Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007943.1 Hibiscus syriacus cultivar Beakdansim tig00110365_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: 1187827
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:402626 original size:31 final size:31
Alignment explanation
Indices: 402542--402619 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
402532 AAAAGGTCAG
402542 TGGGTTCCACTACTTGTGTCACGGTCACTACT
1 TGGG-TCCACTACTTGTGTCACGGTCACTACT
*
402574 TGGGTCCACTACTTGTGTCACGGTTACTACT
1 TGGGTCCACTACTTGTGTCACGGTCACTACT
402605 TGGGTCCACTACTTG
1 TGGGTCCACTACTTG
402620 GATCACGATT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 41 0.91
32 4 0.09
ACGTcount: A:0.15, C:0.27, G:0.23, T:0.35
Consensus pattern (31 bp):
TGGGTCCACTACTTGTGTCACGGTCACTACT
Found at i:406133 original size:36 final size:36
Alignment explanation
Indices: 406029--406248 Score: 163
Period size: 36 Copynumber: 6.3 Consensus size: 36
406019 AAGTTTATGC
* *
406029 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATATGA
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
406065 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
* * * * **
406101 TTCAAGGGAAACTATCTCAAGAGAGATAAAATTCAT
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
* * * *
406137 TTCAAGGGAAA-TGTTTTCAA---TG-----TTTATGT
1 TTCAAGAGAAACTG-TCTCAAGGGAGACAAAATT-TGT
* * * *
406166 TTCAAGAGAAATTATCTCAAGAGAGACAAAACTTAGT
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGT
* * * *
406203 TCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
406239 TTCAAG-GAAA
1 TTCAAGAGAAA
406249 AGATATTCAA
Statistics
Matches: 143, Mismatches: 29, Indels: 25
0.73 0.15 0.13
Matches are distributed among these distances:
28 2 0.01
29 16 0.11
30 1 0.01
32 1 0.01
33 1 0.01
35 5 0.03
36 88 0.62
37 27 0.19
38 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (36 bp):
TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
Found at i:406271 original size:102 final size:102
Alignment explanation
Indices: 406060--406301 Score: 265
Period size: 102 Copynumber: 2.4 Consensus size: 102
406050 GGAGACAAAA
* * * * ** *
406060 TATGATTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAACTATCTCAAGAG
1 TATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATATCTCAAGAG
* * * *
406124 AGATAAAATTCATTTCAAGGGAAATGTTTTCAATGTT
66 AGACAAAATTCATTTCAAGGGAAAAGTATTCAAAGTT
* * * *
406161 TATGTTTCAAGAGAAATTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGG
1 TATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATATCTCAAGAG
* **
406226 AGACGAAATTTGTTTCAA-GGAAAAGATATTCAAAGATT
66 AGACAAAATTCATTTCAAGGGAAAAG-TATTCAAAG-TT
* *
406264 T-TGTTTCAAGGGAAACTGTCTTAAGAGAGACAAAACTT
1 TATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
406302 GGAAACTGTC
Statistics
Matches: 116, Mismatches: 22, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
101 38 0.33
102 75 0.65
103 3 0.03
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.28
Consensus pattern (102 bp):
TATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATATCTCAAGAG
AGACAAAATTCATTTCAAGGGAAAAGTATTCAAAGTT
Found at i:406602 original size:106 final size:106
Alignment explanation
Indices: 406417--406678 Score: 407
Period size: 106 Copynumber: 2.5 Consensus size: 106
406407 GTATAGTTCT
* * * *
406417 AAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTTTTTGTTGACAA
1 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
* *
406482 CCAGTCTTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
* * *
406523 AAGTCCAATATCCTTCGCTGTGAAGCTGAAATTGGTTTTGAAACTGGGAAATTGTTTGTTGACAA
1 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
*
406588 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
* * *
406629 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
1 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAA
406679 GCCCCCTCGT
Statistics
Matches: 140, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 140 1.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (106 bp):
AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
Found at i:407363 original size:33 final size:33
Alignment explanation
Indices: 407271--407379 Score: 141
Period size: 32 Copynumber: 3.4 Consensus size: 33
407261 TTCGCATCAG
* * * *
407271 GATGTTGAAT-TCCCAAAGATGCCCCAATATTC
1 GATGTTGAATCTCCAAAAAATGCCCCAACATTT
* *
407303 GATGTTGAATCT-AAAAAAATGCTCCAACATTT
1 GATGTTGAATCTCCAAAAAATGCCCCAACATTT
*
407335 GATGTTAAATCTCCAAAAAATGCCCCAACATTT
1 GATGTTGAATCTCCAAAAAATGCCCCAACATTT
407368 GATGTTGAATCT
1 GATGTTGAATCT
407380 TTAAAGATGC
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
32 35 0.54
33 30 0.46
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (33 bp):
GATGTTGAATCTCCAAAAAATGCCCCAACATTT
Found at i:408501 original size:19 final size:19
Alignment explanation
Indices: 408479--408515 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
408469 TTTTGTTTCT
408479 CTTTTTTATTTTCTCTTTA
1 CTTTTTTATTTTCTCTTTA
*
408498 CTTTTTTTTTTTCTCTTT
1 CTTTTTTATTTTCTCTTT
408516 TTTCTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78
Consensus pattern (19 bp):
CTTTTTTATTTTCTCTTTA
Found at i:408515 original size:14 final size:14
Alignment explanation
Indices: 408457--408518 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 14
408447 TTTTCTTCAC
408457 TTTTTC-CTTTATTT
1 TTTTTCTCTTT-TTT
408471 TTGTTTCTCTTTTTT
1 TT-TTTCTCTTTTTT
408486 ATTTTCTCTTTACTTTTTT
1 -TTTT-TC--T-CTTTTTT
408505 TTTTTCTCTTTTTT
1 TTTTTCTCTTTTTT
408519 CTATTTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
14 9 0.22
15 10 0.24
16 8 0.20
17 2 0.05
18 5 0.12
19 7 0.17
ACGTcount: A:0.05, C:0.15, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTTCTCTTTTTT
Found at i:408525 original size:21 final size:20
Alignment explanation
Indices: 408474--408528 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
408464 TTTATTTTTG
*
408474 TTTCTCTTTTTTATTTTCTCT
1 TTTCTATTTTTT-TTTTCTCT
*
408495 TTACT-TTTTTTTTTTCTCTTT
1 TTTCTATTTTTTTTTTCTC--T
408516 TTTCTATTTTTTT
1 TTTCTATTTTTTT
408529 GATTGGATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 7 0.24
20 6 0.21
21 9 0.31
22 7 0.24
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTCTATTTTTTTTTTCTCT
Found at i:408878 original size:53 final size:53
Alignment explanation
Indices: 408806--408918 Score: 199
Period size: 53 Copynumber: 2.1 Consensus size: 53
408796 AGGATTAATT
* *
408806 TTATTCACATGAAAACAGTGTAATTAATGCATGATAGAATTATTTAGAATGAA
1 TTATTCTCACGAAAACAGTGTAATTAATGCATGATAGAATTATTTAGAATGAA
*
408859 TTCTTCTCACGAAAACAGTGTAATTAATGCATGATAGAATTATTTAGAATGAA
1 TTATTCTCACGAAAACAGTGTAATTAATGCATGATAGAATTATTTAGAATGAA
408912 TTATTCT
1 TTATTCT
408919 TTCTGCTTCT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (53 bp):
TTATTCTCACGAAAACAGTGTAATTAATGCATGATAGAATTATTTAGAATGAA
Found at i:421428 original size:18 final size:18
Alignment explanation
Indices: 421405--421441 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
421395 ATCGGTACAC
421405 TATGTGTAAAATTCAAAT
1 TATGTGTAAAATTCAAAT
421423 TATGTGTAAAATTCAAAT
1 TATGTGTAAAATTCAAAT
421441 T
1 T
421442 TTTCGACCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (18 bp):
TATGTGTAAAATTCAAAT
Found at i:427799 original size:23 final size:22
Alignment explanation
Indices: 427769--427841 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 22
427759 ACAGTGTATT
427769 GATGCATCCCTTGAATGTGCATC
1 GATGCAT-CCTTGAATGTGCATC
* *
427792 GATGCAT-CATGAA-GATGCACC
1 GATGCATCCTTGAATG-TGCATC
427813 GATGCATTCCTTGAATGTGCATC
1 GATGCA-TCCTTGAATGTGCATC
427836 GATGCA
1 GATGCA
427842 CTATGCTGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
20 1 0.02
21 16 0.38
22 1 0.02
23 23 0.55
24 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (22 bp):
GATGCATCCTTGAATGTGCATC
Found at i:429721 original size:64 final size:64
Alignment explanation
Indices: 429635--429773 Score: 176
Period size: 64 Copynumber: 2.2 Consensus size: 64
429625 CTAGGGGTGG
* * *
429635 ATCGGTACACTAATTACATTCGATGTTTCAA-AGA-GCTAGGAGTGCATCGATGCATTGGTTGTG
1 ATCGGTACACTAATTACATTCGATGTTTAAATAAATGCCA-GAGTGCATCGATGCA-TGGTTGTG
429698 C
64 C
* * *
429699 ATCGGTACACTGAA-TGCTTTCGATGTTTAAATAAATTCCAGAGTGCATCGATGCATGGTTGTGC
1 ATCGGTACACT-AATTACATTCGATGTTTAAATAAATGCCAGAGTGCATCGATGCATGGTTGTGC
429763 ATCGGTACACT
1 ATCGGTACACT
429774 TTTGGTTCGA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
64 45 0.68
65 19 0.29
66 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (64 bp):
ATCGGTACACTAATTACATTCGATGTTTAAATAAATGCCAGAGTGCATCGATGCATGGTTGTGC
Found at i:431079 original size:21 final size:18
Alignment explanation
Indices: 431022--431079 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
431012 CAACAATTGG
431022 TAACAATTGGTATCTTTT
1 TAACAATTGGTATCTTTT
* *
431040 TAACAATTAGTGTCCTTTT
1 TAACAATTGGTAT-CTTTT
431059 GTAAACAATTGGTATCTTTT
1 -T-AACAATTGGTATCTTTT
431079 T
1 T
431080 CAGTAAACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 11 0.33
19 6 0.18
20 6 0.18
21 10 0.30
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (18 bp):
TAACAATTGGTATCTTTT
Found at i:432442 original size:15 final size:16
Alignment explanation
Indices: 432422--432454 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
432412 TCAATTTAAG
432422 TATAGAATTTAT-TTT
1 TATAGAATTTATATTT
432437 TATAGAATTTATATTT
1 TATAGAATTTATATTT
432453 TA
1 TA
432455 AATTTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
TATAGAATTTATATTT
Found at i:433469 original size:18 final size:18
Alignment explanation
Indices: 433438--433546 Score: 143
Period size: 18 Copynumber: 6.1 Consensus size: 18
433428 CTGCCCAAGT
433438 ATGATATTTACAGTTATCAG
1 ATGAT-TTT-CAGTTATCAG
