Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012878.1 Kokia drynarioides strain JFW-HI SEQ_127892, 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: 38384
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 73 characters in sequence are not A, C, G, or T
Found at i:4293 original size:30 final size:29
Alignment explanation
Indices: 4254--4463 Score: 152
Period size: 30 Copynumber: 7.0 Consensus size: 29
4244 GTAATATTTT
* * *
4254 AAAATTTTAGGGGTTAAAATGCAATTTAAA
1 AAAAGTTTAAGGGTTAAAATGAAATTT-AA
* *
4284 AAAAGTTTAGGGGTTAAAATAAAATTTTCAA
1 AAAAGTTTAAGGGTTAAAATGAAA-TTT-AA
* *
4315 AAAATTTTAAGGGTTAAAATGAAAATTTTA
1 AAAAGTTTAAGGGTTAAAATG-AAATTTAA
* * *
4345 AAAAGTATAAGTGTTAAAATGAAATTTCTA
1 AAAAGTTTAAGGGTTAAAATGAAATTT-AA
* * * *
4375 GAAAGATTAAGGGTTAAAAATAAAATTTTA
1 AAAAGTTTAAGGGTT-AAAATGAAATTTAA
* ** *
4405 GAAAGTTCGAGGGTTGAAAATGAAATTTTAG
1 AAAAGTTTAAGGGTT-AAAATGAAA-TTTAA
* *
4436 AAAA-TTTAGGGGTAAAAATGAAAATTTA
1 AAAAGTTTAAGGGTTAAAATG-AAATTTA
4464 GAAAGTTCGA
Statistics
Matches: 146, Mismatches: 28, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
29 16 0.11
30 84 0.58
31 43 0.29
32 3 0.02
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.32
Consensus pattern (29 bp):
AAAAGTTTAAGGGTTAAAATGAAATTTAA
Found at i:4318 original size:91 final size:92
Alignment explanation
Indices: 4223--4403 Score: 215
Period size: 91 Copynumber: 2.0 Consensus size: 92
4213 CGAAATCTTG
* * * * *
4223 AAAAATTTT-AGAGGCTAAAATGTAATATTTT-AAAATTTTAGGGGTTAAAATGCAATTTAAAAA
1 AAAAATTTTAAG-GGCTAAAATG-AAAATTTTAAAAAGTATAAGGGTTAAAATGAAATTTAAAAA
* *
4286 AAGTTTAGGGGTT-AAAATAAAATTTTCA
64 AAGATTAAGGGTTAAAAATAAAATTTTCA
* * ** *
4314 AAAAATTTTAAGGGTTAAAATGAAAATTTTAAAAAGTATAAGTGTTAAAATGAAATTTCTAGAAA
1 AAAAATTTTAAGGGCTAAAATGAAAATTTTAAAAAGTATAAGGGTTAAAATGAAATTTAAAAAAA
4379 GATTAAGGGTTAAAAATAAAATTTT
66 GATTAAGGGTTAAAAATAAAATTTT
4404 AGAAAGTTCG
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
90 7 0.09
91 53 0.71
92 15 0.20
ACGTcount: A:0.49, C:0.02, G:0.15, T:0.34
Consensus pattern (92 bp):
AAAAATTTTAAGGGCTAAAATGAAAATTTTAAAAAGTATAAGGGTTAAAATGAAATTTAAAAAAA
GATTAAGGGTTAAAAATAAAATTTTCA
Found at i:4410 original size:60 final size:60
Alignment explanation
Indices: 4285--4497 Score: 206
Period size: 59 Copynumber: 3.5 Consensus size: 60
4275 CAATTTAAAA
* * * * *
4285 AAAGTTTAGGGGTT-AAAATAAAATTTTCAAAAAATTTTAAGGGTT-AAAATGAAAATTTTAA
1 AAAGTTCAAGGGTTGAAAATGAAATTTT-AGAAAA--TTAAGGGTTAAAAATGAAAATTTTAG
*
4346 AAAGTAT-AAGTGTT-AAAATGAAATTTCTAGAAAGATTAAGGGTTAAAAAT-AAAATTTTAG
1 AAAGT-TCAAGGGTTGAAAATGAAATTT-TAGAAA-ATTAAGGGTTAAAAATGAAAATTTTAG
