Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007422.1 Kokia drynarioides strain JFW-HI SEQ_122042, 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: 97524
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:42 original size:15 final size:15
Alignment explanation
Indices: 22--71 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
12 TGGGTTTGGC
22 GGTGGAGCTGGTGCA
1 GGTGGAGCTGGTGCA
37 GGTGGAG--GGTTTGGC-
1 GGTGGAGCTGG--T-GCA
52 GGTGGAGCTGGTGCA
1 GGTGGAGCTGGTGCA
67 GGTGG
1 GGTGG
72 TGGGCTTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
13 2 0.07
14 2 0.07
15 21 0.72
16 2 0.07
17 2 0.07
ACGTcount: A:0.10, C:0.10, G:0.58, T:0.22
Consensus pattern (15 bp):
GGTGGAGCTGGTGCA
Found at i:48 original size:30 final size:30
Alignment explanation
Indices: 13--80 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
3 TGGAGGAGGT
13 GGGTTTGGCGGTGGAGCTGGTGCAGGTGGA
1 GGGTTTGGCGGTGGAGCTGGTGCAGGTGGA
*
43 GGGTTTGGCGGTGGAGCTGGTGCAGGTGGT
1 GGGTTTGGCGGTGGAGCTGGTGCAGGTGGA
*
73 GGGCTTGG
1 GGGTTTGG
81 AGGAGGACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.07, C:0.10, G:0.57, T:0.25
Consensus pattern (30 bp):
GGGTTTGGCGGTGGAGCTGGTGCAGGTGGA
Found at i:902 original size:120 final size:113
Alignment explanation
Indices: 682--903 Score: 275
Period size: 120 Copynumber: 1.9 Consensus size: 113
672 AAATGTCTAG
*
682 TTGAAATATTTCACATATAAAAATAATGATATTTGAAATAATTATTTTTATAATATTAGAATTTA
1 TTGAAATATTTCACATATAAAAATAATGATATTTGAAATAATTATTTTTATAATATTAGAATCTA
* * * * **
747 TCATACCCACAATGTAGGTGAAAATATAAGGATATTTGAAGCAATTAT
66 ACATACCCACAATATAGGTCAAAATAAAAAAATATTTGAAGCAATTAT
* *
795 TTGAAATATTTTACATATAAAAATAATAATGATATTTGAAATAATTATTTGATTTTATGATATTA
1 TTGAAATATTTCACATAT--AAA-AATAATGATATTTGAAATAATTA--T--TTTTATAATATTA
*
860 GAATCTAACATACCCACTATATAGG-CAAAATAAAACAAATATTT
59 GAATCTAACATACCCACAATATAGGTCAAAATAAAA-AAATATTT
904 TACATATAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
113 17 0.19
115 3 0.03
116 23 0.25
118 1 0.01
119 8 0.09
120 39 0.43
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (113 bp):
TTGAAATATTTCACATATAAAAATAATGATATTTGAAATAATTATTTTTATAATATTAGAATCTA
ACATACCCACAATATAGGTCAAAATAAAAAAATATTTGAAGCAATTAT
Found at i:11409 original size:84 final size:84
Alignment explanation
Indices: 11268--11436 Score: 338
Period size: 84 Copynumber: 2.0 Consensus size: 84
11258 ATTCACCAAG
11268 TAAGACCCGAATTTGAATCGCAAATTAATAATCCAGATTATATTTGAATAGAAAATACTATAACA
1 TAAGACCCGAATTTGAATCGCAAATTAATAATCCAGATTATATTTGAATAGAAAATACTATAACA
11333 AACCTTTTATTCTATAAAA
66 AACCTTTTATTCTATAAAA
11352 TAAGACCCGAATTTGAATCGCAAATTAATAATCCAGATTATATTTGAATAGAAAATACTATAACA
1 TAAGACCCGAATTTGAATCGCAAATTAATAATCCAGATTATATTTGAATAGAAAATACTATAACA
11417 AACCTTTTATTCTATAAAA
66 AACCTTTTATTCTATAAAA
11436 T
1 T
11437 TAATTCGATT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (84 bp):
TAAGACCCGAATTTGAATCGCAAATTAATAATCCAGATTATATTTGAATAGAAAATACTATAACA
