Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011521.1 Kokia drynarioides strain JFW-HI SEQ_126507, 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: 77625
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 182 characters in sequence are not A, C, G, or T
Found at i:696 original size:37 final size:37
Alignment explanation
Indices: 635--733 Score: 103
Period size: 37 Copynumber: 2.6 Consensus size: 37
625 AAAAATATAA
* *
635 AAAAGTTATAGAAAATTATATAAAAA-TATTGAAAAATGT
1 AAAATTTATA-AAATTTAT-TAAAAATTATT-AAAAATGT
* * *
674 AAATTTTATAAAATTTATTAAAAATTATTAAAAGTTT
1 AAAATTTATAAAATTTATTAAAAATTATTAAAAATGT
*
711 AAAATTT-TGAAATTTATTAAAAA
1 AAAATTTATAAAATTTATTAAAAA
734 GTAAATGTTG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
36 15 0.29
37 18 0.35
38 11 0.21
39 8 0.15
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (37 bp):
AAAATTTATAAAATTTATTAAAAATTATTAAAAATGT
Found at i:5824 original size:5 final size:5
Alignment explanation
Indices: 5806--5840 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
5796 GAAAATAATT
*
5806 TGATG -GATG AGATG TGATG TGATG TGATG TGATG T
1 TGATG TGATG TGATG TGATG TGATG TGATG TGATG T
5841 TTAAAAGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.37
Consensus pattern (5 bp):
TGATG
Found at i:10448 original size:21 final size:22
Alignment explanation
Indices: 10410--10455 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
10400 TCCCAAAACC
10410 CTCCGCCGCCACCGTTTCCGCCGT
1 CTCCGCCGCCA-C-TTTCCGCCGT
*
10434 CTCCGCCGCCA-TTTCCGTCGT
1 CTCCGCCGCCACTTTCCGCCGT
10455 C
1 C
10456 CCCGACCTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
24 11 0.52
ACGTcount: A:0.04, C:0.52, G:0.20, T:0.24
Consensus pattern (22 bp):
CTCCGCCGCCACTTTCCGCCGT
Found at i:14387 original size:22 final size:23
Alignment explanation
Indices: 14359--14410 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
14349 ATGCAGGCTA
14359 TTAAAATAATA-AAATTATATTG
1 TTAAAATAATATAAATTATATTG
*
14381 TTAAAATAATAGTTTAATTATATTG
1 TTAAAATAATA--TAAATTATATTG
14406 TTAAA
1 TTAAA
14411 TTATATGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 11 0.42
25 15 0.58
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (23 bp):
TTAAAATAATATAAATTATATTG
Found at i:14412 original size:13 final size:13
Alignment explanation
Indices: 14370--14416 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
14360 TAAAATAATA
14370 AAATTATATTGTT
1 AAATTATATTGTT
* *
14383 AAAATA-ATAGTT
1 AAATTATATTGTT
*
14395 TAATTATATTGTT
1 AAATTATATTGTT
14408 AAATTATAT
1 AAATTATAT
14417 GAAATGGTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (13 bp):
