Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015331.1 Kokia drynarioides strain JFW-HI SEQ_130378, 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: 253177
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 428 characters in sequence are not A, C, G, or T
Found at i:20221 original size:8 final size:9
Alignment explanation
Indices: 20204--20240 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
20194 TTTGAAATTT
20204 TAATAAATA
1 TAATAAATA
20213 TAA-AAATA
1 TAATAAATA
20221 TAATAAA-A
1 TAATAAATA
*
20229 TAATATATA
1 TAATAAATA
20238 TAA
1 TAA
20241 AATTGTTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
8 15 0.60
9 10 0.40
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
TAATAAATA
Found at i:23602 original size:15 final size:17
Alignment explanation
Indices: 23577--23608 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
23567 GAAAATTATT
23577 TAAAGCAAAGTA-ATTG
1 TAAAGCAAAGTAGATTG
23593 TAAA-CAAAGTAGATTG
1 TAAAGCAAAGTAGATTG
23609 ATATTGATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (17 bp):
TAAAGCAAAGTAGATTG
Found at i:34868 original size:3 final size:3
Alignment explanation
Indices: 34860--34884 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
34850 AACTCGAATT
34860 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
34885 AAAAGTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:36660 original size:10 final size:11
Alignment explanation
Indices: 36645--36673 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
36635 ATTGAGCTTA
36645 GAGTCGAGTC-
1 GAGTCGAGTCG
36655 GAGTCGAGTCG
1 GAGTCGAGTCG
36666 GAGTCGAG
1 GAGTCGAG
36674 ATTCAGATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.21, C:0.17, G:0.45, T:0.17
Consensus pattern (11 bp):
GAGTCGAGTCG
Found at i:41257 original size:2 final size:2
Alignment explanation
Indices: 41250--41274 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41240 AGGCTTAAAC
41250 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
41275 GAGGGAAAGG
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:63422 original size:18 final size:18
Alignment explanation
Indices: 63399--63445 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
63389 AGGAACTCTG
*
63399 AAAGAAAAGGACAAAATA
1 AAAGAAAAGGACAAAACA
*
63417 AAAGAAAAGGGCAAAACA
1 AAAGAAAAGGACAAAACA
63435 AAAGAAAAGGA
1 AAAGAAAAGGA
63446 AGAAATTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.70, C:0.06, G:0.21, T:0.02
Consensus pattern (18 bp):
AAAGAAAAGGACAAAACA
Found at i:64202 original size:9 final size:9
Alignment explanation
Indices: 64190--64227 Score: 67
Period size: 9 Copynumber: 4.1 Consensus size: 9
64180 TTAATCCCTT
64190 TAAAAAAAA
1 TAAAAAAAA
64199 TAAAAAAAA
1 TAAAAAAAA
64208 TAAAAAAAAA
1 T-AAAAAAAA
64218 TAAAAAAAA
1 TAAAAAAAA
64227 T
1 T
64228 TAATTAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 19 0.68
10 9 0.32
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:64206 original size:10 final size:10
Alignment explanation
Indices: 64191--64226 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
64181 TAATCCCTTT
64191 AAAAAAAAT-
1 AAAAAAAATA
64200 AAAAAAAATA
1 AAAAAAAATA
64210 AAAAAAAATA
1 AAAAAAAATA
64220 AAAAAAA
1 AAAAAAA
64227 TTAATTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:64215 original size:19 final size:19
Alignment explanation
Indices: 64191--64227 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
64181 TAATCCCTTT
64191 AAAAAAAATAAAAAAAATA
1 AAAAAAAATAAAAAAAATA
64210 AAAAAAAATAAAAAAAAT
1 AAAAAAAATAAAAAAAAT
64228 TAATTAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (19 bp):
AAAAAAAATAAAAAAAATA
Found at i:67461 original size:17 final size:18
Alignment explanation
Indices: 67427--67464 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
67417 TAATTTAATA
* *
67427 TTTTATGTTTTTATAATT
1 TTTTATGTTATTAAAATT
67445 TTTTAT-TTATTAAAATT
1 TTTTATGTTATTAAAATT
67462 TTT
1 TTT
