Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007954.1 Kokia drynarioides strain JFW-HI SEQ_122602, 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: 151835
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1198 original size:31 final size:31
Alignment explanation
Indices: 1134--1199 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
1124 GTTGAAAAAC
* *
1134 AATTCAACTCTTTTTAAAGGAATGAGGGTCA
1 AATTCAACTCTTTTTAAAGGAATAAGGGACA
* *
1165 AATTCAACTTTTTTTAAATGG-TTAAGGGACA
1 AATTCAACTCTTTTTAAA-GGAATAAGGGACA
1196 AATT
1 AATT
1200 TAGTTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (31 bp):
AATTCAACTCTTTTTAAAGGAATAAGGGACA
Found at i:44284 original size:17 final size:17
Alignment explanation
Indices: 44205--44299 Score: 102
Period size: 17 Copynumber: 5.6 Consensus size: 17
44195 AATTGAATCC
*
44205 AAATTTTAATTTATTTT
1 AAATTTAAATTTATTTT
*
44222 AAGTTT-AATTTATTTT
1 AAATTTAAATTTATTTT
* *
44238 AAATTTAAACTCATTTT
1 AAATTTAAATTTATTTT
* * * *
44255 GAGTTTGAATTTACTTT
1 AAATTTAAATTTATTTT
44272 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
*
44289 AAATTGAAATT
1 AAATTTAAATT
44300 AATTAAAAAG
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
16 15 0.24
17 47 0.76
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:44967 original size:3 final size:3
Alignment explanation
Indices: 44954--44999 Score: 65
Period size: 3 Copynumber: 14.7 Consensus size: 3
44944 TTTACTTTGC
*
44954 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATTT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AA
45000 ACAAACAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 34 0.87
4 5 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:47207 original size:20 final size:20
Alignment explanation
Indices: 47182--47220 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
47172 TAATAATATT
47182 TAATTAATTTAATATTAAAA
1 TAATTAATTTAATATTAAAA
*
47202 TAATTATTTTAATATTAAA
1 TAATTAATTTAATATTAAA
47221 TTAAATCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATTAATTTAATATTAAAA
Found at i:47221 original size:19 final size:19
Alignment explanation
Indices: 47161--47221 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
47151 AATCTAATTT
* *
47161 AATAATTATCTTAATAATA
1 AATAATTATTTTAATATTA
** *
47180 TTTAATTAATTTAATATTAA
1 AATAATTATTTTAATATT-A
47200 AATAATTATTTTAATATTA
1 AATAATTATTTTAATATTA
47219 AAT
1 AAT
47222 TAAATCTAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
AATAATTATTTTAATATTA
Found at i:54129 original size:20 final size:19
Alignment explanation
Indices: 54092--54128 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
54082 AAAAAAAGAG
*
54092 TTTGGAGGATTTTTTTTTA
1 TTTGGAAGATTTTTTTTTA
54111 TTTGGAAGATTTTTTTTT
1 TTTGGAAGATTTTTTTTT
54129 TTTAAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.19, T:0.65
Consensus pattern (19 bp):
TTTGGAAGATTTTTTTTTA
Found at i:58469 original size:16 final size:18
Alignment explanation
Indices: 58435--58476 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
58425 ACAGTTATTC
58435 AATTAAATATATACGAT-AA
1 AATT-AATATATAC-ATAAA
58454 AATTAATATATA-ATAAA
1 AATTAATATATACATAAA
58471 AATTAA
1 AATTAA
58477 CTTATTTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 2 0.09
17 8 0.36
18 8 0.36
19 4 0.18
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
AATTAATATATACATAAA
Found at i:59179 original size:2 final size:2
Alignment explanation
