Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001099.1 Kokia drynarioides strain JFW-HI SEQ_112371, 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: 31454
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:2315 original size:6 final size:6
Alignment explanation
Indices: 2306--2336 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2296 AAGTTATCAT
2306 TATTAA TATTAA TATTAA TATTAA T-TTAA TA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TA
2337 ATAACAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATTAA
Found at i:3766 original size:117 final size:118
Alignment explanation
Indices: 3589--4192 Score: 451
Period size: 117 Copynumber: 5.2 Consensus size: 118
3579 AAACTTTTTG
* * * ** ** * *
3589 AAAATTACAATTTTACCCC-GAACTATCCGAAATTAGATTTTTGACCCCAAACTTTC--CAAAAA
1 AAAATTACCATTTTACCCCTAAACTTTCAAAAATTCCATTTTTAACCCTAAA-TTTCTTCAAAAA
*
3651 TTACACATTTACCC-CTAAACTTTCCAAAATTCCA-TTTTAACCTTAATTTTTCAA
65 TTACACATTTACCCTC-AAACTTTCCAAAATTCTATTTTTAACCTTAATTTTTC-A
*
3705 AAAATTACCATTTTACCCCTAAACTTTCAAAAATTCCACTTTTAACCCT-AATTTCTTCAAAAAT
1 AAAATTACCATTTTACCCCTAAACTTTCAAAAATTCCATTTTTAACCCTAAATTTCTTCAAAAAT
* * * * ** *
3769 TACTA-TTTTACCCTCAAACTTCCCAAAATTCTATTTTTGACCCTAAAATTTCC
66 TAC-ACATTTACCCTCAAACTTTCCAAAATTCTATTTTTAACCTTAATTTTTCA
** * **
3822 AAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAA-CCTCGATTTCTTCAAAAAT
1 AAAATTACCATTTTACCCCTAAACTTTCAAAAATTCCATTTTTAACCCTAAATTTCTTCAAAAAT
* **
3886 TAC-CATTTTACCCTCAAAC-TTCCAAAAATTCTATTTTAAACCTCGATTTCTTCA
66 TACACA-TTTACCCTCAAACTTTCC-AAAATTCTATTTTTAACCTTAATTT-TTCA
** * * * **
3940 AATGTTACCGTTTTTCTCCC-AAACTTTCCAAAATTCCATTTTCGACCCTAAAATTTC--CAAAA
1 AAAATTACCATTTTAC-CCCTAAACTTTCAAAAATTCCATTTTTAACCCT-AAATTTCTTCAAAA
* * * *
4002 ATTATCA-TTTTACCCCCGAAC-TTCCAAAAATTCTATTTTTAACCTGT-ATTTCTCCA
64 ATTA-CACATTTACCCTCAAACTTTCC-AAAATTCTATTTTTAACCT-TAATTT-TTCA
* * * * *
4058 AAAAATACCATTTTTA-CCCTCGAAC-TTCCAAAATTCCATTTTTGACCCTAATTTTC-T-AAAA
1 AAAATTACCA-TTTTACCCCT-AAACTTTCAAAAATTCCATTTTTAACCCTAAATTTCTTCAAAA
* * * * **
4119 ATTAC-CATTTTACCCTCGAACTTTCAAAAATT-TCATTTTTGATCGCAATTTTTTCA
64 ATTACACA-TTTACCCTCAAACTTTCCAAAATTCT-ATTTTTAACCTTAA-TTTTTCA
*
4175 AAAATTAACATTTTACCC
1 AAAATTACCATTTTACCC
4193 TCAGATGCCC
Statistics
Matches: 392, Mismatches: 68, Indels: 55
0.76 0.13 0.11
Matches are distributed among these distances:
115 4 0.01
116 33 0.08
117 199 0.51
118 137 0.35
119 14 0.04
120 5 0.01
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (118 bp):
AAAATTACCATTTTACCCCTAAACTTTCAAAAATTCCATTTTTAACCCTAAATTTCTTCAAAAAT
TACACATTTACCCTCAAACTTTCCAAAATTCTATTTTTAACCTTAATTTTTCA
Found at i:3777 original size:59 final size:59
Alignment explanation
Indices: 3645--4192 Score: 448
Period size: 59 Copynumber: 9.3 Consensus size: 59