433458 ATGATTTTCAGTTATCAG
1 ATGATTTTCAGTTATCAG
* *
433476 AT-ATTTACAATTATCAG
1 ATGATTTTCAGTTATCAG
433493 ATGATTTTCAGTTATCAG
1 ATGATTTTCAGTTATCAG
*
433511 ATG-TTTTCAGTTATTAG
1 ATGATTTTCAGTTATCAG
433528 ATG-TTTTACAGTTATCAG
1 ATGATTTT-CAGTTATCAG
433546 A
1 A
433547 CATATATTAA
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
17 35 0.43
18 38 0.47
19 3 0.04
20 5 0.06
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (18 bp):
ATGATTTTCAGTTATCAG
Found at i:433490 original size:35 final size:35
Alignment explanation
Indices: 433440--433546 Score: 162
Period size: 35 Copynumber: 3.1 Consensus size: 35
433430 GCCCAAGTAT
433440 GATATTTACAGTTATCAGATGATTTTCAGTTATCA
1 GATATTTACAGTTATCAGATGATTTTCAGTTATCA
*
433475 GATATTTACAATTATCAGATGATTTTCAGTTATCA
1 GATATTTACAGTTATCAGATGATTTTCAGTTATCA
* * *
433510 GATGTTTTCAGTTATTAGATG-TTTTACAGTTATCA
1 GATATTTACAGTTATCAGATGATTTT-CAGTTATCA
433545 GA
1 GA
433547 CATATATTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
34 4 0.06
35 62 0.94
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (35 bp):
GATATTTACAGTTATCAGATGATTTTCAGTTATCA
Found at i:436260 original size:104 final size:103
Alignment explanation
Indices: 436077--436298 Score: 268
Period size: 104 Copynumber: 2.1 Consensus size: 103
436067 CATCTAATCG
* * * *
436077 ACACAATTATCAATATAAATTGTGATGATTTTTTGACACTAAAAATATAGTTTGTGACCATCAAT
1 ACACTATTATCAATAGAAATTGTGATAATTTTTTGACACTAAAAATATAGTTTGTGACCACCAAT
* *
436142 GTGATCACACTAAGT-ATTTTTAGTGATCAAATGTTCG
66 GTGATCACACTAAGTGATTTTTAGTGACCAAATGTTCA
* * * * *
436179 ATACTATTATTAATAGAAATTGTGATAAATTTATTTGACACTGAAAGTATATTTTGTGACCACCA
1 ACACTATTATCAATAGAAATTGTGAT-AATTT-TTTGACACTAAAAATATAGTTTGTGACCACCA
* * *
436244 ATATTG-TCACAGTAAGTGTTTTTTAGTGACCAAATGTTCA
64 AT-GTGATCACACTAAGTGATTTTTAGTGACCAAATGTTCA
*
436284 ACACTATTAACAATA
1 ACACTATTATCAATA
436299 ACTCTATCAC
Statistics
Matches: 99, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
102 22 0.22
103 4 0.04
104 40 0.40
105 33 0.33
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (103 bp):
ACACTATTATCAATAGAAATTGTGATAATTTTTTGACACTAAAAATATAGTTTGTGACCACCAAT
GTGATCACACTAAGTGATTTTTAGTGACCAAATGTTCA
Found at i:438057 original size:44 final size:43
Alignment explanation
Indices: 438006--438125 Score: 152
Period size: 44 Copynumber: 2.7 Consensus size: 43
437996 TTGAGAATTA
438006 GCGGCGTTTCTAGTGCAAAAACGCCGCTAAATGCATGGTATATT
1 GCGGCGTTTCTAGTGC-AAAACGCCGCTAAATGCATGGTATATT
** **
438050 GCGGCGTTTCTAGTATATAAACGCCGCTAAATGTTTGGTATATT
1 GCGGCGTTTCTAGTGCA-AAACGCCGCTAAATGCATGGTATATT
*
438094 GCGGCATTTCTAGTTTGC-AAACGCCGCTAAAT
1 GCGGCGTTTCTAG--TGCAAAACGCCGCTAAAT
438126 AACACAGGAT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
43 1 0.02
44 64 0.97
46 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (43 bp):
GCGGCGTTTCTAGTGCAAAACGCCGCTAAATGCATGGTATATT
Found at i:438531 original size:15 final size:15
Alignment explanation
Indices: 438513--438542 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
438503 CCCTTTCTTC
438513 ATTTTCCGCTTTCAA
1 ATTTTCCGCTTTCAA
438528 ATTTTCCGCTTTCAA
1 ATTTTCCGCTTTCAA
438543 GTTAGCCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.47
Consensus pattern (15 bp):
ATTTTCCGCTTTCAA
Found at i:441477 original size:52 final size:52
Alignment explanation
Indices: 441414--441572 Score: 284
Period size: 52 Copynumber: 3.1 Consensus size: 52
441404 TAACAACAAA
*
441414 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAATCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
*
441466 ATACATTATAATTTAGAAACATTAAAGTACTTATAG-ATAAACAGTCTTCAAC
1 ATACATTATAATTTAGAAACATTAAAGTACTTAT-GCATAAACAGTCTTCACC
441518 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
441570 ATA
1 ATA
441573 TTGTTCAGTA
Statistics
Matches: 102, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
51 1 0.01
52 100 0.98
53 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.33
Consensus pattern (52 bp):
ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
Found at i:442705 original size:42 final size:40
Alignment explanation
Indices: 442636--442754 Score: 116
Period size: 40 Copynumber: 2.9 Consensus size: 40
442626 GTTTATACAA
* * * * * * *
442636 AAAACGCCGCTAATTTACCACTCTATTGTGGCATTTTTGGT
1 AAAATGCCGCTAAATTAACACTATATTGCGGC-GTTTTAGT
442677 ATAAATGCCGCTAAATTAACACTATATTGCGGCGTTTTAGT
1 A-AAATGCCGCTAAATTAACACTATATTGCGGCGTTTTAGT
*
442718 AAAATGCCGCTACATGT--CTACTATATTGCGGCGTTTT
1 AAAATGCCGCTAAAT-TAAC-ACTATATTGCGGCGTTTT
442755 TACTATAAAC
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
39 1 0.01
40 31 0.46
41 9 0.13
42 26 0.39
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (40 bp):
AAAATGCCGCTAAATTAACACTATATTGCGGCGTTTTAGT
Found at i:442969 original size:80 final size:80
Alignment explanation
Indices: 442830--442977 Score: 196
Period size: 80 Copynumber: 1.9 Consensus size: 80
442820 TATTAATTAC
*
442830 GGCGTTTGTTGAAAAACGCCGCTATATTTATACTCTATTGTAGCGTTTTCATAAAAAACGCCGCT
1 GGCGTTTGTTGAAAAACGCCGCTATATTAATACTCTATTGTAGCGTTTTCATAAAAAACGCCGCT
442895 AAAGTCTCAATTTGT
66 AAAGTCTCAATTTGT
* * *
442910 GGCGTTTGGATTG-AAAACGCTGCTATATGTAATACT-T-TTGTGGCGTTTT-ATCAACAAACGC
1 GGCGTTT-G-TTGAAAAACGCCGCTATAT-TAATACTCTATTGTAGCGTTTTCAT-AAAAAACGC
442971 CGCTAAA
62 CGCTAAA
442978 AACGCCGCTA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
79 2 0.03
80 33 0.55
81 16 0.27
82 9 0.15
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (80 bp):
GGCGTTTGTTGAAAAACGCCGCTATATTAATACTCTATTGTAGCGTTTTCATAAAAAACGCCGCT
AAAGTCTCAATTTGT
Found at i:442982 original size:12 final size:13
Alignment explanation
Indices: 442965--442993 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
442955 TTTTATCAAC
442965 AAACGCCGCTA-A
1 AAACGCCGCTACA
442977 AAACGCCGCTACA
1 AAACGCCGCTACA
442990 AAAC
1 AAAC
442994 AGTTTTGCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.45, C:0.34, G:0.14, T:0.07
Consensus pattern (13 bp):
AAACGCCGCTACA
Found at i:443399 original size:26 final size:26
Alignment explanation
Indices: 443369--443421 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
443359 ACAAATCACC
443369 AACTAAGACCAGTGACAAAAACAATT
1 AACTAAGACCAGTGACAAAAACAATT
* * *
443395 AACTAAGACTAGTGACGAAAATAATT
1 AACTAAGACCAGTGACAAAAACAATT
443421 A
1 A
443422 TCGTCACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.53, C:0.15, G:0.13, T:0.19
Consensus pattern (26 bp):
AACTAAGACCAGTGACAAAAACAATT
Found at i:444025 original size:3 final size:3
Alignment explanation
Indices: 444019--444096 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
444009 GATGATGATG
444019 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
444067 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
444097 TGTTGTAGGA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:446674 original size:6 final size:6
Alignment explanation
Indices: 446663--446689 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
446653 ATTGAAACTA
446663 GGGGAT GGGGAT GGGGAT GGGGAT GGG
1 GGGGAT GGGGAT GGGGAT GGGGAT GGG
446690 TTGGGTGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.70, T:0.15
Consensus pattern (6 bp):
GGGGAT
Found at i:449275 original size:2 final size:2
Alignment explanation
Indices: 449268--449300 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
449258 GCATACATGC
449268 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
449301 CAATCATTAT
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:449720 original size:19 final size:21
Alignment explanation
Indices: 449684--449723 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
449674 TCTCGTATCA
449684 TATAACATGTGCATTATCATT
1 TATAACATGTGCATTATCATT
*
449705 TATAACA-GTTCA-TATCATT
1 TATAACATGTGCATTATCATT
449724 GCTCTTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.42
Consensus pattern (21 bp):
TATAACATGTGCATTATCATT
Found at i:457381 original size:15 final size:15
Alignment explanation
Indices: 457361--457390 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
457351 ATAGTTCATA
*
457361 ATTTTATTTTAATTT
1 ATTTTAATTTAATTT
457376 ATTTTAATTTAATTT
1 ATTTTAATTTAATTT
457391 TTCACTTTTG
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTAATTTAATTT
Found at i:460950 original size:14 final size:15
Alignment explanation
Indices: 460933--460974 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
460923 TATGTATACA
460933 TGAC-TATGAAAATG
1 TGACATATGAAAATG
*
460947 TGACATGTGAAAATG
1 TGACATATGAAAATG
*
460962 TG-CATACGAAAAT
1 TGACATATGAAAAT
460975 ACTCGATGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (15 bp):
TGACATATGAAAATG
Found at i:466530 original size:73 final size:74
Alignment explanation
Indices: 466428--466623 Score: 198
Period size: 74 Copynumber: 2.6 Consensus size: 74
466418 CCTCGAAGGG
* * * * * * * *
466428 AGTCATCCAAAAAATCAATACTAGCTTAAACTGTAAAG-GG-GGCTTTCTCACTTGACTTAAACC
1 AGTCATCCAAAGAATCAAGACTGGCTTAAACCGCAAAGTGGAGTC-ATCTCACTTAACTTAAACC
*
466491 TACAAAGAGA
65 CACAAAGAGA
* * *
466501 AGTCATCTAAAGAATCAAGACTGGCTTAAACCGCGAAGTGGAGTCATCTCGCTTAACTTAAACCC
1 AGTCATCCAAAGAATCAAGACTGGCTTAAACCGCAAAGTGGAGTCATCTCACTTAACTTAAACCC
* *
466566 ACAAAGGGG
66 ACAAAGAGA
* * * *
466575 AGTCATCCAAAGCATCAAGACAGGCTTAAACCCGCTAAGGGGAGTCATC
1 AGTCATCCAAAGAATCAAGACTGGCTTAAA-CCGCAAAGTGGAGTCATC
466624 CAAAGCATTA
Statistics
Matches: 101, Mismatches: 19, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
73 31 0.31
74 52 0.51
75 18 0.18
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (74 bp):
AGTCATCCAAAGAATCAAGACTGGCTTAAACCGCAAAGTGGAGTCATCTCACTTAACTTAAACCC
ACAAAGAGA
Found at i:466580 original size:74 final size:75
Alignment explanation
Indices: 466473--466623 Score: 205
