Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 20 of 187
Found at i:6752113 original size:11 final size:11
Alignment explanation
Indices: 6752097--6752137 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
6752087 CATTGGCCTC
6752097 TCCTTTTTCTT
1 TCCTTTTTCTT
6752108 TCCTTTTT-TT
1 TCCTTTTTCTT
6752118 TCTCTTTTTCTT
1 TC-CTTTTTCTT
*
6752130 TTCTTTTT
1 TCCTTTTT
6752138 TGAAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 4 0.15
11 20 0.74
12 3 0.11
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TCCTTTTTCTT
Found at i:6757385 original size:12 final size:12
Alignment explanation
Indices: 6757368--6757400 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
6757358 CGGCCCTCCA
6757368 ATATTAATTTTT
1 ATATTAATTTTT
6757380 ATATT-ATTTTT
1 ATATTAATTTTT
6757391 ATA-TAATTTT
1 ATATTAATTTT
6757401 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:6762487 original size:30 final size:31
Alignment explanation
Indices: 6762451--6762515 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
6762441 ATTTAACTAA
*
6762451 AAAAG-TTACAATTTAA-TCACTGAACTATTC
1 AAAAGTTTAC-ATTTAAGCCACTGAACTATTC
* *
6762481 AAAAGTTTTCATTTAAGCCATTGAACTATTC
1 AAAAGTTTACATTTAAGCCACTGAACTATTC
6762512 AAAA
1 AAAA
6762516 CTTTTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (31 bp):
AAAAGTTTACATTTAAGCCACTGAACTATTC
Found at i:6765746 original size:20 final size:22
Alignment explanation
Indices: 6765721--6765763 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
6765711 TTGTCAGAAC
6765721 TATTAA-ATA-TAATTCAAATA
1 TATTAACATATTAATTCAAATA
*
6765741 TATTAACTTATTAATTCAAATA
1 TATTAACATATTAATTCAAATA
6765763 T
1 T
6765764 TATAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 2 0.10
22 12 0.60
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
TATTAACATATTAATTCAAATA
Found at i:6768794 original size:28 final size:29
Alignment explanation
Indices: 6768751--6768822 Score: 94
Period size: 28 Copynumber: 2.4 Consensus size: 29
6768741 TTTAATAAAC
6768751 TTAAATTATTAATTAAAATTTAAAATTT-TT
1 TTAAATTATT--TTAAAATTTAAAATTTATT
*
6768781 TATAAA-TATTTTAAATTTTAAAATTTATT
1 T-TAAATTATTTTAAAATTTAAAATTTATT
6768810 TTAAATTATTTTA
1 TTAAATTATTTTA
6768823 TAGTTTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 19 0.50
29 10 0.26
30 5 0.13
31 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
TTAAATTATTTTAAAATTTAAAATTTATT
Found at i:6769079 original size:7 final size:7
Alignment explanation
Indices: 6769067--6769104 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
6769057 GCAAGAGGAG
6769067 TGAACAT
1 TGAACAT
6769074 TGAACAT
1 TGAACAT
6769081 TGAACAT
1 TGAACAT
6769088 TGAAGCA-
1 TGAA-CAT
*
6769095 TGACCAT
1 TGAACAT
6769102 TGA
1 TGA
6769105 GGTGGTGCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 2 0.07
7 24 0.86
8 2 0.07
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (7 bp):
TGAACAT
Found at i:6771102 original size:27 final size:27
Alignment explanation
Indices: 6771072--6771157 Score: 163
Period size: 27 Copynumber: 3.2 Consensus size: 27
6771062 CCTATCAGGT
6771072 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
6771099 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
*
6771126 AGGCGCCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
6771153 AGGCG
1 AGGCG
6771158 GCATTACTAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.29, C:0.21, G:0.35, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:6771308 original size:25 final size:23
Alignment explanation
Indices: 6771263--6771323 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 23
6771253 AATAAACACC
6771263 AAAAAA-ATTTTAAAAATAAAAA
1 AAAAAATATTTTAAAAATAAAAA
6771285 AAAAAAGTATTTTAAAAATAAAAA
1 AAAAAA-TATTTTAAAAATAAAAA
6771309 ATAAAAATATATTTA
1 A-AAAAATAT-TTTA
6771324 TTGTATTCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.17
24 20 0.57
25 9 0.26
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAAAATATTTTAAAAATAAAAA
Found at i:6771493 original size:19 final size:19
Alignment explanation
Indices: 6771471--6771508 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6771461 AATTTAATTT
*
6771471 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
6771490 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
6771509 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:6771638 original size:27 final size:27
Alignment explanation
Indices: 6771607--6771678 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
6771597 TACTGACATT
* *
6771607 CAATATTCATACAAAATTATAATATTA
1 CAATATTCATACAAAATTACAAAATTA
6771634 CAATATTCATACAAAATTACAAAATTA
1 CAATATTCATACAAAATTACAAAATTA
*
6771661 CAATATTCATATAAAATT
1 CAATATTCATACAAAATT
6771679 GCAATTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (27 bp):
CAATATTCATACAAAATTACAAAATTA
Found at i:6771750 original size:22 final size:24
Alignment explanation
Indices: 6771717--6771888 Score: 148
Period size: 27 Copynumber: 7.1 Consensus size: 24
6771707 ATAAATTATC
*
6771717 TATATTTAGTATGAATATTGTAAT
1 TATATTTTGTATGAATATTGTAAT
6771741 T-T-TTTTGTATGAATATTGTAATAT
1 TATATTTTGTATGAATATTGT-A-AT
* *
6771765 TATAATTTTGTGTGAATATTGCAAT
1 TAT-ATTTTGTATGAATATTGTAAT
6771790 T-T-TTTTGTATGAATATTGTAATAT
1 TATATTTTGTATGAATATTGT-A-AT
6771814 TATAATTTTGTATGAATATTGTAAT
1 TAT-ATTTTGTATGAATATTGTAAT
6771839 GTCGATATATATTG--T-AATATTGTAA-
1 -T--ATAT-T-TTGTATGAATATTGTAAT
6771864 T-T-TTTTGTATGAATATTGTAAT
1 TATATTTTGTATGAATATTGTAAT
6771886 TAT
1 TAT
6771889 TTTATAATTA
Statistics
Matches: 123, Mismatches: 5, Indels: 41
0.73 0.03 0.24
Matches are distributed among these distances:
18 3 0.02
19 1 0.01
20 2 0.02
21 11 0.09
22 32 0.26
23 4 0.03
24 9 0.07
25 7 0.06
26 13 0.11
27 35 0.28
28 3 0.02
29 3 0.02
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (24 bp):
TATATTTTGTATGAATATTGTAAT
Found at i:6771791 original size:49 final size:49
Alignment explanation
Indices: 6771720--6771834 Score: 203
Period size: 49 Copynumber: 2.3 Consensus size: 49
6771710 AATTATCTAT
* *
6771720 ATTTAGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
1 ATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTATA
*
6771769 ATTTTGTGTGAATATTGCAATTTTTTTGTATGAATATTGTAATATTATA
1 ATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTATA
6771818 ATTTTGTATGAATATTG
1 ATTTTGTATGAATATTG
6771835 TAATGTCGAT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 62 1.00
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (49 bp):
ATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTATA
Found at i:6771956 original size:19 final size:19
Alignment explanation
Indices: 6771934--6771971 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6771924 TATAAATTTA
*
6771934 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
6771953 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
6771972 AAATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:6772225 original size:27 final size:27
Alignment explanation
Indices: 6772187--6772290 Score: 165
Period size: 27 Copynumber: 3.9 Consensus size: 27
6772177 CCGGGTCGGC
* *
6772187 CCATTGGCGCCTCTCA-GAATGGCACCA
1 CCATTGGCGCCTCCCAGGTA-GGCACCA
6772214 CCATTGGCGCCTCCCAGGTAGGCACCA
1 CCATTGGCGCCTCCCAGGTAGGCACCA
6772241 CCATTGGCGCCTCCCAGGTAGGCACCA
1 CCATTGGCGCCTCCCAGGTAGGCACCA
*
6772268 CCATTGGCGCCTCCCAGATAGGC
1 CCATTGGCGCCTCCCAGGTAGGC
6772291 GCCAATACTA
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
27 71 0.97
28 2 0.03
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.16
Consensus pattern (27 bp):
CCATTGGCGCCTCCCAGGTAGGCACCA
Found at i:6773833 original size:103 final size:99
Alignment explanation
Indices: 6773616--6773837 Score: 286
Period size: 103 Copynumber: 2.2 Consensus size: 99
6773606 AAATGGAAAA
* * *
6773616 AAAAAAGGAAAAAAAAA-TTTGGGTGCTGGCCTGTCAATAGCCGGCACCCAGTACAATTTAAAAA
1 AAAAAAGTAAAAAAAAATTTTAGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAA
