Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012484.1 Kokia drynarioides strain JFW-HI SEQ_127488, 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: 78184
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 116 characters in sequence are not A, C, G, or T
Found at i:7303 original size:15 final size:14
Alignment explanation
Indices: 7280--7340 Score: 68
Period size: 15 Copynumber: 4.1 Consensus size: 14
7270 TGTGAAAGTT
7280 TTTTAAAAATAAAA
1 TTTTAAAAATAAAA
7294 TTTTATAAAATAAAA
1 TTTTA-AAAATAAAA
*
7309 TCTTAAAAATAATTAA
1 TTTTAAAAATAA--AA
*
7325 TTTTAATAATCAAAA
1 TTTTAAAAAT-AAAA
7340 T
1 T
7341 AAATAGAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 12 0.30
15 16 0.40
16 10 0.25
17 2 0.05
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
TTTTAAAAATAAAA
Found at i:7704 original size:16 final size:16
Alignment explanation
Indices: 7658--7708 Score: 65
Period size: 14 Copynumber: 3.4 Consensus size: 16
7648 ATGTGAAAAT
7658 TTTTAAAAATAATT--
1 TTTTAAAAATAATTAA
7672 TTTTATAAAATAA--AA
1 TTTTA-AAAATAATTAA
7687 TTTTAAAAATAATTAA
1 TTTTAAAAATAATTAA
7703 TTTTAA
1 TTTTAA
7709 TAACCAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 12 0.38
15 12 0.38
16 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTTAAAAATAATTAA
Found at i:7907 original size:378 final size:369
Alignment explanation
Indices: 7162--7847 Score: 904
Period size: 378 Copynumber: 1.8 Consensus size: 369
7152 AAATTTTAAA
* * *
7162 GAGTAAAATTTAATTAGATATTTTTAAAATATAAATTATGACGGTAAATTTACATTTTAGTCCTT
1 GAGTAAAATTCAATTAGATATTTGTAAAATATAAATTATGACGATAAATTTACATTTTAGTCCTT
* *
7227 TTATATAATTTTGAATACTATGTATTAATGATGGCTAAAATGATGTGAAAGTTTTTTAAAAATAA
66 TTATATAATTTTGAATACTATGTATTAATGACGGCTAAAATGATGTGAAAGATTTTTAAAAATAA
*
7292 AATTTTATAAAATAAAATCTTAAAAATAATTAATTTTAATAATCAAAATAAATAGAATTTCTTAA
131 AATTTTATAAAATAAAATCTTAAAAATAATTAATTTTAATAACCAAAATAAATAGAATTTCTTAA
* * *
7357 TTAAACTACGAAATTTATGCCAACAAATTAAGGATTCAATTTTAAATCTGATAGGATAAAAAGAT
196 TTAAACTACGAAATCTATACCAACAAATTAAGGATTCAATTTTAAATCCGATAGGATAAAAAGAT
* * * *
7422 AAAATCATGATTTGGTCATATCCAAATTATCCAAATTATATTTTGTTTCATTTTAATTAATTGTG
261 AAAATCATGATTTAGTCATAT-C-AATTAT-C-AATTATAATATGTTTC---TTAAGTAA-TGTG
**
7487 ATGGAAATATTTTTATTCCATTTTTATGTTTGTCAACGAAAAAATGTTGAAG
318 ATACAAATATTTTTATTCCATTTTTATGTTTGTCAACGAAAAAATGTTGAAG
* * * *
7539 GAGTAAAATTCAATTAGATATTTGTCAAATATAAATTATGATGATAAATTTATATTTTAGCTCTT
1 GAGTAAAATTCAATTAGATATTTGTAAAATATAAATTATGACGATAAATTTACATTTTAG-TCCT
*
7604 TTTATATAACTTTT-AATACTATGCT-TTAATCGACGGTTAAAATGATGTGAAA-ATTTTTAAAA
65 TTTATATAA-TTTTGAATACTATG-TATTAAT-GACGGCTAAAATGATGTGAAAGATTTTTAAAA
** * *
7666 ATAATTTTTTATAAAATAAAATTTTAAAAATAATTAATTTTAATAACCAAAATAAATAGAATTTG
127 ATAAAATTTTATAAAATAAAATCTTAAAAATAATTAATTTTAATAACCAAAATAAATAGAATTTC
* * * **
7731 TTAATTAAATTACGAAATCTATACCAATAAATTAGGGATTTCAATTTTAAATCCGATAGG-TTGA
192 TTAATTAAACTACGAAATCTATACCAACAAATTAAGGA-TTCAATTTTAAATCCGATAGGATAAA
* *
7795 AAGATAAAATCATGATTATAGT-AT-T-TATTAT-AATTTTAATATGTTTC-TAAGTA
256 AAGATAAAATCATGATT-TAGTCATATCAATTATCAATTATAATATGTTTCTTAAGTA
7848 GGAACAAACT
Statistics
Matches: 274, Mismatches: 29, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
