Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015887.1 Corchorus capsularis cultivar CVL-1 contig15908, 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: 41635
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:13967 original size:34 final size:36
Alignment explanation
Indices: 13878--13979 Score: 109
Period size: 37 Copynumber: 2.8 Consensus size: 36
13868 AAGTTTTTCC
* * *
13878 AAGTTTTCAAAGTGGGAAAGTTCCCATCAAGTTATCA
1 AAGTTTTCAAATTAGGAAAGTTCCCATCAGGTTAT-A
*
13915 AAGTTTTCAAATTGGGAAAGTTCCCATCAGGTT-T-
1 AAGTTTTCAAATTAGGAAAGTTCCCATCAGGTTATA
* * *
13949 TAGTTTTCAATTTAGGAAAAGTTCCCGTCAG
1 AAGTTTTCAAATTAGG-AAAGTTCCCATCAG
13980 TTTCAGGTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
34 13 0.22
35 13 0.22
36 1 0.02
37 31 0.53
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (36 bp):
AAGTTTTCAAATTAGGAAAGTTCCCATCAGGTTATA
Found at i:14664 original size:24 final size:22
Alignment explanation
Indices: 14630--14675 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
14620 GTTTGCTTGC
14630 GTTTTCATGTTCATTCATGCCT
1 GTTTTCATGTTCATTCATGCCT
* *
14652 GTTTATCATTGTTTATTCTTGCCT
1 GTTT-TCA-TGTTCATTCATGCCT
14676 TTCTTTATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 3 0.15
24 13 0.65
ACGTcount: A:0.13, C:0.20, G:0.13, T:0.54
Consensus pattern (22 bp):
GTTTTCATGTTCATTCATGCCT
Found at i:16789 original size:279 final size:280
Alignment explanation
Indices: 16288--16849 Score: 1063
Period size: 279 Copynumber: 2.0 Consensus size: 280
16278 TGATAAAACA
* *
16288 AGAAAAAGTATTTTCAATATAAAAGTTACGAATAAACGAAAAGTATTTCGATTTTTTGTTAACAC
1 AGAAAAAGTATTTTCAATATAAAAGTTACAAATAAACAAAAAGTATTTCGATTTTTTGTTAACAC
16353 TTTGCCTAACCCAATTTTTTTTTATACCAAAAGAGCCCATTCTTTTTCTTGGAACCAAATTGAAC
66 TTTGCCTAACCCAATTTTTTTTTATACCAAAAGAGCCCATTCTTTTTCTTGGAACCAAATTGAAC
*
16418 AAAAATTACAGATTCCCATTAACATGTTCCATAGAGGAAATCACTTAAAAGGCCAAATTCAAATC
131 AAAAATTACAGATTCCCATTAACATGTGCCATAGAGGAAATCACTTAAAAGGCCAAATTCAAATC
16483 ACTTTCAGGCCTTGAGAAGACAAATTGGTTCGGAGATAAAATAAGCCAATCTAAGTAACACCTTT
196 ACTTTCAGGCCTTGAGAAGACAAATTGGTTCGGAGATAAAATAAGCCAATCTAAGTAACACCTTT
*
16548 TCCAACCACTTCAATTGTTG
261 TCAAACCACTTCAATTGTTG
16568 AGAAAAAGTATTTTCAATATAAAAGTTACAAATAAACAAAAAGTATTTCGATTTTTTGTTAACAC
1 AGAAAAAGTATTTTCAATATAAAAGTTACAAATAAACAAAAAGTATTTCGATTTTTTGTTAACAC
16633 TTTGCCTAACCCAA-TTTTTTTTATACCAAAAGAGCCCATTCTTTTTCTTGGAACCAAATTGAAC
66 TTTGCCTAACCCAATTTTTTTTTATACCAAAAGAGCCCATTCTTTTTCTTGGAACCAAATTGAAC
*
16697 AAAAATTACAGATTCCCATTAACATGTGCCATAGAGGAAATCACTTAAATGGCCAAATTCAAATC
131 AAAAATTACAGATTCCCATTAACATGTGCCATAGAGGAAATCACTTAAAAGGCCAAATTCAAATC
*
16762 ACTTTCAGGCCTTGAGAAGACAAATTGGTTCGGAGATCAAATAAGCCAATCTAAGTAACACCTTT
196 ACTTTCAGGCCTTGAGAAGACAAATTGGTTCGGAGATAAAATAAGCCAATCTAAGTAACACCTTT
16827 TCAAACCACTTCAATTGTTG
261 TCAAACCACTTCAATTGTTG
16847 AGA
1 AGA
16850 CACCTTTATT
Statistics
Matches: 276, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
279 199 0.72
280 77 0.28
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (280 bp):
AGAAAAAGTATTTTCAATATAAAAGTTACAAATAAACAAAAAGTATTTCGATTTTTTGTTAACAC
TTTGCCTAACCCAATTTTTTTTTATACCAAAAGAGCCCATTCTTTTTCTTGGAACCAAATTGAAC
AAAAATTACAGATTCCCATTAACATGTGCCATAGAGGAAATCACTTAAAAGGCCAAATTCAAATC
ACTTTCAGGCCTTGAGAAGACAAATTGGTTCGGAGATAAAATAAGCCAATCTAAGTAACACCTTT
TCAAACCACTTCAATTGTTG
Found at i:16992 original size:14 final size:14
Alignment explanation
Indices: 16973--17018 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
16963 TTCCCATACG
16973 AAAAGAAAAATAGA
1 AAAAGAAAAATAGA
16987 AAAAGAAAAAGT-G-
1 AAAAGAAAAA-TAGA
*
17000 AAAAGAATAAAAAGA
1 AAAAGAA-AAATAGA
17015 AAAA
1 AAAA
17019 AATTGAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
