Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010815.1 Kokia drynarioides strain JFW-HI SEQ_125782, 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: 184722
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:6672 original size:17 final size:16
Alignment explanation
Indices: 6629--6670 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
6619 GAAAAGAAAA
6629 CTTAAATTTTCTATCC
1 CTTAAATTTTCTATCC
*
6645 CTTAACTTTTCTATCC
1 CTTAAATTTTCTATCC
*
6661 CTTTAATTTT
1 CTTAAATTTT
6671 TCATCTTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (16 bp):
CTTAAATTTTCTATCC
Found at i:9058 original size:69 final size:69
Alignment explanation
Indices: 8947--9089 Score: 286
Period size: 69 Copynumber: 2.1 Consensus size: 69
8937 TTACCCATGT
8947 CTTTAGAGGGTCATATCTAGAGGTGCTCATGGGCCAGGTCAGACTGAGCTTATGCATAATATTAA
1 CTTTAGAGGGTCATATCTAGAGGTGCTCATGGGCCAGGTCAGACTGAGCTTATGCATAATATTAA
9012 CATA
66 CATA
9016 CTTTAGAGGGTCATATCTAGAGGTGCTCATGGGCCAGGTCAGACTGAGCTTATGCATAATATTAA
1 CTTTAGAGGGTCATATCTAGAGGTGCTCATGGGCCAGGTCAGACTGAGCTTATGCATAATATTAA
9081 CATA
66 CATA
9085 CTTTA
1 CTTTA
9090 TGCTTGCCCA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 74 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (69 bp):
CTTTAGAGGGTCATATCTAGAGGTGCTCATGGGCCAGGTCAGACTGAGCTTATGCATAATATTAA
CATA
Found at i:9144 original size:10 final size:9
Alignment explanation
Indices: 9126--9158 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
9116 AGGCTTAAAA
9126 TATTTATAT
1 TATTTATAT
9135 TATATTATAT
1 TAT-TTATAT
9145 TATTT-TAT
1 TATTTATAT
9153 TATTTA
1 TATTTA
9159 ATAATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.36
9 5 0.23
10 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTTATAT
Found at i:9165 original size:16 final size:18
Alignment explanation
Indices: 9127--9168 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
9117 GGCTTAAAAT
*
9127 ATTTATATTATATTATATT
1 ATTT-TATTATATTATATA
9146 ATTTTATTAT-TTA-ATA
1 ATTTTATTATATTATATA
9162 ATTTTAT
1 ATTTTAT
9169 ACATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 9 0.41
17 3 0.14
18 6 0.27
19 4 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTATTATATTATATA
Found at i:19564 original size:23 final size:22
Alignment explanation
Indices: 19514--19565 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
19504 AGGGTTTTAA
*
19514 AGTTTTTTTAAAAGTCAGATAT
1 AGTTTTTTTAAAAATCAGATAT
*
19536 -GATTTTTTTAAAAAATCAGATTT
1 AG-TTTTTTT-AAAAATCAGATAT
19559 AGTTTTT
1 AGTTTTT
19566 CGTTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 1 0.04
22 7 0.28
23 16 0.64
24 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.50
Consensus pattern (22 bp):
AGTTTTTTTAAAAATCAGATAT
Found at i:19748 original size:24 final size:25
Alignment explanation
Indices: 19719--19767 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
19709 ATTTCATATT
19719 TTTGAAAC-AAAAAAATAGAAAATA
1 TTTGAAACAAAAAAAATAGAAAATA
19743 TTTGAAACAAAAAAAATAGAAAATA
1 TTTGAAACAAAAAAAATAGAAAATA
19768 AGTAAATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.20
Consensus pattern (25 bp):
TTTGAAACAAAAAAAATAGAAAATA
Found at i:20630 original size:39 final size:39
Alignment explanation
Indices: 20588--20920 Score: 373
Period size: 39 Copynumber: 8.4 Consensus size: 39
