Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 9 of 182
Found at i:3500456 original size:24 final size:24
Alignment explanation
Indices: 3500429--3500475 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3500419 TAATCTTCCA
3500429 ATTAAACTT-TGCTTATTTGTTTCG
1 ATTAAA-TTCTGCTTATTTGTTTCG
*
3500453 ATTAAATTCTGTTTATTTGTTTC
1 ATTAAATTCTGCTTATTTGTTTC
3500476 AGTCAAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.57
Consensus pattern (24 bp):
ATTAAATTCTGCTTATTTGTTTCG
Found at i:3500483 original size:24 final size:24
Alignment explanation
Indices: 3500441--3500491 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3500431 TAAACTTTGC
*
3500441 TTATTTGTTTCGATTAAATTCTGT
1 TTATTTGTTTCGATCAAATTCTGT
*
3500465 TTATTTGTTTC-AGTCAAATTCTTT
1 TTATTTGTTTCGA-TCAAATTCTGT
3500489 TTA
1 TTA
3500492 ATTTAGATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.59
Consensus pattern (24 bp):
TTATTTGTTTCGATCAAATTCTGT
Found at i:3504403 original size:34 final size:34
Alignment explanation
Indices: 3504305--3504405 Score: 132
Period size: 34 Copynumber: 3.0 Consensus size: 34
3504295 GTGTCATTTT
* * *
3504305 TACATTCTAA-TTCTTCAGTTTGAAAACTTAAAA
1 TACATACTAATTTCTTGAGTTTGAAAACTTACAA
*
3504338 TACATACTAATTTCTTGAGTTTAAAAACTTACAA
1 TACATACTAATTTCTTGAGTTTGAAAACTTACAA
* * *
3504372 TACATATTGATTTCTTGAGCTTGAAAACTTACAA
1 TACATACTAATTTCTTGAGTTTGAAAACTTACAA
3504406 AATGAGTTGT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 9 0.15
34 50 0.85
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.39
Consensus pattern (34 bp):
TACATACTAATTTCTTGAGTTTGAAAACTTACAA
Found at i:3505352 original size:33 final size:34
Alignment explanation
Indices: 3505315--3505395 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 34
3505305 ATGATTATAT
3505315 TTAAATATTTAAAATATAATTTA-TATATT-CTAA
1 TTAAATATTTAAAATATAATTTATTAT-TTACTAA
*
3505348 TTAAAT-TTTATAA-ATAA-TTATTATTTACTAA
1 TTAAATATTTAAAATATAATTTATTATTTACTAA
3505379 --AAATATTTAAAAT-TAAT
1 TTAAATATTTAAAATATAAT
3505396 ATTTCATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
29 4 0.10
30 14 0.34
31 11 0.27
32 6 0.15
33 6 0.15
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (34 bp):
TTAAATATTTAAAATATAATTTATTATTTACTAA
Found at i:3505861 original size:29 final size:31
Alignment explanation
Indices: 3505800--3505882 Score: 93
Period size: 30 Copynumber: 2.7 Consensus size: 31
3505790 ATTATAGAGG
3505800 AATTTTGATTTAGTATATAATTTTATACTT-A
1 AATTTTGATTTA-TATATAATTTTATACTTAA
*
3505831 AATTTTGATTT-TTTATAATTTTATA-TATAA
1 AATTTTGATTTATATATAATTTTATACT-TAA
* *
3505861 AATTTTAATTTA-ATTTAATTTT
1 AATTTTGATTTATATATAATTTT
3505883 CATAAATTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
28 1 0.02
29 14 0.31
30 19 0.42
31 11 0.24
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (31 bp):
AATTTTGATTTATATATAATTTTATACTTAA
Found at i:3509205 original size:2 final size:2
Alignment explanation
Indices: 3509200--3509229 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3509190 TGTGTGTGTG
3509200 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
3509230 ATTAAGTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3522008 original size:3 final size:3
Alignment explanation
Indices: 3522000--3522029 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3521990 AGAAACTCAC
3522000 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3522030 GAATACTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3540287 original size:18 final size:18
Alignment explanation
Indices: 3540247--3540298 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
3540237 TTTTTAGTTG
*
3540247 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
*
3540265 CAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
3540283 TAATTAA--AAATTTATT
1 TAATTAATTAAATTTATT
3540299 CTTATCCCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:3544352 original size:2 final size:2
Alignment explanation
Indices: 3544347--3544374 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3544337 TTTTTAAATA
3544347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3544375 TATTTTCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3546850 original size:13 final size:13
Alignment explanation
Indices: 3546828--3546858 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3546818 TTAATATAAT
*
3546828 ATTTGGTATTTAA
1 ATTTGATATTTAA
3546841 ATTTGATATTTAA
1 ATTTGATATTTAA
3546854 ATTTG
1 ATTTG
3546859 TTTTGGGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
ATTTGATATTTAA
Found at i:3547199 original size:27 final size:26
Alignment explanation
Indices: 3547168--3547257 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 26
3547158 AAATTGGTTT
3547168 AAAAAAAAGTCTAGACACCAAATTAGG
1 AAAAAAAAGTCTAGA-ACCAAATTAGG
* *
3547195 AAAAAATGTCAAGTTCAAGAATCAAATT-GG
1 AAAAAA----AAG-TCTAGAACCAAATTAGG
* *
3547225 ATAAAAAAAGTTTAGGTACCAAATTAGG
1 A-AAAAAAAGTCTA-GAACCAAATTAGG
3547253 AAAAA
1 AAAAA
3547258 GTGTCAAGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 16
0.69 0.08 0.23
Matches are distributed among these distances:
26 2 0.04
27 21 0.43
28 3 0.06
30 3 0.06
31 15 0.31
32 5 0.10
ACGTcount: A:0.54, C:0.10, G:0.16, T:0.20
Consensus pattern (26 bp):
AAAAAAAAGTCTAGAACCAAATTAGG
Found at i:3547250 original size:58 final size:59
Alignment explanation
Indices: 3547167--3547338 Score: 206
Period size: 58 Copynumber: 2.9 Consensus size: 59
3547157 GAAATTGGTT
* * * *
3547167 TAAAAAAAAGTCTAGACACCAAATTAGGAAAAAATGTCAAGTTCAAGA-ATCAAATTGGA
1 TAAAAAAAAGTTTAGATACCAAATTAGGAAAAAATGTCAAGTT-AAGATACCAAATTAGA
* * *
3547226 T-AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTTAGATACCAAATTAGA
1 TAAAAAAAAGTTTAGATACCAAATTAGGAAAAAATGTCAAGTTAAGATACCAAATTAGA
* * * *
3547284 TAAAAAAAAGATTAGTTATCAAATTAGGAAAAAATGACAAGCTT-AGATACCAAAT
1 TAAAAAAAAGTTTAGATACCAAATTAGGAAAAAATGTCAAG-TTAAGATACCAAAT
3547339 GATATATTAA
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
57 3 0.03
58 47 0.48
59 46 0.47
60 2 0.02
ACGTcount: A:0.52, C:0.10, G:0.15, T:0.23
Consensus pattern (59 bp):
TAAAAAAAAGTTTAGATACCAAATTAGGAAAAAATGTCAAGTTAAGATACCAAATTAGA
Found at i:3547316 original size:28 final size:28
Alignment explanation
Indices: 3547168--3547338 Score: 105
Period size: 31 Copynumber: 5.8 Consensus size: 28
3547158 AAATTGGTTT
* *
3547168 AAAAAAAAGTCTAGACACCAAATTAGGA
1 AAAAAAAAGTTTAGATACCAAATTAGGA
* * *
3547196 AAAAATGTCAAGTTCAAGA-ATCAAATT-GGA
1 AAAAA---AAAGTT-TAGATACCAAATTAGGA
* *
3547226 TAAAAAAAGTTTAGGTACCAAATTAGGA
1 AAAAAAAAGTTTAGATACCAAATTAGGA
**
3547254 AAAAGTGTCAAGTTTAGATACCAAATTA-GA
1 AAAA---AAAAGTTTAGATACCAAATTAGGA
* * *
3547284 TAAAAAAAAGATTAGTTATCAAATTAGGA
1 -AAAAAAAAGTTTAGATACCAAATTAGGA
*
3547313 AAAAATGACAAGCTTAGATACCAAAT
1 AAAAA--A-AAGTTTAGATACCAAAT
3547339 GATATATTAA
Statistics
Matches: 108, Mismatches: 21, Indels: 25
0.70 0.14 0.16
Matches are distributed among these distances:
26 2 0.02
27 12 0.11
28 32 0.30
29 2 0.02
30 10 0.09
31 47 0.44
32 3 0.03
ACGTcount: A:0.52, C:0.10, G:0.15, T:0.23
Consensus pattern (28 bp):
AAAAAAAAGTTTAGATACCAAATTAGGA
Found at i:3547330 original size:59 final size:57
Alignment explanation
Indices: 3547184--3547338 Score: 195
Period size: 59 Copynumber: 2.6 Consensus size: 57
3547174 AAGTCTAGAC
* * *
3547184 ACCAAATTAGGAAAAAATGTCAAGTTCAAGA-ATCAAATTGGATAAAAAAAGTTTAGGT
1 ACCAAATTAGGAAAAAATGTCAAGTT--AGATACCAAATTAGATAAAAAAAGATTAGGT
* *
3547242 ACCAAATTAGGAAAAAGTGTCAAGTTTAGATACCAAATTAGATAAAAAAAAGATTAGTT
1 ACCAAATTAGGAAAAAATGTCAAG-TTAGATACCAAATTAGAT-AAAAAAAGATTAGGT
* *
3547301 ATCAAATTAGGAAAAAATGACAAGCTTAGATACCAAAT
1 ACCAAATTAGGAAAAAATGTCAAG-TTAGATACCAAAT
3547339 GATATATTAA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
57 3 0.04
58 33 0.39
59 49 0.58
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.24
Consensus pattern (57 bp):
ACCAAATTAGGAAAAAATGTCAAGTTAGATACCAAATTAGATAAAAAAAGATTAGGT
Found at i:3553006 original size:35 final size:35
Alignment explanation
Indices: 3552967--3553037 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
3552957 TGGGTATATA
*
3552967 TAAACTCATAAAAAACAGTAATTTTATGTTGTTAG
1 TAAACTCATAAAAAACAGTAATCTTATGTTGTTAG
*
3553002 TAAACTCATAAAAAATAGTAATCTTATGTTGTTAG
1 TAAACTCATAAAAAACAGTAATCTTATGTTGTTAG
3553037 T
1 T
3553038 TTAAAGAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.38
Consensus pattern (35 bp):
TAAACTCATAAAAAACAGTAATCTTATGTTGTTAG
Found at i:3553594 original size:29 final size:29
Alignment explanation
Indices: 3553537--3553595 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
3553527 CGCTTTCAAC
* *
3553537 TTTTCATAAAATCAATATATTTTTATAAA
1 TTTTCATAAAATCAACATATTTCTATAAA
3553566 TTTTC-TAAAGATCAACATATTTACT-TAAA
1 TTTTCATAAA-ATCAACATATTT-CTATAAA
3553595 T
1 T
3553596 AATCATCAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 4 0.15
29 21 0.81
30 1 0.04
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (29 bp):
TTTTCATAAAATCAACATATTTCTATAAA
Found at i:3559267 original size:162 final size:162
Alignment explanation
