Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013015.1 Kokia drynarioides strain JFW-HI SEQ_128033, 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: 47976
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:11370 original size:16 final size:18
Alignment explanation
Indices: 11328--11363 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
11318 AATAAAAATT
11328 ATAATTT-TATTATTTAA
1 ATAATTTATATTATTTAA
11345 ATAATTTATATT-TTTAA
1 ATAATTTATATTATTTAA
11362 AT
1 AT
11364 TTTTATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATAATTTATATTATTTAA
Found at i:12611 original size:6 final size:6
Alignment explanation
Indices: 12600--12653 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
12590 GCGGGACCTT
* ** * *
12600 TTTTAA TTTTAA ATTTAA AATTAA TCTTAA ATTTAA TTTTAA TTTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
12648 TTTTAA
1 TTTTAA
12654 AATTAAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (6 bp):
TTTTAA
Found at i:12629 original size:18 final size:18
Alignment explanation
Indices: 12602--12659 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
12592 GGGACCTTTT
12602 TTAATTTTAAATTTAAAA
1 TTAATTTTAAATTTAAAA
* **
12620 TTAATCTTAAATTTAATT
1 TTAATTTTAAATTTAAAA
*
12638 TTAATTTTAATTTTAAAA
1 TTAATTTTAAATTTAAAA
12656 TTAA
1 TTAA
12660 AAAATTCAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATTTTAAATTTAAAA
Found at i:13388 original size:30 final size:29
Alignment explanation
Indices: 13354--13427 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 29
13344 AGTAACTATT
13354 TTAATAATAATAA-TAATATTAATGATATCA
1 TTAATAATAATAAGTAATATTAAT-AT-TCA
** *
13384 TTAATAATAAATAAGTTTTTCTTAATATTCA
1 TTAATAAT-AATAAG-TAATATTAATATTCA
13415 TTAATAATAATAA
1 TTAATAATAATAA
13428 ATGTTTTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
30 13 0.34
31 16 0.42
32 2 0.05
33 7 0.18
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (29 bp):
TTAATAATAATAAGTAATATTAATATTCA
Found at i:13441 original size:31 final size:31
Alignment explanation
Indices: 13381--13441 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
13371 ATTAATGATA
* *
13381 TCATTAATAATAAATAAGTTTTTCTTAATAT
1 TCATTAATAATAAATAAATTTTTCATAATAT
*
13412 TCATTAATAAT-AATAAATGTTTTGATAATA
1 TCATTAATAATAAATAAAT-TTTTCATAATA
13442 ATAATATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (31 bp):
TCATTAATAATAAATAAATTTTTCATAATAT
Found at i:13460 original size:21 final size:19
Alignment explanation
Indices: 13407--13469 Score: 74
Period size: 18 Copynumber: 3.2 Consensus size: 19
13397 AGTTTTTCTT
13407 AATATTCATTAATAATAATA
1 AATATT-ATTAATAATAATA
* *
13427 AATGTT-TTGATAATAATA
1 AATATTATTAATAATAATA
13445 ATATTATTATTAATAATAATA
1 A-A-TATTATTAATAATAATA
13466 AATA
1 AATA
13470 AAAAAAAGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 12 0.33
19 3 0.08
20 9 0.25
21 12 0.33
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (19 bp):
AATATTATTAATAATAATA
