Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009480.1 Kokia drynarioides strain JFW-HI SEQ_124189, 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: 17653
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2985 original size:3 final size:3
Alignment explanation
Indices: 2977--3010 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2967 ACTATCTCAC
*
2977 CTT CTT CTT CTC CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
3011 ATGTTCATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:5616 original size:29 final size:31
Alignment explanation
Indices: 5584--5654 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 31
5574 ACTCGTATTT
* *
5584 AATTATTATTTTTACCCTTG-AACTT-TCAA
1 AATTATTATTTTTAACCTTGAAACTTCTAAA
* *
5613 AATT-CTAATTTTAACCTTGAAACTTCTAAA
1 AATTATTATTTTTAACCTTGAAACTTCTAAA
*
5643 AATTATCATTTT
1 AATTATTATTTT
5655 ACCTCCGAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
28 12 0.38
29 9 0.28
30 7 0.22
31 4 0.12
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.46
Consensus pattern (31 bp):
AATTATTATTTTTAACCTTGAAACTTCTAAA
Found at i:5658 original size:29 final size:27
Alignment explanation
Indices: 5584--5658 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
5574 ACTCGTATTT
* *
5584 AATTATTATTTTTACCCTTGAACTTTCAA
1 AATTA-TAATTTTA-CCTTGAACTTTAAA
*
5613 AATTCTAATTTTAACCTTGAAACTTCTAAA
1 AATTATAATTTT-ACCTTG-AACTT-TAAA
*
5643 AATTATCATTTTACCT
1 AATTATAATTTTACCT
5659 CCGAATTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 11 0.29
29 14 0.37
30 13 0.34
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (27 bp):
AATTATAATTTTACCTTGAACTTTAAA
Found at i:5673 original size:29 final size:29
Alignment explanation
Indices: 5640--5734 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
5630 TGAAACTTCT
5640 AAAAATTATCATTTTACCTCCGAATTTTC
1 AAAAATTATCATTTTACCTCCGAATTTTC
* ** *
5669 AAAAAAT-TCATTTTTGACCTCAAAACTTTC
1 AAAAATTATCA-TTTT-ACCTCCGAATTTTC
* * * * * *
5699 AAAGATTACCCTTTTACCTCCGGATGTCC
1 AAAAATTATCATTTTACCTCCGAATTTTC
5728 AAAAATT
1 AAAAATT
5735 CCATTTTTGA
Statistics
Matches: 48, Mismatches: 15, Indels: 6
0.70 0.22 0.09
Matches are distributed among these distances:
28 3 0.06
29 24 0.50
30 20 0.42
31 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (29 bp):
AAAAATTATCATTTTACCTCCGAATTTTC
Found at i:5786 original size:60 final size:58
Alignment explanation
Indices: 5703--5858 Score: 163
Period size: 60 Copynumber: 2.7 Consensus size: 58
5693 ACTTTCAAAG
* * * *
5703 ATTACCCTTTTACCTCCGGATGTCCAAAAATTCCATTTTTGATCCCGATTTTTTCTA-AA
1 ATTACCGTCTTACCCCCGAATGTCCAAAAATTCCATTTTTGATCCCGA--TTTTCTAGAA
* * *
5762 AGTTACCGTCTTACCCCCGAATGTCCAAAAATTCCGTTTTTTATCTCGATTTTCTAGAA
1 A-TTACCGTCTTACCCCCGAATGTCCAAAAATTCCATTTTTGATCCCGATTTTCTAGAA
* * * **
5821 ATTACCTTTTTACCCTCGAATGT-TTAAAATTCCATTTT
1 ATTACCGTCTTACCCCCGAATGTCCAAAAATTCCATTTT