Indices: 3559000--3559332 Score: 666
Period size: 162 Copynumber: 2.1 Consensus size: 162
3558990 TTACATTTTT
3559000 ATACATTGAAAGAAGAAATTATTGTTACAAGCTCGATCCCTAGCTGTGATGTGAATGCAAGTGTA
1 ATACATTGAAAGAAGAAATTATTGTTACAAGCTCGATCCCTAGCTGTGATGTGAATGCAAGTGTA
3559065 TAATCAGACAAGGCATAATCATCTTCTAACTTAAAAAAATGTCATTTTAATGGGTCTATAGAATG
66 TAATCAGACAAGGCATAATCATCTTCTAACTTAAAAAAATGTCATTTTAATGGGTCTATAGAATG
3559130 TGAAGGATTAGTTATCGGGCTCAATCTAATAG
131 TGAAGGATTAGTTATCGGGCTCAATCTAATAG
3559162 ATACATTGAAAGAAGAAATTATTGTTACAAGCTCGATCCCTAGCTGTGATGTGAATGCAAGTGTA
1 ATACATTGAAAGAAGAAATTATTGTTACAAGCTCGATCCCTAGCTGTGATGTGAATGCAAGTGTA
3559227 TAATCAGACAAGGCATAATCATCTTCTAACTTAAAAAAATGTCATTTTAATGGGTCTATAGAATG
66 TAATCAGACAAGGCATAATCATCTTCTAACTTAAAAAAATGTCATTTTAATGGGTCTATAGAATG
3559292 TGAAGGATTAGTTATCGGGCTCAATCTAATAG
131 TGAAGGATTAGTTATCGGGCTCAATCTAATAG
3559324 ATACATTGA
1 ATACATTGA
3559333 GAAATAAAAA
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
162 171 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.31
Consensus pattern (162 bp):
ATACATTGAAAGAAGAAATTATTGTTACAAGCTCGATCCCTAGCTGTGATGTGAATGCAAGTGTA
TAATCAGACAAGGCATAATCATCTTCTAACTTAAAAAAATGTCATTTTAATGGGTCTATAGAATG
TGAAGGATTAGTTATCGGGCTCAATCTAATAG
Found at i:3560664 original size:3 final size:3
Alignment explanation
Indices: 3560658--3560686 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3560648 AAAAGTCTAA
3560658 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3560687 ATAAAAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3561883 original size:17 final size:18
Alignment explanation
Indices: 3561851--3561884 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3561841 TATGTTTTAC
3561851 TTTTACATTCTATAACAA
1 TTTTACATTCTATAACAA
*
3561869 TTTTTCATT-TATAACA
1 TTTTACATTCTATAACA
3561885 CTAACAACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTACATTCTATAACAA
Found at i:3565067 original size:22 final size:23
Alignment explanation
Indices: 3565039--3565085 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
3565029 AATTAGACAA
*
3565039 AAAAAAAT-TTAAATATCAA-ATT
1 AAAAAAATATCAAAT-TCAACATT
3565061 AAAAAAATATCAAATTCAACATT
1 AAAAAAATATCAAATTCAACATT
3565084 AA
1 AA
3565086 GCTAAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAAAAATATCAAATTCAACATT
Found at i:3565518 original size:28 final size:29
Alignment explanation
Indices: 3565467--3565531 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
3565457 AAATTTTAAA
*
3565467 TTAATAATAATAAAAATTATATTTTAA-CTT
1 TTAA-AATAATAAAAAATATA-TTTAATCTT
3565497 TTAAAATAATAAAAAATA-ATTTAATCTT
1 TTAAAATAATAAAAAATATATTTAATCTT
3565525 TTAAAAT
1 TTAAAAT
3565532 TAACAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
27 5 0.15
28 11 0.33
29 13 0.39
30 4 0.12
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (29 bp):
TTAAAATAATAAAAAATATATTTAATCTT
Found at i:3565543 original size:28 final size:27
Alignment explanation
Indices: 3565467--3565543 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 27
3565457 AAATTTTAAA
*
3565467 TTAATAATAATAAAAATTATATTTTAACTT
1 TTAA-AAT-ATAAAAA-TATAATTTAACTT
3565497 TTAAAATAATAAAAA-ATAATTTAATCTT
1 TTAAAAT-ATAAAAATATAATTTAA-CTT
3565525 TTAAAAT-TAACAAATATAA
1 TTAAAATATAA-AAATATAA
3565544 ATTACAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
26 3 0.07
27 11 0.26
28 14 0.33
29 11 0.26
30 4 0.09
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (27 bp):
TTAAAATATAAAAATATAATTTAACTT
Found at i:3576853 original size:22 final size:21
Alignment explanation
Indices: 3576828--3576869 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3576818 TTATTTTTTA
3576828 TTTTT-TTATAAAATTTAAAAC
1 TTTTTATTA-AAAATTTAAAAC
*
3576849 TTTTTATTAAAAATTTTAAAC
1 TTTTTATTAAAAATTTAAAAC
3576870 ATTGTCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTTATTAAAAATTTAAAAC
Found at i:3577851 original size:27 final size:26
Alignment explanation
Indices: 3577819--3577876 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
3577809 AATTTTGAAA
*
3577819 ATTCAATATACATAACAATATAAATAT
1 ATTCAATATACATAA-AAAATAAATAT
***
3577846 ATTCAATATGTGTAAAAAATAAATAT
1 ATTCAATATACATAAAAAATAAATAT
3577872 ATTCA
1 ATTCA
3577877 GTATTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.34
Consensus pattern (26 bp):
ATTCAATATACATAAAAAATAAATAT
Found at i:3577919 original size:16 final size:17
Alignment explanation
Indices: 3577898--3577931 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3577888 TTATTGGTAT
3577898 AAATTTAATACT-AATA
1 AAATTTAATACTGAATA
*
3577914 AAATTTAGTACTGAATA
1 AAATTTAATACTGAATA
3577931 A
1 A
3577932 GTTTGATAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (17 bp):
AAATTTAATACTGAATA
Found at i:3578599 original size:28 final size:30
Alignment explanation
Indices: 3578537--3578599 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
3578527 AATAGTTTAT
* *
3578537 ATTTTTATATTTTAAAAGAATTAAATTATT
1 ATTTTTATATTTTAAAAGAATTAAAATATA
* *
3578567 TTTTTTATTTTTTAAAA-AA-TAAAATATA
1 ATTTTTATATTTTAAAAGAATTAAAATATA
3578595 ATTTT
1 ATTTT
3578600 ACTTCCACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
28 11 0.39
29 2 0.07
30 15 0.54
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
ATTTTTATATTTTAAAAGAATTAAAATATA
Found at i:3585418 original size:37 final size:37
Alignment explanation
Indices: 3585368--3585571 Score: 255
Period size: 37 Copynumber: 5.5 Consensus size: 37
3585358 ACAAAACCTG
* * * *
3585368 CTAGGCACATAGCCCGAATACACTGGCACGAAGCCTA
1 CTAGGCACAAAGCCTGAAAACACCGGCACGAAGCCTA
* **
3585405 CTAGGCACATAGCCTGAAATTACCGGCACGAAGCCTA
1 CTAGGCACAAAGCCTGAAAACACCGGCACGAAGCCTA
* * * *
3585442 CTAGGCATACAGCCTAAAAACACTGGCACGAAGCCTA
1 CTAGGCACAAAGCCTGAAAACACCGGCACGAAGCCTA
* *
3585479 CTAAGCACAAAGCCTGAAAACACCGGCATGAAGCCTA
1 CTAGGCACAAAGCCTGAAAACACCGGCACGAAGCCTA
* * * *
3585516 CTAAGCACAAAGCCTGAAAACACCGACACGAAACGTA
1 CTAGGCACAAAGCCTGAAAACACCGGCACGAAGCCTA
3585553 CTAGGCACAAAGCCTGAAA
1 CTAGGCACAAAGCCTGAAA
3585572 TTTTAGATGC
Statistics
Matches: 145, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 145 1.00
ACGTcount: A:0.38, C:0.30, G:0.20, T:0.12
Consensus pattern (37 bp):
CTAGGCACAAAGCCTGAAAACACCGGCACGAAGCCTA
Found at i:3589999 original size:29 final size:29
Alignment explanation
Indices: 3589957--3590016 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
3589947 AGAGCAAGTG
3589957 TAAGAAATGCTAAACAAATGATCGGACCT
1 TAAGAAATGCTAAACAAATGATCGGACCT
*
3589986 TAAGAAATGCTAAACCAATGATCGGACCT
1 TAAGAAATGCTAAACAAATGATCGGACCT
3590015 TA
1 TA
3590017 GCTCAAGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (29 bp):
TAAGAAATGCTAAACAAATGATCGGACCT
Found at i:3594056 original size:37 final size:37
Alignment explanation
Indices: 3594004--3594079 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
3593994 CAACCACAAC
3594004 AACAGTTCCCAATCCCCAGCC-TGATTTAGATTACGAT
1 AACAGTTCCCAAT-CCCAGCCTTGATTTAGATTACGAT
* *
3594041 AACAGCTTCCC-ATCCCAGCCTTGGTTTAGATTATGAT
1 AACAG-TTCCCAATCCCAGCCTTGATTTAGATTACGAT
3594078 AA
1 AA
3594080 TCATGTCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 7 0.20
37 23 0.66
38 5 0.14
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (37 bp):
AACAGTTCCCAATCCCAGCCTTGATTTAGATTACGAT
Found at i:3603654 original size:47 final size:48
Alignment explanation
Indices: 3603559--3603654 Score: 108
Period size: 47 Copynumber: 2.0 Consensus size: 48
3603549 GGTTTTTTAT
* *
3603559 TTTTATTTTTATTAATGATTTTAATTAATAAATATATTTTTTTAAAAA
1 TTTTATTTTTATTAATGATTTTAATTAATAAATATATCTATTTAAAAA
* * *
3603607 TTTTATTTTTAATT-AT-TTTTTAATTAATAACTCT-TCTATTTATAAAA
1 TTTTATTTTT-ATTAATGATTTTAATTAATAAATATATCTATTTA-AAAA
3603654 T
1 T
3603655 CAAATAATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
46 6 0.15
47 20 0.49
48 12 0.29
49 3 0.07
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (48 bp):
TTTTATTTTTATTAATGATTTTAATTAATAAATATATCTATTTAAAAA
Found at i:3610265 original size:2 final size:2
Alignment explanation
Indices: 3610238--3610291 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
3610228 TCCACCATCT
* * *
3610238 TA TA T- TA TA CA TA CA TA TA TA CA 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
3610279 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
3610292 GTAACTTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3612867 original size:22 final size:21
Alignment explanation
Indices: 3612842--3612913 Score: 87
Period size: 20 Copynumber: 3.4 Consensus size: 21
3612832 ATTATATTAT
3612842 TGTTTTGGTGCTGTTTTTTTAC
1 TGTTTTGGTG-TGTTTTTTTAC
3612864 TGTTTTGGT-TGCTTTTTTTAC
1 TGTTTTGGTGTG-TTTTTTTAC
*
3612885 T-TTTTTGTGT-TGTTTTTTAC
1 TGTTTTGGTGTGT-TTTTTTAC
3612905 TGTTTTGGT
1 TGTTTTGGT
3612914 TATTATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
19 1 0.02
20 17 0.39
21 17 0.39
22 9 0.20
ACGTcount: A:0.04, C:0.07, G:0.21, T:0.68
Consensus pattern (21 bp):
TGTTTTGGTGTGTTTTTTTAC
Found at i:3612881 original size:21 final size:21
Alignment explanation
Indices: 3612842--3612914 Score: 89
Period size: 21 Copynumber: 3.5 Consensus size: 21
