Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold180
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: 1398530
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.31
Warning! 86668 characters in sequence are not A, C, G, or T
File 3 of 6
Found at i:481515 original size:128 final size:128
Alignment explanation
Indices: 481344--481622 Score: 477
Period size: 128 Copynumber: 2.2 Consensus size: 128
481334 GGAAAATCTT
*
481344 ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTACAGTGG
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTACAGTAG
* * *
481409 AGCGGATTAAAATCACAGATCTTATTTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAATATC
66 AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAATATC
* * *
481472 ATCTCCCTGAAGCTGCAGTGGAGCAGATTAAAGTCGATAATCCTATCTCCCTGAAGTTGCAGTAG
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTACAGTAG
**
481537 AGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAATATC
66 AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAATATC
481600 ATCTCCCTGAAGTTGCAGTGGAG
1 ATCTCCCTGAAGTTGCAGTGGAG
481623 TAGACCCCAG
Statistics
Matches: 141, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
128 141 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (128 bp):
ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTACAGTAG
AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAATATC
Found at i:481523 original size:44 final size:43
Alignment explanation
Indices: 480567--481622 Score: 632
Period size: 44 Copynumber: 24.6 Consensus size: 43
480557 TCTCATCTAG
* * *
480567 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCA-TAA
* *
480610 GTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA-AA
1 -TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GTCATAA
* *
480656 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTC-ATAA
* ** *
480700 TCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACAAAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATA-A
* ** * * ***
480744 TATTATCTCTTTGAAGTTGTAG-AGAGCAGATCGCA-TC-TAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
* * *
480784 TCTTATATCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TCATAA
* ** * *
480828 T-TCTAT-TCCCTGAAGTTGTAGTGGAGTGGATTAAAATCA-GA
1 TCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
* * * *** *
480869 TCTTATCTCTCTGAATTTGCAG-AGAGCAGATCGCA-TC-TAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
* * * *
480909 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCA-TAA
* * *
480952 GTCTTATC-CTTCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA-AA
1 -TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GTCATAA
* *
480998 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTC-ATAA
* * * ** *
481042 TCCTAT-TCGCTAAAGTTGCAGTGGAGCAGATTAAAAACACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATA-A
* * * ***
481085 TCTTATCTCTCTGAAGTTACAG-AGAGCAGATCGCA-TC-TAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
* *
481125 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTC-ATAA
* * ** * *
481169 TCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAATCA-GA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
* * * * * * * *
481211 TCTTATCTCTCTGAAGTTGTAG-AGAGCATATCACA-T-TTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
* * *
481251 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCA-TAA
* * * *
481294 GTCTTATC-CTCCTGAAGTTGCAGT-GAGACAGACTGAAGATGGAAAA
1 -TCTTATCTC-CCTGAAGTTGCAGTGGAG-CAGATTAAAG-T-CATAA
*
481340 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTC-ATAA
* * * * *
481384 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATA-A
* * * ***
481428 TCTTATTTCTCTGAAGTTGCAG-AGAGCAGATCGCA-TC-TAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
* * *
481468 TATCATCTCCCTGAAGCTGCAGTGGAGCAGATTAAAGTCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTC-ATAA
* * * ** *
481512 TCCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAACCTTAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATA-A
* * * ***
481556 TCTTATCTCTCTGAAGTTACAG-AGAGCAGATCGCA-TC-TAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
* *
481596 TATCATCTCCCTGAAGTTGCAGTGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
481623 TAGACCCCAG
Statistics
Matches: 773, Mismatches: 178, Indels: 125
0.72 0.17 0.12
Matches are distributed among these distances:
40 120 0.16
41 69 0.09
42 50 0.06
43 118 0.15
44 309 0.40
45 81 0.10
46 19 0.02
47 3 0.00
48 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (43 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
Found at i:481585 original size:215 final size:215
Alignment explanation
Indices: 481123--481586 Score: 580
Period size: 217 Copynumber: 2.2 Consensus size: 215
481113 GATCGCATCT
* *
481123 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTA
* * * * * * *
481188 TAGTGGAGTGGATTAAAATCAGATCTTATCTCTCTGAAGTTGTAGAGAGCATATCACATTTAGTC
66 CAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCTAATA
* * * *
481253 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGT
131 TCATCTCCCTGAAGCTGCAGTGGAGCAGACTAAGTAAGCAAATCCTATCCTCCTGAAGTTGCAGT
* **
481318 GAGACAGACTGAAGATGGAA
196 GAGACAGACTGAAAACCGAA
481338 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTA
* *
481403 CAGTGGAGCGGATTAAAATCACAGATCTTATTTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAA
66 CAGTGGAGCGGATTAAAAT--CAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCTAA
* *
481468 TATCATCTCCCTGAAGCTGCAGTGGAGCAGATTAAAGT-CG-ATAATCCTAT-CTCCCTGAAGTT
129 TATCATCTCCCTGAAGCTGCAGTGGAGCAGACT-AAGTAAGCA-AATCCTATCCT-CCTGAAGTT
* * **
481530 GCAGT-AGAGCGGA-TTAAAACCTTA
191 GCAGTGAGA-CAGACTGAAAACCGAA
* * * *
481554 GATCTTATCTCTCTGAAGTTACAG-AGAGCAGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
481587 CGCATCTAAT
Statistics
Matches: 215, Mismatches: 28, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
215 88 0.41
216 32 0.15
217 91 0.42
218 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (215 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTA
CAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCTAATA
TCATCTCCCTGAAGCTGCAGTGGAGCAGACTAAGTAAGCAAATCCTATCCTCCTGAAGTTGCAGT
GAGACAGACTGAAAACCGAA
Found at i:487330 original size:23 final size:21
Alignment explanation
Indices: 487304--487359 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 21
487294 TAAAAAATAT
487304 ATTAACTAAAATTTTATATAAAA
1 ATTAA-TAAAATTTTA-ATAAAA
*
487327 ATTAAATAAAATTTTAATTAAA
1 ATT-AATAAAATTTTAATAAAA
487349 A-TAATAAAATT
1 ATTAATAAAATT
487360 AAAGGTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 9 0.29
21 1 0.03
22 6 0.19
23 13 0.42
24 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTAATAAAATTTTAATAAAA
Found at i:490571 original size:22 final size:22
Alignment explanation
Indices: 490530--490572 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
490520 ACAGCAGAAC
* **
490530 AGGTTTTTAGCGGCGGTTTTTT
1 AGGTCTTTAGCGGCACTTTTTT
490552 AGGTCTTTAGCGGCACTTTTT
1 AGGTCTTTAGCGGCACTTTTT
490573 AACGCCACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.14, G:0.28, T:0.47
Consensus pattern (22 bp):
AGGTCTTTAGCGGCACTTTTTT
Found at i:502560 original size:27 final size:27
Alignment explanation
Indices: 502522--502589 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
502512 TTAATTAACA
502522 TACTTAAATTTTAGATATAAGTAAACT
1 TACTTAAATTTTAGATATAAGTAAACT
*
502549 TACTTAAATTTTACATATAAGTAAACT
1 TACTTAAATTTTAGATATAAGTAAACT
502576 TACTTAAATTTTAG
1 TACTTAAATTTTAG
502590 TAAGTAATNN
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (27 bp):
TACTTAAATTTTAGATATAAGTAAACT
Found at i:504678 original size:19 final size:19
Alignment explanation
Indices: 504654--504695 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
504644 GGTCGGGTTT
*
504654 GGGGAGCTGTTAGGGATTA
1 GGGGAGATGTTAGGGATTA
* *
504673 GGGGAGATTTTAGGGATTT
1 GGGGAGATGTTAGGGATTA
504692 GGGG
1 GGGG
504696 GGAGAAAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.02, G:0.50, T:0.29
Consensus pattern (19 bp):
GGGGAGATGTTAGGGATTA
Found at i:505275 original size:74 final size:74
Alignment explanation
Indices: 505197--505425 Score: 209
Period size: 74 Copynumber: 3.1 Consensus size: 74
505187 TCAAGCTTGT
505197 GGCGTTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATA
1 GGCGTTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATA
505262 CAAATTTGC
66 CAAATTTGC
*** * * *** * ***
505271 GGCGTTT-CATGTAAAGCGCCACTAA-A-TATAAGATC-AAACGATGTCGTTTC-CCCAACATTG
1 GGCGTTTCCAAACAAA-CGCCACTAATACCAT-TGA-CAAAACGACAACATTTCGATAAACA-T-
* ** *
505331 AACT-CAAGCTTGT
61 AAATACAAATTTGC
*
505344 GGCGTTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTTGATAAACATAAATA
1 GGCGTTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATA
*
505409 CAATTTTGC
66 CAAATTTGC
505418 GGCGTTTC
1 GGCGTTTC
505426 ATGTAAAGCA
Statistics
Matches: 111, Mismatches: 33, Indels: 22
0.67 0.20 0.13
Matches are distributed among these distances:
72 6 0.05
73 46 0.41
74 53 0.48
75 6 0.05
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.25
Consensus pattern (74 bp):
GGCGTTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATA
CAAATTTGC
Found at i:505291 original size:147 final size:147
Alignment explanation
Indices: 505136--505515 Score: 697
Period size: 147 Copynumber: 2.6 Consensus size: 147
505126 CATTTTAAGC
*
505136 AAAGCGCCACTAAATATAAGATCAAACGATGTCATTTCCCCAACATTTAACTCAAGCTTGTGGCG
1 AAAGCGCCACTAAATATAAGATCAAACGATGTCGTTTCCCCAACATTTAACTCAAGCTTGTGGCG
505201 TTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATACAAA
66 TTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATACAAA
505266 TTTGCGGCGTTTCATGT
131 TTTGCGGCGTTTCATGT
*
505283 AAAGCGCCACTAAATATAAGATCAAACGATGTCGTTTCCCCAACATTGAACTCAAGCTTGTGGCG
1 AAAGCGCCACTAAATATAAGATCAAACGATGTCGTTTCCCCAACATTTAACTCAAGCTTGTGGCG
* *
505348 TTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTTGATAAACATAAATACAAT
66 TTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATACAAA
505413 TTTGCGGCGTTTCATGT
131 TTTGCGGCGTTTCATGT
* * *
505430 AAAGCACCACTAAATATAAGATCAAACAATGTCGTTTCCCCAACATTTAACTCAAGCTTGTGGCA
1 AAAGCGCCACTAAATATAAGATCAAACGATGTCGTTTCCCCAACATTTAACTCAAGCTTGTGGCG
505495 TTTCCAAACAAACGCCACTAA
66 TTTCCAAACAAACGCCACTAA
505516 AATAAAACAT
Statistics
Matches: 225, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 225 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (147 bp):
AAAGCGCCACTAAATATAAGATCAAACGATGTCGTTTCCCCAACATTTAACTCAAGCTTGTGGCG
TTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATACAAA
TTTGCGGCGTTTCATGT
Found at i:506765 original size:72 final size:74
Alignment explanation
Indices: 506609--506785 Score: 175