Indices: 59172--59212 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
59162 TAGGGTTCAC
59172 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
59213 AGAGAGTGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:67442 original size:34 final size:34
Alignment explanation
Indices: 67370--67462 Score: 107
Period size: 34 Copynumber: 2.7 Consensus size: 34
67360 AGTTTTTTAT
* * * * *
67370 ATTTTTATAAATTTTTTAAATATATAAATTTTGAA
1 ATTTTGATAAATATTTTGAAT-TTTAAAATTTGAA
67405 ATTTTGATAAATATTTTGAATTTTAAAATTTGAA
1 ATTTTGATAAATATTTTGAATTTTAAAATTTGAA
*
67439 ATTTTGA-AAATTATTTTGTATTTT
1 ATTTTGATAAA-TATTTTGAATTTT
67463 TTGTTGAAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
33 3 0.06
34 30 0.59
35 18 0.35
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (34 bp):
ATTTTGATAAATATTTTGAATTTTAAAATTTGAA
Found at i:68866 original size:19 final size:20
Alignment explanation
Indices: 68828--68867 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
68818 TTGATTTTTT
**
68828 TCGTTATTCTATATTGTAAA
1 TCGTTATTCTATATACTAAA
68848 TCGTTATT-TATATACTAAA
1 TCGTTATTCTATATACTAAA
68867 T
1 T
68868 AAAAAGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (20 bp):
TCGTTATTCTATATACTAAA
Found at i:70192 original size:19 final size:19
Alignment explanation
Indices: 70168--70206 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
70158 GCAACTTTTC
70168 TCAATTTGGCACCTGAACT
1 TCAATTTGGCACCTGAACT
* *
70187 TCAATTTGGTACTTGAACT
1 TCAATTTGGCACCTGAACT
70206 T
1 T
70207 GGATTGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (19 bp):
TCAATTTGGCACCTGAACT
Found at i:80830 original size:21 final size:20
Alignment explanation
Indices: 80795--80835 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
80785 TTATTTTAAC
80795 TCTTGAATTCCAAATTTCGAA
1 TCTTGAATTCCAAA-TTCGAA
**
80816 TCTTGAATTTTAAATTCGAA
1 TCTTGAATTCCAAATTCGAA
80836 ACTTAAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (20 bp):
TCTTGAATTCCAAATTCGAA
Found at i:81217 original size:22 final size:21
Alignment explanation
Indices: 81182--81224 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
81172 GAAATGAAAA
81182 AATTATAAAAATATCATTAAAT
1 AATTATAAAAATATCA-TAAAT
81204 AATTA-AAAATATATCATAAAT
1 AATTATAAAA-ATATCATAAAT
81225 GATATAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
AATTATAAAAATATCATAAAT
Found at i:102009 original size:25 final size:24
Alignment explanation
Indices: 101973--102033 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
101963 TTAGTAAATA
* *
101973 TTAAAAAATATATTTTTATAATTT
1 TTAAAAAATATAATTTTAAAATTT
101997 TTAAAAAATTATAATTTTAAAATTT
1 TTAAAAAA-TATAATTTTAAAATTT
*
102022 TT-TAAAATATAA
1 TTAAAAAATATAA
102034 AAAGTTTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.15
24 12 0.36
25 16 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAAAAAATATAATTTTAAAATTT
Found at i:102575 original size:25 final size:22
Alignment explanation
Indices: 102532--102588 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 22
102522 ATGGATCTTT
102532 AATTTTT-TTTTTTAATTTTAA
1 AATTTTTATTTTTTAATTTTAA
102553 ATATTTTTATTTTTTATATTTTTAA
1 A-ATTTTTATTTTTTA-A-TTTTAA
102578 AATTATTTATT
1 AATT-TTTATT
102589 CACATGAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 1 0.03
22 6 0.19
23 7 0.23
24 4 0.13
25 13 0.42
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
AATTTTTATTTTTTAATTTTAA
Found at i:105566 original size:6 final size:6
Alignment explanation
Indices: 105555--105580 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