13 7 0.26
14 15 0.56
15 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (14 bp):
AAAAGAAAAATAGA
Found at i:17110 original size:14 final size:15
Alignment explanation
Indices: 17092--17130 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
17082 TTCAGAAGTT
17092 GTTTTCAAGAAAA-GA
1 GTTTTCAA-AAAATGA
17107 -TTTTCAAAAAATGA
1 GTTTTCAAAAAATGA
17121 GTTTTCAAAA
1 GTTTTCAAAA
17131 GGTTTTGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.18
14 9 0.41
15 9 0.41
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (15 bp):
GTTTTCAAAAAATGA
Found at i:27716 original size:21 final size:20
Alignment explanation
Indices: 27687--27726 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
27677 ATAAAAATAT
*
27687 GCATAATTTTGGTTCGATCAG
1 GCATAATTTTAGTTC-ATCAG
*
27708 GCATTATTTTAGTTCATCA
1 GCATAATTTTAGTTCATCA
27727 TATTGCAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (20 bp):
GCATAATTTTAGTTCATCAG
Found at i:28590 original size:53 final size:53
Alignment explanation
Indices: 28474--28581 Score: 146
Period size: 53 Copynumber: 2.0 Consensus size: 53
28464 TATTCAATGC
* **
28474 TTCAACTCTTCCATTATTCAATTATTCAATTCTTCAAAACTTCAATCCATCTC
1 TTCAACTCTTCCATTATTCAATTATTCAATTCTTCAAAACTTCAATACATCAA
* * *
28527 TTCAACTCTTCCATTATTCAATTCTTCAATTCTTCAATTA-TTCAATACTTCAA
1 TTCAACTCTTCCATTATTCAATTATTCAATTCTTCAA-AACTTCAATACATCAA
28580 TT
1 TT
28582 TATTTCTTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
53 47 0.98
54 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.44
Consensus pattern (53 bp):
TTCAACTCTTCCATTATTCAATTATTCAATTCTTCAAAACTTCAATACATCAA
Found at i:28596 original size:8 final size:8
Alignment explanation
Indices: 28416--28602 Score: 120
Period size: 8 Copynumber: 24.0 Consensus size: 8
28406 GTTCAATTAG
28416 CTTCAATT
1 CTTCAATT
* *
28424 ATTCAATC
1 CTTCAATT
*
28432 CTTCAATG
1 CTTCAATT
28440 CTTCAATT
1 CTTCAATT
**
28448 -TATCTCTTT
1 CT-TC-AATT
28457 CTTCAATT
1 CTTCAATT
* *
28465 ATTCAATG
1 CTTCAATT
*
28473 CTTCAACT
1 CTTCAATT
*
28481 CTTCCATT
1 CTTCAATT
*
28489 ATTCAATT
1 CTTCAATT
*
28497 ATTCAATT
1 CTTCAATT
**
28505 CTTCAAAA
1 CTTCAATT
28513 CTTCAA-T
1 CTTCAATT
28520 C--C-ATCT
1 CTTCAAT-T
*
28526 CTTCAACT
1 CTTCAATT
*
28534 CTTCCATT
1 CTTCAATT
*
28542 ATTCAATT
1 CTTCAATT
28550 CTTCAATT
1 CTTCAATT
28558 CTTCAATT
1 CTTCAATT
* *
28566 ATTCAATA
1 CTTCAATT
28574 CTTCAA-T
1 CTTCAATT
*
28581 -TT-ATTT
1 CTTCAATT
28587 CTTCAATT
1 CTTCAATT
28595 CTTCAATT
1 CTTCAATT
28603 ACTTAGAGCT
Statistics
Matches: 134, Mismatches: 34, Indels: 22
0.71 0.18 0.12
Matches are distributed among these distances:
4 1 0.01
5 2 0.01
6 5 0.04
7 4 0.03
8 116 0.87
9 5 0.04
10 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.01, T:0.47
Consensus pattern (8 bp):
CTTCAATT
Found at i:29003 original size:8 final size:8
Alignment explanation
Indices: 28990--29035 Score: 65
Period size: 8 Copynumber: 5.8 Consensus size: 8
28980 TCTTATTGTT
28990 TCAATTCC
1 TCAATTCC
28998 TCAATTCC
1 TCAATTCC
*
29006 TCAATTAC
1 TCAATTCC
* *
29014 TCAATGCT
1 TCAATTCC
29022 TCAATTCC
1 TCAATTCC
29030 TCAATT
1 TCAATT
29036 TACTTCAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.28, C:0.30, G:0.02, T:0.39
Consensus pattern (8 bp):
TCAATTCC
Found at i:29017 original size:24 final size:26
Alignment explanation
Indices: 28989--29045 Score: 82
Period size: 24 Copynumber: 2.3 Consensus size: 26
28979 CTCTTATTGT
*
28989 TTCAATTCCTCAATTCCTCAA-TTAC
1 TTCAATGCCTCAATTCCTCAATTTAC
*
29014 -TCAATGCTTCAATTCCTCAATTTAC
1 TTCAATGCCTCAATTCCTCAATTTAC
29039 TTCAATG
1 TTCAATG
29046 ATCCAGGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 18 0.64
25 4 0.14
26 6 0.21
