Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003580.1 Hibiscus syriacus cultivar Beakdansim tig00007555_pilon, 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: 160925
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5563 original size:13 final size:14
Alignment explanation
Indices: 5545--5573 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5535 ATCAGTTTCA
5545 TTCAA-TATTTTTT
1 TTCAATTATTTTTT
5558 TTCAATTATTTTTT
1 TTCAATTATTTTTT
5572 TT
1 TT
5574 TTTAAGTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (14 bp):
TTCAATTATTTTTT
Found at i:11361 original size:14 final size:14
Alignment explanation
Indices: 11317--11364 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
11307 TATTATTATT
11317 ATTATTATTAAAT-
1 ATTATTATTAAATA
*
11330 ATTATTATT-AGTA
1 ATTATTATTAAATA
11343 TATTATTATTAAATA
1 -ATTATTATTAAATA
11358 ATTATTA
1 ATTATTA
11365 CAAGCCCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 2 0.07
13 9 0.30
14 16 0.53
15 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
ATTATTATTAAATA
Found at i:11364 original size:3 final size:3
Alignment explanation
Indices: 11306--11353 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
11296 TCATTTAAAT
* *
11306 TTA TTA TTA TTA TTA TTA TTAA ATA TTA TTA TTA GTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
11351 TTA
1 TTA
11354 AATAATTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.90
4 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:12729 original size:3 final size:3
Alignment explanation
Indices: 12721--12750 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
12711 TTTACTCTTA
*
12721 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12751 TAGTCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:13606 original size:18 final size:18
Alignment explanation
Indices: 13585--13652 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 18
13575 TTTTATATAC
13585 TTATTATTTTCATAGTAT
1 TTATTATTTTCATAGTAT
*
13603 TTATATATTTTCTTATTAATAT
1 TTAT-TATTTTC--A-TAGTAT
*
13625 TTCATTATTTGCA-AGTATT
1 TT-ATTATTTTCATAGTA-T
13644 TTATTATTT
1 TTATTATTT
13653 ATTTTTCTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
18 14 0.34
19 10 0.24
20 1 0.02
21 1 0.02
22 13 0.32
23 2 0.05
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (18 bp):
TTATTATTTTCATAGTAT
Found at i:20610 original size:114 final size:114
Alignment explanation
Indices: 20410--20622 Score: 365
Period size: 114 Copynumber: 1.9 Consensus size: 114
20400 GTGCCACGTT
* *
20410 CTCGTAGTAAAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCGTAGTAAAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTAATCTG
20475 ATTTGGTATAAACCTCAAAACCAATCATTGGATTTGAAAGATAAATTTG
66 ATTTGGTATAAACCTCAAAACCAATCATTGGATTTGAAAGATAAATTTG
*
20524 CTCGTAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTAATCTG
1 CTCGTAGTAAAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTAATCTG
* *
20589 GTTTGGTA-AGAACCTTAAAACCAATCATTGGATT
66 ATTTGGTATA-AACCTCAAAACCAATCATTGGATT
20623 AGGAAGATGA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
113 1 0.01
114 92 0.99
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32
Consensus pattern (114 bp):
CTCGTAGTAAAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTAATCTG
ATTTGGTATAAACCTCAAAACCAATCATTGGATTTGAAAGATAAATTTG
Found at i:23940 original size:45 final size:47
Alignment explanation
Indices: 23876--23966 Score: 159
Period size: 45 Copynumber: 2.0 Consensus size: 47
23866 CTATTTCCCA
*
23876 CATCTGTAAGCCCTTCAGTGCATGATGTTT-TCAAAA-CCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCTAAAAAGCCTTCGGGT
23921 CATCTGTAAGCCCTTCAGTGCATGATGTTTCTAAAAAGCCTTCGGG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCTAAAAAGCCTTCGGG
23967 AGCTTTTTGA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
45 30 0.70
46 5 0.12
47 8 0.19
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (47 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCTAAAAAGCCTTCGGGT
Found at i:23985 original size:76 final size:76
Alignment explanation
Indices: 23898--24192 Score: 513
Period size: 76 Copynumber: 3.9 Consensus size: 76
23888 CTTCAGTGCA
*
23898 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCTAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
23963 CGGGAGCTTTT
66 CGGGAGCTTTT
23974 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
24039 CGGGAGCTTTT
66 CGGGAGCTTTT
* * *
24050 TGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
24115 CGGGAGCTTTT
66 CGGGAGCTTTT
* * *
24126 TGATGTTTTCAAAGCCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
24189 CGGG
66 CGGG
24193 TCATCTGTAA
Statistics
Matches: 211, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
74 8 0.04
75 4 0.02
76 199 0.94
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (76 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTT
Found at i:24175 original size:45 final size:45
Alignment explanation
Indices: 24126--24223 Score: 178
Period size: 45 Copynumber: 2.2 Consensus size: 45
24116 GGGAGCTTTT
*
24126 TGATGTTTTCAAAGCCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
*
24171 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
24216 TGATGTTT
1 TGATGTTT
24224 CTAAAAAGCC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.36
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:24189 original size:121 final size:121
Alignment explanation
Indices: 24050--24315 Score: 451
Period size: 121 Copynumber: 2.2 Consensus size: 121
24040 GGGAGCTTTT
* * *
24050 TGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
24115 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
66 CGGGAGCTTTTTGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
*
24171 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCTAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
