Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013893.1 Kokia drynarioides strain JFW-HI SEQ_128921, 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: 71754
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5790 original size:15 final size:15
Alignment explanation
Indices: 5772--5805 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
5762 GTGGTGATGC
5772 TGGCGACGGTGGTGG
1 TGGCGACGGTGGTGG
5787 TGGCGACGGTGGTGG
1 TGGCGACGGTGGTGG
5802 TGGC
1 TGGC
5806 TCATGCATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.15, G:0.59, T:0.21
Consensus pattern (15 bp):
TGGCGACGGTGGTGG
Found at i:6822 original size:30 final size:31
Alignment explanation
Indices: 6750--6828 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
6740 CTTCTCGCTT
**
6750 TATTTATTTTTCCAA-TTTTTTTCTATTTCATT
1 TATTTATTTTT--AATTTTTTTTCTATTTCACC
* * *
6782 TGTTTATTTTTAGTTTTTTTTCTGTTTCACC
1 TATTTATTTTTAATTTTTTTTCTATTTCACC
6813 TATTT-TTTTTAATTTT
1 TATTTATTTTTAATTTT
6829 CATCGGTGCC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
30 11 0.28
31 18 0.46
32 10 0.26
ACGTcount: A:0.15, C:0.10, G:0.04, T:0.71
Consensus pattern (31 bp):
TATTTATTTTTAATTTTTTTTCTATTTCACC
Found at i:11981 original size:2 final size:2
Alignment explanation
Indices: 11976--12005 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11966 CATCGATAAA
11976 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12006 TGTGTATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12054 original size:101 final size:101
Alignment explanation
Indices: 11885--12075 Score: 373
Period size: 101 Copynumber: 1.9 Consensus size: 101
11875 TATGAAAAGC
11885 ATATATATATATATATATATTGTGTATATGCTCAATACCTAAATTTATGGTTCCTAGAATTTATA
1 ATATATATATATATATATATTGTGTATATGCTCAATACCTAAATTTATGGTTCCTAGAATTTATA
11950 TGTTCATAATATATATCATCGATAAAATATATATAT
66 TGTTCATAATATATATCATCGATAAAATATATATAT
*
11986 ATATATATATATATATATATTGTGTATATGCTCAATACCTAAATTTATGGTTCCTGGAATTTATA
1 ATATATATATATATATATATTGTGTATATGCTCAATACCTAAATTTATGGTTCCTAGAATTTATA
12051 TGTTCATAATATATATCATCGATAA
66 TGTTCATAATATATATCATCGATAA
12076 TAATTAAAAT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 89 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.43
Consensus pattern (101 bp):
ATATATATATATATATATATTGTGTATATGCTCAATACCTAAATTTATGGTTCCTAGAATTTATA
TGTTCATAATATATATCATCGATAAAATATATATAT
Found at i:14808 original size:17 final size:15
Alignment explanation
Indices: 14771--14808 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
14761 CAAAATAACA
14771 TGAATTATTTAATTT
1 TGAATTATTTAATTT
14786 TG-ATTATTTTAATATT
1 TGAATTA-TTTAAT-TT
14802 TGAATTA
1 TGAATTA
14809 ATCCTTGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.20
15 8 0.40
16 4 0.20
17 4 0.20
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (15 bp):
TGAATTATTTAATTT
Found at i:21336 original size:72 final size:72
Alignment explanation
Indices: 21173--21318 Score: 193
Period size: 72 Copynumber: 2.0 Consensus size: 72
21163 TCCTTTCCCG
* * * * * * *
21173 TCTCTTTAGCATTTGAAGAATCTTCTATAAGCTTTGGTAACCATTCAATGTTCATCTCCATAGTC
1 TCTCTTTAGCACTTGTAGAATCTTCTAAAAGATATGGTAACAATTCAATGTTCACCTCCATAGTC
*
21238 TTACCCA
66 ATACCCA
* * *
21245 TCTCTTTAGCACTTGTAGAATCTTCTAAAAGATATGGTAGCAATTCAGTGTTCACCTCCATATTC
1 TCTCTTTAGCACTTGTAGAATCTTCTAAAAGATATGGTAACAATTCAATGTTCACCTCCATAGTC
21310 ATACCCA
66 ATACCCA
21317 TC
1 TC
21319 CTGTTGGCAA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (72 bp):
TCTCTTTAGCACTTGTAGAATCTTCTAAAAGATATGGTAACAATTCAATGTTCACCTCCATAGTC
ATACCCA
Found at i:21356 original size:72 final size:71
Alignment explanation
Indices: 21173--21364 Score: 190
Period size: 72 Copynumber: 2.7 Consensus size: 71
21163 TCCTTTCCCG
* * * * * * *
21173 TCTCTTTAGCATTTGAAGAATCTTCTATAAGCTTTGGTAACCATTCAATGTTCATCTCCATAGTC
1 TCTCTTTAGCACTTGTAGAACCATCTAAAAGC-TTGGTAGCCATTCAATGTTCACCTCCATAGTC
*
21238 TTACCCA
65 ATACCCA
* * * * * *
21245 TCTCTTTAGCACTTGTAGAATCTTCTAAAAGATATGGTAGCAATTCAGTGTTCACCTCCATATTC
1 TCTCTTTAGCACTTGTAGAACCATCTAAAAGCT-TGGTAGCCATTCAATGTTCACCTCCATAGTC
21310 ATACCCA
65 ATACCCA
*
21317 TC-CTGTTGGCAAC-TGTAGAACCATCTAAAAGCTTCGGTAGCCATTCAA
1 TCTCT-TTAGC-ACTTGTAGAACCATCTAAAAGCTT-GGTAGCCATTCAA
21365 CGCCCACCTC
Statistics
Matches: 100, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
71 4 0.04
