Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009674.1 Kokia drynarioides strain JFW-HI SEQ_124392, 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: 83509
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:309 original size:18 final size:18
Alignment explanation
Indices: 286--322 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
276 TTTGTGATCA
286 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
*
304 AAATTGAAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
322 A
1 A
323 TATGAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:311 original size:12 final size:12
Alignment explanation
Indices: 286--322 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
276 TTTGTGATCA
286 AAATTGAAAGTG
1 AAATTGAAAGTG
* *
298 AAAGTGAAATTG
1 AAATTGAAAGTG
310 AAATTGAAAGTG
1 AAATTGAAAGTG
322 A
1 A
323 TATGAATTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
AAATTGAAAGTG
Found at i:1204 original size:45 final size:43
Alignment explanation
Indices: 1096--1204 Score: 111
Period size: 45 Copynumber: 2.5 Consensus size: 43
1086 GGTTGTTAAA
*
1096 AAAAAGTATACTAT--ATTTTGATATTAGTTTAATAAAATGGT
1 AAAAAGTATATTATAAATTTTGATATTAGTTTAATAAAATGGT
* *
1137 AAAGAGTATATTATAAAATTTGATATTAAGTTTGAATAAAAAT-G-
1 AAAAAGTATATTATAAATTTTGATATT-AGTTT-AAT-AAAATGGT
1181 AATAAAGT-TATTAGTAAATTTTGA
1 AA-AAAGTATATTA-TAAATTTTGA
1205 GTAATATTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
41 12 0.21
43 10 0.18
44 12 0.21
45 17 0.30
46 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.13, T:0.39
Consensus pattern (43 bp):
AAAAAGTATATTATAAATTTTGATATTAGTTTAATAAAATGGT
Found at i:7387 original size:17 final size:18
Alignment explanation
Indices: 7365--7400 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7355 TAGATGAGTT
7365 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
7382 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
7400 A
1 A
7401 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:7720 original size:18 final size:18
Alignment explanation
Indices: 7697--7733 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7687 TTTGTGATCA
7697 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
7715 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
7733 A
1 A
7734 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:11197 original size:36 final size:36
Alignment explanation
Indices: 11150--11333 Score: 253
Period size: 36 Copynumber: 5.1 Consensus size: 36
11140 ATTGACTGGT
* * * *
11150 CTCGTATGAGCTAAAATTACTGGGATACTTGAAGAG
1 CTCGTAAGAGCTGAATTTACTGGGAAACTTGAAGAG
* *
11186 CTCGTAAGAGCTGGATTTATTGGGAAACTTGAAGAG
1 CTCGTAAGAGCTGAATTTACTGGGAAACTTGAAGAG
*
11222 CTCATAAGAGCTGAATTTACTGGGAAACTTGAAGAG
1 CTCGTAAGAGCTGAATTTACTGGGAAACTTGAAGAG
*
11258 CTCATAAGAGCTGAATTTACTGGGAAACTTGAAGAG
1 CTCGTAAGAGCTGAATTTACTGGGAAACTTGAAGAG
* * *
11294 CTCGTAAGAGATGAA-TTATTGGGAAACTGGAAGAG
