Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002264.1 Kokia drynarioides strain JFW-HI SEQ_114283, 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: 33887
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:3911 original size:23 final size:23
Alignment explanation
Indices: 3885--3950 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
3875 TACAAAACCT
* *
3885 TAAACCTTAACCTTAATAAAATA
1 TAAACCCTAACCCTAATAAAATA
3908 TAAACCCTAACCCTAATAAAATA
1 TAAACCCTAACCCTAATAAAATA
3931 TAAACCCTAACCCTAA-AAAA
1 TAAACCCTAACCCTAATAAAA
3951 CCCTCTTATC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 4 0.10
23 37 0.90
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.23
Consensus pattern (23 bp):
TAAACCCTAACCCTAATAAAATA
Found at i:5801 original size:15 final size:15
Alignment explanation
Indices: 5781--5833 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
5771 AAACATCAGT
5781 AATAAATTGATGCAA
1 AATAAATTGATGCAA
* *
5796 AATAAATAGCAT-CAGT
1 AATAAATTG-ATGCA-A
*
5812 AATAAATTAATGCAA
1 AATAAATTGATGCAA
5827 AATAAAT
1 AATAAAT
5834 AACATTATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 19 0.63
16 11 0.37
ACGTcount: A:0.57, C:0.08, G:0.09, T:0.26
Consensus pattern (15 bp):
AATAAATTGATGCAA
Found at i:5812 original size:31 final size:31
Alignment explanation
Indices: 5774--5834 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
5764 ATAAGTAAAA
*
5774 CATCAGTAATAAATTGATGCAAAATAAATAG
1 CATCAGTAATAAATTAATGCAAAATAAATAG
5805 CATCAGTAATAAATTAATGCAAAATAAATA
1 CATCAGTAATAAATTAATGCAAAATAAATA
5835 ACATTATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (31 bp):
CATCAGTAATAAATTAATGCAAAATAAATAG
Found at i:8146 original size:32 final size:32
Alignment explanation
Indices: 8110--8174 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
8100 AACTATGATT
* *
8110 AAACTTAATC-ACTTTAATATTAAATTAATTTA
1 AAACTT-ATCAACTTAAATATTAAATTAAATTA
* *
8142 AAACTTATCAAGTTAAATATTAGATTAAATTA
1 AAACTTATCAACTTAAATATTAAATTAAATTA
8174 A
1 A
8175 TATAAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 3 0.11
32 25 0.89
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (32 bp):
AAACTTATCAACTTAAATATTAAATTAAATTA
Found at i:8191 original size:21 final size:22
Alignment explanation
Indices: 8156--8197 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
8146 TTATCAAGTT
8156 AAATATTAGATTAAATTAATATA
1 AAATATTA-ATTAAATTAATATA
8179 AAATATT-ATTAAATTAATA
1 AAATATTAATTAAATTAATA
8198 GAATATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATATTAATTAAATTAATATA
Found at i:12236 original size:26 final size:25
Alignment explanation
Indices: 12151--12263 Score: 111
Period size: 25 Copynumber: 4.5 Consensus size: 25
12141 ATCCAAACCT
*
12151 AGCCTTTGTGGCAAATTATTTGTAA
1 AGCCTTTGTGGCGAATTATTTGTAA
**
12176 AGCCTTTGTGGCGAATTAGCTGTAA
1 AGCCTTTGTGGCGAATTATTTGTAA
* *
12201 AGCCTTTGTGGCGAGTTATTTAGAAA
1 AGCCTTTGTGGCGAATTATTT-GTAA
* * * *
12227 AGCCTATGTGGTGTATTATTCAG-AA
1 AGCCTTTGTGGCGAATTATT-TGTAA
*
12252 AGCCTTAGTGGC
1 AGCCTTTGTGGC
12264 AAAGTTATCT
Statistics
Matches: 71, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
25 51 0.72
26 20 0.28
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.35
