Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 99 of 207
Found at i:29490666 original size:9 final size:9
Alignment explanation
Indices: 29490606--29490674 Score: 52
Period size: 9 Copynumber: 7.2 Consensus size: 9
29490596 CCAAAAGTTT
*
29490606 ATTTTAAAA
1 ATTTAAAAA
29490615 A-TTAAAAA
1 ATTTAAAAA
29490623 ATTTTTAAAAA
1 A--TTTAAAAA
29490634 GTATTTTAAAAA
1 --A-TTTAAAAA
*
29490646 TATTT-TAAA
1 -ATTTAAAAA
29490655 ATTTAAAAA
1 ATTTAAAAA
29490664 ATTTAAAAA
1 ATTTAAAAA
29490673 AT
1 AT
29490675 AAATATATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
8 11 0.22
9 18 0.35
10 3 0.06
11 9 0.18
12 9 0.18
13 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (9 bp):
ATTTAAAAA
Found at i:29493323 original size:22 final size:19
Alignment explanation
Indices: 29493292--29493331 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 19
29493282 ATGATTCTTT
29493292 ATTTCTTATTCCACTCCCCAA
1 ATTTCTTATT--ACTCCCCAA
29493313 ATTTCATTATTACTCCCCA
1 ATTTC-TTATTACTCCCCA
29493332 GCTTTGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTTCTTATTACTCCCCAA
Found at i:29500472 original size:9 final size:9
Alignment explanation
Indices: 29500458--29500483 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
29500448 ATGATCTATT
29500458 ATAAAATAA
1 ATAAAATAA
29500467 ATAAAATAA
1 ATAAAATAA
29500476 ATAAAATA
1 ATAAAATA
29500484 TTAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
ATAAAATAA
Found at i:29501370 original size:17 final size:18
Alignment explanation
Indices: 29501348--29501382 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
29501338 AACTTCAAGG
*
29501348 CAATGATA-CATTAAGTT
1 CAATGATATCATAAAGTT
29501365 CAATGATATCATAAAGTT
1 CAATGATATCATAAAGTT
29501383 TTTGGTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (18 bp):
CAATGATATCATAAAGTT
Found at i:29504255 original size:71 final size:71
Alignment explanation
Indices: 29504167--29504308 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
29504157 ATTATGCAGA
29504167 TAGAAATATCCTTATTTTGAAATTCTTCATTCATATCTTTTCATGCAAAAACTGTATCTTAGACT
1 TAGAAATATCCTTATTTTGAAATTCTTCATTCATATCTTTTCATGCAAAAACTGTATCTTAGACT
29504232 TTTAAT
66 TTTAAT
29504238 TAGAAATATCCTTATTTTGAAATTCTTCATTCATATCTTTTCATGCAAAAACTGTATCTTAGACT
1 TAGAAATATCCTTATTTTGAAATTCTTCATTCATATCTTTTCATGCAAAAACTGTATCTTAGACT
29504303 TTTAAT
66 TTTAAT
29504309 CTAGTTCTTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.45
Consensus pattern (71 bp):
TAGAAATATCCTTATTTTGAAATTCTTCATTCATATCTTTTCATGCAAAAACTGTATCTTAGACT
TTTAAT
Found at i:29526905 original size:28 final size:27
Alignment explanation
Indices: 29526840--29526905 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
29526830 TTTAACAGTA
*
29526840 ACAATACAGTGTGGGCCTTAGCCCAAT
1 ACAATACAGTGTGGGCCTAAGCCCAAT
* * *
29526867 ATAGAAACAGTGTGGGCCTAAGCCCGAT
1 ACA-ATACAGTGTGGGCCTAAGCCCAAT
29526895 ACAATATCAGT
1 ACAATA-CAGT
29526906 ATGGTGCAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (27 bp):
ACAATACAGTGTGGGCCTAAGCCCAAT
Found at i:29527186 original size:32 final size:32
Alignment explanation
Indices: 29527116--29527382 Score: 252
Period size: 32 Copynumber: 8.4 Consensus size: 32
29527106 GAATGGCTAC
* * * *
29527116 AAGCCATAAGT-ATAGTAATGTGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
29527147 AAGCCATCAGTAGCAGTGATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
29527179 CAA-CCATCAGTAATAGTAACATGATCGGCACA
1 -AAGCCATCAGTAACAGTAATATGATCGGCACA
* * ** *
29527211 AACCCATCAGTAGCAGTGGTATGATCAGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * *
29527243 CAGCCATCAGTAATAGTCAA-ATGATTGGTACA
1 AAGCCATCAGTAACAGT-AATATGATCGGCACA
* **
29527275 CAGCCATTGGTAACAGTAATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
29527307 AAGCCATCAGTAACGGTATTATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * *
29527339 AAGCCATCAGTAACGGTACTACGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
29527371 AAGCCATCAGTA
1 AAGCCATCAGTA
29527383 GCATCGCAGC
Statistics
Matches: 191, Mismatches: 40, Indels: 9
0.80 0.17 0.04
Matches are distributed among these distances:
31 14 0.07
32 175 0.92
33 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:29527456 original size:27 final size:26
Alignment explanation
Indices: 29527425--29527489 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
29527415 AACAAGGCTG
29527425 CCAGTAATAGTATATGTAGCCA-AGCCA
1 CCAGTAATAGTAT-TGT-GCCAGAGCCA
*
29527452 CCAGTAATAGTGATTGTGGCAGAGCCA
1 CCAGTAATAGT-ATTGTGCCAGAGCCA
29527479 CCAGTAA-AGTA
1 CCAGTAATAGTA
29527490 CTTCCTCCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 1 0.03
26 6 0.17
27 26 0.74
28 2 0.06
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CCAGTAATAGTATTGTGCCAGAGCCA
Found at i:29527599 original size:23 final size:24
Alignment explanation
Indices: 29527553--29527601 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
29527543 CCATGCTCAG
*
29527553 AATCAGTCATTCAAATCACAGACA
1 AATCAGTCATTCAAACCACAGACA
*
29527577 AATCAGTCATT-TAACCACAGACA
1 AATCAGTCATTCAAACCACAGACA
29527600 AA
1 AA
29527602 ACGATCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.47, C:0.24, G:0.08, T:0.20
Consensus pattern (24 bp):
AATCAGTCATTCAAACCACAGACA
Found at i:29527684 original size:27 final size:26
Alignment explanation
Indices: 29527632--29528154 Score: 484
Period size: 27 Copynumber: 19.6 Consensus size: 26
29527622 GGCAAAAATA
29527632 GTCA-TTTACCC-ACCAGGGCATTACG
1 GTCATTTTACCCTA-CAGGGCATTACG
* *
29527657 GTCATTTTACCTTACATGGGTATTACG
1 GTCATTTTACCCTACA-GGGCATTACG
*
29527684 GTCATTTTACCTTACAGGGGCATTAC-
1 GTCATTTTACCCTACA-GGGCATTACG
* *
29527710 GTCATTTTACCTTACAGGGGTATTACG
1 GTCATTTTACCCTACA-GGGCATTACG
** *
29527737 AACATTTTACCCTATAAGGGCATTACG
1 GTCATTTTACCCTA-CAGGGCATTACG
*
29527764 GTCATTTTACCCTACAAGGGCATTACA
1 GTCATTTTACCCTAC-AGGGCATTACG
29527791 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACA-GGGCATTACG
29527818 GTCATTTTACCCCTACAGGGGC-TTACG
1 GTCATTTTA-CCCTACA-GGGCATTACG
* *
29527845 GTCATTTTACCCTATAAGGGTATTACG
1 GTCATTTTACCCTA-CAGGGCATTACG
* * * *
29527872 ATCATTTTATCCTATAAGGGTATTACG
1 GTCATTTTACCCTA-CAGGGCATTACG
*
29527899 GTCATTTTACCCTACAGAG-ATGTTACG
1 GTCATTTTACCCTACAGGGCA--TTACG
* *
29527926 GTCATTTTACCTTATAGGGGCATTACG
1 GTCATTTTACCCTACA-GGGCATTACG
* * * *
29527953 ATCATTTTACCTTACAGGGGTATTACA
1 GTCATTTTACCCTACA-GGGCATTACG
*
29527980 GTCATTTTACCCTATAGAGGCATTACG
1 GTCATTTTACCCTACAG-GGCATTACG
*
29528007 GTCATTTTACCCTATAGAGGCATTACG
1 GTCATTTTACCCTACAG-GGCATTACG
*
29528034 GTCATTTTACCCTATAGAGGCATTACG
1 GTCATTTTACCCTACAG-GGCATTACG
* *
29528061 GTTATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACA-GGGCATTACG
* * * *
29528088 ATCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTA-CAGGGCATTACG
* * * *
29528115 GT-ATTCTACCCTACGGGGGTATTTCG
1 GTCATTTTACCCTAC-AGGGCATTACG
*
29528141 GT-ATTCTACCCTAC
1 GTCATTTTACCCTAC
29528155 GGGGGTATTT
Statistics
Matches: 434, Mismatches: 46, Indels: 35
0.84 0.09 0.07
Matches are distributed among these distances:
25 5 0.01
26 80 0.18
27 331 0.76
28 17 0.04
29 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.34
Consensus pattern (26 bp):
GTCATTTTACCCTACAGGGCATTACG
Found at i:29527827 original size:81 final size:80
Alignment explanation
Indices: 29527651--29528154 Score: 536
Period size: 81 Copynumber: 6.3 Consensus size: 80
29527641 CCACCAGGGC
* * * * * *
29527651 ATTACGGTCATTTTACCTTACATGGGTATTACGGTCATTTTACCTTACAGGGGCATTACGTCATT
1 ATTACGGTCATTTTACCCTACAAGGGCATTACGGTCATTTTACCCTATAAGGGCATTACGTCATT
*
29527716 TTACCTTACAGGGGT
66 TTACCCTACAGGGGT
** * *
29527731 ATTACGAACATTTTACCCTATAAGGGCATTACGGTCATTTTACCCTACAAGGGCATTACAGTCAT
1 ATTACGGTCATTTTACCCTACAAGGGCATTACGGTCATTTTACCCTATAAGGGCATTAC-GTCAT
*
29527796 TTTACCCTACAGGGGC
65 TTTACCCTACAGGGGT
* *
29527812 ATTACGGTCATTTTACCCCTACAGGGGC-TTACGGTCATTTTACCCTATAAGGGTATTACGATCA
1 ATTACGGTCATTTTA-CCCTACAAGGGCATTACGGTCATTTTACCCTATAAGGGCATTACG-TCA
* * *
29527876 TTTTATCCTATAAGGGT
64 TTTTACCCTACAGGGGT
* * *
29527893 ATTACGGTCATTTTACCCTAC-AGAG-ATGTTACGGTCATTTTACCTTATAGGGGCATTACGATC
1 ATTACGGTCATTTTACCCTACAAGGGCA--TTACGGTCATTTTACCCTATAAGGGCATTACG-TC
*
29527956 ATTTTACCTTACAGGGGT
63 ATTTTACCCTACAGGGGT
* *
29527974 ATTACAGTCATTTTACCCTA-TAGAGGCATTACGGTCATTTTACCCTAT-AGAGGCATTACGGTC
1 ATTACGGTCATTTTACCCTACAAG-GGCATTACGGTCATTTTACCCTATAAG-GGCATTAC-GTC
* * *
29528037 ATTTTACCCTATAGAGGC
63 ATTTTACCCTACAGGGGT
* * * * * * *
29528055 ATTACGGTTATTTTACCCTACAGGGGTATTACGATCATTTTACCCTATGAGGGTATTTCGGT-AT
1 ATTACGGTCATTTTACCCTACAAGGGCATTACGGTCATTTTACCCTATAAGGGCATTAC-GTCAT
* *
29528119 TCTACCCTACGGGGGT
65 TTTACCCTACAGGGGT
* *
29528135 ATTTCGGT-ATTCTACCCTAC
1 ATTACGGTCATTTTACCCTAC
29528155 GGGGGTATTT
Statistics
Matches: 359, Mismatches: 52, Indels: 27
0.82 0.12 0.06
Matches are distributed among these distances:
79 13 0.04
80 79 0.22
81 251 0.70
82 15 0.04
83 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (80 bp):
ATTACGGTCATTTTACCCTACAAGGGCATTACGGTCATTTTACCCTATAAGGGCATTACGTCATT
TTACCCTACAGGGGT
Found at i:29528134 original size:26 final size:26
Alignment explanation
Indices: 29528063--29528168 Score: 140
Period size: 26 Copynumber: 4.0 Consensus size: 26
29528053 GCATTACGGT
* * * *
29528063 TATTTTACCCTACAGGGGTATTACGA
1 TATTCTACCCTACGGGGGTATTTCGG
* * *
29528089 TCATTTTACCCTATGAGGGTATTTCGG
1 T-ATTCTACCCTACGGGGGTATTTCGG
29528116 TATTCTACCCTACGGGGGTATTTCGG
1 TATTCTACCCTACGGGGGTATTTCGG
29528142 TATTCTACCCTACGGGGGTATTTCGG
1 TATTCTACCCTACGGGGGTATTTCGG
29528168 T
1 T
29528169 CCAGATATCG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
26 50 0.70
27 21 0.30
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.37
Consensus pattern (26 bp):
TATTCTACCCTACGGGGGTATTTCGG
Found at i:29532986 original size:33 final size:33
Alignment explanation
Indices: 29532944--29533007 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
29532934 AGGCAAGAAC
29532944 TCTGATTAGAAGGGTTAAAGAACTCAATTAAAA
1 TCTGATTAGAAGGGTTAAAGAACTCAATTAAAA
29532977 TCTGATTAGAAGGGTTAAAGAACTCAATTAA
1 TCTGATTAGAAGGGTTAAAGAACTCAATTAA
29533008 TTCTGGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (33 bp):
TCTGATTAGAAGGGTTAAAGAACTCAATTAAAA
Found at i:29542877 original size:20 final size:20
Alignment explanation
Indices: 29542852--29542950 Score: 110
Period size: 20 Copynumber: 5.0 Consensus size: 20
29542842 CCAATAGGGT
29542852 TTGCACTTTGGTGCCTCTGA
1 TTGCACTTTGGTGCCTCTGA
* ** *
29542872 TTGCACATTCATGCCTCTGT
1 TTGCACTTTGGTGCCTCTGA
*
29542892 TTGCACTTCGGTGCCTCTGA
1 TTGCACTTTGGTGCCTCTGA
* *
29542912 TTGCACATTCGTGCCTCT-A
1 TTGCACTTTGGTGCCTCTGA
*
29542931 TCTACACTTTGGTGCCTCTG
1 T-TGCACTTTGGTGCCTCTG
29542951 TTATGCATAA
Statistics
Matches: 62, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
19 2 0.03
20 60 0.97
