Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010840.1 Kokia drynarioides strain JFW-HI SEQ_125807, 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: 144851
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 234 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--43 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
* *
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43 T
1 T
44 GTTAAAATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9369 original size:20 final size:20
Alignment explanation
Indices: 9337--9374 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9327 AAAAGGGGGA
9337 ATTTGGATCCATGTTTTGCC
1 ATTTGGATCCATGTTTTGCC
9357 ATTTGTGAT-CATGTTTTG
1 ATTTG-GATCCATGTTTTG
9375 ATAAACATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.16, C:0.13, G:0.21, T:0.50
Consensus pattern (20 bp):
ATTTGGATCCATGTTTTGCC
Found at i:13940 original size:16 final size:15
Alignment explanation
Indices: 13903--13945 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
13893 GGTTAATATG
13903 ATCTCCCAAAATTAA
1 ATCTCCCAAAATTAA
* * *
13918 ATATCCCTAATTTGAA
1 ATCTCCCAAAATT-AA
13934 ATCTCCCAAAAT
1 ATCTCCCAAAAT
13946 CACTACTGCC
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (15 bp):
ATCTCCCAAAATTAA
Found at i:21028 original size:18 final size:19
Alignment explanation
Indices: 20989--21033 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
20979 ACATTTTATG
*
20989 TTTTAAACTTTATATATAT
1 TTTTAAAATTTATATATAT
*
21008 TTTTAAAATTTATA-ATTT
1 TTTTAAAATTTATATATAT
21026 TTTTAAAA
1 TTTTAAAA
21034 ATATAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTAAAATTTATATATAT
Found at i:21038 original size:17 final size:19
Alignment explanation
Indices: 21007--21044 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
20997 TTTATATATA
*
21007 TTTTTAAAATTTAT-AATT
1 TTTTTAAAATATATAAATT
21025 TTTTTAAAA-ATATAAATT
1 TTTTTAAAATATATAAATT
21043 TT
1 TT
21045 GGAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTAAAATATATAAATT
Found at i:25212 original size:13 final size:13
Alignment explanation
Indices: 25194--25219 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25184 AAATTATTAT
25194 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
25207 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
25220 CTTTACATGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:27074 original size:26 final size:25
Alignment explanation
Indices: 27045--27096 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
27035 TTGACTTCAA
*
27045 TATTCAAATTGGTACCTAAGTTTTTT
1 TATT-AAATTGATACCTAAGTTTTTT
* * *
27071 TATTTATTTGATACCTGAGTTTTTT
1 TATTAAATTGATACCTAAGTTTTTT
27096 T
1 T
27097 GGTCCTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.23, C:0.10, G:0.12, T:0.56
Consensus pattern (25 bp):
TATTAAATTGATACCTAAGTTTTTT
Found at i:39478 original size:6 final size:6
Alignment explanation
Indices: 39467--39562 Score: 75
