Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, 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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 100 of 100
Found at i:17759842 original size:15 final size:15
Alignment explanation
Indices: 17759822--17759857 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
17759812 TATGAAATAT
*
17759822 GATAAAACAAACATC
1 GATAAAACAAACATA
17759837 GATAAAACAAACATA
1 GATAAAACAAACATA
17759852 GATAAA
1 GATAAA
17759858 GAGTTACACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.64, C:0.14, G:0.08, T:0.14
Consensus pattern (15 bp):
GATAAAACAAACATA
Found at i:17762624 original size:62 final size:62
Alignment explanation
Indices: 17762558--17763328 Score: 255
Period size: 63 Copynumber: 12.3 Consensus size: 62
17762548 GTTTATGACT
* *
17762558 AAAAATGCCTTTAATAATCCCCTGATAAAAATTTGAAGGGATTATTGAAGGTGTTTTCTGTA
1 AAAAATGCCTTCAATAATCCTCTGATAAAAATTTGAAGGGATTATTGAAGGTGTTTTCTGTA
* * * * * *
17762620 AAAAATGCCTTCAATAAT--TTTTA-AAAAATTTTTTTAGGGGATTATTGAAGGTATTTT-TAAT
1 AAAAATGCCTTCAATAATCCTCTGATAAAAA---TTTGAAGGGATTATTGAAGGTGTTTTCT-GT
*
17762681 CT
62 -A
* ** * * *
17762683 AAAAATAG-CTTCAATAATCCTCTGATAGAAAATTAGAATAG-TCTTTTAAAAGGCATTTTTTAC
1 AAAAAT-GCCTTCAATAATCCTCTGATA-AAAATTTGAAGGGAT-TATT-GAAGG--TGTTTT-C
**
17762746 -AAA
59 TGTA
* * * * * *
17762749 AAAAATACCTTTAATAAT-TTCT-TTAAAAATTTTTAAGGGATTATTGAAGGCAT-TTTTTTGTC
1 AAAAATGCCTTCAATAATCCTCTGATAAAAA-TTTGAAGGGATTATTGAAGG--TGTTTTCTGT-
*
17762811 T
62 A
** * * * * *
17762812 AAAAACACCTTCAATAATCC-CTTGATAAAAAATTCAACAGGATTATTGAAGGTATTTT-TCATA
1 AAAAATGCCTTCAATAATCCTC-TGATAAAAATTTGAA-GGGATTATTGAAGGTGTTTTCT-GTA
* ** * * * * *
17762875 AAAAATGCCTTCAATAAT-TTCTTTTAAAATTTTTTAGGGGATTATTGAAGGCG-TTTGTG-A
1 AAAAATGCCTTCAATAATCCTCTGATAAAA-ATTTGAAGGGATTATTGAAGGTGTTTTCTGTA
* * * * * *
17762935 CTAAAAATGCCTTTAATAATCCTTTGATAAAAAATT-AGAGTGGATTATTAAATGCGTTTTCTGT
1 --AAAAATGCCTTCAATAATCCTCTGATAAAAATTTGA-AG-GGATTATTGAAGGTGTTTTCTGT
17762999 A
62 A
* * ** * * * *
17763000 AAAAATACCTTCAATAAT--TTTTTTAAAATTTTTTG-AGGGATTATTAAAGGTG-TTTGTGATT
1 AAAAATGCCTTCAATAATCCTCTGATAAAA--ATTTGAAGGGATTATTGAAGGTGTTTTCTG-TA
* * * ** * *
17763061 GAAAATGCCTTCAATAATCCCCTGATAAAAAATT-AGAGTGGATTATTGAAGGAATTTTTTGCA
1 AAAAATGCCTTCAATAATCCTCTGATAAAAATTTGA-AG-GGATTATTGAAGGTGTTTTCTGTA
* * * * *** *
17763124 AAAAATGCCTTCAATAATCCCCTAATAAAAAATTAGAATGGATTATTGAAGACATTTTCTGCA
1 AAAAATGCCTTCAATAATCCTCTGAT-AAAAATTTGAAGGGATTATTGAAGGTGTTTTCTGTA
* * * * ** ** **
17763187 AAAAAAGCTTTCAATAAT-TTTTTTTAAAAATTTTTAGAGGATTATTGAAGGCATTTT-T-TA
1 AAAAATGCCTTCAATAATCCTCTGATAAAAATTTGAAG-GGATTATTGAAGGTGTTTTCTGTA
** * * * * *
17763247 CTAAAAACACCTTCACTAAT-TTCAT-TTAAAAAATTGAAGGGAATTATTGAAGGTATTTT-TAG
1 --AAAAATGCCTTCAATAATCCTC-TGATAAAAATTTGAAGGG-ATTATTGAAGGTGTTTTCT-G
*
17763309 TC
61 TA
17763311 AAAAATGCCTTCAATAAT
1 AAAAATGCCTTCAATAAT
17763329 GTTAAATGTA
Statistics
Matches: 527, Mismatches: 126, Indels: 112
0.69 0.16 0.15
Matches are distributed among these distances:
59 5 0.01
60 9 0.02
61 56 0.11
62 168 0.32
63 185 0.35
64 46 0.09
65 32 0.06
66 16 0.03
67 10 0.02
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (62 bp):
AAAAATGCCTTCAATAATCCTCTGATAAAAATTTGAAGGGATTATTGAAGGTGTTTTCTGTA
Found at i:17763066 original size:61 final size:61
Alignment explanation
Indices: 17762851--17763078 Score: 203
Period size: 62 Copynumber: 3.7 Consensus size: 61
17762841 AAATTCAACA
* * * * *
17762851 GGATTATTGAAGGTATTTTTCATAAAAAATGCCTTCAATAATTTCTTTTAAAATTTTTT-AGG
1 GGATTATTAAAGGTGTTTGTGATTAAAAATGCCTTCAATAATTT-TTTTAAAATTTTTTGA-G
* * * * ** ** *
17762913 GGATTATTGAAGGCGTTTGTGACTAAAAATGCCTTTAATAATCCTTTGATAAAA-AATTAGAG
1 GGATTATTAAAGGTGTTTGTGATTAAAAATGCCTTCAATAAT--TTTTTTAAAATTTTTTGAG
* * *
17762975 TGGATTATTAAATGCGT-TTTCTG-TAAAAAATACCTTCAATAATTTTTTTAAAATTTTTTGAG
1 -GGATTATTAAA-G-GTGTTTGTGATTAAAAATGCCTTCAATAATTTTTTTAAAATTTTTTGAG
*
17763037 GGATTATTAAAGGTGTTTGTGATTGAAAATGCCTTCAATAAT
1 GGATTATTAAAGGTGTTTGTGATTAAAAATGCCTTCAATAAT
17763079 CCCCTGATAA
Statistics
Matches: 129, Mismatches: 28, Indels: 19
0.73 0.16 0.11
Matches are distributed among these distances:
59 2 0.02
60 6 0.05
61 36 0.28
62 43 0.33
63 33 0.26
64 8 0.06
65 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (61 bp):
GGATTATTAAAGGTGTTTGTGATTAAAAATGCCTTCAATAATTTTTTTAAAATTTTTTGAG
Found at i:17763279 original size:187 final size:180
Alignment explanation
Indices: 17762850--17763328 Score: 451