105545 GGGAGACTTC
105555 CTGATT CTGATT CTGATT CTGATT CT
1 CTGATT CTGATT CTGATT CTGATT CT
105581 CTCCTATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.50
Consensus pattern (6 bp):
CTGATT
Found at i:110310 original size:17 final size:17
Alignment explanation
Indices: 110253--110314 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 17
110243 TTTCAAATTT
110253 TTTTCTTTATTT-TTCA
1 TTTTCTTTATTTCTTCA
*
110269 TTTTCTTTTGTTTCTCTCTCTA
1 TTTTC-TTT-ATT-TCT-TC-A
110291 TTTTCTTTATTTCTTCA
1 TTTTCTTTATTTCTTCA
110308 -TTTCTTT
1 TTTTCTTT
110315 TAATATAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
16 12 0.32
17 4 0.11
18 4 0.11
19 4 0.11
20 3 0.08
21 5 0.13
22 6 0.16
ACGTcount: A:0.08, C:0.18, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTTCTTTATTTCTTCA
Found at i:126163 original size:26 final size:27
Alignment explanation
Indices: 126129--126185 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
126119 ACTCGTGAGG
* *
126129 TTATTAAAA-TTTTACATAATACTTTT
1 TTATGAAAATTTTTACACAATACTTTT
*
126155 TTATGAAAATTTTTATACAATACTTTT
1 TTATGAAAATTTTTACACAATACTTTT
126182 TTAT
1 TTAT
126186 AAATATACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 8 0.30
27 19 0.70
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (27 bp):
TTATGAAAATTTTTACACAATACTTTT
Found at i:126190 original size:14 final size:14
Alignment explanation
Indices: 126146--126190 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
126136 AATTTTACAT
126146 AATACTTTTTTATGA
1 AATACTTTTTTAT-A
126161 AA-A--TTTTTATA
1 AATACTTTTTTATA
126172 CAATACTTTTTTATA
1 -AATACTTTTTTATA
126187 AATA
1 AATA
126191 TACATTTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
11 1 0.04
12 9 0.35
13 1 0.04
14 5 0.19
15 10 0.38
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (14 bp):
AATACTTTTTTATA
Found at i:142432 original size:36 final size:36
Alignment explanation
Indices: 142377--142481 Score: 131
Period size: 42 Copynumber: 2.8 Consensus size: 36
142367 TCTCTCCCCT
* *
142377 AAATTATATAGCATCAATTTTCACTTTTATTTTTTA
1 AAATTATATAGTATTAATTTTCACTTTTATTTTTTA
142413 AAATTATATAGTATTAATTTTCATTTTCACTTTTATTTTTTA
1 AAATTATATAGTATT-A-----ATTTTCACTTTTATTTTTTA
142455 AAATTATATAGTATTAATTTTCA-TTTT
1 AAATTATATAGTATTAATTTTCACTTTT
142482 CATAACATTA
Statistics
Matches: 61, Mismatches: 2, Indels: 13
0.80 0.03 0.17
Matches are distributed among these distances:
35 4 0.07
36 20 0.33
37 1 0.02
41 1 0.02
42 35 0.57
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (36 bp):
AAATTATATAGTATTAATTTTCACTTTTATTTTTTA
Found at i:142452 original size:42 final size:42
Alignment explanation
Indices: 142393--142483 Score: 182
Period size: 42 Copynumber: 2.2 Consensus size: 42
142383 TATAGCATCA
142393 ATTTTCACTTTTATTTTTTAAAATTATATAGTATTAATTTTC
1 ATTTTCACTTTTATTTTTTAAAATTATATAGTATTAATTTTC
142435 ATTTTCACTTTTATTTTTTAAAATTATATAGTATTAATTTTC
1 ATTTTCACTTTTATTTTTTAAAATTATATAGTATTAATTTTC
142477 ATTTTCA
1 ATTTTCA
142484 TAACATTAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (42 bp):
ATTTTCACTTTTATTTTTTAAAATTATATAGTATTAATTTTC
Found at i:142781 original size:137 final size:137
Alignment explanation
Indices: 142620--143376 Score: 962
Period size: 137 Copynumber: 5.6 Consensus size: 137
142610 TGAATGCATT
*
142620 ATCAAGGGTCTATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACC
1 ATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACC
* *
