Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002661.1 Kokia drynarioides strain JFW-HI SEQ_114911, 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: 50119
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3907 original size:206 final size:206
Alignment explanation
Indices: 3547--4317 Score: 1195
Period size: 206 Copynumber: 3.7 Consensus size: 206
3537 TCCACAAAAT
* *
3547 GACGCAGTCATCTTCCCGATGAGATACTGAGAAGACGACCAAATCAAATCCACGCTCGACGTAAG
1 GACGCGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGACGTAAG
* * *
3612 CAAATCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGAAATAAAACGGTTG
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGTCGAAGCAATAAAACGGTTG
*
3677 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCCTCCTGATGAGATACAGAGAAGCGAA
131 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
3742 TTGAAACAAAC
196 TTGAAACAAAC
* * *
3753 GACGTGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAATCCATGTTCGACGTAAG
1 GACGCGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGACGTAAG
* *
3818 CAAATCTTTGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGTCGAAGCAATAAAATGGTTG
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGTCGAAGCAATAAAACGGTTG
*
3883 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAT
131 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
* **
3948 TTGGAACAAGT
196 TTGAAACAAAC
** * * * *
3959 GACGCGGTCATCTTCTTGATGAGATCCCGAGAAGAAGACCAAATCAAGTCCACGCTCGATGTAAG
1 GACGCGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGACGTAAG
4024 CAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGTCGAAGCAATAAAACGGTTG
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGTCGAAGCAATAAAACGGTTG
*
4089 GCTTCCTGATGAGATACTGAAAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
131 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
4154 TTGAAACAAAC
196 TTGAAACAAAC
* ** * * **
4165 GACGCGGTCATCTTCCTGATGAGATTTTGAGAAGAAGACCAAATTAAACCCACGCTCGATATAAG
1 GACGCGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGACGTAAG
** * * * * *
4230 CAAATCTTCGAATACCAGCTTCCTGATGAGACACGGAGAAGCGGGTCGAAGCAAT-GAACGGTTA
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGTCGAAGCAATAAAACGGTTG
4294 G-TGTCCTGATGAGATACTGAGAAG
131 GCT-TCCTGATGAGATACTGAGAAG
4318 AAGGCCAAGA
Statistics
Matches: 519, Mismatches: 45, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
204 1 0.00
205 28 0.05
206 490 0.94
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (206 bp):
GACGCGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGACGTAAG
CAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAAAAGCAGGTCGAAGCAATAAAACGGTTG
GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
TTGAAACAAAC
Found at i:4594 original size:23 final size:22
Alignment explanation
Indices: 4568--4616 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
4558 TTAAATTTAT
*
4568 TTTAAAATTAAGTTTATCGTAAA
1 TTTAAAATTAAATTTAT-GTAAA
* *
4591 TTTAAATTTAAATTTATTTAAA
1 TTTAAAATTAAATTTATGTAAA
4613 TTTA
1 TTTA
4617 TTATGAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (22 bp):