ACGTcount: A:0.12, C:0.29, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCACTTTGGTGCCTCTGA
Found at i:29542895 original size:40 final size:40
Alignment explanation
Indices: 29542850--29542950 Score: 157
Period size: 40 Copynumber: 2.5 Consensus size: 40
29542840 TGCCAATAGG
29542850 GTTTGCACTTTGGTGCCTCTGATTGCACATTCATGCCTCT
1 GTTTGCACTTTGGTGCCTCTGATTGCACATTCATGCCTCT
* *
29542890 GTTTGCACTTCGGTGCCTCTGATTGCACATTCGTGCCTCT
1 GTTTGCACTTTGGTGCCTCTGATTGCACATTCATGCCTCT
* * *
29542930 ATCTACACTTTGGTGCCTCTG
1 GTTTGCACTTTGGTGCCTCTG
29542951 TTATGCATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.12, C:0.29, G:0.21, T:0.39
Consensus pattern (40 bp):
GTTTGCACTTTGGTGCCTCTGATTGCACATTCATGCCTCT
Found at i:29559687 original size:10 final size:9
Alignment explanation
Indices: 29559672--29559740 Score: 61
Period size: 10 Copynumber: 7.4 Consensus size: 9
29559662 TACCCTTTTC
29559672 TTTATTCTAT
1 TTTATT-TAT
29559682 TTTATTTTAT
1 TTTA-TTTAT
29559692 TTTATTTA-
1 TTTATTTAT
29559700 TTTATTTAT
1 TTTATTTAT
*
29559709 TATTATTTGT
1 T-TTATTTAT
*
29559719 TATA-TTAT
1 TTTATTTAT
*
29559727 TTATTTTTAT
1 TT-TATTTAT
29559737 TTTA
1 TTTA
29559741 CTGATCTGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
8 12 0.25
9 9 0.19
10 25 0.52
11 2 0.04
ACGTcount: A:0.23, C:0.01, G:0.01, T:0.74
Consensus pattern (9 bp):
TTTATTTAT
Found at i:29559726 original size:22 final size:21
Alignment explanation
Indices: 29559697--29559738 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
29559687 TTTATTTTAT
29559697 TTATTTATTTATTATTATTTG
1 TTATTTATTTATTATTATTTG
*
29559718 TTATATTATTTATTTTTATTT
1 TTAT-TTATTTATTATTATTT
29559739 TACTGATCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (21 bp):
TTATTTATTTATTATTATTTG
Found at i:29559878 original size:3 final size:3
Alignment explanation
Indices: 29559870--29559931 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
29559860 GTTGTCATTT
* *
29559870 TTA TTA TTA TT- TTCA TTA CTA TTA TTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
29559915 TTA TCA TTGA TT- TTA TT
1 TTA TTA TT-A TTA TTA TT
29559932 TGTTTTTCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
2 4 0.08
3 40 0.82
4 5 0.10
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:29559961 original size:33 final size:33
Alignment explanation
Indices: 29559924--29560003 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 33
29559914 ATTATCATTG
*
29559924 ATTTTATTTGTTTTTCAT-TTTAG-TTTTAGTTTT
1 ATTTT-TTTATTTTT-ATGTTTAGTTTTTAGTTTT
*
29559957 ATTTTTTTATTTTTATGTTTTGTTTTTAGTTGTT
1 ATTTTTTTATTTTTATGTTTAGTTTTTAGTT-TT
29559991 -TTATTTTTATTTT
1 ATT-TTTTTATTTT
29560004 CTTAGACTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
31 2 0.05
32 12 0.29
33 15 0.37
34 12 0.29
ACGTcount: A:0.14, C:0.01, G:0.09, T:0.76
Consensus pattern (33 bp):
ATTTTTTTATTTTTATGTTTAGTTTTTAGTTTT
Found at i:29559970 original size:20 final size:21
Alignment explanation
Indices: 29559941--29560008 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
29559931 TTGTTTTTCA
29559941 TTTTAGTTTTA-GTTTTATTT
1 TTTTAGTTTTATGTTTTATTT
* *
29559961 TTTTATTTTTATGTTTTGTTT
1 TTTTAGTTTTATGTTTTATTT
29559982 TTAGTT-GTTTTAT-TTTTATTT
1 TT--TTAGTTTTATGTTTTATTT
*
29560003 TCTTAG
1 TTTTAG
29560009 ACTTATTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
19 2 0.05
20 11 0.28
21 18 0.46
22 6 0.15
23 2 0.05
ACGTcount: A:0.13, C:0.01, G:0.10, T:0.75
Consensus pattern (21 bp):
TTTTAGTTTTATGTTTTATTT
Found at i:29571789 original size:50 final size:50
Alignment explanation
Indices: 29571710--29571901 Score: 195
Period size: 50 Copynumber: 3.7 Consensus size: 50
29571700 TTTTCTGTAC
* * * * ** *
29571710 TGCCAATGTCATATCCCAGATATGATCTTACATGGGAGTTTTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
29571760 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
29571810 TGCCAACGCCATGTCCAAGACATGGTCTTACATGGGACCTCTCATAATCTCAATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC--GG
* *
29571865 AGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
29571902 TCTCGTTCCC
Statistics
Matches: 116, Mismatches: 21, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
50 79 0.68
53 2 0.02
55 35 0.30
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:29573853 original size:29 final size:31
Alignment explanation
Indices: 29573819--29573880 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
29573809 ATTTCTGAAC
29573819 TTTAGGG-CTAAAA-TGTAAATATG-CAAAAG
1 TTTAGGGAC-AAAATTGTAAATATGTCAAAAG
* *
29573848 TTTAGGGACAAAATTGTAATTTTGTCAAAAG
1 TTTAGGGACAAAATTGTAAATATGTCAAAAG
29573879 TT
1 TT
29573881 GAGTCGAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 11 0.39
30 9 0.32
31 8 0.29
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.34
Consensus pattern (31 bp):
TTTAGGGACAAAATTGTAAATATGTCAAAAG
Found at i:29580442 original size:21 final size:21
Alignment explanation
Indices: 29580416--29580462 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
29580406 TGTGGGTGTC
29580416 CACACGCCCATGTGAAGGCCA
1 CACACGCCCATGTGAAGGCCA
** *
29580437 CACACGCCTGTGTGGAGGCCA
1 CACACGCCCATGTGAAGGCCA
*
29580458 TACAC
1 CACAC
29580463 TTCCGTGTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.36, G:0.26, T:0.13
Consensus pattern (21 bp):
CACACGCCCATGTGAAGGCCA
Found at i:29580774 original size:62 final size:63
Alignment explanation
Indices: 29580699--29580818 Score: 215
Period size: 64 Copynumber: 1.9 Consensus size: 63
29580689 CACATGGCTG
29580699 TGTGGCACCAAAAATCA-CAAAAAGCCTAATTCCCAATTTCACATGACCGTGTGGACCATCTA
1 TGTGGCACCAAAAATCACCAAAAAGCCTAATTCCCAATTTCACATGACCGTGTGGACCATCTA
*
29580761 TGTGGCACCAAAAATCACCCAAAAAGCCTAATTCCCAATTTCACATGGCCGTGTGGAC
1 TGTGGCACCAAAAATCA-CCAAAAAGCCTAATTCCCAATTTCACATGACCGTGTGGAC
29580819 TGCCCATGTG
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
62 17 0.31
64 38 0.69
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (63 bp):
TGTGGCACCAAAAATCACCAAAAAGCCTAATTCCCAATTTCACATGACCGTGTGGACCATCTA
Found at i:29591143 original size:18 final size:19
Alignment explanation
Indices: 29591105--29591145 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
29591095 ACTAGTTGGG
* *
29591105 AAATTTTGCAATTTCTCTA
1 AAATTTTGAAATATCTCTA
29591124 AAATTTTGAAATAT-TCTA
1 AAATTTTGAAATATCTCTA
29591142 AAAT
1 AAAT
29591146 AATTCCTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATTTTGAAATATCTCTA
Found at i:29591688 original size:17 final size:20
Alignment explanation
Indices: 29591672--29591716 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
29591662 TGATTCGATC
29591672 AATTTTGGG-TCTCGATCCT
1 AATTTTGGGTTCTCGATCCT
* *
29591691 GATTTTGGGTTCTCGATTCT
1 AATTTTGGGTTCTCGATCCT
29591711 AATTTT
1 AATTTT
29591717 CGATCTAAAG
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:0.16, C:0.16, G:0.20, T:0.49
Consensus pattern (20 bp):
AATTTTGGGTTCTCGATCCT
Found at i:29591738 original size:13 final size:13
Alignment explanation
Indices: 29591722--29591746 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29591712 ATTTTCGATC
29591722 TAAAGTTCAATTT
1 TAAAGTTCAATTT
29591735 TAAAGTTCAATT
1 TAAAGTTCAATT
29591747 ACCTATTGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TAAAGTTCAATTT
Found at i:29596106 original size:25 final size:26
Alignment explanation
Indices: 29596067--29596138 Score: 103
Period size: 25 Copynumber: 2.8 Consensus size: 26
29596057 CAAGCCCATT
29596067 TTCACAGCTCGTGTAAGCATACT-GA
1 TTCACAGCTCGTGTAAGCATACTCGA
* *
29596092 TTTACAGCTCATGTAAGCATA-TCGA
1 TTCACAGCTCGTGTAAGCATACTCGA
*
29596117 TTCACAGCTCGTGTGAGCATAC
1 TTCACAGCTCGTGTAAGCATAC
29596139 ATGTACAGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
24 1 0.03
25 39 0.98
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (26 bp):
TTCACAGCTCGTGTAAGCATACTCGA
Found at i:29600491 original size:12 final size:12
Alignment explanation
Indices: 29600474--29600502 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
29600464 ATAGGGACAC
29600474 AAACATGAACCT
1 AAACATGAACCT
29600486 AAACATGAACCT
1 AAACATGAACCT
29600498 AAACA
1 AAACA
29600503 CATTTACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.55, C:0.24, G:0.07, T:0.14
Consensus pattern (12 bp):
AAACATGAACCT
Found at i:29603697 original size:39 final size:40
Alignment explanation
Indices: 29603605--29603710 Score: 196
Period size: 40 Copynumber: 2.7 Consensus size: 40
29603595 ACATAGTCGG
*
29603605 TTTAGTAACTCGCACAAATGCCTTCGAGACTTAACCCGGA
1 TTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
29603645 TTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCC-GA
1 TTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
29603684 TTTAGTAACTCGCACAAATGCCTTCGG
1 TTTAGTAACTCGCACAAATGCCTTCGG
29603711 ATCTTGCATT
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
39 29 0.45
40 36 0.55
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (40 bp):
TTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
Found at i:29608152 original size:27 final size:27
Alignment explanation
Indices: 29608119--29608294 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
29608109 TATATAAGTC
* *
29608119 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
29608146 CGCACACTTAGTGCTACGTAATCAA-T
1 CGCACACTTAGTGCTACATAATCAACT
29608172 CGCAACACTTAGTGCTACATAATC-ACT
1 CGC-ACACTTAGTGCTACATAATCAACT
** ** *
29608199 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
29608226 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
29608253 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
29608280 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29608295 GTACAATTTA
Statistics
Matches: 127, Mismatches: 17, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
26 21 0.17
27 105 0.83
28 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:29608260 original size:80 final size:81
Alignment explanation
Indices: 29608140--29608293 Score: 206
Period size: 80 Copynumber: 1.9 Consensus size: 81
29608130 TGCTATATAA
* * *
29608140 TCAACTCGCACACTTAGTGCTACGTAATCAATCGCAACACTTAGTGCTACATAATC-ACTCGCAC
1 TCAACTCGCACACTTAGTGCTACATAATCAATCGCAACACTTAGTGCAACATAATCAAATCGCAC
29608204 ACTTAGTGCCGCATGG
66 ACTTAGTGCCGCATGG
* * * *
29608220 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGC-ACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCTA-CATAATCA-ATCGCAACACTTAGTGCAACATAATCAAATCGC
29608283 ACACTTAGTGC
64 ACACTTAGTGC
29608294 TGTACAATTT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 1 0.02
80 43 0.67
81 20 0.31
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAATCGCAACACTTAGTGCAACATAATCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:29616256 original size:27 final size:27
Alignment explanation
Indices: 29616224--29616400 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29616214 TATATTAGTC
* *
29616224 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
