Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002419.1 Kokia drynarioides strain JFW-HI SEQ_114517, 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: 62897
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:7514 original size:47 final size:49
Alignment explanation
Indices: 7442--7537 Score: 151
Period size: 47 Copynumber: 2.0 Consensus size: 49
7432 ACAATATGAA
*
7442 CATATTAAAAGATAGCAAATAAGCTTTAGCA-AGTGAGTGAAATCACAG
1 CATATTAAAAGATAGCAAATAAGCTTTAGCACACTGAGTGAAATCACAG
*
7490 CATATTGAAAGAT-GCAAATAAGCTTTAGCACTACTGAGTGAAATCACA
1 CATATTAAAAGATAGCAAATAAGCTTTAGCAC-ACTGAGTGAAATCACA
7538 TGCCTTGTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
47 17 0.39
48 12 0.27
49 15 0.34
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.24
Consensus pattern (49 bp):
CATATTAAAAGATAGCAAATAAGCTTTAGCACACTGAGTGAAATCACAG
Found at i:10228 original size:4 final size:4
Alignment explanation
Indices: 10182--10208 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
10172 ATATGTATTT
10182 ATGG ATGG ATGG ATGG ATGG ATGG ATG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATG
10209 TATGAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.48, T:0.26
Consensus pattern (4 bp):
ATGG
Found at i:15269 original size:21 final size:21
Alignment explanation
Indices: 15243--15283 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
15233 AGTACGATAC
15243 TATTA-TAGTATTTTATTTTAT
1 TATTATTAGTATTTT-TTTTAT
*
15264 TATTATTATTATTTTTTTTA
1 TATTATTAGTATTTTTTTTA
15284 CATTATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TATTATTAGTATTTTTTTTAT
Found at i:15603 original size:45 final size:45
Alignment explanation
Indices: 15533--15619 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
15523 ATACTTTAAA
* * * *
15533 TACAATATTATATTTAAAATTAACATTTTATTTTATTAAAAAAAT
1 TACAATATTATATCTAAAATAAACATTTTATCTTATCAAAAAAAT
*
15578 TACAATATTATATCTATAATAAACATTTTATCTTATCAAAAA
1 TACAATATTATATCTAAAATAAACATTTTATCTTATCAAAAA
15620 CACTTTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (45 bp):
TACAATATTATATCTAAAATAAACATTTTATCTTATCAAAAAAAT
Found at i:16533 original size:28 final size:28
Alignment explanation
Indices: 16501--16559 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
16491 CTAATACTTA
* *
16501 ACAACAACGCTAACATAACTATTAATAG
1 ACAACAACGCTAACATAACCATTAACAG
* *
16529 ACAACAACGTTAATATAACCATTAACAG
1 ACAACAACGCTAACATAACCATTAACAG
16557 ACA
1 ACA
16560 CCATATCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.51, C:0.22, G:0.07, T:0.20
Consensus pattern (28 bp):
ACAACAACGCTAACATAACCATTAACAG
Found at i:17242 original size:17 final size:18
Alignment explanation
Indices: 17222--17255 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17212 TTTTTTATGG
17222 TTTTTAAT-AAATTTATT
1 TTTTTAATAAAATTTATT
*
17239 TTTTTTATAAAATTTAT
1 TTTTTAATAAAATTTAT
17256 AAAATTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTAATAAAATTTATT
Found at i:18457 original size:33 final size:35
Alignment explanation