Period size: 74 Copynumber: 2.0 Consensus size: 75
466463 AAGGGGGCTT
* * * *
466473 TCTCACTTGACTTAAACCTACAAAGAGAAGTCATCTAAAGAATCAAGACTGGCTTAAA-CCGCGA
1 TCTCACTTAACTTAAACCCACAAAGAGAAGTCATCCAAAGAATCAAGACAGGCTTAAACCCGCGA
*
466537 AGTGGAGTCA
66 AGGGGAGTCA
* * * * *
466547 TCTCGCTTAACTTAAACCCACAAAGGGGAGTCATCCAAAGCATCAAGACAGGCTTAAACCCGCTA
1 TCTCACTTAACTTAAACCCACAAAGAGAAGTCATCCAAAGAATCAAGACAGGCTTAAACCCGCGA
466612 AGGGGAGTCA
66 AGGGGAGTCA
466622 TC
1 TC
466624 CAAAGCATTA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
74 50 0.76
75 16 0.24
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (75 bp):
TCTCACTTAACTTAAACCCACAAAGAGAAGTCATCCAAAGAATCAAGACAGGCTTAAACCCGCGA
AGGGGAGTCA
Found at i:466703 original size:42 final size:42
Alignment explanation
Indices: 466556--466696 Score: 219
Period size: 42 Copynumber: 3.4 Consensus size: 42
466546 ATCTCGCTTA
* * * * *
466556 ACTTAAACCCACAAAGGGGAGTCATCCAAAGCATCAAGACAG
1 ACTTAAACCCGCGAAGGGGAGTCATCCAAAGCATTAAGATAT
* *
466598 GCTTAAACCCGCTAAGGGGAGTCATCCAAAGCATTAAGATAT
1 ACTTAAACCCGCGAAGGGGAGTCATCCAAAGCATTAAGATAT
466640 ACTTAAACCCGCGAAGGGGAGTCATCCAAAGCATTAAGATAT
1 ACTTAAACCCGCGAAGGGGAGTCATCCAAAGCATTAAGATAT
466682 ACTTAAACCCGCGAA
1 ACTTAAACCCGCGAA
466697 TTGGAGTTGT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (42 bp):
ACTTAAACCCGCGAAGGGGAGTCATCCAAAGCATTAAGATAT
Found at i:468195 original size:20 final size:23
Alignment explanation
Indices: 468149--468198 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
468139 TGATTTTCCC
468149 TTTATTTTATTTATTTTGATTCAAT
1 TTTATTTTATTTATTTT-ATT-AAT
468174 TTTATTTT-TTTATTTT-TT-AT
1 TTTATTTTATTTATTTTATTAAT
468194 TTTAT
1 TTTAT
468199 ATTCGCTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.28
22 2 0.08
24 8 0.32
25 8 0.32
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTATTTTATTTATTTTATTAAT
Found at i:470305 original size:33 final size:33
Alignment explanation
Indices: 470229--470306 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
470219 ATCCAACCTG
* *
470229 AACCCGATCCGAATATCACACTTAAAAAAACCC
1 AACCCGACCCGAATATCAAACTTAAAAAAACCC
* * * *
470262 GATCCGACCCGAATATTAAACTT-AAAAAGCCC
1 AACCCGACCCGAATATCAAACTTAAAAAAACCC
470294 AACCCGAACCCGA
1 AACCCG-ACCCGA
470307 TTTTTTTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
32 12 0.33
33 24 0.67
ACGTcount: A:0.42, C:0.33, G:0.10, T:0.14
Consensus pattern (33 bp):
AACCCGACCCGAATATCAAACTTAAAAAAACCC
Found at i:470322 original size:33 final size:33
Alignment explanation
Indices: 470292--470354 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
470282 CTTAAAAAGC
470292 CCAACCCGAACCCGATTTTTTTTAAAAAAAAAA
1 CCAACCCGAACCCGATTTTTTTTAAAAAAAAAA
* *
470325 CCAACCCGATCCCGATTTTTTTTTAAAAAA
1 CCAACCCGAACCCGATTTTTTTTAAAAAAA
470355 TCCTACCCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.40, C:0.25, G:0.06, T:0.29
Consensus pattern (33 bp):
CCAACCCGAACCCGATTTTTTTTAAAAAAAAAA
Found at i:479089 original size:122 final size:123
Alignment explanation
Indices: 478957--479181 Score: 317
Period size: 123 Copynumber: 1.8 Consensus size: 123
478947 TATTTATAAA
** *
478957 TAAGATATTTATTTACTTGGAAATA-TCAGAAAAGGGCTCCTAGGTGCCTTAAGACAACTCTTTT
1 TAAGATATTTATTTACTTAAAAATATTCAGAAAAGGGCTCCTAGGTGCCTTAAGACAACTCTTTC
** *
479021 CTTTGATATTAAAAAATAAATAAATAACTAAAACATTTAAAAATTTATTTTAATATAG
66 CTTCAACATTAAAAAATAAATAAATAACTAAAACATTTAAAAATTTATTTTAATATAG
* * * * * * *
479079 TAAGATATTTATTTATTTAAAAATATTTAGAAAAGTGCTTCTAGTTGCTTTAAGACAGCTCTTTC
1 TAAGATATTTATTTACTTAAAAATATTCAGAAAAGGGCTCCTAGGTGCCTTAAGACAACTCTTTC
*
479144 CTTCAACATTAAAAAATAAATAAATAACTAAAATATTT
66 CTTCAACATTAAAAAATAAATAAATAACTAAAACATTT
479182 TCTTAAAATA
Statistics
Matches: 88, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
122 22 0.25
123 66 0.75
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (123 bp):
TAAGATATTTATTTACTTAAAAATATTCAGAAAAGGGCTCCTAGGTGCCTTAAGACAACTCTTTC
CTTCAACATTAAAAAATAAATAAATAACTAAAACATTTAAAAATTTATTTTAATATAG
Found at i:480969 original size:3 final size:3
Alignment explanation
Indices: 480961--481018 Score: 55
Period size: 3 Copynumber: 19.7 Consensus size: 3
480951 TAAAATTATT
* * * * *
480961 TAA TAA TAA TAA TAA -AA TAA TTA TAA TTA TAA TTA TAA TTA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
481008 TAA AAA TAA TA
1 TAA TAA TAA TA
481019 GAACCGGGAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:481580 original size:112 final size:113
Alignment explanation
Indices: 481322--481849 Score: 633
Period size: 112 Copynumber: 4.6 Consensus size: 113
481312 AAATTAAGGC
*
481322 AAGGTTGAACAAATTCTTCTCATTATGAA-TATCTTC-TCCTTCTTCAGATGAGTTCTTCTCATT
1 AAGGTTGAACAAATTCTTCTCATTATGAACT-TCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
** *** **
481385 ATGAACACT-TCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTAA-TAGAGTCAAACA
65 ATGAACTTTCTCTGGAAATGTTGA---T--TC-ATCAAGTGATG-AATTAGAG-C--A-A
* *
481443 AAGGTTGAACAAATTCTTCTTATTATGAACTTCTTTTTCC-TCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
* *
481507 TGAACTTTCTCTGGAAAAGTTAATTCATCAAGTGATGAATTCAG-GCAA
66 TGAACTTTCTCTGGAAATGTTGATTCATCAAGTGATGAATT-AGAGCAA
*
481555 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
481619 TGAACTTTCTCTGGAAATGTTGA-TCTATCAAGTGATGAATTAGAGCAA
66 TGAACTTTCTCTGGAAATGTTGATTC-ATCAAGTGATGAATTAGAGCAA
* * *
481667 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
** * * * *
481732 TGAACACT-TCTGGAAATGTTGATCCATCAAGTGAAGGATTTGAGCAA
66 TGAACTTTCTCTGGAAATGTTGATTCATCAAGTGATGAATTAGAGCAA
** * *
481779 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
481844 TGAACT
66 TGAACT
481850 CTACCTGGTA
Statistics
Matches: 367, Mismatches: 31, Indels: 27
0.86 0.07 0.06
Matches are distributed among these distances:
111 4 0.01
112 239 0.65
113 31 0.08
115 3 0.01
116 8 0.02
117 4 0.01
119 1 0.00
121 61 0.17
122 16 0.04
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (113 bp):
AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
TGAACTTTCTCTGGAAATGTTGATTCATCAAGTGATGAATTAGAGCAA
Found at i:482093 original size:76 final size:76
Alignment explanation
Indices: 481865--482095 Score: 381
Period size: 76 Copynumber: 3.0 Consensus size: 76
481855 TGGTAATGCT
* * * * *
481865 GATGACCCGAAGGTTTTGAAAATATTAAAAAGCTCCCGAAGGCTTTTTGGAAATATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
* *
481930 TAGGACTTATA
66 CAGGACTTACA
*
481941 AATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
482006 CAGGACTTACA
66 CAGGACTTACA
*
482017 GATGACCCTAAGGCTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
482082 CAGGACTTACA
66 CAGGACTTACA
482093 GAT
1 GAT
482096 ATGGGAAATA
Statistics
Matches: 145, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 145 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (76 bp):
GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
CAGGACTTACA
Found at i:482329 original size:37 final size:37
Alignment explanation
Indices: 482270--482471 Score: 194
Period size: 37 Copynumber: 5.5 Consensus size: 37
482260 GAAATAACTG
*
482270 TCTCAAGCGAGACAAATCTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATTTTTGTTTTAAGAAAAACAA
* * * ** **
482307 TCTCAAGTGAGATAAATTTTTGTTTCAAGTGAAACTG
1 TCTCAAGCGAGACAAATTTTTGTTTTAAGAAAAACAA
*
482344 TCTCAAGCGAGACAAA-ATTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATTTTTGTTTTAAGAAAAACAA
* * * * ** ** **
482380 TCTCAAGTGAGATAAAGTTCTGTTTCGAGTGAAACTG
1 TCTCAAGCGAGACAAATTTTTGTTTTAAGAAAAACAA
482417 TCTCAAGCGAGACAAA--TTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATTTTTGTTTTAAGAAAAACAA
* *
482452 TCTCAAGTGAGATAAATTTT
1 TCTCAAGCGAGACAAATTTT
482472 ATTTGAAAAC
Statistics
Matches: 125, Mismatches: 37, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
35 26 0.21
36 28 0.22
37 71 0.57
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (37 bp):
TCTCAAGCGAGACAAATTTTTGTTTTAAGAAAAACAA
Found at i:482385 original size:73 final size:73
Alignment explanation
Indices: 482265--482471 Score: 362
Period size: 73 Copynumber: 2.8 Consensus size: 73
482255 AACTCGAAAT
*
482265 AACTGTCTCAAGCGAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
1 AACTGTCTCAAGCGAGACAAA-ATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
482330 TTCAAGTGA
65 TTCAAGTGA
* *
482339 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGTT
*
482404 TCGAGTGA
66 TCAAGTGA
482412 AACTGTCTCAAGCGAGAC-AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTT
482472 ATTTGAAAAC
Statistics
Matches: 127, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
72 40 0.31
73 66 0.52
74 21 0.17
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (73 bp):
AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGTT
TCAAGTGA
Found at i:482788 original size:165 final size:164
Alignment explanation
Indices: 482510--482833 Score: 515
Period size: 165 Copynumber: 2.0 Consensus size: 164
482500 TATGGATGTG
* * * * *
482510 GGAAATGGTTTACTAAGTAAGATACTATGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
**
482575 AGAAAAGATTGAATGAGAAATATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGATT
66 AGAAAAGATAAAATGAGAAATATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGATT
*
482640 GGGTAACATGCCCCAATCTCAAGATAATGTTGTT
131 GGGTAACATGACCCAATCTCAAGATAATGTTGTT
*
482674 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAATAATTTCATTTT
1 GGAAATAGTTTACTAAGT-AAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
* * *
482739 C-GAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTGTTTTTCAAAATATCATGTTGA
65 CAGAAAAGATAAAATGAGAAA-TATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGA
482803 TTGGGTAACATGACCCAATCTCAAGATAATG
129 TTGGGTAACATGACCCAATCTCAAGATAATG
482834 CTCATTCTTA
Statistics