* * *
4406 AAAGTTCGAGGGTTGAAAATGAAATTTTAGAAAATTTAGGGGTAAAAATGAAAA-TTTAG
1 AAAGTTCAAGGGTTGAAAATGAAATTTTAGAAAATTAAGGGTTAAAAATGAAAATTTTAG
** *
4465 AAAGTTCGAA-GGTCAAAAATGAATTTTTAGAAA
1 AAAGTTC-AAGGGTTGAAAATGAAATTTTAGAAA
4498 GCTCGGGGGG
Statistics
Matches: 131, Mismatches: 13, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
59 47 0.36
60 39 0.30
61 42 0.32
62 3 0.02
ACGTcount: A:0.48, C:0.02, G:0.18, T:0.31
Consensus pattern (60 bp):
AAAGTTCAAGGGTTGAAAATGAAATTTTAGAAAATTAAGGGTTAAAAATGAAAATTTTAG
Found at i:4470 original size:59 final size:59
Alignment explanation
Indices: 4238--4497 Score: 217
Period size: 61 Copynumber: 4.3 Consensus size: 59
4228 TTTTAGAGGC
* * * * * *
4238 TAAAATGTAATATTTTA-AAATTTTAGGGGTTAAAATG-CAATTTAAAAAAAGTT-TAGGGGT
1 TAAAATG-AA-ATTTTAGAAAATTTAGGGGTAAAAATGAAAATTT-TAGAAAGTTCGA-GGGT
* * * * * * *
4298 TAAAATAAAATTTTCAAAAAATTTTAAGGGTTAAAATGAAAATTTTAAAAAGTAT-AAGTGT
1 TAAAATGAAATTTT-AGAAAA-TTTAGGGGTAAAAATGAAAATTTTAGAAAGT-TCGAGGGT
* *
4359 TAAAATGAAATTTCTAGAAAGATTAAGGGTTAAAAAT-AAAATTTTAGAAAGTTCGAGGGT
1 TAAAATGAAATTT-TAGAAA-ATTTAGGGGTAAAAATGAAAATTTTAGAAAGTTCGAGGGT
*
4419 TGAAAATGAAATTTTAGAAAATTTAGGGGTAAAAATGAAAA-TTTAGAAAGTTCGAAGGT
1 T-AAAATGAAATTTTAGAAAATTTAGGGGTAAAAATGAAAATTTTAGAAAGTTCGAGGGT
* *
4478 CAAAAATGAATTTTTAGAAA
1 -TAAAATGAAATTTTAGAAA
4498 GCTCGGGGGG
Statistics
Matches: 168, Mismatches: 21, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
58 5 0.03
59 52 0.31
60 38 0.23
61 64 0.38
62 9 0.05
ACGTcount: A:0.48, C:0.02, G:0.17, T:0.32
Consensus pattern (59 bp):
TAAAATGAAATTTTAGAAAATTTAGGGGTAAAAATGAAAATTTTAGAAAGTTCGAGGGT
Found at i:4483 original size:30 final size:29
Alignment explanation
Indices: 4326--4498 Score: 147
Period size: 30 Copynumber: 5.8 Consensus size: 29
4316 AAATTTTAAG
*
4326 GGTT-AAAATGAAAATTTTAAAAAGTAT-AA
1 GGTTAAAAATG-AAATTTTAGAAAGT-TGAA
4355 GTGTT-AAAATGAAATTTCTAGAAAGATT-AA
1 G-GTTAAAAATGAAATTT-TAGAAAG-TTGAA
* *
4385 GGGTTAAAAATAAAATTTTAGAAAGTTCGAG
1 -GGTTAAAAATGAAATTTTAGAAAGTT-GAA
* * * *
4416 GGTTGAAAATGAAATTTTAGAAAATTTAG
1 GGTTAAAAATGAAATTTTAGAAAGTTGAA
* *
4445 GGGTAAAAATGAAAATTTAGAAAGTTCGAA
1 GGTTAAAAATGAAATTTTAGAAAGTT-GAA
* *
4475 GGTCAAAAATGAATTTTTAGAAAG
1 GGTTAAAAATGAAATTTTAGAAAG
4499 CTCGGGGGGT
Statistics
Matches: 119, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
29 33 0.28
30 72 0.61
31 14 0.12
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.30
Consensus pattern (29 bp):
GGTTAAAAATGAAATTTTAGAAAGTTGAA
Found at i:6401 original size:77 final size:77
Alignment explanation
Indices: 6315--6641 Score: 451
