Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013646.1 Kokia drynarioides strain JFW-HI SEQ_128674, 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: 104312
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 126 characters in sequence are not A, C, G, or T
Found at i:350 original size:96 final size:96
Alignment explanation
Indices: 185--365 Score: 222
Period size: 96 Copynumber: 1.9 Consensus size: 96
175 AAGACTTTAA
* * * * **
185 AATCGAGGTAATATTTTTTTATTTCGAGTTTTGAAAATTTGTGTCTTAACTTACTAGATGCAATT
1 AATCGAGGCAATATTTCTTTATTTCGAGTTCTGAAAATTTGTGCCTTAACTTACTAGATGCAACC
*
250 TTTCTTCAAATTGAAATAATTGAATACCCTT
66 TTTCTTCAAATCGAAATAATTGAATACCCTT
* * *
281 AATCGAGGCAATGTTTCTTTATCTTCGA-TTCTG-AAATATTGTGCCTTAACTTACTAGGTGTAA
1 AATCGAGGCAATATTTCTTTAT-TTCGAGTTCTGAAAAT-TTGTGCCTTAACTTACTAGATGCAA
* *
344 CCTTTCTTTAAATCGAGATAAT
64 CCTTTCTTCAAATCGAAATAAT
366 CGTATATCCT
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
95 4 0.06
96 62 0.87
97 5 0.07
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (96 bp):
AATCGAGGCAATATTTCTTTATTTCGAGTTCTGAAAATTTGTGCCTTAACTTACTAGATGCAACC
TTTCTTCAAATCGAAATAATTGAATACCCTT
Found at i:2602 original size:16 final size:18
Alignment explanation
Indices: 2581--2616 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2571 CAAATAAATT
2581 AAAATTA-AAA-ATTAAA
1 AAAATTATAAATATTAAA
2597 AAAATTATAAATATTAAA
1 AAAATTATAAATATTAAA
2615 AA
1 AA
2617 TTAAATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATTATAAATATTAAA
Found at i:26831 original size:18 final size:19
Alignment explanation
Indices: 26808--26859 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
26798 GATTTACAAT
26808 ATTTTTCAATTTCT-AATA
1 ATTTTTCAATTTCTAAATA
*
26826 ATTTTTCATAGTTTTTAAATA
1 ATTTTTCA-A-TTTCTAAATA
26847 ATTTTTACAATTT
1 ATTTTT-CAATTT
26860 TATAAAATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 8 0.28
19 1 0.03
20 7 0.24
21 11 0.38
22 2 0.07
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTTTCAATTTCTAAATA
Found at i:42118 original size:11 final size:12
Alignment explanation
Indices: 42097--42121 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42087 TCGATTTGTC
42097 TTTCTTTTTTTT
1 TTTCTTTTTTTT
42109 TTTCTTTTTTTT
1 TTTCTTTTTTTT
42121 T
1 T
42122 AGATTACTTT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:42445 original size:4 final size:4
Alignment explanation
Indices: 42436--42467 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
42426 TACAGGTGAG
42436 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
42468 CAACCTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:43274 original size:21 final size:21
Alignment explanation
Indices: 43250--43297 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
43240 TGAAATTTTT
43250 TTAAAAAAAATTCTAAAAATA
1 TTAAAAAAAATTCTAAAAATA
** * *
43271 TTAAAAATTATTTTAAAATTA
1 TTAAAAAAAATTCTAAAAATA
43292 TTAAAA
1 TTAAAA
43298 TGCAGAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAAAAAAAATTCTAAAAATA
Found at i:44746 original size:2 final size:2
Alignment explanation
