Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011959.1 Kokia drynarioides strain JFW-HI SEQ_126957, 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: 397225
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 35 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:17 original size:2 final size:2
Alignment explanation
Indices: 12--36 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2 AAAAAAAAAT
12 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 T
37 TTGAATCATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:122 original size:12 final size:11
Alignment explanation
Indices: 105--136 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
95 CTTTTTATAC
105 AATTTTTTTAG
1 AATTTTTTTAG
116 AATTTTTTTAG
1 AATTTTTTTAG
127 AATTTTTTTA
1 AATTTTTTTA
137 AAATATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (11 bp):
AATTTTTTTAG
Found at i:176 original size:19 final size:22
Alignment explanation
Indices: 152--200 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 22
142 TAAATTTTAA
152 AATTTTTAT-AAAT-ATTTTG-
1 AATTTTTATAAAATGATTTTGT
171 AATTTTT-TAAAATGATTTTGT
1 AATTTTTATAAAATGATTTTGT
*
192 AAGTTTTAT
1 AATTTTTAT
201 TGTGAGACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 1 0.04
19 11 0.44
20 6 0.24
21 6 0.24
22 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (22 bp):
AATTTTTATAAAATGATTTTGT
Found at i:621 original size:16 final size:16
Alignment explanation
Indices: 600--633 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
590 TCTTTTTTTT
600 AATTTATATTCATAAA
1 AATTTATATTCATAAA
616 AATTTATATTCATAAA
1 AATTTATATTCATAAA
632 AA
1 AA
634 CCATTATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTATATTCATAAA
Found at i:3977 original size:2 final size:2
Alignment explanation
Indices: 3972--4010 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3962 TATATATATA
3972 TG TG TG TG 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 TG TG TG TG T
4011 TTGAACTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:4359 original size:19 final size:19
Alignment explanation
Indices: 4287--4407 Score: 88
Period size: 19 Copynumber: 6.4 Consensus size: 19
4277 CTATATAGGT
*
4287 GTATGCACTTCGTGTGCCA
1 GTATGCACTTCATGTGCCA
* * * *
4306 ATATACACTTCGTGTGTCA
1 GTATGCACTTCATGTGCCA
* *
4325 GGAATGCACCT-ATGTGCCA
1 -GTATGCACTTCATGTGCCA
*
4344 GTATGCACTTCGTGTGCCAA
1 GTATGCACTTCATGTGCC-A
*
4364 GAAT--A-TGTCTATGTGCCA
1 GTATGCACT-TC-ATGTGCCA
*
4382 GAATGCACTTCATGTGCCA
1 GTATGCACTTCATGTGCCA
4401 GTATGCA
1 GTATGCA
4408 ATTTTTATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 16
0.72 0.14 0.15
Matches are distributed among these distances:
17 1 0.01
18 16 0.20
19 48 0.61
20 13 0.16
21 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (19 bp):
GTATGCACTTCATGTGCCA
Found at i:4397 original size:57 final size:57
Alignment explanation
Indices: 4287--4407 Score: 149
Period size: 57 Copynumber: 2.1 Consensus size: 57
4277 CTATATAGGT
* * *
4287 GTATGCACTTCGTGTGCCAATATACACTTCGTGTGTCAGGAATGCACCTATGTGCCA
1 GTATGCACTTCGTGTGCCAAGATACACTTCATGTGCCAGGAATGCACCTATGTGCCA
* *
4344 GTATGCACTTCGTGTGCCAAGA-ATA-TGTCTATGTGCCA-GAATGCACTTCATGTGCCA
1 GTATGCACTTCGTGTGCCAAGATACACT-TC-ATGTGCCAGGAATGCACCT-ATGTGCCA
4401 GTATGCA
1 GTATGCA
4408 ATTTTTATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
55 1 0.02
56 13 0.23
57 42 0.75
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (57 bp):
GTATGCACTTCGTGTGCCAAGATACACTTCATGTGCCAGGAATGCACCTATGTGCCA
Found at i:6747 original size:21 final size:20
Alignment explanation
Indices: 6703--6753 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
6693 TGCACTCATA
6703 CCCCTCAAGTATTTGATGTC
1 CCCCTCAAGTATTTGATGTC
6723 CCCCTCAAGTATTTGA-GAATC
1 CCCCTCAAGTATTTGATG--TC
6744 CCCCTCAAGT
1 CCCCTCAAGT
6754 TAGATAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.03
20 16 0.55
21 12 0.41
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (20 bp):
CCCCTCAAGTATTTGATGTC
Found at i:8584 original size:38 final size:38
Alignment explanation
Indices: 8542--8674 Score: 144
Period size: 38 Copynumber: 3.5 Consensus size: 38
8532 TATGCGTCAG
* *
8542 TATGCACTTCGTATGCCAGGAATGTGCTTATGTGCCAA
1 TATGCACTTCGTGTGCCAGGAATGTGCTTATGTACCAA
* * *
8580 TATGCACTTCGTGTGCTAAGAATGTGCTTATGCACCAA
1 TATGCACTTCGTGTGCCAGGAATGTGCTTATGTACCAA
* *
8618 TATGCACATT-GTGTACCAGG-ATGCGCTTCATGTACCAA
1 TATGCAC-TTCGTGTGCCAGGAATGTGCTT-ATGTACCAA
* * *
8656 TATGTACTACATGTGCCAG
1 TATGCACTTCGTGTGCCAG
8675 TTTCCCTTAC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
37 8 0.10
38 68 0.87
39 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (38 bp):
TATGCACTTCGTGTGCCAGGAATGTGCTTATGTACCAA
Found at i:12113 original size:3 final size:3
Alignment explanation
Indices: 12105--12130 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12095 GAAGATTCAA
12105 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
12131 AGTGTGGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:25815 original size:18 final size:18
Alignment explanation
Indices: 25789--25823 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25779 TGCGGAAGGA
25789 TGAGCATACAGGCTCGTT
1 TGAGCATACAGGCTCGTT
* *
25807 TGAGTATACTGGCTCGT
1 TGAGCATACAGGCTCGT
25824 AAGAGCATTA
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:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (18 bp):
TGAGCATACAGGCTCGTT
Found at i:30518 original size:15 final size:15
Alignment explanation
Indices: 30486--30514 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30476 TTGCACAGTG
30486 CTTCTTCTTCCTCCT
1 CTTCTTCTTCCTCCT
30501 CTTCTTC-TCCTCCT
1 CTTCTTCTTCCTCCT
30515 TCTTGCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (15 bp):
CTTCTTCTTCCTCCT
Found at i:41868 original size:28 final size:29
Alignment explanation
Indices: 41828--41887 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
41818 AACCTTTCCC
41828 TTAGCTTTAGTGGCTCAACT-AAAACCCT
1 TTAGCTTTAGTGGCTCAACTAAAAACCCT
* *
41856 TTAGCTTTTGTGGCTTAACTAAAAACCCT
1 TTAGCTTTAGTGGCTCAACTAAAAACCCT
41885 TTA
1 TTA
41888 CAATCCTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 18 0.62
29 11 0.38
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (29 bp):
TTAGCTTTAGTGGCTCAACTAAAAACCCT
Found at i:46139 original size:88 final size:88
Alignment explanation
Indices: 46035--46220 Score: 354
Period size: 88 Copynumber: 2.1 Consensus size: 88
46025 AAAATTAACC
*
46035 GAATTAACCAACTAATTTATTAAGTGGGCTAATACTTATATATTATAATATTATTTCTTAAGTTC
1 GAATTAACCGACTAATTTATTAAGTGGGCTAATACTTATATATTATAATATTATTTCTTAAGTTC
*
46100 TGTTAACCGACCGTTTTCGAACT
66 GGTTAACCGACCGTTTTCGAACT
46123 GAATTAACCGACTAATTTATTAAGTGGGCTAATACTTATATATTATAATATTATTTCTTAAGTTC
1 GAATTAACCGACTAATTTATTAAGTGGGCTAATACTTATATATTATAATATTATTTCTTAAGTTC
46188 GGTTAACCGACCGTTTTCGAACT
66 GGTTAACCGACCGTTTTCGAACT
46211 GAATTAACCG
1 GAATTAACCG
46221 TTAATCAAAC
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 96 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (88 bp):
GAATTAACCGACTAATTTATTAAGTGGGCTAATACTTATATATTATAATATTATTTCTTAAGTTC
GGTTAACCGACCGTTTTCGAACT
Found at i:48109 original size:37 final size:37
Alignment explanation
Indices: 48042--48164 Score: 119
Period size: 37 Copynumber: 3.3 Consensus size: 37
48032 TAAATTATTT
* *
48042 TATTACTAATACATAA-A-ATAATAATATATTATAATG
1 TATTACTATTAC-TAATACATAATAATATATTATAATA
*
48078 TATTAGTATTACTAATACATAA-AATAGTATTATAATA
1 TATTACTATTACTAATACATAATAATA-TATTATAATA
* *
48115 TATTACTATTACTAAAAGATTAATACATATATTAT-ATA
1 TATTACTATTACTAATACA-TAATA-ATATATTATAATA
*
48153 TTATTATTATTA
1 -TATTACTATTA
48165 TTATTATTAT
Statistics
Matches: 73, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
35 3 0.04
36 15 0.21
37 29 0.40
38 6 0.08
39 17 0.23
40 3 0.04
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (37 bp):
TATTACTATTACTAATACATAATAATATATTATAATA
Found at i:48159 original size:3 final size:3
Alignment explanation
Indices: 48144--48174 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
48134 TTAATACATA
48144 TAT TAT ATAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
48175 AAAAGATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:52793 original size:2 final size:2
Alignment explanation
Indices: 52786--52812 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52776 ATAAAGTCTC
52786 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA C
52813 CAAGGAATCG
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:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:55887 original size:88 final size:84
Alignment explanation
Indices: 55764--56029 Score: 277
Period size: 89 Copynumber: 3.0 Consensus size: 84
55754 TTAAGGGTGT
*
55764 AAAAAACCTTCAAA-TTAAAAAAAAAAAACTAATTAAGTCATTGTTTTTTTTACACTCAATTTGA
1 AAAAAACC-TCAAACTT--AAAAAAAAAAC-AATTAAGTC-TTGATTTTTTT-CACTCAA-TTGA
*
55828 -TACTTAAACTGTCAAATGCATAAAA
59 GTACTTAAACTATCAAATGCATAAAA
* * *
55853 AAAAAACACTCAAACTTTAAAAAAAAAGCAATTAAGCCTCTGGCTTTTTTTGCACTCAATTGAGT
1 AAAAAAC-CTCAAAC-TTAAAAAAAAAACAATTAAG--TCTTGATTTTTTT-CACTCAATTGAGT
* * *
55918 ACTTAAACTTTCAAAATGTAT-CAA
61 ACTTAAACTATC-AAATGCATAAAA
* * * *
55942 AAAGATCCTCAAACTTAAAAAAAAAACAATTTAGCCCTTGATTTTTTTCACTCAATTGAGTACTT
1 AAAAAACCTCAAACTTAAAAAAAAAACAATTAAG-TCTTGATTTTTTTCACTCAATTGAGTACTT
56007 AAACTATCAAATGCATAAAA
65 AAACTATCAAATGCATAAAA
56027 AAA
1 AAA
56030 TATTTTGGCT
Statistics
Matches: 152, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
84 7 0.05
85 29 0.19
86 11 0.07
87 18 0.12
88 18 0.12
89 57 0.38
90 10 0.07
91 2 0.01
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (84 bp):
AAAAAACCTCAAACTTAAAAAAAAAACAATTAAGTCTTGATTTTTTTCACTCAATTGAGTACTTA
AACTATCAAATGCATAAAA
Found at i:56169 original size:9 final size:9
Alignment explanation
Indices: 56132--56281 Score: 54
Period size: 10 Copynumber: 15.3 Consensus size: 9
56122 ACATGTGACA
*
56132 AAAAACTAT
1 AAAAATTAT
56141 AAAAA-TAT
1 AAAAATTAT
56149 AAATAA--AT
1 AAA-AATTAT
56157 AAAAATTAT
1 AAAAATTAT
56166 AAAAATTATT
1 AAAAATTA-T
**
56176 AAATTTTAAT
1 AAAAATT-AT
*
56186 GAAAATATAT
1 AAAAAT-TAT
*
56196 AAAACTTATT
1 AAAAATTA-T
56206 AAAAATTAGAAT
1 AAAAATT---AT
56218 AAAAATTTTAT
1 AAAAA--TTAT
*
56229 AAAAATGGTAAA
1 AAAAAT--T-AT
*
56241 AAAAAGTAT
1 AAAAATTAT
*
56250 AAAATATTGT
1 AAAA-ATTAT
**
56260 AAACTTTTAT
1 AAA-AATTAT
56270 AAAAATTAT
1 AAAAATTAT
56279 AAA
1 AAA
56282 TTTTTTTTAT
Statistics
Matches: 106, Mismatches: 18, Indels: 34
0.67 0.11 0.22
Matches are distributed among these distances:
7 2 0.02
8 11 0.10
9 32 0.30
10 36 0.34
11 10 0.09
12 12 0.11
13 1 0.01
14 2 0.02
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:56286 original size:19 final size:20
Alignment explanation
Indices: 56247--56285 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
56237 TAAAAAAAAG
*
56247 TATAAAATATTGTAAACTTT
1 TATAAAATATTATAAACTTT
56267 TATAAAA-ATTATAAA-TTT
1 TATAAAATATTATAAACTTT
56285 T
1 T
56286 TTTTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 7 0.39
20 7 0.39
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (20 bp):
TATAAAATATTATAAACTTT
Found at i:56599 original size:10 final size:10
Alignment explanation
Indices: 56482--56778 Score: 74
Period size: 9 Copynumber: 30.8 Consensus size: 10