72 94 0.94
73 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (71 bp):
TCTCTTTAGCACTTGTAGAACCATCTAAAAGCTTGGTAGCCATTCAATGTTCACCTCCATAGTCA
TACCCA
Found at i:24591 original size:13 final size:13
Alignment explanation
Indices: 24572--24615 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 13
24562 CTAATGTACG
24572 AAATTAA-TAATT
1 AAATTAATTAATT
24584 AAACTTAATTAATT
1 AAA-TTAATTAATT
24598 AAATTAAGATTAATT
1 AAATT-A-ATTAATT
24613 AAA
1 AAA
24616 ACTAAAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.11
13 6 0.21
14 9 0.32
15 10 0.36
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
AAATTAATTAATT
Found at i:26398 original size:30 final size:28
Alignment explanation
Indices: 26255--26543 Score: 187
Period size: 30 Copynumber: 9.9 Consensus size: 28
26245 TGGGAAAATC
* *
26255 CGGGGTTAAAAATGGACTTTTTAGACA-TT
1 CGGGG-TAAAAATGGAATTTTTGGA-AGTT
*
26284 CGGGGGT-AAAAGGGTAA-TTTTGTG-AGTTT
1 C-GGGGTAAAAATGG-AATTTTTG-GAAG-TT
*
26313 CGAGGTCAAAAATGGAATTTTTGGACA-TT
1 CGGGGT-AAAAATGGAATTTTTGGA-AGTT
* * * *
26342 CAAGGGCATAAATGGTAATTTATGGAAGTTT
1 C-GGGGTAAAAATGG-AATTTTTGGAAG-TT
*
26373 TGGGGTTAAAAATGGAATTTTTGGAAGTT
1 CGGGG-TAAAAATGGAATTTTTGGAAGTT
* * * *
26402 TGAGGGTAATAATGAAATTTTTTGAAGTTT
1 CG-GGGTAAAAATGGAATTTTTGGAAG-TT
*
26432 CGGGGTCAAAAATGGAATTTTGGGAAGTT
1 CGGGGT-AAAAATGGAATTTTTGGAAGTT
* *
26461 CGGGGGAAAAAATAGAATTTTTAGGAAGTT
1 C-GGGGTAAAAATGGAATTTTT-GGAAGTT
*
26491 TGAGGGTAAAAAT-GAGATTTTTGGAAGTT
1 CG-GGGTAAAAATGGA-ATTTTTGGAAGTT
*
26520 CGGGGGTAAAAA-GGAATTTGTGGA
1 C-GGGGTAAAAATGGAATTTTTGGA
26544 CAATTTAGGG
Statistics
Matches: 206, Mismatches: 30, Indels: 49
0.72 0.11 0.17
Matches are distributed among these distances:
27 1 0.00
28 22 0.11
29 84 0.41
30 89 0.43
31 10 0.05
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (28 bp):
CGGGGTAAAAATGGAATTTTTGGAAGTT
Found at i:26443 original size:59 final size:59
Alignment explanation
Indices: 26308--26528 Score: 211
Period size: 59 Copynumber: 3.7 Consensus size: 59
26298 TAATTTTGTG
* * * * *
26308 AGTTTCGAGGTCAAAAATGGAATTTTTGGACA-TTCAAGGG-CATAAATGGTAATTTATGGA
1 AGTTTCGGGGTCAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAT-AAT-GAAATTTTTGGA
* * * *
26368 AGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTTGAGGGTAATAATGAAATTTTTTGA
1 AGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAATAATGAAATTTTTGGA
* * * *
26427 AGTTTCGGGGTCAAAAATGGAATTTTGGGAAGTTCGGGGGAAAAAAT-AGAATTTTTAGGA
1 AGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAATAATGA-AATTTTT-GGA
*
26487 AGTTT-GAGGGT-AAAAAT-GAGATTTTTGGAAGTTCGGGGGTAA
1 AGTTTCG-GGGTCAAAAATGGA-ATTTTTGGAAGTTCGAGGGTAA
26529 AAAGGAATTT
Statistics
Matches: 136, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
58 3 0.02
59 84 0.62
60 47 0.35
61 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.33
Consensus pattern (59 bp):
AGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAATAATGAAATTTTTGGA
Found at i:26526 original size:29 final size:30
Alignment explanation
Indices: 26320--26543 Score: 173
Period size: 29 Copynumber: 7.6 Consensus size: 30
26310 TTTCGAGGTC
** *
26320 AAAAATG-GAATTTTTGGACA-TTCAAGGGC
1 AAAAATGAGAATTTTTGGA-AGTTCGGGGGT
* * * *
26349 ATAAATG-GTAATTTATGGAAGTTTTGGGGTT
1 AAAAATGAG-AATTTTTGGAAG-TTCGGGGGT
* *
26380 AAAAATG-GAATTTTTGGAAGTTTGAGGGT
1 AAAAATGAGAATTTTTGGAAGTTCGGGGGT
* *
26409 AATAATGA-AATTTTTTGAAGTTTC-GGGGT
1 AAAAATGAGAATTTTTGGAAG-TTCGGGGGT
* *
26438 CAAAAATG-GAATTTTGGGAAGTTCGGGGGA
1 -AAAAATGAGAATTTTTGGAAGTTCGGGGGT
* *
26468 AAAAAT-AGAATTTTTAGGAAGTTTGAGGGT
1 AAAAATGAGAATTTTT-GGAAGTTCGGGGGT
26498 AAAAATGAG-ATTTTTGGAAGTTCGGGGGT
1 AAAAATGAGAATTTTTGGAAGTTCGGGGGT
*
26527 AAAAA-G-GAATTTGTGGA
1 AAAAATGAGAATTTTTGGA
26544 CAATTTAGGG
Statistics
Matches: 157, Mismatches: 26, Indels: 25
0.75 0.12 0.12
Matches are distributed among these distances:
27 1 0.01
28 9 0.06
29 69 0.44
30 65 0.41
31 13 0.08
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (30 bp):
AAAAATGAGAATTTTTGGAAGTTCGGGGGT
Found at i:26531 original size:59 final size:58
Alignment explanation
Indices: 26256--26531 Score: 201
Period size: 59 Copynumber: 4.7 Consensus size: 58
26246 GGGAAAATCC
* * ** *
26256 GGGGTTAAAAATGGACTTTTTAGACA-TTCGGGGGTAAAAGGGTAA-TTTT-GTG-AGTTT
1 GGGG-TAAAAATGGAATTTTTGGA-AGTTCGGGGGTAAAAATGAAATTTTTAG-GAAGTTT
