Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013225.1 Kokia drynarioides strain JFW-HI SEQ_128244, 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: 147328
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:906 original size:18 final size:16
Alignment explanation
Indices: 885--921 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
875 TGATAATTTC
885 AAATAAAATAATAAAATA
1 AAATAAAAT-A-AAAATA
903 AAATAAAATAAAAATA
1 AAATAAAATAAAAATA
919 AAA
1 AAA
922 CAAGTTCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 1 0.05
18 9 0.47
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
AAATAAAATAAAAATA
Found at i:918 original size:6 final size:5
Alignment explanation
Indices: 885--921 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
875 TGATAATTTC
885 AAATA AAAT- -AATA AAATA AAATA AAATAA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAAT-A AAATA AAA
922 CAAGTTCCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 3 0.10
5 21 0.72
6 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:2857 original size:23 final size:23
Alignment explanation
Indices: 2829--2875 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2819 CTTATTATTG
2829 ATATTGAGGGTCAAGGTACCAAT
1 ATATTGAGGGTCAAGGTACCAAT
2852 ATATTGAGGGTCAAGGTACCAAT
1 ATATTGAGGGTCAAGGTACCAAT
2875 A
1 A
2876 CATGCCTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.26
Consensus pattern (23 bp):
ATATTGAGGGTCAAGGTACCAAT
Found at i:4084 original size:16 final size:15
Alignment explanation
Indices: 4063--4096 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
4053 CCATCCTAAT
4063 CATTGCTTGATTTAAG
1 CATTGCTTGATTT-AG
4079 CATTGCTTGATTTAG
1 CATTGCTTGATTTAG
4094 CAT
1 CAT
4097 GATTGAATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.44
Consensus pattern (15 bp):
CATTGCTTGATTTAG
Found at i:9732 original size:16 final size:16
Alignment explanation
Indices: 9701--9730 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9691 AATAAGACCA
9701 ATAGATATTTTCAAAT
1 ATAGATATTTTCAAAT
9717 ATAGATA-TTTCAAA
1 ATAGATATTTTCAAA
9731 ATTTATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (16 bp):
ATAGATATTTTCAAAT
Found at i:9997 original size:18 final size:18
Alignment explanation
Indices: 9974--10008 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9964 TAAATTATTT
* *
9974 AAAAATTTTGTAAAAATA
1 AAAAATATTATAAAAATA
9992 AAAAATATTATAAAAAT
1 AAAAATATTATAAAAAT
10009 TTTAAAAAAT
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:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAAATATTATAAAAATA
Found at i:10016 original size:28 final size:31
Alignment explanation
Indices: 9969--10032 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
9959 TTATTTAAAT
*
9969 TATT-TAAAAATTTTGTAAAAA-T-AAAAAA
1 TATTATAAAAATTTTGAAAAAATTAAAAAAA
9997 TATTATAAAAATTTT-AAAAAATTCAAAAAAA
1 TATTATAAAAATTTTGAAAAAATT-AAAAAAA
10028 TATTA
1 TATTA
10033 AAAGTTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 9 0.29
29 11 0.35
31 11 0.35
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (31 bp):
TATTATAAAAATTTTGAAAAAATTAAAAAAA
Found at i:11641 original size:12 final size:12
Alignment explanation
Indices: 11626--11685 Score: 84
Period size: 12 Copynumber: 5.0 Consensus size: 12
11616 AAATGAGTCA
11626 ATAAACGAGCTT
1 ATAAACGAGCTT
*
11638 ATAAATGAGCTT
1 ATAAACGAGCTT
*
11650 TTAAACGAGCTT
1 ATAAACGAGCTT
*
11662 ATAAATGAGCTT
1 ATAAACGAGCTT
*
11674 TTAAACGAGCTT
1 ATAAACGAGCTT
11686 GTTCATGAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:11641 original size:24 final size:24
Alignment explanation
Indices: 11614--11685 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
11604 TCATTAATAA
11614 ATAAATGAG-TCAATAAACGAGCTT
1 ATAAATGAGCT-AATAAACGAGCTT
**
11638 ATAAATGAGCTTTTAAACGAGCTT
1 ATAAATGAGCTAATAAACGAGCTT
**
11662 ATAAATGAGCTTTTAAACGAGCTT
1 ATAAATGAGCTAATAAACGAGCTT
11686 GTTCATGAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
24 44 0.98
25 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (24 bp):
ATAAATGAGCTAATAAACGAGCTT
Found at i:11693 original size:24 final size:24
Alignment explanation
Indices: 11627--11685 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
11617 AATGAGTCAA
11627 TAAACGAGCTTATAAATGAGCTTT
1 TAAACGAGCTTATAAATGAGCTTT
11651 TAAACGAGCTTATAAATGAGCTTT
1 TAAACGAGCTTATAAATGAGCTTT
11675 TAAACGAGCTT
1 TAAACGAGCTT
11686 GTTCATGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (24 bp):
TAAACGAGCTTATAAATGAGCTTT
Found at i:18766 original size:18 final size:18
Alignment explanation
Indices: 18726--18768 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
18716 ATAAGTATAA
*
18726 AAATTACCCGAATTAATC
1 AAATTAACCGAATTAATC
* **
18744 GAATTAACCGAATTTCTC
1 AAATTAACCGAATTAATC