Indices: 44739--44773 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
44729 ATTTAAGCCA
44739 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44774 GAATTACTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47311 original size:37 final size:37
Alignment explanation
Indices: 47261--47517 Score: 255
Period size: 37 Copynumber: 6.9 Consensus size: 37
47251 CATCTACAAA
* * * * * *
47261 TTCAAGCTGTGTGCCTAGCAGGCTCCGTGCCGGTATA
1 TTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTT
* * * *
47298 TTCAGGCTTTGTGCTTAGTAAGCTTCGTGTCGGTATT
1 TTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTT
* * * * * *
47335 TTCAAGCTTTGGGCTTAGTAAGCTTTGAGCCGGTGTT
1 TTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTT
* * * *
47372 TTCAGGCTTTGTGCTTAGTAAGCTTTGTGCCAGTGTT
1 TTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTT
* *
47409 TTCAGGCTTTATGCCTAGTAGGCTTCGTGCCAGTGTT
1 TTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTT
* * *
47446 TTTAGACTTTGTGCCTAGCAGGCTTCGTGCCGGTGTT
1 TTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTT
* *
47483 TTCAGG-TTATGTGCCTAGCAGGCTTTGTGCCGGTG
1 TTCAGGCTT-TGTGCCTAGTAGGCTTCGTGCCGGTG
47518 ACCCAAGAAC
Statistics
Matches: 189, Mismatches: 30, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
36 2 0.01
37 187 0.99
ACGTcount: A:0.14, C:0.20, G:0.29, T:0.37
Consensus pattern (37 bp):
TTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTT
Found at i:49095 original size:24 final size:23
Alignment explanation
Indices: 49041--49104 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
49031 TAATTTTAAA
*
49041 AATATATTTATATTATTTCAATTT
1 AATAAATTTATA-TATTTCAATTT
**
49065 AATAAATTTATATATTTTTATTT
1 AATAAATTTATATATTTCAATTT
*
49088 ATTGAAATTTTATATAT
1 AAT-AAA-TTTATATAT
49105 AGTGATCTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.32
24 14 0.41
25 9 0.26
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
AATAAATTTATATATTTCAATTT
Found at i:49625 original size:2 final size:2
Alignment explanation
Indices: 49620--49648 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49610 AAACATTCTA
49620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49649 AAACTCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61620 original size:150 final size:151
Alignment explanation
Indices: 61351--61626 Score: 355
Period size: 150 Copynumber: 1.8 Consensus size: 151
61341 CAAATTTGCC
* * *
61351 TAAGTCAACCTTACACTCGAAAAATGAGAATTTTCCCAAAAATTCACTATGGCACCAAAAAAATA
1 TAAGTCAACCTTACACTCGAAAAATAAGAATTTTCCCAAAAATTCACTAAGACACCAAAAAAATA
* * * *
61416 TAATGAAAAAAACTCGAAACAAAAGAGTAATGAGAGAATTGAAAAGTCACAAGAAAGCAATATAC
66 TAATGAAAAAAACTCAAAACAAAAGAGCAATAAGAGAATTGAAAAGCCACAAGAAAGCAATATAC
61481 ACCAAGTGTTTCAAATCTTCA
131 ACCAAGTGTTTCAAATCTTCA
* * * *
61502 TAAGTCAA-CTTAACACTC-AAAAAGTAAGAGTTTTCTCGAAAATTCTCTAAGACACC-AAAAAA
1 TAAGTCAACCTT-ACACTCGAAAAA-TAAGAATTTTCCCAAAAATTCACTAAGACACCAAAAAAA
* * *
61564 TAT-A-GCAAAAGCAACTCAAAACGAAAGAGCAATAAGAGAATTGAAAAGCCATAAGAAAGCAAT
64 TATAATG-AAAA-AAACTCAAAACAAAAGAGCAATAAGAGAATTGAAAAGCCACAAGAAAGCAAT
