Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007834.1 Hibiscus syriacus cultivar Beakdansim tig00110183_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: 925658
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:253330 original size:6 final size:6
Alignment explanation
Indices: 253314--253345 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
253304 TCTCGTCTCG
253314 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
253346 AATACATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:255168 original size:17 final size:17
Alignment explanation
Indices: 255136--255168 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
255126 TCGTATGAAT
255136 ATTATTTATTACTTTGG
1 ATTATTTATTACTTTGG
255153 ATTATATTATTA-TTTG
1 ATTAT-TTATTACTTTG
255169 TGTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.27, C:0.03, G:0.09, T:0.61
Consensus pattern (17 bp):
ATTATTTATTACTTTGG
Found at i:256012 original size:11 final size:11
Alignment explanation
Indices: 255996--256070 Score: 64
Period size: 11 Copynumber: 6.6 Consensus size: 11
255986 TTACGTGATC
255996 ATAATTTTAAT
1 ATAATTTTAAT
256007 ATAA-TTTAAT
1 ATAATTTTAAT
*
256017 AAAATTTTAAT
1 ATAATTTTAAT
*
256028 ATAATTAATTTAGTT
1 ATAA-T--TTTA-AT
256043 ATAATTTTAAT
1 ATAATTTTAAT
*
256054 GTAA-TTTAAT
1 ATAATTTTAAT
*
256064 AAAATTT
1 ATAATTT
256071 AATCTCCAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
10 17 0.33
11 19 0.37
12 5 0.10
14 5 0.10
15 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (11 bp):
ATAATTTTAAT
Found at i:256023 original size:21 final size:21
Alignment explanation
Indices: 255998--256070 Score: 76
Period size: 21 Copynumber: 3.2 Consensus size: 21
255988 ACGTGATCAT
255998 AATTTTAATATAATTTAATAA
1 AATTTTAATATAATTTAATAA
256019 AATTTTAATATAA-TTAATTTAGTTA
1 AATTTTAATATAATTTAA--TA---A
*
256044 TAATTTTAATGTAATTTAATAA
1 -AATTTTAATATAATTTAATAA
256066 AATTT
1 AATTT
256071 AATCTCCAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
20 4 0.09
21 18 0.41
22 3 0.07
25 3 0.07
26 12 0.27
27 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
AATTTTAATATAATTTAATAA
Found at i:256032 original size:26 final size:26
Alignment explanation
Indices: 256003--256059 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
255993 ATCATAATTT
256003 TAATATAATTTA-ATAAAATTTTAATA
1 TAAT-TAATTTAGATAAAATTTTAATA
* * *
256029 TAATTAATTTAGTTATAATTTTAATG
1 TAATTAATTTAGATAAAATTTTAATA
256055 TAATT
1 TAATT
256060 TAATAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (26 bp):
TAATTAATTTAGATAAAATTTTAATA
Found at i:256632 original size:31 final size:31
Alignment explanation
Indices: 256594--256652 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
256584 ATAGTCATAC
* * *
256594 TTTTTAAATAAAGTTTAACATAAAATATATA
1 TTTTTAAATAAACTTGAAAATAAAATATATA
*
256625 TTTTTAAATGAACTTGAAAATAAAATAT
1 TTTTTAAATAAACTTGAAAATAAAATAT
256653 TTTTAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (31 bp):
TTTTTAAATAAACTTGAAAATAAAATATATA
Found at i:256652 original size:27 final size:27
Alignment explanation
Indices: 256622--256685 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
256612 CATAAAATAT
256622 ATATTTTTAAATGAACTTGAA-AATAAA
1 ATATTTTTAAATGAACTT-AATAATAAA
* *
256649 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATTTTTAAATGAACTTAATAATAAA
*
256676 ATATATTTAA
1 ATATTTTTAA
256686 TAAGTTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 2 0.06
27 31 0.94
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (27 bp):
ATATTTTTAAATGAACTTAATAATAAA
Found at i:256703 original size:22 final size:25
Alignment explanation
Indices: 256643--256705 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 25
256633 TGAACTTGAA
*
256643 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATATTT-AA-TAAGTTAAT
256670 AATAAAATATATTTAATAAGTT-AT
1 AATAAAATATATTTAATAAGTTAAT
256694 -ATAAAA-ATATTT
1 AATAAAATATATTT
256706 TTTAAGTCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
22 6 0.17
23 6 0.17
24 2 0.06
25 6 0.17
26 2 0.06
27 13 0.37
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (25 bp):
AATAAAATATATTTAATAAGTTAAT
Found at i:256709 original size:25 final size:25
Alignment explanation
Indices: 256646--256710 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
256636 ACTTGAAAAT
*
256646 AAAATATTTTTAAATTAAGTTAATA
1 AAAATATTTTTTAATTAAGTTAATA
*
256671 ATAAA-ATATATTTAA-TAAGTTATATA
1 A-AAATAT-TTTTTAATTAAGTTA-ATA
256697 AAAATATTTTTTAA
1 AAAATATTTTTTAA
256711 GTCGATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
25 19 0.58
26 14 0.42
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (25 bp):
AAAATATTTTTTAATTAAGTTAATA
Found at i:256711 original size:22 final size:25
Alignment explanation
Indices: 256643--256731 Score: 76
Period size: 27 Copynumber: 3.5 Consensus size: 25
256633 TGAACTTGAA
*
256643 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATATTT--ATTAAGTTAAT
*
256670 AATAAAATATATTTAATAAGTT-AT
1 AATAAAATATATTTATTAAGTTAAT
* *
256694 -ATAAAA-ATATTTTTTAAGTCGATAT
1 AATAAAATATATTTATTAAGT-TA-AT
256719 ATATAAAATATAT
1 A-ATAAAATATAT
256732 ACACCATGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
22 11 0.22
23 6 0.12
24 2 0.04
25 9 0.18
27 19 0.37
28 4 0.08
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (25 bp):
AATAAAATATATTTATTAAGTTAAT
Found at i:257256 original size:22 final size:22
Alignment explanation
Indices: 257212--257256 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
257202 TTAACCCTTA
*
257212 ATTTTAAAACATTACATTTTTT
1 ATTTTAAAACATTACATTGTTT
*
257234 ATTTTAAAAC-TTATATTAGTTT
1 ATTTTAAAACATTACATT-GTTT
257256 A
1 A
257257 AAACATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTTAAAACATTACATTGTTT
Found at i:262705 original size:13 final size:14
Alignment explanation
Indices: 262687--262719 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
262677 TACACGTACC
262687 ATTAAAAATT-TTG
1 ATTAAAAATTATTG
262700 ATTAAAAAATTATTG
1 ATT-AAAAATTATTG
262715 ATTAA
1 ATTAA
262720 TTGCTGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 9 0.50
15 6 0.33
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (14 bp):
ATTAAAAATTATTG
Found at i:262709 original size:14 final size:15
Alignment explanation
Indices: 262690--262719 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
262680 ACGTACCATT
262690 AAAAATT-TTGATTA
1 AAAAATTATTGATTA
262704 AAAAATTATTGATTA
1 AAAAATTATTGATTA
262719 A
1 A
262720 TTGCTGGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (15 bp):
AAAAATTATTGATTA
Found at i:262958 original size:20 final size:21
Alignment explanation
Indices: 262920--262959 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
262910 GGAAAACCCT
*
262920 TTTATATCAAAAGTAAAAACC
1 TTTAAATCAAAAGTAAAAACC
*
262941 TTTAAATCAAAGGTAAAAA
1 TTTAAATCAAAAGTAAAAA
262960 TCAAGGGACT
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:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (21 bp):
TTTAAATCAAAAGTAAAAACC
Found at i:263497 original size:17 final size:17
Alignment explanation
Indices: 263473--263604 Score: 94
Period size: 18 Copynumber: 7.6 Consensus size: 17
263463 TAAGCAACCT
263473 ATTTTTAAGTTGCACTCC
1 ATTTTTAAGTTGCAC-CC
*
263491 A-TTTTAAGTTGCAACCT
1 ATTTTTAAGTTGC-ACCC
*
263508 ATTTTTAAGTTGCAACCT
1 ATTTTTAAGTTGC-ACCC
* *
263526 ATTTTTAAGTTGTAACCT
1 ATTTTTAAGTTG-CACCC
* * *
263544 ATTTTTAAGTTACAATCT
1 ATTTTTAAGTTGC-ACCC
*
263562 ATTTTTAAATTGCAACCC
1 ATTTTTAAGTTGC-ACCC
263580 ATTTTCT-AGTTG--CCC
1 ATTTT-TAAGTTGCACCC
263595 A-TTTTAAGTT
1 ATTTTTAAGTT
263605 ATAGCCTATT
Statistics
Matches: 98, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
13 1 0.01
14 7 0.07
15 4 0.04
17 13 0.13
18 72 0.73
19 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (17 bp):
ATTTTTAAGTTGCACCC
Found at i:263543 original size:36 final size:34
Alignment explanation
Indices: 263466--263604 Score: 149
Period size: 36 Copynumber: 4.0 Consensus size: 34
263456 AACAAAATAA
*
263466 GCAACCTATTTTTAAGTTGCACTCCATTTTAAGTT
1 GCAACCTATTTTTAAGTTGCAC-CTATTTTAAGTT
263501 GCAACCTATTTTTAAGTTGCAACCTATTTTTAAGTT
1 GCAACCTATTTTTAAGTTGC-ACCTA-TTTTAAGTT
* * * *
263537 GTAACCTATTTTTAAGTTACAATCTATTTTTAAATT
1 GCAACCTATTTTTAAGTTGC-ACCTA-TTTTAAGTT
*
263573 GCAACCCATTTTCT-AGTTGC-CC-ATTTTAAGTT
1 GCAACCTATTTT-TAAGTTGCACCTATTTTAAGTT
263605 ATAGCCTATT
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
32 8 0.09
33 1 0.01
34 1 0.01
35 22 0.24
36 58 0.64
37 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (34 bp):
GCAACCTATTTTTAAGTTGCACCTATTTTAAGTT
Found at i:263575 original size:54 final size:53
Alignment explanation
Indices: 263466--263616 Score: 168
Period size: 54 Copynumber: 2.9 Consensus size: 53
263456 AACAAAATAA
* * *
263466 GCAACCTATTTTTAAGTTGCACTCCATTTTAAGTTGCAACCTATTTTTAAGTT
1 GCAACCTATTTTTAAGTTGAACTCCATTTTAAGTTACAACCTATTTTTAAATT
* *
263519 GCAACCTATTTTTAAGTTGTAAC-CTATTTTTAAGTTACAATCTATTTTTAAATT
1 GCAACCTATTTTTAAGTTG-AACTCCA-TTTTAAGTTACAACCTATTTTTAAATT
* * *
263573 GCAACCCATTTTCT-AGTTG--C-CCATTTTAAGTTATAGCCTATTTT
1 GCAACCTATTTT-TAAGTTGAACTCCATTTTAAGTTACAACCTATTTT
