATTTGCTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTTTCA
66 GCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGAGTCGTTTGTTTCA
** * *
18146 ATCCACTTCTCTGTATCTCATCAAGAAGATGAATTTGGTCCACTTCTCGTTATCTCATCAGGAAG
131 ATCTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCG-TATCTCATCAGGAAG
*
18211 CTAATCATTTT
195 CTAACCATTTT
* * ** *
18222 AATGCTTCGACCAGCTTCTCAGTATCTCATCAGAAAATTAGGATTCGAAGATTTGCTCACATCGA
1 ATTGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGATTCGAAGATTTGCTCACATCGA
* * *
18287 GCGTGGGTTTGATTTGGTCTTCTTCTTAGTGTCTCATCAGGAAGATGACCGCA-TCGTTTATTTC
66 GCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCG-AGTCGTTTGTTTC
*
18351 AATCTGCTTCTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAA
130 AATCTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTC-GTATCTCATCAGGAA
18416 GCTAACCATTTT
194 GCTAACCATTTT
*
18428 ATTGCTTCGACCCGCTTCTCAGTATCTCATCA-AGAAGCTGGGATTCGAAGATTTGCTCACATCG
1 ATTGCTTCGACCTGCTTCTCAGTATCTCATCAGA-AAGCTGGGATTCGAAGATTTGCTCACATCG
* * *
18492 AGCATGGATTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACCGAGTCGTTTGTTTC
65 AGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGAGTCGTTTGTTTC
* * *
18557 AATCTGCTTCTCTGTATCTCGTCAGGAAGACGAATTTGGTCCGCTTCTCAATATCTCATCAGGAA
130 AATCTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTC-GTATCTCATCAGGAA
18622 GCTAACCATTTT
194 GCTAACCATTTT
* * * *
18634 ATTGCTTCGACCTGCTTCTCAGTATCACATTAGGAAGCTGTGATTCGAAGATTTGCTCACATCGA
1 ATTGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGATTCGAAGATTTGCTCACATCGA
*
18699 GCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACC
66 GCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACC
18749 ACCACACTAT
Statistics
Matches: 481, Mismatches: 41, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
205 2 0.00
206 478 0.99
207 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (205 bp):
ATTGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGATTCGAAGATTTGCTCACATCGA
GCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGAGTCGTTTGTTTCA
ATCTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCGTATCTCATCAGGAAGC
TAACCATTTT
Found at i:18944 original size:77 final size:77
Alignment explanation
Indices: 18773--18994 Score: 257
Period size: 77 Copynumber: 2.9 Consensus size: 77
18763 GAATAATCAC
** * * * * *
18773 AATCTGCCCCGTGATCGGGGTAGGAGTTTGGTTGACGATGATCTGCCTCATGCTCGGGGTAAGAG
1 AATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCC-CAAGCTCGGGGTAAGAG
*
18838 ATCGAATGGCTAT
65 ATCAAATGGCTAT
* ** * * * * *
18851 AATCTGCCTCTGGCTCGGGGTAAGAGATTGGTTGATAATGATTTGCCCAGGCTCGGGATAAAAGA
1 AATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCAAGCTCGGGGTAAGAGA
18916 TCAAATGGCT-T
66 TCAAATGGCTAT
*
18927 CAATTTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAGA
1 -AATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATGATGATCTG-CCCAAGCTCGGGGTAAGA
18992 GAT
64 GAT
18995 TGGTTAACAA
Statistics
Matches: 120, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
