Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008225.1 Hibiscus syriacus cultivar Beakdansim tig00110858_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: 1890193
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 10
Found at i:473853 original size:53 final size:53
Alignment explanation
Indices: 473791--473901 Score: 215
Period size: 53 Copynumber: 2.1 Consensus size: 53
473781 GGGGTGGTAG
473791 TATG-TGATCGTTTGGATTGGGAATTTACAAGAGTGTTAAAAAGAATCAAATT
1 TATGTTGATCGTTTGGATTGGGAATTTACAAGAGTGTTAAAAAGAATCAAATT
473843 TATGTTGATCGTTTGGATTGGGAATTTACAAGAGTGTTAAAAAGAATCAAATT
1 TATGTTGATCGTTTGGATTGGGAATTTACAAGAGTGTTAAAAAGAATCAAATT
473896 TATGTT
1 TATGTT
473902 ACTTGGACGT
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 4 0.07
53 54 0.93
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (53 bp):
TATGTTGATCGTTTGGATTGGGAATTTACAAGAGTGTTAAAAAGAATCAAATT
Found at i:475677 original size:12 final size:12
Alignment explanation
Indices: 475660--475684 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
475650 TCAGGATAAA
475660 AACCGGTTTTTT
1 AACCGGTTTTTT
475672 AACCGGTTTTTT
1 AACCGGTTTTTT
475684 A
1 A
475685 TTTGGTAAAA
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:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:477569 original size:30 final size:31
Alignment explanation
Indices: 477504--477566 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
477494 AAAAATATAA
* * * *
477504 TTTAAAAAAAAACTTAAAATTTTTGAAAATC
1 TTTATAAAAAAACTCAAAATCTTTAAAAATC
477535 TTTATAAAAAAACTCAAAA-CTTTAAAAA-C
1 TTTATAAAAAAACTCAAAATCTTTAAAAATC
477564 TTT
1 TTT
477567 TATTCCAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 4 0.14
30 7 0.25
31 17 0.61
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.35
Consensus pattern (31 bp):
TTTATAAAAAAACTCAAAATCTTTAAAAATC
Found at i:485679 original size:25 final size:23
Alignment explanation
Indices: 485642--485687 Score: 74
Period size: 25 Copynumber: 1.9 Consensus size: 23
485632 AATTTTATAA
485642 AATTTTATTCAAATTAATTACTT
1 AATTTTATTCAAATTAATTACTT
485665 AATTATTATTACAAATTAATTAC
1 AATT-TTATT-CAAATTAATTAC
485688 GATAACTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.19
24 5 0.24
25 12 0.57
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (23 bp):
AATTTTATTCAAATTAATTACTT
Found at i:486239 original size:9 final size:9
Alignment explanation
Indices: 486227--486260 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
486217 TAATATTTTG
486227 TATTTAATT
1 TATTTAATT
*
486236 TATTTAA-G
1 TATTTAATT
486244 TATTTAATT
1 TATTTAATT
486253 TATTTAAT
1 TATTTAAT
486261 ATTTTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:486266 original size:17 final size:17
Alignment explanation
Indices: 486226--486264 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
486216 TTAATATTTT
486226 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
486243 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
486260 -TATTT
1 GTATTT
486265 TACTTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:488533 original size:13 final size:13
Alignment explanation
Indices: 488492--488535 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
488482 TATTTAATAC
*
488492 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* * *
488505 TGTTTATTGGACT
1 TTTTTATTGTAAT
488518 TTTTTATTGTAAT
1 TTTTTATTGTAAT
488531 TTTTT
1 TTTTT
488536 TATTATTTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (13 bp):
TTTTTATTGTAAT
Found at i:488605 original size:33 final size:35
Alignment explanation
Indices: 488568--488641 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 35
488558 ACTTTAATTC
488568 GTTAATA-TGGTTGGA-TTTATTTTAATTTATTTT
1 GTTAATATTGGTTGGACTTTATTTTAATTTATTTT
* * *
488601 GTTAA-ATTTGTTGGACTTTTTTTTAATTTTTTTT
1 GTTAATATTGGTTGGACTTTATTTTAATTTATTTT
488635 GCTTAAT
1 G-TTAAT
488642 TTTGTTTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
32 1 0.03
33 12 0.35
34 17 0.50
35 4 0.12
ACGTcount: A:0.22, C:0.03, G:0.14, T:0.62
Consensus pattern (35 bp):
GTTAATATTGGTTGGACTTTATTTTAATTTATTTT
Found at i:488635 original size:34 final size:34
Alignment explanation
Indices: 488577--488647 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
488567 CGTTAATATG
488577 GTTGGATTTATTTTAATTTATTTTG-TTAAATTT
1 GTTGGATTTATTTTAATTTATTTTGCTTAAATTT
* * *
488610 GTTGGACTTTTTTTTAATTTTTTTTGCTTAATTTT
1 GTTGGA-TTTATTTTAATTTATTTTGCTTAAATTT
488645 GTT
1 GTT
488648 TAATACCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 6 0.18
34 17 0.52
35 10 0.30
ACGTcount: A:0.18, C:0.03, G:0.13, T:0.66
Consensus pattern (34 bp):
GTTGGATTTATTTTAATTTATTTTGCTTAAATTT
Found at i:492690 original size:18 final size:19
Alignment explanation
Indices: 492662--492698 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
492652 CATGTCATAT
*
492662 TTTTATTAATATTTTAATA
1 TTTTATTAATATTATAATA
492681 TTTT-TTAATATTATAATA
1 TTTTATTAATATTATAATA
492699 AAAAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTATTAATATTATAATA
Found at i:493746 original size:13 final size:13
Alignment explanation
Indices: 493728--493766 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
493718 TTAGTCAAGT
493728 TGAGTCAACTCAC
1 TGAGTCAACTCAC
* *
493741 TGAGTCAACCCAAT
1 TGAGTCAACTC-AC
493755 TGAGTCAACTCA
1 TGAGTCAACTCA
493767 AACAAAGTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.23
Consensus pattern (13 bp):
TGAGTCAACTCAC
Found at i:495244 original size:11 final size:11
Alignment explanation
Indices: 495228--495256 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
495218 AAATACTTTG
495228 TAAAATTGTTT
1 TAAAATTGTTT
495239 TAAAATTGTTT
1 TAAAATTGTTT
495250 TAAAATT
1 TAAAATT
495257 AAAACTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (11 bp):
TAAAATTGTTT
Found at i:505755 original size:12 final size:12
Alignment explanation
Indices: 505738--505770 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
505728 CAAAAAATTT
505738 CACTGTTCATGG
1 CACTGTTCATGG
505750 CACTGTTCATGG
1 CACTGTTCATGG
*
505762 TACTGTTCA
1 CACTGTTCA
505771 CATTACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.36
Consensus pattern (12 bp):
CACTGTTCATGG
Found at i:510203 original size:24 final size:24
Alignment explanation
Indices: 510149--510207 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
510139 TGAAATTTTT
*
510149 CATTGTTCATGGTACTGTTCACGA
1 CATTGTTCATAGTACTGTTCACGA
*
510173 CACTGTTCATAGTACTGTTCAC-A
1 CATTGTTCATAGTACTGTTCACGA
*
510196 GTATTGTTCATA
1 -CATTGTTCATA
510208 AATACATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.03
24 29 0.97
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (24 bp):
CATTGTTCATAGTACTGTTCACGA
Found at i:513326 original size:14 final size:15
Alignment explanation
Indices: 513273--513330 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
513263 TTGGTTTTCC
513273 GGAAAATGAATTACT
1 GGAAAATGAATTACT
*
513288 -GAAATTTGAATTACT
1 GGAAA-ATGAATTACT
**
513303 GGAATTTGAATT-CT
1 GGAAAATGAATTACT
513317 GGAAAATGAATTAC
1 GGAAAATGAATTAC
513331 ATTTTTGGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 16 0.44
15 17 0.47
16 3 0.08
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:513550 original size:21 final size:22
Alignment explanation
Indices: 513524--513565 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
513514 ATAAAACTTT
513524 TTTATTATTAAA-AATAATTTA
1 TTTATTATTAAATAATAATTTA
*
513545 TTTATTATTAAATAGTAATTT
1 TTTATTATTAAATAATAATTT
513566 TATAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTATTATTAAATAATAATTTA
Found at i:513594 original size:29 final size:33
Alignment explanation
Indices: 513554--513623 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
513544 ATTTATTATT
* *
513554 AAATAGTAA-TTTTATA-ATTTTA-T-TAATAA
1 AAATATTAATTTTTATATATTTTAGTGAAATAA
*
513583 AAATATTAATTTTTGTATATTTTAGTGAAATAA
1 AAATATTAATTTTTATATATTTTAGTGAAATAA
513616 AAATATTA
1 AAATATTA
513624 TAAATATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.24
30 6 0.18
31 6 0.18
32 1 0.03
33 13 0.38
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (33 bp):
AAATATTAATTTTTATATATTTTAGTGAAATAA
Found at i:513714 original size:23 final size:23
Alignment explanation
Indices: 513665--513727 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
513655 GTGTTATATT
**
513665 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
513688 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
513711 ATATTATTAAAATATAT
1 ATATT-TTAAAA-ATAT
513728 AAATAATATT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
23 23 0.74
24 5 0.16
25 3 0.10
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:513719 original size:11 final size:11
Alignment explanation
Indices: 513703--513740 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
513693 TTAAATATCT
513703 TTATTAAAATA
1 TTATTAAAATA
513714 TTATTAAAATA
1 TTATTAAAATA
*
