Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009086.1 Hibiscus syriacus cultivar Beakdansim tig00112530_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: 1596699
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:199537 original size:28 final size:28
Alignment explanation
Indices: 199505--199583 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
199495 GATAAATGTT
* *
199505 TTTAAAATACAAATTATATTATTCAAAA
1 TTTAAAATAAAAATAATATTATTCAAAA
*
199533 TTTAAAATAAAAATAATATTATTCGAAA
1 TTTAAAATAAAAATAATATTATTCAAAA
199561 TTTAAAATTAAAATATAA-ATTAT
1 TTTAAAA-TAAAA-ATAATATTAT
199584 AGTATTCGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 32 0.70
29 10 0.22
30 4 0.09
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (28 bp):
TTTAAAATAAAAATAATATTATTCAAAA
Found at i:199572 original size:34 final size:34
Alignment explanation
Indices: 199529--199606 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
199519 TATATTATTC
*
199529 AAAATTTAAAATAAAAATAATATTATTCGAAATTT
1 AAAA-TTAAAATAAAAATAATAGTATTCGAAATTT
* *
199564 AAAATTAAAATATAAATTATAGTATTCGAAATTT
1 AAAATTAAAATAAAAATAATAGTATTCGAAATTT
*
199598 AACATTAAA
1 AAAATTAAA
199607 TTTTAACTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 35 0.90
35 4 0.10
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (34 bp):
AAAATTAAAATAAAAATAATAGTATTCGAAATTT
Found at i:200318 original size:8 final size:8
Alignment explanation
Indices: 200305--200345 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
200295 TCACAAGCTT
200305 TCAAATTC
1 TCAAATTC
200313 TCAAATTC
1 TCAAATTC
* *
200321 CCAAACTC
1 TCAAATTC
200329 T-AAATTC
1 TCAAATTC
200336 TCAAATTC
1 TCAAATTC
200344 TC
1 TC
200346 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:210642 original size:42 final size:42
Alignment explanation
Indices: 210583--210667 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
210573 GAATTGAGCT
210583 TAACTCTGGTTTTAGTTCTGGGAAAGTATGGGGTATGTTTGG
1 TAACTCTGGTTTTAGTTCTGGGAAAGTATGGGGTATGTTTGG
210625 TAACTCTGGTTTTAGTTCTGGGAAAGTATGGGGTATGTTTGG
1 TAACTCTGGTTTTAGTTCTGGGAAAGTATGGGGTATGTTTGG
210667 T
1 T
210668 TACTGAGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.19, C:0.07, G:0.33, T:0.41
Consensus pattern (42 bp):
TAACTCTGGTTTTAGTTCTGGGAAAGTATGGGGTATGTTTGG
Found at i:211347 original size:15 final size:15
Alignment explanation
Indices: 211300--211347 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
211290 TCGGGTCGGG
* *
211300 TATATATATTTAAAT
1 TATATATATATATAT
* *
211315 TAAATATATAAATAT
1 TATATATATATATAT
211330 TATATATATATATAT
1 TATATATATATATAT
211345 TAT
1 TAT
211348 TTAAATTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:211354 original size:39 final size:38
Alignment explanation
Indices: 211300--211378 Score: 131
Period size: 39 Copynumber: 2.1 Consensus size: 38
211290 TCGGGTCGGG
211300 TATATATATTTAAATTAAATATATAAATATTATATATA
1 TATATATATTTAAATTAAATATATAAATATTATATATA
* *
211338 TATATATTATTTAAATTAAATTTATTAATATTATATATA
1 TATATA-TATTTAAATTAAATATATAAATATTATATATA
211377 TA
1 TA
211379 AAAATAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 6 0.16
39 32 0.84
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (38 bp):
TATATATATTTAAATTAAATATATAAATATTATATATA
Found at i:219554 original size:34 final size:33
Alignment explanation
Indices: 219478--219584 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
219468 GTGGTAAGAA
* *
219478 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
219512 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
219547 A-TTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
219581 ATTT
1 ATTT
219585 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 33 0.54
35 9 0.15
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:219566 original size:36 final size:34
Alignment explanation
Indices: 219511--219589 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
219501 TTTAAATAGT
*
219511 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
219543 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
219577 TATTATTTATTTA
1 TATTATTTTTTTA
219590 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:220094 original size:12 final size:13
Alignment explanation
Indices: 220061--220098 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
220051 AAATACATAA
220061 ATATATTTAATAT
1 ATATATTTAATAT
*
220074 ATTTATTTAATAT
1 ATATATTTAATAT
220087 A-ATATTTAATAT
1 ATATATTTAATAT
220099 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:223019 original size:21 final size:21
Alignment explanation
Indices: 222994--223037 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
222984 GGAAATGTTA
* *
222994 AAAAACATTAATGTTTTAGGT
1 AAAAACAATAATGATTTAGGT
*
223015 AAAAATAATAATGATTTAGGT
1 AAAAACAATAATGATTTAGGT
223036 AA
1 AA
223038 TTTTTTACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.34
Consensus pattern (21 bp):
AAAAACAATAATGATTTAGGT
Found at i:229009 original size:17 final size:17
Alignment explanation
Indices: 228989--229044 Score: 112
Period size: 17 Copynumber: 3.3 Consensus size: 17
228979 GAAAGTCAAC
228989 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
229006 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
229023 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
229040 GGTCA
1 GGTCA
229045 GATCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.12, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:229064 original size:19 final size:19
Alignment explanation
Indices: 229042--229097 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
229032 TCGGGTCGGG
229042 TCAGATCGGTCAAACCGGT
1 TCAGATCGGTCAAACCGGT
* *
229061 TCAGACCGGTTCGAACCGGT
1 TCAGATCGG-TCAAACCGGT
* *
229081 TGAAATCGGTCAAACCG
1 TCAGATCGGTCAAACCG
229098 ATTGAAAACC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (19 bp):
TCAGATCGGTCAAACCGGT
Found at i:229102 original size:19 final size:19
Alignment explanation
Indices: 229046--229104 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
229036 GTCGGGTCAG
* *
229046 ATCGGTCAAACCGGTTCAG
1 ATCGGTCAAACCGGTTGAA
* *
229065 ACCGGTTCGAACCGGTTGAA
1 ATCGG-TCAAACCGGTTGAA
*
229085 ATCGGTCAAACCGATTGAA
1 ATCGGTCAAACCGGTTGAA
229104 A
1 A
229105 ACCGGTTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (19 bp):
ATCGGTCAAACCGGTTGAA
Found at i:229115 original size:20 final size:19
Alignment explanation
Indices: 229048--229116 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 19
229038 CGGGTCAGAT
* * *
229048 CGGTCAAACCGGTTCAGAC
1 CGGTCAAACCGATTGAAAC
* * *
229067 CGGTTCGAACCGGTTGAAAT
1 CGG-TCAAACCGATTGAAAC
229087 CGGTCAAACCGATTGAAAAC
1 CGGTCAAACCGATTG-AAAC
*
229107 CGGTTAAACC
1 CGGTCAAACC
229117 AGTTTCCAGC
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 13 0.32
20 27 0.68
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (19 bp):
CGGTCAAACCGATTGAAAC
Found at i:237305 original size:17 final size:17
Alignment explanation
Indices: 237283--237321 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
237273 AACGGTCAAC
237283 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
237300 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
237317 GGTCA
1 GGTCA
237322 GACCGGTCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:237310 original size:7 final size:7
Alignment explanation
Indices: 237249--237293 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
237239 GTCAAAGAAA
237249 GTCAACG
1 GTCAACG
*
237256 ATCAACG
1 GTCAACG
237263 GTCAACG
1 GTCAACG
237270 GTCAACG
1 GTCAACG
237277 GTCAACG
1 GTCAACG
237284 GTCAACG
1 GTCAACG
237291 GTC
1 GTC
237294 GGGTCGGGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:237341 original size:19 final size:19
Alignment explanation
Indices: 237319--237386 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
237309 TCGGGTCGGG
237319 TCAGACCGGTCAGACCGGT
1 TCAGACCGGTCAGACCGGT
237338 TCAGACCGGTTC-GAACCGGT
1 TCAGACCGG-TCAG-ACCGGT
* * *
237358 TGAAACCGGTCAAACCGG-
1 TCAGACCGGTCAGACCGGT
237376 TCAGAACCGGT
1 TCAG-ACCGGT
237387 TGAAAACCGG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
18 2 0.05
19 23 0.57
20 15 0.38
ACGTcount: A:0.25, C:0.29, G:0.29, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAGACCGGT
Found at i:237367 original size:39 final size:38
Alignment explanation
Indices: 237323--237406 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 38
237313 GTCGGGTCAG
*
237323 ACCGGTCAGACCGGTTCAG-ACCGGTTCG-AACCGGTTGAA
1 ACCGGTCAAACCGG-TCAGAACCGGTT-GAAACCGGTT-AA
237362 ACCGGTCAAACCGGTCAGAACCGGTTGAAAACCGGTTAA
1 ACCGGTCAAACCGGTCAGAACCGGTTG-AAACCGGTTAA
237401 ACCGGT
1 ACCGGT
237407 TTCCAGCAGC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
38 5 0.12
39 28 0.68
40 8 0.20
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (38 bp):
ACCGGTCAAACCGGTCAGAACCGGTTGAAACCGGTTAA
Found at i:237404 original size:9 final size:10
Alignment explanation
Indices: 237323--237407 Score: 79
