Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 20 of 32
Found at i:2699023 original size:17 final size:17
Alignment explanation
Indices: 2699001--2699066 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 17
2698991 AAAATAATTT
2699001 AAATATTAAATTTAATA
1 AAATATTAAATTTAATA
* *
2699018 AAATA-TATATTTAATT
1 AAATATTAAATTTAATA
* *
2699034 AAATAATATATTTTAAATA
1 AAATATTA-AATTT-AATA
*
2699053 TAAATTTTAAATTT
1 -AAATATTAAATTT
2699067 TAAATTTTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
16 14 0.38
17 7 0.19
18 3 0.08
19 7 0.19
20 6 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATATTAAATTTAATA
Found at i:2699027 original size:21 final size:20
Alignment explanation
Indices: 2699003--2699056 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
2698993 AATAATTTAA
2699003 ATATTAAATTTAATAAAATAT
1 ATATTAAATTTAA-AAAATAT
* *
2699024 ATATTTAA-TTAAATAATAT
1 ATATTAAATTTAAAAAATAT
* *
2699043 ATTTTAAATATAAA
1 ATATTAAATTTAAA
2699057 TTTTAAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 12 0.44
20 8 0.30
21 7 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATTAAATTTAAAAAATAT
Found at i:2699051 original size:14 final size:13
Alignment explanation
Indices: 2699032--2699093 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 13
2699022 ATATATTTAA
*
2699032 TTAAATAATATATT
1 TTAAAT-ATAAATT
2699046 TTAAATATAAATT
1 TTAAATATAAATT
*
2699059 TTAAATTTTAAATTT
1 TTAAA-TATAAA-TT
*
2699074 TTATATATAATAATT
1 TTAAATAT-A-AATT
2699089 TTAAA
1 TTAAA
2699094 AAATTAAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 11 0.28
14 13 0.33
15 13 0.33
16 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAAATATAAATT
Found at i:2699147 original size:20 final size:20
Alignment explanation
Indices: 2699124--2699167 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2699114 AATTTTTTAA
*
2699124 AATTTTATTAAGTTTTTATC
1 AATTTAATTAAGTTTTTATC
* * *
2699144 AATTTAATTTATTTTTTATT
1 AATTTAATTAAGTTTTTATC
2699164 AATT
1 AATT
2699168 AAAAAATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
AATTTAATTAAGTTTTTATC
Found at i:2699644 original size:9 final size:9
Alignment explanation
Indices: 2699618--2699655 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
2699608 TAAAATAATG
2699618 ATTTATTTA
1 ATTTATTTA
2699627 ATTT-TTTA
1 ATTTATTTA
*
2699635 ATTTAATTA
1 ATTTATTTA
*
2699644 ATTTATATA
1 ATTTATTTA
2699653 ATT
1 ATT
2699656 ATTATTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
ATTTATTTA
Found at i:2702234 original size:6 final size:6
Alignment explanation
Indices: 2702225--2702282 Score: 71
Period size: 6 Copynumber: 9.2 Consensus size: 6
2702215 AAAAATTTTT
* *
2702225 AATTTA AATTTA AATTTA AATTTA AGTTTA AATATA AATAATTA AATTTAA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT--TTA AATTT-A
2702276 AATTTA A
1 AATTTA A
2702283 CATGAAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
6 34 0.76
7 6 0.13
8 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:2702295 original size:33 final size:32
Alignment explanation
Indices: 2702234--2702295 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 32
2702224 TAATTTAAAT
** * *
2702234 TTAAATTTAAATTTAAGTTTAAATATAAATAA
1 TTAAATTTAAATTTAACATGAAAAATAAATAA
2702266 TTAAATTTAAAATTTAACATGAAAAATAAA
1 TTAAATTT-AAATTTAACATGAAAAATAAA
2702296 CTTATTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 8 0.32
33 17 0.68
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (32 bp):
TTAAATTTAAATTTAACATGAAAAATAAATAA
Found at i:2702423 original size:36 final size:38
Alignment explanation
Indices: 2702356--2702426 Score: 94
Period size: 36 Copynumber: 1.9 Consensus size: 38
2702346 ATTAAATAAA
* *
2702356 TTTAAATAATTAATTTTATCTTAAATCAAATTAAAACT
1 TTTAAATAATAAAATTTATCTTAAATCAAATTAAAACT
2702394 TTTAAA-AATAAAATTTA-CTTAAA-CTAAATTAAA
1 TTTAAATAATAAAATTTATCTTAAATC-AAATTAAA
2702427 TTTTAATCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 1 0.03
36 14 0.47
37 9 0.30
38 6 0.20
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (38 bp):
TTTAAATAATAAAATTTATCTTAAATCAAATTAAAACT
Found at i:2702899 original size:59 final size:57
Alignment explanation
Indices: 2702834--2702943 Score: 143
Period size: 60 Copynumber: 1.9 Consensus size: 57
2702824 ATTTTTTAAT
*
2702834 TAATTA-TTTAAAA-AAATATGATTTAAATAAATATTTATATTATGATTTTTTAAAATATA
1 TAATTATTTTAAAATAAATATCA-TTAAATAAATA-TTA-A-TATGATTTTTTAAAATATA
* *
2702893 TAATTATTTTAAAATTAATGTCATTAAATAAATATTAATATGATTTTTTAA
1 TAATTATTTTAAAATAAATATCATTAAATAAATATTAATATGATTTTTTAA
2702944 TATCTAATGA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
57 13 0.28
58 1 0.02
59 9 0.20
60 18 0.39
61 5 0.11
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (57 bp):
TAATTATTTTAAAATAAATATCATTAAATAAATATTAATATGATTTTTTAAAATATA
Found at i:2704264 original size:19 final size:18
Alignment explanation
Indices: 2704242--2704292 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
2704232 TATACAAATA
2704242 TAAATTTAATATAAATTAT
1 TAAATTTAATATAAATT-T
* *
2704261 TAAATATATTA-AAATTT
1 TAAATTTAATATAAATTT
*
2704278 TAAATATAAATATAA
1 TAAAT-TTAATATAA
2704293 TACGTATATT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
17 6 0.24
18 8 0.32
19 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAATTTAATATAAATTT
Found at i:2704490 original size:3 final size:3
Alignment explanation
Indices: 2704482--2704519 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2704472 GCCAAATCGA
2704482 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2704520 AGAACTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2707448 original size:154 final size:154
Alignment explanation
Indices: 2707267--2707711 Score: 494
Period size: 153 Copynumber: 2.9 Consensus size: 154
2707257 TGTTTTATTT
** *
2707267 TCAAAATAAAAAGTTTTTTACTTCGTAAATTTTTTTGATAAGATTTTTCTGAATTTATAATTTCC
1 TCAAAATACGAAGTTTTCTACTTCGTAAATTTTTTTGATAAGATTTTTCTGAATTTATAATTTCC
* * *
2707332 AAATTCTTCAAATATTATTTTTTTAATTTATATTAAATCAGTTTTGAAAAATTCAATTCATTTTA
66 AAATTCTTCAAATATTATTTATTTAATTCATATTAAATCAGTTTTGAAAAATTCAATTTATTTTA
*
2707397 CGAGTTTTAGAAATTTTCCTAATAC
131 TGAGTTTTAGAAATTTTCCT-ATAC
* ** * *
2707422 T-GAAATGTGAAGTTTTCTACTCCGTAAATTTTTTTTGA-AAGA-TTTTCTAAATTTATAATTTC
1 TCAAAATACGAAGTTTTCTACTTCGTAAA-TTTTTTTGATAAGATTTTTCTGAATTTATAATTTC
* * * * *
2707484 CAAAATTTTTCAAATATTA-TTGTCTAATTCGTATTAAATCAGTTTTAAAAAATTCAATTTATTT
65 C-AAATTCTTCAAATATTATTTATTTAATTCATATTAAATCAGTTTTGAAAAATTCAATTTATTT
* * **
2707548 TATGAGTTTTAGAACTTTTTCTATTT
129 TATGAGTTTTAGAAATTTTCCTATAC
* * * *
2707574 TCAAAATACGAAGTTTTCTACTTCGTAAATTTCTTTGGTTAGATTTTTCCCTG--TTTAAAATTT
1 TCAAAATACGAAGTTTTCTACTTCGTAAATTTTTTTGATAAGATTTTT--CTGAATTTATAA-TT
** * * *
2707637 TTAAAATTCATCAAATATT-TTTATTAAATTCAT-TTAAATTAGTTTGTG-AAAATTCAATTTAT
63 TCCAAATTCTTCAAATATTATTTATTTAATTCATATTAAATCAGTTT-TGAAAAATTCAATTTAT
2707699 TTTATGAGTTTTA
127 TTTATGAGTTTTA
2707712 CATTTTTTTT
Statistics
Matches: 242, Mismatches: 38, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
152 10 0.04
153 142 0.59
154 75 0.31
155 13 0.05
156 2 0.01
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.49
Consensus pattern (154 bp):
TCAAAATACGAAGTTTTCTACTTCGTAAATTTTTTTGATAAGATTTTTCTGAATTTATAATTTCC
AAATTCTTCAAATATTATTTATTTAATTCATATTAAATCAGTTTTGAAAAATTCAATTTATTTTA
TGAGTTTTAGAAATTTTCCTATAC
Found at i:2708372 original size:23 final size:23
Alignment explanation
