Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009990.1 Kokia drynarioides strain JFW-HI SEQ_124745, 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: 64064
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2528 original size:78 final size:77
Alignment explanation
Indices: 2398--2553 Score: 294
Period size: 78 Copynumber: 2.0 Consensus size: 77
2388 CAACTAACAG
2398 TGTGGCTAGTGTCTGTAACGCATCGAAGTCGGTGTGTAAGCATTGCAAAAGAATTCATTCAGGTC
1 TGTGGCTAGTGTCTGTAACGCATCGAAGTCGGTGTGTAAGCATTGCAAAAGAATTCATTCAGGTC
2463 AATGCCGACTGA
66 AATGCCGACTGA
*
2475 TNGTGGCTAGTGTCTGTAACGCATCGAAGTCGGTGTGTGAGCATTGCAAAAGAATTCATTCAGGT
1 T-GTGGCTAGTGTCTGTAACGCATCGAAGTCGGTGTGTAAGCATTGCAAAAGAATTCATTCAGGT
2540 CAATGCCGACTGA
65 CAATGCCGACTGA
2553 T
1 T
2554 TAAGTGAGCC
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
77 1 0.01
78 76 0.99
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (77 bp):
TGTGGCTAGTGTCTGTAACGCATCGAAGTCGGTGTGTAAGCATTGCAAAAGAATTCATTCAGGTC
AATGCCGACTGA
Found at i:9461 original size:18 final size:18
Alignment explanation
Indices: 9438--9490 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
9428 ACAATTCATA
9438 TCACTTTCAATTTCAATC
1 TCACTTTCAATTTCAATC
* * *
9456 TCACTTTCACTTTCACTT
1 TCACTTTCAATTTCAATC
9474 TCACTTT-AACTTTCAAT
1 TCACTTTCAA-TTTCAAT
9491 TTTGATCACA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 1 0.03
18 28 0.97
ACGTcount: A:0.25, C:0.28, G:0.00, T:0.47
Consensus pattern (18 bp):
TCACTTTCAATTTCAATC
Found at i:9471 original size:12 final size:12
Alignment explanation
Indices: 9438--9488 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
9428 ACAATTCATA
*
9438 TCACTTTCAATT
1 TCACTTTCACTT
* *
9450 TCAATCTCACTT
1 TCACTTTCACTT
9462 TCACTTTCACTT
1 TCACTTTCACTT
*
9474 TCACTTTAACTT
1 TCACTTTCACTT
9486 TCA
1 TCA
9489 ATTTTGATCA
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:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (12 bp):
TCACTTTCACTT
Found at i:15595 original size:47 final size:48
Alignment explanation
Indices: 15495--15813 Score: 152
Period size: 47 Copynumber: 6.6 Consensus size: 48
15485 ACTAACATTG
* * * * *
15495 GCAAATCTTTATCTCCCTAAAGTTGTAGTCAAGCAAGATGAAGTCACA
1 GCAAATCTTTATCTCCCTAAAGTTGCAGTGAAGCAAGATAAAATAACA
* * *
15543 CCAAATC-TTATCTTCCTAAAGTTGCAGTGAAGCAA-ATTAAAATAATA
1 GCAAATCTTTATCTCCCTAAAGTTGCAGTGAAGCAAGA-TAAAATAACA
* * * *
15590 GCAAATCTTTATCTCCCTGAAGTTGCAATGGAGCAAGATGAAGCTATAACA
1 GCAAATCTTTATCTCCCTAAAGTTGCAGTGAAGCAAGAT-AA--AATAACA
* * * * * *
15641 -CAAAATC-ATATATCCCTGAAGTTACAAG-G-ATCGAA-TTAAAACTAACA
1 GC-AAATCTTTATCTCCCTAAAGTTGC-AGTGAAGC-AAGATAAAA-TAACA
* * * * ***
15688 TTGGCAAATCTTTATCTCCCTAAAGTTGTAGTGGAGTAAGATGAAGCCACA
1 ---GCAAATCTTTATCTCCCTAAAGTTGCAGTGAAGCAAGATAAAATAACA
* * * * * **
15739 CCAAATC-CTATCTTCCTGAAGTTGCAGTGAA-CTCAGATTAAAATAGTA
1 GCAAATCTTTATCTCCCTAAAGTTGCAGTGAAGC-AAGA-TAAAATAACA
* *
15787 GCAAATCTTTATCTCCTTGAAGTTGCA
1 GCAAATCTTTATCTCCCTAAAGTTGCA
15814 ATGGAGTAAA
Statistics
Matches: 198, Mismatches: 52, Indels: 41
0.68 0.18 0.14
