Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009906.1 Kokia drynarioides strain JFW-HI SEQ_124644, 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: 55698
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 14 characters in sequence are not A, C, G, or T
Found at i:4276 original size:2 final size:2
Alignment explanation
Indices: 4269--4295 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4259 AAGTAGGTTT
4269 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4296 TTAGATTCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5253 original size:24 final size:25
Alignment explanation
Indices: 5223--5306 Score: 77
Period size: 24 Copynumber: 3.4 Consensus size: 25
5213 TTATATTCTG
5223 TTTTTTAAAATTAAAT-C-ATTTTT
1 TTTTTTAAAATTAAATCCTATTTTT
*
5246 ATTTTTT--AGTTAAATCCTATTTTT
1 -TTTTTTAAAATTAAATCCTATTTTT
* *
5270 TGTTTTTAAAATTAAATTCTTTTTTT
1 T-TTTTTAAAATTAAATCCTATTTTT
5296 GTTGTTTTAAA
1 -TT-TTTTAAA
5307 TTTTCCCATC
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
22 7 0.14
23 2 0.04
24 17 0.35
26 15 0.31
27 8 0.16
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (25 bp):
TTTTTTAAAATTAAATCCTATTTTT
Found at i:5276 original size:26 final size:25
Alignment explanation
Indices: 5247--5305 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
5237 ATCATTTTTA
*
5247 TTTTTTAGTTAAATCCTATTTTTTGT
1 TTTTTTAATTAAATCCT-TTTTTTGT
** *
5273 TTTTAAAATTAAATTCTTTTTTTGT
1 TTTTTTAATTAAATCCTTTTTTTGT
*
5298 TGTTTTAA
1 TTTTTTAA
5306 ATTTTCCCAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.64
Consensus pattern (25 bp):
TTTTTTAATTAAATCCTTTTTTTGT
Found at i:5307 original size:26 final size:26
Alignment explanation
Indices: 5224--5308 Score: 83
Period size: 26 Copynumber: 3.4 Consensus size: 26
5214 TATATTCTGT
5224 TTTTTAAAATTAAAT-C-ATTTTTAT-
1 TTTTTAAAATTAAATCCTATTTTT-TG
*
5248 TTTTT--AGTTAAATCCTATTTTTTG
1 TTTTTAAAATTAAATCCTATTTTTTG
*
5272 TTTTTAAAATTAAATTCT-TTTTTTG
1 TTTTTAAAATTAAATCCTATTTTTTG
*
5297 TTGTTTTAAATT
1 TT-TTTAAAATT
5309 TTCCCATCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
22 7 0.14
23 2 0.04
24 16 0.31
25 9 0.18
26 17 0.33
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (26 bp):
TTTTTAAAATTAAATCCTATTTTTTG
Found at i:9727 original size:22 final size:22
Alignment explanation
Indices: 9699--9741 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
9689 AATTTCACCC
* * *
9699 AAAAAAATAAAGAAAGGAAAAG
1 AAAAAAAGAAAAAAAAGAAAAG
9721 AAAAAAAGAAAAAAAAGAAAA
1 AAAAAAAGAAAAAAAAGAAAA
9742 AAGAGAGGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAAAAAGAAAAAAAAGAAAAG
Found at i:9730 original size:18 final size:17
Alignment explanation
Indices: 9702--9743 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
9692 TTCACCCAAA
*
9702 AAAATAAAGAAAGGAAAAG
1 AAAA-AAAGAAA-AAAAAG
9721 AAAAAAAGAAAAAAAAG
1 AAAAAAAGAAAAAAAAG
9738 AAAAAA
1 AAAAAA
9744 GAGAGGTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.50
18 7 0.32
19 4 0.18
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAAG
Found at i:9735 original size:9 final size:9
Alignment explanation
Indices: 9701--9743 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
9691 TTTCACCCAA
9701 AAAAATAAAG
1 AAAAA-AAAG
*
9711 AAAGGAAAAG
1 AAA-AAAAAG
9721 -AAAAAAAG
1 AAAAAAAAG
9729 AAAAAAAAG
1 AAAAAAAAG
9738 AAAAAA
1 AAAAAA
9744 GAGAGGTCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 5 0.17
9 16 0.55
10 7 0.24
11 1 0.03
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:11715 original size:21 final size:20
Alignment explanation
Indices: 11690--11736 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 20
11680 ACAGTAAGCA
11690 CACACAGTGCAATCCAATAGG
1 CACACAGTGCAAT-CAATAGG
*
11711 CACACAGTGCAATCAGTAGG
1 CACACAGTGCAATCAATAGG
11731 CACACA
1 CACACA
11737 TAGCGCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.38, C:0.30, G:0.19, T:0.13
Consensus pattern (20 bp):
CACACAGTGCAATCAATAGG
Found at i:11774 original size:23 final size:23
Alignment explanation
Indices: 11743--11801 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
11733 CACATAGCGC