513725 -TATAAATAATA
1 TTATTAA-AATA
513736 TTATT
1 TTATT
513741 CATTATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 5 0.22
11 15 0.65
12 3 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTATTAAAATA
Found at i:513755 original size:19 final size:20
Alignment explanation
Indices: 513703--513781 Score: 58
Period size: 20 Copynumber: 4.0 Consensus size: 20
513693 TTAAATATCT
513703 TTATTAAA-ATATTATTAAA
1 TTATTAAATATATTATTAAA
* *
513722 ATATATAAATAATATTATT-CA
1 TTAT-TAAAT-ATATTATTAAA
* ***
513743 TTATTAAATATATAATTTTT
1 TTATTAAATATATTATTAAA
513763 TTATT--ATATATTATTAAA
1 TTATTAAATATATTATTAAA
513781 T
1 T
513782 ATATATATAT
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
18 10 0.22
19 10 0.22
20 14 0.30
21 4 0.09
22 8 0.17
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (20 bp):
TTATTAAATATATTATTAAA
Found at i:513756 original size:30 final size:30
Alignment explanation
Indices: 513711--513889 Score: 122
Period size: 30 Copynumber: 5.9 Consensus size: 30
513701 CTTTATTAAA
*
513711 ATATTATTAAA-ATATATAAATAATATTAT
1 ATATTATTAAATATATATATATAATATTAT
* **
513740 -TCATTATTAAATATATA-ATTTTTTTATTAT
1 AT-ATTATTAAATATATATA-TATAATATTAT
513770 ATATTATTAAATATATATATATAATATCT-T
1 ATATTATTAAATATATATATATAATAT-TAT
* *
513800 ATATTATTATAATATA-AT-TGATTATTTTAT
1 ATATTATTA-AATATATATAT-ATAATATTAT
* * *
513830 ATAATATTAAAAATATAATATTATATTATTAT
1 ATATTATTAAATATAT-ATA-TATAATATTAT
* *
513862 AAATATTAATAAAT-TA-ATAAATAATATT
1 --ATATTATTAAATATATATATATAATATT
513890 TTGATGAAAA
Statistics
Matches: 116, Mismatches: 19, Indels: 29
0.71 0.12 0.18
Matches are distributed among these distances:
28 1 0.01
29 17 0.15
30 65 0.56
31 14 0.12
32 7 0.06
33 3 0.03
34 9 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
ATATTATTAAATATATATATATAATATTAT
Found at i:513786 original size:60 final size:58
Alignment explanation
Indices: 513702--513861 Score: 166
Period size: 60 Copynumber: 2.7 Consensus size: 58
513692 TTTAAATATC
*
513702 TTTATTAAAATATTATTAAAATATATAAATAATATTATTCATTATTAAATATATAATT-TT
1 TTTATT-ATATATTATTAAAATATATAAATAATATTATT-ATTATTAAA-ATATAATTATT
* *
513762 TTTATTATATATTATTAAATATATATATATAATATCT-TATATTATTATAATATAATTGATT
1 TTTATTATATATTATTAAA-ATATATAAATAATAT-TAT-TATTATTAAAATATAATT-ATT
* * *
513823 ATT-TTATATAATATTAAAA-ATATAATATTATATTATTAT
1 TTTATTATATATTATTAAAATATATAA-ATAATATTATTAT
513862 AAATATTAAT
Statistics
Matches: 86, Mismatches: 7, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
58 9 0.10
59 28 0.33
60 43 0.50
61 6 0.07
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (58 bp):
TTTATTATATATTATTAAAATATATAAATAATATTATTATTATTAAAATATAATTATT
Found at i:513854 original size:22 final size:23
Alignment explanation
Indices: 513829--513872 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
513819 GATTATTTTA
513829 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
513851 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
513873 AATTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:513880 original size:31 final size:31
Alignment explanation
Indices: 513744--513880 Score: 101
Period size: 31 Copynumber: 4.5 Consensus size: 31
513734 TATTATTCAT
* * *
513744 TATTAAATATATAAT-TT-TTTTATTATATAT
1 TATTAAAAATATAATATTATATT-TTATATAA
* * *
513774 TATTAAATATATATATATAATATCTTATAT--
1 TATTAAAAATATA-ATATTATATTTTATATAA
* *
513804 TATT-ATAATATAAT-TGATTATTTTATATAA
1 TATTAAAAATATAATATTA-TATTTTATATAA
513834 TATTAAAAATATAATATTATATTATTATA-AA
1 TATTAAAAATATAATATTATATT-TTATATAA
513865 TATTAATAAAT-TAATA
1 TATTAA-AAATATAATA
513881 AATAATATTT
Statistics
Matches: 88, Mismatches: 9, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
27 2 0.02
28 11 0.12
29 6 0.07
30 21 0.24
31 28 0.32
32 18 0.20
33 2 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
TATTAAAAATATAATATTATATTTTATATAA
Found at i:514151 original size:42 final size:43
Alignment explanation
Indices: 514069--514178 Score: 195
Period size: 42 Copynumber: 2.6 Consensus size: 43
514059 TATGTTCAGG
* *
514069 AAAACCAATTACGTGAAACAAACACTGGAAAACATTTTTCCGA
1 AAAACGAATTACGTGAAACAAACACGGGAAAACATTTTTCCGA
514112 AAAACGAATTACGTGAAACAAACACGGGAAAACA-TTTTCCGA
1 AAAACGAATTACGTGAAACAAACACGGGAAAACATTTTTCCGA
514154 AAAACGAATTACGTGAAACAAACAC
1 AAAACGAATTACGTGAAACAAACAC
514179 AAGAATTCGG
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
42 33 0.51
43 32 0.49
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.17
Consensus pattern (43 bp):
AAAACGAATTACGTGAAACAAACACGGGAAAACATTTTTCCGA
Found at i:520388 original size:42 final size:42
Alignment explanation
Indices: 520342--520426 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
520332 TAAATCATAC
520342 TTATAATCGGTGATGAATGATGATTAAATTTGTATCAGATAG
1 TTATAATCGGTGATGAATGATGATTAAATTTGTATCAGATAG
520384 TTATAATCGGTGATGAATGATGATTAAATTTGTATCAGATAG
1 TTATAATCGGTGATGAATGATGATTAAATTTGTATCAGATAG
520426 T
1 T
520427 AATGGATGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (42 bp):
TTATAATCGGTGATGAATGATGATTAAATTTGTATCAGATAG
Found at i:521086 original size:20 final size:21
Alignment explanation
Indices: 521061--521112 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
521051 GACCAACAAA
*
521061 TTCGCAACGCGA-ACTCCAAT
1 TTCGCAACGCCAGACTCCAAT
**
521081 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCCAGACTCCAAT
521101 TTCGCAACGCCA
1 TTCGCAACGCCA
521113 ATTTGTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.27, C:0.37, G:0.13, T:0.23
Consensus pattern (21 bp):
TTCGCAACGCCAGACTCCAAT
Found at i:521125 original size:20 final size:20
Alignment explanation
Indices: 521102--521189 Score: 72
Period size: 20 Copynumber: 4.4 Consensus size: 20
521092 GTTTCCAATT
* *
521102 TCGCAACGCCAATTTGTAAA
1 TCGCAACACCAATCTGTAAA
* **
521122 TCGCAA-AACAA-AAGTCAAA
1 TCGCAACACCAATCTGT-AAA
* *
521141 TTCGCAACGCGAATCTGTAAA
1 -TCGCAACACCAATCTGTAAA
*
521162 TCGCAACACGAATCTGTAAA
1 TCGCAACACCAATCTGTAAA
521182 TCGCAACA
1 TCGCAACA
521190 TAGAAGTCAA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
18 2 0.04
19 6 0.11
20 39 0.72
21 5 0.09
22 2 0.04
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.19
Consensus pattern (20 bp):
TCGCAACACCAATCTGTAAA
Found at i:521205 original size:20 final size:20
Alignment explanation
Indices: 521182--521269 Score: 88
Period size: 20 Copynumber: 4.3 Consensus size: 20
521172 AATCTGTAAA
* *
521182 TCGCAACATAGAAGTCAAAG
1 TCGCAACACAGAAGTCAAAT
*
521202 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
521222 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* * *
521242 TCGCAACGCGGAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
521263 TCGCAAC
1 TCGCAAC
521270 TAGATTTTCG
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.04
20 40 0.71
21 14 0.25
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:521226 original size:60 final size:61
Alignment explanation
Indices: 521101--521230 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 61
521091 AGTTTCCAAT
* * * *
521101 TTCGCAACGCCAATTTGTAAATCGCAAAACAAAAGTCAAATTCGCAACGCGAATCTGTAAA
1 TTCGCAACACCAATCTGTAAATCGCAAAACAAAAGTCAAAGTCGCAACGCGAATCAGTAAA
* * * *
521162 -TCGCAACACGAATCTGTAAATCGCAACATAGAAGTCAAAGTCGCAACGCG-AT-AGTCAAA
1 TTCGCAACACCAATCTGTAAATCGCAAAACAAAAGTCAAAGTCGCAACGCGAATCAGT-AAA
521221 TTCGCAACAC
1 TTCGCAACAC
521231 AAAAGTCAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
58 2 0.03
59 5 0.08
60 52 0.88
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (61 bp):
TTCGCAACACCAATCTGTAAATCGCAAAACAAAAGTCAAAGTCGCAACGCGAATCAGTAAA
Found at i:521249 original size:40 final size:41
Alignment explanation
Indices: 521182--521269 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 41
521172 AATCTGTAAA
* *
521182 TCGCAACATAGAAGTCAAAGTCGCAACGC-G-ATAGTCAAAT
1 TCGCAACACAAAAGTCAAAGTCGCAACGCGGAAT-GTCAAAT
* *
521222 TCGCAACACAAAAGTCAAATTCGCAACGCGGAATTTCAAAT
1 TCGCAACACAAAAGTCAAAGTCGCAACGCGGAATGTCAAAT
521263 TCGCAAC
1 TCGCAAC
521270 TAGATTTTCG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
40 26 0.62
41 14 0.33
42 2 0.05
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (41 bp):
TCGCAACACAAAAGTCAAAGTCGCAACGCGGAATGTCAAAT
Found at i:521262 original size:21 final size:19
Alignment explanation
Indices: 521216--521308 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 19
521206 AACGCGATAG
* **
521216 TCAAATTCGCAACACAAAAG
1 TCAAATTCGCAAC-CGAATT
521236 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAAC-C-GAATT
* *
521257 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAAC-CGAATT
*
521277 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-CGAATT
*
521297 T-AATTTCGCAAC
1 TCAAATTCGCAAC
521309 TGGTTTTAGC
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
19 9 0.15
20 35 0.59
21 15 0.25
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.26
Consensus pattern (19 bp):
TCAAATTCGCAACCGAATT
