Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002220.1 Kokia drynarioides strain JFW-HI SEQ_114214, 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: 86567
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 42 characters in sequence are not A, C, G, or T
Found at i:1355 original size:80 final size:80
Alignment explanation
Indices: 1213--1519 Score: 395
Period size: 80 Copynumber: 3.8 Consensus size: 80
1203 ACAATTATGA
* * * * **
1213 CACCCAGTGCCTAGCGGA-ATAACCGTGAAA-GTGAGCCCAGCTCTAGTTGGATT-AACCAACAA
1 CACCCAGTGCTTAGCGGATA-AACCG-CAAATGTGAGCCCAGCTCTAATCGG-TTAAACTGACAA
*
1275 ATATTCGTCAAATCTTAG
63 ATATCCGTCAAATCTTAG
* *
1293 CACCCAGTGCTTAGCAGATAAACCGCAAATGTAAGCCCAGCTCTAATCGGTTAAACTGACAAATA
1 CACCCAGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAATCGGTTAAACTGACAAATA
*
1358 TCCGTCAAATCCTAG
66 TCCGTCAAATCTTAG
* * * *
1373 CACCCAATGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCCAATCGGTTAAATTGACATATA
1 CACCCAGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAATCGGTTAAACTGACAAATA
*
1438 TCCATCAAATCTTAG
66 TCCGTCAAATCTTAG
* * *
1453 CACCCAGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCGATTAAACCGACAACAT
1 CACCCAGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAATCGGTTAAACTGACAA-AT
1518 AT
65 AT
1520 ATTCATCAAA
Statistics
Matches: 198, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
79 5 0.03
80 188 0.95
81 5 0.03
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (80 bp):
CACCCAGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAATCGGTTAAACTGACAAATA
TCCGTCAAATCTTAG
Found at i:2945 original size:20 final size:20
Alignment explanation
Indices: 2920--2958 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2910 AATAATATTC
*
2920 TGAAATTTGAGGATCTCTTT
1 TGAAATCTGAGGATCTCTTT
2940 TGAAATCTGAGGATCTCTT
1 TGAAATCTGAGGATCTCTT
2959 AACTCTGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.41
Consensus pattern (20 bp):
TGAAATCTGAGGATCTCTTT
Found at i:3281 original size:35 final size:35
Alignment explanation
Indices: 3220--3297 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 35
3210 GCTTAGCACG
*
3220 TATGTGCTCTATAGTATGTCTTGAGGATTAGTACT
1 TATGTGCTCTATAGTATGTCTTGAGGATTAATACT
*
3255 TATGTGCTC-ATTGT-TGTGCTTAGAGGATTAATACT
1 TATGTGCTCTATAGTATGT-CTT-GAGGATTAATACT
3290 TATGTGCT
1 TATGTGCT
3298 TTCTAGTGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
33 3 0.08
34 7 0.18
35 29 0.74
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.44
Consensus pattern (35 bp):
TATGTGCTCTATAGTATGTCTTGAGGATTAATACT
Found at i:4087 original size:24 final size:23
Alignment explanation
Indices: 4060--4112 Score: 54
Period size: 24 Copynumber: 2.2 Consensus size: 23
4050 TAACTTAAGT
4060 TTAATAATGAAATAATT-AACTAAA
1 TTAATAA-G-AATAATTAAACTAAA
* *
4084 TTAAGTAAGATTAATTAAACTAAT
1 TTAA-TAAGAATAATTAAACTAAA
4108 TTAAT
1 TTAAT
4113 GTTAATGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 15 0.60
25 3 0.12
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.38
Consensus pattern (23 bp):
TTAATAAGAATAATTAAACTAAA
Found at i:6431 original size:28 final size:28
Alignment explanation