* *
11743 AAATCAGTAGGCACACGAGGTACG
1 AAAT-AGTAAGCACACGAAGTACG
*
11767 AAATAGTAAGCACACGAAGTGCG
1 AAATAGTAAGCACACGAAGTACG
11790 AAATAGTAAGCA
1 AAATAGTAAGCA
11802 TGCTAGCTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 28 0.88
24 4 0.12
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.14
Consensus pattern (23 bp):
AAATAGTAAGCACACGAAGTACG
Found at i:13770 original size:14 final size:14
Alignment explanation
Indices: 13751--13780 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
13741 GAGGAACTCT
13751 TTTATTGGCTCTTC
1 TTTATTGGCTCTTC
13765 TTTATTGGCTCTTC
1 TTTATTGGCTCTTC
13779 TT
1 TT
13781 CATAAGTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.20, G:0.13, T:0.60
Consensus pattern (14 bp):
TTTATTGGCTCTTC
Found at i:18953 original size:22 final size:22
Alignment explanation
Indices: 18902--18970 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 22
18892 TTAATTGTAA
18902 GCACACACAGTGCAATCCAGTAG
1 GCACACACAGTGCAAT-CAGTAG
*
18925 GCACACACAGTGCAATCAATAG
1 GCACACACAGTGCAATCAGTAG
* *
18947 GCGCACACAGCGCAAATCAGTAG
1 GCACACACAGTGC-AATCAGTAG
18970 G
1 G
18971 TACAAGAGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.39
23 25 0.61
ACGTcount: A:0.36, C:0.29, G:0.23, T:0.12
Consensus pattern (22 bp):
GCACACACAGTGCAATCAGTAG
Found at i:22805 original size:99 final size:99
Alignment explanation
Indices: 22388--23331 Score: 677
Period size: 99 Copynumber: 9.7 Consensus size: 99
22378 TATCAATCTC
* * * * ***
22388 CCTT-AGGTTACAGTGGAATGGAGTAAAGTTACAACACCAAATCTTATAACCCTGAAGTTGCAGT
1 CCTTGAGGTTACAGTGGAATGGAGTGAAGCTACAACAACAAATCCTATCTTCCTGAAGTTGCAGT
* * *
22452 G-GGTCGGATTAAAGCCAA-AAGCAAAACTCAATGT
66 GAAG-CGGATTAAAG-CAAGAAGCAGATCTCAATGT
* * * * * * * *
22486 CCCTAAAGTTATAGTGGCATGGAGTGAAGCT------TCAAATCCTATCTTCCTAAAGTTGCGGT
1 CCTTGAGGTTACAGTGGAATGGAGTGAAGCTACAACAACAAATCCTATCTTCCTGAAGTTGCAGT
** * *
22545 GAAGCATATTAAAACAAGTAA-C-GAATCTCAATCT
66 GAAGCGGATTAAAGCAAG-AAGCAG-ATCTCAATGT
* * * * * **
22579 CCCTGAGGTTACAGTGGAATGGAGTAAAGTTACAACACCAAATCCTATAC--CCTTGAGGTTATA
1 CCTTGAGGTTACAGTGGAATGGAGTGAAGCTACAACAACAAATCCTAT-CTTCC-TGAAGTTGCA
* * *
22642 GTG-GGTCGGATTAAAATGACAA-AA-TAGATCTTAATGT
64 GTGAAG-CGGATT-AAA-G-CAAGAAGCAGATCTCAATGT
* * * * * *
22679 CCCTGAGGTTACAATGGAATAGAGTGAAGCTCCAACAACAAATCTTATCTTCCTTAAGTTGCAGT
1 CCTTGAGGTTACAGTGGAATGGAGTGAAGCTACAACAACAAATCCTATCTTCCTGAAGTTGCAGT
* *
22744 GAAGCGGATTAAAGCTACAAGCAGATCTCAATGT
66 GAAGCGGATTAAAGCAAGAAGCAGATCTCAATGT
* * * * ** *
22778 CCTTGAGGTTATAGTAGAATGGCGTGAAGCTTCAACAATGAATCCTATCTTCCTAAAGTTGCAGT
1 CCTTGAGGTTACAGTGGAATGGAGTGAAGCTACAACAACAAATCCTATCTTCCTGAAGTTGCAGT
* *
22843 GAAGCGGATTAAAACAAGTAGCAGATCTCAATGT
66 GAAGCGGATTAAAGCAAGAAGCAGATCTCAATGT
* * * * * * * * *
22877 CCTTAAGGTTACAGTGGAATTGAATGAAGCTACTACACCAAATCTTATATCCCTGAAGTTGCAAT
1 CCTTGAGGTTACAGTGGAATGGAGTGAAGCTACAACAACAAATCCTATCTTCCTGAAGTTGCAGT
* * **
22942 GGATCGGATT--------AA--AGATCTCAAAAT
66 GAAGCGGATTAAAGCAAGAAGCAGATCTCAATGT
* * * * *** * *
22966 CCCTAAGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATAACCCTAAAATTGCAGT
1 CCTTGAGGTTACAGTGGAATGGAGTGAAGCTACAACAACAAATCCTATCTTCCTGAAGTTGCAGT
* * * * *
23031 G-GGTCGAATTAAAGCCAGAAGCAAAACTCAATGT
66 GAAG-CGGATTAAAGCAAGAAGCAGATCTCAATGT
* * *
23065 CCTTGAGGTTACAGTGGAATGGAGTGAAGCTTCAATAACAAATCCTATCTTCCTGAAGTTGCAAT
1 CCTTGAGGTTACAGTGGAATGGAGTGAAGCTACAACAACAAATCCTATCTTCCTGAAGTTGCAGT
* * * *
23130 GAAGCGAATTAAAACAAGTAGCAAATCTCAATGT
66 GAAGCGGATTAAAGCAAGAAGCAGATCTCAATGT
* * * * * * * **
23164 CCTTGAGGTTACAGTGAAACGGAGTAAAGTTACAACATCAAATCTTATAC-CCCTGAAGTTATAG
1 CCTTGAGGTTACAGTGGAATGGAGTGAAGCTACAACAACAAATCCTAT-CTTCCTGAAGTTGCAG
* *
23228 TG-GGTCGGATTAAAGCCAGAAGCAGATCTCAATGT
65 TGAAG-CGGATTAAAGCAAGAAGCAGATCTCAATGT
* * * * *
23263 CCCTGAGGTTACAGTGGAATGGAGTGAAGCTTCAACAACCAATCCTATATTCCTGAAGTTGTAGT
1 CCTTGAGGTTACAGTGGAATGGAGTGAAGCTACAACAACAAATCCTATCTTCCTGAAGTTGCAGT
23328 GAAG
66 GAAG
23332 TTAAAACAAG
Statistics
Matches: 652, Mismatches: 155, Indels: 76
0.74 0.18 0.09
Matches are distributed among these distances:
89 71 0.11
91 1 0.00
92 3 0.00
93 63 0.10
94 3 0.00
