Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001558.1 Kokia drynarioides strain JFW-HI SEQ_113152, 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: 132351
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 102 characters in sequence are not A, C, G, or T
Found at i:5242 original size:15 final size:14
Alignment explanation
Indices: 5222--5251 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5212 AAAAAAGGCC
5222 TTTTATTTTTTATTT
1 TTTTATTTTTT-TTT
5237 TTTTATTTTTTTTT
1 TTTTATTTTTTTTT
5251 T
1 T
5252 GGCATCTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTATTTTTTTTT
Found at i:8187 original size:14 final size:14
Alignment explanation
Indices: 8168--8209 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
8158 AGCACGAATG
8168 AATAAATATACGAA
1 AATAAATATACGAA
*
8182 AATAAATATAAGAAA
1 AATAAATATACG-AA
8197 AATAAA-ATACGAA
1 AATAAATATACGAA
8210 TTATTAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 2 0.08
14 15 0.60
15 8 0.32
ACGTcount: A:0.69, C:0.05, G:0.07, T:0.19
Consensus pattern (14 bp):
AATAAATATACGAA
Found at i:8443 original size:28 final size:29
Alignment explanation
Indices: 8387--8463 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 29
8377 TTGGACATTT
* *
8387 GGGAGCAAAATGGTAACTTTTGGATGTCCG
1 GGGAGCAAAATGGTAA-TTTTGAATGTCCA
8417 GGGA-CAAAATGGTAATTTTGAATGTCCA
1 GGGAGCAAAATGGTAATTTTGAATGTCCA
**
8445 GGGATAAAAAT-GTAATTTT
1 GGGAGCAAAATGGTAATTTT
8464 TAGAAGTTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 23 0.53
29 16 0.37
30 4 0.09
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (29 bp):
GGGAGCAAAATGGTAATTTTGAATGTCCA
Found at i:8481 original size:29 final size:29
Alignment explanation
Indices: 8449--8705 Score: 169
Period size: 29 Copynumber: 8.6 Consensus size: 29
8439 TGTCCAGGGA
8449 TAAAAATGTAATTTTTAGAAGTTTGGGGG
1 TAAAAATGTAATTTTTAGAAGTTTGGGGG
** *
8478 TAAAAAACATAATTTTTAAGAAGTTTTGGGG
1 T-AAAAATGTAATTTTT-AGAAGTTTGGGGG
* *
8509 TAAAAAATG--ATTTTTAAAAGTTTAGGGG
1 T-AAAAATGTAATTTTTAGAAGTTTGGGGG
* * *
8537 CAAATATGTAATTTTTTTAAAGAAGTTTGAAGGG
1 TAAAAATGTAA--TTTTT--AGAAGTTTG-GGGG
* * **
8571 TAAAAATGTGATTTTTGGAAGTTTGATGG
1 TAAAAATGTAATTTTTAGAAGTTTGGGGG
* **
8600 TGAAAATGTAATTTTTGAGAAGTTTATGGG
1 TAAAAATGTAATTTTT-AGAAGTTTGGGGG
* **
8630 TAAAAAATGTGA-TTTTAGAAAAGTTTAAGGG
1 T-AAAAATGTAATTTTTAG--AAGTTTGGGGG
* **
8661 TTAAAATGTAATTTAGAGAAGTTTGGGGG
1 TAAAAATGTAATTTTTAGAAGTTTGGGGG
* * *
8690 TCAAAATATGATTTTT
1 TAAAAATGTAATTTTT
8706 GGAAAGTTCA
Statistics
Matches: 177, Mismatches: 37, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
27 6 0.03
28 11 0.06
29 47 0.27
30 43 0.24
31 47 0.27
32 5 0.03
33 7 0.04
34 11 0.06
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (29 bp):
TAAAAATGTAATTTTTAGAAGTTTGGGGG
Found at i:8503 original size:31 final size:29
Alignment explanation
Indices: 8457--8637 Score: 109
Period size: 30 Copynumber: 6.0 Consensus size: 29
8447 GATAAAAATG
*
8457 TAATTTTT-AGAAGTTTGGGGGTAAAAAACA
1 TAATTTTTAAGAAGTTTAGGGGT-AAAAA-A
*
8487 TAATTTTTAAGAAGTTTTGGGGTAAAAAA
1 TAATTTTTAAGAAGTTTAGGGGTAAAAAA
* * **
8516 TGATTTTTAA-AAGTTTAGGGGCAAATATG
1 TAATTTTTAAGAAGTTTAGGGGTAAA-AAA
* *
8545 TAATTTTTTTAAAGAAGTTTGAAGGGTAAAAATG
1 TAA--TTTTT-AAGAAGTTT-AGGGGTAAAAA-A
* * * **
8579 TGATTTTT-GGAAGTTT-GATGGTGAAAATG
1 TAATTTTTAAGAAGTTTAG-GGGT-AAAAAA
* *
8608 TAATTTTTGAGAAGTTTATGGGTAAAAAA
1 TAATTTTTAAGAAGTTTAGGGGTAAAAAA
8637 T
1 T
8638 GTGATTTTAG
Statistics
Matches: 118, Mismatches: 21, Indels: 25
0.72 0.13 0.15
Matches are distributed among these distances:
28 13 0.11
29 29 0.25
30 34 0.29
31 18 0.15
32 7 0.06
33 7 0.06
34 10 0.08
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (29 bp):
TAATTTTTAAGAAGTTTAGGGGTAAAAAA
Found at i:8669 original size:30 final size:30
Alignment explanation
Indices: 8551--8727 Score: 126
Period size: 30 Copynumber: 5.9 Consensus size: 30
8541 TATGTAATTT
8551 TTTTA-AAGAAGTTTGAAGGGTAAAAATGTGA
1 TTTTAGAA-AAGTTT-AAGGGTAAAAATGTGA
* * * * * *
8582 TTTTTG-GAAGTTTGATGGTGAAAATGTAA
1 TTTTAGAAAAGTTTAAGGGTAAAAATGTGA
* * *
8611 TTTTTGAGAAGTTTATGGGTAAAAAATGTGA
1 TTTTAGAAAAGTTTAAGGGT-AAAAATGTGA
*
8642 TTTTAGAAAAGTTTAAGGGTTAAAATGT-A
1 TTTTAGAAAAGTTTAAGGGTAAAAATGTGA