Period size: 77 Copynumber: 4.2 Consensus size: 77
6305 TGTTTCAACT
* * * * * *
6315 TGCCTCATGATTGGGGTAAAAGACTGCATGTCTTTAATTTGCCTTCTGATTAAGTTAAGAGATTG
1 TGCCCCATGATCGGGGTAAGAGACTGCATGTCTTCAATCTGCCTTCTGATTAAGGTAAGAGATTG
6380 AAATT-TTCAATC
66 -AATTCTTCAATC
* * * *
6392 TGGCCCATGATCAGGGTAAGAGACTGAATGTCTTCAATCTGCCTTTTGATTAAGGTAAGAGATTG
1 TGCCCCATGATCGGGGTAAGAGACTGCATGTCTTCAATCTGCCTTCTGATTAAGGTAAGAGATTG
*
6457 AATTCTTCAATT
66 AATTCTTCAATC
* * *
6469 TGCCCCATGATCGGGGTAAGAGACTGCATGTCTTTAATCTGTCTTCTAATTAAGGTAAGAGATTG
1 TGCCCCATGATCGGGGTAAGAGACTGCATGTCTTCAATCTGCCTTCTGATTAAGGTAAGAGATTG
*
6534 AATTCTTTAATC
66 AATTCTTCAATC
*
6546 TGCCCCATGATCAGGGTAAGAGACTGCATGTCTTCAAT-TGGCCTTCTGATTAAGGTAAGAGATT
1 TGCCCCATGATCGGGGTAAGAGACTGCATGTCTTCAATCT-GCCTTCTGATTAAGGTAAGAGATT
* *
6610 GGATTCTTTAATC
65 GAATTCTTCAATC
*
6623 TGCCCCATGATTGGGGTAA
1 TGCCCCATGATCGGGGTAA
6642 AAGATTAGGT
Statistics
Matches: 221, Mismatches: 27, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
76 5 0.02
77 216 0.98
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (77 bp):
TGCCCCATGATCGGGGTAAGAGACTGCATGTCTTCAATCTGCCTTCTGATTAAGGTAAGAGATTG
AATTCTTCAATC
Found at i:6571 original size:154 final size:154
Alignment explanation
Indices: 6308--6645 Score: 509
Period size: 154 Copynumber: 2.2 Consensus size: 154
6298 AATTTGATGT
* * * * *
6308 TTCAACTTGCCTCATGATTGGGGTAAAAGACTGCATGTCTTTAATTTGCCTTCTGATTAAGTTAA
1 TTCAATTTGCCCCATGATTGGGGTAAAAGACTGCATGTCTTTAATCTGCCTTCTAATTAAGGTAA
*
6373 GAGATTGAAATTTTCAATCTGGCCCATGATCAGGGTAAGAGACTGAATGTCTTCAATCT-GCCTT
66 GAGATTGAAATTTTCAATCTGCCCCATGATCAGGGTAAGAGACTGAATGTCTTCAAT-TGGCCTT
*
6437 TTGATTAAGGTAAGAGATTGAATTC
130 CTGATTAAGGTAAGAGATTGAATTC
* * *
6462 TTCAATTTGCCCCATGATCGGGGTAAGAGACTGCATGTCTTTAATCTGTCTTCTAATTAAGGTAA
1 TTCAATTTGCCCCATGATTGGGGTAAAAGACTGCATGTCTTTAATCTGCCTTCTAATTAAGGTAA
* *
6527 GAGATTG-AATTCTTTAATCTGCCCCATGATCAGGGTAAGAGACTGCATGTCTTCAATTGGCCTT
66 GAGATTGAAATT-TTCAATCTGCCCCATGATCAGGGTAAGAGACTGAATGTCTTCAATTGGCCTT
*
6591 CTGATTAAGGTAAGAGATTGGATTC
130 CTGATTAAGGTAAGAGATTGAATTC
* *
6616 TTTAATCTGCCCCATGATTGGGGTAAAAGA
1 TTCAATTTGCCCCATGATTGGGGTAAAAGA
6646 TTAGGTGCTT
Statistics
Matches: 165, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
153 5 0.03
154 160 0.97
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (154 bp):
TTCAATTTGCCCCATGATTGGGGTAAAAGACTGCATGTCTTTAATCTGCCTTCTAATTAAGGTAA
GAGATTGAAATTTTCAATCTGCCCCATGATCAGGGTAAGAGACTGAATGTCTTCAATTGGCCTTC
TGATTAAGGTAAGAGATTGAATTC
Found at i:6671 original size:192 final size:192
Alignment explanation
Indices: 6461--6833 Score: 545
Period size: 192 Copynumber: 1.9 Consensus size: 192
