Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 8 of 171
Found at i:3411225 original size:24 final size:24
Alignment explanation
Indices: 3411197--3411306 Score: 98
Period size: 23 Copynumber: 4.7 Consensus size: 24
3411187 TTATTTTTCG
*
3411197 TAAACATGTACAATTATATGTTCA
1 TAAACATGTTCAATTATATGTTCA
** *
3411221 TAAACATGTTCGTTTA-ATGTTCG
1 TAAACATGTTCAATTATATGTTCA
* *
3411244 TGAACATGTTCAATTTTATGTTCA
1 TAAACATGTTCAATTATATGTTCA
* ** *
3411268 TGAACATGTTCGTTTA-ATGTTCG
1 TAAACATGTTCAATTATATGTTCA
* *
3411291 TGAACATGTTCGATTA
1 TAAACATGTTCAATTA
3411307 AATTAATATG
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
23 39 0.55
24 32 0.45
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (24 bp):
TAAACATGTTCAATTATATGTTCA
Found at i:3411249 original size:23 final size:23
Alignment explanation
Indices: 3411214--3411307 Score: 125
Period size: 23 Copynumber: 4.0 Consensus size: 23
3411204 GTACAATTAT
*
3411214 ATGTTCATAAACATGTTCGTTTA
1 ATGTTCATGAACATGTTCGTTTA
* * *
3411237 ATGTTCGTGAACATGTTCAATTTT
1 ATGTTCATGAACATGTTC-GTTTA
3411261 ATGTTCATGAACATGTTCGTTTA
1 ATGTTCATGAACATGTTCGTTTA
* *
3411284 ATGTTCGTGAACATGTTCGATTA
1 ATGTTCATGAACATGTTCGTTTA
3411307 A
1 A
3411308 ATTAATATGT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 41 0.67
24 20 0.33
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.43
Consensus pattern (23 bp):
ATGTTCATGAACATGTTCGTTTA
Found at i:3411264 original size:47 final size:47
Alignment explanation
Indices: 3411193--3411306 Score: 183
Period size: 47 Copynumber: 2.4 Consensus size: 47
3411183 GTATTTATTT
* *
3411193 TTCGTAAACATGTACAATTATATGTTCATAAACATGTTCGTTTAATG
1 TTCGTGAACATGTTCAATTATATGTTCATAAACATGTTCGTTTAATG
* *
3411240 TTCGTGAACATGTTCAATTTTATGTTCATGAACATGTTCGTTTAATG
1 TTCGTGAACATGTTCAATTATATGTTCATAAACATGTTCGTTTAATG
*
3411287 TTCGTGAACATGTTCGATTA
1 TTCGTGAACATGTTCAATTA
3411307 AATTAATATG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 61 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (47 bp):
TTCGTGAACATGTTCAATTATATGTTCATAAACATGTTCGTTTAATG
Found at i:3411276 original size:12 final size:12
Alignment explanation
Indices: 3411261--3411302 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
3411251 GTTCAATTTT
*
3411261 ATGTTCATGAAC
1 ATGTTCGTGAAC
**
3411273 ATGTTCGTTTA-
1 ATGTTCGTGAAC
3411284 ATGTTCGTGAAC
1 ATGTTCGTGAAC
3411296 ATGTTCG
1 ATGTTCG
3411303 ATTAAATTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (12 bp):
ATGTTCGTGAAC
Found at i:3412693 original size:25 final size:26
Alignment explanation
Indices: 3412660--3412714 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
3412650 GGGAACATTT
3412660 TTTTTATTTAATATTAATATAAT-TA
1 TTTTTATTTAATATTAATATAATATA
**
3412685 TTTTTATTTAATATTTGTATAATATA
1 TTTTTATTTAATATTAATATAATATA
3412711 TTTT
1 TTTT
3412715 AAATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 21 0.78
26 6 0.22
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTTTATTTAATATTAATATAATATA
Found at i:3416861 original size:2 final size:2
Alignment explanation
Indices: 3416856--3416889 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3416846 ACATATATAC
3416856 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3416890 TCAGTTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3418216 original size:19 final size:19
Alignment explanation
Indices: 3418172--3418218 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
3418162 ATGTTTAAAT
*
3418172 TTCGATTAAAATTAAATTAA
1 TTCGATT-AAATTAAAGTAA
* *
3418192 CT-GATTAAATTAAAGTAG
1 TTCGATTAAATTAAAGTAA
3418210 TTCGATTAA
1 TTCGATTAA
3418219 TTGATTAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 11 0.50
19 10 0.45
20 1 0.05
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (19 bp):
TTCGATTAAATTAAAGTAA
Found at i:3425476 original size:24 final size:24
Alignment explanation
Indices: 3425390--3425464 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
3425380 AAAAATAATC
* * * *
3425390 TTTCAGTTAAATTTTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
3425414 TTTCAATTAAACTCTGTATATTTA
1 TTTCAATTAAACTCTGTTTATTTG
3425438 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
3425462 TTT
1 TTT
3425465 GGATCAAACT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.27, C:0.09, G:0.08, T:0.56
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:3427351 original size:24 final size:24
Alignment explanation
Indices: 3427323--3427373 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3427313 AGAAATAATC
* *
3427323 TTTCAGTTATACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
*
3427347 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAATTG
3427371 TTT
1 TTT
3427374 GAGTCAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAATTG
Found at i:3427382 original size:24 final size:24
Alignment explanation
Indices: 3427333--3427385 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3427323 TTTCAGTTAT
*
3427333 ACTCTGTTTAATTGTTTCAATTAA
1 ACTCTGTTTAATTGTTTCAATCAA
* * *
3427357 ACTCTGTTTATTTGTTTGAGTCAA
1 ACTCTGTTTAATTGTTTCAATCAA
3427381 ACTCT
1 ACTCT
3427386 TATTAGCCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.49
Consensus pattern (24 bp):
ACTCTGTTTAATTGTTTCAATCAA
Found at i:3439362 original size:3 final size:3
Alignment explanation
Indices: 3439354--3439387 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3439344 ATTAAATTAC
3439354 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3439388 ACTCTCTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3443496 original size:6 final size:6
Alignment explanation
Indices: 3443485--3443515 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3443475 TTCCAAAGGG
3443485 AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA A
1 AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA A
3443516 CTAAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAGGAA
Found at i:3445512 original size:23 final size:22
Alignment explanation
Indices: 3445482--3445524 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3445472 AGTTTTTATA
3445482 TTTTTATTTTTAAGAATTTAACC
1 TTTTTATTTTT-AGAATTTAACC
*
3445505 TTTTTATTTTTCGAATTTAA
1 TTTTTATTTTTAGAATTTAA
3445525 AAATTCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (22 bp):
TTTTTATTTTTAGAATTTAACC
Found at i:3447577 original size:6 final size:6
Alignment explanation
Indices: 3447566--3447595 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3447556 CTCAAAGTTT
3447566 TATCCC TATCCC TATCCC TATCCC TATCCC
1 TATCCC TATCCC TATCCC TATCCC TATCCC
3447596 GTGCATGCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
TATCCC
Found at i:3449053 original size:22 final size:21
Alignment explanation
Indices: 3449028--3449072 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3449018 TTAGAGCGAG
*
3449028 ATGTTTACACCTTCAAAATAAA
1 ATGTTTACA-CTTCAAAAAAAA
**
3449050 ATGTTTTGACTTCAAAAAAAA
1 ATGTTTACACTTCAAAAAAAA
3449071 AT
1 AT
3449073 TTAAATGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (21 bp):
ATGTTTACACTTCAAAAAAAA
Found at i:3449744 original size:18 final size:18
Alignment explanation
Indices: 3449710--3449749 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
3449700 TTTAACTCTT
3449710 TAAA-TATTATAAAGATA
1 TAAATTATTATAAAGATA
3449727 TAAATTATTA-AAATGATA
1 TAAATTATTATAAA-GATA
3449745 -AAATT
1 TAAATT
3449750 GTATTTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
TAAATTATTATAAAGATA
Found at i:3452063 original size:52 final size:52
Alignment explanation
Indices: 3451985--3452085 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 52
3451975 ATAATTTCAA
* *
3451985 TAAATGAGTTTTTTAATAAAAATAGATTGACTTGACGAAATCTTCCAAACAG
1 TAAATGAATTTCTTAATAAAAATAGATTGACTTGACGAAATCTTCCAAACAG
* * * *
3452037 TAAATGAATTTCTTACTGAAAATAGATTGACTTGATGAAATGTTCCAAA
1 TAAATGAATTTCTTAATAAAAATAGATTGACTTGACGAAATCTTCCAAA
3452086 ATGAGATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (52 bp):
TAAATGAATTTCTTAATAAAAATAGATTGACTTGACGAAATCTTCCAAACAG
Found at i:3455628 original size:60 final size:60
Alignment explanation
Indices: 3455455--3455619 Score: 280
Period size: 60 Copynumber: 2.8 Consensus size: 60
3455445 ATACAGGAAA
* *
3455455 AGGGAAGCCTGGGGGTGGCACCCATGTGAACGTTGGAGGCAAAGGAGTTGGAGTGAACAC
1 AGGGAAGCCAGGGGGTGGCACTCATGTGAACGTTGGAGGCAAAGGAGTTGGAGTGAACAC
3455515 -GGGAAAGCCAGGGGGTGGCACTCATGTGAACGTTGG-GCGCAAAGGAGTTGGAGTGAACAC
1 AGGG-AAGCCAGGGGGTGGCACTCATGTGAACGTTGGAG-GCAAAGGAGTTGGAGTGAACAC
3455575 AGGGAAGCCAGGGGGTGGCACTCATGTGAACGTTGGAGGCAAAGG
1 AGGGAAGCCAGGGGGTGGCACTCATGTGAACGTTGGAGGCAAAGG
3455620 TGGAGGAGTA
Statistics
Matches: 99, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
59 4 0.04
60 91 0.92
61 4 0.04
ACGTcount: A:0.27, C:0.16, G:0.42, T:0.15
Consensus pattern (60 bp):
AGGGAAGCCAGGGGGTGGCACTCATGTGAACGTTGGAGGCAAAGGAGTTGGAGTGAACAC
Found at i:3468919 original size:3 final size:3
Alignment explanation
Indices: 3468911--3468946 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
3468901 CCTCGCTATT
* *
3468911 GAA GAA GAA GAG GAA GAA GAA GAA GAA GAT GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3468947 CATCACGAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:3475796 original size:27 final size:29
Alignment explanation
Indices: 3475766--3475819 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
3475756 TTCTTTTTGC
3475766 CTTTTATAGTAA-AT-ATTATATAAGTCG
1 CTTTTATAGTAATATGATTATATAAGTCG
* *
3475793 CTTTTTTAGTAATATGATTTTATAAGT
1 CTTTTATAGTAATATGATTATATAAGT
3475820 TAAAAAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 11 0.48
28 2 0.09
29 10 0.43
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (29 bp):
CTTTTATAGTAATATGATTATATAAGTCG
Found at i:3476064 original size:19 final size:20
Alignment explanation
Indices: 3476042--3476079 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3476032 GTAAAATAAT
* *
3476042 AATATTATTTAAAT-TATTG
1 AATATAATTAAAATATATTG
3476061 AATATAATTAAAATATATT
1 AATATAATTAAAATATATT
3476080 AATTTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
AATATAATTAAAATATATTG
Found at i:3482531 original size:32 final size:32
Alignment explanation
Indices: 3482490--3482550 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
3482480 AAGAGACATT
3482490 TCCTTCATCCTGTTAGACATGTATGACAGGAC
1 TCCTTCATCCTGTTAGACATGTATGACAGGAC
*
3482522 TCCTTCATCCTGTTAGGCATGTATGACAG
1 TCCTTCATCCTGTTAGACATGTATGACAG
3482551 AAAATAAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (32 bp):
TCCTTCATCCTGTTAGACATGTATGACAGGAC
Found at i:3486432 original size:8 final size:8
Alignment explanation
Indices: 3486419--3486452 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
3486409 TTTTTGCACT
*
3486419 CACTTAGA
