Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012272.1 Kokia drynarioides strain JFW-HI SEQ_127273, 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: 91749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:16 original size:2 final size:2
Alignment explanation
Indices: 11--38 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1 AAAAAAAAAA
11 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
39 TAAAATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5291 original size:30 final size:31
Alignment explanation
Indices: 5237--5296 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
5227 TTGATTTAAT
5237 GTGTAATTTAATATATATAAATTTTAATTTA
1 GTGTAATTTAATATATATAAATTTTAATTTA
5268 GTGTAA-TT-ATATATATGAAATTTTAATTT
1 GTGTAATTTAATATATAT-AAATTTTAATTT
5297 TAATTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 8 0.29
30 14 0.50
31 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (31 bp):
GTGTAATTTAATATATATAAATTTTAATTTA
Found at i:5816 original size:10 final size:10
Alignment explanation
Indices: 5803--5851 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
5793 TTAATTTTGA
5803 AATAATTTTT
1 AATAATTTTT
* *
5813 AATAGTTTTA
1 AATAATTTTT
5823 AATAATTTCTT
1 AATAATTT-TT
*
5834 -ATAATTCTT
1 AATAATTTTT
5843 AATAATTTT
1 AATAATTTT
5852 CTATATATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
9 2 0.06
10 28 0.90
11 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (10 bp):
AATAATTTTT
Found at i:5827 original size:20 final size:19
Alignment explanation
Indices: 5794--5856 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 19
5784 AAATTAATAT
5794 TAATTTTGAAATAATTTTTAA
1 TAATTTT-AAATAATTTTT-A
*
5815 TAGTTTTAAATAATTTCTTA
1 TAATTTTAAATAATTT-TTA
5835 TAATTCTT-AATAATTTTCTA
1 TAATT-TTAAATAATTTT-TA
5855 TA
1 TA
5857 TATATTTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 1 0.03
20 26 0.70
21 10 0.27
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (19 bp):
TAATTTTAAATAATTTTTA
Found at i:15212 original size:18 final size:19
Alignment explanation
Indices: 15189--15230 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
15179 TGTATATAAA
*
15189 TATATAA-TATAGTTTTAT
1 TATATAATTACAGTTTTAT
*
15207 TATATAATTACATTTTTAT
1 TATATAATTACAGTTTTAT
15226 TATAT
1 TATAT
15231 TGTCTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TATATAATTACAGTTTTAT
Found at i:15286 original size:6 final size:6
Alignment explanation
Indices: 15262--15297 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
15252 TATTAATTAA
15262 AAACAT -AA-AT AAA-AT AAACAT AAACAT AAACAT AAA
1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAA
15298 AACCATGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 2 0.07
5 9 0.32
6 17 0.61
ACGTcount: A:0.72, C:0.11, G:0.00, T:0.17
Consensus pattern (6 bp):
AAACAT
Found at i:20678 original size:90 final size:90
Alignment explanation
Indices: 20525--20710 Score: 257
Period size: 90 Copynumber: 2.1 Consensus size: 90
20515 CCCATCATTA
* * * * * *
20525 GAATTTTCATTAATCACATCACCTGCTATCGTGATCTTTGCAAGGTTATCTAGTGAATTAGCTAA
1 GAATTTTCATTAAACACAGCACCTACTAGCGTGATCTTAGCAAGGTTATCCAGTGAATTAGCTAA
*
20590 TTTCCCTCCCTCAACTACTCCTAAG
66 TTTCCCTCCCTCAACTACTCCCAAG
* *
20615 GAATTTTCATTAAACACGGCACCTACTAGCGTGTTCTTAGC-AGGATTATCCAGTGAATTAGCTA
1 GAATTTTCATTAAACACAGCACCTACTAGCGTGATCTTAGCAAGG-TTATCCAGTGAATTAGCTA
* *
20679 TTTTCCTTCCCTCAACTACTCCCAAG
65 ATTTCCCTCCCTCAACTACTCCCAAG
20705 GAATTT
1 GAATTT
20711 GAATCCCTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
89 3 0.04
90 81 0.96
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.34
Consensus pattern (90 bp):
GAATTTTCATTAAACACAGCACCTACTAGCGTGATCTTAGCAAGGTTATCCAGTGAATTAGCTAA
TTTCCCTCCCTCAACTACTCCCAAG
Found at i:21908 original size:29 final size:29
Alignment explanation
Indices: 21875--21934 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
21865 TTAGAACGAA