67465 ATATATTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTATGTTATTAAAATT
Found at i:81257 original size:25 final size:23
Alignment explanation
Indices: 81216--81270 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
81206 GCCATGTTAA
*
81216 ACACGCAATGCACAAAAAACGCG
1 ACACACAATGCACAAAAAACGCG
81239 ACACACAATGCACAAAAAACGCG
1 ACACACAATGCACAAAAAACGCG
81262 ACACACAAT
1 ACACACAAT
81271 ACGACCCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.51, C:0.31, G:0.13, T:0.05
Consensus pattern (23 bp):
ACACACAATGCACAAAAAACGCG
Found at i:88166 original size:4 final size:4
Alignment explanation
Indices: 88159--88191 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
88149 GAGAAGGAAG
88159 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA A
88192 GAAGGAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:88221 original size:8 final size:7
Alignment explanation
Indices: 88150--88217 Score: 55
Period size: 8 Copynumber: 8.7 Consensus size: 7
88140 AGCTAAGAGG
*
88150 AGAAGGA
1 AGAAGAA
88157 AGAAGAA
1 AGAAGAA
88164 AGAAAGAA
1 AG-AAGAA
88172 AGAAAGAA
1 AG-AAGAA
88180 AGAAAGAA
1 AG-AAGAA
88188 AGAAGAA
1 AGAAGAA
*
88195 GGAGAATAA
1 --AGAAGAA
88204 ATGAATGAA
1 A-GAA-GAA
88213 AGAAG
1 AGAAG
88218 GAAAAGAAGG
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
7 15 0.28
8 29 0.55
9 9 0.17
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.04
Consensus pattern (7 bp):
AGAAGAA
Found at i:94382 original size:23 final size:23
Alignment explanation
Indices: 94305--94430 Score: 98
Period size: 23 Copynumber: 5.5 Consensus size: 23
94295 ACACTAGTGC
* *
94305 GCTCTTTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* * *
94328 GCTCTCTGGTCAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
94351 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
94374 GCTCTCTGTTGCCCAGCACTTATGTGT
1 GCTCTCTGTT---TAGCACTT-TGTGT
*
94401 --TCTCTG-TTAGTACTTTG-GT
1 GCTCTCTGTTTAGCACTTTGTGT
*
94420 ACTCTCTGTTT
1 GCTCTCTGTTT
94431 GTTCCGTATA
Statistics
Matches: 82, Mismatches: 14, Indels: 15
0.74 0.13 0.14
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 12 0.15
22 2 0.02
23 46 0.56
24 1 0.01
25 6 0.07
26 6 0.07
27 5 0.06
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.45
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTTTGTGT
Found at i:110699 original size:14 final size:16
Alignment explanation
Indices: 110680--110711 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
110670 TTGGATCACC
110680 AAAAAA-CGTTTT-AA
1 AAAAAACCGTTTTGAA
110694 AAAAAACCGTTTTGAA
1 AAAAAACCGTTTTGAA
110710 AA
1 AA
110712 CATGTAGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 6 0.38
16 4 0.25
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.25
Consensus pattern (16 bp):
AAAAAACCGTTTTGAA
Found at i:111495 original size:28 final size:28
Alignment explanation
Indices: 111434--111495 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
111424 AAAATGAGCT
* *
111434 TTTTGAATACTCGGGGGCAAAATGGTAA
1 TTTTGGATACTCGGGGGAAAAATGGTAA
* *
111462 TTTTGGATTCTCGGGGTAAAAATGGTAA
1 TTTTGGATACTCGGGGGAAAAATGGTAA
111490 TTTTGG
1 TTTTGG
111496 GAAAATTCGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.27, C:0.08, G:0.29, T:0.35
Consensus pattern (28 bp):
TTTTGGATACTCGGGGGAAAAATGGTAA
Found at i:111592 original size:30 final size:30
Alignment explanation
Indices: 111551--111884 Score: 418
Period size: 29 Copynumber: 11.4 Consensus size: 30
111541 AAAAGGTTAA
* * *
111551 TTTGGAAGTTTCGAGAGTAAAAATAGAATT
1 TTTGGAAGTTTCGAGGGTAAAAATGGGATT
** *
111581 TTTACAAGTTTCGA-GGTCAAAATGGGATT
1 TTTGGAAGTTTCGAGGGTAAAAATGGGATT
*
111610 TTTGGAAGTTTAG-GGGTAAAAATGGGATT
1 TTTGGAAGTTTCGAGGGTAAAAATGGGATT
* *
111639 TTTGGAAGTTTTGGGGGTAAAAATGGGATT
1 TTTGGAAGTTTCGAGGGTAAAAATGGGATT
*
111669 TCTT-GAAGTTTCGAGCGTAAAAATGGGATT
1 T-TTGGAAGTTTCGAGGGTAAAAATGGGATT
**
111699 TTTGGAAGTTT-GAGGGTAAAAATGAAATT
1 TTTGGAAGTTTCGAGGGTAAAAATGGGATT