5859 AAACTTCAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
57 12 0.15
58 26 0.32
59 4 0.05
60 40 0.49
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (58 bp):
ATTACCGTCTTACCCCCGAATGTCCAAAAATTCCATTTTTGATCCCGATTTTCTAGAA
Found at i:5907 original size:28 final size:28
Alignment explanation
Indices: 5874--5935 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
5864 TCAAATTTTC
*
5874 CCAAAATTACCGTTTTG-CTCTCGAG-AGT
1 CCAAAATTACCATTTTGAC-CTCGAGTA-T
5902 CCAAAATTACCATTTTGACCTCGAGTAT
1 CCAAAATTACCATTTTGACCTCGAGTAT
5930 CCAAAA
1 CCAAAA
5936 AGTCTCATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (28 bp):
CCAAAATTACCATTTTGACCTCGAGTAT
Found at i:7866 original size:146 final size:148
Alignment explanation
Indices: 7603--7876 Score: 349
Period size: 146 Copynumber: 1.9 Consensus size: 148
7593 AAACATGACG
* ** *
7603 GGAAAGATCTAAGACCGCAACGGCGGATCTAGTACTGCAAAGATACAAAAGGGAAGGGTTTAAGT
1 GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGA-ACAAAAGGGAAAGGTTTAAGT
* * * * *
7668 CGCAACGGTGAACCTTATACCTCAGAGACATGATGAGAAATATCTAAGCCGCAACGGTGGATCCA
65 CGCAACGGCGAACCTTATACCTCAGAGACATAAAGAGAAAGATCTAAGCCGCAACGGCGGATCCA
7733 GTGCCGCGAAGACATGAAA
130 GTGCCGCGAAGACATGAAA
* *
7752 GGAAAGATCTAAG-TCGCAACGGCGGATCCAGTACCACAAAG-ACAGAAGGGAAAGGTTTAAGTC
1 GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGAACAAAAGGGAAAGGTTTAAGTC
* * * * *
7815 GTAATGGCGGA-CTTAGTACCTCAGAGACATAAAGGGAAAGAT-TTAGACCGCAACGGCGGATC
66 GCAACGGCGAACCTTA-TACCTCAGAGACATAAAGAGAAAGATCTAAG-CCGCAACGGCGGATC
7877 TAGTACTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
145 7 0.07
146 63 0.59
148 24 0.22
149 13 0.12
ACGTcount: A:0.36, C:0.20, G:0.28, T:0.16
Consensus pattern (148 bp):
GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGAACAAAAGGGAAAGGTTTAAGTC
GCAACGGCGAACCTTATACCTCAGAGACATAAAGAGAAAGATCTAAGCCGCAACGGCGGATCCAG
TGCCGCGAAGACATGAAA
Found at i:7899 original size:146 final size:147
Alignment explanation
Indices: 7602--7970 Score: 325
Period size: 146 Copynumber: 2.5 Consensus size: 147
7592 GAAACATGAC
* * ** * *
7602 GGGAAAGATCTAAGACCGCAACGGCGGATCTAGTACTGCAAAGATACAAAAGGGAAGGGTTTAAG
1 GGGAAAGATCTAAG-TCGCAACGGCGGATCCAGTACCACAAAG--ACAGAAGGGAAAGGTTTAAG
* * * * * * *
7667 TCGCAACGGTGAACCTTATACCTCAGAGACATGATGAGAAATATCTAAGCCGCAACGGTGGATCC
63 TCGTAATGGCGAACCTTATACCTCAGAGACATAAAGAGAAAGATCTAAGCCGCAACGGCGGATCC
* * * **
7732 AGTGCCGCGAAGACATGAAA
128 AGTACCACAAAGACACAAAA
7752 -GGAAAGATCTAAGTCGCAACGGCGGATCCAGTACCACAAAGACAGAAGGGAAAGGTTTAAGTCG
1 GGGAAAGATCTAAGTCGCAACGGCGGATCCAGTACCACAAAGACAGAAGGGAAAGGTTTAAGTCG
* * * *
7816 TAATGGCGGA-CTTAGTACCTCAGAGACATAAAGGGAAAGAT-TTAGACCGCAACGGCGGATCTA
66 TAATGGCGAACCTTA-TACCTCAGAGACATAAAGAGAAAGATCTAAG-CCGCAACGGCGGATCCA
* *
7879 GTACTACAAAGATACAAAA
129 GTACCACAAAGACACAAAA
* * ** * * * *
7898 GGGAAAGGTTTAAGTTACAACGGC-GA-ACTGTGAACCTCAGAAGACAAGAAGGGAAAGATTTAA
