Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000310.1 Hibiscus syriacus cultivar Beakdansim tig00000584_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 102229
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:344 original size:54 final size:53
Alignment explanation
Indices: 183--345 Score: 249
Period size: 51 Copynumber: 3.1 Consensus size: 53
173 AGAATAGCAG
* * * *
183 GTTCGTAAAAACATTTAACAACGCATTCTCATTTCCTGTGGCTTCTGCTCAAAT
1 GTTCGT-AAAACATTTGACAACACATTCTCCTTTCCTGTGGCTTCTGCTCAGAT
237 GTTCGTAAAACATTTGACAACACA-T-TCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCTCCTTTCCTGTGGCTTCTGCTCAGAT
*
288 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTC-TCCTTTCCTGTGGCTTCTGCTCAGAT
342 GTTC
1 GTTC
346 TCAATCATTG
Statistics
Matches: 101, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
51 48 0.48
52 2 0.02
53 16 0.16
54 35 0.35
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.36
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCTCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:2590 original size:114 final size:114
Alignment explanation
Indices: 2390--2609 Score: 404
Period size: 114 Copynumber: 1.9 Consensus size: 114
2380 GATCATGCAG
* *
2390 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
2455 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* *
2504 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
2569 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
2610 CGAGAATATG
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:4759 original size:15 final size:15
Alignment explanation
Indices: 4739--4814 Score: 89
Period size: 15 Copynumber: 5.0 Consensus size: 15
4729 CTTGATTCAA
*
4739 TTTTCCTTCTTCTTT
1 TTTTTCTTCTTCTTT
* * *
4754 TTTTCCTTTTTATTT
1 TTTTTCTTCTTCTTT
* *
4769 TTTTTATTTTTCTTT
1 TTTTTCTTCTTCTTT
4784 TTTTTCTTCTTCTTTT
1 TTTTTCTTCTTC-TTT
4800 TTTTTCTTCTTCTTT
1 TTTTTCTTCTTCTTT
4815 CTTTGCTGGA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
15 38 0.72
16 15 0.28
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTCTTCTTCTTT
Found at i:5113 original size:2 final size:2
Alignment explanation
Indices: 5106--5154 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
5096 TGGGGACAAC
5106 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5148 AT AT AT A
1 AT AT AT A
5155 AAAGGATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9732 original size:14 final size:14
Alignment explanation
Indices: 9713--9739 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9703 TTAATACCTG
9713 AATAAAATAATATT
1 AATAAAATAATATT
9727 AATAAAATAATAT
1 AATAAAATAATAT
9740 AAAATAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAAAATAATATT
Found at i:10486 original size:15 final size:14
Alignment explanation
Indices: 10465--10497 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
10455 TATTGAAAAA
10465 TAAATATAT-ATTAT
1 TAAA-ATATGATTAT
10479 TAAAATATGATTAT
1 TAAAATATGATTAT
10493 TAAAA
1 TAAAA
10498 GTAATTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
TAAAATATGATTAT
Found at i:10620 original size:35 final size:36
Alignment explanation
Indices: 10579--10647 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
10569 TATTTATATA
10579 AATAATAAAAATAATAATG-AAATAATAATTAAAGC
1 AATAATAAAAATAATAATGCAAATAATAATTAAAGC
* * *
10614 AATAATAATAATAATATTGCAAATAATGATTAAA
1 AATAATAAAAATAATAATGCAAATAATAATTAAA
10648 ATAAAAGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 17 0.57
36 13 0.43
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (36 bp):
AATAATAAAAATAATAATGCAAATAATAATTAAAGC
Found at i:10706 original size:29 final size:28
Alignment explanation
Indices: 10657--10717 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
10647 AATAAAAGGA
* *
10657 ATTAAAAATATAGTATTAAAATGTAAAAT
1 ATTAAAAATATAATATCAAAATG-AAAAT
10686 ATTAAAAATA-AATAGTCAAAATGAAAAT
1 ATTAAAAATATAATA-TCAAAATGAAAAT
10714 -TTAA
1 ATTAA
10718 TGATTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 4 0.14
28 8 0.28
29 17 0.59
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.31
Consensus pattern (28 bp):
ATTAAAAATATAATATCAAAATGAAAAT
Found at i:11164 original size:23 final size:25
Alignment explanation
Indices: 11107--11163 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
11097 TCATTTCTCT
11107 TTTCTCTCTTAAACTGAGAGAGAGA
1 TTTCTCTCTTAAACTGAGAGAGAGA
11132 TTTCTCTCTTAAACTGAGAGAGAGA
1 TTTCTCTCTTAAACTGAGAGAGAGA
11157 TTTCTCT
1 TTTCTCT
11164 TTCGCGTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (25 bp):
TTTCTCTCTTAAACTGAGAGAGAGA
Found at i:11957 original size:3 final size:3
Alignment explanation
Indices: 11941--11997 Score: 54
Period size: 3 Copynumber: 21.0 Consensus size: 3
11931 GTCTGGTTTG
* *
11941 TAA TAA -AA -AA TAA TAA T-A TTA TAA T-A TAA TAA TAA TAT TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11984 TAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA
11998 ATAAAACAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
2 12 0.26
3 34 0.74
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:11973 original size:19 final size:19
Alignment explanation
Indices: 11947--11996 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
11937 TTTGTAATAA
*
11947 AAAATAATAATATTATAAT
1 AAAATAATAATATTAAAAT
*
11966 ATAATAATAATATTAAAAT
1 AAAATAATAATATTAAAAT
11985 AAAATAATAATA
1 AAAATAATAATA
11997 AATAAAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATAATAATATTAAAAT
Found at i:12008 original size:19 final size:22
Alignment explanation
Indices: 11942--11997 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
11932 TCTGGTTTGT
11942 AATAAAA-AATAATAATATT--
1 AATAAAATAATAATAATATTAA
*
11961 -ATAATATAATAATAATATTAA
1 AATAAAATAATAATAATATTAA
11982 AATAAAATAATAATAA
1 AATAAAATAATAATAA
11998 ATAAAACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 5 0.16
19 12 0.39
22 14 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
AATAAAATAATAATAATATTAA
Found at i:12608 original size:63 final size:65
Alignment explanation
Indices: 12540--12701 Score: 208
Period size: 63 Copynumber: 2.6 Consensus size: 65
12530 ATCCCTTGAC
* * * *
12540 GGGTGCATCGATGCACTATC-TATGCATCGGTACA-TAAATCCTATTCGATGTTTGTA-TTTAAT
1 GGGTGCATCGATGCACTATCATGTGCATCGATACACT-AATCATATTCGATGTTTGTATTTTAAA
12602 G
65 G
* * *
12603 GGGTGCATCGATGCACTA-CTTGTGCATCGATACACTAATGATATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACTATCATGTGCATCGATACACTAATCATATTCGATGTTTGTATTTTAAAG
*
12667 GAGTGCATCGATGCACT-TCATGTGCATCGATACAC
1 GGGTGCATCGATGCACTATCATGTGCATCGATACAC
12702 CTTGAACAAT
Statistics
Matches: 87, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
62 1 0.01
63 47 0.54
64 39 0.45
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (65 bp):
GGGTGCATCGATGCACTATCATGTGCATCGATACACTAATCATATTCGATGTTTGTATTTTAAAG
Found at i:15291 original size:12 final size:12
Alignment explanation
Indices: 15262--15305 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
15252 CTCGAGACTC
15262 GAGCTCGA--TT
1 GAGCTCGATTTT
15272 GAAGCTCGATTTT
1 G-AGCTCGATTTT
15285 GAGCTCGATTTT
1 GAGCTCGATTTT
15297 GAGCTCGAT
1 GAGCTCGAT
15306 ACAAGCTCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 1 0.03
11 7 0.23
12 20 0.65
13 3 0.10
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.34
Consensus pattern (12 bp):
GAGCTCGATTTT
Found at i:15334 original size:17 final size:17
Alignment explanation
Indices: 15312--15344 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
