Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397272.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.0, 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: 3572271
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 44823 characters in sequence are not A, C, G, or T
File 9 of 9
Found at i:3403684 original size:51 final size:51
Alignment explanation
Indices: 3403620--3403748 Score: 159
Period size: 51 Copynumber: 2.5 Consensus size: 51
3403610 TCATTGCACT
* * * *
3403620 ATCTCTTATTAATGTGGTATGCTATACTCTCATTAGATTATCTAGTTAGCC
1 ATCTCTTACTAATGTAGTATGCTATACTCTCATCAAATTATCTAGTTAGCC
* ** ** *
3403671 ATCTCTTACTAATGTAGTATGCTATACTTTTGTCAAATTATCTCTTTAGCT
1 ATCTCTTACTAATGTAGTATGCTATACTCTCATCAAATTATCTAGTTAGCC
*
3403722 ATCTCTTACTAATGTAGTATGCAATAC
1 ATCTCTTACTAATGTAGTATGCTATAC
3403749 CCTCGTTGCA
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (51 bp):
ATCTCTTACTAATGTAGTATGCTATACTCTCATCAAATTATCTAGTTAGCC
Found at i:3410986 original size:33 final size:33
Alignment explanation
Indices: 3410949--3411034 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
3410939 TTTTAAAGTC
3410949 ATATATTTTATTTTTATTT-ATTAATATAATCTT
1 ATATATTTTATTTTTATTTCATTAATAT-ATCTT
* *
3410982 ATATATTTTATTTTTATTTCTTTAATATATTTT
1 ATATATTTTATTTTTATTTCATTAATATATCTT
* *
3411015 TTATATTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
3411035 TAAGTTGATT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
33 32 0.68
34 15 0.32
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTCATTAATATATCTT
Found at i:3411133 original size:15 final size:15
Alignment explanation
Indices: 3411110--3411141 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3411100 TTCTTATATT
3411110 ATATATTTTATTTTA
1 ATATATTTTATTTTA
*
3411125 ATATTTTTTATTTTA
1 ATATATTTTATTTTA
3411140 AT
1 AT
3411142 TATAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATATTTTATTTTA
Found at i:3411144 original size:33 final size:34
Alignment explanation
Indices: 3411082--3411150 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
3411072 TTATATTTTG
3411082 TTTTATTTTAATTTTTGATTCTTATATTAT-ATA
1 TTTTATTTTAATTTTTGATTCTTATATTATAATA
*
3411115 TTTTATTTTAATATTTTTTATT-TTA-ATTATAATA
1 TTTTATTTT-A-ATTTTTGATTCTTATATTATAATA
3411149 TT
1 TT
3411151 ATAAAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
33 14 0.44
34 9 0.28
35 9 0.28
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (34 bp):
TTTTATTTTAATTTTTGATTCTTATATTATAATA
Found at i:3416682 original size:28 final size:28
Alignment explanation
Indices: 3416595--3416682 Score: 95
Period size: 28 Copynumber: 3.1 Consensus size: 28
3416585 AAAGTAGATG
* * * *
3416595 AATACTTTTTACCCATCGAGAATGAATA
1 AATACTTTTAACCCACCAAGAATGGATA
* * *
3416623 AATACTTTTAACCCACAAAGAGTTGATA
1 AATACTTTTAACCCACCAAGAATGGATA
* *
3416651 AATACTTTTAACCAACCAAGAATGGATG
1 AATACTTTTAACCCACCAAGAATGGATA
3416679 AATA
1 AATA
3416683 GTGAAGAGAT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.28
Consensus pattern (28 bp):
AATACTTTTAACCCACCAAGAATGGATA
Found at i:3419198 original size:27 final size:29
Alignment explanation
Indices: 3419167--3419227 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 29
3419157 TTTCTCCATC
*
3419167 TCCTCC-CAT-GTTTCTTCCTTTTTTCCT
1 TCCTCCACATAGTTTCTTCCCTTTTTCCT
*
3419194 TCCTCCATATGAAGTTTCTTCCCTTTTTCCT
1 TCCTCCACAT--AGTTTCTTCCCTTTTTCCT
3419225 TCC
1 TCC
3419228 CCATTACTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 6 0.21
28 2 0.07
31 20 0.71
ACGTcount: A:0.08, C:0.36, G:0.05, T:0.51
Consensus pattern (29 bp):
TCCTCCACATAGTTTCTTCCCTTTTTCCT
Found at i:3422659 original size:18 final size:19
Alignment explanation
Indices: 3422619--3422666 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
3422609 TTAATATTTT
3422619 AATATTATTTTATTTATAA
1 AATATTATTTTATTTATAA
3422638 AATATTATTTTATTTA-AA
1 AATATTATTTTATTTATAA
*
3422656 AATATTCTTTT
1 AATATTATTTT
3422667 CACTTGTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
AATATTATTTTATTTATAA
Found at i:3439925 original size:28 final size:27
Alignment explanation
Indices: 3439892--3439991 Score: 130
Period size: 28 Copynumber: 3.6 Consensus size: 27