AACCTTTTATTCTATAAAA
Found at i:17587 original size:89 final size:89
Alignment explanation
Indices: 17434--17610 Score: 309
Period size: 89 Copynumber: 2.0 Consensus size: 89
17424 CGAACTTCGA
*
17434 ATGTTATACGGTCAACTCCAAACTACTATCAATCAAACTAGATATTCACTCAATAACCCCTTTTT
1 ATGTTACACGGTCAACTCCAAACTACTATCAATCAAACTAGATATTCACTCAATAACCCCTTTTT
17499 TCAGGCAATTTCAGTTTTCTACGC
66 TCAGGCAATTTCAGTTTTCTACGC
* * *
17523 ATGTTACACGGTCAACTCCAAACTATTATCGATCAAACTAGATATTCACTCAATAACCCTTTTTT
1 ATGTTACACGGTCAACTCCAAACTACTATCAATCAAACTAGATATTCACTCAATAACCCCTTTTT
*
17588 TCAGTCAATTTCAGTTTTCTACG
66 TCAGGCAATTTCAGTTTTCTACG
17611 ATTCTAAAAC
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.35
Consensus pattern (89 bp):
ATGTTACACGGTCAACTCCAAACTACTATCAATCAAACTAGATATTCACTCAATAACCCCTTTTT
TCAGGCAATTTCAGTTTTCTACGC
Found at i:18168 original size:18 final size:19
Alignment explanation
Indices: 18147--18191 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
18137 AATAGTAATG
18147 ATAATAAAATTA-AATACA
1 ATAATAAAATTATAATACA
* *
18165 ATAATAATATTATAATATA
1 ATAATAAAATTATAATACA
18184 A-AATAAAA
1 ATAATAAAA
18192 AATATAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAATAAAATTATAATACA
Found at i:50486 original size:11 final size:10
Alignment explanation
Indices: 50460--50484 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
50450 GACAAAAGAG
50460 AAAAATAAAA
1 AAAAATAAAA
50470 AAAAATAAAA
1 AAAAATAAAA
50480 AAAAA
1 AAAAA
50485 ATTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:57797 original size:26 final size:26
Alignment explanation
Indices: 57748--57855 Score: 110
Period size: 26 Copynumber: 4.2 Consensus size: 26
57738 TTATGCGCTT
** * *
57748 TCCTTGCGAGCTATGCCCACGAGCTC
1 TCCTTGCGAGCCCTGTCGACGAGCTC
* *
57774 TCATTGCGAGCCCTGTCGATGAGCTC
1 TCCTTGCGAGCCCTGTCGACGAGCTC
* *
57800 TCCTTGCGAACACTGTCGACGAGCTC
1 TCCTTGCGAGCCCTGTCGACGAGCTC
* *
57826 TCCTTGCAAGCCCTATCTG-CGAGCTC
1 TCCTTGCGAGCCCTGTC-GACGAGCTC
57852 TCCT
1 TCCT
57856 CTTGTGAGCT
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
26 66 0.99
27 1 0.01
ACGTcount: A:0.16, C:0.36, G:0.22, T:0.26
Consensus pattern (26 bp):
TCCTTGCGAGCCCTGTCGACGAGCTC
Found at i:58698 original size:26 final size:26
Alignment explanation
Indices: 58652--58704 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
58642 CGTCGATAGT
*
58652 GCTCGCAAGAAGAGGTCACCGACAGG
1 GCTCGCAAGAAGAGCTCACCGACAGG
* *
58678 GCTCGC-AGAGAGAGCTTACCGATAGG
1 GCTCGCAAGA-AGAGCTCACCGACAGG
58704 G
1 G
58705 ATCACAGGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.28, C:0.25, G:0.36, T:0.11
Consensus pattern (26 bp):
GCTCGCAAGAAGAGCTCACCGACAGG
Found at i:59261 original size:54 final size:54
Alignment explanation
Indices: 59179--59288 Score: 193
Period size: 54 Copynumber: 2.0 Consensus size: 54
59169 GTAGATTGAA
* *
59179 TAATAATAAGTCTCCCAGTAAGGGAGAAGAGATTCACTTTCCAAGCTCTTAGCT
