Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014373.1 Kokia drynarioides strain JFW-HI SEQ_129411, 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: 813680
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 179 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:216 original size:19 final size:18
Alignment explanation
Indices: 188--250 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
178 TAAAATAGAG
*
188 AAAATTATAAAAATAATAA
1 AAAATCATAAAAAT-ATAA
*
207 AAAATCATAAATATATACA
1 AAAATCATAAAAATATA-A
226 TAAAA-CATAAAAAATTATAA
1 -AAAATCAT-AAAAA-TATAA
246 AAAAT
1 AAAAT
251 TAGCAAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
18 3 0.08
19 20 0.56
20 9 0.25
21 4 0.11
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATCATAAAAATATAA
Found at i:3451 original size:20 final size:21
Alignment explanation
Indices: 3426--3471 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
3416 TACTTTAAAA
3426 TTATTTTTTCAAATT-TTTTT
1 TTATTTTTTCAAATTATTTTT
**
3446 TTATTTTTTCGGATTATTTTT
1 TTATTTTTTCAAATTATTTTT
3467 TTATT
1 TTATT
3472 GATTTTAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (21 bp):
TTATTTTTTCAAATTATTTTT
Found at i:7057 original size:2 final size:2
Alignment explanation
Indices: 7050--7080 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7040 TGATGTTATA
7050 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
7081 TAAGCTTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:12533 original size:46 final size:47
Alignment explanation
Indices: 12420--12536 Score: 132
Period size: 51 Copynumber: 2.5 Consensus size: 47
12410 AGCAGATAAA
*
12420 GAATATGCAT-CAG-AAAAATAACTTGCACCAATAATGTAGGCAAGGAAAG
1 GAATATGCATGCAGAAAAAATAACTTACACCAATAATGTAGGC----AAAG
** *
12469 GAATACCCATGCAAAAAAAATAACTTACACCAATAATGTAGGC-AAG
1 GAATATGCATGCAGAAAAAATAACTTACACCAATAATGTAGGCAAAG
*
12515 GAATATGCGTGCAGAAAAAATA
1 GAATATGCATGCAGAAAAAATA
12537 GGCAAAGAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
46 21 0.36
49 8 0.14
50 2 0.03
51 27 0.47
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (47 bp):
GAATATGCATGCAGAAAAAATAACTTACACCAATAATGTAGGCAAAG
Found at i:16245 original size:121 final size:123
Alignment explanation
Indices: 16047--16269 Score: 326
Period size: 121 Copynumber: 1.8 Consensus size: 123
16037 AAATCGAGAA
16047 AATAAGAAATAAAGAAATAAGTGGCGAGATCCACAAGAAAAAAAAACTTAAAAAATTAAAGACAT
1 AATAAGAAATAAAGAAATAAGTGGCGAGATCCACAAGAAAAAAAAACTTAAAAAATTAAAGACAT
* *
16112 GGCATTCAAGTCAATATTTAACAGGCCATGAGTGATTCAAGTCAACATTTAACAAGCT
66 GACATTCAAGTCAACATTTAACAGGCCATGAGTGATTCAAGTCAACATTTAACAAGCT
* * * * * *
16170 AATAAGAAATAAATAAATAAGTGGC-AGAATCC-TAA-ATAAAAAAATTTTAAAAATTAAAGACT
1 AATAAGAAATAAAGAAATAAGTGGCGAG-ATCCACAAGAAAAAAAAACTTAAAAAATTAAAGACA
* *
16232 TGACATTCAAGTCAACATTTAATAGGCCATGCGTGATT
65 TGACATTCAAGTCAACATTTAACAGGCCATGAGTGATT
16270 TTTGTTACGC
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
121 57 0.64
122 4 0.04
123 28 0.31
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.24
Consensus pattern (123 bp):
AATAAGAAATAAAGAAATAAGTGGCGAGATCCACAAGAAAAAAAAACTTAAAAAATTAAAGACAT
GACATTCAAGTCAACATTTAACAGGCCATGAGTGATTCAAGTCAACATTTAACAAGCT
Found at i:24585 original size:20 final size:20
Alignment explanation
Indices: 24545--24581 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
24535 ATGAGAAGAG
24545 AGAAATAAAAAGGAAAATAA
1 AGAAATAAAAAGGAAAATAA
24565 AGAAATAAAAA-GAAAAT
1 AGAAATAAAAAGGAAAAT
24582 TAAATTGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.11
Consensus pattern (20 bp):
AGAAATAAAAAGGAAAATAA
Found at i:33115 original size:16 final size:16
Alignment explanation
Indices: 33094--33125 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
33084 TTAGGATGAA
33094 AGAGAAAACAAATATC
1 AGAGAAAACAAATATC
33110 AGAGAAAACAAATATC
1 AGAGAAAACAAATATC
33126 TCCTCTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.12
Consensus pattern (16 bp):
AGAGAAAACAAATATC
Found at i:38599 original size:18 final size:19
Alignment explanation
Indices: 38562--38604 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
38552 AACTAGATCC
38562 TAATTAATTAAGGATTAAT
1 TAATTAATTAAGGATTAAT
* *
38581 TAATTAA-TGAGGTTTAAT
1 TAATTAATTAAGGATTAAT
38599 TAATTA
1 TAATTA
38605 TTAGTCTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (19 bp):
TAATTAATTAAGGATTAAT
Found at i:43830 original size:18 final size:19
Alignment explanation
Indices: 43799--43851 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 19
43789 TTTTTAAATA
* *
43799 AAAATTTAATTTAATATTT
1 AAAATTTAAATTAAAATTT
43818 AAAA-TTAAATTAAAATTT
1 AAAATTTAAATTAAAATTT
*
43836 --AATTTAATTTAAAATT
1 AAAATTTAAATTAAAATT
43852 ATTGACACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 2 0.07
17 12 0.40
18 12 0.40
19 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATTTAAATTAAAATTT
Found at i:43833 original size:30 final size:28
Alignment explanation
Indices: 43792--43852 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 28
43782 CTCTTTTTTT
43792 TTAAATAAAAATTTAATTTAATATTTAAAA
1 TTAAATAAAAATTTAATTT-A-ATTTAAAA
*
43822 TTAAATTAAAATTTAATTTAATTTAAAA
1 TTAAATAAAAATTTAATTTAATTTAAAA
43850 TTA
1 TTA
43853 TTGACACATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 11 0.37
29 1 0.03
30 18 0.60
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TTAAATAAAAATTTAATTTAATTTAAAA
Found at i:47984 original size:21 final size:21
Alignment explanation
Indices: 47959--47998 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
47949 GAAGGAATCA
*
47959 AATTGAACTTCATTCTCTTCG
1 AATTGAACTTCACTCTCTTCG
47980 AATTGAACTTCACTCTCTT
1 AATTGAACTTCACTCTCTT
47999 TGAGTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.42
Consensus pattern (21 bp):
AATTGAACTTCACTCTCTTCG
Found at i:54795 original size:19 final size:20
Alignment explanation
Indices: 54766--54811 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
54756 AAACGAAATT
*
54766 AAAATAATTTGTAAA-ACAAC
1 AAAA-AATTTGAAAATACAAC
*
54786 AAAAAATTTGAAAATACAAT
1 AAAAAATTTGAAAATACAAC
54806 AAAAAA
1 AAAAAA
54812 AACTTTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (20 bp):
AAAAAATTTGAAAATACAAC
Found at i:58381 original size:72 final size:70
Alignment explanation
Indices: 58263--58402 Score: 167
Period size: 72 Copynumber: 2.0 Consensus size: 70
58253 AATATCAATG
* * * * *
58263 AATAAATAAAATTAAATGAAGGCAAAAATATAAATAGCGTAAAAAAT-AACAAATAAATATAATA
1 AATAAATAAAATTAAATAAAAGCAAAAATATAAATAACGAAAAAAATGAA-AAACAAATA-AATA
58327 CATAAAAC
64 -ATAAAAC
* *
58335 AATAAATAAAATTAAATAAAAGCAAGAATGTAAATAAC-AAATAAAATGAAAAACAAATAAATAA
1 AATAAATAAAATTAAATAAAAGCAAAAATATAAATAACGAAA-AAAATGAAAAACAAATAAATAA
58399 TAAA
65 TAAA
58403 TGCTAAAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
70 5 0.08
71 6 0.10
72 46 0.78
73 2 0.03
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.20
Consensus pattern (70 bp):
AATAAATAAAATTAAATAAAAGCAAAAATATAAATAACGAAAAAAATGAAAAACAAATAAATAAT
AAAAC
Found at i:58440 original size:13 final size:14
Alignment explanation
Indices: 58407--58440 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
58397 AATAAATGCT
58407 AAAATAAACAAATA
1 AAAATAAACAAATA
*
58421 AATATAAAC-AATA
1 AAAATAAACAAATA
58434 AAAATAA
1 AAAATAA
58441 TAGGGACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAATAAACAAATA
Found at i:58440 original size:27 final size:27
Alignment explanation
Indices: 58385--58436 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
58375 ATAAAATGAA
***
58385 AAACAAATAAATAATAAATGCTAAAAT
1 AAACAAATAAATAATAAACAATAAAAT
58412 AAACAAATAAAT-ATAAACAATAAAA
1 AAACAAATAAATAATAAACAATAAAA
58437 ATAATAGGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.19
Consensus pattern (27 bp):
AAACAAATAAATAATAAACAATAAAAT
Found at i:62519 original size:21 final size:21
Alignment explanation
Indices: 62495--62548 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
62485 CTTGTGATAG
*
62495 TTCTACCGATACAAGT-GTAAC
1 TTCTACCGATACAAGTCAT-AC
* * *
62516 TTCTATCGAAACAAGTCATGC
1 TTCTACCGATACAAGTCATAC
62537 TTCTACCGATAC
1 TTCTACCGATAC
62549 TAAAAACTCC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATAC
Found at i:63585 original size:20 final size:19
Alignment explanation
Indices: 63553--63591 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
63543 TCGTTGTTTC
*
63553 CATCTTTCTCATTTCCAAT
1 CATCTTTCCCATTTCCAAT
*
63572 CATCGTTTCCCATTTGCAAT
1 CATC-TTTCCCATTTCCAAT
63592 AGTTGTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.21, C:0.31, G:0.05, T:0.44
Consensus pattern (19 bp):
CATCTTTCCCATTTCCAAT
Found at i:68124 original size:27 final size:27
Alignment explanation
Indices: 68082--68134 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
68072 CTGATGGCAT
* *
68082 ATGTCCGTGTAGGTGCTCGGACCTTAC
1 ATGTCCGTGTAAGTGCTCGAACCTTAC
68109 ATGTCCGTGTAAGTGCTCGAACCTTA
1 ATGTCCGTGTAAGTGCTCGAACCTTA
68135 GATCTGGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (27 bp):
ATGTCCGTGTAAGTGCTCGAACCTTAC