3439882 ATTATTTATC
*
3439892 CACTTTTAGTGGGTTAAAAGTATT-AGT
1 CACTTTTAGTGGGTTACAAGTATTCA-T
3439919 CTACTTTTAGTGGGTTACAAGTATTCATT
1 C-ACTTTTAGTGGGTTACAAGTATTCA-T
*
3439948 CACTTTTGGTGGGTTACAAGTATTCAT
1 CACTTTTAGTGGGTTACAAGTATTCAT
*
3439975 CCACTTTTGGTGGGTTA
1 -CACTTTTAGTGGGTTA
3439992 TCCACGTTTG
Statistics
Matches: 67, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.03
28 62 0.93
29 3 0.04
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.42
Consensus pattern (27 bp):
CACTTTTAGTGGGTTACAAGTATTCAT
Found at i:3439996 original size:18 final size:18
Alignment explanation
Indices: 3439973--3440027 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
3439963 ACAAGTATTC
3439973 ATCCACTTTTGGTGGGTT
1 ATCCACTTTTGGTGGGTT
*
3439991 ATCCACGTTTGGTGGGTT
1 ATCCACTTTTGGTGGGTT
*
3440009 ATCCACTTTTTGTGGGTT
1 ATCCACTTTTGGTGGGTT
3440027 A
1 A
3440028 GTGGGTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.13, C:0.16, G:0.27, T:0.44
Consensus pattern (18 bp):
ATCCACTTTTGGTGGGTT
Found at i:3440089 original size:26 final size:26
Alignment explanation
Indices: 3440060--3440120 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
3440050 TTCTTATGGT
3440060 AAAATTATTTATCCACTTC-GAGTGGC
1 AAAATTATTTATCCACTTCTG-GTGGC
* * *
3440086 AAAATTATCTATGCACTTCTGGTGGT
1 AAAATTATTTATCCACTTCTGGTGGC
3440112 AAAATTATT
1 AAAATTATT
3440121 CTGACGGCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 29 0.97
27 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (26 bp):
AAAATTATTTATCCACTTCTGGTGGC
Found at i:3441506 original size:22 final size:22
Alignment explanation
Indices: 3441453--3441542 Score: 83
Period size: 22 Copynumber: 4.1 Consensus size: 22
3441443 AACTTTGGAC
* * *
3441453 ATTGCATGACTAGTTTTTAAGC
1 ATTGCGTGACTAATTTTTAAGT
* *
3441475 ATTACATGACTAATTTTTAAGT
1 ATTGCGTGACTAATTTTTAAGT
* * * *
3441497 ATTGTGTGACTAA-CTTTGAGC
1 ATTGCGTGACTAATTTTTAAGT
*
3441518 ATTGCGTGACTAGTTTTTAAGT
1 ATTGCGTGACTAATTTTTAAGT
3441540 ATT
1 ATT
3441543 ATGAAATTGA
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
21 16 0.30
22 37 0.70
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (22 bp):
ATTGCGTGACTAATTTTTAAGT
Found at i:3441526 original size:21 final size:21
Alignment explanation
Indices: 3441409--3441529 Score: 57
Period size: 21 Copynumber: 5.7 Consensus size: 21
3441399 TTGCGTGATG
* *
3441409 GCATTGCATAACTGACTTT-A
1 GCATTGCATGACTAACTTTAA
* * * *
3441429 GACATTACGTGATTAACTTT-G
1 G-CATTGCATGACTAACTTTAA
**
3441450 GACATTGCATGACTAGTTTTTAA
1 G-CATTGCATGACTA-ACTTTAA
* *
3441473 GCATTACATGACTAATTTTTAA
1 GCATTGCATGACTAA-CTTTAA
* ** *
3441495 GTATTGTGTGACTAACTTTGA
1 GCATTGCATGACTAACTTTAA
*
3441516 GCATTGCGTGACTA
1 GCATTGCATGACTA
3441530 GTTTTTAAGT
Statistics
Matches: 75, Mismatches: 22, Indels: 7
0.72 0.21 0.07
Matches are distributed among these distances:
20 1 0.01
21 41 0.55
22 32 0.43
23 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (21 bp):
GCATTGCATGACTAACTTTAA
Found at i:3444266 original size:73 final size:74
Alignment explanation
Indices: 3444131--3444331 Score: 182
Period size: 73 Copynumber: 2.7 Consensus size: 74
3444121 TTATATAATA
* * * * * *
3444131 TCATCTCTTAAATATATTTTTAATGTCATATATGTTATTTTTATTTATTATTATAAACTTATAT-
1 TCATATCTTTAATATATTTTTTATATTATATAT-TTATTTTAATTTATT-TTATAAACTTATATA
3444195 ATTTT-A-TTT
64 ATTTTAAGTTT
* *
3444204 TCATTTCTTTAATATAATTTTTTATATTATATATTTATTTTAATTTATTTTACCTATA-TTATAT
1 TCATATCTTTAATAT-ATTTTTTATATTATATATTTATTTTAATTTATTTTA--TAAACTTATAT
3444268 AAATTTTAAGTTT
63 -AATTTTAAGTTT
* * *
3444281 TTATAT-TTTATTTTA-TTTTTATATTATATATTTTATTTTAATATT-TTTTAT
1 TCATATCTTTAATATATTTTTTATATTATATA-TTTATTTTAAT-TTATTTTAT
3444332 TTTAATTATA
Statistics
Matches: 108, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
72 3 0.03
73 34 0.31
74 33 0.31
75 22 0.20
76 9 0.08
77 7 0.06
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (74 bp):
TCATATCTTTAATATATTTTTTATATTATATATTTATTTTAATTTATTTTATAAACTTATATAAT
TTTAAGTTT
Found at i:3444289 original size:7 final size:7
Alignment explanation
Indices: 3444279--3444335 Score: 59
Period size: 7 Copynumber: 8.7 Consensus size: 7
