Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006270.1 Hibiscus syriacus cultivar Beakdansim tig00014949_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: 949592
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 1 of 5
Found at i:3909 original size:30 final size:31
Alignment explanation
Indices: 3875--3937 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
3865 TTGAAAAATC
* *
3875 ATTATATATTATTAAAATAAAAG-TTATAAT
1 ATTATATATCATTAAAATAAAAGAATATAAT
* *
3905 ATTATATATCATTAATATTAAAGAATATAAT
1 ATTATATATCATTAAAATAAAAGAATATAAT
3936 AT
1 AT
3938 ATAAGAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (31 bp):
ATTATATATCATTAAAATAAAAGAATATAAT
Found at i:4353 original size:2 final size:2
Alignment explanation
Indices: 4346--4381 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4336 TTAATTCTTG
4346 AT AT AT AT AT AT 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 AT
4382 TTTTCTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7505 original size:2 final size:2
Alignment explanation
Indices: 7498--7524 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7488 TTTAATTCTT
7498 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 T
7525 TTTTTTCTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13379 original size:2 final size:2
Alignment explanation
Indices: 13372--13396 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13362 TTTCTTGGAA
13372 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13397 CATAAGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14778 original size:2 final size:2
Alignment explanation
Indices: 14773--14802 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14763 GAAAAAAATA
14773 AT AT AT 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
14803 CAAGAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15704 original size:24 final size:24
Alignment explanation
Indices: 15599--15704 Score: 85
Period size: 24 Copynumber: 4.4 Consensus size: 24
15589 AACGGAGATA
* *
15599 TCAGAAATCAAAACAAAATTCAGAA
1 TCAGAAATCATAACAAAATTCA-AG
* * *
15624 T-A-AATATCAGAACAGAA-TCCAG
1 TCAGAA-ATCATAACAAAATTCAAG
*
15646 ATCAGAAATCATAACATAATTCAAG
1 -TCAGAAATCATAACAAAATTCAAG
*
15671 TCATG-TATCATAACAAAATTCAAG
1 TCA-GAAATCATAACAAAATTCAAG
15695 TCAGAAATCA
1 TCAGAAATCA
15705 GATAAAATAT
Statistics
Matches: 64, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
22 1 0.02
23 6 0.09
24 49 0.77
25 8 0.12
ACGTcount: A:0.52, C:0.17, G:0.09, T:0.22
Consensus pattern (24 bp):
TCAGAAATCATAACAAAATTCAAG
Found at i:24256 original size:59 final size:58
Alignment explanation
Indices: 24126--24468 Score: 245
Period size: 59 Copynumber: 5.8 Consensus size: 58
24116 TATCAGTGCT
* * * * *
24126 CTATCTAGAAAAT-CATACACTTAGTATGCTTCCCTTTTCATTTTAGCACACAA-AGTGCC
1 CTATCT-GGAAATCCATACA-TTAGTATGATTTCCTTATCATTTTAGCACATAATA-TGCC
** ** *
24185 CTAT-TCAAAAATCCATACCATTAGTATGATTTTGTTACCATTTTAGCACATAATATGCC
1 CTATCT-GGAAATCCATA-CATTAGTATGATTTCCTTATCATTTTAGCACATAATATGCC
* ** * *** *
24244 CTATCTGGAAATCCTTATTTTAAATATGATTTCCTTATCA-TTTAGCAC-CCCTAGTGCT
1 CTATCTGGAAATCCATACATT-AGTATGATTTCCTTATCATTTTAGCACATAATA-TGCC
* * * * *
24302 TTATCTGGAAACCCATACACTCAGTATGATTCCCTTATCATTTTAGCACATAATATTCC
1 CTATCTGGAAATCCATACA-TTAGTATGATTTCCTTATCATTTTAGCACATAATATGCC
* * *
24361 CTATCTGGAAATCCATA-ATTTCAATATGATTTCCTTATCA-TTTAGCACACTCA-GTGCTC
1 CTATCTGGAAATCCATACA-TT-AGTATGATTTCCTTATCATTTTAGCACA-TAATATGC-C
* * *
24420 C-ATATGGAAATCCATACACTCAGTATGATTTCCTTATCATTATAGCACA
1 CTATCTGGAAATCCATACA-TTAGTATGATTTCCTTATCATTTTAGCACA
24469 CAAAGTGCCA
Statistics
Matches: 221, Mismatches: 49, Indels: 28
0.74 0.16 0.09
Matches are distributed among these distances:
57 2 0.01
58 93 0.42
59 120 0.54
60 6 0.03
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (58 bp):
CTATCTGGAAATCCATACATTAGTATGATTTCCTTATCATTTTAGCACATAATATGCC
Found at i:24319 original size:117 final size:117
Alignment explanation
Indices: 24219--24468 Score: 367
Period size: 117 Copynumber: 2.1 Consensus size: 117
24209 TATGATTTTG
* *
24219 TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCTTATTTTAAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTAAATATGATTTCCTTATCA
24284 TTTAGCACCCCTAGTGCTTTATCTGGAAACCCATACACTCAGTATGATTCCC
66 TTTAGCACCCCTAGTGCTTTATCTGGAAACCCATACACTCAGTATGATTCCC
* * *
24336 TTATCATTTTAGCACATAATATTCCCTATCTGGAAATCCATAATTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTAAATATGATTTCCTTATCA
* ** * * *
24401 TTTAGCA-CACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTTCC
66 TTTAGCACCCCT-AGTGCTTTATCTGGAAACCCATACACTCAGTATGATTCCC
* *
24453 TTATCATTATAGCACA
1 TTACCATTTTAGCACA
24469 CAAAGTGCCA
Statistics
Matches: 120, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
116 3 0.03
117 117 0.98
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.37
Consensus pattern (117 bp):
TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTAAATATGATTTCCTTATCA
TTTAGCACCCCTAGTGCTTTATCTGGAAACCCATACACTCAGTATGATTCCC
Found at i:24987 original size:19 final size:19
Alignment explanation
Indices: 24942--24990 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
24932 TTAGGTGTGC
* * *
24942 ATCGATGAACTACTTATGC
1 ATCGATGCACCACTTATGA
24961 ATCGATGCACCACTTATGA
1 ATCGATGCACCACTTATGA
24980 ATCGATGCACC
1 ATCGATGCACC
24991 TTACCTAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (19 bp):
ATCGATGCACCACTTATGA
Found at i:33081 original size:27 final size:29
Alignment explanation
Indices: 33028--33096 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 29
33018 ACTTTTATTT
* *
33028 TAATATTATATAATGAATTTTCAATAAAAA
1 TAATATTAT-TAATGAAATTACAATAAAAA
**
33058 TAATATTATTAAT-AAATTAC-ATAAATG
1 TAATATTATTAATGAAATTACAATAAAAA
*
33085 TATTATTATTAA
1 TAATATTATTAA
33097 ATTATTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 16 0.47
28 5 0.15
29 4 0.12
30 9 0.26
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (29 bp):
TAATATTATTAATGAAATTACAATAAAAA
Found at i:40480 original size:18 final size:18
Alignment explanation
Indices: 40450--40498 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
40440 GAGGACTTTT
40450 ATATTATTTATAAAAATA
1 ATATTATTTATAAAAATA
40468 ATATT-TTTCATAAAAATA
1 ATATTATTT-ATAAAAATA
40486 ATATATATTTATA
1 ATAT-TATTTATA
40499 TCAAATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.11
18 18 0.64
19 4 0.14
20 3 0.11
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTATTTATAAAAATA
Found at i:49003 original size:27 final size:29
Alignment explanation
Indices: 48950--49018 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 29
48940 ACTTTTATTT
* *
48950 TAATATTATATAATGAATTTTCAATAAAAA
1 TAATATTAT-TAATGAAATTACAATAAAAA
**
48980 TAATATTATTAAT-AAATTAC-ATAAATG
1 TAATATTATTAATGAAATTACAATAAAAA
*
49007 TATTATTATTAA
1 TAATATTATTAA
49019 ATTATTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 16 0.47
28 5 0.15
29 4 0.12
30 9 0.26
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (29 bp):
TAATATTATTAATGAAATTACAATAAAAA
Found at i:50287 original size:2 final size:2
Alignment explanation
Indices: 50280--50312 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
50270 TTCCTTGGAA
50280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50313 AGATATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59599 original size:65 final size:64
Alignment explanation
Indices: 59402--59611 Score: 171
Period size: 65 Copynumber: 3.3 Consensus size: 64
59392 TGCACTAAGA
* ** * * * * *
59402 GTGCATCGATGCATCATGTGCATTCGATGTTTCAA-AATAGC-CAGAGTGTAT-GATGCATGGCT
1 GTGCATCAATGCATCAAATGCATTCGATGTTTTAATAAAATCTC--AGTGCATCGATGCATGGTT
59464 G
64 G
* * *
59465 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCAATGCATCAAATGCATTCGATGTTTTAATAAAAT-CTCAGTGCATCGATGCATGGT-T
59530 -
64 G
* * **
59530 GTGCATCAATGCATGAAATGCATTCTATG-TTTAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCAATGCATCAAATGCATTCGATGTTTTAATAAAATCTCA--GTGCATCGATGCATGG-T
59593 TG
63 TG
*
59595 GTGCATCAGTGCATCAA
1 GTGCATCAATGCATCAA