15302 CGATACAAGC
*
15312 TCGATTCAAGCTCGAAT
1 TCGATTAAAGCTCGAAT
15329 TCGATTAAAGCTCGAA
1 TCGATTAAAGCTCGAA
15345 CTCAAACTCG
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:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (17 bp):
TCGATTAAAGCTCGAAT
Found at i:15343 original size:11 final size:11
Alignment explanation
Indices: 15263--15326 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
15253 TCGAGACTCG
*
15263 AGCTCGATTGA
1 AGCTCGATTTA
*
15274 AGCTCGATTTTG
1 AGCTCGA-TTTA
*
15286 AGCTCGATTTTG
1 AGCTCGA-TTTA
**
15298 AGCTCGATACA
1 AGCTCGATTTA
*
15309 AGCTCGATTCA
1 AGCTCGATTTA
15320 AGCTCGA
1 AGCTCGA
15327 ATTCGATTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
11 25 0.54
12 21 0.46
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (11 bp):
AGCTCGATTTA
Found at i:15650 original size:21 final size:21
Alignment explanation
Indices: 15625--15739 Score: 90
Period size: 21 Copynumber: 5.5 Consensus size: 21
15615 TGGCATAACT
15625 TAAACCCTAATACATAAACCC
1 TAAACCCTAATACATAAACCC
* * *
15646 TAAACCTTAACACATATACCC
1 TAAACCCTAATACATAAACCC
* *
15667 TAAACCCTAA-ACTTTAAACCT
1 TAAACCCTAATAC-ATAAACCC
* * *
15688 TAAATCCTATTACATAAACCT
1 TAAACCCTAATACATAAACCC
* * *
15709 TAAATCCT-ATGAAATAAACTC
1 TAAACCCTAAT-ACATAAACCC
*
15730 TAAATCCTAA
1 TAAACCCTAA
15740 ACCCTACACC
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
20 3 0.04
21 70 0.92
22 3 0.04
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (21 bp):
TAAACCCTAATACATAAACCC
Found at i:16030 original size:14 final size:14
Alignment explanation
Indices: 16013--16053 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
16003 TTTATTCATC
16013 AATAATGTATTTTT
1 AATAATGTATTTTT
16027 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
16038 AATAATGTAATTTT
1 AATAATGTATTTTT
16052 AA
1 AA
16054 AAAATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:16208 original size:11 final size:11
Alignment explanation
Indices: 16192--16219 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
16182 CCGAATATTT
16192 ATCGAGCCAAG
1 ATCGAGCCAAG
16203 ATCGAGCCAAG
1 ATCGAGCCAAG
16214 ATCGAG
1 ATCGAG
16220 TAACTCGCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.25, G:0.29, T:0.11
Consensus pattern (11 bp):
ATCGAGCCAAG
Found at i:19716 original size:3 final size:3
Alignment explanation
Indices: 19708--19742 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
19698 TTACTATTTA
19708 ATT ATT ATT ATT -TT ATT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
19743 ATACAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:19728 original size:17 final size:17
Alignment explanation
Indices: 19708--19742 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
19698 TTACTATTTA
*
19708 ATTATTATTATTTTATT
1 ATTATTATTATTATATT
19725 ATTATTATTATTATATT
1 ATTATTATTATTATATT
19742 A
1 A
19743 ATACAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTATTATTATTATATT
Found at i:19741 original size:14 final size:14
Alignment explanation
Indices: 19691--19742 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
19681 TGTACGGATC
*
19691 TTTTA-TATTACTA
1 TTTTATTATTATTA
*
19704 TTTAATTATTATTA
1 TTTTATTATTATTA
19718 TTTTATTATTATTA
1 TTTTATTATTATTA
19732 TTATTA-TATTA
1 TT-TTATTATTA
19743 ATACAAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 4 0.12
14 27 0.79
15 3 0.09
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTATTATTATTA
Found at i:22012 original size:15 final size:17
Alignment explanation
Indices: 21984--22020 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
21974 GAACACCATT
21984 TTTTTGTCTAAAAA-TG
1 TTTTTGTCTAAAAATTG
*
22000 TTTTT-TCTTAAAATTG
1 TTTTTGTCTAAAAATTG
22016 TTTTT
1 TTTTT
22021 AAAAAGATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (17 bp):
TTTTTGTCTAAAAATTG
Found at i:22991 original size:32 final size:32
Alignment explanation
Indices: 22955--23015 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
22945 ATTGTGGGTA
22955 GAAAGCATGTCAGAGTAGGATTGCTATATATT
1 GAAAGCATGTCAGAGTAGGATTGCTATATATT
22987 GAAAGCATGTCAGAGTAGGATTGCTATAT
1 GAAAGCATGTCAGAGTAGGATTGCTATAT
23016 TTGTTAGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (32 bp):
GAAAGCATGTCAGAGTAGGATTGCTATATATT
Found at i:24013 original size:22 final size:22
Alignment explanation
Indices: 23983--24045 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
23973 ATACGGTATG
* *
23983 AACAGTACCATGAACAATAATT
1 AACAATACCATGAACAATAATA
* * *
24005 AACATTACCGTGAACAGTAATA
1 AACAATACCATGAACAATAATA
* *
24027 AACAATATCAGGAACAATA
1 AACAATACCATGAACAATA
24046 CTCGAATGTT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.21
Consensus pattern (22 bp):
AACAATACCATGAACAATAATA
Found at i:24961 original size:31 final size:31
Alignment explanation
Indices: 24866--24979 Score: 95
Period size: 31 Copynumber: 3.7 Consensus size: 31
24856 CTGTCCATTG
* * * * *
24866 GTCCCGAAGAACCTAGGTAAAATGTCCATAT
1 GTCCCGAAGAACATAGGTAAATTATGCACAT
* ** *
24897 GTTCCTTAGAACATAAGTAAATTATGCACAT
1 GTCCCGAAGAACATAGGTAAATTATGCACAT
* * * *
24928 GTCTCGAA-AGACATAGGTAAATTGTTCATAT
1 GTCCCGAAGA-ACATAGGTAAATTATGCACAT
24959 GTCCCGAAGAACATAGGTAAA
1 GTCCCGAAGAACATAGGTAAA
24980 CCCTCGACTC
Statistics
Matches: 63, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
30 1 0.02
31 61 0.97
32 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (31 bp):
GTCCCGAAGAACATAGGTAAATTATGCACAT
Found at i:25357 original size:30 final size:31
Alignment explanation
Indices: 25270--25357 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 31
25260 ATATATATAT
*
25270 ATATGGTTCACTTTTACATATCACATTTAATC
1 ATATGGTTCACTTTCACATATCACATTT-ATC
* * *
25302 ATATGGTTCACTTGCACGTAACACATTT-TC
1 ATATGGTTCACTTTCACATATCACATTTATC
25332 ATA-GGATTCACTTTCACATATCACAT
1 ATATGG-TTCACTTTCACATATCACAT
25358 ATTCCTTTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 2 0.04
30 22 0.46
32 24 0.50
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.39
Consensus pattern (31 bp):
ATATGGTTCACTTTCACATATCACATTTATC
Found at i:29435 original size:27 final size:27
Alignment explanation
Indices: 29374--29480 Score: 94
Period size: 27 Copynumber: 3.9 Consensus size: 27
29364 TTTTGTCTCT
* * *
29374 TTTGAGACAATTTCTCTCGAAACAAATC
1 TTTGAGTCTATTTCTCTTGAAA-AAATC
*
29402 TTTGAGTCTATTTCTTTTGAAAAAATC
1 TTTGAGTCTATTTCTCTTGAAAAAATC
* *
29429 TTTGAGTATGTTTCTCTT-AACAAAATC
1 TTTGAGTCTATTTCTCTTGAA-AAAATC
29456 ATCTGTGAGTCTATTTCT-TT-AAAAA
1 -T-T-TGAGTCTATTTCTCTTGAAAAA
29481 CAAATTTTGT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
26 2 0.03
27 26 0.39
28 22 0.33
29 5 0.08
30 11 0.17
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (27 bp):
TTTGAGTCTATTTCTCTTGAAAAAATC
Found at i:29619 original size:65 final size:65
Alignment explanation
Indices: 29450--29619 Score: 182
Period size: 65 Copynumber: 2.6 Consensus size: 65
29440 TTCTCTTAAC
* * * *
29450 AAAATCATCTGTGAGTCTATTTCTTTAAAAAC-AAATTTTGTCTCTCTTGAGAAAGTTTCTAATG
1 AAAAACATCTTTGAGTTTATTTCTTTGAAAACAAAATTTTGTCTCTCTTGAGAAAGTTTCTAATG
* * * * * * **
29514 AAAAACCAACATTTGAGATTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTTAGACAGTTTCTTT
1 AAAAA-CATC-TTTGAGTTTATTTCTTTGAAAACAAAATTTTGTCTCTCTTGAGAAAGTTTCTAA
29579 TG
64 TG
*
29581 AGAAAA-ATCTTTGAGTTTATTTTTTTGAAAACAAAATTT
1 A-AAAACATCTTTGAGTTTATTTCTTTGAAAACAAAATTT
29620 ATCATCTTTG
Statistics
Matches: 85, Mismatches: 17, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
