Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015247.1 Kokia drynarioides strain JFW-HI SEQ_130292, 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: 112077
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 97 characters in sequence are not A, C, G, or T
Found at i:10408 original size:20 final size:19
Alignment explanation
Indices: 10371--10406 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10361 AATAATTTTT
10371 AAATTTAAAATATTTATAA
1 AAATTTAAAATATTTATAA
*
10390 AAATTTCAAA-ATTTATA
1 AAATTTAAAATATTTATA
10407 TATATAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTTAAAATATTTATAA
Found at i:22145 original size:17 final size:18
Alignment explanation
Indices: 22120--22161 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
22110 GATCGGGCCC
* *
22120 TTTTAGGTTTAGGG-TTA
1 TTTTGGGTTTAGGGCTGA
*
22137 TTTTGGGTTTGGGGCTGA
1 TTTTGGGTTTAGGGCTGA
22155 TTTTGGG
1 TTTTGGG
22162 CCACTTTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.10, C:0.02, G:0.38, T:0.50
Consensus pattern (18 bp):
TTTTGGGTTTAGGGCTGA
Found at i:22303 original size:16 final size:17
Alignment explanation
Indices: 22219--22304 Score: 106
Period size: 17 Copynumber: 5.2 Consensus size: 17
22209 TTGGACTTTC
*
22219 TAAATTT-AATTTTATAA
1 TAAATTTAAATTTCA-AA
22236 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
22253 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
*
22270 TAAACTTAAATTT-AAA
1 TAAATTTAAATTTCAAA
* *
22286 TAAA-TTCAATTTCCAA
1 TAAATTTAAATTTCAAA
22302 TAA
1 TAA
22305 GTCCAAACAA
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
15 7 0.11
16 12 0.19
17 38 0.60
18 6 0.10
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:24593 original size:9 final size:9
Alignment explanation
Indices: 24579--24603 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
24569 TATATTTTTA
24579 AAAAATTAT
1 AAAAATTAT
24588 AAAAATTAT
1 AAAAATTAT
24597 AAAAATT
1 AAAAATT
24604 TTCTAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:27279 original size:16 final size:16
Alignment explanation
Indices: 27238--27279 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
27228 AATTCGGAAG
*
27238 ATTTGAATTTAAAATA
1 ATTTAAATTTAAAATA
*
27254 ATTTAGATTTAAAAT-
1 ATTTAAATTTAAAATA
27269 ATTCTAAATTT
1 ATT-TAAATTT
27280 CATATGACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (16 bp):
ATTTAAATTTAAAATA
Found at i:28338 original size:24 final size:24
Alignment explanation
Indices: 28241--28339 Score: 137
Period size: 24 Copynumber: 4.1 Consensus size: 24
28231 AGTTTGACTC
*
28241 AAACAAATAAACAGAGTTTAATTA
1 AAACAAATAAACAGAGTTTAATTG
*
28265 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
28289 AAACAAATAAACA-AGGTTTAATTG
1 AAACAAATAAACAGA-GTTTAATTG
* * *
28313 AAATAATTAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
28337 AAA
1 AAA
28340 GATTATTTCT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
23 1 0.01
24 66 0.97
25 1 0.01
ACGTcount: A:0.57, C:0.08, G:0.10, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:29508 original size:29 final size:27
Alignment explanation
Indices: 29460--29570 Score: 80