AAATTATATTGTT
Found at i:14648 original size:10 final size:10
Alignment explanation
Indices: 14613--14646 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
14603 TTCCATCTCC
*
14613 CAACCCAACC
1 CAACCCAACT
14623 CAACCCAACT
1 CAACCCAACT
*
14633 CAACTCAACT
1 CAACCCAACT
14643 CAAC
1 CAAC
14647 TCTATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.50, G:0.00, T:0.09
Consensus pattern (10 bp):
CAACCCAACT
Found at i:25855 original size:285 final size:283
Alignment explanation
Indices: 25276--26394 Score: 1273
Period size: 285 Copynumber: 4.0 Consensus size: 283
25266 TACCAGTTAG
* *
25276 GTCTAAAAAATAAATTATTTTAACCGAATTTACATTGTTAAAAATTTGAATTAAAATTCTCATGT
1 GTCTAAAAAATAAATTATTTTAACCGAATTTACATTGTTAAAATTTTGAATTAAAATTCTCATAT
** * * *
25341 CATATTGCATATTAAATCAAAAATAAAAAT-----GGA-TTAATTAGGTGAAGATCAAATTATTA
66 CATATTGCATATTAAATCAAAAATAAAAATAAAAACAATTTAACTAGATGAAGATGAAATTATT-
* * *
25400 AAAAAAACATATTTTAAACAAATCAGTTTTATATGATATCACTAGAGCAAATAATTAAATG----
130 -AAAAAACATATTTTAAACAAATCAATTTAATATGATATCACTAGAGAAAATAATTAAATGATTT
* * * * *
25461 ATTTATTTATC-AGTTTTTATTTTATGTATGACTACAGGTTCTGAGGAAAAACATAATAAAGAAC
194 ATTTATTTATCTA-TTTTTATTTTAGGTACGACTACAGGTTCAGAGAAAAAACATAATGAAGAAC
*
25525 CGAAAGGTAAATACTTTACTCTACAC
258 CGAAAGGTAAATACTTTAATCTACAC
** * * * *
25551 GTCTAAAAAATAAATTATTTTAGTCAAATTTACATTGTTAAAATTTTGAATCAAAAATCTTATAT
1 GTCTAAAAAATAAATTATTTTAACCGAATTTACATTGTTAAAATTTTGAATTAAAATTCTCATAT
25616 CATATTGCATATTAAATCAAAAATAAAAATAAAAACAATTTAACTAGATGAAGATGAAATTATGT
66 CATATTGCATATTAAATCAAAAATAAAAATAAAAACAATTTAACTAGATGAAGATGAAATTAT-T
* * *
25681 AAAAATATATATTTTAAACAAATCAGTTTAACATCG-TATCACTAGAGAAAATAATTAAATGATT
130 AAAAA-ACATATTTTAAACAAATCAATTTAATAT-GATATCACTAGAGAAAATAATTAAATGATT
* * * *
25745 TGTTTATTTATCTGTTTTTATTTTAGGTACGACAACAGGTTC-GAAGAAAAAATATAATGAAGAA
193 TATTTATTTATCTATTTTTATTTTAGGTACGACTACAGGTTCAG-AGAAAAAACATAATGAAGAA
*
25809 CCGAAAGGTAAATACTTTAATCTACAT
257 CCGAAAGGTAAATACTTTAATCTACAC
** * * *
25836 GTCTAAAAAATAAATTATTTTAGTCGAATTTAAATCGTTAAAAATTTT-AAATAAAATTCTCATA
1 GTCTAAAAAATAAATTATTTTAACCGAATTTACATTGTT-AAAATTTTGAATTAAAATTCTCATA
* * *** *
25900 TCATGTTGCATATTAAATCAAAAATAAAAAATGAAAATGGTTTAACTAGACGAAGATGAAATTAT
65 TCATATTGCATATTAAATCAAAAAT-AAAAATAAAAACAATTTAACTAGATGAAGATGAAATTAT
*
25965 TAGAAAAACATATTTTAAACAAATCAATTTAATATGATATCAC-AGGAGAAAATAACTAAATGAT
129 TA-AAAAACATATTTTAAACAAATCAATTTAATATGATATCACTA-GAGAAAATAATTAAATGAT
* ** * * ** * *
26029 TTATTTATTTATTTATTTTTATTTTATTTATGATTACAATTTCAGAGGAAAAACGTAATGAAGAA
192 TTATTTATTTATCTATTTTTATTTTAGGTACGACTACAGGTTCAGAGAAAAAACATAATGAAGAA
*