**
6773680 AAAAATTTTTTTTGTCAGAATCAAATATCAGTATACG
66 AAAAA---TTCGTGTCAGAATCAAATATCAGTATACG
* ***
6773717 AAAAAAGTAAAAAAAAATTGTTAGGTGCTGGCCTGTCAATGGTCGGCACCCAGTACAATTTTTTA
1 AAAAAAGTAAAAAAAAATT-TTAGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAA
*
6773782 AAAAAA-TCGTGTCAGAATCAGATATCAGTATACG
65 AAAAAATTCGTGTCAGAATCAAATATCAGTATACG
*
6773816 AAAAAAGTAAACCAAAAATTTT
1 AAAAAAGTAAA-AAAAAATTTT
6773838 TTTTTGGTAC
Statistics
Matches: 107, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
99 38 0.36
100 7 0.07
101 16 0.15
102 1 0.01
103 45 0.42
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (99 bp):
AAAAAAGTAAAAAAAAATTTTAGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAA
AAAAATTCGTGTCAGAATCAAATATCAGTATACG
Found at i:6781585 original size:16 final size:16
Alignment explanation
Indices: 6781560--6781593 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
6781550 CATTAATCAG
6781560 TTAAAAATATATATTA
1 TTAAAAATATATATTA
*
6781576 TTAAATATATATATTA
1 TTAAAAATATATATTA
6781592 TT
1 TT
6781594 TTTGTATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAAAATATATATTA
Found at i:6781800 original size:19 final size:19
Alignment explanation
Indices: 6781776--6781827 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
6781766 ACAAACACAA
6781776 AAATTTATAACATAATCCT
1 AAATTTATAACATAATCCT
6781795 AAATTTATAACATAATCCT
1 AAATTTATAACATAATCCT
6781814 AAATTT-TAA-ATAAT
1 AAATTTATAACATAAT
6781828 TTGTATGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.15
18 3 0.09
19 25 0.76
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTTATAACATAATCCT
Found at i:6781848 original size:8 final size:8
Alignment explanation
Indices: 6781835--6781906 Score: 63
Period size: 8 Copynumber: 8.4 Consensus size: 8
6781825 AATTTGTATG
6781835 AATATTGT
1 AATATTGT
6781843 AATATTGT
1 AATATTGT
*
6781851 AATTTTGTAT
1 AATATTG--T
6781861 GAATATTGT
1 -AATATTGT
* * *
6781870 AATGTCGGG
1 AATAT-TGT
6781879 ATATATTGT
1 A-ATATTGT
6781888 AATATTGT
1 AATATTGT
6781896 AATATTGT
1 AATATTGT
6781904 AAT
1 AAT
6781907 TTTTTGTATG
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
8 36 0.71
9 5 0.10
10 4 0.08
11 6 0.12
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.47
Consensus pattern (8 bp):
AATATTGT
Found at i:6782070 original size:19 final size:19
Alignment explanation
Indices: 6782046--6782097 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
6782036 ACAAACACAA
6782046 AAATTTATAACATAATCCT
1 AAATTTATAACATAATCCT
6782065 AAATTTATAACATAATCCT
1 AAATTTATAACATAATCCT
6782084 AAATTT-TAA-ATAAT
1 AAATTTATAACATAAT
6782098 TTGTATGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.15
18 3 0.09
19 25 0.76
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTTATAACATAATCCT
Found at i:6782076 original size:270 final size:270
Alignment explanation
Indices: 6781593--6782356 Score: 1413
Period size: 270 Copynumber: 2.9 Consensus size: 270
6781583 TATATATTAT
6781593 TTTTGTATGAATATTGTAATGTCGGGATATATTGTAATA---T--TA---TAATTTTTTGTATGA
1 TTTTGTATGAATATTGTAATGTCGGGATATATTGTAATATTGTAATATTGTAATTTTTTGTATGA
6781650 ATATTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTATTAG--T
66 ATATTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTATTAGTAT
* *
6781713 AACTTATTAGTAATTTTGTAATTTATTATTAATAAATTAAATTTTAAATAATTACAAACACAAAA
131 AACTTATTAGTAATTTTGTAATTTATTACTAATAAATTGAATTTTAAATAATTACAAACACAAAA
6781778 ATTTATAACATAATCCTAAATTTATAACATAATCCTAAATTTTAAATAATTTGTATGAATATTGT
196 ATTTATAACATAATCCTAAATTTATAACATAATCCTAAATTTTAAATAATTTGTATGAATATTGT
6781843 AATATTGTAA
261 AATATTGTAA
6781853 TTTTGTATGAATATTGTAATGTCGGGATATATTGTAATATTGTAATATTGTAATTTTTTGTATGA
1 TTTTGTATGAATATTGTAATGTCGGGATATATTGTAATATTGTAATATTGTAATTTTTTGTATGA
6781918 ATATTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTATTAGTAT
66 ATATTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTATTAGTAT
*
6781983 AACTTATTAGTAATTTTGTAATTTATTACTAATAAATTGAATTTTAAGTAATTACAAACACAAAA
131 AACTTATTAGTAATTTTGTAATTTATTACTAATAAATTGAATTTTAAATAATTACAAACACAAAA
6782048 ATTTATAACATAATCCTAAATTTATAACATAATCCTAAATTTTAAATAATTTGTATGAATATTGT
196 ATTTATAACATAATCCTAAATTTATAACATAATCCTAAATTTTAAATAATTTGTATGAATATTGT
*
6782113 AATTTTGTAA
261 AATATTGTAA
6782123 TTTTGTATGAATATTGTAATGTCGGGATATATTGTAATATTGTAATATTGTAATTTTTTGTATGA
1 TTTTGTATGAATATTGTAATGTCGGGATATATTGTAATATTGTAATATTGTAATTTTTTGTATGA
6782188 ATATTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTATTAGTAT
66 ATATTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTATTAGTAT
6782253 AACTTATTAGTAATTTTGTAATTTATTACTAATAAATTGAATTTTAAATAATTACAAACACAAAA
131 AACTTATTAGTAATTTTGTAATTTATTACTAATAAATTGAATTTTAAATAATTACAAACACAAAA
*
6782318 ATTTATAACATAATCCTAAATTTATAACATAACCCTAAA
196 ATTTATAACATAATCCTAAATTTATAACATAATCCTAAA
6782357 CCCGAAAAAA
Statistics
Matches: 488, Mismatches: 6, Indels: 10
0.97 0.01 0.02
Matches are distributed among these distances:
260 39 0.08
263 1 0.00
265 2 0.00
268 77 0.16
270 369 0.76
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (270 bp):
TTTTGTATGAATATTGTAATGTCGGGATATATTGTAATATTGTAATATTGTAATTTTTTGTATGA
ATATTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTATTAGTAT
AACTTATTAGTAATTTTGTAATTTATTACTAATAAATTGAATTTTAAATAATTACAAACACAAAA
ATTTATAACATAATCCTAAATTTATAACATAATCCTAAATTTTAAATAATTTGTATGAATATTGT
AATATTGTAA
Found at i:6782164 original size:8 final size:8
Alignment explanation
Indices: 6782151--6782176 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
6782141 ATGTCGGGAT
6782151 ATATTGTA
1 ATATTGTA
6782159 ATATTGTA
1 ATATTGTA
6782167 ATATTGTA
1 ATATTGTA
6782175 AT
1 AT
6782177 TTTTTGTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (8 bp):
ATATTGTA
Found at i:6782340 original size:19 final size:19
Alignment explanation
Indices: 6782316--6782356 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
6782306 ACAAACACAA
*
6782316 AAATTTATAACATAATCCT
1 AAATTTATAACATAACCCT
6782335 AAATTTATAACATAACCCT
1 AAATTTATAACATAACCCT
6782354 AAA
1 AAA
6782357 CCCGAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATTTATAACATAACCCT
Found at i:6788857 original size:25 final size:25
Alignment explanation
Indices: 6788824--6788876 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
6788814 ATAAACTCTT
6788824 ATTCTCAATTATAAAATCTTAAAAA
1 ATTCTCAATTATAAAATCTTAAAAA
6788849 ATTCTCAATTATAAAATCTTAAAAA
1 ATTCTCAATTATAAAATCTTAAAAA
6788874 ATT
1 ATT
6788877 AGAACATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (25 bp):
ATTCTCAATTATAAAATCTTAAAAA
Found at i:6789571 original size:27 final size:27
Alignment explanation
Indices: 6789541--6789592 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
6789531 TGCCGCTTCT
6789541 GCCAGCTCCTCCACCAGTGCCGCCTGC
1 GCCAGCTCCTCCACCAGTGCCGCCTGC
* *
6789568 GCCAGCTCTTCCACCAGTGCTGCCT
1 GCCAGCTCCTCCACCAGTGCCGCCT
6789593 CTTCCCTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.12, C:0.48, G:0.21, T:0.19
Consensus pattern (27 bp):
GCCAGCTCCTCCACCAGTGCCGCCTGC
Found at i:6790364 original size:6 final size:6
Alignment explanation
Indices: 6790353--6790380 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6790343 CAATGCAATA
6790353 AAAAGG AAAAGG AAAAGG AAAAGG AAAA
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAA
6790381 AACGAACCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:6790909 original size:3 final size:3
Alignment explanation
Indices: 6790895--6790929 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
6790885 AAAGAAAACA
* *
6790895 CAG CAA CAG CAG CAG CAG CAG CAG CAG CAG GAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
6790930 AGAAAAGAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.37, C:0.31, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:6790946 original size:9 final size:8
Alignment explanation
Indices: 6790929--6790962 Score: 50
Period size: 9 Copynumber: 4.0 Consensus size: 8
6790919 CAGCAGGAGC
6790929 AAGAAAAG
1 AAGAAAAG
6790937 AAGAAGAAG
1 AAGAA-AAG