3444269 AATTTTAAGT
3444279 TTTTATA
1 TTTTATA
3444286 -TTT-TA
1 TTTTATA
3444291 TTTTAT-
1 TTTTATA
3444297 TTTTATA
1 TTTTATA
*
3444304 TTATATA
1 TTTTATA
3444311 TTTTAT-
1 TTTTATA
*
3444317 TTTAATA
1 TTTTATA
*
3444324 TTTTTTA
1 TTTTATA
3444331 TTTTA
1 TTTTA
3444336 ATTATAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
5 2 0.05
6 17 0.43
7 21 0.52
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTATA
Found at i:3444298 original size:25 final size:25
Alignment explanation
Indices: 3444222--3444320 Score: 71
Period size: 25 Copynumber: 4.0 Consensus size: 25
3444212 TTAATATAAT
*
3444222 TTTTTATATTATATA-TTTATTTTA
1 TTTTAATATTATATATTTTATTTTA
* * * **
3444246 ATTT-ATTTTACCTATATTATA-TAAA
1 TTTTAATATTA--TATATTTTATTTTA
*
3444271 TTTTAAGT-TTTTATATTTTATTTTA
1 TTTTAA-TATTATATATTTTATTTTA
*
3444296 TTTTTATATTATATATTTTATTTTA
1 TTTTAATATTATATATTTTATTTTA
3444321 ATATTTTTTA
Statistics
Matches: 56, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
23 5 0.09
24 12 0.21
25 32 0.57
26 6 0.11
27 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (25 bp):
TTTTAATATTATATATTTTATTTTA
Found at i:3444324 original size:20 final size:21
Alignment explanation
Indices: 3444259--3444349 Score: 73
Period size: 20 Copynumber: 4.4 Consensus size: 21
3444249 TATTTTACCT
*
3444259 ATATTATATAAATTTTAAGTTTTT
1 ATATTATAT--ATTTTAA-TTTTA
*
3444283 ATATT-T-TATTTT-ATTTTT
1 ATATTATATATTTTAATTTTA
3444301 ATATTATATATTTT-ATTTTA
1 ATATTATATATTTTAATTTTA
* * *
3444321 ATATTTTTTATTTTAATTATA
1 ATATTATATATTTTAATTTTA
*
3444342 ACATTATA
1 ATATTATA
3444350 AAATATTTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
18 10 0.18
19 2 0.04
20 28 0.49
21 10 0.18
22 1 0.02
23 1 0.02
24 5 0.09
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (21 bp):
ATATTATATATTTTAATTTTA
Found at i:3444333 original size:15 final size:15
Alignment explanation
Indices: 3444296--3444337 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
3444286 TTTTATTTTA
*
3444296 TTTTTATATT-ATAT
1 TTTTTATTTTAATAT
*
3444310 ATTTTATTTTAATAT
1 TTTTTATTTTAATAT
3444325 TTTTTATTTTAAT
1 TTTTTATTTTAAT
3444338 TATAACATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTATTTTAATAT
Found at i:3452182 original size:35 final size:36
Alignment explanation
Indices: 3452143--3452248 Score: 90
Period size: 39 Copynumber: 2.9 Consensus size: 36
3452133 TATCTTGATG
* *
3452143 AATTAATTTTTTATTAATTAATATATAAATTAATAA
1 AATTAATTTTTGATTAAATAATATATAAATTAATAA
* * *
3452179 ATTATTAATTTCTTGATTAAATAATATTTTAATTAAT-T
1 A--ATTAATTT-TTGATTAAATAATATATAAATTAATAA
* *
3452217 AATTAATTTTCATAATTAAA-AATATATTAATT
1 AATTAATTTT--TGATTAAATAATATATAAATT
3452249 TGTAGTGGTT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
35 1 0.02
36 20 0.34
37 7 0.12
38 9 0.16
39 21 0.36
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (36 bp):
AATTAATTTTTGATTAAATAATATATAAATTAATAA
Found at i:3452204 original size:39 final size:38
Alignment explanation
Indices: 3452144--3452221 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
3452134 ATCTTGATGA
* *
3452144 ATTAATTTTTTATTAATTAATATATAAATTAATAAATT
1 ATTAATTTTTGATTAAATAATATATAAATTAATAAATT
* * *
3452182 ATTAATTTCTTGATTAAATAATATTTTAATTAATTAATT
1 ATTAATTT-TTGATTAAATAATATATAAATTAATAAATT
3452221 A
1 A
3452222 ATTTTCATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
38 8 0.24
39 26 0.76
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (38 bp):
ATTAATTTTTGATTAAATAATATATAAATTAATAAATT
Found at i:3455727 original size:2 final size:2
Alignment explanation
Indices: 3455720--3455744 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3455710 TTAGTTTAGC
3455720 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
3455745 TTTGATAAGC
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:3466732 original size:12 final size:14
Alignment explanation
Indices: 3466701--3466749 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 14
3466691 TTTAACATGT
* *
3466701 ATATTTTTATTGTC
1 ATATTTTTAATATC
3466715 AT-TTTTTAA-AT-
1 ATATTTTTAATATC
3466726 ATATTTTTAATATC
1 ATATTTTTAATATC
3466740 ATATATTTTA
1 ATAT-TTTTA
3466750 TTTTTCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 2 0.07
