Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002130.1 Kokia drynarioides strain JFW-HI SEQ_114064, 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: 88365
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:461 original size:30 final size:30
Alignment explanation
Indices: 427--543 Score: 123
Period size: 30 Copynumber: 3.9 Consensus size: 30
417 TAATTTTGAG
* *
427 AGTTTCGAGGTCGAAAATGGAGTTTTTGGA
1 AGTTTCGGGGTCAAAAATGGAGTTTTTGGA
* *
457 AGTTTCGGGGCCAAAAATGGAATTTTTGGA
1 AGTTTCGGGGTCAAAAATGGAGTTTTTGGA
*
487 AGTTTGGGGGTCAAAAATGG-GATTTTTGGA
1 AGTTTCGGGGTCAAAAATGGAG-TTTTTGGA
* * *
517 AGCTT-GAGGGT-AAAAATGTAATTTTTG
1 AGTTTCG-GGGTCAAAAATGGAGTTTTTG
544 AATAGTTTAG
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
29 14 0.19
30 60 0.81
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.33
Consensus pattern (30 bp):
AGTTTCGGGGTCAAAAATGGAGTTTTTGGA
Found at i:551 original size:60 final size:59
Alignment explanation
Indices: 401--545 Score: 154
Period size: 60 Copynumber: 2.5 Consensus size: 59
391 TTTTTAAACA
** * *
401 TTCGAGGGTAAAAGGGTAA-TTTTGAGAGTTTCGAGGTCGAAAATGGAGTTTTTGGAAGT
1 TTCGAGGGTAAAAATGTAATTTTTGA-AGTTTCGAGGTCAAAAATGGAGTTTTTGGAAGC
* * * *
460 TTCG-GGGCCAAAAATGGAATTTTTGGAAGTTTGGGGGTCAAAAATGG-GATTTTTGGAAGC
1 TTCGAGGG-TAAAAATGTAATTTTT-GAAGTTTCGAGGTCAAAAATGGAG-TTTTTGGAAGC
520 TT-GAGGGTAAAAATGTAATTTTTGAA
1 TTCGAGGGTAAAAATGTAATTTTTGAA
546 TAGTTTAGGG
Statistics
Matches: 71, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
58 6 0.08
59 27 0.38
60 36 0.51
61 2 0.03
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.32
Consensus pattern (59 bp):
TTCGAGGGTAAAAATGTAATTTTTGAAGTTTCGAGGTCAAAAATGGAGTTTTTGGAAGC
Found at i:1650 original size:12 final size:12
Alignment explanation
Indices: 1615--1735 Score: 97
Period size: 12 Copynumber: 10.2 Consensus size: 12
1605 TTTCGGCTCT
1615 TATTATTATTAA
1 TATTATTATTAA
*
1627 TATTAATA-TAA
1 TATTATTATTAA
1638 TATTATTATTAA
1 TATTATTATTAA
* *
1650 TGTTTTTATTAA
1 TATTATTATTAA
1662 TATTA--A-TAA
1 TATTATTATTAA
*
1671 TATTTTTATTAA
1 TATTATTATTAA
* **
1683 TACTTATTAATGC
1 TA-TTATTATTAA
**
1696 TATTTATTGCTAA
1 TA-TTATTATTAA
1709 TATTTATTATTAA
1 TA-TTATTATTAA
*
1722 TGTTATTATTAA
1 TATTATTATTAA
1734 TA
1 TA
1736 ACAATATTTA
Statistics
Matches: 84, Mismatches: 20, Indels: 10
0.74 0.18 0.09
Matches are distributed among these distances:
9 7 0.08
10 1 0.01
11 11 0.13
12 39 0.46
13 26 0.31
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.56
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:1671 original size:21 final size:21
Alignment explanation
Indices: 1641--1703 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
1631 AATATAATAT
1641 TATTATTAATGTTTTTATTAA
1 TATTATTAATGTTTTTATTAA
* *
1662 TATTAATAATATTTTTATTAA
1 TATTATTAATGTTTTTATTAA
*
1683 TACTTATTAATGCTATTTATT
1 TA-TTATTAATG-TTTTTATT
1704 GCTAATATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 21 0.60
22 7 0.20
23 7 0.20
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (21 bp):
TATTATTAATGTTTTTATTAA
Found at i:1690 original size:25 final size:25
Alignment explanation