Matches: 146, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
164 34 0.23
165 112 0.77
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (164 bp):
GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
AGAAAAGATAAAATGAGAAATATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGATT
GGGTAACATGACCCAATCTCAAGATAATGTTGTT
Found at i:483428 original size:22 final size:22
Alignment explanation
Indices: 483349--483426 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
483339 AATAAAGCTT
483349 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
483371 TCATCTTTTAAAAAGAGAATCTA
1 TCATC-TTTGAAAAGAGAATCTA
* * *
483394 TCCTCTTTGAAGAGAAAATCTA
1 TCATCTTTGAAAAGAGAATCTA
483416 TCATCTTTGAA
1 TCATCTTTGAA
483427 GAATATAGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
22 29 0.59
23 20 0.41
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:484691 original size:74 final size:74
Alignment explanation
Indices: 484570--484710 Score: 178
Period size: 74 Copynumber: 1.9 Consensus size: 74
484560 ATGGGCCTTC
* *
484570 AGCATGCCCCAACATTGGCTAATACAAATGTTCAAAAATACCTCAACA-TTCTTCATTCTGATTG
1 AGCATGCCCCAACATTGGCTAATACAAATGTTCAAAAATACATCAACATTTC-TCATTCTAATTG
484634 AAAGGGTTTT
65 AAAGGGTTTT
* ** * * *
484644 AGCATGCCCCAACATTTTGCTGCTATAAATGTTC-AGAATACATCAACATTTCTGATTCTAATTG
1 AGCATGCCCCAACA-TTGGCTAATACAAATGTTCAAAAATACATCAACATTTCTCATTCTAATTG
484708 AAA
65 AAA
484711 TGGGCTTTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
74 39 0.68
75 18 0.32
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (74 bp):
AGCATGCCCCAACATTGGCTAATACAAATGTTCAAAAATACATCAACATTTCTCATTCTAATTGA
AAGGGTTTT
Found at i:489754 original size:14 final size:14
Alignment explanation
Indices: 489735--489821 Score: 58
Period size: 14 Copynumber: 6.5 Consensus size: 14
489725 AAATGTAATT
489735 ATGTAAAAATGAAA
1 ATGTAAAAATGAAA
489749 ATGT--AAAT-ACAA
1 ATGTAAAAATGA-AA
* *
489761 ACGTAAAAATGCAA
1 ATGTAAAAATGAAA
*
489775 ATGT--AAATGCAA
1 ATGTAAAAATGAAA
* **
489787 ATGTAAATATGTGA
1 ATGTAAAAATGAAA
* *
489801 ATGTAACAATAAAA
1 ATGTAAAAATGAAA
489815 ATGTAAA
1 ATGTAAA
489822 TTGTATAGTA
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
11 1 0.02
12 21 0.38
14 33 0.60
ACGTcount: A:0.56, C:0.06, G:0.14, T:0.24
Consensus pattern (14 bp):
ATGTAAAAATGAAA
Found at i:489766 original size:12 final size:12
Alignment explanation
Indices: 489747--489795 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
489737 GTAAAAATGA
489747 AAATGTAAATAC
1 AAATGTAAATAC
* *
489759 AAACGTAAAAATGC
1 AAATGT--AAATAC
*
489773 AAATGTAAATGC
1 AAATGTAAATAC
489785 AAATGTAAATA
1 AAATGTAAATA
489796 TGTGAATGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 21 0.68
14 10 0.32
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.22
Consensus pattern (12 bp):
AAATGTAAATAC
Found at i:489806 original size:26 final size:26
Alignment explanation
Indices: 489737--489793 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
489727 ATGTAATTAT
*
489737 GTAAAAATGAAAATGTAAATACAAAC
1 GTAAAAATGCAAATGTAAATACAAAC
* *
489763 GTAAAAATGCAAATGTAAATGCAAAT
1 GTAAAAATGCAAATGTAAATACAAAC
489789 GTAAA
1 GTAAA
489794 TATGTGAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.58, C:0.07, G:0.14, T:0.21
Consensus pattern (26 bp):
GTAAAAATGCAAATGTAAATACAAAC
Found at i:492072 original size:123 final size:123
Alignment explanation
Indices: 491935--492160 Score: 328
Period size: 123 Copynumber: 1.8 Consensus size: 123
491925 TATTTATAAA
** *
491935 TAAGATATTTATTTATTTGGAAATA-TCAGAAAAGGGCTTCTAGGTGCCTTAAGACAACTCTTTT
1 TAAGATATTTATTTATTTAAAAATATTCAGAAAAGGGCTTCTAGGTGCCTTAAGACAACTCTTTC
** * *
491999 CTTTGATATTAAAAAAATAGATAAATAACTAAAACATTTAAAAATTTATTTTAATATAG
66 CTTCAACATT-AAAAAATAAATAAATAACTAAAACATTTAAAAATTTATTTTAATATAG
* * * *
492058 TAAGATATTTATTTATTTAAAAATATTTAGAAAAGGGCTTCTAGTTGCTTTAAGACAGCTCTTTC
1 TAAGATATTTATTTATTTAAAAATATTCAGAAAAGGGCTTCTAGGTGCCTTAAGACAACTCTTTC
*
492123 CTTCAACATTAAAAAATAAATAAATAACTAAAATATTT
66 CTTCAACATTAAAAAATAAATAAATAACTAAAACATTT
492161 TCTTAAAATA
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
123 49 0.54
124 41 0.46
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (123 bp):
TAAGATATTTATTTATTTAAAAATATTCAGAAAAGGGCTTCTAGGTGCCTTAAGACAACTCTTTC
CTTCAACATTAAAAAATAAATAAATAACTAAAACATTTAAAAATTTATTTTAATATAG
Found at i:494032 original size:26 final size:26
Alignment explanation
Indices: 494002--494064 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
493992 TGGCCTGTAA
494002 AATAAATAAAATTATT-TAATAATAAT
1 AATAAA-AAAATTATTATAATAATAAT
* * *
494028 AATAAAATAATTATTATTATAATTAT
1 AATAAAAAAATTATTATAATAATAAT
*
494054 TATAAAAAAAT
1 AATAAAAAAAT
494065 AATAGAACCG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 8 0.26
26 23 0.74
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
AATAAAAAAATTATTATAATAATAAT
Found at i:500202 original size:30 final size:29
Alignment explanation
Indices: 500167--500225 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
500157 CAATTTAAGG
500167 CAAAATGGT-TTTGGACTTGAATTGAATTTA
1 CAAAAT-GTATTTGGACTT-AATTGAATTTA
500197 CAAAATGTATTTGGACTTAATTGAATTTA
1 CAAAATGTATTTGGACTTAATTGAATTTA
500226 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.41
Consensus pattern (29 bp):
CAAAATGTATTTGGACTTAATTGAATTTA
Found at i:500312 original size:19 final size:19
Alignment explanation
Indices: 500301--500352 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
500291 GAATAGTAAT
500301 TTACTATTTGAACAATAAA
1 TTACTATTTGAACAATAAA
500320 TTACTATTTGAACAATAAA
1 TTACTATTTGAACAATAAA
* *
500339 TCACTGTTTGAACA
1 TTACTATTTGAACA
500353 GTAACCCGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (19 bp):
TTACTATTTGAACAATAAA
Found at i:500467 original size:21 final size:21
Alignment explanation
Indices: 500441--500482 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
500431 ATTTGAATAT
*
500441 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
500462 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
500483 CCCATTTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:500544 original size:21 final size:21
Alignment explanation
Indices: 500511--500550 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
500501 TTTTTGCAGA
*
500511 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
500533 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
500551 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:509217 original size:53 final size:53
Alignment explanation
Indices: 509137--509253 Score: 155
Period size: 53 Copynumber: 2.2 Consensus size: 53
509127 GTCCACCCTA
* * * * *
509137 AAATTTAATTTTTTTTATATTAATTATTTATTTTATTGATAGTATTCATCCTG
1 AAATTTAATTTTTTTTATATCAATTATTTAGTTTATTGACAATATTCAACCTG
*
509190 AAATTTAAGTTTTTTTT-TATCAATTATTTAGTTTATTGACAATATTCAACTTG
1 AAATTTAA-TTTTTTTTATATCAATTATTTAGTTTATTGACAATATTCAACCTG
*
509243 AAATTTTATTT
1 AAATTTAATTT
509254 ATACTTAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
52 3 0.05
53 45 0.80
54 8 0.14
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (53 bp):
AAATTTAATTTTTTTTATATCAATTATTTAGTTTATTGACAATATTCAACCTG
Found at i:513640 original size:15 final size:15
Alignment explanation
Indices: 513622--513677 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
513612 TAACCGGTTT
513622 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
513637 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
513654 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
513669 CGATTTTAA
1 CGGTTTTAA
513678 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:513650 original size:17 final size:17
Alignment explanation
Indices: 513625--513675 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
513615 CCGGTTTCGG
513625 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
513642 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
513657 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
513674 TT
1 TT
513676 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:513900 original size:21 final size:21
Alignment explanation
Indices: 513848--513888 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
513838 ACACTTAGGG
513848 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
513869 AACCGATTCCCTATGAGAGG
1 AACCGATTCCCTATGAGAGG
513889 GTATCGATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:514117 original size:13 final size:13
Alignment explanation
Indices: 514096--514150 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
514086 AAGTTCGATA
*
514096 AATTCAAATACTT
1 AATTGAAATACTT
514109 AATTGAAATACTT
1 AATTGAAATACTT
* *
514122 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
514136 AATTGAAATACTT
1 AATTGAAATACTT
514149 AA
1 AA
514151 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:514232 original size:32 final size:32
Alignment explanation
Indices: 514136--514234 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 32
514126 AACTCAACAT
* * *
514136 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAA-AATTCCAAGTTCGATA
514169 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAA-TTCCAAGTTCGATA
*
514202 AATTCAAATACTTAAAAATTTCAAGTTCGATA
1 AATTCAAATACTTAAAAATTCCAAGTTCGATA
514234 A
1 A
514235 TTGAAACAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
32 15 0.25
33 46 0.75
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (32 bp):
AATTCAAATACTTAAAAATTCCAAGTTCGATA
Found at i:514254 original size:21 final size:21
Alignment explanation
Indices: 514229--514268 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
514219 ATTTCAAGTT
514229 CGATAATTGAAACAAAGTTTG
1 CGATAATTGAAACAAAGTTTG
*
514250 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