56472 TTATAATTTT
56482 TTTTTTATAA
1 TTTTTTATAA
*
56492 -ATTTTAT-A
1 TTTTTTATAA
*
56500 TTTCTTTA-CA
1 TTT-TTTATAA
*
56510 TTTTCTATAA
1 TTTTTTATAA
*
56520 CTTTTTTATGA
1 -TTTTTTATAA
*
56531 --CTTTATAA
1 TTTTTTATAA
**
56539 AATTTTAT-A
1 TTTTTTATAA
*
56548 TTTTTTCTAA
1 TTTTTTATAA
*
56558 -TTTCTAT-A
1 TTTTTTATAA
* *
56566 TATCTTATAA
1 TTTTTTATAA
* *
56576 TTATTTACAA
1 TTTTTTATAA
56586 -TTTTTATAA
1 TTTTTTATAA
*
56595 TTTTTTCT-A
1 TTTTTTATAA
56604 TTTTTTAATAA
1 TTTTTT-ATAA
** *
56615 -AATTTAAATA
1 TTTTTTATA-A
56625 TTTTTTAT-A
1 TTTTTTATAA
56634 TTTTTTATTAA
1 TTTTTTA-TAA
** *
56645 AATTTAAT-A
1 TTTTTTATAA
*
56654 TTTTTTAAAACA
1 TTTTTT-ATA-A
* *
56666 TTTATTGTAA
1 TTTTTTATAA
*
56676 TTTTATAT-A
1 TTTTTTATAA
*
56685 TTTTTTCTAA
1 TTTTTTATAA
*
56695 -TTTCTAT-A
1 TTTTTTATAA
* *
56703 TATCTTATAA
1 TTTTTTATAA
* *
56713 TTATTTACAA
1 TTTTTTATAA
56723 -TTTTTATAA
1 TTTTTTATAA
*
56732 TTTTTTCTAA
1 TTTTTTATAA
*
56742 TTTTTAATAA
1 TTTTTTATAA
**
56752 -AATTTA-AA
1 TTTTTTATAA
*
56760 TATTTTTATAG
1 T-TTTTTATAA
56771 TTTTTTAT
1 TTTTTTAT
56779 TAAAATTTAA
Statistics
Matches: 194, Mismatches: 66, Indels: 54
0.62 0.21 0.17
Matches are distributed among these distances:
8 11 0.06
9 79 0.41
10 77 0.40
11 21 0.11
12 6 0.03
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:56659 original size:29 final size:30
Alignment explanation
Indices: 56594--56660 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
56584 AATTTTTATA
*
56594 ATTTTTTCTATTTTTTAATAAAATTTAAAT
1 ATTTTTTATATTTTTTAATAAAATTTAAAT
*
56624 ATTTTTTATATTTTTTATTAAAATTT-AAT
1 ATTTTTTATATTTTTTAATAAAATTTAAAT
56653 ATTTTTTA
1 ATTTTTTA
56661 AAACATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 11 0.31
30 24 0.69
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (30 bp):
ATTTTTTATATTTTTTAATAAAATTTAAAT
Found at i:56668 original size:19 final size:19
Alignment explanation
Indices: 56631--56669 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
56621 AATATTTTTT
56631 ATATTTTTTATTAAAATTTA
1 ATATTTTTTA-TAAAATTTA
56651 ATATTTTTTA-AAACATTTA
1 ATATTTTTTATAAA-ATTTA
56670 TTGTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 5 0.28
20 10 0.56
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTTTTTATAAAATTTA
Found at i:56669 original size:29 final size:29
Alignment explanation
Indices: 56607--56690 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
56597 TTTTCTATTT
* * ***
56607 TTTAATAAAATTTAAATATTTTTTATATTT
1 TTTATTAAAATTT-AATATTTTTTAAAACA
56637 TTTATTAAAATTTAATATTTTTTAAAACA
1 TTTATTAAAATTTAATATTTTTTAAAACA
* *
56666 TTTATTGTAATTTTATATATTTTTT
1 TTTATT-AAAATTTA-ATATTTTTT
56691 CTAATTTCTA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
29 18 0.40
30 18 0.40
31 9 0.20
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (29 bp):
TTTATTAAAATTTAATATTTTTTAAAACA
Found at i:56687 original size:19 final size:20
Alignment explanation
Indices: 56665--56710 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
56655 TTTTTAAAAC
*
56665 ATTTATTGTAATTT-TATAT
1 ATTTATTCTAATTTCTATAT
*
56684 ATTTTTTCTAATTTCTATAT
1 ATTTATTCTAATTTCTATAT
56704 ATCTTAT
1 AT-TTAT
56711 AATTATTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 12 0.55
20 7 0.32
21 3 0.14
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (20 bp):
ATTTATTCTAATTTCTATAT
Found at i:56708 original size:137 final size:137
Alignment explanation
Indices: 56544--56810 Score: 491
Period size: 137 Copynumber: 1.9 Consensus size: 137
56534 TATAAAATTT
*
56544 TATATTTTTTCTAATTTCTATATATCTTATAATTATTTACAATTTTTATAATTTTTTCTATTTTT
1 TATATTTTTTCTAATTTCTATATATCTTATAATTATTTACAATTTTTATAATTTTTTCTAATTTT
56609 TAATAAAATTTAAATATTTTTTATA-TTTTTTATTAAAATTTAATATTTTTTAAAACATTTATTG
66 TAATAAAATTTAAATA-TTTTTATAGTTTTTTATTAAAATTTAATATTTTTTAAAACATTTATTG
56673 TAATTTTA
130 TAATTTTA
56681 TATATTTTTTCTAATTTCTATATATCTTATAATTATTTACAATTTTTATAATTTTTTCTAATTTT
1 TATATTTTTTCTAATTTCTATATATCTTATAATTATTTACAATTTTTATAATTTTTTCTAATTTT
* *
56746 TAATAAAATTTAAATATTTTTATAGTTTTTTATTAAAATTTAATATTTTTTAAAACTTTTGTTGT
66 TAATAAAATTTAAATATTTTTATAGTTTTTTATTAAAATTTAATATTTTTTAAAACATTTATTGT
56811 TTTTTATTTT
Statistics
Matches: 126, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
136 8 0.06
137 118 0.94
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (137 bp):
TATATTTTTTCTAATTTCTATATATCTTATAATTATTTACAATTTTTATAATTTTTTCTAATTTT
TAATAAAATTTAAATATTTTTATAGTTTTTTATTAAAATTTAATATTTTTTAAAACATTTATTGT
AATTTTA
Found at i:56731 original size:19 final size:19
Alignment explanation
Indices: 56707--56769 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
56697 TCTATATATC
56707 TTATAATTATTTACAATTT
1 TTATAATTATTTACAATTT
*
56726 TTATAATT-TTTTCTAATTT
1 TTATAATTATTTAC-AATTT
* *
56745 TTAATAA-AATTTAAATATTT
1 TT-ATAATTATTTACA-ATTT
56765 TTATA
1 TTATA
56770 GTTTTTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 4 0.11
19 19 0.53
20 13 0.36
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATAATTATTTACAATTT
Found at i:56757 original size:29 final size:29
Alignment explanation
Indices: 56725--56797 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 29
56715 ATTTACAATT
*
56725 TTTATAATTTTTTCTA-ATTTTTAATAAAA
1 TTTA-AATTTTTTATAGATTTTTAATAAAA
* *
56754 TTTAAATATTTTTATAGTTTTTTATTAAAA
1 TTTAAAT-TTTTTATAGATTTTTAATAAAA
56784 TTTAATATTTTTTA
1 TTTAA-ATTTTTTA
56798 AAACTTTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 3 0.08
29 11 0.29
30 22 0.58
31 2 0.05
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (29 bp):
TTTAAATTTTTTATAGATTTTTAATAAAA
Found at i:57056 original size:93 final size:92
Alignment explanation
Indices: 56891--57125 Score: 257
Period size: 93 Copynumber: 2.6 Consensus size: 92
56881 ATTAGGAGTG
* * * * *
56891 ATTCAAGTACCCAATTGAGTGC---AAAATAAATCAGGGGCTTAATTATTTTTTTTTGAAAAAGT
1 ATTCAAATACCCAATTAAGTGCAAAAAAAAAAAT-AAGGGCTTAATTTTTTTTTTTTGAAAAAGT
* *
56953 TTGATAGCCTTTTTTATGCATTTT-GAA
65 TTGATAGCCTTTTTGAGGCATTTTGGAA
*
56980 AGTTCAAATACCCAATTAAGTG-AAAAAAAAAATGTAAGGGCTTAATTGTTTTTTTTTTGAAAAA
1 A-TTCAAATACCCAATTAAGTGCAAAAAAAAAA-ATAAGGGCTTAATT-TTTTTTTTTTGAAAAA
* * *
57044 GTTTG-TGGGCCTTTTTGAGGTATTTTGGTA
63 GTTTGAT-AGCCTTTTTGAGGCATTTTGGAA
* * *
57074 ATTCAAGTACCCAATTGAGTGCAAAAAAAAAAATAGGGGCTTAATTTTTTTT
1 ATTCAAATACCCAATTAAGTGCAAAAAAAAAAATAAGGGCTTAATTTTTTTT
57126 AAAAAAGTTT
Statistics
Matches: 122, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
89 1 0.01
90 18 0.15
92 24 0.20
93 66 0.54
94 13 0.11
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (92 bp):
ATTCAAATACCCAATTAAGTGCAAAAAAAAAAATAAGGGCTTAATTTTTTTTTTTTGAAAAAGTT
TGATAGCCTTTTTGAGGCATTTTGGAA
Found at i:57240 original size:31 final size:29
Alignment explanation
Indices: 57202--57271 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
57192 ATCTCAAAAC
57202 TATACATGAACTATAATTTAATGTGCAATTG
1 TATACATGAACTATAATTT--TGTGCAATTG
* * * *
57233 TATACATGAACTTTGATTTTGTGTAATTT
1 TATACATGAACTATAATTTTGTGCAATTG
57262 TATACATGAA
1 TATACATGAA
57272 ATTTTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.51
31 17 0.49
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (29 bp):
TATACATGAACTATAATTTTGTGCAATTG
Found at i:57265 original size:29 final size:30
Alignment explanation
Indices: 57202--57281 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
57192 ATCTCAAAAC
* *
57202 TATACATGAACTATAATTTAATGTGCAATTG
1 TATACATGAACTTTGATTT-ATGTGCAATTG
* *
57233 TATACATGAACTTTGATTT-TGTGTAATTT
1 TATACATGAACTTTGATTTATGTGCAATTG
*
57262 TATACATGAAATTTTGATTT
1 TATACATG-AACTTTGATTT
57282 GATCCAATTC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 16 0.37
30 10 0.23
31 17 0.40
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.46
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATGTGCAATTG
Found at i:57605 original size:29 final size:30
Alignment explanation
Indices: 57521--57605 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 30
57511 GATTAAATCA
**
57521 AAATTAAAGTTTCAAGTATACTTTTGAACC
1 AAATTAAAGTTTCAAGTATACAATTGAACC
* * *
57551 ACAATTAGAGTTTCAAGTATATAATTGCACC
1 A-AATTAAAGTTTCAAGTATACAATTGAACC
*
57582 AAATTAAAG-TTCATGTATACAATT
1 AAATTAAAGTTTCAAGTATACAATT
57606 ACATATTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 13 0.28
30 8 0.17
31 25 0.54
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATACAATTGAACC
Found at i:58966 original size:23 final size:23
Alignment explanation
Indices: 58940--59013 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
58930 GATTAAGAAG
*
58940 CAGATACATAATAGAAACAGATT
1 CAGATGCATAATAGAAACAGATT
* **
58963 CAGATGCATAATTGGTACAGATT
1 CAGATGCATAATAGAAACAGATT
* *
58986 CAGATGCATAACA-AATTCAGATT
1 CAGATGCATAATAGAA-ACAGATT
59009 CAGAT
1 CAGAT
59014 CTTATCTCCA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (23 bp):
CAGATGCATAATAGAAACAGATT
Found at i:69429 original size:59 final size:59
Alignment explanation
Indices: 69337--69452 Score: 214
Period size: 59 Copynumber: 2.0 Consensus size: 59
69327 AAAGAAATCA
* *
69337 AGTTTTTATTTTGGCTTAGGTTGTAGATGACAATTCAAGGTTCTAACAAAGACATATTT
1 AGTTTTTATTTTGGCTCAGGTGGTAGATGACAATTCAAGGTTCTAACAAAGACATATTT
69396 AGTTTTTATTTTGGCTCAGGTGGTAGATGACAATTCAAGGTTCTAACAAAGACATAT
1 AGTTTTTATTTTGGCTCAGGTGGTAGATGACAATTCAAGGTTCTAACAAAGACATAT
69453 GCAAGTCACC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (59 bp):
AGTTTTTATTTTGGCTCAGGTGGTAGATGACAATTCAAGGTTCTAACAAAGACATATTT
Found at i:70401 original size:4 final size:4
Alignment explanation
Indices: 70386--70503 Score: 110
Period size: 4 Copynumber: 29.5 Consensus size: 4
70376 TTGTATAATA
* * * * *
70386 ATAT ACAT ATAT ATAT ATAT ATAC ATAT ATAT ATGT ATGT ATGT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * * *
70434 ATGT ATGT ATAT ATGT ATAT ATGT ATAT ATGT ATGT ATGT ATAT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
70482 ATAT ATGT ATAT ATAT ATAT AT
1 ATAT ATAT ATAT ATAT ATAT AT
70504 GTTTTTTCTT
Statistics
Matches: 96, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 96 1.00
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (4 bp):
ATAT
Found at i:70428 original size:8 final size:8
Alignment explanation
Indices: 70392--70505 Score: 137
Period size: 8 Copynumber: 14.8 Consensus size: 8
70382 AATAATATAC
*
70392 ATATATAT
1 ATATGTAT
*
70400 ATATATAT
1 ATATGTAT
* *
70408 ACATATAT
1 ATATGTAT
70416 ATATGTAT
1 ATATGTAT
*
70424 GTATGTAT
1 ATATGTAT
70432 ATATG---
1 ATATGTAT
70437 -TATGTAT
1 ATATGTAT
70444 ATATGTAT
1 ATATGTAT
70452 ATATGTAT
1 ATATGTAT
70460 ATATGTAT
1 ATATGTAT
*
70468 GTATGTAT
1 ATATGTAT
70476 ATATGTAT
1 ATATGTAT
70484 ATATGTAT
1 ATATGTAT
*
70492 ATATATAT
1 ATATGTAT
70500 ATATGT
1 ATATGT
70506 TTTTTCTTTT
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
4 4 0.04
8 89 0.96
ACGTcount: A:0.39, C:0.01, G:0.11, T:0.49
Consensus pattern (8 bp):
ATATGTAT
Found at i:102394 original size:32 final size:30
Alignment explanation
Indices: 102350--102414 Score: 85
Period size: 32 Copynumber: 2.1 Consensus size: 30
102340 AACATAAATG
102350 AAATAACAAAGGAAATAAAAATAACTAAACAT
1 AAATAACAAAGGAAATAAAAAT-ACTAAAC-T
* * *
102382 AAATTACAAAGGAAGTGAAAATACTAAACT
1 AAATAACAAAGGAAATAAAAATACTAAACT
102412 AAA
1 AAA
102415 GATGTGTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 4 0.13