Indices: 1662--1735 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 25
1652 TTTTTATTAA
1662 TATTAATAATATTTTTATTAATACT
1 TATTAATAATATTTTTATTAATACT
** ** *
1687 TATTAATGCTATTTATTGCTAATATT
1 TATTAATAATATTT-TTATTAATACT
* * *
1713 TATTATTAATGTTATTATTAATA
1 TATTAATAATATTTTTATTAATA
1736 ACAATATTTA
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
25 19 0.53
26 17 0.47
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (25 bp):
TATTAATAATATTTTTATTAATACT
Found at i:2380 original size:17 final size:17
Alignment explanation
Indices: 2360--2442 Score: 62
Period size: 17 Copynumber: 4.9 Consensus size: 17
2350 AATTTATAAA
2360 AAATTTAAATTTAAAGT
1 AAATTTAAATTTAAAGT
* ** *
2377 AAATTTTAACTAAAAAAT
1 AAA-TTTAAATTTAAAGT
*
2395 AAATTTAAATTTAGAA-C
1 AAATTTAAATTTA-AAGT
* *
2412 AAATTCAAACTTAAAGT
1 AAATTTAAATTTAAAGT
*
2429 AAA-TTAAAGTTAAA
1 AAATTTAAATTTAAA
2443 ATTTGGACTC
Statistics
Matches: 50, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
16 11 0.22
17 24 0.48
18 15 0.30
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.34
Consensus pattern (17 bp):
AAATTTAAATTTAAAGT
Found at i:5131 original size:30 final size:31
Alignment explanation
Indices: 5095--5163 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
5085 CATTTAACGC
*
5095 AACAGTCACTCAAC-TT-TGAAAACGTGACAA
1 AACAGTCACT-AACATTATCAAAACGTGACAA
*
5125 AACAGTCACTAACATTATCAAAATGTGACAA
1 AACAGTCACTAACATTATCAAAACGTGACAA
5156 AACAGTCA
1 AACAGTCA
5164 TTGAAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 3 0.09
30 12 0.34
31 20 0.57
ACGTcount: A:0.46, C:0.22, G:0.12, T:0.20
Consensus pattern (31 bp):
AACAGTCACTAACATTATCAAAACGTGACAA
Found at i:6529 original size:53 final size:53
Alignment explanation
Indices: 6417--6529 Score: 131
Period size: 54 Copynumber: 2.1 Consensus size: 53
6407 AATTTACCCT
* * * ***
6417 TTTTTTTATTACTCAACTATGAAAAGTTAATAAAATAGTCACTCAATTGTTAG
1 TTTTTTTATCACTCAACTATGAAAAGTTAACAAAATAGTCACCCAACAATTAG
6470 TATTTTTTATCAC-CTAACTATGAAAAGTT-ACAAAATAGTCACCCAACAATTCAG
1 T-TTTTTTATCACTC-AACTATGAAAAGTTAACAAAATAGTCACCCAACAATT-AG
6524 TTTTTT
1 TTTTTT
6530 CGTTTTTGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
53 24 0.47
54 27 0.53
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (53 bp):
TTTTTTTATCACTCAACTATGAAAAGTTAACAAAATAGTCACCCAACAATTAG
Found at i:14025 original size:3 final size:3
Alignment explanation
Indices: 14017--14042 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
14007 TATGAAAATA
14017 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
14043 AGTAGGCGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:14994 original size:20 final size:20
Alignment explanation
Indices: 14969--15008 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
14959 CCTATTTTTT
14969 TGAATA-GACGGACCAAAATA
1 TGAATAGGA-GGACCAAAATA
14989 TGAATAGGAGGACCAAAATA
1 TGAATAGGAGGACCAAAATA
15009 CAATCAATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.50, C:0.12, G:0.23, T:0.15
Consensus pattern (20 bp):
TGAATAGGAGGACCAAAATA
Found at i:17085 original size:19 final size:22
Alignment explanation