* * ** * *
8671 ATTTAGAGAAGTTTGGGGGTCAAAATATGA
1 TTTTAGAAAAGTTTAAGGGTAAAAATGTGA
* * * *
8701 TTTTTGGAAAGTTCAAGGGTCAAAATG
1 TTTTAGAAAAGTTTAAGGGTAAAAATG
8728 CAATTTGGAA
Statistics
Matches: 113, Mismatches: 29, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
29 41 0.36
30 43 0.38
31 29 0.26
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.36
Consensus pattern (30 bp):
TTTTAGAAAAGTTTAAGGGTAAAAATGTGA
Found at i:8680 original size:60 final size:58
Alignment explanation
Indices: 8492--8776 Score: 200
Period size: 60 Copynumber: 4.8 Consensus size: 58
8482 AAACATAATT
** * * *
8492 TTTA-AGAAGTTTTGGGGTAAAAA-ATGATTTTTAAAAGTTT-AGGGGCAAATATGTAA
1 TTTAGAGAAGTTTAAGGGTAAAAATGTGATTTTTGAAAGTTTAAGGGTCAAA-ATGTAA
* * * * *
8548 TTTTTTTAAAGAAGTTTGAAGGGTAAAAATGTGATTTTTGGAAGTTTGATGGTGAAAATGTAA
1 ----TTTAGAGAAGTTT-AAGGGTAAAAATGTGATTTTTGAAAGTTTAAGGGTCAAAATGTAA
* * * *
8611 TTTTTGAGAAGTTTATGGGTAAAAAATGTGATTTTAGAAAAGTTTAAGGGTTAAAATGTAA
1 -TTTAGAGAAGTTTAAGGGT-AAAAATGTGATTTTTG-AAAGTTTAAGGGTCAAAATGTAA
** * * * *
8672 TTTAGAGAAGTTTGGGGGTCAAAATATGATTTTTGGAAAGTTCAAGGGTCAAAATGCAA
1 TTTAGAGAAGTTTAAGGGTAAAAATGTGATTTTT-GAAAGTTTAAGGGTCAAAATGTAA
* * * * * * *
8731 TTTGGAAAAGCTT-GGGGTCAAAATATGATTTTTGGAAAGCTTAAGG
1 TTTAGAGAAGTTTAAGGGTAAAAATGTGATTTTT-GAAAGTTTAAGG
8777 ACCTTTTAGA
Statistics
Matches: 188, Mismatches: 30, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
58 31 0.16
59 47 0.25
60 48 0.26
61 27 0.14
62 9 0.05
63 20 0.11
64 6 0.03
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.35
Consensus pattern (58 bp):
TTTAGAGAAGTTTAAGGGTAAAAATGTGATTTTTGAAAGTTTAAGGGTCAAAATGTAA
Found at i:8761 original size:28 final size:27
Alignment explanation
Indices: 8686--8761 Score: 64
Period size: 28 Copynumber: 2.7 Consensus size: 27
8676 GAGAAGTTTG
8686 GGGGTCAAAATATGATTTTTGGAAAGTTCA
1 GGGGTCAAAATATGA--TTTGGAAAGTT-A
* ***
8716 AGGGTCAAAATGCAATTTGGAAAAGCTT-
1 GGGGTCAAAATATGATTTGG-AAAG-TTA
8744 GGGGTCAAAATATGATTT
1 GGGGTCAAAATATGATTT
8762 TTGGAAAGCT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
28 19 0.53
29 4 0.11
30 13 0.36
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (27 bp):
GGGGTCAAAATATGATTTGGAAAGTTA
Found at i:8767 original size:30 final size:30
Alignment explanation
Indices: 8686--8773 Score: 96
Period size: 29 Copynumber: 3.0 Consensus size: 30
8676 GAGAAGTTTG
8686 GGGGTCAAAATATGATTTTTGGAAAG-TTCA
1 GGGGTCAAAATATGATTTTTGGAAAGCTT-A
* *
8716 AGGGTC-AAA-ATGCA-ATTTGGAAAAGCTT-
1 GGGGTCAAAATATG-ATTTTTGG-AAAGCTTA
8744 GGGGTCAAAATATGATTTTTGGAAAGCTTA
1 GGGGTCAAAATATGATTTTTGGAAAGCTTA
8774 AGGACCTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
28 13 0.28
29 19 0.40
30 15 0.32
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.31
Consensus pattern (30 bp):
GGGGTCAAAATATGATTTTTGGAAAGCTTA
Found at i:10562 original size:6 final size:6
Alignment explanation
Indices: 10545--10634 Score: 53
Period size: 6 Copynumber: 14.8 Consensus size: 6
10535 GGACTTTTAA
* *
10545 TTAAACT TTAAAT TTAAAT TCAAA- ATAAAT TTAAAT TTAGAA- -TAAAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTA-AAT TTAAAT
* * * *
10592 TTAACT CATAAA- ATAAAT TAAAAT TTAAAAT TTAAAAT TTAAA
1 TTAAAT -TTAAAT TTAAAT TTAAAT TT-AAAT TT-AAAT TTAAA
10635 ATTGGGTTCA
Statistics
Matches: 66, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
4 2 0.03
5 10 0.15
6 31 0.47
7 23 0.35
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:10608 original size:18 final size:17
Alignment explanation
Indices: 10553--10622 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
10543 AATTAAACTT
10553 TAAATTTAAAT-TCAAAA
1 TAAATTTAAATAT-AAAA
* *
10570 TAAATTTAAATTTAGAA
1 TAAATTTAAATATAAAA
*
10587 TAAATTTAACTCATAAAA
1 TAAATTTAAAT-ATAAAA
* *
10605 TAAATTAAAATTTAAAA
1 TAAATTTAAATATAAAA
10622 T
1 T
10623 TTAAAATTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
17 30 0.68
18 14 0.32
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATATAAAA
Found at i:10621 original size:7 final size:7
Alignment explanation
Indices: 10609--10637 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
10599 ATAAAATAAA
10609 TTAAAAT
1 TTAAAAT
10616 TTAAAAT
1 TTAAAAT
10623 TTAAAAT
