Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010879.1 Kokia drynarioides strain JFW-HI SEQ_125847, 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: 146454
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 211 characters in sequence are not A, C, G, or T
Found at i:1697 original size:37 final size:37
Alignment explanation
Indices: 1656--1734 Score: 158
Period size: 37 Copynumber: 2.1 Consensus size: 37
1646 AGGTTAGCTC
1656 CCTGATGAGATACTGAGGAGTGAACCAAATTCATCTT
1 CCTGATGAGATACTGAGGAGTGAACCAAATTCATCTT
1693 CCTGATGAGATACTGAGGAGTGAACCAAATTCATCTT
1 CCTGATGAGATACTGAGGAGTGAACCAAATTCATCTT
1730 CCTGA
1 CCTGA
1735 CGAGGTACAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (37 bp):
CCTGATGAGATACTGAGGAGTGAACCAAATTCATCTT
Found at i:2955 original size:59 final size:59
Alignment explanation
Indices: 2852--3232 Score: 523
Period size: 59 Copynumber: 6.5 Consensus size: 59
2842 ACCTGGAGGT
* * *
2852 CCCCGAACCTTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCAAATTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
* *
2911 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
* * * *
2970 CCTCGAACCTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
* *
3029 CCCCGAACCTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
* * * ***
3088 CCCTGAACCTTCCAGAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
* * * *
3147 CCCCTAACCTT-TCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCGTTTTTAA
1 CCCCGAACCTTCT-AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
* * *
3206 CTCCGAACCTTC-CAAAACTACCATTTT
1 CCCCGAACCTTCTAAAAATTACCATTTT
3233 TGCCCCCGTG
Statistics
Matches: 287, Mismatches: 33, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
58 13 0.05
59 274 0.95
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (59 bp):
CCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
Found at i:4608 original size:39 final size:38
Alignment explanation
Indices: 4509--4611 Score: 102
Period size: 38 Copynumber: 2.7 Consensus size: 38
4499 TGCTTAAAGT
* * *
4509 TTCACTCTTCCCTATGATCAGGGTAAGAGATCGTGTAC
1 TTCAATCTTCCCTCTGATCAGGGTAAGAGATAGTGTAC
* * *
4547 TTCAATTTTCCC-CATGATCAGGGTTAGTA-CTAGTGTATC
1 TTCAATCTTCCCTC-TGATCAGGGTAAG-AGATAGTGTA-C
*
4586 TTCGATCTTCCCTCTGATCAGGGTAA
1 TTCAATCTTCCCTCTGATCAGGGTAA
4612 AAAGATCGGA
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
38 28 0.54
39 23 0.44
40 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.35
Consensus pattern (38 bp):
TTCAATCTTCCCTCTGATCAGGGTAAGAGATAGTGTAC
Found at i:5652 original size:24 final size:24
Alignment explanation
Indices: 5625--5670 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5615 TTTCTGTTAG
* *
5625 AATGAGAGCTCCTCTTGAGAAACT
1 AATGAGAACTCCTCCTGAGAAACT
5649 AATGAGAACTCCTCCTGAGAAA
1 AATGAGAACTCCTCCTGAGAAA
5671 GCTTTCTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (24 bp):
AATGAGAACTCCTCCTGAGAAACT
Found at i:9026 original size:6 final size:6
Alignment explanation
Indices: 9015--9043 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
9005 ATGATTATTG
9015 GTATGA GTATGA GTATGA GTATGA GTATG
1 GTATGA GTATGA GTATGA GTATGA GTATG
9044 TTTGCGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (6 bp):
GTATGA
Found at i:10256 original size:26 final size:26
Alignment explanation
Indices: 10225--10287 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
10215 GAGTACTCCG
10225 GGTAATGTGTACCCTTTACAACGGGT
1 GGTAATGTGTACCCTTTACAACGGGT
10251 GGTAATGTGTACCCTTTACAACGGGT
1 GGTAATGTGTACCCTTTACAACGGGT
10277 GGTAATGTGTA
1 GGTAATGTGTA
10288 AGGCTTTCGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.32
Consensus pattern (26 bp):
GGTAATGTGTACCCTTTACAACGGGT
Found at i:16460 original size:30 final size:30
Alignment explanation
Indices: 16426--16829 Score: 300
Period size: 30 Copynumber: 13.7 Consensus size: 30
16416 GGTCAAAACA
* *
16426 TAATTTTGGAAAAGTTTAGGGGTAAAAAGG
1 TAATTTTGGAAAAGTTTAGGGGTTAAAATG
* *
16456 TAATTATGGGAAAGTTTAGGGGTTAAAATG
1 TAATTTTGGAAAAGTTTAGGGGTTAAAATG
* * * *