Period size: 187 Copynumber: 2.6 Consensus size: 180
17762840 AAAATTCAAC
* ** *
17762850 AGGATTATTGAAGGTATTTTTCATAAAAAATGCCTTCAATAATTTCTTTTAAAATTTTTTAGGGG
1 AGGATTATTGAAGGTATTTTTCATAAAAAA--CCTTCAATAATTTCATTTAAAA-AATTGA-GGG
** * * ** * *
17762915 ATTATTGAAGGCGTTTGTGACTAAAAATGCCTTTAATAATCCTTTGATAAAAAATTAGAGTGGAT
62 ATTATTGAAGGATTTTTTGAC-AAAAATGCCTTCAATAATCCCCTAATAAAAAATTAGAATGGAT
* * *
17762980 TATTAAATGCGTTTTCTGTAAAAAATACCTTCAATAATTTTTTTAAAATTTTTTG
126 TATTAAATGCATTTTCTGCAAAAAATACCTTCAATAATTTTTTTAAAATTTTTAG
* * * * ** ** * *
17763035 AGGGATTATTAAAGGTGTTTGTGATTGAAAATGCCTTCAATAATCCCCTGATAAAAAATTAGAGT
1 A-GGATTATTGAAGGTATTTTTCA-T-AAAAAACCTTCAATAATTTCAT-TTAAAAAATT-GAG-
17763100 GGATTATTGAAGGAATTTTTTG-CAAAAAATGCCTTCAATAATCCCCTAATAAAAAATTAGAATG
60 GGATTATTGAAGG-ATTTTTTGAC-AAAAATGCCTTCAATAATCCCCTAATAAAAAATTAGAATG
* *
17763164 GATTATTGAA-GACATTTTCTGCAAAAAA-AGCTTTCAATAATTTTTTTTAAAAATTTTTAG
123 GATTATTAAATG-CATTTTCTGCAAAAAATA-CCTTCAATAA-TTTTTTT-AAAATTTTTAG
* * *
17763224 AGGATTATTGAAGGCATTTTTTACTAAAAACACCTTCACTAATTTCATTTAAAAAATTGAAGGGA
1 AGGATTATTGAAGGTATTTTTCA-TAAAAA-ACCTTCAATAATTTCATTTAAAAAATTG-AGGG-
* *
17763289 ATTATTGAAGGTATTTTTAGTCAAAAATGCCTTCAATAAT
62 ATTATTGAAGG-ATTTTTTGACAAAAATGCCTTCAATAAT
17763329 GTTAAATGTA
Statistics
Matches: 237, Mismatches: 42, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
185 1 0.00
186 39 0.16
187 139 0.59
188 47 0.20
189 11 0.05
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (180 bp):
AGGATTATTGAAGGTATTTTTCATAAAAAACCTTCAATAATTTCATTTAAAAAATTGAGGGATTA
TTGAAGGATTTTTTGACAAAAATGCCTTCAATAATCCCCTAATAAAAAATTAGAATGGATTATTA
AATGCATTTTCTGCAAAAAATACCTTCAATAATTTTTTTAAAATTTTTAG
Found at i:17766364 original size:32 final size:32
Alignment explanation
Indices: 17766328--17766392 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
17766318 TAACACACTC
*
17766328 ATTAGTGCTTTTCACTTT-AGTCCCTAAAGTAA
1 ATTAGTGCTTTTCACTTTCA-TCCCTAAAATAA
17766360 ATTAGTGCTTTTCACTTTCATCCCTAAAATAA
1 ATTAGTGCTTTTCACTTTCATCCCTAAAATAA
17766392 A
1 A
17766393 AATTGAATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 30 0.97
33 1 0.03
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (32 bp):
ATTAGTGCTTTTCACTTTCATCCCTAAAATAA
Found at i:17769480 original size:20 final size:20
Alignment explanation
Indices: 17769440--17769491 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
17769430 CATATATCAT
*
17769440 TTCCTTTCTTTTAAATAACC
1 TTCCTTTCCTTTAAATAACC
* *
17769460 TTCCTTTCCTTTACATTACC
1 TTCCTTTCCTTTAAATAACC
**
17769480 TTTTTTTCCTTT
1 TTCCTTTCCTTT
17769492 CTTTTACTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.58
Consensus pattern (20 bp):
TTCCTTTCCTTTAAATAACC
Found at i:17770140 original size:22 final size:23
Alignment explanation
Indices: 17770115--17770158 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
17770105 TTTCTATTTT
17770115 TGTTATTATAG-TATAT-ATTATA
1 TGTTATTAT-GTTATATCATTATA
17770137 TGTTATTATGTTATATCATTAT
1 TGTTATTATGTTATATCATTAT
17770159 TAATGTCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 1 0.05
22 14 0.70
23 5 0.25
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (23 bp):
TGTTATTATGTTATATCATTATA
Found at i:17770174 original size:3 final size:3
Alignment explanation
Indices: 17770168--17770336 Score: 81
Period size: 3 Copynumber: 58.3 Consensus size: 3
17770158 TTAATGTCAC
* *
17770168 TAT TAT TAT TAT TAT TAT TAT TAC TA- TAT GAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
17770214 T-G TAT T-T TCCT T-T TTT TCT T-T GGTAT T-T T-T GTAT ATAT TA-
1 TAT TAT TAT T-AT TAT TAT TAT TAT --TAT TAT TAT -TAT -TAT TAT
* * * * * *
17770254 TAT TA- TAG TAT TAT TAA TGT CAC TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
17770301 TAT TAT TAT TAT T-T TAT TTT TAT TTT TAT TTT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
17770337 TTTTCTTTTC
Statistics
Matches: 128, Mismatches: 24, Indels: 28
0.71 0.13 0.16
Matches are distributed among these distances:
2 19 0.15
3 101 0.79
4 7 0.05
5 1 0.01
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:17770339 original size:109 final size:109
Alignment explanation
Indices: 17770140--17770344 Score: 292
Period size: 109 Copynumber: 1.9 Consensus size: 109
17770130 TATTATATGT
* *
17770140 TATTATGTTATATCATTATTAATGTCACTATTATTATTATTATTATTATTACTATATGATTATTA
1 TATTATATTATATCATTATTAATGTCACTATTATTATTATTATTACTATTACTATATGATTATTA
17770205 TTATTTTATTGTATTTTCCT-TTTTTTCTTTGGTATTTTTGTATA