64 4 0.05
65 29 0.34
66 19 0.22
67 29 0.34
68 4 0.05
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (65 bp):
AAAAACATCTTTGAGTTTATTTCTTTGAAAACAAAATTTTGTCTCTCTTGAGAAAGTTTCTAATG
Found at i:29882 original size:27 final size:27
Alignment explanation
Indices: 29807--29886 Score: 97
Period size: 27 Copynumber: 2.8 Consensus size: 27
29797 GAGATAGTTG
29807 CTTTTAAAACATATCATCTTTGAGTTTGTT
1 CTTTTAAAACA-A--ATCTTTGAGTTTGTT
* * *
29837 TTTCTTGAAACAAATCTTTGGGTTTGTT
1 CTT-TTAAAACAAATCTTTGAGTTTGTT
29865 CTTTTAAAACAAATCTTTGAGT
1 CTTTTAAAACAAATCTTTGAGT
29887 CGGTTTCCCT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
27 17 0.40
28 16 0.37
30 3 0.07
31 7 0.16
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (27 bp):
CTTTTAAAACAAATCTTTGAGTTTGTT
Found at i:30259 original size:135 final size:134
Alignment explanation
Indices: 29913--30262 Score: 368
Period size: 135 Copynumber: 2.6 Consensus size: 134
29903 CCTTATCCCA
* * * * * ** *
29913 AAAGATGGCCAACCGTCCTCATCAC-TAGAAACCATGTCCTCTCCCGACCAGACCTCTTCATCAC
1 AAAGATGGCCAACCATCCTCATCACGTAGGAACCGTGTCATCACTTGACCAGACCTCCTCATCAC
* * * * *
29977 GTAGGAGCCGTGTCA-ACCTAGATAACCAGCCTTCCTCATCACGTAAGAATCGAGTTATCACCAC
66 GTAGGAGCCGTGTCACCCCTAGATAACCAGCCATCCTCATCACGTAAGAACCAAGTAATCACCAC
30041 TCCT
131 TCCT
* * * *
30045 AAAGATGGTCAACCATCCTGATCACGTAGGAACTGTGTCATCCCTTGACCAGACCTCCTCATCAC
1 AAAGATGGCCAACCATCCTCATCACGTAGGAACCGTGTCATCACTTGACCAGACCTCCTCATCAC
* ** *
30110 GTAGGAGCCATGTCACCCCTAGATAACCAGTGATCCTCATCACGTAGGAACCAAGTAATCACC-C
66 GTAGGAGCCGTGTCACCCCTAGATAACCAGCCATCCTCATCACGTAAGAACCAAGTAATCACCAC
30174 TTCCT
131 -TCCT
* ** * * * *
30179 AAAGATGGCCAGGAGC-TTTTCATCACTTATGAGCCGTGTCATCTAC-TGACCAGATCTCCTCAT
1 AAAGATGGCCA--ACCATCCTCATCACGTAGGAACCGTGTCATC-ACTTGACCAGACCTCCTCAT
*
30242 CACGTAGGAGTCGTGTCACCC
63 CACGTAGGAGCCGTGTCACCC
30263 TTAAACGACT
Statistics
Matches: 179, Mismatches: 33, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
132 22 0.12
133 46 0.26
134 53 0.30
135 55 0.31
136 3 0.02
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.23
Consensus pattern (134 bp):
AAAGATGGCCAACCATCCTCATCACGTAGGAACCGTGTCATCACTTGACCAGACCTCCTCATCAC
GTAGGAGCCGTGTCACCCCTAGATAACCAGCCATCCTCATCACGTAAGAACCAAGTAATCACCAC
TCCT
Found at i:30460 original size:3 final size:3
Alignment explanation
Indices: 30452--30503 Score: 79
Period size: 3 Copynumber: 17.0 Consensus size: 3
30442 TGGGTCTTTT
30452 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA
30499 -TA TTA
1 TTA TTA
30504 ATACAAATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 38 0.81
4 7 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:31520 original size:32 final size:32
Alignment explanation
Indices: 31479--31540 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
31469 AATTTTGGCC
31479 CCATTTTGGGGTTTATAAGCTCTTTAATGTCG
1 CCATTTTGGGGTTTATAAGCTCTTTAATGTCG
31511 CCATTTTGGGGTTTATAAGCTCTTTAATGT
1 CCATTTTGGGGTTTATAAGCTCTTTAATGT
31541 GACACAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.45
Consensus pattern (32 bp):
CCATTTTGGGGTTTATAAGCTCTTTAATGTCG
Found at i:36896 original size:60 final size:60
Alignment explanation
Indices: 36782--36897 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
36772 TTTTTTCATA
* *
36782 AACTTTTAATAGTTAATAGACTCAACAAACCAATACCCTATAATCGAATTACCATTTTAT
1 AACTTTTAATAGTTAATAGACTCAACAAAACAATACCCTATAATCGAATAACCATTTTAT
* * * * *
36842 AACTTTTAATAGTTGATAGACTTAACAAAATAATATCCTATATTCGAGA-AACCATT
1 AACTTTTAATAGTTAATAGACTCAACAAAACAATACCCTATAATCGA-ATAACCATT
36898 CGTGTATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 47 0.98
61 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (60 bp):
AACTTTTAATAGTTAATAGACTCAACAAAACAATACCCTATAATCGAATAACCATTTTAT
Found at i:37981 original size:64 final size:65
Alignment explanation
Indices: 37868--38014 Score: 183
Period size: 64 Copynumber: 2.3 Consensus size: 65
37858 CATTCATAAG
* * *
37868 TGCATCGATGCATTCC-TTTAAAAGAAAGAACATCGAATGCCTTTGATGCATCGATGCA-TAGCT
1 TGCATCGATGCA-TCCTTTTAAAAGAAAGAACATCGAATGCATTTGATGCACCGATGCACAAG-T
37931 AA
64 AA
* * * *
37933 TGCATCGATGCATCCTTTTAAAATAAA-AATATCGAATGCATTTTATGCACCGATGCACAAGTAG
1 TGCATCGATGCATCCTTTTAAAAGAAAGAACATCGAATGCATTTGATGCACCGATGCACAAGTAA
37997 TGCATCGATGCATACCTT
1 TGCATCGATGCAT-CCTT
38015 CATTGAAAGA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
64 44 0.61
65 28 0.39
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29
Consensus pattern (65 bp):
TGCATCGATGCATCCTTTTAAAAGAAAGAACATCGAATGCATTTGATGCACCGATGCACAAGTAA
Found at i:38711 original size:31 final size:31
Alignment explanation
Indices: 38673--38778 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 31
38663 TCGAGGGTTT
38673 TACCTATG-TCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTTT-GAGACATATGGACAGTA
** *
38704 TACCTATGTTCTAAG-GAACATATGGACAGTT
1 TACCTATGTTCTTTGAG-ACATATGGACAGTA
* * *
38735 TACCTAGGTTCTTTGGGACCTATGGACAGT-
1 TACCTATGTTCTTTGAGACATATGGACAGTA
* *
38765 TGCCGATGTTCTTT
1 TACCTATGTTCTTT
38779 ATGACCTCTG
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
30 12 0.19
31 46 0.74
32 4 0.06
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.35
Consensus pattern (31 bp):
TACCTATGTTCTTTGAGACATATGGACAGTA
Found at i:38785 original size:30 final size:30
Alignment explanation
Indices: 38693--38799 Score: 81
Period size: 31 Copynumber: 3.5 Consensus size: 30
38683 TTTCGAGACA
* * * *
38693 TATGGACAGTATACCTATGTTC-TAAGGAACA
1 TATGGACAGT-TACCGAGGTTCTTTAGG-ACC
* *
38724 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* * *
38755 TATGGACAGTTGCCGATGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
38785 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
38800 GGGTCTGTGT
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
30 28 0.45
31 30 0.48
32 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:39999 original size:5 final size:5
Alignment explanation
Indices: 39985--40028 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
39975 GTCCGTCCGT
* * * *
39985 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
40029 TGGTCGTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.07, C:0.41, G:0.36, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:40037 original size:6 final size:6
Alignment explanation
Indices: 40026--40104 Score: 131
Period size: 6 Copynumber: 13.2 Consensus size: 6
40016 TCGGCTCGGC
* * *
40026 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
40074 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
40105 AATACGTGTC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.04, C:0.16, G:0.49, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:40404 original size:22 final size:22
Alignment explanation
Indices: 40379--40433 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
40369 TCAGGAGTTA
* *
40379 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
40401 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
40423 CGGGAGTTATA
1 CAGGAGTTATA
40434 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:43480 original size:5 final size:5
Alignment explanation
Indices: 43466--43509 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
43456 GTCCGTCCGT
* * * *
43466 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
43510 TGGTCGTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.07, C:0.41, G:0.36, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:43518 original size:6 final size:6
