Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 45 of 138
Found at i:9719991 original size:14 final size:13
Alignment explanation
Indices: 9719967--9719999 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
9719957 TAATTTATTG
9719967 ATTTGAATTTTAT
1 ATTTGAATTTTAT
9719980 ATTTGAATTTT-T
1 ATTTGAATTTTAT
9719992 ATTT-AATT
1 ATTTGAATT
9720000 ATTTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 5 0.25
13 11 0.55
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (13 bp):
ATTTGAATTTTAT
Found at i:9721133 original size:13 final size:13
Alignment explanation
Indices: 9721115--9721139 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9721105 ATTTCTTAGT
9721115 TCTTTACTTTGAA
1 TCTTTACTTTGAA
9721128 TCTTTACTTTGA
1 TCTTTACTTTGA
9721140 TAAGAAAGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
TCTTTACTTTGAA
Found at i:9729557 original size:26 final size:26
Alignment explanation
Indices: 9729528--9729579 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
9729518 TGGCATGTAT
9729528 GATGCATTTCATTACATTTTCTCTTC
1 GATGCATTTCATTACATTTTCTCTTC
* *
9729554 GATGCATTTTATTACATTTTTTCTTC
1 GATGCATTTCATTACATTTTCTCTTC
9729580 AAACCACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.08, T:0.54
Consensus pattern (26 bp):
GATGCATTTCATTACATTTTCTCTTC
Found at i:9731904 original size:45 final size:47
Alignment explanation
Indices: 9731804--9731906 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 47
9731794 ATTTAAATAT
*
9731804 CTAAAGTTTTTTGAATGACAATCTTTTGAAATCTTAAATGTGAATTC
1 CTAAAGTTTTTTGAATGACAATATTTTGAAATCTTAAATGTGAATTC
* * *
9731851 CTAAAGTTTTTTTAATGAGAA-ATTTTGAAAT-TTGAATGTGAA-TC
1 CTAAAGTTTTTTGAATGACAATATTTTGAAATCTTAAATGTGAATTC
9731895 CTTAAAGTTTTT
1 C-TAAAGTTTTT
9731907 ATTGAATAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
44 3 0.06
45 20 0.39
46 9 0.18
47 19 0.37
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.45
Consensus pattern (47 bp):
CTAAAGTTTTTTGAATGACAATATTTTGAAATCTTAAATGTGAATTC
Found at i:9731964 original size:43 final size:43
Alignment explanation
Indices: 9731917--9732096 Score: 161
Period size: 43 Copynumber: 4.1 Consensus size: 43
9731907 ATTGAATAAA
*
9731917 AATCTTTGAATTTTAGG-TCTGAATTTCTAAAATTTT-GAATGTG
1 AATCTTTGAATTTT-GGATGTGAATTT-TAAAATTTTCGAATGTG
*** * *
9731960 AATCTTTGAATTTTGGATGTGAGCCTTGAAATTTTCAAATGTG
1 AATCTTTGAATTTTGGATGTGAATTTTAAAATTTTCGAATGTG
* **
9732003 AATCTTTGAATTTTGGATGTAAATCACTAACAAAAATCTTTCGAATGTG
1 AATCTTTGAATTTTGGATGTGAAT---T--TTAAAAT-TTTCGAATGTG
*
9732052 AATCTTTGAATTTTAGATGTGAA-TTTAGAAATTTT-GAATGTG
1 AATCTTTGAATTTTGGATGTGAATTTTA-AAATTTTCGAATGTG
9732094 AAT
1 AAT
9732097 TTCTAAAAAT
Statistics
Matches: 110, Mismatches: 18, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
42 20 0.18
43 50 0.45
44 4 0.04
45 1 0.01
48 4 0.04
49 31 0.28
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (43 bp):
AATCTTTGAATTTTGGATGTGAATTTTAAAATTTTCGAATGTG
Found at i:9731973 original size:21 final size:21
Alignment explanation
Indices: 9731947--9732096 Score: 90
Period size: 21 Copynumber: 6.8 Consensus size: 21
9731937 GAATTTCTAA
9731947 AATTTTGAATGTGAATCTTTG
1 AATTTTGAATGTGAATCTTTG
* * *
9731968 AATTTTGGATGTG-AGCCTTG
1 AATTTTGAATGTGAATCTTTG
*
9731988 AAATTTTCAAATGTGAATCTTTG
1 -AATTTT-GAATGTGAATCTTTG
* * ***
9732011 AATTTTGGATGTAAATCACTAACAAA
1 AATTTTGAATGTGAAT--CT---TTG
9732037 AATCTTTCGAATGTGAATCTTTG
1 AAT-TTT-GAATGTGAATCTTTG
*
9732060 AATTTT-AGATGTGAAT-TTAG
1 AATTTTGA-ATGTGAATCTTTG
9732080 AAATTTTGAATGTGAAT
1 -AATTTTGAATGTGAAT
9732097 TTCTAAAAAT
Statistics
Matches: 97, Mismatches: 19, Indels: 26
0.68 0.13 0.18
Matches are distributed among these distances:
20 9 0.09
21 47 0.48
22 15 0.15
23 10 0.10
26 5 0.05
27 3 0.03
28 8 0.08
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.41
Consensus pattern (21 bp):
AATTTTGAATGTGAATCTTTG
Found at i:9732050 original size:49 final size:43
Alignment explanation
Indices: 9731945--9732096 Score: 139
Period size: 49 Copynumber: 3.4 Consensus size: 43
9731935 CTGAATTTCT
* *
9731945 AAAATTTT-GAATGTGAATCTTTGAATTTTGGATGTGAGCCTT
1 AAAATTTTCGAATGTGAATCTTTGAATTTTGGATGTAAGCCTA
* * *
9731987 GAAATTTTCAAATGTGAATCTTTGAATTTTGGATGTAAATCACTAACA
1 AAAATTTTCGAATGTGAATCTTTGAATTTTGGATGT-AAGC-CT---A
* **
9732035 AAAATCTTTCGAATGTGAATCTTTGAATTTTAGATGTGAA-TTTA
1 AAAAT-TTTCGAATGTGAATCTTTGAATTTTGGATGT-AAGCCTA
*
9732079 GAAATTTT-GAATGTGAAT
1 AAAATTTTCGAATGTGAAT
9732097 TTCTAAAAAT
Statistics
Matches: 91, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
42 17 0.19
43 29 0.32
44 7 0.08
45 2 0.02
47 1 0.01
48 4 0.04
49 31 0.34
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (43 bp):
AAAATTTTCGAATGTGAATCTTTGAATTTTGGATGTAAGCCTA
Found at i:9732724 original size:20 final size:19
Alignment explanation
Indices: 9732689--9732730 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
9732679 TTATTTGTAC
*
9732689 TTTTTTTTTAT-TTTTTTA
1 TTTTTTTTTATCTTTTCTA
9732707 TTTTTTATTCTATCTTTTCTA
1 TTTTTT-TT-TATCTTTTCTA
9732728 TTT
1 TTT
9732731 ATCTTTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 6 0.30
19 2 0.10
20 3 0.15
21 9 0.45
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTTTTATCTTTTCTA
Found at i:9735653 original size:16 final size:17
Alignment explanation
Indices: 9735622--9735654 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9735612 ATATTTTATT
9735622 AATTAAAATAATAAAAA
1 AATTAAAATAATAAAAA
*
9735639 AATTTAAAT-ATAAAAA
1 AATTAAAATAATAAAAA
9735655 CTCGATTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATTAAAATAATAAAAA
Found at i:9736197 original size:76 final size:79
Alignment explanation
Indices: 9736090--9736237 Score: 203
Period size: 76 Copynumber: 1.9 Consensus size: 79
9736080 AAAGACTACA
* * * * * *
9736090 TTTTTTATCTTAAAAATATTGTTTTTGTTGAATTTTG-AAATT-T-TTTTTTCATATTTTCAATA
1 TTTTTTATCTTAAAAACATTATCTTTATTGAATTATGAAAATTATATTTTTTCATATTTTCAACA
9736152 AAGATTGTGTTTTT
66 AAGATTGTGTTTTT
* *
9736166 TTTTTTATCTTAAAAACATTATCTTTATTGAATTATGAAAATTATATTTTTTGATGTTTTCAACA
1 TTTTTTATCTTAAAAACATTATCTTTATTGAATTATGAAAATTATATTTTTTCATATTTTCAACA
9736231 AAGATTG
66 AAGATTG
9736238 CATTTTCTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
76 32 0.52
77 5 0.08
78 1 0.02
79 23 0.38
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.55
Consensus pattern (79 bp):
TTTTTTATCTTAAAAACATTATCTTTATTGAATTATGAAAATTATATTTTTTCATATTTTCAACA
AAGATTGTGTTTTT
Found at i:9736279 original size:74 final size:74
Alignment explanation
Indices: 9736187--9736404 Score: 237
Period size: 76 Copynumber: 2.9 Consensus size: 74
9736177 AAAAACATTA
* *
9736187 TCTTTATTGAATTATGAAAATTATATTTTTTGATGTTTTCAACAAAGATTGCATTTTCTATTTTC
1 TCTTTATTGAATTATGAAAATTATATTTTTTCATGTTTTCAACAAAGATTGCATTTTCTATTTTA
9736252 GAAACATCG
66 GAAACATCG
* * * * * * *
9736261 TCTTTATTGAATTTTGAAAAATATTTTTTTTTTTATGATTTCAACAGAGACTATG--TTTTCTAG
1 TCTTTATTGAATTATG-AAAAT-TATATTTTTTCATGTTTTCAACAAAGA-T-TGCATTTTCTAT
*
9736324 TTTAGAAACTTCG
62 TTTAGAAACATCG
* * * *
9736337 TCTTTGTTGAATTAT-AAAA-AATAGTTTTTTCATGTTTTCAACAAAGATTGCATTCTCTATATT
1 TCTTTATTGAATTATGAAAATTATA-TTTTTTCATGTTTTCAACAAAGATTGCATTTTCTATTTT
9736400 AGAAA
65 AGAAA
9736405 TGTTATCAGT
Statistics
Matches: 117, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
71 2 0.02
72 2 0.02
73 33 0.28
74 19 0.16
75 5 0.04
76 53 0.45
77 1 0.01
78 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.47
Consensus pattern (74 bp):
TCTTTATTGAATTATGAAAATTATATTTTTTCATGTTTTCAACAAAGATTGCATTTTCTATTTTA
GAAACATCG
Found at i:9736612 original size:20 final size:20
Alignment explanation
Indices: 9736587--9736624 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9736577 CTCTACCAAC
9736587 AAAAAACTATAT-TTTTATAT
1 AAAAAA-TATATATTTTATAT
9736607 AAAAAATATATATTTTAT
1 AAAAAATATATATTTTAT
9736625 CAATTACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAAAATATATATTTTATAT
Found at i:9736824 original size:30 final size:30
Alignment explanation
Indices: 9736783--9736842 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
9736773 TTGCAAGTGT
* * *
9736783 CCAATTTTGTGGTTAGAAATGTAGCTTTGC
1 CCAATTATGTGGCTAGAAATGTACCTTTGC
*
9736813 CCAATTATGTGGCTAGCAATGTACCTTTGC
1 CCAATTATGTGGCTAGAAATGTACCTTTGC
9736843 ATGTTAGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (30 bp):
CCAATTATGTGGCTAGAAATGTACCTTTGC
Found at i:9741261 original size:23 final size:25
Alignment explanation
Indices: 9741229--9741276 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
9741219 TATTTATTAG
*
9741229 TCAAATATAT-CAAAT-AAGCACAA
1 TCAAACATATGCAAATCAAGCACAA
*
9741252 TCAAACATATGCATATCAAGCACAA
1 TCAAACATATGCAAATCAAGCACAA
9741277 GTAAATTCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 4 0.19
25 8 0.38
ACGTcount: A:0.52, C:0.21, G:0.06, T:0.21
Consensus pattern (25 bp):
TCAAACATATGCAAATCAAGCACAA
Found at i:9743945 original size:9 final size:9
Alignment explanation
Indices: 9743931--9743957 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
9743921 CAATATGCAT
9743931 AAAAATCAC
1 AAAAATCAC
9743940 AAAAATCAC
1 AAAAATCAC
9743949 AAAAATCAC
1 AAAAATCAC
9743958 TTTCATCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.22, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAATCAC
Found at i:9762465 original size:16 final size:16
Alignment explanation
Indices: 9762440--9762496 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
9762430 AAATTCAATC
9762440 ATTTTAAATTTAGATT
1 ATTTTAAATTTAGATT
*
9762456 ATTTTGAATTTA-ATT
1 ATTTTAAATTTAGATT
*
9762471 ATTTTAAGTTTGAGA-T
1 ATTTTAAATTT-AGATT
9762487 ATTTTAAATT
1 ATTTTAAATT
9762497 CAAAATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 12 0.34
16 22 0.63
17 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (16 bp):
ATTTTAAATTTAGATT
Found at i:9762490 original size:31 final size:31
Alignment explanation
Indices: 9762425--9762499 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
9762415 GATTTTAACC
*
9762425 ATTTCAAATTCAATCATTTTAAATTTAGATT
1 ATTTTAAATTCAATCATTTTAAATTTAGATT
* * * *
9762456 ATTTTGAATTTAATTATTTTAAGTTTGAGA-T
1 ATTTTAAATTCAATCATTTTAAATTT-AGATT