97 4 0.01
98 10 0.02
99 417 0.64
100 73 0.11
101 4 0.01
102 3 0.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (99 bp):
CCTTGAGGTTACAGTGGAATGGAGTGAAGCTACAACAACAAATCCTATCTTCCTGAAGTTGCAGT
GAAGCGGATTAAAGCAAGAAGCAGATCTCAATGT
Found at i:23028 original size:89 final size:89
Alignment explanation
Indices: 22865--23044 Score: 234
Period size: 89 Copynumber: 2.0 Consensus size: 89
22855 AACAAGTAGC
** * * * * *
22865 AGATCTCAATGTCCTTAAGGTTACAGTGGAATTGAATGAAGCTACTACACCAAATCTTATATCCC
1 AGATCTCAAAATCCCTAAGGTTACAGTGGAATGGAATGAAGCTACAACACCAAATCCTATAACCC
* * *
22930 TGAAGTTGCAATGGATCGGATTAA
66 TAAAATTGCAATGGATCGAATTAA
* *
22954 AGATCTCAAAATCCCTAAGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATAACCC
1 AGATCTCAAAATCCCTAAGGTTACAGTGGAATGGAATGAAGCTACAACACCAAATCCTATAACCC
* *
23019 TAAAATTGCAGTGGGTCGAATTAA
66 TAAAATTGCAATGGATCGAATTAA
23043 AG
1 AG
23045 CCAGAAGCAA
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
89 77 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (89 bp):
AGATCTCAAAATCCCTAAGGTTACAGTGGAATGGAATGAAGCTACAACACCAAATCCTATAACCC
TAAAATTGCAATGGATCGAATTAA
Found at i:23127 original size:287 final size:286
Alignment explanation
Indices: 22386--23242 Score: 976
Period size: 287 Copynumber: 3.0 Consensus size: 286
22376 AATATCAATC
* * *
22386 TCCCTTAGGTTACAGTGGAATGGAGTAAAGTTACAACACCAAATCTTATAACCCTGAAGTTGCAG
1 TCCCTAAGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCTTATAACCCTAAAGTTGCAG
* * * *
22451 TGGGTCGGATTAAAGCCAAAAGCAAAACTCAATGTCCCTAAAGTTATAGTGGCATGGAGTGAAGC
66 TGGGTCGGATTAAAGCCAAAAGCAAAACTCAATGTCCTTGAGGTTATAGTGGAATGGAGTGAAGC
* *
22516 -T---T--CAAATCCTATCTTCCTAAAGTTGCGGTGAAGC-ATATTAAAACAAGTAAC-GAATCT
131 TTCAATAACAAATCCTATCTTCCTAAAGTTGCAGTGAAGCGA-ATTAAAACAAGTAGCAG-ATCT
* * * *
22573 CAATCTCCCTGAGGTTACAGTGGAATGGAGTAAAGTTACAACACCAAATCCTATACCCTTGAGGT
194 CAATGTCCTTGAGGTTACAGTGGAATGGAGTAAAGTTACAACACCAAATCTTATACCC-TGAAGT
* **
22638 TATAGTGGGTCGGATTAAAATGACAAAATAGATCTTAATG
258 TATAGTGGGTCGGA-T----T-----AA-AGATCTCAAAA
* * * * * * *** *
22678 TCCCTGAGGTTACAATGGAATAGAGTGAAGCTCCAACAACAAATCTTATCTTCCTTAAGTTGCAG
1 TCCCTAAGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCTTATAACCCTAAAGTTGCAG
* * * * * * *
22743 TGAAG-CGGATTAAAGCTACAAGCAGATCTCAATGTCCTTGAGGTTATAGTAGAATGGCGTGAAG
66 TG-GGTCGGATTAAAGCCAAAAGCAAAACTCAATGTCCTTGAGGTTATAGTGGAATGGAGTGAAG
* ** *
22807 CTTCAACAATGAATCCTATCTTCCTAAAGTTGCAGTGAAGCGGATTAAAACAAGTAGCAGATCTC
130 CTTCAATAACAAATCCTATCTTCCTAAAGTTGCAGTGAAGCGAATTAAAACAAGTAGCAGATCTC
* * * * * *
22872 AATGTCCTTAAGGTTACAGTGGAATTGAATGAAGCTACTACACCAAATCTTATATCCCTGAAGTT
195 AATGTCCTTGAGGTTACAGTGGAATGGAGTAAAGTTACAACACCAAATCTTATA-CCCTGAAGTT
** * *
22937 GCAATGGATCGGATTAAAGATCTCAAAA
259 ATAGTGGGTCGGATTAAAGATCTCAAAA
* *
22965 TCCCTAAGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATAACCCTAAAATTGCAG
1 TCCCTAAGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCTTATAACCCTAAAGTTGCAG
* * *
23030 TGGGTCGAATTAAAGCCAGAAGCAAAACTCAATGTCCTTGAGGTTACAGTGGAATGGAGTGAAGC
66 TGGGTCGGATTAAAGCCAAAAGCAAAACTCAATGTCCTTGAGGTTATAGTGGAATGGAGTGAAGC
* * *
23095 TTCAATAACAAATCCTATCTTCCTGAAGTTGCAATGAAGCGAATTAAAACAAGTAGCAAATCTCA
131 TTCAATAACAAATCCTATCTTCCTAAAGTTGCAGTGAAGCGAATTAAAACAAGTAGCAGATCTCA
* * *
23160 ATGTCCTTGAGGTTACAGTGAAACGGAGTAAAGTTACAACATCAAATCTTATACCCCTGAAGTTA
196 ATGTCCTTGAGGTTACAGTGGAATGGAGTAAAGTTACAACACCAAATCTTATA-CCCTGAAGTTA
23225 TAGTGGGTCGGATTAAAG
260 TAGTGGGTCGGATTAAAG
23243 CCAGAAGCAG
Statistics
Matches: 467, Mismatches: 87, Indels: 27
0.80 0.15 0.05
Matches are distributed among these distances:
286 1 0.00
287 242 0.52
288 2 0.00
292 106 0.23
293 3 0.01
297 1 0.00
298 108 0.23
299 4 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (286 bp):
TCCCTAAGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCTTATAACCCTAAAGTTGCAG
TGGGTCGGATTAAAGCCAAAAGCAAAACTCAATGTCCTTGAGGTTATAGTGGAATGGAGTGAAGC
TTCAATAACAAATCCTATCTTCCTAAAGTTGCAGTGAAGCGAATTAAAACAAGTAGCAGATCTCA
ATGTCCTTGAGGTTACAGTGGAATGGAGTAAAGTTACAACACCAAATCTTATACCCTGAAGTTAT
AGTGGGTCGGATTAAAGATCTCAAAA
Found at i:23246 original size:198 final size:198