* ** * * * *
26313 CGAGGTCAAAAATGGAATTTTTGGACA-TTCAAGGGCATAAATGGTAATTTAT-GGAAGTTTT
1 -GGGGT-AAAAATGGAATTTTTGGA-AGTTCGGGGGTAAAAAT-GAAATTTTTAGGAAG-TTT
* * * *
26374 GGGGTTAAAAATGGAATTTTTGGAAGTTTGAGGGTAATAATGAAATTTTT-TGAAGTTT
1 GGGG-TAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGAAATTTTTAGGAAGTTT
* *
26432 CGGGGTCAAAAATGGAATTTTGGGAAGTTCGGGGGAAAAAAT-AGAATTTTTAGGAAGTTT
1 -GGGGT-AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGA-AATTTTTAGGAAGTTT
26492 GAGGGTAAAAAT-GAGATTTTTGGAAGTTCGGGGGTAAAAA
1 G-GGGTAAAAATGGA-ATTTTTGGAAGTTCGGGGGTAAAAA
26532 GGAATTTGTG
Statistics
Matches: 178, Mismatches: 27, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
57 1 0.01
58 37 0.21
59 88 0.49
60 48 0.27
61 4 0.02
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (58 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGAAATTTTTAGGAAGTTT
Found at i:27705 original size:30 final size:31
Alignment explanation
Indices: 27671--27729 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
27661 ATTATTAATG
*
27671 TCATTAATATTATTATTA-TTATCAAAACAA
1 TCATTAATATTATTAATAGTTATCAAAACAA
*
27701 TCATTAATATTATTAATAGTTATTAAAAC
1 TCATTAATATTATTAATAGTTATCAAAAC
27730 GTTTTCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (31 bp):
TCATTAATATTATTAATAGTTATCAAAACAA
Found at i:28403 original size:18 final size:17
Alignment explanation
Indices: 28374--28454 Score: 90
Period size: 17 Copynumber: 4.6 Consensus size: 17
28364 TAAATAGGTT
*
28374 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTAAAA
* *
28392 TAAATTTAAAATTTTAAG
1 TAAATTT-AAATTTAAAA
*
28410 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
28427 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
28444 TGAATTTAAAT
1 TAAATTTAAAT
28455 CCTGTTGGGC
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
17 34 0.65
18 18 0.35
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:29282 original size:201 final size:204
Alignment explanation
Indices: 28780--29411 Score: 481
Period size: 201 Copynumber: 3.1 Consensus size: 204
28770 CTTCTTCTTA
* ** ** ** ***
28780 GTATCTCATCAGGAAGACGACCATATCACTTGTTTTGGTCCACTTCTCTGTGTTTCATCAGGAAG
1 GTATCTCATCAGGAAGATGACCACCTCACTTGTTTTAATCTGCTTCTCTGTACCTCATCAGGAAG
* ** ** * * * * * *
28845 ATGGTTTTGGTTCACTTCCCCGTA-CTTCACCAGTG-AGCTAA-CTATTTTATTACTTTGACCTG
66 AAGAATTTGGCCCACTTCTCAGTATC-TCATCAG-GAAGCTAACCCA-TTTATTACTTCGACCTA
* * * *** * * * *
28907 CTTCTCAGTATCTCATCAAGAAGCCGGGG-TTCGAAGATTTGCTCATATCGAGCGTGAGTTTGAT
128 CTTCTCAATATCTCATCAAAAAGCTGGGGTTTC-AAGATTTGCTCGCGTTGAGCCT-TGTATGA-
* * *
28971 TTGGTCTTCTTCTCA
190 TTGGTATACTTCTCT
* * * *** ** * *** * *
28986 GTACCTCATCAGAAAGATGGCCGTGTCGTTTGTTTCAATCCATTTCTTTGTATCTCATCAGGAAG
1 GTATCTCATCAGGAAGATGACCACCTCACTTGTTTTAATCTGCTTCTCTGTACCTCATCAGGAAG
* * * * * * *
29051 ACGAATTTGGTCGACTTCTCAGTTTCTCATCAGGAAGAC-GACCCATTTATTGCTTCGACCTGCT
66 AAGAATTTGGCCCACTTCTCAGTATCTCATCAGGAAG-CTAACCCATTTATTACTTCGACCTACT
*
29115 TTTCAATATCTCATCAAAAAGCTGGGG-TTCGAAGATTTGCTCGCGTTGAGCCTTG-A-G-TTGG
130 TCTCAATATCTCATCAAAAAGCTGGGGTTTC-AAGATTTGCTCGCGTTGAGCCTTGTATGATTGG
29176 TATACTTCTCT
194 TATACTTCTCT
29187 GTATCTCATCAGGAAGATGACCACCTCACTTGTTTTAATCTGCTTCTCTGTACCTCATCAGGAAG
1 GTATCTCATCAGGAAGATGACCACCTCACTTGTTTTAATCTGCTTCTCTGTACCTCATCAGGAAG
* ***
29252 AATAATTTGGCCCACTTCTCAGTATCTCATCAGGAAGCTAACTTTTTTATTACTTCGACCTACTT
66 AAGAATTTGGCCCACTTCTCAGTATCTCATCAGGAAGCTAACCCATTTATTACTTCGACCTACTT
* * ** * *
29317 CTCAGTATCTTATCAGGAAGTTGGGGTTTCAAGATTTGCTCGCTTTGAGCCTTGTTTCATTGATT
131 CTCAATATCTCATCAAAAAGCTGGGGTTTCAAGATTTGCTCGCGTTGAGCCTTG--T-A-TGA-T
*
29382 TGGTCTACTTCTCT
191 TGGTATACTTCTCT
29396 GTATCTCATCAGGAAG
1 GTATCTCATCAGGAAG
29412 TTAACCATTT
Statistics
Matches: 337, Mismatches: 75, Indels: 25
0.77 0.17 0.06
Matches are distributed among these distances:
200 1 0.00
201 158 0.47
202 3 0.01
203 1 0.00
205 3 0.01
206 136 0.40
207 5 0.01
209 30 0.09
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (204 bp):
GTATCTCATCAGGAAGATGACCACCTCACTTGTTTTAATCTGCTTCTCTGTACCTCATCAGGAAG
AAGAATTTGGCCCACTTCTCAGTATCTCATCAGGAAGCTAACCCATTTATTACTTCGACCTACTT
CTCAATATCTCATCAAAAAGCTGGGGTTTCAAGATTTGCTCGCGTTGAGCCTTGTATGATTGGTA
TACTTCTCT
Found at i:29523 original size:122 final size:123
Alignment explanation
Indices: 29265--29533 Score: 339