Alignment explanation
Indices: 43507--43579 Score: 119
Period size: 6 Copynumber: 12.2 Consensus size: 6
43497 TCGGCTCGGC
* * *
43507 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
43555 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
43580 AATACGTGTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.04, C:0.16, G:0.49, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:43877 original size:22 final size:22
Alignment explanation
Indices: 43852--43906 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
43842 TCAGGAGTTA
* *
43852 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
43874 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
43896 CGGGAGTTATA
1 CAGGAGTTATA
43907 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:49450 original size:5 final size:5
Alignment explanation
Indices: 49436--49479 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
49426 GTCCGTCCGT
* * * *
49436 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
49480 TGGTCATGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.07, C:0.41, G:0.36, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:49495 original size:6 final size:6
Alignment explanation
Indices: 49477--49549 Score: 110
Period size: 6 Copynumber: 12.2 Consensus size: 6
49467 TCGGCTCGGC
* * * *
49477 TCGTGG TCATGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
49525 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
49550 AATACGTGTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.05, C:0.16, G:0.48, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:49849 original size:22 final size:22
Alignment explanation
Indices: 49824--49878 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
49814 TCAGGAGTTA
* *
49824 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
49846 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
49868 CGGGAGTTATA
1 CAGGAGTTATA
49879 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:51023 original size:11 final size:12
Alignment explanation
Indices: 50989--51031 Score: 63
Period size: 11 Copynumber: 3.8 Consensus size: 12
50979 ATACAACACA
50989 TAATTAAAAA-T
1 TAATTAAAAATT
51000 TAATTAAAAATT
1 TAATTAAAAATT
51012 TAA-TAAAAATT
1 TAATTAAAAATT
*
51023 TATTTAAAA
1 TAATTAAAA
51032 GAAAATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TAATTAAAAATT
Found at i:51153 original size:21 final size:21
Alignment explanation
Indices: 51129--51177 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
51119 AAAATAATAC
51129 AATTAATATTTT-ATTTTAAAT
1 AATT-ATATTTTAATTTTAAAT
*
51150 AATT-TATTTTAAATTTTAACT
1 AATTATATTTT-AATTTTAAAT
51171 AATTATA
1 AATTATA
51178 ATTATACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 6 0.25
21 16 0.67
22 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTATATTTTAATTTTAAAT
Found at i:51155 original size:14 final size:14
Alignment explanation
Indices: 51133--51163 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
51123 TAATACAATT
*
51133 AATATTTTATTTTA
1 AATAATTTATTTTA
51147 AATAATTTATTTTA
1 AATAATTTATTTTA
51161 AAT
1 AAT
51164 TTTAACTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATAATTTATTTTA
Found at i:51814 original size:21 final size:21
Alignment explanation
Indices: 51788--51840 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
51778 ATTCTGACTA
51788 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
51809 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
51830 TCGCAATGCGA
1 TCGCATTGCGA
51841 ATACGTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:51854 original size:41 final size:41
Alignment explanation
Indices: 51816--51943 Score: 132
Period size: 41 Copynumber: 3.1 Consensus size: 41
51806 AATTCGCATT
* * *
51816 GCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAAC
1 GCGAATTTCCAAAATCGCAATGCGAATACGTAAATCGCAAC
** * *
51857 GCGAATTTGGAAAATCGCAATGCGATTACGTAAATCGTAAC
1 GCGAATTTCCAAAATCGCAATGCGAATACGTAAATCGCAAC
* ** * * *
51898 GCGAA-TACGTAAATCGCAACGCGGATACGTAAATTGCAAC
1 GCGAATTTCCAAAATCGCAATGCGAATACGTAAATCGCAAC
51938 GCGAAT
1 GCGAAT
51944 CTGACTATCG
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 32 0.45
41 39 0.55
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (41 bp):
GCGAATTTCCAAAATCGCAATGCGAATACGTAAATCGCAAC
Found at i:51855 original size:20 final size:20
Alignment explanation
Indices: 51830--51943 Score: 138
Period size: 20 Copynumber: 5.7 Consensus size: 20
51820 TTTTCCTAAT
*
51830 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
** *
51850 TCGCAACGCGAATTTGGAAAA
1 TCGCAACGCGAA-TACGTAAA
* *
51871 TCGCAATGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
*
51891 TCGTAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
51911 TCGCAACGCGGATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
51931 TTGCAACGCGAAT
1 TCGCAACGCGAAT
51944 CTGACTATCG
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
20 62 0.81
21 15 0.19
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:51954 original size:40 final size:39
Alignment explanation
Indices: 51830--51958 Score: 127
Period size: 40 Copynumber: 3.2 Consensus size: 39
51820 TTTTCCTAAT
* * *
51830 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAACGCGGATACGTAAATCGCAACGCGAATCT-G-AAA
* *
51871 TCGCAATGC-GATTACGTAAATCGTAACGCGAATAC-GTAAA
1 TCGCAACGCGGA-TACGTAAATCGCAACGCGAAT-CTG-AAA
* *
51911 TCGCAACGCGGATACGTAAATTGCAACGCGAATCTGACTA
1 TCGCAACGCGGATACGTAAATCGCAACGCGAATCTGA-AA
51951 TCGCAACG
1 TCGCAACG
51959 AGATTCTGAC
Statistics
Matches: 75, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
39 2 0.03
40 42 0.56
41 31 0.41
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (39 bp):
TCGCAACGCGGATACGTAAATCGCAACGCGAATCTGAAA
Found at i:51956 original size:20 final size:20
Alignment explanation
Indices: 51933--51976 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
51923 TACGTAAATT
*
51933 GCAACGCGAATCTGACTATC
1 GCAACGAGAATCTGACTATC
*
51953 GCAACGAGATTCTGACTATC
1 GCAACGAGAATCTGACTATC
51973 GCAA
1 GCAA
51977 TACTGAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (20 bp):
GCAACGAGAATCTGACTATC
Found at i:53080 original size:15 final size:14
Alignment explanation
Indices: 53062--53097 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
53052 GAAAAAGAAG
53062 AAGAAGAAATCCCCA
1 AAGAA-AAATCCCCA
*
53077 AAGAAAAGTCCCCA
1 AAGAAAAATCCCCA
53091 AAGAAAA
1 AAGAAAA
53098 TGTCACGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.58, C:0.22, G:0.14, T:0.06
Consensus pattern (14 bp):
AAGAAAAATCCCCA
Found at i:55332 original size:20 final size:21
Alignment explanation
Indices: 55305--55393 Score: 114
Period size: 20 Copynumber: 4.4 Consensus size: 21
55295 CAACGCGGAA
55305 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAATATGACT
* *
55325 ACCGCAACACGGAA-ATGACT
1 ATCGCAACGCGGAATATGACT
55345 ATCGCAACGCGGAAT-TGACT
1 ATCGCAACGCGGAATATGACT
*
55365 ATCGCAACGC-GAAAATGACT
1 ATCGCAACGCGGAATATGACT
*
55385 ATCGTAACG
1 ATCGCAACG
55394 AGAGAATCGC
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.05
20 54 0.90
21 3 0.05
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGGAATATGACT
Found at i:55364 original size:40 final size:40
Alignment explanation
Indices: 55305--55393 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
55295 CAACGCGGAA
*
55305 ATCGCAACGCGAATATGACTACCGCAACACGGAAATGACT
1 ATCGCAACGCGAATATGACTACCGCAACACGAAAATGACT