24236 CGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
66 CGGGAGCTTTTTGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
*
24292 TGATGTTTCCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
24316 AGCTTTTTGA
Statistics
Matches: 136, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
121 124 0.91
122 4 0.03
123 8 0.06
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (121 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:24211 original size:197 final size:197
Alignment explanation
Indices: 23974--24391 Score: 764
Period size: 197 Copynumber: 2.1 Consensus size: 197
23964 GGGAGCTTTT
23974 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
* * *
24039 CGGGAGCTTTTTGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
66 CGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTC
24104 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCAGGTCATCTGTAAGCCCTTCAGTG
131 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCAGGTCATCTGTAAGCCCTTCAGTG
24169 CA
196 CA
*
24171 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCTAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
24236 CGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTC
66 CGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTC
*
24301 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTG
131 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCAGGTCATCTGTAAGCCCTTCAGTG
24366 CA
196 CA
*
24368 TGATGTTTCCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
24392 AGCTTTTTGA
Statistics
Matches: 213, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
197 201 0.94
198 4 0.02
199 8 0.04
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (197 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTC
CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCAGGTCATCTGTAAGCCCTTCAGTG
CA
Found at i:24251 original size:76 final size:76
Alignment explanation
Indices: 24171--24465 Score: 540
Period size: 76 Copynumber: 3.9 Consensus size: 76
24161 CTTCAGTGCA
*
24171 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCTAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
24236 CGGGAGCTTTT
66 CGGGAGCTTTT
24247 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
24312 CGGGAGCTTTT
66 CGGGAGCTTTT
*
24323 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
24388 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
24399 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
24462 CGGG
66 CGGG
24466 TCATCTGTAA
Statistics
Matches: 216, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
74 8 0.04
75 4 0.02
76 204 0.94
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (76 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTT
Found at i:24363 original size:273 final size:273
Alignment explanation
Indices: 23876--24496 Score: 1206
Period size: 273 Copynumber: 2.3 Consensus size: 273
23866 CTATTTCCCA
23876 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
23941 CATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAA
66 CATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAA
*
24006 GCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTTCGG
131 GCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGG
*
24071 GTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
196 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
24136 AAAGCCTTCAGGT
261 AAAGCCTTCAGGT
24149 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
24214 CATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAA
66 CATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAA
24279 GCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGG
131 GCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGG
24344 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
196 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
*
24409 AAAGCCTTCGGGT
261 AAAGCCTTCAGGT
*
24422 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
24487 CATGATGTTT
66 CATGATGTTT
24497 TCAAACATTT
Statistics
Matches: 344, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
273 344 1.00
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (273 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
CATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAA
GCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGG
GTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
AAAGCCTTCAGGT
Found at i:24448 original size:45 final size:45
Alignment explanation
Indices: 24399--24501 Score: 188
Period size: 45 Copynumber: 2.3 Consensus size: 45
24389 GGGAGCTTTT
*
24399 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
24444 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
24489 TGATGTTTTCAAA
1 TGATGTTTTCAAA
24502 CATTTACATC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.36
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:24647 original size:18 final size:18
Alignment explanation
Indices: 24624--24662 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
24614 TTTTTTTCAT
24624 TTAAATTTATTATTATTA
1 TTAAATTTATTATTATTA
24642 TTAAATTTATTATTATTA
1 TTAAATTTATTATTATTA
24660 TTA
1 TTA
24663 TTATTAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAAATTTATTATTATTA
Found at i:24657 original size:24 final size:23
Alignment explanation
Indices: 24630--24706 Score: 100
Period size: 25 Copynumber: 3.1 Consensus size: 23
24620 TCATTTAAAT
24630 TTATTATTATTATTAAATTTATTA
1 TTATTATTATTATTAAA-TTATTA
24654 TTATTATTATTATTAAACATTATTA
1 TTATTATTATTATT-AA-ATTATTA
*
24679 TTAGTATATTATTATTAAATAATTA
1 TTA-T-TATTATTATTAAATTATTA
24704 TTA
1 TTA
24707 CAAGCCCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
24 14 0.29
25 20 0.42
26 4 0.08
27 10 0.21
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (23 bp):
TTATTATTATTATTAAATTATTA
Found at i:24706 original size:3 final size:3
