Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013628.1 Kokia drynarioides strain JFW-HI SEQ_128656, 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: 48281
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 74 characters in sequence are not A, C, G, or T
Found at i:599 original size:16 final size:16
Alignment explanation
Indices: 580--610 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
570 ATATTAATGG
*
580 TATTTAATTTTAAAAA
1 TATTTAATATTAAAAA
596 TATTTAATATTAAAA
1 TATTTAATATTAAAA
611 TTATACAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTAATATTAAAAA
Found at i:5651 original size:59 final size:60
Alignment explanation
Indices: 5585--5831 Score: 204
Period size: 59 Copynumber: 4.2 Consensus size: 60
5575 GAGAATTCGA
*
5585 GGTTAAAACATAATTTTAGAAAAG-TTTAGGGGTAAAAATGCAATTTTA-AGAAAG-TTTAG
1 GGTTAAAATATAATTTTAGAAAAGTTTTA-GGGTAAAAATGCAATTTTAGA-AAAGTTTTAG
* * * * *
5644 GGTTAAAATATGATTTTAGAGAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTAG
1 GGTTAAAATATAATTTTAGAAAAGTTTTAGGGTAAAAATGCAATTTTAGAAAAGTTTTAG
* * ** * **
5704 GGTTAAAATGTAATTTTAG-GAAGTTCAAGGGTTAAATAT--AATTTT-GAAAAGTTAGAG
1 GGTTAAAATATAATTTTAGAAAAGTTTTAGGG-TAAAAATGCAATTTTAGAAAAGTTTTAG
* * * * * * *
5761 GGTCAAAATGTAATTTTAGAGAAGTTTTGAGGGTCAAAATAG-GATTTTAGAGAAGTTTAAG
1 GGTTAAAATATAATTTTAGAAAAGTTTT-AGGGTAAAAAT-GCAATTTTAGAAAAGTTTTAG
*
5822 GGTCAAAATA
1 GGTTAAAATA
5832 GGATATTTTT
Statistics
Matches: 155, Mismatches: 24, Indels: 16
0.79 0.12 0.08
Matches are distributed among these distances:
57 28 0.18
58 17 0.11
59 55 0.35
60 37 0.24
61 18 0.12
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (60 bp):
GGTTAAAATATAATTTTAGAAAAGTTTTAGGGTAAAAATGCAATTTTAGAAAAGTTTTAG
Found at i:5700 original size:89 final size:86
Alignment explanation
Indices: 5595--5831 Score: 253
Period size: 89 Copynumber: 2.7 Consensus size: 86
5585 GGTTAAAACA
*
5595 TAATTTTAGAAAAGTTTAGGGGTAAAAATGCAATTTTAAGAAAGTTTAGGGTTAAAATATGATTT
1 TAATTTTAGAAAAGTTTAGGGGTAAAAATG-AATTTT-AGAAAGTTTAGGGTTAAAATATAATTT
* **
5660 TAGAGAAGTTTTAGGGTCAAAATG
64 T-GAAAAGTTAGAGGGTCAAAATG
* * * *
5684 TAATTTTGGAAAAGTTTTA-GGGTTAAAATGTAATTTTAGGAAGTTCAAGGGTT-AAATATAATT
1 TAATTTTAGAAAAG-TTTAGGGGTAAAAATG-AATTTTAGAAAGTT-TAGGGTTAAAATATAATT
5747 TTGAAAAGTTAGAGGGTCAAAATG
63 TTGAAAAGTTAGAGGGTCAAAATG
* * * * *
5771 TAATTTTAGAGAAGTTTTGAGGGTCAAAATAGGATTTTAGAGAAGTTTAAGGGTCAAAATA
1 TAATTTTAGAAAAGTTTAG-GGGTAAAAAT-GAATTTTAGA-AAGTTT-AGGGTTAAAATA
5832 GGATATTTTT
Statistics
Matches: 123, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
86 3 0.02
87 31 0.25
88 34 0.28
89 46 0.37
90 9 0.07
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.35
Consensus pattern (86 bp):
TAATTTTAGAAAAGTTTAGGGGTAAAAATGAATTTTAGAAAGTTTAGGGTTAAAATATAATTTTG
AAAAGTTAGAGGGTCAAAATG
Found at i:5835 original size:30 final size:30
Alignment explanation