1 GGGAAAGATCTAAGTCGCAACGGCGGATCCAGT--ACCACA-AAGAC-AGAAGGGAAAGGTTTAA
*
7961 GCCGTAATGG
62 GTCGTAATGG
7971 TGGATCCAGT
Statistics
Matches: 179, Mismatches: 33, Indels: 15
0.79 0.15 0.07
Matches are distributed among these distances:
145 10 0.06
146 78 0.44
147 24 0.13
148 29 0.16
149 38 0.21
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (147 bp):
GGGAAAGATCTAAGTCGCAACGGCGGATCCAGTACCACAAAGACAGAAGGGAAAGGTTTAAGTCG
TAATGGCGAACCTTATACCTCAGAGACATAAAGAGAAAGATCTAAGCCGCAACGGCGGATCCAGT
ACCACAAAGACACAAAA
Found at i:7919 original size:50 final size:50
Alignment explanation
Indices: 7618--8112 Score: 211
Period size: 50 Copynumber: 10.0 Consensus size: 50
7608 GATCTAAGAC
* *
7618 CGCAACGGCGGATCTAGTACTGCAAAGATACAAAAGGGAAGGGTTTAAGT
1 CGCAACGGCGGATCTAGTACTACAAAGATACAAAAGGGAAAGGTTTAAGT
* * * * * * * ** * *
7668 CGCAACGGTGAACCTTA-TACCT-C--AGAGACATGATGAGAAATATCTAAGC
1 CGCAACGGCGGATC-TAGTA-CTACAAAGATACA-AAAGGGAAAGGTTTAAGT
* * * ** * * ** * *
7717 CGCAACGGTGGATCCAGTGCCGCGAAGACATGAAA-GGAAAGATCTAAGT
1 CGCAACGGCGGATCTAGTACTACAAAGATACAAAAGGGAAAGGTTTAAGT
* * *
7766 CGCAACGGCGGATCCAGTACCACAAAG--ACAGAAGGGAAAGGTTTAAGT
1 CGCAACGGCGGATCTAGTACTACAAAGATACAAAAGGGAAAGGTTTAAGT
* * * * *
7814 CGTAATGGCGGA-CTTAGTACCT-C--AGAGACATAAAGGGAAAGATTT-AGAC
1 CGCAACGGCGGATC-TAGTA-CTACAAAGATACA-AAAGGGAAAGGTTTAAG-T
7863 CGCAACGGCGGATCTAGTACTACAAAGATACAAAAGGGAAAGGTTTAAGT
1 CGCAACGGCGGATCTAGTACTACAAAGATACAAAAGGGAAAGGTTTAAGT
** * * *
7913 TACAACGGC-GAACT-GTGAACCT-CAGAAG--ACAAGAAGGGAAAGATTTAAGC
1 CGCAACGGCGGATCTAGT--A-CTACA-AAGATACAA-AAGGGAAAGGTTTAAGT
* * * * * *
7963 CGTAATGGTGGATCCAGTACCACAAATATACAAAAGGGAAAGGTTTAAGT
1 CGCAACGGCGGATCTAGTACTACAAAGATACAAAAGGGAAAGGTTTAAGT
* * * * * *
8013 CGCAACGGCAGACCGT-GTACCTTA-GAAGATA-AGAAGGGAAAGATTTAAGC
1 CGCAACGGCGGATC-TAGTA-C-TACAAAGATACAAAAGGGAAAGGTTTAAGT
* * * *** *
8063 CGCAACGGCGAATCTAATACCACAAAGATTTGAAGGGGAAAGGTTTAAGT
1 CGCAACGGCGGATCTAGTACTACAAAGATACAAAAGGGAAAGGTTTAAGT
8113 TACAATGACG
Statistics
Matches: 324, Mismatches: 86, Indels: 70
0.68 0.18 0.15
Matches are distributed among these distances:
46 2 0.01
47 4 0.01
48 45 0.14
49 105 0.32
50 131 0.40
51 34 0.10
52 3 0.01
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.18
Consensus pattern (50 bp):
CGCAACGGCGGATCTAGTACTACAAAGATACAAAAGGGAAAGGTTTAAGT
Found at i:7982 original size:100 final size:100
Alignment explanation
Indices: 7740--8117 Score: 410
Period size: 100 Copynumber: 3.8 Consensus size: 100
7730 CCAGTGCCGC
* * * * *
7740 GAAGACATGAAAGGAAAGATCTAAGTCGCAACGGCGGATCCAGTACCACAAAG--ACAGAAGGGA
1 GAAGACAAGAAGGGAAAGATTTAAGCCGCAACGGCGGATCCAGTACCACAAAGATACAAAAGGGA
** * *
7803 AAGGTTTAAGTCGTAATGGCGGACT-TAGTACCTCA
66 AAGGTTTAAGTCACAACGGCGAACTGT-GTACCTCA
* *
7838 G-AGACATA-AAGGGAAAGATTT-AGACCGCAACGGCGGATCTAGTACTACAAAGATACAAAAGG
1 GAAGACA-AGAAGGGAAAGATTTAAG-CCGCAACGGCGGATCCAGTACCACAAAGATACAAAAGG
* *