* *
55345 ATCGCAACGCGGAAT-TGACTATCGCAACGCGAAAATGACT
1 ATCGCAACGC-GAATATGACTACCGCAACACGAAAATGACT
*
55385 ATCGTAACG
1 ATCGCAACG
55394 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 40 0.91
41 4 0.09
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (40 bp):
ATCGCAACGCGAATATGACTACCGCAACACGAAAATGACT
Found at i:55422 original size:33 final size:34
Alignment explanation
Indices: 55365--55454 Score: 137
Period size: 33 Copynumber: 2.7 Consensus size: 34
55355 GGAATTGACT
* **
55365 ATCGCAACGCGAAAATGACTATCGTAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGTAACGAGAGA
*
55399 ATCGCAATGCG-AAATGAAAATCGTAACGAGTGA
1 ATCGCAATGCGAAAATGAAAATCGTAACGAGAGA
55432 ATCGCAATGCGAAAATGAAAATC
1 ATCGCAATGCGAAAATGAAAATC
55455 ATATACGCGT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 30 0.59
34 21 0.41
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGTAACGAGAGA
Found at i:55595 original size:14 final size:14
Alignment explanation
Indices: 55576--55612 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
55566 CATCAATTAA
55576 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
55590 ACAAATCATCTTTT
1 ACAAATCAACATTT
55604 ACAAATCAA
1 ACAAATCAA
55613 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:56974 original size:42 final size:42
Alignment explanation
Indices: 56895--56987 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
56885 CCTCTTCAAC
* * *
56895 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
56937 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
56979 GATGACAGG
1 GATGACAGG
56988 TGAGTCGGAC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:57509 original size:34 final size:34
Alignment explanation
Indices: 57462--57612 Score: 133
Period size: 34 Copynumber: 4.3 Consensus size: 34
57452 TGAAACTTAA
*
57462 AATCGCAACGCGAAAATGACTATCGCAACGAGAG
1 AATCGCAATGCGAAAATGACTATCGCAACGAGAG
** * * *
57496 AATCGCAATGCG-AAATGAAAATCGCAACAACAA
1 AATCGCAATGCGAAAATGACTATCGCAACGAGAG
* * *
57529 AATTGCAACGCGAAAATGACTATCGCAATGCGAAAATG
1 AATCGCAATGCGAAAATGACTATCGCAA--CG-AGA-G
* **
57567 ACTATCACAATGCGAATTTGACTATCGCAACGAGAG
1 A--ATCGCAATGCGAAAATGACTATCGCAACGAGAG
57603 AATCGCAATG
1 AATCGCAATG
57613 TGGTTTTCAT
Statistics
Matches: 90, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
33 26 0.29
34 32 0.36
36 3 0.03
37 4 0.04
38 3 0.03
40 22 0.24
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (34 bp):
AATCGCAATGCGAAAATGACTATCGCAACGAGAG
Found at i:57542 original size:33 final size:33
Alignment explanation
Indices: 57460--57543 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
57450 TCTGAAACTT
** * *
57460 AAAATCGCAACGCGAAAATGACTATCGCAACGAG
1 AAAATCGCAACGCG-AAATGAAAATCGCAACAAC
* *
57494 AGAATCGCAATGCGAAATGAAAATCGCAACAAC
1 AAAATCGCAACGCGAAATGAAAATCGCAACAAC
*
57527 AAAATTGCAACGCGAAA
1 AAAATCGCAACGCGAAA
57544 ATGACTATCG
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
33 29 0.71
34 12 0.29
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACAAC
Found at i:57561 original size:20 final size:20
Alignment explanation
Indices: 57533--57596 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
57523 CAACAAAATT
*
57533 GCAACGCGAAAATGACTATC
1 GCAATGCGAAAATGACTATC
57553 GCAATGCGAAAATGACTATC
1 GCAATGCGAAAATGACTATC
* **
57573 ACAATGCGAATTTGACTATC
1 GCAATGCGAAAATGACTATC
57593 GCAA
1 GCAA
57597 CGAGAGAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (20 bp):
GCAATGCGAAAATGACTATC
Found at i:57668 original size:20 final size:20
Alignment explanation
Indices: 57643--57819 Score: 130
Period size: 20 Copynumber: 9.5 Consensus size: 20
57633 GATTCTTTCG
** *
57643 TTGCGATAGTCAAATTCGTA
1 TTGCGATAGTCATTTTCGCA
57663 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
57683 TTACGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
57703 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
57723 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
** *
57737 TTGCGATTTTCA-TTTCGTA
1 TTGCGATAGTCATTTTCGCA
* *
57756 TTGTGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
**
57770 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCA
*
57790 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
57810 TTGCGATAGT
1 TTGCGATAGT
57820 AAACTATTCT
Statistics
Matches: 129, Mismatches: 14, Indels: 28
0.75 0.08 0.16
Matches are distributed among these distances:
14 13 0.10
16 12 0.09
17 6 0.05
18 5 0.04
19 6 0.05
20 87 0.67
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.44
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:57783 original size:33 final size:33
Alignment explanation
Indices: 57701--57784 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
57691 GTCATTTTCG
* *
57701 CGTTGCGATAGTCATTTTCGCATTGCGATTTTGT
1 CGTTGCGATAGTCA-TTTCGCATTGCGATTCTCT
* ** * *
57735 TGTTGCGATTTTCATTTCGTATTGTGATTCTCT
1 CGTTGCGATAGTCATTTCGCATTGCGATTCTCT
57768 CGTTGCGATAGTCATTT
1 CGTTGCGATAGTCATTT
57785 TCGTGTTGCG
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
33 29 0.73
34 11 0.28
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCATTGCGATTCTCT
Found at i:59731 original size:20 final size:20
Alignment explanation
Indices: 59673--59742 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
59663 GAAACTTTAA
* **
59673 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
59693 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
59713 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
59733 ATCGCAACGC
1 ATCGCAACGC
59743 AAGAATCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:59781 original size:33 final size:34
Alignment explanation
Indices: 59672--59785 Score: 88
Period size: 33 Copynumber: 3.2 Consensus size: 34
59662 TGAAACTTTA
* * *
59672 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATG
1 AATCGCAACGCGAATATGAAAATCGC-A-ACG-CAA-G
* **
59710 ACTATCGCAACGCGAATTTGACTATCGCAACGCAAG
1 A--ATCGCAACGCGAATATGAAAATCGCAACGCAAG
*
59746 AATCGCAACGCGAA-ATGAAAATTGCAACG-ACAG
1 AATCGCAACGCGAATATGAAAATCGCAACGCA-AG
59779 AATCGCA
1 AATCGCA
59786 TTGCGATAGT
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
32 1 0.02
33 20 0.32
34 13 0.21
36 2 0.03
37 2 0.03
38 4 0.06
39 1 0.02
40 20 0.32
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.14
Consensus pattern (34 bp):
AATCGCAACGCGAATATGAAAATCGCAACGCAAG
Found at i:60357 original size:20 final size:20
Alignment explanation
Indices: 60332--60500 Score: 212
Period size: 20 Copynumber: 8.3 Consensus size: 20
60322 GCTATGTAAA
60332 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
*
60352 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAT
* *
60372 TCGTATTGCAATTTACGTAT
1 TCGCATTGCGATTTACGTAT
*
60392 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAT
* **
60412 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACGTAT
* *
60433 TCGCGTTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAT
* **
60453 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACGTAT
60474 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
60494 TCGCATT
1 TCGCATT
60501 ACGAATTAGG
Statistics
Matches: 123, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
20 92 0.75
21 31 0.25
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:60447 original size:41 final size:41
Alignment explanation
Indices: 60330--60500 Score: 238
Period size: 41 Copynumber: 4.2 Consensus size: 41
60320 GCGCTATGTA