111728 TTTGGAAG-TTC--GGGTAAAAATGGGATT
1 TTTGGAAGTTTCGAGGGTAAAAATGGGATT
111755 TTTGGAAGTTTCG-GGGTAAAAATGGGATT
1 TTTGGAAGTTTCGAGGGTAAAAATGGGATT
*
111784 TTTGGAAGTTTCAAGGGTAAAAATGGGATT
1 TTTGGAAGTTTCGAGGGTAAAAATGGGATT
* **
111814 TTTGGAAGTTTCG-GAGTCAAAAAAAGGATT
1 TTTGGAAGTTTCGAGGGT-AAAAATGGGATT
111844 TTTGGAAGTTT-GAGGGTAAAAATGGGATT
1 TTTGGAAGTTTCGAGGGTAAAAATGGGATT
*
111873 TTTTGACAGTTT
1 TTTGGA-AGTTT
111885 AGGGACCCTT
Statistics
Matches: 265, Mismatches: 28, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
27 22 0.08
28 5 0.02
29 119 0.45
30 117 0.44
31 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.35
Consensus pattern (30 bp):
TTTGGAAGTTTCGAGGGTAAAAATGGGATT
Found at i:111779 original size:145 final size:148
Alignment explanation
Indices: 111551--111884 Score: 466
Period size: 145 Copynumber: 2.3 Consensus size: 148
111541 AAAAGGTTAA
* *
111551 TTTGGAAGTTTCGAGAGTAAAAAT-AGAATTTTTACAAGTTTCGAGGTCAAAATGGGATTTTTGG
1 TTTGGAAGTTT-GAGGGTAAAAATGAGAATTTTTACAAGTTTCGAGGTAAAAATGGGATTTTTGG
***
111615 AAGTTTAGGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGGTAAAAATGGGATTTCTT-GAAGTT
65 AAGTTTAGGGGTAAAAATGGGATTTTTGGAAGTTTCAAGGGTAAAAATGGGATTT-TTGGAAGTT
* **
111679 TCGAGCGT-AAAAATGGGATT
129 TCG-GAGTCAAAAAAAGGATT
**
111699 TTTGGAAGTTTGAGGGTAAAAATGA-AATTTTTGGAAG-TTCG-GGTAAAAATGGGATTTTTGGA
1 TTTGGAAGTTTGAGGGTAAAAATGAGAATTTTTACAAGTTTCGAGGTAAAAATGGGATTTTTGGA
*
111761 AGTTTCGGGGTAAAAATGGGATTTTTGGAAGTTTCAAGGGTAAAAATGGGATTTTTGGAAGTTTC
66 AGTTTAGGGGTAAAAATGGGATTTTTGGAAGTTTCAAGGGTAAAAATGGGATTTTTGGAAGTTTC
111826 GGAGTCAAAAAAAGGATT
131 GGAGTCAAAAAAAGGATT
* *
111844 TTTGGAAGTTTGAGGGTAAAAATGGGATTTTTTGAC-AGTTT
1 TTTGGAAGTTTGAGGGTAAAAATGAGAATTTTT-ACAAGTTT
111885 AGGGACCCTT
Statistics
Matches: 165, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
144 5 0.03
145 113 0.68
146 12 0.07
147 23 0.14
148 12 0.07
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.35
Consensus pattern (148 bp):
TTTGGAAGTTTGAGGGTAAAAATGAGAATTTTTACAAGTTTCGAGGTAAAAATGGGATTTTTGGA
AGTTTAGGGGTAAAAATGGGATTTTTGGAAGTTTCAAGGGTAAAAATGGGATTTTTGGAAGTTTC
GGAGTCAAAAAAAGGATT
Found at i:113021 original size:3 final size:3
Alignment explanation
Indices: 112973--113003 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
112963 AATGAGGTAG
112973 TTA TTA CTTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
113004 ATAGCACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:113795 original size:11 final size:11
Alignment explanation
Indices: 113778--113828 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
113768 TATGGACTTT
113778 TTAAAATTAAAA
1 TTAAAATT-AAA
*
113790 TTAAATTTAAA
1 TTAAAATTAAA
* *
113801 TTTAATTTAAA
1 TTAAAATTAAA
113812 TTTAAAA-TAAA
1 -TTAAAATTAAA
113823 TTAAAA
1 TTAAAA
113829 AGGGACCCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
10 6 0.18
11 17 0.50
12 11 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAAAATTAAA
Found at i:113824 original size:17 final size:17
Alignment explanation
Indices: 113777--113824 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
113767 TTATGGACTT
*
113777 TTTAAAATTAAAATTAAA
1 TTTAAAA-TAAATTTAAA
* *
113795 TTTAAATTTAATTTAAA
1 TTTAAAATAAATTTAAA
113812 TTTAAAATAAATT
1 TTTAAAATAAATT
113825 AAAAAGGGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:118662 original size:29 final size:30
Alignment explanation
Indices: 118612--118672 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
118602 AATAAAACTT
* * *
118612 TAATATTAAATAATTATTTATGTT-AATAA
1 TAATAATAAATAAATATGTATGTTAAATAA
*
118641 TAATAATAATTAAATATGTATGTTAAATAA
1 TAATAATAAATAAATATGTATGTTAAATAA
118671 TA
1 TA
118673 TTCAACAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (30 bp):
TAATAATAAATAAATATGTATGTTAAATAA
Found at i:120530 original size:5 final size:5
Alignment explanation
Indices: 120516--120549 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