12 8 0.28
13 8 0.28
14 6 0.21
15 5 0.17
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (14 bp):
ATATTTTTAATATC
Found at i:3472999 original size:24 final size:23
Alignment explanation
Indices: 3472958--3473008 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
3472948 TTTCCTAATC
*
3472958 TTTTGTATTATGTATTTTTCTTAT
1 TTTTGTATTATGTATTTTT-ATAT
* * *
3472982 TTTTGTATTTTTTGTTTTTATAT
1 TTTTGTATTATGTATTTTTATAT
3473005 TTTT
1 TTTT
3473009 ATTTGTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.14, C:0.02, G:0.08, T:0.76
Consensus pattern (23 bp):
TTTTGTATTATGTATTTTTATAT
Found at i:3473011 original size:21 final size:22
Alignment explanation
Indices: 3472958--3473021 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
3472948 TTTCCTAATC
3472958 TTTTGTATTATGTATT-TTTCTTAT
1 TTTTGTATT-TGT-TTATTT-TTAT
*
3472982 TTTTGTATTT-TTTGTTTTTAT
1 TTTTGTATTTGTTTATTTTTAT
3473003 ATTTT-TATTTGTTTATTTT
1 -TTTTGTATTTGTTTATTTT
3473022 AATTCACGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 11 0.31
22 15 0.42
23 1 0.03
24 9 0.25
ACGTcount: A:0.14, C:0.02, G:0.08, T:0.77
Consensus pattern (22 bp):
TTTTGTATTTGTTTATTTTTAT
Found at i:3473271 original size:30 final size:30
Alignment explanation
Indices: 3473220--3473276 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
3473210 ATATGGTTTT
* *
3473220 AATGGGATTGTGATAACTACCCATTATTTG
1 AATGAGATTATGATAACTACCCATTATTTG
*
3473250 AATGAGATTATGATAATTACCCATTAT
1 AATGAGATTATGATAACTACCCATTAT
3473277 CTTTTGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (30 bp):
AATGAGATTATGATAACTACCCATTATTTG
Found at i:3479497 original size:30 final size:30
Alignment explanation
Indices: 3479462--3479518 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
3479452 ATATGGTTTT
*
3479462 AATGGGATTGTGATAACTACCCATTATTTG
1 AATGGGATTATGATAACTACCCATTATTTG
*
3479492 AATGGGATTATGATAATTACCCATTAT
1 AATGGGATTATGATAACTACCCATTAT
3479519 CTTTTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (30 bp):
AATGGGATTATGATAACTACCCATTATTTG
Found at i:3482858 original size:16 final size:15
Alignment explanation
Indices: 3482837--3482871 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
3482827 ATTTAGTTTC
*
3482837 TTTTATTTTGTGGTT
1 TTTTATTTTATGGTT
3482852 ATTTTATTTTATGGTT
1 -TTTTATTTTATGGTT
3482868 TTTT
1 TTTT
3482872 GGTTTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.11, C:0.00, G:0.14, T:0.74
Consensus pattern (15 bp):
TTTTATTTTATGGTT
Found at i:3489395 original size:120 final size:121
Alignment explanation
Indices: 3489161--3489399 Score: 390
Period size: 120 Copynumber: 2.0 Consensus size: 121
3489151 ATTGAGTGTA
*
3489161 TAGGTTCTAACTCAGCCTAAAAAAGTTAGTTTTTGGGTTTTGGTTGATCCCGAAAAAAAAACCAT
1 TAGGTTCTAACTCAGCCTAAAAAAGTTAGTTTTTGGATTTTGGTTGATCCCGAAAAAAAAACCAT
* * *
3489226 TATTGAAGGTTGTGGCTGAGCCTGTGAATAGCCATTGTAAAAGCTTGGTGAAAGCT
66 TATTGAAGGTTGTGACTGAGCCTATGAAAAGCCATTGTAAAAGCTTGGTGAAAGCT
** * *
3489282 TAGGTTCTAACTCAGCCTAGTAAAGTTAGTTTTTGGATTTTGGTTGATCTCG-GAAAAAAACCAT
1 TAGGTTCTAACTCAGCCTAAAAAAGTTAGTTTTTGGATTTTGGTTGATCCCGAAAAAAAAACCAT
*
3489346 TGTTGAAGGTTGTGACTGAGCCTATGAAAAGCCATTGTAAAAGCTTGGTGAAAG
66 TATTGAAGGTTGTGACTGAGCCTATGAAAAGCCATTGTAAAAGCTTGGTGAAAG
3489400 ATTTGGAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
120 61 0.56
121 48 0.44
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (121 bp):
TAGGTTCTAACTCAGCCTAAAAAAGTTAGTTTTTGGATTTTGGTTGATCCCGAAAAAAAAACCAT
TATTGAAGGTTGTGACTGAGCCTATGAAAAGCCATTGTAAAAGCTTGGTGAAAGCT
Found at i:3494376 original size:2 final size:2
Alignment explanation
Indices: 3494367--3494415 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
3494357 TTTGTTCCCT
3494367 TA TA -A TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
3494408 TA TA TA TA
1 TA TA TA TA
3494416 AGATTCAGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3497009 original size:15 final size:16
Alignment explanation
Indices: 3496983--3497012 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3496973 TTTTTAATTT
3496983 TTAAAAATTAAAATCG
1 TTAAAAATTAAAATCG
3496999 TTAAAAA-TAAAATC
1 TTAAAAATTAAAATC