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (26 bp):
TTCAATGCCTCAATTCCTCAATTTAC
Found at i:29129 original size:22 final size:21
Alignment explanation
Indices: 29088--29576 Score: 185
Period size: 22 Copynumber: 22.6 Consensus size: 21
29078 ATTCAATACC
*
29088 TCAATTTCAATAT-TTTAATGT
1 TCAATTTCAAT-TCTTCAATGT
29109 TGCAATTTCAATTCTTCAATGTT
1 T-CAATTTCAATTCTTCAATG-T
29132 TC--TTTCAATTCTTCAATGCT
1 TCAATTTCAATTCTTCAATG-T
* *
29152 TCAATTTGAATAT-GTCAAT-T
1 TCAATTTCAAT-TCTTCAATGT
* *
29172 TCAATTCTCCAATTTTTCAAAGCT
1 TCAATT-T-CAATTCTTCAATG-T
*
29196 TCAATTTCAATTCTTCAA-AT
1 TCAATTTCAATTCTTCAATGT
* * *
29216 TCAATCCTCCAA-T-TTCAGCTCT
1 TCAAT--TTCAATTCTTCA-ATGT
* *
29238 TCAAATTCAATCCTTCAATGT
1 TCAATTTCAATTCTTCAATGT
* *
29259 CTCAATTCCAATTCTTCAATTCT
1 -TCAATTTCAATTCTTCAA-TGT
*
29282 TCAAATTCAATTCTTCAATGTT
1 TCAATTTCAATTCTTCAATG-T
* *
29304 TCAATTTCAATAT-TCCAATCCT
1 TCAATTTCAAT-TCTTCAAT-GT
*
29326 TCAATGTCTCAA-T-TTCAATTCT
1 TCAAT-T-TCAATTCTTCAA-TGT
* *
29348 TCAAATTCAATCCTTCAAT-T
1 TCAATTTCAATTCTTCAATGT
* *
29368 TCAA-TTCTATTCTTCAGTGTT
1 TCAATTTCAATTCTTCAATG-T
* *
29389 TCATGTTTCAATCCTTCAATGTT
1 TCA-ATTTCAATTCTTCAATG-T
*
29412 TCAAAGCTTCAA-T-TTCAA--T
1 TC-AA-TTTCAATTCTTCAATGT
* * *
29431 TCTATCCTTCAGTGT-TTCCAT-T
1 TCAAT--TTCAAT-TCTTCAATGT
*
29453 TCAATTCTTCAATGT-TTCAAAGCT
1 TCAA-T-TTCAAT-TCTTCAATG-T
* **
29477 TCAAATTCAATTCCCCAATGCT
1 TCAATTTCAATTCTTCAATG-T
**
29499 TCAATTTCGGTAT-TTCAATGTT
1 TCAATTTCAAT-TCTTCAATG-T
29521 TCAATTTCAATTCTTCAATGTT
1 TCAATTTCAATTCTTCAATG-T
29543 TCAATTTCAATAT-TTCAATGCT
1 TCAATTTCAAT-TCTTCAATG-T
*
29565 TTAATTTCAATT
1 TCAATTTCAATT
29577 TCAATCCCAA
Statistics
Matches: 361, Mismatches: 62, Indels: 90
0.70 0.12 0.18
Matches are distributed among these distances:
18 1 0.00
19 18 0.05
20 49 0.14
21 22 0.06
22 221 0.61
23 28 0.08
24 22 0.06
ACGTcount: A:0.28, C:0.22, G:0.05, T:0.45
Consensus pattern (21 bp):
TCAATTTCAATTCTTCAATGT
Found at i:29421 original size:16 final size:16
Alignment explanation
Indices: 29391--29424 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29381 TCAGTGTTTC
*
29391 ATGTTTCAATCCTTCA
1 ATGTTTCAAACCTTCA
*
29407 ATGTTTCAAAGCTTCA
1 ATGTTTCAAACCTTCA
29423 AT
1 AT
29425 TTCAATTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (16 bp):
ATGTTTCAAACCTTCA
Found at i:29486 original size:57 final size:57
Alignment explanation
Indices: 29303--29489 Score: 218
Period size: 58 Copynumber: 3.2 Consensus size: 57
29293 TCTTCAATGT
* * * * * **
29303 TTCAATTTCAATATTCCAATCCTTCAATGTCTCAATTTCAATTCTTCAA--ATTCAATCC
1 TTCAATTTC-A-ATT-CTATCCTTCAGTGTTTCCATTTCAATTCTTCAATGTTTCAAAGC
* *
29361 TTCAATTTCAATTCTATTCTTCAGTGTTT-CATGTTTCAATCCTTCAATGTTTCAAAGC
1 TTCAATTTCAATTCTATCCTTCAGTGTTTCCA--TTTCAATTCTTCAATGTTTCAAAGC
29419 TTCAATTTCAATTCTATCCTTCAGTGTTTCCATTTCAATTCTTCAATGTTTCAAAGC
1 TTCAATTTCAATTCTATCCTTCAGTGTTTCCATTTCAATTCTTCAATGTTTCAAAGC
*
29476 TTCAAATTCAATTC
1 TTCAATTTCAATTC
29490 CCCAATGCTT
Statistics
Matches: 112, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
54 1 0.01
55 12 0.11
56 16 0.14
57 38 0.34
58 43 0.38
59 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.44
Consensus pattern (57 bp):
TTCAATTTCAATTCTATCCTTCAGTGTTTCCATTTCAATTCTTCAATGTTTCAAAGC
Found at i:29522 original size:8 final size:7
Alignment explanation
Indices: 29511--29581 Score: 53
Period size: 8 Copynumber: 10.0 Consensus size: 7
29501 AATTTCGGTA
29511 TTTCAAT
1 TTTCAAT
29518 GTTTCAA-
1 -TTTCAAT
29525 TTTCAAT
1 TTTCAAT
29532 TCTTCAAT
1 T-TTCAAT
29540 GTTTCAA-
1 -TTTCAAT
29547 TTTCAAT
1 TTTCAAT
29554 ATTTCAAT
1 -TTTCAAT
29562 GCTTT-AA-
1 --TTTCAAT
29569 TTTCAA-
1 TTTCAAT
29575 TTTCAAT
1 TTTCAAT
29582 CCCAAATGTC
Statistics