Period size: 29 Copynumber: 3.8 Consensus size: 27
29450 TTGGGAAAGT
*
29460 TCGAGGTTAAAATCGGAATTTTTAGACA
1 TCGAGGGTAAAA-CGGAATTTTTAGACA
*
29488 CTCGAGGGTAAAACGGTAATTTTTAGAAAAAA
1 -TCGAGGGTAAAACGG-AATTTTTAG---ACA
** *
29520 TCG-GAATCAAAACGGAATTTTTGGACA
1 TCGAGGGT-AAAACGGAATTTTTAGACA
*
29547 TCCGAGGGTAAAAAGGTAATTTTT
1 T-CGAGGGTAAAACGG-AATTTTT
29571 GAAAGTTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
27 3 0.05
28 11 0.17
29 29 0.45
30 10 0.15
31 10 0.15
32 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (27 bp):
TCGAGGGTAAAACGGAATTTTTAGACA
Found at i:29584 original size:29 final size:29
Alignment explanation
Indices: 29552--29864 Score: 103
Period size: 29 Copynumber: 10.7 Consensus size: 29
29542 GGACATCCGA
*
29552 GGGTAAAAAGGTAATTTTTGAAAGTTTTT
1 GGGTAAAAAGGTAATTTTTGAAAGTTTTG
* * * *
29581 GGGTCAAAAA--TAGAATTTTGGAA-CTCTG
1 GGGT-AAAAAGGTA-ATTTTTGAAAGTTTTG
* *
29609 GGGATAAAATA-GTATTTTTTGAGAGTTTTAG
1 GGG-TAAAA-AGGTAATTTTTGAAAGTTTT-G
* * **
29640 GGTTAAAAATGG-AATTTTTGAAGGTTTAA
1 GGGTAAAAA-GGTAATTTTTGAAAGTTTTG
* * * *
29669 GGGTAATATGGTAATTTTTGGAAGTTTCG
1 GGGTAAAAAGGTAATTTTTGAAAGTTTTG
* * *
29698 AGGTCAAAATCAGG---TTTTTGGAAGTTTGG
1 GGGT-AAAA--AGGTAATTTTTGAAAGTTTTG
* *
29727 GGGTAATATGGTAATTTTTGAAAGTTTTG
1 GGGTAAAAAGGTAATTTTTGAAAGTTTTG
* * * *
29756 GGGTCAAAATTGG-GATTTTTGGAAG-TTCG
1 GGGT-AAAA-AGGTAATTTTTGAAAGTTTTG
* *
29785 AGGGTAATATGGTAATTTTTCG-AAGTTTTG
1 -GGGTAAAAAGGTAATTTTT-GAAAGTTTTG
* ** * *
29815 GGATCAAAATCG-AGATTTTTGGAAG-TTCG
1 GGGT-AAAAAGGTA-ATTTTTGAAAGTTTTG
*
29844 AGGGTAAAAATGTAATTTTTG
1 -GGGTAAAAAGGTAATTTTTG
29865 GATAGTTTAA
Statistics
Matches: 210, Mismatches: 47, Indels: 54
0.68 0.15 0.17
Matches are distributed among these distances:
26 2 0.01
28 19 0.09
29 112 0.53
30 68 0.32
31 7 0.03
32 2 0.01
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (29 bp):
GGGTAAAAAGGTAATTTTTGAAAGTTTTG
Found at i:29597 original size:59 final size:59
Alignment explanation
Indices: 29534--29864 Score: 254
Period size: 59 Copynumber: 5.6 Consensus size: 59
29524 AATCAAAACG
*
29534 GAATTTTTGGACA-TCCGAGGGTAAAAAGGTAATTTTTGAAAGTTTTTGGGTCAAAAATA
1 GAATTTTTGGA-AGTTCGAGGGTAAAAAGGTAATTTTTGAAAGTTTTTGGGTCAAAAATA
* * * * * *
29593 GAA-TTTTGGAA-CTCTG-GGGATAAAATA-GTATTTTTTGAGAGTTTTAGGGTTAAAAATG
1 GAATTTTTGGAAGTTC-GAGGG-TAAAA-AGGTAATTTTTGAAAGTTTTTGGGTCAAAAATA
** * * * *
29651 GAATTTTT-GAAGGTTTAAGGGTAATATGGTAATTTTTGGAAG-TTTCGAGGTC-AAAATCA
1 GAATTTTTGGAA-GTTCGAGGGTAAAAAGGTAATTTTTGAAAGTTTTTG-GGTCAAAAAT-A
* * * * * * * *
29710 G-GTTTTTGGAAGTTTGGGGGTAATATGGTAATTTTTGAAAGTTTTGGGGTCAAAATTG
1 GAATTTTTGGAAGTTCGAGGGTAAAAAGGTAATTTTTGAAAGTTTTTGGGTCAAAAATA
* * * *
29768 GGATTTTTGGAAGTTCGAGGGTAATATGGTAATTTTTCG-AAG-TTTTGGGATC-AAAATC
1 GAATTTTTGGAAGTTCGAGGGTAAAAAGGTAATTTTT-GAAAGTTTTTGGG-TCAAAAATA
*
29826 GAGATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTG
1 GA-ATTTTTGGAAGTTCGAGGGTAAAAAGGTAATTTTTG
29865 GATAGTTTAA
Statistics
Matches: 220, Mismatches: 35, Indels: 35
0.76 0.12 0.12
Matches are distributed among these distances:
57 5 0.02
58 103 0.47
59 107 0.49
60 5 0.02
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.38