59612 TCTGAAACAT
Statistics
Matches: 120, Mismatches: 18, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
62 3 0.03
63 31 0.26
64 33 0.28
65 51 0.43
66 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCAATGCATCAAATGCATTCGATGTTTTAATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:64838 original size:24 final size:24
Alignment explanation
Indices: 64810--64869 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
64800 AATTTTCGAT
64810 TTGGATTCTGATCTGATATC-TGA-
1 TTGGATTCTGATCTGATA-CATGAC
64833 TATGGATTCTGATCTGATACATGAC
1 T-TGGATTCTGATCTGATACATGAC
64858 TTGGATTCTGAT
1 TTGGATTCTGAT
64870 ATGTTACTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
23 2 0.06
24 31 0.91
25 1 0.03
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.42
Consensus pattern (24 bp):
TTGGATTCTGATCTGATACATGAC
Found at i:64890 original size:24 final size:24
Alignment explanation
Indices: 64839--64912 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
64829 CTGATATGGA
* * *
64839 TTCTGATCTGATACATGACTTGGA-
1 TTCTGATATGATACTTGACCT-GAT
* *
64863 TTCTGATATGTTACTTTACCTGAT
1 TTCTGATATGATACTTGACCTGAT
64887 TTCTGATATGATACTTGACCTGAT
1 TTCTGATATGATACTTGACCTGAT
64911 TT
1 TT
64913 ATGTTTTGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 2 0.05
24 40 0.95
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (24 bp):
TTCTGATATGATACTTGACCTGAT
Found at i:67014 original size:13 final size:13
Alignment explanation
Indices: 66996--67032 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
66986 GTCACAACCC
66996 GACCCGACCCGTT
1 GACCCGACCCGTT
67009 GACCCGACCCGTT
1 GACCCGACCCGTT
67022 GACCCGACCCG
1 GACCCGACCCG
67033 ACCGACTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.24, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:69614 original size:24 final size:24
Alignment explanation
Indices: 69587--69681 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 24
69577 ATTTTCGATT
69587 TGGATTCTGATCTGATATC-TGACA
1 TGGATTCTGATCTGATA-CATGACA
*
69611 TGGATTCTGATCTGATACATGACT
1 TGGATTCTGATCTGATACATGACA
* * * *
69635 TGGATTCTGATATGTTACTTGACC
1 TGGATTCTGATCTGATACATGACA
* *
69659 T-GATTTCTGATATGATACTTGAC
1 TGGA-TTCTGATCTGATACATGAC
69682 CTGATTTATG
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
23 3 0.05
24 60 0.95
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (24 bp):
TGGATTCTGATCTGATACATGACA
Found at i:69682 original size:24 final size:24
Alignment explanation
Indices: 69615--69688 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
69605 CTGACATGGA
* * *
69615 TTCTGATCTGATACATGACTTGGA-
1 TTCTGATATGATACTTGACCT-GAT
*
69639 TTCTGATATGTTACTTGACCTGAT
1 TTCTGATATGATACTTGACCTGAT
69663 TTCTGATATGATACTTGACCTGAT
1 TTCTGATATGATACTTGACCTGAT
69687 TT
1 TT
69689 ATGTTTTGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (24 bp):
TTCTGATATGATACTTGACCTGAT
Found at i:71793 original size:13 final size:13
Alignment explanation
Indices: 71775--71811 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
71765 GTCACAACCC
71775 GACCCGACCCGTT
1 GACCCGACCCGTT
71788 GACCCGACCCGTT
1 GACCCGACCCGTT
71801 GACCCGACCCG
1 GACCCGACCCG
71812 ACCGACTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.24, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:74431 original size:24 final size:24
Alignment explanation
Indices: 74364--74437 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
74354 TCGATTTGGA
* * *
74364 TTCTGATCTGATACATGACTTGGA-
1 TTCTGATATGATACTTGACCT-GAT
*
74388 TTCTGATATGTTACTTGACCTGAT
1 TTCTGATATGATACTTGACCTGAT
74412 TTCTGATATGATACTTGACCTGAT
1 TTCTGATATGATACTTGACCTGAT
74436 TT
1 TT
74438 ATGTTTTGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (24 bp):
TTCTGATATGATACTTGACCTGAT
Found at i:75410 original size:12 final size:12
Alignment explanation
Indices: 75384--75416 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
75374 TTATTATACT
*
75384 ATTTT-ATTAAC
1 ATTTTAATTAAA
75395 ATTTTAATTAAA
1 ATTTTAATTAAA
75407 ATTTTAATTA
1 ATTTTAATTA
75417 TTAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTTAATTAAA
Found at i:78581 original size:12 final size:12
Alignment explanation
Indices: 78555--78587 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
78545 TTATTATACT
*
78555 ATTTT-ATTAAC
1 ATTTTAATTAAA
78566 ATTTTAATTAAA
1 ATTTTAATTAAA
78578 ATTTTAATTA
1 ATTTTAATTA
78588 TTAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTTAATTAAA
Found at i:78812 original size:41 final size:41
Alignment explanation
Indices: 78767--78844 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
78757 AAAACAACCC
* *
78767 TTAATATATTATATAATATTCTTATTTT-AATAATAATGTTT
1 TTAATATATTA-AAAATATTATTATTTTCAATAATAATGTTT
* *
78808 TTAATATTTTAAAAATATTATTATTTTCAATAGTAAT
1 TTAATATATTAAAAATATTATTATTTTCAATAATAAT
78845 TAAAATAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 14 0.44
41 18 0.56
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (41 bp):
TTAATATATTAAAAATATTATTATTTTCAATAATAATGTTT
Found at i:78870 original size:3 final size:3
Alignment explanation
Indices: 78862--78892 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
78852 ATCAAGAATA
78862 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
78893 GTAAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:81806 original size:12 final size:12
Alignment explanation
Indices: 81780--81812 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
81770 TTATTATACT
*
81780 ATTTT-ATTAAC
1 ATTTTAATTAAA
81791 ATTTTAATTAAA
1 ATTTTAATTAAA
81803 ATTTTAATTA
1 ATTTTAATTA
81813 TTAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTTAATTAAA
Found at i:88119 original size:12 final size:12
Alignment explanation
Indices: 88093--88125 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
88083 TTATTATACT
*
88093 ATTTT-ATTAAC
1 ATTTTAATTAAA
88104 ATTTTAATTAAA
1 ATTTTAATTAAA
88116 ATTTTAATTA
1 ATTTTAATTA
88126 TTAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTTAATTAAA
Found at i:88948 original size:29 final size:29
Alignment explanation
Indices: 88915--89090 Score: 257
Period size: 29 Copynumber: 6.1 Consensus size: 29
88905 ATCGGGTGAC
* *
88915 ATTTTGGGAATTAATTTGAAATGAGTGCT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
88944 ATTTTGGGAATTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
*
88973 ATTTTGGGAATTAATTCAAAATGGGTGCT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
*
89002 ATTTTGGGAATTAATTCAAAATGGGTGCT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
* * *
89031 ATTTTGGGAATTAATT-GAAA-AGATGAT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
* *
89058 ATTTTGGGAATTAATTTGAAAAGGGTGCT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
89087 ATTT
1 ATTT
89091 ATGTAAAATG
Statistics
Matches: 135, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
27 20 0.15
28 7 0.05
29 108 0.80
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (29 bp):
ATTTTGGGAATTAATTCGAAATGGGTGCT
Found at i:89848 original size:14 final size:16
Alignment explanation
Indices: 89824--89856 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
89814 TGATACATGA
89824 TTCCTGAATAT-TGAT
1 TTCCTGAATATCTGAT
89839 TTCCTG-ATATCTGAT
1 TTCCTGAATATCTGAT
89854 TTC
1 TTC
89857 TGTATTTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.48
Consensus pattern (16 bp):
TTCCTGAATATCTGAT
Found at i:90368 original size:18 final size:18
Alignment explanation
Indices: 90332--90379 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
90322 ATATCTATAT
** *
90332 TATTAATATTTTGTTTTG
1 TATTAATATAATGTATTG
90350 TATTAATATAATGTATTG
1 TATTAATATAATGTATTG
*
90368 TAATATATATAA
1 TATTA-ATATAA
90380 AAAAAACCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (18 bp):
TATTAATATAATGTATTG
Found at i:96134 original size:18 final size:18
Alignment explanation
Indices: 96113--96157 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
96103 TCGACTCGAC
96113 CCGTTGACCCGACCCGAA
1 CCGTTGACCCGACCCGAA
*
96131 CCGTTGACCCGACCCGAC
1 CCGTTGACCCGACCCGAA