120506 CTTTTAGCCT
120516 GGCT- GGCTA GGCTA GGCTA GGCTA GGCTA GGCTA
1 GGCTA GGCTA GGCTA GGCTA GGCTA GGCTA GGCTA
120550 AGCGGAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.18, C:0.21, G:0.41, T:0.21
Consensus pattern (5 bp):
GGCTA
Found at i:121635 original size:24 final size:25
Alignment explanation
Indices: 121608--121660 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
121598 AACATTAAAA
*
121608 TTAACA-TTAAAAAAATAATCAAAT
1 TTAACATTTAAAAAAATAAACAAAT
* *
121632 TTAATATTTTAAAAAATAAACAAAT
1 TTAACATTTAAAAAAATAAACAAAT
121657 TTAA
1 TTAA
121661 AATACATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (25 bp):
TTAACATTTAAAAAAATAAACAAAT
Found at i:121992 original size:18 final size:17
Alignment explanation
Indices: 121969--122003 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
121959 GAATAGATTT
121969 TTAATTAAATAAATTTAA
1 TTAATTAAA-AAATTTAA
121987 TTAATTAAAAAATTTAA
1 TTAATTAAAAAATTTAA
122004 ACCATAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTAAAAAATTTAA
Found at i:122659 original size:18 final size:17
Alignment explanation
Indices: 122628--122662 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
122618 GATTTAGGGT
122628 TTAAATTTTTTAATTAA
1 TTAAATTTTTTAATTAA
122645 TTAAATTTATTTAATTAA
1 TTAAATTT-TTTAATTAA
122663 AAATCTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTAATTAA
Found at i:122997 original size:24 final size:23
Alignment explanation
Indices: 122915--123010 Score: 90
Period size: 24 Copynumber: 4.2 Consensus size: 23
122905 AGACAATAGT
* *
122915 AAAAAC-GCATAAAAAATAACAT
1 AAAAACAGCAAAAAAAATAACAC
* * *
122937 TAAAACAACAAAAAACAATAA-TC
1 AAAAACAGCAAAAAA-AATAACAC
*
122960 -AAAACAGCAGAAAAAATAACAGC
1 AAAAACAGCAAAAAAAATAACA-C
122983 AAAAACAGCAAAAAAAATAACAAC
1 AAAAACAGCAAAAAAAATAAC-AC
123007 AAAA
1 AAAA
123011 GCAATACTGA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
21 5 0.08
22 17 0.29
23 7 0.12
24 29 0.49
25 1 0.02
ACGTcount: A:0.71, C:0.16, G:0.05, T:0.08
Consensus pattern (23 bp):
AAAAACAGCAAAAAAAATAACAC
Found at i:123013 original size:21 final size:20
Alignment explanation
Indices: 122915--123014 Score: 65
Period size: 22 Copynumber: 4.5 Consensus size: 20
122905 AGACAATAGT
* *
122915 AAAAACGCATAAAAAATAAC
1 AAAAAAGCAAAAAAAATAAC
*
122935 ATTAAAACAACAAAAAACAATAATC
1 A--AAAA-AGCAAAAAA-AATAA-C
* *
122960 AAAACAGCAGAAAAAATAACAGC
1 AAAAAAGCAAAAAAAAT-A-A-C
122983 AAAAACAGCAAAAAAAATAAC
1 AAAAA-AGCAAAAAAAATAAC
123004 AACAAAAGCAA
1 AA-AAAAGCAA
123015 TACTGAAACA
Statistics
Matches: 62, Mismatches: 9, Indels: 17
0.70 0.10 0.19
Matches are distributed among these distances:
20 1 0.02
21 11 0.18
22 16 0.26
23 16 0.26
24 16 0.26
25 2 0.03
ACGTcount: A:0.70, C:0.16, G:0.06, T:0.08
Consensus pattern (20 bp):
AAAAAAGCAAAAAAAATAAC
Found at i:126309 original size:32 final size:31
Alignment explanation
Indices: 126240--126309 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 31
126230 GATAACTATG
** * *
126240 AATAAAATGTAAATATATTATAAATTACATT
1 AATAAAAACTAAATATATTATAAATTAAAAT
126271 AA-AAAAACTAAATATA-TATAAGAATTAAAAT
1 AATAAAAACTAAATATATTAT-A-AATTAAAAT
126302 AATAAAAA
1 AATAAAAA
126310 TGATTACAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
29 3 0.09
30 13 0.41
31 11 0.34
32 5 0.16
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (31 bp):
AATAAAAACTAAATATATTATAAATTAAAAT
Found at i:136719 original size:26 final size:30
Alignment explanation
Indices: 136690--136747 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 30
136680 TTTATTATTT
*
136690 TAATA-GAAT-TA-TATTTTTTAA-ATTAA
1 TAATATGAATATATTATTTTTAAATATTAA
*
136716 TAATATTAATATATTATTTTTAAATATTAA
1 TAATATGAATATATTATTTTTAAATATTAA
136746 TA
1 TA
136748 TTTTATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 5 0.19
27 3 0.12
28 2 0.08
29 9 0.35
30 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (30 bp):
TAATATGAATATATTATTTTTAAATATTAA