16486 TGATTTTAGG-AAAGATT-GAGGTCAAAATG
1 TAATTTT-GGAAAAGTTTAGGGGTTAAAATG
* *
16515 TAATTTT-GAAAAGGTTTAAGGGTTAAAATA
1 TAATTTTGGAAAA-GTTTAGGGGTTAAAATG
* * *
16545 TAATTTTGGGAATGTTTGGGGGTTAAAATG
1 TAATTTTGGAAAAGTTTAGGGGTTAAAATG
* * *
16575 TAAGTTTGTAAAAGTTTA-AGGTTAAAATG
1 TAATTTTGGAAAAGTTTAGGGGTTAAAATG
* *
16604 TGATTTTGGGAAAGTTTA-GGGTTAAAATG
1 TAATTTTGGAAAAGTTTAGGGGTTAAAATG
** *
16633 TGTTTTTTGG-AAAGTTTGGGGGTTAAAATG
1 T-AATTTTGGAAAAGTTTAGGGGTTAAAATG
*
16663 TAATTTTAAGAAAA-TTTA-GGGTTAAAATG
1 TAATTTT-GGAAAAGTTTAGGGGTTAAAATG
* ** *
16692 TGATTTAAG-AAAGTTTAAGGGTTAAAATG
1 TAATTTTGGAAAAGTTTAGGGGTTAAAATG
*
16721 -AATTTTTTGGGAAAA-TTTAGGGGTTAAAATA
1 TAA--TTTT-GGAAAAGTTTAGGGGTTAAAATG
* * *
16752 TGATTTTAGG-AAAGTTTA-AGG-TCAAATG
1 TAATTTT-GGAAAAGTTTAGGGGTTAAAATG
* * *
16780 TGATTTT-GAGAAAGTTT-GAGGTCAAAATG
1 TAATTTTGGA-AAAGTTTAGGGGTTAAAATG
**
16809 TAATTTTTAAAAAGTTTAGGG
1 TAATTTTGGAAAAGTTTAGGG
16830 ACCTTCTGAG
Statistics
Matches: 296, Mismatches: 55, Indels: 46
0.75 0.14 0.12
Matches are distributed among these distances:
26 1 0.00
27 4 0.01
28 32 0.11
29 115 0.39
30 117 0.40
31 23 0.08
32 4 0.01
ACGTcount: A:0.37, C:0.01, G:0.26, T:0.37
Consensus pattern (30 bp):
TAATTTTGGAAAAGTTTAGGGGTTAAAATG
Found at i:16532 original size:59 final size:58
Alignment explanation
Indices: 16466--16829 Score: 258
Period size: 59 Copynumber: 6.2 Consensus size: 58
16456 TAATTATGGG
* *
16466 AAAGTTTAGGGGTTAAAATGTGATTTTAGGAAAGATTGAGGTCAAAATGTAATTTTGA
1 AAAGTTTAGGGGTTAAAATGTGATTTTGGGAAAGATTGAGGTTAAAATGTAATTTTGA
* * * * * * *
16524 AAAGGTTTAAGGGTTAAAATATAATTTTGGGAATGTTTGGGGGTTAAAATGTAAGTTTGTA
1 AAA-GTTTAGGGGTTAAAATGTGATTTTGGGAAAGATT-GAGGTTAAAATGTAATTTTG-A
* * ** *
16585 AAAGTTTA-AGGTTAAAATGTGATTTTGGGAAAG-TTTAGGGTTAAAATGTGTTTTTTGG
1 AAAGTTTAGGGGTTAAAATGTGATTTTGGGAAAGATTGA-GGTTAAAATGT-AATTTTGA
* * ** * * *
16643 AAAGTTTGGGGGTTAAAATGTAATTTTAAGAAA-ATTTAGGGTTAAAATGTGA-TTTAA
1 AAAGTTTAGGGGTTAAAATGTGATTTTGGGAAAGATTGA-GGTTAAAATGTAATTTTGA
* * * * * *
16700 GAAAGTTTAAGGGTTAAAATGAAT-TTTTTGGGAAA-ATTTAGGGGTTAAAATATGATTTTAGG
1 -AAAGTTTAGGGGTTAAAATG--TGATTTTGGGAAAGA-TT-GAGGTTAAAATGTAATTTT-GA
* * * * * *
16762 AAAGTTTA-AGG-TCAAATGTGATTTTGAGAAAGTTTGAGGTCAAAATGTAATTTTTAA
1 AAAGTTTAGGGGTTAAAATGTGATTTTGGGAAAGATTGAGGTTAAAATGTAA-TTTTGA
16819 AAAGTTTAGGG
1 AAAGTTTAGGG
16830 ACCTTCTGAG
Statistics
Matches: 238, Mismatches: 50, Indels: 36
0.73 0.15 0.11
Matches are distributed among these distances:
57 23 0.10
58 57 0.24
59 104 0.44
60 39 0.16
61 15 0.06
ACGTcount: A:0.37, C:0.01, G:0.26, T:0.37
Consensus pattern (58 bp):
AAAGTTTAGGGGTTAAAATGTGATTTTGGGAAAGATTGAGGTTAAAATGTAATTTTGA
Found at i:16664 original size:88 final size:87
Alignment explanation
Indices: 16428--16829 Score: 375
Period size: 89 Copynumber: 4.6 Consensus size: 87
16418 TCAAAACATA
* * * * * *
16428 ATTTTGGAAAAGTTTAGGGGTAAAAAGGTAATTATGGGAAAGTTTAGGGGTTAAAATGTGATTTT
1 ATTTTGGGAAAGTTTA-GGGTTAAAATGTATTTTTGGGAAAGTTTAGGGGTTAAAATGTAATTTT
* * * *
16493 AGGAAAGATTGAGGTCAAAATGTA
65 A-GAAAGTTTAAGGTTAAAATGTG
* * * * *
16517 ATTTT-GAAAAGGTTTAAGGGTTAAAATATAATTTTGGGAATGTTTGGGGGTTAAAATGTAAGTT
1 ATTTTGGGAAA-GTTT-AGGGTTAAAATGTATTTTTGGGAAAGTTTAGGGGTTAAAATGTAA-TT
16581 TGTA-AAAGTTTAAGGTTAAAATGTG
63 T-TAGAAAGTTTAAGGTTAAAATGTG
* * *
16606 ATTTTGGGAAAGTTTAGGGTTAAAATGTGTTTTTTGGAAAGTTTGGGGGTTAAAATGTAATTTTA
1 ATTTTGGGAAAGTTTAGGGTTAAAATGTATTTTTGGGAAAGTTTAGGGGTTAAAATGTAATTTT-
* *
16671 AGAAAATTTAGGGTTAAAATGTG
65 AGAAAGTTTAAGGTTAAAATGTG
** * * * *
16694 A-TTTAAGAAAGTTTAAGGGTTAAAATGAATTTTTTGGGAAAATTTAGGGGTTAAAATATGATTT
1 ATTTTGGGAAAGTTT-AGGGTTAAAATGTA-TTTTTGGGAAAGTTTAGGGGTTAAAATGTAATTT
*
16758 TAGGAAAGTTTAAGG-TCAAATGTG
64 TA-GAAAGTTTAAGGTTAAAATGTG
* * **
16782 ATTTTGAGAAAGTTT-GAGGTCAAAATGTAATTTTT-AAAAAGTTTAGGG
1 ATTTTGGGAAAGTTTAG-GGTTAAAATGT-ATTTTTGGGAAAGTTTAGGG
16830 ACCTTCTGAG
Statistics
Matches: 263, Mismatches: 37, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
86 1 0.00
87 26 0.10
88 101 0.38
89 125 0.48
90 8 0.03
91 2 0.01
ACGTcount: A:0.37, C:0.01, G:0.26, T:0.37