Period size: 10 Copynumber: 8.7 Consensus size: 10
237313 GTCGGGTCAG
*
237323 ACCGG-TCAG
1 ACCGGTTCAA
*
237332 ACCGGTTCAG
1 ACCGGTTCAA
*
237342 ACCGGTTCGA
1 ACCGGTTCAA
*
237352 ACCGGTTGAA
1 ACCGGTTCAA
237362 ACCGG-TCAA
1 ACCGGTTCAA
237371 ACCGG-TCAGA
1 ACCGGTTCA-A
*
237381 ACCGGTTGAAA
1 ACCGGTT-CAA
237392 ACCGGTT-AA
1 ACCGGTTCAA
237401 ACCGGTT
1 ACCGGTT
237408 TCCAGCAGCC
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
9 25 0.38
10 31 0.47
11 9 0.14
12 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:241476 original size:4 final size:4
Alignment explanation
Indices: 241467--241497 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
241457 ACTGTTCAAC
241467 TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
241498 ACATGCATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:241892 original size:24 final size:24
Alignment explanation
Indices: 241860--241916 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
241850 TTTATGAATT
* *
241860 TAATATTAAT-AAAATATTTTAATA
1 TAATTTTAATCAAAATA-TTTAAAA
241884 TAATTTTAATCAAAATATTTAAAA
1 TAATTTTAATCAAAATATTTAAAA
241908 TATATTTTA
1 TA-ATTTTA
241917 TTAATATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATTTTAATCAAAATATTTAAAA
Found at i:241931 original size:22 final size:22
Alignment explanation
Indices: 241897--241961 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
241887 TTTTAATCAA
* **
241897 AATATTTAAAATATATTTTATT
1 AATATTTATAATATATAATATT
*
241919 AATATTTCTAATAATATAATATT
1 AATATTTATAAT-ATATAATATT
*
241942 -ATATTTTTAATATTATAATA
1 AATATTTATAATA-TATAATA
241962 AAATAATCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 27 0.75
23 8 0.22
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATTTATAATATATAATATT
Found at i:242023 original size:55 final size:53
Alignment explanation
Indices: 241927--242030 Score: 140
Period size: 55 Copynumber: 1.9 Consensus size: 53
241917 TTAATATTTC
*
241927 TAATAATATAATATTATATTTTTAATATTATAATAAAATAATCAATTATATTA
1 TAATAATATAATATTATATTTTTAATATTATAATAAAATAATAAATTATATTA
*
241980 TAATAATATAAGATATTATATTTTT-AT-TTTTAATAATATATAATAAATTAT
1 TAATAATAT-A-ATATTATATTTTTAATATTATAATAA-A-ATAATAAATTAT
242031 TAATAAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
53 17 0.38
54 4 0.09
55 24 0.53
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (53 bp):
TAATAATATAATATTATATTTTTAATATTATAATAAAATAATAAATTATATTA
Found at i:242103 original size:19 final size:18
Alignment explanation
Indices: 242079--242147 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
242069 ATATTATTAA
242079 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
242098 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
242116 ATTAATCTAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
242138 ATT-TTAATAA
1 ATTATTAATAA
242148 ATATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:242252 original size:31 final size:31
Alignment explanation
Indices: 242227--242324 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 31
242217 ATATAATTTA
242227 TAATATTTTTATTTCAATAAAATAT-ATCAATAT
1 TAATATTTTTA-TT-AATAAAATATAAT-AATAT
242260 TAATATTTTTATTAATAAAATTATAA-AA-A-
1 TAATATTTTTATTAATAAAA-TATAATAATAT
* * *
242289 TAATA--TTTAATAAT-AAATA-AATTATTT
1 TAATATTTTTATTAATAAAATATAATAATAT
242316 TAATATTTT
1 TAATATTTT
242325 AAAAATAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
24 2 0.04
25 3 0.05
26 3 0.05
27 13 0.24
29 7 0.13
30 1 0.02
31 9 0.16
32 5 0.09
33 12 0.22
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (31 bp):
TAATATTTTTATTAATAAAATATAATAATAT
Found at i:242265 original size:33 final size:29
Alignment explanation
Indices: 242226--242296 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 29
242216 AATATAATTT
*
242226 ATAATATTTTTATTTCAATAAAATATATCAATA
1 ATAATATTTTTA-TT-AATAAAAT-TAT-AAAA
*
242259 TTAATATTTTTATTAATAAAATTATAAAA
1 ATAATATTTTTATTAATAAAATTATAAAA
242288 ATAATATTT
1 ATAATATTT
242297 AATAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.31
30 3 0.09
31 8 0.23
32 2 0.06
33 11 0.31
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (29 bp):
ATAATATTTTTATTAATAAAATTATAAAA
Found at i:242539 original size:14 final size:14
Alignment explanation
Indices: 242520--242578 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
242510 CCAGAAATAT
*
242520 AATTCATTTTTCAG
1 AATTCAATTTTCAG
* *
242534 AATTCAAATTCCAG
1 AATTCAATTTTCAG
* *
242548 TAATTCATTTTTAAG
1 -AATTCAATTTTCAG
242563 AATTCAATTTTCAG
1 AATTCAATTTTCAG
242577 AA
1 AA
242579 AATCAATTAC
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 25 0.71
15 10 0.29
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (14 bp):
AATTCAATTTTCAG
Found at i:244562 original size:34 final size:35
Alignment explanation
Indices: 244504--244584 Score: 96
Period size: 34 Copynumber: 2.3 Consensus size: 35
244494 AAATCTTATG
*
244504 ATTATAATTTGAAT-ATTAACTATAATAT-ATA-AT
1 ATTATAATTT-TATCATTAACTATAATATAATATAT
* *
244537 ATATATATTTTTATCATTAATTATAATATAATATAT
1 AT-TATAATTTTATCATTAACTATAATATAATATAT
244573 ATTATAATTTTA
1 ATTATAATTTTA
244585 ATATTAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
33 4 0.10
34 20 0.50
35 12 0.30
36 4 0.10
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (35 bp):
ATTATAATTTTATCATTAACTATAATATAATATAT
Found at i:244979 original size:25 final size:25
Alignment explanation
Indices: 244945--244993 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
244935 TGTTTGAATT
* *
244945 CATATTTTATTTGCTTGACAAATGA
1 CATAATTTATTCGCTTGACAAATGA
244970 CATAATTTATTCGCTTGACAAATG
1 CATAATTTATTCGCTTGACAAATG
244994 TCTTTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (25 bp):
CATAATTTATTCGCTTGACAAATGA
Found at i:245093 original size:32 final size:32
Alignment explanation
Indices: 245050--245115 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
245040 TTCAAAGTCC
245050 TACCATCAGGGGTGTTCAAAATC-GAGTACCCG
1 TACCATCAGGGGTGTTCAAAATCAG-GTACCCG
*
245082 TACCATTAGGGGTGTTCAAAATCAGGTACCCG
1 TACCATCAGGGGTGTTCAAAATCAGGTACCCG
245114 TA
1 TA
245116 TTTTCGGATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 31 0.97
33 1 0.03
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (32 bp):
TACCATCAGGGGTGTTCAAAATCAGGTACCCG
Found at i:245560 original size:2 final size:2
Alignment explanation
Indices: 245555--245587 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
245545 AATATAAAAA
245555 AT 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 AT A
245588 ATAAACCGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:248577 original size:7 final size:7
Alignment explanation
Indices: 248565--248625 Score: 88
Period size: 7 Copynumber: 8.9 Consensus size: 7
248555 TGAAAATAAT
248565 GAAGGGC
1 GAAGGGC
248572 GAAGGGC
1 GAAGGGC
*
248579 GAACGGC
1 GAAGGGC
248586 GAAGGGC
1 GAAGGGC
248593 GAAGGGC
1 GAAGGGC
248600 GAAGGGC
1 GAAGGGC
*
248607 GAAGGGT
1 GAAGGGC
*
248614 GAAAGG-
1 GAAGGGC
248620 GAAGGG
1 GAAGGG
248626 GTGAAAAGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
6 5 0.10
7 44 0.90
ACGTcount: A:0.31, C:0.11, G:0.56, T:0.02
Consensus pattern (7 bp):
GAAGGGC
Found at i:253486 original size:18 final size:18
Alignment explanation
Indices: 253463--253512 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
253453 AACCCCTCCA
253463 CAAGTGCCACCCCTAATC
1 CAAGTGCCACCCCTAATC
*
253481 CAAGTGTCACCCCTAATC
1 CAAGTGCCACCCCTAATC
253499 CAAGTGCCACCCCT
1 CAAGTGCCACCCCT
253513 CAAAAGTGCT
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:0.26, C:0.44, G:0.12, T:0.18
Consensus pattern (18 bp):
CAAGTGCCACCCCTAATC
Found at i:256983 original size:3 final size:3
Alignment explanation
Indices: 256970--257017 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
256960 AGCCAGTTTG
* *
256970 TAA TAAA TAA TAA TTA TAA -AA TAA TAA TAA TAA TTTA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
257016 TA
1 TA
257018 GTATATTGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 31 0.82
4 5 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:256993 original size:14 final size:14
Alignment explanation
Indices: 256970--257017 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
256960 AGCCAGTTTG
256970 TAAT-AAATAATAA
1 TAATAAAATAATAA
*
256983 TTATAAAATAATAA
1 TAATAAAATAATAA
*
256997 TAATAATTTATAATAA
1 TAATAA--AATAATAA
257013 TAATA
1 TAATA
257018 GTATATTGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 3 0.10
14 14 0.48
16 12 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATAAAATAATAA
Found at i:259832 original size:7 final size:7
Alignment explanation
Indices: 259820--259845 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
259810 CTTAATAATT
259820 TTTTATA
1 TTTTATA
259827 TTTTATA
1 TTTTATA
259834 TTTTATA
1 TTTTATA
259841 TTTTA
1 TTTTA
259846 AATAACATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTATA
Found at i:265201 original size:20 final size:21
Alignment explanation
Indices: 265149--265210 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
