Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013859.1 Kokia drynarioides strain JFW-HI SEQ_128887, 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: 257970
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 66 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:180091 original size:95 final size:96
Alignment explanation
Indices: 179908--180098 Score: 235
Period size: 95 Copynumber: 2.0 Consensus size: 96
179898 TTTTTGGGAA
* ** *
179908 AAGGATATTTGATTATCTTGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGTGCAATATTTCA
1 AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGAGCAATATTTCA
**
179973 GAATCCAAGATAAGGAAACATTGCCTCGATT
66 GAATCCAAGATAAAAAAACATTGCCTCGATT
* *
180004 AAGGGTATTCGATTAT-TTCGATTTGAAGAAAAATTGCA-CTAGTAAGTTAAGGAGCAA-ATTTT
1 AAGGATATTCGATTATCTT-GATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGAGCAATATTTC
* * * *
180066 TGAAATTCGAGATAAAAAAATATTGCCTCGATT
65 AG-AATCCAAGATAAAAAAACATTGCCTCGATT
180099 TTAAAGTCTT
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
94 5 0.06
95 45 0.56
96 31 0.38
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (96 bp):
AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGAGCAATATTTCA
GAATCCAAGATAAAAAAACATTGCCTCGATT
Found at i:180526 original size:30 final size:30
Alignment explanation
Indices: 180490--180821 Score: 337
Period size: 29 Copynumber: 11.3 Consensus size: 30
180480 GTAAAATAGT
*
180490 AATTTTTGGAAGTTTTGGGGTTATAAATGG
1 AATTTTTGGAAGTTTTGGGGTTAAAAATGG
180520 AATTTTTGGAAG-TTTGGGGTTAAAAATGG
1 AATTTTTGGAAGTTTTGGGGTTAAAAATGG
* *
180549 AATTTTTGGAA-ATTCGAGGG-TAAAAATGGG
1 AATTTTTGGAAGTTTTG-GGGTTAAAAAT-GG
* *
180579 ATTTTTTGGAAG-TTTGGAGG-TAAAAATGA
1 AATTTTTGGAAGTTTTGG-GGTTAAAAATGG
*
180608 AATTTTTGGAAGTTTTGGGGTCAAAAATTGG
1 AATTTTTGGAAGTTTTGGGGTTAAAAA-TGG
* *
180639 GATTTTTGGAAGTTTAGGGG-TAAAAATGG
1 AATTTTTGGAAGTTTTGGGGTTAAAAATGG
*
180668 AATTTTTAGAAGTTTTGGGGTT-AAAATGG
1 AATTTTTGGAAGTTTTGGGGTTAAAAATGG
* * * *
180697 AATTTTTTGAAGTTTCGAGGTCAAAAAT-G
1 AATTTTTGGAAGTTTTGGGGTTAAAAATGG
* * *
180726 AGTTTTTTGAAAG-TTTGAGGG-TAGAAATGG
1 A-ATTTTTGGAAGTTTTG-GGGTTAAAAATGG
* * *
180756 AATTTTTAGAAGTTTTAGGGTCAAAAATGG
1 AATTTTTGGAAGTTTTGGGGTTAAAAATGG
**
180786 AATTTTT-GAAGTTTAAGGG-TAAAAATGG
1 AATTTTTGGAAGTTTTGGGGTTAAAAATGG
180814 AATTTTTG
1 AATTTTTG
180822 AATAGTTTAG
Statistics
Matches: 253, Mismatches: 33, Indels: 33
0.79 0.10 0.10
Matches are distributed among these distances:
28 15 0.06
29 129 0.51
30 89 0.35
31 20 0.08
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.38
Consensus pattern (30 bp):
AATTTTTGGAAGTTTTGGGGTTAAAAATGG
Found at i:180526 original size:59 final size:59
Alignment explanation
Indices: 180386--180821 Score: 340
Period size: 59 Copynumber: 7.4 Consensus size: 59
180376 TCTGGGAAAA
* * * * **
180386 TTTGGGTTTAAAAATGGAATTTTTAGACA-TTCGAGGGTAAAAGGGTAA-TTTT-GAGAGT
1 TTTGGGGTTAAAAATGGAATTTTTGGA-AGTTTGGGGGTAAAAATGTAATTTTTGGA-AGT
** ** * **
180444 TTTGAAGTCGAAAATGGAGTTTTTGGACA-TCCGGGGGT-AAAATAGTAATTTTTGGAAGT
1 TTTGGGGTTAAAAATGGAATTTTTGGA-AGTTTGGGGGTAAAAAT-GTAATTTTTGGAAGT
* * * *
180503 TTTGGGGTTATAAATGGAATTTTTGGAAGTTTGGGGTTAAAAATGGAATTTTTGGAA-A
1 TTTGGGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAGT
* * * *
180561 TTCGAGGG-TAAAAATGGGATTTTTTGGAAGTTTGGAGGTAAAAATGAAATTTTTGGAAGT
1 TTTG-GGGTTAAAAAT-GGAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAGT
* * * * *
180621 TTTGGGGTCAAAAATTGGGATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTAGAAGT
1 TTTGGGGTTAAAAA-TGGAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAGT
* * * * *
180681 TTTGGGGTT-AAAATGGAATTTTTTGAAGTTTCGAGGTCAAAAATG-AGTTTTTTGAAAG-
1 TTTGGGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGT-AAAAATGTA-ATTTTTGGAAGT
* * ** *
180739 TTTGAGGG-TAGAAATGGAATTTTTAGAAGTTTTAGGGTCAAAAATGGAATTTTT-GAAGT
1 TTTG-GGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGT-AAAAATGTAATTTTTGGAAGT
**
180798 TTAAGGG-TAAAAATGGAATTTTTG
1 TTTGGGGTTAAAAATGGAATTTTTG
180822 AATAGTTTAG
Statistics
Matches: 306, Mismatches: 56, Indels: 32
0.78 0.14 0.08
Matches are distributed among these distances:
57 3 0.01
58 90 0.29
59 150 0.49
60 62 0.20
61 1 0.00
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (59 bp):
TTTGGGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAGT
Found at i:180549 original size:88 final size:90
Alignment explanation
Indices: 180454--180821 Score: 368
Period size: 88 Copynumber: 4.2 Consensus size: 90
180444 TTTGAAGTCG
* * * * * *
180454 AAAATGGAGTTTTTGGACA-TCCGGGGGTAAAATAGTAATTTTTGGAAGTTTTGGGGTTATAAAT
1 AAAATGGAGTTTTTGGAAAGTTCGAGGGTAAAATAGGAATTTTTAGAAGTTTTGGGGTTAAAAAT
*
180518 GGAATTTTTGGAAGTTT-GGGGTTA
66 GGAATTTTTGGAAGTTTAGGGGTCA
* * * *
180542 AAAATGGAATTTTTGGAAA-TTCGAGGGTAAAAATGGGATTTTTTGGAAG-TTTGGAGG-TAAAA
1 AAAATGGAGTTTTTGGAAAGTTCGAGGGT-AAAATAGGAATTTTTAGAAGTTTTGG-GGTTAAAA
* *
180604 ATGAAATTTTTGGAAGTTTTGGGGTCA
64 ATGGAATTTTTGGAAGTTTAGGGGTCA
*
180631 AAAATTGG-GATTTTTGG-AAGTT-TAGGGGTAAAA-ATGGAATTTTTAGAAGTTTTGGGGTT-A