Consensus pattern (87 bp):
ATTTTGGGAAAGTTTAGGGTTAAAATGTATTTTTGGGAAAGTTTAGGGGTTAAAATGTAATTTTA
GAAAGTTTAAGGTTAAAATGTG
Found at i:19549 original size:19 final size:20
Alignment explanation
Indices: 19525--19565 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
19515 ATATTTTATT
19525 TTATTACAAATTAAAA-AAA
1 TTATTACAAATTAAAAGAAA
* *
19544 TTATTACTACTTAAAAGAAA
1 TTATTACAAATTAAAAGAAA
19564 TT
1 TT
19566 CGTTTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (20 bp):
TTATTACAAATTAAAAGAAA
Found at i:23139 original size:24 final size:24
Alignment explanation
Indices: 23112--23181 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
23102 TCCAAATCAA
* *
23112 ATTTTGGGTCGAACCCCGAGTCCG
1 ATTTTGGGTCAAACCCCGAATCCG
* * *
23136 ATTTTGAGTCAAACCTCGAATCGG
1 ATTTTGGGTCAAACCCCGAATCCG
*
23160 ATTTTGGGTCAAACCTCGAATC
1 ATTTTGGGTCAAACCCCGAATC
23182 AGGTTCTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (24 bp):
ATTTTGGGTCAAACCCCGAATCCG
Found at i:25119 original size:55 final size:55
Alignment explanation
Indices: 25008--25259 Score: 283
Period size: 55 Copynumber: 4.6 Consensus size: 55
24998 TGTAGTTGCA
* * * * * * *
25008 AAACAGTATGTTCACACGGCCT-GACCCACGCCCATGTGCCTAGCCCGTGTATCACT
1 AAACAGTATGTACACACGGTCTAG-CACACGCTCGTG-GCTTAGCCCGTGTACCACT
* * * * *
25064 AAACAGTATATACCCACGGTCTAGCACACACTCATGGCTTAGCCCGTGTGCCACT
1 AAACAGTATGTACACACGGTCTAGCACACGCTCGTGGCTTAGCCCGTGTACCACT
* * * *
25119 AAACAGTATGTACACAC-GTCTAGCATACGTTCGTGCCTCAGCCCGTGTACCACT
1 AAACAGTATGTACACACGGTCTAGCACACGCTCGTGGCTTAGCCCGTGTACCACT
* * * *
25173 AAACAATATGTACATACGATCTAGCACACGCTCGTGGCTTAGCCCGAGTACCACT
1 AAACAGTATGTACACACGGTCTAGCACACGCTCGTGGCTTAGCCCGTGTACCACT
*
25228 AAACAGTATGTACATACGGTCTAGCACACGCT
1 AAACAGTATGTACACACGGTCTAGCACACGCT
25260 TGTAGCTCCA
Statistics
Matches: 165, Mismatches: 29, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
54 45 0.27
55 92 0.56
56 27 0.16
57 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (55 bp):
AAACAGTATGTACACACGGTCTAGCACACGCTCGTGGCTTAGCCCGTGTACCACT
Found at i:25173 original size:109 final size:109
Alignment explanation
Indices: 25043--25253 Score: 307
Period size: 109 Copynumber: 1.9 Consensus size: 109
25033 CCACGCCCAT
* * * *
25043 GTGCCTAGCCCGTGTATCACTAAACAGTATATACCCACGGTCTAGCACACACTCATGGCTTAGCC
1 GTGCCTAGCCCGTGTACCACTAAACAATATATACACACGATCTAGCACACACTCATGGCTTAGCC
* *
25108 CGTGTGCCACTAAACAGTATGTACACAC-GTCTAGCATACGTTC
66 CGAGTACCACTAAACAGTATGTACACACGGTCTAGCATACGTTC
* * * *
25151 GTGCCTCAGCCCGTGTACCACTAAACAATATGTACATACGATCTAGCACACGCTCGTGGCTTAGC
1 GTGCCT-AGCCCGTGTACCACTAAACAATATATACACACGATCTAGCACACACTCATGGCTTAGC
*
25216 CCGAGTACCACTAAACAGTATGTACATACGGTCTAGCA
65 CCGAGTACCACTAAACAGTATGTACACACGGTCTAGCA
25254 CACGCTTGTA
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
108 6 0.07
109 76 0.84
110 8 0.09
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (109 bp):
GTGCCTAGCCCGTGTACCACTAAACAATATATACACACGATCTAGCACACACTCATGGCTTAGCC
CGAGTACCACTAAACAGTATGTACACACGGTCTAGCATACGTTC
Found at i:36705 original size:27 final size:28
Alignment explanation
Indices: 36675--36730 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
36665 CTCATTTTAT
36675 CTTTTTAAAAAATAATTTT-TTTTTTCA
1 CTTTTTAAAAAATAATTTTATTTTTTCA
* * *
36702 CTTTTTTAGAATTAATTTTAGTTTTTTCA
1 CTTTTTAAAAAATAATTTTA-TTTTTTCA
36731 ATAAATGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 16 0.67
29 8 0.33
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.61
Consensus pattern (28 bp):
CTTTTTAAAAAATAATTTTATTTTTTCA
Found at i:36806 original size:21 final size:21
Alignment explanation
Indices: 36767--36807 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
36757 GAAGGAATTA
* *
36767 CTTGGATTTTTATAGGAAAAT
1 CTTGGATTTTTACAAGAAAAT
*
36788 CTTGGATTTTTGCAAGAAAA
1 CTTGGATTTTTACAAGAAAA
36808 ACTATTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (21 bp):
CTTGGATTTTTACAAGAAAAT
Found at i:40199 original size:120 final size:118
Alignment explanation
Indices: 40056--40345 Score: 472