265139 TTCCCCTGTG
265149 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
* *
265172 AGGAGGAATCGGTTCCCTC-A
1 GGGGGGAATCGGTTCCCTCAA
*
265192 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
265211 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 12 0.35
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:271730 original size:29 final size:30
Alignment explanation
Indices: 271694--271751 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
271684 AACCTTTTGA
*
271694 TTTGGTCCC-AAAATTAATTAAAATTTTAT
1 TTTGGTCCCTAAAATTAATCAAAATTTTAT
* *
271723 TTTGGTCCCTAAATTTCATCAAAATTTTA
1 TTTGGTCCCTAAAATTAATCAAAATTTTA
271752 ATTTAATCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (30 bp):
TTTGGTCCCTAAAATTAATCAAAATTTTAT
Found at i:272364 original size:15 final size:15
Alignment explanation
Indices: 272344--272373 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
272334 AGATATCAAA
*
272344 TTTATTTTTATTATT
1 TTTATTTTTAATATT
272359 TTTATTTTTAATATT
1 TTTATTTTTAATATT
272374 AAGTTTTCAT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATTTTTAATATT
Found at i:274018 original size:29 final size:28
Alignment explanation
Indices: 273977--274031 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
273967 TTTTTTTTAA
* *
273977 AAAAAATACCCAACATTTTATAAAACTAT
1 AAAAAATACCCAAAACTTT-TAAAACTAT
274006 AAAAAA-ACTCCAAAACTTTTAAAACT
1 AAAAAATAC-CCAAAACTTTTAAAACT
274032 CTAATTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.25
Consensus pattern (28 bp):
AAAAAATACCCAAAACTTTTAAAACTAT
Found at i:275839 original size:75 final size:76
Alignment explanation
Indices: 275739--275879 Score: 230
Period size: 75 Copynumber: 1.9 Consensus size: 76
275729 CATGGAACTA
* *
275739 TGGCTTTTTTTTTCGACCTTAAATTCTACCGTTTTCCCCTTCGAATCACTAGATTTATATATTTT
1 TGGCTTTTTTTTTC-ACCTCAAATTCTACCGTTTTCCCATTCGAATCACTAGATTTATATATTTT
275804 TATAGCTCAATG
65 TATAGCTCAATG
* *
275816 TGGCTTTTTTTTT-ACCTCAAATTCTGCCGTTTTTCCATTCGAATCACTAGATTTATATATTTTT
1 TGGCTTTTTTTTTCACCTCAAATTCTACCGTTTTCCCATTCGAATCACTAGATTTATATATTTTT
275880 TACTATTTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
75 47 0.78
77 13 0.22
ACGTcount: A:0.21, C:0.20, G:0.10, T:0.49
Consensus pattern (76 bp):
TGGCTTTTTTTTTCACCTCAAATTCTACCGTTTTCCCATTCGAATCACTAGATTTATATATTTTT
ATAGCTCAATG
Found at i:281444 original size:76 final size:77
Alignment explanation
Indices: 281273--281461 Score: 281
Period size: 76 Copynumber: 2.5 Consensus size: 77
281263 CAAAGCCAAA
* * * **
281273 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
281338 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
* *
281351 ATTTCCAGAATGGTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
281416 TTT-GCTCCGAG
66 TTTGGCCCCGAG
*
281427 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCC
281462 TTATACAACG
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
76 39 0.39
77 37 0.37
78 24 0.24
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.21
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:287300 original size:21 final size:21
Alignment explanation
Indices: 287274--287313 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
287264 CCCCCTTTGA
*
287274 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
287295 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
287314 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:289257 original size:9 final size:8
Alignment explanation
Indices: 289235--289285 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
289225 TGTTTCAACA
289235 TTTTGGAT
1 TTTTGGAT
289243 ATTTTGGAT
1 -TTTTGGAT
289252 TGTTT-GAT
1 T-TTTGGAT
289260 TTTGTGGAT
1 TTT-TGGAT
*
289269 TGTTGGA-
1 TTTTGGAT
289276 TTTTGGAT
1 TTTTGGAT
289284 TT
1 TT
289286 ATGAATAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:289269 original size:17 final size:17
Alignment explanation
Indices: 289237--289280 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
289227 TTTCAACATT
289237 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
289254 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
289271 TTGGATTTTG
1 TTGGATTTTG
289281 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:290077 original size:75 final size:77
Alignment explanation
Indices: 289869--290078 Score: 293
Period size: 75 Copynumber: 2.8 Consensus size: 77
289859 CAAAGCCAAA
* * **
289869 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTAAATGG
1 AATTCCAGATTGCTCGGAGGGAACCGA-TCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
289934 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
* *
289947 ATTTCCAGATTGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATT-CCCCCTAAACAGT
1 AATTCCAGATTGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
290011 TTT-GCTCCGAG
66 TTTGGCCCCGAG
* *
290022 AATTCCAG-TATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAT-TGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCT
290079 TGTACAACGG
Statistics
Matches: 119, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
74 13 0.11
75 45 0.38
76 14 0.12
77 23 0.19
78 24 0.20
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGATTGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:291593 original size:30 final size:30
Alignment explanation
Indices: 291529--291623 Score: 120
Period size: 29 Copynumber: 3.2 Consensus size: 30
291519 AAATTATTTA
*
291529 TTTATTTTTGTTTTAACTTATTAAATAT-T
1 TTTATTTTTGTTTTAATTTATTAAATATAT
*
291558 TTTATTTTTGTCTTAATTTATTAAATATAT
1 TTTATTTTTGTTTTAATTTATTAAATATAT
* * **
291588 TTTATTTTTATTTTAATATAAAAATATATAT
1 TTTATTTTTGTTTTAATTTATTAA-ATATAT
291619 TTTAT
1 TTTAT
291624 CTTTATCATC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 26 0.46
30 20 0.35
31 11 0.19
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (30 bp):
TTTATTTTTGTTTTAATTTATTAAATATAT
Found at i:291629 original size:31 final size:30
Alignment explanation
Indices: 291582--291738 Score: 104
Period size: 31 Copynumber: 4.9 Consensus size: 30
291572 AATTTATTAA
*
291582 ATATATTTTATTTTTATTTTAATATAAAAAT
1 ATATATTTTATCTTTATTTTAAT-TAAAAAT
* * *
291613 ATATATTTTATCTTTATCATCACTTAAAAAT
1 ATATATTTTATCTTTAT-TTTAATTAAAAAT
***
291644 ATATATTTT-TAAATATTTTAATTTGAAATATATTT
1 ATATATTTTATCTTTATTTTAA-TT-AAA-A-A--T
* *
291679 AAATATTTTA-CTATTAATTTAATATAAAAAT
1 ATATATTTTATCT-TTATTTTAAT-TAAAAAT
291710 ATATATTTTA-CTCTTATTTTTAATTAAAA
1 ATATATTTTATCT-TTA-TTTTAATTAAAA
291739 TAATTTAATA
Statistics
Matches: 97, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
29 2 0.02
30 6 0.06
31 55 0.57
32 10 0.10
33 2 0.02
34 1 0.01
35 13 0.13
36 8 0.08
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (30 bp):
ATATATTTTATCTTTATTTTAATTAAAAAT
Found at i:303110 original size:26 final size:26
Alignment explanation
Indices: 303077--303135 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
303067 TTGTACCAAC
303077 AAAGAAAATGAAAATGTCTGAGGCAA
1 AAAGAAAATGAAAATGTCTGAGGCAA
*
303103 AAAGAAAATGAAAATGTCTGAGGTAA
1 AAAGAAAATGAAAATGTCTGAGGCAA
*
303129 GAAGAAA
1 AAAGAAA
303136 GGAGAGCCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.56, C:0.05, G:0.24, T:0.15
Consensus pattern (26 bp):
AAAGAAAATGAAAATGTCTGAGGCAA
Found at i:306808 original size:31 final size:30
Alignment explanation
Indices: 306773--306842 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
306763 TGACTTATAA
*
306773 ATATTAATAAAAGACATCAGAGTATAGTAAC
1 ATATT-ATAAAACACATCAGAGTATAGTAAC
* * *
306804 ATATT-TATAACATATCAGAGTATAGTACC
1 ATATTATAAAACACATCAGAGTATAGTAAC
306833 ATATTCATAA
1 ATATT-ATAA
306843 CATATTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
29 25 0.78
31 7 0.22
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.31
Consensus pattern (30 bp):
ATATTATAAAACACATCAGAGTATAGTAAC
Found at i:306824 original size:29 final size:29
Alignment explanation
Indices: 306788--306847 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
306778 AATAAAAGAC
*
306788 ATCAGAGTATAGTAACATATTTATAACAT
1 ATCAGAGTATAGTAACATATTCATAACAT
*
306817 ATCAGAGTATAGTACCATATTCATAACAT
1 ATCAGAGTATAGTAACATATTCATAACAT
306846 AT
1 AT
306848 TTTTTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (29 bp):
ATCAGAGTATAGTAACATATTCATAACAT
Found at i:310061 original size:19 final size:19
Alignment explanation
Indices: 310037--310076 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
310027 ACTAGATTGT
310037 ATAATTAGGTGGTGATACA
1 ATAATTAGGTGGTGATACA
310056 ATAATTAGGTGGTGATACA
1 ATAATTAGGTGGTGATACA
310075 AT
1 AT
310077 CTTTGTATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.33
Consensus pattern (19 bp):
ATAATTAGGTGGTGATACA
Found at i:316421 original size:34 final size:33
Alignment explanation
Indices: 316383--316451 Score: 129
Period size: 34 Copynumber: 2.1 Consensus size: 33
316373 AACATCGTCG
316383 TTTGTTAAACGAGCCGAGTCGAACTTGAAAACTT
1 TTTGTTAAACGAGCCGAGTCGAACTTGAAAA-TT
316417 TTTGTTAAACGAGCCGAGTCGAACTTGAAAATT
1 TTTGTTAAACGAGCCGAGTCGAACTTGAAAATT
316450 TT