Found at i:77995 original size:51 final size:51
Alignment explanation
Indices: 77940--78040 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
77930 ACTTGCTTAG
* * *
77940 CAACATTATCCACTCCATCTGATGTTGTAAAATTAGCATCATATTCATCAA
1 CAACATTATCCACTCCATCTGATGTTGCAAAATCAGCAACATATTCATCAA
* * *
77991 CAACATTATCCTCTTCATCTGATGTTGCAAAATCAGTAACATATTCATCA
1 CAACATTATCCACTCCATCTGATGTTGCAAAATCAGCAACATATTCATCA
78041 GTAGCAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.34
Consensus pattern (51 bp):
CAACATTATCCACTCCATCTGATGTTGCAAAATCAGCAACATATTCATCAA
Found at i:79146 original size:16 final size:16
Alignment explanation
Indices: 79113--79170 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
79103 TGTTCTTGGG
*
79113 TTAGGGA-TTCAATGAT
1 TTAGGGATTTTAAT-AT
*
79129 TTGGGGATTTTAATAT
1 TTAGGGATTTTAATAT
*
79145 TTAGGTATTTTAATATT
1 TTAGGGATTTTAATA-T
79162 TTAGGGATT
1 TTAGGGATT
79171 CAAAGAAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
16 21 0.60
17 14 0.40
ACGTcount: A:0.28, C:0.02, G:0.22, T:0.48
Consensus pattern (16 bp):
TTAGGGATTTTAATAT
Found at i:80464 original size:40 final size:40
Alignment explanation
Indices: 80420--80524 Score: 138
Period size: 40 Copynumber: 2.6 Consensus size: 40
80410 CCAAGTTTGC
* *
80420 ACATCTGTGCCCTTGTATACACTTCGGTTTCCCTGTTTAA
1 ACATCTGTGCCCTTGTATACACTTCGATTTCCCTATTTAA
* * **
80460 ACATCTGTGCCCTTGTATAAACTTCGATTTCGCTATTTGC
1 ACATCTGTGCCCTTGTATACACTTCGATTTCCCTATTTAA
* *
80500 ACATCTGTGCCCTTGTTTGCACTTC
1 ACATCTGTGCCCTTGTATACACTTC
80525 AGTGCCCTTG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.17, C:0.28, G:0.15, T:0.40
Consensus pattern (40 bp):
ACATCTGTGCCCTTGTATACACTTCGATTTCCCTATTTAA
Found at i:80520 original size:20 final size:20
Alignment explanation
Indices: 80495--80536 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
80485 GATTTCGCTA
*
80495 TTTGCACATCTGTGCCCTTG
1 TTTGCACATCAGTGCCCTTG
*
80515 TTTGCACTTCAGTGCCCTTG
1 TTTGCACATCAGTGCCCTTG
80535 TT
1 TT
80537 ATGTGTCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.29, G:0.19, T:0.43
Consensus pattern (20 bp):
TTTGCACATCAGTGCCCTTG
Found at i:90212 original size:23 final size:22
Alignment explanation
Indices: 90180--90225 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
90170 AAAGAAACTG
*
90180 AAATGCATTA-AACTAAAGCTAA
1 AAATGCATTACAACCAAAG-TAA
90202 AAATGTCATTACAACCAAAGTAA
1 AAATG-CATTACAACCAAAGTAA
90225 A
1 A
90226 GGGATTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 9 0.43
24 7 0.33
ACGTcount: A:0.54, C:0.15, G:0.09, T:0.22
Consensus pattern (22 bp):
AAATGCATTACAACCAAAGTAA
Found at i:90832 original size:36 final size:36
Alignment explanation
Indices: 90792--90863 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
90782 TATATGGGGA
90792 TACAAAGTAAAAAGAATGACAATAAAATTATCAATT
1 TACAAAGTAAAAAGAATGACAATAAAATTATCAATT
90828 TACAAAGTAAAAAGAATGACAATAAAATTATCAATT
1 TACAAAGTAAAAAGAATGACAATAAAATTATCAATT
90864 GTCAAAACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.25
Consensus pattern (36 bp):
TACAAAGTAAAAAGAATGACAATAAAATTATCAATT
Found at i:104837 original size:17 final size:17
Alignment explanation
Indices: 104804--104835 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
104794 AAAAGAATGC
104804 AAAATATAATATGAAAT
1 AAAATATAATATGAAAT
104821 AAAAT-TAATATGAAA
1 AAAATATAATATGAAA
104836 ATGCATTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (17 bp):
AAAATATAATATGAAAT
Found at i:106587 original size:12 final size:12
Alignment explanation
Indices: 106574--106652 Score: 77
Period size: 12 Copynumber: 6.6 Consensus size: 12
106564 AATATGTCTG
*
106574 ACAATAATAATG
1 ACAATAATAATA
* *
106586 ACAATAATGATC
1 ACAATAATAATA
* * *
106598 ACGATGATGATA
1 ACAATAATAATA
106610 ACAATAATAATA
1 ACAATAATAATA
*
106622 ATAATAATAATA
1 ACAATAATAATA
*
106634 ATAATAATAATA
1 ACAATAATAATA
*
106646 ATAATAA
1 ACAATAA
106653 ATAGAGTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 58 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (12 bp):
ACAATAATAATA
Found at i:106618 original size:3 final size:3
Alignment explanation
Indices: 106607--106652 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
106597 CACGATGATG
*
106607 ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
106653 ATAGAGTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:108250 original size:10 final size:10
Alignment explanation
Indices: 108235--108366 Score: 55
Period size: 10 Copynumber: 13.5 Consensus size: 10
108225 CATAAAAAAA
108235 TAAAAATTAT
1 TAAAAATTAT
*
108245 TAAAAATTAA
1 TAAAAATTAT
* *
108255 TATATA-TAT
1 TAAAAATTAT
* *
108264 ATATATATATAT
1 -TAAAAAT-TAT
108276 TAAAAA-TA-
1 TAAAAATTAT
*
108284 -AAAAAATAT
1 TAAAAATTAT
108293 T-AAAATTGA-
1 TAAAAATT-AT
*
108302 GAAATAATTAT
1 TAAA-AATTAT
108313 TAAAAATTAT
1 TAAAAATTAT
*
108323 TAAGAAATTAA
1 TAA-AAATTAT
* *
108334 TAAAAA-GAG
1 TAAAAATTAT
108343 T-AAAATTAT
1 TAAAAATTAT
* *
108352 AAAAAAATAT
1 TAAAAATTAT
108362 TAAAA
1 TAAAA
108367 TGGTAAAAAG
Statistics
Matches: 92, Mismatches: 17, Indels: 26
0.68 0.13 0.19
Matches are distributed among these distances:
7 5 0.05
8 6 0.07
9 12 0.13
10 46 0.50
11 20 0.22
12 3 0.03
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:108469 original size:21 final size:23
Alignment explanation
Indices: 108443--108487 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
108433 TAGAAAAAAT
*
108443 ATTAAA-ATTGTAAAAAA-GTTA
1 ATTAAATATTATAAAAAATGTTA
*
108464 ATTAAATTTTATAAAAAATGTTA
1 ATTAAATATTATAAAAAATGTTA
108487 A
1 A
108488 AATTTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 9 0.45
23 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (23 bp):
ATTAAATATTATAAAAAATGTTA
Found at i:110703 original size:24 final size:24
Alignment explanation
Indices: 110660--110724 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
110650 AAATGCAAAA
* *
110660 AAAAAACATAAAATAAAAAATAATC
1 AAAAAA-ATAAAATAAAAAAAAACC
* * *
110685 AAACAAATGAAATACAAAAAAACC
1 AAAAAAATAAAATAAAAAAAAACC
110709 AAAAAAATAAAATAAA
1 AAAAAAATAAAATAAA
110725 TAAAGGTGAT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 27 0.84
25 5 0.16
ACGTcount: A:0.77, C:0.09, G:0.02, T:0.12
Consensus pattern (24 bp):
AAAAAAATAAAATAAAAAAAAACC
Found at i:110876 original size:32 final size:32
Alignment explanation
Indices: 110838--110903 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
110828 AAAAATAGTC
*
110838 GGGTTTATTTTGTGAAAACAAACACTAAATGG
1 GGGTTTATTTTGAGAAAACAAACACTAAATGG
* *
110870 GGGTTTATTTTGAGAAAATAGACACTAAATGG
1 GGGTTTATTTTGAGAAAACAAACACTAAATGG
110902 GG
1 GG
110904 TAAAATTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (32 bp):
GGGTTTATTTTGAGAAAACAAACACTAAATGG
Found at i:113056 original size:101 final size:101
Alignment explanation
Indices: 112938--113180 Score: 314
Period size: 101 Copynumber: 2.4 Consensus size: 101
112928 TCAATCCAAT
* * *
112938 CCACTGCAACTTCAGGGGTATAAGATCTGATGTTGTAGCTTCATCTTGCTCCATTGCAA-CTTCA
1 CCACTGCAACTTCAGGGGTATAAGATTTGATGTTGTAGCTTCATCTTGCTCCAGT-AAATCTT-A
* *
113002 AG-GAGATAAATATTTTCTTTCATGACTTTAATCCGAC
64 AGAGAGATAAAGATTTGCTTTCATGACTTTAATCCGAC
* * * *
113039 CCACTGCAACTTCAGGGGTATAAGATTTGGT-TCTATAGCTTCATCTTGCTCTAGTAAATCTTTA
1 CCACTGCAACTTCAGGGGTATAAGATTTGATGT-TGTAGCTTCATCTTGCTCCAGTAAATCTTAA
113103 GAGAGATAAAGATTTGCTTTCATGACTTTAATCCGAC
65 GAGAGATAAAGATTTGCTTTCATGACTTTAATCCGAC
* ** *
113140 CCACTACAAC-TCAGGGGTATGGGATTTGATGTTGTAACTTC
1 CCACTGCAACTTCAGGGGTATAAGATTTGATGTTGTAGCTTC
113181 TCTCCATTCT
Statistics
Matches: 123, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
100 29 0.24
101 94 0.76
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (101 bp):
CCACTGCAACTTCAGGGGTATAAGATTTGATGTTGTAGCTTCATCTTGCTCCAGTAAATCTTAAG
AGAGATAAAGATTTGCTTTCATGACTTTAATCCGAC
Found at i:113574 original size:49 final size:49
Alignment explanation
Indices: 113544--113710 Score: 217
Period size: 49 Copynumber: 3.4 Consensus size: 49
113534 TAGGATTTGT
*
113544 CGTTGCGGCTTCAATCTTTCCCTACACATCTCTAAGGTATAAGGTTCGC
1 CGTTGCGGCTTCAATCTTTCCCTACACATCTCTAGGGTATAAGGTTCGC
* * * * *
113593 CGTTACGACTTCAACCTTTTCCTCCACATCTCTAGGGTATAAGGTTCGC
1 CGTTGCGGCTTCAATCTTTCCCTACACATCTCTAGGGTATAAGGTTCGC
* * * * *
113642 CGTTGCAGCTTTAATCTTTCCCTTCGCATCTCTAGGGTATAAGATTCGC
1 CGTTGCGGCTTCAATCTTTCCCTACACATCTCTAGGGTATAAGGTTCGC
* *
113691 CGTTGTGGCTTCAATATTTC
1 CGTTGCGGCTTCAATCTTTC
113711 ATTTTATATC
Statistics
Matches: 99, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 99 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (49 bp):
CGTTGCGGCTTCAATCTTTCCCTACACATCTCTAGGGTATAAGGTTCGC
Found at i:113631 original size:98 final size:98
Alignment explanation
Indices: 113516--113694 Score: 245
Period size: 98 Copynumber: 1.8 Consensus size: 98
113506 CAATTTGCTT
* * * *
113516 CTCCTCATCTTCTGGGTAT-AGGATTTGTCGTTGCGGCTTCAATCTTTCCCTACACATCTCTAAG
1 CTCCACATCTTCTGGGTATAAGG-TTCGCCGTTGCAGCTTCAATCTTTCCCTACACATCTCTAAG
*
113580 GTATAAGGTTCGCCGTTACGACTTCAACCTTTTC