29616251 CGCACACTTAGTGCTACGTAATCAA-T
1 CGCACACTTAGTGCTACATAATCAACT
29616277 CGCACACTTAGTGCTACATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
** ** *
29616304 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
29616331 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
29616358 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
29616385 CGCACACTTAGTGCTA
1 CGCACACTTAGTGCTA
29616401 TACAATTTAA
Statistics
Matches: 130, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
26 25 0.19
27 104 0.80
28 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:29621118 original size:29 final size:30
Alignment explanation
Indices: 29621076--29621262 Score: 99
Period size: 29 Copynumber: 6.4 Consensus size: 30
29621066 ACCATAAAAT
*
29621076 TATGACAAGGGATGGTGACGACCATCAATA
1 TATGAAAAGGGATGGTGACGACCATCAATA
29621106 T-TGAAAAGGGA---TGACGACCAT-AGA-A
1 TATGAAAAGGGATGGTGACGACCATCA-ATA
* *** * *
29621131 CTATGAAAAGGGATAGTTTTGACTATTTAAT-
1 -TATGAAAAGGGATGGTGACGACCA-TCAATA
* ** * *
29621162 TATGAAAAGGGATAGCT-TTGGCTATCAA-A
1 TATGAAAAGGGAT-GGTGACGACCATCAATA
* * * *
29621191 TTATGAAAAGGAATGGTGATGAGCATCAA-C
1 -TATGAAAAGGGATGGTGACGACCATCAATA
*
29621221 TATGAAAAGGGATGGTGACGA-CATCAAAA
1 TATGAAAAGGGATGGTGACGACCATCAATA
29621250 TATGAAAAGGGAT
1 TATGAAAAGGGAT
29621263 AGCTTCGACT
Statistics
Matches: 124, Mismatches: 19, Indels: 29
0.72 0.11 0.17
Matches are distributed among these distances:
25 2 0.02
26 12 0.10
27 10 0.08
28 6 0.05
29 46 0.37
30 44 0.35
31 3 0.02
32 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (30 bp):
TATGAAAAGGGATGGTGACGACCATCAATA
Found at i:29621124 original size:26 final size:27
Alignment explanation
Indices: 29621091--29621144 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
29621081 CAAGGGATGG
29621091 TGACGACCAT-CAA-TATTGAAAAGGGA
1 TGACGACCATACAACTA-TGAAAAGGGA
*
29621117 TGACGACCATAGAACTATGAAAAGGGA
1 TGACGACCATACAACTATGAAAAGGGA
29621144 T
1 T
29621145 AGTTTTGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 10 0.40
27 13 0.52
28 2 0.08
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.19
Consensus pattern (27 bp):
TGACGACCATACAACTATGAAAAGGGA
Found at i:29621168 original size:30 final size:30
Alignment explanation
Indices: 29621132--29621288 Score: 117
Period size: 30 Copynumber: 5.3 Consensus size: 30
29621122 ACCATAGAAC
* **
29621132 TATGAAAAGGGATAGTTTTGACTATTTAAT
1 TATGAAAAGGGATAGCTTTGACTATCAAAT
*
29621162 TATGAAAAGGGATAGCTTTGGCTATCAAAT
1 TATGAAAAGGGATAGCTTTGACTATCAAAT
* * * *
29621192 TATGAAAAGGAAT-GGTGATGAGC-ATC-AAC
1 TATGAAAAGGGATAGCT-TTGA-CTATCAAAT
* ** *
29621221 TATGAAAAGGGAT-GGTGACGAC-ATCAAAA
1 TATGAAAAGGGATAGCT-TTGACTATCAAAT
* *
29621250 TATGAAAAGGGATAGCTTCGACTATCGAAT
1 TATGAAAAGGGATAGCTTTGACTATCAAAT
29621280 TATGGAAAA
1 TAT-GAAAA
29621289 AGATGGTCAC
Statistics
Matches: 105, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
28 4 0.04
29 42 0.40
30 53 0.50
31 6 0.06
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (30 bp):
TATGAAAAGGGATAGCTTTGACTATCAAAT
Found at i:29621227 original size:116 final size:116
Alignment explanation
Indices: 29621020--29621288 Score: 319
Period size: 116 Copynumber: 2.3 Consensus size: 116
29621010 TCAACCAATA
* * *
29621020 AAAAGGAATAGCTTCGACTATCGAGTTATGAAAAGGGATAGCTTCAACCATAAAATTATGACAAG
1 AAAAGGGATAGCTTCGACTATCGAATTATGAAAAGGGATAGCTTCAACCATAAAATTATGAAAAG
* *
29621085 GGATGGTGACGACCATCAATATTGAAAAGGGA-TGACGACCAT-AGAACTATG
66 GAATGGTGACGACCATCAATATTGAAAAGGGAGTGACGA-CATCA-AAATATG
* * ** *** * *
29621136 AAAAGGGATAGTTTTGACTATTTAATTATGAAAAGGGATAGCTTTGGCTATCAAATTATGAAAAG
1 AAAAGGGATAGCTTCGACTATCGAATTATGAAAAGGGATAGCTTCAACCATAAAATTATGAAAAG
* *
29621201 GAATGGTGATGAGCATCAACTA-TGAAAAGGGATGGTGACGACATCAAAATATG
66 GAATGGTGACGACCATCAA-TATTGAAAAGGGA--GTGACGACATCAAAATATG
29621254 AAAAGGGATAGCTTCGACTATCGAATTATGGAAAA
1 AAAAGGGATAGCTTCGACTATCGAATTAT-GAAAA
29621289 AGATGGTCAC
Statistics
Matches: 127, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
116 79 0.62
117 2 0.02
118 34 0.27
119 12 0.09
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (116 bp):
AAAAGGGATAGCTTCGACTATCGAATTATGAAAAGGGATAGCTTCAACCATAAAATTATGAAAAG
GAATGGTGACGACCATCAATATTGAAAAGGGAGTGACGACATCAAAATATG
Found at i:29621246 original size:28 final size:30
Alignment explanation
Indices: 29621185--29621262 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 30
29621175 AGCTTTGGCT
* * *
29621185 ATCAAATTATGAAAAGGAATGGTGATGAGC
1 ATCAAAATATGAAAAGGGATGGTGACGAGC
*
29621215 ATC-AACTATGAAAAGGGATGGTGACGA-C
1 ATCAAAATATGAAAAGGGATGGTGACGAGC
29621243 ATCAAAATATGAAAAGGGAT
1 ATCAAAATATGAAAAGGGAT
29621263 AGCTTCGACT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 4 0.09
29 36 0.84
30 3 0.07
ACGTcount: A:0.45, C:0.09, G:0.26, T:0.21
Consensus pattern (30 bp):
ATCAAAATATGAAAAGGGATGGTGACGAGC
Found at i:29621271 original size:29 final size:29
Alignment explanation
Indices: 29621020--29621271 Score: 94
Period size: 30 Copynumber: 8.6 Consensus size: 29
29621010 TCAACCAATA
* * **
29621020 AAAAGGAATAGCTTCGACTATCGAGTTATG
1 AAAAGGGATAGCTTCGAC-ATCAAAATATG
*
29621050 AAAAGGGATAGCTTCAACCAT-AAAATTATG
1 AAAAGGGATAGCTTCGA-CATCAAAA-TATG
* * * *
29621080 ACAAGGGAT-GGTGACGACCATCAATAT-TG
1 AAAAGGGATAGCT-TCGA-CATCAAAATATG
* *
29621109 AAAAGGGAT-G--ACGACCAT-AGAACTATG
1 AAAAGGGATAGCTTCGA-CATCA-AAATATG
* * ** *
29621136 AAAAGGGATAGTTTTGACTATTTAATTATG
1 AAAAGGGATAGCTTCGAC-ATCAAAATATG
* * *
29621166 AAAAGGGATAGCTTTGGCTATCAAATTATG
1 AAAAGGGATAGCTTCGAC-ATCAAAATATG
* * *
29621196 AAAAGGAAT-GGTGAT-GAGCATC-AACTATG
1 AAAAGGGATAGCT--TCGA-CATCAAAATATG
* *
29621225 AAAAGGGAT-GGTGACGACATCAAAATATG
1 AAAAGGGATAGCT-TCGACATCAAAATATG
29621254 AAAAGGGATAGCTTCGAC
1 AAAAGGGATAGCTTCGAC
29621272 TATCGAATTA
Statistics
Matches: 174, Mismatches: 31, Indels: 35
0.73 0.13 0.15
Matches are distributed among these distances:
25 1 0.01
26 10 0.06
27 11 0.06
28 5 0.03
29 55 0.32
30 86 0.49
31 6 0.03
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (29 bp):
AAAAGGGATAGCTTCGACATCAAAATATG
Found at i:29623900 original size:20 final size:20
Alignment explanation
Indices: 29623847--29623904 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
29623837 ATGCCTCTGT
*
29623847 TTGCACTTTAGTGCCCCTGA
1 TTGCACTTTAGTGCTCCTGA
* *
29623867 TCGCA-TATTCGTGCTCCTGA
1 TTGCACT-TTAGTGCTCCTGA
*
29623887 TTGCACTTTGGTGCTCCT
1 TTGCACTTTAGTGCTCCT
29623905 ATTATGCATC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.12, C:0.29, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCACTTTAGTGCTCCTGA
Found at i:29640568 original size:27 final size:27
Alignment explanation
Indices: 29640507--29640571 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
29640497 GTCGAATGAT
*
29640507 TGAAATACCCCCATAGGGTAAAATAAC
1 TGAAATACCCTCATAGGGTAAAATAAC
*
29640534 TGAAATACCCTCATAGGGTAAAATGAC
1 TGAAATACCCTCATAGGGTAAAATAAC
**
29640561 TGTTATACCCT
1 TGAAATACCCT
29640572 TCAGAGATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (27 bp):
TGAAATACCCTCATAGGGTAAAATAAC
Found at i:29640826 original size:26 final size:26
Alignment explanation
Indices: 29640794--29640857 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
29640784 TTTGCCACAT
* *
29640794 ATACTATTACTGGTAGCTTTACTGCG
1 ATACTATTACTGGCAGCTTTACTACG
*
29640820 ATACTATTACTGGCAGCTTTACTACT
1 ATACTATTACTGGCAGCTTTACTACG
29640846 ATACTATTACTG
1 ATACTATTACTG
29640858 ACAAATTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTACTACG
Found at i:29640870 original size:26 final size:26
Alignment explanation
Indices: 29640793--29640870 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 26
29640783 TTTTGCCACA
** ** *
29640793 TATACTATTACTGGTAGCTTTACTGC
1 TATACTATTACTGACAAATTTACTAC
* * **
29640819 GATACTATTACTGGCAGCTTTACTAC
1 TATACTATTACTGACAAATTTACTAC
*
29640845 TATACTATTACTGACAAATTTGCTAC
1 TATACTATTACTGACAAATTTACTAC
29640871 GATATTGGTG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (26 bp):
TATACTATTACTGACAAATTTACTAC
Found at i:29641023 original size:28 final size:28
Alignment explanation
Indices: 29640981--29641069 Score: 135
Period size: 28 Copynumber: 3.2 Consensus size: 28
29640971 CACTGCATTG
29640981 TACTGTATTGGGCTAAGGCCCACACTGA
1 TACTGTATTGGGCTAAGGCCCACACTGA
*
29641009 TTCTGTATTGGGCTAAGGCCCACACTGA
1 TACTGTATTGGGCTAAGGCCCACACTGA
* * *
29641037 TACTGTATTAGGATAAGGCTCACACT-A
1 TACTGTATTGGGCTAAGGCCCACACTGA
29641064 TACTGT
1 TACTGT
29641070 CACTGAGTAG
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 7 0.12
28 49 0.88
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCCACACTGA
Found at i:29646188 original size:7 final size:7
Alignment explanation
Indices: 29646178--29646202 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29646168 AAATATTTTT
29646178 AAATTGA
1 AAATTGA
29646185 AAATTGA
1 AAATTGA
29646192 AAATTGA
1 AAATTGA
29646199 AAAT
1 AAAT
29646203 AGTTACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (7 bp):
AAATTGA
Found at i:29649120 original size:20 final size:20
Alignment explanation
Indices: 29649095--29649142 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
29649085 GAACATTTGG
29649095 GAGCAAAAGGAGTGAAATAC
1 GAGCAAAAGGAGTGAAATAC
29649115 GAGCAAAAGGAGTGAAATAC
1 GAGCAAAAGGAGTGAAATAC
29649135 GAGCAAAA
1 GAGCAAAA
29649143 ATCGGAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.52, C:0.10, G:0.29, T:0.08
Consensus pattern (20 bp):
GAGCAAAAGGAGTGAAATAC
Found at i:29653152 original size:338 final size:342
Alignment explanation
Indices: 29652523--29653216 Score: 1270
Period size: 338 Copynumber: 2.0 Consensus size: 342
29652513 TTTAAGGGCC
29652523 GAAACCAAAAGTACTAAGAATGATGGGGATAAAATGGGGCAACGGTACTCCCTTTTTTCAGATGA
1 GAAACCAAAAGTACTAAGAATGATGGGGATAAAATGGGGCAACGGTACTCCC----TT---AT--
29652588 ATTTTGTAAACCGATACGATAATACCACTAAGAGAGCAAGAGCATATTCGGCCAAGTATCCTCAA
57 ATTTTGTAAACCGATACGATAATACCACTAAGAGAGCAAGAGCATATTCGGCCAAGTATCCTCAA
29652653 AAGAGAAGGACGAAGAACGGAGACTAGTATTCGACAAGGGTAGAGAATAAAAATGTAAGAACTAT
122 AAGAGAAGGACGAAGAACGGAGACTAGTATTCGACAAGGGTAGAGAATAAAAATGTAAGAACTAT
29652718 TGAAAGAAGAGGAGAATGAGAATGGAGGAGAGGAAACGAGAAGAGTAAAGATCCGGCCAGAGAAT
187 TGAAAGAAGAGGAGAATGAGAATGGAGGAGAGGAAACGAGAAGAGTAAAGATCCGGCCAGAGAAT
29652783 GTGGAGAGATTAAGAACACTTAAAGAGTATACAGTTAAGGCTCAGACAGAAAGAGGAGGAGCAAA
252 GTGGAGAGATTAAGAACACTTAAAGAGTATACAGTTAAGGCTCAGACAGAAAGAGGAGGAGCAAA
29652848 GTTCAGCTTTGGCACATAAAAGGATT
317 GTTCAGCTTTGGCACATAAAAGGATT
29652874 GAAACCAAAAGTACTAAGAATGATGGGGATAAAATGGGGCAACGGTACTCCC-T-T-TTTT-TAA
1 GAAACCAAAAGTACTAAGAATGATGGGGATAAAATGGGGCAACGGTACTCCCTTATATTTTGTAA
29652935 ACCGATACGATAATACCACTAAGAGAGCAAGAGCATATTCGGCCAAGTATCCTCAAAAGAGAAGG
66 ACCGATACGATAATACCACTAAGAGAGCAAGAGCATATTCGGCCAAGTATCCTCAAAAGAGAAGG
29653000 ACGAAGAACGGAGACTAGTATTCGACAAGGGTAGAGAATAAAAATGTAAGAACTATTGAAAGAAG