Indices: 18420--18484 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
18410 CAAATAATTA
18420 TATTTATTT-AATATAAAAAT-AATTAAAATTTTT
1 TATTTATTTAAATATAAAAATGAATTAAAATTTTT
* * *
18453 TATTTTTTTAAATATATAATTGAATTAAAATT
1 TATTTATTTAAATATAAAAATGAATTAAAATT
18485 AAAATTCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 8 0.30
34 9 0.33
35 10 0.37
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (35 bp):
TATTTATTTAAATATAAAAATGAATTAAAATTTTT
Found at i:18985 original size:20 final size:21
Alignment explanation
Indices: 18960--19000 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
18950 CTGATGTTTC
*
18960 GTTATTTTTCTCTT-TATTTT
1 GTTATTTTTCTATTATATTTT
18980 GTTATTTTTCTATTATATTTT
1 GTTATTTTTCTATTATATTTT
19001 AATTTCGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.15, C:0.07, G:0.05, T:0.73
Consensus pattern (21 bp):
GTTATTTTTCTATTATATTTT
Found at i:20346 original size:24 final size:23
Alignment explanation
Indices: 20302--20364 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
20292 TAACAACATT
* *
20302 AAAATAAAATTATATCAAATTAA
1 AAAATAAAACTAAATCAAATTAA
*
20325 AAAATAAACACTAAATCAAATT-T
1 AAAATAAA-ACTAAATCAAATTAA
* *
20348 AACATAAAAATAAATCA
1 AAAATAAAACTAAATCA
20365 GATTGTCGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 8 0.24
23 15 0.44
24 11 0.32
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (23 bp):
AAAATAAAACTAAATCAAATTAA
Found at i:20478 original size:2 final size:2
Alignment explanation
Indices: 20471--20500 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20461 GCCCCACCTC
20471 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
20501 GACATCAATG
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:21647 original size:20 final size:20
Alignment explanation
Indices: 21622--21661 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
21612 GCCGAATCAC
21622 AGCTTGAAC-AAAGATGTTCT
1 AGCTTG-ACTAAAGATGTTCT
*
21642 AGCTTGACTAAAGATTTTCT
1 AGCTTGACTAAAGATGTTCT
21662 GCTCAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (20 bp):
AGCTTGACTAAAGATGTTCT
Found at i:21980 original size:20 final size:20
Alignment explanation
Indices: 21944--21997 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
21934 ATTATTTTTA
*
21944 ATATTT-TTTTA-AAAATAT
1 ATATTTATTTTATATAATAT
21962 ATATTTATTTTATATAATAT
1 ATATTTATTTTATATAATAT
* * *
21982 TTAATAATTTTATATA
1 ATATTTATTTTATATA
21998 TTTTATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 6 0.20
19 5 0.17
20 19 0.63
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTTATTTTATATAATAT
Found at i:26150 original size:31 final size:30
Alignment explanation
Indices: 26099--26156 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
26089 ATTGGATTTT
*
26099 AATTTTAAAATTTAACGAGTAAAAGGACTA
1 AATTTTAAAATTGAACGAGTAAAAGGACTA
*
26129 AATTTCTAAATATTGAA-GAGTACAAGGA
1 AATTT-TAAA-ATTGAACGAGTAAAAGGA
26157 TTGCAAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 5 0.21
31 14 0.58
32 5 0.21
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (30 bp):