76 1 0.01
77 63 0.52
78 56 0.47
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (77 bp):
AATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCAAGCTCGGGGTAAGAGA
TCAAATGGCTAT
Found at i:18975 original size:39 final size:38
Alignment explanation
Indices: 18787--18999 Score: 148
Period size: 39 Copynumber: 5.5 Consensus size: 38
18777 TGCCCCGTGA
* * * * *
18787 TCGGGGTAGGAGTTTGGTTGACGATGATCTGCCTCATGC
1 TCGGGGTAAGAGATTGGTTGA-TATGATCTGCCCCAAGC
* * * * * * **
18826 TCGGGGTAAGAGATCGAATGGCTATAATCTGCCTCTGGC
1 TCGGGGTAAGAGATTG-GTTGATATGATCTGCCCCAAGC
* *
18865 TCGGGGTAAGAGATTGGTTGATAATGATTTG-CCCAGGC
1 TCGGGGTAAGAGATTGGTTGAT-ATGATCTGCCCCAAGC
* * *
18903 TCGGGATAAAAGATCAAATGGCTTCA-AT--T-TGCCCCAAGC
1 TCGGGGTAAGAGAT----TGG-TTGATATGATCTGCCCCAAGC
18942 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGC
1 TCGGGGTAAGAGATTGGTTGAT-ATGATCTGCCCCAAGC
18981 TCGGGGTAAGAGATTGGTT
1 TCGGGGTAAGAGATTGGTT
19000 AACAATGTAC
Statistics
Matches: 136, Mismatches: 25, Indels: 26
0.73 0.13 0.14
Matches are distributed among these distances:
34 3 0.02
35 3 0.02
36 2 0.01
38 23 0.17
39 95 0.70
40 2 0.01
41 2 0.01
42 3 0.02
43 3 0.02
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.27
Consensus pattern (38 bp):
TCGGGGTAAGAGATTGGTTGATATGATCTGCCCCAAGC
Found at i:19206 original size:101 final size:101
Alignment explanation
Indices: 19077--19262 Score: 282
Period size: 101 Copynumber: 1.8 Consensus size: 101
19067 TTCAACTTCG
* * * * * *
19077 CTGTAACTTCAGGAAGATAGGATTTGATGTTGATGCTTCATCTTGCTCTTACTATAACTTCAGAG
1 CTGTAACTTCAAGAAGATAGGAATTGATGTTAACGATTCATCTTGCTCTTACTACAACTTCAGAG
*
19142 AGATAAAGACTTGCTATTGTTTTTAATCCGACTTTA
66 AGATAAAGACTTGCCATTGTTTTTAATCCGACTTTA
* * *
19178 CTGTAACTTCAAGAGGATAGGAATTGATGTTAACGATTCATCTTGCTCTTGCTGCAACTTCAGAG
1 CTGTAACTTCAAGAAGATAGGAATTGATGTTAACGATTCATCTTGCTCTTACTACAACTTCAGAG
19243 AGATAAAGACTTGCCATTGT
66 AGATAAAGACTTGCCATTGT
19263 AGTTTTGATT
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 75 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (101 bp):
CTGTAACTTCAAGAAGATAGGAATTGATGTTAACGATTCATCTTGCTCTTACTACAACTTCAGAG
AGATAAAGACTTGCCATTGTTTTTAATCCGACTTTA
Found at i:19487 original size:100 final size:99
Alignment explanation
Indices: 19356--19606 Score: 255
Period size: 100 Copynumber: 2.5 Consensus size: 99
19346 CGGGTTTGCC
** *
19356 ATTGCGACTTAAACATTT-CCTTTTCAAATCTTCGTGGTACTGGATTCGCCGTTGCGG-CTTAAA
1 ATTGCGACTTAAACATTTCCCTTTT-GTATCTTCGTGGTACTGGATCCGCCGTTGCGGTCTT-AA
* * *
19419 TATTTCTCTTCT-TGTCTTTTGAGCT-TTAGAGTCTG-T
64 TATTTCCCTT-TATGTC-TTTGAGCTACTAG-GTCCGCT
* * * * *
19455 CGTTGCGACTTAAACTTTTCCCTTTTGTATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTGAT
1 -ATTGCGACTTAAACATTTCCCTTTTGTATCTTCGTGGTACTGGATCCGCCGTTGCGGTCTTAAT
* *
19520 CTTTCCCTTTATGTCTTTGAGGTACTAGGTCCGCT
65 ATTTCCCTTTATGTCTTTGAGCTACTAGGTCCGCT
* * *
19555 ATTACGACTTAAACCTTTCCC--TTGTGTCTTCGTGGTACTGGATCCGCCGTTG
1 ATTGCGACTTAAACATTTCCCTTTTGTATCTTCGTGGTACTGGATCCGCCGTTG