Period size: 6 Copynumber: 17.0 Consensus size: 6
39457 GACCCAACAT
* * *
39467 AATTTA AATTT- ATTTTA AATTTA AATTT- -ATTTCA AGTTTA AATCT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
39512 -ATTTAA AATTTA AATTT- -ATTATA AATTTA AATTTA AATTT- -ATTTA
1 AATTT-A AATTTA AATTTA AATT-TA AATTTA AATTTA AATTTA AATTTA
39557 AATTTA
1 AATTTA
39563 TAATGTCCAA
Statistics
Matches: 72, Mismatches: 6, Indels: 24
0.71 0.06 0.24
Matches are distributed among these distances:
4 14 0.19
5 5 0.07
6 43 0.60
7 10 0.14
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:39489 original size:17 final size:17
Alignment explanation
Indices: 39467--39563 Score: 117
Period size: 17 Copynumber: 5.8 Consensus size: 17
39457 GACCCAACAT
39467 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
*
39484 AATTTAAATTTATTTCA
1 AATTTAAATTTATTTTA
* * *
39501 AGTTTAAATCTATTTAA
1 AATTTAAATTTATTTTA
*
39518 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
*
39535 AATTTAAATTTAAATTT-
1 AATTTAAATTT-ATTTTA
39552 -ATTTAAATTTAT
1 AATTTAAATTTAT
39564 AATGTCCAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
15 1 0.01
16 10 0.15
17 54 0.79
18 3 0.04
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:39529 original size:23 final size:21
Alignment explanation
Indices: 39512--39562 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 21
39502 GTTTAAATCT
39512 ATTTAAAATTTAAATTTATTATAA
1 ATTT-AAATTTAAA-TTATT-TAA
39536 ATTTAAATTTAAATTTATTTAA
1 ATTTAAATTTAAA-TTATTTAA
39558 ATTTA
1 ATTTA
39563 TAATGTCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 8 0.30
23 15 0.56
24 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAAATTTAAATTATTTAA
Found at i:40277 original size:9 final size:9
Alignment explanation
Indices: 40266--40351 Score: 82
Period size: 9 Copynumber: 9.6 Consensus size: 9
40256 TAAATATTTT
*
40266 TAATAACAT
1 TAATAACAA
*
40275 TAATAATAA
1 TAATAACAA
*
40284 TAATAATAA
1 TAATAACAA
40293 TAATAACAA
1 TAATAACAA
* *
40302 CAACAACAA
1 TAATAACAA
* *
40311 CAACAACAA
1 TAATAACAA
*
40320 TAATAATAA
1 TAATAACAA
*
40329 TAATAATAA
1 TAATAACAA
*
40338 TAATAATAA
1 TAATAACAA
40347 TAATA
1 TAATA
40352 TAAAAAAGTT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 69 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (9 bp):
TAATAACAA
Found at i:40283 original size:3 final size:3
Alignment explanation
Indices: 40275--40351 Score: 91
Period size: 3 Copynumber: 25.7 Consensus size: 3
40265 TTAATAACAT
* * * * * * *
40275 TAA TAA TAA TAA TAA TAA TAA TAA CAA CAA CAA CAA CAA CAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40323 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
40352 TAAAAAAGTT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (3 bp):
TAA
Found at i:44897 original size:24 final size:24
Alignment explanation
Indices: 44869--44917 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
44859 ATCCGAAAAG
*
44869 TAAAATTCTTATACATTTTGGAAA