Period size: 73 Copynumber: 2.4 Consensus size: 74
506599 AAATAATTAT
* * * *
506609 TTTGCGGCGCTTATCAATAAATGCCGCTAAATCACCCAAATACTAAGTAAAACGATCGCATTGGG
1 TTTGCGGCGCTTATCAAGAAACGCCGCTAAAACACCCAAATACTAAGTAAAACGATCGCATTCGG
506674 CTTATGTTA
66 CTTATGTTA
* * * * * * *
506683 TTGGCAGCGCTTATCCA-AAACGCCGCTAAAAC-CCCGAATACTCAG-AGAACGAT-GTCGTTCG
1 TTTGCGGCGCTTATCAAGAAACGCCGCTAAAACACCCAAATACTAAGTAAAACGATCG-CATTCG
*
506744 GCTTATATTTA
65 GCTTAT-GTTA
*
506755 TTTGCGGCGCTT-TCGTAGAAACGCCGCTAAA
1 TTTGCGGCGCTTATC-AAGAAACGCCGCTAAA
506786 GTACTGAACA
Statistics
Matches: 85, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
70 1 0.01
71 19 0.22
72 25 0.29
73 26 0.31
74 14 0.16
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (74 bp):
TTTGCGGCGCTTATCAAGAAACGCCGCTAAAACACCCAAATACTAAGTAAAACGATCGCATTCGG
CTTATGTTA
Found at i:515805 original size:20 final size:19
Alignment explanation
Indices: 515779--515817 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
515769 ATTGCAAGCC
515779 TAAAAAAATCTAAAGATGG
1 TAAAAAAATCTAAAGATGG
515798 TAAAAAAATCTAAAGATGG
1 TAAAAAAATCTAAAGATGG
515817 T
1 T
515818 GACAATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.23
Consensus pattern (19 bp):
TAAAAAAATCTAAAGATGG
Found at i:517563 original size:32 final size:32
Alignment explanation
Indices: 517509--517584 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
517499 CATTATAAAT
* * *
517509 TTATAAATTCATTACTTGAATTTAATAACTTA
1 TTATTAATTAATTAATTGAATTTAATAACTTA
* *
517541 TTATTAATTAATTAATTTAATTTGATAACTTA
1 TTATTAATTAATTAATTGAATTTAATAACTTA
*
517573 -TATTGATTAATT
1 TTATTAATTAATT
517585 GAACTTGTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 11 0.29
32 27 0.71
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.51
Consensus pattern (32 bp):
TTATTAATTAATTAATTGAATTTAATAACTTA
Found at i:520947 original size:42 final size:36
Alignment explanation
Indices: 520899--520982 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 36
520889 TTTTTTCATT
520899 ATTTTTCCTTTTTCTCTCATTTTCATTTTGACCTTGATTTTG
1 ATTTTTCCTTTTTCT-TC-TTTTCATTTT----TTGATTTTG
* *
520941 ATTTTTCTTTTTTCTTCTTTTTATTTTTTGATTTTG
1 ATTTTTCCTTTTTCTTCTTTTCATTTTTTGATTTTG
520977 ATTTTT
1 ATTTTT
520983 GATTTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
36 15 0.38
40 9 0.22
41 2 0.05
42 14 0.35
ACGTcount: A:0.11, C:0.13, G:0.06, T:0.70
Consensus pattern (36 bp):
ATTTTTCCTTTTTCTTCTTTTCATTTTTTGATTTTG
Found at i:520970 original size:30 final size:30
Alignment explanation
Indices: 520936--520999 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
520926 TTGACCTTGA
** **
520936 TTTTGATTTTTCTTTTTTCTTCTTTTTATT
1 TTTTGATTTTGATTTTTGATTCTTTTTATT
*
520966 TTTTGATTTTGATTTTTGATTTTTTTTATT
1 TTTTGATTTTGATTTTTGATTCTTTTTATT
520996 TTTT
1 TTTT
521000 TTGGGCTCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.09, C:0.05, G:0.06, T:0.80
Consensus pattern (30 bp):
TTTTGATTTTGATTTTTGATTCTTTTTATT
Found at i:529009 original size:24 final size:23
Alignment explanation
Indices: 528977--529023 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
528967 GTGCAATCTT
528977 AGATATGATATATGCAATCTTAGA
1 AGATATGAT-TATGCAATCTTAGA
* * *
529001 AGATGTGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
529024 GATTTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:529504 original size:10 final size:10
Alignment explanation
Indices: 529485--529516 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
529475 ATCATTATCA
*
529485 TTATTATTAT
1 TTATTTTTAT
529495 TTATTTTTAT
1 TTATTTTTAT
529505 TTATTTTTAT
1 TTATTTTTAT
529515 TT
1 TT
529517 TATATTCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
TTATTTTTAT
Found at i:529522 original size:17 final size:17
Alignment explanation
Indices: 529488--529522 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
529478 ATTATCATTA
529488 TTATTATTTATTTTTAT
1 TTATTATTTATTTTTAT
529505 TTATT-TTTATTTTATAT
1 TTATTATTTATTTT-TAT
529522 T
1 T
529523 CATGCGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATTATTTATTTTTAT
Found at i:533604 original size:27 final size:24
Alignment explanation
Indices: 533548--533608 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
533538 TTTTAAAATT
533548 AATATTATTTTAATGATCAAGCTC
1 AATATTATTTTAATGATCAAGCTC
533572 AATATTATTTTAATGATCAAGCTC
1 AATATTATTTTAATGATCAAGCTC
*
533596 AACATTATTTTAA
1 AATATTATTTTAA
533609 ATTTATTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (24 bp):
AATATTATTTTAATGATCAAGCTC
Found at i:533765 original size:18 final size:19
Alignment explanation
Indices: 533719--533765 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
533709 TTATATATTA
533719 ATATTTTAATTTCCATATAT
1 ATATTTT-ATTTCCATATAT
* *
533739 ATATATTATTT-CATATGT
1 ATATTTTATTTCCATATAT
*
533757 TTATTTTAT
1 ATATTTTAT
533766 GTAAATTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 13 0.57
19 4 0.17
20 6 0.26
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (19 bp):
ATATTTTATTTCCATATAT
Found at i:544585 original size:12 final size:12
Alignment explanation
Indices: 544568--544593 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
544558 GAAAATAGAC
544568 TTTTAGCGGCAT
1 TTTTAGCGGCAT
544580 TTTTAGCGGCAT
1 TTTTAGCGGCAT
544592 TT
1 TT
544594 AGACCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCAT
Found at i:544901 original size:114 final size:114
Alignment explanation
Indices: 544700--545191 Score: 553
Period size: 113 Copynumber: 4.3 Consensus size: 114
544690 CAAAAGATCA
* * * * * *
544700 GCATTAGCAGTGTTTATG-AGAGAAACGCCGCAATAGTTCAAGCATTAGCGGCGCTTTTCCAAAA
1 GCATTAGCGGTGCTTATGCA-A-AAACGCCGCTATAGGTCGAGCATTAGCGGCGCTTTTCTAAAA
* *
544764 ACGCCG-TAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCCTAGTG
64 ACGCCGCAAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTAGTG
* * * *
544814 GCATTAGTGGTGCTTATGCAAAAACACCGTTATAGGTCGAGCATTAGCGGCGCTTTTCTAAAAAT
1 GCATTAGCGGTGCTTATGCAAAAACGCCGCTATAGGTCGAGCATTAGCGGCGCTTTTCTAAAAAC
* *
544879 GCCGCAAAAAATGTTAATCAAAATGCATTGTTCTATCTTGAGCTTAGTG
66 GCCGCAAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTAGTG
* * * * * * *
544928 GAATTAGCGACT-TTTATGC-AAAATGCCGCTATAGGTCAAGAATTAGCGGCGGTTTTCTAAAAA
1 GCATTAGCG-GTGCTTATGCAAAAACGCCGCTATAGGTCGAGCATTAGCGGCGCTTTTCTAAAAA
* * * * *
544991 TGCCGCAAAAAATGTTAATCAAAGCACATTGTTCTATCTTGAGCTTAATG
65 CGCCGCAAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTAGTG
* * *
545041 GCATTAGCGGTGGTGCTTATGCAAAAACGCCACTATAGATCGAG-ATTTAGCGGCGCTTTTATAA
1 GCATTAGC---GGTGCTTATGCAAAAACGCCGCTATAGGTCGAGCA-TTAGCGGCGCTTTTCTAA
** * *
545105 AAACATCGCAAAAAATGTTGATCAAAACGCACCGTTCTATCTTGAGCTTAGTG
62 AAACGCCGCAAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTAGTG
* * * *
545158 GTATTAGCGGCGCTTATGCAAAAGCGCTGCTATA
1 GCATTAGCGGTGCTTATGCAAAAACGCCGCTATA
545192 TATATGTCGA
Statistics
Matches: 318, Mismatches: 51, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
113 132 0.42
114 91 0.29
115 3 0.01
116 8 0.03
117 84 0.26
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (114 bp):
GCATTAGCGGTGCTTATGCAAAAACGCCGCTATAGGTCGAGCATTAGCGGCGCTTTTCTAAAAAC
GCCGCAAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTAGTG
Found at i:545177 original size:230 final size:226
Alignment explanation
Indices: 544726--545180 Score: 606
Period size: 230 Copynumber: 2.0 Consensus size: 226
544716 TGAGAGAAAC
* * * *
544726 GCCGCAATAGTTCAAGCATTAGCGGCGCTTTTCCAAAAACGCCGTAAAAATGTTAATCAAAACGC
1 GCCGCAATAGGTCAAGAATTAGCGGCGCTTTTCCAAAAACGCCGAAAAAATGTTAATCAAAACAC
* ** *
544791 ATCGTTCTATCTTGAGCCTAGTGGCATTAGTGGTGCTTATGCAAAAACACCGTTATAGGTCGAGC
66 ATCGTTCTATCTTGAGCCTAATGGCATTAGTGGTGCTTATGCAAAAACACCACTATAGATCGAGC
* ** * **
544856 ATTAGCGGCGCTTTTCTAAAAATGCCGCAAAAAATGTTAATCAAAATGCATTGTTCTATCTTGAG
131 ATTAGCGGCGCTTTTATAAAAACACCGCAAAAAATGTTAATCAAAACGCACCGTTCTATCTTGAG
**
544921 CTTAGTGGAATTAGCGACTTTTATGCAAAAT
196 CTTAGTGGAATTAGCGACGCTTATGCAAAAT
* * * * *
544952 GCCGCTATAGGTCAAGAATTAGCGGCGGTTTTCTAAAAATGCCGCAAAAAATGTTAATCAAAGCA
1 GCCGCAATAGGTCAAGAATTAGCGGCGCTTTTCCAAAAACGCCG-AAAAAATGTTAATCAAAACA
* * *
545017 CATTGTTCTATCTTGAGCTTAATGGCATTAGCGGTGGTGCTTATGCAAAAACGCCACTATAGATC
65 CATCGTTCTATCTTGAGCCTAATGGCATTA---GTGGTGCTTATGCAAAAACACCACTATAGATC
* *
545082 GAG-ATTTAGCGGCGCTTTTATAAAAACATCGCAAAAAATGTTGATCAAAACGCACCGTTCTATC
127 GAGCA-TTAGCGGCGCTTTTATAAAAACACCGCAAAAAATGTTAATCAAAACGCACCGTTCTATC
* *
545146 TTGAGCTTAGTGGTATTAGCGGCGCTTATGCAAAA
191 TTGAGCTTAGTGGAATTAGCGACGCTTATGCAAAA
545181 GCGCTGCTAT
Statistics
Matches: 196, Mismatches: 28, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
226 38 0.19
227 44 0.22
229 1 0.01
230 113 0.58
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (226 bp):
GCCGCAATAGGTCAAGAATTAGCGGCGCTTTTCCAAAAACGCCGAAAAAATGTTAATCAAAACAC
ATCGTTCTATCTTGAGCCTAATGGCATTAGTGGTGCTTATGCAAAAACACCACTATAGATCGAGC
ATTAGCGGCGCTTTTATAAAAACACCGCAAAAAATGTTAATCAAAACGCACCGTTCTATCTTGAG
CTTAGTGGAATTAGCGACGCTTATGCAAAAT
Found at i:545625 original size:14 final size:14
Alignment explanation
Indices: 545590--545675 Score: 68
Period size: 14 Copynumber: 6.1 Consensus size: 14
545580 TTCCCAAAGA
*
545590 TATGGTTTA-GGAT
1 TATGGTTTAGGGTT
*
545603 TATGATTTAGGGTT
1 TATGGTTTAGGGTT
*
545617 TATGGTTTAGAGTT
1 TATGGTTTAGGGTT
*
545631 TAGGGTTT-GGGTTT
1 TATGGTTTAGGG-TT
** * *
545645 TATAATTTAAGATT
1 TATGGTTTAGGGTT
545659 TATGGTTTAAGGGTT
1 TATGGTTT-AGGGTT
545674 TA
1 TA
545676 GAGAATATTG
Statistics
Matches: 54, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
13 10 0.19
14 37 0.69
15 7 0.13
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (14 bp):
TATGGTTTAGGGTT
Found at i:545642 original size:27 final size:27
Alignment explanation
Indices: 545590--545644 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
545580 TTCCCAAAGA
*
545590 TATGGTTTAGGATTATGATTTAGGGTT
1 TATGGTTTAGGATTAGGATTTAGGGTT
* *
545617 TATGGTTTAGAGTTTAGGGTTT-GGGTT
1 TATGGTTTAG-GATTAGGATTTAGGGTT
545644 T
1 T
545645 TATAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (27 bp):
TATGGTTTAGGATTAGGATTTAGGGTT
Found at i:545653 original size:21 final size:21
Alignment explanation
Indices: 545593--545667 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
545583 CCAAAGATAT
* *
545593 GGTTTA-GGATTATGATTTAG
1 GGTTTAGGGTTTATAATTTAG
* * *
545613 GGTTTATGGTTTAGAGTTTAG
1 GGTTTAGGGTTTATAATTTAG
*
545634 GGTTT-GGGTTTTATAATTTAA
1 GGTTTAGGG-TTTATAATTTAG
* *
545655 GATTTATGGTTTA
1 GGTTTAGGGTTTA
545668 AGGGTTTAGA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
20 8 0.19
21 32 0.76
22 2 0.05
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (21 bp):
GGTTTAGGGTTTATAATTTAG
Found at i:545851 original size:15 final size:15
Alignment explanation
Indices: 545831--545860 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