1 TT
316452 AAAAGTAAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 4 0.11
34 31 0.89
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (33 bp):
TTTGTTAAACGAGCCGAGTCGAACTTGAAAATT
Found at i:319611 original size:60 final size:59
Alignment explanation
Indices: 319516--319690 Score: 199
Period size: 60 Copynumber: 2.9 Consensus size: 59
319506 GTATATACGT
* * *
319516 ATAGTTTGGGATGAAATTGGAATATTCAAAAAGTTTAGGGACCAATTTAGAATGA-AAGTC
1 ATAGTTTGGGATGAAATTGAAATATT-TAAAAGTTTAAGGACCAATTTAGAATGATAA-TC
*
319576 ATAGTTTGGGGATGAAATTGAAATATTTAAAAGTTTAAGGACTAATTTAGAATGATAATC
1 ATAGTTT-GGGATGAAATTGAAATATTTAAAAGTTTAAGGACCAATTTAGAATGATAATC
* * * * * * * *
319636 ATAGTTTAAGGATAAAATTGAAACATTTGAAAGATTAAAGACTAATTTAAAATGA
1 ATAGTTT-GGGATGAAATTGAAATATTTAAAAGTTTAAGGACCAATTTAGAATGA
319691 GGATCATACT
Statistics
Matches: 101, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
60 81 0.80
61 20 0.20
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (59 bp):
ATAGTTTGGGATGAAATTGAAATATTTAAAAGTTTAAGGACCAATTTAGAATGATAATC
Found at i:319697 original size:60 final size:60
Alignment explanation
Indices: 319559--319707 Score: 174
Period size: 60 Copynumber: 2.5 Consensus size: 60
319549 TTTAGGGACC
* ** * * * *
319559 AATTTAGAATGA-AAGTCATAGTTTGGGGATGAAATTGAAATATTTAAAAGTTTAAGGACT
1 AATTTAAAATGAGAA-TCATAGTTTAAGGATAAAATTGAAACATTTAAAAGATTAAAGACT
* * *
319619 AATTTAGAATGATAATCATAGTTTAAGGATAAAATTGAAACATTTGAAAGATTAAAGACT
1 AATTTAAAATGAGAATCATAGTTTAAGGATAAAATTGAAACATTTAAAAGATTAAAGACT
* *
319679 AATTTAAAATGAGGATCATACTTTAAGGA
1 AATTTAAAATGAGAATCATAGTTTAAGGA
319708 CATATGACGC
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 75 0.97
61 2 0.03
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (60 bp):
AATTTAAAATGAGAATCATAGTTTAAGGATAAAATTGAAACATTTAAAAGATTAAAGACT
Found at i:321509 original size:29 final size:29
Alignment explanation
Indices: 321464--321521 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
321454 GTGTTGATCG
*
321464 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
*
321493 TAGGTCGCCATGTCTTCCCGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
321522 AAGAGATTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.38, G:0.26, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:321583 original size:14 final size:14
Alignment explanation
Indices: 321564--321591 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
321554 TTCTGGGCAT
321564 CCGAGGCTATCCGA
1 CCGAGGCTATCCGA
321578 CCGAGGCTATCCGA
1 CCGAGGCTATCCGA
321592 GAGCATCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.36, G:0.29, T:0.14
Consensus pattern (14 bp):
CCGAGGCTATCCGA
Found at i:321639 original size:23 final size:23
Alignment explanation
Indices: 321613--321662 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
321603 GCCATCCAAA
321613 CGAGCTATGCGAGGGCAA-CCGAG
1 CGAGCTATGCGAGGG-AAGCCGAG
321636 CGAGCTATGCGAGGGAAGCCGAG
1 CGAGCTATGCGAGGGAAGCCGAG
321659 CGAG
1 CGAG
321663 GGTAGGTCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.26, C:0.24, G:0.42, T:0.08
Consensus pattern (23 bp):
CGAGCTATGCGAGGGAAGCCGAG
Found at i:321699 original size:29 final size:29
Alignment explanation
Indices: 321666--321750 Score: 152
Period size: 29 Copynumber: 2.9 Consensus size: 29
321656 GAGCGAGGGT
*
321666 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
*
321695 AGGTCGTCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
321724 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
321751 TGTGTTGGGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.20, C:0.29, G:0.38, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:321796 original size:12 final size:12
Alignment explanation
Indices: 321779--321803 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
321769 TGCCATGCAA
321779 CACGTTCATTCT
1 CACGTTCATTCT
321791 CACGTTCATTCT
1 CACGTTCATTCT
321803 C
1 C
321804 TTTGTTTAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CACGTTCATTCT
Found at i:321863 original size:29 final size:29
Alignment explanation
Indices: 321821--321906 Score: 172
Period size: 29 Copynumber: 3.0 Consensus size: 29
321811 AAGCAAGGGT
321821 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
321850 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
321879 AGGTCGCCCGGAGTGCATGGCGACCTAC
1 AGGTCGCCCGGAGTGCATGGCGACCTAC
321907 GACCAACACT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.20, C:0.31, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:329455 original size:3 final size:3
Alignment explanation
Indices: 329447--329549 Score: 116
Period size: 3 Copynumber: 33.7 Consensus size: 3
329437 TTTAAATTTG
** * *
329447 TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
329495 TTA TTA TAA TAA TTA TTA TTA TTTA TTA ATA TTA ATA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA
329542 TTA TTA TT
1 TTA TTA TT
329550 TAATAAATAA
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
3 78 0.93
4 6 0.07
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:331693 original size:18 final size:18
Alignment explanation
Indices: 331672--331742 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 18
331662 ATTTTTTATA
331672 TATTTATTATTTTCATAG
1 TATTTATTATTTTCATAG
*
331690 TATTTATATATTTTCTTATTAA
1 TATTTAT-TATTTTC--A-TAG
*
331712 TATTTCATTATTTGCA-AG
1 TATTT-ATTATTTTCATAG
331730 TATTTTATTATTT
1 TA-TTTATTATTT
331743 ATTTTTCTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
18 17 0.39
19 10 0.23
20 1 0.02
21 1 0.02
22 13 0.30
23 2 0.05
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (18 bp):
TATTTATTATTTTCATAG
Found at i:333754 original size:7 final size:7
Alignment explanation
Indices: 333719--333759 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
333709 TTTTCATACA
333719 TGCATTT
1 TGCATTT
333726 T-CATTT
1 TGCATTT
333732 TGCATCTT
1 TGCAT-TT
333740 TGCATTT
1 TGCATTT
*
333747 TTCATTT
1 TGCATTT
333754 TGCATT
1 TGCATT
333760 CATACTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:338129 original size:114 final size:114
Alignment explanation
Indices: 337929--338148 Score: 377
Period size: 114 Copynumber: 1.9 Consensus size: 114
337919 CACGTTCTCG
*
337929 TAGTAGAAATAAGGAGATCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGGAGATCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
* * *
337994 GGTATAAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTAGAAACCCCAAAACCAATCATTGGAATTAAAAGATGAATTTGCTCA
* *
338043 TAGTAGAAATAAGGAGATCCAATATCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGATCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
*
338108 GGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAA
66 GGTAGAAACCCCAAAACCAATCATTGGAATTAAAAGATGAA
338149 ATGCATGATC
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGATCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
GGTAGAAACCCCAAAACCAATCATTGGAATTAAAAGATGAATTTGCTCA
Found at i:338964 original size:41 final size:41
Alignment explanation
Indices: 338914--339023 Score: 109
Period size: 42 Copynumber: 2.7 Consensus size: 41
338904 ACATTGAGAG
338914 TCAACCAGAAATAGAATATTGGGGCATATCGAA-AGCCCATT
1 TCAACCAGAAATAGAATATTGGGGCATATCGAAGA-CCCATT
** * * * *
338955 TCAGA-CAGAAATA-TTTCATGTGGGACATCTTGAGGACCCATT
1 TCA-ACCAGAAATAGAAT-AT-TGGGGCATATCGAAGACCCATT
338997 TCAACCAGAAATAGAATATTGGGGCAT
1 TCAACCAGAAATAGAATATTGGGGCAT
339024 TTTGAAGGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
40 1 0.02
41 21 0.39
42 30 0.56
43 2 0.04
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (41 bp):
TCAACCAGAAATAGAATATTGGGGCATATCGAAGACCCATT
Found at i:340208 original size:54 final size:54
Alignment explanation
Indices: 340121--340286 Score: 251
Period size: 54 Copynumber: 3.1 Consensus size: 54
340111 CAATGATTGA
* *
340121 GAACATCTGAGCAGAAGTCACAAAAAATGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
* *
340175 GAACGTCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTATCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
** ***
340229 GAACATCTGAGCAGAAGCCACAGGAAAGGATGAATGCACTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
340283 GAAC
1 GAAC
340287 CTGCTATTCT
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 101 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (54 bp):
GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
Found at i:340666 original size:22 final size:22
Alignment explanation
Indices: 340637--340691 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
340627 ATCTACACTC
340637 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
340659 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
340681 TTCAAAGATGA
1 TTCAAAGATGA
340692 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:341731 original size:76 final size:76
Alignment explanation
Indices: 341540--342327 Score: 1357
Period size: 76 Copynumber: 10.4 Consensus size: 76
341530 CTATTTCCCA
* *
341540 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