3497013 CACATAATAG
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:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (16 bp):
TTAAAAATTAAAATCG
Found at i:3503447 original size:33 final size:33
Alignment explanation
Indices: 3503379--3503448 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 33
3503369 CAATTTTAAC
* *
3503379 TTTTATTAATTTTAAAAATTATTATTATATATT
1 TTTTATTAATTTTAAAAATTACTAATATATATT
*
3503412 TTTTATTAA-TTT-AAAATTACTAATATAATCTT
1 TTTTATTAATTTTAAAAATTACTAATAT-ATATT
3503444 TTTTA
1 TTTTA
3503449 AAAAATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 12 0.36
32 12 0.36
33 9 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (33 bp):
TTTTATTAATTTTAAAAATTACTAATATATATT
Found at i:3503479 original size:20 final size:19
Alignment explanation
Indices: 3503454--3503492 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3503444 TTTTAAAAAA
3503454 TAAAATAATAATTATATATT
1 TAAAATAATAATTAT-TATT
* *
3503474 TAAAATTATTATTATTATT
1 TAAAATAATAATTATTATT
3503493 ATCTCTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAAATAATAATTATTATT
Found at i:3504594 original size:22 final size:22
Alignment explanation
Indices: 3504532--3504594 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
3504522 TTGCTTGGGT
* *
3504532 AGAAAAAGAA-AAGGAGAGA-G
1 AGAAAGAGAAGAAAGAGAGAGG
* **
3504552 AGAAAG-GAAGAAACATCGAGG
1 AGAAAGAGAAGAAAGAGAGAGG
3504573 AGAAAGAGAAGAAAGAGAGAGG
1 AGAAAGAGAAGAAAGAGAGAGG
3504595 GGTGGAGGGA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 3 0.09
20 10 0.31
21 7 0.22
22 12 0.38
ACGTcount: A:0.59, C:0.03, G:0.37, T:0.02
Consensus pattern (22 bp):
AGAAAGAGAAGAAAGAGAGAGG
Found at i:3504813 original size:18 final size:17
Alignment explanation
Indices: 3504779--3504813 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3504769 AGATCCCTTA
*
3504779 TTTTAGGTTTTTAATTT
1 TTTTAAGTTTTTAATTT
3504796 TTTTAAGTTTTGTAATTT
1 TTTTAAGTTTT-TAATTT
3504814 GCAATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (17 bp):
TTTTAAGTTTTTAATTT
Found at i:3510788 original size:8 final size:8
Alignment explanation
Indices: 3510775--3510802 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3510765 AATATTAGGC
3510775 TTTTTTTA
1 TTTTTTTA
3510783 TTTTTTTA
1 TTTTTTTA
3510791 TTTTTTTA
1 TTTTTTTA
3510799 TTTT
1 TTTT
3510803 AAATCCTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTA
Found at i:3511169 original size:28 final size:28
Alignment explanation
Indices: 3511137--3511237 Score: 100
Period size: 28 Copynumber: 3.7 Consensus size: 28
3511127 TCAGACTTAG
3511137 TCTTGATCACGAACTTCGCTACTTGATA
1 TCTTGATCACGAACTTCGCTACTTGATA
* *
3511165 TCTTGATCACAAACTT--C-ACTTAATA
1 TCTTGATCACGAACTTCGCTACTTGATA
* * * * *
3511190 ACTTGATCATGAACTTTGGTTCTTGATA
1 TCTTGATCACGAACTTCGCTACTTGATA
* *
3511218 TCTTGATTATGAACTTCGCT
1 TCTTGATCACGAACTTCGCT
3511238 TGATATATTA
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
25 20 0.34
26 1 0.02
28 37 0.64
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.40
Consensus pattern (28 bp):
TCTTGATCACGAACTTCGCTACTTGATA
Found at i:3511204 original size:25 final size:27
Alignment explanation
Indices: 3511138--3511205 Score: 77
Period size: 25 Copynumber: 2.6 Consensus size: 27
3511128 CAGACTTAGT
* *
3511138 CTTGATCACGAACTTCGCTACTTGATAT
1 CTTGATCACGAACTTC-CTACTTAATAA
*
3511166 CTTGATCACAAACTT-C-ACTTAATAA
1 CTTGATCACGAACTTCCTACTTAATAA
*
3511191 CTTGATCATGAACTT
1 CTTGATCACGAACTT
3511206 TGGTTCTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 20 0.57
26 1 0.03
28 14 0.40
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (27 bp):
CTTGATCACGAACTTCCTACTTAATAA
Found at i:3511276 original size:25 final size:25
Alignment explanation
Indices: 3511162--3511302 Score: 81
Period size: 25 Copynumber: 5.5 Consensus size: 25
3511152 TCGCTACTTG
*
3511162 ATATCTTGATCACAAAC-TTCACTTA
1 ATATCTTGATCACAAACTTTC-CTTT
* ** * *
3511187 ATAACTTGATCATGAACTTTGGTTCTTG
1 ATATCTTGATCACAAAC-TT--TCCTTT
* ** *
3511215 ATATCTTGATTATGAAC-TTCGCTTG
1 ATATCTTGATCACAAACTTTC-CTTT
* *
3511240 ATATATTAATCACAAACGTTT-CTTT
1 ATATCTTGATCACAAAC-TTTCCTTT
3511265 ATATCTTGATCACAAACTTTCCTTT