96149 CCGTTGACC
1 CCGTTGACC
96158 GTTGACCGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.13
Consensus pattern (18 bp):
CCGTTGACCCGACCCGAA
Found at i:96308 original size:29 final size:29
Alignment explanation
Indices: 96172--96319 Score: 178
Period size: 29 Copynumber: 5.1 Consensus size: 29
96162 ACCGGGTGAC
*
96172 ATTTTGGGAATTAATTC-GAAATGGGTGCT
1 ATTTTGGGAATTAATTCAAAAAT-GGTGCT
*
96201 ATTTTGGGAATTAATT--TAAATGGGTGCT
1 ATTTTGGGAATTAATTCAAAAAT-GGTGCT
*
96229 ATTTTGGGAATTTAATTCAAAAA-GGTGAT
1 ATTTTGGGAA-TTAATTCAAAAATGGTGCT
*
96258 ATTTTGGGAATTAATTCGAAAATGGTGCT
1 ATTTTGGGAATTAATTCAAAAATGGTGCT
* * *
96287 ATTTTGGTAATTATTTTAAAAATGGTGCT
1 ATTTTGGGAATTAATTCAAAAATGGTGCT
96316 ATTT
1 ATTT
96320 CTGTAAAATG
Statistics
Matches: 106, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
28 32 0.30
29 71 0.67
31 3 0.03
ACGTcount: A:0.31, C:0.05, G:0.22, T:0.42
Consensus pattern (29 bp):
ATTTTGGGAATTAATTCAAAAATGGTGCT
Found at i:96319 original size:58 final size:58
Alignment explanation
Indices: 96172--96319 Score: 180
Period size: 57 Copynumber: 2.6 Consensus size: 58
96162 ACCGGGTGAC
* *
96172 ATTTTGGGAA-TTAATTC-GAAATGGGTGCTATTTTGGGAATTAATTTAAATGGGTGCT
1 ATTTTGGGAATTTAATTCAAAAAT-GGTGCTATTTTGGGAATTAATTAAAATGGGTGCT
*
96229 ATTTTGGGAATTTAATTCAAAAA-GGTGATATTTTGGGAATTAATTCGAAAAT-GGTGCT
1 ATTTTGGGAATTTAATTCAAAAATGGTGCTATTTTGGGAATTAATT--AAAATGGGTGCT
* * *
96287 ATTTTGGTAA-TTATTTTAAAAATGGTGCTATTT
1 ATTTTGGGAATTTAATTCAAAAATGGTGCTATTT
96320 CTGTAAAATG
Statistics
Matches: 79, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
57 41 0.52
58 31 0.39
59 7 0.09
ACGTcount: A:0.31, C:0.05, G:0.22, T:0.42
Consensus pattern (58 bp):
ATTTTGGGAATTTAATTCAAAAATGGTGCTATTTTGGGAATTAATTAAAATGGGTGCT
Found at i:97090 original size:14 final size:16
Alignment explanation
Indices: 97066--97098 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
97056 TGATACATGA
97066 TTCCTGAATAT-TGAT
1 TTCCTGAATATCTGAT
97081 TTCCTG-ATATCTGAT
1 TTCCTGAATATCTGAT
97096 TTC
1 TTC
97099 TGTATTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.48
Consensus pattern (16 bp):
TTCCTGAATATCTGAT
Found at i:97767 original size:27 final size:25
Alignment explanation
Indices: 97741--97789 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
97731 TTTTCAATAA
97741 AAATAATATTATTAATAAATTACAT
1 AAATAATATTATTAATAAATTACAT
* *
97766 AAAT-GTATTATTATTAAATTACAT
1 AAATAATATTATTAATAAATTACAT
97790 CAATTATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (25 bp):
AAATAATATTATTAATAAATTACAT
Found at i:97939 original size:50 final size:50
Alignment explanation
Indices: 97880--97983 Score: 199
Period size: 50 Copynumber: 2.1 Consensus size: 50
97870 CTCGTAAGCC
97880 AAATTCTATTGCAATTCTTCGAACTCACTTTTCAGTTGCTACAGTAAAAT
1 AAATTCTATTGCAATTCTTCGAACTCACTTTTCAGTTGCTACAGTAAAAT
*
97930 AAATTCTATTGCTATTCTTCGAACTCACTTTTCAGTTGCTACAGTAAAAT
1 AAATTCTATTGCAATTCTTCGAACTCACTTTTCAGTTGCTACAGTAAAAT
97980 AAAT
1 AAAT
97984 AAATATTATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (50 bp):
AAATTCTATTGCAATTCTTCGAACTCACTTTTCAGTTGCTACAGTAAAAT
Found at i:98006 original size:50 final size:49
Alignment explanation
Indices: 97893--98000 Score: 148
Period size: 50 Copynumber: 2.2 Consensus size: 49
97883 TTCTATTGCA
* **
97893 ATTCTTCGAACTCACTTTTCAGTTGCTACAGTAAAATAAATTCTATTGCT
1 ATTCTTCAAACTCACTTTTCAGTTGCTACAGTAAAATAAATAATATT-CT
*
97943 ATTCTTCGAACTCACTTTTCAGTTGCTACAGTAAAATAAATAA-ATAT-T
1 ATTCTTCAAACTCACTTTTCAGTTGCTACAGTAAAATAAATAATAT-TCT
97991 ATTCTTCAAA
1 ATTCTTCAAA
98001 GACTCATGAG
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
48 10 0.19
49 2 0.04
50 42 0.78
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (49 bp):
ATTCTTCAAACTCACTTTTCAGTTGCTACAGTAAAATAAATAATATTCT
Found at i:98295 original size:27 final size:30
Alignment explanation
Indices: 98242--98296 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
98232 ATTTTCATTT
* *
98242 TAATATTATATAATGAATTTTCAATAAAAA
1 TAATATTATATAATGAAATTACAATAAAAA
98272 TAATATTAT-TAAT-AAATTAC-ATAAA
1 TAATATTATATAATGAAATTACAATAAA
98297 TGTATTGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 5 0.22
29 4 0.17
30 9 0.39
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (30 bp):
TAATATTATATAATGAAATTACAATAAAAA
Found at i:101502 original size:27 final size:30
Alignment explanation
Indices: 101449--101503 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
101439 ATTTTCATTT
* *
101449 TAATATTATATAATGAACTTTCAATAAAAA
1 TAATATTATATAATGAAATTACAATAAAAA
101479 TAATATTAT-TAAT-AAATTAC-ATAAA
1 TAATATTATATAATGAAATTACAATAAA
101504 TGTATTGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 5 0.22
29 4 0.17
30 9 0.39
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (30 bp):
TAATATTATATAATGAAATTACAATAAAAA
Found at i:104668 original size:25 final size:26
Alignment explanation
Indices: 104634--104685 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
104624 TCAGTTTTAT
104634 TCCATTCATTTCAGAGCTCGAGGATA
1 TCCATTCATTTCAGAGCTCGAGGATA
* * *
104660 TCCA-TCATTTCTGAGCTTGATGATA
1 TCCATTCATTTCAGAGCTCGAGGATA
104685 T
1 T
104686 TCTTGGGTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (26 bp):
TCCATTCATTTCAGAGCTCGAGGATA
Found at i:106093 original size:17 final size:16
Alignment explanation
Indices: 106061--106107 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
106051 GGTCAAATCC
106061 GGTCAACAATGGTCAACG
1 GGTCAAC-A-GGTCAACG
106079 CCGGTCAAC-GGTCAACG
1 --GGTCAACAGGTCAACG
106096 GGTCAACAGGTC
1 GGTCAACAGGTC
106108 GGGTCAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.27
16 4 0.15
17 8 0.31
20 7 0.27
ACGTcount: A:0.28, C:0.28, G:0.30, T:0.15
Consensus pattern (16 bp):
GGTCAACAGGTCAACG
Found at i:108287 original size:24 final size:24
Alignment explanation
Indices: 108260--108335 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
108250 TATATCAAAA
108260 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
108284 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * **
108308 ATCAGATCAGAATCCAAATCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
108332 ATCA
1 ATCA
108336 GATCAGAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.09
24 41 0.91
ACGTcount: A:0.46, C:0.20, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:108336 original size:24 final size:24
Alignment explanation
Indices: 108277--108440 Score: 179
Period size: 24 Copynumber: 6.8 Consensus size: 24
108267 CATAAATCAG
* * *
108277 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAA
108301 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
* * *
108325 ATCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAA
* *
108349 GT-TAGATATCAGATCATAATCCAA
1 GTCAAG-TATCAGATCAGAATCCAA
* *
108373 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAA
* *
108397 GT-TAGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
*
108421 TTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
108441 TCAAATCGAA
Statistics
Matches: 117, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
23 4 0.03
24 109 0.93
25 4 0.03
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:108340 original size:12 final size:12
Alignment explanation
Indices: 108272--108340 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
108262 CAAAACATAA
*
108272 ATCAGGTCAAGT
1 ATCAGATCAAGT
* *
108284 ATCATATCAA-A
1 ATCAGATCAAGT
*
108295 ATCCAGGTCAAGT
1 AT-CAGATCAAGT
*
108308 ATCAGATC-AGA
1 ATCAGATCAAGT
*
108319 ATCCAAATCAAGT
1 AT-CAGATCAAGT
108332 ATCAGATCA
1 ATCAGATCA
108341 GAATCTATGT
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
11 6 0.14
12 30 0.71
13 6 0.14
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.23
Consensus pattern (12 bp):
ATCAGATCAAGT
Found at i:108359 original size:48 final size:48
Alignment explanation
Indices: 108307--108440 Score: 232
Period size: 48 Copynumber: 2.8 Consensus size: 48
108297 CCAGGTCAAG
108307 TATCAGATCAGAATCCAAATCAAGTATCAGATCAGAATCTATGTTAGA
1 TATCAGATCAGAATCCAAATCAAGTATCAGATCAGAATCTATGTTAGA