*
21875 ATTTTAATTTTGGTACATTTGAAAAGTTG
1 ATTTTAATTTCGGTACATTTGAAAAGTTG
21904 ATTTTAATTTCGGTACATTTGAAAAGTTG
1 ATTTTAATTTCGGTACATTTGAAAAGTTG
21933 AT
1 AT
21935 ATTTTAATCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.47
Consensus pattern (29 bp):
ATTTTAATTTCGGTACATTTGAAAAGTTG
Found at i:21949 original size:29 final size:28
Alignment explanation
Indices: 21888--21949 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
21878 TTAATTTTGG
**
21888 TACATTTGAAAAGTTGATTTTAATTTCGG
1 TACATTTGAAAAGTTGATTTTAA-TTCCC
21917 TACATTTGAAAAGTTGATATTTTAA-TCCC
1 TACATTTGAAAAGTTG--ATTTTAATTCCC
21946 TACA
1 TACA
21950 CATTAGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 22 0.76
31 7 0.24
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (28 bp):
TACATTTGAAAAGTTGATTTTAATTCCC
Found at i:23570 original size:3 final size:3
Alignment explanation
Indices: 23564--23600 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
23554 ACGTGGTGGT
* *
23564 GGA GGA GGA GGA GGA GGA GGA GGA GAA GGA GAA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA G
23601 AAGGCGATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:23601 original size:6 final size:6
Alignment explanation
Indices: 23566--23604 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
23556 GTGGTGGTGG
* * *
23566 AGGAGG AGGAGG AGGAGG AGGAGA AGGAGA AGGAGA AGG
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGG
23605 CGATTGTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (6 bp):
AGGAGA
Found at i:23601 original size:12 final size:12
Alignment explanation
Indices: 23566--23604 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
23556 GTGGTGGTGG
*
23566 AGGAGGAGGAGG
1 AGGAGGAGGAGA
23578 AGGAGGAGGAGA
1 AGGAGGAGGAGA
*
23590 AGGAGAAGGAGA
1 AGGAGGAGGAGA
23602 AGG
1 AGG
23605 CGATTGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (12 bp):
AGGAGGAGGAGA
Found at i:23669 original size:13 final size:13
Alignment explanation
Indices: 23651--23721 Score: 70
Period size: 13 Copynumber: 5.0 Consensus size: 13
23641 AAAAAACATG
23651 GAAAATGAAGGAA
1 GAAAATGAAGGAA
23664 GAAAATGAAGGAA
1 GAAAATGAAGGAA
*
23677 CGGGAAAATGAATGAA
1 ---GAAAATGAAGGAA
*
23693 GAAAATAAAGGAACA
1 GAAAATGAAGG-A-A
23708 GAAAAATGAAGGAA
1 G-AAAATGAAGGAA
23722 AAGGAGAAGC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
13 22 0.46
14 2 0.04
15 3 0.06
16 21 0.44
ACGTcount: A:0.61, C:0.03, G:0.28, T:0.08
Consensus pattern (13 bp):
GAAAATGAAGGAA
Found at i:23693 original size:29 final size:29
Alignment explanation
Indices: 23645--23721 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
23635 TGCCCAAAAA
*
23645 AACATGGAAAATGAAGGAAGAAAATGAAGG
1 AACA-GGAAAATGAAGGAAGAAAATAAAGG
* *
23675 AACGGGAAAATGAATGAAGAAAATAAAGG
1 AACAGGAAAATGAAGGAAGAAAATAAAGG
*
23704 AACAGAAAAATGAAGGAA
1 AACAGGAAAATGAAGGAA
23722 AAGGAGAAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 38 0.93
30 3 0.07
ACGTcount: A:0.60, C:0.04, G:0.27, T:0.09
Consensus pattern (29 bp):
AACAGGAAAATGAAGGAAGAAAATAAAGG
Found at i:23996 original size:27 final size:28
Alignment explanation
Indices: 23955--24018 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 28
23945 AATAAATATT
23955 TAAAATATAAAAAAAGTTAGAATTTTTAAAAA
1 TAAAAT-T-AAAAAAG--AGAATTTTTAAAAA
23987 -AAAATTAAAAAAGAGAATTTTTAAAAA
1 TAAAATTAAAAAAGAGAATTTTTAAAAA
24014 TAAAA
1 TAAAA
24019 ATATTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
27 14 0.45
28 4 0.13
29 7 0.23
30 1 0.03
31 5 0.16
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (28 bp):
TAAAATTAAAAAAGAGAATTTTTAAAAA
Found at i:24019 original size:29 final size:29
Alignment explanation
Indices: 23955--24021 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
23945 AATAAATATT
23955 TAAAATATAAAAAAAGTTAGAATTTTTAAAA
1 TAAAA-ATAAAAAAAG-TAGAATTTTTAAAA
*
23986 -AAAAATTAAAAAAG-AGAATTTTTAAAAA
1 TAAAAATAAAAAAAGTAGAATTTTT-AAAA