Found at i:136743 original size:21 final size:22
Alignment explanation
Indices: 136717--136767 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
136707 TTAAATTAAT
136717 AATATTAATATATTATTTT-TA
1 AATATTAATATATTATTTTATA
* *
136738 AATATTAATATTTTATTTTATT
1 AATATTAATATATTATTTTATA
136760 AATATTAA
1 AATATTAA
136768 CAGAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATATTAATATATTATTTTATA
Found at i:136799 original size:18 final size:18
Alignment explanation
Indices: 136776--136821 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
136766 AACAGAAAAT
136776 TTATATTATAATATTTTA
1 TTATATTATAATATTTTA
* * *
136794 TTATATTTTAGTATTTTT
1 TTATATTATAATATTTTA
*
136812 TTAAATTATA
1 TTATATTATA
136822 TAAAAATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TTATATTATAATATTTTA
Found at i:137064 original size:20 final size:20
Alignment explanation
Indices: 137027--137263 Score: 83
Period size: 20 Copynumber: 11.8 Consensus size: 20
137017 AATATCTAAT
* * *
137027 GATTTGCCAATATATCTAGC
1 GATTTACCAAAATTTCTAGC
**
137047 GATTTACCAAAATTTCTATT
1 GATTTACCAAAATTTCTAGC
* *
137067 GATTTATCAAAACTTT-T-GA
1 GATTTACCAAAA-TTTCTAGC
* *
137086 GATTTTACCAAAATATCTAAC
1 GA-TTTACCAAAATTTCTAGC
*
137107 GATTTACCTAAATTTCTAAG-
1 GATTTACCAAAATTTCT-AGC
* ** ** *
137127 GATTTACTATTATACCTAAC
1 GATTTACCAAAATTTCTAGC
* * *
137147 GATTTACCAATATTT-TTGAA
1 GATTTACCAAAATTTCTAG-C
* **
137167 GATTTATCAAAATATT-TAAA
1 GATTTACCAAAAT-TTCTAGC
* *
137187 GATTTATCAAAATTTCTATC
1 GATTTACCAAAATTTCTAGC
* * *
137207 AATTTACCAATATTTATGAG-
1 GATTTACCAAAATTTCT-AGC
* *
137227 GCTTTACCAAAATGTCTAAG-
1 GATTTACCAAAATTTCT-AGC
*
137247 GTTTTACCAATAATTTC
1 GATTTACCAA-AATTTC
137264 AAAATTTCTA
Statistics
Matches: 158, Mismatches: 48, Indels: 21
0.70 0.21 0.09
Matches are distributed among these distances:
19 8 0.05
20 135 0.85
21 15 0.09
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (20 bp):
GATTTACCAAAATTTCTAGC
Found at i:137111 original size:40 final size:38
Alignment explanation
Indices: 137015--137201 Score: 122
Period size: 40 Copynumber: 4.7 Consensus size: 38
137005 CGAGTTTGCT
* * * * *
137015 AAAATATCTAATGATTTGCCAATATATCTAGCGATTTACC
1 AAAATATCTAACGATTTACCAA-A-ATTTTGAGATTTACC
* ** *
137055 AAAATTTCTATTGATTTATCAAAACTTTTGAGATTTTACC
1 AAAATATCTAACGATTTACCAAAA-TTTTGAGA-TTTACC
* * *
137095 AAAATATCTAACGATTTACCTAAATTTCTAAGGATTTACT
1 AAAATATCTAACGATTTACCAAAATTT-TGA-GATTTACC
** * * *
137135 ATTATACCTAACGATTTACCAATATTTTTGAAGATTTATC
1 AAAATATCTAACGATTTACCAA-AATTTTG-AGATTTACC
* * *
137175 AAAATATTTAAAGATTTATCAAAATTT
1 AAAATATCTAACGATTTACCAAAATTT
137202 CTATCAATTT
Statistics
Matches: 112, Mismatches: 29, Indels: 13
0.73 0.19 0.08
Matches are distributed among these distances:
38 1 0.01
39 13 0.12
40 91 0.81
41 7 0.06
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.40
Consensus pattern (38 bp):
AAAATATCTAACGATTTACCAAAATTTTGAGATTTACC
Found at i:137364 original size:40 final size:40
Alignment explanation
Indices: 137287--137407 Score: 102
Period size: 40 Copynumber: 3.0 Consensus size: 40
137277 CTATACCAAG
* * **
137287 TTTTAACA-TTTACCAAAAATTC-AATGAATTTTCCAAAAT
1 TTTTAACATTTTACCAATATTTCTAATG-ATTCACCAAAAT
** * * * *
137326 TTTTGTCATTTTACCTATATTTCTAATGATTTATCAAAAA
1 TTTTAACATTTTACCAATATTTCTAATGATTCACCAAAAT
* * *
137366 TTTTAAGATTTTATCAATATTTCTAATGGTTCACCAAAAT
1 TTTTAACATTTTACCAATATTTCTAATGATTCACCAAAAT
137406 TT
1 TT
137408 ATAAGAATTT
Statistics
Matches: 63, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
39 6 0.10
40 53 0.84
41 4 0.06
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.45
Consensus pattern (40 bp):
TTTTAACATTTTACCAATATTTCTAATGATTCACCAAAAT
Found at i:137387 original size:19 final size:21
Alignment explanation
Indices: 137342--137393 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
137332 CATTTTACCT
137342 ATATTTCTAATGATTTATCAA
1 ATATTTCTAATGATTTATCAA
*
137363 AAATTT-TAA-GATTTTATC-A
1 ATATTTCTAATGA-TTTATCAA