Alignment explanation
Indices: 24630--24695 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
24620 TCATTTAAAT
* **
24630 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTAA ACA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
24676 TTA TTA GTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
24696 AATAATTATT
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
2 3 0.06
3 47 0.90
4 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:26104 original size:3 final size:3
Alignment explanation
Indices: 26096--26125 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
26086 TTTACTCTTA
*
26096 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
26126 TAGTCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:26339 original size:2 final size:2
Alignment explanation
Indices: 26334--26398 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
26324 TTATTTTAAT
26334 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
26376 TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
26399 CAAAGAAAAG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29946 original size:21 final size:18
Alignment explanation
Indices: 29908--29961 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 18
29898 CTTTACATTC
*
29908 ATATTTTTAATTATATAA
1 ATATTTTTAATTAAATAA
29926 TATATTTATTATATTAAATAA
1 -ATATTT-TTA-ATTAAATAA
29947 ATATGTTTGTAATTA
1 ATAT-TTT-TAATTA
29962 TTGAAATGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 6 0.20
20 12 0.40
21 12 0.40
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
ATATTTTTAATTAAATAA
Found at i:31840 original size:39 final size:39
Alignment explanation
Indices: 31650--31833 Score: 194
Period size: 39 Copynumber: 4.7 Consensus size: 39
31640 CGCCTTCCGA
* * *
31650 AGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTATTGC
1 AGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTGC
* * *
31689 AGGCTCCTC-GACTTTGTGCTCAGGGTAAATCCTTACTGT
1 AGGCTCCTCTG-CTTTGTGCACAGGGTAAGTCCTTACTGC
* * *
31728 AGGCTCCT-TGGTTTTGTTCTA-AGGGTAAGTCCTTACTGT
1 AGGCTCCTCT-GCTTTGTGC-ACAGGGTAAGTCCTTACTGC
* * * *
31767 AGGCTCCTATGCTTTGTGCACAGGATAAGACCTTACTCC
1 AGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTGC
*
31806 AGGCTCCTCTGCTTCGTGCACAGGGTAA
1 AGGCTCCTCTGCTTTGTGCACAGGGTAA
31834 CCCCTTATTC
Statistics
Matches: 123, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.02
39 119 0.97
40 2 0.02
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (39 bp):
AGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTGC
Found at i:32636 original size:21 final size:20
Alignment explanation
Indices: 32606--32645 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
32596 ATCATAATTC
32606 TTAAACTTAAACCCTAAAGT
1 TTAAACTTAAACCCTAAAGT
32626 TTAAATCTTAAACCCTAAAG
1 TTAAA-CTTAAACCCTAAAG
32646 CCTACACCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (20 bp):
TTAAACTTAAACCCTAAAGT
Found at i:32939 original size:21 final size:21
Alignment explanation
Indices: 32895--32936 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
32885 GGGCTTAGGG
* *
32895 TTTATGATTTGAGTTTTAGAA
1 TTTAGGATTTGAGTTTGAGAA
32916 TTTAGGATTTGAGGTTTGAGA
1 TTTAGGATTTGA-GTTTGAGA
32937 TTTTGGGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (21 bp):
TTTAGGATTTGAGTTTGAGAA
Found at i:38458 original size:43 final size:43
Alignment explanation
Indices: 38410--38512 Score: 163
Period size: 43 Copynumber: 2.4 Consensus size: 43
38400 TAAAAAGTAA
38410 ATTAATAATTTTATTTAAAAAATGTTTACAAACTAATATGTAC
1 ATTAATAATTTTATTTAAAAAATGTTTACAAACTAATATGTAC
**
38453 ATTAATTTTTTTATTTAAAAAATGTTTACAAACTAATATGTAC
1 ATTAATAATTTTATTTAAAAAATGTTTACAAACTAATATGTAC
*
38496 A-TAATAAAATTTATTTA
1 ATTAAT-AATTTTATTTA
38513 TATTTTATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
42 4 0.07
43 50 0.93
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (43 bp):
ATTAATAATTTTATTTAAAAAATGTTTACAAACTAATATGTAC
Found at i:39537 original size:11 final size:11
Alignment explanation
Indices: 39521--39584 Score: 55
Period size: 11 Copynumber: 5.7 Consensus size: 11
39511 TGGCACTATC
39521 TAAAAAATATA
1 TAAAAAATATA
39532 TAAAAAATGAT-
1 TAAAAAAT-ATA
39543 TAAAAAGATATA
1 TAAAAA-ATATA
39555 -AAAATAA-AT-
1 TAAAA-AATATA
39564 TAAATAAATATA
1 TAAA-AAATATA
39576 TTAAAAAAT
1 -TAAAAAAT
39585 TAGTTAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 17
0.72 0.00 0.28
Matches are distributed among these distances:
10 7 0.16
11 24 0.55
12 9 0.20
13 4 0.09
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (11 bp):
TAAAAAATATA
Found at i:39548 original size:21 final size:21
Alignment explanation
Indices: 39523--39594 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 21
39513 GCACTATCTA
*
39523 AAAAATATATAAAAAATGATT
1 AAAAATATATAAAAAATAATT
*
39544 AAAAAGATAT-AAAAATAAATT
1 AAAAATATATAAAAAAT-AATT
*
39565 AAATAAATATATTAAAAAATTAGTT
1 -AA-AAATATA-TAAAAAA-TAATT
39590 AAAAA
1 AAAAA
39595 AAGTAAAGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 6 0.15
21 12 0.29
22 2 0.05
23 9 0.22
24 3 0.07
25 8 0.20
26 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAAATATATAAAAAATAATT
Found at i:39578 original size:13 final size:12
Alignment explanation
Indices: 39554--39611 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 12
39544 AAAAAGATAT
39554 AAAAATAAATTA
1 AAAAATAAATTA
*
39566 AATAAATATATTA
1 AA-AAATAAATTA
* *
39579 AAAAATTAGTTAA
1 AAAAATAAATT-A
39592 AAAAAGTAAAGTTA
1 AAAAA-TAAA-TTA
39606 AAAAAT
1 AAAAAT
39612 TACCTTCCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
12 8 0.22
13 18 0.50
14 8 0.22
15 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (12 bp):
AAAAATAAATTA
Found at i:39582 original size:25 final size:27
Alignment explanation
Indices: 39554--39611 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
39544 AAAAAGATAT
* *
39554 AAAAATAAATTAAATAAA-TATA-TTA