6451 AGATTGAATT
** * * * *
6461 CTTCAATTTGCCCCATGATCGGGGTAAGAGACTG-CATGTCTTTAATCTGTCTTCTAATTAAGGT
1 CTTCAATTTGCCCCATGATCGGAATAAAAGACTGTC-TATCTTCAATCTGCCTTCTAATTAAGGT
* * *
6525 AAGAGATTGAATTCTTTAATCTGCCCCATGATCAGGGTAAGAGACTG-CATGTCTTCAAT-TGGC
65 AAGAGATTGAATTCTTTAATCTGCACCATGATCAGGGAAAAAGACTGTC-TGTCTTCAATCT-GC
*
6588 CTTCTGATTAAGGTAAGAGATTGGATTCTTTAATCTGCCCCATGATTGGGGTAAAAGATTAGGTG
128 CTTCTGATTAAGGTAAGAGATTGGATTCTTCAATCTGCCCCATGATTGGGGTAAAAGATTAGGTG
* * *
6653 CTTCAATTTGCTCCATGATCGGAATAAAATATTGTCTATCTTCAATCTGCCTTCTAATTAAGGTA
1 CTTCAATTTGCCCCATGATCGGAATAAAAGACTGTCTATCTTCAATCTGCCTTCTAATTAAGGTA
* *
6718 AGAGATTGAATTCTTTAATCTGCACCATGATCAGGGAAAAAGATTGTCTGTCTTCAATCTGCTTT
66 AGAGATTGAATTCTTTAATCTGCACCATGATCAGGGAAAAAGACTGTCTGTCTTCAATCTGCCTT
* *
6783 CTGATTAAGGTAAGAGATTGTATTCTTCAATCTGCTCCATGATTGGGGTAA
131 CTGATTAAGGTAAGAGATTGGATTCTTCAATCTGCCCCATGATTGGGGTAA
6834 GAGACTGCAT
Statistics
Matches: 161, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
192 158 0.98
193 3 0.02
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (192 bp):
CTTCAATTTGCCCCATGATCGGAATAAAAGACTGTCTATCTTCAATCTGCCTTCTAATTAAGGTA
AGAGATTGAATTCTTTAATCTGCACCATGATCAGGGAAAAAGACTGTCTGTCTTCAATCTGCCTT
CTGATTAAGGTAAGAGATTGGATTCTTCAATCTGCCCCATGATTGGGGTAAAAGATTAGGTG
Found at i:6764 original size:77 final size:76
Alignment explanation
Indices: 6653--6906 Score: 312
Period size: 77 Copynumber: 3.3 Consensus size: 76
6643 AGATTAGGTG
* * * * * *
6653 CTTCAATTTGCTCCATGATCGGAATAAAATATTGTCTATCTTCAATCTGCCTTCTAATTAAGGTA
1 CTTCAATCTGCACCATGATCGGGA-AAAAGATTGTCTGTCTTCAATCTGCCTTCTGATTAAGGTA
6718 AGAGATTGAATT
65 AGAGATTGAATT
* *
6730 CTTTAATCTGCACCATGATCAGGGAAAAAGATTGTCTGTCTTCAATCTGCTTTCTGATTAAGGTA
1 CTTCAATCTGCACCATGATC-GGGAAAAAGATTGTCTGTCTTCAATCTGCCTTCTGATTAAGGTA
*
6795 AGAGATTGTATT
65 AGAGATTGAATT
* * * * * * *
6807 CTTCAATCTGCTCCATGATTGGGGTAAGAGACTG-CATGTCTTCAATCTTCCTTTTGATTAAGGT
1 CTTCAATCTGCACCATGA-TCGGGAAAAAGATTGTC-TGTCTTCAATCTGCCTTCTGATTAAGGT
6871 AAGAGATTGAATT
64 AAGAGATTGAATT
*
6884 CTTCAATCTGCCCCATGATCGGG
1 CTTCAATCTGCACCATGATCGGG
6907 GTAACAGACG
Statistics
Matches: 153, Mismatches: 21, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
76 5 0.03
77 144 0.94
78 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (76 bp):
CTTCAATCTGCACCATGATCGGGAAAAAGATTGTCTGTCTTCAATCTGCCTTCTGATTAAGGTAA
GAGATTGAATT
Found at i:6792 original size:269 final size:269
Alignment explanation
Indices: 6422--6948 Score: 756
Period size: 269 Copynumber: 2.0 Consensus size: 269
6412 AGACTGAATG
* * * * * *
6422 TCTTCAATCTGCCTTTTGATTAAGGTAAGAGATTGAATTCTTCAATTTGCCCCATGATCGGGGTA