26094 CAGAAAGGTAAATACTTTAATCTACAC
257 CCGAAAGGTAAATACTTTAATCTACAC
* * * *
26121 ATCTAAAATATAAATTATTTTAACCGAATTTACATTGCTAGAAA-TTTGAATTAAAGTTCTCATA
1 GTCTAAAAAATAAATTATTTTAACCGAATTTACATTGTTA-AAATTTTGAATTAAAATTCTCATA
* * *
26185 TCATATTGCATA-T---T---AAAT--AAA-AAAAACAGTTTAACTAGGTGAACATGAAATTATT
65 TCATATTGCATATTAAATCAAAAATAAAAATAAAAACAATTTAACTAGATGAAGATGAAATTATT
* * *
26240 AAAAAACATATTTTAAAAAAATCAATTTAATATGTTATCACTAGAGAAAATATTTAAATGATTTA
130 AAAAAACATATTTTAAACAAATCAATTTAATATGATATCACTAGAGAAAATAATTAAATGATTTA
* * * *
26305 TTTATTTTTTTTATCTATTTTTAATTTAGGTACGACTACAGGTTCAGAGAACAAACGTAATGAAA
195 TTTA-----TTTATCTATTTTTATTTTAGGTACGACTACAGGTTCAGAGAAAAAACATAATGAAG
* * * *
26370 AACTGAAAGATAAACACTATAATCT
255 AACCGAAAGGTAAATACTTTAATCT
26395 GCATATATAA
Statistics
Matches: 721, Mismatches: 94, Indels: 55
0.83 0.11 0.06
Matches are distributed among these distances:
273 62 0.09
274 30 0.04
275 90 0.12
278 70 0.10
280 6 0.01
281 71 0.10
282 2 0.00
284 8 0.01
285 335 0.46
286 47 0.07
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.35
Consensus pattern (283 bp):
GTCTAAAAAATAAATTATTTTAACCGAATTTACATTGTTAAAATTTTGAATTAAAATTCTCATAT
CATATTGCATATTAAATCAAAAATAAAAATAAAAACAATTTAACTAGATGAAGATGAAATTATTA
AAAAACATATTTTAAACAAATCAATTTAATATGATATCACTAGAGAAAATAATTAAATGATTTAT
TTATTTATCTATTTTTATTTTAGGTACGACTACAGGTTCAGAGAAAAAACATAATGAAGAACCGA
AAGGTAAATACTTTAATCTACAC
Found at i:26755 original size:21 final size:22
Alignment explanation
Indices: 26717--26761 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
26707 ATAAATTTTA
*
26717 AAATTATATATGAATTTTGATT
1 AAATTATATATGAATTTTAATT
* *
26739 AAATT-TATATTATTTTTAATT
1 AAATTATATATGAATTTTAATT
26760 AA
1 AA
26762 TGTATTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
AAATTATATATGAATTTTAATT
Found at i:27532 original size:22 final size:23
Alignment explanation
Indices: 27507--27571 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 23
27497 TTTGAGATAA
27507 ATTTTAAAAT-TATATATGAATT
1 ATTTTAAAATATATATATGAATT
*
27529 ATTTCAAAAATATATATATGAATT
1 ATTT-TAAAATATATATATGAATT
*
27553 ATGTTTAAAATGTATATAT
1 AT-TTTAAAATATATATAT
27572 AATATAATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 4 0.11
23 5 0.14
24 26 0.70
25 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (23 bp):
ATTTTAAAATATATATATGAATT
Found at i:31838 original size:271 final size:271
Alignment explanation
Indices: 31105--32068 Score: 942
Period size: 287 Copynumber: 3.4 Consensus size: 271
31095 CTGCCACTTG
* * * *
31105 AATAATTAAATGATTTAATTATTTATTTGT-TTTTATTTTAGGTACTACAGTACGTTCGGAGGAA
