Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000219.1 Hibiscus syriacus cultivar Beakdansim tig00000387_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 169236
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
File 1 of 2
Found at i:1818 original size:23 final size:23
Alignment explanation
Indices: 1766--1818 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1756 AGAATAAGTT
* *
1766 TATCTTCGTGACACGTTTATCTC
1 TATCTTTGTGACACATTTATCTC
*
1789 TACCTTTGTGACACATTTATCTC
1 TATCTTTGTGACACATTTATCTC
*
1812 TTTCTTT
1 TATCTTT
1819 TGGTAGTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.17, C:0.25, G:0.09, T:0.49
Consensus pattern (23 bp):
TATCTTTGTGACACATTTATCTC
Found at i:2748 original size:15 final size:16
Alignment explanation
Indices: 2724--2760 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2714 GTTATTGAAT
*
2724 TGACTAGATA-TTACC
1 TGACTTGATATTTACC
2739 TGACTTGATATTTACC
1 TGACTTGATATTTACC
2755 TGACTT
1 TGACTT
2761 ATAAGTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (16 bp):
TGACTTGATATTTACC
Found at i:2943 original size:19 final size:18
Alignment explanation
Indices: 2909--2946 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2899 ATTAATTCCA
2909 ATTCTTTATATTATTTAT
1 ATTCTTTATATTATTTAT
*
2927 ATTCTTATATTTTATTTAT
1 ATTCTT-TATATTATTTAT
2946 A
1 A
2947 ATCATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTCTTTATATTATTTAT
Found at i:3682 original size:20 final size:20
Alignment explanation
Indices: 3657--3724 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
3647 AACCCTTACA
*
3657 AATATCAAGCAGAATCAAAC
1 AATATCAAACAGAATCAAAC
3677 AATATCAAACAGAAGT-AAAC
1 AATATCAAACAGAA-TCAAAC
* * *
3697 AATATCAAACATAAGCAAGC
1 AATATCAAACAGAATCAAAC
3717 AATATCAA
1 AATATCAA
3725 GCACCAACTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 41 0.98
21 1 0.02
ACGTcount: A:0.57, C:0.18, G:0.09, T:0.16
Consensus pattern (20 bp):
AATATCAAACAGAATCAAAC
Found at i:6254 original size:6 final size:6
Alignment explanation
Indices: 6244--6366 Score: 77
Period size: 6 Copynumber: 20.5 Consensus size: 6
6234 GTTTGGATAC
* * * *
6244 GGGTTC GGGTTT GGGTTT GGATTC GAGTTT GGGTTT GGGTTT GGGTTT
1 GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT
* * * * ** * * * ** *
6292 GAGATC GAGTTT GGAATC AGGTTC AAGTTT GGGTTT GGGTTT -GGTTCC
1 GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTT-T
*
6340 GGGTTC GGGTTT GGGTTT GGGTTT GGG
1 GGGTTT GGGTTT GGGTTT GGGTTT GGG
6367 CTCTGGTTAG
Statistics
Matches: 90, Mismatches: 25, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
5 4 0.04
6 82 0.91
7 4 0.04
ACGTcount: A:0.08, C:0.07, G:0.44, T:0.41
Consensus pattern (6 bp):
GGGTTT
Found at i:6278 original size:30 final size:30
Alignment explanation
Indices: 6244--6305 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
6234 GTTTGGATAC
6244 GGGTTCGGGTTTGGGTTTG-GATTCGAGTTT
1 GGGTTCGGGTTTGGGTTTGAGA-TCGAGTTT
*
6274 GGGTTTGGGTTTGGGTTTGAGATCGAGTTT
1 GGGTTCGGGTTTGGGTTTGAGATCGAGTTT
6304 GG
1 GG
6306 AATCAGGTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.08, C:0.05, G:0.45, T:0.42
Consensus pattern (30 bp):
GGGTTCGGGTTTGGGTTTGAGATCGAGTTT
Found at i:6380 original size:30 final size:30
Alignment explanation
Indices: 6318--6380 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
6308 TCAGGTTCAA
* *
6318 GTTTGGGTTTGGGTTTGGTTCCGGGTTCGG
1 GTTTGGGTTTGGGTTTGGCTCCGGGTTAGG
*
6348 GTTTGGGTTTGGGTTTGGGCT-CTGGTTAGG
1 GTTTGGGTTTGGGTTT-GGCTCCGGGTTAGG
6378 GTT
1 GTT
6381 AGAGAATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.02, C:0.08, G:0.46, T:0.44
Consensus pattern (30 bp):
GTTTGGGTTTGGGTTTGGCTCCGGGTTAGG
Found at i:6796 original size:103 final size:104
Alignment explanation
Indices: 6664--6889 Score: 355
Period size: 104 Copynumber: 2.2 Consensus size: 104
6654 GGGGAAGAAC
* * * *
6664 TGAGATGAACACGAATGAACAAGGGTTGAATTTTTGGGTGTTTGGTCGAAAAAATAC-TAAATAG
1 TGAGATGAAAACGAATGAACAAGGGTTGAATTTTTGGGTGTTTGATCGAAAAAAAACACAAATAG
6728 TTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGGGTTTT
66 TTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGGGTTTT
* * *
6767 TGAGATGAAAATGAATGAATAAGGGTTGAATTTTTGGGTGTTTGATCGAAAAAAAACACAAATGG
1 TGAGATGAAAACGAATGAACAAGGGTTGAATTTTTGGGTGTTTGATCGAAAAAAAACACAAATAG
6832 TTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGGGTTTT
66 TTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGGGTTTT
* * *
6871 TGGGATGAACACGGATGAA
1 TGAGATGAAAACGAATGAA
6890 AAAAATGAAA
Statistics
Matches: 111, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
103 52 0.47
104 59 0.53
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (104 bp):
TGAGATGAAAACGAATGAACAAGGGTTGAATTTTTGGGTGTTTGATCGAAAAAAAACACAAATAG
TTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGGGTTTT
Found at i:6905 original size:104 final size:103
Alignment explanation
Indices: 6664--6904 Score: 306
Period size: 103 Copynumber: 2.3 Consensus size: 103
6654 GGGGAAGAAC
* * *** * * *
6664 TGAGATGAACACGAATGAACAAGGGTTGAATTTTTGGGTGTTTGGTCGAAAAAATACTAAATAGT
1 TGAGATGAAAACGAATGAATAAGAAATGAATTTTTGGGTGTTTGATCGAAAAAAAACCAAATAGT
6729 TTGGGTTTTGGTGTTTGTGAAGATCAAATGAGGGTTTT
66 TTGGGTTTTGGTGTTTGTGAAGATCAAATGAGGGTTTT
* *** *
6767 TGAGATGAAAATGAATGAATAAGGGTTGAATTTTTGGGTGTTTGATCGAAAAAAAACACAAATGG
1 TGAGATGAAAACGAATGAATAAGAAATGAATTTTTGGGTGTTTGATCGAAAAAAAAC-CAAATAG
6832 TTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGGGTTTT
65 TTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGGGTTTT
* * *
6871 TGGGATGAACACGGATGAA-AA-AAATGAAATTTTT
1 TGAGATGAAAACGAATGAATAAGAAATG-AATTTTT
6905 TTAGAGAATC
Statistics
Matches: 122, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
102 2 0.02
103 61 0.50
104 59 0.48
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (103 bp):
TGAGATGAAAACGAATGAATAAGAAATGAATTTTTGGGTGTTTGATCGAAAAAAAACCAAATAGT
TTGGGTTTTGGTGTTTGTGAAGATCAAATGAGGGTTTT
Found at i:7210 original size:25 final size:25
Alignment explanation
Indices: 7161--7231 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
7151 CAATTCTTTC
7161 AATTAATATATATGCTTATATTAATA
1 AATTAATATATA-GCTTATATTAATA
* *
7187 AATTAACATATAGTTTATATTAATA
1 AATTAATATATAGCTTATATTAATA
*
7212 AATTAATATATAGGTTATAT
1 AATTAATATATAGCTTATAT
7232 ATTCTAATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 30 0.73
26 11 0.27
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (25 bp):
AATTAATATATAGCTTATATTAATA
Found at i:7249 original size:51 final size:51
Alignment explanation
Indices: 7202--7310 Score: 148
Period size: 51 Copynumber: 2.1 Consensus size: 51
7192 ACATATAGTT
* *
7202 TATA-TTAATAAATTAATATATAGGTTATATATTCTAATGAACTATATAATA
1 TATAGTTAATAAA-TAATATATAGGTTATATATACTAATAAACTATATAATA
* * * *
7253 TATAGTTTATATATACTATATAGTTTATATATACTAATAAACTATATAATA
1 TATAGTTAATAAATAATATATAGGTTATATATACTAATAAACTATATAATA
7304 TATAGTT
1 TATAGTT
7311 TATATATACC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
51 45 0.88
52 6 0.12
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.45
Consensus pattern (51 bp):
TATAGTTAATAAATAATATATAGGTTATATATACTAATAAACTATATAATA
Found at i:7267 original size:18 final size:18
Alignment explanation
Indices: 7244--7403 Score: 107
Period size: 18 Copynumber: 8.7 Consensus size: 18
7234 TCTAATGAAC
*
7244 TATATAATATATAGTTTA
1 TATATACTATATAGTTTA
7262 TATATACTATATAGTTTA
1 TATATACTATATAGTTTA
***
7280 TATATACTA-ATAAACTA
1 TATATACTATATAGTTTA
7297 TATA-A-TATATAGTTTA
1 TATATACTATATAGTTTA
* *
7313 TATATACCATATACTTTA
1 TATATACTATATAGTTTA
*
7331 TAAATAGTTTTTA-TATATAGTTCA
1 T--ATA-----TACTATATAGTTTA
*
7355 TATATAACTACATAG-TTA
1 TATAT-ACTATATAGTTTA
* *
7373 TATAAACTATATA-TGTA
1 TATATACTATATAGTTTA
7390 CTATATACTATATA
1 -TATATACTATATA
7404 AATAGTTTAT
Statistics
Matches: 110, Mismatches: 18, Indels: 28
0.71 0.12 0.18
Matches are distributed among these distances:
15 2 0.02
16 10 0.09
17 20 0.18
18 55 0.50
19 6 0.05
20 3 0.03
22 3 0.03
24 9 0.08
25 2 0.02
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (18 bp):
TATATACTATATAGTTTA
Found at i:7311 original size:51 final size:51
Alignment explanation
Indices: 7218--7332 Score: 185
Period size: 51 Copynumber: 2.3 Consensus size: 51
7208 AATAAATTAA
* * *
7218 TATATAGGTTATATATTCTAATGAACTATATAATATATAGTTTATATATAC
1 TATATAGTTTATATATACTAATAAACTATATAATATATAGTTTATATATAC
7269 TATATAGTTTATATATACTAATAAACTATATAATATATAGTTTATATATAC
1 TATATAGTTTATATATACTAATAAACTATATAATATATAGTTTATATATAC
* *
7320 CATATACTTTATA
1 TATATAGTTTATA
7333 AATAGTTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (51 bp):
TATATAGTTTATATATACTAATAAACTATATAATATATAGTTTATATATAC
Found at i:7371 original size:19 final size:17
Alignment explanation
Indices: 7347--7381 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
7337 GTTTTTATAT
7347 ATAGTTCATATATAACTAC
1 ATAGTT-ATATA-AACTAC
7366 ATAGTTATATAAACTA
1 ATAGTTATATAAACTA
7382 TATATGTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (17 bp):
ATAGTTATATAAACTAC
Found at i:7482 original size:15 final size:15
Alignment explanation
Indices: 7467--7501 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
7457 TACTTTGAAT
7467 TTATAT-AGTATAAA
1 TTATATAAGTATAAA
7481 TTATATAAGTATAAA
1 TTATATAAGTATAAA
7496 TTATAT
1 TTATAT
7502 TATATTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (15 bp):
TTATATAAGTATAAA
Found at i:7592 original size:13 final size:13
Alignment explanation
Indices: 7560--7784 Score: 99