AATTTTAAAATTGAACGAGTAAAAGGACTA
Found at i:29008 original size:20 final size:20
Alignment explanation
Indices: 28982--29039 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
28972 TCAAAAAATA
28982 ATAAAAATATTTAAAAATTC
1 ATAAAAATATTTAAAAATTC
*
29002 ATTAAAAT-TTTAAAAAATTC
1 ATAAAAATATTT-AAAAATTC
*
29022 ATAAAAATATTAAAAAAT
1 ATAAAAATATTTAAAAAT
29040 ATTCATGTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 3 0.09
20 28 0.85
21 2 0.06
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
ATAAAAATATTTAAAAATTC
Found at i:36511 original size:2 final size:2
Alignment explanation
Indices: 36504--36528 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36494 ATACATAAGA
36504 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
36529 AAGTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:41575 original size:3 final size:3
Alignment explanation
Indices: 41564--41605 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
41554 AAAGGAAAAA
* *
41564 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG GAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
41606 GAAAAATTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:41617 original size:15 final size:15
Alignment explanation
Indices: 41570--41611 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
41560 AAAAAAGAAA
* *
41570 AGAAGAAGAAGAAGA
1 AGAAGAAGAAAAAGG
41585 AGAAGAAGAAAAAGG
1 AGAAGAAGAAAAAGG
41600 AGAAG-AGAAAAA
1 AGAAGAAGAAAAA
41612 TTGAGATGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (15 bp):
AGAAGAAGAAAAAGG
Found at i:42608 original size:59 final size:57
Alignment explanation
Indices: 42540--42685 Score: 168
Period size: 58 Copynumber: 2.5 Consensus size: 57
42530 GATAAACATG
* * *
42540 GCCGACACCCCCTTTTTGTCAAATAAAAAATTCAATTTTTTTATGTTGACCATGCCAAGA
1 GCCGACA-CCCCTTTTT-TCAGATAAAAAAATCAACTTTTTTATGTTGACCATG-CAAGA
* * * * *
42600 -CCGACACCCCTATTTATCTGATAAAAAAATCAACTTTTTTGTGTTGGCCATGCAATA
1 GCCGACACCCCT-TTTTTCAGATAAAAAAATCAACTTTTTTATGTTGACCATGCAAGA
*
42657 GCCGACACCCATTTTTTCAGATAAAAAAA
1 GCCGACACCCCTTTTTTCAGATAAAAAAA
42686 ATTCAAAATT
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
57 19 0.26
58 45 0.62
59 9 0.12
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.32
Consensus pattern (57 bp):
GCCGACACCCCTTTTTTCAGATAAAAAAATCAACTTTTTTATGTTGACCATGCAAGA
Found at i:42737 original size:93 final size:92
Alignment explanation
Indices: 42611--42793 Score: 262
Period size: 93 Copynumber: 2.0 Consensus size: 92
42601 CGACACCCCT
* *
42611 ATTTATCTGATAAAAAAATCAACTTTTTTGTGTTGGCCATGCAATAGCCGACAC-CCATTTTT-T
1 ATTTATCTGATAAAAAAATCAAATTTTTTGTGTTAGCCATGCAATAGCCGACACTCCATTTTTGT
*
42674 CAGATAAAAAAAATTCAAAATTTTTGG
66 CAAATAAAAAAAATTCAAAATTTTTGG
* *
42701 ATTTATCTGATAAAAAAAAATCAAATTTTTTAGTGTTAGCCATGCAATGGCCGACACTCCTTTTT
1 ATTTATCTGAT--AAAAAAATCAAATTTTTT-GTGTTAGCCATGCAATAGCCGACACTCCATTTT
* *
42766 TGTCAAATAAAAAAATTTCAAATTTTTT
63 TGTCAAATAAAAAAAATTCAAAATTTTT
42794 TAGTTTTGGC
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
90 11 0.14
92 17 0.21