1 TCTTCAATCTGCCTTCTAATTAAGGTAAGAGATTGAATTCTTCAATCTGCACCATGATCAGGGAA
* * *
6487 AGAGACTGCATGTCTTTAATCTGTCTTCTAATTAAGGTAAGAGATTGAATTCTTTAATCTGCCCC
66 AAAGACTGCATGTCTTCAATCTGTCTTCTAATTAAGGTAAGAGATTGAATTCTTCAATCTGCCCC
*
6552 ATGATCAGGGTAAGAGACTGCATGTCTTCAAT-TGGCCTTCTGATTAAGGTAAGAGATTGGATTC
131 ATGATCAGGGTAAGAGACTGCATGTCTTCAATCT-GCCTTCTGATTAAGGTAAGAGATTGAATTC
* * * *
6616 TTTAATCTGCCCCATGATTGGGGTAAAAGATTAGG-TGCTTCAATTTGCTCCATGATCGGAATAA
195 TTCAATCTGCCCCATGATCGGGGTAAAAGA-CAGGATGCTTCAATCTGCTCCATGATCGGAATAA
6680 AATATTGTCTA
259 AATATTGTCTA
*
6691 TCTTCAATCTGCCTTCTAATTAAGGTAAGAGATTGAATTCTTTAATCTGCACCATGATCAGGGAA
1 TCTTCAATCTGCCTTCTAATTAAGGTAAGAGATTGAATTCTTCAATCTGCACCATGATCAGGGAA
* * * *
6756 AAAGATTGTC-TGTCTTCAATCTG-CTTTCTGATTAAGGTAAGAGATTGTATTCTTCAATCTGCT
66 AAAGACTG-CATGTCTTCAATCTGTC-TTCTAATTAAGGTAAGAGATTGAATTCTTCAATCTGCC
** * *
6819 CCATGATTGGGGTAAGAGACTGCATGTCTTCAATCTTCCTTTTGATTAAGGTAAGAGATTGAATT
129 CCATGATCAGGGTAAGAGACTGCATGTCTTCAATCTGCCTTCTGATTAAGGTAAGAGATTGAATT
* * *
6884 CTTCAATCTGCCCCATGATCGGGGTAACAGACGGGATGCTTCAATCTGCTCCATGATTGGAATAA
194 CTTCAATCTGCCCCATGATCGGGGTAAAAGACAGGATGCTTCAATCTGCTCCATGATCGGAATAA
6949 GAGATTGGTG
Statistics
Matches: 228, Mismatches: 26, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
268 3 0.01
269 223 0.98
270 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (269 bp):
TCTTCAATCTGCCTTCTAATTAAGGTAAGAGATTGAATTCTTCAATCTGCACCATGATCAGGGAA
AAAGACTGCATGTCTTCAATCTGTCTTCTAATTAAGGTAAGAGATTGAATTCTTCAATCTGCCCC
ATGATCAGGGTAAGAGACTGCATGTCTTCAATCTGCCTTCTGATTAAGGTAAGAGATTGAATTCT
TCAATCTGCCCCATGATCGGGGTAAAAGACAGGATGCTTCAATCTGCTCCATGATCGGAATAAAA
TATTGTCTA
Found at i:6889 original size:192 final size:190
Alignment explanation
Indices: 6461--6895 Score: 495
Period size: 192 Copynumber: 2.3 Consensus size: 190
6451 AGATTGAATT
* * * * * *
6461 CTTCAATTTGCC-CCATGATCGGGGTAAGAGACTGCATGTCTTTAATCTGTCTTCTAATTAAGGT
1 CTTCAATTT-CCTCCATGAT--AGGTAAGAGATTGAATATCTTCAATCTGCCTTCTAATTAAGGT
* * *
6525 AAGAGATTGAATTCTTTAATCTGCCCCATGATCAGGGTAAGAGACTGCATGTCTTCAATTGGCCT
63 AAGAGATTGAATTCTTTAATCTGCACCATGATCAGGGAAAAAGACTGCATGTCTTCAATTGGCCT
* *
6590 TCTGATTAAGGTAAGAGATTGGATTCTTTAATCTGCCCCATGATTGGGGTAAAAGATTAGGTG
128 TCTGATTAAGGTAAGAGATTGGATTCTTCAATCTGCCCCATGATTGGGGTAAAAGATCAGGTG
* * * * **
6653 CTTCAATTTGCTCCATGATCGGAATAAAATATTGTCTATCTTCAATCTGCCTTCTAATTAAGGTA
1 CTTCAATTTCCTCCATGATAGG--TAAGAGATTGAATATCTTCAATCTGCCTTCTAATTAAGGTA
* *
6718 AGAGATTGAATTCTTTAATCTGCACCATGATCAGGGAAAAAGATTGTC-TGTCTTCAATCT-GCT
64 AGAGATTGAATTCTTTAATCTGCACCATGATCAGGGAAAAAGACTG-CATGTCTTCAAT-TGGCC