367 5 0.02
371 13 0.05
374 5 0.02
377 55 0.20
378 149 0.54
379 47 0.17
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.41
Consensus pattern (369 bp):
GAGTAAAATTCAATTAGATATTTGTAAAATATAAATTATGACGATAAATTTACATTTTAGTCCTT
TTATATAATTTTGAATACTATGTATTAATGACGGCTAAAATGATGTGAAAGATTTTTAAAAATAA
AATTTTATAAAATAAAATCTTAAAAATAATTAATTTTAATAACCAAAATAAATAGAATTTCTTAA
TTAAACTACGAAATCTATACCAACAAATTAAGGATTCAATTTTAAATCCGATAGGATAAAAAGAT
AAAATCATGATTTAGTCATATCAATTATCAATTATAATATGTTTCTTAAGTAATGTGATACAAAT
ATTTTTATTCCATTTTTATGTTTGTCAACGAAAAAATGTTGAAG
Found at i:9378 original size:17 final size:16
Alignment explanation
Indices: 9342--9384 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
9332 AAAAGCATTT
*
9342 AAAT-AAATTTGAATA
1 AAATCAAATTGGAATA
*
9357 GAATCAATATTGGAATA
1 AAATCAA-ATTGGAATA
9374 AAATCAAATTG
1 AAATCAAATTG
9385 AGATATTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 3 0.13
16 6 0.26
17 14 0.61
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30
Consensus pattern (16 bp):
AAATCAAATTGGAATA
Found at i:11317 original size:23 final size:24
Alignment explanation
Indices: 11269--11317 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
11259 AACCATTAAG
11269 TTAAAAAGCAAAACTACATCGTTT
1 TTAAAAAGCAAAACTACATCGTTT
* *
11293 TTAAAAGGCAAAACTACGTCGTTT
1 TTAAAAAGCAAAACTACATCGTTT
11317 T
1 T
11318 GATAAATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (24 bp):
TTAAAAAGCAAAACTACATCGTTT
Found at i:11362 original size:94 final size:94
Alignment explanation
Indices: 11201--11387 Score: 331
Period size: 94 Copynumber: 2.0 Consensus size: 94
11191 TCCGAATAAG
*
11201 AAAAGTCAAAACTACGTCATTTTGATAAATGTTTACCTTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAGGCAAAACTACGTCATTTTGATAAATGTTTACCTTTTCTAAAGTTAAAAGTCAAAACCATT
11266 AAGTTAAAAAG-CAAAACTACATCGTTTTT
66 AAGTT-AAAAGTCAAAACTACATCGTTTTT
*
11295 AAAAGGCAAAACTACGTCGTTTTGATAAATGTTTACCTTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAGGCAAAACTACGTCATTTTGATAAATGTTTACCTTTTCTAAAGTTAAAAGTCAAAACCATT
*
11360 AAGTTAAAAGTCAAAACTACGTCGTTTT
66 AAGTTAAAAGTCAAAACTACATCGTTTT
11388 AATAAATGTT
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
93 5 0.06
94 84 0.94
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (94 bp):
AAAAGGCAAAACTACGTCATTTTGATAAATGTTTACCTTTTCTAAAGTTAAAAGTCAAAACCATT
AAGTTAAAAGTCAAAACTACATCGTTTTT
Found at i:13021 original size:83 final size:82
Alignment explanation
Indices: 12823--13100 Score: 276
Period size: 83 Copynumber: 3.3 Consensus size: 82
12813 CAGAATTTAA
* * * *
12823 TTAATTCTTGTTTGAAAACAAAATCAAAATCA-AATCACATCAAATCTGTTGAACGACAGGAATA
1 TTAATTCTTGTTTGGAAACAAAATCAAAAT-AGAAT---A--AAATCTGTTAAACAACGGGAATA
* ** * *
12887 AATCCCGAAACAAAATTATTTAATT
60 AATCTCGAAACAGGATTA-TTCA-C
* ** * *
12912 TTAATTATTGTTTGGAAATTAAATCAAAATAGAATAAAATCTGTTAAACAGCGGGAATAAATTTC
1 TTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAAAATCTGTTAAACAACGGGAATAAATCTC
12977 -AAGACA-GATTTATTCAAC
66 GAA-ACAGGA-TTATTC-AC
* *
12995 TT-ATTCTTGTTTTGGAAACAAAATCAAAATAGAATAAAATTTGTTAAACAACGGTAATAAATCT
1 TTAATTCTTG-TTTGGAAACAAAATCAAAATAGAATAAAATCTGTTAAACAACGGGAATAAATCT
13059 CGAAACAGGATTATTCAC