Alignment explanation
Indices: 22367--23323 Score: 923
Period size: 198 Copynumber: 4.9 Consensus size: 198
22357 GTTACAAGAG
* *
22367 CAAGTAACAAATATCAATCTCCCTT-AGGTTACAGTGGAATGGAGTAAAGTTACAACACCAAATC
1 CAAGTAGCAAATCTCAATCT-CCTTGAGGTTACAGTGGAATGGAGTAAAGTTACAACACCAAATC
* * * * * * *
22431 TTATAACCCTGAAGTTGCAGTGGGTCGGATTAAAGCCAAAAGCAAAACTCAATGTCCCTAAAGTT
65 CTATACCCCTGAAGTTGCAGTGGGTCGGATTAAAGCCAGAAGCAGATCTCAATGTCCCTGAGGTT
* * * **
22496 ATAGTGGCATGGAGTGAAGCTT------CAAATCCTATCTTCCTAAAGTTGCGGTGAAGC-ATAT
130 ACAGTGGAATGGAGTGAAGCTTCAACAACAAATCCTATCTTCCTGAAGTTGCAATGAAGCGA-AT
22554 TAAAA
194 TAAAA
* * *
22559 CAAGTAACGAATCTCAATCTCCCTGAGGTTACAGTGGAATGGAGTAAAGTTACAACACCAAATCC
1 CAAGTAGCAAATCTCAATCTCCTTGAGGTTACAGTGGAATGGAGTAAAGTTACAACACCAAATCC
* * ** * ** *
22624 TATACCCTTGAGGTTATAGTGGGTCGGATTAAAATGACA-AAATAGATCTTAATGTCCCTGAGGT
66 TATACCCCTGAAGTTGCAGTGGGTCGGATT-AAA-GCCAGAAGCAGATCTCAATGTCCCTGAGGT
* * * * * * *
22688 TACAATGGAATAGAGTGAAGCTCCAACAACAAATCTTATCTTCCTTAAGTTGCAGTGAAGCGGAT
129 TACAGTGGAATGGAGTGAAGCTTCAACAACAAATCCTATCTTCCTGAAGTTGCAATGAAGCGAAT
*
22753 TAAAG
194 TAAAA
* ** * * * * * * ***
22758 CTACAAGCAGATCTCAATGTCCTTGAGGTTATAGTAGAATGGCGTGAAGCTT-CAACAATGAATC
1 CAAGTAGCAAATCTCAATCTCCTTGAGGTTACAGTGGAATGGAGTAAAG-TTACAACACCAAATC
* * * * * * * *
22822 CTAT-CTTCCTAAAGTTGCAGTGAAG-CGGATTAAAACAAGTAGCAGATCTCAATGTCCTTAAGG
65 CTATAC-CCCTGAAGTTGCAGTG-GGTCGGATTAAAGCCAGAAGCAGATCTCAATGTCCCTGAGG
* * * * * * * * * * *
22885 TTACAGTGGAATTGAATGAAGCTACTACACCAAATCTTATATCCCTGAAGTTGCAATGGATCGGA
128 TTACAGTGGAATGGAGTGAAGCTTCAACAACAAATCCTATCTTCCTGAAGTTGCAATGAAGCGAA
22950 TT----
193 TTAAAA
** * * *
22952 -AA--AG---ATCTCAAAATCCCTAAGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCC
1 CAAGTAGCAAATCTCAATCTCCTTGAGGTTACAGTGGAATGGAGTAAAGTTACAACACCAAATCC
* * * * * * *
23011 TATAACCCTAAAATTGCAGTGGGTCGAATTAAAGCCAGAAGCAAAACTCAATGTCCTTGAGGTTA
66 TATACCCCTGAAGTTGCAGTGGGTCGGATTAAAGCCAGAAGCAGATCTCAATGTCCCTGAGGTTA
*
23076 CAGTGGAATGGAGTGAAGCTTCAATAACAAATCCTATCTTCCTGAAGTTGCAATGAAGCGAATTA
131 CAGTGGAATGGAGTGAAGCTTCAACAACAAATCCTATCTTCCTGAAGTTGCAATGAAGCGAATTA
23141 AAA
196 AAA
* * * * *
23144 CAAGTAGCAAATCTCAATGTCCTTGAGGTTACAGTGAAACGGAGTAAAGTTACAACATCAAATCT
1 CAAGTAGCAAATCTCAATCTCCTTGAGGTTACAGTGGAATGGAGTAAAGTTACAACACCAAATCC
**
23209 TATACCCCTGAAGTTATAGTGGGTCGGATTAAAGCCAGAAGCAGATCTCAATGTCCCTGAGGTTA
66 TATACCCCTGAAGTTGCAGTGGGTCGGATTAAAGCCAGAAGCAGATCTCAATGTCCCTGAGGTTA
* *
23274 CAGTGGAATGGAGTGAAGCTTCAACAACCAATCCTATATTCCTGAAGTTG
131 CAGTGGAATGGAGTGAAGCTTCAACAACAAATCCTATCTTCCTGAAGTTG
23324 TAGTGAAGTT
Statistics
Matches: 613, Mismatches: 125, Indels: 48
0.78 0.16 0.06
Matches are distributed among these distances:
187 3 0.00
188 145 0.24
191 5 0.01
192 82 0.13
193 42 0.07
194 3 0.00
195 2 0.00
197 1 0.00
198 226 0.37
199 101 0.16
200 3 0.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (198 bp):
CAAGTAGCAAATCTCAATCTCCTTGAGGTTACAGTGGAATGGAGTAAAGTTACAACACCAAATCC
TATACCCCTGAAGTTGCAGTGGGTCGGATTAAAGCCAGAAGCAGATCTCAATGTCCCTGAGGTTA
CAGTGGAATGGAGTGAAGCTTCAACAACAAATCCTATCTTCCTGAAGTTGCAATGAAGCGAATTA
AAA
Found at i:23467 original size:50 final size:50
Alignment explanation
Indices: 23374--23733 Score: 344
Period size: 50 Copynumber: 7.2 Consensus size: 50
23364 CAAATATTAT
* * * ** ** * *
23374 AAGCTGTAAAGGAGCAGATTGAAGCTGGGAGGGAAAATTTTATACACCTA
1 AAGCTGTAGAGGGGCAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTA
* * *
23424 AAGTTGTAGAGGGGCAGATTGAAGCCGCGAGGGCTAATCTTATACCCCTA
1 AAGCTGTAGAGGGGCAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTA
* * * *
23474 GAGCTATAGAGGAGCAGATTGAAGCCGCAAGGGCGAATCTTATACACCTA
1 AAGCTGTAGAGGGGCAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTA
* * *
23524 AAGCTGTAGAGGGGCATATTGAAGCCCGTAAGGGTGAATCTTATACCCCTA
1 AAGCTGTAGAGGGGCAGATTGAAG-CCGCAAGGGCGAATCTTATACCCCTA
* * * * **
23575 AAGCTTTAGAGGAGCAGATTGAAGTCGCAAGAGCGAATCTTATACATCTA
1 AAGCTGTAGAGGGGCAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTA
* ** * * * *
23625 AAGCTGTAAAATGGCAGATTGAAGCCACAAGAGCAAATATTATACCCCTA
1 AAGCTGTAGAGGGGCAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTA
* * * * * * *
23675 AAGCTATAAAAGGGCAGATTGAAG-TGTAAAGACGAATCTTATACCCCTA
1 AAGCTGTAGAGGGGCAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTA
*
23724 AAGTTGTAGA
1 AAGCTGTAGA
23734 AAAGAGAATC
Statistics
Matches: 253, Mismatches: 56, Indels: 3
0.81 0.18 0.01
Matches are distributed among these distances:
49 24 0.09
50 185 0.73
51 44 0.17
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (50 bp):
AAGCTGTAGAGGGGCAGATTGAAGCCGCAAGGGCGAATCTTATACCCCTA
Found at i:23517 original size:100 final size:99
Alignment explanation
Indices: 23374--23733 Score: 384
Period size: 100 Copynumber: 3.6 Consensus size: 99
23364 CAAATATTAT
* * * ** ** * *
23374 AAGCTGTAAAGGAGCAGATTGAAGCTGGGAGGGAAAATTTTATACACCTAAAGTTGTAGAGGGGC
1 AAGCTATAGAGGAGCAGATTGAAGCCGCAAGGGCGAATCTTATACACCTAAAGCTGTAGAGGGGC
23439 AGATTGAAGCCGCGAGGGCTAATCTTATACCCCTA
66 AGATTGAAGCC-CGAGGGCTAATCTTATACCCCTA
*
23474 GAGCTATAGAGGAGCAGATTGAAGCCGCAAGGGCGAATCTTATACACCTAAAGCTGTAGAGGGGC
1 AAGCTATAGAGGAGCAGATTGAAGCCGCAAGGGCGAATCTTATACACCTAAAGCTGTAGAGGGGC
*
23539 ATATTGAAGCCCGTAAGGG-TGAATCTTATACCCCTA
66 AGATTGAAGCCCG--AGGGCT-AATCTTATACCCCTA
* * * * * **
23575 AAGCTTTAGAGGAGCAGATTGAAGTCGCAAGAGCGAATCTTATACATCTAAAGCTGTAAAATGGC
1 AAGCTATAGAGGAGCAGATTGAAGCCGCAAGGGCGAATCTTATACACCTAAAGCTGTAGAGGGGC
* * * *
23640 AGATTGAAGCCACAAGAGCAAATATTATACCCCTA
66 AGATTGAAGCC-CGAGGGCTAATCTTATACCCCTA
* * * * * * *
23675 AAGCTATAAAAGG-GCAGATTGAAG-TGTAAAGACGAATCTTATACCCCTAAAGTTGTAGA
1 AAGCTAT-AGAGGAGCAGATTGAAGCCGCAAGGGCGAATCTTATACACCTAAAGCTGTAGA
23734 AAAGAGAATC
Statistics
Matches: 219, Mismatches: 35, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
99 28 0.13
100 100 0.46
101 90 0.41
102 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (99 bp):
AAGCTATAGAGGAGCAGATTGAAGCCGCAAGGGCGAATCTTATACACCTAAAGCTGTAGAGGGGC
AGATTGAAGCCCGAGGGCTAATCTTATACCCCTA
Found at i:23604 original size:101 final size:100
Alignment explanation
Indices: 23413--23733 Score: 373
Period size: 101 Copynumber: 3.2 Consensus size: 100
23403 AGGGAAAATT
* * *
23413 TTATACACCTAAAGTTGTAGAGGGGCAGATTGAAGCCGCG-AGGGCTAATCTTATACCCCTAGAG
1 TTATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCCACGAAGGG-TAATCTTATACCCCTAAAG
* *
23477 CTATAGAGGAGCAGATTGAAGCCGCAAGGGCGAATC
65 CTTTAGAGGAGCAGATTGAAGTCGCAAGGGCGAATC
*
23513 TTATACACCTAAAGCTGTAGAGGGGCATATTGAAGCC-CGTAAGGGTGAATCTTATACCCCTAAA
1 TTATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCCACG-AAGGGT-AATCTTATACCCCTAAA
*
23577 GCTTTAGAGGAGCAGATTGAAGTCGCAAGAGCGAATC
64 GCTTTAGAGGAGCAGATTGAAGTCGCAAGGGCGAATC
* * ** ** *
23614 TTATACATCTAAAGCTGTAAAATGGCAGATTGAAGCCAC-AAGAGCAAATATTATACCCCTAAAG
1 TTATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCCACGAAG-GGTAATCTTATACCCCTAAAG
* * * * *
23678 CTATAAAAGG-GCAGATTGAAGT-GTAAAGACGAATC
65 CT-TTAGAGGAGCAGATTGAAGTCGCAAGGGCGAATC
* *
23713 TTATACCCCTAAAGTTGTAGA
1 TTATACACCTAAAGCTGTAGA
23734 AAAGAGAATC
Statistics
Matches: 191, Mismatches: 24, Indels: 13
0.84 0.11 0.06
Matches are distributed among these distances:
99 28 0.15
100 70 0.37
101 92 0.48
102 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (100 bp):
TTATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCCACGAAGGGTAATCTTATACCCCTAAAGC
TTTAGAGGAGCAGATTGAAGTCGCAAGGGCGAATC
Found at i:23614 original size:151 final size:149
Alignment explanation
Indices: 23413--23733 Score: 367
Period size: 151 Copynumber: 2.1 Consensus size: 149
23403 AGGGAAAATT
* * * * * * *
23413 TTATACACCTAAAGTTGTAGAGGGGCAGATTGAAGCCGCGAGGGCTAATCTTATACCCCTAGAGC
1 TTATACCCCTAAAGTTGTAGAGGAGCAGATTGAAGCCGCAAGAGCGAATCTTATACACCTAAAGC
* * * * * * * * *
23478 TAT-AGAGGAGCAGATTGAAGCCGCAAGGGCGAATCTTATACACCTAAAGCTGTAGAGGGGCATA
66 TATAAAAGG-GCAGATTGAAGCCACAAGAGCAAATATTATACACCTAAAGCTATAAAAGGGCAGA
* **
23542 TTGAAGCCCGTAAGGGTGAATC
130 TTGAAG--CGTAAAGACGAATC
* *
23564 TTATACCCCTAAAGCTT-TAGAGGAGCAGATTGAAGTCGCAAGAGCGAATCTTATACATCTAAAG
1 TTATACCCCTAAAG-TTGTAGAGGAGCAGATTGAAGCCGCAAGAGCGAATCTTATACACCTAAAG
* * *
23628 CTGTAAAATGGCAGATTGAAGCCACAAGAGCAAATATTATACCCCTAAAGCTATAAAAGGGCAGA