9762487 ATTTTAAATTCAA
1 ATTTTAAATTCAA
9762500 AATATTTAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 33 0.92
32 3 0.08
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (31 bp):
ATTTTAAATTCAATCATTTTAAATTTAGATT
Found at i:9762789 original size:20 final size:19
Alignment explanation
Indices: 9762764--9762814 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 19
9762754 TGATTAATCA
9762764 AAAATAAATTAATAAATTTT
1 AAAAT-AATTAATAAATTTT
*
9762784 AAAATAATTTATAAATTTT
1 AAAATAATTAATAAATTTT
9762803 AAGAAATAATTA
1 -A-AAATAATTA
9762815 GTCATGTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 13 0.48
20 6 0.22
21 8 0.30
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
AAAATAATTAATAAATTTT
Found at i:9762864 original size:17 final size:18
Alignment explanation
Indices: 9762831--9762866 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9762821 TAAAAGTAAT
9762831 ATATTAAAAATAATATAA
1 ATATTAAAAATAATATAA
*
9762849 ATATTAAATA-AATATAA
1 ATATTAAAAATAATATAA
9762866 A
1 A
9762867 AAAGTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATATTAAAAATAATATAA
Found at i:9765116 original size:38 final size:38
Alignment explanation
Indices: 9765074--9765167 Score: 109
Period size: 39 Copynumber: 2.4 Consensus size: 38
9765064 AGTTTAGCTA
* *
9765074 AGGTTGAGAGTTTGGGGCTTT-GATATAGGGTTTAAGAT
1 AGGTTTAGAGTTTGGGG-TTTCGATATAAGGTTTAAGAT
* * *
9765112 AGGTTTAGAGGTTTGGGGTTTCGGTTTAAGGTTTAGGAT
1 AGGTTTAGA-GTTTGGGGTTTCGATATAAGGTTTAAGAT
*
9765151 AGATTTAGAGTTTGGGG
1 AGGTTTAGAGTTTGGGG
9765168 GTTTAGTTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
38 19 0.40
39 29 0.60
ACGTcount: A:0.21, C:0.02, G:0.38, T:0.38
Consensus pattern (38 bp):
AGGTTTAGAGTTTGGGGTTTCGATATAAGGTTTAAGAT
Found at i:9765239 original size:19 final size:19
Alignment explanation
Indices: 9765186--9765240 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
9765176 AAAGTTTACG
* *
9765186 TAAGGGTTTAGGGTTGGCA
1 TAAGGGTTTAAGGTTTGCA
*
9765205 TAAGGGTTTATGGTTTGCA
1 TAAGGGTTTAAGGTTTGCA
*
9765224 TTAGGGTTTAAGGTTTG
1 TAAGGGTTTAAGGTTTG
9765241 TATTTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.20, C:0.04, G:0.36, T:0.40
Consensus pattern (19 bp):
TAAGGGTTTAAGGTTTGCA
Found at i:9765348 original size:38 final size:39
Alignment explanation
Indices: 9765268--9765368 Score: 136
Period size: 38 Copynumber: 2.7 Consensus size: 39
9765258 TGGTATGAGA
* *
9765268 GTTTAGGGTTTGTG--TAAGGTTTTACGATTTGCATGGG
1 GTTTAGGGTTTGTGTTTAAGGTTTAAAGATTTGCATGGG
*
9765305 ATTTAGGGTTTGTGTTTAAGGTTTAAAG-TTTGCATGGG
1 GTTTAGGGTTTGTGTTTAAGGTTTAAAGATTTGCATGGG
* *
9765343 GTTTAGGGTTTATGTTTAGGGTTTAA
1 GTTTAGGGTTTGTGTTTAAGGTTTAA
9765369 GTGGTGCATG
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
37 13 0.23
38 33 0.59
39 10 0.18
ACGTcount: A:0.19, C:0.03, G:0.33, T:0.46
Consensus pattern (39 bp):
GTTTAGGGTTTGTGTTTAAGGTTTAAAGATTTGCATGGG
Found at i:9765361 original size:13 final size:13
Alignment explanation
Indices: 9765343--9765367 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9765333 TTTGCATGGG
9765343 GTTTAGGGTTTAT
1 GTTTAGGGTTTAT
9765356 GTTTAGGGTTTA
1 GTTTAGGGTTTA
9765368 AGTGGTGCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (13 bp):
GTTTAGGGTTTAT
Found at i:9765377 original size:38 final size:38
Alignment explanation
Indices: 9765297--9765378 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 38
9765287 TTTTACGATT
* *
9765297 TGCATGGGATTTAGGGTTTGTGTTTAAGGTTTAAAGTT
1 TGCATGGGATTTAGGGTTTATGTTTAAGGTTTAAAGTG
* *
9765335 TGCATGGGGTTTAGGGTTTATGTTTAGGGTTT-AAGTGG
1 TGCATGGGATTTAGGGTTTATGTTTAAGGTTTAAAGT-G
9765373 TGCATG
1 TGCATG
9765379 TGACAAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 4 0.10
38 35 0.90
ACGTcount: A:0.18, C:0.04, G:0.35, T:0.43
Consensus pattern (38 bp):
TGCATGGGATTTAGGGTTTATGTTTAAGGTTTAAAGTG
Found at i:9768757 original size:19 final size:20
Alignment explanation
Indices: 9768735--9768787 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 20
9768725 TTTTTCACAA
9768735 CTTTATTACTTT-TGTTTTT
1 CTTTATTACTTTATGTTTTT
*
9768754 CTTT-TT-TTTTCATGTTTTT
1 CTTTATTACTTT-ATGTTTTT
9768773 CTTTATATACTTTAT
1 CTTTAT-TACTTTAT
9768788 ACATTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
17 3 0.11
18 2 0.07
19 15 0.56
20 1 0.04
21 3 0.11
22 3 0.11
ACGTcount: A:0.13, C:0.11, G:0.04, T:0.72
Consensus pattern (20 bp):
CTTTATTACTTTATGTTTTT
Found at i:9776152 original size:144 final size:142
Alignment explanation
Indices: 9775905--9776464 Score: 462
Period size: 144 Copynumber: 3.9 Consensus size: 142
9775895 TAATACACCA
* * * * * * * ** * **
9775905 AAAATT-ATAAAATAATATAAAAACATGATATATAGTTTTTCATGAAAAATCAACCTTAAGAAGG
1 AAAATTCATGAAATAATATTAAAATAAGATCTAAAGCTTTTCACAAAAAATCAACCTTAAAAAAT
** ** * * *
9775969 TCAAATTACAAAAATACTTGTAAAAGGTATTTTGGTAATTTTGCATCTTTTAAGGTACAATCAAG
66 TCAAATTATGAAAATAC-CCTAAAAGGTATTTTAGTAATTTTACA-CTTTTAAGGTGCAATCAAG
9776034 GTTTTTAATGCATC
129 GTTTTTAATGCATC
* * * * *
9776048 AAAATTCATGAAACAATATTAAAATAAAATCTAAAGCCTTTCACAAAAAATCAACCTTGAAAATT
1 AAAATTCATGAAATAATATTAAAATAAGATCTAAAGCTTTTCACAAAAAATCAACCTTAAAAAAT
* **
9776113 TCAAATTATGAAAATAACCCTAAAAGGTATTTTAGTAATTTAACACATTTCGAGGTGCAATCAAG
66 TCAAATTATGAAAAT-ACCCTAAAAGGTATTTTAGTAATTTTACAC-TTTTAAGGTGCAATCAAG
* **
9776178 GCTTTTAATATATC
129 GTTTTTAATGCATC
* * * * ** * *
9776192 AAAATTCATGAAATAATATTAAAACATGATTTAAAGTTTTTCATTAAAAATCTACCTTAAGAAAG
1 AAAATTCATGAAATAATATTAAAATAAGATCTAAAGCTTTTCACAAAAAATCAACCTTAA-AAAA
* * * * * * * *
9776257 TT-AATTTATAAAAATACCTTAAAAGGCATTTCAATAATTTTACACCTTTTGAA-GTGCGATAAA
65 TTCAAATTATGAAAATACCCTAAAAGGTATTTTAGTAATTTTACA-CTTTT-AAGGTGCAATCAA
*
9776320 GGTTTTGTAATGCATA
128 GGTTTT-TAATGCATC
* * * * *
9776336 AAAAATCATGAAATAATATTAAAATAAGATCTAAAGCTTTTCGCAACAAATCAA-CTTTAAAAAG
1 AAAATTCATGAAATAATATTAAAATAAGATCTAAAGCTTTTCACAAAAAATCAACCTTAAAAAAT
* * * * * * * *
9776400 TCAAATTATGAAACTACCTTAAAATGATAATTTGGTAATTTAACAGCTTCTGAGGTGCAATCAAG
66 TCAAATTATGAAAATACCCTAAAA-GGTATTTTAGTAATTTTACA-CTTTTAAGGTGCAATCAAG
9776465 ACTTTTAGTA
Statistics
Matches: 323, Mismatches: 84, Indels: 19
0.76 0.20 0.04
Matches are distributed among these distances:
142 4 0.01
143 71 0.22
144 241 0.75
145 7 0.02
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (142 bp):
AAAATTCATGAAATAATATTAAAATAAGATCTAAAGCTTTTCACAAAAAATCAACCTTAAAAAAT
TCAAATTATGAAAATACCCTAAAAGGTATTTTAGTAATTTTACACTTTTAAGGTGCAATCAAGGT
TTTTAATGCATC
Found at i:9786249 original size:17 final size:16
Alignment explanation
Indices: 9786223--9786268 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 16
9786213 GTATATTTCA
*
9786223 TTTTATTTTTACTTTATT
1 TTTTATTTTT--TTAATT
9786241 TTTTATTTTTTTAATT
1 TTTTATTTTTTTAATT
9786257 TTATTATTTTTT
1 TT-TTATTTTTT
9786269 GTATATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 7 0.27
17 9 0.35
18 10 0.38
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTATTTTTTTAATT
Found at i:9793065 original size:18 final size:18
Alignment explanation
Indices: 9793042--9793078 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9793032 AGAAAAACAT
9793042 GAAAAAAAAAGAAAGAAA
1 GAAAAAAAAAGAAAGAAA
**
9793060 GAAAAAAAATTAAAGAAA
1 GAAAAAAAAAGAAAGAAA
9793078 G
1 G
9793079 CTTGAAGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.05
Consensus pattern (18 bp):
GAAAAAAAAAGAAAGAAA
Found at i:9797546 original size:12 final size:13
Alignment explanation
Indices: 9797517--9797549 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
9797507 TGTTTTCGTC
*
9797517 GCTCTCCCCTCTT
1 GCTCTCCCCACTT
9797530 GCTCTCCCCAC-T
1 GCTCTCCCCACTT
9797542 GCTCTCCC
1 GCTCTCCC
9797550 TATTCTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.03, C:0.58, G:0.09, T:0.30
Consensus pattern (13 bp):
GCTCTCCCCACTT
Found at i:9811765 original size:159 final size:157
Alignment explanation
Indices: 9811408--9811857 Score: 471
Period size: 159 Copynumber: 2.9 Consensus size: 157
9811398 CATATTTTGC
* * **
9811408 TTTGTGATTCTTGTTGTGTATTGTACTTGTTGC-TAAACAACTTTTATAGTAATTTCAAAGTATA
1 TTTGTGATTCTTGTTGTGTATTGTGCTTGTT-CATAAACTACTTTTATA-TAA-TTCAAAGCCTA
* * * **
9811472 AAATTTATTGAAAATTCTTTATTAAACTAGATAGTGTATTGTGTGTTTTGCGATGCAATAACTTT
63 AAATTTGTAGAAAATTCTTTATTAAACTAGATAGTGTATTGTGTGTATTAAGATGCAATAACTTT
* * *
9811537 GTAAAATGTGAAAATTATTATGTATTTTAG
128 GTAAAAGGTGAAAACTATTATGTATGTTAG
* * * * **
9811567 TTTCTGTTTCTTATTGTGTATTGTGCTTGTTGACGAACTACTTTTATACTAATTCAAAAGCCTAA
1 TTTGTGATTCTTGTTGTGTATTGTGCTTGTTCATAAACTACTTTTATA-TAATTC-AAAGCCTAA
* **
9811632 AATTTGTAGAAAATTCTTTGTTAAACTAGATAGTGTATTGTGTGTATTAAGATGTTATAACTTTG
64 AATTTGTAGAAAATTCTTTATTAAACTAGATAGTGTATTGTGTGTATTAAGATGCAATAACTTTG
* *
9811697 TGAAAGGTGAAAACTATTATGTATGTTAT
129 TAAAAGGTGAAAACTATTATGTATGTTAG
* * *
9811726 TTTGTGACTCTTGTTGTGTATTATGCTT-TTCAATAAACTAC-TTT-TAT-AGTCAAAGCCTAAA
1 TTTGTGATTCTTGTTGTGTATTGTGCTTGTTC-ATAAACTACTTTTATATAATTCAAAGCCTAAA
* * * * * * * * *
9811787 ATTTGTA-AGAAATTCTTTATTGAATTAGAAAATATTTTTTGTATATTAGGATGCAATAACTTTG
65 ATTTGTAGA-AAATTCTTTATTAAACTAGATAGTGTATTGTGTGTATTAAGATGCAATAACTTTG
9811851 TGAAAAG
129 T-AAAAG
9811858 TAAAACCTGT
Statistics
Matches: 240, Mismatches: 46, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
153 1 0.00
154 61 0.25
155 7 0.03
156 1 0.00
157 2 0.01
158 8 0.03
159 160 0.67
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (157 bp):
TTTGTGATTCTTGTTGTGTATTGTGCTTGTTCATAAACTACTTTTATATAATTCAAAGCCTAAAA
TTTGTAGAAAATTCTTTATTAAACTAGATAGTGTATTGTGTGTATTAAGATGCAATAACTTTGTA
AAAGGTGAAAACTATTATGTATGTTAG
Found at i:9813250 original size:23 final size:23
Alignment explanation
Indices: 9813202--9813250 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
9813192 ACCCTAAAGC
**
9813202 AAGAATTGAAATATTGCAAGTAA
1 AAGAATTGAAATATTGCAAACAA
*
9813225 AAGAATT-AAATATTGTAAACAGA
1 AAGAATTGAAATATTGCAAACA-A
9813248 AAG
1 AAG
9813251 TAAAGATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.55, C:0.04, G:0.16, T:0.24
Consensus pattern (23 bp):
AAGAATTGAAATATTGCAAACAA
Found at i:9821665 original size:62 final size:61
Alignment explanation
Indices: 9821530--9821666 Score: 143
Period size: 62 Copynumber: 2.2 Consensus size: 61