Found at i:14487 original size:30 final size:29
Alignment explanation
Indices: 14431--14798 Score: 307
Period size: 29 Copynumber: 12.5 Consensus size: 29
14421 TAAACCTACA
* * *
14431 AAAAATTCTATTTTTACCCCCGAACTTCC
1 AAAAATTCCATTTTTACCCTCAAACTTCC
*
14460 AAAAATTCCATTTTTAACCCTAAAACTTCC
1 AAAAATTCCATTTTT-ACCCTCAAACTTCC
***
14490 AAAAATTTTGTTTTTACCC-CTAAACTTCC
1 AAAAATTCCATTTTTACCCTC-AAACTTCC
* * *
14519 AAAAATTCCATTTTTACACTCGAATTTCC
1 AAAAATTCCATTTTTACCCTCAAACTTCC
* * *
14548 AAAAATTCAATTTTTTTAACCACGAAACTTCC
1 AAAAATTCCA--TTTTTACCCTC-AAACTTCC
* * *
14580 AAAAATTCCATTTTTACCCCCGAACATCC
1 AAAAATTCCATTTTTACCCTCAAACTTCC
* *
14609 AAAAATCCCATTTTTAACCCTAAAACTTCC
1 AAAAATTCCATTTTT-ACCCTCAAACTTCC
* * * *
14639 AAAAATTCCAATTTTATCCTCAAATTTCT
1 AAAAATTCCATTTTTACCCTCAAACTTCC
*
14668 AAAAA-TCCTATTTTTAGCCC-CAAAACTTTC
1 AAAAATTCC-ATTTTTA-CCCTC-AAACTTCC
** *
14698 AAAAATTCCATTTTTACCCTTGAATTTCC
1 AAAAATTCCATTTTTACCCTCAAACTTCC
* *
14727 AAGAATCCCATTTTTTACCC-CGAAACTTCC
1 AAAAATTCCA-TTTTTACCCTC-AAACTTCC
* * *
14757 AAAAATTCCATTTTTGCCCT-TAACCTCC
1 AAAAATTCCATTTTTACCCTCAAACTTCC
14785 -AAAATCTCCATTTT
1 AAAAAT-TCCATTTT
14799 CGACCTTGAA
Statistics
Matches: 268, Mismatches: 55, Indels: 33
0.75 0.15 0.09
Matches are distributed among these distances:
27 5 0.02
28 17 0.06
29 122 0.46
30 98 0.37
31 11 0.04
32 15 0.06
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCTCAAACTTCC
Found at i:14516 original size:59 final size:58
Alignment explanation
Indices: 14431--14776 Score: 361
Period size: 59 Copynumber: 5.8 Consensus size: 58
14421 TAAACCTACA
* ** *
14431 AAAAATTCTATTTTTACCCCCG-AACTTCCAAAAATTCCATTTTTAACCCTAAAACTTCC
1 AAAAATCCTATTTTTA-CCCCGAAACTTCCAAAAATTCCATTTTT-ACCCTCGAATTTCC
** * * *
14490 AAAAATTTTGTTTTTACCCCTAAACTTCCAAAAATTCCATTTTTACACTCGAATTTCC
1 AAAAATCCTATTTTTACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAATTTCC
* * * * **
14548 AAAAATTCAATTTTTTTAACCACGAAACTTCCAAAAATTCCATTTTTACCCCCGAACATCC
1 AAAAA-TC-CTATTTTT-ACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAATTTCC
* ** * * * *
14609 AAAAATCCCATTTTTAACCCTAAAACTTCCAAAAATTCCAATTTTATCCTCAAATTTCT
1 AAAAATCCTATTTTT-ACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAATTTCC
* * *
14668 AAAAATCCTATTTTTAGCCCCAAAACTTTCAAAAATTCCATTTTTACCCTTGAATTTCC
1 AAAAATCCTATTTTTA-CCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAATTTCC
* * *
14727 AAGAATCCCATTTTTTACCCCGAAACTTCCAAAAATTCCATTTTTGCCCT
1 AAAAATCCTA-TTTTTACCCCGAAACTTCCAAAAATTCCATTTTTACCCT
14777 TAACCTCCAA
Statistics
Matches: 239, Mismatches: 42, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
58 20 0.08
59 163 0.68
60 14 0.06
61 42 0.18
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (58 bp):
AAAAATCCTATTTTTACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAATTTCC
Found at i:14805 original size:28 final size:29
Alignment explanation
Indices: 14758--14820 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
14748 GAAACTTCCA