Indices: 17045--17088 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 22
17035 ATTTTGACAA
17045 AAGAAAATGTAAATACTAATTT
1 AAGAAAATGTAAATACTAATTT
17067 AAGAAAAT-T-AATA-TAATTT
1 AAGAAAATGTAAATACTAATTT
17086 AAG
1 AAG
17089 TATTATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.41
20 4 0.18
21 1 0.05
22 8 0.36
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (22 bp):
AAGAAAATGTAAATACTAATTT
Found at i:33958 original size:77 final size:77
Alignment explanation
Indices: 33877--34019 Score: 200
Period size: 77 Copynumber: 1.9 Consensus size: 77
33867 ACCATATGAC
* * *
33877 AAATCTATGACAT-GAGGGCTGAA-CCCAAACTCAGATTACAAATGCAGCTCATACAAAGTCTAA
1 AAATCTATGA-ATAGAGAGCT-AATCCCAAAATCAGATTACAAATGCAGCTCACACAAAGTCTAA
33940 CTTCACCATAACAT
64 CTTCACCATAACAT
* * *
33954 AAATCTATGATTAGAGAGCTAATCCCAAAATCGGATTGCAAATGCAGCTCACACAAAGTCTAACT
1 AAATCTATGAATAGAGAGCTAATCCCAAAATCAGATTACAAATGCAGCTCACACAAAGTCTAACT
34019 T
66 T
34020 TCAGCAACAC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
76 3 0.05
77 55 0.95
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (77 bp):
AAATCTATGAATAGAGAGCTAATCCCAAAATCAGATTACAAATGCAGCTCACACAAAGTCTAACT
TCACCATAACAT
Found at i:34181 original size:84 final size:83
Alignment explanation
Indices: 33944--34188 Score: 240
Period size: 85 Copynumber: 2.9 Consensus size: 83
33934 GTCTAACTTC
* * * * * * *
33944 ACCATAACATAAATCTATGATTAGAGAGCTAATCCCAAAATCGGATTGCAAATGCAGCTCACACA
1 ACCATAACATAAATCTAT-ATAATAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTCATACA
* *
34009 AAGTCTAACTTTCAGCAAC
65 AAGTCTAACATTCAGCAAA
* * * * *
34028 ACCATAACATAAAATCTATA-ATTCAAGAGCTAAACCTGAACTTGGATTACAAATACAACTCATA
1 ACCATAACAT-AAATCTATATAAT--AGAGCTAAACCCGAACTCGGATTACAAATGCAGCTCATA
* *
34092 AAAAGTCTTACATTCAGCAAA
63 CAAAGTCTAACATTCAGCAAA
* * * * *
34113 ACCATAATATAAATCTAATATAATAGAGCTAAGCCCGAACTCGGGTTATAAATGCAGCTCATGCA
1 ACCATAACATAAATCT-ATATAATAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTCATACA
*
34178 AAGTTTAACAT
65 AAGTCTAACAT
34189 AAATCTATCA
Statistics
Matches: 127, Mismatches: 29, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
84 58 0.46
85 67 0.53
86 2 0.02
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (83 bp):
ACCATAACATAAATCTATATAATAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTCATACAA
AGTCTAACATTCAGCAAA
Found at i:34330 original size:84 final size:84
Alignment explanation
Indices: 34183--34697 Score: 502
Period size: 84 Copynumber: 6.1 Consensus size: 84
34173 ATGCAAAGTT
* * * * *
34183 TAACATAAATCTATCAAAAGAGGGCTAAACCAGAACTCAGG-TTATAAATGCAGCTCATGCAAAG
1 TAACATAAATATATCAAATGAGGGCTAAACCAGAACTC-GGATTACAAATGCAGCTTATACAAAG
*
34247 TCTAACTTTCAGCGACACAA
65 TCTAACTTTCAGTGACACAA
* * * * *
34267 TAACATAAATCTATCAAACGAGGGCTAAACCTGAACTTGGATTACAAATGCAACTTATACAAAGT
1 TAACATAAATATATCAAATGAGGGCTAAACCAGAACTCGGATTACAAATGCAGCTTATACAAAGT
* *
34332 ATAACTTTCAGTGACACCA
66 CTAACTTTCAGTGACACAA
* ** * * * * *
34351 TAACATAAATATATTATGTGAGAGCTGAACCCGAACTTGGATTACAAATGCAGCTT-TGCAAAGT
1 TAACATAAATATATCAAATGAGGGCTAAACCAGAACTCGGATTACAAATGCAGCTTATACAAAGT
* *
34415 CGAACTTTCAGTGACACCA