Period size: 120 Copynumber: 2.4 Consensus size: 118
40046 TTTAAATTAT
* * * *
40056 ATCTTAATATTACTTTTAACACAAATCTAATCATTTAAACAAAAGTATAATATTCAATGTTATAT
1 ATCTTAATATTACTTTCAACACAAATCTAATCATTCAAACAAAAATATAATATTCAATATTATAT
* *
40121 CTTAAAATATACAAATTATTATTACAATATAAAAAAACATACACGAGTCAAACCA
66 CTTAAAATATACAAATTATTATTACAATAT-AAAAAA-ATAAACGAATCAAACCA
* *
40176 ATCTTAATATTACTTTCAACACAAATCTAATCATTCAAACAAAAATATAATGTTCTATATTATAT
1 ATCTTAATATTACTTTCAACACAAATCTAATCATTCAAACAAAAATATAATATTCAATATTATAT
40241 CTTAAAATATACAAATTATTATTACAATATAAAAAAATAAACGAATCAAACCA
66 CTTAAAATATACAAATTATTATTACAATATAAAAAAATAAACGAATCAAACCA
*
40294 ATCTTAATATTACTTTCTAACACAAATCTAATCATTCAAGCAAAAATATAAT
1 ATCTTAATATTACTTTC-AACACAAATCTAATCATTCAAACAAAAATATAAT
40346 GTTGAATGCT
Statistics
Matches: 160, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
118 32 0.20
119 39 0.24
120 89 0.56
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.33
Consensus pattern (118 bp):
ATCTTAATATTACTTTCAACACAAATCTAATCATTCAAACAAAAATATAATATTCAATATTATAT
CTTAAAATATACAAATTATTATTACAATATAAAAAAATAAACGAATCAAACCA
Found at i:40412 original size:16 final size:15
Alignment explanation
Indices: 40391--40422 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
40381 ATTTAACACA
40391 AATCTAATCTAATAAT
1 AATCTAATCTAA-AAT
40407 AATCTAATCTAAAAT
1 AATCTAATCTAAAAT
40422 A
1 A
40423 TAAATAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (15 bp):
AATCTAATCTAAAAT
Found at i:44875 original size:2 final size:2
Alignment explanation
Indices: 44868--44906 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
44858 TGCAAGGGCT
44868 TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA T
44907 CCTGTTGGCG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:46071 original size:13 final size:12
Alignment explanation
Indices: 46053--46111 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 12
46043 TTAACGTTGC
46053 TTTTAAAAAGTAT
1 TTTTAAAAA-TAT
*
46066 TTTTAAAAAACAT
1 TTTT-AAAAATAT
*
46079 TTTGAAAAATCAT
1 TTTTAAAAAT-AT
* *
46092 TCTGAAAAATAT
1 TTTTAAAAATAT
46104 TTTTAAAA
1 TTTTAAAA
46112 CTTTTAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
12 13 0.34
13 20 0.53
14 5 0.13
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (12 bp):
TTTTAAAAATAT
Found at i:46639 original size:48 final size:48
Alignment explanation
Indices: 46564--46666 Score: 172
Period size: 48 Copynumber: 2.1 Consensus size: 48
46554 TTCAAATTCA
*
46564 ATTAAAATGCTAAAAGTCATAAGAAAAAA-TTTGATTTATCATTCTCTT
1 ATTAAAATGCTAAAAGTCATAAAAAAAAATTTTGA-TTATCATTCTCTT
*
46612 ATTAAAATGCTAAGAGTCATAAAAAAAAATTTTGATTATCATTCTCTT
1 ATTAAAATGCTAAAAGTCATAAAAAAAAATTTTGATTATCATTCTCTT
46660 ATTAAAA
1 ATTAAAA
46667 AAGATAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
48 47 0.90
49 5 0.10
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.37
Consensus pattern (48 bp):
ATTAAAATGCTAAAAGTCATAAAAAAAAATTTTGATTATCATTCTCTT
Found at i:49000 original size:21 final size:21
Alignment explanation
Indices: 48952--49000 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
48942 AATTAGATTT
* **
48952 ATTTA-AAGTAAAAATATTAA
1 ATTTATAATTAAAAATAGAAA
48972 ATTT-TAATTAAAAATAGAAA
1 ATTTATAATTAAAAATAGAAA
48992 ATTTATAAT
1 ATTTATAAT
49001 ATTAAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (21 bp):
ATTTATAATTAAAAATAGAAA
Found at i:50886 original size:6 final size:6
Alignment explanation
Indices: 50877--50902 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
50867 GGCTCCACCG
50877 ACCGAT ACCGAT ACCGAT ACCGAT AC
1 ACCGAT ACCGAT ACCGAT ACCGAT AC
50903 GATCACTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.35, G:0.15, T:0.15
Consensus pattern (6 bp):
ACCGAT
Found at i:53943 original size:20 final size:20
Alignment explanation
Indices: 53920--53963 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
53910 CTCAAACAAA
*
53920 AACCGTGAA-TCTCAAACTCG
1 AACCGTGAACCCT-AAACTCG
*
53940 AACCTTGAACCCTAAACTCG
1 AACCGTGAACCCTAAACTCG
53960 AACC
1 AACC
53964 TTAAACTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.36, C:0.34, G:0.11, T:0.18