6790946 AAGAAAAAG
1 AAG-AAAAG
6790955 AAGAAAAG
1 AAGAAAAG
6790963 TAGTAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 10 0.42
9 12 0.50
10 2 0.08
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (8 bp):
AAGAAAAG
Found at i:6795073 original size:26 final size:26
Alignment explanation
Indices: 6795024--6795074 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
6795014 TATTTTAAAT
* *
6795024 ATTTTTAATTTAAATTATTCATTTTC
1 ATTTTTAATATAAAATATTCATTTTC
* *
6795050 ATTTTTAATATAAAATGTTTATTTT
1 ATTTTTAATATAAAATATTCATTTT
6795075 TTATATCATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (26 bp):
ATTTTTAATATAAAATATTCATTTTC
Found at i:6796053 original size:2 final size:2
Alignment explanation
Indices: 6796046--6796073 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6796036 GTAAGGAGTA
6796046 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6796074 CTTATAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6797520 original size:23 final size:24
Alignment explanation
Indices: 6797494--6797546 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
6797484 GGAACAAGAT
6797494 ATTATCTCCT-GAGAGATTAGGAA
1 ATTATCTCCTCGAGAGATTAGGAA
*
6797517 ATTATC-CCTCGAGGGATTAGGAA
1 ATTATCTCCTCGAGAGATTAGGAA
6797540 ATTATCT
1 ATTATCT
6797547 ATGAAGGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (24 bp):
ATTATCTCCTCGAGAGATTAGGAA
Found at i:6814977 original size:13 final size:13
Alignment explanation
Indices: 6814961--6814998 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
6814951 TTTAAACCAA
6814961 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
* *
6814974 ACTTTTCCACAGT
1 ACTTTTCAAAAGT
6814987 ACTTTTCAAAAG
1 ACTTTTCAAAAG
6814999 CAATGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:6815643 original size:94 final size:94
Alignment explanation
Indices: 6815540--6815729 Score: 362
Period size: 94 Copynumber: 2.0 Consensus size: 94
6815530 CACCAGTTAA
*
6815540 AATATTGTGCACCAACTAGTACATTATTTAAAATTTACCAACTTTAAACTTAATTTTATTTATTT
1 AATATTGTGCACCAACTAGTACAGTATTTAAAATTTACCAACTTTAAACTTAATTTTATTTATTT
6815605 TAAAATAAAAAATTAATAAATAATAAAAG
66 TAAAATAAAAAATTAATAAATAATAAAAG
*
6815634 AATATTGTGCACCAACTAGTACAGTATTTAAAGTTTACCAACTTTAAACTTAATTTTATTTATTT
1 AATATTGTGCACCAACTAGTACAGTATTTAAAATTTACCAACTTTAAACTTAATTTTATTTATTT
6815699 TAAAATAAAAAATTAATAAATAATAAAAG
66 TAAAATAAAAAATTAATAAATAATAAAAG
6815728 AA
1 AA
6815730 GCGTTGGGTT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.37
Consensus pattern (94 bp):
AATATTGTGCACCAACTAGTACAGTATTTAAAATTTACCAACTTTAAACTTAATTTTATTTATTT
TAAAATAAAAAATTAATAAATAATAAAAG
Found at i:6815818 original size:7 final size:7
Alignment explanation
Indices: 6815808--6815849 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
6815798 GGAACTTAAT
*
6815808 TTTATAT
1 TTTATAA
6815815 TTTA-AA
1 TTTATAA
6815821 TTATATAA
1 TT-TATAA
6815829 TTTATAA
1 TTTATAA
6815836 TTTATAA
1 TTTATAA
6815843 TTTATAA
1 TTTATAA
6815850 AACAAATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 3 0.09
7 25 0.78
8 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTTATAA
Found at i:6816368 original size:20 final size:21
Alignment explanation
Indices: 6816343--6816402 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
6816333 ATTAATTATT
*
6816343 TATAAAATT-TAATTTGAATA
1 TATAAAATTATAATTTAAATA
*
6816363 TAT-AAATTATATTTTAAATA
1 TATAAAATTATAATTTAAATA
*
6816383 TATAATATTATATATTTAAA
1 TATAAAATTATA-ATTTAAA
6816403 ATAAATGTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.15
20 15 0.45
21 7 0.21
22 6 0.18
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TATAAAATTATAATTTAAATA
Found at i:6828877 original size:2 final size:2
Alignment explanation
Indices: 6828870--6828899 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6828860 GCAAAACACT
6828870 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6828900 TCCAAGATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6840655 original size:21 final size:21
Alignment explanation
Indices: 6840609--6840655 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
6840599 TTTACCGATT
6840609 GTTGATCGATGTTGAACGAGC
1 GTTGATCGATGTTGAACGAGC
* * *
6840630 ATTGATTGATTGTTG-ACTAGC
1 GTTGATCGA-TGTTGAACGAGC
6840651 GTTGA
1 GTTGA
6840656 CCATCCATTG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.36
Consensus pattern (21 bp):
GTTGATCGATGTTGAACGAGC
Found at i:6840814 original size:17 final size:17
Alignment explanation
Indices: 6840758--6840831 Score: 78
Period size: 17 Copynumber: 4.2 Consensus size: 17
6840748 ATTAAAAATG
*
6840758 TAAAATATATAATATATA
1 TAAAAT-TAAAATATATA
*
6840776 TAAAAGTAAAATAGTATA
1 TAAAATTAAAATA-TATA
6840794 TAAAATTGAAAATAT-TA
1 TAAAATT-AAAATATATA
* *
6840811 TAAAATTAATATATATT
1 TAAAATTAAAATATATA
6840828 TAAA
1 TAAA
6840832 TTTCAATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
16 6 0.12
17 20 0.42
18 16 0.33
19 6 0.12
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.36
Consensus pattern (17 bp):
TAAAATTAAAATATATA
Found at i:6840881 original size:20 final size:18
Alignment explanation
Indices: 6840836--6840881 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
6840826 TTTAAATTTC
*
6840836 AATTTTTGTATATTTTTT
1 AATTTTTATATATTTTTT
*
6840854 AATATTTATATATTATTTT
1 AATTTTTATATATT-TTTT
6840873 GAATTTTTA
1 -AATTTTTA
6840882 AAATTTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 12 0.52
19 4 0.17
20 7 0.30
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (18 bp):
AATTTTTATATATTTTTT
Found at i:6841583 original size:18 final size:17
Alignment explanation
Indices: 6841542--6841583 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
6841532 ATTTTACACA
6841542 TTTTGTAATTTGATTCT
1 TTTTGTAATTTGATTCT
* *
6841559 TTTTGTAATTTTATTTT
1 TTTTGTAATTTGATTCT
6841576 TCTTTGTA
1 T-TTTGTA
6841584 TCCCTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.17, C:0.05, G:0.10, T:0.69
Consensus pattern (17 bp):
TTTTGTAATTTGATTCT
Found at i:6843813 original size:26 final size:26
Alignment explanation
Indices: 6843783--6843834 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
6843773 CTTAGTTTTA
6843783 GCCTTAGTTTTCTCTAGGTTTTCTCT
1 GCCTTAGTTTTCTCTAGGTTTTCTCT
6843809 GCCTTAGTTTTCTCTAGGTTTTCTCT
1 GCCTTAGTTTTCTCTAGGTTTTCTCT
6843835 TAGTCTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.08, C:0.23, G:0.15, T:0.54
Consensus pattern (26 bp):
GCCTTAGTTTTCTCTAGGTTTTCTCT
Found at i:6846175 original size:21 final size:23
Alignment explanation
Indices: 6846145--6846186 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
6846135 TTGGCACAAA
*
6846145 ATTGAATGAAGAGGTT-TATTTG
1 ATTGAATGAAGAAGTTGTATTTG
6846167 ATTG-ATGAAGAAGTTGTATT
1 ATTGAATGAAGAAGTTGTATT
6846187 CTAATCGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.40
Consensus pattern (23 bp):
ATTGAATGAAGAAGTTGTATTTG
Found at i:6853328 original size:22 final size:22
Alignment explanation
Indices: 6853302--6853346 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
6853292 TCAATGAGTA
6853302 AGGTCTTCAAGAATTCATGCAC
1 AGGTCTTCAAGAATTCATGCAC
6853324 AGGTCTTCAAGAATTCATGCAC
1 AGGTCTTCAAGAATTCATGCAC
6853346 A
1 A
6853347 TTTCAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (22 bp):
AGGTCTTCAAGAATTCATGCAC
Found at i:6856526 original size:19 final size:19
Alignment explanation
Indices: 6856502--6856540 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
6856492 ATAGCATGCG
6856502 AAGCATGAACCTAAAATCT
1 AAGCATGAACCTAAAATCT
6856521 AAGCATGAACCTAAAATCT
1 AAGCATGAACCTAAAATCT
6856540 A
1 A
6856541 TCTTTTATCC
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:0.49, C:0.21, G:0.10, T:0.21
Consensus pattern (19 bp):
AAGCATGAACCTAAAATCT
Found at i:6862795 original size:6 final size:7
Alignment explanation
Indices: 6862777--6862802 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6862767 AAATTCAAAG
6862777 TAAAAAA
1 TAAAAAA
6862784 TAAAAAA
1 TAAAAAA