65 CGAAACAGGATTATTCAC
13077 TTAATTCTTGTTTGGAAACAAAAT
1 TTAATTCTTGTTTGGAAACAAAAT
13101 TAAAGTAGGA
Statistics
Matches: 161, Mismatches: 20, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
82 24 0.15
83 72 0.45
84 34 0.21
86 1 0.01
88 1 0.01
89 29 0.18
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (82 bp):
TTAATTCTTGTTTGGAAACAAAATCAAAATAGAATAAAATCTGTTAAACAACGGGAATAAATCTC
GAAACAGGATTATTCAC
Found at i:13835 original size:31 final size:31
Alignment explanation
Indices: 13780--13838 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
13770 TGGAGACTTT
*
13780 AAATCAATTTGAATAAAATCAAATCAAAATG
1 AAATCAATTTGAATAAAATAAAATCAAAATG
* **
13811 AAATCAATTTGATTGGAATAAAATCAAA
1 AAATCAATTTGAATAAAATAAAATCAAA
13839 TTAAGATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.27
Consensus pattern (31 bp):
AAATCAATTTGAATAAAATAAAATCAAAATG
Found at i:14782 original size:30 final size:30
Alignment explanation
Indices: 14748--14804 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
14738 TAATCGATCA
14748 AATTTGGTTAATCAGTCAGTTAACCGACTG
1 AATTTGGTTAATCAGTCAGTTAACCGACTG
*
14778 AATTTGGTTAATCAGTCGGTTAACCGA
1 AATTTGGTTAATCAGTCAGTTAACCGA
14805 ATTAATTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (30 bp):
AATTTGGTTAATCAGTCAGTTAACCGACTG
Found at i:17195 original size:27 final size:27
Alignment explanation
Indices: 17164--17215 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
17154 TGATCGGCTA
* * *
17164 TTGACTATTGACTGTTGACCGTTGAAT
1 TTGACCATTGACTATTGACCATTGAAT
*
17191 TTGACCGTTGACTATTGACCATTGA
1 TTGACCATTGACTATTGACCATTGA
17216 CCGTTGACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (27 bp):
TTGACCATTGACTATTGACCATTGAAT
Found at i:17196 original size:13 final size:14
Alignment explanation
Indices: 17178--17215 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
17168 CTATTGACTG
17178 TTGACCGTTGAAT-
1 TTGACCGTTGAATA
*
17191 TTGACCGTTGACTA
1 TTGACCGTTGAATA
*
17205 TTGACCATTGA
1 TTGACCGTTGA
17216 CCGTTGACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (14 bp):
TTGACCGTTGAATA
Found at i:17200 original size:20 final size:20
Alignment explanation
Indices: 17171--17256 Score: 67
Period size: 20 Copynumber: 4.6 Consensus size: 20
17161 CTATTGACTA
*
17171 TTGACTGTTGACCGTTGAAT
1 TTGACCGTTGACCGTTGAAT
17191 TTGACCGTTGA-C--T--A-
1 TTGACCGTTGACCGTTGAAT
* *
17205 TTGACCATTGACCGTTGACT
1 TTGACCGTTGACCGTTGAAT
* * *
17225 TTGATCGTTGATCGTTGACT
1 TTGACCGTTGACCGTTGAAT
*
17245 TTGATCGTTGAC
1 TTGACCGTTGAC
17257 TTTTTTTTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
14 10 0.19
15 2 0.04
17 2 0.04
19 1 0.02
20 38 0.72
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (20 bp):
TTGACCGTTGACCGTTGAAT
Found at i:17207 original size:34 final size:34
Alignment explanation
Indices: 17164--17235 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
17154 TGATCGGCTA
**
17164 TTGACTATTGACTGTTGACCGTTGAATTTGACCG
1 TTGACTATTGACCATTGACCGTTGAATTTGACCG
* *
17198 TTGACTATTGACCATTGACCGTTGACTTTGATCG
1 TTGACTATTGACCATTGACCGTTGAATTTGACCG
17232 TTGA
1 TTGA
17236 TCGTTGACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (34 bp):
TTGACTATTGACCATTGACCGTTGAATTTGACCG
