Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001470.1 Hibiscus syriacus cultivar Beakdansim tig00002847_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: 1178067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:179592 original size:26 final size:27
Alignment explanation
Indices: 179559--179618 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
179549 CTAAGCGAGG
179559 AGAAGAAAAGTGAAG-AGAA-AGAAAGA
1 AGAAGAAAAGTGAAGAAGAAGA-AAAGA
179585 AGAAGAAAAGTGAAGAAGAAGAAAAGA
1 AGAAGAAAAGTGAAGAAGAAGAAAAGA
*
179612 AAAAGAA
1 AGAAGAA
179619 TAACAAGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 15 0.48
27 15 0.48
28 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.28, T:0.03
Consensus pattern (27 bp):
AGAAGAAAAGTGAAGAAGAAGAAAAGA
Found at i:181661 original size:20 final size:20
Alignment explanation
Indices: 181625--181662 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
181615 ATCATATTCC
**
181625 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
181645 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
181663 GTGAACCAAA
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:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:183166 original size:21 final size:22
Alignment explanation
Indices: 183118--183176 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
183108 ATTTCAATTA
*
183118 CAGTATCGATA-T-CTCCATAT
1 CAGTATCGATACTACTTCATAT
183138 CA-TATCGATACTACTTCA-AT
1 CAGTATCGATACTACTTCATAT
183158 CAGTATCGATACTA-TTCAT
1 CAGTATCGATACTACTTCAT
183177 CATATTTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
19 8 0.24
20 11 0.32
21 15 0.44
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (22 bp):
CAGTATCGATACTACTTCATAT
Found at i:183519 original size:19 final size:19
Alignment explanation
Indices: 183487--183532 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
183477 ATTGAGAAGT
183487 CAAATATT-CTTTAGAATC
1 CAAATATTCCTTTAGAATC
183505 CAAATATTCCTTTAGAATC
1 CAAATATTCCTTTAGAATC
183524 CAAATATTC
1 CAAATATTC
183533 ATAATTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (19 bp):
CAAATATTCCTTTAGAATC
Found at i:189014 original size:29 final size:29
Alignment explanation
Indices: 188966--189033 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
188956 CGCTTGAATT
*
188966 TTAA-ATAAAATACAAATTTAACAT-TAAC
1 TTAAGATAAAATACAAATTTAAC-TCAAAC
* *
188994 TTAAGATAAAATATAACTTTAACTCAAAC
1 TTAAGATAAAATACAAATTTAACTCAAAC
*
189023 TTTAGATAAAA
1 TTAAGATAAAA
189034 AAATCAATTC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.15
29 29 0.85
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.32
Consensus pattern (29 bp):
TTAAGATAAAATACAAATTTAACTCAAAC
Found at i:191338 original size:72 final size:72
Alignment explanation
Indices: 191209--191343 Score: 198
Period size: 72 Copynumber: 1.9 Consensus size: 72
191199 ATGGAACCCC
* ** * * *
191209 ACTAAATTATTATATTTTTGAGTTTTTTAAATAAAAATGATGTTTAAAAATATTTTTTAATTGTT
1 ACTAAATTATCATATTTTCAAGTATTTAAAATAAAAAAGATGTTTAAAAATATTTTTTAATTGTT
191274 GGGCCCT
66 GGGCCCT
*
191281 ACTAAATTGTCATATTTTCAAGTATTTAAAATAAAAAAGTATGTTTAAAAATATTTTTTAATT
1 ACTAAATTATCATATTTTCAAGTATTTAAAATAAAAAAG-ATGTTTAAAAATATTTTTTAATT
191344 ATTAAACTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
72 32 0.58
73 23 0.42
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (72 bp):
ACTAAATTATCATATTTTCAAGTATTTAAAATAAAAAAGATGTTTAAAAATATTTTTTAATTGTT
GGGCCCT
Found at i:191870 original size:19 final size:19
Alignment explanation
Indices: 191833--191877 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
191823 ATCGAAAAAA
*
191833 TTATTA-TTTCTATCGATT
1 TTATTATTTTCTACCGATT
*
191851 TTATTATTTTTTACCGATT
1 TTATTATTTTCTACCGATT
191870 TTATTATT
1 TTATTATT
191878 GTTGAACACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.64
Consensus pattern (19 bp):
TTATTATTTTCTACCGATT
Found at i:191956 original size:24 final size:21
Alignment explanation
Indices: 191904--191947 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
191894 AAAACGTTAA
* *
191904 AAAAATATTAATGTTTTAAGT
1 AAAAATAATAATATTTTAAGT
191925 AAAAATAATAATATTTTAAGT
1 AAAAATAATAATATTTTAAGT
191946 AA
1 AA
191948 TTTAAATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAGT
Found at i:193073 original size:23 final size:23
Alignment explanation
Indices: 193045--193115 Score: 115
Period size: 23 Copynumber: 3.1 Consensus size: 23
193035 ATCAAGTACA
*
193045 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
193068 ATAATATAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
* *
193091 ATAATATAATAGGTAACGTTTAT
1 ATAATATAATAGGTAGCGCTTAT
193114 AT
1 AT
193116 TGACCTATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:194035 original size:162 final size:162
Alignment explanation
Indices: 193761--194093 Score: 585
Period size: 162 Copynumber: 2.1 Consensus size: 162
193751 TCGAGATCGA
193761 TTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTGTATAAAGTATCGACACTT
1 TTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTGTATAAAGTATCGACACTT
* * *
193826 TATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGTATCGA
66 TATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTATCGATACTTATAATAAAGTATCGA
* *
193891 CACTATCAACATATCTGATAGCTCTTTACCGG
131 CACTATCAACATATCCGATAGCGCTTTACCGG
*
193923 TTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
1 TTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTGTATAAAGTATCGACACTT
193988 TATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTATCGATACTTATAATAAAGTATCGA
66 TATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTATCGATACTTATAATAAAGTATCGA
* *
194053 CACTATCAACATATCCGGTAGCGCTTTACCTG
131 CACTATCAACATATCCGATAGCGCTTTACCGG
*
194085 TTTTGTCAT
1 TTTTATCAT
194094 TTATAGACCA
Statistics
Matches: 162, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
162 162 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (162 bp):
TTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTGTATAAAGTATCGACACTT
TATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTATCGATACTTATAATAAAGTATCGA
CACTATCAACATATCCGATAGCGCTTTACCGG
Found at i:194128 original size:19 final size:20
Alignment explanation
Indices: 194077--194129 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
194067 CCGGTAGCGC
*
194077 TTTACCTGTTTTGTCATTTA
1 TTTACCTGTTTTATCATTTA
** *
194097 TAGACCAGTTTTATCATTT-
1 TTTACCTGTTTTATCATTTA
194116 TTTACCTGTTTTAT
1 TTTACCTGTTTTAT
194130 TGTTATAGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.19, C:0.15, G:0.09, T:0.57
Consensus pattern (20 bp):
TTTACCTGTTTTATCATTTA
Found at i:194302 original size:112 final size:112
Alignment explanation
Indices: 194028--194385 Score: 621
Period size: 112 Copynumber: 3.2 Consensus size: 112
194018 TTCCAAAAGT
* *
194028 ATCGATAC-TTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
1 ATCGATACATTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
* * * *
194092 ATTTATAGACCAGTTTTATCA-TTTTTTACCTGTTTTATTGTTATAG
66 ATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGG
*
194138 ATCGATACATTTTTATAAAGTATTGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
1 ATCGATACATTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
*
194203 ATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTATTATGG
66 ATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGG
194250 ATCGATACATTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
1 ATCGATACATTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
194315 ATTTATAGACCGGTTTTGTCATTTTTTTTACCTGTTATATTGTTATGG
66 ATTTATAGACCGGTTTTGTCA-TTTTTTTACCTGTTATATTGTTATGG
194363 ATCGATACATTTTTATAAAGTAT
1 ATCGATACATTTTTATAAAGTAT
194386 TGAGCGCTTT
Statistics
Matches: 235, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
110 8 0.03
111 72 0.31
112 107 0.46
113 48 0.20
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (112 bp):
ATCGATACATTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
ATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGG
Found at i:194404 original size:93 final size:92
Alignment explanation
Indices: 194295--194477 Score: 285
Period size: 93 Copynumber: 2.0 Consensus size: 92
194285 CATATCCGGT
* ** *
194295 AGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTTACCTGTTATATTGTTA
1 AGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTAATTTTTTTT-CCTGCCATATTATTA
*
194360 TGGATCGATACATTTTTATAAAGTATTG
65 TGGATCAATACATTTTTATAAAGTATTG
*
194388 AGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTAATTTTTTTTCTTGCCATATTATTAT
1 AGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTAATTTTTTTTCCTGCCATATTATTAT
* *
194453 GGATTAATATATTTTTATAAAGTAT
66 GGATCAATACATTTTTATAAAGTAT
194478 CGACAGAAAT
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
92 34 0.41
93 48 0.59
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (92 bp):
AGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTAATTTTTTTTCCTGCCATATTATTAT
GGATCAATACATTTTTATAAAGTATTG