3635 CCAAACTTTC
* *
3645 CAAAAATTACACA-TTTACCCCTAAACTTTCCAAAATTCCA-TTTTAACCTTAATTT-TT
1 CAAAAATTAC-CATTTTACCCCTAAACTTTCAAAAATTCCATTTTTAACCCTAATTTCTT
*
3702 CAAAAAATTACCATTTTACCCCTAAACTTTCAAAAATTCCACTTTTAACCCTAATTTCTT
1 C-AAAAATTACCATTTTACCCCTAAACTTTCAAAAATTCCATTTTTAACCCTAATTTCTT
* * * * * **
3762 CAAAAATTACTATTTTA-CCCTCAAACTTCCCAAAATTCTATTTTTGACCCTAAAAT-TT
1 CAAAAATTACCATTTTACCCCT-AAACTTTCAAAAATTCCATTTTTAACCCTAATTTCTT
* ** * *
3820 CCAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAA-CCTCGATTTCTT
1 CAAAAATTACCATTTTACCCCTAAACTTTCAAAAATTCCATTTTTAACCCT-AATTTCTT
* * * *
3879 CAAAAATTACCATTTTA-CCCTCAAACTTCCAAAAATTCTA-TTTTAAACCTCGATTTCTT
1 CAAAAATTACCATTTTACCCCT-AAACTTTCAAAAATTCCATTTTTAACCCT-AATTTCTT
** * * * **
3938 CAAATGTTACCGTTTTTCTCCC-AAACTTTCCAAAATTCCATTTTCGACCCTAAAATTTC--
1 CAAAAATTACCATTTTAC-CCCTAAACTTTCAAAAATTCCATTTTTAACCCT--AATTTCTT
* ** * * * *
3997 CAAAAATTATCATTTTACCCCCGAACTTCCAAAAATTCTATTTTTAA-CCTGTATTTCTC
1 CAAAAATTACCATTTTACCCCTAAACTTTCAAAAATTCCATTTTTAACCCT-AATTTCTT
* * * *
4056 CAAAAAATACCATTTTTA-CCCTCGAAC-TTCCAAAATTCCATTTTTGACCCTAA-TT-TT
1 CAAAAATTACCA-TTTTACCCCT-AAACTTTCAAAAATTCCATTTTTAACCCTAATTTCTT
* * * * *
4113 CTAAAAATTACCATTTTA-CCCTCGAACTTTCAAAAATTTCATTTTTGATCGC-AATTTTTT
1 C-AAAAATTACCATTTTACCCCT-AAACTTTCAAAAATTCCATTTTT-AACCCTAATTTCTT
*
4173 CAAAAATTAACATTTTACCC
1 CAAAAATTACCATTTTACCC
4193 TCAGATGCCC
Statistics
Matches: 400, Mismatches: 65, Indels: 49
0.78 0.13 0.10
Matches are distributed among these distances:
57 27 0.07
58 124 0.31
59 214 0.54
60 27 0.07
61 8 0.02
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.38
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCAAAAATTCCATTTTTAACCCTAATTTCTT
Found at i:3929 original size:29 final size:29
Alignment explanation
Indices: 3589--4150 Score: 256
Period size: 29 Copynumber: 19.2 Consensus size: 29
3579 AAACTTTTTG
* *
3589 AAAATTACAATTTTACCC-CGAACTATCC-
1 AAAATTACCATTTTACCCTCAAACT-TCCA
* *
3617 GAAATTA-GATTTTTGACCC-CAAACTTTCCA
1 AAAATTACCA-TTTT-ACCCTCAAAC-TTCCA
3647 AAAATTACACA-TTTACCC-CTAAACTTTCC-
1 AAAATTAC-CATTTTACCCTC-AAAC-TTCCA
* * ** *
3676 AAAATT-CCATTTTAACCTTAATTTTTCAA
1 AAAATTACCATTTTACCCTCAA-ACTTCCA
*
3705 AAAATTACCATTTTACCC-CTAAACTTTCA
1 AAAATTACCATTTTACCCTC-AAACTTCCA
*
3734 AAAATT-CCACTTTTAACCCT--AATTTCTTCA
1 AAAATTACCA-TTTT-ACCCTCAAACTTC--CA
* *
3764 AAAATTACTATTTTACCCTCAAACTTCCC
1 AAAATTACCATTTTACCCTCAAACTTCCA
* * *
3793 AAAATT-CTATTTTTGACCCTAAAATTTCC-
1 AAAATTACCA-TTTT-ACCCTCAAACTTCCA
* *
3822 AAAATTACCATTTTACCCCCGAACTTCCA
1 AAAATTACCATTTTACCCTCAAACTTCCA
* * *
3851 AAAATT-CCATTTTTAACCTC-GATTTCTTCA
1 AAAATTACCA-TTTTACCCTCAAACTTC--CA
3881 AAAATTACCATTTTACCCTCAAACTTCCA
1 AAAATTACCATTTTACCCTCAAACTTCCA
* * * *
3910 AAAATT-CTATTTTAAACCTC-GATTTCTTCA