* * *
14758 AAAATTCCATTTTTGCCCTT-AACCTC-C
1 AAAATTCCATTTTCGACCTTGAAACTCTC
14785 AAAATCTCCATTTTCGACCTTGAAACTCTC
1 AAAAT-TCCATTTTCGACCTTGAAACTCTC
14815 AAAATT
1 AAAATT
14821 ACCCTTTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 5 0.17
28 13 0.43
29 6 0.20
30 6 0.20
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAATTCCATTTTCGACCTTGAAACTCTC
Found at i:14818 original size:58 final size:58
Alignment explanation
Indices: 14448--14818 Score: 185
Period size: 59 Copynumber: 6.3 Consensus size: 58
14438 CTATTTTTAC
** * * **** *
14448 CCCCG-AACTTCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAATTTTGTTTT-TA
1 CCCCGAAACTT-CAAAAATTCCATTTTT-ACCCTTGAACCTCCAAGAATCCCATTTTCGA
* * * ** * * * **
14506 CCCCTAAACTTCCAAAAATTCCATTTTTACACTCGAATTTCCAAAAATTCAATTTTTTTAA
1 CCCCGAAACTT-CAAAAATTCCATTTTTACCCTTGAACCTCCAAGAATCCCA--TTTTCGA
* ** * * **
14567 CCACGAAACTTCCAAAAATTCCATTTTTACCCCCGAACATCCAAAAATCCCATTTTTAA
1 CCCCGAAACTT-CAAAAATTCCATTTTTACCCTTGAACCTCCAAGAATCCCATTTTCGA
** * * ** ** * * * *
14626 CCCTAAAACTTCCAAAAATTCCAATTTTATCCTCAAATTTCTAAAAATCCTATTTT-TA
1 CCCCGAAACTT-CAAAAATTCCATTTTTACCCTTGAACCTCCAAGAATCCCATTTTCGA
* ** **
14684 GCCCCAAAACTTTCAAAAATTCCATTTTTACCCTTGAATTTCCAAGAATCCCATTTTTTA
1 -CCCCGAAAC-TTCAAAAATTCCATTTTTACCCTTGAACCTCCAAGAATCCCATTTTCGA
*
14744 CCCCGAAACTTCCAAAAATTCCATTTTTGCCCTT-AACCTCCAA-AATCTCCATTTTCGA
1 CCCCGAAACTT-CAAAAATTCCATTTTTACCCTTGAACCTCCAAGAATC-CCATTTTCGA
**
14802 CCTTGAAACTCTCAAAA
1 CCCCGAAACT-TCAAAA
14819 TTACCCTTTT
Statistics
Matches: 258, Mismatches: 45, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
57 4 0.02
58 52 0.20
59 149 0.58
60 8 0.03
61 45 0.17
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (58 bp):
CCCCGAAACTTCAAAAATTCCATTTTTACCCTTGAACCTCCAAGAATCCCATTTTCGA
Found at i:15925 original size:12 final size:12
Alignment explanation
Indices: 15908--15934 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
15898 ATTATATTAT
15908 GTGATATTGCTA
1 GTGATATTGCTA
15920 GTGATATTGCTA
1 GTGATATTGCTA
15932 GTG
1 GTG
15935 TAAATTTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.07, G:0.30, T:0.41
Consensus pattern (12 bp):
GTGATATTGCTA
Found at i:26230 original size:206 final size:207
Alignment explanation
Indices: 25788--26261 Score: 481
Period size: 206 Copynumber: 2.3 Consensus size: 207
25778 AACAGCGATG
* * *
25788 CGGTCATCTTCCTGATGAGATACTGAGAAGAAAACCAAATCAATGAAACGAGGCTCAAAGTGAGC
1 CGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA-GAAACGAGCCTCAAAGTAAGC
* * *
25853 AAATCTTCGAACCCCAGCTTCCTGATGAGATACGGAGAAGGAATGTGAAGCAATAAAAGGTTAGC
65 AAATCTTCGAACCCCAACTTCCTGATGAGACACGGAGAAGCAATGTGAAGCAATAAAAGGTTAGC
* ** * * * * * *
25918 TTCCTAATGAGATATTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATT
130 TTCCTAATGAAATACGGAGAAGTGAACCAAAATCATCTTCCTGATGAAACACAGAGAAGCGAATC
* *
25983 GAAACAAACGACG
195 AAAACAAACGACA
* * * ** * *
25996 CAGTCATCTTCTTGATGTGATACTGAGAAGAAGACCAAATCAA-ACTC-ACGCCT-GATGTAAGC