1 TTAAAAT
10630 TTAAAAT
1 TTAAAAT
10637 T
1 T
10638 GGGTTCAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TTAAAAT
Found at i:53800 original size:56 final size:56
Alignment explanation
Indices: 53685--53876 Score: 269
Period size: 56 Copynumber: 3.4 Consensus size: 56
53675 TGAAATAACC
* * ** *
53685 TTACGCTCTAACCGAGACGTAAGCAAGT-CAGAGCTTTACCCGAGCTATAATAGCT
1 TTACGCTCTAACCGAGACGTAAGCATGTCCAAAGCTTTACATGAGCTATAATAGCA
* * * *
53740 TTACGCTTTAACAGAGATGTAAGCATGTCCAAAGCTCTACATGAGCTATAATAGCA
1 TTACGCTCTAACCGAGACGTAAGCATGTCCAAAGCTTTACATGAGCTATAATAGCA
* *
53796 TTACGCTCTAACCGAGACGTAAGCATGTCCAAAGCTTTACTTGAGCTATAATAACA
1 TTACGCTCTAACCGAGACGTAAGCATGTCCAAAGCTTTACATGAGCTATAATAGCA
*
53852 TTACGCTTTAACCGAGACGTAAGCA
1 TTACGCTCTAACCGAGACGTAAGCA
53877 GATCGGAGCT
Statistics
Matches: 120, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
55 24 0.20
56 96 0.80
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (56 bp):
TTACGCTCTAACCGAGACGTAAGCATGTCCAAAGCTTTACATGAGCTATAATAGCA
Found at i:72531 original size:16 final size:17
Alignment explanation
Indices: 72505--72537 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
72495 CTTTAAATCT
72505 GTTTATAGGTCGATTGA
1 GTTTATAGGTCGATTGA
72522 GTTT-TAGGTCGATTGA
1 GTTTATAGGTCGATTGA
72538 TATGAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.21, C:0.06, G:0.30, T:0.42
Consensus pattern (17 bp):
GTTTATAGGTCGATTGA
Found at i:80028 original size:22 final size:21
Alignment explanation
Indices: 79987--80030 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
79977 TTTTCATTTC
*
79987 TTTTCTTTTTTTCTCTCAAGA
1 TTTTCTTTTTTTCTCCCAAGA
80008 TTTTCCTTTCTTTT-TCCCAAGA
1 TTTT-CTTT-TTTTCTCCCAAGA
80030 T
1 T
80031 CAAGGAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.14, C:0.23, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTTCTTTTTTTCTCCCAAGA
Found at i:80907 original size:21 final size:21
Alignment explanation
Indices: 80881--80929 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
80871 GAAGAATGAA
*
80881 TAGGGTTAGGGTTTGGG-TGAT
1 TAGGGTTAGAG-TTGGGTTGAT
*
80902 TAGGGTTAGAGTTGGGTTTAT
1 TAGGGTTAGAGTTGGGTTGAT
80923 TAGGGTT
1 TAGGGTT
80930 CTGGGATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.16, C:0.00, G:0.43, T:0.41
Consensus pattern (21 bp):
TAGGGTTAGAGTTGGGTTGAT
Found at i:83483 original size:38 final size:36
Alignment explanation
Indices: 83387--83498 Score: 134
Period size: 37 Copynumber: 3.0 Consensus size: 36
83377 GTTTGCACAA
* *
83387 TTTTCAGGCTATGTACCTAGTCGGCTTCGTGCAGGTG
1 TTTTCAGGCTATGTGCCTAGTAGGCTTCGTGC-GGTG
*
83424 TTTTCAGACTATGTGCCTAGTAGGCTTCGTGTCGGTG
1 TTTTCAGGCTATGTGCCTAGTAGGCTTCGTG-CGGTG
* * *
83461 TTTTCGGGGCTATGTGCTTAGTAGGCTTTGTGCCGGTG
1 TTTTC-AGGCTATGTGCCTAGTAGGCTTCGTG-CGGTG
83499 ATCCAAGAAG
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
37 37 0.57
38 28 0.43
ACGTcount: A:0.12, C:0.19, G:0.32, T:0.38
Consensus pattern (36 bp):
TTTTCAGGCTATGTGCCTAGTAGGCTTCGTGCGGTG
Found at i:84231 original size:93 final size:93
Alignment explanation
Indices: 84121--84314 Score: 379
Period size: 93 Copynumber: 2.1 Consensus size: 93
84111 GAATTTATAC
84121 TACCGGTAGAACTATGAAACTAGTATAGATATAATAGGAGAAGTATCGGTAGAAATATGCCATAC
1 TACCGGTAGAACTATGAAACTAGTATAGATATAATAGGAGAAGTATCGGTAGAAATATGCCATAC
84186 TTGTCAATCTTGCTCTCTATTAATTTAG
66 TTGTCAATCTTGCTCTCTATTAATTTAG
84214 TACCGGTAGAACTATGAAACTAGTATAGATATAATAGGAGAAGTATCGGTAGAAATATGCCATAC
1 TACCGGTAGAACTATGAAACTAGTATAGATATAATAGGAGAAGTATCGGTAGAAATATGCCATAC
84279 TTGTCAATCTTGCTCTCTATTAATTTAG
66 TTGTCAATCTTGCTCTCTATTAATTTAG
*
84307 TATCGGTA
1 TACCGGTA
84315 ATTAGAAGAG
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 100 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (93 bp):
TACCGGTAGAACTATGAAACTAGTATAGATATAATAGGAGAAGTATCGGTAGAAATATGCCATAC
TTGTCAATCTTGCTCTCTATTAATTTAG
Found at i:87027 original size:19 final size:19
Alignment explanation
Indices: 87003--87040 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
86993 TAAAAATGTG
87003 CAAAATAAAG-AGAAAAAGT
1 CAAAAT-AAGTAGAAAAAGT
*
87022 CAAAATGAGTAGAAAAAGT
1 CAAAATAAGTAGAAAAAGT
87041 ACTTGAGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.63, C:0.05, G:0.18, T:0.13