Found at i:17233 original size:13 final size:13
Alignment explanation
Indices: 17232--17259 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17222 ACTTTGATCG
17232 TTGATCGTTGACT
1 TTGATCGTTGACT
17245 TTGATCGTTGACT
1 TTGATCGTTGACT
17258 TT
1 TT
17260 TTTTTGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (13 bp):
TTGATCGTTGACT
Found at i:18326 original size:3 final size:3
Alignment explanation
Indices: 18318--18351 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
18308 TTACATCATT
*
18318 TTA TTA TTA TTA TTA TTA TT- TTG TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
18352 TTTGTTTGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:18346 original size:14 final size:14
Alignment explanation
Indices: 18327--18353 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18317 TTTATTATTA
18327 TTATTATTATTTTG
1 TTATTATTATTTTG
18341 TTATTATTATTTT
1 TTATTATTATTTT
18354 TGTTTGGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (14 bp):
TTATTATTATTTTG
Found at i:19237 original size:13 final size:13
Alignment explanation
Indices: 19219--19243 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19209 TGGCTGAAGG
19219 ATTTATAGAGATT
1 ATTTATAGAGATT
19232 ATTTATAGAGAT
1 ATTTATAGAGAT
19244 GAGCTACCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTTATAGAGATT
Found at i:33109 original size:19 final size:20
Alignment explanation
Indices: 33085--33141 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
33075 TTATAATTTT
33085 TTAAAATAATAAAAAAT-TC
1 TTAAAATAATAAAAAATATC
*
33104 TTAAAAATGAA-AAAAAATATT
1 TT-AAAAT-AATAAAAAATATC
33125 TTAAAAT-ATAAAAAATA
1 TTAAAATAATAAAAAATA
33142 AAAAGTTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 1 0.03
19 10 0.30
20 17 0.52
21 5 0.15
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
TTAAAATAATAAAAAATATC
Found at i:34248 original size:33 final size:33
Alignment explanation
Indices: 34178--34248 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
34168 ACTAGGGAGG
* **
34178 GTGATGATGAAGGGGTAGAATCTAATGGGGAGG
1 GTGATGATGAAGGGGTAGAATCTAATGGGAAAA
* * *
34211 GTGATGATGAAGGGGTAGAATTTGATGGTAAAA
1 GTGATGATGAAGGGGTAGAATCTAATGGGAAAA
34244 GTGAT
1 GTGAT
34249 TTGGAAAGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.01, G:0.41, T:0.25
Consensus pattern (33 bp):
GTGATGATGAAGGGGTAGAATCTAATGGGAAAA
Found at i:34281 original size:33 final size:33
Alignment explanation
Indices: 34190--34326 Score: 89
Period size: 33 Copynumber: 4.2 Consensus size: 33
34180 GATGATGAAG
* * * * *
34190 GGGTAGAATCTAATGGGGAGGGTGA-TGATGAA
1 GGGTAGAACCTGATGGGGAAGGTGATTTAGGAA
** ** *
34222 GGGGTAGAATTTGATGGTAAAAGTGATTT-GGAAA
1 -GGGTAGAACCTGATGGGGAAGGTGATTTAGG-AA
** * *
34256 GGGTAGAAGTTGTTGGGGAAGGTGATTTAGGAG
1 GGGTAGAACCTGATGGGGAAGGTGATTTAGGAA
* * *
34289 GGGTAGAACCTGATGGGGAGGGTGATGTAGGAG
1 GGGTAGAACCTGATGGGGAAGGTGATTTAGGAA
34322 GGGTA
1 GGGTA
34327 CAAGATAATG
Statistics
Matches: 82, Mismatches: 19, Indels: 6
0.77 0.18 0.06
Matches are distributed among these distances:
33 77 0.94
34 5 0.06
ACGTcount: A:0.28, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
GGGTAGAACCTGATGGGGAAGGTGATTTAGGAA