1 CGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAGAAACGA-GCCTCAAAGTAAGC
* *
26058 AAATCTTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAA-GTCGAAGTAATGAAACA-GTT
65 AAATCTTCGAACCCCAACTTCCTGATGAGACACGGAGAAGCAATGT-GAAGCAAT-AAA-AGGTT
* * * * * *
26121 AGCTTCCTAGTGAAATACGGGGAAGTGAACCAAAATCATTTTCTTGATGAAACACAGAGAAGTGG
127 AGCTTCCTAATGAAATACGGAGAAGTGAACCAAAATCATCTTCCTGATGAAACACAGAGAAGCGA
** *
26186 ATCAAAACAAGTGATA
192 ATCAAAACAAACGACA
* * ** * * *
26202 TGGTCGTCTTCCTGATGAGATACTGAGAAGAAGGTCAAGTCAATGAAACCAGACTCAAAG
1 CGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA-GAAACGAGCCTCAAAG
26262 ACTACGGTGA
Statistics
Matches: 210, Mismatches: 48, Indels: 15
0.77 0.18 0.05
Matches are distributed among these distances:
204 2 0.01
205 53 0.25
206 107 0.51
207 1 0.00
208 44 0.21
209 3 0.01
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (207 bp):
CGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAGAAACGAGCCTCAAAGTAAGCA
AATCTTCGAACCCCAACTTCCTGATGAGACACGGAGAAGCAATGTGAAGCAATAAAAGGTTAGCT
TCCTAATGAAATACGGAGAAGTGAACCAAAATCATCTTCCTGATGAAACACAGAGAAGCGAATCA
AAACAAACGACA
Found at i:26559 original size:6 final size:6
Alignment explanation
Indices: 26548--26617 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
26538 CCGGGCCCCT
* * * *
26548 TTTTAA TTTTAA ATTTAGA -TTT-A TTTTAA ATTTAA -ATTAA TCTTAA
1 TTTTAA TTTTAA TTTTA-A TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
* *
26594 ATTTAA ATTTAA TTTTAA TTTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA
26618 AATTAAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
4 1 0.02
5 7 0.13
6 44 0.83
7 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (6 bp):
TTTTAA
Found at i:26575 original size:17 final size:17
Alignment explanation
Indices: 26553--26618 Score: 87
Period size: 17 Copynumber: 3.8 Consensus size: 17
26543 CCCCTTTTTA
*
26553 ATTTTAAATTTAGATTT
1 ATTTTAAATTTAAATTT
*
26570 ATTTTAAATTTAAATTA
1 ATTTTAAATTTAAATTT
*
26587 ATCTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
26604 AATTTTAATTTTAAA
1 -ATTTTAAATTTAAA
26619 ATTAAAAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
17 30 0.71
18 12 0.29
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:26594 original size:34 final size:36
Alignment explanation
Indices: 26550--26623 Score: 107
Period size: 34 Copynumber: 2.1 Consensus size: 36
26540 GGGCCCCTTT
* *
26550 TTAATTTTAAATTTAGATTT-ATTTTAAATTT-AAA
1 TTAATCTTAAATTTAAATTTAATTTTAAATTTAAAA
*
26584 TTAATCTTAAATTTAAATTTAATTTTAATTTTAAAA
1 TTAATCTTAAATTTAAATTTAATTTTAAATTTAAAA
26620 TTAA
1 TTAA
26624 AAAAGTTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
34 18 0.51
35 10 0.29
36 7 0.20
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (36 bp):
TTAATCTTAAATTTAAATTTAATTTTAAATTTAAAA
Found at i:27329 original size:30 final size:29
Alignment explanation
Indices: 27295--27368 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 29