93 23 0.28
94 7 0.09
95 23 0.28
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (92 bp):
ATTTATCTGATAAAAAAATCAAATTTTTTGTGTTAGCCATGCAATAGCCGACACTCCATTTTTGT
CAAATAAAAAAAATTCAAAATTTTTGG
Found at i:42873 original size:61 final size:61
Alignment explanation
Indices: 42701--42882 Score: 220
Period size: 63 Copynumber: 2.9 Consensus size: 61
42691 AAATTTTTGG
* * * *
42701 ATTTATCTGATAAAAAAAAATCAAATTTTTTAGTGTTAGCCATGCAATGGCCGACACTCCTT
1 ATTTATCTGAT-AAAAAAAATCAAATTTTTTTGTGTTAGCCATGCAATGGTCGACACCCCCT
* * ** * * *
42763 TTTTGTCAAATAAAAAAATTTCAAATTTTTTTAGTTTTGGCCATGCAATGGTCGACACCCCCT
1 ATTTATCTGATAAAAAAA-ATCAAATTTTTTT-GTGTTAGCCATGCAATGGTCGACACCCCCT
* *
42826 ATTTATCTGATAAAAAAAATCAAATTTTTTTGTGTTAGCCATACAATGGTTGACACC
1 ATTTATCTGATAAAAAAAATCAAATTTTTTTGTGTTAGCCATGCAATGGTCGACACC
42883 AACTTTCTCT
Statistics
Matches: 98, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
61 29 0.30
62 30 0.31
63 39 0.40
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (61 bp):
ATTTATCTGATAAAAAAAATCAAATTTTTTTGTGTTAGCCATGCAATGGTCGACACCCCCT
Found at i:43719 original size:30 final size:30
Alignment explanation
Indices: 43675--43812 Score: 159
Period size: 30 Copynumber: 4.6 Consensus size: 30
43665 ATAAATTTTC
* *
43675 AAAAAATAATAATTAGAATATACAGGAAATT
1 AAAAATTAA-AATTAAAATATACAGGAAATT
*
43706 AAAAATTAAAATTAGAATATACAGGAAATT
1 AAAAATTAAAATTAAAATATACAGGAAATT
* *
43736 ATAAATTAAATTTAAAATATACAGGAAATT
1 AAAAATTAAAATTAAAATATACAGGAAATT
* * * * *
43766 AGAAATTAAATTTAAAATAAAAACGAAATT
1 AAAAATTAAAATTAAAATATACAGGAAATT
* *
43796 ACAAATTAAATTTAAAA
1 AAAAATTAAAATTAAAA
43813 AATAAACGAA
Statistics
Matches: 98, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
30 90 0.92
31 8 0.08
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (30 bp):
AAAAATTAAAATTAAAATATACAGGAAATT
Found at i:43755 original size:60 final size:60
Alignment explanation
Indices: 43691--43812 Score: 181
Period size: 60 Copynumber: 2.0 Consensus size: 60
43681 TAATAATTAG
* * * * *
43691 AATATACAGGAAATTAAAAATTAAAATTAGAATATACAGGAAATTATAAATTAAATTTAA
1 AATATACAGGAAATTAAAAATTAAAATTAAAATAAAAACGAAATTACAAATTAAATTTAA
* *
43751 AATATACAGGAAATTAGAAATTAAATTTAAAATAAAAACGAAATTACAAATTAAATTTAA
1 AATATACAGGAAATTAAAAATTAAAATTAAAATAAAAACGAAATTACAAATTAAATTTAA
43811 AA
1 AA
43813 AATAAACGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (60 bp):
AATATACAGGAAATTAAAAATTAAAATTAAAATAAAAACGAAATTACAAATTAAATTTAA
Found at i:46174 original size:22 final size:22
Alignment explanation
Indices: 46146--46189 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
46136 AATGTATAAA
*
46146 GATTGCGACGACTTCGTTACTT
1 GATTGCGACAACTTCGTTACTT
46168 GATTGCGACAACTTCGTTACTT
1 GATTGCGACAACTTCGTTACTT
46190 TATAATCGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (22 bp):
GATTGCGACAACTTCGTTACTT
Found at i:49762 original size:63 final size:60
Alignment explanation
Indices: 49636--49795 Score: 166
Period size: 63 Copynumber: 2.6 Consensus size: 60
49626 GGTGTCGGCT
* * * * * *