**
60330 AATCGCATTGCGA-TTTACGTATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTTACAAATTCGCATTGCGATTTACGT
* * **
60370 AATCGTATTGC-AATTTACGTATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTTACAAATTCGCATTGCGATTTACGT
* *
60410 AATCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGT
1 AATCGCATTGCGATTTTACAAATTCGCATTGCGATTTACGT
*
60451 AATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTTACAAATTCGCATTGCGATTTACGT
*
60492 ATTCGCATT
1 AATCGCATT
60501 ACGAATTAGG
Statistics
Matches: 120, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 1 0.01
40 47 0.39
41 72 0.60
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.38
Consensus pattern (41 bp):
AATCGCATTGCGATTTTACAAATTCGCATTGCGATTTACGT
Found at i:60526 original size:21 final size:22
Alignment explanation
Indices: 60502--60547 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
60492 ATTCGCATTA
60502 CGAA-TTAGGAAAATCGCAACG
1 CGAATTTAGGAAAATCGCAACG
* * *
60523 CGAATTTGGGAAAATCTCAATG
1 CGAATTTAGGAAAATCGCAACG
60545 CGA
1 CGA
60548 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (22 bp):
CGAATTTAGGAAAATCGCAACG
Found at i:60999 original size:23 final size:24
Alignment explanation
Indices: 60948--61002 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 24
60938 GTTACAAAAA
60948 GTTAATATATGTAGATTATAATTTT
1 GTTAATA-ATGTAGATTATAATTTT
60973 -TTAATAATG-AGAATTA-AATTTT
1 GTTAATAATGTAG-ATTATAATTTT
60995 GTTAATAA
1 GTTAATAA
61003 AAATAATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 8 0.29
23 14 0.50
24 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (24 bp):
GTTAATAATGTAGATTATAATTTT
Found at i:61010 original size:23 final size:22
Alignment explanation
Indices: 60962--61015 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
60952 ATATATGTAG
**
60962 ATTATAATTTTTTAATAATGAGA
1 ATTA-AATTTTTTAATAAAAAGA
*
60985 ATTAAATTTTGTTAATAAAAATA
1 ATTAAATTTT-TTAATAAAAAGA
61008 ATTGAAAT
1 ATT-AAAT
61016 CATAACGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 6 0.23
23 16 0.62
24 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (22 bp):
ATTAAATTTTTTAATAAAAAGA
Found at i:62373 original size:52 final size:54
Alignment explanation
Indices: 62295--62401 Score: 155
Period size: 52 Copynumber: 2.0 Consensus size: 54
62285 TTATAATATT
* *
62295 CTTGTGATTAGTTGCAATTCCCTAACTCTAGACTAGTCTCCTA-TT-TATGTGC
1 CTTGTAATTAGTTGCAATCCCCTAACTCTAGACTAGTCTCCTATTTCTATGTGC
* * *
62347 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATGTGC
1 CTTGTAATTAGTTGCAATCCCCTAACTCTAGACTAGTCTCCTATTTCTATGTGC
62401 C
1 C
62402 CCATCTTGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
52 38 0.79
53 2 0.04
54 8 0.17
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (54 bp):
CTTGTAATTAGTTGCAATCCCCTAACTCTAGACTAGTCTCCTATTTCTATGTGC
Found at i:65965 original size:52 final size:54
Alignment explanation
Indices: 65887--65987 Score: 161
Period size: 52 Copynumber: 1.9 Consensus size: 54
65877 TATTCTAATG
*
65887 ATTAGTTGCAATTCCCTAACTCTAGGCTAGTCTCCTA-TT-TATGTGCCTTGTA
1 ATTAGTTGCAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGTGCCTTGTA
* *
65939 ATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATGTGCC
1 ATTAGTTGCAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGTGCC
65988 ACATCTTGTG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 34 0.77
53 2 0.05
54 8 0.18
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41
Consensus pattern (54 bp):
ATTAGTTGCAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGTGCCTTGTA
Found at i:68949 original size:42 final size:42
Alignment explanation
Indices: 68903--69275 Score: 683
Period size: 42 Copynumber: 8.9 Consensus size: 42
68893 GTTGCGATAG
*
68903 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
68945 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* * *
68987 TCCAAATTTGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
69029 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
69071 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
69113 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
69155 TCCAAGTTCGTTGCGATAGTCGAAGTTCGTGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
69197 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* *
69239 TCTAAGTTCGTTGCGATAGTCGATGTTCGCGTTGCGA
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGA
69276 ATCTGGAAAC
Statistics
Matches: 320, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 320 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (42 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:69629 original size:16 final size:16
Alignment explanation
Indices: 69608--69646 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
69598 GTGTTTCTAA
*
69608 AAATTTTAATTTTTTT
1 AAATTTTAAGTTTTTT
69624 AAA-TTTAAGTTTTTT
1 AAATTTTAAGTTTTTT
69639 AATATTTT
1 AA-ATTTT
69647 TATTGATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 13 0.65
16 4 0.20
17 3 0.15
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
AAATTTTAAGTTTTTT
Found at i:77900 original size:17 final size:17
Alignment explanation
Indices: 77878--77913 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
77868 AATAACTTAA
77878 TATAATTT-TATATTATT
1 TATAATTTATATA-TATT
77895 TATAATTTATATATATT
1 TATAATTTATATATATT
77912 TA
1 TA
77914 ATAAAATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATAATTTATATATATT
Found at i:79436 original size:24 final size:25
Alignment explanation
Indices: 79408--79459 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
79398 TAAATGGTTG
* * *
79408 AATATTTATTCTAAA-TTAATAAAA
1 AATATATATTCAAAATTTAAAAAAA
79432 AATATATATTCAAAATTTAAAAAAA
1 AATATATATTCAAAATTTAAAAAAA
79457 AAT
1 AAT
79460 CTAAAATCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (25 bp):
AATATATATTCAAAATTTAAAAAAA
Found at i:79878 original size:21 final size:21
Alignment explanation
Indices: 79854--79898 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
79844 AAATTATACA
*
79854 TTTAGTACCTAAACTATTAGT
1 TTTAGTACATAAACTATTAGT
* *
79875 TTTAGTACATAAACTTTTATT
1 TTTAGTACATAAACTATTAGT
79896 TTT
1 TTT
79899 TTAAAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (21 bp):
TTTAGTACATAAACTATTAGT
Found at i:80351 original size:15 final size:15
Alignment explanation
Indices: 80331--80379 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
80321 CTACCTCCTA
80331 AAATTTTATAAATTT
1 AAATTTTATAAATTT
** *
80346 AAA-TTTATCCATTA
1 AAATTTTATAAATTT
*
80360 AAATTTTAAAAATTT
1 AAATTTTATAAATTT
80375 AAATT
1 AAATT
80380 CATCTTCTTA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATTTTATAAATTT
Found at i:85009 original size:25 final size:25
Alignment explanation
Indices: 84980--85027 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
84970 GCTGTCCCTT
84980 ATTCTCATATGTAATGGGATAAGAG
1 ATTCTCATATGTAATGGGATAAGAG
85005 ATTCTCATATGTAATGGGATAAG
1 ATTCTCATATGTAATGGGATAAG
85028 GGAGAGGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.33
Consensus pattern (25 bp):
ATTCTCATATGTAATGGGATAAGAG
Found at i:85385 original size:28 final size:27
Alignment explanation
Indices: 85347--85400 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
85337 ATTTAACTTA
*
85347 TTTTTTTTCGTATTTTTCCTGACCAAT
1 TTTTTTTTCGTATTTTTCCTAACCAAT
85374 TTTTTTTCTCGTATTTTTCCTAACCAA
1 TTTTTTT-TCGTATTTTTCCTAACCAA
85401 ATAAGTTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (27 bp):
TTTTTTTTCGTATTTTTCCTAACCAAT
Found at i:87307 original size:21 final size:21