18762 AAATTAA
1 AAATTAA
18769 AAAATTAACC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (18 bp):
AAATTAACCGAATTAATC
Found at i:20849 original size:18 final size:17
Alignment explanation
Indices: 20828--20882 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
20818 TTTTAAAAGA
20828 TATATTAATTAATAATAT
1 TATATTAA-TAATAATAT
*
20846 TATAATAAATAATAATAT
1 TAT-ATTAATAATAATAT
*
20864 TTTATT-AT-ATAATAT
1 TATATTAATAATAATAT
20879 TATA
1 TATA
20883 AAATATAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 10 0.31
16 2 0.06
17 2 0.06
18 14 0.44
19 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATATTAATAATAATAT
Found at i:20888 original size:15 final size:15
Alignment explanation
Indices: 20839--20890 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
20829 ATATTAATTA
20839 ATAATATTATAATAAAT
1 ATAATATTAT-A-AAAT
* **
20856 AATAATATTTTATTAT
1 -ATAATATTATAAAAT
20872 ATAATATTATAAAAT
1 ATAATATTATAAAAT
20887 ATAA
1 ATAA
20891 GAAAAGAAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 16 0.57
16 2 0.07
17 1 0.04
18 9 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATATTATAAAAT
Found at i:24402 original size:2 final size:2
Alignment explanation
Indices: 24395--24419 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24385 AGGAAGATCG
24395 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
24420 CTTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24650 original size:2 final size:2
Alignment explanation
Indices: 24643--24668 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24633 TATTTATAAC
24643 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
24669 AGTAGCTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29481 original size:30 final size:29
Alignment explanation
Indices: 29447--29550 Score: 106
Period size: 29 Copynumber: 3.6 Consensus size: 29
29437 ATTTTCGAGG
29447 AATTTGAGGGTCAAAATTAAATTTTTTGGA
1 AATTTGAGGGTCAAAATTAAA-TTTTTGGA
* *
29477 AATTTG-GGGATTAAAATTAAACTTTTGGA
1 AATTTGAGGG-TCAAAATTAAATTTTTGGA
* * *
29506 AATTTGAGGTTAAAAATGT-GATTTTTGGA
1 AATTTGAGGGTCAAAAT-TAAATTTTTGGA
*
29535 AATTT-AGGGGCAAAAT
1 AATTTGAGGGTCAAAAT
29551 GGTAATTTTG
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
28 8 0.13
29 35 0.56
30 19 0.31
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTGAGGGTCAAAATTAAATTTTTGGA
Found at i:29558 original size:29 final size:29
Alignment explanation
Indices: 29429--29559 Score: 83
Period size: 29 Copynumber: 4.4 Consensus size: 29
29419 ATTCGAGATG
* * **
29429 AAAATGTAATTTTCGAGGAATTTGAGGGTC
1 AAAATGTAATTTTTG-GAAATTTGAGGGGA
29459 AAAAT-TAAATTTTTTGGAAATTT--GGGGA
1 AAAATGT-AA-TTTTTGGAAATTTGAGGGGA
* **
29487 TTAAAAT-TAAACTTTTGGAAATTTGAGGTTA
1 --AAAATGT-AATTTTTGGAAATTTGAGGGGA
* *
29518 AAAATGTGATTTTTGGAAATTT-AGGGGC
1 AAAATGTAATTTTTGGAAATTTGAGGGGA
29546 AAAATGGTAATTTT
1 AAAAT-GTAATTTT
29560 GGATGTTTGG
Statistics
Matches: 80, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
28 11 0.14
29 38 0.47
30 23 0.29
31 8 0.10
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAATTTGAGGGGA
Found at i:29572 original size:28 final size:28
Alignment explanation
Indices: 29541--29605 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
29531 TGGAAATTTA
* * *
29541 GGGGCAAAATGGTAATTT-TGGATGTTT
1 GGGGGAAAATAGTAATTTCTAGATGTTT
*
29568 GGGGGTAAATAGTAATTTCTAGATGTTT
1 GGGGGAAAATAGTAATTTCTAGATGTTT
*
29596 GGGGTAAAAT
1 GGGGGAAAAT
29606 CATAGTTTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.29, C:0.03, G:0.32, T:0.35
Consensus pattern (28 bp):
GGGGGAAAATAGTAATTTCTAGATGTTT
Found at i:29582 original size:27 final size:27
Alignment explanation
Indices: 29547--29603 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
29537 TTTAGGGGCA
* *
29547 AAATGGTAATTT-TGGATGTTTGGGGGT
1 AAATAGTAATTTCTAGATGTTT-GGGGT
29574 AAATAGTAATTTCTAGATGTTTGGGGT
1 AAATAGTAATTTCTAGATGTTTGGGGT
29601 AAA
1 AAA
29604 ATCATAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.30, T:0.39
Consensus pattern (27 bp):
AAATAGTAATTTCTAGATGTTTGGGGT
Found at i:29646 original size:30 final size:30
Alignment explanation
Indices: 29611--29764 Score: 154
Period size: 30 Copynumber: 5.1 Consensus size: 30
29601 AAAATCATAG
*
29611 TTTTGGAGAAGTTTAGAGGTTAAAATGTAA
1 TTTTAGAGAAGTTTAGAGGTTAAAATGTAA
* * *
29641 TTTTGGA-AATGTTTAGGGGGTTAAATTGTAA
1 TTTTAGAGAA-GTTTA-GAGGTTAAAATGTAA
* *
29672 TTTTAAAGAAGTTTAG-TGTTAAAATGTAA
1 TTTTAGAGAAGTTTAGAGGTTAAAATGTAA
* *
29701 TTTTAGAAAAGTTGA-AGGGTTAAAATGTAA
1 TTTTAGAGAAGTTTAGA-GGTTAAAATGTAA
* *
29731 TTTTAGAAAAGTTT-GATGGTTAAAATGTGA
1 TTTTAGAGAAGTTTAGA-GGTTAAAATGTAA
29761 TTTT
1 TTTT
29765 GGGAAAGTTT
Statistics
Matches: 105, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
29 25 0.24
30 55 0.52