24014 TAAAAATA
1 TAAAAATA
24022 TTAAAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 9 0.28
28 4 0.12
29 15 0.47
30 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (29 bp):
TAAAAATAAAAAAAGTAGAATTTTTAAAA
Found at i:24054 original size:18 final size:18
Alignment explanation
Indices: 23993--24057 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
23983 AAAAAAAATT
23993 AAAA-AAGAGAATTT-TTA
1 AAAATAAGA-AATTTATTA
24010 AAAATAA-AAA--TATTA
1 AAAATAAGAAATTTATTA
*
24025 AAAATAATAGAAATTTATTT
1 AAAAT-A-AGAAATTTATTA
24045 AAAATAAGAAATT
1 AAAATAAGAAATT
24058 AAATTTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
14 1 0.03
15 8 0.20
16 3 0.08
17 6 0.15
18 12 0.30
19 1 0.03
20 9 0.22
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
AAAATAAGAAATTTATTA
Found at i:24059 original size:34 final size:30
Alignment explanation
Indices: 23956--24060 Score: 90
Period size: 34 Copynumber: 3.3 Consensus size: 30
23946 ATAAATATTT
23956 AAAATATAAAAAAAGTTAGAA-TTTTTAAAA-A
1 AAAAT-TAAAAAAAG--AGAATTTTTTAAAATA
*
23987 AAAATT-AAAAAAGAGAATTTTTAAAAATAA
1 AAAATTAAAAAAAGAGAATTTTTTAAAAT-A
*
24017 AAATATTAAAAATAATAGAAATTTATTTAAAATA
1 AAA-ATTAAAAA-AAGAG-AATTT-TTTAAAATA
24051 AGAAATTAAA
1 A-AAATTAAA
24061 TTTTTTTAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
27 4 0.06
28 8 0.13
29 7 0.11
30 5 0.08
31 8 0.13
32 4 0.06
33 4 0.06
34 13 0.21
35 9 0.15
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.30
Consensus pattern (30 bp):
AAAATTAAAAAAAGAGAATTTTTTAAAATA
Found at i:24088 original size:9 final size:9
Alignment explanation
Indices: 24067--24121 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
24057 TAAATTTTTT
24067 TAAAAATT-
1 TAAAAATTA
*
24075 CAAAAATTA
1 TAAAAATTA
24084 TAAAAA--A
1 TAAAAATTA
*
24091 TAGAAATTCA
1 TAAAAATT-A
24101 -AAAAATTA
1 TAAAAATTA
24109 TAAAAATTA
1 TAAAAATTA
24118 TAAA
1 TAAA
24122 TGGAAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
7 6 0.16
8 8 0.21
9 23 0.61
10 1 0.03
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (9 bp):
TAAAAATTA
Found at i:24128 original size:25 final size:25
Alignment explanation
Indices: 24076--24131 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
24066 TTAAAAATTC
*
24076 AAAAATTATAAAAAATAGAAATTCA
1 AAAAATTATAAAAAATAGAAATGCA
* * *
24101 AAAAATTATAAAAATTATAAATGGA
1 AAAAATTATAAAAAATAGAAATGCA
24126 AAAAAT
1 AAAAAT
24132 CAAAATATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (25 bp):
AAAAATTATAAAAAATAGAAATGCA
Found at i:24160 original size:18 final size:20
Alignment explanation
Indices: 24137--24174 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
24127 AAAATCAAAA
24137 TATTAAAAT-AT-TAAAATT
1 TATTAAAATAATATAAAATT
24155 TATTAAAATAATATAAAATT
1 TATTAAAATAATATAAAATT
24175 GCAAAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TATTAAAATAATATAAAATT
Found at i:24180 original size:18 final size:19
Alignment explanation
Indices: 24159--24229 Score: 74
Period size: 18 Copynumber: 3.7 Consensus size: 19
24149 AAAATTTATT
*
24159 AAAATAATATAAAATTGCAAA
1 AAAATATTA-AAAATTGC-AA
*
24180 ACAAATATTAAAAATTACAA
1 A-AAATATTAAAAATTGCAA
*
24200 AAAGTA-TAAAAATTG-AA
1 AAAATATTAAAAATTGCAA
24217 AAAATATTAAAAA
1 AAAATATTAAAAA
24230 ATAGTTTGCA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
17 7 0.16
18 14 0.33
19 4 0.09
20 3 0.07
21 8 0.19
22 7 0.16
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.24
Consensus pattern (19 bp):
AAAATATTAAAAATTGCAA
Found at i:24187 original size:40 final size:36
Alignment explanation
Indices: 24141--24229 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 36
24131 TCAAAATATT
* *
24141 AAAATATTAAAATTTATTAAAATAATAT-AAAATTGCAAA
1 AAAATATTAAAAATTA-CAAAA-AATATAAAAATTG--AA
*
24180 ACAAATATTAAAAATTACAAAAAGTATAAAAATTGAA
1 A-AAATATTAAAAATTACAAAAAATATAAAAATTGAA
24217 AAAATATTAAAAA
1 AAAATATTAAAAA