341605 A-CCTTCGGGT
66 AGCCTTAGGGT
*
341615 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
341680 ATCCTTAGGGT
66 AGCCTTAGGGT
341691 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
341756 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
341767 CATCTGTAAGTCCTACAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
341832 AGCCTTAGGGT
66 AGCCTTAGGGT
*
341843 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
341908 A-CCTTCGGGT
66 AGCCTTAGGGT
*
341918 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
341983 ATCCTTAGGGT
66 AGCCTTAGGGT
* * *
341994 CTTCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGCTGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
342059 ATCCTTCGGGT
66 AGCCTTAGGGT
*
342070 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
342135 AGCCTTAGGGT
66 AGCCTTAGGGT
342146 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCC-TCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
342210 AGCCTTAGGGT
66 AGCCTTAGGGT
*
342221 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* *
342286 AAACCTTCGGGT
65 AAGCCTTAGGGT
*
342298 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
342328 TCAACATTTC
Statistics
Matches: 680, Mismatches: 29, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
75 209 0.31
76 432 0.64
77 39 0.06
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:341935 original size:227 final size:227
Alignment explanation
Indices: 341540--342327 Score: 1382
Period size: 227 Copynumber: 3.5 Consensus size: 227
341530 CTATTTCCCA
* *
341540 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
341605 ACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTG
66 ACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
*
341670 ATGTTTTCAAATCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
131 ATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
341735 GGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
196 GGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
*
341767 CATCTGTAAGTCCTACAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
341832 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 A-CCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
341897 GATGTTTTCAAA-CCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
130 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
* *
341961 GGGATCTTTTTGATGTTTTCAAATCCTTAGGGT
195 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
* * * *
341994 CTTCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGCTGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
342059 ATCCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 A-CCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
342124 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCC-TC
130 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
342188 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
195 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
342221 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC--
*
342286 AAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTT
64 AAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
342328 TCAACATTTC
Statistics
Matches: 531, Mismatches: 26, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
227 371 0.70
228 157 0.30
229 3 0.01
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (227 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
ATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
GGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
Found at i:342087 original size:303 final size:303
Alignment explanation
Indices: 341540--342327 Score: 1425
Period size: 303 Copynumber: 2.6 Consensus size: 303
341530 CTATTTCCCA
*
341540 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
341605 ACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTG
66 ACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTG
341670 ATGTTTTCAAATCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
131 ATGTTTTCAAATCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
341735 GGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTCTCCA
196 GGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTCTCCA
341800 AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
261 AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
341843 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
341908 ACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTG
66 ACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTG
*
341973 ATGTTTTCAAATCCTTAGGGTCTTCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
131 ATGTTTTCAAATCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
* * * * *
342038 GGATCTTTTTGCTGTTTTCAAATCCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCA
196 GGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTCTCCA
342103 AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
261 AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
*
342146 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCC-TCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * *
342210 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 A-CCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTT
* * *
342275 GATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTT
130 GATGTTTTC-AAATCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
342328 TCAACATTTC
Statistics
Matches: 468, Mismatches: 15, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
302 25 0.05
303 404 0.86
304 39 0.08
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (303 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTG
ATGTTTTCAAATCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
GGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTCTCCA
AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
Found at i:342469 original size:3 final size:3
Alignment explanation
Indices: 342461--342563 Score: 98
Period size: 3 Copynumber: 33.7 Consensus size: 3
342451 TTTAAATTTG
** ** * *
342461 TTA TTA TTA TTA AAA TTA AAA TTA TTA GTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
342509 GTA TTA TAA TTA TTA TTA TTTA TTA TTA ATA TTA ATA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA TTA
342556 TTA TTA TT
1 TTA TTA TT
342564 TAATAAATAA
Statistics
Matches: 78, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
3 72 0.92
4 6 0.08
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:357246 original size:18 final size:18
Alignment explanation
Indices: 357223--357261 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
357213 ATAACTAAAA
357223 TTGATTAAATTATGGATT
1 TTGATTAAATTATGGATT
* * *
357241 TTGATTATATTTTGTATT
1 TTGATTAAATTATGGATT
357259 TTG
1 TTG
357262 TGGATTAGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (18 bp):
TTGATTAAATTATGGATT
Found at i:357681 original size:12 final size:12
Alignment explanation
Indices: 357664--357693 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
357654 TAGGGCCATT
357664 AGTTTTACATCA
1 AGTTTTACATCA
*
357676 AGTTTTACATTA
1 AGTTTTACATCA
357688 AGTTTT
1 AGTTTT
357694 CTTTATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:358048 original size:3 final size:3
Alignment explanation
Indices: 358040--358088 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
358030 TTTCTATCTA
* * *
358040 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATG CTT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
358088 A
1 A
358089 ACATATTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:359688 original size:2 final size:2
Alignment explanation
Indices: 359676--359711 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
359666 ATATTTATTT
359676 TA TA T- 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 TA T
359712 CCCTTATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:364522 original size:30 final size:30
Alignment explanation
Indices: 364465--364532 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
364455 ATGCATAAGT
**
364465 AAATGCATCATTTATAATGCATCACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
* * *
364495 AAATGTATCATTTATAGCACATTACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
*
364525 ATATGCAT
1 AAATGCAT
364533 TCGAATTTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (30 bp):
AAATGCATCATTTATAACACATCACCAATA
Found at i:372827 original size:141 final size:141
Alignment explanation
Indices: 372609--372879 Score: 402
Period size: 141 Copynumber: 1.9 Consensus size: 141
372599 AACATCAACT
372609 GACCAGATCTCCTCATCACATAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
1 GACCAGATCTCCTCATCACATAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
* ** *
372674 GGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCATC
66 GGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATC
372739 TACCCTTAGAC
131 TACCCTTAGAC
* * * *
372750 GACCAGA-CTTCCTCATCACGTAGGAGCCGTGTCAACCTTA-GATAATCAGCCGTCCTCATCACG
