Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012594.1 Kokia drynarioides strain JFW-HI SEQ_127603, 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: 29314
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Warning! 77 characters in sequence are not A, C, G, or T
Found at i:570 original size:9 final size:10
Alignment explanation
Indices: 530--562 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
520 GAAACGTTTC
530 AATAACTATT
1 AATAACTATT
540 AATAA-TATT
1 AATAACTATT
*
549 AATAACTGTT
1 AATAACTATT
559 AATA
1 AATA
563 TTAATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (10 bp):
AATAACTATT
Found at i:570 original size:19 final size:19
Alignment explanation
Indices: 530--580 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
520 GAAACGTTTC
* *
530 AATAACTATTAATAATATT
1 AATAACTGTTAATAATAAT
*
549 AATAACTGTTAATATTAAT
1 AATAACTGTTAATAATAAT
* *
568 AATTATTGTTAAT
1 AATAACTGTTAAT
581 GACCTATTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (19 bp):
AATAACTGTTAATAATAAT
Found at i:1854 original size:59 final size:59
Alignment explanation
Indices: 1722--2485 Score: 984
Period size: 59 Copynumber: 12.9 Consensus size: 59
1712 CGGAGGTCCT
* *
1722 TAAACTTTCCAAAAATTACCATTTTACCCTCGAACTTTCAAAAAATTCCATTTTTGACCC
1 TAAACTTTCCAAAAATTACCATTTTACCCTCGAAC-TTCCAAAAATCCCATTTTTGACCC
* **
1782 CAAACTTTCCAAAAATTACCATTTTACCCTTTAACTTCCAAAAATCCCATTTTTGACCC
1 TAAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCC
*
1841 TAAACTTTCC-AAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCC
1 TAAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCC
* * *
1899 TAAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAACATCTCATTTTTGACCT
1 TAAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCC
* * * *
1958 TAAACTTTCTAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTAACCC
1 TAAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCC
* ** * * * *
2017 CAAACCATCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCAATTTTTTACCC
1 TAAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCC
** * *
2076 CGAGCTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCT
1 TAAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCC
2135 TAAACTTTCCAAAAATTACCATTTTACCCTCGAAC-TCCAAAAAATCCCATTTTTGA-CC
1 TAAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCC-AAAAATCCCATTTTTGACCC
* * * *
2193 TCAAACTTTCCAAAAAATACCATTTTACCCCCTGAACTTCCACAAATCCTATTTTTGACCTC
1 T-AAACTTTCCAAAAATTACCATTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGACC-C
* * * * *
2255 GAAACCTT-CTAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCT
1 TAAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCC
* * * **
2313 TAAACTTTCCAAAAAATACCATTTTACCCCTTGAACTTCCATAAATCCTGTTTTTGACCC
1 TAAACTTTCCAAAAATTACCATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTGACCC
** * * * * *
2373 CGAACCTT-CTAAAATTATCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGA-TC
1 TAAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCC
* * *
2430 TGAACCTTT-CGAAAATTATCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
1 T-AAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
2486 TTTTGAACCT
Statistics
Matches: 618, Mismatches: 76, Indels: 22
0.86 0.11 0.03
Matches are distributed among these distances:
57 1 0.00
58 140 0.23
59 363 0.59
60 103 0.17
61 10 0.02
62 1 0.00
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (59 bp):
TAAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCC
Found at i:3807 original size:45 final size:45
Alignment explanation
Indices: 3745--3832 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
3735 GTGAAGGAGA
3745 TTTTTTTAAGATGCCCTTTACGGGTTTTCATCTTGA-CTTTTCCT
1 TTTTTTTAAGATGCCCTTTACGGGTTTTCATCTTGATCTTTTCCT
*
3789 TTTTTTTAAAGATGCCCTTTGCGGGTTTTCATCTTGATCTTTTC
1 TTTTTTT-AAGATGCCCTTTACGGGTTTTCATCTTGATCTTTTC
3833 TTTCTTTCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 7 0.17
45 28 0.68
46 6 0.15
ACGTcount: A:0.14, C:0.19, G:0.15, T:0.52
Consensus pattern (45 bp):
TTTTTTTAAGATGCCCTTTACGGGTTTTCATCTTGATCTTTTCCT
Found at i:10577 original size:17 final size:17
Alignment explanation
Indices: 10535--10581 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
10525 AAATCAATTT
*
10535 TAATATAAAT-ATTTAA
1 TAATATAAATAATTCAA
10551 TACGAT-TAAATAATTCAA
1 TA--ATATAAATAATTCAA
10569 TAATATAAATAAT
1 TAATATAAATAAT
10582 ACAAAATGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 4 0.15
17 13 0.50
18 9 0.35
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (17 bp):
TAATATAAATAATTCAA
Found at i:10914 original size:21 final size:20
Alignment explanation
Indices: 10877--10915 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
10867 ATGAGAGGGG
* *
10877 AGTAAAAGTTTTGGGGGTAA
1 AGTAAAAATTTTAGGGGTAA
10897 AGTAAAAATGTTTAGGGGT
1 AGTAAAAAT-TTTAGGGGT
10916 TTAGGGTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (20 bp):
AGTAAAAATTTTAGGGGTAA
Found at i:11527 original size:2 final size:2
Alignment explanation
Indices: 11520--11552 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
11510 AAATCAAGAA
*
11520 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11553 GATTTTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:17057 original size:96 final size:96
Alignment explanation
Indices: 16873--17064 Score: 239
Period size: 96 Copynumber: 2.0 Consensus size: 96
16863 TCTTTGGAAA
* ** *
16873 AAGGATATTCGATTATCTTGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCGCAGTATTTCA
1 AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGAACAATATTTCA
*
16938 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAGAAAACATTGCCTCGATT
* *
16969 AAGGGTATTCGATTAT-TTCGATTTGAGGAAAAATTGCACCTAGTAAGTTAAGGAACAA-ATTTT
1 AAGGATATTCGATTATCTT-GATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGAACAATA-TTT
* *
17032 CGGAACTCGAA-ATAA-AAAGATATTGCCTCGATT
64 CAGAA-TCGAAGATAAGAAA-ACATTGCCTCGATT
17065 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
95 5 0.06
96 73 0.88
97 5 0.06
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGAACAATATTTCA
GAATCGAAGATAAGAAAACATTGCCTCGATT
Found at i:17455 original size:59 final size:59
Alignment explanation
Indices: 17341--17959 Score: 700
Period size: 59 Copynumber: 10.5 Consensus size: 59
17331 ATTCAAAACA
* * * * *
17341 TTCGAGGGTAAAAATGGCAATTTTGAG-AGTTTCGAGGTCGAAAAT-GGAGTCTTTGGACA-
1 TTCGAGGGT-AAAATGGTAATTTTTAGAAGTTTCGGGGTCAAAAATGGGA-TTTTTGGA-AG
* * * *
17400 TCCGAGAGTAAAATAGTAATCTTT-GAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTAG-AAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * * * *
17459 TTCTAGGGTAAAATGGTATTTTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTGGGAG
1 TTCGAGGGTAAAATGGTAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* *** *
17518 TT-TAGGGGTAAAATGGTAATTTTTAGAAGTTTTAAGGTCAAAAATGGGATTTTTGGGAG