Found at i:199263 original size:34 final size:35
Alignment explanation
Indices: 199220--199300 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 35
199210 TTTAAATATA
* * * * *
199220 TAGTTGTTTAGAAATATTTTAAAAGTAG-TATTGG
1 TAGTCGTTTAAAAATATTTGAAAAGTAGTTAATAG
199254 TAGTCGTTTAAAAATATTTGAAAAGTAGTTAATAG
1 TAGTCGTTTAAAAATATTTGAAAAGTAGTTAATAG
199289 TAGTCG-TTAAAA
1 TAGTCGTTTAAAA
199301 CTCATAGGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
34 31 0.76
35 10 0.24
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (35 bp):
TAGTCGTTTAAAAATATTTGAAAAGTAGTTAATAG
Found at i:199590 original size:37 final size:36
Alignment explanation
Indices: 199520--199591 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
199510 TGGAAAATAA
* *
199520 TTATATATTTTCTTTAAAAATTTAAATTCATAAAAT
1 TTATATATTTTCTTTAAAAATTAAAAATCATAAAAT
*
199556 TTATATAATTTTTTTTACAAAATTAAAAAT-ATAAAA
1 TTATAT-ATTTTCTTTA-AAAATTAAAAATCATAAAA
199592 AAGGTTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 6 0.19
37 15 0.48
38 10 0.32
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
TTATATATTTTCTTTAAAAATTAAAAATCATAAAAT
Found at i:200441 original size:13 final size:13
Alignment explanation
Indices: 200423--200448 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
200413 AATTTCTAAT
200423 TAATATATATTTG
1 TAATATATATTTG
200436 TAATATATATTTG
1 TAATATATATTTG
200449 ATATGTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TAATATATATTTG
Found at i:201538 original size:18 final size:18
Alignment explanation
Indices: 201515--201553 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
201505 ATCCAATCAT
201515 TATTTTTTCGTTCGGTGC
1 TATTTTTTCGTTCGGTGC
201533 TATTTTTTCGTTCGGTGC
1 TATTTTTTCGTTCGGTGC
201551 TAT
1 TAT
201554 AAGGGGGTCC
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:0.08, C:0.15, G:0.21, T:0.56
Consensus pattern (18 bp):
TATTTTTTCGTTCGGTGC
Found at i:204241 original size:3 final size:3
Alignment explanation
Indices: 204233--204335 Score: 55
Period size: 3 Copynumber: 32.0 Consensus size: 3
204223 TAGTCATTGT
* **
204233 TTA TTA TTA ATA TTA TTA TTAA TTA TTAA TGG TGT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TT-A TTA T-TA TTA TTA TTA TTA
* * * * *
204280 GTCA TTAA TTA TTTA TTA ATA TTA TTA TCA TTTA ATA TTA CTA TTTA
1 -TTA TT-A TTA -TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA
204327 TTA TTA TTA
1 TTA TTA TTA
204336 GATAATATTA
Statistics
Matches: 76, Mismatches: 15, Indels: 18
0.70 0.14 0.17
Matches are distributed among these distances:
2 1 0.01
3 58 0.76
4 17 0.22
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:204250 original size:12 final size:13
Alignment explanation
Indices: 204233--204335 Score: 66
Period size: 13 Copynumber: 7.7 Consensus size: 13
204223 TAGTCATTGT
204233 TTATTATTAA-TA
1 TTATTATTAATTA
204245 TTATTATTAATTA
1 TTATTATTAATTA
* *
204258 TTAATGGTGTTTATTA
1 TT-AT--TATTAATTA
* *
204274 TTATTAGTCATTAA
1 TTATTATTAATT-A
204288 TTATTTATTAA-TA
1 TTA-TTATTAATTA
* *
204301 TTATTATCATTTA
1 TTATTATTAATTA
* * *
204314 ATATTACTATTTA
1 TTATTATTAATTA
204327 TTATTATTA
1 TTATTATTA
204336 GATAATATTA
Statistics
Matches: 70, Mismatches: 14, Indels: 13
0.72 0.14 0.13
Matches are distributed among these distances:
12 15 0.21
13 32 0.46
14 7 0.10
15 7 0.10
16 9 0.13
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (13 bp):
TTATTATTAATTA
Found at i:204250 original size:26 final size:26
Alignment explanation
Indices: 204219--204311 Score: 80
Period size: 26 Copynumber: 3.5 Consensus size: 26
204209 TTTGTCCAGG
*
204219 TTATTAGTCATTGTTTATTATTAATA
1 TTATTAGTCATTATTTATTATTAATA
* * * * *
204245 TTATTATTAATTATTAATGGTGTTTATTA
1 TTATTAGTCATTATTTAT--T-ATTAATA
*
204274 TTATTAGTCATTAATTATTTATTAATA
1 TTATTAGTCATTATTTA-TTATTAATA
204301 TTATTA-TCATT
1 TTATTAGTCATT
204312 TAATATTACT
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
26 19 0.37
27 11 0.22
28 2 0.04
29 18 0.35
30 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (26 bp):
TTATTAGTCATTATTTATTATTAATA
Found at i:204327 original size:56 final size:55
Alignment explanation
Indices: 204219--204336 Score: 146
Period size: 56 Copynumber: 2.1 Consensus size: 55
204209 TTTGTCCAGG
** * * ** *
204219 TTATTAGTCATTGTTTATTATTAATATTATTATTAATTATTAATGGTGTTTATTA
1 TTATTAGTCATTAATTATTATTAATATTATTATCAATTAATAATACTATTTATTA
* *
204274 TTATTAGTCATTAATTATTTATTAATATTATTATCATTTAATATTACTATTTATTA
1 TTATTAGTCATTAATTA-TTATTAATATTATTATCAATTAATAATACTATTTATTA
204330 TTATTAG
1 TTATTAG
204337 ATAATATTAC
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
55 15 0.28
56 38 0.72
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (55 bp):
TTATTAGTCATTAATTATTATTAATATTATTATCAATTAATAATACTATTTATTA
Found at i:204328 original size:26 final size:26
Alignment explanation
Indices: 204299--204354 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
204289 TATTTATTAA
** *
204299 TATTATTATCATTTAATATTACTATT
1 TATTATTATCAGATAATATTACTAGT
*
204325 TATTATTATTAGATAATATTACTAGT
1 TATTATTATCAGATAATATTACTAGT
204351 TATT
1 TATT
204355 CATATGATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (26 bp):
TATTATTATCAGATAATATTACTAGT
Found at i:209470 original size:91 final size:90
Alignment explanation
Indices: 209315--209497 Score: 230
Period size: 91 Copynumber: 2.0 Consensus size: 90
209305 ATTTTCAAAG
*
209315 TGATGCATCGATGCACCAATCCATGCATCGATGCACCATGGAATTAATTGAACATCGAATGCATT
1 TGATGCATCGATGCACCAAACCATGCATCGATGCACCATGGAATTAA-T-AACATCGAATGCATT
*
209380 TTATGCATCGATGCA-CTTAGTGCACT
64 TCATGCATCGATGCACCTTAGTGCACT
* *
209406 TGATGCATCGATGCA-CAAGACCATGCATCGATGCACTCA-GGCTATTTCAA-AACATTGAATGC
1 TGATGCATCGATGCACCAA-ACCATGCATCGATGCAC-CATGG--AATT-AATAACATCGAATGC
209468 ATTTCATGCATCGATGCACTCTTAGTGCAC
61 ATTTCATGCATCGATGCAC-CTTAGTGCAC
209498 CGATGCACTG
Statistics
Matches: 81, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
90 3 0.04
91 61 0.75
92 2 0.02
93 13 0.16
94 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.28
Consensus pattern (90 bp):
TGATGCATCGATGCACCAAACCATGCATCGATGCACCATGGAATTAATAACATCGAATGCATTTC
ATGCATCGATGCACCTTAGTGCACT
Found at i:211481 original size:22 final size:21
Alignment explanation
Indices: 211459--211498 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
211449 AAGACTATAT
211459 TTTCAAAATAT-AAAAATGATA
1 TTTCAAAAT-TGAAAAATGATA
211480 TTTCAAAATTGAAAAATGA
1 TTTCAAAATTGAAAAATGA
211499 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
TTTCAAAATTGAAAAATGATA
Found at i:218026 original size:45 final size:46
Alignment explanation
Indices: 217977--218064 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
217967 GAACATCAGA
* * *
217977 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGAACAAGACCATGCATCGATGCACTTAG
218022 TGCATTTGATGCATCGATGAACAAGACCATGCATCGATGCACT
1 TGCATTTGATGCATCGATGAACAAGACCATGCATCGATGCACT
218065 CAGGCTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 20 0.51
46 19 0.49
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGAACAAGACCATGCATCGATGCACTTAG
Found at i:219586 original size:19 final size:18
Alignment explanation
Indices: 219564--219604 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
219554 TTCTGCTTCC
*
219564 TTTTAATTGACTATTTTG
1 TTTTTATTGACTATTTTG
*
219582 TTTTTCTTGACTATTTTG
1 TTTTTATTGACTATTTTG
219600 TTTTT
1 TTTTT
219605 CTTTGCAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (18 bp):
TTTTTATTGACTATTTTG
Found at i:219604 original size:18 final size:18
Alignment explanation
Indices: 219570--219607 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
219560 TTCCTTTTAA
219570 TTGACTATTTTGTTTTTC
1 TTGACTATTTTGTTTTTC
219588 TTGACTATTTTGTTTTTC
1 TTGACTATTTTGTTTTTC
219606 TT
1 TT
219608 TGCAAGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.68
Consensus pattern (18 bp):
TTGACTATTTTGTTTTTC
Found at i:220073 original size:13 final size:13
Alignment explanation
Indices: 220055--220082 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
220045 AAACTCCACT
220055 AAAAATGAAAAAA
1 AAAAATGAAAAAA
220068 AAAAATGAAAAAA
1 AAAAATGAAAAAA
220081 AA
1 AA
220083 TTGAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (13 bp):
AAAAATGAAAAAA
Found at i:227119 original size:25 final size:25
Alignment explanation
Indices: 227085--227209 Score: 196
Period size: 25 Copynumber: 5.0 Consensus size: 25
227075 GAGTAGGGGA
* *
227085 TTAGGGTTTGAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGAT
227110 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
* * *
227135 TTAGGGTTTGGAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGAT
*
227160 TTAGGGGTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
227185 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
227210 GGGTTGTTGG
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 90 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:227160 original size:50 final size:50
Alignment explanation
Indices: 227085--227204 Score: 222
Period size: 50 Copynumber: 2.4 Consensus size: 50