1 TAATAATAAGTCTCCCAATAAGGGAGAAGAGATTCACTTTCCAAACTCTTAGCT
*
59233 TAATAATAAGTCTCCCAATAAGGGAGAAGAGATTCTCTTTCCAAACTCTTAGCT
1 TAATAATAAGTCTCCCAATAAGGGAGAAGAGATTCACTTTCCAAACTCTTAGCT
59287 TA
1 TA
59289 CTCCTAACTT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (54 bp):
TAATAATAAGTCTCCCAATAAGGGAGAAGAGATTCACTTTCCAAACTCTTAGCT
Found at i:60459 original size:15 final size:16
Alignment explanation
Indices: 60425--60456 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
60415 TAAATTGTCA
*
60425 TATTTTTTAAAATATT
1 TATTTTTAAAAATATT
60441 TATTTTTAAAAATATT
1 TATTTTTAAAAATATT
60457 ATTCTATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTTTAAAAATATT
Found at i:67749 original size:30 final size:31
Alignment explanation
Indices: 67705--67767 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
67695 TAGTAAAAGT
67705 AAAATTTCACTTTAATCCCTTAAAAATGATA
1 AAAATTTCACTTTAATCCCTTAAAAATGATA
* ** *
67736 AAAATTTGA-TTTAATCTTTTAAAAATTATA
1 AAAATTTCACTTTAATCCCTTAAAAATGATA
67766 AA
1 AA
67768 GATATAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.40
Consensus pattern (31 bp):
AAAATTTCACTTTAATCCCTTAAAAATGATA
Found at i:68699 original size:27 final size:25
Alignment explanation
Indices: 68669--68719 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
68659 AAAGGTTTTT
68669 TTTATATATTAAGTATATAATAATATA
1 TTTATATATT-A-TATATAATAATATA
* *
68696 TTTATTTATTATATATATTAATAT
1 TTTATATATTATATATAATAATAT
68720 TTTCATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.55
26 1 0.05
27 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTATATATTATATATAATAATATA
Found at i:68720 original size:19 final size:19
Alignment explanation
Indices: 68671--68721 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
68661 AGGTTTTTTT
*
68671 TATATATTAAGTATATAATA
1 TATATATTAA-TATTTAATA
*
68691 -ATATATT--TATTTATTA
1 TATATATTAATATTTAATA
68707 TATATATTAATATTT
1 TATATATTAATATTT
68722 TCATTAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
16 7 0.27
17 7 0.27
19 12 0.46
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TATATATTAATATTTAATA
Found at i:69950 original size:87 final size:87
Alignment explanation
Indices: 69810--70120 Score: 264
Period size: 88 Copynumber: 3.5 Consensus size: 87
69800 AAAAGGTCCC
* * * * * * *
69810 CGAACTATCCAAAAATCATATTTTAACCCCTAAACTTTTCAAAAATTACATTTTAACCCTTAAAC
1 CGAACTTTCC-AAAATTACATTTTGACCCC-GAACTTCTCAAAAATTACATTTTTACCCTTAAAC
**
69875 TTTCCAAAATTACATTTTGACCCCT
64 TTTTAAAAATTACATTTT-ACCCCT
* *
69900 -TAACTTTCCAAAATTACATTTTGACCCCGAACTTCTCAAAATTTACATTTTTACTCC-TAAACT
1 CGAACTTTCCAAAATTACATTTTGACCCCGAACTTCTCAAAAATTACATTTTTAC-CCTTAAACT
69963 TCTTAAAAATCT-CATTTTTA-CCCT
65 T-TTAAAAAT-TACA-TTTTACCCCT
* ** *
69987 CGAAC-TTCCAAAAATTACCATTTT-ACCCCAAACTTC-CAAAAAATCCCATTTTTA-CCTTGAA
1 CGAACTTTCC-AAAATTA-CATTTTGACCCCGAACTTCTC-AAAAATTACATTTTTACCCTTAAA
**
70048 CTTTTTGAAATTACCATTTTACCCCT