Found at i:34338 original size:33 final size:33
Alignment explanation
Indices: 34269--34345 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
34259 TAGAAGTTGT
* * * * *
34269 TGGGGAAGGTGATTTAGGAGGGGTAGAACCTGA
1 TGGGGAGGGTGATGTAGGAGGGGTACAACATAA
*
34302 TGGGGAGGGTGATGTAGGAGGGGTACAAGATAA
1 TGGGGAGGGTGATGTAGGAGGGGTACAACATAA
34335 TGGGGAGGGTG
1 TGGGGAGGGTG
34346 TGTCTACTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.26, C:0.04, G:0.51, T:0.19
Consensus pattern (33 bp):
TGGGGAGGGTGATGTAGGAGGGGTACAACATAA
Found at i:39605 original size:25 final size:23
Alignment explanation
Indices: 39542--39605 Score: 56
Period size: 25 Copynumber: 2.6 Consensus size: 23
39532 TAAAAAGATG
* * *
39542 AATTAAAATAAAAAATTGAAAAC
1 AATTTAAATAAAAAATAGAAAAA
*
39565 AATTTATTAATTAAAAATAAGAAAAA
1 AATTTA--AATAAAAAAT-AGAAAAA
39591 AATATTAAATAAAAA
1 AAT-TTAAATAAAAA
39606 TTACAAATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
23 5 0.16
25 16 0.50
26 8 0.25
27 3 0.09
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.27
Consensus pattern (23 bp):
AATTTAAATAAAAAATAGAAAAA
Found at i:43220 original size:12 final size:12
Alignment explanation
Indices: 43203--43227 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43193 AAATAACATA
43203 AAAGAGATGGAG
1 AAAGAGATGGAG
43215 AAAGAGATGGAG
1 AAAGAGATGGAG
43227 A
1 A
43228 TGTGAGGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.40, T:0.08
Consensus pattern (12 bp):
AAAGAGATGGAG
Found at i:44805 original size:88 final size:88
Alignment explanation
Indices: 44666--44844 Score: 204
Period size: 88 Copynumber: 2.0 Consensus size: 88
44656 TTTATTTAAC
* *
44666 TAAAATTTAAATTTAAAAAAATATATTATTTTATTAGTGAAGTCACAAAATATAGCGACATCACT
1 TAAAATTTAAATTTAAAAAAATATATTATTTTATTAGTGAAGTCACAAAATATAGAGACACCACT
*
44731 TTG-TATCATATTTTTTATTTTTT
66 TTGCTATAAT-TTTTTTATTTTTT
* * * * * *
44754 TAAAATTTAAATTTTAAAAAATATATTA-TTTA-TAGGATGGAG-CCCTTAAATATGGAGCCACC
1 TAAAATTTAAATTTAAAAAAATATATTATTTTATTA-G-TGAAGTCAC-AAAATATAGAGACACC
*
44816 ACTTTGCTTTAATTTTTTTATTTTTT
63 ACTTTGCTATAATTTTTTTATTTTTT
44842 TAA
1 TAA
44845 TTTAAAAATA
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
86 2 0.03
87 7 0.09
88 64 0.83
89 4 0.05
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.45
Consensus pattern (88 bp):
TAAAATTTAAATTTAAAAAAATATATTATTTTATTAGTGAAGTCACAAAATATAGAGACACCACT
TTGCTATAATTTTTTTATTTTTT
Found at i:47642 original size:84 final size:84
Alignment explanation
Indices: 47501--47668 Score: 300
Period size: 84 Copynumber: 2.0 Consensus size: 84
47491 CCAACATTAT
*
47501 ATAGCATTATGGAACGCCCGATACAACAGGCAGGTTGAGATGCACTCCTGTATGAATGACTTTAA
1 ATAGCACTATGGAACGCCCGATACAACAGGCAGGTTGAGATGCACTCCTGTATGAATGACTTTAA
*
47566 TCCCTCGACTAAATACATG
66 CCCCTCGACTAAATACATG
* *
47585 ATAGCACTATGGAACGCTCGATACAACAGGCAGGTTGAGATGCACTCCTGTATGAATGACTTTAG
1 ATAGCACTATGGAACGCCCGATACAACAGGCAGGTTGAGATGCACTCCTGTATGAATGACTTTAA
47650 CCCCTCGACTAAATACATG
66 CCCCTCGACTAAATACATG
47669 CACTGGTACA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (84 bp):
ATAGCACTATGGAACGCCCGATACAACAGGCAGGTTGAGATGCACTCCTGTATGAATGACTTTAA
CCCCTCGACTAAATACATG
Found at i:49032 original size:16 final size:18