6862791 TAAAAAA
1 TAAAAAA
6862798 TAAAA
1 TAAAA
6862803 TATTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:6871140 original size:16 final size:17
Alignment explanation
Indices: 6871116--6871192 Score: 61
Period size: 16 Copynumber: 4.5 Consensus size: 17
6871106 CCTTTACAAT
*
6871116 TGTGTGAGCT-TATATG
1 TGTGCGAGCTCTATATG
*
6871132 TGTGCGAGCTCTGTAT-
1 TGTGCGAGCTCTATATG
* *
6871148 TATGCGAGC-CTATATACA
1 TGTGCGAGCTCTATAT--G
*
6871166 TGTGCGAGCTCTATGTTG
1 TGTGCGAGCTCTAT-ATG
6871184 TGTGCGAGC
1 TGTGCGAGC
6871193 CATATACTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
15 5 0.10
16 17 0.35
17 4 0.08
18 17 0.35
19 4 0.08
20 1 0.02
ACGTcount: A:0.18, C:0.17, G:0.30, T:0.35
Consensus pattern (17 bp):
TGTGCGAGCTCTATATG
Found at i:6871175 original size:50 final size:52
Alignment explanation
Indices: 6871095--6871192 Score: 123
Period size: 50 Copynumber: 1.9 Consensus size: 52
6871085 CCCTGTCGCA
*
6871095 TATTATGCGAACCTTTACAATTGTGTGAGCT-TAT-ATGTGTGCGAGCTCTG
1 TATTATGCGAACCTTTACAATTGTGCGAGCTCTATGATGTGTGCGAGCTCTG
* *
6871145 TATTATGCGAGCCTATATAC-A-TGTGCGAGCTCTATGTTGTGTGCGAGC
1 TATTATGCGAACCT-T-TACAATTGTGCGAGCTCTATGATGTGTGCGAGC
6871193 CATATACTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
50 22 0.54
51 5 0.12
52 14 0.34
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (52 bp):
TATTATGCGAACCTTTACAATTGTGCGAGCTCTATGATGTGTGCGAGCTCTG
Found at i:6871963 original size:22 final size:24
Alignment explanation
Indices: 6871933--6871978 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
6871923 TTACAAGATA
*
6871933 TTAATAATATCA-TTAAA-ATATT
1 TTAAAAATATCATTTAAACATATT
6871955 TTAAAAATATCATTTAAACATATT
1 TTAAAAATATCATTTAAACATATT
6871979 ACTTACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.52
23 5 0.24
24 5 0.24
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAAAAATATCATTTAAACATATT
Found at i:6872975 original size:28 final size:29
Alignment explanation
Indices: 6872921--6872998 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
6872911 GGGTTTAGGG
*
6872921 GTTCTAAAAAAATAATTTTGACAAGAT-A
1 GTTCTGAAAAAATAATTTTGACAAGATGA
* * *
6872949 GGTTTTGAAAAAATAATTTT-TCGAGATGA
1 -GTTCTGAAAAAATAATTTTGACAAGATGA
*
6872978 GTTCTGAAGAAATAATTTTGA
1 GTTCTGAAAAAATAATTTTGA
6872999 AGAAAAAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 22 0.55
29 18 0.45
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.36
Consensus pattern (29 bp):
GTTCTGAAAAAATAATTTTGACAAGATGA
Found at i:6876456 original size:2 final size:2
Alignment explanation
Indices: 6876449--6876483 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6876439 GTCTTAGGCA
6876449 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
6876484 TATGAGTCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6881583 original size:10 final size:10
Alignment explanation
Indices: 6881570--6881624 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
6881560 AAATATAAAA
6881570 AAAATTATAT
1 AAAATTATAT
*
6881580 AAAATTATGT
1 AAAATTATAT
6881590 AAAATT-TATT
1 AAAATTATA-T
*
6881600 AATAATTATAA
1 AA-AATTATAT
*
6881611 AAAATTATAG
1 AAAATTATAT
6881621 AAAA
1 AAAA
6881625 AATTATTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 1 0.03
10 29 0.76
11 6 0.16
12 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (10 bp):
AAAATTATAT
Found at i:6881593 original size:21 final size:20
Alignment explanation
Indices: 6881568--6881624 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
6881558 AAAAATATAA
6881568 AAAAAATTATATAAAATTAT
1 AAAAAATTATATAAAATTAT
**
6881588 GTAAAATT-TATTAATAATTAT
1 AAAAAATTATA-TAA-AATTAT
*
6881609 AAAAAATTATAGAAAA
1 AAAAAATTATATAAAA
6881625 AATTATTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 2 0.07
20 11 0.38
21 14 0.48
22 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (20 bp):
AAAAAATTATATAAAATTAT
Found at i:6881640 original size:30 final size:31
Alignment explanation
Indices: 6881572--6881655 Score: 100
Period size: 30 Copynumber: 2.7 Consensus size: 31
6881562 ATATAAAAAA
* * *
6881572 AATTATATAAAATTAT-GTAAAATTTATTAAT
1 AATTATAAAAAATTATAGAAAAAATTATT-AT
6881603 AATTATAAAAAATTATAGAAAAAATTATT-T
1 AATTATAAAAAATTATAGAAAAAATTATTAT
* *
6881633 GATTATAAAAATTTATAGAAAAA
1 AATTATAAAAAATTATAGAAAAA
6881656 TGTTTTCGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
30 22 0.47
31 15 0.32
32 10 0.21
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (31 bp):
AATTATAAAAAATTATAGAAAAAATTATTAT
Found at i:6882974 original size:19 final size:19
Alignment explanation
Indices: 6882950--6882988 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
6882940 TTCAGACAAG
6882950 TTCAGTGCAGAGGAATGCA
1 TTCAGTGCAGAGGAATGCA
6882969 TTCAGTGCAGAGGAATGCA
1 TTCAGTGCAGAGGAATGCA
6882988 T
1 T
6882989 AAGTCCAGCT
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:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (19 bp):
TTCAGTGCAGAGGAATGCA
Found at i:6886846 original size:20 final size:20
Alignment explanation
Indices: 6886821--6886860 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6886811 CGTAAAATGA
*
6886821 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
6886841 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
6886861 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:6886850 original size:34 final size:35
Alignment explanation
Indices: 6886806--6886872 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
6886796 CAGTAAAATA
*
6886806 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
6886840 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
6886873 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:6886876 original size:14 final size:15
Alignment explanation
Indices: 6886800--6886876 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
6886790 GATTGCCAGT
* *
6886800 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
6886814 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
6886828 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
6886848 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
6886863 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
6886877 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:6888546 original size:27 final size:25
Alignment explanation
Indices: 6888516--6888599 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 25
6888506 ATATTCTTAA
6888516 AAATAAAAAATATTAAAAATATGATAG
1 AAATAAAAAATATTAAAAAT-T-ATAG
6888543 AAATTCAAAAAAT-TGGTAAAAATTATAG
1 AAA-T-AAAAAATAT--TAAAAATTATAG
6888571 AAAAATAAAAAA-ATTATAAAATTATAG
1 --AAATAAAAAATATTA-AAAATTATAG
6888598 AA
1 AA
6888600 GAACTATATA
Statistics
Matches: 49, Mismatches: 0, Indels: 18
0.73 0.00 0.27
Matches are distributed among these distances:
25 2 0.04
26 2 0.04
27 13 0.27
28 13 0.27
29 9 0.18
30 10 0.20
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.26
Consensus pattern (25 bp):
AAATAAAAAATATTAAAAATTATAG
Found at i:6888570 original size:28 final size:27
Alignment explanation
Indices: 6888515--6888599 Score: 84
Period size: 28 Copynumber: 3.1 Consensus size: 27
6888505 AATATTCTTA
*
6888515 AAAATAAAAAATATTA-AAAATATGATAG
1 AAAATAAAAAA-ATTATAAAA-ATTATAG
* * *
6888543 AAATTCAAAAAATTGGTAAAAATTATAG
1 AAAATAAAAAAATT-ATAAAAATTATAG
6888571 AAAAATAAAAAAATTAT-AAAATTATAG
1 -AAAATAAAAAAATTATAAAAATTATAG
6888598 AA
1 AA
6888600 GAACTATATA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.04
27 13 0.28
28 16 0.34
29 16 0.34
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.26
Consensus pattern (27 bp):
AAAATAAAAAAATTATAAAAATTATAG
Found at i:6899956 original size:21 final size:23
Alignment explanation
Indices: 6899930--6899975 Score: 78
Period size: 21 Copynumber: 2.1 Consensus size: 23
6899920 TCTATTTAAT
6899930 TATTTTAA-TTATTTAA-TTATA
1 TATTTTAATTTATTTAATTTATA
6899951 TATTTTAATTTATTTAATTTATA
1 TATTTTAATTTATTTAATTTATA
6899974 TA
1 TA
6899976 AGTAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.35