3612832 ATTATATTAT
3612842 TGTTTTGG-TGCTGTTTTTTTAC
1 TGTTTTGGTTGC--TTTTTTTAC
3612864 TGTTTTGGTTGCTTTTTTTAC
1 TGTTTTGGTTGCTTTTTTTAC
*
3612885 TTTTTTGTGTTG--TTTTTTAC
1 TGTTTTG-GTTGCTTTTTTTAC
3612905 TGTTTTGGTT
1 TGTTTTGGTT
3612915 ATTATTTTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.06
20 14 0.30
21 15 0.32
22 12 0.26
23 3 0.06
ACGTcount: A:0.04, C:0.07, G:0.21, T:0.68
Consensus pattern (21 bp):
TGTTTTGGTTGCTTTTTTTAC
Found at i:3612922 original size:20 final size:19
Alignment explanation
Indices: 3612856--3612922 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 19
3612846 TTGGTGCTGT
*
3612856 TTTTTTACTGTTTTGGTTGCT
1 TTTTTTACTGTTTTGGTT--A
* *
3612877 TTTTTTACTTTTTTGTGTTG
1 TTTTTTACTGTTTTG-GTTA
3612897 TTTTTTACTGTTTTGGTTA
1 TTTTTTACTGTTTTGGTTA
3612916 TTATTTT
1 TT-TTTT
3612923 TGTGTTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 5 0.12
20 18 0.45
21 14 0.35
22 3 0.08
ACGTcount: A:0.07, C:0.06, G:0.15, T:0.72
Consensus pattern (19 bp):
TTTTTTACTGTTTTGGTTA
Found at i:3612933 original size:23 final size:24
Alignment explanation
Indices: 3612907--3612957 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
3612897 TTTTTTACTG
*
3612907 TTTTGGTTATTATTTTTG-TGTTA
1 TTTTGGCTATTATTTTTGTTGTTA
* * *
3612930 TTTTTGCTGTTATTTTTGTTGTTG
1 TTTTGGCTATTATTTTTGTTGTTA
3612954 TTTT
1 TTTT
3612958 TTATTGCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.08, C:0.02, G:0.18, T:0.73
Consensus pattern (24 bp):
TTTTGGCTATTATTTTTGTTGTTA
Found at i:3612934 original size:12 final size:12
Alignment explanation
Indices: 3612916--3612958 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
3612906 GTTTTGGTTA
3612916 TTATTTTTG-TG
1 TTATTTTTGCTG
3612927 TTATTTTTGCTG
1 TTATTTTTGCTG
*
3612939 TTATTTTTGTTG
1 TTATTTTTGCTG
*
3612951 TTGTTTTT
1 TTATTTTT
3612959 TATTGCTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.07, C:0.02, G:0.16, T:0.74
Consensus pattern (12 bp):
TTATTTTTGCTG
Found at i:3612951 original size:26 final size:28
Alignment explanation
Indices: 3612912--3612965 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
3612902 TACTGTTTTG
3612912 GTTATTATTTTTG-TGTTATTT-TTGCT
1 GTTATTATTTTTGTTGTTATTTATTGCT
*
3612938 GTTATT-TTTGTTGTTGTTTTTTATTGCT
1 GTTATTATTT-TTGTTGTTATTTATTGCT
3612966 ATTTTTGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.12
26 9 0.38
27 7 0.29
28 5 0.21
ACGTcount: A:0.09, C:0.04, G:0.17, T:0.70
Consensus pattern (28 bp):
GTTATTATTTTTGTTGTTATTTATTGCT
Found at i:3612977 original size:57 final size:55
Alignment explanation
Indices: 3612886--3613004 Score: 134
Period size: 57 Copynumber: 2.1 Consensus size: 55
3612876 TTTTTTTACT
* * *
3612886 TTTTTGTGTTGTTTTTTACTGTTTTGGTTATTATTTTT-GTGTTATTTTTGCTGTTA
1 TTTTTGTGTTGTTTTTTACTGTTTT-GTTATTATTTTTAATATT-GTTTTGCTGTTA
* *
3612942 TTTTTGTTGTTGTTTTTTATTGCTATTT-TTGTTATTTTTAATATTGTTTTGCTGTTA
1 TTTTTG-TGTTGTTTTTTACTG-T-TTTGTTATTATTTTTAATATTGTTTTGCTGTTA
3612999 TTTTTG
1 TTTTTG
3613005 CTAATGTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
56 6 0.11
57 41 0.76
58 4 0.07
59 3 0.06
ACGTcount: A:0.10, C:0.03, G:0.16, T:0.71
Consensus pattern (55 bp):
TTTTTGTGTTGTTTTTTACTGTTTTGTTATTATTTTTAATATTGTTTTGCTGTTA
Found at i:3612997 original size:23 final size:24
Alignment explanation
Indices: 3612971--3613027 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
3612961 TTGCTATTTT
* *
3612971 TGTTATTTTTAATATTGTTTT-GC
1 TGTTATTTTTAATAATGTTTTAGA
**
3612994 TGTTATTTTTGCTAATGTTTTAGA
1 TGTTATTTTTAATAATGTTTTAGA
3613018 TGTTATTTTT
1 TGTTATTTTT
3613028 CATGCGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.18, C:0.04, G:0.14, T:0.65
Consensus pattern (24 bp):
TGTTATTTTTAATAATGTTTTAGA
Found at i:3613183 original size:26 final size:27
Alignment explanation
Indices: 3613142--3613210 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
3613132 TAATATAAAT
* *
3613142 TTTTTTAATGTATTTTAAATTTATTT-A
1 TTTTTTAATAT-TTTTAAATGTATTTGA
*
3613169 TTTTTTAATATTTTTAAGTGTATTTGA
1 TTTTTTAATATTTTTAAATGTATTTGA
* *
3613196 TATATTAATATTTTT
1 TTTTTTAATATTTTT
3613211 TAAAATTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
26 12 0.33
27 24 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (27 bp):
TTTTTTAATATTTTTAAATGTATTTGA
Found at i:3614425 original size:56 final size:55
Alignment explanation
Indices: 3614354--3614484 Score: 199
Period size: 56 Copynumber: 2.3 Consensus size: 55
3614344 TTTTGGGTGT
* * *
3614354 TGGCGACACTCCCTATTTCAAAAAACAATTGCATTTTTGGATGTTGGCCATCAAA
1 TGGCGACACTCCCTATTTCAAAAAAAAATTACATTTTTGAATGTTGGCCATCAAA
3614409 TGGCTGACACTCCCTATTTCAAAAAAAAATTACATTTTTGAATGTTGGCCATCAAA
1 TGGC-GACACTCCCTATTTCAAAAAAAAATTACATTTTTGAATGTTGGCCATCAAA
* *
3614465 TGGCCAACACCCCCTATTTC
1 TGG-CGACACTCCCTATTTC
3614485 TCGAGAAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
55 4 0.06
56 64 0.93
57 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (55 bp):
TGGCGACACTCCCTATTTCAAAAAAAAATTACATTTTTGAATGTTGGCCATCAAA
Found at i:3614522 original size:62 final size:60
Alignment explanation
Indices: 3614451--3614569 Score: 186
Period size: 62 Copynumber: 1.9 Consensus size: 60
3614441 CATTTTTGAA
*
3614451 TGTTGGCCATCAAATGGCCAACACCCCCTAT-TTCTCGAGAAAAAAATTTTAAATTTTTTTGG
1 TGTTAGCCATCAAATGGCCAACA--CCCTATGTTCTCGAGAAAAAAA-TTTAAATTTTTTTGG
*
3614513 TGTTAGCCATCAAATGGCCGACACCCTATGTTCTCGAGAAAAAAATTTAAATTTTTT
1 TGTTAGCCATCAAATGGCCAACACCCTATGTTCTCGAGAAAAAAATTTAAATTTTTT
3614570 CGTGTTGGTC
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
60 18 0.33
61 15 0.28
62 21 0.39
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (60 bp):
TGTTAGCCATCAAATGGCCAACACCCTATGTTCTCGAGAAAAAAATTTAAATTTTTTTGG
Found at i:3614549 original size:61 final size:60
Alignment explanation
Indices: 3614387--3614569 Score: 191
Period size: 56 Copynumber: 3.1 Consensus size: 60
3614377 AACAATTGCA
* ** * *
3614387 TTTTTGGATGTTGGCCATCAAATGGCTGACACTCCCTA-TT-TC-A-AAAAAAAATTACA--
1 TTTTTGG-TGTTAGCCATCAAATGGCCAACAC-CCCTATTTCTCGAGAAAAAAATTTAAATT
* *
3614443 TTTTTGAATGTTGGCCATCAAATGGCCAACACCCCCTATTTCTCGAGAAAAAAATTTTAAATT
1 TTTTTG-GTGTTAGCCATCAAATGGCCAACA-CCCCTATTTCTCGAGAAAAAAA-TTTAAATT
*
3614506 TTTTTGGTGTTAGCCATCAAATGGCCGACA-CCCTATGTTCTCGAGAAAAAAATTTAAATT
1 TTTTTGGTGTTAGCCATCAAATGGCCAACACCCCTAT-TTCTCGAGAAAAAAATTTAAATT
3614566 TTTT
1 TTTT
3614570 CGTGTTGGTC
Statistics
Matches: 109, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
56 32 0.29
57 3 0.03
58 2 0.02
59 1 0.01
60 25 0.23
61 19 0.17
62 21 0.19
63 6 0.06
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.34
Consensus pattern (60 bp):
TTTTTGGTGTTAGCCATCAAATGGCCAACACCCCTATTTCTCGAGAAAAAAATTTAAATT
Found at i:3617762 original size:20 final size:20
Alignment explanation
Indices: 3617734--3617779 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3617724 TGAAACTCGA
*
3617734 TCAAAGGTGAACAAAGTCGG
1 TCAACGGTGAACAAAGTCGG
* *
3617754 TCAACGGTGGACAAAGTTGG
1 TCAACGGTGAACAAAGTCGG
3617774 TCAACG
1 TCAACG
3617780 ACGGTCAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.17
Consensus pattern (20 bp):
TCAACGGTGAACAAAGTCGG
Found at i:3617787 original size:10 final size:10
Alignment explanation
Indices: 3617772--3617805 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3617762 GGACAAAGTT
3617772 GGTCAACGAC
1 GGTCAACGAC
**
3617782 GGTCAACGGT
1 GGTCAACGAC
3617792 GGTCAACGAC
1 GGTCAACGAC
3617802 GGTC
1 GGTC
3617806 TCGGGACGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (10 bp):
GGTCAACGAC
Found at i:3618183 original size:162 final size:164
Alignment explanation
Indices: 3617966--3618409 Score: 579
Period size: 165 Copynumber: 2.6 Consensus size: 164
3617956 TAAATATAAA
* *
3617966 ATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATATA
1 ATATGATAAAAATTGT-A-AT-ATAAAAAAA-TTATTTAAAAATATAAAATTAATAAATAATGTA
3618031 TTGTCAAATCAACACATTATATGATAAAAATTGTAATATAA-AA-AGAT-TTTTTATTTAAAGAT
62 TTGTCAAATCAACACATTATATGATAAAAATTGTAATATAATAATA-ATATTTTTATTTAAAGAT
*
3618093 ATAAAATTAATAAATAATGTATTGTCAAATCAACACATT
126 ATAAAATTAATAAATAATGTATTATCAAATCAACACATT
* *
3618132 ATATGATAAAAATTATAATATAAAAAAATTATTTAAAAATATAAAATTAATAAATATTGTATTGT
1 ATATGATAAAAATTGTAATATAAAAAAATTATTTAAAAATATAAAATTAATAAATAATGTATTGT
3618197 CAAATCAACACATTATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAA
66 CAAATCAACACATTATATGATAAAAATTGTAATATAATAATAAT-ATTTTTATTTAAAGATATAA
* * *
3618262 AATTAATAAATATTGTATTATCAAATTAACATATT
130 AATTAATAAATAATGTATTATCAAATCAACACATT
* * * *
3618297 ATATGATAAAAATTGTAATATAATAATAATAATTTGTACTTTAAATATGAAAATTTGATAAATAA
1 ATATGATAAAAATTGTAATATAA-AAAAATTA-TT-TA---AAAATAT-AAAA-TTAATAAATAA
* ** * * *
3618362 TGTATTGTCAAATTAGTACAATATTTGATATAAATTGTAATATAATAA
58 TGTATTGTCAAATCAACACATTATATGATAAAAATTGTAATATAATAA
3618410 CTATTTTTTT
Statistics
Matches: 246, Mismatches: 20, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
162 71 0.29
163 13 0.05
164 3 0.01
165 73 0.30
166 21 0.09
167 2 0.01
168 2 0.01
171 6 0.02
172 4 0.02
173 51 0.21
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (164 bp):