1 CTCGTAAGAGCTGAATTTACTGGGAAACTTGAAGAG
*
11329 ATCGT
1 CTCGT
11334 TTGAGATACG
Statistics
Matches: 134, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 22 0.16
36 112 0.84
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.26
Consensus pattern (36 bp):
CTCGTAAGAGCTGAATTTACTGGGAAACTTGAAGAG
Found at i:14875 original size:17 final size:19
Alignment explanation
Indices: 14846--14880 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
14836 ATTTACTCTT
14846 TTAAAATAAAAA-TAATTC
1 TTAAAATAAAAATTAATTC
14864 TTAAAA-AAAAATTAATT
1 TTAAAATAAAAATTAATT
14881 TGTAATACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
TTAAAATAAAAATTAATTC
Found at i:16452 original size:24 final size:24
Alignment explanation
Indices: 16415--16475 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
16405 GACTAATAAA
* *
16415 AGTTTGACTCAAACAAATAAACAG
1 AGTTTAACTGAAACAAATAAACAG
* *
16439 AGTTTAATTGAAACAAATAAATAG
1 AGTTTAACTGAAACAAATAAACAG
*
16463 TGTTTAACTGAAA
1 AGTTTAACTGAAA
16476 GATTATTTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAACAG
Found at i:18448 original size:24 final size:24
Alignment explanation
Indices: 18383--18449 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
18373 AATCTAGACT
* * *
18383 AATAAGAGTTTGACTCAAATAAATA
1 AATAA-AGTTTAACTGAAACAAATA
* *
18408 AACAAAGTTTAATTGAAACAAATA
1 AATAAAGTTTAACTGAAACAAATA
18432 AATAAAGTTTAACTGAAA
1 AATAAAGTTTAACTGAAA
18450 GATTATTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
24 31 0.89
25 4 0.11
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.27
Consensus pattern (24 bp):
AATAAAGTTTAACTGAAACAAATA
Found at i:21131 original size:68 final size:69
Alignment explanation
Indices: 21018--21157 Score: 183
Period size: 68 Copynumber: 2.0 Consensus size: 69
21008 AGTCTGGAGG
* **
21018 TTGAATATAGCATAAAGTACTTCTTTGAACATAGTGCTTGGAATA-TGCCAATTAATTGATTTAG
1 TTGAATATAGCACAAAGTACTTCTTTGAACATAGTGCTTGGAATATTGCCAATTAATAAATTTAG
21082 TAGT
66 TAGT
* * * * * * *
21086 TTGAATATAGCACAAATTACTTGTTTTAATATATTGCTTGTAATATTGCTAATTAATAAATTTAG
1 TTGAATATAGCACAAAGTACTTCTTTGAACATAGTGCTTGGAATATTGCCAATTAATAAATTTAG
21151 TAGT
66 TAGT
21155 TTG
1 TTG
21158 GTAAGAAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
68 38 0.62
69 23 0.38
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (69 bp):
TTGAATATAGCACAAAGTACTTCTTTGAACATAGTGCTTGGAATATTGCCAATTAATAAATTTAG
TAGT
Found at i:35467 original size:7 final size:7
Alignment explanation
Indices: 35457--35538 Score: 64
Period size: 7 Copynumber: 11.6 Consensus size: 7
35447 AGAAAAGTGA
35457 AAAATAT
1 AAAATAT
35464 -AAA-A-
1 AAAATAT
35468 AAAATAT
1 AAAATAT
35475 AAAAATAT
1 -AAAATAT
*
35483 AAAAATAA
1 -AAAATAT
35491 AAAATAT
1 AAAATAT
35498 ATAAA-ATT
1 A-AAATA-T
*
35506 ACAAATAA
1 A-AAATAT
*
35514 AAAATAA
1 AAAATAT
35521 AAAATAT
1 AAAATAT
35528 AAAATAT
1 AAAATAT
35535 AAAA
1 AAAA
35539 CATATTTACA