TTTAAAATTAAATTTATGTAAA
Found at i:5544 original size:30 final size:27
Alignment explanation
Indices: 5489--6024 Score: 401
Period size: 30 Copynumber: 18.2 Consensus size: 27
5479 CCTGGAGGTC
*
5489 CCCCGAACTCCCAAAAATTACCATTTTA
1 CCCCGAACTTCCAAAAATT-CCATTTTA
*
5517 CCCTCGAACTTCCAAAAAAATTTCATTTTA
1 CCC-CGAACTTCC--AAAAATTCCATTTTA
*
5547 CCCCTGAACTT-CAAAAAATCTCATTTTTAA
1 CCCC-GAACTTCCAAAAATTC-CA-TTTT-A
*
5577 CCCCAAAACTTCCAAAAATTACCATTTTA
1 CCCC-GAACTTCCAAAAATT-CCATTTTA
* *
5606 CCCCCAAACTTCCAAAAATCCCATTTTTGA
1 -CCCCGAACTTCCAAAAATTCCA-TTTT-A
*
5636 CCCCGAACCTTCCAAAAATCACCATTTTA
1 CCCCGAA-CTTCCAAAAAT-TCCATTTTA
*
5665 CCCTCGAACTTCCAAAAATCCCATTTTTTA
1 CCC-CGAACTTCCAAAAATTCCA--TTTTA
** *
5695 TCCCAAAACTTCTAAAAATTACCATTTTA
1 -CCCCGAACTTCCAAAAATT-CCATTTTA
* * *
5724 CCCCTAAACTCCCAAAAATCCCATTTTTAA
1 CCCC-GAACTTCCAAAAATTCCA-TTTT-A
*
5754 CCCCAAAACTTCCAAAAATTACCATTTTA
1 CCCC-GAACTTCCAAAAATT-CCATTTTA
* * *
5783 CTCCCAAACTTCTAAAAAATTTCATTTTTA
1 C-CCCGAACTTC-CAAAAATTCCA-TTTTA
*
5813 CCCCCGAACTTCCAAAAATCCCATTTTTGA
1 -CCCCGAACTTCCAAAAATTCCA-TTTT-A
**
5843 CCCCGAAACTTTGAAAAATTACCATTTTA
1 CCCCG-AACTTCCAAAAATT-CCATTTTA
* * *
5872 CCCTCAAACTTCCAAAAGTCCCAATTTTGA
1 CCC-CGAACTTCCAAAAATTCC-ATTTT-A
5902 CCCCGAAGCTTCCAAAAATTACCATTTTA
1 CCCCGAA-CTTCCAAAAATT-CCATTTTA
*
5931 CCCCCGAACTTCCTAAAATTACCATTTTA
1 -CCCCGAACTTCCAAAAATT-CCATTTTA
*
5960 CCCTTGAACTTCCAAAAA-TCTCATTTTTGA
1 CCC-CGAACTTCCAAAAATTC-CA-TTTT-A
5990 CCCCGACACTTCCAAAAATTACCATTTTA
1 CCCCGA-ACTTCCAAAAATT-CCATTTTA
6019 CTCCCG
1 C-CCCG
6025 GATGTTCGAG
Statistics
Matches: 421, Mismatches: 43, Indels: 86
0.77 0.08 0.16
Matches are distributed among these distances:
27 7 0.02
28 25 0.06
29 167 0.40
30 183 0.43
31 37 0.09
32 2 0.00
ACGTcount: A:0.35, C:0.32, G:0.04, T:0.30
Consensus pattern (27 bp):
CCCCGAACTTCCAAAAATTCCATTTTA
Found at i:5594 original size:59 final size:58
Alignment explanation
Indices: 5523--6019 Score: 451
Period size: 59 Copynumber: 8.4 Consensus size: 58
5513 TTTACCCTCG
* *
5523 AACTTCCAAAAAAATT-TCATTTTACCCCTGAACTTCAAAAAATCTCATTTTTAACCCCAA
1 AACTTCC--AAAAATTACCATTTTACCCCTGAACTTCCAAAAATCTCATTTTT-ACCCCAA
** * *
5583 AACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGA
1 AACTTCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCTCATTTTT-ACCCCAA
* * * *
5642 ACCTTCCAAAAATCACCATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTTATCCCAA
1 AACTTCCAAAAATTACCATTTTACCCCT-GAACTTCCAAAAATCTCA-TTTTTACCCCAA
* * * *
5701 AACTTCTAAAAATTACCATTTTACCCCTAAACTCCCAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCTCATTTTT-ACCCCAA
* * * **
5760 AACTTCCAAAAATTACCATTTTACTCCC-AAACTTCTAAAAAATTTCATTTTTACCCCCG
1 AACTTCCAAAAATTACCATTTTAC-CCCTGAACTTC-CAAAAATCTCATTTTTACCCCAA
* **
5819 AACTTCCAAAAA-TCCCATTTTTGACCCC-GAAACTTTGAAAAAT-TACCA-TTTTACCCTC-A
1 AACTTCCAAAAATTACCA-TTTT-ACCCCTG-AACTTCCAAAAATCT--CATTTTTACCC-CAA
* * **
5878 AACTTCC-AAAAGTCCCAATTTTGACCCC-GAAGCTTCCAAAAAT-TACCA-TTTTACCCCCG
1 AACTTCCAAAAATTACC-ATTTT-ACCCCTGAA-CTTCCAAAAATCT--CATTTTTACCCCAA
* * *
5937 AACTTCCTAAAATTACCATTTTACCCTTGAACTTCCAAAAATCTCATTTTTGACCCCGA