514269 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTG
Found at i:516598 original size:23 final size:24
Alignment explanation
Indices: 516549--516595 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
516539 TTAAACCCAT
*
516549 ACCGGTTTTTTTTTCCGGATAAAA
1 ACCGGTTTTTTTATCCGGATAAAA
516573 ACCGG-TTTTTTATCCGG-TAAAA
1 ACCGGTTTTTTTATCCGGATAAAA
516595 A
1 A
516596 ACCCGGTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.27
23 11 0.50
24 5 0.23
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (24 bp):
ACCGGTTTTTTTATCCGGATAAAA
Found at i:517793 original size:20 final size:18
Alignment explanation
Indices: 517757--517836 Score: 65
Period size: 18 Copynumber: 4.3 Consensus size: 18
517747 ATGTTAGTAT
* *
517757 TTTTTTAAATAGTTATTA
1 TTTTTTATATAATTATTA
517775 TTTTTTATATTAATATATT-
1 TTTTTTATA-TAAT-TATTA
*
517794 TATGTTTATATAATTATTA
1 T-TTTTTATATAATTATTA
* *
517813 TTTATT-TAGAATTATTAA
1 TTTTTTATATAATTATT-A
517831 TTTTTT
1 TTTTTT
517837 TTGCTAATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
17 9 0.18
18 21 0.42
19 9 0.18
20 11 0.22
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (18 bp):
TTTTTTATATAATTATTA
Found at i:519605 original size:21 final size:21
Alignment explanation
Indices: 519581--519673 Score: 73
Period size: 21 Copynumber: 4.4 Consensus size: 21
519571 GCCCACCAGT
*
519581 TTATATACC-ATCTCCGCAGGG
1 TTATATACCGAGC-CCGCAGGG
*
519602 TTATATTCCGAGCCCGCAGGG
1 TTATATACCGAGCCCGCAGGG
* * *
519623 TTACATTCCTAGCCCGCCA-GG
1 TTATATACCGAGCCCG-CAGGG
* * *
519644 TTACATGCCTAGCCCGCAGGG
1 TTATATACCGAGCCCGCAGGG
*
519665 TTTTATACC
1 TTATATACC
519674 ATATGGAGGT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.03
21 55 0.90
22 4 0.07
ACGTcount: A:0.20, C:0.31, G:0.22, T:0.27
Consensus pattern (21 bp):
TTATATACCGAGCCCGCAGGG
Found at i:520239 original size:34 final size:34
Alignment explanation
Indices: 520189--520286 Score: 124
Period size: 34 Copynumber: 2.9 Consensus size: 34
520179 AAATGTTTTT
*
520189 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * * * *
520223 AAAATAAAAATAATATTATTCAAAATTGAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
520257 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
520287 CATTAAATTT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:520918 original size:128 final size:128
Alignment explanation
Indices: 520687--521184 Score: 912
Period size: 128 Copynumber: 3.9 Consensus size: 128
520677 TTACCTGATT
* *
520687 TACTGATATATCTAGTATCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
*
520752 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACACGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
520815 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
*
520880 TGACAAAATAATGGAAGGCGTGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
520943 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
*
521008 TGACAAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
521071 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
521136 TG---AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
521185 ACTCCGATTA
Statistics
Matches: 360, Mismatches: 10, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
125 46 0.13
128 314 0.87
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:521266 original size:8 final size:8
Alignment explanation
Indices: 521255--521295 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
521245 TCACAAACTT
521255 TCAAATTC
1 TCAAATTC
521263 TCAAATTC
1 TCAAATTC
* *
521271 CCAAACTC
1 TCAAATTC
521279 T-AAATTC
1 TCAAATTC
521286 TCAAATTC
1 TCAAATTC
521294 TC
1 TC
521296 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:524308 original size:13 final size:13
Alignment explanation
Indices: 524290--524327 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
524280 TACATAAATA
524290 TATTTAATATATT
1 TATTTAATATATT
*
524303 TATTTAATATA-A
1 TATTTAATATATT
*
524315 TAATTAATATATT
1 TATTTAATATATT
524328 AGTTATAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTTAATATATT
Found at i:524324 original size:34 final size:35
Alignment explanation
Indices: 524286--524353 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
524276 TAAATACATA
524286 AATATATTTA-ATAT-ATTTATTT-AATATAATAATT
1 AATATA-TTAGATATAATTT-TTTAAATATAATAATT
*
524320 AATATATTAGTTATAATTTTTTAAATATAATAAT
1 AATATATTAGATATAATTTTTTAAATATAATAAT
524354 AATTCCACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 3 0.10
34 12 0.40
35 15 0.50
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (35 bp):
AATATATTAGATATAATTTTTTAAATATAATAATT
Found at i:527014 original size:16 final size:16
Alignment explanation
Indices: 526973--527016 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
526963 AATTTTTTTA
526973 AAATATTTTATT-AAT
1 AAATATTTTATTAAAT
*
526988 TAATATTTTATTAAAT
1 AAATATTTTATTAAAT
*
527004 AAATTTTTTATTA
1 AAATATTTTATTA
527017 TTTTAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATATTTTATTAAAT
Found at i:527696 original size:29 final size:29
Alignment explanation
Indices: 527661--527731 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
527651 TATTGTTGAG
527661 CTCGACTCAAACTTTAAAAGTAAGCTCAA
1 CTCGACTCAAACTTTAAAAGTAAGCTCAA
527690 CTCGACTCAAACTTTAAAAGTAAGCTCAA
1 CTCGACTCAAACTTTAAAAGTAAGCTCAA
527719 CTCGACTCAAACT
1 CTCGACTCAAACT
527732 CACGAACTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (29 bp):
CTCGACTCAAACTTTAAAAGTAAGCTCAA
Found at i:528724 original size:16 final size:16
Alignment explanation
Indices: 528700--528730 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
528690 TATTTGATTT
*
528700 TTTTTAAATCAAAATA
1 TTTTAAAATCAAAATA
528716 TTTTAAAATCAAAAT
1 TTTTAAAATCAAAAT
528731 TTAAAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTTAAAATCAAAATA
Found at i:530578 original size:21 final size:21
Alignment explanation
Indices: 530554--530598 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
530544 TTTTTTGGTT
530554 TTTTAAATTT-ATTTTTTTATA
1 TTTTAAATTTAATTTTTTT-TA
*
530575 TTTTGAATTTAATTTTTTTTA
1 TTTTAAATTTAATTTTTTTTA
530596 TTT
1 TTT
530599 AAAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTAAATTTAATTTTTTTTA
Found at i:530781 original size:18 final size:18
Alignment explanation
Indices: 530754--530798 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
530744 AAAATATACT
530754 TATT-ATTTTAATAAAAA
1 TATTAATTTTAATAAAAA
*
530771 TATTAATTTTAATTAAAA
1 TATTAATTTTAATAAAAA
* *
530789 CAATAATTTT
1 TATTAATTTT
530799 GTGGTCTACG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTAATTTTAATAAAAA
Found at i:536768 original size:34 final size:32
Alignment explanation
Indices: 536729--536798 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
536719 TTTTGTAAAT
* *
536729 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAAGTTCTAGCTTAGCCCG-G-AAAAACTA
*
536763 GGGAAAAGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
536795 GGGA
1 GGGA
536799 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (32 bp):
GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:540544 original size:21 final size:21
Alignment explanation
Indices: 540518--540559 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
540508 CAATTAAGAA
**
540518 TCAAGGAGCTTTACTTCAAAG
1 TCAAGGAGCCGTACTTCAAAG
*
540539 TCAAGGCGCCGTACTTCAAAG
1 TCAAGGAGCCGTACTTCAAAG
540560 CCATAGTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (21 bp):
TCAAGGAGCCGTACTTCAAAG
Found at i:545111 original size:21 final size:20
Alignment explanation
Indices: 545087--545130 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
545077 TAACTTTTTA
*
545087 TTTTCTCTGTCATCCTTAACT
1 TTTTCTATGTCAT-CTTAACT
* *
545108 TTTTCTATTTCATTTTAACT
1 TTTTCTATGTCATCTTAACT
545128 TTT
1 TTT
545131 ACTTTTTCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTCTATGTCATCTTAACT
Found at i:556485 original size:20 final size:20
Alignment explanation
Indices: 556460--556498 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
556450 CAATTAAGAA
556460 TCAAGGAG-CTTTACTTCAAG
1 TCAAGGAGTC-TTACTTCAAG
*
556480 TCAAGGTGTCTTACTTCAA
1 TCAAGGAGTCTTACTTCAA
556499 ATCCATAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (20 bp):
TCAAGGAGTCTTACTTCAAG
Found at i:561070 original size:21 final size:21
Alignment explanation
Indices: 561004--561073 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 21
560994 CTATCACCCA
* *
561004 TTTTCCCTCTCATTTTTAACT
1 TTTTCTCTTTCATTTTTAACT
* *
561025 TTTTCTTTTATCTTTATTATTAACT
1 TTTTCTCTT-TC---ATTTTTAACT
561050 TTTTCTCTTTCATTTTTAACT
1 TTTTCTCTTTCATTTTTAACT
561071 TTT
1 TTT
561074 ACTTTTTCTC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
21 18 0.46
22 2 0.05
24 2 0.05
25 17 0.44
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTCTCTTTCATTTTTAACT
Found at i:565933 original size:3 final size:3
Alignment explanation
Indices: 565920--565981 Score: 108
Period size: 3 Copynumber: 20.7 Consensus size: 3
565910 TCTTTTATAT
565920 TTA TT- TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
565965 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
565982 TACAATATAC
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 52 0.91
4 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:567479 original size:18 final size:17
Alignment explanation
Indices: 567450--567491 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
567440 TATATGTATA
*
567450 ATTTATTTTTTTTACTT
1 ATTTATTGTTTTTACTT
567467 ATGTTATTGTTTTTACTT
1 AT-TTATTGTTTTTACTT
567485 ATTTATT
1 ATTTATT
567492 ATATTTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (17 bp):
ATTTATTGTTTTTACTT
Found at i:572189 original size:30 final size:30
Alignment explanation