24230 ATAGTTTGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
36 12 0.27
37 3 0.07
38 4 0.09
39 12 0.27
40 14 0.31
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.28
Consensus pattern (36 bp):
AAAATATTAAAAATTACAAAAAATATAAAAATTGAA
Found at i:24202 original size:22 final size:22
Alignment explanation
Indices: 24160--24201 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
24150 AAATTTATTA
*
24160 AAATAATATAAAATTGCAAAAC
1 AAATAATATAAAATTACAAAAC
*
24182 AAATATTA-AAAATTACAAAA
1 AAATAATATAAAATTACAAAA
24202 AGTATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (22 bp):
AAATAATATAAAATTACAAAAC
Found at i:24231 original size:19 final size:18
Alignment explanation
Indices: 24141--24229 Score: 67
Period size: 18 Copynumber: 4.7 Consensus size: 18
24131 TCAAAATATT
* *
24141 AAAATATT-AAAATTTATT
1 AAAATATTAAAAATTGA-A
*
24159 AAAATAATATAAAATTGCAAA
1 AAAATATTA-AAAATTG--AA
24180 ACAAATATTAAAAATT-ACA
1 A-AAATATTAAAAATTGA-A
24199 AAAAGTA-TAAAAATTGAA
1 AAAA-TATTAAAAATTGAA
24217 AAAATATTAAAAA
1 AAAATATTAAAAA
24230 ATAGTTTGCA
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
17 2 0.03
18 30 0.52
19 5 0.09
20 6 0.10
21 7 0.12
22 8 0.14
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAATATTAAAAATTGAA
Found at i:26451 original size:6 final size:6
Alignment explanation
Indices: 26440--26466 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
26430 ATAATCTAAG
26440 AGCCAC AGCCAC AGCCAC AGCCAC AGC
1 AGCCAC AGCCAC AGCCAC AGCCAC AGC
26467 AAGCGTGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.48, G:0.19, T:0.00
Consensus pattern (6 bp):
AGCCAC
Found at i:29806 original size:29 final size:30
Alignment explanation
Indices: 29772--29830 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
29762 AAACCGAGTC
* *
29772 AAATTT-GAATTTTTTAAAAGTTTGGGGGT
1 AAATTTGGAATTTTTGAAAAGCTTGGGGGT
*
29801 AAATTTGGAATTTTTGGAAAGCTTGGGGGT
1 AAATTTGGAATTTTTGAAAAGCTTGGGGGT
29831 TAAAACATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.29, C:0.02, G:0.29, T:0.41
Consensus pattern (30 bp):
AAATTTGGAATTTTTGAAAAGCTTGGGGGT
Found at i:30169 original size:25 final size:25
Alignment explanation
Indices: 30141--30190 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
30131 TTTCTCAAAA
30141 ACAAACCCAAATCCCCTTTATTTTT
1 ACAAACCCAAATCCCCTTTATTTTT
**
30166 ACAATTCCAAATCCCCTTTATTTTT
1 ACAAACCCAAATCCCCTTTATTTTT
30191 TCTCTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (25 bp):
ACAAACCCAAATCCCCTTTATTTTT
Found at i:31103 original size:13 final size:13
Alignment explanation
Indices: 31085--31109 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31075 CTTTTTTTTA
31085 TTTTTAATTAATG
1 TTTTTAATTAATG
31098 TTTTTAATTAAT
1 TTTTTAATTAAT
31110 AAGAATGTTA
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:31353 original size:15 final size:16
Alignment explanation
Indices: 31333--31365 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
31323 TGTGGGTTTC
*
31333 ATAAATTTTAAT-ATT
1 ATAAATTTAAATAATT
31348 ATAAATTTAAATAATT
1 ATAAATTTAAATAATT
31364 AT
1 AT
31366 TTCAAATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAAATTTAAATAATT
Found at i:31627 original size:17 final size:17
Alignment explanation
Indices: 31607--31639 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31597 TATTTGACAT
31607 AAAAAT-TATATATAAAG
1 AAAAATATATA-ATAAAG
31624 AAAAATATATAATAAA
1 AAAAATATATAATAAA
31640 AAATAGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAAATATATAATAAAG
Found at i:32073 original size:14 final size:14
Alignment explanation
Indices: 32054--32084 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
32044 TATAAAAATT
*
32054 ATATATAAAGAAAA
1 ATATATAAAAAAAA
32068 ATATATAAAAAAAA
1 ATATATAAAAAAAA
32082 ATA
1 ATA
32085 GTTAATGTTT
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:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (14 bp):
ATATATAAAAAAAA