263617 CTGGTTACTC
Statistics
Matches: 85, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
50 18 0.21
51 3 0.04
53 21 0.25
54 42 0.49
55 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (53 bp):
GCAACCTATTTTTAAGTTGAACTCCATTTTAAGTTACAACCTATTTTTAAATT
Found at i:263592 original size:18 final size:18
Alignment explanation
Indices: 263466--263584 Score: 161
Period size: 18 Copynumber: 6.7 Consensus size: 18
263456 AACAAAATAA
263466 GCAACCTATTTTTAAGTT
1 GCAACCTATTTTTAAGTT
*
263484 GC-ACTCCA-TTTTAAGTT
1 GCAAC-CTATTTTTAAGTT
263501 GCAACCTATTTTTAAGTT
1 GCAACCTATTTTTAAGTT
263519 GCAACCTATTTTTAAGTT
1 GCAACCTATTTTTAAGTT
*
263537 GTAACCTATTTTTAAGTT
1 GCAACCTATTTTTAAGTT
* * *
263555 ACAATCTATTTTTAAATT
1 GCAACCTATTTTTAAGTT
*
263573 GCAACCCATTTT
1 GCAACCTATTTT
263585 CTAGTTGCCC
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
17 15 0.17
18 73 0.83
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.45
Consensus pattern (18 bp):
GCAACCTATTTTTAAGTT
Found at i:271158 original size:20 final size:20
Alignment explanation
Indices: 271064--271472 Score: 513
Period size: 20 Copynumber: 20.4 Consensus size: 20
271054 GATTTTCCAT
* ** *
271064 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
271084 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
271104 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
271124 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
271144 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
271164 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
271184 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
271204 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
271224 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
271244 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
271264 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
271284 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
271304 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
271324 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
271344 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
271364 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
271384 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
271404 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
271424 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
271444 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
271464 AATCACAAC
1 AATCGCAAC
271473 ACTGAAATTT
Statistics
Matches: 341, Mismatches: 38, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.01
20 333 0.98
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:272185 original size:24 final size:24
Alignment explanation
Indices: 272146--272192 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
272136 AAATTTGGTC
272146 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
272170 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
272193 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:274714 original size:19 final size:19
Alignment explanation
Indices: 274692--275017 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
274682 CGGAAAATAC
*
274692 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
274711 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
274725 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
274745 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
274759 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
274778 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
274797 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
274811 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
274830 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
274849 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
274863 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
274882 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
274901 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
274920 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
274939 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
274958 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
274972 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
274991 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
275010 AATCGCAA
1 AATCGCAA
275018 CGAGATAATC
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 50 0.19
15 3 0.01
16 13 0.05
17 12 0.04
18 4 0.01
19 174 0.65
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:274779 original size:33 final size:34
Alignment explanation
Indices: 274692--275017 Score: 321
Period size: 33 Copynumber: 9.2 Consensus size: 34
274682 CGGAAAATAC
* *
274692 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
274725 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
274759 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
274797 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
274830 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
274863 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
274901 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
274939 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
274971 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
275010 AATCGCAA
1 AATCGCAA
275018 CGAGATAATC
Statistics
Matches: 257, Mismatches: 12, Indels: 43
0.82 0.04 0.14
Matches are distributed among these distances:
32 2 0.01
33 111 0.43
34 32 0.12
35 9 0.04
36 6 0.02
37 4 0.02
38 91 0.35
39 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:274953 original size:161 final size:157
Alignment explanation
Indices: 274720--275039 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
274710 AAATCCCAAC
*
274720 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
274785 ATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
66 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
274850 ATCGCAACGAGAGAATCGCAATGCGAA
131 ATCGCAACGAGAGAATCGCAATGCGAA
*
274877 ATGAAAATCGCAATGC-GAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGC-A-ACG--A-GAAAATCGCAATGCGAAATGAAAA
274941 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
61 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
*
275006 TGAAAATCGCAACGAGATAATCGCAATGCGAA
126 TGAAAATCGCAACGAGAGAATCGCAATGCGAA
275038 AT
1 AT
275040 TATAAACGCA
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 13 0.08
157 17 0.11
158 3 0.02
160 1 0.01
161 120 0.78
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (157 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
ATCGCAACGAGAGAATCGCAATGCGAA
Found at i:275055 original size:52 final size:52
Alignment explanation
Indices: 274720--275039 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
274710 AAATCCCAAC
274720 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
274773 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
274825 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
274877 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
*
274934 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
274986 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
275038 AT
1 AT
275040 TATAAACGCA
Statistics
Matches: 255, Mismatches: 7, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
52 184 0.72
53 18 0.07
54 3 0.01
55 3 0.01
56 2 0.01
57 45 0.18
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:275155 original size:19 final size:19
Alignment explanation
Indices: 275046--275147 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
275036 AAATTATAAA
275046 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
275065 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
275085 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
275101 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
275118 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
275137 CGCATTGCGAT
1 CGCATTGCGAT
275148 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:275273 original size:14 final size:14
Alignment explanation
Indices: 275254--275290 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
275244 CATCAATTAC
275254 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
275268 ACAAATCATCTTTT
1 ACAAATCAACTTTT
275282 ACAAATCAA
1 ACAAATCAA
275291 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:275318 original size:37 final size:37
Alignment explanation
Indices: 275271--275341 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
275261 AACTTTTACA
*
275271 AATCATCTTTTACAAATCAATTAAACAATCAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAATTG
275308 AATCAACTTTTACAAATCAATTAAACAATCAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAA
275342 AACAATCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.52, C:0.17, G:0.01, T:0.30
Consensus pattern (37 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAATTG
Found at i:275349 original size:37 final size:37
Alignment explanation
Indices: 275271--275350 Score: 124
Period size: 37 Copynumber: 2.2 Consensus size: 37
275261 AACTTTTACA