66 TTATTTTATTGTATTTT-CTATTTTTTCTTTGGTATTTTTGTATA
* *
17770249 TATTATATTATAGT-ATTATTAATGTCACTATTATTATTATTATTACTATTATTATTATTATTAT
1 TATTATATTATA-TCATTATTAATGTCACTATTATTATTATTATTACTATTACTA-TATGATTAT
*
17770313 T-TTATTTTTATTTTTATTTT-TATTTTTTCTTT
64 TATTA-TTTTA-TTGTATTTTCTATTTTTTCTTT
17770345 TCTTTCTTTT
Statistics
Matches: 86, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
109 53 0.62
110 25 0.29
111 8 0.09
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.64
Consensus pattern (109 bp):
TATTATATTATATCATTATTAATGTCACTATTATTATTATTATTACTATTACTATATGATTATTA
TTATTTTATTGTATTTTCTATTTTTTCTTTGGTATTTTTGTATA
Found at i:17770765 original size:21 final size:21
Alignment explanation
Indices: 17770720--17770759 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17770710 TCTAGGTGGT
*
17770720 TTTGGGAGTAAAT-TAGGCAGA
1 TTTGGGAG-AAATCTAGGAAGA
17770741 TTTGGGAGAAATCTAGGAA
1 TTTGGGAGAAATCTAGGAA
17770760 AGTTTGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.05, G:0.33, T:0.28
Consensus pattern (21 bp):
TTTGGGAGAAATCTAGGAAGA
Found at i:17771357 original size:23 final size:21
Alignment explanation
Indices: 17771331--17771378 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
17771321 AAAATGATTC
17771331 AATAAAAAAAAGATATCTTTTCA
1 AATAAAAAAAA-A-ATCTTTTCA
17771354 AAT--AAAAAAAATCTTTTCA
1 AATAAAAAAAAAATCTTTTCA
17771373 AATAAA
1 AATAAA
17771379 GTTTTCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 12 0.52
20 1 0.04
21 7 0.30
23 3 0.13
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.29
Consensus pattern (21 bp):
AATAAAAAAAAAATCTTTTCA
Found at i:17771473 original size:22 final size:24
Alignment explanation
Indices: 17771445--17771488 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
17771435 TTATATATAT
17771445 AAAAAAATC-TTTTC-AATAAATC
1 AAAAAAATCTTTTTCAAATAAATC
17771467 AAAAAAATCTTTTTCAAATAAA
1 AAAAAAATCTTTTTCAAATAAA
17771489 AATCCTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (24 bp):
AAAAAAATCTTTTTCAAATAAATC
Found at i:17780616 original size:6 final size:6
Alignment explanation
Indices: 17780605--17780629 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17780595 GTGCTAACTT
17780605 GGAAGA GGAAGA GGAAGA GGAAGA G
1 GGAAGA GGAAGA GGAAGA GGAAGA G
17780630 CATGTCCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
GGAAGA
Found at i:17781981 original size:54 final size:53
Alignment explanation
Indices: 17781856--17781981 Score: 123
Period size: 53 Copynumber: 2.4 Consensus size: 53
17781846 TGCCATGAAG
* * * *
17781856 AAGTTGAAAACCTAAAAAGGTGACCTGAACCAAAAAAAAAAAAGAAAGAGTTC
1 AAGTTGAAAACCTAAAAGGGTGACCTCAACCAAAAAAAAAAAAGAAAAAATTC
* * * *
17781909 AAGTTAAAAACTTGAAAGGGT-AGCTTCAA-CAAAAAAAAACCAAA-AAACAAATTC
1 AAGTTGAAAACCTAAAAGGGTGA-CCTCAACCAAAAAAAAA--AAAGAAA-AAATTC
17781963 AAGTTGAAAACCTAAAAGG
1 AAGTTGAAAACCTAAAAGG
17781982 ACAGCTTGGA
Statistics
Matches: 58, Mismatches: 11, Indels: 7
0.76 0.14 0.09
Matches are distributed among these distances:
52 11 0.19
53 24 0.41
54 23 0.40
ACGTcount: A:0.56, C:0.13, G:0.15, T:0.15
Consensus pattern (53 bp):
AAGTTGAAAACCTAAAAGGGTGACCTCAACCAAAAAAAAAAAAGAAAAAATTC
Found at i:17783514 original size:116 final size:115
Alignment explanation
Indices: 17783280--17783515 Score: 264
Period size: 115 Copynumber: 2.0 Consensus size: 115
17783270 GTACTTACCT
* *
17783280 GATCTATCCCTCCCTTAAAAGGATCGATCTATTTTTTATACAAAATGCAAACTTGGTTAAAAATT
1 GATCGATCCCTCCCTTAAAAGGATCGATCTATTTTTTATACAAAATGCAAAATTGGTTAAAAATT
* * * *
17783345 CCCAAAAGAGATCGATCCCCCCACATAGGAGATCGATAACCTAAGCATGG
66 CACAAAAGAGATCGATCCCCCCACATAAGAGATCAATAACCTAAGAATGG
* * * * *
17783395 GATCGATCCCTTCCTTAAAGGGATCGATCTATTTTTTATATAGAAA-GTAAAATTGGTTTGAAAA
1 GATCGATCCCTCCCTTAAAAGGATCGATCTATTTTTTATACA-AAATGCAAAATTGG-TTAAAAA
* * * *
17783459 -TCAACAAAAGGGATTGATCCCCTCACATAA-AGGATCAATCACCTAAGGAAT-G
64 TTC-ACAAAAGAGATCGATCCCCCCACATAAGA-GATCAATAACCTAA-GAATGG
17783511 GATCG
1 GATCG
17783516 GTTAGGTATA
Statistics
Matches: 101, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
115 49 0.49
116 49 0.49
117 3 0.03
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (115 bp):
GATCGATCCCTCCCTTAAAAGGATCGATCTATTTTTTATACAAAATGCAAAATTGGTTAAAAATT
CACAAAAGAGATCGATCCCCCCACATAAGAGATCAATAACCTAAGAATGG
Found at i:17783660 original size:17 final size:17
Alignment explanation
Indices: 17783620--17783661 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
17783610 TTGATCCCTT
*
17783620 AATAGCCAGAAAGCCCC