1 AAAAATAAATTAAAAAAAGTAAAGTTA
* *
39579 AAAAATTAGTTAAAAAAAGTAAAGTTA
1 AAAAATAAATTAAAAAAAGTAAAGTTA
39606 AAAAAT
1 AAAAAT
39612 TACCTTCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 15 0.56
26 3 0.11
27 9 0.33
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (27 bp):
AAAAATAAATTAAAAAAAGTAAAGTTA
Found at i:39591 original size:12 final size:12
Alignment explanation
Indices: 39521--39595 Score: 63
Period size: 10 Copynumber: 6.6 Consensus size: 12
39511 TGGCACTATC
39521 TAAAAAATATA-
1 TAAAAAATATAT
*
39532 TAAAAAAT-GAT
1 TAAAAAATATAT
*
39543 T-AAAAAGATA-
1 TAAAAAATATAT
*
39553 T-AAAAATAAAT
1 TAAAAAATATAT
39564 TAAATAAATATAT
1 TAAA-AAATATAT
39577 TAAAAAAT-TAGT
1 TAAAAAATATA-T
39589 TAAAAAA
1 TAAAAAA
39596 AGTAAAGTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
10 14 0.27
11 13 0.25
12 14 0.27
13 11 0.21
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (12 bp):
TAAAAAATATAT
Found at i:41424 original size:3 final size:3
Alignment explanation
Indices: 41416--41450 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
41406 CTCAATCTCT
* *
41416 TTC TTC TTC TTC TTC TTC TTC TTC GTC TTC ATC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
41451 GGTCTGTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.31, G:0.03, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:47021 original size:21 final size:21
Alignment explanation
Indices: 46991--47108 Score: 118
Period size: 21 Copynumber: 5.6 Consensus size: 21
46981 GATTTACATA
*
46991 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
47012 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
47035 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
47054 TTTGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
47077 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
47096 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
47109 TTATTCCAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
19 18 0.22
21 44 0.55
23 18 0.22
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:47048 original size:42 final size:42
Alignment explanation
Indices: 46997--47122 Score: 225
Period size: 42 Copynumber: 3.0 Consensus size: 42
46987 CATATTCGCA
*
46997 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
47039 TTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
47081 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
47123 CAACGACGGT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 79 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:47870 original size:21 final size:21
Alignment explanation
Indices: 47846--47904 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 21
47836 TTTAGAATAA
47846 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
47867 ATCGCAATTCGATCGAACTTGGACT
1 ATCGCAA--CG--CGAACTTCGACT
*
47892 ATCGCAATGCGAA
1 ATCGCAACGCGAA
47905 TATGTAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 11 0.34
23 3 0.09
25 18 0.56
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:47938 original size:21 final size:21
Alignment explanation
Indices: 47913--47965 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
47903 AATATGTAAA
47913 TCGCATTGCGATAGTCCG-AGT
1 TCGCATTGCGATAGT-CGAAGT
47934 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
47955 TCGCGTTGCGA
1 TCGCATTGCGA
47966 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:49503 original size:3 final size:3
Alignment explanation
Indices: 49495--49523 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
49485 CATATAATTG
49495 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
49524 GTAATTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:54108 original size:15 final size:15
Alignment explanation
Indices: 54088--54179 Score: 55
Period size: 15 Copynumber: 6.0 Consensus size: 15
54078 AAATTAAAAT
54088 AATATT-TATAATATA
1 AATATTATAT-ATATA
54103 AATATTATATATATA
1 AATATTATATATATA
* *
54118 AGT-TTCTATATAATA
1 AATATTATATAT-ATA
* *
54133 AATAATATAAATATA
1 AATATTATATATATA
** *
54148 CTTCTTATAATATTATA
1 AATATTAT-ATA-TATA
54165 AA-ATTACTATATATA
1 AATATTA-TATATATA
54180 TAATTTTTAT
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
14 7 0.12
15 29 0.51
16 16 0.28
17 5 0.09
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (15 bp):
AATATTATATATATA
Found at i:63552 original size:15 final size:15
Alignment explanation
Indices: 63532--63561 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
63522 TTGTTTTCCC
63532 AACTAACTTACACCG
1 AACTAACTTACACCG
*
63547 AACTAATTTACACCG
1 AACTAACTTACACCG
63562 GTGTAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.30, G:0.07, T:0.23
Consensus pattern (15 bp):
AACTAACTTACACCG
Found at i:64721 original size:21 final size:21
Alignment explanation
Indices: 64696--64748 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
64686 TGGAGCGTGG
64696 GGGGAATCGGTACCCCCTCAT
1 GGGGAATCGGTACCCCCTCAT
64717 GGGGAATCGGTACCCCCTCAT
1 GGGGAATCGGTACCCCCTCAT
64738 GGGGAATCGGT
1 GGGGAATCGGT
64749 TCCATAAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.28, G:0.34, T:0.19
Consensus pattern (21 bp):
GGGGAATCGGTACCCCCTCAT
Found at i:75968 original size:15 final size:15
Alignment explanation
Indices: 75948--75979 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
75938 AAAATCTTTC
*
75948 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
75963 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
75978 TT
1 TT
75980 GGATCTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:77405 original size:30 final size:29
Alignment explanation
Indices: 77354--77732 Score: 223
Period size: 30 Copynumber: 12.7 Consensus size: 29
77344 TTAGTTTTTA
*
77354 TATCTTAACATTAAAAAATATATTTTATTTT
1 TATCTTAAC-TT-AAAAATATATTTTATTCT
* *
77385 TATATTAACTTATTAAATATATTTTATTCT
1 TATCTTAACTTA-AAAATATATTTTATTCT
* * *
77415 TGTCTTAACCTAAAAATATATTTTATTTT