27285 AATAATTGTT
27295 TTAATAATAATAA-TAATATTAATGATATCA
1 TTAATAATAATAAGTAATATTAAT-AT-TCA
** *
27325 TTAATAATAAATAAGTTTTTCTTAATATTCA
1 TTAATAAT-AATAAG-TAATATTAATATTCA
27356 TTAATAATAATAA
1 TTAATAATAATAA
27369 ATGTTTTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
30 13 0.34
31 16 0.42
32 2 0.05
33 7 0.18
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (29 bp):
TTAATAATAATAAGTAATATTAATATTCA
Found at i:27382 original size:31 final size:31
Alignment explanation
Indices: 27322--27382 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
27312 ATTAATGATA
* *
27322 TCATTAATAATAAATAAGTTTTTCTTAATAT
1 TCATTAATAATAAATAAATTTTTCATAATAT
*
27353 TCATTAATAAT-AATAAATGTTTTGATAATA
1 TCATTAATAATAAATAAAT-TTTTCATAATA
27383 ATAATATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (31 bp):
TCATTAATAATAAATAAATTTTTCATAATAT
Found at i:27401 original size:21 final size:19
Alignment explanation
Indices: 27348--27410 Score: 74
Period size: 18 Copynumber: 3.2 Consensus size: 19
27338 AGTTTTTCTT
27348 AATATTCATTAATAATAATA
1 AATATT-ATTAATAATAATA
* *
27368 AATGTT-TTGATAATAATA
1 AATATTATTAATAATAATA
27386 ATATTATTATTAATAATAATA
1 A-A-TATTATTAATAATAATA
27407 AATA
1 AATA
27411 AACAAAAAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 12 0.33
19 3 0.08
20 9 0.25
21 12 0.33
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (19 bp):
AATATTATTAATAATAATA
Found at i:28474 original size:30 final size:28
Alignment explanation
Indices: 28377--28835 Score: 323
Period size: 30 Copynumber: 15.7 Consensus size: 28
28367 GTCCCTAAAC
** **
28377 CTTCCAAAAATTTTGTTTTTACCCCCGAA
1 CTTCCAAAAA-TTCATTTTTACCCCAAAA
*
28406 CTTCCAAAAATTCCATTTTTAACCCC-GAA
1 CTTCCAAAAATT-CATTTTT-ACCCCAAAA
* *
28435 CTTCTAAAAATCTCATTTTTAACCTCAAAA
1 CTTCCAAAAAT-TCATTTTT-ACCCCAAAA
*
28465 CTTCCAAAAATTCCA-TTTTACCCCCAAA
1 CTTCCAAAAATT-CATTTTTACCCCAAAA
* * * **
28493 CTTCCAAAAATCCCCTTTTGACCTTAAAA
1 CTTCCAAAAAT-TCATTTTTACCCCAAAA
**
28522 CTTCCAAAAATTCCA-TTTT-CCCCCGAA
1 CTTCCAAAAATT-CATTTTTACCCCAAAA
*
28549 TTTCCAAAAATTCCATTTTTAACCCCAAAA
1 CTTCCAAAAATT-CATTTTT-ACCCCAAAA
* **
28579 CTTCCGAAAATTCTATTTTTACCCCCGAA
1 CTTCCAAAAATTC-ATTTTTACCCCAAAA
* * *
28608 CTTCCTAAAATCCCATTTTTGACCCCAAAG
1 CTTCCAAAAAT-TCATTTTT-ACCCCAAAA
28638 CTTCCAAAAAATTCATTTTTACCCCAAAA
1 CTTCC-AAAAATTCATTTTTACCCCAAAA
* * * *
28667 TTTCCAAAAATACCACTTTTGACCCTAAAA
1 CTTCCAAAAAT-TCA-TTTTTACCCCAAAA
* *
28697 CTTCCAAAAAATTCCATTTTTACCACTAAA
1 CTTCC-AAAAATT-CATTTTTACCCCAAAA
* * * *
28727 TTTCCAAGAATCCCATTTTTTACCTCAAAA
1 CTTCCAAAAAT-TCA-TTTTTACCCCAAAA
* * **
28757 CTTTCTAAAATTCCATTTTTACCCCCGAA
1 CTTCCAAAAATT-CATTTTTACCCCAAAA
* *
28786 CTTCCAAAAATCCCATTTTTGACCCCGAAA
1 CTTCCAAAAAT-TCATTTTT-ACCCCAAAA
*
28816 CTTCCAAAAATCCCATTTTT
1 CTTCCAAAAAT-TCATTTTT
28836 GCCCTTAATC
Statistics
Matches: 342, Mismatches: 64, Indels: 47
0.75 0.14 0.10
Matches are distributed among these distances:
27 18 0.05
28 34 0.10
29 138 0.40
30 139 0.41
31 13 0.04