Matches are distributed among these distances:
46 2 0.01
47 64 0.32
48 49 0.25
49 22 0.11
50 26 0.13
51 31 0.16
52 4 0.02
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (48 bp):
GCAAATCTTTATCTCCCTAAAGTTGCAGTGAAGCAAGATAAAATAACA
Found at i:15708 original size:101 final size:101
Alignment explanation
Indices: 15441--16131 Score: 535
Period size: 101 Copynumber: 7.0 Consensus size: 101
15431 GGATCAACGA
* * * * *
15441 AACAACAAATCCTATATCCTTGAAGTTGCAAGGATCGAATTAAAACTAACATTGGCAAATCTTTA
1 AACACCAAATCCTATATCCCTGAAGTTACAAGGATCGAATTAAAACTAACAGTAGCAAATCTTTA
* **
15506 TCTCCCTAAAGTTGTAGTCAAGCAAGATGAAG---T
66 TCTCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTAT
* * * * * * * *
15539 CACACCAAATCTTATCTTCCTAAAGTTGC-AGTGAAGCAAATTAAAA-T-A-A-TAGCAAATCTT
1 AACACCAAATCCTATATCCCTGAAGTTACAAG-G-ATCGAATTAAAACTAACAGTAGCAAATCTT
* *
15599 TATCTCCCTGAAGTTGCAATGGAGCAAGATGAAGCTAT
64 TATCTCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTAT
* * * *
15637 AACACAAAATCATATATCCCTGAAGTTACAAGGATCGAATTAAAACTAACATTGGCAAATCTTTA
1 AACACCAAATCCTATATCCCTGAAGTTACAAGGATCGAATTAAAACTAACAGTAGCAAATCTTTA
* *
15702 TCTCCCTAAAGTTGTAGTGGAGTAAGATGAAGC---
66 TCTCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTAT
* * * *
15735 CACACCAAATCCTATCTTCCTGAAGTTGC-AGTGAACTC-AGATTAAAA-T---AGTAGCAAATC
1 AACACCAAATCCTATATCCCTGAAGTTACAAG-G-A-TCGA-ATTAAAACTAACAGTAGCAAATC
* * * * * *
15794 TTTATCTCCTTGAAGTTGCAATGGAGTAAAATGAAGCTAC
62 TTTATCTCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTAT
* * * ** *
15834 AACCCCAAATCCTATATCCCTAAAGTTACAAGGATCGAATTAAAACTAACAATAATAAATATTTA
1 AACACCAAATCCTATATCCCTGAAGTTACAAGGATCGAATTAAAACTAACAGTAGCAAATCTTTA
* * * * * *
15899 TCACCCTAAAGTTACAATAGAGCAAGGTTAAGCTAT
66 TCTCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTAT
* * * * * *
15935 AACCCCAAATCTTACATCCCTAAAGTTATAAAGATC-AGATTAAAACTAACAGTAGCAAATCTTT
1 AACACCAAATCCTATATCCCTGAAGTTACAAGGATCGA-ATTAAAACTAACAGTAGCAAATCTTT
* * * * *
15999 ATCTCCTTAAAATTACAGTGGAGCAAGATAAAGCTAA
65 ATCTCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTAT
* * * * * * * *
16036 AACCCCAAA-CTTTATATCCTTGAAGTTATAA-GAT-TAGATTAAAACTAATAGT-GATAAAACT
1 AACACCAAATC-CTATATCCCTGAAGTTACAAGGATCGA-ATTAAAACTAACAGTAG-CAAATCT
* *
16097 TTATCTCCCTGAAGTTACAGTGGAGCAAGATGAAG
63 TTATCTCCCTAAAGTTGCAGTGGAGCAAGATGAAG
16132 TCACGTCACC
Statistics
Matches: 478, Mismatches: 88, Indels: 52
0.77 0.14 0.08
Matches are distributed among these distances:
95 39 0.08
96 42 0.09
97 24 0.05
98 76 0.16
99 41 0.09
100 69 0.14
101 187 0.39
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (101 bp):
AACACCAAATCCTATATCCCTGAAGTTACAAGGATCGAATTAAAACTAACAGTAGCAAATCTTTA
TCTCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTAT
Found at i:15908 original size:197 final size:196
Alignment explanation
Indices: 15441--15911 Score: 699
Period size: 197 Copynumber: 2.4 Consensus size: 196
15431 GGATCAACGA
* * *
15441 AACAACAAATCCTATATCCTTGAAGTTGCAAGGATCGAATTAAAACTAACATTGGCAAATCTTTA
1 AACACCAAATCCTATATCCCTGAAGTTACAAGGATCGAATTAAAACTAACATTGGCAAATCTTTA
* *