Consensus pattern (19 bp):
CAAAATAAGTAGAAAAAGT
Found at i:92389 original size:15 final size:15
Alignment explanation
Indices: 92369--92403 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
92359 AGCAGTCACA
*
92369 CATTTGGATCGGGTC
1 CATTTGGAACGGGTC
92384 CATTTGGAACGGGTC
1 CATTTGGAACGGGTC
92399 CATTT
1 CATTT
92404 CTGAAGCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.29, T:0.34
Consensus pattern (15 bp):
CATTTGGAACGGGTC
Found at i:99830 original size:17 final size:18
Alignment explanation
Indices: 99783--99830 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
99773 AATTTGTATT
99783 TAAAA-ATTAAAAATATC
1 TAAAATATTAAAAATATC
* *
99800 TAATAT-TTACAAATA-C
1 TAAAATATTAAAAATATC
99816 TAAAATATTAAAAAT
1 TAAAATATTAAAAAT
99831 TCAATAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATATTAAAAATATC
Found at i:100280 original size:22 final size:21
Alignment explanation
Indices: 100252--100333 Score: 80
Period size: 22 Copynumber: 3.9 Consensus size: 21
100242 GTTTTGATGC
100252 TATTTTTTGCTGTTTTGGTTAT
1 TATTTTTTGCTGTTTTGGTT-T
*
100274 TATTTTTTGTTGTTTTGGTGTT
1 TATTTTTTGCTGTTTTGGT-TT
100296 GTATTTTTAT-C-GTTTTGGTTT
1 -TATTTTT-TGCTGTTTTGGTTT
* *
100317 T-TTTTTTACTATTTTGG
1 TATTTTTTGCTGTTTTGG
100334 CTTCTGTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
18 1 0.02
19 6 0.12
20 7 0.13
21 2 0.04
22 27 0.52
23 8 0.15
24 1 0.02
ACGTcount: A:0.09, C:0.04, G:0.18, T:0.70
Consensus pattern (21 bp):
TATTTTTTGCTGTTTTGGTTT
Found at i:100359 original size:35 final size:36
Alignment explanation
Indices: 100317--100417 Score: 116
Period size: 35 Copynumber: 2.8 Consensus size: 36
100307 GTTTTGGTTT
* *
100317 TTTTTTTACTATTTTGGCTTCTGTTTTGGTGCTA-G
1 TTTTTTTACTATTTTTGCTACTGTTTTGGTGCTATG
* ** *
100352 TTTTTTTACTATTTTTG-TGCTGTTTTTATTGCTATT
1 TTTTTTTACTATTTTTGCTACTG-TTTTGGTGCTATG
*
100388 TTTTTTTATTATTTTTGCTACTGTTTTGGT
1 TTTTTTTACTATTTTTGCTACTGTTTTGGT
100418 TATTATTTTG
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
34 4 0.07
35 25 0.46
36 21 0.39
37 4 0.07
ACGTcount: A:0.10, C:0.09, G:0.15, T:0.66
Consensus pattern (36 bp):
TTTTTTTACTATTTTTGCTACTGTTTTGGTGCTATG
Found at i:100371 original size:23 final size:23
Alignment explanation
Indices: 100340--100390 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
100330 TTGGCTTCTG
*
100340 TTTTGGTGCTAGTTTTT-TTACTA
1 TTTTTGTGCT-GTTTTTATTACTA
*
100363 TTTTTGTGCTGTTTTTATTGCTA
1 TTTTTGTGCTGTTTTTATTACTA
100386 TTTTT
1 TTTTT
100391 TTTTATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.10, C:0.08, G:0.16, T:0.67
Consensus pattern (23 bp):
TTTTTGTGCTGTTTTTATTACTA
Found at i:100414 original size:24 final size:22
Alignment explanation
Indices: 100354--100426 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 22
100344 GGTGCTAGTT
* * *
100354 TTTTTACTATTTTTGTGCTGTT-
1 TTTTTGCTATTTTTG-GTTATTA
**
100376 TTTATTGCTATTTTTTTTTATTA
1 TTT-TTGCTATTTTTGGTTATTA
100399 TTTTTGCTACTGTTTTGGTTATTA
1 TTTTTGCTA-T-TTTTGGTTATTA
100423 TTTT
1 TTTT
100427 GGTTGTTTGG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
22 12 0.30
23 14 0.35
24 14 0.35
ACGTcount: A:0.12, C:0.07, G:0.11, T:0.70
Consensus pattern (22 bp):
TTTTTGCTATTTTTGGTTATTA
Found at i:101728 original size:20 final size:20
Alignment explanation
Indices: 101705--101748 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
101695 AAAAAAAAAC
101705 CATAAAT-TTCTTAAAATTTT
1 CATAAATATTC-TAAAATTTT
101725 CAT-AATATTCTAAAATTTT
1 CATAAATATTCTAAAATTTT
101744 C-TAAA
1 CATAAA
101749 AATCTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.05
19 15 0.68
20 6 0.27
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.45
Consensus pattern (20 bp):
CATAAATATTCTAAAATTTT
Found at i:101756 original size:18 final size:19
Alignment explanation
Indices: 101716--101756 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
101706 ATAAATTTCT
* *
101716 TAAAATTTTCATAATATTC
1 TAAAATTTTCATAAAAATC
101735 TAAAATTTTC-TAAAAATC
1 TAAAATTTTCATAAAAATC
101753 TAAA
1 TAAA
101757 TTTCCAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAATTTTCATAAAAATC
Found at i:101926 original size:10 final size:10
Alignment explanation