1 GACCAGATC-TCCTCATCACATAGGAG-AGTGTCAACATTAGGATAACCAGCCGTCCTCATCACG
* * * *
372813 TAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTATGAGCCGTGTCA
64 TAGGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCA
372878 TC
129 TC
372880 CCTTGATCAG
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
140 1 0.01
141 104 0.90
142 11 0.09
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (141 bp):
GACCAGATCTCCTCATCACATAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
GGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATC
TACCCTTAGAC
Found at i:372873 original size:94 final size:91
Alignment explanation
Indices: 372762--373008 Score: 361
Period size: 91 Copynumber: 2.7 Consensus size: 91
372752 CCAGACTTCC
* *
372762 TCATCACGTAGGAGCCGTGTCA-ACCTTAGATAATCAGCCGTCCTCATCACGTAGGAACCGAGTT
1 TCATCGCGTATGAGCCGTGTCATACCTT-G---ATCAGCCGTCCTCATCACGTAGGAACCGAGTT
372826 ATCACCCTTCTTAAAGATGACCAGAACTCT
62 ATCACCCTTCTTAAAGATGACCAGAACTCT
*
372856 TCATCGCGTATGAGCCGTGTCATCCCTTGATCAGCCGTCCTCATCACGTAGGAACCGAGTTATCA
1 TCATCGCGTATGAGCCGTGTCATACCTTGATCAGCCGTCCTCATCACGTAGGAACCGAGTTATCA
372921 CCCTTCTTAAAGATGACCAGAACTCT
66 CCCTTCTTAAAGATGACCAGAACTCT
* * * *** *
372947 TCATCGCGTATGAGCCGTGTCATCCCTCGACCAGATTTCCTCATCACGTAGGAACCGCGTTA
1 TCATCGCGTATGAGCCGTGTCATACCTTGATCAGCCGTCCTCATCACGTAGGAACCGAGTTA
373009 ACCTTAAAAC
Statistics
Matches: 143, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
91 118 0.83
94 21 0.15
95 4 0.03
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (91 bp):
TCATCGCGTATGAGCCGTGTCATACCTTGATCAGCCGTCCTCATCACGTAGGAACCGAGTTATCA
CCCTTCTTAAAGATGACCAGAACTCT
Found at i:372908 original size:91 final size:91
Alignment explanation
Indices: 372794--373008 Score: 376
Period size: 91 Copynumber: 2.4 Consensus size: 91
372784 ACCTTAGATA
372794 ATCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCA
1 ATCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCA
*
372859 TCGCGTATGAGCCGTGTCATCCCTTG
66 TCGCGTATGAGCCGTGTCATCCCTCG
372885 ATCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCA
1 ATCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCA
372950 TCGCGTATGAGCCGTGTCATCCCTCG
66 TCGCGTATGAGCCGTGTCATCCCTCG
* *** *
372976 ACCAGATTTCCTCATCACGTAGGAACCGCGTTA
1 ATCAGCCGTCCTCATCACGTAGGAACCGAGTTA
373009 ACCTTAAAAC
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 118 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (91 bp):
ATCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCA
TCGCGTATGAGCCGTGTCATCCCTCG
Found at i:373221 original size:3 final size:3
Alignment explanation
Indices: 373213--373267 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
373203 TTTCTATCTA
* *
373213 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATG CTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
373261 TTT ATT A
1 ATT ATT A
373268 ACATATTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:374866 original size:2 final size:2
Alignment explanation
Indices: 374854--374893 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
374844 ATATTTATTT
374854 TA TA T- 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 TA TA TA T
374894 TCCCTTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:382186 original size:5 final size:5
Alignment explanation
Indices: 382176--382205 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
382166 ACCATCCACG
382176 CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC
1 CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC
382206 ACTTCTCTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
CTTTC
Found at i:385500 original size:18 final size:17
Alignment explanation
Indices: 385470--385575 Score: 72
Period size: 18 Copynumber: 5.6 Consensus size: 17
385460 AGACACTAGT
*
385470 TTTTTCTTA-TATATTTGG
1 TTTTT-TTATTATATTT-A
385488 TTTTTTTATTATATTTA
1 TTTTTTTATTATATTTA
385505 TTATTTTTATTACTATTATTA
1 TT-TTTTTATTA-TA-T-TTA
385526 TTATTTTTATTATTAATATTA
1 TT-TTTTTATTA-T-AT-TTA
385547 TTTTTATTATTA-ATATTA
1 TTTTT-TTATTATAT-TTA
*
385565 TTATTTTATTA
1 TTTTTTTATTA
385576 CAGATACAAC
Statistics
Matches: 78, Mismatches: 3, Indels: 15
0.81 0.03 0.16
Matches are distributed among these distances:
17 11 0.14
18 31 0.40
19 2 0.03
20 4 0.05
21 29 0.37
22 1 0.01
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTTTTATTATATTTA
Found at i:385506 original size:9 final size:10
Alignment explanation
Indices: 385492--385575 Score: 81
Period size: 9 Copynumber: 8.7 Consensus size: 10
385482 ATTTGGTTTT
385492 TTTATTA-TA
1 TTTATTATTA
385501 TTTATTATT-
1 TTTATTATTA
*
385510 TTTATTACTA
1 TTTATTATTA
385520 -TTATTATTA
1 TTTATTATTA
385529 TTT-TTATTA
1 TTTATTATTA
385538 TTAATATTATT-
1 TT--TATTATTA
385549 TTTATTATTA
1 TTTATTATTA
*
385559 -ATATTATTA
1 TTTATTATTA
385568 TTTTATTA
1 -TTTATTA
385576 CAGATACAAC
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
9 46 0.74
10 3 0.05
11 8 0.13
12 5 0.08
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTATTATTA
Found at i:385512 original size:21 final size:21
Alignment explanation
Indices: 385488--385575 Score: 107
Period size: 21 Copynumber: 4.4 Consensus size: 21
385478 ATATATTTGG
385488 TTTTT-TTATT-ATATTTATTA
1 TTTTTATTATTAATA-TTATTA
* *
385508 TTTTTATTACTATTATTATTA
1 TTTTTATTATTAATATTATTA
385529 TTTTTATTATT-A-A-TATTA
1 TTTTTATTATTAATATTATTA
385547 TTTTTATTATTAATATTATTA
1 TTTTTATTATTAATATTATTA
385568 -TTTTATTA
1 TTTTTATTA
385576 CAGATACAAC
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
18 16 0.27
19 2 0.03
20 14 0.24
21 25 0.42
22 2 0.03
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTTATTATTAATATTATTA
Found at i:391183 original size:15 final size:15
Alignment explanation
Indices: 391163--391194 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
391153 GATCAATACC
391163 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
391178 TTTTGCATACATTCA
1 TTTTGCATACATGCA
391193 TT
1 TT
391195 ATTCATTGCA
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:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:394009 original size:22 final size:22
Alignment explanation
Indices: 393984--394027 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
393974 GGTATTTTAA
393984 AATTAAATATTATAAAAATTAT
1 AATTAAATATTATAAAAATTAT
* * **
394006 AATTTAATTTTATTTAAATTAT
1 AATTAAATATTATAAAAATTAT
394028 TATATTATTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTAAATATTATAAAAATTAT
Found at i:402685 original size:37 final size:37
Alignment explanation
Indices: 402627--402745 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
402617 TCCCATTATT
* * *
402627 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACC
402663 ATTTTTCAAAGAAACATTTACCAAACTTT-AAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACC
402699 A-TTTTCAAAGAAACATTTACCAAACTTTG-AAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACC
402734 ATTTTTTCAAAG
1 A-TTTTTCAAAG
402746 TTGGTTACCA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 34 0.45
36 14 0.18
37 28 0.37
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (37 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACC
Found at i:407266 original size:37 final size:35
Alignment explanation
Indices: 407204--407315 Score: 131
Period size: 34 Copynumber: 3.2 Consensus size: 35
407194 TCCCATTATC
* * *
407204 ATTTTTC-AACAAACATCTACTAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTT-AAAAA-T
407240 ATTTTTCAAAGAAACATTTACCAAACTTTAAAAAT
1 ATTTTTCAAAGAAACATTTACCAAACTTTAAAAAT
*
407275 CA--TTTCAAAGAAATATTTACCAAACTTTAAAAATT
1 -ATTTTTCAAAGAAACATTTACCAAACTTTAAAAA-T
407310 ATTTTT
1 ATTTTT
407316 TTAAAATTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
34 31 0.46
35 2 0.03
36 16 0.24
37 18 0.27
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.37
Consensus pattern (35 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTAAAAAT
Found at i:414333 original size:46 final size:46
Alignment explanation
Indices: 414270--414362 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
414260 CAAAACAATG
414270 TTCAACCTTCAAAGAAACTTGTGTCAAGAAGACTTGACAAAGACAA
1 TTCAACCTTCAAAGAAACTTGTGTCAAGAAGACTTGACAAAGACAA
*
414316 TTCAACCTTCACAGAAACTTGTGTCAAGAAGACTTGACAAAGACAA
1 TTCAACCTTCAAAGAAACTTGTGTCAAGAAGACTTGACAAAGACAA
414362 T
1 T
414363 GTTAAGAACA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (46 bp):
TTCAACCTTCAAAGAAACTTGTGTCAAGAAGACTTGACAAAGACAA
Found at i:415072 original size:3 final size:3
Alignment explanation
Indices: 415064--415088 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
415054 ATTTTTAACC
415064 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
415089 CCGGAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:416166 original size:21 final size:21
Alignment explanation
Indices: 416140--416189 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
416130 GCGTTACATT
416140 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