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
5 4 0.06
6 4 0.06
7 31 0.49
8 23 0.37
9 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.22
Consensus pattern (7 bp):
AAAATAT
Found at i:35496 original size:23 final size:23
Alignment explanation
Indices: 35466--35543 Score: 106
Period size: 23 Copynumber: 3.4 Consensus size: 23
35456 AAAAATATAA
35466 AAAAAATATAAAAATATAAAAAT
1 AAAAAATATAAAAATATAAAAAT
*
35489 AAAAAATATATAAAAT-TACAAAT
1 AAAAAATATA-AAAATATAAAAAT
35512 AAAAAATA-AAAAATATAAAATAT
1 AAAAAATATAAAAATATAAAA-AT
*
35535 AAAACATAT
1 AAAAAATAT
35544 TTACAATTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
21 5 0.10
22 5 0.10
23 33 0.69
24 5 0.10
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (23 bp):
AAAAAATATAAAAATATAAAAAT
Found at i:35536 original size:16 final size:15
Alignment explanation
Indices: 35467--35543 Score: 93
Period size: 16 Copynumber: 5.0 Consensus size: 15
35457 AAAATATAAA
35467 AAAAATATAAAAATAT
1 AAAAATA-AAAAATAT
35483 AAAAATAAAAAATAT
1 AAAAATAAAAAATAT
* *
35498 ATAAAATTACAAATA-
1 A-AAAATAAAAAATAT
35513 AAAAATAAAAAATAT
1 AAAAATAAAAAATAT
*
35528 AAAATATAAAACATAT
1 AAAA-ATAAAAAATAT
35544 TTACAATTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
14 11 0.21
15 14 0.26
16 28 0.53
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAATAAAAAATAT
Found at i:38231 original size:11 final size:11
Alignment explanation
Indices: 38212--38246 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
38202 AGCTTATTTG
38212 GATTCAAATAT
1 GATTCAAATAT
*
38223 GATTTAAATAT
1 GATTCAAATAT
*
38234 GAATCAAATAT
1 GATTCAAATAT
38245 GA
1 GA
38247 CAAATCAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (11 bp):
GATTCAAATAT
Found at i:51533 original size:157 final size:158
Alignment explanation
Indices: 51289--51576 Score: 386
Period size: 157 Copynumber: 1.8 Consensus size: 158
51279 GTGAGCCCAT
**
51289 CTCTAGTTGGATTAACCAACAAATAACCGTCAAATCCTAGCACCCAATACCTACTGGATAAACCG
1 CTCTAGTTGGATTAACCAACAAATAACCGTCAAATCCTAGCACCCAATACCTACTGGATAAACAA
* * * * *
51354 CAATTGTGAGCGCAGCTTTAGTTGGATTAATCAACAATATCCGTCAAATCCTGACACCCAGTGCC
66 CAATTATGAGCGCAGATATAGTTGGATTAACCAACAATATCCATCAAATCCTGACACCCAGTGCC
51419 TGCAGGTAAACTGCAATTGTGAGATCAG
131 TGCAGGTAAACTGCAATTGTGAGATCAG
* * * *
51447 CTCTAGTTTGATTAACCAAC-AATATCTGTCAAATCCT-GACACCCAATGCCTAGC-GGATAAAC
1 CTCTAGTTGGATTAACCAACAAATAACCGTCAAATCCTAG-CACCCAATACCTA-CTGGATAAAC
* * * *
51509 AACAATTATGAGTC-CAGATATAGTTGGATTAACCAACAATTTTCATTAAATCCTGGCACCCAGT
64 AACAATTATGAG-CGCAGATATAGTTGGATTAACCAACAATATCCATCAAATCCTGACACCCAGT
51573 GCCT
128 GCCT
51577 AGTAGATAAA
Statistics
Matches: 112, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
156 1 0.01
157 90 0.80
158 21 0.19
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (158 bp):
CTCTAGTTGGATTAACCAACAAATAACCGTCAAATCCTAGCACCCAATACCTACTGGATAAACAA
CAATTATGAGCGCAGATATAGTTGGATTAACCAACAATATCCATCAAATCCTGACACCCAGTGCC