Consensus pattern (25 bp):
AGCCTTTGTGGCGAATTATTTGTAA
Found at i:12254 original size:51 final size:50
Alignment explanation
Indices: 12151--12271 Score: 127
Period size: 51 Copynumber: 2.4 Consensus size: 50
12141 ATCCAAACCT
* * *
12151 AGCCTTTGTGGCAAATTATTTGTAAAGCCTTTGTGGCGAATTAGCTGTAA
1 AGCCTTTGTGGCAAATTATTTGAAAAGCCTATGTGGCGAATTAGCAGTAA
* * * * *
12201 AGCCTTTGTGGCGAGTTATTTAGAAAAGCCTATGTGGTGTATTATTCAG-AA
1 AGCCTTTGTGGCAAATTATTT-GAAAAGCCTATGTGGCGAATTA-GCAGTAA
*
12252 AGCCTTAGTGGCAAAGTTAT
1 AGCCTTTGTGGCAAA-TTAT
12272 CTAGGAAGCC
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
50 19 0.33
51 32 0.56
52 6 0.11
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (50 bp):
AGCCTTTGTGGCAAATTATTTGAAAAGCCTATGTGGCGAATTAGCAGTAA
Found at i:16840 original size:24 final size:24
Alignment explanation
Indices: 16794--16877 Score: 123
Period size: 24 Copynumber: 3.5 Consensus size: 24
16784 AGCTCATACA
*
16794 AGCCCAGATAGAATTAGCTCTTATG
1 AGCCCAGATAG-GTTAGCTCTTATG
* *
16819 AGCCCAGATAGGTTAGCCCTTACG
1 AGCCCAGATAGGTTAGCTCTTATG
*
16843 AGCCTAGATAGGTTAGCTCTTATG
1 AGCCCAGATAGGTTAGCTCTTATG
16867 AGCCCAGATAG
1 AGCCCAGATAG
16878 ATTTTAACCA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
24 41 0.79
25 11 0.21
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (24 bp):
AGCCCAGATAGGTTAGCTCTTATG
Found at i:22554 original size:12 final size:12
Alignment explanation
Indices: 22537--22566 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
22527 AATTTTCATT
22537 ATCATGATTATA
1 ATCATGATTATA
22549 ATCATGATTATA
1 ATCATGATTATA
*
22561 AGCATG
1 ATCATG
22567 TCACATGGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (12 bp):
ATCATGATTATA
Found at i:23194 original size:6 final size:6
Alignment explanation
Indices: 23185--23314 Score: 90
Period size: 6 Copynumber: 22.2 Consensus size: 6
23175 AACTTTTTGT
* * * * * **
23185 TTTAAA TTTATA -TTAAG TTTAAA -TTGAT TTTTAA TTTATT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* **
23231 TTTAAAA TTT-AT TTTAAA TTTAAA TTTAAA TTTATT TTTAAA TTTAAA
1 TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** *
23279 TTT-GT TTTAAA TTTAAA TTT-AG TTTAAA TTTGAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA T
23315 GGTTTTAAAC
Statistics
Matches: 92, Mismatches: 25, Indels: 13
0.71 0.19 0.10
Matches are distributed among these distances:
5 17 0.18
6 65 0.71
7 10 0.11
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:23246 original size:24 final size:23
Alignment explanation
Indices: 23185--23299 Score: 105
Period size: 23 Copynumber: 5.2 Consensus size: 23
23175 AACTTTTTGT
* *
23185 TTTAAATTTATATTAAGTTTAAA
1 TTTAAATTTATTTTAAATTTAAA
* ** * **
23208 TTGATTTTTAATTTATTTTTAAA
1 TTTAAATTTATTTTAAATTTAAA
23231 TTTAAAATTTATTTTAAATTTAAA
1 TTT-AAATTTATTTTAAATTTAAA
23255 TTTAAATTTA--TT---TTTAAA
1 TTTAAATTTATTTTAAATTTAAA
*
23273 TTTAAATTTGTTTTAAATTTAAA
1 TTTAAATTTATTTTAAATTTAAA
23296 TTTA
1 TTTA
23300 GTTTAAATTT
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
18 15 0.21
20 2 0.03
21 2 0.03
23 35 0.49
24 18 0.25
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (23 bp):
TTTAAATTTATTTTAAATTTAAA