Matches: 54, Mismatches: 1, Indels: 17
0.75 0.01 0.24
Matches are distributed among these distances:
5 3 0.06
6 20 0.37
7 1 0.02
8 26 0.48
9 4 0.07
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (7 bp):
TTTCAAT
Found at i:29639 original size:22 final size:22
Alignment explanation
Indices: 29596--29646 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
29586 AATGTCAGTG
**
29596 CTTCAATTTTGATTCTTCAATA
1 CTTCAATTTCCATTCTTCAATA
* *
29618 CTTCAATTTCCATTTTTTAATA
1 CTTCAATTTCCATTCTTCAATA
*
29640 TTTCAAT
1 CTTCAAT
29647 CCTTCAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.18, G:0.02, T:0.53
Consensus pattern (22 bp):
CTTCAATTTCCATTCTTCAATA
Found at i:29698 original size:22 final size:22
Alignment explanation
Indices: 29641--29745 Score: 74
Period size: 22 Copynumber: 4.7 Consensus size: 22
29631 TTTTTAATAT
*
29641 TTCAATCCTTCAAATTC-T-AAA
1 TTCAATTCTTC-AATTCTTCAAA
*
29662 TGTCAATGCTTCAATTCTTCAAA
1 T-TCAATTCTTCAATTCTTCAAA
*
29685 TTCAATTCTTCAATGT-TTCAAT
1 TTCAATTCTTCAAT-TCTTCAAA
* * *
29707 TTCAATAT-TTCAATGCTTGAAT
1 TTCAAT-TCTTCAATTCTTCAAA
*
29729 TTCAATTCCTCGAATTC
1 TTCAATTCTTC-AATTC
29746 AATCCTTCAA
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
21 7 0.10
22 52 0.75
23 10 0.14
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (22 bp):
TTCAATTCTTCAATTCTTCAAA
Found at i:29698 original size:30 final size:30
Alignment explanation
Indices: 29611--29765 Score: 104
Period size: 30 Copynumber: 5.2 Consensus size: 30
29601 ATTTTGATTC
* * * * * *
29611 TTCAATACTTCAATTTCCATTTTTTAATAT
1 TTCAATTCTTCAAATTCAATTCTTCAATGT
* * * *
29641 TTCAATCCTTCAAATTCTAAAT-GTCAATGC
1 TTCAATTCTTCAAATTC-AATTCTTCAATGT
29671 TTCAATTCTTCAAATTCAATTCTTCAATGT
1 TTCAATTCTTCAAATTCAATTCTTCAATGT
* *
29701 TTCAA-T-TTCAATATTTCAATGCTTGAA--T
1 TTCAATTCTTCAA-A-TTCAATTCTTCAATGT
* * * *
29729 TTCAATTCCTCGAATTCAATCCTTCAACGT
1 TTCAATTCTTCAAATTCAATTCTTCAATGT
29759 TTCAATT
1 TTCAATT
29766 TCAATAAGTT
Statistics
Matches: 99, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
28 22 0.22
29 7 0.07
30 68 0.69
31 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.45
Consensus pattern (30 bp):
TTCAATTCTTCAAATTCAATTCTTCAATGT
Found at i:29780 original size:58 final size:58
Alignment explanation
Indices: 29671--29782 Score: 163
Period size: 58 Copynumber: 1.9 Consensus size: 58
29661 ATGTCAATGC
* * * *
29671 TTCAATTCTTCAAATTCAATTCTTCAATGTTTCAATTTCAATATTTCAATGCTTGAAT
1 TTCAATTCCTCAAATTCAATCCTTCAACGTTTCAATTTCAATAGTTCAATGCTTGAAT
*
29729 TTCAATTCCTCGAATTCAATCCTTCAACGTTTCAATTTCAATAAGTT-AATGCTT
1 TTCAATTCCTCAAATTCAATCCTTCAACGTTTCAATTTCAAT-AGTTCAATGCTT
29783 CAATGATCCA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
58 45 0.94
59 3 0.06
ACGTcount: A:0.30, C:0.20, G:0.06, T:0.44
Consensus pattern (58 bp):
TTCAATTCCTCAAATTCAATCCTTCAACGTTTCAATTTCAATAGTTCAATGCTTGAAT
Found at i:31617 original size:16 final size:17
Alignment explanation
Indices: 31562--31619 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
31552 CGTATTCTTC
* *
31562 TTTTTATTAATT-GCCA
1 TTTTTACTAATTATCCA
*
31578 TTTTTACTAATTATCCTC
1 TTTTTACTAATTATCC-A
*
31596 TTTTTACTGATTA-CCA
1 TTTTTACTAATTATCCA
31612 TTTTTACT
1 TTTTTACT
31620 TTTGCTACTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 19 0.54
17 4 0.11
18 12 0.34
ACGTcount: A:0.22, C:0.17, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTTTACTAATTATCCA
Found at i:31649 original size:49 final size:50
Alignment explanation
Indices: 31596--31721 Score: 139
Period size: 49 Copynumber: 2.5 Consensus size: 50
31586 AATTATCCTC
** *
31596 TTTTTACTGATTACCATTTTTACTTTTGCTACT-TTTATCATTTTTA-GCT
1 TTTTTACTGATTACCATTTTTACTTTT-CTACTGAATACCATTTTTATGCT