66 CTAACTTTCAGTGACACAA
* * * ** * * * *
34434 TAACATAAATATATTATATGAGAGCCGAACCCGAACTCAGATTACAAATGCGGCTTATACAATGT
1 TAACATAAATATATCAAATGAGGGCTAAACCAGAACTCGGATTACAAATGCAGCTTATACAAAGT
34499 CTAACTTTCAGTGACACAA
66 CTAACTTTCAGTGACACAA
** *
34518 TAACATAAATATATCAAATGAGGGCTAAACCAGAACTCGGATCGCAAATACAGCTTATACAAAGT
1 TAACATAAATATATCAAATGAGGGCTAAACCAGAACTCGGATTACAAATGCAGCTTATACAAAGT
* * *
34583 CTTAACTTTCAAT-AAAAACA
66 C-TAACTTTCAGTGACACA-A
** * * * * *
34603 TAACATAAATCCATTATATGAGAGCTGAAGCC-GAAATC-GATTTAACAAATGCAGCTTATACAA
1 TAACATAAATATATCAAATGAGGGCT-AAACCAGAACTCGGA-TT-ACAAATGCAGCTTATACAA
*
34666 AGCCTAACTTTCAGTGACATC-A
63 AGTCTAACTTTCAGTGACA-CAA
*
34688 TAACACAAAT
1 TAACATAAAT
34698 TCAGCTTATA
Statistics
Matches: 361, Mismatches: 61, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
83 77 0.21
84 200 0.55
85 58 0.16
86 26 0.07
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (84 bp):
TAACATAAATATATCAAATGAGGGCTAAACCAGAACTCGGATTACAAATGCAGCTTATACAAAGT
CTAACTTTCAGTGACACAA
Found at i:34402 original size:234 final size:234
Alignment explanation
Indices: 33993--34414 Score: 564
Period size: 234 Copynumber: 1.8 Consensus size: 234
33983 ATCGGATTGC
* *
33993 AAATGCAGCTCACACAAAGTCTAACTTTCAGCAACACCATAACATAAAATCTATAATTCAAGAGC
1 AAATGCAGCTCACACAAAGTCTAACTTTCAGCAACACAATAACATAAAATCTATAATACAAGAGC
* * *
34058 TAAACCTGAACTTGGATTACAAATACAACTCATAAAAAGTCTTACATTCAGCAAAACCATAATAT
66 TAAACCTGAACTTGGATTACAAATACAACTCATAAAAAGTATAACATTCAGCAAAACCATAACAT
* * *
34123 AAATCTAATATAATAGAGCTAAGCCCGAACTCGGGTTATAAATGCAGCTCATGCAAAGTTTAACA
131 AAATATAATATAATAGAGCTAAGCCCGAACTCGGATTACAAATGCAGCT-ATGCAAAGTTTAACA
34188 TAAATCTATCAAAAGAGGGCTAAACCAGAACTCAGGTTAT
195 TAAATCTATCAAAAGAGGGCTAAACCAGAACTCAGGTTAT
** * * *
34228 AAATGCAGCTCATGCAAAGTCTAACTTTCAGCGACACAATAACAT-AAATCTATCAA-ACGAGGG
1 AAATGCAGCTCACACAAAGTCTAACTTTCAGCAACACAATAACATAAAATCTAT-AATACAAGAG
* * * * ** *
34291 CTAAACCTGAACTTGGATTACAAATGCAACTTATACAAAGTATAACTTTCAGTGACACCATAACA
65 CTAAACCTGAACTTGGATTACAAATACAACTCATAAAAAGTATAACATTCAGCAAAACCATAACA
* * * *
34356 TAAATATATTAT-GTGAGAGCTGAA-CCCGAACTTGGATTACAAATGCAGCTTTGCAAAGT
130 TAAATATAATATAAT-AGAGCT-AAGCCCGAACTCGGATTACAAATGCAGCTATGCAAAGT
34415 CGAACTTTCA
Statistics
Matches: 160, Mismatches: 24, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
233 9 0.06
234 106 0.66
235 45 0.28
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (234 bp):
AAATGCAGCTCACACAAAGTCTAACTTTCAGCAACACAATAACATAAAATCTATAATACAAGAGC
TAAACCTGAACTTGGATTACAAATACAACTCATAAAAAGTATAACATTCAGCAAAACCATAACAT
AAATATAATATAATAGAGCTAAGCCCGAACTCGGATTACAAATGCAGCTATGCAAAGTTTAACAT
AAATCTATCAAAAGAGGGCTAAACCAGAACTCAGGTTAT
Found at i:34479 original size:167 final size:166
Alignment explanation
Indices: 34183--34697 Score: 555
Period size: 167 Copynumber: 3.1 Consensus size: 166
34173 ATGCAAAGTT
* * * * * *
34183 TAACATAAATCTATCAAAAGAGGGCTAAACCAGAACTCAGG-TTATAAATGCAGCTCATGCAAAG
1 TAACATAAATATATCAAATGAGAGCTAAACCAGAACTC-GGATCACAAATGCAGCT-TTGCAAAG
* * * * * * * * *
34247 TCTAACTTTCAGCGACACAATAACATAAATCTATCAAACGAGGGCTAAACCTGAACTTGGATTAC
64 TCTAACTTTCAGTGACACCATAACATAAATCTATTATATGAGAGCTGAACCCGAAC-TCGATTAC