227075 GAGTAGGGGA
*
227085 TTAGGGTTTGAAACCCTAATTTGTTTTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATTTGTTTTAGGGGTTGAAACCCTAATCTGAT
*
227135 TTAGGGTTTGGAACCCTAATTTGTTTTAGGGGTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATTTGTTTTAGGGGTTGAAACCCTAATCTGAT
227185 TTAGGGTTTGAAACCCTAAT
1 TTAGGGTTTGAAACCCTAAT
227205 CTGATGGGTT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (50 bp):
TTAGGGTTTGAAACCCTAATTTGTTTTAGGGGTTGAAACCCTAATCTGAT
Found at i:227294 original size:15 final size:15
Alignment explanation
Indices: 227274--227310 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
227264 GATTGGGCCA
*
227274 ATTGGGCTTCGGGTT
1 ATTGGGCTCCGGGTT
227289 ATTGGGCTCCGGGTT
1 ATTGGGCTCCGGGTT
227304 ATTGGGC
1 ATTGGGC
227311 CTCTGTAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.16, G:0.41, T:0.35
Consensus pattern (15 bp):
ATTGGGCTCCGGGTT
Found at i:227299 original size:37 final size:37
Alignment explanation
Indices: 227210--227311 Score: 168
Period size: 37 Copynumber: 2.7 Consensus size: 37
227200 CTAATCTGAT
*
227210 GGGTTGTTGGGCTCCAGGATTGGGCCAATTGGGCTTC
1 GGGTTGTTGGGCTCCGGGATTGGGCCAATTGGGCTTC
227247 GGGTTGTTGGGCTCCGGGATTGGGCCAATTGGGCTTC
1 GGGTTGTTGGGCTCCGGGATTGGGCCAATTGGGCTTC
*
227284 GGGTTATTGGGCTCCGGGTTATTGGGCC
1 GGGTTGTTGGGCTCCGGG--ATTGGGCC
227312 TCTGTAATCT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
37 53 0.87
39 8 0.13
ACGTcount: A:0.09, C:0.19, G:0.42, T:0.30
Consensus pattern (37 bp):
GGGTTGTTGGGCTCCGGGATTGGGCCAATTGGGCTTC
Found at i:227361 original size:3 final size:3
Alignment explanation
Indices: 227355--227409 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
227345 AAAAAAATTG
*
227355 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
227399 TAA TAA -AA TAA
1 TAA TAA TAA TAA
227410 CGGAAAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 5 0.11
3 38 0.83
4 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:227766 original size:85 final size:89
Alignment explanation
Indices: 227608--227814 Score: 257
Period size: 85 Copynumber: 2.4 Consensus size: 89
227598 CGTCTAAGGG
* * * * * *
227608 TGACACGGCTCCTACGTGATGAGGAAATCTGGTCATCTTTAGGGATGATAACTCGGTTCCTACGT
1 TGACACGGCT-CTACGTGATGAAGAGATCTGGTCA-CATAAAGGATGATAACACGGTTCCTACGT
227673 AATGAGGACGACTGGTTATC-A-GGT
64 AATGAGGACGACTGGTTATCTATGGT
*
227697 TGACACGGCTCTTACGTGATGAAGAGATCTGG-C-CATAAAGG-TGATAACACGGTTCCTACGTG
1 TGACACGGCTC-TACGTGATGAAGAGATCTGGTCACATAAAGGATGATAACACGGTTCCTACGTA
*
227759 ATGAGGACGGCTGGTTATCTATGGT
65 ATGAGGACGACTGGTTATCTATGGT
*
227784 TGACACGG--CTACGTGATGAAGAGGTCTGGTC
1 TGACACGGCTCTACGTGATGAAGAGATCTGGTC
227815 TGGGGATGAC
Statistics
Matches: 105, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
84 19 0.18
85 39 0.37
86 6 0.06
87 11 0.10
88 2 0.02
89 28 0.27
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (89 bp):
TGACACGGCTCTACGTGATGAAGAGATCTGGTCACATAAAGGATGATAACACGGTTCCTACGTAA
TGAGGACGACTGGTTATCTATGGT
Found at i:228932 original size:20 final size:20
Alignment explanation
Indices: 228894--228931 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
228884 TTTATTTATT
* *
228894 ATTTTTTCTTTTTCATTTTC
1 ATTTTTTCATTTCCATTTTC
228914 ATTTTTTCATTTCC-TTTT
1 ATTTTTTCATTTCCATTTT
228932 TTTTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.74
Consensus pattern (20 bp):
ATTTTTTCATTTCCATTTTC
Found at i:242142 original size:25 final size:25
Alignment explanation
Indices: 242108--242231 Score: 205
Period size: 25 Copynumber: 5.0 Consensus size: 25
242098 GAGTAGGGGA
*
242108 TTAGGGTTTGAAACCCTAATCTGTT
1 TTAGGGTTTGAAACCCTAATCTGAT
*
242133 TTAGGGTTTGAAACCCTAAAT-TGTT
1 TTAGGGTTTGAAACCCT-AATCTGAT
242158 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
*
242183 TTAGGGTTTGAAACCCTAATCTAAT
1 TTAGGGTTTGAAACCCTAATCTGAT
242208 TTAGGGTTTGAAACCCTAATCTGA
1 TTAGGGTTTGAAACCCTAATCTGA
242232 CGGGTTGCTG
Statistics
Matches: 94, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
24 3 0.03
25 88 0.94
26 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.37
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:242356 original size:3 final size:3
Alignment explanation
Indices: 242348--242403 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
242338 GCAAAAATTG
* **
242348 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
242392 TAA TAA TAA TAA
1 TAA TAA TAA TAA
242404 CGGAAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 3 0.07
3 38 0.86
4 3 0.07
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:242683 original size:2 final size:2
Alignment explanation
Indices: 242676--242713 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
242666 AATTAAATTA
242676 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
242714 GAAAAAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:243143 original size:20 final size:21
Alignment explanation
Indices: 243118--243194 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 21
243108 AACCCGACTC
243118 AAAATAATATATTTATT-TAA
1 AAAATAATATATTTATTATAA
* *
243138 AAAATATTATTTTTATTCAATAA
1 AAAATAATATATTTATT--ATAA
*
243161 AAAATAA-AGATTTAATTGA-AA
1 AAAATAATATATTT-ATT-ATAA
243182 GAAAATAATATAT
1 -AAAATAATATAT
243195 AAATAGATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
20 15 0.34
21 2 0.05
22 12 0.27
23 15 0.34
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (21 bp):
AAAATAATATATTTATTATAA
Found at i:244141 original size:6 final size:6
Alignment explanation
Indices: 244132--244157 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
244122 GCATCATCAT
244132 CATCTC CATCTC CATCTC CATCTC CA
1 CATCTC CATCTC CATCTC CATCTC CA
244158 GCAGTTAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.50, G:0.00, T:0.31
Consensus pattern (6 bp):
CATCTC
Found at i:247691 original size:2 final size:2
Alignment explanation
Indices: 247684--247714 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
247674 AAATAAACAA
247684 AT AT AT 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 AT AT AT A
247715 AAAAAACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:248740 original size:18 final size:19
Alignment explanation
Indices: 248717--248762 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
248707 TGTTTATGAG
*
248717 GGAATTGA-AATCTGTGAA
1 GGAATTGAGAATCTGTCAA
248735 GGAATT-AGAATCTGTCAA
1 GGAATTGAGAATCTGTCAA
248753 -GAATTG-GAAT
1 GGAATTGAGAAT
248763 TTAACTCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.39, C:0.07, G:0.26, T:0.28
Consensus pattern (19 bp):
GGAATTGAGAATCTGTCAA
Found at i:249342 original size:32 final size:32
Alignment explanation
Indices: 249301--249413 Score: 129
Period size: 32 Copynumber: 3.3 Consensus size: 32
249291 AAACCCGAAC
249301 CCGACCCGACCCGAATATCACACTTAAAAAAA
1 CCGACCCGACCCGAATATCACACTTAAAAAAA
* *
249333 CCGACCCGACCCGAACAACACAC-TAAAAAAA
1 CCGACCCGACCCGAATATCACACTTAAAAAAA
*
249364 CCCCGACCCGACTCGACCCGAATATCACACTTAAAAAAC
1 --CCGA--C--C-CGACCCGAATATCACACTTAAAAAAA
249403 CCGACCCGACC
1 CCGACCCGACC
249414 TGAACAAAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
31 8 0.12
32 26 0.38
33 5 0.07
35 2 0.03
37 5 0.07
38 15 0.22
39 7 0.10
ACGTcount: A:0.40, C:0.41, G:0.11, T:0.09
Consensus pattern (32 bp):
CCGACCCGACCCGAATATCACACTTAAAAAAA
Found at i:249382 original size:38 final size:37
Alignment explanation
Indices: 249291--249413 Score: 130
Period size: 38 Copynumber: 3.4 Consensus size: 37
249281 TTTTCACCCT
* * *
249291 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAA
1 AAACCCG-ACCCGACCCGACCCGAACAACACACTAAAA
249329 AAA----A-CCGACCCGACCCGAACAACACACTAAAA
1 AAACCCGACCCGACCCGACCCGAACAACACACTAAAA
* * * *
249361 AAACCCCGACCCGACTCGACCCGAATATCACACTTAAA
1 AAA-CCCGACCCGACCCGACCCGAACAACACACTAAAA
249399 AAACCCGACCCGACC
1 AAACCCGACCCGACC
249414 TGAACAAAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
32 28 0.39
33 1 0.01
37 12 0.17
38 30 0.42
ACGTcount: A:0.41, C:0.41, G:0.11, T:0.08
Consensus pattern (37 bp):
AAACCCGACCCGACCCGACCCGAACAACACACTAAAA
Found at i:251430 original size:2 final size:2
Alignment explanation
Indices: 251418--251481 Score: 112
Period size: 2 Copynumber: 32.0 Consensus size: 2
251408 AAAATGTTCA
251418 AT AT GAT AT AT AT AT AT AT AT AT AT A- 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
251460 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
251482 TTCTAAAATA
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 57 0.95
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:252732 original size:4 final size:4
Alignment explanation
Indices: 252723--252755 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
252713 CATATATGTC
252723 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
252756 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:252760 original size:2 final size:2
Alignment explanation
Indices: 252753--252797 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
252743 ACATACATAC
252753 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