* *
108355 TATCAGATCATAATCCAAGTCAAGTATCAGATCAGAATCTATGTTAGA
1 TATCAGATCAGAATCCAAATCAAGTATCAGATCAGAATCTATGTTAGA
**
108403 TATCAGATCAGAATCCATTTCAAGTATCAGATCAGAAT
1 TATCAGATCAGAATCCAAATCAAGTATCAGATCAGAAT
108441 TCAAATCGAA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 81 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.28
Consensus pattern (48 bp):
TATCAGATCAGAATCCAAATCAAGTATCAGATCAGAATCTATGTTAGA
Found at i:108431 original size:72 final size:73
Alignment explanation
Indices: 108278--108436 Score: 200
Period size: 72 Copynumber: 2.2 Consensus size: 73
108268 ATAAATCAGG
* *
108278 TCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATCAAGTATCAGATCAGA
1 TCAAGTATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAAGTATCAGATCAGA
*
108343 ATCTATGT
66 ATCCATGT
* * ** *
108351 T--AGATATCAGATCATAATCCAAGTCAAGTATCAGATCAGAATCTATGT-TAGATATCAGATCA
1 TCAAG-TATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAAG-TATCAGATCA
108413 GAATCCAT-T
64 GAATCCATGT
108422 TCAAGTATCAGATCA
1 TCAAGTATCAGATCA
108437 GAATTCAAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
71 6 0.08
72 65 0.88
73 3 0.04
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (73 bp):
TCAAGTATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAAGTATCAGATCAGA
ATCCATGT
Found at i:109456 original size:25 final size:26
Alignment explanation
Indices: 109414--109465 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
109404 TCAGTTTTAT
*
109414 TCCATTCATTTCAAAGCTCGA-GATA
1 TCCAATCATTTCAAAGCTCGATGATA
** *
109439 TCCAATCATTTCTGAGCTTGATGATA
1 TCCAATCATTTCAAAGCTCGATGATA
109465 T
1 T
109466 TCTTGGGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (26 bp):
TCCAATCATTTCAAAGCTCGATGATA
Found at i:112398 original size:2 final size:2
Alignment explanation
Indices: 112391--112423 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
112381 TTTCTTGGAA
112391 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
112424 AGATATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:114195 original size:12 final size:12
Alignment explanation
Indices: 114173--114205 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
114163 TTAATATACT
114173 ATTTT-ATTAAC
1 ATTTTAATTAAC
114184 ATTTTAATTAAC
1 ATTTTAATTAAC
114196 ATTTTAATTA
1 ATTTTAATTA
114206 TTAAATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTTAATTAAC
Found at i:115611 original size:2 final size:2
Alignment explanation
Indices: 115604--115632 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
115594 TATTTCTTGG
115604 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
115633 AGATATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:121006 original size:36 final size:36
Alignment explanation
Indices: 120959--121040 Score: 137
Period size: 36 Copynumber: 2.2 Consensus size: 36
120949 AGTTCTGGAA
*
120959 TTAAGTGATAAAAGAATCAGCCATGGATATGTAGAT
1 TTAAGTTATAAAAGAATCAGCCATGGATATGTAGAT
120995 TTAAGTTATAAAAGAATCAGCCATGGATATGTAGAT
1 TTAAGTTATAAAAGAATCAGCCATGGATATGTAGAT
*
121031 TATAATTTAT
1 T-TAAGTTAT
121041 CTCATTAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
36 36 0.84
37 7 0.16
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.33
Consensus pattern (36 bp):
TTAAGTTATAAAAGAATCAGCCATGGATATGTAGAT
Found at i:122837 original size:24 final size:24
Alignment explanation
Indices: 122810--122899 Score: 137
Period size: 24 Copynumber: 3.8 Consensus size: 24
122800 TTTTATCTGA
122810 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACTTGG
*
122834 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACTTGG
*
122858 ATTTTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACTTGG
*
122882 ATTCTTATCTGATACTTG
1 ATTCTGATCTGATACTTG
122900 GCCTGATTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
23 1 0.02
24 57 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACTTGG
Found at i:125713 original size:36 final size:36
Alignment explanation
Indices: 125666--125738 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
125656 AGTTCTGGAA
*
125666 TTAAGTGATAAAAGAATCAGCCATGGATATGTAGAT
1 TTAAGTGATAAAAGAATCAACCATGGATATGTAGAT
125702 TTAAGTGATAAAAGAATCAACCATGGATATGTAGAT
1 TTAAGTGATAAAAGAATCAACCATGGATATGTAGAT
125738 T
1 T
125739 ATAATTTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (36 bp):
TTAAGTGATAAAAGAATCAACCATGGATATGTAGAT
Found at i:127508 original size:24 final size:24
Alignment explanation
Indices: 127476--127587 Score: 163
Period size: 24 Copynumber: 4.7 Consensus size: 24
127466 ATTTGAATTT
127476 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
*
127500 TGATATGATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
*
127524 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* *
127548 TGATCTGATACTTGACTTGGATTT
1 TGATCTGATACTTGACATGGATTC
*
127572 TGATATGATACTTGAC
1 TGATCTGATACTTGAC
127588 CTGATTTATG
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:127525 original size:12 final size:12
Alignment explanation
Indices: 127488--127526 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
127478 ATCTGATACT
127488 TGACATGGATTC
1 TGACATGGATTC
*
127500 TGATAT-GATATC
1 TGACATGGAT-TC
127512 TGACATGGATTC
1 TGACATGGATTC
127524 TGA
1 TGA
127527 TCTGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:129539 original size:22 final size:22
Alignment explanation
Indices: 129514--129565 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
129504 ATATTATTAT
*
129514 TTTAATAAAAATAATAATATAA
1 TTTAATAAAAATAATAATAAAA
* * **
129536 TTTATTAAAAGTTTTAATAAAA
1 TTTAATAAAAATAATAATAAAA
129558 TTTAATAA
1 TTTAATAA
129566 TCTTAATATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TTTAATAAAAATAATAATAAAA
Found at i:132025 original size:24 final size:24
Alignment explanation
Indices: 132004--132101 Score: 124
Period size: 24 Copynumber: 4.1 Consensus size: 24
131994 TATATCAAAA
* *
132004 ATCAAAACATAATCCAGGTCAAGT
1 ATCAAATCAAAATCCAGGTCAAGT
*
132028 ATCAAATCAAAATCCATGTCAAGT
1 ATCAAATCAAAATCCAGGTCAAGT
132052 ATCAAATCAAAATCCAGGTCAAGT
1 ATCAAATCAAAATCCAGGTCAAGT
** * * *
132076 ATCCGATCAGAATCCAAGTCAGGT
1 ATCAAATCAAAATCCAGGTCAAGT
132100 AT
1 AT
132102 TATAATATAA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAATCAAAATCCAGGTCAAGT
Found at i:133264 original size:18 final size:18
Alignment explanation
Indices: 133243--133278 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
133233 CTTCCATCCG
*
133243 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
133261 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
133279 GTCCTTTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:140080 original size:23 final size:24
Alignment explanation
Indices: 140054--140135 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 24
140044 ATGAATTTAT
140054 TATTATTAAATTA-TTTAATAATA
1 TATTATTAAATTATTTTAATAATA
*
140077 TATTAAAAATAATATTATTTTAATAATA
1 TATT---ATTAA-ATTATTTTAATAATA
*
140105 TAGTT-TTTAA-TATTTTAATAATA
1 TA-TTATTAAATTATTTTAATAATA
140128 TTATTATT
1 -TATTATT
140136 TTCAATAGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
23 19 0.40
24 5 0.10
25 2 0.04
26 4 0.08
27 4 0.08
28 12 0.25
29 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (24 bp):
TATTATTAAATTATTTTAATAATA
Found at i:140137 original size:26 final size:23
Alignment explanation
Indices: 140092--140142 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
140082 AAAATAATAT
* *
140092 TATTTTAATAATATAGTTTTTAA
1 TATTTTAATAATATAATTTTCAA
140115 TATTTTAATAATATTATTATTTTCAA
1 TATTTTAATAATA-TA--ATTTTCAA
140141 TA
1 TA
140143 GTAATTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 13 0.57
24 2 0.09
26 8 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TATTTTAATAATATAATTTTCAA
Found at i:140202 original size:26 final size:26
Alignment explanation
Indices: 140139--140199 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
140129 TATTATTTTC
* * *
140139 AATAGTAATTAATATAATCAATAATAT
1 AATA-TAATTATTTTAATAAATAATAT
*
140166 ATTATAATTATTTTAATAAATAAT-T