1 AAAA-TGGAG-TTTTTGGAAAGTTCGA-GGGTAAAATA-GGAATTTTTAGAAGTTTTGGGGTTAA
* * *
180691 AAATGGAATTTTTTGAAGTTTCGAGGTCA
62 AAATGGAATTTTTGGAAGTTTAGGGGTCA
* * * *
180720 AAAAT-GAGTTTTTTGAAAGTTTGAGGGTAGAAAT-GGAATTTTTAGAAGTTTTAGGGTCAAAAA
1 AAAATGGAGTTTTTGGAAAGTTCGAGGGTA-AAATAGGAATTTTTAGAAGTTTTGGGGTTAAAAA
*
180783 TGGAATTTTT-GAAGTTTAAGGGT-A
65 TGGAATTTTTGGAAGTTTAGGGGTCA
*
180807 AAAATGGAATTTTTG
1 AAAATGGAGTTTTTG
180822 AATAGTTTAG
Statistics
Matches: 235, Mismatches: 28, Indels: 34
0.79 0.09 0.11
Matches are distributed among these distances:
87 13 0.06
88 102 0.43
89 98 0.42
90 22 0.09
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (90 bp):
AAAATGGAGTTTTTGGAAAGTTCGAGGGTAAAATAGGAATTTTTAGAAGTTTTGGGGTTAAAAAT
GGAATTTTTGGAAGTTTAGGGGTCA
Found at i:180829 original size:59 final size:57
Alignment explanation
Indices: 180490--180833 Score: 350
Period size: 59 Copynumber: 5.8 Consensus size: 57
180480 GTAAAATAGT
* * *
180490 AATTTTTGGAAGTTTTGGGGTTATAAATGGAATTTTTGGAAGTTTGGGGTTAAAAATGG
1 AATTTTTGGAAGTTTTAGGG-TAAAAATGGAATTTTTGGAAGTTTAGGG-TAAAAATGG
* ** * * *
180549 AATTTTTGGAAATTCGAGGGTAAAAATGGGATTTTTTGGAAGTTTGGAGGTAAAAATGA
1 AATTTTTGGAAGTTTTAGGGTAAAAAT-GGAATTTTTGGAAGTTTAG-GGTAAAAATGG
* *
180608 AATTTTTGGAAGTTTTGGGGTCAAAAATTGGGATTTTTGGAAGTTTAGGGGTAAAAATGG
1 AATTTTTGGAAGTTTTAGGGT-AAAAA-TGGAATTTTTGGAAGTTTA-GGGTAAAAATGG
* * * * *
180668 AATTTTTAGAAGTTTTGGGGTTAAAATGGAATTTTTTGAAGTTTCGAGGTCAAAAAT-G
1 AATTTTTGGAAGTTTTAGGGTAAAAATGGAATTTTTGGAAGTTTAG-GGT-AAAAATGG
* * * * *
180726 AGTTTTTTGAAAGTTTGAGGGTAGAAATGGAATTTTTAGAAGTTTTAGGGTCAAAAATGG
1 A-ATTTTTGGAAGTTTTAGGGTAAAAATGGAATTTTTGGAAG-TTTAGGGT-AAAAATGG
* *
180786 AATTTTT-GAAGTTTAAGGGTAAAAATGGAATTTTTGAATAGTTTAGGG
1 AATTTTTGGAAGTTTTAGGGTAAAAATGGAATTTTTGGA-AGTTTAGGG
180834 ACCTCCAAGG
Statistics
Matches: 239, Mismatches: 35, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
57 1 0.00
58 60 0.25
59 118 0.49
60 58 0.24
61 2 0.01
ACGTcount: A:0.33, C:0.01, G:0.28, T:0.38
Consensus pattern (57 bp):
AATTTTTGGAAGTTTTAGGGTAAAAATGGAATTTTTGGAAGTTTAGGGTAAAAATGG
Found at i:181929 original size:3 final size:3
Alignment explanation
Indices: 181912--182035 Score: 61
Period size: 3 Copynumber: 39.0 Consensus size: 3
181902 TTTCCCTTTT
* * * * *
181912 TTA TTCA TT- TTA TTA TTA ATA TTT TTA TTA ATA TTTA TTA ATG TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* * * * *
181958 TTTA TTA CTA CTA TTTA TTA TTA ATA TTA TTA TTA TCTA TTAA ATA GTTT
1 -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA TT-A TTA -TTA
* *
182008 TTA TTA TTA TTAA CTA TTA TTA CTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA
182036 ATGTTACTTA
Statistics
Matches: 90, Mismatches: 22, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
2 2 0.02
3 70 0.78
4 18 0.20
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:181998 original size:13 final size:12
Alignment explanation
Indices: 181921--182029 Score: 56
Period size: 13 Copynumber: 8.5 Consensus size: 12
181911 TTTATTCATT
*
181921 TTATTATTAATA
1 TTATTATTACTA
* *
181933 TTTTTATTAATA
1 TTATTATTACTA
* **
181945 TTTATTAATGTTA
1 -TTATTATTACTA
*
181958 TTTATTACTACTA
1 -TTATTATTACTA
*
181971 TTTATTATTAATA
1 -TTATTATTACTA
181984 TTATTATTATCTA
1 TTATTATTA-CTA
* **
181997 TTAAATAGTTTTTA
1 TT-ATTA-TTACTA
182011 TTATTATTAACTA
1 TTATTATT-ACTA
182024 TTATTA
1 TTATTA
182030 CTATTAATGT
Statistics
Matches: 75, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
12 22 0.29
13 44 0.59
14 7 0.09
15 2 0.03
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (12 bp):
TTATTATTACTA
Found at i:182810 original size:17 final size:17
Alignment explanation
Indices: 182790--182862 Score: 92
Period size: 17 Copynumber: 4.2 Consensus size: 17
182780 TTTTAAATCC
* * *
182790 ATTTGAATTTTAATTAA
1 ATTTAAATTTAAAATAA
**
182807 ATTTAAATTTAAAGCAA
1 ATTTAAATTTAAAATAA
182824 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
182841 ATTTAAATTTAAAAATAA
1 ATTTAAATTT-AAAATAA
182859 ATTT
1 ATTT
182863 GAATCAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
17 38 0.78
18 11 0.22
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:182812 original size:6 final size:6
Alignment explanation
Indices: 182790--182853 Score: 62
Period size: 6 Copynumber: 11.2 Consensus size: 6
182780 TTTTAAATCC
* * **
182790 ATTTGA ATTTTA A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
182836 A-ATAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA A
182854 AATAAATTTG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
5 11 0.23
6 36 0.77
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:184761 original size:15 final size:14
Alignment explanation
Indices: 184743--184772 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
184733 TGAAGAAGAT
184743 GAAGAAGAAGACAAA
1 GAAGAAGAAGA-AAA
184758 GAAGAAGAAGAAAA
1 GAAGAAGAAGAAAA
184772 G
1 G
184773 GATGATCGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.67, C:0.03, G:0.30, T:0.00
Consensus pattern (14 bp):
GAAGAAGAAGAAAA
Found at i:187118 original size:148 final size:148