Indices: 572132--572199 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
572122 ATGCATAAGT
* **
572132 AAATTCATCATTTATAATGCATCACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
* *
572162 AAATGCATCATTTATAGCACATTACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
*
572192 ATATGCAT
1 AAATGCAT
572200 TCGAATTTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (30 bp):
AAATGCATCATTTATAACACATCACCAATA
Found at i:579318 original size:14 final size:14
Alignment explanation
Indices: 579299--579329 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
579289 TATTACACTT
579299 AAATCAATCAAAAA
1 AAATCAATCAAAAA
579313 AAATCAATCAAAAA
1 AAATCAATCAAAAA
579327 AAA
1 AAA
579330 AGAAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.74, C:0.13, G:0.00, T:0.13
Consensus pattern (14 bp):
AAATCAATCAAAAA
Found at i:580454 original size:47 final size:46
Alignment explanation
Indices: 580279--580502 Score: 163
Period size: 43 Copynumber: 4.9 Consensus size: 46
580269 CAACATCAAC
*
580279 TGACCAGACTTCCTCATCACGTAGGAGCCGTGTCA--A-CCTTAGA
1 TGACCAGACTTCCTCATCACGTAGGAACCGTGTCATCACCCTTAGA
* * * * * *
580322 TAATCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCCTAAAGA
1 TGACCAGACTTCCTCATCACGTAGGAACCGTGTCATCACCC-T--T--AGA
* * * * * *
580373 TGGCCAGAGTTCTTCATCATGTATGAACCATGTCATCTACCCTTAGA
1 TGACCAGACTTCCTCATCACGTAGGAACCGTGTCATC-ACCCTTAGA
* *
580420 CGACCAGACTTCCTCATCACGTAGGAGCCGTGTCA--A-CCTTAGA
1 TGACCAGACTTCCTCATCACGTAGGAACCGTGTCATCACCCTTAGA
* * * * * *
580463 TAATCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACC
1 TGACCAGACTTCCTCATCACGTAGGAACCGTGTCATCACC
580503 TTTCCTAAAG
Statistics
Matches: 134, Mismatches: 35, Indels: 21
0.71 0.18 0.11
Matches are distributed among these distances:
43 62 0.46
44 1 0.01
45 2 0.01
46 3 0.02
47 31 0.23
49 2 0.01
51 29 0.22
52 4 0.03
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (46 bp):
TGACCAGACTTCCTCATCACGTAGGAACCGTGTCATCACCCTTAGA
Found at i:580498 original size:141 final size:142
Alignment explanation
Indices: 580280--580595 Score: 508
Period size: 141 Copynumber: 2.2 Consensus size: 142
580270 AACATCAACT
580280 GACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAATCAGCCGTCCTCATCACGTA
1 GACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAATCAGCCGTCCTCATCACGTA
** *
580345 GGAACCGAGTTATCACCCTTCCTAAAGATGGCCAG-AGTTCTTCATCATGTATGAACCATGTCAT
66 GGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAAACTCTTCATCACGTATGAACCATGTCAT
*
580409 CTACCCTTAGAC
131 CCACCCTTAGAC
580421 GACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAATCAGCCGTCCTCATCACGTA
1 GACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAATCAGCCGTCCTCATCACGTA
* ** *
580486 GGAACCGAGTTATCACCTTTCCTAAAGATGGCCAGAAACTCTTCATCACGTATGAGTCGTGTCAT
66 GGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAAACTCTTCATCACGTATGAACCATGTCAT
580551 CCACCCTTAGAC
131 CCACCCTTAGAC
* * * * *
580563 GACCAGACCTCTTCATCATGTATGAGCAGTGTC
1 GACCAGACTTCCTCATCACGTAGGAGCCGTGTC
580596 GTCCCCAACA
Statistics
Matches: 161, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
141 99 0.61
142 62 0.39
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (142 bp):
GACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAATCAGCCGTCCTCATCACGTA
GGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAAACTCTTCATCACGTATGAACCATGTCAT
CCACCCTTAGAC
Found at i:580762 original size:3 final size:3
Alignment explanation
Indices: 580749--580849 Score: 170
Period size: 3 Copynumber: 33.7 Consensus size: 3
580739 TCTTTTATAT
580749 TTA TT- TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
580795 TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
580842 TTA TTA TT
1 TTA TTA TT
580850 TACAATATAC
Statistics
Matches: 94, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.04
3 84 0.89
4 6 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:582345 original size:18 final size:17
Alignment explanation
Indices: 582316--582357 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
582306 TATATGTATA
*
582316 ATTTATTTTTTTTACTT
1 ATTTATTGTTTTTACTT
582333 ATGTTATTGTTTTTACTT
1 AT-TTATTGTTTTTACTT
582351 ATTTATT
1 ATTTATT
582358 ATATTTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (17 bp):
ATTTATTGTTTTTACTT
Found at i:585939 original size:2 final size:2
Alignment explanation
Indices: 585934--586015 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
585924 GCGCGCGCAC
585934 AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
585975 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
586016 ATCTTTTACA
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 78 0.99
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:587298 original size:18 final size:18
Alignment explanation
Indices: 587265--587299 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
587255 AATCAGGTTT
587265 TTCTGCATTTTAATTTAG
1 TTCTGCATTTTAATTTAG
587283 TTCTCGCATTTT-ATTTA
1 TTCT-GCATTTTAATTTA
587300 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.20, C:0.14, G:0.09, T:0.57
Consensus pattern (18 bp):
TTCTGCATTTTAATTTAG
Found at i:595053 original size:36 final size:36
Alignment explanation
Indices: 595006--595323 Score: 394
Period size: 36 Copynumber: 8.8 Consensus size: 36
594996 CTCAAGTCAA
* *
595006 TCCAGCCTTCACGGAAAAGTAGTAAAGTAAATCATT
1 TCCAGCCTTCACGGAAGAGTAGTGAAGTAAATCATT
595042 TCCAGCCTTCACGGAAGAGTAGTGAAGTAAATCA-T
1 TCCAGCCTTCACGGAAGAGTAGTGAAGTAAATCATT
*
595077 TCTCAGCCTTCAAGGAAGAGTAGTGAAGTAAATCATT
1 TC-CAGCCTTCACGGAAGAGTAGTGAAGTAAATCATT
* *
595114 TCCAGCCTTCACGGAATATTAGTGAAGTAAATCA-T
1 TCCAGCCTTCACGGAAGAGTAGTGAAGTAAATCATT
595149 TCTCAGCCTTCACGGAAGAGTAGTGAAGTAAATCA-T
1 TC-CAGCCTTCACGGAAGAGTAGTGAAGTAAATCATT
* *
595185 TCTTAGCCTTCACAGAAGAGTAGTGAAGTAAATCATT
1 TC-CAGCCTTCACGGAAGAGTAGTGAAGTAAATCATT
** * *
595222 AT-CAGCCTTCACAAAAGAGTAGTGAAGTTAATCAAAT
1 -TCCAGCCTTCACGGAAGAGTAGTGAAGTAAATC-ATT
* * *
595259 CCCAACCTTCACGAAAGAGTAGTGAAGTAAATCA-T
1 TCCAGCCTTCACGGAAGAGTAGTGAAGTAAATCATT
* * *
595294 TCTTAGCCTTCATGAAAGAGTAGTGAAGTA
1 TC-CAGCCTTCACGGAAGAGTAGTGAAGTA
595324 GGAGCAGATC
Statistics
Matches: 252, Mismatches: 22, Indels: 16
0.87 0.08 0.06
Matches are distributed among these distances:
35 8 0.03
36 209 0.83
37 34 0.13
38 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (36 bp):
TCCAGCCTTCACGGAAGAGTAGTGAAGTAAATCATT
Found at i:595195 original size:108 final size:109
Alignment explanation
Indices: 595005--595323 Score: 459
Period size: 108 Copynumber: 2.9 Consensus size: 109
594995 TCTCAAGTCA
*
595005 ATCCAGCCTTCACGGAAAAGTAGTAAAGTAAATCATT-TCCAGCCTTCACGGAAGAGTAGTGAAG
1 ATCCAGCCTTCACGGAAAAGTAGTGAAGTAAATCATTCT-CAGCCTTCACGGAAGAGTAGTGAAG
*
595069 TAAATCATTCTCAGCCTTCAAGGAAGAGTAGTGAAGTAAATCATT
65 TAAATCATTCTTAGCCTTCAAGGAAGAGTAGTGAAGTAAATCATT
* *
595114 -TCCAGCCTTCACGGAATATTAGTGAAGTAAATCATTCTCAGCCTTCACGGAAGAGTAGTGAAGT
1 ATCCAGCCTTCACGGAAAAGTAGTGAAGTAAATCATTCTCAGCCTTCACGGAAGAGTAGTGAAGT
595178 AAATCATTCTTAGCCTTCACA-GAAGAGTAGTGAAGTAAATCATT
66 AAATCATTCTTAGCCTTCA-AGGAAGAGTAGTGAAGTAAATCATT
* * * * * *
595222 AT-CAGCCTTCAC-AAAAGAGTAGTGAAGTTAATCAAATCCCAACCTTCACGAAAGAGTAGTGAA
1 ATCCAGCCTTCACGGAAA-AGTAGTGAAGTAAATC-ATTCTCAGCCTTCACGGAAGAGTAGTGAA
* *
595285 GTAAATCATTCTTAGCCTTCATGAAAGAGTAGTGAAGTA
64 GTAAATCATTCTTAGCCTTCAAGGAAGAGTAGTGAAGTA
595324 GGAGCAGATC
Statistics
Matches: 190, Mismatches: 14, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
107 2 0.01
108 124 0.65
109 64 0.34
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (109 bp):
ATCCAGCCTTCACGGAAAAGTAGTGAAGTAAATCATTCTCAGCCTTCACGGAAGAGTAGTGAAGT
AAATCATTCTTAGCCTTCAAGGAAGAGTAGTGAAGTAAATCATT
Found at i:595510 original size:3 final size:3
Alignment explanation
Indices: 595496--595559 Score: 92
Period size: 3 Copynumber: 21.0 Consensus size: 3
595486 CATTCTCATT
**
595496 TTA TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CCA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
595542 TTA TTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
595560 CAAGGCTTGA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:598315 original size:4 final size:4
Alignment explanation
Indices: 598306--598389 Score: 59
Period size: 4 Copynumber: 20.5 Consensus size: 4
598296 GCATTTTTTG
* *
598306 TTAT TTA- TT-T TTAT TT-T TTAT TCTAT TTA- ATATT TTACA TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT T-TAT TTAT TTA-T TTA-T TTAT TTAT
*
598353 TTAT TTAT TTATT TTAT TTATCT TTAT TTAT CTAT TT
1 TTAT TTAT TTA-T TTAT TTA--T TTAT TTAT TTAT TT
598390 TATTATTATT
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
3 9 0.14
4 38 0.59
5 13 0.20
6 4 0.06
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:598324 original size:46 final size:47
Alignment explanation
Indices: 598272--598362 Score: 118
Period size: 46 Copynumber: 2.0 Consensus size: 47
598262 TTTAAAAAAC
598272 ATTTTTTATTACT-TTTAA-AATTTAGCATT-TTT-TGTTATTTATTTTT
1 ATTTTTTATT-CTATTTAATAATTTA-CATTATTTAT-TTATTTATTTTT
*
598318 ATTTTTTATTCTATTTAATATTTTACATTATTTATTTATTTATTT
1 ATTTTTTATTCTATTTAATAATTTACATTATTTATTTATTTATTT
598363 ATTTTATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
45 2 0.05
46 19 0.47
47 18 0.45
48 1 0.03
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.68
Consensus pattern (47 bp):
ATTTTTTATTCTATTTAATAATTTACATTATTTATTTATTTATTTTT
Found at i:598326 original size:17 final size:17
Alignment explanation
Indices: 598301--598416 Score: 63
Period size: 19 Copynumber: 6.1 Consensus size: 17
598291 ATTTAGCATT
598301 TTTTGTTATTTATTTTTA
1 TTTT-TTATTTATTTTTA
*
598319 TTTTTTATTCTATTTAATA
1 TTTTTTATT-TATTT-TTA
598338 TTTTACATTATTTATTTATTTA
1 TTTT---TTATTTA-TT-TTTA
*
598360 TTTATTTTATTTATCTTTA