416161 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
416182 TCGCGTTG
1 TCGCGTTG
416190 TGATTTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:416227 original size:19 final size:19
Alignment explanation
Indices: 416205--416250 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
416195 TTTCAGTCCG
*
416205 CGTTGCGATTTTCTAAATT
1 CGTTGCGATTTTCCAAATT
416224 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
416243 CGTTGCGA
1 CGTTGCGA
416251 AAATCGCGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:416300 original size:21 final size:21
Alignment explanation
Indices: 416274--416330 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
416264 ATTTTTCATT
416274 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
416295 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
416316 TCGTGTTGCGATAGT
1 TCGCGTTGCGATAGT
416331 CTACAGTTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:416988 original size:6 final size:6
Alignment explanation
Indices: 416979--417021 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
416969 CCGTCTCGTC
416979 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
417022 GTCTTGAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:419581 original size:3 final size:3
Alignment explanation
Indices: 419538--419563 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
419528 TAAATAGCTT
419538 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
419564 CTGCAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:419837 original size:2 final size:2
Alignment explanation
Indices: 419830--419884 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
419820 CATCTCAGGT
419830 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
419872 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
419885 ATTTTCTTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:422072 original size:120 final size:120
Alignment explanation
Indices: 421859--422234 Score: 743
Period size: 120 Copynumber: 3.1 Consensus size: 120
421849 TTTTCTCTGT
421859 TCATGACCTCCAATTTTCTTAACACAACTACACAAGTGGTATGAATCTTGTAACGATGTTTTTCT
1 TCATGACCTCCAATTTTCTTAACACAACTACACAAGTGGTATGAATCTTGTAACGATGTTTTTCT
421924 TGTATTCGAGTTGTAATTTCTTTCAAGCTCTATATAACAACCTTGGTATAGCATC
66 TGTATTCGAGTTGTAATTTCTTTCAAGCTCTATATAACAACCTTGGTATAGCATC
*
421979 TCATGACCTCCAATTTTCTTAACACAACTACACAAGTGGTATGAATCTTGTAATGATGTTTTTCT
1 TCATGACCTCCAATTTTCTTAACACAACTACACAAGTGGTATGAATCTTGTAACGATGTTTTTCT
422044 TGTATTCGAGTTGTAATTTCTTTCAAGCTCTATATAACAACCTTGGTATAGCATC
66 TGTATTCGAGTTGTAATTTCTTTCAAGCTCTATATAACAACCTTGGTATAGCATC
422099 TCATGACCTCCAATTTTCTTAACACAACTACACAAGTGGTATGAATCTTGTAACGATGTTTTTCT
1 TCATGACCTCCAATTTTCTTAACACAACTACACAAGTGGTATGAATCTTGTAACGATGTTTTTCT
422164 TGTATTCGAGTTGTAATTTCTTTCAAGCTCTATATAACAACCTTGGTATAGCATC
66 TGTATTCGAGTTGTAATTTCTTTCAAGCTCTATATAACAACCTTGGTATAGCATC
422219 TCATGACCTCCAATTT
1 TCATGACCTCCAATTT
422235 CTTTCAGCAC
Statistics
Matches: 254, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 254 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (120 bp):
TCATGACCTCCAATTTTCTTAACACAACTACACAAGTGGTATGAATCTTGTAACGATGTTTTTCT
TGTATTCGAGTTGTAATTTCTTTCAAGCTCTATATAACAACCTTGGTATAGCATC
Found at i:423049 original size:27 final size:27
Alignment explanation
Indices: 422996--423049 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
422986 GTTAATGATT
*
422996 TTTTATATTTAAATTTAATATATAATA
1 TTTTATATTTAAATTGAATATATAATA
* *
423023 TTTTATTTTTAAAATTGCATATA-AATA
1 TTTTATATTT-AAATTGAATATATAATA
423050 ATTCATATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
TTTTATATTTAAATTGAATATATAATA
Found at i:423471 original size:25 final size:25
Alignment explanation
Indices: 423408--423472 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 25
423398 AATTGTCTCT
*
423408 ATTAT-TAAAAATTAAAAATTCAAA
1 ATTATATAAAAATTATAAATTCAAA
** * *
423432 A-TATATTTAATTTATAATTTCAAA
1 ATTATATAAAAATTATAAATTCAAA
423456 ATTATATAAAAATTATA
1 ATTATATAAAAATTATA
423473 TAAAAAATAT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
23 3 0.10
24 16 0.52
25 12 0.39
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTATATAAAAATTATAAATTCAAA
Found at i:423479 original size:13 final size:11
Alignment explanation
Indices: 423453--423490 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
423443 TTATAATTTC
423453 AAAATTATATA
1 AAAATTATATA
423464 AAAATTATATA
1 AAAATTATATA
* *
423475 AAAAATATTTA
1 AAAATTATATA
423486 AAAAT
1 AAAAT
423491 ATCAGAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAATTATATA
Found at i:424997 original size:14 final size:14
Alignment explanation
Indices: 424978--425005 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
424968 TTGTATTTTA
424978 TTTTATTATTATTT
1 TTTTATTATTATTT
424992 TTTTATTATTATTT
1 TTTTATTATTATTT
425006 ATATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTATTATTATTT
Found at i:425038 original size:9 final size:9
Alignment explanation
Indices: 425026--425106 Score: 81
Period size: 9 Copynumber: 9.0 Consensus size: 9
425016 TTAATATATT
425026 TAATAATAA
1 TAATAATAA
*
425035 TAATAATTA
1 TAATAATAA
* * *
425044 TTATTATTA
1 TAATAATAA
* *
425053 TTATTATAA
1 TAATAATAA
* *
425062 TATTTATAA
1 TAATAATAA
425071 TAATAATAA
1 TAATAATAA
*
425080 TTATAATAA
1 TAATAATAA
425089 TAATAATAA
1 TAATAATAA
425098 TAATAATAA
1 TAATAATAA
425107 ATAAATCAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 62 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TAATAATAA
Found at i:425073 original size:3 final size:3
Alignment explanation
Indices: 425067--425106 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
425057 TATAATATTT
*
425067 ATA ATA ATA ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
425107 ATAAATCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:425405 original size:36 final size:36
Alignment explanation
Indices: 425358--425452 Score: 145
Period size: 36 Copynumber: 2.6 Consensus size: 36
425348 TTGAATAAGC
*
425358 TCTTCTTATTATGAACTTTCTTTTCTTCAAATGAGT
1 TCTTCTCATTATGAACTTTCTTTTCTTCAAATGAGT
* *
425394 TCTTTTCATTATGAACTTTCTTTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTTCTTTTCTTCAAATGAGT
* *
425430 TCTTCTCATTACGAACTCTCTTT
1 TCTTCTCATTATGAACTTTCTTT
425453 GGCGCTGCTG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.20, C:0.20, G:0.08, T:0.52
Consensus pattern (36 bp):
TCTTCTCATTATGAACTTTCTTTTCTTCAAATGAGT
Found at i:425432 original size:18 final size:17
Alignment explanation
Indices: 425375--425433 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 17
425365 ATTATGAACT
425375 TTCTTTTCTTCAAATGAG
1 TTCTTTTCTTC-AATGAG
*
425393 TTCTTTTCATT--ATGAACT
1 TTCTTTTC-TTCAATG-A-G
425411 TTCTTTTCTTCAGATGAG
1 TTCTTTTCTTCA-ATGAG
425429 TTCTT
1 TTCTT
425434 CTCATTACGA
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 3 0.09
17 3 0.09
18 21 0.64
19 3 0.09
20 3 0.09
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (17 bp):
TTCTTTTCTTCAATGAG
Found at i:425687 original size:113 final size:112
Alignment explanation
Indices: 425393--425953 Score: 877
Period size: 113 Copynumber: 5.1 Consensus size: 112
425383 TTCAAATGAG
* * ****
425393 TTCTTTTCATTATGAACT-TTCTT--TTCTTCAGATGAGTTCTTCTCATTACGAACTCTCTTTGG
1 TTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
**** * * ** * * *
425455 CGCTGCTGATCCATCAAATGATGAATTCAAGCAAAGGGTTAAACAAG
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
425502 TTCTTCTCATTATGAACT-TTCTT--TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
1 TTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
* *
425564 AAAAGTTGATCCATCAAGTGATGGGTTTGAGCAAAAGGTTGAACAAA
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
425611 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
425676 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
65 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
425724 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
425789 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
65 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
425837 TTCTTCTCATTATGAA--CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
1 TTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
425900 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
425947 TTCTTCT
1 TTCTTCT
425954 TCCTTCTTCA
Statistics
Matches: 427, Mismatches: 21, Indels: 7
0.94 0.05 0.02
Matches are distributed among these distances:
109 107 0.25
110 102 0.24
111 5 0.01
113 213 0.50
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (112 bp):
TTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
Found at i:425808 original size:226 final size:221
Alignment explanation
Indices: 425393--426107 Score: 1070
Period size: 206 Copynumber: 3.3 Consensus size: 221
425383 TTCAAATGAG
* * ****
425393 TTCTTTTCATTATGAACT-TTCTT--TTCTTCAGATGAGTTCTTCTCATTACGAACTCTCTTTGG
1 TTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
**** * * ** * * *
425455 CGCTGCTGATCCATCAAATGATGAATTCAAGCAAAGGGTTAAACAAGTTCTTCTCATTATGAACT