Indices: 6368--6500 Score: 169
Period size: 28 Copynumber: 4.7 Consensus size: 28
6358 TACATAAAAT
*
6368 AGAGAACAACCACAAAGGCTTTCACATACC
1 AGAGAACAACCACAAAGGC--TCACATATC
* * *
6398 AAAGAATAGCCACAAAGGCTCACATATC
1 AGAGAACAACCACAAAGGCTCACATATC
* * *
6426 AGAGAATAGCCACAAAGGCTCACATATT
1 AGAGAACAACCACAAAGGCTCACATATC
6454 AGAGAACAACCACAAAGGCTCACATATC
1 AGAGAACAACCACAAAGGCTCACATATC
*
6482 A-ATAACAACCACAAAGGCT
1 AGAGAACAACCACAAAGGCT
6501 TCCACATTTT
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
27 17 0.18
28 60 0.65
30 16 0.17
ACGTcount: A:0.46, C:0.26, G:0.14, T:0.14
Consensus pattern (28 bp):
AGAGAACAACCACAAAGGCTCACATATC
Found at i:16174 original size:20 final size:20
Alignment explanation
Indices: 16132--16174 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
16122 ACTTTCACAA
* *
16132 TTAAGCTTAATTAACCTCCT
1 TTAAACTTAATTAACCTCAT
16152 TTAAACTTAATTAATCCT-AT
1 TTAAACTTAATTAA-CCTCAT
16172 TTA
1 TTA
16175 TATTCAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (20 bp):
TTAAACTTAATTAACCTCAT
Found at i:18364 original size:53 final size:54
Alignment explanation
Indices: 18260--18546 Score: 241
Period size: 52 Copynumber: 5.5 Consensus size: 54
18250 TTGATAACTT
* * * * *
18260 ACGATGACATAAAGTCATCGGACCT--TTAATCCGTAATAGGATCCATGTACTC
1 ACGATGACACATAGTCATCGGACCTAGTAAATCCGTAATAGGATTCATATACTC
* * * *
18312 ACAATGACACATAATCATCGGA-CTAGTAAATCCGTAGTAGGATTCGTATACTC
1 ACGATGACACATAGTCATCGGACCTAGTAAATCCGTAATAGGATTCATATACTC
* * * * * *
18365 ACGATGACATATAGTCATTGGATCT-GTTAATCCATAAT-GGATTTATATACTC
1 ACGATGACACATAGTCATCGGACCTAGTAAATCCGTAATAGGATTCATATACTC
* * * * * * * *
18417 ATGATGACATATAGTCATAGGA-CTTGCAAATCCGTAGTAGAATTCGTATACTC
1 ACGATGACACATAGTCATCGGACCTAGTAAATCCGTAATAGGATTCATATACTC
* *
18470 ACGATGACACATAGTCATCGGACCTCA-T-AATCTGTAA-AGGATTCATATACTT
1 ACGATGACACATAGTCATCGGACCT-AGTAAATCCGTAATAGGATTCATATACTC
* * * *
18522 ACAATGACACACAGTAATCAGACCT
1 ACGATGACACATAGTCATCGGACCT
18547 TTTACATTTA
Statistics
Matches: 187, Mismatches: 41, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
51 4 0.02
52 92 0.49
53 87 0.47
54 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (54 bp):
ACGATGACACATAGTCATCGGACCTAGTAAATCCGTAATAGGATTCATATACTC
Found at i:18448 original size:105 final size:105
Alignment explanation
Indices: 18260--18532 Score: 325
Period size: 105 Copynumber: 2.6 Consensus size: 105
18250 TTGATAACTT
* * *
18260 ACGATGACATAAAGTCATCGGACCTTTAATCCGTAATAGGATCCATGTACTCACAATGACACATA
1 ACGATGACATATAGTCATCGGACCTTTAATCCATAATAGGATCCATATACTCACAATGACACATA
* * *
18325 ATCATCGGACTAGTAAATCCGTAGTAGGATTCGTATACTC
66 ATCATAGGACTAGCAAATCCGTAGTAGAATTCGTATACTC
* * ** ** *
18365 ACGATGACATATAGTCATTGGATCTGTTAATCCATAAT-GGATTTATATACTCATGATGACATAT
1 ACGATGACATATAGTCATCGGACCT-TTAATCCATAATAGGATCCATATACTCACAATGACACAT
* *
18429 AGTCATAGGACTTGCAAATCCGTAGTAGAATTCGTATACTC
65 AATCATAGGACTAGCAAATCCGTAGTAGAATTCGTATACTC
* * ** * *
18470 ACGATGACACATAGTCATCGGACCTCATAATCTGTAA-AGGATTCATATACTTACAATGACACA
1 ACGATGACATATAGTCATCGGACCT-TTAATCCATAATAGGATCCATATACTCACAATGACACA
18533 CAGTAATCAG
Statistics
Matches: 139, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
