Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003818.1 Kokia drynarioides strain JFW-HI SEQ_116814, 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: 50228
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:205 original size:16 final size:17
Alignment explanation
Indices: 172--208 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
162 TTTTTTTTCC
172 TCTCCTTCTTCCCCTTAT
1 TCTCCTTCTT-CCCTTAT
190 TCTCCTTCTT-CCTTAT
1 TCTCCTTCTTCCCTTAT
206 TCT
1 TCT
209 TTCTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
18 10 0.53
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (17 bp):
TCTCCTTCTTCCCTTAT
Found at i:1021 original size:21 final size:22
Alignment explanation
Indices: 997--1055 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 22
987 TATTGTTAGT
*
997 ATTATTATAAAAATTG-TAAAA
1 ATTATTATAAAAATTGAAAAAA
*
1018 ATTA-TAAAAGAAATTGAAAAAA
1 ATTATTATAA-AAATTGAAAAAA
1040 ATTAATATATAAAAAT
1 ATT-AT-TATAAAAAT
1056 AATATTAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
20 4 0.13
21 10 0.33
22 7 0.23
23 1 0.03
24 4 0.13
25 4 0.13
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (22 bp):
ATTATTATAAAAATTGAAAAAA
Found at i:4080 original size:19 final size:18
Alignment explanation
Indices: 4058--4107 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
4048 AATTATGAAT
4058 CAAAATAAATAAGAAAATA
1 CAAAATAAATAA-AAAATA
* *
4077 CAAAATTAATTAAAAATA
1 CAAAATAAATAAAAAATA
4095 -AAAA-AAATTAAAA
1 CAAAATAAA-TAAAA
4108 TTTATATACG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 2 0.08
17 8 0.31
18 6 0.23
19 10 0.38
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.20
Consensus pattern (18 bp):
CAAAATAAATAAAAAATA
Found at i:4196 original size:29 final size:28
Alignment explanation
Indices: 4164--4342 Score: 146
Period size: 29 Copynumber: 6.1 Consensus size: 28
4154 AGTTTCAGAG
*
4164 AGTTTGGGGTTAAAAATGTAATTTTTGAA
1 AGTTAGGGG-TAAAAATGTAATTTTTGAA
* *
4193 AGTTCAAGGGTAAAAATGTAATTTTGGAGA
1 AGTT-AGGGGTAAAAATGTAATTTTTGA-A
* * *
4223 AGTTCGAGGGT-AAAATGTGATTTTTGGA
1 AGTTAG-GGGTAAAAATGTAATTTTTGAA
* *
4251 AGTTTAGGGGT-AAAATGTGATTTTTGGA
1 AG-TTAGGGGTAAAAATGTAATTTTTGAA
*
4279 AGTTCAAGGGTAAAAATGTAATTTTTGATA
1 AGTT-AGGGGTAAAAATGTAATTTTTGA-A
* * * *
4309 AGTTCAAGGGTTAAAATGCAATTTTGGCAA
1 AGTT-AGGGGTAAAAATGTAATTTTTG-AA
4339 AGTT
1 AGTT
4343 TGAGGGTCAA
Statistics
Matches: 127, Mismatches: 15, Indels: 15
0.81 0.10 0.10
Matches are distributed among these distances:
27 2 0.02
28 31 0.24
29 51 0.40
30 42 0.33
31 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (28 bp):
AGTTAGGGGTAAAAATGTAATTTTTGAA
Found at i:4233 original size:30 final size:30
Alignment explanation
Indices: 4174--4333 Score: 204
Period size: 29 Copynumber: 5.5 Consensus size: 30
4164 AGTTTGGGGT
4174 TAAAAATGTAATTTTTGA-AAGTTCAAGGG
1 TAAAAATGTAATTTTTGAGAAGTTCAAGGG
* *
4203 TAAAAATGTAATTTTGGAGAAGTTCGAGGG
1 TAAAAATGTAATTTTTGAGAAGTTCAAGGG
* * *
4233 T-AAAATGTGATTTTTG-GAAGTTTAGGGG
1 TAAAAATGTAATTTTTGAGAAGTTCAAGGG
*
4261 T-AAAATGTGATTTTTG-GAAGTTCAAGGG
1 TAAAAATGTAATTTTTGAGAAGTTCAAGGG
*
4289 TAAAAATGTAATTTTTGATAAGTTCAAGGG
1 TAAAAATGTAATTTTTGAGAAGTTCAAGGG
* *
4319 TTAAAATGCAATTTT
1 TAAAAATGTAATTTT
4334 GGCAAAGTTT
Statistics
Matches: 115, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
28 36 0.31
29 44 0.38
30 35 0.30
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.36
Consensus pattern (30 bp):
TAAAAATGTAATTTTTGAGAAGTTCAAGGG
Found at i:4334 original size:86 final size:88
Alignment explanation
Indices: 4176--4364 Score: 251
Period size: 86 Copynumber: 2.2 Consensus size: 88
4166 TTTGGGGTTA
* *
4176 AAAATGTAATTTTTGAAAGTTCAAGGGTAAAAATGTAATTTTGGAGAAGTTCGAGGGTAAAATGT
1 AAAATGTGATTTTTGAAAGTTCAAGGGTAAAAATGTAATTTTGGAGAAGTTCAAGGGTAAAATGT
* *
4241 GATTTTTGG-AAGTTT-AGGGGT-
66 CAATTTTGGAAAGTTTGA-GGGTC
* * *
4262 AAAATGTGATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGATAAGTTCAAGGGTTAAAATG
1 AAAATGTGATTTTTGAAAGTTCAAGGGTAAAAATGTAATTTTGGAGAAGTTCAAGGG-TAAAATG
4327 -CAATTTTGGCAAAGTTTGAGGGTC
65 TCAATTTTGG-AAAGTTTGAGGGTC
*
4351 AAAATATGATTTTT
1 AAAATGTGATTTTT
4365 AGACAATTTA
Statistics
Matches: 90, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
86 59 0.66
87 7 0.08
88 10 0.11
89 14 0.16
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (88 bp):
AAAATGTGATTTTTGAAAGTTCAAGGGTAAAAATGTAATTTTGGAGAAGTTCAAGGGTAAAATGT
CAATTTTGGAAAGTTTGAGGGTC
Found at i:4355 original size:30 final size:28
Alignment explanation
Indices: 4176--4342 Score: 176
Period size: 30 Copynumber: 5.8 Consensus size: 28
4166 TTTGGGGTTA
*
4176 AAAATGTAATTTTTGAAAGTTCAAGGGT
1 AAAATGTAATTTTGGAAAGTTCAAGGGT
*
4204 AAAAATGTAATTTTGGAGAAGTTCGAGGGT
1 -AAAATGTAATTTTGGA-AAGTTCAAGGGT
* * *
4234 AAAATGTGATTTTTGG-AAGTTTAGGGGT
1 AAAATGT-AATTTTGGAAAGTTCAAGGGT
*
4262 AAAATGTGATTTTTGG-AAGTTCAAGGGT
1 AAAATGT-AATTTTGGAAAGTTCAAGGGT
*
4290 AAAAATGTAATTTTTGATAAGTTCAAGGGTT
1 -AAAATGTAATTTTGGA-AAGTTCAAGGG-T
*
4321 AAAATGCAATTTTGGCAAAGTT
1 AAAATGTAATTTTGG-AAAGTT
4343 TGAGGGTCAA
Statistics
