Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003573.1 Kokia drynarioides strain JFW-HI SEQ_116444, 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: 42751
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:867 original size:11 final size:11
Alignment explanation
Indices: 851--887 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
841 TCCCTTTTTA
851 TTATTAAATAT
1 TTATTAAATAT
*
862 TTATTATATA-
1 TTATTAAATAT
872 TTA-TAAATAT
1 TTATTAAATAT
882 TTATTA
1 TTATTA
888 TAAAACGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 5 0.23
10 6 0.27
11 11 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTATTAAATAT
Found at i:878 original size:20 final size:21
Alignment explanation
Indices: 849--889 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
839 TCTCCCTTTT
849 TATTATTAAATATTTATTATA
1 TATTATTAAATATTTATTATA
870 TATTA-TAAATATTTATTATA
1 TATTATTAAATATTTATTATA
890 AAACGTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTATTAAATATTTATTATA
Found at i:1579 original size:18 final size:18
Alignment explanation
Indices: 1556--1591 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1546 AACAACTTTC
* *
1556 AAATTTTAAATTTAAAAT
1 AAATTTAAAATTAAAAAT
1574 AAATTTAAAATTAAAAAT
1 AAATTTAAAATTAAAAAT
1592 TGGGTTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATTTAAAATTAAAAAT
Found at i:2082 original size:39 final size:39
Alignment explanation
Indices: 2014--2801 Score: 323
Period size: 39 Copynumber: 20.2 Consensus size: 39
2004 TGCCTCATGT
* * * *
2014 TCGGAGTAAGAGATTGACTGA-TGATAATCTGCCCCAAGC
1 TCGGGGTAAGAGATCGAATGATTG-TAATCTGCCCCAGGC
* * * * *
2053 TCGGGGTAAGAGATCGAATGGTTGCAATCTACCCCAAGA
1 TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
* * * ** * * * *
2092 TCAGGGTAAGAAATTGGCTGATGGTGATCTGCCTCAAGC
1 TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
* * * ** * * * *
2131 TCGGGGTAAAATAT-TAGATGGA-TGCCATTTACCTCAGGT
1 TCGGGGTAAGAGATCGA-AT-GATTGTAATCTGCCCCAGGC
* * ** * * * *
2170 TTGGGGTAAGAGATTGGCTGATGGTGAT-TTCCCCAAGC
1 TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
* * * **
2208 TCGAGGTAAGGGATCGAATGATTGCAATCTGCCTTAGGC
1 TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
* * * * * * *
2247 ACGAGGTAAGAGATTTG-CTGA-TGATGATCTGCCTCAAGC
1 TCGGGGTAAGAGA-TCGAATGATTG-TAATCTGCCCCAGGC
* * * * *
2286 TCGAGGTAAAAGATCGAATGACTGCAATCTACCCCAGGC
1 TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
* * ** * **
2325 TCGGGTTAAGAGATTGGCTGATGGTAATCTGCCCTTGGC
1 TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
* * * ** *
2364 TCGGGGTAAAAGATCGAATGACTGCAATCTGCTTCAAGC
1 TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
* ** * * * *