31 7 0.23
32 19 0.63
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.17
Consensus pattern (30 bp):
AAATAACAAAGGAAATAAAAATACTAAACT
Found at i:113398 original size:27 final size:27
Alignment explanation
Indices: 113367--113441 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
113357 GCTTTTGTAG
* *
113367 GAAAGCCTTTGTGGCTAGACTGTATAA
1 GAAAGCCTTTGTGGCTAAACTATATAA
* * * *
113394 GAAAGCATTTGTGACTAAACTATGTGA
1 GAAAGCCTTTGTGGCTAAACTATATAA
113421 GAAAGCCTTTGTGGCTAAACT
1 GAAAGCCTTTGTGGCTAAACT
113442 CTAAGTAGGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (27 bp):
GAAAGCCTTTGTGGCTAAACTATATAA
Found at i:113627 original size:26 final size:28
Alignment explanation
Indices: 113598--113660 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
113588 AAAAGGCCAT
*
113598 CTTTCTGGCAT-ATAT-GAAAGGAAAAC
1 CTTTATGGCATAATATAGAAAGGAAAAC
* *
113624 CTTTATGGC-TAATCTAGAAAGGAACAC
1 CTTTATGGCATAATATAGAAAGGAAAAC
*
113651 CTTTGTGGCA
1 CTTTATGGCA
113661 CAATCAAAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 1 0.03
26 11 0.37
27 18 0.60
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (28 bp):
CTTTATGGCATAATATAGAAAGGAAAAC
Found at i:124065 original size:21 final size:20
Alignment explanation
Indices: 124016--124066 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
124006 GTATCACAGA
124016 TTGTTGTGGCTACATCTGAT
1 TTGTTGTGGCTACATCTGAT
* *
124036 TCTGGTGTGGCTGCATCTGACT
1 T-TGTTGTGGCTACATCTGA-T
124058 TTGTTGTGG
1 TTGTTGTGG
124067 ATGAATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.88
22 2 0.08
ACGTcount: A:0.10, C:0.16, G:0.31, T:0.43
Consensus pattern (20 bp):
TTGTTGTGGCTACATCTGAT
Found at i:124104 original size:21 final size:22
Alignment explanation
Indices: 124075--124115 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
124065 GGATGAATTT
*
124075 ATGTATGTTGATTGTAATTCTG
1 ATGTATGTTGACTGTAATTCTG
*
124097 ATGT-TGTTGGCTGTAATTC
1 ATGTATGTTGACTGTAATTC
124116 CCTTGTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.20, C:0.07, G:0.24, T:0.49
Consensus pattern (22 bp):
ATGTATGTTGACTGTAATTCTG
Found at i:126664 original size:200 final size:200
Alignment explanation
Indices: 126319--126686 Score: 506
Period size: 200 Copynumber: 1.8 Consensus size: 200
126309 ATAGGTTTCT
* * * *
126319 TTTCATCAGAATCAAGCTATCTCTAGTCGTACAAGTTGGTTATACCAGACTGGATAGCTCACACA
1 TTTCATCAGAATCAAGCTATCACTAGTCGTACAAGTTGGTTATACCAGACTAGACAACTCACACA
* * * * * * * *
126384 TTTTTATTCTTATCTGGACAGCTGTCAGATGTGGCGAGAATTCTAGATGTAATCTGAAATTACTT
66 TTTCTATTCTTATCTGGACAACTATCAGATGCGACGAGAATCCTAGACGGAATCTGAAATTACTT
*
126449 ATGCAACGACATCTGTACCAAAACATGACAAAATTAAGCATAAGTACAAGTTGTCCTTGTGTATA
131 ATGCAACGACATCTGTACCAAAACAAGACAAAATTAAGCATAAGTACAAGTTGTCCTTGTGTATA
126514 TGTCC
196 TGTCC
* *
126519 TTTCATCATAATCAAGCTATCAC-AGGTTGTACAAGTTGGTTATACCAGACTAGACAACTCACAC
1 TTTCATCAGAATCAAGCTATCACTA-GTCGTACAAGTTGGTTATACCAGACTAGACAACTCACAC
* * *
126583 ATTTCTGTTCTTATTTGGACAACTATCAGATGCGACG-GCAATCCTAGACGGAATCTGAAATTTC
65 ATTTCTATTCTTATCTGGACAACTATCAGATGCGACGAG-AATCCTAGACGGAATCTGAAATTAC
** * *
126647 TTATGCAGTGCCATCTGTACCAAAACAAGACAAATTTAAG
129 TTATGCAACGACATCTGTACCAAAACAAGACAAAATTAAG
126687 AGTAAATAGG
Statistics
Matches: 144, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
199 2 0.01
200 142 0.99
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (200 bp):
TTTCATCAGAATCAAGCTATCACTAGTCGTACAAGTTGGTTATACCAGACTAGACAACTCACACA
TTTCTATTCTTATCTGGACAACTATCAGATGCGACGAGAATCCTAGACGGAATCTGAAATTACTT
ATGCAACGACATCTGTACCAAAACAAGACAAAATTAAGCATAAGTACAAGTTGTCCTTGTGTATA
TGTCC
Found at i:135820 original size:20 final size:21
Alignment explanation
Indices: 135784--135822 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
135774 CATTTGTTTA
*
135784 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
135805 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
135823 AATTCCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:137230 original size:18 final size:15
Alignment explanation
Indices: 137188--137220 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
137178 ATGACTTGCT
137188 GAAG-AAAA-AGGAA
1 GAAGAAAAAGAGGAA
137201 GAAGAAAAAGAGGAA
1 GAAGAAAAAGAGGAA
137216 GAAGA
1 GAAGA
137221 GAATGAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 4 0.22
15 10 0.56
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
GAAGAAAAAGAGGAA
Found at i:142193 original size:17 final size:17
Alignment explanation
Indices: 142171--142203 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
142161 ATGCTAAAAT
142171 AAAATGCAAAGACAATA
1 AAAATGCAAAGACAATA
*
142188 AAAATGCAATGACAAT
1 AAAATGCAAAGACAAT
142204 TTAAAATAAA
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:0.61, C:0.12, G:0.12, T:0.15
Consensus pattern (17 bp):
AAAATGCAAAGACAATA
Found at i:142645 original size:15 final size:16
Alignment explanation
Indices: 142625--142665 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
142615 CGTCCTTCTC
*
142625 CTCTTCACTT-ACTTT
1 CTCTTCACTTAACTCT
142640 CTCTTC-CTTAACTCT
1 CTCTTCACTTAACTCT
142655 CTCCTTCACTT
1 CT-CTTCACTT
142666 CTATGCCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 3 0.14
15 12 0.55
16 4 0.18
17 3 0.14
ACGTcount: A:0.12, C:0.39, G:0.00, T:0.49
Consensus pattern (16 bp):
CTCTTCACTTAACTCT
Found at i:152810 original size:16 final size:17
Alignment explanation
Indices: 152785--152822 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
152775 TCTTGATTGG
*
152785 TTTTATTTGTTTGTTAA
1 TTTTATTTGTTTATTAA
*
152802 TTTTA-TTGTTTATTTA
1 TTTTATTTGTTTATTAA
152818 TTTTA
1 TTTTA
152823 GATATTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (17 bp):
TTTTATTTGTTTATTAA
Found at i:154280 original size:13 final size:13
Alignment explanation
Indices: 154262--154286 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
154252 TATACATATA
154262 AAAATAAAATAAT
1 AAAATAAAATAAT
154275 AAAATAAAATAA
1 AAAATAAAATAA
154287 AGAAACTATA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:158130 original size:50 final size:50
Alignment explanation
Indices: 158059--158161 Score: 152
Period size: 50 Copynumber: 2.1 Consensus size: 50
158049 TAAAATTAAG
* **
158059 AATTCGATAGGTTAGAATTGTGTAATTCGAATCCCATCGTTTGTTAAAAA
1 AATTCGATAGATTAGAATTGTGTAACCCGAATCCCATCGTTTGTTAAAAA
* * *
158109 AATTCGATAGATTAGAGTTGTGTGACCCGAATCCCATTGTTTGTTAAAAA
1 AATTCGATAGATTAGAATTGTGTAACCCGAATCCCATCGTTTGTTAAAAA
158159 AAT
1 AAT
158162 AAAATACAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (50 bp):
AATTCGATAGATTAGAATTGTGTAACCCGAATCCCATCGTTTGTTAAAAA
Found at i:158719 original size:3 final size:3
Alignment explanation
Indices: 158711--158758 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
158701 TTAAAAAGTA
*
158711 AAT AAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
158759 CCAAAAGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:161752 original size:23 final size:23
Alignment explanation
Indices: 161726--161895 Score: 114
Period size: 23 Copynumber: 7.5 Consensus size: 23
161716 AAAAATTATA
* *
161726 TTGTTTTTTTTTTACTGTTTTGG
1 TTGTTTTTTTTTTGCTGTTTTTG
*
161749 TTGTTATTTTTTTGCTGTTTTTG
1 TTGTTTTTTTTTTGCTGTTTTTG
* * *
161772 -TG-TTGTTTTTTACTGTTTTGG
1 TTGTTTTTTTTTTGCTGTTTTTG
* ** *
161793 TTGTTGTTTTCGTGTTGTTTTTG
1 TTGTTTTTTTTTTGCTGTTTTTG
* *
161816 TTGTTATTTTTGTTGCTATTTTTG
1 TTGTT-TTTTTTTTGCTGTTTTTG
** *
161840 TTG--TTTTTAATGTTGTTTTTG
1 TTGTTTTTTTTTTGCTGTTTTTG
** * *
161861 TTGTTATTTTTGCTGCTATTTTGG
1 TTGTT-TTTTTTTTGCTGTTTTTG
*
161885 TTGTTATTTTT
1 TTGTTTTTTTT
161896 GTTATTTGAA
Statistics
Matches: 111, Mismatches: 30, Indels: 12
0.73 0.20 0.08
Matches are distributed among these distances:
21 32 0.29
22 4 0.04
23 41 0.37
24 34 0.31
ACGTcount: A:0.06, C:0.04, G:0.19, T:0.71
Consensus pattern (23 bp):
TTGTTTTTTTTTTGCTGTTTTTG
Found at i:161781 original size:12 final size:10
Alignment explanation
Indices: 161756--161870 Score: 81
Period size: 12 Copynumber: 10.6 Consensus size: 10
161746 TGGTTGTTAT
*
161756 TTTTTTGCTG
1 TTTTTTGTTG
161766 TTTTTGTGTTG
1 TTTTT-TGTTG
**
161777 TTTTTTACTG
1 TTTTTTGTTG
161787 TTTTGGTTGTTG
1 TTTT--TTGTTG
*
161799 TTTTCGTGTTG
1 TTTT-TTGTTG
161810 -TTTTTGTTG
1 TTTTTTGTTG
161819 TTATTTTTGTTG
1 -T-TTTTTGTTG
161831 CTATTTTTGTTG
1 -T-TTTTTGTTG
161843 TTTTTAATGTTG
1 TTTTT--TGTTG
161855 -TTTTTGTTG
1 TTTTTTGTTG
161864 TTATTTT
1 TT-TTTT
161871 TGCTGCTATT
Statistics
Matches: 86, Mismatches: 9, Indels: 19
0.75 0.08 0.17
Matches are distributed among these distances:
9 10 0.12
10 20 0.23
11 23 0.27
12 33 0.38
ACGTcount: A:0.05, C:0.03, G:0.20, T:0.71
Consensus pattern (10 bp):
TTTTTTGTTG
Found at i:161791 original size:44 final size:45
Alignment explanation
Indices: 161726--161894 Score: 150
Period size: 44 Copynumber: 3.8 Consensus size: 45
161716 AAAAATTATA
**
161726 TTGTT-TT-TTTTTTACTGTTTTGGTTGTTATTTTTTTGCTGTTT
1 TTGTTGTTATTTTTTACTGTTTTGGTTGTTATTTTCGTGCTGTTT
* * *
161769 TTG-TGTTGTTTTTTACTGTTTTGGTTGTTGTTTTCGTGTTGTTT
1 TTGTTGTTATTTTTTACTGTTTTGGTTGTTATTTTCGTGCTGTTT
* * * ** *
161813 TTGTTGTTATTTTTGTTGCTATTTTTGTTG-T-TTTTAATGTTGTTT
1 TTGTTGTTA-TTTT-TTACTGTTTTGGTTGTTATTTTCGTGCTGTTT
* *
161858 TTGTTGTTATTTTTGCTGCTATTTTGGTTGTTATTTT
1 TTGTTGTTATTTTT--TACTGTTTTGGTTGTTATTTT
161895 TGTTATTTGA
Statistics
Matches: 106, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
42 1 0.01
43 6 0.06
44 39 0.37
45 38 0.36
46 6 0.06
47 16 0.15
ACGTcount: A:0.06, C:0.04, G:0.20, T:0.70
Consensus pattern (45 bp):
TTGTTGTTATTTTTTACTGTTTTGGTTGTTATTTTCGTGCTGTTT
Found at i:161842 original size:33 final size:33
Alignment explanation
Indices: 161741--161898 Score: 126
Period size: 33 Copynumber: 4.7 Consensus size: 33
161731 TTTTTTTTAC
* *
161741 TGTTTTGGTTGTTATTTTT-TTGCTGTTTTTG-
1 TGTTTTTGTTGTTATTTTTGTTGCTATTTTTGT
* * *
161772 TGTTGTT-TT-TTACTGTTTTGGTTGTTGTTTTCGTGT
1 TGTTTTTGTTGTTA-T-TTTT-GTTGCTATTTT--TGT
161808 TGTTTTTGTTGTTATTTTTGTTGCTATTTTTGT
1 TGTTTTTGTTGTTATTTTTGTTGCTATTTTTGT
** * * *
161841 TGTTTTTAATGTTGTTTTTGTTGTTATTTTTGC
1 TGTTTTTGTTGTTATTTTTGTTGCTATTTTTGT
161874 TGCTATTTTGGTTGTTATTTTTGTT
1 TG-T-TTTT-GTTGTTATTTTTGTT
161899 ATTTGAATGT
Statistics
Matches: 101, Mismatches: 14, Indels: 19
0.75 0.10 0.14
Matches are distributed among these distances:
29 3 0.03
30 3 0.03
31 9 0.09
33 42 0.42
34 1 0.01
35 15 0.15
36 22 0.22
37 3 0.03
38 3 0.03
ACGTcount: A:0.06, C:0.04, G:0.21, T:0.70
Consensus pattern (33 bp):
TGTTTTTGTTGTTATTTTTGTTGCTATTTTTGT
Found at i:161871 original size:12 final size:12
Alignment explanation
Indices: 161787--161898 Score: 99
Period size: 12 Copynumber: 9.7 Consensus size: 12
161777 TTTTTTACTG
* *
161787 TTTTGGTTGTTG
1 TTTTTGTTGTTA
* *
161799 TTTTCG-TGTTG
1 TTTTTGTTGTTA
161810 TTTTTGTTGTTA
1 TTTTTGTTGTTA
*
161822 TTTTTGTTGCTA
1 TTTTTGTTGTTA
161834 TTTTTGTTGTT-
1 TTTTTGTTGTTA
*
161845 TTTAATGTTG---
1 TTT-TTGTTGTTA
161855 TTTTTGTTGTTA
1 TTTTTGTTGTTA
* *
161867 TTTTTGCTGCTA
1 TTTTTGTTGTTA
*
161879 TTTTGGTTGTTA
1 TTTTTGTTGTTA
161891 TTTTTGTT
1 TTTTTGTT
161899 ATTTGAATGT
Statistics
Matches: 82, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
9 5 0.06
10 3 0.04
11 13 0.16
12 61 0.74
ACGTcount: A:0.06, C:0.04, G:0.21, T:0.70