1 CACTTAAA
3486427 CACTTAAA
1 CACTTAAA
3486435 CACTTAAAA
1 CACTT-AAA
3486444 CACTTAAA
1 CACTTAAA
3486452 C
1 C
3486453 TTTCAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.47, C:0.26, G:0.03, T:0.24
Consensus pattern (8 bp):
CACTTAAA
Found at i:3486596 original size:20 final size:20
Alignment explanation
Indices: 3486560--3486597 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3486550 AATAAATCAT
**
3486560 TTGACCGTTAACTTTAACAG
1 TTGACCGTTAAAATTAACAG
3486580 TTGACCGTTAAAATTAAC
1 TTGACCGTTAAAATTAAC
3486598 TGCTTCTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (20 bp):
TTGACCGTTAAAATTAACAG
Found at i:3486716 original size:19 final size:20
Alignment explanation
Indices: 3486672--3486716 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
3486662 GTGACAAAAG
*
3486672 AATTTATAAAAATTATTAAA
1 AATTAATAAAAATTATTAAA
**
3486692 TTTTAATAAAAA-TATTAAA
1 AATTAATAAAAATTATTAAA
3486711 AATTAA
1 AATTAA
3486717 AATTAAAAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTAATAAAAATTATTAAA
Found at i:3509795 original size:32 final size:31
Alignment explanation
Indices: 3509774--3509833 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
3509764 GTGTTCTAAT
3509774 TGTGATTCATTATATGGATTTTTAATTATAAC
1 TGTGATT-ATTATATGGATTTTTAATTATAAC
3509806 TGTGATTATTATATGGA-TTTT-ATTATAA
1 TGTGATTATTATATGGATTTTTAATTATAA
3509834 TAAATTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 7 0.25
30 4 0.14
31 10 0.36
32 7 0.25
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.52
Consensus pattern (31 bp):
TGTGATTATTATATGGATTTTTAATTATAAC
Found at i:3509845 original size:29 final size:29
Alignment explanation
Indices: 3509779--3509868 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
3509769 CTAATTGTGA
**
3509779 TTCATTATATGGATTTTTAATTATAACTGTGA-
1 TTCATTATATGGA-TTTT-ATTATAA-T-AAAT
3509811 TT-ATTATATGGATTTTATTATAATAAAT
1 TTCATTATATGGATTTTATTATAATAAAT
* *
3509839 TTCATTATAGGGATTTTA-TATAATATAT
1 TTCATTATATGGATTTTATTATAATAAAT
3509867 TT
1 TT
3509869 AGAATATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
27 1 0.02
28 14 0.27
29 21 0.40
30 4 0.08
31 10 0.19
32 2 0.04
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.52
Consensus pattern (29 bp):
TTCATTATATGGATTTTATTATAATAAAT
Found at i:3510096 original size:17 final size:17
Alignment explanation
Indices: 3510060--3510109 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
3510050 CAATATTTGT
* *
3510060 TTAAAATAAAATATTGAA
1 TTAAAAT-AAATAATAAA
3510078 TTAAAATAAATAATAAA
1 TTAAAATAAATAATAAA
*
3510095 TTATAAAAAAATAAT
1 TTA-AAATAAATAAT
3510110 TTTTTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
TTAAAATAAATAATAAA
Found at i:3510908 original size:31 final size:30
Alignment explanation
Indices: 3510838--3510909 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
3510828 ATTATATATG
*
3510838 AACTTTAATTTGATATAATTATATACGTGA
1 AACTTTAATTTGATATAAATATATACGTGA
** *
3510868 AACACTAATTGTGAT-TCAAATATATACTTGA
1 AACTTTAATT-TGATAT-AAATATATACGTGA
3510899 AACTTTAATTT
1 AACTTTAATTT
3510910 CGATTTATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
30 10 0.29
31 24 0.71
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (30 bp):
AACTTTAATTTGATATAAATATATACGTGA
Found at i:3511075 original size:29 final size:28
Alignment explanation
Indices: 3511016--3511083 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
3511006 GAATGAAATC
*
3511016 AAATCAAAATTTATATATAAAATTACATA
1 AAATCAAAATTTAGATAT-AAATTACATA
* *
3511045 AAATCAAAGTTTAGATAT-AATTACACTT
1 AAATCAAAATTTAGATATAAATTACA-TA
*
3511073 AAATCATAATT
1 AAATCAAAATT
3511084 CTTATATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 7 0.21
28 10 0.30
29 16 0.48
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (28 bp):
AAATCAAAATTTAGATATAAATTACATA
Found at i:3524394 original size:278 final size:277
Alignment explanation
Indices: 3523897--3524424 Score: 869
Period size: 278 Copynumber: 1.9 Consensus size: 277
3523887 GGAAGATGGG
* * * * *
3523897 AAATGTTACTACTAATTAAAGAAGGGTAAATTCTAAAAATAGTCACTTTAGTTTGTCTCAAGTTA
1 AAATGTTACTACTAATTAAAAAAAGATAAA-TCTAAAAAAAGTCACTTTAGTTTGCCTCAAGTTA
*
3523962 TATTTTAGTCACTTATGTTTGAAATGTTACGTTTTAGTCACTTATGTTATTATTTTATTACGAAG
65 CATTTTAGTCACTTATGTTTGAAATGTTACGTTTTAGTCACTTATGTTATTATTTTATTACGAAG
* * *
3524027 TGATCACTCTACCGTTAAGTTCCGTTACCTCTCTAACGGTAATCCTACGTGGCAGTCCAATTAGA
130 TGATCACTCTACCGTTAAGTTCCATTACCTCCCTAACGGTAATCCTACGTGGCAATCCAATTAGA
*
3524092 ATTTAAGTGTCAACTTGAATTTCCAAATGAGATGAGAATAGATTTTTAAATAAATTTAAAATTTA
195 ATTTAAGTGCCAACTTGAATTTCCAAATGAGATGAGAATAGATTTTTAAATAAATTTAAAATTTA
3524157 AACCTAAACCTTAGCTTA
260 AACCTAAACCTTAGCTTA
3524175 AAATGTTACGTACTAATTAAAAAAAGATAAA-CTAAAAAAAAGTCACTTTAGTTTGCCTCAAGTT
1 AAATGTTAC-TACTAATTAAAAAAAGATAAATCT-AAAAAAAGTCACTTTAGTTTGCCTCAAGTT
* *
3524239 ACATTTTAGTCACTTATGTTTGAAATGTTACGTTTTTGTCACTTATGTTATTATTTTGTTACGAA
64 ACATTTTAGTCACTTATGTTTGAAATGTTACGTTTTAGTCACTTATGTTATTATTTTATTACGAA
* **
3524304 GTGATCACTCTACCGTTAAGTTCTATTGTCTCCCTAACGGTAATCCTACGTGGCAATCCAATTAG
129 GTGATCACTCTACCGTTAAGTTCCATTACCTCCCTAACGGTAATCCTACGTGGCAATCCAATTAG
* *
3524369 AATTTAAGTGCCAACTTGAATTTCCAAATGGGATGAGAATAGATTTTTAATTAAAT
194 AATTTAAGTGCCAACTTGAATTTCCAAATGAGATGAGAATAGATTTTTAAATAAAT
3524425 AAATTTAATT
Statistics
Matches: 231, Mismatches: 17, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
277 2 0.01
278 211 0.91
279 18 0.08
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.38
Consensus pattern (277 bp):
AAATGTTACTACTAATTAAAAAAAGATAAATCTAAAAAAAGTCACTTTAGTTTGCCTCAAGTTAC
ATTTTAGTCACTTATGTTTGAAATGTTACGTTTTAGTCACTTATGTTATTATTTTATTACGAAGT
GATCACTCTACCGTTAAGTTCCATTACCTCCCTAACGGTAATCCTACGTGGCAATCCAATTAGAA
TTTAAGTGCCAACTTGAATTTCCAAATGAGATGAGAATAGATTTTTAAATAAATTTAAAATTTAA
ACCTAAACCTTAGCTTA
Found at i:3525439 original size:2 final size:2
Alignment explanation
Indices: 3525432--3525473 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
3525422 AAGAAATTCC
* *
3525432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3525474 TTGAGATTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3534369 original size:8 final size:8
Alignment explanation
Indices: 3534356--3534383 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3534346 GGAGACGAGA
3534356 TTCGGCAG
1 TTCGGCAG
3534364 TTCGGCAG
1 TTCGGCAG
3534372 TTCGGCAG
1 TTCGGCAG
3534380 TTCG
1 TTCG
3534384 ACTTATTAAT
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:0.25, G:0.36, T:0.29
Consensus pattern (8 bp):
TTCGGCAG
Found at i:3535654 original size:28 final size:28
Alignment explanation
Indices: 3535614--3535672 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
3535604 AGTTTAAAAC
* *
3535614 TTGTCCACATGTCGTTCGACATCCTATG
1 TTGTCCACATGTCATTCGACACCCTATG
*
3535642 TTGTCCACGTGTCATTCGACACCCTATG
1 TTGTCCACATGTCATTCGACACCCTATG
3535670 TTG
1 TTG
3535673 AAAGCTTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.36
Consensus pattern (28 bp):
TTGTCCACATGTCATTCGACACCCTATG
Found at i:3545958 original size:31 final size:29
Alignment explanation
Indices: 3545911--3546014 Score: 120
Period size: 28 Copynumber: 3.4 Consensus size: 29
3545901 CAAATGATTT
3545911 TAAAATTATTAAAATTATTTTTTTAAAAATA
1 TAAAATTATTAAAATTATTTTTTT--AAATA
* * * *
3545942 TATAGTTTTTTAAATTA-TTTTTTAAATA
1 TAAAATTATTAAAATTATTTTTTTAAATA
3545970 TAAAATTATTAAAATTATTTTTTTTGAAATAA
1 TAAAATTATTAAAATTA-TTTTTTT-AAAT-A
3546002 TAAAATTATTAAA
1 TAAAATTATTAAA
3546015 TAATTTTAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
28 18 0.30
30 12 0.20
31 17 0.28
32 14 0.23
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTTAAATA
Found at i:3546021 original size:31 final size:30
Alignment explanation
Indices: 3545911--3546021 Score: 102
Period size: 31 Copynumber: 3.7 Consensus size: 30
3545901 CAAATGATTT
* *
3545911 TAAAATTATTAAAATTATTTTTTTAAAAATA
1 TAAAATTATTAAAATAATTTTTTT-TAAATA
* * * * *
3545942 TATAGTTTTTTAAAT--TATTTTTTAAATA
1 TAAAATTATTAAAATAATTTTTTTTAAATA
*
3545970 TAAAATTATTAAAATTATTTTTTTTGAAATAA
1 TAAAATTATTAAAATAATTTTTTTT-AAAT-A
3546002 TAAAATTATT-AAATAATTTT
1 TAAAATTATTAAAATAATTTT
3546022 AATTTCTAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
28 16 0.25
29 6 0.09
30 7 0.11
31 24 0.38
32 11 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (30 bp):
TAAAATTATTAAAATAATTTTTTTTAAATA
Found at i:3547667 original size:52 final size:52
Alignment explanation
Indices: 3547589--3547693 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
3547579 TTTAGCCATC
3547589 TTTATATAGTGCAAGTTACAAATGCAAAGCTTTATTCCTAACCTATGATATT
1 TTTATATAGTGCAAGTTACAAATGCAAAGCTTTATTCCTAACCTATGATATT
3547641 TTTATATAGTGCAAGTTACAAATGCAAAGCTTTATTCCTAACCTATGATATT
1 TTTATATAGTGCAAGTTACAAATGCAAAGCTTTATTCCTAACCTATGATATT
3547693 T
1 T
3547694 GGATTTTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.39
Consensus pattern (52 bp):
TTTATATAGTGCAAGTTACAAATGCAAAGCTTTATTCCTAACCTATGATATT
Found at i:3581098 original size:27 final size:27
Alignment explanation
Indices: 3581068--3581126 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
3581058 ATCAATTTAA
3581068 ATGTTTAAAAAGATACATGGAATTCAT
1 ATGTTTAAAAAGATACATGGAATTCAT
* * * *
3581095 ATGTTTAAAATGTTAGATGGCATTCAT
1 ATGTTTAAAAAGATACATGGAATTCAT
3581122 ATGTT
1 ATGTT
3581127 ATATCAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (27 bp):
ATGTTTAAAAAGATACATGGAATTCAT
Found at i:3581521 original size:19 final size:19
Alignment explanation
Indices: 3581476--3581527 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
3581466 AAATTGAATG
3581476 AAATAATTAAAAATAAATTT
1 AAATAA-TAAAAATAAATTT
*
3581496 TAA-AATAAAAATCAAA-TT
1 AAATAATAAAAAT-AAATTT
*
3581514 AAATAATAATAATA
1 AAATAATAAAAATA
3581528 TTTTTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 12 0.44
19 13 0.48
20 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATAATAAAAATAAATTT
Found at i:3581595 original size:23 final size:22
Alignment explanation
Indices: 3581527--3581596 Score: 54
Period size: 22 Copynumber: 3.0 Consensus size: 22
3581517 TAATAATAAT
*
3581527 ATTTTTTTAAATGTAATTATAATA
1 ATTTTTTAAAAT-TAATTA-AATA
* *
3581551 A--ATTTAAATATTAAGGTAAATA
1 ATTTTTTAAA-ATTAA-TTAAATA
3581573 ATTTTTTAAAATTAATTAGAATA
1 ATTTTTTAAAATTAATTA-AATA
3581596 A
1 A
3581597 ATAATATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
22 15 0.42
23 14 0.39
24 7 0.19
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (22 bp):
ATTTTTTAAAATTAATTAAATA
Found at i:3583271 original size:20 final size:20
Alignment explanation
Indices: 3583243--3583354 Score: 64
Period size: 20 Copynumber: 5.9 Consensus size: 20
3583233 TCACGTCAGC
*
3583243 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