20578 TTGATTTTAA
*
20588 GGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCA
1 GGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCG
* *
20627 GGGTAAGAGATTGGATGGCTTCAATCTGCCTCATCATCG
1 GGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCG
*
20666 GGGTAAGAGATTGGATAATGTCTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGG---ATGGCTTCAATCTGCCCCATGATCG
* * * * *
20708 GGGTAAGAGATCGGGTGGCTGT-GATCTGCCCTATGATCT
1 GGGTAAGAGATTGGATGGCT-TCAATCTGCCCCATGATCG
* *
20747 GGGTAAGAGATCGGATGGTTTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGG-CTTCAATCTGCCCCATGATCG
* * *
20787 GGGTAAGAGATTGGATGGC-TCGATCTGCCCTACGATCG
1 GGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCG
*** * * * *
20825 GGGTAAGAGATCAAATGGTTTTCAATCTACCCCATAATCA
1 GGGTAAGAGATTGGATGG-CTTCAATCTGCCCCATGATCG
* * *
20865 GGGTAAGAGATTGGATGGCTGCGATCTGCCCTATGATCG
1 GGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCG
*
20904 GGGTAAGAGATCGGATG
1 GGGTAAGAGATTGGATG
20921 ACTGATGTAG
Statistics
Matches: 243, Mismatches: 43, Indels: 16
0.80 0.14 0.05
Matches are distributed among these distances:
38 31 0.13
39 116 0.48
40 61 0.25
42 35 0.14
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.26
Consensus pattern (39 bp):
GGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCG
Found at i:20806 original size:79 final size:78
Alignment explanation
Indices: 20588--20920 Score: 436
Period size: 78 Copynumber: 4.2 Consensus size: 78
20578 TTGATTTTAA
* *
20588 GGGTAAGAGATTGGATGG-CTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGGCTTCAAT
1 GGGTAAGAGATCGGATGGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGGC-TCGAT
*
20652 CTG-CCTCATCATCG
65 CTGCCCT-ATGATCG
* * * * * *
20666 GGGTAAGAGATTGGATAATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATCGGGTGGCTGTG
1 GGGTAAGAGATCGGAT--GGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGGCT-CG
*
20731 ATCTGCCCTATGATCT
63 ATCTGCCCTATGATCG
* *
20747 GGGTAAGAGATCGGATGGTTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTCGATC
1 GGGTAAGAGATCGGATGGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGGCTCGATC
*
20812 TGCCCTACGATCG
66 TGCCCTATGATCG
** * * *
20825 GGGTAAGAGATCAAATGGTTTTCAATCTACCCCATAATCAGGGTAAGAGATTGGATGGCTGCGAT
1 GGGTAAGAGATCGGATGGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGGCT-CGAT
20890 CTGCCCTATGATCG
65 CTGCCCTATGATCG
20904 GGGTAAGAGATCGGATG
1 GGGTAAGAGATCGGATG
20921 ACTGATGTAG
Statistics
Matches: 225, Mismatches: 24, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
78 86 0.38
79 72 0.32
80 2 0.01
81 62 0.28
82 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.26
Consensus pattern (78 bp):
GGGTAAGAGATCGGATGGTCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGGCTCGATC
TGCCCTATGATCG
Found at i:21474 original size:48 final size:47
Alignment explanation
Indices: 21381--21595 Score: 178
Period size: 48 Copynumber: 4.4 Consensus size: 47
21371 CGGATTTGTT
* * * * *
21381 GTTGCAGCCTTAATCCTTCCCATCACATTTCTAAGGTATCGGGTTCACC
1 GTTGCGGCCTTAA-CCTTTCCATCAAATTTC-ATGGTACCGGGTTCACC
* *
21430 GTTGTGGCCTTAACCTTTCCTTCAAATATTCATGGTACCGGGTTCACC
1 GTTGCGGCCTTAACCTTTCCATCAAAT-TTCATGGTACCGGGTTCACC
** ** * *
21478 GTTGCGGCCTCGACCTTTCCAATCGCATTTCATGGTACCGGATTCACT