Alignment explanation
Indices: 87251--87307 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
87241 TTTTTTACTT
* *
87251 TTTAAATATTTAT-TTATAAA
1 TTTAAAAATTTATATTGTAAA
*
87271 -ATAAAAA-TTATCATTGTAAA
1 TTTAAAAATTTAT-ATTGTAAA
87291 TTTAAAAATTTATATTG
1 TTTAAAAATTTATATTG
87308 AATTAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
18 4 0.14
19 5 0.17
20 6 0.21
21 10 0.34
22 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (21 bp):
TTTAAAAATTTATATTGTAAA
Found at i:88527 original size:11 final size:13
Alignment explanation
Indices: 88503--88534 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
88493 TTTGATTTTA
88503 TCAAACTAATATC
1 TCAAACTAATATC
*
88516 TCAAACTAATCTC
1 TCAAACTAATATC
88529 TCAAAC
1 TCAAAC
88535 AGGTATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (13 bp):
TCAAACTAATATC
Found at i:90035 original size:16 final size:16
Alignment explanation
Indices: 90014--90047 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
90004 CCAATAATCC
* *
90014 AATTTAAATTGATTTG
1 AATTTAAAATAATTTG
90030 AATTTAAAATAATTTG
1 AATTTAAAATAATTTG
90046 AA
1 AA
90048 CGTGTAATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (16 bp):
AATTTAAAATAATTTG
Found at i:93200 original size:31 final size:32
Alignment explanation
Indices: 93164--93224 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
93154 ATGCCTTTAA
93164 AAAATTGAAAGTTTAGGTATTAAA-GTGTATT
1 AAAATTGAAAGTTTAGGTATTAAATGTGTATT
*
93195 AAAATTGATAGTTTAGGTATTAAATGTGTA
1 AAAATTGAAAGTTTAGGTATTAAATGTGTA
93225 GTTTATCCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (32 bp):
AAAATTGAAAGTTTAGGTATTAAATGTGTATT
Found at i:94872 original size:48 final size:48
Alignment explanation
Indices: 94820--94915 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
94810 ATCTCTTATC
94820 TCTCTTAATTTTCAAATTTAAATACTTAGTATACGTTCGCATATCTTA
1 TCTCTTAATTTTCAAATTTAAATACTTAGTATACGTTCGCATATCTTA
*
94868 TCTCTTAATTTTCAAATTTAAATACTTAGTATACGTTTGCATATCTTA
1 TCTCTTAATTTTCAAATTTAAATACTTAGTATACGTTCGCATATCTTA
94916 ATGTATGATT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (48 bp):
TCTCTTAATTTTCAAATTTAAATACTTAGTATACGTTCGCATATCTTA
Found at i:95186 original size:14 final size:14
Alignment explanation
Indices: 95167--95194 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
95157 TTTTAAGCAC
95167 CTATTTGAGAATAA
1 CTATTTGAGAATAA
95181 CTATTTGAGAATAA
1 CTATTTGAGAATAA
95195 GGGTATAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
CTATTTGAGAATAA
Found at i:95439 original size:40 final size:40
Alignment explanation
Indices: 95390--95491 Score: 195
Period size: 40 Copynumber: 2.5 Consensus size: 40
95380 GCGTTTATTT
95390 ATTAAATGAACGAACATGAACAAGATTTTGTGTTCGTTTA
1 ATTAAATGAACGAACATGAACAAGATTTTGTGTTCGTTTA
95430 ATTAAATGAACGAACATGAACAAGATTTTGTGTTCGTTTA
1 ATTAAATGAACGAACATGAACAAGATTTTGTGTTCGTTTA
*
95470 ATTAAATGAACGAACACGAACA
1 ATTAAATGAACGAACATGAACA
95492 TAGGTCTCAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (40 bp):
ATTAAATGAACGAACATGAACAAGATTTTGTGTTCGTTTA
Found at i:95551 original size:14 final size:14
Alignment explanation
Indices: 95543--95574 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
95533 TGTTCGTTTT
95543 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
95557 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
95571 TGTT
1 TGTT
95575 TATCCCAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.59
Consensus pattern (14 bp):
TGTTCGTTCATTTA
Found at i:96675 original size:16 final size:16
Alignment explanation
Indices: 96649--96713 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
96639 CCAACGTTTA
*
96649 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
* *
96665 TGTTCAATTATGTTTG
1 TGTTCATTTATGTTCG
96681 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
96697 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
96713 T
1 T
96714 TAATTATTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.11, C:0.11, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:97547 original size:31 final size:31
Alignment explanation
Indices: 97500--97568 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
97490 TGTATTAAAC
* * *
97500 AACGTTTGTAATATTAGATATTTAAAATGGT
1 AACGTTTATAACATTAGATACTTAAAATGGT
97531 AACGTTTATAACATTAGATACTTAAAATGGT
1 AACGTTTATAACATTAGATACTTAAAATGGT
97562 AACGTTT
1 AACGTTT
97569 GTTTGTAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (31 bp):
AACGTTTATAACATTAGATACTTAAAATGGT
Found at i:98450 original size:36 final size:35
Alignment explanation
Indices: 98352--98569 Score: 252
Period size: 34 Copynumber: 6.3 Consensus size: 35
98342 TTTATTTATT
** **
98352 TATAT-TATATAGTTTGCAAATGATTTTG-AAATA
1 TATATATATATAGTTTTTAAAACATTTTGAAAATA
*
98385 TATATATATATAGTTTTTAAAATATTTTTGAAAACT-
1 TATATATATATAGTTTTTAAAACA-TTTTGAAAA-TA
98421 TATATAATATATAGTTTTTAAAACATTTTGAAAATA
1 TATAT-ATATATAGTTTTTAAAACATTTTGAAAATA
* * * *
98457 TGTATATATATATTTTTTAAAAAATTATGAAAATA
1 TATATATATATAGTTTTTAAAACATTTTGAAAATA
* *
98492 TATA-ATATAGAGTTTTTAAAACATTTTGAATATA
1 TATATATATATAGTTTTTAAAACATTTTGAAAATA
*
98526 TATA-ATATATAGTTTTT-AAA-ATTTTGAATATA
1 TATATATATATAGTTTTTAAAACATTTTGAAAATA
98558 TATATATATATA
1 TATATATATATA
98570 TATATATATA
Statistics
Matches: 162, Mismatches: 16, Indels: 14
0.84 0.08 0.07
Matches are distributed among these distances:
32 16 0.10
33 15 0.09
34 55 0.34
35 36 0.22
36 21 0.13
37 19 0.12
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (35 bp):
TATATATATATAGTTTTTAAAACATTTTGAAAATA
Found at i:98560 original size:2 final size:2
Alignment explanation
Indices: 98553--98581 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
98543 AAAATTTTGA
98553 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
98582 ATTAGTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:98641 original size:33 final size:34
Alignment explanation
Indices: 98569--98674 Score: 133
Period size: 33 Copynumber: 3.0 Consensus size: 34
98559 ATATATATAT
*
98569 ATATATATATATAATTAGTTTTTAAAACATTTTGAAAAA
1 ATATATA-ATAT-A-TAGTTTTT-AAATATTTTG-AAAA
98608 ATATATAATATATAGTTTTTAAATA-TTTGAAAA
1 ATATATAATATATAGTTTTTAAATATTTTGAAAA
* *
98641 AAATATAATATATAGTTTTAAAATATTTTGAAAA
1 ATATATAATATATAGTTTTTAAATATTTTGAAAA
98675 TATTATATTT
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
33 27 0.43
34 12 0.19
35 4 0.06
36 8 0.13
37 1 0.02
38 4 0.06
39 7 0.11
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.43
Consensus pattern (34 bp):
ATATATAATATATAGTTTTTAAATATTTTGAAAA
Found at i:98642 original size:35 final size:34
Alignment explanation
Indices: 98588--98674 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 34
98578 TATAATTAGT
*
98588 TTTTAAAACATTTTGAAAAAATATATAATATATAG
1 TTTTAAAATATTTTGAAAAAA-ATATAATATATAG
*
98623 TTTTTAAATA-TTTGAAAAAAATATAATATATAG
1 TTTTAAAATATTTTGAAAAAAATATAATATATAG
98656 TTTTAAAATATTTTGAAAA
1 TTTTAAAATATTTTGAAAA
98675 TATTATATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
33 22 0.46
34 18 0.38
35 8 0.17
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.43
Consensus pattern (34 bp):
TTTTAAAATATTTTGAAAAAAATATAATATATAG
Found at i:98652 original size:83 final size:83
Alignment explanation
Indices: 98502--98654 Score: 231
Period size: 85 Copynumber: 1.8 Consensus size: 83
98492 TATAATATAG
* * *
98502 AGTTTTTAAAACATTTTGAATATATATAATATATAGTTTTTAAAATTTTGAATATATATATATAT
1 AGTTTTTAAAACATTTTGAAAATATATAATATATAGTTTTTAAAATTTTGAATAAAAATATATAT
98567 ATATATATATATATAATT