3583263 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
*
3583283 AAATTA--TTAAATTTATTTTA
1 AAATTATTTTAAAATTA--TTA
* * *
3583303 AAATTAATTT-AATTTTTTA
1 AAATTATTTTAAAATTATTA
3583322 AAA-TA---TAAAATTATTA
1 AAATTATTTTAAAATTATTA
*
3583338 AATTTATTTT-AAATTAT
1 AAATTATTTTAAAATTAT
3583355 AATCATTGTC
Statistics
Matches: 73, Mismatches: 6, Indels: 27
0.69 0.06 0.25
Matches are distributed among these distances:
15 1 0.01
16 14 0.19
17 4 0.05
18 2 0.03
19 13 0.18
20 22 0.30
21 7 0.10
22 10 0.14
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:3583316 original size:29 final size:29
Alignment explanation
Indices: 3583252--3583306 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 29
3583242 CAAATGATTT
*
3583252 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATATTTTAAAATA
3583281 TAAAATTATT-AAATT-TATTTTAAAAT
1 TAAAATTATTAAAATTATATTTTAAAAT
3583307 TAATTTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 10 0.40
28 5 0.20
29 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TAAAATTATTAAAATTATATTTTAAAATA
Found at i:3583334 original size:26 final size:25
Alignment explanation
Indices: 3583268--3583356 Score: 91
Period size: 27 Copynumber: 3.6 Consensus size: 25
3583258 TATTAAAATT
3583268 ATTTTTTAAAATATAAAATTATTAA
1 ATTTTTTAAAATATAAAATTATTAA
3583293 ATTTATTTTAAAAT-T--AA-T-TT-A
1 A-TT-TTTTAAAATATAAAATTATTAA
3583314 ATTTTTTAAAATATAAAATTATTAA
1 ATTTTTTAAAATATAAAATTATTAA
*
3583339 ATTTATTTTAAATTATAA
1 A-TT-TTTTAAAATATAA
3583357 TCATTGTCAT
Statistics
Matches: 53, Mismatches: 1, Indels: 18
0.74 0.01 0.25
Matches are distributed among these distances:
19 9 0.17
20 3 0.06
21 2 0.04
22 4 0.08
23 2 0.04
24 4 0.08
25 3 0.06
26 5 0.09
27 21 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTTTTAAAATATAAAATTATTAA
Found at i:3583355 original size:27 final size:26
Alignment explanation
Indices: 3583268--3583356 Score: 84
Period size: 25 Copynumber: 3.6 Consensus size: 26
3583258 TATTAAAATT
3583268 ATTTTTTAAAATATAAAATT-ATTAA
1 ATTTTTTAAAATATAAAATTAATTAA
* *
3583293 ATTTATT----T-TAAAATTAATTTA
1 ATTTTTTAAAATATAAAATTAATTAA
3583314 ATTTTTTAAAATATAAAATT-ATTAA
1 ATTTTTTAAAATATAAAATTAATTAA
*
3583339 ATTTATTTTAAATTATAA
1 A-TT-TTTTAAAATATAA
3583357 TCATTGTCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
20 7 0.14
21 11 0.22
25 12 0.24
26 9 0.18
27 12 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTTTTTAAAATATAAAATTAATTAA
Found at i:3585707 original size:22 final size:23
Alignment explanation
Indices: 3585684--3585726 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3585674 TCATATATTA
3585684 AAATA-AATAT-AAAATTAAAAT
1 AAATAGAATATAAAAATTAAAAT
3585705 AAATAGAATATAAAAATTAAAA
1 AAATAGAATATAAAAATTAAAA
3585727 GTTAAAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.25
22 5 0.25
23 10 0.50
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (23 bp):
AAATAGAATATAAAAATTAAAAT
Found at i:3585720 original size:17 final size:17
Alignment explanation
Indices: 3585678--3585721 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
3585668 TTTAAATCAT
*
3585678 ATATTAAAATAAATATA
1 ATATTAAAATAAATAGA
*
3585695 AAATTAAAATAAATAGA
1 ATATTAAAATAAATAGA
*
3585712 ATATAAAAAT
1 ATATTAAAAT
3585722 TAAAAGTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
ATATTAAAATAAATAGA
Found at i:3585740 original size:23 final size:22
Alignment explanation
Indices: 3585680--3585740 Score: 54
Period size: 23 Copynumber: 2.6 Consensus size: 22
3585670 TAAATCATAT
3585680 ATTAAA-ATAAATATAAAATTAAA
1 ATTAAAGAT-AATA-AAAATTAAA
*
3585703 ATAAATAGA-ATATAAAAATTAAA
1 ATTAA-AGATA-ATAAAAATTAAA
3585726 AGTTAAAGATAATAA
1 A-TTAAAGATAATAA
3585741 TGGATTCAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
23 22 0.71
24 8 0.26
25 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (22 bp):
ATTAAAGATAATAAAAATTAAA
Found at i:3595647 original size:195 final size:195
Alignment explanation
Indices: 3595315--3595704 Score: 771
Period size: 195 Copynumber: 2.0 Consensus size: 195
3595305 CATGTACGCA
3595315 ACCGAGTGAACCTAAGGAGGTCGGTGGTTTATGATTTCGCGATCTGTCCAAATTTAATATTGCAT
1 ACCGAGTGAACCTAAGGAGGTCGGTGGTTTATGATTTCGCGATCTGTCCAAATTTAATATTGCAT
3595380 TGTTAGCTAAACAAGATTGACGTTTATTTACTTATCCGGATTCATTATTAGCTCGTGTTATGAAA
66 TGTTAGCTAAACAAGATTGACGTTTATTTACTTATCCGGATTCATTATTAGCTCGTGTTATGAAA
3595445 GCAAAATATTACCCGAACACAGATTTTTTAAATTCGAGTTTAGGGACTTCACCTTCATATACCTG
131 GCAAAATATTACCCGAACACAGATTTTTTAAATTCGAGTTTAGGGACTTCACCTTCATATACCTG
*
3595510 ACCGAGTGAACCTAAGGAGGTCGGTGGTTTATGATTTCGTGATCTGTCCAAATTTAATATTGCAT
1 ACCGAGTGAACCTAAGGAGGTCGGTGGTTTATGATTTCGCGATCTGTCCAAATTTAATATTGCAT
3595575 TGTTAGCTAAACAAGATTGACGTTTATTTACTTATCCGGATTCATTATTAGCTCGTGTTATGAAA
66 TGTTAGCTAAACAAGATTGACGTTTATTTACTTATCCGGATTCATTATTAGCTCGTGTTATGAAA
3595640 GCAAAATATTACCCGAACACAGATTTTTTAAATTCGAGTTTAGGGACTTCACCTTCATATACCTG
131 GCAAAATATTACCCGAACACAGATTTTTTAAATTCGAGTTTAGGGACTTCACCTTCATATACCTG
3595705 GAAAAGCATT
Statistics
Matches: 194, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
195 194 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (195 bp):
ACCGAGTGAACCTAAGGAGGTCGGTGGTTTATGATTTCGCGATCTGTCCAAATTTAATATTGCAT
TGTTAGCTAAACAAGATTGACGTTTATTTACTTATCCGGATTCATTATTAGCTCGTGTTATGAAA
GCAAAATATTACCCGAACACAGATTTTTTAAATTCGAGTTTAGGGACTTCACCTTCATATACCTG
Found at i:3599242 original size:22 final size:23
Alignment explanation
Indices: 3599217--3599264 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
3599207 GAAAATACAG
* *
3599217 AATTTTAAAATATAAT-ATATAA
1 AATTTTAAAAAATAATAATAGAA
3599239 AATTTTAAAAAATAATAATAGAA
1 AATTTTAAAAAATAATAATAGAA
3599262 AAT
1 AAT
3599265 ACAAAACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AATTTTAAAAAATAATAATAGAA
Found at i:3599260 original size:52 final size:52
Alignment explanation
Indices: 3599200--3599300 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
3599190 CACCGTTCAA
* *
3599200 AATAATAGAAAATACAGAATTTTAAAATATAATATATAAAATTTTAAAAAAT
1 AATAATAGAAAATACAAAACTTTAAAATATAATATATAAAATTTTAAAAAAT
* *
3599252 AATAATAGAAAATACAAAACTTTAAAATATAATATTTAAACTTTTAAAA
1 AATAATAGAAAATACAAAACTTTAAAATATAATATATAAAATTTTAAAA
3599301 TTAACATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (52 bp):
AATAATAGAAAATACAAAACTTTAAAATATAATATATAAAATTTTAAAAAAT
Found at i:3599292 original size:21 final size:21
Alignment explanation
Indices: 3599268--3599309 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3599258 AGAAAATACA
*
3599268 AAAC-TTTAAAATATAATATTT
1 AAACTTTTAAAAT-TAACATTT
3599289 AAACTTTTAAAATTAACATTT
1 AAACTTTTAAAATTAACATTT
3599310 TTATCTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (21 bp):
AAACTTTTAAAATTAACATTT
Found at i:3600563 original size:24 final size:24
Alignment explanation
Indices: 3600517--3600565 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3600507 CTCTCTTCTC
*
3600517 AAAAATAATTTATTTCCTAAATTA
1 AAAAATAATTTATTTACTAAATTA
* *
3600541 AAAAATAATTTATTTAGTCAATTA
1 AAAAATAATTTATTTACTAAATTA
3600565 A
1 A
3600566 TTTTTTTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (24 bp):
AAAAATAATTTATTTACTAAATTA
Found at i:3604059 original size:29 final size:31
Alignment explanation
Indices: 3604025--3604093 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 31
3604015 CAAAGATTTG
*
3604025 AAATTTAGTCATTATA-TTTTTATTTTTAT-
1 AAATTTAGTCATTATATTTTTTATTTATATC
* *
3604054 AAATTTAGTCTTTCTATTTTTTATTTATATC
1 AAATTTAGTCATTATATTTTTTATTTATATC
3604085 ACAATTTAG
1 A-AATTTAG
3604094 GTACAATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 14 0.41
30 12 0.35
31 1 0.03
32 7 0.21
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.58
Consensus pattern (31 bp):
AAATTTAGTCATTATATTTTTTATTTATATC
Found at i:3627933 original size:21 final size:21
Alignment explanation
Indices: 3627907--3627952 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3627897 ACTTATATTC
3627907 TTAATAAT-TTTCAAATAATT-T
1 TTAATAATATTT--AATAATTAT
3627928 TTAATAATATTTAATAATTAT
1 TTAATAATATTTAATAATTAT
3627949 TTAA
1 TTAA
3627953 GAAAGCACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.30
21 13 0.57
22 3 0.13
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTAATAATATTTAATAATTAT
Found at i:3627951 original size:11 final size:10
Alignment explanation
Indices: 3627907--3627952 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
3627897 ACTTATATTC
3627907 TTAATAATTT
1 TTAATAATTT
*
3627917 TCAAATAATTT
1 T-TAATAATTT
*
3627928 TTAATAATAT
1 TTAATAATTT
3627938 TTAATAATTAT
1 TTAATAATT-T
3627949 TTAA
1 TTAA
3627953 GAAAGCACTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 16 0.53
11 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (10 bp):
TTAATAATTT
Found at i:3628207 original size:16 final size:17
Alignment explanation
Indices: 3628178--3628221 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
3628168 AATAATTATA
3628178 AAAATTTATTTATTTTT
1 AAAATTTATTTATTTTT
*
3628195 TAAATTT-TTTATTTTT
1 AAAATTTATTTATTTTT
3628211 AAAATATTATT
1 AAAAT-TTATT
3628222 ATATCAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 13 0.57
17 8 0.35
18 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
AAAATTTATTTATTTTT
Found at i:3634263 original size:25 final size:23
Alignment explanation
Indices: 3634235--3634296 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 23
3634225 TTTTTAATTG
3634235 AATTATAAATTAATTAAATATTCCA
1 AATTATAAATTAATTAAA-A-TCCA
*
3634260 AATT-TCAAATTTAATTTAAATCCA
1 AATTAT-AAA-TTAATTAAAATCCA
3634284 AATTCATAAATTA
1 AATT-ATAAATTA
3634297 GCTGAATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
24 12 0.38
25 11 0.34
26 9 0.28
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTATAAATTAATTAAAATCCA
Found at i:3634691 original size:19 final size:19
Alignment explanation
Indices: 3634642--3634695 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
3634632 ATAATATATC
3634642 AAATATACTTAAAAACATTA
1 AAATATA-TTAAAAACATTA
* *
3634662 AACAAACATTAAAAA-ATTTA
1 AA-ATATATTAAAAACA-TTA
3634682 AAATATATTAAAAA
1 AAATATATTAAAAA
3634696 TTCTTTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 11 0.39
20 14 0.50
21 3 0.11
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATATATTAAAAACATTA
Found at i:3640628 original size:33 final size:33
Alignment explanation
Indices: 3640567--3640630 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
3640557 CACAAGGGTT
* *
3640567 AATAAAAAATTAGTCATGCTAGAACAAAAAATA
1 AATAAAAAACTAGTCATGCTAAAACAAAAAATA
* *
3640600 AATAAATAACTAGTCATGC-AAAACCAAAAAT
1 AATAAAAAACTAGTCATGCTAAAACAAAAAAT
3640631 TATATTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 10 0.37
33 17 0.63
ACGTcount: A:0.59, C:0.12, G:0.08, T:0.20
Consensus pattern (33 bp):
AATAAAAAACTAGTCATGCTAAAACAAAAAATA