Indices: 101911--101944 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
101901 TATTTTTGGA
101911 TTTTTAATTT
1 TTTTTAATTT
101921 TTTTTAATTTT
1 TTTTTAA-TTT
101932 TTTTTAATTT
1 TTTTTAATTT
101942 TTT
1 TTT
101945 GCCAAGTGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTAATTT
Found at i:101932 original size:11 final size:11
Alignment explanation
Indices: 101911--101944 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
101901 TATTTTTGGA
101911 TTTTTAA-TTT
1 TTTTTAATTTT
101921 TTTTTAATTTT
1 TTTTTAATTTT
101932 TTTTTAATTTT
1 TTTTTAATTTT
101943 TT
1 TT
101945 GCCAAGTGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 7 0.30
11 16 0.70
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTAATTTT
Found at i:106373 original size:26 final size:26
Alignment explanation
Indices: 106330--106379 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
106320 TAAATAAAAA
* *
106330 AAAATTTTAACCGTTAAATATATATT
1 AAAATTTTAACCGGTAAAAATATATT
106356 AAAATTTTCAA-CGGTAAAAATATA
1 AAAATTTT-AACCGGTAAAAATATA
106380 ATTTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (26 bp):
AAAATTTTAACCGGTAAAAATATATT
Found at i:107085 original size:18 final size:17
Alignment explanation
Indices: 107034--107085 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 17
107024 AACCGACCTA
* *
107034 TTTTAAATT-TATAATA
1 TTTTATATTATATAATT
* *
107050 TTTTATATTATGTTATT
1 TTTTATATTATATAATT
107067 TTTATATATTATATAATT
1 TTT-TATATTATATAATT
107085 T
1 T
107086 ACAATACATA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 8 0.29
17 7 0.25
18 13 0.46
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTATATTATATAATT
Found at i:109902 original size:11 final size:10
Alignment explanation
Indices: 109871--109901 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
109861 CTCCAAATAC
109871 ATAAAAAAAA
1 ATAAAAAAAA
109881 ATAAAAAAAA
1 ATAAAAAAAA
109891 ATAAAAAAAA
1 ATAAAAAAAA
109901 A
1 A
109902 ACCCTAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (10 bp):
ATAAAAAAAA
Found at i:112161 original size:23 final size:23
Alignment explanation
Indices: 112075--112185 Score: 125
Period size: 23 Copynumber: 4.8 Consensus size: 23
112065 TTAATGTTTA
**
112075 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-CGAACATTAAT
112098 CGAACATGTTCACGAACATTAAT
1 CGAACATGTTCACGAACATTAAT
* * *
112121 CAAACATGTTCACAAACATTAAA
1 CGAACATGTTCACGAACATTAAT
*
112144 CGAACATGTTCATGAACATATAAT
1 CGAACATGTTCACGAACAT-TAAT
* *
112168 TGAACACGTTCACGAACA
1 CGAACATGTTCACGAACA
112186 ATGTTAATGA
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
22 3 0.04
23 53 0.72
24 18 0.24
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.27
Consensus pattern (23 bp):
CGAACATGTTCACGAACATTAAT
Found at i:112210 original size:4 final size:4
Alignment explanation
Indices: 112201--112235 Score: 61
Period size: 4 Copynumber: 8.5 Consensus size: 4
112191 AATGAATAAT
112201 AAAC AAAC AAAC AAAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC -AAAC AAAC AAAC AAAC AAAC AA
112236 TAAAAACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:112226 original size:21 final size:21
Alignment explanation
Indices: 112201--112243 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
112191 AATGAATAAT
112201 AAACAAACAAACAA-AACAAAC
1 AAACAAACAAACAATAA-AAAC
112222 AAACAAACAAACAATAAAAAC
1 AAACAAACAAACAATAAAAAC
112243 A
1 A
112244 TACACATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.77, C:0.21, G:0.00, T:0.02
Consensus pattern (21 bp):
AAACAAACAAACAATAAAAAC
Found at i:112344 original size:12 final size:12
Alignment explanation
Indices: 112293--112347 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
112283 TCATTAATAA
*
112293 ATAAACGAAC-T
1 ATAAACGAGCTT
112304 ATAAACGAGCTT
1 ATAAACGAGCTT
* **
112316 AAAAACGAGCCA
1 ATAAACGAGCTT
112328 ATAAACGAGCTT
1 ATAAACGAGCTT
*
112340 TTAAACGA
1 ATAAACGA
112348 ACTTGTTCGT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
11 9 0.26
12 26 0.74
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.18
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:113494 original size:17 final size:18
Alignment explanation
Indices: 113474--113519 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 18