7900 GAAAGGTTTAAGTTACAACGGCGAACTGTGAACCTCA
64 GAAAGGTTTAAGTCACAACGGCGAACTGTGTACCTCA
* * * *
7937 GAAGACAAGAAGGGAAAGATTTAAGCCGTAATGGTGGATCCAGTACCACAAATATACAAAAGGGA
1 GAAGACAAGAAGGGAAAGATTTAAGCCGCAACGGCGGATCCAGTACCACAAAGATACAAAAGGGA
* * *
8002 AAGGTTTAAGTCGCAACGGC-AGACCGTGTACCTTA
66 AAGGTTTAAGTCACAACGGCGA-ACTGTGTACCTCA
* * * * *** *
8037 GAAGATAAGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAATACCACAAAGATTTGAAGGGGA
1 GAAGACAAGAAGGGAAAGATTTAAGCCGCAACGGCGGATCCAGTACCACAAAGATACAAAAGGGA
*
8102 AAGGTTTAAGTTACAA
66 AAGGTTTAAGTCACAA
8118 TGACGAACCC
Statistics
Matches: 233, Mismatches: 38, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
96 2 0.01
97 41 0.18
98 1 0.00
99 39 0.17
100 148 0.64
101 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.17
Consensus pattern (100 bp):
GAAGACAAGAAGGGAAAGATTTAAGCCGCAACGGCGGATCCAGTACCACAAAGATACAAAAGGGA
AAGGTTTAAGTCACAACGGCGAACTGTGTACCTCA
Found at i:8090 original size:200 final size:197
Alignment explanation
Indices: 7740--8117 Score: 483
Period size: 200 Copynumber: 1.9 Consensus size: 197
7730 CCAGTGCCGC
* * *
7740 GAAGACATGAAAGGAAAGATCTAAGTCGCAACGGCGGATCCAGTACCACAAAGACAGAAGGGAAA
1 GAAGACAAGAAAGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAAAGACAAAAGGGAAA
* * * *
7805 GGTTTAAGTCGTAATGGCGGACTTAGTACCTCAGAGACATAAAGGGAAAGATTTAGACCGCAACG
66 GGTTTAAGTCGCAACGGCAGACGTAGTACCTCAGAGACATAAAGGGAAAGATTTAGACCGCAACG
* * *
7870 GCGGATCTAGTACTACAAAGATACAAAAGGGAAAGGTTTAAGTTACAACGGCGAACTGTGAACCT
131 GCGAATCTAATACCACAAAGATACAAAAGGGAAAGGTTTAAGTTACAACGGCGAACTGTGAACCT
7935 CA
196 CA
* * * * * *
7937 GAAGACAAGAAGGGAAAGATTTAAGCCGTAATGGTGGATCCAGTACCACAAATATACAAAAGGGA
1 GAAGACAAGAAAGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC-AA-AGACAAAAGGGA
* *
8002 AAGGTTTAAGTCGCAACGGCAGACCGT-GTACCTTAGA-AGATAAGAAGGGAAAGATTTA-AGCC
64 AAGGTTTAAGTCGCAACGGCAGA-CGTAGTACCTCAGAGACAT-A-AAGGGAAAGATTTAGA-CC
*** *
8064 GCAACGGCGAATCTAATACCACAAAGATTTGAAGGGGAAAGGTTTAAGTTACAA
125 GCAACGGCGAATCTAATACCACAAAGATACAAAAGGGAAAGGTTTAAGTTACAA
8118 TGACGAACCC
Statistics
Matches: 153, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
197 42 0.27
198 5 0.03
199 41 0.27
200 65 0.42
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.17
Consensus pattern (197 bp):
GAAGACAAGAAAGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAAAGACAAAAGGGAAA
GGTTTAAGTCGCAACGGCAGACGTAGTACCTCAGAGACATAAAGGGAAAGATTTAGACCGCAACG
GCGAATCTAATACCACAAAGATACAAAAGGGAAAGGTTTAAGTTACAACGGCGAACTGTGAACCT
CA
Found at i:8396 original size:101 final size:101
Alignment explanation
Indices: 8220--8413 Score: 262
Period size: 101 Copynumber: 1.9 Consensus size: 101
8210 CTACAATGAC
* * * *
8220 AAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAAATAAAGCTTTAACGTCAATTCCTATCCTC
1 AAGTCTTTATCTCTCTGAAGTTGCAATAAGAGCAAAATAAAGCTTCAACATCAAATCCTATCCTC
* * * *
8285 TTGAATTTGCAGTAAAGTTGGATTAAAAACAATAGT