Period size: 122 Copynumber: 2.2 Consensus size: 123
29255 AATTTGGCCC
** * * *
29265 ACTTCTC-AGTATCTCATCAGGAAGCTAACTTTTTTATTACTTCGACCTACTTCTCAGTATCTTA
1 ACTTCTCGA-TATCTCATCAGGAAGCTAACCATTTTATTACTTCAAACTACTTCTCAGTATCTCA
* * * * * * *
29329 TCAGGAAGTTGGGGTTTCAAGATTTGCTCGCTTTGAGCCTTGTTTCATTGATTTGGTCT
65 TCAGGAAGCTGGGGTTTCAAGATTTGCTCACATCGAGCCTCGTTTCATTGATTCGATCT
* * *
29388 ACTTCTCTG-TATCTCATCAGGAAGTTAACCATTTTATTATTTCAAACTGCTTCTCAGTATCTCA
1 ACTTCTC-GATATCTCATCAGGAAGCTAACCATTTTATTACTTCAAACTACTTCTCAGTATCTCA
29452 TCA-GAAGCTGGGG-TTCGAAGATTTGCTCACATCGAGCCTCGTTTCATTGATTCGATCT
65 TCAGGAAGCTGGGGTTTC-AAGATTTGCTCACATCGAGCCTCGTTTCATTGATTCGATCT
*
29510 TCTTCTCGATATCTCATCAGGAAG
1 ACTTCTCGATATCTCATCAGGAAG
29534 ATGATCGCAT
Statistics
Matches: 126, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
121 4 0.03
122 65 0.52
123 57 0.45
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (123 bp):
ACTTCTCGATATCTCATCAGGAAGCTAACCATTTTATTACTTCAAACTACTTCTCAGTATCTCAT
CAGGAAGCTGGGGTTTCAAGATTTGCTCACATCGAGCCTCGTTTCATTGATTCGATCT
Found at i:30543 original size:21 final size:17
Alignment explanation
Indices: 30497--30533 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
30487 CTCCTCCTGA
30497 GAAATTTTTATGTATGG
1 GAAATTTTTATGTATGG
30514 GAAATTTTTATGTATGG
1 GAAATTTTTATGTATGG
30531 GAA
1 GAA
30534 GTATCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.43
Consensus pattern (17 bp):
GAAATTTTTATGTATGG
Found at i:39876 original size:29 final size:28
Alignment explanation
Indices: 39844--39943 Score: 76
Period size: 29 Copynumber: 3.5 Consensus size: 28
39834 TTTTGTGAAA
39844 ATTCGGGGTTAAAAATGGACTTTTTAGAC
1 ATTCGGGGTTAAAAATGGA-TTTTTAGAC
* * *
39873 ATTCGGGGGT-AAAAGGGTATTTTTAGAG
1 ATTCGGGGTTAAAAATGG-ATTTTTAGAC
* ** * *
39901 TTTCAAGGTCAAAAATGGAATTTTTGGAC
1 ATTCGGGGTTAAAAATGG-ATTTTTAGAC
* *
39930 ATTTGGGGATAAAA
1 ATTCGGGGTTAAAA
39944 TGGTAAATTT
Statistics
Matches: 51, Mismatches: 18, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
28 19 0.37
29 32 0.63
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (28 bp):
ATTCGGGGTTAAAAATGGATTTTTAGAC
Found at i:39879 original size:58 final size:58
Alignment explanation
Indices: 39817--40106 Score: 176
Period size: 59 Copynumber: 5.0 Consensus size: 58
39807 TTTTGAATTC
* ** *
39817 TCGGGGTGAAATGGTAATTTTGTGAAAATTCGGGGTTAAAAATGGACTTTTTAGACAT
1 TCGGGGTAAAATGGTAATTTTGTGAAGTTTCGGGGTTAAAAATGGAATTTTTAGACAT
* ** * *
39875 TCGGGGGTAAAAGGGT-ATTTT-T-AGAGTTTCAAGGTCAAAAATGGAATTTTTGGACAT
1 TC-GGGGTAAAATGGTAATTTTGTGA-AGTTTCGGGGTTAAAAATGGAATTTTTAGACAT
* * *
39932 TTGGGGATAAAATGGTAAATTTTG-GAAGTTTTGGGGTTAAAAA-GGAATTTTTGGA-AGTT
1 TCGGGG-TAAAATGGT-AATTTTGTGAAGTTTCGGGGTTAAAAATGGAATTTTTAGACA--T
* *
39991 TTGGGGTCAAAAATGG-AATTTT-TGGAAG-TTCGGCAG-TAAAAATGGAATTTTTAGGA-AGT
1 TCGGGGT--AAAATGGTAATTTTGT-GAAGTTTCGG-GGTTAAAAATGGAATTTTTA-GACA-T
* * * * *
40050 TTGAGGGTAAAAATGAG-ATTTTTG-GAAG-TTCGGGGGTAAAAATAGAATTTTTGGACA
1 TCG-GGGT-AAAATG-GTAATTTTGTGAAGTTTCGGGGTTAAAAATGGAATTTTTAGACA
40107 ATTTAGGGAC
Statistics
Matches: 188, Mismatches: 23, Indels: 41
0.75 0.09 0.16
Matches are distributed among these distances:
56 5 0.03
57 37 0.20
58 39 0.21
59 86 0.46
60 21 0.11
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (58 bp):
TCGGGGTAAAATGGTAATTTTGTGAAGTTTCGGGGTTAAAAATGGAATTTTTAGACAT
Found at i:39983 original size:29 final size:28
Alignment explanation
Indices: 39911--40104 Score: 207
Period size: 29 Copynumber: 6.6 Consensus size: 28
39901 TTTCAAGGTC
39911 AAAAATGGAATTTTTGGACA-TTTGGGG-
1 AAAAATGGAATTTTTGGA-AGTTTGGGGT
*
39938 ATAAAATGGTAAATTTTGGAAGTTTTGGGGTT
1 A-AAAATGG-AATTTTTGGAAG-TTTGGGG-T
39970 AAAAA-GGAATTTTTGGAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAAG-TTTGGGGT
* *
39998 CAAAAATGGAATTTTTGGAAGTTCGGCAGT
1 -AAAAATGGAATTTTTGGAAGTTTGG-GGT
40028 AAAAATGGAATTTTTAGGAAGTTTGAGGGT
1 AAAAATGGAATTTTT-GGAAGTTTG-GGGT
*
40058 AAAAAT-GAGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGA-ATTTTTGGAAGTT-TGGGGT
*
40087 AAAAATAGAATTTTTGGA
1 AAAAATGGAATTTTTGGA
40105 CAATTTAGGG
Statistics
Matches: 146, Mismatches: 7, Indels: 26
0.82 0.04 0.15
Matches are distributed among these distances:
27 1 0.01
28 9 0.06
29 80 0.55
30 50 0.34
31 5 0.03
32 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.34
Consensus pattern (28 bp):
AAAAATGGAATTTTTGGAAGTTTGGGGT