65 GTATAAGATTCGCCGTTACGACTTCAACCTTTTC
* * * *
113614 CTCCACATC-TCTAGGGTATAAGGTTCGCCGTTGCAGCTTTAATCTTTCCCTTCGCATCTCTAGG
1 CTCCACATCTTCT-GGGTATAAGGTTCGCCGTTGCAGCTTCAATCTTTCCCTACACATCTCTAAG
113678 GTATAAGATTCGCCGTT
65 GTATAAGATTCGCCGTT
113695 GTGGCTTCAA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
97 3 0.04
98 64 0.91
99 3 0.04
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (98 bp):
CTCCACATCTTCTGGGTATAAGGTTCGCCGTTGCAGCTTCAATCTTTCCCTACACATCTCTAAGG
TATAAGATTCGCCGTTACGACTTCAACCTTTTC
Found at i:114448 original size:113 final size:113
Alignment explanation
Indices: 114134--114441 Score: 390
Period size: 113 Copynumber: 2.7 Consensus size: 113
114124 CTAACCACTA
* * *
114134 TTTCAATGCAAAAATGCTTGAACAGGATTGTAAAGTGGATAAAATTAAATTTTATTGGAGGCAAA
1 TTTCAATGCAAAAATGCTTGAACAGGGTTCTAAAGTGGATAAAATTGAATTTTATTGGAGGCAAA
*
114199 GTTCGCATGAATGAAAAGATTAAAAAATCATTGATCCACTAACCGTAAT
66 GCTCGCATGAATGAAAAGATT-AAAAATCATTGATCCACTAACCGTAAT
* *
114248 TTT-GATGCAAAAATGCTTGAACAGGG-TC-ACAAGGTGAATAAAATTGAATTTTATTGGAGGCA
1 TTTCAATGCAAAAATGCTTGAACAGGGTTCTA-AA-GTGGATAAAATTGAATTTTATTGGAGGCA
* * * * *
114310 AAGCTCGCGTGAATGATAAGATTAAAAATTATT-AGTCCACTAATCGTTAT
64 AAGCTCGCATGAATGAAAAGATTAAAAATCATTGA-TCCACTAACCGTAAT
** * * *
114360 TTTCAATGCAAACGTGCTTAAACAGGGTTCTAATGTGGATAAAATTGAATTTTATTGGAGGTAAA
1 TTTCAATGCAAAAATGCTTGAACAGGGTTCTAAAGTGGATAAAATTGAATTTTATTGGAGGCAAA
* *
114425 ACTCGCATAAATGAAAA
66 GCTCGCATGAATGAAAA
114442 TGTTAAAGGT
Statistics
Matches: 166, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
111 2 0.01
112 28 0.17
113 129 0.78
114 6 0.04
115 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (113 bp):
TTTCAATGCAAAAATGCTTGAACAGGGTTCTAAAGTGGATAAAATTGAATTTTATTGGAGGCAAA
GCTCGCATGAATGAAAAGATTAAAAATCATTGATCCACTAACCGTAAT
Found at i:119302 original size:31 final size:31
Alignment explanation
Indices: 119267--119334 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
119257 ATAAAAATAG
* *
119267 TGGGGTTTATTTTGTGAAAACGGACACTAAA
1 TGGGGTTTATTTTGAGAAAACAGACACTAAA
*
119298 TGGGGTTTATTTTGAGAAAATAGACACTAAA
1 TGGGGTTTATTTTGAGAAAACAGACACTAAA
*
119329 TTGGGT
1 TGGGGT
119335 AAAATTAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.32, C:0.07, G:0.26, T:0.34
Consensus pattern (31 bp):
TGGGGTTTATTTTGAGAAAACAGACACTAAA
Found at i:120622 original size:17 final size:19
Alignment explanation
Indices: 120600--120641 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
120590 AAATTAAAAG
*
120600 TTTATTTTA-TTATTTGT-
1 TTTATTTTATTTATTTATA
120617 TTTA-TTTATTTATTTATA
1 TTTATTTTATTTATTTATA
120635 TTTATTT
1 TTTATTT
120642 AACAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 11 0.52
18 4 0.19
19 2 0.10
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTATTTTATTTATTTATA
Found at i:120627 original size:13 final size:13
Alignment explanation
Indices: 120600--120642 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 13
120590 AAATTAAAAG
120600 TTTATTTTA-TTA
1 TTTATTTTATTTA
*
120612 TTTGTTTTATTTA
1 TTTATTTTATTTA
120625 TTTATTTATATTTA
1 TTTATTT-TATTTA
120639 TTTA
1 TTTA
120643 ACAATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 8 0.30
13 9 0.33
14 10 0.37
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:127568 original size:16 final size:16
Alignment explanation
Indices: 127544--127575 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
127534 TCCTTACAAA
*
127544 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
127560 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
127576 AAAAATCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:132018 original size:28 final size:28
Alignment explanation
Indices: 131974--132166 Score: 206
Period size: 28 Copynumber: 6.9 Consensus size: 28
131964 CAAAATAATT
* * *
131974 CTCTACCCAAGCTAAAAATAGAGTAACG
1 CTCTACCCGAGCCAAAAATAGAATAACG
* * **
132002 CTTTACCCAAGCCAAAAACGGAATAACG
1 CTCTACCCGAGCCAAAAATAGAATAACG
* * *
132030 TTTTACCCGAGCCAAAAATAGAATAACA
1 CTCTACCCGAGCCAAAAATAGAATAACG
* * *
132058 CTCTACCTGAGCCCAAAATAGAATAATG
1 CTCTACCCGAGCCAAAAATAGAATAACG
* *
132086 CTCTACCCGAGTCAAAAACAGAATAACG
1 CTCTACCCGAGCCAAAAATAGAATAACG
**
132114 CTCTACTTGAGCCAAAAATAGAATAACG
1 CTCTACCCGAGCCAAAAATAGAATAACG
* * *
132142 CTCTACGCGAGCCAGAAACAGAATA
1 CTCTACCCGAGCCAAAAATAGAATA
132167 GTTATTAAGC
Statistics
Matches: 136, Mismatches: 29, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 136 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.18
Consensus pattern (28 bp):
CTCTACCCGAGCCAAAAATAGAATAACG
Found at i:132055 original size:84 final size:84
Alignment explanation
Indices: 131929--132166 Score: 217
Period size: 84 Copynumber: 2.8 Consensus size: 84
131919 TTATTCGAGC
* * ** * * ** *
131929 CCAAATACAGAATAACACTCTTTCCGAG-CAAGAAACAAAATAATTCTCTACCCAAGCTAAAAAT
1 CCAAAAACAGAATAACGCTCTACCCGAGCCAA-AAATAGAATAACACTCTACCCAAGCCAAAAAT
* *
131993 AGAGTAACGCTTTACCCAAG
65 AGAATAACGCTCTACCCAAG
* * * ** *
132013 CCAAAAACGGAATAACGTTTTACCCGAGCCAAAAATAGAATAACACTCTACCTGAGCCCAAAATA
1 CCAAAAACAGAATAACGCTCTACCCGAGCCAAAAATAGAATAACACTCTACCCAAGCCAAAAATA
* *
132078 GAATAATGCTCTACCCGAG
66 GAATAACGCTCTACCCAAG
* ** * * * * *
132097 TCAAAAACAGAATAACGCTCTACTTGAGCCAAAAATAGAATAACGCTCTACGCGAGCCAGAAACA
1 CCAAAAACAGAATAACGCTCTACCCGAGCCAAAAATAGAATAACACTCTACCCAAGCCAAAAATA
132162 GAATA
66 GAATA
132167 GTTATTAAGC
Statistics
Matches: 122, Mismatches: 31, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
84 119 0.98
85 3 0.02
ACGTcount: A:0.44, C:0.25, G:0.13, T:0.18
Consensus pattern (84 bp):
CCAAAAACAGAATAACGCTCTACCCGAGCCAAAAATAGAATAACACTCTACCCAAGCCAAAAATA
GAATAACGCTCTACCCAAG
Found at i:134330 original size:30 final size:30
Alignment explanation
Indices: 134294--134369 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 30
134284 TTATTGAAAA
134294 GTGGAAGCCTTTGTGGCTGTTCTCTGA-TAT
1 GTGGAAGCCTTTGTGGCTGTTCTCT-ATTAT
*
134324 GTGGAAGCCTTTAG-GGTTGTTCTCTATTAT
1 GTGGAAGCCTTT-GTGGCTGTTCTCTATTAT
*
134354 ATGTG-AGCCTTTGTGG
1 GTG-GAAGCCTTTGTGG
134370 TGAAGGCTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 2 0.05
30 36 0.90
31 2 0.05
ACGTcount: A:0.14, C:0.14, G:0.30, T:0.41
Consensus pattern (30 bp):
GTGGAAGCCTTTGTGGCTGTTCTCTATTAT
Found at i:134626 original size:29 final size:30
Alignment explanation
Indices: 134541--134641 Score: 106
Period size: 29 Copynumber: 3.6 Consensus size: 30
134531 GTTTGGATGT
*
134541 CTTTGTGGATATCTAATGTTATGTGGACGC
1 CTTTGTGGCTATCTAATGTTATGTGGACGC
* * *
134571 C--T-T--CTACCTAATATTATGTGGATGC
1 CTTTGTGGCTATCTAATGTTATGTGGACGC
134596 CTTTGTGGCTATCTAA-GTTATGTGGACGC
1 CTTTGTGGCTATCTAATGTTATGTGGACGC
**
134625 CTTCATGGCTATCTAAT
1 CTTTGTGGCTATCTAAT
134642 TTTCAAGGAT
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
25 19 0.34
27 2 0.04
28 2 0.04
29 25 0.45
30 8 0.14
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (30 bp):
CTTTGTGGCTATCTAATGTTATGTGGACGC
Found at i:144786 original size:37 final size:37
Alignment explanation
Indices: 144737--144882 Score: 179
Period size: 37 Copynumber: 4.0 Consensus size: 37
144727 AATTACTTTG
* * * *
144737 ATGG-AGGCTTACGTCTAGGTTAAAGCGTAATGCTAT
1 ATGGAAGGCTTACGTCTCGATTAGAGCATAATGCTAT
*
144773 ATGGAAGGCTTACGTCTCGATTAGAGCATAATGTTAT
1 ATGGAAGGCTTACGTCTCGATTAGAGCATAATGCTAT
* * *
144810 ATGGAAAGCTTACATCTCGATTAGAGCATAATGTTAT
1 ATGGAAGGCTTACGTCTCGATTAGAGCATAATGCTAT
* * *
144847 ATGGAA-GCTTACGTCTTGGTTAGAGCGTAATGCTAT
1 ATGGAAGGCTTACGTCTCGATTAGAGCATAATGCTAT
144883 GTGATTTGCT
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
36 29 0.30
37 68 0.70
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (37 bp):
ATGGAAGGCTTACGTCTCGATTAGAGCATAATGCTAT
Found at i:144871 original size:73 final size:73
Alignment explanation
Indices: 144764--144918 Score: 188
Period size: 73 Copynumber: 2.1 Consensus size: 73
144754 GGTTAAAGCG
*
144764 TAATGCTATATGGAAGGCTTACGTCTCGATTAGAGCATAATGTTATATGGA-AAGCTTACATCTC
1 TAATGCTATATGGAAGGCTTACGTCTCGATTAGAGCATAATGCTATAT-GATAAGC-TACATCTC
144828 GATTAGAGCA
64 GATTAGAGCA
* * * * * ** *
144838 TAATGTTATATGGAA-GCTTACGTCTTGGTTAGAGCGTAATGCTATGTGATTTGCTACATCTCGG
1 TAATGCTATATGGAAGGCTTACGTCTCGATTAGAGCATAATGCTATATGATAAGCTACATCTCGA
144902 TTAGAGCA
66 TTAGAGCA
*
144910 TAATTCTAT
1 TAATGCTAT
144919 GTGATCTGCT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
72 26 0.38
73 29 0.42
74 14 0.20
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (73 bp):
TAATGCTATATGGAAGGCTTACGTCTCGATTAGAGCATAATGCTATATGATAAGCTACATCTCGA
TTAGAGCA
Found at i:144943 original size:109 final size:110
Alignment explanation
Indices: 144737--144949 Score: 254
Period size: 109 Copynumber: 1.9 Consensus size: 110
144727 AATTACTTTG
* *
144737 ATGGAGGCTTACGTCTAGGTTAAAGCGTAATGCTATATGGAAGGCTTACGTCTCGATTAGAGCAT
1 ATGGAAGCTTACGTCTAGGTTAAAGCGTAATGCTATATGGAAGGCTTACATCTCGATTAGAGCAT
*
144802 AATGTTATATGGAAAGCTTACATCTCGATTAGAGCATAATGTTAT
66 AATGTTATATGGAAAGCTTACATCTCAATTAGAGCATAATGTTAT
* * * ** *
144847 ATGGAAGCTTACGTCTTGGTTAGAGCGTAATGCTATGT-GATTTGC-TACATCTCGGTTAGAGCA