66 CTGAAGTTGCAGCAAAGTTGGAATAAAAACAATAGT
* * * * *
8321 AAGTCTTTATTTCTCTGAAGTTGTAATAAGAGCAAGATGAAGCTTCAACATCAAATCCTATCTTC
1 AAGTCTTTATCTCTCTGAAGTTGCAATAAGAGCAAAATAAAGCTTCAACATCAAATCCTATCCTC
*
8386 CTGAAGTTGCAGCGAAGTTGGAATAAAA
66 CTGAAGTTGCAGCAAAGTTGGAATAAAA
8414 CTACAGCAGC
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 79 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (101 bp):
AAGTCTTTATCTCTCTGAAGTTGCAATAAGAGCAAAATAAAGCTTCAACATCAAATCCTATCCTC
CTGAAGTTGCAGCAAAGTTGGAATAAAAACAATAGT
Found at i:8928 original size:206 final size:206
Alignment explanation
Indices: 8634--10262 Score: 2346
Period size: 206 Copynumber: 7.9 Consensus size: 206
8624 TCAAAGCGAG
* *
8634 AAATCTTCGAACCCCGGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAA
1 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
* * *
8699 CTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCAGAT
66 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* * * * * *
8764 TGAAACAAACGATGCGATCGTCTTCCTAATGAGATACTGAGCAGAAGACCAAATCAAACTCA-GA
131 TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACG-
*
8828 CTCGATATGAGC
195 CTCGATGTGAGC
* * *
8840 AAATATTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGAAATAAAATGGTTAG
1 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
* * *
8905 CTTTCTGATGAGATACCGAGAAGTGGACCAAATTCGTCTTCCTGAT-ATGATACAGAGAAACGGA
66 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGA-GATACAGAGAAGCGGA
* * *
8969 TTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACC
130 TTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACG
9034 CTCG-TGGTGAGC
195 CTCGAT-GTGAGC
* * * * *
9046 AAATCTTCAAATCCCAGCTTCCTGATGAGATACTGAGAAACGGGTCGAAGCAATAAAATAGTTAG
1 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
*
9111 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGATAAGCGGAT
66 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* * ** *
9176 TGAAACAAACGACACAGTCATCTTTTTGATGAGATACTGAGAAGAAGACCAAATCAAACGCACGC
131 TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
9241 TCGATGTGAGC
196 TCGATGTGAGC
* * *
9252 AAATCTTCGAACCCCAACTTCCTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAG
1 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
* * *
9317 CTTCCTGATGAGATACTGAGAAGTGGACTAAATTCATCTTCTTGATGAGATACAGAGAAGCGGAT
66 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* ** *
9382 TAAAACAAACGACGCGGTCATCTTCCTGAAAAGATACTGAGAAGAATACCAAATCAAACCCACGC
131 TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
9447 TCGATGTGAGC
196 TCGATGTGAGC
* * * *
9458 AAATCTTCGAATCCCAGCTTCTTGATGAGATACTGAGAAGCGGGTCGAAACAATAAAATGGTTAG
1 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
* ** * *
9523 CTTCCTGATGAGATACTGAGAAGTAGAGTAAATTCATCTTCTTGATGAGATACAGAGAAGCGGAT
66 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* * * *
9588 TGAAACAAACGACGCGGTCATCTTCTTGATGAGATACTGAGAATAAGACCAAATCAAACCTATGC