49636 ATTGCAT-GACCAACAC-AAAAAAATTGA-TTTGTTACCAGATAAAAAAAGGGGTGTCGATC
1 ATTGCATAG-CCAACACAAAAAAAATTGATTTTTTTATCTGA-CAAAAAAGGGGCGTCGACC
*
49695 ATTGCAT-GACCAACACAAAAAAAAATTGAAATTTTTTTATCTGACAAAAAGGGGGCGTCGACC
1 ATTGCATAG-CCAACAC-AAAAAAAATTG--ATTTTTTTATCTGACAAAAAAGGGGCGTCGACC
*
49758 ATTGCATAGCCAACACAAAAAAATTTGATTTTTTTATC
1 ATTGCATAGCCAACACAAAAAAAATTGATTTTTTTATC
49796 AAATAACCAA
Statistics
Matches: 87, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
59 16 0.18
60 11 0.13
61 10 0.11
62 10 0.11
63 30 0.34
64 10 0.11
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (60 bp):
ATTGCATAGCCAACACAAAAAAAATTGATTTTTTTATCTGACAAAAAAGGGGCGTCGACC
Found at i:49966 original size:84 final size:87
Alignment explanation
Indices: 49712--49954 Score: 334
Period size: 91 Copynumber: 2.8 Consensus size: 87
49702 GACCAACACA
* * *
49712 AAAAAAAATTGAAATTTTTTTATCTGACAAAAAGGGGGCGTCGACCATTGCAT-AGCCAACACAA
1 AAAAAAAATTGAAATTTTTTTATCTGACAAAAAAGGGGTGTCGGCCATTGCATGA-CCAACACAA
*
49776 AAAAATTTGATTTTTTTATCAAAT
65 AAAAATTTGATTTTTTTATC-AAG
* * *
49800 AACCAAAAAATTTTGAAATTTTTTTATCTGA-AAAAAAGAGGTGTCGGCTATTGCACGACCAACA
1 AA--AAAAAA--TTGAAATTTTTTTATCTGACAAAAAAGGGGTGTCGGCCATTGCATGACCAACA
49864 CAAAAAAATTTGATTTTTTTATC-AG
62 CAAAAAAATTTGATTTTTTTATCAAG
49889 AAAAAAAATT-AAA-TTTTTTATCTGACAAAAAAGGGGTGTCGGCCATTGCATGACCAACACAAA
1 AAAAAAAATTGAAATTTTTTTATCTGACAAAAAAGGGGTGTCGGCCATTGCATGACCAACACAAA
49952 AAA
66 AAA
49955 TACAAATTTT
Statistics
Matches: 139, Mismatches: 10, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
83 12 0.09
84 40 0.29
85 2 0.01
87 6 0.04
88 2 0.01
89 3 0.02
90 6 0.04
91 48 0.35
92 20 0.14
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (87 bp):
AAAAAAAATTGAAATTTTTTTATCTGACAAAAAAGGGGTGTCGGCCATTGCATGACCAACACAAA
AAAATTTGATTTTTTTATCAAG
Found at i:52306 original size:28 final size:27
Alignment explanation
Indices: 52266--52321 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
52256 ACAATATTTT
*
52266 AAAATTATTTTTATTAATTTAAATATAA
1 AAAATTATTTTTA-TAATATAAATATAA
52294 AAAATCTA-TTTTATAATATAAATATAA
1 AAAAT-TATTTTTATAATATAAATATAA
52321 A
1 A
52322 TTTAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 14 0.54
28 10 0.38
29 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATTATTTTTATAATATAAATATAA
Found at i:56447 original size:17 final size:17
Alignment explanation
Indices: 56415--56447 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
56405 AATAAATTTA
56415 TATTAAATATATAATAC
1 TATTAAATATATAATAC
56432 TATTATAATATA-AATA
1 TATTA-AATATATAATA
56448 TTAAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TATTAAATATATAATAC
Found at i:56455 original size:14 final size:15
Alignment explanation
Indices: 56413--56474 Score: 60
Period size: 14 Copynumber: 4.3 Consensus size: 15
56403 AAAATAAATT
56413 TATATTAAATATATAA
1 TATATTAAA-ATATAA
*
56429 TACTATTATAATATAA
1 TA-TATTAAAATATAA
*
56445 -ATATTAAAATA-AT
1 TATATTAAAATATAA
56458 TATA-TAAAA-ATAA
1 TATATTAAAATATAA
56471 TATA
1 TATA
56475 AAATTAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