1 AACTTCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCTCATTTTT-ACCCCAA
*
5996 CACTTCCAAAAATTACCATTTTAC
1 AACTTCCAAAAATTACCATTTTAC
6020 TCCCGGATGT
Statistics
Matches: 374, Mismatches: 41, Indels: 45
0.81 0.09 0.10
Matches are distributed among these distances:
57 2 0.01
58 46 0.12
59 276 0.74
60 50 0.13
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.30
Consensus pattern (58 bp):
AACTTCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCTCATTTTTACCCCAA
Found at i:5700 original size:118 final size:116
Alignment explanation
Indices: 5540--6024 Score: 514
Period size: 118 Copynumber: 4.1 Consensus size: 116
5530 AAAAAAATTT
*
5540 CATTTTACCCCTGAACTTCAAAAAATCTCATTTTTAACCCCAAAACTTCCAAAAATTACCATTTT
1 CATTTTACCCC-GAACTTCAAAAAATCCCATTTTT-ACCCCAAAACTTCCAAAAATTACCATTTT
* *
5605 ACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATCAC
64 ACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATCAC
* * *
5658 CATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTATCCCAAAACTTCTAAAAATTACCATTTT
1 CATTTTACCC-CGAACTTCAAAAAATCCCA-TTTTTACCCCAAAACTTCCAAAAATTACCATTTT
* * * *
5723 ACCCCTAAACTCCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTAC
64 ACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATCAC
* ** ** *
5776 CATTTTACTCCCAAACTTCTAAAAAATTTCATTTTTACCCCCGAACTTCCAAAAA-TCCCATTTT
1 CATTTTAC-CCCGAACTTC-AAAAAATCCCATTTTTACCCCAAAACTTCCAAAAATTACCA-TTT
* ** * *
5840 TGACCCCGAAACTTTGAAAAATTACCA-TTTT-ACCCTC-AAACTTCCAAAAGTC-C
63 T-ACCCCTAAACTTCCAAAAA-TCCCATTTTTGACCC-CGAAACTTCCAAAAATCAC
* * ** *
5893 CAATTTTGACCCCGAAGCTTCCAAAAATTACCA-TTTTACCCCCGAACTTCCTAAAATTACCATT
1 C-ATTTT-ACCCCGAA-CTT-CAAAAAATCCCATTTTTACCCCAAAACTTCCAAAAATTACCATT
* * * * *
5957 TTACCCTTGAACTTCCAAAAATCTCATTTTTGACCCCGACACTTCCAAAAATTAC
62 TTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATCAC
6012 CATTTTACTCCCG
1 CATTTTAC-CCCG
6025 GATGTTCGAG
Statistics
Matches: 307, Mismatches: 42, Indels: 36
0.80 0.11 0.09
Matches are distributed among these distances:
116 3 0.01
117 27 0.09
118 217 0.71
119 55 0.18
120 5 0.02
ACGTcount: A:0.35, C:0.32, G:0.04, T:0.30
Consensus pattern (116 bp):
CATTTTACCCCGAACTTCAAAAAATCCCATTTTTACCCCAAAACTTCCAAAAATTACCATTTTAC
CCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATCAC
Found at i:11638 original size:73 final size:74
Alignment explanation
Indices: 11555--11701 Score: 269
Period size: 75 Copynumber: 2.0 Consensus size: 74
11545 TTGATCTGCC
11555 CTTCTGTTCGCCAGGTAG-ATTTTTTTGGTTTATTTTTACTTTTAGATCTTAAAGGATTTAGTTT
1 CTTCTGTTCGCCAGGTAGTATTTTTTTGGTTTATTTTTACTTTTAGATCTTAAAGGATTTAGTTT
11619 TGATTTAAG
66 TGATTTAAG
*
11628 CTTCTGTTCGCCAGGTAGTTTTTTTTTTGGTTTATTTTTACTTTTAGATCTTAAAGGATTTAGTT
1 CTTCTGTTCGCCAGGTAG-TATTTTTTTGGTTTATTTTTACTTTTAGATCTTAAAGGATTTAGTT
11693 TTGATTTAA
65 TTGATTTAA
11702 TAAAAATGTC
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
73 18 0.25
75 53 0.75
ACGTcount: A:0.20, C:0.10, G:0.17, T:0.54
Consensus pattern (74 bp):
CTTCTGTTCGCCAGGTAGTATTTTTTTGGTTTATTTTTACTTTTAGATCTTAAAGGATTTAGTTT