15506 TCTCCCTAAAGTTGTAGTCAAGCAAGATGAAGTCACACCAAATCTTATCTTCCTAAAGTTGCAGT
66 TCTCCCTAAAGTTGTAGTCAAGCAAGATGAAGCCACACCAAATCCTATCTTCCTAAAGTTGCAGT
*
15571 GAAGCAAATTAAAATAATAGCAAATCTTTATCTCCCTGAAGTTGCAATGGAGCAAGATGAAGCTA
131 GAAGCAAATTAAAATAATAGCAAATCTTTATCTCCCTGAAGTTGCAATGGAGCAAAATGAAGCTA
*
15636 T
196 C
* *
15637 AACACAAAATCATATATCCCTGAAGTTACAAGGATCGAATTAAAACTAACATTGGCAAATCTTTA
1 AACACCAAATCCTATATCCCTGAAGTTACAAGGATCGAATTAAAACTAACATTGGCAAATCTTTA
** * *
15702 TCTCCCTAAAGTTGTAGTGGAGTAAGATGAAGCCACACCAAATCCTATCTTCCTGAAGTTGCAGT
66 TCTCCCTAAAGTTGTAGTCAAGCAAGATGAAGCCACACCAAATCCTATCTTCCTAAAGTTGCAGT
* * * * *
15767 GAACTCAGATTAAAATAGTAGCAAATCTTTATCTCCTTGAAGTTGCAATGGAGTAAAATGAAGCT
131 GAA-GCAAATTAAAATAATAGCAAATCTTTATCTCCCTGAAGTTGCAATGGAGCAAAATGAAGCT
15832 AC
195 AC
* * * *** *
15834 AACCCCAAATCCTATATCCCTAAAGTTACAAGGATCGAATTAAAACTAACAATAATAAATATTTA
1 AACACCAAATCCTATATCCCTGAAGTTACAAGGATCGAATTAAAACTAACATTGGCAAATCTTTA
*
15899 TCACCCTAAAGTT
66 TCTCCCTAAAGTT
15912 ACAATAGAGC
Statistics
Matches: 246, Mismatches: 28, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
196 122 0.50
197 124 0.50
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.27
Consensus pattern (196 bp):
AACACCAAATCCTATATCCCTGAAGTTACAAGGATCGAATTAAAACTAACATTGGCAAATCTTTA
TCTCCCTAAAGTTGTAGTCAAGCAAGATGAAGCCACACCAAATCCTATCTTCCTAAAGTTGCAGT
GAAGCAAATTAAAATAATAGCAAATCTTTATCTCCCTGAAGTTGCAATGGAGCAAAATGAAGCTA
C
Found at i:19504 original size:37 final size:37
Alignment explanation
Indices: 19463--19534 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
19453 AGGTACATAA
19463 ATATTTATCCATCTATTGTAAAACATTTTAACAAATT
1 ATATTTATCCATCTATTGTAAAACATTTTAACAAATT
* *
19500 ATATTTATCCATCTGTTGTAAAATATTTTAACAAA
1 ATATTTATCCATCTATTGTAAAACATTTTAACAAA
19535 ATACATTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.43
Consensus pattern (37 bp):
ATATTTATCCATCTATTGTAAAACATTTTAACAAATT
Found at i:27796 original size:5 final size:5
Alignment explanation
Indices: 27786--27814 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
27776 TAAATTATAA
27786 AAATC AAATC AAATC AAATC AAATC AAAT
1 AAATC AAATC AAATC AAATC AAATC AAAT
27815 TAAAGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATC
Found at i:29154 original size:19 final size:19
Alignment explanation
Indices: 29130--29196 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
29120 TTCAGAAAGA
*
29130 AGCAATATTGGCTCGCAAG
1 AGCAATACTGGCTCGCAAG
29149 AGCAATACTGGCTCGCAAG
1 AGCAATACTGGCTCGCAAG
* *
29168 AACAATACTGGCTCGTAAG
1 AGCAATACTGGCTCGCAAG
*
29187 AGCATTACTG
1 AGCAATACTG
29197 ACTCATAGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (19 bp):
AGCAATACTGGCTCGCAAG
Found at i:29238 original size:19 final size:19
Alignment explanation
Indices: 29146--29238 Score: 87
Period size: 19 Copynumber: 4.9 Consensus size: 19
29136 ATTGGCTCGC
* **
29146 AAGAGCAATACTGGCTCGC
1 AAGAGCATTACTGGCTCAT
* * *
29165 AAGAACAATACTGGCTCGT
1 AAGAGCATTACTGGCTCAT
*
29184 AAGAGCATTACTGACTCAT
1 AAGAGCATTACTGGCTCAT
* * *
29203 AGGAGAATTATTGGCTCAT
1 AAGAGCATTACTGGCTCAT
*