Found at i:32352 original size:439 final size:436
Alignment explanation
Indices: 31537--32388 Score: 1517
Period size: 439 Copynumber: 1.9 Consensus size: 436
31527 ATATTCAAAA
* *
31537 TAATTATTTTATTTTATTATATTAAAAATTACCATACACACAATGTACACGGAAAAAAAATATTT
1 TAATTATATTATTTTATTATATTAAAAATTACCATACACAAAATGTACACGGAAAAAAAATATTT
*
31602 GACATAAAAATTATATATAAAGAAAAATATATAATAAAAAATAGTTAATGTTTTTTAAAAAATAA
66 GACATAAAAATTATATATAAAGAAAAATATATAAAAAAAAATAGTTAATGTTTTTTAAAAAATAA
* * *
31667 AAGATTTAAAAAAAAATTCTTTTGGGATTCATCAAATGCCATGTTTGTGTGGGTGTGAAACTAGT
131 AAGATTTAAAAAAAAATTCTATTGGGATTCATAAAATGCCATGTTTGTGTGGGTGTGAAACAAGT
31732 GTTGGTCGAAAGGGTTGGTTAAAGAAACTGTTTTTACTTCCATATACCACAAAAGGGAAATTCCA
196 GTTGGTCGAAAGGGTTGGTTAAAGAAACTGTTTTTACTTCCATATACCACAAAAGGGAAATTCCA
*
31797 TGTTCAAACTTGCTTCTGTGTTGCAACAGAAACTTCCAAAAGGGAAGGAAGAAATAATATTTCAC
261 TGCTCAAACTTGCTTCTGTGTTGCAACAGAAACTTCCAAAAGGGAAGGAAGAAATAATATTTCAC
*
31862 TGGGCAAAAGGGGCGTTCTGAGAATCGAACTCGGGACCTCTCGCACCCAAAGCGAGAATCATACC
326 TGGGCAAAAGGGGCGTTCCGAGAATCGAACTCGGGACCTCTCGCACCCAAAGCGAGAATCATACC
*
31927 ATTAGACCAAACGCCCACTCGATAAGTAATACTACAACTATAGCTC
391 ACTAGACCAAACGCCCACTCGATAAGTAATACTACAACTATAGCTC
*
31973 TAATTATATTATTTTATTATATTAGAAATTACCATACACAAAATGTACACGGGAAAAAAAAATAT
1 TAATTATATTATTTTATTATATTAAAAATTACCATACACAAAATGTACAC-GG-AAAAAAAATAT
32038 TTGACATATAAAAATTATATATAAAGAAAAATATATAAAAAAAAATAGTTAATGTTTTTTAAAAA
64 TTGAC--ATAAAAATTATATATAAAGAAAAATATATAAAAAAAAATAGTTAATGTTTTTTAAAAA
*
32103 ATAAAAGATTTAAAAAAAAATTC-ATTGGGATTCCTAAAATGCCATGTTTGTGTGGGTGTGAAAC
127 ATAAAAGATTTAAAAAAAAATTCTATTGGGATTCATAAAATGCCATGTTTGTGTGGGTGTGAAAC
* *
32167 AAGTGTTGGTCGAAAGGGTTGGTTAACGAAGCTGTTTTTACTTCCATATACCACAAAAGGGAAAT
192 AAGTGTTGGTCGAAAGGGTTGGTTAAAGAAACTGTTTTTACTTCCATATACCACAAAAGGGAAAT
*
32232 TCCATGCTCAAACTTGCTTCTGTGTTGCAACAGAACCTTCCAAAAGGGAAGGAAGAAATAATATT
257 TCCATGCTCAAACTTGCTTCTGTGTTGCAACAGAAACTTCCAAAAGGGAAGGAAGAAATAATATT
*
32297 TCACTGGGCTAAAGGGGCGTTCCGAGAATCGAACTCGGGACCTCTCGCACCCAAAGCGAGAATCA
322 TCACTGGGCAAAAGGGGCGTTCCGAGAATCGAACTCGGGACCTCTCGCACCCAAAGCGAGAATCA
*
32362 TACCACTAGACCAAACGCCCATTCGAT
387 TACCACTAGACCAAACGCCCACTCGAT
32389 GCTTGTTCGA
Statistics
Matches: 396, Mismatches: 16, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
436 47 0.12
437 2 0.01
438 16 0.04
439 251 0.63
440 80 0.20
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (436 bp):
TAATTATATTATTTTATTATATTAAAAATTACCATACACAAAATGTACACGGAAAAAAAATATTT
GACATAAAAATTATATATAAAGAAAAATATATAAAAAAAAATAGTTAATGTTTTTTAAAAAATAA
AAGATTTAAAAAAAAATTCTATTGGGATTCATAAAATGCCATGTTTGTGTGGGTGTGAAACAAGT
GTTGGTCGAAAGGGTTGGTTAAAGAAACTGTTTTTACTTCCATATACCACAAAAGGGAAATTCCA
TGCTCAAACTTGCTTCTGTGTTGCAACAGAAACTTCCAAAAGGGAAGGAAGAAATAATATTTCAC
TGGGCAAAAGGGGCGTTCCGAGAATCGAACTCGGGACCTCTCGCACCCAAAGCGAGAATCATACC
ACTAGACCAAACGCCCACTCGATAAGTAATACTACAACTATAGCTC
Found at i:33259 original size:18 final size:18
Alignment explanation
Indices: 33221--33259 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
33211 ATTTTCAATG
* * *
33221 TTTTCATTTTTTTTTTGT
1 TTTTCAATTTTTTTGTAT
33239 TTTTCAATTTTTTTGTAT
1 TTTTCAATTTTTTTGTAT
33257 TTT
1 TTT
33260 AAAAATATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.79
Consensus pattern (18 bp):
TTTTCAATTTTTTTGTAT
Found at i:34506 original size:32 final size:33
Alignment explanation
Indices: 34463--34544 Score: 118
Period size: 31 Copynumber: 2.6 Consensus size: 33
34453 GGTTGATATG
*
34463 TTTTTTT-TTAATTTGGTACT-TGAACTTGACA
1 TTTTTTTCTTAATTTGGTACTATGAACTTAACA
34494 TTTTTTTCTTAATTTGGTA-TATGAACTTAACA
1 TTTTTTTCTTAATTTGGTACTATGAACTTAACA
*
34526 -TTTTTTCCTAATTTGGTAC
1 TTTTTTTCTTAATTTGGTAC
34545 CTAAGGTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
31 25 0.54
32 21 0.46
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (33 bp):
TTTTTTTCTTAATTTGGTACTATGAACTTAACA
Found at i:36102 original size:22 final size:20
Alignment explanation