* ***
275271 AATCATCTTTTACAAATCAATTAAACAATCAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAAAC
275308 AATCAACTTTTACAAATCAATTAAACAATCAAAAAAC
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAAAC
275345 AATCAA
1 AATCAA
275351 TTAAACTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.54, C:0.17, G:0.01, T:0.28
Consensus pattern (37 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAAAC
Found at i:277235 original size:14 final size:14
Alignment explanation
Indices: 277216--277272 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
277206 GCGAAATGAA
*
277216 AATCGCAACGACAG
1 AATCGCAACGAAAG
277230 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
277247 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
277263 AATCGCAACG
1 AATCGCAACG
277273 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:277243 original size:33 final size:33
Alignment explanation
Indices: 277197--277289 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
277187 GCGAAACCAA
*
277197 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
277230 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
277263 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
277290 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:277254 original size:19 final size:19
Alignment explanation
Indices: 277160--277294 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
277150 TAGTTTACTT
* *
277160 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
277180 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
277199 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
277218 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
277232 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
277251 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
277265 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
277284 TCGCAATGCGA
1 TCGCAACGCGA
277295 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:277312 original size:19 final size:19
Alignment explanation
Indices: 277290--277418 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
277280 AAAATCGCAA
277290 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
277309 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
277323 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
277342 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
277356 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
277375 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
277394 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
277414 TGCGA
1 TGCGA
277419 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:277332 original size:33 final size:33
Alignment explanation
Indices: 277290--277381 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
277280 AAAATCGCAA
277290 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
277323 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
277356 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
277382 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:277621 original size:93 final size:93
Alignment explanation
Indices: 277462--277841 Score: 753
Period size: 93 Copynumber: 4.1 Consensus size: 93
277452 TTGAATGGAT
277462 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
277527 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
277555 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
277620 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
277648 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
277712 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
277740 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
277805 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
277833 AAATTTACT
1 AAATTTACT
277842 AAGCAATCTA
Statistics
Matches: 286, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 194 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:277775 original size:185 final size:186
Alignment explanation
Indices: 277462--277841 Score: 753
Period size: 185 Copynumber: 2.0 Consensus size: 186
277452 TTGAATGGAT
277462 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
277527 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
277592 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
277648 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
277712 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
277777 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
277833 AAATTTACT
1 AAATTTACT
277842 AAGCAATCTA
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 155 0.80
186 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:279566 original size:14 final size:14
Alignment explanation
Indices: 279547--279636 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
279537 TTGAAATGAA
279547 AATCGCAACGAGAG
1 AATCGCAACGAGAG
279561 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
279578 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
279594 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
279613 AATCGCAACGAGAG
1 AATCGCAACGAGAG
279627 AATCGCAACG
1 AATCGCAACG
279637 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:279584 original size:33 final size:33
Alignment explanation
Indices: 279539--279653 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
279529 TCTTTTGGTT
279539 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
279572 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
279605 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
279638 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
279654 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:279585 original size:19 final size:18
Alignment explanation
Indices: 279546--279658 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
279536 GTTGAAATGA
279546 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
279561 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
279578 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
279594 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
279611 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
279627 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
279644 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
279659 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:279689 original size:14 final size:14
Alignment explanation
Indices: 279670--279724 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
279660 TTTGGTTTCG
279670 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
279684 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
279703 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
279717 CGTTGCGA
1 CGTTGCGA
279725 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:279702 original size:33 final size:33
Alignment explanation
Indices: 279654--279724 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
279644 AAAATCGCAA
**
279654 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
279687 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
279720 TGCGA
1 TGCGA
279725 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:279732 original size:33 final size:33
Alignment explanation
Indices: 279665--279746 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
279655 GCGATTTTGG
***
279665 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
279698 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
279731 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
279747 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:279751 original size:20 final size:20
Alignment explanation
Indices: 279677--279765 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
279667 TCGCGTTGCG
279677 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
279697 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
279710 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
279730 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
279750 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
279766 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:279887 original size:33 final size:33
Alignment explanation
Indices: 279845--279915 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
279835 AATACTAACT
*
279845 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
279878 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
279911 TGAAA
1 TGAAA
279916 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:280148 original size:22 final size:22
Alignment explanation
Indices: 280096--280150 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
280086 TGGTTGTGAG
**
280096 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
280118 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
280140 GGATTTCTTCG
1 GGATTTCTTCG
280151 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:280321 original size:20 final size:20
Alignment explanation
Indices: 280296--280489 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
280286 CTTTAAATAT
280296 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