Alignment explanation
Indices: 186838--187200 Score: 446
Period size: 148 Copynumber: 2.4 Consensus size: 148
186828 AAATTTGAAG
* * * * * *
186838 GGAAAGGTTGAGGGCACAACGGCGAACCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCT
1 GGAAAGGTTGAGGCCGCAACAGTGAACCCGGTACC-ATGAAGATGTGATGGGAAAGGTTGAGGCC
* *
186903 GCAACGGCGAATCCAGTACCATGAAGAGATAGAGGGAAGGATTGAGGCCGCAATGGCAAATCCGG
65 GCAACGGCGAACCCAGTACCATGAAGAGATAGAGGGAAGGATTGAGGCCGCAATGACAAATCCGG
* *
186968 TACCTTAGAAGATGTGATG
130 TACATTAGAAGATGTGATA
* *
186987 GGAAAGGTTGAGGCCGTAATAGTGAACCCGGTACCATGAAGATGTGATGGGAAAGGTTGAGGCCG
1 GGAAAGGTTGAGGCCGCAACAGTGAACCCGGTACCATGAAGATGTGATGGGAAAGGTTGAGGCCG
* * * * *
187052 CAACGGCGAACCCAGTACCATGAAGAGAT-GAAGGGAAGGATTGAGGTCGTGACT-ACGAATCTG
66 CAACGGCGAACCCAGTACCATGAAGAGATAG-AGGGAAGGATTGAGGCCG-CAATGACAAATCCG
*
187115 GTACATTAGGAGATGTGATA
129 GTACATTAGAAGATGTGATA
* * ** *
187135 GGAAAGGTTTAGGCCGCAACGGTGAACCCAATACCATGAAGA-GATGAAGGG-AAGGATTGAGGC
1 GGAAAGGTTGAGGCCGCAACAGTGAACCCGGTACCATGAAGATG-TGATGGGAAAGG-TTGAGGC
187198 CGC
64 CGC
187201 GACGATGAAT
Statistics
Matches: 185, Mismatches: 25, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
147 6 0.03
148 148 0.80
149 31 0.17
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.17
Consensus pattern (148 bp):
GGAAAGGTTGAGGCCGCAACAGTGAACCCGGTACCATGAAGATGTGATGGGAAAGGTTGAGGCCG
CAACGGCGAACCCAGTACCATGAAGAGATAGAGGGAAGGATTGAGGCCGCAATGACAAATCCGGT
ACATTAGAAGATGTGATA
Found at i:187388 original size:247 final size:248
Alignment explanation
Indices: 186887--187444 Score: 603
Period size: 247 Copynumber: 2.3 Consensus size: 248
186877 AAGATGTGAT
* * *
186887 GGGAAAGGTTGAGGCTGCAACGGCGAATCCAGTACCATGAAGAGAT-AGAGGGAAGGATTGAGGC
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCAATACCATGAAGAGATGA-AGGGAAGGATTGAGGC
* * * * *
186951 CGCAATGGCAAATCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGTAATAGTGAACCC
65 CGCAACGACAAATCCGGTACCTCAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACAGTAAACCC
* ** * * *
187016 GGTACCATGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGAGAT
130 GATACCATGAAGATACGAAGGGAAAGGTTGAGACCGCAACGGCGAACCCAGTACCAAGAAGAGAT
** * * * * * * * **
187081 GAAGGGAAGGATTGAGGTCGTGACTACGAATCTGGTACATTAGGAGATGTGATA
195 GAAGGGAAGGATTGAGACCGTAACGACAAACCCGATACATTAGAAGATACGATA
* *
187135 -GGAAAGGTTTAGGCCGCAACGGTGAACCCAATACCATGAAGAGATGAAGGGAAGGATTGAGGCC
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCAATACCATGAAGAGATGAAGGGAAGGATTGAGGCC
* ** * * *
187199 GCGACGATGAATCTGGTACCTCAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACGGTAAACTCG
66 GCAACGACAAATCCGGTACCTCAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACAGTAAACCCG
* * *
187264 ATACCATTAAGATACGAAGGGAAAGGTTGAGACCGTAATGGCGAACCCAGTACCTAAGAAGATG-
131 ATACCATGAAGATACGAAGGGAAAGGTTGAGACCGCAACGGCGAACCCAGTACC-AAGAAGA-GA
* *
187328 TGATGGGAAAGG-TTGAGACCGTAACGATAAACCCGATACCA-T-GAAGATACGA-A
194 TGAAGGG-AAGGATTGAGACCGTAACGACAAACCCGATA-CATTAGAAGATACGATA
* * * *
187381 GGGAAAGGTTGAGGCCACAGCGGCGAACCCGATACC-T-AAGAAGATGCGATGGGAAGGATTGAG
1 GGGAAAGGTTGAGGCCGCAACGGCGAACCCAATACCATGAAG-AGAT--GAAGGGAAGGATTGAG
187444 G
63 G
187445 TCGTAACGGT
Statistics
Matches: 257, Mismatches: 44, Indels: 18
0.81 0.14 0.06
Matches are distributed among these distances:
245 3 0.01
246 6 0.02
247 194 0.75
248 47 0.18
249 7 0.03
ACGTcount: A:0.33, C:0.16, G:0.33, T:0.17
Consensus pattern (248 bp):
GGGAAAGGTTGAGGCCGCAACGGCGAACCCAATACCATGAAGAGATGAAGGGAAGGATTGAGGCC
GCAACGACAAATCCGGTACCTCAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACAGTAAACCCG
ATACCATGAAGATACGAAGGGAAAGGTTGAGACCGCAACGGCGAACCCAGTACCAAGAAGAGATG
AAGGGAAGGATTGAGACCGTAACGACAAACCCGATACATTAGAAGATACGATA
Found at i:187468 original size:297 final size:297
Alignment explanation
Indices: 186986--187629 Score: 699
Period size: 297 Copynumber: 2.2 Consensus size: 297
186976 AAGATGTGAT
* * * *
186986 GGGAAAGGTTGAGGCCGTAATAGTGAACCCGGTACC-ATGAAGATGTGATGGGAAAGGTTGAGGC
1 GGGAAAGGTTGAGGCCGTAATGGTGAACCCAGTACCTAAGAAGATGTGATGGGAAAGGTTGAGAC
* * * * ** * * *
187050 CGCAACGGCGAACCCAGTACCATGAAGAGATGAAGGGAAGGATTGAGGTCGTGACTACGAATCTG
66 CGCAACGACAAACCCAGTACCATGAAGAGACGAAGGGAAGGATTGAGGCCCAGACGACGAACCCG
* * * * * *
187115 GTACATTAGGAGATGTGATAGGAAAGGTTTAGGCCGCAACGGTGAACCCAATACCATGAAGAGAT
131 ATACATAAGAAGATGCGATAGGAAAGGTTGAGGCCGCAACGGTGAACCCAATACCATGAAAAGAT
* * * * * *
187180 GAAGGGAAGGATTGAGGCCGCGACGATGAA-TCTGGTACCTCAGAAGATGTGATGGGAAAGGTTG
196 GAAAGGAAGGATTGAGGCCACGACGATGAATTC-GGTACCTAAGAAGATGCGATGCGAAAGGTTA
* * * **
187244 AGGCCGTAACGGTAAACTCGATACCATTAAGATACGAA
260 AAGCCGCAACGGTAAACCCGATACCACGAAGATACGAA
* *
187282 GGGAAAGGTTGAGACCGTAATGGCGAACCCAGTACCTAAGAAGATGTGATGGGAAAGGTTGAGAC
1 GGGAAAGGTTGAGGCCGTAATGGTGAACCCAGTACCTAAGAAGATGTGATGGGAAAGGTTGAGAC
* * * *
187347 CGTAACGATAAACCC-GATACCATGAAGATACGAAGGGAAAGG-TTGAGGCCACAG-CGGCGAAC
66 CGCAACGACAAACCCAG-TACCATGAAGAGACGAAGGG-AAGGATTGAGGCC-CAGACGACGAAC
* * * * * *
187409 CCGATACCTAAGAAGATGCGAT-GGGAAGGATTGAGGTCGTAACGGTGAATCCGATACCATGAAA