1 ATGGAAGCTTACGTCTAGGTTAAAGCGTAATGCTATATGGA-AGGCTTACATCTCGATTAGAGCA
* ** *
144910 TAA--TTCTATGTGATCTGCTTATATCTCAATTAGAGCATAA
65 TAATGTTATATG-GA-AAGCTTACATCTCAATTAGAGCATAA
144950 GGCCATTTCA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
107 6 0.07
108 2 0.02
109 43 0.49
110 36 0.41
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34
Consensus pattern (110 bp):
ATGGAAGCTTACGTCTAGGTTAAAGCGTAATGCTATATGGAAGGCTTACATCTCGATTAGAGCAT
AATGTTATATGGAAAGCTTACATCTCAATTAGAGCATAATGTTAT
Found at i:144944 original size:37 final size:36
Alignment explanation
Indices: 144866--144949 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 36
144856 TACGTCTTGG
* * **
144866 TTAGAGCGTAATGCTATGTGATTTGCTACATCTCGG
1 TTAGAGCATAATGCTATGTGATCTGCTACATCTCAA
* *
144902 TTAGAGCATAATTCTATGTGATCTGCTTATATCTCAA
1 TTAGAGCATAATGCTATGTGATCTGC-TACATCTCAA
144939 TTAGAGCATAA
1 TTAGAGCATAA
144950 GGCCATTTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
36 23 0.56
37 18 0.44
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (36 bp):
TTAGAGCATAATGCTATGTGATCTGCTACATCTCAA
Found at i:147683 original size:26 final size:26
Alignment explanation
Indices: 147654--147752 Score: 94
Period size: 26 Copynumber: 3.8 Consensus size: 26
147644 CACTGTATTA
147654 GCTCGAAAGAGTGATATACTGAACTG
1 GCTCGAAAGAGTGATATACTGAACTG
* *
147680 GCTC-ATAAGAGTGTTATACTGTACTG
1 GCTCGA-AAGAGTGATATACTGAACTG
* * *
147706 GCTCAAAAGA-TCGATATTCTGAACAG
1 GCTCGAAAGAGT-GATATACTGAACTG
* * *
147732 GCTCGTAAGAGCGTTATACTG
1 GCTCGAAAGAGTGATATACTG
147753 TACCGAGAGC
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
25 2 0.03
26 55 0.95
27 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (26 bp):
GCTCGAAAGAGTGATATACTGAACTG
Found at i:147715 original size:52 final size:52
Alignment explanation
Indices: 147645--147755 Score: 143
Period size: 52 Copynumber: 2.1 Consensus size: 52
147635 TTGAAGATAC
* * * *
147645 ACTGTATTAGCTCGAAAGAGT-GATATACTGAACTGGCTCATAAGAGTGTTAT
1 ACTGTACTAGCTCAAAAGA-TCGATATACTGAACAGGCTCATAAGAGCGTTAT
* * *
147697 ACTGTACTGGCTCAAAAGATCGATATTCTGAACAGGCTCGTAAGAGCGTTAT
1 ACTGTACTAGCTCAAAAGATCGATATACTGAACAGGCTCATAAGAGCGTTAT
147749 ACTGTAC
1 ACTGTAC
147756 CGAGAGCGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 1 0.02
52 50 0.98
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.29
Consensus pattern (52 bp):
ACTGTACTAGCTCAAAAGATCGATATACTGAACAGGCTCATAAGAGCGTTAT
Found at i:147870 original size:35 final size:37
Alignment explanation
Indices: 147803--147885 Score: 116
Period size: 35 Copynumber: 2.3 Consensus size: 37
147793 TACTAACTGG
*
147803 GCTCGTATGAGCTAAAATTTACTAGGAGACTTGAAGA
1 GCTCGTATGAGCTAAAATTTACTAGGAAACTTGAAGA
*
147840 GCTCGTATGAGCT-AAA-TTACTGGGAAACTTGAAGA
1 GCTCGTATGAGCTAAAATTTACTAGGAAACTTGAAGA
* *
147875 GATCGTTTGAG
1 GCTCGTATGAG
147886 ATACGAATGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 26 0.62
36 3 0.07
37 13 0.31
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.28
Consensus pattern (37 bp):
GCTCGTATGAGCTAAAATTTACTAGGAAACTTGAAGA
Found at i:149982 original size:19 final size:19
Alignment explanation
Indices: 149958--150010 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
149948 GAACCAAGCC
* *
149958 CGACCCTAACCCTTTGACT
1 CGACCCAAACCCGTTGACT
*
149977 CGACCCAAACCCGTTGACC
1 CGACCCAAACCCGTTGACT
* *
149996 CAACTCAAACCCGTT
1 CGACCCAAACCCGTT
150011 AACCATTGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.26, C:0.43, G:0.11, T:0.19
Consensus pattern (19 bp):
CGACCCAAACCCGTTGACT
Found at i:174166 original size:16 final size:16
Alignment explanation
Indices: 174147--174180 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
174137 TTTTTATTTT
174147 ATTTTAACTTAGATTA
1 ATTTTAACTTAGATTA
**
174163 ATTTTAGTTTAGATTA
1 ATTTTAACTTAGATTA
174179 AT
1 AT
174181 ATTCATCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (16 bp):
ATTTTAACTTAGATTA
Found at i:176090 original size:27 final size:28
Alignment explanation
Indices: 176060--176139 Score: 110
Period size: 27 Copynumber: 2.9 Consensus size: 28
176050 AGTCCATTTA
*
176060 GAGTATGCCATAAAGGTTGTTCTTTC-T
1 GAGTATGCCACAAAGGTTGTTCTTTCAT
* * *
176087 GAGTACGCTACAAATGTTGTTCTTTCAT
1 GAGTATGCCACAAAGGTTGTTCTTTCAT
176115 -AGTATGCCACAAAGGTTGTTCTTTC
1 GAGTATGCCACAAAGGTTGTTCTTTC
176140 CTGACGTGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 44 0.98
28 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (28 bp):
GAGTATGCCACAAAGGTTGTTCTTTCAT
Found at i:182799 original size:137 final size:136
Alignment explanation
Indices: 182477--182897 Score: 630
Period size: 138 Copynumber: 3.1 Consensus size: 136
182467 GTGAATATAG
**
182477 ATATAATTAATATATGAATTTGATTCATACAAAATATTAACAGTATATATTTTACTAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAC-AAATTTATT
182542 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGACATTAATATTCTTT
65 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGA-ATTAATATTCTTT
*
182607 TGGAAAAA
129 TGGAAAGA
* *
182615 ATATAATTAATATATTAATTTGATTCAAACAAAATATTAATTGTATATATTTTACAAGATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAA-ATTTATT
* *
182680 AAT-TAAA-ATAGTTATATTAATTAATGTCGGTCAAAATATAAAAGAAATGGAATTAATATTCTT
65 AATATAAACA-A-TTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAATTAATATTCTT
182743 TTGGAAAGA
128 TTGGAAAGA
* *
182752 ATATAATTAATATATGAATTAGATTCATACAAAATATTAATTGTATATATTTTACAAAATGTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAC-AAATTTATT
* ** * *
182817 CATATAAACAATTATATTAATTAATTTTAGTCAAAATATACAAGACATGAAAATTAATATTCTTT
65 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATG-GAATTAATATTCTTT
*
182882 TGCAAAGA
129 TGGAAAGA
182890 ATATAATT
1 ATATAATT
182898 CCCTTTTCTA
Statistics
Matches: 257, Mismatches: 19, Indels: 14
0.89 0.07 0.05
Matches are distributed among these distances:
136 1 0.00
137 120 0.47
138 135 0.53
139 1 0.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (136 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAAATTTATTA
ATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAATTAATATTCTTTTG
GAAAGA
Found at i:182964 original size:75 final size:75
Alignment explanation
Indices: 182873--183019 Score: 197
Period size: 75 Copynumber: 2.0 Consensus size: 75
182863 ATGAAAATTA
* * * *
182873 ATATTCTTTTGCAAAGAATATAATTCCCTTTTCTAACTTTCCATTT-TCATTTTGTATTAATAAG
1 ATATTCTTTTGCAAAGAATATAATTCACTTTTCTAACTTTCCATTTGACATCTT-TATTAATAAA
*
182937 GGAATAATTTT
65 AGAATAATTTT
* * * *
182948 ATATTCTTTTGGAAAGAATATAATTCATTTTTTTAACTTTTCATTTGACATCTTTATTAATAAAA
1 ATATTCTTTTGCAAAGAATATAATTCACTTTTCTAACTTTCCATTTGACATCTTTATTAATAAAA
183013 GAATAAT
66 GAATAAT
183020 CCTGATTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
75 57 0.92
76 5 0.08
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (75 bp):
ATATTCTTTTGCAAAGAATATAATTCACTTTTCTAACTTTCCATTTGACATCTTTATTAATAAAA
GAATAATTTT
Found at i:186071 original size:37 final size:37
Alignment explanation
Indices: 186030--186125 Score: 113
Period size: 37 Copynumber: 2.6 Consensus size: 37
186020 TTTAATCCAG
* * *
186030 AATTGCGCCC-AAACATGTCGCTACATGAGTACTTCTA
1 AATTGCACCCAAAAC-TATCGCCACATGAGTACTTCTA
186067 AATTGCACCCAAAACTATCGCCACATGAGTACTTCTA
1 AATTGCACCCAAAACTATCGCCACATGAGTACTTCTA
* * * *
186104 GATTTCACCCAACACTGTCGCC
1 AATTGCACCCAAAACTATCGCC
186126 GTAAGAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
37 47 0.92
38 4 0.08
ACGTcount: A:0.30, C:0.31, G:0.14, T:0.25
Consensus pattern (37 bp):
AATTGCACCCAAAACTATCGCCACATGAGTACTTCTA
Found at i:190748 original size:37 final size:37
Alignment explanation
Indices: 190707--190806 Score: 101
Period size: 37 Copynumber: 2.7 Consensus size: 37
190697 CATGTCGCTA
* *
190707 CATGAGTACTTCTAGATTGCACCCAAAACTATCGCCG
1 CATGAGTAATTCCAGATTGCACCCAAAACTATCGCCG
* * * * *
190744 CATGAGCAATTCCAAATTTCACCCAAAATTGTCGCCG
1 CATGAGTAATTCCAGATTGCACCCAAAACTATCGCCG
* * * *
190781 CAAGAGTATTTCCGGAATGCACCCAA
1 CATGAGTAATTCCAGATTGCACCCAA
190807 TACTGTCACT
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (37 bp):
CATGAGTAATTCCAGATTGCACCCAAAACTATCGCCG
Found at i:190866 original size:38 final size:38
Alignment explanation
Indices: 190798--190914 Score: 191
Period size: 38 Copynumber: 3.1 Consensus size: 38
190788 ATTTCCGGAA
* * * *
190798 TGCACCCAATACTGTCACTGCATAAATATTCTTCAAAT
1 TGCATCCAAAACTATCACTGCATAAGTATTCTTCAAAT
190836 TGCATCCAAAACTATCACTGCATAAGTATTCTTCAAAT
1 TGCATCCAAAACTATCACTGCATAAGTATTCTTCAAAT
190874 TGCATCCAAAACTATCACTGCATAAGTATTCTTC-AAT
1 TGCATCCAAAACTATCACTGCATAAGTATTCTTCAAAT
190911 TGCA
1 TGCA
190915 CCCAGGAATG
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
37 7 0.09
38 68 0.91
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.32
Consensus pattern (38 bp):
TGCATCCAAAACTATCACTGCATAAGTATTCTTCAAAT
Found at i:201055 original size:138 final size:138
Alignment explanation
Indices: 200807--201227 Score: 682
Period size: 138 Copynumber: 3.1 Consensus size: 138
200797 GAGAACATAG