545821 GATTATTTAG
*
545831 AATATAAATCTAAAT
1 AATATAAATATAAAT
545846 AATATAAATATAAAT
1 AATATAAATATAAAT
545861 TATTATTTAA
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:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
AATATAAATATAAAT
Found at i:546063 original size:16 final size:18
Alignment explanation
Indices: 546032--546066 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
546022 ATATATTGCA
546032 TACATAAATATTTTAAAT
1 TACATAAATATTTTAAAT
546050 TACA-AAAT-TTTTAAAT
1 TACATAAATATTTTAAAT
546066 T
1 T
546067 TTGTTGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 4 0.24
18 4 0.24
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
TACATAAATATTTTAAAT
Found at i:546665 original size:17 final size:19
Alignment explanation
Indices: 546644--546688 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
546634 AAATTTTCCC
* *
546644 CATTTCCCCCAATTCC-AA
1 CATTTCCCCAAATCCCTAA
546662 -ATTTCCCCAAATCCCTAA
1 CATTTCCCCAAATCCCTAA
546680 CATTTCCCC
1 CATTTCCCC
546689 TAACCCTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 13 0.57
18 2 0.09
19 8 0.35
ACGTcount: A:0.27, C:0.44, G:0.00, T:0.29
Consensus pattern (19 bp):
CATTTCCCCAAATCCCTAA
Found at i:547225 original size:153 final size:154
Alignment explanation
Indices: 547021--547328 Score: 609
Period size: 153 Copynumber: 2.0 Consensus size: 154
547011 TCCTGTTCAT
547021 TGATCCTCTACTTTTAACCTTTTTTTTTTACAGAATATAATATACCTAAATATGAAGTTCTTTTT
1 TGATCCTCTACTTTTAACCTTTTTTTTTTACAGAATATAATATACCTAAATATGAAGTTCTTTTT
547086 TTGTTGGTAATTACAAATTTTTTATCAAATCTGATTATTTTATTGAGAAATTATATATCTTTTGA
66 TTGTTGGTAATTACAAATTTTTTATCAAATCTGATTATTTTATTGAGAAATTATATATCTTTTGA
547151 ATTGTTTTTGTTGTTGTATAAATA
131 ATTGTTTTTGTTGTTGTATAAATA
547175 TGATCCTCTAC-TTTAACCTTTTTTTTTTACAGAATATAATATACCTAAATATGAAGTTCTTTTT
1 TGATCCTCTACTTTTAACCTTTTTTTTTTACAGAATATAATATACCTAAATATGAAGTTCTTTTT
547239 TTGTTGGTAATTACAAATTTTTTATCAAATCTGATTATTTTATTGAGAAATTATATATCTTTTGA
66 TTGTTGGTAATTACAAATTTTTTATCAAATCTGATTATTTTATTGAGAAATTATATATCTTTTGA
547304 ATTGTTTTTGTTGTTGTATAAATA
131 ATTGTTTTTGTTGTTGTATAAATA
547328 T
1 T
547329 TATTATTTTG
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
153 143 0.93
154 11 0.07
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.51
Consensus pattern (154 bp):
TGATCCTCTACTTTTAACCTTTTTTTTTTACAGAATATAATATACCTAAATATGAAGTTCTTTTT
TTGTTGGTAATTACAAATTTTTTATCAAATCTGATTATTTTATTGAGAAATTATATATCTTTTGA
ATTGTTTTTGTTGTTGTATAAATA
Found at i:548111 original size:27 final size:26
Alignment explanation
Indices: 548081--548132 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
548071 ATTTGAGCTT
*
548081 GTTA-ATTTGCAATAATTTGTATTTAAA
1 GTTATATTTGAAAT-ATTT-TATTTAAA
*
548108 GTTATATTTTAAATATTTTATTTAA
1 GTTATATTTGAAATATTTTATTTAA
548133 TTTTAATGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 7 0.32
27 8 0.36
28 7 0.32
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.54
Consensus pattern (26 bp):
GTTATATTTGAAATATTTTATTTAAA
Found at i:548231 original size:9 final size:9
Alignment explanation
Indices: 548213--548292 Score: 79
Period size: 9 Copynumber: 8.6 Consensus size: 9
548203 GTTCAAATTT
548213 CATAACTTA
1 CATAACTTA
*
548222 CATAAATTA
1 CATAACTTA
548231 CATAACTTA
1 CATAACTTA
*
548240 CATAATTTAAA
1 CATAACTT--A
* * *
548251 GATCAAATTT
1 CAT-AACTTA
548261 CATAACTTA
1 CATAACTTA
*
548270 CATAATTTA
1 CATAACTTA
548279 CATAACTTA
1 CATAACTTA
548288 CATAA
1 CATAA
548293 TTTAGAGATC
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
9 48 0.84
10 2 0.04
11 3 0.05
12 4 0.07
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:548247 original size:48 final size:48
Alignment explanation
Indices: 548190--548315 Score: 225
Period size: 48 Copynumber: 2.6 Consensus size: 48
548180 TCAAATTTAC
*
548190 TACATAATTTAAAGTTCAAATTTCATAACTTACATAAATTACATAACT
1 TACATAATTTAAAGATCAAATTTCATAACTTACATAAATTACATAACT
*
548238 TACATAATTTAAAGATCAAATTTCATAACTTACATAATTTACATAACT
1 TACATAATTTAAAGATCAAATTTCATAACTTACATAAATTACATAACT
*
548286 TACATAATTTAGAGATCAAATTTCATAACT
1 TACATAATTTAAAGATCAAATTTCATAACT
548316 ATTTATGAAC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 75 1.00
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.37
Consensus pattern (48 bp):
TACATAATTTAAAGATCAAATTTCATAACTTACATAAATTACATAACT
Found at i:548293 original size:18 final size:18
Alignment explanation
Indices: 548208--548296 Score: 104
Period size: 18 Copynumber: 5.3 Consensus size: 18
548198 TTAAAGTTCA
548208 AATTT-CATAACTTACAT
1 AATTTACATAACTTACAT
*
548225 AAATTACATAACTTACAT
1 AATTTACATAACTTACAT
548243 AATTTA-A-AGA--T-CA-
1 AATTTACATA-ACTTACAT
548256 AATTT-CATAACTTACAT
1 AATTTACATAACTTACAT
548273 AATTTACATAACTTACAT
1 AATTTACATAACTTACAT
548291 AATTTA
1 AATTTA
548297 GAGATCAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 17
0.76 0.03 0.21
Matches are distributed among these distances:
13 7 0.11
14 3 0.05
15 2 0.03
16 3 0.05
17 11 0.18
18 35 0.57
ACGTcount: A:0.46, C:0.15, G:0.01, T:0.38
Consensus pattern (18 bp):
AATTTACATAACTTACAT
Found at i:548348 original size:17 final size:19
Alignment explanation
Indices: 548326--548365 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
548316 ATTTATGAAC
548326 GAAGATA-TTACG-ATTAT
1 GAAGATATTTACGAATTAT
*
548343 GAAGATATTTATGAATTAT
1 GAAGATATTTACGAATTAT
548362 GAAG
1 GAAG
548366 TAGTAAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 4 0.20
19 9 0.45
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (19 bp):
GAAGATATTTACGAATTAT
Found at i:549665 original size:13 final size:14
Alignment explanation
Indices: 549649--549677 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
549639 TTGTAAATAT
549649 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
549662 TTATAATGGTTTAA
1 TTATAATGGTTTAA
549676 TT
1 TT
549678 CTTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:550439 original size:43 final size:43
Alignment explanation
Indices: 550392--550624 Score: 116
Period size: 43 Copynumber: 5.4 Consensus size: 43
550382 GGCGTTTGTA
*
550392 AAAAAAAGCGCCGCTAAAGACCACGAACTATAGCGGCATTTTC
1 AAAAAAAGCGCCGCTAAAGACCAAGAACTATAGCGGCATTTTC
* * * * **
550435 AAAAAATGCGTCGC-AAAGTGCCATG-ACTTATAGCGGCGCTTT-
1 AAAAAAAGCGCCGCTAAAG-ACCAAGAAC-TATAGCGGCATTTTC
* * * ** * * *
550477 ATAAAAAAGTGCTGCTAAAGATCTTGAATTTTCGCGGCATTTTC
1 A-AAAAAAGCGCCGCTAAAGACCAAGAACTATAGCGGCATTTTC
* * * ** *
550521 TACAAAAGCGCCGCTAAAG-GCAATTACTTATAGCGGCGTTTT-
1 AAAAAAAGCGCCGCTAAAGACCAAGAAC-TATAGCGGCATTTTC
** * * * *
550563 ATAAATTAGCGCAGCTAAAGGCCAAGACCTTTAGCGGCATTTTC
1 A-AAAAAAGCGCCGCTAAAGACCAAGAACTATAGCGGCATTTTC
* * *
550607 TATAAAAGCGCCACTAAA
1 AAAAAAAGCGCCGCTAAA
550625 AGTCATGATC
Statistics
Matches: 132, Mismatches: 48, Indels: 20
0.66 0.24 0.10
Matches are distributed among these distances:
42 9 0.07
43 114 0.86
44 9 0.07
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (43 bp):
AAAAAAAGCGCCGCTAAAGACCAAGAACTATAGCGGCATTTTC
Found at i:550494 original size:86 final size:86
Alignment explanation
Indices: 550393--550624 Score: 243
Period size: 86 Copynumber: 2.7 Consensus size: 86
550383 GCGTTTGTAA
* * * *
550393 AAAAAAGCGCCGCTAAAGACCACGAACTATAGCGGCATTTTC-AAAAAATGCGTCGC-AAAGTGC
1 AAAAAAGCGCAGCTAAAGACCAAGAACTTTAGCGGCATTTTCTAAAAAA-GCGCCGCTAAAG-GC
*
550456 CATGACTTATAGCGGCGCTTTAT
64 AATGACTTATAGCGGCGCTTTAT
* * * ** * * *
550479 AAAAAAGTGCTGCTAAAGATCTTGAATTTTCGCGGCATTTTCTACAAAAGCGCCGCTAAAGGCAA
1 AAAAAAGCGCAGCTAAAGACCAAGAACTTTAGCGGCATTTTCTAAAAAAGCGCCGCTAAAGGCAA
* *
550544 TTACTTATAGCGGCGTTTTAT
66 TGACTTATAGCGGCGCTTTAT
** * * * *
550565 AAATTAGCGCAGCTAAAGGCCAAGACCTTTAGCGGCATTTTCTATAAAAGCGCCACTAAA
1 AAAAAAGCGCAGCTAAAGACCAAGAACTTTAGCGGCATTTTCTAAAAAAGCGCCGCTAAA
550625 AGTCATGATC
Statistics
Matches: 118, Mismatches: 26, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
86 109 0.92
87 9 0.08
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (86 bp):
AAAAAAGCGCAGCTAAAGACCAAGAACTTTAGCGGCATTTTCTAAAAAAGCGCCGCTAAAGGCAA
TGACTTATAGCGGCGCTTTAT
Found at i:551171 original size:32 final size:32
Alignment explanation
Indices: 551123--551188 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
551113 AATAAAATAT
*
551123 TTAAAATATATATTTTTA-TAATTAAATTTAAA
1 TTAAAAAATATATTTTTATTAATTAAA-TTAAA
* *
551155 TTAAAAAATATTTTTTTATTATTTAAATTAAA
1 TTAAAAAATATATTTTTATTAATTAAATTAAA
551187 TT
1 TT
551189 TGAATCTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 23 0.77
33 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TTAAAAAATATATTTTTATTAATTAAATTAAA
Found at i:552876 original size:28 final size:28
Alignment explanation
Indices: 552799--552880 Score: 94
Period size: 28 Copynumber: 3.0 Consensus size: 28
552789 CATGGGATTC
* * *
552799 ATTTGCTCACACAAGTTGTAATATTCAA
1 ATTTGCTCACACAAGCTGTGATATTTAA
* * * *
552827 ATTTTCTCTCA-GAGCTGTGATATTTGA
1 ATTTGCTCACACAAGCTGTGATATTTAA
552854 ATTTGCTCACACAAGCTGTGATATTTA
1 ATTTGCTCACACAAGCTGTGATATTTA
552881 GGCCACTCAC
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 20 0.48
28 22 0.52
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (28 bp):
ATTTGCTCACACAAGCTGTGATATTTAA
Found at i:554094 original size:6 final size:6
Alignment explanation
Indices: 554083--554108 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
554073 TTATTTTCAT
554083 ATTTTA ATTTTA ATTTTA ATTTTA AT
1 ATTTTA ATTTTA ATTTTA ATTTTA AT
554109 ATAATTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATTTTA
Found at i:577272 original size:12 final size:12
Alignment explanation
Indices: 577255--577281 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
577245 TTCATGCACT
577255 TTGTAACACCCA
1 TTGTAACACCCA
577267 TTGTAACACCCA
1 TTGTAACACCCA
577279 TTG
1 TTG
577282 CTCGATCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.30
Consensus pattern (12 bp):
TTGTAACACCCA
Found at i:590816 original size:28 final size:28
Alignment explanation
Indices: 590736--590818 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 28
590726 CATGGGATTG
* * * *
590736 ATTTGCTCACACAAGTTTTAATATTCAA
1 ATTTGCTCACACAAGCTATGATATTTAA
* * * *
590764 ATTTTCTCACACGAGCTATGGTATTTGA
1 ATTTGCTCACACAAGCTATGATATTTAA
*
590792 ATTTGCTCACACAAGCTGTGATATTTA
1 ATTTGCTCACACAAGCTATGATATTTA
590819 GGCTGCTCAC
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (28 bp):
ATTTGCTCACACAAGCTATGATATTTAA
Found at i:592641 original size:4 final size:4
Alignment explanation
Indices: 592632--592666 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
592622 CTAACATTTT
592632 CATA CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CAT
592667 TTCATTTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:595379 original size:31 final size:30
Alignment explanation
Indices: 595334--595396 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