Indices: 2708346--2708411 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
2708336 TTGTTTTAAT
*
2708346 TGGGCTTTTAGTTTAGGTTTAGA
1 TGGGCTTTTAGTTTAGATTTAGA
*
2708369 TGGGCTTTTAGTTTAGATTTAAA
1 TGGGCTTTTAGTTTAGATTTAGA
* * *
2708392 TAGG-TTTAAGTTTAAATTTA
1 TGGGCTTTTAGTTTAGATTTA
2708412 TATTTTATTG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
22 14 0.37
23 24 0.63
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (23 bp):
TGGGCTTTTAGTTTAGATTTAGA
Found at i:2708840 original size:21 final size:21
Alignment explanation
Indices: 2708814--2708856 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2708804 GTTTTATGAT
2708814 TGCTTGAGCTCATGGATTTCA
1 TGCTTGAGCTCATGGATTTCA
2708835 TGCTTGAGCTCATGGATTTCA
1 TGCTTGAGCTCATGGATTTCA
2708856 T
1 T
2708857 TACATGTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (21 bp):
TGCTTGAGCTCATGGATTTCA
Found at i:2710368 original size:21 final size:21
Alignment explanation
Indices: 2710344--2710389 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
2710334 ATTATTATTA
*
2710344 TTATTATTATAAAAATTCATT
1 TTATTATTATAAAAATTAATT
*
2710365 TTATTATTTTAAAAATTAATT
1 TTATTATTATAAAAATTAATT
2710386 TTAT
1 TTAT
2710390 GTTAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTATTATAAAAATTAATT
Found at i:2710372 original size:3 final size:3
Alignment explanation
Indices: 2710308--2710353 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2710298 TTTAGGGTCC
2710308 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2710354 AAAAATTCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2715555 original size:15 final size:15
Alignment explanation
Indices: 2715531--2715565 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2715521 TTAATTTAAT
* *
2715531 AATAATAATATATTA
1 AATAAAAATAAATTA
2715546 AATAAAAATAAATTA
1 AATAAAAATAAATTA
2715561 AATAA
1 AATAA
2715566 TGCTTTACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAAAAATAAATTA
Found at i:2722213 original size:35 final size:34
Alignment explanation
Indices: 2722130--2722217 Score: 131
Period size: 34 Copynumber: 2.6 Consensus size: 34
2722120 TAACCAGGCC
*
2722130 AGAAACACATTTCTAGAACAAAAAAAGAAGCCAT
1 AGAAACACATTTATAGAACAAAAAAAGAAGCCAT
* * *
2722164 ACAAACACATTTATAGAACAAAAAAGGAAGGCAT
1 AGAAACACATTTATAGAACAAAAAAAGAAGCCAT
2722198 AGAAACACATGTTATAGAAC
1 AGAAACACAT-TTATAGAAC
2722218 TTGCAAGATA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 39 0.81
35 9 0.19
ACGTcount: A:0.55, C:0.16, G:0.14, T:0.16
Consensus pattern (34 bp):
AGAAACACATTTATAGAACAAAAAAAGAAGCCAT
Found at i:2723396 original size:21 final size:20
Alignment explanation
Indices: 2723364--2723402 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2723354 CATTTTAACA
*
2723364 TATTTAAAAAAACTAGACAT
1 TATTGAAAAAAACTAGACAT
2723384 TATTGAAACAAAACTAGAC
1 TATTGAAA-AAAACTAGAC
2723403 CTTACTGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.54, C:0.13, G:0.08, T:0.26
Consensus pattern (20 bp):
TATTGAAAAAAACTAGACAT
Found at i:2724824 original size:16 final size:16
Alignment explanation
Indices: 2724805--2724946 Score: 58
Period size: 16 Copynumber: 8.6 Consensus size: 16
2724795 ATATAATTTA
2724805 ATATTTATATTTTATT
1 ATATTTATATTTTATT
2724821 ATATTTAAAATATTTTATT
1 ATATTT---ATATTTTATT
* ** * *
2724840 TTAAAATAAATTTTAAT
1 AT-ATTTATATTTTATT
* *
2724857 AAATTAATAATTTATATT
1 ATATTTAT-ATTT-TATT
** *
2724875 ATATACA-ATTTAATAT
1 ATATTTATATTTTAT-T
**
2724891 ATATTTATATGATATT
1 ATATTTATATTTTATT
*
2724907 ATA-TTATATATTA-T
1 ATATTTATATTTTATT
*
2724921 ATATTTTTTATTTT-TT
1 ATA-TTTATATTTTATT
2724937 ATATTTATAT
1 ATATTTATAT
2724947 AATTATATAT
Statistics
Matches: 89, Mismatches: 26, Indels: 23
0.64 0.19 0.17
Matches are distributed among these distances:
14 4 0.04
15 16 0.18
16 33 0.37
17 16 0.18
18 7 0.08
19 11 0.12
20 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.58
Consensus pattern (16 bp):
ATATTTATATTTTATT
Found at i:2724879 original size:7 final size:7
Alignment explanation
Indices: 2724869--2724956 Score: 51
Period size: 7 Copynumber: 12.7 Consensus size: 7
2724859 ATTAATAATT
2724869 TATATTA
1 TATATTA
**
2724876 TATACAA
1 TATATTA
* *
2724883 TTTAATA
1 TATATTA
2724890 TATATT-
1 TATATTA
2724896 TATATGATA
1 TATAT--TA
2724905 TTATATTA
1 -TATATTA
2724913 TATATTA
1 TATATTA
2724920 TATATT-
1 TATATTA
2724926 T-T-TTA
1 TATATTA
* *
2724931 TTTTTTA
1 TATATTA
2724938 TAT-TTA
1 TATATTA
2724944 TATAATTA
1 TAT-ATTA
2724952 TATAT
1 TATAT
2724957 AAAATAAGTT
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
6 13 0.20
7 33 0.52
8 9 0.14
10 5 0.08
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (7 bp):
TATATTA
Found at i:2726085 original size:14 final size:14
Alignment explanation
Indices: 2726060--2726102 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2726050 TTAAAATTTA
2726060 TATAATATATAATAT
1 TATAA-ATATAATAT
* *
2726075 TTTAAATATAATAA
1 TATAAATATAATAT
*
2726089 TATAAATGTAATAT
1 TATAAATATAATAT
2726103 GAATATATGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
TATAAATATAATAT
Found at i:2726800 original size:26 final size:26
Alignment explanation
Indices: 2726771--2726825 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
2726761 TCAATTTTTT
2726771 AAAAAATATAA-TAAAAATTAAATCTA
1 AAAAAATATAATTAAAAATTAAAT-TA
* *
2726797 AAAAATTATAATTTAAAATTAAATTA
1 AAAAAATATAATTAAAAATTAAATTA
2726823 AAA
1 AAA
2726826 TTTAAAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAAAATATAATTAAAAATTAAATTA
Found at i:2726946 original size:3 final size:3
Alignment explanation
Indices: 2726938--2726975 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2726928 AATCTGTCAC
2726938 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2726976 CTTTGGGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2728646 original size:23 final size:23
Alignment explanation
Indices: 2728594--2728648 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
2728584 AAAATATTTG
* * *
2728594 ATATATTTAAAAATAAAATTTAT
1 ATATAATTAAAAATAAAATATAA
*
2728617 ATTTAATTAAAAATAAAATATAA
1 ATATAATTAAAAATAAAATATAA
2728640 ATATAATTA
1 ATATAATTA
2728649 TTATATGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATATAATTAAAAATAAAATATAA
Found at i:2728721 original size:52 final size:52
Alignment explanation
Indices: 2728623--2728721 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 52
2728613 TTATATTTAA
* **
2728623 TTAAAAATAAAATATAAATATAATTATTATATGATATTATTTTATTACTTTT
1 TTAAAAATAAAATATAAATATAATTATTATATAATATTATAATATTACTTTT
2728675 TTAAAAAT-AAATATAAATAATAATT-TTA-ATAATATGTATAAATATTA
1 TTAAAAATAAAATATAAAT-ATAATTATTATATAATAT-TAT-AATATTA
2728722 TTAATGTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
50 6 0.15
51 16 0.39
52 19 0.46
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (52 bp):
TTAAAAATAAAATATAAATATAATTATTATATAATATTATAATATTACTTTT
Found at i:2731333 original size:15 final size:15
Alignment explanation
Indices: 2731313--2731343 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2731303 GAGGACTATA
2731313 CCCTATACTCATGTT
1 CCCTATACTCATGTT
2731328 CCCTATACTCATGTT
1 CCCTATACTCATGTT
2731343 C
1 C
2731344 GAATATGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.35, G:0.06, T:0.39
Consensus pattern (15 bp):
CCCTATACTCATGTT
Found at i:2734499 original size:23 final size:24
Alignment explanation
Indices: 2734450--2734501 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
2734440 TATTAGAATC