* * * * **
200807 ATATAATAAATATATGAATTTGATTCATATAAATTATTAATAGTATATATTTTACTAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* * * *
200872 AATATAAATAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAAATATTATTCTTT
66 AATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
200937 TGGAAAGA
131 TGGAAAGA
* *
200945 ATATAATTAATATCTGAATTTGATTCCTACAAAATATTAATTGTATATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
*
201010 AATATAAATAGTTATATTAGTTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
66 AATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
*
201075 TGGAATGA
131 TGGAAAGA
*
201083 ATATAATCAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
* *
201148 AATATAAAT-GTTATATTAATTAATTTCGGTCAAAAAATAAAATACATGGAAATTAATATTCTTT
66 AATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
201212 TGGAAAGA
131 TGGAAAGA
201220 ATATAATT
1 ATATAATT
201228 CCTTTTTTCT
Statistics
Matches: 261, Mismatches: 22, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
137 66 0.25
138 195 0.75
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
AATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
TGGAAAGA
Found at i:201339 original size:75 final size:76
Alignment explanation
Indices: 201203--201350 Score: 228
Period size: 75 Copynumber: 2.0 Consensus size: 76
201193 ATGGAAATTA
* * *
201203 ATATTCTTTTGGAAAGAATATAATTCCTTTTTTCTAACTTTCCATTTGTCTTCTTTAATAATAAG
1 ATATTCTTTTGAAAAGAATATAATTCCATTTTTCTAACTTTCCATTTGTCTTCTCTAATAATAAG
201268 GAAATAATTCT
66 GAAATAATTCT
*
201279 ATATTCTTTTGAAAAGAATATAATT-CATTTTTCTAACTTTTCATTT-TCCTTCTCTAATAATAA
1 ATATTCTTTTGAAAAGAATATAATTCCATTTTTCTAACTTTCCATTTGT-CTTCTCTAATAATAA
*
201342 GGGAATAAT
65 GGAAATAAT
201351 CATGATTTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
74 1 0.02
75 41 0.62
76 24 0.36
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (76 bp):
ATATTCTTTTGAAAAGAATATAATTCCATTTTTCTAACTTTCCATTTGTCTTCTCTAATAATAAG
GAAATAATTCT
Found at i:205509 original size:58 final size:59
Alignment explanation
Indices: 205419--205534 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 59
205409 TAAGGCATAC
205419 TTCTATTTGATTAAATGATACAATATAAAAATAATGTGTA-AAAAATATTCAAAATAAT
1 TTCTATTTGATTAAATGATACAATATAAAAATAATGTGTACAAAAATATTCAAAATAAT
*
205477 TTCTATTTTATTAAATGATACAATATAAAAATAATGTGTACAAAAATATTCAAAATAA
1 TTCTATTTGATTAAATGATACAATATAAAAATAATGTGTACAAAAATATTCAAAATAA
205535 CATCAATGCA
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 39 0.70
59 17 0.30
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (59 bp):
TTCTATTTGATTAAATGATACAATATAAAAATAATGTGTACAAAAATATTCAAAATAAT
Found at i:206668 original size:25 final size:23
Alignment explanation
Indices: 206635--206692 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
206625 GTCTCCCCCT
*
206635 TTATGTCTCATTCCATCTCACCTCC
1 TTATTTCTCATT-C-TCTCACCTCC
* *
206660 TTATTTCTCCTTCTCTCACCTTC
1 TTATTTCTCATTCTCTCACCTCC
206683 TCTATTTCTC
1 T-TATTTCTC
206693 CATTTTAGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.34
24 9 0.31
25 10 0.34
ACGTcount: A:0.12, C:0.38, G:0.02, T:0.48
Consensus pattern (23 bp):
TTATTTCTCATTCTCTCACCTCC
Found at i:213795 original size:19 final size:20
Alignment explanation
Indices: 213771--213815 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
213761 AATTATAAAA
* * *
213771 AAAAATTAAATTAAATTA-T
1 AAAAATGAAATAAAAATATT
213790 AAAAATGAAATAAAAATATT
1 AAAAATGAAATAAAAATATT
213810 AAAAAT
1 AAAAAT
213816 ATTTTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAATGAAATAAAAATATT
Found at i:213806 original size:20 final size:20
Alignment explanation
Indices: 213756--213816 Score: 54
Period size: 23 Copynumber: 2.9 Consensus size: 20
213746 ATCTTTTCAC
213756 ATAAAAATTATAAAAA-AAA
1 ATAAAAATTATAAAAATAAA
*
213775 ATTAAATTAAATTATAAAAATGAA
1 A-T-AA--AAATTATAAAAATAAA
213799 ATAAAAA-TATTAAAAATA
1 ATAAAAATTA-TAAAAATA
213817 TTTTAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
19 3 0.09
20 11 0.32
21 2 0.06
22 2 0.06
23 13 0.38
24 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (20 bp):
ATAAAAATTATAAAAATAAA
Found at i:222540 original size:28 final size:25
Alignment explanation
Indices: 222508--222578 Score: 88
Period size: 25 Copynumber: 2.7 Consensus size: 25
222498 TCAATAACTT
*
222508 ATTCAAAGCCACTACTTTTGTTGGTTGA
1 ATTCAAA-CC-CTAC-TTCGTTGGTTGA
*
222536 ATTCAAACCTTACTTCGTTGGTTGA
1 ATTCAAACCCTACTTCGTTGGTTGA
*
222561 ATTCAAACCTTACTTCGT
1 ATTCAAACCCTACTTCGT
222579 GAGGAAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
25 29 0.71
26 3 0.07
27 2 0.05
28 7 0.17
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (25 bp):
ATTCAAACCCTACTTCGTTGGTTGA
Found at i:222558 original size:25 final size:25
Alignment explanation
Indices: 222527--222578 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
222517 CACTACTTTT
222527 GTTGGTTGAATTCAAACCTTACTTC
1 GTTGGTTGAATTCAAACCTTACTTC
222552 GTTGGTTGAATTCAAACCTTACTTC
1 GTTGGTTGAATTCAAACCTTACTTC
222577 GT
1 GT
222579 GAGGAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (25 bp):
GTTGGTTGAATTCAAACCTTACTTC
Found at i:225355 original size:18 final size:17
Alignment explanation
Indices: 225326--225412 Score: 62
Period size: 16 Copynumber: 5.3 Consensus size: 17
225316 TTCTTTTTTT
*
225326 AATTGTAATTAATTTAA
1 AATTTTAATTAATTTAA
225343 AATTTTCAATTAA-TT-A
1 AATTTT-AATTAATTTAA
225359 AATTTT--TTAGATTTTAA
1 AATTTTAATTA-A-TTTAA
225376 AATTTTTAATTAA-TT-A
1 AA-TTTTAATTAATTTAA
* *
225392 AA-TTTATTTAATTAAA
1 AATTTTAATTAATTTAA
225408 AATTT
1 AATTT
225413 ATTCTCATCC
Statistics
Matches: 56, Mismatches: 3, Indels: 22
0.69 0.04 0.27
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
15 1 0.02
16 15 0.27
17 14 0.25
18 10 0.18
19 1 0.02
20 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
AATTTTAATTAATTTAA
Found at i:225363 original size:16 final size:17
Alignment explanation
Indices: 225331--225406 Score: 84
Period size: 18 Copynumber: 4.4 Consensus size: 17
225321 TTTTTAATTG
225331 TAATTAATTTAAAATTTT
1 TAATTAA-TTAAAATTTT
* *
225349 CAATTAATTAAATTTTT
1 TAATTAATTAAAATTTT
225366 TAGATT--TTAAAATTTT
1 TA-ATTAATTAAAATTTT
*
225382 TAATTAATTAAATTTATT
1 TAATTAATTAAAATT-TT
225400 TAATTAA
1 TAATTAA
225407 AAATTTATTC
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
15 3 0.06
16 11 0.22
17 17 0.35
18 18 0.37
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
TAATTAATTAAAATTTT
Found at i:225375 original size:33 final size:34
Alignment explanation
Indices: 225338--225401 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 34
225328 TTGTAATTAA
225338 TTTAAAATTTTCAATTAATTAAATTT-TTTAGAT
1 TTTAAAATTTTCAATTAATTAAATTTATTTAGAT
*
225371 TTTAAAATTTTTAATTAATTAAATTTATTTA
1 TTTAAAATTTTCAATTAATTAAATTTATTTA
225402 ATTAAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (34 bp):
TTTAAAATTTTCAATTAATTAAATTTATTTAGAT
Found at i:225746 original size:21 final size:20
Alignment explanation
Indices: 225721--225768 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
225711 AATATATGAT
225721 TATATTTTAAAAAATAAAATA
1 TATATTTT-AAAAATAAAATA
* *
225742 TATATCTTAAAATTAAAATA
1 TATATTTTAAAAATAAAATA
225762 T-TATTTT
1 TATATTTT
225769 TATCATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 5 0.21
20 12 0.50
21 7 0.29
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TATATTTTAAAAATAAAATA
Found at i:229418 original size:11 final size:12
Alignment explanation
Indices: 229402--229431 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
229392 GGTTGGTGGT
229402 TGCTTGA-TTCA
1 TGCTTGATTTCA
229413 TGCTTGATTTCA
1 TGCTTGATTTCA
229425 TGCTTGA
1 TGCTTGA
229432 ATAATGCACG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.47
Consensus pattern (12 bp):
TGCTTGATTTCA
Found at i:241036 original size:21 final size:19
Alignment explanation
Indices: 240994--241037 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
240984 AAAAAATCTG
240994 AAAAAGAAAACAATTAGAA
1 AAAAAGAAAACAATTAGAA
* *
241013 AAAAATAATAACAGATTAGTA
1 AAAAAGAA-AACA-ATTAGAA
241034 AAAA
1 AAAA
241038 TAAAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 4 0.19
21 10 0.48
ACGTcount: A:0.70, C:0.05, G:0.09, T:0.16
Consensus pattern (19 bp):
AAAAAGAAAACAATTAGAA
Found at i:241047 original size:17 final size:18
Alignment explanation
Indices: 240994--241052 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 18
240984 AAAAAATCTG
* *
240994 AAAAAGAAAACAATTAGAA
1 AAAAATAAAACAATTAG-T
241013 AAAAATAATAACAGATTAGT
1 AAAAATAA-AACA-ATTAGT
241033 AAAAATAAAA-AATTAAGT
1 AAAAATAAAACAATT-AGT
241051 AA
1 AA
241053 GTAAAATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
17 3 0.09
18 6 0.17
19 9 0.26
20 12 0.34
21 5 0.14
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.19
Consensus pattern (18 bp):
AAAAATAAAACAATTAGT
Found at i:246292 original size:16 final size:16
Alignment explanation
Indices: 246271--246308 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
246261 CTTCCTCTAA
246271 TCTCTCT-TC-GTCTC