1 ATATCTTGATCACAAACTTTCCTTT
* *
3511290 GTATCTTTATCAC
1 ATATCTTGATCAC
3511303 GAACCTCGCT
Statistics
Matches: 90, Mismatches: 18, Indels: 16
0.73 0.15 0.13
Matches are distributed among these distances:
24 4 0.04
25 63 0.70
26 1 0.01
27 3 0.03
28 18 0.20
29 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (25 bp):
ATATCTTGATCACAAACTTTCCTTT
Found at i:3512199 original size:33 final size:33
Alignment explanation
Indices: 3512158--3512250 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
3512148 TTGTTGGTGC
*
3512158 AATGGGGTTTAAATGAAATTCAAGGAACCCATA
1 AATGGGGTTTAAATGAAATTCAAGGAACACATA
* ** *
3512191 AATTGGGTTTAGCT-AGAATTCAAGGAACATATA
1 AATGGGGTTTAAATGA-AATTCAAGGAACACATA
*
3512224 AATGGGGTATAAATGAAATTCAAGGAA
1 AATGGGGTTTAAATGAAATTCAAGGAA
3512251 TCAGCAAAAC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
32 1 0.02
33 47 0.96
34 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.26
Consensus pattern (33 bp):
AATGGGGTTTAAATGAAATTCAAGGAACACATA
Found at i:3517845 original size:17 final size:17
Alignment explanation
Indices: 3517823--3517858 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3517813 TCTTTTTGCA
3517823 AAGAACTTTGGCAAATG
1 AAGAACTTTGGCAAATG
3517840 AAGAACTTTGGCAAATG
1 AAGAACTTTGGCAAATG
3517857 AA
1 AA
3517859 TGATGGAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (17 bp):
AAGAACTTTGGCAAATG
Found at i:3518491 original size:28 final size:28
Alignment explanation
Indices: 3518452--3518519 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
3518442 TTGAACTTCA
3518452 CTTGATATCTTGATCACAAACTTCG-TT
1 CTTGATATCTTGATCACAAACTTCGCTT
**
3518479 GCTTGATATCTTGATCATGAACTTCGCTT
1 -CTTGATATCTTGATCACAAACTTCGCTT
*
3518508 TTTGATATCTTG
1 CTTGATATCTTG
3518520 GTTATGAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 34 0.94
29 2 0.06
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (28 bp):
CTTGATATCTTGATCACAAACTTCGCTT
Found at i:3518597 original size:28 final size:25
Alignment explanation
Indices: 3518384--3518581 Score: 161
Period size: 25 Copynumber: 7.8 Consensus size: 25
3518374 TTGGACTTGG
*
3518384 TCTTGATCATGAACTTCGCTTGAGAA
1 TCTTGATCATGAACTTCGCTTGA-TA
* ** * *
3518410 T-TTAATCAAAAACTTCACTTGAGA
1 TCTTGATCATGAACTTCGCTTGATA
* * *
3518434 ACTTGATCTTGAACTTCACTTGATA
1 TCTTGATCATGAACTTCGCTTGATA
**
3518459 TCTTGATCACAAACTTCGTTGCTTGATA
1 TCTTGATCATGAACTTC---GCTTGATA
3518487 TCTTGATCATGAACTTCGCTTTTTGATA
1 TCTTGATCATGAACTTCGC---TTGATA
* *
3518515 TCTTGGTTATGAA-TT-GCTTGATA
1 TCTTGATCATGAACTTCGCTTGATA
*
3518538 TCTTGATCACGAA-TCTCGCTTGATA
1 TCTTGATCATGAACT-TCGCTTGATA
*
3518563 TCTTCATCATGAACTTCGC
1 TCTTGATCATGAACTTCGC
3518582 CGGTTGATAT
Statistics
Matches: 137, Mismatches: 25, Indels: 21
0.75 0.14 0.11
Matches are distributed among these distances:
23 17 0.12
24 2 0.01
25 73 0.53
26 4 0.03
27 2 0.01
28 39 0.28
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (25 bp):
TCTTGATCATGAACTTCGCTTGATA
Found at i:3528429 original size:22 final size:22
Alignment explanation
Indices: 3528379--3528429 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3528369 CAATATTCAA
*
3528379 AACTTTTCATATGAAAAAACAT
1 AACTTTTCATATGAAAAAACAC
* * *
3528401 AATTTTTCATATGAAGAATCAC
1 AACTTTTCATATGAAAAAACAC
3528423 AACTTTT
1 AACTTTT
3528430 AATTTTGAAA
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:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (22 bp):
AACTTTTCATATGAAAAAACAC
Found at i:3529331 original size:31 final size:31
Alignment explanation
Indices: 3529296--3529359 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
3529286 TGGCCATATT
3529296 TAAATATTAAAGCACTTTACACCTTTAAAGG
1 TAAATATTAAAGCACTTTACACCTTTAAAGG
*
3529327 TAAATATTTAAGCACTTTACACCTTTAAAGG
1 TAAATATTAAAGCACTTTACACCTTTAAAGG
3529358 TA
1 TA
3529360 TTGAGCCGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (31 bp):
TAAATATTAAAGCACTTTACACCTTTAAAGG
Found at i:3530541 original size:23 final size:24
Alignment explanation
Indices: 3530481--3530544 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 24
3530471 TAAGTAATGC
3530481 CTAAGTCACACAATGCCTTACTAA
1 CTAAGTCACACAATGCCTTACTAA
* * *