1 AATAGCTAGAAAGCCCC
17783637 AATAGCTAGAAAGCCCC
1 AATAGCTAGAAAGCCCC
17783654 AATAGCTA
1 AATAGCTA
17783662 TTTTTTTGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.43, C:0.29, G:0.17, T:0.12
Consensus pattern (17 bp):
AATAGCTAGAAAGCCCC
Found at i:17787564 original size:16 final size:16
Alignment explanation
Indices: 17787543--17787576 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
17787533 ATAGAAAGAG
17787543 CACTTTCGATACTTGT
1 CACTTTCGATACTTGT
*
17787559 CACTTTCGATATTTGT
1 CACTTTCGATACTTGT
17787575 CA
1 CA
17787577 ATTGTTTGGA
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:0.21, C:0.24, G:0.12, T:0.44
Consensus pattern (16 bp):
CACTTTCGATACTTGT
Found at i:17790119 original size:15 final size:14
Alignment explanation
Indices: 17790094--17790127 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
17790084 TATCACTTTG
17790094 AAATTTGGCTTGTC
1 AAATTTGGCTTGTC
*
17790108 AAATTATGGCTTGTG
1 AAATT-TGGCTTGTC
17790123 AAATT
1 AAATT
17790128 GGTATATTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (14 bp):
AAATTTGGCTTGTC
Found at i:17790335 original size:37 final size:38
Alignment explanation
Indices: 17790285--17790362 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 38
17790275 AAATTATATG
* * *
17790285 AAAATTTTCTATTTGATTGATGATCTTGGTGGTATGGA
1 AAAATTTTCTATTTCATTGATGATCTTGATGGTATGCA
17790323 AAAATTTT-TATTTCATTGATGATCTTGATGGTATGCA
1 AAAATTTTCTATTTCATTGATGATCTTGATGGTATGCA
17790360 AAA
1 AAA
17790363 TTTGTACTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
37 29 0.78
38 8 0.22
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (38 bp):
AAAATTTTCTATTTCATTGATGATCTTGATGGTATGCA
Found at i:17790376 original size:32 final size:35
Alignment explanation
Indices: 17790300--17790382 Score: 91
Period size: 37 Copynumber: 2.4 Consensus size: 35
17790290 TTTCTATTTG
* *
17790300 ATTGATGATCTTGGTGGTATGGAAAAATTTTTATTTC
1 ATTGATGATCTTGATGGTATGGAAAAATTTGTA--TC
*
17790337 ATTGATGATCTTGATGGTAT-GCAAAATTTGTA-C
1 ATTGATGATCTTGATGGTATGGAAAAATTTGTATC
*
17790370 -TTGATGATATTGA
1 ATTGATGATCTTGA
17790383 CATTGTTCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 12 0.29
33 1 0.02
36 10 0.24
37 19 0.45
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (35 bp):
ATTGATGATCTTGATGGTATGGAAAAATTTGTATC
Found at i:17792149 original size:56 final size:56
Alignment explanation
Indices: 17792026--17792134 Score: 157
Period size: 56 Copynumber: 1.9 Consensus size: 56
17792016 TTGTAGTTCA
* * * *
17792026 TCCCAATCATTTGATCTTGGCTTAGTCCAAATCACTTCTTATGATTCATGGTTTCG
1 TCCCAGTCATTTAATCTTGGCTCAATCCAAATCACTTCTTATGATTCATGGTTTCG
*
17792082 TCCCAGTCATTTAATCTTGGCTCAATCCAAATCA-TCTCTTATGATTCGTGGTT
1 TCCCAGTCATTTAATCTTGGCTCAATCCAAATCACT-TCTTATGATTCATGGTT
17792135 CTGTCCTGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
55 1 0.02
56 46 0.98
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (56 bp):
TCCCAGTCATTTAATCTTGGCTCAATCCAAATCACTTCTTATGATTCATGGTTTCG
Found at i:17792436 original size:3 final size:3
Alignment explanation
Indices: 17792430--17792499 Score: 101
Period size: 3 Copynumber: 24.3 Consensus size: 3
17792420 TTAATGTCAC
* *
17792430 TAT TAT TAT TAT TAC TA- TAT GAT TAT TAT TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17792476 TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
17792500 TTCCTTTTCT
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
2 6 0.10
3 55 0.90
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:17792456 original size:23 final size:23
Alignment explanation
Indices: 17792430--17792499 Score: 97
Period size: 23 Copynumber: 3.0 Consensus size: 23
17792420 TTAATGTCAC
17792430 TATTATTATTATTACTA-TATGAT
1 TATTATTATTATTACTATTAT-AT
*
17792453 TATTATTATTATTATTATTATAT
1 TATTATTATTATTACTATTATAT
* *
17792476 TATTATTATTATTATTATTTTAT
1 TATTATTATTATTACTATTATAT
17792499 T
1 T
17792500 TTCCTTTTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (23 bp):
TATTATTATTATTACTATTATAT
Found at i:17792498 original size:20 final size:20
Alignment explanation
Indices: 17792432--17792499 Score: 91
Period size: 20 Copynumber: 3.2 Consensus size: 20
17792422 AATGTCACTA
*
17792432 TTATTATTATTACTATATGATT
1 TTATTATTATTA-T-TATTATT
*
17792454 ATTATTATTATTATTATTATA
1 -TTATTATTATTATTATTATT
17792475 TTATTATTATTATTATTATT
1 TTATTATTATTATTATTATT
17792495 TTATT
1 TTATT
17792500 TTCCTTTTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 24 0.57
21 5 0.12