595324 AATAAAATAT
*
595334 TTAAAATATATTTTTA-TAATTAAATTTAAA
1 TTAAAAAATATTTTTATTAATTAAA-TTAAA
*
595364 TTAAAAAATACTTTTTATTATTTAAATTAAA
1 TTAAAAAATA-TTTTTATTAATTAAATTAAA
595395 TT
1 TT
595397 TGAATTTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 9 0.31
31 13 0.45
32 7 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (30 bp):
TTAAAAAATATTTTTATTAATTAAATTAAA
Found at i:608478 original size:15 final size:16
Alignment explanation
Indices: 608448--608480 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
608438 TTTACCCATA
608448 ATAATATTAAAAAATT
1 ATAATATTAAAAAATT
*
608464 ATAATATT-GAAAATT
1 ATAATATTAAAAAATT
608479 AT
1 AT
608481 TACATTGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
ATAATATTAAAAAATT
Found at i:611047 original size:14 final size:14
Alignment explanation
Indices: 611018--611063 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
611008 ATATTAATTT
*
611018 TATATAGGTAACACA
1 TATATA-GTAAAACA
611033 TATATAGTAAAACA
1 TATATAGTAAAACA
611047 TA-ATAGTAATAACA
1 TATATAGTAA-AACA
611061 TAT
1 TAT
611064 GTATACTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 7 0.25
14 15 0.54
15 6 0.21
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (14 bp):
TATATAGTAAAACA
Found at i:615874 original size:23 final size:22
Alignment explanation
Indices: 615831--615888 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
615821 AAAGGGTATC
* *
615831 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
615852 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
615875 TGCATATCATATCT
1 TACAAATCATATCT
615889 AAGATTCCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:622578 original size:15 final size:15
Alignment explanation
Indices: 622558--622587 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
622548 TAATTACCCA
622558 CGCTTCATAATTCAG
1 CGCTTCATAATTCAG
622573 CGCTTCATAATTCAG
1 CGCTTCATAATTCAG
622588 TCATTTTAGT
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:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (15 bp):
CGCTTCATAATTCAG
Found at i:622909 original size:21 final size:21
Alignment explanation
Indices: 622879--622918 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
622869 TTAATATCAA
622879 TATTAATATAAAATTTGAATT
1 TATTAATATAAAATTTGAATT
* * *
622900 TATTATTATATATTTTGAA
1 TATTAATATAAAATTTGAA
622919 AATATTTATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TATTAATATAAAATTTGAATT
Found at i:622924 original size:21 final size:21
Alignment explanation
Indices: 622877--622924 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
622867 ATTTAATATC
622877 AATATTAATATAAAATTTGAA
1 AATATTAATATAAAATTTGAA
** * * *
622898 TTTATTATTATATATTTTGAA
1 AATATTAATATAAAATTTGAA
622919 AATATT
1 AATATT
622925 TATGTTTTTT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (21 bp):
AATATTAATATAAAATTTGAA
Found at i:645745 original size:17 final size:18
Alignment explanation
Indices: 645725--645758 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
645715 GGATTGTGTT
*
645725 AATA-GAAATTTAAAAAA
1 AATACGAAAATTAAAAAA
645742 AATACGAAAATTAAAAA
1 AATACGAAAATTAAAAA
645759 TGATGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (18 bp):
AATACGAAAATTAAAAAA
Found at i:647802 original size:42 final size:40
Alignment explanation
Indices: 647701--647857 Score: 233
Period size: 41 Copynumber: 3.8 Consensus size: 40
647691 CTAAAATGCT
* *
647701 TTTAGCGGCGCTTAAAAAAACGCCGCTAAAGATAATGTTC
1 TTTAGCGGCGCTTAAAAAAACGCCCCTAAAGATCATGTTC
*
647741 TTTAGCGGCGCTTAGAAAAAAAGCCCCTAAAGATCATGTTC
1 TTTAGCGGCGCTTA-AAAAAACGCCCCTAAAGATCATGTTC
647782 TTTAGCGGCGCTTTAAAAAAACGCCCCTAAAGATCATGTTC
1 TTTAGCGGCGC-TTAAAAAAACGCCCCTAAAGATCATGTTC
* *
647823 TTTAGCAGCGCTTAGAAAAAAACGCCGCTAAAGAT
1 TTTAGCGGCGCTT--AAAAAAACGCCCCTAAAGAT
647858 TATTAAAAAA
Statistics
Matches: 107, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
40 16 0.15
41 69 0.64
42 22 0.21
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (40 bp):
TTTAGCGGCGCTTAAAAAAACGCCCCTAAAGATCATGTTC
Found at i:647837 original size:82 final size:82
Alignment explanation
Indices: 647701--647857 Score: 262
Period size: 82 Copynumber: 1.9 Consensus size: 82
647691 CTAAAATGCT
* *
647701 TTTAGCGGCGCTTAAAAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTAGAAAAAAA-GC
1 TTTAGCGGCGCTTAAAAAAACGCCCCTAAAGATAATGTTCTTTAGCAGCGCTTAGAAAAAAACGC
647765 CCCTAAAGATCATGTTC
66 CCCTAAAGATCATGTTC
*
647782 TTTAGCGGCGCTTTAAAAAAACGCCCCTAAAGATCATGTTCTTTAGCAGCGCTTAGAAAAAAACG
1 TTTAGCGGCGC-TTAAAAAAACGCCCCTAAAGATAATGTTCTTTAGCAGCGCTTAGAAAAAAACG
*
647847 CCGCTAAAGAT
65 CCCCTAAAGAT
647858 TATTAAAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
81 11 0.16
82 48 0.69
83 11 0.16
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (82 bp):
TTTAGCGGCGCTTAAAAAAACGCCCCTAAAGATAATGTTCTTTAGCAGCGCTTAGAAAAAAACGC
CCCTAAAGATCATGTTC
Found at i:649015 original size:23 final size:23
Alignment explanation
Indices: 648925--649020 Score: 70
Period size: 23 Copynumber: 4.0 Consensus size: 23
648915 CGAAGAAGTG
648925 ATCATAATTATAATAATTACATAA
1 ATCATAATTATAATAATTA-ATAA
* * * * *
648949 TTACA-ATTTATATACTAATAAACAT
1 AT-CATAATTATA-A-TAATTAATAA
* *
648974 ATAATATTTA-AATAAATTAATAA
1 ATCATAATTATAAT-AATTAATAA
648997 ATCATAATTATAATAATTAATAA
1 ATCATAATTATAATAATTAATAA
649020 A
1 A
649021 AAATAATTGC
Statistics
Matches: 54, Mismatches: 12, Indels: 13
0.68 0.15 0.16
Matches are distributed among these distances:
22 1 0.02
23 25 0.46
24 12 0.22
25 11 0.20
26 5 0.09
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (23 bp):
ATCATAATTATAATAATTAATAA
Found at i:653114 original size:3 final size:3
Alignment explanation
Indices: 653106--653140 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
653096 AAATTAGTTA
653106 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
653141 AAAGGATAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:653538 original size:31 final size:31
Alignment explanation
Indices: 653445--653540 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
653435 GGCAAATTAC
*
653445 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
653476 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
653508 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
653539 AA
1 AA
653541 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:659141 original size:23 final size:23
Alignment explanation
Indices: 659051--659146 Score: 70
Period size: 23 Copynumber: 4.0 Consensus size: 23
659041 CGAAGAAGTG
659051 ATCATAATTATAATAATTACATAA
1 ATCATAATTATAATAATTA-ATAA
* * * * *
659075 TTACA-ATTTATATACTAATAAACAT
1 AT-CATAATTATA-A-TAATTAATAA
* *
659100 ATAATATTTA-AATAAATTAATAA
1 ATCATAATTATAAT-AATTAATAA
659123 ATCATAATTATAATAATTAATAA
1 ATCATAATTATAATAATTAATAA
659146 A
1 A
659147 AAATAATTGC
Statistics
Matches: 54, Mismatches: 12, Indels: 13
0.68 0.15 0.16
Matches are distributed among these distances:
22 1 0.02
23 25 0.46
24 12 0.22
25 11 0.20
26 5 0.09
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (23 bp):
ATCATAATTATAATAATTAATAA
Found at i:663240 original size:3 final size:3
Alignment explanation
Indices: 663232--663266 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
663222 AAATTAGTTA
663232 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
663267 AAAGGATAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:667793 original size:17 final size:17
Alignment explanation
Indices: 667771--667809 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
667761 GCAACTTTTT
667771 TTTTTGCGCTTTTTTGC
1 TTTTTGCGCTTTTTTGC
** *
667788 TTTTTGCTTTTTTTTTC
1 TTTTTGCGCTTTTTTGC
667805 TTTTT
1 TTTTT
667810 TTTTGCGCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.77
Consensus pattern (17 bp):
TTTTTGCGCTTTTTTGC
Found at i:667854 original size:22 final size:21
Alignment explanation
Indices: 667788--667856 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
667778 GCTTTTTTGC
*
667788 TTTTTGC-TTTTTTTTTCTTTT
1 TTTTTGCGCTTTTTTTT-TTTT
* ***
667809 TTTTTGCGCTTTTTACTCACTT
1 TTTTTGCGCTTTTT-TTTTTTT
*
667831 TTTTTGCGCTTTTTTTGTTTT
1 TTTTTGCGCTTTTTTTTTTTT
667852 TTTTT
1 TTTTT
667857 AAAGAATAAG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
21 15 0.41
22 21 0.57
23 1 0.03
ACGTcount: A:0.03, C:0.13, G:0.09, T:0.75
Consensus pattern (21 bp):
TTTTTGCGCTTTTTTTTTTTT
Found at i:668890 original size:17 final size:18
Alignment explanation
Indices: 668856--668896 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
668846 TTATCGAGCA
668856 AAAAGAAAAGCAAAAAGAG
1 AAAA-AAAAGCAAAAAGAG
*
668875 AAAAAAAAG-AAGAAGAG
1 AAAAAAAAGCAAAAAGAG
668892 AAAAA
1 AAAAA
668897 CCTCCATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.57
18 5 0.24
19 4 0.19
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGCAAAAAGAG
Found at i:669522 original size:27 final size:27
Alignment explanation
Indices: 669457--669522 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 27
669447 TCCTCTTTTC
*
669457 CTTTATCGTTCTTCTTCTTCCCTATTGT
1 CTTTATCCTTC-TCTTCTTCCCTATTGT
* **
669485 -TTTCTTTTTCTCTTCTTCCCTTATT-T
1 CTTTATCCTTCTCTTCTTCCC-TATTGT
669511 CTTTATCCTTCT
1 CTTTATCCTTCT
669523 TGCTTTTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
26 11 0.37
27 19 0.63
ACGTcount: A:0.06, C:0.29, G:0.03, T:0.62
Consensus pattern (27 bp):
CTTTATCCTTCTCTTCTTCCCTATTGT
Found at i:673935 original size:19 final size:19
Alignment explanation
Indices: 673913--673949 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
673903 AGGGAGTTGT
*
673913 TTTTCACTTGATTTAAAAG
1 TTTTCAATTGATTTAAAAG
673932 TTTTCAATTGATTTAAAA
1 TTTTCAATTGATTTAAAA
673950 CTGTTCCATT
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:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (19 bp):
TTTTCAATTGATTTAAAAG
Found at i:677092 original size:20 final size:21
Alignment explanation
Indices: 677059--677098 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
677049 GGGGGAAAGT
677059 GGGAAGAAGT-AAAAGTTTGA
1 GGGAAGAAGTAAAAAGTTTGA
677079 GGGAA-AAGTAAAAAAGTTTG
1 GGGAAGAAGT-AAAAAGTTTG
677099 GGAGTTTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.20
Consensus pattern (21 bp):
GGGAAGAAGTAAAAAGTTTGA
Found at i:681085 original size:4 final size:4
Alignment explanation
Indices: 681078--681105 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
681068 TACATACATA
681078 CATG CATG CATG CATG CATG CATG CATG
1 CATG CATG CATG CATG CATG CATG CATG
681106 ATTATTGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (4 bp):
CATG
Found at i:682129 original size:10 final size:11
Alignment explanation
Indices: 682098--682140 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
682088 CGTGAATTAC
*
682098 AAAATATTTAT
1 AAAATATATAT