Found at i:521484 original size:14 final size:15
Alignment explanation
Indices: 521465--521502 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
521455 TCCATATCTC
521465 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
521479 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
521495 TAATTTTT
1 TAATTTTT
521503 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:522118 original size:12 final size:12
Alignment explanation
Indices: 522097--522130 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
522087 ACCACATTTC
*
522097 CAATACCAAACA
1 CAATATCAAACA
522109 CAATATCAAACA
1 CAATATCAAACA
*
522121 CAATCTCAAA
1 CAATATCAAA
522131 ACCTATAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:522283 original size:24 final size:24
Alignment explanation
Indices: 522256--522309 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
522246 GTATTCGAAA
522256 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
522280 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
522304 TTTGAT
1 TTTGAT
522310 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:524554 original size:12 final size:12
Alignment explanation
Indices: 524537--524583 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
524527 AGCAAAAGGA
*
524537 AATCAAAATCGC
1 AATCAAAATCAC
*
524549 AATCAAAATCAA
1 AATCAAAATCAC
*
524561 AATCAAAATCCC
1 AATCAAAATCAC
*
524573 AATCACAATCA
1 AATCAAAATCA
524584 GCTTCACCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.55, C:0.26, G:0.02, T:0.17
Consensus pattern (12 bp):
AATCAAAATCAC
Found at i:524558 original size:6 final size:6
Alignment explanation
Indices: 524536--524570 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
524526 AAGCAAAAGG
* *
524536 AAATCA AAATCG CAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
524571 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:525149 original size:64 final size:65
Alignment explanation
Indices: 525013--525152 Score: 255
Period size: 65 Copynumber: 2.2 Consensus size: 65
525003 TTAAAACAAT
525013 AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTAAAC
1 AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTAAAC
* *
525078 AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATC-AATTAAAC
1 AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTAAAC
525142 AAATCAACTTT
1 AAATCAACTTT
525153 CAATGTAAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 19 0.26
65 54 0.74
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.31
Consensus pattern (65 bp):
AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTAAAC
Found at i:526555 original size:21 final size:21
Alignment explanation
Indices: 526530--526605 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
526520 GCGGGTGAGA
*
526530 CCTCTTAAACGATGACAGGGG
1 CCTCTTGAACGATGACAGGGG
* *
526551 GCTCTTGAAC-AGTGAGAGGGG
1 CCTCTTGAACGA-TGACAGGGG
* *
526572 CCTCTTCG-ATGATGATAGGGG
1 CCTCTT-GAACGATGACAGGGG
526593 CCTCTTGAACGAT
1 CCTCTTGAACGAT
526606 AGGAGGCGTC
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
20 2 0.05
21 40 0.91
22 2 0.05
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGGGG
Found at i:527959 original size:56 final size:57
Alignment explanation
Indices: 527897--528003 Score: 137
Period size: 57 Copynumber: 1.9 Consensus size: 57
527887 AGTGCACCGA
* *
527897 TGCATCAAGTGTAATCGATG-TTTCA-AAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCAAATGCAATCGATGTTTTCATAAA-AGCCAGAGTGCATCGATGCATGGCTGG
* ** *
527953 TGCATCAAATGCATTCGATGTTTTCATAAAATTCTGAGTGCATCGATGCAT
1 TGCATCAAATGCAATCGATGTTTTCATAAAAGCCAGAGTGCATCGATGCAT
528004 AGTATGTGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
56 17 0.40
57 23 0.53
58 3 0.07
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (57 bp):
TGCATCAAATGCAATCGATGTTTTCATAAAAGCCAGAGTGCATCGATGCATGGCTGG
Found at i:528475 original size:20 final size:21
Alignment explanation
Indices: 528426--528473 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
528416 TTTGAAATTA
528426 CTCCCCCTTACTTTAACACTT
1 CTCCCCCTTACTTTAACACTT
528447 CTCCCCCTTACTTTAACACTT
1 CTCCCCCTTACTTTAACACTT
528468 CTCCCC
1 CTCCCC
528474 TTTTAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.35
Consensus pattern (21 bp):
CTCCCCCTTACTTTAACACTT
Found at i:540121 original size:28 final size:28
Alignment explanation
Indices: 540089--540154 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
540079 TACAGATCAT
*
540089 AAGAGCTTGAAGTATCTGATGACTCAAA
1 AAGAGCTTAAAGTATCTGATGACTCAAA
540117 AAGAGCTTAAAGTATCTGATGACTCAAA
1 AAGAGCTTAAAGTATCTGATGACTCAAA
540145 AAGAGCTTAA
1 AAGAGCTTAA
540155 TCTGAGACAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (28 bp):
AAGAGCTTAAAGTATCTGATGACTCAAA
Found at i:547207 original size:23 final size:23
Alignment explanation
Indices: 547178--547238 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
547168 CAGCTCGTAT
*
547178 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACATAG
* * * *
547201 AATTGCACCGTAGTGCCGCATGG
1 AAATGCACCGAAGTGCCACATAG
547224 AAATGCACCGAAGTG
1 AAATGCACCGAAGTG
547239 TCATATAAGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.28, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:549629 original size:25 final size:24
Alignment explanation
Indices: 549585--549635 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
549575 CTATTACCTC
549585 ATTTCTTAATATTTTCTT-CCTTT
1 ATTTCTTAATATTTTCTTCCCTTT
*
549608 ATTTCTTCAACTATTTTTTTCCCTTT
1 ATTTCTT-AA-TATTTTCTTCCCTTT
549634 AT
1 AT
549636 ACATTTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 7 0.29
24 2 0.08
25 8 0.33
26 7 0.29
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTTCTTAATATTTTCTTCCCTTT
Found at i:552173 original size:23 final size:23
Alignment explanation
Indices: 552147--552215 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
552137 CACCACAGCT
*
552147 CGTATAAATACACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* * *
552170 CGTAGAATTACACCGTAGTGCCG
1 CGTAGAAATACACCGAAGTGCCA
*
552193 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
552216 TATAAGGTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.17
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:553652 original size:19 final size:19
Alignment explanation
Indices: 553628--553678 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
553618 TCCCTTGAAG
553628 TGCATCGATGCATTCCTTA
1 TGCATCGATGCATTCCTTA
**
553647 TGCATCGATAAATTCCTTA
1 TGCATCGATGCATTCCTTA
553666 TGCATCGATGCAT
1 TGCATCGATGCAT
553679 AAATTGCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (19 bp):
TGCATCGATGCATTCCTTA
Found at i:555607 original size:22 final size:22
Alignment explanation
Indices: 555580--555638 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
555570 ATATGGAGAT
555580 AGACGGATTTCGTCGGAGATGG
1 AGACGGATTTCGTCGGAGATGG
*
555602 AGACGGATTTCGCCGGAGATGG
1 AGACGGATTTCGTCGGAGATGG
* * *
555624 GGATGGATGTCGTCG
1 AGACGGATTTCGTCG
555639 TAGAGAGTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.20, C:0.15, G:0.42, T:0.22
Consensus pattern (22 bp):
AGACGGATTTCGTCGGAGATGG
Found at i:555776 original size:20 final size:20
Alignment explanation
Indices: 555751--555854 Score: 127
Period size: 20 Copynumber: 5.2 Consensus size: 20
555741 TTTCGCGTTA
555751 CGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTTTGTGTTG
* **
555771 CGAATTTGAAATTCAGTGTTG
1 CGAATTTG-ACTTTTGTGTTG
* * *
555792 CGAATTTGACTATCGCGTTG
1 CGAATTTGACTTTTGTGTTG
555812 CGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTTTGTGTTG
* *
555832 CGGATTTGACTTCTGTGTTG
1 CGAATTTGACTTTTGTGTTG
555852 CGA
1 CGA
555855 TTTACAAATT
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
20 52 0.75
21 17 0.25
ACGTcount: A:0.18, C:0.13, G:0.26, T:0.42
Consensus pattern (20 bp):
CGAATTTGACTTTTGTGTTG
Found at i:555867 original size:40 final size:40
Alignment explanation
Indices: 555754--555917 Score: 137
Period size: 40 Copynumber: 4.1 Consensus size: 40
555744 CGCGTTACGA
* * *
555754 ATTTGACTTTTGTGTTGCGAATTT-GAAATTCAGTGTTGCG
1 ATTTGACTTCTGTGTTGCGAATTTACAAATT-TGTGTTGCG
* *
555794 AATTTGACTATC-GCGTTGCGAATTTGAC--TTTTGTGTTGCGG
1 -ATTTGACT-TCTGTGTTGCGAATTT-ACAAATTTGTGTTGC-G
555835 ATTTGACTTCTGTGTTGCG-ATTTACAAATTTGTGTTGCG
1 ATTTGACTTCTGTGTTGCGAATTTACAAATTTGTGTTGCG
* *
555874 ATTT-ACAAATT-TGTGTTGCG-ATTTACAAATTCGCGTTGCG
1 ATTTGAC---TTCTGTGTTGCGAATTTACAAATTTGTGTTGCG
555914 ATTT
1 ATTT
555918 ACATATTCGC
Statistics
Matches: 104, Mismatches: 9, Indels: 21
0.78 0.07 0.16
Matches are distributed among these distances:
38 4 0.04
39 11 0.11
40 63 0.61
41 25 0.24
42 1 0.01
ACGTcount: A:0.20, C:0.13, G:0.23, T:0.44
Consensus pattern (40 bp):
ATTTGACTTCTGTGTTGCGAATTTACAAATTTGTGTTGCG
Found at i:555868 original size:20 final size:20
Alignment explanation
Indices: 555845--555920 Score: 134
Period size: 20 Copynumber: 3.8 Consensus size: 20