63 CTTTTAAAAATTA-CATTTTACCCCT
* *
70074 CGAA-TGTCCAAAATTTACAATTTTGACCCCGAACTT-TCCAAAATTAC
1 CGAACTTTCCAAAA-TTAC-ATTTTGACCCCGAACTTCTCAAAAATTAC
70121 CAGTTTACCC
Statistics
Matches: 180, Mismatches: 24, Indels: 37
0.75 0.10 0.15
Matches are distributed among these distances:
85 1 0.01
86 18 0.10
87 71 0.39
88 72 0.40
89 18 0.10
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (87 bp):
CGAACTTTCCAAAATTACATTTTGACCCCGAACTTCTCAAAAATTACATTTTTACCCTTAAACTT
TTAAAAATTACATTTTACCCCT
Found at i:70029 original size:29 final size:28
Alignment explanation
Indices: 69807--70338 Score: 168
Period size: 29 Copynumber: 18.2 Consensus size: 28
69797 CCCAAAAGGT
* * * *
69807 CCCCGAACTATCCAAAAATCATATTTTAA
1 CCCCAAACT-TCCAAAAATTACATTTTGA
* *
69836 CCCCTAAACTTTTCAAAAATTACATTTTAA
1 CCCC-AAAC-TTCCAAAAATTACATTTTGA
*
69866 CCCTTAAACTTTCC-AAAATTACATTTTGA
1 CCC-CAAAC-TTCCAAAAATTACATTTTGA
*
69895 CCCCTTAACTTTCC-AAAATTACATTTTGA
1 CCCC-AAAC-TTCCAAAAATTACATTTTGA
* * *
69924 CCCCGAACTTCTCAAAATTTACATTTTTA
1 CCCCAAACTTC-CAAAAATTACATTTTGA
* * *
69953 CTCCTAAACTTCTTAAAAATCT-CATTTTTA
1 C-CCCAAACTTC-CAAAAAT-TACATTTTGA
*
69983 CCCTCGAACTTCCAAAAATTACCATTTT-A
1 CCC-CAAACTTCCAAAAATTA-CATTTTGA
** *
70012 CCCCAAACTTCCAAAAAATCCCATTTTTA
1 CCCCAAACTTCC-AAAAATTACATTTTGA
*** ****
70041 CCTTGAACTTTTTGAAATTACCATTTT-A
1 CCCCAAACTTCCAAAAATTA-CATTTTGA
* *
70069 CCCCTCGAA-TGTCCAAAATTTACAATTTTGA
1 -CCC-CAAACT-TCCAAAAATTAC-ATTTTGA
* *
70100 CCCCGAACTTTCC-AAAATTACCAGTTT-A
1 CCCCAAAC-TTCCAAAAATTA-CATTTTGA
* * *
70128 CCCCTCGAA-TGTCCAAAAAATATATTTTTG-
1 -CCC-CAAACT-TCCAAAAATTACA-TTTTGA
* **
70158 CCCTCGAGTTTCCAAAAATTACATTTTTG-
1 CCC-CAAACTTCCAAAAATTACA-TTTTGA
70187 CCACCAAA-TGTCCAAAAATTATCATTTT-A
1 CC-CCAAACT-TCCAAAAATTA-CATTTTGA
*
70216 CCTCTCGAA-TGTCCAAAAATTACCATTTT-A
1 CC-C-CAAACT-TCCAAAAATTA-CATTTTGA
** *
70246 CCTCCGGA-TGTCCAAAAATTACATTTTTA
1 CC-CCAAACT-TCCAAAAATTACATTTTGA
* *
70275 CCACCGAA-TGTCCAAAAATTACCGTTTT-A
1 CC-CCAAACT-TCCAAAAATTA-CATTTTGA
*
70304 CCCCTAAA-TCTCTAAAAATTATCATTTT-A
1 CCCC-AAACT-TCCAAAAATTA-CATTTTGA
70333 CCCCAA
1 CCCCAA
70339 GTATCCTAAA
Statistics
Matches: 406, Mismatches: 60, Indels: 75
0.75 0.11 0.14
Matches are distributed among these distances:
27 3 0.01
28 37 0.09
29 227 0.56
30 135 0.33
31 4 0.01
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (28 bp):
CCCCAAACTTCCAAAAATTACATTTTGA
Found at i:70118 original size:59 final size:59
Alignment explanation
Indices: 69807--70336 Score: 320
Period size: 59 Copynumber: 9.1 Consensus size: 59
69797 CCCAAAAGGT
* * * * * *
69807 CCCCGAACTATCCAAAAATCA-TATTTTAACCCCT-AAACTTTTCAAAAATTACATTTTAA
1 CCCCGAACTTTCCAAAAATTACCATTTT-ACCCCTCAAA-TGTCCAAAAATTACATTTTGA
** * * *
69866 CCCTTAAACTTTCC-AAAATTA-CATTTTGACCCCTTAACTTTCC-AAAATTACATTTTGA
1 CCC-CGAACTTTCCAAAAATTACCATTTT-ACCCCTCAAATGTCCAAAAATTACATTTTGA
* * * *
69924 CCCCGAAC-TTCTCAAAATTTA-CATTTTTACTCCT-AAACT-TCTTAAAAATCT-CATTTTTA