Matches: 119, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
28 41 0.34
29 29 0.24
30 47 0.39
31 2 0.02
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (28 bp):
AAAATGTAATTTTGGAAAGTTCAAGGGT
Found at i:6058 original size:12 final size:11
Alignment explanation
Indices: 6052--6119 Score: 52
Period size: 11 Copynumber: 6.0 Consensus size: 11
6042 TAATTAAATT
6052 TTAAATTTAAA
1 TTAAATTTAAA
*
6063 TTCAAA-ATAAA
1 TT-AAATTTAAA
6074 TTTAAATTTTAAA
1 -TTAAA-TTTAAA
6087 -TAAATTTAAA
1 TTAAATTTAAA
*
6097 CTTAAA-ATAAA
1 -TTAAATTTAAA
6108 TTGAAATTTAAA
1 TT-AAATTTAAA
6120 ATTTAAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 15
0.70 0.06 0.23
Matches are distributed among these distances:
10 8 0.18
11 20 0.44
12 13 0.29
13 4 0.09
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:6062 original size:6 final size:6
Alignment explanation
Indices: 6045--6126 Score: 64
Period size: 6 Copynumber: 13.8 Consensus size: 6
6035 GGATTTTTAA
* *
6045 TTAAATT TTAAAT TTAAAT TCAAA- ATAAAT TTAAATT TTAAA- -TAAAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT TTAAAT
* * *
6092 TTAAAC TTAAA- ATAAAT TGAAAT TTAAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TTAAA
6127 ATTGAGTTCA
Statistics
Matches: 60, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
4 4 0.07
5 7 0.12
6 32 0.53
7 17 0.28
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:6073 original size:17 final size:17
Alignment explanation
Indices: 6053--6121 Score: 102
Period size: 17 Copynumber: 4.1 Consensus size: 17
6043 AATTAAATTT
*
6053 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
*
6070 TAAATTTAAATTTTAAA
1 TAAATTTAAATTTAAAA
*
6087 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
6104 TAAATTGAAATTTAAAA
1 TAAATTTAAATTTAAAA
6121 T
1 T
6122 TTAAAATTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 46 1.00
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:6096 original size:23 final size:23
Alignment explanation
Indices: 6043--6126 Score: 66
Period size: 23 Copynumber: 3.6 Consensus size: 23
6033 TTGGATTTTT
6043 AATTAAATTTTAAATTTAAATTCA
1 AATTAAA-TTTAAATTTAAATTCA
*
6067 AAATAAATTTAAATTTTAAA-T-A
1 AATTAAATTTAAA-TTTAAATTCA
* * *
6089 AATTTAAACTTAAA-ATAAATTGA
1 AA-TTAAATTTAAATTTAAATTCA
6112 AATTTAAAATTTAAA
1 AA-TT-AAATTTAAA
6127 ATTGAGTTCA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
21 4 0.08
22 4 0.08
23 22 0.44
24 20 0.40
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (23 bp):
AATTAAATTTAAATTTAAATTCA
Found at i:6446 original size:23 final size:23
Alignment explanation
Indices: 6385--6448 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
6375 TGTCTTCTAA
6385 TATTTTT-GAAGGTTATAATT-TTG
1 TATTTTTAGAA-GTTAT-ATTATTG
* *
6408 TA-TCTTA-AATTTATATTATTG
1 TATTTTTAGAAGTTATATTATTG
6429 TATTTTTAGAAGTTATATTA
1 TATTTTTAGAAGTTATATTA
6449 GACCTGTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 3 0.09
21 9 0.27
22 9 0.27
23 12 0.36
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (23 bp):
TATTTTTAGAAGTTATATTATTG
Found at i:22451 original size:21 final size:21
Alignment explanation
Indices: 22425--22488 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
22415 TTTAAAATAA
* *
22425 GACTAAGTCCTAGGGGGATTT
1 GACTAAGTCCTAAGGAGATTT
22446 GACTAAGTCCTAAGGAGATTT
1 GACTAAGTCCTAAGGAGATTT
22467 GACTAAGTCC-AAGAGAGATTT
1 GACTAAGTCCTAAG-GAGATTT
22488 G
1 G
22489 TTGGCTTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
20 3 0.08
21 37 0.93
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (21 bp):
GACTAAGTCCTAAGGAGATTT
Found at i:27747 original size:89 final size:88
Alignment explanation
Indices: 27583--27985 Score: 298
Period size: 89 Copynumber: 4.5 Consensus size: 88
27573 TGAAAGTTTG
* * * * * * *
27583 GGGTTAAAATGTGATTTTGGAAAAGTTTAAGAG-AAAAAAGTAATTTTGGAGAAATTT-AGGATG
1 GGGTAAAAATATGATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAGAGAAATTTAAGG-T-
* *** *
27646 AAAATATTATTTTAGAAAAACTTGA
64 TAAATGCAATTTTAGAAAAACTTAA
* * * * *
27671 GGGTTAAAATATAAGTTTGGAGAAGTTTAGGGGTCAAATTGTAATTTTAGAGAAATTTAAGTGTT
1 GGGTAAAAATATGATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAGAGAAATTTAAG-GTT
* ** *
27736 AAATGCAATTTTGGAAAAGTTTAG
65 AAATGCAATTTTAGAAAAACTTAA
* * * * *
27760 GGGTGAAAATGTGATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTAGAGAAGTTTAGCGGTT
1 GGGTAAAAATATGATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAGAGAAATTTA-AGGTT
* **
27825 AAATTGAAATTTTA-AAGAAGTTTAA
65 AAA-TGCAATTTTAGAA-AAACTTAA
*
27850 GGGTAAAAATTATGATTTTGGAAAAGCTT-GGGGTCAAAATGTAATTTTAGAG-AATTTCATAGG
1 GGGTAAAAA-TATGATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAGAGAAATTT-A-AGG
* * **
27913 TTAAAATGCAATTTTGGAGAAGTTTAA
63 TT-AAATGCAATTTTAGAAAAACTTAA
* * * * * * *
27940 -TGTCAAAATGTAATTTTGGAAAAGTTTA-GAGTGAAAATGTGATTTT
1 GGGTAAAAATATGATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTT
27986 GAAAATGTTT
Statistics
Matches: 255, Mismatches: 49, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
88 58 0.23
89 105 0.41
90 70 0.27
91 22 0.09