1 AAAATTACCATTTT-ACCCTCAAACTTC--CA
** * *
3940 AATGTTACCGTTTTTCTCC-CAAACTTTCC-
1 AAAATTACCATTTTAC-CCTCAAAC-TTCCA
* *
3969 AAAATT-CCATTTTCGACCCTAAAATTTCCA
1 AAAATTACCATTTT--ACCCTCAAACTTCCA
* * *
3999 AAAATTATCATTTTACCCCCGAACTTCCA
1 AAAATTACCATTTTACCCTCAAACTTCCA
* * ** **
4028 AAAATT-CTATTTTTAACCTGTATTTCTCCA
1 AAAATTACCA-TTTTACCCTCAAACT-TCCA
* *
4058 AAAAATACCATTTTTACCCTCGAACTTCC-
1 AAAATTACCA-TTTTACCCTCAAACTTCCA
** *
4087 AAAATT-CCATTTTTGACCCT-AATTTTCTA
1 AAAATTACCA-TTTT-ACCCTCAAACTTCCA
* *
4116 AAAATTACCATTTTACCCTCGAACTTTCA
1 AAAATTACCATTTTACCCTCAAACTTCCA
4145 AAAATT
1 AAAATT
4151 TCATTTTTGA
Statistics
Matches: 402, Mismatches: 83, Indels: 97
0.69 0.14 0.17
Matches are distributed among these distances:
27 3 0.01
28 83 0.21
29 160 0.40
30 111 0.28
31 41 0.10
32 4 0.01
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCAAACTTCCA
Found at i:4243 original size:28 final size:28
Alignment explanation
Indices: 4209--4273 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
4199 GCCCCGAATT
* *
4209 TATCCAAAATTATCATTTT-GCCCTCGAG
1 TATCCAAAATTACCATTTTACCCCT-GAG
*
4237 TGTCCAAAATTACCATTTTACCCCTGAG
1 TATCCAAAATTACCATTTTACCCCTGAG
4265 TATCCAAAA
1 TATCCAAAA
4274 ATCACATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 28 0.88
29 4 0.12
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (28 bp):
TATCCAAAATTACCATTTTACCCCTGAG
Found at i:4618 original size:96 final size:97
Alignment explanation
Indices: 4480--4666 Score: 238
Period size: 98 Copynumber: 1.9 Consensus size: 97
4470 AAAACTTTAA
* *
4480 AATCGAGGCAATATTCTTTTATTTCGAGTTTTGAAAATTTGTGCCTT-AACTTA-TCAGGTGCAA
1 AATCGAGGCAATATTCTCTTATTTCGAGTTCTGAAAATTTGTGCCTTAAACTTACT-AGGTGCAA
** *
4543 TTTTTCTTCAAATCGAAATAATCGAATACCCTT
65 CCTTTCTTCAAATCGAAATAAACGAATACCCTT
* *
4576 AATCGAGGCAATGTT-TCCTTATCTTCGA-TTCTGGAAATTTGTGCCTTAAAACTTACTAGGTGC
1 AATCGAGGCAATATTCT-CTTAT-TTCGAGTTCTGAAAATTTGTGCCTT-AAACTTACTAGGTGC
*
4639 AACCTTTCTTCAAATCGAGATAAACGAA
63 AACCTTTCTTCAAATCGAAATAAACGAA
4667 CATCCTTTTC
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
95 1 0.01
96 35 0.45
97 5 0.06
98 36 0.46
99 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (97 bp):
AATCGAGGCAATATTCTCTTATTTCGAGTTCTGAAAATTTGTGCCTTAAACTTACTAGGTGCAAC
CTTTCTTCAAATCGAAATAAACGAATACCCTT
Found at i:16129 original size:155 final size:154
Alignment explanation
Indices: 15844--16405 Score: 743
Period size: 155 Copynumber: 3.6 Consensus size: 154
15834 TAGTACCCCA
* * * *
15844 AAAGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCTCGAAGACACAAAGGGAA
1 AAAGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAG-CAAAAAGGGAA
* *** * *
15909 AGGTTTAAGTCGTAACGGTAAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAGCCACAAT
65 AGGTTTAAGTCGCAACGACGAACCTAGTACCTCAGAGGCATGAAGGGAAAGATCTAAGCCGCAAT