Consensus pattern (59 bp):
GAATTTTTGGAAGTTCGAGGGTAAAAAGGTAATTTTTGAAAGTTTTTGGGTCAAAAATA
Found at i:29654 original size:117 final size:115
Alignment explanation
Indices: 29528--29838 Score: 306
Period size: 117 Copynumber: 2.6 Consensus size: 115
29518 AATCGGAATC
* * * *
29528 AAAACGGAATTTTTGGACATCCGAGGGTAAAAAGGTAATTTTTGAAAGTTTTTGGGTCAAAAAT-
1 AAAATGGAATTTTTGGA-ATTCGAGGGTAATATGGTAATTTTTG-AAG-TTTTGGGTCAAAAATC
* * *
29592 AGAATTTTGGAACTCTGGGGATAAAATAGTATTTTTTGAGAGTTTTAGGGTTA
63 AGAATTTTGGAACTCTGGGGATAAAATAGTAATTTTTGAAAGTTTTAGGGTCA
** *
29645 AAAATGGAATTTTT-GAAGGTTTAAGGGTAATATGGTAATTTTTGGAAGTTTCGAGGTC-AAAAT
1 AAAATGGAATTTTTGGAA--TTCGAGGGTAATATGGTAATTTTT-GAAGTTTTG-GGTCAAAAAT
** * * * * * *
29708 CAGGTTTTTGGAAGTTTGGGGGTAATATGGTAATTTTTGAAAGTTTTGGGGTCA
62 CAGAATTTTGGAACTCTGGGGATAAAATAGTAATTTTTGAAAGTTTTAGGGTCA
* *
29762 AAATTGGGATTTTTGGAAGTTCGAGGGTAATATGGTAATTTTTCGAAGTTTTGGGATC-AAAATC
1 AAAATGGAATTTTTGGAA-TTCGAGGGTAATATGGTAATTTTT-GAAGTTTTGGG-TCAAAAATC
*
29826 GAGATTTTTGGAA
63 -AGAATTTTGGAA
29839 GTTCGAGGGT
Statistics
Matches: 161, Mismatches: 25, Indels: 15
0.80 0.12 0.07
Matches are distributed among these distances:
115 1 0.01
116 13 0.08
117 132 0.82
118 15 0.09
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (115 bp):
AAAATGGAATTTTTGGAATTCGAGGGTAATATGGTAATTTTTGAAGTTTTGGGTCAAAAATCAGA
ATTTTGGAACTCTGGGGATAAAATAGTAATTTTTGAAAGTTTTAGGGTCA
Found at i:29672 original size:30 final size:29
Alignment explanation
Indices: 29613--29876 Score: 79
Period size: 30 Copynumber: 9.0 Consensus size: 29
29603 ACTCTGGGGA
* * *
29613 TAAAATAGTATTTTTTGAGAGTTTTAGGG
1 TAAAATGGTAATTTTTGAGAGTTTAAGGG
29642 TTAAAAATGG-AATTTTTGA-AGGTTTAAGGG
1 -T-AAAATGGTAATTTTTGAGA-GTTTAAGGG
* *
29672 TAATATGGTAATTTTTG-GAAGTTT-CGAGG
1 TAAAATGGTAATTTTTGAG-AGTTTAAG-GG
* **
29701 TCAAAATCAGGT--TTTTGGA-AGTTTGGGGG
1 T-AAAAT--GGTAATTTTTGAGAGTTTAAGGG
* * **
29730 TAATATGGTAATTTTTGAAAGTTTTGGGG
1 TAAAATGGTAATTTTTGAGAGTTTAAGGG
* **
29759 TCAAAATTGG-GATTTTTG-GAAGTTCGAGGG
1 T-AAAA-TGGTAATTTTTGAG-AGTTTAAGGG
* *
29789 TAATATGGTAATTTTTCGA-AGTTT-TGGG
1 TAAAATGGTAATTTTT-GAGAGTTTAAGGG
* **
29817 ATCAAAATCG-AGATTTTTG-GAAGTTCGAGGG
1 -T-AAAATGGTA-ATTTTTGAG-AGTTTAAGGG
*
29848 TAAAAAT-GTAATTTTTGGATAGTTTAAGG
1 T-AAAATGGTAATTTTT-GAGAGTTTAAGG
29877 ACCTCCGGGG
Statistics
Matches: 176, Mismatches: 29, Indels: 58
0.67 0.11 0.22
Matches are distributed among these distances:
26 3 0.02
28 23 0.13
29 58 0.33
30 77 0.44
31 12 0.07
32 3 0.02
ACGTcount: A:0.30, C:0.03, G:0.28, T:0.39
Consensus pattern (29 bp):
TAAAATGGTAATTTTTGAGAGTTTAAGGG
Found at i:30925 original size:24 final size:25
Alignment explanation
Indices: 30884--30932 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
30874 TAATATTTCC
*
30884 AAAAATATTTATTAATTATTTTTAA
1 AAAAATATTTATTAATTATTATTAA
30909 AAAAAT-TATTATT-ATTATTATTAA
1 AAAAATAT-TTATTAATTATTATTAA
30933 TATTAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AAAAATATTTATTAATTATTATTAA
Found at i:31888 original size:6 final size:6
Alignment explanation
Indices: 31877--31943 Score: 61
Period size: 6 Copynumber: 11.7 Consensus size: 6