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (88 bp):
GGGTAAAAATATGATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAGAGAAATTTAAGGTTA
AATGCAATTTTAGAAAAACTTAA
Found at i:27749 original size:59 final size:60
Alignment explanation
Indices: 27576--28015 Score: 280
Period size: 59 Copynumber: 7.4 Consensus size: 60
27566 AATTTTATGA
* * * * * * *
27576 AAGTTT-GGGGTTAAAATGTGATTTTGGA-AAAGTTTAAGAG-AAAAAAGTAATTTTGGAG
1 AAGTTTAGGGGTCAAAATGTAATTTTAGAGAAA-TTTAAGGGTTAAAATGCAATTTTGGAG
* * * * * * * * ** *
27634 AAATTTA-GGATGAAAATATTATTTTAGAAAAACTTGAGGGTTAAAATATAAGTTTGGAG
1 AAGTTTAGGGGTCAAAATGTAATTTTAGAGAAATTTAAGGGTTAAAATGCAATTTTGGAG
* * *
27693 AAGTTTAGGGGTCAAATTGTAATTTTAGAGAAATTTAAGTGTT-AAATGCAATTTTGGAA
1 AAGTTTAGGGGTCAAAATGTAATTTTAGAGAAATTTAAGGGTTAAAATGCAATTTTGGAG
* * * * * *
27752 AAGTTTAGGGGTGAAAATGTGATTTTGGA-AAAGTTTAGGGGTTAAAATGTAATTTTAGAG
1 AAGTTTAGGGGTCAAAATGTAATTTTAGAGAAA-TTTAAGGGTTAAAATGCAATTTTGGAG
* * * * * * * * *
27812 AAGTTTAGCGGTTAAATTGAAATTTTAAAGAAGTTTAAGGGTAAAAAT-TATGATTTTGGAA
1 AAGTTTAGGGGTCAAAATGTAATTTTAGAGAAATTTAAGGGTTAAAATGCA--ATTTTGGAG
*
27873 AAGCTT-GGGGTCAAAATGTAATTTTAGAG-AATTTCATA-GGTTAAAATGCAATTTTGGAG
1 AAGTTTAGGGGTCAAAATGTAATTTTAGAGAAATTT-A-AGGGTTAAAATGCAATTTTGGAG
** * * * ** *
27932 AAGTTTA-ATGTCAAAATGTAATTTTGGA-AAAGTTT-AGAGTGAAAATGTGATTTT-GAA
1 AAGTTTAGGGGTCAAAATGTAATTTTAGAGAAA-TTTAAGGGTTAAAATGCAATTTTGGAG
*
27989 AATGTTT-GAGGGTCAAAATGTGATTTT
1 AA-GTTTAG-GGGTCAAAATGTAATTTT
28016 TGGGTAAAAT
Statistics
Matches: 293, Mismatches: 70, Indels: 37
0.73 0.17 0.09
Matches are distributed among these distances:
57 5 0.02
58 46 0.16
59 122 0.42
60 104 0.35
61 16 0.05
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.35
Consensus pattern (60 bp):
AAGTTTAGGGGTCAAAATGTAATTTTAGAGAAATTTAAGGGTTAAAATGCAATTTTGGAG
Found at i:27777 original size:30 final size:30
Alignment explanation
Indices: 27575--28015 Score: 273
Period size: 30 Copynumber: 14.9 Consensus size: 30
27565 TAATTTTATG
*
27575 AAAGTTT-GGGGTTAAAATGTGATTTTGGA
1 AAAGTTTAGGGGTTAAAATGTAATTTTGGA
* * * *
27604 AAAGTTTAAGAG-AAAAAAGTAATTTTGGA
1 AAAGTTTAGGGGTTAAAATGTAATTTTGGA
* * * * *
27633 GAAA-TTTA-GGATGAAAATATTATTTTAGA
1 -AAAGTTTAGGGGTTAAAATGTAATTTTGGA
** * *
27662 AAAACTT-GAGGGTTAAAATATAAGTTTGGA
1 AAAGTTTAG-GGGTTAAAATGTAATTTTGGA
* * * *
27692 GAAGTTTAGGGGTCAAATTGTAATTTTAGA
1 AAAGTTTAGGGGTTAAAATGTAATTTTGGA
* * *
27722 GAAA-TTTAAGTGTT-AAATGCAATTTTGGA
1 -AAAGTTTAGGGGTTAAAATGTAATTTTGGA
* *
27751 AAAGTTTAGGGGTGAAAATGTGATTTTGGA
1 AAAGTTTAGGGGTTAAAATGTAATTTTGGA
*
27781 AAAGTTTAGGGGTTAAAATGTAATTTTAGA
1 AAAGTTTAGGGGTTAAAATGTAATTTTGGA
* * * * *
27811 GAAGTTTAGCGGTTAAATTGAAATTTT-AA
1 AAAGTTTAGGGGTTAAAATGTAATTTTGGA
* *
27840 AGAAGTTTAAGGGTAAAAAT-TATGATTTTGGA
1 A-AAGTTTAGGGGTTAAAATGTA--ATTTTGGA
* * *
27872 AAAGCTT-GGGGTCAAAATGTAATTTTAGA
1 AAAGTTTAGGGGTTAAAATGTAATTTTGGA
* ** *
27901 GAA-TTTCATAGGTTAAAATGCAATTTTGGA
1 AAAGTTT-AGGGGTTAAAATGTAATTTTGGA
* ** *
27931 GAAGTTTA-ATGTCAAAATGTAATTTTGGA
1 AAAGTTTAGGGGTTAAAATGTAATTTTGGA
* * *
27960 AAAGTTTA-GAGTGAAAATGTGATTTT-GA
1 AAAGTTTAGGGGTTAAAATGTAATTTTGGA
* *
27988 AAATGTTT-GAGGGTCAAAATGTGATTTT
1 AAA-GTTTAG-GGGTTAAAATGTAATTTT
28016 TGGGTAAAAT
Statistics
Matches: 317, Mismatches: 74, Indels: 41
0.73 0.17 0.09
Matches are distributed among these distances:
28 14 0.04
29 112 0.35
30 171 0.54
31 18 0.06
32 2 0.01
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (30 bp):
AAAGTTTAGGGGTTAAAATGTAATTTTGGA
Found at i:27883 original size:90 final size:89
Alignment explanation
Indices: 27686--27985 Score: 312
Period size: 90 Copynumber: 3.4 Consensus size: 89
27676 AAAATATAAG
* * *
27686 TTTGGAGAAGTTTAGGGGTCAAATTGTAATTTTAGAGAAATTTAAGTGTTAAATGCAATTTTGGA
1 TTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAGAG-AATTTAAGGGTTAAATGCAATTTT-GA
* * *
27751 A-AAGTTTAGGGGTGAAAA-TGTGAT
64 AGAAGTTTAAGGGTAAAAATTATGAT
* * *
27775 TTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTAGAGAAGTTT-AGCGGTTAAATTGAAATTTTA
1 TTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAGAGAA-TTTAAG-GGTTAAA-TGCAATTTTG
27839 AAGAAGTTTAAGGGTAAAAATTATGAT
63 AAGAAGTTTAAGGGTAAAAATTATGAT
*
27866 TTTGGAAAAGCTT-GGGGTCAAAATGTAATTTTAGAGAATTTCATA-GGTTAAAATGCAATTTTG
1 TTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAGAGAATTT-A-AGGGTT-AAATGCAATTTTG
* * *
27929 GAGAAGTTTAA-TGTCAAAATGTA--AT
63 AAGAAGTTTAAGGGTAAAAAT-TATGAT
* * *
27954 TTTGGAAAAGTTTA-GAGTGAAAATGTGATTTT
1 TTTGGAAAAGTTTAGGGGTCAAAATGTAATTTT
27986 GAAAATGTTT
Statistics
Matches: 180, Mismatches: 20, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
88 33 0.18
89 55 0.31
90 71 0.39
91 20 0.11
92 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (89 bp):
TTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAGAGAATTTAAGGGTTAAATGCAATTTTGAAG
AAGTTTAAGGGTAAAAATTATGAT
Found at i:30165 original size:207 final size:207
Alignment explanation
Indices: 29799--30207 Score: 674
Period size: 207 Copynumber: 2.0 Consensus size: 207
29789 GCTTCATTTC
* ****
29799 TTGGTCTACTCCTCTGTATCTCATCAAGAAGATGATGGTTTTATTACTTCGACCCACTTCTCTGT