2734450 TTAATAAAAAGTTAGATAATTAAT
1 TTAATAAAAAGTTAGATAATTAAT
* *
2734474 TTAATCAAAAATTTA-A-AATTATT
1 TTAAT-AAAAAGTTAGATAATTAAT
2734497 TTAAT
1 TTAAT
2734502 TTAATATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 11 0.44
24 6 0.24
25 8 0.32
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (24 bp):
TTAATAAAAAGTTAGATAATTAAT
Found at i:2735472 original size:19 final size:19
Alignment explanation
Indices: 2735448--2735492 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
2735438 TTGATTCAAT
2735448 TTAAAATAATA-ATTTTATA
1 TTAAAATAATATATTTT-TA
2735467 TTAAAATAATATATTTTTA
1 TTAAAATAATATATTTTTA
*
2735486 TTTAAAT
1 TTAAAAT
2735493 TTAATTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAATAATATATTTTTA
Found at i:2736560 original size:23 final size:21
Alignment explanation
Indices: 2736512--2736568 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
2736502 AATATTAATA
2736512 ATATTTA-ATTATTTTAAAATT
1 ATATTTATATT-TTTTAAAATT
*
2736533 TTATTTATATTTTTTAAAAAATT
1 ATATTTATATTTTTT--AAAATT
2736556 ATATTTTATATTT
1 ATA-TTTATATTT
2736569 ATATTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 10 0.33
22 3 0.10
23 8 0.27
24 9 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTTATATTTTTTAAAATT
Found at i:2736923 original size:65 final size:66
Alignment explanation
Indices: 2736806--2736967 Score: 160
Period size: 65 Copynumber: 2.5 Consensus size: 66
2736796 ATTAAAATAA
* * * *
2736806 TATTATTTTATATTTA-A-ATTATATCTTTATTAATGATCTTTAATATTATATTA-GTGTAAAAA
1 TATTATGTTATTTTTATATATTATATATTTATTAATAATCTTTAATATTATATTATGT-TAAAAA
2736868 TTT
65 -TT
* *
2736871 TATTATGTTATTTTTATATATTATTATATTTATTATTAAT-TTTAA-ATT-TATTATGTTATAAA
1 TATTATGTTATTTTTATATATTA-TATATTTATTAATAATCTTTAATATTATATTATGTTAAAAA
2736933 TT
65 TT
* * *
2736935 T-TTATGTTATTTATATATAATA-AAATTTATTAA
1 TATTATGTTATTTTTATATATTATATATTTATTAA
2736968 AATAATATTA
Statistics
Matches: 83, Mismatches: 10, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
61 9 0.11
63 19 0.23
64 3 0.04
65 24 0.29
66 6 0.07
67 9 0.11
68 13 0.16
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (66 bp):
TATTATGTTATTTTTATATATTATATATTTATTAATAATCTTTAATATTATATTATGTTAAAAAT
T
Found at i:2736939 original size:15 final size:16
Alignment explanation
Indices: 2736913--2736944 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2736903 TTATTAATTT
2736913 TAAATTTATTATGTTA
1 TAAATTTATTATGTTA
2736929 TAAATTT-TTATGTTA
1 TAAATTTATTATGTTA
2736944 T
1 T
2736945 TTATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
TAAATTTATTATGTTA
Found at i:2736996 original size:16 final size:16
Alignment explanation
Indices: 2736977--2737030 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
2736967 AAATAATATT
2736977 ATTTTATATTAATTAA
1 ATTTTATATTAATTAA
* * *
2736993 ATTTTAAATTATTTATT
1 ATTTTATATTAATTA-A
2737010 ATTTTATATTTAAATTAA
1 ATTTTATA-TT-AATTAA
2737028 ATT
1 ATT
2737031 ATTTTTATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
16 13 0.45
17 7 0.24
18 5 0.17
19 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTATATTAATTAA
Found at i:2737020 original size:40 final size:40
Alignment explanation
Indices: 2736975--2737055 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
2736965 TAAAATAATA
*
2736975 TTAT-TTTATATT-AATTAAATTTTA-AATTATTTATTATT
1 TTATATTTAAATTAAATT-AATTTTATAATTATTTATTATT
* *
2737013 TTATATTTAAATTAAATTATTTTTATTATTATTTATTATT
1 TTATATTTAAATTAAATTAATTTTATAATTATTTATTATT
2737053 TTA
1 TTA
2737056 GATGAGATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 4 0.11
39 13 0.35
40 20 0.54
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (40 bp):
TTATATTTAAATTAAATTAATTTTATAATTATTTATTATT
Found at i:2737023 original size:30 final size:30
Alignment explanation
Indices: 2736973--2737050 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 30
2736963 ATTAAAATAA
2736973 TATTATTTTATATTAATTAAATTTTAAATTATT
1 TATTATTTTATATT-ATTAAA--TTAAATTATT
2737006 TATTATTTTATA-T-TTAAATTAAATTATT
1 TATTATTTTATATTATTAAATTAAATTATT
2737034 T-TTATTATTAT-TTATTA
1 TATTATT-TTATATTATTA
2737051 TTTTAGATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
27 5 0.12
28 16 0.38
29 3 0.07
30 5 0.12
32 1 0.02
33 12 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (30 bp):
TATTATTTTATATTATTAAATTAAATTATT
Found at i:2737042 original size:33 final size:32
Alignment explanation
Indices: 2736973--2737046 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 32
2736963 ATTAAAATAA
2736973 TATTATTTTATATTAATTAAATTTTAAATTATT
1 TATTATTTTATATTAATTAAATTTT-AATTATT
*
2737006 TATTATTTTATATTTAAATTAAATTATT-TTTA-T
1 TATTATTTTATA-TT-AATTAAATT-TTAATTATT
2737039 TATTATTT
1 TATTATTT
2737047 ATTATTTTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
33 21 0.57
34 5 0.14
35 9 0.24
36 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (32 bp):
TATTATTTTATATTAATTAAATTTTAATTATT
Found at i:2737053 original size:33 final size:31
Alignment explanation
Indices: 2736973--2737053 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 31
2736963 ATTAAAATAA
*
2736973 TATTATTTTATATTAATTAAATTTTAAATTATT
1 TATTATTTT-TATTATTTAAA-TTTAAATTATT
2737006 TATTA-TTTTA-TATTTAAA-TTAAATTATTTT
1 TATTATTTTTATTATTTAAATTTAAATTA--TT
2737036 TATTATTATTTATTATTT
1 TATTATT-TTTATTATTT
2737054 TAGATGAGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
28 8 0.19
30 14 0.33
31 3 0.07
32 7 0.17
33 10 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (31 bp):
TATTATTTTTATTATTTAAATTTAAATTATT
Found at i:2737689 original size:12 final size:13
Alignment explanation
Indices: 2737656--2737693 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
2737646 GATAGTAAAA
2737656 TAAATTATAAATAT
1 TAAATT-TAAATAT
2737670 TAAAATTTAAAT-T
1 T-AAATTTAAATAT
2737683 TAAATTTAAAT
1 TAAATTTAAAT
2737694 CTGATATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.43
13 2 0.09
14 6 0.26
15 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAATTTAAATAT
Found at i:2739321 original size:5 final size:5
Alignment explanation
Indices: 2739304--2739341 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
2739294 TTTTCTTGGC
* *
2739304 AGGCA GGGC- AGGCC AGGCA AGGCA AGGCA AGGCA AGGC
1 AGGCA AGGCA AGGCA AGGCA AGGCA AGGCA AGGCA AGGC
2739342 TAAACTAAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
4 3 0.10
5 26 0.90
ACGTcount: A:0.32, C:0.24, G:0.45, T:0.00
Consensus pattern (5 bp):
AGGCA
Found at i:2739697 original size:18 final size:18
Alignment explanation
Indices: 2739674--2739743 Score: 57
Period size: 16 Copynumber: 4.3 Consensus size: 18
2739664 AATTAAAATA
2739674 TAATATAATATAAATTAT
1 TAATATAATATAAATTAT
2739692 TAATAT-AT-TAAA--AT
1 TAATATAATATAAATTAT
* *
2739706 TTATATATATATAAAATAT
1 TAATATA-ATATAAATTAT
2739725 T-ATA-AATAT-AATTA-
1 TAATATAATATAAATTAT
2739739 TAATA
1 TAATA
2739744 ATACATAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
14 8 0.18
15 7 0.16
16 10 0.23
17 7 0.16
18 9 0.20
19 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATATAATATAAATTAT
Found at i:2739728 original size:16 final size:16
Alignment explanation
Indices: 2739667--2739735 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
2739657 TTAAAAAAAT
*
2739667 TAAAATATAATATAATA
1 TAAAATATTATAT-ATA
*
2739684 TAAATTATTA-ATATA
1 TAAAATATTATATATA
*
2739699 TTAAAATTTATATATATA
1 -TAAAATAT-TATATATA
*
2739717 TAAAATATTATAAATA
1 TAAAATATTATATATA
2739733 TAA
1 TAA