Found at i:39994 original size:59 final size:58
Alignment explanation
Indices: 39911--40104 Score: 195
Period size: 59 Copynumber: 3.3 Consensus size: 58
39901 TTTCAAGGTC
* *
39911 AAAAATGGAATTTTTGGACA--TTTGGGG-ATAAAATGGTAAATTTTGGAAGTTTTGG-GGTT
1 AAAAATGGAATTTTTGGA-AGTTTTGGGGTA-AAAATGG-AAATTTTGGAAG-TTCGGCAG-T
*
39970 AAAAA-GGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGGCAGT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGT-AAAAATGGAAATTTTGGAAGTTCGGCAGT
* **
40028 AAAAATGGAATTTTTAGGAAG-TTTGAGGGTAAAAAT-GAGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTT-GGAAGTTTTG-GGGTAAAAATGGA-AATTTTGGAAGTTCGGCAGT
*
40087 AAAAATAGAATTTTTGGA
1 AAAAATGGAATTTTTGGA
40105 CAATTTAGGG
Statistics
Matches: 120, Mismatches: 6, Indels: 19
0.83 0.04 0.13
Matches are distributed among these distances:
57 1 0.01
58 27 0.22
59 75 0.62
60 16 0.13
61 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.34
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAAGTTTTGGGGTAAAAATGGAAATTTTGGAAGTTCGGCAGT
Found at i:41941 original size:17 final size:17
Alignment explanation
Indices: 41916--41996 Score: 90
Period size: 17 Copynumber: 4.6 Consensus size: 17
41906 TAAATAGATT
*
41916 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTAAAA
* *
41934 TAAATTTAAATTTTTAAG
1 TAAATTTAAA-TTTAAAA
*
41952 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
41969 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
41986 TGAATTTAAAT
1 TAAATTTAAAT
41997 CCTGTTGGGC
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
17 34 0.65
18 18 0.35
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:41971 original size:35 final size:34
Alignment explanation
Indices: 41916--41995 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 34
41906 TAAATAGATT
* * * *
41916 TAAACTTTAAATTTATAATAAATTTAAATTTTTAAG
1 TAAA-TTTAAACTTAAAATAAATTT-AATTTTAAAA
41952 TAAATTTAAACTTAAAATAAATTTAATTTTAAAA
1 TAAATTTAAACTTAAAATAAATTTAATTTTAAAA
*
41986 TGAATTTAAA
1 TAAATTTAAA
41996 TCCTGTTGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 17 0.44
35 18 0.46
36 4 0.10
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (34 bp):
TAAATTTAAACTTAAAATAAATTTAATTTTAAAA
Found at i:47670 original size:41 final size:41
Alignment explanation
Indices: 47618--47705 Score: 158
Period size: 41 Copynumber: 2.1 Consensus size: 41
47608 TCACAGCTTA
*
47618 ATTATTATTTTTTACATATGACAAATTGAGATGATGATAAC
1 ATTATTATTTTTTACATATGACAAATTGAGATGATAATAAC
47659 ATTATTATTTTTTACATATGACAAATTGAGATGATAATAAC
1 ATTATTATTTTTTACATATGACAAATTGAGATGATAATAAC
*
47700 AATATT
1 ATTATT
47706 TGAACTTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (41 bp):
ATTATTATTTTTTACATATGACAAATTGAGATGATAATAAC
Found at i:52882 original size:17 final size:18
Alignment explanation
Indices: 52843--52939 Score: 98
Period size: 18 Copynumber: 5.5 Consensus size: 18
52833 TTAAACCCAT
52843 TTTAAGATTT-ATTTTAAGA
1 TTTAA-ATTTGATTTTAA-A
*
52862 -TT-AATTTGATTTTGAA
1 TTTAAATTTGATTTTAAA
52878 TTTAAATTT-ATTTTAAA
1 TTTAAATTTGATTTTAAA
52895 TTTAAATTTG-TTTTAAAA
1 TTTAAATTTGATTTT-AAA
*
52913 TTTAAATTTAGA-TTTATA
1 TTTAAATTT-GATTTTAAA
52931 TTTAAATTT
1 TTTAAATTT
52940 AAAACTTATT
Statistics
Matches: 68, Mismatches: 3, Indels: 15
0.79 0.03 0.17
Matches are distributed among these distances:
16 5 0.07
17 29 0.43
18 30 0.44
19 4 0.06
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTAAATTTGATTTTAAA
Found at i:52885 original size:6 final size:6
Alignment explanation
Indices: 52876--52942 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
52866 TTTGATTTTG
* **
52876 AATTTA AATTT- ATTTTA AATTTA AATTT- GTTTTAA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
* *
52923 GATTTA TATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AA
52943 ACTTATTATA
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.14
6 39 0.80
7 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
AATTTA
Found at i:52916 original size:24 final size:24
Alignment explanation
Indices: 52876--52942 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
52866 TTTGATTTTG
* *
52876 AATTTAAATTT-ATTTTAAATTTA
1 AATTTATATTTAAATTTAAATTTA
*
52899 AATTTGT-TTTAAAATTTAAATTTA
1 AATTTATATTT-AAATTTAAATTTA
*
52923 GATTTATATTTAAATTTAAA
1 AATTTATATTTAAATTTAAA