Period size: 14 Copynumber: 16.5 Consensus size: 13
7550 AACTATAGTT
*
7560 TATATAATTTATA
1 TATATAGTTTATA
* *
7573 TACATAGTTTTTA
1 TATATAGTTTATA
*
7586 TATATAGTTCATATG
1 TATATAGTT--TATA
*
7601 TAACTATA-TGTATA
1 T-A-TATAGTTTATA
*
7615 GTATATAGTATATA
1 -TATATAGTTTATA
*
7629 GTATATAGTATATA
1 -TATATAGTTTATA
7643 GTATATAG--TATA
1 -TATATAGTTTATA
*
7655 TAGTATAGTATATA
1 TA-TATAGTTTATA
7669 GTATATAG-TTATA
1 -TATATAGTTTATA
7682 GTATATAG--TATA
1 -TATATAGTTTATA
7694 TAGTATAG--TATA
1 TA-TATAGTTTATA
*
7706 GTATATAGTATAAGTA
1 -TATATAGT-TTA-TA
7722 TAGTATAGTATATATA
1 TA-TATAGT-T-TATA
*
7738 GTATATAGTATATA
1 -TATATAGTTTATA
* *
7752 TATATAATATATCA
1 TATATAGTTTAT-A
7766 -ACTATAGTTTATA
1 TA-TATAGTTTATA
7779 TATATA
1 TATATA
7785 CTATATATTG
Statistics
Matches: 174, Mismatches: 16, Indels: 44
0.74 0.07 0.19
Matches are distributed among these distances:
11 4 0.02
12 27 0.16
13 53 0.30
14 54 0.31
15 9 0.05
16 20 0.11
17 7 0.04
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:7623 original size:7 final size:7
Alignment explanation
Indices: 7611--7763 Score: 205
Period size: 7 Copynumber: 22.4 Consensus size: 7
7601 TAACTATATG
7611 TATAGTA
1 TATAGTA
7618 TATAGTA
1 TATAGTA
7625 TATAGTA
1 TATAGTA
7632 TATAGTA
1 TATAGTA
7639 TATAGTA
1 TATAGTA
7646 TATAGTA
1 TATAGTA
7653 TATAG--
1 TATAGTA
7658 TATAGTA
1 TATAGTA
7665 TATAGTA
1 TATAGTA
7672 TATAGT-
1 TATAGTA
7678 TATAGTA
1 TATAGTA
7685 TATAGTA
1 TATAGTA
7692 TATAGTATA
1 TATAG--TA
7701 GTATAGTA
1 -TATAGTA
7709 TATAGTA
1 TATAGTA
7716 TA-AG--
1 TATAGTA
7720 TATAGTA
1 TATAGTA
7727 TAGTA-TA
1 TA-TAGTA
7734 TATAGTA
1 TATAGTA
7741 TATAGTA
1 TATAGTA
7748 TATA-TA
1 TATAGTA
*
7754 TATAATA
1 TATAGTA
7761 TAT
1 TAT
7764 CAACTATAGT
Statistics
Matches: 134, Mismatches: 0, Indels: 24
0.85 0.00 0.15
Matches are distributed among these distances:
4 2 0.01
5 7 0.05
6 16 0.12
7 98 0.73
8 4 0.03
9 2 0.01
10 5 0.04
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (7 bp):
TATAGTA
Found at i:7749 original size:5 final size:5
Alignment explanation
Indices: 7605--7742 Score: 109
Period size: 5 Copynumber: 27.8 Consensus size: 5
7595 CATATGTAAC
7605 TATATG TATAG TATA- TAGTA- TATAG TATA- TAGTA- TATAG TATA-
1 TATA-G TATAG TATAG TA-TAG TATAG TATAG TA-TAG TATAG TATAG
7648 TAGTA- TATAG TATAG TATA- TAGTA- TATAG TTATAG TATA- TAGTA-
1 TA-TAG TATAG TATAG TATAG TA-TAG TATAG -TATAG TATAG TA-TAG
7692 TATAG TATAG TATAG TATATAG TATAAG TATAG TATAG TATA- TATAG
1 TATAG TATAG TATAG --TATAG TAT-AG TATAG TATAG TATAG TATAG
7739 TATA
1 TATA
7743 TAGTATATAT
Statistics
Matches: 117, Mismatches: 0, Indels: 31
0.79 0.00 0.21
Matches are distributed among these distances:
4 24 0.21
5 74 0.63
6 14 0.12
7 5 0.04
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (5 bp):
TATAG
Found at i:7820 original size:30 final size:31
Alignment explanation
Indices: 7768--8005 Score: 93
Period size: 30 Copynumber: 8.1 Consensus size: 31
7758 ATATATCAAC
* * * *
7768 TATAGTTTATATATATACTATATATTGTTTA
1 TATAGTTCATATATAAACTATATATAGTTCA
7799 TATAGTTCAT-TATAAACTATATATAGTTCA
1 TATAGTTCATATATAAACTATATATAGTTCA
*
7829 TAT-G--CAATAATGTAAAC--TATATA-TT-A
1 TATAGTTC-AT-ATATAAACTATATATAGTTCA
* * *
7855 TATAGTAT-AAATATCAACTATATATATAGTTTA
1 TATAGT-TCATATATAAAC--TATATATAGTTCA
* * *
7888 TATAATTTATATATATA-TATATATAGTTCA
1 TATAGTTCATATATAAACTATATATAGTTCA
** * * *
7918 TAT-GTAAAT-TATATAGTA-A-ATAGTTTA
1 TATAGTTCATATATAAACTATATATAGTTCA
* * *
7945 TAT-G-T-AGTATAT--ACTATAAATAATTTA
1 TATAGTTCA-TATATAAACTATATATAGTTCA
7972 TATAGTTCAT-TAATAAACTATATATATGTTCA
1 TATAGTTCATAT-ATAAACTATATATA-GTTCA
8004 TA
1 TA
8006 CGTAAATTAT
Statistics
Matches: 158, Mismatches: 23, Indels: 51
0.68 0.10 0.22
Matches are distributed among these distances:
25 4 0.03
26 6 0.04
27 34 0.22
28 18 0.11
29 10 0.06
30 42 0.27
31 24 0.15
32 8 0.05
33 12 0.08
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (31 bp):
TATAGTTCATATATAAACTATATATAGTTCA
Found at i:7858 original size:2 final size:2
Alignment explanation
Indices: 7846--7912 Score: 50
Period size: 2 Copynumber: 33.0 Consensus size: 2
7836 TAATGTAAAC
* *
7846 TA TA TA T- TA TA TA GTA TA AA TA TCA -A CTA TA TA TA TA GTT TA
1 TA TA TA TA TA TA TA -TA TA TA TA T-A TA -TA TA TA TA TA -TA TA
*
7888 TA TA -A TT TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
7913 GTTCATATGT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
1 3 0.06
2 44 0.85
3 5 0.10
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:7957 original size:27 final size:25
Alignment explanation
Indices: 7897--7974 Score: 84
Period size: 27 Copynumber: 3.0 Consensus size: 25
7887 ATATAATTTA
* *
7897 TATATATATATATATAGTTCATATG
1 TATATATATATAAATAGTTTATATG
*
7922 TAAATTATATAGTAAATAGTTTATATG
1 TATA-TATATA-TAAATAGTTTATATG
*
7949 TAGTATATACTATAAATAATTTATAT
1 TA-TATATA-TATAAATAGTTTATAT
7975 AGTTCATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
25 3 0.07
26 6 0.14
27 32 0.73
28 3 0.07
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (25 bp):
TATATATATATAAATAGTTTATATG
Found at i:8116 original size:29 final size:27
Alignment explanation
Indices: 8069--8132 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 27
8059 TATATATATT
* *
8069 TATACATATAGTTCTATGTAAACTATA
1 TATATATATAGTTCAATGTAAACTATA
8096 TAGTATATATAGTTCAAATGTAAACTATA
1 TA-TATATATAGTTC-AATGTAAACTATA
8125 TATATATA
1 TATATATA
8133 ATTTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.06
28 17 0.52
29 14 0.42
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (27 bp):
TATATATATAGTTCAATGTAAACTATA
Found at i:8143 original size:77 final size:80
Alignment explanation
Indices: 7993--8144 Score: 186
Period size: 77 Copynumber: 1.9 Consensus size: 80
7983 AATAAACTAT
* * * *
7993 ATATATGTTCATACGTAAATTATATAGTTTATATATAATTCATATGTAAACATGTAAACTATATT
1 ATATATGTTCATACGTAAACTATATAG-TTATATATAATTCAAATGTAAACATATAAACTATAAT
*
8058 TTATATATATTTATAC
65 TTACATATATTTATAC
* * *
8074 ATATA-GTTC-TATGTAAACTATATAG-TATATATAGTTCAAATGTAAACTATATATA-TATAAT
1 ATATATGTTCATACGTAAACTATATAGTTATATATAATTCAAATGTAAAC-ATATAAACTATAAT
8135 TTACATATAT
65 TTACATATAT
8145 AATAAGTTAG
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
77 34 0.55
78 5 0.08
79 14 0.23
80 4 0.06
81 5 0.08
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (80 bp):
ATATATGTTCATACGTAAACTATATAGTTATATATAATTCAAATGTAAACATATAAACTATAATT
TACATATATTTATAC
Found at i:8295 original size:33 final size:33
Alignment explanation
Indices: 8256--8321 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
8246 ATATATAAAT
* * *
8256 ATAAACTATATAGTTCATATATAGTTTATATTA
1 ATAAACTATATACTTCATACATAGTATATATTA
*
8289 ATAAACTATATACTTTATACATAGTATATATTA
1 ATAAACTATATACTTCATACATAGTATATATTA
8322 TTTATAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (33 bp):
ATAAACTATATACTTCATACATAGTATATATTA
Found at i:12152 original size:30 final size:30
Alignment explanation
Indices: 12116--12180 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
12106 ATTTTTTTGT
12116 AGTGTCTAACGTTTTCTCCATTATCATTTA
1 AGTGTCTAACGTTTTCTCCATTATCATTTA
12146 AGTGTCTAACGTTTTCTCCATTATCATTTA
1 AGTGTCTAACGTTTTCTCCATTATCATTTA
12176 AGTGT
1 AGTGT
12181 TTAGTCGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.46
Consensus pattern (30 bp):
AGTGTCTAACGTTTTCTCCATTATCATTTA
Found at i:14476 original size:4 final size:4
Alignment explanation
Indices: 14467--14495 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
14457 TTACAGAGAC
14467 AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA A
14496 TGGAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:14996 original size:3 final size:3
Alignment explanation
Indices: 14988--15037 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
14978 ATAAATATTA
* *
14988 AAT AAT AAT AAT AAT AAAT ATT AAT AAT AAT -AT AAT -AT AAAT AAC
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
15033 AAT AA
1 AAT AA
15038 CCAAGACAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 4 0.10
3 30 0.77
4 5 0.13
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:15005 original size:16 final size:16
Alignment explanation
Indices: 14981--15037 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
14971 AATTAACATA
*
14981 AATATTAAATAATAAT
1 AATAATAAATAATAAT
*
14997 AATAATAAATATTAAT
1 AATAATAAATAATAAT
15013 AATAATATAAT-ATAAAT
1 AATAATA-AATAAT-AAT
*
15030 AACAATAA
1 AATAATAA
15038 CCAAGACAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
16 23 0.66
17 12 0.34
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAATAAATAATAAT
Found at i:15596 original size:20 final size:20
Alignment explanation
Indices: 15571--15628 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
15561 AATTTTCTTA
**
15571 TGGTTTCGAAACCCCCTTGC
1 TGGTTTCGAAACCCCCTAAC
* *
15591 TGGTTTTGAAACCCTCTAAC
1 TGGTTTCGAAACCCCCTAAC
*
15611 TGGTTTCTAAACTCCCCT
1 TGGTTTCGAAAC-CCCCT
15629 GCCTCGTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34
Consensus pattern (20 bp):
TGGTTTCGAAACCCCCTAAC
Found at i:17342 original size:30 final size:30
Alignment explanation
Indices: 17308--17366 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
17298 CTAAATTTAG
17308 AGTATAGTTTAATGATTTAAGTAACCCAAT
1 AGTATAGTTTAATGATTTAAGTAACCCAAT
*
17338 AGTATAGTTTAATGATTTAAGTAATCCAA
1 AGTATAGTTTAATGATTTAAGTAACCCAA
17367 GCACCAACTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (30 bp):
AGTATAGTTTAATGATTTAAGTAACCCAAT
Found at i:18377 original size:17 final size:18
Alignment explanation