2739736 TTATAATAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
15 3 0.07
16 18 0.42
17 17 0.40
18 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAATATTATATATA
Found at i:2739744 original size:25 final size:25
Alignment explanation
Indices: 2739667--2739744 Score: 65
Period size: 25 Copynumber: 3.1 Consensus size: 25
2739657 TTAAAAAAAT
*
2739667 TAAAATATAATATAATATAAATTAT--
1 TAAAATATTATA-AATAT-AATTATAA
* *
2739692 TAATATATTA-AAAT-TTATATATATA
1 TAAAATATTATAAATATAAT-TATA-A
2739717 TAAAATATTATAAATATAATTATAA
1 TAAAATATTATAAATATAATTATAA
2739742 TAA
1 TAA
2739745 TACATAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
21 2 0.05
22 4 0.10
23 3 0.07
24 1 0.02
25 21 0.50
26 8 0.19
27 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TAAAATATTATAAATATAATTATAA
Found at i:2742846 original size:19 final size:17
Alignment explanation
Indices: 2742820--2742854 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
2742810 TTTTTTACTC
2742820 AAAATATTTTTTAATTAT
1 AAAATA-TTTTTAATTAT
2742838 AAAATTATTTTTAATTA
1 AAAA-TATTTTTAATTA
2742855 CTACTAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAAATATTTTTAATTAT
Found at i:2743571 original size:41 final size:41
Alignment explanation
Indices: 2743526--2743606 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
2743516 AACCAAAAAG
*
2743526 TATATTTATTTTTTATTTAAAATTAATCTAAAAATAATAAC
1 TATATTTATTTTTTATTTAAAATTAACCTAAAAATAATAAC
2743567 TATATTTATTTTTTATTTAAAATTAACCTAAAAATAATAA
1 TATATTTATTTTTTATTTAAAATTAACCTAAAAATAATAA
2743607 TTTGAGATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (41 bp):
TATATTTATTTTTTATTTAAAATTAACCTAAAAATAATAAC
Found at i:2746285 original size:15 final size:17
Alignment explanation
Indices: 2746267--2746304 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2746257 AAATAATTAT
2746267 AAATCAC-A-AGTAATA
1 AAATCACTATAGTAATA
2746282 AAATCACTATAGTAATA
1 AAATCACTATAGTAATA
*
2746299 AGATCA
1 AAATCA
2746305 GCTTGATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 1 0.05
17 12 0.60
ACGTcount: A:0.55, C:0.13, G:0.08, T:0.24
Consensus pattern (17 bp):
AAATCACTATAGTAATA
Found at i:2746820 original size:14 final size:14
Alignment explanation
Indices: 2746792--2746839 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
2746782 AATTTAATTT
*
2746792 AATTAATTTAT-AA
1 AATTAATTTTTAAA
*
2746805 AATTATTTTTTAAA
1 AATTAATTTTTAAA
*
2746819 AAATAATTTTTAATA
1 AATTAATTTTTAA-A
2746834 AATTAA
1 AATTAA
2746840 AATTTAAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 9 0.32
14 13 0.46
15 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTAATTTTTAAA
Found at i:2748684 original size:13 final size:13
Alignment explanation
Indices: 2748666--2748695 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2748656 ATCTTTTATA
2748666 AATATTTATATTC
1 AATATTTATATTC
*
2748679 AATATTTATATTT
1 AATATTTATATTC
2748692 AATA
1 AATA
2748696 CATATGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
AATATTTATATTC
Found at i:2749591 original size:27 final size:28
Alignment explanation
Indices: 2749539--2749593 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
2749529 ACCCCTTGCT
*
2749539 TTTTAGTTTAATTTTTTATCTAATTTTA
1 TTTTAATTTAATTTTTTATCTAATTTTA
* *
2749567 TTTTAATTT-ATTTTTTATTTGATTTTA
1 TTTTAATTTAATTTTTTATCTAATTTTA
2749594 AACTTATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (28 bp):
TTTTAATTTAATTTTTTATCTAATTTTA
Found at i:2750097 original size:15 final size:15
Alignment explanation
Indices: 2750045--2750103 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 15
2750035 ATTATTTTTT
2750045 AATTT-ATTTTTGAGAA
1 AATTTAATTTTT-A-AA
2750061 AA-TTATATTTTTAAA
1 AATTTA-ATTTTTAAA
*
2750076 AATTTAATTTTTAAT
1 AATTTAATTTTTAAA
2750091 AATTTAATATTTT
1 AATTTAAT-TTTT
2750104 TTTTATTAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
15 22 0.58
16 10 0.26
17 6 0.16
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
AATTTAATTTTTAAA
Found at i:2750553 original size:19 final size:19
Alignment explanation
Indices: 2750529--2750579 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
2750519 ATATTAGATC
*
2750529 ATATTTATTCAAAAATTTT
1 ATATTTATTCAAAAATATT
*
2750548 ATATTTATT-AAATATATT
1 ATATTTATTCAAAAATATT
*
2750566 AAATTTATATCAAA
1 ATATTTAT-TCAAA
2750580 TTTTGTAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 14 0.52
19 10 0.37
20 3 0.11
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATTCAAAAATATT
Found at i:2750936 original size:22 final size:22
Alignment explanation
Indices: 2750911--2750953 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2750901 AATTTTTATT
*
2750911 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TAAAAAAATATA
2750933 TAAATATTAATAAAAAAATAT
1 TAAATATTAATAAAAAAATAT
2750954 TTTTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATATTAATAAAAAAATATA
Found at i:2751857 original size:22 final size:22
Alignment explanation
Indices: 2751817--2751858 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2751807 ATTTAAATAT
*
2751817 TATTTTTATATTAATATTTATA
1 TATTTTAATATTAATATTTATA
2751839 TATTTTAATAATTAA-ATTTA
1 TATTTTAAT-ATTAATATTTA
2751859 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTAATATTAATATTTATA
Found at i:2760581 original size:19 final size:20
Alignment explanation
Indices: 2760545--2760586 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
2760535 AAAGTTATAC
* *
2760545 AATAAATTAAAGAAAAAATA
1 AATAAATTAAACAAAAAACA
*
2760565 AATAAA-TAAACACAAAACA
1 AATAAATTAAACAAAAAACA
2760584 AAT
1 AAT
2760587 TGAAACTTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.17
Consensus pattern (20 bp):
AATAAATTAAACAAAAAACA
Found at i:2767598 original size:51 final size:50
Alignment explanation
Indices: 2767542--2767679 Score: 143
Period size: 51 Copynumber: 2.7 Consensus size: 50
2767532 AATTGTTTAT
* **
2767542 ATGTATCGATACATTAAAGAATGTATCAATA-ATTTGGATCAAAAATTCAAA
1 ATGTATCGATACATGAAA-AATGTATCAATACATTTGGATC-AAAACCCAAA
* * * *
2767593 ATGTATCGATATAATGAAAAATATATCTATACATTTGGGTCAAAACCCAAA
1 ATGTATCGATA-CATGAAAAATGTATCAATACATTTGGATCAAAACCCAAA
* **
2767644 ATGTATTGATACAATGAAAAATGTATTGATACATTT
1 ATGTATCGATAC-ATGAAAAATGTATCAATACATTT
2767680 TTCTTTCAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
51 59 0.82
52 13 0.18
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (50 bp):
ATGTATCGATACATGAAAAATGTATCAATACATTTGGATCAAAACCCAAA
Found at i:2768766 original size:2 final size:2
Alignment explanation
Indices: 2768759--2768800 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2768749 CTTATAGTAT
2768759 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2768801 CATGAGGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2769398 original size:17 final size:17
Alignment explanation
Indices: 2769376--2769415 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2769366 GAAGAATATG
2769376 AAAAAAAATAAAAAATA
1 AAAAAAAATAAAAAATA
** *
2769393 AAAAAATCTAAAAGATA
1 AAAAAAAATAAAAAATA
2769410 AAAAAA
1 AAAAAA
2769416 TAATGTAGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (17 bp):
AAAAAAAATAAAAAATA
Found at i:2769416 original size:17 final size:17
Alignment explanation
Indices: 2769384--2769416 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2769374 TGAAAAAAAA
2769384 TAAAAAATAAAAAAATC
1 TAAAAAATAAAAAAATC
*
2769401 TAAAAGATAAAAAAAT
1 TAAAAAATAAAAAAAT
2769417 AATGTAGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
TAAAAAATAAAAAAATC