52943 ACTTATTATA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
22 3 0.08
23 5 0.14
24 25 0.69
25 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (24 bp):
AATTTATATTTAAATTTAAATTTA
Found at i:53648 original size:27 final size:27
Alignment explanation
Indices: 53616--53690 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
53606 ATAAATATAT
*
53616 ATATATATATATATATATTAAATGTTTTA
1 ATATATATA-ATA-ATAATAAATGTTTTA
* * *
53645 ATATTTTTAATAATAATAATTGTTTTA
1 ATATATATAATAATAATAAATGTTTTA
53672 ATA-ATAATAATAATAATAA
1 ATATAT-ATAATAATAATAA
53691 TAAATAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 1 0.03
27 28 0.72
28 3 0.08
29 7 0.18
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (27 bp):
ATATATATAATAATAATAAATGTTTTA
Found at i:53664 original size:18 final size:19
Alignment explanation
Indices: 53643--53683 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
53633 TTAAATGTTT
53643 TAATAT-TTTTAATAATAA
1 TAATATGTTTTAATAATAA
53661 TAAT-TGTTTTAATAATAA
1 TAATATGTTTTAATAATAA
53679 TAATA
1 TAATA
53684 ATAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TAATATGTTTTAATAATAA
Found at i:53676 original size:3 final size:3
Alignment explanation
Indices: 53670--53705 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
53660 ATAATTGTTT
*
53670 TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAT TAA TA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA
53706 CCATTAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:53691 original size:27 final size:27
Alignment explanation
Indices: 53638--53691 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
53628 ATATATTAAA
* **
53638 TGTTTTAATATTTTTAATAATAATAAT
1 TGTTTTAATAATAATAATAATAATAAT
53665 TGTTTTAATAATAATAATAATAATAAT
1 TGTTTTAATAATAATAATAATAATAAT
53692 AAATAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (27 bp):
TGTTTTAATAATAATAATAATAATAAT
Found at i:54770 original size:59 final size:59
Alignment explanation
Indices: 54697--54955 Score: 235
Period size: 59 Copynumber: 4.4 Consensus size: 59
54687 AGAGGTCTCT
* ** * * *
54697 AAACTGTCCAAAAATTCCATTTTTACCCTCGAACTTTTAGAAATTCCATTTTTGACCTCG
1 AAACT-TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCA
54757 AAACTTCCAAAAATTCCATTTTTA-CCTCCAAAACTTCCAAAAATTCCA-TTTTAACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCT-C-AAACTTCCAAAAATTCCATTTTTAACCTCA
* * * * * * *
54816 AAACTTCCAAAAATTTCATTTTAACCCTAAAACTTCTAAAAAATCCAATTTTACCCTC-
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCA
* * * *
54874 -AACTTTCTAAAAATTCTATTTTTACACC-CGAACCT-CAAAAATTTCCATTTTTAACC-CTA
1 AAAC-TTCCAAAAATTCCATTTTTAC-CCTCAAACTTCCAAAAA-TTCCATTTTTAACCTC-A
*
54933 AAACTTTCAAAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
54956 GCCCATGGAT
Statistics
Matches: 162, Mismatches: 26, Indels: 22
0.77 0.12 0.10
Matches are distributed among these distances:
57 9 0.06
58 51 0.31
59 71 0.44
60 31 0.19
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.35
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCA
Found at i:54771 original size:30 final size:29
Alignment explanation
Indices: 54697--55070 Score: 204
Period size: 29 Copynumber: 12.8 Consensus size: 29
54687 AGAGGTCTCT
54697 AAACTGTCCAAAAATTCCATTTTTACCCTCG
1 AAACT-TCCAAAAATTCCATTTTTA-CCTCG
** *
54728 -AACTTTTAGAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
*
54757 AAACTTCCAAAAATTCCATTTTTACCTCCA
1 AAACTTCCAAAAATTCCATTTTTACCT-CG
* *
54787 AAACTTCCAAAAATTCCATTTTAACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCTCG
* * *
54816 AAACTTCCAAAAATTTCATTTTAACC-CTA
1 AAACTTCCAAAAATTCCATTTTTACCTC-G
* * *
54845 AAACTTCTAAAAAATCCAATTTTACCCTC-
1 AAACTTCCAAAAATTCCATTTTTA-CCTCG
* * *
54874 -AACTTTCTAAAAATTCTATTTTTACACCCG
1 AAAC-TTCCAAAAATTCCATTTTTAC-CTCG
* *
54904 -AACCT-CAAAAATTTCCATTTTTAACC-CTA
1 AAACTTCCAAAAA-TTCCATTTTT-ACCTC-G
* ** *
54933 AAACTTTCAAAAATTACCATTTTGCCCATGG
1 AAACTTCCAAAAATT-CCATTTTTACC-TCG
* * *
54964 ATA--TCCAAAAACTCCATTTTCGACCTCG
1 AAACTTCCAAAAATTCCATTTT-TACCTCG
54992 AAAC-TCTC-AAAATTACC-TTTTT-CCTC-
1 AAACTTC-CAAAAATT-CCATTTTTACCTCG
* * *
55018 AAA-TGTCTAAAAATTCTATTTTTAACCCCG
1 AAACT-TCCAAAAATTCCATTTTT-ACCTCG
*
55048 -AACTTTCCCAAAATTACCATTTT
1 AAAC-TTCCAAAAATT-CCATTTT
55071 GCTCCCGAAA
Statistics
Matches: 271, Mismatches: 41, Indels: 62
0.72 0.11 0.17