Found at i:23247 original size:18 final size:17
Alignment explanation
Indices: 23185--23314 Score: 109
Period size: 17 Copynumber: 7.4 Consensus size: 17
23175 AACTTTTTGT
* *
23185 TTTAAATTTATATTAAG
1 TTTAAATTTATTTTAAA
* *
23202 TTTAAATTGATTTTTAA
1 TTTAAATTTATTTTAAA
** *
23219 TTTATTTTTAAATTTAAAA
1 TTTAAATTT--ATTTTAAA
* *
23238 TTT-ATTTTAAATTTAAA
1 TTTAAATTT-ATTTTAAA
23255 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
*
23273 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
23290 TTTAAATTTAGTTTAAA
1 TTTAAATTTATTTTAAA
23307 TTTGAAAT
1 TTT-AAAT
23315 GGTTTTAAAC
Statistics
Matches: 91, Mismatches: 17, Indels: 9
0.78 0.15 0.08
Matches are distributed among these distances:
17 55 0.60
18 27 0.30
19 9 0.10
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:23321 original size:17 final size:15
Alignment explanation
Indices: 23242--23328 Score: 60
Period size: 17 Copynumber: 5.8 Consensus size: 15
23232 TTAAAATTTA
23242 TTTTAAATTTAAA--
1 TTTTAAATTTAAATG
23255 -TTTAAATTT--AT-
1 TTTTAAATTTAAATG
23266 TTTTAAATTTAAATTTG
1 TTTTAAATTTAAA--TG
*
23283 TTTTAAATTTAAATT
1 TTTTAAATTTAAATG
23298 TAGTTTAAATTTGAAATGG
1 T--TTTAAATTT-AAAT-G
*
23317 TTTTAAACTTAA
1 TTTTAAATTTAA
23329 TTCTAAATTT
Statistics
Matches: 60, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
10 1 0.02
12 18 0.30
14 1 0.02
15 2 0.03
16 3 0.05
17 30 0.50
18 4 0.07
19 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (15 bp):
TTTTAAATTTAAATG
Found at i:25509 original size:28 final size:28
Alignment explanation
Indices: 25474--25532 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
25464 ATTTCTTAGT
25474 CATCAAATGACAAGTAAAAATAATCTTA
1 CATCAAATGACAAGTAAAAATAATCTTA
*
25502 CATCAAATGACATGTAAAAATAATCTTA
1 CATCAAATGACAAGTAAAAATAATCTTA
25530 CAT
1 CAT
25533 GATATTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.51, C:0.15, G:0.07, T:0.27
Consensus pattern (28 bp):
CATCAAATGACAAGTAAAAATAATCTTA
Found at i:26343 original size:30 final size:28
Alignment explanation
Indices: 26309--26494 Score: 156
Period size: 30 Copynumber: 6.2 Consensus size: 28
26299 AGTTTTTAGA
* *
26309 AATTTTTCGAAAGTTCAAGGTCAAAAATGA
1 AATTTTT-GAAAGTTCAAGGT-TAAAATGT
*
26339 AATTTTTGTAAAGTTCAGGGTTAAAATGT
1 AATTTTTG-AAAGTTCAAGGTTAAAATGT
* * * *
26368 AATTTTTAAGAAGTTTAGGAGTCAAAATGT
1 AATTTTTGA-AAGTTCAAG-GTTAAAATGT
26398 AATTTTTAGAAAGTTCAAAGGTTAAAATGT
1 AATTTTT-GAAAGTTC-AAGGTTAAAATGT
* * *
26428 AATTTTTGAGAAGTATGAGGGTTAACATGT
1 AATTTTTGA-AAGT-TCAAGGTTAAAATGT
* *
26458 AATTTTTGAGAAGTTTGAGGGTTAAAATGT
1 AATTTTTGA-AAG-TTCAAGGTTAAAATGT
*
26488 GATTTTT
1 AATTTTT
26495 AGACAGTTTA
Statistics
Matches: 133, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
28 1 0.01
29 24 0.18
30 103 0.77
31 5 0.04
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (28 bp):
AATTTTTGAAAGTTCAAGGTTAAAATGT
Found at i:26394 original size:60 final size:56
Alignment explanation
Indices: 26309--26504 Score: 194
Period size: 60 Copynumber: 3.3 Consensus size: 56
26299 AGTTTTTAGA
* * * *
26309 AATTTTTCGAAAGTTCAAGGTCAAAAATGAAATTTTTGTAAAGTTCAGGGTTAAAATGT
1 AATTTTTAG-AAGTTTAGGGTC-AAAATGTAATTTTTG-AAAGTTCAGGGTTAAAATGT
*