Found at i:2769418 original size:8 final size:8
Alignment explanation
Indices: 2769377--2769418 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
2769367 AAGAATATGA
2769377 AAAAAAAT
1 AAAAAAAT
2769385 -AAAAAAT
1 AAAAAAAT
2769392 AAAAAAAT
1 AAAAAAAT
* *
2769400 CTAAAAGAT
1 -AAAAAAAT
2769409 AAAAAAAT
1 AAAAAAAT
2769417 AA
1 AA
2769419 TGTAGCATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 7 0.25
8 15 0.54
9 6 0.21
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (8 bp):
AAAAAAAT
Found at i:2773523 original size:27 final size:27
Alignment explanation
Indices: 2773486--2773546 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
2773476 ACACCATATA
2773486 AATATAATAAAAAAATAAT-TAAATTAT
1 AATATAATAAAAAAATAATAT-AATTAT
*
2773513 AATATATTAAAAAAATAATATAATTAT
1 AATATAATAAAAAAATAATATAATTAT
2773540 AATATAA
1 AATATAA
2773547 AATATATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
AATATAATAAAAAAATAATATAATTAT
Found at i:2775432 original size:2 final size:2
Alignment explanation
Indices: 2775425--2775465 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2775415 ACTATACTTG
2775425 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2775466 GCATTAATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2776094 original size:22 final size:23
Alignment explanation
Indices: 2776066--2776114 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
2776056 AAAAATAGTA
*
2776066 TAAAAAT-ATGATATAATATATT
1 TAAAAATGATAATATAATATATT
*
2776088 TAAAAATGGTTAATATAATATATT
1 TAAAAAT-GATAATATAATATATT
2776112 TAA
1 TAA
2776115 TGTATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 7 0.30
24 16 0.70
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (23 bp):
TAAAAATGATAATATAATATATT
Found at i:2776156 original size:9 final size:9
Alignment explanation
Indices: 2776103--2776162 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
2776093 ATGGTTAATA
2776103 TAATATATT
1 TAATATATT
* *
2776112 TAATGTATA
1 TAATATATT
*
2776121 TATTATA-T
1 TAATATATT
2776129 T-A-ATATT
1 TAATATATT
*
2776136 TAAAAT-TT
1 TAATATATT
2776144 TAATATATT
1 TAATATATT
2776153 TAATATATT
1 TAATATATT
2776162 T
1 T
2776163 TTATCGTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
6 3 0.08
7 2 0.05
8 9 0.22
9 26 0.65
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
TAATATATT
Found at i:2779149 original size:12 final size:12
Alignment explanation
Indices: 2779125--2779157 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2779115 AGAAGAACCC
2779125 CACACAC-CACA
1 CACACACGCACA
*
2779136 CACGCACGCACA
1 CACACACGCACA
2779148 CACACACGCA
1 CACACACGCA
2779158 AGACAGCCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.39, C:0.52, G:0.09, T:0.00
Consensus pattern (12 bp):
CACACACGCACA
Found at i:2779928 original size:18 final size:20
Alignment explanation
Indices: 2779905--2779952 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2779895 ATTAATATAA
*
2779905 AAATATAAAA-TA-TAATAT
1 AAATATAAAATTATTAAAAT
2779923 AAATATATAAATTATTAAAAT
1 AAATATA-AAATTATTAAAAT
2779944 -AATATAAAA
1 AAATATAAAA
2779953 CTCAATCCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.27
19 6 0.23
20 8 0.31
21 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATAAAATTATTAAAAT
Found at i:2779951 original size:26 final size:26
Alignment explanation
Indices: 2779890--2779951 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
2779880 ATTTATATTT
2779890 ATATAAT-T-AATATAAAAATATAAA
1 ATATAATATAAATATAAAAATATAAA
* *
2779914 ATATAATATAAATATATAAATTATTAA
1 ATATAATATAAATATA-AAAATATAAA
2779941 A-ATAATATAAA
1 ATATAATATAAA
2779952 ACTCAATCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 7 0.21
25 1 0.03
26 16 0.48
27 9 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
ATATAATATAAATATAAAAATATAAA
Found at i:2782476 original size:28 final size:28
Alignment explanation
Indices: 2782423--2782476 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
2782413 TTATTTGGAA
* * *
2782423 ATATAATATGTCATATAATGTTTCTAAC
1 ATATAATATGTCATAAAAAGTGTCTAAC
2782451 ATATAATATGTCA-AAAAAGTAGTCTA
1 ATATAATATGTCATAAAAAGT-GTCTA
2782477 GAGAAATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (28 bp):
ATATAATATGTCATAAAAAGTGTCTAAC
Found at i:2783080 original size:2 final size:2
Alignment explanation
Indices: 2783073--2783107 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2783063 AAGCTTTTGT
2783073 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2783108 TTTCAAATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:2792513 original size:17 final size:17
Alignment explanation
Indices: 2792491--2792532 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2792481 CCATTATTTC
2792491 AAAATT-TTAAAGATAAA
1 AAAATTATTAAA-ATAAA
2792508 AAAATTGATTAAAAT-AA
1 AAAATT-ATTAAAATAAA
2792525 AAAATTAT
1 AAAATTAT
2792533 ATTTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.09
17 14 0.61
18 2 0.09
19 5 0.22
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (17 bp):
AAAATTATTAAAATAAA
Found at i:2792656 original size:11 final size:10
Alignment explanation
Indices: 2792631--2792655 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2792621 TTTATATATA
2792631 TTTTTATTCT
1 TTTTTATTCT
2792641 TTTTTATTCT
1 TTTTTATTCT
2792651 TTTTT
1 TTTTT
2792656 TCATTTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTATTCT
Found at i:2792896 original size:15 final size:17
Alignment explanation
Indices: 2792865--2792898 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
2792855 AAATTCTGAT
2792865 TATTTTATAATTAAAAA
1 TATTTTATAATTAAAAA
2792882 TATTTTA-AA-TAAAAA
1 TATTTTATAATTAAAAA
2792897 TA
1 TA
2792899 ATAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 2 0.12
17 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTTTATAATTAAAAA
Found at i:2792917 original size:7 final size:7
Alignment explanation
Indices: 2792907--2792947 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
2792897 TAATAAAAAA
2792907 TAATAAT
1 TAATAAT
2792914 TAATAAT
1 TAATAAT
2792921 TAATAAT
1 TAATAAT
2792928 TAATAAT
1 TAATAAT
2792935 TAATAAT
1 TAATAAT
2792942 TAATAA
1 TAATAA
2792948 ATAGTATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TAATAAT
Found at i:2793147 original size:18 final size:17
Alignment explanation
Indices: 2793126--2793175 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
2793116 AAAATAAATT
2793126 ATATATATAAAATTAAAA
1 ATATATATAAAATT-AAA
* *
2793144 ATATAAATAAACTTAAA
1 ATATATATAAAATTAAA
2793161 ATAATATATTAAAAT
1 AT-ATATA-TAAAAT
2793176 ATAATAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 5 0.19
18 16 0.62
19 5 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATATATAAAATTAAA
Found at i:2793166 original size:20 final size:19
Alignment explanation
Indices: 2793114--2793168 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
2793104 TTAAAAAATT
* * *
2793114 TAAAAATAAATTATATATA
1 TAAAATTAAATAATATAAA
2793133 TAAAATTAAA-AATATAAA
1 TAAAATTAAATAATATAAA
*
2793151 TAAACTTAAAATAATATA
1 TAAAATT-AAATAATATA
2793169 TTAAAATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 12 0.40
19 12 0.40
20 6 0.20
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATTAAATAATATAAA
Found at i:2793183 original size:18 final size:18
Alignment explanation
Indices: 2793116--2793183 Score: 50
Period size: 18 Copynumber: 3.7 Consensus size: 18
2793106 AAAAAATTTA
*
2793116 AAAATA-AATTATATATAT