ATATGATAAAAATTGTAATATAAAAAAATTATTTAAAAATATAAAATTAATAAATAATGTATTGT
CAAATCAACACATTATATGATAAAAATTGTAATATAATAATAATATTTTTATTTAAAGATATAAA
ATTAATAAATAATGTATTATCAAATCAACACATT
Found at i:3618253 original size:86 final size:85
Alignment explanation
Indices: 3617966--3618409 Score: 590
Period size: 83 Copynumber: 5.3 Consensus size: 85
3617956 TAAATATAAA
* *
3617966 ATATGATAAAAATTGTAATATAATAAAA-AA-ATTTATTTAAAGATATAAAATTAATAAATAATA
1 ATATGATAAAAATTGTAATATAATAAAATAATTTTTATTTAAAGATATAAAATTAATAAATAATG
3618029 TATTGTCAAATCAACACATT
66 TATTGTCAAATCAACACATT
3618049 ATATGATAAAAATTGTAATATAA-AAAGAT--TTTTTATTTAAAGATATAAAATTAATAAATAAT
1 ATATGATAAAAATTGTAATATAATAAA-ATAATTTTTATTTAAAGATATAAAATTAATAAATAAT
3618111 GTATTGTCAAATCAACACATT
65 GTATTGTCAAATCAACACATT
* * *
3618132 ATATGATAAAAATTATAATAT-A-AAAA-AA---TTATTTAAAAATATAAAATTAATAAATATTG
1 ATATGATAAAAATTGTAATATAATAAAATAATTTTTATTTAAAGATATAAAATTAATAAATAATG
3618191 TATTGTCAAATCAACACATT
66 TATTGTCAAATCAACACATT
*
3618211 ATATGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATATT
1 ATATGATAAAAATTGTAATATAATAA-AATAATTTTTATTTAAAGATATAAAATTAATAAATAAT
* * *
3618276 GTATTATCAAATTAACATATT
65 GTATTGTCAAATCAACACATT
* *
3618297 ATATGATAAAAATTGTAATATAATAATAATAATTTGTACTTT-AA-ATATGAAAATTTGATAAAT
1 ATATGATAAAAATTGTAATATAATAA-AATAATTTTTA-TTTAAAGATAT-AAAA-TTAATAAAT
* ** *
3618360 AATGTATTGTCAAATTAGTACAAT
62 AATGTATTGTCAAATCAACACATT
* *
3618384 ATTTGATATAAATTGTAATATAATAA
1 ATATGATAAAAATTGTAATATAATAA
3618410 CTATTTTTTT
Statistics
Matches: 326, Mismatches: 20, Indels: 26
0.88 0.05 0.07
Matches are distributed among these distances:
79 69 0.21
80 1 0.00
81 3 0.01
82 9 0.03
83 97 0.30
85 4 0.01
86 90 0.28
87 53 0.16
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (85 bp):
ATATGATAAAAATTGTAATATAATAAAATAATTTTTATTTAAAGATATAAAATTAATAAATAATG
TATTGTCAAATCAACACATT
Found at i:3618555 original size:12 final size:12
Alignment explanation
Indices: 3618538--3618585 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
3618528 AAACATGTTC
3618538 ATTAATTTCCAA
1 ATTAATTTCCAA
3618550 ATTAATTTCAACTTAA
1 ATTAATTTC--C--AA
*
3618566 ATTAATTTTCAA
1 ATTAATTTCCAA
3618578 ATTAATTT
1 ATTAATTT
3618586 TTACACAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTAATTTCCAA
Found at i:3618584 original size:16 final size:16
Alignment explanation
Indices: 3618548--3618582 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3618538 ATTAATTTCC
*
3618548 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
3618564 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
3618581 AA
1 AA
3618583 TTTTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:3618595 original size:28 final size:28
Alignment explanation
Indices: 3618538--3618595 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
3618528 AAACATGTTC
**
3618538 ATTAATTTCCAAATTAATTTCAACTTAA
1 ATTAATTTCCAAATTAATTTCAACACAA
* **
3618566 ATTAATTTTCAAATTAATTTTTACACAA
1 ATTAATTTCCAAATTAATTTCAACACAA
3618594 AT
1 AT
3618596 ATACTTTGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTAATTTCCAAATTAATTTCAACACAA
Found at i:3622438 original size:60 final size:61
Alignment explanation
Indices: 3622319--3622627 Score: 391
Period size: 61 Copynumber: 5.1 Consensus size: 61
3622309 GAAAAGTTGA
* * *
3622319 TGTCGGCCATTTGATGGCCAACACCAAAAAAAATTGAATTTTTTTTCTCGAGAATAGGGGC
1 TGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTTCTCGAGAAAAGGGGG
* * *
3622380 TGTCGGCTATTTGATGGCCAACATCAAAAAAATTTGAA-TTTTTTTCTCAAGAAAAGGGGG
1 TGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTTCTCGAGAAAAGGGGG
* * * *
3622440 TGTCGACCA--TGCAGTGGCCAACATCAAAAAAATTTAAATTTTTTTTCTCGAGAAAAGTGGG
1 TGTCGGCCATTTG-A-TGGCCAACACCAAAAAAATTTGAATTTTTTTTCTCGAGAAAAGGGGG
* *
3622501 TGTCGGCCA--TGCAGTGGCCGACA-C-AAAAAATTTGAATTTTTTTTCTCGAGAATAGGGGG
1 TGTCGGCCATTTG-A-TGGCCAACACCAAAAAAATTTGAATTTTTTTTCTCGAGAAAAGGGGG
* *
3622560 TGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAAATTTTTTT-TCGAGAAATAGGGGG
1 TGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTTCTCGAGAAA-AGGGGG
3622621 TGTCGGC
1 TGTCGGC
3622628 GGCCAACACC
Statistics
Matches: 220, Mismatches: 20, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
58 2 0.01
59 50 0.23
60 59 0.27
61 109 0.50
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (61 bp):
TGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTTCTCGAGAAAAGGGGG
Found at i:3622444 original size:121 final size:119
Alignment explanation
Indices: 3622319--3622627 Score: 396
Period size: 120 Copynumber: 2.6 Consensus size: 119
3622309 GAAAAGTTGA
* *
3622319 TGTCGGCCATTTGATGGCCAACACCAAAAAAAATTGAATTTTTTTTCTCGAGAATAGGGGCTGTC
1 TGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAATTTTTTTTCTCGAGAATAGGGG-TGTC
*
3622384 GGCTATTTG-A-TGGCCAACATCAAAAAAATTTGAA-TTTTTTTCTCAAGAAAAGGGGG
65 GGCCA--TGCAGTGGCCAACA-C-AAAAAATTTGAATTTTTTTTCTCAAGAAAAGGGGG
* * *
3622440 TGTCGACCA--TGCAGTGGCCAACATCAAAAAAATTTAAATTTTTTTTCTCGAGAAAAGTGGGTG
1 TGTCGGCCATTTG-A-TGGCCAACACCAAAAAAATTTAAATTTTTTTTCTCGAGAATAG-GGGTG
* * *
3622503 TCGGCCATGCAGTGGCCGACACAAAAAATTTGAATTTTTTTTCTCGAGAATAGGGGG
63 TCGGCCATGCAGTGGCCAACACAAAAAATTTGAATTTTTTTTCTCAAGAAAAGGGGG
*
3622560 TGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAAATTTTTTT-TCGAGAAATAGGGGGTGT
1 TGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAATTTTTTTTCTCGAG-AATA-GGGGTGT
3622624 CGGC
64 CGGC
3622628 GGCCAACACC
Statistics
Matches: 165, Mismatches: 13, Indels: 21
0.83 0.07 0.11
Matches are distributed among these distances:
119 21 0.13
120 74 0.45
121 65 0.39
122 5 0.03
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (119 bp):
TGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAATTTTTTTTCTCGAGAATAGGGGTGTCG
GCCATGCAGTGGCCAACACAAAAAATTTGAATTTTTTTTCTCAAGAAAAGGGGG
Found at i:3639460 original size:21 final size:21
Alignment explanation
Indices: 3639434--3639473 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3639424 TAAAACCTTA
**
3639434 AACCCTAATTATTAAAAAAAT
1 AACCCTAACAATTAAAAAAAT
3639455 AACCCTAACAATTAAAAAA
1 AACCCTAACAATTAAAAAA
3639474 GGTCGAGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (21 bp):
AACCCTAACAATTAAAAAAAT
Found at i:3644332 original size:6 final size:6
Alignment explanation
Indices: 3644321--3644355 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
3644311 CCAAAAGGAT
* *
3644321 AAAGAC AAAGAC AAAGAC AAAAAC AAAGAT AAAGA
1 AAAGAC AAAGAC AAAGAC AAAGAC AAAGAC AAAGA
3644356 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.71, C:0.11, G:0.14, T:0.03
Consensus pattern (6 bp):
AAAGAC
Found at i:3644356 original size:6 final size:6
Alignment explanation
Indices: 3644318--3644369 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
3644308 TATCCAAAAG
* * * * * *
3644318 GATAAA GACAAA GACAAA GACAAA AACAAA GATAAA GATAAA AATAAA
1 GATAAA GATAAA GATAAA GATAAA GATAAA GATAAA GATAAA GATAAA
3644366 GATA
1 GATA
3644370 GAGAGGTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.69, C:0.08, G:0.13, T:0.10
Consensus pattern (6 bp):
GATAAA
Found at i:3644368 original size:18 final size:18
Alignment explanation
Indices: 3644325--3644369 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3644315 AAGGATAAAG
*
3644325 ACAAAGACAAAGACAAAA
1 ACAAAGATAAAGACAAAA
*
3644343 ACAAAGATAAAGATAAAA
1 ACAAAGATAAAGACAAAA
*
3644361 ATAAAGATA
1 ACAAAGATA
3644370 GAGAGGTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.71, C:0.09, G:0.11, T:0.09
Consensus pattern (18 bp):
ACAAAGATAAAGACAAAA
Found at i:3667137 original size:19 final size:19
Alignment explanation
Indices: 3667113--3667153 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
3667103 AAGATGGATA
3667113 ATATGAGATGGATAAGCTG
1 ATATGAGATGGATAAGCTG
3667132 ATATGAGATGGATAAGCTG
1 ATATGAGATGGATAAGCTG
3667151 ATA
1 ATA
3667154 AGGTAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.05, G:0.29, T:0.27
Consensus pattern (19 bp):
ATATGAGATGGATAAGCTG
Found at i:3683406 original size:18 final size:16
Alignment explanation
Indices: 3683371--3683424 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 16
3683361 AAATTATAAG
*
3683371 AATATAAAAATATTAAA
1 AATATAAAAATA-AAAA
*
3683388 AATATTAAAATGCAAAAA
1 AATATAAAAAT--AAAAA
3683406 AATATAAAAATAAAAA
1 AATATAAAAATAAAAA
3683422 AAT
1 AAT
3683425 TGATTTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.25
17 10 0.31
18 13 0.41
19 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (16 bp):
AATATAAAAATAAAAA
Found at i:3683410 original size:35 final size:35
Alignment explanation
Indices: 3683345--3683417 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
3683335 TTGATATTTT
* * * *
3683345 ATATTTAAAATCATTAAAATTATAAGAATATAAAA
1 ATATTAAAAATCATTAAAATCAAAAAAATATAAAA
3683380 ATATTAAAAAT-ATTAAAATGCAAAAAAATATAAAA
1 ATATTAAAAATCATTAAAAT-CAAAAAAATATAAAA
3683415 ATA
1 ATA
3683418 AAAAAATTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 8 0.24
35 25 0.76
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (35 bp):
ATATTAAAAATCATTAAAATCAAAAAAATATAAAA