* * * *
6781 TTCTGATTAAGGTAAGAGATTGTATTCTTCAATCTGCTCCATGATTGGGGTAAGAGACTGCATGT
127 TTCTGATTAAGGTAAGAGATTGGATTCTTCAATCTGCCCCATGATTGGGGTAAAAGA-T-CAGGT
6846 -
190 G
**
6846 CTTCAATCTTCCT-TTTGATTAAGGTAAGAGATTGAAT-TCTTCAATCTGCC
1 CTTCAAT-TTCCTCCATGA-T-AGGTAAGAGATTGAATATCTTCAATCTGCC
6896 CCATGATCGG
Statistics
Matches: 204, Mismatches: 29, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
190 2 0.01
191 1 0.00
192 169 0.83
193 22 0.11
194 8 0.04
195 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (190 bp):
CTTCAATTTCCTCCATGATAGGTAAGAGATTGAATATCTTCAATCTGCCTTCTAATTAAGGTAAG
AGATTGAATTCTTTAATCTGCACCATGATCAGGGAAAAAGACTGCATGTCTTCAATTGGCCTTCT
GATTAAGGTAAGAGATTGGATTCTTCAATCTGCCCCATGATTGGGGTAAAAGATCAGGTG
Found at i:19195 original size:30 final size:30
Alignment explanation
Indices: 19141--19305 Score: 210
Period size: 30 Copynumber: 5.5 Consensus size: 30
19131 TAGAATTCGA
* *
19141 GGGTTAAAATGCAA-TTTTAAAAAGTTTAG
1 GGGTTAAAATGAAATTTTTAGAAAGTTTAG
* *
19170 GGGTTAAAATAAAATTTTTAGAAAGTGTAG
1 GGGTTAAAATGAAATTTTTAGAAAGTTTAG
*
19200 GGGTTAAAATGAATTTTTTAGAAAGTTTAG
1 GGGTTAAAATGAAATTTTTAGAAAGTTTAG
* *
19230 GGGTTAAAATGAAATTTCTAAAAAGTTT-G
1 GGGTTAAAATGAAATTTTTAGAAAGTTTAG
*
19259 GGGTCAAAAATGAAA-TTTTAGAAAGTTTAG
1 GGGT-TAAAATGAAATTTTTAGAAAGTTTAG
*
19289 GGGTCAAAAATGAAATT
1 GGGT-TAAAATGAAATT
19306 ATACAAAATT
Statistics
Matches: 119, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
29 28 0.24
30 90 0.76
31 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.33
Consensus pattern (30 bp):
GGGTTAAAATGAAATTTTTAGAAAGTTTAG
Found at i:19226 original size:60 final size:57
Alignment explanation
Indices: 19141--19341 Score: 199
Period size: 59 Copynumber: 3.4 Consensus size: 57
19131 TAGAATTCGA
* * *
19141 GGGTTAAAATGCAATTTTAAAAAGTTTAGGGGTTAAAATAAAATTTTTAGAAAGTGTAG
1 GGGTTAAAATG-AATTTTAGAAAGTTTAGGGGTTAAAATAAAATTTCTAAAAAGT-TAG
* *
19200 GGGTTAAAATGAATTTTTTAGAAAGTTTAGGGGTTAAAATGAAATTTCTAAAAAGTTTG
1 GGGTTAAAATGAA--TTTTAGAAAGTTTAGGGGTTAAAATAAAATTTCTAAAAAGTTAG
* * * * *
19259 GGGTCAAAAATGAAATTTTAGAAAGTTTAGGGGTCAAAAATGAAA-TTATACAAAA-TTAA
1 GGGT-TAAAATG-AATTTTAGAAAGTTTAGGGGT-TAAAATAAAATTTCTA-AAAAGTTAG
*
19318 TGGTTAAAAATGAAGTTTTAGAAA
1 GGGTT-AAAATGAA-TTTTAGAAA
19342 ACTCGAGGGT
Statistics
Matches: 122, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
58 4 0.03
59 60 0.49
60 56 0.46
61 2 0.02
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (57 bp):
GGGTTAAAATGAATTTTAGAAAGTTTAGGGGTTAAAATAAAATTTCTAAAAAGTTAG
Found at i:19342 original size:29 final size:29
Alignment explanation
Indices: 19235--19342 Score: 101