Consensus pattern (20 bp):
AACCGTGAACCCTAAACTCG
Found at i:56926 original size:34 final size:34
Alignment explanation
Indices: 56879--56949 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
56869 GAAGAATGTA
56879 TAGATATCAATCATATACTCTTTCAACTTACCTT
1 TAGATATCAATCATATACTCTTTCAACTTACCTT
* *
56913 TAGATATCGATCATATTCTCTTTCAACTTACCTT
1 TAGATATCAATCATATACTCTTTCAACTTACCTT
56947 TAG
1 TAG
56950 CTCTCAGCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.42
Consensus pattern (34 bp):
TAGATATCAATCATATACTCTTTCAACTTACCTT
Found at i:63183 original size:5 final size:5
Alignment explanation
Indices: 63167--63220 Score: 60
Period size: 5 Copynumber: 11.0 Consensus size: 5
63157 TAAGATACTT
*
63167 TTAAA TTAAAA TTAAA TTAAA TTAAA TTATAA --AAA TAAAA TT-AA TTAAA
1 TTAAA TT-AAA TTAAA TTAAA TTAAA TTA-AA TTAAA TTAAA TTAAA TTAAA
63216 TTAAA
1 TTAAA
63221 ACTTTTCAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
3 2 0.05
4 5 0.12
5 29 0.67
6 7 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
TTAAA
Found at i:63205 original size:23 final size:23
Alignment explanation
Indices: 63174--63218 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
63164 CTTTTAAATT
*
63174 AAAATTAAATTAAATTAAATTATA
1 AAAATAAAATT-AATTAAATTATA
63198 AAAATAAAATTAATTAAATTA
1 AAAATAAAATTAATTAAATTA
63219 AAACTTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATAAAATTAATTAAATTATA
Found at i:64241 original size:21 final size:20
Alignment explanation
Indices: 64216--64259 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
64206 TAGGTTTTAG
*
64216 TATTTATTTATAATTAATAAT
1 TATTTAATTATAATTAA-AAT
*
64237 TATTTAATTATATTTAAAAT
1 TATTTAATTATAATTAAAAT
64257 TAT
1 TAT
64260 CAATATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTTAATTATAATTAAAAT
Found at i:67762 original size:21 final size:21
Alignment explanation
Indices: 67709--67763 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
67699 CCCGTTAACC
* *
67709 GTTGACCGTTGACTCTTGATA
1 GTTGACCGTTGACACTTGACA
* * * *
67730 ATTGATCATTGACAGTTGACA
1 GTTGACCGTTGACACTTGACA
67751 GTTGACCGTTGAC
1 GTTGACCGTTGAC
67764 CATTAATTTT
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (21 bp):
GTTGACCGTTGACACTTGACA
Found at i:74690 original size:20 final size:19
Alignment explanation
Indices: 74645--74699 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
74635 AAGCTCGAAT
*
74645 GACCCGACCCGAACCCGAC
1 GACCCAACCCGAACCCGAC
* *
74664 GACCCAACCCGAATCCGTC
1 GACCCAACCCGAACCCGAC
74683 GAACCCAACCCG-ACCCG
1 G-ACCCAACCCGAACCCG
74700 TTAACCATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 21 0.68
20 10 0.32
ACGTcount: A:0.27, C:0.51, G:0.18, T:0.04
Consensus pattern (19 bp):
GACCCAACCCGAACCCGAC
Found at i:75797 original size:17 final size:17
Alignment explanation
Indices: 75777--75810 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
75767 TTATATTATC
75777 TTATTATTATT-ATTTTG
1 TTATTATT-TTGATTTTG
75794 TTATTATTTTGATTTTG
1 TTATTATTTTGATTTTG
75811 GGTTTTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (17 bp):
TTATTATTTTGATTTTG
Found at i:75951 original size:12 final size:12
Alignment explanation
Indices: 75934--75960 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
75924 CTTTATATTA
75934 TATATTTATAAT
1 TATATTTATAAT
75946 TATATTTATAAT
1 TATATTTATAAT
75958 TAT
1 TAT
75961 GAAGGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATATTTATAAT
Found at i:76795 original size:23 final size:22
Alignment explanation
Indices: 76769--76846 Score: 84
Period size: 23 Copynumber: 3.4 Consensus size: 22
76759 GACAAACATA
76769 GAAGATTCTTTGCAATAAGCAGT
1 GAAGATTCTTTGCAATAA-CAGT
* * *
76792 GAAGATTCTTTGTAATGAAAAAT
1 GAAGATTCTTTGCAAT-AACAGT
* *
76815 AAAGATTCTCTGCAATAACCAGT
1 GAAGATTCTTTGCAATAA-CAGT
76838 GAAGATTCT
1 GAAGATTCT
76847 CTATAAAAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
22 2 0.05
23 40 0.91
24 2 0.05
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (22 bp):
GAAGATTCTTTGCAATAACAGT