61627 GCACACAAAG
Statistics
Matches: 107, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
148 1 0.01
149 5 0.05
150 62 0.58
151 39 0.36
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (151 bp):
TAAGTCAACCTTACACTCGAAAAATAAGAATTTTCCCAAAAATTCACTAAGACACCAAAAAAATA
TAATGAAAAAAACTCAAAACAAAAGAGCAATAAGAGAATTGAAAAGCCACAAGAAAGCAATATAC
ACCAAGTGTTTCAAATCTTCA
Found at i:63314 original size:3 final size:3
Alignment explanation
Indices: 63306--63350 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
63296 ATAGCATTAC
*
63306 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
63351 TCGGCTTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:75063 original size:6 final size:6
Alignment explanation
Indices: 75052--75076 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
75042 CGTCATCATT
75052 CATTGC CATTGC CATTGC CATTGC C
1 CATTGC CATTGC CATTGC CATTGC C
75077 GTTGGTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.16, T:0.32
Consensus pattern (6 bp):
CATTGC
Found at i:76041 original size:22 final size:22
Alignment explanation
Indices: 75989--76043 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
75979 ATTTTATAAT
* * * *
75989 CAGATACAAACGCAGAGCATAT
1 CAGATACAGATGCAGAGCACAC
76011 CAGATACAGATGCAGAGCACAC
1 CAGATACAGATGCAGAGCACAC
76033 CAGATACAGAT
1 CAGATACAGAT
76044 TCAAAATTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.13
Consensus pattern (22 bp):
CAGATACAGATGCAGAGCACAC
Found at i:78941 original size:59 final size:59
Alignment explanation
Indices: 78765--79095 Score: 413
Period size: 59 Copynumber: 5.6 Consensus size: 59
78755 GTAATTTTGG
* * *
78765 GGAAGTTCGAGGTTAAAAGATGGAATTTTTAGAT-ATTCGGGGT-AAAAATG-GAATTTTT
1 GGAAGTTCGAGGGTAAAA-ATGGAATTTTTGGATGTTTCGGGGTCAAAAATGAG-ATTTTT
* * * *
78823 GG-AGTTTCGA-GGTCAAAAATGAAATTTTTTGA-GTTTCGAGGTTAAAAATGAGATTTTT
1 GGAAG-TTCGAGGGT-AAAAATGGAATTTTTGGATGTTTCGGGGTCAAAAATGAGATTTTT
* * *
78881 GGAAGTTCGGGGGTAAAAATGGAATTTTTAGATGTTTTGGGGTCAAAAATGAGATTTTT
1 GGAAGTTCGAGGGTAAAAATGGAATTTTTGGATGTTTCGGGGTCAAAAATGAGATTTTT
* * *
78940 GGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGTGGTTAAAAATGAGATTTTT
1 GGAAGTTCGAGGGTAAAAATGGAATTTTTGGATGTTTCGGGGTCAAAAATGAGATTTTT
* * * * *
78999 GTAAGTTTGAGGGTAAAAATGAAATTTTTGGAAGTTTCGGGGTCAAAAATAAGATTTTT
1 GGAAGTTCGAGGGTAAAAATGGAATTTTTGGATGTTTCGGGGTCAAAAATGAGATTTTT
79058 GGAAGTTCGAGGGTAAAAATGGAATTTTTGGATAGTTT
1 GGAAGTTCGAGGGTAAAAATGGAATTTTTGGAT-GTTT
79096 AGGGACCTTC
Statistics
Matches: 237, Mismatches: 27, Indels: 16
0.85 0.10 0.06
Matches are distributed among these distances:
57 23 0.10
58 46 0.19
59 164 0.69
60 4 0.02
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.36
Consensus pattern (59 bp):
GGAAGTTCGAGGGTAAAAATGGAATTTTTGGATGTTTCGGGGTCAAAAATGAGATTTTT
Found at i:79099 original size:29 final size:28
Alignment explanation
Indices: 78749--79099 Score: 239
Period size: 29 Copynumber: 11.9 Consensus size: 28
78739 ACCTAGGGGC
* * *
78749 AAAATGGTAATTTTGGGGAAGTTCGAGGTTA
1 AAAATGG-AATTTT-TGGAAGTT-TAGGGTA
* **