Found at i:3683414 original size:9 final size:8
Alignment explanation
Indices: 3683359--3683424 Score: 60
Period size: 8 Copynumber: 7.9 Consensus size: 8
3683349 TTAAAATCAT
*
3683359 TAAAATTA
1 TAAAAATA
*
3683367 TAAGAATA
1 TAAAAATA
3683375 TAAAAATA
1 TAAAAATA
3683383 TTAAAAATA
1 -TAAAAATA
*
3683392 TTAAAATGCA
1 TAAAAAT--A
*
3683402 AAAAAATA
1 TAAAAATA
3683410 TAAAAATA
1 TAAAAATA
*
3683418 AAAAAAT
1 TAAAAAT
3683425 TGATTTATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
8 33 0.70
9 8 0.17
10 6 0.13
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.26
Consensus pattern (8 bp):
TAAAAATA
Found at i:3684356 original size:113 final size:113
Alignment explanation
Indices: 3684158--3684387 Score: 460
Period size: 113 Copynumber: 2.0 Consensus size: 113
3684148 AATTCTAATT
3684158 CAAAATTACTTTTAATTTACAAGTATAAATGCAACTATATATTTAAGCAACCACAAAGTATATAA
1 CAAAATTACTTTTAATTTACAAGTATAAATGCAACTATATATTTAAGCAACCACAAAGTATATAA
3684223 TCAAACTATTATAATACAGACGAATTAAAAATTGATTATGAATTGAAA
66 TCAAACTATTATAATACAGACGAATTAAAAATTGATTATGAATTGAAA
3684271 CAAAATTACTTTTAATTTACAAGTATAAATGCAACTATATATTTAAGCAACCACAAAGTATATAA
1 CAAAATTACTTTTAATTTACAAGTATAAATGCAACTATATATTTAAGCAACCACAAAGTATATAA
3684336 TCAAACTATTATAATACAGACGAATTAAAAATTGATTATGAATTGAAA
66 TCAAACTATTATAATACAGACGAATTAAAAATTGATTATGAATTGAAA
3684384 CAAA
1 CAAA
3684388 TTATATTAAA
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 117 1.00
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (113 bp):
CAAAATTACTTTTAATTTACAAGTATAAATGCAACTATATATTTAAGCAACCACAAAGTATATAA
TCAAACTATTATAATACAGACGAATTAAAAATTGATTATGAATTGAAA
Found at i:3687518 original size:46 final size:45
Alignment explanation
Indices: 3687451--3687551 Score: 157
Period size: 46 Copynumber: 2.2 Consensus size: 45
3687441 CACTAGCGCG
* * *
3687451 CTCTCTGATTAGCACTGTGTGTGCTCTCTGATCAGTATTTTGTGTA
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATCAGTACTTCG-GTA
*
3687497 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTCAGTACTTCGGTA
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATCAGTACTTCGGTA
3687542 CTCTCTGTTT
1 CTCTCTGTTT
3687552 GTTCCGTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 13 0.25
46 38 0.75
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (45 bp):
CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATCAGTACTTCGGTA
Found at i:3687528 original size:23 final size:23
Alignment explanation
Indices: 3687450--3687526 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
3687440 ACACTAGCGC
3687450 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * * *
3687473 GCTCTCTGATCAGTATTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
3687496 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
3687519 GCTCTCTG
1 GCTCTCTG
3687527 TTCAGTACTT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:3688628 original size:17 final size:17
Alignment explanation
Indices: 3688608--3688649 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
3688598 TACTTTGAGA
3688608 TTAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAT
* *
3688625 TTAAATGTATTTTATAT
1 TTAAATTTATTTTAAAT
3688642 TT-AATTTA
1 TTAAATTTA
3688650 AGTTTGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:3688637 original size:45 final size:45
Alignment explanation
Indices: 3688590--3688690 Score: 116
Period size: 45 Copynumber: 2.3 Consensus size: 45
3688580 CCCAAACCAT
* * *
3688590 TTTTA-ATTTACTTTGAGATTAAATTTATTTTAAATTTAAATGTA
1 TTTTATATTTAATTTAAGATTAAATTTAATTTAAATTTAAATGTA
* *
3688634 TTTTATATTTAATTTAAGTTTGAATTTAATTTAAATTTAATAT-TA
1 TTTTATATTTAATTTAAGATTAAATTTAATTTAAATTTAA-ATGTA
* *
3688679 TTATAAATTTAA
1 TTTTATATTTAA
3688691 AAGTCTAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 5 0.10
45 41 0.85
46 2 0.04
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (45 bp):
TTTTATATTTAATTTAAGATTAAATTTAATTTAAATTTAAATGTA
Found at i:3688649 original size:11 final size:12
Alignment explanation
Indices: 3688608--3688677 Score: 51
Period size: 11 Copynumber: 6.1 Consensus size: 12
3688598 TACTTTGAGA
3688608 TTAAATTTAT-T
1 TTAAATTTATAT
*
3688619 TTAAATTTAAAT
1 TTAAATTTATAT
* *
3688631 GT-ATTTTATAT
1 TTAAATTTATAT
3688642 TT-AATTTA-AGT
1 TTAAATTTATA-T
*
3688653 TTGAATTTA-AT
1 TTAAATTTATAT
3688664 TTAAATTTAATAT
1 TTAAATTT-ATAT
3688677 T
1 T
3688678 ATTATAAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
10 1 0.02
11 33 0.70
12 10 0.21
13 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (12 bp):
TTAAATTTATAT
Found at i:3688666 original size:28 final size:28
Alignment explanation
Indices: 3688608--3688674 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
3688598 TACTTTGAGA
* *
3688608 TTAAATTTATTTTAAATTTAAATGTATT
1 TTAAATTTAATTTAAATTTAAATGTAAT
* * * *
3688636 TTATATTTAATTTAAGTTTGAATTTAAT
1 TTAAATTTAATTTAAATTTAAATGTAAT
3688664 TTAAATTTAAT
1 TTAAATTTAAT
3688675 ATTATTATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (28 bp):
TTAAATTTAATTTAAATTTAAATGTAAT
Found at i:3690178 original size:12 final size:12
Alignment explanation
Indices: 3690163--3690191 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3690153 ATTAATTACA
3690163 AAATTGGCCCAG
1 AAATTGGCCCAG
3690175 AAATTGGCCCAG
1 AAATTGGCCCAG
3690187 AAATT
1 AAATT
3690192 TTTCAAGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (12 bp):
AAATTGGCCCAG
Found at i:3690350 original size:30 final size:28
Alignment explanation
Indices: 3690294--3690452 Score: 108
Period size: 29 Copynumber: 5.6 Consensus size: 28
3690284 CTAAATTGTC
* **
3690294 CAAAAATTACATTTCGATCTCGAACTTCT
1 CAAAAATTACATTTTGATCTAAAACTT-T
*
3690323 CCAAAATTACATTTTGATTCTAAAACTTT
1 CAAAAATTACATTTTGA-TCTAAAACTTT
* * *
3690352 TAAAAATTACATTTTAACCCCT-AAACTTT
1 CAAAAATTACATTTTGA--TCTAAAACTTT
* * * *
3690381 CAAAAAAATCCATTTTAACCCTAAAAC-TT
1 C-AAAAATTACATTTTGA-TCTAAAACTTT
* * **
3690410 CCAAAATTACATTTTG-CCCCAAACTTT
1 CAAAAATTACATTTTGATCTAAAACTTT
3690437 CAAAAATTACATTTTG
1 CAAAAATTACATTTTG
3690453 CCCCCAAACT
Statistics
Matches: 106, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
26 6 0.06
27 17 0.16
28 11 0.10
29 44 0.42
30 28 0.26
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.35
Consensus pattern (28 bp):
CAAAAATTACATTTTGATCTAAAACTTT
Found at i:3690377 original size:29 final size:29
Alignment explanation
Indices: 3690345--3690538 Score: 166
Period size: 29 Copynumber: 6.8 Consensus size: 29
3690335 TTTGATTCTA
*
3690345 AAACTTTTAAAAATTACATTTTAACCCCT
1 AAACTTTCAAAAATTACATTTTAACCCCT
* *
3690374 AAACTTTCAAAAAAATCCATTTTAA-CCCT
1 AAACTTTC-AAAAATTACATTTTAACCCCT
* *
3690403 AAAAC-TTCCAAAATTACATTTT-GCCCC-
1 -AAACTTTCAAAAATTACATTTTAACCCCT
* *
3690430 AAACTTTCAAAAATTACATTTT-GCCCCC
1 AAACTTTCAAAAATTACATTTTAACCCCT
* * * *
3690458 AAACTTCCAAAATTTCCATTTTTAACCTCT
1 AAACTTTCAAAAATTACA-TTTTAACCCCT
* ** *
3690488 AAACTTCCAAAAATTACATTTTTGCCCCC
1 AAACTTTCAAAAATTACATTTTAACCCCT
*
3690517 AAAC-TTCAAAAAATTCCATTTT
1 AAACTTTC-AAAAATTACATTTT
3690539 TGACCTCGAA
Statistics
Matches: 135, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
26 4 0.03
27 21 0.16
28 31 0.23
29 42 0.31
30 37 0.27
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.34
Consensus pattern (29 bp):
AAACTTTCAAAAATTACATTTTAACCCCT
Found at i:3690494 original size:30 final size:29
Alignment explanation
Indices: 3690404--3690586 Score: 160
Period size: 29 Copynumber: 6.4 Consensus size: 29
3690394 TTTAACCCTA
* *
3690404 AAACTTCC-AAAATTACA-TTTTG-CCCC
1 AAACTTCCAAAAATTCCATTTTTGACCTC
* * * *
3690430 AAACTTTCAAAAATTACA-TTTTGCCCCC
1 AAACTTCCAAAAATTCCATTTTTGACCTC
* *
3690458 AAACTTCCAAAATTTCCATTTTTAACCTC
1 AAACTTCCAAAAATTCCATTTTTGACCTC
* * *
3690487 TAAACTTCCAAAAATTACATTTTTGCCCCC
1 -AAACTTCCAAAAATTCCATTTTTGACCTC
*
3690517 AAACTTCAAAAAATTCCATTTTTGACCTC
1 AAACTTCCAAAAATTCCATTTTTGACCTC
* * * *
3690546 GAATTTTC-AAAATTCCATTTTTGACCGC
1 AAACTTCCAAAAATTCCATTTTTGACCTC
*
3690574 GAAACTCCCAAAA
1 -AAACTTCCAAAA
3690587 TTACCCTTTT
Statistics
Matches: 126, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
26 7 0.06
27 14 0.11
28 38 0.30
29 40 0.32
30 27 0.21
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTGACCTC
Found at i:3690502 original size:58 final size:59
Alignment explanation
Indices: 3690430--3690545 Score: 189
Period size: 59 Copynumber: 2.0 Consensus size: 59
3690420 ATTTTGCCCC
* * *
3690430 AAACTTTCAAAAATTACA-TTTTGCCCCCAAACTTCCAAAATTTCCATTTTTAACCTCT
1 AAACTTCCAAAAATTACATTTTTGCCCCCAAACTTCAAAAAATTCCATTTTTAACCTCT
*
3690488 AAACTTCCAAAAATTACATTTTTGCCCCCAAACTTCAAAAAATTCCATTTTTGACCTC
1 AAACTTCCAAAAATTACATTTTTGCCCCCAAACTTCAAAAAATTCCATTTTTAACCTC
3690546 GAATTTTCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
58 17 0.32
59 36 0.68
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (59 bp):
AAACTTCCAAAAATTACATTTTTGCCCCCAAACTTCAAAAAATTCCATTTTTAACCTCT
Found at i:3690539 original size:29 final size:28
Alignment explanation
Indices: 3690353--3690540 Score: 148
Period size: 30 Copynumber: 6.6 Consensus size: 28
3690343 TAAAACTTTT