* *
34312 AAATGCAACTTATACAAAGTATAACTTTCAGTGACACCA
128 AAATGCAGCTTATACAAAGTCTAACTTTCAGTGACACCA
* ** * * * *
34351 TAACATAAATATATTATGTGAGAGCTGAACCCGAACTTGGATTACAAATGCAGCTTTGCAAAGTC
1 TAACATAAATATATCAAATGAGAGCTAAACCAGAACTCGGATCACAAATGCAGCTTTGCAAAGTC
* * *
34416 GAACTTTCAGTGACACCATAACATAAATATATTATATGAGAGCCGAACCCGAACTCAGATTACAA
66 TAACTTTCAGTGACACCATAACATAAATCTATTATATGAGAGCTGAACCCGAACTC-GATTACAA
* * *
34481 ATGCGGCTTATACAATGTCTAACTTTCAGTGACACAA
130 ATGCAGCTTATACAAAGTCTAACTTTCAGTGACACCA
* * * *
34518 TAACATAAATATATCAAATGAGGGCTAAACCAGAACTCGGATCGCAAATACAGCTTATACAAAGT
1 TAACATAAATATATCAAATGAGAGCTAAACCAGAACTCGGATCACAAATGCAGCTT-TGCAAAGT
* * * * * * *
34583 CTTAACTTTCAATAAAAACATAACATAAATCCATTATATGAGAGCTGAAGCCGAAATCGATTTAA
65 C-TAACTTTCAGTGACACCATAACATAAATCTATTATATGAGAGCTGAACCCGAACTCGA-TT-A
* *
34648 CAAATGCAGCTTATACAAAGCCTAACTTTCAGTGACATCA
127 CAAATGCAGCTTATACAAAGTCTAACTTTCAGTGACACCA
*
34688 TAACACAAAT
1 TAACATAAAT
34698 TCAGCTTATA
Statistics
Matches: 286, Mismatches: 55, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
166 1 0.00
167 140 0.49
168 52 0.18
169 48 0.17
170 45 0.16
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (166 bp):
TAACATAAATATATCAAATGAGAGCTAAACCAGAACTCGGATCACAAATGCAGCTTTGCAAAGTC
TAACTTTCAGTGACACCATAACATAAATCTATTATATGAGAGCTGAACCCGAACTCGATTACAAA
TGCAGCTTATACAAAGTCTAACTTTCAGTGACACCA
Found at i:34696 original size:45 final size:45
Alignment explanation
Indices: 34647--34743 Score: 158
Period size: 45 Copynumber: 2.2 Consensus size: 45
34637 AATCGATTTA
*
34647 ACAAATGCAGCTTATACAAAGCCTAACTTTCAGTGACATCATAAC
1 ACAAATGCAGCTTATACAAAGCCTAACTTTCAGTGACACCATAAC
* *
34692 ACAAATTCAGCTTATACAAAGCCTAACTTTCAGTGACACCATGAC
1 ACAAATGCAGCTTATACAAAGCCTAACTTTCAGTGACACCATAAC
*
34737 ATAAATG
1 ACAAATG
34744 AATGATAGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.25
Consensus pattern (45 bp):
ACAAATGCAGCTTATACAAAGCCTAACTTTCAGTGACACCATAAC
Found at i:36060 original size:25 final size:23
Alignment explanation
Indices: 36019--36064 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
36009 CCAATTAGGT
36019 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
36042 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
36065 TGGATTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:38796 original size:179 final size:179
Alignment explanation
Indices: 38496--38855 Score: 711
Period size: 179 Copynumber: 2.0 Consensus size: 179
38486 ATAATTAGTA
38496 TTGATGAAAATTATTAAAATTTAACTTCTAATTCTTTAATAAAATCATATAAATTTTCATCAAAT
1 TTGATGAAAATTATTAAAATTTAACTTCTAATTCTTTAATAAAATCATATAAATTTTCATCAAAT
38561 TGTTTTGCATTTCATTGACTCGGGATGGTCTAACTGGTCATACCAACACTGTGAACTTGTTTTCA
66 TGTTTTGCATTTCATTGACTCGGGATGGTCTAACTGGTCATACCAACACTGTGAACTTGTTTTCA
38626 CTATCTCTATATCATTCATATCAGTGTAATGTACTCTTTATAAGAATAT
131 CTATCTCTATATCATTCATATCAGTGTAATGTACTCTTTATAAGAATAT
38675 TTGATGAAAATTATTAAAATTTAACTTCTAATTCTTTAATAAAATCATATAAATTTTCATCAAAT
1 TTGATGAAAATTATTAAAATTTAACTTCTAATTCTTTAATAAAATCATATAAATTTTCATCAAAT
38740 TGTTTTGCATTTCATTGACTCGGGATGGTCTAACTGGTCATACCAACACTGTGAACTTGTTTTCA