Indices: 5595--5830 Score: 225
Period size: 30 Copynumber: 8.0 Consensus size: 30
5585 GGTTAAAACA
* * *
5595 TAATTTTAGAAAAGTTTAGGGGTAAAAATG
1 TAATTTTAGAGAAGTTTAAGGGTCAAAATG
* * *
5625 CAATTTTA-AGAAAGTTT-AGGGTTAAAATA
1 TAATTTTAGAG-AAGTTTAAGGGTCAAAATG
* *
5654 TGATTTTAGAGAAGTTTTAGGGTCAAAATG
1 TAATTTTAGAGAAGTTTAAGGGTCAAAATG
* * * *
5684 TAATTTTGGAAAAGTTTTAGGGTTAAAATG
1 TAATTTTAGAGAAGTTTAAGGGTCAAAATG
* * *
5714 TAATTTTAG-GAAGTTCAAGGGT-TAAATA
1 TAATTTTAGAGAAGTTTAAGGGTCAAAATG
*
5742 TAATTTT-GAAAAG-TTAGAGGGTCAAAATG
1 TAATTTTAGAGAAGTTTA-AGGGTCAAAATG
*
5771 TAATTTTAGAGAAGTTTTGAGGGTCAAAATAG
1 TAATTTTAGAGAAG-TTTAAGGGTCAAAAT-G
*
5803 -GATTTTAGAGAAGTTTAAGGGTCAAAAT
1 TAATTTTAGAGAAGTTTAAGGGTCAAAAT
5831 AGGATATTTT
Statistics
Matches: 169, Mismatches: 27, Indels: 20
0.78 0.12 0.09
Matches are distributed among these distances:
27 3 0.02
28 19 0.11
29 43 0.25
30 78 0.46
31 23 0.14
32 3 0.02
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (30 bp):
TAATTTTAGAGAAGTTTAAGGGTCAAAATG
Found at i:6977 original size:14 final size:15
Alignment explanation
Indices: 6958--6986 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6948 TGACTCTTGA
6958 ATATTTTGC-TCTGT
1 ATATTTTGCTTCTGT
6972 ATATTTTGCTTCTGT
1 ATATTTTGCTTCTGT
6987 TGTATTGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (15 bp):
ATATTTTGCTTCTGT
Found at i:8142 original size:39 final size:39
Alignment explanation
Indices: 8012--8505 Score: 162
Period size: 39 Copynumber: 12.7 Consensus size: 39
8002 TGATGGTGAC
* *
8012 CTGCCCCAAGCTTGGGGTAAGAGATCTA-ATTG-CTACAAT
1 CTGCCCCAAGCTCGGGGTAAGAGATC-AGA-TGACTGCAAT
* * * ** * **
8051 CTGCCCTAAGCTTGAGGTAAGAGATTGGTTGA-TAGTGAT
1 CTGCCCCAAGCTCGGGGTAAGAGATCAGATGACT-GCAAT
* * * * * * *
8090 TTACCTCAGGCTCGGGGTGAGAGATCGGATGATTGCAAT
1 CTGCCCCAAGCTCGGGGTAAGAGATCAGATGACTGCAAT
* *
8129 CTGCCCCAAGCTCGGGGTAAGAGATCAGATGGCTCCAAT
1 CTGCCCCAAGCTCGGGGTAAGAGATCAGATGACTGCAAT
* * * * *
8168 CTGCCCCAGGCTCGAGGTAAGAGATTAGCTGA-TGGTAAT
1 CTGCCCCAAGCTCGGGGTAAGAGATCAGATGACT-GCAAT
* *** *
8207 CTGTCCCAAGCTCAAAGTAAGAGATCGGAT-AGCTGCAAT
1 CTGCCCCAAGCTCGGGGTAAGAGATCAGATGA-CTGCAAT
* * * ** * * **
8246 CTACCCCAGGCTCGGGGTAAGAGGTTGGCT-AATGGTGAT
1 CTGCCCCAAGCTCGGGGTAAGAGATCAGATGACT-GCAAT
* * * * * *
8285 CTGCCTCAGGCTCGGGATAAGAGATCGGATGGCTGTAAT
1 CTGCCCCAAGCTCGGGGTAAGAGATCAGATGACTGCAAT
* * ** ** * **
8324 TTTCCTTAAGCTCGGGGTAAGAGATTGGTTGA-TGGTGAT
1 CTGCCCCAAGCTCGGGGTAAGAGATCAGATGACT-GCAAT
* * * ** *
8363 TTGCCCTAAGCTCGGGGTCAGAGATTGGGT-AGCTGCAAT
1 CTGCCCCAAGCTCGGGGTAAGAGATCAGATGA-CTGCAAT
* * * * * * * **
8402 TTG-CCCAGGCTTGGGGTAAAATATTAGCTGA-TGGTGAT
1 CTGCCCCAAGCTCGGGGTAAGAGATCAGATGACT-GCAAT
* * ** *
8440 CTGCCCCAAACTCGGGGTAAAAGATTGGATGGCTGCAAT
1 CTGCCCCAAGCTCGGGGTAAGAGATCAGATGACTGCAAT
* *
8479 TTGCCCCAGGCTCGGGGTAAGAGATCA
1 CTGCCCCAAGCTCGGGGTAAGAGATCA
8506 AAATCTTCAA
Statistics
Matches: 333, Mismatches: 106, Indels: 32