Indices: 18357--18392 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
18347 ATAATATAAG
18357 TTTATA-TATAAACTATA
1 TTTATATTATAAACTATA
18374 TTTATATTATAAACTATA
1 TTTATATTATAAACTATA
18392 T
1 T
18393 AATTATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATATTATAAACTATA
Found at i:18399 original size:18 final size:17
Alignment explanation
Indices: 18358--18403 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
18348 TAATATAAGT
*
18358 TTATATATAAACTATATT
1 TTAT-TATAAACTATATA
18376 TATATTATAAACTATATAA
1 T-TATTATAAACTATAT-A
18395 TTATTATAA
1 TTATTATAA
18404 GTTATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATTATAAACTATATA
Found at i:18450 original size:28 final size:26
Alignment explanation
Indices: 18406--18466 Score: 86
Period size: 28 Copynumber: 2.3 Consensus size: 26
18396 TATTATAAGT
* *
18406 TATATATATAAATTATGTTTATATGAAC
1 TATATATATAAACTATG--TATATAAAC
18434 TATATATATAAACTATGTATATAAAC
1 TATATATATAAACTATGTATATAAAC
18460 TATATAT
1 TATATAT
18467 GTATAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 15 0.48
28 16 0.52
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (26 bp):
TATATATATAAACTATGTATATAAAC
Found at i:18498 original size:81 final size:78
Alignment explanation
Indices: 18412--18624 Score: 247
Period size: 81 Copynumber: 2.7 Consensus size: 78
18402 AAGTTATATA
* *
18412 TATAAATTATGTTTATATGAACTATATATATAAACTATGTATATAAACTATATATGTATAAATTA
1 TATAAATTATATTTATAT-AA-TATATATATAAACTAT-TATATAAACTATATATGTATAAACTA
18477 TA-AAAAGTATATAGTT
63 TATAAAA-TATATAGTT
*
18493 TATAAAATATAATTTATACTAATATAGTATATATATAC-A-TATATAAACTATATATGTATAAAC
1 TATAAATTAT-ATTTATA-TAATATA-TATATA-A-ACTATTATATAAACTATATATGTATAAAC
18556 TATATAAAATATATAGTT
61 TATATAAAATATATAGTT
* *
18574 TATAAATTATAATTATAT-ATATATATAGAAAC-ATTATGCATAAACTATATA
1 TATAAATTATATTTATATAATATATATATAAACTATTAT--ATAAACTATATA
18625 AAGTAATAAA
Statistics
Matches: 117, Mismatches: 6, Indels: 21
0.81 0.04 0.15
Matches are distributed among these distances:
75 3 0.03
76 4 0.03
77 5 0.04
78 17 0.15
79 1 0.01
80 6 0.05
81 58 0.50
82 18 0.15
83 3 0.03
84 2 0.02
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (78 bp):
TATAAATTATATTTATATAATATATATATAAACTATTATATAAACTATATATGTATAAACTATAT
AAAATATATAGTT
Found at i:18544 original size:17 final size:16
Alignment explanation
Indices: 18360--18568 Score: 77
Period size: 15 Copynumber: 13.4 Consensus size: 16
18350 ATATAAGTTT
*
18360 ATATATAAACTATATTT
1 ATATATAAACTATA-TA
18377 ATATTATAAACTATATA
1 ATA-TATAAACTATATA
*
18394 AT-TATTATAAGT-TAT-
1 ATATA-TA-AACTATATA
* *
18409 ATATATAAATTATGT-
1 ATATATAAACTATATA
* *
18424 TTATATGAAC--TAT-
1 ATATATAAACTATATA
18437 ATATATAAAC--TAT-
1 ATATATAAACTATATA
*
18450 GTATATAAACTATAT-
1 ATATATAAACTATATA
* *
18465 ATGTATAAATTATA-A
1 ATATATAAACTATATA
* * * *
18480 AAAGTATATAGTTTATA
1 ATA-TATAAACTATATA
* **
18497 AAATATAATTTATACTA
1 ATATATAAACTATA-TA
*
18514 ATATAGTATA-TATATA
1 ATATA-TAAACTATATA
18530 CATATATAAACTATAT-
1 -ATATATAAACTATATA
*
18546 ATGTATAAACTATATA
1 ATATATAAACTATATA
*
18562 AAATATA
1 ATATATA
18569 TAGTTTATAA
Statistics
Matches: 147, Mismatches: 30, Indels: 31
0.71 0.14 0.15
Matches are distributed among these distances:
13 22 0.15
14 3 0.02
15 44 0.30
16 32 0.22
17 33 0.22
18 13 0.09
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (16 bp):
ATATATAAACTATATA
Found at i:18560 original size:15 final size:14
Alignment explanation
Indices: 18376--18561 Score: 90
Period size: 15 Copynumber: 13.3 Consensus size: 14
18366 AAACTATATT
18376 TATATTATAAACTA
1 TATATTATAAACTA
*
18390 TATAATTATTATAAGT-
1 TAT-ATTA-TA-AACTA
*
18406 TATATATATAAATTA
1 TATAT-TATAAACTA
*
18421 TGT-TTATATGAACTA
1 TATATTATA--AACTA
18436 TATA-TATAAACTA
1 TATATTATAAACTA
*
18449 TGTA-TATAAACTA
1 TATATTATAAACTA
18462 TATATGTATAAA-T-
1 TATAT-TATAAACTA
*
18475 TATA--A-AAAGTA
1 TATATTATAAACTA
*
18486 TATAGTTTATAAAATA
1 TATA--TTATAAACTA
*
18502 TA-ATT-TATACTAA
1 TATATTATAAACT-A
* *
18515 TATAGTATATA-TA
1 TATATTATAAACTA
*
18528 TACATATATAAACTA
1 TATAT-TATAAACTA
18543 TATATGTATAAACTA
1 TATAT-TATAAACTA
18558 TATA
1 TATA
18562 AAATATATAG
Statistics
Matches: 134, Mismatches: 16, Indels: 43
0.69 0.08 0.22
Matches are distributed among these distances:
9 3 0.02
10 2 0.01
11 4 0.03
12 4 0.03
13 37 0.28
14 16 0.12
15 51 0.38
16 14 0.10
17 3 0.02
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (14 bp):
TATATTATAAACTA
Found at i:18623 original size:63 final size:64
Alignment explanation
Indices: 18493--18626 Score: 168
Period size: 65 Copynumber: 2.1 Consensus size: 64
18483 GTATATAGTT
* * *
18493 TATAAAATATAATTTATACTAATATAGTATATATATACATATATAAACTATATATGTATAAACTA
1 TATAAAATATAATTTATAC-AATATAATATATATATACATATAGAAACTATATATGCATAAACTA
*
18558 TATAAAATATATAGTTTATA-AATTATAAT-TATATATATATATAGAAAC-AT-TATGCATAAAC
1 TATAAAATATA-A-TTTATACAA-TATAATATATATATACATATAGAAACTATATATGCATAAAC
18619 TA
63 TA
18621 TATAAA
1 TATAAA
18627 GTAATAAAGT
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
63 18 0.29
64 2 0.03
65 30 0.48
66 6 0.10
67 6 0.10
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (64 bp):
TATAAAATATAATTTATACAATATAATATATATATACATATAGAAACTATATATGCATAAACTA
Found at i:18873 original size:35 final size:36
Alignment explanation
Indices: 18803--18876 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
18793 ACAATAGTTA
* *
18803 ATATATGTAACCTATAGTATATGTATACATGTAAACT
1 ATATATGTAACCTATAGTACATGTATA-ATATAAACT
* *
18840 ATATATGTAACTTATAGTACATGTAT-GTATAAACT
1 ATATATGTAACCTATAGTACATGTATAATATAAACT
18875 AT
1 AT
18877 GTATAGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 9 0.27
37 24 0.73
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (36 bp):
ATATATGTAACCTATAGTACATGTATAATATAAACT
Found at i:18890 original size:2 final size:2
Alignment explanation
Indices: 18878--18914 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
18868 ATAAACTATG
18878 TA TA GTA 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
18915 ACCTATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:19013 original size:48 final size:49
Alignment explanation
Indices: 18925--19018 Score: 145
Period size: 48 Copynumber: 1.9 Consensus size: 49
18915 ACCTATAAAT
* **
18925 ATAAACCATATAAAGTAAATTACTTATATAGTTTATAAAAACCCTATAC
1 ATAAACCATATAAAGTAAATAAAGTATATAGTTTATAAAAACCCTATAC
*
18974 ATAAACTATATAAAGT-AATAAAGTATATAGTTTATAAAAACCCTA
1 ATAAACCATATAAAGTAAATAAAGTATATAGTTTATAAAAACCCTA
19019 AACCCTAAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 26 0.63
49 15 0.37
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (49 bp):
ATAAACCATATAAAGTAAATAAAGTATATAGTTTATAAAAACCCTATAC
Found at i:19021 original size:7 final size:7
Alignment explanation
Indices: 19011--19112 Score: 66
Period size: 7 Copynumber: 14.6 Consensus size: 7
19001 TAGTTTATAA
19011 AAACCCT
1 AAACCCT
19018 AAACCCT
1 AAACCCT
**
19025 AAACTTT
1 AAACCCT
* *
19032 AAAACAT
1 AAACCCT
19039 AAACCCT
1 AAACCCT
*
19046 AAA-CCA
1 AAACCCT
*
19052 AAATCCT
1 AAACCCT
*
19059 AAACCCA
1 AAACCCT
**
19066 AAAATCT
1 AAACCCT
19073 CAAACCCT
1 -AAACCCT
19081 AAACCCT
1 AAACCCT
*
19088 AAA-CAT
1 AAACCCT
19094 CAAA-CCT
1 -AAACCCT
19101 CAAACCCT
1 -AAACCCT
19109 AAAC
1 AAAC
19113 ACTATACATA
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
6 7 0.10
7 58 0.79
8 8 0.11
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (7 bp):
AAACCCT
Found at i:19048 original size:14 final size:14
Alignment explanation
Indices: 19011--19125 Score: 60
Period size: 14 Copynumber: 8.3 Consensus size: 14
19001 TAGTTTATAA
*
19011 AAACCCTAAACCCT
1 AAACCCTAAACCAT
** *
19025 AAACTTTAAAACAT
1 AAACCCTAAACCAT
19039 AAACCCTAAACCA-
1 AAACCCTAAACCAT
*
19052 AAATCCTAAACCCA-
1 AAACCCTAAA-CCAT
** *
19066 AAAATCTCAAACCCT
1 AAACCCT-AAACCAT
19081 AAACCCTAAA-CAT
1 AAACCCTAAACCAT
*
19094 CAAA-CCTCAAACCCT
1 -AAACCCT-AAACCAT
* *
19109 AAACACTATA-CAT
1 AAACCCTAAACCAT
19122 AAAC
1 AAAC
19126 AATAGTTAAT
Statistics
Matches: 76, Mismatches: 18, Indels: 15
0.70 0.17 0.14
Matches are distributed among these distances:
13 20 0.26
14 44 0.58
15 12 0.16
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (14 bp):
AAACCCTAAACCAT
Found at i:19098 original size:21 final size:21
Alignment explanation
Indices: 19011--19113 Score: 88
Period size: 21 Copynumber: 4.9 Consensus size: 21
19001 TAGTTTATAA
* *
19011 AAACCCTAAACCCTAAACTTT
1 AAACCCTAAACCCTAAACATC
* *
19032 AAAACATAAACCCTAAAC--C
1 AAACCCTAAACCCTAAACATC
* *
19051 AAAATCCTAAACCC-AAAAATCTC
1 -AAACCCTAAACCCTAAACA--TC
19074 AAACCCTAAACCCTAAACATC
1 AAACCCTAAACCCTAAACATC
19095 AAA-CCTCAAACCCTAAACA
1 AAACCCT-AAACCCTAAACA
19114 CTATACATAA
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
19 3 0.04
20 14 0.21
21 33 0.49
22 12 0.18
23 5 0.07
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (21 bp):
AAACCCTAAACCCTAAACATC
Found at i:19102 original size:28 final size:27
Alignment explanation
Indices: 19071--19125 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
19061 ACCCAAAAAT
*
19071 CTCAAACCCTAAACCCTAAACATCAAAC
1 CTCAAACCCTAAACACTAAACAT-AAAC
*
19099 CTCAAACCCTAAACACTATACATAAAC
1 CTCAAACCCTAAACACTAAACATAAAC
19126 AATAGTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.47, C:0.36, G:0.00, T:0.16
Consensus pattern (27 bp):
CTCAAACCCTAAACACTAAACATAAAC
Found at i:19204 original size:35 final size:36
Alignment explanation
Indices: 19134--19207 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