Indices: 36072--36112 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
36062 AATCAGCATA
36072 ATACAAAAAATATATATATTAT
1 ATAC-AAAAATA-ATATATTAT
*
36094 ATACCAAAATAATATATTA
1 ATACAAAAATAATATATTA
36113 GAAATCAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (20 bp):
ATACAAAAATAATATATTAT
Found at i:36162 original size:51 final size:53
Alignment explanation
Indices: 36057--36162 Score: 189
Period size: 51 Copynumber: 2.0 Consensus size: 53
36047 AATCAGATCT
*
36057 TTAGAAATCAGCATAATACAAAAAATATATATATTATATACCAAAATAATATA
1 TTAGAAATCAGCATAATACAAAAAATATAAATATTATATACCAAAATAATATA
36110 TTAGAAATCAGCATAATACAAAAAA-A-AAATATTATATACCAAAATAATATA
1 TTAGAAATCAGCATAATACAAAAAATATAAATATTATATACCAAAATAATATA
36161 TT
1 TT
36163 CTCCCCATTA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
51 26 0.50
52 1 0.02
53 25 0.48
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.29
Consensus pattern (53 bp):
TTAGAAATCAGCATAATACAAAAAATATAAATATTATATACCAAAATAATATA
Found at i:36404 original size:27 final size:27
Alignment explanation
Indices: 36365--36428 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
36355 TTTTTGGGTG
*
36365 GTGCCTACCTGATAGGCGGCACCAATA
1 GTGCCTACCTGATAGGCAGCACCAATA
* *
36392 GTGCCTACTTGATAGGCAGCACCAATG
1 GTGCCTACCTGATAGGCAGCACCAATA
36419 GTGCCTACCT
1 GTGCCTACCT
36429 ACCAGGTGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (27 bp):
GTGCCTACCTGATAGGCAGCACCAATA
Found at i:36772 original size:17 final size:17
Alignment explanation
Indices: 36750--36783 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
36740 CTAAAAATTC
*
36750 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
36767 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
36784 TCATGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:37282 original size:33 final size:32
Alignment explanation
Indices: 37211--37282 Score: 76
Period size: 33 Copynumber: 2.2 Consensus size: 32
37201 TTCTACTATA
*
37211 TTAAAATTTAAAAAATATATATTTTTGAATAT
1 TTAAAATTTAAAAAATAAATATTTTTGAATAT
* *
37243 TAAAAATTTGAAATAAA-AAATATTTTT-AATTTT
1 TTAAAATTT-AAA-AAATAAATATTTTTGAA-TAT
37276 TTAAAAT
1 TTAAAAT
37283 GAAAAATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
32 10 0.30
33 20 0.61
34 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (32 bp):
TTAAAATTTAAAAAATAAATATTTTTGAATAT
Found at i:42703 original size:25 final size:26
Alignment explanation
Indices: 42654--42704 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
42644 AACCTTCTGT
* *
42654 TTCCTTTTCTTCTTCAAAACTTTTGC
1 TTCCTTTCCTTCTTCAAAACATTTGC
42680 TTCCTTTCCTTCTTCAAAA-ATTTGC
1 TTCCTTTCCTTCTTCAAAACATTTGC
42705 GGTTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.18, C:0.27, G:0.04, T:0.51
Consensus pattern (26 bp):
TTCCTTTCCTTCTTCAAAACATTTGC
Found at i:43327 original size:27 final size:27
Alignment explanation
Indices: 43270--43331 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
43260 GGCTACCAGG
* *
43270 TAGGCACCTTTGGTGCCGCCTGGTAGG
1 TAGGCACCTGTGGTGCCGCCTGGTAGA
*
43297 TAGGCACCTGTGGTGCCG-CTTGTCAGA
1 TAGGCACCTGTGGTGCCGCCTGGT-AGA
43324 TAGGCACC
1 TAGGCACC
43332 ACCCCTTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.15, C:0.27, G:0.34, T:0.24
Consensus pattern (27 bp):
TAGGCACCTGTGGTGCCGCCTGGTAGA
Found at i:46830 original size:23 final size:23
Alignment explanation
Indices: 46787--46832 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
46777 AATAATTATA
*
46787 ATATATTTAATATTTTTAATTTG
1 ATATATTTAATATTTTAAATTTG
*
46810 ATATATTT-ATGTGTTTAAATTTG
1 ATATATTTAATAT-TTTAAATTTG
46833 GTTTTACTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.59
Consensus pattern (23 bp):
ATATATTTAATATTTTAAATTTG
Found at i:47327 original size:2 final size:2
Alignment explanation
Indices: 47320--47345 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47310 AATGCGACTT
47320 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