0.71 0.23 0.07
Matches are distributed among these distances:
37 1 0.00
38 31 0.09
39 296 0.89
40 5 0.02
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.25
Consensus pattern (39 bp):
CTGCCCCAAGCTCGGGGTAAGAGATCAGATGACTGCAAT
Found at i:8178 original size:78 final size:78
Alignment explanation
Indices: 8096--8503 Score: 422
Period size: 78 Copynumber: 5.2 Consensus size: 78
8086 TGATTTACCT
* * * * ** *
8096 CAGGCTCGGGGTGAGAGATCGGATGATTGCAATCTGCCCCAAGCTCGGGGTAAGAGATCAGATGG
1 CAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGGATGG
* *
8161 CTCCAATCTGCCC
66 CTGCAATTTGCCC
* * * * *** *
8174 CAGGCTCGAGGTAAGAGATTAGCTGATGGTAATCTGTCCCAAGCTCAAAGTAAGAGATCGGATAG
1 CAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGGATGG
* *
8239 CTGCAATCTACCC
66 CTGCAATTTGCCC
* * * * *
8252 CAGGCTCGGGGTAAGAGGTTGGCTAATGGTGATCTGCCTCAGGCTCGGGATAAGAGATCGGATGG
1 CAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGGATGG
* * *
8317 CTGTAATTTTCCT
66 CTGCAATTTGCCC
* * * * * * * * *
8330 TAAGCTCGGGGTAAGAGATTGGTTGATGGTGATTTGCCCTAAGCTCGGGGTCAGAGATTGGGTAG
1 CAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGGATGG
8395 CTGCAATTTG-CC
66 CTGCAATTTGCCC
* * * * * * *
8407 CAGGCTTGGGGTAAAATATTAGCTGATGGTGATCTGCCCCAAACTCGGGGTAAAAGATTGGATGG
1 CAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGGATGG
8472 CTGCAATTTGCCC
66 CTGCAATTTGCCC
8485 CAGGCTCGGGGTAAGAGAT
1 CAGGCTCGGGGTAAGAGAT
8504 CAAAATCTTC
Statistics
Matches: 263, Mismatches: 66, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
77 62 0.24
78 201 0.76
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (78 bp):
CAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGGATGG
CTGCAATTTGCCC
Found at i:8230 original size:117 final size:117
Alignment explanation
Indices: 8012--8268 Score: 288
Period size: 117 Copynumber: 2.2 Consensus size: 117
8002 TGATGGTGAC
* * * *
8012 CTGCCCCAAGCTTGGGGTAAGAGATCTAATTGCTACAATCTGCCCTAAGCTTGAGGTAAGAGATT
1 CTGCCCCAAGCTCGGGGTAAGAGATCTAATGGCTACAATCTGCCCCAAGCTCGAGGTAAGAGATT
* * * * *** * *
8077 GGTTGATAGTGATTTACCTCAGGCTCGGGGTGAGAGATCGGAT-GATTGCAAT
66 AGCTGATAGTAATTTACCTCAAGCTCAAAGTAAGAGATCGGATAG-CTGCAAT
* *
8129 CTGCCCCAAGCTCGGGGTAAGAGATC-AGATGGCTCCAATCTGCCCCAGGCTCGAGGTAAGAGAT
1 CTGCCCCAAGCTCGGGGTAAGAGATCTA-ATGGCTACAATCTGCCCCAAGCTCGAGGTAAGAGAT
*
8193 TAGCTGATGGTAATCTGT-CC-CAAGCTCAAAGTAAGAGATCGGATAGCTGCAAT
65 TAGCTGATAGTAAT-T-TACCTCAAGCTCAAAGTAAGAGATCGGATAGCTGCAAT
* *
8246 CTACCCCAGGCTCGGGGTAAGAG
1 CTGCCCCAAGCTCGGGGTAAGAG
8269 GTTGGCTAAT
Statistics
Matches: 118, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
116 1 0.01
117 112 0.95
118 4 0.03
119 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (117 bp):
CTGCCCCAAGCTCGGGGTAAGAGATCTAATGGCTACAATCTGCCCCAAGCTCGAGGTAAGAGATT
AGCTGATAGTAATTTACCTCAAGCTCAAAGTAAGAGATCGGATAGCTGCAAT
Found at i:16964 original size:14 final size:15