1 TAAAACTCTTATACATTTTGGAAA
44893 TAAAACTCTTATACATTTTGGAAA
1 TAAAACTCTTATACATTTTGGAAA
44917 T
1 T
44918 TTAAAATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (24 bp):
TAAAACTCTTATACATTTTGGAAA
Found at i:45141 original size:23 final size:23
Alignment explanation
Indices: 45128--45179 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
45118 TTTAACAATG
45128 ATAAAAATTAAATTTGAAAAAGT
1 ATAAAAATTAAATTTGAAAAAGT
* * *
45151 ATAAAGATTAAATTT-CAAATGT
1 ATAAAAATTAAATTTGAAAAAGT
45173 ATAAAAA
1 ATAAAAA
45180 AATAGGAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.31
Consensus pattern (23 bp):
ATAAAAATTAAATTTGAAAAAGT
Found at i:45177 original size:22 final size:23
Alignment explanation
Indices: 45107--45179 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 23
45097 AATCTAAATT
* *
45107 TAAAAAAT-AATTTTAACAATG-A
1 TAAAAATTAAATTTGAA-AATGTA
*
45129 TAAAAATTAAATTTGAAAAAGTA
1 TAAAAATTAAATTTGAAAATGTA
* *
45152 TAAAGATTAAATTT-CAAATGTA
1 TAAAAATTAAATTTGAAAATGTA
45174 TAAAAA
1 TAAAAA
45180 AATAGGAAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
22 21 0.50
23 21 0.50
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.32
Consensus pattern (23 bp):
TAAAAATTAAATTTGAAAATGTA
Found at i:45524 original size:3 final size:3
Alignment explanation
Indices: 45516--45545 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
45506 TTACTAAAAT
45516 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
45546 TACAATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:45843 original size:6 final size:6
Alignment explanation
Indices: 45832--45871 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
45822 ATGGCGAAAT
45832 TCTTCG TCTTCG TCTTCG TCTTCG TCTTCG TCTTCG TCTT
1 TCTTCG TCTTCG TCTTCG TCTTCG TCTTCG TCTTCG TCTT
45872 TCACTTGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.53
Consensus pattern (6 bp):
TCTTCG
Found at i:48591 original size:21 final size:21
Alignment explanation
Indices: 48567--48606 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
48557 TTTTTGAAAA
*
48567 ATTAAATTAAATTTTTATCGG
1 ATTAAATCAAATTTTTATCGG
48588 ATTAAATCAAATTTTTATC
1 ATTAAATCAAATTTTTATC
48607 ATTTTTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (21 bp):
ATTAAATCAAATTTTTATCGG
Found at i:50042 original size:22 final size:24
Alignment explanation
Indices: 49990--50043 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
49980 AACATCCAAT
*
49990 CAACAAAAATAACAACCAAAACAG
1 CAACAAAAATAACAAACAAAACAG
*
50014 CAGCAAAAA-AA-AAACAAAAC-G
1 CAACAAAAATAACAAACAAAACAG
50035 ACAACAAAA
1 -CAACAAAA
50044 TAGCAACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 1 0.04
22 15 0.58
23 2 0.08
24 8 0.31
ACGTcount: A:0.70, C:0.22, G:0.06, T:0.02
Consensus pattern (24 bp):
CAACAAAAATAACAAACAAAACAG
Found at i:50090 original size:35 final size:33
Alignment explanation
Indices: 49990--50112 Score: 97
Period size: 34 Copynumber: 3.6 Consensus size: 33
49980 AACATCCAAT