Alignment explanation
Indices: 49006--49042 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
48996 TAATTTTTAA
49006 ATTTGAAAAAATAT-CAC
1 ATTTGAAAAAATATACAC
49023 ATTT-AAAAAATATACAC
1 ATTTGAAAAAATATACAC
49040 ATT
1 ATT
49043 AGATTGGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.32
Consensus pattern (18 bp):
ATTTGAAAAAATATACAC
Found at i:59451 original size:21 final size:21
Alignment explanation
Indices: 59427--59496 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
59417 GTGAAAAGTA
59427 AAAAATTGGTTGAATTAAGCT
1 AAAAATTGGTTGAATTAAGCT
** * *
59448 AAAAAAAGATTGAATCTATAGTT
1 AAAAATTGGTTGAAT-TA-AGCT
* **
59471 GAACTTTGGTTGAATTAAGCT
1 AAAAATTGGTTGAATTAAGCT
59492 AAAAA
1 AAAAA
59497 AAGATTGAAT
Statistics
Matches: 33, Mismatches: 14, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
21 17 0.52
22 4 0.12
23 12 0.36
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (21 bp):
AAAAATTGGTTGAATTAAGCT
Found at i:59482 original size:44 final size:44
Alignment explanation
Indices: 59432--59519 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
59422 AAGTAAAAAA
59432 TTGGTTGAATTAAGCTAAAAAAAGATTGAATCTATAGTTGAACT
1 TTGGTTGAATTAAGCTAAAAAAAGATTGAATCTATAGTTGAACT
59476 TTGGTTGAATTAAGCTAAAAAAAGATTGAATCTATAGTTGAACT
1 TTGGTTGAATTAAGCTAAAAAAAGATTGAATCTATAGTTGAACT
59520 AATTTCGAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (44 bp):
TTGGTTGAATTAAGCTAAAAAAAGATTGAATCTATAGTTGAACT
Found at i:59506 original size:21 final size:21
Alignment explanation
Indices: 59436--59506 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
59426 AAAAAATTGG
59436 TTGAATTAAGCTAAAAAAAGA
1 TTGAATTAAGCTAAAAAAAGA
* * **** *
59457 TTGAATCTATAGTTGAACTTTGG
1 TTGAAT-TA-AGCTAAAAAAAGA
59480 TTGAATTAAGCTAAAAAAAGA
1 TTGAATTAAGCTAAAAAAAGA
59501 TTGAAT
1 TTGAAT
59507 CTATAGTTGA
Statistics
Matches: 34, Mismatches: 14, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
21 18 0.53
22 4 0.12
23 12 0.35
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (21 bp):
TTGAATTAAGCTAAAAAAAGA
Found at i:65154 original size:43 final size:42
Alignment explanation
Indices: 65081--65161 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 42
65071 TAGTTGATAT
*
65081 TTTTATAAAATAAAATATATTTAACATAATTATAAATATCAA
1 TTTTATAAAATAAAATATATTTAACATAATTAGAAATATCAA
* * *
65123 TTTTATAAAA-AATATATTTTTATTATATAATTAGAAATA
1 TTTTATAAAATAAAATATATTTA--ACATAATTAGAAATA
65162 ATTATTTGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 10 0.30
42 10 0.30
43 13 0.39
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (42 bp):
TTTTATAAAATAAAATATATTTAACATAATTAGAAATATCAA
Found at i:65178 original size:26 final size:24
Alignment explanation
Indices: 65131--65204 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 24
65121 AATTTTATAA
*
65131 AAAATATATT-TTTATTATATAATT
1 AAAATA-ATTATTTATTATATAAAT
*
65155 AGAAATAATTATTTGATTTTATAAAT
1 A-AAATAATTATTT-ATTATATAAAT
* *
65181 AAAAGAATTATTAATTA-A-AAAT
1 AAAATAATTATTTATTATATAAAT
65203 AA
1 AA
65205 TTAAAAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
22 6 0.14
23 1 0.02
24 7 0.17
25 18 0.43
26 10 0.24
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