19124 ACAATAGTTA
* *
19134 ATATATGTAACCTATAGTATATGTATACATGTAAACT
1 ATATATGTAACCTATAGTACATGTATA-ATATAAACT
* *
19171 ATATATGTAACTTATAGTACATGTAT-TTATAAACT
1 ATATATGTAACCTATAGTACATGTATAATATAAACT
19206 AT
1 AT
19208 GTGTAGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 9 0.27
37 24 0.73
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (36 bp):
ATATATGTAACCTATAGTACATGTATAATATAAACT
Found at i:20113 original size:24 final size:24
Alignment explanation
Indices: 20076--20152 Score: 100
Period size: 24 Copynumber: 3.2 Consensus size: 24
20066 AAATCAAAAT
* *
20076 AGAATTCAGATCAGATATCATAAC
1 AGAATCCAGGTCAGATATCATAAC
* * *
20100 ATAATCCATGTCAGAAATCATAAC
1 AGAATCCAGGTCAGATATCATAAC
*
20124 AGAATCCAGGTCAGGTATCATAAC
1 AGAATCCAGGTCAGATATCATAAC
20148 AGAAT
1 AGAAT
20153 GCAAATCGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.23
Consensus pattern (24 bp):
AGAATCCAGGTCAGATATCATAAC
Found at i:25678 original size:24 final size:24
Alignment explanation
Indices: 25623--25678 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
25613 CTCTCAAGGG
*
25623 TAATTTCATAATTTCTTAGCCATA
1 TAATTTCGTAATTTCTTAGCCATA
25647 TAATTTCGTAATTTCTTAGCCATA
1 TAATTTCGTAATTTCTTAGCCATA
25671 TAATTTCG
1 TAATTTCG
25679 GTATTAAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.46
Consensus pattern (24 bp):
TAATTTCGTAATTTCTTAGCCATA
Found at i:28099 original size:24 final size:24
Alignment explanation
Indices: 28047--28100 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
28037 GTATTCGAAA
*
28047 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* * *
28071 ATTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
28095 TTTGAT
1 TTTGAT
28101 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:30676 original size:140 final size:140
Alignment explanation
Indices: 30424--30706 Score: 521
Period size: 140 Copynumber: 2.0 Consensus size: 140
30414 GCAAATGTTG
* *
30424 TATTATGTGTATTTTATCTGTAAACTTTTAACAATTTCAGTTAGGTATGTATTAGTAACTTGAGT
1 TATTATGTATATTTTATCTGTAAACTTTTAACAATTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
30489 TTGAACATTGCTATGATTTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
30554 CGAATTTGAC
131 CGAATTTGAC
* *
30564 TATTATGTATATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTATATTTTATCTGTAAACTTTTAACAATTTCAGTTAGGCATGTATTAGTAACTTGAGT
30629 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
30694 CGAATTTGAC
131 CGAATTTGAC
30704 TAT
1 TAT
30707 CGCAACGCTA
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 138 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TATTATGTATATTTTATCTGTAAACTTTTAACAATTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:30702 original size:20 final size:20
Alignment explanation
Indices: 30677--30805 Score: 128
Period size: 20 Copynumber: 6.8 Consensus size: 20
30667 TTACACATTC
*
30677 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
30697 ATTTGACTATCGCAACGCTA
1 ATTTGACTATCGCAACGCGA
30717 ATTTGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
30736 A----A-AATCGAAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
30751 ATTTGATTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
30771 ATTTGATTATCACAACAG-GA
1 ATTTGACTATCGCAAC-GCGA
30791 ATTTGACTATCGCAA
1 ATTTGACTATCGCAA
30806 TGAGAAAATC
Statistics
Matches: 92, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
14 9 0.10
15 3 0.03
19 3 0.03
20 76 0.83
21 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:30798 original size:74 final size:74
Alignment explanation
Indices: 30677--30847 Score: 213
Period size: 74 Copynumber: 2.3 Consensus size: 74
30667 TTACACATTC
* *
30677 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGCTAATTTGACTATCGCAACGCA-AAAAT
1 ATTTGAATATCGCAACGCGAATTTGACTATCACAACGCGAATTTGACTATCGCAACG-AGAAAAT
30741 CG-AAACGCGA
65 CGCAAA-GCGA
* * * *
30751 ATTTGATTATCGCAACGTGAATTTGATTATCACAACAG-GAATTTGACTATCGCAATGAGAAAAT
1 ATTTGAATATCGCAACGCGAATTTGACTATCACAAC-GCGAATTTGACTATCGCAACGAGAAAAT
*
30815 CGCAAAGCGT
65 CGCAAAGCGA
* *
30825 ATTAGACTATCGCAACGCGAATT
1 ATTTGAATATCGCAACGCGAATT
30848 AACTTTCGCG
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
73 1 0.01
74 79 0.94
75 4 0.05
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (74 bp):
ATTTGAATATCGCAACGCGAATTTGACTATCACAACGCGAATTTGACTATCGCAACGAGAAAATC
GCAAAGCGA
Found at i:30875 original size:20 final size:20
Alignment explanation
Indices: 30849--30909 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
30839 ACGCGAATTA
*
30849 ACTTTCGCGTTGCGATTTTG
1 ACTTTCGCATTGCGATTTTG
* *
30869 GCTTTCGCATTGCGATTTTT
1 ACTTTCGCATTGCGATTTTG
*
30889 ACTTTCGTATTGCGATTTTG
1 ACTTTCGCATTGCGATTTTG
30909 A
1 A
30910 GTTTAGCGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (20 bp):
ACTTTCGCATTGCGATTTTG
Found at i:31087 original size:67 final size:69
Alignment explanation
Indices: 30975--31154 Score: 185
Period size: 72 Copynumber: 2.6 Consensus size: 69
30965 GATTGAAATC
*
30975 AACAAATCAACTTTTACATTTCAATCAATTAAACAAGC---ACAAATAAGAA-TTA-TTTACACA
1 AACAAATCAACTTTTACA--T-AATCAATTAAACAAGCAAAAAAAATAAGAATTTATTTTACACA
31035 TCAATTA
63 TCAATTA
* * *
31042 AACAAATCAACTTTTACA-AATCAATTAAACAAGCAAAAAATAATAATAATTCTTATTTTCCTCA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAAA-AATAAGAA-T-TTATTTTACACA
31106 TCAATTA
63 TCAATTA
* * *
31113 AATAAATCAGACTTTTA-AGAATCAATTAAACAATCAAAAAAA
1 AACAAATCA-ACTTTTACATAATCAATTAAACAAGCAAAAAAA
31155 GTGTACCCCA
Statistics
Matches: 97, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
63 16 0.16
66 2 0.02
67 25 0.26
70 3 0.03
71 23 0.24
72 28 0.29
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.29
Consensus pattern (69 bp):
AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAAAAATAAGAATTTATTTTACACATCA
ATTA
Found at i:32505 original size:42 final size:41
Alignment explanation
Indices: 32446--32568 Score: 133
Period size: 42 Copynumber: 2.9 Consensus size: 41
32436 GTGAATCGGG
*
32446 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAAT-GTGGGAGGGACCTCTTGAACGATGACAGGGGC
** *
32488 CTCTTGAACTGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAA-TGTGGGA-GGGACCTCTTGAACGATGACAGGGGC
* *
32530 CTCTTGAATGATAGGAGAGG-CCTCTTGAATGATGACAGG
1 CTCTTGAATG-TGGGAG-GGACCTCTTGAACGATGACAGG
32569 TGAGTCGGGC
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
41 3 0.04
42 60 0.88
43 5 0.07
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAATGTGGGAGGGACCTCTTGAACGATGACAGGGGC
Found at i:32506 original size:21 final size:21
Alignment explanation
Indices: 32446--32563 Score: 103
Period size: 21 Copynumber: 5.6 Consensus size: 21
32436 GTGAATCGGG
* *
32446 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGATGGGAGGGGC
* * **
32467 CTCTTCAACGATGACAGGGGC
1 CTCTTGAATGATGGGAGGGGC
*
32488 CTCTTGAACTG-TGGGAGGGGA
1 CTCTTGAA-TGATGGGAGGGGC
** **
32509 CTCTTGAGGGATGATAGGGGC
1 CTCTTGAATGATGGGAGGGGC
* *
32530 CTCTTGAATGATAGGAGAGGC
1 CTCTTGAATGATGGGAGGGGC
32551 CTCTTGAATGATG
1 CTCTTGAATGATG
32564 ACAGGTGAGT
Statistics
Matches: 72, Mismatches: 23, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 1 0.01
21 70 0.97
22 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGATGGGAGGGGC
Found at i:33069 original size:20 final size:20
Alignment explanation
Indices: 33044--33148 Score: 88
Period size: 20 Copynumber: 5.3 Consensus size: 20
33034 AATAGTTTCT
*
33044 GAAACTTAAAATCGCAACAC
1 GAAACTGAAAATCGCAACAC
* *
33064 GAAACTTAAAATCGCATCAC
1 GAAACTGAAAATCGCAACAC
* ** *
33084 GAAAATGACTATCGCAACGC
1 GAAACTGAAAATCGCAACAC
**
33104 GGAAA-TGACTATCGCAACAC
1 -GAAACTGAAAATCGCAACAC
* *
33124 GAAAC-CAAAATCGCAACGC
1 GAAACTGAAAATCGCAACAC
33143 GAAACT
1 GAAACT
33149 AAATTCGCGT
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
19 19 0.27
20 47 0.67
21 4 0.06
ACGTcount: A:0.45, C:0.26, G:0.15, T:0.14
Consensus pattern (20 bp):
GAAACTGAAAATCGCAACAC
Found at i:33217 original size:33 final size:34
Alignment explanation
Indices: 33156--33231 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 34
33146 ACTAAATTCG
* *
33156 CGTTGTGATTTTCATTTTCGCATAGCGATTTTCA
1 CGTTGCGATTTTCATTTTCGCATAGCGATTATCA
* * *
33190 CGTTGCGATTTTTA-TTTCGCATTGCGATTATCC
1 CGTTGCGATTTTCATTTTCGCATAGCGATTATCA
33223 CGTTGCGAT
1 CGTTGCGAT
33232 AATCAAATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 25 0.68
34 12 0.32
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATAGCGATTATCA
Found at i:33248 original size:20 final size:20
Alignment explanation
Indices: 33223--33291 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
33213 GCGATTATCC
* *
33223 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAATTTCG
33243 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
* *
33263 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
33283 CGTTGCGAT
1 CGTTGCGAT
33292 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:33467 original size:22 final size:21
Alignment explanation
Indices: 33427--33467 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
33417 CAGTATTGGT
*
33427 AGCAATCGAATGAATTTACTA
1 AGCAATCGAATGAAATTACTA
*
33448 AGCAATCTAAGTGAAATTAC
1 AGCAATCGAA-TGAAATTAC
33468 GAGTAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (21 bp):
AGCAATCGAATGAAATTACTA
Found at i:35157 original size:20 final size:20
Alignment explanation
Indices: 35134--35174 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
35124 TCTGAAACTT
35134 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