* * * *
31645 TTTTTACTGAATGCCATTTTTACTCTTTTTACTGAATACCATTTTTATTCT
1 TTTTTACTGATTACCATTTTTACT-TTTCTACTGAATACCATTTTTATGCT
* *
31696 TTTCTACTGATTACCATTTTCACTTT
1 TTTTTACTGATTACCATTTTTACTTT
31722 ACTAATTACT
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
49 26 0.41
50 15 0.24
51 22 0.35
ACGTcount: A:0.20, C:0.18, G:0.06, T:0.56
Consensus pattern (50 bp):
TTTTTACTGATTACCATTTTTACTTTTCTACTGAATACCATTTTTATGCT
Found at i:31652 original size:24 final size:24
Alignment explanation
Indices: 31596--31721 Score: 128
Period size: 25 Copynumber: 5.1 Consensus size: 24
31586 AATTATCCTC
31596 TTTTTACTGATTACCATTTTTACT
1 TTTTTACTGATTACCATTTTTACT
* * *
31620 TTTGCTACT-TTTATCATTTTTAGCT
1 TTT-TTACTGATTACCATTTTTA-CT
* *
31645 TTTTTACTGAATGCCATTTTTACT
1 TTTTTACTGATTACCATTTTTACT
*
31669 CTTTTTACTGAATACCATTTTTATTCT
1 -TTTTTACTGATTACCATTTTTA--CT
* *
31696 TTTCTACTGATTACCATTTTCACT
1 TTTTTACTGATTACCATTTTTACT
31720 TT
1 TT
31722 ACTAATTACT
Statistics
Matches: 84, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
24 24 0.29
25 39 0.46
26 19 0.23
27 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.06, T:0.56
Consensus pattern (24 bp):
TTTTTACTGATTACCATTTTTACT
Found at i:31724 original size:21 final size:21
Alignment explanation
Indices: 31700--31744 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
31690 TATTCTTTTC
* *
31700 TACTGATTACCATTTTCACTT
1 TACTAATTACCATTTACACTT
* *
31721 TACTAATTACTATTTACTCTT
1 TACTAATTACCATTTACACTT
31742 TAC
1 TAC
31745 CATTTTACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.22, G:0.02, T:0.49
Consensus pattern (21 bp):
TACTAATTACCATTTACACTT
Found at i:31743 original size:7 final size:7
Alignment explanation
Indices: 31727--32369 Score: 280
Period size: 7 Copynumber: 88.7 Consensus size: 7
31717 ACTTTACTAA
*
31727 TTACTAT
1 TTACTCT
31734 TTACTCT
1 TTACTCT
31741 TTAC-CATT
1 TTACTC--T
*
31749 TTACTTT
1 TTACTCT
**
31756 TTACTGA
1 TTACTCT
31763 TTACTCT
1 TTACTCT
*
31770 TTACTTT
1 TTACTCT
31777 TTAC-CATT
1 TTACTC--T
*
31785 TTACCCT
1 TTACTCT
**
31792 TTACTGA
1 TTACTCT
31799 TTACTCT
1 TTACTCT
31806 TTACTCT
1 TTACTCT
**
31813 TTACTAA
1 TTACTCT
*
31820 TTACTATT
1 TTACT-CT
31828 TTACTCT
1 TTACTCT
* *
31835 CTTGAATTT
1 -TT-ACTCT
31844 AATTAC-CATT
1 --TTACTC--T
31854 TTAC-CATT
1 TTACTC--T
*
31862 TTTCTCT
1 TTACTCT
**
31869 TTACTGA
1 TTACTCT
31876 TTACTCT
1 TTACTCT
*
31883 TTACTTT
1 TTACTCT
31890 TTACTCT
1 TTACTCT
*
31897 TTTCTCT
1 TTACTCT
**
31904 TTACTGA
1 TTACTCT
31911 TTACTCT
1 TTACTCT
*
31918 ATACTCT
1 TTACTCT
31925 TTACTCT
1 TTACTCT
*
31932 TTTCTCT
1 TTACTCT
***
31939 TTACGGA
1 TTACTCT
31946 TTACTCT
1 TTACTCT
*
31953 ATACTCT
1 TTACTCT
*
31960 TTACTGT
1 TTACTCT
*
31967 TTTCTCT
1 TTACTCT
**
31974 TTACTGA
1 TTACTCT
31981 TTACTCT
1 TTACTCT
*
31988 ATACTCT
1 TTACTCT
31995 TTAC-CATT
1 TTACTC--T
* *
32003 TTCCCCT
1 TTACTCT
**
32010 TTACTGA
1 TTACTCT
32017 TTACTCT
1 TTACTCT
*
32024 TTACTTT
1 TTACTCT
32031 TTAC-CAT
1 TTACTC-T
*
32038 TTCACTAT
1 TT-ACTCT
* **
32046 TTATTGA
1 TTACTCT
32053 TTACTCT
1 TTACTCT
32060 TTACTCT
1 TTACTCT
**
32067 TTACTAA
1 TTACTCT
*
32074 TTACTATT
1 TTACT-CT
32082 TTACTCT
1 TTACTCT
* *
32089 CTTGAATTT
1 -TT-ACTCT
32098 AATTAC-CATT
1 --TTACTC--T
32108 TTAC-CATT
1 TTACTC--T
*
32116 TTTCTCT
1 TTACTCT
**
32123 TTACTGA
1 TTACTCT
32130 TTACTCT
1 TTACTCT
*
32137 TTACTTT
1 TTACTCT
32144 TTACTCT
1 TTACTCT
*
32151 TTTCTCT
1 TTACTCT
**
32158 TTACTGA
1 TTACTCT
32165 TTACTCT
1 TTACTCT
*
32172 ATACTCT
1 TTACTCT
32179 TTACTCT
1 TTACTCT
*
32186 TTTCTCT
1 TTACTCT
**
32193 TTACTGA
1 TTACTCT
32200 TTACTCT
1 TTACTCT
*
32207 ATACTCT
1 TTACTCT
32214 TTACTCT
1 TTACTCT
*
32221 TTTCTCT
1 TTACTCT