Found at i:3643594 original size:32 final size:35
Alignment explanation
Indices: 3643558--3643624 Score: 104
Period size: 32 Copynumber: 2.0 Consensus size: 35
3643548 ACCCTTCAAT
*
3643558 TTTATTTTATTTTTT-AT-TTTTTAAT-ATTTAAA
1 TTTATGTTATTTTTTAATATTTTTAATAATTTAAA
3643590 TTTATGTTATTTTTTAATATTTTTAATAATTTAAA
1 TTTATGTTATTTTTTAATATTTTTAATAATTTAAA
3643625 ATTTTAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 14 0.45
33 2 0.06
34 8 0.26
35 7 0.23
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (35 bp):
TTTATGTTATTTTTTAATATTTTTAATAATTTAAA
Found at i:3644592 original size:9 final size:9
Alignment explanation
Indices: 3644578--3644604 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3644568 TTTTTTGTCA
3644578 CTCATTCAC
1 CTCATTCAC
3644587 CTCATTCAC
1 CTCATTCAC
3644596 CTCATTCAC
1 CTCATTCAC
3644605 TTACTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.44, G:0.00, T:0.33
Consensus pattern (9 bp):
CTCATTCAC
Found at i:3658935 original size:10 final size:10
Alignment explanation
Indices: 3658907--3658936 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3658897 ACCAAATTAA
*
3658907 TTTCTTTTCT
1 TTTCTTTTTT
3658917 TTTCTTTTTT
1 TTTCTTTTTT
3658927 TTTCTTTTTT
1 TTTCTTTTTT
3658937 GAAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:3664175 original size:3 final size:3
Alignment explanation
Indices: 3664167--3664191 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3664157 CCCCAACTAA
3664167 AAC AAC AAC AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC A
3664192 GATATAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:3668603 original size:13 final size:14
Alignment explanation
Indices: 3668581--3668623 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
3668571 AAATCGAATT
*
3668581 AATTCAGTT-ATCG
1 AATTCGGTTAATCG
3668594 AATTCGGTTAATC-
1 AATTCGGTTAATCG
3668607 AA-TCGGTTAATCG
1 AATTCGGTTAATCG
3668620 AATT
1 AATT
3668624 AATTCAGTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 10 0.38
13 12 0.46
14 4 0.15
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (14 bp):
AATTCGGTTAATCG
Found at i:3677933 original size:52 final size:52
Alignment explanation
Indices: 3677840--3678081 Score: 295
Period size: 52 Copynumber: 4.7 Consensus size: 52
3677830 TTCATTTCAC
* * * * * * *
3677840 TCATATACTCACGATGACACATAGCCACCGGATCTTATAATCCATGAGGGAT
1 TCATATACTCACGATGACACATAGTCATCGGACCTTTTAATCCGTAAAGGAT
* * * *
3677892 TCGTATACTCACGATGACACAGAGTCATCAGACCTCTTAATCCGTAAAGGAT
1 TCATATACTCACGATGACACATAGTCATCGGACCTTTTAATCCGTAAAGGAT
* * * *
3677944 CCATATACTCACGATGACACTTAGTCATTGGACCTTTTAATCCGTAAAGTAT
1 TCATATACTCACGATGACACATAGTCATCGGACCTTTTAATCCGTAAAGGAT
* * * *
3677996 TCATATACTCATGATGACACTTAATCATCGGACCTTTTAAACCGTAAAGGAT
1 TCATATACTCACGATGACACATAGTCATCGGACCTTTTAATCCGTAAAGGAT
* *
3678048 TCATATACTCACGATGACACTTAGTCATTGGACC
1 TCATATACTCACGATGACACATAGTCATCGGACC
3678082 CCTTTTCATT
Statistics
Matches: 162, Mismatches: 28, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 162 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (52 bp):
TCATATACTCACGATGACACATAGTCATCGGACCTTTTAATCCGTAAAGGAT
Found at i:3679610 original size:20 final size:20
Alignment explanation
Indices: 3679585--3679633 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
3679575 CTCCAGTGAG
3679585 ACTTCTACCAGTAGAACTCC
1 ACTTCTACCAGTAGAACTCC
3679605 ACTTCTACCAGTAGAACTCC
1 ACTTCTACCAGTAGAACTCC
3679625 ACTTCTACC
1 ACTTCTACC
3679634 GATACAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.37, G:0.08, T:0.27
Consensus pattern (20 bp):
ACTTCTACCAGTAGAACTCC
Found at i:3679642 original size:20 final size:20
Alignment explanation
Indices: 3679585--3679653 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
3679575 CTCCAGTGAG
*
3679585 ACTTCTACCAGTAGAACTCC
1 ACTTCTACCAGTACAACTCC
*
3679605 ACTTCTACCAGTAGAACTCC
1 ACTTCTACCAGTACAACTCC
*
3679625 ACTTCTACC-GATACAACTAC
1 ACTTCTACCAG-TACAACTCC
*
3679645 AGTTCTACC
1 ACTTCTACC
3679654 GATACCTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 1 0.02
20 44 0.98
ACGTcount: A:0.30, C:0.35, G:0.09, T:0.26
Consensus pattern (20 bp):
ACTTCTACCAGTACAACTCC
Found at i:3697498 original size:15 final size:14
Alignment explanation
Indices: 3697450--3697489 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
3697440 TTTTTCTCAA
3697450 ATTATATTTTAATT
1 ATTATATTTTAATT
* *
3697464 ATTTATATTTGAAAT
1 A-TTATATTTTAATT
3697479 ATTATATTTTA
1 ATTATATTTTA
3697490 GTTACTTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (14 bp):
ATTATATTTTAATT
Found at i:3697942 original size:51 final size:51
Alignment explanation
Indices: 3697857--3697953 Score: 158
Period size: 51 Copynumber: 1.9 Consensus size: 51
3697847 TGGCTCAGTG
* *
3697857 ATTAAAATGTTACAACACGTTAACATAAGTAACTAAAATGTAACATTTCAA
1 ATTAAAATGTTACAACACGTTAACATAAGCAACTAAAATATAACATTTCAA
* *
3697908 ATTAAAATGTTACAATACGTTAACCTAAGCAACTAAAATATAACAT
1 ATTAAAATGTTACAACACGTTAACATAAGCAACTAAAATATAACAT
3697954 AACATTTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.29
Consensus pattern (51 bp):
ATTAAAATGTTACAACACGTTAACATAAGCAACTAAAATATAACATTTCAA
Found at i:3702193 original size:35 final size:36
Alignment explanation
Indices: 3702126--3702194 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
3702116 TCATTAATTG
* * * *
3702126 TAATTAAAAATTATTAACTTATCAATTTAAATATCA
1 TAATAAAAAATTATCAAATTATCAATTAAAATATCA
*
3702162 TAATAAAAAATTCTCAAATTAT-AATTAAAATAT
1 TAATAAAAAATTATCAAATTATCAATTAAAATAT
3702195 TATTATCATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 10 0.36
36 18 0.64
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (36 bp):
TAATAAAAAATTATCAAATTATCAATTAAAATATCA
Found at i:3718181 original size:26 final size:24
Alignment explanation
Indices: 3718136--3718245 Score: 76
Period size: 27 Copynumber: 4.1 Consensus size: 24
3718126 ATCTTACACG
3718136 AAATATATATTTTAAATAATTAATAT
1 AAAT-TAT-TTTTAAATAATTAATAT
* *
3718162 AAATTATTTTTAAAATTAATGATACAT
1 AAATTATTTTT-AAA-TAATTA-ATAT
* *
3718189 AAAATATTTTAAAAATTTAAATATAATAAT
1 AAATTATTTT-TAAA--T-AAT-TAAT-AT
3718219 AAATTATTTTTAAATAATTTAATAT
1 AAATTATTTTTAAATAA-TTAATAT
3718244 AA
1 AA
3718246 TGATACATAA
Statistics
Matches: 67, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
24 4 0.06
25 10 0.15
26 15 0.22
27 17 0.25
28 2 0.03
29 7 0.10
30 12 0.18
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.45
Consensus pattern (24 bp):
AAATTATTTTTAAATAATTAATAT
Found at i:3723545 original size:18 final size:18
Alignment explanation
Indices: 3723511--3723545 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3723501 TGCCTCTCGT
**
3723511 TTAAATTATTATTATTTA
1 TTAAATTATTAAAATTTA
3723529 TTAAATTATTAAAATTT
1 TTAAATTATTAAAATTT
3723546 TCAAAATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAATTATTAAAATTTA
Found at i:3723813 original size:33 final size:33
Alignment explanation
Indices: 3723776--3723846 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
3723766 TAATTATGGT
* *
3723776 ATTATAAAAAAGTAACCATGGATTACAAATTTA
1 ATTATAAAAAAGTAACCATGGATTACAAAGTCA
*** *
3723809 ATTATGGTAAATTAACCATGGATTACAAAGTCA
1 ATTATAAAAAAGTAACCATGGATTACAAAGTCA
3723842 ATTAT
1 ATTAT
3723847 GGTACTATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.32
Consensus pattern (33 bp):
ATTATAAAAAAGTAACCATGGATTACAAAGTCA
Found at i:3723847 original size:33 final size:33
Alignment explanation
Indices: 3723788--3723850 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
3723778 TATAAAAAAG
* *
3723788 TAACCATGGATTACAAATTTAATTATGGTAAAT
1 TAACCATGGATTACAAAGTCAATTATGGTAAAT
3723821 TAACCATGGATTACAAAGTCAATTATGGTA
1 TAACCATGGATTACAAAGTCAATTATGGTA
3723851 CTATAACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.33
Consensus pattern (33 bp):
TAACCATGGATTACAAAGTCAATTATGGTAAAT
Found at i:3734158 original size:2 final size:2
Alignment explanation
Indices: 3734151--3734191 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3734141 TTATTAGAAA
3734151 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3734192 AGTTCTTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3746146 original size:43 final size:43
Alignment explanation
Indices: 3746092--3746192 Score: 177
Period size: 43 Copynumber: 2.4 Consensus size: 43
3746082 TTTTAATACT
3746092 TGATA-TTTGGTTATTAGATCAGCAAGCCTACACTCCTTAATG
1 TGATAGTTTGGTTATTAGATCAGCAAGCCTACACTCCTTAATG
*
3746134 TGATAGTTTGGTTATTAGATCAGCAAGCCTACTCTCCTTAATG
1 TGATAGTTTGGTTATTAGATCAGCAAGCCTACACTCCTTAATG
*
3746177 TGATAGTTCGGTTATT
1 TGATAGTTTGGTTATT
3746193 TGTGATTACA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
42 5 0.09
43 51 0.91
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (43 bp):
TGATAGTTTGGTTATTAGATCAGCAAGCCTACACTCCTTAATG
Found at i:3782903 original size:12 final size:13
Alignment explanation
Indices: 3782869--3782905 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
3782859 GAAATATATA
3782869 TATATATAATTTT
1 TATATATAATTTT
*
3782882 TTTA-ATAATTTT
1 TATATATAATTTT
3782894 TATATA-AATTTT
1 TATATATAATTTT
3782906 ATAAAAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATATATAATTTT
Found at i:3798392 original size:12 final size:12
Alignment explanation
Indices: 3798375--3798399 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3798365 CTCAATTAAT
3798375 TAAATATTATTA
1 TAAATATTATTA
3798387 TAAATATTATTA
1 TAAATATTATTA
3798399 T
1 T
3798400 TAAGATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAATATTATTA
Found at i:3813236 original size:71 final size:70
Alignment explanation
Indices: 3813115--3813260 Score: 265
Period size: 71 Copynumber: 2.1 Consensus size: 70
3813105 TTTTATCATA
3813115 ATATCATGATTAAGTTTATATCATTAAATTTTAAATTTTACTCCGCATTTTTTTTTATTTGATAT
1 ATATCATGATTAAGTTTATATCATTAAATTTTAAATTTTACTCCGCA-TTTTTTTTATTTGATAT
3813180 TTTATG
65 TTTATG
*
3813186 ATATCATGATTAAGTTTATATCATTAAATTTTAAATTTTACTCCGTATTTTTTTTATTTGATATT
1 ATATCATGATTAAGTTTATATCATTAAATTTTAAATTTTACTCCGCATTTTTTTTATTTGATATT
3813251 TTATG
66 TTATG
*
3813256 TTATC
1 ATATC
3813261 TATATTTGCT
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
70 27 0.37
71 46 0.63
ACGTcount: A:0.29, C:0.08, G:0.07, T:0.55
Consensus pattern (70 bp):
ATATCATGATTAAGTTTATATCATTAAATTTTAAATTTTACTCCGCATTTTTTTTATTTGATATT
TTATG
Found at i:3829199 original size:17 final size:15
Alignment explanation
Indices: 3829177--3829216 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
3829167 ATAATCTAAT
3829177 AAAATAATTAAATATAA
1 AAAATAA-TAAA-ATAA
3829194 AAAATAATAAAATAA
1 AAAATAATAAAATAA
3829209 ATAAATAA
1 A-AAATAA
3829217 ATTATGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.23
16 10 0.45
17 7 0.32
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATAATAAAATAA
Found at i:3829230 original size:21 final size:21
Alignment explanation
Indices: 3829182--3829235 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
3829172 CTAATAAAAT
3829182 AATTAAATATAAAAAATAATA
1 AATTAAATATAAAAAATAATA
* * *
3829203 AAATAAATA-AATAAATTATGA
1 AATTAAATATAAAAAATAAT-A
*
3829224 AATTAAAAATAA
1 AATTAAATATAA
3829236 CTCTTAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 8 0.31
21 16 0.62
22 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (21 bp):
AATTAAATATAAAAAATAATA
Found at i:3846620 original size:342 final size:342
Alignment explanation
Indices: 3845995--3846680 Score: 1336
Period size: 342 Copynumber: 2.0 Consensus size: 342
3845985 TCAATTCCAT
3845995 TAGCTTGGTGGATGTTTGATTGCTGCTTTATTCACTTGATTTTTTGTTTATAAGCTCACGTTAAC
1 TAGCTTGGTGGATGTTTGATTGCTGCTTTATTCACTTGATTTTTTGTTTATAAGCTCACGTTAAC
*
3846060 CATGGTCCCATGGGGCATGGAGCACCTAGGACACAATGGTCGACGGTGATGCCTAAATTCTGCGT
66 CATGGTCCCATGGGGCATGGAGCACCTAGGACACAATGGTCGACGATGATGCCTAAATTCTGCGT
3846125 GGACCACCATGTAAGTGTCAAATTATGATTCCCCTCGATGATAACCAGGCTCAAACACAGGAGAA
131 GGACCACCATGTAAGTGTCAAATTATGATTCCCCTCGATGATAACCAGGCTCAAACACAGGAGAA
* *
3846190 TTTTACAAGTCAATGGTGGCTTAAAAGTTAAAAACTGTGTATATGCATTTAATGCCTCCCCTTCT
196 TTTTACAAGTCAATGGGGGCTTAAAAGTTAAAAACGGTGTATATGCATTTAATGCCTCCCCTTCT
3846255 CCAAGATTTCCTCAGCTCCAAAGCCAGCACAACTAAGCAGTTGCAGTGAAAGGGAATGTTCCAGG
261 CCAAGATTTCCTCAGCTCCAAAGCCAGCACAACTAAGCAGTTGCAGTGAAAGGGAATGTTCCAGG
3846320 TAGAACAAAGTCCTATC
326 TAGAACAAAGTCCTATC
*
3846337 TAGCTTGGTGGATGTTTGATTGCTGCTTTATTCACTTGATTTTTTGTTTATAAGCTCATGTTAAC
1 TAGCTTGGTGGATGTTTGATTGCTGCTTTATTCACTTGATTTTTTGTTTATAAGCTCACGTTAAC
3846402 CATGGTCCCATGGGGCATGGAGCACCTAGGACACAATGGTCGACGATGATGCCTAAATTCTGCGT
66 CATGGTCCCATGGGGCATGGAGCACCTAGGACACAATGGTCGACGATGATGCCTAAATTCTGCGT
3846467 GGACCACCATGTAAGTGTCAAATTATGATTCCCCTCGATGATAACCAGGCTCAAACACAGGAGAA
131 GGACCACCATGTAAGTGTCAAATTATGATTCCCCTCGATGATAACCAGGCTCAAACACAGGAGAA
3846532 TTTTACAAGTCAATGGGGGCTTAAAAGTTAAAAACGGTGTATATGCATTTAATGCCTCCCCTTCT
196 TTTTACAAGTCAATGGGGGCTTAAAAGTTAAAAACGGTGTATATGCATTTAATGCCTCCCCTTCT
3846597 CCAAGATTTCCTCAGCTCCAAAGCCAGCACAACTAAGCAGTTGCAGTGAAAGGGAATGTTCCAGG
261 CCAAGATTTCCTCAGCTCCAAAGCCAGCACAACTAAGCAGTTGCAGTGAAAGGGAATGTTCCAGG
3846662 TAGAACAAAGTCCTATC
326 TAGAACAAAGTCCTATC
3846679 TA
1 TA
3846681 TATTATAAAT
Statistics
Matches: 340, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
342 340 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (342 bp):
TAGCTTGGTGGATGTTTGATTGCTGCTTTATTCACTTGATTTTTTGTTTATAAGCTCACGTTAAC
CATGGTCCCATGGGGCATGGAGCACCTAGGACACAATGGTCGACGATGATGCCTAAATTCTGCGT
GGACCACCATGTAAGTGTCAAATTATGATTCCCCTCGATGATAACCAGGCTCAAACACAGGAGAA
TTTTACAAGTCAATGGGGGCTTAAAAGTTAAAAACGGTGTATATGCATTTAATGCCTCCCCTTCT
CCAAGATTTCCTCAGCTCCAAAGCCAGCACAACTAAGCAGTTGCAGTGAAAGGGAATGTTCCAGG
TAGAACAAAGTCCTATC
Found at i:3862414 original size:43 final size:43
Alignment explanation
Indices: 3862304--3868869 Score: 4166
Period size: 43 Copynumber: 154.4 Consensus size: 43
3862294 ATTCTCAGAA
* * * * *
3862304 TGTGCCAGTGTAGATGCATCGGTTTACCCGACGATGCA-T-TA
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* *
3862345 TGTGTCAGTATAGATGCCTCGATTTACCCAATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * *
3862388 TGTGCCACTATAAATACCTCGATTTACTCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * *
3862431 TGTGCTAGTATAGATGCCTCGGTTTACCCGATGATACA-TGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * *
3862473 TGTGTCAGTATAAATGCCTCGGTTTACTCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* *
3862516 TGT--CAGTATAGATGCC-CCAGTTTACCCGATGATACACTGTG
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * * * *
3862557 TGTGCCAATACAGATGCCTTGGTTTACCCGATGATGCACTGTA
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* *
3862600 TGTGCCAGTATAGATGCCTCGATTTACCTGATGATGCACTATG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* *
3862643 TGTGCCAGTATAGATGCCTC-AGTTTACCCGATAATGCACTTTG
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * * * * *
3862686 TGTGCCAATATAAATGCCTCGATTTACCTGATAATACACTATG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * *
3862729 TGTGCTAGTATAGATGCCTCGGTTTACCTGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
** *
3862772 TGTGCCAGTATAGATATCTCGATTTACCCGATGATGCACTTTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * *
3862815 TGTGCCAGTATAGATGCCTTGGTTTACCCAATGATACACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * *
3862858 TGTGCTAGTGTAGATGTCTCGGTTTACTCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * *
3862901 TGTGCCAGTATAGATTCTTC-AGTTTACTCGATGATTCATTATG
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * * * * * * *
3862944 TGTGCCAATATAAATACCTCAATTTACCCGATGATGTATTCTA
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* ** * * *
3862987 TGTGTCAGTATAGATGTATCGATTTACCCAATGATACACTCTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * *
3863030 TGTGCCAGTATAGATACCTCGATTTACCCAATGATACACTATG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * ** *
3863073 TGTGCCAGTATAAATACCTCGATTTACTTGATGATGCACTATG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * *
3863116 TGTGTCAGTATAGATACCTCGATTTATCCGATGATGTACTATG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * *
3863159 TGTGCCAATAAAGATGTCTCGATTTACCCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* *
3863202 TGTGCCAGTGTAGATGCCTCGATTTACCCGATGGTGCAC--TG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * *
3863243 TGT--CGGTATAGATACCTCAATTTACCCGATGATACACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * *
3863284 TGTGCCAATATAGATGCCTTGGTTTACCTGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* ** * *
3863327 TGTGCTAGTATAGATGTATC-AGTTTACCCGGTGATGCACTCTG
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * *
3863370 TGTGCCAATATAGATGCCTCGGTTTACTCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* **
3863413 TGTGCCAGTATAGACGCCTTTATTTACCCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * *
3863456 TGTTCTAGTATAGATACCTCGGTTTACCCGATGATACACTCTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
3863499 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * * *
3863542 TGTGCTAGTATAGATACATTGGTTTACTCGATGATGCATTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* *** * * *
3863585 TGTGCCAATATAGATTATTCGGTTTACTCGATGATGCACTATG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * ** * ** *
3863628 TGTGCAAGTATAAATACCTCGATTTAGTCGATGGTATACTATG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * *
3863671 TGTGTCAGTATAGATGCCTTGGTTTACCCGATGATACACTTTA
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * *
3863714 TGTGACAATATAGATGCCTCGATTTACTCGATGATGTACTTTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* ** *
3863757 TGTGCCAGTATAGATGCCTCAATTTACCCGATGATATACTTTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * *
3863800 TGTGTCAATATAGATACCTCGATTTACCTGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * * *
3863843 TGTGCTAGTATAGGTGCCT-TAGCTTACTCGAAGATGCACTATG
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * ** * * *
3863886 TGTACCAATATAGATGTATCGGTTTACCTGATGATGCATTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * *
3863929 TATGCCAGTATAGATGCCTCGACTTATCTGATTATACACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
3863972 TGTG-CAGGTATAGATGCCTC-AGTTTACCCGATGATGCACTGTG
1 TGTGCCA-GTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * * * *
3864015 TGTGCCAGTATATAGATGCCT-TAGTTTATCCGATGATTCACTTTT
1 TGTGCCAG--TATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * *
3864060 TGTGCCAGTATAAATGCCAC-AGGTTACCCGATGATGCACT-TG
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * * * * *
3864102 TGTGCTAGTATAGATGTCTCGGTTTACTCGATGATGTACTATG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * ** * * *
3864145 TGTGTCAGTATAGATTCTTTGGTTTAATCGATGATGCATTATT
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
** ** * * * * * *
3864188 TGTGGAAGTATAGACACTTCGGTTTATCCAATGATGCATTGTC
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
** * * **
3864231 TGTGTTAGTATAGCTGCCTCGATTTAACTAATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * *** *
3864274 TGTGTCAGTATAGATACCTTGATTTACTTTATGATGTAC--TG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * *
3864315 TATGCGAGTATAGATGTCTCGGTTTACCCGATGATGCA-T-TG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * *
3864356 TGTGCTAGTATAGATTCCTCGATTTACCCTATGATGTAC--TG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * ** * *** *
3864397 TGTACTAGTATAAATGCCTCGATTTACCAAATAAAATACTATG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * *
3864440 TATGCCAGTATAGATGCCTCGATTTTCCCGATGATGCATTATA
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * *
3864483 TATGCCAATATAAATACCTCGATTTTCCAGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * *
3864526 TGTGCCAGTATAGATACCTCGATTTACTCGATAATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* ** * *
3864569 TGTGCTAGTATAGATTTCTCAATTTACTCGATGATGCAC--TG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * *
3864610 TATACCAGTATAGATGCCTCGATTTACCAGATGAAGCACTATA
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* ** * * * * *
3864653 TGTGCTAGTATAGATATCTCGGTTTTACTCAATGATGTATTGTG
1 TGTGCCAGTATAGATGCCTC-GATTTACCCGATGATGCACTGTG
* * * * * *
3864697 TATGCTAGTATAAATGCCT-AATTTTACCAG-TGATGCATTGTG
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * * *
3864739 TGTACCAGTATAGATGCCTCGATTTACTCGATAATACACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * * *
3864782 TATGCCAGTATAGATTCTTCGATTTACCCGACGATGCATTATA
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
*** * *
3864825 TGTATAAGTATAGATGCCTCGGTTTACTCGATGATGCAC--TG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * **** *
3864866 TGTGCAAGTATAAATACC-CTGATTTACTCGATGATATTTTATG
1 TGTGCCAGTATAGATGCCTC-GATTTACCCGATGATGCACTGTG
* ** * * *
3864909 TGTACCAGTATAGATGCCTCGATTTACCCGATGATATATTTTA
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * *
3864952 TGTGCCAGTATAAATACCTTGATTTACCCGATGATGTATTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
*
3864995 TGTGCTAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * ** **
3865038 TGTGCCAATATAGATACCTCGGTTTATCAAATGACACACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * *
3865081 TGT-CTAGTATAGATGCATTGGTTTACCCGATGATGCACTGTA
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* ** ** * *
3865123 TGTGCCAGTATAGATGTCTCGGCTTATTCGATTATGCATTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * ** *
3865166 TGTGCTAGTTTAGATATCTCGGTTTACCCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * *
3865209 TGTGCTAGTATAGATGCCTCGATTTACCTGATGATGTATTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * *
3865252 TGTGCCAATATAAATGCCTCAATTTACCCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * *
3865295 TGTACCAATATAGATGCTTCAATTTACCCGA-G--GCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * ** *
3865335 TGTGCCAGTATAGATGCTTGGGTTTACTAGACGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * *
3865378 TGTGCCAGTATAGATTCTTCAATTTACCCGATGATGCACT-T-
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * *
3865419 TGT-CCTAGTGTAGATTCCTCTG-TTTACCCGATGATGCACTATG
1 TGTGCC-AGTATAGATGCCTC-GATTTACCCGATGATGCACTGTG
* * * * * *
3865462 TGTGCCATTATAAATCCCTC-AGTTTACTCGATAATGCATTGTG
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* *
3865505 TGTGCCAGTATAGATGCCTCGATTTACCCTATGATGTAC----
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * * *
3865544 TGTGCTAATATAGATTCTTTGATTTACTCGATGATGCACTGTA
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
** ** * *
3865587 TGTGCCAGTATAGATGCCTCGGCTTATTCGATTATGCATTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * ** * *
3865630 TGTGCTAGTTTAGATATCTCGGTTTACCCGGTGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * ** * *
3865673 TGTGCTAGTATAGATGCCTTGATTTACTTGATGATGTATTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * *
3865716 TGTGCCAATATAAATGCCTCAATTTACCCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * *
3865759 TGTGCCAATATAGATGCTTCAATTTACCCGA-G--GCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * *
3865799 TGTGCCAGTATAAATGCTTGGGTTTACCAGACGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * *
3865842 TGTGCCAGTATAGATTCTTCAATTTACCCGATGATGCACT-T-
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * **
3865883 TGT-CCTAATGTAGATTCCTCGGTTTACCCGATGATGCACCATG
1 TGTGCC-AGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * *
3865926 TGTACCATTATAAATGCCTC-AGTTTACTCGATCATGCATTGTG
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * * * *
3865969 TGTGCAAGTATATATGCCTCGGTTTACCCTATGATGTAC----
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * * * *
3866008 TGTGCTAATATAGATTCTTTGATTTACTCGATGATGCATTGTA
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * ** * *
3866051 TGTGGCAGTATAGATGCCTCGACTTATTCGATTATGCATTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * ** *
3866094 TGTGCTAGTTTAGATATCTCGGTTTACCCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* ** * *
3866137 TGTGCTAGTATAGATGCCTCGATTTACTTGATGATGTATTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * *
3866180 TGTGCCAATATAAATGCCTCAATTTACCCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * *
3866223 TGTGCCAATATAGATGCTTCAATTTACCCGA-G--GCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * *
3866263 TGTGCCAGTATAGATGCTTGGGTTTACCAGATGATGTACTTTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
** *
3866306 TGTGCCTA-TATAGATGCCTCGATTTAATCGATGATGCAGTGTG
1 TGTGCC-AGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * *
3866349 TGTGCCAGTATAGATTCTTCAATTTACCCGATGATGCACT-T-
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * *
3866390 TGT-CCTAGTGTAGATTCCTCGATTTACCCGATGATGCACTATG
1 TGTGCC-AGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * *
3866433 TGTGTCATTATAAATGCCTC-AGTTTACTCGATCATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * *
3866476 TGTGCAAGTATAGATGCCTCGATTTACCCGATAATGTAC----
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * *
3866515 TGTGCTAATATAGATTCCTTGATTTACTCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* ***
3866558 TGTGCCAGTATAGATGTCTCGATTTATTAGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* *
3866601 TGTGCCAGTAAAGATGCCTCGATTTACTCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * *
3866644 TGTGCCAGTATAGATGCTTGGGTTTACCCAATGATGCATTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
** * * *
3866687 TGTGATAGTATAGATGCTTTGATTTACCCGATGATGCACTTTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
** * ** * * * *
3866730 CATGTCAGTATAGATG-CTTTAGTTTATCCTATGATGCATTGTA
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * * **
3866773 TGTGTCAGTATAGATGCTTCGGTTTATTCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* **
3866816 TGTGCCAGTATAGATGCTTCGATTTATTCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * ** * *** *
3866859 TATGCGAGTATAAATGGTTCAATTTTTTCGATGATGCACTGTA
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
** * ** * *** * *
3866902 TGTGTGAGTATAAATGGTTCGGTTTTTTCAATGATGCACTGTA
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * ** *
3866945 TGTGCGAGTATAGATGCTTCGATTTATTCGATGGTGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
** * * ****
3866988 TGTGTTAGTATAGATGCTTCAATTTTTTTGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * * * * *
3867031 GGTACCAATATAAATGCTTCGATTTACCCAATAATGCACTATA
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * ** * *
3867074 CGTGTCAGTATAGATGATTCGATTTATCCGATGATGCACTATG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* ** * * * *
3867117 TGTGCCAGTATAGTTGTTTCGATGTATCCGATGATGTACTATG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
** * * *
3867160 TGTGTCC-GTATAGATG-CTTTAGTTTATCCGATGATCCTCTGTG
1 TGTG-CCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
** * * * * *
3867203 TGTGCCAGTATAGATG-CTTTAGTTTATCTGATGATGCATTCTA
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * * *
3867246 TGTGTCAATATAGATGCTTC-AGTTTATCCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * * * *** **
3867289 TATGCTAGTATA-ATTGCTTCAATTTATTTGATGATGCAGAGTG
1 TGTGCCAGTATAGA-TGCCTCGATTTACCCGATGATGCACTGTG
* * ** * * *
3867332 TGTGCCAGTATAGATGCTTCGGTTTATTCAACGATGCATTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
** * * ** * * *
3867375 TGTGAGAGTAGAGATG-TTTTAGTTTATCCGATGATGCAATGTA
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * ** * * * * *
3867418 TGTGCTAGTATAGGTGTTTCGGTGTATCC-A--ATGCATTTTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * ** ** *
3867458 TTTGCTAGTTTAGGTGTTTCG-TTGTATTC---GATGCACTTTG
1 TGTGCCAGTATAGATGCCTCGATT-TACCCGATGATGCACTGTG
* * * * *
3867498 TTTGCTAGTATAGATGCTTCGATTTATCCGATGATGCATTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
** * * * * *
3867541 TGTGATAGTATATATTCTTC-AGTTTATCCGATGTTGCA-T-TG
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * * ** * *
3867582 TGGGCCAATATAGATGCTTCGATTTATTCGATGTTGCA--ATG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
** * * ** * *
3867623 TGTGCCAGGGTAGATGCTTCGCTTTATTCAATGATGCATTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
** * * * *
3867666 TGTGCCA--ATATTTTCGGT-GAATT---CGAT-AGTGTACTGTG
1 TGTGCCAGTATAGATGC-CTCGATTTACCCGATGA-TGCACTGTG
* *** ** * ** * *
3867704 TGTGCCAGTGTAGATATTTTAATATATTCGATGATGCTCTATG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * *
3867747 TTTGTCAGTATAGATGCTTC-AGTTTATCCGATGATG--TTGTG
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * ** * ** * *
3867788 TGTGCTAGTATGGATGTTTC-AGTGTATTCAATGATGCACTATG
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
** ** * * * *
3867831 TGTTTCAGTATAGATGTTTTGATTTATCTGATGATGTACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* *** * * * *
3867874 TGTGCTAGTATAGATTTTTCGCTTTATCTGATGATACAC--TG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * * * * *
3867915 TGTGCTAGTATAAATGCTTTGGTTTATCCAATTATGCATTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * ** * *
3867958 TTTGCTATGT-TAGATGCTTCGGTTTATTCGATGATGCATTATG
1 TGTGCCA-GTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * * * *
3868001 TGTGTCAGTAT---T--TTTGGTGTATCTGATGATGCAATGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * **
3868039 TGT--TAGTATAAATGCTTC-AGTTTATACGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* * * * * **
3868080 TGTACTAGTATAGATGCTTTGGTTTATACGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* ** * *
3868123 TGTGTCAGTATAGATG-CTTTAGTTTATCCGATGATGCACTATG
1 TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
** * * * ** * *
3868166 TGTGAGAGCATAGATGCTTCGGTTTATTCGGTGATGCACTTTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * **
3868209 TGTGCCAGTATACATGCTTCGATTTATTCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * ** *
3868252 AGTGCCAGTATAGATGCTTCGGTTTATTCGATAATGCAC--TG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * *
3868293 TGTGCTAGTATAGATGCTTGGGTTTACTCGATGATGTACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * *
3868336 TATGCCAGTATAGATGCTTCGGTTTACCCGATGATTCACTTTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * *
3868379 CT-TGTCAGTATGGATGCTTC-AGTTTATCCTATGATGCATTGTG
1 -TGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTGTG
* ** * * *
3868422 TGTGCCAGTATATATGTTTTGGTTTATCCGATGATGCA-TGGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACT-GTG
* * * * *** * *
3868465 TGTCCCAATATAGATGCTTCGGTTTAATTGATGATGCATTAT-
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* ** * * * * *
3868507 TCATGTTAGTATAGATGCTTCGATTTATCCAATGAGGCATTGTG
1 T-GTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * *
3868551 TGAGTGCTAGTATAGATGCTTCGGTATATCCGATGATGCACTGTA
1 T--GTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * * ** * *
3868596 TGTGCCAGTATAGTTACTTTGGTATATTCGATGATGCATTGTC
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
** * * * *
3868639 CATGTCAGTATAGATGCTTCGGTTTACTCGATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * * *
3868682 TGTGCCAGTATAGATGCTTTGGTTTATCCGATTATGCATTGCG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * *
3868725 TGTGCCAATGTTGATGCCTCGATTTATCCAATGATGCACTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* ** * **** * *
3868768 TGTGCCAATATAGATGATTCGATTGATTTAATTATGCATTGTG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
* * * * * * *
3868811 TGTGCCAGTATAGATACTTTGATTTATCCGATTATGTACTATG
1 TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
3868854 TGTGCCAGTATAGATG
1 TGTGCCAGTATAGATG
3868870 TTTTGGTGTA
Statistics
Matches: 5163, Mismatches: 1215, Indels: 292
0.77 0.18 0.04
Matches are distributed among these distances:
36 5 0.00
37 1 0.00
38 40 0.01
39 122 0.02
40 174 0.03
41 525 0.10
42 172 0.03
43 3993 0.77
44 58 0.01
45 73 0.01
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (43 bp):
TGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTGTG
Found at i:3867464 original size:40 final size:40
Alignment explanation
Indices: 3867420--3867510 Score: 137
Period size: 40 Copynumber: 2.3 Consensus size: 40
3867410 GCAATGTATG
*
3867420 TGCTAGTATAGGTGTTTCGGTGTATCCAATGCATTTTGTT
1 TGCTAGTATAGGTGTTTCGGTGTATCCAATGCACTTTGTT
* * * *
3867460 TGCTAGTTTAGGTGTTTCGTTGTATTCGATGCACTTTGTT
1 TGCTAGTATAGGTGTTTCGGTGTATCCAATGCACTTTGTT
3867500 TGCTAGTATAG
1 TGCTAGTATAG
3867511 ATGCTTCGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.16, C:0.12, G:0.25, T:0.46
Consensus pattern (40 bp):
TGCTAGTATAGGTGTTTCGGTGTATCCAATGCACTTTGTT