35154 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
35174 A
1 A
35175 CTGTCACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.20, G:0.15, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:35189 original size:20 final size:20
Alignment explanation
Indices: 35141--35210 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
35131 CTTAAAATCG
* ** *
35141 CAACACGAAAATGAAAATCG
1 CAACGCGAAAATGACTATCA
* *
35161 CAACACGAAAATGACTGTCA
1 CAACGCGAAAATGACTATCA
** *
35181 CAACGCGAATTTGACTATCG
1 CAACGCGAAAATGACTATCA
35201 CAACGCGAAA
1 CAACGCGAAA
35211 CTAAAATCGC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.44, C:0.24, G:0.17, T:0.14
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCA
Found at i:35830 original size:21 final size:21
Alignment explanation
Indices: 35806--35880 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
35796 CGCTTTGAAA
35806 ATCGCATTGCGATTTTGTATT
1 ATCGCATTGCGATTTTGTATT
** * **
35827 ATCGCAACGCGA--TAGTCAGA
1 ATCGCATTGCGATTTTGT-ATT
*
35847 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGATTTTGTATT
*
35868 ATCGCGTTGCGAT
1 ATCGCATTGCGAT
35881 AGTCAGAATC
Statistics
Matches: 39, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
19 3 0.08
20 11 0.28
21 23 0.59
22 2 0.05
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (21 bp):
ATCGCATTGCGATTTTGTATT
Found at i:35852 original size:20 final size:20
Alignment explanation
Indices: 35835--35920 Score: 102
Period size: 20 Copynumber: 4.2 Consensus size: 20
35825 TTATCGCAAC
35835 GCGATAGTCAGAATCGCATT
1 GCGATAGTCAGAATCGCATT
** *
35855 GCGATTATGT-ATTATCGCGTT
1 GCGA-TA-GTCAGAATCGCATT
*
35876 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCATT
*
35896 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCATT
35916 GCGAT
1 GCGAT
35921 TATGTATTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
19 2 0.03
20 40 0.69
21 14 0.24
22 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCATT
Found at i:35866 original size:41 final size:41
Alignment explanation
Indices: 35805--35900 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
35795 GCGCTTTGAA
*
35805 AATCGCATTGCGATTTTGTATTATCGCAACGCGATAGTCAG
1 AATCGCATTGCGATTATGTATTATCGCAACGCGATAGTCAG
***
35846 AATCGCATTGCGATTATGTATTATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATTATGTATTATCGCAACGCGATAGTCAG
*
35887 AATCGCGTTGCGAT
1 AATCGCATTGCGAT
35901 AGTCAGAATC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (41 bp):
AATCGCATTGCGATTATGTATTATCGCAACGCGATAGTCAG
Found at i:36060 original size:20 final size:19
Alignment explanation
Indices: 36037--36082 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
36027 GGAAACTGAT
* *
36037 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
36057 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
36076 TTGCGAT
1 TTGCGAT
36083 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:36072 original size:19 final size:19
Alignment explanation
Indices: 36048--36084 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
36038 TGCGATACTG
*
36048 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
36067 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
36085 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:36271 original size:21 final size:21
Alignment explanation
Indices: 36245--36284 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
36235 TAGTGTACTA
* *
36245 TATAGTTTATACTTTATAACC
1 TATAGTATATAATTTATAACC
36266 TATAGTATATAATTTATAA
1 TATAGTATATAATTTATAA
36285 ACTACAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (21 bp):
TATAGTATATAATTTATAACC
Found at i:36297 original size:21 final size:21
Alignment explanation
Indices: 36250--36297 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
36240 TACTATATAG
* * * *
36250 TTTATACTTTATAACCTATAG
1 TTTATAATTTATAAACTACAA
*
36271 TATATAATTTATAAACTACAA
1 TTTATAATTTATAAACTACAA
36292 TTTATA
1 TTTATA
36298 TTAATATGCT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTATAATTTATAAACTACAA
Found at i:36345 original size:15 final size:15
Alignment explanation
Indices: 36308--36358 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
36298 TTAATATGCT
*
36308 ATATAGTTTATATTA
1 ATATAATTTATATTA
*
36323 ATGTTAA-TTATATTA
1 AT-ATAATTTATATTA
36338 ACTATAATTTATATTA
1 A-TATAATTTATATTA
36354 ATATA
1 ATATA
36359 GCATATAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (15 bp):
ATATAATTTATATTA
Found at i:36480 original size:31 final size:30
Alignment explanation
Indices: 36308--36493 Score: 96
Period size: 31 Copynumber: 5.8 Consensus size: 30
36298 TTAATATGCT
*
36308 ATATAGTTTATATTAATGTTAATTATATTAAC
1 ATATAGTTTATATTAATATTAATT-TA-TAAC
* *
36340 -TATAATTTATATTAATATAGCATATAGTTTACAA-
1 ATATAGTTTATATTAATAT----TA-A-TTTATAAC
*
36374 ACTATA--CTATATTAATATTAATTATATTAAC
1 A-TATAGTTTATATTAATATTAATT-TA-TAAC
* *
36405 -TGTAGTTTATAAACTATACTATATAATTTATAAC
1 ATATAGTTTAT--A-T-TAATAT-TAATTTATAAC
36439 ATATAGTTTATATTAATATTAATGTTATATAC
1 ATATAGTTTATATTAATATTAAT-TTATA-AC
* *
36471 -TATATTTTATATTGATATTAATT
1 ATATAGTTTATATTAATATTAATT
36494 ACAAATTATA
Statistics
Matches: 121, Mismatches: 12, Indels: 44
0.68 0.07 0.25
Matches are distributed among these distances:
28 2 0.02
29 6 0.05
30 9 0.07
31 49 0.40
32 3 0.02
33 2 0.02
34 16 0.13
35 20 0.17
36 12 0.10
37 2 0.02
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (30 bp):
ATATAGTTTATATTAATATTAATTTATAAC
Found at i:37310 original size:6 final size:6
Alignment explanation
Indices: 37295--37384 Score: 54
Period size: 6 Copynumber: 14.7 Consensus size: 6
37285 TCTATAACTC
* ** * * * *
37295 AACCTT AACCTA AACCCTA AATATA AACTCGA ACCCTA AACCTG AACCCA
1 AACCTA AACCTA AA-CCTA AACCTA AAC-CTA AACCTA AACCTA AACCTA
* * * * *
37345 AACCTA AACCCA AACATG AACTTA AACTTA AACCTA AACC
1 AACCTA AACCTA AACCTA AACCTA AACCTA AACCTA AACC
37385 CTAACCCAAA
Statistics
Matches: 62, Mismatches: 20, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
6 53 0.85
7 9 0.15
ACGTcount: A:0.47, C:0.32, G:0.03, T:0.18
Consensus pattern (6 bp):
AACCTA
Found at i:37349 original size:12 final size:12
Alignment explanation
Indices: 37325--37429 Score: 70
Period size: 12 Copynumber: 8.8 Consensus size: 12
37315 ATATAAACTC
37325 GAACCCTAAACCT
1 GAACCC-AAACCT
37338 GAACCCAAACCT
1 GAACCCAAACCT
* *
37350 AAACCCAAACAT
1 GAACCCAAACCT
** *
37362 GAACTTAAACTT
1 GAACCCAAACCT
* *
37374 AAACCTAAACCCT
1 GAACCCAAA-CCT
**
37387 -AACCCAAATTT
1 GAACCCAAACCT
*
37398 GAACCCGAACC-
1 GAACCCAAACCT
* *
37409 CAACCCGAACCT
1 GAACCCAAACCT
37421 GAACCCAAA
1 GAACCCAAA
37430 TTCAAACCCG
Statistics
Matches: 71, Mismatches: 18, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
11 11 0.15
12 52 0.73
13 8 0.11
ACGTcount: A:0.44, C:0.36, G:0.07, T:0.13
Consensus pattern (12 bp):
GAACCCAAACCT
Found at i:37408 original size:18 final size:18
Alignment explanation
Indices: 37381--37443 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
37371 CTTAAACCTA
* *
37381 AACCCTAACCCAAATTTG
1 AACCCGAACCCAAATTCG
**
37399 AACCCGAACCC-AACCCG
1 AACCCGAACCCAAATTCG
* *
37416 AACCTGAACCCAAATTCA
1 AACCCGAACCCAAATTCG
37434 AACCCGAACC
1 AACCCGAACC
37444 TAAAAAACCC
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
17 13 0.37
18 22 0.63
ACGTcount: A:0.40, C:0.41, G:0.08, T:0.11
Consensus pattern (18 bp):
AACCCGAACCCAAATTCG
Found at i:39471 original size:21 final size:21
Alignment explanation
Indices: 39447--39489 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
39437 TCTAGTTGAA
* *
39447 TTTTAACTTATTTATTTCTTG
1 TTTTAACTTACTAATTTCTTG
* *
39468 TTTTCATTTACTAATTTCTTG
1 TTTTAACTTACTAATTTCTTG
39489 T
1 T
39490 CTTTTGTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.12, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTTAACTTACTAATTTCTTG
Found at i:40904 original size:23 final size:23
Alignment explanation
Indices: 40873--40921 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
40863 TTATTTTTTC
40873 TTTACATAAATTAAACTATATAA
1 TTTACATAAATTAAACTATATAA
* *
40896 TTTATATAAATTAAACTATATTA
1 TTTACATAAATTAAACTATATAA
40919 TTT
1 TTT
40922 TTTCTTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTACATAAATTAAACTATATAA
Found at i:40978 original size:9 final size:9
Alignment explanation
Indices: 40966--40995 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
40956 TACATTTAAA
40966 TAATTTTAT
1 TAATTTTAT
40975 TAATTTTAT
1 TAATTTTAT
40984 TAATTTTAT
1 TAATTTTAT
40993 TAA
1 TAA
40996 ATAATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TAATTTTAT
Found at i:41221 original size:16 final size:16
Alignment explanation
Indices: 41200--41258 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
41190 CGAATCATTT
* **
41200 ACAGGTCAGGTTTATC
1 ACAGGTCAGGTTAAAA
41216 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
41232 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
41248 ACAGGTCAGGT
1 ACAGGTCAGGT
41259 AAATACCAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.22
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:43971 original size:20 final size:20
Alignment explanation
Indices: 43943--43985 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 20
43933 TTTATTTTTT
43943 ATAAAATTATT--TT-AAGA
1 ATAAAATTATTAATTGAAGA
*
43960 ATAAAATTATTAATTGAAGT
1 ATAAAATTATTAATTGAAGA
43980 ATAAAA
1 ATAAAA
43986 AATTAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 11 0.50
19 2 0.09
20 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (20 bp):