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (28 bp):
CTTCCAAAAATTCATTTTTACCCCAAAA
Found at i:28474 original size:59 final size:59
Alignment explanation
Indices: 28404--28835 Score: 514
Period size: 59 Copynumber: 7.4 Consensus size: 59
28394 TTTACCCCCG
* * * * *
28404 AACTTCCAAAAATTCCATTTTTAACCCCGAACTTCTAAAAATCTCATTTTTAACCTCAA
1 AACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAA
* * **
28463 AACTTCCAAAAATTCCA-TTTTACCCCCAAACTTCCAAAAATCCC-CTTTTGACCTTAA
1 AACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAA
* * *
28520 AACTTCCAAAAATTCCA-TTTT-CCCCCGAATTTCCAAAAATTCCATTTTTAACCCCAA
1 AACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAA
* * *
28577 AACTTCCGAAAATTCTATTTTTACCCCCGAACTTCCTAAAATCCCATTTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAA
* ** * * * *
28636 AGCTTCCAAAAAATT-CATTTTTACCCCAAAATTTCCAAAAATACCACTTTTGACCCTAA
1 AACTTCC-AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAA
* ** * * * *
28695 AACTTCCAAAAAATTCCATTTTTACCACTAAATTTCCAAGAATCCCATTTTTTACCTCAA
1 AACTTCC-AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAA
* * *
28755 AACTTTCTAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGA
1 AACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAA
*
28814 AACTTCCAAAAATCCCATTTTT
1 AACTTCCAAAAATTCCATTTTT
28836 GCCCTTAATC
Statistics
Matches: 316, Mismatches: 52, Indels: 10
0.84 0.14 0.03
Matches are distributed among these distances:
56 19 0.06
57 55 0.17
58 27 0.09
59 167 0.53
60 48 0.15
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (59 bp):
AACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAA
Found at i:28836 original size:30 final size:29
Alignment explanation
Indices: 28377--28835 Score: 417
Period size: 29 Copynumber: 15.7 Consensus size: 29
28367 GTCCCTAAAC
*** **
28377 CTTCCAAAAATTTTGTTTTTACCCCCGAA
1 CTTCCAAAAATTCCATTTTTACCCCAAAA
*
28406 CTTCCAAAAATTCCATTTTTAACCCC-GAA
1 CTTCCAAAAATTCCATTTTT-ACCCCAAAA
* *
28435 CTTCTAAAAA-TCTCATTTTTAACCTCAAAA
1 CTTCCAAAAATTC-CATTTTT-ACCCCAAAA
*
28465 CTTCCAAAAATTCCA-TTTTACCCCCAAA
1 CTTCCAAAAATTCCATTTTTACCCCAAAA
* * * **
28493 CTTCCAAAAATCCCCTTTTGACCTTAAAA
1 CTTCCAAAAATTCCATTTTTACCCCAAAA
**
28522 CTTCCAAAAATTCCA-TTTT-CCCCCGAA
1 CTTCCAAAAATTCCATTTTTACCCCAAAA
*
28549 TTTCCAAAAATTCCATTTTTAACCCCAAAA
1 CTTCCAAAAATTCCATTTTT-ACCCCAAAA
* * **
28579 CTTCCGAAAATTCTATTTTTACCCCCGAA
1 CTTCCAAAAATTCCATTTTTACCCCAAAA
* * *
28608 CTTCCTAAAATCCCATTTTTGACCCCAAAG
1 CTTCCAAAAATTCCATTTTT-ACCCCAAAA
28638 CTTCCAAAAAATT-CATTTTTACCCCAAAA
1 CTTCC-AAAAATTCCATTTTTACCCCAAAA
* * * *
28667 TTTCCAAAAATACCACTTTTGACCCTAAAA
1 CTTCCAAAAATTCCA-TTTTTACCCCAAAA
* *
28697 CTTCCAAAAAATTCCATTTTTACCACTAAA
1 CTTCC-AAAAATTCCATTTTTACCCCAAAA
* * * *
28727 TTTCCAAGAATCCCATTTTTTACCTCAAAA
1 CTTCCAAAAATTCCA-TTTTTACCCCAAAA
* * **
28757 CTTTCTAAAATTCCATTTTTACCCCCGAA
1 CTTCCAAAAATTCCATTTTTACCCCAAAA
* *
28786 CTTCCAAAAATCCCATTTTTGACCCCGAAA
1 CTTCCAAAAATTCCATTTTT-ACCCCAAAA