12 1 0.03
13 11 0.28
14 12 0.31
15 1 0.03
16 8 0.21
17 6 0.15
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
TATATTAAAATATAA
Found at i:61127 original size:69 final size:68
Alignment explanation
Indices: 60856--61140 Score: 275
Period size: 69 Copynumber: 4.1 Consensus size: 68
60846 TGGCCCCAGT
* * * *
60856 TGTCATTTTAAGGTTCGCAAGCGAAGAGCCGCAACCTCCAACACAATTAGCAAGAGCAAAGCTCT
1 TGTCATATTAAGGTTCGC-AGCGAAGAGCTGCAACCTCCAACACAATTAGCGAGAGCAAAGCTCC
* **
60921 TAGT
65 CAAC
* * * * * * *
60925 TGTCATTTTGAGGTTCGCAGGCAAAGAGTTGCAACCTCCAATACAGTTAGCGAGAGCAAAGCTTC
1 TGTCATATTAAGGTTCGCA-GCGAAGAGCTGCAACCTCCAACACAATTAGCGAGAGCAAAGCTCC
*
60990 CAAA
65 CAAC
* * * ** * * *
60994 TGTCATATTGAGGTTTGCAGGCGAAGAG-TCGTAACCTTTAATATAGTTAGCGAGAGCAAAGCTC
1 TGTCATATTAAGGTTCGCA-GCGAAGAGCT-GCAACCTCCAACACAATTAGCGAGAGCAAAGCTC
61058 CCAAC
64 CCAAC
* * * *
61063 TTTCATATTAAGGTTCGTAGCTGCAGAGCTGCAACCTCCAACACAATTAGTGAGAGCAAAGCTCC
1 TGTCATATTAAGGTTCGCAGC-GAAGAGCTGCAACCTCCAACACAATTAGCGAGAGCAAAGCTCC
61128 CAAC
65 CAAC
61132 TGTCATATT
1 TGTCATATT
61141 GAGTCGCAAC
Statistics
Matches: 178, Mismatches: 34, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
68 4 0.02
69 173 0.97
70 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (68 bp):
TGTCATATTAAGGTTCGCAGCGAAGAGCTGCAACCTCCAACACAATTAGCGAGAGCAAAGCTCCC
AAC
Found at i:61173 original size:53 final size:53
Alignment explanation
Indices: 61093--61193 Score: 148
Period size: 53 Copynumber: 1.9 Consensus size: 53
61083 CTGCAGAGCT
*
61093 GCAACCTCCAACACAATTAGTGAGAGCAAAGCTCCCAACTGTCATATTGAGTC
1 GCAACCTCCAACACAATTAGCGAGAGCAAAGCTCCCAACTGTCATATTGAGTC
** * * *
61146 GCAACCTCCAATGCAGTTAGCGAGAGCAAAGCTCTCAGCTGTCATATT
1 GCAACCTCCAACACAATTAGCGAGAGCAAAGCTCCCAACTGTCATATT
61194 AAGGTTTGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.22
Consensus pattern (53 bp):
GCAACCTCCAACACAATTAGCGAGAGCAAAGCTCCCAACTGTCATATTGAGTC
Found at i:61236 original size:122 final size:121
Alignment explanation
Indices: 61038--61262 Score: 317
Period size: 122 Copynumber: 1.8 Consensus size: 121
61028 CCTTTAATAT
* * *
61038 AGTTAGCGAGAGCAAAGCTCCCAACTTTCATATTAAGGTTCGTAGCTGCAGAGCTGCAACCTCCA
1 AGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGTTCGCAGC-GCAAAGCTGCAACCTCCA
61103 ACACAATTAGTGAGAGCAAAGCTCCCAACTGTCATATTGAGTCGCAACCTCCAATGC
65 ACACAATTAGTGAGAGCAAAGCTCCCAACTGTCATATTGAGTCGCAACCTCCAATGC
* * * * *
61160 AGTTAGCGAGAGCAAAGCTCTCAGCTGTCATATTAAGGTTTGCAG-GCAAAAAGCTGTAACCTTC
1 AGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGTTCGCAGCGC--AAAGCTGCAACCTCC
* * *
61224 AATACAGTTAGTGAGAGCAAAGTTCCCAACTGTCATATT
64 AACACAATTAGTGAGAGCAAAGCTCCCAACTGTCATATT
61263 AAGGTTCACT
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
120 2 0.02
122 88 0.98
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (121 bp):
AGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGTTCGCAGCGCAAAGCTGCAACCTCCAA
CACAATTAGTGAGAGCAAAGCTCCCAACTGTCATATTGAGTCGCAACCTCCAATGC
Found at i:61288 original size:69 final size:69