31867 CTGGGCTCAA
* * * *
31877 TAAATT TAAATT T-ATTT TAAAAT TAAGTT T-ATTT TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
31923 T--ATT ATAAATT TAAATT TAAA
1 TAAATT -TAAATT TAAATT TAAA
31944 ATTCATTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
4 3 0.06
5 9 0.18
6 34 0.69
7 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:31902 original size:17 final size:17
Alignment explanation
Indices: 31877--31941 Score: 103
Period size: 17 Copynumber: 3.8 Consensus size: 17
31867 CTGGGCTCAA
31877 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* *
31894 TAAAATTAAGTTTATTT
1 TAAATTTAAATTTATTT
*
31911 TAAATTTAAATTTATTA
1 TAAATTTAAATTTATTT
31928 TAAATTTAAATTTA
1 TAAATTTAAATTTA
31942 AAATTCATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:31918 original size:23 final size:24
Alignment explanation
Indices: 31879--31955 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 24
31869 GGGCTCAATA
*
31879 AATT-TAAATTT-ATTTTAAAATT
1 AATTATAAATTTAAATTTAAAATT
*
31901 AAGTT-T-ATTTTAAATTT-AAATT
1 AA-TTATAAATTTAAATTTAAAATT
*
31923 TATTATAAATTTAAATTTAAAATT
1 AATTATAAATTTAAATTTAAAATT
*
31947 CATT-TAAAT
1 AATTATAAAT
31956 AATGTCCAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
21 2 0.04
22 13 0.29
23 22 0.49
24 8 0.18
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (24 bp):
AATTATAAATTTAAATTTAAAATT
Found at i:33621 original size:29 final size:29
Alignment explanation
Indices: 33584--33767 Score: 176
Period size: 29 Copynumber: 6.3 Consensus size: 29
33574 GTTCCCGAAT
* *
33584 TTCCCAAAATCCCATTTTTGACCTCGAAAC
1 TTCCAAAAATCCCATTTTT-ACCCCGAAAC
**
33614 TTCCAAAAATTTCA-TTTTACCCCCGAAAC
1 TTCCAAAAATCCCATTTTTA-CCCCGAAAC
**
33643 TTCCAAAAATTTCATTTTTACCCCCG-AAC
1 TTCCAAAAATCCCATTTTTA-CCCCGAAAC
* * *
33672 TTCCCAAAATCTCATTTTTAACCCCAAAAC
1 TTCCAAAAATCCCATTTTT-ACCCCGAAAC
*
33702 TTCCAAAAATTCCATTTTTACCCCG-AAC
1 TTCCAAAAATCCCATTTTTACCCCGAAAC
* **
33730 TTCCAAAAATCCCACTTTTGACCTTGAAAC
1 TTCCAAAAATCCCA-TTTTTACCCCGAAAC
*
33760 TCCCAAAA
1 TTCCAAAA
33768 TTACCCTTTT
Statistics
Matches: 132, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
28 17 0.13
29 63 0.48
30 52 0.39
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (29 bp):
TTCCAAAAATCCCATTTTTACCCCGAAAC
Found at i:33630 original size:30 final size:29
Alignment explanation
Indices: 33596--33739 Score: 186
Period size: 29 Copynumber: 4.9 Consensus size: 29
33586 CCCAAAATCC
*
33596 CATTTTTGACCTCGAAACTTCCAAAAATTT
1 CATTTTT-ACCCCGAAACTTCCAAAAATTT
33626 CA-TTTTACCCCCGAAACTTCCAAAAATTT
1 CATTTTTA-CCCCGAAACTTCCAAAAATTT
* *
33655 CATTTTTACCCCCG-AACTTCCCAAAATCT
1 CATTTTTA-CCCCGAAACTTCCAAAAATTT
* *
33684 CATTTTTAACCCCAAAACTTCCAAAAATTC
1 CATTTTT-ACCCCGAAACTTCCAAAAATTT
33714 CATTTTTACCCCG-AACTTCCAAAAAT
1 CATTTTTACCCCGAAACTTCCAAAAAT
33740 CCCACTTTTG
Statistics
Matches: 102, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
28 14 0.14
29 55 0.54
30 33 0.32
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (29 bp):
CATTTTTACCCCGAAACTTCCAAAAATTT
Found at i:33673 original size:58 final size:58
Alignment explanation
Indices: 33584--33740 Score: 208