1 AATATAATTATTTTAATAAATAATAT
140191 AATATAATT
1 AATATAATT
140200 TATAAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 9 0.31
26 17 0.59
27 3 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
AATATAATTATTTTAATAAATAATAT
Found at i:143035 original size:20 final size:19
Alignment explanation
Indices: 142993--143035 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
142983 TGAGGACTTT
142993 TATATTATTTATAAAAATA
1 TATATTATTTATAAAAATA
143012 -ATATT-TTTCATAAAAAATA
1 TATATTATTT-AT-AAAAATA
143031 TATAT
1 TATAT
143036 ATATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.14
18 7 0.33
19 7 0.33
20 4 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATTATTTATAAAAATA
Found at i:143722 original size:15 final size:15
Alignment explanation
Indices: 143702--143751 Score: 100
Period size: 15 Copynumber: 3.3 Consensus size: 15
143692 AATGAAGCAT
143702 ATGCTCTTATCACCC
1 ATGCTCTTATCACCC
143717 ATGCTCTTATCACCC
1 ATGCTCTTATCACCC
143732 ATGCTCTTATCACCC
1 ATGCTCTTATCACCC
143747 ATGCT
1 ATGCT
143752 AGGTAATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.20, C:0.38, G:0.08, T:0.34
Consensus pattern (15 bp):
ATGCTCTTATCACCC
Found at i:144296 original size:21 final size:20
Alignment explanation
Indices: 144251--144296 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
144241 AACCAGTTGC
144251 AGAGAAAAAAGAAAGGAAAT
1 AGAGAAAAAAGAAAGGAAAT
144271 A-AGAAAAATATGAAAGGAAA-
1 AGAGAAAAA-A-GAAAGGAAAT
144291 AGAGAA
1 AGAGAA
144297 CACGTGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.30
20 3 0.13
21 13 0.57
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.07
Consensus pattern (20 bp):
AGAGAAAAAAGAAAGGAAAT
Found at i:146861 original size:48 final size:48
Alignment explanation
Indices: 146805--146901 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
146795 AAATATTTTA
146805 TCTTATTTCTGA-CTTGAATTCTGTTCTGATACATGACCTGAATTATGT
1 TCTTATTTCTGATC-TGAATTCTGTTCTGATACATGACCTGAATTATGT
* * ** *
146853 TCTTATTTCTGATCTGCATTCTGTTCTGATATATGTTCTGAATTCTGT
1 TCTTATTTCTGATCTGAATTCTGTTCTGATACATGACCTGAATTATGT
146901 T
1 T
146902 TTGATTTATG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 42 0.98
49 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.49
Consensus pattern (48 bp):
TCTTATTTCTGATCTGAATTCTGTTCTGATACATGACCTGAATTATGT
Found at i:146911 original size:24 final size:24
Alignment explanation
Indices: 146819--146913 Score: 100
Period size: 24 Copynumber: 4.0 Consensus size: 24
146809 ATTTCTGACT
* *
146819 TGAATTCTGTTCTGATACATGACC
1 TGAATTCTGTTCTGATATATGATC
* * * *
146843 TGAATTATGTTCTTATTTCTGATC
1 TGAATTCTGTTCTGATATATGATC
* *
146867 TGCATTCTGTTCTGATATATGTTC
1 TGAATTCTGTTCTGATATATGATC
* *
146891 TGAATTCTGTTTTGATTTATGAT
1 TGAATTCTGTTCTGATATATGAT
146914 ATTTCCGTTT
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATATGATC
Found at i:149310 original size:24 final size:24
Alignment explanation
Indices: 149218--149312 Score: 77
Period size: 24 Copynumber: 4.0 Consensus size: 24
149208 ATTTCTGACT
* ** *
149218 TGAATTCTGTTCTGATACATGACC
1 TGAATTCTGTTTTGATTTATGATC
* *
149242 TGAATTTTGTTCTT-ATTTCTGATC
1 TGAATTCTGTT-TTGATTTATGATC
* * *
149266 TGCATTCTGTTATG-TTATATGTTC
1 TGAATTCTGTTTTGATT-TATGATC
149290 TGAATTCTGTTTTGATTTATGAT
1 TGAATTCTGTTTTGATTTATGAT
149313 ATTTTCATTT
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
23 3 0.06
24 47 0.89
25 3 0.06
ACGTcount: A:0.20, C:0.13, G:0.16, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTTTGATTTATGATC
Found at i:151710 original size:24 final size:24
Alignment explanation
Indices: 151618--151712 Score: 100
Period size: 24 Copynumber: 4.0 Consensus size: 24
151608 ATCTCCGACT
* *
151618 TGAATTCTGTTCTGATACATGACC
1 TGAATTCTGTTCTGATATATGATC
* * * *
151642 TGAATTTTGTTCTTATTTCTGATC
1 TGAATTCTGTTCTGATATATGATC
* *
151666 TGCATTCTGTTCTGATATATGTTC
1 TGAATTCTGTTCTGATATATGATC
* *
151690 TGAATTCTGTTTTGATTTATGAT
1 TGAATTCTGTTCTGATATATGAT
151713 ATTTTCGTTT
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATATGATC
Found at i:154003 original size:48 final size:48
Alignment explanation
Indices: 153951--154044 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
153941 TCCGACTTGT
153951 ATTCTGTTCTGATA-CATGACCTGAATTATGTTTTGATTTCTGATATGG
1 ATTCTGTTCTGATATC-TGACCTGAATTATGTTTTGATTTCTGATATGG
** *
153999 ATTCTGTTCTGATATCTGTTCTGAATTCTGTTTTGATTTCTGATAT
1 ATTCTGTTCTGATATCTGACCTGAATTATGTTTTGATTTCTGATAT
154045 TTCCATTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
48 41 0.98
49 1 0.02
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (48 bp):
ATTCTGTTCTGATATCTGACCTGAATTATGTTTTGATTTCTGATATGG
Found at i:154006 original size:24 final size:24
Alignment explanation
Indices: 153972--154044 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
153962 ATACATGACC
*
153972 TGAATTATGTTTTGATTTCTGATA
1 TGAATTCTGTTTTGATTTCTGATA
* * * * *
153996 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTTTGATTTCTGATA
154020 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTTTGATTTCTGATA
154044 T
1 T
154045 TTCCATTTAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.19, C:0.10, G:0.18, T:0.53
Consensus pattern (24 bp):
TGAATTCTGTTTTGATTTCTGATA
Found at i:158320 original size:24 final size:24
Alignment explanation
Indices: 158228--158322 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 24
158218 ATTTCCGACT
* * *
158228 TGAATTCTGTTCTGA-TACATGACC
1 TGAATTCTGTTTTGATTTC-TGATC
*
158252 TGAATTCTGTTTTGATTTCTAATC
1 TGAATTCTGTTTTGATTTCTGATC
* * * *
158276 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTTTGATTTCTGATC
*
158300 TGAATTATGTTTTGATTTCTGAT
1 TGAATTCTGTTTTGATTTCTGAT
158323 ATTTTCATTT
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
24 54 0.96
25 2 0.04
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTTTGATTTCTGATC
Found at i:159125 original size:21 final size:21
Alignment explanation
Indices: 159101--159150 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
159091 TTCAACAAAA
159101 ATAATATTATTCA-TAAATTAC
1 ATAATATTATT-ATTAAATTAC
*
159122 ATAA-ATGTATTATTAAATTAT
1 ATAATAT-TATTATTAAATTAC
*
159143 TTAATATT
1 ATAATATT
159151 TATAACACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
20 3 0.12
21 19 0.79
22 2 0.08
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (21 bp):
ATAATATTATTATTAAATTAC
Found at i:163684 original size:372 final size:372
Alignment explanation
Indices: 162999--163725 Score: 1170
Period size: 372 Copynumber: 2.0 Consensus size: 372
162989 TTATTGATGT
*
162999 AAACTGATAATTAAAGTGAAAATGTTATTAATTTCTCTTAAAACCTTAGATTCATGTCACAACCA
1 AAACTGATAATTAAAGTGAAAATGTTATTAATTTCTATTAAAACCTTAGATTCATGTCACAACCA
* * * *
163064 CTAAGATACTCTAAAATAACCATATTTGATGTCAAACAATTGTTCCAACAGTAGTAAGGTCTTCT
66 CTAAAACACTCTAAAATAACCATATTTGATATCAAACAATTGCTCCAACAGTAGTAAGGTCTTCT
* * *
163129 GCCGACCAAAGTCATAAAATCATTTTGCCCCTAAAAGCTTCAATGGCTAGTCTAAACATTTTTGC
131 ACCGAACAAAGTCATAAAATCATTTTGCCCCTAAAAGCTTCAATGGCTAGCCTAAACATTTTTGC
* *
163194 TACAATAAAGATTCTTGTTATTTTTGCAAGTGGAGGTGTAATGGCTCAAGACTTTTACGATTGTG
196 TACAATAAAGATTCTTGTTATTTTTGCAAGAGGACGTGTAATGGCTCAAGACTTTTACGATTGTG
* *
163259 AAACCCAGAACAAGATGGACTTGCATTGTATTTTTGAAGTATTTGATAACATATTTAAAGTTGGA
261 AAACCCAGAACAAGATGGACTTGCATTGTATTTTTGAAGTAATTGACAACATATTTAAAGTTGGA
*
163324 ACGGTCACGAATGAATGTTGTCATCAACTTCTTAGATTCATGTTATG
326 ACGGTCACGAATAAATGTTGTCATCAACTTCTTAGATTCATGTTATG
**
163371 AAACTGATAATTAAAGTGAAAATGTTATTAATTTCTATTAAAACCTTAGATTCATGTCACGGCCA
1 AAACTGATAATTAAAGTGAAAATGTTATTAATTTCTATTAAAACCTTAGATTCATGTCACAACCA
* * * * *
163436 TTAAAACACTCTATAAATGACCATATTTGTTATCAAACAATTGCTGCAATAGTAGTAAGGTCTTC
66 CTAAAACACTCTA-AAATAACCATATTTGATATCAAACAATTGCTCCAACAGTAGTAAGGTCTTC
* * *
163501 TACCGAACAAAGTCAT-AAATCCTTTTGCCCCTAAAAGCTTCAATGGGTGGCCTAAACATTTTTG
130 TACCGAACAAAGTCATAAAATCATTTTGCCCCTAAAAGCTTCAATGGCTAGCCTAAACATTTTTG
* ** *
163565 CTACTATAGCGATTCTTGTTATTTTTGCAAGAGGACTTGTAATGGCTCAAGACTTTTACGATTGT
195 CTACAATAAAGATTCTTGTTATTTTTGCAAGAGGACGTGTAATGGCTCAAGACTTTTACGATTGT