Alignment explanation
Indices: 16932--16965 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
16922 AACAAGTTTC
16932 TTTACATAAAGCAGT
1 TTTACATAAAGCAGT
*
16947 TTTACATAAA-CGGT
1 TTTACATAAAGCAGT
16961 TTTAC
1 TTTAC
16966 CTTAATACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (15 bp):
TTTACATAAAGCAGT
Found at i:20646 original size:29 final size:29
Alignment explanation
Indices: 20489--20759 Score: 192
Period size: 30 Copynumber: 9.2 Consensus size: 29
20479 AACGGAGTCG
* * *
20489 AAAATG-AAGTTTTAGAGAA-TTCGAGGTT
1 AAAATGTAA-TTTTAGAAAAGTTTGAGGGT
** * *
20517 AAAACATAATTTTAGAAAAGTTTAAGGGCA
1 AAAATGTAATTTTAGAAAAGTTTGAGGG-T
*
20547 AAAATGTAATTTTAGGAAAGTTT-AGGGT
1 AAAATGTAATTTTAGAAAAGTTTGAGGGT
* * *
20575 TAAATGTGATTTTAGAGAAGTTTGAGGGTT
1 AAAATGTAATTTTAGAAAAGTTTGAGGG-T
* * *
20605 AAAATGCAATTTTGGAAAAGTTTTAGGGT
1 AAAATGTAATTTTAGAAAAGTTTGAGGGT
* * * *
20634 AAAATGTGATTTTGGGAAAGTTCGAGGGT
1 AAAATGTAATTTTAGAAAAGTTTGAGGGT
**
20663 CAAAATACAATTTT-GAATAAGTTTGAGGGT
1 -AAAATGTAATTTTAGAA-AAGTTTGAGGGT
* * *
20693 CAAATGTAATTTTAGAGAAGTTTTGTGGGT
1 AAAATGTAATTTTAGAAAAG-TTTGAGGGT
* * *
20723 CAAAATAG-GATTTTAGAGAAGTTTGAAGGT
1 -AAAAT-GTAATTTTAGAAAAGTTTGAGGGT
20753 CAAAATG
1 -AAAATG
20760 GGAATTTAAA
Statistics
Matches: 192, Mismatches: 40, Indels: 21
0.76 0.16 0.08
Matches are distributed among these distances:
28 32 0.17
29 56 0.29
30 87 0.45
31 16 0.08
32 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAAGTTTGAGGGT
Found at i:20655 original size:59 final size:58
Alignment explanation
Indices: 20525--20715 Score: 199
Period size: 59 Copynumber: 3.2 Consensus size: 58
20515 TTAAAACATA
* * * *
20525 ATTTTAGAAAAGTTTAAGGGCAAAAATGTAATTTTAGG-AAAG-TTTAGGGTTAAATGTG
1 ATTTTAG-AAAGTTTGAGGGTAAAAATGCAATTTT-GGAAAAGTTTTAGGGTAAAATGTG
*
20583 ATTTTAGAGAAGTTTGAGGGTTAAAATGCAATTTTGGAAAAGTTTTAGGGTAAAATGTG
1 ATTTTAGA-AAGTTTGAGGGTAAAAATGCAATTTTGGAAAAGTTTTAGGGTAAAATGTG
* * * * * * *
20642 ATTTTGGGAAAGTTCGAGGGTCAAAATACAATTTT-GAATAAGTTTGAGGGTCAAATGTA
1 ATTTT-AGAAAGTTTGAGGGTAAAAATGCAATTTTGGAA-AAGTTTTAGGGTAAAATGTG
20701 ATTTTAGAGAAGTTT
1 ATTTTAGA-AAGTTT
20716 TGTGGGTCAA
Statistics
Matches: 113, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
57 3 0.03
58 38 0.34
59 70 0.62
60 2 0.02
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (58 bp):
ATTTTAGAAAGTTTGAGGGTAAAAATGCAATTTTGGAAAAGTTTTAGGGTAAAATGTG
Found at i:24589 original size:45 final size:45
Alignment explanation
Indices: 24525--24614 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
24515 GGATCAAACC
24525 CAAAAAAAGAATAATTTAGACAAAATTGAAAATTTTTTACCTTAT
1 CAAAAAAAGAATAATTTAGACAAAATTGAAAATTTTTTACCTTAT
24570 CAAAAAAAGAATAATTTAGACAAAATTGAAAATTTTTTACCTTAT
1 CAAAAAAAGAATAATTTAGACAAAATTGAAAATTTTTTACCTTAT
24615 AGGGGTCACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (45 bp):
CAAAAAAAGAATAATTTAGACAAAATTGAAAATTTTTTACCTTAT