131 TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
*
9653 TCGAGGTGAGC
196 TCGATGTGAGC
* * * *
9664 AAATCTTCGAACACCAGCTTCCTGATGAGACACTGAGCAGTAGGTCGAAGCAATAAAATGGTTAG
1 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
* * *
9729 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGTGATACAAAAAAGCGGAT
66 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* *
9794 TGAAATAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAAAAGACCAAATCAAACCCACGC
131 TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
9859 TCGATGTGAGC
196 TCGATGTGAGC
*
9870 AAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
1 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
* * *
9935 CTTCCTGATGAGATACTAAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGGAT
66 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* * * * * *
10000 TTAAACAAATGACACGGTCATCTTCCTGATGAGACACAGAGAAGAAGACCAAATCTAACCCACGC
131 TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
10065 TCGATGTGAGC
196 TCGATGTGAGC
* * * *
10076 AAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCAAGTCGAAGCAATTAAGTGGTTAG
1 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
* * * * * * * * *
10141 CTTCCTGATGAGATACAGAGAAGTGAACCTAATCCTTCTTCCTAATGAAACACAGAGAAGTGGAT
66 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
** ** * * * *
10206 CAAAACAAGTGATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAGTCAA
131 TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
10263 TGAAACCAGA
Statistics
Matches: 1276, Mismatches: 142, Indels: 10
0.89 0.10 0.01
Matches are distributed among these distances:
205 2 0.00
206 1272 1.00
207 2 0.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (206 bp):
AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
TCGATGTGAGC
Found at i:10640 original size:6 final size:6
Alignment explanation
Indices: 10631--10696 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
10621 GATTTATTTC
* ** * *
10631 TAAATT TAAATT TAAATT CATTTT TAAATT TAAATT T-AGTT TAAACT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
10678 TAAACTT TAAAAT TAAATT
1 TAAA-TT TAAATT TAAATT
10697 CAAAGTCCAT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
5 4 0.09
6 37 0.80
7 5 0.11
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (6 bp):
TAAATT
Found at i:10653 original size:24 final size:24
Alignment explanation
Indices: 10617--10668 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
10607 TTTAAATTAT
* *
10617 TTTAGATTTATTTCTAAATTTAAA
1 TTTAAATTCATTTCTAAATTTAAA
*
10641 TTTAAATTCATTTTTAAATTTAAA
1 TTTAAATTCATTTCTAAATTTAAA
10665 TTTA
1 TTTA
10669 GTTTAAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTAAATTCATTTCTAAATTTAAA
Found at i:12620 original size:29 final size:29
Alignment explanation
Indices: 12549--12778 Score: 114
Period size: 28 Copynumber: 7.9 Consensus size: 29