*
163630 G-AACACCAGAACAAGATGGACTTGTATTGTATTTTTGAAGTAATTGACAACATATTTAAAGTTG
260 GAAAC-CCAGAACAAGATGGACTTGCATTGTATTTTTGAAGTAATTGACAACATATTTAAAGTTG
163694 GAACGGTCACGAATAAATGTTGTCATCAACTT
324 GAACGGTCACGAATAAATGTTGTCATCAACTT
163726 GTTAATCTAG
Statistics
Matches: 325, Mismatches: 28, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
371 3 0.01
372 263 0.81
373 59 0.18
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (372 bp):
AAACTGATAATTAAAGTGAAAATGTTATTAATTTCTATTAAAACCTTAGATTCATGTCACAACCA
CTAAAACACTCTAAAATAACCATATTTGATATCAAACAATTGCTCCAACAGTAGTAAGGTCTTCT
ACCGAACAAAGTCATAAAATCATTTTGCCCCTAAAAGCTTCAATGGCTAGCCTAAACATTTTTGC
TACAATAAAGATTCTTGTTATTTTTGCAAGAGGACGTGTAATGGCTCAAGACTTTTACGATTGTG
AAACCCAGAACAAGATGGACTTGCATTGTATTTTTGAAGTAATTGACAACATATTTAAAGTTGGA
ACGGTCACGAATAAATGTTGTCATCAACTTCTTAGATTCATGTTATG
Found at i:165134 original size:2 final size:2
Alignment explanation
Indices: 165127--165154 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
165117 CTGAAAAATA
165127 AT AT 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
165155 CAAGAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:170468 original size:20 final size:20
Alignment explanation
Indices: 170432--170469 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
170422 TTATAATTTT
*
170432 ATTTTAATAATATATAATGA
1 ATTTTAATAATAAATAATGA
170452 ATTTTCAATAA-AAATAAT
1 ATTTT-AATAATAAATAAT
170470 ATTATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTTTAATAATAAATAATGA
Found at i:170543 original size:14 final size:15
Alignment explanation
Indices: 170492--170548 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 15
170482 TTACATAAAT
*
170492 TTATTATTATTAA-A
1 TTATTATTAATAATA
170506 TTA-T-TTAATAATA
1 TTATTATTAATAATA
**
170519 -TATTAAAAATAATA
1 TTATTATTAATAATA
170533 TTATT-TTAATAATA
1 TTATTATTAATAATA
170547 TT
1 TT
170549 TTTAATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
12 8 0.24
13 3 0.09
14 19 0.56
15 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATTATTAATAATA
Found at i:171559 original size:13 final size:14
Alignment explanation
Indices: 171543--171576 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
171533 GGGCTGATCC
171543 GACCCACTGA-CCA
1 GACCCACTGACCCA
171556 GACCCACTGACCCA
1 GACCCACTGACCCA
171570 -ACCCACT
1 GACCCACT
171577 AATCCGACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 17 0.85
14 3 0.15
ACGTcount: A:0.29, C:0.50, G:0.12, T:0.09
Consensus pattern (14 bp):
GACCCACTGACCCA
Found at i:171655 original size:14 final size:14
Alignment explanation
Indices: 171636--171668 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
171626 TAATCGACCG
171636 TTGATTGTTGATCA
1 TTGATTGTTGATCA
*
171650 TTGATTGTTGATCG
1 TTGATTGTTGATCA
171664 TTGAT
1 TTGAT
171669 CGACCGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.24, T:0.52
Consensus pattern (14 bp):
TTGATTGTTGATCA
Found at i:172459 original size:39 final size:39
Alignment explanation
Indices: 172419--172599 Score: 200
Period size: 39 Copynumber: 4.6 Consensus size: 39
172409 AGGCTCTTCG
* * **
172419 GCTTTGTACTCAGGGTAAGTCCTTACTGCAGGTTCCTCG
1 GCTTTGTACACAGGGTAAGTCCTTACTGCAGGCTCCTAT
* * * * *
172458 GCATTGTTCTCAGGGTAAGTCCTTACTGTAGTCTCCTAT
1 GCTTTGTACACAGGGTAAGTCCTTACTGCAGGCTCCTAT
* * * * *
172497 GCTTTGTGCACAGGATAAGACCTTACTGCAGGCTCATTT
1 GCTTTGTACACAGGGTAAGTCCTTACTGCAGGCTCCTAT
* *
172536 GCTTTGTACAAAGGGTAAGACCTTACTGCAGGCTCCTAT
1 GCTTTGTACACAGGGTAAGTCCTTACTGCAGGCTCCTAT
* *
172575 ACTTTGTGCACAGGGTAAGTCCTTA
1 GCTTTGTACACAGGGTAAGTCCTTA
172600 TTGGGTGTAC
Statistics
Matches: 117, Mismatches: 25, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 117 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (39 bp):
GCTTTGTACACAGGGTAAGTCCTTACTGCAGGCTCCTAT
Found at i:172996 original size:28 final size:29
Alignment explanation
Indices: 172959--173015 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
172949 ATTTTATACG
* *
172959 GTTTTCTATAGTATTTTG-ATATGTATAT
1 GTTTTATATAGTATTCTGAATATGTATAT
172987 GTTTTATATAGTATTCTGACATATGTATA
1 GTTTTATATAGTATTCTGA-ATATGTATA
173016 CATATATGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 16 0.64
30 9 0.36
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (29 bp):
GTTTTATATAGTATTCTGAATATGTATAT
Found at i:173211 original size:19 final size:19
Alignment explanation
Indices: 173187--173224 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
173177 AGGGTTTTGG
*
173187 TAAAAAGAGATTTAAATAA
1 TAAAAAGAAATTTAAATAA
173206 TAAAAAGAAATTTAAATAA
1 TAAAAAGAAATTTAAATAA
173225 AGAATAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (19 bp):
TAAAAAGAAATTTAAATAA
Found at i:174127 original size:27 final size:26
Alignment explanation
Indices: 174096--174149 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
174086 CCAGAAGGCG
*
174096 CTGACTAGATCATCTAGAAAACTGCCA
1 CTGACTAGACCATCTAG-AAACTGCCA
* *
174123 CTGACTGGACCTTCTAGAAACTGCCA
1 CTGACTAGACCATCTAGAAACTGCCA
174149 C
1 C
174150 ATCAGACCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (26 bp):
CTGACTAGACCATCTAGAAACTGCCA
Found at i:176361 original size:68 final size:68
Alignment explanation
Indices: 176252--176388 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
176242 AAGGCTAATC
176252 TATTTGGGGTTTAGCTGACGAAATGTATAAGAAGGGTGACAATATGATTTTGGGGAAAAAGAATG
1 TATTTGGGGTTTAGCTGACGAAATGTATAAGAAGGGTGACAATATGATTTTGGGGAAAAAGAATG
176317 AGT
66 AGT
176320 TATTTGGGGTTTAGCTGACGAAATGTATAAGAAGGGTGACAATATGATTTTGGGGAAAAAGAATG
1 TATTTGGGGTTTAGCTGACGAAATGTATAAGAAGGGTGACAATATGATTTTGGGGAAAAAGAATG
176385 AGT
66 AGT
176388 T
1 T
176389 GGCAGTTAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.35, C:0.04, G:0.31, T:0.30
Consensus pattern (68 bp):
TATTTGGGGTTTAGCTGACGAAATGTATAAGAAGGGTGACAATATGATTTTGGGGAAAAAGAATG
AGT
Found at i:182687 original size:17 final size:17
Alignment explanation
Indices: 182662--182694 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
182652 AGCATGTTTA
*
182662 AAAATAAAAATTAAAAG
1 AAAAGAAAAATTAAAAG
182679 AAAAGAAAAATTAAAA
1 AAAAGAAAAATTAAAA
182695 CTTGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAAGAAAAATTAAAAG
Found at i:182970 original size:27 final size:26
Alignment explanation
Indices: 182939--182992 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
182929 TTCCAAAAGA
* * *
182939 CGCTGATTAGATCTTTTAGAAAACTGC
1 CGCTGACTAGACCTTCTAG-AAACTGC
182966 CGCTGACTAGACCTTCTAGAAACTGC
1 CGCTGACTAGACCTTCTAGAAACTGC
182992 C
1 C
182993 ACGTCATACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (26 bp):
CGCTGACTAGACCTTCTAGAAACTGC
Found at i:187194 original size:16 final size:16
Alignment explanation
Indices: 187173--187205 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
187163 CTCATTTATC
187173 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
187189 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
187205 A
1 A
187206 AAACACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTTAAAACACACTT
Found at i:189477 original size:21 final size:21
Alignment explanation
Indices: 189451--189490 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
189441 CAGAACCCCA
*
189451 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
189472 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
189491 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:189525 original size:20 final size:21
Alignment explanation
Indices: 189471--189533 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
189461 GATTCCCCTG
189471 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
189495 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
189515 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
189534 TACACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:199277 original size:39 final size:39
Alignment explanation
Indices: 199234--199429 Score: 239
Period size: 39 Copynumber: 5.0 Consensus size: 39
199224 ACCACTTTTC
* * *
199234 GCAGGCTCCTCGGCTTTGTACTCAGGGTAAGTCCTTACT