*
28816 CTTCCAAAAATCCCATTTTT
1 CTTCCAAAAATTCCATTTTT
28836 GCCCTTAATC
Statistics
Matches: 348, Mismatches: 67, Indels: 29
0.78 0.15 0.07
Matches are distributed among these distances:
27 18 0.05
28 35 0.10
29 141 0.41
30 138 0.40
31 16 0.05
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (29 bp):
CTTCCAAAAATTCCATTTTTACCCCAAAA
Found at i:28883 original size:30 final size:29
Alignment explanation
Indices: 28735--28883 Score: 103
Period size: 30 Copynumber: 5.1 Consensus size: 29
28725 AATTTCCAAG
* * *
28735 AATCCCATTTTTTACCTCAAAACTTTCTAA
1 AATCCCATTTTTGACCTCGAAACTCTC-AA
* *
28765 AATTCCATTTTT-ACCCCCG-AACT-TCCAAA
1 AATCCCATTTTTGA-CCTCGAAACTCT-C-AA
*
28794 AATCCCATTTTTGACCCCGAAACT-TCCAAA
1 AATCCCATTTTTGACCTCGAAACTCT-C-AA
* * *
28824 AATCCCATTTTTGCCCT-TAATCTCT-AA
1 AATCCCATTTTTGACCTCGAAACTCTCAA
*
28851 AATCTCCATTTTCGACCTCGAAACTCTCAA
1 AATC-CCATTTTTGACCTCGAAACTCTCAA
28881 AAT
1 AAT
28884 TACCCTTTTA
Statistics
Matches: 98, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
27 6 0.06
28 12 0.12
29 34 0.35
30 46 0.47
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.34
Consensus pattern (29 bp):
AATCCCATTTTTGACCTCGAAACTCTCAA
Found at i:31854 original size:58 final size:58
Alignment explanation
Indices: 31758--31932 Score: 314
Period size: 58 Copynumber: 3.0 Consensus size: 58
31748 CGCAGAATAT
*
31758 CCATTTGAATCGTTCATCTTCTCTCCAATCTGACAATAGTTCTGATGCTATGAGTTTG
1 CCATTTGAATCGTTCATCTTCTCTCCAATCTGATAATAGTTCTGATGCTATGAGTTTG
* *
31816 CCGTTTGAATTGTTCATCTTCTCTCCAATCTGATAATAGTTCTGATGCTATGAGTTTG
1 CCATTTGAATCGTTCATCTTCTCTCCAATCTGATAATAGTTCTGATGCTATGAGTTTG
*
31874 CCATTTGAATCGTTCATCTTCTCTCCAATCTGATAATAGTTCTGATCCTATGAGTTTG
1 CCATTTGAATCGTTCATCTTCTCTCCAATCTGATAATAGTTCTGATGCTATGAGTTTG
31932 C
1 C
31933 AGCTGGGTGG
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 111 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (58 bp):
CCATTTGAATCGTTCATCTTCTCTCCAATCTGATAATAGTTCTGATGCTATGAGTTTG
Found at i:32232 original size:128 final size:129
Alignment explanation
Indices: 31984--32235 Score: 380
Period size: 128 Copynumber: 2.0 Consensus size: 129
31974 CTAATATTGA
* *
31984 TGTTGTGTGCTACTGTTTGTTTCTCCTCATCTTCCTCTGGGACTTCAGTTTACTATCTATGGTGT
1 TGTTATGTGCTACTGTTTGTTTCTCCTCATCTTCCTCTCGGACTTCAGTTTACTATCTATGGTGT
* * **
32049 ATCTTGCTGCTCTTTACTCGTATGCTCTATGTATGAGTACATGTTTGAATTATATCTTCTGGCT
66 ATCTTGCTCCTCTTTACTCGTATGCTCTATGTATGAGTACAAGTCCGAATTATATCTTCTGGCT
* * * * *
32113 TGTTATGTGCTACTGTTTGTTTCTCCTCGTCTTCTTTTCGGACTTCAGTTTACTATCTGT-GTTT
1 TGTTATGTGCTACTGTTTGTTTCTCCTCATCTTCCTCTCGGACTTCAGTTTACTATCTATGGTGT
* *
32177 ATCTTGCTCCTCTTTACTCGTATGCTCTATGTGTGAGTACAAGTCCGACTTATATCTTC
66 ATCTTGCTCCTCTTTACTCGTATGCTCTATGTATGAGTACAAGTCCGAATTATATCTTC
32236 CGACTACGGG
Statistics
Matches: 110, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
128 56 0.51
129 54 0.49
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (129 bp):