131 ACGAAGAACGGAGACTAGTATTCGACAAGGGTAGAGAATAAAAATGTAAGAACTATTGAAAGAAG
*
29653065 AGGAGAATGAGAATGGAGGAGAGGAAACGAGAAGAGTAAAGATTCGGCCAGAGAATGTGGAGAGA
196 AGGAGAATGAGAATGGAGGAGAGGAAACGAGAAGAGTAAAGATCCGGCCAGAGAATGTGGAGAGA
29653130 TTAAGAACACTTAAAGAGTATACAGTTAAGGCTCAGACAGAAAGAGGAGGAGCAAAGTTCAGCTT
261 TTAAGAACACTTAAAGAGTATACAGTTAAGGCTCAGACAGAAAGAGGAGGAGCAAAGTTCAGCTT
29653195 TGGCACATAAAAGGATT
326 TGGCACATAAAAGGATT
29653212 GAAAC
1 GAAAC
29653217 AAAGTAAGGT
Statistics
Matches: 342, Mismatches: 1, Indels: 13
0.96 0.00 0.04
Matches are distributed among these distances:
338 284 0.83
339 4 0.01
342 1 0.00
346 1 0.00
351 52 0.15
ACGTcount: A:0.42, C:0.13, G:0.27, T:0.18
Consensus pattern (342 bp):
GAAACCAAAAGTACTAAGAATGATGGGGATAAAATGGGGCAACGGTACTCCCTTATATTTTGTAA
ACCGATACGATAATACCACTAAGAGAGCAAGAGCATATTCGGCCAAGTATCCTCAAAAGAGAAGG
ACGAAGAACGGAGACTAGTATTCGACAAGGGTAGAGAATAAAAATGTAAGAACTATTGAAAGAAG
AGGAGAATGAGAATGGAGGAGAGGAAACGAGAAGAGTAAAGATCCGGCCAGAGAATGTGGAGAGA
TTAAGAACACTTAAAGAGTATACAGTTAAGGCTCAGACAGAAAGAGGAGGAGCAAAGTTCAGCTT
TGGCACATAAAAGGATT
Found at i:29654647 original size:11 final size:11
Alignment explanation
Indices: 29654631--29654655 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29654621 TAGAAAACGA
29654631 ACAAATGCAAT
1 ACAAATGCAAT
29654642 ACAAATGCAAT
1 ACAAATGCAAT
29654653 ACA
1 ACA
29654656 TCCAGAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.20, G:0.08, T:0.16
Consensus pattern (11 bp):
ACAAATGCAAT
Found at i:29657204 original size:29 final size:29
Alignment explanation
Indices: 29657141--29657208 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
29657131 TAATCAACCG
29657141 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
29657170 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
29657199 CGCACACTTA
1 CGCACACTTA
29657209 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:29657320 original size:174 final size:174
Alignment explanation
Indices: 29657030--29657357 Score: 620
Period size: 174 Copynumber: 1.9 Consensus size: 174
29657020 AACTCAAGGT
* *
29657030 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
29657095 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
29657160 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
29657204 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
29657269 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
29657334 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
29657358 TGTACAATTT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:29657349 original size:29 final size:30
Alignment explanation
Indices: 29657310--29657388 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
29657300 CTTAATAATC
29657310 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
29657340 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
29657369 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
29657389 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:29660991 original size:24 final size:24
Alignment explanation
Indices: 29660901--29661010 Score: 103
Period size: 24 Copynumber: 4.6 Consensus size: 24
29660891 CCCCTCGAGG
* * * *
29660901 TTAAATGATTGTTTTGCCTATGAT
1 TTAAATGACTGATTTGTCTGTGAT
* * * * *
29660925 GTAAATGAATGATTTTTCCGAGAT
1 TTAAATGACTGATTTGTCTGTGAT
*
29660949 GTAAATGACTGATTTGTCTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
*
29660973 TTAAATGACTGATTTGTCTTTGAT
1 TTAAATGACTGATTTGTCTGTGAT
**
29660997 TTGTATGACTGATT
1 TTAAATGACTGATT
29661011 CCGTGTAGGG
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.45
Consensus pattern (24 bp):
TTAAATGACTGATTTGTCTGTGAT
Found at i:29661294 original size:64 final size:64
Alignment explanation
Indices: 29661182--29661370 Score: 200
Period size: 64 Copynumber: 3.0 Consensus size: 64
29661172 GCTGCGATGC
* * * * ** **
29661182 TATTGATGGATT-TGTGCAGATCATATTACCATTATTGGTGGCCGTGTGCCAATCATATTACCAT
1 TATTGATGG-TTGTGTGCCGATCATATTACTACTACTAATGGCTTTGTGCCAATCATATTACCAT
* * * ** * **
29661246 TATTGATGGTTGTGTGCTGATCATATTACTTCTACTAATTGCTTTGTGCTGATCATACTAATAT
1 TATTGATGGTTGTGTGCCGATCATATTACTACTACTAATGGCTTTGTGCCAATCATATTACCAT
* *
29661310 TATTGATGGTTGTGTGCCGATCATATTACTACTACTGATGGCTTTGTGCCAATCATTTTAC
1 TATTGATGGTTGTGTGCCGATCATATTACTACTACTAATGGCTTTGTGCCAATCATATTAC
29661371 TGTACTTATG
Statistics
Matches: 100, Mismatches: 24, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
63 2 0.02
64 98 0.98
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.41
Consensus pattern (64 bp):
TATTGATGGTTGTGTGCCGATCATATTACTACTACTAATGGCTTTGTGCCAATCATATTACCAT
Found at i:29661326 original size:32 final size:32
Alignment explanation
Indices: 29661182--29661370 Score: 143
Period size: 32 Copynumber: 5.9 Consensus size: 32
29661172 GCTGCGATGC
*
29661182 TATTGATGGATT-TGTGCAGATCATATTACCAT
1 TATTGATGG-TTGTGTGCCGATCATATTACCAT
* ** *
29661214 TATTGGTGGCCGTGTGCCAATCATATTACCAT
1 TATTGATGGTTGTGTGCCGATCATATTACCAT
* *
29661246 TATTGATGGTTGTGTGCTGATCATATTA-CTT
1 TATTGATGGTTGTGTGCCGATCATATTACCAT
* * * * * **
29661277 CTACTAATTGCTT-TGTGCTGATCATACTAATAT
1 -TATTGA-TGGTTGTGTGCCGATCATATTACCAT
* *
29661310 TATTGATGGTTGTGTGCCGATCATATTACTAC
1 TATTGATGGTTGTGTGCCGATCATATTACCAT
* * *
29661342 TACTGATGGCTT-TGTGCCAATCATTTTAC
1 TATTGATGG-TTGTGTGCCGATCATATTAC
29661371 TGTACTTATG
Statistics
Matches: 124, Mismatches: 27, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
31 6 0.05
32 111 0.90
33 7 0.06
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.41
Consensus pattern (32 bp):
TATTGATGGTTGTGTGCCGATCATATTACCAT
Found at i:29661365 original size:96 final size:96
Alignment explanation
Indices: 29661192--29661371 Score: 218
Period size: 96 Copynumber: 1.9 Consensus size: 96
29661182 TATTGATGGA
* * * * *
29661192 TTTGTGCAGATCATATTACCATTATTGGTGGCCGTGTGCCAATCATATTACCATTATTGATGGTT
1 TTTGTGCAGATCATACTAACATTATTGATGGCCGTGTGCCAATCATATTACCACTACTGATGGTT
**
29661257 GTGTGCTGATCATATTACTTCTACTAATTGC
66 GTGTGCCAATCATATTACTTCTACTAATTGC
* * ** * *
29661288 TTTGTGCTGATCATACTAATATTATTGATGGTTGTGTGCCGATCATATTACTACTACTGATGGCT
1 TTTGTGCAGATCATACTAACATTATTGATGGCCGTGTGCCAATCATATTACCACTACTGATGG-T
*
29661353 T-TGTGCCAATCATTTTACT
65 TGTGTGCCAATCATATTACT
29661372 GTACTTATGG
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
96 67 0.97
97 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (96 bp):
TTTGTGCAGATCATACTAACATTATTGATGGCCGTGTGCCAATCATATTACCACTACTGATGGTT
GTGTGCCAATCATATTACTTCTACTAATTGC
Found at i:29661406 original size:22 final size:22
Alignment explanation
Indices: 29661376--29661422 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
29661366 TTTACTGTAC
* *
29661376 TTATGGCTTATAGCCATTCTAT
1 TTATAGCTTATAGCCATCCTAT
*
29661398 TTATAGCTTATAGCTATCCTAT
1 TTATAGCTTATAGCCATCCTAT
29661420 TTA
1 TTA
29661423 CGGCTCTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.47
Consensus pattern (22 bp):
TTATAGCTTATAGCCATCCTAT
Found at i:29664367 original size:21 final size:23
Alignment explanation
Indices: 29664326--29664373 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
29664316 TATTAACCTT
*
29664326 TTAACTTTATAATAATAAT-AAA
1 TTAACTTTATAAAAATAATAAAA
29664348 TTAAC-TTATAAAACAT-ATAAAA
1 TTAACTTTATAAAA-ATAATAAAA
29664370 TTAA
1 TTAA
29664374 AATATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAACTTTATAAAAATAATAAAA
Found at i:29667090 original size:14 final size:15
Alignment explanation
Indices: 29667068--29667100 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
29667058 ATGATATTTC
*
29667068 TATTATTTTTAGTAT
1 TATTATTTTTACTAT
29667083 TATT-TTTTTACTAT
1 TATTATTTTTACTAT
29667097 TATT
1 TATT
29667101 CTTACTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (15 bp):
TATTATTTTTACTAT
Found at i:29667105 original size:12 final size:12
Alignment explanation
Indices: 29667067--29667110 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
29667057 TATGATATTT
29667067 CTATTATTTTTA
1 CTATTATTTTTA
*
29667079 GTATTATTTTTTTA
1 CTATTA--TTTTTA
*
29667093 CTATTATTCTTA
1 CTATTATTTTTA
29667105 CTATTA
1 CTATTA
29667111 CCTTTAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 16 0.59
14 11 0.41
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (12 bp):
CTATTATTTTTA
Found at i:29667159 original size:6 final size:6
Alignment explanation
Indices: 29667144--29667192 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
29667134 ATTGATTTTA
* *
29667144 TTTC-T TTTCAT TTTCAT TTTCAT TTTC-T TTTTAT CTTT-AT TTTTAT
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT -TTTCAT TTTCAT
29667190 TTT
1 TTT
29667193 TGTTTTAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 11 0.28
6 25 0.64
7 3 0.08
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTCAT
Found at i:29667174 original size:23 final size:23
Alignment explanation
Indices: 29667144--29667192 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
29667134 ATTGATTTTA
29667144 TTTCTTTTCAT-TTTCATTTTCAT
1 TTTCTTTTCATCTTT-ATTTTCAT
* *
29667167 TTTCTTTTTATCTTTATTTTTAT
1 TTTCTTTTCATCTTTATTTTCAT
29667190 TTT
1 TTT
29667193 TGTTTTAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTCTTTTCATCTTTATTTTCAT
Found at i:29667175 original size:12 final size:11
Alignment explanation
Indices: 29667139--29667192 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 11
29667129 TCATCATTGA
29667139 TTTTA-TTTCT
1 TTTTATTTTCT
*
29667149 TTTCATTTTCAT
1 TTTTATTTTC-T
*
29667161 TTTCATTTTCT
1 TTTTATTTTCT
*
29667172 TTTTATCTTTAT
1 TTTTAT-TTTCT
29667184 TTTTATTTT
1 TTTTATTTT
29667193 TGTTTTAGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
10 4 0.11
11 13 0.34
12 21 0.55
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTATTTTCT
Found at i:29667198 original size:23 final size:25
Alignment explanation
Indices: 29667159--29667222 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 25
29667149 TTTCATTTTC
*
29667159 ATTTTCATTTTCTTTTTA-T-CTTT
1 ATTTTTATTTTCTTTTTAGTACTTT
29667182 ATTTTTATTTT-TGTTTTAGTTACTTT
1 ATTTTTATTTTCT-TTTTAG-TACTTT
*
29667208 ATTTTTTATCTTCTT
1 A-TTTTTATTTTCTT
29667223 AGGCTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
22 1 0.03
23 15 0.45
25 1 0.03
26 5 0.15
27 10 0.30
28 1 0.03
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.73
Consensus pattern (25 bp):
ATTTTTATTTTCTTTTTAGTACTTT
Found at i:29675707 original size:340 final size:341
Alignment explanation
Indices: 29673675--29675720 Score: 3914
Period size: 341 Copynumber: 6.0 Consensus size: 341
29673665 AACTACTTAT
29673675 ACAGTAAATCATTGTCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
1 ACAGTAAATCATTGTCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
29673740 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTCTTTTTTTTAC
66 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTCTTTTTTTTAC
29673805 GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
131 GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
29673870 TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAAGGTTAGAAAAACAGGATGCA
196 TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAAGGTTAGAAAAACAGGATGCA
29673935 ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGGAATGAAAA
261 ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGGAATGAAAA
29674000 TAAACCTAAACATTAA
326 TAAACCTAAACATTAA
29674016 ACAGTAAATCATTGTCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
1 ACAGTAAATCATTGTCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
*
29674081 AAACTTGACGTCGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTCTTTTTTTTAC
66 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTCTTTTTTTTAC
29674146 GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
131 GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
*
29674211 TAATCGAGTTATAAATATAAGAAAATTCACAGCCGTGAGCTTAAAGGTTAGAAAAACAGGATGCA
196 TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAAGGTTAGAAAAACAGGATGCA
29674276 ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGGAATGAAAA
261 ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGGAATGAAAA
29674341 TAAACCTAAACATTAA
326 TAAACCTAAACATTAA
29674357 ACAGTAAATCATTGTCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
1 ACAGTAAATCATTGTCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
*
29674422 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTATTTTTTTTAC
66 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTCTTTTTTTTAC
*
29674487 ATTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
131 GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
* *
29674552 TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAACGTTAGAAAAATAGGATGCA
196 TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAAGGTTAGAAAAACAGGATGCA
*
29674617 ACAATTTTATTAATCACCAGTTTACTAAAAACAAATAGTTGAGATGCTGATAATTGGAATGAAAA
261 ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGGAATGAAAA
*
29674682 TAACCCTAAACATTAA
326 TAAACCTAAACATTAA
*
29674698 ACAGTAAATCATTGTCGATCAATCATTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
1 ACAGTAAATCATTGTCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
29674763 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTCTTTTTTTTAC
66 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTCTTTTTTTTAC
29674828 GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
131 GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
*
29674893 TAATCGAGTTATAAATATAAGAAAATTCACAGCCGTGAGCTTAAAGGTTAGAAAAACAGGATGCA
196 TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAAGGTTAGAAAAACAGGATGCA
29674958 ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGGAATGAAAA
261 ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGGAATGAAAA
29675023 TAAACCTAAACATTAA
326 TAAACCTAAACATTAA
29675039 ACAGTAAATCATTGTCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
1 ACAGTAAATCATTGTCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
29675104 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTCTTTTTTTTAC
66 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTCTTTTTTTTAC
29675169 GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
131 GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
* *
29675234 TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAACGTTAGAAAAATAGGATGCA
196 TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAAGGTTAGAAAAACAGGATGCA
29675299 ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGGAATGAAAA
261 ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGGAATGAAAA
*
29675364 TAACCCTAAACATTAA
326 TAAACCTAAACATTAA
*
29675380 ACAGTAAATCATTGTCAATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
1 ACAGTAAATCATTGTCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
29675445 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTC-TTTTTTTAC
66 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTCTTTTTTTTAC
*
29675509 GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCTTGAATTGAAACT
131 GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
29675574 TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAAGGTTAGAAAAACAGGATGCA
196 TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAAGGTTAGAAAAACAGGATGCA
* * *
29675639 ACAATTTTATTAATCACTAGTTTACTAAAAGCAAATAGTTGAAAAGCTGATAATTGGAATGAAAA
261 ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGGAATGAAAA
*
29675704 TAACCCTAAACATTAA
326 TAAACCTAAACATTAA
29675720 A
1 A
29675721 TAGTCAAGGC
Statistics
Matches: 1675, Mismatches: 30, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
340 215 0.13
341 1460 0.87
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (341 bp):
ACAGTAAATCATTGTCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTCTTTTTTTTAC
GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAAGGTTAGAAAAACAGGATGCA
ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGGAATGAAAA
TAAACCTAAACATTAA
Found at i:29676460 original size:23 final size:23
Alignment explanation
Indices: 29676434--29676480 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
29676424 TCATTTTCAT
*
29676434 TGATCTTAATCTTGATT-TTTTGC
1 TGATCTTAATCCTG-TTGTTTTGC
29676457 TGATCTTAATCCTGTTGTTTTGC
1 TGATCTTAATCCTGTTGTTTTGC
29676480 T
1 T
29676481 TTCCTCTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (23 bp):
TGATCTTAATCCTGTTGTTTTGC
Found at i:29677723 original size:7 final size:7
Alignment explanation
Indices: 29677711--29677739 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
29677701 AACATTTAAA
29677711 TAAATTT
1 TAAATTT
29677718 TAAATTT
1 TAAATTT
29677725 TAAATTT
1 TAAATTT
29677732 TAAATTT
1 TAAATTT
29677739 T
1 T
29677740 TTAGTTAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TAAATTT
Found at i:29678655 original size:12 final size:12
Alignment explanation
Indices: 29678637--29678679 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
29678627 TGTGTTATTT
29678637 CTATTATTTTTA
1 CTATTATTTTTA
*
29678649 GTATTATTTTTTA
1 CTATTA-TTTTTA
*
29678662 CTATTATTCTTA
1 CTATTATTTTTA
*
29678674 CAATTA
1 CTATTA
29678680 CATTTAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.60
Consensus pattern (12 bp):
CTATTATTTTTA
Found at i:29678661 original size:13 final size:13
Alignment explanation
Indices: 29678637--29678669 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
29678627 TGTGTTATTT
29678637 CTATTA-TTTTTA
1 CTATTATTTTTTA
*
29678649 GTATTATTTTTTA
1 CTATTATTTTTTA
29678662 CTATTATT
1 CTATTATT
29678670 CTTACAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (13 bp):
CTATTATTTTTTA
Found at i:29678725 original size:6 final size:6
Alignment explanation
Indices: 29678714--29678774 Score: 68
Period size: 6 Copynumber: 9.7 Consensus size: 6
29678704 ATTTTATTTC
* * *
29678714 TTTTAT TTTTAT TTTTAT TTTTAT CTTTAT TTTTGT TTGTAGT TGCTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T T--TTTAT
29678765 TTTTAT TTTT
1 TTTTAT TTTT
29678775 TTAGACTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
6 39 0.85
7 2 0.04
8 2 0.04
9 3 0.07
ACGTcount: A:0.13, C:0.03, G:0.07, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:29678825 original size:5 final size:6
Alignment explanation
Indices: 29678810--29678834 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29678800 TTGAACTATG
29678810 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
29678835 GGTTGTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:29689965 original size:42 final size:42
Alignment explanation
Indices: 29689910--29690030 Score: 120
Period size: 42 Copynumber: 2.8 Consensus size: 42
29689900 TCAAATATTG
* *
29689910 ATGCCACTGTCCCAGATAGGGTCTTACACGAAAT-T-ATATACA
1 ATGCCAATGTCCCAGA-AGGGTCTTACACGAAATCTCAAAT-CA
* **
29689952 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAATTG
1 ATGCCAATGTCCCAGA-AGGGTCTTACACG-AAATCTCAAATCA
* *
29689996 ATTCCAATGTCCCAGACGTGGTCTTACACGAAATC
1 ATGCCAATGTCCCAGAAG-GGTCTTACACGAAATC
29690031 AGATATCAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
42 27 0.41
43 9 0.14
44 27 0.41
45 3 0.05
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (42 bp):
ATGCCAATGTCCCAGAAGGGTCTTACACGAAATCTCAAATCA
Found at i:29694779 original size:37 final size:37
Alignment explanation
Indices: 29694693--29694779 Score: 86
Period size: 37 Copynumber: 2.3 Consensus size: 37
29694683 ATTCTACTTT
** * * *
29694693 TTCATAATTTCACTTTTTCAATTTCAATTACTATTTAA
1 TTCA-AATTTCACTTTGCCAATTTCAATCAATATTCAA
* *
29694731 TTCAAAATTCACTTTGCCATTTTCAAGTCAATATTCAA
1 TTCAAATTTCACTTTGCCAATTTCAA-TCAATATTCAA
29694769 TT-AAATTTCAC
1 TTCAAATTTCAC
29694780 ACATATATTC
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
37 26 0.65
38 14 0.35
ACGTcount: A:0.33, C:0.18, G:0.02, T:0.46
Consensus pattern (37 bp):
TTCAAATTTCACTTTGCCAATTTCAATCAATATTCAA
Found at i:29695042 original size:51 final size:51
Alignment explanation
Indices: 29694980--29695159 Score: 213
Period size: 51 Copynumber: 3.5 Consensus size: 51
29694970 GTTCACATAT
* * *
29694980 TAGCCTACACATAGTACTACACATGTGACCATCA-CTATCCGATACACGTAG
1 TAGCCTGCACATAGTACTACACACGTGACCAT-AGCTATCCGGTACACGTAG
* ** *
29695031 TAGCCTGCACATAGTACTACACACGTGATCGA-AGCTATCCGGTATGCATAG
1 TAGCCTGCACATAGTACTACACACGTGA-CCATAGCTATCCGGTACACGTAG
* * * * *
29695082 TAGCCTGCACATAGTACTACACATGCGACC-TATCTTTCTGGTACACGTAG
1 TAGCCTGCACATAGTACTACACACGTGACCATAGCTATCCGGTACACGTAG
29695132 TAGCCTGCACATAGTACTACACACGTGA
1 TAGCCTGCACATAGTACTACACACGTGA
29695160 TCATCACTTT
Statistics
Matches: 108, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
50 41 0.38
51 65 0.60
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (51 bp):
TAGCCTGCACATAGTACTACACACGTGACCATAGCTATCCGGTACACGTAG
Found at i:29695144 original size:101 final size:101
Alignment explanation
Indices: 29694975--29695161 Score: 295
Period size: 101 Copynumber: 1.8 Consensus size: 101
29694965 TACCGGTTCA
* *
29694975 CATATTAGCCTACACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCAT-ACTATCCGATACACGTAGTAGCCTGCA
29695040 CATAGTACTACACACGTGATCGAAGCTATCCGGTATG
65 CATAGTACTACACACGTGATCGAAGCTATCCGGTATG
* * * *
29695077 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCTTTCTGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCATA-CTATCCGATACACGTAGTAGCCTGCA
29695141 CATAGTACTACACACGTGATC
65 CATAGTACTACACACGTGATC
29695162 ATCACTTTCA
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
100 1 0.01
101 45 0.58
102 32 0.41
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTACACATAGTACTACACATGCGACCATACTATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAGCTATCCGGTATG
Found at i:29697753 original size:58 final size:58
Alignment explanation
Indices: 29697688--29697956 Score: 276
Period size: 58 Copynumber: 4.6 Consensus size: 58