105 128 0.92
106 11 0.08
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (105 bp):
ACGATGACATATAGTCATCGGACCTTTAATCCATAATAGGATCCATATACTCACAATGACACATA
ATCATAGGACTAGCAAATCCGTAGTAGAATTCGTATACTC
Found at i:18449 original size:52 final size:54
Alignment explanation
Indices: 18260--18530 Score: 164
Period size: 53 Copynumber: 5.2 Consensus size: 54
18250 TTGATAACTT
* * ** * * * *
18260 ACGATGACATAAAGTCATCGGAC-CT-TTAATCCGTAATAGGATCCATGTACTC
1 ACGATGACATATAGTCATAGGACTCTGCAAATCCATAATAGAATTCATATACTC
* * * * * * * * * *
18312 ACAATGACACATAATCATCGGACT-AGTAAATCCGTAGTAGGATTCGTATACTC
1 ACGATGACATATAGTCATAGGACTCTGCAAATCCATAATAGAATTCATATACTC
* ** * *
18365 ACGATGACATATAGTCATTGGA-TCTGTTAATCCATAAT-GGATTTATATACTC
1 ACGATGACATATAGTCATAGGACTCTGCAAATCCATAATAGAATTCATATACTC
* * * *
18417 ATGATGACATATAGTCATAGGACT-TGCAAATCCGTAGTAGAATTCGTATACTC
1 ACGATGACATATAGTCATAGGACTCTGCAAATCCATAATAGAATTCATATACTC
* * ** * *
18470 ACGATGACACATAGTCATCGGAC-CT-CATAATCTGTAA-AGGATTCATATACTT
1 ACGATGACATATAGTCATAGGACTCTGCA-AATCCATAATAGAATTCATATACTC
*
18522 ACAATGACA
1 ACGATGACA
18531 CACAGTAATC
Statistics
Matches: 174, Mismatches: 38, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
52 84 0.48
53 90 0.52
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (54 bp):
ACGATGACATATAGTCATAGGACTCTGCAAATCCATAATAGAATTCATATACTC
Found at i:27276 original size:52 final size:53
Alignment explanation
Indices: 27114--27456 Score: 358
Period size: 52 Copynumber: 6.5 Consensus size: 53
27104 ACCTTTGATA
* * * * *
27114 ACTCACGATGACACAAAGTCATCGGA-CTTTTAATCCATAGTAGGATCCATGA-
1 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCGTAATAGGATTCAT-AT
* * * * * * * * **
27166 ACTCACGATAACATATAATCATC-AAACTAGTAAATTCGTAGTAGGATTTGTAT
1 ACTCACGATGACACATAGTCATCGGACCT-GTTAATCCGTAATAGGATTCATAT
27219 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCGTAAT-GGATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCGTAATAGGATTCATAT
* * *
27271 ACTCACGATGACACATAGTCATCGGA-CTAGTAAATCCGTAGTAGGATTCGTAT
1 ACTCACGATGACACATAGTCATCGGACCT-GTTAATCCGTAATAGGATTCATAT
* * *
27324 ACTCACGATGACACATAGTCATTGGAACTGTTAATCCATAAT-GGATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCGTAATAGGATTCATAT
* * ** * *
27376 AGTCACGATGACACATAGTCAACGGACCTCATATTCCGTAA-AAGATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCGTAATAGGATTCATAT
*
27428 ACTCACGATGGCACATAGTCATCGGACCT
1 ACTCACGATGACACATAGTCATCGGACCT
27457 TTTACATTTA
Statistics
Matches: 241, Mismatches: 42, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
51 3 0.01
52 144 0.60
53 89 0.37
54 5 0.02
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (53 bp):
ACTCACGATGACACATAGTCATCGGACCTGTTAATCCGTAATAGGATTCATAT
Found at i:27300 original size:105 final size:105
Alignment explanation
Indices: 27114--27456 Score: 419
Period size: 105 Copynumber: 3.3 Consensus size: 105
27104 ACCTTTGATA
* * * * *
27114 ACTCACGATGACACAAAGTCATCGGA-CTTTTAATCCATAGTAGGATCCATGA-ACTCACGATAA
1 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCATAAT-GGATTCAT-ATACTCACGATGA
* * ** *
27177 CATATAATCATCAAACTAGTAAATTCGTAGTAGGATTTGTAT