* * *
49990 CAACAAAAATAACAACCAAAACAGCAGCAAAAAAAA
1 CAAC-AAAACAACAA-CAAAATAGCA-AAAAAAAAA
* *
50026 -AACAAAACGACAACAAAATAGCAACAAAAATAA
1 CAACAAAACAACAACAAAATAGCAA-AAAAAAAA
* *
50059 CAACATAAACAACACCAAAATAGTAAAAAAAAAA
1 CAACA-AAACAACAACAAAATAGCAAAAAAAAAA
*
50093 C-ACTAAAACAGCAATCAAAA
1 CAAC-AAAACAACAA-CAAAA
50113 CAGTGAAAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
33 25 0.35
34 26 0.37
35 20 0.28
ACGTcount: A:0.68, C:0.20, G:0.05, T:0.07
Consensus pattern (33 bp):
CAACAAAACAACAACAAAATAGCAAAAAAAAAA
Found at i:50106 original size:57 final size:56
Alignment explanation
Indices: 49990--50112 Score: 128
Period size: 57 Copynumber: 2.1 Consensus size: 56
49980 AACATCCAAT
* * *
49990 CAACAAAAATAACAACCAAAACAGCAGCAAAAAAAAAACAAAACGACAACAAAATAG
1 CAACAAAAATAACAACCAAAACAACACCAAAAAAAAAACAAAAC-ACAACAAAACAG
50047 CAACAAAAATAACAA-CATAAACAACACCAAAATAGTAAAAA-AAAA-AC-ACTAAAACAG
1 CAACAAAAATAACAACCA-AAACAACACCAAAA-A--AAAAACAAAACACAAC-AAAACAG
50104 CAATCAAAA
1 CAA-CAAAA
50113 CAGTGAAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
56 4 0.07
57 38 0.67
58 6 0.11
59 4 0.07
60 5 0.09
ACGTcount: A:0.68, C:0.20, G:0.05, T:0.07
Consensus pattern (56 bp):
CAACAAAAATAACAACCAAAACAACACCAAAAAAAAAACAAAACACAACAAAACAG
Found at i:50114 original size:20 final size:19
Alignment explanation
Indices: 50089--50143 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
50079 TAGTAAAAAA
* *
50089 AAAACACTAAAACAGCAATC
1 AAAACAATAAAAAAGC-ATC
*
50109 AAAACAGTGAAAAAAAGCATC
1 AAAACAAT--AAAAAAGCATC
50130 AAAACAATAAAAAA
1 AAAACAATAAAAAA
50144 CAATAACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 6 0.20
20 7 0.23
21 10 0.33
22 7 0.23
ACGTcount: A:0.67, C:0.16, G:0.07, T:0.09
Consensus pattern (19 bp):
AAAACAATAAAAAAGCATC
Found at i:50121 original size:21 final size:20
Alignment explanation
Indices: 50089--50143 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
50079 TAGTAAAAAA
*
50089 AAAACACT-AAAACAGCAATC
1 AAAACACTAAAAAAAGC-ATC
*
50109 AAAACAGTGAAAAAAAGCATC
1 AAAACACT-AAAAAAAGCATC
*
50130 AAAACAATAAAAAA
1 AAAACACTAAAAAA
50144 CAATAACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.43
21 10 0.33
22 7 0.23
ACGTcount: A:0.67, C:0.16, G:0.07, T:0.09
Consensus pattern (20 bp):
AAAACACTAAAAAAAGCATC
Found at i:50122 original size:22 final size:22
Alignment explanation
Indices: 50097--50165 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
50087 AAAAAACACT
50097 AAAACAGCAATCAAAACAGTGAA
1 AAAACAGCAATCAAAACAGT-AA
*
50120 AAAA-AGC-ATCAAAACAATAA
1 AAAACAGCAATCAAAACAGTAA
** *
50140 AAAACAATAACCAAAACAGTAA
1 AAAACAGCAATCAAAACAGTAA
50162 AAAA
1 AAAA
50166 AACAACACCA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.15
21 11 0.28
22 18 0.46
23 4 0.10
ACGTcount: A:0.68, C:0.16, G:0.07, T:0.09
Consensus pattern (22 bp):
AAAACAGCAATCAAAACAGTAA
Found at i:59602 original size:26 final size:26
Alignment explanation