Found at i:80345 original size:76 final size:76
Alignment explanation
Indices: 80219--80372 Score: 299
Period size: 76 Copynumber: 2.0 Consensus size: 76
80209 ATGGCCATGG
80219 GTGTTAAACCTGAAGTTGGGCATACCTGTCTCAGACACATTTCTGTATCAGACACTAACACTCAA
1 GTGTTAAACCTGAAGTTGGGCATACCTGTCTCAGACACATTTCTGTATCAGACACTAACACTCAA
80284 ATCGAAGTAAT
66 ATCGAAGTAAT
*
80295 GTGTTAAACCTGAAGTTGGGCATACCTGTCTCATACACATTTCTGTATCAGACACTAACACTCAA
1 GTGTTAAACCTGAAGTTGGGCATACCTGTCTCAGACACATTTCTGTATCAGACACTAACACTCAA
80360 ATCGAAGTAAT
66 ATCGAAGTAAT
80371 GT
1 GT
80373 AGGGAACTTC
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (76 bp):
GTGTTAAACCTGAAGTTGGGCATACCTGTCTCAGACACATTTCTGTATCAGACACTAACACTCAA
ATCGAAGTAAT
Found at i:88156 original size:43 final size:43
Alignment explanation
Indices: 88095--88180 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
88085 GTATTGATAA
88095 GTTTCTGTTTTTGTCACTTAACTAAAAAAATTACAATTTGGTC
1 GTTTCTGTTTTTGTCACTTAACTAAAAAAATTACAATTTGGTC
88138 GTTTCTGTTTTTGTCACTTAACTAAAAAAATTACAATTTGGTC
1 GTTTCTGTTTTTGTCACTTAACTAAAAAAATTACAATTTGGTC
88181 ACTTAACTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (43 bp):
GTTTCTGTTTTTGTCACTTAACTAAAAAAATTACAATTTGGTC
Found at i:96608 original size:42 final size:41
Alignment explanation
Indices: 96558--96640 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 41
96548 AATTTGTTTT
*
96558 CACTATAGTTTATTTAGGACTTCCTATTTTTAAATTCTAACA
1 CACTATAGTTTATTGAGGACTTCCTA-TTTTAAATTCTAACA
* *
96600 CACTATAGTTTATTGAGGACTTCTTATTTTCAATTCTAACA
1 CACTATAGTTTATTGAGGACTTCCTATTTTAAATTCTAACA
96641 ACAATTTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 14 0.37
42 24 0.63
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (41 bp):
CACTATAGTTTATTGAGGACTTCCTATTTTAAATTCTAACA
Found at i:99650 original size:4 final size:4
Alignment explanation
Indices: 99643--99673 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
99633 GGAAAAAGAA
99643 AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGG
1 AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGG
99674 ATAAAGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (4 bp):
AGGG
Found at i:102183 original size:16 final size:16
Alignment explanation
Indices: 102162--102194 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
102152 TCAAGCATGG
*
102162 TTTTTAATATTTTTTA
1 TTTTTAATATATTTTA
102178 TTTTTAATATATTTTA
1 TTTTTAATATATTTTA
102194 T
1 T
102195 AATTATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTAATATATTTTA
Found at i:104540 original size:21 final size:21
Alignment explanation
Indices: 104515--104557 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
104505 AAAATTTCAA
*
104515 TAAA-TAAAAATATATAATTAT
1 TAAATTAAAAA-ATATAAATAT
104536 TAAATTAAAAAATATAAATAT
1 TAAATTAAAAAATATAAATAT
104557 T
1 T
104558 TAAAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATTAAAAAATATAAATAT
Found at i:107408 original size:4 final size:4
Alignment explanation
Indices: 107378--107439 Score: 53
Period size: 4 Copynumber: 16.2 Consensus size: 4
107368 ACGATAGAAC
*
107378 AAAG AAA- AAA- AAAG AAA- AGAAG AAAAG AAAG AAAG AAAG -AAG GAAG
1 AAAG AAAG AAAG AAAG AAAG A-AAG -AAAG AAAG AAAG AAAG AAAG AAAG
*
107424 GAAG AAAG -AAG AAAG A
1 AAAG AAAG AAAG AAAG A
107440 GAATGATAGA
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
3 13 0.25
4 34 0.67
5 3 0.06
6 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:107436 original size:7 final size:7
Alignment explanation
Indices: 107373--107439 Score: 57
Period size: 7 Copynumber: 9.4 Consensus size: 7
107363 GACCAACGAT
*
107373 AGAACAA
1 AGAAGAA
*
107380 AGAAAAA
1 AGAAGAA
*
107387 AAAAGAAA
1 AGAAG-AA
107395 AGAAG-A
1 AGAAGAA
107401 A-AAGAA
1 AGAAGAA
107407 AGAAAGAA
1 AG-AAGAA
107415 AGAAGGAA
1 AGAA-GAA
*
107423 GGAAGAA
1 AGAAGAA
107430 AGAAGAA
1 AGAAGAA
107437 AGA
1 AGA
107440 GAATGATAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
5 3 0.06
6 4 0.08
7 23 0.47
8 19 0.39
ACGTcount: A:0.73, C:0.01, G:0.25, T:0.00
Consensus pattern (7 bp):
AGAAGAA