64 CACATAGTCATCGGACTAGTAAATTCGTAGTAGGATTCGTAT
*
27219 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCGTAATGGATTCATATACTCACGATGACA
1 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCATAATGGATTCATATACTCACGATGACA
*
27284 CATAGTCATCGGACTAGTAAATCCGTAGTAGGATTCGTAT
66 CATAGTCATCGGACTAGTAAATTCGTAGTAGGATTCGTAT
* * *
27324 ACTCACGATGACACATAGTCATTGGAACTGTTAATCCATAATGGATTCATATAGTCACGATGACA
1 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCATAATGGATTCATATACTCACGATGACA
* * * *
27389 CATAGTCAACGGACCTCA-T--ATTCCGTA-AAAGATTCATAT
66 CATAGTCATCGGA-CT-AGTAAATT-CGTAGTAGGATTCGTAT
*
27428 ACTCACGATGGCACATAGTCATCGGACCT
1 ACTCACGATGACACATAGTCATCGGACCT
27457 TTTACATTTA
Statistics
Matches: 209, Mismatches: 24, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
104 38 0.18
105 155 0.74
106 15 0.07
107 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (105 bp):
ACTCACGATGACACATAGTCATCGGACCTGTTAATCCATAATGGATTCATATACTCACGATGACA
CATAGTCATCGGACTAGTAAATTCGTAGTAGGATTCGTAT
Found at i:27402 original size:157 final size:157
Alignment explanation
Indices: 27114--27454 Score: 409
Period size: 157 Copynumber: 2.2 Consensus size: 157
27104 ACCTTTGATA
* * *
27114 ACTCACGATGACACAAAGTCATCGGACTTTTAATCCATAGTAGGATCCATGAACTCACGATAACA
1 ACTCACGATGACACATAGTCATCGGACTGTAAATCCATAGTAGGATCCATGAACTCACGATAACA
* * * * ** *
27179 TATAATCATCAAACTAGTAAATTCGTAGTAGGATTTGTATACTCACGATGACACATAGTCATCGG
66 CATAATCATCAAACTAGTAAATCCATAATAGGATTCATATACTCACGATGACACATAGTCAACGG
** **
27244 ACCTGTTAATCCGTAATGGATTCATAT
131 ACCTCATAATCCGTAAAAGATTCATAT
* * * *
27271 ACTCACGATGACACATAGTCATCGGACTAGTAAATCCGTAGTAGGATTCGT-ATACTCACGATGA
1 ACTCACGATGACACATAGTCATCGGACT-GTAAATCCATAGTAGGATCCATGA-ACTCACGATAA
* ** * *
27335 CACATAGTCATTGGAACT-GTTAATCCATAAT-GGATTCATATAGTCACGATGACACATAGTCAA
64 CACATAATCA-TCAAACTAGTAAATCCATAATAGGATTCATATACTCACGATGACACATAGTCAA
*
27398 CGGACCTCATATTCCGTAAAAGATTCATAT
128 CGGACCTCATAATCCGTAAAAGATTCATAT
*
27428 ACTCACGATGGCACATAGTCATCGGAC
1 ACTCACGATGACACATAGTCATCGGAC
27455 CTTTTACATT
Statistics
Matches: 156, Mismatches: 25, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
157 107 0.69
158 44 0.28
159 5 0.03
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (157 bp):
ACTCACGATGACACATAGTCATCGGACTGTAAATCCATAGTAGGATCCATGAACTCACGATAACA
CATAATCATCAAACTAGTAAATCCATAATAGGATTCATATACTCACGATGACACATAGTCAACGG
ACCTCATAATCCGTAAAAGATTCATAT
Found at i:28735 original size:17 final size:18
Alignment explanation
Indices: 28715--28751 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
28705 TTAAAGCTAG
28715 TTTTT-TTCTT-TTTTCT
1 TTTTTCTTCTTCTTTTCT
*
28731 TTTTTCTTCTTCTTTTGT
1 TTTTTCTTCTTCTTTTCT
28749 TTT
1 TTT
28752 CTCCCTACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
18 8 0.44
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.84
Consensus pattern (18 bp):
TTTTTCTTCTTCTTTTCT
Found at i:31895 original size:25 final size:25
Alignment explanation
Indices: 31840--31898 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
31830 CTAACCTAAA
* *
31840 CTTTAAACCTAAAACCCTTATTACC
1 CTTTAAAACTAAAACCCTTATAACC
*
31865 CATTTAAAACTCAAA-CCTTATAAACC
1 C-TTTAAAACTAAAACCCTTAT-AACC