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:161916 original size:45 final size:44
Alignment explanation
Indices: 161805--161915 Score: 136
Period size: 45 Copynumber: 2.5 Consensus size: 44
161795 GTTGTTTTCG
* * * *
161805 TGTTGTTTTTGTTGTTATTTTTGTTGCTATTTTTGTTGTTTTTAA
1 TGTTGTTTTTGATGTTATTTTTGCTGCTATTTTGGTTGTTATT-A
*
161850 TGTTGTTTTTGTTGTTATTTTTGCTGCTATTTTGGTTGTTATT-
1 TGTTGTTTTTGATGTTATTTTTGCTGCTATTTTGGTTGTTATTA
161893 T-TTGTTATTTGAATGTTATTTTT
1 TGTTGTT-TTTG-ATGTTATTTTT
161916 TATGCGTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
42 5 0.08
43 5 0.08
44 10 0.17
45 40 0.67
ACGTcount: A:0.10, C:0.03, G:0.18, T:0.69
Consensus pattern (44 bp):
TGTTGTTTTTGATGTTATTTTTGCTGCTATTTTGGTTGTTATTA
Found at i:162064 original size:16 final size:16
Alignment explanation
Indices: 162030--162060 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
162020 AATATAAAAA
162030 AAATTTAATTTATTTT
1 AAATTTAATTTATTTT
162046 AAATTT-ATTTATTTT
1 AAATTTAATTTATTTT
162061 TAAACGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AAATTTAATTTATTTT
Found at i:163099 original size:2 final size:2
Alignment explanation
Indices: 163094--163119 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
163084 TATATTCATT
163094 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
163120 GAATGTTATT
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):
TA
Found at i:166855 original size:19 final size:20
Alignment explanation
Indices: 166817--166856 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
166807 TGTCTAATTG
* *
166817 TGATGCGAAGCCTTTAAATA
1 TGATGCGAAACCTATAAATA
166837 TGATGC-AAACCTATAAATA
1 TGATGCGAAACCTATAAATA
166856 T
1 T
166857 TTCTAGGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (20 bp):
TGATGCGAAACCTATAAATA
Found at i:168025 original size:21 final size:22
Alignment explanation
Indices: 167990--168030 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
167980 ATTTCGTGTT
167990 CAGGAGTCGATGTCACGACACA
1 CAGGAGTCGATGTCACGACACA
* *
168012 CAGGATTCG-TGTCATGACA
1 CAGGAGTCGATGTCACGACA
168031 TAGCAAGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (22 bp):
CAGGAGTCGATGTCACGACACA
Found at i:173427 original size:52 final size:52
Alignment explanation
Indices: 173342--173632 Score: 350
Period size: 52 Copynumber: 5.6 Consensus size: 52
173332 TAAATGAAAT
* * * *
173342 AGGTCCGATGACTATGTGTCATCGTGAGAATATGAATCCTTAACGGATTATA
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
* *
173394 AGGTCCAATGACTATGTGTCATCATAAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
* * * *
173446 AGGTCCGATGACTATATGTCATCATGAGAATATGAATCCTTTATGAATTATG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
* * ** *
173498 AGGTCCGATGACTATATGTGATTGTGAGTATGTGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
** * * *
173550 AGGTCTAATGACTATGTGTTATCATGAGTATATGAATTCTTTACGGATTA-A
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
* ** * *
173601 ATGTCCGATGACTCCGTTTCATCGTGAGTATA
1 AGGTCCGATGACTATGTGTCATCATGAGTATA
173633 AAATACACAT
Statistics
Matches: 203, Mismatches: 36, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
51 24 0.12
52 179 0.88
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
Found at i:179893 original size:72 final size:72
Alignment explanation
Indices: 179771--179916 Score: 231
Period size: 72 Copynumber: 2.0 Consensus size: 72
179761 TGAAACTAAA
* * * *
179771 ACATAGGTGGCGATCTTATTAGCGATAAAGTCCTCATAACAAAGTGCTCGCCTTAATTGAAATTT
1 ACATAGGTGGCGATCTTATTAGCGATAAAGTCCTCATAACAAAGTCCTCGCCCTAACTAAAATTT
179836 CTCTATC
66 CTCTATC
*
179843 ACATAGGTGGCGA-CGTTATTAGCGATAAAGTCCTCCTAACAAAGTCCTCGCCCTAACTAAAATT
1 ACATAGGTGGCGATC-TTATTAGCGATAAAGTCCTCATAACAAAGTCCTCGCCCTAACTAAAATT
179907 TCTCTATC
65 TCTCTATC
179915 AC
1 AC
179917 TCGGACTGGT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
71 1 0.01
72 67 0.99
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (72 bp):
ACATAGGTGGCGATCTTATTAGCGATAAAGTCCTCATAACAAAGTCCTCGCCCTAACTAAAATTT
CTCTATC
Found at i:182249 original size:57 final size:57
Alignment explanation
Indices: 182183--182297 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 57
182173 GATTGATTGG
* * * *
182183 ACATATATAATTAGGGCTCAAATGGTTTATAATTAAGTTCTATCTTTTTGCCTATTA
1 ACATATATAATTAGGGCTCAAATGATTTATAATTAAGTACAAGCTTTTTGCCTATTA
* *
182240 ACATATATAATTAGGGTTCAAATTATTTATAATTAAGTACAAGCTTTTTGCCTATTA
1 ACATATATAATTAGGGCTCAAATGATTTATAATTAAGTACAAGCTTTTTGCCTATTA
182297 A
1 A
182298 TTATAAACTC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (57 bp):
ACATATATAATTAGGGCTCAAATGATTTATAATTAAGTACAAGCTTTTTGCCTATTA
Found at i:186695 original size:21 final size:21
Alignment explanation
Indices: 186653--186695 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
186643 TTGTATGTTT
* *
186653 AGAACTACCGATACATGCAAG
1 AGAACTACCGAAACAAGCAAG
*
186674 AGAACTACCGAAACAAGTAAG
1 AGAACTACCGAAACAAGCAAG
186695 A
1 A
186696 ATATTACTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.12
Consensus pattern (21 bp):
AGAACTACCGAAACAAGCAAG
Found at i:187241 original size:18 final size:18
Alignment explanation
Indices: 187200--187304 Score: 120
Period size: 18 Copynumber: 5.8 Consensus size: 18
187190 AATTTACTCT
*
187200 AACGAGCCAGTATTGCTCT
1 AACGAGCCAGTA-TGCTCA
* *
187219 TACGAGCCATTATGCTCA
1 AACGAGCCAGTATGCTCA
*
187237 AACGAGCCAGTATGCTTA
1 AACGAGCCAGTATGCTCA
** *
187255 ATTGAGGCAGTATGCTCA
1 AACGAGCCAGTATGCTCA
*
187273 AACGAGCCAGTATGCTCT
1 AACGAGCCAGTATGCTCA
*
187291 AACGAGCCAATATG
1 AACGAGCCAGTATG
187305 TTATTCCTTC
Statistics
Matches: 71, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
18 61 0.86
19 10 0.14
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (18 bp):
AACGAGCCAGTATGCTCA
Found at i:188671 original size:22 final size:22
Alignment explanation
Indices: 188647--188689 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
188637 AATGATGCTT
* *
188647 TTTTGGTTGGTTTG-TACTTAA
1 TTTTGGATGGTTAGATACTTAA
188668 TTTTGGATGGTTAGATACTTAA
1 TTTTGGATGGTTAGATACTTAA
188690 GATACTTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.21, C:0.05, G:0.23, T:0.51
Consensus pattern (22 bp):
TTTTGGATGGTTAGATACTTAA
Found at i:193306 original size:2 final size:2
Alignment explanation
Indices: 193294--193326 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
193284 AAGCATGAGT
*
193294 GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
193327 GAATCTGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:193637 original size:3 final size:3
Alignment explanation
Indices: 193629--193657 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
193619 CAGTCGGAAG
193629 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
193658 TACTCAGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:212720 original size:49 final size:49
Alignment explanation
Indices: 212667--213037 Score: 224
Period size: 49 Copynumber: 7.5 Consensus size: 49
212657 CATGAAGATT
*
212667 TGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
1 TGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
* * * *
212716 TGAAGGAAAAGATTTAAGCCGCAACGGCGAATCTAGTA-C-CATGAAG-A
1 TGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCA-GAAGCA
* * * ** *
212763 TATAGAGGGAAA-AGTTTAAGTCGTAAAGGTAAACCTTATACCTCA-AGAGCA
1 T-GA-AGGGAAAGA-TTTAAGTCGCAACGGCGAACCTTGTACCTCAGA-AGCA
** * * * *
212814 CAAAGGGAAAGATTTAA-TC-CATAATGGCGAATCC-AGTACCAC-GAAGATAA
1 TGAAGGGAAAGATTTAAGTCGC--AACGGCGAA-CCTTGTACCTCAGAAG--CA
* * * * * * *
212864 TGGAGGTAAAGGTTTAAGCCACAACAGTGAACCTTGTACCTCAGAAGCA
1 TGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
* * * * **
212913 TGAAGGGAAAGATTTAAG-CTGCAACGGTGAATCC-AGTACCATGAAAATAA
1 TGAAGGGAAAGATTTAAGTC-GCAACGGCGAA-CCTTGTACC-TCAGAAGCA
* * * *
212963 TGGAGGAAAAGGTTTAAGCCGCAACGGCGAACCTTGTACCTCAGAAGCA
1 TGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
* *
213012 TGGAGGGAAAGATTTTAGTCGCAACG
1 TGAAGGGAAAGATTTAAGTCGCAACG
213038 ACAAATCTAG
Statistics
Matches: 238, Mismatches: 60, Indels: 48
0.69 0.17 0.14
Matches are distributed among these distances:
47 4 0.02
48 12 0.05
49 143 0.60
50 69 0.29
51 9 0.04
52 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (49 bp):
TGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
Found at i:212921 original size:99 final size:98
Alignment explanation
Indices: 212651--213074 Score: 476
Period size: 99 Copynumber: 4.3 Consensus size: 98
212641 CTACAGGCTT
* * * *
212651 CAGTACCATGAAGATTTGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
1 CAGTACCATGAAGATATGGAGGGAAAGGTTTAAGCCGCAACAGCGAACCTTGTACCTCAGAAGCA
*
212716 TGAAGGAAAAGATTTAAGCCGCAACGGCGAATC
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * * *
212749 TAGTACCATGAAGATATAGAGGGAAAAGTTTAAGTCGTAA-AG-GTAAACCTTATACCTCA-AGA
1 CAGTACCATGAAGATATGGAGGGAAAGGTTTAAGCCGCAACAGCG--AACCTTGTACCTCAGA-A
** * ** *
212811 GCACAAAGGGAAAGATTTAATCCATAATGGCGAATC
63 GCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * *
212847 CAGTACCACGAAGATAATGGAGGTAAAGGTTTAAGCCACAACAGTGAACCTTGTACCTCAGAAGC
1 CAGTACCATGAAGAT-ATGGAGGGAAAGGTTTAAGCCGCAACAGCGAACCTTGTACCTCAGAAGC
* *
212912 ATGAAGGGAAAGATTTAAGCTGCAACGGTGAATC
65 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * *
212946 CAGTACCATGAAAATAATGGAGGAAAAGGTTTAAGCCGCAACGGCGAACCTTGTACCTCAGAAGC
1 CAGTACCATGAAGAT-ATGGAGGGAAAGGTTTAAGCCGCAACAGCGAACCTTGTACCTCAGAAGC
* * * * *
213011 ATGGAGGGAAAGATTTTAGTCGCAACGACAAATC
65 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * *
213045 TAGTACCACGAAGATATGGAGGGAAGGGTT
1 CAGTACCATGAAGATATGGAGGGAAAGGTT
213075 ACAACCGCAA
Statistics
Matches: 269, Mismatches: 50, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
96 1 0.00
97 2 0.01
98 103 0.38
99 159 0.59
100 3 0.01
101 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (98 bp):
CAGTACCATGAAGATATGGAGGGAAAGGTTTAAGCCGCAACAGCGAACCTTGTACCTCAGAAGCA
TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
Found at i:213066 original size:197 final size:195
Alignment explanation
Indices: 212651--213074 Score: 503
Period size: 197 Copynumber: 2.2 Consensus size: 195
212641 CTACAGGCTT
* * * * * *
212651 CAGTACCATGAAGATTTGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGCCACAACAGCGAACCTTGTACCTCAGAAGCA
* *
212716 TGAAGGAAAAGATTTAAGCCGCAACGGCGAATCTAGTACCATGAAGATATAGAGGGAAAAGTTTA
66 TGAAGGAAAAGATTTAAGCCGCAACGGCGAATCCAGTACCATGAAAATATAGAGGGAAAAGTTTA
* * * * * *
212781 AGTCGTAAAGGTAAACCTTATACCTCAAGAGCACAAAGGGAAAGATTTAATCCATAATGGCGAAT
131 AGCCGCAAAGGCAAACCTTATACCTCAAGAGCACAAAGGGAAAGATTTAATCCA-AACGACAAAT
212846 C
195 C
* *
212847 CAGTACCACGAAGATAATGGAGGTAAAGGTTTAAGCCACAACAGTGAACCTTGTACCTCAGAAGC
1 CAGTACCACGAAGAT-ATGGAGGGAAAGGTTTAAGCCACAACAGCGAACCTTGTACCTCAGAAGC
* * * *
212912 ATGAAGGGAAAGATTTAAGCTGCAACGGTGAATCCAGTACCATGAAAATAATGGA-GGAAAAGGT
65 ATGAAGGAAAAGATTTAAGCCGCAACGGCGAATCCAGTACCATGAAAAT-ATAGAGGGAAAA-GT
* * * *** *
212976 TTAAGCCGCAACGGCGAACCTTGTACCTC-AGAAGCATGGAGGGAAAGATTTTAGTCGC-AACGA
128 TTAAGCCGCAAAGGCAAACCTTATACCTCAAG-AGCACAAAGGGAAAGA-TTTAATC-CAAACGA
213039 CAAATC
190 CAAATC
* *
213045 TAGTACCACGAAGATATGGAGGGAAGGGTT
1 CAGTACCACGAAGATATGGAGGGAAAGGTT
213075 ACAACCGCAA
Statistics
Matches: 192, Mismatches: 30, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
196 14 0.07
197 107 0.56