**
32228 TTACTGA
1 TTACTCT
32235 TTACTCT
1 TTACTCT
*
32242 ATACTCT
1 TTACTCT
32249 TTAC-CATT
1 TTACTC--T
*
32257 TTCCTCT
1 TTACTCT
**
32264 TTACTGA
1 TTACTCT
32271 TTACTCT
1 TTACTCT
*
32278 TTACTTT
1 TTACTCT
32285 TTAC-CATT
1 TTACTC--T
32293 TTACTCT
1 TTACTCT
* **
32300 TTATTGA
1 TTACTCT
32307 TTACTCT
1 TTACTCT
32314 TTACTCTT
1 TTACTC-T
*
32322 TTTCTCT
1 TTACTCT
**
32329 TTACTGA
1 TTACTCT
32336 TTACTCT
1 TTACTCT
32343 TTACTCT
1 TTACTCT
32350 TTACTCTT
1 TTACTC-T
*
32358 TTTCTCT
1 TTACTCT
32365 TTACT
1 TTACT
32370 AATTACTATT
Statistics
Matches: 463, Mismatches: 139, Indels: 68
0.69 0.21 0.10
Matches are distributed among these distances:
6 3 0.01
7 364 0.79
8 76 0.16
9 14 0.03
10 6 0.01
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.55
Consensus pattern (7 bp):
TTACTCT
Found at i:31744 original size:14 final size:14
Alignment explanation
Indices: 31727--32490 Score: 180
Period size: 14 Copynumber: 54.1 Consensus size: 14
31717 ACTTTACTAA
31727 TTACTATTTACTCT
1 TTACTATTTACTCT
* *
31741 TTACCATTTTACTTT
1 TTACTA-TTTACTCT
31756 TTACTGA-TTACTCT
1 TTACT-ATTTACTCT
*
31770 TTACTTTTTAC-C-
1 TTACTATTTACTCT
*
31782 --A-T-TTTACCCT
1 TTACTATTTACTCT
31792 TTACTGA-TTACTCT
1 TTACT-ATTTACTCT
* **
31806 TTACTCTTTACTAA
1 TTACTATTTACTCT
31820 TTACTATTTTACTCT
1 TTACTA-TTTACTCT
* *
31835 CTTGAATTTAATTAC-CATT
1 -TT--A-CTATTTACTC--T
* *
31854 TTACCATTTTTCTCT
1 TTACTA-TTTACTCT
31869 TTACTGA-TTACTCT
1 TTACT-ATTTACTCT
*
31883 TTACTTTTTACTCT
1 TTACTATTTACTCT
* * **
31897 TTTCTCTTTACTGA
1 TTACTATTTACTCT
* *
31911 TTACTCTATACTCT
1 TTACTATTTACTCT
* *
31925 TTACTCTTTTCTCT
1 TTACTATTTACTCT
*
31939 TTACGGA-TTACTCT
1 TTAC-TATTTACTCT
* * *
31953 ATACTCTTTACTGT
1 TTACTATTTACTCT
* * **
31967 TTTCTCTTTACTGA
1 TTACTATTTACTCT
* *
31981 TTACTCTATACTCT
1 TTACTATTTACTCT
* * *
31995 TTACCATTTTCCCCT
1 TTACTA-TTTACTCT
32010 TTACTGA-TTACTCT
1 TTACT-ATTTACTCT
*
32024 TTACTTTTTAC-CAT
1 TTACTATTTACTC-T
* **
32038 TTCACTATTTATTGA
1 TT-ACTATTTACTCT
*
32053 TTACTCTTTACTCT
1 TTACTATTTACTCT
* *
32067 TTACTAATTACTATT
1 TTACTATTTACT-CT
* *
32082 TTACTCTCTTGA--AT
1 TTACTAT-TT-ACTCT
32096 TTA--A-TTAC-CATT
1 TTACTATTTACTC--T
* *
32108 TTACCATTTTTCTCT
1 TTACTA-TTTACTCT
32123 TTACTGA-TTACTCT
1 TTACT-ATTTACTCT
*
32137 TTACTTTTTACTCT
1 TTACTATTTACTCT
* * **
32151 TTTCTCTTTACTGA
1 TTACTATTTACTCT
* *
32165 TTACTCTATACTCT
1 TTACTATTTACTCT
* *
32179 TTACTCTTTTCTCT
1 TTACTATTTACTCT
32193 TTACTGA-TTACTCT
1 TTACT-ATTTACTCT
* *
32207 ATACTCTTTACTCT
1 TTACTATTTACTCT
* * **
32221 TTTCTCTTTACTGA
1 TTACTATTTACTCT
* *
32235 TTACTCTATACTCT
1 TTACTATTTACTCT
* *
32249 TTACCATTTTCCTCT
1 TTACTA-TTTACTCT
32264 TTACTGA-TTACTCT
1 TTACT-ATTTACTCT
*
32278 TTACTTTTTAC-C-
1 TTACTATTTACTCT
32290 --A-T-TTTACTCT
1 TTACTATTTACTCT
*
32300 TTATTGA-TTACTCT
1 TTACT-ATTTACTCT
* *
32314 TTACTCTTTTTCTCT
1 TTACT-ATTTACTCT
32329 TTACTGA-TTACTCT
1 TTACT-ATTTACTCT
*
32343 TTACTCTTTACTCTT
1 TTACTATTTACTC-T
* * **
32358 TTTCTCTTTACTAA
1 TTACTATTTACTCT
32372 TTACTATTTTACTCT
1 TTACTA-TTTACTCT
* *
32387 CTTGAATTTAATTAC-CATT
1 -TT--A-CTATTTACTC--T
*
32406 TTACCATTTTACTCT
1 TTACTA-TTTACTCT
32421 TTACTGA-TTACTCT
1 TTACT-ATTTACTCT
*
32435 TTACTTTTTAC-CAT
1 TTACTATTTACTC-T
*
32449 TT--TTTTTACTCT
1 TTACTATTTACTCT
32461 TTACTGA-TTACTTCTT
1 TTACT-ATTTAC-TC-T
32477 TTACT-TTTACTCT
1 TTACTATTTACTCT
32490 T
1 T
32491 AATTACCAAC
Statistics
Matches: 547, Mismatches: 126, Indels: 155
0.66 0.15 0.19
Matches are distributed among these distances:
8 10 0.02
9 5 0.01
10 4 0.01
12 16 0.03
13 9 0.02
14 344 0.63
15 103 0.19
16 30 0.05
17 6 0.01
18 14 0.03
19 6 0.01
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.55