1 AATAATTAAATGATTTATTTATTTATTTTTATTTTA-TGTACG-ACTACAG---GTTCGGAGGAA
* * * * *
31169 AAACATATTGAAGAACCGAAAGATAAATACTTTAATCTACGTGTTTAAAAAATAAATTATTTTAA
61 AAACATAATGAAAAACCGAAAGATAAATACTTTAATCTACATATCTAAAAAATAAATTATTTTAA
** * * *
31234 TAGAATTTACATTGTTAAAAAGTTGAATTAAAATTCTCATGTCATATTGCATATTAAATCAAAAA
126 CCGAATTTACATTGTTAGAAATTTGAATTAAAATTCTCATATCATATTGCATATTAAATCAAAAA
*
31299 T-AAAAATAAAAACAATTTAACTAGATAAAGATGAAATTATTTAATAAAAACTATATTTTAAACA
191 TAAAAAATAAAAACAGTTTAACTAGATAAAGATG-----A---AAT----ACTATATTTTAAACA
*
31363 AATCAATTTAACATCGTATCACTAGAGAA
244 AATCAATTTAATAT-GTATCACTAGAGAA
* * * * * * *
31392 AAAAATTAAATGATTTGTTTATTTATCTGTTTTTATTTTA-GATACAACAATAAGTTCGGAGAAA
1 AATAATTAAATGATTTATTTATTTA----TTTTTATTTTATG-TACGACTACAGGTTCGGAGGAA
* * * * * * *
31456 AAACATAATGAAGAATCGAAAGGTAAATATTTTAACCTACATGTCTAAAAAATAAATTATTTTAG
61 AAACATAATGAAAAACCGAAAGATAAATACTTTAATCTACATATCTAAAAAATAAATTATTTTAA
* * * * *
31521 CCAAATTTACATAGTTTGAAATTTGAAATAAAATTCTCAAATCATATTGCATATTAAATCAAAAA
126 CCGAATTTACATTGTTAGAAATTTGAATTAAAATTCTCATATCATATTGCATATTAAATCAAAAA
** *
31586 TAAAAAATAAAAATGGTTTAACTAGATGAAGATGAAATA-TATATTTTAAACAAATCAATTTAAT
191 TAAAAAATAAAAACAGTTTAACTAGATAAAGATGAAATACTATATTTTAAACAAATCAATTTAAT
31650 ATGATATCAC-AGGAGAA
256 ATG-TATCACTA-GAGAA
* *
31667 AATAATTAAATGATTTATTTATTTATTTTTATTTTATGTACGATTACAGGTTCGGAGGAAAAACG
1 AATAATTAAATGATTTATTTATTTATTTTTATTTTATGTACGACTACAGGTTCGGAGGAAAAACA
* * *
31732 TAATGAAAAACCGAAAGGTAAATACTTTAATCTACACATCTAAAATATAAATTATTTTAACCGAA
66 TAATGAAAAACCGAAAGATAAATACTTTAATCTACATATCTAAAAAATAAATTATTTTAACCGAA
* * *
31797 TTTACGTTGCTAGAAATTTGAATTAAAGTTCTCATATCATATTGCATATTAAAT-AAAAA-AGAA
131 TTTACATTGTTAGAAATTTGAATTAAAATTCTCATATCATATTGCATATTAAATCAAAAATA-AA
* * *
31860 AGACAAAAACAGTTTAACTA-AGTAAAGATGAAATTATTAAAAAACATATTTTAAACAAATCAAT
195 AAATAAAAACAGTTTAACTAGA-TAAAGATGAAA-TACT-------ATATTTTAAACAAATCAAT
*
31924 TTAATATGTTACCACTAGAGAA
251 TTAATATG-TATCACTAGAGAA
* * *
31946 AATAATTAAATGATTTATTTATTTTTTAATCTATTTTTATTTTAGGTACGATTACAGGCTT-AGA
1 AATAATTAAATGATTTATTTA-----T--T-TATTTTTATTTTATGTACGACTACAGG-TTCGGA
* *
32010 -GAACAAACATAATGAAAAACTGAAAGATAAATACTTTAATCTACATATAT-AAAAATAAA
57 GGAA-AAACATAATGAAAAACCGAAAGATAAATACTTTAATCTACATATCTAAAAAATAAA
32069 AAATTTATCC
Statistics
Matches: 571, Mismatches: 74, Indels: 65
0.80 0.10 0.09
Matches are distributed among these distances:
269 2 0.00
270 33 0.06
271 136 0.24
272 2 0.00
274 2 0.00
275 60 0.11
276 1 0.00
279 58 0.10
280 4 0.01
283 1 0.00
284 1 0.00
286 12 0.02
287 214 0.37
288 30 0.05
290 4 0.01
291 6 0.01
292 5 0.01
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (271 bp):