1 -TT-TTTTATTTATTTTTA
* *
598379 TTTATCTATTTTATTATTA
1 TTT-TTTA-TTTATTTTTA
*
598398 TTATTTT-TTTCTTTTTA
1 TT-TTTTATTTATTTTTA
598415 TT
1 TT
598417 ACTTCTTTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 25
0.69 0.08 0.23
Matches are distributed among these distances:
17 16 0.21
18 14 0.18
19 22 0.29
20 2 0.03
21 9 0.12
22 9 0.12
23 3 0.04
24 2 0.03
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (17 bp):
TTTTTTATTTATTTTTA
Found at i:598382 original size:23 final size:21
Alignment explanation
Indices: 598345--598393 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 21
598335 ATATTTTACA
*
598345 TTATTTATTTATTTATTTATT
1 TTATTTATTTATTTATCTATT
598366 TTATTTATCTTTATTTATCTATT
1 TTATTTA--TTTATTTATCTATT
598389 TTATT
1 TTATT
598394 ATTATTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 7 0.28
23 18 0.72
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (21 bp):
TTATTTATTTATTTATCTATT
Found at i:602533 original size:35 final size:34
Alignment explanation
Indices: 602446--602533 Score: 81
Period size: 35 Copynumber: 2.5 Consensus size: 34
602436 CATTTTTTTG
**
602446 TTATTTATTTTTATTATTTTTTTCTATTTAATATT
1 TTATTTA-TTTTATTATTTTTTAATATTTAATATT
* *
602481 TTACATT-TTTTATTTATTTTTTAAT-TTTATTTATCT
1 TTA-TTTATTTTA-TTATTTTTTAATATTTA-ATAT-T
602517 TTATTTATTTTATTATT
1 TTATTTATTTTATTATT
602534 ATTATTATTC
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
34 9 0.21
35 23 0.53
36 11 0.26
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (34 bp):
TTATTTATTTTATTATTTTTTAATATTTAATATT
Found at i:602541 original size:27 final size:28
Alignment explanation
Indices: 602489--602546 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
602479 TTTTACATTT
602489 TTTATTTATTTTTTAATTTTATTTA-TC
1 TTTATTTATTTTTTAATTTTATTTATTC
602516 TTTATTTATTTTATT-ATTATTA-TTATTC
1 TTTATTTATTTT-TTAATT-TTATTTATTC
602544 TTT
1 TTT
602547 TTCTTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 18 0.64
28 10 0.36
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.74
Consensus pattern (28 bp):
TTTATTTATTTTTTAATTTTATTTATTC
Found at i:603576 original size:32 final size:34
Alignment explanation
Indices: 603507--603577 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 34
603497 TTGTTTAGTA
*
603507 TTTTTATATTAAATATATTAAATATTTTAATAAT
1 TTTTTATATTAAATATATTAAATATTTAAATAAT
** * *
603541 TTTTTATATTTTATAT-TTTAA-ATTTAAATATT
1 TTTTTATATTAAATATATTAAATATTTAAATAAT
603573 TTTTT
1 TTTTT
603578 TAGTTTTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 14 0.44
33 4 0.12
34 14 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (34 bp):
TTTTTATATTAAATATATTAAATATTTAAATAAT
Found at i:614969 original size:35 final size:35
Alignment explanation
Indices: 614918--614987 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
614908 AAAACATTCC
* * *
614918 TCAATTTCATTTTAAACCCCAAATTCTAAAATAAT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATAAT
614953 TCAATTACATTCTAAACCCCAAATTCCAAAATAAT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATAAT
614988 CAAAAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATAAT
Found at i:615532 original size:35 final size:35
Alignment explanation
Indices: 615486--615559 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
615476 AGTCAATATT
*
615486 TTGAAGTATTTTAGAATTTGGGGTTTAGAATGTAA
1 TTGAAGTATTTTAGAATTTGGGGTTTAGAATGAAA
* *
615521 TTGAATTATTTTGGAATTTGGGGTTTAGAATGAAA
1 TTGAAGTATTTTAGAATTTGGGGTTTAGAATGAAA
615556 TTGA
1 TTGA
615560 GGTTTGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (35 bp):
TTGAAGTATTTTAGAATTTGGGGTTTAGAATGAAA
Found at i:616162 original size:12 final size:12
Alignment explanation
Indices: 616147--616214 Score: 55
Period size: 12 Copynumber: 5.7 Consensus size: 12
616137 TAAAGAGTCG
*
616147 ATAAACGAGTTT
1 ATAAAAGAGTTT
* **
616159 ATAAAAAAGTCG
1 ATAAAAGAGTTT
*
616171 ATAAACGAGTTT
1 ATAAAAGAGTTT
* **
616183 ATAAAAGAATCA
1 ATAAAAGAGTTT
*
616195 ATAAATGAGTTT
1 ATAAAAGAGTTT
616207 ATAAAAGA
1 ATAAAAGA
616215 ATTTGCTCGT
Statistics
Matches: 39, Mismatches: 17, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (12 bp):
ATAAAAGAGTTT
Found at i:616169 original size:24 final size:25
Alignment explanation
Indices: 616138--616215 Score: 117
Period size: 24 Copynumber: 3.2 Consensus size: 25
616128 ATAACCGAGT
616138 AAAG-AGTCGATAAACGAGTTTATA
1 AAAGAAGTCGATAAACGAGTTTATA
616162 AAA-AAGTCGATAAACGAGTTTATA
1 AAAGAAGTCGATAAACGAGTTTATA
* *
616186 AAAGAA-TCAATAAATGAGTTTATA
1 AAAGAAGTCGATAAACGAGTTTATA
616210 AAAGAA
1 AAAGAA
616216 TTTGCTCGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
24 48 0.96
25 2 0.04
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.24
Consensus pattern (25 bp):
AAAGAAGTCGATAAACGAGTTTATA
Found at i:620353 original size:20 final size:20
Alignment explanation
Indices: 620328--620379 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
620318 TTCAGGGCGC
*
620328 AAAGTTTCGAAACTCTTACA
1 AAAGTTTCCAAACTCTTACA
620348 AAAGTTTCCAAACTCTTAC-
1 AAAGTTTCCAAACTCTTACA
620367 -AAGTTTCCAAACT
1 AAAGTTTCCAAACT
620380 ATGAATAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 13 0.42
20 18 0.58
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (20 bp):
AAAGTTTCCAAACTCTTACA
Found at i:627146 original size:181 final size:182
Alignment explanation
Indices: 626862--627316 Score: 600
Period size: 182 Copynumber: 2.5 Consensus size: 182
626852 ATTCATATTA
** * * * * *
626862 ATATAACAGGTAAAAATATGATAAAATTGGTCA-CGAAAA-GACAATACCGGTAATGTC-TTACC
1 ATATAACAGGTAAAAATATGATAAAACCGAT-ATC-AAAATGATAAAACCGGTAAAG-CGCTACC
* *
626924 GGATATATTGAACGTGTCGATACTTTAATATAAAGATCGACAC-TTGTAAATTTAAAAGAGAAGC
63 GGATATATTGAAAGTGTCGATACTTTAATATAAAGATCGACACTTTGTAAATTTAAAAGAGAAAC
*
626988 AGTTTTAACGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATCCACAACG
128 AGTTTTAACGCCTATAAAGTATCGATACTTTATAAAAATGTATCAATCCACAACG
* * *
627043 ATATAACAGGTAAAAATAT-TTCAAAACCGATATCGAAATGATAAAACCGGTAAAGCGCTACCAG
1 ATATAACAGGTAAAAATATGAT-AAAACCGATATCAAAATGATAAAACCGGTAAAGCGCTACCGG
* * *
627107 ATATATTTAAAGTGTC-AGTACTTTAATAT-AAGTATCGACACTTTGTGAATTTAAAAGAGAAAT
65 ATATATTGAAAGTGTCGA-TACTTTAATATAAAG-ATCGACACTTTGTAAATTTAAAAGAGAAAC
* *
627170 AGTTTTAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTATCAATCCACAACG
128 AGTTTTAACGCCTATAAAGTATCGATACTTTATAAAAATGTATCAATCCACAACG
* * * *
627225 ATATAACATGTAAAAATATGATAAAATCGGTATCAAAATGATAAAATCGGTAAAGCGCTACCGGA
1 ATATAACAGGTAAAAATATGATAAAACCGATATCAAAATGATAAAACCGGTAAAGCGCTACCGGA
*
627290 TATATTGAAAGTGTCGACACTTTAATA
66 TATATTGAAAGTGTCGATACTTTAATA
627317 AGTACGTGTA
Statistics
Matches: 238, Mismatches: 27, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
180 10 0.04
181 77 0.32
182 149 0.63
183 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (182 bp):
ATATAACAGGTAAAAATATGATAAAACCGATATCAAAATGATAAAACCGGTAAAGCGCTACCGGA
TATATTGAAAGTGTCGATACTTTAATATAAAGATCGACACTTTGTAAATTTAAAAGAGAAACAGT
TTTAACGCCTATAAAGTATCGATACTTTATAAAAATGTATCAATCCACAACG
Found at i:628060 original size:21 final size:21
Alignment explanation
Indices: 628010--628051 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
628000 CCAAAGGGTA
628010 GATATATGTACTTCTAGTAAG
1 GATATATGTACTTCTAGTAAG
628031 GATATATGTACTTCTAGTAAG
1 GATATATGTACTTCTAGTAAG
628052 TATCAATGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (21 bp):
GATATATGTACTTCTAGTAAG
Found at i:629448 original size:15 final size:15
Alignment explanation
Indices: 629425--629456 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
629415 TGGTTGTATT
629425 GGGGAATGACGGTGA
1 GGGGAATGACGGTGA
*
629440 GGGGGATGACGGTGA
1 GGGGAATGACGGTGA
629455 GG
1 GG
629457 TAAAACAAAG
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:0.22, C:0.06, G:0.59, T:0.12
Consensus pattern (15 bp):
GGGGAATGACGGTGA
Found at i:629564 original size:21 final size:21
Alignment explanation
Indices: 629540--629583 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
629530 AAGACAATCA
629540 AGAGTCAAAGAGAAACTTGAG
1 AGAGTCAAAGAGAAACTTGAG
* *
629561 AGAGTCAAAGATACACTTGAG
1 AGAGTCAAAGAGAAACTTGAG
629582 AG
1 AG
629584 GCATAAGGGG
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:0.45, C:0.11, G:0.27, T:0.16
Consensus pattern (21 bp):
AGAGTCAAAGAGAAACTTGAG
Found at i:631491 original size:19 final size:19
Alignment explanation
Indices: 631464--631512 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
631454 AATGTAGGGT
*
631464 TAATGTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
631483 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
631502 TAATTTTGTAT
1 TAATTTTGTAT
631513 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:631994 original size:200 final size:200
Alignment explanation
Indices: 631754--632913 Score: 1863
Period size: 200 Copynumber: 5.8 Consensus size: 200
631744 GTAAGCATAT
* *
631754 GTGTCGATCCATATATAAAAAGTATCGATCGCAGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* * *
631819 GGTAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTACAAAAGAATAGGTCTACAACATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
* * * * * * *
631884 ATCGACACTTTTTGATTTTGTGTCAATACTTTTGGTCCAGAATGAATGCCAGAAAGGGCGAAACC
131 ATCGACACTTTTTAATTTTATGTCGATACTTTTGGTCCAGAATGAATCCCAAAAAGGGTGCAACC
631949 ATAAA
196 ATAAA
* *
631954 GTGTCGATCCATTTATAAAAAGTATCAATCCCAGAAACATCAAAACCCATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* * *
632019 GGTAAATTTTCAATGTAACCGGTATAAATATACCAGTTTTACGAGATAATAGGTCTACAACATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
* * * *
632084 ATC-AAACCTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATACAAAAAAGGGTGCAAC
131 ATCGACA-CTTTTTAATTTTATGTCGATACTTTTGGTCCAGAATGAATCCCAAAAAGGGTGCAAC