19607 TGATTTAGAT
Statistics
Matches: 127, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
97 28 0.22
99 30 0.24
100 60 0.47
101 9 0.07
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (99 bp):
ATTGCGACTTAAACATTTCCCTTTTGTATCTTCGTGGTACTGGATCCGCCGTTGCGGTCTTAATA
TTTCCCTTTATGTCTTTGAGCTACTAGGTCCGCT
Found at i:19511 original size:50 final size:50
Alignment explanation
Indices: 19353--19602 Score: 142
Period size: 50 Copynumber: 5.1 Consensus size: 50
19343 TATCGGGTTT
* ** * *
19353 GCCATTGCGACTTAAACATTT-CCTTTTCAAATCTTCGTGGTACTGGATTC
1 GCCATTGCGACTTAAACTTTTCCCTTTT-GTATCTTTGTGGTACTGGATCC
* * * * * * * * *
19403 GCCGTTGCGGCTTAAA-TATTTCTCTTCTTGTCT-TTTGAGCT-TTAGAGTCT
1 GCCATTGCGACTTAAACT-TTTCCCTT-TTGTATCTTTGTGGTACTGGA-TCC
* *
19453 GTCGTTGCGACTTAAACTTTTCCCTTTTGTATCTTTGTGGTACTGGATCC
1 GCCATTGCGACTTAAACTTTTCCCTTTTGTATCTTTGTGGTACTGGATCC
* * * *
19503 GCCATTGCGGTCTTGATC-TTTCCCTTTATG--TCTTTGAGGTACTAGG-TCC
1 GCCATTGC-GACTTAAACTTTTCCCTTT-TGTATCTTTGTGGTACT-GGATCC
* * * * *
19552 GCTATTACGACTTAAACCTTTCCC--TTGTGTCTTCGTGGTACTGGATCC
1 GCCATTGCGACTTAAACTTTTCCCTTTTGTATCTTTGTGGTACTGGATCC
19600 GCC
1 GCC
19603 GTTGTGATTT
Statistics
Matches: 149, Mismatches: 37, Indels: 30
0.69 0.17 0.14
Matches are distributed among these distances:
46 2 0.01
47 3 0.02
48 22 0.15
49 35 0.23
50 69 0.46
51 16 0.11
52 2 0.01
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.41
Consensus pattern (50 bp):
GCCATTGCGACTTAAACTTTTCCCTTTTGTATCTTTGTGGTACTGGATCC
Found at i:19573 original size:49 final size:49
Alignment explanation
Indices: 19460--19602 Score: 132
Period size: 49 Copynumber: 2.9 Consensus size: 49
19450 TCTGTCGTTG
* * *
19460 CGACTTAAACTTTTCCCTTTTGTATCTTTGTGGTACTGGATCCGCCATTG
1 CGACTTAAACCTTTCCCTTTTG-ATCTTTGAGGTACTGGATCCGCCATTA
* * * *
19510 CGGTCTT-GATCTTTCCCTTTATG-TCTTTGAGGTACTAGG-TCCGCTATTA
1 C-GACTTAAACCTTTCCCTTT-TGATCTTTGAGGTACT-GGATCCGCCATTA
* * *
19559 CGACTTAAACCTTTCCCTTGTG-TCTTCGTGGTACTGGATCCGCC
1 CGACTTAAACCTTTCCCTTTTGATCTTTGAGGTACTGGATCCGCC
19603 GTTGTGATTT
Statistics
Matches: 74, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
47 2 0.03
48 22 0.30
49 31 0.42
50 13 0.18
51 6 0.08
ACGTcount: A:0.15, C:0.26, G:0.20, T:0.40
Consensus pattern (49 bp):
CGACTTAAACCTTTCCCTTTTGATCTTTGAGGTACTGGATCCGCCATTA
Found at i:19621 original size:48 final size:49
Alignment explanation
Indices: 19471--19622 Score: 148
Period size: 48 Copynumber: 3.1 Consensus size: 49
19461 GACTTAAACT
* *
19471 TTTCCCTTTTGTATCTTTGTGGTACTGGATCCGCCATTGCGGTCTT-GATC
1 TTTCCC-TTTGTGTCTTTGTGGTACTGGATCCGCCATTGCGAT-TTAGATC
* * * * * * *
19521 TTTCCCTTTATGTCTTTGAGGTACTAGG-TCCGCTATTACGACTTAAACC
1 TTTCCCTTTGTGTCTTTGTGGTACT-GGATCCGCCATTGCGATTTAGATC
* * *
19570 TTTCCC-TTGTGTCTTCGTGGTACTGGATCCGCCGTTGTGATTTAGATC
1 TTTCCCTTTGTGTCTTTGTGGTACTGGATCCGCCATTGCGATTTAGATC
19618 TTTCC
1 TTTCC
19623 TTTTAAATCT
Statistics
Matches: 80, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
47 2 0.03
48 36 0.45