1 TTCGA-GGGTAAAATGGTAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * *
17577 TTCGTGAGTAAAATGGTAATTTTTAGAAGTTTCGGGGTCAAAAAAGGGATTTTTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * *
17636 CTCAAGGGTAAAATGGTAATTTTTAGAAGTTTCGGGGT-TAAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * * * * ***
17694 TTTGGGGGTAAATTGGTAATTTTTAGAAGTTTCGAGGTTAAAAATGGGATTTTCAAAAG
1 TTCGAGGGTAAAATGGTAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * * *
17753 TTCG-GGAGTAAAATGGTAATTTTTAGAAGGTTCGAGGTTAAAAATGGGATTTTTAGAAG
1 TTCGAGG-GTAAAATGGTAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* *
17812 TTCGAGGGTAAAAAGGTAATTTTTAGAAGGTTT-GGGGT-TAAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTAGAA-GTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * * *
17870 TTTGGGGGTAAAATGGTAGTTTTTAGAAGATTCGGGGTC-AAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* *
17928 TTCGGGGGTAAAATGGTAATTTTTGGAAGTTT
1 TTCGAGGGTAAAATGGTAATTTTTAGAAGTTT
17960 AGGGACCTCC
Statistics
Matches: 482, Mismatches: 65, Indels: 27
0.84 0.11 0.05
Matches are distributed among these distances:
57 4 0.01
58 160 0.33
59 309 0.64
60 9 0.02
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (59 bp):
TTCGAGGGTAAAATGGTAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
Found at i:17482 original size:29 final size:28
Alignment explanation
Indices: 17440--17958 Score: 324
Period size: 29 Copynumber: 17.8 Consensus size: 28
17430 TTCGGGGTCA
* *
17440 AAAATGGGATTTTTGGAAGTTCTAGGGT
1 AAAATGGGATTTTTAGAAGTTCTGGGGT
* *
17468 AAAATGGTATTTTTTAGAAGTTTTGGGGTT
1 AAAATGGGA-TTTTTAGAAGTTCTGGGG-T
* *
17498 AAAAATGGGATTTTTGGGAGTT-TAGGGGT
1 -AAAATGGGATTTTTAGAAGTTCT-GGGGT
* * **
17527 AAAATGGTAATTTTTAGAAGTTTTAAGGT
1 AAAATGG-GATTTTTAGAAGTTCTGGGGT
* * *
17556 CAAAAATGGGATTTTTGGGAGTTC-GTGAGT
1 --AAAATGGGATTTTTAGAAGTTCTG-GGGT
*
17586 AAAATGGTAATTTTTAGAAGTT-TCGGGGT
1 AAAATGG-GATTTTTAGAAGTTCT-GGGGT
* * * **
17615 CAAAAAAGGGATTTTTGGAAGCTCAAGGGT
1 --AAAATGGGATTTTTAGAAGTTCTGGGGT
*
17645 AAAATGGTAATTTTTAGAAGTT-TCGGGGTT
1 AAAATGG-GATTTTTAGAAGTTCT-GGGG-T
*
17675 AAAATGGGATTTTTGGAAGTT-TGGGGGT
1 AAAATGGGATTTTTAGAAGTTCT-GGGGT
* * *
17703 AAATTGGTAATTTTTAGAAGTT-TCGAGGTT
1 AAAATGG-GATTTTTAGAAGTTCT-G-GGGT
* *
17733 AAAAATGGGATTTTCAAAAGTTC-GGGAGT
1 -AAAATGGGATTTTTAGAAGTTCTGGG-GT
* *
17762 AAAATGGTAATTTTTAGAAGGTTC-GAGGTT
1 AAAATGG-GATTTTTAGAA-GTTCTG-GGGT
17792 AAAAATGGGATTTTTAGAAGTTC-GAGGGT
1 -AAAATGGGATTTTTAGAAGTTCTG-GGGT
* *
17821 AAAAAGGTAATTTTTAGAAGGTT-TGGGGTT
1 AAAATGG-GATTTTTAGAA-GTTCTGGGG-T
*
17851 AAAATGGGATTTTTGGAAGTT-TGGGGGT
1 AAAATGGGATTTTTAGAAGTTCT-GGGGT
*
17879 AAAATGGTAGTTTTTAGAAGATTC-GGGGT
1 AAAATGGGA-TTTTTAGAAG-TTCTGGGGT
* *
17908 CAAAATGGGATTTTTGGAAGTTCGGGGGT
1 -AAAATGGGATTTTTAGAAGTTCTGGGGT
* *
17937 AAAATGGTAATTTTTGGAAGTT
1 AAAATGG-GATTTTTAGAAGTT
17959 TAGGGACCTC
Statistics
Matches: 389, Mismatches: 64, Indels: 75
0.74 0.12 0.14
Matches are distributed among these distances:
28 73 0.19
29 176 0.45
30 104 0.27
31 36 0.09
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (28 bp):
AAAATGGGATTTTTAGAAGTTCTGGGGT
Found at i:17769 original size:176 final size:175
Alignment explanation
Indices: 17346--17959 Score: 797
Period size: 176 Copynumber: 3.5 Consensus size: 175
17336 AAACATTCGA
* * ** * * *
17346 GGGTAAAAATGGCAATTTTGAG-AGTTTCGAGGTCGAAAAT-GGAGTCTTTGGACA-TCCGAGAG
1 GGGT-AAAATGGTAATTTTTAGAAGTTTCGAGGTTAAAAATGGGA-TTTTTGGA-AGTTCGGGAG
* * *