Period size: 59 Copynumber: 2.7 Consensus size: 58
33574 GTTCCCGAAT
* * * * * *
33584 TTCCCAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTTCA-TTTTACCCCCGAAAC
1 TTCCAAAAATTCCATTTTT-ACCCCG-AACTTCCAAAAATCTCATTTTTAACCCCAAAAC
* *
33643 TTCCAAAAATTTCATTTTTACCCCCGAACTTCCCAAAATCTCATTTTTAACCCCAAAAC
1 TTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATCTCATTTTTAACCCCAAAAC
33702 TTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATC
1 TTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATC
33741 CCACTTTTGA
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
58 34 0.40
59 52 0.60
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (58 bp):
TTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATCTCATTTTTAACCCCAAAAC
Found at i:33760 original size:58 final size:56
Alignment explanation
Indices: 33584--33767 Score: 197
Period size: 58 Copynumber: 3.1 Consensus size: 56
33574 GTTCCCGAAT
* * * *
33584 TTCCCAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTTCATTTTACCCCCGAAAC
1 TTCCAAAAATTCCATTTTT-ACCCCG-AACTTCCAAAAATCTCATTTTA-CCCCGAAAC
* * *
33643 TTCCAAAAATTTCATTTTTACCCCCGAACTTCCCAAAATCTCATTTTTAACCCCAAAAC
1 TTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATCTCA-TTTT-ACCCCGAAAC
* **
33702 TTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATCCCACTTTTGACCTTGAAAC
1 TTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATCTCA-TTTT-ACCCCGAAAC
*
33760 TCCCAAAA
1 TTCCAAAA
33768 TTACCCTTTT
Statistics
Matches: 106, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
58 54 0.51
59 51 0.48
60 1 0.01
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (56 bp):
TTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATCTCATTTTACCCCGAAAC
Found at i:33784 original size:58 final size:58
Alignment explanation
Indices: 33611--33829 Score: 160
Period size: 58 Copynumber: 3.8 Consensus size: 58
33601 TTGACCTCGA
** * ** * * *
33611 AACTTCCAAAAATTTCATTTTACCCCCGAAACTTCCAAAAATT-TCATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTAACCTTGAAAC-TCCCAAAATTACCACTTTTACCCCCG
* * *** * *
33669 AACTTCCCAAAATCTCATTTTTAACCCCAAAACTTCCAAAAATT-CCATTTTTA-CCCCG
1 AACTTCCAAAAATCCCA-TTTTAACCTTGAAAC-TCCCAAAATTACCACTTTTACCCCCG
*
33727 AACTTCCAAAAATCCCACTTTTGACCTTGAAACTCCCAAAATTACC-CTTTTACCCCCG
1 AACTTCCAAAAATCCCA-TTTTAACCTTGAAACTCCCAAAATTACCACTTTTACCCCCG
* * * **
33785 AA-TGTCTAAAAATTCCATTTTAACGTTGAATTTTCCCAAAATTAC
1 AACT-TCCAAAAATCCCATTTTAACCTTGAA-ACTCCCAAAATTAC
33830 TATTTCACCC
Statistics
Matches: 136, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
57 26 0.19
58 78 0.57
59 32 0.24
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (58 bp):
AACTTCCAAAAATCCCATTTTAACCTTGAAACTCCCAAAATTACCACTTTTACCCCCG
Found at i:39982 original size:12 final size:11
Alignment explanation
Indices: 39964--39988 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39954 ATTAAATGTT
39964 ATATTTTTAAA
1 ATATTTTTAAA
39975 ATATTTTTAAA
1 ATATTTTTAAA
39986 ATA
1 ATA
39989 AATATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATTTTTAAA
Found at i:43002 original size:3 final size:3
Alignment explanation