632148 CATAAA
195 CATAAA
* ** *
632154 GTGACGATATATTTATAAAAAGTATCGATCTCAGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
*
632219 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGATAATAGGTCTACAACATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
* * *
632284 ATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATCCCAAAAAAGGTGCAACC
131 ATCGACACTTTTTAATTTTATGTCGATACTTTTGGTCCAGAATGAATCCCAAAAAGGGTGCAACC
632349 ATAAA
196 ATAAA
632354 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* *
632419 GGTAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTACGATAGAATAGGTCTACAACATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
* * * *
632484 ATCAACACTTTTTAATTTTATGTCAATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGTAACC
131 ATCGACACTTTTTAATTTTATGTCGATACTTTTGGTCCAGAATGAATCCCAAAAAGGGTGCAACC
632549 ATAAA
196 ATAAA
* *
632554 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAGTATAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* * * *
632619 GGTAATTTTTCAATATAACCGGTATAAATATATCAGTTTTACGAGATAATAGGTCTACAACATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
* *
632684 ATCGACACTTTTTAATTTTATCTCGATACTTTTGGTCCAGAATGAATCCCAAAAAAGGTGCAACC
131 ATCGACACTTTTTAATTTTATGTCGATACTTTTGGTCCAGAATGAATCCCAAAAAGGGTGCAACC
632749 ATAAA
196 ATAAA
632754 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* * * * * *
632819 GGTAAATTTTCAATGTAACCGGTATAAATATATCGGTTTTATGAGAGAATATGTCTATAGCATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
632884 ATCGACACTTTTTAATTTTATGTCGATACT
131 ATCGACACTTTTTAATTTTATGTCGATACT
632914 AATTTAAATA
Statistics
Matches: 888, Mismatches: 70, Indels: 4
0.92 0.07 0.00
Matches are distributed among these distances:
199 2 0.00
200 884 1.00
201 2 0.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (200 bp):
GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
ATCGACACTTTTTAATTTTATGTCGATACTTTTGGTCCAGAATGAATCCCAAAAAGGGTGCAACC
ATAAA
Found at i:635323 original size:19 final size:19
Alignment explanation
Indices: 635269--635323 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
635259 AACCAATAAT
*
635269 AATAAACATAACA-AAATTG
1 AATAAA-ATAAAATAAATTG
* *
635288 GATTAAA-AAAATGAAATTG
1 AATAAAATAAAAT-AAATTG
635307 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
635324 GAAGATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
17 3 0.11
18 1 0.04
19 19 0.68
20 5 0.18
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.24
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:635436 original size:22 final size:21
Alignment explanation
Indices: 635410--635522 Score: 70
Period size: 25 Copynumber: 4.9 Consensus size: 21
635400 AAACTAAAAA
635410 TATAATGAAAATAAATAAATAG
1 TATAAT-AAAATAAATAAATAG
*
635432 TATAAATAAAAT-AATAAA-AA
1 TAT-AATAAAATAAATAAATAG
635452 TATATATAAAAATATAA-AAATGTATG
1 TATA-AT-AAAATA-AATAAA--TA-G
*
635478 TATAATATAATAAAATACTAATAG
1 TATAATAAAAT-AAATA--AATAG
635502 TAATAATAATAATAAATAAAT
1 T-ATAATAA-AATAAATAAAT
635523 GAAAAATAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 29
0.69 0.04 0.28
Matches are distributed among these distances:
19 1 0.01
20 6 0.08
21 11 0.15
22 11 0.15
23 8 0.11
24 8 0.11
25 18 0.25
26 7 0.10
27 2 0.03
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (21 bp):
TATAATAAAATAAATAAATAG
Found at i:635450 original size:42 final size:42
Alignment explanation
Indices: 635404--635492 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
635394 GCAAAGAAAC
*
635404 TAAAAATATA-ATGAAAATA-AATAAATAGTATAAATAAAATAA
1 TAAAAATATATATAAAAATATAA-AAAT-GTATAAATAAAATAA
** *
635446 TAAAAATATATATAAAAATATAAAAATGTATGTATAATATAA
1 TAAAAATATATATAAAAATATAAAAATGTATAAATAAAATAA
635488 TAAAA
1 TAAAA
635493 TACTAATAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 27 0.66
43 12 0.29
44 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.29
Consensus pattern (42 bp):
TAAAAATATATATAAAAATATAAAAATGTATAAATAAAATAA
Found at i:635760 original size:23 final size:23
Alignment explanation
Indices: 635726--635772 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
635716 ACGTAAAGAA
635726 AAATGAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAA-TATAATTAAAT
635749 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAA-AAAATATAATTAAAT
635772 A
1 A
635773 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATGAAAAAAATATAATTAAAT
Found at i:637074 original size:18 final size:18
Alignment explanation
Indices: 637051--637096 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
637041 CAAGCGGTCA
637051 ATGAAGATGAAGATGACG
1 ATGAAGATGAAGATGACG
* *
637069 ATGAAGATGACGATGATG
1 ATGAAGATGAAGATGACG
*
637087 ATGATGATGA
1 ATGAAGATGA
637097 TCCAAACAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.41, C:0.04, G:0.33, T:0.22
Consensus pattern (18 bp):
ATGAAGATGAAGATGACG
Found at i:637097 original size:6 final size:6
Alignment explanation
Indices: 637051--637096 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
637041 CAAGCGGTCA
* * * *
637051 ATGAAG ATGAAG ATGACG ATGAAG ATGACG ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
637097 TCCAAACAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.41, C:0.04, G:0.33, T:0.22
Consensus pattern (6 bp):
ATGAAG
Found at i:637097 original size:12 final size:12
Alignment explanation
Indices: 637051--637096 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
637041 CAAGCGGTCA
*
637051 ATGAAGATGAAG
1 ATGACGATGAAG
637063 ATGACGATGAAG
1 ATGACGATGAAG
*
637075 ATGACGATGATG
1 ATGACGATGAAG
*
637087 ATGATGATGA
1 ATGACGATGA
637097 TCCAAACAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.41, C:0.04, G:0.33, T:0.22
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:638601 original size:51 final size:53
Alignment explanation
Indices: 638546--638655 Score: 147
Period size: 51 Copynumber: 2.1 Consensus size: 53
638536 AGAATGGATG
638546 CCAAAAAGGG-TGAACGCACAAAGTGTCGATACATTT-TCAAAGAGTGTCGAT-
1 CCAAAAAGGGTTGAACGCACAAAGTGTCGATACATTTATCAAA-AGTGTCGATC
* * * *
638597 CC-AAAAGGGTTGCACGCATAAAGTTTCGATACATTTATTAAAAGTGTCGATC
1 CCAAAAAGGGTTGAACGCACAAAGTGTCGATACATTTATCAAAAGTGTCGATC
638649 CCAAAAA
1 CCAAAAA
638656 TATCGAAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
50 7 0.14
51 34 0.67
52 6 0.12
53 4 0.08
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (53 bp):
CCAAAAAGGGTTGAACGCACAAAGTGTCGATACATTTATCAAAAGTGTCGATC
Found at i:638786 original size:250 final size:248
Alignment explanation
Indices: 638399--638848 Score: 672
Period size: 250 Copynumber: 1.8 Consensus size: 248
638389 AAATAACGAC
* *
638399 CCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAATTTTTCAATGTAACCAGTATAAAT
1 CCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATATAACCAGTATAAAT
* * * *
638464 ATACTGGTTTATGAAAAATAGGTCTACAACATGTATCGATACTTATCAATATTGTGTCGATACTT
66 ATACCGGTTTATGAAAAATAGGTATACAACA-GTATCGACACTTATCAATATTGTGTCGATAATT
* *
638529 TTTGTCCAGAATGGATGCCAAAAAGGGTGAACGCACAAAGTGTCGATACATTTTCAAAGAGTGTC
130 TTTGTCCAGAATGGACGCCAAAAAGGGTGAACGCACAAAGTGTCGATACATTTTCAAAAAGTGTC
638594 GATCCAAAAGGGTTGCACGCATAAAGTTTCGATACATTTATTAAAAGTGTCGAT
195 GATCCAAAAGGGTTGCACGCATAAAGTTTCGATACATTTATTAAAAGTGTCGAT
*
638648 CCCAAAAATATCGAAATCCCATAATTATAATGTAATAGGTAATTTTGT-AATATAACC-GATATA
1 CCCAAAAACATCGAAA-CCCATAATTATAATGTAATAGGTAATTTT-TCAATATAACCAG-TATA
* * * * * *
638711 CATATACCGATTTTATGAGAGAATAGGTATATAACA-TATCGACACTTCTTAATATTGTGTCGAT
63 AATATACCG-GTTTATGA-AAAATAGGTATACAACAGTATCGACACTTATCAATATTGTGTCGAT
* *
638775 AATTTTTGTCCAGAATGGACGCCAAAAATGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAG
126 AATTTTTGTCCAGAATGGACGCCAAAAAGGGTGAACGCACAAAGTGTCGATACATTTTCAAAAAG
638840 TGTCGATCC
191 TGTCGATCC
638849 CGAAAACATC
Statistics
Matches: 179, Mismatches: 17, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
249 16 0.09
250 141 0.79
251 8 0.04
252 14 0.08
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (248 bp):
CCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATATAACCAGTATAAAT
ATACCGGTTTATGAAAAATAGGTATACAACAGTATCGACACTTATCAATATTGTGTCGATAATTT
TTGTCCAGAATGGACGCCAAAAAGGGTGAACGCACAAAGTGTCGATACATTTTCAAAAAGTGTCG
ATCCAAAAGGGTTGCACGCATAAAGTTTCGATACATTTATTAAAAGTGTCGAT
Found at i:638909 original size:175 final size:176
Alignment explanation
Indices: 638712--639065 Score: 552
Period size: 177 Copynumber: 2.0 Consensus size: 176
638702 ACCGATATAC
* * *
638712 ATATACCGATTTTATGAGAGAATAGGTATATAACA-TATCGACACT-TCTTAATATTGTGTCGAT
1 ATATACCGATTTTATGAGAGAATAGGTATATAACAGTATCGACACTATATAAAT-TTGTGACGAT
*
638775 AATTTTTGTCCAGAATGGACGCCAAAAATGG-TGAACGCATAAAGTGTCGATACATTTTCAAAAA
65 AATTTTTGTCCAGAATGGACGCCAAAAA-GGATGAACGCACAAAGTGTCGATACATTTTCAAAAA
*
638839 GTGTCGATCCCGAAAACATCGAAACCCATAATTATAATGTAATAGGTA
129 GTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTA
* *
638887 ATATACCGGTTTTATGAGAGAATAGGTCTATAACATGTATCGACACTATATAAATTTGTGACGAT
1 ATATACCGATTTTATGAGAGAATAGGTATATAACA-GTATCGACACTATATAAATTTGTGACGAT
* * * *
638952 ACTTTTTGTCCATAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATTTTCAAAGAG
65 AATTTTTGTCCAGAATGGACGCCAAAAAGGATGAACGCACAAAGTGTCGATACATTTTCAAAAAG
*
639017 TGTCGATCCCAAAAATATCGAAACCCATAATTATAATGTAATAGGTA
130 TGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTA
639064 AT
1 AT
639066 TTTGTAATAT
Statistics
Matches: 163, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
175 33 0.20
176 2 0.01
177 123 0.75
178 5 0.03
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (176 bp):
ATATACCGATTTTATGAGAGAATAGGTATATAACAGTATCGACACTATATAAATTTGTGACGATA
ATTTTTGTCCAGAATGGACGCCAAAAAGGATGAACGCACAAAGTGTCGATACATTTTCAAAAAGT
GTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTA
Done.