* *
15974 GACGGATCCAGTACTGTAAAGATAC
130 GGCGGATCCAGTACCGTAAAGATAC
* *
15999 AAAGACATGAAGGGAAAGATTTAAGCCGTAACGACGAATCCAGTACCATGAATGCAAAAAGGGAA
1 AAAGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAA-GCAAAAAGGGAA
* *
16064 AGGTTTAAGTCGCAACGACGAACCTAGTACCTTAGAGGCATGAAGCGAAAGATCTAAGCCGCAAT
65 AGGTTTAAGTCGCAACGACGAACCTAGTACCTCAGAGGCATGAAGGGAAAGATCTAAGCCGCAAT
16129 GGCGGATCCAGTACCGTAAAGATAC
130 GGCGGATCCAGTACCGTAAAGATAC
* * ** *
16154 GAAGACATGAAGGGAAAGATTTAAGCCGTAACGGTGAATCCAGTACCACGAACGCACAAAGGGAA
1 AAAGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAA-GCAAAAAGGGAA
16219 AGGTTTAAGTCGCAAC-AGCGAACCTAGTACCTCAGAGGCATGAAGGGAAAGATCTAAGCCGCAA
65 AGGTTTAAGTCGCAACGA-CGAACCTAGTACCTCAGAGGCATGAAGGGAAAGATCTAAGCCGCAA
* * * *
16283 CGGCGAATCCAGAACCGCAAAGATAC
129 TGGCGGATCCAGTACCGTAAAGATAC
* ***
16309 GAAGACATGAAGGGAAAGATTTAAGCCGCAACGGTAAATCCAGTACCACGAAGGCACAAAA-GGA
1 AAAGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAA-GCA-AAAAGGGA
* * * *
16373 AGGGTTTAGGTCGCAATGGCGAACCCT-GTACCT
64 AAGGTTTAAGTCGCAACGACGAA-CCTAGTACCT
16406 TAAAAACATA
Statistics
Matches: 366, Mismatches: 36, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
154 1 0.00
155 358 0.98
156 7 0.02
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.15
Consensus pattern (154 bp):
AAAGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGCAAAAAGGGAAA
GGTTTAAGTCGCAACGACGAACCTAGTACCTCAGAGGCATGAAGGGAAAGATCTAAGCCGCAATG
GCGGATCCAGTACCGTAAAGATAC
Found at i:16195 original size:57 final size:52
Alignment explanation
Indices: 15806--16355 Score: 320
Period size: 49 Copynumber: 10.7 Consensus size: 52
15796 CGCAGAGAAC
* * *
15806 GGAAAGATTTAAGCCGCAACGGTGAATCTAGTACCCCAA-AA--GACATGAAG
1 GGAAAGATTTAAGCCGCAACGGCGAATCCAGTA-CCTAAGAACGGACATGAAG
* * * * **
15856 GGAAAGATCTAAGCCGCAACGACGGATCCAGTACCT-CGAA--GACACAAAG
1 GGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCTAAGAACGGACATGAAG
* * * * * *
15905 GGAAAGGTTTAAGTCGTAACGG-TAAACCTAGTACCTCAG-A--GACATGAAG
1 GGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCTAAGAACGGACATGAAG
* * * * * * *
15954 GGAAAGATCTAAGCCACAATGACGGATCCAGTACTGTAAAGATACAAAGACATGAAG
1 GGAAAGATTTAAGCCGCAACGGCGAATCCAGTAC-CT-AAGA-AC--GGACATGAAG
* * * * **
16011 GGAAAGATTTAAGCCGTAACGACGAATCCAGTACC-ATGAA-TG-CAAAAAG
1 GGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCTAAGAACGGACATGAAG
* * * *
16060 GGAAAGGTTTAAGTCGCAACGACGAA-CCTAGTACCTTAG-A-GG-CATGAAG
1 GGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCTAAGAACGGACATGAAG
* * * *
16109 CGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCGTAAAGATACGAAGACATGAAG
1 GGAAAGATTTAAGCCGCAACGGCGAATCCAGTACC-T-AAGA-ACG--GACATGAAG
* * * *
16166 GGAAAGATTTAAGCCGTAACGGTGAATCCAGTACC-ACGAACGCACA--AAG