31891 CTTTAAAA
1 CTTTAAAA
31899 AGCTATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (25 bp):
CTTTAAAACTAAAACCCTTATAACC
Found at i:31971 original size:15 final size:16
Alignment explanation
Indices: 31939--31973 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
31929 ACCCAATAAC
31939 CCAAACCCAAAGTGAA
1 CCAAACCCAAAGTGAA
*
31955 CCAAACCC-AATTGAA
1 CCAAACCCAAAGTGAA
31970 CCAA
1 CCAA
31974 GTCCAAACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.49, C:0.34, G:0.09, T:0.09
Consensus pattern (16 bp):
CCAAACCCAAAGTGAA
Found at i:32722 original size:6 final size:6
Alignment explanation
Indices: 32711--32735 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
32701 TGGGATATAA
32711 ATTGAG ATTGAG ATTGAG ATTGAG A
1 ATTGAG ATTGAG ATTGAG ATTGAG A
32736 CAATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (6 bp):
ATTGAG
Found at i:33143 original size:22 final size:24
Alignment explanation
Indices: 33116--33160 Score: 67
Period size: 22 Copynumber: 1.9 Consensus size: 24
33106 ACAAATTTAC
33116 ATTATTTT-ATTTT-ATTATTATT
1 ATTATTTTGATTTTGATTATTATT
33138 ATTATTTTGATTTTGGATTATTA
1 ATTATTTTGATTTT-GATTATTA
33161 ATATACTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 5 0.25
25 7 0.35
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (24 bp):
ATTATTTTGATTTTGATTATTATT
Found at i:33995 original size:23 final size:23
Alignment explanation
Indices: 33939--33995 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
33929 AAAGTCAATG
33939 GTCAATGAGTC-GACCGGTCAAA
1 GTCAATGAGTCGGACCGGTCAAA
* *
33961 GTCAA-CAGGTCGGATCGGTCAAA
1 GTCAATGA-GTCGGACCGGTCAAA
33984 GTCAATGAGTCG
1 GTCAATGAGTCG
33996 CGTCGGGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 1 0.03
22 8 0.28
23 19 0.66
24 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.19
Consensus pattern (23 bp):
GTCAATGAGTCGGACCGGTCAAA
Found at i:50586 original size:136 final size:136
Alignment explanation
Indices: 50342--50614 Score: 494
Period size: 136 Copynumber: 2.0 Consensus size: 136
50332 TTTGTTCTCC
*
50342 AGGGATGTAACGTAAGGATCATTGATTCTCTTGTAACAAAATACTTCGAATTCGTCTAATCAAGG
1 AGGGATGTAACGTAAGGACCATTGATTCTCTTGTAACAAAATACTTCGAATTCGTCTAATCAAGG
*
50407 TTGAGTACGATGTGATGAAAACGTTTTCTTGAATGACTCGAATAACTTCTAATCTATCGGATTGA
66 TTGAGTACGATGTGATGAAAACATTTTCTTGAATGACTCGAATAACTTCTAATCTATCGGATTGA
50472 ATTATT
131 ATTATT
50478 AGGGATGTAACGTAAGGACCATTGATTCTCTTGTAACAAAATACTTCGAATTCGTCTAATCAAGG
1 AGGGATGTAACGTAAGGACCATTGATTCTCTTGTAACAAAATACTTCGAATTCGTCTAATCAAGG
* *
50543 TTGAGTACGATGTGATGAAAACA-TTTCTTTGAATGATTTGAATAACTTCTAATCTATCGGATTG
66 TTGAGTACGATGTGATGAAAACATTTTC-TTGAATGACTCGAATAACTTCTAATCTATCGGATTG
50607 AATTATT
130 AATTATT
50614 A
1 A
50615 TTTTGTTATG
Statistics
Matches: 132, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
135 4 0.03
136 128 0.97
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (136 bp):
AGGGATGTAACGTAAGGACCATTGATTCTCTTGTAACAAAATACTTCGAATTCGTCTAATCAAGG
TTGAGTACGATGTGATGAAAACATTTTCTTGAATGACTCGAATAACTTCTAATCTATCGGATTGA
ATTATT
Found at i:58677 original size:24 final size:24
Alignment explanation