280316 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
280338 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
280357 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
280377 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
280397 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
280417 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
280437 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
280457 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
280477 CGCGTTGCGATTT
1 CGCGTTGCGATTT
280490 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:280483 original size:60 final size:60
Alignment explanation
Indices: 280296--280489 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
280286 CTTTAAATAT
**
280296 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
280357 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
280417 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
280477 CGCGTTGCGATTT
1 CGCGTTGCGATTT
280490 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:280506 original size:21 final size:20
Alignment explanation
Indices: 280482--280558 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
280472 ATATTCGCGT
280482 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
280503 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
280523 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
280545 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
280559 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:280569 original size:20 final size:20
Alignment explanation
Indices: 280544--280595 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
280534 AAGAATCGCG
*
280544 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
280564 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
280584 TTGCGATTCTGG
1 TTGCGATTCTGG
280596 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:284782 original size:41 final size:42
Alignment explanation
Indices: 284737--284840 Score: 111
Period size: 52 Copynumber: 2.3 Consensus size: 42
284727 TCGTATATTT
284737 TAATCAAATTGCTTACATTCTAAAAATAATGCAAGAAACTGTAA
1 TAATCAAATTGCTTACATTCTAAAAATAATGCAAGAAACTG--A
284781 TCAATTAGACAAAAAATTGCTTACATTCTAAAAATAATGCAAGAAACTG-
1 T-AA-T---C---AAATTGCTTACATTCTAAAAATAATGCAAGAAACTGA
284830 TAATCAAATTG
1 TAATCAAATTG
284841 ATACATGAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 19
0.73 0.00 0.27
Matches are distributed among these distances:
41 6 0.12
44 2 0.04
45 2 0.04
46 1 0.02
47 1 0.02
48 2 0.04
49 2 0.04
52 36 0.69
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (42 bp):
TAATCAAATTGCTTACATTCTAAAAATAATGCAAGAAACTGA
Found at i:286875 original size:20 final size:21
Alignment explanation
Indices: 286850--286942 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
286840 TTTTCCCAAT
*
286850 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
286870 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
286891 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
286911 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
286932 TCGCAATGCGA
1 TCGCAATGCGA
286943 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:286895 original size:41 final size:41
Alignment explanation
Indices: 286850--286942 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
286840 TTTTCCCAAT
286850 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
286891 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
286932 TCGCAATGCGA
1 TCGCAATGCGA
286943 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:286955 original size:41 final size:41
Alignment explanation
Indices: 286869--287003 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
286859 GAATAAGTAA
* *
286869 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
286910 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
286951 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
286992 TTCGCAACGCGA
1 ATCGCAACGCGA
287004 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:286956 original size:20 final size:20
Alignment explanation
Indices: 286931--287019 Score: 79
Period size: 20 Copynumber: 4.4 Consensus size: 20
286921 AATTGGGAAA
*
286931 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
286951 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
286972 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
286992 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
287012 TTCGCAAC
1 ATCGCAAC
287020 ACAATAATAC
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
20 41 0.75
21 14 0.25
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:287241 original size:22 final size:22
Alignment explanation
Indices: 287213--287256 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
287203 CACTCTCTCA
287213 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
287235 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
287257 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:287545 original size:20 final size:20
Alignment explanation
Indices: 287520--287557 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
287510 CGATTCTCTC
287520 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
287540 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
287558 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:288897 original size:18 final size:18
Alignment explanation
Indices: 288876--288920 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
288866 TCCACTTCGG
*
288876 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
288894 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
288912 GAGCCATCA
1 GAGCCATCA
288921 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:289427 original size:20 final size:20
Alignment explanation
Indices: 289402--289447 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
289392 TAGTTTACTT
289402 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
289422 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
289442 TCGCAA
1 TCGCAA
289448 TGCGATCTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:289476 original size:14 final size:14
Alignment explanation
Indices: 289457--289514 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
289447 ATGCGATCTG
289457 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
289471 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
289487 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
289503 AAAATCGCAACG
1 AAAATCGCAACG
289515 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:289499 original size:32 final size:33
Alignment explanation
Indices: 289441--289531 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
289431 GGAAATGGCT
**
289441 ATCGCAATGCGATCTGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
289474 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
289506 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
289532 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:289604 original size:19 final size:19
Alignment explanation
Indices: 289582--289665 Score: 78
Period size: 20 Copynumber: 4.3 Consensus size: 19
289572 GATTTTGTCA
*
289582 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
***
289601 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
**
289621 TTGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
289640 TTGCGATTTTAAGTTTCGTG
1 TTGCGATTTTCA-TTTCGCG
289660 TTGCGA
1 TTGCGA
289666 AAGTAAACTA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
19 25 0.46
20 29 0.54
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.40
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:289626 original size:20 final size:19
Alignment explanation
Indices: 289592--289646 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
289582 TTGCGATTTT
*
289592 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
289611 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
289631 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
289647 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:291635 original size:888 final size:888
Alignment explanation
Indices: 289879--291659 Score: 3528
Period size: 889 Copynumber: 2.0 Consensus size: 888
289869 TAGCGACCCG
*
289879 ATAAGGTGGATGCTTTACGTCGGGTTTTCCTTGCACGACGGAGTTCACGCATCAGACGGCGTGGA
1 ATAAGGTGGATGCTTTACGTCGGGTTTTCCTTACACGACGGAGTTCACGCATCAGACGGCGTGGA
289944 CGTGCTATTACGTCTCCGTTCACCCCAATGGTGCGAAGACTCCGCAAGAAGAAGCCCGACTCACC
66 CGTGCTATTACGTCTCCGTTCACCCCAATGGTGCGAAGACTCCGCAAGAAGAAGCCCGACTCACC
290009 GGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCTATTCTCCCTCAAGATTCCCCCCC
131 GGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCTATTCTCCCTCAAGATTCCCCCCC
290074 CCCACCGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTCCAGAGCCCGATTC
196 CCCACCGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTCCAGAGCCCGATTC
290139 ACATGGGGTAATATATCGAAGTATTGAGAAACCCCCACCGGTTCCGGACATGATGGATGAGAGTT
261 ACATGGGGTAATATATCGAAGTATTGAGAAACCCCCACCGGTTCCGGACATGATGGATGAGAGTT
290204 GGCTCTCGTATGAGTTACCGGCTAGTACCCTTCCGGTATCTGAAGTGGAGAGGAGACAACTACCG