65 CTATAAAAGGGCAGATTGAAGCCACAAGAGCAAATATTATACACCTAAAGCTATAAAAGGGCAGA
*
23693 TTGAAGTGTAAAGACGAATC
130 TTGAAGCGTAAAGACGAATC
23713 TTATACCCCTAAAGTTGTAGA
1 TTATACCCCTAAAGTTGTAGA
23734 AAAGAGAATC
Statistics
Matches: 142, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
148 2 0.01
149 28 0.20
151 107 0.75
152 5 0.04
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (149 bp):
TTATACCCCTAAAGTTGTAGAGGAGCAGATTGAAGCCGCAAGAGCGAATCTTATACACCTAAAGC
TATAAAAGGGCAGATTGAAGCCACAAGAGCAAATATTATACACCTAAAGCTATAAAAGGGCAGAT
TGAAGCGTAAAGACGAATC
Found at i:23957 original size:14 final size:13
Alignment explanation
Indices: 23922--23963 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
23912 GTCTGGCCCT
*
23922 AAACAAAA-AAAA
1 AAACAAAACAAAC
23934 AAACAAAACAAAC
1 AAACAAAACAAAC
23947 AAACTAAAACAAAC
1 AAAC-AAAACAAAC
23961 AAA
1 AAA
23964 AAATCCTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 8 0.30
13 7 0.26
14 12 0.44
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.02
Consensus pattern (13 bp):
AAACAAAACAAAC
Found at i:24923 original size:30 final size:30
Alignment explanation
Indices: 24867--24923 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
24857 GAGGATGGAG
*
24867 AGAAGAAAGAAATTTTTATTAAAAAAACTA
1 AGAAGAAAGAAATTTTTATGAAAAAAACTA
*
24897 AGAAGAAAAGAAATTTTT-TGAGAAAAA
1 AGAAG-AAAGAAATTTTTATGAAAAAAA
24924 TTGGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.60, C:0.02, G:0.14, T:0.25
Consensus pattern (30 bp):
AGAAGAAAGAAATTTTTATGAAAAAAACTA
Found at i:25406 original size:24 final size:22
Alignment explanation
Indices: 25367--25411 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
25357 GTTTTTAAAA
*
25367 ATTAAATCCTTTTTATTTTTTG
1 ATTAAATCCTTTTTATGTTTTG
*
25389 ATTAAATTCTATTATTATGTTTT
1 ATTAAATCCT-TT-TTATGTTTT
25412 AAAAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 2 0.11
24 8 0.42
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (22 bp):
ATTAAATCCTTTTTATGTTTTG
Found at i:28292 original size:12 final size:12
Alignment explanation
Indices: 28257--28294 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
28247 CATTGGTTAG
*
28257 TATTAACAAAAA
1 TATTAATAAAAA
28269 TATTAATAAAAA
1 TATTAATAAAAA
28281 TATTAGATAAAAA
1 TATTA-ATAAAAA
28294 T
1 T
28295 TAAAAACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (12 bp):
TATTAATAAAAA
Found at i:28379 original size:12 final size:11
Alignment explanation
Indices: 28358--28387 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
28348 TAGACCTTAT
28358 TATATTAAATA
1 TATATTAAATA
28369 TATATTCAAATA
1 TATATT-AAATA
28381 TATATTA
1 TATATTA
28388 TCTATTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (11 bp):
TATATTAAATA
Found at i:33988 original size:45 final size:48
Alignment explanation
Indices: 33939--34036 Score: 130
Period size: 50 Copynumber: 2.1 Consensus size: 48
33929 TATTTAGTTT
*
33939 TTAAT-TTATTCAA-GAA-AAATTAGAAACGAAAAGAGATATTTTATC
1 TTAATATTATTCAATAAACAAATTAGAAACGAAAAGAGATATTTTATC
* *
33984 TTAATAATTTTTTAATAAACTAAATTAGAAACGAAAAGAGATATTTTATC
1 TTAAT-ATTATTCAATAAAC-AAATTAGAAACGAAAAGAGATATTTTATC
34034 TTA
1 TTA
34037 TTAATTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
45 5 0.11
47 6 0.13
48 2 0.04
50 32 0.71
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (48 bp):
TTAATATTATTCAATAAACAAATTAGAAACGAAAAGAGATATTTTATC
Found at i:34010 original size:50 final size:50
Alignment explanation
Indices: 33955--34055 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
33945 TATTCAAGAA
33955 AAATTAGAAACGAAAAGAGATATTTTATCTTAATAATTTTTTAATAAACT
1 AAATTAGAAACGAAAAGAGATATTTTATCTTAATAATTTTTTAATAAACT
*
34005 AAATTAGAAACGAAAAGAGATATTTTATCTTATTAATTTTTTAATAAACT
1 AAATTAGAAACGAAAAGAGATATTTTATCTTAATAATTTTTTAATAAACT
34055 A
1 A
34056 TTTTATAAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.39
Consensus pattern (50 bp):
AAATTAGAAACGAAAAGAGATATTTTATCTTAATAATTTTTTAATAAACT
Found at i:36997 original size:3 final size:3
Alignment explanation
Indices: 36989--37019 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
36979 TTAGAGATTT
*