Indices: 58649--58699 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
58639 AGAAATAATC
* * *
58649 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAATTAAAATCTATTTAGTTG
*
58673 TTTCAATTAAAATCTGTTTAGTTG
1 TTTCAATTAAAATCTATTTAGTTG
58697 TTT
1 TTT
58700 GAGTCAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAAATCTATTTAGTTG
Found at i:60658 original size:24 final size:24
Alignment explanation
Indices: 60630--60680 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
60620 AGAAATAATC
* * *
60630 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAAATCTGTTTAGTTG
60654 TTTCAATTAAAATCTGTTTAGTTG
1 TTTCAATTAAAATCTGTTTAGTTG
60678 TTT
1 TTT
60681 GAGTCAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAAATCTGTTTAGTTG
Found at i:65692 original size:35 final size:36
Alignment explanation
Indices: 65653--65725 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 36
65643 TCTTTTACTG
*
65653 TATTAATTATAATTCAAATTATATAT-TTATAAA-TT
1 TATTAATTATAACTCAAATTATAT-TGTTATAAAGTT
65688 TATTAATTATAACTCAAATTATATTGTTATAAAGTT
1 TATTAATTATAACTCAAATTATATTGTTATAAAGTT
65724 TA
1 TA
65726 CATCAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
34 1 0.03
35 30 0.86
36 4 0.11
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (36 bp):
TATTAATTATAACTCAAATTATATTGTTATAAAGTT
Found at i:66647 original size:35 final size:35
Alignment explanation
Indices: 66601--66668 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
66591 ATACATTAAT
66601 TGAATCATTATTGTGATTATGCTCATCCTATGAGC
1 TGAATCATTATTGTGATTATGCTCATCCTATGAGC
* *
66636 TGAATCTTTATTGTGATTATGCTCATCTTATGA
1 TGAATCATTATTGTGATTATGCTCATCCTATGA
66669 ATTGGAGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (35 bp):
TGAATCATTATTGTGATTATGCTCATCCTATGAGC
Found at i:66926 original size:14 final size:15
Alignment explanation
Indices: 66895--66929 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
66885 AATATTATAT
*
66895 TGAATTTTGAATTTG
1 TGAATTTTGAATTAG
66910 TGAATTTT-AATTAG
1 TGAATTTTGAATTAG
66924 TGAATT
1 TGAATT
66930 AATTGTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.51
Consensus pattern (15 bp):
TGAATTTTGAATTAG
Found at i:69649 original size:21 final size:21
Alignment explanation
Indices: 69610--69663 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
69600 GGAGTTTTCA
*
69610 GTATCGGTAGAAGAGTCACTT
1 GTATCGGTAGAAGAGTCACAT
*
69631 GTATCGGTAGAACTA-TCACAT
1 GTATCGGTAGAA-GAGTCACAT
*
69652 GTGTCGGTAGAA
1 GTATCGGTAGAA
69664 AATTTGCCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (21 bp):
GTATCGGTAGAAGAGTCACAT
Found at i:78616 original size:2 final size:2
Alignment explanation
Indices: 78609--78646 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
78599 AGGCTTTGAT
* *
78609 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
78647 AACTCATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:82639 original size:5 final size:5
Alignment explanation
Indices: 82629--82653 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
82619 AATTTTCAAT
82629 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
82654 CCAAATAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Done.