Period size: 30 Copynumber: 3.7 Consensus size: 29
19225 TTTAGGGGTT
**
19235 AAAATGAAATTTCTA-AAAAGTTTGGGGTCA
1 AAAATGAAATTT-TAGAAAA-TTAAGGGTCA
* *
19265 AAAATGAAATTTTAGAAAGTTTAGGGGTCA
1 AAAATGAAATTTTAGAAA-ATTAAGGGTCA
* * * *
19295 AAAATGAAATTATACAAAATTAATGGTTA
1 AAAATGAAATTTTAGAAAATTAAGGGTCA
*
19324 AAAATGAAGTTTTAGAAAA
1 AAAATGAAATTTTAGAAAA
19343 CTCGAGGGTA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
29 25 0.38
30 40 0.62
ACGTcount: A:0.49, C:0.04, G:0.18, T:0.30
Consensus pattern (29 bp):
AAAATGAAATTTTAGAAAATTAAGGGTCA
Found at i:22740 original size:22 final size:22
Alignment explanation
Indices: 22713--22790 Score: 102
Period size: 22 Copynumber: 3.4 Consensus size: 22
22703 GTGATGGGGA
*
22713 AACAGAAGCACACACAATGCTG
1 AACAGAAGCACACACAGTGCTG
22735 AACAGAAGCACACACAGTGCTGGG
1 AACAGAAGCACACACAGTGCT--G
*
22759 TAACAGAAGCACACATAGTGCTG
1 -AACAGAAGCACACACAGTGCTG
*
22782 AACAAAAGC
1 AACAGAAGC
22791 GCGCTAGCGT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
22 28 0.56
23 1 0.02
24 1 0.02
25 20 0.40
ACGTcount: A:0.44, C:0.24, G:0.22, T:0.10
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:22998 original size:21 final size:21
Alignment explanation
Indices: 22974--23014 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
22964 TGTCACAAAT
*
22974 TAATTACACA-ATCAATATTTA
1 TAATTAAACATAT-AATATTTA
22995 TAATTAAACATATAATATTT
1 TAATTAAACATATAATATTT
23015 CACAGATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATTAAACATATAATATTTA
Found at i:26972 original size:6 final size:6
Alignment explanation
Indices: 26961--27024 Score: 71
Period size: 6 Copynumber: 11.0 Consensus size: 6
26951 TTTAATTTAT
26961 TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAAA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
27007 TTTGAT TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA
27025 AAGTCCATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
4 2 0.04
5 7 0.14
6 38 0.78
7 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:26976 original size:17 final size:18
Alignment explanation
Indices: 26954--27024 Score: 85
Period size: 17 Copynumber: 4.1 Consensus size: 18
26944 GCCGCTTTTT
26954 AATTT-ATTTTAAATTTA
1 AATTTAATTTTAAATTTA
*
26971 AATTT-ATCTTAAATTTA
1 AATTTAATTTTAAATTTA
*
26988 AATTTAAATTT-AATTTA
1 AATTTAATTTTAAATTTA
* *
27005 AATTTGATTTTAAAATTA
1 AATTTAATTTTAAATTTA
27023 AA
1 AA
27025 AAGTCCATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
17 36 0.78
18 10 0.22
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (18 bp):
AATTTAATTTTAAATTTA
Found at i:26988 original size:23 final size:23