ATAAAATTATTAATTGAAGA
Found at i:44590 original size:3 final size:3
Alignment explanation
Indices: 44584--44641 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
44574 ACACTTCCTT
44584 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44632 TTA TTA TTA T
1 TTA TTA TTA T
44642 CATAAATCAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:50463 original size:30 final size:32
Alignment explanation
Indices: 50419--50494 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 32
50409 TTAATAATTC
* * *
50419 TAAATAAATAATAATTATATAATATTATTTTAATA
1 TAAA-AAATAATTATTACATAA-A-TATATTAATA
50454 -AAAAAATAA-TATTACATAAATATATTAATA
1 TAAAAAATAATTATTACATAAATATATTAATA
50484 TAAAAAATAAT
1 TAAAAAATAAT
50495 AACTATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
30 9 0.25
31 10 0.28
32 8 0.22
33 6 0.17
34 3 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAAAAATAATTATTACATAAATATATTAATA
Found at i:50476 original size:33 final size:29
Alignment explanation
Indices: 50419--50495 Score: 82
Period size: 33 Copynumber: 2.4 Consensus size: 29
50409 TTAATAATTC
* *
50419 TAAATAAATAATAATTATATAATATTATTTTAA
1 TAAAAAAATAAT-ATTACATAATA-TA--TTAA
50452 TAAAAAAATAATATTACATAAATATATTAA
1 TAAAAAAATAATATTACAT-AATATATTAA
50482 TATAAAAAATAATA
1 TA-AAAAAATAATA
50496 ACTATTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
30 6 0.15
31 11 0.28
32 8 0.20
33 15 0.38
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (29 bp):
TAAAAAAATAATATTACATAATATATTAA
Found at i:51662 original size:21 final size:21
Alignment explanation
Indices: 51629--51668 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
51619 TTATCAATTG
* *
51629 TATAATTTTTTAAATTAAAAA
1 TATAATATATTAAATTAAAAA
*
51650 TATAATATATTAATTTAAA
1 TATAATATATTAAATTAAA
51669 TTAAACTTAA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATAATATATTAAATTAAAAA
Found at i:53775 original size:41 final size:41
Alignment explanation
Indices: 53730--53911 Score: 328
Period size: 41 Copynumber: 4.4 Consensus size: 41
53720 ATTCGCGTTG
* *
53730 CATTTTGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
53771 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
53812 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
53853 CATTTCGCGTTGCGATAGTTGAAAATCGCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAAT--CGCGTTGCGATTTTC
53896 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
53912 TTTCCATTTC
Statistics
Matches: 137, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
41 106 0.77
43 31 0.23
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:53780 original size:20 final size:20
Alignment explanation
Indices: 53755--53931 Score: 174
Period size: 20 Copynumber: 8.6 Consensus size: 20
53745 TAGTTGAAAA
53755 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
53775 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
53796 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
53816 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
53837 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*** *
53857 TCGCGTTGCGATAGTTGAAAATC
1 TCGCGTTGCGAT--TT-TCCATT
*
53880 GCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
53900 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
53920 TCGCGTTGCGAT
1 TCGCGTTGCGAT
53932 AGTCTACAGT
Statistics
Matches: 122, Mismatches: 30, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
20 75 0.61
21 32 0.26
22 2 0.02
23 13 0.11
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:54063 original size:6 final size:6
Alignment explanation
Indices: 54052--54113 Score: 117
Period size: 6 Copynumber: 10.5 Consensus size: 6
54042 GACACGTATT
54052 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
54100 ACCACG A-CACG ACC
1 ACCACG ACCACG ACC
54114 CGAGACGAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.09
6 50 0.91
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:54615 original size:6 final size:6
Alignment explanation
Indices: 54602--54711 Score: 204
Period size: 6 Copynumber: 18.5 Consensus size: 6
54592 CCGCCGTCCG
*
54602 GGTCG- GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
54649 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
54697 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
54712 AATACGTGTC
Statistics
Matches: 103, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
5 5 0.05
6 98 0.95
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:54853 original size:41 final size:41
Alignment explanation
Indices: 54808--55042 Score: 249
Period size: 41 Copynumber: 5.5 Consensus size: 41
54798 ACAACTGTAG
54808 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
***
54849 ACTATCGCAACGCGAAATGCGTTGCGATGATGGAGATCGCGTTGCGA-TTTCA
1 ACTATCGCAACGCGAAA-----TG-GA--A---A-ATCGCAACGCGATTTTCA
* * *
54901 ACTATCGCAACGCGAAATGGAAAATCGCAACACGATCTCCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* *
54942 ACTATCGCAACGCGAAATGGAAAAAT-GCAACGCGATCTCCA
1 ACTATCGCAACGCGAAATGG-AAAATCGCAACGCGATTTTCA
*
54983 ACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
55024 ACTATCGCAATGCGAAATG
1 ACTATCGCAACGCGAAATG
55043 CAACGTGAAT
Statistics
Matches: 165, Mismatches: 14, Indels: 30
0.79 0.07 0.14
Matches are distributed among these distances:
40 12 0.07
41 106 0.64
42 5 0.03
44 1 0.01
46 4 0.02
47 4 0.02
49 1 0.01
52 23 0.14
53 9 0.05
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:54915 original size:20 final size:20
Alignment explanation
Indices: 54892--55038 Score: 66
Period size: 20 Copynumber: 7.2 Consensus size: 20
54882 AGATCGCGTT
*
54892 GCGATTTCAACTATCGCAAC
1 GCGATTGCAACTATCGCAAC
* * *
54912 GCGAAATGGAA-AATCGCAAC
1 GCG-ATTGCAACTATCGCAAC
* *
54932 ACGATCTCCAACTATCGCAAC
1 GCGAT-TGCAACTATCGCAAC
* * **
54953 GCGAAATGGAAAAAT-GCAAC
1 GCG-ATTGCAACTATCGCAAC
*
54973 GCGATCTCCAACTATCGCAAC
1 GCGAT-TGCAACTATCGCAAC
* * * *
54994 GCGAAATGGAA-AAACGCAAC
1 GCG-ATTGCAACTATCGCAAC
* *
55014 GCGATTTTCAACTATCGCAAT
1 GCGA-TTGCAACTATCGCAAC
55035 GCGA
1 GCGA
55039 AATGCAACGT
Statistics
Matches: 87, Mismatches: 31, Indels: 17
0.64 0.23 0.13
Matches are distributed among these distances:
19 3 0.03
20 42 0.48
21 40 0.46
22 2 0.02
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (20 bp):
GCGATTGCAACTATCGCAAC
Found at i:55046 original size:21 final size:21
Alignment explanation
Indices: 54899--55046 Score: 104
Period size: 21 Copynumber: 7.2 Consensus size: 21
54889 GTTGCGATTT
54899 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
54920 GAA-AATCGCAACACGATCTC
1 CAACTATCGCAACGCGAAATG
54940 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* ** ** *
54961 GAAAAAT-GCAACGCGATCTC
1 CAACTATCGCAACGCGAAATG
54981 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
55002 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
55022 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
55043 CAAC
1 CAAC
55047 GTGAATTTGC
Statistics
Matches: 87, Mismatches: 37, Indels: 6
0.67 0.28 0.05
Matches are distributed among these distances:
20 42 0.48
21 45 0.52
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.16
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:57282 original size:26 final size:27
Alignment explanation
Indices: 57252--57302 Score: 95
Period size: 26 Copynumber: 1.9 Consensus size: 27
57242 AAAATATATA
57252 TTTAATATCTAAATTAT-TATTTTTAT
1 TTTAATATCTAAATTATATATTTTTAT
57278 TTTAATATCTAAATTATATATTTTT
1 TTTAATATCTAAATTATATATTTTT
57303 TAAAATCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTAATATCTAAATTATATATTTTTAT
Found at i:57313 original size:28 final size:26
Alignment explanation
Indices: 57254--57313 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
57244 AATATATATT
***
57254 TAATATCTAAATTATTATTTTTATTT
1 TAATATCTAAATTATTATTTTTAAAA
57280 TAATATCTAAATTATATATTTTTTAAAA
1 TAATATCTAAATTAT-TA-TTTTTAAAA
*
57308 TCATAT
1 TAATAT
57314 GTAACATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 15 0.54
27 2 0.07
28 11 0.39
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (26 bp):
TAATATCTAAATTATTATTTTTAAAA
Found at i:57754 original size:13 final size:13
Alignment explanation
Indices: 57722--57747 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57712 AGTTTGAGTA
57722 TAAATTTAATTTT
1 TAAATTTAATTTT
57735 TAAATTTAATTTT
1 TAAATTTAATTTT
57748 ATTATTTTAG
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:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TAAATTTAATTTT
Found at i:58066 original size:31 final size:31
Alignment explanation
Indices: 58023--58082 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
58013 TAGTTTAAAA
58023 AAAACTAAAGTTTAGATATTAAAA-TATAAT
1 AAAACTAAAGTTTAGATATTAAAAGTATAAT
* *
58053 AAAATTAATAGTTTAGTTATTAAAAGTATA
1 AAAACTAA-AGTTTAGATATTAAAAGTATA
58083 TTTTACCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 7 0.27
31 15 0.58
32 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (31 bp):
AAAACTAAAGTTTAGATATTAAAAGTATAAT
Found at i:62001 original size:154 final size:153
Alignment explanation
Indices: 61673--62025 Score: 410
Period size: 153 Copynumber: 2.3 Consensus size: 153
61663 CTTTCCCTAC
* *
61673 CTTGTTAGGTTATGGTCATATGCACTAATCTATGCTACTTAT-CCTAGTTTTTTTATTATGTATA
1 CTTGTTAGGTTATGGTCATATGCACTAATCTGTGCTACTTATCCCTAGTTTTTTCATTATGTATA
* * *
61737 TAAAATTATATTTGAATTCATATTAATATTTAAAATATACATTCAAATCCGAATAATATAACCTT
66 TAAAATTACATTTGAATTCATAATAATATGTAAAATATACATTCAAATCCGAATAATATAACCTT