3530505 CTAA-CCACAAAATGGCTTACTAA
1 CTAAGTCACACAATGCCTTACTAA
*
3530528 C-AAGTCACGCAATGCCT
1 CTAAGTCACACAATGCCT
3530545 ATCAACTAGC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
22 2 0.06
23 26 0.81
24 4 0.12
ACGTcount: A:0.38, C:0.30, G:0.11, T:0.22
Consensus pattern (24 bp):
CTAAGTCACACAATGCCTTACTAA
Found at i:3530590 original size:23 final size:23
Alignment explanation
Indices: 3530529--3530591 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
3530519 GCTTACTAAC
** *
3530529 AAGTCACGCAATGCCTATCAACT
1 AAGTCACGCAATGCCTAAAAAAT
* *
3530552 -AGCCACGCAATACCTAAAAAAT
1 AAGTCACGCAATGCCTAAAAAAT
*
3530574 AAGTCACGTAATGCCTAA
1 AAGTCACGCAATGCCTAA
3530592 GTCAGTCACA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.41, C:0.27, G:0.13, T:0.19
Consensus pattern (23 bp):
AAGTCACGCAATGCCTAAAAAAT
Found at i:3537364 original size:16 final size:17
Alignment explanation
Indices: 3537322--3537370 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
3537312 TTTCTAAAGT
*
3537322 TTTTATTTA-CTTTTTA
1 TTTTATTTATTTTTTTA
3537338 TTTTATATTATTTTTTTA
1 TTTTAT-TTATTTTTTTA
3537356 -TTTATTTATTATTTT
1 TTTTATTTATT-TTTT
3537371 CAATTCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 11 0.38
17 12 0.41
18 6 0.21
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTTATTTTTTTA
Found at i:3537365 original size:19 final size:18
Alignment explanation
Indices: 3537332--3537370 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
3537322 TTTTATTTAC
3537332 TTTTTATTTTATATTATT
1 TTTTTATTTTATATTATT
*
3537350 TTTTTATTTATTTATTATT
1 TTTTTATTT-TATATTATT
3537369 TT
1 TT
3537371 CAATTCTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTATTTTATATTATT
Found at i:3539594 original size:24 final size:23
Alignment explanation
Indices: 3539540--3539594 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
3539530 CACCCTTTTG
* * *
3539540 ATTTTTTGTTTATATTTTATGTT
1 ATTTTTTCTTTATATTTAAGGTT
*
3539563 TTTATTTTCTTTAGTATTTAAGGTT
1 ATT-TTTTCTTTA-TATTTAAGGTT
3539588 ATTTTTT
1 ATTTTTT
3539595 TATATTGAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.08
24 12 0.48
25 11 0.44
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.71
Consensus pattern (23 bp):
ATTTTTTCTTTATATTTAAGGTT
Found at i:3539595 original size:25 final size:23
Alignment explanation
Indices: 3539541--3539595 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 23
3539531 ACCCTTTTGA
* * *
3539541 TTTTTTGTTTATATTTTATGTTT
1 TTTTTTCTTTATATTTAAGGTTT
3539564 TTATTTTCTTTAGTATTTAAGGTTAT
1 TT-TTTTCTTTA-TATTTAAGGTT-T
3539590 TTTTTT
1 TTTTTT
3539596 ATATTGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 2 0.08
24 8 0.31
25 13 0.50
26 3 0.12
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.73
Consensus pattern (23 bp):
TTTTTTCTTTATATTTAAGGTTT
Found at i:3542939 original size:12 final size:12
Alignment explanation
Indices: 3542924--3542949 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3542914 ACATTCTCCT
3542924 TTTATATTCATC
1 TTTATATTCATC
3542936 TTTATATTCATC
1 TTTATATTCATC
3542948 TT
1 TT
3542950 CAAATTCGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTATATTCATC
Found at i:3546821 original size:19 final size:19
Alignment explanation
Indices: 3546799--3546858 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 19
3546789 ATATATTCTT
3546799 ATTTTTATTAATTATTTTA
1 ATTTTTATTAATTATTTTA
* *
3546818 ATTTTAATTATTTACTTATTA
1 ATTTTTATTAATTA-TT-TTA
3546839 A-TTTTATATAATTATATTTA
1 ATTTTTAT-TAATTAT-TTTA
3546859 TTTAATAGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
19 12 0.36
20 11 0.33
21 10 0.30
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTATTAATTATTTTA
Found at i:3546839 original size:15 final size:16
Alignment explanation
Indices: 3546803--3546841 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
3546793 ATTCTTATTT
3546803 TTATTAATTATTTTAA
1 TTATTAATTATTTTAA
*
3546819 TT-TTAATTA-TTTAC
1 TTATTAATTATTTTAA
3546833 TTATTAATT
1 TTATTAATT
3546842 TTATATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 13 0.62
16 2 0.10
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTAATTATTTTAA
Found at i:3551524 original size:31 final size:31