29697678 ACCTTAGATA
* * * * * *
29697688 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGAT-GATGACGACCATCAACT
1 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAAGGATAGCT-TCGACTATCAAAT
* * * *
29697746 ATGAAAAGGGATGGTGATTACCG-TA--GAATATGAAAAGGGATAGCTTCGACTATCAAAT
1 ATGAAAAGGGAT--AGCTT-CGGCTATCGAATATGAAAAAGGATAGCTTCGACTATCAAAT
* *
29697804 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAAGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAAGGATAGCTTCGACTATCAAAT
* * * *
29697862 GTGAAAAGGGATAGCTTCTGCTATCGAATATGAAAATGGATAGCTTCGGCTATCAAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAAGGATAGCTTCGACTATCAAAT
* * * * * *
29697920 GTGAAAAAGGATAGCTTTGGCTAGCGATTATAAAAAA
1 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAA
29697957 AGATGGTGAT
Statistics
Matches: 179, Mismatches: 25, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
55 2 0.01
56 5 0.03
58 163 0.91
59 2 0.01
60 5 0.03
61 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (58 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAAGGATAGCTTCGACTATCAAAT
Found at i:29697816 original size:29 final size:29
Alignment explanation
Indices: 29697688--29697942 Score: 248
Period size: 29 Copynumber: 8.8 Consensus size: 29
29697678 ACCTTAGATA
* *
29697688 ATGAAAAGGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCAAAT
* * * * *
29697717 ATGAAAAGGGAT-GATGACGACCATCAACT
1 ATGAAAAGGGATAGCT-TCGGCTATCAAAT
* * * *
29697746 ATGAAAAGGGATGGTGATTACCG-TA--GAAT
1 ATGAAAAGGGAT--AGCTT-CGGCTATCAAAT
*
29697775 ATGAAAAGGGATAGCTTCGACTATCAAAT
1 ATGAAAAGGGATAGCTTCGGCTATCAAAT
*
29697804 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCAAAT
* *
29697833 ATGAAAAAGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCAAAT
* * *
29697862 GTGAAAAGGGATAGCTTCTGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCAAAT
*
29697891 ATGAAAATGGATAGCTTCGGCTATCAAAT
1 ATGAAAAGGGATAGCTTCGGCTATCAAAT
* * *
29697920 GTGAAAAAGGATAGCTTTGGCTA
1 ATGAAAAGGGATAGCTTCGGCTA
29697943 GCGATTATAA
Statistics
Matches: 188, Mismatches: 30, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
26 1 0.01
27 5 0.03
28 2 0.01
29 175 0.93
31 1 0.01
32 4 0.02
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGGCTATCAAAT
Found at i:29697934 original size:87 final size:87
Alignment explanation
Indices: 29697771--29697942 Score: 274
Period size: 87 Copynumber: 2.0 Consensus size: 87
29697761 GATTACCGTA
*
29697771 GAATATGAAAAGGGATAGCTTCGACTATCAAATATGAAAAGGGATAGCTTCGGCTATCGAATATG
1 GAATATGAAAAGGGATAGCTTCGACTATCAAATATGAAAAGGGATAGCTTCGGCTATCAAATATG
29697836 AAAAAGGATAGCTTCGGCTATC
66 AAAAAGGATAGCTTCGGCTATC
* * * *
29697858 GAATGTGAAAAGGGATAGCTTCTG-CTATCGAATATGAAAATGGATAGCTTCGGCTATCAAATGT
1 GAATATGAAAAGGGATAGCTTC-GACTATCAAATATGAAAAGGGATAGCTTCGGCTATCAAATAT
*
29697922 GAAAAAGGATAGCTTTGGCTA
65 GAAAAAGGATAGCTTCGGCTA
29697943 GCGATTATAA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
87 77 0.99
88 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.26
Consensus pattern (87 bp):
GAATATGAAAAGGGATAGCTTCGACTATCAAATATGAAAAGGGATAGCTTCGGCTATCAAATATG
AAAAAGGATAGCTTCGGCTATC
Found at i:29698014 original size:30 final size:29
Alignment explanation
Indices: 29697977--29698062 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
29697967 GACCATCAGC
* * * *
29697977 TATGAAAATGGATGGTGACGACCATTGAT
1 TATGAAAAGGGATGGTTACGACCATCGAA
* *
29698006 TAATGAAAAGGGATAGTTTCGACCATCGAA
1 T-ATGAAAAGGGATGGTTACGACCATCGAA
*
29698036 TATGAAAAGGGATGGTTACAACCATCG
1 TATGAAAAGGGATGGTTACGACCATCG
29698063 TTTAGCACAC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 24 0.51
30 23 0.49
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (29 bp):
TATGAAAAGGGATGGTTACGACCATCGAA
Found at i:29698044 original size:29 final size:29
Alignment explanation
Indices: 29697688--29698048 Score: 198
Period size: 29 Copynumber: 12.4 Consensus size: 29
29697678 ACCTTAGATA
* * *
29697688 ATGAAAAGGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGTTTCGACTATCGAAT
** *
29697717 ATGAAAAGGGAT-GATGACGACCATC-AACT
1 ATGAAAAGGGATAG-TTTCGACTATCGAA-T
* ** *
29697746 ATGAAAAGGGATGGTGATT--ACCGTAGAAT
1 ATGAAAAGGGATAGT--TTCGACTATCGAAT
* *
29697775 ATGAAAAGGGATAGCTTCGACTATCAAAT
1 ATGAAAAGGGATAGTTTCGACTATCGAAT
* *
29697804 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGTTTCGACTATCGAAT
* * *
29697833 ATGAAAAAGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGTTTCGACTATCGAAT
* *
29697862 GTGAAAAGGGATAGCTTCTG-CTATCGAAT
1 ATGAAAAGGGATAGTTTC-GACTATCGAAT
* * * *
29697891 ATGAAAATGGATAGCTTCGGCTATCAAAT
1 ATGAAAAGGGATAGTTTCGACTATCGAAT
* * * * *
29697920 GTGAAAAAGGATAGCTTT-GGCTAGCGATT
1 ATGAAAAGGGATAG-TTTCGACTATCGAAT
* ** * * * *
29697949 ATAAAAAAAGATGGTGAT-GACCATC-AGCT
1 ATGAAAAGGGATAGT-TTCGACTATCGA-AT
* * ** * * *
29697978 ATGAAAATGGATGGTGACGACCATTGATT
1 ATGAAAAGGGATAGTTTCGACTATCGAAT
*
29698007 AATGAAAAGGGATAGTTTCGACCATCGAAT
1 -ATGAAAAGGGATAGTTTCGACTATCGAAT
29698037 ATGAAAAGGGAT
1 ATGAAAAGGGAT
29698049 GGTTACAACC
Statistics
Matches: 264, Mismatches: 52, Indels: 32
0.76 0.15 0.09
Matches are distributed among these distances:
27 2 0.01
28 5 0.02
29 227 0.86
30 30 0.11
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.24
Consensus pattern (29 bp):
ATGAAAAGGGATAGTTTCGACTATCGAAT
Found at i:29701586 original size:22 final size:23
Alignment explanation
Indices: 29701552--29701595 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
29701542 TAATGATGAG
*
29701552 CAAACTATGAAATAATTAAAAACA
1 CAAACTA-GAAATAACTAAAAACA
29701576 CAAACTA-AAATAACTAAAAA
1 CAAACTAGAAATAACTAAAAA
29701596 TTAATGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.66, C:0.14, G:0.02, T:0.18
Consensus pattern (23 bp):
CAAACTAGAAATAACTAAAAACA
Found at i:29703338 original size:27 final size:25
Alignment explanation
Indices: 29703308--29703357 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
29703298 TTTTGTTTAA
*
29703308 TCTCAATCTCGTTTTTCTTTTTCTCAC
1 TCTCAATCTC-TTTTT-TTCTTCTCAC
*
29703335 TCTCACTCTCTTTTTTTCTTCTC
1 TCTCAATCTCTTTTTTTCTTCTC
29703358 TCGAGTTCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 5 0.24
27 9 0.43
ACGTcount: A:0.08, C:0.32, G:0.02, T:0.58
Consensus pattern (25 bp):
TCTCAATCTCTTTTTTTCTTCTCAC
Found at i:29704318 original size:15 final size:14
Alignment explanation
Indices: 29704296--29704330 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
29704286 TTTTTTGCTT
29704296 TCACAATTTTTTTG
1 TCACAATTTTTTTG
*
29704310 TCACGAATTTTTTTT
1 TCAC-AATTTTTTTG
29704325 TCACAA
1 TCACAA
29704331 CTTGATATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (14 bp):
TCACAATTTTTTTG
Found at i:29704382 original size:11 final size:11
Alignment explanation
Indices: 29704366--29704400 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
29704356 AATGGAAACT
29704366 AATTTTTTTCG
1 AATTTTTTTCG
29704377 AATTTTTTTTCG
1 AA-TTTTTTTCG
*
29704389 AGTTTTTTTCG
1 AATTTTTTTCG
29704400 A
1 A
29704401 GAAACTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.63
Consensus pattern (11 bp):
AATTTTTTTCG
Found at i:29704385 original size:12 final size:12
Alignment explanation
Indices: 29704368--29704397 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29704358 TGGAAACTAA
29704368 TTTTTTTCGAAT
1 TTTTTTTCGAAT
*
29704380 TTTTTTTCGAGT
1 TTTTTTTCGAAT
29704392 TTTTTT
1 TTTTTT
29704398 CGAGAAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.73
Consensus pattern (12 bp):
TTTTTTTCGAAT
Found at i:29715237 original size:20 final size:20
Alignment explanation
Indices: 29715212--29715262 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
29715202 GTATTGATTT
*
29715212 GGTATCGATACT-TTTCTTAA
1 GGTATCGATA-TATTTCCTAA
29715232 GGTATCGATATATTTCCTAA
1 GGTATCGATATATTTCCTAA
29715252 GGTATCGATAT
1 GGTATCGATAT
29715263 TCCTGCTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (20 bp):
GGTATCGATATATTTCCTAA
Found at i:29734991 original size:21 final size:19
Alignment explanation
Indices: 29734962--29735000 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
29734952 GTCCTAGTTT
29734962 ATTTATGTTATAATTGTTGCA
1 ATTTATGTT-TAATT-TTGCA
*
29734983 ATTTGTGTTTAATTTTGC
1 ATTTATGTTTAATTTTGC
29735001 TAAAATCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 5 0.29
21 8 0.47
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.56
Consensus pattern (19 bp):
ATTTATGTTTAATTTTGCA
Found at i:29740270 original size:61 final size:62
Alignment explanation
Indices: 29740193--29740316 Score: 198
Period size: 61 Copynumber: 2.0 Consensus size: 62
29740183 GACAATCAAA
* *
29740193 TGTTGAACATCAAATTTGATCACCTAATTTAATTAGTTTTAAC-TTTAATTTCTAGGGGTTT
1 TGTTGAACATCAAATTTCATCACCTAATTTAATTAGTTTTAACATTTAATTTCTAGGGCTTT
*
29740254 TGTTGAAC-TCCAAATTTCATCGCCTAATTTAATTAGTTTTAACATTTAATTTCTAGGGCTTT
1 TGTTGAACAT-CAAATTTCATCACCTAATTTAATTAGTTTTAACATTTAATTTCTAGGGCTTT
29740316 T
1 T
29740317 TTTGCATATA
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
60 1 0.02
61 39 0.67
62 18 0.31
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (62 bp):
TGTTGAACATCAAATTTCATCACCTAATTTAATTAGTTTTAACATTTAATTTCTAGGGCTTT
Found at i:29742144 original size:7 final size:7
Alignment explanation
Indices: 29742132--29742157 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29742122 GCTAAGCTAC
29742132 CACTTAT
1 CACTTAT
29742139 CACTTAT
1 CACTTAT
29742146 CACTTAT
1 CACTTAT
29742153 CACTT
1 CACTT
29742158 GCCACTTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (7 bp):
CACTTAT
Found at i:29742163 original size:14 final size:14
Alignment explanation
Indices: 29742129--29742164 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
29742119 GTGGCTAAGC
29742129 TACCACTTATCACT
1 TACCACTTATCACT
*
29742143 TATCACTTATCACT
1 TACCACTTATCACT
*
29742157 TGCCACTT
1 TACCACTT
29742165 GTCATTGATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.25, C:0.33, G:0.03, T:0.39
Consensus pattern (14 bp):
TACCACTTATCACT
Found at i:29742166 original size:64 final size:65
Alignment explanation
Indices: 29742080--29742212 Score: 187
Period size: 64 Copynumber: 2.1 Consensus size: 65
29742070 CTTACACGGA
* * * * * *
29742080 ATCACTTATCATTTATCTCTTGTCACTGGTCAGATAAGTGTGGCT-AAGCTACCACTTATCACTT
1 ATCACTTATCACTTACCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTG
* *
29742144 ATCACTTATCACTTGCCACTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTG
1 ATCACTTATCACTTACCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTG
29742209 ATCA
1 ATCA
29742213 GAAGTACTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
64 38 0.63
65 22 0.37
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.35
Consensus pattern (65 bp):
ATCACTTATCACTTACCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTG
Found at i:29744707 original size:29 final size:31
Alignment explanation