12539 GGAGGTCCTT
* * *
12549 AAACTTCCCAAAATTCCATTTTTGA-CCTC
1 AAACTTCCAAAAATTAC-TTTTTTACCCTC
*
12578 GAAACTTTTCAAAAATTACTTTTTTACCCTC
1 -AAAC-TTCCAAAAATTACTTTTTTACCCTC
* * * * *
12609 GAGCTTCC-AAAATTCCATTTTTAACCCTA
1 AAACTTCCAAAAATTAC-TTTTTTACCCTC
* ** *
12638 AAACTTCTAAAAATTAC-CATTTACCCCC
1 AAACTTCCAAAAATTACTTTTTTACCCTC
* * *
12666 AAACTTCCAAAAATTTCATTTTTGA-TCTC
1 AAACTTCCAAAAATTAC-TTTTTTACCCTC
* **
12695 -AACTTTCAAAAATTACCATTTTACCC-C
1 AAACTTCCAAAAATTACTTTTTTACCCTC
* * *
12722 GAACTTCCAAAAATTCCATTTTTGACCC-C
1 AAACTTCCAAAAATTAC-TTTTTTACCCTC
* * **
12751 AAAACTTTCAAAGATTACCCTTTTACCC
1 -AAACTTCCAAAAATTACTTTTTTACCC
12779 CCGGATGTCC
Statistics
Matches: 146, Mismatches: 44, Indels: 21
0.69 0.21 0.10
Matches are distributed among these distances:
27 5 0.03
28 57 0.39
29 35 0.24
30 35 0.24
31 14 0.10
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTACTTTTTTACCCTC
Found at i:12629 original size:28 final size:29
Alignment explanation
Indices: 12550--12749 Score: 123
Period size: 28 Copynumber: 6.9 Consensus size: 29
12540 GAGGTCCTTA
12550 AACTTCCCAAAATTCCATTTTTGA-CCTCG
1 AACTT-CCAAAATTCCATTTTTGACCCTCG
* * *
12579 AAACTTTTCAAAAATTAC-TTTTTTACCCTCG
1 -AAC--TTCCAAAATTCCATTTTTGACCCTCG
* * **
12610 AGCTTCCAAAATTCCATTTTTAACCCTAA
1 AACTTCCAAAATTCCATTTTTGACCCTCG
* * *
12639 AACTTCTAAAAATTACCA--TTT-ACCCCCA
1 AACTTC-CAAAATT-CCATTTTTGACCCTCG
* *
12667 AACTTCCAAAAATTTCATTTTTGA-TCTC-
1 AACTTCC-AAAATTCCATTTTTGACCCTCG
*
12695 AACTTTCAAAAATTACCA-TTTT-ACCC-CG
1 AAC-TTCCAAAATT-CCATTTTTGACCCTCG
12723 AACTTCCAAAAATTCCATTTTTGACCC
1 AACTTCC-AAAATTCCATTTTTGACCC
12750 CAAAACTTTC
Statistics
Matches: 132, Mismatches: 21, Indels: 35
0.70 0.11 0.19
Matches are distributed among these distances:
27 10 0.08
28 54 0.41
29 32 0.24
30 18 0.14
31 16 0.12
32 2 0.02
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.35
Consensus pattern (29 bp):
AACTTCCAAAATTCCATTTTTGACCCTCG
Found at i:12686 original size:58 final size:57
Alignment explanation
Indices: 12549--12780 Score: 229
Period size: 56 Copynumber: 4.0 Consensus size: 57
12539 GGAGGTCCTT
* * ** *
12549 AAACTTCCCAAAATTCCATTTTTGACCTCGAAACTTTTCAAAAATTACTTTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTGACCT-AAAAC-TTTCAAAAATTAC-CATTTACCCCC
* * *
12609 GAGCTTCC-AAAATTCCATTTTTAACCCTAAAAC-TTCTAAAAATTACCATTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTGA-CCTAAAACTTTC-AAAAATTACCATTTACCCCC
* * *
12666 AAACTTCCAAAAATTTCATTTTTGATCT-CAACTTTCAAAAATTACCATTTTA-CCCC
1 AAACTTCCAAAAATTCCATTTTTGACCTAAAACTTTCAAAAATTACCA-TTTACCCCC
* * * *
12722 GAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTTCAAAGATTACCCTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTGA-CCTAAAACTTTCAAAAATTA-CCATTTACCCCC
12781 GGATGTCCAA
Statistics
Matches: 143, Mismatches: 20, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