1 GTTGCGGCCTTAACCTTTCC-ATCAAATTTCATGGTACCGGGTTCACC
* * * * *
21526 GTTGCGGGCTTAATCCTTCCCATCATATCTTTTAAGGTACCGGGTTCACC
1 GTTGCGGCCTTAA-CCTTTCCATCA-A-ATTTCATGGTACCGGGTTCACC
* * *
21576 GTTACGACCTCAACCTTTCC
1 GTTGCGGCCTTAACCTTTCC
21596 CTTCATATCT
Statistics
Matches: 130, Mismatches: 31, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
48 74 0.57
49 30 0.23
50 26 0.20
ACGTcount: A:0.19, C:0.30, G:0.18, T:0.33
Consensus pattern (47 bp):
GTTGCGGCCTTAACCTTTCCATCAAATTTCATGGTACCGGGTTCACC
Found at i:21596 original size:50 final size:50
Alignment explanation
Indices: 21198--21605 Score: 199
Period size: 50 Copynumber: 8.3 Consensus size: 50
21188 GCCTCGATCC
* * * * ** *
21198 TTCCCATCATATC-TTCATGGTACCGAGTTTTCCGTTGCGGCCTCAACCT
1 TTCCCATCACATCTTTTAAGGTACCGGGTTCACCGTTGCGACCTCAACCT
* * ** * * * *
21247 TTCCCATAACATCTTCTAAGGTATTGGGTTCGCTGTTGCAACCTCAACAT
1 TTCCCATCACATCTTTTAAGGTACCGGGTTCACCGTTGCGACCTCAACCT
* * * *** *
21297 TTCCCTTCACATCTTCTAAGATACCGGGTTTGTCGTCGCGACCTCAACCT
1 TTCCCATCACATCTTTTAAGGTACCGGGTTCACCGTTGCGACCTCAACCT
* * * **** *
21347 TTCCC-T-ACATTTTTTTCATGGTACCGGATTTGTTGTTGC-AGCCTTAATCC-
1 TTCCCATCACA-TCTTTT-AAGGTACCGGGTTCACCGTTGCGA-CCTCAA-CCT
* * * * *
21397 TTCCCATCACAT-TTCTAAGGTATCGGGTTCACCGTTGTGGCCTTAACCT
1 TTCCCATCACATCTTTTAAGGTACCGGGTTCACCGTTGCGACCTCAACCT
* * * * * * *
21446 TT-CCTTCAAAT-ATTCATGGTACCGGGTTCACCGTTGCGGCCTCGACCT
1 TTCCCATCACATCTTTTAAGGTACCGGGTTCACCGTTGCGACCTCAACCT
* * * * * * ** *
21494 TTCCAATCGCA--TTTCATGGTACCGGATTCACTGTTGCGGGCTTAATCC-
1 TTCCCATCACATCTTTTAAGGTACCGGGTTCACCGTTGCGACCTCAA-CCT
* *
21542 TTCCCATCATATCTTTTAAGGTACCGGGTTCACCGTTACGACCTCAACCT
1 TTCCCATCACATCTTTTAAGGTACCGGGTTCACCGTTGCGACCTCAACCT
* *
21592 TTCCCTTCATATCT
1 TTCCCATCACATCT
21606 CTATGTTTCC
Statistics
Matches: 270, Mismatches: 75, Indels: 27
0.73 0.20 0.07
Matches are distributed among these distances:
48 79 0.29
49 47 0.17
50 137 0.51
51 4 0.01
52 3 0.01
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.35
Consensus pattern (50 bp):
TTCCCATCACATCTTTTAAGGTACCGGGTTCACCGTTGCGACCTCAACCT
Found at i:22603 original size:26 final size:26
Alignment explanation
Indices: 22553--22603 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
22543 AGACCTCACA
* **
22553 TTTTTCTCTTTTTTAATTTTTCTTTC
1 TTTTTCACTTTTTTAATTTCCCTTTC
*
22579 TTTTTCACTTTTTTTATTTCCCTTT
1 TTTTTCACTTTTTTAATTTCCCTTT
22604 TTTATTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTTCACTTTTTTAATTTCCCTTTC
Found at i:27652 original size:3 final size:3
Alignment explanation
Indices: 27644--27675 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
27634 TATAACGTGT
27644 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
27676 GATGAGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:30824 original size:25 final size:23
Alignment explanation
Indices: 30746--30896 Score: 130
Period size: 23 Copynumber: 6.5 Consensus size: 23
30736 TATACGGAAC
* * *
30746 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
*
30768 -AACAGAGAGCACATA-AGTGCT
1 AAACAGAGAGCACACACAGTGCT
* *
30789 GGGCAACAGAGAGCACACACAGTACT
1 ---AAACAGAGAGCACACACAGTGCT
*
30815 AAACAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
30838 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
* *