252795 AT A
1 AT A
252798 ATCATATCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:253319 original size:13 final size:13
Alignment explanation
Indices: 253295--253347 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
253285 GTTTTGAAAT
253295 AAGTCAACGGTCA
1 AAGTCAACGGTCA
* *
253308 AATTCAATGGTCA
1 AAGTCAACGGTCA
* *
253321 TAGTCAACAGTCA
1 AAGTCAACGGTCA
*
253334 AAGTCAATGGTCA
1 AAGTCAACGGTCA
253347 A
1 A
253348 TCGATCGCTC
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (13 bp):
AAGTCAACGGTCA
Found at i:253333 original size:26 final size:26
Alignment explanation
Indices: 253296--253346 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
253286 TTTTGAAATA
* *
253296 AGTCAACGGTCAAATTCAATGGTCAT
1 AGTCAACAGTCAAAGTCAATGGTCAT
253322 AGTCAACAGTCAAAGTCAATGGTCA
1 AGTCAACAGTCAAAGTCAATGGTCA
253347 ATCGATCGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (26 bp):
AGTCAACAGTCAAAGTCAATGGTCAT
Found at i:255542 original size:15 final size:17
Alignment explanation
Indices: 255509--255545 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
255499 AAAAAGTATT
255509 ATAAT-TACAATTATAA
1 ATAATATACAATTATAA
255525 ATAATATAC-ATT-TAA
1 ATAATATACAATTATAA
255540 ATAATA
1 ATAATA
255546 ATTAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
16 8 0.40
17 3 0.15
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATATACAATTATAA
Found at i:257621 original size:16 final size:16
Alignment explanation
Indices: 257597--257648 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
257587 CTGTCCTTGT
257597 CGCCCGTCACACGTGC
1 CGCCCGTCACACGTGC
*
257613 CGTCCGTCACACGTGC
1 CGCCCGTCACACGTGC
257629 CGCCCGTCACACGTGC
1 CGCCCGTCACACGTGC
257645 CGCC
1 CGCC
257649 ACGCACCACG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.12, C:0.50, G:0.25, T:0.13
Consensus pattern (16 bp):
CGCCCGTCACACGTGC
Found at i:268749 original size:149 final size:149
Alignment explanation
Indices: 268266--268729 Score: 865
Period size: 149 Copynumber: 3.1 Consensus size: 149
268256 GGGTAGAGGG
*
268266 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGGGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
268331 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
268396 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
268415 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
268480 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
268545 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
268564 TCTACGCGGTCCTTCGAGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGATACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
*
268629 ACTTGATCCCTAGTATGTGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
*
268694 TATAGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
268713 TCTACGTGGTACTTCGG
1 TCTACGCGGTCCTTCGG
268730 TGCAATTATA
Statistics
Matches: 307, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 307 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:270901 original size:20 final size:20
Alignment explanation
Indices: 270878--270923 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
270868 CTCTTTATAA
270878 ACATCTATTTCTATTTCCCT
1 ACATCTATTTCTATTTCCCT
270898 ACATCTATTTCTATTTCCCT
1 ACATCTATTTCTATTTCCCT
270918 ACATCT
1 ACATCT
270924 CTCGACTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.30, G:0.00, T:0.48
Consensus pattern (20 bp):
ACATCTATTTCTATTTCCCT
Found at i:275017 original size:18 final size:19
Alignment explanation
Indices: 274994--275041 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
274984 GCTGATTTTG
*
274994 GTATCGATACTCATGG-GA
1 GTATCGATACTCAGGGAGA
*
275012 GTATCGATATTCAGGGTAGA
1 GTATCGATACTCAGGG-AGA
275032 GTATCGATAC
1 GTATCGATAC
275042 CAAGGTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 14 0.56
20 11 0.44
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (19 bp):
GTATCGATACTCAGGGAGA
Found at i:281879 original size:20 final size:20
Alignment explanation
Indices: 281856--281911 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
281846 TAGTTCACGA
*
281856 AATGTAAGATTACGAGTGGG
1 AATGTAAGATTACCAGTGGG
*
281876 AATGTAAGATTACCAGTTGG
1 AATGTAAGATTACCAGTGGG
281896 AATGTAAGATTACCAG
1 AATGTAAGATTACCAG
281912 GGAATATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.27
Consensus pattern (20 bp):
AATGTAAGATTACCAGTGGG
Found at i:284411 original size:127 final size:130
Alignment explanation
Indices: 284191--284448 Score: 486
Period size: 127 Copynumber: 2.0 Consensus size: 130
284181 GAACATTGTT
284191 AAAGGAGGTGGTGTGGATGTGAACCTCCCATTGTTGTATTTTTTTTGTGTGGGGGGGGGGGGTTA
1 AAAGGAGGTGGTGTGGATGTGAACCTCCCATTGTTGTATTTTTTTTGTGTGGGGGGGGGGGGTTA
*
284256 AGTCGTAATTTTGTTACTATTCTTTTATCAATAAACTTTTTAAAAGAACTCTTTCGTTAATTAAA
66 AGTCGTAATTTTGTTACTATTCTTTTATCAATAAACTTTTTAAAAGAACTCTTTCATTAATTAAA
284321 AAAGGAGGTGGTGTGGATGTGAACCTCCCATTGTTGTA-TTTTTTT-T-TGGGGGGGGGGGGTTA
1 AAAGGAGGTGGTGTGGATGTGAACCTCCCATTGTTGTATTTTTTTTGTGTGGGGGGGGGGGGTTA
284383 AGTCGTAATTTTGTTACTATTCTTTTATCAATAAACTTTTTAAAAGAACTCTTTCATTAATTAAA
66 AGTCGTAATTTTGTTACTATTCTTTTATCAATAAACTTTTTAAAAGAACTCTTTCATTAATTAAA
284448 A
1 A
284449 TTTTCAGAGT
Statistics
Matches: 127, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
127 81 0.64
128 1 0.01
129 7 0.06
130 38 0.30
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.41
Consensus pattern (130 bp):
AAAGGAGGTGGTGTGGATGTGAACCTCCCATTGTTGTATTTTTTTTGTGTGGGGGGGGGGGGTTA
AGTCGTAATTTTGTTACTATTCTTTTATCAATAAACTTTTTAAAAGAACTCTTTCATTAATTAAA
Found at i:285778 original size:7 final size:7
Alignment explanation
Indices: 285766--285798 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
285756 AATTTAATTC
285766 ATAAAAA
1 ATAAAAA
285773 ATAAAAA
1 ATAAAAA
285780 ATAAAAA
1 ATAAAAA
285787 ATAAAAA
1 ATAAAAA
285794 ATAAA
1 ATAAA
285799 GAAAGTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
ATAAAAA
Found at i:289719 original size:16 final size:16
Alignment explanation
Indices: 289663--289722 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
289653 GTATGAATTG
289663 TTGACTTTGACCTAACT
1 TTGACTTTGACC-AACT
* * * *
289680 GTCGACGTTGACTAGAGT
1 -TTGACTTTGACCA-ACT
289698 TT-ACTTTGACCAACT
1 TTGACTTTGACCAACT
289713 TTGACTTTGA
1 TTGACTTTGA
289723 ACAAAAGTTG
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
15 4 0.12
16 15 0.47
17 2 0.06
18 11 0.34
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.38
Consensus pattern (16 bp):
TTGACTTTGACCAACT
Found at i:294482 original size:34 final size:34
Alignment explanation
Indices: 294441--294505 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
294431 ACAACAAAGG
* *
294441 AAGAGATTTATGGATATGGGAAATAGATAAAGCA
1 AAGAGATTTATAGATATGGAAAATAGATAAAGCA
* *
294475 AAGAGATTTGTAGATATGTAAAATAGATAAA
1 AAGAGATTTATAGATATGGAAAATAGATAAA
294506 AGGCGATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.23, T:0.26
Consensus pattern (34 bp):
AAGAGATTTATAGATATGGAAAATAGATAAAGCA
Found at i:306459 original size:32 final size:32
Alignment explanation
Indices: 306418--306524 Score: 107
Period size: 31 Copynumber: 3.4 Consensus size: 32
306408 AGTCGAGGGT
*
306418 TTACCTATGTTCTACAGAATATATGGACAGAA
1 TTACCTATGTTCTACAGAACATATGGACAGAA
* *
306450 TTACCTATG-TCTTTC-GAGACATATGGACAGTA
1 TTACCTATGTTC-TACAGA-ACATATGGACAGAA
*
306482 -TACCTATGTTCTA-AGGAACATATGGACA-AT
1 TTACCTATGTTCTACA-GAACATATGGACAGAA
*
306512 TTACCTAGGTTCT
1 TTACCTATGTTCT
306525 TTGGGACCTA
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
31 35 0.56
32 27 0.44
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (32 bp):
TTACCTATGTTCTACAGAACATATGGACAGAA
Found at i:306537 original size:31 final size:31
Alignment explanation
Indices: 306438--306538 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 31
306428 TCTACAGAAT
* *
306438 ATATGGACAGAATTACCTATG-TCTTTCGAGAC
1 ATATGGACA-ATTTACCTATGTTCTTT-GGGAC
* * ** *
306470 ATATGGACAGTATACCTATGTTCTAAGGAAC
1 ATATGGACAATTTACCTATGTTCTTTGGGAC
*
306501 ATATGGACAATTTACCTAGGTTCTTTGGGAC
1 ATATGGACAATTTACCTATGTTCTTTGGGAC
*
306532 CTATGGA
1 ATATGGA
306539 TAGTTGCCGA
Statistics
Matches: 54, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
31 42 0.78
32 12 0.22
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (31 bp):
ATATGGACAATTTACCTATGTTCTTTGGGAC
Found at i:309371 original size:14 final size:15
Alignment explanation
Indices: 309347--309377 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
309337 TCTCCAGAGT
309347 TTTCATTCTTCTTCC
1 TTTCATTCTTCTTCC
309362 TTTC-TTCTTCTTCC
1 TTTCATTCTTCTTCC
309376 TT
1 TT
309378 CATGCATGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTCATTCTTCTTCC
Found at i:309987 original size:30 final size:31
Alignment explanation
Indices: 309931--309991 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
309921 TAATTTTAGG
309931 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
309962 CAAAATGGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
309992 TTCAAAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:310122 original size:23 final size:21