9821520 GGTGGGAAGT
* *
9821530 CATTTTTGTAATTATGATAGGAGGACATTATAGCAATTTTGCTCAATCATAGTAGTAGAGA
1 CATTTTTGTAATTATGATAGGAGGACATTATAGCAATTTTGCTCAATCAGAGGAGTAGAGA
** * * * * * *
9821591 CATTTTCATAATTATGGTAGGAGGAATATTATAGTAATTTTAGC-CAATTAGAGGA-TAAGGGG
1 CATTTTTGTAATTATGATAGGAGG-ACATTATAGCAATTTT-GCTCAATCAGAGGAGT-AGAGA
9821653 CATTTTTGTAATTA
1 CATTTTTGTAATTA
9821667 CGACATAAAG
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
61 22 0.36
62 37 0.61
63 2 0.03
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.37
Consensus pattern (61 bp):
CATTTTTGTAATTATGATAGGAGGACATTATAGCAATTTTGCTCAATCAGAGGAGTAGAGA
Found at i:9821814 original size:58 final size:57
Alignment explanation
Indices: 9821648--9821814 Score: 155
Period size: 57 Copynumber: 2.9 Consensus size: 57
9821638 TTAGAGGATA
* * * * * *
9821648 AGGGGCATTTTTGT-AATTACGACATAAAGGTATCATAGTAATTTTTCATTTATAGG
1 AGGGGCATTTTTGTCATTTAAGACATAAAGGTATTATAGTAGTTTATCATTTATAAG
** * *
9821704 AGGGGCA-TTTTCACATTTAAGACATAAAAGGCATTATAAT-GATTTGAT-ATTTATAAG
1 AGGGGCATTTTTGTCATTTAAGACAT-AAAGGTATTATAGTAG-TTT-ATCATTTATAAG
*
9821761 AGGGGTATTTTTGTCATTTAAGA-ATAAAGGGATATTATAGTAGTTTATCATTTA
1 AGGGGCATTTTTGTCATTTAAGACATAAA-GG-TATTATAGTAGTTTATCATTTA
9821815 AAAAATGGAT
Statistics
Matches: 87, Mismatches: 15, Indels: 16
0.74 0.13 0.14
Matches are distributed among these distances:
55 4 0.05
56 19 0.22
57 34 0.39
58 29 0.33
59 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (57 bp):
AGGGGCATTTTTGTCATTTAAGACATAAAGGTATTATAGTAGTTTATCATTTATAAG
Found at i:9825168 original size:15 final size:15
Alignment explanation
Indices: 9825136--9825169 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
9825126 AGTATATATT
*
9825136 AAAGCTATCCCTAAG
1 AAAGCTATCCCCAAG
*
9825151 AAAGCTATCCCCAGG
1 AAAGCTATCCCCAAG
9825166 AAAG
1 AAAG
9825170 GCTTACAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.26, G:0.18, T:0.15
Consensus pattern (15 bp):
AAAGCTATCCCCAAG
Found at i:9829470 original size:49 final size:49
Alignment explanation
Indices: 9829417--9829561 Score: 108
Period size: 49 Copynumber: 3.1 Consensus size: 49
9829407 TAGATCGCTT
9829417 AAATGTAAGCTCATTGAATGGTTTAACTCATGTGTTCAAGTACAAAATA
1 AAATGTAAGCTCATTGAATGGTTTAACTCATGTGTTCAAGTACAAAATA
* * * ** ** * * * *
9829466 AAATGCAAG-----TGTA-GGTTTAAGGTCAAAT-TT-ATTTAGATCACTT
1 AAATGTAAGCTCATTGAATGGTTTAA-CTCATGTGTTCAAGTACA-AAATA
*
9829509 AGATGTAAGCTCATTGAATGGTTTAACTCATGTGTTCAAGTACAAAATA
1 AAATGTAAGCTCATTGAATGGTTTAACTCATGTGTTCAAGTACAAAATA
9829558 AAAT
1 AAAT
9829562 CCAAGTGTAA
Statistics
Matches: 62, Mismatches: 24, Indels: 20
0.58 0.23 0.19
Matches are distributed among these distances:
42 4 0.06
43 18 0.29
44 7 0.11
48 7 0.11
49 22 0.35
50 4 0.06
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (49 bp):
AAATGTAAGCTCATTGAATGGTTTAACTCATGTGTTCAAGTACAAAATA
Found at i:9829501 original size:92 final size:92
Alignment explanation
Indices: 9829399--9829570 Score: 317
Period size: 92 Copynumber: 1.9 Consensus size: 92
9829389 TTCAAGGTTG
*
9829399 AATTTATTTAGATCGCTTAAATGTAAGCTCATTGAATGGTTTAACTCATGTGTTCAAGTACAAAA
1 AATTTATTTAGATCACTTAAATGTAAGCTCATTGAATGGTTTAACTCATGTGTTCAAGTACAAAA
*
9829464 TAAAATGCAAGTGTAGGTTTAAGGTCA
66 TAAAATCCAAGTGTAGGTTTAAGGTCA
*
9829491 AATTTATTTAGATCACTTAGATGTAAGCTCATTGAATGGTTTAACTCATGTGTTCAAGTACAAAA
1 AATTTATTTAGATCACTTAAATGTAAGCTCATTGAATGGTTTAACTCATGTGTTCAAGTACAAAA
9829556 TAAAATCCAAGTGTA
66 TAAAATCCAAGTGTA
9829571 AGCTTAATTT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 77 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (92 bp):
AATTTATTTAGATCACTTAAATGTAAGCTCATTGAATGGTTTAACTCATGTGTTCAAGTACAAAA
TAAAATCCAAGTGTAGGTTTAAGGTCA
Found at i:9835244 original size:16 final size:15
Alignment explanation
Indices: 9835225--9835254 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
9835215 GATTCAGGTT
9835225 GGAAAGAAAGTAGGAA
1 GGAAAGAAA-TAGGAA
9835241 GGAAAGAAATAGGA
1 GGAAAGAAATAGGA
9835255 TAAGATCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.07
Consensus pattern (15 bp):
GGAAAGAAATAGGAA
Found at i:9837331 original size:2 final size:2
Alignment explanation
Indices: 9837324--9837360 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
9837314 AGTTAATCTT
*
9837324 TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9837361 TAGAAGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:9839778 original size:34 final size:33
Alignment explanation
Indices: 9839724--9839802 Score: 81
Period size: 34 Copynumber: 2.4 Consensus size: 33
9839714 CAAATTTTTC
* *
9839724 TTTTTTTTATTTTCTTTTTTC-CTTTTAGTTTAT
1 TTTTTTTTATTTTCTATTTTCTCTTTTA-TATAT
*
9839757 TTTTTTTTATTTAT-TAATTTTCTTTTTTATATAT
1 TTTTTTTTATTT-TCT-ATTTTCTCTTTTATATAT
*
9839791 TTATTTTTATTT
1 TTTTTTTTATTT
9839803 GCATACATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
33 13 0.33
34 21 0.54
35 5 0.13
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.78
Consensus pattern (33 bp):
TTTTTTTTATTTTCTATTTTCTCTTTTATATAT
Found at i:9839782 original size:20 final size:20
Alignment explanation
Indices: 9839759--9839797 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9839749 TAGTTTATTT
*
9839759 TTTTTTATTTATTAATTTTC
1 TTTTTTATATATTAATTTTC
*
9839779 TTTTTTATATATTTATTTT
1 TTTTTTATATATTAATTTT
9839798 TATTTGCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTTATATATTAATTTTC
Found at i:9841910 original size:21 final size:20
Alignment explanation
Indices: 9841880--9841946 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
9841870 AATTATATTG
* *
9841880 ATAATAAGATTAATTATTGTA
1 ATAATGAGATTAA-TATTATA
* *
9841901 GTGATGAGATTGAATATTATA
1 ATAATGAGATT-AATATTATA
*
9841922 ATAATGAGATTAAAATTAATA
1 ATAATGAGATTAATATT-ATA
9841943 ATAA
1 ATAA
9841947 AATATATGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 5 0.14
21 30 0.81
22 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (20 bp):
ATAATGAGATTAATATTATA
Found at i:9850162 original size:39 final size:39
Alignment explanation
Indices: 9850097--9850172 Score: 93
Period size: 38 Copynumber: 1.9 Consensus size: 39
9850087 ATACGAGAAT
*
9850097 AAAAAATTTATCAATCTAATAGTTAAACT-ATAAATTAA
1 AAAAAAATTATCAATCTAATAGTTAAACTAATAAATTAA
* *
9850135 AAAAAAATTATCAATTTTAATTA-TTAAATTAATAAATT
1 AAAAAAATTATCAA-TCTAA-TAGTTAAACTAATAAATT
9850173 TTTCATCATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 13 0.41
39 10 0.31
40 9 0.28
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.38
Consensus pattern (39 bp):
AAAAAAATTATCAATCTAATAGTTAAACTAATAAATTAA
Found at i:9850325 original size:3 final size:3
Alignment explanation
Indices: 9850317--9850355 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
9850307 TCAAAAAATG
9850317 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9850356 CAACAAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:9858238 original size:32 final size:31
Alignment explanation
Indices: 9858194--9858263 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 31
9858184 TTTAAAATTT
9858194 TTAATATGATATTTAAATTATAA-ATATATTAA
1 TTAATATGATATTTAAATT-TAATATA-ATTAA
* * *
9858226 TTAATATTATATTTATATTTAATTTAATTAA
1 TTAATATGATATTTAAATTTAATATAATTAA
9858257 TTAATAT
1 TTAATAT
9858264 ATTTATAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 15 0.44
32 19 0.56
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (31 bp):
TTAATATGATATTTAAATTTAATATAATTAA
Found at i:9858278 original size:28 final size:28
Alignment explanation
Indices: 9858222--9858288 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
9858212 TATAAATATA
*
9858222 TTAATTAA-TATTATATTTATATTTAAT
1 TTAATTAATTAATATATTTATATTTAAT
9858249 TTAATTAATTAATATATTTATAATTT-AT
1 TTAATTAATTAATATATTTAT-ATTTAAT
9858277 TT-ATTATATTAA
1 TTAATTA-ATTAA
9858289 ATTTCTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 12 0.33
28 20 0.56
29 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TTAATTAATTAATATATTTATATTTAAT
Found at i:9858686 original size:11 final size:11
Alignment explanation
Indices: 9858657--9858706 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 11
9858647 AATTTATTAG
*
9858657 ATTTTAAAATT
1 ATTTTAATATT
9858668 -TTTT-ATATT
1 ATTTTAATATT
*
9858677 ATTTTAATATA
1 ATTTTAATATT
9858688 ATTTTAATA-T
1 ATTTTAATATT
*
9858698 ATTTAAATA
1 ATTTTAATA
9858707 GATTTAGATG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 4 0.12
10 16 0.48
11 13 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTTAATATT
Found at i:9862268 original size:4 final size:4
Alignment explanation
Indices: 9862259--9862283 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
9862249 ATCATTCGAT
9862259 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
9862284 CATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:9862291 original size:13 final size:12
Alignment explanation
Indices: 9862275--9862322 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
9862265 TATTTATTTA
*
9862275 TTTATTTATCATT
1 TTTATTT-TTATT
9862288 TTTATTTTTATTT
1 TTTATTTTTA-TT
9862301 TTTATTCTTTATT
1 TTTATT-TTTATT
9862314 TTTATTTTT
1 TTTATTTTT
9862323 TTGTTATCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
12 5 0.16
13 23 0.72
14 4 0.12
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTATTTTTATT
Found at i:9864641 original size:120 final size:120
Alignment explanation
Indices: 9864490--9864728 Score: 334
Period size: 120 Copynumber: 2.0 Consensus size: 120
9864480 TTAAACCGAA
* * * * *
9864490 ACATACACATTTGTCAGCAGAACTGAGCTATTAAGCTGGTTAAGAGAAAATTCAAAATACAAATT
1 ACATACACATTTCTCAACAGAACTGAGCTATTAAGCTAGCTAAGAGAAAATTCAAAATACAAATC
* * * *
9864555 TACATTTTGATTCAGTTCTACTTTTTTACTATATACCATTTTACTAACAACAAAC
66 TACATTTTGATTCAGTTCTACTTTATTACTATATACCATTCTACAAAAAACAAAC
* * * *
9864610 ACATACACATTTCTCAATAGGATTGAGCTATTAAGCTAGCTAAGAGAAAATTTAAAATACAAATC
1 ACATACACATTTCTCAACAGAACTGAGCTATTAAGCTAGCTAAGAGAAAATTCAAAATACAAATC
* * *
9864675 TACATTTTGATTTAGTTCTACTTTATTATTATATGCCATTCTACAAAAAACAAA
66 TACATTTTGATTCAGTTCTACTTTATTACTATATACCATTCTACAAAAAACAAA
9864729 AAACTAACTC
Statistics
Matches: 103, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