22 1 0.02
23 12 0.29
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (20 bp):
TTATTATTATTATTATTATT
Found at i:17792616 original size:5 final size:5
Alignment explanation
Indices: 17792606--17792642 Score: 56
Period size: 5 Copynumber: 7.0 Consensus size: 5
17792596 TTATTAATTA
17792606 TTCTT TTCTT TTCTT TTCTT CTTCTCT TTCTT TTCTT
1 TTCTT TTCTT TTCTT TTCTT -TTCT-T TTCTT TTCTT
17792643 CTTTCTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 21 0.70
6 8 0.27
7 1 0.03
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
TTCTT
Found at i:17792637 original size:17 final size:17
Alignment explanation
Indices: 17792606--17792654 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
17792596 TTATTAATTA
17792606 TTCTT-TTCT-TTTCTT
1 TTCTTCTTCTCTTTCTT
17792621 TTCTTCTTCTCTTTCTT
1 TTCTTCTTCTCTTTCTT
17792638 TTCTTCTT-TCTTT-TT
1 TTCTTCTTCTCTTTCTT
17792653 TT
1 TT
17792655 GTTTCGATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.28
16 9 0.28
17 14 0.44
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
TTCTTCTTCTCTTTCTT
Found at i:17792650 original size:12 final size:11
Alignment explanation
Indices: 17792606--17792651 Score: 60
Period size: 12 Copynumber: 4.2 Consensus size: 11
17792596 TTATTAATTA
17792606 TTCT-TTTCTT
1 TTCTCTTTCTT
17792616 TTCT-TTTCTT
1 TTCTCTTTCTT
17792626 CTTCTCTTTCTT
1 -TTCTCTTTCTT
17792638 TTCTTCTTTCTT
1 TTC-TCTTTCTT
17792650 TT
1 TT
17792652 TTTGTTTCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.30
11 7 0.21
12 16 0.48
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTCTCTTTCTT
Found at i:17793484 original size:19 final size:18
Alignment explanation
Indices: 17793462--17793502 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
17793452 CAGGTTTTCC
17793462 TTTTTTCATTTTATTTTTA
1 TTTTTTCATTTTA-TTTTA
*
17793481 TTTTTTGATTTTATTTTA
1 TTTTTTCATTTTATTTTA
17793499 TTTT
1 TTTT
17793503 ATTTTTAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTTTCATTTTATTTTA
Found at i:17793733 original size:21 final size:21
Alignment explanation
Indices: 17793709--17793755 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
17793699 TTAAGTTGTC
* *
17793709 AAAAAATAGTTTT-ATATATA
1 AAAAAATACTTTTCATAAATA
*
17793729 AAAAAATCCTTTTCATAAATA
1 AAAAAATACTTTTCATAAATA
17793750 AAAAAA
1 AAAAAA
17793756 ATCTTTTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAAAATACTTTTCATAAATA
Found at i:17801395 original size:200 final size:199
Alignment explanation
Indices: 17800960--17801633 Score: 710
Period size: 200 Copynumber: 3.4 Consensus size: 199
17800950 AAAATGAGAA
* * *
17800960 AAATGAAAAAATTCAAA-ATATTAGTGACTAAAGGTAAATCGTCACAATATTAG-ACACAAAATT
1 AAATGATAAAA-TCAAATATATTAGTGACGAAAGGTAAATCGTCACAATATTAGTA-ACACAATT
* * ** ***
17801023 ATTGTCACCAATGATTGTAAGATAATGTTTACCATGACAATAAAATCAAACGTCACCTTATGCTT
64 ATCGTCACAAATGATTGTAAGATAATGTCAAATGTGACAATAAAATCAAACGTCACCTTATGCTT
* * * *
17801088 TAATATTTGTGATGTTAGTTTTAGTCAGCTATTTATGAACAAAAACATCATTAAAGGCTATAATC
129 T--T-TTTGTGACGTTAGTTTTCGTTAGCTATTTAT-AAAAAAAACATCATTAAAGGCTATAATC
17801153 ATCACAAAAT
190 ATCACAAAAT
* * * *
17801163 AAATGATAAAATCAGATATATTAGTGACGAAAGATATATCGTCACAATATTAGTGACACAATTAT
1 AAATGATAAAATCAAATATATTAGTGACGAAAGGTAAATCGTCACAATATTAGTAACACAATTAT
** * * * *
17801228 CGTCATGAATGATTATAAGATAATATCAAATGTGACAATAAAATCAAACATCACCTTGTGCTTTT
66 CGTCACAAATGATTGTAAGATAATGTCAAATGTGACAATAAAATCAAACGTCACCTTATGCTTTT
* * * *
17801293 TTTATGACGTTAGTTTTCGTTAGCTATTTATAAAAAAGAACATGATTGAAA-GTTATAATCGTCA
131 TTTGTGACGTTAGTTTTCGTTAGCTATTTATAAAAAA-AACATCATT-AAAGGCTATAATCATCA
17801357 CAAAAT
194 CAAAAT
* * * * *
17801363 AAATGATAAAATCAAATATATTAATAACGAAAGGTAAATCATCACAGTATTGGTAACACAATTAT
1 AAATGATAAAATCAAATATATTAGTGACGAAAGGTAAATCGTCACAATATTAGTAACACAATTAT
* * * * * *
17801428 CATTACAAATGATTGTAAGATAACGTCAAATGTGATAATAAAATCAAATGTCACATTATGCTTTA
66 CGTCACAAATGATTGTAAGATAATGTCAAATGTGACAATAAAATCAAACGTCACCTTATGC----
* * * ** *
17801493 TTTTTTTGTGACATTAGTTTTCATTAGCTATTTAT-GAAAAAATGTCATTAAAGGCCATAATCAT
127 TTTTTTTGTGACGTTAGTTTTCGTTAGCTATTTATAAAAAAAACATCATTAAAGGCTATAATCAT
17801557 CACAAAAT
192 CACAAAAT
* ** * * * * * * *
17801565 AAATGAT-AAATCTAATATATTAGTGATAAAAAGTAAATCATCACAGTATTGGTGACATAATTAA
1 AAATGATAAAATCAAATATATTAGTGACGAAAGGTAAATCGTCACAATATTAGTAACACAATTAT
17801629 CGTCA
66 CGTCA
17801634 TTAAATCCTA
Statistics
Matches: 393, Mismatches: 69, Indels: 20
0.82 0.14 0.04
Matches are distributed among these distances:
199 5 0.01