Found at i:3867530 original size:40 final size:39
Alignment explanation
Indices: 3867420--3867530 Score: 132
Period size: 40 Copynumber: 2.8 Consensus size: 39
3867410 GCAATGTATG
* * *
3867420 TGCTAGTATAGGTGTTTCGGTGTATCCAATGCATTTTGTT
1 TGCTAGTATAGGTGTTTC-GTTTATCCGATGCACTTTGTT
* *
3867460 TGCTAGTTTAGGTGTTTCGTTGTATTCGATGCACTTTGTT
1 TGCTAGTATAGGTGTTTCGTT-TATCCGATGCACTTTGTT
* *
3867500 TGCTAGTATAGATGCTTCGATTTATCCGATG
1 TGCTAGTATAGGTGTTTCG-TTTATCCGATG
3867531 ATGCATTGTG
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
39 2 0.03
40 56 0.93
41 2 0.03
ACGTcount: A:0.17, C:0.14, G:0.24, T:0.45
Consensus pattern (39 bp):
TGCTAGTATAGGTGTTTCGTTTATCCGATGCACTTTGTT
Found at i:3868062 original size:122 final size:122
Alignment explanation
Indices: 3867786--3868389 Score: 340
Period size: 127 Copynumber: 4.8 Consensus size: 122
3867776 GATGATGTTG
** * * * * * *
3867786 TGTGTGCTAGTATGGATGTTTCAGTGTATTCAATGATGCACTATGTGT-TTCAGTATAGATGTTT
1 TGTGTGCTAGTATAAATGCTTCAGTTTATACAATGATGCACTGTGTGTACT-AGTATAGATGCTT
* * * * * * *
3867850 TGATTTAT-CTGATGATGTACTGTGTGTG-CTAGTATAGATTTTTCGCTTTATCTGATGATACAC
65 CGGTTTATAC-GATGATGCACTATGTGTGTC-AG--T--ATTTTT-GGTGTATCTGATGATACAA
** * * * * *
3867913 TGTGTGCTAGTATAAATGCTTTGGTTTATCCAATTATGCATTGTGTTTGCTATGT-TAGATGCTT
1 TGTGTGCTAGTATAAATGCTTCAGTTTATACAATGATGCACTGTGTGTACTA-GTATAGATGCTT
* * *
3867977 CGGTTTATTCGATGATGCATTATGTGTGTCAGTATTTTTGGTGTATCTGATGATGCAA
65 CGGTTTATACGATGATGCACTATGTGTGTCAGTATTTTTGGTGTATCTGATGATACAA
* * *
3868035 TGTGTGTTAGTATAAATGCTTCAGTTTATACGATGATGCACTGTGTGTACTAGTATAGATGCTTT
1 TGTGTGCTAGTATAAATGCTTCAGTTTATACAATGATGCACTGTGTGTACTAGTATAGATGCTTC
* * * * *
3868100 GGTTTATACGATGATGCACTGTGTGTGTCAGTATAGATGCTTTAGTTTATCCGATGATGCACTA
66 GGTTTATACGATGATGCACTATGTGTGTCAGTAT---T--TTTGGTGTATCTGATGAT--ACAA
** * * * * ** * * * *
3868164 TGTGTGAGAGCATAGATGCTTCGGTTTATTCGGTGATGCACTTTGTGTGCCAGTATACATGCTTC
1 TGTGTGCTAGTATAAATGCTTCAGTTTATACAATGATGCACTGTGTGTACTAGTATAGATGCTTC
* * * * * * * * * *
3868229 GATTTATTCGATGATGCACTGTGAGTGCCAGTATAGATGCTTCGGTTTAT-TCGATAATGCAC
66 GGTTTATACGATGATGCACTATGTGTGTCAGTAT---T--TTTGGTGTATCT-GATGATACAA
* ** * * * * *
3868291 TGTGTGCTAGTATAGATGCTTGGGTTTACT-CGATGATGTACTGTGTATGCCAGTATAGATGCTT
1 TGTGTGCTAGTATAAATGCTTCAGTTTA-TACAATGATGCACTGTGTGTACTAGTATAGATGCTT
** * *
3868355 CGGTTTACCCGATGATTCACTTTGCT-TGTCAGTAT
65 CGGTTTATACGATGATGCACTATG-TGTGTCAGTAT
3868390 GGATGCTTCA
Statistics
Matches: 383, Mismatches: 79, Indels: 30
0.78 0.16 0.06
Matches are distributed among these distances:
121 2 0.01
122 98 0.26
123 6 0.02
125 2 0.01
127 165 0.43
128 6 0.02
129 104 0.27
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.41
Consensus pattern (122 bp):
TGTGTGCTAGTATAAATGCTTCAGTTTATACAATGATGCACTGTGTGTACTAGTATAGATGCTTC
GGTTTATACGATGATGCACTATGTGTGTCAGTATTTTTGGTGTATCTGATGATACAA
Found at i:3868974 original size:41 final size:40
Alignment explanation
Indices: 3868816--3868978 Score: 139
Period size: 42 Copynumber: 3.9 Consensus size: 40
3868806 TTGTGTGTGC
* * * * * *
3868816 CAGTATAGATACTTTGATTTATCCGATTATGTACTATGTGT
1 CAGTATAGAT-GTTTCAGTTATCCGATGATGCACTATGTAT
** *
3868857 GCCAGTATAGATGTTTTGGTGTATCCGATGATGCATTATGTAAGT
1 --CAGTATAGATGTTTCAGT-TATCCGATGATGCACTATGT-A-T
* *
3868902 C-GTATAGATGCTTCAGTTTATTCGATGATGCACTATGTAT
1 CAGTATAGATGTTTCAG-TTATCCGATGATGCACTATGTAT
*
3868942 CAGTATAGATGTTTCAAGTTATCCGATAATGCACTAT
1 CAGTATAGATGTTTC-AGTTATCCGATGATGCACTAT
3868979 ATGTGTCAGT
Statistics
Matches: 98, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
40 2 0.02
41 30 0.31
42 36 0.37
43 29 0.30
45 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.39
Consensus pattern (40 bp):
CAGTATAGATGTTTCAGTTATCCGATGATGCACTATGTAT
Found at i:3869462 original size:18 final size:19
Alignment explanation
Indices: 3869436--3869488 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
3869426 ATGCTCTTCA
3869436 TGTTATTG-TTTTAAATAT
1 TGTTATTGTTTTTAAATAT
*
3869454 TGTTTTTGTTTTTAAATAT
1 TGTTATTGTTTTTAAATAT
* *
3869473 TTTTA-TATTTTTAAAT
1 TGTTATTGTTTTTAAAT
3869489 TATTTTTGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 17 0.57
19 13 0.43
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (19 bp):
TGTTATTGTTTTTAAATAT
Found at i:3869468 original size:19 final size:18
Alignment explanation
Indices: 3869444--3869495 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
3869434 CATGTTATTG
* *
3869444 TTTTAAATATTGTTTTTGT
1 TTTTAAATATT-TTTATAT
3869463 TTTTAAATATTTTTATAT
1 TTTTAAATATTTTTATAT
3869481 TTTTAAATTATTTTT
1 TTTTAAA-TATTTTT
3869496 GGATATTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 12 0.40
19 18 0.60
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (18 bp):
TTTTAAATATTTTTATAT
Found at i:3870486 original size:6 final size:6
Alignment explanation
Indices: 3870478--3870510 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
3870468 CAAAAATAAA
*
3870478 TGAAGA TGAAGG TGAAGG TGAAGG TGAAGG TGA
1 TGAAGG TGAAGG TGAAGG TGAAGG TGAAGG TGA
3870511 GGCATATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.45, T:0.18
Consensus pattern (6 bp):
TGAAGG
Found at i:3871705 original size:37 final size:37
Alignment explanation
Indices: 3871655--3871725 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
3871645 TTAACGTTTT
3871655 TGAATAATTGTTCTCTACAGCTAAAACTAGTTTCTTA
1 TGAATAATTGTTCTCTACAGCTAAAACTAGTTTCTTA
3871692 TGAATAATTGTTCTCTACAGCTAAAACTAGTTTC
1 TGAATAATTGTTCTCTACAGCTAAAACTAGTTTC
3871726 ATACTCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (37 bp):
TGAATAATTGTTCTCTACAGCTAAAACTAGTTTCTTA
Found at i:3888009 original size:12 final size:11
Alignment explanation
Indices: 3887988--3888015 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3887978 ATCAAAACCC
3887988 AAAAAGAAAAA
1 AAAAAGAAAAA
3887999 AAAAAGAAAAA
1 AAAAAGAAAAA
3888010 AAAAAG
1 AAAAAG
3888016 CTTGTGGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:3901533 original size:29 final size:29
Alignment explanation
Indices: 3901509--3901591 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 29
3901499 TTAAAATTTT
* *
3901509 AAATTAAGTAGATATTAATTAAAAACTCA
1 AAATTAAGTAAATATTAATTAAAAACTTA
* * * *
3901538 AAATTACGTAAATACTAATAAAAACACTTC
1 AAATTAAGTAAATATTAATTAAAA-ACTTA
*
3901568 AAATTAAGTAAATATTTATTAAAA
1 AAATTAAGTAAATATTAATTAAAA
3901592 GAATTCAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
29 20 0.47
30 23 0.53
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.31
Consensus pattern (29 bp):
AAATTAAGTAAATATTAATTAAAAACTTA
Found at i:3901579 original size:30 final size:29
Alignment explanation
Indices: 3901509--3901581 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
3901499 TTAAAATTTT
* * *
3901509 AAATTAAGTAGATATTAATTAAAAACTCA
1 AAATTAAGTAAATACTAATAAAAAACTCA
*
3901538 AAATTACGTAAATACTAATAAAAACACTTC-
1 AAATTAAGTAAATACTAATAAAAA-AC-TCA
3901568 AAATTAAGTAAATA
1 AAATTAAGTAAATA
3901582 TTTATTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.54
30 15 0.41
31 2 0.05
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.29
Consensus pattern (29 bp):
AAATTAAGTAAATACTAATAAAAAACTCA
Found at i:3902594 original size:111 final size:111
Alignment explanation
Indices: 3902400--3902621 Score: 383
Period size: 111 Copynumber: 2.0 Consensus size: 111
3902390 GTTTTAACAA
* * *
3902400 ATGCTGGAAAATCTTTTATTAAATGAAAAAAAAGGTTTTGAACGGTGAGTTCTTTAACAAAAACT
1 ATGCTGGAAAATCTTTTATTAAATGAAAAAAAAGATTTTGAACAGTGAGTTCTTTAACAAAAACC
*
3902465 CATTCAATACTGCTTATATCAAATGGTTCATGATCGAGTCTAAATT
66 CATTCAATACTGCTTATATCAAATGGTTCATGATCGAGTATAAATT
*
3902511 ATGCTGGAAAATCTTTTATTAGATGAAAAAAAAGATTTTGAACAGTGAGTTCTTTAAC-AAAACC
1 ATGCTGGAAAATCTTTTATTAAATGAAAAAAAAGATTTTGAACAGTGAGTTCTTTAACAAAAACC
3902575 CAATTCAATACTGCTTATATCAAATGGTTCATGATCGAGTATAAATT
66 C-ATTCAATACTGCTTATATCAAATGGTTCATGATCGAGTATAAATT
3902622 TTATAGCAGA
Statistics
Matches: 105, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
110 6 0.06
111 99 0.94
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (111 bp):
ATGCTGGAAAATCTTTTATTAAATGAAAAAAAAGATTTTGAACAGTGAGTTCTTTAACAAAAACC
CATTCAATACTGCTTATATCAAATGGTTCATGATCGAGTATAAATT
Found at i:3915241 original size:22 final size:22
Alignment explanation
Indices: 3915216--3915267 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
3915206 GTTAAAGTGT
3915216 AATTTTATTATTATCAACTTAA
1 AATTTTATTATTATCAACTTAA
*
3915238 AATTTTATTATTATTAACTTAA
1 AATTTTATTATTATCAACTTAA
3915260 AATTTTAT
1 AATTTTAT
3915268 AAATTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTTTATTATTATCAACTTAA
Found at i:3918976 original size:2 final size:2
Alignment explanation
Indices: 3918969--3918996 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3918959 TTCTCGATCT
3918969 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3918997 CTATAACAGT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3924225 original size:15 final size:17
Alignment explanation
Indices: 3924184--3924225 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
3924174 ACCTTTTTTT
3924184 TAAATTTATAATTACAAA
1 TAAA-TTATAATTACAAA
3924202 TATAATTAT-ATTA-AAA
1 TA-AATTATAATTACAAA
3924218 TAAATTAT
1 TAAATTAT
3924226 CATCAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 6 0.26
16 5 0.22
17 4 0.17
18 6 0.26
19 2 0.09
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTATAATTACAAA
Found at i:3927186 original size:30 final size:30
Alignment explanation
Indices: 3927150--3927207 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
3927140 CATCTACAAA
3927150 TGATGTTTTAACTCTATAGTTATTCAGGTT
1 TGATGTTTTAACTCTATAGTTATTCAGGTT
3927180 TGATGTTTTAACTCTATAGTTATTCAGG
1 TGATGTTTTAACTCTATAGTTATTCAGG
3927208 ATAACCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.48
Consensus pattern (30 bp):
TGATGTTTTAACTCTATAGTTATTCAGGTT
Found at i:3931843 original size:9 final size:9
Alignment explanation
Indices: 3931818--3931871 Score: 72
Period size: 9 Copynumber: 6.0 Consensus size: 9
3931808 GTGGCTGAAG
3931818 TTCTTCCTC
1 TTCTTCCTC
*
3931827 TTCGTCCTC
1 TTCTTCCTC
*
3931836 GTCTTCCTC
1 TTCTTCCTC
*
3931845 TTCTTCTTC
1 TTCTTCCTC
3931854 TTCTTCCTC
1 TTCTTCCTC
*
3931863 CTCTTCCTC
1 TTCTTCCTC
3931872 ACCATCATCG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.00, C:0.44, G:0.04, T:0.52
Consensus pattern (9 bp):
TTCTTCCTC
Found at i:3932044 original size:21 final size:21
Alignment explanation
Indices: 3931996--3932063 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
3931986 TGCATCCTCC
*
3931996 TCCTCAT-CTGCATCTTCATCT
1 TCCTCATCCT-CATCCTCATCT
** *
3932017 TGATCAT-CTCCTGCCTCATCT
1 TCCTCATCCTCAT-CCTCATCT
*
3932038 TCCTCATCCTCATCCTCATCA
1 TCCTCATCCTCATCCTCATCT
3932059 TCCTC
1 TCCTC