1 AAAATATAATAATATAT-T
* *
2793134 AAAAT-TAAAAATATAAAT
1 AAAATATAATAATAT-ATT
* *
2793152 AAACTTAAAATAATATATT
1 AAA-ATATAATAATATATT
2793171 AAAATATAATAAT
1 AAAATATAATAAT
2793184 TTTAATACAT
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
18 23 0.62
19 7 0.19
20 7 0.19
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATATAATAATATATT
Found at i:2796153 original size:42 final size:42
Alignment explanation
Indices: 2796099--2796208 Score: 175
Period size: 42 Copynumber: 2.6 Consensus size: 42
2796089 AAGAGAAAGA
* *
2796099 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGT
1 AGAGAGAAGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
2796141 AGAGATAAGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
1 AGAGAGAAGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
* *
2796183 AGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGAGAAGAGGGATGATAGGAGGAG
2796209 GAGAGAAGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.42, C:0.03, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGAGAAGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
Found at i:2802662 original size:26 final size:27
Alignment explanation
Indices: 2802607--2802661 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
2802597 ACTTAATTAA
2802607 TTATAATTTATTATATTTTTTAATATT
1 TTATAATTTATTATATTTTTTAATATT
* *
2802634 TTAT-ATTTATTTTATTTATTTGATATT
1 TTATAATTTATTATATTT-TTTAATATT
2802661 T
1 T
2802662 AAAAGTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (27 bp):
TTATAATTTATTATATTTTTTAATATT
Found at i:2803635 original size:15 final size:15
Alignment explanation
Indices: 2803615--2803644 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2803605 TAATAATTAT
2803615 TTAATTTAACAATAA
1 TTAATTTAACAATAA
2803630 TTAATTTAACAATAA
1 TTAATTTAACAATAA
2803645 ATTTTGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAATTTAACAATAA
Found at i:2803684 original size:15 final size:17
Alignment explanation
Indices: 2803653--2803685 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2803643 AAATTTTGAT
2803653 TATTTTATAATTAAAAA
1 TATTTTATAATTAAAAA
2803670 TATTTTA-AA-TAAAAA
1 TATTTTATAATTAAAAA
2803685 T
1 T
2803686 GATGAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATTTTATAATTAAAAA
Found at i:2803707 original size:7 final size:7
Alignment explanation
Indices: 2803695--2803721 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2803685 TGATGAAAAA
2803695 TAATAAT
1 TAATAAT
2803702 TAATAAT
1 TAATAAT
2803709 TAATAAT
1 TAATAAT
2803716 TAATAA
1 TAATAA
2803722 GAAGTGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TAATAAT
Found at i:2804471 original size:25 final size:25
Alignment explanation
Indices: 2804434--2804496 Score: 108
Period size: 25 Copynumber: 2.4 Consensus size: 25
2804424 TTAAATCAAT
2804434 TTAAGAGATAGATTTACACAACCATCA
1 TTAA-AGA-AGATTTACACAACCATCA
2804461 TTAAAGAAGATTTACACAACCATCA
1 TTAAAGAAGATTTACACAACCATCA
2804486 TTAAAGAAGAT
1 TTAAAGAAGAT
2804497 GCTATTAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 29 0.81
26 3 0.08
27 4 0.11
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (25 bp):
TTAAAGAAGATTTACACAACCATCA
Found at i:2806404 original size:34 final size:35
Alignment explanation
Indices: 2806361--2806426 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
2806351 AACCTTGCAA
*
2806361 CCCTATC-TTTTCATAGACTAAGATAGAACCTTTT
1 CCCTATCTTTTTCAAAGACTAAGATAGAACCTTTT
*
2806395 CCCTATCTTTTTCAAAGGCTAAGATAGAACCT
1 CCCTATCTTTTTCAAAGACTAAGATAGAACCT
2806427 CTCAATCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 7 0.24
35 22 0.76
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (35 bp):
CCCTATCTTTTTCAAAGACTAAGATAGAACCTTTT
Found at i:2806894 original size:20 final size:20
Alignment explanation
Indices: 2806868--2806925 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
2806858 CGTTAGGCCA
2806868 AATGTATCGATACAATTCTTG
1 AATGTATCGATACAATT-TTG
*
2806889 -ATGTATCGATAC-ACTTTG
1 AATGTATCGATACAATTTTG
2806907 AAATGTATCGATACAATTT
1 -AATGTATCGATACAATTT
2806926 CAACGTTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 24 0.75
21 3 0.09
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (20 bp):
AATGTATCGATACAATTTTG
Found at i:2807735 original size:21 final size:21
Alignment explanation
Indices: 2807693--2807740 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2807683 CGAACCTTTC
* **
2807693 TCTCCCCGAATTTATAGTACT
1 TCTCCCCGAATTTACAACACT
*
2807714 TCTCCCCGAGTTTACAACACT
1 TCTCCCCGAATTTACAACACT
2807735 TCTCCC
1 TCTCCC
2807741 TTTTTGACAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.38, G:0.08, T:0.33
Consensus pattern (21 bp):
TCTCCCCGAATTTACAACACT
Found at i:2812057 original size:13 final size:13
Alignment explanation
Indices: 2812041--2812083 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
2812031 ACAATTCATC
*
2812041 ATGTATCGACACA
1 ATGTATCGATACA
2812054 ATGTATCGATACA
1 ATGTATCGATACA
2812067 ATGTATCGATACA
1 ATGTATCGATACA
2812080 ATGT
1 ATGT
2812084 GTCATGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2812092 original size:20 final size:20
Alignment explanation
Indices: 2812067--2812182 Score: 69
Period size: 20 Copynumber: 5.7 Consensus size: 20
2812057 TATCGATACA
2812067 ATGTATCGATACAATGTGTC
1 ATGTATCGATACAATGTGTC
*
2812087 ATGTATTGATACAACTAGTGGT-
1 ATGTATCGATACAA-T-GT-GTC
* * * * *
2812109 AGGGTAGCTACTACCA-GTTTC
1 A-TGTATCGA-TACAATGTGTC
2812130 ATGTATCGATACAAT-TGTCC
1 ATGTATCGATACAATGTGT-C
* **
2812150 TTGTATCGATACAATG-AAC
1 ATGTATCGATACAATGTGTC
2812169 ATGTATCGATACAA
1 ATGTATCGATACAA
2812183 AACATAATGT
Statistics
Matches: 71, Mismatches: 16, Indels: 19
0.67 0.15 0.18
Matches are distributed among these distances:
19 20 0.28
20 34 0.48
21 4 0.06
22 3 0.04
23 6 0.08
24 4 0.06
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTGTC
Found at i:2812175 original size:19 final size:20
Alignment explanation
Indices: 2812129--2812182 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
2812119 CTACCAGTTT
**
2812129 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
2812149 CTTGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
2812168 CATGTATCGATACAA
1 CATGTATCGATACAA
2812183 AACATAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:2814712 original size:13 final size:13
Alignment explanation
Indices: 2814694--2814719 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2814684 TAGTAACCCT
2814694 TGTATCGATACAA
1 TGTATCGATACAA
2814707 TGTATCGATACAA
1 TGTATCGATACAA
2814720 AGAATATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2820963 original size:20 final size:20
Alignment explanation
Indices: 2820938--2820975 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2820928 TACTGCCAGT
2820938 TTCATGTATCGATACAATTG
1 TTCATGTATCGATACAATTG
2820958 TTCATGTATCGATACAAT
1 TTCATGTATCGATACAAT
2820976 GAACATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (20 bp):
TTCATGTATCGATACAATTG
Found at i:2820984 original size:19 final size:20
Alignment explanation
Indices: 2820940--2820992 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
2820930 CTGCCAGTTT
**
2820940 CATGTATCGATACAATTGTT
1 CATGTATCGATACAATTGAA
2820960 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
2820979 CATGTATTGATACA
1 CATGTATCGATACA
2820993 TTATATCGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:2823093 original size:33 final size:33
Alignment explanation