Matches are distributed among these distances:
26 4 0.01
27 17 0.06
28 22 0.08
29 128 0.47
30 77 0.28
31 23 0.08
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCTCG
Found at i:54974 original size:88 final size:86
Alignment explanation
Indices: 54823--54983 Score: 184
Period size: 88 Copynumber: 1.8 Consensus size: 86
54813 TCAAAACTTC
* * *
54823 CAAAAATTTCATTTTAACCCTAAAACTTCTAAAAAATCCAATTTTACCCTCAACTTTCTAAAAAT
1 CAAAAATTTCATTTTAACCCTAAAACTTCTAAAAAATCCAATTTTACCCTCAACTATCCAAAAAC
*
54888 TCTATTTTTACACCCGAACCT
66 TCCATTTTTACACCCGAACCT
* * **
54909 CAAAAATTTCCATTTTTAACCCTAAAACTT-TCAAAAATTACC-ATTTTGCCCATGGA-TATCCA
1 CAAAAATTT-CA-TTTTAACCCTAAAACTTCT-AAAAAAT-CCAATTTTACCC-TCAACTATCCA
54971 AAAACTCCATTTT
61 AAAACTCCATTTT
54984 CGACCTCGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
86 9 0.15
87 3 0.05
88 46 0.74
89 4 0.06
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (86 bp):
CAAAAATTTCATTTTAACCCTAAAACTTCTAAAAAATCCAATTTTACCCTCAACTATCCAAAAAC
TCCATTTTTACACCCGAACCT
Found at i:65907 original size:114 final size:114
Alignment explanation
Indices: 65685--65900 Score: 321
Period size: 114 Copynumber: 1.9 Consensus size: 114
65675 AATGAAACAA
*
65685 GGCTCAAAGCAAGCAAATCTTCGAACCTCAGCTTCCTGATAAGATACTGAGAAGCAGGTCGAAGA
1 GGCTCAAAGCAAGCAAATCTTCAAACCTCAGCTTCCTGATAAGATACTGAGAAGCAGGTCGAAGA
*
65750 CATAAAATGTTAGCTTCCTGATGAGATACAGAGAAGTATACCAACTTAG
66 CATAAAATGTTACCTTCCTGATGAGATACAGAGAAGTATACCAACTTAG
* * *
65799 GGCTCAATGTAAGCAAATCTTTAAATCC-CAGCTTCCTGATGAA-ATACTGAGAAGCAGGTCGAA
1 GGCTCAAAGCAAGCAAATCTTCAAA-CCTCAGCTTCCTGAT-AAGATACTGAGAAGCAGGTCGAA
* *
65862 G-CAATAAAATGTTACCTTCTTGATGAGATACTGAGAAGT
64 GAC-ATAAAATGTTACCTTCCTGATGAGATACAGAGAAGT
65901 GAACCAAATT
Statistics
Matches: 92, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
113 1 0.01
114 87 0.95
115 4 0.04
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (114 bp):
GGCTCAAAGCAAGCAAATCTTCAAACCTCAGCTTCCTGATAAGATACTGAGAAGCAGGTCGAAGA
CATAAAATGTTACCTTCCTGATGAGATACAGAGAAGTATACCAACTTAG
Found at i:66170 original size:115 final size:113
Alignment explanation
Indices: 66005--66335 Score: 378
Period size: 116 Copynumber: 2.9 Consensus size: 113
65995 TCAAACCCAC
* *
66005 GCTCGATGTGAGCAAATCCTT-GAACCCAGCTTCTTGATCAGATACTGAGAAGTAAGTGAAAATA
1 GCTCGATGTGAGCAAAT-CTTCGAACCCAGCTTCTTGATGAGATACTGAGAAGTAAGTG-AAACA
* *
66069 ATGAAATGGTTAGCTTCCTGATGAGACACAAAGGAGTATACCAACTCAGG
64 ATGAAATGGTTAGCTTCCTGATGAGACACAAAGAAGAATACCAACTCAGG
* * * * *
66119 GCTCGATGTGATCAAATCTTCAAATCCCAGCTTCTTGATGAGATACAGAGAAGCAGATTGAAACA
1 GCTCGATGTGAGCAAATCTTCGAA-CCCAGCTTCTTGATGAGATACTGAGAAGTA-AGTGAAACA
** * * * *
66184 A-GTAAGGCGGTCATCTTCCTGATGAGATACAAAGAAGAATATCAACTCAGG
64 ATG-AA-ATGGTTAGCTTCCTGATGAGACACAAAGAAGAATACCAACTCAGG
* * * *
66235 ACTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAA-CCCAGCTTCTTGATGAGATACTGAGAAGTAAGT-GAAACA
* * *
66300 ATAAAATGGTTAGCTTCCTGATGAGATACTAAGAAG
64 ATGAAATGGTTAGCTTCCTGATGAGACACAAAGAAG
66336 TGAACCAAAT
Statistics
Matches: 179, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
113 3 0.02
114 19 0.11
115 61 0.34
116 96 0.54
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (113 bp):
GCTCGATGTGAGCAAATCTTCGAACCCAGCTTCTTGATGAGATACTGAGAAGTAAGTGAAACAAT
GAAATGGTTAGCTTCCTGATGAGACACAAAGAAGAATACCAACTCAGG
Found at i:66230 original size:116 final size:113
Alignment explanation
Indices: 65914--66287 Score: 349
Period size: 116 Copynumber: 3.2 Consensus size: 113
65904 CCAAATTCAT
* * * * *
65914 CTTCCTGATGAGATACAGAGAAGCGGATTGAAATAAGCGATGCAGTCATCTTCCTGATGAGATTC
1 CTTCCTGATGAGATACAGAGAAGCAGATTGAAA-AAG-TAAGCGGTCATCTTCCTGATGAGATAC
* * *
65979 TGAGAAGAAGACCAAATCAAACCCA-CGCTCGATGTGAGCAAATCCTT-GAACCCAG
64 --A-AAGAAGA--ATATC-AACTCAGGGCTCGATGTGAGCAAAT-CTTCGAACCCAG
* * * * * * ** * * *
66034 CTTCTTGATCAGATACTGAGAAGTA-AGTGAAAATAATGAAATGGTTAGCTTCCTGATGAGACAC
1 CTTCCTGATGAGATACAGAGAAGCAGATTGAAAA-AGT-AAGCGGTCATCTTCCTGATGAGATAC
* * * * *
66098 AAAGGAGTATACCAACTCAGGGCTCGATGTGATCAAATCTTCAAATCCCAG
64 AAAGAAGAATATCAACTCAGGGCTCGATGTGAGCAAATCTTCGAA-CCCAG
*
66149 CTTCTTGATGAGATACAGAGAAGCAGATTGAAACAAGTAAGGCGGTCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCAGATTGAAA-AAGTAA-GCGGTCATCTTCCTGATGAGATAC
*
66214 AAAGAAGAATATCAACTCAGGACTCGATGTGAGCAAATCTTCGAACCCCAG
64 AAAGAAGAATATCAACTCAGGGCTCGATGTGAGCAAATCTTCGAA-CCCAG