Indices: 59563--59612 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
59553 CTTTTTAAAG
*
59563 TCAATAAAACATTTGAACATAATTCT
1 TCAAGAAAACATTTGAACATAATTCT
*
59589 TCAAGAAAATATTTGAACATAATT
1 TCAAGAAAACATTTGAACATAATT
59613 ACATTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (26 bp):
TCAAGAAAACATTTGAACATAATTCT
Found at i:66785 original size:2 final size:2
Alignment explanation
Indices: 66778--66803 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
66768 ACGAAGACAA
66778 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
66804 TACCAAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67131 original size:20 final size:20
Alignment explanation
Indices: 67097--67137 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
67087 TCTAATTGAG
67097 TTATTTTTTAAAATTT-TAT
1 TTATTTTTTAAAATTTGTAT
*
67116 TTATTTATTTACAATTTGTAT
1 TTATTT-TTTAAAATTTGTAT
67137 T
1 T
67138 ACACCAGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 9 0.47
21 4 0.21
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
TTATTTTTTAAAATTTGTAT
Found at i:76635 original size:131 final size:131
Alignment explanation
Indices: 76370--76840 Score: 694
Period size: 131 Copynumber: 3.6 Consensus size: 131
76360 GCTTGAGTTA
* ** * * * *
76370 TAAAAAGATGGTATTTTTATTATAGGCTTATCAATGATTTCAGGTTGCTTCTTGATAAAATCTTT
1 TAAAAAAATGGTAACTTTATTTTAGTCTTATCAATGATTTCAGGTTGCTTGTTAATAAAATCTTT
* * * *
76435 TGCTTT-CCTTGT-TTTAGAAAAAAGGAAATTCTAGTGATGAATTCAAGTGCTAATCATGTAATT
66 TACTTTCCCTT-TCTTT--ATAAGATGAAATTCTAGTGATGAATTCAAGTGCTAATCATGTAATT
76498 TGAT
128 TGAT
* * * *
76502 TAAACAAATGGCAACTTTATTTTAGTCTTATCAATGATTTCAGGTTCCTTGTTAATAAAGTCTTT
1 TAAAAAAATGGTAACTTTATTTTAGTCTTATCAATGATTTCAGGTTGCTTGTTAATAAAATCTTT
* * * *
76567 TTCTTTCCCTTTCTTTATAAGATGAAATTCTAATGATGAATTCAAATGCTAATCCTGTAATTTGA
66 TACTTTCCCTTTCTTTATAAGATGAAATTCTAGTGATGAATTCAAGTGCTAATCATGTAATTTGA
76632 T
131 T
* *
76633 TAAAAAAATGGTAACTTTATTTTAGTCTTATCAATGATTTCTGGTTGCTTGCTAATAAAATCTTT
1 TAAAAAAATGGTAACTTTATTTTAGTCTTATCAATGATTTCAGGTTGCTTGTTAATAAAATCTTT
76698 TACTTTCCCTTTCTTTATAAGATGAAATTCTAGTGATGAATTCAAGTGCTAATCATGTAATTTGA
66 TACTTTCCCTTTCTTTATAAGATGAAATTCTAGTGATGAATTCAAGTGCTAATCATGTAATTTGA
76763 T
131 T
* *
76764 TAAAAAAATGGTAACTTTATTTTAGTCTTATCAATGATTTCAGGTTGCTTGTTGATAAAATCTTG
1 TAAAAAAATGGTAACTTTATTTTAGTCTTATCAATGATTTCAGGTTGCTTGTTAATAAAATCTTT
76829 TACTTTCCCTTT
66 TACTTTCCCTTT
76841 TTTGTAGAAA
Statistics
Matches: 305, Mismatches: 32, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
131 238 0.78
132 60 0.20
133 7 0.02
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (131 bp):
TAAAAAAATGGTAACTTTATTTTAGTCTTATCAATGATTTCAGGTTGCTTGTTAATAAAATCTTT
TACTTTCCCTTTCTTTATAAGATGAAATTCTAGTGATGAATTCAAGTGCTAATCATGTAATTTGA
T
Found at i:83755 original size:30 final size:31
Alignment explanation
Indices: 83687--83756 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
83677 AAATTATATA
*
83687 ATTTTGGTACCAGAATTTAGTAGCTGGATTC
1 ATTTTGGTCCCAGAATTTAGTAGCTGGATTC