Found at i:25454 original size:32 final size:32
Alignment explanation
Indices: 25413--25642 Score: 307
Period size: 32 Copynumber: 7.1 Consensus size: 32
25403 AAAAACTGTA
* * *
25413 AACAGTAAGCTCATAGGAGCTATCAATCTATG
1 AACAATAAGCTCGTAAGAGCTATCAATCTATG
25445 AACAATAAGCTCGTAAGAGCTATCAAATCTATG
1 AACAATAAGCTCGTAAGAGCTATC-AATCTATG
* *
25478 AACAATAAGCTCGTAAGAGCTATCGATCTACG
1 AACAATAAGCTCGTAAGAGCTATCAATCTATG
* * *
25510 AACAATAAGCTCGTAAGAGTTGTAAAATCTATG
1 AACAATAAGCTCGTAAGAGCTAT-CAATCTATG
*
25543 AACAATAAGCTCGTAAGAGCTGTCAATCTATG
1 AACAATAAGCTCGTAAGAGCTATCAATCTATG
* * * *
25575 AACAATAAGCTCTTAAAAGCTGTAAATCTATG
1 AACAATAAGCTCGTAAGAGCTATCAATCTATG
* *
25607 AACAATAAGCTCGTAAGAGCTTTCAATCTGTG
1 AACAATAAGCTCGTAAGAGCTATCAATCTATG
25639 AACA
1 AACA
25643 TTAGTTAATG
Statistics
Matches: 176, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
32 116 0.66
33 60 0.34
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (32 bp):
AACAATAAGCTCGTAAGAGCTATCAATCTATG
Found at i:25522 original size:65 final size:64
Alignment explanation
Indices: 25413--25642 Score: 334
Period size: 65 Copynumber: 3.6 Consensus size: 64
25403 AAAAACTGTA
* * * *
25413 AACAGTAAGCTCATAGGAGCTATCAATCTATGAACAATAAGCTCGTAAGAGCTATCAAATCTATG
1 AACAATAAGCTCGTAAGAGCTATCAATCTATGAACAATAAGCTCGTAAGAGCTGT-AAATCTATG
* * *
25478 AACAATAAGCTCGTAAGAGCTATCGATCTACGAACAATAAGCTCGTAAGAGTTGTAAAATCTATG
1 AACAATAAGCTCGTAAGAGCTATCAATCTATGAACAATAAGCTCGTAAGAGCTGT-AAATCTATG
* * *
25543 AACAATAAGCTCGTAAGAGCTGTCAATCTATGAACAATAAGCTCTTAAAAGCTGTAAATCTATG
1 AACAATAAGCTCGTAAGAGCTATCAATCTATGAACAATAAGCTCGTAAGAGCTGTAAATCTATG
* *
25607 AACAATAAGCTCGTAAGAGCTTTCAATCTGTGAACA
1 AACAATAAGCTCGTAAGAGCTATCAATCTATGAACA
25643 TTAGTTAATG
Statistics
Matches: 149, Mismatches: 16, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
64 43 0.29
65 106 0.71
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (64 bp):
AACAATAAGCTCGTAAGAGCTATCAATCTATGAACAATAAGCTCGTAAGAGCTGTAAATCTATG
Found at i:28218 original size:22 final size:22
Alignment explanation
Indices: 28192--28242 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
28182 TAAAATTTTG
* * *
28192 ATTTAATCTTTTAAAAATTGCA
1 ATTTAATATTATAAAAATTACA
* *
28214 CTTTACTATTATAAAAATTACA
1 ATTTAATATTATAAAAATTACA
28236 ATTTAAT
1 ATTTAAT
28243 TTCAGTCTCT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTTAATATTATAAAAATTACA
Found at i:32992 original size:12 final size:12
Alignment explanation
Indices: 32975--33008 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
32965 TTATTAATTC
*
32975 ATAAACGAGTCA
1 ATAAACGAGCCA
*
32987 ATAAACGAACCA
1 ATAAACGAGCCA
32999 ATAAACGAGC
1 ATAAACGAGC
33009 TTTTAAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.21, G:0.15, T:0.12
Consensus pattern (12 bp):
ATAAACGAGCCA
Found at i:35396 original size:18 final size:20
Alignment explanation