66 TGTTTTGCATTTCATTGACTCGGGATGGTCTAACTGGTCATACCAACACTGTGAACTTGTTTTCA
*
38805 CTATCTCTATGTCATTCATATCAGTGTAATGTACTCTTTATAAGAATAT
131 CTATCTCTATATCATTCATATCAGTGTAATGTACTCTTTATAAGAATAT
38854 TT
1 TT
38856 ATAATAGGAA
Statistics
Matches: 180, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
179 180 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (179 bp):
TTGATGAAAATTATTAAAATTTAACTTCTAATTCTTTAATAAAATCATATAAATTTTCATCAAAT
TGTTTTGCATTTCATTGACTCGGGATGGTCTAACTGGTCATACCAACACTGTGAACTTGTTTTCA
CTATCTCTATATCATTCATATCAGTGTAATGTACTCTTTATAAGAATAT
Found at i:41536 original size:27 final size:27
Alignment explanation
Indices: 41504--41567 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
41494 TTCTAGAATA
* *
41504 TAAATTTTTGAAAAATTAAGT-TTTTTT
1 TAAATTTTT-AAAAATTAAATATATTTT
* *
41531 TGAATTTTTTAAAATTAAATATATTTT
1 TAAATTTTTAAAAATTAAATATATTTT
41558 TAAATTTTTA
1 TAAATTTTTA
41568 TATAATATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 9 0.30
27 21 0.70
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (27 bp):
TAAATTTTTAAAAATTAAATATATTTT
Found at i:47000 original size:19 final size:17
Alignment explanation
Indices: 46959--47034 Score: 55
Period size: 18 Copynumber: 4.2 Consensus size: 17
46949 AGTCAAATGG
* *
46959 TAATTTTTTTATAGTTTC
1 TAATTTTTTT-TATTTTA
46977 TAATTATTTTTTATTTTA
1 TAATT-TTTTTTATTTTA
** *
46995 TAAATTTTATTAGAATTTA
1 T-AATTTT-TTTTATTTTA
47014 TAATTTTTTTTTATTTT-
1 TAA-TTTTTTTTATTTTA
47031 TAAT
1 TAAT
47035 ACATATTGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
16 1 0.02
17 3 0.07
18 21 0.46
19 21 0.46
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (17 bp):
TAATTTTTTTTATTTTA
Found at i:47181 original size:20 final size:20
Alignment explanation
Indices: 47156--47203 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
47146 ATCAAAATGA
47156 GAAAATGATATATTTTAAGG
1 GAAAATGATATATTTTAAGG
47176 GAAAATGATATATTTTAAGG
1 GAAAATGATATATTTTAAGG
47196 GAAAATGA
1 GAAAATGA
47204 AGCTTTAAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31
Consensus pattern (20 bp):
GAAAATGATATATTTTAAGG
Found at i:47678 original size:2 final size:2
Alignment explanation
Indices: 47671--47695 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47661 TTTGGAAAAG
47671 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 A
47696 AAGGGATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53791 original size:20 final size:20
Alignment explanation
Indices: 53768--53805 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53758 TAAAAAATGT
*
53768 TAAAAACTATTTTAAAATTA
1 TAAAAACTATTTAAAAATTA
*
53788 TAAAAATTATTTAAAAAT
1 TAAAAACTATTTAAAAAT
53806 GAGAATACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAAACTATTTAAAAATTA
Found at i:66948 original size:19 final size:18
Alignment explanation
Indices: 66910--66954 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
66900 TGAATCAAAA
66910 TTTTTAATTTTTAAATAT
1 TTTTTAATTTTTAAATAT
66928 TTTTTGAATTTTT-AATGA-
1 TTTTT-AATTTTTAAAT-AT
66946 TTTTTAATT
1 TTTTTAATT
66955 GAATTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.16
18 13 0.52
19 8 0.32