Alignment explanation
Indices: 310071--310130 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 21
310061 AGGGTGTCTA
*
310071 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTAC
310092 AGTGCATCCATGCACCTGCC-AC
1 AGTGCATCCATGCACC--CCTAC
310114 TAGTGCATCCATGCACC
1 -AGTGCATCCATGCACC
310131 ATGTAGTGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
21 16 0.46
22 1 0.03
23 18 0.51
ACGTcount: A:0.22, C:0.40, G:0.18, T:0.20
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:310194 original size:20 final size:20
Alignment explanation
Indices: 310169--310241 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
310159 AATGCACTTA
**
310169 GTGCATCGATGCATTTTGTT
1 GTGCATCGATGCATCCTGTT
310189 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCTGTT
*
310209 GTTCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCTGTT
*
310229 GTGCATCCATGCA
1 GTGCATCGATGCA
310242 CCAAGGCTGC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.37
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGTT
Found at i:313463 original size:31 final size:30
Alignment explanation
Indices: 313422--313482 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 30
313412 CAATTTAAGG
313422 CAAAAAGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAAGGTTTTTGGACTT-AATTGAATTTA
* *
313453 CAAAATGGTTTTTGGACTTAATTTAATTTA
1 CAAAAAGGTTTTTGGACTTAATTGAATTTA
313483 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 10 0.36
31 18 0.64
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (30 bp):
CAAAAAGGTTTTTGGACTTAATTGAATTTA
Found at i:313588 original size:21 final size:21
Alignment explanation
Indices: 313562--313621 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
313552 AGGGTGTCTA
313562 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
313583 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
313604 AGTGAATCCATGCACCCC
1 AGTGCATCCATGCACCCC
313622 CACTAGTGCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.22, C:0.42, G:0.18, T:0.18
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:313659 original size:42 final size:42
Alignment explanation
Indices: 313562--313660 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
313552 AGGGTGTCTA
** *
313562 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCCACAGTGCATCCATGCACCCATGC
* ** *
313604 AGTGAATCCATGCACCCCCACTAGTGCATTGATGCA-CCATGT
1 AGTGCATCCATGCACCCCCAC-AGTGCATCCATGCACCCATGC
*
313646 AGTGCATCTATGCAC
1 AGTGCATCCATGCAC
313661 TGCATTTCGA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 35 0.74
43 12 0.26
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (42 bp):
AGTGCATCCATGCACCCCCACAGTGCATCCATGCACCCATGC
Found at i:316947 original size:31 final size:31
Alignment explanation
Indices: 316909--316970 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
316899 CAATTTAAGG
316909 CAAAATGG-TTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTTGGACTT-AATTGAATTTA
* *
316940 CAAAATGGTTTTTTTGACTTAATTTAATTTA
1 CAAAATGGTTTTTTGGACTTAATTGAATTTA
316971 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (31 bp):
CAAAATGGTTTTTTGGACTTAATTGAATTTA
Found at i:317101 original size:23 final size:23
Alignment explanation
Indices: 317050--317131 Score: 125
Period size: 23 Copynumber: 3.7 Consensus size: 23
317040 AAGGTGTCTA
*
317050 AGTGCATCCATGCACC--CCTGC-
1 AGTGCATCCATGCACCTGCC-ACT
317071 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACCTGCCACT
317094 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACCTGCCACT
317117 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
317132 TCCATTTCGG
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
21 16 0.28
22 1 0.02
23 40 0.70
ACGTcount: A:0.22, C:0.39, G:0.18, T:0.21
Consensus pattern (23 bp):
AGTGCATCCATGCACCTGCCACT
Found at i:317176 original size:20 final size:20
Alignment explanation
Indices: 317151--317243 Score: 132
Period size: 20 Copynumber: 4.7 Consensus size: 20
317141 GATGCACTTA
*
317151 GTGCATCGATGCATTCTGCT
1 GTGCATCGATGCATCCTGCT
*
317171 GTGCATGGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
317191 GTGCATGGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
**
317211 GTGCATCGATGCATCCTATT
1 GTGCATCGATGCATCCTGCT
*
317231 GTGCATCCATGCA
1 GTGCATCGATGCA
317244 CCAAGGCTGC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:318160 original size:11 final size:11
Alignment explanation
Indices: 318144--318188 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
318134 GCATCGATGC
*
318144 ACTGCTATAGT
1 ACTGCTACAGT
318155 ACTGCTACAGT
1 ACTGCTACAGT
* *
318166 GCCGCTACAGT
1 ACTGCTACAGT
318177 ACTGCTACAGT
1 ACTGCTACAGT
318188 A
1 A
318189 ACTTTCGTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (11 bp):
ACTGCTACAGT
Found at i:318872 original size:31 final size:31
Alignment explanation
Indices: 318837--318938 Score: 143
Period size: 31 Copynumber: 3.3 Consensus size: 31
318827 CCCGAAGGAC
* *
318837 CAGTCCATAGATTTCGAAGAACCTAAGTAAA
1 CAGTCCATAGATTCCGAAGAACCTAGGTAAA
318868 CAGTCCATAGATTCCGAAGAACCTAGGTAAA
1 CAGTCCATAGATTCCGAAGAACCTAGGTAAA
* * *
318899 CAGTCCATATG-TCCCTAAGAACATAGGTAAA
1 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
318930 CAGTCCATA
1 CAGTCCATA
318939 TGTCTCGAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 64 0.98
32 1 0.02
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.22
Consensus pattern (31 bp):
CAGTCCATAGATTCCGAAGAACCTAGGTAAA
Found at i:318939 original size:31 final size:31
Alignment explanation
Indices: 318851--318961 Score: 143
Period size: 31 Copynumber: 3.6 Consensus size: 31
318841 CCATAGATTT
* * *
318851 CGAAGAACCTAAGTAAACAGTCCATA-GATTC
1 CGAAGAACATAGGTAAACAGTCCATATG-TCC
*
318882 CGAAGAACCTAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
* *
318913 CTAAGAACATAGGTAAACAGTCCATATGTCT
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
*
318944 CGAAAAACATAGGTAAAC
1 CGAAGAACATAGGTAAAC
318962 CCTCGACCCT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
31 71 0.99
32 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (31 bp):
CGAAGAACATAGGTAAACAGTCCATATGTCC
Found at i:321137 original size:2 final size:2
Alignment explanation
Indices: 321130--321164 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
321120 TGTACATGCG
321130 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
321165 TATTGTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:329135 original size:21 final size:21
Alignment explanation
Indices: 329094--329159 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
329084 GTAAAATAAA
329094 TAAAT-AAATAAT-ATACTAAAG
1 TAAATAAAATAATAATA--AAAG
329115 TAAATAAAATAATAATAAAAG
1 TAAATAAAATAATAATAAAAG
* *
329136 AAAACAAAATGAATAA-AAAA-
1 TAAATAAAAT-AATAATAAAAG
329156 TAAA
1 TAAA
329160 AAGTAAAAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 3 0.08
21 21 0.54
22 12 0.31
23 3 0.08
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (21 bp):
TAAATAAAATAATAATAAAAG
Found at i:329208 original size:14 final size:15
Alignment explanation
Indices: 329184--329226 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
329174 GTTAAAAAAT
*
329184 AAAAAT-GAGAATAAA
1 AAAAATAGAAAAT-AA
329199 AAAAATAGAAAATAA
1 AAAAATAGAAAATAA
*
329214 AAAAATAAAAAAT
1 AAAAATAGAAAAT
329227 TTAAACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAAATAGAAAATAA
Found at i:329220 original size:15 final size:16
Alignment explanation
Indices: 329184--329218 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
329174 GTTAAAAAAT
*
329184 AAAAAT-GAGAATAAA
1 AAAAATAGAAAATAAA
329199 AAAAATAGAAAATAAA
1 AAAAATAGAAAATAAA
329215 AAAA
1 AAAA
329219 TAAAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (16 bp):
AAAAATAGAAAATAAA
Found at i:330607 original size:3 final size:3
Alignment explanation
Indices: 330594--330653 Score: 59
Period size: 3 Copynumber: 19.3 Consensus size: 3
330584 AAAGTAAATA
**
330594 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAAT ACC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
*
330639 ATAT ATT ATAT AAT A
1 A-AT AAT A-AT AAT A
330654 TATACATTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 2 0.04
3 37 0.79
4 8 0.17
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:330789 original size:38 final size:36
Alignment explanation
Indices: 330708--331122 Score: 295
Period size: 38 Copynumber: 11.5 Consensus size: 36
330698 AAAATTTTCC
**
330708 AAAACTATATATTATATAGTTTT-AAAAA-ATAATT
1 AAAACTATATATTATATAGTTTTCAAAAATATTTTT
*
330742 AAAA--A-ATATTATATGAGTTTTCAAAAAATGTTTTT
1 AAAACTATATATTATAT-AGTTTTC-AAAAATATTTTT
* * * *
330777 AAAACTACATATTATTTACTTTTCAAAAATGTTTTT
1 AAAACTATATATTATATAGTTTTCAAAAATATTTTT
*
330813 AAAACTATATATTATATAATCTTTCAAAAAATATTTTT
1 AAAACTATATATTATATAGT-TTTC-AAAAATATTTTT
** *
330851 TTAACTATATATTATATAATTTTTCAAAAATATTTTT
1 AAAACTATATATTATAT-AGTTTTCAAAAATATTTTT
* *
330888 AAAACCATATATT-TATA-TTTT-AAAAATATTTTA
1 AAAACTATATATTATATAGTTTTCAAAAATATTTTT