Indices: 35373--35412 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
35363 TTAAAAATTG
*
35373 GAATTTTT-ATAA-TATTTT
1 GAATTTTTGAAAATTATTTT
35391 GAATTTTTGAAAATTATTTT
1 GAATTTTTGAAAATTATTTT
35411 GA
1 GA
35413 TTATCTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 3 0.16
20 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (20 bp):
GAATTTTTGAAAATTATTTT
Found at i:35848 original size:7 final size:7
Alignment explanation
Indices: 35836--35877 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
35826 AGCAAAGAGA
35836 CTAAACC
1 CTAAACC
35843 CTAAACC
1 CTAAACC
35850 CTAAACC
1 CTAAACC
35857 CTAAACC
1 CTAAACC
35864 CTAAACC
1 CTAAACC
35871 CTAAACC
1 CTAAACC
35878 TTAATTAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14
Consensus pattern (7 bp):
CTAAACC
Found at i:36204 original size:12 final size:14
Alignment explanation
Indices: 36176--36264 Score: 50
Period size: 12 Copynumber: 6.7 Consensus size: 14
36166 TTAAACATAC
36176 ATATTTAATTATTT
1 ATATTTAATTATTT
36190 ATATTTAA-T-TTT
1 ATATTTAATTATTT
*
36202 ATA-TAAATTA-TT
1 ATATTTAATTATTT
* *
36214 A-ATATAATTA-AT
1 ATATTTAATTATTT
36226 ATAATTT-ATTATTT
1 AT-ATTTAATTATTT
* *
36240 -TAATCAATTATTT
1 ATATTTAATTATTT
36253 AATATTTCAATT
1 -ATATTT-AATT
36265 TTATTTTAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 18
0.66 0.12 0.22
Matches are distributed among these distances:
11 4 0.07
12 19 0.35
13 13 0.24
14 12 0.22
15 3 0.05
16 4 0.07
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATTTAATTATTT
Found at i:36283 original size:13 final size:14
Alignment explanation
Indices: 36267--36308 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
36257 TTTCAATTTT
36267 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
36280 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
36295 ATTTTAAATAATAT
1 ATTTT-AATAATAT
36309 CCTTAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:36293 original size:16 final size:16
Alignment explanation
Indices: 36271--36307 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
36261 AATTTTATTT
36271 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
36288 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
36303 TAATA
1 TAATA
36308 TCCTTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:36360 original size:15 final size:15
Alignment explanation
Indices: 36326--36396 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
36316 ATATTATTGA
36326 AAATA-TTTAAT-AT
1 AAATATTTTAATAAT
*
36339 TAATATTTTAATAAT
1 AAATATTTTAATAAT
* *
36354 AAATATTTATTGCAGTTAT
1 AAATA-TT-TT--AATAAT
*
36373 AAATATATTAATAAT
1 AAATATTTTAATAAT
36388 AAATATTTT
1 AAATATTTT
36397 GTAGTATAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
13 4 0.09
14 6 0.14
15 18 0.41
16 2 0.05
17 4 0.09
18 1 0.02
19 9 0.20
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:41009 original size:25 final size:26