2403 TCGGGGTAAGAGATTGGCTGATGGTGATCTACCCTAGGC
1 TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
** * *
2442 TCGGGGTAAGAGATCGAATGGCTGTAATCTGCCCTAAGC
1 TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
** * * * * *
2481 TCAAGGTAAGAGATTTG-CTGATGGTGATTTGCCCC-GTGC
1 TCGGGGTAAGAGA-TCGAATGATTGTAATCTGCCCCAG-GC
* * * * *
2520 TCGGGGTAAAAGATCGAATGGTTGTAATTTTCCCCAGGT
1 TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
** * ** * * *
2559 TCGGGGTAAGAGATTTACTGATAATGATCTACCCTAGGC
1 TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
* * * *
2598 TCGGGGTAAGAGATCGGATGACTGTAATCTACCCCAGGT
1 TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
* * * * * *
2637 TCGGGCTAAGAGATCGAATGGTTGCAATTTGCCCCATGA
1 TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
** * * * * **
2676 TCGGGGTAAGAGATTTACTGATGGTGATTTGCCTTAGGC
1 TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
* * * * * *
2715 TCGGGGTAAAAGATTGAATGGTTGCAATCTTCCCCAAGC
1 TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
* ** * * *
2754 TCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCTAGGC
1 TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
2793 TCGGGGTAA
1 TCGGGGTAA
2802 AGGATCAGAA
Statistics
Matches: 527, Mismatches: 208, Indels: 28
0.69 0.27 0.04
Matches are distributed among these distances:
38 33 0.06
39 483 0.92
40 11 0.02
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (39 bp):
TCGGGGTAAGAGATCGAATGATTGTAATCTGCCCCAGGC
Found at i:2130 original size:78 final size:77
Alignment explanation
Indices: 1988--2650 Score: 492
Period size: 78 Copynumber: 8.5 Consensus size: 77
1978 CTTTATTGCT
* * * * * * * *
1988 TCGAATGACTGCCATCTGCCTCATGTTC-GGAGTAAGAGATTGACTGATGATAATCTGCCCCAAG
1 TCGAATGACTGCAATCTACCCCAAGCTCAGG-GTAAGAGATTGGCTGATGGTGATCTG-CCCAAG
*
2052 CTCGGGGTAAGAGA
64 CTCGGGGTAAAAGA
** * *
2066 TCGAATGGTTGCAATCTACCCCAAGATCAGGGTAAGAAATTGGCTGATGGTGATCTGCCTCAAGC
1 TCGAATGACTGCAATCTACCCCAAGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCC-CAAGC
*
2131 TCGGGGTAAAATA
65 TCGGGGTAAAAGA
* * * * * * ** * *
2144 T-TAGATGGA-TGCCATTTACCTCAGGTTTGGGGTAAGAGATTGGCTGATGGTGATTTCCCCAAG
1 TCGA-AT-GACTGCAATCTACCCCAAGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCAAG
* **
2207 CTCGAGGTAAGGGA
64 CTCGGGGTAAAAGA
* * ** * * * *
2221 TCGAATGATTGCAATCTGCCTTAGGCAC-GAGGTAAGAGATTTGCTGATGATGATCTGCCTCAAG
1 TCGAATGACTGCAATCTACCCCAAGCTCAG-GGTAAGAGATTGGCTGATGGTGATCTGCC-CAAG
*
2285 CTCGAGGTAAAAGA
64 CTCGGGGTAAAAGA
* * **
2299 TCGAATGACTGCAATCTACCCCAGGCTC-GGGTTAAGAGATTGGCTGATGGTAATCTGCCCTTGG
1 TCGAATGACTGCAATCTACCCCAAGCTCAGGG-TAAGAGATTGGCTGATGGTGATCTGCCC-AAG
2363 CTCGGGGTAAAAGA
64 CTCGGGGTAAAAGA
* ** * * *