128 CCGATACATAAGAAGATGCGATAGGAAAGG-TTGAGGCCGCAACGGTGAACCCAATACCATGAAA
** * * *
187473 ATTTGAAAGGAAGGATTGAGGCCACGATGGTGAATTCGGTACCTAAGAAGATGCGATGCGATAGG
192 AGATGAAAGGAAGGATTGAGGCCACGACGATGAATTCGGTACCTAAGAAGATGCGATGCGAAAGG
* * *
187538 TTAAAGCCGCAACGGTGAACCCGTTACCACGAAGATATGAA
257 TTAAAGCCGCAACGGTAAACCCGATACCACGAAGATACGAA
* * * * *
187579 GGGAAAGGTTTAGGCCGTAATGGTGAACCTAGCACCTTAGAA-ACGTGATGG
1 GGGAAAGGTTGAGGCCGTAATGGTGAACCCAGTACCTAAGAAGATGTGATGG
187630 AACAGATTGA
Statistics
Matches: 285, Mismatches: 57, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
296 47 0.16
297 231 0.81
298 7 0.02
ACGTcount: A:0.33, C:0.17, G:0.32, T:0.18
Consensus pattern (297 bp):
GGGAAAGGTTGAGGCCGTAATGGTGAACCCAGTACCTAAGAAGATGTGATGGGAAAGGTTGAGAC
CGCAACGACAAACCCAGTACCATGAAGAGACGAAGGGAAGGATTGAGGCCCAGACGACGAACCCG
ATACATAAGAAGATGCGATAGGAAAGGTTGAGGCCGCAACGGTGAACCCAATACCATGAAAAGAT
GAAAGGAAGGATTGAGGCCACGACGATGAATTCGGTACCTAAGAAGATGCGATGCGAAAGGTTAA
AGCCGCAACGGTAAACCCGATACCACGAAGATACGAA
Found at i:187602 original size:99 final size:99
Alignment explanation
Indices: 186837--187607 Score: 601
Period size: 99 Copynumber: 7.8 Consensus size: 99
186827 AAAATTTGAA
* * * * * * *
186837 GGGAAAGGTTGAGGGCACAACGGCGAACCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGC
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGATACC-ATGAAGATATGAAGGGAAAGGTTGAGGC
* * * * * * *
186902 TGCAACGGCGAATCCAGTACCATGAAG-AGAT-AGA-
65 CGTAATGGTGAACCCGGTACC-T-AAGAAGATGTGAT
* ** * * * * *
186936 GGG-AAGGATTGAGGCCGCAATGGCAAATCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGG
1 GGGAAAGG-TTGAGGCCGCAACGGTGAACCCGATACCAT-GAAGATATGAAGGGAAAGGTTGAGG
* *
187000 CCGTAATAGTGAACCCGGTACC-ATGAAGATGTGAT
64 CCGTAATGGTGAACCCGGTACCTAAGAAGATGTGAT
* *
187035 GGGAAAGGTTGAGGCCGCAACGGCGAACCC-AGTACCATGAAGAGATGAAGGG-AAGGATTGAGG
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGA-TACCATGAAGATATGAAGGGAAAGG-TTGAGG
* * ** * * * * *
187098 TCGTGACT-ACGAATCTGGTACATTAGGAGATGTGAT
64 CCGT-AATGGTGAACCCGGTACCTAAGAAGATGTGAT
* * * *
187134 AGGAAAGGTTTAGGCCGCAACGGTGAACCCAATACCATGAAGAGATGAAGGG-AAGGATTGAGGC
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGATACCATGAAGATATGAAGGGAAAGG-TTGAGGC
** * * * * *
187198 CGCGACGATGAATCTGGTACCTCAGAAGATGTGAT
65 CGTAATGGTGAACCCGGTACCTAAGAAGATGTGAT
* * * * * *
187233 GGGAAAGGTTGAGGCCGTAACGGTAAACTCGATACCATTAAGATACGAAGGGAAAGGTTGAGACC
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCC
* *
187298 GTAATGGCGAACCCAGTACCTAAGAAGATGTGAT
66 GTAATGGTGAACCCGGTACCTAAGAAGATGTGAT
* * * * *
187332 GGGAAAGGTTGAGACCGTAACGATAAACCCGATACCATGAAGATACGAAGGGAAAGGTTGAGGCC
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCC
** ** * * *
187397 ACAGCGGCGAACCCGATACCTAAGAAGATGCGAT
66 GTAATGGTGAACCCGGTACCTAAGAAGATGTGAT
* * * * * *
187431 GGG-AAGGATTGAGGTCGTAACGGTGAATCCGATACCATGAAAATTTGAAAGG-AAGGATTGAGG
1 GGGAAAGG-TTGAGGCCGCAACGGTGAACCCGATACCATGAAGATATGAAGGGAAAGG-TTGAGG
*** ** *
187494 CCACGATGGTGAATTCGGTACCTAAGAAGATGCGAT
64 CCGTAATGGTGAACCCGGTACCTAAGAAGATGTGAT
* * * * * * *
187530 GCGATAGGTTAAAGCCGCAACGGTGAACCCGTTACCACGAAGATATGAAGGGAAAGGTTTAGGCC
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCC
187595 GTAATGGTGAACC
66 GTAATGGTGAACC
187608 TAGCACCTTA
Statistics
Matches: 544, Mismatches: 111, Indels: 34
0.79 0.16 0.05
Matches are distributed among these distances:
96 2 0.00
97 8 0.01
98 43 0.08
99 475 0.87
100 16 0.03
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.18
Consensus pattern (99 bp):
GGGAAAGGTTGAGGCCGCAACGGTGAACCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCC
GTAATGGTGAACCCGGTACCTAAGAAGATGTGAT
Found at i:187604 original size:49 final size:49
Alignment explanation
Indices: 186823--187607 Score: 430
Period size: 49 Copynumber: 15.9 Consensus size: 49
186813 CTGTGAAAAA
* * * ** * *
186823 CATGAAAATTTGAAGGGAAAGGTTGAGGGCACAACGGCGAACCCGGTAC
1 CATGAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGTGAACCCGATAC
* * * * * *
186872 CTAAGAAGATGTGATGGGAAAGGTTGAGGCTGCAACGGCGAATCC-AGTAC
1 C-ATGAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGTGAACCCGA-TAC
* * ** * *
186922 CATGAAGA-GAT-AGAGGG-AAGGATTGAGGCCGCAATGGCAAATCCGGTAC
1 CATGAAGATG-TGA-AGGGAAAGG-TTGAGGCCGTAACGGTGAACCCGATAC
* * ** *
186971 CTTAGAAGATGTGATGGGAAAGGTTGAGGCCGTAATAGTGAACCCGGTAC
1 CAT-GAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGTGAACCCGATAC
* * *
187021 CATGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCC-AGTAC
1 CATGAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGTGAACCCGA-TAC
* * *** * * *
187070 CATGAAGA-GATGAAGGG-AAGGATTGAGGTCGTGACTACGAATCTGGTA-
1 CATGAAGATG-TGAAGGGAAAGG-TTGAGGCCGTAACGGTGAACCCGATAC
* * * *
187118 CATTAGGAGATGTGATA-GGAAAGGTTTAGGCCGCAACGGTGAACCCAATAC
1 CA-T-GAAGATGTGA-AGGGAAAGGTTGAGGCCGTAACGGTGAACCCGATAC
** * * * *
187169 CATGAAGA-GATGAAGGG-AAGGATTGAGGCCGCGACGATGAATCTGGTAC
1 CATGAAGATG-TGAAGGGAAAGG-TTGAGGCCGTAACGGTGAACCCGATAC
* * *
187218 C-TCAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACGGTAAACTCGATAC
1 CAT--GAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGTGAACCCGATAC
* ** * * *
187268 CATTAAGATACGAAGGGAAAGGTTGAGACCGTAATGGCGAACCC-AGTAC
1 CATGAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGTGAACCCGA-TAC
* * * * *
187317 CTAAGAAGATGTGATGGGAAAGGTTGAGACCGTAACGATAAACCCGATAC
1 C-ATGAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGTGAACCCGATAC
** ** * *
187367 CATGAAGATACGAAGGGAAAGGTTGAGGCCACAGCGGCGAACCCGATAC
1 CATGAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGTGAACCCGATAC
* * * * *
187416 CTAAGAAGATGCGATGGG-AAGGATTGAGGTCGTAACGGTGAATCCGATAC
1 C-ATGAAGATGTGAAGGGAAAGG-TTGAGGCCGTAACGGTGAACCCGATAC
* * * *** * ** *
187466 CATGAAAATTTGAAAGG-AAGGATTGAGGCCACGATGGTGAATTCGGTAC
1 CATGAAGATGTGAAGGGAAAGG-TTGAGGCCGTAACGGTGAACCCGATAC
* * * * * * * * *
187515 CTAAGAAGATGCGATGCGATAGGTTAAAGCCGCAACGGTGAACCCGTTAC
1 C-ATGAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGTGAACCCGATAC
* * * *
187565 CACGAAGATATGAAGGGAAAGGTTTAGGCCGTAATGGTGAACC
1 CATGAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGTGAACC
187608 TAGCACCTTA
Statistics
Matches: 558, Mismatches: 143, Indels: 70
0.72 0.19 0.09
Matches are distributed among these distances:
48 21 0.04
49 283 0.51
50 230 0.41
51 24 0.04
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.18
Consensus pattern (49 bp):
CATGAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGTGAACCCGATAC
Found at i:188196 original size:5 final size:5
Alignment explanation
Indices: 188186--188210 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
188176 AAAGATTTGG
188186 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
188211 AATATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:188559 original size:19 final size:18
Alignment explanation
Indices: 188519--188561 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
188509 TGTTCTTCCC
188519 AAAAAATCATGAGTAACT
1 AAAAAATCATGAGTAACT
188537 AAAAAATCATGAGTAACT
1 AAAAAATCATGAGTAACT
188555 AAAAAAT
1 AAAAAAT
188562 TCTTCTCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.21
Consensus pattern (18 bp):
AAAAAATCATGAGTAACT
Found at i:189095 original size:22 final size:22
Alignment explanation
Indices: 189069--189111 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
189059 TCGACTTCTT
189069 TATTTTCTATTT-CTTTTAATTA
1 TATTTTCT-TTTACTTTTAATTA
*
189091 TATTTTCTTTTATTTTTAATT
1 TATTTTCTTTTACTTTTAATT
189112 TTGTTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (22 bp):
TATTTTCTTTTACTTTTAATTA
Found at i:194791 original size:22 final size:20
Alignment explanation
Indices: 194733--194791 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 20
194723 ATTATTTTTA
*
194733 TTTTTATTTTATTATTATTAT
1 TTTTTA-TTTATTTTTATTAT
194754 TTTTCTATCTTA-TTTTATTTAT
1 TTTT-TAT-TTATTTTTA-TTAT
194776 TTATTTATTTATTTTT
1 TT-TTTATTTATTTTT
194792 GTCTAGGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
21 12 0.38
22 18 0.56
23 2 0.06
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTATTTATTTTTATTAT
Found at i:196301 original size:19 final size:19
Alignment explanation
Indices: 196279--196323 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
196269 TTATATTAGG
196279 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
196298 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
196317 ATTTAAT
1 ATTTAAT
196324 TTAAGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:197161 original size:21 final size:22
Alignment explanation
Indices: 197125--197171 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
197115 TTTCTATTTC
*
197125 TTTTAATTATATTTTCGTTTAT
1 TTTTAATTATAGTTTCGTTTAT
*
197147 TTTTAATTAT-GTTTCTTTTAT
1 TTTTAATTATAGTTTCGTTTAT
197168 TTTT
1 TTTT
197172 CCTCAGATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (22 bp):
TTTTAATTATAGTTTCGTTTAT
Found at i:197409 original size:6 final size:6
Alignment explanation
Indices: 197388--197479 Score: 54
Period size: 6 Copynumber: 16.5 Consensus size: 6
197378 CCCAATTTTA
* *
197388 AAATTT AAA-TT --ATTT AAGTTT AAATTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * * * * * *
197432 -ATTTT GAGTTT GAATTT -ATTTT AAA-TT AAATTT AAAATT AAGTTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
197477 AAA
1 AAA
197480 ATGTCCAAAT
Statistics
Matches: 66, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
3 1 0.02
4 2 0.03
5 19 0.29
6 44 0.67
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:197420 original size:17 final size:17
Alignment explanation
Indices: 197391--197479 Score: 94
Period size: 17 Copynumber: 5.4 Consensus size: 17
197381 AATTTTAAAA
197391 TTTAAA-TTA-TTTAAG
1 TTTAAATTTATTTTAAG
*
197406 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAG
*
197423 TTTAAATTTATTTTGAG
1 TTTAAATTTATTTTAAG
*
197440 TTTGAATTTATTTTAA-
1 TTTAAATTTATTTTAAG
* **
197456 ATTAAATTTAAAATTAAG
1 TTTAAATTT-ATTTTAAG
197474 TTTAAA
1 TTTAAA
197480 ATGTCCAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
15 6 0.10
16 10 0.17
17 39 0.65
18 5 0.08
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAG
Found at i:197476 original size:34 final size:34