30861 AATAACGGAGAGCACGAGAC-GTGCT
1 -A-AACAGAGAGCAC-ACACAGTGCT
30886 AAACAGAGAGC
1 AAACAGAGAGC
30897 GCGCTAGTGT
Statistics
Matches: 106, Mismatches: 14, Indels: 17
0.77 0.10 0.12
Matches are distributed among these distances:
21 16 0.15
22 1 0.01
23 50 0.47
24 2 0.02
25 29 0.27
26 8 0.08
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.11
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Found at i:30885 original size:48 final size:46
Alignment explanation
Indices: 30746--30896 Score: 139
Period size: 48 Copynumber: 3.2 Consensus size: 46
30736 TATACGGAAC
* * *
30746 AAACAGAGAGTAC-CAAAGTACT-AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACACAGTACTAAACAGAGAGCACACAAAGTGCT
*
30789 GGGCAACAGAGAGCACACACAGTACTAAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACACAGTACTAAACAGAGAGCACACAAAGTGCT
* * * * *
30838 AATCAGAGAGCACACACAGTGCTAATAACGGAGAGCACGA-GACGTGCT
1 AAACAGAGAGCACACACAGTACT-A-AACAGAGAGCAC-ACAAAGTGCT
30886 AAACAGAGAGC
1 AAACAGAGAGC
30897 GCGCTAGTGT
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
46 31 0.35
47 9 0.10
48 40 0.45
49 8 0.09
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.11
Consensus pattern (46 bp):
AAACAGAGAGCACACACAGTACTAAACAGAGAGCACACAAAGTGCT
Found at i:34893 original size:30 final size:29
Alignment explanation
Indices: 34846--34903 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
34836 CCTTATTACT
* *
34846 TTTTCCCAAAAACTTTTACTCCTTCCCAC
1 TTTTCCCAAAAACTTTTACCCCCTCCCAC
* *
34875 TTTTCCCTTAAAATTTTTACCCCCTCCCA
1 TTTTCCC-AAAAACTTTTACCCCCTCCCA
34904 TCTCACCCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.22, C:0.38, G:0.00, T:0.40
Consensus pattern (29 bp):
TTTTCCCAAAAACTTTTACCCCCTCCCAC
Found at i:35158 original size:20 final size:21
Alignment explanation
Indices: 35133--35173 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
35123 AAAACCTCCA
35133 AAACTTTTTA-TTTTC-CCCTT
1 AAAC-TTTTACTTTTCACCCTT
35153 AAACTTTTACTTTTCACCCTT
1 AAACTTTTACTTTTCACCCTT
35174 TACCCCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 9 0.47
21 5 0.26
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (21 bp):
AAACTTTTACTTTTCACCCTT
Found at i:38655 original size:8 final size:8
Alignment explanation
Indices: 38644--38674 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
38634 TTTGTTAAAA
38644 GTAGTTAG
1 GTAGTTAG
38652 GTAGTTAG
1 GTAGTTAG
38660 GTAGTTAG
1 GTAGTTAG
*
38668 TTAGTTA
1 GTAGTTA
38675 TCAGTTCGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (8 bp):
GTAGTTAG
Found at i:40453 original size:56 final size:56
Alignment explanation
Indices: 40393--40606 Score: 227
Period size: 56 Copynumber: 3.8 Consensus size: 56
40383 TCTTGCCCAA
* *
40393 AAGAGCATTGCTCTGTATTCTGGCTCATAAGAACATTATTCTGTATTTTGGCTTGG
1 AAGAGCATTGCTCTGTATTCTGGCTCAGAAGAGCATTATTCTGTATTTTGGCTTGG
* * ** *
40449 AAGAGCGTTACTCTGTATTCTGGCTTGGAAGAGCATTATTCTGTATTCTGGCTTGG
1 AAGAGCATTGCTCTGTATTCTGGCTCAGAAGAGCATTATTCTGTATTTTGGCTTGG
* * * * *
40505 AAGAGCATTGCTTTGTATTCTAGCTCAGAAGAGCGTTA-CCTTGT-TTTCTGGCTCGG
1 AAGAGCATTGCTCTGTATTCTGGCTCAGAAGAGCATTATTC-TGTATTT-TGGCTTGG
* * * * *
40561 AAGAGCACTGCTTTGTATTTTGGCTC-GTAAGGGCATTATTTTGTAT
1 AAGAGCATTGCTCTGTATTCTGGCTCAG-AAGAGCATTATTCTGTAT
40607 CTAGCTTGAA
Statistics
Matches: 129, Mismatches: 24, Indels: 9