Alignment explanation
Indices: 3551489--3551550 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
3551479 CTCCTAAAAA
3551489 ATGAAAAAGATGTATGTTGATGTGATATTCC
1 ATGAAAAAGATGTATGTTGATGTGATATTCC
*
3551520 ATGAAAAAGATGTATGTTGCTGTGATATTCC
1 ATGAAAAAGATGTATGTTGATGTGATATTCC
3551551 TTTACGTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (31 bp):
ATGAAAAAGATGTATGTTGATGTGATATTCC
Found at i:3566346 original size:23 final size:23
Alignment explanation
Indices: 3566275--3566471 Score: 127
Period size: 23 Copynumber: 8.7 Consensus size: 23
3566265 ATGTGTTAGC
* *
3566275 ACATGGCGTGTAATATTTTTATTGA
1 ACATGGCGTGTAACA-ATTT-TTGA
* * *
3566300 ATATGGCATGTAAC-ATGTTATGA
1 ACATGGCGTGTAACAAT-TTTTGA
3566323 ACATGGCGTGTAACAATTTTTGA
1 ACATGGCGTGTAACAATTTTTGA
** *
3566346 AC-TTACGTATAAC-A-TTTTGA
1 ACATGGCGTGTAACAATTTTTGA
* *
3566366 ACATGGTGTGTAACATTTTTTGA
1 ACATGGCGTGTAACAATTTTTGA
* *** *
3566389 AC-TTGCACCTAAC-ATTTGTGA
1 ACATGGCGTGTAACAATTTTTGA
* * * * *
3566410 ACATGACTTGCAACATTTTTTAA
1 ACATGGCGTGTAACAATTTTTGA
*
3566433 ACATGGCGTGTAACAGTTTTTGA
1 ACATGGCGTGTAACAATTTTTGA
*
3566456 ACATGGTGTGTAACAA
1 ACATGGCGTGTAACAA
3566472 CATGACTGAC
Statistics
Matches: 126, Mismatches: 39, Indels: 16
0.70 0.22 0.09
Matches are distributed among these distances:
20 8 0.06
21 16 0.13
22 19 0.15
23 68 0.54
24 4 0.03
25 11 0.09
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (23 bp):
ACATGGCGTGTAACAATTTTTGA
Found at i:3566368 original size:43 final size:44
Alignment explanation
Indices: 3566310--3566471 Score: 146
Period size: 43 Copynumber: 3.6 Consensus size: 44
3566300 ATATGGCATG
*
3566310 TAACATGTTATGAACATGGCGTGTAACAATTTTTGAACTTACGTA
1 TAACAT-TTATGAACATGGCGTGTAACAATTTTTGAACTTGCGTA
* * ***
3566355 TAACATTT-TGAACATGGTGTGTAACATTTTTTGAACTTGCACC
1 TAACATTTATGAACATGGCGTGTAACAATTTTTGAACTTGCGTA
* * * * * * * *
3566398 TAACATTTGTGAACATGACTTGCAACATTTTTTAAACATGGCGTG
1 TAACATTTATGAACATGGCGTGTAACAATTTTTGAAC-TTGCGTA
* *
3566443 TAACAGTTTTTGAACATGGTGTGTAACAA
1 TAACA-TTTATGAACATGGCGTGTAACAA
3566472 CATGACTGAC
Statistics
Matches: 93, Mismatches: 21, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
43 37 0.40
44 25 0.27
45 14 0.15
46 17 0.18
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36
Consensus pattern (44 bp):
TAACATTTATGAACATGGCGTGTAACAATTTTTGAACTTGCGTA
Found at i:3569263 original size:24 final size:24
Alignment explanation
Indices: 3569230--3569286 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
3569220 ATTAGTTTTG
*
3569230 GACTGTAATCACATTACATCCCTT
1 GACTGCAATCACATTACATCCCTT
*
3569254 GACTGCAATCACATTACGTCCCTT
1 GACTGCAATCACATTACATCCCTT
3569278 GACTGCAAT
1 GACTGCAAT
3569287 GTGATTGCAN
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.30
Consensus pattern (24 bp):
GACTGCAATCACATTACATCCCTT
Found at i:3569804 original size:17 final size:17
Alignment explanation
Indices: 3569778--3569812 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3569768 CACTACATCA
*
3569778 TTTTGGAACTTTCATAT
1 TTTTGAAACTTTCATAT
*
3569795 TTTTGAAACTTTCTTAT
1 TTTTGAAACTTTCATAT
3569812 T
1 T
3569813 AAGTTTGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (17 bp):
TTTTGAAACTTTCATAT
Found at i:3570109 original size:108 final size:108
Alignment explanation
Indices: 3569916--3570118 Score: 343
Period size: 108 Copynumber: 1.9 Consensus size: 108
3569906 TAAAATGACT
*
3569916 AAATATGTTAATTTAGTTACAACTTTCACAATTTACAAATACACATTCGTTTAAAATTATTCAAC
1 AAATATATTAATTTAGTTACAACTTTCACAATTTACAAATACACATTCGTTTAAAATTATTCAAC
3569981 ACTTACCCAATTTACCTTTTATTTAAATTTGCTCAAAGTAGCA
66 ACTTACCCAATTTACCTTTTATTTAAATTTGCTCAAAGTAGCA
* * * *
3570024 AAATATATTGATTTAGTTACAATTTTCACAATTTACAAATAGACATTCGTTTGAAATTATTCAAC
1 AAATATATTAATTTAGTTACAACTTTCACAATTTACAAATACACATTCGTTTAAAATTATTCAAC
* *
3570089 TCTTACCCAATTTACTTTTTATTTAAATTT
66 ACTTACCCAATTTACCTTTTATTTAAATTT
3570119 ACTTAAAATT
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
108 88 1.00
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (108 bp):
AAATATATTAATTTAGTTACAACTTTCACAATTTACAAATACACATTCGTTTAAAATTATTCAAC
ACTTACCCAATTTACCTTTTATTTAAATTTGCTCAAAGTAGCA
Done.