26368 AATTTTTAAGAAGTTTAGGAGTCAAAATGTAATTTTTAGAAAGTTCAAAGGTTAAAATGT
1 AATTTTT-AGAAGTTTAGG-GTCAAAATGTAATTTTT-GAAAGTTC-AGGGTTAAAATGT
* * * *
26428 AATTTTTGAGAAGTATGAGGGTTAACATGTAATTTTTGAGAAGTTTGAGGGTTAAAATGT
1 AATTTTT-AGAAGT-TTAGGGTCAAAATGTAATTTTTGA-AAG-TTCAGGGTTAAAATGT
*
26488 GATTTTTAGACAGTTTA
1 AATTTTTAGA-AGTTTA
26505 AGGACCTTTT
Statistics
Matches: 116, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
59 41 0.35
60 69 0.59
61 6 0.05
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (56 bp):
AATTTTTAGAAGTTTAGGGTCAAAATGTAATTTTTGAAAGTTCAGGGTTAAAATGT
Found at i:26472 original size:90 final size:89
Alignment explanation
Indices: 26309--26507 Score: 251
Period size: 90 Copynumber: 2.2 Consensus size: 89
26299 AGTTTTTAGA
*
26309 AATTTTTCGAAAGTTCAAGGTCAAAAATGAAATTTTTGTAAAGTTCAGGGTTAAAATGTAATTTT
1 AATTTTTAGAAAGTTCAAGGTCAAAAATGAAATTTTTGTAAAGTTCAGGGTTAAAATGTAATTTT
26374 TAAGAAGTTT-AGGAGTCAAAATGT
66 TAAGAAGTTTGAGG-GTCAAAATGT
* * * *
26398 AATTTTTAGAAAGTTCAAAGGT-TAAAATGTAATTTTTG-AGAAGTATGAGGGTTAACATGTAAT
1 AATTTTTAGAAAGTTC-AAGGTCAAAAATGAAATTTTTGTA-AAGT-TCAGGGTTAAAATGTAAT
* *
26461 TTTTGAGAAGTTTGAGGGTTAAAATGT
63 TTTTAAGAAGTTTGAGGGTCAAAATGT
* * *
26488 GATTTTTAGACAGTTTAAGG
1 AATTTTTAGAAAGTTCAAGG
26508 ACCTTTTGAG
Statistics
Matches: 96, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
88 1 0.01
89 37 0.39
90 55 0.57
91 3 0.03
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (89 bp):
AATTTTTAGAAAGTTCAAGGTCAAAAATGAAATTTTTGTAAAGTTCAGGGTTAAAATGTAATTTT
TAAGAAGTTTGAGGGTCAAAATGT
Found at i:26503 original size:30 final size:30
Alignment explanation
Indices: 26332--26503 Score: 183
Period size: 30 Copynumber: 5.8 Consensus size: 30
26322 TTCAAGGTCA
* *
26332 AAAATGAAATTTTTGTA-AAG-TTCAGGGTT
1 AAAATGTAATTTTTG-AGAAGTTTGAGGGTT
* *
26361 AAAATGTAATTTTTAAGAAGTTT-AGGAGTC
1 AAAATGTAATTTTTGAGAAGTTTGAGG-GTT
** *
26391 AAAATGTAATTTTT-AGAAAGTTCAAAGGTT
1 AAAATGTAATTTTTGAG-AAGTTTGAGGGTT
*
26421 AAAATGTAATTTTTGAGAAGTATGAGGGTT
1 AAAATGTAATTTTTGAGAAGTTTGAGGGTT
*
26451 AACATGTAATTTTTGAGAAGTTTGAGGGTT
1 AAAATGTAATTTTTGAGAAGTTTGAGGGTT
*
26481 AAAATGTGATTTTT-AGACAGTTT
1 AAAATGTAATTTTTGAGA-AGTTT
26504 AAGGACCTTT
Statistics
Matches: 122, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.01
29 24 0.20
30 93 0.76
31 4 0.03
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (30 bp):
AAAATGTAATTTTTGAGAAGTTTGAGGGTT
Found at i:28304 original size:17 final size:16
Alignment explanation
Indices: 28279--28338 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
28269 ATTATTAATT
*
28279 TAAACTTAAATTTATAA
1 TAAATTTAAATTTA-AA
28296 TAAATTTAAATTTCAAA
1 TAAATTTAAATTT-AAA
* *
28313 TAAATTTAAACCTAAAA
1 TAAATTTAAA-TTTAAA
28330 TAAATTTAA
1 TAAATTTAA
28339 TTTTTGTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 36 0.95
18 2 0.05
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:29090 original size:209 final size:208
Alignment explanation
Indices: 28632--29638 Score: 1444
Period size: 209 Copynumber: 4.8 Consensus size: 208
28622 TTGTTTGGTG
* * *
28632 TCATTGATTTGATCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATAACTTGTTTTGATCTA
1 TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCA
* *
28697 CTTCTCTGTGTCTCATCAAGAAGACGGATCTGGTTCACTTCTCTGTATCTCATC-AGAAAGGTAA
66 CTTCTCTGTGTCTCATCAGGAAGACAGATCTGGTTCACTTCTCTGTATCTCATCAAG-AAGGTAA
* * *
28761 CCCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCG
130 CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
*
28826 CTTTGAGCCTGGTT
195 CTTTGAGCCTCGTT
* * *
28840 TCATTGATTTGGTTTACTTCTCAGTATCTCATCAAGAAAATGACCGCATCACTTGTTTTGATCCA
1 TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCA
* *
28905 CTTCTCCGTGTCTCATCAGGAAGACAGATCTGGTCCACTTCTCTGTATCTCATCAAGAAGGTAAT
66 CTTCTCTGTGTCTCATCAGGAAGACAGATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAA-
* *
28970 CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGCAGATTTGCTCA
130 CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
29035 CTTTGAGCCTCGTT
195 CTTTGAGCCTCGTT
* * *
29049 TCATTGATTTGGTCTACTTCTCAATATATCATCAGGAAAATGACCGCATCACTTGTTTTGATCCA
1 TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCA
* * * * * *
29114 CTTCTCTGCGTCTCATAAGAAAGACTGATCTGGTTCACTTCTTTGTATCTCATCAGGAAGGTAAC
66 CTTCTCTGTGTCTCATCAGGAAGACAGATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAA-
* * * * *
29179 CACTTTATTGCTTCAACCTGCTTCTCAATATCTCATCAGGAAGCTGTGGTTCTAAGATTTGCTCA
130 CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* *
29244 CTTTAAGTCTCGTT
195 CTTTGAGCCTCGTT
* * * *
29258 TCATTAATTTGATCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATTACTTGTTTTGATCAA
1 TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCA
* * * * *
29323 CTTCTTTGTGTCTCATCAGGAAGA-AGGATTTGGTTCACTTCTCTATATTTCATCAGGAAGGTAA
66 CTTCTCTGTGTCTCATCAGGAAGACA-GATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAA
* ** ***
29387 CTGTTTTATTGCTTCGACCTGCTTCTTGGTATCTCATCAGGAAGCAATGGTTCGAAGATTTGCTC
130 C-GCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC
*
29452 ACTTTGAGCCTTGTT
194 ACTTTGAGCCTCGTT
* * *
29467 TCATTGATTTGGTCTACTTCTCAGTATATCATCAAGAAGATGACCACATCACTTGTTTTGATCCA
1 TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCA
* * *
29532 CTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTAGCTCATCAAGAAGGTGAC
66 CTTCTCTGTGTCTCATCAGGAAGACAGATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGT-AA
*
29597 CGCTTTATTGCTTCGACTTGCTTCTCA-TATCTCATCAGGAAG
130 CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAG
29639 ATGATCGCCT
Statistics
Matches: 708, Mismatches: 85, Indels: 12
0.88 0.11 0.01
Matches are distributed among these distances:
208 132 0.19
209 574 0.81
210 2 0.00
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (208 bp):
TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCA
CTTCTCTGTGTCTCATCAGGAAGACAGATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAAC
GCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAC
TTTGAGCCTCGTT
Found at i:32688 original size:46 final size:46
Alignment explanation
Indices: 32633--32722 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
32623 TAGTATATCA
*
32633 CCCTTTCCTTCTTTCCAGATTCATCGTGTTGGCCTAGTACACATCG
1 CCCTTTCCTTCTTTCCAGATTCATCGTGTTAGCCTAGTACACATCG
32679 CCCTTTCCTTCTTTCCAGATTCATCGTGTTAGCCTAGTACACAT
1 CCCTTTCCTTCTTTCCAGATTCATCGTGTTAGCCTAGTACACAT