1 GGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCTAAGAACGGACATGAAG
* * * *
16215 GGAAAGGTTTAAGTCGCAACAGCGAA-CCTAGTACCTCAG-A-GG-CATGAAG
1 GGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCTAAGAACGGACATGAAG
* * *
16264 GGAAAGATCTAAGCCGCAACGGCGAATCCAGAACCGCAAAGATACGAAGACATGAAG
1 GGAAAGATTTAAGCCGCAACGGCGAATCCAGTA-C-CTAAGA-ACG--GACATGAAG
**
16321 GGAAAGATTTAAGCCGCAACGGTAAATCCAGTACC
1 GGAAAGATTTAAGCCGCAACGGCGAATCCAGTACC
16356 ACGAAGGCAC
Statistics
Matches: 379, Mismatches: 85, Indels: 67
0.71 0.16 0.13
Matches are distributed among these distances:
47 2 0.01
48 8 0.02
49 188 0.50
50 42 0.11
51 10 0.03
53 7 0.02
54 8 0.02
55 1 0.00
56 3 0.01
57 110 0.29
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.15
Consensus pattern (52 bp):
GGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCTAAGAACGGACATGAAG
Found at i:16844 original size:17 final size:17
Alignment explanation
Indices: 16800--16856 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
16790 AAATCTTTAT
*
16800 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
*
16817 CTTAGAA-TTATTTTAAA
1 TTTA-AATTTATTTTAAA
16834 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
16851 TTTAAA
1 TTTAAA
16857 ATTTGAGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 2 0.06
17 31 0.89
18 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:17600 original size:12 final size:12
Alignment explanation
Indices: 17553--17632 Score: 54
Period size: 12 Copynumber: 6.2 Consensus size: 12
17543 GAAAGTTATC
*
17553 AATATTAATATT
1 AATATTAATAAT
17565 AAT-TTAATAAT
1 AATATTAATAAT
* *
17576 AACAATGACAATAAT
1 AA-TAT--TAATAAT
17591 AATATTAATAACAAAT
1 AATATTAAT----AAT
*
17607 AATATTAGTAAT
1 AATATTAATAAT
17619 AATATTAATAAT
1 AATATTAATAAT
17631 AA
1 AA
17633 CAGTAATCAT
Statistics
Matches: 53, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
11 9 0.17
12 22 0.42
13 1 0.02
14 2 0.04
15 8 0.15
16 11 0.21
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (12 bp):
AATATTAATAAT
Found at i:20766 original size:29 final size:29
Alignment explanation
Indices: 20707--20785 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
20697 TTGGAAAATT
* ** *
20707 GAGGGTAAAATGGTAATTTTTTGATGCTC
1 GAGGGTAAAATAGTAATTTTTCAAAGCTC
* *
20736 GAGGGTAAAATAGTGATTTTTCAAAGTTC
1 GAGGGTAAAATAGTAATTTTTCAAAGCTC
*
20765 GAGGGCAAAATTA-TAATTTTT
1 GAGGGTAAAA-TAGTAATTTTT
20786 GAGAAGTTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 39 0.95
30 2 0.05
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (29 bp):
GAGGGTAAAATAGTAATTTTTCAAAGCTC
Found at i:20829 original size:87 final size:89
Alignment explanation
Indices: 20738--20921 Score: 207
Period size: 87 Copynumber: 2.1 Consensus size: 89
20728 TGATGCTCGA