113464 GATTAGGTAG
113474 ATAAAAGATATACAAAA-
1 ATAAAAGATATACAAAAT
113491 ATAAAA-A-ATACAAAAT
1 ATAAAAGATATACAAAAT
*
113507 ACAAAAGCATATA
1 ATAAAAG-ATATA
113520 TTCAAAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 8 0.33
16 6 0.25
17 6 0.25
18 1 0.04
19 3 0.12
ACGTcount: A:0.70, C:0.09, G:0.04, T:0.17
Consensus pattern (18 bp):
ATAAAAGATATACAAAAT
Found at i:113614 original size:28 final size:29
Alignment explanation
Indices: 113580--113647 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 29
113570 AGTCAAAAAT
* **
113580 GTAATTTTTGATTC-TCGAGGGTAAAACA
1 GTAATTTTTGATGCTTCGAGAATAAAACA
* **
113608 GTAATTTTGGATGCTTCGAGAATAAAAGG
1 GTAATTTTTGATGCTTCGAGAATAAAACA
113637 GTAATTTTTGA
1 GTAATTTTTGA
113648 AAGGTTCGAG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
28 12 0.38
29 20 0.62
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.37
Consensus pattern (29 bp):
GTAATTTTTGATGCTTCGAGAATAAAACA
Found at i:113753 original size:58 final size:58
Alignment explanation
Indices: 113657--114010 Score: 260
Period size: 58 Copynumber: 6.0 Consensus size: 58
113647 AAAGGTTCGA
* * * *
113657 GGTCAAAAATGAAATTTTAGAAATTTTA-AGGTAAAAAATGGAATTTT-GAAAAGTTTAGG
1 GGTCAAAAATGGAATTTTGGAAAATTTAGGGGT--AAAATGGAATTTTGGAAAA-TTTAGG
* ** * ** *
113716 GGT-AAAAATGTAATTTTTGGAAAATTTAGGGGTAAAATGTGTTTTTTTTTGAAGGTTT-GA
1 GGTCAAAAATGGAA-TTTTGGAAAATTTAGGGGTAAAATG-G--AATTTTGGAAAATTTAGG
* * *
113776 GGTCAAAAATGGAA-TTTGGGAAGTTT-GAGGGTAAAATGTAATTTTTGGAAAATTTA-G
1 GGTCAAAAATGGAATTTTGGAAAATTTAG-GGGTAAAATGGAA-TTTTGGAAAATTTAGG
* * *
113833 GGTCAAAAATGAAATTTTGGAAAGTTTAGGGGTAAAATGTAATTTTTGGAAAATTTA-G
1 GGTCAAAAATGGAATTTTGGAAAATTTAGGGGTAAAATGGAA-TTTTGGAAAATTTAGG
* * *
113891 GGTTAAAAATGGAATTTTGG-AAATTTCGAGGGTAAAAGTGTAAATTTTGGAAAATTT-GG
1 GGTCAAAAATGGAATTTTGGAAAATTTAG-GGGTAAAA-TG-GAATTTTGGAAAATTTAGG
* * * * * *
113950 GGTCAAATATGGAATTTTGAAAAAGTTTAAGGGTTAAAATATGATTTTTGGACAATTTAGG
1 GGTCAAAAATGGAATTTTGGAAAA-TTT-AGGGGTAAAAT-GGAATTTTGGAAAATTTAGG
114011 TCCTTTAGGG
Statistics
Matches: 239, Mismatches: 35, Indels: 40
0.76 0.11 0.13
Matches are distributed among these distances:
57 29 0.12
58 82 0.34
59 70 0.29
60 26 0.11
61 28 0.12
62 4 0.02
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.36
Consensus pattern (58 bp):
GGTCAAAAATGGAATTTTGGAAAATTTAGGGGTAAAATGGAATTTTGGAAAATTTAGG
Found at i:113764 original size:31 final size:30
Alignment explanation
Indices: 113637--113999 Score: 183
Period size: 29 Copynumber: 12.3 Consensus size: 30
113627 GAATAAAAGG
* * *
113637 GTAATTTTTG-AAAGGTTCGAGGTCAAAAAT
1 GTAATTTTTGAAAAGTTTAGGGGT-AAAAAT
* * * *
113667 GAAATTTTAG-AAATTTTA-AGGTAAAAAAT
1 GTAATTTTTGAAAAGTTTAGGGGT-AAAAAT
*
113696 GGAA-TTTTGAAAAGTTTAGGGGTAAAAAT
1 GTAATTTTTGAAAAGTTTAGGGGTAAAAAT
*
113725 GTAATTTTTGGAAAA-TTTAGGGGTAAAATGT
1 GTAATTTTT-GAAAAGTTTAGGGGTAAAA-AT
** * *
113756 GTTTTTTTTTG-AAGGTTT-GAGGTCAAAAAT
1 G-TAATTTTTGAAAAGTTTAGGGGT-AAAAAT
* **
113786 GGAA--TTTGGGAAGTTT-GAGGGT-AAAAT
1 GTAATTTTTGAAAAGTTTAG-GGGTAAAAAT
113813 GTAATTTTTGGAAAA-TTTA-GGGTCAAAAAT
1 GTAATTTTT-GAAAAGTTTAGGGGT-AAAAAT
* *
113843 G-AAATTTTGGAAAGTTTAGGGGT-AAAAT
1 GTAATTTTTGAAAAGTTTAGGGGTAAAAAT
*
113871 GTAATTTTTGGAAAA-TTTAGGGTTAAAAAT
1 GTAATTTTT-GAAAAGTTTAGGGGTAAAAAT
* * * *
113901 GGAA-TTTTGGAAA-TTTCGAGGGTAAAAGT
1 GTAATTTTTGAAAAGTTTAG-GGGTAAAAAT
* *
113930 GTAAATTTTGGAAAA-TTT-GGGGTCAAATAT
1 GT-AATTTTTGAAAAGTTTAGGGGT-AAAAAT
* * *
113960 GGAA-TTTTGAAAAAGTTTAAGGGTTAAAAT
1 GTAATTTTTG-AAAAGTTTAGGGGTAAAAAT
* *
113990 ATGATTTTTG
1 GTAATTTTTG
114000 GACAATTTAG
Statistics
Matches: 255, Mismatches: 49, Indels: 57
0.71 0.14 0.16
Matches are distributed among these distances:
27 12 0.05
28 36 0.14
29 85 0.33
30 82 0.32
31 34 0.13
32 6 0.02
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.36
Consensus pattern (30 bp):
GTAATTTTTGAAAAGTTTAGGGGTAAAAAT
Found at i:113811 original size:28 final size:28
Alignment explanation
Indices: 113780--114010 Score: 184
Period size: 29 Copynumber: 7.9 Consensus size: 28
113770 GTTTGAGGTC
* *
113780 AAAAATGGAA-TTTGGGAAGTTTGAGGGT
1 AAAAATGGAATTTTGGAAAATTT-AGGGT
*
113808 -AAAATGTAATTTTTGGAAAATTTAGGGT
1 AAAAATGGAA-TTTTGGAAAATTTAGGGT