1 GCAGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACT
*
199273 GCAGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACT
1 GCAGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACT
* * * * * * *
199312 GCATGCTCCTTTGCTTTGTGAACATGATAAGACATTACT
1 GCAGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACT
* ** * *
199351 ACAGGCTCCTCCACTTTGTGCACAGGATAAGACCTTACT
1 GCAGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACT
*
199390 GCAGGCTCCTCTACTTTGTGCACAGGGTAAGTCCTTACT
1 GCAGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACT
199429 G
1 G
199430 TTGTACAGGT
Statistics
Matches: 135, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 135 1.00
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.31
Consensus pattern (39 bp):
GCAGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACT
Found at i:200572 original size:21 final size:21
Alignment explanation
Indices: 200548--200595 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
200538 GTGCTAATGG
200548 GGTAGCCCATAAGGCTTACAT
1 GGTAGCCCATAAGGCTTACAT
* *
200569 GGTAGCCCATAATGCTTAGAT
1 GGTAGCCCATAAGGCTTACAT
200590 GGTAGC
1 GGTAGC
200596 TCATTGTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (21 bp):
GGTAGCCCATAAGGCTTACAT
Found at i:201262 original size:20 final size:20
Alignment explanation
Indices: 201226--201264 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
201216 TTATAATTTT
*
201226 ATTTTAATAATATATAATAA
1 ATTTTAATAATAAATAATAA
201246 ATTTTCAATAA-AAATAATA
1 ATTTT-AATAATAAATAATA
201265 TTAATTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTTAATAATAAATAATAA
Found at i:201381 original size:23 final size:23
Alignment explanation
Indices: 201339--201386 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
201329 ATAATATCCT
*
201339 TATTTTAATAATATAGTTTTTAA
1 TATTTTAATAATATAGTTTTCAA
*
201362 TATTTTAATATTATTA-TTTTCAA
1 TATTTTAATAATA-TAGTTTTCAA
201385 TA
1 TA
201387 GTAATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTTTAATAATATAGTTTTCAA
Found at i:201398 original size:45 final size:45
Alignment explanation
Indices: 201347--201452 Score: 117
Period size: 45 Copynumber: 2.3 Consensus size: 45
201337 CTTATTTTAA
* * *
201347 TAATATAGTTTTTAATATTTTA-ATATTATTATTTTCAAT-AGTAAT
1 TAATATAATTTTTAATATATTATA-ATTATTATTTT-AATAAATAAT
***
201392 TAATATAATCAATAATATATTATAATTATTATTTTAATAAATAAT
1 TAATATAATTTTTAATATATTATAATTATTATTTTAATAAATAAT
201437 TAATATAATTTATTAA
1 TAATATAATTT-TTAA
201453 AACTTTCAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
44 3 0.06
45 42 0.86
46 4 0.08
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (45 bp):
TAATATAATTTTTAATATATTATAATTATTATTTTAATAAATAAT
Found at i:204092 original size:2 final size:2
Alignment explanation
Indices: 204085--204176 Score: 184
Period size: 2 Copynumber: 46.0 Consensus size: 2
204075 TTTCAAGTAC
204085 AT AT AT AT AT AT AT AT AT 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 AT AT AT AT
204127 AT AT AT AT AT AT AT AT AT 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 AT AT AT AT
204169 AT AT AT AT
1 AT AT AT AT
204177 GGGAAACTTT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 90 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:212270 original size:20 final size:20
Alignment explanation
Indices: 212234--212271 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
212224 TTATACTTTT
*
212234 ATTTTAATAATATATAATGA
1 ATTTTAATAATAAATAATGA
212254 ATTTTCAATAA-AAATAAT
1 ATTTT-AATAATAAATAAT
212272 ATTATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTTTAATAATAAATAATGA
Found at i:218941 original size:21 final size:21
Alignment explanation
Indices: 218915--218954 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
218905 CCCCCTTTGA
*
218915 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
218936 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
218955 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:220954 original size:17 final size:17
Alignment explanation
Indices: 220921--220954 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
220911 TTGAATATTT
* *
220921 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
220938 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
220955 GATTTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:223218 original size:24 final size:24
Alignment explanation
Indices: 223191--223275 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
223181 TTCGATTTGA
*
223191 ATTATGTTATGATACCTGACATGG
1 ATTATGTTATGATACCTGACCTGG
* *
223215 ATTATGTTATAATACCTGACCTCG
1 ATTATGTTATGATACCTGACCTGG
* * ** *
223239 ATTCTGATATGATATTTGACCTGA
1 ATTATGTTATGATACCTGACCTGG
*
223263 ATTATGTTTTGAT
1 ATTATGTTATGAT
223276 TTTTGATATA
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.42
Consensus pattern (24 bp):
ATTATGTTATGATACCTGACCTGG
Found at i:227480 original size:24 final size:24
Alignment explanation
Indices: 227453--227505 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
227443 TTCGATTTGA
* *
227453 ATTCTGTTATTATACCTGACATGG
1 ATTCTGTTATAATACATGACATGG
* *
227477 ATTCTGTTCTAATACATGACCTGG
1 ATTCTGTTATAATACATGACATGG
227501 ATTCT
1 ATTCT
227506 AATATGATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (24 bp):
ATTCTGTTATAATACATGACATGG
Found at i:229450 original size:2 final size:2
Alignment explanation
Indices: 229445--229470 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
229435 ATTTTTTAAA
229445 AT 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
229471 TAAGAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:229454 original size:18 final size:19
Alignment explanation
Indices: 229414--229454 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
229404 TGAGGACTTT
229414 TATATTCTTTATAAAAATA
1 TATATTCTTTATAAAAATA
229433 -ATATT-TTT-TAAAATATA
1 TATATTCTTTATAAAA-ATA
229450 TATAT
1 TATAT
229455 ATATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATTCTTTATAAAAATA
Found at i:230969 original size:39 final size:39
Alignment explanation
Indices: 230926--231001 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
230916 ATAAACTTGT
* * *
230926 AGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCCTAC
1 AGTAAGGACTTACCCTAAGCACAAAGCCAAGGAGCCTAC
*
230965 AGTAAGGACTTACCCTAAGCACAGAGCCAAGGAGCCT
1 AGTAAGGACTTACCCTAAGCACAAAGCCAAGGAGCCT
231002 GGGGAAAGCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.34, C:0.26, G:0.25, T:0.14
Consensus pattern (39 bp):
AGTAAGGACTTACCCTAAGCACAAAGCCAAGGAGCCTAC
Found at i:241840 original size:14 final size:15
Alignment explanation
Indices: 241789--241844 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 15
241779 TTACATAAAT
*
241789 TTATTATTATTAA-A
1 TTATTATTAATAATA
241803 TTA-T-TTAATAATA
1 TTATTATTAATAATA
**
241816 -TATTAAAAATAATA
1 TTATTATTAATAATA
241830 TTATT-TTAATAATA
1 TTATTATTAATAATA
241844 T
1 T
241845 AGTTTTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
12 8 0.24
13 3 0.09
14 18 0.55
15 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATTATTAATAATA
Found at i:243789 original size:39 final size:38
Alignment explanation
Indices: 243746--243892 Score: 152
Period size: 39 Copynumber: 3.8 Consensus size: 38
243736 CCGCTTTCCG
* *
243746 TAGGCTCCTCGACTTTGTGCTCAGGGTAAGTCCTTACTC
1 TAGGCTCCTCG-CTTTGTGCACAGGGTAAGACCTTACTC
* *
243785 TAGGCTCCTCTGCTTTGTGCACAGGATAAGACCTTACTA
1 TAGGCTCCTC-GCTTTGTGCACAGGGTAAGACCTTACTC
* * *
243824 TAGGCTCATTTGCTTTGTGCATAGGGTAAGACCTTACTGC
1 TAGGCTC-CTCGCTTTGTGCACAGGGTAAGACCTTACT-C
** *
243864 -AGGCTCCTATACTTTGTGCACGGGGTAAG
1 TAGGCTCCT-CGCTTTGTGCACAGGGTAAG
243893 TTCTTATGGG
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
38 1 0.01
39 88 0.97
40 2 0.02
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (38 bp):
TAGGCTCCTCGCTTTGTGCACAGGGTAAGACCTTACTC
Found at i:244293 original size:28 final size:30
Alignment explanation
Indices: 244247--244309 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 30
244237 GTAAATGTTT
* * *
244247 TATATTGTTTTCTATAGTATTTTG-ATATG