Consensus pattern (14 bp):
TTACTATTTACTCT
Found at i:31774 original size:43 final size:41
Alignment explanation
Indices: 31727--31834 Score: 109
Period size: 36 Copynumber: 2.7 Consensus size: 41
31717 ACTTTACTAA
*
31727 TTACTATTTACTCTTTACCATTTTACTTTTTACTGATTACTCT
1 TTACT-TTTACT-TTTACCATTTTACTCTTTACTGATTACTCT
*
31770 TTAC---T--TTTTACCATTTTACCCTTTACTGATTACTCT
1 TTACTTTTACTTTTACCATTTTACTCTTTACTGATTACTCT
* *
31806 TTACTCTTTACTAATTACTATTTTACTCT
1 TTACT-TTTACT-TTTACCATTTTACTCT
31835 CTTGAATTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
36 32 0.60
37 1 0.02
39 1 0.02
40 1 0.02
42 1 0.02
43 17 0.32
ACGTcount: A:0.21, C:0.22, G:0.02, T:0.55
Consensus pattern (41 bp):
TTACTTTTACTTTTACCATTTTACTCTTTACTGATTACTCT
Found at i:31907 original size:35 final size:35
Alignment explanation
Indices: 31861--32386 Score: 554
Period size: 35 Copynumber: 14.8 Consensus size: 35
31851 ATTTTACCAT
*
31861 TTTTCTCTTTACTGATTACTCTTTACTTTTTACTC
1 TTTTCTCTTTACTGATTACTCTTTACTCTTTACTC
*
31896 TTTTCTCTTTACTGATTACTCTATACTCTTTACTC
1 TTTTCTCTTTACTGATTACTCTTTACTCTTTACTC
* * *
31931 TTTTCTCTTTACGGATTACTCTATACTCTTTACTG
1 TTTTCTCTTTACTGATTACTCTTTACTCTTTACTC
*
31966 TTTTCTCTTTACTGATTACTCTATACTCTTTAC-C
1 TTTTCTCTTTACTGATTACTCTTTACTCTTTACTC
* *
32000 ATTTTCCCCTTTACTGATTACTCTTTACTTTTTAC-C
1 -TTTT-CTCTTTACTGATTACTCTTTACTCTTTACTC
* * * *
32036 ATTTCACTATTTATTGATTACTCTTTACTCTTTACTA
1 -TTT-TCTCTTTACTGATTACTCTTTACTCTTTACTC
* * * ** * *
32073 ATTACTATTTTACTCTCTTGAATTTAATTAC-CATTTTAC-C
1 TTTTCT-CTTTACT-GATT-ACTCT--TTACTC--TTTACTC
*
32113 ATTTTTCTCTTTACTGATTACTCTTTACTTTTTACTC
1 --TTTTCTCTTTACTGATTACTCTTTACTCTTTACTC
*
32150 TTTTCTCTTTACTGATTACTCTATACTCTTTACTC
1 TTTTCTCTTTACTGATTACTCTTTACTCTTTACTC
*
32185 TTTTCTCTTTACTGATTACTCTATACTCTTTACTC
1 TTTTCTCTTTACTGATTACTCTTTACTCTTTACTC
*
32220 TTTTCTCTTTACTGATTACTCTATACTCTTTAC-C
1 TTTTCTCTTTACTGATTACTCTTTACTCTTTACTC
*
32254 ATTTTCCTCTTTACTGATTACTCTTTACTTTTTAC-C
1 -TTTT-CTCTTTACTGATTACTCTTTACTCTTTACTC
*
32290 ATTTTACTCTTTATTGATTACTCTTTA--C--T-CT-
1 -TTTT-CTCTTTACTGATTACTCTTTACTCTTTACTC
32321 TTTTCTCTTTACTGATTACTCTTTACTCTTTACTC
1 TTTTCTCTTTACTGATTACTCTTTACTCTTTACTC
* *
32356 TTTTTCTCTTTACTAATTACTATTTTACTCT
1 -TTTTCTCTTTACTGATTACT-CTTTACTCT
32387 CTTGAATTTA
Statistics
Matches: 424, Mismatches: 41, Indels: 50
0.82 0.08 0.10
Matches are distributed among these distances:
29 20 0.05
30 4 0.01
31 2 0.00
32 1 0.00
33 1 0.00
34 3 0.01
35 210 0.50
36 140 0.33
37 15 0.04
38 3 0.01
39 4 0.01
40 6 0.01
41 11 0.03
42 4 0.01
ACGTcount: A:0.18, C:0.24, G:0.03, T:0.55
Consensus pattern (35 bp):
TTTTCTCTTTACTGATTACTCTTTACTCTTTACTC
Found at i:32021 original size:254 final size:254
Alignment explanation
Indices: 31712--32322 Score: 1105
Period size: 254 Copynumber: 2.4 Consensus size: 254
31702 CTGATTACCA
* * * * * *
31712 TTTTCACTTTACTAATTACTATTTACTCTTTACCATTTTACTTTTTACTGATTACTCTTTACTTT
1 TTTTCTCTTTACTGATTACTCTATACTCTTTACCATTTTCCTCTTTACTGATTACTCTTTACTTT
* *
31777 TTACCATTTTACCCTTTACTGATTACTCTTTACTCTTTACTAATTACTATTTTACTCTCTTGAAT
66 TTACCATTTTACTCTTTATTGATTACTCTTTACTCTTTACTAATTACTATTTTACTCTCTTGAAT
31842 TTAATTACCATTTTACCATTTTTCTCTTTACTGATTACTCTTTACTTTTTACTCTTTTCTCTTTA
131 TTAATTACCATTTTACCATTTTTCTCTTTACTGATTACTCTTTACTTTTTACTCTTTTCTCTTTA
*
31907 CTGATTACTCTATACTCTTTACTCTTTTCTCTTTACGGATTACTCTATACTCTTTACTG
196 CTGATTACTCTATACTCTTTACTCTTTTCTCTTTACGGATTACTCTATACTCTTTACTC
*
31966 TTTTCTCTTTACTGATTACTCTATACTCTTTACCATTTTCCCCTTTACTGATTACTCTTTACTTT
1 TTTTCTCTTTACTGATTACTCTATACTCTTTACCATTTTCCTCTTTACTGATTACTCTTTACTTT
* *
32031 TTACCATTTCACTATTTATTGATTACTCTTTACTCTTTACTAATTACTATTTTACTCTCTTGAAT
66 TTACCATTTTACTCTTTATTGATTACTCTTTACTCTTTACTAATTACTATTTTACTCTCTTGAAT