Alignment explanation
Indices: 61148--61327 Score: 207
Period size: 69 Copynumber: 2.6 Consensus size: 69
61138 ATTGAGTCGC
* * * ** *
61148 AACCTCCAATGCAGTTAGCGAGAGCAAAGCTCTCAGCTGTCATATTAAGGTTTGCAGGCAAAAAG
1 AACCTCCAATACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGTTCACAGACAAAAAG
*
61213 CTGT
66 CCGT
* * * * ** *
61217 AACCTTCAATACAGTTAGTGAGAGCAAAGTTCCCAACTGTCATATTAAGGTTCACTGATGAAGAG
1 AACCTCCAATACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGTTCACAGACAAAAAG
61282 CCGT
66 CCGT
* * *
61286 AACCTCCAACACAGTTAGCGAGAGCAAAGCTCCTAATTGTCA
1 AACCTCCAATACAGTTAGCGAGAGCAAAGCTCCCAACTGTCA
61328 CTTTAAATTT
Statistics
Matches: 91, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
69 91 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (69 bp):
AACCTCCAATACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGTTCACAGACAAAAAG
CCGT
Found at i:61292 original size:191 final size:191
Alignment explanation
Indices: 60950--61327 Score: 519
Period size: 191 Copynumber: 2.0 Consensus size: 191
60940 CGCAGGCAAA
* *
60950 GAGTTGCAACCTCCAATACAGTTAGCGAGAGCAAAGCTTCCAAATGTCATATTGAGGTTTGCAGG
1 GAGTCGCAACCTCCAATACAGTTAGCGAGAGCAAAGCTTCCAAATGTCATATTAAGGTTTGCAGG
* * * * * *
61015 CGAAGAGTCGTAACCTTTAATATAGTTAGCGAGAGCAAAGCTCCCAACTTTCATATTAAGGTTCG
66 CAAAAAGTCGTAACCTTCAATACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGTTCC
* * * *
61080 TAGCTGCAGAGCTGCAACCTCCAACACAATTAGTGAGAGCAAAGCTCCCAACTGTCATATT
131 TAGATGAAGAGCCGCAACCTCCAACACAATTAGCGAGAGCAAAGCTCCCAACTGTCATATT
* **
61141 GAGTCGCAACCTCCAATGCAGTTAGCGAGAGCAAAGC-TCTCAGCTGTCATATTAAGGTTTGCAG
1 GAGTCGCAACCTCCAATACAGTTAGCGAGAGCAAAGCTTC-CAAATGTCATATTAAGGTTTGCAG
* *
61205 GCAAAAAG-CTGTAACCTTCAATACAGTTAGTGAGAGCAAAGTTCCCAACTGTCATATTAAGGTT
65 GCAAAAAGTC-GTAACCTTCAATACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGTT
* * * *
61269 CACT-GATGAAGAGCCGTAACCTCCAACACAGTTAGCGAGAGCAAAGCTCCTAATTGTCA
129 C-CTAGATGAAGAGCCGCAACCTCCAACACAATTAGCGAGAGCAAAGCTCCCAACTGTCA
61328 CTTTAAATTT
Statistics
Matches: 163, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
190 3 0.02
191 159 0.98
192 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (191 bp):
GAGTCGCAACCTCCAATACAGTTAGCGAGAGCAAAGCTTCCAAATGTCATATTAAGGTTTGCAGG
CAAAAAGTCGTAACCTTCAATACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGTTCC
TAGATGAAGAGCCGCAACCTCCAACACAATTAGCGAGAGCAAAGCTCCCAACTGTCATATT
Found at i:61459 original size:42 final size:42
Alignment explanation
Indices: 61423--61522 Score: 141
Period size: 42 Copynumber: 2.4 Consensus size: 42
61413 CACATCTAAG
61423 CTCATTATTGTTAAGAAAATAGCTTGCAGACTCACATCCCAA
1 CTCATTATTGTTAAGAAAATAGCTTGCAGACTCACATCCCAA
* * * *
61465 CTCATTATTGTTAAGAAAATAGCTCGCGGATTCATATCCCAA
1 CTCATTATTGTTAAGAAAATAGCTTGCAGACTCACATCCCAA
*
61507 CTGATTATT-TT-AGAAA
1 CTCATTATTGTTAAGAAA
61523 TTTTTCACAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
40 5 0.09
41 2 0.04
42 46 0.87
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (42 bp):
CTCATTATTGTTAAGAAAATAGCTTGCAGACTCACATCCCAA
Done.