78780 AAAGATGGAATTTTTAGATA-TTCGGGGTA
1 AAA-ATGGAATTTTTGGA-AGTTTAGGGTA
*
78809 AAAATGGAATTTTTGG-AGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTAG-GGT-A
* * *
78838 AAAATGAAATTTTTTG-AGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTTT--AGGGTA
**
78867 AAAAT-GAGATTTTTGGAAGTTCGGGGGTA
1 AAAATGGA-ATTTTTGGAAGTT-TAGGGTA
* * *
78896 AAAATGGAATTTTTAGATGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAG-TTTAGGGT-A
*
78926 AAAAT-GAGATTTTTGGAAGTTCGAGGGTA
1 AAAATGGA-ATTTTTGGAAGTT-TAGGGTA
*
78955 AAAATGGAATTTTTGGAAGTTTCGTGGTTA
1 AAAATGGAATTTTTGGAAGTTTAG-GG-TA
*
78985 AAAAT-GAGATTTTTGTAAGTTTGAGGGTA
1 AAAATGGA-ATTTTTGGAAGTTT-AGGGTA
* *
79014 AAAATGAAATTTTTGGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTT-AGGGT-A
* *
79044 AAAAT-AAGATTTTTGGAAGTTCGAGGGTA
1 AAAATGGA-ATTTTTGGAAGTT-TAGGGTA
79073 AAAATGGAATTTTTGGATAGTTTAGGG
1 AAAATGGAATTTTTGGA-AGTTTAGGG
79100 ACCTTCGAGG
Statistics
Matches: 258, Mismatches: 36, Indels: 54
0.74 0.10 0.16
Matches are distributed among these distances:
26 1 0.00
27 3 0.01
28 17 0.07
29 135 0.52
30 86 0.33
31 12 0.05
32 4 0.02
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.35
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTAGGGTA
Found at i:80142 original size:3 final size:3
Alignment explanation
Indices: 80134--80206 Score: 83
Period size: 3 Copynumber: 24.0 Consensus size: 3
80124 TTTTCCTTTT
* ** **
80134 TTA TTA TTAA TTA ATA TTA TTA TTA TTA TTA TTA AAA CAA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
80180 CTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
80207 ATGCTATCAG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:80830 original size:16 final size:15
Alignment explanation
Indices: 80792--80830 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
80782 GGTTTGGGCT
80792 GATTTGGGTCATTTA
1 GATTTGGGTCATTTA
* *
80807 GGTTTGGGTCTTTTA
1 GATTTGGGTCATTTA
80822 GAATTTGGG
1 G-ATTTGGG
80831 CTTAGGTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.15, C:0.05, G:0.33, T:0.46
Consensus pattern (15 bp):
GATTTGGGTCATTTA
Found at i:80922 original size:18 final size:18
Alignment explanation
Indices: 80899--80984 Score: 72
Period size: 17 Copynumber: 4.8 Consensus size: 18
80889 TTTTTTAATT
80899 AATTAAATTTTAAA-TTCA
1 AATTAAATTTTAAACTT-A
80917 AATT-AATTTTAAACTTA
1 AATTAAATTTTAAACTTA
*
80934 ATTTAAA-TTTAAACTTAA
1 AATTAAATTTTAAACTT-A
** *
80952 AAGAAAAGTTTAAACTTTA
1 AATTAAATTTTAAAC-TTA
*
80971 AACTAAA-TTTAAAC
1 AATTAAATTTTAAAC
80985 CCAAAATGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
17 22 0.39
18 20 0.35
19 13 0.23
20 2 0.04
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (18 bp):
AATTAAATTTTAAACTTA
Found at i:88132 original size:96 final size:96
Alignment explanation
Indices: 87951--88142 Score: 257
Period size: 96 Copynumber: 2.0 Consensus size: 96
87941 TTTTTGGGAA
* * **
87951 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCA
*
88016 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* *
88047 AAGGGTATTCGATTATTTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATA-TTTC