* * *
330921 AAAACTATATACTATATAAGTTTTC-AAAATGTTTTA
1 AAAACTATATATTATAT-AGTTTTCAAAAATATTTTT
* * * *
330957 AAAACTACACAATATATAAATGTTTTC-AAAATATTTTC
1 AAAACTATA-TAT-TATATA-GTTTTCAAAAATATTTTT
* * * *
330995 CAAATTATACA-T-TATA-TTTT-AAAAATATTTTCA
1 AAAACTATATATTATATAGTTTTCAAAAATATTTT-T
* * *
331028 AAAACTATATAGTATATAAATTTTCAAAAATCGTTTTCT
1 AAAACTATATATTATAT-AGTTTTCAAAAAT-ATTTT-T
* *
331067 AAAAATTATATATTATAT--TTTGTCAAAAATATTTTC
1 -AAAACTATATATTATATAGTTT-TCAAAAATATTTTT
*
331103 ACAAACTATATTACTATATA
1 A-AAACTATA-TATTATATA
331123 CATATATAAA
Statistics
Matches: 309, Mismatches: 42, Indels: 56
0.76 0.10 0.14
Matches are distributed among these distances:
31 9 0.03
32 21 0.07
33 30 0.10
34 20 0.06
35 14 0.05
36 62 0.20
37 54 0.17
38 77 0.25
39 7 0.02
40 15 0.05
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (36 bp):
AAAACTATATATTATATAGTTTTCAAAAATATTTTT
Found at i:331047 original size:71 final size:73
Alignment explanation
Indices: 330869--331122 Score: 192
Period size: 70 Copynumber: 3.5 Consensus size: 73
330859 ATATTATATA
* * *
330869 ATTTTTCAAAAATATTTT-TAAAACCATAT-AT-T-TATATTTT-AAAAAT-ATTTT-AAAAACT
1 ATTTTT-AAAAATATTTTCAAAAACTATATAATATATAAATTTTCAAAAATCATTTTCAAAAA-T
330927 ATATAC-TATAT
64 -TATACAT-TAT
* * * * * *
330938 AAGTTTTCAAAATGTTTT-AAAAACTACACAATATATAAATGTTTTC-AAAAT-ATTTTC-CAAA
1 -ATTTTTAAAAATATTTTCAAAAACTATATAATATATAAA--TTTTCAAAAATCATTTTCAAAAA
330999 TTATACATTAT
63 TTATACATTAT
* *
331010 A-TTTTAAAAATATTTTCAAAAACTATATAGTATATAAATTTTCAAAAATCGTTTTCTAAAAATT
1 ATTTTTAAAAATATTTTCAAAAACTATATAATATATAAATTTTCAAAAATCATTTTC-AAAAATT
*
331074 ATATATTAT
65 ATACATTAT
* *
331083 ATTTTGTCAAAAATATTTTCACAAACTATATTACTATATA
1 ATTTT-T-AAAAATATTTTCAAAAACTATA-TAATATATA
331123 CATATATAAA
Statistics
Matches: 148, Mismatches: 19, Indels: 27
0.76 0.10 0.14
Matches are distributed among these distances:
69 21 0.14
70 25 0.17
71 25 0.17
72 11 0.07
73 16 0.11
74 20 0.14
75 1 0.01
76 21 0.14
77 8 0.05
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (73 bp):
ATTTTTAAAAATATTTTCAAAAACTATATAATATATAAATTTTCAAAAATCATTTTCAAAAATTA
TACATTAT
Found at i:331093 original size:107 final size:108
Alignment explanation
Indices: 330796--331112 Score: 287
Period size: 108 Copynumber: 2.9 Consensus size: 108
330786 TATTATTTAC
* * * * *** *
330796 TTTTCAAAAATGTTTTTAAAACTATATATTATAT-AATCTTTCAAAAAATATTTTTTTAACTATA
1 TTTT-AAAAATATTTTAAAAACTATATACTATATAAAT-TTTC--AAAATGTTTTAAAAACTACA
* * * * *
330860 TATTATAT-AAT-TTTTCAAAAATATTTTTA-AAACCATATATTTATA
62 CAATATATAAATGTTTTCAAAAATATTTTCACAAACTATACA-TTATA
*
330905 TTTTAAAAATATTTTAAAAACTATATACTATATAAGTTTTCAAAATGTTTTAAAAACTACACAAT
1 TTTTAAAAATATTTTAAAAACTATATACTATATAAATTTTCAAAATGTTTTAAAAACTACACAAT
*
330970 ATATAAATGTTTTC-AAAATATTTTC-CAAATTATACATTATA
66 ATATAAATGTTTTCAAAAATATTTTCACAAACTATACATTATA
* *
331011 TTTTAAAAATATTTTCAAAAACTATATAGTATATAAATTTTCAAAAATCGTTTTCTAAAAA-T-T
1 TTTTAAAAATATTTT-AAAAACTATATACTATATAAATTTTC-AAAAT-G-TTT-TAAAAACTAC
* *
331074 A-TATAT-TATAT-TTTGTCAAAAATATTTTCACAAACTATA
61 ACAATATATAAATGTTT-TCAAAAATATTTTCACAAACTATA
331113 TTACTATATA
Statistics
Matches: 175, Mismatches: 21, Indels: 24
0.80 0.10 0.11
Matches are distributed among these distances:
106 44 0.25
107 50 0.29
108 55 0.31
109 16 0.09
110 4 0.02
111 6 0.03
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (108 bp):
TTTTAAAAATATTTTAAAAACTATATACTATATAAATTTTCAAAATGTTTTAAAAACTACACAAT
ATATAAATGTTTTCAAAAATATTTTCACAAACTATACATTATA
Found at i:332952 original size:58 final size:58
Alignment explanation
Indices: 332863--332981 Score: 184
Period size: 58 Copynumber: 2.1 Consensus size: 58
332853 TTGAGATATG
* *
332863 ATGATTGCGATAGTTCGAACGTAGGTTTCCAGGTGATCCGGCAACCAAGGAGATCGCC
1 ATGATTGCGACAGTTCGAACGTAGGTCTCCAGGTGATCCGGCAACCAAGGAGATCGCC
* * * *
332921 ATGATTGCGACAGTTTGAATGTTGGTCTCCAGGTGATCCGGCAACCAAGGAGGTCGCC
1 ATGATTGCGACAGTTCGAACGTAGGTCTCCAGGTGATCCGGCAACCAAGGAGATCGCC
332979 ATG
1 ATG
332982 CCATCCCATG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (58 bp):
ATGATTGCGACAGTTCGAACGTAGGTCTCCAGGTGATCCGGCAACCAAGGAGATCGCC
Found at i:333387 original size:24 final size:24
Alignment explanation
Indices: 333330--333417 Score: 63
Period size: 24 Copynumber: 3.7 Consensus size: 24
333320 TGATATTAAC
* *
333330 GATTTAGTAATAATTAGTAATACTAA
1 GATTTAATAATAATTACTAATA--AA
* *
333356 -AATT-ATAATAATTATTAATAAA
1 GATTTAATAATAATTACTAATAAA
* * *
333378 GATTTAATAATGATTACTCATAAT
1 GATTTAATAATAATTACTAATAAA
* *
333402 TATTTAATAATGATTA
1 GATTTAATAATAATTA
333418 AATATTTAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
22 2 0.04
23 3 0.06
24 43 0.84
25 3 0.06
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (24 bp):
GATTTAATAATAATTACTAATAAA
Found at i:333532 original size:17 final size:15
Alignment explanation
Indices: 333498--333537 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
333488 AGAGATATGC
333498 ATATTTAATATTATA
1 ATATTTAATATTATA
*
333513 ATATTTAAGTTTTAATA
1 ATATTTAA-TATT-ATA
333530 ATATTTAA
1 ATATTTAA
333538 CAAAACCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 3 0.14
17 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATATTTAATATTATA
Found at i:333992 original size:14 final size:14
Alignment explanation
Indices: 333973--334002 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
333963 TGTAGCAAAC
333973 ATCATATCTCAGCA
1 ATCATATCTCAGCA
333987 ATCATATCTCAGCA
1 ATCATATCTCAGCA
334001 AT
1 AT
334003 TAATTGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (14 bp):
ATCATATCTCAGCA
Found at i:335453 original size:26 final size:26
Alignment explanation
Indices: 335424--335478 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
335414 CGGTGTAATT
*
335424 TACACAAAAATTTTTAAGGTAAAGCA
1 TACACAAAAATTTTAAAGGTAAAGCA
*
335450 TACACTAAAATTTTAAAGGTAAAGCA
1 TACACAAAAATTTTAAAGGTAAAGCA
335476 TAC
1 TAC
335479 TATTTATTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (26 bp):
TACACAAAAATTTTAAAGGTAAAGCA
Found at i:335639 original size:35 final size:35
Alignment explanation
Indices: 335591--335661 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
335581 CTACCATTAA
*
335591 ATAATTAACGATGTTATGATAGAGTAACTAACACC
1 ATAATTAACGATGTTATGATAGAGCAACTAACACC
* * *
335626 ATAATTAATGATGTTATGATAGGGCAATTAACACC
1 ATAATTAACGATGTTATGATAGAGCAACTAACACC
335661 A
1 A
335662 AAATGACGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (35 bp):
ATAATTAACGATGTTATGATAGAGCAACTAACACC
Found at i:336235 original size:2 final size:2
Alignment explanation
Indices: 336224--336256 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
336214 TATTTTTTTC
*
336224 AT AT AC AT 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 AT AT AT AT A
336257 ATTAAGGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:339857 original size:53 final size:53
Alignment explanation
Indices: 339777--339884 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
339767 TAATGTAAAC
339777 ATAAGCATGACATGAAGTGTCAGAGACCATTTATACAATTTTCTGGAATATCT
1 ATAAGCATGACATGAAGTGTCAGAGACCATTTATACAATTTTCTGGAATATCT
*
339830 ATAAGCATGACATGAAGTGTCAGAGACCATTTATATAATTTTCTGGAATATCT
1 ATAAGCATGACATGAAGTGTCAGAGACCATTTATACAATTTTCTGGAATATCT
339883 AT
1 AT
339885 TGTATATTGC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (53 bp):
ATAAGCATGACATGAAGTGTCAGAGACCATTTATACAATTTTCTGGAATATCT
Found at i:340847 original size:24 final size:24
Alignment explanation
Indices: 340815--340862 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
340805 GGAATTGGGT
* * *
340815 TGAATATAAGCAAACAGACATAAA
1 TGAACATAAACAAACAAACATAAA
*
340839 TGAACATAAACGAACAAACATAAA
1 TGAACATAAACAAACAAACATAAA
340863 CAAATGAACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.60, C:0.15, G:0.10, T:0.15
Consensus pattern (24 bp):
TGAACATAAACAAACAAACATAAA
Found at i:340876 original size:14 final size:14
Alignment explanation
Indices: 340836--340881 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
340826 AAACAGACAT
340836 AAATGAACATAAAC
1 AAATGAACATAAAC
* **
340850 GAACAAACATAAAC
1 AAATGAACATAAAC
*
340864 AAATGAACTTAAAC
1 AAATGAACATAAAC
340878 AAAT
1 AAAT
340882 AGATTACCGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.63, C:0.15, G:0.07, T:0.15
Consensus pattern (14 bp):
AAATGAACATAAAC
Found at i:344111 original size:22 final size:23
Alignment explanation
Indices: 344050--344111 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
344040 TAAAATATTT
*
344050 TTTATATCGAAAT-AATTTAGCG
1 TTTATATCGAAATAAATTTAGAG
* *
344072 TATATAT-GAAATATATTT-GAG
1 TTTATATCGAAATAAATTTAGAG
344093 TTTATATCGAAATAAATTT
1 TTTATATCGAAATAAATTT
344112 TGATAATATC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 13 0.39
22 20 0.61
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (23 bp):
TTTATATCGAAATAAATTTAGAG
Found at i:344113 original size:23 final size:23
Alignment explanation
Indices: 344050--344114 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 23
344040 TAAAATATTT
* *
344050 TTTATATCGAAAT-AATTTAGCG