137382 ATATTTCTAATG
1 ATATTTCTAATG
137394 GTTCACCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 8 0.31
20 12 0.46
21 6 0.23
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (21 bp):
ATATTTCTAATGATTTATCAA
Found at i:137413 original size:40 final size:41
Alignment explanation
Indices: 137333--137420 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 41
137323 AATTTTTGTC
* *
137333 ATTTTACCTATATTTCTAATGATTTATCAAAAATTTTAAG-
1 ATTTTACCAATATTTCTAATGATTCATCAAAAATTTTAAGA
* * *
137373 ATTTTATCAATATTTCTAATGGTTCA-CCAAAATTTATAAGA
1 ATTTTACCAATATTTCTAATGATTCATCAAAAATTT-TAAGA
137414 ATTTTAC
1 ATTTTAC
137421 AAAAATTCCA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 8 0.20
40 26 0.65
41 6 0.15
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (41 bp):
ATTTTACCAATATTTCTAATGATTCATCAAAAATTTTAAGA
Found at i:137591 original size:20 final size:20
Alignment explanation
Indices: 137537--137592 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
137527 ATTTTACTAG
137537 AATTTCTAATGATTTATCAA
1 AATTTCTAATGATTTATCAA
* **
137557 AACTTT-TGACAATTTATCAA
1 AA-TTTCTAATGATTTATCAA
*
137577 TATTTCTAATGATTTA
1 AATTTCTAATGATTTA
137593 AAATTTTTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
19 3 0.11
20 21 0.78
21 3 0.11
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (20 bp):
AATTTCTAATGATTTATCAA
Found at i:137733 original size:40 final size:39
Alignment explanation
Indices: 137692--137850 Score: 178
Period size: 40 Copynumber: 4.0 Consensus size: 39
137682 ATTTATCAAT
*
137692 ATATTTT-TTAATTTACCAAAATATCTAAAATTTTACCA
1 ATATTTTATGAATTTACCAAAATATCTAAAATTTTACCA
* * *
137730 ATATTTTCATGGATTTACCAAAATATTTAAAACTTTACCA
1 ATATTTT-ATGAATTTACCAAAATATCTAAAATTTTACCA
* *
137770 ATATTTTTATTG-ATTTATCAAAATATCTAAAATTTTTCCA
1 ATA-TTTTA-TGAATTTACCAAAATATCTAAAATTTTACCA
** * *
137810 ATATTTATATGAATTTATAAAAATATTTAACATTTTACCA
1 ATATTT-TATGAATTTACCAAAATATCTAAAATTTTACCA
137850 A
1 A
137851 AAATTTTAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
38 7 0.07
39 5 0.05
40 85 0.83
41 6 0.06
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.45
Consensus pattern (39 bp):
ATATTTTATGAATTTACCAAAATATCTAAAATTTTACCA
Found at i:137766 original size:20 final size:19
Alignment explanation
Indices: 137701--137861 Score: 69
Period size: 20 Copynumber: 8.1 Consensus size: 19
137691 TATATTTTTT
*
137701 AATTTACCAAAATATCTAA
1 AATTTACCAAAATATTTAA
* *
137720 AATTTTACCAATAT-TTTCATG
1 AA-TTTACCAAAATATTT-A-A
*
137741 GATTTACCAAAATATTTAA
1 AATTTACCAAAATATTTAA
* * *
137760 AACTTTACCAATATTTTTATT
1 AA-TTTACCAAAATATTTA-A
* * *
137781 GATTTATCAAAATATCTAA
1 AATTTACCAAAATATTTAA
*
137800 AATTTTTCC--AATATTTATA
1 AA-TTTACCAAAATATTTA-A
**
137819 TGAATTTATAAAAATATTTAA
1 --AATTTACCAAAATATTTAA
*
137840 CATTTTACCAAAA-ATTTTAA
1 -AATTTACCAAAATA-TTTAA
137860 AA
1 AA
137862 CTAAACCTTT
Statistics
Matches: 101, Mismatches: 28, Indels: 26
0.65 0.18 0.17
Matches are distributed among these distances:
18 7 0.07
19 9 0.09
20 69 0.68
21 8 0.08
22 8 0.08
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.42
Consensus pattern (19 bp):
AATTTACCAAAATATTTAA
Found at i:137792 original size:80 final size:80
Alignment explanation
Indices: 137683--137850 Score: 223
Period size: 80 Copynumber: 2.1 Consensus size: 80
137673 TTTTTATGGA
* *
137683 TTTATCAATATATTTTTTAATTTACCAAAATATCTAAAATTTTACCAATATTT-TCATGGATTTA
1 TTTACCAATATATTTTTTAATTTACCAAAATATCTAAAATTTTACCAATATTTAT-ATGAATTTA
*
137747 CCAAAATATTTAAAAC
65 CAAAAATATTTAAAAC
* * *
137763 TTTACCAATAT-TTTTATTGATTTATCAAAATATCTAAAATTTTTCCAATATTTATATGAATTTA
1 TTTACCAATATATTTT-TTAATTTACCAAAATATCTAAAATTTTACCAATATTTATATGAATTTA
* * *
137827 TAAAAATATTTAACAT
65 CAAAAATATTTAAAAC
137843 TTTACCAA
1 TTTACCAA
137851 AAATTTTAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
79 4 0.05
80 72 0.94
81 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.45
Consensus pattern (80 bp):