120 103 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (120 bp):
ACATACACATTTCTCAACAGAACTGAGCTATTAAGCTAGCTAAGAGAAAATTCAAAATACAAATC
TACATTTTGATTCAGTTCTACTTTATTACTATATACCATTCTACAAAAAACAAAC
Found at i:9880576 original size:17 final size:16
Alignment explanation
Indices: 9880543--9880584 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
9880533 GTAATGATTA
* *
9880543 GTTTTATTCATTTATTT
1 GTTTTATTTATTCA-TT
9880560 GTTTTATTTATTCATT
1 GTTTTATTTATTCATT
9880576 -TTTTATTTA
1 GTTTTATTTA
9880585 CACGCATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 2 0.09
17 12 0.52
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (16 bp):
GTTTTATTTATTCATT
Found at i:9884707 original size:71 final size:70
Alignment explanation
Indices: 9884596--9884875 Score: 268
Period size: 71 Copynumber: 4.0 Consensus size: 70
9884586 TTTGGGGTAA
* *
9884596 ATAGAATCATTACTTTTGAATGTTGCATTTGCATTGTTGTTTAAACCATGCATTTGCATTATTTT
1 ATAG-ATCATTA-TTTTGAATGTTGCATTTGCA-TCTTGTTTGAACCATGCATTTGCATTATTTT
9884661 GTGAATAT
63 GTGAATAT
* * *
9884669 ATAGATCATTATTTTGAATGTTACATTTGCATCATTGTTTGAACCATACATTTGCACTA-TTTGA
1 ATAGATCATTATTTTGAATGTTGCATTTGCATC-TTGTTTGAACCATGCATTTGCATTATTTTG-
* *
9884733 TGAGTAC
64 TGAATAT
* * * * *
9884740 ATAGATCATTGTTTTGAATGTTGCATTTGCATCTATGTTTGGACGATGCATTTGTATTATTTGGT
1 ATAGATCATTATTTTGAATGTTGCATTTGCATCT-TGTTTGAACCATGCATTTGCATTATTTTGT
9884805 GAATAT
65 GAATAT
* * ** * * * *
9884811 TTAAATC-TT-TGAT-AA--TTGCATTTGCATCATGGTTTGGA-CATGCATTTGCATCATTTAGT
1 ATAGATCATTATTTTGAATGTTGCATTTGCATC-TTGTTTGAACCATGCATTTGCATTATTTTGT
9884870 GAATAT
65 GAATAT
9884876 TTGAATCATG
Statistics
Matches: 176, Mismatches: 26, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
65 23 0.13
66 20 0.11
67 1 0.01
68 2 0.01
69 2 0.01
70 8 0.05
71 106 0.60
72 10 0.06
73 4 0.02
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (70 bp):
ATAGATCATTATTTTGAATGTTGCATTTGCATCTTGTTTGAACCATGCATTTGCATTATTTTGTG
AATAT
Found at i:9884846 original size:66 final size:65
Alignment explanation
Indices: 9884760--9884882 Score: 185
Period size: 65 Copynumber: 1.9 Consensus size: 65
9884750 GTTTTGAATG
* * *
9884760 TTGCATTTGCATCTATGTTTGGACGATGCATTTGTATTATTTGGTGAATATTTAAATCTTTGATA
1 TTGCATTTGCATCTATGTTTGGAC-ATGCATTTGCATCATTTAGTGAATATTTAAATCTTTGATA
9884825 A
65 A
*
9884826 TTGCATTTGCATC-ATGGTTTGGACATGCATTTGCATCATTTAGTGAATATTTGAATC
1 TTGCATTTGCATCTAT-GTTTGGACATGCATTTGCATCATTTAGTGAATATTTAAATC
9884883 ATGGTATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
65 31 0.60
66 21 0.40
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (65 bp):
TTGCATTTGCATCTATGTTTGGACATGCATTTGCATCATTTAGTGAATATTTAAATCTTTGATAA
Found at i:9885006 original size:20 final size:20
Alignment explanation
Indices: 9884956--9885009 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
9884946 TTGAATTGTT
*
9884956 GCATTTGCATCATTTAGAAA
1 GCATTTGCATTATTTAGAAA
*
9884976 GCATTAGCATTATTTAGAAA
1 GCATTTGCATTATTTAGAAA
9884996 GCATTTGCATTATT
1 GCATTTGCATTATT
9885010 ATCATTCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (20 bp):
GCATTTGCATTATTTAGAAA
Found at i:9885174 original size:38 final size:38
Alignment explanation
Indices: 9885121--9885295 Score: 117
Period size: 38 Copynumber: 4.6 Consensus size: 38
9885111 AGATAAAATA
* * *
9885121 TTGAATTCTTAAATGATGAAAATTTTTCAACATGAGAT
1 TTGAATCCTCAAATGAAGAAAATTTTTCAACATGAGAT
* * * *
9885159 TTGAATCCTCGAATGAGGAAAGCTTTTT-AAGAT-ATGATT
1 TTGAATCCTCAAATGAAGAAA-ATTTTTCAACATGA-GA-T
* *
9885198 TTGAATCCTCAAATGAAAAAAATTTTCCAACATGAGAT
1 TTGAATCCTCAAATGAAGAAAATTTTTCAACATGAGAT
* * * * *
9885236 TTAAAACCTTC-AATG-AGAAAAACTTTTCAAGATAAGAT
1 TTGAATCC-TCAAATGAAG-AAAATTTTTCAACATGAGAT
* *
9885274 TTTAATTCGTCAAATG-AGAAAA
1 TTGAA-TCCTCAAATGAAGAAAA
9885296 ACTATTTCTA
Statistics
Matches: 106, Mismatches: 22, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
37 2 0.02
38 64 0.60
39 39 0.37
40 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (38 bp):
TTGAATCCTCAAATGAAGAAAATTTTTCAACATGAGAT
Found at i:9885296 original size:77 final size:76
Alignment explanation
Indices: 9885094--9885296 Score: 230
Period size: 77 Copynumber: 2.6 Consensus size: 76
9885084 GAATTCTTGG
* * * *
9885094 ATGAGGAAAGCTTTTAAAGATAAAATATTGAATTCTTAAATGATG-AAAATTTTTCAACATGAGA
1 ATGAGGAAAGCTTTTAAAGATAAGAT-TTTAATTCTCAAATGA-GAAAAATTTTCCAACATGAGA
* *
9885158 TTTGAATCCTCGA
64 TTTAAAACCTCGA
* * * *
9885171 ATGAGGAAAGCTTTTTAAGATATGATTTTGAATCCTCAAATGAAAAAAATTTTCCAACATGAGAT
1 ATGAGGAAAGCTTTTAAAGATAAGATTTT-AATTCTCAAATGAGAAAAATTTTCCAACATGAGAT
9885236 TTAAAACCTTC-A
65 TTAAAACC-TCGA
* * *
9885248 ATGAGAAAAACTTTTCAAGATAAGATTTTAATTCGTCAAATGAGAAAAA
1 ATGAGGAAAGCTTTTAAAGATAAGATTTTAATTC-TCAAATGAGAAAAA
9885297 CTATTTCTAG
Statistics
Matches: 106, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
76 6 0.06
77 98 0.92
78 2 0.02
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32
Consensus pattern (76 bp):
ATGAGGAAAGCTTTTAAAGATAAGATTTTAATTCTCAAATGAGAAAAATTTTCCAACATGAGATT
TAAAACCTCGA
Found at i:9885297 original size:39 final size:38
Alignment explanation
Indices: 9885094--9885308 Score: 148
Period size: 39 Copynumber: 5.6 Consensus size: 38
9885084 GAATTCTTGG
* * * * * *
9885094 ATGAGGAAAGCTTTTAAAGATAAAATATTGAATTCTTAA
1 ATGAGAAAAACTTTTCAAGATAAGAT-TTGAATCCTCAA
* * * *
9885133 ATGATG-AAAATTTTTCAACATGAGATTTGAATCCTCGA
1 ATGA-GAAAAACTTTTCAAGATAAGATTTGAATCCTCAA
* * * *
9885171 ATGAGGAAAGCTTTTTAAGATATGATTTTGAATCCTCAA
1 ATGAGAAAAACTTTTCAAGATAAGA-TTTGAATCCTCAA
* * * * *
9885210 ATGA-AAAAAATTTTCCAACATGAGATTTAAAACCTTC-A
1 ATGAGAAAAACTTTT-CAAGATAAGATTTGAATCC-TCAA
* *
9885248 ATGAGAAAAACTTTTCAAGATAAGATTTTAATTCGTCAA
1 ATGAGAAAAACTTTTCAAGATAAGATTTGAA-TCCTCAA
*
9885287 ATGAGAAAAACTATTTCTAGAT
1 ATGAGAAAAACT-TTTCAAGAT
9885309 GATATTTTGA
Statistics
Matches: 135, Mismatches: 32, Indels: 17
0.73 0.17 0.09
Matches are distributed among these distances:
37 1 0.01
38 60 0.44
39 65 0.48
40 9 0.07
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (38 bp):
ATGAGAAAAACTTTTCAAGATAAGATTTGAATCCTCAA
Found at i:9885456 original size:43 final size:44
Alignment explanation
Indices: 9885409--9885614 Score: 179
Period size: 44 Copynumber: 4.8 Consensus size: 44
9885399 TACTCTTTGG
* *
9885409 ATGAAATGAACCTTTTA-ATTTTTCAAAAGTTGATGAGCCTTTT
1 ATGAAATGAACCTTTTATATTTTTCAAAAGTTGTTGAGCCTTTA
* * * *
9885452 ATGAAA-GGACCTTTAATATTTCTT-AAAAGTTGTTGAGCCTATG
1 ATGAAATGAACCTTTTATATTT-TTCAAAAGTTGTTGAGCCTTTA
** * *
9885495 ACAAAATGCACATTTTATATTTTTCAAAAGTTGTTGAGCCTTTA
1 ATGAAATGAACCTTTTATATTTTTCAAAAGTTGTTGAGCCTTTA
* * * * * * *
9885539 ATGAGAT-AAGCCTTTTATGTTTTTTAAAAGTTATTAAGTCTCTA
1 ATGAAATGAA-CCTTTTATATTTTTCAAAAGTTGTTGAGCCTTTA
* * *
9885583 ATGAGATGAGCTTTTTATATTTTTC-AAAGTTG
1 ATGAAATGAACCTTTTATATTTTTCAAAAGTTG
9885615 CTAAACCTTT
Statistics
Matches: 129, Mismatches: 28, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
42 8 0.06
43 39 0.30
44 81 0.63
45 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (44 bp):
ATGAAATGAACCTTTTATATTTTTCAAAAGTTGTTGAGCCTTTA
Found at i:9885713 original size:24 final size:25
Alignment explanation
Indices: 9885668--9885714 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
9885658 AACTATTAAA
* **
9885668 AAAATCTTTTTAGATGTGAATTTCT
1 AAAATCTTTTTAAATGCAAATTTCT
9885693 AAAAT-TTTTTAAATGCAAATTT
1 AAAATCTTTTTAAATGCAAATTT
9885715 ATGAATTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (25 bp):
AAAATCTTTTTAAATGCAAATTTCT
Found at i:9885811 original size:46 final size:44
Alignment explanation
Indices: 9885675--9885962 Score: 219
Period size: 45 Copynumber: 6.4 Consensus size: 44
9885665 AAAAAAATCT
* * *
9885675 TTTTAGATGTGAATTTCTAAAATTTTTTAAATGCA-AAT-TTATGAA
1 TTTTGGATGTGAATCTCTAAAA-TTTTCAAATG-AGAATCTT-TGAA
* * * * *
9885720 TTTTGGATATGAATC-CTTAAAAATTCTCTAATTAGAATATTTGAA
1 TTTTGGATGTGAATCTC-T-AAAATTTTCAAATGAGAATCTTTGAA
* *
9885765 TCTTGGATGTGAA-CATGTAAAAAGTTTTCAAATGAGAATCTTTGAA
1 TTTTGGATGTGAATC-TCT-AAAA-TTTTCAAATGAGAATCTTTGAA
* ** * *
9885811 TTTTAGATGTGAATCTCTAAAATTTTTTGAATGTGAATCTATGAA
1 TTTTGGATGTGAATCTCTAAAA-TTTTCAAATGAGAATCTTTGAA
*
9885856 TTTTGGATGTGAATCTCTAAAATTTCTCAAATGAAAATCTTTGAAA
1 TTTTGGATGTGAATCTCTAAAATTT-TCAAATGAGAATCTTTG-AA
* * *
9885902 TTTTGGATGTGAATC-CTTAAATTTTGTCAAA-CATGAATATTTGAA
1 TTTTGGATGTGAATCTC-TAAAATTT-TCAAATGA-GAATCTTTGAA
* *
9885947 TCTTGGATATGAATCT
1 TTTTGGATGTGAATCT
9885963 TTAATGTGAA
Statistics
Matches: 195, Mismatches: 35, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
44 6 0.03
45 115 0.59
46 73 0.37
47 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (44 bp):
TTTTGGATGTGAATCTCTAAAATTTTCAAATGAGAATCTTTGAA
Found at i:9885825 original size:91 final size:90
Alignment explanation
Indices: 9885680--9885962 Score: 265
Period size: 91 Copynumber: 3.1 Consensus size: 90
9885670 AATCTTTTTA
* * * * *
9885680 GATGTGAATTTCTAAAATTTTTTAAATGCAAAT-TTATGAATTTTGGATATGAATCCTTAAAAAT
1 GATGTGAATCTCTAAAATTTCTCAAATGAAAATCTT-TGAATTTTGGATGTGAATCCTTAAAAAT
9885744 TCTCTAATTAGAATATTTGAATCTTG
65 TCTCTAATTAGAATATTTGAATCTTG
* * *
9885770 GATGTGAA-CATGTAAAAAGTTT-TCAAATGAGAATCTTTGAATTTTAGATGTGAAT-CTCT-AA
1 GATGTGAATC-TCT-AAAA-TTTCTCAAATGAAAATCTTTGAATTTTGGATGTGAATCCT-TAAA
* * * * *
9885831 AATTTTTTGAATGT-GAATCTATGAATTTTG
62 AATTCTCT-AAT-TAGAATATTTGAATCTTG
**
9885861 GATGTGAATCTCTAAAATTTCTCAAATGAAAATCTTTGAAATTTTGGATGTGAATCCTTAAATTT
1 GATGTGAATCTCTAAAATTTCTCAAATGAAAATCTTTG-AATTTTGGATGTGAATCCTTAAAAAT
* **
9885926 TGTC-AAACATGAATATTTGAATCTTG
65 TCTCTAATTA-GAATATTTGAATCTTG
*
9885952 GATATGAATCT
1 GATGTGAATCT
9885963 TTAATGTGAA
Statistics
Matches: 154, Mismatches: 25, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
89 3 0.02
90 42 0.27
91 95 0.62
92 14 0.09
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (90 bp):
GATGTGAATCTCTAAAATTTCTCAAATGAAAATCTTTGAATTTTGGATGTGAATCCTTAAAAATT
CTCTAATTAGAATATTTGAATCTTG
Found at i:9885834 original size:22 final size:22
Alignment explanation
Indices: 9885809--9885926 Score: 87
Period size: 24 Copynumber: 5.3 Consensus size: 22
9885799 AGAATCTTTG
9885809 AATTTTAGATGTGAATCTCTAA
1 AATTTTAGATGTGAATCTCTAA