31 23 0.22
32 2 0.02
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.40
Consensus pattern (30 bp):
TTTTAGAGAAGTTTAGAGGTTAAAATGTAA
Found at i:29703 original size:60 final size:61
Alignment explanation
Indices: 29617--29778 Score: 199
Period size: 60 Copynumber: 2.7 Consensus size: 61
29607 ATAGTTTTGG
* *
29617 AGAAGTTTAGAGGTTAAAATGTAATTTTGGAAATGTTTAGGGGGTTAAATTGTAATTTTA-A
1 AGAAGTTTAGATGTTAAAATGTAATTTTGGAAA-GTTTAGGGGGTTAAAATGTAATTTTAGA
* * *
29678 AGAAGTTTAG-TGTTAAAATGTAATTTTAGAAAAGTTGA-AGGGTTAAAATGTAATTTTAGA
1 AGAAGTTTAGATGTTAAAATGTAATTTT-GGAAAGTTTAGGGGGTTAAAATGTAATTTTAGA
*
29738 A-AAGTTT-GATGGTTAAAATGTGATTTTGGGAAAGTTTAGGG
1 AGAAGTTTAGAT-GTTAAAATGTAATTTT-GGAAAGTTTAGGG
29779 ACTACCTGGA
Statistics
Matches: 86, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
58 1 0.01
59 25 0.29
60 45 0.52
61 15 0.17
ACGTcount: A:0.37, C:0.00, G:0.25, T:0.38
Consensus pattern (61 bp):
AGAAGTTTAGATGTTAAAATGTAATTTTGGAAAGTTTAGGGGGTTAAAATGTAATTTTAGA
Found at i:36331 original size:30 final size:30
Alignment explanation
Indices: 36297--36354 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
36287 AGTTTTAAAA
*
36297 ACAATTTAAAAACCCTAATTTTCTTTAAGG
1 ACAATTTAAAAACCATAATTTTCTTTAAGG
36327 ACAATTTAAAAACCATAATTTTCTTTAA
1 ACAATTTAAAAACCATAATTTTCTTTAA
36355 AAACCCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (30 bp):
ACAATTTAAAAACCATAATTTTCTTTAAGG
Found at i:37083 original size:26 final size:26
Alignment explanation
Indices: 37044--37132 Score: 108
Period size: 26 Copynumber: 3.3 Consensus size: 26
37034 AACTAAACCG
*
37044 TTGACTTGATCGTTGATCGTTGACCA
1 TTGACTTGACCGTTGATCGTTGACCA
*
37070 TTGACTTGACCGTTGATTGTTGACCA
1 TTGACTTGACCGTTGATCGTTGACCA
* *
37096 TTGACCATTG-CCTGTTCATCGTTGACTA
1 TTGA-C-TTGACC-GTTGATCGTTGACCA
37124 TTGACTTGA
1 TTGACTTGA
37133 TCGTGACTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
26 31 0.57
27 4 0.07
28 19 0.35
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.39
Consensus pattern (26 bp):
TTGACTTGACCGTTGATCGTTGACCA
Found at i:40547 original size:37 final size:37
Alignment explanation
Indices: 40497--40573 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
40487 AGTTGTCTGC
* *
40497 ACACGACCGTGTGCCCTTATTTCACACA-GAAGCTGGG
1 ACACGACCATGTGCCCCTATTTCACACATG-AGCTGGG
*
40534 ACACGACCATGTGCCCCTATTTCACATATGAGCTGGG
1 ACACGACCATGTGCCCCTATTTCACACATGAGCTGGG
40571 ACA
1 ACA
40574 ACTCACACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 35 0.97
38 1 0.03
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (37 bp):
ACACGACCATGTGCCCCTATTTCACACATGAGCTGGG
Found at i:48403 original size:10 final size:10
Alignment explanation
Indices: 48388--48412 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
48378 ACTTTGCTCA
48388 AAAAAGAAAG
1 AAAAAGAAAG
48398 AAAAAGAAAG
1 AAAAAGAAAG
48408 AAAAA
1 AAAAA
48413 ATGGCCGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:52297 original size:22 final size:22
Alignment explanation
Indices: 52244--52297 Score: 54
Period size: 25 Copynumber: 2.3 Consensus size: 22
52234 ATTCAATATA
*
52244 AATATTTTAAAATAAAAAGAAT
1 AATATTCTAAAATAAAAAGAAT
* *
52266 AATTAAATTCTAAAATGAAAATAAT
1 AA-T--ATTCTAAAATAAAAAGAAT
52291 AATATTC
1 AATATTC
52298 ATTTTAATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
22 6 0.23
23 1 0.04
24 1 0.04
25 18 0.69
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (22 bp):
AATATTCTAAAATAAAAAGAAT
Found at i:54778 original size:25 final size:25
Alignment explanation
Indices: 54746--54825 Score: 91
Period size: 25 Copynumber: 3.4 Consensus size: 25
54736 TATAATTTTT
54746 AAGTTAAAATTTTTATCATTTTTAA
1 AAGTTAAAATTTTTATCATTTTTAA
* *
54771 AAGTTAAAA-ATGTA--ATTTTT--
1 AAGTTAAAATTTTTATCATTTTTAA
54791 AAGTTAAAATTTTTATCATTTTTAA
1 AAGTTAAAATTTTTATCATTTTTAA
54816 GAA-TTAAAAT
1 -AAGTTAAAAT
54826 ATAATTTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
20 9 0.20
21 3 0.07
22 6 0.13
23 6 0.13
24 3 0.07
25 16 0.36
26 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (25 bp):
AAGTTAAAATTTTTATCATTTTTAA
Found at i:54796 original size:20 final size:20
Alignment explanation
Indices: 54730--54799 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 20
54720 TTAAAGATAA
54730 TAAAAATATAATTTTTAAGT
1 TAAAAATATAATTTTTAAGT
* *
54750 TAAAATTTTTATCATTTTTAAAAGT
1 TAAAA---ATATAATTTTT--AAGT
*
54775 TAAAAATGTAATTTTTAAGT
1 TAAAAATATAATTTTTAAGT
54795 TAAAA
1 TAAAA
54800 TTTTTATCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
20 14 0.35
22 8 0.20
23 9 0.22
25 9 0.22
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (20 bp):
TAAAAATATAATTTTTAAGT
Found at i:54847 original size:45 final size:45
Alignment explanation
Indices: 54730--54833 Score: 176
Period size: 45 Copynumber: 2.3 Consensus size: 45