* *
83718 ATTTTGGTCCCTGAATTTAGTAGTTGGATT-
1 ATTTTGGTCCCAGAATTTAGTAGCTGGATTC
*
83748 TTTTTGGTC
1 ATTTTGGTC
83757 TTGGAACTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
30 8 0.23
31 27 0.77
ACGTcount: A:0.20, C:0.11, G:0.23, T:0.46
Consensus pattern (31 bp):
ATTTTGGTCCCAGAATTTAGTAGCTGGATTC
Found at i:88833 original size:12 final size:12
Alignment explanation
Indices: 88816--88840 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
88806 TCATCCCATC
88816 AAATAAATAAGA
1 AAATAAATAAGA
88828 AAATAAATAAGA
1 AAATAAATAAGA
88840 A
1 A
88841 TATATTCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AAATAAATAAGA
Found at i:111745 original size:12 final size:12
Alignment explanation
Indices: 111728--111752 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
111718 TAAATGATTG
111728 ATTTTTTTTTTT
1 ATTTTTTTTTTT
111740 ATTTTTTTTTTT
1 ATTTTTTTTTTT
111752 A
1 A
111753 CAATTTTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (12 bp):
ATTTTTTTTTTT
Found at i:117490 original size:40 final size:39
Alignment explanation
Indices: 117438--117523 Score: 154
Period size: 40 Copynumber: 2.2 Consensus size: 39
117428 GAAAAAAGGT
*
117438 AAAAATAAATAAATAAATAAACATTGAAAAGTTCAAAAA
1 AAAAAAAAATAAATAAATAAACATTGAAAAGTTCAAAAA
117477 AAAAAAAANATAAATAAATAAACATTGAAAAGTTCAAAAA
1 AAAAAAAA-ATAAATAAATAAACATTGAAAAGTTCAAAAA
117517 AAAAAAA
1 AAAAAAA
117524 GGGTCGGCTT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 7 0.16
40 38 0.84
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.17
Consensus pattern (39 bp):
AAAAAAAAATAAATAAATAAACATTGAAAAGTTCAAAAA
Found at i:127946 original size:236 final size:232
Alignment explanation
Indices: 127526--127995 Score: 753
Period size: 236 Copynumber: 2.0 Consensus size: 232
127516 ATTTTTTTTA
*
127526 TTCATTTATTTGAAACGGTTTTTTTCTCTTCTATCATCGTCATCATTCTACCAAGTCTATCTCTT
1 TTCATTTATTTGAAACGGTTTTTTTATCTTCTATCATCGTCATCATTCTACCAAGTCTATCTCTT
* *
127591 CTCTCTCATATTTTCAAATCAAAGTGTTTCTTTATTTTTTTTTTCTCTCTTATCAGTTCTCACCC
66 CTCTCTCATATTTGCAAATCAAAGTGTTTCTTTATTTCTTTTTTCTCTCTTATCAGTTCTCACCC
* * *
127656 ACCGCCATGTCCACCGCTTTTCACCAGATCTGATCCATATCCCACGTTGGATCATGTTAACACGG
131 ACCGCCATGTCCACCGCTTTTCACCAGATCCGATCCATATCCCACGTAGGATCATGTCAACACGG
127721 GTACGGCACCCCAAACTGCCAAATCCGGCTAAGGAAG
196 GTACGGCACCCCAAACTGCCAAATCCGGCTAAGGAAG
* *
127758 TTCATTTATTTTAAACGGTTTTTTTTTATCTTCTATCATCGTCATCATTCTACCATGTCTATCTC
1 TTCATTTATTTGAAACGG--TTTTTTTATCTTCTATCATCGTCATCATTCTACCAAGTCTATCTC
* * * *
127823 TTCTCTCTCATCTTTGCAAATCAAAGTGTTTTTTTCGTCTTCTTTTTTCTCTCTTATCAGTTCTT
64 TTCTCTCTCATATTTGCAAATCAAAGTGTTTCTTT-AT-TTCTTTTTTCTCTCTTATCAGTTCTC
127888 ACCCACCGCCATGTCCACCGCTTTTCACCAGATCCGAT-CAGTATCCCACGTAGGATCATGTCAA
127 ACCCACCGCCATGTCCACCGCTTTTCACCAGATCCGATCCA-TATCCCACGTAGGATCATGTCAA
* * *
127952 CACGGGTATGGCACCCCAAACTGCCAAATCTGGCTAATGAAG
191 CACGGGTACGGCACCCCAAACTGCCAAATCCGGCTAAGGAAG
127994 TT
1 TT
127996 TCTCACTAGT
Statistics