198 64 0.33
199 6 0.03
200 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (195 bp):
CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGCCACAACAGCGAACCTTGTACCTCAGAAGCA
TGAAGGAAAAGATTTAAGCCGCAACGGCGAATCCAGTACCATGAAAATATAGAGGGAAAAGTTTA
AGCCGCAAAGGCAAACCTTATACCTCAAGAGCACAAAGGGAAAGATTTAATCCAAACGACAAATC
Found at i:213386 original size:103 final size:102
Alignment explanation
Indices: 213169--213392 Score: 252
Period size: 103 Copynumber: 2.2 Consensus size: 102
213159 TCAAGTCTTC
* * * *
213169 ATCTCTCTAAAGTTACAGTAAGAGCAAGATGAAGCCTCAACGTCAAATCTTATCCTCTTGAAGTT
1 ATCTCTCTGAAGTTACAGTAAGAGCAAGATGAAGCCTCAACATCAAATCCTATCCTCCTGAAGTT
* * * **
213234 ACAATAAAGTTGTATTAAAAACAAATAATAAGTCTTT
66 ACAATAAAGTTGGATTAAAAACAAATAACAAATCTCG
* * *
213271 ATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAAAATCCTATCTTCCTGAAGT
1 ATCTCTCTGAAGTTACAGTAAGAGCAAGATGAAGCCTCAACATC-AAATCCTATCCTCCTGAAGT
** * * *
213336 TGTAATGAAGTTGGATTAGAAACAAATAGCAAATCTCG
65 TACAATAAAGTTGGATTAAAAACAAATAACAAATCTCG
* *
213374 ATTTC-CTCGAAGTCACAGT
1 ATCTCTCT-GAAGTTACAGT
213393 GGAATGTAGT
Statistics
Matches: 100, Mismatches: 20, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
102 42 0.42
103 58 0.58
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (102 bp):
ATCTCTCTGAAGTTACAGTAAGAGCAAGATGAAGCCTCAACATCAAATCCTATCCTCCTGAAGTT
ACAATAAAGTTGGATTAAAAACAAATAACAAATCTCG
Found at i:224917 original size:44 final size:44
Alignment explanation
Indices: 224867--224954 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
224857 ATTAAATATG
224867 TTAATTTGTAAAGGAATGGCCTAGAAAGGTCCTTAAAAGTAATT
1 TTAATTTGTAAAGGAATGGCCTAGAAAGGTCCTTAAAAGTAATT
224911 TTAATTTGTAAAGGAATGGCCTAGAAAGGTCCTTAAAAGTAATT
1 TTAATTTGTAAAGGAATGGCCTAGAAAGGTCCTTAAAAGTAATT
224955 ATACCTTTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (44 bp):
TTAATTTGTAAAGGAATGGCCTAGAAAGGTCCTTAAAAGTAATT
Found at i:225893 original size:27 final size:27
Alignment explanation
Indices: 225865--225981 Score: 153
Period size: 27 Copynumber: 4.3 Consensus size: 27
225855 TGCTATTCTG
* * *
225865 TTCTGGGCTCATAAGAGCTAAACTTTG
1 TTCTGGGCTCGTAAGAGCTAAACTCTA
* *
225892 TTCTAGGCTCGTAAGAGCTGAACTCTA
1 TTCTGGGCTCGTAAGAGCTAAACTCTA
* * *
225919 TTTTAGGCTCGTAAGAGCTGAACTCTA
1 TTCTGGGCTCGTAAGAGCTAAACTCTA
*
225946 TTTTGGGCTCGTAAGAGCTAAACTCTA
1 TTCTGGGCTCGTAAGAGCTAAACTCTA
225973 TTCTGGGCT
1 TTCTGGGCT
225982 TGAATGAGCT
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 81 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (27 bp):
TTCTGGGCTCGTAAGAGCTAAACTCTA
Found at i:230358 original size:218 final size:219
Alignment explanation
Indices: 229917--230339 Score: 613
Period size: 218 Copynumber: 1.9 Consensus size: 219
229907 AAAAATTTAT
* *
229917 GTTCGTTATTTCATGATTTGAAAAGTCAAGCCCTAACTTACTGGGTGCGTTTTCCTTCGAATTGA
1 GTTCATTATTTCATGATTTGAAAAGTCAAGCCCTAACTTACTGAGTGCGTTTTCCTTCGAATTGA
* * *
229982 AATATTCGAATGCTTTTCTCTTTAAAAAATAATAAACCTGAGATTTAAAAAAAAATCGGATTGCT
66 AATATTCGAATGCTTTTCTCTTAAAAAAATAATAAACATGAGATTT--AAAAAAATAGGATTGCT
* * * *
230047 TGTTATTTTTGGAAACATGAGGTGTCGAGCCCTAACTTACTGGACCCGACTTCCTTTCTCGATTT
129 TGTGATTTTTGAAAACATAAGGTGTCGAGCCCTAACTTACTAGACCCGACTTCCTTTCTCGATTT
230112 TCAAAATAACGATTCTTCCTCGTAAA
194 TCAAAATAACGATTCTTCCTCGTAAA
* * *
230138 GTTCATTATTT-ATTGATTTGAAAAGTCGAGCCCTAACTTACTGAGTGAGGTTTTTCTTCGAATT
1 GTTCATTATTTCA-TGATTTGAAAAGTCAAGCCCTAACTTACTGAGTG-CGTTTTCCTTCGAATT
*
230202 GAAATATTCGAATGCTTTTCTC-TAAAAAAATAATAAATCATGAGATTT-TAAAAATAGG-TATG
64 GAAATATTCGAATGCTTTTCTCTTAAAAAAATAATAAA-CATGAGATTTAAAAAAATAGGAT-TG
* * *
230264 TTTGTGA-TTTTGAAAACGTAAGGTGTCGAGCCCTAACTTACTAGACCCGATTTCCTTTCTCGAT
127 CTTGTGATTTTTGAAAACATAAGGTGTCGAGCCCTAACTTACTAGACCCGACTTCCTTTCTCGAT
230328 TTTCAAAATAAC
192 TTTCAAAATAAC
230340 AAGCTTTTCT
Statistics
Matches: 182, Mismatches: 16, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
218 65 0.36
219 15 0.08
220 1 0.01
221 56 0.31
222 45 0.25
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (219 bp):
GTTCATTATTTCATGATTTGAAAAGTCAAGCCCTAACTTACTGAGTGCGTTTTCCTTCGAATTGA
AATATTCGAATGCTTTTCTCTTAAAAAAATAATAAACATGAGATTTAAAAAAATAGGATTGCTTG
TGATTTTTGAAAACATAAGGTGTCGAGCCCTAACTTACTAGACCCGACTTCCTTTCTCGATTTTC
AAAATAACGATTCTTCCTCGTAAA
Found at i:233563 original size:11 final size:11
Alignment explanation
Indices: 233547--233578 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
233537 CAGTTAAATC
*
233547 AGAAACCATAA
1 AGAAACCACAA
233558 AGAAACCACAA
1 AGAAACCACAA
233569 AGAAACCACA
1 AGAAACCACA
233579 TCGCTCCAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.62, C:0.25, G:0.09, T:0.03
Consensus pattern (11 bp):
AGAAACCACAA
Found at i:241896 original size:38 final size:39
Alignment explanation
Indices: 241854--241938 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 39
241844 TAATCAAGAA
* *
241854 GGGCAGATTGA-AG-ATTTCGATCTCTTACCCCAAGCCTG
1 GGGCAGATTCACAGCATTT-GATATCTTACCCCAAGCCTG
*
241892 GGGCAGA-TCACAGCCATTTGATATCTTACCCCGAGCCTG
1 GGGCAGATTCACAG-CATTTGATATCTTACCCCAAGCCTG
241931 GGGCAGAT
1 GGGCAGAT
241939 CACCATCAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
37 2 0.05
38 9 0.22
39 25 0.62
40 4 0.10
ACGTcount: A:0.24, C:0.27, G:0.26, T:0.24
Consensus pattern (39 bp):
GGGCAGATTCACAGCATTTGATATCTTACCCCAAGCCTG
Found at i:241958 original size:39 final size:39
Alignment explanation
Indices: 241915--243093 Score: 588
Period size: 39 Copynumber: 30.3 Consensus size: 39
241905 CCATTTGATA
* *
241915 TCTTACCCCGAGCCTGGGGCAGATCACCATCAACCAATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
* * * * **
241954 TCTTACCCCGAGCTTAGGACAGATTA-CAGCCATTCAATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCA-TCAGCCAATC
* * *
241993 TTTTACCCCGATCTTGGGGCAGATTACCATCAGCCAATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
* * *
242032 TCTTACCCTGAGCTTGAGGCAGATTGCAGCCAT---CCGATC
1 TCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGCCAATC
* ** *
242071 TCTTACCTCGAGCTTGAAGCAGATCACCATCAGCGAATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
* * * * * * * * * * *
242110 TCTTACTCCAAGCCTGGGGTAGTTTA-TAGCCGTTCGATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAG-CCAATC
* * ** ** *
242149 TCTTACCTCGAGCTTGAGGCAGAT-TGCAGTCATTCGATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCA-TCAGCCAATC
*
242188 TCTTACCCCGAGCTTGGGGCAGATCACCATTAGCCAATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
*
242227 TCTTACCCCGAGCTTAGGGCAGATTGCAGCCAT---CCAATC
1 TCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGCCAATC
* * * * * * *
242266 TCTTACCTCGAGCCTGGGGCAAATTA-CAGCCGTCCGATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAG-CCAATC
** * * *
242305 TCTTACCCTAAGCTTGGGGTAAATCACCATCAACCAATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
* * *** *
242344 TCTTACCTCGAGCCTACAGCAGATTGCAGCCATCTG---ATC
1 TCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGCCAATC
* ** * * * *
242383 TTTTACCCTAAGCTTGTGGTAAATCACCATCAACCAATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
* * * ** * * ** *
242422 TCTTACCTCGAACTTGGGGCAAATTGCAACCATTCGATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
* * *
242461 TCTTACCCCGAGCTTGAGGCAAATCACCATCAGCTAATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
* * * *
242500 TCTTACCTCGAGCTTGAGGCAAATCACCATCAGCTAATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
* * * * *
242539 TCTTACCCCGAGCCTAGGGTAGATTGTATCCATCTG---ATC
1 TCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGCCAATC
* *
242578 TCTTATCTCGAGCTTGGGGCAGATCACCATCAGCCAATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
* * * * * * *
242617 TATTACCCCGAGCTTGGGACAAATTA-CAACCGTCCGATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAG-CCAATC
* * *
242656 TCTTACTCTGAGCTTGGGGTAGATCACCATCAGCCAATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
* * * *
242695 TCTTACCTCAAGCCTAGGGCAGATTGCAGCCATTC-G---ATC
1 TCTTACCCCGAGCTTGGGGCAGA-T-CA-CCA-TCAGCCAATC
* * *
242734 TTTTACCCCAAGCTTAGGGCAGATCACCATCAGCCAATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
* * * ** * * * ** *
242773 -CATACCCTGAGCCTAAGGCAGATTACAACCATTCGATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
* *
242811 TCTTACCCCGAGCCT-GGGCTAGATCACCATTAGCCAATC
1 TCTTACCCCGAGCTTGGGGC-AGATCACCATCAGCCAATC
* * *
242850 TCTTACCCCGAGCATAGGGCAGACTGCAGCCATCTG---ATC
1 TCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGCCAATC
* * * *
242889 TTTTACTCCGAGCCTAGGGCAGATCACCATCAGCCAATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
* *
242928 TGTTACCCCGAGCTTAGGGCAGATTGCAGCCATTC-G---ATC
1 TCTTACCCCGAGCTTGGGGCAGA-T-CA-CCA-TCAGCCAATC
* * * * *
242967 TTTTACCCTGAGCTTGAGGTAGATCACCATCAACCAATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
** * * *
243006 TCTTACCTTGAGCCTGGGGTAGATTGCAGCCATCTG---ATC
1 TCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGCCAATC
* * *
243045 TCTTACCCTGAGCTTGGGGCAGATCGCCATCAGTCAATC
1 TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
243084 TCTTACCCCG
1 TCTTACCCCG
243094 CGACAAGGGC
Statistics
Matches: 854, Mismatches: 221, Indels: 130
0.71 0.18 0.11
Matches are distributed among these distances:
35 6 0.01
36 34 0.04
37 13 0.02
38 46 0.05
39 676 0.79
40 24 0.03
41 14 0.02
42 37 0.04
43 4 0.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (39 bp):
TCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATC
Found at i:242206 original size:195 final size:195
Alignment explanation
Indices: 241915--242709 Score: 718
Period size: 195 Copynumber: 4.1 Consensus size: 195
241905 CCATTTGATA
* * * * * * * *
241915 TCTTACCCCGAGCCTGGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCTTA-GGACAGATT
1 TCTTACCTCAAGCCTGGGGTAAATCACCACCGATCAATCTCTTACCCCGAGCCTACGG-CAGATT
* * * * * *
241979 ACAGCCAT-TCAATCTTTTACCCCGATCTTGGGGCAGATTACCATCAGCCAATCTCTTACCCTGA
65 GCAGCCATCT-GATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGA
* * * *
242043 GCTTGAGGCAGATTGCAGCCATCCGATCTCTTACCTCGAGCTTGAAGCAGATCACCATCAGCGAA
129 GCTTGAGGCAAATTGCAACCATCCGATCTCTTACCTCGAGCTTGAGGCAAATCACCATCAGCGAA
242108 TC
194 TC
** * * * * * *
242110 TCTTA-CTCCAAGCCTGGGGTAGTTTA-TAGCCGTTCGATCTCTTACCTCGAGCTTGA-GGCAGA
1 TCTTACCT-CAAGCCTGGGGTAAATCACCA-CCGATCAATCTCTTACCCCGAGCCT-ACGGCAGA
* *
242172 TTGCAGTCAT-TCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGCCAATCTCTTACCCC
63 TTGCAGCCATCT-GATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCC
* * * * * *
242236 GAGCTT-AGGGCAGATTGCAGCCATCCAATCTCTTACCTCGAGCCTGGGGCAAATTACAGCCGTC
127 GAGCTTGA-GGCAAATTGCAACCATCCGATCTCTTACCTCGAGCTTGAGGCAAA-T-CA-CCATC
242300 --CG-ATC
188 AGCGAATC
* * * * * *
242305 TCTTACC-CTAAGCTTGGGGTAAATCACCATCAACCAATCTCTTACCTCGAGCCTACAGCAGATT
1 TCTTACCTC-AAGCCTGGGGTAAATCACCACCGATCAATCTCTTACCCCGAGCCTACGGCAGATT
* ** * * * * * *
242369 GCAGCCATCTGATCTTTTACCCTAAGCTTGTGGTAAATCACCATCAACCAATCTCTTACCTCGAA
65 GCAGCCATCTGATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAG
* * * *
242434 CTTGGGGCAAATTGCAACCATTCGATCTCTTACCCCGAGCTTGAGGCAAATCACCATCAGCTAAT
130 CTTGAGGCAAATTGCAACCATCCGATCTCTTACCTCGAGCTTGAGGCAAATCACCATCAGCGAAT
242499 C
195 C
* * * * * * * *
242500 TCTTACCTCGAGCTTGAGGCAAATCACCATC-AGCTAATCTCTTACCCCGAGCCTAGGGTAGATT
1 TCTTACCTCAAGCCTGGGGTAAATCACCACCGATC-AATCTCTTACCCCGAGCCTACGGCAGATT