TGTTATGTGCTACTGTTTGTTTCTCCTCATCTTCCTCTCGGACTTCAGTTTACTATCTATGGTGT
ATCTTGCTCCTCTTTACTCGTATGCTCTATGTATGAGTACAAGTCCGAATTATATCTTCTGGCT
Found at i:36011 original size:6 final size:6
Alignment explanation
Indices: 36000--36050 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
35990 TGATCAAAAT
* * * * *
36000 TGAAAG TGAAAG TGAAAA TGAAAG TGAAAA TGAAAT TGGAAT TGAAAG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
36048 TGA
1 TGA
36051 TATAAATTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:36021 original size:12 final size:12
Alignment explanation
Indices: 36000--36050 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
35990 TGATCAAAAT
*
36000 TGAAAGTGAAAG
1 TGAAAATGAAAG
36012 TGAAAATGAAAG
1 TGAAAATGAAAG
*
36024 TGAAAATGAAAT
1 TGAAAATGAAAG
* *
36036 TGGAATTGAAAG
1 TGAAAATGAAAG
36048 TGA
1 TGA
36051 TATAAATTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (12 bp):
TGAAAATGAAAG
Found at i:36023 original size:18 final size:18
Alignment explanation
Indices: 35995--36050 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
35985 ATTTGTGATC
35995 AAAATTGAAAGTGAAAGTG
1 AAAA-TGAAAGTGAAAGTG
*
36014 AAAATGAAAGTGAAAATG
1 AAAATGAAAGTGAAAGTG
* * *
36032 AAATTGGAATTGAAAGTG
1 AAAATGAAAGTGAAAGTG
36050 A
1 A
36051 TATAAATTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 28 0.88
19 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.25, T:0.21
Consensus pattern (18 bp):
AAAATGAAAGTGAAAGTG
Found at i:36254 original size:37 final size:39
Alignment explanation
Indices: 36154--36255 Score: 91
Period size: 37 Copynumber: 2.6 Consensus size: 39
36144 GACCTCGAGT
* * **
36154 CGATGAGACACTTGGTGTCATTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA--CTTTTACTTCGGATAGAGC
** ** *
36195 CGATGAGGTACTGGGTAACACTTTT-CTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCACTTTTACTTCGGATAGAGC
36232 CGATGAGACACTGGGTGTCACTTT
1 CGATGAGACACTGGGTGTCACTTT
36256 ATTGCTTCGA
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
37 20 0.42
38 9 0.19
39 4 0.08
41 15 0.31
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCACTTTTACTTCGGATAGAGC
Found at i:37928 original size:21 final size:21
Alignment explanation
Indices: 37904--37947 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
37894 CCTCAATTTT
*
37904 CTTTTGAAAATCCATAGTTTG
1 CTTTTGAAAATCCATAGATTG
*
37925 CTTTTGAAAATCTATAGATTG
1 CTTTTGAAAATCCATAGATTG
37946 CT
1 CT
37948 GCTAAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (21 bp):
CTTTTGAAAATCCATAGATTG
Found at i:38063 original size:27 final size:27
Alignment explanation
Indices: 38032--38090 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
38022 TATGGGGCTC
*
38032 GATTTTGAAATGGCTAGTTATAACGTG
1 GATTTCGAAATGGCTAGTTATAACGTG
*
38059 GATTTCGAAATGGCTAGTTATAATGTG
1 GATTTCGAAATGGCTAGTTATAACGTG
38086 GATTT
1 GATTT
38091 GTCCCAAGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.07, G:0.25, T:0.39
Consensus pattern (27 bp):
GATTTCGAAATGGCTAGTTATAACGTG
Done.