Matches: 218, Mismatches: 15, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
232 17 0.08
234 75 0.34
235 3 0.01
236 123 0.56
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.38
Consensus pattern (232 bp):
TTCATTTATTTGAAACGGTTTTTTTATCTTCTATCATCGTCATCATTCTACCAAGTCTATCTCTT
CTCTCTCATATTTGCAAATCAAAGTGTTTCTTTATTTCTTTTTTCTCTCTTATCAGTTCTCACCC
ACCGCCATGTCCACCGCTTTTCACCAGATCCGATCCATATCCCACGTAGGATCATGTCAACACGG
GTACGGCACCCCAAACTGCCAAATCCGGCTAAGGAAG
Found at i:128935 original size:109 final size:110
Alignment explanation
Indices: 128744--128944 Score: 311
Period size: 109 Copynumber: 1.8 Consensus size: 110
128734 GCTATAAATA
*
128744 GCATACCTGTAAAAGTGCAGCAATAGTACCAAAAGAATTCCACAACAATGGAGCCAAATCTTGAA
1 GCATACCTGTAAAAGTGCAGCAATAGTACCAAAAGAATTCCACAACAAAGGAGCCAAATCTTGAA
128809 ATAATTCTCTCTTCT-AAAAATAAAAACAAAAACAAGTTTATTAG
66 ATAATTCTCTCTTCTAAAAAATAAAAACAAAAACAAGTTTATTAG
* *
128853 GCATACCTG-AATGAGTGCAGCTATAGTACCAAAAGAATTCCAC-ACGAAAGGAGCCAAATCTTG
1 GCATACCTGTAA-AAGTGCAGCAATAGTACCAAAAGAATTCCACAAC-AAAGGAGCCAAATCTTG
*
128916 AAATAATTC-CTTGTTCTAAAAAATAAAAA
64 AAATAATTCTC-TCTTCTAAAAAATAAAAA
128945 GGTAGACGCT
Statistics
Matches: 84, Mismatches: 4, Indels: 7
0.88 0.04 0.07
Matches are distributed among these distances:
108 5 0.06
109 68 0.81
110 11 0.13
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.23
Consensus pattern (110 bp):
GCATACCTGTAAAAGTGCAGCAATAGTACCAAAAGAATTCCACAACAAAGGAGCCAAATCTTGAA
ATAATTCTCTCTTCTAAAAAATAAAAACAAAAACAAGTTTATTAG
Found at i:133538 original size:19 final size:18
Alignment explanation
Indices: 133492--133542 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
133482 ATAAAAAAAA
*
133492 AAAATTCAAAATAATGTT
1 AAAATTCAAATTAATGTT
*
133510 AAGAACTTCAAATTAAATTTT
1 AA-AA-TTCAAATT-AATGTT
133531 AAAATTCAAATT
1 AAAATTCAAATT
133543 TTATATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 2 0.07
19 10 0.36
20 9 0.32
21 7 0.25
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (18 bp):
AAAATTCAAATTAATGTT
Found at i:135345 original size:17 final size:18
Alignment explanation
Indices: 135306--135348 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
135296 TCTTTGAAAT
135306 TAAAATTAAGAATTATAA
1 TAAAATTAAGAATTATAA
* * *
135324 AAAAATTAA-ATTTATTA
1 TAAAATTAAGAATTATAA
135341 TAAAATTA
1 TAAAATTA
135349 TTTGTAAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
TAAAATTAAGAATTATAA
Found at i:140759 original size:39 final size:39
Alignment explanation
Indices: 140704--140783 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 39
140694 GCCGGTTAGT
***
140704 GTTTTGTGTTTATGTGACATTGATTTGCTTCTATTAGCG
1 GTTTTGTGTTTATGTGACAGCCATTTGCTTCTATTAGCG
* *
140743 GTTTTGTGTTTGTGTGACGGCCATTTGCTTCTATTAGCG
1 GTTTTGTGTTTATGTGACAGCCATTTGCTTCTATTAGCG
140782 GT
1 GT
140784 ACGTGAGTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.12, C:0.12, G:0.26, T:0.49
Consensus pattern (39 bp):
GTTTTGTGTTTATGTGACAGCCATTTGCTTCTATTAGCG
Done.