1 TATCTTAACTTAAAAATATATTTTATTCT
* *
77444 TATTTTAACTTAAAAATATATTTTAATCTT
1 TATCTTAACTTAAAAATATATTTTATTC-T
* *
77474 TATCTTAATTTTAAAAAAAAAAGATATTTTATTCT
1 TATCTTAA-CTT-----AAAAATATATTTTATTCT
* * * * *
77509 TATCTTAA-TCTATTACATAAATTATATTAT
1 TATCTTAACT-TA-AAAATATATTTTATTCT
* * * * **
77539 TAACTTAAATTATTAAATATACTCAATTCT
1 TATCTTAACTTA-AAAATATATTTTATTCT
* * * * *
77569 TACCTTAAATTATTAAATATAATTAATTCT
1 TATCTTAACTTA-AAAATATATTTTATTCT
* *
77599 TATTTTAACTTAAAACATATCTTTTATTCT
1 TATCTTAACTTAAAA-ATATATTTTATTCT
77629 TATCTTAACTT-AAAATATATTTTTATT-T
1 TATCTTAACTTAAAAATATA-TTTTATTCT
* *
77657 TAAC-T-AC--AAAAATATATTTTATTTT
1 TATCTTAACTTAAAAATATATTTTATTCT
* * *
77682 TATCTTAACTACAAAAAACTATATTATATTTT
1 TATCTTAACT--TAAAAA-TATATTTTATTCT
* *
77714 TATCTTAAATTTAAAATAT
1 TATCTTAACTTAAAAATAT
77733 TGTCATAATA
Statistics
Matches: 278, Mismatches: 48, Indels: 46
0.75 0.13 0.12
Matches are distributed among these distances:
24 7 0.03
25 12 0.04
26 3 0.01
27 3 0.01
28 8 0.03
29 55 0.20
30 127 0.46
31 16 0.06
32 21 0.08
33 1 0.00
34 1 0.00
35 9 0.03
36 15 0.05
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.50
Consensus pattern (29 bp):
TATCTTAACTTAAAAATATATTTTATTCT
Found at i:77480 original size:59 final size:59
Alignment explanation
Indices: 77367--77481 Score: 178
Period size: 59 Copynumber: 1.9 Consensus size: 59
77357 CTTAACATTA
* * *
77367 AAAAATATATTTTATTTTTATATTAACTTATTAAATATATTTTATTCTTGTCTTAACCT
1 AAAAATATATTTTATTTTTATATTAACTTATAAAATATATTTTAATCTTATCTTAACCT
*
77426 AAAAATATATTTTATTTTTATTTTAACTTA-AAAATATATTTTAATCTTTATCTTAA
1 AAAAATATATTTTATTTTTATATTAACTTATAAAATATATTTTAATC-TTATCTTAA
77482 TTTTAAAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 14 0.27
59 37 0.73
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (59 bp):
AAAAATATATTTTATTTTTATATTAACTTATAAAATATATTTTAATCTTATCTTAACCT
Found at i:77654 original size:23 final size:24
Alignment explanation
Indices: 77623--77676 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
77613 ACATATCTTT
* *
77623 TATTCTTATCTTAACT-TAAAATA
1 TATTTTTATCTTAACTAAAAAATA
*
77646 TATTTTTATTTTAACTACAAAAATA
1 TATTTTTATCTTAACTA-AAAAATA
77671 TATTTT
1 TATTTT
77677 ATTTTTATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 14 0.54
25 12 0.46
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTTTTATCTTAACTAAAAAATA
Found at i:77712 original size:32 final size:30
Alignment explanation
Indices: 77644--77721 Score: 120
Period size: 32 Copynumber: 2.5 Consensus size: 30
77634 TAACTTAAAA
*
77644 TATATTTTTATTTTAACTACAAAAATATAT
1 TATATTTTTATCTTAACTACAAAAATATAT
*
77674 TTTATTTTTATCTTAACTACAAAAAACTATAT
1 TATATTTTTATCTTAACTAC-AAAAA-TATAT
77706 TATATTTTTATCTTAA
1 TATATTTTTATCTTAA
77722 ATTTAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 18 0.42
31 5 0.12
32 20 0.47
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (30 bp):
TATATTTTTATCTTAACTACAAAAATATAT
Found at i:77789 original size:31 final size:31
Alignment explanation
Indices: 77739--77845 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 31
77729 ATATTGTCAT
** * * *
77739 AATAAAATATAAATATTTAAGTTAAGTTAAG
1 AATAAAATATATTTTTTTAAATTAAGATAAG
* * *
77770 AATAAATTATATTTTTTTAATTTAAGATAAT
1 AATAAAATATATTTTTTTAAATTAAGATAAG
* * * * *
77801 ATTAAACTGTA-TTTTTAAAATTAAAATAAG
1 AATAAAATATATTTTTTTAAATTAAGATAAG
77831 AATAAAATATATTTT
1 AATAAAATATATTTT
77846 CAGGTTACAA
Statistics
Matches: 58, Mismatches: 17, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
30 23 0.40
31 35 0.60
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.43
Consensus pattern (31 bp):
AATAAAATATATTTTTTTAAATTAAGATAAG
Found at i:77844 original size:30 final size:30
Alignment explanation
Indices: 77766--77873 Score: 85
Period size: 30 Copynumber: 3.6 Consensus size: 30
77756 TAAGTTAAGT
* * * *
77766 TAAGAATAAATTATATTTTTTTAATTTAAGA
1 TAAGAATAAAATATA-TTTTTAAAATTAAAA
* * * *
77797 TAATATTAAACTGTATTTTTAAAATTAAAA
1 TAAGAATAAAATATATTTTTAAAATTAAAA
* **
77827 TAAGAATAAAATATA-TTTTCAGGTTACAAA
1 TAAGAATAAAATATATTTTTAAAATTA-AAA
77857 -AAGAATAAAATATATTT
1 TAAGAATAAAATATATTT
77874 AATAAAATAT
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
29 22 0.36
30 28 0.46
31 11 0.18
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (30 bp):
TAAGAATAAAATATATTTTTAAAATTAAAA
Found at i:77845 original size:29 final size:29
Alignment explanation
Indices: 77813--77873 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
77803 TAAACTGTAT
77813 TTTTAAAATTA-AAATAAGAATAAAATATA
1 TTTTAAAATTACAAA-AAGAATAAAATATA
* **
77842 TTTTCAGGTTACAAAAAGAATAAAATATA
1 TTTTAAAATTACAAAAAGAATAAAATATA
77871 TTT
1 TTT
77874 AATAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (29 bp):
TTTTAAAATTACAAAAAGAATAAAATATA
Found at i:78421 original size:16 final size:16
Alignment explanation
Indices: 78402--78433 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
78392 ATAAATTAAA
78402 TTATTAGTGCTCGTCG
1 TTATTAGTGCTCGTCG
*
78418 TTATTGGTGCTCGTCG
1 TTATTAGTGCTCGTCG
78434 AACGTAGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (16 bp):
TTATTAGTGCTCGTCG
Found at i:79164 original size:19 final size:19
Alignment explanation
Indices: 79119--79165 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
79109 TAAACAAATA
*
79119 TAATATTTATTTTTTATAAT
1 TAAT-TTTATATTTTATAAT
*
79139 TATTTTTATATTTTA-AAT
1 TAATTTTATATTTTATAAT
79157 TAAATTTTA
1 T-AATTTTA
79166 AACTTACAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 4 0.17
19 16 0.70
20 3 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TAATTTTATATTTTATAAT
Found at i:79281 original size:136 final size:136
Alignment explanation
Indices: 79131--79448 Score: 424
Period size: 136 Copynumber: 2.3 Consensus size: 136
79121 ATATTTATTT
* * * *
79131 TTTATAATTATTTTTATATTTTAAATTAAATTTTAAACT-TACAATTTTTTAAATTATTTTTATT