*
66265 CTTCCTGATGAGATACTGAGAAG
1 CTTCCTGATGAGATACAGAGAAG
66288 TAGGTCGAAG
Statistics
Matches: 203, Mismatches: 43, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
113 8 0.04
114 21 0.10
115 29 0.14
116 97 0.48
117 2 0.01
118 1 0.00
119 25 0.12
120 20 0.10
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (113 bp):
CTTCCTGATGAGATACAGAGAAGCAGATTGAAAAAGTAAGCGGTCATCTTCCTGATGAGATACAA
AGAAGAATATCAACTCAGGGCTCGATGTGAGCAAATCTTCGAACCCAG
Found at i:66616 original size:206 final size:206
Alignment explanation
Indices: 66193--66633 Score: 491
Period size: 206 Copynumber: 2.2 Consensus size: 206
66183 AAGTAAGGCG
* * * * **
66193 GTCATCTTCCTGATGAGATAC--A-AAGAAGA--ATATC-AACTCAGGACTCGATGTGAGCAAAT
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACG-CTCGATATGAAAAAAT
* * * *
66252 CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAATGGTTAGCTTC
65 CCTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGAAGGTCGAAGCAATAAAATGGTTAACTTC
* * * ** * * * * * **
66317 CTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAATGGATTGAA
130 CTGACGAAATACGAAGAAGTGAACCAAAACCATCTCCCTGATGAAACACAAAGAAATGAATCAAA
* *
66382 ATAAGCGATGCA
195 ACAAGCGATACA
* *
66394 GTCATCTTCTTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAAAAAATC
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAAAAAATC
* *
66459 CTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGCAAGTTC-AAGTAATAAAATGGTTAACTTC
66 CTCGAACCCCAGCTTCCTGATAAGATACTGAGAAG-AAGGTCGAAGCAATAAAATGGTTAACTTC
** * *
66523 CTGACGAAATACGGGGAAGTGAACCAAAACCATCTCCCTGATGAAACACAGAGAAGTGAATCAAA
130 CTGACGAAATACGAAGAAGTGAACCAAAACCATCTCCCTGATGAAACACAAAGAAATGAATCAAA
* **
66588 ACAAGTGATATG
195 ACAAGCGATACA
*
66600 GTCGTCTTCCTGATGAGATACTGAGAAGAAGACC
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACC
66634 TAGTCAATGA
Statistics
Matches: 195, Mismatches: 38, Indels: 9
0.81 0.16 0.04
Matches are distributed among these distances:
201 19 0.10
203 1 0.01
204 7 0.04
206 158 0.81
207 10 0.05
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.22
Consensus pattern (206 bp):
GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAAAAAATC
CTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGAAGGTCGAAGCAATAAAATGGTTAACTTCC
TGACGAAATACGAAGAAGTGAACCAAAACCATCTCCCTGATGAAACACAAAGAAATGAATCAAAA
CAAGCGATACA
Found at i:66979 original size:17 final size:17
Alignment explanation
Indices: 66949--67011 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
66939 GGCCTAACAG
*
66949 AATTTGAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
66966 AAATTAAGTTTATTTTA
1 AATTTAAATTTATTTTA
*
66983 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTTA
67000 AATTTAAATTTA
1 AATTTAAATTTA
67012 AATTTATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:67004 original size:7 final size:6
Alignment explanation
Indices: 66949--67017 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
66939 GGCCTAACAG
* * * * *
66949 AATTTG AATTT- ATTTTA AAATTA AGTTT- ATTTTA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
66994 -ATTTGA AATTTA AATTTA AATTTA
1 AATTT-A AATTTA AATTTA AATTTA
67018 TTTAAATAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.08
5 8 0.16
6 35 0.69
7 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (6 bp):
AATTTA
Found at i:67005 original size:23 final size:22
Alignment explanation
Indices: 66979--67024 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 22
66969 TTAAGTTTAT
66979 TTTAAATTTAAATTTATTTGAAA
1 TTTAAATTTAAATTTATTT-AAA
67002 TTTAAATTTAAATTTATTTAAA
1 TTTAAATTTAAATTTATTTAAA
67024 T
1 T
67025 AATGTCCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTAAATTTAAATTTATTTAAA
Found at i:69200 original size:60 final size:60
Alignment explanation
Indices: 69130--69248 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
69120 ATGTACTTAG
* ** *
69130 GATGGTTTTGGATAGGTAGTGGGATGTGGTACGGTGCGTTTAGTTTATTTTTTGTCTCAA
1 GATGGGTTTGGATAAATAGTGGGATGTGGTACGGTGCGTTTAATTTATTTTTTGTCTCAA
69190 GATGGGTTTGGATAAATAGTGGGATGTGGTACGGTGCGTTTAATTTATTTTTTGTCTCA
1 GATGGGTTTGGATAAATAGTGGGATGTGGTACGGTGCGTTTAATTTATTTTTTGTCTCA
69249 CGCTATAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.18, C:0.07, G:0.32, T:0.43
Consensus pattern (60 bp):
GATGGGTTTGGATAAATAGTGGGATGTGGTACGGTGCGTTTAATTTATTTTTTGTCTCAA
Done.