66 ATATATATATATATAATT
98585 AGTTTTTAAAACATTTTGAAAAAATATATAATATATAGTTTTT-AAATATTTGAA-AAAAATATA
1 AGTTTTTAAAACATTTTG--AAAATATATAATATATAGTTTTTAAAAT-TTTGAATAAAAATATA
98648 -ATATATA
63 TATATATA
98655 GTTTTAAAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
83 25 0.39
84 11 0.17
85 28 0.44
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.46
Consensus pattern (83 bp):
AGTTTTTAAAACATTTTGAAAATATATAATATATAGTTTTTAAAATTTTGAATAAAAATATATAT
ATATATATATATATAATT
Found at i:98675 original size:31 final size:31
Alignment explanation
Indices: 98605--98682 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 31
98595 ACATTTTGAA
*
98605 AAAATATATAATATATAGTTTTTAAATATTTG
1 AAAA-ATATAATATATAGTTTTAAAATATTTG
98637 AAAAAAATATAATATATAGTTTTAAAATATTTTG
1 --AAAAATATAATATATAGTTTTAAAATA-TTTG
*
98671 -AAAATATTATAT
1 AAAAATATAATAT
98683 TTTATGGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
31 11 0.27
33 22 0.54
34 8 0.20
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (31 bp):
AAAAATATAATATATAGTTTTAAAATATTTG
Found at i:98693 original size:34 final size:34
Alignment explanation
Indices: 98588--98700 Score: 138
Period size: 34 Copynumber: 3.3 Consensus size: 34
98578 TATAATTAGT
*
98588 TTTTAAAACATTTTGAAAAAATATATAATATATAG
1 TTTTAAAATATTTTGAAAAAAT-TATAATATATAG
* *
98623 TTTTTAAATA-TTTGAAAAAAATATAATATATAG
1 TTTTAAAATATTTTGAAAAAATTATAATATATAG
* * * *
98656 TTTTAAAATATTTTGAAAATATTATATTTTATGG
1 TTTTAAAATATTTTGAAAAAATTATAATATATAG
98690 TTTTGAAAATA
1 TTTT-AAAATA
98701 ATTATTTTTA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
33 21 0.31
34 32 0.48
35 14 0.21
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (34 bp):
TTTTAAAATATTTTGAAAAAATTATAATATATAG
Found at i:98693 original size:152 final size:149
Alignment explanation
Indices: 98421--98699 Score: 375
Period size: 152 Copynumber: 1.9 Consensus size: 149
98411 TTTGAAAACT
* * *
98421 TATATAATATATAGTTTTTAAAACATTTTGAAAATATGTATATATATATTTTTTAAAAAATTATG
1 TATATAATATATAGTTTTTAAAACATTTTGAAAAAATATATATATATAGTTTTTAAAAAATTATG
* * *
98486 AAAATATATAATATAGAGTTTTTAAAACATTTTGAATATATATAATATATAGTTTTTAAAATTTT
66 AAAAAATATAATATAGAGTTTTTAAAACATTTTGAAAATATATAATATATAGTTTTGAAAATTTT
98551 GAATATATATATATATATA
131 GAATATATATATATATATA
*
98570 TATATATATATAATTAGTTTTTAAAACATTTTGAAAAAATATATAATATATAGTTTTT-AAATAT
1 TATATA-ATAT-A-TAGTTTTTAAAACATTTTGAAAAAATATAT-ATATATAGTTTTTAAAAAAT
* * * * *
98634 T-TGAAAAAAATATAATATATAG-TTTTAAAATATTTTGAAAATATTATATTTTATGGTTTTGAA
62 TATG-AAAAAATATAATATAGAGTTTTTAAAACATTTTGAAAATA-TATAATATATAGTTTTGAA
98697 AAT
125 AAT
98700 AATTATTTTT
Statistics
Matches: 112, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
149 6 0.05
150 4 0.04
151 22 0.20
152 68 0.61
153 12 0.11
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.46
Consensus pattern (149 bp):
TATATAATATATAGTTTTTAAAACATTTTGAAAAAATATATATATATAGTTTTTAAAAAATTATG
AAAAAATATAATATAGAGTTTTTAAAACATTTTGAAAATATATAATATATAGTTTTGAAAATTTT
GAATATATATATATATATA
Found at i:98704 original size:119 final size:116
Alignment explanation
Indices: 98470--98682 Score: 279
Period size: 119 Copynumber: 1.8 Consensus size: 116
98460 ATATATATAT
* * *
98470 TTTTTAAAAAATTATGAAAATATATAATATAGAGTTTTTAAAACATTTTGAATATATATAATATA
1 TTTTTAAAACATTATGAAAATATATAATATAGAGTTTTTAAAACATTTTGAAAAAATATAATATA
* * *
98535 TAGTTTTTAAAATTTTGAATATATATATATATATATATATATATATAATTA
66 TAGTTTTAAAAATTTTGAAAATATATATATATATATATATATAAATAATTA
* * *
98586 GTTTTTAAAACATTTTGAAAAAATATATAATATATAGTTTTT-AAATA-TTTGAAAAAAATATAA
1 -TTTTTAAAACATTATG--AAAATATATAATATAGAGTTTTTAAAACATTTTG-AAAAAATATAA
98649 TATATAGTTTTAAAATATTTTGAAAATAT-TATAT
62 TATATAGTTTTAAAA-ATTTTGAAAATATATATAT
98683 TTTATGGTTT
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
117 18 0.21
118 32 0.38
119 34 0.40
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.46
Consensus pattern (116 bp):
TTTTTAAAACATTATGAAAATATATAATATAGAGTTTTTAAAACATTTTGAAAAAATATAATATA
TAGTTTTAAAAATTTTGAAAATATATATATATATATATATATAAATAATTA
Found at i:98756 original size:3 final size:3
Alignment explanation
Indices: 98750--98798 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
98740 AAAATTATTG
*
98750 TAT TAT TAT TAT TA- TAT TAT ATAT TAA TAT TAT T-T T-T TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
98792 TAT TAT T
1 TAT TAT T
98799 TATTTAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 8 0.20
3 29 0.73
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:98762 original size:14 final size:15
Alignment explanation
Indices: 98743--98798 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 15
98733 TTTTAAAAAA
*
98743 ATTATTGTATTAT-T
1 ATTATTATATTATAT
98757 ATTATTATATTATAT
1 ATTATTATATTATAT
98772 ATTA--ATATTAT-T
1 ATTATTATATTATAT
98784 -TT-TTATATTAT-T
1 ATTATTATATTATAT
98796 ATT
1 ATT
98799 TATTTAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
11 2 0.05
12 9 0.24
13 9 0.24
14 12 0.32
15 5 0.14
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
ATTATTATATTATAT
Found at i:98780 original size:18 final size:18
Alignment explanation
Indices: 98753--98802 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
98743 ATTATTGTAT
98753 TATTATTATTATATTATA
1 TATTATTATTATATTATA
* * *
98771 TATTAATATTATTTTTTA
1 TATTATTATTATATTATA
98789 TATTATTATT-TATT
1 TATTATTATTATATT
98803 TAATTTATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 3 0.11
18 24 0.89
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTATTATTATATTATA
Found at i:98809 original size:21 final size:20
Alignment explanation
Indices: 98750--98813 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
98740 AAAATTATTG
98750 TATTATTATTA-TTATATTATA
1 TATTATTATTATTTA-ATT-TA
*
98771 TATTAATATTATTT--TTTA
1 TATTATTATTATTTAATTTA
98789 TATTATTATTTATTTAATTTA
1 TATTATTA-TTATTTAATTTA
98810 TATT
1 TATT
98814 TACTTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 9 0.24
19 8 0.22
21 18 0.49
22 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTATTATTATTTAATTTA
Found at i:98813 original size:18 final size:18
Alignment explanation
Indices: 98756--98813 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 18
98746 ATTGTATTAT
*
98756 TATTATTATATTATATATTAA
1 TATTATT-TATT-TA-ATTTA
*
98777 TATTATTT-TTT-ATAT-
1 TATTATTTATTTAATTTA
98792 TATTATTTATTTAATTTA
1 TATTATTTATTTAATTTA
98810 TATT
1 TATT
98814 TACTTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
15 8 0.26
16 5 0.16
17 3 0.10
18 5 0.16
19 2 0.06
20 1 0.03
21 7 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTATTTATTTAATTTA
Found at i:98813 original size:33 final size:38
Alignment explanation
Indices: 98753--98822 Score: 96
Period size: 35 Copynumber: 2.0 Consensus size: 38
98743 ATTATTGTAT
98753 TATTATTATTATATTATATATTAATA-TTA-TTTTTTA
1 TATTATTATTATATTATATATTAATATTTACTTTTTTA
*
98789 TATTATTATT-TATT-TA-ATTTATATTTACTTTTTT
1 TATTATTATTATATTATATATTAATATTTACTTTTTT
98823 TCTTTATTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
33 6 0.19
34 5 0.16
35 10 0.32
36 10 0.32
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (38 bp):
TATTATTATTATATTATATATTAATATTTACTTTTTTA
Found at i:100537 original size:13 final size:13
Alignment explanation
Indices: 100519--100543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
100509 ACGAATATAC
100519 TTAGAAAATCTTT
1 TTAGAAAATCTTT
100532 TTAGAAAATCTT
1 TTAGAAAATCTT
100544 AAATTTATTT
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTAGAAAATCTTT
Done.