22 8 0.35
23 7 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTTTAATTTATTTAATTTATA
Found at i:6899984 original size:21 final size:21
Alignment explanation
Indices: 6899935--6899986 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
6899925 TTAATTATTT
**
6899935 TAATTATTTAATTATATATTT
1 TAATTATTTAATTATATATAG
6899956 TAATTTATTTAATT-TATATAAG
1 TAA-TTATTTAATTATATAT-AG
6899978 TAATTATTT
1 TAATTATTT
6899987 CATAAATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TAATTATTTAATTATATATAG
Found at i:6902782 original size:48 final size:48
Alignment explanation
Indices: 6902715--6902872 Score: 244
Period size: 48 Copynumber: 3.3 Consensus size: 48
6902705 GATTTGTACA
* * *
6902715 AAAAATGGACAGCATTTAAGCACCAATTTGGACAACATTAATATACTC
1 AAAAATGGACAGCAATTAAGCATCAATTTGGACAGCATTAATATACTC
*
6902763 AAAAATGGGCAGCAATTAAGCATCAATTTGGACAGCATTAATATACTC
1 AAAAATGGACAGCAATTAAGCATCAATTTGGACAGCATTAATATACTC
* * * *
6902811 AAAAATAGACAGCAATTAACCATCAATTTGGACAGCATTAATATGCTA
1 AAAAATGGACAGCAATTAAGCATCAATTTGGACAGCATTAATATACTC
6902859 AAAAATGGACAGCA
1 AAAAATGGACAGCA
6902873 TCTTATCATT
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 100 1.00
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (48 bp):
AAAAATGGACAGCAATTAAGCATCAATTTGGACAGCATTAATATACTC
Found at i:6903485 original size:43 final size:42
Alignment explanation
Indices: 6903437--6903532 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
6903427 AGATATGGTG
** *
6903437 TTACATGTTATAATATATCGATGCCACTGTCCCAGACAGGGTC
1 TTACATGAAATAATATA-CGATGCCAATGTCCCAGACAGGGTC
* *
6903480 TTACATGAAATCATATACGATGCCAATGTCCCAGACATGGTC
1 TTACATGAAATAATATACGATGCCAATGTCCCAGACAGGGTC
*
6903522 TTACACGAAAT
1 TTACATGAAAT
6903533 CACACCTCGA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 33 0.70
43 14 0.30
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (42 bp):
TTACATGAAATAATATACGATGCCAATGTCCCAGACAGGGTC
Found at i:6903501 original size:42 final size:43
Alignment explanation
Indices: 6903449--6903534 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 43
6903439 ACATGTTATA
* *
6903449 ATATATCGATGCCACTGTCCCAGACAGGGTCTTACATGAAATC
1 ATATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAAATC
*
6903492 ATATA-CGATGCCAATGTCCCAGACATGGTCTTACACGAAATC
1 ATATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAAATC
6903534 A
1 A
6903535 CACCTCGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 35 0.88
43 5 0.12
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (43 bp):
ATATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAAATC
Found at i:6907819 original size:9 final size:9
Alignment explanation
Indices: 6907799--6907847 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
6907789 GTAGTGATTC
*
6907799 AATTCAGTT
1 AATTCGGTT
*
6907808 AATTCGGGT
1 AATTCGGTT
*
6907817 AATTCAGTT
1 AATTCGGTT
6907826 AATTCGGTT
1 AATTCGGTT
6907835 AATTCGGTT
1 AATTCGGTT
6907844 AATT
1 AATT
6907848 TTTAACCAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:6907822 original size:18 final size:18
Alignment explanation
Indices: 6907799--6907847 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
6907789 GTAGTGATTC
6907799 AATTCAGTTAATTCGGGT
1 AATTCAGTTAATTCGGGT
*
6907817 AATTCAGTTAATTCGGTT
1 AATTCAGTTAATTCGGGT
*
6907835 AATTCGGTTAATT
1 AATTCAGTTAATT
6907848 TTTAACCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (18 bp):
AATTCAGTTAATTCGGGT
Found at i:6908196 original size:58 final size:58
Alignment explanation
Indices: 6908101--6908218 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
6908091 ATTCACAACC
6908101 AAATAGGCCCATACATCATTAAATATCATAGCCTGAGATTTGGTTCCCTAATTAAAAA
1 AAATAGGCCCATACATCATTAAATATCATAGCCTGAGATTTGGTTCCCTAATTAAAAA
*
6908159 AAATAGGCCCATACATCATTAAATATCATAGCTTGAGATTTGGTTCCCTAATTAAAAA
1 AAATAGGCCCATACATCATTAAATATCATAGCCTGAGATTTGGTTCCCTAATTAAAAA
6908217 AA
1 AA
6908219 TAACTTATAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.30
Consensus pattern (58 bp):
AAATAGGCCCATACATCATTAAATATCATAGCCTGAGATTTGGTTCCCTAATTAAAAA
Found at i:6914334 original size:146 final size:146
Alignment explanation
Indices: 6914070--6914354 Score: 561
Period size: 146 Copynumber: 2.0 Consensus size: 146
6914060 AATATCGATA
6914070 ATGACAATATATCGCAAAGAAATTAGAAATAGAAAAATAAAGAACACAGAGATTTTACGTGGAAA
1 ATGACAATATATCGCAAAGAAATTAGAAATAGAAAAATAAAGAACACAGAGATTTTACGTGGAAA
*
6914135 TCCTTTCGGGAAAAAACCACGGGCAGAGGAGAAGAAAATTTACTATGTCGAATTTGAATTCATTA
66 TCCTTTCGGGAAAAAACCACGGGCAGAGGAGAAGAAAATTCACTATGTCGAATTTGAATTCATTA
6914200 CAAGAGAAAATTCACT
131 CAAGAGAAAATTCACT
6914216 ATGACAATATATCGCAAAGAAATTAGAAATAGAAAAATAAAGAACACAGAGATTTTACGTGGAAA
1 ATGACAATATATCGCAAAGAAATTAGAAATAGAAAAATAAAGAACACAGAGATTTTACGTGGAAA
6914281 TCCTTTCGGGAAAAAACCACGGGCAGAGGAGAAGAAAATTCACTATGTCGAATTTGAATTCATTA
66 TCCTTTCGGGAAAAAACCACGGGCAGAGGAGAAGAAAATTCACTATGTCGAATTTGAATTCATTA
6914346 CAAGAGAAA
131 CAAGAGAAA
6914355 TAGACTATGG
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
146 138 1.00
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.22
Consensus pattern (146 bp):
ATGACAATATATCGCAAAGAAATTAGAAATAGAAAAATAAAGAACACAGAGATTTTACGTGGAAA
TCCTTTCGGGAAAAAACCACGGGCAGAGGAGAAGAAAATTCACTATGTCGAATTTGAATTCATTA
CAAGAGAAAATTCACT
Found at i:6914935 original size:13 final size:13
Alignment explanation
Indices: 6914919--6914958 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
6914909 TTTAAACCAA
6914919 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
6914932 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
6914945 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
6914958 A
1 A
6914959 ATGAAGAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:6915345 original size:11 final size:11
Alignment explanation
Indices: 6915329--6915377 Score: 53
Period size: 11 Copynumber: 4.0 Consensus size: 11
6915319 TTTTAAGTAT
6915329 TTAATTTTTAA
1 TTAATTTTTAA
6915340 TTAATTTTAAAATAA
1 TTAATTTT----TAA
6915355 TTAATTTTTAA
1 TTAATTTTTAA
6915366 TTAATTTATTAA
1 TTAATTT-TTAA
6915378 AATTTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 18 0.55
12 4 0.12
15 11 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTAATTTTTAA
Found at i:6915365 original size:26 final size:25
Alignment explanation
Indices: 6915316--6915372 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 25
6915306 GCGTTGCATG
* *
6915316 TAATTTTAAGTATTTAATTTTTAAT
1 TAATTTTAAATAATTAATTTTTAAT
6915341 TAATTTTAAAATAATTAATTTTTAAT
1 TAATTTT-AAATAATTAATTTTTAAT
6915367 TAATTT
1 TAATTT
6915373 ATTAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 7 0.24
26 22 0.76
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
TAATTTTAAATAATTAATTTTTAAT
Found at i:6915370 original size:15 final size:15
Alignment explanation
Indices: 6915336--6915371 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6915326 TATTTAATTT
6915336 TTAATTAATTTTAAA
1 TTAATTAATTTTAAA
* *
6915351 ATAATTAATTTTTAA
1 TTAATTAATTTTAAA
6915366 TTAATT
1 TTAATT
6915372 TATTAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAATTAATTTTAAA
Found at i:6915403 original size:20 final size:20
Alignment explanation
Indices: 6915357--6915405 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
6915347 TAAAATAATT
6915357 AATTTTTAATTAATTTATTA
1 AATTTTTAATTAATTTATTA
* * *
6915377 AAATTTTAATTCA-TTATTTG
1 AATTTTTAATTAATTTA-TTA
6915397 AATTTTTAA
1 AATTTTTAA
6915406 ATATAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
AATTTTTAATTAATTTATTA
Found at i:6915694 original size:7 final size:7
Alignment explanation
Indices: 6915682--6915708 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
6915672 TAAAATAAAT
6915682 TATTCAC
1 TATTCAC
6915689 TATTCAC
1 TATTCAC
6915696 TATTCAC
1 TATTCAC
6915703 TATTCA
1 TATTCA
6915709 ATTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.44
Consensus pattern (7 bp):
TATTCAC
Found at i:6921762 original size:17 final size:19