61802 TTAACATGATAAATTTTTCTTGG
131 TTAACATGATAAATTTTTCTTGG
* *
61825 CTTGTTAGGTTATGGTCGTATGCATTAATCTGTGCTACTTATCCCTA-TTTTTTCA-TATGTATA
1 CTTGTTAGGTTATGGTCATATGCACTAATCTGTGCTACTTATCCCTAGTTTTTTCATTATGTATA
** * * * ** * *
61888 TAAAACATTACATTTGAATAT-ATAATCGTATGTGAAATTTACATTCGAATCTTAATAATATCAT
66 T-AAA-ATTACATTTGAAT-TCATAATAATATGTAAAATATACATTCAAATCCGAATAATATAAC
* * * *
61952 CTCTTTGATATGATGATTTTTTCTTGG
128 CT-TTTAACATGATAAATTTTTCTTGG
* *
61979 CTTGTTGGGTTATGGTCCTATGCACTAATCCATGAT-CTACTTATCCC
1 CTTGTTAGGTTATGGTCATATGCACTAAT-C-TG-TGCTACTTATCCC
62026 CCCTAGTTTA
Statistics
Matches: 170, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
151 9 0.05
152 49 0.29
153 50 0.29
154 47 0.28
155 1 0.01
156 13 0.08
157 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (153 bp):
CTTGTTAGGTTATGGTCATATGCACTAATCTGTGCTACTTATCCCTAGTTTTTTCATTATGTATA
TAAAATTACATTTGAATTCATAATAATATGTAAAATATACATTCAAATCCGAATAATATAACCTT
TTAACATGATAAATTTTTCTTGG
Found at i:62118 original size:83 final size:83
Alignment explanation
Indices: 61998--62163 Score: 332
Period size: 83 Copynumber: 2.0 Consensus size: 83
61988 TTATGGTCCT
61998 ATGCACTAATCCATGATCTACTTATCCCCCCTAGTTTAGGTGGATGCTAATAGTATTGTTATTGT
1 ATGCACTAATCCATGATCTACTTATCCCCCCTAGTTTAGGTGGATGCTAATAGTATTGTTATTGT
62063 TGTTTTGATGTGTTAAGG
66 TGTTTTGATGTGTTAAGG
62081 ATGCACTAATCCATGATCTACTTATCCCCCCTAGTTTAGGTGGATGCTAATAGTATTGTTATTGT
1 ATGCACTAATCCATGATCTACTTATCCCCCCTAGTTTAGGTGGATGCTAATAGTATTGTTATTGT
62146 TGTTTTGATGTGTTAAGG
66 TGTTTTGATGTGTTAAGG
62164 GATATGGGTT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (83 bp):
ATGCACTAATCCATGATCTACTTATCCCCCCTAGTTTAGGTGGATGCTAATAGTATTGTTATTGT
TGTTTTGATGTGTTAAGG
Found at i:70528 original size:174 final size:173
Alignment explanation
Indices: 70240--70589 Score: 675
Period size: 174 Copynumber: 2.0 Consensus size: 173
70230 GTTAGCCAGT
70240 AAAGGGTTTAGGGATAACAATGAGTGTTGGAGTAACATCATCATTGGAAATACTCCAAGCGTACA
1 AAAGGGTTTAGGGATAACAATGAGTGTTGGAGTAACATCATCATTGGAAATACTCCAAGCGTACA
70305 TAGCAGACAATAAGTAAATTATTTGGCTTCATGTTTCTCAAAGGTTTTCGCTTAAAGTTCAAC-T
66 TAGCAGACAATAAGTAAATTATTTGGCTTCATGTTTCTCAAAGGTTTTCGCTTAAAGTTCAACAT
70369 TAGTAACACCCTCAGAAAATCGTAGACCAATTTTACAGGTCCC
131 TAGTAACACCCTCAGAAAATCGTAGACCAATTTTACAGGTCCC
70412 AAAGGGTTTAGGGATAACAATGAGTGTTGGAGTAACATCATCATTGGAAAATACTCCAAGCGTAC
1 AAAGGGTTTAGGGATAACAATGAGTGTTGGAGTAACATCATCATTGG-AAATACTCCAAGCGTAC
70477 AGTAGCAGACAATAAGTAAATTATTTGGCTTCATGTTTCTCAAAGGTTTTCGCTTAAAGTTCAAC
65 A-TAGCAGACAATAAGTAAATTATTTGGCTTCATGTTTCTCAAAGGTTTTCGCTTAAAGTTCAAC
70542 ATTAGTAACACCCTCAGAAAATCGTAGACCAATTTTACAGGTCCC
129 ATTAGTAACACCCTCAGAAAATCGTAGACCAATTTTACAGGTCCC
70587 AAA
1 AAA
70590 CAACATGTGA
Statistics
Matches: 175, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
172 47 0.27
173 18 0.10
174 63 0.36
175 47 0.27
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (173 bp):
AAAGGGTTTAGGGATAACAATGAGTGTTGGAGTAACATCATCATTGGAAATACTCCAAGCGTACA
TAGCAGACAATAAGTAAATTATTTGGCTTCATGTTTCTCAAAGGTTTTCGCTTAAAGTTCAACAT
TAGTAACACCCTCAGAAAATCGTAGACCAATTTTACAGGTCCC
Found at i:71540 original size:20 final size:20
Alignment explanation
Indices: 71515--71565 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
71505 TCTGGGCAGA
71515 GAGTATCGATACTTCTAAAG
1 GAGTATCGATACTTCTAAAG
71535 GAGTATCGATACTTCTAAAG
1 GAGTATCGATACTTCTAAAG
71555 GAGTATCGATA
1 GAGTATCGATA
71566 TTGCCCCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (20 bp):
GAGTATCGATACTTCTAAAG
Found at i:83848 original size:59 final size:60
Alignment explanation
Indices: 83741--83853 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 60
83731 AAATAGTATC
83741 TCGATTATAAGATGTTCATTTATTGAGTCTCTCAATTATTAAAAGTTACAAAATATTCTT
1 TCGATTATAAGATGTTCATTTATTGAGTCTCTCAATTATTAAAAGTTACAAAATATTCTT
* * * *
83801 TCGATTATAGGATGTT-ATTTCTAT-AGTCTTTCTATTATTAAAAGTTACAAAAT
1 TCGATTATAAGATGTTCATTTAT-TGAGTCTCTCAATTATTAAAAGTTACAAAAT
83854 GATCATCTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
59 32 0.67
60 16 0.33
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (60 bp):
TCGATTATAAGATGTTCATTTATTGAGTCTCTCAATTATTAAAAGTTACAAAATATTCTT
Found at i:84779 original size:42 final size:42
Alignment explanation
Indices: 84718--84802 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
84708 CACTTCTTAT
* *
84718 TCTCATAAATTAGATAATATTTACTGTATAAATATATTTAAA
1 TCTCATAAATTAGAGAATATTAACTGTATAAATATATTTAAA
* *
84760 TCTCATCAATTAGAGAATATTAAGTGTATAAATATATTTAAA
1 TCTCATAAATTAGAGAATATTAACTGTATAAATATATTTAAA
84802 T
1 T
84803 AGTTTGATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (42 bp):
TCTCATAAATTAGAGAATATTAACTGTATAAATATATTTAAA
Found at i:87791 original size:11 final size:11
Alignment explanation
Indices: 87777--87802 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
87767 TGTGGGGCGA
87777 GCGGATGCGGG
1 GCGGATGCGGG
87788 GCGGATGCGGG
1 GCGGATGCGGG
87799 GCGG
1 GCGG
87803 GTAATGTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.19, G:0.65, T:0.08
Consensus pattern (11 bp):
GCGGATGCGGG
Found at i:91742 original size:56 final size:53
Alignment explanation
Indices: 91677--91788 Score: 161
Period size: 56 Copynumber: 2.1 Consensus size: 53
91667 TATAAAAATA
* *
91677 TCAAGAACACACACAAGCACTATAAGCATAGCAATTAACAAACAAAGAACAAAAAC
1 TCAAGAACACACACAAGCACTATAAACATAACAATT---AAACAAAGAACAAAAAC
* *
91733 TCAAGAACACACACAAGTACTATAAACATAATAATTAAACAAAGAACAAAAAC
1 TCAAGAACACACACAAGCACTATAAACATAACAATTAAACAAAGAACAAAAAC
91786 TCA
1 TCA
91789 CTACGTGGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
53 20 0.38
56 32 0.62
ACGTcount: A:0.58, C:0.21, G:0.07, T:0.13
Consensus pattern (53 bp):
TCAAGAACACACACAAGCACTATAAACATAACAATTAAACAAAGAACAAAAAC
Found at i:98530 original size:23 final size:23
Alignment explanation
Indices: 98499--98550 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
98489 AGAATTGATA
98499 CCCCC-TTGAAGGGGAACCGATT
1 CCCCCTTTGAAGGGGAACCGATT
98521 CCCCCTTTGAAGGGGAACCGATT
1 CCCCCTTTGAAGGGGAACCGATT
98544 CCCCCTT
1 CCCCCTT
98551 GGGGTTCTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 5 0.17
23 24 0.83
ACGTcount: A:0.19, C:0.37, G:0.23, T:0.21
Consensus pattern (23 bp):
CCCCCTTTGAAGGGGAACCGATT
Found at i:101132 original size:23 final size:23
Alignment explanation
Indices: 101095--101151 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
101085 CTCAGAGGGA
*
101095 ACCGATT-CCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCCAAGGGAGT
101117 ACCGATTCCCCCCCCAAGGGAGT
1 ACCGATTCCCCCCCCAAGGGAGT
101140 ACCGATTCCCCC
1 ACCGATTCCCCC
101152 TGAATGGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 7 0.21
23 26 0.79
ACGTcount: A:0.19, C:0.46, G:0.21, T:0.14
Consensus pattern (23 bp):
ACCGATTCCCCCCCCAAGGGAGT
Found at i:107068 original size:154 final size:154
Alignment explanation
Indices: 106781--107087 Score: 494
Period size: 154 Copynumber: 2.0 Consensus size: 154
106771 GAGGTCATTG
106781 AATTCGAAGTGATATTAACCCTGTCGAGTGAAAAACACTGAACTTTACCTATCAATCCAAACCCA
1 AATTCGAAGTGATATTAACCCTGTCGAGTGAAAAACACTGAACTTTACCTATCAATCCAAACCCA
*
106846 ATATGACATGGAAATATGAGATATGTACATAAATTCCAATCCGATCCGAATGTAAAGATATATTC
66 ATATGACATGGAAATATGAGATATGTACATAAATTCCAATCCGATCCGAATGTAAAGATATATAC
*
106911 ATAATTTCTGAATGCATAACATATA
131 ATAA-TTCCGAATGCATAACATATA
* *
106936 AATTCGAAGTGATATTAACCTTGTC-AGGTGAAAAACACTGAA-TTTTCCTATCAATCCAAACCC
1 AATTCGAAGTGATATTAACCCTGTCGA-GTGAAAAACACTGAACTTTACCTATCAATCCAAACCC
* * *
106999 ACTATGACATGGCAATATGAGATATGTACATAAATTTCAATCCGATCCGAATGTAAAGATAT-TC
65 AATATGACATGGAAATATGAGATATGTACATAAATTCCAATCCGATCCGAATGTAAAGATATAT-
*
107063 ACATAATTCCGAATGCATAATATAT
129 ACATAATTCCGAATGCATAACATAT
107088 CATCCGAATT
Statistics
Matches: 142, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
153 18 0.13
154 85 0.60
155 39 0.27
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (154 bp):
AATTCGAAGTGATATTAACCCTGTCGAGTGAAAAACACTGAACTTTACCTATCAATCCAAACCCA
ATATGACATGGAAATATGAGATATGTACATAAATTCCAATCCGATCCGAATGTAAAGATATATAC
ATAATTCCGAATGCATAACATATA
Found at i:108268 original size:64 final size:64
Alignment explanation
Indices: 108215--108378 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 64
108205 CGGTGCACCA
*
108215 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * * ** *
108279 CTTGCGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCACCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
108344 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
108379 CAATTAATTC
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
64 31 0.37
65 52 0.63
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:108618 original size:20 final size:21
Alignment explanation
Indices: 108595--108634 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
108585 GAATCGAATA
108595 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
108615 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
108635 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:109991 original size:44 final size:42
Alignment explanation
Indices: 109877--109994 Score: 128
Period size: 44 Copynumber: 2.7 Consensus size: 42
109867 AAAACCTGCC
* * *
109877 GGATGCATCGGTGCATGGTCTTATGCATCGATGCATATTCAAG
1 GGATGCATCGGTGCATTGT-TAATGCATCGATACATATTCAAG
* * *
109920 GCATGCATCGGTGCATCATGGTGATGCATCGATACATATTCAAAG
1 GGATGCATCGGTGCAT--TGTTAATGCATCGATACATATTC-AAG
*
109965 GGATGCATCGATGCATTGTTAAATGCATCG
1 GGATGCATCGGTGCATTGTT-AATGCATCG
109995 GTGCATGAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