TGCAGGTAAACTGCAATTGTGAGATCAG
Found at i:51560 original size:79 final size:80
Alignment explanation
Indices: 51292--51598 Score: 306
Period size: 79 Copynumber: 3.9 Consensus size: 80
51282 AGCCCATCTC
* * *
51292 TAGTTGGATTAACCAACAAATAACCGTCAAATCCT-AGCACCCAATACCTA-CTGGATAAACCGC
1 TAGTTGGATTAACCAAC-AATAACCGTCAAATCCTGA-CACCCAATGCCTAGCAGGATAAACCAC
*
51355 AATTGTGAG-CGCAGCTT
64 AATTGTGAGTC-CAGCTA
* * * **
51372 TAGTTGGATTAATCAACAATATCCGTCAAATCCTGACACCCAGTGCCT-GCAGG-TAAACTGCAA
1 TAGTTGGATTAACCAACAATAACCGTCAAATCCTGACACCCAATGCCTAGCAGGATAAACCACAA
*
51435 TTGTGAGAT-CAGCTC
66 TTGTGAG-TCCAGCTA
* * * *
51450 TAGTTTGATTAACCAACAATATCTGTCAAATCCTGACACCCAATGCCTAGC-GGATAAACAACAA
1 TAGTTGGATTAACCAACAATAACCGTCAAATCCTGACACCCAATGCCTAGCAGGATAAACCACAA
* *
51514 TTATGAGTCCAGATA
66 TTGTGAGTCCAGCTA
*** * * * * *
51529 TAGTTGGATTAACCAACAATTTTCATTAAATCCTGGCACCCAGTGCCTAGTA-GATAAACCACAA
1 TAGTTGGATTAACCAACAATAACCGTCAAATCCTGACACCCAATGCCTAGCAGGATAAACCACAA
51593 TTGTGA
66 TTGTGA
51599 TCCGAACTCT
Statistics
Matches: 192, Mismatches: 27, Indels: 17
0.81 0.11 0.07
Matches are distributed among these distances:
78 68 0.35
79 107 0.56
80 17 0.09
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (80 bp):
TAGTTGGATTAACCAACAATAACCGTCAAATCCTGACACCCAATGCCTAGCAGGATAAACCACAA
TTGTGAGTCCAGCTA
Found at i:53203 original size:34 final size:34
Alignment explanation
Indices: 53152--53233 Score: 146
Period size: 34 Copynumber: 2.4 Consensus size: 34
53142 TGTTCTTATA
* *
53152 TGTCTCATTGCATTGATCTTGGGCGTTATCTTGG
1 TGTCCCATTGCACTGATCTTGGGCGTTATCTTGG
53186 TGTCCCATTGCACTGATCTTGGGCGTTATCTTGG
1 TGTCCCATTGCACTGATCTTGGGCGTTATCTTGG
53220 TGTCCCATTGCACT
1 TGTCCCATTGCACT
53234 TTGGCCGTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.12, C:0.23, G:0.24, T:0.40
Consensus pattern (34 bp):
TGTCCCATTGCACTGATCTTGGGCGTTATCTTGG
Found at i:55203 original size:37 final size:37
Alignment explanation
Indices: 55152--55272 Score: 161
Period size: 38 Copynumber: 3.2 Consensus size: 37
55142 CAAACGATAC
*
55152 ATTGGGTTCATTTTAAGCAAACAAAAGAGCAATGTGA
1 ATTGGGTTCTTTTTAAGCAAACAAAAGAGCAATGTGA
* * *
55189 ATTGAGTTCTTTTTAAGCAAACAAAAGAGACAATTTTA
1 ATTGGGTTCTTTTTAAGCAAACAAAAGAG-CAATGTGA
* * *
55227 ACTGGGTTCTTTTTAAGAAAACAAAAGAGGTAATGTGA
1 ATTGGGTTCTTTTTAAGCAAACAAAAGA-GCAATGTGA
55265 ATTGGGTT
1 ATTGGGTT
55273 GTTGTTTTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
37 27 0.38
38 43 0.61
39 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (37 bp):
ATTGGGTTCTTTTTAAGCAAACAAAAGAGCAATGTGA
Found at i:64150 original size:80 final size:78
Alignment explanation
Indices: 63939--64152 Score: 194
Period size: 78 Copynumber: 2.7 Consensus size: 78
63929 TTGTAAATAG
** * * ** ** * * * *
63939 AAAATTAATCGAATAATTCTATTTCAGGATTTATTTATGTCATTCAATAGAATTTATTTGATTTT
1 AAAATTAATTAAACAATTATATTTCAGGATTTATTCCTACCGTTCAATAGAATTTACTCGAGTTT