54720 TTAAAGATAA
54730 TAAAAATATAATTTTTAAGTTAAAATTTTTATCATTTTTAAAAGT
1 TAAAAATATAATTTTTAAGTTAAAATTTTTATCATTTTTAAAAGT
*
54775 TAAAAATGTAATTTTTAAGTTAAAATTTTTATCATTTTTAAGAA-T
1 TAAAAATATAATTTTTAAGTTAAAATTTTTATCATTTTTAA-AAGT
54820 T-AAAATATAATTTT
1 TAAAAATATAATTTT
54834 ATTTTTATTA
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
44 12 0.21
45 42 0.75
46 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (45 bp):
TAAAAATATAATTTTTAAGTTAAAATTTTTATCATTTTTAAAAGT
Found at i:63879 original size:6 final size:7
Alignment explanation
Indices: 63862--63887 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
63852 AAATATATTA
63862 AAAAATT
1 AAAAATT
63869 AAAAATT
1 AAAAATT
63876 AAAAATT
1 AAAAATT
63883 AAAAA
1 AAAAA
63888 CAATACATGA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAAATT
Found at i:65196 original size:39 final size:40
Alignment explanation
Indices: 65104--65196 Score: 143
Period size: 40 Copynumber: 2.4 Consensus size: 40
65094 AGTCGTGCGA
*
65104 TGTTTACAGTGTCACCGCCAGTTCAAAATAGCAATCGTAG
1 TGTTTACAGTGTCACCGCCAGTTCAAAATAGCAATCGCAG
* * *
65144 TGTTTACAGTGTCACTGCCAGTTCAACATAGCTA-CGCAG
1 TGTTTACAGTGTCACCGCCAGTTCAAAATAGCAATCGCAG
65183 TGTTTACAGTGTCA
1 TGTTTACAGTGTCA
65197 TTGCTAGCTC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 18 0.37
40 31 0.63
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (40 bp):
TGTTTACAGTGTCACCGCCAGTTCAAAATAGCAATCGCAG
Found at i:65248 original size:39 final size:39
Alignment explanation
Indices: 65142--65284 Score: 109
Period size: 39 Copynumber: 3.7 Consensus size: 39
65132 TAGCAATCGT
* *
65142 AGTGTTTACAGTGTCACTGCCAGTTCA--ACA-TAGCTACGC
1 AGTGTTTACAGTGTCACTGTCAGTTCAGTACATTA-TTA--C
* *
65181 AGTGTTTACAGTGTCATTG-CTAGCTCAGTACATTATTAC
1 AGTGTTTACAGTGTCACTGTC-AGTTCAGTACATTATTAC
* * *
65220 AGTGTTTACAGTGTCACCGTCAGTTCAGT--ATTGGTTTGC
1 AGTGTTTACAGTGTCACTGTCAGTTCAGTACATT--ATTAC
* *
65259 AATGTTTACAGTGTCACTGTCGGTTC
1 AGTGTTTACAGTGTCACTGTCAGTTC
65285 GATACAATAT
Statistics
Matches: 86, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
37 3 0.03
38 1 0.01
39 74 0.86
40 1 0.01
41 5 0.06
42 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (39 bp):
AGTGTTTACAGTGTCACTGTCAGTTCAGTACATTATTAC
Found at i:65265 original size:78 final size:78
Alignment explanation
Indices: 65142--65348 Score: 211
Period size: 78 Copynumber: 2.7 Consensus size: 78
65132 TAGCAATCGT
* * ** * * ** * *
65142 AGTGTTTACAGTGTCACTGCCAGTTCAACATAGCTACGCAGTGTTTACAGTGTCATTG-CTAGCT
1 AGTGTTTACAGTGTCACCGTCAGTTCAGTATTGGTTTGCAATGTTTACAGTGTCACTGTC-AGCT
*
65206 C-AGTACATTATTAC
65 CGA-TACAATATTAC
* *
65220 AGTGTTTACAGTGTCACCGTCAGTTCAGTATTGGTTTGCAATGTTTACAGTGTCACTGTCGGTTC
1 AGTGTTTACAGTGTCACCGTCAGTTCAGTATTGGTTTGCAATGTTTACAGTGTCACTGTCAGCTC
*
65285 GATACAATATTAT
66 GATACAATATTAC
* * * * *
65298 GGTGTTTATAGTATCACCATAAGTTCAGTATTGGTTTGCAATGTTTACAGT
1 AGTGTTTACAGTGTCACCGTCAGTTCAGTATTGGTTTGCAATGTTTACAGT
65349 TTTACGATGT
Statistics
Matches: 108, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
78 106 0.98
79 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (78 bp):
AGTGTTTACAGTGTCACCGTCAGTTCAGTATTGGTTTGCAATGTTTACAGTGTCACTGTCAGCTC
GATACAATATTAC
Found at i:67701 original size:17 final size:17
Alignment explanation
Indices: 67681--67716 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
67671 TTTTTTCAAA
67681 AATAAATTTTCAACAAT
1 AATAAATTTTCAACAAT
* *
67698 AATAACTTTTTAACAAT
1 AATAAATTTTCAACAAT
67715 AA
1 AA
67717 AATAATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAAATTTTCAACAAT
Found at i:75375 original size:21 final size:21
Alignment explanation
Indices: 75321--75380 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
75311 AATAGTTCAG
*
75321 ACTTCTACCAATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
* * * *
75342 AATTTTACTGATACAAGTGTC
1 ACTTCTACCGATACAAGTGAC
* *
75363 TCTTCTACCGATATAAGT
1 ACTTCTACCGATACAAGT
75381 CTTACTTCTT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:81650 original size:21 final size:21
Alignment explanation
Indices: 81624--81673 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
81614 CATGCTTGTT
*
81624 TCAGTAGAGCTCTTGCATGTA
1 TCAGTAGAGATCTTGCATGTA
81645 TCAGTAGAGATCTTGCATGTA
1 TCAGTAGAGATCTTGCATGTA
81666 TCAGTAGA
1 TCAGTAGA
81674 AGTACAGAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (21 bp):
TCAGTAGAGATCTTGCATGTA
Found at i:84609 original size:20 final size:20
Alignment explanation
Indices: 84586--84627 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
84576 AAAATTAAAA
*
84586 AAATTATGAATAATTTTAGC
1 AAATTATGAATAATCTTAGC
84606 AAATTATGAATAATCTTAGC
1 AAATTATGAATAATCTTAGC
84626 AA
1 AA
84628 TTTTTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.36