1 TATATTGTTTTATACAGTATTCTGAATATG
244276 TATA-TGTTTTATACAGTATTCTGACATATG
1 TATATTGTTTTATACAGTATTCTGA-ATATG
244306 TATA
1 TATA
244310 CATGTATGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 16 0.55
29 4 0.14
30 9 0.31
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (30 bp):
TATATTGTTTTATACAGTATTCTGAATATG
Found at i:244523 original size:20 final size:19
Alignment explanation
Indices: 244483--244537 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
244473 GGGGTTTTGG
244483 TAAAAAGAAATTAAAATAA
1 TAAAAAGAAATTAAAATAA
244502 TAAAAAGAAATTCAAAGA-AA
1 TAAAAAGAAATT-AAA-ATAA
*
244522 TAATAAAGAAAATAAA
1 TAA-AAAGAAATTAAA
244538 GAGTGAAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 12 0.38
20 11 0.34
21 9 0.28
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (19 bp):
TAAAAAGAAATTAAAATAA
Found at i:244538 original size:20 final size:20
Alignment explanation
Indices: 244483--244539 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
244473 GGGGTTTTGG
244483 TAAAAAGAAATTAAA-ATAA
1 TAAAAAGAAATTAAAGATAA
244502 TAAAAAGAAATTCAAAGA-AA
1 TAAAAAGAAATT-AAAGATAA
*
244522 TAATAAAGAAAATAAAGA
1 TAA-AAAGAAATTAAAGA
244540 GTGAAACGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 12 0.35
20 13 0.38
21 9 0.26
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.18
Consensus pattern (20 bp):
TAAAAAGAAATTAAAGATAA
Found at i:246642 original size:18 final size:19
Alignment explanation
Indices: 246619--246657 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
246609 AATATCTTAA
*
246619 CCTAAACAATCAT-GTGTT
1 CCTAAACAAGCATGGTGTT
246637 CCTAAACAAGCATGGTGTT
1 CCTAAACAAGCATGGTGTT
246656 CC
1 CC
246658 AAAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (19 bp):
CCTAAACAAGCATGGTGTT
Found at i:253837 original size:17 final size:17
Alignment explanation
Indices: 253812--253844 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
253802 AGCATGTTTA
*
253812 AAAATAAAAATTAAAAG
1 AAAAGAAAAATTAAAAG
253829 AAAAGAAAAATTAAAA
1 AAAAGAAAAATTAAAA
253845 CTTGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAAGAAAAATTAAAAG
Found at i:260776 original size:39 final size:39
Alignment explanation
Indices: 260718--260815 Score: 169
Period size: 39 Copynumber: 2.5 Consensus size: 39
260708 ACCACTTTTC
* *
260718 GTAGGCTCCTCGGCATTGTGCTCAGGGTAAGTCCTTACT
1 GTAGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACT
260757 GTAGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACT
1 GTAGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACT
*
260796 GTAGGCTCCTTTGCTTTGTG
1 GTAGGCTCCTCTGCTTTGTG
260816 AGTATGATAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.12, C:0.24, G:0.28, T:0.36
Consensus pattern (39 bp):
GTAGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACT
Found at i:260835 original size:39 final size:39
Alignment explanation
Indices: 260718--260836 Score: 123
Period size: 39 Copynumber: 3.1 Consensus size: 39
260708 ACCACTTTTC
* * * * *
260718 GTAGGCTCCTCGGCATTGTGCTCAGGGTAAGTCCTTACT
1 GTAGGCTCCTCTGCTTTGTGCTCAGGATAAGACCATACT
* * *
260757 GTAGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACT
1 GTAGGCTCCTCTGCTTTGTGCTCAGGATAAGACCATACT
* * *
260796 GTAGGCTCCTTTGCTTTGTGAGT-ATGATAAGACCATACT
1 GTAGGCTCCTCTGCTTTGTG-CTCAGGATAAGACCATACT
260835 GT
1 GT
260837 TGTGCATAGG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
39 70 0.99
40 1 0.01
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (39 bp):
GTAGGCTCCTCTGCTTTGTGCTCAGGATAAGACCATACT
Found at i:262258 original size:2 final size:2
Alignment explanation
Indices: 262222--262250 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
262212 TTTCTTGGAA
262222 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
262251 AGATATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:263478 original size:21 final size:21
Alignment explanation
Indices: 263418--263470 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
263408 TGTGCTAATG
263418 TGGTAGCTCATAATGCTTACA
1 TGGTAGCTCATAATGCTTACA
*
263439 TGGTAGCCCATAATGCTTACA
1 TGGTAGCTCATAATGCTTACA
263460 TGGTAGCTCAT
1 TGGTAGCTCAT
263471 TGTACTTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (21 bp):
TGGTAGCTCATAATGCTTACA
Found at i:265299 original size:31 final size:31
Alignment explanation
Indices: 265264--265363 Score: 77
Period size: 31 Copynumber: 3.2 Consensus size: 31
265254 TTAATTGCTT
265264 TCTTAAACACTCTCTGATCTTGAAACGGTTC
1 TCTTAAACACTCTCTGATCTTGAAACGGTTC
* *
265295 TCTTAACAGACT-TCTAGTATCCTTCACAAAC---TC
1 TCTTAA-ACACTCTCT-G-AT-CTT--GAAACGGTTC
265328 T-TCT-AACACTCTCTGATCTTGAAACGGTTC
1 TCT-TAAACACTCTCTGATCTTGAAACGGTTC
265358 TCTTAA
1 TCTTAA
265364 CAGACTTCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 26
0.63 0.05 0.32
Matches are distributed among these distances:
27 4 0.08
29 3 0.06
30 6 0.12
31 16 0.31
32 10 0.19
33 6 0.12
34 3 0.06
36 4 0.08
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (31 bp):
TCTTAAACACTCTCTGATCTTGAAACGGTTC
Found at i:265368 original size:63 final size:63
Alignment explanation
Indices: 265269--265391 Score: 246
Period size: 63 Copynumber: 2.0 Consensus size: 63
265259 TGCTTTCTTA
265269 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
265332 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
265392 CCTCGGATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (63 bp):
AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
Found at i:266309 original size:8 final size:8
Alignment explanation
Indices: 266296--266335 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
266286 TTCCGGTCAC
266296 GGTCAACG
1 GGTCAACG
266304 GGTCAAC-
1 GGTCAACG
266311 GGTCAACG
1 GGTCAACG
266319 GGT---CG
1 GGTCAACG
266324 GGTCAACG
1 GGTCAACG
266332 GGTC
1 GGTC
266336 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.20, C:0.25, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:266314 original size:15 final size:14
Alignment explanation
Indices: 266290--266335 Score: 67
Period size: 15 Copynumber: 3.3 Consensus size: 14
266280 GGTCAATTCC
266290 GGTCACGGTCAACG
1 GGTCACGGTCAACG
266304 GGTCAACGGTCAACG
1 GGTC-ACGGTCAACG
*
266319 GGTC-GGGTCAACG
1 GGTCACGGTCAACG
266332 GGTC
1 GGTC
266336 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 12 0.40
14 4 0.13
15 14 0.47
ACGTcount: A:0.20, C:0.26, G:0.39, T:0.15
Consensus pattern (14 bp):
GGTCACGGTCAACG
Found at i:266329 original size:13 final size:13
Alignment explanation
Indices: 266296--266363 Score: 88
Period size: 13 Copynumber: 5.3 Consensus size: 13
266286 TTCCGGTCAC
*
266296 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
266311 GGTCAACGGGTCG
1 GGTCAACGGGTCG
266324 GGTCAACGGGTCG
1 GGTCAACGGGTCG
266337 GGT---CGGGTCG
1 GGTCAACGGGTCG
266347 GGTCAACGGGTCG
1 GGTCAACGGGTCG
266360 GGTC
1 GGTC
266364 GGGTTGTGAC
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
10 10 0.20
13 27 0.55
15 12 0.24
ACGTcount: A:0.15, C:0.24, G:0.46, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:266343 original size:23 final size:23
Alignment explanation
Indices: 266317--266367 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
266307 CAACGGTCAA
266317 CGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCGGGTCAACGGGTCGGGT
266340 CGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCGGGTCAACGGGTCGGGT
266363 CGGGT
1 CGGGT
266368 TGTGACCGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.08, C:0.22, G:0.53, T:0.18
Consensus pattern (23 bp):
CGGGTCGGGTCAACGGGTCGGGT
Found at i:268373 original size:12 final size:12
Alignment explanation
Indices: 268348--268417 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
268338 ACGAAGATAT
* *
268348 CAGAAATCAAAA
1 CAGAATTCAGAA
268360 CAGAATTCAGAA
1 CAGAATTCAGAA
268372 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
268384 CAGAATCCAGAT
1 CAGAATTCAGAA
*
268396 CAGAAATCAGAA
1 CAGAATTCAGAA
268408 CAGAATTCAG
1 CAGAATTCAG
268418 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Done.