* *
113836 CAAAAATGAAATTTTGGAAAGTTTAGGGGT
1 -AAAAATGGAATTTTGGAAAATTTA-GGGT
*
113866 -AAAATGTAATTTTTGGAAAATTTAGGGTT
1 AAAAATGGAA-TTTTGGAAAATTTAGGG-T
113895 AAAAATGGAATTTTGG-AAATTTCGAGGGT
1 AAAAATGGAATTTTGGAAAATTT--AGGGT
* * *
113924 AAAAGTGTAAATTTTGGAAAATTTGGGGT
1 AAAAATG-GAATTTTGGAAAATTTAGGGT
* *
113953 CAAATATGGAATTTTGAAAAAGTTTAAGGGTT
1 -AAAAATGGAATTTTGGAAAA-TTT-AGGG-T
* *
113985 AAAATAT-GATTTTTGGACAATTTAGG
1 AAAA-ATGGAATTTTGGAAAATTTAGG
114011 TCCTTTAGGG
Statistics
Matches: 166, Mismatches: 20, Indels: 33
0.76 0.09 0.15
Matches are distributed among these distances:
27 8 0.05
28 22 0.13
29 68 0.41
30 43 0.26
31 22 0.13
32 3 0.02
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.35
Consensus pattern (28 bp):
AAAAATGGAATTTTGGAAAATTTAGGGT
Found at i:115111 original size:19 final size:19
Alignment explanation
Indices: 115087--115177 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 19
115077 TTCTCTTTTT
115087 TTATTAATAATATTATTAA
1 TTATTAATAATATTATTAA
*
115106 TTATT-ATATTTATTATT-A
1 TTATTAATA-ATATTATTAA
* *
115124 TTATTATTAAATAGTTATTATT
1 TTATTAAT-AATA-TTATTA-A
* *
115146 TTTTTAAAGAAATATTATTAA
1 TTATT-AA-TAATATTATTAA
*
115167 TTATTATTAAT
1 TTATTAATAAT
115178 GCTATTTATG
Statistics
Matches: 53, Mismatches: 11, Indels: 16
0.66 0.14 0.20
Matches are distributed among these distances:
18 9 0.17
19 18 0.34
20 7 0.13
21 4 0.08
22 10 0.19
23 5 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:115115 original size:12 final size:13
Alignment explanation
Indices: 115087--115129 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
115077 TTCTCTTTTT
*
115087 TTATTAA-TAATA
1 TTATTAATTATTA
115099 TTATTAATTATTA
1 TTATTAATTATTA
*
115112 -TATTTATTATTA
1 TTATTAATTATTA
115124 TTATTA
1 TTATTA
115130 TTAAATAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATTAATTATTA
Found at i:115881 original size:17 final size:17
Alignment explanation
Indices: 115861--115895 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
115851 ATAATAATTT
115861 TAAATTTAAACTTAAAA
1 TAAATTTAAACTTAAAA
*
115878 TAAATTTAAATTTAAAA
1 TAAATTTAAACTTAAAA
115895 T
1 T
115896 GGGTTTAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:116608 original size:49 final size:48
Alignment explanation
Indices: 116548--116710 Score: 157
Period size: 49 Copynumber: 3.3 Consensus size: 48
116538 AGGTATAAGG
* * * *
116548 TTCGCCATTGCGGCTTAAACCTTTCTCTTCGTGTCTTCGTGGCACTGGA
1 TTCGCCGTTGCGGCTTAAACCTTTCCCTTCATGTCTTCGTGG-AATGGA
* * * *
116597 TTCACCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGAATAAGG-
1 TTCGCCGTTGCGGCTTAAACCTTTCCCTTCATGTCTTCGTGGAAT--GGA
* ** * *
116646 TTCGCCGTTGCGGATTAAACCTTTCCCTTTTTGTCTTCATGGTATTGGA
1 TTCGCCGTTGCGGCTTAAACCTTTCCCTTCATGTCTTCGTGG-AATGGA
*
116695 TTCGCAGTTGCGGCTT
1 TTCGCCGTTGCGGCTT
116711 CATGTCTCTG
Statistics
Matches: 91, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
48 4 0.04
49 83 0.91
50 4 0.04
ACGTcount: A:0.15, C:0.25, G:0.22, T:0.39
Consensus pattern (48 bp):
TTCGCCGTTGCGGCTTAAACCTTTCCCTTCATGTCTTCGTGGAATGGA
Found at i:116681 original size:98 final size:98
Alignment explanation
Indices: 116504--116921 Score: 447
Period size: 98 Copynumber: 4.4 Consensus size: 98
116494 CTAAATTCGT
* * * *
116504 CGTTGCGGCTTAAAAT-TTTTCTTTCATG-CTTCTAAGGTATAAGGTTCGCCATTGCGGCTTAAA
1 CGTTGCGGCTT-AAATCTTTCCCTTCATGTCTT-TGAGGTATAAGGTTCGCCATTGCGACTTAAA
* * *
116567 CCTTTCTCTTCGTGTCTTCGTGGCACTGGATTCAC
64 CCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCAC
* *
116602 CGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGAATAAGGTTCGCCGTTGCGGA-TTAAAC
1 CGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCGCCATTGC-GACTTAAAC
* * * *
116666 CTTTCCCTTTTTGTCTTCATGGTATTGGATTCGC
65 CTTTCCCTTTGTGTCTTCGTGGTACTGGATTCAC
* *
116700 AGTTGCGG-------------CTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACC
1 CGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCGCCATTGCGACTTAAACC
116752 TTTCCCTTTGTGTCTTCGTGGTACTGGATTCAC
66 TTTCCCTTTGTGTCTTCGTGGTACTGGATTCAC
* * * * * * *
116785 CGTTACGGCTTAAATCTTTCCCTTCATGTCTCTAAGGTATAAGTTTCGCCACTACGACTTAAATC
1 CGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCGCCATTGCGACTTAAACC
*
116850 TTTCCCTTTTTGTCTTCGTGGTACTGGATTCAC
66 TTTCCCTTTGTGTCTTCGTGGTACTGGATTCAC
* * * *
116883 CGTTGCAGCTTAAATCTTTCTCATCATG-CTTTGTGGTAT
1 CGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTAT
116922 TGAGACCTAT
Statistics
Matches: 267, Mismatches: 36, Indels: 35
0.79 0.11 0.10
Matches are distributed among these distances:
84 2 0.01
85 73 0.27
97 12 0.04
98 176 0.66
99 4 0.01
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.39
Consensus pattern (98 bp):
CGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCGCCATTGCGACTTAAACC
TTTCCCTTTGTGTCTTCGTGGTACTGGATTCAC
Found at i:116766 original size:85 final size:85
Alignment explanation
Indices: 116623--116782 Score: 250
Period size: 85 Copynumber: 1.9 Consensus size: 85
116613 AAATCTTTCC
* * *
116623 CTTCATGTCTTTGAGGAATAAGGTTCGCCGTTGCGGATTAAACCTTTCCCTTTTTGTCTTCATGG
1 CTTCATGTCTCTGAGGAATAAGGTTCGCCATTGCGGATTAAACCTTTCCCTTTGTGTCTTCATGG
*
116688 TATTGGATTCGCAGTTGCGG
66 TACTGGATTCGCAGTTGCGG
* *
116708 CTTCATGTCTCTGAGGTATAAGGTTCGCCATTGC-GACTTAAACCTTTCCCTTTGTGTCTTCGTG
1 CTTCATGTCTCTGAGGAATAAGGTTCGCCATTGCGGA-TTAAACCTTTCCCTTTGTGTCTTCATG
116772 GTACTGGATTC
65 GTACTGGATTC
116783 ACCGTTACGG
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
84 2 0.03
85 66 0.97
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (85 bp):
CTTCATGTCTCTGAGGAATAAGGTTCGCCATTGCGGATTAAACCTTTCCCTTTGTGTCTTCATGG
TACTGGATTCGCAGTTGCGG
Found at i:116804 original size:49 final size:49
Alignment explanation
Indices: 116744--116902 Score: 162
Period size: 49 Copynumber: 3.2 Consensus size: 49
116734 GCCATTGCGA
* *
116744 CTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCACCGTTACGG
1 CTTAAATCTTTCCCTTTATGTCTTCGTGGTACTGGATTCACCGTTACGG
* * * * ** *
116793 CTTAAATCTTTCCCTTCATGTC-TC-TAAGGTA-TAAGTTTCGCCACTACGA
1 CTTAAATCTTTCCCTTTATGTCTTCGT--GGTACT-GGATTCACCGTTACGG
* * *
116842 CTTAAATCTTTCCCTTTTTGTCTTCGTGGTACTGGATTCACCGTTGCAG
1 CTTAAATCTTTCCCTTTATGTCTTCGTGGTACTGGATTCACCGTTACGG
116891 CTTAAATCTTTC
1 CTTAAATCTTTC
116903 TCATCATGCT
Statistics
Matches: 85, Mismatches: 19, Indels: 12
0.73 0.16 0.10
Matches are distributed among these distances:
47 1 0.01
48 3 0.04
49 77 0.91
50 3 0.04
51 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.16, T:0.40
Consensus pattern (49 bp):
CTTAAATCTTTCCCTTTATGTCTTCGTGGTACTGGATTCACCGTTACGG
Found at i:116855 original size:183 final size:183
Alignment explanation
Indices: 116538--116880 Score: 535
Period size: 183 Copynumber: 1.9 Consensus size: 183
116528 CATGCTTCTA
* *
116538 AGGTATAAGGTTCGCCATTGCGGCTTAAACCTTTCTCTTCGTGTCTTCGTGGCACTGGATTCACC
1 AGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCGTGTCTTCGTGGCACTGGATTCACC
* * * ** *
116603 GTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGAATAAGGTTCGCCGTTGCGGATTAAACCT
66 GTTACGGCTTAAATCTTTCCCTTCATGTCTCTAAGGAATAAGGTTCGCCACTACGGATTAAACCT
*
116668 TTCCCTTTTTGTCTTCATGGTATTGGATTCGCAGTTGCGGCTTCATGTCTCTG
131 TTCCCTTTTTGTCTTCATGGTACTGGATTCGCAGTTGCGGCTTCATGTCTCTG
* *
116721 AGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCACC
1 AGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCGTGTCTTCGTGGCACTGGATTCACC
* * *
116786 GTTACGGCTTAAATCTTTCCCTTCATGTCTCTAAGGTATAAGTTTCGCCACTAC-GACTTAAATC
66 GTTACGGCTTAAATCTTTCCCTTCATGTCTCTAAGGAATAAGGTTCGCCACTACGGA-TTAAACC
*
116850 TTTCCCTTTTTGTCTTCGTGGTACTGGATTC
130 TTTCCCTTTTTGTCTTCATGGTACTGGATTC
116881 ACCGTTGCAG
Statistics
Matches: 144, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
182 2 0.01
183 142 0.99
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (183 bp):
AGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCGTGTCTTCGTGGCACTGGATTCACC
GTTACGGCTTAAATCTTTCCCTTCATGTCTCTAAGGAATAAGGTTCGCCACTACGGATTAAACCT
TTCCCTTTTTGTCTTCATGGTACTGGATTCGCAGTTGCGGCTTCATGTCTCTG
Found at i:117358 original size:18 final size:18
Alignment explanation
Indices: 117332--117367 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
117322 AAAATTGATG
*
117332 AATATTTACAAGGAACAA
1 AATAATTACAAGGAACAA
117350 AATAATTACAAGGAACAA
1 AATAATTACAAGGAACAA
117368 TATTAGATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.19
Consensus pattern (18 bp):
AATAATTACAAGGAACAA
Done.