Indices: 29744673--29744732 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
29744663 GAATCAAAAT
29744673 AACCTATACACATTCGAAC-T-TAATCATCC
1 AACCTATACACATTCGAACATATAATCATCC
29744702 AACCTATACACATTCGAACATATAATCATCC
1 AACCTATACACATTCGAACATATAATCATCC
29744733 TTTTACTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 19 0.66
30 1 0.03
31 9 0.31
ACGTcount: A:0.40, C:0.30, G:0.03, T:0.27
Consensus pattern (31 bp):
AACCTATACACATTCGAACATATAATCATCC
Found at i:29745592 original size:36 final size:36
Alignment explanation
Indices: 29745540--29745622 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
29745530 ATATATAATT
* * * *
29745540 ATCACTTTTAAATATTACAACTATATCATTATG-CCGA
1 ATCACTTAT-AATATTACAACTACACCAATA-GACCGA
*
29745577 ATCACTTATAATATTACAATTACACCAATAGACCGA
1 ATCACTTATAATATTACAACTACACCAATAGACCGA
29745613 ATCACTTATA
1 ATCACTTATA
29745623 TGCTCAATTG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
35 1 0.03
36 31 0.77
37 8 0.20
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (36 bp):
ATCACTTATAATATTACAACTACACCAATAGACCGA
Found at i:29746895 original size:28 final size:28
Alignment explanation
Indices: 29746837--29746892 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
29746827 TTTTTTAATA
* *
29746837 ATAACTTTATAATATAATATATATTATT
1 ATAACTTTATAATATAATATAAACTATT
29746865 ATAACCTTTATAA-ATAATATAAAACTAT
1 ATAA-CTTTATAATATAATAT-AAACTAT
29746893 ATATTATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (28 bp):
ATAACTTTATAATATAATATAAACTATT
Found at i:29749511 original size:27 final size:26
Alignment explanation
Indices: 29749481--29749591 Score: 100
Period size: 27 Copynumber: 4.2 Consensus size: 26
29749471 TATAACGGTC
*
29749481 ATTTTGCCCTTCAGGGTTATTTCAGTA
1 ATTTTACCCTTCAGGG-TATTTCAGTA
* * *
29749508 ATTTTACCTTTCGGGGGTATTT-TGATA
1 ATTTTACCCTTC-AGGGTATTTCAG-TA
* **
29749535 ATTTTACCCTTTGAGGGTATTTTGGTA
1 ATTTTACCC-TTCAGGGTATTTCAGTA
29749562 ATTTTACCCTTCGAGGGTA-TTCAGTA
1 ATTTTACCCTTC-AGGGTATTTCAGTA
29749588 ATTT
1 ATTT
29749592 AACAACTTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
26 12 0.18
27 50 0.74
28 6 0.09
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (26 bp):
ATTTTACCCTTCAGGGTATTTCAGTA
Found at i:29751655 original size:40 final size:39
Alignment explanation
Indices: 29751611--29751687 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
29751601 CGTTTGGATA
* * *
29751611 AAAAACGCCACTAAAGATCGAGTATTAGCGGCGCTTTCTG
1 AAAAACACCACTAAAAAT-GAGCATTAGCGGCGCTTTCTG
* *
29751651 AAAAACACCGCTAAAAATGAGCATTAGCGGCGTTTTC
1 AAAAACACCACTAAAAATGAGCATTAGCGGCGCTTTC
29751688 CAAAAAGAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
39 17 0.53
40 15 0.47
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (39 bp):
AAAAACACCACTAAAAATGAGCATTAGCGGCGCTTTCTG
Found at i:29751809 original size:41 final size:41
Alignment explanation
Indices: 29751741--29752056 Score: 311
Period size: 41 Copynumber: 7.8 Consensus size: 41
29751731 TGAGTTTTCG
* * * * *
29751741 GGGCATTAGTGGCGTTTTTTAAAAAGCGTCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
*
29751782 GGGCTTTAGCAGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
* * *
29751823 GGGCTTTAGCGACGCTTTTGAAGAAGCGCCGCTAATACTCTA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC-A
** * * *
29751865 --TTTTTAGCGGCATTTTT-ATAAAAGCGCCACTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGA-AGAAGCGCCGCTAATGCTCA
* * * *
29751904 GGGTTTTAGCAGCATTTTTTAAGAAGCGCCGCTAATGCTC-
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
* * * *
29751944 GAGTCTTTAGCGGCGTTTCTGAAAAAGCGCCTCTAATGCTCA
1 G-GGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
*
29751986 GGGCTTTAGCGGCGTTTTTGAAGAAGCACCGCTAATGCT-A
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
*** * *
29752026 -TATTTTAGCGGCGTTTCTGAAAAAGCGCCGC
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGC
29752057 AAAAAATTCA
Statistics
Matches: 227, Mismatches: 41, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
39 27 0.12
40 30 0.13
41 167 0.74
42 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
Found at i:29751972 original size:122 final size:121
Alignment explanation
Indices: 29751756--29751980 Score: 328
Period size: 122 Copynumber: 1.9 Consensus size: 121
29751746 TTAGTGGCGT
* * *
29751756 TTTTTAAAAAGCGTCGCTAATGCTCAGGGCTTTAGCAGCGTTTTTGAAGAAGCGCCGCTAATGCT
1 TTTTTAAAAAGCGCCACTAATGCTCAGGGCTTTAGCAGCATTTTTGAAGAAGCGCCGCTAATGCT
*
29751821 CAGGGCTTTAGCGACGCTTTTGAAGAAGCGCCGCTAATACTCTATTTTTAGCGGCA
66 CAGGGCTTTAGCGACGCTTTTGAAAAAGCGCCGCTAATACTCTATTTTTAGCGGCA
* *
29751877 TTTTTATAAAAGCGCCACTAATGCTCAGGGTTTTAGCAGCATTTTTTAAGAAGCGCCGCTAATGC
1 TTTTTA-AAAAGCGCCACTAATGCTCAGGGCTTTAGCAGCATTTTTGAAGAAGCGCCGCTAATGC
* * *
29751942 TC-GAGTCTTTAGCGGCG-TTTCTGAAAAAGCGCCTCTAAT
65 TCAG-GGCTTTAGCGACGCTTT-TGAAAAAGCGCCGCTAAT
29751981 GCTCAGGGCT
Statistics
Matches: 92, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
121 10 0.11
122 82 0.89
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (121 bp):
TTTTTAAAAAGCGCCACTAATGCTCAGGGCTTTAGCAGCATTTTTGAAGAAGCGCCGCTAATGCT
CAGGGCTTTAGCGACGCTTTTGAAAAAGCGCCGCTAATACTCTATTTTTAGCGGCA
Found at i:29751974 original size:163 final size:162
Alignment explanation
Indices: 29751755--29752054 Score: 433
Period size: 163 Copynumber: 1.8 Consensus size: 162
29751745 ATTAGTGGCG
* * *
29751755 TTTTTTAAAAAGCGTCGCTAATGCTCAGGGCTTTAGCAGCGTTTTTGAAGAAGCGCCGCTAATGC
1 TTTTTTAAAAAGCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTCTGAAAAAGCGCCGCTAATGC
* * *
29751820 TCAGGGCTTTAGCGACGCTTTTGAAGAAGCGCCGCTAATACTCTATTTTTAGCGGCATTT-TTAT
66 TCAGGGCTTTAGCGACGCTTTTGAAGAAGCACCGCTAATACTATA-TTTTAGCGGCATTTCTGA-
29751884 AAAAGCGCCACTAATGCTCAGGGTTTTAGCAGCA
129 AAAAGCGCCACTAATGCTCAGGGTTTTAGCAGCA
* * * *
29751918 TTTTTTAAGAAGCGCCGCTAATGCTC-GAGTCTTTAGCGGCGTTTCTGAAAAAGCGCCTCTAATG
1 TTTTTTAAAAAGCGCCGCTAATGCTCAG-GGCTTTAGCAGCGTTTCTGAAAAAGCGCCGCTAATG
* * * *
29751982 CTCAGGGCTTTAGCGGCGTTTTTGAAGAAGCACCGCTAATGCTATATTTTAGCGGCGTTTCTGAA
65 CTCAGGGCTTTAGCGACGCTTTTGAAGAAGCACCGCTAATACTATATTTTAGCGGCATTTCTGAA
29752047 AAAGCGCC
130 AAAGCGCC
29752055 GCAAAAAATT
Statistics
Matches: 121, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
162 23 0.19
163 98 0.81
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (162 bp):
TTTTTTAAAAAGCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTCTGAAAAAGCGCCGCTAATGC
TCAGGGCTTTAGCGACGCTTTTGAAGAAGCACCGCTAATACTATATTTTAGCGGCATTTCTGAAA
AAGCGCCACTAATGCTCAGGGTTTTAGCAGCA
Found at i:29752431 original size:22 final size:21
Alignment explanation
Indices: 29752383--29752502 Score: 75
Period size: 22 Copynumber: 5.6 Consensus size: 21
29752373 ATGGTTTAGA
* *
29752383 GTTTAAGGTTTAGGAGTTACTA
1 GTTTAAGGTTTATGAGTTA-TG
*
29752405 TTTTAAGGTTTATG-GATTATGG
1 GTTTAAGGTTTATGAG-TTAT-G
* *
29752427 GTTTAGGGGTTATGAGTTATG
1 GTTTAAGGTTTATGAGTTATG
* ** **
29752448 GTTTAAAGTTTAAAAGTTGGG
1 GTTTAAGGTTTATGAGTTATG
29752469 GTTTAAGGTTTA-GAGGTTAT-
1 GTTTAAGGTTTATGA-GTTATG
29752489 GTGTTAAGGGTTTA
1 GT-TTAA-GGTTTA
29752503 GGGTTTTAGG
Statistics
Matches: 75, Mismatches: 17, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
20 3 0.04
21 35 0.47
22 36 0.48
23 1 0.01
ACGTcount: A:0.25, C:0.01, G:0.31, T:0.43
Consensus pattern (21 bp):
GTTTAAGGTTTATGAGTTATG
Found at i:29752465 original size:21 final size:21
Alignment explanation
Indices: 29752441--29752489 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
29752431 AGGGGTTATG
29752441 AGTTATGGTTTAAAGTTTAAA
1 AGTTATGGTTTAAAGTTTAAA
** * *
29752462 AGTTGGGGTTTAAGGTTTAGA
1 AGTTATGGTTTAAAGTTTAAA
*
29752483 GGTTATG
1 AGTTATG
29752490 TGTTAAGGGT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.41
Consensus pattern (21 bp):
AGTTATGGTTTAAAGTTTAAA
Found at i:29752505 original size:7 final size:7
Alignment explanation
Indices: 29752467--29752533 Score: 55
Period size: 7 Copynumber: 9.1 Consensus size: 7
29752457 TTAAAAGTTG
29752467 GGGTTTA
1 GGGTTTA
*
29752474 AGGTTTA
1 GGGTTTA
29752481 GAGG-TTA
1 G-GGTTTA
* *
29752488 TGTGTTAA
1 -GGGTTTA
29752496 GGGTTTA
1 GGGTTTA
29752503 GGGTTTTA
1 GGG-TTTA
29752511 GGGTTTA
1 GGGTTTA
*
29752518 GGATTTTA
1 GG-GTTTA
29752526 GGGTTTA
1 GGGTTTA
29752533 G
1 G
29752534 ATTAACTAGT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
7 29 0.62
8 18 0.38
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.43
Consensus pattern (7 bp):
GGGTTTA
Found at i:29752512 original size:8 final size:8
Alignment explanation
Indices: 29752495--29752531 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
29752485 TTATGTGTTA
29752495 AGGG-TTT
1 AGGGTTTT
29752502 AGGGTTTT
1 AGGGTTTT
29752510 AGGG-TTT
1 AGGGTTTT
*
29752517 AGGATTTT
1 AGGGTTTT
29752525 AGGGTTT
1 AGGGTTT
29752532 AGATTAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 10 0.38
8 16 0.62
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.46
Consensus pattern (8 bp):
AGGGTTTT
Found at i:29752515 original size:15 final size:15
Alignment explanation
Indices: 29752495--29752533 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
29752485 TTATGTGTTA
*
29752495 AGGGTTTAGGGTTTT
1 AGGGTTTAGGATTTT
29752510 AGGGTTTAGGATTTT
1 AGGGTTTAGGATTTT
29752525 AGGGTTTAG
1 AGGGTTTAG
29752534 ATTAACTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.38, T:0.44
Consensus pattern (15 bp):
AGGGTTTAGGATTTT
Found at i:29754654 original size:21 final size:21
Alignment explanation
Indices: 29754609--29754654 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
29754599 ATATATATAT
*
29754609 GTTTAGCTTAGTGTTGATCTA
1 GTTTAGCTTAGTATTGATCTA
* *
29754630 GTTTAGCTTAGTATTGGTCTG
1 GTTTAGCTTAGTATTGATCTA
29754651 GTTT
1 GTTT
29754655 TTTTACATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.09, G:0.26, T:0.50
Consensus pattern (21 bp):
GTTTAGCTTAGTATTGATCTA
Found at i:29756608 original size:14 final size:14
Alignment explanation
Indices: 29756589--29756616 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29756579 TCATTACAAG
29756589 ATTTCCTTGATTAA
1 ATTTCCTTGATTAA
29756603 ATTTCCTTGATTAA
1 ATTTCCTTGATTAA
29756617 GTTAATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
ATTTCCTTGATTAA
Found at i:29756680 original size:43 final size:43
Alignment explanation
Indices: 29756603--29756685 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
29756593 CCTTGATTAA
* ** *
29756603 ATTTCCTTGATTAAGTTAATGTATTATATCTTTTATTACCAAG
1 ATTTACTTGATTAAGAAAATGCATTATATCTTTTATTACCAAG
* *
29756646 ATTTACTTGATTAAGAAAATGCATTGTATTTTTTATTACC
1 ATTTACTTGATTAAGAAAATGCATTATATCTTTTATTACC
29756686 TTGCAATGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (43 bp):
ATTTACTTGATTAAGAAAATGCATTATATCTTTTATTACCAAG
Found at i:29756976 original size:5 final size:5
Alignment explanation
Indices: 29756966--29756991 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29756956 TCAAATTTAA