*
64004 CTGTTTCCAAACA
66 ATGTTTCCAAACA
* * * * * * ** *
64017 GAAATTATTTGAACAATTCTGTTTCGGGATTTATTCCTATTGTTTAATAGAATTTACTCGAGTTT
1 AAAATTAATTAAACAATTATATTTCAGGATTTATTCCTACCGTTCAATAGAATTTACTCGAGTTT
64082 ATGTTTCCAAACA
66 ATGTTTCCAAACA
* *
64095 AAAATTAAATTAAATAATTATATTTTAGGATTTTATTCCTACCGTTCAATAGAATTTA
1 AAAATT-AATTAAACAATTATATTTCAGGA-TTTATTCCTACCGTTCAATAGAATTTA
64153 TTCAATTTCT
Statistics
Matches: 107, Mismatches: 27, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
78 67 0.63
79 16 0.15
80 24 0.22
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (78 bp):
AAAATTAATTAAACAATTATATTTCAGGATTTATTCCTACCGTTCAATAGAATTTACTCGAGTTT
ATGTTTCCAAACA
Found at i:66235 original size:25 final size:25
Alignment explanation
Indices: 66207--66274 Score: 118
Period size: 25 Copynumber: 2.7 Consensus size: 25
66197 TATGAATTAG
*
66207 ATAGAATATCACTCTTACAAGTCAA
1 ATAGAATATCGCTCTTACAAGTCAA
66232 ATAGAATATCGCTCTTACAAGTCAA
1 ATAGAATATCGCTCTTACAAGTCAA
*
66257 ACAGAATATCGCTCTTAC
1 ATAGAATATCGCTCTTAC
66275 GAGCAAGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (25 bp):
ATAGAATATCGCTCTTACAAGTCAA
Found at i:71168 original size:70 final size:70
Alignment explanation
Indices: 71079--71230 Score: 259
Period size: 70 Copynumber: 2.2 Consensus size: 70
71069 TTTAAGGGAC
* *
71079 TTCTACTGGTACCTCATGGTTAAGTATCGGTAGTAGTCAATTCAATGAACAATTTTAGAACTGTG
1 TTCTACTGGTACCTCATGGTCAAGTATCGGTAGTAGTCAATTCAATGAACAATTGTAGAACTGTG
71144 CAGAT
66 CAGAT
* * *
71149 TTCTACTGGTACCTGATGGTCAAGTATTGGTAGTAGTCAATTCAATGAACAATTGTAGAATTGTG
1 TTCTACTGGTACCTCATGGTCAAGTATCGGTAGTAGTCAATTCAATGAACAATTGTAGAACTGTG
71214 CAGAT
66 CAGAT
71219 TTCTACTGGTAC
1 TTCTACTGGTAC
71231 TTTTACTCAT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 77 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (70 bp):
TTCTACTGGTACCTCATGGTCAAGTATCGGTAGTAGTCAATTCAATGAACAATTGTAGAACTGTG
CAGAT
Found at i:72105 original size:52 final size:51
Alignment explanation
Indices: 71950--72186 Score: 285
Period size: 52 Copynumber: 4.6 Consensus size: 51
71940 TTTCATTTAA
** ** * * *
71950 TACTCACGATGACAAATAGTCATCGAACCTCTTGTTCCGTATAGGAATTCATA
1 TACTCACGATGACACTTAGTCATCGAACCT-TTAATCCATAAAGG-ATTCATT
* * * * *
72003 TACTCACGATGAAACTAAGTCATCGGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCATAAAGGATTCATT
*
72054 TACTCACGATGACACTTAGTCATCGAATCCTTTAGTCCATAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGAA-CCTTTAATCCATAAAGGATTCATT
** * *
72106 TACTCACGATGACACTTAGTCATCAGGCCCTTTAATCCGTAAAGGATTCGTT
1 TACTCACGATGACACTTAGTCATC-GAACCTTTAATCCATAAAGGATTCATT
72158 TACTCACGATGACACTTAGTCATCGAACC
1 TACTCACGATGACACTTAGTCATCGAACC
72187 CTTTCGTTTA
Statistics
Matches: 157, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
51 33 0.21
52 98 0.62
53 26 0.17
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGAACCTTTAATCCATAAAGGATTCATT
Found at i:72190 original size:104 final size:103