36989 AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
37020 GACGATAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:37787 original size:111 final size:112
Alignment explanation
Indices: 37591--37806 Score: 380
Period size: 111 Copynumber: 1.9 Consensus size: 112
37581 AAATATTCTT
37591 GCATAACAAATTTAAGTCATAATCATTAAAAAGTGAAAACCAACAAACAAGTTGCAACCATGATT
1 GCATAACAAATTTAAGTCATAATCATT-AAAAGTGAAAACCAACAAACAAGTTGCAACCATGATT
* *
37656 AAAAAACTATAAAAGAAAGAAATAGATAAGAGAAGGAAAGAAAGGATG
65 AAAAAACAATAAAAGAAAGAAATAGATAAGAGAAAGAAAGAAAGGATG
*
37704 GCATAACAAATTTAAGTCATAATTATT-AAAGTGAAAACCAACAAACAAGTTGCAACCATGATTA
1 GCATAACAAATTTAAGTCATAATCATTAAAAGTGAAAACCAACAAACAAGTTGCAACCATGATTA
*
37768 AAAAACAATAGAAGAAAGAAATAGATAAGAGAAAGAAAG
66 AAAAACAATAAAAGAAAGAAATAGATAAGAGAAAGAAAG
37807 GACGTTAGCC
Statistics
Matches: 99, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
111 73 0.74
113 26 0.26
ACGTcount: A:0.56, C:0.11, G:0.15, T:0.18
Consensus pattern (112 bp):
GCATAACAAATTTAAGTCATAATCATTAAAAGTGAAAACCAACAAACAAGTTGCAACCATGATTA
AAAAACAATAAAAGAAAGAAATAGATAAGAGAAAGAAAGAAAGGATG
Found at i:38677 original size:55 final size:55
Alignment explanation
Indices: 38616--38735 Score: 143
Period size: 55 Copynumber: 2.2 Consensus size: 55
38606 CAAGCACTAC
* ** *
38616 ATGCGAGCTGCAGACAGAGAGCTTGTGAACTAAGATGGAGCTA-CGAACTAGTGAA
1 ATGCGAGCTGCAAACAGAGAGCTTACGAACTAAGACGGAG-TAGCGAACTAGTGAA
* * * *
38671 ATGCGAGTTGTAAACAGAGAGCTTACGAACTGAGACGGAGTAGCGAACTGGTGAA
1 ATGCGAGCTGCAAACAGAGAGCTTACGAACTAAGACGGAGTAGCGAACTAGTGAA
*
38726 GTGCGAGCTG
1 ATGCGAGCTG
38736 TCTCCAAGCA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 2 0.04
55 52 0.96
ACGTcount: A:0.33, C:0.16, G:0.33, T:0.18
Consensus pattern (55 bp):
ATGCGAGCTGCAAACAGAGAGCTTACGAACTAAGACGGAGTAGCGAACTAGTGAA
Found at i:38785 original size:80 final size:79
Alignment explanation
Indices: 38671--38861 Score: 247
Period size: 80 Copynumber: 2.4 Consensus size: 79
38661 AACTAGTGAA
* * * * *
38671 ATGCGAGTTGTAAACAGAGAGCTTACGAACTGAGACGGAGTAGCGAACTGGTGAAGTGCGAGCTG
1 ATGCGAGCTGTAAACAGAGAGCTTGCGAACTGAGACGAAGTAGCAAACTGGTGAAGTGCGAGCTA
*
38736 TCTCCAAGCACTGC
66 TCTCCAAACACTGC
* * * *
38750 ATGCGAGCTGTAAAAAAGAGAGCTTGCGAAGTGAGATGAAGTTGCAAACTGGTGAAGTGCGAGCT
1 ATGCGAGCTGT-AAACAGAGAGCTTGCGAACTGAGACGAAGTAGCAAACTGGTGAAGTGCGAGCT
* * *
38815 ATCTTCAAACATTGT
65 ATCTCCAAACACTGC
*
38830 ATGCGAGCTGCAAACAGAGAGCTTGCGAACTG
1 ATGCGAGCTGTAAACAGAGAGCTTGCGAACTG
38862 TCCGTGAGCA
Statistics
Matches: 95, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
79 29 0.31
80 66 0.69
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.20
Consensus pattern (79 bp):
ATGCGAGCTGTAAACAGAGAGCTTGCGAACTGAGACGAAGTAGCAAACTGGTGAAGTGCGAGCTA
TCTCCAAACACTGC
Found at i:54466 original size:96 final size:96
Alignment explanation
Indices: 54292--54466 Score: 246
Period size: 96 Copynumber: 1.8 Consensus size: 96
54282 ATTTTGGGAA
** * *
54292 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAATAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGACACAATATTTCA
54357 AAATCGAAGATAAAGAAACATTGCCTCGATC
66 AAATCGAAGATAAAGAAACATTGCCTCGATC
* * *
54388 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGACACAATA-TTTC
*
54452 GAAACTCGAA-ATAAA
65 -AAAATCGAAGATAAA
54467 AGAATATTAC
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
95 1 0.01
96 60 0.87
97 8 0.12
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGACACAATATTTCA
AAATCGAAGATAAAGAAACATTGCCTCGATC
Found at i:54804 original size:58 final size:58
Alignment explanation
Indices: 54706--55164 Score: 286
Period size: 59 Copynumber: 7.8 Consensus size: 58
54696 CGGATACTTT
* ** * * *
54706 GGGGCAAAATGGTAATTTTGGGAAAATTCGAAGTTAAAAATGGAATTCTTAGACATTCG
1 GGGGTAAAATGGTAATTTT-GGAAGTTTCGAGGTCAAAAATGGAATTTTTAGACATTCG
* * * * *
54765 GGGGTAAAAGGGTAATTTT-GAGAGTTTCGAGGTCCAAAATGGAGTTTTTGGACA-CCG
1 GGGGTAAAATGGTAATTTTGGA-AGTTTCGAGGTCAAAAATGGAATTTTTAGACATTCG
* * * *
54822 GGGGCAAAATGGTAATTTTGGAAGTTT-TAGGGTCAAAAATAGAATTTTTTGA-AGTTCG
1 GGGGTAAAATGGTAATTTTGGAAGTTTCGA-GGTCAAAAATGGAATTTTTAGACA-TTCG
* * *