Alignment explanation
Indices: 197382--197479 Score: 112
Period size: 34 Copynumber: 2.9 Consensus size: 34
197372 ATGAAGCCCA
*
197382 ATTTTAAAATTTAAA-TT-ATTTAAGTTTAAATTT
1 ATTTT-AAATTTAAATTTAAATTAAGTTTAAATTT
** * *
197415 ATTTTAAATTTAAATTTATTTTGAGTTTGAATTT
1 ATTTTAAATTTAAATTTAAATTAAGTTTAAATTT
197449 ATTTTAAA-TTAAATTTAAAATTAAGTTTAAA
1 ATTTTAAATTTAAATTT-AAATTAAGTTTAAA
197480 ATGTCCAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
32 9 0.16
33 15 0.27
34 31 0.56
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (34 bp):
ATTTTAAATTTAAATTTAAATTAAGTTTAAATTT
Found at i:197547 original size:18 final size:18
Alignment explanation
Indices: 197524--197558 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
197514 CAAACCCAAT
*
197524 AACCCAAGCCCAATTACA
1 AACCCAAGACCAATTACA
*
197542 AACCCATGACCAATTAC
1 AACCCAAGACCAATTAC
197559 CCACCTAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.37, G:0.06, T:0.14
Consensus pattern (18 bp):
AACCCAAGACCAATTACA
Found at i:198184 original size:16 final size:16
Alignment explanation
Indices: 198165--198214 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
198155 AAATAATTTT
*
198165 AATAATGATATTAATA
1 AATAATAATATTAATA
198181 AATAATAATATTAATA
1 AATAATAATATTAATA
* *
198197 ATTAATAATAATAATA
1 AATAATAATATTAATA
198213 AA
1 AA
198215 AGAGAAATCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
AATAATAATATTAATA
Found at i:198187 original size:3 final size:3
Alignment explanation
Indices: 198164--198213 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
198154 TAAATAATTT
* * *
198164 TAA TAA TGA TAT TAA TAAA TAA TAA TAT TAA TAA TTAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
198211 TAA
1 TAA
198214 AAGAGAAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:198195 original size:25 final size:23
Alignment explanation
Indices: 198150--198213 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 23
198140 CATTAAAGTT
**
198150 TTAATAAATAATTTTAATAATGATA
1 TTAATAAATAATAATAATAAT-A-A
*
198175 TTAATAAATAATAATATTAATAA
1 TTAATAAATAATAATAATAATAA
198198 TTAAT-AATAATAATAA
1 TTAATAAATAATAATAA
198214 AAGAGAAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 10 0.29
23 6 0.17
24 1 0.03
25 18 0.51
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TTAATAAATAATAATAATAATAA
Found at i:198208 original size:13 final size:13
Alignment explanation
Indices: 198150--198211 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 13
198140 CATTAAAGTT
*
198150 TTAATAAATAAT-T
1 TTAAT-AATAATAA
*
198163 TTAATAATGAT-A
1 TTAATAATAATAA
198175 TTAAT-A-AATAA
1 TTAATAATAATAA
*
198186 -TAATATTAATAA
1 TTAATAATAATAA
198198 TTAATAATAATAA
1 TTAATAATAATAA
198211 T
1 T
198212 AAAAGAGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
10 6 0.15
11 2 0.05
12 15 0.38
13 17 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
TTAATAATAATAA
Found at i:198506 original size:3 final size:3
Alignment explanation
Indices: 198500--198533 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
198490 TTTAAAAAAG
198500 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
198534 CGGTTTTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:199326 original size:29 final size:28
Alignment explanation
Indices: 199221--199564 Score: 228
Period size: 30 Copynumber: 11.8 Consensus size: 28
199211 AAAAATCAAG
* *
199221 TTTTGACCTTAAACTTTCCCAAAAATTACA
1 TTTTAACCCTAAACTTT--CAAAAATTACA
* *
199251 TTTTGACTCCCAAACTTTCCAAAAATTACA
1 TTTTAAC-CCTAAACTTT-CAAAAATTACA
* * *
199281 TTTTGACCCTTGAACTTATCAAAAATCACA
1 TTTTAACCC-TAAACTT-TCAAAAATTACA
* * *
199311 TTTTAACTCTAAACTTCCAAAATTTACA
1 TTTTAACCCTAAACTTTCAAAAATTACA
* * *
199339 TTTTGACCCCTAAACTTTCCCAAAATTATA
1 TTTT-AACCCTAAACTTT-CAAAAATTACA
* * *
199369 TGTTGACCCCCAAACTTCTCAAAAA-TACA
1 T-TTTAACCCTAAACTT-TCAAAAATTACA
* *
199398 TTTTAA-CCTCGAACTTTCAAAAATTAGA
1 TTTTAACCCT-AAACTTTCAAAAATTACA
* *
199426 TTTTTACCCTCGAACTTCTCAAAAATTACA
1 TTTTAACCCT-AAACTT-TCAAAAATTACA
** * * *
199456 TTTTTCCCCTAAGCGTCTC-AAAATCACA
1 TTTTAACCCTAAAC-TTTCAAAAATTACA
* * *
199484 TTTTGACCCTAAACTTCCACAAATTACA
1 TTTTAACCCTAAACTTTCAAAAATTACA
* *
199512 TTGTT-ACTCGAAACTTCTCAAAAATTACA
1 TT-TTAACCCTAAACTT-TCAAAAATTACA
*
199541 TTTTTACCCCTAAACTTTCAAAAA
1 -TTTTAACCCTAAACTTTCAAAAA
199565 AACACCATTT
Statistics
Matches: 250, Mismatches: 47, Indels: 35
0.75 0.14 0.11
Matches are distributed among these distances:
27 11 0.04
28 66 0.26
29 57 0.23
30 104 0.42
31 12 0.05
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.34
Consensus pattern (28 bp):
TTTTAACCCTAAACTTTCAAAAATTACA
Found at i:199355 original size:58 final size:55
Alignment explanation
Indices: 199230--199563 Score: 224
Period size: 58 Copynumber: 5.7 Consensus size: 55
199220 GTTTTGACCT
* * *
199230 TAAACTTTCCCAAAAATTACATTTTGACTCCCAAACTTTCCAAAAATTACATTTTGACCCT
1 TAAACTTT--CAAAAATTACATTTTAAC-CCTAAAC-TTCC-AAAATTACATTTT-ACCCC
* * *
199291 TGAACTTATCAAAAATCACATTTTAACTCTAAACTTCCAAAATTTACATTTTGACCCC
1 TAAACTT-TCAAAAATTACATTTTAACCCTAAACTTCCAAAA-TTACATTTT-ACCCC