1 TTGGTCCACTCCTCTGTATCTCATCAAGAAGATGACCACTTTATTACTTCGACCCACTTCTCTGT
* *
29864 ATCTCATCAAGAAGATGGGGTTTGAAGTCTTATTCGTATTGAGCTTTGCTTCATTGATTTGGTCT
66 ATCTCATCAAGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCT
29929 ACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTCAATCCACTTATCTATATCTCAT
131 ACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTCAATCCACTTATCTATATCTCAT
29994 CAGGAAGGCAGA
196 CAGGAAGGCAGA
* * * * * * *
30006 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCTATTTCTTTGT
1 TTGGTCCACTCCTCTGTATCTCATCAAGAAGATGACCACTTTATTACTTCGACCCACTTCTCTGT
*
30071 ATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCT
66 ATCTCATCAAGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCT
*
30136 ACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTCAATCCACTTCTCTATATCTCAT
131 ACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTCAATCCACTTATCTATATCTCAT
30201 CAGGAAG
196 CAGGAAG
30208 ATGAGCACTT
Statistics
Matches: 186, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
207 186 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (207 bp):
TTGGTCCACTCCTCTGTATCTCATCAAGAAGATGACCACTTTATTACTTCGACCCACTTCTCTGT
ATCTCATCAAGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCT
ACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTCAATCCACTTATCTATATCTCAT
CAGGAAGGCAGA
Found at i:30174 original size:48 final size:48
Alignment explanation
Indices: 30119--30258 Score: 199
Period size: 48 Copynumber: 2.9 Consensus size: 48
30109 TTGAGCTTCG
* *
30119 CTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCA
1 CTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGACCA
** * *
30167 CTTCATTGATTCAATCCACTTCTCTATATCTCATCAGGAAGATGAGCA
1 CTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGACCA
* * *
30215 CTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATG
1 CTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATG
30259 GAGTTTGAAG
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 80 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (48 bp):
CTTCATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGACCA
Found at i:30295 original size:171 final size:171
Alignment explanation
Indices: 30010--30378 Score: 630
Period size: 171 Copynumber: 2.2 Consensus size: 171
30000 GGCAGATTGG
* * *
30010 TCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCTATTTCTTTGTATCT
1 TCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTGTATCT
*
30075 CATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTT
66 CATCAGGAAGATGGAGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTT
30140 CTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTCAA
131 CTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTCAA
* *
30181 TCCACTTCTCTATATCTCATCAGGAAGATGAGCACTTTATTGCTTTGACCCACTTCTCTGTATCT
1 TCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTGTATCT
*
30246 CATCAGGAAGATGGAGTTTGAAGTTTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTT
66 CATCAGGAAGATGGAGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTT
**
30311 CTCTGTATCTCATCAGGAAGATGACTGCTTCATTGATTCAA
131 CTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTCAA
* * *
30352 TCCACTTGTTTGTATCTCATCAAGAAG
1 TCCACTTCTCTGTATCTCATCAGGAAG
30379 GCGAATTTGG
Statistics
Matches: 185, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
171 185 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (171 bp):
TCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTGTATCT
CATCAGGAAGATGGAGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTT
CTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTCAA
Found at i:30442 original size:85 final size:85
Alignment explanation
Indices: 30298--30458 Score: 214
Period size: 85 Copynumber: 1.9 Consensus size: 85
30288 CGCTTCATTG
** * * *
30298 ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTGATTCAATCCACTTGTTT
1 ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTCAACCCACTTCTCT
30363 GTATCTCATCAAGAAGGCGA
66 GTATCTCATCAAGAAGGCGA
* * * * **
30383 ATTTGGTCTACTTCTTTGTATCTCATCAGGGAGATGACCACTTTATTGCTTTGACCCACTTCTCT
1 ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTCAACCCACTTCTCT
*
30448 GTATCTTATCA
66 GTATCTCATCA
30459 GAAAGATGAG
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
85 64 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (85 bp):
ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTCAACCCACTTCTCT
GTATCTCATCAAGAAGGCGA
Found at i:30561 original size:208 final size:208
Alignment explanation
Indices: 30181--30641 Score: 710
Period size: 208 Copynumber: 2.2 Consensus size: 208
30171 ATTGATTCAA
* * *
30181 TCCACTTCTCTATATCTCATCAGGAAGATGAGCACTTTATTGCTTTGACCCACTTCTCTGTATCT
1 TCCACTTCTTTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTGTATCT
* * *
30246 CATCAGGAAGATGGAGTTTGAAGTTTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTT
66 CATCAGAAAGATGGAGTTTGAAGTCTCACTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTT
* * * * *
30311 CTCTGTATCTCATCAGGAAGATGACTGCTTCATTGATTCAATCCACTTGTTTGTATCTCATCAAG