1 TTTATAATAATTTTTATATTTTAAATTAAATTTTAAAATATACAA-ATTATAAATTATTTTTATT
*
79195 GTAAATTTTTCATCAATTACAATTTAAAATATTAGATTTATTTAATTATTTATGTGATATTTTAA
65 GTAAATCTTTCATCAATTACAATTTAAAATATTAGATTTATTTAATTATTTATGTGATATTTTAA
79260 TTTAAAA
130 TTTAAAA
* *
79267 TTTATAATAATTTTTATATTTTAAATTAAATTTTAAAATATAGAAATTATAATTTATTTTTATTG
1 TTTATAATAATTTTTATATTTTAAATTAAATTTTAAAATATACAAATTATAAATTATTTTTATTG
* * * * * *
79332 TAAATCTTTCATCAATTACAATTTAAACTATTATATTTGTTTAATTATTTATGTTATTTTTTATT
66 TAAATCTTTCATCAATTACAATTTAAAATATTAGATTTATTTAATTATTTATGTGATATTTTAAT
79397 TTAAAA
131 TTAAAA
* * * * * * * *
79403 TTTATAGTTATTATAAAATTTAAAATTTAA-TTTAAAATATAAAAAT
1 TTTATAATAATTTTTATATTTTAAATTAAATTTTAAAATATACAAAT
79449 AATTATAAAA
Statistics
Matches: 160, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
135 15 0.09
136 141 0.88
137 4 0.03
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (136 bp):
TTTATAATAATTTTTATATTTTAAATTAAATTTTAAAATATACAAATTATAAATTATTTTTATTG
TAAATCTTTCATCAATTACAATTTAAAATATTAGATTTATTTAATTATTTATGTGATATTTTAAT
TTAAAA
Found at i:85873 original size:17 final size:17
Alignment explanation
Indices: 85851--85884 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
85841 CTATGTTCAT
85851 CGAAGTGGAGTTCTTTC
1 CGAAGTGGAGTTCTTTC
85868 CGAAGTGGAGTTCTTTC
1 CGAAGTGGAGTTCTTTC
85885 TGTGGTTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (17 bp):
CGAAGTGGAGTTCTTTC
Found at i:86482 original size:2 final size:2
Alignment explanation
Indices: 86477--86502 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
86467 ATAAAAAAAA
86477 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
86503 TGTTAGTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89031 original size:17 final size:16
Alignment explanation
Indices: 88991--89045 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
88981 CAGATTCAGA
*
88991 TTCAGATTCTAATTCC
1 TTCAGATTCCAATTCC
*
89007 TTCAGATTTCAATTCC
1 TTCAGATTCCAATTCC
89023 TTACAGATTCCAATTCC
1 TT-CAGATTCCAATTCC
*
89040 CTCAGA
1 TTCAGA
89046 AACATTCCAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 20 0.59
17 14 0.41
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.38
Consensus pattern (16 bp):
TTCAGATTCCAATTCC
Found at i:94404 original size:2 final size:2
Alignment explanation
Indices: 94399--94423 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
94389 TCTCTCTCTA
94399 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
94424 CACACAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:95761 original size:26 final size:25
Alignment explanation
Indices: 95697--95761 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
95687 GGAGAGTGAT
* *
95697 AAAAAATAGAGTAAATATAAAAATGA
1 AAAAAATACA-TAAATAAAAAAATGA
*
95723 ATAAAATACATAAATAAATAAAATGA
1 AAAAAATACATAAATAAA-AAAATGA
95749 AGAAAAATA-ATAA
1 A-AAAAATACATAA
95762 CACATATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 7 0.21
26 20 0.61
27 6 0.18
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.20
Consensus pattern (25 bp):
AAAAAATACATAAATAAAAAAATGA
Found at i:95815 original size:17 final size:18
Alignment explanation
Indices: 95793--95833 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
95783 ACCAAATAAG
*
95793 AATAAAATG-ATAATGCA
1 AATAAAATGAATAAAGCA
95810 AAT-AAATGAATAAAGCA
1 AATAAAATGAATAAAGCA
95827 AATAAAA
1 AATAAAA
95834 GGAAGATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 5 0.24
17 13 0.62
18 3 0.14
ACGTcount: A:0.66, C:0.05, G:0.10, T:0.20
Consensus pattern (18 bp):
AATAAAATGAATAAAGCA
Found at i:95870 original size:38 final size:40
Alignment explanation
Indices: 95826--95931 Score: 103
Period size: 38 Copynumber: 2.6 Consensus size: 40
95816 TGAATAAAGC
*
95826 AAATAAAAGGAAGATAGA-AAGATAAA-AA-TAGAGA-ATAA
1 AAATAAAAGGAAAATAGATAA-ATAAATAAGTAGA-ATATAA
*
95864 AAATAAAAAGAAAATAGATAAATAAATAAGTAGAATATAA
1 AAATAAAAGGAAAATAGATAAATAAATAAGTAGAATATAA
* * *
95904 AAAGTAAAAGTATATATATATAAATAAA
1 AAA-TAAAAGGA-AAATAGATAAATAAA
95932 ATGATAATAA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
38 21 0.38
39 5 0.09
40 11 0.20
41 6 0.11
42 13 0.23
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (40 bp):
AAATAAAAGGAAAATAGATAAATAAATAAGTAGAATATAA
Found at i:95886 original size:19 final size:18
Alignment explanation
Indices: 95826--95889 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
95816 TGAATAAAGC
* *
95826 AAATAAAAGGAAGATAGA
1 AAATAAAAAGAAAATAGA
*
95844 AAGATAAAAATAGAGAATA-A
1 AA-AT-AAAA-AGAAAATAGA
95864 AAATAAAAAGAAAATAGA
1 AAATAAAAAGAAAATAGA
95882 TAAATAAA
1 -AAATAAA
95890 TAAGTAGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
17 7 0.19
18 7 0.19
19 11 0.30
20 7 0.19
21 5 0.14
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (18 bp):
AAATAAAAAGAAAATAGA
Found at i:96029 original size:2 final size:2
Alignment explanation
Indices: 96016--96079 Score: 80
Period size: 2 Copynumber: 32.5 Consensus size: 2
96006 AAAATAGGAA
*
96016 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT ACT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
96057 AT GAT A- AT AT AT AT AT AT AT AT A
1 AT -AT AT AT AT AT AT AT AT AT AT A
96080 AATAATAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
1 3 0.05
2 48 0.87
3 4 0.07
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:96070 original size:31 final size:30
Alignment explanation
Indices: 96032--96106 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 30
96022 ATATATATAT
* *
96032 ATATATATATATATATATAATACTAATGA-TA
1 ATATATATATATATATA-AATAATAA-AACTA
96063 ATATATATATATATATAAATAATAAAACGTA
1 ATATATATATATATATAAATAATAAAAC-TA
96094 ATATATATATATA
1 ATATATATATATA
96107 ACAAAAACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 1 0.03
30 7 0.17
31 32 0.80
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (30 bp):
ATATATATATATATATAAATAATAAAACTA
Found at i:96119 original size:23 final size:23