555835 ATTTGACTTC
555845 TGTGTTGCGATTTACAAATT
1 TGTGTTGCGATTTACAAATT
555865 TGTGTTGCGATTTACAAATT
1 TGTGTTGCGATTTACAAATT
555885 TGTGTTGCGATTTACAAATT
1 TGTGTTGCGATTTACAAATT
* *
555905 CGCGTTGCGATTTACA
1 TGTGTTGCGATTTACA
555921 TATTCGCATT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (20 bp):
TGTGTTGCGATTTACAAATT
Found at i:555925 original size:20 final size:20
Alignment explanation
Indices: 555848--555935 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
555838 TGACTTCTGT
* *
555848 GTTGCGATTTACAAATTTGT
1 GTTGCGATTTACAAATTCGC
* *
555868 GTTGCGATTTACAAATTTGT
1 GTTGCGATTTACAAATTCGC
555888 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
555908 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
*
555928 ATTGCGAT
1 GTTGCGAT
555936 ATTGAAAACT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:559473 original size:3 final size:3
Alignment explanation
Indices: 559465--559507 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
559455 GTTTGTGGGT
559465 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
559508 CTTTGATGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:563728 original size:22 final size:22
Alignment explanation
Indices: 563703--563746 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
563693 AAATCATGCT
*
563703 CCATATTATTCA-TCTTTCAAGA
1 CCATACTATTCACT-TTTCAAGA
*
563725 CCATACTGTTCACTTTTCAAGA
1 CCATACTATTCACTTTTCAAGA
563747 TGTCTACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (22 bp):
CCATACTATTCACTTTTCAAGA
Found at i:565587 original size:56 final size:55
Alignment explanation
Indices: 565352--565588 Score: 276
Period size: 56 Copynumber: 4.2 Consensus size: 55
565342 TAGATAATTT
* * * *
565352 GATTTCAGGCCCCCTATTTTTATACTTCTTAATGATAATAACTAATAGATATACTC
1 GATTTC-GGACCCCTATTTTTATACTTCTTAATGACAACAACTGATAGATATACTC
* **
565408 GATTTCGGACCTCTTATTTTTATACTTCTTAATGGTAACAACTGATAGATATACTC
1 GATTTCGGACC-CCTATTTTTATACTTCTTAATGACAACAACTGATAGATATACTC
** * * * *
565464 GATTTCGGAACTTCTATTTTTATGCTTCTTAATGACAACAATTGATAAATACACTC
1 GATTTCGG-ACCCCTATTTTTATACTTCTTAATGACAACAACTGATAGATATACTC
* * * *
565520 TATTTCAAGACCCCTATTTTTATGCTTATTAATGACAACAACTGATAGATATACTC
1 GATTTC-GGACCCCTATTTTTATACTTCTTAATGACAACAACTGATAGATATACTC
565576 GATTTCGAGACCC
1 GATTTCG-GACCC
565589 TTTCGAAACC
Statistics
Matches: 153, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
55 4 0.03
56 146 0.95
57 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.38
Consensus pattern (55 bp):
GATTTCGGACCCCTATTTTTATACTTCTTAATGACAACAACTGATAGATATACTC
Found at i:571207 original size:13 final size:13
Alignment explanation
Indices: 571186--571222 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
571176 ACTTTGTAAA
571186 TTGTGTCTCAAAG
1 TTGTGTCTCAAAG
*
571199 TTGTTTCTCAAAG
1 TTGTGTCTCAAAG
571212 TTGTGTCTCAA
1 TTGTGTCTCAA
571223 CTAACCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (13 bp):
TTGTGTCTCAAAG
Found at i:572467 original size:13 final size:13
Alignment explanation
Indices: 572449--572474 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
572439 TCATCCTATA
572449 TTTGACCATATTT
1 TTTGACCATATTT
572462 TTTGACCATATTT
1 TTTGACCATATTT
572475 GATCATATTC
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:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
TTTGACCATATTT
Found at i:573237 original size:51 final size:50
Alignment explanation
Indices: 573126--573237 Score: 125
Period size: 51 Copynumber: 2.2 Consensus size: 50
573116 AATGAGATTA
* * *
573126 AAACCCGAAATAGAACCAATTTCTATTTAACGACGAGAATTTAATAAATT
1 AAACCCGAAATAGAACCAACTTCTATTGAACGACGAAAATTTAATAAATT
* * * * * *
573176 AATTCTCGAAATAGAACTAACTTCTGTTGAACGATGAAAATTTAGTAAATT
1 AA-ACCCGAAATAGAACCAACTTCTATTGAACGACGAAAATTTAATAAATT
573227 GAAACCCGAAA
1 -AAACCCGAAA
573238 CAAAAGTACA
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
50 2 0.04
51 45 0.92
52 2 0.04
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (50 bp):
AAACCCGAAATAGAACCAACTTCTATTGAACGACGAAAATTTAATAAATT
Found at i:576322 original size:22 final size:22
Alignment explanation
Indices: 576297--576343 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
576287 ACTAAGTGAC
576297 CATATGAAAATGTTACATGAAA
1 CATATGAAAATGTTACATGAAA
576319 CATATGAAAATGTTACATGAAA
1 CATATGAAAATGTTACATGAAA
576341 CAT
1 CAT
576344 GTGAGATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.28
Consensus pattern (22 bp):
CATATGAAAATGTTACATGAAA
Found at i:576575 original size:44 final size:44
Alignment explanation
Indices: 576508--576594 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
576498 GTTGAGGGTT
* ** * * *
576508 CTATGTGGTCCTTCGGGATAATTATGTGGCACTTCGTTGCAAAC
1 CTATGTGGTCCTGCGAAACAATTATGTGACACTTCGGTGCAAAC
576552 CTATGTGGTCCTGCGAAACAATTATGTGACACTTCGGTGCAAA
1 CTATGTGGTCCTGCGAAACAATTATGTGACACTTCGGTGCAAA
576595 TTATGAGCTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (44 bp):
CTATGTGGTCCTGCGAAACAATTATGTGACACTTCGGTGCAAAC
Found at i:577636 original size:35 final size:35
Alignment explanation
Indices: 577579--577647 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
577569 ATTAAAAAAT
*
577579 AAATCTATTCATCAAGTGACATAACTTATTATAAC
1 AAATCTATTCATCAAGTAACATAACTTATTATAAC
577614 AAATCTATTCA-CTAAGTAACATAACTTATTATAA
1 AAATCTATTCATC-AAGTAACATAACTTATTATAA
577648 ATAATATCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 1 0.03
35 31 0.97
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (35 bp):
AAATCTATTCATCAAGTAACATAACTTATTATAAC
Found at i:586036 original size:3 final size:3
Alignment explanation
Indices: 586028--586073 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
586018 TGAAGAGTGT
586028 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
586074 GTAGGAGCAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:590583 original size:29 final size:29
Alignment explanation
Indices: 590542--590598 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
590532 TATATCATGG
590542 TATATATGGTATTTTGGATTAGAAATAGA
1 TATATATGGTATTTTGGATTAGAAATAGA
590571 TATATATGGTATTTTGGATTAGAAATAG
1 TATATATGGTATTTTGGATTAGAAATAG
590599 GTGTAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (29 bp):
TATATATGGTATTTTGGATTAGAAATAGA
Found at i:595920 original size:15 final size:15
Alignment explanation
Indices: 595900--595937 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
595890 TTTGTATTTT
595900 TAATTTGCCATATAC
1 TAATTTGCCATATAC
595915 TAATTTGCCATATAC
1 TAATTTGCCATATAC
595930 TAATTTGC
1 TAATTTGC
595938 TTTGTTGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (15 bp):
TAATTTGCCATATAC
Found at i:597298 original size:23 final size:23
Alignment explanation
Indices: 597272--597319 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
597262 AATAACATAT
597272 TAGGTAGAACTTATATAATGTAA
1 TAGGTAGAACTTATATAATGTAA
**
597295 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGAACTTATATAATGTAA
597318 TA
1 TA
597320 AGCATTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (23 bp):
TAGGTAGAACTTATATAATGTAA
Found at i:597381 original size:87 final size:87
Alignment explanation
Indices: 597235--597394 Score: 293
Period size: 87 Copynumber: 1.8 Consensus size: 87
597225 AATGTTATAT
597235 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGAACTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGAACTTATATAATGTAATAGGT
597300 AGCGCTTATATAATGTAATAAG
66 AGCGCTTATATAATGTAATAAG
**
597322 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCTCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGAACTTATATAATGTAATAGGT
*
597387 ATCGCTTA
66 AGCGCTTA
597395 CATTGACCTA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGAACTTATATAATGTAATAGGT
AGCGCTTATATAATGTAATAAG
Found at i:605164 original size:201 final size:201
Alignment explanation
Indices: 604819--605355 Score: 1013
Period size: 201 Copynumber: 2.7 Consensus size: 201
604809 TTTAAATTAA
*
604819 TATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGTAT
1 TATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTAT
604884 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTGGG
66 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTGGG
604949 ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTGTGGAC
131 ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTGTGGAC
605014 CAAAAG
196 CAAAAG
*
605020 TATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTC-TACAAATCGGTA
1 TATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATA-AAACCGGTA
*
605084 TATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTAG
65 TATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTGG
605149 GATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTGTGGA
130 GATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTGTGGA
605214 CCAAAAG
195 CCAAAAG
*
605221 TATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTAT
1 TATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTAT
*
605286 ATTTATACCGGTTATATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTGGG
66 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTGGG
605351 ATCGA
131 ATCGA
605356 TAAATTTTAC
Statistics
Matches: 327, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
200 2 0.01
201 323 0.99
202 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (201 bp):
TATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTAT
ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTGGG
ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTGTGGAC
CAAAAG
Found at i:607513 original size:21 final size:21
Alignment explanation
Indices: 607488--607531 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
607478 CCTCTTATGC
607488 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
607509 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
607530 CT
1 CT
607532 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:607632 original size:15 final size:15
Alignment explanation
Indices: 607614--607646 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
607604 ACACTGTTTT
*
607614 CCCTTACCGTCATCC
1 CCCTCACCGTCATCC
607629 CCCTCACCGTCATCC
1 CCCTCACCGTCATCC
607644 CCC
1 CCC
607647 AATACAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.61, G:0.06, T:0.21
Consensus pattern (15 bp):
CCCTCACCGTCATCC
Found at i:607962 original size:22 final size:24
Alignment explanation
Indices: 607934--607984 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
607924 AACCTGCATT
*
607934 TATAATAA-AAT-TTATAATTTTA
1 TATAATAATAATACTATAATTTTA
*
607956 TATAATAATTATACTATAATTTTA
1 TATAATAATAATACTATAATTTTA
607980 TATAA
1 TATAA
607985 AAACACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.32
23 2 0.08
24 15 0.60
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TATAATAATAATACTATAATTTTA
Found at i:609762 original size:20 final size:19
Alignment explanation
Indices: 609717--609762 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
609707 TCGATAGCGC
*
609717 TTTACCGATTTTATCATTT
1 TTTACCGACTTTATCATTT
*
609736 TGATACCGACTTTATCATATT
1 T-TTACCGACTTTATCAT-TT
609757 TTTACC
1 TTTACC
609763 TGTTATATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.50
Consensus pattern (19 bp):
TTTACCGACTTTATCATTT
Found at i:614433 original size:21 final size:21
Alignment explanation
Indices: 614407--614450 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
614397 AAGACAATCA
614407 AGAGTCGAAAAGAAACTTGAG
1 AGAGTCGAAAAGAAACTTGAG
* * *
614428 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAAAGAAACTTGAG
614449 AG
1 AG
614451 GCATAAGGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.30, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAAAGAAACTTGAG
Found at i:614521 original size:33 final size:33
Alignment explanation
Indices: 614484--614549 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
614474 AAATAGATGG
*
614484 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
614517 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
614550 TCTTAAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:617194 original size:2 final size:2
Alignment explanation
Indices: 617187--617227 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
617177 TATATTCATC
617187 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
617228 CCACGCATAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:617578 original size:29 final size:30
Alignment explanation
Indices: 617536--617632 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
617526 CCCGAAGGAC
*
617536 CTATCCAGAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGTAA
* *
617565 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGTAA
* * * *
617595 CTGTCCATAGGTCCCAAAGAACCTAGGTAAA
1 CTATCCAGAGGTCACAAAGAACCTCGGT-AA
617626 CTATCCA
1 CTATCCA
617633 TATGTTCCTT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 18 0.32
30 30 0.54
31 8 0.14
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.18
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGTAA
Found at i:617647 original size:31 final size:31
Alignment explanation
Indices: 617593--617720 Score: 114
Period size: 31 Copynumber: 4.1 Consensus size: 31
617583 GAACCTCGGC
* * * * *
617593 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTATCCATATGTTCCATAGAACATAGGTA
*
617624 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTTCCATAGAACATAGGTA
* * * * * *
617655 TATTGTTCATATGTCTCGAAAG-ACATAGGTAA
1 AACTATCCATATGT-TCCATAGAACATAGGT-A
*
617687 AACTATCCATATGTTCCGTAGAACATAGGTA
1 AACTATCCATATGTTCCATAGAACATAGGTA
617718 AAC
1 AAC
617721 CCTCGACTCT
Statistics
Matches: 74, Mismatches: 20, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
31 51 0.69
32 23 0.31
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (31 bp):
AACTATCCATATGTTCCATAGAACATAGGTA
Found at i:621449 original size:31 final size:31
Alignment explanation
Indices: 621395--621522 Score: 123
Period size: 31 Copynumber: 4.1 Consensus size: 31
621385 GAACCTCGAG
* * * *
621395 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
* *
621426 AACTGTCCATATATTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
* * * *
621457 TACTGTTCATATGTCTCGAAAG-ACATAGGTAA
1 AACTGTCCATATGT-TCCATAGAACATAGGT-A
* *
621489 AATTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
621520 AAC
1 AAC
621523 CCTCGACTCT
Statistics
Matches: 75, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
31 51 0.68
32 24 0.32
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGTTCCATAGAACATAGGTA
Found at i:623676 original size:201 final size:201
Alignment explanation
Indices: 623081--623755 Score: 1163
Period size: 201 Copynumber: 3.4 Consensus size: 201
623071 GGATGTTACA
623081 ATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTG
1 ATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTG
623146 TCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCA
66 TCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCA
*
623211 AAAAGTGTCGATCCCATAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTA
131 AAAAGTGTCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTA
*
623276 ATCGGT
196 ACCGGT
* *
623282 ATAAATATACCAGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTGTTTAATTTTGTG
1 ATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTG
*
623347 TCGATAC-TTTGGTCCACAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCA
66 TCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCA
623411 AAAAGTGTCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTA
131 AAAAGTGTCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTA
623476 ACCGGT
196 ACCGGT
* *
623482 ATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTAATTTTGTG
1 ATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTG
* * * *
623547 TCGATACTTTTGGTTCAGAATTGATGTCAAAAAGGGTGAATGCATAAAGTGTCGATACATTTTCA
66 TCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCA
* *
623612 AAACGTGTTGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTA
131 AAAAGTGTCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTA
**
623677 ACTAGT
196 ACCGGT
** * * *
623683 ATAAATATACATGTTTTATGAGAGAATAGGTCTACAACATGTATCGACATTTTTTTAATGTTGTG
1 ATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTG
623748 TCGATACT
66 TCGATACT
623756 AATTTAAATA
Statistics
Matches: 452, Mismatches: 21, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
200 195 0.43
201 257 0.57
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (201 bp):
ATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTG
TCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCA
AAAAGTGTCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTA
ACCGGT
Found at i:625234 original size:18 final size:18
Alignment explanation
Indices: 625207--625252 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
625197 CAAGCGGTCA
*
625207 ATGAATATGAAGATGACG
1 ATGAAGATGAAGATGACG
* *
625225 ATGAAGATGACGATGATG
1 ATGAAGATGAAGATGACG
*
625243 ATGATGATGA
1 ATGAAGATGA
625253 TCCAAACAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.30, T:0.24
Consensus pattern (18 bp):
ATGAAGATGAAGATGACG
Found at i:625253 original size:12 final size:12
Alignment explanation
Indices: 625213--625252 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
625203 GTCAATGAAT
625213 ATGAAGATGACG
1 ATGAAGATGACG
625225 ATGAAGATGACG
1 ATGAAGATGACG
* *
625237 ATGATGATGATG
1 ATGAAGATGACG
625249 ATGA
1 ATGA
625253 TCCAAACAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.33, T:0.23
Consensus pattern (12 bp):
ATGAAGATGACG
Found at i:629206 original size:23 final size:23
Alignment explanation
Indices: 629177--629224 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
629167 AAATAGGTCA
* *
629177 ATATAAGCGCTACCTATTATATT
1 ATATAAGAGCTACCTAATATATT
* *
629200 ATATAAGAGTTACCTAATATGTT