Consensus pattern (20 bp):
AAATTATGAATAATCTTAGC
Found at i:96009 original size:31 final size:31
Alignment explanation
Indices: 95971--96033 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
95961 TTCATCTCAA
* * *
95971 TTAAATATTGATTTTTAGATTTTAGTTTGAG
1 TTAAATATTAATTTTTAGATGTTAATTTGAG
96002 TTAAATATTAATTTTTAGATGTTAATTTGAG
1 TTAAATATTAATTTTTAGATGTTAATTTGAG
96033 T
1 T
96034 CTTATTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (31 bp):
TTAAATATTAATTTTTAGATGTTAATTTGAG
Found at i:96768 original size:18 final size:17
Alignment explanation
Indices: 96745--96779 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
96735 ATTTTTTTTT
*
96745 TATTTTGATATATTTATA
1 TATTTTAATAT-TTTATA
96763 TATTTTAATATTTTATA
1 TATTTTAATATTTTATA
96780 GAATAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:102333 original size:19 final size:19
Alignment explanation
Indices: 102282--102323 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
102272 ACGAATAATA
* *
102282 AAAATAACATATAATAAAAT
1 AAAATAATATAT-TTAAAAT
102302 AAAATAATATATTTAAAAT
1 AAAATAATATATTTAAAAT
102321 AAA
1 AAA
102324 TTATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAATATATTTAAAAT
Found at i:102815 original size:58 final size:58
Alignment explanation
Indices: 102724--102847 Score: 212
Period size: 58 Copynumber: 2.1 Consensus size: 58
102714 TATTATATTT
* *
102724 AAATTATATAATTTCTTTTTTATTGATCGATGTAATCGTGTAGTGGACGTTGCCCTCCA
1 AAATTA-ATAATTTCCTTTTCATTGATCGATGTAATCGTGTAGTGGACGTTGCCCTCCA
102783 AAATTAATAATTTCCTTTTCATTGATCGATGTAATCGTGTAGTGGACGTTGCCCTCCA
1 AAATTAATAATTTCCTTTTCATTGATCGATGTAATCGTGTAGTGGACGTTGCCCTCCA
*
102841 AGATTAA
1 AAATTAA
102848 CACAGTAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
58 56 0.90
59 6 0.10
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (58 bp):
AAATTAATAATTTCCTTTTCATTGATCGATGTAATCGTGTAGTGGACGTTGCCCTCCA
Found at i:107133 original size:21 final size:21
Alignment explanation
Indices: 107059--107127 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
107049 AGTAGCAGAC
107059 TTCTACATATACTTGTAATGG
1 TTCTACATATACTTGTAATGG
* **
107080 TTCTACCA-ATACAAATGT-A-CC
1 TTCTA-CATATAC--TTGTAATGG
107101 TTCTACATATACTTGTAATGG
1 TTCTACATATACTTGTAATGG
107122 TTCTAC
1 TTCTAC
107128 CAATACAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
19 3 0.08
20 3 0.08
21 24 0.67
22 3 0.08
23 3 0.08
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.39
Consensus pattern (21 bp):
TTCTACATATACTTGTAATGG
Found at i:107146 original size:21 final size:21
Alignment explanation
Indices: 107080--107154 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
107070 CTTGTAATGG
107080 TTCTACCAATACAAATGTACC
1 TTCTACCAATACAAATGTACC
* **
107101 TTCTA-CATATAC--TTGTAATGG
1 TTCTACCA-ATACAAATGT-A-CC
107122 TTCTACCAATACAAATGTACC
1 TTCTACCAATACAAATGTACC
*
107143 TTCTACTAATAC
1 TTCTACCAATAC
107155 TCGACATACT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
19 3 0.07
20 3 0.07
21 29 0.71
22 3 0.07
23 3 0.07
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.35
Consensus pattern (21 bp):
TTCTACCAATACAAATGTACC
Found at i:107155 original size:42 final size:42
Alignment explanation
Indices: 107058--107148 Score: 182
Period size: 42 Copynumber: 2.2 Consensus size: 42
107048 CAGTAGCAGA
107058 CTTCTACATATACTTGTAATGGTTCTACCAATACAAATGTAC
1 CTTCTACATATACTTGTAATGGTTCTACCAATACAAATGTAC
107100 CTTCTACATATACTTGTAATGGTTCTACCAATACAAATGTAC
1 CTTCTACATATACTTGTAATGGTTCTACCAATACAAATGTAC
107142 CTTCTAC
1 CTTCTAC
107149 TAATACTCGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (42 bp):
CTTCTACATATACTTGTAATGGTTCTACCAATACAAATGTAC
Found at i:107168 original size:42 final size:42
Alignment explanation
Indices: 107058--107175 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
107048 CAGTAGCAGA
* **
107058 CTTCTACATATACTTGTAATGGTTCTACCAATACAAATGTAC
1 CTTCTACATATACTCGTAATACTTCTACCAATACAAATGTAC
* **
107100 CTTCTACATATACTTGTAATGGTTCTACCAATACAAATGTAC
1 CTTCTACATATACTCGTAATACTTCTACCAATACAAATGTAC
*
107142 CTTCTAC-TAATACTCG-ACATACTTCTACCTATAC
1 CTTCTACAT-ATACTCGTA-ATACTTCTACCAATAC
107176 TAAAAACTCT
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
41 2 0.03
42 68 0.97
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.36
Consensus pattern (42 bp):
CTTCTACATATACTCGTAATACTTCTACCAATACAAATGTAC
Found at i:107868 original size:18 final size:18
Alignment explanation
Indices: 107847--107937 Score: 105
Period size: 18 Copynumber: 5.1 Consensus size: 18
107837 AAGAAATTAA
*
107847 CTCTTACGAGCCAATATG
1 CTCTAACGAGCCAATATG
* * *
107865 CTCTAATGAGCTAGTATG
1 CTCTAACGAGCCAATATG
*
107883 CT-TAAACGAGCCAGTATG
1 CTCT-AACGAGCCAATATG
107901 CTC-AACGAGCCAATATG
1 CTCTAACGAGCCAATATG
*