1 CCCCGAACTTTC-CAAAAATTACCA-TTTTACCCCTCAAA-TGTC-CAAAAAT-TACATTTTGA
** *
69983 CCCTCGAAC-TTCCAAAAATTACCATTTTA-CCC-CAAACT-TCCAAAAAATCCCATTTTTA
1 CCC-CGAACTTTCCAAAAATTACCATTTTACCCCTCAAA-TGTCC-AAAAATTACATTTTGA
** *** * *
70041 CCTTGAACTTT-TTGAAATTACCATTTTACCCCTCGAATGTCCAAAATTTACAATTTTGA
1 CCCCGAACTTTCCAAAAATTACCATTTTACCCCTCAAATGTCCAAAAATTAC-ATTTTGA
* * * *
70100 CCCCGAACTTTCC-AAAATTACCAGTTTACCCCTCGAATGTCCAAAAAATATATTTTTG-
1 CCCCGAACTTTCCAAAAATTACCATTTTACCCCTCAAATGTCCAAAAATTACA-TTTTGA
* * *
70158 CCCTCG-AGTTTCCAAAAATTA-CATTTTTGCCAC-CAAATGTCCAAAAATTATCATTTT-A
1 CCC-CGAACTTTCCAAAAATTACCA-TTTTACCCCTCAAATGTCCAAAAATTA-CATTTTGA
* * ** *
70216 CCTCTCGAA-TGTCCAAAAATTACCATTTTACCTC-CGGATGTCCAAAAATTACATTTTTA
1 CC-C-CGAACTTTCCAAAAATTACCATTTTACCCCTCAAATGTCCAAAAATTACATTTTGA
* * * *
70275 CCACCGAA-TGTCCAAAAATTACCGTTTTACCCCT-AAATCTCTAAAAATTATCATTTT-A
1 CC-CCGAACTTTCCAAAAATTACCATTTTACCCCTCAAATGTCCAAAAATTA-CATTTTGA
70333 CCCC
1 CCCC
70337 AAGTATCCTA
Statistics
Matches: 382, Mismatches: 57, Indels: 66
0.76 0.11 0.13
Matches are distributed among these distances:
56 3 0.01
57 28 0.07
58 149 0.39
59 179 0.47
60 23 0.06
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (59 bp):
CCCCGAACTTTCCAAAAATTACCATTTTACCCCTCAAATGTCCAAAAATTACATTTTGA
Found at i:70172 original size:88 final size:88
Alignment explanation
Indices: 70070--70308 Score: 254
Period size: 88 Copynumber: 2.7 Consensus size: 88
70060 ACCATTTTAC
* * *
70070 CCCTCGAATGTCCAAAATTTACAATTTTGACC-CCGAACTTTCC-AAAATTACCAGTTTACCCCT
1 CCCTCGAATGTCCAAAAATTACAATTTTG-CCACC-AAATGTCCAAAAATTACCAGTTTACCCCT
70133 CGAATGTCCAAAAAATATATTTTTG
64 CGAATGTCCAAAAAATATATTTTTG
* * * * * *
70158 CCCTCGAGTTTCCAAAAATTACATTTTTGCCACCAAATGTCCAAAAATTATCATTTTACCTCTCG
1 CCCTCGAATGTCCAAAAATTACAATTTTGCCACCAAATGTCCAAAAATTACCAGTTTACCCCTCG
* *
70223 AATGTCCAAAAATTACCA-TTTT-
66 AATGTCCAAAAAATA-TATTTTTG
* * * * *
70245 ACCTCCGGATGTCCAAAAATTACATTTTTACCACCGAATGTCCAAAAATTACC-GTTTTACCCCT
1 CCCT-CGAATGTCCAAAAATTACAATTTTGCCACCAAATGTCCAAAAATTACCAG-TTTACCCCT
70309 AAATCTCTAA
Statistics
Matches: 126, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
87 11 0.09
88 114 0.90
89 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.32
Consensus pattern (88 bp):
CCCTCGAATGTCCAAAAATTACAATTTTGCCACCAAATGTCCAAAAATTACCAGTTTACCCCTCG
AATGTCCAAAAAATATATTTTTG
Found at i:70349 original size:29 final size:29
Alignment explanation
Indices: 70055--70334 Score: 223
Period size: 29 Copynumber: 9.6 Consensus size: 29
70045 GAACTTTTTG
*
70055 AAATTACCATTTTACCCCTCGAATGTCCAA
1 AAATTACCATTTTACCTC-CGAATGTCCAA
* * *
70085 AATTTACAATTTTGACC-CCGAACTTTCC-A
1 AAATTACCATTTT-ACCTCCGAA-TGTCCAA
* *
70114 AAATTACCAGTTTACCCCTCGAATGTCCAA
1 AAATTACCATTTTACCTC-CGAATGTCCAA
* * * * *
70144 AAAATA-TATTTTTGCC-CTCGAGTTTCCAA
1 AAATTACCA-TTTTACCTC-CGAATGTCCAA
* * *
70173 AAATTA-CATTTTTGCCACCAAATGTCCAA