1 TTTATATCGAAATAAATTTTGAG
* *
344072 TATATAT-GAAATATA-TTTGAG
1 TTTATATCGAAATAAATTTTGAG
344093 TTTATATCGAAATAAATTTTGA
1 TTTATATCGAAATAAATTTTGA
344115 TAATATCAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
21 15 0.44
22 14 0.41
23 5 0.15
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (23 bp):
TTTATATCGAAATAAATTTTGAG
Found at i:352750 original size:47 final size:47
Alignment explanation
Indices: 352683--352818 Score: 132
Period size: 55 Copynumber: 2.7 Consensus size: 47
352673 ATTTTTTTAT
* *
352683 AATGACAATTTAGGGTTAAAAATAATATAAAAAATT-ATCATATTTAA
1 AATGGCAATTTAGGGTTAAAAATAATATAAAAAATTAAT-ATACTTAA
*
352730 AATGGTAATTTAGGGTTAAAAATTTTAAAATATTATAAAAAATTAATATACTTAA
1 AATGGCAATTTAGGGTTAAAAA---T---A-A-TATAAAAAATTAATATACTTAA
* *
352785 AATGGCAATTTAGGGTT-AAAATGATATTAAAAAT
1 AATGGCAATTTAGGGTTAAAAATAATATAAAAAAT
352819 AAAATTATAT
Statistics
Matches: 74, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
46 9 0.12
47 21 0.28
50 1 0.01
51 1 0.01
53 1 0.01
54 5 0.07
55 34 0.46
56 2 0.03
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.35
Consensus pattern (47 bp):
AATGGCAATTTAGGGTTAAAAATAATATAAAAAATTAATATACTTAA
Found at i:352770 original size:55 final size:55
Alignment explanation
Indices: 352701--352805 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 55
352691 TTTAGGGTTA
* *
352701 AAAATAATATAAAAAATT-ATCATATTTAAAATGGTAATTTAGGGTTAAAAATTTT
1 AAAATAATATAAAAAATTAAT-ATACTTAAAATGGCAATTTAGGGTTAAAAATTTT
*
352756 AAAATATTATAAAAAATTAATATACTTAAAATGGCAATTTAGGGTTAAAA
1 AAAATAATATAAAAAATTAATATACTTAAAATGGCAATTTAGGGTTAAAA
352806 TGATATTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
55 44 0.96
56 2 0.04
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.35
Consensus pattern (55 bp):
AAAATAATATAAAAAATTAATATACTTAAAATGGCAATTTAGGGTTAAAAATTTT
Found at i:352948 original size:18 final size:18
Alignment explanation
Indices: 352922--352971 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
352912 TAAAATATTT
352922 AAATGATAAAATATAAAG
1 AAATGATAAAATATAAAG
*
352940 AAATTATAAAATATAAAG
1 AAATGATAAAATATAAAG
352958 AAATGATAAAATAT
1 AAATGATAAAATAT
352972 TAATTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (18 bp):
AAATGATAAAATATAAAG
Found at i:353288 original size:12 final size:12
Alignment explanation
Indices: 353271--353298 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
353261 GTTGAATTAC
353271 AATTATGACCAA
1 AATTATGACCAA
353283 AATTATGACCAA
1 AATTATGACCAA
353295 AATT
1 AATT
353299 GATATAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (12 bp):
AATTATGACCAA
Found at i:368268 original size:12 final size:11
Alignment explanation
Indices: 368247--368289 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 11
368237 ATTTTCACCT
368247 AGAGAAGAGAG
1 AGAGAAGAGAG
368258 AGAGTAAGAGAG
1 AGAG-AAGAGAG
*
368270 AGA-CAGAGAG
1 AGAGAAGAGAG
*
368280 AGAGATGAGA
1 AGAGAAGAGA
368290 TCCAAAGATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 9 0.33
11 8 0.30
12 10 0.37
ACGTcount: A:0.51, C:0.02, G:0.42, T:0.05
Consensus pattern (11 bp):
AGAGAAGAGAG
Found at i:369524 original size:40 final size:39
Alignment explanation
Indices: 369459--369534 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 39
369449 TGGTTATCTA
* * *
369459 GGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCG
1 GGGGTGACACGACTCATACGCGATGAAGAGATCTGGTCG
* *
369498 GGGGATGACACGACTCATACGTGATGAAGAGTTCTGG
1 GGGG-TGACACGACTCATACGCGATGAAGAGATCTGG
369535 CCATCTTTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 4 0.13
40 27 0.87
ACGTcount: A:0.22, C:0.20, G:0.38, T:0.20
Consensus pattern (39 bp):
GGGGTGACACGACTCATACGCGATGAAGAGATCTGGTCG
Found at i:369602 original size:134 final size:134
Alignment explanation
Indices: 369319--369679 Score: 476
Period size: 134 Copynumber: 2.7 Consensus size: 134
369309 AGTTTGGGTC
* * * * *
369319 ATCTAAGGGTGACATGGTTCCTACGTGATGAGGA-ACTCTGGTCGAGAGATGACACTG-CTCACA
1 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGA-TCTGGTCGGGAGATGACAC-GACTCATA
* * * *
369382 CGTGATGAAGAGTTCTTGGCCATTTTTAGGAAGGGTGATAACTCGATTCCTACGCGATGAGGACG
64 CGTGATGAAGAGTTC-TGGCCATCTTTAGGAAGGGCGATAACACGATTCCCACGCGATGAGGACG
369447 GTTGGTT
128 GTTGGTT
* *
369454 ATCTAGGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACG
1 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGAGATGACACGACTCATACG
* * *
369519 TGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCCACGTGATGAGGAC-TTC
66 TGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGATTCCCACGCGATGAGGACGGT-
369583 TGGTT
130 TGGTT
* * * * * *
369588 ATCTAGGGGTGACACGACTCCTGCGTGATAAAGAGATCTGGTCAGGAGATGACACGACTTATACG
1 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGAGATGACACGACTCATACG
*
369653 TGATGAAGAGTTCTAGCCATCTTTAGG
66 TGATGAAGAGTTCTGGCCATCTTTAGG
369680 GATAATGATT
Statistics
Matches: 200, Mismatches: 23, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
133 1 0.00
134 131 0.65
135 67 0.34
136 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (134 bp):
ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGAGATGACACGACTCATACG
TGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGATTCCCACGCGATGAGGACGGTT
GGTT
Found at i:370044 original size:66 final size:63
Alignment explanation
Indices: 369859--370037 Score: 180
Period size: 66 Copynumber: 2.8 Consensus size: 63
369849 CCAAAGCAAC
* * * * **
369859 TGTCTCGAAAGAGACAAAATTCGTTTCAAAGGAAAC-AACCCAAAGATGGCATTTAAAGGGAAT
1 TGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGGTGTTTAAAGGGAAT
* ** * * * *
369922 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAACGTTCTCAAAGATCGGTGTTTCATGGGAA
1 TGTCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACGATCTCAAAGAT-GGTGTTTAAAGGG-A
369987 AT
62 AT
369989 TGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1 TGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
370038 TTTGTTTTGT
Statistics
Matches: 93, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
62 2 0.02
63 15 0.16
64 13 0.14
65 9 0.10
66 34 0.37
67 20 0.22
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (63 bp):
TGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGGTGTTTAAAGGGAAT
Found at i:370583 original size:65 final size:66
Alignment explanation
Indices: 370514--370637 Score: 187
Period size: 66 Copynumber: 1.9 Consensus size: 66
370504 GTGGGTATTT
* *
370514 TCAAAAGAAATTGTC-TCGAGAGACAAAAGTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTT
1 TCAAAAGAAATTGTCATCAAGAGACAAAAGTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTT
370578 C
66 C
* * * *
370579 TCAAAAGAAATTGTCATTAAGATATAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
1 TCAAAAGAAATTGTCATCAAGAGACAAAAGTTTGTTTCAAAAGAAACAAACTCAAAGAT
370638 GGATTACATC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
65 15 0.29
66 37 0.71
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (66 bp):
TCAAAAGAAATTGTCATCAAGAGACAAAAGTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTT
C
Found at i:371029 original size:37 final size:37
Alignment explanation
Indices: 370988--371059 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
370978 AAGAGACAAA
*
370988 ATTTTGTTTCCAA-AGAAACATACTCAAAGATTTTTTC
1 ATTTTGTTT-CAAGAGAAACAAACTCAAAGATTTTTTC
* *
371025 ATTTTGTTTTAAGTGAAACAAACTCAAAGATTTTT
1 ATTTTGTTTCAAGAGAAACAAACTCAAAGATTTTT
371060 CAAGAAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 2 0.06
37 29 0.94
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (37 bp):
ATTTTGTTTCAAGAGAAACAAACTCAAAGATTTTTTC
Found at i:371143 original size:30 final size:32
Alignment explanation
Indices: 371088--371160 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 32
371078 GAGACAAAGT
371088 TTTGTTTCAAAAGAAATAAACTCAAAGATCA-
1 TTTGTTTCAAAAGAAATAAACTCAAAGATCAG
* * *
371119 TTTGTTTCAAAATAAAT-GACTCAAAGATGATG
1 TTTGTTTCAAAAGAAATAAACTCAAAGATCA-G
371151 TTTGTTTCAA
1 TTTGTTTCAA
371161 GTGAAACAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.30
31 16 0.43
32 10 0.27
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (32 bp):
TTTGTTTCAAAAGAAATAAACTCAAAGATCAG
Found at i:371227 original size:36 final size:36
Alignment explanation
Indices: 371184--371321 Score: 172
Period size: 36 Copynumber: 3.8 Consensus size: 36
371174 ATAATTTGGA
*
371184 AAATTGTCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* * * *
371220 AAATTGTCTCAAACGACACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
371256 AAATTGTCTCAAGCGAGACAACATTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
** *
371291 AAAACGATCTCAAGTGAGATCAAC-TTTGTTT
1 AAATTG-TCTCAAGCGAGA-CAACATTTGTTT
371322 AATATGAAAA
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
35 7 0.08
36 77 0.88
37 4 0.05
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
Found at i:371406 original size:36 final size:37
Alignment explanation
Indices: 371355--371426 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 37
371345 TTTATTCTCA
*
371355 AAAGAAAAATGTCTCAAACGAGACGAAATTTGTTTTG