32723 TGTTGAAGCC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.17, C:0.32, G:0.13, T:0.38
Consensus pattern (46 bp):
CCCTTTCCTTCTTTCCAGATTCATCGTGTTAGCCTAGTACACATCG
Found at i:32789 original size:17 final size:17
Alignment explanation
Indices: 32761--32834 Score: 96
Period size: 17 Copynumber: 4.4 Consensus size: 17
32751 TTGGAAATTG
32761 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
32777 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
32794 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
32811 AATTTATTATAAAAATTA
1 AATTTATT-TTAAATTTA
32829 AATTTA
1 AATTTA
32835 GAAAATCCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
16 5 0.10
17 33 0.65
18 13 0.25
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:32809 original size:7 final size:6
Alignment explanation
Indices: 32766--32816 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
32756 AATTGAATTT
* *
32766 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTTGAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA
32812 ATTTA
1 ATTTA
32817 TTATAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 4 0.11
5 4 0.11
6 26 0.68
7 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (6 bp):
ATTTAA
Found at i:32817 original size:34 final size:34
Alignment explanation
Indices: 32755--32834 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 34
32745 GACTTATTGG
* * *
32755 AAATTGAATTTATTTAAATTTAAGTTTATT-TTA
1 AAATTAAATTTATTTAAATTTAAATTTATTATAA
*
32788 AATTTAAATTTATTTGAAATTTAAATTTATTATAA
1 AAATTAAATTTATTT-AAATTTAAATTTATTATAA
32823 AAATTAAATTTA
1 AAATTAAATTTA
32835 GAAAATCCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 13 0.32
34 14 0.35
35 13 0.32
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (34 bp):
AAATTAAATTTATTTAAATTTAAATTTATTATAA
Found at i:32894 original size:15 final size:15
Alignment explanation
Indices: 32866--32919 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
32856 AAAACAAAGT
32866 CCAATTACAGATGGC
1 CCAATTACAGATGGC
* *
32881 CCAATAACAAATGGC
1 CCAATTACAGATGGC
32896 CCAATTACAGATGGC
1 CCAATTACAGATGGC
*
32911 CCAAATACA
1 CCAATTACA
32920 AACTACCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.41, C:0.28, G:0.15, T:0.17
Consensus pattern (15 bp):
CCAATTACAGATGGC
Found at i:33467 original size:18 final size:19
Alignment explanation
Indices: 33433--33474 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
33423 AAAACGTTTC
*
33433 AATAACTTTTATTAATATT
1 AATAACTGTTATTAATATT
33452 AATAACTGTT-TTAATATT
1 AATAACTGTTATTAATATT
33470 AATAA
1 AATAA
33475 TAATACTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (19 bp):
AATAACTGTTATTAATATT
Found at i:33578 original size:7 final size:7
Alignment explanation
Indices: 33546--33589 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
33536 ATGTTTTGAT
33546 ATTAATA
1 ATTAATA
33553 A-TAATA
1 ATTAATA
33559 ATATCAATA
1 AT-T-AATA
*
33568 ATTATTA
1 ATTAATA
33575 ATTAATA
1 ATTAATA
33582 ATTAATA
1 ATTAATA
33589 A
1 A
33590 AAAAAACACG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 6 0.19
7 18 0.56
8 2 0.06
9 6 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (7 bp):
ATTAATA
Done.