0.80 0.15 0.06
Matches are distributed among these distances:
55 4 0.03
56 124 0.96
57 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.38
Consensus pattern (56 bp):
AAGAGCATTGCTCTGTATTCTGGCTCAGAAGAGCATTATTCTGTATTTTGGCTTGG
Found at i:40603 original size:28 final size:28
Alignment explanation
Indices: 40393--40606 Score: 189
Period size: 28 Copynumber: 7.6 Consensus size: 28
40383 TCTTGCCCAA
* * **
40393 AAGAGCATTGCTCTGTATTCTGGCTCAT
1 AAGAGCATTACTTTGTATTCTGGCTCGG
* * *
40421 AAGAACATTA-TTCTGTATTTTGGCTTGG
1 AAGAGCATTACTT-TGTATTCTGGCTCGG
* * *
40449 AAGAGCGTTACTCTGTATTCTGGCTTGG
1 AAGAGCATTACTTTGTATTCTGGCTCGG
*
40477 AAGAGCATTA-TTCTGTATTCTGGCTTGG
1 AAGAGCATTACTT-TGTATTCTGGCTCGG
* * *
40505 AAGAGCATTGCTTTGTATTCTAGCTCAG
1 AAGAGCATTACTTTGTATTCTGGCTCGG
* * *
40533 AAGAGCGTTACCTTGTTTTCTGGCTCGG
1 AAGAGCATTACTTTGTATTCTGGCTCGG
* * * *
40561 AAGAGCACTGCTTTGTATTTTGGCTCGT
1 AAGAGCATTACTTTGTATTCTGGCTCGG
* *
40589 AAGGGCATTATTTTGTAT
1 AAGAGCATTACTTTGTAT
40607 CTAGCTTGAA
Statistics
Matches: 148, Mismatches: 34, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
27 2 0.01
28 143 0.97
29 3 0.02
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.38
Consensus pattern (28 bp):
AAGAGCATTACTTTGTATTCTGGCTCGG
Found at i:46834 original size:2 final size:2
Alignment explanation
Indices: 46827--46854 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
46817 AAATTGACAA
46827 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46855 GGTATAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55638 original size:28 final size:28
Alignment explanation
Indices: 55598--55655 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
55588 AATGACATAC
55598 TAATCTATTCTAAGACGGAGTCGAACCA
1 TAATCTATTCTAAGACGGAGTCGAACCA
55626 TAATCTATTCTAAGACGGAGTCGAACCA
1 TAATCTATTCTAAGACGGAGTCGAACCA
55654 TA
1 TA
55656 CTCAGCATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (28 bp):
TAATCTATTCTAAGACGGAGTCGAACCA
Found at i:59072 original size:28 final size:28
Alignment explanation
Indices: 59040--59322 Score: 287
Period size: 28 Copynumber: 10.1 Consensus size: 28
59030 AATTATTCTA
* * *
59040 TATTCTAGCTCGAAAGAGAGTTACTCTG
1 TATTCTGGCTCGGAAGAGCGTTACTCTG
* * *
59068 TATTCTGGCTCGAAAGACCGTTGCTCTG
1 TATTCTGGCTCGGAAGAGCGTTACTCTG
* * *
59096 TATTCTGGCTCGTAAGAGCATTATTCTG
1 TATTCTGGCTCGGAAGAGCGTTACTCTG
* *
59124 TATTCTGGCTCGAAAGAGCGTTACTCTT
1 TATTCTGGCTCGGAAGAGCGTTACTCTG
* * *
59152 TACTCTGGCTCGGAAGAGCGTTGCTTTG
1 TATTCTGGCTCGGAAGAGCGTTACTCTG
* * * *
59180 TATTCTAGCTTGGAAGAGCGTTGCTTTG
1 TATTCTGGCTCGGAAGAGCGTTACTCTG
* *
59208 TATTCTGGCTCGTAAGAGCGTTACTCTT
1 TATTCTGGCTCGGAAGAGCGTTACTCTG
* * *
59236 TACTCTGGCTCGGAAGAGCGTTGCTTTG
1 TATTCTGGCTCGGAAGAGCGTTACTCTG
* * * *
59264 TATTCTAGCTTGGAAGAGCGTTGCTTTG
1 TATTCTGGCTCGGAAGAGCGTTACTCTG
* * * *
59292 TATTCTGGCTCGTAAGGGCATTATTCTG
1 TATTCTGGCTCGGAAGAGCGTTACTCTG
59320 TAT
1 TAT
59323 CTAGCTTGAA
Statistics
Matches: 212, Mismatches: 43, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 212 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (28 bp):
TATTCTGGCTCGGAAGAGCGTTACTCTG
Found at i:59307 original size:84 final size:84
Alignment explanation
Indices: 59040--59303 Score: 395
Period size: 84 Copynumber: 3.1 Consensus size: 84