29222 AAGAGCATTACTAGCTC
1 AAGAGCATTACTGGCTC
29239 GTGAGAGCAA
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 60 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (19 bp):
AAGAGCATTACTGGCTCAT
Found at i:30721 original size:3 final size:3
Alignment explanation
Indices: 30713--30744 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
30703 ATCACCATTC
30713 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
30745 AATTAGTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:42271 original size:30 final size:30
Alignment explanation
Indices: 42235--42317 Score: 148
Period size: 30 Copynumber: 2.8 Consensus size: 30
42225 ACATTAACAA
42235 GACACCCTCCACATTTTCAAGTGGTTCTAG
1 GACACCCTCCACATTTTCAAGTGGTTCTAG
42265 GACACCCTCCACATTTTCAAGTGGTTCTAG
1 GACACCCTCCACATTTTCAAGTGGTTCTAG
* *
42295 GACACCCCCCACATTTCCAAGTG
1 GACACCCTCCACATTTTCAAGTG
42318 CTTTTGGAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.27
Consensus pattern (30 bp):
GACACCCTCCACATTTTCAAGTGGTTCTAG
Found at i:56865 original size:14 final size:14
Alignment explanation
Indices: 56846--56874 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
56836 CTTTAGGCAT
56846 GACTAGTAAGTGAA
1 GACTAGTAAGTGAA
56860 GACTAGTAAGTGAA
1 GACTAGTAAGTGAA
56874 G
1 G
56875 CCATGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.31, T:0.21
Consensus pattern (14 bp):
GACTAGTAAGTGAA
Found at i:61077 original size:61 final size:62
Alignment explanation
Indices: 60955--61172 Score: 218
Period size: 62 Copynumber: 3.6 Consensus size: 62
60945 GTGTTGGCCA
** * * *
60955 TTATCT-GAATAAAAAA-TCAAATTTTTTGGGTGATACCCATGCCATGATGACACC-TTTTTT
1 TTATCTAG-ATAAAAAATTCAAATTTTTTTTGTGTTAACCATGCAATGATGACACCTTTTTTT
* *
61015 TTGTC-AGATAAAAAATTCAAATTTTTTTTGTGTTAACCATGCAATGGTCGACACCTTTTTTT
1 TTATCTAGATAAAAAATTCAAATTTTTTTTGTGTTAACCATGCAATGAT-GACACCTTTTTTT
* * *
61077 TTATCTAG-TAAAAAATTC-AATTTTTTTTGTGTTGACCATACAATGACTGACACCCCTTTTTT
1 TTATCTAGATAAAAAATTCAAATTTTTTTTGTGTTAACCATGCAATGA-TGACA-CCTTTTTTT
* * *
61139 TTAT-TTGGTAAAAAA-TCAATTTTTTTTTTGTGTT
1 TTATCTAGATAAAAAATTCAA-ATTTTTTTTGTGTT
61173 GATCATTGTA
Statistics
Matches: 134, Mismatches: 14, Indels: 17
0.81 0.08 0.10
Matches are distributed among these distances:
59 8 0.06
60 31 0.23
61 39 0.29
62 41 0.31
63 15 0.11
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.44
Consensus pattern (62 bp):
TTATCTAGATAAAAAATTCAAATTTTTTTTGTGTTAACCATGCAATGATGACACCTTTTTTT
Found at i:61103 original size:63 final size:61
Alignment explanation
Indices: 60955--61245 Score: 240
Period size: 61 Copynumber: 4.8 Consensus size: 61
60945 GTGTTGGCCA
* * ** * * *
60955 TTATCTGAATAAAAAATCAAATTTTTTGGGTGAT-ACCCATGCCAT-GATGACA-CCTTTTTT
1 TTATCT-AGTAAAAAATCAATTTTTTTTTGTGTTGA-CCATGCAATGGACGACACCCTTTTTT
* * * * *
61015 TTGTC-AGATAAAAAATTCAAATTTTTTTTGTGTTAACCATGCAATGGTCGACACCTTTTTTT
1 TTATCTAG-TAAAAAA-TCAATTTTTTTTTGTGTTGACCATGCAATGGACGACACCCTTTTTT
*
61077 TTATCTAGTAAAAAATTCAA-TTTTTTTTGTGTTGACCATACAAT-GACTGACACCCCTTTTTT
1 TTATCTAGTAAAAAA-TCAATTTTTTTTTGTGTTGACCATGCAATGGAC-GACA-CCCTTTTTT
* * * * *