2377 TCGAATGACTGCAATCTGCTTCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCTAGGC
1 TCGAATGACTGCAATCTACCCCAAGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCC-AAGC
*
2442 TCGGGGTAAGAGA
65 TCGGGGTAAAAGA
* * * * * * * **
2455 TCGAATGGCTGTAATCTGCCCTAAGCTCAAGGTAAGAGATTTGCTGATGGTGATTTGCCCCGTGC
1 TCGAATGACTGCAATCTACCCCAAGCTCAGGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGC
2520 TCGGGGTAAAAGA
65 TCGGGGTAAAAGA
** * * * * * * ** ** * *
2533 TCGAATGGTTGTAATTTTCCCCAGGTTCGGGGTAAGAGATTTACTGATAATGATCTACCCTAGGC
1 TCGAATGACTGCAATCTACCCCAAGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCC-AAGC
*
2598 TCGGGGTAAGAGA
65 TCGGGGTAAAAGA
* * * *
2611 TCGGATGACTGTAATCTACCCCAGGTTC-GGGCTAAGAGAT
1 TCGAATGACTGCAATCTACCCCAAGCTCAGGG-TAAGAGAT
2651 CGAATGGTTG
Statistics
Matches: 475, Mismatches: 96, Indels: 28
0.79 0.16 0.05
Matches are distributed among these distances:
76 3 0.01
77 66 0.14
78 397 0.84
79 9 0.02
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (77 bp):
TCGAATGACTGCAATCTACCCCAAGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCAAGCT
CGGGGTAAAAGA
Found at i:2424 original size:156 final size:155
Alignment explanation
Indices: 1988--2650 Score: 598
Period size: 156 Copynumber: 4.3 Consensus size: 155
1978 CTTTATTGCT
* * * * * *
1988 TCGAATGACTGCCATCTGCCTCATGTTCGGAGTAAGAGATTGACTGATGATAATCTGCCCCAAGC
1 TCGAATGACTGCAATCTACCCCAGGTTCGG-GTAAGAGATTGGCTGATGGTAATCTGCCCCAAGC
* * * * * * *
2053 TCGGGGTAAGAGATCGAATGGTTGCAATCTACCCCAAGATCAGGGTAAGAAATTGGCTGATGGTG
65 TCGGGGTAAAAGATCGAATGATTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATG
* *
2118 ATCT-GCCTCAAGCTCGGGGTAAAATA
130 ATCTACCCT-AAGCTCGGGGTAAAAGA
* * * * * * *
2144 T-TAGATGGA-TGCCATTTACCTCAGGTTTGGGGTAAGAGATTGGCTGATGGTGAT-TTCCCCAA
1 TCGA-AT-GACTGCAATCTACCCCAGG-TTCGGGTAAGAGATTGGCTGATGGTAATCTGCCCCAA
* ** ** * * * *
2206 GCTCGAGGTAAGGGATCGAATGATTGCAATCTGCCTTAGGCACGAGGTAAGAGATTTGCTGATGA
63 GCTCGGGGTAAAAGATCGAATGATTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGA
* *
2271 TGATCT-GCCTCAAGCTCGAGGTAAAAGA
128 TGATCTACCCT-AAGCTCGGGGTAAAAGA
* ***
2299 TCGAATGACTGCAATCTACCCCAGGCTCGGGTTAAGAGATTGGCTGATGGTAATCTGCCCTTGGC
1 TCGAATGACTGCAATCTACCCCAGGTTCGGG-TAAGAGATTGGCTGATGGTAATCTGCCCCAAGC
* ** *
2364 TCGGGGTAAAAGATCGAATGACTGCAATCTGCTTCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
65 TCGGGGTAAAAGATCGAATGATTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATG
* *
2429 ATCTACCCTAGGCTCGGGGTAAGAGA
130 ATCTACCCTAAGCTCGGGGTAAAAGA
* * * * * * * * * * **
2455 TCGAATGGCTGTAATCTGCCCTAAGCTCAAGGTAAGAGATTTGCTGATGGTGATTTGCCCCGTGC
1 TCGAATGACTGCAATCTACCCCAGGTTC-GGGTAAGAGATTGGCTGATGGTAATCTGCCCCAAGC
* * * * * * ** *