200 157 0.40
201 58 0.15
202 33 0.08
203 108 0.27
204 32 0.08
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (199 bp):
AAATGATAAAATCAAATATATTAGTGACGAAAGGTAAATCGTCACAATATTAGTAACACAATTAT
CGTCACAAATGATTGTAAGATAATGTCAAATGTGACAATAAAATCAAACGTCACCTTATGCTTTT
TTTGTGACGTTAGTTTTCGTTAGCTATTTATAAAAAAAACATCATTAAAGGCTATAATCATCACA
AAAT
Found at i:17804305 original size:7 final size:7
Alignment explanation
Indices: 17804289--17804319 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
17804279 AATTATATTT
*
17804289 TTTAATA
1 TTTAAAA
17804296 TTTAAAA
1 TTTAAAA
17804303 TTTAAAA
1 TTTAAAA
17804310 TTTAAAA
1 TTTAAAA
17804317 TTT
1 TTT
17804320 TTATTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TTTAAAA
Found at i:17804360 original size:29 final size:29
Alignment explanation
Indices: 17804287--17804366 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
17804277 AAAATTATAT
* *
17804287 TTTTTAATATTTAAAATTTAAAATTTAAAA
1 TTTTTAAT-TTTAATATTAAAAATTTAAAA
*
17804317 TTTTTATTTTTTAATATTAAAAATTATAAAA
1 TTTTTA-ATTTTAATATTAAAAATT-TAAAA
17804348 -TTTTAATTTTAATATTAAA
1 TTTTTAATTTTAATATTAAA
17804367 TACATTAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 13 0.30
30 25 0.57
31 6 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TTTTTAATTTTAATATTAAAAATTTAAAA
Found at i:17805850 original size:234 final size:235
Alignment explanation
Indices: 17805035--17805997 Score: 1083
Period size: 241 Copynumber: 4.0 Consensus size: 235
17805025 TAACATCATT
** * * * *
17805035 TAAAAGTTTGTGACATTTATGTTATTGTCATATAACACCACACATTAACGTAATCAAATTGCAAT
1 TAAAAGTTTGTGACATTTATGTTATCATCATATAACACCATACATTAACGTGATGAAATTACAAT
* * * * * *
17805100 ATCATTAATAGTAAACTAAAATATTCAATTTGTGACAAAAATTCATAACATCACCTTAAATCTAT
66 GTCATTAATAATTAACTAAAGTATTCAATTTGTGACAAAAATTAATAACATCACCTAAAATCTAT
* ** **
17805165 TAGAAAAAATTCATCACAGTTAAAATTTTAAATTGGTGATAAAATTATAATGTCACCTAAAATAA
131 T--AAAAAATTTATCACAAATAAAATTTTAAATTGGTGATAAAATTATAACATCACCTAAAAT--
**
17805230 AAACAAAAACATCACAAGGAAATTTTCCACCAAATAAATTTGGCGG
192 AAA-AAAAA-ATCACAAAAAAATTTTCCACCAAATAAATTTGGCGG
* * * *
17805276 TAAAAGTTTGTGACATTTATGTTATCATCATATGACACCATACATTGACGTGATGAAATTGCAAC
1 TAAAAGTTTGTGACATTTATGTTATCATCATATAACACCATACATTAACGTGATGAAATTACAAT
* * * * ** ** * *
17805341 GTTATTAATAGTTAACTAAAGTGTTCAATTTATGACAACTATTAATAATGTTACCTATAATCTAT
66 GTCATTAATAATTAACTAAAGTATTCAATTTGTGACAAAAATTAATAACATCACCTAAAATCTAT
* * * * * *
17805406 AAAAAAAAAATTTGTCATAGATAAAATTTTAAATTGGTGATGAAATTATAACATCACCTAAAA-C
131 ---TAAAAAATTTATCACAAATAAAATTTTAAATTGGTGATAAAATTATAACATCACCTAAAATA
*
17805470 AAAAAACATCACAAAAAAAAAATTTTCCCACCAAATAAATTTAGG-GG
193 AAAAAAAATCAC---AAAAAAATTTT-CCACCAAATAAATTT-GGCGG
* * * *
17805517 TAAAAGTTTGTGACATTTATGTTATCGTCATATAACACCATACATTAATGTGACGAAATTATAAT
1 TAAAAGTTTGTGACATTTATGTTATCATCATATAACACCATACATTAACGTGATGAAATTACAAT
* **
17805582 GTCATTAATAATTAACTAAAGTGTTCAATTTGTGACAAAAATTAATAATGTCACCTAAAATCTAT
66 GTCATTAATAATTAACTAAAGTATTCAATTTGTGACAAAAATTAATAACATCACCTAAAATCTAT
* * * *
17805647 TAAAAAATTAATCACAAATAAAATTTTAAATTGGTGACAAAAATTATAACATTAGCTAAAAT-AA
131 TAAAAAATTTATCACAAATAAAATTTTAAATTGGTGA-TAAAATTATAACATCACCTAAAATAAA
* * * **
17805711 AAAAAATCACAAATAAATTTTTCACCATATAAATTTGGCAA
195 AAAAAATCACAAAAAAATTTTCCACCAAATAAATTTGGCGG
* * *
17805752 TAAAAGTTTGTGGCATTTATGTTATCATTATATAA-ACCATACATTAACGTGATGAAACTACAAT
1 TAAAAGTTTGTGACATTTATGTTATCATCATATAACACCATACATTAACGTGATGAAATTACAAT
* * * *
17805816 GTCATTAATAATTAACTAAAGCATTTATTTTGTGACAAGAATTAATAACATCACCTAAAATCTAT
66 GTCATTAATAATTAACTAAAGTATTCAATTTGTGACAAAAATTAATAACATCACCTAAAATCTAT
* * * * *
17805881 CAGAAAAATTTGTCA-AAGATAAAATTTTAAGTTGGTGACAAAATTATAACGTCACCTAAAATAA
131 TA-AAAAATTTATCACAA-ATAAAATTTTAAATTGGTGATAAAATTATAACATCACCTAAAATAA
* *
17805945 AAAAAAATGTCACAAAAAAATTTCCCACCAAATAAATTTGGTGG
194 AAAAAAA--TCACAAAAAAATTTTCCACCAAATAAATTTGGCGG
17805989 TAAAA-TTTG
1 TAAAAGTTTG
17805998 GCAATAAGAT
Statistics
Matches: 613, Mismatches: 93, Indels: 37
0.83 0.13 0.05
Matches are distributed among these distances:
234 108 0.18
235 82 0.13
236 14 0.02
237 38 0.06
238 36 0.06
239 32 0.05
240 9 0.01
241 240 0.39
242 54 0.09
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (235 bp):
TAAAAGTTTGTGACATTTATGTTATCATCATATAACACCATACATTAACGTGATGAAATTACAAT
GTCATTAATAATTAACTAAAGTATTCAATTTGTGACAAAAATTAATAACATCACCTAAAATCTAT
TAAAAAATTTATCACAAATAAAATTTTAAATTGGTGATAAAATTATAACATCACCTAAAATAAAA
AAAAATCACAAAAAAATTTTCCACCAAATAAATTTGGCGG