* * *
9885831 AATTTTTTGAATGTGAATCTAT-G
1 AA-TTTTAG-ATGTGAATCTCTAA
*
9885854 AATTTTGGATGTGAATCTCTAA
1 AATTTTAGATGTGAATCTCTAA
* ** * *
9885876 AATTTCTCAAATGAAAATCTTTGA
1 AATTT-T-AGATGTGAATCTCTAA
* *
9885900 AATTTTGGATGTGAATC-CTTA
1 AATTTTAGATGTGAATCTCTAA
9885921 AATTTT
1 AATTTT
9885927 GTCAAACATG
Statistics
Matches: 73, Mismatches: 18, Indels: 11
0.72 0.18 0.11
Matches are distributed among these distances:
21 19 0.26
22 19 0.26
23 9 0.12
24 26 0.36
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.43
Consensus pattern (22 bp):
AATTTTAGATGTGAATCTCTAA
Found at i:9885844 original size:24 final size:24
Alignment explanation
Indices: 9885817--9885880 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 24
9885807 TGAATTTTAG
9885817 ATGTGAATCTCTAAAATTTTTTGA
1 ATGTGAATCTCTAAAATTTTTTGA
* * *
9885841 ATGTGAATCTAT-GAA--TTTTGG
1 ATGTGAATCTCTAAAATTTTTTGA
9885862 ATGTGAATCTCTAAAATTT
1 ATGTGAATCTCTAAAATTT
9885881 CTCAAATGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 16 0.50
22 2 0.06
23 2 0.06
24 12 0.38
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.44
Consensus pattern (24 bp):
ATGTGAATCTCTAAAATTTTTTGA
Found at i:9885945 original size:136 final size:135
Alignment explanation
Indices: 9885675--9885962 Score: 323
Period size: 136 Copynumber: 2.1 Consensus size: 135
9885665 AAAAAAATCT
* *
9885675 TTTTAGATGTGAATTTCTAAAATTTTTTAAATGCAAATTTATGAATTTTGGATATGAATCCTTAA
1 TTTTAGATGTGAATCTCTAAAATTTTTTAAATGCAAATCTATGAATTTTGGATATGAATCCTTAA
* * * * *
9885740 AAATTCTCTAATTAGAATATTTGAATCTTGGATGTGAACATGTAAAAAGTTTTCAAATGAGAATC
66 AAATTCTCAAATGAAAATATTTGAATCTTGGATGTGAACATGT-AAAAGTTTTCAAATCAGAATA
9885805 TTTGAA
130 TTTGAA
* ** *
9885811 TTTTAGATGTGAATCTCTAAAATTTTTTGAATGTGAATCTATGAATTTTGGATGTGAAT-CTCTA
1 TTTTAGATGTGAATCTCTAAAATTTTTTAAATGCAAATCTATGAATTTTGGATATGAATCCT-TA
* * * * *
9885875 AAATTTCTCAAATGAAAATCTTTGAAATTTTGGATGTGAATCCT-T-AAATTTTGTCAAA-CATG
65 AAAATTCTCAAATGAAAATATTTG-AATCTTGGATGTGAA-CATGTAAAAGTTT-TCAAATCA-G
9885937 AATATTTGAA
126 AATATTTGAA
* * *
9885947 TCTTGGATATGAATCT
1 TTTTAGATGTGAATCT
9885963 TTAATGTGAA
Statistics
Matches: 128, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
135 9 0.07
136 102 0.80
137 15 0.12
138 2 0.02
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (135 bp):
TTTTAGATGTGAATCTCTAAAATTTTTTAAATGCAAATCTATGAATTTTGGATATGAATCCTTAA
AAATTCTCAAATGAAAATATTTGAATCTTGGATGTGAACATGTAAAAGTTTTCAAATCAGAATAT
TTGAA
Found at i:9886651 original size:144 final size:142
Alignment explanation
Indices: 9886478--9886812 Score: 411
Period size: 144 Copynumber: 2.3 Consensus size: 142
9886468 GTTTTTAGTG
* * * * * *
9886478 AAAAGCTTCAGATCGTGTTTTGATATTATTTCATAATTTTTTATGCATTGAAAATCCTTATTGCA
1 AAAAGCTCCAAATCATGTTTTAATATTATTTCATAATTTTTTATGCATTGAAAACCCTGATTGCA
* * * * * *
9886543 CCTTAAAAGGAGTGAAATTACCAATATATCCTTTAGGGGTATTTTCATAATTTAACTTTTTTAAA
66 CCTCAAAAGGAGTAAAATTACCAAAATATCATTTAGGGGTATTTT-ATAATTTAA-TCTTTCAAA
**
9886608 GTCAATTTTTTGCGA
129 GTCAATTTTTCAC-A
*
9886623 AAAA-CTCCAAATCATGTTTTAATATTATTTCATAATTTTTAATGCATTGAAAACCCTGATTGCA
1 AAAAGCTCCAAATCATGTTTTAATATTATTTCATAATTTTTTATGCATTGAAAACCCTGATTGCA
* * * * * * * *
9886687 CCTCGAAAGGATTAAAATTACTAAAATGTCATTTAGGGGTATTTTGTAATTTGATCTTTCGATGT
66 CCTCAAAAGGAGTAAAATTACCAAAATATCATTTAGGGGTATTTTATAATTTAATCTTTCAAAGT
*
9886752 CAGTTTTTCACA
131 CAATTTTTCACA
*
9886764 AAAAGCTCCAAATCATGTTTTAATATTATTTCATAATTTTTTATACATT
1 AAAAGCTCCAAATCATGTTTTAATATTATTTCATAATTTTTTATGCATT
9886813 AAATTGATCT
Statistics
Matches: 163, Mismatches: 26, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
141 5 0.03
142 57 0.35
143 7 0.04
144 90 0.55
145 4 0.02
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (142 bp):
AAAAGCTCCAAATCATGTTTTAATATTATTTCATAATTTTTTATGCATTGAAAACCCTGATTGCA
CCTCAAAAGGAGTAAAATTACCAAAATATCATTTAGGGGTATTTTATAATTTAATCTTTCAAAGT
CAATTTTTCACA
Found at i:9888397 original size:59 final size:58
Alignment explanation
Indices: 9888299--9888441 Score: 182
Period size: 59 Copynumber: 2.4 Consensus size: 58
9888289 CAAAACCTTG
* *
9888299 AAACCCCAAACCAAACCCTTAAACTCTAAATCAAACCTTAAACAC-TAAACTTAAAC-CTC
1 AAACCACAAACCAAACCCTTAAAC-CCAAATCAAACCTTAAAC-CTTAAACTTAAACTC-C
*
9888358 AAACTACAAACCAAACCCTTAAACCCAAATCAAACCCTTAAACCTTAAACTTAAACTCC
1 AAACCACAAACCAAACCCTTAAACCCAAATCAAA-CCTTAAACCTTAAACTTAAACTCC
* * *
9888417 AAACCCCAAACCAAACACTCAAACC
1 AAACCACAAACCAAACCCTTAAACC
9888442 TTAAACTTAC
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
58 10 0.14
59 63 0.85
60 1 0.01
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (58 bp):
AAACCACAAACCAAACCCTTAAACCCAAATCAAACCTTAAACCTTAAACTTAAACTCC
Found at i:9888401 original size:19 final size:20
Alignment explanation
Indices: 9888289--9888400 Score: 95
Period size: 19 Copynumber: 5.7 Consensus size: 20
9888279 ATTATTCATG
* * *
9888289 CAAAACCTTGAAACCCCAAAC
1 CAAACCCTT-AAACTCCAAAT
*
9888310 CAAACCCTTAAACTCTAAAT
1 CAAACCCTTAAACTCCAAAT
* *
9888330 CAAA-CCTTAAACACTAAACT
1 CAAACCCTTAAACTCCAAA-T
* * * *
9888350 TAAA-CCTCAAACTACAAAC
1 CAAACCCTTAAACTCCAAAT
9888369 CAAACCCTTAAAC-CCAAAT
1 CAAACCCTTAAACTCCAAAT
9888388 CAAACCCTTAAAC
1 CAAACCCTTAAAC
9888401 CTTAAACTTA
Statistics
Matches: 74, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
19 33 0.45
20 33 0.45
21 8 0.11
ACGTcount: A:0.48, C:0.34, G:0.01, T:0.17
Consensus pattern (20 bp):
CAAACCCTTAAACTCCAAAT
Found at i:9888426 original size:40 final size:40
Alignment explanation
Indices: 9888381--9888470 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
9888371 AACCCTTAAA
* *
9888381 CCCAAATCAAACCCTTAAACCTTAAACTTAAACTCCAAAC
1 CCCAAATCAAACACTCAAACCTTAAACTTAAACTCCAAAC
* **
9888421 CCCAAACCAAACACTCAAACCTTAAACTTACTCTCCAAAC
1 CCCAAATCAAACACTCAAACCTTAAACTTAAACTCCAAAC
*
9888461 CCCAAGTCAA
1 CCCAAATCAA
9888471 CTTGAAACCC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.43, C:0.38, G:0.01, T:0.18
Consensus pattern (40 bp):
CCCAAATCAAACACTCAAACCTTAAACTTAAACTCCAAAC
Found at i:9888441 original size:20 final size:20
Alignment explanation
Indices: 9888289--9888432 Score: 91
Period size: 20 Copynumber: 7.2 Consensus size: 20
9888279 ATTATTCATG
*
9888289 CAAAACCTTGAAACCCCAAAC
1 CAAACCCTT-AAACCCCAAAC
* * *
9888310 CAAACCCTTAAACTCTAAAT
1 CAAACCCTTAAACCCCAAAC
* *
9888330 CAAA-CCTTAAACACTAAAC
1 CAAACCCTTAAACCCCAAAC
* * **
9888349 TTAAA-CCTCAAACTACAAAC
1 -CAAACCCTTAAACCCCAAAC
*
9888369 CAAACCCTTAAA-CCCAAAT
1 CAAACCCTTAAACCCCAAAC
**
9888388 CAAACCCTTAAACCTTAAAC
1 CAAACCCTTAAACCCCAAAC
*
9888408 TTAAACTCC--AAACCCCAAAC
1 -CAAAC-CCTTAAACCCCAAAC
9888428 CAAAC
1 CAAAC
9888433 ACTCAAACCT
Statistics
Matches: 95, Mismatches: 23, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
19 36 0.38
20 45 0.47
21 12 0.13
22 2 0.02
ACGTcount: A:0.48, C:0.35, G:0.01, T:0.17
Consensus pattern (20 bp):
CAAACCCTTAAACCCCAAAC
Found at i:9888623 original size:30 final size:30
Alignment explanation
Indices: 9888587--9888646 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
9888577 AATCGAGCAT
9888587 AAACCCTAAACTAA-TCTCAAACCCTAAACC
1 AAACCCTAAACTAACTC-CAAACCCTAAACC
*
9888617 AAACCCTAAACTAACTCCAAACCTTAAACC
1 AAACCCTAAACTAACTCCAAACCCTAAACC
9888647 CCAAATCTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 26 0.93
31 2 0.07
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (30 bp):
AAACCCTAAACTAACTCCAAACCCTAAACC
Found at i:9889848 original size:17 final size:17
Alignment explanation
Indices: 9889826--9889875 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
9889816 AACTCTTGCG
*
9889826 AATCTTTAAATTTTGTA
1 AATCTTTAAATATTGTA
* *
9889843 AATCTTCAACTATTGTA
1 AATCTTTAAATATTGTA
*
9889860 AATCTTTAAATGTTGT
1 AATCTTTAAATATTGT
9889876 GAATTTTCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (17 bp):
AATCTTTAAATATTGTA
Found at i:9889852 original size:34 final size:34
Alignment explanation
Indices: 9889813--9889890 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
9889803 TTGTGAATTT
* *
9889813 TTCAACTCTTGCGAATCTTTAAATTTTGTAAATC
1 TTCAACTCTTGCAAATCTTTAAATGTTGTAAATC
* * * *
9889847 TTCAACTATTGTAAATCTTTAAATGTTGTGAATT
1 TTCAACTCTTGCAAATCTTTAAATGTTGTAAATC
9889881 TTCAACTCTT
1 TTCAACTCTT
9889891 TCTTTAAATC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.46
Consensus pattern (34 bp):
TTCAACTCTTGCAAATCTTTAAATGTTGTAAATC
Found at i:9889907 original size:29 final size:30
Alignment explanation
Indices: 9889862--9889920 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
9889852 CTATTGTAAA
* *
9889862 TCTTTAAATGTTGTGAAT-TTTCAACTCTT
1 TCTTTAAATCTTATGAATCTTTCAACTCTT
*
9889891 TCTTTAAATCTTATGAATCTTTCAATTCTT
1 TCTTTAAATCTTATGAATCTTTCAACTCTT
9889921 GTGAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (30 bp):
TCTTTAAATCTTATGAATCTTTCAACTCTT
Found at i:9890011 original size:37 final size:35
Alignment explanation
Indices: 9889943--9890015 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 35
9889933 ATCTTACAAA
*
9889943 TCTTAAAATCTTTGAATTCTTGCGAATCTTTAAAT
1 TCTTAAAACCTTTGAATTCTTGCGAATCTTTAAAT
* *
9889978 TCTTATAAACCTTTGAATTTTTTGTGAATCTTTAAAT
1 TCTTA-AAACCTTTGAA-TTCTTGCGAATCTTTAAAT
9890015 T
1 T
9890016 TTTCTATGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 5 0.15
36 10 0.30
37 18 0.55
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.49
Consensus pattern (35 bp):
TCTTAAAACCTTTGAATTCTTGCGAATCTTTAAAT
Found at i:9890025 original size:20 final size:19
Alignment explanation
Indices: 9889966--9890037 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
9889956 GAATTCTTGC
*
9889966 GAATCTTTAAA-TTCTTAT
1 GAATCTTTAAATTTTTTAT
* * * *
9889984 AAACCTTTGAATTTTTTGT
1 GAATCTTTAAATTTTTTAT
9890003 GAATCTTTAAATTTTTCTAT
1 GAATCTTTAAATTTTT-TAT
* *
9890023 GAATCATTGAATTTT
1 GAATCTTTAAATTTT
9890038 AAATCTTTGG
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
18 8 0.20
19 18 0.44
20 15 0.37
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (19 bp):
GAATCTTTAAATTTTTTAT
Found at i:9890520 original size:12 final size:11
Alignment explanation
Indices: 9890495--9890530 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
9890485 GCCTGAAATA