17408 TAAAATAGTAATCTTT-GAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCTAGGGTAAAA
63 TAAAATGGTAATTTTTAG-AAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAAGGGTAAAA
* * *
17472 TGGTATTTTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTGGGAGTTTAG
127 TGGTAATTTTTAGAAG-TTTGGGGTT-AAAATGGGATTTTTGGAAGTTTGG
** * * *
17523 GGGTAAAATGGTAATTTTTAGAAGTTTTAAGGTCAAAAATGGGATTTTTGGGAGTTCGTGAGTAA
1 GGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGGGAGTAA
* *
17588 AATGGTAATTTTTAGAAGTTTCGGGGTCAAAAAAGGGATTTTTGGAAGCTCAAGGGTAAAATGGT
66 AATGGTAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAAGGGTAAAATGGT
17653 AATTTTTAGAAGTTTCGGGGTTAAAATGGGATTTTTGGAAGTTTGG
131 AATTTTTAGAAGTTT-GGGGTTAAAATGGGATTTTTGGAAGTTTGG
* ***
17699 GGGTAAATTGGTAATTTTTAGAAGTTTCGAGGTTAAAAATGGGATTTTCAAAAGTTCGGGAGTAA
1 GGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGGGAGTAA
* * * * * *
17764 AATGGTAATTTTTAGAAGGTTCGAGGTTAAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAAGGT
66 AATGGTAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAAGGGTAAAATGGT
17829 AATTTTTAGAAGGTTTGGGGTTAAAATGGGATTTTTGGAAGTTTGG
131 AATTTTTAGAA-GTTTGGGGTTAAAATGGGATTTTTGGAAGTTTGG
* * * * *
17875 GGGTAAAATGGTAGTTTTTAGAAGATTCG-GGGTCAAAATGGGATTTTTGGAAGTTCGGGGGTAA
1 GGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGGGAGTAA
*
17939 AATGGTAATTTTTGGAAGTTT
66 AATGGTAATTTTTAGAAGTTT
17960 AGGGACCTCC
Statistics
Matches: 386, Mismatches: 45, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
175 48 0.12
176 221 0.57
177 113 0.29
178 4 0.01
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (175 bp):
GGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGGGAGTAA
AATGGTAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAAGGGTAAAATGGT
AATTTTTAGAAGTTTGGGGTTAAAATGGGATTTTTGGAAGTTTGG
Found at i:19708 original size:23 final size:22
Alignment explanation
Indices: 19681--19748 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
19671 TTTTGGACTT
*
19681 TTTAATTTTGAAATTAAATTTAA
1 TTTAAATTT-AAATTAAATTTAA
19704 TTTAAATTTAAGATT-AATTTAAA
1 TTTAAATTTAA-ATTAAATTT-AA
* *
19727 ATTAAATTTAAATCAAATTTAA
1 TTTAAATTTAAATTAAATTTAA
19749 AATAAATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 11 0.28
23 28 0.72
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (22 bp):
TTTAAATTTAAATTAAATTTAA
Found at i:19710 original size:11 final size:11
Alignment explanation
Indices: 19691--19755 Score: 78
Period size: 11 Copynumber: 5.8 Consensus size: 11
19681 TTTAATTTTG
19691 AAATTAAATTT
1 AAATTAAATTT
*
19702 AATTTAAATTT
1 AAATTAAATTT
19713 AAGATT-AATTT
1 AA-ATTAAATTT
19724 AAAATTAAATTT
1 -AAATTAAATTT
*
19736 AAATCAAATTT
1 AAATTAAATTT
*
19747 AAAATAAAT
1 AAATTAAAT
19756 AAAAAAGGGC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
11 37 0.80
12 9 0.20
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:19737 original size:17 final size:17
Alignment explanation
Indices: 19681--19737 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
19671 TTTTGGACTT
*
19681 TTTAATTTTGAAATTAAA
1 TTTAA-TTTAAAATTAAA
*
19699 TTTAATTTAAATTTAAGA
1 TTTAATTTAAAATTAA-A
19717 -TTAATTTAAAATTAAA
1 TTTAATTTAAAATTAAA
19733 TTTAA
1 TTTAA
19738 ATCAAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 1 0.03
17 27 0.79
18 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (17 bp):
TTTAATTTAAAATTAAA
Found at i:19748 original size:17 final size:17
Alignment explanation