* * * * *
242564 GTATCCATCTGATCTCTTATCTCGAGCTTGGGGCAGATCACCATCAGCCAATCTATTACCCCGAG
65 GCAGCCATCTGATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAG
* * * * * *
242629 CTTG-GGACAAATTACAACCGTCCGATCTCTTA-CTCTGAGCTTGGGGTAGATCACCATCAGCCA
130 CTTGAGG-CAAATTGCAACCATCCGATCTCTTACCTC-GAGCTTGAGGCAAATCACCATCAGCGA
242692 ATC
193 ATC
242695 TCTTACCTCAAGCCT
1 TCTTACCTCAAGCCT
242710 AGGGCAGATT
Statistics
Matches: 489, Mismatches: 91, Indels: 40
0.79 0.15 0.06
Matches are distributed among these distances:
192 4 0.01
193 2 0.00
194 13 0.03
195 454 0.93
196 10 0.02
197 2 0.00
198 4 0.01
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (195 bp):
TCTTACCTCAAGCCTGGGGTAAATCACCACCGATCAATCTCTTACCCCGAGCCTACGGCAGATTG
CAGCCATCTGATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGC
TTGAGGCAAATTGCAACCATCCGATCTCTTACCTCGAGCTTGAGGCAAATCACCATCAGCGAATC
Found at i:242734 original size:156 final size:154
Alignment explanation
Indices: 242497--243128 Score: 707
Period size: 156 Copynumber: 4.1 Consensus size: 154
242487 CCATCAGCTA
* * * *
242497 ATCTCTTA-CCTCGAGCTTGAGGCAAATCACCATCAGCTAATCTCTTACCCCGAGCCTAGGGTAG
1 ATCTCTTACCCT-GAGCTTGAGGTAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAG
* * * *
242561 ATTGTATCCATCTGATCTCTTATCTCGAGCTTGGGGCAGATCACCATCAGCCAATCTATTACCCC
65 ATTGCAGCCATCTGATCTCTTA-CCCGAGCTTAGGGCAGATCACCATCAGCCAATCTATTACCCC
* * *
242626 GAGCTTGGGACAAATTACAACCGTCCG
129 GAGCTTGGG-CAGATTACAACCATTCG
* * * *
242653 ATCTCTTACTCTGAGCTTGGGGTAGATCACCATCAGCCAATCTCTTACCTCAAGCCTAGGGCAGA
1 ATCTCTTACCCTGAGCTTGAGGTAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGA
* * * *
242718 TTGCAGCCAT-TCGATCTTTTACCCCAAGCTTAGGGCAGATCACCATCAGCCAATCCA-TACCCT
66 TTGCAGCCATCT-GATCTCTTA-CCCGAGCTTAGGGCAGATCACCATCAGCCAATCTATTACCCC
**
242781 GAGCCTAAGGCAGATTACAACCATTCG
129 GAG-CTTGGGCAGATTACAACCATTCG
* * * *
242808 ATCTCTTACCCCGAGCCTG-GGCTAGATCACCATTAGCCAATCTCTTACCCCGAGCATAGGGCAG
1 ATCTCTTACCCTGAGCTTGAGG-TAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAG
* * * *
242872 ACTGCAGCCATCTGATCTTTTACTCCGAGCCTAGGGCAGATCACCATCAGCCAATCTGTTACCCC
65 ATTGCAGCCATCTGATCTCTTAC-CCGAGCTTAGGGCAGATCACCATCAGCCAATCTATTACCCC
* *
242937 GAGCTTAGGGCAGATTGCAGCCATTCG
129 GAGCTT-GGGCAGATTACAACCATTCG
* * ** * *
242964 ATCTTTTACCCTGAGCTTGAGGTAGATCACCATCAACCAATCTCTTACCTTGAGCCTGGGGTAGA
1 ATCTCTTACCCTGAGCTTGAGGTAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGA
* * * *
243029 TTGCAGCCATCTGATCTCTTACCCTGAGCTTGGGGCAGATCGCCATCAGTCAATCTCTTACCCCG
66 TTGCAGCCATCTGATCTCTTACCC-GAGCTTAGGGCAGATCACCATCAGCCAATCTATTACCCCG
* ** * *
243094 CGACAAGGGCAGATTGCAACC-TTCCA
130 AG-CTTGGGCAGATTACAACCATT-CG
243120 ATCTCTTAC
1 ATCTCTTAC
243129 AAAAAAACCA
Statistics
Matches: 402, Mismatches: 62, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
154 3 0.01
155 132 0.33
156 262 0.65
157 5 0.01
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.25
Consensus pattern (154 bp):
ATCTCTTACCCTGAGCTTGAGGTAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGA
TTGCAGCCATCTGATCTCTTACCCGAGCTTAGGGCAGATCACCATCAGCCAATCTATTACCCCGA
GCTTGGGCAGATTACAACCATTCG
Found at i:242742 original size:195 final size:190
Alignment explanation
Indices: 241915--243090 Score: 701
Period size: 195 Copynumber: 6.0 Consensus size: 190
241905 CCATTTGATA
* * * * * * * *
241915 TCTTACCCCGAGCCTGGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCTTAGGACAGATTA
1 TCTTACCTCAAGCCTGGGGCAAATCACCAT---TCGATCTCTTACCCCGAGCCTAGGGCAGATTG
* * * * * *
241980 CAGCCAT-TCAATCTTTTACCCCGATCTTGGGGCAGATTACCATCAGCCAATCTCTTACCCTGAG
63 CATCCATCT-GATCTCTTA-CCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAG
* * * * *
242044 CTTGAGGCAGATTGCAGCCATCCGATCTCTTACCTCGAGCTTGAAGCAGATCACCATCAGCGAAT
126 CTTG-GGCAAATTGCAACCATCCGATCTCTTACCTCGAGCTTGAGGCAAATCACCATCAGCCAAT
242109 C
190 C
* * * * *
242110 TCTTA-CTCCAAGCCTGGGGTAGTTTAT-AGCCGTTCGATCTCTTACCTCGAG-CTTGAGGCAGA
1 TCTTACCT-CAAGCCTGGGGCA---AATCA-CCATTCGATCTCTTACCCCGAGCCTAG-GGCAGA
*
242172 TTGCAGT-CAT-TCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGCCAATCTCTTACCC
60 TTGCA-TCCATCT-GATCTCTTA-CCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCC
* * * * * * * *
242235 CGAGCTTAGGGCAGATTGCAGCCATCCAATCTCTTACCTCGAGCCTGGGGCAAATTA-CAGCCGT
122 CGAGCTT-GGGCAAATTGCAACCATCCGATCTCTTACCTCGAGCTTGAGGCAAATCACCATCAG-
*
242299 CCGATC
185 CCAATC
* * * * * **
242305 TCTTACC-CTAAGCTTGGGGTAAATCACCATCAACCAATCTCTTACCTCGAGCCTACAGCAGATT
1 TCTTACCTC-AAGCCTGGGGCAAATCACCAT---TCGATCTCTTACCCCGAGCCTAGGGCAGATT
* * * * * * * * *
242369 GCAGCCATCTGATCTTTTACCCTAAGCTTGTGGTAAATCACCATCAACCAATCTCTTACCTCGAA
62 GCATCCATCTGATCTCTTACCC-GAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAG
* * *
242434 CTTGGGGCAAATTGCAACCATTCGATCTCTTACCCCGAGCTTGAGGCAAATCACCATCAGCTAAT
126 CTT-GGGCAAATTGCAACCATCCGATCTCTTACCTCGAGCTTGAGGCAAATCACCATCAGCCAAT
242499 C
190 C
* * * *
242500 TCTTACCTCGAGCTTGAGGCAAATCACCA-TCAGCTAATCTCTTACCCCGAGCCTAGGGTAGATT
1 TCTTACCTCAAGCCTGGGGCAAATCACCATTC-G---ATCTCTTACCCCGAGCCTAGGGCAGATT
* * *
242564 GTATCCATCTGATCTCTTATCTCGAGCTTGGGGCAGATCACCATCAGCCAATCTATTACCCCGAG
62 GCATCCATCTGATCTCTTA-CCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAG
* * * * *
242629 CTTGGGACAAATTACAACCGTCCGATCTCTTA-CTCTGAGCTTGGGGTAGATCACCATCAGCCAA
126 CTTGGG-CAAATTGCAACCATCCGATCTCTTACCTC-GAGCTTGAGGCAAATCACCATCAGCCAA
242693 TC
189 TC
* * * * *
242695 TCTTACCTCAAGCCTAGGGCAGATTGCAGCCATTCGATCTTTTACCCCAAGCTTAGGGCAGA-T-
1 TCTTACCTCAAGCCTGGGGCA-AAT-CA-CCATTCGATCTCTTACCCCGAGCCTAGGGCAGATTG
* * * ** * * * ** *
242758 CA-CCATCAGCCAATC-CATACCCTGAGCCTAAGGCAGATTACAACCATTCGATCTCTTACCCCG
63 CATCCATCTG---ATCTCTTACCC-GAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCG
* * * * * *
242821 AGCCTGGGCTAGA-T-C-ACCATTAGCCAATCTCTTACCCCGAGCAT-AGGGCAGACTGCAGCCA
124 AGCTTGGGC-AAATTGCAACCA-T--CCGATCTCTTACCTCGAGCTTGA-GGCA-AAT-CA-CCA
*
242882 TCTG---ATC
181 TCAGCCAATC
* * * * * *
242889 TTTTA-CTCCGAGCCTAGGGCAGATCACCA-TCAGCCAATCTGTTACCCCGAGCTTAGGGCAGAT
1 TCTTACCT-CAAGCCTGGGGCAAATCACCATTC-G---ATCTCTTACCCCGAGCCTAGGGCAGAT
* * * * * **
242952 TGCAGCCAT-TCGATCTTTTACCCTGAGCTTGAGGTAGATCACCATCAACCAATCTCTTACCTTG
61 TGCATCCATCT-GATCTCTTACCC-GAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCG
* * * * * * * * *
243016 AGCCTGGGGTAGATTGCAGCCATCTGATCTCTTACC-CTGAGCTTGGGGCAGATCGCCATCAGTC
124 AG-CTTGGGCAAATTGCAACCATCCGATCTCTTACCTC-GAGCTTGAGGCAAATCACCATCAGCC
243080 AATC
187 AATC
243084 TCTTACC
1 TCTTACC
243091 CCGCGACAAG
Statistics
Matches: 760, Mismatches: 156, Indels: 129
0.73 0.15 0.12
Matches are distributed among these distances:
190 2 0.00
191 8 0.01
192 21 0.03
193 10 0.01
194 125 0.16
195 540 0.71
196 24 0.03
197 16 0.02
198 12 0.02
199 2 0.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (190 bp):
TCTTACCTCAAGCCTGGGGCAAATCACCATTCGATCTCTTACCCCGAGCCTAGGGCAGATTGCAT
CCATCTGATCTCTTACCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGG
GCAAATTGCAACCATCCGATCTCTTACCTCGAGCTTGAGGCAAATCACCATCAGCCAATC
Found at i:243067 original size:311 final size:311
Alignment explanation
Indices: 242497--243083 Score: 813
Period size: 311 Copynumber: 1.9 Consensus size: 311
242487 CCATCAGCTA
* * * * *
242497 ATCTCTTACCTCGAGCTTGAGGCAAATCACCATCAGCTAATCTCTTACCCCGAGCCTAGGGTAGA
1 ATCTCTTACCCCGAGCCTGAGGCAAATCACCATCAGCCAATCTCTTACCCCGAGCATAGGGCAGA
* * * * *
242562 TTGTATCCATCTGATCTCTTATCTCGAGCTTGGGGCAGATCACCATCAGCCAATCTATTACCCCG
66 CTGCAGCCATCTGATCTCTTATCTCGAGCCTAGGGCAGATCACCATCAGCCAATCTATTACCCCG
* * * *
242627 AGCTTGGGACAAATTACAACCGTCCGATCTCTTACTCTGAGCTTGGGGTAGATCACCATCAGCCA
131 AGCTTGGGACAAATTACAACCATCCGATCTCTTACCCTGAGCTTGAGGTAGATCACCATCAACCA
*
242692 ATCTCTTACCTCAAGCCTAGGGCAGATTGCAGCCATTCGATCTTTTACCCCAAGCTTAGGGCAGA
196 ATCTCTTACCTCAAGCCTAGGGCAGATTGCAGCCATTCGATCTCTTACCCCAAGCTTAGGGCAGA
242757 TCACCATCAGCCAATCCATACCCTGAGCCTAAGGCAGATTACAACCATTCG
261 TCACCATCAGCCAATCCATACCCTGAGCCTAAGGCAGATTACAACCATTCG
* *
242808 ATCTCTTACCCCGAGCCTG-GGCTAGATCACCATTAGCCAATCTCTTACCCCGAGCATAGGGCAG
1 ATCTCTTACCCCGAGCCTGAGGC-AAATCACCATCAGCCAATCTCTTACCCCGAGCATAGGGCAG
* *
242872 ACTGCAGCCATCTGATCTTTTA-CTCCGAGCCTAGGGCAGATCACCATCAGCCAATCTGTTACCC
65 ACTGCAGCCATCTGATCTCTTATCT-CGAGCCTAGGGCAGATCACCATCAGCCAATCTATTACCC
* * * * *
242936 CGAGCTTAGGG-CAGATTGCAGCCATTCGATCTTTTACCCTGAGCTTGAGGTAGATCACCATCAA
129 CGAGCTT-GGGACAAATTACAACCATCCGATCTCTTACCCTGAGCTTGAGGTAGATCACCATCAA
** * * ** *
243000 CCAATCTCTTACCTTGAGCCTGGGGTAGATTGCAGCCA-TCTGATCTCTTACCCTGAGCTTGGGG
193 CCAATCTCTTACCTCAAGCCTAGGGCAGATTGCAGCCATTC-GATCTCTTACCCCAAGCTTAGGG
* *
243064 CAGATCGCCATCAGTCAATC
257 CAGATCACCATCAGCCAATC
243084 TCTTACCCCG
Statistics
Matches: 239, Mismatches: 33, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
310 7 0.03
311 229 0.96
312 3 0.01
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (311 bp):
ATCTCTTACCCCGAGCCTGAGGCAAATCACCATCAGCCAATCTCTTACCCCGAGCATAGGGCAGA
CTGCAGCCATCTGATCTCTTATCTCGAGCCTAGGGCAGATCACCATCAGCCAATCTATTACCCCG
AGCTTGGGACAAATTACAACCATCCGATCTCTTACCCTGAGCTTGAGGTAGATCACCATCAACCA
ATCTCTTACCTCAAGCCTAGGGCAGATTGCAGCCATTCGATCTCTTACCCCAAGCTTAGGGCAGA
TCACCATCAGCCAATCCATACCCTGAGCCTAAGGCAGATTACAACCATTCG
Found at i:256530 original size:21 final size:21
Alignment explanation
Indices: 256504--256545 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
256494 TGTTACGAAA
*
256504 TCTTTTATATGCTATGAGAAC
1 TCTTTTAGATGCTATGAGAAC
* *
256525 TCTTTTAGATGTTATGCGAAC
1 TCTTTTAGATGCTATGAGAAC
256546 ATTTTCACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (21 bp):
TCTTTTAGATGCTATGAGAAC
Found at i:260985 original size:197 final size:199
Alignment explanation
Indices: 260625--261009 Score: 639
Period size: 197 Copynumber: 1.9 Consensus size: 199
260615 CCTTGTGTTC
*
260625 TTGAATTTATTGCATTTGCAATCTGGCCAACTTGATTTTCCAATGCTCTTAATGACGCACCTTGG
1 TTGAATTTATTGCATTT-CAATCTGGCCAACTTGATTTTCCAATGCTCTTAATGACGCAACTTGG
* * * *
260690 CTTTGGATGATAGCATCATTTTGGACATGTATTCCTTCATCAAATTCTTGATAGACGAGAAATCT
65 CTTTGGATGATAACATCATTTTGGACATGTATTCCTTCAACAAATTCTAGATAGAAGAGAAATCT
*
260755 CCATTTTGCTATTGATTTTGCTTTGAAAAATTTGGCTCAAATCCAGGTGCTCTGTCTTAGAGAAC
130 CCATTTTGCTATTGATTTTGCTTTGAAAAATTTGGCTCAAATCCAGGTGCTATGTCTTAGAGAAC
260820 AACAT
195 AACAT
* *
260825 TTGAATTTATTGCA-TT-AATCTGGCCAACTTGATTTTCTAATGCTCTTAATGATGCAACTTGGC
1 TTGAATTTATTGCATTTCAATCTGGCCAACTTGATTTTCCAATGCTCTTAATGACGCAACTTGGC
* *
260888 TTTGGATGATAACATCATTTTGGACATTTATTCCTTCAACAAATTCTAGATGGAAGAGAAATCTC
66 TTTGGATGATAACATCATTTTGGACATGTATTCCTTCAACAAATTCTAGATAGAAGAGAAATCTC
* *
260953 CATTTTGCTATTGATTTTGCTTTGACAAATTTGGCTCAAATCCATGTGCTATGTCTT
131 CATTTTGCTATTGATTTTGCTTTGAAAAATTTGGCTCAAATCCAGGTGCTATGTCTT
261010 GGTGAACAGC
Statistics
Matches: 173, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
197 157 0.91
199 2 0.01
200 14 0.08
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (199 bp):
TTGAATTTATTGCATTTCAATCTGGCCAACTTGATTTTCCAATGCTCTTAATGACGCAACTTGGC
TTTGGATGATAACATCATTTTGGACATGTATTCCTTCAACAAATTCTAGATAGAAGAGAAATCTC
CATTTTGCTATTGATTTTGCTTTGAAAAATTTGGCTCAAATCCAGGTGCTATGTCTTAGAGAACA
ACAT
Found at i:264089 original size:19 final size:19
Alignment explanation
Indices: 263998--264095 Score: 65
Period size: 20 Copynumber: 4.8 Consensus size: 19
263988 TATTTAAGTT
* *