131 CTCTATATCTCATCAGGAAGATGACCGCCTCATTGATTCAATCCACTTCTCTGTATCTCATCAAG
*
30376 AAGGCGAATTTGG
196 AAGACGAATTTGG
* *
30389 TCTACTTCTTTGTATCTCATCAGGGAGATGACCACTTTATTGCTTTGACCCACTTCTCTGTATCT
1 TCCACTTCTTTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTGTATCT
* *
30454 TATCAGAAAGAT-GAGGTTTGAAGTCTCACTCGTATTGAGCTTCGCTTTATTGATTTGGTCTACT
66 CATCAGAAAGATGGA-GTTTGAAGTCTCACTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACT
* * *
30518 TTTCTATATCTCATTAGGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAA
130 TCTCTATATCTCATCAGGAAGATGACCGCCTCATTGATTCAATCCACTTCTCTGTATCTCATCAA
30583 GAAGACGAATTTGG
195 GAAGACGAATTTGG
*
30597 TCCACTT-TTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTT
1 TCCACTTCTT-TGTATCTCATCAGGAAGATGACCACTTTATTGCTT
30642 CGGATGATTG
Statistics
Matches: 229, Mismatches: 22, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
207 4 0.02
208 225 0.98
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (208 bp):
TCCACTTCTTTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTGTATCT
CATCAGAAAGATGGAGTTTGAAGTCTCACTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTT
CTCTATATCTCATCAGGAAGATGACCGCCTCATTGATTCAATCCACTTCTCTGTATCTCATCAAG
AAGACGAATTTGG
Found at i:30711 original size:39 final size:39
Alignment explanation
Indices: 30652--30818 Score: 201
Period size: 39 Copynumber: 4.3 Consensus size: 39
30642 CGGATGATTG
*
30652 CAATCTGCCCTATGATCGGGGTAAGAGATTGAATGGCTA
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGAATGGCTA
* * * *
30691 CAATTTGCCCCATGATCGGGGTAAGAGATTGGATGACTG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGAATGGCTA
** * *
30730 CAATCTGCCTAATGATCGAGGTAAGAGATT-AGATGGCTG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGA-ATGGCTA
* * * *
30769 CAATCTACCCCATGATCGGTGTAAGAGATTGGATGGTTA
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGAATGGCTA
30808 CAATCTGCCCC
1 CAATCTGCCCC
30819 TTTTGACTTA
Statistics
Matches: 106, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 106 1.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (39 bp):
CAATCTGCCCCATGATCGGGGTAAGAGATTGAATGGCTA
Found at i:30780 original size:78 final size:78
Alignment explanation
Indices: 30643--30817 Score: 237
Period size: 78 Copynumber: 2.2 Consensus size: 78
30633 TTATTGCTTC
* * * *
30643 GGATGATTGCAATCTGCCCTATGATCGGGGTAAGAGATTGAATGGCTACAATTTGCCCCATGATC
1 GGATGACTGCAATCTGCCCTATGATCGAGGTAAGAGATTGAATGGCTACAATCTACCCCATGATC
30708 GGGGTAAGAGATT
66 GGGGTAAGAGATT
*
30721 GGATGACTGCAATCTG-CCTAATGATCGAGGTAAGAGATT-AGATGGCTGCAATCTACCCCATGA
1 GGATGACTGCAATCTGCCCT-ATGATCGAGGTAAGAGATTGA-ATGGCTACAATCTACCCCATGA
*
30784 TCGGTGTAAGAGATT
64 TCGGGGTAAGAGATT
** *
30799 GGATGGTTACAATCTGCCC
1 GGATGACTGCAATCTGCCC
30818 CTTTTGACTT
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
77 4 0.05
78 79 0.93
79 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.26
Consensus pattern (78 bp):
GGATGACTGCAATCTGCCCTATGATCGAGGTAAGAGATTGAATGGCTACAATCTACCCCATGATC
GGGGTAAGAGATT
Found at i:31212 original size:99 final size:99
Alignment explanation
Indices: 31048--31705 Score: 506
Period size: 99 Copynumber: 6.7 Consensus size: 99
31038 TAAGATTCGT
* * * ** * * *
31048 CGTTGCAGCCTCAATCTTTCCCGTCATGT-TTTTAAGGTATCGGGTTTGCCGTTACGGCCTCAAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAAC
* * *
31112 CTTTCCTTTCATATCTTCATGGTACCAGATTCAC
66 CTTTCCCTTCAAATCTTCATGGTACCGGATTCAC
* * * ** *
31146 CGTTGCGGCCTCAACCCTTCCCATCACATCTTCTAAGGTATTGGGTTTGTTGTTGCGGCCTTAAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAAC
* * * *
31211 CTTTCCCTTCAAATCTTTATGGTACTGGGTTCGC
66 CTTTCCCTTCAAATCTTCATGGTACCGGATTCAC
* * * * ** * * *
31245 CATTGCGGCCTCAACCTTTCCC-T-TCATATT-TAATGGTACCGAATTCACCGTTGTGGCTTCTA
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAA-GGTATCGGGTTCGCCGTTGCGGCCTC-A
* * * ** * * * *
31307 TCC-TTCCCATGACGTCTTCTAAGGTATC-GAGTTTAT
64 ACCTTTCCCTTCAAATCTTC-ATGGTACCGGA-TTCAC
* * * * *
31343 CGTTGCTGCCTCAACCTTTGCCATTACATCTTCTAATGTATCAGGTTCGCCGTTGCGGCCTCAAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAAC
* * ** * ** **
31408 CTTTCGCATCATGT-TTCTTGGTATTGGATTCGT
66 CTTTCCCTTCAAATCTTCATGGTACCGGATTCAC
* ** * * * * * *
31441 CGTTGGGGCCTCAATATTTCCCATCACATCTTTTAAGGTATTGGTTTTGCCATTGCAGCCTCAAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAAC
* *
31506 CTTTCCCTTCAAATCTTCATGGTACCGGGTTCAT
66 CTTTCCCTTCAAATCTTCATGGTACCGGATTCAC
* * * *
31540 CGTTACGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCAGGTTCGTCGTTGCGGCCTCAAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAAC
* *
31605 CTTTCCCTTCAAATCTTCATGGTATCGGGTTCAC
66 CTTTCCCTTCAAATCTTCATGGTACCGGATTCAC
* * * * * * * *
31639 CGTTGTGACCTAAACCTTTCCCATTACAT-TTC-ATGGTACCGGATTCGCCGTTGCGGACTCAAT
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAA-
31702 CCTT
65 CCTT
31706 CCCGTCCCGT
Statistics
Matches: 431, Mismatches: 117, Indels: 24
0.75 0.20 0.04
Matches are distributed among these distances:
96 3 0.01
97 57 0.13
98 129 0.30
99 207 0.48
100 32 0.07
101 3 0.01