TTTACCAATATATTTTTTAATTTACCAAAATATCTAAAATTTTACCAATATTTATATGAATTTAC
AAAAATATTTAAAAC
Found at i:144306 original size:21 final size:21
Alignment explanation
Indices: 144264--144308 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
144254 TATAAAAAAA
*
144264 TTATTTTAGTTTTTTATTTAT
1 TTATTTTAGTTTTTTATGTAT
*
144285 TTATTTTTGTCTTTTTA-GTAT
1 TTATTTTAGT-TTTTTATGTAT
144306 TTA
1 TTA
144309 AATTTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.73
Consensus pattern (21 bp):
TTATTTTAGTTTTTTATGTAT
Found at i:145202 original size:55 final size:54
Alignment explanation
Indices: 145127--145235 Score: 155
Period size: 55 Copynumber: 2.0 Consensus size: 54
145117 ATATTATAAA
* *
145127 ATATTATGTTAATAATATTAATATTACAAAATAAATAATTTAAAAAAATCAAGAT
1 ATATTATGTTAATAACATTAAAATTACAAAATAAATAATTT-AAAAAATCAAGAT
* * * *
145182 ATATTATTTTATTAACATTAAAATTACAACATAAGTAATTTAAAAAATCAAGAT
1 ATATTATGTTAATAACATTAAAATTACAAAATAAATAATTTAAAAAATCAAGAT
145236 TTACTTTTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
54 13 0.27
55 35 0.73
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (54 bp):
ATATTATGTTAATAACATTAAAATTACAAAATAAATAATTTAAAAAATCAAGAT
Found at i:149371 original size:3 final size:3
Alignment explanation
Indices: 149363--149439 Score: 118
Period size: 3 Copynumber: 25.7 Consensus size: 3
149353 TGTTGAATCT
* * * *
149363 TTA TTA TTA TTA TTA TTG TTA TTG TTG TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
149411 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
149440 TCTTGATGTC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:159881 original size:1 final size:1
Alignment explanation
Indices: 159875--159899 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
159865 TCTCTCCTAA
159875 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
159900 GTGGATTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:163551 original size:19 final size:20
Alignment explanation
Indices: 163500--163551 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
163490 TTAATTTTTT
163500 AAAATT-TAAAAAAGTTATA
1 AAAATTATAAAAAAGTTATA
**
163519 AAAA-TATTTTAAAAG-TATA
1 AAAATTA-TAAAAAAGTTATA
163538 AAAATTATAAAAAA
1 AAAATTATAAAAAA
163552 ATATTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
18 1 0.04
19 17 0.65
20 8 0.31
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
AAAATTATAAAAAAGTTATA
Found at i:165921 original size:20 final size:20
Alignment explanation
Indices: 165896--165933 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
165886 TATTTTATGG
165896 TATCATTAATAATTCAATTT
1 TATCATTAATAATTCAATTT
165916 TATCATTAATAATTCAAT
1 TATCATTAATAATTCAAT
165934 ATGATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
TATCATTAATAATTCAATTT
Found at i:181870 original size:28 final size:27
Alignment explanation
Indices: 181826--181878 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
181816 AAGTTAATTA
* *
181826 TATAAAAATTTTTAATAAATAAAAAATG
1 TATAAAAATATTAAAT-AATAAAAAATG
*
181854 TATAAAAATATTAAATATTAAAAAA
1 TATAAAAATATTAAATAATAAAAAA
181879 ACATAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (27 bp):
TATAAAAATATTAAATAATAAAAAATG
Found at i:188439 original size:23 final size:24
Alignment explanation
Indices: 188410--188457 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
188400 CAAGAAAACT
* *
188410 AATAAGAAAACCGCAGAAA-GAAA
1 AATAAGAAAAACGAAGAAACGAAA
188433 AATAAGAAAAACGAAGAAACGAAA
1 AATAAGAAAAACGAAGAAACGAAA
188457 A
1 A
188458 GCACATGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.69, C:0.10, G:0.17, T:0.04
Consensus pattern (24 bp):
AATAAGAAAAACGAAGAAACGAAA
Found at i:199724 original size:18 final size:18
Alignment explanation
Indices: 199697--199746 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
199687 TCATTGTACA
199697 TTTT-TATAATATTTTTT
1 TTTTATATAATATTTTTT
199714 TTTTATATAATATTTTTT
1 TTTTATATAATATTTTTT
*
199732 TTTTACATAATATTT
1 TTTTATATAATATTT