Alignment explanation
Indices: 6921726--6921783 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
6921716 ATTACAAAAT
*
6921726 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTATAA
6921745 AATT-AAAAT-ATTTATAAA
1 AATTCAAAATAATTTAT-AA
*
6921763 AATTCTAAAATAATATATAA
1 AATTC-AAAATAATTTATAA
6921783 A
1 A
6921784 TAAAGTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
17 5 0.15
18 11 0.33
19 4 0.12
20 8 0.24
21 5 0.15
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:6921784 original size:19 final size:19
Alignment explanation
Indices: 6921726--6921784 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
6921716 ATTACAAAAT
* *
6921726 AATTC-AAAATAATTTTTA
1 AATTCTAAAATAATATATA
* * *
6921744 AAAT-TAAAATATTTATAAA
1 AATTCTAAAATA-ATATATA
6921763 AATTCTAAAATAATATATA
1 AATTCTAAAATAATATATA
6921782 AAT
1 AAT
6921785 AAAGTTAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 5
0.70 0.19 0.12
Matches are distributed among these distances:
18 9 0.30
19 14 0.47
20 7 0.23
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTCTAAAATAATATATA
Found at i:6922196 original size:2 final size:2
Alignment explanation
Indices: 6922189--6922215 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6922179 TAAGGTACTT
6922189 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6922216 GGGGGTTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6923060 original size:25 final size:24
Alignment explanation
Indices: 6923004--6923060 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
6922994 AGCAATTAAT
* * *
6923004 TATTTTTTAAAATTTTTAAAATTA
1 TATTTTATAAAAATTTTAAAAATA
*
6923028 TAAATTTATAAAAATTTTAAAGAATA
1 T-ATTTTATAAAAATTTTAAA-AATA
6923054 TATTTTA
1 TATTTTA
6923061 ATTTTTTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 1 0.04
25 21 0.81
26 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TATTTTATAAAAATTTTAAAAATA
Found at i:6923778 original size:27 final size:27
Alignment explanation
Indices: 6923748--6923802 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
6923738 TAACAAAGAG
6923748 TTTGGAACCGTTAATAGTAGCATTCAA
1 TTTGGAACCGTTAATAGTAGCATTCAA
6923775 TTTGGAACCGTTAATAGTAGCATTCAA
1 TTTGGAACCGTTAATAGTAGCATTCAA
6923802 T
1 T
6923803 CTCACAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (27 bp):
TTTGGAACCGTTAATAGTAGCATTCAA
Found at i:6923968 original size:16 final size:16
Alignment explanation
Indices: 6923947--6923977 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6923937 GAACGAAAGA
*
6923947 GGAAAAAAAATAGAAT
1 GGAAAAAAAAAAGAAT
6923963 GGAAAAAAAAAAGAA
1 GGAAAAAAAAAAGAA
6923978 AAAGAAAGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (16 bp):
GGAAAAAAAAAAGAAT
Found at i:6925131 original size:13 final size:13
Alignment explanation
Indices: 6925113--6925146 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
6925103 TATTCAAAAG
6925113 CACTTTTCCACAA
1 CACTTTTCCACAA
* *
6925126 CACTTTTCCGCAG
1 CACTTTTCCACAA
6925139 CACTTTTC
1 CACTTTTC
6925147 AAAAGCATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.06, T:0.35
Consensus pattern (13 bp):
CACTTTTCCACAA
Found at i:6928172 original size:46 final size:46
Alignment explanation
Indices: 6928113--6928297 Score: 219
Period size: 46 Copynumber: 4.0 Consensus size: 46
6928103 CAGGGCTTAA
* * *
6928113 TATTCATGTATTCTCAAGCCCACAACATATGCAGGAGCTCAAAACC
1 TATTCCTGTATTCTCAAGTCCACAACATATGCAGGAGCTCGAAACC
** ** *
6928159 TAAACCTGTATTCTCAAGTCTGCAACATATGCAGAAGCTCGAAACC
1 TATTCCTGTATTCTCAAGTCCACAACATATGCAGGAGCTCGAAACC
**
6928205 TATTCCTGTATTCTCGAA-TCCACAACATATATAGGAGCTCGAAACC
1 TATTCCTGTATTCTC-AAGTCCACAACATATGCAGGAGCTCGAAACC
* * * * *
6928251 TATTCATGTATTCTCGAGTCCGCAACATATGTAGGAGCTCGGAACC
1 TATTCCTGTATTCTCAAGTCCACAACATATGCAGGAGCTCGAAACC
6928297 T
1 T
6928298 GGGAAAAACT
Statistics
Matches: 117, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
45 1 0.01
46 114 0.97
47 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (46 bp):
TATTCCTGTATTCTCAAGTCCACAACATATGCAGGAGCTCGAAACC
Found at i:6943002 original size:2 final size:2
Alignment explanation
Indices: 6942995--6943027 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6942985 AAATTTACAA
6942995 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6943028 AAGATAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6945474 original size:2 final size:2
Alignment explanation
Indices: 6945467--6945527 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
6945457 ACACTTGATT
6945467 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6945509 TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA
6945528 AAACTGTTAA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6947731 original size:14 final size:14
Alignment explanation
Indices: 6947711--6947743 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6947701 ATAATTACTT
6947711 TTAAATT-TAAAAA
1 TTAAATTATAAAAA
6947724 TGTAAATTATAAAAA
1 T-TAAATTATAAAAA
6947739 TTAAA
1 TTAAA
6947744 AAATTTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 10 0.56
15 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
TTAAATTATAAAAA
Found at i:6950122 original size:3 final size:3
Alignment explanation
Indices: 6950114--6950160 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
6950104 TGTGCTCTAA
6950114 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
6950161 GAAGAAGATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:6952203 original size:18 final size:17
Alignment explanation
Indices: 6952182--6952223 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
6952172 ACATAGGGGG
6952182 TTTTTTT-AACATTTCACT
1 TTTTTTTCAAC-TTT-ACT
6952200 TTTTCTTTCAACTTTACT
1 TTTT-TTTCAACTTTACT
6952218 TTTTTT
1 TTTTTT
6952224 AAAGGTGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.09
18 11 0.50
19 6 0.27
20 3 0.14
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTTTCAACTTTACT
Found at i:6960409 original size:32 final size:34
Alignment explanation
Indices: 6960345--6960409 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
6960335 CCATTAAGTA
*
6960345 ATTAATATTATGATATATAGAATATATGAAATTC
1 ATTAATATTATGATATATAGAATATATAAAATTC
*
6960379 ATTAATATTATGATATA-CGAA-ATATAAAATT
1 ATTAATATTATGATATATAGAATATATAAAATT
6960410 TATAATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 9 0.31
33 3 0.10
34 17 0.59
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (34 bp):
ATTAATATTATGATATATAGAATATATAAAATTC
Found at i:6960718 original size:30 final size:31
Alignment explanation
Indices: 6960664--6960724 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
6960654 GTACTTTTAT
* *
6960664 TTGATCAATTTTAGTCTATATACTTTTCAAA
1 TTGATCAATTTTAGACCATATACTTTTCAAA
*
6960695 TTGATCAATTTTA-ACCCTATACTTTTCAAA
1 TTGATCAATTTTAGACCATATACTTTTCAAA
6960725 CAAATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 14 0.52
31 13 0.48
ACGTcount: A:0.33, C:0.16, G:0.05, T:0.46
Consensus pattern (31 bp):
TTGATCAATTTTAGACCATATACTTTTCAAA
Found at i:6963764 original size:44 final size:44
Alignment explanation
Indices: 6963683--6963773 Score: 110
Period size: 44 Copynumber: 2.1 Consensus size: 44
6963673 TCAGTATAGT
* *
6963683 TTCATCAAGATGTTGAGTAAAAGAATAATATAAAAGATTCAAAC
1 TTCATCAAGATGTTGAGTAAAAGAACAAGATAAAAGATTCAAAC
* * * * * *
6963727 TTCATTAAGATGTTGATTAAAATAACCAGATACAAGATTCAAGC
1 TTCATCAAGATGTTGAGTAAAAGAACAAGATAAAAGATTCAAAC
6963771 TTC
1 TTC
6963774 TAGTTGCAGG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (44 bp):
TTCATCAAGATGTTGAGTAAAAGAACAAGATAAAAGATTCAAAC
Found at i:6964188 original size:102 final size:102
Alignment explanation
Indices: 6964012--6964208 Score: 376
Period size: 102 Copynumber: 1.9 Consensus size: 102
6964002 CTTCATGAAG
6964012 AATTTCCATATCAGATTCAACTTTCGGAGGTCCAGCAGCATCTTGAGGTGGTTCCCCATGCACAA
1 AATTTCCATATCAGATTCAACTTTCGGAGGTCCAGCAGCATCTTGAGGTGGTTCCCCATGCACAA
6964077 ATGCAGTATTTTCAGTAACTATTTCATTCTCCTCAAC
66 ATGCAGTATTTTCAGTAACTATTTCATTCTCCTCAAC