Indices: 2823037--2823100 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
2823027 AATTTCATAG
* *
2823037 TGTATCGATACATAGCAATTTGTATCGATACGA
1 TGTATCAATACATAGCAACTTGTATCGATACGA
* * *
2823070 TGTATCAATACTTTGCAACTTGTATTGATAC
1 TGTATCAATACATAGCAACTTGTATCGATAC
2823101 ATCTGCATGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (33 bp):
TGTATCAATACATAGCAACTTGTATCGATACGA
Found at i:2825373 original size:20 final size:21
Alignment explanation
Indices: 2825341--2825381 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2825331 GGAGGTGCTG
2825341 AACATGCTGT-AAATGCATGA
1 AACATGCTGTAAAATGCATGA
2825361 AACATAGCT-TAAAATGCATGA
1 AACAT-GCTGTAAAATGCATGA
2825382 TTCATGGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (21 bp):
AACATGCTGTAAAATGCATGA
Found at i:2826275 original size:52 final size:52
Alignment explanation
Indices: 2826197--2826325 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
2826187 CGAAATATGA
* *
2826197 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCAATACATCTGGGC
*
2826249 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCAATACATCTGGGC
2826301 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2826326 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCAATACATCTGGGC
Found at i:2826338 original size:52 final size:51
Alignment explanation
Indices: 2826197--2826345 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
2826187 CGAAATATGA
2826197 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* * *
2826249 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
2826301 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
2826346 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 86 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:2826352 original size:13 final size:13
Alignment explanation
Indices: 2826334--2826358 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2826324 CAAAGATCAG
2826334 TGTATCGATACAA
1 TGTATCGATACAA
2826347 TGTATCGATACA
1 TGTATCGATACA
2826359 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2826438 original size:13 final size:13
Alignment explanation
Indices: 2826420--2826444 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2826410 ACAAAATTTA
2826420 TGTATCGATACAT
1 TGTATCGATACAT
2826433 TGTATCGATACA
1 TGTATCGATACA
2826445 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2826440 original size:32 final size:33
Alignment explanation
Indices: 2826399--2826464 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
2826389 AGTAGCTTAA
2826399 ATTGTATCGATACAA-AATTTATGTATCGATAC
1 ATTGTATCGATACAACAATTTATGTATCGATAC
*
2826431 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAATTTATGTATCGATAC
2826464 A
1 A
2826465 AATCCTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 15 0.47
33 17 0.53
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (33 bp):
ATTGTATCGATACAACAATTTATGTATCGATAC
Found at i:2829413 original size:21 final size:21
Alignment explanation
Indices: 2829362--2829417 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
2829352 ATTAGAGGAG
*
2829362 AAATGAATGAGTTGGAAAAGA
1 AAATGAATGAGTTGCAAAAGA
2829383 AAA-GAAATGAGTTGCAAAATGA
1 AAATG-AATGAGTTGCAAAA-GA
2829405 AAATG-ATGAGTTG
1 AAATGAATGAGTTG
2829418 GCTAATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 1 0.03
21 24 0.77
22 5 0.16
23 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.27, T:0.21
Consensus pattern (21 bp):
AAATGAATGAGTTGCAAAAGA
Found at i:2830959 original size:13 final size:13
Alignment explanation
Indices: 2830918--2830959 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2830908 ACAAAGAAAG
2830918 TTATATCGATACA
1 TTATATCGATACA
* * *
2830931 CTGTATCGATATA
1 TTATATCGATACA
2830944 TTATATCGATACA
1 TTATATCGATACA
2830957 TTA
1 TTA
2830960 CTTTGGTATG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (13 bp):
TTATATCGATACA
Found at i:2832546 original size:10 final size:10
Alignment explanation
Indices: 2832527--2832557 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2832517 ATCTCATTTT
2832527 TCACTGTTCA
1 TCACTGTTCA
*
2832537 TCACTATTCA
1 TCACTGTTCA
2832547 TCACTGTTCA
1 TCACTGTTCA
2832557 T
1 T
2832558 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:2832661 original size:73 final size:73
Alignment explanation
Indices: 2832537--2832685 Score: 201
Period size: 73 Copynumber: 2.0 Consensus size: 73
2832527 TCACTGTTCA
* * * * *
2832537 TCACTATTCATCACTGTTCATGTATCGATACATCATTGTTCATTACTATACATTGAGC-CTAACG
1 TCACTATTCATCACTGTTCATGTATCGATACATCACTGTTCATCACGATACATTAAGCTC-AACA
*
2832601 GCTATAATT
65 ACTATAATT
* * *
2832610 TCACTGTTCATCAGTGTTCATGTATCGATACATCACTGTTTATCACGATACATTAAGCTCAACAA
1 TCACTATTCATCACTGTTCATGTATCGATACATCACTGTTCATCACGATACATTAAGCTCAACAA
2832675 CTATAATT
66 CTATAATT
2832683 TCA
1 TCA
2832686 AATACATGTA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
73 65 0.98
74 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (73 bp):
TCACTATTCATCACTGTTCATGTATCGATACATCACTGTTCATCACGATACATTAAGCTCAACAA
CTATAATT
Found at i:2835534 original size:21 final size:22
Alignment explanation
Indices: 2835475--2835536 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 22
2835465 AAATATTTTG
2835475 AATTTTTATATTTTTTAAAAAATC
1 AATTTTTA-ATTTTTT-AAAAATC
* * *
2835499 ACTTATTTGATTTTTTAAAACT-
1 AATT-TTTAATTTTTTAAAAATC
2835521 AATTTTTAATTTTTTA
1 AATTTTTAATTTTTTA
2835537 TCTTGATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 11 0.34
22 3 0.09
23 5 0.16
24 10 0.31
25 3 0.09
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (22 bp):
AATTTTTAATTTTTTAAAAATC
Found at i:2837692 original size:20 final size:19
Alignment explanation
Indices: 2837650--2837702 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
2837640 ATCAATGGAG
**
2837650 TGTATCGATACATGTTCAT
1 TGTATCGATACATGGACAT
2837669 TGTATCGATACATGGACAAT
1 TGTATCGATACATGGAC-AT
2837689 TGTAT-GAATACATG
1 TGTATCG-ATACATG
2837703 AAACTAGCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATGGACAT
Found at i:2837768 original size:13 final size:13
Alignment explanation
Indices: 2837750--2837801 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
2837740 TACATAGGAC
2837750 ATTGTATCGATAT
1 ATTGTATCGATAT
** * *
2837763 ATTGTATATAGGAC
1 ATTGTATCGA-TAT
2837777 ATTGTATCGATAT
1 ATTGTATCGATAT
2837790 ATTGTATCGATA
1 ATTGTATCGATA
2837802 CATGATGAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
13 21 0.70
14 9 0.30
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (13 bp):
ATTGTATCGATAT
Found at i:2837781 original size:27 final size:27
Alignment explanation
Indices: 2837743--2837796 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2837733 GTATCGATAC
2837743 ATAGGACATTGTATCGATATATTGTAT
1 ATAGGACATTGTATCGATATATTGTAT
2837770 ATAGGACATTGTATCGATATATTGTAT
1 ATAGGACATTGTATCGATATATTGTAT
2837797 CGATACATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (27 bp):
ATAGGACATTGTATCGATATATTGTAT
Found at i:2840048 original size:21 final size:20
Alignment explanation
Indices: 2840014--2840056 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2840004 TATTAAAAAG
*
2840014 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAACAA-GAA
2840035 TTAGCTAA-GAAAAACAAGAA
1 TTAGCTAATG-AAAACAAGAA
2840055 TT
1 TT
2840057 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (20 bp):
TTAGCTAATGAAAACAAGAA
Found at i:2840055 original size:20 final size:21
Alignment explanation