59030 AATTATTCTA
* * * * * * * *
59040 TATTCTAGCTCGAAAGAGAGTTACTCTGTATTCTGGCTCGAAAGACCGTTGCTCTGTATTCTGGC
1 TATTCTGGCTCGAAAGAGCGTTACTCTTTACTCTGGCTCGGAAGAGCGTTGCTTTGTATTCTAGC
* * * *
59105 TCGTAAGAGCATT-ATTCTG
66 TTGGAAGAGCGTTGCTT-TG
59124 TATTCTGGCTCGAAAGAGCGTTACTCTTTACTCTGGCTCGGAAGAGCGTTGCTTTGTATTCTAGC
1 TATTCTGGCTCGAAAGAGCGTTACTCTTTACTCTGGCTCGGAAGAGCGTTGCTTTGTATTCTAGC
59189 TTGGAAGAGCGTTGCTTTG
66 TTGGAAGAGCGTTGCTTTG
*
59208 TATTCTGGCTCGTAAGAGCGTTACTCTTTACTCTGGCTCGGAAGAGCGTTGCTTTGTATTCTAGC
1 TATTCTGGCTCGAAAGAGCGTTACTCTTTACTCTGGCTCGGAAGAGCGTTGCTTTGTATTCTAGC
59273 TTGGAAGAGCGTTGCTTTG
66 TTGGAAGAGCGTTGCTTTG
59292 TATTCTGGCTCG
1 TATTCTGGCTCG
59304 TAAGGGCATT
Statistics
Matches: 166, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
84 164 0.99
85 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (84 bp):
TATTCTGGCTCGAAAGAGCGTTACTCTTTACTCTGGCTCGGAAGAGCGTTGCTTTGTATTCTAGC
TTGGAAGAGCGTTGCTTTG
Found at i:75140 original size:41 final size:43
Alignment explanation
Indices: 75045--75141 Score: 103
Period size: 41 Copynumber: 2.3 Consensus size: 43
75035 GTTTTTGAGA
* * *
75045 AAACATCGTTATTGCTCTATACCTATTGCGGCATTTTTCCTAT
1 AAACGTCGTTATTACTCTATACCTATTACGGCATTTTTCCTAT
* *
75088 AAATG-CTGTTATTACT-T-TACCTTTTACGGCATTTTT-CTCAT
1 AAACGTC-GTTATTACTCTATACCTATTACGGCATTTTTCCT-AT
75129 AAACGTCGTTATT
1 AAACGTCGTTATT
75142 GTTTAATCTT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
40 2 0.04
41 29 0.64
42 3 0.07
43 11 0.24
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.44
Consensus pattern (43 bp):
AAACGTCGTTATTACTCTATACCTATTACGGCATTTTTCCTAT
Found at i:75253 original size:22 final size:22
Alignment explanation
Indices: 75225--75271 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
75215 TAAAAATTGA
75225 AATATATTTTAACTTGTAATGT
1 AATATATTTTAACTTGTAATGT
75247 AATATATTTTAACTTGTAATGT
1 AATATATTTTAACTTGTAATGT
75269 AAT
1 AAT
75272 GTAATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (22 bp):
AATATATTTTAACTTGTAATGT
Found at i:77063 original size:41 final size:42
Alignment explanation
Indices: 77006--77096 Score: 132
Period size: 41 Copynumber: 2.2 Consensus size: 42
76996 ATTGCTTAAC
* *
77006 CTTTAGCGATGTTTTTC-CTATAAATGTCGCTAATGTTCTGAT
1 CTTTAGCGATGTTTTTCTC-ATAAACGCCGCTAATGTTCTGAT
*
77048 CTTTAGCGATG-TTTTCTCGTAAACGCCGCTAATGTTCTGAT
1 CTTTAGCGATGTTTTTCTCATAAACGCCGCTAATGTTCTGAT
77089 CTTTAGCG
1 CTTTAGCG
77097 GCGTTTATGC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 33 0.73
42 12 0.27
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.42
Consensus pattern (42 bp):
CTTTAGCGATGTTTTTCTCATAAACGCCGCTAATGTTCTGAT
Found at i:77187 original size:40 final size:40
Alignment explanation
Indices: 77142--77239 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
77132 ATAAATGCCA
*
77142 CTATTGCTTTACCTTTTGC-GACTTTTATGTAAAAACG-TCG
1 CTATTGCTTTACCTTTTGCAG-CGTTTATGTAAAAACGCT-G
77182 CTATTGCTTTACCTTTTGCAGCGTTTATGTAAAAACGCTG
1 CTATTGCTTTACCTTTTGCAGCGTTTATGTAAAAACGCTG
* *
77222 CTATTGATTTACTTTTTG
1 CTATTGCTTTACCTTTTG
77240 TGGTGTTTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
40 51 0.96
41 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.45
Consensus pattern (40 bp):
CTATTGCTTTACCTTTTGCAGCGTTTATGTAAAAACGCTG