49 34 0.43
50 8 0.10
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.42
Consensus pattern (49 bp):
TTTCCCTTTGTGTCTTTGTGGTACTGGATCCGCCATTGCGATTTAGATC
Found at i:20888 original size:32 final size:32
Alignment explanation
Indices: 20840--20909 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
20830 TTTTTTCTAT
* * *
20840 TTTTTTTATTTTTCTTCTTGTTTTTGCTT-TTC
1 TTTTTTTATTTCTCTTCTTCTTCTT-CTTCTTC
*
20872 TTTTTTTCTTTCTCTTCTTCTTCTTCTTCTTC
1 TTTTTTTATTTCTCTTCTTCTTCTTCTTCTTC
20904 TTTTTT
1 TTTTTT
20910 GTTTTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 3 0.09
32 30 0.91
ACGTcount: A:0.01, C:0.19, G:0.03, T:0.77
Consensus pattern (32 bp):
TTTTTTTATTTCTCTTCTTCTTCTTCTTCTTC
Found at i:26521 original size:29 final size:29
Alignment explanation
Indices: 26357--26646 Score: 103
Period size: 29 Copynumber: 9.9 Consensus size: 29
26347 TTTGGATACC
*
26357 CGGGGGTAAAATTGTAA-TTTTGGAC-TT
1 CGGGGGTAAAATGGTAATTTTTGGACATT
** * *
26384 ATAGGGGTAAAATGGGAATTTTGGGA-AGTT
1 -CGGGGGTAAAATGGTAATTTTTGGACA-TT
* *** * *
26414 CGGGGTTAAAATCAAAATTTTTAGACACT
1 CGGGGGTAAAATGGTAATTTTTGGACATT
* * * * * *
26443 CTGGGGTAAAACGATAATTTTTAGAAAAAAT
1 CGGGGGTAAAATGGTAATTTTT-G-GACATT
** *
26474 CGGGATTAAAAACGG-AATTTTTGGACATT
1 CGGGGGT-AAAATGGTAATTTTTGGACATT
*
26503 CGGGGGTAAAATGGTAATTTTT-GAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGACA-TT
***
26532 TTTGGGTCAAAAATGG-AATTTTTGGA-AGTT
1 CGGGGGT--AAAATGGTAATTTTTGGACA-TT
* * **
26562 TGGGGGTAAAATAGTAATTTTTGAGAGGTT
1 CGGGGGTAAAATGGTAATTTTTG-GACATT
* * **
26592 C-GAGGTAAAAAAATGG-AATTTTTAGAGGTT
1 CGGGGGT---AAAATGGTAATTTTTGGACATT
*
26622 TGGGGGTAAAATGGTAATTTTTGGA
1 CGGGGGTAAAATGGTAATTTTTGGA
26647 AGTGTCGGTG
Statistics
Matches: 194, Mismatches: 48, Indels: 39
0.69 0.17 0.14
Matches are distributed among these distances:
28 35 0.18
29 83 0.43
30 30 0.15
31 34 0.18
32 12 0.06
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (29 bp):
CGGGGGTAAAATGGTAATTTTTGGACATT
Found at i:26557 original size:59 final size:58
Alignment explanation
Indices: 26445--26764 Score: 252
Period size: 60 Copynumber: 5.4 Consensus size: 58
26435 TAGACACTCT
* * *** * *
26445 GGGGTAAAACGATAATTTTTAGAAAAAATCGGGATTAAAAACGGAATTTTTGGACA-TTCG
1 GGGGTAAAATGGTAATTTTT-GAAAGTTTCGGG-TCAAAAATGGAATTTTTGGA-AGTTCG
* *
26505 GGGGTAAAATGGTAATTTTTGAAAGTTTTTGGGTCAAAAATGGAATTTTTGGAAGTTTG
1 GGGGTAAAATGGTAATTTTTGAAAG-TTTCGGGTCAAAAATGGAATTTTTGGAAGTTCG
* * * * * * *
26564 GGGGTAAAATAGTAATTTTTGAGAGGTTCGAGGTAAAAAAATGGAATTTTTAGAGGTTTG
1 GGGGTAAAATGGTAATTTTTGAAAGTTTCG-GGT-CAAAAATGGAATTTTTGGAAGTTCG
* * * *
26624 GGGGTAAAATGGTAATTTTTGGAAGTGTCGGTGTCAAAATTGGGATTTTTTGGAAGTTCG
1 GGGGTAAAATGGTAATTTTTGAAAGTTTCGG-GTCAAAAAT-GGAATTTTTGGAAGTTCG
* * * * * *
26684 AGGGTAAAAAT-CTAATTTTT-AGAAGTTTAAGGGTCAAAAGTGGAATTTTGGAGAAGTTTG
1 GGGGT-AAAATGGTAATTTTTGA-AAGTTT-CGGGTCAAAAATGGAATTTTTG-GAAGTTCG
*
26744 GGGGTCAAAAT-ATAATTTTTG
1 GGGGT-AAAATGGTAATTTTTG
26765 GATAGTTTAA
Statistics