1 ATATAAGAGCTACCTAATATATT
629223 AT
1 AT
629225 TGTACTTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (23 bp):
ATATAAGAGCTACCTAATATATT
Found at i:629282 original size:87 final size:86
Alignment explanation
Indices: 629177--629350 Score: 276
Period size: 87 Copynumber: 2.0 Consensus size: 86
629167 AAATAGGTCA
* * * *
629177 ATATAAGCGCTACCTATTATATTATATAAGAGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGATACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTAATAATATTT
*
629242 CCGGTTAAATGACTATTACATT
66 CCGGTTAAATGA-TATAACATT
* *
629264 ATATAAGCGATATCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
1 ATATAAGCGATACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTAATAATATTT
629329 CCGGTTAAATGATATAACATT
66 CCGGTTAAATGATATAACATT
629350 A
1 A
629351 CCGGTCAAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
86 9 0.11
87 71 0.89
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (86 bp):
ATATAAGCGATACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTAATAATATTT
CCGGTTAAATGATATAACATT
Found at i:629311 original size:23 final size:23
Alignment explanation
Indices: 629258--629305 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
629248 AAATGACTAT
* *
629258 TACATTATATAAGCGATATCTAT
1 TACATTATATAAGCGATACCTAA
*
629281 TACATTATATAAGCGCTACCTAA
1 TACATTATATAAGCGATACCTAA
629304 TA
1 TA
629306 TGTTATTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (23 bp):
TACATTATATAAGCGATACCTAA
Found at i:629445 original size:4 final size:4
Alignment explanation
Indices: 629438--629464 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
629428 CTTTCGTCAA
629438 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
629465 ACATCCCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:632849 original size:31 final size:30
Alignment explanation
Indices: 632782--632858 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
632772 TTAATTGCTT
*
632782 AGTGATCAAAATATAACAAGAAATAACATA
1 AGTGATCAAAATTTAACAAGAAATAACATA
* * *
632812 ACTGATCAAAATTTAATAA-ATCAATAATATA
1 AGTGATCAAAATTTAACAAGA--AATAACATA
*
632843 AGTGATCAAAACTTAA
1 AGTGATCAAAATTTAA
632859 GTTTTTAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 1 0.03
30 16 0.41
31 22 0.56
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (30 bp):
AGTGATCAAAATTTAACAAGAAATAACATA
Found at i:635234 original size:21 final size:21
Alignment explanation
Indices: 635203--635274 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
635193 AGTTGATCTT
635203 ATTATTAAATAATTTTTTTATA
1 ATTA-TAAATAATTTTTTTATA
* *
635225 ATTATAAATAA----TATAGA
1 ATTATAAATAATTTTTTTATA
*
635242 CA-TAAAAATAATTTTTTTATA
1 -ATTATAAATAATTTTTTTATA
635263 ATTATAAATAAT
1 ATTATAAATAAT
635275 ATAAACATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 13
0.67 0.11 0.23
Matches are distributed among these distances:
17 12 0.32
18 1 0.03
20 1 0.03
21 20 0.53
22 4 0.11
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (21 bp):
ATTATAAATAATTTTTTTATA
Found at i:635252 original size:38 final size:38
Alignment explanation
Indices: 635209--635282 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
635199 TCTTATTATT
*
635209 AAATAATTTTTTTATAATTATAAATAATATAGACATAA
1 AAATAATTTTTTTATAATTATAAATAATATAAACATAA
635247 AAATAATTTTTTTATAATTATAAATAATATAAACAT
1 AAATAATTTTTTTATAATTATAAATAATATAAACAT
635283 TTATGTCGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (38 bp):
AAATAATTTTTTTATAATTATAAATAATATAAACATAA
Found at i:637254 original size:6 final size:6
Alignment explanation
Indices: 637236--637300 Score: 85
Period size: 6 Copynumber: 10.8 Consensus size: 6
637226 CATACCAGAA
* * *
637236 GGGGCT GGAGCT GGGGCT GGGGCT GGGGCT GGGGCT GGAGCT GGAGCT
1 GGGGCT GGGGCT GGGGCT GGGGCT GGGGCT GGGGCT GGGGCT GGGGCT
* *
637284 GCGGCT GCGGCT GGGGC
1 GGGGCT GGGGCT GGGGC
637301 AGGGTCTGCT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.05, C:0.20, G:0.60, T:0.15
Consensus pattern (6 bp):
GGGGCT
Found at i:647536 original size:36 final size:36
Alignment explanation
Indices: 647469--647760 Score: 397
Period size: 36 Copynumber: 8.0 Consensus size: 36
647459 AAAAATGAAC
* * * *
647469 ACTTGAATTGAAAGTG-CGACGCCTCATTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCCTCCTTCCGTTCG
**
647504 ACTTGAATCGGAAGTGTTGATGCCTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCCTCCTTCCGTTCG
* *
647540 ACTTGACTCGGAAGGGCCGATGCCTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCCTCCTTCCGTTCG
* * *
647576 ACTTGACTCGGAGGTGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCCTCCTTCCGTTCG
*
647612 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCCTCCTTCCGTTCG
647648 ACTTGAATCGGAAGTGCCGATGCCTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCCTCCTTCCGTTCG
*
647684 ACTTGAATCGGAAACAGAAGTGCCGATGCCTCCTTCCATTCG
1 ACTTGAATC-G-----GAAGTGCCGATGCCTCCTTCCGTTCG
*
647726 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTC
1 ACTTGAATCGGAAGTGCCGATGCCTCCTTCCGTTC
647761 TTGTATTTCT
Statistics
Matches: 232, Mismatches: 18, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
35 14 0.06
36 182 0.78
37 1 0.00
41 1 0.00
42 34 0.15
ACGTcount: A:0.18, C:0.29, G:0.25, T:0.29
Consensus pattern (36 bp):
ACTTGAATCGGAAGTGCCGATGCCTCCTTCCGTTCG
Found at i:648826 original size:36 final size:36
Alignment explanation
Indices: 648785--648855 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
648775 AAATGGAGGG
648785 ACTAATTGATGCGAGCAACCAAGATGCCAACGCACT
1 ACTAATTGATGCGAGCAACCAAGATGCCAACGCACT
648821 ACTAATTGATGCGAGCAACCAAGATGCCAACGCAC
1 ACTAATTGATGCGAGCAACCAAGATGCCAACGCAC
648856 AATCTTGCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.37, C:0.28, G:0.20, T:0.15
Consensus pattern (36 bp):
ACTAATTGATGCGAGCAACCAAGATGCCAACGCACT
Found at i:652422 original size:21 final size:20
Alignment explanation
Indices: 652371--652447 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 20
652361 AGATTGCTCG
652371 GATGGTACCGATACCCCCCA
1 GATGGTACCGATACCCCCCA
* *
652391 GA-GGTATCGATACCCCATGCA
1 GATGGTACCGATACCCC--CCA
*
652412 -ATGGTACCGATACCCCCTTA
1 GATGGTACCGATACCCCC-CA
652432 GGA-GGTACCGATACCC
1 -GATGGTACCGATACCC
652448 TCAGGCATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
19 13 0.28
20 4 0.09
21 28 0.61
22 1 0.02
ACGTcount: A:0.26, C:0.34, G:0.22, T:0.18
Consensus pattern (20 bp):
GATGGTACCGATACCCCCCA
Found at i:654450 original size:23 final size:23
Alignment explanation
Indices: 654424--654492 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
654414 CACCACAGCT
*
654424 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
654447 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
654470 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
654493 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:654676 original size:102 final size:103
Alignment explanation
Indices: 654507--654718 Score: 374
Period size: 102 Copynumber: 2.1 Consensus size: 103
654497 ATAATGTCAT
* *
654507 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCAATCCTTAAGAATCATATACATATACAAGAGATCAAGTATGTGTCTCACCA
654572 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
654610 AAGGACCACATAT-AATCCTTAAGAATCATATACATATGCCAAG-GATCAAGTATGTGTCTCACC
1 AAGGACCACATATCAATCCTTAAGAATCATATACATAT-ACAAGAGATCAAGTATGTGTCTCACC
654673 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
654712 AAGGACC
1 AAGGACC
654719 GCGTAGACCC
Statistics
Matches: 105, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
102 89 0.85
103 16 0.15
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCAATCCTTAAGAATCATATACATATACAAGAGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:656086 original size:20 final size:21
Alignment explanation
Indices: 656045--656098 Score: 92
Period size: 20 Copynumber: 2.6 Consensus size: 21
656035 TTCGCTTGAG
656045 GGGTATCGATTCCCCATTGAAT
1 GGGTATCGATT-CCCATTGAAT
656067 GGGTATCGATTCCC-TTGAAT
1 GGGTATCGATTCCCATTGAAT
656087 GGGTATCGATTC
1 GGGTATCGATTC
656099 TCTTTGCCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 18 0.56
21 3 0.09
22 11 0.34
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.33
Consensus pattern (21 bp):
GGGTATCGATTCCCATTGAAT
Found at i:662067 original size:17 final size:17
Alignment explanation
Indices: 662036--662070 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
662026 AGCTTAGAGA
**
662036 TTCTAAAAATGTATTTT
1 TTCTAAAAAAATATTTT
662053 TTCTAAAAAAATATTTT
1 TTCTAAAAAAATATTTT
662070 T
1 T
662071 ACTTTCAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (17 bp):
TTCTAAAAAAATATTTT
Found at i:662314 original size:17 final size:17
Alignment explanation
Indices: 662292--662339 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
662282 ACTCAAGTAA
**
662292 TTTTAAAATTTTATTTT
1 TTTTAAAATTTTATAAT
*
662309 TTTTAAAA--ATATAAT
1 TTTTAAAATTTTATAAT
662324 TTTTAAAATTTTATAA
1 TTTTAAAATTTTATAA