Found at i:17807359 original size:20 final size:20
Alignment explanation
Indices: 17807327--17807365 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
17807317 ACCATTAAAC
*
17807327 AAAAAATCAAATAA-AAAAT
1 AAAAAATAAAATAACAAAAT
17807346 AAAAAATAATAATAACAAAA
1 AAAAAATAA-AATAACAAAA
17807366 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 5 0.29
21 4 0.24
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.15
Consensus pattern (20 bp):
AAAAAATAAAATAACAAAAT
Found at i:17807499 original size:12 final size:12
Alignment explanation
Indices: 17807484--17807510 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17807474 TTAAAAGTCT
17807484 AAAAAAAAAAAG
1 AAAAAAAAAAAG
17807496 AAAAAAAAAAAG
1 AAAAAAAAAAAG
17807508 AAA
1 AAA
17807511 GCAAATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:17807504 original size:17 final size:17
Alignment explanation
Indices: 17807484--17807540 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 17
17807474 TTAAAAGTCT
17807484 AAAAAAAAAAAG-AAAA
1 AAAAAAAAAAAGAAAAA
*
17807500 AAAAAAAGAAAGCAAATGAA
1 AAAAAAAAAAAG-AAA--AA
17807520 AAAAGACAAAAAAGAAAAA
1 AAAA-A-AAAAAAGAAAAA
17807539 AA
1 AA
17807541 TGGATTCCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
16 11 0.33
18 2 0.06
19 4 0.12
20 6 0.18
21 4 0.12
22 6 0.18
ACGTcount: A:0.84, C:0.04, G:0.11, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAAAGAAAAA
Found at i:17812844 original size:9 final size:9
Alignment explanation
Indices: 17812827--17812868 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
17812817 AACTTATGAA
17812827 AAAACAGAAG
1 AAAA-AGAAG
* *
17812837 AAGAAGAAA
1 AAAAAGAAG
17812846 AAAAAGAAG
1 AAAAAGAAG
17812855 AAAAAGAAG
1 AAAAAGAAG
17812864 AAAAA
1 AAAAA
17812869 CCAAATCTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 25 0.89
10 3 0.11
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:17812847 original size:18 final size:18
Alignment explanation
Indices: 17812824--17812868 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
17812814 TGAAACTTAT
* *
17812824 GAAAAAACAGAAGAAGAA
1 GAAAAAAAAGAAGAAAAA
17812842 GAAAAAAAAGAAGAAAAA
1 GAAAAAAAAGAAGAAAAA
17812860 GAAGAAAAA
1 GAA-AAAAA
17812869 CCAAATCTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
GAAAAAAAAGAAGAAAAA
Found at i:17818917 original size:13 final size:13
Alignment explanation
Indices: 17818896--17818938 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
17818886 TTCATTTCAC
*
17818896 TTCTCTTTTTTTT
1 TTCTTTTTTTTTT
17818909 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
*
17818922 TTGTTTTGGTTTTTT
1 TTCTTTT--TTTTTT
17818937 TT
1 TT
17818939 TGGGCATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 18 0.69
15 8 0.31
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (13 bp):
TTCTTTTTTTTTT
Found at i:17826569 original size:207 final size:205
Alignment explanation
Indices: 17826315--17826718 Score: 623
Period size: 209 Copynumber: 2.0 Consensus size: 205
17826305 CATAATTGGA
*
17826315 AATTCTCATTACTCAATTTTATGAAAAATAAATGCATTTATAAATATTTATTTTTTATCTTTTCA
1 AATTCCCATTACTCAATTTTATGAAAAATAAATGCATTTATAAATATTTATTTTTTATCTTTTCA
* * *
17826380 AGATAATTGTTTAAATTGAT-AAAAAAATTTATATTGAAAAGAGTTTCTAAATATTCCAATACTT
66 AGAGAATTGTTCAAATTGATAAAAAAAATTTATATTGAAAAGAGTTTCTAAATATTCCAATACCT
* *
17826444 TGGTAGTTTTTAGAAATCTTTTCTCACCT-AGGTAATTCTCAAGAATCACTATTCGAACTTTCTG
131 TGGTAATTTTTAGAAATCTTTTCTCACCTAAGG-AATTCTCAAGAATCACTA---GAACTTCCTG
17826508 AGGTCCCATCATCG
192 AGGTCCCATCATCG
** *
17826522 AATTCCCATTACTCAATTTTATGAAAAATCCATGCTTTTATAAATATTTATTTTTTATCTTTTCA
1 AATTCCCATTACTCAATTTTATGAAAAATAAATGCATTTATAAATATTTATTTTTTATCTTTTCA
*
17826587 AGAGAATTGTTCAAATTGATAAAAAAAAATTTATATTGAAAAGAGTTTCTAAATATTCTAATACC
66 AGAGAATTGTTCAAATTGAT-AAAAAAAATTTATATTGAAAAGAGTTTCTAAATATTCCAATACC
* * * *
17826652 TTGGTAATTTTTAGAAATCTTTTCTTACTTAAGGAATTCTTAGGAATCACTAGAACTTCCTGAGG
130 TTGGTAATTTTTAGAAATCTTTTCTCACCTAAGGAATTCTCAAGAATCACTAGAACTTCCTGAGG
17826717 TC
195 TC
17826719 TTACCATCGA
Statistics
Matches: 180, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
206 14 0.08
207 79 0.44
209 84 0.47
210 3 0.02
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (205 bp):
AATTCCCATTACTCAATTTTATGAAAAATAAATGCATTTATAAATATTTATTTTTTATCTTTTCA
AGAGAATTGTTCAAATTGATAAAAAAAATTTATATTGAAAAGAGTTTCTAAATATTCCAATACCT
TGGTAATTTTTAGAAATCTTTTCTCACCTAAGGAATTCTCAAGAATCACTAGAACTTCCTGAGGT
CCCATCATCG
Found at i:17828021 original size:2 final size:2