Alignment explanation
Indices: 26951--27023 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
26941 CGGGCCGCTT
*
26951 TTTAATTT-ATTTTAAATTTAAA
1 TTTAATTTAAATTTAAATTTAAA
26973 TTT-ATCTTAAATTTAAATTTAAA
1 TTTAAT-TTAAATTTAAATTTAAA
* *
26996 TTTAATTTAAATTTGATTTTAAA
1 TTTAATTTAAATTTAAATTTAAA
*
27019 ATTAA
1 TTTAA
27024 AAAGTCCATT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
21 2 0.05
22 5 0.11
23 35 0.80
24 2 0.05
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (23 bp):
TTTAATTTAAATTTAAATTTAAA
Found at i:29045 original size:60 final size:58
Alignment explanation
Indices: 28962--29179 Score: 280
Period size: 60 Copynumber: 3.7 Consensus size: 58
28952 TTACCCGACG
*
28962 AACTTCCAAAAA-TCTCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCTCAA
1 AACTTCCAAAAATTC-CATTTTTACCCT-GAACTTCCAAAAATCTCATTTTTGACCTCGA
* *
29021 AACTTTCCAAAAATTCCATTTTTACCACTGAACTTCCAAAAATCTCATTCTTGACCCCGA
1 AAC-TTCCAAAAATTCCATTTTTACC-CTGAACTTCCAAAAATCTCATTTTTGACCTCGA
* * *
29081 AACTTCCAAAAATTCCA-TTTTATCCCTAAACTTCCAAAAATTTCATTTTTAACCTCGA
1 AACTTCCAAAAATTCCATTTTTA-CCCTGAACTTCCAAAAATCTCATTTTTGACCTCGA
*
29139 AACATT-CAAAAATTCCATTTTTACCCTCGAAACTCCCAAAA
1 AAC-TTCCAAAAATTCCATTTTTACCCT-G-AACTTCCAAAA
29180 TTATCCTTTT
Statistics
Matches: 141, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
58 51 0.36
59 26 0.18
60 60 0.43
61 4 0.03
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (58 bp):
AACTTCCAAAAATTCCATTTTTACCCTGAACTTCCAAAAATCTCATTTTTGACCTCGA
Found at i:29181 original size:29 final size:30
Alignment explanation
Indices: 28930--29179 Score: 229
Period size: 30 Copynumber: 8.4 Consensus size: 30
28920 GGAGGTCCCT
*** *
28930 AAACTGTCCAAAAATTTTGTTTTTACCCGACG
1 AAACT-TCCAAAAATTCCATTTTTACCC-TCG
28962 -AACTTCCAAAAA-TCTCATTTTTACCCTCG
1 AAACTTCCAAAAATTC-CATTTTTACCCTCG
*
28991 -AACTTCCAAAAA-TCTCATTTTTGA-CCTCA
1 AAACTTCCAAAAATTC-CATTTTT-ACCCTCG
29020 AAACTTTCCAAAAATTCCATTTTTACCACT-G
1 AAAC-TTCCAAAAATTCCATTTTTACC-CTCG
*
29051 -AACTTCCAAAAA-TCTCATTCTTGACCC-CG
1 AAACTTCCAAAAATTC-CATT-TTTACCCTCG
29080 AAACTTCCAAAAATTCCA-TTTTATCCCT--
1 AAACTTCCAAAAATTCCATTTTTA-CCCTCG
* *
29108 AAACTTCCAAAAATTTCATTTTTAACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCG
29138 AAACATT-CAAAAATTCCATTTTTACCCTCG
1 AAAC-TTCCAAAAATTCCATTTTTACCCTCG
*
29168 AAACTCCCAAAA
1 AAACTTCCAAAA
29180 TTATCCTTTT
Statistics
Matches: 186, Mismatches: 13, Indels: 40
0.78 0.05 0.17
Matches are distributed among these distances:
28 25 0.13
29 54 0.29
30 78 0.42
31 25 0.13
32 4 0.02
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCG
Done.