AATAATTAAATGATTTATTTATTTATTTTTATTTTATGTACGACTACAGGTTCGGAGGAAAAACA
TAATGAAAAACCGAAAGATAAATACTTTAATCTACATATCTAAAAAATAAATTATTTTAACCGAA
TTTACATTGTTAGAAATTTGAATTAAAATTCTCATATCATATTGCATATTAAATCAAAAATAAAA
AATAAAAACAGTTTAACTAGATAAAGATGAAATACTATATTTTAAACAAATCAATTTAATATGTA
TCACTAGAGAA
Found at i:40488 original size:14 final size:15
Alignment explanation
Indices: 40469--40503 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
40459 TTGTCTTGTT
40469 TAATTGAA-CAAAAA
1 TAATTGAAGCAAAAA
*
40483 TAATTGAAGCAATAA
1 TAATTGAAGCAAAAA
40498 TAATTG
1 TAATTG
40504 CAACTAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (15 bp):
TAATTGAAGCAAAAA
Found at i:49000 original size:3 final size:3
Alignment explanation
Indices: 48992--49020 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
48982 ATTGTCTTAA
48992 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
49021 ATGTTGAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:50505 original size:169 final size:170
Alignment explanation
Indices: 50218--50748 Score: 550
Period size: 169 Copynumber: 3.0 Consensus size: 170
50208 TTCAAGCTTA
* *
50218 AATTTAAAGCATGCAATGGGGTTTGTGAGATAGGGAAGATTATATTTCATGGTATAGTTTAAGGT
1 AATTTAAAGCATGCAATGGGG-TTGTAAGATAGGAAAGATTATATTTCAT-GTATAGTTTAAGGT
* * * ** * * * *
50283 CGAATGATATTTTGTATTATAATAGCGAAGGTTCTAGTGTTTTTGAGCTTTTAGCTTTATAGTAG
64 CAAATGATATTTTGTATTGTAACAAAGAAGGTTTTAGTGTTTTTAAACTTTTAGCTTTATAATAG
*
50348 TTAACTTTGTTTT-ATATGAAGC-TATGTATATATATATAAT
129 TTAACTTTGTTTTAATATGAAGCATATATATATATATATAAT
* ** *
50388 -ATTTAAAGCATGCAATGGGAGTTGTAAGATAGGAAAGATTATACTTCATAGCCTAGTTCAAGGT
1 AATTTAAAGCATGCAATGGG-GTTGTAAGATAGGAAAGATTATATTTCAT-GTATAGTTTAAGGT
50452 CAAATGATATTTTGTATTGTAACAAAGAAGGTTTTAGTGTTTTTAAACTTTTAGCTTTGAACTTT
64 CAAATGATATTTTGTATTGTAACAAAGAAGGTTTTAGTGTTTTTAAACTTTTA-----G--CTTT
*
50517 ATAATAGTGAACTTTGTTTTAATATGAAGCAATATATATATATATATATATAT
122 ATAATAGTTAACTTTGTTTTAATATGAAGC---ATATATATATATATATA-AT
* * * *
50570 AATTTAGAAGAATGCAATGAGGTTTGTAGGATAGGAAAGATTATATTTCATGTATTGTTTAAGGT
1 AATTTA-AAGCATGCAATG-GGGTTGTAAGATAGGAAAGATTATATTTCATGTATAGTTTAAGGT
* *
50635 CAAATGATATTTTATA-TGATAACAGAA-AAGGTTTTAGTGTTTTTGAACCTTTAGCTTTGAGCT
64 CAAATGATATTTTGTATTG-TAACA-AAGAAGGTTTTAGTGTTTTT-AA-----A-CTTTTAGCT
* * * *
50698 TTATAATAGTTAAATTTGTTTTGATATGAAGCAAATTTATATATATATAAT
120 TTATAATAGTTAACTTTGTTTTAATATGAAGCATATATATATATATATAAT
50749 TTATAATTGA
Statistics
Matches: 302, Mismatches: 33, Indels: 43
0.80 0.09 0.11
Matches are distributed among these distances:
169 100 0.33
170 1 0.00
174 1 0.00
176 22 0.07
177 9 0.03
179 2 0.01
180 15 0.05
181 15 0.05