662340 AGGTAAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 12 0.48
17 13 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTAAAATTTTATAAT
Found at i:663099 original size:183 final size:184
Alignment explanation
Indices: 662791--663160 Score: 733
Period size: 183 Copynumber: 2.0 Consensus size: 184
662781 TTTATGTCGT
662791 TTTGATTGAGGACAACATCTTTGAGGAAGGTCTCGTAGCTTCAAAGCCCTAGGAGAGAGAGATAG
1 TTTGATTGAGGACAACATCTTTGAGGAAGGTCTCGTAGCTTCAAAGCCCTAGGAGAGAGAGATAG
662856 GAGGTAAACATATCGCTACAAAGAGCGGGAACGTTCGGGTGCTCCTCGGTGCTTTGCCCTAGTTC
66 GAGGTAAACATATCGCTACAAAGAGCGGGAACGTTCGGGTGCTCCTCGGTGCTTTGCCCTAGTTC
662921 CAAATTGCTGGAATCCCTACCCCAATTCAGGTTTTTGTTCG-CCTTAATTTTCG
131 CAAATTGCTGGAATCCCTACCCCAATTCAGGTTTTTGTTCGCCCTTAATTTTCG
662974 TTTGATTGAGGACAACATCTTTGAGGAAGGTCTCGTAGCTTCAAAGCCCTAGGAGAGAGAGATAG
1 TTTGATTGAGGACAACATCTTTGAGGAAGGTCTCGTAGCTTCAAAGCCCTAGGAGAGAGAGATAG
663039 GAGGTAAACATATCGCTACAAAGAGCGGGAACGTTCGGGTGCTCCTCGGTGCTTTGCCCTAGTTC
66 GAGGTAAACATATCGCTACAAAGAGCGGGAACGTTCGGGTGCTCCTCGGTGCTTTGCCCTAGTTC
663104 CAAATTGCTGGAATCCCTACCCCAATTCAGGTTTTTGTTCGCCCTTAATTTTCG
131 CAAATTGCTGGAATCCCTACCCCAATTCAGGTTTTTGTTCGCCCTTAATTTTCG
663158 TTT
1 TTT
663161 TGGAAACCCT
Statistics
Matches: 186, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
183 171 0.92
184 15 0.08
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (184 bp):
TTTGATTGAGGACAACATCTTTGAGGAAGGTCTCGTAGCTTCAAAGCCCTAGGAGAGAGAGATAG
GAGGTAAACATATCGCTACAAAGAGCGGGAACGTTCGGGTGCTCCTCGGTGCTTTGCCCTAGTTC
CAAATTGCTGGAATCCCTACCCCAATTCAGGTTTTTGTTCGCCCTTAATTTTCG
Found at i:670608 original size:27 final size:27
Alignment explanation
Indices: 670577--670671 Score: 167
Period size: 27 Copynumber: 3.6 Consensus size: 27
670567 TCTATTTACA
670577 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
670604 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
*
670631 AAATCATAACTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
670658 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
670672 ATTCCTACAC
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
25 8 0.12
27 58 0.88
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:674179 original size:27 final size:27
Alignment explanation
Indices: 674148--674242 Score: 149
Period size: 27 Copynumber: 3.6 Consensus size: 27
674138 TCTATTTACA
*
674148 AAATCATATCTCTATAGGAATGATAAC
1 AAATCATATCTCTATAGGAATGGTAAC
674175 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
* *
674202 AAATCATAACTCTATAGGAATGGTAGC
1 AAATCATATCTCTATAGGAATGGTAAC
674229 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
674243 ATTCCTACAG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
25 8 0.12
27 56 0.88
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:683074 original size:15 final size:14
Alignment explanation
Indices: 683054--683083 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
683044 CCCAGCAAAT
683054 CTCAAGCTGAGCCAA
1 CTCAAGCTGA-CCAA
683069 CTCAAGCTGACCAA
1 CTCAAGCTGACCAA
683083 C
1 C
683084 AGCAAATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.37, G:0.17, T:0.13
Consensus pattern (14 bp):
CTCAAGCTGACCAA
Found at i:688811 original size:55 final size:55
Alignment explanation
Indices: 688752--688856 Score: 176
Period size: 55 Copynumber: 1.9 Consensus size: 55
688742 TAAATTGAAC
688752 ATCGAATGCATTTCATGCATCGATGCA-CATACCATGCATCGATGCACTCATGGTT
1 ATCGAATGCATTTCATGCATCGATGCACCA-ACCATGCATCGATGCACTCATGGTT
* *
688807 ATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCA
1 ATCGAATGCATTTCATGCATCGATGCACCAACCATGCATCGATGCACTCA
688857 GGCTTTTTCA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
55 45 0.96
56 2 0.04
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (55 bp):
ATCGAATGCATTTCATGCATCGATGCACCAACCATGCATCGATGCACTCATGGTT
Found at i:696634 original size:19 final size:20
Alignment explanation
Indices: 696602--696639 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
696592 TTCTCTCATC
696602 TCTTCTTCCTTCTT-TCTTA
1 TCTTCTTCCTTCTTCTCTTA
696621 TCTTCTTCAC-TCTTCTCTT
1 TCTTCTTC-CTTCTTCTCTT
696640 CTTCCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTCTTCCTTCTTCTCTTA
Found at i:697637 original size:21 final size:22
Alignment explanation
Indices: 697611--697670 Score: 95
Period size: 21 Copynumber: 2.8 Consensus size: 22
697601 GTCGAGGGTT
697611 TCATAGGTCCTTCGGGACA-AC
1 TCATAGGTCCTTCGGGACATAC
*
697632 TCATAGGTCCTTCGGGACATAT
1 TCATAGGTCCTTCGGGACATAC
*
697654 TCACAGGTCCTTCGGGA
1 TCATAGGTCCTTCGGGA
697671 AAAATTTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 19 0.53
22 17 0.47
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.27
Consensus pattern (22 bp):
TCATAGGTCCTTCGGGACATAC
Found at i:698188 original size:11 final size:11
Alignment explanation
Indices: 698172--698216 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
698162 TTTTTACGGA
698172 AGTACTGTAGC
1 AGTACTGTAGC
*
698183 AGTACTGTAGT
1 AGTACTGTAGC
* *
698194 AGCACTGTAGT
1 AGTACTGTAGC
*
698205 GGTACTGTAGC
1 AGTACTGTAGC
698216 A
1 A
698217 AGGGAATCGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (11 bp):
AGTACTGTAGC
Found at i:698234 original size:22 final size:22
Alignment explanation
Indices: 698209--698254 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
698199 TGTAGTGGTA
*
698209 CTGTAGCAAGGGAATCGTTTCC
1 CTGTAGCAAGGGAATCGATTCC
*
698231 CTGTAGCAGGGGAATCGATTCC
1 CTGTAGCAAGGGAATCGATTCC
698253 CT
1 CT
698255 ATTTGTAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.26
Consensus pattern (22 bp):
CTGTAGCAAGGGAATCGATTCC
Found at i:698685 original size:25 final size:23
Alignment explanation
Indices: 698644--698692 Score: 55
Period size: 25 Copynumber: 2.0 Consensus size: 23
698634 CTGGTATGGT
*
698644 AATGAGTATGTTGTTTTGCTAATAG
1 AATGAGTATGTTATTTT--TAATAG
698669 AATGA-TATGTTTATTTTTAATAG
1 AATGAGTATG-TTATTTTTAATAG
698692 A
1 A
698693 TGTCCGGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 7 0.32
24 4 0.18
25 11 0.50
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (23 bp):
AATGAGTATGTTATTTTTAATAG
Found at i:703540 original size:19 final size:20
Alignment explanation
Indices: 703508--703545 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
703498 TTCTCTCATC
703508 TCTTCTTCCTTCTT-TCTTA
1 TCTTCTTCCTTCTTCTCTTA
703527 TCTTCTTCAC-TCTTCTCTT
1 TCTTCTTC-CTTCTTCTCTT
703546 CTTCCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTCTTCCTTCTTCTCTTA
Found at i:704571 original size:22 final size:21
Alignment explanation
Indices: 704517--704580 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
704507 AGTCGAGGGT
704517 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
*
704538 CTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
*
704560 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
704581 ATTTCATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:705131 original size:22 final size:22
Alignment explanation
Indices: 705106--705150 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
705096 GTAACGGCAT
*
705106 TGTAGCAGGGGAATCGTTTCCC
1 TGTAGCAGGGGAATCGATTCCC
705128 TGTAGCAGGGGAATCGATTCCC
1 TGTAGCAGGGGAATCGATTCCC
705150 T
1 T
705151 ATTTGTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.27
Consensus pattern (22 bp):
TGTAGCAGGGGAATCGATTCCC
Found at i:712321 original size:21 final size:22
Alignment explanation
Indices: 712272--712323 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
712262 ATTCCCCTGT
712272 GGGGGGGAATCGGTTCCCCTTCA
1 GGGGGGGAATCGGTT-CCCTTCA
**
712295 AAGGGGGAATCGGTT-CCTTCA
1 GGGGGGGAATCGGTTCCCTTCA
712316 GGGGGGGA
1 GGGGGGGA
712324 TCGATTCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 12 0.48
23 13 0.52
ACGTcount: A:0.17, C:0.19, G:0.44, T:0.19
Consensus pattern (22 bp):
GGGGGGGAATCGGTTCCCTTCA
Found at i:722604 original size:291 final size:291
Alignment explanation
Indices: 722080--722662 Score: 1139
Period size: 291 Copynumber: 2.0 Consensus size: 291
722070 ACTATGAAAG
722080 AAACTACTACAAACAAAAAAGACAGACAGCACATCCTTCATAAACAACAAGATAGAAAAAGATGC
1 AAACTACTACAAACAAAAAAGACAGACAGCACATCCTTCATAAACAACAAGATAGAAAAAGATGC
722145 TATCTAATTCATCTAATCGTGAAGTGCAGTAAAAATTCAAATAATCCAATTTTAAAGATGATAAG
66 TATCTAATTCATCTAATCGTGAAGTGCAGTAAAAATTCAAATAATCCAATTTTAAAGATGATAAG
722210 AGGAGCACTTTTACCTGTACAATAGTATCTACTCCATACTCTTTCCTCCAGTTCAGCATATCTTC
131 AGGAGCACTTTTACCTGTACAATAGTATCTACTCCATACTCTTTCCTCCAGTTCAGCATATCTTC
*
722275 CCACATCTGCATGGTTTCATCAAGGTCAAACTTCCTTGCTTTCAGAAACCTGCAAAAAACAAATT
196 CCACATCTGCATGGTTTCATCAAGGTCAAACTTCCTTGCTTTCAAAAACCTGCAAAAAACAAATT
722340 CCACATTTTTTAAATGAATGAACATAGCTGA
261 CCACATTTTTTAAATGAATGAACATAGCTGA
* *
722371 AAACTACTACAAACAAAAAGGACAGACAGCACATCCTTCATAAACAACAAGATAGACAAAGATGC
1 AAACTACTACAAACAAAAAAGACAGACAGCACATCCTTCATAAACAACAAGATAGAAAAAGATGC
722436 TATCTAATTCATCTAATCGTGAAGTGCAGTAAAAATTCAAATAATCCAATTTTAAAGATGATAAG