29756966 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
29756992 TTTATCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:29757177 original size:43 final size:43
Alignment explanation
Indices: 29757048--29757254 Score: 170
Period size: 43 Copynumber: 4.8 Consensus size: 43
29757038 ATGATATATT
* * * *
29757048 TTTAGCGGCGTTTTTG-CAAGAAGCGTCACTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGACAA-AAGCGTCGCTAAAGATCATGTTC
* * * * *
29757090 TATAGCGGCGTTTGTGGTAAAAAAAGTGCCGCTAAAGATTATGTTC
1 TTTAGCGGCGTTTGT-G--ACAAAAGCGTCGCTAAAGATCATGTTC
29757136 TTTAGCGGCGTTTGTGACAAAAGCGTCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGACAAAAGCGTCGCTAAAGATCATGTTC
* * * ** *
29757179 TTTAGTGGCATTTGTGACAAAAGCATTC-CTAAATCTCATG-AC
1 TTTAGCGGCGTTTGTGACAAAAGC-GTCGCTAAAGATCATGTTC
* * *
29757221 TTTTAGCGGCGTTTATGATAAAAGCGCCGCTAAA
1 -TTTAGCGGCGTTTGTGACAAAAGCGTCGCTAAA
29757255 TTTAGTGGCG
Statistics
Matches: 132, Mismatches: 25, Indels: 15
0.77 0.15 0.09
Matches are distributed among these distances:
42 15 0.11
43 81 0.61
44 2 0.02
45 13 0.10
46 21 0.16
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.32
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGACAAAAGCGTCGCTAAAGATCATGTTC
Found at i:29775258 original size:147 final size:147
Alignment explanation
Indices: 29775067--29775516 Score: 542
Period size: 147 Copynumber: 3.1 Consensus size: 147
29775057 GTTTTGATTT
* *
29775067 TTTTTTTAAAAAAGAGAAAGTTTAGATTTAAAAAAATAAAAATATGGTTTTTTAGTCATTTTAAA
1 TTTTTTT--AAAAGAGAAAATTTAGATTTTAAAAAATAAAAATAT-GTTTTTTAGTCATTTTAAA
* *
29775132 GGAAAG-TTAAAATTTTAAAACAAAGCTTTGATTTTCTTTTCAACTATTTCAAAATAAAAGTTTT
63 GGAAAGTTTAAAATTTTAAAACAAAGCTTTAATTTT-TTTTCAACTATTTCAAAATAAAAGCTTT
29775196 GATCTTTAAGAAAAATAGT-A
127 GATCTTTAAGAAAAATAGTGA
29775216 TTTTTTTAAAAGAGAAAATTTAGATTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGA
1 TTTTTTTAAAAGAGAAAATTTAGATTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGA
** *
29775281 AAGTTTAAAATTTTAAAACAAATTTTTAATTTTTTTTCAACTATTTCAAAATTAAAGCTTTGATC
66 AAGTTTAAAATTTTAAAACAAAGCTTTAATTTTTTTTCAACTATTTCAAAATAAAAGCTTTGATC
*
29775346 TTTAAGAAAAATAGTGT
131 TTTAAGAAAAATAGTGA
* ** *
29775363 TTTTTTTAAAA-AAAAGAGAGTTTAGATTTT-TTAAATAAAAATATGTTTTTTATTCATTTTAAA
1 TTTTTTTAAAAGAGAA-A-A-TTTAGATTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAA
** * * * * * *
29775426 GGAAAAGTTTAAAA--TTAAAA-AAA-AATTCA-TCTTTTTCATCTCTTTCGAAAT-AAAGTTTT
63 GG-AAAGTTTAAAATTTTAAAACAAAGCTTTAATTTTTTTTCAACTATTTCAAAATAAAAGCTTT
* * *
29775485 GATTTTTAAGAAAAGTAATGA
127 GATCTTTAAGAAAAATAGTGA
29775506 TTGTTTTTAAA
1 TT-TTTTTAAA
29775517 GAAAATTTTT
Statistics
Matches: 270, Mismatches: 24, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
143 26 0.10
144 26 0.10
145 3 0.01
146 76 0.28
147 78 0.29
148 33 0.12
149 28 0.10
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (147 bp):
TTTTTTTAAAAGAGAAAATTTAGATTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGA
AAGTTTAAAATTTTAAAACAAAGCTTTAATTTTTTTTCAACTATTTCAAAATAAAAGCTTTGATC
TTTAAGAAAAATAGTGA
Found at i:29775355 original size:146 final size:148
Alignment explanation
Indices: 29775067--29775441 Score: 544
Period size: 146 Copynumber: 2.5 Consensus size: 148
29775057 GTTTTGATTT
* *
29775067 TTTTTTTAAAAAAGAGAAAGTTTAGATTTAAAAAAATAAAAATATGGTTTTTTAGTCATTTTAAA
1 TTTTTTT--AAAAGAGAAAATTTAGATTTTAAAAAATAAAAATAT-GTTTTTTAGTCATTTTAAA
* *
29775132 GGAAAG-TTAAAATTTTAAAACAAAGCTTTGATTTTCTTTTCAACTATTTCAAAATAAAAGTTTT
63 GGAAAGTTTAAAATTTTAAAACAAAGCTTTAATTTTCTTTTCAACTATTTCAAAATAAAAGCTTT
29775196 GATCTTTAAGAAAAATAGT-A
128 GATCTTTAAGAAAAATAGTGA
29775216 TTTTTTTAAAAGAGAAAATTTAGATTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGA
1 TTTTTTTAAAAGAGAAAATTTAGATTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGA
** *
29775281 AAGTTTAAAATTTTAAAACAAATTTTTAATTTT-TTTTCAACTATTTCAAAATTAAAGCTTTGAT
66 AAGTTTAAAATTTTAAAACAAAGCTTTAATTTTCTTTTCAACTATTTCAAAATAAAAGCTTTGAT
*
29775345 CTTTAAGAAAAATAGTGT
131 CTTTAAGAAAAATAGTGA
* ** *
29775363 TTTTTTTAAAA-AAAAGAGAGTTTAGATTTT-TTAAATAAAAATATGTTTTTTATTCATTTTAAA
1 TTTTTTTAAAAGAGAA-A-A-TTTAGATTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAA
29775426 GGAAAAGTTTAAAATT
63 GG-AAAGTTTAAAATT
29775442 AAAAAAAAAT
Statistics
Matches: 208, Mismatches: 12, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
146 73 0.35
147 72 0.35
148 33 0.16
149 30 0.14
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.42
Consensus pattern (148 bp):
TTTTTTTAAAAGAGAAAATTTAGATTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGA
AAGTTTAAAATTTTAAAACAAAGCTTTAATTTTCTTTTCAACTATTTCAAAATAAAAGCTTTGAT
CTTTAAGAAAAATAGTGA
Found at i:29775385 original size:21 final size:21
Alignment explanation
Indices: 29775346--29775385 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29775336 AGCTTTGATC
* * *
29775346 TTTAAGAAAAATAGTGTTTTT
1 TTTAAAAAAAAGAGAGTTTTT
29775367 TTTAAAAAAAAGAGAGTTT
1 TTTAAAAAAAAGAGAGTTT
29775386 AGATTTTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (21 bp):
TTTAAAAAAAAGAGAGTTTTT
Found at i:29775461 original size:146 final size:146
Alignment explanation
Indices: 29775066--29775521 Score: 534
Period size: 146 Copynumber: 3.1 Consensus size: 146
29775056 AGTTTTGATT
* *
29775066 TTTTTTTTAAAAAAGAGAAAGTTTAGATTTAAAAAAATAAAAATATGGTTTTTTAGTCATTTTAA
1 TTTTTTTTAAAAAAAAG-AAGTTTAGATTT-TAAAAATAAAAATAT-GTTTTTTAGTCATTTTAA
* * *
29775131 AGGAAAG-TTAAAATTTTAAAACAAAGCTTTGATTTTCTTTTCAACTATTTCAAAATAAAAGTTT
63 AGGAAAGTTTAAAA-TTTAAAACAAAGATTTAATTTT-TTTTCAACTATTTCAAAATTAAAGTTT
29775195 TGATCTTTAAGAAAAATAGT-
126 TGATCTTTAAGAAAAATAGTG
* *
29775215 ATTTTTTTAAAAGAGAA-AA-TTTAGATTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAA
1 TTTTTTTTAAAA-AAAAGAAGTTTAGATTTT-AAAAATAAAAATATGTTTTTTAGTCATTTTAAA
** *
29775278 GGAAAGTTTAAAATTTTAAAACAAATTTTTAATTTTTTTTCAACTATTTCAAAATTAAAGCTTTG
64 GGAAAGTTTAAAA-TTTAAAACAAAGATTTAATTTTTTTTCAACTATTTCAAAATTAAAGTTTTG
29775343 ATCTTTAAGAAAAATAGTG
128 ATCTTTAAGAAAAATAGTG
** *
29775362 TTTTTTTTAAAAAAAAGAGAGTTTAGATTTTTTAAATAAAAATATGTTTTTTATTCATTTTAAAG
1 TTTTTTTTAAAAAAAAGA-AGTTTAGATTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAAG
* * * * * *
29775427 GAAAAGTTTAAAA-TTAAAA-AAA-AATTCA-TCTTTTTCATCTCTTTCGAAA-TAAAGTTTTGA
65 G-AAAGTTTAAAATTTAAAACAAAGATTTAATTTTTTTTCAACTATTTCAAAATTAAAGTTTTGA
* * *
29775487 TTTTTAAGAAAAGTAATG
129 TCTTTAAGAAAAATAGTG
* *
29775505 ATTGTTTTTAAAGAAAA
1 -TTTTTTTTAAAAAAAA
29775522 TTTTTATTTT
Statistics
Matches: 271, Mismatches: 27, Indels: 23
0.84 0.08 0.07
Matches are distributed among these distances:
143 25 0.09
144 31 0.11
145 3 0.01
146 76 0.28
147 67 0.25
148 35 0.13
149 32 0.12
150 2 0.01
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (146 bp):
TTTTTTTTAAAAAAAAGAAGTTTAGATTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGG
AAAGTTTAAAATTTAAAACAAAGATTTAATTTTTTTTCAACTATTTCAAAATTAAAGTTTTGATC
TTTAAGAAAAATAGTG
Found at i:29777853 original size:14 final size:14
Alignment explanation
Indices: 29777834--29777866 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
29777824 GGGCTTATTC
29777834 ATAAAAAGTAAAAA
1 ATAAAAAGTAAAAA
29777848 ATAAAAAGTAAAAA
1 ATAAAAAGTAAAAA
29777862 A-AAAA
1 ATAAAA
29777867 GATGAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (14 bp):
ATAAAAAGTAAAAA
Found at i:29777877 original size:16 final size:16
Alignment explanation
Indices: 29777858--29777893 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
29777848 ATAAAAAGTA
29777858 AAAAAAAAAGATGAAC
1 AAAAAAAAAGATGAAC
29777874 AAAAAAAAAGATGAAC
1 AAAAAAAAAGATGAAC
29777890 AAAA
1 AAAA
29777894 TATTTGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.78, C:0.06, G:0.11, T:0.06
Consensus pattern (16 bp):
AAAAAAAAAGATGAAC
Found at i:29779577 original size:27 final size:27
Alignment explanation
Indices: 29779535--29779586 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
29779525 GAAATGTGAA
*
29779535 AGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCCG
29779562 AGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTTGCTAAGTGCTGATTCCCC
29779587 GGTTCATTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.25, G:0.33, T:0.29
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:29779599 original size:103 final size:104
Alignment explanation
Indices: 29779459--29779681 Score: 369
Period size: 103 Copynumber: 2.2 Consensus size: 104
29779449 TGTATATAAA
** * *
29779459 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
29779523 TTGAAATGTGAAA-GGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
29779562 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGATATCCACCATATCTT
29779627 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
29779666 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
29779682 GATATCCATT
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 69 0.62
104 43 0.38
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:29779733 original size:71 final size:72
Alignment explanation
Indices: 29779600--29779751 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
29779590 TCATTGGTGG
* *
29779600 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
29779665 GAGGGGT
66 GAGGGGT
***
29779672 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
29779736 GAGGGGT
66 GAGGGGT
29779743 TGCTAAGTG
1 TGCTAAGTG
29779752 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:29786669 original size:5 final size:5
Alignment explanation
Indices: 29786659--29786696 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
29786649 TCTTAAGACA
29786659 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
29786697 GAGATGGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:29786881 original size:37 final size:37
Alignment explanation
Indices: 29786834--29786909 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
29786824 TATTTTGTGC
* *
29786834 AAAATTAACATTTATACCTAGAGTTATTTTGTAAAAA
1 AAAATGAACATTTATACCTAAAGTTATTTTGTAAAAA
29786871 AAAATGAACATTTATACCTAAAGTTATTTTGTAAAAA
1 AAAATGAACATTTATACCTAAAGTTATTTTGTAAAAA
29786908 AA
1 AA
29786910 TTAACATGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (37 bp):
AAAATGAACATTTATACCTAAAGTTATTTTGTAAAAA
Found at i:29787433 original size:33 final size:34
Alignment explanation
Indices: 29787364--29787433 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 34
29787354 TACTTTCAAA
* * *
29787364 ATTAAACTTATTTAAAACTCATTTTCAAAAATTG
1 ATTAAACTTATTTAAAACTCATGTTAAAAAAATG
*
29787398 ATTAAA-TTTTTTAAAAC-CATGTTAAAAAACATG
1 ATTAAACTTATTTAAAACTCATGTTAAAAAA-ATG
29787431 ATT
1 ATT
29787434 GATCTACCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
32 10 0.32
33 15 0.48
34 6 0.19
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (34 bp):
ATTAAACTTATTTAAAACTCATGTTAAAAAAATG
Done.