Indices: 2840014--2840056 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
2840004 TATTAAAAAG
*
2840014 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAATAAAGAA
2840035 TTAGCTAA-GAAAA-ACAAGAA
1 TTAGCTAATGAAAATA-AAGAA
2840055 TT
1 TT
2840057 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.55
21 8 0.40
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (21 bp):
TTAGCTAATGAAAATAAAGAA
Found at i:2845363 original size:20 final size:20
Alignment explanation
Indices: 2845319--2845376 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2845309 ATTTCAATGA
***
2845319 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACATATTTT
*
2845339 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
2845359 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
2845377 AAGCTACTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:2845433 original size:13 final size:13
Alignment explanation
Indices: 2845415--2845439 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2845405 ATCACTTAAA
2845415 TGTATCGATACAT
1 TGTATCGATACAT
2845428 TGTATCGATACA
1 TGTATCGATACA
2845440 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2849388 original size:13 final size:13
Alignment explanation
Indices: 2849370--2849421 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
2849360 GATACATAGG
2849370 ACATTGTATCGAT
1 ACATTGTATCGAT
2849383 ACATTGTATCGAT
1 ACATTGTATCGAT
2849396 ACA-TG-AT-G--
1 ACATTGTATCGAT
2849404 A-ATTGTATCGAT
1 ACATTGTATCGAT
2849416 ACATTG
1 ACATTG
2849422 CTTATAACGG
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 20 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:2849395 original size:33 final size:33
Alignment explanation
Indices: 2849353--2849421 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
2849343 TTACCACTGT
2849353 TTGTATCGATACAT-AGGACATTGTATCGATACA
1 TTGTATCGATACATGAGGA-ATTGTATCGATACA
*
2849386 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGAGGAATTGTATCGATACA
2849419 TTG
1 TTG
2849422 CTTATAACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 31 0.91
34 3 0.09
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGAGGAATTGTATCGATACA
Found at i:2852394 original size:12 final size:11
Alignment explanation
Indices: 2852377--2852441 Score: 57
Period size: 12 Copynumber: 5.9 Consensus size: 11
2852367 AAAAAGAAAG
2852377 AGGAGGGATGAT
1 AGGAGGGA-GAT
2852389 AGGAGGAGAGAT
1 AGGAGG-GAGAT
2852401 AGGA--GAGAT
1 AGGAGGGAGAT
*
2852410 AGTA--GAGAT
1 AGGAGGGAGAT
2852419 AGGAGGGATGAT
1 AGGAGGGA-GAT
2852431 AGGAGGAGAGA
1 AGGAGG-GAGA
2852442 CATGAGAGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
9 16 0.35
11 2 0.04
12 24 0.52
13 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.48, T:0.12
Consensus pattern (11 bp):
AGGAGGGAGAT
Found at i:2852417 original size:11 final size:9
Alignment explanation
Indices: 2852392--2852423 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2852382 GGATGATAGG
2852392 AGGAGAGAT
1 AGGAGAGAT
2852401 AGGAGAGAT
1 AGGAGAGAT
*
2852410 AGTAGAGAT
1 AGGAGAGAT
2852419 AGGAG
1 AGGAG
2852424 GGATGATAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:2852424 original size:42 final size:42
Alignment explanation
Indices: 2852375--2852480 Score: 158
Period size: 42 Copynumber: 2.5 Consensus size: 42
2852365 GAAAAAAGAA
* * *
2852375 AGAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAGTAGAG
1 AGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAAAG
* *
2852417 ATAGGAGGGATGATAGGAGGAGAGACATGAGAGATAATAAAG
1 AGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAAAG
*
2852459 AGAGGAGGGATGACAGGAGGAG
1 AGAGGAGGGATGATAGGAGGAG
2852481 GAGAGAAGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.11
Consensus pattern (42 bp):
AGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAAAG
Found at i:2859002 original size:63 final size:63
Alignment explanation
Indices: 2858903--2859055 Score: 225
Period size: 63 Copynumber: 2.4 Consensus size: 63
2858893 ACATGCTCCT
* ** * *
2858903 ATGTATCGATAGAATTCATAATGTATCGATACAATGCATTTAAAATTCTAGCCGTTGGGCTCA
1 ATGTATCGATAAAATTCACCATGTATCGATACAATGCATTTAAAATTATAGCCGTTGAGCTCA
* *
2858966 ATGTATCGATAAAATTCACCATGTATTGATACAATGCATTTAAAATTATAGCCGTTGAGCTTA
1 ATGTATCGATAAAATTCACCATGTATCGATACAATGCATTTAAAATTATAGCCGTTGAGCTCA
* *
2859029 ATGTATCGATATAATTTACCATGTATC
1 ATGTATCGATAAAATTCACCATGTATC
2859056 ACAATTGAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 80 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (63 bp):
ATGTATCGATAAAATTCACCATGTATCGATACAATGCATTTAAAATTATAGCCGTTGAGCTCA
Found at i:2860740 original size:21 final size:22
Alignment explanation
Indices: 2860716--2860760 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2860706 TTTAATGTGT
*
2860716 AATTGAAGAAATTTGA-G-TTGG
1 AATTAAAG-AATTTGATGATTGG
2860737 AATTAAAGAATTTGATGATTGG
1 AATTAAAGAATTTGATGATTGG
2860759 AA
1 AA
2860761 ATCAAGGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 8 0.38
22 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.33
Consensus pattern (22 bp):
AATTAAAGAATTTGATGATTGG
Found at i:2860880 original size:13 final size:13
Alignment explanation
Indices: 2860862--2860886 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2860852 ATAATTTTAA
2860862 TGTATCGATACAT
1 TGTATCGATACAT
2860875 TGTATCGATACA
1 TGTATCGATACA
2860887 ATTTCTTTGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2860890 original size:32 final size:32
Alignment explanation
Indices: 2860843--2860903 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2860833 ATAGTTGAAA
*
2860843 TGTATAGATATAATTT-TAATGTATCGATACAT
1 TGTATAGATACAATTTCT-ATGTATCGATACAT
* *
2860875 TGTATCGATACAATTTCTTTGTATCGATA
1 TGTATAGATACAATTTCTATGTATCGATA
2860904 AATCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 24 0.96
33 1 0.04
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (32 bp):
TGTATAGATACAATTTCTATGTATCGATACAT
Found at i:2866949 original size:20 final size:20
Alignment explanation
Indices: 2866924--2866962 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2866914 ACACACTCTT
*
2866924 ATGTATCGATAGAATTCATA
1 ATGTATCGATACAATTCATA
2866944 ATGTATCGATACAATTCAT
1 ATGTATCGATACAATTCAT
2866963 TTAAACTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:2867012 original size:20 final size:20
Alignment explanation
Indices: 2866987--2867024 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2866977 ATTGGGCTTA
2866987 ATGTATCGATACAATTCACT
1 ATGTATCGATACAATTCACT
2867007 ATGTATCGATACAATTCA
1 ATGTATCGATACAATTCA
2867025 TTTAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATTCACT
Found at i:2867023 original size:63 final size:63
Alignment explanation
Indices: 2866924--2867087 Score: 240
Period size: 63 Copynumber: 2.6 Consensus size: 63
2866914 ACACACTCTT
* * *
2866924 ATGTATCGATAGAATTCA-TAATGTATCGATACAATTCATTTAAACTTCTAGCCATTGGGCTTA
1 ATGTATCGATACAATTCACT-ATGTATCGATACAATTCATTTAAAATTATAGCCATTGGGCTTA
*
2866987 ATGTATCGATACAATTCACTATGTATCGATACAATTCATTTAAAATTATAGCCGTTGGGCTTA
1 ATGTATCGATACAATTCACTATGTATCGATACAATTCATTTAAAATTATAGCCATTGGGCTTA
* * * *
2867050 ATGTATCAATACAATTTACCATGTATTGATACAATTCA
1 ATGTATCGATACAATTCACTATGTATCGATACAATTCA
2867088 ATTATGAACA
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
63 91 0.99
64 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (63 bp):
ATGTATCGATACAATTCACTATGTATCGATACAATTCATTTAAAATTATAGCCATTGGGCTTA
Done.