107918 CTCAAACGAGCCAATATG
1 CTCTAACGAGCCAATATG
107936 CT
1 CT
107938 TATCCTTTCG
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
17 17 0.27
18 46 0.73
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (18 bp):
CTCTAACGAGCCAATATG
Found at i:107925 original size:35 final size:36
Alignment explanation
Indices: 107852--107937 Score: 120
Period size: 35 Copynumber: 2.4 Consensus size: 36
107842 ATTAACTCTT
* * * *
107852 ACGAGCCAATATGCTCTAATGAGCTAGTATGCTTAA
1 ACGAGCCAATATGCTCTAACGAGCCAATATGCTCAA
*
107888 ACGAGCCAGTATGCTC-AACGAGCCAATATGCTCAA
1 ACGAGCCAATATGCTCTAACGAGCCAATATGCTCAA
107923 ACGAGCCAATATGCT
1 ACGAGCCAATATGCT
107938 TATCCTTTCG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 29 0.66
36 15 0.34
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (36 bp):
ACGAGCCAATATGCTCTAACGAGCCAATATGCTCAA
Found at i:116334 original size:82 final size:82
Alignment explanation
Indices: 116197--116357 Score: 304
Period size: 82 Copynumber: 2.0 Consensus size: 82
116187 AACAAAATTT
116197 GAATTCCCATATCATCGATAACTCCCCATTACTCTCATTCTCCCCCTTTATTATCAACAAGATTG
1 GAATTCCCATATCATCGATAACTCCCCATTACTCTCATTCTCCCCCTTTATTATCAACAAGATTG
116262 CTAACTTACTCTTCGTC
66 CTAACTTACTCTTCGTC
* *
116279 GAATTCCCATATCATCGATAACTCTCCATTACTCTCATTCTCCCCCTTTTTTATCAACAAGATTG
1 GAATTCCCATATCATCGATAACTCCCCATTACTCTCATTCTCCCCCTTTATTATCAACAAGATTG
116344 CTAACTTACTCTTC
66 CTAACTTACTCTTC
116358 ATCGGGAAGG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.25, C:0.32, G:0.06, T:0.37
Consensus pattern (82 bp):
GAATTCCCATATCATCGATAACTCCCCATTACTCTCATTCTCCCCCTTTATTATCAACAAGATTG
CTAACTTACTCTTCGTC
Found at i:122196 original size:11 final size:11
Alignment explanation
Indices: 122180--122207 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
122170 ATGTAGGTTA
122180 TCACGTGGATG
1 TCACGTGGATG
122191 TCACGTGGATG
1 TCACGTGGATG
122202 TCACGT
1 TCACGT
122208 TAGCAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (11 bp):
TCACGTGGATG
Found at i:122269 original size:19 final size:19
Alignment explanation
Indices: 122247--122283 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
122237 CAAAAAACTA
*
122247 TAAAGATTATTTAAAAAAT
1 TAAAAATTATTTAAAAAAT
122266 TAAAAATTATTTAAAAAA
1 TAAAAATTATTTAAAAAA
122284 GTACATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (19 bp):
TAAAAATTATTTAAAAAAT
Found at i:122383 original size:26 final size:26
Alignment explanation
Indices: 122344--122394 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
122334 AATATGGCAT
* *
122344 ACACATGAATTGGCATTTGGATGCCC
1 ACACATGAACTGGCATGTGGATGCCC
*
122370 ACACATGGACTGGCATGTGGATGCC
1 ACACATGAACTGGCATGTGGATGCC
122395 ACCATGTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (26 bp):
ACACATGAACTGGCATGTGGATGCCC
Found at i:123001 original size:20 final size:19
Alignment explanation
Indices: 122959--123003 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
122949 TATTTTATAA
** *
122959 AATTTTTATATTTTTTTTT
1 AATTTTTATATTTTCATTG
122978 AATTTTTATAATTTTCATTG
1 AATTTTTAT-ATTTTCATTG
122998 AATTTT
1 AATTTT
123004 ATTTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
AATTTTTATATTTTCATTG
Found at i:123028 original size:26 final size:27
Alignment explanation
Indices: 122980--123030 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
122970 TTTTTTTTAA
122980 TTTTTATAATTTTCATTGAATTTTATT
1 TTTTTATAATTTTCATTGAATTTTATT
* * *
123007 TTTTTTTATTTTTTATTG-ATTTTA
1 TTTTTATAATTTTCATTGAATTTTA
123031 GTGCACAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.73
Consensus pattern (27 bp):
TTTTTATAATTTTCATTGAATTTTATT
Found at i:123212 original size:18 final size:18
Alignment explanation
Indices: 123170--123212 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
123160 AATATGAAAT
*
123170 ATTTTTAAAATAAATTTC
1 ATTTTTAAAATAAATTTA
*
123188 ATATTTAAAATAAATTTA
1 ATTTTTAAAATAAATTTA
123206 ATTTTTA
1 ATTTTTA
123213 TTTCTTAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTTAAAATAAATTTA
Found at i:123215 original size:42 final size:41
Alignment explanation
Indices: 123169--123254 Score: 122
Period size: 42 Copynumber: 2.0 Consensus size: 41
123159 TAATATGAAA
123169 TATTT-TTAA-AATAAATTTCATATTTAAAATAAATTTAATTTT
1 TATTTCTTAAGAATAAA--TCAT-TTTAAAATAAATTTAATTTT
123211 TATTTCTTAAGTAATAAATCATTTTAAAATAAATTTAATTTT
1 TATTTCTTAAG-AATAAATCATTTTAAAATAAATTTAATTTT
123253 TA
1 TA
123255 GTCCAAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
42 27 0.66
43 8 0.20
45 6 0.15
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (41 bp):
TATTTCTTAAGAATAAATCATTTTAAAATAAATTTAATTTT
Found at i:124668 original size:9 final size:9
Alignment explanation
Indices: 124654--124718 Score: 53
Period size: 8 Copynumber: 7.2 Consensus size: 9
124644 GTAATTAATT