32096 TTAATTACCATTTTACCATTTTTCTCTTTACTGATTACTCTTTACTTTTTACTCTTTTCTCTTTA
131 TTAATTACCATTTTACCATTTTTCTCTTTACTGATTACTCTTTACTTTTTACTCTTTTCTCTTTA
*
32161 CTGATTACTCTATACTCTTTACTCTTTTCTCTTTACTGATTACTCTATACTCTTTACTC
196 CTGATTACTCTATACTCTTTACTCTTTTCTCTTTACGGATTACTCTATACTCTTTACTC
32220 TTTTCTCTTTACTGATTACTCTATACTCTTTACCATTTTCCTCTTTACTGATTACTCTTTACTTT
1 TTTTCTCTTTACTGATTACTCTATACTCTTTACCATTTTCCTCTTTACTGATTACTCTTTACTTT
32285 TTACCATTTTACTCTTTATTGATTACTCTTTACTCTTT
66 TTACCATTTTACTCTTTATTGATTACTCTTTACTCTTT
32323 TTCTCTTTAC
Statistics
Matches: 341, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
254 341 1.00
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.54
Consensus pattern (254 bp):
TTTTCTCTTTACTGATTACTCTATACTCTTTACCATTTTCCTCTTTACTGATTACTCTTTACTTT
TTACCATTTTACTCTTTATTGATTACTCTTTACTCTTTACTAATTACTATTTTACTCTCTTGAAT
TTAATTACCATTTTACCATTTTTCTCTTTACTGATTACTCTTTACTTTTTACTCTTTTCTCTTTA
CTGATTACTCTATACTCTTTACTCTTTTCTCTTTACGGATTACTCTATACTCTTTACTC
Found at i:32438 original size:29 final size:29
Alignment explanation
Indices: 32278--32438 Score: 114
Period size: 29 Copynumber: 5.4 Consensus size: 29
32268 TGATTACTCT
* *
32278 TTACTTTTTACCATTTTACTCTTTATTGA
1 TTACTCTTTACCATTTTACTCTTTACTGA
*
32307 TTACTCTTTACTC-TTTTTCTCTTTACTGA
1 TTACTCTTTAC-CATTTTACTCTTTACTGA
* **
32336 TTACTCTTTA-C-TCTTTACTCTTTTTCTCT
1 TTACTCTTTACCAT-TTTACTC-TTTACTGA
** * * *
32365 TTACTAATTACTATTTTACTCTCTTGAATTTAA
1 TTACTCTTTACCATTTTACTCT-TT--A-CTGA
32398 TTAC-CATTTTACCATTTTACTCTTTACTGA
1 TTACTC--TTTACCATTTTACTCTTTACTGA
32428 TTACTCTTTAC
1 TTACTCTTTAC
32439 TTTTTACCAT
Statistics
Matches: 101, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
27 2 0.02
28 6 0.06
29 53 0.52
30 16 0.16
31 3 0.03
33 7 0.07
34 14 0.14
ACGTcount: A:0.20, C:0.22, G:0.02, T:0.56
Consensus pattern (29 bp):
TTACTCTTTACCATTTTACTCTTTACTGA
Found at i:32545 original size:32 final size:32
Alignment explanation
Indices: 32502--32578 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
32492 ATTACCAACT
* *
32502 TACTGACTACTTCTTTTACTTTTACTCCATT-
1 TACTGATTACTTCTTTTACTTTCACTCCATTC
32533 TCACTGATTACTTCTTTTACTTTCACTCCATTC
1 T-ACTGATTACTTCTTTTACTTTCACTCCATTC
*
32566 TACTGATCACTTC
1 TACTGATTACTTC
32579 CTCTTTTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
31 1 0.02
32 39 0.95
33 1 0.02
ACGTcount: A:0.19, C:0.29, G:0.04, T:0.48
Consensus pattern (32 bp):
TACTGATTACTTCTTTTACTTTCACTCCATTC
Found at i:32762 original size:32 final size:32
Alignment explanation
Indices: 32694--32766 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
32684 CTAATTAATC
* * * *
32694 CTTTTACCTTGACTCTTAATTATTGACTTACC
1 CTTTTACTTTGACCCTTAATTACTGACTTACA
*
32726 CTTTTACTTTGACCCTTAATTACTGA-TTGCTA
1 CTTTTACTTTGACCCTTAATTACTGACTTAC-A
32758 CTTTTACTT
1 CTTTTACTT
32767 CCTCTCTTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 3 0.09
32 32 0.91
ACGTcount: A:0.21, C:0.23, G:0.07, T:0.49
Consensus pattern (32 bp):
CTTTTACTTTGACCCTTAATTACTGACTTACA
Found at i:32840 original size:38 final size:39
Alignment explanation
Indices: 32743--32840 Score: 92
Period size: 38 Copynumber: 2.5 Consensus size: 39
32733 TTTGACCCTT
* * * *
32743 AATTACTGATTGCTACTTTTACTTCCTCTCTTAGTTATC
1 AATTACTGATTACTACTTTTACTTCCTCTCTTAATCACC
* * * *
32782 AATTTACTAATGAATCCTTTTACTT-C-CTCTTAATCACC
1 AA-TTACTGATTACTACTTTTACTTCCTCTCTTAATCACC
32820 AATTGACTGATTACTACTTTT
1 AATT-ACTGATTACTACTTTT
32841 TTATCTTTTC
Statistics
Matches: 45, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
37 2 0.04
38 23 0.51
39 3 0.07
40 17 0.38
ACGTcount: A:0.26, C:0.22, G:0.06, T:0.46
Consensus pattern (39 bp):
AATTACTGATTACTACTTTTACTTCCTCTCTTAATCACC
Done.