9890495 AAAAAGAATTG
1 AAAAAGAATTG
9890506 AAAAAGAATTG
1 AAAAAGAATTG
* *
9890517 GAAAAGGATTG
1 AAAAAGAATTG
9890528 AAA
1 AAA
9890531 TTCCTAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (11 bp):
AAAAAGAATTG
Found at i:9891185 original size:17 final size:17
Alignment explanation
Indices: 9891159--9891205 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
9891149 AATTGGGTAA
*
9891159 TTATTAGTTTTATTCAT
1 TTATTTGTTTTATTCAT
*
9891176 TTATTTGTTTTATTTAT
1 TTATTTGTTTTATTCAT
*
9891193 TCATTT-TTTTATT
1 TTATTTGTTTTATT
9891206 TACACGCGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 7 0.26
17 20 0.74
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (17 bp):
TTATTTGTTTTATTCAT
Found at i:9892325 original size:18 final size:17
Alignment explanation
Indices: 9892243--9892325 Score: 58
Period size: 18 Copynumber: 4.6 Consensus size: 17
9892233 ATTTGAATCA
* *
9892243 TGTGAATATTTGAATTCT
1 TGTGAAT-TTTAAATTTT
* *
9892261 TGTAAATTTTTGAATTTT
1 TGTGAA-TTTTAAATTTT
* *
9892279 TGCGAATCTTTAAATTCT
1 TGTGAAT-TTTAAATTTT
*
9892297 TATGAACTTTTAAATTTTT
1 TGTGAA-TTTTAAA-TTTT
9892316 TGTGAATTTT
1 TGTGAATTTT
9892326 TTAATCTTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
17 1 0.02
18 40 0.78
19 10 0.20
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.54
Consensus pattern (17 bp):
TGTGAATTTTAAATTTT
Found at i:9892445 original size:35 final size:34
Alignment explanation
Indices: 9892368--9892447 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 34
9892358 TCTTTGGAAT
* *
9892368 CTTTGAATTTCAAATTAAAAATATTTGAATTTCA
1 CTTTGAATTTCAAATTAAAAACATTTGAATTGCA
* ** *
9892402 GTTGTGAATTTCAAATTGTAAACCTTTGAATTGCAA
1 CTT-TGAATTTCAAATTAAAAACATTTGAATTGC-A
9892438 CTTTGAATTT
1 CTTTGAATTT
9892448 GTGAATTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
34 2 0.05
35 32 0.86
36 3 0.08
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (34 bp):
CTTTGAATTTCAAATTAAAAACATTTGAATTGCA
Found at i:9893294 original size:32 final size:32
Alignment explanation
Indices: 9893239--9893302 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
9893229 GGAAATTACT
9893239 GGCTCAGCGAAAGACTTGAAAGTAGATTTTTA
1 GGCTCAGCGAAAGACTTGAAAGTAGATTTTTA
* *
9893271 GGCTTAGCGGAAGACTT-ACAAGTAGATTTTTA
1 GGCTCAGCGAAAGACTTGA-AAGTAGATTTTTA
9893303 CCAGCCCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 1 0.03
32 28 0.97
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (32 bp):
GGCTCAGCGAAAGACTTGAAAGTAGATTTTTA
Found at i:9894624 original size:72 final size:73
Alignment explanation
Indices: 9894506--9894677 Score: 195
Period size: 72 Copynumber: 2.4 Consensus size: 73
9894496 TAAAAATTAG
* * * ** * *
9894506 AAATAATAAATTTGCTAATAGAATCAAGATCAATTTCCTAAAACAAATGCAATATTAATAGTAAC
1 AAATAATAAGTTTGCTAGTAAAATCATTATCAATTTCCTAAAACAAATGCAACATCAATAGTAAC
9894571 AATCCCAA
66 AATCCCAA
** * * *
9894579 AAAT-ATAAGTTTTTTAGTAAAATCATTATCAATGTT-CTAAGACAAATGCAACATCGATAGTGA
1 AAATAATAAGTTTGCTAGTAAAATCATTATCAAT-TTCCTAAAACAAATGCAACATCAATAGTAA
*
9894642 CAATCCCAT
65 CAATCCCAA
*
9894651 AAATAATAAGTTTGCTAGTAGAATCAT
1 AAATAATAAGTTTGCTAGTAAAATCAT
9894678 GGATGAAAAT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
72 56 0.69
73 25 0.31
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (73 bp):
AAATAATAAGTTTGCTAGTAAAATCATTATCAATTTCCTAAAACAAATGCAACATCAATAGTAAC
AATCCCAA
Found at i:9902151 original size:20 final size:20
Alignment explanation
Indices: 9902126--9902165 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
9902116 ATGTTTTTCA
9902126 ATCTAAAGGTGGCAATAAGT
1 ATCTAAAGGTGGCAATAAGT
*
9902146 ATCTAAGGGTGGCAATAAGT
1 ATCTAAAGGTGGCAATAAGT
9902166 GAAGGTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.28, T:0.25
Consensus pattern (20 bp):
ATCTAAAGGTGGCAATAAGT
Found at i:9904691 original size:20 final size:19
Alignment explanation
Indices: 9904666--9904706 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
9904656 ATGCTTCGCC
* * *
9904666 TTTTTTCCCTTTTTTTTGT
1 TTTTTTTCCTATTTTTTCT
9904685 TTTTTTTCCTATTTTTTCT
1 TTTTTTTCCTATTTTTTCT
9904704 TTT
1 TTT
9904707 GTTGTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTTTCCTATTTTTTCT
Found at i:9906194 original size:15 final size:15
Alignment explanation
Indices: 9906176--9906210 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9906166 ACTCTTAGGG
9906176 TTTAGCATTTTGGAT
1 TTTAGCATTTTGGAT
**
9906191 TTTAGTGTTTTGGAT
1 TTTAGCATTTTGGAT
9906206 TTTAG
1 TTTAG
9906211 GGTTAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.03, G:0.23, T:0.57
Consensus pattern (15 bp):
TTTAGCATTTTGGAT
Found at i:9906371 original size:20 final size:20
Alignment explanation
Indices: 9906326--9906371 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
9906316 AAGTTAAAAT
9906326 TAATTTATTTAGTTTTAATA
1 TAATTTATTTAGTTTTAATA
* *
9906346 TTATTTA-TTATTTTTAATAA
1 TAATTTATTTAGTTTTAAT-A
9906366 TAATTT
1 TAATTT
9906372 CTCAACATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TAATTTATTTAGTTTTAATA
Found at i:9906590 original size:20 final size:19
Alignment explanation
Indices: 9906563--9906611 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
9906553 ATTTGAATTT
* *
9906563 TTATTATTGTTATTGTTAT
1 TTATTATTATTATTGTTAA
9906582 TTAATTATTATTATTGTTAA
1 TT-ATTATTATTATTGTTAA
9906602 TTATTATTAT
1 TTATTATTAT
9906612 AAAACAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (19 bp):
TTATTATTATTATTGTTAA
Found at i:9907868 original size:18 final size:17
Alignment explanation
Indices: 9907847--9907889 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
9907837 TTTTGTTTTC
*
9907847 TTTTTGTTTTTAATTAAA
1 TTTTTATTTTT-ATTAAA
*
9907865 TTTTTATTTTTATTATA
1 TTTTTATTTTTATTAAA
9907882 -TTTTATTT
1 TTTTTATTT
9907890 AATTAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 8 0.35
17 5 0.22
18 10 0.43
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTTTATTTTTATTAAA
Found at i:9908346 original size:34 final size:36
Alignment explanation
Indices: 9908308--9908375 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
9908298 GAATTTAATT
*
9908308 GCAAGTC-ATAAAATAA-AAAGATCGAGATTAAACC
1 GCAAGTCAAAAAAATAATAAAGATCGAGATTAAACC
* *
9908342 GCAAGTCAAAAAAATAATGAGGATCGAGATTAAA
1 GCAAGTCAAAAAAATAATAAAGATCGAGATTAAA
9908376 TCGTGACTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 7 0.24
35 8 0.28
36 14 0.48
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (36 bp):
GCAAGTCAAAAAAATAATAAAGATCGAGATTAAACC
Found at i:9908370 original size:36 final size:36
Alignment explanation
Indices: 9908327--9908537 Score: 98
Period size: 34 Copynumber: 6.1 Consensus size: 36
9908317 AAAATAAAAA
9908327 GATCGAGATTAAACCGCAAGTCAAAAAAATAATGAG
1 GATCGAGATTAAACCGCAAGTCAAAAAAATAATGAG
* * * ** * *
9908363 GATCGAGATTAAATCG--TGACTTAAAAGTAAAGA-
1 GATCGAGATTAAACCGCAAGTCAAAAAAATAATGAG
* * *** *
9908396 GATCGGGATTAAATCATGAGTCAAAGAAATAATGAG
1 GATCGAGATTAAACCGCAAGTCAAAAAAATAATGAG
* * * * ** * *
9908432 GATTGGGATTAAA-C-CATGACTTAAAAGTAAAGA-
1 GATCGAGATTAAACCGCAAGTCAAAAAAATAATGAG
* * * *
9908465 GATCGAGATTAAACCGCCAGTTAAGAAAATAA--AA
1 GATCGAGATTAAACCGCAAGTCAAAAAAATAATGAG
* **
9908499 AACTCG-GATTAAACCAAAAGTCAAAAAAATAATGAG
1 GA-TCGAGATTAAACCGCAAGTCAAAAAAATAATGAG
9908535 GAT
1 GAT
9908538 TGGGGATCAA
Statistics
Matches: 122, Mismatches: 44, Indels: 19
0.66 0.24 0.10
Matches are distributed among these distances:
33 26 0.21
34 44 0.36
35 23 0.19
36 29 0.24
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.20
Consensus pattern (36 bp):
GATCGAGATTAAACCGCAAGTCAAAAAAATAATGAG
Found at i:9908406 original size:33 final size:33
Alignment explanation
Indices: 9908363--9908477 Score: 122
Period size: 33 Copynumber: 3.4 Consensus size: 33
9908353 AAATAATGAG
*
9908363 GATCGAGATTAAATCGTGACTTAAAAGTAAAGA
1 GATCGAGATTAAATCATGACTTAAAAGTAAAGA
* * * * *
9908396 GATCGGGATTAAATCATGAGTCAAAGAAATAATGA
1 GATCGAGATTAAATCATGACT-TAA-AAGTAAAGA
* * *
9908431 GGATTGGGATTAAACCATGACTTAAAAGTAAAGA
1 -GATCGAGATTAAATCATGACTTAAAAGTAAAGA
9908465 GATCGAGATTAAA
1 GATCGAGATTAAA
9908478 CCGCCAGTTA
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
33 29 0.45
34 9 0.14
35 9 0.14
36 18 0.28
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (33 bp):
GATCGAGATTAAATCATGACTTAAAAGTAAAGA
Found at i:9908495 original size:69 final size:68
Alignment explanation
Indices: 9908316--9908496 Score: 220
Period size: 69 Copynumber: 2.6 Consensus size: 68
9908306 TTGCAAGTCA
* * *
9908316 TAAAA-TAAAAAGATCGAGATTAAACCGCAAGTCAAAAAAATAATGAGGATCGAGATTAAATCGT
1 TAAAAGTAAAGAGATCGAGATTAAACCGCAAGTC-AAAAAATAATGAGGATCGAGATTAAACCAT
9908380 GACT
65 GACT
* * *** * *
9908384 TAAAAGTAAAGAGATCGGGATTAAATCATGAGTCAAAGAAATAATGAGGATTGGGATTAAACCAT
1 TAAAAGTAAAGAGATCGAGATTAAACCGCAAGTCAAA-AAATAATGAGGATCGAGATTAAACCAT
9908449 GACT
65 GACT
* *
9908453 TAAAAGTAAAGAGATCGAGATTAAACCGCCAGTTAAGAAAATAA
1 TAAAAGTAAAGAGATCGAGATTAAACCGCAAGTCAA-AAAATAA
9908497 AAAACTCGGA
Statistics
Matches: 94, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
68 8 0.09
69 85 0.90
70 1 0.01
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.21
Consensus pattern (68 bp):
TAAAAGTAAAGAGATCGAGATTAAACCGCAAGTCAAAAAATAATGAGGATCGAGATTAAACCATG
ACT
Found at i:9908833 original size:72 final size:70
Alignment explanation
Indices: 9908659--9908833 Score: 153
Period size: 72 Copynumber: 2.4 Consensus size: 70
9908649 ACTGAACCAT
* * * * * *
9908659 GAGTCAAGGAATCACAGGGACTGGGGTTAAACCACGAGTCAAGGAATAATGAAGATTAGGGTTGA
1 GAGTCAAGGAATCACAGGGACTAGGGTTAAACAACGAGTCAAGAAATAATGAAGACTAGGATTAA
9908724 ACCGC
66 ACCGC
* *
9908729 -ACGTCCAGAGGAAT-A-ATGAGGA-TTGGGATTAAACAACGAGTCAAGAAAATAATGATGACT-
1 GA-GT-CA-AGGAATCACA-G-GGACTAGGG-TTAAACAACGAGTCAAG-AAATAATGAAGACTA
*
9908789 GGAATTAAAACTGC
59 GG-ATT-AAACCGC
9908803 GAGTCAAGGAATCACAGGGACTAGGGTTAAA
1 GAGTCAAGGAATCACAGGGACTAGGGTTAAA
9908834 TCACAAGTCA
Statistics
Matches: 83, Mismatches: 9, Indels: 24
0.72 0.08 0.21
Matches are distributed among these distances:
69 1 0.01
70 3 0.04
71 8 0.10
72 41 0.49
73 21 0.25
74 8 0.10
75 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.29, T:0.18
Consensus pattern (70 bp):