43 18 0.29
44 26 0.42
45 18 0.29
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (42 bp):
GGATGCATCGGTGCATTGTTAATGCATCGATACATATTCAAG
Found at i:113851 original size:22 final size:21
Alignment explanation
Indices: 113809--113848 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
113799 GAGTTTGTTT
*
113809 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
113830 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
113849 ACAGTTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:115828 original size:64 final size:64
Alignment explanation
Indices: 115775--115938 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 64
115765 CGGTGCACCA
*
115775 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * **
115839 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
115904 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
115939 CAATTAATTC
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 32 0.37
65 54 0.63
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:115927 original size:17 final size:19
Alignment explanation
Indices: 115889--115935 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
115879 ATATTCAGAG
115889 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
115908 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
115925 TGCATTCGATG
1 TGCA-TCGATG
115936 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:116178 original size:20 final size:21
Alignment explanation
Indices: 116155--116194 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
116145 GAATCGAATA
116155 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
116175 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
116195 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:119806 original size:24 final size:24
Alignment explanation
Indices: 119770--119824 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
119760 GTTCGCCCTA
* *
119770 ATTTTTTTCTTTAAATT-ATAAAT
1 ATTTTTATCTTTAAATTAAAAAAT
* *
119793 CATTTTTATGTTTAATTTAAAAAAT
1 -ATTTTTATCTTTAAATTAAAAAAT
119818 ATTTTTA
1 ATTTTTA
119825 ATGGACTCGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (24 bp):
ATTTTTATCTTTAAATTAAAAAAT
Found at i:121106 original size:15 final size:16
Alignment explanation
Indices: 121081--121110 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
121071 CTCAAAACAA
121081 AAAATAAAATAAAATG
1 AAAATAAAATAAAATG
121097 AAAA-AAAATAAAAT
1 AAAATAAAATAAAAT
121111 AAGATAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAATAAAATAAAATG
Found at i:122823 original size:42 final size:42
Alignment explanation
Indices: 122736--122877 Score: 162
Period size: 42 Copynumber: 3.4 Consensus size: 42
122726 AGGTCTTATG
* ** * * *
122736 GATGGCTCGAAGGACTTA-TTATCTTGCTCAAAAGACTCA-T
1 GATGGCCCGAAGGACTTACACATCATGCTCGAAAGACTTACT
*
122776 AGATGGCCCGAAGGACTTACACATCATGCTTGAAAGACTTACT
1 -GATGGCCCGAAGGACTTACACATCATGCTCGAAAGACTTACT
* * *
122819 GATGGCCCGAATGACTTACACATCATTCTCGAAAGACTTATT
1 GATGGCCCGAAGGACTTACACATCATGCTCGAAAGACTTACT
*
122861 GATGGCCTGAAGGACTT
1 GATGGCCCGAAGGACTT
122878 CAACTGATTC
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
41 17 0.20
42 68 0.79
43 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (42 bp):
GATGGCCCGAAGGACTTACACATCATGCTCGAAAGACTTACT
Found at i:122856 original size:22 final size:22
Alignment explanation
Indices: 122784--122858 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
122774 ATAGATGGCC
*
122784 CGAAGGACTTACACATCATGCT
1 CGAAAGACTTACACATCATGCT
* * *
122806 TGAAAGACTT--AC-TGATGGCC
1 CGAAAGACTTACACATCAT-GCT
* *
122826 CGAATGACTTACACATCATTCT
1 CGAAAGACTTACACATCATGCT
122848 CGAAAGACTTA
1 CGAAAGACTTA
122859 TTGATGGCCT
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
19 3 0.08
20 12 0.31
22 21 0.54
23 3 0.08
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (22 bp):
CGAAAGACTTACACATCATGCT
Found at i:123059 original size:84 final size:84
Alignment explanation
Indices: 122940--123274 Score: 483
Period size: 84 Copynumber: 4.0 Consensus size: 84
122930 GTAGGGCGTT
122940 GCTGATTCAAAGTGTTGTGAATCGAGCAAAGGAAATGTTGAAAACATCTTGCCCGAAGGTCTTAT
1 GCTGATTCAAAGTG-TGTGAATCGAGCAAAGGAAATGTTGAAAACATCTTGCCCGAAGGTCTTAT
* *
123005 GGATGGCCCAAAGGACTTAA
65 AGATGGCCCGAAGGACTTAA
* * * *
123025 GCTGATTCGAAGTGTATGAATCGAGCAAATGAAATGTTGAAAACATCTTGCCCGAAGGTCTTATG
1 GCTGATTCAAAGTGTGTGAATCGAGCAAAGGAAATGTTGAAAACATCTTGCCCGAAGGTCTTATA
*
123090 GATGGCCTGAAGGACTTAA
66 GATGGCCCGAAGGACTTAA
* ** * * *
123109 GCTAATTTGAAGTATGTGAATCGAGCAAAGGAAATGTTGAAAACATCCTGCCCGAAGTTCTTATA
1 GCTGATTCAAAGTGTGTGAATCGAGCAAAGGAAATGTTGAAAACATCTTGCCCGAAGGTCTTATA
*
123174 GATGGCCCGAAGAACTTAA
66 GATGGCCCGAAGGACTTAA
* * * *
123193 GTTGATTCAAAGTGTGTGAATCGAGCAAATGAAATGTTTAAAAAATC-TGCCCGAAGGTCTTATA
1 GCTGATTCAAAGTGTGTGAATCGAGCAAAGGAAATGTTGAAAACATCTTGCCCGAAGGTCTTATA
*
123257 GATGGCCTGAAGGACTTA
66 GATGGCCCGAAGGACTTA
123275 TCACCTTGCT
Statistics
Matches: 224, Mismatches: 26, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
83 32 0.14
84 179 0.80
85 13 0.06
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.26
Consensus pattern (84 bp):
GCTGATTCAAAGTGTGTGAATCGAGCAAAGGAAATGTTGAAAACATCTTGCCCGAAGGTCTTATA
GATGGCCCGAAGGACTTAA
Found at i:123153 original size:168 final size:167
Alignment explanation
Indices: 122955--123274 Score: 532
Period size: 168 Copynumber: 1.9 Consensus size: 167
122945 TTCAAAGTGT
* * *
122955 TGTGAATCGAGCAAAGGAAATGTTGAAAACATCTTGCCCGAAGGTCTTATGGATGGCCCAAAGGA
1 TGTGAATCGAGCAAAGGAAATGTTGAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCAAAGAA
* *
123020 CTTAAGCTGATTCGAAGTGTATGAATCGAGCAAATGAAATGTTGAAAACATCTTGCCCGAAGGTC
66 CTTAAGCTGATTCAAAGTGTATGAATCGAGCAAATGAAATGTTGAAAAAATC-TGCCCGAAGGTC
*
123085 TTATGGATGGCCTGAAGGACTTAAGCTAATTTGAAGTA
130 TTATAGATGGCCTGAAGGACTTAAGCTAATTTGAAGTA
* *
123123 TGTGAATCGAGCAAAGGAAATGTTGAAAACATCCTGCCCGAAGTTCTTATAGATGGCCCGAAGAA
1 TGTGAATCGAGCAAAGGAAATGTTGAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCAAAGAA
* * *
123188 CTTAAGTTGATTCAAAGTGTGTGAATCGAGCAAATGAAATGTTTAAAAAATCTGCCCGAAGGTCT
66 CTTAAGCTGATTCAAAGTGTATGAATCGAGCAAATGAAATGTTGAAAAAATCTGCCCGAAGGTCT
123253 TATAGATGGCCTGAAGGACTTA
131 TATAGATGGCCTGAAGGACTTA
123275 TCACCTTGCT
Statistics
Matches: 141, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
167 34 0.24
168 107 0.76
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.26
Consensus pattern (167 bp):
TGTGAATCGAGCAAAGGAAATGTTGAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCAAAGAA
CTTAAGCTGATTCAAAGTGTATGAATCGAGCAAATGAAATGTTGAAAAAATCTGCCCGAAGGTCT
TATAGATGGCCTGAAGGACTTAAGCTAATTTGAAGTA
Found at i:123355 original size:20 final size:20
Alignment explanation
Indices: 123241--123357 Score: 58
Period size: 20 Copynumber: 5.7 Consensus size: 20
123231 TAAAAAATCT
* *
123241 GCCCGAAGGTCTTATAGATG
1 GCCCGAAGGACTTATTGATG
* * *
123261 GCCTGAAGGACTTA-TCACCTT
1 GCCCGAAGGACTTATTGA--TG
* * *
123282 GCTCGAAAGACTTATAGATG
1 GCCCGAAGGACTTATTGATG
* * *
123302 ACCCGAAGGATTTAAGTATCAT-
1 GCCCGAAGGACTT-A-T-TGATG
* *
123324 GCTCGAAAGACTTATTGATG
1 GCCCGAAGGACTTATTGATG
123344 GCCCGAAGGACTTA
1 GCCCGAAGGACTTA
123358 CTCATCAAAA
Statistics
Matches: 66, Mismatches: 24, Indels: 14
0.63 0.23 0.13
Matches are distributed among these distances:
19 4 0.06
20 35 0.53
21 14 0.21
22 11 0.17
23 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (20 bp):
GCCCGAAGGACTTATTGATG
Found at i:123536 original size:52 final size:51
Alignment explanation
Indices: 123401--123659 Score: 202
Period size: 52 Copynumber: 4.7 Consensus size: 51
123391 TTCTTAGTTG
*
123401 TCAAGGAAACTCTAAAAATTAGGCTTAGTTTCCTTTAAAAAACTCA-TTGAAAATCATCA
1 TCAA-GAAACCCT-AAAATTAGGCTTAGTTT-C-TT-AAAAACTCATTTG-AAA--A-CA
* *
123460 TCAAGAAACCTCTAAAAATCAGGCTTAGTTTC-TAAAAACTCATTTGACAACA
1 TCAAGAAACC-CT-AAAATTAGGCTTAGTTTCTTAAAAACTCATTTGAAAACA
* ** *
123512 TCAAGAAATCCCTAAATATTAGGCTTAATTTCTTTGAAATTCATTTGAAAACA
1 TCAAGAAA-CCCTAAA-ATTAGGCTTAGTTTCTTAAAAACTCATTTGAAAACA
*
123565 TCAAGAAACCCCTAAAATTAGGCTCAGTTTCCTTTTAAAAACTCA-TTGAAAATCATCA
1 TCAAGAAA-CCCTAAAATTAGGCTTAGTTT-C--TTAAAAACTCATTTG-AAA--A-CA
**
123623 TCAAGAAACCACTAAAACCAGGCTTAGTTTC-TAAAAA
1 TCAAGAAACC-CTAAAATTAGGCTTAGTTTCTTAAAAA
123660 TCTTTTGTTT
Statistics
Matches: 169, Mismatches: 18, Indels: 31
0.78 0.08 0.14
Matches are distributed among these distances:
51 3 0.02
52 37 0.22
53 35 0.21
54 9 0.05
55 22 0.13
56 4 0.02
57 4 0.02
58 32 0.19
59 23 0.14
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (51 bp):
TCAAGAAACCCTAAAATTAGGCTTAGTTTCTTAAAAACTCATTTGAAAACA
Found at i:123700 original size:39 final size:39
Alignment explanation
Indices: 123656--123819 Score: 238
Period size: 39 Copynumber: 4.2 Consensus size: 39
123646 TTAGTTTCTA
* *
123656 AAAATCTTTTGTTTCGAGCGAAACTATCTCAAGCGAGAT
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAT
** ** *
123695 AAAATCTTCTGTTTCGAGTAAAAGAATCTTAAGCGAGAT
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAT
* *
123734 AAAATCCTCTGTTTCAAGGGAAACTATCTCAAGCGAGAT
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAT
*
123773 AAAATCTTCTGCTTCGAGGGAAACTATCTCAAGCGAGAT
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAT
123812 AAAATCTT
1 AAAATCTT
123820 TTGTAGCAGA
Statistics
Matches: 109, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 109 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (39 bp):
AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAT
Done.