** *
3690353 AAAAATTACATTTTAACCCCTAAACTTTC
1 AAAAATTACATTTTTGCCCCCAAAC-TTC
* * ** **
3690382 AAAAAAATCCATTTTAACCCTAAAACTTC
1 -AAAAATTACATTTTTGCCCCCAAACTTC
*
3690411 CAAAATTACA-TTTTG-CCCCAAACTTTC
1 AAAAATTACATTTTTGCCCCCAAAC-TTC
3690438 AAAAATTACA-TTTTGCCCCCAAACTTCC
1 AAAAATTACATTTTTGCCCCCAAACTT-C
* * * * *
3690466 AAAATTTCCATTTTTAACCTCTAAACTTCC
1 AAAAATTACATTTTT-GCCCCCAAACTT-C
3690496 AAAAATTACATTTTTGCCCCCAAACTTC
1 AAAAATTACATTTTTGCCCCCAAACTTC
*
3690524 AAAAAATTCCATTTTTG
1 -AAAAATTACATTTTTG
3690541 ACCTCGAATT
Statistics
Matches: 129, Mismatches: 23, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
26 6 0.05
27 22 0.17
28 25 0.19
29 31 0.24
30 45 0.35
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (28 bp):
AAAAATTACATTTTTGCCCCCAAACTTC
Found at i:3690557 original size:29 final size:29
Alignment explanation
Indices: 3690462--3690712 Score: 131
Period size: 29 Copynumber: 8.6 Consensus size: 29
3690452 GCCCCCAAAC
* * * *
3690462 TTCCAAAATTTCCATTTTTAACCTCTAAAC
1 TTCCAAAAATTCCATTTTTGACCTC-GAAT
* * * * *
3690492 TTCCAAAAATTACATTTTTGCCCCCAAAC
1 TTCCAAAAATTCCATTTTTGACCTCGAAT
*
3690521 TTCAAAAAATTCCATTTTTGACCTCGAAT
1 TTCCAAAAATTCCATTTTTGACCTCGAAT
* * *
3690550 TTTC-AAAATTCCATTTTTGACCGCGAAA
1 TTCCAAAAATTCCATTTTTGACCTCGAAT
* * *
3690578 CTCCCAAAATTACC-CTTTT-ACCCTCGAAT
1 TTCCAAAAATT-CCATTTTTGA-CCTCGAAT
* *
3690607 TTCCAAAAA-TCCTGTTTTTGATCC-CGATTT
1 TTCCAAAAATTCC-ATTTTTGA-CCTCGA-AT
* *
3690637 TTCTAAAAATTACCA-TTTT-ACCTCCGAAC
1 TTCCAAAAATT-CCATTTTTGACCT-CGAAT
* * * * *
3690666 GT-CTAAAATTTCATTTTTAATCTCGAAT
1 TTCCAAAAATTCCATTTTTGACCTCGAAT
*
3690694 TTCCCAAAATTACCATTTT
1 TTCCAAAAATT-CCATTTT
3690713 GCCCCCGAAA
Statistics
Matches: 168, Mismatches: 38, Indels: 30
0.71 0.16 0.13
Matches are distributed among these distances:
27 4 0.02
28 43 0.26
29 71 0.42
30 47 0.28
31 1 0.01
32 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.38
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTGACCTCGAAT
Found at i:3690587 original size:57 final size:55
Alignment explanation
Indices: 3690434--3690614 Score: 168
Period size: 57 Copynumber: 3.2 Consensus size: 55
3690424 TGCCCCAAAC
* * *
3690434 TTTCAAAAATTACA-TTTTGCCCCCAAACTTCCAAAATTTCCATTTTTAACCTCTAAA
1 TTTCCAAAATTACATTTTTGCCCCCAAACTCCCAAAA-TTCCATTTTT-ACCTC-GAA
* **
3690491 CTTCCAAAAATTACATTTTTGCCCCCAAACTTCAAAAAATTCCATTTTTGACCTCGAA
1 TTTCC-AAAATTACATTTTTGCCCCCAAAC-TCCCAAAATTCCATTTTT-ACCTCGAA
* * * * *
3690549 TTTTCAAAATTCCATTTTTGACCGCGAAACTCCCAAAATTACC-CTTTTACCCTCGAA
1 TTTCCAAAATTACATTTTTG-CCCCCAAACTCCCAAAATT-CCATTTTTA-CCTCGAA
3690606 TTTCCAAAA
1 TTTCCAAAA
3690615 ATCCTGTTTT
Statistics
Matches: 102, Mismatches: 16, Indels: 12
0.78 0.12 0.09
Matches are distributed among these distances:
56 1 0.01
57 44 0.43
58 23 0.23
59 29 0.28
60 5 0.05
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (55 bp):
TTTCCAAAATTACATTTTTGCCCCCAAACTCCCAAAATTCCATTTTTACCTCGAA
Found at i:3694841 original size:2 final size:2
Alignment explanation
Indices: 3694834--3694871 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3694824 AACCCCAATA
3694834 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3694872 ATATATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3694876 original size:2 final size:2
Alignment explanation
Indices: 3694871--3694938 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
3694861 TCTCTCTCTC
3694871 TA TA TA 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
3694913 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
3694939 AGTGTCTTGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3696168 original size:58 final size:58
Alignment explanation
Indices: 3696050--3696208 Score: 180
Period size: 58 Copynumber: 2.8 Consensus size: 58
3696040 GGTGTCGGTA
* * *
3696050 ATTAGTTGCCAAACACTAAAAAAATTATTTTTTAATTCGTATTTTTATGAGTGTCAACC
1 ATTAGTTGACAAACAC-CAAAAAATTATTTTTTAATTCATATTTTTATGAGTGTCAACC
* * * * * *
3696109 ATTAGTTGTCAAATACCAAAAAATTATTTTTTTATTTATATTTTTGTG-GATGTCGACC
1 ATTAGTTGACAAACACCAAAAAATTATTTTTTAATTCATATTTTTATGAG-TGTCAACC
* *
3696167 ATTAGATGACAAACACCAAAAAATAATTTTTT-ATTCAT-TTTT
1 ATTAGTTGACAAACACCAAAAAATTATTTTTTAATTCATATTTT
3696209 AAGTGTCGGT
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
56 4 0.05
57 6 0.07
58 62 0.72
59 14 0.16
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (58 bp):
ATTAGTTGACAAACACCAAAAAATTATTTTTTAATTCATATTTTTATGAGTGTCAACC
Found at i:3700811 original size:4 final size:4
Alignment explanation
Indices: 3700798--3700843 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
3700788 AAAATTGAGG
*
3700798 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA G-AA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAA
3700844 GAAGGAGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
3 6 0.16
4 28 0.76
5 3 0.08
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:3700812 original size:11 final size:11
Alignment explanation
Indices: 3700798--3700843 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
3700788 AAAATTGAGG
3700798 GAAAAAAGAAA
1 GAAAAAAGAAA
3700809 GAAAAAAG--A
1 GAAAAAAGAAA
3700818 GAAAGAAAGAAA
1 GAAA-AAAGAAA
*
3700830 GAAAGAAGAAA
1 GAAAAAAGAAA
3700841 GAA
1 GAA
3700844 GAAGGAGAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
9 5 0.16
10 4 0.13
11 17 0.55
12 5 0.16
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:3700828 original size:21 final size:20
Alignment explanation
Indices: 3700798--3700838 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
3700788 AAAATTGAGG
3700798 GAAAAAAGAAAGAAAAAAGA
1 GAAAAAAGAAAGAAAAAAGA
*
3700818 GAAAGAAAGAAAGAAAGAAGA
1 GAAA-AAAGAAAGAAAAAAGA
3700839 AAGAAGAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
GAAAAAAGAAAGAAAAAAGA
Found at i:3700844 original size:7 final size:7
Alignment explanation
Indices: 3700798--3700846 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
3700788 AAAATTGAGG
*
3700798 GAAAAAA
1 GAAAGAA
3700805 GAAAGAA
1 GAAAGAA
*
3700812 AAAAG-A
1 GAAAGAA
3700818 GAAAGAA
1 GAAAGAA
*
3700825 -AGA-AA
1 GAAAGAA
3700830 GAAAGAA
1 GAAAGAA
3700837 GAAAGAA
1 GAAAGAA
3700844 GAA
1 GAA
3700847 GGAGAAGAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
5 2 0.06
6 9 0.26
7 23 0.68
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
GAAAGAA
Found at i:3700854 original size:9 final size:9
Alignment explanation
Indices: 3700840--3700870 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3700830 GAAAGAAGAA
3700840 AGAAGAAGG
1 AGAAGAAGG
3700849 AGAAGAAGG
1 AGAAGAAGG
*
3700858 GGAAGAAGG
1 AGAAGAAGG
3700867 AGAA
1 AGAA
3700871 AGAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (9 bp):
AGAAGAAGG
Found at i:3701256 original size:20 final size:21
Alignment explanation
Indices: 3701215--3701257 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3701205 TAATTTACTT
3701215 TAATTTTATTTTGCTAGTTAG
1 TAATTTTATTTTGCTAGTTAG
*
3701236 TAATTTTATTTTG-TTGTTAG
1 TAATTTTATTTTGCTAGTTAG
3701256 TA
1 TA
3701258 GTAGTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.23, C:0.02, G:0.14, T:0.60
Consensus pattern (21 bp):
TAATTTTATTTTGCTAGTTAG
Found at i:3701393 original size:98 final size:98
Alignment explanation
Indices: 3701222--3701491 Score: 396
Period size: 98 Copynumber: 2.8 Consensus size: 98
3701212 CTTTAATTTT
*
3701222 ATTTTGCTAGTTAGTAATTTTA--TT-TTGTT-GT-TAGTAGTAGTAAGTAAAAAATATTATTCA
1 ATTTTGCTAGTTAGTAATTTTATTTTGTTGTTAGTATAGTAGTAGTAAGTAAAAAATATTGTTCA
*
3701282 TATTTATTGATTTAAAATTTAATAATGTTT-AA
66 TATTTATTAATTTAAAATTTAATAATGTTTAAA
*
3701314 ATTTTGCTAGTTAATAATTTTATTTTGTTGTTAGTAGTAGTAGTAGTAAGTAAAAAATATTGTTC
1 ATTTTGCTAGTTAGTAATTTTATTTTGTTGTTAGTA-TAGTAGTAGTAAGTAAAAAATATTGTTC
3701379 ATATTTATTAATTTAAAATTTAATAATGTTTAAA
65 ATATTTATTAATTTAAAATTTAATAATGTTTAAA
*** *
3701413 AAAAT--TAGTTAGTAATTTTATTTTGTTGTTAGTA-AGTAGCAGTAAGTAAAAAATATTGTTCA
1 ATTTTGCTAGTTAGTAATTTTATTTTGTTGTTAGTATAGTAGTAGTAAGTAAAAAATATTGTTCA
*
3701475 TATTTATTTATTTAAAA
66 TATTTATTAATTTAAAA
3701492 AAATAATATA
Statistics
Matches: 162, Mismatches: 9, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
92 21 0.13
94 2 0.01
95 48 0.30
96 2 0.01
97 28 0.17
98 57 0.35
99 4 0.02
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.48
Consensus pattern (98 bp):
ATTTTGCTAGTTAGTAATTTTATTTTGTTGTTAGTATAGTAGTAGTAAGTAAAAAATATTGTTCA
TATTTATTAATTTAAAATTTAATAATGTTTAAA
Found at i:3703074 original size:43 final size:43
Alignment explanation
Indices: 3702992--3703076 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
3702982 ATTAACATGT
* * *
3702992 TAAATTATACTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAACTATACTACTTGACTCGTATTAATATGCTTGCATGTTAC
* * *
3703035 TAAACTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAACTATACTACTTGACTCGTATTAATATGCTTG-CATGTTA
3703077 TTAATTGTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 3 0.09
43 32 0.91
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (43 bp):
TAAACTATACTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:3703723 original size:21 final size:21