** *
20738 GGGTAAAATA-GTGATTTTTCAAAGTTCGAGGGCAAAATTATAATTTTTGAGAAGTTTG-GGGC-
1 GGGTAAAATATGTGATTTTTCAAAGTAAGAGGGCAAAAATATAA-TTTT-AGAAGTTTGAGGGCA
* *
20800 AAAAATTTATTTTTTG-GAAGTACGG
64 AAAAATGTAATTTTTGAGAAGTACGG
** * * *
20825 GGGTAAAA-ATGTGATTTTTGGAAGTAAGAGGGTAAAAATGTGATTTTAGAAGTTTGAGGGCAAA
1 GGGTAAAATATGTGATTTTTCAAAGTAAGAGGGCAAAAATATAATTTTAGAAGTTTGAGGGCAAA
*
20889 AAATGTAATTTTTGAGAAGTTCGG
66 AAATGTAATTTTTGAGAAGTACGG
*
20913 GGTTAAAAT
1 GGGTAAAAT
20922 GCATTTTTAG
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
85 9 0.11
86 9 0.11
87 47 0.59
88 15 0.19
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (89 bp):
GGGTAAAATATGTGATTTTTCAAAGTAAGAGGGCAAAAATATAATTTTAGAAGTTTGAGGGCAAA
AAATGTAATTTTTGAGAAGTACGG
Found at i:20920 original size:29 final size:29
Alignment explanation
Indices: 20738--20990 Score: 144
Period size: 29 Copynumber: 8.7 Consensus size: 29
20728 TGATGCTCGA
* *
20738 GGGT-AAAATAGTGATTTTTCA-AAGTTCG
1 GGGTAAAAAT-GTAATTTTTGAGAAGTTCG
* * * *
20766 AGGGCAAAATTATAATTTTTGAGAAGTTTG
1 -GGGTAAAAATGTAATTTTTGAGAAGTTCG
* * * *
20796 GGGCAAAAATTTATTTTTTG-GAAGTACGG
1 GGGTAAAAATGTAATTTTTGAGAAGTTC-G
* **
20825 GGGTAAAAATGTGATTTTTG-GAAGTAAG
1 GGGTAAAAATGTAATTTTTGAGAAGTTCG
* *
20853 AGGGTAAAAATGTGA-TTTT-AGAAGTTTG
1 -GGGTAAAAATGTAATTTTTGAGAAGTTCG
*
20881 AGGGCAAAAAATGTAATTTTTGAGAAGTTCG
1 -GGG-TAAAAATGTAATTTTTGAGAAGTTCG
* *
20912 GGGTTAAAATG-CATTTTT-AGAAAGTTCG
1 GGGTAAAAATGTAATTTTTGAG-AAGTTCG
* * * * **
20940 ATGGTTAAAATGTAATTTTTAGAAAATTTAT
1 -GGGTAAAAATGTAATTTTT-GAGAAGTTCG
*
20971 GGGTTAAAATGTAATTTTTG
1 GGGTAAAAATGTAATTTTTG
20991 GAAAGTTTAG
Statistics
Matches: 180, Mismatches: 31, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
27 2 0.01
28 33 0.18
29 91 0.51
30 41 0.23
31 12 0.07
32 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGAGAAGTTCG
Found at i:20921 original size:58 final size:58
Alignment explanation
Indices: 20758--20997 Score: 178
Period size: 58 Copynumber: 4.1 Consensus size: 58
20748 GTGATTTTTC
* * * * ** * * *
20758 AAAGTTCGAGGGCAAAATTATAATTTTTGAGAAGTTTGGGGCAAAAATTTATTTTTTG
1 AAAGTTCGAGGGAAAAAATGTAATTTTTGAGAAGTTAGGGGTTAAAATGTAATTTTAG
* * * * * * * *
20816 GAAGTACGGGGGTAAAAATGTGATTTTTG-GAAGTAAGAGGGTAAAAATGTGATTTTAG
1 AAAGTTCGAGGGAAAAAATGTAATTTTTGAGAAGTTAG-GGGTTAAAATGTAATTTTAG
* * * *
20874 -AAGTTTGAGGGCAAAAAATGTAATTTTTGAGAAGTTCGGGGTTAAAATGCATTTTTAG
1 AAAGTTCGAGGG-AAAAAATGTAATTTTTGAGAAGTTAGGGGTTAAAATGTAATTTTAG
* ** * * * *
20932 AAAGTTCGATGGTTAAAATGTAATTTTTAGAAAATTTATGGGTTAAAATGTAATTTTTGG
1 AAAGTTCGAGGGAAAAAATGTAATTTTT-GAGAAGTTAGGGGTTAAAATGTAA-TTTTAG
20992 AAAGTT
1 AAAGTT
20998 TAGGGGTCAA
Statistics
Matches: 140, Mismatches: 36, Indels: 10
0.75 0.19 0.05
Matches are distributed among these distances:
57 14 0.10
58 82 0.59
59 33 0.24
60 11 0.08