Alignment explanation
Indices: 96071--96119 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
96061 TAATATATAT
* *
96071 ATATATATAAATAATAAAACGTA
1 ATATATATAAATAAAAAAACGAA
*
96094 ATATATATATATAACAAAAAC-AA
1 ATATATATAAATAA-AAAAACGAA
96117 ATA
1 ATA
96120 AAAATAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (23 bp):
ATATATATAAATAAAAAAACGAA
Found at i:98273 original size:106 final size:106
Alignment explanation
Indices: 98088--98455 Score: 594
Period size: 106 Copynumber: 3.5 Consensus size: 106
98078 GTATTGTTCC
* * * *
98088 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAA-CTGGGAAATTATTTTTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAGTTGGGAAATTATTTGTTGACA
98152 GTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTT
65 GTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTT
* * *
98194 GAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAGTCGGGAAATTATTTGTTGATAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
*
98259 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTATT
66 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTT
*
98300 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
* * *
98365 TCAGCCTCCCCTTCGCCGTGAAGTTGAGATTGTGCTGTCTT
66 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTT
* *
98406 AAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAA
98456 GCCCCTTCGT
Statistics
Matches: 242, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
105 3 0.01
106 239 0.99
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTT
Found at i:99491 original size:18 final size:18
Alignment explanation
Indices: 99444--99498 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
99434 ACTCACTTTA
99444 TTTTTCTCTTTATTT-TTC
1 TTTTTCTCTTT-TTTGTTC
99462 -TTTTC-C--TTTTGTTC
1 TTTTTCTCTTTTTTGTTC
99476 TTTTTCTCTTTTTTGTTC
1 TTTTTCTCTTTTTTGTTC
99494 TTTTT
1 TTTTT
99499 AATTTAGGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.09
14 4 0.12
15 5 0.16
16 2 0.06
17 5 0.16
18 13 0.41
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (18 bp):
TTTTTCTCTTTTTTGTTC
Found at i:99580 original size:15 final size:14
Alignment explanation
Indices: 99562--99600 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
99552 TTTTTTTCTC
99562 TTTTCTTTTCTATTT
1 TTTTCTTTTCT-TTT
99577 TTTTCTTTTTCTTTT
1 TTTTC-TTTTCTTTT
99592 TATTTCTTT
1 T-TTTCTTT
99601 GACTTTAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTCTTTTCTTTT
Found at i:99588 original size:16 final size:15
Alignment explanation
Indices: 99562--99600 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
99552 TTTTTTTCTC
99562 TTTTC-TTTTCTATTT
1 TTTTCTTTTTCT-TTT
99577 TTTTCTTTTTCTTTT
1 TTTTCTTTTTCTTTT
99592 TATTTCTTT
1 T-TTTCTTT
99601 GACTTTAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTTCTTTT
Found at i:99595 original size:20 final size:21
Alignment explanation
Indices: 99546--99596 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
99536 TTTTTCCTCA
*
99546 TTTTTGTTTTTTTCTCTTTTC
1 TTTTTATTTTTTTCTCTTTTC
99567 TTTTCTATTTTTTTCT-TTTTC
1 TTTT-TATTTTTTTCTCTTTTC
99588 TTTTTATTT
1 TTTTTATTT
99597 CTTTGACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 5 0.18
21 13 0.46
22 10 0.36
ACGTcount: A:0.04, C:0.12, G:0.02, T:0.82
Consensus pattern (21 bp):
TTTTTATTTTTTTCTCTTTTC
Found at i:99597 original size:10 final size:11
Alignment explanation
Indices: 99563--99600 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
99553 TTTTTTCTCT
99563 TTTCTTTTCTA
1 TTTCTTTTCTA
*
99574 TTT-TTTTCTT
1 TTTCTTTTCTA
99584 TTTCTTTT-TA
1 TTTCTTTTCTA
99594 TTTCTTT
1 TTTCTTT
99601 GACTTTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTCTTTTCTA
Found at i:109727 original size:26 final size:25
Alignment explanation
Indices: 109662--109727 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
109652 GGAGAGTGAT
* *
109662 AAAAAAATAGAGTAAATATAAAAATG
1 AAAAAAATACA-TAAATAAAAAAATG
*
109688 AATAAAATACATAAATAAATAAAATG
1 AAAAAAATACATAAATAAA-AAAATG
109714 AAGAAAAATA-ATAA
1 AA-AAAAATACATAA
109728 CACATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 7 0.21
26 21 0.62
27 6 0.18
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.20
Consensus pattern (25 bp):
AAAAAAATACATAAATAAAAAAATG
Found at i:109781 original size:17 final size:18
Alignment explanation
Indices: 109759--109799 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
109749 ACCAAATAAG
*
109759 AATAAAATG-ATAATGCA
1 AATAAAATGAATAAAGCA
109776 AAT-AAATGAATAAAGCA
1 AATAAAATGAATAAAGCA
109793 AATAAAA
1 AATAAAA
109800 GGAAGATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 5 0.24
17 13 0.62
18 3 0.14
ACGTcount: A:0.66, C:0.05, G:0.10, T:0.20
Consensus pattern (18 bp):
AATAAAATGAATAAAGCA
Found at i:109847 original size:38 final size:40
Alignment explanation
Indices: 109792--109879 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 40
109782 TGAATAAAGC
*
109792 AAATAAAAGGAAGATAGA-AAGATAAA-AA-TAGAGA-ATAA
1 AAATAAAAGGAAAATAGATAA-ATAAATAAGTAGA-ATATAA
109830 AAATAGAAA-GAAAATAGATAAATAAATAAGTAGAATATAA
1 AAATA-AAAGGAAAATAGATAAATAAATAAGTAGAATATAA
109870 AAAGTAAAAG
1 AAA-TAAAAG
109880 TATATATATA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
38 18 0.43
39 8 0.19
40 14 0.33
41 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (40 bp):
AAATAAAAGGAAAATAGATAAATAAATAAGTAGAATATAA
Found at i:110100 original size:2 final size:2
Alignment explanation
Indices: 109998--110080 Score: 152
Period size: 2 Copynumber: 42.5 Consensus size: 2
109988 GGAATATAAA
109998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
110040 AT AT AT AT AT A- AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
110080 A
1 A
110081 ATAAAACGTA
Statistics
Matches: 79, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 77 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:110116 original size:23 final size:23