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.36
Consensus pattern (99 bp):
CGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAAC
CTTTCCCTTCAAATCTTCATGGTACCGGATTCAC
Found at i:31217 original size:50 final size:50
Alignment explanation
Indices: 31043--31832 Score: 450
Period size: 50 Copynumber: 16.1 Consensus size: 50
31033 AGGTATAAGA
* * * ** *
31043 TTCGTCGTTGCAGCCTCAATCTTTCCCGTCATGT-TTTTAAGGTATCGGG
1 TTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGG
* * * ** * * * * *
31092 TTTGCCGTTACGGCCTCAACCTTTCCTTTCATATCTTC-ATGGTACCAGA
1 TTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGG
** * *
31141 TTCACCGTTGCGGCCTCAACCCTTCCCATCACATCTTCTAAGGTATTGGG
1 TTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGG
* * * * * *
31191 TTTGTTGTTGCGGCCTTAACCTTTCCCTTCAAATCTT-TATGGTA-CTGGG
1 TTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATC-GGG
* * * * * **
31240 TTCGCCATTGCGGCCTCAACCTTTCCC-T-TCATATT-TAATGGTACCGAA
1 TTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAA-GGTATCGGG
** * * * * * *
31288 TTCACCGTTGTGGCTTCTATCC-TTCCCATGACGTCTTCTAAGGTATCGAG
1 TTCGTCGTTGCGGCCTC-AACCTTTCCCATCACATCTTCTAAGGTATCGGG
** * * * * *
31338 TTTATCGTTGCTGCCTCAACCTTTGCCATTACATCTTCTAATGTATCAGG
1 TTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGG
* * ** * * *
31388 TTCGCCGTTGCGGCCTCAACCTTTCGCATCATGT-TTCT-TGGTATTGGA
1 TTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGG
* ** * * *
31436 TTCGTCGTTGGGGCCTCAATATTTCCCATCACATCTTTTAAGGTATTGGT
1 TTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGG
* * * * * * * *
31486 TTTGCCATTGCAGCCTCAACCTTTCCCTTCAAATCTTC-ATGGTACCGGG
1 TTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGG
* * * *
31535 TTCATCGTTACGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCAGG
1 TTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGG
* * *
31585 TTCGTCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTC-ATGGTATCGGG
1 TTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGG
** * * * * * * *
31634 TTCACCGTTGTGACCTAAACCTTTCCCATTACAT-TTC-ATGGTACCGGA
1 TTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGG
* * * * * * *
31682 TTCGCCGTTGCGGACTCAATCC-TTCCCGTCCCGTCTTCAAAGGTA-CTAGG
1 TTCGTCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTCTAAGGTATC-GGG
* ** ** * *
31732 TTCG-CAGTTGCGGTCTCAACCTTTCTGATCATGT-TTC-ATGGTA-CTGGA
1 TTCGTC-GTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATC-GGG
* * * *
31780 TTCATCGTTGCGACCTCAATCTTTCCCATCACATCTTCTAAGGTATCGAG
1 TTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGG
31830 TTC
1 TTC
31833 ACCATTGTGG
Statistics
Matches: 553, Mismatches: 165, Indels: 45
0.72 0.22 0.06
Matches are distributed among these distances:
47 6 0.01
48 122 0.22
49 197 0.36
50 224 0.41
51 4 0.01
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (50 bp):
TTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGG
Found at i:31571 original size:197 final size:195
Alignment explanation
Indices: 31041--31628 Score: 561
Period size: 197 Copynumber: 3.0 Consensus size: 195
31031 TAAGGTATAA
* ** * *
31041 GATTCGTCGTTGCAGCCTCAATCTTTCCCGTCATGTTTTTAAGGTATCGGGTTTGCCGTTACGGC
1 GATTCGTCGTTGCGGCCTCAATCTTTCCC-TCACATTTTTAAGGTATCGGATTTGCCGTTGCGGC
* * * * * *
31106 CTCAACCTTTCCTTTCATATCTTCATGGTACCAGATTCACCGTTGCGGCCTCAACCCTTCCCATC
65 CTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTCATCGTTGCGGCCTCAACCTTTCCCATC
** * * * *
31171 ACATCTTCTAAGGTATTGGGTTTGTTGTTGCGGCCTTAACCTTTCCCTTCAAATCTTTATGGTAC
130 ACATCTTCTAAGGTATCAGGTTCGTCGTTGCGGCCTCAACCTTTCCCATC-AATCTTTATGGTAC
31236 TG
194 TG
* * * * * * * * ** *
31238 GGTTCGCCATTGCGGCCTCAACCTTTCCCT-TCATATTTAATGGTACCGAATTCACCGTTGTGGC
1 GATTCGTCGTTGCGGCCTCAATCTTTCCCTCACATTTTTAA-GGTATCGGATTTGCCGTTGCGGC
* * * * ** * * * * * *
31302 TTCTATCC-TTCCCATGACGTCTTCTAAGGTATCGAGTTTATCGTTGCTGCCTCAACCTTTGCCA
65 CTC-AACCTTTCCCTTCAAATCTTC-ATGGTACCGGGTTCATCGTTGCGGCCTCAACCTTTCCCA
* * * * * *
31366 TTACATCTTCTAATGTATCAGGTTCGCCGTTGCGGCCTCAACCTTTCGCATC-ATGTTTCTTGGT
128 TCACATCTTCTAAGGTATCAGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCAATCTTT-ATGGT
*
31430 ATTG
192 ACTG
* * * * * *
31434 GATTCGTCGTTGGGGCCTCAATATTTCCCATCACATCTTTTAAGGTATTGGTTTTGCCATTGCAG
1 GATTCGTCGTTGCGGCCTCAATCTTTCCC-TCACAT-TTTTAAGGTATCGGATTTGCCGTTGCGG
*
31499 CCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTCATCGTTACGGCCTCAACCTTTCCCAT
64 CCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTCATCGTTGCGGCCTCAACCTTTCCCAT
* * *
31564 CACATCTTCTAAGGTACCAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTA
129 CACATCTTCTAAGGTATCAGGTTCGTCGTTGCGGCCTCAACCTTTCCCATC-AATCTTTATGGTA
31629 TCGGGTTCAC
Statistics
Matches: 296, Mismatches: 85, Indels: 19
0.74 0.21 0.05
Matches are distributed among these distances:
195 11 0.04
196 60 0.20
197 180 0.61
198 36 0.12
199 9 0.03
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.36
Consensus pattern (195 bp):
GATTCGTCGTTGCGGCCTCAATCTTTCCCTCACATTTTTAAGGTATCGGATTTGCCGTTGCGGCC
TCAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTCATCGTTGCGGCCTCAACCTTTCCCATCA
CATCTTCTAAGGTATCAGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCAATCTTTATGGTACTG
Found at i:31851 original size:98 final size:97
Alignment explanation
Indices: 31499--31870 Score: 257
Period size: 98 Copynumber: 3.8 Consensus size: 97
31489 GCCATTGCAG
* * * * * * * * ** *
31499 CCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTCATCGTTACGGCCTCAACCTTTCCCAT
1 CCTCAATCTTTCCCATCACATCTTCAAGGTATCGAGTTCACCATTGTGGCCTAAACCTTTCCCAT
* * *
31564 CACATCTTCTAAGGTACCAGG-TTCGTCGTTGCGG
66 CACAT-TTC-ATGGTACC-GGATTCATCGTTGCGA
* * * * * * *
31598 CCTCAACCTTTCCCTTCAAATCTTCATGGTATCGGGTTCACCGTTGTGACCTAAACCTTTCCCAT
1 CCTCAATCTTTCCCATCACATCTTCAAGGTATCGAGTTCACCATTGTGGCCTAAACCTTTCCCAT
* **
31663 TACATTTCATGGTACCGGATTCGCCGTTGCGGA
66 CACATTTCATGGTACCGGATTCATCGTTGC-GA
* * * * * * * * * *
31696 -CTCAATCCTTCCCGTCCCGTCTTCAAAGGTA-CTAGGTTC-GCAGTTGCGGTCTCAACCTTTCT
1 CCTCAATCTTTCCCATCACATCTTC-AAGGTATCGA-GTTCACCA-TTGTGGCCTAAACCTTTCC
* ** *
31758 GATCATGTTTCATGGTACTGGATTCATCGTTGCGA
63 CATCACATTTCATGGTACCGGATTCATCGTTGCGA
* * *
31793 CCTCAATCTTTCCCATCACATCTTCTAAGGTATCGAGTTCACCATTGTGGCCTTAACCTCTCCCT
1 CCTCAATCTTTCCCATCACATCTTC-AAGGTATCGAGTTCACCATTGTGGCCTAAACCTTTCCCA
*
31858 TCAAATGTTCATG
65 TCACAT-TTCATG
31871 TTTCCTTGCT
Statistics
Matches: 215, Mismatches: 49, Indels: 18
0.76 0.17 0.06
Matches are distributed among these distances:
96 2 0.01
97 39 0.18
98 101 0.47
99 73 0.34
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (97 bp):
CCTCAATCTTTCCCATCACATCTTCAAGGTATCGAGTTCACCATTGTGGCCTAAACCTTTCCCAT
CACATTTCATGGTACCGGATTCATCGTTGCGA
Found at i:37615 original size:30 final size:30
Alignment explanation
Indices: 37566--38097 Score: 482
Period size: 30 Copynumber: 17.9 Consensus size: 30
37556 TAATTTTATG
37566 AAAGTTTA-GGGTTAAAATGTGATTTTGGA
1 AAAGTTTAGGGGTTAAAATGTGATTTTGGA
* *
37595 AAAGTTTAGGGGTAAAAATGTGGTTTT-GA
1 AAAGTTTAGGGGTTAAAATGTGATTTTGGA
*
37624 AAAGGTTTAGAGGTTAAAATGTGATTTTGG-
1 AAA-GTTTAGGGGTTAAAATGTGATTTTGGA
*
37654 AAAGTTTTA-GGGTTAAAACT-TGATTTTAGA
1 AAAG-TTTAGGGGTTAAAA-TGTGATTTTGGA
*
37684 GAAGTTTA-GGGTTAAAATGTGATTTTGGGA
1 AAAGTTTAGGGGTTAAAATGTGATTTT-GGA
* * *
37714 AAATTTTAAGGGTTAAAATGTAATTTTGGA
1 AAAGTTTAGGGGTTAAAATGTGATTTTGGA
* ** *
37744 AAAGATTAAAGGTTAAAATG-CATATTTGGA
1 AAAGTTTAGGGGTTAAAATGTGAT-TTTGGA
* *
37774 GAAA-TTTA-GGGTGAAAATG-GAATTTTAGA
1 -AAAGTTTAGGGGTTAAAATGTG-ATTTTGGA
* ** *
37803 GAAGTTTAGGGGTTAAAATGAAATTTTAGA
1 AAAGTTTAGGGGTTAAAATGTGATTTTGGA
* * *
37833 GATA-TTT-GAGGGTTAAAATGTAATTTTAGA
1 -AAAGTTTAG-GGGTTAAAATGTGATTTTGGA
*
37863 AAAGTTT-TGGGTTAAAAATGTGATTTTGGA
1 AAAGTTTAGGGGTT-AAAATGTGATTTTGGA
* * *
37893 AAAGTTTAGGGGTTAAAATATAATTTTAGA
1 AAAGTTTAGGGGTTAAAATGTGATTTTGGA
* ** * * *
37923 GAAGTTTATTGGTCAAAATGTAATTTTGTA
1 AAAGTTTAGGGGTTAAAATGTGATTTTGGA
* * *
37953 AAATTTTAAGGGTAAAAATGTGATTTTGGA
1 AAAGTTTAGGGGTTAAAATGTGATTTTGGA
*
37983 AAAGTTTA-GGGTTAAAATGTAATTTTGGA
1 AAAGTTTAGGGGTTAAAATGTGATTTTGGA
* * *
38012 AAAGTTTAAGGGTTAAAATGTAATTTTAGA
1 AAAGTTTAGGGGTTAAAATGTGATTTTGGA
* *
38042 AAAGTTTAGGGGTAAAAATATGATTTTGGA
1 AAAGTTTAGGGGTTAAAATGTGATTTTGGA
* * *
38072 AAAGTTT-GGTGTCAAAATGTAATTTT
1 AAAGTTTAGGGGTTAAAATGTGATTTT
38098 TGGGTAAAAA
Statistics
Matches: 420, Mismatches: 62, Indels: 42
0.80 0.12 0.08
Matches are distributed among these distances:
28 3 0.01
29 120 0.29
30 270 0.64
31 27 0.06
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.37
Consensus pattern (30 bp):
AAAGTTTAGGGGTTAAAATGTGATTTTGGA
Found at i:37645 original size:60 final size:59
Alignment explanation
Indices: 37550--38097 Score: 551
Period size: 60 Copynumber: 9.2 Consensus size: 59
37540 TTCGAGGATC
* *
37550 AAAAGGTAATTTTATG-AAAGTTTAGGGTTAAAATGTGATTTTGGAAAAGTTTAGGGGTA
1 AAAATGTAATTTTA-GAAAAGTTTAGGGTTAAAATGTGATTTTGGAAAAGTTTAGGGGTT
**
37609 AAAATGTGGTTTT-GAAAAGGTTTAGAGGTTAAAATGTGATTTTGG-AAAGTTTTA-GGGTT
1 AAAATGTAATTTTAGAAAA-GTTTAG-GGTTAAAATGTGATTTTGGAAAAG-TTTAGGGGTT
* * * *
37668 AAAACT-TGATTTTAGAGAAGTTTAGGGTTAAAATGTGATTTTGGGAAAATTTTAAGGGTT
1 AAAA-TGTAATTTTAGAAAAGTTTAGGGTTAAAATGTGATTTT-GGAAAAGTTTAGGGGTT
* * * * *
37728 AAAATGTAATTTTGGAAAAGATTAAAGGTTAAAATG-CATATTTGGAGAAA-TTTA-GGGTG
1 AAAATGTAATTTTAGAAAAG-TTTAGGGTTAAAATGTGAT-TTTGGA-AAAGTTTAGGGGTT
* * ** * *
37787 AAAATGGAATTTTAGAGAAGTTTAGGGGTTAAAATGAAATTTTAGAGATA-TTT-GAGGGTT
1 AAAATGTAATTTTAGAAAAGTTTA-GGGTTAAAATGTGATTTTGGA-AAAGTTTAG-GGGTT
*
37847 AAAATGTAATTTTAGAAAAGTTTTGGGTTAAAAATGTGATTTTGGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTAGAAAAGTTTAGGGTT-AAAATGTGATTTTGGAAAAGTTTAGGGGTT
* * * * * * * * *
37907 AAAATATAATTTTAGAGAAGTTTATTGGTCAAAATGTAATTTTGTAAAATTTTAAGGGTA
1 AAAATGTAATTTTAGAAAAGTTTA-GGGTTAAAATGTGATTTTGGAAAAGTTTAGGGGTT
* * * *
37967 AAAATGTGATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTT
1 AAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTGATTTTGGAAAAGTTTAGGGGTT
* * * *
38026 AAAATGTAATTTTAGAAAAGTTTAGGGGTAAAAATATGATTTTGGAAAAGTTT-GGTGTC
1 AAAATGTAATTTTAGAAAAGTTTA-GGGTTAAAATGTGATTTTGGAAAAGTTTAGGGGTT
38085 AAAATGTAATTTT
1 AAAATGTAATTTT
38098 TGGGTAAAAA