Found at i:107488 original size:13 final size:12
Alignment explanation
Indices: 107460--107484 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
107450 AATGTAATGT
107460 ATTTATTTTTAA
1 ATTTATTTTTAA
107472 ATTTATTTTTAA
1 ATTTATTTTTAA
107484 A
1 A
107485 ATTTTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTATTTTTAA
Found at i:109403 original size:43 final size:43
Alignment explanation
Indices: 109321--109405 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
109311 ATTAACATGT
* *
109321 TAAATTATATTACTTGACTAATGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTAATATTAATATGATTGCATGTTAC
* **
109364 TAAATTATATTACTTTACTCTTATTAATAT-ATTGACATGTTA
1 TAAATTATATTACTTGACTAATATTAATATGATTG-CATGTTA
109406 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTAATATTAATATGATTGCATGTTAC
Found at i:109890 original size:6 final size:6
Alignment explanation
Indices: 109876--109910 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
109866 AGCCAAAGCG
* *
109876 AGAGCA AGAGGA AGAGGA AGAGAA AGAGGA AGAGG
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGG
109911 CATTGGATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (6 bp):
AGAGGA
Found at i:109897 original size:18 final size:18
Alignment explanation
Indices: 109876--109910 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
109866 AGCCAAAGCG
*
109876 AGAGCAAGAGGAAGAGGA
1 AGAGAAAGAGGAAGAGGA
109894 AGAGAAAGAGGAAGAGG
1 AGAGAAAGAGGAAGAGG
109911 CATTGGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (18 bp):
AGAGAAAGAGGAAGAGGA
Found at i:110336 original size:7 final size:7
Alignment explanation
Indices: 110313--110434 Score: 62
Period size: 7 Copynumber: 17.6 Consensus size: 7
110303 TTCATACTTA
110313 TAAACCT
1 TAAACCT
110320 TAAACTCT
1 TAAAC-CT
110328 TAAACCT
1 TAAACCT
110335 TAAATCC-
1 TAAA-CCT
*
110342 TAAA-TT
1 TAAACCT
110348 TAAAACCT
1 T-AAACCT
*
110356 TAAATCT
1 TAAACCT
*
110363 TAAACCC
1 TAAACCT
*
110370 TAAA-AT
1 TAAACCT
*
110376 TAAAACT
1 TAAACCT
110383 TAAAACCCT
1 T-AAA-CCT
*
110392 T-AACCC
1 TAAACCT
110398 T-AACCT
1 TAAACCT
110404 TAAA-CT
1 TAAACCT
*
110410 ATAAA-TT
1 -TAAACCT
110417 TAAAGCC-
1 TAAA-CCT
110424 TAAACCT
1 TAAACCT
110431 TAAA
1 TAAA
110435 TTCAAAAACA
Statistics
Matches: 89, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
6 21 0.24
7 51 0.57
8 14 0.16
9 3 0.03
ACGTcount: A:0.47, C:0.23, G:0.01, T:0.30
Consensus pattern (7 bp):
TAAACCT
Found at i:110351 original size:28 final size:27
Alignment explanation
Indices: 110319--110400 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 27
110309 CTTATAAACC
* *
110319 TTAAACTCTTAAACCTTAAATCCTAAAT
1 TTAAAC-CTTAAACCTTAAACCCTAAAA
*
110347 TTAAAACCTTAAATCTTAAACCCTAAAA
1 TT-AAACCTTAAACCTTAAACCCTAAAA
*
110375 TTAAAACTTAAAACCCTT-AACCCTAA
1 TTAAACCTT-AAA-CCTTAAACCCTAA
110401 CCTTAAACTA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
27 6 0.13
28 33 0.72
29 7 0.15
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.30
Consensus pattern (27 bp):
TTAAACCTTAAACCTTAAACCCTAAAA
Found at i:112943 original size:24 final size:24
Alignment explanation
Indices: 112908--112954 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
112898 CCACCATACA
112908 TGGAGTTAGATCTTTATTTTCTAC
1 TGGAGTTAGATCTTTATTTTCTAC
*
112932 TGGAGTTGGATCTTTATTTTCTA
1 TGGAGTTAGATCTTTATTTTCTA
112955 TAAGTTCCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.11, G:0.19, T:0.51
Consensus pattern (24 bp):
TGGAGTTAGATCTTTATTTTCTAC
Found at i:113397 original size:4 final size:4
Alignment explanation
Indices: 113388--113481 Score: 88
Period size: 4 Copynumber: 24.0 Consensus size: 4
113378 AAACACACTA
* * * * *
113388 TCTT TCTT TCTT TC-T TCTT TTTT TCCTC TCCT TC-T TCAT TCCT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT T-CTT TCTT TCTT TCTT TCTT TCTT
*
113435 TCTT TCTT TCTT T-TT T-TT TCTTT TTTT TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TC-TT TCTT TCTT TCTT TCTT TCTT TCTT
113482 CTTATGTCCG
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
3 12 0.16
4 59 0.78