Indices: 42994--43026 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
42984 AGCTAACGAG
42994 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
43027 GATCAATGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:56341 original size:17 final size:18
Alignment explanation
Indices: 56319--56361 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
56309 TAAAAATATA
*
56319 ATTTTATTATTTT-TAAT
1 ATTTTATAATTTTATAAT
56336 ATTTTATAATTTTATAAT
1 ATTTTATAATTTTATAAT
56354 -TTTTATAA
1 ATTTTATAA
56362 ATTAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTATAATTTTATAAT
Found at i:56347 original size:8 final size:8
Alignment explanation
Indices: 56315--56361 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
56305 CCAGTAAAAA
56315 TATAATTT
1 TATAATTT
*
56323 TATTATTT
1 TATAATTT
56331 T-TAATATTT
1 TAT-A-ATTT
56340 TATAATTT
1 TATAATTT
56348 TATAATTTT
1 TATAA-TTT
56357 TATAA
1 TATAA
56362 ATTAAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
7 1 0.03
8 17 0.52
9 14 0.42
10 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATAATTT
Found at i:56833 original size:30 final size:30
Alignment explanation
Indices: 56792--56867 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 30
56782 AAATTCTATT
* *
56792 ATTAATTTTTATACTATATTTATAT-TATAG
1 ATTAGTTTTTATACTAT-TTTATATGAATAG
* *
56822 ATTAGTTTTTATA-T-TTTTTTGTGAATAG
1 ATTAGTTTTTATACTATTTTATATGAATAG
56850 ATTAGTTTTTATACTATT
1 ATTAGTTTTTATACTATT
56868 AAATGTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 5 0.13
28 18 0.46
29 2 0.05
30 14 0.36
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.59
Consensus pattern (30 bp):
ATTAGTTTTTATACTATTTTATATGAATAG
Found at i:63563 original size:19 final size:19
Alignment explanation
Indices: 63541--63587 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
63531 TAATTTTTAA
63541 AATT-TTAAAAATATAAAAT
1 AATTATTAAAAA-ATAAAAT
*
63560 AATTATTTAAAAATAAAAT
1 AATTATTAAAAAATAAAAT
63579 --TTATTAAAA
1 AATTATTAAAA
63588 CCATTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 8 0.32
19 11 0.44
20 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTATTAAAAAATAAAAT
Found at i:63585 original size:16 final size:17
Alignment explanation
Indices: 63538--63587 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
63528 AATTAATTTT
*
63538 TAAAATTT-TAAAAATA
1 TAAAATTTATTAAAATA
63554 TAAAATAATTATTTAAAA-A
1 TAAAAT--TTA-TTAAAATA
63573 TAAAATTTATTAAAA
1 TAAAATTTATTAAAA
63588 CCATTTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
16 12 0.41
17 3 0.10
18 2 0.07
19 7 0.24
20 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATTTATTAAAATA
Found at i:65605 original size:18 final size:18
Alignment explanation
Indices: 65582--65616 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
65572 GGACCGTAAC
*
65582 CACCATCACCACCAAAAT
1 CACCATAACCACCAAAAT
*
65600 CACCATAATCACCAAAA
1 CACCATAACCACCAAAA
65617 CCATCATTGT
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:0.49, C:0.40, G:0.00, T:0.11
Consensus pattern (18 bp):
CACCATAACCACCAAAAT
Found at i:74650 original size:19 final size:19
Alignment explanation