GAGTCAAGGAATCACAGGGACTAGGGTTAAACAACGAGTCAAGAAATAATGAAGACTAGGATTAA
ACCGC
Found at i:9908968 original size:142 final size:142
Alignment explanation
Indices: 9908796--9909103 Score: 343
Period size: 142 Copynumber: 2.2 Consensus size: 142
9908786 ACTGGAATTA
* * *
9908796 AAACTGCGAGTCAAGGAATCACAGGGACTAGGGTTAAATCACAAGT-CATGAGG-ATAAAGACGA
1 AAACTGCGAGTCAAGGAATAATAAGGACTAGGGTTAAATCACAAGTCCA-GAGGAATAAAGACGA
* * *
9908859 CCGA-GATTGAACCACAAGTCAAAAAGATAAAAACGACTAGGACTGAACCAAGAGTCAAAGAATC
65 -CGAGGATTAAACCACAAGTCAAAAA-ATAAAAACGACTAGGACTAAACCAAGACTCAAAGAATC
*
9908923 ATAAGGACTGGGGTT
128 ACAAGGACTGGGGTT
* * * * *
9908938 AAACTGCGAGTCAAGGAATAATAAGGACTAGGGTTAAATCGCGAGTCCAGAGGAATAATGAGGAT
1 AAACTGCGAGTCAAGGAATAATAAGGACTAGGGTTAAATCACAAGTCCAGAGGAATAAAGACGAC
* * * ** * * *
9909003 TAGGATTAAACCACGAGTCAAGAAATAATGACGACTGGGATTAAACCATGACTCAAAGAATCACA
66 GAGGATTAAACCACAAGTCAAAAAATAAAAACGACTAGGACTAAACCAAGACTCAAAGAATCACA
*
9909068 GGGACTGGGGTT
131 AGGACTGGGGTT
* *
9909080 AAACTGGCAAGTCAGAGAAATAAT
1 AAACT-GCGAGTCA-AGGAATAAT
9909104 GAAGATCGGG
Statistics
Matches: 138, Mismatches: 23, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
142 95 0.69
143 35 0.25
144 8 0.06
ACGTcount: A:0.42, C:0.16, G:0.25, T:0.17
Consensus pattern (142 bp):
AAACTGCGAGTCAAGGAATAATAAGGACTAGGGTTAAATCACAAGTCCAGAGGAATAAAGACGAC
GAGGATTAAACCACAAGTCAAAAAATAAAAACGACTAGGACTAAACCAAGACTCAAAGAATCACA
AGGACTGGGGTT
Found at i:9908996 original size:251 final size:249
Alignment explanation
Indices: 9908553--9909083 Score: 735
Period size: 251 Copynumber: 2.1 Consensus size: 249
9908543 ATCAACCGCA
* * * *
9908553 AGTCAAGGAATCATAGGGATTGGGGTTAAACCACGAGTCAAGAGGATAAAGACGATCAAGATTAA
1 AGTCAAGGAATCACAGGGACTGGGGTTAAACCACAAGTCAAGAGGATAAAGACGACCAAGATTAA
* * * * * *
9908618 ACCACAAGTTAAGAAGATAAAGACAACTAGGACTGAACCATGAGTCAAGGAATCACAGGGACTGG
66 ACCACAAGTCAAAAAGATAAAAACAACTAGGACTGAACCAAGAGTCAAAGAATCACAAGGACTGG
* *
9908683 GGTTAAACCACGAGTCAAGGAATAATGAAGATTAGGGTTGAACCGCACGTCCAGAGGAATAATGA
131 GGTTAAACCACGAGTCAAGGAATAATGAAGACTAGGGTTAAACCGCACGTCCAGAGGAATAATGA
* *
9908748 GGATTGGGATTAAACAACGAGTCAAGAAAATAATGATGACTGGAATTAAAAC-TGCG
196 GGATTAGGATTAAACAACGAGTCAAG-AAATAATGACGACTGGAATTAAAACAT--G
* * * * *
9908804 AGTCAAGGAATCACAGGGACTAGGGTTAAATCACAAGTCATGAGGATAAAGACGACCGAGATTGA
1 AGTCAAGGAATCACAGGGACTGGGGTTAAACCACAAGTCAAGAGGATAAAGACGACCAAGATTAA
* *
9908869 ACCACAAGTCAAAAAGATAAAAACGACTAGGACTGAACCAAGAGTCAAAGAATCATAAGGACTGG
66 ACCACAAGTCAAAAAGATAAAAACAACTAGGACTGAACCAAGAGTCAAAGAATCACAAGGACTGG
** *
9908934 GGTTAAACTGCGAGTCAAGGAATAAT-AAGGACTAGGGTTAAATCGCGA-GTCCAGAGGAATAAT
131 GGTTAAACCACGAGTCAAGGAATAATGAA-GACTAGGGTTAAACCGC-ACGTCCAGAGGAATAAT
* * *
9908997 GAGGATTAGGATTAAACCACGAGTCAAGAAATAATGACGACTGGGATTAAACCATG
194 GAGGATTAGGATTAAACAACGAGTCAAGAAATAATGACGACTGGAATTAAAACATG
* *
9909053 ACTCAAAGAATCACAGGGACTGGGGTTAAAC
1 AGTCAAGGAATCACAGGGACTGGGGTTAAAC
9909084 TGGCAAGTCA
Statistics
Matches: 246, Mismatches: 31, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
249 28 0.11
250 24 0.10
251 193 0.78
252 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.26, T:0.18
Consensus pattern (249 bp):
AGTCAAGGAATCACAGGGACTGGGGTTAAACCACAAGTCAAGAGGATAAAGACGACCAAGATTAA
ACCACAAGTCAAAAAGATAAAAACAACTAGGACTGAACCAAGAGTCAAAGAATCACAAGGACTGG
GGTTAAACCACGAGTCAAGGAATAATGAAGACTAGGGTTAAACCGCACGTCCAGAGGAATAATGA
GGATTAGGATTAAACAACGAGTCAAGAAATAATGACGACTGGAATTAAAACATG
Found at i:9909012 original size:37 final size:35
Alignment explanation
Indices: 9908659--9909049 Score: 159
Period size: 35 Copynumber: 10.9 Consensus size: 35
9908649 ACTGAACCAT
* * *
9908659 GAGTCAAGGAATCACA-G-GGACTGGGGTTAAACCAC
1 GAGTCAAGGAAT-A-ATGAGGACTAGGATTAAACCGC
* * * *
9908694 GAGTCAAGGAATAATGAAGATTAGGGTTGAACCGC
1 GAGTCAAGGAATAATGAGGACTAGGATTAAACCGC
* * **
9908729 -ACGTCCAGAGGAATAATGAGGATTGGGATTAAACAAC
1 GA-GT-CA-AGGAATAATGAGGACTAGGATTAAACCGC
* * *
9908766 GAGTCAAGAAAATAATGATGACT-GGAATTAAAACTGC
1 GAGTCAAG-GAATAATGAGGACTAGG-ATT-AAACCGC
* * *
9908803 GAGTCAAGGAATCACA-G-GGACTAGGGTTAAATCAC
1 GAGTCAAGGAAT-A-ATGAGGACTAGGATTAAACCGC
* * * * * *
9908838 AAGTCATGAGG-ATAAAGACGAC-CGAGATTGAACCAC
1 GAGTCA--AGGAATAATGAGGACTAG-GATTAAACCGC
* ** ** * * * **
9908874 AAGTCAAAAAGATAAAAACGACTAGGACTGAACCAA
1 GAGTCAAGGA-ATAATGAGGACTAGGATTAAACCGC
* * * * * *
9908910 GAGTCAAAGAATCATAAGGACTGGGGTTAAACTGC
1 GAGTCAAGGAATAATGAGGACTAGGATTAAACCGC
* * *
9908945 GAGTCAAGGAATAATAAGGACTAGGGTTAAATCGC
1 GAGTCAAGGAATAATGAGGACTAGGATTAAACCGC
* *
9908980 GAGTCCAGAGGAATAATGAGGATTAGGATTAAACCAC
1 GAGT-CA-AGGAATAATGAGGACTAGGATTAAACCGC
* * *
9909017 GAGTCAAGAAATAATGACGACTGGGATTAAACC
1 GAGTCAAGGAATAATGAGGACTAGGATTAAACC
9909050 ATGACTCAAA
Statistics
Matches: 274, Mismatches: 60, Indels: 44
0.72 0.16 0.12
Matches are distributed among these distances:
33 1 0.00
34 5 0.02
35 115 0.42
36 77 0.28
37 74 0.27
38 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (35 bp):
GAGTCAAGGAATAATGAGGACTAGGATTAAACCGC
Found at i:9909263 original size:36 final size:35
Alignment explanation
Indices: 9909223--9909342 Score: 109
Period size: 36 Copynumber: 3.4 Consensus size: 35
9909213 ATTGAGGTTG
*
9909223 AACCACGAGTCAAAAAGATAAAGAAGATCGGGATTA
1 AACCACGAGTCAAAAA-ATAAAGACGATCGGGATTA
* ** *
9909259 AACCACAAGTCAAGGAATAATA-ACGA-CTGGGACTA
1 AACCACGAGTCAAAAAATAA-AGACGATC-GGGATTA
* * *
9909294 AACCATGAGTCAAAAAAATAATGACGATCGGGGTTA
1 AACCACGAGTC-AAAAAATAAAGACGATCGGGATTA
*
9909330 AACCATGAGTCAA
1 AACCACGAGTCAA
9909343 GAGAAGAAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
34 1 0.01
35 24 0.36
36 41 0.61
37 1 0.01
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.16
Consensus pattern (35 bp):
AACCACGAGTCAAAAAATAAAGACGATCGGGATTA
Found at i:9914023 original size:304 final size:305
Alignment explanation
Indices: 9913455--9914065 Score: 1010
Period size: 304 Copynumber: 2.0 Consensus size: 305
9913445 CAGGCATATC
*
9913455 TTGATAGGACCATACAAATACATCCACATATTCTTATAGTAAATTCACTAGTTTTTTTTTCTCAA
1 TTGATAAGACCATACAAATACATCCACATATTCTTATAGTAAATTCACTAGTTTTTTTTTCTCAA
* *
9913520 TCAGTGATAATGAAGTATCGATCCTAACTTCTTTCTTATTCTCATCGTCTCTCAAATTTAACATG
66 TCAGTGATAATGAAGTACCAATCCTAACTTCTTTCTTATTCTCATCGTCTCTCAAATTTAACATG
* * * *
9913585 TCAGTCAATTTTCGATGGGGTTATATAATTTTCTTCTCTTGCTTCATCCATTTCAGCAGATTGTG
131 TCAGTCAATTCTCGATAGGGTTATATAATTTTCTCCTCTTACTTCATCCATTTCAGCAGATTGTG
* * *
9913650 AGGTAAATCATAGTCTTTTGAATCAACATCATTATCAAGCTTGCTAATGTGAATCGAATTTTTAA
196 AGGTAAATCATAGTCTTTTGAATCAACATCATTATCAAGCTCGCTAATGTGAATCAAATTTTCAA
*
9913715 AATCAAACCTGGTGTTATTGCCTTGGTTGTCCATAATGTTCATTA
261 AATCAAACCTGGTGTTATTGCCTTGGTCGTCCATAATGTTCATTA
*
9913760 TTGATAAGACCATGCAAATACATCCACATATTCTTATAGTAAATTCACTAGTTTTTATTTT-TCA
1 TTGATAAGACCATACAAATACATCCACATATTCTTATAGTAAATTCACTAGTTTTT-TTTTCTCA
* * *
9913824 ATCGGTGATAATGAAGTACCAAT-TTAACTTCTTTCTTATTCTTATCGTCTCTCAAATTTAACAT
65 ATCAGTGATAATGAAGTACCAATCCTAACTTCTTTCTTATTCTCATCGTCTCTCAAATTTAACAT
* * * *
9913888 GTCAGTCAATTCTCGATAGGGTTTTATAATTTTCTCCTCTTATTTCATCTATTTCAGTAGATTGT
130 GTCAGTCAATTCTCGATAGGGTTATATAATTTTCTCCTCTTACTTCATCCATTTCAGCAGATTGT
* *
9913953 GAGGTAAATCATAGTCTTTTGAATCCATATCATTATCAAGCTCGCTAATGTGAATCAAATTTTCA
195 GAGGTAAATCATAGTCTTTTGAATCAACATCATTATCAAGCTCGCTAATGTGAATCAAATTTTCA
9914018 AAATCAAACCTGGTGTTATTGCCTTGGTCGTCCATAATGTTCATTA
260 AAATCAAACCTGGTGTTATTGCCTTGGTCGTCCATAATGTTCATTA
9914064 TT
1 TT
9914066 AGAAAACTTG
Statistics
Matches: 284, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
304 203 0.71
305 77 0.27
306 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.41
Consensus pattern (305 bp):
TTGATAAGACCATACAAATACATCCACATATTCTTATAGTAAATTCACTAGTTTTTTTTTCTCAA
TCAGTGATAATGAAGTACCAATCCTAACTTCTTTCTTATTCTCATCGTCTCTCAAATTTAACATG
TCAGTCAATTCTCGATAGGGTTATATAATTTTCTCCTCTTACTTCATCCATTTCAGCAGATTGTG
AGGTAAATCATAGTCTTTTGAATCAACATCATTATCAAGCTCGCTAATGTGAATCAAATTTTCAA
AATCAAACCTGGTGTTATTGCCTTGGTCGTCCATAATGTTCATTA
Found at i:9922061 original size:15 final size:15
Alignment explanation
Indices: 9922041--9922105 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 15
9922031 GGGTTTGGGA
9922041 TTTTGGATTTTAGTG
1 TTTTGGATTTTAGTG
9922056 TTTTGGATTTTAAGGCTTG
1 TTTTGGATTTT-A-G--TG
*
9922075 AAATTTTGAATTTTAGTG
1 ---TTTTGGATTTTAGTG
9922093 TTTTGGATTTTAG
1 TTTTGGATTTTAG
9922106 GGTTAAAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
15 23 0.56
16 1 0.02
17 1 0.02
18 2 0.05
19 2 0.05
20 1 0.02
21 1 0.02
22 10 0.24
ACGTcount: A:0.20, C:0.02, G:0.23, T:0.55
Consensus pattern (15 bp):
TTTTGGATTTTAGTG
Found at i:9922256 original size:19 final size:21
Alignment explanation
Indices: 9922213--9922264 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
9922203 TTATGAAGAG
9922213 TTAATATTAATTTATTTAGTT
1 TTAATATTAATTTATTTAGTT
*
9922234 TTAATATT-ATTTA-TTATTT
1 TTAATATTAATTTATTTAGTT
*
9922253 TTAATAATAATT
1 TTAATATTAATT
9922265 CTCCAACATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.43
20 8 0.29
21 8 0.29
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TTAATATTAATTTATTTAGTT
Found at i:9923609 original size:3 final size:3
Alignment explanation
Indices: 9923601--9923651 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
9923591 ACTAAAGTAA
* *
9923601 AAT AAT AAT AAT AAT AA- AAT AAT TAT AAT AAT TAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9923648 AAT A
1 AAT A
9923652 TGTAAATATG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:9924085 original size:19 final size:19
Alignment explanation
Indices: 9924049--9924088 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
9924039 ATTTTTTCAC
9924049 TTTTTTATATTTAATAAATA
1 TTTTTTATATTT-ATAAATA
9924069 TTTTTTAATATTT-TAAATA
1 TTTTTT-ATATTTATAAATA
9924088 T
1 T
9924089 GAACCCGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 6 0.32
21 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTTATATTTATAAATA
Found at i:9924234 original size:6 final size:7
Alignment explanation
Indices: 9924208--9924244 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
9924198 TTTTTAACTT
9924208 TTTTTAA
1 TTTTTAA
9924215 TTTTTCATA
1 TTTTT-A-A
9924224 TTTTTAA
1 TTTTTAA
9924231 TTTTTAA
1 TTTTTAA