5 5 0.07
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:113473 original size:39 final size:40
Alignment explanation
Indices: 113388--113481 Score: 120
Period size: 39 Copynumber: 2.4 Consensus size: 40
113378 AAACACACTA
113388 TCTTTCTTTCTTTC-TTCTTTTTTTCCTCTCCTTCTTCAT
1 TCTTTCTTTCTTTCTTTCTTTTTTTCCTCTCCTTCTTCAT
* * ** * *
113427 TCCTTCTTTCTTTCTTTCTTTTTTT-TTCTTTTTTTTCTT
1 TCTTTCTTTCTTTCTTTCTTTTTTTCCTCTCCTTCTTCAT
113466 TCTTTCTTTCTTTCTT
1 TCTTTCTTTCTTTCTT
113482 CTTATGTCCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 37 0.79
40 10 0.21
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (40 bp):
TCTTTCTTTCTTTCTTTCTTTTTTTCCTCTCCTTCTTCAT
Found at i:116148 original size:15 final size:14
Alignment explanation
Indices: 116120--116148 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
116110 TACAGACGCA
116120 TAAAAAACTATTTT
1 TAAAAAACTATTTT
116134 TAAAAAACTATTTT
1 TAAAAAACTATTTT
116148 T
1 T
116149 GTGGAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAAAAACTATTTT
Found at i:133681 original size:18 final size:18
Alignment explanation
Indices: 133658--133694 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
133648 AAATAAAGTG
* *
133658 TGTATAATAATATTAAAA
1 TGTATAAAAATATCAAAA
133676 TGTATAAAAATATCAAAA
1 TGTATAAAAATATCAAAA
133694 T
1 T
133695 AAAGCTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (18 bp):
TGTATAAAAATATCAAAA
Found at i:135472 original size:18 final size:20
Alignment explanation
Indices: 135436--135477 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
135426 ATTAAGGTAA
135436 TAAAGTGTACACAATTAAAT
1 TAAAGTGTACACAATTAAAT
*
135456 TAAATTGTACA-AA-TAAAT
1 TAAAGTGTACACAATTAAAT
135474 TAAA
1 TAAA
135478 ATAAAGTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 2 0.10
20 10 0.48
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (20 bp):
TAAAGTGTACACAATTAAAT
Found at i:136181 original size:18 final size:18
Alignment explanation
Indices: 136150--136226 Score: 52
Period size: 18 Copynumber: 4.2 Consensus size: 18
136140 TAATTATTTA
**
136150 AAAATTATCGAAAAATAT
1 AAAATTATTTAAAAATAT
136168 AAAATTATTTAAAAATGAAT
1 AAAATTATTTAAAAAT--AT
*
136188 AAGAATTA--TAAGAATATAA
1 AA-AATTATTTAA-AA-ATAT
*
136207 AAAATTATTAAAAAAT-T
1 AAAATTATTTAAAAATAT
136224 AAA
1 AAA
136227 GATAATTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 15
0.70 0.07 0.22
Matches are distributed among these distances:
17 3 0.06
18 21 0.45
19 8 0.17
20 8 0.17
21 7 0.15
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAATTATTTAAAAATAT
Found at i:142413 original size:97 final size:95
Alignment explanation
Indices: 142224--142414 Score: 240
Period size: 98 Copynumber: 2.0 Consensus size: 95
142214 TTCATTTAAT
* * *
142224 TCAATCAATTATTTAATAAAAAAATATTTACCGTAAAAATATTAAATCCAATAAATCATATTTAA
1 TCAATCAATTATTTAAAAAAAAAATATTTACCATAAAAATACTAAATCCAATAAATCATATTTAA
*
142289 TAAATTTATCTAAATTAATCTATTATTTAC
66 TAAAGTTATCTAAATTAATCTATTATTTAC
* * ** ** *
142319 TCAATCAATTATTTATGAAAAAAAAAATGTTTACCATAAAATTACTAAATTTAATCCATCGTATT
1 TCAATCAATTA-TT-T-AAAAAAAAAATATTTACCATAAAAATACTAAATCCAATAAATCATATT
*
142384 TAAT-AAGTTATCTAAATTAATTTATTATTTA
63 TAATAAAGTTATCTAAATTAATCTATTATTTA
142415 TTAAATATGA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
95 11 0.14
96 2 0.02
97 26 0.32
98 42 0.52
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.41
Consensus pattern (95 bp):
TCAATCAATTATTTAAAAAAAAAATATTTACCATAAAAATACTAAATCCAATAAATCATATTTAA
TAAAGTTATCTAAATTAATCTATTATTTAC
Found at i:145567 original size:33 final size:33
Alignment explanation
Indices: 145541--145606 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
145531 AAACGTATGT
145541 CAAATCAGAATATCATATTTTCAAAACATATAC
1 CAAATCAGAATATCATATTTTCAAAACATATAC
* *
145574 CAGATCAGAATATCATATTTTTAAGAACATATA
1 CAAATCAGAATATCATATTTTCAA-AACATATA
145607 TTATATCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 22 0.73
34 8 0.27
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (33 bp):
CAAATCAGAATATCATATTTTCAAAACATATAC
Done.