2520 TCGGGGTAAAAGATCGAATGGTTGTAATTTTCCCCAGGTTCGGGGTAAGAGATTTACTGATAATG
65 TCGGGGTAAAAGATCGAATGATTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATG
* *
2585 ATCTACCCTAGGCTCGGGGTAAGAGA
130 ATCTACCCTAAGCTCGGGGTAAAAGA
* *
2611 TCGGATGACTGTAATCTACCCCAGGTTCGGGCTAAGAGAT
1 TCGAATGACTGCAATCTACCCCAGGTTCGGG-TAAGAGAT
2651 CGAATGGTTG
Statistics
Matches: 414, Mismatches: 83, Indels: 20
0.80 0.16 0.04
Matches are distributed among these distances:
154 6 0.01
155 124 0.30
156 273 0.66
157 11 0.03
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (155 bp):
TCGAATGACTGCAATCTACCCCAGGTTCGGGTAAGAGATTGGCTGATGGTAATCTGCCCCAAGCT
CGGGGTAAAAGATCGAATGATTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATGA
TCTACCCTAAGCTCGGGGTAAAAGA
Found at i:2787 original size:117 final size:117
Alignment explanation
Indices: 2039--2801 Score: 393
Period size: 117 Copynumber: 6.5 Consensus size: 117
2029 GACTGATGAT
* * * * * * * * *
2039 AATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGTTGCAATCTACCCCAAGATCAGGGTAAGAA
1 AATCTTCCCCAAGCTCGGGGTAAGAGATCGAATGATGGTAATCTGCCCCAGGCTCGGGGTAAGAG
* * * * *
2104 ATTGGCTGATGGTGATCTG-CCTCAAGCTCGGGGTAAAATAT-TAGATGGA-TGC
66 ATTGACTGATGGTAATCTGCCCT-AGGCTCGGGGTAAAAGATCGA-AT-GACTGC
* * * * * * ** * * * * *
2156 CAT-TTACCTCAGGTTTGGGGTAAGAGATTGGCTGATGGTGAT-TTCCCCAAGCTCGAGGTAAGG
1 AATCTT-CCCCAAGCTCGGGGTAAGAGATCGAATGATGGTAATCTGCCCCAGGCTCGGGGTAAGA
* * * * * * * *
2219 GATCGAATGATTGCAATCTGCCTTAGGCACGAGGTAAGAGATTTGCTG-ATGA-TG-
65 GATTGACTGATGGTAATCTGCCCTAGGCTCGGGGTAAAAGA--T-C-GAATGACTGC
* * * * * * *
2273 -ATCTGCCTCAAGCTCGAGGTAAAAGATCGAATGACT-GCAATCTACCCCAGGCTCGGGTTAAGA
1 AATCTTCCCCAAGCTCGGGGTAAGAGATCGAATGA-TGGTAATCTGCCCCAGGCTCGGGGTAAGA
* *
2336 GATTGGCTGATGGTAATCTGCCCTTGGCTCGGGGTAAAAGATCGAATGACTGC
65 GATTGACTGATGGTAATCTGCCCTAGGCTCGGGGTAAAAGATCGAATGACTGC
* ** * ** * * *
2389 AATCTGCTTCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCTAGGCTCGGGGTAAGAG
1 AATCTTCCCCAAGCTCGGGGTAAGAGATCGAATGATGGTAATCTGCCCCAGGCTCGGGGTAAGAG
* * * * ** * * * *
2454 ATCGAATGGCT-GTAATCTGCCCTAAGCTCAAGGTAAGAGATTTG-CTGA-TGGT
66 ATTGACT-GATGGTAATCTGCCCTAGGCTCGGGGTAAAAGA-TCGAATGACT-GC
* ** * * * * * *
2506 GAT-TTGCCCCGTGCTCGGGGTAAAAGATCGAATGGTTGTAATTTTCCCCAGGTTCGGGGTAAGA
1 AATCTT-CCCCAAGCTCGGGGTAAGAGATCGAATGATGGTAATCTGCCCCAGGCTCGGGGTAAGA
* ** * * * * *
2570 GATTTACTGATAATGATCTACCCTAGGCTCGGGGTAAGAGATCGGATGACTGT
65 GATTGACTGATGGTAATCTGCCCTAGGCTCGGGGTAAAAGATCGAATGACTGC
* * * * * * * * * *
2623 AATCTACCCCAGGTTCGGGCTAAGAGATCGAATGGTTGCAATTTGCCCCATGATCGGGGTAAGAG
1 AATCTTCCCCAAGCTCGGGGTAAGAGATCGAATGATGGTAATCTGCCCCAGGCTCGGGGTAAGAG
* * * * * **
2688 ATTTACTGATGGTGATTTGCCTTAGGCTCGGGGTAAAAGATTGAATGGTTGC
66 ATTGACTGATGGTAATCTGCCCTAGGCTCGGGGTAAAAGATCGAATGACTGC