142685 CGGTTGGGCCCTTTTTAGTTTTAATTTTATTTCATTAAATATCATCTATTATTATAGTTCATTTT
66 CGGTTGGGCCCTTATTAGTTTTAATTTTATTTCATTAAACATCATCTATTATTATAGTTCATTTT
142750 ACACAGC
131 ACACAGC
*
142757 ATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTACAGATC-A-A-GT----GG-TC---CC
1 ATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACC
* * * * *
142811 CGGTTGAGCCCTTATTACTTTTAATTTTATTCCATTAAATATCATCTATTATCATAGTTCATTTT
66 CGGTTGGGCCCTTATTAGTTTTAATTTTATTTCATTAAACATCATCTATTATTATAGTTCATTTT
* *
142876 GCCCAGC
131 ACACAGC
*
142883 TTCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACC
1 ATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACC
* * * *
142948 CGGTTGGGCCC-TATTATTTTTAATTTTATATT-ATT--A-ATCATCTATAACTATAGTTCATGT
66 CGGTTGGGCCCTTATTAGTTTTAATTTTAT-TTCATTAAACATCATCTATTATTATAGTTCATTT
143008 TACACAGC
130 TACACAGC
* *
143016 ATCAAGGGTCCATAGCTCAGTGATAGAGCATTTGACTGCAGATCAAGAGGTCACCTGTTCGAACC
1 ATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACC
* * *
143081 CGGTTGAGG-CC-TATTATTTTTAAACTAAATGTTTAATGTTTTATTAAACATCATTTATTATTA
66 CGGTTG-GGCCCTTATTA-GTTT----T-AAT-TTT-A--TTTCATTAAACATCATCTATTATTA
* * * *
143144 TATTTCA-CTTGCACTGC
120 TAGTTCATTTTACACAGC
**
143161 ATCGGGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACC
1 ATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACC
* * *
143226 CGGTTGGGCCCTTACT-GCTTTTAATTTTATTTTATTAAACATCATTTATTATTATAGTTCA-TT
66 CGGTTGGGCCCTTATTAG-TTTTAATTTTATTTCATTAAACATCATCTATTATTATAGTTCATTT
*
143289 TAGAACAGC
130 TA-CACAGC
143298 ATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACC
1 ATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACC
143363 CGGTTGGGCCCTTA
66 CGGTTGGGCCCTTA
143377 CTGCTCTAAA
Statistics
Matches: 546, Mismatches: 43, Indels: 62
0.84 0.07 0.10
Matches are distributed among these distances:
126 109 0.20
127 1 0.00
128 1 0.00
129 4 0.01
130 2 0.00
133 103 0.19
134 11 0.02
135 1 0.00
136 54 0.10
137 136 0.25
138 2 0.00
139 6 0.01
140 6 0.01
141 2 0.00
142 2 0.00
143 4 0.01
144 2 0.00
145 80 0.15
146 20 0.04
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (137 bp):
ATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACC
CGGTTGGGCCCTTATTAGTTTTAATTTTATTTCATTAAACATCATCTATTATTATAGTTCATTTT
ACACAGC
Found at i:142908 original size:126 final size:126
Alignment explanation
Indices: 142682--143356 Score: 490
Period size: 126 Copynumber: 5.1 Consensus size: 126
142672 ACCGGTTCGA
* * *
142682 ACCCGGTTGGGCCCTTTTTAGTTTTAATTTTATTTCATTAAATATCATCTATTATTATAGTTCAT
1 ACCCGGTTGGGCCCTTATTACTTTTAATTTTA-TTCATTAAATATCATCTATTATCATAGTTCAT
*
142747 TTTACACAGCATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTACAGATCAAGTGGTC
65 TTTACACAGCATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGTGGTC
*
142809 -CCCGGTTGAGCCCTTATTACTTTTAATTTTATTCCATTAAATATCATCTATTATCATAGTTCAT
1 ACCCGGTTGGGCCCTTATTACTTTTAATTTTATT-CATTAAATATCATCTATTATCATAGTTCAT
* * *
142873 TTTGCCCAGCTTCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACC
65 TTTACACAGCATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATC-A-A-GT----
142938 GGTTC
123 GG-TC
* * *
142943 GAACCCGGTTGGGCCC-TATTATTTTTAATTTTA-T-ATT-ATTAATCATCTA-TAACTATAGTT
1 --ACCCGGTTGGGCCCTTATTACTTTTAATTTTATTCATTAAAT-ATCATCTATTATC-ATAGTT
* *
143003 CATGTTACACAGCATCAAGGGTCCATAGCTCAGTGATAGAGCATTTGACTGCAGATCAAGAGGTC
62 CATTTTACACAGCATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATC-A-A-G--
*
143068 ACCTGTTC
122 ---TGGTC
* * ** * * *