Alignment explanation
Indices: 3703697--3703743 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
3703687 ACGAGCCACC
*
3703697 GCAATACTTTACTCCTCCCGG
1 GCAATACTCTACTCCTCCCGG
*
3703718 GCAATACTCTACTCCTCCGGG
1 GCAATACTCTACTCCTCCCGG
3703739 GCAAT
1 GCAAT
3703744 TGGACCCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.26
Consensus pattern (21 bp):
GCAATACTCTACTCCTCCCGG
Found at i:3707054 original size:17 final size:15
Alignment explanation
Indices: 3707019--3707059 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
3707009 AACAAATTAC
*
3707019 CTTTCTTTCCTTTTT
1 CTTTCTTTCCTTCTT
3707034 CTTTCTTTCCTCTCCTT
1 CTTTCTTTCCT-T-CTT
3707051 CTTTCTTTC
1 CTTTCTTTC
3707060 TTTCCCGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.48
16 1 0.04
17 11 0.48
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (15 bp):
CTTTCTTTCCTTCTT
Found at i:3707056 original size:21 final size:20
Alignment explanation
Indices: 3707026--3707064 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
3707016 TACCTTTCTT
3707026 TCCTTTTTCTTTCTTTCCTC
1 TCCTTTTTCTTTCTTTCCTC
3707046 TCCTTCTTTCTTTCTTTCC
1 TCCTT-TTTCTTTCTTTCC
3707065 CGTTTATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (20 bp):
TCCTTTTTCTTTCTTTCCTC
Found at i:3713257 original size:7 final size:7
Alignment explanation
Indices: 3713244--3713278 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
3713234 TCCATGTTTG
3713244 TTGAAAC
1 TTGAAAC
*
3713251 GTGAAAC
1 TTGAAAC
3713258 TTGAAAC
1 TTGAAAC
3713265 TTGAAAC
1 TTGAAAC
3713272 TTGAAAC
1 TTGAAAC
3713279 CTTCATTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (7 bp):
TTGAAAC
Found at i:3714443 original size:31 final size:33
Alignment explanation
Indices: 3714388--3714472 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 33
3714378 TTATTTATTA
*
3714388 TTTTTATAATTTTTAAAAAAATTAA-AT-TAAT
1 TTTTTATTATTTTTAAAAAAATTAATATATAAT
* **
3714419 TTTTTATTATTTTTAAGAGGATTAATATATAAT
1 TTTTTATTATTTTTAAAAAAATTAATATATAAT
*
3714452 TTTATTTTTATTAATTTAAAA
1 TTT-TTATTATT--TTTAAAA
3714473 TTTTAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
31 21 0.49
32 2 0.05
33 7 0.16
34 7 0.16
36 6 0.14
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (33 bp):
TTTTTATTATTTTTAAAAAAATTAATATATAAT
Found at i:3727365 original size:16 final size:16
Alignment explanation
Indices: 3727344--3727376 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3727334 TGCACGATGT
3727344 CAAGATTAAATTTTTA
1 CAAGATTAAATTTTTA
3727360 CAAGATTAAATTTTTA
1 CAAGATTAAATTTTTA
3727376 C
1 C
3727377 TTAGTATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (16 bp):
CAAGATTAAATTTTTA
Found at i:3728614 original size:29 final size:30
Alignment explanation
Indices: 3728572--3728630 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
3728562 GAATTGAATC
* *
3728572 AAATCAAAATTTCATGTATA-ATATTACACA
1 AAATCAAAAGTTCATATATATA-ATTACACA
3728602 AAATC-AAAGTTCATATATATAATTACACA
1 AAATCAAAAGTTCATATATATAATTACACA
3728631 TTAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (30 bp):
AAATCAAAAGTTCATATATATAATTACACA
Found at i:3731636 original size:7 final size:7
Alignment explanation
Indices: 3731624--3731665 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
3731614 CTATTTCTAC
3731624 ATATATA
1 ATATATA
3731631 ATATATA
1 ATATATA
*
3731638 ATCTATA
1 ATATATA
*
3731645 ATCTAT-
1 ATATATA
3731651 ATAATATA
1 AT-ATATA
3731659 ATATATA
1 ATATATA
3731666 TAAAAACACA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 2 0.06
7 27 0.87
8 2 0.06
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATATA
Found at i:3731667 original size:23 final size:23
Alignment explanation
Indices: 3731625--3731668 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3731615 TATTTCTACA
*
3731625 TATATAATATATAATCTATAATC
1 TATATAATATATAATATATAATC
3731648 TATATAATATA-ATATATATAA
1 TATATAATATATA-ATATATAA
3731669 AAACACAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (23 bp):
TATATAATATATAATATATAATC
Found at i:3734263 original size:19 final size:19
Alignment explanation
Indices: 3734221--3734263 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
3734211 AAAAAGCATT
*
3734221 AAATTTTTAATAATTTCAA
1 AAATTTTTAATAATTTAAA
* * *
3734240 CAATTTTTTATATTTTAAA
1 AAATTTTTAATAATTTAAA
3734259 AAATT
1 AAATT
3734264 AATTAATTAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATTTTTAATAATTTAAA
Found at i:3747125 original size:70 final size:70
Alignment explanation
Indices: 3747012--3747151 Score: 271
Period size: 70 Copynumber: 2.0 Consensus size: 70
3747002 CATTAAGTAT
3747012 ATAACATAATATAACTAAGGATTGATTATAAAAATAAATGATTCTTATTTTATTGAAGGAAATGC
1 ATAACATAATATAACTAAGGATTGATTATAAAAATAAATGATTCTTATTTTATTGAAGGAAATGC
3747077 AAGAA
66 AAGAA
*
3747082 ATAACATAATATAACTAAGGATTGATTGTAAAAATAAATGATTCTTATTTTATTGAAGGAAATGC
1 ATAACATAATATAACTAAGGATTGATTATAAAAATAAATGATTCTTATTTTATTGAAGGAAATGC
3747147 AAGAA
66 AAGAA
3747152 TGTGGATTTC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.48, C:0.06, G:0.14, T:0.33
Consensus pattern (70 bp):
ATAACATAATATAACTAAGGATTGATTATAAAAATAAATGATTCTTATTTTATTGAAGGAAATGC
AAGAA
Found at i:3750515 original size:12 final size:13
Alignment explanation
Indices: 3750493--3750542 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
3750483 TTAGTATTGC
3750493 TTTTAAGAAA-TGA
1 TTTTAA-AAAGTGA
*
3750506 TTTTAAAAATTG-
1 TTTTAAAAAGTGA
3750518 TTTTAGAAAAGTGA
1 TTTTA-AAAAGTGA
*
3750532 TTTTGAAAAGT
1 TTTTAAAAAGT
3750543 AGTTTTGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 8 0.25
13 20 0.62
14 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (13 bp):
TTTTAAAAAGTGA
Found at i:3750517 original size:26 final size:26
Alignment explanation
Indices: 3750503--3750554 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3750493 TTTTAAGAAA
3750503 TGATTTTAAAAATTGTTTTAGAAAAG
1 TGATTTTAAAAATTGTTTTAGAAAAG
* *
3750529 TGATTTTGAAAAGTAGTTTT-GAAAAG
1 TGATTTT-AAAAATTGTTTTAGAAAAG
3750555 CTTGGTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (26 bp):
TGATTTTAAAAATTGTTTTAGAAAAG
Found at i:3750554 original size:13 final size:12
Alignment explanation
Indices: 3750506--3750554 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
3750496 TAAGAAATGA
* *
3750506 TTTTAAAAATTG
1 TTTTGAAAAGTG
3750518 TTTTAGAAAAGTG
1 TTTT-GAAAAGTG
3750531 ATTTTGAAAAGTAG
1 -TTTTGAAAAGT-G
3750545 TTTTGAAAAG
1 TTTTGAAAAG
3750555 CTTGGTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 4 0.12
13 23 0.72
14 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (12 bp):
TTTTGAAAAGTG
Found at i:3760618 original size:2 final size:2
Alignment explanation
Indices: 3760613--3760648 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3760603 TCCCAGTTGT
3760613 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
3760649 AGGCATTCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3762600 original size:21 final size:21
Alignment explanation
Indices: 3762576--3762615 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3762566 TGGATACCCA
3762576 GGGGCAAAACGATAATTTTCG
1 GGGGCAAAACGATAATTTTCG
* *
3762597 GGGGTAAAATGATAATTTT
1 GGGGCAAAACGATAATTTT
3762616 TAGACACTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (21 bp):
GGGGCAAAACGATAATTTTCG
Found at i:3762672 original size:29 final size:29
Alignment explanation
Indices: 3762593--3762731 Score: 92
Period size: 29 Copynumber: 4.8 Consensus size: 29
3762583 AACGATAATT
* * * * *
3762593 TTCGGGGGTAAAATGATAATTTTTAGACAC
1 TTCGGGGTTAAAATG-GAATTTTTGGAAAG
* *
3762623 TTAGGGG-TAAAATGGTATTTTTGGAAAG
1 TTCGGGGTTAAAATGGAATTTTTGGAAAG
*
3762651 TTC-GGGTTAAAATTGGAA-TTTTCGAACA-
1 TTCGGGGTTAAAA-TGGAATTTTTGGAA-AG
*
3762679 -TCTGGGAG-TAAAATGGTAATTTTTGGAAGG
1 TTC-GGG-GTTAAAATGG-AATTTTTGGAAAG
*
3762709 TTCGGGGTCAAAATGGAATTTTT
1 TTCGGGGTTAAAATGGAATTTTT
3762732 ATGAAGTTCG
Statistics
Matches: 86, Mismatches: 12, Indels: 23
0.71 0.10 0.19
Matches are distributed among these distances:
27 5 0.06
28 26 0.30
29 29 0.34
30 24 0.28
31 2 0.02
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.35
Consensus pattern (29 bp):
TTCGGGGTTAAAATGGAATTTTTGGAAAG
Found at i:3762753 original size:30 final size:30
Alignment explanation
Indices: 3762631--3762753 Score: 80
Period size: 29 Copynumber: 4.2 Consensus size: 30
3762621 ACTTAGGGGT
* *
3762631 AAAATGGT-ATTTTTGGAAAGTTCGG-GTT
1 AAAATGGTAATTTTTGGAAGGTTCGGAGTC
* ** *
3762659 AAAATTGG-AA-TTTTCGAACATCTGGGAGT-
1 AAAA-TGGTAATTTTTGGAAGGT-TCGGAGTC
*
3762688 AAAATGGTAATTTTTGGAAGGTTCGGGGTC
1 AAAATGGTAATTTTTGGAAGGTTCGGAGTC
*
3762718 AAAATGG-AATTTTTATGAA-GTTCGAGAGTC
1 AAAATGGTAATTTTT-GGAAGGTTCG-GAGTC
*
3762748 CAAATG
1 AAAATG
3762754 TGATTTTGGA
Statistics
Matches: 74, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
28 15 0.20
29 30 0.41
30 29 0.39
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAGGTTCGGAGTC
Found at i:3764602 original size:6 final size:6
Alignment explanation
Indices: 3764591--3764672 Score: 62
Period size: 6 Copynumber: 14.2 Consensus size: 6