682109 AAAATATATAT
1 AAAATATATAT
*
682120 AAAAATATATTTT
1 -AAAATATA-TAT
682133 AAAATATA
1 AAAATATA
682141 AAGGATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 10 0.36
12 16 0.57
13 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAATATATAT
Found at i:682171 original size:17 final size:17
Alignment explanation
Indices: 682151--682184 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
682141 AAGGATAAAT
*
682151 AAATATGTATATATATA
1 AAATATGTACATATATA
*
682168 AAATGTGTACATATATA
1 AAATATGTACATATATA
682185 TTTAGGTACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (17 bp):
AAATATGTACATATATA
Found at i:683517 original size:116 final size:116
Alignment explanation
Indices: 683397--683628 Score: 464
Period size: 116 Copynumber: 2.0 Consensus size: 116
683387 TTTTTTGATC
683397 AGTTTCTATCTATTACAAAAGGAAAATGAAAAAAAGGCCCCCCTTTTACAAATTCAAAGTCAGTC
1 AGTTTCTATCTATTACAAAAGGAAAATGAAAAAAAGGCCCCCCTTTTACAAATTCAAAGTCAGTC
683462 CCCTTAGAACCGATTCCCCCCCAAAGTTATATTTTCTTTTTGCTTTTATAG
66 CCCTTAGAACCGATTCCCCCCCAAAGTTATATTTTCTTTTTGCTTTTATAG
683513 AGTTTCTATCTATTACAAAAGGAAAATGAAAAAAAGGCCCCCCTTTTACAAATTCAAAGTCAGTC
1 AGTTTCTATCTATTACAAAAGGAAAATGAAAAAAAGGCCCCCCTTTTACAAATTCAAAGTCAGTC
683578 CCCTTAGAACCGATTCCCCCCCAAAGTTATATTTTCTTTTTGCTTTTATAG
66 CCCTTAGAACCGATTCCCCCCCAAAGTTATATTTTCTTTTTGCTTTTATAG
683629 CAGATTGATA
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 116 1.00
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (116 bp):
AGTTTCTATCTATTACAAAAGGAAAATGAAAAAAAGGCCCCCCTTTTACAAATTCAAAGTCAGTC
CCCTTAGAACCGATTCCCCCCCAAAGTTATATTTTCTTTTTGCTTTTATAG
Found at i:684950 original size:375 final size:375
Alignment explanation
Indices: 684256--684991 Score: 1183
Period size: 375 Copynumber: 2.0 Consensus size: 375
684246 TTCGTCATTA
*
684256 TGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTATT
1 TGGCTTTAATCTTTTTAACTGCAATGTCAGAGAAACAAGATTCACCAATTTGGCTTTAATCTATT
* * * *
684321 CCACTGCATCGTTTGGGGTGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGATGTGGCT
66 CCACTGCATCGCTTGGGGCGTAAGATTCGCTGGTGTAGCTTTAATCAAGATTCAACGATGTGGCT
* * *
684386 TTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTATTCCACT
131 TGAATCTTTTTAACTGCAATGTAGGAGAAACAAGATTAACCAATTTGGCTTTAATCTATTCCACT
* *
684451 GCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGATTTGGCTTTAAT
196 GCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGACTCACCGATGTGGCTTTAAT
* *
684516 CTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTATTCCACTGC-AT
261 CTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTAGCTTCAATCTATTCCACTGCAAT
* *** * *
684580 CGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGATT
326 -GCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCAAGATTCACCGATT
684631 TGGCTTTAATCTTTTTAACTGCAATGTCAGAGAAACAAGATTCACCAATTTGGCTTTAATCTATT
1 TGGCTTTAATCTTTTTAACTGCAATGTCAGAGAAACAAGATTCACCAATTTGGCTTTAATCTATT
*
684696 CCACTGCATCGCTTGTGGCGTAAGATTCGCTGGTGTAGCTTTAATCAAGATTCAACGATGTGGCT
66 CCACTGCATCGCTTGGGGCGTAAGATTCGCTGGTGTAGCTTTAATCAAGATTCAACGATGTGGCT
684761 TGAATCTTTTTAACTGCAATGTAGGAGAAACAAGATTAACCAATTTGGCTTTAATCTATTCCACT
131 TGAATCTTTTTAACTGCAATGTAGGAGAAACAAGATTAACCAATTTGGCTTTAATCTATTCCACT
684826 GCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGACTCACCGATGTGGCTTTAAT
196 GCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGACTCACCGATGTGGCTTTAAT
* ** ** *
684891 CTTTTTAATTGCAATGTCAGG-GAAGTAAGA-TC-CGCTGTTGTAGCTTCAATCTGTTCCACTGC
261 CTTTTTAACTGCAATGTC-GGAGAAACAAGATTCAC-CAATT-TAGCTTCAATCTATTCCACTGC
684953 AATGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATC
323 AATGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATC
684992 TTCTTATTTG
Statistics
Matches: 332, Mismatches: 25, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
373 1 0.00
374 5 0.02
375 322 0.97
376 4 0.01
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (375 bp):
TGGCTTTAATCTTTTTAACTGCAATGTCAGAGAAACAAGATTCACCAATTTGGCTTTAATCTATT
CCACTGCATCGCTTGGGGCGTAAGATTCGCTGGTGTAGCTTTAATCAAGATTCAACGATGTGGCT
TGAATCTTTTTAACTGCAATGTAGGAGAAACAAGATTAACCAATTTGGCTTTAATCTATTCCACT
GCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGACTCACCGATGTGGCTTTAAT
CTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTAGCTTCAATCTATTCCACTGCAAT
GCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCAAGATTCACCGATT
Found at i:684953 original size:125 final size:125
Alignment explanation
Indices: 684256--684908 Score: 1189
Period size: 125 Copynumber: 5.2 Consensus size: 125
684246 TTCGTCATTA
684256 TGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTATT
1 TGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTATT
* *
684321 CCACTGCATCGTTTGGGGTGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGATG
66 CCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGATG
684381 TGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTATT
1 TGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTATT
*
684446 CCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGATT
66 CCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGATG
684506 TGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTATT
1 TGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTATT
*
684571 CCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGATT
66 CCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGATG
*
684631 TGGCTTTAATCTTTTTAACTGCAATGTCAGAGAAACAAGATTCACCAATTTGGCTTTAATCTATT
1 TGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTATT
* * *
684696 CCACTGCATCGCTTGTGGCGTAAGATTCGCTGGTGTAGCTTTAATCAAGATTCAACGATG
66 CCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGATG
* * *
684756 TGGCTTGAATCTTTTTAACTGCAATGTAGGAGAAACAAGATTAACCAATTTGGCTTTAATCTATT
1 TGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTATT
*
684821 CCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGACTCACCGATG
66 CCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGATG
*
684881 TGGCTTTAATCTTTTTAATTGCAATGTC
1 TGGCTTTAATCTTTTTAACTGCAATGTC
684909 AGGGAAGTAA
Statistics
Matches: 509, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 509 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (125 bp):
TGGCTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTATT
CCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGATG
Found at i:684967 original size:50 final size:50
Alignment explanation
Indices: 684900--685041 Score: 209
Period size: 50 Copynumber: 2.8 Consensus size: 50
684890 TCTTTTTAAT
684900 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGT-TCCA-C
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT-TCT-CATC
* * *
684950 TGCAATG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTATT
1 TGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTCATC
685000 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATC
1 TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATC
685042 AAGATTCACC
Statistics
Matches: 84, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
49 3 0.04
50 80 0.95
51 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (50 bp):
TGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTCATC
Found at i:685090 original size:300 final size:300
Alignment explanation
Indices: 684715--685304 Score: 1072
Period size: 300 Copynumber: 2.0 Consensus size: 300
684705 CGCTTGTGGC
* * *
684715 GTAAGATTCGCTGGTGTAGCTTTAATCAAGATTCAACGATGTGGCTTGAATCTTTTTAACTGCAA
1 GTAAGATCCGCTGGTGTAGCTTCAATCAAGATTCAACGATGTGGCTTGAATCATTTTAACTGCAA
684780 TGTAGGAGAAACAAGATTAACCAATTTGGCTTTAATCTATTCCACTGCATCGCTTGGGGCGTAAG
66 TGTAGGAGAAACAAGATTAACCAATTTGGCTTTAATCTATTCCACTGCATCGCTTGGGGCGTAAG
*
684845 ATTCGCTGTTGTAGCTTTAATCAAGACTCACCGATGTGGCTTTAATCTTTTTAATTGCAATGTCA
131 ATTCACTGTTGTAGCTTTAATCAAGACTCACCGATGTGGCTTTAATCTTTTTAATTGCAATGTCA
*
684910 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAATGCTAGGAAAGTAAGATCCG
196 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCG
*
684975 CTGTTGTAGCTTCAATCTTCTTATTTGCAATGTCAGGGAA
261 CTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAA
* * * *
685015 GTAAGATCCGCTGTTGTAGCTTCAATCAAGATTCACCGATTTGGCTTTAATCATTTTAACTGCAA
1 GTAAGATCCGCTGGTGTAGCTTCAATCAAGATTCAACGATGTGGCTTGAATCATTTTAACTGCAA
* *
685080 TGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTATTCCACTGCATCGCTTGGGGCGTAAG
66 TGTAGGAGAAACAAGATTAACCAATTTGGCTTTAATCTATTCCACTGCATCGCTTGGGGCGTAAG
685145 ATTCACTGTTGTAGCTTTAATCAAGACTCACCGATGTGGCTTTAATCTTTTTAATTGCAATGTCA
131 ATTCACTGTTGTAGCTTTAATCAAGACTCACCGATGTGGCTTTAATCTTTTTAATTGCAATGTCA
685210 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCG
196 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCG
685275 CTGTTGTAGCTTCAATCTTCTTAATTGCAA
261 CTGTTGTAGCTTCAATCTTCTTAATTGCAA
685305 ACTATGGTTT
Statistics
Matches: 278, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
300 278 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (300 bp):
GTAAGATCCGCTGGTGTAGCTTCAATCAAGATTCAACGATGTGGCTTGAATCATTTTAACTGCAA
TGTAGGAGAAACAAGATTAACCAATTTGGCTTTAATCTATTCCACTGCATCGCTTGGGGCGTAAG
ATTCACTGTTGTAGCTTTAATCAAGACTCACCGATGTGGCTTTAATCTTTTTAATTGCAATGTCA
GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCG
CTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAA
Found at i:685146 original size:175 final size:175
Alignment explanation
Indices: 684840--685166 Score: 410
Period size: 175 Copynumber: 1.9 Consensus size: 175
684830 CGCTTGGGGC
* * * *
684840 GTAAGATTCGCTGTTGTAGCTTTAATCAAGACTCACCGATGTGGCTTTAATCTTTTTAATTGCAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCAAGACTCACCGATGTGGCTTTAATCATTTTAACTGCAA
** ** *
684905 TGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAATGCTAGGAAAGTAAG
66 TGTCAGGGAAACAAGATCCGCAATTGTAGCTTCAATCTATTCCACTGCAATGCTAGGAAAGTAAG
*
684970 ATCCGCTGTTGTAGCTTCAATCTTCTTATTTGCAATGTCAGGGAA
131 ATCCACTGTTGTAGCTTCAATCTTCTTATTTGCAATGTCAGGGAA
* *
685015 GTAAGATCCGCTGTTGTAGCTTCAATCAAGATTCACCGATTTGGCTTTAATCATTTTAACTGCAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCAAGACTCACCGATGTGGCTTTAATCATTTTAACTGCAA
* * * ***
685080 TGTC-GGAGAAACAAGATTCAC-CAATT-TGGCTTTAATCTATTCCACTGC-ATCGCTTGGGGCG
66 TGTCAGG-GAAACAAGA-TC-CGCAATTGTAGCTTCAATCTATTCCACTGCAAT-GCTAGGAAAG
* *
685141 TAAGATTCACTGTTGTAGCTTTAATC
127 TAAGATCCACTGTTGTAGCTTCAATC
685167 AAGACTCACC
Statistics
Matches: 128, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
174 4 0.03
175 118 0.92
176 5 0.04
177 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (175 bp):
GTAAGATCCGCTGTTGTAGCTTCAATCAAGACTCACCGATGTGGCTTTAATCATTTTAACTGCAA
TGTCAGGGAAACAAGATCCGCAATTGTAGCTTCAATCTATTCCACTGCAATGCTAGGAAAGTAAG
ATCCACTGTTGTAGCTTCAATCTTCTTATTTGCAATGTCAGGGAA
Found at i:685242 original size:125 final size:125
Alignment explanation
Indices: 685013--685291 Score: 339