Matches: 210, Mismatches: 39, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
58 4 0.02
59 65 0.31
60 134 0.64
61 7 0.03
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.34
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGAAAGTTTCGGGTCAAAAATGGAATTTTTGGAAGTTCG
Found at i:26731 original size:30 final size:28
Alignment explanation
Indices: 26506--26772 Score: 126
Period size: 30 Copynumber: 8.9 Consensus size: 28
26496 GGACATTCGG
**
26506 GGGTAAAATGGTAATTTTT-GAAAGTTTTT
1 GGGTAAAATGG-AATTTTTAG-AAGTTTGA
* *
26535 GGGTCAAAAATGGAATTTTTGGAAGTTTGG
1 GGGT--AAAATGGAATTTTTAGAAGTTTGA
* * *
26565 GGGTAAAATAGTAATTTTTGAGAGGTTCGA
1 GGGTAAAAT-GGAATTTTT-AGAAGTTTGA
* *
26595 -GGTAAAAAAATGGAATTTTTAGAGGTTTGG
1 GGGT---AAAATGGAATTTTTAGAAGTTTGA
* *
26625 GGGTAAAATGGTAATTTTTGGAAGTGTCG-
1 GGGTAAAATGG-AATTTTTAGAAGT-TTGA
* * * *
26654 GTGTCAAAATTGGGATTTTTTGGAAGTTCGA
1 GGGT-AAAA-T-GGAATTTTTAGAAGTTTGA
** *
26685 GGGTAAAAATCTAATTTTTAGAAGTTTAA
1 GGGT-AAAATGGAATTTTTAGAAGTTTGA
* *
26714 GGGTCAAAAGTGGAATTTTGGAGAAGTTTGG
1 GGGT-AAAA-TGGAATTTT-TAGAAGTTTGA
** *
26745 GGGTCAAAATATAATTTTTGGATAGTTT
1 GGGT-AAAATGGAATTTTTAGA-AGTTT
26773 AAGGACCTTC
Statistics
Matches: 187, Mismatches: 33, Indels: 35
0.73 0.13 0.14
Matches are distributed among these distances:
28 12 0.06
29 52 0.28
30 60 0.32
31 56 0.30
32 7 0.04
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (28 bp):
GGGTAAAATGGAATTTTTAGAAGTTTGA
Found at i:26764 original size:31 final size:30
Alignment explanation
Indices: 26504--26772 Score: 132
Period size: 29 Copynumber: 9.0 Consensus size: 30
26494 TTGGACATTC
*
26504 GGGGGT-AAAATGGTAATTTTTGA-AAGTTT
1 GGGGGTCAAAAT-ATAATTTTTGAGAAGTTT
**
26533 TTGGGTCAAAA-ATGGAATTTTTG-GAAGTTT
1 GGGGGTCAAAATAT--AATTTTTGAGAAGTTT
*
26563 GGGGGT-AAAATAGTAATTTTTGAG-AGGTT
1 GGGGGTCAAAATA-TAATTTTTGAGAAGTTT
* * * * *
26592 CGAGGTAAAAAAATGGAATTTTT-AGAGGTTT
1 GGGGGTCAAAATAT--AATTTTTGAGAAGTTT
* *
26623 GGGGGT-AAAATGGTAATTTTTG-GAAGTGT
1 GGGGGTCAAAAT-ATAATTTTTGAGAAGTTT
* * * *
26652 CGGTGTCAAAAT-TGGGATTTTTTG-GAAGTTC
1 GGGGGTCAAAATAT---AATTTTTGAGAAGTTT
* * *
26683 GAGGGTAAAAATCTAATTTTT-AGAAGTTT
1 GGGGGTCAAAATATAATTTTTGAGAAGTTT
** ** *
26712 AAGGGTCAAAAGTGGAATTTTGGAGAAGTTT
1 GGGGGTCAAAA-TATAATTTTTGAGAAGTTT
26743 GGGGGTCAAAATATAATTTTTG-GATAGTTT
1 GGGGGTCAAAATATAATTTTTGAGA-AGTTT
26773 AAGGACCTTC
Statistics
Matches: 180, Mismatches: 38, Indels: 43
0.69 0.15 0.16
Matches are distributed among these distances:
28 2 0.01
29 64 0.36
30 60 0.33
31 53 0.29
32 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (30 bp):
GGGGGTCAAAATATAATTTTTGAGAAGTTT
Found at i:27937 original size:12 final size:12
Alignment explanation
Indices: 27918--27966 Score: 80
Period size: 12 Copynumber: 4.1 Consensus size: 12
27908 ATATTACTAT
27918 TTATTATTAATA
1 TTATTATTAATA
* *
27930 TGATTATTAAAA
1 TTATTATTAATA
27942 TTATTATTAATA
1 TTATTATTAATA
27954 TTATTATTAATA
1 TTATTATTAATA
27966 T
1 T
27967 CAATAAGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TTATTATTAATA
Done.