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACT
*
425520 TTCTTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGA
131 TTCTTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGA
*
425585 TGGGTTTGAGCAAAAGGTTGAACAAA
196 TGGATTTGAGCAAAAGGTTGAACAAA
425611 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
425676 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
425741 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCA
130 -T-TTCTT--TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCA
425806 AGTGATGGATTTGAGCAAAAGGTTGAACAAA
191 AGTGATGGATTTGAGCAAAAGGTTGAACAAA
425837 TTCTTCTCATTATGAA--CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
1 TTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
425900 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTC-T-TC--T-T---C-
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACT
425956 --C--TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGA
131 TTCTTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGA
426017 TGGATTTGAGCAAAAGGTTGAACAAA
196 TGGATTTGAGCAAAAGGTTGAACAAA
*
426043 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAACTG
1 TTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
426108 ACACTGTTGA
Statistics
Matches: 466, Mismatches: 20, Indels: 31
0.90 0.04 0.06
Matches are distributed among these distances:
206 102 0.22
209 45 0.10
210 1 0.00
215 1 0.00
218 17 0.04
219 2 0.00
220 5 0.01
221 2 0.00
222 88 0.19
223 98 0.21
224 5 0.01
226 100 0.21
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (221 bp):
TTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACT
TTCTTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGA
TGGATTTGAGCAAAAGGTTGAACAAA
Found at i:426017 original size:96 final size:96
Alignment explanation
Indices: 425853--426049 Score: 394
Period size: 96 Copynumber: 2.1 Consensus size: 96
425843 TCATTATGAA
425853 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAG
1 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAG
425918 TGATGGATTTGAGCAAAAGGTTGAACAAATT
66 TGATGGATTTGAGCAAAAGGTTGAACAAATT
425949 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAG
1 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAG
426014 TGATGGATTTGAGCAAAAGGTTGAACAAATT
66 TGATGGATTTGAGCAAAAGGTTGAACAAATT
426045 CTTCT
1 CTTCT
426050 CATTATGAAC
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 101 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (96 bp):
CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAG
TGATGGATTTGAGCAAAAGGTTGAACAAATT
Found at i:436026 original size:12 final size:12
Alignment explanation
Indices: 436009--436041 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
435999 ACACCATATT
436009 ACTTCTTTCTTC
1 ACTTCTTTCTTC
436021 ACTTCTTTCTTC
1 ACTTCTTTCTTC
436033 ACTTCTTTC
1 ACTTCTTTC
436042 CACATAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.33, G:0.00, T:0.58
Consensus pattern (12 bp):
ACTTCTTTCTTC
Found at i:439779 original size:13 final size:13
Alignment explanation
Indices: 439744--439781 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
439734 GATATTAAAG
439744 AATAAATA-TTAA
1 AATAAATATTTAA
*
439756 AATAATTTATTTAA
1 AATAA-ATATTTAA
439770 AATAAATATTTA
1 AATAAATATTTA
439782 TTTATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 5 0.23
13 8 0.36
14 9 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATAAATATTTAA
Found at i:441086 original size:19 final size:18
Alignment explanation
Indices: 441055--441092 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
441045 TGGGCTTGTA
441055 TTTTATTTTATTATTATT
1 TTTTATTTTATTATTATT
441073 TTTTATTGTTATTATTATT
1 TTTTATT-TTATTATTATT
441092 T
1 T
441093 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTTATTTTATTATTATT
Found at i:441119 original size:12 final size:11
Alignment explanation
Indices: 441101--441176 Score: 65
Period size: 12 Copynumber: 7.2 Consensus size: 11
441091 TTATATATAT
441101 ATTTAAT-AT-
1 ATTTAATAATA
441110 ATTTAATAATA
1 ATTTAATAATA
441121 A--TAATAATA
1 ATTTAATAATA
441130 A--TAATAATA
1 ATTTAATAATA
*
441139 ATATTTATAATA
1 AT-TTAATAATA
441151 ATTATAATAATA
1 ATT-TAATAATA
*
441163 ATAATAATAATA
1 AT-TTAATAATA
441175 AT
1 AT
441177 AATAAATAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
9 25 0.44
10 2 0.04
11 2 0.04
12 28 0.49
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:441121 original size:3 final size:3
Alignment explanation
Indices: 441113--441181 Score: 111
Period size: 3 Copynumber: 23.0 Consensus size: 3
441103 TTAATATATT
* * *
441113 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
441161 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
441182 ATAAATAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:443345 original size:30 final size:30
Alignment explanation
Indices: 443311--443376 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
443301 AAAAAAATAG
*
443311 AAACTTTAGGGACTAAAATAAATAAAACAA
1 AAACTTTAGGGACCAAAATAAATAAAACAA
* * *
443341 AAACTTTAGGTACCAAAATAGATAAAACAG
1 AAACTTTAGGGACCAAAATAAATAAAACAA
443371 AAACTT
1 AAACTT
443377 AAATAACTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.56, C:0.12, G:0.11, T:0.21
Consensus pattern (30 bp):
AAACTTTAGGGACCAAAATAAATAAAACAA
Found at i:443389 original size:30 final size:29
Alignment explanation
Indices: 443322--443411 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 29
443312 AACTTTAGGG
* * **
443322 ACTAAAATAAATAAAACAAAAACTTTAGGT
1 ACTAAAATAGATAAAACAGAAAC-TTAAAT
*
443352 ACCAAAATAGATAAAACAGAAACTTAAAT
1 ACTAAAATAGATAAAACAGAAACTTAAAT
* * *
443381 AACTAAAATAGAAAAAAATAGAAACTAAAAT
1 -ACTAAAATAG-ATAAAACAGAAACTTAAAT
443412 GGGCTAAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 4 0.08
30 29 0.59
31 16 0.33
ACGTcount: A:0.64, C:0.10, G:0.07, T:0.19
Consensus pattern (29 bp):
ACTAAAATAGATAAAACAGAAACTTAAAT
Found at i:444845 original size:3 final size:3
Alignment explanation
Indices: 444837--444897 Score: 88
Period size: 3 Copynumber: 20.0 Consensus size: 3
444827 GTATTTGTAT
*
444837 TAA TAA TAA TAGT TAA TAA -ATA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
444883 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
444898 AATTAAATAG
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 1 0.02
3 49 0.92
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:445375 original size:134 final size:134
Alignment explanation
Indices: 445069--445451 Score: 527
Period size: 134 Copynumber: 2.9 Consensus size: 134
445059 ACACTACTCA
* * * * * * *
445069 TACGTGATGAAGA-GTTCGGGTCATCTAAGGGTGACAC-AGTTCCTACATGATGAGGAAATCTGG
1 TACGTGATGAGGACGTT-TGGTTATCTAGGGGTGACACGA-CTCCTACGTGATGAGGAGATCTGG
* * * * *
445132 TCGAGGGATGACACTGCTCATACGTGATGAAAAGTTCTTGGCCATCTTTAGGAAGGGTGATAACT
64 TCGGGGGATGACACGGCTCATACGTGATGAAGAGTTC-TGGCCATCTTTAGGAAGGGCGATAACA
*
445197 CGGTTCC
128 CGATTCC
* * **
445204 TACGCGATGAGGGCGGCTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTC
1 TACGTGATGAGGACGTTTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTC
* *
445269 GGGGGATGACACGGCCCATACGTGATGAAGAGTTCTAGCCATCTTTAGGAAGGGCGATAACACGA
66 GGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGA
445334 TTCC
131 TTCC
*
445338 TACGTGATGAGGACGTTTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAAGAGATCTGGTC
1 TACGTGATGAGGACGTTTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTC
* *
445403 AGGAGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGG
66 GGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGG
445452 GATAATGATT
Statistics
Matches: 218, Mismatches: 28, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
134 135 0.62
135 81 0.37
136 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (134 bp):
TACGTGATGAGGACGTTTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTC
GGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGA
TTCC
Found at i:445823 original size:91 final size:90
Alignment explanation
Indices: 445659--445885 Score: 282
Period size: 91 Copynumber: 2.5 Consensus size: 90
445649 GTTAAGATAT
*
445659 ACAAGCTCAAAG--TTTTTTCAAAAAGAACAGACTCAAAGATTTTTCTCAAGAAAAACTGTCTCA
1 ACAAACTCAAAGAATTTTTTC-AAAAGAA-AGACTCAAAGATTTTTCTCAAG-AAAACTGTCTCA
* *
445722 AGAGAGACAAAACTTTGTTTCAAAAGAA
63 AGAGAAACAAAACTTTGGTTCAAAAGAA
* * * *
445750 ACAAACTCAAAGATTTTGGTTTCAAAAGAAATGACTCAAAGATTTTT-TCACG-AAATTGTCTTA
1 ACAAACTCAAAGAATTT--TTTCAAAAGAAA-GACTCAAAGATTTTTCTCAAGAAAACTGTCTCA
445813 AGAGAAACAAAACTTTGGTTCAAAAGAA
63 AGAGAAACAAAACTTTGGTTCAAAAGAA
* *
445841 ACAGACTCAAAGAATTTTTTCAAAAGAAACAACTCAAAGATTTTT
1 ACAAACTCAAAGAATTTTTTCAAAAGAAA-GACTCAAAGATTTTT
445886 ATTTCAAAAG
Statistics
Matches: 121, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
89 26 0.21
91 61 0.50
93 8 0.07
94 22 0.18
95 4 0.03
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (90 bp):
ACAAACTCAAAGAATTTTTTCAAAAGAAAGACTCAAAGATTTTTCTCAAGAAAACTGTCTCAAGA
GAAACAAAACTTTGGTTCAAAAGAA
Done.