* ** * *
2740 AATCTTCCCCAAGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCTAGGCTCGGGGTAA
1 AATCTTCCCCAAGCTCGGGGTAAGAGATCGAATGATGGTAATCTGCCCCAGGCTCGGGGTAA
2802 AGGATCAGAA
Statistics
Matches: 477, Mismatches: 146, Indels: 46
0.71 0.22 0.07
Matches are distributed among these distances:
113 1 0.00
114 5 0.01
115 3 0.01
116 75 0.16
117 380 0.80
118 11 0.02
119 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (117 bp):
AATCTTCCCCAAGCTCGGGGTAAGAGATCGAATGATGGTAATCTGCCCCAGGCTCGGGGTAAGAG
ATTGACTGATGGTAATCTGCCCTAGGCTCGGGGTAAAAGATCGAATGACTGC
Found at i:14859 original size:30 final size:29
Alignment explanation
Indices: 14730--15122 Score: 396
Period size: 29 Copynumber: 13.3 Consensus size: 29
14720 GAAGTTTCAA
*
14730 AAGTTTGAGGTTAAAAATGTAATTTTTGG
1 AAGTTTGAGGGTAAAAATGTAATTTTTGG
* * *
14759 AAGTTCGAGAGCAAAAATGTAATTTTTGAG
1 AAGTTTGAGGGTAAAAATGTAATTTTTG-G
* *
14789 AAGTTTGGGGGT-AAAATGTGATTTTTGG
1 AAGTTTGAGGGTAAAAATGTAATTTTTGG
* *
14817 AAGCTCGAGGGTAAAAATGTAATTTTTGAG
1 AAGTTTGAGGGTAAAAATGTAATTTTTG-G
* ** *
14847 AAATTTGAGGGTAAAAACATGATTTTTGG
1 AAGTTTGAGGGTAAAAATGTAATTTTTGG
* * * *
14876 AAGTTAGAGGGCAAAAATGTATTTTTTAG
1 AAGTTTGAGGGTAAAAATGTAATTTTTGG
* *
14905 AAGTTTGAGGGTAAAAATATAATTTTTGAA
1 AAGTTTGAGGGTAAAAATGTAATTTTTG-G
* * *
14935 AAGTTTAAGGTTAAAAATGTGATTTTTTTGG
1 AAGTTTGAGGGTAAAAATGT-A-ATTTTTGG
* *
14966 AAGTTCGAGGGTAAAAATGTAAATTTTGG
1 AAGTTTGAGGGTAAAAATGTAATTTTTGG
* *
14995 AAAGTTCGAGGGTAAAAATGTGATTTTTGG
1 -AAGTTTGAGGGTAAAAATGTAATTTTTGG
* *
15025 AAGTTCGAGGGAAAAAATGTAATTTTTGAG
1 AAGTTTGAGGGTAAAAATGTAATTTTTG-G
* *
15055 AAGTTTGGGGGTAAATATGTAA-TTTTGG
1 AAGTTTGAGGGTAAAAATGTAATTTTTGG
* *
15083 AAAGGTTTGGGGGTCAAAATGTAA-TTTTGG
1 -AA-GTTTGAGGGTAAAAATGTAATTTTTGG
15113 AAAGTTTGAG
1 -AAGTTTGAG
15123 ATCAAAATAT
Statistics
Matches: 300, Mismatches: 54, Indels: 20
0.80 0.14 0.05
Matches are distributed among these distances:
28 11 0.04
29 142 0.47
30 123 0.41
31 18 0.06
32 6 0.02
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
AAGTTTGAGGGTAAAAATGTAATTTTTGG
Found at i:14902 original size:59 final size:59
Alignment explanation
Indices: 14730--15114 Score: 377
Period size: 59 Copynumber: 6.5 Consensus size: 59
14720 GAAGTTTCAA
* * * *
14730 AAGTTTGAGGTTAAAAATGTAATTTTTGGAAGTTCGAGAGCAAAAATGTAATTTTTGAG
1 AAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAG
* * * *
14789 AAGTTTGGGGGT-AAAATGTGATTTTTGGAAGCTCGAGGGTAAAAATGTAATTTTTGAG
1 AAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAG
* * * * * *
14847 AAATTTGAGGGTAAAAACATGATTTTTGGAAGTTAGAGGGCAAAAATGT-ATTTTTTAG
1 AAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAG
* ** * *