1 AAATTACCA-TTTTACCTCCGAATGTCCAA
*
70202 AAATTATCATTTTACCTCTCGAATGTCCAA
1 AAATTACCATTTTACCTC-CGAATGTCCAA
*
70232 AAATTACCATTTTACCTCCGGATGTCCAA
1 AAATTACCATTTTACCTCCGAATGTCCAA
*
70261 AAATTA-CATTTTTACCACCGAATGTCCAA
1 AAATTACCA-TTTTACCTCCGAATGTCCAA
* * * *
70290 AAATTACCGTTTTACC-CCTAAATCTCTAA
1 AAATTACCATTTTACCTCC-GAATGTCCAA
*
70319 AAATTATCATTTTACC
1 AAATTACCATTTTACC
70335 CCAAGTATCC
Statistics
Matches: 207, Mismatches: 31, Indels: 25
0.79 0.12 0.10
Matches are distributed among these distances:
28 7 0.03
29 135 0.65
30 62 0.30
31 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.33
Consensus pattern (29 bp):
AAATTACCATTTTACCTCCGAATGTCCAA
Found at i:79147 original size:6 final size:6
Alignment explanation
Indices: 79136--79163 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
79126 GTACTCACAT
79136 CATGTG CATGTG CATGTG CATGTG CATG
1 CATGTG CATGTG CATGTG CATGTG CATG
79164 CATAAGTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (6 bp):
CATGTG
Found at i:80547 original size:14 final size:14
Alignment explanation
Indices: 80530--80568 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
80520 TAAAATATTG
*
80530 GATTTAATGTTTAA
1 GATTTAATATTTAA
80544 GATTTAATATTTAA
1 GATTTAATATTTAA
*
80558 AATTT-ATATTT
1 GATTTAATATTT
80569 GTGAGTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (14 bp):
GATTTAATATTTAA
Found at i:81668 original size:2 final size:2
Alignment explanation
Indices: 81656--81685 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
81646 GTTTTATTGT
81656 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
81686 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:82949 original size:24 final size:25
Alignment explanation
Indices: 82890--82949 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 25
82880 TTATAAAAAG
*
82890 TTAAAATTATATATTATTATGACTTT
1 TTAAAATT-TATATTATTATGAATTT
82916 TTAAAATTTATATT-TT-TGAATTT
1 TTAAAATTTATATTATTATGAATTT
82939 TATAAAATTTA
1 T-TAAAATTTA
82950 AACATCCGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 7 0.22
24 11 0.34
25 6 0.19
26 8 0.25
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (25 bp):
TTAAAATTTATATTATTATGAATTT
Found at i:84118 original size:14 final size:14
Alignment explanation
Indices: 84101--84134 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
84091 TCTCCCACAG
84101 TTTTTTTATTCTTC
1 TTTTTTTATTCTTC
* *
84115 TTTTTTTTTTTTTC
1 TTTTTTTATTCTTC
84129 TTTTTT
1 TTTTTT
84135 NGTATCTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTATTCTTC
Found at i:84121 original size:17 final size:16
Alignment explanation
Indices: 84101--84134 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
84091 TCTCCCACAG
84101 TTTTTTTATTCTTCTTT
1 TTTTTTTATTCTT-TTT
*
84118 TTTTTTTTTTCTTTTT
1 TTTTTTTATTCTTTTT
84134 T
1 T
84135 NGTATCTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTTATTCTTTTT
Done.