1 TCTCTCTCTCTGTCTC
246285 TCTCTCTCTCTGTCTC
1 TCTCTCTCTCTGTCTC
*
246301 TCGCTCTC
1 TCTCTCTC
246309 CCCCCCTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 2 0.10
16 12 0.57
ACGTcount: A:0.00, C:0.45, G:0.08, T:0.47
Consensus pattern (16 bp):
TCTCTCTCTCTGTCTC
Found at i:251095 original size:18 final size:18
Alignment explanation
Indices: 251061--251095 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
251051 CTTCCTCATA
* *
251061 TTTCTCTCTCTCTCTCTT
1 TTTCTCTCTCCCCCTCTT
251079 TTTCTCTCTCCCCCTCT
1 TTTCTCTCTCCCCCTCT
251096 CTCTCCCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTCTCTCTCCCCCTCTT
Found at i:261550 original size:7 final size:7
Alignment explanation
Indices: 261540--261574 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
261530 TGCAAACACT
261540 AAAACAA
1 AAAACAA
261547 AAAACAA
1 AAAACAA
261554 AAAACAA
1 AAAACAA
261561 AAAACAA
1 AAAACAA
261568 AAAACAA
1 AAAACAA
261575 CCTTAAACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAACAA
Found at i:261735 original size:19 final size:19
Alignment explanation
Indices: 261708--261748 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
261698 AGGTTGAAGC
* *
261708 AAAAGTAGAAGTAGCCAGA
1 AAAACTAGAACTAGCCAGA
*
261727 AAAACTAGATCTAGCCAGA
1 AAAACTAGAACTAGCCAGA
261746 AAA
1 AAA
261749 GTGAAGTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.54, C:0.15, G:0.20, T:0.12
Consensus pattern (19 bp):
AAAACTAGAACTAGCCAGA
Found at i:272405 original size:112 final size:112
Alignment explanation
Indices: 272200--272417 Score: 259
Period size: 112 Copynumber: 1.9 Consensus size: 112
272190 TCGTCGAATG
* *
272200 ATAGCTCGGTTAGAGCTTCGATATGCTTACGTCTCTGTTAGAGAGTAATGCTATGTATACCTCTA
1 ATAGCTCGGGTAGAGCTTCGATATGCTTACGTCTCTGTTAGAGAGTAATGCTATGTATACCTCGA
272265 TTAGAGCTTTGAATTGCTTATGAATCGGTTAGAA-CATAAAGATATAT
66 TTAGAGCTTTGAATTGCTTATGAATCGGTTA-AAGCATAAAGATATAT
* * *
272312 ATAGCTCGGGTAGAGCTATGGA-ATGCTTACGT-TTTGGTTAGAGCA-TAATGCTATGTATAGCT
1 ATAGCTCGGGTAGAGCT-TCGATATGCTTACGTCTCT-GTTAGAG-AGTAATGCTATGTATACCT
* * **
272374 CGATTATAGCTTTG-TTCTGCTTACT-TCTCGGTTAAAGCATAAAG
63 CGATTAGAGCTTTGAAT-TGCTTA-TGAATCGGTTAAAGCATAAAG
272418 CTAATTCAAT
Statistics
Matches: 91, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
111 5 0.05
112 81 0.89
113 5 0.05
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.36
Consensus pattern (112 bp):
ATAGCTCGGGTAGAGCTTCGATATGCTTACGTCTCTGTTAGAGAGTAATGCTATGTATACCTCGA
TTAGAGCTTTGAATTGCTTATGAATCGGTTAAAGCATAAAGATATAT
Found at i:282190 original size:182 final size:181
Alignment explanation
Indices: 281887--282243 Score: 450
Period size: 182 Copynumber: 2.0 Consensus size: 181
281877 CACATATTCG
* * * * *
281887 TCGGTTTATCTGACTAGCGTTGGGCTCAAAACTGTTGGTTAATCCAACTTCAGCTGGGTTCACTT
1 TCGGTTTATCCGACTAGCGTTGGGCGCAAAACTATTGGTTAATCCAACTACAGCTGGGCTCACTT
* * * * *
281952 TTGCGGTTTATCTGCTAGGTACTAGGTGCCAGGATTTGATGGACTATTCGTTGGTTAATCCAACT
66 TTGCGGTTTATCCGCTAGGCACTAGGTGCCAAGAATTGACGGACTATTCGTTGGTT-ATCC-ACT
* **
282017 AGAGCTGGGCTCAATT-TTGCGGTTTATCCGCTAGGCATTGGGTGCCTGATTT
129 AGAGCTGGGCTCAATTATTACGGTTTATCCGCTAGGCACCGGGTGCCTGATTT
* * *
282069 TCGGTTTATCCGACTAGCGTTGGGCGCAAAA-TCATTGGTTAATCCAACTAGAGTTGTGCTCACT
1 TCGGTTTATCCGACTAGCGTTGGGCGCAAAACT-ATTGGTTAATCCAACTACAGCTGGGCTCACT
* * **
282133 TTTGC-GTTTATCCGCTAGGCACTGGGTGCCAAGAATTGACGGAATTATTTTTTGGTTATCCACT
65 TTTGCGGTTTATCCGCTAGGCACTAGGTGCCAAGAATTGACGG-ACTATTCGTTGGTTATCCACT
* * *
282197 AGAGCTGGGCTCACTTATTATGGTTTATCTGCTAGGCACCGGGTGCC
129 AGAGCTGGGCTCAATTATTACGGTTTATCCGCTAGGCACCGGGTGCC
282244 ATGAGTTGAA
Statistics
Matches: 149, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
180 18 0.12
181 61 0.41
182 70 0.47
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (181 bp):
TCGGTTTATCCGACTAGCGTTGGGCGCAAAACTATTGGTTAATCCAACTACAGCTGGGCTCACTT
TTGCGGTTTATCCGCTAGGCACTAGGTGCCAAGAATTGACGGACTATTCGTTGGTTATCCACTAG
AGCTGGGCTCAATTATTACGGTTTATCCGCTAGGCACCGGGTGCCTGATTT
Found at i:282241 original size:81 final size:82
Alignment explanation
Indices: 282103--282262 Score: 202
Period size: 81 Copynumber: 2.0 Consensus size: 82
282093 CGCAAAATCA
* * *
282103 TTGGTTAATCCAACTAGAGTTGTGCTCACTTTTGCGTTTATCCGCTAGGCACTGGGTGCCAAGAA
1 TTGGTTAATCCAACTAGAGCTGGGCTCACTTTTGCGTTTATCCGCTAGGCACCGGGTGCCAAGAA
*
282168 TTGACGGAA-TTATTTT
66 TTGAAGGAAGTTATTTT
* *
282184 TTGGTT-ATCC-ACTAGAGCTGGGCTCACTTATTATG-GTTTATCTGCTAGGCACCGGGTGCCAT
1 TTGGTTAATCCAACTAGAGCTGGGCTCAC-T-TT-TGCGTTTATCCGCTAGGCACCGGGTGCCAA
*
282246 GAGTTGAAGGAAGTTAT
63 GAATTGAAGGAAGTTAT
282263 AACGAAAAGA
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
79 15 0.22
80 5 0.07
81 42 0.62
82 6 0.09
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (82 bp):
TTGGTTAATCCAACTAGAGCTGGGCTCACTTTTGCGTTTATCCGCTAGGCACCGGGTGCCAAGAA
TTGAAGGAAGTTATTTT
Found at i:286429 original size:18 final size:18
Alignment explanation
Indices: 286381--286436 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 18
286371 AATGCAACTC
286381 AATGCAAATGCACTAAAT-AA
1 AATGC-AATG-AC-AAATAAA
* *
286401 AATTCAGTGACAAATAAA
1 AATGCAATGACAAATAAA
*
286419 AATGCAATGACAACTAAA
1 AATGCAATGACAAATAAA
286437 TGCTATGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 4 0.13
18 19 0.63
19 3 0.10
20 4 0.13
ACGTcount: A:0.55, C:0.14, G:0.11, T:0.20
Consensus pattern (18 bp):
AATGCAATGACAAATAAA
Found at i:286914 original size:18 final size:18
Alignment explanation
Indices: 286875--286921 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
286865 CCTTCTTTTC
**
286875 TTCCTTCATT-TCCTCATT
1 TTCCTTC-TTCTCCTCAGG
286893 TTCCTTCTTCTCCTCAGG
1 TTCCTTCTTCTCCTCAGG
*
286911 TTCCTCCTTCT
1 TTCCTTCTTCT
286922 TAGTTGTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.06, C:0.38, G:0.04, T:0.51
Consensus pattern (18 bp):
TTCCTTCTTCTCCTCAGG
Found at i:293192 original size:2 final size:2
Alignment explanation
Indices: 293185--293218 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
293175 TTGTACAGTA
*
293185 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
293219 TAGTAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:301031 original size:13 final size:13
Alignment explanation
Indices: 301013--301037 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
301003 AATTAAAAAA
301013 ATGCTAAAAATGT
1 ATGCTAAAAATGT
301026 ATGCTAAAAATG
1 ATGCTAAAAATG
301038 ACTCAATAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (13 bp):
ATGCTAAAAATGT
Found at i:303938 original size:81 final size:81
Alignment explanation
Indices: 303790--303939 Score: 187
Period size: 81 Copynumber: 1.9 Consensus size: 81
303780 GGCGCAAAAC
* * * * * *
303790 CGTTGGTTAATCCAACTAGAGTTGGATTCACTTTTTTGGTTTATCCGTTAGGCACTTAGTGCCAG
1 CGTTGGTTAATCCAACTAGAGCTGGATTCAATTTTGTAGTTTATCCGCTAGGCACTGAGTGCCAG
303855 GATTTGACGGACTATT
66 GATTTGACGGACTATT
* * *
303871 CGTTGGTTAATCTAACTAGAGCTGG-TCTCAATTTTGTAGTTTA-CTCGCTAGGCACTGGGTGCT
1 CGTTGGTTAATCCAACTAGAGCTGGAT-TCAATTTTGTAGTTTATC-CGCTAGGCACTGAGTGCC
303934 AGGATT
64 AGGATT
303940 GTCAGATTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
80 2 0.03
81 56 0.97
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (81 bp):
CGTTGGTTAATCCAACTAGAGCTGGATTCAATTTTGTAGTTTATCCGCTAGGCACTGAGTGCCAG
GATTTGACGGACTATT
Found at i:306452 original size:17 final size:17
Alignment explanation
Indices: 306402--306463 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
306392 ATTAAATTAC
*
306402 AATGACAAATGGAAATGC
1 AATGAC-AATGGAAATGT
**
306420 AATGACAATTAAAATGT
1 AATGACAATGGAAATGT
*
306437 AATGACAATGGGAATGT
1 AATGACAATGGAAATGT
*
306454 GATGACAATG
1 AATGACAATG
306464 CTTACTAACA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 31 0.84
18 6 0.16
ACGTcount: A:0.47, C:0.08, G:0.23, T:0.23
Consensus pattern (17 bp):
AATGACAATGGAAATGT
Found at i:310723 original size:17 final size:17
Alignment explanation
Indices: 310680--310725 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
310670 TATAGCAATA
310680 TTTCTTTTTTT-T-TCT
1 TTTCTTTTTTTCTCTCT
*
310695 TTTCTCTTTTTCTCTCT
1 TTTCTTTTTTTCTCTCT
*
310712 TTTTTTTTTTTCTC
1 TTTCTTTTTTTCTC
310726 ATTCAACATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 10 0.38
16 1 0.04
17 15 0.58
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTCTTTTTTTCTCTCT
Found at i:311461 original size:20 final size:19
Alignment explanation
Indices: 311436--311479 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
311426 AGTTTTCTTT
311436 TTCTT-CTTCCTTGGGCTCTC
1 TTCTTCCTT-CTTGGGCT-TC
*
311456 TTCTTCCTTCTTGTGCTTC
1 TTCTTCCTTCTTGGGCTTC
311475 TTCTT
1 TTCTT
311480 TTTGTCCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 12 0.55
21 3 0.14
ACGTcount: A:0.00, C:0.32, G:0.11, T:0.57
Consensus pattern (19 bp):
TTCTTCCTTCTTGGGCTTC
Found at i:311494 original size:21 final size:21
Alignment explanation
Indices: 311465--311509 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
311455 CTTCTTCCTT
* * *
311465 CTTGTGCTTCTTCTTTTTGTC
1 CTTGCGCTTCCTCTTTTTATC