47346 AAACATAAAT
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:54703 original size:16 final size:16
Alignment explanation
Indices: 54682--54717 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
54672 CATGCTATTT
* *
54682 AAATTTTGGATTTTTA
1 AAATTTAGGATTTTCA
54698 AAATTTAGGATTTTCA
1 AAATTTAGGATTTTCA
54714 AAAT
1 AAAT
54718 CCAAGATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (16 bp):
AAATTTAGGATTTTCA
Found at i:56400 original size:23 final size:23
Alignment explanation
Indices: 56345--56401 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
56335 CTATTTTTAT
*
56345 ATAAAATAAATTTAAAAAAAATA
1 ATAAAATAAATATAAAAAAAATA
* * **
56368 ATACATTAAATATACTAAAAATA
1 ATAAAATAAATATAAAAAAAATA
*
56391 TTAAAATAAAT
1 ATAAAATAAAT
56402 GTTTCTCAAC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (23 bp):
ATAAAATAAATATAAAAAAAATA
Found at i:61864 original size:21 final size:21
Alignment explanation
Indices: 61840--61895 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
61830 GCATCCAAGT
61840 ATTATTAAATTGACATCTAAA
1 ATTATTAAATTGACATCTAAA
*
61861 ATTATTATAAGTT-A-ATTTAAA
1 ATTATTA-AA-TTGACATCTAAA
61882 ATTATT-AATTGACA
1 ATTATTAAATTGACA
61896 GTTAAACGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
18 2 0.07
19 3 0.10
20 1 0.03
21 19 0.63
22 3 0.10
23 2 0.07
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (21 bp):
ATTATTAAATTGACATCTAAA
Found at i:63527 original size:40 final size:40
Alignment explanation
Indices: 63422--63529 Score: 137
Period size: 40 Copynumber: 2.7 Consensus size: 40
63412 TATCAAATTT
*
63422 TGAACTAGCAGTGACATTGAAAACACTGCGATATCTCTAC
1 TGAACTGGCAGTGACATTGAAAACACTGCGATATCTCTAC
* * * **
63462 TGAACTGGCAGTCATACTGTGAACACTAG-GATATCTCTAC
1 TGAACTGGCAGTGACATTGAAAACACT-GCGATATCTCTAC
*
63502 TGAATTGGCAGTGACATTGAAAACACTG
1 TGAACTGGCAGTGACATTGAAAACACTG
63530 TGGTAATATT
Statistics
Matches: 55, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
39 1 0.02
40 53 0.96
41 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (40 bp):
TGAACTGGCAGTGACATTGAAAACACTGCGATATCTCTAC
Found at i:70312 original size:29 final size:28
Alignment explanation
Indices: 70243--70550 Score: 215
Period size: 29 Copynumber: 10.8 Consensus size: 28
70233 TTGGACATCC
* * *
70243 GGGGGAAAAATGGTAATTTTCAAAAGTTTT
1 GGGGTAAAAATGG-AATTTTTAGAAG-TTT
70273 GGGGTCAAAAATGGAATTTTTAGAAGTTT
1 GGGGT-AAAAATGGAATTTTTAGAAGTTT
70302 GTGGGTAAAAATGGAA----T-----TTT
1 G-GGGTAAAAATGGAATTTTTAGAAGTTT
70322 GGGGTCAAAAATGGAATTTTTAGAAGTTT
1 GGGGT-AAAAATGGAATTTTTAGAAGTTT
70351 GAGGGTAAAAATGGAATTTTT-GAAAGTTT
1 G-GGGTAAAAATGGAATTTTTAG-AAGTTT
* * * *
70380 CGGCGTTAAAAATAGAATTTTTGGAAGTTC
1 -GG-GGTAAAAATGGAATTTTTAGAAGTTT
* * * *
70410 GAGGGTTAAAATGAAATTTTTGGAAGTTC
1 G-GGGTAAAAATGGAATTTTTAGAAGTTT
* * *
70439 GAGAGTAAAAATGGAA-TTTTCGAAAGTTC
1 G-GGGTAAAAATGGAATTTTTAG-AAGTTT
* *
70468 GGAGGTAAAAATGGAATTTTTGGAAATTT
1 GG-GGTAAAAATGGAATTTTTAGAAGTTT
* *
70497 CGGGGTCGAAAATGGAATTTTTGGAAGTTT
1 -GGGGT-AAAAATGGAATTTTTAGAAGTTT
* *
70527 GGGGGCAAAAATGTAATTTTTAGA
1 -GGGGTAAAAATGGAATTTTTAGA
70551 TAATTTAAGG
Statistics
Matches: 230, Mismatches: 25, Indels: 47
0.76 0.08 0.16
Matches are distributed among these distances:
19 4 0.02
20 14 0.06
24 1 0.00
25 1 0.00
28 7 0.03
29 117 0.51
30 77 0.33
31 9 0.04
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (28 bp):
GGGGTAAAAATGGAATTTTTAGAAGTTT
Found at i:70328 original size:49 final size:49
Alignment explanation
Indices: 70269--70370 Score: 195
Period size: 49 Copynumber: 2.1 Consensus size: 49
70259 TTTTCAAAAG
*
70269 TTTTGGGGTCAAAAATGGAATTTTTAGAAGTTTGTGGGTAAAAATGGAA
1 TTTTGGGGTCAAAAATGGAATTTTTAGAAGTTTGAGGGTAAAAATGGAA
70318 TTTTGGGGTCAAAAATGGAATTTTTAGAAGTTTGAGGGTAAAAATGGAA
1 TTTTGGGGTCAAAAATGGAATTTTTAGAAGTTTGAGGGTAAAAATGGAA
70367 TTTT
1 TTTT
70371 TGAAAGTTTC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.36