326 GGCTCTCGTATGAGTTACCGGCTAGTACCCTTCCGGTATCTGAAGTGGAGAGGAGACAACTACCG
290269 GAAACAATTGTGGATAATACCCTTTGGGCTAAGACCGCAGTTGATTTTTATCTACATGAGCGGAG
391 GAAACAATTGTGGATAATACCCTTTGGGCTAAGACCGCAGTTGATTTTTATCTACATGAGCGGAG
290334 CCAAGGGTGTTACACTGACATCAACAAACTCAACGATGAAATGTTTTTGTTGCTTGATCGGTCTT
456 CCAAGGGTGTTACACTGACATCAACAAACTCAACGATGAAATGTTTTTGTTGCTTGATCGGTCTT
290399 GGTGGGGTGTGCTATTAGGGGTTGAAGATAGTGGCTATTTGGATGGGGAGGTAAGACTATATTTG
521 GGTGGGGTGTGCTATTAGGGGTTGAAGATAGTGGCTATTTGGATGGGGAGGTAAGACTATATTTG
290464 TCTTATATATGATTTTGATTAATTTGTTTAAAAATTAATGTAATTCACTAATATATGTATTTTTT
586 TCTTATATATGATTTTGATTAATTTGTTTAAAAATTAATGTAATTCACTAATATATGTATTTTTT
290529 TTGTAAAACAGCATATCGATGCGTGGGTGTCACGTCTACTAATAATAAGGAAGCTTAGGAAAAAT
651 TTGTAAAACAGCATATCGATGCGTGGGTGTCACGTCTACTAATAATAAGGAAGCTTAGGAAAAAT
290594 AAAAAAAAAATCGCTATATACAATAATGCCGACGGCTTTTCACGCAGTTCACTTGAAGAATCAAC
716 AAAAAAAAAATCGCTATATACAATAATGCCGACGGCTTTTCACGCAGTTCACTTGAAGAATCAAC
290659 GAGATGAATCATTTTTGTTGGGCAATGGACAAGCTAAACTTTATCCTGCATGGTGGGAGGTCGAT
781 GAGATGAATCATTTTTGTTGGGCAATGGACAAGCTAAACTTTATCCTGCATGGTGGGAGGTCGAT
290724 AAGGTTAGTGTTTATTTTTAAAATTTTTTAAAGGTGTTCATAA
846 AAGGTTAGTGTTTATTTTTAAAATTTTTTAAAGGTGTTCATAA
290767 ATAAGGTGGATGCTTTACGTCGGGTTTTCCTTACACGACGGAGTTCACGCATCAGACGGCGTGGA
1 ATAAGGTGGATGCTTTACGTCGGGTTTTCCTTACACGACGGAGTTCACGCATCAGACGGCGTGGA
290832 CGTGCTATTACGTCTCCGTTCACCCCAATGGTGCGAAGACTCCGCAAGAAGAAGCCCGACTCACC
66 CGTGCTATTACGTCTCCGTTCACCCCAATGGTGCGAAGACTCCGCAAGAAGAAGCCCGACTCACC
290897 GGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTATTCTCCCTCAAGATTCCCCCC
131 GGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGG-CCCTATTCTCCCTCAAGATTCCCCCC
290962 CCCCACCGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTCCAGAGCCCGATT
195 CCCCACCGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTCCAGAGCCCGATT
291027 CACATGGGGTAATATATCGAAGTATTGAGAAACCCCCACCGGTTCCGGACATGATGGATGAGAGT
260 CACATGGGGTAATATATCGAAGTATTGAGAAACCCCCACCGGTTCCGGACATGATGGATGAGAGT
*
291092 TGGCTCTTGTATGAGTTACCGGCTAGTACCCTTCCGGTATCTGAAGTGGAGAGGAGACAACTACC
325 TGGCTCTCGTATGAGTTACCGGCTAGTACCCTTCCGGTATCTGAAGTGGAGAGGAGACAACTACC
291157 GGAAACAATTGTGGATAATACCCTTTGGGCTAAGACCGCAGTTGATTTTTATCTACATGAGCGGA
390 GGAAACAATTGTGGATAATACCCTTTGGGCTAAGACCGCAGTTGATTTTTATCTACATGAGCGGA
291222 GCCAAGGGTGTTACACTGACATCAACAAACTCAACGATGAAATGTTTTTGTTGCTTGATCGGTCT
455 GCCAAGGGTGTTACACTGACATCAACAAACTCAACGATGAAATGTTTTTGTTGCTTGATCGGTCT
291287 TGGTGGGGTGTGCTATTAGGGGTTGAAGATAGTGGCTATTTGGATGGGGAGGTAAGACTATATTT
520 TGGTGGGGTGTGCTATTAGGGGTTGAAGATAGTGGCTATTTGGATGGGGAGGTAAGACTATATTT
291352 GTCTTATATATGATTTTGATTAATTTGTTTAAAAATTAATGTAATTCACTAATATATGTATTTTT
585 GTCTTATATATGATTTTGATTAATTTGTTTAAAAATTAATGTAATTCACTAATATATGTATTTTT
291417 TTTGTAAAACAGCATATCGATGCGTGGGTGTCACGTCTACTAATAATAAGGAAGCTTAGGAAAAA
650 TTTGTAAAACAGCATATCGATGCGTGGGTGTCACGTCTACTAATAATAAGGAAGCTTAGGAAAAA
291482 T-AAAAAAAAATCGCTATATACAATAATGCCGACGGCTTTTCACGCAGTTCACTTGAAGAATCAA
715 TAAAAAAAAAATCGCTATATACAATAATGCCGACGGCTTTTCACGCAGTTCACTTGAAGAATCAA
291546 CGAGATGAATCATTTTTGTTGGGCAATGGACAAGCTAAACTTTATCCTGCATGGTGGGAGGTCGA
780 CGAGATGAATCATTTTTGTTGGGCAATGGACAAGCTAAACTTTATCCTGCATGGTGGGAGGTCGA
291611 TAAGGTTAGTGTTTATTTTTAAAATTTTTTAAAGGTGTTCATAA
845 TAAGGTTAGTGTTTATTTTTAAAATTTTTTAAAGGTGTTCATAA
291655 ATAAG
1 ATAAG
291660 TGCGCAAATA
Statistics
Matches: 890, Mismatches: 2, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
888 344 0.39
889 546 0.61
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (888 bp):
ATAAGGTGGATGCTTTACGTCGGGTTTTCCTTACACGACGGAGTTCACGCATCAGACGGCGTGGA
CGTGCTATTACGTCTCCGTTCACCCCAATGGTGCGAAGACTCCGCAAGAAGAAGCCCGACTCACC
GGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCTATTCTCCCTCAAGATTCCCCCCC
CCCACCGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTCCAGAGCCCGATTC
ACATGGGGTAATATATCGAAGTATTGAGAAACCCCCACCGGTTCCGGACATGATGGATGAGAGTT
GGCTCTCGTATGAGTTACCGGCTAGTACCCTTCCGGTATCTGAAGTGGAGAGGAGACAACTACCG
GAAACAATTGTGGATAATACCCTTTGGGCTAAGACCGCAGTTGATTTTTATCTACATGAGCGGAG
CCAAGGGTGTTACACTGACATCAACAAACTCAACGATGAAATGTTTTTGTTGCTTGATCGGTCTT
GGTGGGGTGTGCTATTAGGGGTTGAAGATAGTGGCTATTTGGATGGGGAGGTAAGACTATATTTG
TCTTATATATGATTTTGATTAATTTGTTTAAAAATTAATGTAATTCACTAATATATGTATTTTTT
TTGTAAAACAGCATATCGATGCGTGGGTGTCACGTCTACTAATAATAAGGAAGCTTAGGAAAAAT
AAAAAAAAAATCGCTATATACAATAATGCCGACGGCTTTTCACGCAGTTCACTTGAAGAATCAAC
GAGATGAATCATTTTTGTTGGGCAATGGACAAGCTAAACTTTATCCTGCATGGTGGGAGGTCGAT
AAGGTTAGTGTTTATTTTTAAAATTTTTTAAAGGTGTTCATAA
Found at i:292571 original size:19 final size:19
Alignment explanation
Indices: 292549--292616 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
292539 ATCACAACGA
292549 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
292568 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
292587 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
292601 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
292617 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:292637 original size:19 final size:19
Alignment explanation
Indices: 292606--292692 Score: 103
Period size: 19 Copynumber: 4.8 Consensus size: 19
292596 AACGAGAAAA
*
292606 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
292625 TCGCATTGTGA--TTC-TA
1 TCGCATTGCGATTTTCATT
*
292641 TCG--TTGCGATTTGCATT
1 TCGCATTGCGATTTTCATT
292658 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
292677 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
292693 TCGTTGCGAT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
14 5 0.09
16 6 0.11
17 7 0.12
19 38 0.68
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:292710 original size:52 final size:52
Alignment explanation
Indices: 292606--292721 Score: 162
Period size: 52 Copynumber: 2.2 Consensus size: 52
292596 AACGAGAAAA
* * *
292606 TCGCAATGCGATTTTCATTTCGCATTGTGATTCTATCGTTGCGATTTGCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCGATTAGCATT
* *
292658 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGA-TAGCCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCGATTAG-CATT
*
292710 TCGCGTTGCGAT
1 TCGCATTGCGAT
292722 AGCCTGTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 2 0.04
52 55 0.96
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.42
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCGATTAGCATT
Found at i:292711 original size:19 final size:19
Alignment explanation
Indices: 292689--292725 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
292679 GCATTGCGAT
*
292689 TTTCTCGTTGCGATAGCCA
1 TTTCGCGTTGCGATAGCCA
292708 TTTCGCGTTGCGATAGCC
1 TTTCGCGTTGCGATAGCC
292726 TGTTTTGCAA
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:0.14, C:0.27, G:0.24, T:0.35
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGCCA
Found at i:293707 original size:24 final size:24
Alignment explanation
Indices: 293673--293726 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
293663 GTATTCGAAA
* * *
293673 TTTGATCTTGGTTAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
293697 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
293721 TTTGAT
1 TTTGAT
293727 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:296250 original size:33 final size:33
Alignment explanation
Indices: 296208--296330 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
296198 ATTACTATCA
296208 CAATGCGAAATGAAAATCGCAACGAAAGAATCG
1 CAATGCGAAATGAAAATCGCAACGAAAGAATCG
* **
296241 CAATGCGAAATGAAAATCGCAACGCTAA-TTTCG
1 CAATGCGAAATGAAAATCGCAACG-AAAGAATCG
**
296274 CAATGCGAAATGAAAATCGCAACGAGGGAATCG
1 CAATGCGAAATGAAAATCGCAACGAAAGAATCG
296307 CAATGCGAAATGAAAATCGCAACG
1 CAATGCGAAATGAAAATCGCAACG
296331 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
33 78 0.98
34 2 0.03
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAAAGAATCG
Found at i:296314 original size:66 final size:66
Alignment explanation
Indices: 296208--296337 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
296198 ATTACTATCA
*
296208 CAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTC
1 CAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTC
296273 G
66 G
**
296274 CAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 CAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
296338 AATTTCGCGT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (66 bp):
CAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTC
G
Found at i:296365 original size:20 final size:19
Alignment explanation
Indices: 296339--296459 Score: 91
Period size: 19 Copynumber: 6.8 Consensus size: 19
296329 CGCGAATTTA
296339 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
296358 ATTTTCGCGTTGAGA--TTC
1 A-TTTCGCGTTGCGATTTTC
*
296376 ---TCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
296392 ATTTCGCATTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
296411 ATTTTCGCGTTGAGA--TTC
1 A-TTTCGCGTTGCGATTTTC
* *
296429 ---TCTCATTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
296445 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
296460 AGTACTTTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
14 17 0.22
16 6 0.08