14905 AAGTTTGAGGGTAAAAATATAATTTTTGAAAAGTTTAAGGTTAAAAATGTGATTTTTTTG-G
1 AAGTTTGAGGGTAAAAATATAATTTTTG-GAAGTTCGAGGGTAAAAATGT-A-ATTTTTGAG
* * * *
14966 AAGTTCGAGGGTAAAAATGTAAATTTTGGAAAGTTCGAGGGTAAAAATGTGATTTTTG-G
1 AAGTTTGAGGGTAAAAATATAATTTTTGG-AAGTTCGAGGGTAAAAATGTAATTTTTGAG
* * * * * * *
15025 AAGTTCGAGGGAAAAAATGTAATTTTTGAGAAGTTTGGGGGTAAATATGTAATTTTGGA-
1 AAGTTTGAGGGTAAAAATATAATTTTTG-GAAGTTCGAGGGTAAAAATGTAATTTTTGAG
* * *
15084 AAGGTTTGGGGGTCAAAATGTAA-TTTTGGAA
1 AA-GTTTGAGGGTAAAAATATAATTTTTGGAA
15115 AGTTTGAGAT
Statistics
Matches: 273, Mismatches: 44, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
58 88 0.32
59 120 0.44
60 17 0.06
61 43 0.16
62 5 0.02
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.35
Consensus pattern (59 bp):
AAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAG
Found at i:15120 original size:29 final size:29
Alignment explanation
Indices: 14729--15147 Score: 320
Period size: 30 Copynumber: 14.2 Consensus size: 29
14719 TGAAGTTTCA
*
14729 AAAGTTTGAGGTTAAAAATGTAATTTTTGG
1 AAAGTTTGAGGGTAAAAATGTAA-TTTTGG
* * * *
14759 -AAGTTCGAGAGCAAAAATGTAATTTTTG
1 AAAGTTTGAGGGTAAAAATGTAATTTTGG
* *
14787 AGAAGTTTGGGGGT-AAAATGTGATTTTTGG
1 A-AAGTTTGAGGGTAAAAATGT-AATTTTGG
* *
14817 -AAGCTCGAGGGTAAAAATGTAATTTTTGAG
1 AAAGTTTGAGGGTAAAAATGTAA-TTTTG-G
*
14847 AAA-TTTGAGGGTAAAAACATG-ATTTTTGG
1 AAAGTTTGAGGGT-AAAA-ATGTAATTTTGG
* * **
14876 -AAGTTAGAGGGCAAAAATGT-ATTTTTT
1 AAAGTTTGAGGGTAAAAATGTAATTTTGG
* *
14903 AGAAGTTTGAGGGTAAAAATATAATTTTTGA
1 A-AAGTTTGAGGGTAAAAATGTAA-TTTTGG
* * *
14934 AAAGTTTAAGGTTAAAAATGTGATTTTTTTGG
1 AAAGTTTGAGGGTAAAAATGT-A--ATTTTGG
*
14966 -AAGTTCGAGGGTAAAAATGTAAATTTTGG
1 AAAGTTTGAGGGTAAAAATGT-AATTTTGG
* *
14995 AAAGTTCGAGGGTAAAAATGTGATTTTTGG
1 AAAGTTTGAGGGTAAAAATGT-AATTTTGG
* * *
15025 -AAGTTCGAGGGAAAAAATGTAATTTTTG
1 AAAGTTTGAGGGTAAAAATGTAATTTTGG
* *
15053 AGAAGTTTGGGGGTAAATATGTAATTTTGG
1 A-AAGTTTGAGGGTAAAAATGTAATTTTGG
* *
15083 AAAGGTTTGGGGGTCAAAATGTAATTTTGG
1 AAA-GTTTGAGGGTAAAAATGTAATTTTGG
* *
15113 AAAGTTTGA-GATCAAAATATG-ATTTTTGG
1 AAAGTTTGAGGGT-AAAA-ATGTAATTTTGG
15142 AAAGTT
1 AAAGTT
15148 CAGTGACCTT
Statistics
Matches: 311, Mismatches: 54, Indels: 49
0.75 0.13 0.12
Matches are distributed among these distances:
27 7 0.02
28 29 0.09
29 110 0.35
30 126 0.41
31 31 0.10
32 8 0.03
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
AAAGTTTGAGGGTAAAAATGTAATTTTGG
Found at i:15967 original size:11 final size:11
Alignment explanation
Indices: 15953--15990 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
15943 TCTCCTTTTT
15953 TTTATTAAATA
1 TTTATTAAATA
*
15964 TTTATTATATA
1 TTTATTAAATA
15975 -TTA-TAAATA
1 TTTATTAAATA
15984 TTTATTA
1 TTTATTA