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (58 bp):
AAAGTTCGAGGGAAAAAATGTAATTTTTGAGAAGTTAGGGGTTAAAATGTAATTTTAG
Found at i:20960 original size:30 final size:30
Alignment explanation
Indices: 20888--20997 Score: 129
Period size: 30 Copynumber: 3.7 Consensus size: 30
20878 TTGAGGGCAA
*
20888 AAAATGTAATTTTT-GAGAAGTTCG-GGGTT
1 AAAATGTAATTTTTAGA-AAGTTCGATGGTT
*
20917 AAAATG-CATTTTTAGAAAGTTCGATGGTT
1 AAAATGTAATTTTTAGAAAGTTCGATGGTT
* *
20946 AAAATGTAATTTTTAGAAAATT-TATGGGTT
1 AAAATGTAATTTTTAGAAAGTTCGAT-GGTT
*
20976 AAAATGTAATTTTTGGAAAGTT
1 AAAATGTAATTTTTAGAAAGTT
20998 TAGGGGTCAA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
28 13 0.19
29 20 0.29
30 37 0.53
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.40
Consensus pattern (30 bp):
AAAATGTAATTTTTAGAAAGTTCGATGGTT
Found at i:21018 original size:30 final size:30
Alignment explanation
Indices: 20984--21049 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
20974 TTAAAATGTA
* * *
20984 ATTTTTGGAAAGTTTAGGGGTCAAAACATG
1 ATTTTTGAAAAGTTTAAGGATCAAAACATG
* *
21014 ATTTTTGAAAAGTTTAAGGATTAAAATATG
1 ATTTTTGAAAAGTTTAAGGATCAAAACATG
21044 ATTTTT
1 ATTTTT
21050 AGACAATTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.41
Consensus pattern (30 bp):
ATTTTTGAAAAGTTTAAGGATCAAAACATG
Found at i:22241 original size:13 final size:13
Alignment explanation
Indices: 22223--22252 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
22213 CTGTTTTTGA
22223 AATAAATGAGAAT
1 AATAAATGAGAAT
*
22236 AATAAATGATAAT
1 AATAAATGAGAAT
22249 AATA
1 AATA
22253 GTACAGCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (13 bp):
AATAAATGAGAAT
Found at i:22962 original size:11 final size:10
Alignment explanation
Indices: 22926--22983 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
22916 GGACATTATT
22926 AATTTAAATA
1 AATTTAAATA
22936 AATTTAAACTTA
1 AATTTAAA--TA
22948 AATTTACAATA
1 AATTTA-AATA
22959 AATTTAAAT-
1 AATTTAAATA
*
22968 --TTCAAATA
1 AATTTAAATA
22976 AATTTAAA
1 AATTTAAA
22984 CTTAAAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 6 0.15
10 16 0.40
11 8 0.20
12 8 0.20
13 2 0.05
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (10 bp):
AATTTAAATA
Found at i:22965 original size:17 final size:17
Alignment explanation
Indices: 22940--23002 Score: 83
Period size: 17 Copynumber: 3.7 Consensus size: 17
22930 TAAATAAATT
*
22940 TAAACTTAAATTTACAA
1 TAAATTTAAATTTACAA
22957 TAAATTTAAATTT-CAAA
1 TAAATTTAAATTTAC-AA
* *
22974 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTACAA
22991 TAAATTTAAATT
1 TAAATTTAAATT
23003 CTTTTGAGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
16 1 0.03
17 39 0.98
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTACAA
Found at i:22966 original size:6 final size:6
Alignment explanation