18 6 0.08
19 27 0.34
20 23 0.29
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:296419 original size:53 final size:53
Alignment explanation
Indices: 296330--296459 Score: 224
Period size: 53 Copynumber: 2.5 Consensus size: 53
296320 AAATCGCAAC
* * * *
296330 GCGAATTTAATTTCGCGTTGCGATTTTCATTTTCGCGTTGAGATTCTCTCGTT
1 GCGATTTTCATTTCGCATTGCGATTTTCATTTTCGCGTTGAGATTCTCTCATT
296383 GCGATTTTCATTTCGCATTGCGATTTTCATTTTCGCGTTGAGATTCTCTCATT
1 GCGATTTTCATTTCGCATTGCGATTTTCATTTTCGCGTTGAGATTCTCTCATT
296436 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCATTGCGAT
296460 AGTACTTTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 73 1.00
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.45
Consensus pattern (53 bp):
GCGATTTTCATTTCGCATTGCGATTTTCATTTTCGCGTTGAGATTCTCTCATT
Found at i:296585 original size:14 final size:14
Alignment explanation
Indices: 296566--296602 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
296556 CATCAATTAA
296566 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
296580 ACAAATCACCTTTT
1 ACAAATCAACTTTT
296594 ACAAATCAA
1 ACAAATCAA
296603 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:298023 original size:21 final size:21
Alignment explanation
Indices: 297957--298023 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
297947 GTGAATCGGG
*
297957 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
297977 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
297999 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
298020 CTCT
1 CTCT
298024 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:298042 original size:42 final size:41
Alignment explanation
Indices: 297957--298079 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
297947 GTGAATCGGG
* * * * *
297957 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
297999 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
298041 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
298080 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:300107 original size:20 final size:19
Alignment explanation
Indices: 300062--300246 Score: 149
Period size: 19 Copynumber: 10.1 Consensus size: 19
300052 TCTTTTGGTT
*
300062 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
300081 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
300101 GGAAATGACTATTGCAA--C
1 -GAAATGAAAATCGCAACGC
*
300119 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
300135 GAAATGACTATCGCAAC-C
1 GAAATGAAAATCGCAACGC
*
300153 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
300168 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
* *
300188 GAAATAAAAATCGCAACAC
1 GAAATGAAAATCGCAACGC
300207 GAAA-GTAAAATCGCAACGC
1 GAAATG-AAAATCGCAACGC
*
300226 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
300245 GA
1 GA
300247 TTTTGGTTTC
Statistics
Matches: 134, Mismatches: 17, Indels: 30
0.74 0.09 0.17
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 58 0.43
20 45 0.34
21 2 0.01
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:300144 original size:33 final size:33
Alignment explanation
Indices: 300087--300185 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
300077 ACGAGATAAT
* *
300087 GAGAATCGCAACGCGGAAATGACTATTGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
300121 GAGAATCGCAACGCGAAATGACTATCGCAACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
300154 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
300186 GCGAAATAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 46 0.77
34 14 0.23
ACGTcount: A:0.40, C:0.25, G:0.22, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:300217 original size:39 final size:38
Alignment explanation
Indices: 300157--300241 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 38
300147 GCAACCAGAC
*
300157 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACACGAAATGAAAATCGCAA-CGCGAAATAAA
*
300196 AATCGCAACACGAAA-GTAAAATCGCAACGCGAAATGAA
1 AATCGCAACACGAAATG-AAAATCGCAACGCGAAATAAA
300234 AATCGCAA
1 AATCGCAA
300242 TGCGATTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
38 19 0.44
39 24 0.56
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (38 bp):
AATCGCAACACGAAATGAAAATCGCAACGCGAAATAAA
Found at i:300264 original size:19 final size:19
Alignment explanation
Indices: 300242--300289 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
300232 AAAATCGCAA
*
300242 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
300261 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
300281 TGCGATTTT
1 TGCGATTTT
300290 CATTCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:300833 original size:20 final size:20
Alignment explanation
Indices: 300808--300900 Score: 71
Period size: 20 Copynumber: 4.6 Consensus size: 20
300798 CGCTATGTAA
300808 ATCGCGTTGCGAAAGTCAA-T
1 ATCGCGTTGCGAAAGT-AAGT
*
300828 ATCGCGTTGTGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
* *** * *
300848 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-AAGTAAGT
* *
300869 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
300889 ATCGCATTGCGA
1 ATCGCGTTGCGA
300901 TTTTCCCAAT
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.04
20 42 0.74
21 13 0.23
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:300919 original size:21 final size:21
Alignment explanation
Indices: 300890--300982 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
300880 ATAGTAAGTA
300890 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
300911 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
300931 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
300952 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
300972 TCGCATTGCGA
1 TCGCATTGCGA
300983 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:300920 original size:41 final size:42
Alignment explanation
Indices: 300824--300963 Score: 144
Period size: 41 Copynumber: 3.4 Consensus size: 42
300814 TTGCGAAAGT
* * * * *
300824 CAATATCGCGTTGTGAAAGTAAGTATCTCGTTGCGATTTT-T
1 CAATATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCC
* * *
300865 TATTATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCC
1 CAATATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCC
* **
300907 CAAT-TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCC
1 CAATATCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCC
300948 CAAT-TCGCGTTGCGAT
1 CAATATCGCGTTGCGAT
300964 TTACTTATTC
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 4 0.05
41 77 0.93
42 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (42 bp):
CAATATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCC
Found at i:300964 original size:41 final size:41
Alignment explanation
Indices: 300890--300982 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
300880 ATAGTAAGTA
300890 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
300931 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
300972 TCGCATTGCGA
1 TCGCATTGCGA
300983 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:301955 original size:131 final size:132
Alignment explanation
Indices: 301798--302062 Score: 505
Period size: 131 Copynumber: 2.0 Consensus size: 132
301788 CTACGTCATG
301798 ATTTTAGTTAAAAATCGTTATCCAATACATGTCACAATTATATACATTTAAAAAAAAATTAGAAA
1 ATTTTAGTTAAAAATCGTTATCCAATACATGTCACAATTATATACATTTAAAAAAAAATTAGAAA
*
301863 ACTTAAAAATTTA-TTTAAAAAAAAATTTCTAAAATCCAAAAATAAAAACTTATAATCGTTAATT
66 ACTTAAAAATTTATTTTAAAAAAAAAATTCTAAAATCCAAAAATAAAAACTTATAATCGTTAATT
301927 TT
131 TT
301929 ATTTTAGTTAAAAATCGTTATCCAATACATGTCACAATTATATACATTTAAAAAAAAATTAGAAA
1 ATTTTAGTTAAAAATCGTTATCCAATACATGTCACAATTATATACATTTAAAAAAAAATTAGAAA
*
301994 ACTTAAAAATTTATTTTAAAAAAAAAATTCTAAAATCCAAAACTAAAAACTTATAATCGTTAATT
66 ACTTAAAAATTTATTTTAAAAAAAAAATTCTAAAATCCAAAAATAAAAACTTATAATCGTTAATT
302059 TT
131 TT
302061 AT
1 AT
302063 CTCACCCCGG
Statistics
Matches: 131, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
131 78 0.60
132 53 0.40
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (132 bp):
ATTTTAGTTAAAAATCGTTATCCAATACATGTCACAATTATATACATTTAAAAAAAAATTAGAAA
ACTTAAAAATTTATTTTAAAAAAAAAATTCTAAAATCCAAAAATAAAAACTTATAATCGTTAATT
TT
Found at i:304870 original size:12 final size:13
Alignment explanation
Indices: 304851--304881 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
304841 TATTTAGAAT
304851 ATATTAATATTTA
1 ATATTAATATTTA
304864 A-ATTAATATTTA
1 ATATTAATATTTA
304876 ATATTA
1 ATATTA
304882 TTAATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTAATATTTA
Found at i:304928 original size:17 final size:17
Alignment explanation
Indices: 304876--304940 Score: 76
Period size: 17 Copynumber: 3.6 Consensus size: 17
304866 TTAATATTTA
*
304876 ATATTATTAATTTTTATT
1 ATATTATTTATTTTT-TT
* *
304894 ATTTTTATATTCTTTTTTT
1 A-TATTAT-TTATTTTTTT
304913 ATATTATTTATTTTTTT
1 ATATTATTTATTTTTTT
304930 ATATTATTTAT
1 ATATTATTTAT
304941 ATATTCTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
17 20 0.50
18 6 0.15
19 8 0.20
20 6 0.15
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (17 bp):
ATATTATTTATTTTTTT