1 AAAGAAAAATGTCTCAAACGAGACAAAATTTGTTTTG
* *
371392 AAAG-AAATTGTCTCAAGCGAGACAAAATTTGTTTT
1 AAAGAAAAATGTCTCAAACGAGACAAAATTTGTTTT
371427 TAGAAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 28 0.88
37 4 0.12
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (37 bp):
AAAGAAAAATGTCTCAAACGAGACAAAATTTGTTTTG
Found at i:373026 original size:12 final size:12
Alignment explanation
Indices: 373009--373049 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
372999 TCTTTGTCCT
373009 TTTTTTCTTTGC
1 TTTTTTCTTTGC
373021 TTTTTTCTTTG-
1 TTTTTTCTTTGC
*
373032 TTGTTTT-TTTTC
1 TT-TTTTCTTTGC
373044 TTTTTT
1 TTTTTT
373050 TTATTGGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (12 bp):
TTTTTTCTTTGC
Found at i:378073 original size:12 final size:11
Alignment explanation
Indices: 378052--378094 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 11
378042 ATTTTCACCT
378052 AGAGAAGAGAG
1 AGAGAAGAGAG
378063 AGAGTAAGAGAG
1 AGAG-AAGAGAG
*
378075 AGA-CAGAGAG
1 AGAGAAGAGAG
*
378085 AGAGATGAGA
1 AGAGAAGAGA
378095 TCCAGAGATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 9 0.33
11 8 0.30
12 10 0.37
ACGTcount: A:0.51, C:0.02, G:0.42, T:0.05
Consensus pattern (11 bp):
AGAGAAGAGAG
Found at i:384749 original size:41 final size:39
Alignment explanation
Indices: 384579--384751 Score: 120
Period size: 41 Copynumber: 4.3 Consensus size: 39
384569 CCGAACTATT
* * *
384579 GCGGCGTTTGTTGAAAAACGCCACTAAAGAACAATTCTTTT
1 GCGGCGTTTGTTTAAAAACGCCACTAAAGAAC--TTATTTA
* * **
384620 GCGGCGTTTGTTTAGAAACACCACTAAATTA-TTAGGTTTTA
1 GCGGCGTTTGTTTAAAAACGCCACTAAAGAACTTA---TTTA
* * * * *
384661 CCAGCGTTTGTCTAAAAACGACAC-AATATATACTCTA-TT-
1 GCGGCGTTTGTTTAAAAACGCCACTAA-AGA-ACT-TATTTA
384700 GCGGCGTTTGTTTAAAAACGCCACTAAAGAACTTATATGTA
1 GCGGCGTTTGTTTAAAAACGCCACTAAAGAACTTAT-T-TA
384741 GCGGCGTTTGT
1 GCGGCGTTTGT
384752 GAAATAAACG
Statistics
Matches: 101, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
37 2 0.02
38 5 0.05
39 23 0.23
40 7 0.07
41 60 0.59
42 1 0.01
43 1 0.01
44 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (39 bp):
GCGGCGTTTGTTTAAAAACGCCACTAAAGAACTTATTTA
Found at i:387499 original size:13 final size:12
Alignment explanation
Indices: 387468--387509 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 12
387458 TGACCTAAGT
*
387468 AATATATA-CTA
1 AATATATATTTA
387479 AA-ATATATTTA
1 AATATATATTTA
387490 ATATATATATTTA
1 A-ATATATATTTA
387503 AATATAT
1 AATATAT
387510 TCAATTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 5 0.19
11 5 0.19
12 7 0.26
13 10 0.37
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (12 bp):
AATATATATTTA
Found at i:387505 original size:23 final size:23
Alignment explanation
Indices: 387469--387519 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
387459 GACCTAAGTA
*
387469 ATATATACTAAAATATATTTAAT
1 ATATATACTAAAATATATTCAAT
* *
387492 ATATATATTTAAATATATTCAAT
1 ATATATACTAAAATATATTCAAT
*
387515 TTATA
1 ATATA
387520 AGATCATAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATATACTAAAATATATTCAAT
Found at i:398101 original size:21 final size:22
Alignment explanation
Indices: 398059--398103 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
398049 AATTACAAAT
398059 AGGGAACTGATTCCCTTGCTAC
1 AGGGAACTGATTCCCTTGCTAC
398081 AGGGAACTGATTCCC-TGCTAC
1 AGGGAACTGATTCCCTTGCTAC
398102 AG
1 AG
398104 TACTTCCGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (22 bp):
AGGGAACTGATTCCCTTGCTAC
Found at i:401768 original size:21 final size:21
Alignment explanation
Indices: 401689--401790 Score: 66
Period size: 21 Copynumber: 4.9 Consensus size: 21
401679 AAATCAGTTC
*
401689 CCAGAATCGCAACGTGATTAT
1 CCAGAATCGCAACGCGATTAT
** *
401710 AAAGAATCGCAATGCGA-TAGT
1 CCAGAATCGCAACGCGATTA-T
* ** *
401731 ACA-AATTCGCATTGCGATTTT
1 CCAGAA-TCGCAACGCGATTAT
*
401752 CCAGAATCGCAACGCGAATAT
1 CCAGAATCGCAACGCGATTAT
* *
401773 -GAAAATCGCAACGCGATT
1 CCAGAATCGCAACGCGATT
401791 CTGACTATCG
Statistics
Matches: 62, Mismatches: 15, Indels: 9
0.72 0.17 0.10
Matches are distributed among these distances:
20 19 0.31
21 40 0.65
22 3 0.05
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (21 bp):
CCAGAATCGCAACGCGATTAT
Found at i:401781 original size:20 final size:20
Alignment explanation
Indices: 401756--402007 Score: 202
Period size: 20 Copynumber: 12.5 Consensus size: 20
401746 GATTTTCCAG
** *
401756 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
* *
401776 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * *
401795 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCCGT-A
* *
401817 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
**
401837 AATCGCAACGAC-AATATGTAA
1 AATCGCAACG-CGAATCCGT-A
*
401858 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* * *
401878 AATCACAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
401898 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
* * *
401918 AATCCCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* * *
401938 AATCGTAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
401958 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
401978 AATCGCAATGCGAATCTGTA
1 AATCGCAACGCGAATCCGTA
401998 AATCGCAACG
1 AATCGCAACG
402008 AGATTCTGAC
Statistics
Matches: 183, Mismatches: 43, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
19 1 0.01
20 149 0.81
21 32 0.17
22 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:401912 original size:40 final size:40
Alignment explanation
Indices: 401756--402010 Score: 280
Period size: 40 Copynumber: 6.3 Consensus size: 40
401746 GATTTTCCAG
* * * *
401756 AATCGCAACGCGAATATGAAAATCGCAACGCG-ATTC-TGA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGT-A
* * * *
401795 CTATCGCAACGAGTATCCGTAAAATCGTAACGCGTATCCGTA
1 -AATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTA
* *
401837 AATCGCAACGACAATATGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTA
* *
401878 AATCACAACGAGAATACGTAAATCGCAACGCGTATCTGTA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTA
* * *
401918 AATCCCAACGAGAATACGTAAATCGTAATGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTA
* * * * *
401958 AATCGCAATGCGAATACGTAAATCGCAATGCGAATCTGTA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTA
401998 AATCGCAACGAGA
1 AATCGCAACGAGA
402011 TTCTGACTAT
Statistics
Matches: 182, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
40 114 0.63
41 63 0.35
42 4 0.02
43 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (40 bp):
AATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTA
Found at i:402894 original size:24 final size:24
Alignment explanation
Indices: 402867--402944 Score: 138
Period size: 24 Copynumber: 3.2 Consensus size: 24
402857 GTATTCGAAA
402867 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
402891 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
402915 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
402939 TTTGAT
1 TTTGAT
402945 GATTTTTCAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:405518 original size:19 final size:19
Alignment explanation
Indices: 405494--405592 Score: 101
Period size: 19 Copynumber: 5.7 Consensus size: 19
405484 GCAACGAGAG
405494 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
405513 AATCGCAA--CG---TGAA
1 AATCGCAATGCGAAATGAA
405527 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
**
405546 AATCGCAA--CG--A-GGG
1 AATCGCAATGCGAAATGAA
405560 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
405579 AATCGCAACGCGAA
1 AATCGCAATGCGAA
405593 TTTATTTTCG
Statistics
Matches: 65, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 21 0.32
15 1 0.02
16 4 0.06
17 4 0.06
18 1 0.02
19 34 0.52
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:405518 original size:33 final size:33
Alignment explanation
Indices: 405481--405588 Score: 189
Period size: 33 Copynumber: 3.3 Consensus size: 33
405471 GGAAATTACT
405481 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* *
405514 ATCGCAACGTGAAAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
*
405547 ATCGCAACGAGGGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
405580 ATCGCAACG
1 ATCGCAACG
405589 CGAATTTATT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 70 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:405615 original size:19 final size:19
Alignment explanation
Indices: 405588--405664 Score: 74
Period size: 19 Copynumber: 4.3 Consensus size: 19
405578 AAATCGCAAC
* *
405588 GCGAATTTATTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
405607 GTGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
405626 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
* *
405640 GCGATTTTAATTTCGCATT
1 GCGATTTTAGTTTCGCGTT
405659 GCGATT
1 GCGATT
405665 CTCTTGTTGC
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
14 12 0.26
16 1 0.02
17 1 0.02
18 1 0.02
19 32 0.68
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.48
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Done.