311486 CTTGCGCTTCCTCTTTTTATC
1 CTTGCGCTTCCTCTTTTTATC
311507 CTT
1 CTT
311510 CGAACCAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.29, G:0.11, T:0.58
Consensus pattern (21 bp):
CTTGCGCTTCCTCTTTTTATC
Found at i:312760 original size:13 final size:12
Alignment explanation
Indices: 312725--312767 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
312715 ATAGAATTTA
312725 AAAAGGAACAAGT
1 AAAAGGAA-AAGT
312738 AAAAGTGAAAAGAT
1 AAAAG-GAAAAG-T
*
312752 AAAAGGAAATGT
1 AAAAGGAAAAGT
312764 AAAA
1 AAAA
312768 TGAGTTGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 5 0.19
13 13 0.48
14 9 0.33
ACGTcount: A:0.65, C:0.02, G:0.21, T:0.12
Consensus pattern (12 bp):
AAAAGGAAAAGT
Found at i:323108 original size:21 final size:21
Alignment explanation
Indices: 323084--323124 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
323074 TGGCTGTACA
* *
323084 TGATTTTGATGTGGATGCATT
1 TGATCTTGATGTGAATGCATT
323105 TGATCTTGATGTGAATGCAT
1 TGATCTTGATGTGAATGCAT
323125 CTGAGTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.07, G:0.27, T:0.44
Consensus pattern (21 bp):
TGATCTTGATGTGAATGCATT
Found at i:324358 original size:17 final size:16
Alignment explanation
Indices: 324316--324359 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
324306 TAGTAGCAAA
324316 AAGAAAAAA-ATTAGT
1 AAGAAAAAATATTAGT
*
324331 AACAAATAAATATTAGAT
1 AAGAAA-AAATATTAG-T
324349 AAGAAAAAATA
1 AAGAAAAAATA
324360 AGTGCAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 5 0.21
16 3 0.12
17 10 0.42
18 6 0.25
ACGTcount: A:0.68, C:0.02, G:0.09, T:0.20
Consensus pattern (16 bp):
AAGAAAAAATATTAGT
Found at i:328375 original size:16 final size:17
Alignment explanation
Indices: 328336--328376 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
328326 TAAATTAACA
328336 AAAT-AAATGCAATGAC
1 AAATAAAATGCAATGAC
*
328352 AAAATAAAATGCGATGAC
1 -AAATAAAATGCAATGAC
328370 -AATAAAA
1 AAATAAAA
328377 ATGTATGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 4 0.18
18 11 0.50
ACGTcount: A:0.61, C:0.10, G:0.12, T:0.17
Consensus pattern (17 bp):
AAATAAAATGCAATGAC
Found at i:328379 original size:17 final size:18
Alignment explanation
Indices: 328333--328371 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
328323 AACTAAATTA
328333 ACAAAAT-AAATGCAATG
1 ACAAAATAAAATGCAATG
*
328350 ACAAAATAAAATGCGATG
1 ACAAAATAAAATGCAATG
328368 ACAA
1 ACAA
328372 TAAAAATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.15
Consensus pattern (18 bp):
ACAAAATAAAATGCAATG
Found at i:341398 original size:21 final size:21
Alignment explanation
Indices: 341366--341444 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
341356 AACAGTGTAG
* *
341366 ACTTCTATCGATAACTA-TGAC
1 ACTTCTACCGAT-ACTAGTGAA
*
341387 AGTTCTACCGATACTAGTGAA
1 ACTTCTACCGATACTAGTGAA
* * * * *
341408 ACTTCTACCGAAACAAATCAT
1 ACTTCTACCGATACTAGTGAA
341429 ACTTCTACCGATACTA
1 ACTTCTACCGATACTA
341445 AAAACTCCAG
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 4 0.09
21 42 0.91
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.29
Consensus pattern (21 bp):
ACTTCTACCGATACTAGTGAA
Found at i:352210 original size:26 final size:26
Alignment explanation
Indices: 352132--352281 Score: 79
Period size: 26 Copynumber: 6.0 Consensus size: 26
352122 AATCAGTAAT
352132 TCGCTCTTAT-GAGCCAGTACAGTATAA
1 TCGCTCTT-TCGAGCCAGTACAGTAT-A
* * * *
352159 T-GCT-TTTACAAGTCAGTTCAATATA
1 TCGCTCTTT-CGAGCCAGTACAGTATA
352184 TCGCTCTTTCGAGCCAGTACAGTATA
1 TCGCTCTTTCGAGCCAGTACAGTATA
* *
352210 TCACT-TTT--A---A-TATAGTATA
1 TCGCTCTTTCGAGCCAGTACAGTATA
* * **
352229 ACGCTCTTACGAGCCAGTTTAGTATA
1 TCGCTCTTTCGAGCCAGTACAGTATA
* *
352255 TCGCTCTTTCAAGCTC-GTACAATATA
1 TCGCTCTTTCGAGC-CAGTACAGTATA
352281 T
1 T
352282 TTTCAAATCT
Statistics
Matches: 91, Mismatches: 20, Indels: 25
0.67 0.15 0.18
Matches are distributed among these distances:
19 11 0.12
20 3 0.03
22 1 0.01
23 1 0.01
24 1 0.01
25 8 0.09
26 61 0.67
27 5 0.05
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (26 bp):
TCGCTCTTTCGAGCCAGTACAGTATA
Found at i:354995 original size:27 final size:27
Alignment explanation
Indices: 354957--355008 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
354947 TCAGAGTAGT
*
354957 CCACGACCCTCTAGGAATTGGGACTGC
1 CCACGACCCTCTAGGAATTGAGACTGC
*
354984 CCACGACCCTCTGGGAATTGAGACT
1 CCACGACCCTCTAGGAATTGAGACT
355009 AACAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.19
Consensus pattern (27 bp):
CCACGACCCTCTAGGAATTGAGACTGC
Found at i:357606 original size:27 final size:26
Alignment explanation
Indices: 357575--357644 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
357565 TGACAGTAAA
* *
357575 ATAATAATTTATTAATATT-ATTATGT
1 ATAATAATATATTAATATTAATTA-AT
*
357601 GATAATAATAAATTTAATATTAATTAAT
1 -ATAATAATATA-TTAATATTAATTAAT
357629 ATAATAATATATTAAT
1 ATAATAATATATTAAT
357645 GTGAAAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 5 0.14
27 19 0.51
28 9 0.24
29 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (26 bp):
ATAATAATATATTAATATTAATTAAT
Found at i:357657 original size:22 final size:20
Alignment explanation
Indices: 357617--357657 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
357607 AATAAATTTA
*
357617 ATATTAATTAATATAATAAT
1 ATATTAATTAAAATAATAAT
357637 ATATTAATGTGAAAATAATAA
1 ATATTAAT-T-AAAATAATAA
357658 ATTTTATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
ATATTAATTAAAATAATAAT
Found at i:357987 original size:15 final size:15
Alignment explanation
Indices: 357964--358023 Score: 95
Period size: 15 Copynumber: 4.1 Consensus size: 15
357954 TTTTAAGTTA
*
357964 TTTTAAAATTTAATT
1 TTTTTAAATTTAATT
357979 TTTTTAAATTTAA-T
1 TTTTTAAATTTAATT
*
357993 TTTTTAAATTTAAAT
1 TTTTTAAATTTAATT
358008 TTTTTAAATTTAATT
1 TTTTTAAATTTAATT
358023 T
1 T
358024 AAAAAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
14 14 0.33
15 28 0.67
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTAAATTTAATT
Found at i:358001 original size:29 final size:29
Alignment explanation
Indices: 357964--358023 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
357954 TTTTAAGTTA
*
357964 TTTTAAAATTTAATTTTTTTAAATTTAAT
1 TTTTAAAATTTAAATTTTTTAAATTTAAT
*
357993 TTTTTAAATTTAAATTTTTTAAATTTAAT
1 TTTTAAAATTTAAATTTTTTAAATTTAAT
358022 TT
1 TT
358024 AAAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
TTTTAAAATTTAAATTTTTTAAATTTAAT
Found at i:363667 original size:20 final size:20
Alignment explanation
Indices: 363629--363668 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
363619 TAGTCTCTTC
*
363629 ATTATGATATTTTAATTTTT
1 ATTATGATATGTTAATTTTT
*
363649 ATTATGATGTGTT-ATTTTT
1 ATTATGATATGTTAATTTTT
363668 A
1 A
363669 AAGATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (20 bp):
ATTATGATATGTTAATTTTT
Found at i:370014 original size:13 final size:14
Alignment explanation
Indices: 369993--370021 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
369983 CTCAAAGTAG
369993 AAATCAAGGTATGA
1 AAATCAAGGTATGA
370007 AAAT-AAGGTATGA
1 AAATCAAGGTATGA
370020 AA
1 AA
370022 TTCTCTACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (14 bp):
AAATCAAGGTATGA
Found at i:374009 original size:8 final size:8
Alignment explanation
Indices: 373996--374021 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
373986 TTAAATTATC
373996 TCTATAAT
1 TCTATAAT
374004 TCTATAAT
1 TCTATAAT
374012 TCTATAAT
1 TCTATAAT
374020 TC
1 TC
374022 CTTTCTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (8 bp):
TCTATAAT
Found at i:374242 original size:16 final size:18
Alignment explanation
Indices: 374211--374244 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
374201 CGTTATATAA
374211 TTTCTTCACTTTCTTTTT
1 TTTCTTCACTTTCTTTTT
374229 TTTCTTC-C-TTCTTTTT
1 TTTCTTCACTTTCTTTTT
374245 GACGCAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTCTTCACTTTCTTTTT
Found at i:374895 original size:20 final size:19
Alignment explanation
Indices: 374861--374899 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
374851 TTTTTTTACA
374861 ACATTTATCACACTTCTTTT
1 ACATTTATCACACTT-TTTT
374881 ACATTT-TCACAACTTTTTT
1 ACATTTATCAC-ACTTTTTT
374900 TTTTACACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (19 bp):
ACATTTATCACACTTTTTT
Found at i:382383 original size:36 final size:36
Alignment explanation
Indices: 382333--382404 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
382323 CTAAAAATCC
382333 AGTCATAAACTAGTATATTCTACATAAATTTAAATG
1 AGTCATAAACTAGTATATTCTACATAAATTTAAATG
* *
382369 AGTCATAAATTAGTATATTCTAGATAAATTTAAATG
1 AGTCATAAACTAGTATATTCTACATAAATTTAAATG
382405 GCAACATAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (36 bp):
AGTCATAAACTAGTATATTCTACATAAATTTAAATG
Found at i:382907 original size:18 final size:17
Alignment explanation
Indices: 382880--382913 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
382870 ATTATAATTA
382880 TCATCTTTCAATTTTTT
1 TCATCTTTCAATTTTTT
382897 TCATCCTTTCAATTTTT
1 TCAT-CTTTCAATTTTT
382914 CATCTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.62