88111 -GAAATTCG-AGATAAA-AGAACATTGCCTCGATT
65 AG-AA-TCGAAGATAAAGA-AACATTGCCTCGATT
88143 TTAAAGTCTT
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
95 3 0.04
96 79 0.93
97 3 0.04
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:88456 original size:59 final size:59
Alignment explanation
Indices: 88431--88773 Score: 512
Period size: 59 Copynumber: 5.9 Consensus size: 59
88421 TTTTGGGAAA
* * *
88431 TTTTGGGGTTAAAAATGGAATTTTTGGAAGTTCGAGGCTAAAAATGGAATTTTTGGAAG
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAG
* * *
88490 TTTCGGGGCTAAAAATGGGATTTTTGTAAGTTCGAGGGTAAAAATGGAATTTTTAGAAG
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAG
* * *
88549 TTTTGAGGTTAAAATTGGGATTTTTGGAAGTTCGTGGGTAAAAATGGAATTTTTAGAAG
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAG
*
88608 TTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAG
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAG
*
88667 TTTT-GGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGATTTTTTAGAAG
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAG
* * * * * *
88725 TTTTAGGGTCAAAAATAGGATTTCTGAAAGTTTG-GGGT-AAAATGGAATT
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATT
88774 CTTGGATAGT
Statistics
Matches: 259, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
57 10 0.04
58 60 0.23
59 189 0.73
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (59 bp):
TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAG
Found at i:88478 original size:29 final size:29
Alignment explanation
Indices: 88440--88784 Score: 351
Period size: 29 Copynumber: 11.8 Consensus size: 29
88430 ATTTTGGGGT
*
88440 TAAAAATGGAATTTTTGGAAGTTCGAGGC
1 TAAAAATGGAATTTTTGGAAGTTCGAGGG
88469 TAAAAATGGAATTTTTGGAAGTTTCG-GGG
1 TAAAAATGGAATTTTTGGAAG-TTCGAGGG
* *
88498 CTAAAAATGGGATTTTTGTAAGTTCGAGGG
1 -TAAAAATGGAATTTTTGGAAGTTCGAGGG
* * *
88528 TAAAAATGGAATTTTTAGAAGTTTTGAGGT
1 TAAAAATGGAATTTTTGGAAG-TTCGAGGG
* * *
88558 TAAAATTGGGATTTTTGGAAGTTCGTGGG
1 TAAAAATGGAATTTTTGGAAGTTCGAGGG
* *
88587 TAAAAATGGAATTTTTAGAAGTTTTG-GGG
1 TAAAAATGGAATTTTTGGAAG-TTCGAGGG
*
88616 TCAAAAATGGGATTTTTGGAAGTTCGAGGG
1 T-AAAAATGGAATTTTTGGAAGTTCGAGGG
* * *
88646 TAAAAATGGAATTTTTAGAAGTTTTG-GGT
1 TAAAAATGGAATTTTTGGAAG-TTCGAGGG
*
88675 TAAAAATGGGATTTTTGGAAGTTCGAGGG
1 TAAAAATGGAATTTTTGGAAGTTCGAGGG
* * **
88704 TAAAAATGGATTTTTTAGAAGTTTTAGGG
1 TAAAAATGGAATTTTTGGAAGTTCGAGGG
* * *
88733 TCAAAAATAGG-ATTTCTGAAAGTTTG-GGG
1 T-AAAAAT-GGAATTTTTGGAAGTTCGAGGG
*
88762 T-AAAATGGAATTCTTGGATAGTT
1 TAAAAATGGAATTTTTGGA-AGTT
88785 TAGGGACCTC
Statistics
Matches: 261, Mismatches: 42, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
26 2 0.01
27 11 0.04
28 7 0.03
29 145 0.56
30 94 0.36
31 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.36
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTCGAGGG
Found at i:89467 original size:30 final size:30
Alignment explanation
Indices: 89433--89523 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
89423 CGCGCTGTCA
* *
89433 TCCCGCAGTCCTCTGATGCACGCGCCACTG