Indices: 74626--74672 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
74616 AACAATTTTA
*
74626 ATTACGATAGATAAA-TCTG
1 ATTACGAT-GAAAAATTCTG
*
74645 ATTACGATGAAAAATTTTG
1 ATTACGATGAAAAATTCTG
74664 ATTACGATG
1 ATTACGATG
74673 GGAGACAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (19 bp):
ATTACGATGAAAAATTCTG
Found at i:78462 original size:13 final size:13
Alignment explanation
Indices: 78444--78468 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
78434 TCCCTTCACC
78444 TTTAAAAAAATAT
1 TTTAAAAAAATAT
78457 TTTAAAAAAATA
1 TTTAAAAAAATA
78469 CACATCATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTTAAAAAAATAT
Found at i:82434 original size:20 final size:21
Alignment explanation
Indices: 82409--82449 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
82399 ATTTTTAAAA
82409 TTAAAAA-TCATT-AAAATTAT
1 TTAAAAAGT-ATTAAAAATTAT
82429 TTAAAAAGTATTAAAAATTAT
1 TTAAAAAGTATTAAAAATTAT
82450 AAAAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
TTAAAAAGTATTAAAAATTAT
Found at i:82463 original size:37 final size:37
Alignment explanation
Indices: 82405--82480 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
82395 TAAAATTTTT
**
82405 AAAATTAAAAATCATTAAAATTATTTAAAAAG-T-ATTA
1 AAAATTAAAAAAAATTAAAA-T-TTTAAAAAGCTAATTA
82442 AAAATTATAAAAAAATT-AAATTTTAAAAAGCTAATTA
1 AAAATTA-AAAAAAATTAAAATTTTAAAAAGCTAATTA
82479 AA
1 AA
82481 TGCTGACATG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
35 9 0.26
36 2 0.06
37 16 0.47
38 7 0.21
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (37 bp):
AAAATTAAAAAAAATTAAAATTTTAAAAAGCTAATTA
Found at i:93785 original size:2 final size:2
Alignment explanation
Indices: 93778--93802 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
93768 CCACCTGTTT
93778 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 T
93803 GAGGCTGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:97472 original size:21 final size:19
Alignment explanation
Indices: 97434--97478 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
97424 TACTCTGAAC
*
97434 TTTGAATCTCGACTTAAAT
1 TTTGAATCACGACTTAAAT
97453 TTTGAATCACGAATCTTAAAT
1 TTTGAATCACG-A-CTTAAAT
*
97474 CTTGA
1 TTTGA
97479 TCCTTGAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 10 0.45
20 1 0.05
21 11 0.50
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (19 bp):
TTTGAATCACGACTTAAAT
Found at i:97669 original size:21 final size:23
Alignment explanation
Indices: 97627--97669 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
97617 GAGTATGAAG
**
97627 CTTGATGTTTGAGGTTTGAGATT
1 CTTGATGTTTGAGGTTCAAGATT
97650 CTTGAT-TTTG-GGTTCAAGAT
1 CTTGATGTTTGAGGTTCAAGAT
97670 AAAAGAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
22 4 0.22
23 6 0.33
ACGTcount: A:0.19, C:0.07, G:0.28, T:0.47
Consensus pattern (23 bp):
CTTGATGTTTGAGGTTCAAGATT
Found at i:98418 original size:17 final size:18
Alignment explanation
Indices: 98398--98436 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
98388 TATAAAATTT
98398 TTTGTATTGT-ATTTTTG
1 TTTGTATTGTAATTTTTG
* *
98415 TTTGTATTTTAATTTTTT
1 TTTGTATTGTAATTTTTG
98433 TTTG
1 TTTG
98437 AAAAATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (18 bp):