9924238 TTTTTAA
1 TTTTTAA
9924245 AATTCATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 20 0.71
8 2 0.07
9 6 0.21
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTTAA
Found at i:9924248 original size:16 final size:14
Alignment explanation
Indices: 9924208--9924244 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 14
9924198 TTTTTAACTT
9924208 TTTTTAATTTTTCATA
1 TTTTTAATTTTT-A-A
9924224 TTTTTAATTTTTAA
1 TTTTTAATTTTTAA
9924238 TTTTTAA
1 TTTTTAA
9924245 AATTCATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 12 0.57
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTAATTTTTAA
Found at i:9924908 original size:29 final size:28
Alignment explanation
Indices: 9924876--9924931 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
9924866 TTTTTTATAT
*
9924876 ATATATT-ATATTAATAAAATTATTATTTG
1 ATATATTAAT-TTAA-AAAATTAATATTTG
*
9924905 ATATTTTAATTTAAAAAATTAATATTT
1 ATATATTAATTTAAAAAATTAATATTT
9924932 TAAGCTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 12 0.50
29 10 0.42
30 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (28 bp):
ATATATTAATTTAAAAAATTAATATTTG
Found at i:9926078 original size:2 final size:2
Alignment explanation
Indices: 9926073--9926097 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9926063 AATGCTTTTT
9926073 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 T
9926098 CATTGAGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9926669 original size:29 final size:29
Alignment explanation
Indices: 9926632--9926691 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
9926622 AATTAATAGA
*
9926632 TTTATAATTTAAATATCATATTAAAAATT
1 TTTAAAATTTAAATATCATATTAAAAATT
* *
9926661 TTTAAAATTTAAATATTATATTAAATATT
1 TTTAAAATTTAAATATCATATTAAAAATT
9926690 TT
1 TT
9926692 ATTATAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTAAAATTTAAATATCATATTAAAAATT
Found at i:9927180 original size:12 final size:13
Alignment explanation
Indices: 9927163--9927199 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
9927153 TAAAAATCAC
9927163 TGAAT-AATCAAA
1 TGAATAAATCAAA
9927175 TGAATAAATC-AA
1 TGAATAAATCAAA
*
9927187 TCAATAAATCAAA
1 TGAATAAATCAAA
9927200 AGCTAATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.24
Consensus pattern (13 bp):
TGAATAAATCAAA
Found at i:9928182 original size:15 final size:16
Alignment explanation
Indices: 9928155--9928187 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
9928145 CAAATGAAGG
9928155 CATTTTAAAATTTCTT
1 CATTTTAAAATTTCTT
9928171 CATTTT-AAATTTCTT
1 CATTTTAAAATTTCTT
9928186 CA
1 CA
9928188 AAATTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (16 bp):
CATTTTAAAATTTCTT
Found at i:9928673 original size:2 final size:2
Alignment explanation
Indices: 9928666--9928690 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9928656 GCACGTGTTC
9928666 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 A
9928691 AAGAGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9929911 original size:28 final size:26
Alignment explanation
Indices: 9929856--9929914 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
9929846 TGTTTGTTTA
* *
9929856 TTTTAATATTTTATTATTATATATAT
1 TTTTAATATTTTATTATTATAAACAT
9929882 TTTTAGATATTTTAATTACTTA-AAACAT
1 TTTTA-ATATTTT-ATTA-TTATAAACAT
9929910 TTTTA
1 TTTTA
9929915 TTAAACACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 5 0.18
27 7 0.25
28 13 0.46
29 3 0.11
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (26 bp):
TTTTAATATTTTATTATTATAAACAT
Found at i:9931158 original size:23 final size:22
Alignment explanation
Indices: 9931132--9931194 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
9931122 TTTAATATTA
9931132 AATAATAATTATAATAAATAATT
1 AATAATAATTATAA-AAATAATT
9931155 AATAA-AA-TATAAAAA-AATT
1 AATAATAATTATAAAAATAATT
*
9931174 AATTAATTAATTAAAAAAATA
1 AA-TAA-TAATTATAAAAATA
9931195 GAAAGTAGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
19 6 0.18
20 6 0.18
21 5 0.15
22 4 0.12
23 12 0.35
24 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAATAATTATAAAAATAATT
Found at i:9931287 original size:12 final size:11
Alignment explanation
Indices: 9931250--9931279 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
9931240 ACCCTTGTGT
9931250 AGCCACCCTAC
1 AGCCACCCTAC
*
9931261 CGCCACCCTAC
1 AGCCACCCTAC
9931272 AGCCACCC
1 AGCCACCC
9931280 CTATAGCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.23, C:0.60, G:0.10, T:0.07
Consensus pattern (11 bp):
AGCCACCCTAC
Found at i:9932649 original size:29 final size:28
Alignment explanation
Indices: 9932605--9932663 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
9932595 TCGGACCGTA
* *
9932605 TTTTTTTTTTGAATTTT-TTATATATTAT
1 TTTTTTTTTTAAATTTTATTAT-TAATAT
9932633 TTTTGTTTTTTAAATTTTATTATTAATAT
1 TTTT-TTTTTTAAATTTTATTATTAATAT
9932662 TT
1 TT
9932664 ATGCATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 4 0.15
29 19 0.70
30 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (28 bp):
TTTTTTTTTTAAATTTTATTATTAATAT
Found at i:9932650 original size:27 final size:26
Alignment explanation
Indices: 9932603--9932657 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
9932593 GATCGGACCG
*
9932603 TATTTTTTTTTTGAATTTTTTATATAT
1 TATTTTTTTTTTGAATATTTTAT-TAT
*
9932630 TATTTTTGTTTTTTAA-ATTTTATTAT
1 TATTTTT-TTTTTGAATATTTTATTAT
9932656 TA
1 TA
9932658 ATATTTATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.20
27 13 0.52
28 7 0.28
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (26 bp):
TATTTTTTTTTTGAATATTTTATTAT
Found at i:9932652 original size:20 final size:21
Alignment explanation
Indices: 9932604--9932653 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
9932594 ATCGGACCGT
* *
9932604 ATTTTTTTTTTGAATTTTTTAT
1 ATTTTATTTTTG-ATTTTTTAA
*
9932626 ATATTATTTTTG-TTTTTTAA
1 ATTTTATTTTTGATTTTTTAA
9932646 ATTTTATT
1 ATTTTATT
9932654 ATTAATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 14 0.58
22 10 0.42
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (21 bp):
ATTTTATTTTTGATTTTTTAA
Found at i:9932964 original size:3 final size:3
Alignment explanation
Indices: 9932958--9933013 Score: 94
Period size: 3 Copynumber: 18.3 Consensus size: 3
9932948 AAAAAAAGAG
*
9932958 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATTG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
9933004 ATA ATA ATA A
1 ATA ATA ATA A
9933014 ATTTCCATAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 48 0.96
4 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:9933254 original size:29 final size:29
Alignment explanation
Indices: 9933210--9933349 Score: 129
Period size: 29 Copynumber: 4.8 Consensus size: 29
9933200 CCTAAAGTTA
*
9933210 AAACCCCAAAATTAAACCCTAAACCCTCC
1 AAACCCCAAAACTAAACCCTAAACCCTCC
* * * **
9933239 AAACCCTAAAACTAAACTCTAAAACCTTT
1 AAACCCCAAAACTAAACCCTAAACCCTCC
* * *
9933268 AAACCCCGAAATTGAAATCCTAAACCCTCC
1 AAACCCCAAAACT-AAACCCTAAACCCTCC
** * *
9933298 AAGTCCTAAAACTAAACCCTAAACTCT-C
1 AAACCCCAAAACTAAACCCTAAACCCTCC
*
9933326 AAACCCCAAAACTGAAACCTTAAA
1 AAACCCCAAAACT-AAACCCTAAA
9933350 ATCCAAAATC
Statistics
Matches: 84, Mismatches: 25, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
28 11 0.13
29 54 0.64
30 19 0.23
ACGTcount: A:0.46, C:0.34, G:0.03, T:0.18
Consensus pattern (29 bp):
AAACCCCAAAACTAAACCCTAAACCCTCC
Found at i:9933260 original size:13 final size:13
Alignment explanation
Indices: 9933194--9933263 Score: 50
Period size: 13 Copynumber: 5.1 Consensus size: 13
9933184 CCTAAATCCT
*
9933194 CTAAACCCTAAAG
1 CTAAACCCTAAAA
* *
9933207 TTAAAACCCCAAAA
1 CT-AAACCCTAAAA
* *
9933221 TTAAACCCTAAACC
1 CTAAACCCTAAA-A
9933235 CTCCAAACCCTAAAA
1 CT--AAACCCTAAAA
*
9933250 CTAAACTCTAAAA
1 CTAAACCCTAAAA
9933263 C
1 C
9933264 CTTTAAACCC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
13 21 0.47
14 12 0.27
15 2 0.04
16 10 0.22
ACGTcount: A:0.49, C:0.33, G:0.01, T:0.17
Consensus pattern (13 bp):
CTAAACCCTAAAA
Found at i:9933270 original size:59 final size:57
Alignment explanation
Indices: 9933194--9933349 Score: 188
Period size: 58 Copynumber: 2.7 Consensus size: 57
9933184 CCTAAATCCT
* *
9933194 CTAAACCCTAAAGTTAAAACCCCAAAATT-AAACCCTAAACCCTCCAAACCCTAAAA
1 CTAAACCCTAAACTTTAAACCCCAAAATTGAAACCCTAAACCCTCCAAACCCTAAAA
* * * **
9933250 CTAAACTCTAAAACCTTTAAACCCCGAAATTGAAATCCTAAACCCTCCAAGTCCTAAAA
1 CTAAACCCT-AAA-CTTTAAACCCCAAAATTGAAACCCTAAACCCTCCAAACCCTAAAA
* * *
9933309 CTAAACCCTAAACTCTCAAACCCCAAAACTGAAACCTTAAA
1 CTAAACCCTAAACT-TTAAACCCCAAAATTGAAACCCTAAA
9933350 ATCCAAAATC
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
56 8 0.10
57 5 0.06
58 38 0.46
59 32 0.39
ACGTcount: A:0.46, C:0.33, G:0.03, T:0.19
Consensus pattern (57 bp):
CTAAACCCTAAACTTTAAACCCCAAAATTGAAACCCTAAACCCTCCAAACCCTAAAA
Found at i:9933367 original size:22 final size:21
Alignment explanation
Indices: 9933331--9933431 Score: 63
Period size: 22 Copynumber: 5.0 Consensus size: 21
9933321 CTCTCAAACC
*
9933331 CCAAAA-CTGAAACCTTAAAAT
1 CCAAAATCTCAAACC-TAAAAT
9933352 CCAAAATCTCAAACCT--AA-
1 CCAAAATCTCAAACCTAAAAT
*
9933370 --AAAA-CTAAAACCCTAAAAT
1 CCAAAATCTCAAA-CCTAAAAT
* **
9933389 CCAAAATCTTAAATTTTAAAAT
1 CCAAAATCTCAAA-CCTAAAAT
*
9933411 CCAAAATCCCAAATCCTAAAA
1 CCAAAATCTCAAA-CCTAAAA
9933432 GTCTAAACCC
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
15 5 0.08
16 7 0.11
18 2 0.03
19 2 0.03
21 11 0.18
22 35 0.56
ACGTcount: A:0.53, C:0.25, G:0.01, T:0.21
Consensus pattern (21 bp):
CCAAAATCTCAAACCTAAAAT
Found at i:9936904 original size:4 final size:4
Alignment explanation
Indices: 9936888--9936969 Score: 69
Period size: 4 Copynumber: 20.5 Consensus size: 4
9936878 GTCAGTTGTG
* * **
9936888 CATT CACT CATT CATT CATT CATT TATT CATT TGTGT -ATT CATT CATT
1 CATT CATT CATT CATT CATT CATT CATT CATT CAT-T CATT CATT CATT
* * *
9936936 CATT CATC CATT CATC CATT TATGT -ATT CATT CA
1 CATT CATT CATT CATT CATT CAT-T CATT CATT CA
9936970 ATATAATGCA
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
3 2 0.03
4 58 0.94
5 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.04, T:0.49
Consensus pattern (4 bp):
CATT
Done.