3932064 GGTGTCTCCG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 2 0.05
21 31 0.84
22 4 0.11
ACGTcount: A:0.15, C:0.43, G:0.04, T:0.38
Consensus pattern (21 bp):
TCCTCATCCTCATCCTCATCT
Found at i:3932050 original size:15 final size:15
Alignment explanation
Indices: 3932030--3932063 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3932020 TCATCTCCTG
* *
3932030 CCTCATCTTCCTCAT
1 CCTCATCCTCATCAT
3932045 CCTCATCCTCATCAT
1 CCTCATCCTCATCAT
3932060 CCTC
1 CCTC
3932064 GGTGTCTCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.50, G:0.00, T:0.35
Consensus pattern (15 bp):
CCTCATCCTCATCAT
Found at i:3941954 original size:20 final size:20
Alignment explanation
Indices: 3941900--3941956 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
3941890 TATTATCGGC
* * *
3941900 TAAAATTTCAAAAAAATTCA
1 TAAAATTTTAAAAAAAATAA
*
3941920 TAAATATTTT--TAAAAATAA
1 TAAA-ATTTTAAAAAAAATAA
3941939 TAAAATTTTAAAAAAAAT
1 TAAAATTTTAAAAAAAAT
3941957 TCAATTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 5 0.17
19 10 0.34
20 10 0.34
21 4 0.14
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAAATTTTAAAAAAAATAA
Found at i:3942008 original size:21 final size:20
Alignment explanation
Indices: 3941984--3942028 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
3941974 TTTAAATACA
* *
3941984 AAATATTTATATTTATATAAT
1 AAATAATTAAATTTA-ATAAT
*
3942005 AAATAATTAAATTTAATTAT
1 AAATAATTAAATTTAATAAT
3942025 AAAT
1 AAAT
3942029 TAAATAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATAATTAAATTTAATAAT
Found at i:3942036 original size:21 final size:21
Alignment explanation
Indices: 3941994--3942036 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3941984 AAATATTTAT
*
3941994 ATTTATATAATAAATAATTAA
1 ATTTATATAATAAATAAATAA
*
3942015 ATTTA-ATTATAAATTAAATAA
1 ATTTATATAATAAA-TAAATAA
3942036 A
1 A
3942037 ATAGAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTATATAATAAATAAATAA
Found at i:3942648 original size:72 final size:72
Alignment explanation
Indices: 3942570--3942731 Score: 315
Period size: 72 Copynumber: 2.2 Consensus size: 72
3942560 AAGAGATTGA
*
3942570 AATTAAAGAAAATTTAATCGCTTATTTCTTCTAGGGCTCTTTTGAATGCCCAATAAGTTGATTAG
1 AATTAAAGAAAGTTTAATCGCTTATTTCTTCTAGGGCTCTTTTGAATGCCCAATAAGTTGATTAG
3942635 AGGGTTT
66 AGGGTTT
3942642 AATTAAAGAAAGTTTAATCGCTTATTTCTTCTAGGGCTCTTTTGAATGCCCAATAAGTTGATTAG
1 AATTAAAGAAAGTTTAATCGCTTATTTCTTCTAGGGCTCTTTTGAATGCCCAATAAGTTGATTAG
3942707 AGGGTTT
66 AGGGTTT
3942714 AATTAAAGAAAGTTTAAT
1 AATTAAAGAAAGTTTAAT
3942732 ACTTCTAACT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 89 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (72 bp):
AATTAAAGAAAGTTTAATCGCTTATTTCTTCTAGGGCTCTTTTGAATGCCCAATAAGTTGATTAG
AGGGTTT
Found at i:3943193 original size:165 final size:165
Alignment explanation
Indices: 3942916--3943238 Score: 531
Period size: 165 Copynumber: 2.0 Consensus size: 165
3942906 TAAAATACTT
* * *
3942916 TTTTTTATTTAGATCTTTAAAATTTTTTAAAACTTTAAATTAGTGAAGATAAAATTTCACTTTGG
1 TTTTCTATTTAGATCCTTAAAATTTTTTAAAACTTTAAATTAGTAAAGATAAAATTTCACTTTGG
* * *
3942981 TCCTCTTAAAAATAATAAAATTTTAATTTAATCCTTTAAAAAATGCACTTTTACTACCGTAAAAA
66 ACCCCCTAAAAATAATAAAATTTTAATTTAATCCTTTAAAAAATGCACTTTTACTACCGTAAAAA
*
3943046 TTACAATTTAACTTCGGCCTCCCTAAAATAAAAAA
131 TTACAATTTAACTTCGGCCCCCCTAAAATAAAAAA
* *
3943081 TTTTCTATTTAGATCCTTAAAATTTTTTAAAATTTTTAAATTAGTAAAGGTAAAATTTCACTTT-
1 TTTTCTATTTAGATCCTTAAAATTTTTTAAAA-CTTTAAATTAGTAAAGATAAAATTTCACTTTG
* *
3943145 GACCCCCTAAAAATGATAAAATTTTAATTTAATCCTTTAAAAAATGCACTTTTACTATCGTAAAA
65 GACCCCCTAAAAATAATAAAATTTTAATTTAATCCTTTAAAAAATGCACTTTTACTACCGTAAAA
3943210 ATTACAATTTAACTTCGGCCCCCCTAAAA
130 ATTACAATTTAACTTCGGCCCCCCTAAAA
3943239 AAATTTTTGG
Statistics
Matches: 146, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
165 118 0.81
166 28 0.19
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (165 bp):
TTTTCTATTTAGATCCTTAAAATTTTTTAAAACTTTAAATTAGTAAAGATAAAATTTCACTTTGG
ACCCCCTAAAAATAATAAAATTTTAATTTAATCCTTTAAAAAATGCACTTTTACTACCGTAAAAA
TTACAATTTAACTTCGGCCCCCCTAAAATAAAAAA
Found at i:3946573 original size:10 final size:10
Alignment explanation
Indices: 3946558--3946672 Score: 71
Period size: 10 Copynumber: 11.6 Consensus size: 10
3946548 GCATTTTTTA
3946558 TATATTAAAT
1 TATATTAAAT
*
3946568 TATATTAAAA
1 TATATTAAAT
3946578 TATTATTAAAT
1 TA-TATTAAAT
*
3946589 TATA-TATTAT
1 TATATTA-AAT
*
3946599 TTTATTAAAT
1 TATATTAAAT
* *
3946609 TGTATTTAA-
1 TATATTAAAT
3946618 TA-A-T-AAT
1 TATATTAAAT
* *
3946625 TATGTTAAAA
1 TATATTAAAT
3946635 TATAATTAAAT
1 TAT-ATTAAAT
3946646 TA-ATTAATATT
1 TATATTAA-A-T
*
3946657 TTTATTAAAT
1 TATATTAAAT
3946667 TATATT
1 TATATT
3946673 TAATAATAAT
Statistics
Matches: 80, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 1 0.01
9 9 0.11
10 39 0.49
11 21 0.26
12 5 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (10 bp):
TATATTAAAT
Found at i:3946684 original size:58 final size:57
Alignment explanation
Indices: 3946565--3946685 Score: 181
Period size: 58 Copynumber: 2.1 Consensus size: 57
3946555 TTATATATTA
* * *
3946565 AATTATATTAAAATATTATTAAATTATATATTATTTTATTAAATTGTATTTAATAAT
1 AATTATATTAAAATATAATTAAATTATATAATATTTTATTAAATTATATTTAATAAT
*
3946622 AATTATGTTAAAATATAATTAAATTA-ATTAATATTTTTATTAAATTATATTTAATAAT
1 AATTATATTAAAATATAATTAAATTATA-TAATA-TTTTATTAAATTATATTTAATAAT
3946680 AATTAT
1 AATTAT
3946686 TAAAATTTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
56 1 0.02
57 28 0.48
58 29 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (57 bp):
AATTATATTAAAATATAATTAAATTATATAATATTTTATTAAATTATATTTAATAAT
Found at i:3946885 original size:16 final size:16
Alignment explanation
Indices: 3946850--3946901 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
3946840 TGAATTATTG
* *
3946850 ATTACAGTCCTATTCC
1 ATTACAGTTCTATTCT
*
3946866 ATTACAGTTCTATTTT
1 ATTACAGTTCTATTCT
**
3946882 ATTACACCTCTATTCT
1 ATTACAGTTCTATTCT
3946898 ATTA
1 ATTA
3946902 TAGTCCATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.27, C:0.23, G:0.04, T:0.46
Consensus pattern (16 bp):
ATTACAGTTCTATTCT
Found at i:3967064 original size:46 final size:46
Alignment explanation
Indices: 3967013--3967106 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
3967003 TTTTTTTTTA
3967013 TATTTTATGCTTAGAGTTTTATTCAATGAATAATTCTATTTTAAAT
1 TATTTTATGCTTAGAGTTTTATTCAATGAATAATTCTATTTTAAAT
*
3967059 TATTTTATGCTTATAGTTTTATTCAATGAATAATTCTATTTTAAAT
1 TATTTTATGCTTAGAGTTTTATTCAATGAATAATTCTATTTTAAAT
3967105 TA
1 TA
3967107 GTAAAACTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.53
Consensus pattern (46 bp):
TATTTTATGCTTAGAGTTTTATTCAATGAATAATTCTATTTTAAAT
Found at i:3967272 original size:23 final size:24
Alignment explanation
Indices: 3967245--3967290 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3967235 TTTAATTCAC
*
3967245 ATTTTAAAT-TAAATATTATAATT
1 ATTTTAAATGTAAATATAATAATT
*
3967268 ATTTTAAATGTCAATATAATAAT
1 ATTTTAAATGTAAATATAATAAT
3967291 ATGATGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
ATTTTAAATGTAAATATAATAATT
Found at i:3967838 original size:30 final size:30
Alignment explanation
Indices: 3967753--3967851 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
3967743 AGTTGAATCA
* ** * * *
3967753 AAATCAAAGTGTCATATATATATTTGAATC
1 AAATCAAAGTTTCATATGCATAATTGCACC
* ** *
3967783 ATAATCAAAGTTTTACGTGCTTAATTGCACC
1 A-AATCAAAGTTTCATATGCATAATTGCACC
*
3967814 AAATCAAAGTTTCATATGCATAATTACACC
1 AAATCAAAGTTTCATATGCATAATTGCACC
*
3967844 AAACCAAA
1 AAATCAAA
3967852 ATTGATGTAC
Statistics
Matches: 52, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
30 32 0.62
31 20 0.38
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.31
Consensus pattern (30 bp):
AAATCAAAGTTTCATATGCATAATTGCACC
Found at i:3969467 original size:2 final size:2
Alignment explanation
Indices: 3969450--3969487 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
3969440 TAAAATTAAA
*
3969450 AT AT AT AA AT AGT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A
3969488 AATGTTTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3970857 original size:19 final size:21
Alignment explanation
Indices: 3970819--3970860 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
3970809 TAGTCATAAC
3970819 TTTTAAAAATTAACTCTCAAT
1 TTTTAAAAATTAACTCTCAAT
*
3970840 TTTTACAAA-TAA-TCTCAAT
1 TTTTAAAAATTAACTCTCAAT
3970859 TT
1 TT
3970861 GATTCCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 3 0.15
21 8 0.40
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTTAAAAATTAACTCTCAAT
Found at i:3970898 original size:18 final size:18
Alignment explanation
Indices: 3970875--3970910 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3970865 CCAATTCTAA
3970875 AAAAATAAATAAATATAT
1 AAAAATAAATAAATATAT
*
3970893 AAAAATACATAAATATAT
1 AAAAATAAATAAATATAT
3970911 TTTAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAATAAATAAATATAT
Found at i:3972513 original size:18 final size:18
Alignment explanation
Indices: 3972490--3972526 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3972480 TCTTTTATCC
3972490 CTTCACTTTTCCATCCAA
1 CTTCACTTTTCCATCCAA
3972508 CTTCACTTTTCCATCCAA
1 CTTCACTTTTCCATCCAA
3972526 C
1 C
3972527 CAAGTACATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.38
Consensus pattern (18 bp):
CTTCACTTTTCCATCCAA
Found at i:3976566 original size:23 final size:24
Alignment explanation
Indices: 3976527--3976571 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
3976517 GATTGATTTT
3976527 TTAAATTTATACTACA-TAAAATA
1 TTAAATTTATACTACATTAAAATA
3976550 TTAAATTTATA-TGACATTAAAA
1 TTAAATTTATACT-ACATTAAAA
3976572 AAAATGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 1 0.05
23 14 0.70
24 5 0.25
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (24 bp):
TTAAATTTATACTACATTAAAATA
Found at i:3978274 original size:20 final size:19
Alignment explanation
Indices: 3978249--3978293 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3978239 TTATATGAAT
*
3978249 ATTATATCATAATCCGACCA
1 ATTATATCAAAATCCG-CCA
*
3978269 ATTATATGAAAATCCGCCA
1 ATTATATCAAAATCCGCCA
*
3978288 AGTATA
1 ATTATA
3978294 ATCCGACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (19 bp):
ATTATATCAAAATCCGCCA
Found at i:3982722 original size:28 final size:28
Alignment explanation
Indices: 3982665--3982723 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
3982655 TTATGGATCG
** *
3982665 AATTTAATTTAAATAATAAATATTTTTT
1 AATTTAATTTAAATAATAAATAAATATT
*
3982693 AATTTAATTATAAA-AATACATAAATATT
1 AATTTAATT-TAAATAATAAATAAATATT
3982721 AAT
1 AAT
3982724 ATAAAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 22 0.85
29 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
AATTTAATTTAAATAATAAATAAATATT
Done.