66 TATCTAATTCATCTAATCGTGAAGTGCAGTAAAAATTCAAATAATCCAATTTTAAAGATGATAAG
722501 AGGAGCACTTTTACCTGTACAATAGTATCTACTCCATACTCTTTCCTCCAGTTCAGCATATCTTC
131 AGGAGCACTTTTACCTGTACAATAGTATCTACTCCATACTCTTTCCTCCAGTTCAGCATATCTTC
722566 CCACATCTGCATGGTTTCATCAAGGTCAAACTTCCTTGCTTTCAAAAACCTGCAAAAAACAAATT
196 CCACATCTGCATGGTTTCATCAAGGTCAAACTTCCTTGCTTTCAAAAACCTGCAAAAAACAAATT
722631 CCACATTTTTTAAATGAATGAACATAGCTGA
261 CCACATTTTTTAAATGAATGAACATAGCTGA
722662 A
1 A
722663 TGGAGGCTCT
Statistics
Matches: 289, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
291 289 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (291 bp):
AAACTACTACAAACAAAAAAGACAGACAGCACATCCTTCATAAACAACAAGATAGAAAAAGATGC
TATCTAATTCATCTAATCGTGAAGTGCAGTAAAAATTCAAATAATCCAATTTTAAAGATGATAAG
AGGAGCACTTTTACCTGTACAATAGTATCTACTCCATACTCTTTCCTCCAGTTCAGCATATCTTC
CCACATCTGCATGGTTTCATCAAGGTCAAACTTCCTTGCTTTCAAAAACCTGCAAAAAACAAATT
CCACATTTTTTAAATGAATGAACATAGCTGA
Found at i:724659 original size:23 final size:22
Alignment explanation
Indices: 724633--724699 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
724623 TCAAATGATC
*
724633 GAAAACGTGTCATGAAGGTAGAA
1 GAAAACGTGTCATAAAGGTAG-A
* * *
724656 GAAAACATATCATAAATGTAGA
1 GAAAACGTGTCATAAAGGTAGA
* * *
724678 GAAAATGTGTTATAAAGATAGA
1 GAAAACGTGTCATAAAGGTAGA
724700 ATTATTAGAA
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
22 17 0.50
23 17 0.50
ACGTcount: A:0.49, C:0.06, G:0.22, T:0.22
Consensus pattern (22 bp):
GAAAACGTGTCATAAAGGTAGA
Found at i:726415 original size:76 final size:76
Alignment explanation
Indices: 726288--726507 Score: 307
Period size: 76 Copynumber: 2.9 Consensus size: 76
726278 AAGTTATAAA
* * *
726288 TATTTTATCGTTTACATTATTATTATACATTTAAACAAATCGATA-ATTAGTTTAACGTAATAGG
1 TATTTTATCGTTTATATTATTATTATACCTTTAAACAAATCGGTAGA-TAGTTTAACGTAATAGG
726352 TTGCGCCTATTT
65 TTGCGCCTATTT
* * * * *
726364 TATTTTACCGTTTATAATATTATTATACCTTTAAACAAATCGGTCGCTAGTTTAACGTAATAGAT
1 TATTTTATCGTTTATATTATTATTATACCTTTAAACAAATCGGTAGATAGTTTAACGTAATAGGT
* *
726429 TACGTCTATTT
66 TGCGCCTATTT
* * *
726440 TATTTTATCATTTATATTATTATTATACCTTTAAACAAACCGGTAGATAATTTAACGTAATAGGT
1 TATTTTATCGTTTATATTATTATTATACCTTTAAACAAATCGGTAGATAGTTTAACGTAATAGGT
726505 TGC
66 TGC
726508 AATTTTTTTA
Statistics
Matches: 124, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
76 124 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (76 bp):
TATTTTATCGTTTATATTATTATTATACCTTTAAACAAATCGGTAGATAGTTTAACGTAATAGGT
TGCGCCTATTT
Found at i:726617 original size:100 final size:100
Alignment explanation
Indices: 726440--726620 Score: 281
Period size: 100 Copynumber: 1.8 Consensus size: 100
726430 ACGTCTATTT
* *
726440 TATTTTATCATTTATATTATTATTATACCTTTAAACAAACCGGTAGATAATTTAACGTAATAGGT
1 TATTTTACCATTTACATTATTATTATACCTTTAAACAAACCGGTAGATAATTTAACGTAATAGGT
* *
726505 TGCAATTTTTTTATTTTAACTGATTAAGTTGTAAA
66 TGCAACTATTTTATTTTAACTGATTAAGTTGTAAA
* * * *
726540 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACTGGTAGCTAGTTTAACGTAATAGGT
1 TATTTTACCATTTACATTATTATTATACCTTTAAACAAACCGGTAGATAATTTAACGTAATAGGT
*
726605 TGCACCTATTTTATTT
66 TGCAACTATTTTATTT
726621 GACCATTTAT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 72 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (100 bp):
TATTTTACCATTTACATTATTATTATACCTTTAAACAAACCGGTAGATAATTTAACGTAATAGGT
TGCAACTATTTTATTTTAACTGATTAAGTTGTAAA
Found at i:726690 original size:76 final size:76
Alignment explanation
Indices: 726540--726696 Score: 224
Period size: 76 Copynumber: 2.1 Consensus size: 76
726530 AAGTTGTAAA
* * * *
726540 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACTGGTAGCTAGTTTAACGTAATAGGT
1 TATTTGACCATTTACATTATTATTATACCTTTAAACAAACTGGTAGATAGTTTAACGTAATAGAT
*
726605 TGCACCTATTT
66 TACACCTATTT
* * *
726616 TATTTGACCATTTATATTATTATTATACCTTTAAACAAACTGGTAGATAGTTTAATGTAATATAT
1 TATTTGACCATTTACATTATTATTATACCTTTAAACAAACTGGTAGATAGTTTAACGTAATAGAT
**
726681 TACGTCTATTT
66 TACACCTATTT
726692 TATTT
1 TATTT
726697 TAACCGGTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (76 bp):
TATTTGACCATTTACATTATTATTATACCTTTAAACAAACTGGTAGATAGTTTAACGTAATAGAT
TACACCTATTT
Found at i:726695 original size:176 final size:176
Alignment explanation
Indices: 726364--726719 Score: 500
Period size: 176 Copynumber: 2.0 Consensus size: 176
726354 GCGCCTATTT
* *
726364 TATTTTACCGTTTATAATATTATTATACCTTTAAACAAATCGGTCGCTAGTTTAACGTAATAGAT
1 TATTTTACCGTTTACAATATTATTATACCTTTAAACAAATCGGTAGCTAGTTTAACGTAATAGAT
** * *
726429 TACGTCTATTTTATTTTATCATTTATATTATTATTATACCTTTAAACAAACCGGTAGATAATTTA
66 TACACCTATTTTATTTGACCATTTATATTATTATTATACCTTTAAACAAACCGGTAGATAATTTA
* * * *
726494 ACGTAATAGGTTGCAATTTTTTTATTTTAACTGATTAAGTTGTAAA
131 ACGTAATAGATTACAATTATTTTATTTTAACCGATTAAGTTGTAAA
* *
726540 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAA-CTGGTAGCTAGTTTAACGTAATAGG
1 TATTTTACCGTTTACAATATTATTATACCTTTAAACAAATC-GGTAGCTAGTTTAACGTAATAGA
* * *
726604 TTGCACCTATTTTATTTGACCATTTATATTATTATTATACCTTTAAACAAACTGGTAGATAGTTT
65 TTACACCTATTTTATTTGACCATTTATATTATTATTATACCTTTAAACAAACCGGTAGATAATTT
* * * * *
726669 AATGTAATATATTAC-GTCTATTTTATTTTAACCGGTTAAGTTGTAAT
130 AACGTAATAGATTACAAT-TATTTTATTTTAACCGATTAAGTTGTAAA
726716 TATT
1 TATT
726720 ATTAGACTAT
Statistics
Matches: 158, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
175 2 0.01
176 156 0.99
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (176 bp):
TATTTTACCGTTTACAATATTATTATACCTTTAAACAAATCGGTAGCTAGTTTAACGTAATAGAT
TACACCTATTTTATTTGACCATTTATATTATTATTATACCTTTAAACAAACCGGTAGATAATTTA
ACGTAATAGATTACAATTATTTTATTTTAACCGATTAAGTTGTAAA
Found at i:727073 original size:72 final size:70
Alignment explanation
Indices: 726982--727145 Score: 213
Period size: 72 Copynumber: 2.3 Consensus size: 70
726972 CTTTTTTTAT
* ** * *
726982 TTTTTTTAAAATTCGAAAGTATTGATATTTGTAGAAAAATATTAAAATTTTATAACATTCTCATT
1 TTTTTTTAAAATTTGAAAGTATCAATATTTGTAGAAAAATATTAAAACTTTACAACATTCTCATT
727047 TTCAA
66 TTCAA
* * * *
727052 TATTTTTCTAAAATTTGAAAGTGTCAATATTTGTAGAAAACTATTAATACTTTACAACCTTCTCA
1 T-TTTTT-TAAAATTTGAAAGTATCAATATTTGTAGAAAAATATTAAAACTTTACAACATTCTCA
*
727117 TTTTTAA
64 TTTTCAA
727124 TTTTTTT-AAATTTGAAAGTATC
1 TTTTTTTAAAATTTGAAAGTATC
727146 TATTATCGTA
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
69 14 0.17
70 2 0.02
71 10 0.12
72 55 0.68
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.46
Consensus pattern (70 bp):
TTTTTTTAAAATTTGAAAGTATCAATATTTGTAGAAAAATATTAAAACTTTACAACATTCTCATT
TTCAA
Found at i:729945 original size:41 final size:41
Alignment explanation
Indices: 729900--729980 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
729890 TTGTAGATAG
*
729900 CTGTCTTTCGGATGAGAGCGACTTTAATCAGTAATATTATT
1 CTGTCTTTCGGATGAGAGCGACTTTAATAAGTAATATTATT
*
729941 CTGTCTTTCGGATGAGAGTGACTTTAATAAGTAATATTAT
1 CTGTCTTTCGGATGAGAGCGACTTTAATAAGTAATATTAT
729981 CATCATTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (41 bp):
CTGTCTTTCGGATGAGAGCGACTTTAATAAGTAATATTATT
Found at i:736234 original size:21 final size:21
Alignment explanation
Indices: 736210--736348 Score: 138
Period size: 21 Copynumber: 6.7 Consensus size: 21
736200 GTGTTGCATT
*
736210 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
736231 TCGCGTTACGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
736251 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
736272 TCGCGTTGCGCT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
736292 TCGCGTTGTGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
736313 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
736334 TCGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
736349 CTACAGTTGT
Statistics
Matches: 89, Mismatches: 27, Indels: 4
0.74 0.22 0.03
Matches are distributed among these distances:
20 27 0.30
21 62 0.70
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:736260 original size:41 final size:41
Alignment explanation
Indices: 736206--736324 Score: 202
Period size: 41 Copynumber: 2.9 Consensus size: 41
736196 ATTCGTGTTG
* *
736206 CATTTCGCATTGCGATAGTTGAAAATCGCGTTACGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
736247 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
736288 CATTTCGCGTTGTGATAGTTGAAAATCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
736325 AGTTGAAAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:736297 original size:20 final size:20
Alignment explanation
Indices: 736231--736299 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
736221 TAGTTGAAAA
*
736231 TCGCGTTACGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
736251 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
736272 TCGCGTTGCGCTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
736292 TCGCGTTG
1 TCGCGTTG
736300 TGATAGTTGA
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 22 0.61
21 14 0.39
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Done.