TGATTTAAG
Found at i:23872 original size:33 final size:33
Alignment explanation
Indices: 23835--23900 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
23825 CATAAAATTT
23835 TTATT-TTTATTTATTTTGAGAAG-AAAAGCTTAA
1 TTATTATTT-TTTATTTTGA-AAGAAAAAGCTTAA
*
23868 TTATTATTTTTTTTTTTGAAAGAAAAAGCTTAA
1 TTATTATTTTTTATTTTGAAAGAAAAAGCTTAA
23901 AATTTCTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 3 0.10
33 24 0.80
34 3 0.10
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.50
Consensus pattern (33 bp):
TTATTATTTTTTATTTTGAAAGAAAAAGCTTAA
Found at i:35197 original size:3 final size:3
Alignment explanation
Indices: 35189--35231 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
35179 CTAAATGCCA
35189 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
35232 GCAATCTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:36316 original size:127 final size:127
Alignment explanation
Indices: 36085--36327 Score: 324
Period size: 127 Copynumber: 1.9 Consensus size: 127
36075 TTAAGTGCAG
* * * * ** *
36085 ACAAGCTGCCGTTTGGTTGAGGATTCACAATTCCTCATAGATAAAAGCTATTAGAGAAAATCGTG
1 ACAAGCTGCCATATGGTTAAGGATCCACAACCCCTCACAGATAAAAGCTATTAGAGAAAATCGTG
* * * *
36150 GATGCTTTGTTCATATAGTCGTAGTTGGAATTTGCTAAGCTATGGATACACAGAGGGTGTAC
66 GATGCTCTGTTCATATAGCCGCAGTTGGAATCTGCTAAGCTATGGATACACAGAGGGTGTAC
* * * *
36212 ACAAGCTGCCATATGGTTAAGGATCCACAACCCCTCGCAGATAAGAGCTGTTAGAGAAAGTCGTG
1 ACAAGCTGCCATATGGTTAAGGATCCACAACCCCTCACAGATAAAAGCTATTAGAGAAAATCGTG
* * *
36277 GATGCTCTGTTCATATAGCCGCAGTTGTAATCTGTTAAGCTGTGGATACAC
66 GATGCTCTGTTCATATAGCCGCAGTTGGAATCTGCTAAGCTATGGATACAC
36328 GGCTAACATA
Statistics
Matches: 98, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
127 98 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (127 bp):
ACAAGCTGCCATATGGTTAAGGATCCACAACCCCTCACAGATAAAAGCTATTAGAGAAAATCGTG
GATGCTCTGTTCATATAGCCGCAGTTGGAATCTGCTAAGCTATGGATACACAGAGGGTGTAC
Found at i:38007 original size:19 final size:20
Alignment explanation
Indices: 37978--38015 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
37968 CATTGACTCT
37978 ACAATAATAAAATATTTATA
1 ACAATAATAAAATATTTATA
37998 ACAA-AATAAAATATTTAT
1 ACAATAATAAAATATTTAT
38016 TGAATTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
ACAATAATAAAATATTTATA
Found at i:38348 original size:5 final size:5
Alignment explanation
Indices: 38334--38364 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
38324 TTTCACGTAC
38334 ATTTT A-TTT ATTTT ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
38365 ACATTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:38413 original size:29 final size:29
Alignment explanation
Indices: 38381--38437 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
38371 TAAAACAAAT
*
38381 TTTTAT-A-TTTTATTAGTTTTATATTTATA
1 TTTTATAATTTTTA-TAATTTTAT-TTTATA
38410 TTTTATAATTTTTATAATTTTATTTTAT
1 TTTTATAATTTTTATAATTTTATTTTAT
38438 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 11 0.44
30 9 0.36
31 5 0.20
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (29 bp):
TTTTATAATTTTTATAATTTTATTTTATA