199747 AAAATTATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 4 0.13
18 27 0.87
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATATAATATTTTTT
Found at i:206034 original size:22 final size:20
Alignment explanation
Indices: 206009--206056 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
205999 TTTAACAATT
206009 CAAATATTATAATAAAAAATAA
1 CAAATATT-T-ATAAAAAATAA
*
206031 CAAAT-TTTATAAATAATAA
1 CAAATATTTATAAAAAATAA
206050 -AAATATT
1 CAAATATT
206057 GAAAATAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 4 0.17
19 12 0.50
20 1 0.04
21 2 0.08
22 5 0.21
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
CAAATATTTATAAAAAATAA
Found at i:226073 original size:22 final size:20
Alignment explanation
Indices: 226041--226084 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
226031 TTTTAACAAA
*
226041 AATAATTTTTAACTTTTTTT
1 AATAATTTTTAACATTTTTT
*
226061 AATATATTCTTTAAGATTTTTT
1 AATA-ATT-TTTAACATTTTTT
226083 AA
1 AA
226085 GATCTTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 3 0.15
22 13 0.65
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (20 bp):
AATAATTTTTAACATTTTTT
Found at i:239728 original size:23 final size:23
Alignment explanation
Indices: 239698--239800 Score: 136
Period size: 23 Copynumber: 4.4 Consensus size: 23
239688 CACTAGCACA
*
239698 CTCTCTGTTTAGCAC-GTCTCGTG
1 CTCTCTGTTTAGCACTGTGT-GTG
239721 CTCTCTGTTTTTAGCACTGTGTGTG
1 CTCTCTG--TTTAGCACTGTGTGTG
* * *
239746 CTCTCTGATTAGCACTTTGTGTA
1 CTCTCTGTTTAGCACTGTGTGTG
239769 CTCTCTGTTTAGCACTGTGTGTG
1 CTCTCTGTTTAGCACTGTGTGTG
239792 CTCTCTGTT
1 CTCTCTGTT
239801 GCCCAGCACT
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
23 49 0.70
25 18 0.26
26 3 0.04
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (23 bp):
CTCTCTGTTTAGCACTGTGTGTG
Found at i:241603 original size:16 final size:16
Alignment explanation
Indices: 241582--241612 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
241572 TTCATAAGGT
241582 CATATGAAATTTTTAG
1 CATATGAAATTTTTAG
*
241598 CATATGAATTTTTTA
1 CATATGAAATTTTTA
241613 TGGTTGTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
CATATGAAATTTTTAG
Found at i:242204 original size:37 final size:37
Alignment explanation
Indices: 242163--242273 Score: 141
Period size: 37 Copynumber: 3.0 Consensus size: 37
242153 CTTACACAAT
*
242163 TTTTCAGGCTTTGTGCCTAGTAGGCTTAGTGCTGGTG
1 TTTTCAGGCTTTGTGCCTAGTAGGCTTAGTGCCGGTG
* * *
242200 TTTTCAGGCTTCGTGCCTAGTAGGCTTCGTGCCGGAG
1 TTTTCAGGCTTTGTGCCTAGTAGGCTTAGTGCCGGTG
* * * * *
242237 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTG
1 TTTTCAGGCTTTGTGCCTAGTAGGCTTAGTGCCGGTG
242274 ATCCAAAAAC
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.11, C:0.21, G:0.33, T:0.35
Consensus pattern (37 bp):
TTTTCAGGCTTTGTGCCTAGTAGGCTTAGTGCCGGTG
Found at i:244360 original size:23 final size:22
Alignment explanation
Indices: 244330--244404 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 22
244320 GAAACAATAA
244330 GCACACACAGTGCAATCCAGTAG
1 GCACACACAGTGCAAT-CAGTAG
*
244353 GCACACACATTGCAATCAGTAG
1 GCACACACAGTGCAATCAGTAG
* * * *
244375 ACGCACATAGCGCAAATCAGTAG
1 GCACACACAGTGC-AATCAGTAG
244398 GCACACA
1 GCACACA
244405 AGGTGCGAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 14 0.33
23 29 0.67
ACGTcount: A:0.37, C:0.29, G:0.20, T:0.13
Consensus pattern (22 bp):
GCACACACAGTGCAATCAGTAG
Found at i:246725 original size:13 final size:13
Alignment explanation
Indices: 246681--246740 Score: 59
Period size: 13 Copynumber: 4.6 Consensus size: 13
246671 TTGAAGTTAG
246681 AATTAAATTAATT
1 AATTAAATTAATT
* *
246694 GA-GAAATTAACTT
1 AATTAAATTAA-TT
* *
246707 AGTTAATTTAATT
1 AATTAAATTAATT
246720 AATTAAATTAATT
1 AATTAAATTAATT
*
246733 GATTAAAT
1 AATTAAAT
246741 AGATAATATT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
12 7 0.19
13 23 0.64
14 6 0.17
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (13 bp):
AATTAAATTAATT
Done.