Alignment explanation
Indices: 110068--110116 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
110058 ATATATATAT
* *
110068 ATATATATATATAATAAAACGTA
1 ATATATATATATAAAAAAACGAA
110091 ATATATATATATAACAAAAAC-AA
1 ATATATATATATAA-AAAAACGAA
110114 ATA
1 ATA
110117 AAAATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (23 bp):
ATATATATATATAAAAAAACGAA
Found at i:113195 original size:14 final size:14
Alignment explanation
Indices: 113176--113206 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
113166 TACTTCCTTA
*
113176 TTTTCTTTTTCTTT
1 TTTTCTTCTTCTTT
113190 TTTTCTTCTTCTTT
1 TTTTCTTCTTCTTT
113204 TTT
1 TTT
113207 ATAAGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTCTTCTTCTTT
Found at i:114747 original size:45 final size:45
Alignment explanation
Indices: 114683--114773 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
114673 TAATATTACA
114683 AGTATTTTGTTGCATTATATCTAATTTTAATGGACAGAAGAATTG
1 AGTATTTTGTTGCATTATATCTAATTTTAATGGACAGAAGAATTG
114728 AGTATTTTGTTGCATTATATCTAATTTTAATGGACAGAAGAATTG
1 AGTATTTTGTTGCATTATATCTAATTTTAATGGACAGAAGAATTG
114773 A
1 A
114774 TATGCCAGAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.42
Consensus pattern (45 bp):
AGTATTTTGTTGCATTATATCTAATTTTAATGGACAGAAGAATTG
Found at i:117552 original size:17 final size:17
Alignment explanation
Indices: 117532--117574 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
117522 GATTGGTCAG
*
117532 CGAACCGGATCGATCAA
1 CGAAACGGATCGATCAA
*
117549 CGAAATGGATCGATCAA
1 CGAAACGGATCGATCAA
*
117566 CGAATCGGA
1 CGAAACGGA
117575 CCGGTCAGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (17 bp):
CGAAACGGATCGATCAA
Found at i:122730 original size:14 final size:14
Alignment explanation
Indices: 122711--122750 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
122701 ATTTTCCTAA
122711 AACATAATCTTCGG
1 AACATAATCTTCGG
*
122725 AACATAATTTTCGG
1 AACATAATCTTCGG
122739 AA-ACTAATCTTC
1 AACA-TAATCTTC
122751 TATTGTACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 1 0.04
14 22 0.96
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (14 bp):
AACATAATCTTCGG
Found at i:135426 original size:20 final size:20
Alignment explanation
Indices: 135401--135438 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
135391 ATATTAATTG
* *
135401 GATTTGTTTAATGAATATAA
1 GATTTGTATAATAAATATAA
135421 GATTTGTATAATAAATAT
1 GATTTGTATAATAAATAT
135439 TATTAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (20 bp):
GATTTGTATAATAAATATAA
Found at i:142419 original size:14 final size:14
Alignment explanation
Indices: 142392--142435 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
142382 AATGGTCGGT
142392 TTTCTCATTTCTCTC
1 TTTCTCA-TTCTCTC
142407 TTTCTCATTCTCTC
1 TTTCTCATTCTCTC
142421 TTTCTCATTCTCTC
1 TTTCTCATTCTCTC
142435 T
1 T
142436 CTAAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 22 0.76
15 7 0.24
ACGTcount: A:0.07, C:0.34, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTCTCATTCTCTC
Found at i:148955 original size:2 final size:2
Alignment explanation
Indices: 148948--149034 Score: 52
Period size: 2 Copynumber: 49.0 Consensus size: 2
148938 GCGCCCCGAT
* * *
148948 TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT TA TA TT TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
148988 T- TA -A T- TA TA TA TA TA -A TA T- TT TA TA TA T- TT TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
149023 TA -A T- TA TA TA TA
1 TA TA TA TA TA TA TA
149035 AAATATTTTC
Statistics
Matches: 69, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
1 11 0.16
2 58 0.84
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:149019 original size:34 final size:33
Alignment explanation
Indices: 148960--149043 Score: 150
Period size: 34 Copynumber: 2.5 Consensus size: 33
148950 TATATATATA
148960 TATATATATAATATTTTATATTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTATATTAAT
148993 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATAT-TTTTATATTAAT
*
149027 TATATATAAAATATTTT
1 TATATATATAATATTTT
149044 CGGGTTCGGG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 21 0.43
34 28 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
TATATATATAATATTTTATATTTTTATATTAAT
Found at i:149066 original size:20 final size:20
Alignment explanation
Indices: 149036--149073 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
149026 TTATATATAA
149036 AATATTTTCGGGTTCGGGTAT
1 AATATTTTCGGG-TCGGGTAT
149057 AATA-TTTCGGGTCGGGT
1 AATATTTTCGGGTCGGGT
149074 TCGGGGATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.18, C:0.11, G:0.32, T:0.39
Consensus pattern (20 bp):
AATATTTTCGGGTCGGGTAT
Found at i:150654 original size:34 final size:34
Alignment explanation
Indices: 150602--150679 Score: 131
Period size: 34 Copynumber: 2.3 Consensus size: 34
150592 AAAACCAAGC
150602 CGGTGCCCA-CCCCTTTGTTAATTTCAATTTAGG
1 CGGTGCCCACCCCCTTTGTTAATTTCAATTTAGG
*
150635 CGGTGCCCACCCCCTTTGTTAATTTCCATTTAGG
1 CGGTGCCCACCCCCTTTGTTAATTTCAATTTAGG
*
150669 CGGTGCTCACC
1 CGGTGCCCACC
150680 ACCCCTTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
33 9 0.21
34 33 0.79
ACGTcount: A:0.15, C:0.32, G:0.19, T:0.33
Consensus pattern (34 bp):
CGGTGCCCACCCCCTTTGTTAATTTCAATTTAGG
Found at i:155113 original size:2 final size:2
Alignment explanation
Indices: 155102--155143 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
155092 CATTTTCTTT
155102 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
155143 T
1 T
155144 TGCATGAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:155241 original size:2 final size:2
Alignment explanation
Indices: 155234--155274 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
155224 TTAAAACATA
155234 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
155275 CAAATCTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.