Found at i:38430 original size:8 final size:7
Alignment explanation
Indices: 38381--38437 Score: 55
Period size: 7 Copynumber: 7.9 Consensus size: 7
38371 TAAAACAAAT
38381 TTTTATA
1 TTTTATA
38388 TTTTATTA
1 TTTTA-TA
38396 GTTTTATA
1 -TTTTATA
38404 -TTTATA
1 TTTTATA
38410 TTTTATAA
1 TTTTAT-A
38418 TTTTTATA
1 -TTTTATA
*
38426 ATTT-TA
1 TTTTATA
38432 TTTTAT
1 TTTTAT
38438 TTAAAAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
6 11 0.26
7 14 0.33
8 6 0.14
9 11 0.26
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (7 bp):
TTTTATA
Found at i:38503 original size:23 final size:24
Alignment explanation
Indices: 38475--38521 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
38465 TTCAGAACTC
38475 TATAAATTTTT-AATATTTAAAAT
1 TATAAATTTTTGAATATTTAAAAT
*
38498 TATAAATTTTTGAATATTTGAAAT
1 TATAAATTTTTGAATATTTAAAAT
38522 AATGTCCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
TATAAATTTTTGAATATTTAAAAT
Found at i:38683 original size:16 final size:17
Alignment explanation
Indices: 38630--38680 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
38620 ACCTTTTATA
38630 ATTAAAAT-TTTATTTT
1 ATTAAAATATTTATTTT
***
38646 -TTATTTTATTTATTTT
1 ATTAAAATATTTATTTT
*
38662 ATTAAAATATTTTTTTT
1 ATTAAAATATTTATTTT
38679 AT
1 AT
38681 AAATGATGTT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
15 4 0.15
16 8 0.31
17 14 0.54
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTAAAATATTTATTTT
Found at i:48648 original size:17 final size:17
Alignment explanation
Indices: 48626--48688 Score: 101
Period size: 17 Copynumber: 3.7 Consensus size: 17
48616 TTGGAAATTG
*
48626 AATTTAAGTTTATTTAA
1 AATTTAAATTTATTTAA
48643 AATTTAAATTTATTTAA
1 AATTTAAATTTATTTAA
48660 AATTTAAATTTATTATAA
1 AATTTAAATTTATT-TAA
48678 AA-TTAAATTTA
1 AATTTAAATTTA
48689 GAAAAGTCCA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
17 39 0.89
18 5 0.11
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
AATTTAAATTTATTTAA
Found at i:48764 original size:30 final size:30
Alignment explanation
Indices: 48728--48796 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
48718 CAAAAGTCCA
*
48728 AATTACAAATGG-CCTAATAACAAATGGCCC
1 AATTACAAATGGCCCAAAT-ACAAATGGCCC
* *
48758 AGTTACAGATGGCCCAAATACAAATGGCCC
1 AATTACAAATGGCCCAAATACAAATGGCCC
48788 AATTACAAA
1 AATTACAAA
48797 GTGCCCGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 28 0.85
31 5 0.15
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.19
Consensus pattern (30 bp):
AATTACAAATGGCCCAAATACAAATGGCCC
Found at i:48802 original size:15 final size:15
Alignment explanation
Indices: 48725--48796 Score: 74
Period size: 15 Copynumber: 4.7 Consensus size: 15
48715 AAACAAAAGT
48725 CCAAATTACAAATGG-
1 CCAAA-TACAAATGGC
*
48740 CCTAATAACAAATGGC
1 CCAAAT-ACAAATGGC
** *
48756 CCAGTTACAGATGGC
1 CCAAATACAAATGGC
48771 CCAAATACAAATGGC
1 CCAAATACAAATGGC
*
48786 CCAATTACAAA
1 CCAAATACAAA
48797 GTGCCCGAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
14 1 0.02
15 42 0.91
16 3 0.07
ACGTcount: A:0.43, C:0.25, G:0.14, T:0.18
Consensus pattern (15 bp):
CCAAATACAAATGGC
Done.