Found at i:304943 original size:28 final size:31
Alignment explanation
Indices: 304888--304945 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 31
304878 ATTATTAATT
* *
304888 TTTATTATTTTTATATTCTTTTTTTATATTA
1 TTTATTATTTTTATATTCTATTTATATATTA
304919 TTTATT-TTTTTATA-T-TATTTATATATT
1 TTTATTATTTTTATATTCTATTTATATATT
304946 CTTATTTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.40
29 1 0.04
30 8 0.32
31 6 0.24
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (31 bp):
TTTATTATTTTTATATTCTATTTATATATTA
Found at i:313493 original size:2 final size:2
Alignment explanation
Indices: 313486--313524 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
313476 TTCTCAAATA
313486 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
313525 ATCTGACAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:318377 original size:2 final size:2
Alignment explanation
Indices: 318370--318404 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
318360 GGAAAATTAA
318370 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
318405 AAAAATCAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:320182 original size:44 final size:44
Alignment explanation
Indices: 320131--320246 Score: 115
Period size: 44 Copynumber: 2.6 Consensus size: 44
320121 TTCCTATTCG
* * **
320131 CGGGTTTAATCCATGTGAAATATTCTTCGGATGACTTCCCTTTG
1 CGGGTTTAAGCCATGTGAAATATTCTTCGGATGACTCCCCTTCA
* * * * * * *
320175 TGGGTTTAAGCTAGGTGAAGTATTTTTTGGATTACTCCCCTTCA
1 CGGGTTTAAGCCATGTGAAATATTCTTCGGATGACTCCCCTTCA
* *
320219 CGGGTTTAGGCCATGTGAAATGTTCTTC
1 CGGGTTTAAGCCATGTGAAATATTCTTC
320247 CATTCGTGAG
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (44 bp):
CGGGTTTAAGCCATGTGAAATATTCTTCGGATGACTCCCCTTCA
Found at i:320345 original size:45 final size:45
Alignment explanation
Indices: 320285--320580 Score: 269
Period size: 45 Copynumber: 6.6 Consensus size: 45
320275 GTATTCTTCA
* *
320285 AATGACTCCTATTCGCGGGTTTAAGCCGGGTGAAATGTTTTTTCG
1 AATGACTCCTCTTCGCGGGTTTAAGCCGGGTGAAATGTTCTTTCG
* * * *
320330 AATGACTCTTCTTCGCGGGTTTAAACAGGGTGAAATGTTCTTTCA
1 AATGACTCCTCTTCGCGGGTTTAAGCCGGGTGAAATGTTCTTTCG
* * *
320375 AACGACT-CTCCTTTGCGGGTTTAAGCCGGGTGAAATGTTCTTTTG
1 AATGACTCCT-CTTCGCGGGTTTAAGCCGGGTGAAATGTTCTTTCG
* * * * * *
320420 GACGACTCCCCTTCGTGGGTTTAAGTCGGGTAAAATGTTCTTTCG
1 AATGACTCCTCTTCGCGGGTTTAAGCCGGGTGAAATGTTCTTTCG
* * * * *
320465 -ATCAACT-TTCATTTGTGGGTTTAAGCCAGGTGAAATGTTCTTTCG
1 AAT-GACTCCTC-TTCGCGGGTTTAAGCCGGGTGAAATGTTCTTTCG
* * * *
320510 AATAACT-CTCATTTGCTGGTTTAAGTCGGGTGAAATGTTC-TTCG
1 AATGACTCCTC-TTCGCGGGTTTAAGCCGGGTGAAATGTTCTTTCG
* * * *
320554 GATGAATCCCCTTCGCGAGTTTAAGCC
1 AATGACTCCTCTTCGCGGGTTTAAGCC
320581 ATGTGAAGTG
Statistics
Matches: 204, Mismatches: 41, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
44 23 0.11
45 178 0.87
46 3 0.01
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (45 bp):
AATGACTCCTCTTCGCGGGTTTAAGCCGGGTGAAATGTTCTTTCG
Found at i:320531 original size:135 final size:134
Alignment explanation
Indices: 320296--320580 Score: 351
Period size: 135 Copynumber: 2.1 Consensus size: 134
320286 ATGACTCCTA
* * *
320296 TTCGCGGGTTTAAGCCGGGTGAAATGTTTTTTCGAATGACTCTTCTTCGCGGGTTTAAACAGGGT
1 TTCGCGGGTTTAAGCCGGGTAAAATGTTCTTTCGAATAACTCTTCTTCGCGGGTTTAAACAGGGT
* * * *
320361 GAAATGTTCTTTCAAACGACTCTCCTTTGCGGGTTTAAGCCGGGTGAAATGTTCTTTTGGACGAC
66 GAAATGTTCTTTCAAACAACTCTCATTTGCGGGTTTAAGCCGGGTGAAATGTTC-TTCGGACGAA
320426 TCCCC
130 TCCCC
* * * * *
320431 TTCGTGGGTTTAAGTCGGGTAAAATGTTCTTTCG-ATCAACT-TTCATTTGTGGGTTTAAGCCA-
1 TTCGCGGGTTTAAGCCGGGTAAAATGTTCTTTCGAAT-AACTCTTC-TTCGCGGGTTTAA-ACAG
* * * * *
320493 GGTGAAATGTTCTTTCGAATAACTCTCATTTGCTGGTTTAAGTCGGGTGAAATGTTCTTCGGATG
63 GGTGAAATGTTCTTTCAAACAACTCTCATTTGCGGGTTTAAGCCGGGTGAAATGTTCTTCGGACG
320558 AATCCCC
128 AATCCCC
*
320565 TTCGCGAGTTTAAGCC
1 TTCGCGGGTTTAAGCC
320581 ATGTGAAGTG
Statistics
Matches: 127, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
134 30 0.24
135 95 0.75
136 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (134 bp):
TTCGCGGGTTTAAGCCGGGTAAAATGTTCTTTCGAATAACTCTTCTTCGCGGGTTTAAACAGGGT
GAAATGTTCTTTCAAACAACTCTCATTTGCGGGTTTAAGCCGGGTGAAATGTTCTTCGGACGAAT
CCCC
Found at i:325602 original size:25 final size:25
Alignment explanation
Indices: 325574--325652 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 25
325564 TAATGAAAAT
325574 AAATA-ATAGTATAAATAAAATAATA
1 AAATATATA-TATAAATAAAATAATA
* *
325599 AAATATATATATATATAATATAA-A
1 AAATATATATATAAATAAAATAATA
* * *
325623 AATGTATGTATAATATAATAAAATACTA
1 AA-ATATATAT-ATA-AATAAAATAATA
325651 AA
1 AA
325653 TAGTAATAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
24 3 0.07
25 23 0.55
26 6 0.14
27 7 0.17
28 3 0.07
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (25 bp):
AAATATATATATAAATAAAATAATA
Found at i:325607 original size:21 final size:21
Alignment explanation
Indices: 325556--325690 Score: 68
Period size: 21 Copynumber: 6.4 Consensus size: 21
325546 GCAAAGAAAC
325556 TAAAA-ATAT-AATGAAAATAA
1 TAAAATATATAAAT-AAAATAA
*
325576 -ATAATAGTATAAATAAAATAA
1 TAAAATA-TATAAATAAAATAA
*
325597 TAAAATATATATATATATAAT-A
1 TAAAATATATA-A-ATAAAATAA
* ** *
325619 TAAAAATGTATGTATAATATAA
1 T-AAAATATATAAATAAAATAA
* *
325641 TAAAATA-CTAAATAGTAATAA
1 TAAAATATATAAATA-AAATAA
* *
325662 TAATAATAAATAAATGAAA-AA
1 TAA-AATATATAAATAAAATAA
325683 T-AAATATA
1 TAAAATATA
325691 CATATAATAT
Statistics
Matches: 86, Mismatches: 18, Indels: 23
0.68 0.14 0.18
Matches are distributed among these distances:
19 8 0.09
20 6 0.07
21 34 0.40
22 19 0.22
23 19 0.22
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (21 bp):
TAAAATATATAAATAAAATAA
Found at i:325922 original size:2 final size:2
Alignment explanation
Indices: 325915--325939 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
325905 ATATAATTAA
325915 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
325940 AATAATAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:326436 original size:37 final size:37
Alignment explanation
Indices: 326395--326487 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
326385 ATGCTTGTGC
* * *
326395 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
* ** *
326432 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
*
326469 ATCTTATTTTTAGGAGTTT
1 ATCCTATTTTTAGGAGTTT
326488 GAATCCTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
Found at i:340149 original size:3 final size:3
Alignment explanation
Indices: 340141--340184 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
340131 AACAAACGAA
340141 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
340185 AAGGACAAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:344120 original size:20 final size:21
Alignment explanation
Indices: 344095--344187 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
344085 TTTTCCCAAT
*
344095 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
344115 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
344136 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
344156 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
344177 TCGCAATGCGA
1 TCGCAATGCGA
344188 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:344140 original size:41 final size:41
Alignment explanation
Indices: 344095--344187 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
344085 TTTTCCCAAT
344095 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
344136 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
344177 TCGCAATGCGA
1 TCGCAATGCGA
344188 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:344200 original size:41 final size:41
Alignment explanation
Indices: 344114--344248 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
344104 GAATAAGTAA
* *
344114 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
344155 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
344196 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
344237 TTCGCAACGCGA
1 ATCGCAACGCGA
344249 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:344201 original size:20 final size:20
Alignment explanation
Indices: 344176--344270 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
344166 AATTGGGAAA
*
344176 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
344196 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
344217 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
344237 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
344257 TTCGCAACGCGATA
1 ATCGCAACGCGATA
344271 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:344483 original size:22 final size:22
Alignment explanation
Indices: 344455--344498 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
344445 CACTCTCTCA
*
344455 CCCATCTCTGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
344477 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
344499 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:344798 original size:20 final size:20
Alignment explanation
Indices: 344775--344817 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
344765 GATAGTCGAA
344775 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