TTTGTATTGTAATTTTTG
Found at i:98419 original size:12 final size:13
Alignment explanation
Indices: 98396--98424 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
98386 ATTATAAAAT
98396 TTTTTGTATTGTA
1 TTTTTGTATTGTA
98409 TTTTTGT-TTGTA
1 TTTTTGTATTGTA
98421 TTTT
1 TTTT
98425 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.10, C:0.00, G:0.14, T:0.76
Consensus pattern (13 bp):
TTTTTGTATTGTA
Found at i:103151 original size:44 final size:44
Alignment explanation
Indices: 103064--103154 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 44
103054 ATTTAGAAAA
* * *
103064 ATCCGTAATTTATTTTAGTAACAATGTCTCAAAATTGAATAAAG
1 ATCCCTAATTTATTTTAGTAACAAAGTCTCAAAATTCAATAAAG
**
103108 ATCCCTAATTTATTTTAGTAGGAAAGAT-TCAAAA-TCAACTAAAG
1 ATCCCTAATTTATTTTAGTAACAAAG-TCTCAAAATTCAA-TAAAG
103152 ATC
1 ATC
103155 AAATCGATAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 3 0.08
44 36 0.90
45 1 0.03
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (44 bp):
ATCCCTAATTTATTTTAGTAACAAAGTCTCAAAATTCAATAAAG
Found at i:105528 original size:21 final size:21
Alignment explanation
Indices: 105504--105545 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
105494 TTTTTTCTTT
*
105504 AATTAATTAATCAAATATTAA
1 AATTAATAAATCAAATATTAA
* *
105525 AATTACTAAATCAAATTTTAA
1 AATTAATAAATCAAATATTAA
105546 TATTTCACCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTAATAAATCAAATATTAA
Found at i:108859 original size:30 final size:30
Alignment explanation
Indices: 108801--108859 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
108791 TATTTTATTG
**
108801 TTAATTTTGTTATTATTTTAGAGGCATTTA
1 TTAATTTTGTTATTATTTTAGAAACATTTA
108831 TTAATTTTGTTATTATTTTAGAAACATTT
1 TTAATTTTGTTATTATTTTAGAAACATTT
108860 GTTTGTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAGAAACATTTA
Found at i:109240 original size:26 final size:26
Alignment explanation
Indices: 109186--109240 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
109176 ATGATTTTTT
* * *
109186 TGAAGATTTCAGTCTACAATTATTTG
1 TGAAGATTGCAATCTACAATTATTGG
109212 TGAAGATTGCAATCTACAATT-TTAGG
1 TGAAGATTGCAATCTACAATTATT-GG
109238 TGA
1 TGA
109241 CAATCTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (26 bp):
TGAAGATTGCAATCTACAATTATTGG
Found at i:110782 original size:19 final size:19
Alignment explanation
Indices: 110744--110783 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
110734 AATCATTTTA
*
110744 AATATAATTATTTTTAGTG
1 AATATAATTATTTATAGTG
110763 AATATAATT-TTTATATGTG
1 AATATAATTATTTATA-GTG
110782 AA
1 AA
110784 ATATTTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (19 bp):
AATATAATTATTTATAGTG
Found at i:111403 original size:24 final size:24
Alignment explanation
Indices: 111371--111430 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
111361 GTGTTTTGTA
111371 GAAAGCGTTTTCAGGAAGCGCGTG
1 GAAAGCGTTTTCAGGAAGCGCGTG
111395 GAAAGCGTTTTCAGGAAGCGCGTG
1 GAAAGCGTTTTCAGGAAGCGCGTG
111419 GAAAGCGTTTTC
1 GAAAGCGTTTTC
111431 TGACAAAACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23
Consensus pattern (24 bp):
GAAAGCGTTTTCAGGAAGCGCGTG
Done.