*
6964114 AATTTCCATATCAGATTCAACTTTCGGAGGTCCAGCAGCATCTTGAGGTGGTTTCCCATGCACAA
1 AATTTCCATATCAGATTCAACTTTCGGAGGTCCAGCAGCATCTTGAGGTGGTTCCCCATGCACAA
*
6964179 ATGCAGTATTTTCAGTACCTATTTCATTCT
66 ATGCAGTATTTTCAGTAACTATTTCATTCT
6964209 TATCATCTTC
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 93 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (102 bp):
AATTTCCATATCAGATTCAACTTTCGGAGGTCCAGCAGCATCTTGAGGTGGTTCCCCATGCACAA
ATGCAGTATTTTCAGTAACTATTTCATTCTCCTCAAC
Found at i:6964832 original size:31 final size:31
Alignment explanation
Indices: 6964785--6964845 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
6964775 TAATAACTTA
*
6964785 GTAACTTAAATAAAAACTTTTAAATAGTTCG
1 GTAACTTAAATAAAAACTTTCAAATAGTTCG
* *
6964816 GTAAGTTAAATGAAAACTTTCAAATAGTTC
1 GTAACTTAAATAAAAACTTTCAAATAGTTC
6964846 AATAATCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (31 bp):
GTAACTTAAATAAAAACTTTCAAATAGTTCG
Found at i:6966212 original size:3 final size:3
Alignment explanation
Indices: 6966204--6966232 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6966194 ATAATTTATA
6966204 CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
6966233 ATTAGTACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.31, T:0.34
Consensus pattern (3 bp):
CTG
Found at i:6975671 original size:14 final size:14
Alignment explanation
Indices: 6975652--6975691 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
6975642 TTGTTTGGCA
6975652 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
6975666 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
6975680 GAAAAATGTTTT
1 GTAAAATGTTTT
6975692 ACTTTTCTGT
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:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:6975700 original size:20 final size:20
Alignment explanation
Indices: 6975675--6975714 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6975665 CGTAAAATGA
*
6975675 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
6975695 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
6975715 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:6975704 original size:34 final size:35
Alignment explanation
Indices: 6975660--6975726 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
6975650 CAGTAAAATG
*
6975660 TTTTCCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
* *
6975694 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
6975727 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:6975832 original size:14 final size:14
Alignment explanation
Indices: 6975813--6975840 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6975803 TTTTTACATA
6975813 TATTAATATATATT
1 TATTAATATATATT
6975827 TATTAATATATATT
1 TATTAATATATATT
6975841 AATAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTAATATATATT
Found at i:6979937 original size:25 final size:25
Alignment explanation
Indices: 6979898--6979949 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
6979888 AAAATGTCTG
6979898 CTGCTTAGAAGAGAATGGAAAATGT
1 CTGCTTAGAAGAGAATGGAAAATGT
6979923 CTGCTTAG-AGAAGAATGGAAAATGT
1 CTGCTTAGAAG-AGAATGGAAAATGT
6979948 CT
1 CT
6979950 TACCAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25
Consensus pattern (25 bp):
CTGCTTAGAAGAGAATGGAAAATGT
Found at i:6982028 original size:21 final size:21
Alignment explanation
Indices: 6982004--6982043 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6981994 GGTACATGTG
* *
6982004 TTAGTATACTTTGTATAGGAT
1 TTAGAATACTTTATATAGGAT
*
6982025 TTAGAATAGTTTATATAGG
1 TTAGAATACTTTATATAGG
6982044 TTTTTAGGCT
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:0.33, C:0.03, G:0.20, T:0.45
Consensus pattern (21 bp):
TTAGAATACTTTATATAGGAT
Found at i:6984351 original size:9 final size:9
Alignment explanation
Indices: 6984337--6984367 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6984327 GTTAAACGAA
6984337 TCGAGTTAT
1 TCGAGTTAT
*
6984346 TCGAGTTAA
1 TCGAGTTAT
6984355 TCGAGTTAT
1 TCGAGTTAT
6984364 TCGA
1 TCGA
6984368 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:6984439 original size:9 final size:9
Alignment explanation
Indices: 6984420--6984456 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
6984410 TGAATTTTCG
*
6984420 AATTTGAAT
1 AATTCGAAT
*
6984429 AACTCGAAT
1 AATTCGAAT
6984438 AATTCGAAT
1 AATTCGAAT
6984447 AATTCGAAT
1 AATTCGAAT
6984456 A
1 A
6984457 TCAAAGTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:6984692 original size:29 final size:29
Alignment explanation
Indices: 6984660--6984774 Score: 124
Period size: 29 Copynumber: 4.0 Consensus size: 29
6984650 AAAAAATAAA
6984660 AAATTACATTTTAACCCCTAAACTTTTTG
1 AAATTACATTTTAACCCCTAAACTTTTTG
* * * *
6984689 AAATTGCATTTTAACCCTTAAA-TTTCATA
1 AAATTACATTTTAACCCCTAAACTTT-TTG
* * *
6984718 AAATTGCATTTTGACCCATAAACTTTTTG
1 AAATTACATTTTAACCCCTAAACTTTTTG
* * *
6984747 AAATTACGTTTTGACACCTAAACTTTTT
1 AAATTACATTTTAACCCCTAAACTTTTT
6984775 CAAAATTTTG
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
28 3 0.04
29 66 0.92
30 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (29 bp):
AAATTACATTTTAACCCCTAAACTTTTTG
Found at i:6985132 original size:3 final size:3
Alignment explanation
Indices: 6985124--6985178 Score: 74
Period size: 3 Copynumber: 17.3 Consensus size: 3
6985114 CCAAGGCGTA
6985124 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAAG AAG AAAG AAG AAG TAAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG -AAG AAG AAG -AAG
*
6985172 AAA AAG A
1 AAG AAG A
6985179 GAAAAAGAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 38 0.81
4 9 0.19
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:6985138 original size:9 final size:9
Alignment explanation
Indices: 6985124--6985178 Score: 74
Period size: 10 Copynumber: 5.8 Consensus size: 9
6985114 CCAAGGCGTA
6985124 AAGAAGAAG
1 AAGAAGAAG
6985133 AAGAAGAAG
1 AAGAAGAAG
6985142 AAGAAGAAG
1 AAGAAGAAG
6985151 AAAGAAGAAAG
1 -AAGAAG-AAG
6985162 AAGAAGTAAG
1 AAGAAG-AAG
*
6985172 AAAAAGA
1 AAGAAGA
6985179 GAAAAAGAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
9 19 0.45
10 20 0.48
11 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (9 bp):
AAGAAGAAG
Found at i:6985183 original size:8 final size:8
Alignment explanation
Indices: 6985170--6985214 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
6985160 AGAAGAAGTA
6985170 AGAAAAAG
1 AGAAAAAG
6985178 AGAAAAAG
1 AGAAAAAG
*
6985186 AGAAAAAAA
1 AG-AAAAAG
6985195 AGAAAAAG
1 AGAAAAAG
6985203 -GAAAAAG
1 AGAAAAAG
6985210 A-AAAA
1 AGAAAA
6985215 TAATAAAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
7 11 0.33
8 15 0.45
9 7 0.21
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AGAAAAAG
Found at i:6985197 original size:35 final size:35
Alignment explanation
Indices: 6985123--6985211 Score: 96
Period size: 35 Copynumber: 2.6 Consensus size: 35
6985113 ACCAAGGCGT
* * *
6985123 AAAGAAGAAGAAGAAGAAGAAGAAGAAGAAAGAAG
1 AAAGAAGAAGAAGAAAAAGAAGAAAAAGAAAGAAA
6985158 AAAGAAGAAGTAAGAAAAAG-AGAAAAAGAGAA-AAA
1 AAAGAAGAAG-AAGAAAAAGAAGAAAAAGA-AAGAAA
*
6985193 AAAGAA-AA-AGGAAAAAGAA
1 AAAGAAGAAGAAGAAAAAGAA
6985212 AAATAATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
32 8 0.17
33 1 0.02
34 2 0.04
35 26 0.55
36 10 0.21
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (35 bp):
AAAGAAGAAGAAGAAAAAGAAGAAAAAGAAAGAAA
Found at i:6985202 original size:6 final size:6
Alignment explanation
Indices: 6985123--6985214 Score: 69
Period size: 6 Copynumber: 14.5 Consensus size: 6
6985113 ACCAAGGCGT
* * * * *
6985123 AAAGAA GAAGAA GAAGAA GAAGAA GAAGAA AGAAGAA AGAAGAA GTAAGAAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA A-AAGAA -AAAG-AA
*
6985175 AAGAGAA AAAGAG AAA-AA AAAGAA AAAGGAA AAAGAA AAA
1 AA-AGAA AAAGAA AAAGAA AAAGAA AAA-GAA AAAGAA AAA
6985215 TAATAAAGCA
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
5 4 0.05
6 40 0.54
7 26 0.35
8 4 0.05
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (6 bp):