Alignment explanation
Indices: 40981--41030 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
40971 ATCAACCTAA
40981 CGAGAGGAAGATAAATT-CAAATTTG
1 CGAGAGGAAGATAAATTCCAAATTTG
* *
41006 CGAGAGGAATATCAATTCCAAATTT
1 CGAGAGGAAGATAAATTCCAAATTT
41031 TGCAACACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (26 bp):
CGAGAGGAAGATAAATTCCAAATTTG
Found at i:42219 original size:24 final size:22
Alignment explanation
Indices: 42169--42241 Score: 80
Period size: 21 Copynumber: 3.3 Consensus size: 22
42159 CCTGCAACTT
42169 CTACCGATA-C-AAGTACATAAA
1 CTACCGATACCTAAGTACA-AAA
*
42190 CCACCGATACTTCTAAGTACAAAA
1 CTACCGATAC--CTAAGTACAAAA
*
42214 CTACCGATACCT-ACTACAAAA
1 CTACCGATACCTAAGTACAAAA
42235 CTACCGA
1 CTACCGA
42242 CACAACCCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
21 23 0.51
22 2 0.04
24 13 0.29
25 7 0.16
ACGTcount: A:0.42, C:0.30, G:0.08, T:0.19
Consensus pattern (22 bp):
CTACCGATACCTAAGTACAAAA
Found at i:47067 original size:96 final size:96
Alignment explanation
Indices: 46883--47074 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 96
46873 CTTTTGCAAG
* ** *
46883 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCG
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCG
* *
46948 GAATCGAAGATAAGAAAACATTGCCTCGATT
66 AAACCGAAGATAAGAAAACATTGCCTCGATT
* * *
46979 AAGGGTATTCGATTA-CTTCGATTTGAAGAAAAATTTCACCTAGTGAGTTAAGGCACAA-ATTTT
1 AAGGATATTCGATTATC-TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTT
*
47042 CGAAACCCGAA-ATAA-AAGAATATTGCCTCGATT
64 CGAAA-CCGAAGATAAGAA-AACATTGCCTCGATT
47075 TTAAAGTTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
95 4 0.05
96 74 0.90
97 4 0.05
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCG
AAACCGAAGATAAGAAAACATTGCCTCGATT
Found at i:47433 original size:29 final size:29
Alignment explanation
Indices: 47401--47985 Score: 382
Period size: 29 Copynumber: 19.8 Consensus size: 29
47391 AATTCAGGGT
47401 TAAAAATGGGATTTTTGGAAGTTTCGAGG
1 TAAAAATGGGATTTTTGGAAGTTTCGAGG
*
47430 T-AAAATGGTAATTTTTGGAAGTTTCG-GG
1 TAAAAATGG-GATTTTTGGAAGTTTCGAGG
47458 TTGAAAAAT-GGAGTTTTTGGAAGTTT-GAGGG
1 -T-AAAAATGGGA-TTTTTGGAAGTTTCGA-GG
*
47489 T-AAAATGGTAATTTTTGGAAGGTTTCG-GAG
1 TAAAAATGG-GATTTTTGGAA-GTTTCGAG-G
*
47519 TAAAAAATGGGATTTTTGGAAGTTT-GGGG
1 T-AAAAATGGGATTTTTGGAAGTTTCGAGG
* * *
47548 TTAAAATGGTAATTTTTGGAAGTTTTGAGG
1 TAAAAATGG-GATTTTTGGAAGTTTCGAGG
* *
47578 TTAAAAATGGGATTTTTGGAAG-CTCGGGGG
1 -TAAAAATGGGATTTTTGGAAGTTTC-GAGG
* ** * *
47608 TAAAATTGTAATTTTTGGAAGTTTTGGGG
1 TAAAAATGGGATTTTTGGAAGTTTCGAGG
*
47637 TTAAAAATTGGATTTTTGGAA-TTTCGAGGG
1 -TAAAAATGGGATTTTTGGAAGTTTCGA-GG
* * *
47667 T-AAAATGGTAATTTTGGAAGTTTCGAGC
1 TAAAAATGGGATTTTTGGAAGTTTCGAGG
*
47695 TCAAAAATGGGATTTTTGGAAG-CTCGAGGG
1 T-AAAAATGGGATTTTTGGAAGTTTCGA-GG
*** ** *
47725 TAATTTTGTAATTTTTGGAAGTTTTGAGG
1 TAAAAATGGGATTTTTGGAAGTTTCGAGG
* * *