Consensus pattern (17 bp):
TCATCTTTCAATTTTTT
Found at i:382914 original size:16 final size:16
Alignment explanation
Indices: 382880--382929 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
382870 ATTATAATTA
382880 TCAT-CTTTCAATTTTTT
1 TCATCCTTTCAA--TTTT
382897 TCATCCTTTCAATTTT
1 TCATCCTTTCAATTTT
*
382913 TCATCTTTTC-ATTTT
1 TCATCCTTTCAATTTT
382928 TC
1 TC
382930 TTTTCACTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 7 0.23
16 13 0.42
17 4 0.13
18 7 0.23
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (16 bp):
TCATCCTTTCAATTTT
Found at i:385229 original size:29 final size:31
Alignment explanation
Indices: 385179--385250 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
385169 TGCTATTCAC
* *
385179 ATAAAAATTATAA-AAAATATTAATTAA-ATT
1 ATAAAAATGA-AATAAAATATTAATAAAGATT
385209 ATAAAAATGAAATAAAA-ATTAATAAAGATT
1 ATAAAAATGAAATAAAATATTAATAAAGATT
385239 A-AAAAATGAAAT
1 ATAAAAATGAAAT
385251 TAATTCTTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
29 21 0.55
30 17 0.45
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (31 bp):
ATAAAAATGAAATAAAATATTAATAAAGATT
Found at i:389184 original size:18 final size:18
Alignment explanation
Indices: 389161--389211 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
389151 ACCTACAAAC
* *
389161 AAAAAACAAAGAAAGGAA
1 AAAAAACAAAAAAAGAAA
*
389179 AAAAAATAGAAAAAAGAAA
1 AAAAAACA-AAAAAAGAAA
389198 AAAAATACAAAAAA
1 AAAAA-ACAAAAAA
389212 CCATGTAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 7 0.26
19 18 0.67
20 2 0.07
ACGTcount: A:0.82, C:0.04, G:0.10, T:0.04
Consensus pattern (18 bp):
AAAAAACAAAAAAAGAAA
Found at i:389194 original size:19 final size:18
Alignment explanation
Indices: 389161--389211 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
389151 ACCTACAAAC
389161 AAAAA-ACAAAGAAAGGAAA
1 AAAAATACAAA-AAA-GAAA
*
389180 AAAAATAGAAAAAAGAAA
1 AAAAATACAAAAAAGAAA
389198 AAAAATACAAAAAA
1 AAAAATACAAAAAA
389212 CCATGTAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 17 0.59
19 8 0.28
20 4 0.14
ACGTcount: A:0.82, C:0.04, G:0.10, T:0.04
Consensus pattern (18 bp):
AAAAATACAAAAAAGAAA
Found at i:390361 original size:17 final size:17
Alignment explanation
Indices: 390335--390373 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
390325 TATTTCCAGC
390335 TTTT-TTATTTTATGTT
1 TTTTATTATTTTATGTT
* *
390351 TTTTATTATTTTCTTTT
1 TTTTATTATTTTATGTT
390368 TTTTAT
1 TTTTAT
390374 CCTTGATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTATTATTTTATGTT
Found at i:390523 original size:25 final size:25
Alignment explanation
Indices: 390495--390543 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
390485 TCTGTTATCT
390495 TTTATTTA-TGTTATTAATTGTATTA
1 TTTA-TTAGTGTTATTAATTGTATTA
* *
390520 TTTATTAGTGTTATTTATTTTATT
1 TTTATTAGTGTTATTAATTGTATT
390544 TTGTTATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.67
Consensus pattern (25 bp):
TTTATTAGTGTTATTAATTGTATTA
Found at i:403633 original size:21 final size:21
Alignment explanation
Indices: 403609--403658 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
403599 ACAGGAAGAG
403609 GAAGAGAAGGAAGGTGAGAAT
1 GAAGAGAAGGAAGGTGAGAAT
403630 GAAGAGAAGGAAGGTGAGAAT
1 GAAGAGAAGGAAGGTGAGAAT
403651 GAAGAGAA
1 GAAGAGAA
403659 AGACCCTACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.50, C:0.00, G:0.42, T:0.08
Consensus pattern (21 bp):
GAAGAGAAGGAAGGTGAGAAT
Found at i:403905 original size:20 final size:20
Alignment explanation
Indices: 403880--403924 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
403870 TCAGAGGTGA
403880 CAATCGATGAGGTCGCTAAC
1 CAATCGATGAGGTCGCTAAC
403900 CAATCGATGAGGTCGCTAAC
1 CAATCGATGAGGTCGCTAAC
403920 CAATC
1 CAATC
403925 TATTGAGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (20 bp):
CAATCGATGAGGTCGCTAAC
Found at i:404731 original size:16 final size:16
Alignment explanation
Indices: 404694--404740 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
404684 TCAGTCATTT
*
404694 GAAAAAGAAACAAAATAA
1 GAAAAAGAAA-GAAA-AA
*
404712 GAAAAAGGAAGAAAAA
1 GAAAAAGAAAGAAAAA
404728 GAAAAAGAAAGAA
1 GAAAAAGAAAGAA
404741 TTTTTTGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 14 0.54
17 3 0.12
18 9 0.35
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (16 bp):
GAAAAAGAAAGAAAAA
Found at i:412760 original size:100 final size:98
Alignment explanation
Indices: 412656--412997 Score: 364
Period size: 100 Copynumber: 3.4 Consensus size: 98
412646 GTAGCACAGC
** * * *
412656 AAGATGAAGCTACAACATCAAATTATATACCCCTAAAGTTGCAATGGATCGGATTGAAGCTATAA
1 AAGATGAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAATGGATCAGATTGAAGCTA-AA
* * * *
412721 CAACAAATCTTATCTCCCTAAAGATGTAATGGAGT
65 -AGCAAATTTTATCTCCCTAAAGATGCAGTGGAGT
* * * * * * *
412756 AAGATGAAGTTACTACATCAAATCCTATATCCTTGAAGTTGC-AGGGATTAGATTAAAACTACAA
1 AAGATGAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAATGGATCAGATTGAAGCTA-AA
* * *
412820 TAGCAAATGTTTATCTCTCTAAAGTTGCAGTAGAGT
65 -AGCAAAT-TTTATCTCCCTAAAGATGCAGTGGAGT
* * * *
412856 AAGATGAAGCTACCACATCAAATCCTATATCTCTGAAGTTGTAGTGGATCAGATTGAAGCTCAAA
1 AAGATGAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAATGGATCAGATTGAAGCT-AAA
* * *
412921 AGCAAATTTTATCTCCTTGAAGATGCAGTGGAGC
65 AGCAAATTTTATCTCCCTAAAGATGCAGTGGAGT
*
412955 AAGATGAAGTTACGAA-ATCAAATCCTATATCCCTGAAGTTGCA
1 AAGATGAAGCTAC-AACATCAAATCCTATATCCCTGAAGTTGCA
412998 GTAAATCGAA
Statistics
Matches: 197, Mismatches: 41, Indels: 9
0.80 0.17 0.04
Matches are distributed among these distances:
99 80 0.41
100 101 0.51
101 15 0.08
102 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (98 bp):
AAGATGAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAATGGATCAGATTGAAGCTAAAA
GCAAATTTTATCTCCCTAAAGATGCAGTGGAGT
Found at i:412876 original size:200 final size:199
Alignment explanation
Indices: 412560--412998 Score: 567
Period size: 200 Copynumber: 2.2 Consensus size: 199
412550 TGGAATGGAG
* *
412560 TGAAGTTACCACATCAAATCCTATATCCTTGAAATTTG-AGGGATCAGATTAAAACTACAGTAGC
1 TGAAGTTACCACATCAAATCCTATATCCTTG-AAGTTGCAGGGATCAGATTAAAACTACAATAGC
* * * *
412624 AAATCTTTATCTCTGTGAAGTTGTAGCACAGCAAGATGAAGCTACAACATCAAATTATATACCCC
65 AAATCTTTATCTCTCTAAAGTTGCAGCACAGCAAGATGAAGCTACAACATCAAATCATATACCCC
* *
412689 TAAAGTTGCAATGGATCGGATTGAAGCT-ATAACAACAAATCTTATCTCCCTAAAGATGTAATGG
130 TAAAGTTGCAATGGATCAGATTGAAGCTCA-AA-AACAAATCTTATCTCCCTAAAGATGCAATGG
*
412753 AGTAAGA
193 AGCAAGA
* *
412760 TGAAGTTACTACATCAAATCCTATATCCTTGAAGTTGCAGGGATTAGATTAAAACTACAATAGCA
1 TGAAGTTACCACATCAAATCCTATATCCTTGAAGTTGCAGGGATCAGATTAAAACTACAATAGCA
* * * * * * * *
412825 AATGTTTATCTCTCTAAAGTTGCAGTAGAGTAAGATGAAGCTACCACATCAAATCCTATATCTCT
66 AATCTTTATCTCTCTAAAGTTGCAGCACAGCAAGATGAAGCTACAACATCAAATCATATACCCCT
* * * * * * * *
412890 GAAGTTGTAGTGGATCAGATTGAAGCTCAAAAGCAAATTTTATCTCCTTGAAGATGCAGTGGAGC
131 AAAGTTGCAATGGATCAGATTGAAGCTCAAAAACAAATCTTATCTCCCTAAAGATGCAATGGAGC
412955 AAGA
196 AAGA
* * *
412959 TGAAGTTACGAAATCAAATCCTATATCCCTGAAGTTGCAG
1 TGAAGTTACCACATCAAATCCTATATCCTTGAAGTTGCAG
412999 TAAATCGAAT
Statistics
Matches: 207, Mismatches: 30, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
199 73 0.35
200 133 0.64
201 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28
Consensus pattern (199 bp):
TGAAGTTACCACATCAAATCCTATATCCTTGAAGTTGCAGGGATCAGATTAAAACTACAATAGCA
AATCTTTATCTCTCTAAAGTTGCAGCACAGCAAGATGAAGCTACAACATCAAATCATATACCCCT
AAAGTTGCAATGGATCAGATTGAAGCTCAAAAACAAATCTTATCTCCCTAAAGATGCAATGGAGC
AAGA
Found at i:412889 original size:50 final size:49
Alignment explanation
Indices: 412656--412999 Score: 219
Period size: 50 Copynumber: 6.9 Consensus size: 49
412646 GTAGCACAGC
** * * *
412656 AAGATGAAGCTACAACATCAAATTATATACCCCTAAAGTTGCAATGGAT
1 AAGATGAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAGTGGAT
** * * * * * * * *
412705 CGGATTGAAGCTATAACAACAAATCTTATCTCCCTAAAGATGTAATGGAGT
1 AAGA-TGAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAGTGGA-T
* * *
412756 AAGATGAAGTTACTACATCAAATCCTATATCCTTGAAGTTGCAG-GGAT
1 AAGATGAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAGTGGAT
* * * * * * * * *
412804 TAGATTAAAACTACAATAGCAAAT-GTTTATCTCTCTAAAGTTGCAGTAGAGT
1 AAGA-TGAAGCTACAACATCAAATCCTATATC-C-CTGAAGTTGCAGTGGA-T
* * *
412856 AAGATGAAGCTACCACATCAAATCCTATATCTCTGAAGTTGTAGTGGAT
1 AAGATGAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAGTGGAT
* * * ** * * * *
412905 CAGATTGAAGCT-CAAAAGCAAATTTTATCTCCTTGAAGATGCAGTGGAGC
1 AAGA-TGAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAGTGGA-T
*
412955 AAGATGAAGTTACGAA-ATCAAATCCTATATCCCTGAAGTTGCAGT
1 AAGATGAAGCTAC-AACATCAAATCCTATATCCCTGAAGTTGCAGT
413000 AAATCGAATT
Statistics
Matches: 216, Mismatches: 67, Indels: 23
0.71 0.22 0.08
Matches are distributed among these distances:
48 9 0.04
49 55 0.25
50 122 0.56
51 21 0.10
52 9 0.04
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (49 bp):
AAGATGAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAGTGGAT
Done.