AAAGAA
Found at i:6985214 original size:7 final size:7
Alignment explanation
Indices: 6985148--6985214 Score: 53
Period size: 7 Copynumber: 9.1 Consensus size: 7
6985138 GAAGAAGAAG
*
6985148 AAGAAAG
1 AAGAAAA
*
6985155 AAGAAAG
1 AAGAAAA
**
6985162 AAGAAGT
1 AAGAAAA
6985169 AAGAAAA
1 AAGAAAA
6985176 AGAGAAAA
1 A-AGAAAA
6985184 AGAGAAAA
1 A-AGAAAA
*
6985192 AAAAGAAA
1 AAGA-AAA
*
6985200 AAGGAAA
1 AAGAAAA
6985207 AAGAAAA
1 AAGAAAA
6985214 A
1 A
6985215 TAATAAAGCA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
7 30 0.60
8 20 0.40
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.01
Consensus pattern (7 bp):
AAGAAAA
Found at i:6985222 original size:13 final size:13
Alignment explanation
Indices: 6985169--6985214 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
6985159 AAGAAGAAGT
6985169 AAGAAAAAGAGAAA
1 AAGAAAAAG-GAAA
*
6985183 AAGAGAAA--AAA
1 AAGAAAAAGGAAA
6985194 AAGAAAAAGGAAA
1 AAGAAAAAGGAAA
6985207 AAGAAAAA
1 AAGAAAAA
6985215 TAATAAAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 10 0.36
13 11 0.39
14 7 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGGAAA
Found at i:6985338 original size:14 final size:14
Alignment explanation
Indices: 6985318--6985368 Score: 61
Period size: 13 Copynumber: 3.6 Consensus size: 14
6985308 CAAAGCAGCC
*
6985318 CAAAAAAAATAAAG
1 CAAAAAAAACAAAG
6985332 -AAAAAAAACAAAG
1 CAAAAAAAACAAAG
6985345 CAAAAAAAA-AAGCAG
1 CAAAAAAAACAA--AG
6985360 CAAAAAAAA
1 CAAAAAAAA
6985369 GGGGGCAGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
13 14 0.42
14 8 0.24
15 11 0.33
ACGTcount: A:0.80, C:0.10, G:0.08, T:0.02
Consensus pattern (14 bp):
CAAAAAAAACAAAG
Found at i:6985429 original size:26 final size:26
Alignment explanation
Indices: 6985378--6985430 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
6985368 AGGGGGCAGG
** *
6985378 CCAACAGCAGGCCCAATTCCAGCAGC
1 CCAACAGCAGGCCCAAGCCCAACAGC
*
6985404 CCAACAGCAGGCCCCAGCCCAACAGC
1 CCAACAGCAGGCCCAAGCCCAACAGC
6985430 C
1 C
6985431 AGCCTGTCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.47, G:0.19, T:0.04
Consensus pattern (26 bp):
CCAACAGCAGGCCCAAGCCCAACAGC
Found at i:6985526 original size:11 final size:11
Alignment explanation
Indices: 6985510--6985558 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
6985500 GCAGCCCAGC
6985510 AGAAAAAGAAA
1 AGAAAAAGAAA
6985521 AGAAAAA-AAGA
1 AGAAAAAGAA-A
* *
6985532 AAAAAAAG-AG
1 AGAAAAAGAAA
6985542 AGAAAAAGAAA
1 AGAAAAAGAAA
6985553 AGAAAA
1 AGAAAA
6985559 TTTCAATTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 9 0.29
11 22 0.71
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:6985530 original size:13 final size:13
Alignment explanation
Indices: 6985512--6985553 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
6985502 AGCCCAGCAG
6985512 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
6985525 AAAAAGAAAA-AA
1 AAAAAGAAAAGAA
*
6985537 AAGAGAGAAAAAGAA
1 AA-AAAG-AAAAGAA
6985552 AA
1 AA
6985554 GAAAATTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 4 0.16
13 13 0.52
14 4 0.16
15 4 0.16
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Found at i:6985534 original size:19 final size:19
Alignment explanation
Indices: 6985510--6985558 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
6985500 GCAGCCCAGC
6985510 AGAAAAAGAAAAGAAAAAA
1 AGAAAAAGAAAAGAAAAAA
*
6985529 AGAAAAA-AAAGAGAGAAAA
1 AGAAAAAGAAA-AGAAAAAA
6985548 AG-AAAAGAAAA
1 AGAAAAAGAAAA
6985559 TTTCAATTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AGAAAAAGAAAAGAAAAAA
Found at i:6985745 original size:16 final size:16
Alignment explanation
Indices: 6985705--6985748 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
6985695 ATTTTTGTAT
6985705 TTATATTTTCAATTTAA
1 TTATATTTT-AATTTAA
*
6985722 TTAAATTTTAATTTTAA
1 TTATATTTTAA-TTTAA
6985739 TT-TATTTTAA
1 TTATATTTTAA
6985749 ATAATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATATTTTAATTTAA
Found at i:6985943 original size:21 final size:20
Alignment explanation
Indices: 6985911--6985952 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
6985901 TCGGGTTTCG
6985911 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTCAAAA
*
6985931 AAATTTCTCGTGTTTTCAAAA
1 AAATTT-TCGTGTCTTCAAAA
6985952 A
1 A
6985953 TAAAGTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
AAATTTTCGTGTCTTCAAAA
Found at i:6985953 original size:19 final size:19
Alignment explanation
Indices: 6985911--6985952 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
6985901 TCGGGTTTCG
6985911 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTC-AAA
*
6985931 AAATTTCTCGTGTTTTCAAA
1 AAATTT-TCGTGTCTTCAAA
6985951 AA
1 AA
6985953 TAAAGTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (19 bp):
AAATTTTCGTGTCTTCAAA
Found at i:6986108 original size:35 final size:35
Alignment explanation
Indices: 6986058--6986187 Score: 145
Period size: 35 Copynumber: 3.7 Consensus size: 35
6986048 AAAAAATTAG
*
6986058 AAAATTTTTCGTGTTTTCAAAAAATTCCAATTTTC
1 AAAATTTTTCGTGTTTTCAAAAAATTCCAGTTTTC
* *
6986093 AAAATTTTTCATGTTTTCAAAAAATTCCCGTGTTTC
1 AAAATTTTTCGTGTTTTCAAAAAATTCCAGT-TTTC
* ** ** * *
6986129 AAAAATCCTCGTGTTTTCAAAATTTTCGATGTTTTG
1 AAAATTTTTCGTGTTTTCAAAAAATTCCA-GTTTTC
6986165 AAAATTTTT-GTGTTTTCAAAAAA
1 AAAATTTTTCGTGTTTTCAAAAAA
6986188 AAATCTCGTG
Statistics
Matches: 76, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
35 40 0.53
36 34 0.45
37 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (35 bp):
AAAATTTTTCGTGTTTTCAAAAAATTCCAGTTTTC
Found at i:6986151 original size:17 final size:17
Alignment explanation
Indices: 6986058--6986185 Score: 87
Period size: 17 Copynumber: 7.2 Consensus size: 17
6986048 AAAAAATTAG
6986058 AAAATTTTTCGTGTTTTC
1 AAAA-TTTTCGTGTTTTC
** ***
6986076 AAAAAATTCCAATTTTC
1 AAAATTTTCGTGTTTTC
*
6986093 AAAATTTTTCATGTTTTC
1 AAAA-TTTTCGTGTTTTC
**
6986111 AAAAAATTCCCGTG-TTTC
1 --AAAATTTTCGTGTTTTC
**
6986129 AAAAATCCTCGTGTTTTC
1 -AAAATTTTCGTGTTTTC
*
6986147 AAAATTTTCGATGTTTTG
1 AAAATTTTCG-TGTTTTC
*
6986165 AAAATTTTTGTGTTTTC
1 AAAATTTTCGTGTTTTC
6986182 AAAA
1 AAAA
6986186 AAAAATCTCG
Statistics
Matches: 85, Mismatches: 20, Indels: 11
0.73 0.17 0.09
Matches are distributed among these distances:
17 41 0.48
18 35 0.41
19 5 0.06
20 4 0.05
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.45
Consensus pattern (17 bp):
AAAATTTTCGTGTTTTC
Found at i:6986186 original size:18 final size:18
Alignment explanation
Indices: 6986058--6986186 Score: 95
Period size: 18 Copynumber: 7.3 Consensus size: 18
6986048 AAAAAATTAG
*
6986058 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* ***
6986076 AAAAA-ATTCCAATTTTC
1 AAAAATTTTCGTGTTTTC
* *
6986093 AAAATTTTTCATGTTTTC
1 AAAAATTTTCGTGTTTTC
**
6986111 AAAAAATTCCCGTG-TTTC
1 -AAAAATTTTCGTGTTTTC
**
6986129 AAAAATCCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
6986147 -AAAATTTTCGATGTTTT-
1 AAAAATTTTCG-TGTTTTC
* *
6986164 GAAAATTTTTGTGTTTTC
1 AAAAATTTTCGTGTTTTC
6986182 AAAAA
1 AAAAA
6986187 AAAATCTCGT
Statistics
Matches: 85, Mismatches: 20, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
17 37 0.44
18 39 0.46
19 9 0.11
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:6986233 original size:55 final size:57
Alignment explanation
Indices: 6986129--6986240 Score: 133
Period size: 55 Copynumber: 2.0 Consensus size: 57
6986119 CCCGTGTTTC
*** *
6986129 AAAAATCCTCGTGTTTTCAAAATTTTCGATGTTTTGAAAATTTTTGTGTTTTCAAAA
1 AAAAATCCTCGTGTTTTCAAAATTTTCGATGTTTTGAAAAAAATTGTGTTTCCAAAA
*
6986186 AAAAAT-CTCGTG-TTTCATAAATTTTC-AT-TTTTTAAACAAAATTGTGTTTCCAAAA
1 AAAAATCCTCGTGTTTTCA-AAATTTTCGATGTTTTGAAA-AAAATTGTGTTTCCAAAA
6986241 TTCTCGTGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
54 7 0.15
55 21 0.44
56 14 0.29
57 6 0.12
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.44
Consensus pattern (57 bp):
AAAAATCCTCGTGTTTTCAAAATTTTCGATGTTTTGAAAAAAATTGTGTTTCCAAAA
Done.