15991 TAAAACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 5 0.22
10 6 0.26
11 12 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTATTAAATA
Found at i:16687 original size:17 final size:17
Alignment explanation
Indices: 16664--16744 Score: 108
Period size: 17 Copynumber: 4.8 Consensus size: 17
16654 ACTTTCAAAT
* *
16664 TTTAAATTTGAAAGAAA
1 TTTAAATTTAAAATAAA
* *
16681 CTTAAATCTAAAATAAA
1 TTTAAATTTAAAATAAA
16698 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
16715 TTTAAACTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
16732 TTTAAAATTAAAA
1 TTTAAATTTAAAA
16745 ATTGGGTTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:16703 original size:6 final size:6
Alignment explanation
Indices: 16694--16743 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
16684 AAATCTAAAA
* * * *
16694 TAAATT TAAATT TAAA-A TAAATT TAAACT TAAA-A TAAATT TAAAAT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
16740 TAAA
1 TAAA
16744 AATTGGGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
5 8 0.22
6 28 0.78
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (6 bp):
TAAATT
Found at i:22982 original size:21 final size:21
Alignment explanation
Indices: 22940--22983 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
22930 AGGAACCTAC
**
22940 TGTAGAGGAGGAAGTTGATGT
1 TGTAGAGGAGGAAGTCCATGT
*
22961 TGTAGAGGAGGAAGTCCTTGT
1 TGTAGAGGAGGAAGTCCATGT
22982 TG
1 TG
22984 AAGATGTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.41, T:0.30
Consensus pattern (21 bp):
TGTAGAGGAGGAAGTCCATGT
Found at i:23021 original size:15 final size:15
Alignment explanation
Indices: 23003--23042 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
22993 AAGAGAAGGA
*
23003 TGAGGAAGAAGACGC
1 TGAGAAAGAAGACGC
*
23018 TGAGAAAGAAGATGC
1 TGAGAAAGAAGACGC
*
23033 TGATAAAGAA
1 TGAGAAAGAA
23043 TCTGTTGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.47, C:0.07, G:0.33, T:0.12
Consensus pattern (15 bp):
TGAGAAAGAAGACGC
Found at i:29408 original size:78 final size:77
Alignment explanation
Indices: 29275--29432 Score: 228
Period size: 78 Copynumber: 2.0 Consensus size: 77
29265 ATAAGGGTAA
*
29275 TGAAATAAAGGATAGAGATGGATATAACTTATAAAACAAGATTTATCCCAAAAATGAACCAACAC
1 TGAAATAAAGGATAGAGATGGATATAACTTATAAAACAAGACTTATCCCAAAAATGAACCAACAC
*
29340 TATAAAATAGTG
66 TATAAAATAATG
** * * *
29352 TGAAATAAAAGGATAGAGATGGATATAACTTATAAAA-TGGAACTTGTCCCAGAAATGAACTAAC
1 TGAAAT-AAAGGATAGAGATGGATATAACTTATAAAACAAG-ACTTATCCCAAAAATGAACCAAC
29416 ACTATAAAATAATG
64 ACTATAAAATAATG
29430 TGA
1 TGA
29433 CTCGATTTCT
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
77 7 0.10
78 65 0.90
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (77 bp):