3764581 GACTTTCATC
* * ** * *
3764591 ATTTAA ATTTAA A-ATAA TTTTAA ATTTAA AAATAA ATTTAA ACTTAT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* **
3764638 A-TTAA ATTTAA ACTTAA A-ACAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
3764673 GTAAACTTAA
Statistics
Matches: 57, Mismatches: 16, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
5 10 0.18
6 47 0.82
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:3764614 original size:17 final size:17
Alignment explanation
Indices: 3764591--3764697 Score: 117
Period size: 17 Copynumber: 6.2 Consensus size: 17
3764581 GACTTTCATC
3764591 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
3764608 TTTTAAATTTAAAAATAA
1 ATTTAAATTT-AAAATAA
* * *
3764626 ATTTAAACTTATATTAA
1 ATTTAAATTTAAAATAA
* *
3764643 ATTTAAACTTAAAACAA
1 ATTTAAATTTAAAATAA
*
3764660 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAATAA
*
3764677 ACTT-AATCTTAAAATAA
1 ATTTAAAT-TTAAAATAA
3764694 ATTT
1 ATTT
3764698 TAAAAATGGG
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
16 3 0.04
17 56 0.76
18 15 0.20
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:3764628 original size:29 final size:29
Alignment explanation
Indices: 3764594--3764649 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
3764584 TTTCATCATT
*
3764594 TAAATTTAAAATAATTTTAAATTTAAAAA
1 TAAATTTAAAATAATATTAAATTTAAAAA
* *
3764623 TAAATTTAAACTTATATTAAATTTAAA
1 TAAATTTAAAATAATATTAAATTTAAA
3764650 CTTAAAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (29 bp):
TAAATTTAAAATAATATTAAATTTAAAAA
Found at i:3764649 original size:23 final size:22
Alignment explanation
Indices: 3764614--3764681 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
3764604 ATAATTTTAA
**
3764614 ATTTAAAAATAAATTTAAACTT
1 ATTTAAATTTAAATTTAAACTT
* **
3764636 ATATTAAATTTAAACTTAAAACAA
1 AT-TTAAATTTAAA-TTTAAACTT
*
3764660 ATTTAAATTTAAA-GTAAACTT
1 ATTTAAATTTAAATTTAAACTT
3764681 A
1 A
3764682 ATCTTAAAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
21 5 0.14
22 2 0.06
23 20 0.57
24 8 0.23
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.38
Consensus pattern (22 bp):
ATTTAAATTTAAATTTAAACTT
Found at i:3764655 original size:29 final size:29
Alignment explanation
Indices: 3764593--3764655 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
3764583 CTTTCATCAT
*
3764593 TTAAATTTAAAATAATTTTAAATTTAAAA
1 TTAAATTTAAAATAATATTAAATTTAAAA
* * * *
3764622 ATAAATTTAAACTTATATTAAATTTAAAC
1 TTAAATTTAAAATAATATTAAATTTAAAA
3764651 TTAAA
1 TTAAA
3764656 ACAAATTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (29 bp):
TTAAATTTAAAATAATATTAAATTTAAAA
Found at i:3764688 original size:23 final size:23
Alignment explanation
Indices: 3764629--3764689 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
3764619 AAAATAAATT
*
3764629 TAAACTT-ATATTAAATTTAAACT
1 TAAACTTAAT-TTAAATTTAAACG
*
3764652 TAAAAC-AAATTTAAATTTAAA-G
1 T-AAACTTAATTTAAATTTAAACG
3764674 TAAACTTAATCTTAAA
1 TAAACTTAAT-TTAAA
3764690 ATAAATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 4 0.13
22 4 0.13
23 17 0.55
24 6 0.19
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (23 bp):
TAAACTTAATTTAAATTTAAACG
Found at i:3765948 original size:6 final size:6
Alignment explanation
Indices: 3765938--3765987 Score: 82
Period size: 6 Copynumber: 8.3 Consensus size: 6
3765928 ATGGATGTCC
* *
3765938 ATCAAC ATCAAG ATAAAG ATCAAG ATCAAG ATCAAG ATCAAG ATCAAG
1 ATCAAG ATCAAG ATCAAG ATCAAG ATCAAG ATCAAG ATCAAG ATCAAG
3765986 AT
1 AT
3765988 AAGGTTTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.52, C:0.16, G:0.14, T:0.18
Consensus pattern (6 bp):
ATCAAG
Found at i:3772290 original size:19 final size:21
Alignment explanation
Indices: 3772247--3772290 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 21
3772237 GAAAATTTAG
3772247 AAATTATAGAAAAATATATAC
1 AAATTATAGAAAAATATATAC
*
3772268 --ATTATA-AAAATTATA-AC
1 AAATTATAGAAAAATATATAC
3772285 AAATTA
1 AAATTA
3772291 AATATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 6
0.74 0.04 0.22
Matches are distributed among these distances:
17 2 0.10
18 8 0.40
19 10 0.50
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (21 bp):
AAATTATAGAAAAATATATAC
Found at i:3772478 original size:21 final size:22
Alignment explanation
Indices: 3772446--3772500 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
3772436 TTTTAGTGCA
*
3772446 AAAAATACTTTTTGAAAAATTT
1 AAAAATACTTTTTGAAAAATTC
*
3772468 AAAAATATTTTTTGAAAAATTC
1 AAAAATACTTTTTGAAAAATTC
*
3772490 AAAAAGACTTT
1 AAAAATACTTT
3772501 GTTTAGTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (22 bp):
AAAAATACTTTTTGAAAAATTC
Found at i:3772539 original size:18 final size:19
Alignment explanation
Indices: 3772512--3772551 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
3772502 TTTAGTAACG
3772512 TTTTTATTTCAAAAGTG-T
1 TTTTTATTTCAAAAGTGCT
*
3772530 TTTTTGTTTCAAAAGTGCT
1 TTTTTATTTCAAAAGTGCT
3772549 TTT
1 TTT
3772552 GAAAAGCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.23, C:0.07, G:0.12, T:0.57
Consensus pattern (19 bp):
TTTTTATTTCAAAAGTGCT
Found at i:3783965 original size:31 final size:31
Alignment explanation
Indices: 3783927--3783985 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3783917 TATTTGAGTT
3783927 AATTAAGTTATTT-GGATTAACTCGAATAAAA
1 AATTAAGTT-TTTCGGATTAACTCGAATAAAA
*
3783958 AATTAAGTTTTTCGGTTTAACTCGAATA
1 AATTAAGTTTTTCGGATTAACTCGAATA
3783986 TGAATTACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (31 bp):
AATTAAGTTTTTCGGATTAACTCGAATAAAA
Found at i:3791002 original size:6 final size:6
Alignment explanation
Indices: 3790991--3791027 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
3790981 ACTACTAGTT
3790991 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA T
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA T
3791028 GAATAAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:3821727 original size:56 final size:55
Alignment explanation
Indices: 3821667--3821865 Score: 154
Period size: 59 Copynumber: 3.5 Consensus size: 55
3821657 TGCATGGCCA
*
3821667 ACACCTCTTTTTAATCTGATAAAAAAAAATTTTAGGTGGTGGCTATGCAATGGTCG
1 ACACCTCTTTTT-ATCTGATAAAAAAAAATTTTAGGTGGTGGCAATGCAATGGTCG
* * * * * *
3821723 ACACCCTCTTTTTGTCAGATAAAAAATTCAATTTTTTGGTGTTGGCAATGTAATGGTCG
1 ACA-CCTCTTTTTATCTGATAAAAAA---AAATTTTAGGTGGTGGCAATGCAATGGTCG
* * *
3821782 ACACC-CTTATTTATCTAATAAAAAAATCAAATTTTTGG-GAGTTGGTC-ATGCAATGGCCG
1 ACACCTCTT-TTTATCTGAT-AAAAAA--AAATTTTAGGTG-G-TGG-CAATGCAATGGTCG
*
3821841 ACACCTCCTTTTT-TCAGATAAAAAA
1 ACACCT-CTTTTTATCTGATAAAAAA
3821866 TTTCAAATTT
Statistics
Matches: 116, Mismatches: 16, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
56 14 0.12
57 13 0.11
58 26 0.22
59 56 0.48
60 4 0.03
61 3 0.03
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (55 bp):
ACACCTCTTTTTATCTGATAAAAAAAAATTTTAGGTGGTGGCAATGCAATGGTCG
Found at i:3821913 original size:60 final size:60
Alignment explanation
Indices: 3821711--3822066 Score: 314
Period size: 61 Copynumber: 5.9 Consensus size: 60
3821701 GGTGGTGGCT
*
3821711 ATGCAATGGTCGACACCCTCTTTTTGTCAGATAAAAAATTC-AA-TTTTTTGGTGTTGG-C
1 ATGCAATGGCCGACACCCT-TTTTTGTCAGATAAAAAATTCAAATTTTTTTGGTGTTGGTC
* * * * * * *
3821769 AATGTAATGGTCGACACCCTTATTTATCTA-ATAAAAAAATCAAA-TTTTTGGGAGTTGGTC
1 -ATGCAATGGCCGACACCCTTTTTTGTC-AGATAAAAAATTCAAATTTTTTTGGTGTTGGTC
* *
3821829 ATGCAATGGCCGACACCTCCTTTTT-TCAGATAAAAAATTTCAAATTTTTTTGGTATTGGTC
1 ATGCAATGGCCGACACC-CTTTTTTGTCAGATAAAAAA-TTCAAATTTTTTTGGTGTTGGTC
* * ** * *
3821890 ATGCCATGGCCGACACCCTTTTTTGTCTGATAAAAAATTTGAATTTTTTTTGTGTTGGCC
1 ATGCAATGGCCGACACCCTTTTTTGTCAGATAAAAAATTCAAATTTTTTTGGTGTTGGTC
* * ** * * * *
3821950 ATGTC-ATGACCGACATCCCCTTTTTTATTTGGTAAAAAAATC-AATTTTTTTTGTGTTGATC
1 ATG-CAATGGCCGACA--CCCTTTTTTGTCAGATAAAAAATTCAAATTTTTTTGGTGTTGGTC
* * * * *
3822011 ATGCAATGGTCGACACTTCTTTTTTGTGAAATAAAAAATTCAGATTTTTTTGGTGT
1 ATGCAATGGCCGACAC-CCTTTTTTGTCAGATAAAAAATTCAAATTTTTTTGGTGT
3822067 AAAATTTGAT
Statistics
Matches: 242, Mismatches: 41, Indels: 26
0.78 0.13 0.08
Matches are distributed among these distances:
58 17 0.07
59 59 0.24
60 65 0.27
61 81 0.33
62 20 0.08
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.40
Consensus pattern (60 bp):
ATGCAATGGCCGACACCCTTTTTTGTCAGATAAAAAATTCAAATTTTTTTGGTGTTGGTC
Found at i:3822185 original size:17 final size:18
Alignment explanation
Indices: 3822153--3822187 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3822143 TCTTGTATTT
*
3822153 TCGTATATAAATAAAATA
1 TCGTATATAAAAAAAATA
3822171 TCGTAT-TAAAAAAAATA
1 TCGTATATAAAAAAAATA
3822188 CAAAGGTGTC
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:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
TCGTATATAAAAAAAATA
Found at i:3827969 original size:2 final size:2
Alignment explanation
Indices: 3827964--3827991 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3827954 ATATACCATC
3827964 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3827992 TTCAGCTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.