Period size: 125 Copynumber: 2.2 Consensus size: 125
685003 AATGTCAGGG
* *
685013 AAGTAAGATCCGCTGTTGTAGCTTCAATCAAGATTCACCGATTTGGCTTTAATCATTTTAACTGC
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCAAGACTCACCGATGTGGCTTTAATCATTTTAACTGC
* * * * *
685078 AATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCTATTCCACTGCATCGCTTGGG
66 AATGTCGGAGAAACAAGATTCACCAATTTAGCTTCAATCTATTCCACTGCAACGCTAGGA
** * * * * *
685138 GCGTAAGATTCACTGTTGTAGCTTTAATCAAGACTCACCGATGTGGCTTTAATCTTTTTAATTGC
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCAAGACTCACCGATGTGGCTTTAATCATTTTAACTGC
** ** *
685203 AATGTCAGG-GAAGTAAGA-TC-CGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGA
66 AATGTC-GGAGAAACAAGATTCAC-CAATT-TAGCTTCAATCTATTCCACTGCAACGCTAGGA
685263 AAGTAAGATCCGCTGTTGTAGCTTCAATC
1 AAGTAAGATCCGCTGTTGTAGCTTCAATC
685292 TTCTTAATTG
Statistics
Matches: 127, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
123 1 0.01
124 5 0.04
125 119 0.94
126 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (125 bp):
AAGTAAGATCCGCTGTTGTAGCTTCAATCAAGACTCACCGATGTGGCTTTAATCATTTTAACTGC
AATGTCGGAGAAACAAGATTCACCAATTTAGCTTCAATCTATTCCACTGCAACGCTAGGA
Found at i:685304 original size:50 final size:49
Alignment explanation
Indices: 685183--685304 Score: 147
Period size: 50 Copynumber: 2.4 Consensus size: 49
685173 CACCGATGTG
* * *
685183 GCTTTAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTA
1 GCTTCAATC-TTTTAATTGCAACGTCAGGAAAGTAAGATCCGCTGTTGTA
** *
685233 GCTTCAATCTGTTCCACTGCAACG-CTAGGAAAGTAAGATCCGCTGTTGTA
1 GCTTCAATCT-TTTAATTGCAACGTC-AGGAAAGTAAGATCCGCTGTTGTA
685283 GCTTCAATCTTCTTAATTGCAA
1 GCTTCAATCTT-TTAATTGCAA
685305 ACTATGGTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
49 3 0.05
50 57 0.95
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (49 bp):
GCTTCAATCTTTTAATTGCAACGTCAGGAAAGTAAGATCCGCTGTTGTA
Found at i:687526 original size:24 final size:25
Alignment explanation
Indices: 687499--687562 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
687489 TGATTGATTG
687499 ATTTTTTTTATTTTGGTTTTTTT-T
1 ATTTTTTTTATTTTGGTTTTTTTGT
* *
687523 ATTTTTATTATTTTTGTTTTTTTGT
1 ATTTTTTTTATTTTGGTTTTTTTGT
*
687548 CTTGTTTTTT-TTTTG
1 ATT-TTTTTTATTTTG
687563 AGTCTGAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
24 21 0.64
25 7 0.21
26 5 0.15
ACGTcount: A:0.08, C:0.02, G:0.09, T:0.81
Consensus pattern (25 bp):
ATTTTTTTTATTTTGGTTTTTTTGT
Found at i:688156 original size:273 final size:273
Alignment explanation
Indices: 687669--688187 Score: 876
Period size: 273 Copynumber: 1.9 Consensus size: 273
687659 CTTGCATGTG
* *
687669 AAAAACCTTCTTTGGTACCAGATTTCTTTCATAAAGCCCTTTTGGGACGCAACTACGACAGAGAA
1 AAAAACCTTCTTTGATACCAGATTTCTTTCATAAAGCCCTTTTGGGACGCAACTACGACAGAAAA
*
687734 CTTTGGATCTTCCTCTTTAATCAGGATAAAATCCAACAACATCTTGAAGGGATGGAAACTCGACT
66 CTTTAGATCTTCCTCTTTAATCAGGATAAAATCCAACAACATCTTGAAGGGATGGAAACTCGACT
* * *
687799 TCAAATGGGAAAAGCTATGCTGACTCAACGAGAGAGGCATTGCCCCAGCAAAGAATTGTATTGTT
131 TCAAATGGGAAAAGCTATGCTGACTCAACGAGAGAGACATTGCCCCAGCAAAGAATTGCATCGTT
* *
687864 CGCACTGTAAATTTCTGACATCGTGCTGTTGTGCAGATTTTATTATAAGAATCGAGGCATACCCT
196 CGCACTGCAAATTTCTGACATCGTGCTGTTGTACAGATTTTATTATAAGAATCGAGGCATACCCT
687929 GGTATGATCATGC
261 GGTATGATCATGC
* * * *
687942 AAAAACCTTCTTTGATACCATATTTCTTTCATAGAGCCCTTTTGGGATGCAACTATGACAGAAAA
1 AAAAACCTTCTTTGATACCAGATTTCTTTCATAAAGCCCTTTTGGGACGCAACTACGACAGAAAA
* * *
688007 CTTTAGATCTTCCTCTTTAATCAGTATAAAATCCAGCAACATCTTGAAGGGATGGAAACTTGACT
66 CTTTAGATCTTCCTCTTTAATCAGGATAAAATCCAACAACATCTTGAAGGGATGGAAACTCGACT
* *
688072 TCAAATGGGCAAAGCTATGCTGACTCAACGAGAGAGACATTGCCCCGGCAAAGAATTGCATCGTT
131 TCAAATGGGAAAAGCTATGCTGACTCAACGAGAGAGACATTGCCCCAGCAAAGAATTGCATCGTT
*
688137 CGCACTGCGAATTTCTGACATCGTGCTGTTGTACAGATTTTATTATAAGAA
196 CGCACTGCAAATTTCTGACATCGTGCTGTTGTACAGATTTTATTATAAGAA
688188 GACATCTTTG
Statistics
Matches: 228, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
273 228 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (273 bp):
AAAAACCTTCTTTGATACCAGATTTCTTTCATAAAGCCCTTTTGGGACGCAACTACGACAGAAAA
CTTTAGATCTTCCTCTTTAATCAGGATAAAATCCAACAACATCTTGAAGGGATGGAAACTCGACT
TCAAATGGGAAAAGCTATGCTGACTCAACGAGAGAGACATTGCCCCAGCAAAGAATTGCATCGTT
CGCACTGCAAATTTCTGACATCGTGCTGTTGTACAGATTTTATTATAAGAATCGAGGCATACCCT
GGTATGATCATGC
Found at i:694137 original size:19 final size:19
Alignment explanation
Indices: 694110--694179 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
694100 TATGCTAATA
694110 TTTGGTTCTGCCTTGCGTG
1 TTTGGTTCTGCCTTGCGTG
* * *
694129 TTTGTTTCTGTCTTTGCAGGTA
1 TTTGGTTCTG-CCTTGC--GTG
694151 TTTGGTTCTGCCTTGCGTG
1 TTTGGTTCTGCCTTGCGTG
*
694170 TTTGTTTCTG
1 TTTGGTTCTG
694180 TCTTTGCAGG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 20 0.49
20 5 0.12
21 5 0.12
22 11 0.27
ACGTcount: A:0.03, C:0.17, G:0.27, T:0.53
Consensus pattern (19 bp):
TTTGGTTCTGCCTTGCGTG
Found at i:694165 original size:41 final size:41
Alignment explanation
Indices: 694108--694190 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
694098 GTTATGCTAA
694108 TATTTGGTTCTGCCTTGCGTGTTTGTTTCTGTCTTTGCAGG
1 TATTTGGTTCTGCCTTGCGTGTTTGTTTCTGTCTTTGCAGG
694149 TATTTGGTTCTGCCTTGCGTGTTTGTTTCTGTCTTTGCAGG
1 TATTTGGTTCTGCCTTGCGTGTTTGTTTCTGTCTTTGCAGG
694190 T
1 T
694191 GAGCAGTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.05, C:0.17, G:0.27, T:0.52
Consensus pattern (41 bp):
TATTTGGTTCTGCCTTGCGTGTTTGTTTCTGTCTTTGCAGG
Found at i:694835 original size:49 final size:49
Alignment explanation
Indices: 694655--694840 Score: 180
Period size: 49 Copynumber: 3.8 Consensus size: 49
694645 ATATAGTGAT
* * * * * *
694655 TGAAAACCATCATTGTAGGGCCATCTAGGATTGTAGATTAT-ATAAACAA
1 TGAAAACCATCATTGTTGGGCCATCCAAGATGGTAGAATATCA-AAACAG
* * *
694704 T-AAACATCATCATTGTTGGGCCATTCAGGATGGTAGAATATCAAAACAG
1 TGAAA-ACCATCATTGTTGGGCCATCCAAGATGGTAGAATATCAAAACAG
* ** * * *
694753 TGAAAGCCATTGTTCTCGGGCCATCCGAA-ATGGTAGAATATCAAAATAG
1 TGAAAACCATCATTGTTGGGCCATCC-AAGATGGTAGAATATCAAAACAG
*
694802 TGAAAACCATCATTGTTGGGCAATCCAAGATGGTAGAAT
1 TGAAAACCATCATTGTTGGGCCATCCAAGATGGTAGAAT
694841 TTGTAAATTG
Statistics
Matches: 110, Mismatches: 22, Indels: 10
0.77 0.15 0.07
Matches are distributed among these distances:
48 5 0.05
49 100 0.91
50 5 0.05
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (49 bp):
TGAAAACCATCATTGTTGGGCCATCCAAGATGGTAGAATATCAAAACAG
Found at i:704706 original size:28 final size:28
Alignment explanation
Indices: 704672--704728 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
704662 GAAAACCATT
704672 GATCTCTCCAACAATAGCCTATCAGGTA
1 GATCTCTCCAACAATAGCCTATCAGGTA
704700 GATCTCTCCAACAATAGCCTATCAGGTA
1 GATCTCTCCAACAATAGCCTATCAGGTA
704728 G
1 G
704729 TTTGCCTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (28 bp):
GATCTCTCCAACAATAGCCTATCAGGTA
Found at i:713086 original size:18 final size:18
Alignment explanation
Indices: 713063--713106 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
713053 GTGTATGAAC
*
713063 AAATATAT-TTTATATTAA
1 AAATATATATTTATA-AAA
713081 AAATATATATTTATAAAA
1 AAATATATATTTATAAAA
713099 AAATATAT
1 AAATATAT
713107 GTAAAAGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATATATATTTATAAAA
Found at i:713097 original size:16 final size:18
Alignment explanation
Indices: 713063--713106 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
713053 GTGTATGAAC
*
713063 AAATATATTTTATATTAA
1 AAATATATATTATATTAA
713081 AAATATATATT-TA-TAA
1 AAATATATATTATATTAA
*
713097 AAAAATATAT
1 AAATATATAT
713107 GTAAAAGATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 12 0.50
17 2 0.08
18 10 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATATATATTATATTAA
Found at i:714345 original size:49 final size:49
Alignment explanation
Indices: 714248--714393 Score: 212
Period size: 49 Copynumber: 3.0 Consensus size: 49
714238 ATACGTCGCC
* *
714248 GGTTAATAATAATCCACACCAAATAGGT-TAATTT--AT-ACATCA-CATA
1 GGTTAATAATAATCCACACCAAATA-GTCAAATTTACATGGCAT-AGCATA
*
714294 GGTTAATAATAATCCACACTAAATAGTCAAATTTACATGGCATAGCATA
1 GGTTAATAATAATCCACACCAAATAGTCAAATTTACATGGCATAGCATA
714343 GGTTAATAATAATCCACACCAAATAGTCAAATTTACATGGCATAGCATA
1 GGTTAATAATAATCCACACCAAATAGTCAAATTTACATGGCATAGCATA
714392 GG
1 GG
714394 ACGTTAATTT
Statistics
Matches: 91, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
45 2 0.02
46 29 0.32
48 3 0.03
49 57 0.63
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (49 bp):
GGTTAATAATAATCCACACCAAATAGTCAAATTTACATGGCATAGCATA
Found at i:715718 original size:22 final size:22
Alignment explanation
Indices: 715666--715720 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
715656 AAAATTGGTT
* *
715666 ATATATATATGTTTTTCATATA
1 ATATATATATGTTTTTCAAAAA
*
715688 TTATAATATATG-TTTTCAAAAAA
1 ATAT-ATATATGTTTTTC-AAAAA
715711 ATATATATAT
1 ATATATATAT
715721 AAACTACAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (22 bp):
ATATATATATGTTTTTCAAAAA
Found at i:730414 original size:18 final size:17
Alignment explanation
Indices: 730374--730417 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
730364 TTAAAATTTT
* *
730374 GTTTATAATTTTTTTAT
1 GTTTTTAATTTTTTTAA
730391 GATTTTTAATATTTTTTAA
1 G-TTTTTAAT-TTTTTTAA
730410 GTTTTTAA
1 GTTTTTAA
730418 AAGGGATTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 14 0.61
19 8 0.35
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (17 bp):
GTTTTTAATTTTTTTAA
Found at i:733835 original size:94 final size:95
Alignment explanation
Indices: 733711--733902 Score: 377
Period size: 94 Copynumber: 2.0 Consensus size: 95
733701 AATTAAAAAT
733711 CATTAAAACCATTAAAAATTATAAAAATAATTTTAATTTTAAAAAATTAATTAATTACTGATATC
1 CATTAAAACCATTAAAAATTATAAAAATAATTTTAATTTTAAAAAATTAATTAATTACTGATATC
733776 GTATACATTTGGACTACCACATGGATGCCA
66 GTATACATTTGGACTACCACATGGATGCCA
733806 CATTAAAACCATT-AAAATTATAAAAATAATTTTAATTTTAAAAAATTAATTAATTACTGATATC
1 CATTAAAACCATTAAAAATTATAAAAATAATTTTAATTTTAAAAAATTAATTAATTACTGATATC
733870 GTATACATTTGGACTACCACATGGATGCCA
66 GTATACATTTGGACTACCACATGGATGCCA
733900 CAT
1 CAT
733903 AAACAAAGTT
Statistics
Matches: 97, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
94 84 0.87
95 13 0.13
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (95 bp):
CATTAAAACCATTAAAAATTATAAAAATAATTTTAATTTTAAAAAATTAATTAATTACTGATATC
GTATACATTTGGACTACCACATGGATGCCA
Found at i:734807 original size:18 final size:19
Alignment explanation
Indices: 734786--734825 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
734776 AATAAACACC
734786 AAAAA-AAATTTAAAAATA
1 AAAAAGAAATTTAAAAATA
* *
734804 AAAAAGTATTTTAAAAATA
1 AAAAAGAAATTTAAAAATA
734823 AAA
1 AAA
734826 CATTTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (19 bp):
AAAAAGAAATTTAAAAATA
Found at i:734832 original size:17 final size:17
Alignment explanation