182 4 0.01
183 83 0.27
184 41 0.14
185 3 0.01
189 1 0.00
190 5 0.02
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.41
Consensus pattern (170 bp):
AATTTAAAGCATGCAATGGGGTTGTAAGATAGGAAAGATTATATTTCATGTATAGTTTAAGGTCA
AATGATATTTTGTATTGTAACAAAGAAGGTTTTAGTGTTTTTAAACTTTTAGCTTTATAATAGTT
AACTTTGTTTTAATATGAAGCATATATATATATATATAAT
Found at i:50641 original size:183 final size:179
Alignment explanation
Indices: 50218--50756 Score: 622
Period size: 183 Copynumber: 3.0 Consensus size: 179
50208 TTCAAGCTTA
* *
50218 AATTTAAAGCATGCAATGGGGTTTGT-GAGATAGGGAAGATTATATTTCATGGTATAGTTTAAGG
1 AATTTAAAGCATGCAAT-GGGTTTGTAG-GATAGGAAAGATTATATTTCATAGTATAGTTTAAGG
* * * ** * *
50282 TCGAATGATATTTTGTATTATAATAGCGAAGGTTCTAGTGTTTTTGAGCTTTTA-----G-CTTT
64 TCAAATGATATTTTGTATTGTAACAAAGAAGGTTTTAGTGTTTTTGAACTTTTAGCTTTGACTTT
* *
50341 ATAGTAGTTAACTTTGTTTTATATGAAGC---TATGTATATATATATA-AT
129 ATAATAGTTAACTTTGTTTTATATGAAGCAAATATATATATATATATATAT
* * * ** *
50388 -ATTTAAAGCATGCAATGGGAGTTGTAAGATAGGAAAGATTATACTTCATAGCCTAGTTCAAGGT
1 AATTTAAAGCATGCAATGGG-TTTGTAGGATAGGAAAGATTATATTTCATAGTATAGTTTAAGGT
*
50452 CAAATGATATTTTGTATTGTAACAAAGAAGGTTTTAGTGTTTTTAAACTTTTAGCTTTGAACTTT
65 CAAATGATATTTTGTATTGTAACAAAGAAGGTTTTAGTGTTTTTGAACTTTTAGCTTTG-ACTTT
*
50517 ATAATAGTGAACTTTGTTTTAATATGAAGCAATATATATATATATATATATAT
129 ATAATAGTTAACTTTGTTTT-ATATGAAGCAA-ATATATATATATATATATAT
* *
50570 AATTTAGAAGAATGCAATGAGGTTTGTAGGATAGGAAAGATTATATTTCAT-GTATTGTTTAAGG
1 AATTTA-AAGCATGCAATG-GGTTTGTAGGATAGGAAAGATTATATTTCATAGTATAGTTTAAGG
* *
50634 TCAAATGATATTTTATA-TGATAACAGAA-AAGGTTTTAGTGTTTTTGAACCTTTAGCTTTGAGC
64 TCAAATGATATTTTGTATTG-TAACA-AAGAAGGTTTTAGTGTTTTTGAACTTTTAGCTTTGA-C
* * *
50697 TTTATAATAGTTAAATTTGTTTTGATATGAAGCAAATTTATATATATATAATTTAT
126 TTTATAATAGTTAACTTTGTTTT-ATATGAAGCAAATATATATATATAT-ATATAT
50753 AATT
1 AATT
50757 GAAGTAGTTT
Statistics
Matches: 312, Mismatches: 35, Indels: 31
0.83 0.09 0.08
Matches are distributed among these distances:
168 3 0.01
169 96 0.31
174 1 0.00
176 22 0.07
177 9 0.03
181 15 0.05
182 18 0.06
183 107 0.34
184 39 0.12
185 2 0.01
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.41
Consensus pattern (179 bp):
AATTTAAAGCATGCAATGGGTTTGTAGGATAGGAAAGATTATATTTCATAGTATAGTTTAAGGTC
AAATGATATTTTGTATTGTAACAAAGAAGGTTTTAGTGTTTTTGAACTTTTAGCTTTGACTTTAT
AATAGTTAACTTTGTTTTATATGAAGCAAATATATATATATATATATAT
Found at i:52351 original size:20 final size:18
Alignment explanation
Indices: 52302--52337 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
52292 ACTTGTAGTT
52302 TCTTCTCCCTTATCGCAC
1 TCTTCTCCCTTATCGCAC
52320 TCTTCTCCCTTATCGCAC
1 TCTTCTCCCTTATCGCAC