Found at i:77953 original size:19 final size:19
Alignment explanation
Indices: 77910--77955 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
77900 AATATAGTAA
* *
77910 AATATTAAA-AAATTAAAT
1 AATATAAAATAAAATAAAT
*
77928 -ATTTAAAATAAAATAAAT
1 AATATAAAATAAAATAAAT
77946 AATATAAAAT
1 AATATAAAAT
77956 TTTCAAAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 6 0.27
18 8 0.36
19 8 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AATATAAAATAAAATAAAT
Found at i:95998 original size:7 final size:7
Alignment explanation
Indices: 95986--96011 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
95976 TCTTGATGAT
95986 TTCTTCA
1 TTCTTCA
95993 TTCTTCA
1 TTCTTCA
96000 TTCTTCA
1 TTCTTCA
96007 TTCTT
1 TTCTT
96012 TTATTTATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.62
Consensus pattern (7 bp):
TTCTTCA
Found at i:97448 original size:25 final size:25
Alignment explanation
Indices: 97420--97469 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
97410 CTCACCCTTG
*
97420 TCTTGGT-CCTTCTTTTTCTTTTTAT
1 TCTTGGTGCCTT-TTTCTCTTTTTAT
*
97445 TCTTTGTGCCTTTTTCTCTTTTTAT
1 TCTTGGTGCCTTTTTCTCTTTTTAT
97470 CCTTCGACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.04, C:0.20, G:0.08, T:0.68
Consensus pattern (25 bp):
TCTTGGTGCCTTTTTCTCTTTTTAT
Found at i:103985 original size:93 final size:93
Alignment explanation
Indices: 103826--104001 Score: 316
Period size: 93 Copynumber: 1.9 Consensus size: 93
103816 TTGCGATGAG
* * *
103826 CTTATCTTCTTGTGTTGCGTCGAATGATGCATTGACAATAACAGGCAATGTCTTGTTGTCACCAA
1 CTTATCTTCTTGTGTTGCGTCAAAGGATGCATTGACAATAACAGACAATGTCTTGTTGTCACCAA
*
103891 GAAAGACATACTTCAAATACATCGACAA
66 GAAAGACAAACTTCAAATACATCGACAA
103919 CTTATCTTCTTGTGTTGCGTCAAAGGATGCATTGACAATAACAGACAATGTCTTGTTGTCACCAA
1 CTTATCTTCTTGTGTTGCGTCAAAGGATGCATTGACAATAACAGACAATGTCTTGTTGTCACCAA
103984 GAAAGACAAACTTCAAAT
66 GAAAGACAAACTTCAAAT
104002 GCGTCGGCAG
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 79 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (93 bp):
CTTATCTTCTTGTGTTGCGTCAAAGGATGCATTGACAATAACAGACAATGTCTTGTTGTCACCAA
GAAAGACAAACTTCAAATACATCGACAA
Found at i:110216 original size:22 final size:22
Alignment explanation
Indices: 110190--110235 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
110180 TTGTTTGTAT
110190 TGTACTAGGATAATCAAAGTAC
1 TGTACTAGGATAATCAAAGTAC
110212 TGTACTAGGATAATCAAAGTAC
1 TGTACTAGGATAATCAAAGTAC
110234 TG
1 TG
110236 ATGTTAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (22 bp):
TGTACTAGGATAATCAAAGTAC
Found at i:115712 original size:18 final size:18
Alignment explanation
Indices: 115689--115723 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
115679 AAATTCCGAA
*
115689 AAATAAATTAAATAAATC
1 AAATAAAGTAAATAAATC
*
115707 AAATAAAGTAAGTAAAT
1 AAATAAAGTAAATAAAT
115724 ATAATTGTAT
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:0.66, C:0.03, G:0.06, T:0.26
Consensus pattern (18 bp):
AAATAAAGTAAATAAATC
Found at i:117975 original size:61 final size:61
Alignment explanation
Indices: 117906--118028 Score: 228
Period size: 61 Copynumber: 2.0 Consensus size: 61
117896 TCAATTGTCA
117906 ATAATAATTCATCAACATAAAGAGAGGGGTCAACAAATACATCAAAGCTTACTATCTCTAG
1 ATAATAATTCATCAACATAAAGAGAGGGGTCAACAAATACATCAAAGCTTACTATCTCTAG