* * * * * * *
199349 TAAACTTTCCCAAAATTATATGTTGACCCCCAAACTTCTCAAAAATACATTTTA-ACC
1 TAAACTTT-CAAAAATTACAT-TTTAACCCTAAACTTC-CAAAATTACATTTTACCCC
* * * * *
199406 TCGAACTTTCAAAAATTAGATTTTTACCCTCGAACTTCTCAAAAATTACATTTTTCCCC
1 T-AAACTTTCAAAAATTACATTTTAACCCT-AAACTTC-C-AAAATTACATTTTACCCC
* * * * *
199465 TAAGCGTCTC-AAAATCACATTTTGACCCTAAACTTCCACAAATTACATTGTTA-CTC
1 TAAAC-TTTCAAAAATTACATTTTAACCCTAAACTTCCA-AAATTACATT-TTACCCC
* * *
199521 GAAACTTCTCAAAAATTACATTTTTACCCCTAAACTTTCAAAA
1 TAAACTT-TCAAAAATTACA-TTTTAACCCTAAACTTCCAAAA
199564 AAACACCATT
Statistics
Matches: 215, Mismatches: 43, Indels: 34
0.74 0.15 0.12
Matches are distributed among these distances:
55 2 0.01
56 23 0.11
57 45 0.21
58 86 0.40
59 31 0.14
60 21 0.10
61 6 0.03
62 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (55 bp):
TAAACTTTCAAAAATTACATTTTAACCCTAAACTTCCAAAATTACATTTTACCCC
Found at i:208553 original size:179 final size:179
Alignment explanation
Indices: 208253--208610 Score: 698
Period size: 179 Copynumber: 2.0 Consensus size: 179
208243 TATTACATTG
*
208253 TATAATTTATTTTTAAAAAGATCAAATTTATTGTTTCGTCTAAGCCCAAAAATATAAAAAAGGGG
1 TATAATTTATTTTTAAAAAGATCAAATTTATTGTTTCGTCTAAACCCAAAAATATAAAAAAGGGG
208318 CTTGAAGGAACTAAGTTTAAATTTGAATTTTATAAATTTGTTTGTTTGTTTGTAATTTTTTTAAA
66 CTTGAAGGAACTAAGTTTAAATTTGAATTTTATAAATTTGTTTGTTTGTTTGTAATTTTTTTAAA
208383 ATTTAGAATTTACAAATATTTGTCAAGGAGGTCTTGTACTTTATTTATA
131 ATTTAGAATTTACAAATATTTGTCAAGGAGGTCTTGTACTTTATTTATA
208432 TATAATTTATTTTTAAAAAGATCAAATTTATTGTTTCGTCTAAACCCAAAAATATAAAAAAGGGG
1 TATAATTTATTTTTAAAAAGATCAAATTTATTGTTTCGTCTAAACCCAAAAATATAAAAAAGGGG
*
208497 CTTGAAGGAACTAAGTTTAAATTTGAATTTTATAAATTTGTTTGTTTGTTTGTAATTTTTTTTAA
66 CTTGAAGGAACTAAGTTTAAATTTGAATTTTATAAATTTGTTTGTTTGTTTGTAATTTTTTTAAA
208562 ATTTAGAATTTACAAATATTTGTCAAGGAGGTCTTGTACTTTATTTATA
131 ATTTAGAATTTACAAATATTTGTCAAGGAGGTCTTGTACTTTATTTATA
208611 AACAATCAGA
Statistics
Matches: 177, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
179 177 1.00
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (179 bp):
TATAATTTATTTTTAAAAAGATCAAATTTATTGTTTCGTCTAAACCCAAAAATATAAAAAAGGGG
CTTGAAGGAACTAAGTTTAAATTTGAATTTTATAAATTTGTTTGTTTGTTTGTAATTTTTTTAAA
ATTTAGAATTTACAAATATTTGTCAAGGAGGTCTTGTACTTTATTTATA
Found at i:211261 original size:14 final size:14
Alignment explanation
Indices: 211232--211271 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
211222 TATTAAGGAA
* *
211232 TTAATGAATTACGC
1 TTAATTAATTAAGC
*
211246 TTAATTACTTAAGC
1 TTAATTAATTAAGC
211260 TTAATTAATTAA
1 TTAATTAATTAA
211272 CCATTAAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (14 bp):
TTAATTAATTAAGC
Found at i:215968 original size:16 final size:16
Alignment explanation
Indices: 215925--215972 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
215915 ATGATCGTAT
* **
215925 TAGAATAGAGATAAAA
1 TAGAATAGAGTTGTAA
*
215941 TAGAATAAAGTTGTAA
1 TAGAATAGAGTTGTAA
215957 TAGAATAGAGTTGTAA
1 TAGAATAGAGTTGTAA
215973 AGACTATCAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.27
Consensus pattern (16 bp):
TAGAATAGAGTTGTAA
Found at i:217060 original size:13 final size:13
Alignment explanation
Indices: 217038--217075 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
217028 TATCTTCTCG
217038 AAAA-TATTTTTT
1 AAAAGTATTTTTT
*
217050 CAAAGTA-TTTTT
1 AAAAGTATTTTTT
217062 AAAAGTATTTTTT
1 AAAAGTATTTTTT
217075 A
1 A
217076 GCCTTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 14 0.64
13 8 0.36
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (13 bp):
AAAAGTATTTTTT
Found at i:225161 original size:30 final size:32
Alignment explanation
Indices: 225108--225168 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
225098 GAGAAAGGAT
225108 AAAAATGAATTTGGATAAAAATAT-AAGTTTG
1 AAAAATGAATTTGGATAAAAATATAAAGTTTG
**
225139 AAAAATGGGTTTGGAT-AAAATATAAAGTTT
1 AAAAATGAATTTGGATAAAAATATAAAGTTT
225169 ATTTTCTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (32 bp):
AAAAATGAATTTGGATAAAAATATAAAGTTTG
Found at i:232893 original size:26 final size:24
Alignment explanation
Indices: 232863--232916 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
232853 TATTTAATTT
232863 TAAAAACA-TGTTATACTATATATATA
1 TAAAAACACT-TTATA-TATAT-TATA
*
232889 TAAAAACACTTTATATATATTATT
1 TAAAAACACTTTATATATATTATA
232913 TAAA
1 TAAA
232917 TGAATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 7 0.27
25 5 0.19
26 13 0.50
27 1 0.04
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (24 bp):
TAAAAACACTTTATATATATTATA
Found at i:233843 original size:12 final size:12
Alignment explanation
Indices: 233828--233886 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
233818 ATAACATCTA
233828 AACAACAAAAAT
1 AACAACAAAAAT
*
233840 AACAACCAAAAT
1 AACAACAAAAAT
*
233852 AACAGA-AAAAAC
1 AACA-ACAAAAAT
* *
233864 AATAAAAAAAAT
1 AACAACAAAAAT
*
233876 AACAATAAAAA
1 AACAACAAAAA
233887 ACAACGCTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 1 0.03
12 36 0.95
13 1 0.03