Indices: 19681--19749 Score: 70
Period size: 17 Copynumber: 4.0 Consensus size: 17
19671 TTTTGGACTT
19681 TTTAATTTTGAAA-TTAAA
1 TTTAA-TTT-AAATTTAAA
19699 TTTAATTTAAATTTAAGA
1 TTTAATTTAAATTTAA-A
*
19717 -TTAATTTAAAATTAAA
1 TTTAATTTAAATTTAAA
* *
19733 TTTAAATCAAATTTAAA
1 TTTAATTTAAATTTAAA
19750 ATAAATAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
16 4 0.09
17 34 0.77
18 6 0.14
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (17 bp):
TTTAATTTAAATTTAAA
Found at i:19749 original size:23 final size:22
Alignment explanation
Indices: 19695--19755 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
19685 ATTTTGAAAT
*
19695 TAAATTT-AATTTAAATTTAAGA
1 TAAATTTAAAATTAAATTTAA-A
*
19717 TTAATTTAAAATTAAATTTAAA
1 TAAATTTAAAATTAAATTTAAA
19739 TCAAATTTAAAA-TAAAT
1 T-AAATTTAAAATTAAAT
19756 AAAAAAGGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAATTTAAAATTAAATTTAAA
Found at i:20447 original size:194 final size:194
Alignment explanation
Indices: 19983--20623 Score: 805
Period size: 194 Copynumber: 3.2 Consensus size: 194
19973 GGTTTTACCG
* * *
19983 ATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGATCACGTCGCTATTTGTTTCAATTCGCTC
1 ATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACATCGCTATTTGTTTCAATTCGCTC
* * *
20048 CTCTGTATCTTG-TCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGAAAGTTAACCT
66 CTCTGTA-CCTGATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCT
* * * *
20112 TTTATTGCTTCGACCTGCTTTTCAGTGTCTCATCAGGAAGCCGGGGTTCGAAGATTTCGCTCGTT
130 TTTATTGCTT-----T-C---TCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTTGCTTGTT
20177 TTGAGCCTC
186 TTGAGCCTC
*
20186 -----G--TTCTTCTCAGTGTCTCATCAGGAAGATGATCACATCGCTGTTTGTTTCAATTCGCTC
1 ATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACATCGCTATTTGTTTCAATTCGCTC
* *
20244 CTTTGTACCTGATCAGGAAGACAAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTT
66 CTCTGTACCTGATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTT
*
20309 TTATTG-TTTCTCAGTGTCTCATTAGGAAGCTGGGGTTTGAAGATTTTGCTTGTTTTGAGCCTC
131 TTATTGCTTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTTGCTTGTTTTGAGCCTC
* * * *
20372 ATTTAGGTCTTCTTCTTAGTGTCTCATCAGGAGGATGATCACATCGCCATTTGTTTCAATTTGCT
1 ATTT-GGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACATCGCTATTTGTTTCAATTCGCT
* *
20437 CCTCTGTACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCT
65 CCTCTGTACCTGATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCT
* * *
20502 TTTATTGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTAGGGTTTGAAGATTTTGCTTGTT
130 TTTA----TT-G--CT--TTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTTGCTTGTT
20567 TTGAGCCTC
186 TTGAGCCTC
* *
20576 GTTTGGATCTTCTTCTCAGTGTCTCATCAGGAAGATAATCACATCGCT
1 ATTTGG-TCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACATCGCT
20624 GTTTTGATAA
Statistics
Matches: 386, Mismatches: 32, Indels: 39
0.84 0.07 0.09
Matches are distributed among these distances:
186 48 0.12
189 1 0.00
190 1 0.00
192 1 0.00
194 116 0.30
195 5 0.01
196 115 0.30
198 3 0.01
199 1 0.00
202 1 0.00
203 2 0.01
204 92 0.24
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.38
Consensus pattern (194 bp):
ATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACATCGCTATTTGTTTCAATTCGCTC
CTCTGTACCTGATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTT
TTATTGCTTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTTGCTTGTTTTGAGCCTC
Done.