143076 GAACCCGGTTGAGG-CC-TATTATTTTTAAACTAAATGTTTAATGTTTTATTAAACATC-ATTTA
1 --ACCCGGTTG-GGCCCTTATTA-CTTT----T-AAT-TTTATTCATTAAAT-ATCATCTA-TTA
* * **** * * **
143138 TTATTATATTTCACTTGCACTGCATCGGGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGA
54 TCA-TA-GTTCATTTTACACAGCATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGA
143203 TCAAGAGGTCACCGGTTC
117 TC-A-A-GT----GG-TC
* * * * * *
143221 GAACCCGGTTGGGCCCTTACTGCTTTTAATTTTATTTTATTAAACATCATTTATTATTATAGTTC
1 --ACCCGGTTGGGCCCTTATTACTTTTAATTTTA-TTCATTAAATATCATCTATTATCATAGTTC
* *
143286 A-TTTAGAACAGCATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTC
63 ATTTTA-CACAGCATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGTGGTC
143350 A-CCGGTT
1 ACCCGGTT
143357 CGAACCCGGT
Statistics
Matches: 450, Mismatches: 54, Indels: 89
0.76 0.09 0.15
Matches are distributed among these distances:
125 2 0.00
126 113 0.25
127 2 0.00
128 1 0.00
129 4 0.01
130 2 0.00
132 5 0.01
133 97 0.22
134 10 0.02
135 2 0.00
136 19 0.04
137 60 0.13
138 4 0.01
139 17 0.04
140 13 0.03
141 2 0.00
142 3 0.01
143 10 0.02
144 7 0.02
145 74 0.16
146 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (126 bp):
ACCCGGTTGGGCCCTTATTACTTTTAATTTTATTCATTAAATATCATCTATTATCATAGTTCATT
TTACACAGCATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGTGGTC
Found at i:143064 original size:133 final size:135
Alignment explanation
Indices: 142809--143374 Score: 696
Period size: 133 Copynumber: 4.1 Consensus size: 135
142799 TCAAGTGGTC
* * *
142809 CCCGGTTGAGCCCTTATTACTTTTAATTTTATTCCATTA--AATATCATCTATTATCATAGTTCA
1 CCCGGTTGGGCCC-TATTACTTTTAATTTTATT--ATTATTAACATCATCTATTATTATAGTTCA
* * *
142872 TTTTGCCCAGCTTCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCAC
63 -TTTACACAGCATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCAC
142937 CGGTTCGAA
127 CGGTTCGAA
* * *
142946 CCCGGTTGGGCCCTATTATTTTTAATTTTA-TATTATT-A-ATCATCTATAACTATAGTTCATGT
1 CCCGGTTGGGCCCTATTACTTTTAATTTTATTATTATTAACATCATCTATTATTATAGTTCAT-T
* *
143008 TACACAGCATCAAGGGTCCATAGCTCAGTGATAGAGCATTTGACTGCAGATCAAGAGGTCACCTG
65 TACACAGCATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGG
143073 TTCGAA
130 TTCGAA
* * *
143079 CCCGGTTGAGG-CCTATTATTTTTAAACTAAATGTTTAATGTTTTATTAAACATCATTTATTATT
1 CCCGGTTG-GGCCCTATTA-CTTT----T-AAT-TTT-AT-TATTATT-AACATCATCTATTATT
* * * * **
143143 ATATTTCACTTGCACTGCATCGGGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAG
55 ATAGTTCATTTACACAGCATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAG
143208 AGGTCACCGGTTCGAA
120 AGGTCACCGGTTCGAA
* * *
143224 CCCGGTTGGGCCCTTACTGCTTTTAATTTTATT-TTATTAAACATCATTTATTATTATAGTTCAT
1 CCCGGTTGGGCCC-TATTACTTTTAATTTTATTATTATT-AACATCATCTATTATTATAGTTCAT
*
143288 TTAGAACAGCATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACC
64 TTA-CACAGCATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACC
143353 GGTTCGAA
128 GGTTCGAA
143361 CCCGGTTGGGCCCT
1 CCCGGTTGGGCCCT
143375 TACTGCTCTA
Statistics
Matches: 377, Mismatches: 32, Indels: 41
0.84 0.07 0.09
Matches are distributed among these distances:
132 1 0.00
133 104 0.28
134 7 0.02
135 1 0.00
136 48 0.13
137 91 0.24
138 3 0.01
139 6 0.02
140 6 0.02
141 2 0.01
143 6 0.02
144 2 0.01
145 80 0.21
146 20 0.05
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (135 bp):
CCCGGTTGGGCCCTATTACTTTTAATTTTATTATTATTAACATCATCTATTATTATAGTTCATTT
ACACAGCATCAAGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGT
TCGAA
Done.