Indices: 734794--734855 Score: 74
Period size: 16 Copynumber: 3.6 Consensus size: 17
734784 CCAAAAAAAA
734794 TTTAAAAATAAAAAAGTAT
1 TTTAAAAAT-AAAAA-TAT
734813 TTTAAAAATAAAACAT-T
1 TTTAAAAATAAAA-ATAT
*
734830 TTTAAAAA-AAAAGTAT
1 TTTAAAAATAAAAATAT
734846 TTTAAAAATA
1 TTTAAAAATA
734856 TTTTAAAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
15 1 0.03
16 13 0.33
17 10 0.26
18 5 0.13
19 10 0.26
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (17 bp):
TTTAAAAATAAAAATAT
Found at i:734836 original size:16 final size:17
Alignment explanation
Indices: 734794--734855 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
734784 CCAAAAAAAA
*
734794 TTTAAAAATAAAAAAGTAT
1 TTTAAAAAT--AAAAGCAT
734813 TTTAAAAATAAAA-CATT
1 TTTAAAAATAAAAGCA-T
*
734830 TTTAAAAA-AAAAGTAT
1 TTTAAAAATAAAAGCAT
734846 TTTAAAAATA
1 TTTAAAAATA
734856 TTTTAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 14 0.37
17 15 0.39
19 9 0.24
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (17 bp):
TTTAAAAATAAAAGCAT
Found at i:734870 original size:17 final size:17
Alignment explanation
Indices: 734786--734852 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 17
734776 AATAAACACC
* *
734786 AAAAAAAATTTAAAAAT
1 AAAAAATATTTTAAAAT
734803 AAAAAAGTATTTTAAAAAT
1 AAAAAA-TATTTT-AAAAT
*
734822 AAAACAT-TTTTAAAA-
1 AAAAAATATTTTAAAAT
*
734837 AAAAAGTATTTTAAAA
1 AAAAAATATTTTAAAA
734853 ATATTTTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
15 5 0.12
16 12 0.29
17 10 0.24
18 5 0.12
19 10 0.24
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (17 bp):
AAAAAATATTTTAAAAT
Found at i:750816 original size:16 final size:16
Alignment explanation
Indices: 750795--750839 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
750785 ACCTTCCGTG
750795 TTTTTTTTTTTGCTTA
1 TTTTTTTTTTTGCTTA
* * *
750811 TTTTTTGTTTGGTTTA
1 TTTTTTTTTTTGCTTA
750827 TTTTTCTTTTTTG
1 TTTTT-TTTTTTG
750840 TTCTGTTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.04, C:0.04, G:0.11, T:0.80
Consensus pattern (16 bp):
TTTTTTTTTTTGCTTA
Found at i:760013 original size:21 final size:21
Alignment explanation
Indices: 759989--760041 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
759979 AACGATGGCT
* * * *
759989 GTGATATTAGTTACTATAGCG
1 GTGAGATTAGATACCATAGCA
*
760010 GTGAGATTGGATACCATAGCA
1 GTGAGATTAGATACCATAGCA
760031 GTGAGATTAGA
1 GTGAGATTAGA
760042 AATAGTGAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.09, G:0.28, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACCATAGCA
Found at i:766271 original size:21 final size:22
Alignment explanation
Indices: 766228--766276 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
766218 ATAAGTTATG
766228 ATAAAAAATTATAATATTTTTT
1 ATAAAAAATTATAATATTTTTT
*
766250 ATAAATAAA-TATATTA-TTTTT
1 ATAAA-AAATTATAATATTTTTT
766271 ATAAAA
1 ATAAAA
766277 TATAACATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 10 0.40
22 11 0.44
23 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAAAAAATTATAATATTTTTT
Found at i:770776 original size:3 final size:3
Alignment explanation
Indices: 770768--770793 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
770758 TTACCAGAAA
770768 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
770794 GAAAGCCATG
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:774714 original size:19 final size:20
Alignment explanation
Indices: 774686--774723 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
774676 AATTGGAATT
*
774686 AAATTTTAAAAATA-AAAAA
1 AAATTCTAAAAATATAAAAA
774705 AAATTCTAAAAATATAAAA
1 AAATTCTAAAAATATAAAA
774724 TATAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATTCTAAAAATATAAAAA
Found at i:783609 original size:15 final size:15
Alignment explanation
Indices: 783588--783626 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
783578 GATCATCGTT
*
783588 TATTTATAAT-TATT
1 TATTTATAATCTATC
783602 TAATTTATAATCTATC
1 T-ATTTATAATCTATC
783618 TATTTATAA
1 TATTTATAA
783627 ACATTTACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 17 0.77
16 4 0.18
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTATAATCTATC
Found at i:783986 original size:18 final size:19
Alignment explanation
Indices: 783942--783986 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 19
783932 AATTACTTTC
*
783942 TAAAAATTACTTCTTTATA
1 TAAAAATTAATTCTTTATA
*
783961 T--AACTTAATT-TTTATA
1 TAAAAATTAATTCTTTATA
783977 TAAAAATTAA
1 TAAAAATTAA
783987 CTTGAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 5
0.72 0.10 0.17
Matches are distributed among these distances:
16 7 0.33
17 7 0.33
18 6 0.29
19 1 0.05
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAAAATTAATTCTTTATA
Found at i:790615 original size:14 final size:14
Alignment explanation
Indices: 790592--790631 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
790582 ACAGAAAAGT
*
790592 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
790606 AAATCATTTTACGG
1 AAAACATTTTACAG
790620 AAAACATTTTAC
1 AAAACATTTTAC
790632 TGCTAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:801623 original size:478 final size:478
Alignment explanation
Indices: 800727--801678 Score: 1888
Period size: 478 Copynumber: 2.0 Consensus size: 478
800717 ATATGATGAG
800727 ATTTAATCACTCAAGGTCACTAAACTATTATTAATTTTACATTTTGGTCACTCAACTTAAAAAAA
1 ATTTAATCACTCAAGGTCACTAAACTATTATTAATTTTACATTTTGGTCACTCAACTTAAAAAAA
800792 TTACAAAATAGTCATTGAATTATTCTTAAAATTTTTTTTCTTTAATTTAATATTTAAAAATAAAT
66 TTACAAAATAGTCATTGAATTATTCTTAAAATTTTTTTTCTTTAATTTAATATTTAAAAATAAAT
800857 TTATCTATTTTTTAATAAAAATAATAAAATATAATTTAACTCTTAGTACAATATATTTTGCATAT
131 TTATCTATTTTTTAATAAAAATAATAAAATATAATTTAACTCTTAGTACAATATATTTTGCATAT
800922 ATTTTTACTACTAAAAAGATAACAAAATTTGGTGGAATAGGTCAACATTACGAAAAGTTTATCGT
196 ATTTTTACTACTAAAAAGATAACAAAATTTGGTGGAATAGGTCAACATTACGAAAAGTTTATCGT
800987 ATAAATGAAGGAAAAGATTAGTCGGTGGGTTTTTGCCTTTTGGAGTTAATGGGTGGGCATGGAAG
261 ATAAATGAAGGAAAAGATTAGTCGGTGGGTTTTTGCCTTTTGGAGTTAATGGGTGGGCATGGAAG
801052 GGTAATTTTCAAAAGGACAGCGAAAAGAAGAATATAAAATTTGACCCAAAAAGTGCATAAATCTG
326 GGTAATTTTCAAAAGGACAGCGAAAAGAAGAATATAAAATTTGACCCAAAAAGTGCATAAATCTG
801117 TCAATTATGAATTATCTCCTTCAAGTTGGGAACTCCCCCCTGCCCCTTTAGTTTTCGCAGCATTT
391 TCAATTATGAATTATCTCCTTCAAGTTGGGAACTCCCCCCTGCCCCTTTAGTTTTCGCAGCATTT
801182 ATTCCCCCAAGATGCAGAAACAA
456 ATTCCCCCAAGATGCAGAAACAA
801205 ATTTAATCACTCAAGGTCACTAAACTATTATTAATTTTACATTTTGGTCACTCAACTTAAAAAAA
1 ATTTAATCACTCAAGGTCACTAAACTATTATTAATTTTACATTTTGGTCACTCAACTTAAAAAAA
801270 TTACAAAATAGTCATTGAATTATTCTTAAAATTTTTTTTCTTTAATTTAATATTTAAAAATAAAT
66 TTACAAAATAGTCATTGAATTATTCTTAAAATTTTTTTTCTTTAATTTAATATTTAAAAATAAAT
801335 TTATTCTATTTTTT-ATAAAAATAATAAAATATAATTTAACTCTTAGTACAATATATTTTGCATA
131 TTA-TCTATTTTTTAATAAAAATAATAAAATATAATTTAACTCTTAGTACAATATATTTTGCATA
801399 TATTTTTACTACTAAAAAGATAACAAAATTTGGTGGAATAGGTCAACATTACGAAAAGTTTATCG
195 TATTTTTACTACTAAAAAGATAACAAAATTTGGTGGAATAGGTCAACATTACGAAAAGTTTATCG
801464 TATAAATGAAGGAAAAGATTAGTCGGTGGGTTTTTGCCTTTTGGAGTTAATGGGTGGGCATGGAA
260 TATAAATGAAGGAAAAGATTAGTCGGTGGGTTTTTGCCTTTTGGAGTTAATGGGTGGGCATGGAA
801529 GGGTAATTTTCAAAAGGACAGCGAAAAGAAGAATATAAAATTTGACCCAAAAAGTGCATAAATCT
325 GGGTAATTTTCAAAAGGACAGCGAAAAGAAGAATATAAAATTTGACCCAAAAAGTGCATAAATCT
801594 GTCAATTATGAATTATCTCCTTCAAGTTGGGAACTCCCCCCTGCCCCTTTAGTTTTCGCAGCATT
390 GTCAATTATGAATTATCTCCTTCAAGTTGGGAACTCCCCCCTGCCCCTTTAGTTTTCGCAGCATT
801659 TATTCCCCCAAGATGCAGAA
455 TATTCCCCCAAGATGCAGAA
801679 CCAACCTCCC
Statistics
Matches: 473, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
478 463 0.98
479 10 0.02
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (478 bp):
ATTTAATCACTCAAGGTCACTAAACTATTATTAATTTTACATTTTGGTCACTCAACTTAAAAAAA
TTACAAAATAGTCATTGAATTATTCTTAAAATTTTTTTTCTTTAATTTAATATTTAAAAATAAAT
TTATCTATTTTTTAATAAAAATAATAAAATATAATTTAACTCTTAGTACAATATATTTTGCATAT
ATTTTTACTACTAAAAAGATAACAAAATTTGGTGGAATAGGTCAACATTACGAAAAGTTTATCGT
ATAAATGAAGGAAAAGATTAGTCGGTGGGTTTTTGCCTTTTGGAGTTAATGGGTGGGCATGGAAG
GGTAATTTTCAAAAGGACAGCGAAAAGAAGAATATAAAATTTGACCCAAAAAGTGCATAAATCTG
TCAATTATGAATTATCTCCTTCAAGTTGGGAACTCCCCCCTGCCCCTTTAGTTTTCGCAGCATTT
ATTCCCCCAAGATGCAGAAACAA
Found at i:802917 original size:77 final size:78
Alignment explanation
Indices: 802789--802943 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 78
802779 TTTATTTTTT
802789 ACTTATTTGTTTTTAAAATTTAAATCCACAAAAAGTAATATGTATCACTAATAATCTGATTTAGT
1 ACTTATTTGTTTTTAAAATTTAAATCCACAAAAAGTAATATGTATCACTAATAATCTGATTTAGT
802854 GTCAAATTATTTA
66 GTCAAATTATTTA
802867 ACTTATTTGTTTTT-AAATTTAAATCCACAAAAAGTAATATGTATCACTAATAATCTGATTTAGT
1 ACTTATTTGTTTTTAAAATTTAAATCCACAAAAAGTAATATGTATCACTAATAATCTGATTTAGT
802931 GTCAAATTATTTA
66 GTCAAATTATTTA
802944 CCTATTTAAT
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 63 0.82
78 14 0.18
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (78 bp):
ACTTATTTGTTTTTAAAATTTAAATCCACAAAAAGTAATATGTATCACTAATAATCTGATTTAGT
GTCAAATTATTTA
Found at i:803070 original size:17 final size:14
Alignment explanation
Indices: 803032--803074 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
803022 TTCTAAAAAA
803032 AATATTATTTATAT
1 AATATTATTTATAT
*
803046 AATTTTATTATATATT
1 AATATTATT-TATA-T
803062 ATATATTATTTAT
1 A-ATATTATTTAT
803075 TGTAGTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 8 0.33
15 4 0.17
16 5 0.21
17 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AATATTATTTATAT
Found at i:803094 original size:21 final size:19
Alignment explanation
Indices: 803037--803094 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 19
803027 AAAAAAATAT
*
803037 TATTTATATAATTTTATTA
1 TATTTATATATTTTTATTA
*
803056 TATATTATATATTATTTATTG
1 TAT-TTATATATT-TTTATTA
803077 TAGTTTATATTATTTTTA
1 TA-TTTATA-TATTTTTA
803095 ATGGTATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 3 0.09
20 8 0.24
21 17 0.52
22 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TATTTATATATTTTTATTA
Found at i:804040 original size:22 final size:21
Alignment explanation
Indices: 804015--804063 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
804005 CTTAAAACAT
*
804015 TATATGTATGTATATACATGCA
1 TATAT-TATATATATACATGCA
* *
804037 TATACTTATATATGTATATGCA
1 TATA-TTATATATATACATGCA
804059 TATAT
1 TATAT
804064 AAGATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 21 0.91
23 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (21 bp):
TATATTATATATATACATGCA
Found at i:804207 original size:1 final size:1
Alignment explanation
Indices: 804201--804226 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
804191 CTTCTTCTTC
804201 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
804227 CAATTTTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:809817 original size:19 final size:20
Alignment explanation