1 TCCCGCAGTCCTCCGGTGCACGCGCCACTG
* * ** *
89463 TCCCGTAGTCCTCCGGTGCACGTGCTGCCG
1 TCCCGCAGTCCTCCGGTGCACGCGCCACTG
* *
89493 TCCCACAATCCTCCGGTGCACGCGCCACTG
1 TCCCGCAGTCCTCCGGTGCACGCGCCACTG
89523 T
1 T
89524 TTTCGAGTCC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.12, C:0.43, G:0.24, T:0.21
Consensus pattern (30 bp):
TCCCGCAGTCCTCCGGTGCACGCGCCACTG
Found at i:90586 original size:17 final size:17
Alignment explanation
Indices: 90566--90613 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
90556 AAATAAATTT
90566 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
90583 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
90600 TAAATTTAAGTTTA
1 TAAATTTAAATTTA
90614 TTGGGCCCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:90600 original size:24 final size:24
Alignment explanation
Indices: 90551--90598 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
90541 GTACTTGGAC
*
90551 ATTTAAAATAAATTTTAAATTTAA
1 ATTTAAAATAAATCTTAAATTTAA
*
90575 ATTTAAAATAAA-CTTAATTTTAA
1 ATTTAAAATAAATCTTAAATTTAA
90598 A
1 A
90599 ATAAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTAAAATAAATCTTAAATTTAA
Found at i:99149 original size:30 final size:27
Alignment explanation
Indices: 99109--99263 Score: 107
Period size: 30 Copynumber: 5.3 Consensus size: 27
99099 AAATTAAGGG
99109 TTGA-CCCTAAACTTTTCAAAACTTTGATT
1 TTGACCCCTAAACTTTT-AAAA-TTT-ATT
99138 TTGACCCCTAAACTTTTTAAAATTTATAT
1 TTGACCCCTAAAC-TTTTAAAATTTAT-T
* *
99167 TTTAACCCTAAACATTTTAAAAATTATATT
1 TTGACCCCTAAAC-TTTT-AAAATT-TATT
*
99197 TTAACCCCTAAATTCTTTTAAAATCTTATT
1 TTGACCCCTAAA--CTTTTAAAAT-TTATT
* ** *
99227 TTTA-TTCTCGAACTTTCTAAAATTTCATT
1 TTGACCCCT-AAACTTT-TAAAATTT-ATT
99256 TTGACCCC
1 TTGACCCC
99264 CAAGTTTTCT
Statistics
Matches: 102, Mismatches: 12, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
28 8 0.08
29 37 0.36
30 44 0.43
31 12 0.12
32 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.45
Consensus pattern (27 bp):
TTGACCCCTAAACTTTTAAAATTTATT
Found at i:99175 original size:59 final size:60
Alignment explanation
Indices: 99112--99230 Score: 156
Period size: 59 Copynumber: 2.0 Consensus size: 60
99102 TTAAGGGTTG
* *
99112 ACCCTAAAC-TTTTCAAAACTT-TGATTTTGACCCCTAAACT-TTTTAAAAT-TTATATTTTA
1 ACCCTAAACATTTT-AAAAATTAT-ATTTTAACCCCTAAACTCTTTTAAAATCTTAT-TTTTA
*
99171 ACCCTAAACATTTTAAAAATTATATTTTAACCCCTAAATTCTTTTAAAATCTTATTTTTA
1 ACCCTAAACATTTTAAAAATTATATTTTAACCCCTAAACTCTTTTAAAATCTTATTTTTA
99231 TTCTCGAACT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
59 30 0.57
60 19 0.36
61 4 0.08
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.45
Consensus pattern (60 bp):
ACCCTAAACATTTTAAAAATTATATTTTAACCCCTAAACTCTTTTAAAATCTTATTTTTA
Found at i:102908 original size:6 final size:6
Alignment explanation
Indices: 102897--102931 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
102887 TAATAGGTTT
102897 CACACC CACACC CACACC CACACC CACACC CACAC
1 CACACC CACACC CACACC CACACC CACACC CACAC
102932 ACTCAAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (6 bp):
CACACC
Done.