Consensus pattern (49 bp):
TTTTGGGGTCAAAAATGGAATTTTTAGAAGTTTGAGGGTAAAAATGGAA
Found at i:70331 original size:20 final size:20
Alignment explanation
Indices: 70299--70341 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
70289 TTTTTAGAAG
70299 TTTGTGGGTAAAAATGGAAT
1 TTTGTGGGTAAAAATGGAAT
70319 TTTG-GGGTCAAAAATGGAAT
1 TTTGTGGGT-AAAAATGGAAT
70339 TTT
1 TTT
70342 TAGAAGTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (20 bp):
TTTGTGGGTAAAAATGGAAT
Found at i:70421 original size:59 final size:59
Alignment explanation
Indices: 70328--70547 Score: 241
Period size: 59 Copynumber: 3.7 Consensus size: 59
70318 TTTTGGGGTC
* * *
70328 AAAAATGGAATTTTTAGAAGTTTGAGGGTAAAAATGGAATTTTTGAAAGTTTCGGCGTT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGTTTCGGAGTT
* * * *
70387 AAAAATAGAATTTTTGGAAGTTCGAGGGTTAAAATGAAATTTTTGGAAG-TTCGAGAG-T
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGTTTCG-GAGTT
* * * *
70445 AAAAATGGAATTTTCGAAAGTTCG-GAGGTAAAAATGGAATTTTTGGAAA-TTTCGGGGTC
1 AAAAATGGAATTTTTGGAAGTTCGAG-GGTAAAAATGGAATTTTT-GAAAGTTTCGGAGTT
* * * * *
70504 GAAAATGGAATTTTTGGAAGTTTGGGGGCAAAAATGTAATTTTT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTT
70548 AGATAATTTA
Statistics
Matches: 134, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
57 1 0.01
58 44 0.33
59 88 0.66
60 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGTTTCGGAGTT
Found at i:70537 original size:88 final size:88
Alignment explanation
Indices: 70313--70546 Score: 301
Period size: 88 Copynumber: 2.7 Consensus size: 88
70303 TGGGTAAAAA
* * *
70313 TGGAATTTTGGGGTCAAAAATGGAATTTTTAGAAGTTTGAGGGTAAAAATGGAATTTTTGAAAGT
1 TGGAATTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTCGAAAGT
* *
70378 TTCGGCGTTAAAAATAGAATTTT
66 TTCGGAGGTAAAAATAGAATTTT
* * * * *
70401 TGGAAGTTCGAGGGT-TAAAATGAAATTTTTGGAAGTTCGAGAGTAAAAATGGAATTTTCGAAAG
1 TGGAATTTCG-GGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTCGAAAG
*
70465 -TTCGGAGGTAAAAATGGAATTTT
65 TTTCGGAGGTAAAAATAGAATTTT
* * * *
70488 TGGAAATTTCGGGGTCGAAAATGGAATTTTTGGAAGTTTGGGGGCAAAAATGTAATTTT
1 TGG-AATTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTT
70547 TAGATAATTT
Statistics
Matches: 124, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
87 27 0.22
88 93 0.75
89 4 0.03
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (88 bp):
TGGAATTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTCGAAAGT
TTCGGAGGTAAAAATAGAATTTT
Found at i:71130 original size:3 final size:3
Alignment explanation
Indices: 71122--71191 Score: 90
Period size: 3 Copynumber: 24.0 Consensus size: 3
71112 TAATATTTAA
* * * *
71122 TAT TAT TAT TAT TAT TAT TAT TAT TA- AAA CAG T-T TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
71168 TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
71192 ACTTATGAGC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
2 2 0.03
3 58 0.97
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:71897 original size:6 final size:6
Alignment explanation
Indices: 71886--71936 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
71876 TCAAATTTGA
**
71886 TTAAAT TTAAAT TTAAA- GCAAAT TTAAAT TTAAGA- -TAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT
71932 TTAAA
1 TTAAA
71937 AAAGAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 1 0.03
5 6 0.16
6 29 0.78
7 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:71910 original size:17 final size:18
Alignment explanation
Indices: 71888--71936 Score: 75
Period size: 17 Copynumber: 2.8 Consensus size: 18
71878 AAATTTGATT
71888 AAATTTAAATTTAAAG-C
1 AAATTTAAATTTAAAGAC
*
71905 AAATTTAAATTT-AAGAT
1 AAATTTAAATTTAAAGAC
71922 AAATTTAAATTTAAA
1 AAATTTAAATTTAAA
71937 AAAGAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 3 0.10
17 24 0.83
18 2 0.07
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (18 bp):
AAATTTAAATTTAAAGAC
Done.