TGAAATAAAGGATAGAGATGGATATAACTTATAAAACAAGACTTATCCCAAAAATGAACCAACAC
TATAAAATAATG
Found at i:31633 original size:45 final size:45
Alignment explanation
Indices: 31569--31659 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
31559 ACTTTATGCA
31569 TACATGTAGTATCCTCATCAAACAATCATAATTTAATAGCAATAT
1 TACATGTAGTATCCTCATCAAACAATCATAATTTAATAGCAATAT
31614 TACATGTAGTATCCTCATCAAACAATCATAATTTAATAGCAATAT
1 TACATGTAGTATCCTCATCAAACAATCATAATTTAATAGCAATAT
31659 T
1 T
31660 TTTTTTTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.34
Consensus pattern (45 bp):
TACATGTAGTATCCTCATCAAACAATCATAATTTAATAGCAATAT
Found at i:37011 original size:3 final size:3
Alignment explanation
Indices: 37003--37045 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
36993 GGGTCCTAAA
* * *
37003 AAT AAT AAT AAT ATTT AAT AAT AAT GAT AAT GAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
37046 TTAGGCCCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 31 0.94
4 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:41938 original size:30 final size:30
Alignment explanation
Indices: 41902--41969 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
41892 TAACATGAGT
41902 GCTCGCAACACCAGTGCTCGCATCTTCCAG
1 GCTCGCAACACCAGTGCTCGCATCTTCCAG
41932 GCTCGCAACACCAGTGCTCGCATCTTCCAG
1 GCTCGCAACACCAGTGCTCGCATCTTCCAG
41962 GCTCGCAA
1 GCTCGCAA
41970 GGTACATGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.21, C:0.40, G:0.21, T:0.19
Consensus pattern (30 bp):
GCTCGCAACACCAGTGCTCGCATCTTCCAG
Found at i:41965 original size:15 final size:16
Alignment explanation
Indices: 41899--41968 Score: 76
Period size: 15 Copynumber: 4.6 Consensus size: 16
41889 TCATAACATG
* *
41899 AGTGCTCGCAAC-ACC
1 AGTGCTCGCATCTTCC
41914 AGTGCTCGCATCTTCC
1 AGTGCTCGCATCTTCC
* *
41930 AG-GCTCGCAAC-ACC
1 AGTGCTCGCATCTTCC
41944 AGTGCTCGCATCTTCC
1 AGTGCTCGCATCTTCC
41960 AG-GCTCGCA
1 AGTGCTCGCA
41969 AGGTACATGG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
14 4 0.09
15 34 0.74
16 8 0.17
ACGTcount: A:0.20, C:0.39, G:0.21, T:0.20
Consensus pattern (16 bp):
AGTGCTCGCATCTTCC
Found at i:42345 original size:53 final size:53
Alignment explanation
Indices: 42265--42373 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
42255 CTAATCTCCG
42265 GGTTCAAAGATTACTCGTTTACGTCCTTTGTTGGCTTTGCTGGCATATTGCTT
1 GGTTCAAAGATTACTCGTTTACGTCCTTTGTTGGCTTTGCTGGCATATTGCTT
42318 GGTTCAAAGATTACTCGTTTACGTCCTTTGTTGGCTTTGCTGGCATATTGCTT
1 GGTTCAAAGATTACTCGTTTACGTCCTTTGTTGGCTTTGCTGGCATATTGCTT
42371 GGT
1 GGT
42374 CCTCTCCTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.43
Consensus pattern (53 bp):
GGTTCAAAGATTACTCGTTTACGTCCTTTGTTGGCTTTGCTGGCATATTGCTT
Done.