52338 GTTCTTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.44, G:0.06, T:0.39
Consensus pattern (18 bp):
TCTTCTCCCTTATCGCAC
Found at i:53953 original size:2 final size:2
Alignment explanation
Indices: 53946--53980 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
53936 ATTATAAAAT
53946 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53981 TTAACTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:70214 original size:22 final size:22
Alignment explanation
Indices: 70173--70214 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
70163 TAATCTTACC
*
70173 ATTTAATTTTAGAAGGAATTTT
1 ATTTAATTTTAGAAGCAATTTT
*
70195 ATTTAATTTTAGAATCAATT
1 ATTTAATTTTAGAAGCAATT
70215 CTATGCTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (22 bp):
ATTTAATTTTAGAAGCAATTTT
Found at i:70878 original size:6 final size:6
Alignment explanation
Indices: 70867--70913 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
70857 ATATGCCCAA
* *
70867 CACCGC CACCGC CACCGC CACCGC CACCGC CAGCGC CAGCGC CACCG
1 CACCGC CACCGC CACCGC CACCGC CACCGC CACCGC CACCGC CACCG
70914 ACACTCACCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.17, C:0.62, G:0.21, T:0.00
Consensus pattern (6 bp):
CACCGC
Found at i:74215 original size:9 final size:9
Alignment explanation
Indices: 74197--74260 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
74187 ATCAGCAAAT
74197 AATT-TTAA
1 AATTATTAA
74205 AATTATTAA
1 AATTATTAA
74214 AATTATT--
1 AATTATTAA
74221 --TT-TTAA
1 AATTATTAA
*
74227 AAATA-TAA
1 AATTATTAA
74235 AATTATTAA
1 AATTATTAA
74244 AATTATTTTAA
1 AATTA--TTAA
74255 AATTAT
1 AATTAT
74261 AATCATCATC
Statistics
Matches: 45, Mismatches: 2, Indels: 17
0.70 0.03 0.27
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
8 12 0.27
9 20 0.44
11 9 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
AATTATTAA
Found at i:74235 original size:21 final size:22
Alignment explanation
Indices: 74199--74241 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
74189 CAGCAAATAA
*
74199 TTTTAAAATTATTAAAATTATT
1 TTTTAAAAATATTAAAATTATT
74221 TTTTAAAAATA-TAAAATTATT
1 TTTTAAAAATATTAAAATTATT
74242 AAAATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAAATATTAAAATTATT
Found at i:75162 original size:21 final size:23
Alignment explanation
Indices: 75136--75178 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
75126 AATTTTTTTT
75136 AATAATTTT-AT-ATTTTAAAAA
1 AATAATTTTAATAATTTTAAAAA
75157 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
75179 TCATTTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAATTTTAATAATTTTAAAAA
Done.