124654 AATTTTTAA
1 AATTTTTAA
124663 AA-TTTTAA
1 AATTTTTAA
124671 AATATTTTAA
1 AAT-TTTTAA
**
124681 TTTTTTTAA
1 AATTTTTAA
* **
124690 TATTTTTTTG
1 -AATTTTTAA
124700 AATTTTTAA
1 AATTTTTAA
124709 AA-TTTTAA
1 AATTTTTAA
124717 AA
1 AA
124719 ACTTAATTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
8 16 0.36
9 16 0.36
10 13 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (9 bp):
AATTTTTAA
Found at i:131861 original size:146 final size:147
Alignment explanation
Indices: 131549--132066 Score: 505
Period size: 146 Copynumber: 3.4 Consensus size: 147
131539 GATCTTGGAA
* * ** * * *
131549 AAAATTTTGGTTTTTTTAAACAATTTAGAAATAAAAATTT-AAATTTTTAAGTTAAATAGTGATT
1 AAAATTTTGATTTTTTTTAATTATTTCGAAATAAAAATTTGGAA-TTTTAAGTAAAATAGTGATT
* *
131613 TT-ATTTAAAAAAAGAGAAAGTTTATATTTTTAAAAATTAAAATCTATTTTTTTAGTCATTTTAA
65 TTCA-TT--AAAAA-A-AAAGTTTAGATTTTAAAAAATTAAAATCTATTTTTTTAGTCATTTTAA
*
131677 AGAAAAAGTTTAAATTTTTAAAC
125 AGAAAAAGTTTAAAATTTTAAAC
* *
131700 AAAATTTTGATTTTTTTTAATTATTTCGACATAAAAATTTGGAATTTTAAGTAAAATAGTAATTT
1 AAAATTTTGATTTTTTTTAATTATTTCGAAATAAAAATTTGGAATTTTAAGTAAAATAGTGATTT
131765 TCATTAAAAAAAAAGTTTAGA-TTTAAAAAATTAAAAAGTCTA-TTTTTTAGTCATTTTAAAG-A
66 TCATTAAAAAAAAAGTTTAGATTTTAAAAAATT-AAAA-TCTATTTTTTTAGTCATTTTAAAGAA
*
131827 AAAGTTTAAAATTTTAAAT
129 AAAGTTTAAAATTTTAAAC
* * * * * *
131846 AAATTTTTGATTTTTTTTAATTGTTTTGAAATAAAAGTTTGGATTTTTAAGTAAATTAGTGATTT
1 AAAATTTTGATTTTTTTTAATTATTTCGAAATAAAAATTTGGAATTTTAAGTAAAATAGTGATTT
* * * *
131911 TCATTAAAAAAAGAAAGAAAGTTTAGATTTTTTAAAAAAATAAAAATTTGTTTTTTTAGTGATTT
66 TCATT----AAA-AAA-AAAGTTTAGA--TTTT-AAAAAATTAAAATCTATTTTTTTAGTCATTT
*
131976 TAAAGAAAAA-ATTAAAATTTTTAAAC
122 TAAAGAAAAAGTTTAAAA-TTTTAAAC
* * * * * * **
132002 AGAGTTTT-AATTTTTTTAACTATTTCAAAATAAAAGTTCT-G-ATTTTGAAGTAAAGCAGTGAT
1 AAAATTTTGATTTTTTTTAATTATTTCGAAATAAAAATT-TGGAATTTT-AAGTAAAATAGTGAT
132064 TTT
64 TTT
132067 GTTTTAATCA
Statistics
Matches: 311, Mismatches: 37, Indels: 34
0.81 0.10 0.09
Matches are distributed among these distances:
146 90 0.29
147 32 0.10
148 5 0.02
149 5 0.02
150 3 0.01
151 59 0.19
152 13 0.04
154 6 0.02
155 73 0.23
156 25 0.08
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (147 bp):
AAAATTTTGATTTTTTTTAATTATTTCGAAATAAAAATTTGGAATTTTAAGTAAAATAGTGATTT
TCATTAAAAAAAAAGTTTAGATTTTAAAAAATTAAAATCTATTTTTTTAGTCATTTTAAAGAAAA
AGTTTAAAATTTTAAAC
Found at i:132016 original size:155 final size:153
Alignment explanation
Indices: 131549--132066 Score: 537
Period size: 155 Copynumber: 3.4 Consensus size: 153
131539 GATCTTGGAA
* * ** * **
131549 AAAATTTTGGTTTTTTTAAACAATTTAGAAATAAAAATTTAAATTTTTAAGTTAAATAGTGATTT
1 AAAATTTTGATTTTTTTTAATTATTTCGAAATAAAAATTTGGATTTTTAAG-TAAATAGTGATTT
* *
131614 T-ATTTAAAAAAAG--AGAAAGTTTATATTTTT--AAAAATTAAAATCTATTTTTTTAGTCATTT
65 TCA-TTAAAAAAAGAAAGAAAGTTTAGATTTTTAAAAAAATAAAAATCT-TTTTTTTAGTCATTT
* *
131674 TAAAGAAAAAGTTTAAATTTTTAAAC
128 TAAAGAAAAAATTAAAATTTTTAAAC
* * *
131700 AAAATTTTGATTTTTTTTAATTATTTCGACATAAAAATTTGGAATTTTAAGTAAAATAGTAATTT
1 AAAATTTTGATTTTTTTTAATTATTTCGAAATAAAAATTTGGATTTTTAAGT-AAATAGTGATTT
* *
131765 TCATT----AAA-AAA-AAAGTTTAGA--TTTAAAAAATTAAAAAGTCTATTTTTTAGTCATTTT
65 TCATTAAAAAAAGAAAGAAAGTTTAGATTTTTAAAAAAATAAAAA-TCTTTTTTTTAGTCATTTT
** *
131822 AAAGAAAAGTTTAAAA-TTTTAAAT
129 AAAGAAAAAATTAAAATTTTTAAAC
* * * *
131846 AAATTTTTGATTTTTTTTAATTGTTTTGAAATAAAAGTTTGGATTTTTAAGTAAATTAGTGATTT
1 AAAATTTTGATTTTTTTTAATTATTTCGAAATAAAAATTTGGATTTTTAAGTAAA-TAGTGATTT
* *
131911 TCATTAAAAAAAGAAAGAAAGTTTAGATTTTTTAAAAAAATAAAAATTTGTTTTTTTAGTGATTT
65 TCATTAAAAAAAGAAAGAAAGTTTAGA-TTTTTAAAAAAATAAAAATCT-TTTTTTTAGTCATTT
131976 TAAAGAAAAAATTAAAATTTTTAAAC
128 TAAAGAAAAAATTAAAATTTTTAAAC
* * * * * * * *
132002 AGAGTTTT-AATTTTTTTAACTATTTCAAAATAAAAGTTCT-GATTTTGAAGTAAAGCAGTGATT
1 AAAATTTTGATTTTTTTTAATTATTTCGAAATAAAAATT-TGGATTTTTAAGTAAA-TAGTGATT
132065 TT
64 TT
132067 GTTTTAATCA
Statistics
Matches: 305, Mismatches: 42, Indels: 36
0.80 0.11 0.09
Matches are distributed among these distances:
145 6 0.02
146 66 0.22
147 49 0.16
148 4 0.01
150 4 0.01
151 59 0.19
152 11 0.04
154 2 0.01
155 90 0.30
156 14 0.05
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (153 bp):
AAAATTTTGATTTTTTTTAATTATTTCGAAATAAAAATTTGGATTTTTAAGTAAATAGTGATTTT
CATTAAAAAAAGAAAGAAAGTTTAGATTTTTAAAAAAATAAAAATCTTTTTTTTAGTCATTTTAA
AGAAAAAATTAAAATTTTTAAAC
Found at i:133715 original size:13 final size:13
Alignment explanation
Indices: 133697--133722 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
133687 ACCTGAAGTA
133697 AATTTTATATTTT
1 AATTTTATATTTT
133710 AATTTTATATTTT
1 AATTTTATATTTT
133723 TTATAAACCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
AATTTTATATTTT
Found at i:134877 original size:46 final size:46
Alignment explanation