47754 TTAAAAATAGGATTTTTAGAAG-TTCAGGGG
1 -TAAAAATGGGATTTTTGGAAGTTTC-GAGG
* *
47784 T-AAAATGGTAATTTTTGGAAGTTT-TAGGG
1 TAAAAATGG-GATTTTTGGAAGTTTCGA-GG
* *
47813 TCAAAAATGGGATTTCTGGAAG-CTCGAGGG
1 T-AAAAATGGGATTTTTGGAAGTTTCGA-GG
* * **
47843 TAGAATTGTAATTTTTGGAAGTTTCG-GCG
1 TAAAAATGGGATTTTTGGAAGTTTCGAG-G
*
47872 TAAAAAATGGGATTTTTGGAAG-CTCGAGGG
1 T-AAAAATGGGATTTTTGGAAGTTTCGA-GG
* ** *
47902 TAAAATTGTAATTTTTGGAAGTTT-TAGGG
1 TAAAAATGGGATTTTTGGAAGTTTCGA-GG
*
47931 TTAAAAATGGGATTTTTGGAAG-TTCGGGGG
1 -TAAAAATGGGATTTTTGGAAGTTTC-GAGG
*
47961 T-AAAATGGTAATTTTTGGAAAGTTT
1 TAAAAATGG-GATTTTTGG-AAGTTT
47986 AAGGACCTCT
Statistics
Matches: 431, Mismatches: 78, Indels: 92
0.72 0.13 0.15
Matches are distributed among these distances:
28 52 0.12
29 172 0.40
30 164 0.38
31 36 0.08
32 7 0.02
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.37
Consensus pattern (29 bp):
TAAAAATGGGATTTTTGGAAGTTTCGAGG
Found at i:47468 original size:59 final size:58
Alignment explanation
Indices: 47397--47985 Score: 738
Period size: 59 Copynumber: 10.0 Consensus size: 58
47387 GCTAAATTCA
47397 GGGTTAAAAATGGGATTTTTGGAAGTTTCGA-GGTAAAATGGTAATTTTTGGAAGTTTC
1 GGGTTAAAAATGGGATTTTTGGAAG-TTCGAGGGTAAAATGGTAATTTTTGGAAGTTTC
*
47455 GGGTTGAAAAAT-GGAGTTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGGTTTC
1 GGGTT-AAAAATGGGA-TTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAA-GTTTC
* * *
47515 GGAGTAAAAAATGGGATTTTTGGAAGTTTG-GGGTTAAAATGGTAATTTTTGGAAGTTTT
1 GG-GTTAAAAATGGGATTTTTGGAAGTTCGAGGG-TAAAATGGTAATTTTTGGAAGTTTC
* * * *
47574 GAGGTTAAAAATGGGATTTTTGGAAGCTCGGGGGTAAAATTGTAATTTTTGGAAGTTTTG
1 G-GGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAG-TTTC
* *
47634 GGGTTAAAAATTGGATTTTTGGAATTTCGAGGGTAAAATGGTAA-TTTTGGAAGTTTC
1 GGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTC
* * * ** * *
47691 GAGCTCAAAAATGGGATTTTTGGAAGCTCGAGGGTAATTTTGTAATTTTTGGAAGTTTT
1 G-GGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTC
* * *
47750 GAGGTTAAAAATAGGATTTTTAGAAGTTC-AGGGGTAAAATGGTAATTTTTGGAAGTTTTA
1 G-GGTTAAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTTTGGAAG-TTTC
* * * * *
47810 GGGTCAAAAATGGGATTTCTGGAAGCTCGAGGGTAGAATTGTAATTTTTGGAAGTTTC
1 GGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTC
* * * *
47868 GGCGTAAAAAATGGGATTTTTGGAAGCTCGAGGGTAAAATTGTAATTTTTGGAAGTTTTA
1 GG-GTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAG-TTTC
*
47928 GGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAAGTTT
1 GGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGG-AAGTTT
47986 AAGGACCTCT
Statistics
Matches: 465, Mismatches: 48, Indels: 35
0.85 0.09 0.06
Matches are distributed among these distances:
57 4 0.01
58 62 0.13
59 326 0.70
60 68 0.15
61 5 0.01
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.37
Consensus pattern (58 bp):
GGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTC
Done.