Indices: 22926--23002 Score: 60
Period size: 6 Copynumber: 13.7 Consensus size: 6
22916 GGACATTATT
*
22926 AATTTA AA--TA AATTTA AACTTA AATTTA CAA--TA AATTTA AATTTCA
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTT-A
* *
22972 AA--TA AATTTA AACTTA AA-ATA AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATT
23003 CTTTTGAGCA
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
4 9 0.16
5 7 0.12
6 36 0.63
7 5 0.09
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:25599 original size:21 final size:21
Alignment explanation
Indices: 25557--25600 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
25547 TTACCCCAAA
* *
25557 CCCCAAATCTTTTTACTTTTC
1 CCCCAAAACTTTTTACTCTTC
25578 CCCCAAAAC-TTTTACTCCTTC
1 CCCCAAAACTTTTTACT-CTTC
25599 CC
1 CC
25601 ACTTCCCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.20, C:0.41, G:0.00, T:0.39
Consensus pattern (21 bp):
CCCCAAAACTTTTTACTCTTC
Found at i:30354 original size:69 final size:68
Alignment explanation
Indices: 30232--30402 Score: 204
Period size: 69 Copynumber: 2.5 Consensus size: 68
30222 TATACGGAAC
* * *
30232 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACAC
1 AAACAGAGAGTACACAAAGTACTAATAAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACAA
30295 AGTGCT
63 AGTGCT
30301 AAACAGAGAGTACACAAAGTACTAATAAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAA
1 AAACAGAGAGTACACAAAGTACTAATAAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACAAA
30365 GTGCT
64 GTGCT
* * * * *
30370 AATCAGAGAGCACACACAGTGCTAATAACAGAG
1 AAACAGAGAGTACACAAAGTACTAATAAGAGAG
30403 GGCATGAGAC
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
68 2 0.02
69 60 0.67
70 11 0.12
71 10 0.11
72 7 0.08
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.12
Consensus pattern (68 bp):
AAACAGAGAGTACACAAAGTACTAATAAGAGAGCACAAAAGTGCTGAACAGAGAGCACACAAAGT
GCT
Found at i:30395 original size:23 final size:23
Alignment explanation
Indices: 30235--30395 Score: 177
Period size: 23 Copynumber: 7.0 Consensus size: 23
30225 ACGGAACAAA
* *
30235 CAGAGAGTAC-CAAAGTACTAA-
1 CAGAGAGCACACAAAGTGCTAAT
*
30256 CAGAGAGCACA-TAAGTGCTGGGCAA-
1 CAGAGAGCACACAAAGTGCT----AAT
* *
30281 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAT
* *
30304 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
30327 AAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
30350 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
30373 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
30396 AACAGAGGGC
Statistics
Matches: 119, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
21 15 0.13
22 2 0.02
23 83 0.70
25 13 0.11
26 6 0.05
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.13
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Done.