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
TTTTTAATTTTTAAATAT
Found at i:68607 original size:24 final size:24
Alignment explanation
Indices: 68579--68625 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
68569 TAAATTTTCA
*
68579 TAAATT-CAAATAATTTTTATTTTT
1 TAAATTACAAAT-ATTTTAATTTTT
*
68603 TAAATTATAAATATTTTAATTTT
1 TAAATTACAAATATTTTAATTTT
68626 GAATGTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TAAATTACAAATATTTTAATTTTT
Found at i:68625 original size:23 final size:26
Alignment explanation
Indices: 68593--68651 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 26
68583 TTCAAATAAT
*
68593 TTTTATTTTTTAAAT-T-ATAA-ATA
1 TTTTAATTTTTAAATGTAATAATATA
*
68616 TTTTAA-TTTTGAATGTAATAATATA
1 TTTTAATTTTTAAATGTAATAATATA
68641 TTTT-ATTTTTA
1 TTTTAATTTTTA
68652 TAGTACAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 7 0.24
23 6 0.21
24 5 0.17
25 11 0.38
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (26 bp):
TTTTAATTTTTAAATGTAATAATATA
Found at i:69162 original size:18 final size:19
Alignment explanation
Indices: 69139--69181 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
69129 ATTTTTTATT
69139 ATAATTTATA-ATATAATA
1 ATAATTTATATATATAATA
*
69157 ATAA-TTATATATATATTA
1 ATAATTTATATATATAATA
*
69175 ACAATTT
1 ATAATTT
69182 TAGTCATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 14 0.67
19 2 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAATTTATATATATAATA
Found at i:70009 original size:36 final size:36
Alignment explanation
Indices: 69939--70011 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
69929 CTGATTAAAC
**
69939 AATTCAATAATATAAATAGTACAAAATGTGAAAATT
1 AATTCAATAATATAAATAGTACAAAAAATGAAAATT
*
69975 AATTTAATAATATAAATAGTA-AATATAAAT-AAAATT
1 AATTCAATAATATAAATAGTACAA-A-AAATGAAAATT
70011 A
1 A
70012 TTATTATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 2 0.06
36 28 0.88
37 2 0.06
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (36 bp):
AATTCAATAATATAAATAGTACAAAAAATGAAAATT
Found at i:75101 original size:40 final size:40
Alignment explanation
Indices: 75057--75138 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
75047 CTATACATGC
75057 AATTGTATATTTAGTCCATATTATCCAATTGAATCATTCT
1 AATTGTATATTTAGTCCATATTATCCAATTGAATCATTCT
75097 AATTGTATATTTAGTCCATATTATCCAATTGAATCATTCT
1 AATTGTATATTTAGTCCATATTATCCAATTGAATCATTCT
75137 AA
1 AA
75139 GTCCCTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (40 bp):
AATTGTATATTTAGTCCATATTATCCAATTGAATCATTCT
Found at i:81076 original size:16 final size:16
Alignment explanation
Indices: 81058--81087 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
81048 TAAATCTTTA
81058 AAAATT-TAAAAATTC
1 AAAATTATAAAAATTC
81073 AAAATTATAAAAATT
1 AAAATTATAAAAATT
81088 ATTTAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATTATAAAAATTC
Found at i:86319 original size:2 final size:2
Alignment explanation
Indices: 86312--86336 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
86302 TTAAATCTTA
86312 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 A
86337 GTGACATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.