56 41 0.29
57 27 0.19
58 41 0.29
59 25 0.17
60 9 0.06
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (57 bp):
AAACTTCCAAAAATTCCATTTTTGACCTAAAACTTTCAAAAATTACCATTTACCCCC
Found at i:12828 original size:59 final size:60
Alignment explanation
Indices: 12642--12904 Score: 210
Period size: 59 Copynumber: 4.5 Consensus size: 60
12632 ACCCTAAAAC
* * * * * **
12642 TTCTA-AAAATTACCA-TTTACCCCCAAACT-TCCAAAAATTTCATTTTTGATCTC-AACT
1 TTCTAGAAAGTTACCATTTTACCCCCGAA-TGTCCAAAAATTCCGTTTTTGATCCCGATTT
* * * * **
12699 TTC-A-AAAATTACCATTTTA-CCCCGAACT-TCCAAAAATTCCATTTTTGACCCCAAAACT
1 TTCTAGAAAGTTACCATTTTACCCCCGAA-TGTCCAAAAATTCCGTTTTTGATCCC-GATTT
* * *
12757 TTC---AAAGATTACCCTTTTACCCCCGGATGTCCAAAAATTCTGTTTTTGATCCCGATTT
1 TTCTAGAAAG-TTACCATTTTACCCCCGAATGTCCAAAAATTCCGTTTTTGATCCCGATTT
* * *
12815 TTCTA-AAAGTTACCATCTTACCCTCGAATGTCCAAAAATTCCGTTTTTTATCCCGATTT
1 TTCTAGAAAGTTACCATTTTACCCCCGAATGTCCAAAAATTCCGTTTTTGATCCCGATTT
* *
12874 TTCTAGAAA-TTACCTTTTTACCCTCGAATGT
1 TTCTAGAAAGTTACCATTTTACCCCCGAATGT
12905 TTAAAATTCC
Statistics
Matches: 176, Mismatches: 21, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
56 40 0.23
57 10 0.06
58 23 0.13
59 96 0.55
60 7 0.04
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (60 bp):
TTCTAGAAAGTTACCATTTTACCCCCGAATGTCCAAAAATTCCGTTTTTGATCCCGATTT
Found at i:14864 original size:18 final size:18
Alignment explanation
Indices: 14843--14877 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14833 AATACTATAA
14843 AATAAAATAATTATTTTC
1 AATAAAATAATTATTTTC
* *
14861 AATATAATTATTATTTT
1 AATAAAATAATTATTTT
14878 TATATAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
AATAAAATAATTATTTTC
Found at i:16757 original size:17 final size:17
Alignment explanation
Indices: 16735--16767 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
16725 AATTTGTCAC
16735 ATAT-TTTATTT-TTTT
1 ATATATTTATTTCTTTT
16750 ATATATTTATTTCTTTT
1 ATATATTTATTTCTTTT
16767 A
1 A
16768 AAATTTTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 7 0.44
17 5 0.31
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
ATATATTTATTTCTTTT
Found at i:16990 original size:22 final size:22
Alignment explanation
Indices: 16965--17030 Score: 132
Period size: 22 Copynumber: 3.0 Consensus size: 22
16955 ATATATATAT
16965 TTATTGAAAAGACGAAATGACG
1 TTATTGAAAAGACGAAATGACG
16987 TTATTGAAAAGACGAAATGACG
1 TTATTGAAAAGACGAAATGACG
17009 TTATTGAAAAGACGAAATGACG
1 TTATTGAAAAGACGAAATGACG
17031 ACCATTCTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (22 bp):
TTATTGAAAAGACGAAATGACG
Found at i:17635 original size:3 final size:3
Alignment explanation
Indices: 17629--17653 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17619 CCACCACCAC
17629 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
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:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Done.