263998 TTTTTAAAA-CATTATAAA
1 TTTTTAAAATTATTTTAAA
264016 TTTTTTAAAATATAAATTTTAGAA
1 -TTTTTAAAAT-T--ATTTTA-AA
* *
264040 TTTTTATAAA-CATTTTGAA
1 TTTTTA-AAATTATTTTAAA
*
264059 TTTTAAAAAATTATTTTAAA
1 TTTT-TAAAATTATTTTAAA
264079 TTTTTAAAATTTATTTT
1 TTTTTAAAA-TTATTTT
264096 GATTTTTTGT
Statistics
Matches: 62, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
19 22 0.35
20 24 0.39
23 11 0.18
24 5 0.08
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTTAAAATTATTTTAAA
Found at i:264103 original size:20 final size:20
Alignment explanation
Indices: 264017--264102 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 20
264007 CATTATAAAT
*
264017 TTTTTAAAATATAAATTTTAGAA
1 TTTTTAAAA-AT-TATTTT-GAA
* *
264040 TTTTTATAAA-CATTTTGAA
1 TTTTTAAAAATTATTTTGAA
* *
264059 TTTTAAAAAATTATTTTAAA
1 TTTTTAAAAATTATTTTGAA
*
264079 TTTTTAAAATTTATTTTG-A
1 TTTTTAAAAATTATTTTGAA
264098 TTTTT
1 TTTTT
264103 TGTAAATTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
19 17 0.32
20 27 0.51
22 1 0.02
23 8 0.15
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:264965 original size:8 final size:8
Alignment explanation
Indices: 264952--265040 Score: 72
Period size: 8 Copynumber: 10.8 Consensus size: 8
264942 TTACTTTAAA
264952 AAATTTTT
1 AAATTTTT
264960 AAATTTTT
1 AAATTTTT
*
264968 AAAATTTT
1 AAATTTTT
*
264976 AAAATTTT
1 AAATTTTT
*
264984 ATATTTTTT
1 A-AATTTTT
* *
264993 AAA-ATAT
1 AAATTTTT
*
265000 AAATTTTG
1 AAATTTTT
265008 AAATTTTTAT
1 AAA-TTTT-T
265018 AAATATTTT
1 AAAT-TTTT
*
265027 AAATTTTA
1 AAATTTTT
265035 AAATTT
1 AAATTT
265041 ATTTTGAATT
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
7 5 0.08
8 38 0.58
9 16 0.25
10 6 0.09
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (8 bp):
AAATTTTT
Found at i:264983 original size:24 final size:24
Alignment explanation
Indices: 264951--265036 Score: 86
Period size: 23 Copynumber: 3.5 Consensus size: 24
264941 ATTACTTTAA
264951 AAAATTTTTAAATTTTTAAAATTTT
1 AAAA-TTTTAAATTTTTAAAATTTT
* *
264976 AAAATTTTATATTTTTTAAAA-TAT
1 AAAATTTTA-AATTTTTAAAATTTT
265000 -AAATTTTGAAATTTTTATAAATATTT
1 AAAATTTT-AAATTTTTA-AAAT-TTT
*
265026 TAAATTTTAAA
1 AAAATTTTAAA
265037 ATTTATTTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
23 14 0.27
24 11 0.22
25 14 0.27
26 5 0.10
27 7 0.14
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (24 bp):
AAAATTTTAAATTTTTAAAATTTT
Found at i:265062 original size:20 final size:19
Alignment explanation
Indices: 264988--265073 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 19
264978 AATTTTATAT
264988 TTTTTAAAATATAAATTTTGAAA
1 TTTTTAAAAT-T--ATTTTG-AA
265011 TTTTTATAAA-TATTTT-AA
1 TTTTTA-AAATTATTTTGAA
*
265029 ATTTTAAAATTTATTTTGAA
1 TTTTTAAAA-TTATTTTGAA
*
265049 TTTTTGAAAATTATTTTGCA
1 TTTTT-AAAATTATTTTGAA
265069 TTTTT
1 TTTTT
265074 CTGCAATTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
17 3 0.05
18 7 0.13
19 6 0.11
20 25 0.45
21 4 0.07
22 1 0.02
23 6 0.11
24 3 0.05
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTTTAAAATTATTTTGAA
Found at i:269874 original size:24 final size:23
Alignment explanation
Indices: 269847--269892 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
269837 TTAGCCCGAC
*
269847 TAGTTAATAGAGACTTTCAATTTA
1 TAGTTAATA-ACACTTTCAATTTA
* *
269871 TAGTTCATATCACTTTCAATTT
1 TAGTTAATAACACTTTCAATTT
269893 CAATTTCACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.46
Consensus pattern (23 bp):
TAGTTAATAACACTTTCAATTTA
Found at i:270452 original size:49 final size:50
Alignment explanation
Indices: 270337--270458 Score: 151
Period size: 50 Copynumber: 2.5 Consensus size: 50
270327 GATCATTACA
* *
270337 AATCAATAGAAACATTTGGGTTCTTTCTTCTCTTTTTCTTTTTTCAAATT
1 AATCAATAGAAACATTTGAGTTCTTTCTTCTCTTTTTCTTTTTGCAAATT
* *
270387 AATCGATAGAAACATTTGAGTTCTTTCTTCTCTTTCTT-TTTTTGC-AGTT
1 AATCAATAGAAACATTTGAGTTCTTTCTTCTCTTT-TTCTTTTTGCAAATT
* *
270436 ACA-CAATAAAAACATTTAAGTTC
1 A-ATCAATAGAAACATTTGAGTTC
270459 CTTGGTTGGT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
49 21 0.33
50 40 0.63
51 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (50 bp):
AATCAATAGAAACATTTGAGTTCTTTCTTCTCTTTTTCTTTTTGCAAATT
Found at i:275680 original size:15 final size:15
Alignment explanation
Indices: 275662--275710 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
275652 TCGCAACATG
275662 AGTGTTCACAACACT
1 AGTGTTCACAACACT
275677 AGTGTTCACAACA-T
1 AGTGTTCACAACACT
* *
275691 GAGTGCTCGCAACACT
1 -AGTGTTCACAACACT
275707 AGTG
1 AGTG
275711 CTTGCATCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 1 0.03
15 28 0.93
16 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (15 bp):
AGTGTTCACAACACT
Found at i:275712 original size:15 final size:15
Alignment explanation
Indices: 275649--275704 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
275639 CCTTCATCCA
*
275649 TGCTCGCAACATGAG
1 TGCTCACAACATGAG
*
275664 TGTTCACAACACT-AG
1 TGCTCACAACA-TGAG
*
275679 TGTTCACAACATGAG
1 TGCTCACAACATGAG
*
275694 TGCTCGCAACA
1 TGCTCACAACA
275705 CTAGTGCTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
14 1 0.03
15 33 0.94
16 1 0.03
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (15 bp):
TGCTCACAACATGAG
Found at i:284810 original size:21 final size:20
Alignment explanation
Indices: 284786--284840 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
284776 CCTGTAACTT
*
284786 CTACCGATACAAGTACACGAA
1 CTACCGATACAACTACAC-AA
* * *
284807 CTACCAATACCTACTATACAA
1 CTACCGATA-CAACTACACAA
284828 CTACCGATACAAC
1 CTACCGATACAAC
284841 CTAAGTCAGT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 3 0.11
21 18 0.67
22 6 0.22
ACGTcount: A:0.42, C:0.33, G:0.07, T:0.18
Consensus pattern (20 bp):
CTACCGATACAACTACACAA
Found at i:286588 original size:20 final size:20
Alignment explanation
Indices: 286552--286601 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
286542 TCATTAAGCT
*
286552 TTAATTAACCACTTTTA-ATC
1 TTAATTAAACACTTTTACA-C
286572 TTAATTAAAC-CTATTTACAC
1 TTAATTAAACACT-TTTACAC
286592 TTAATATAAA
1 TTAAT-TAAA
286602 TCATGCTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAATTAAACACTTTTACAC
Found at i:288740 original size:3 final size:3
Alignment explanation
Indices: 288723--288779 Score: 78
Period size: 3 Copynumber: 17.7 Consensus size: 3
288713 ATAGTAGTAC
288723 ATT ATAT ATT AATT ATT ATAT ATT ATTT ATT ATT ATT ATT ATT ATT ATT
1 ATT AT-T ATT -ATT ATT AT-T ATT A-TT ATT ATT ATT ATT ATT ATT ATT
288772 ATT ATT AT
1 ATT ATT AT
288780 ATTGATTGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
3 38 0.76
4 12 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:290183 original size:79 final size:79
Alignment explanation
Indices: 290046--290309 Score: 350
Period size: 79 Copynumber: 3.4 Consensus size: 79
290036 TTCTATTTGA
* * * * * * *
290046 AAACATAAATTAATTGAATAATTCTGTTTCAGGATTTTATTCCTGTTGTTCAAAAAAATTTATTC
1 AAACAGAAATCAATTGAACAATTCTATTTCAAGATTTTATTCCTGCTGTTCAACAAAATTTATTC
290111 GATTTTTTGTTTCT
66 GATTTTTTGTTTCT
* * *
290125 AAACAGAAATCAATTGAACAATTCTTTTTCAAGATTTTATTCCTGCTGTTTAACAAAATTTATTT
1 AAACAGAAATCAATTGAACAATTCTATTTCAAGATTTTATTCCTGCTGTTCAACAAAATTTATTC
* *
290190 GATTTTCTATTTCT
66 GATTTTTTGTTTCT
* * * *
290204 AAACAGAAATCATTTGAACAATTCTATTTCAAGATTCTATTCTTGCCGTTCAAC-AAATTTATTC
1 AAACAGAAATCAATTGAACAATTCTATTTCAAGATTTTATTCCTGCTGTTCAACAAAATTTATTC
*
290268 GATTTTTTGTTTCC
66 GATTTTTTGTTTCT
* *
290282 AAATAGAAATCATTTGAACAATTCTATT
1 AAACAGAAATCAATTGAACAATTCTATT
290310 CTTGCCATTC
Statistics
Matches: 163, Mismatches: 22, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
78 47 0.29
79 116 0.71
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (79 bp):
AAACAGAAATCAATTGAACAATTCTATTTCAAGATTTTATTCCTGCTGTTCAACAAAATTTATTC
GATTTTTTGTTTCT
Found at i:294021 original size:65 final size:66
Alignment explanation
Indices: 293945--294085 Score: 266
Period size: 66 Copynumber: 2.2 Consensus size: 66
293935 CGGATCTGCT
293945 AATTAAAGGCTTAAATCGA-ATCAGGTTGATAAAACATCGAAAGGAATTGGGCTAAAGCCCATGA
1 AATTAAAGGCTTAAATCGAGATCAGGTTGATAAAACATCGAAAGGAATTGGGCTAAAGCCCATGA
294009 A
66 A
*
294010 AATTAAAGGCTTAAATCGAGATCAGGTTGATAAAACATCGAAAGGAATTGGGCTAAAGCCTATGA
1 AATTAAAGGCTTAAATCGAGATCAGGTTGATAAAACATCGAAAGGAATTGGGCTAAAGCCCATGA
294075 A
66 A
294076 AATTAAAGGC
1 AATTAAAGGC
294086 ACTATGCGAA
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
65 19 0.26
66 55 0.74
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (66 bp):
AATTAAAGGCTTAAATCGAGATCAGGTTGATAAAACATCGAAAGGAATTGGGCTAAAGCCCATGA
A
Found at i:302634 original size:16 final size:16
Alignment explanation
Indices: 302615--302649 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
302605 CCAACAAAGG
302615 AAGAAAATTTCAAAAC
1 AAGAAAATTTCAAAAC
302631 AAGAAAATTTCAAAAC
1 AAGAAAATTTCAAAAC
302647 AAG
1 AAG
302650 GAAGGACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.09, T:0.17
Consensus pattern (16 bp):
AAGAAAATTTCAAAAC
Found at i:303493 original size:21 final size:21
Alignment explanation
Indices: 303469--303512 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
303459 GGTAATTCAT
303469 TAGTTCTTTATTTTTAATATC
1 TAGTTCTTTATTTTTAATATC
*
303490 TAGTTTTTTATTTTTAATATC
1 TAGTTCTTTATTTTTAATATC
303511 TA
1 TA
303513 TCTTTGAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (21 bp):
TAGTTCTTTATTTTTAATATC
Found at i:305700 original size:33 final size:33
Alignment explanation
Indices: 305658--305723 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
305648 TTGATGTCTA
*
305658 AATGTCGGAGAAATCAATATTTAAATTAAGTGT
1 AATGTCGGAGAAATCAATATTGAAATTAAGTGT
*
305691 AATGTCGGAGAAATCAGTATTGAAATTAAGTGT
1 AATGTCGGAGAAATCAATATTGAAATTAAGTGT
305724 TAATCTAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (33 bp):
AATGTCGGAGAAATCAATATTGAAATTAAGTGT
Found at i:306903 original size:13 final size:13
Alignment explanation
Indices: 306885--306910 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
306875 CAATTTATTC
306885 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
306898 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
306911 CATTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:306919 original size:19 final size:19
Alignment explanation
Indices: 306882--306920 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
306872 CAGCAATTTA
*
306882 TTCTTTTTCTTTTTCTTTT
1 TTCTTTTTCTATTTCTTTT
306901 TTCTTTTTCTCATTT-TTTT
1 TTCTTTTTCT-ATTTCTTTT
306920 T
1 T
306921 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (19 bp):
TTCTTTTTCTATTTCTTTT
Found at i:307987 original size:12 final size:12
Alignment explanation
Indices: 307970--308002 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
307960 CCTCGGCAGG
307970 TTTTTCTTCTTC
1 TTTTTCTTCTTC
307982 TTTTTCTTCTTC
1 TTTTTCTTCTTC
*
307994 TTTCTCTTC
1 TTTTTCTTC
308003 CTCGTCTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTCTTCTTC
Found at i:316704 original size:45 final size:45
Alignment explanation
Indices: 316653--316743 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 45
316643 GACATCTGGG
** * *
316653 AAATTCCTGCATTGGTGCTTCCAGCTGTGGATTCAGCTTGATTCT
1 AAATTCCTGCATTGACGCGTCCAACTGTGGATTCAGCTTGATTCT
** * *
316698 AAATTCCTGTGTTGACGCGTCCAATTGTGGATTTAGCTTGATTCT
1 AAATTCCTGCATTGACGCGTCCAACTGTGGATTCAGCTTGATTCT