ACGTcount: A:0.76, C:0.14, G:0.02, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:233855 original size:21 final size:21
Alignment explanation
Indices: 233814--233865 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
233804 AAAACACATA
* *
233814 AAAAATAAC-ATCTAAACAAC
1 AAAAATAACAACCAAAACAAC
*
233834 AAAAATAACAACCAAAATAAC
1 AAAAATAACAACCAAAACAAC
233855 AGAAAA-AACAA
1 A-AAAATAACAA
233866 TAAAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.33
21 14 0.52
22 4 0.15
ACGTcount: A:0.71, C:0.17, G:0.02, T:0.10
Consensus pattern (21 bp):
AAAAATAACAACCAAAACAAC
Found at i:233879 original size:15 final size:14
Alignment explanation
Indices: 233857--233887 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
233847 AAAATAACAG
233857 AAAAAACAATAAAA
1 AAAAAACAATAAAA
233871 AAAATAACAATAAAA
1 AAAA-AACAATAAAA
233886 AA
1 AA
233888 CAACGCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.84, C:0.06, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAAAACAATAAAA
Found at i:233905 original size:21 final size:21
Alignment explanation
Indices: 233876--233928 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
233866 TAAAAAAAAT
* **
233876 AACAATAAAAAACAACGCTAA
1 AACAGTAAAAAACAACAATAA
* *
233897 AACAGTAAAAAATAGCAATAA
1 AACAGTAAAAAACAACAATAA
233918 AACAGTAAAAA
1 AACAGTAAAAA
233929 TAGAATCAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.68, C:0.13, G:0.08, T:0.11
Consensus pattern (21 bp):
AACAGTAAAAAACAACAATAA
Found at i:233929 original size:20 final size:20
Alignment explanation
Indices: 233894--233942 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 20
233884 AAAACAACGC
233894 TAAAACAGTAAAAAATAGCAA
1 TAAAACAGTAAAAAATAG-AA
233915 TAAAACAGT-AAAAATAGAA
1 TAAAACAGTAAAAAATAGAA
233934 TCAAAACAG
1 T-AAAACAG
233943 CAACTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.11
20 15 0.56
21 9 0.33
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.14
Consensus pattern (20 bp):
TAAAACAGTAAAAAATAGAA
Found at i:235503 original size:27 final size:27
Alignment explanation
Indices: 235466--235517 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
235456 TACCATAAAT
235466 ATAATAAATATTTTATTATATTAAAAA
1 ATAATAAATATTTTATTATATTAAAAA
* *
235493 ATAATGAATATTTTATTGTATTAAA
1 ATAATAAATATTTTATTATATTAAA
235518 TATAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (27 bp):
ATAATAAATATTTTATTATATTAAAAA
Found at i:235518 original size:24 final size:25
Alignment explanation
Indices: 235461--235523 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
235451 AAAACTACCA
235461 TAAATATAATAAATATTTTATTATAT
1 TAAA-ATAATAAATATTTTATTATAT
* *
235487 TAAAAAATAATGAATATTTTATTGTAT
1 T--AAAATAATAAATATTTTATTATAT
235514 TAAATATAAT
1 TAAA-ATAAT
235524 TTTTAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 3 0.09
26 6 0.19
27 20 0.62
28 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (25 bp):
TAAAATAATAAATATTTTATTATAT
Found at i:239838 original size:11 final size:11
Alignment explanation
Indices: 239822--239846 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
239812 TCTTTGAACC
239822 ATGGTGTTGTG
1 ATGGTGTTGTG
239833 ATGGTGTTGTG
1 ATGGTGTTGTG
239844 ATG
1 ATG
239847 TTGGAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (11 bp):
ATGGTGTTGTG
Found at i:240076 original size:13 final size:12
Alignment explanation
Indices: 240061--240105 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 12
240051 TAGAATAATG
240061 ATTAATAAACTA
1 ATTAATAAACTA
240073 GATTAATTAAACTTA
1 -ATTAA-TAAAC-TA
240088 ATTAATAAACTA
1 ATTAATAAACTA
240100 ATTAAT
1 ATTAAT
240106 CTATATCTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.27
13 10 0.33
14 10 0.33
15 2 0.07
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (12 bp):
ATTAATAAACTA
Found at i:248558 original size:2 final size:2
Alignment explanation
Indices: 248551--248597 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
248541 ACGGTCAACG
248551 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
248590 TA T- TA TA T
1 TA TA TA TA T
248598 TGGTTTTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 4 0.10
2 37 0.90
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:248642 original size:13 final size:13
Alignment explanation
Indices: 248604--248647 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 13
248594 ATATTGGTTT
*
248604 TAATATATGATAAA
1 TAATATATTAT-AA
248618 TAATAGTATTATAA
1 TAATA-TATTATAA
248632 TAATATATTATAA
1 TAATATATTATAA
248645 TAA
1 TAA
248648 AAAAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 11 0.39
14 12 0.43
15 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (13 bp):
TAATATATTATAA
Found at i:249798 original size:17 final size:18
Alignment explanation
Indices: 249766--249808 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
249756 GAACTATTTG
* *
249766 ATTGATATGAAAAATGTT
1 ATTGAAATGAAAAATGCT
249784 ATTGAAATG-AAAATGCT
1 ATTGAAATGAAAAATGCT
*
249801 ATTAAAAT
1 ATTGAAAT
249809 AACGAGTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35
Consensus pattern (18 bp):
ATTGAAATGAAAAATGCT
Done.