54880 GGGGTAAAAATGG-AATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGA-AGTTCA
1 GGGGT-AAAATGGTAA-TTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTAGACA-TTCG
* * * * **
54939 AGGGTAAAAATGG-AATTTTTGGAAGTTTCAAGGTCAAAAATGGAATTTTTGGTA-GTTAA
1 GGGGT-AAAATGGTAA-TTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTAG-ACATTCG
* * *
54998 AGGGTAAAAATGG-AATTTTTGGAAGTTTCAAGGTCAAAAATGGAATTTTT-GAAAGTTC-
1 GGGGT-AAAATGGTAA-TTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTAGACA-TTCG
* * * * * *
55056 GAGGTCAAAAATGG-AATTTTTGGAAGTTTGGGGGT--AAAATGGAAGTTTTGGA-AGTTTTG
1 GGGGT--AAAATGGTAA-TTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTAGACA--TTCG
* * *
55115 GGGTCTAAAATGG-AATTTTTGGAAG-TTCGGGGGTAAAAAATGGAATTTTT
1 GGG-GTAAAATGGTAA-TTTTGGAAGTTTC-GAGGTCAAAAATGGAATTTTT
55165 GGAAGTTTTA
Statistics
Matches: 337, Mismatches: 44, Indels: 37
0.81 0.11 0.09
Matches are distributed among these distances:
56 2 0.01
57 61 0.18
58 66 0.20
59 193 0.57
60 15 0.04
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTAGACATTCG
Found at i:54876 original size:30 final size:30
Alignment explanation
Indices: 54827--55202 Score: 439
Period size: 30 Copynumber: 12.7 Consensus size: 30
54817 CACCGGGGGC
*
54827 AAAATGGTAA-TTTTGGAAGTTTTAGGGTCA
1 AAAATGG-AATTTTTGGAAGTTTGAGGGTCA
* * * *
54857 AAAATAGAATTTTTTGAAGTTCGGGGGT-A
1 AAAATGGAATTTTTGGAAGTTTGAGGGTCA
54886 AAAATGGAATTTTTGGAAGTTTCG-GGGTCA
1 AAAATGGAATTTTTGGAAGTTT-GAGGGTCA
**
54916 AAAATGGAATTTTTGGAAGTTCAAGGGT-A
1 AAAATGGAATTTTTGGAAGTTTGAGGGTCA
* *
54945 AAAATGGAATTTTTGGAAGTTTCAAGGTCA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTCA
* **
54975 AAAATGGAATTTTTGGTAGTTAAAGGGT-A
1 AAAATGGAATTTTTGGAAGTTTGAGGGTCA
* *
55004 AAAATGGAATTTTTGGAAGTTTCAAGGTCA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTCA
* *
55034 AAAATGGAATTTTTGAAAGTTCGA-GGTCA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTCA
*
55063 AAAATGGAATTTTTGGAAGTTTGGGGGT--
1 AAAATGGAATTTTTGGAAGTTTGAGGGTCA
* *
55091 AAAATGGAAGTTTTGGAAGTTTTG-GGGTCT
1 AAAATGGAATTTTTGGAAG-TTTGAGGGTCA
* * *
55121 AAAATGGAATTTTTGGAAGTTCGGGGGTAA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTCA
*
55151 AAAATGGAATTTTTGGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTCA
55181 AAAAT-GATATTTTTGGAAGTTT
1 AAAATGGA-ATTTTTGGAAGTTT
55203 CGAGACCTCT
Statistics
Matches: 298, Mismatches: 36, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
28 22 0.07
29 112 0.38
30 164 0.55
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.35
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTGAGGGTCA
Found at i:54906 original size:59 final size:60
Alignment explanation
Indices: 54827--55203 Score: 457
Period size: 59 Copynumber: 6.4 Consensus size: 60
54817 CACCGGGGGC
* * * **
54827 AAAATGGTAA-TTTTGGAAGTTTTAGGGTCAAAAATAGAATTTTTTGAAGTTCGGGGGT-A
1 AAAATGG-AATTTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCAAGGGTCA
*
54886 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCAAGGGT-A
1 AAAATGGAATTTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCAAGGGTCA
* * *
54945 AAAATGGAATTTTTGGAAGTTTCAAGGTCAAAAATGGAATTTTTGGTAGTTAAAGGGT-A
1 AAAATGGAATTTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCAAGGGTCA
* * *
55004 AAAATGGAATTTTTGGAAGTTTCAAGGTCAAAAATGGAATTTTTGAAAGTTCGA-GGTCA
1 AAAATGGAATTTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCAAGGGTCA
** * *** *
55063 AAAATGGAATTTTTGGAAGTTTGGGGGT--AAAATGGAAGTTTTGGAAGTTTTGGGGTCT
1 AAAATGGAATTTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCAAGGGTCA
* * **
55121 AAAATGGAATTTTTGGAAG-TTCGGGGGTAAAAAATGGAATTTTTGGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTC-AGGGTCAAAAATGGAATTTTTGGAAGTTCAAGGGTCA
55181 AAAAT-GATATTTTTGGAAGTTTC
1 AAAATGGA-ATTTTTGGAAGTTTC
55204 GAGACCTCTT
Statistics
Matches: 283, Mismatches: 27, Indels: 14
0.87 0.08 0.04
Matches are distributed among these distances:
57 21 0.07
58 33 0.12
59 183 0.65
60 43 0.15
61 3 0.01
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (60 bp):
AAAATGGAATTTTTGGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCAAGGGTCA
Done.