61139 TTATTTGGTAAAAAATCAATTTTTTTTTTGTGTTGATCATTG-TATGGCCGACATCCC--TTTT
1 TTATCTAGTAAAAAATCAA-TTTTTTTTTGTGTTGACCA-TGCAATGGACGACA-CCCTTTTTT
* * *
61200 GTATCTTGTAAAAAATCAATTTTTTTTTGTGTTGGCCATGCAATGG
1 TTATCTAGTAAAAAATCAATTTTTTTTTGTGTTGACCATGCAATGG
61246 CCGATACCAA
Statistics
Matches: 191, Mismatches: 27, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
58 1 0.01
59 9 0.05
60 50 0.26
61 56 0.29
62 44 0.23
63 28 0.15
64 3 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (61 bp):
TTATCTAGTAAAAAATCAATTTTTTTTTGTGTTGACCATGCAATGGACGACACCCTTTTTT
Found at i:61373 original size:23 final size:23
Alignment explanation
Indices: 61343--61387 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
61333 AATGAGAGTG
61343 TTTTTTTATTTATCATTAGATGT
1 TTTTTTTATTTATCATTAGATGT
61366 TTTTTTTATTTATCATTAGATG
1 TTTTTTTATTTATCATTAGATG
61388 AGTGTTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.04, G:0.09, T:0.64
Consensus pattern (23 bp):
TTTTTTTATTTATCATTAGATGT
Found at i:61395 original size:23 final size:23
Alignment explanation
Indices: 61346--61395 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
61336 GAGAGTGTTT
** *
61346 TTTTATTTATCATTAGATGTTTT
1 TTTTATTTATCATTAGATGAGTG
61369 TTTTATTTATCATTAGATGAGTG
1 TTTTATTTATCATTAGATGAGTG
61392 TTTT
1 TTTT
61396 GTTTTGAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.62
Consensus pattern (23 bp):
TTTTATTTATCATTAGATGAGTG
Found at i:61395 original size:27 final size:24
Alignment explanation
Indices: 61337--61385 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
61327 CAATAAAATG
61337 AGAGTG-TTTTTTTATTTATCATT
1 AGAGTGTTTTTTTTATTTATCATT
61360 AGA-TGTTTTTTTTATTTATCATT
1 AGAGTGTTTTTTTTATTTATCATT
61383 AGA
1 AGA
61386 TGAGTGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.24, C:0.04, G:0.12, T:0.59
Consensus pattern (24 bp):
AGAGTGTTTTTTTTATTTATCATT
Found at i:62101 original size:30 final size:30
Alignment explanation
Indices: 62057--62190 Score: 101
Period size: 30 Copynumber: 4.4 Consensus size: 30
62047 ATAAATTTTC
* * *
62057 AAAAAATAATAATTAGAATATATAGGAAATT
1 AAAAATTAA-AATTAAAATATAAAGGAAATT
* *
62088 AAAAATTAAAATTAAAATCTACAGGAAATT
1 AAAAATTAAAATTAAAATATAAAGGAAATT
** * * *
62118 TGAAATTAAATTTAAAATAAAAACGAAATT
1 AAAAATTAAAATTAAAATATAAAGGAAATT
* * *
62148 ACAAATTAAATTTAAAA-AGTAAACGGAAA-A
1 AAAAATTAAAATTAAAATA-TAAA-GGAAATT
*
62178 AAAAATCAAAATT
1 AAAAATTAAAATT
62191 GAGTAGATTT
Statistics
Matches: 82, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
29 1 0.01
30 69 0.84
31 12 0.15
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.26
Consensus pattern (30 bp):
AAAAATTAAAATTAAAATATAAAGGAAATT
Found at i:63413 original size:18 final size:20
Alignment explanation
Indices: 63371--63415 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
63361 TTTAAAATTC
*
63371 GAAAATATAAAAAACATTTT
1 GAAAATATAAAAAACATTAT
*
63391 GAAAATA-AAAAAATATTAT
1 GAAAATATAAAAAACATTAT
*
63410 AAAAAT
1 GAAAAT
63416 TCGAAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (20 bp):
GAAAATATAAAAAACATTAT
Done.