* *
117967 ATAATAATTCATCAACATAAAGAGAGGGGTCAACAAATACATCGAAGCTTACTGTCTCTAG
1 ATAATAATTCATCAACATAAAGAGAGGGGTCAACAAATACATCAAAGCTTACTATCTCTAG
118028 A
1 A
118029 CTACTAAGAC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (61 bp):
ATAATAATTCATCAACATAAAGAGAGGGGTCAACAAATACATCAAAGCTTACTATCTCTAG
Found at i:125507 original size:28 final size:28
Alignment explanation
Indices: 125426--125510 Score: 107
Period size: 28 Copynumber: 3.0 Consensus size: 28
125416 TTTGATGTGG
* * *
125426 AGATAGTTGGAAACCTTGTTTGCAGTGG
1 AGATAGTTGGAAACCCTGTTTGCAATGA
* *
125454 AGATAGTTGGAAACCCTATTTACAATGA
1 AGATAGTTGGAAACCCTGTTTGCAATGA
**
125482 AGATAGTTAAAAACCCTGTTTGCAATGA
1 AGATAGTTGGAAACCCTGTTTGCAATGA
125510 A
1 A
125511 TGTTACGTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (28 bp):
AGATAGTTGGAAACCCTGTTTGCAATGA
Found at i:135407 original size:22 final size:22
Alignment explanation
Indices: 135381--135427 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
135371 GCAAATGAAA
* *
135381 GGTTTGAATAAGGAACAAAATG
1 GGTTTAAATAACGAACAAAATG
* *
135403 GGTTTAAATACCTAACAAAATG
1 GGTTTAAATAACGAACAAAATG
135425 GGT
1 GGT
135428 AAATTACACG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.26
Consensus pattern (22 bp):
GGTTTAAATAACGAACAAAATG
Found at i:140766 original size:20 final size:20
Alignment explanation
Indices: 140743--140810 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
140733 TAGAAACACC
140743 AAAGTGCATACAAAGATACT
1 AAAGTGCATACAAAGATACT
* * * * **
140763 AAAGTACAAACAAAAACAGG
1 AAAGTGCATACAAAGATACT
* *
140783 GAAGTGCATACAAAGATATT
1 AAAGTGCATACAAAGATACT
140803 AAAGTGCA
1 AAAGTGCA
140811 AACAGTCACA
Statistics
Matches: 34, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.53, C:0.13, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAGTGCATACAAAGATACT
Found at i:140769 original size:40 final size:40
Alignment explanation
Indices: 140724--140814 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 40
140714 GACATCGAAG
* *
140724 AAGTACAAATAGAAACACCAAAGTGCATACAAAGATACTA
1 AAGTACAAACAAAAACACCAAAGTGCATACAAAGATACTA
*** *
140764 AAGTACAAACAAAAACAGGGAAGTGCATACAAAGATATTA
1 AAGTACAAACAAAAACACCAAAGTGCATACAAAGATACTA
*
140804 AAGTGCAAACA
1 AAGTACAAACA
140815 GTCACATTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.55, C:0.15, G:0.15, T:0.14
Consensus pattern (40 bp):
AAGTACAAACAAAAACACCAAAGTGCATACAAAGATACTA
Found at i:142122 original size:21 final size:22
Alignment explanation
Indices: 142074--142122 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
142064 TGCGCATAGG
142074 CCATGTGGCTAAAAGACATGTA
1 CCATGTGGCTAAAAGACATGTA
** *
142096 -TGTGTGGCTAAACGACATG-A
1 CCATGTGGCTAAAAGACATGTA
142116 CCATGTG
1 CCATGTG
142123 CGATCGATAA
Statistics
Matches: 21, Mismatches: 5, Indels: 3
0.72 0.17 0.10
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (22 bp):
CCATGTGGCTAAAAGACATGTA
Found at i:181465 original size:13 final size:13
Alignment explanation
Indices: 181447--181473 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
181437 TATTCCCTTA
181447 ACATTATTAGGTG
1 ACATTATTAGGTG
181460 ACATTATTAGGTG
1 ACATTATTAGGTG
181473 A
1 A
181474 AGGTAACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.37
Consensus pattern (13 bp):
ACATTATTAGGTG
Done.