Alignment explanation
Indices: 71950--72186 Score: 316
Period size: 104 Copynumber: 2.3 Consensus size: 103
71940 TTTCATTTAA
** * *
71950 TACTCACGATGACAAATAGTCATCGAACCTCTTGTTCCGTATAGGAATTCATATACTCACGATGA
1 TACTCACGATGACACTTAGTCATCGAACCT-TTGTTCCATAAAGGAATTCATATACTCACGATGA
* *
72015 AACTAAGTCATCGGACCTTTAATCCATCATGGATTCATT
65 AACTAAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
72054 TACTCACGATGACACTTAGTCATCGAATCCTTTAG-TCCATAAAGG-ATTCATTTACTCACGATG
1 TACTCACGATGACACTTAGTCATCGAA-CCTTT-GTTCCATAAAGGAATTCATATACTCACGATG
* * * * *
72117 ACACTTAGTCATCAGGCCCTTTAATCCGTAAAGGATTCGTT
64 AAACTAAGTCATC-GGACCTTTAATCCATAAAGGATTCATT
72158 TACTCACGATGACACTTAGTCATCGAACC
1 TACTCACGATGACACTTAGTCATCGAACC
72187 CTTTCGTTTA
Statistics
Matches: 118, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
103 30 0.25
104 84 0.71
105 4 0.03
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (103 bp):
TACTCACGATGACACTTAGTCATCGAACCTTTGTTCCATAAAGGAATTCATATACTCACGATGAA
ACTAAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:76164 original size:25 final size:25
Alignment explanation
Indices: 76064--76165 Score: 141
Period size: 25 Copynumber: 4.0 Consensus size: 25
76054 TAAAGTTTAG
*
76064 CTCTTACGAGCCCAGACAGAATATCG
1 CTCTTACGAG-CCAGACAGAATATCT
* * *
76090 CTCTTACAAGCCAGACATAATATCA
1 CTCTTACGAGCCAGACAGAATATCT
*
76115 CTCTTACGAGCCAGACAAAATATCT
1 CTCTTACGAGCCAGACAGAATATCT
*
76140 CTCTTACGAGCCAAACAGAATATCT
1 CTCTTACGAGCCAGACAGAATATCT
76165 C
1 C
76166 CATCGTCTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
25 59 0.87
26 9 0.13
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.23
Consensus pattern (25 bp):
CTCTTACGAGCCAGACAGAATATCT
Found at i:80914 original size:24 final size:24
Alignment explanation
Indices: 80886--80949 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
80876 AGAAATAATC
80886 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
80910 TTTCAATTAAACTCAGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
80934 TTTGAGTCAAACTCTG
1 TTTCAGTTAAACTCTG
80950 ATTAGTCTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.48
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTG
Found at i:82871 original size:24 final size:24
Alignment explanation
Indices: 82842--82892 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
82832 AGAAATAATC
*
82842 TTTCAATTAAGCTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
* *
82866 TTTCAATTAAATTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
82890 TTT
1 TTT
82893 GAGTCAAACT
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:0.08, T:0.59
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:83488 original size:2 final size:2
Alignment explanation
Indices: 83481--83509 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
83471 CACCTATTTG
83481 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.