Statistics
Matches: 410, Mismatches: 57, Indels: 44
0.80 0.11 0.09
Matches are distributed among these distances:
57 1 0.00
58 23 0.06
59 164 0.40
60 199 0.49
61 23 0.06
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.37
Consensus pattern (59 bp):
AAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTGATTTTGGAAAAGTTTAGGGGTT
Found at i:38076 original size:89 final size:89
Alignment explanation
Indices: 37566--38097 Score: 575
Period size: 89 Copynumber: 6.0 Consensus size: 89
37556 TAATTTTATG
* * *
37566 AAAGTTT-AGGGTTAAAATGTGATTTTGGAAAAGTTTAGGGGTAAAAATGTGGTTTT-GAAAAGG
1 AAAGTTTAAGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTAAAAATGTGATTTTGGAAAA-G
*
37629 TTTAGAGGTTAAAATGTGATTTTGG-
65 TTTAG-GGTTAAAATGTAATTTTGGA
* * * *
37654 AAAGTTTTAGGGTTAAAACT-TGATTTTAGAGAAGTTTA-GGGTTAAAATGTGATTTTGGGAAAA
1 AAAGTTTAAGGGTTAAAA-TGTAATTTTAGAAAAGTTTAGGGGTAAAAATGTGATTTT-GGAAAA
*
37717 TTTTAAGGGTTAAAATGTAATTTTGGA
64 GTTT-AGGGTTAAAATGTAATTTTGGA
* * * * * * *
37744 AAAGATTAAAGGTTAAAATG-CATATTTGGAGAAA-TTTA-GGGTGAAAATG-GAATTTTAGAGA
1 AAAGTTTAAGGGTTAAAATGTAAT-TTTAGA-AAAGTTTAGGGGTAAAAATGTG-ATTTTGGAAA
* *
37805 AGTTTAGGGGTTAAAATGAAATTTTAGA
63 AGTTTA-GGGTTAAAATGTAATTTTGGA
* * * *
37833 GATA-TTTGAGGGTTAAAATGTAATTTTAGAAAAGTTTTGGGTTAAAAATGTGATTTTGGAAAAG
1 -AAAGTTTAAGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTAAAAATGTGATTTTGGAAAAG
* *
37897 TTTAGGGGTTAAAATATAATTTTAGA
65 TTTA-GGGTTAAAATGTAATTTTGGA
* ** * * *
37923 GAAGTTTATTGGTCAAAATGTAATTTT-GTAAAATTTTAAGGGTAAAAATGTGATTTTGGAAAAG
1 AAAGTTTAAGGGTTAAAATGTAATTTTAG-AAAAGTTTAGGGGTAAAAATGTGATTTTGGAAAAG
37987 TTTAGGGTTAAAATGTAATTTTGGA
65 TTTAGGGTTAAAATGTAATTTTGGA
*
38012 AAAGTTTAAGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTAAAAATATGATTTTGGAAAAGT
1 AAAGTTTAAGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTAAAAATGTGATTTTGGAAAAGT
*
38077 TT-GGTGTCAAAATGTAATTTT
66 TTAGG-GTTAAAATGTAATTTT
38098 TGGGTAAAAA
Statistics
Matches: 373, Mismatches: 51, Indels: 39
0.81 0.11 0.08
Matches are distributed among these distances:
88 29 0.08
89 192 0.51
90 149 0.40
91 3 0.01
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.37
Consensus pattern (89 bp):
AAAGTTTAAGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTAAAAATGTGATTTTGGAAAAGT
TTAGGGTTAAAATGTAATTTTGGA
Found at i:38100 original size:119 final size:117
Alignment explanation
Indices: 37550--38097 Score: 583
Period size: 119 Copynumber: 4.6 Consensus size: 117
37540 TTCGAGGATC
*
37550 AAAAGGTAATTTTATGA-AAGTTTAGGGTTAAAATGTGATTTTGGAAAAGTTTAGGGGTAAAAAT
1 AAAATGTAATTTTA-GAGAAGTTTAGGGTTAAAATGTGATTTTGGAAAAGTTTA-GGGTAAAAAT
** *
37614 GTGGTTTT-GAAAAGGTTTAGAGGTTAAAATGTGATTTTGG-AAAGTTTTAGGGTT
64 GTAATTTTGGAAAA-GTTTAG-GGTTAAAATGTGATTTTGGAAAAGTTTAAGGGTT
* * *
37668 AAAACT-TGATTTTAGAGAAGTTTAGGGTTAAAATGTGATTTTGGGAAAATTTTAAGGGTTAAAA
1 AAAA-TGTAATTTTAGAGAAGTTTAGGGTTAAAATGTGATTTT-GGAAAAGTTT-AGGGTAAAAA
* * * *
37732 TGTAATTTTGGAAAAGATTAAAGGTTAAAATG-CATATTTGGAGAAA-TTT-AGGGTG
63 TGTAATTTTGGAAAAG-TTTAGGGTTAAAATGTGAT-TTTGGA-AAAGTTTAAGGGTT
* ** * * *
37787 AAAATGGAATTTTAGAGAAGTTTAGGGGTTAAAATGAAATTTTAGAGATA-TTTGAGGGTTAAAA
1 AAAATGTAATTTTAGAGAAGTTTA-GGGTTAAAATGTGATTTTGGA-AAAGTTT-AGGGTAAAAA
* * *
37851 TGTAATTTTAGAAAAGTTTTGGGTTAAAAATGTGATTTTGGAAAAGTTTAGGGGTT
63 TGTAATTTTGGAAAAGTTTAGGGTT-AAAATGTGATTTTGGAAAAGTTTAAGGGTT
* * * * * *
37907 AAAATATAATTTTAGAGAAGTTTATTGGTCAAAATGTAATTTTGTAAAATTTTAAGGGTAAAAAT
1 AAAATGTAATTTTAGAGAAGTTTA-GGGTTAAAATGTGATTTTGGAAAAGTTT-AGGGTAAAAAT
* *
37972 GTGATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTT
64 GTAATTTTGGAAAAGTTTAGGGTTAAAATGTGATTTTGGAAAAGTTTAAGGGTT
* * * *
38026 AAAATGTAATTTTAGAAAAGTTTAGGGGTAAAAATATGATTTTGGAAAAGTTT-GGTGTCAAAAT
1 AAAATGTAATTTTAGAGAAGTTTA-GGGTTAAAATGTGATTTTGGAAAAGTTTAGG-GTAAAAAT
38090 GTAATTTT
64 GTAATTTT
38098 TGGGTAAAAA
Statistics
Matches: 361, Mismatches: 51, Indels: 36
0.81 0.11 0.08
Matches are distributed among these distances:
117 4 0.01
118 62 0.17
119 184 0.51
120 108 0.30
121 3 0.01
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.37
Consensus pattern (117 bp):
AAAATGTAATTTTAGAGAAGTTTAGGGTTAAAATGTGATTTTGGAAAAGTTTAGGGTAAAAATGT
AATTTTGGAAAAGTTTAGGGTTAAAATGTGATTTTGGAAAAGTTTAAGGGTT
Found at i:39725 original size:21 final size:21
Alignment explanation
Indices: 39699--39762 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
39689 GAAAAAATAA
*
39699 GACTAAGTCCTAGGGATATTT
1 GACTAAGTCCTAGGGAGATTT
39720 GACTAAGTCCTAGGGAGATTT
1 GACTAAGTCCTAGGGAGATTT
* *
39741 GACTAACTCCTAGAGAGATTT
1 GACTAAGTCCTAGGGAGATTT
39762 G
1 G
39763 TTGGCTTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (21 bp):
GACTAAGTCCTAGGGAGATTT
Found at i:42785 original size:17 final size:17
Alignment explanation
Indices: 42747--42786 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
42737 AATAATAAAA
*
42747 ATTTTAAATTAAAATTC
1 ATTTTAAATTAAAAGTC
*
42764 ATTTTAATTTAAAAGTC
1 ATTTTAAATTAAAAGTC
*
42781 CTTTTA
1 ATTTTA
42787 CACCCTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTTTAAATTAAAAGTC
Done.