344795 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
344815 TTC
1 TTC
344818 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:346177 original size:18 final size:18
Alignment explanation
Indices: 346133--346177 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
346123 TCCACTTCGG
*
346133 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
346151 TAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
346169 GAGCCATCA
1 GAGCCATCA
346178 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.44, G:0.13, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:346712 original size:19 final size:20
Alignment explanation
Indices: 346658--346724 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
346648 TAGTTTACTT
* *
346658 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
346678 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
346698 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
346717 TCGCAACG
1 TCGCAACG
346725 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:346732 original size:14 final size:14
Alignment explanation
Indices: 346713--346770 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
346703 ATGCGAAATG
346713 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
346727 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
346743 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
346759 AAAATCGCAACG
1 AAAATCGCAACG
346771 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:346755 original size:32 final size:33
Alignment explanation
Indices: 346697--346787 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
346687 GGAAATGGCT
346697 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
346730 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
346762 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
346788 TGTGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:346881 original size:20 final size:19
Alignment explanation
Indices: 346847--346901 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
346837 GTTGCGATTT
*
346847 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
346866 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
346886 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
346902 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:349508 original size:24 final size:24
Alignment explanation
Indices: 349457--349510 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
349447 CTATTCGAAA
* *
349457 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
* *
349481 TTTGATATTGGTCAATACATGGAT
1 TTTGATATTGGTCAATACACGGAC
349505 TTTGAT
1 TTTGAT
349511 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:349702 original size:12 final size:12
Alignment explanation
Indices: 349685--349709 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
349675 ATATAATCCT
349685 GAAGAAGAAAAA
1 GAAGAAGAAAAA
349697 GAAGAAGAAAAA
1 GAAGAAGAAAAA
349709 G
1 G
349710 TCTCCGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:352030 original size:33 final size:33
Alignment explanation
Indices: 351983--352109 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
351973 GGAAATTACT
351983 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
352016 ATCGTAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
352048 TTTCGCAATGCGAAATGAAAATCACAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
352082 ATCACAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
352110 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
32 1 0.01
33 78 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:352066 original size:66 final size:66
Alignment explanation
Indices: 351984--352116 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
351974 GAAATTACTA
* ** *
351984 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGTAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
352049 T
66 T
*
352050 TCGCAATGCGAAATGAAAATCACAACGAGGGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
352115 T
66 T
352116 T
1 T
352117 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCACAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:352131 original size:19 final size:20
Alignment explanation
Indices: 352109--352151 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
352099 AAATCGCAAC
352109 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
352128 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
352148 GCGA
1 GCGA
352152 TTCCCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:352306 original size:14 final size:14
Alignment explanation
Indices: 352287--352323 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
352277 AACATCAAAA
352287 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
352301 ACAAATCACCTTTT
1 ACAAATCAACTTTT
352315 ACAAATCAA
1 ACAAATCAA
352324 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:354011 original size:137 final size:139
Alignment explanation
Indices: 353764--354043 Score: 537
Period size: 137 Copynumber: 2.0 Consensus size: 139
353754 GGAGTGGACT
353764 CTTGAGGGATGATAGGCGAGTCGGGCTTCTTCTTCCGGTGTCTTCGCACTATTGGGGTATACGGA
1 CTTGAGGGATGATAGGCGAGTCGGGCTTCTTCTTCCGGTGTCTTCGCACTATTGGGGTATACGGA
353829 GACTTAATAGCACGTGCACGCCGTCTGATGCGTGAACTCTGTCGTGCAAG-AAAACCCGACGTAA
66 GACTTAATAGCACGTGCACGCCGTCTGATGCGTGAACTCTGTCGTGCAAGAAAAACCCGACGTAA
353893 AGCATCCAC
131 AGCATCCAC
353902 CTTGAGGGATGATAGGCGAGTCGGGCTTCTTCTTCCGG-GTCTTCGCACTATTGGGGTATACGGA
1 CTTGAGGGATGATAGGCGAGTCGGGCTTCTTCTTCCGGTGTCTTCGCACTATTGGGGTATACGGA
353966 GACTTAATAGCACGTGCACGCCGTCTGATGCGTGAACTCTGTCGTGCAAGAAAAAACCCGACGTA
66 GACTTAATAGCACGTGCACGCCGTCTGATGCGTGAACTCTGTCGTGCAAG-AAAAACCCGACGTA
354031 AAGCATCCAC
130 AAGCATCCAC
354041 CTT
1 CTT
354044 ATCGGTCCGC
Statistics
Matches: 140, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
137 76 0.54
138 38 0.27
139 26 0.19
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (139 bp):
CTTGAGGGATGATAGGCGAGTCGGGCTTCTTCTTCCGGTGTCTTCGCACTATTGGGGTATACGGA
GACTTAATAGCACGTGCACGCCGTCTGATGCGTGAACTCTGTCGTGCAAGAAAAACCCGACGTAA
AGCATCCAC
Found at i:355971 original size:32 final size:33
Alignment explanation
Indices: 355916--356010 Score: 129
Period size: 32 Copynumber: 2.9 Consensus size: 33
355906 CGATAATGAG
* *
355916 AATCGCAACGCGGAAATGACTATCGCAACGAGAT
1 AATCGCAACGC-GAAATGACTATCGCAACCAGAC
*
355950 AATCGCAACGCG-AATGACTATCGCGACCAGAC
1 AATCGCAACGCGAAATGACTATCGCAACCAGAC
**
355982 AATCGCAACGCGAAATGAAAATCGCAACC
1 AATCGCAACGCGAAATGACTATCGCAACC
356011 GCGAAATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
32 29 0.54
33 14 0.26
34 11 0.20
ACGTcount: A:0.39, C:0.27, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACCAGAC
Found at i:356015 original size:20 final size:19
Alignment explanation
Indices: 355982--356033 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
355972 GCGACCAGAC
*
355982 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
356001 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATAAA
*
356021 AATCGCAATGCGA
1 AATCGCAACGCGA
356034 TTTTTGTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:356065 original size:19 final size:19
Alignment explanation
Indices: 356029--356073 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
356019 AAAATCGCAA
*
356029 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
356048 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
356067 TGCGATT
1 TGCGATT
356074 ATCTCGTGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:356709 original size:20 final size:20
Alignment explanation
Indices: 356624--356737 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
356614 CGCTATGTAA
* * *
356624 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
*
356644 ATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
356664 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
356685 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
356705 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
356725 ATCGCATTGCGAT
1 ATCGCATTGCGAT
356738 TTCCCAATTC
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 62 0.78
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:356722 original size:61 final size:61
Alignment explanation
Indices: 356624--356739 Score: 169
Period size: 61 Copynumber: 1.9 Consensus size: 61
356614 CGCTATGTAA
* * * *
356624 ATCGCGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
356685 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
356740 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:356749 original size:20 final size:20
Alignment explanation
Indices: 356726--356795 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
356716 ATAGTCAGTA
* **
356726 TCGCATTGCGATTTCCCAAT
1 TCGCATTGCGATTTACTTAT
* *
356746 TCGCGTTTCGA-TTACTTAT
1 TCGCATTGCGATTTACTTAT
*
356765 TCGCATTGTGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
356785 TCGCATTGCGA
1 TCGCATTGCGA
356796 ATTGGGAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
19 13 0.32
20 27 0.68
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Done.