Indices: 809771--809814 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
809761 AATAAACATT
*
809771 AAAAATTATTTTAAAAATAA
1 AAAAATAATTTTAAAAATAA
*
809791 AAAAATAATTTTAAAATTAA
1 AAAAATAATTTTAAAAATAA
809811 AAAA
1 AAAA
809815 TAAAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATAATTTTAAAAATAA
Found at i:813836 original size:5 final size:6
Alignment explanation
Indices: 813809--813834 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
813799 ATTTAGTCCG
813809 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
813835 ATAAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:819929 original size:13 final size:13
Alignment explanation
Indices: 819913--819963 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
819903 TTTAAACCAA
819913 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
819926 ACTTCTCAAAAAC
1 ACTTTTCAAAAGC
*
819939 ACTTTTTC-ACAGC
1 AC-TTTTCAAAAGC
819952 ACTTTTCAAAAG
1 ACTTTTCAAAAG
819964 TAATGAAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
12 5 0.17
13 21 0.70
14 4 0.13
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.31
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:821955 original size:14 final size:15
Alignment explanation
Indices: 821936--821968 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
821926 TCAAAGATTC
*
821936 AAAACAAGA-AATAT
1 AAAACAAAACAATAT
821950 AAAACAAAACAATAT
1 AAAACAAAACAATAT
821965 AAAA
1 AAAA
821969 TATAAAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.12
Consensus pattern (15 bp):
AAAACAAAACAATAT
Found at i:829363 original size:88 final size:88
Alignment explanation
Indices: 829213--829445 Score: 398
Period size: 88 Copynumber: 2.6 Consensus size: 88
829203 CGGAGTCTTA
829213 AACTTTCAAAATGCATCAAAAAAGCCCTCAAACTTCTTTAAAGTAAGCAATTAAGCCTCTGGTTA
1 AACTTTCAAAATGCATCAAAAAA-CCCTCAAACTTCTTTAAAGTAAGCAATTAAGCCTCTGGTTA
829278 TTTTTTCACTTAATTGGGTACTTG
65 TTTTTTCACTTAATTGGGTACTTG
829302 AACTTTCAAAATGCATCAAAAAACCCTCAAACTTCTTTAAAGTAAGCAATTAAGCCTCTGGTTAT
1 AACTTTCAAAATGCATCAAAAAACCCTCAAACTTCTTTAAAGTAAGCAATTAAGCCTCTGGTTAT
829367 TTTTTCACTTAATTGGGTACTTG
66 TTTTTCACTTAATTGGGTACTTG
* * *
829390 AACTTTCAAAATGCAACAAAAAGACCCTCAAAATTTTTCTAAA--AAGCAATTAAGCC
1 AACTTTCAAAATGCATCAAAAA-ACCCTCAAACTTCTT-TAAAGTAAGCAATTAAGCC
829446 CTGCTCTTAT
Statistics
Matches: 139, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
88 99 0.71
89 36 0.26
90 4 0.03
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (88 bp):
AACTTTCAAAATGCATCAAAAAACCCTCAAACTTCTTTAAAGTAAGCAATTAAGCCTCTGGTTAT
TTTTTCACTTAATTGGGTACTTG
Found at i:829680 original size:10 final size:9
Alignment explanation
Indices: 829661--829718 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
829651 TCTTGGTATA
829661 ATAATTTTT
1 ATAATTTTT
829670 ATAATTTTTT
1 ATAA-TTTTT
*
829680 ATGAA-ATTT
1 AT-AATTTTT
*
829689 AT-ATTTCT
1 ATAATTTTT
829697 AT-ATATTTT
1 ATAAT-TTTT
829706 ATAATTTTT
1 ATAATTTTT
829715 ATAA
1 ATAA
829719 AAAAATTCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
7 1 0.03
8 6 0.15
9 22 0.55
10 9 0.22
11 2 0.05
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (9 bp):
ATAATTTTT
Found at i:833173 original size:36 final size:36
Alignment explanation
Indices: 833129--833432 Score: 371
Period size: 36 Copynumber: 8.4 Consensus size: 36
833119 GAAAGCAGCA
* *
833129 TGGTGTTAGCAATGGTATGGGGCCAGGCCGGCCTGG
1 TGGTGCTAGCAATGGTATGGGGCCTGGCCGGCCTGG
*
833165 TGGTGTTAGCAATGGTATGGGGCCTGGCCGGCCTGG
1 TGGTGCTAGCAATGGTATGGGGCCTGGCCGGCCTGG
833201 TGGTGCTAGCAATGGTATGGGGCCTGGCCGGCCTGG
1 TGGTGCTAGCAATGGTATGGGGCCTGGCCGGCCTGG
833237 TGGTGCTAGCAATGGTATGGGGCCTGGCCGGCCTGG
1 TGGTGCTAGCAATGGTATGGGGCCTGGCCGGCCTGG
** * *
833273 TGGTGCTAGCAATGGTACCGGGCCTAGCCGACCTGG
1 TGGTGCTAGCAATGGTATGGGGCCTGGCCGGCCTGG
*
833309 TGGTG-TAAGCAATGGTACT-GGGCCTGGTCGGCCTGG
1 TGGTGCT-AGCAATGGTA-TGGGGCCTGGCCGGCCTGG
* * * * *
833345 TGGTGCTAACAGTGGT-TCTGGTCCTGGCCGGGCTGG
1 TGGTGCTAGCAATGGTAT-GGGGCCTGGCCGGCCTGG
* *** * *
833381 TGCTGCTAGCAATGGTGCAGGGTCTGGCCGGCCTGT
1 TGGTGCTAGCAATGGTATGGGGCCTGGCCGGCCTGG
* *
833417 TGGCGCAAGCAATGGT
1 TGGTGCTAGCAATGGT
833433 GCAGGGTCTG
Statistics
Matches: 235, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
34 1 0.00
35 1 0.00
36 232 0.99
37 1 0.00
ACGTcount: A:0.13, C:0.22, G:0.42, T:0.23
Consensus pattern (36 bp):
TGGTGCTAGCAATGGTATGGGGCCTGGCCGGCCTGG
Found at i:837093 original size:25 final size:25
Alignment explanation
Indices: 837065--837159 Score: 79
Period size: 25 Copynumber: 3.8 Consensus size: 25
837055 TGACTCTTAT
837065 GAGCTTCCTAATAATTGGCTCTTCG
1 GAGCTTCCTAATAATTGGCTCTTCG
** * *
837090 GAGCTTCCCGATAACTGGCTCTTAG
1 GAGCTTCCTAATAATTGGCTCTTCG
* * *
837115 GAGCTTACTGATTAA-TGGCTCTCCG
1 GAGCTTCCT-AATAATTGGCTCTTCG
*
837140 GAGTTTCCCT-AT-ATTGGCTC
1 GAGCTT-CCTAATAATTGGCTC
837160 ACTTGAACTT
Statistics
Matches: 54, Mismatches: 13, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
23 1 0.02
24 7 0.13
25 41 0.76
26 5 0.09
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (25 bp):
GAGCTTCCTAATAATTGGCTCTTCG
Found at i:837094 original size:49 final size:50
Alignment explanation
Indices: 837041--837148 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
837031 TGGTTCTTGC
* * * *
837041 GAGCTTCCCGATTA-TGACTCTTATGAGCTTCCT-AATAATTGGCTCTTCG
1 GAGCTTCCCGATAACTGACTCTTAGGAGCTTACTGAATAA-TGGCTCTCCG
* *
837090 GAGCTTCCCGATAACTGGCTCTTAGGAGCTTACTGATTAATGGCTCTCCG
1 GAGCTTCCCGATAACTGACTCTTAGGAGCTTACTGAATAATGGCTCTCCG
*
837140 GAGTTTCCC
1 GAGCTTCCC
837149 TATATTGGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
49 13 0.26
50 33 0.66
51 4 0.08
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.33
Consensus pattern (50 bp):
GAGCTTCCCGATAACTGACTCTTAGGAGCTTACTGAATAATGGCTCTCCG
Found at i:837247 original size:76 final size:75
Alignment explanation
Indices: 837090--837264 Score: 198
Period size: 76 Copynumber: 2.3 Consensus size: 75
837080 TGGCTCTTCG
* * *
837090 GAGCTTCCCGA-TAACTGGCTC-TTAGGAGCTTACTGATTAATGGCTCTCCGGAGTTTCCCTATA
1 GAGCTTCCCGATTAA-TGGCTCTTTAGGAGCTTACTGATTAATGACTCTCCGGAGCTTCCCGATA
837153 TTGGCTCACTT
65 TTGGCTCACTT
* * * *
837164 GAACTTCCCGATTAAAGGCTCTTTCATGAGCTT-CTTGATTAATGACTCTCTGGAGCTTCCCGAT
1 GAGCTTCCCGATTAATGGCTCTTT-AGGAGCTTAC-TGATTAATGACTCTCCGGAGCTTCCCGAT
*
837228 ATTGGCTC-GTAT
64 ATTGGCTCACT-T
*
837240 GAGCTTCCCG-TTAATGACTCTTTAG
1 GAGCTTCCCGATTAATGGCTCTTTAG
837265 AGTTTTCCGT
Statistics
Matches: 84, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
74 16 0.19
75 18 0.21
76 50 0.60
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.35
Consensus pattern (75 bp):
GAGCTTCCCGATTAATGGCTCTTTAGGAGCTTACTGATTAATGACTCTCCGGAGCTTCCCGATAT
TGGCTCACTT
Found at i:839257 original size:33 final size:33
Alignment explanation
Indices: 839207--839407 Score: 116
Period size: 33 Copynumber: 5.6 Consensus size: 33
839197 TCCCCCAAGG
* *
839207 GGTTACTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCTGAATCATTGGT
* * * *
839240 GGTTGCTAAGTGTTGATTCCACTGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CTG-A--AT-CAT-T---GGT
* *
839282 GGTTGCTAAGTGTTGATTCCCTGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCTGAATCATTGGT
* * * *
839315 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CTGAATC----AT-TG---GT
*
839357 GGTTGCTAAGTGCTGATTCCCTGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCTGAATCATTGGT
839390 GGTTGCT-AGTGCTGATTC
1 GGTTGCTAAGTGCTGATTC
839408 TACCGTATTT
Statistics
Matches: 130, Mismatches: 20, Indels: 37
0.70 0.11 0.20
Matches are distributed among these distances:
32 11 0.08
33 46 0.35
34 6 0.05
35 1 0.01
36 3 0.02
37 5 0.04
38 5 0.04
39 3 0.02
40 1 0.01
41 7 0.05
42 42 0.32
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCTGAATCATTGGT
Found at i:839299 original size:42 final size:41
Alignment explanation
Indices: 839240--839376 Score: 128
Period size: 42 Copynumber: 3.5 Consensus size: 41
839230 AATCATTGGT
*
839240 GGTTGCTAAGTGTTGATTCCACTGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACTGTA-TTTAAATGTGAAGGG
* * * *
839282 GGTTGCTAAGTGTTGATTCC-CTG-A-CT-CAT-T---GGT
1 GGTTGCTAAGTGCTGATTCCACTGTATTTAAATGTGAAGGG
* * *
839315 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACTGTAT-TTAAATGTGAAGGG
839357 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
839377 CTGATTCATT
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
33 20 0.27
34 2 0.03
35 1 0.01
36 1 0.01
37 3 0.04
38 3 0.04
39 1 0.01
40 1 0.01
41 3 0.04
42 40 0.53
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.35
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACTGTATTTAAATGTGAAGGG
Found at i:839347 original size:75 final size:75
Alignment explanation
Indices: 839203--839488 Score: 403
Period size: 75 Copynumber: 3.8 Consensus size: 75
839193 TGATTCCCCC
* * *
839203 AAGGGGTTACTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATTCCACTGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
839268 TTAAATGTGA
66 TTAAATGTGA
* * * * * *
839278 AGGGGGTTGCTAAGTGTTGATTCCCTGACTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
839343 TTAAATGTGA
66 TTAAATGTGA
* * *
839353 AAGGGGTTGCTAAGTGCTGATTCCCTGATTCATTGGTGGTTGCT-AGTGCTGATTCTACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTA-T
* *
839417 TTTGACTGTGA
65 TTTAAATGTGA
* * *
839428 AAAGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCG
839489 ATAACGGATA
Statistics
Matches: 186, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
74 16 0.09
75 156 0.84
76 14 0.08
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
TTAAATGTGA
Found at i:839724 original size:33 final size:33
Alignment explanation
Indices: 839682--839805 Score: 104
Period size: 33 Copynumber: 3.5 Consensus size: 33
839672 ATCAGTGGAT
839682 TCAGCACTTAGCAACCACCAATGAGTCGGGGAA
1 TCAGCACTTAGCAACCACCAATGAGTCGGGGAA
* * *
839715 TCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGA
1 TCAGCACTTAGCAACCAC---CA-A--TGAG-T-CGG-GGAA
* * *
839757 TCAACACTTAGCAACCACTAATGATTCGGGGAA
1 TCAGCACTTAGCAACCACCAATGAGTCGGGGAA
*
839790 TCAGCACTTAACAACC
1 TCAGCACTTAGCAACC
839806 CCTTTATATT
Statistics
Matches: 71, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
33 34 0.48
34 3 0.04
35 1 0.01
36 4 0.06
37 1 0.01
38 1 0.01
39 4 0.06
40 1 0.01
41 3 0.04
42 19 0.27
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (33 bp):
TCAGCACTTAGCAACCACCAATGAGTCGGGGAA
Found at i:841577 original size:11 final size:11
Alignment explanation
Indices: 841563--841590 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
841553 ATAAGGACAA
841563 TATGATTGATT
1 TATGATTGATT
841574 TATGATTGATT
1 TATGATTGATT
841585 TATGAT
1 TATGAT
841591 ACGAATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.54
Consensus pattern (11 bp):
TATGATTGATT
Done.