AAAATAATTATTTATTATATAAAT
Found at i:65220 original size:14 final size:15
Alignment explanation
Indices: 65198--65228 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
65188 TTATTAATTA
65198 AAAATAATTAAAAAT
1 AAAATAATTAAAAAT
65213 AAAA-AATTAAAAAT
1 AAAATAATTAAAAAT
65227 AA
1 AA
65229 TATATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATAATTAAAAAT
Found at i:65897 original size:32 final size:32
Alignment explanation
Indices: 65840--65903 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 32
65830 ATTATTTTGA
65840 AATTTAAAAATTTTCACTATATTTTAA-TTTT
1 AATTTAAAAATTTTCACTATATTTTAAGTTTT
* *
65871 AATTTTAAAATTTT-ATCTATTTTTTTAAGTTTT
1 AATTTAAAAATTTTCA-CTA-TATTTTAAGTTTT
65904 TCGTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 1 0.04
31 16 0.57
32 7 0.25
33 4 0.14
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (32 bp):
AATTTAAAAATTTTCACTATATTTTAAGTTTT
Found at i:70355 original size:38 final size:38
Alignment explanation
Indices: 70304--70379 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
70294 CCATTAAGTT
*
70304 AGCCAAAAATACCACACACTGAATCTCTAACGGAACCC
1 AGCCAAAAATACCACACACTGAATCTCTAACGAAACCC
70342 AGCCAAAAATACCACACACTGAATCTCTAACGAAACCC
1 AGCCAAAAATACCACACACTGAATCTCTAACGAAACCC
70380 GTCCATCAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.43, C:0.34, G:0.09, T:0.13
Consensus pattern (38 bp):
AGCCAAAAATACCACACACTGAATCTCTAACGAAACCC
Found at i:74286 original size:16 final size:15
Alignment explanation
Indices: 74244--74286 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
74234 AAAAAAGGAC
74244 ATAAATTTTTAAAAA
1 ATAAATTTTTAAAAA
*
74259 TTATAATATTTTAAAATA
1 ATA-AAT-TTTTAAAA-A
74277 ATAAATTTTT
1 ATAAATTTTT
74287 TTTAAACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 2 0.09
16 7 0.30
17 11 0.48
18 3 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATAAATTTTTAAAAA
Found at i:74287 original size:17 final size:17
Alignment explanation
Indices: 74244--74287 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
74234 AAAAAAGGAC
* *
74244 ATAAATTTTTAAAAATT
1 ATAAATTTTTTAAAATA
*
74261 AT-AATATTTTAAAATA
1 ATAAATTTTTTAAAATA
74277 ATAAATTTTTT
1 ATAAATTTTTT
74288 TTAAACATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATAAATTTTTTAAAATA
Found at i:77250 original size:34 final size:35
Alignment explanation
Indices: 77203--77274 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 35
77193 AATTCTGTCA
77203 TTTGATTTCTGATTTTACGCAATAAATACTTAGAT
1 TTTGATTTCTGATTTTACGCAATAAATACTTAGAT
77238 TTTGATTT-TGATTTTACGCAATAAATACTTAGAT
1 TTTGATTTCTGATTTTACGCAATAAATACTTAGAT
77272 TTT
1 TTT
77275 TTCTCAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 29 0.78
35 8 0.22
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.49
Consensus pattern (35 bp):
TTTGATTTCTGATTTTACGCAATAAATACTTAGAT
Found at i:78038 original size:15 final size:14
Alignment explanation
Indices: 77999--78029 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
77989 ATTATTTGCA
77999 TTTT-TAATTTAAT
1 TTTTCTAATTTAAT
78012 TTTTCTAATTTAAT
1 TTTTCTAATTTAAT
78026 TTTT
1 TTTT
78030 TCTCTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTAATTTAAT
Done.