316743 A
1 A
316744 CTCATTCAAG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (45 bp):
AAATTCCTGCATTGACGCGTCCAACTGTGGATTCAGCTTGATTCT
Found at i:317955 original size:32 final size:31
Alignment explanation
Indices: 317910--318000 Score: 137
Period size: 32 Copynumber: 2.8 Consensus size: 31
317900 AAATTTTACT
*
317910 ATAATTTAATAAATACAAACATAAACATAAAC
1 ATAA-TTAATAAATACAAATATAAACATAAAC
*
317942 ATAATTAACTAAATACAAATACAAACATAAAC
1 ATAATTAA-TAAATACAAATATAAACATAAAC
317974 ATAATTAAATAAATACAAATATAAACA
1 ATAATT-AATAAATACAAATATAAACA
318001 GAAAATGAGT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
31 4 0.07
32 48 0.89
33 2 0.04
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (31 bp):
ATAATTAATAAATACAAATATAAACATAAAC
Found at i:318278 original size:33 final size:33
Alignment explanation
Indices: 318241--318306 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
318231 ATGGGCCTGG
*
318241 AGGAGTAGAG-TACCGCGATGGTAATGGGCTGAA
1 AGGAGTAGAGAT-CCACGATGGTAATGGGCTGAA
* * *
318274 AGGAGTGGAGATCTACGATGGTAATGGGTTGAA
1 AGGAGTAGAGATCCACGATGGTAATGGGCTGAA
318307 GATATCAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.30, C:0.09, G:0.39, T:0.21
Consensus pattern (33 bp):
AGGAGTAGAGATCCACGATGGTAATGGGCTGAA
Found at i:324315 original size:40 final size:40
Alignment explanation
Indices: 324271--324351 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
324261 GCACAGACCA
324271 CTTCGCAATGAAATATCTTCTTACAAAGAAAGATGCCAAG
1 CTTCGCAATGAAATATCTTCTTACAAAGAAAGATGCCAAG
324311 CTTCGCAATGAAATATCTTCTTACAAAGAAAGATGCCAAG
1 CTTCGCAATGAAATATCTTCTTACAAAGAAAGATGCCAAG
324351 C
1 C
324352 CTAGATTGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (40 bp):
CTTCGCAATGAAATATCTTCTTACAAAGAAAGATGCCAAG
Found at i:340145 original size:15 final size:17
Alignment explanation
Indices: 340109--340149 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
340099 CAATAAAAAT
*
340109 TAAAAGAAAAGTTAAGA
1 TAAAATAAAAGTTAAGA
340126 TAAAATAAAA-TTAA-A
1 TAAAATAAAAGTTAAGA
340141 TAAAATAAA
1 TAAAATAAA
340150 CAAACATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.43
16 4 0.17
17 9 0.39
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (17 bp):
TAAAATAAAAGTTAAGA
Found at i:341183 original size:40 final size:39
Alignment explanation
Indices: 341063--341184 Score: 117
Period size: 40 Copynumber: 3.2 Consensus size: 39
341053 TGATTAATCT
* *
341063 GACTAGTGTTGGGCACACATTTAATACCGTTGGTTTATCC
1 GACTAGTGCTGGGCACACATTTAATA-CGTCGGTTTATCC
* * * * *
341103 GATTAGTGCTAGGCGCAAATCTT--TA--TCGGTTTATCA
1 GACTAGTGCTGGGCACACAT-TTAATACGTCGGTTTATCC
*
341139 GACTAGTACTGGGCACACATTTAATATCGTCGGTTTATCC
1 GACTAGTGCTGGGCACACATTTAATA-CGTCGGTTTATCC
341179 GACTAG
1 GACTAG
341185 CGTTGGGTGC
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
35 2 0.03
36 24 0.38
37 2 0.03
39 2 0.03
40 31 0.49
41 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.34
Consensus pattern (39 bp):
GACTAGTGCTGGGCACACATTTAATACGTCGGTTTATCC
Found at i:341197 original size:76 final size:76
Alignment explanation
Indices: 341016--341197 Score: 229
Period size: 76 Copynumber: 2.4 Consensus size: 76
341006 TTTGTGATCA
* * * * **
341016 TCGGTTTATCCAACTAGCGCTAGGTGCAAATCTTTGTTGATTAATCTGACTAGTGTTGGGCACAC
1 TCGGTTTATCCGACTAGCGCTAGGTGCAAATCTTTATCGATTAATCAGACTAGTACTGGGCACAC
341081 ATTTAATACCG
66 ATTTAATACCG
* * * * * *
341092 TTGGTTTATCCGATTAGTGCTAGGCGCAAATCTTTATCGGTTTATCAGACTAGTACTGGGCACAC
1 TCGGTTTATCCGACTAGCGCTAGGTGCAAATCTTTATCGATTAATCAGACTAGTACTGGGCACAC
*
341157 ATTTAATATCG
66 ATTTAATACCG
* *
341168 TCGGTTTATCCGACTAGCGTTGGGTGCAAA
1 TCGGTTTATCCGACTAGCGCTAGGTGCAAA
341198 ACATTACTAC
Statistics
Matches: 87, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
76 87 1.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (76 bp):
TCGGTTTATCCGACTAGCGCTAGGTGCAAATCTTTATCGATTAATCAGACTAGTACTGGGCACAC
ATTTAATACCG
Found at i:343586 original size:33 final size:33
Alignment explanation
Indices: 343549--343616 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
343539 ATTATGATTA
343549 TTGAGTATGTATAATGAAATGAGAAGAACTTAC
1 TTGAGTATGTATAATGAAATGAGAAGAACTTAC
343582 TTGAGTATGTATAATGAAATGAGAAGAACTTAC
1 TTGAGTATGTATAATGAAATGAGAAGAACTTAC
343615 TT
1 TT
343617 AACCAAATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (33 bp):
TTGAGTATGTATAATGAAATGAGAAGAACTTAC
Found at i:343856 original size:21 final size:21
Alignment explanation
Indices: 343827--343869 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
343817 TGATACAAGG
*
343827 TTAGTATAATTTCAGATTCAC
1 TTAGGATAATTTCAGATTCAC
*
343848 TTAGGATAATTTTAGATTCAC
1 TTAGGATAATTTCAGATTCAC
343869 T
1 T
343870 ATTGGGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (21 bp):
TTAGGATAATTTCAGATTCAC
Found at i:364227 original size:54 final size:54
Alignment explanation
Indices: 364140--364305 Score: 253
Period size: 54 Copynumber: 3.1 Consensus size: 54
364130 ACTTAAAGGA
* *
364140 CATTTAATTAAGTTTTATTTCAATTT-AGTAAGTTTGCATTGTAATTATGTCTTG
1 CATTTAATTAAGTTTTATTTCAGTTTAAG-AAGTTTGCATTTTAATTATGTCTTG
*
364194 CATTTAATTAAGTTTTATTTCAGTTTAAGAAGTTTGCATTTTTATTATGTCTTG
1 CATTTAATTAAGTTTTATTTCAGTTTAAGAAGTTTGCATTTTAATTATGTCTTG
* * * *
364248 CATTTAATAAAGTTTTACTTCAGTTTAATAAGTTTGCATTTTAATTATCTCTTG
1 CATTTAATTAAGTTTTATTTCAGTTTAAGAAGTTTGCATTTTAATTATGTCTTG
364302 CATT
1 CATT
364306 ATATTTATGT
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
54 101 0.98
55 2 0.02
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.52
Consensus pattern (54 bp):
CATTTAATTAAGTTTTATTTCAGTTTAAGAAGTTTGCATTTTAATTATGTCTTG
Found at i:366030 original size:23 final size:23
Alignment explanation
Indices: 366004--366120 Score: 137
Period size: 23 Copynumber: 5.1 Consensus size: 23
365994 TTTTAGCGCA
*
366004 AATTGAAAGTGGCACTTTGGTGC
1 AATTGAAAGTGGCACTTTGATGC
** * *
366027 AATTGACCGTGGCACTCTAATGC
1 AATTGAAAGTGGCACTTTGATGC
*
366050 AATTGACAA-TGACACTTTGATGC
1 AATTGA-AAGTGGCACTTTGATGC
*
366073 AATTGAAAGTGGCACTTCGATGC
1 AATTGAAAGTGGCACTTTGATGC
* *
366096 AATTGAAAATGGCACTTCGATGC
1 AATTGAAAGTGGCACTTTGATGC
366119 AA
1 AA
366121 ATTAGTGATT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
22 2 0.03
23 77 0.97
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (23 bp):
AATTGAAAGTGGCACTTTGATGC
Found at i:368504 original size:82 final size:82
Alignment explanation
Indices: 368326--368596 Score: 316
Period size: 82 Copynumber: 3.3 Consensus size: 82
368316 AAAAAGAGCA
* * * * *
368326 TTTGTGGCAAATTATGAAAGGAAATGCTTTTGTGGTGAATTATGAAAAGAATAGTCTTTATGGCA
1 TTTGTGGCGAATTATGAAAGGAAATG-TCTTGTGGCGAATTATGAAAAGAAT-GTCTTTGTGGCG
*
368391 AATTATGAAAGGAA-ATGCC
64 AATTATGAAAAGAATA-GCC
* *
368410 CTTGTGGTGAATTATGAAAGGAAATGTCTTGTGGCGAATTATGAAAAGAATGTCTTTGTGGCGAA
1 TTTGTGGCGAATTATGAAAGGAAATGTCTTGTGGCGAATTATGAAAAGAATGTCTTTGTGGCGAA
*
368475 TTATGAAAAGAATAGTC
66 TTATGAAAAGAATAGCC
* * * **
368492 TTTGTGACGAATTATGAAA-G-AATAGTCTTTGTGACGAATTATG-AAAGAAATGTTTTTGTGAT
1 TTTGTGGCGAATTATGAAAGGAAAT-GTC-TTGTGGCGAATTATGAAAAG-AATGTCTTTGTGGC
* *
368554 GAATTATGAAAAAAATAACC
63 GAATTATGAAAAGAATAGCC
368574 TTTGTGGCGAATTATGAAAGGAA
1 TTTGTGGCGAATTATGAAAGGAA
368597 GTGCCTTTGT
Statistics
Matches: 161, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
80 3 0.02
81 8 0.05
82 101 0.63
83 25 0.16
84 24 0.15
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (82 bp):
TTTGTGGCGAATTATGAAAGGAAATGTCTTGTGGCGAATTATGAAAAGAATGTCTTTGTGGCGAA
TTATGAAAAGAATAGCC
Found at i:368603 original size:28 final size:28
Alignment explanation
Indices: 368326--368606 Score: 274
Period size: 28 Copynumber: 10.2 Consensus size: 28
368316 AAAAAGAGCA
*
368326 TTTGTGGCAAATTATGAAAGGAAATG-C
1 TTTGTGGCGAATTATGAAAGGAAATGTC
* *
368353 TTTTGTGGTGAATTATGAAAAG-AATAGTC
1 -TTTGTGGCGAATTATGAAAGGAAAT-GTC
* * *
368382 TTTATGGCAAATTATGAAAGGAAATGCC
1 TTTGTGGCGAATTATGAAAGGAAATGTC
* *
368410 CTTGTGGTGAATTATGAAAGGAAATGTC
1 TTTGTGGCGAATTATGAAAGGAAATGTC
*
368438 -TTGTGGCGAATTATGAAAAG-AATGTC
1 TTTGTGGCGAATTATGAAAGGAAATGTC
*
368464 TTTGTGGCGAATTATGAAAAG-AATAGTC
1 TTTGTGGCGAATTATGAAAGGAAAT-GTC
*
368492 TTTGTGACGAATTATGAAA-G-AATAGTC
1 TTTGTGGCGAATTATGAAAGGAAAT-GTC
* *
368519 TTTGTGACGAATTATGAAA-GAAATGTT
1 TTTGTGGCGAATTATGAAAGGAAATGTC
** * **
368546 TTTGTGATGAATTATGAAA-AAAATAACC
1 TTTGTGGCGAATTATGAAAGGAAAT-GTC
* *
368574 TTTGTGGCGAATTATGAAAGGAAGTGCC
1 TTTGTGGCGAATTATGAAAGGAAATGTC
368602 TTTGT
1 TTTGT
368607 AGCGTATTCT
Statistics
Matches: 218, Mismatches: 27, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.03
27 96 0.44
28 109 0.50
29 7 0.03
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (28 bp):
TTTGTGGCGAATTATGAAAGGAAATGTC
Found at i:369463 original size:14 final size:14
Alignment explanation
Indices: 369444--369478 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
369434 TACCCAAGAT
*
369444 TCGAATTCGATTAA
1 TCGAATCCGATTAA
369458 TCGAATCCGATTAA
1 TCGAATCCGATTAA
*
369472 TCAAATC
1 TCGAATC
369479 GAGTTAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (14 bp):
TCGAATCCGATTAA
Found at i:370966 original size:20 final size:20
Alignment explanation
Indices: 370920--370966 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
370910 CTCTTTTCCT
*
370920 TAAAAACAAAAAAAAAAAAG
1 TAAAAATAAAAAAAAAAAAG
*
370940 TAAAAATAAAAAAAAACAAG
1 TAAAAATAAAAAAAAAAAAG
370960 TAAAAAT
1 TAAAAAT
370967 CTTTCTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.11
Consensus pattern (20 bp):
TAAAAATAAAAAAAAAAAAG
Found at i:377692 original size:243 final size:243
Alignment explanation
Indices: 377264--377755 Score: 921
Period size: 243 Copynumber: 2.0 Consensus size: 243
377254 TCTACGTGCA
377264 TAAATTCCACAAAGCAAGAGATCCTACAATCACAAAGTACTAAAGCTTCATATTGCAATGGAGAA
1 TAAATTCCACAAAGCAAGAGATCCTACAATCACAAAGTACTAAAGCTTCATATTGCAATGGAGAA
*
377329 AGTCGGAAACACAAAATTTCATATACATATTCACTTCAATTTAGAAGATTCACACAATGTCAGGC
66 AGTCGGAAACACAAAATTACATATACATATTCACTTCAATTTAGAAGATTCACACAATGTCAGGC
* *
377394 TATAAACATTTTAAAACTTTACAATGCTCCCTCATAATCCTGAACTTGTTCCAGTATTGCTTTCT
131 TATAAACATGTTAAAACTTTACAATGCTCCCTCATAATCCTGAACTTCTTCCAGTATTGCTTTCT
*
377459 ATTTGTTTTAATAGCTAGACTCAATCAAATTATGAACACGTTAATCTT
196 ATTTGTTTTAAAAGCTAGACTCAATCAAATTATGAACACGTTAATCTT
377507 TAAATTCCACAAAGCAAGAGATCCTACAATCACAAAGTACTAAAGCTTCATATTGCAATGGAGAA
1 TAAATTCCACAAAGCAAGAGATCCTACAATCACAAAGTACTAAAGCTTCATATTGCAATGGAGAA
* *
377572 AGTCGGAAACACAAAATTACATATACATATTCATTTCAATTTAGAAGATTCACACAATGTTAGGC
66 AGTCGGAAACACAAAATTACATATACATATTCACTTCAATTTAGAAGATTCACACAATGTCAGGC
*
377637 TATAAACATGTTAAAACTTTACAATGCTTCCTCATAATCCTGAACTTCTTCCAGTATTGCTTTCT
131 TATAAACATGTTAAAACTTTACAATGCTCCCTCATAATCCTGAACTTCTTCCAGTATTGCTTTCT
377702 ATTTGTTTTAAAAGCTAGACTCAATCAAATTATGAACACGTTAATCTT
196 ATTTGTTTTAAAAGCTAGACTCAATCAAATTATGAACACGTTAATCTT
377750 TAAATT
1 TAAATT
377756 GCTCCATCAT
Statistics
Matches: 242, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
243 242 1.00
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (243 bp):
TAAATTCCACAAAGCAAGAGATCCTACAATCACAAAGTACTAAAGCTTCATATTGCAATGGAGAA
AGTCGGAAACACAAAATTACATATACATATTCACTTCAATTTAGAAGATTCACACAATGTCAGGC
TATAAACATGTTAAAACTTTACAATGCTCCCTCATAATCCTGAACTTCTTCCAGTATTGCTTTCT
ATTTGTTTTAAAAGCTAGACTCAATCAAATTATGAACACGTTAATCTT
Done.