Indices: 134821--134913 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
134811 CCTTAGAAAA
*
134821 TACACTCATTAGAGATTAGAACTCATAACACTTTTAGAGAATTTTG
1 TACACCCATTAGAGATTAGAACTCATAACACTTTTAGAGAATTTTG
*
134867 TACACCCATTAGAGATTAGAACTCATAATACTTTTAGAGAATTTTG
1 TACACCCATTAGAGATTAGAACTCATAACACTTTTAGAGAATTTTG
134913 T
1 T
134914 GTTTATATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (46 bp):
TACACCCATTAGAGATTAGAACTCATAACACTTTTAGAGAATTTTG
Found at i:136084 original size:16 final size:17
Alignment explanation
Indices: 136065--136098 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
136055 ATCAACAAAC
*
136065 TAAACTCAAATAT-TTT
1 TAAACCCAAATATATTT
136081 TAAACCCAAATATATTT
1 TAAACCCAAATATATTT
136098 T
1 T
136099 CATTCTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAACCCAAATATATTT
Found at i:136127 original size:58 final size:58
Alignment explanation
Indices: 136061--136180 Score: 197
Period size: 58 Copynumber: 2.1 Consensus size: 58
136051 AACCATCAAC
* *
136061 AAACTAAACTCAAATATTTTTAAACCCAAATAT-ATTTTCATTCTTAAAAAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTT-ATTCCTAAAAAACACTCAT
*
136119 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAATAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAAAAACACTCAT
136177 AAAC
1 AAAC
136181 AATTTCTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
58 53 0.91
59 5 0.09
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAAAAACACTCAT
Found at i:141138 original size:30 final size:31
Alignment explanation
Indices: 141083--141147 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
141073 TGAAAATGTT
* *
141083 AAAAAACTTATAAAACTATAAAAAAATTGTAA
1 AAAAAACTTATAAAAC-ATAAAAAAAATCTAA
* *
141115 AAAAAACTTATTAAA-ATACAAAAAATCTAA
1 AAAAAACTTATAAAACATAAAAAAAATCTAA
141145 AAA
1 AAA
141148 TTAAAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 15 0.52
32 14 0.48
ACGTcount: A:0.68, C:0.08, G:0.02, T:0.23
Consensus pattern (31 bp):
AAAAAACTTATAAAACATAAAAAAAATCTAA
Found at i:141146 original size:8 final size:8
Alignment explanation
Indices: 141135--141240 Score: 61
Period size: 8 Copynumber: 12.0 Consensus size: 8
141125 TTAAAATACA
*
141135 AAAAATCT
1 AAAAATAT
141143 AAAAAT-T
1 AAAAATAT
141150 AAAAATAT
1 AAAAATAT
*
141158 AACAATAT
1 AAAAATAT
141166 AAAAATTCAT
1 AAAAA-T-AT
141176 AAAACCATAT
1 AAAA--ATAT
*
141186 AAAAACTCT
1 AAAAA-TAT
*
141195 ACAAATATTCT
1 A-AAA-A-TAT
*
141206 AATAAATACA
1 AA-AAATA-T
141216 AAAAATAT
1 AAAAATAT
141224 AAAAATAT
1 AAAAATAT
141232 ATAAAATAT
1 A-AAAATAT
141241 TGGAATATAT
Statistics
Matches: 80, Mismatches: 7, Indels: 21
0.74 0.06 0.19
Matches are distributed among these distances:
7 7 0.09
8 28 0.35
9 17 0.21
10 19 0.24
11 8 0.10
12 1 0.01
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAAATAT
Found at i:141155 original size:15 final size:16
Alignment explanation
Indices: 141135--141240 Score: 61
Period size: 20 Copynumber: 6.0 Consensus size: 16
141125 TTAAAATACA
*
141135 AAAAATCTAAAAAT-T
1 AAAAATATAAAAATAT
*
141150 AAAAATATAACAATAT
1 AAAAATATAAAAATAT
141166 AAAAATTCATAAAACCATAT
1 AAAAA-T-ATAAAA--ATAT
* *
141186 AAAAACTCTACAAATATTCT
1 AAAAA-TATA-AAA-A-TAT
*
141206 AATAAATACAAAAAATAT
1 AA-AAATA-TAAAAATAT
141224 AAAAATATATAAAATAT
1 AAAAATATA-AAAATAT
141241 TGGAATATAT
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
15 12 0.17
16 7 0.10
17 13 0.19
18 9 0.13
19 4 0.06
20 21 0.30
21 4 0.06
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATATAAAAATAT
Found at i:141227 original size:9 final size:9
Alignment explanation
Indices: 141127--141237 Score: 50
Period size: 9 Copynumber: 12.2 Consensus size: 9
141117 AAAACTTATT
*
141127 AAAATACAA
1 AAAATATAA
*
141136 AAAATCT-A
1 AAAATATAA
141144 AAAAT-T-A
1 AAAATATAA
141151 AAAATAT-A
1 AAAATATAA
*
141159 ACAATATAA
1 AAAATATAA
*
141168 AAATTCATAA
1 AAAAT-ATAA
*
141178 AACCATATAA
1 AA-AATATAA
* *
141188 AAACTCTACA
1 AAAATATA-A
* *
141198 AATATTCTAA
1 AA-AATATAA
* *
141208 TAAATACAA
1 AAAATATAA
141217 AAAATATAA
1 AAAATATAA
141226 AAATATATAA
1 AAA-ATATAA
141236 AA
1 AA
141238 TATTGGAATA
Statistics
Matches: 78, Mismatches: 17, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
7 7 0.09
8 14 0.18
9 26 0.33
10 25 0.32
11 6 0.08
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATATAA
Found at i:143842 original size:29 final size:29
Alignment explanation
Indices: 143780--143835 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
143770 ACATATTTAG
*
143780 CATGTAATCAGATTAACAGTAGCAGTAAA
1 CATGTAATCAGATTAACAGTAACAGTAAA
* * *
143809 CATGTACTCAGTTTATCAGTAACAGTA
1 CATGTAATCAGATTAACAGTAACAGTA
143836 GTCATGTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (29 bp):
CATGTAATCAGATTAACAGTAACAGTAAA
Done.