Alignment explanation
Indices: 17828014--17828040 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17828004 CGTTGTCTTC
17828014 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
17828041 TTAGCTACCT
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:17830924 original size:32 final size:32
Alignment explanation
Indices: 17830888--17830952 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
17830878 TCATACAATG
17830888 TTGCCAATTTTTTTAAACAGCGTAGGAATCTA
1 TTGCCAATTTTTTTAAACAGCGTAGGAATCTA
17830920 TTGCCAATTTTTTTAAACAGCGTAGGAATCTA
1 TTGCCAATTTTTTTAAACAGCGTAGGAATCTA
17830952 T
1 T
17830953 CTCCTGTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (32 bp):
TTGCCAATTTTTTTAAACAGCGTAGGAATCTA
Found at i:17832828 original size:3 final size:3
Alignment explanation
Indices: 17832806--17832850 Score: 54
Period size: 3 Copynumber: 14.0 Consensus size: 3
17832796 TTAGTAAGCT
*
17832806 TAA TAA TTAA AAA TATA TAA TAA TAA TAA TAA TAA TAA GTAA TAA
1 TAA TAA -TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA -TAA TAA
17832851 ATATGCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
3 28 0.76
4 9 0.24
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:17832836 original size:9 final size:9
Alignment explanation
Indices: 17832806--17832850 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 9
17832796 TTAGTAAGCT
17832806 TAATAATTAA
1 TAATAA-TAA
*
17832816 AAATATATAA
1 TAATA-ATAA
17832826 TAATAATAA
1 TAATAATAA
17832835 TAATAATAA
1 TAATAATAA
17832844 GTAATAA
1 -TAATAA
17832851 ATATGCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 13 0.42
10 17 0.55
11 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (9 bp):
TAATAATAA
Found at i:17833148 original size:13 final size:13
Alignment explanation
Indices: 17833130--17833167 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
17833120 TTTAAAAACC
17833130 TGAAACCCTAAAG
1 TGAAACCCTAAAG
*
17833143 TGAAACCCTAATG
1 TGAAACCCTAAAG
*
17833156 TGAAGCCCTAAA
1 TGAAACCCTAAA
17833168 ATAAAATCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (13 bp):
TGAAACCCTAAAG
Found at i:17833219 original size:19 final size:19
Alignment explanation
Indices: 17833171--17833211 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
17833161 CCCTAAAATA
**
17833171 AAATCCTAGACAAAACCCT
1 AAATCCTAGGTAAAACCCT
17833190 AAATCCTAGGTAAAACCCT
1 AAATCCTAGGTAAAACCCT
17833209 AAA
1 AAA
17833212 CCTTAGGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.27, G:0.07, T:0.17
Consensus pattern (19 bp):
AAATCCTAGGTAAAACCCT
Found at i:17838829 original size:31 final size:31
Alignment explanation
Indices: 17838787--17838847 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
17838777 AAGGAAAAAA
* *
17838787 AGTGAAGAAAAAGAGAAAAAGAAAA-AAGAAT
1 AGTGAA-AAAAAAAGAAAAAAAAAAGAAGAAT
17838818 AGTGAAAAAAAAAGAAAAAAAAAAGAAGAA
1 AGTGAAAAAAAAAGAAAAAAAAAAGAAGAA
17838848 AAGAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (31 bp):
AGTGAAAAAAAAAGAAAAAAAAAAGAAGAAT
Found at i:17838848 original size:24 final size:24
Alignment explanation
Indices: 17838802--17838849 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
17838792 AGAAAAAGAG
* *
17838802 AAAAAGAAAAAAGAATAGTGAAAA
1 AAAAAGAAAAAAGAAAAGAGAAAA
17838826 AAAAAGAAAAAA-AAAAGAAGAAAA
1 AAAAAGAAAAAAGAAAAG-AGAAAA
17838850 GAAATAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (24 bp):
AAAAAGAAAAAAGAAAAGAGAAAA
Found at i:17839764 original size:33 final size:33
Alignment explanation
Indices: 17839727--17839993 Score: 245
Period size: 33 Copynumber: 8.2 Consensus size: 33
17839717 GCATGCAACA
* *
17839727 TAAGCCCAAACTAGCTAGCACATAATGAAAATT
1 TAAGCCCAAATTAGCTAGCACCTAATGAAAATT
* **
17839760 TAAGCCTAGTTTAGCTAGCACAC-AATGAAAATT
1 TAAGCCCAAATTAGCTAGCAC-CTAATGAAAATT
* *
17839793 TAAGCTCAGATTAGCTAGCACCTAATGAAAATT
1 TAAGCCCAAATTAGCTAGCACCTAATGAAAATT
* * * * *
17839826 TATG-CCTAATTAGCTGGCA-CTCATGAAAATC
1 TAAGCCCAAATTAGCTAGCACCTAATGAAAATT
** * * * *
17839857 TAAGCTTAATTTAGCTGGTACCCAATGAAAATT
1 TAAGCCCAAATTAGCTAGCACCTAATGAAAATT
*
17839890 TAAGCCCAAATTAGTTAGCACCTAATGAAAATT
1 TAAGCCCAAATTAGCTAGCACCTAATGAAAATT
* * ** *
17839923 TAAGCCTAATTTAAATGGCACCTAATGAAAATT
1 TAAGCCCAAATTAGCTAGCACCTAATGAAAATT
** * *
17839956 TAATTCTAGATTAGCTAGCACC-AATGAAAATT
1 TAAGCCCAAATTAGCTAGCACCTAATGAAAATT
17839988 TAAGCC
1 TAAGCC
17839994 AATTTTAGTT
Statistics
Matches: 185, Mismatches: 45, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
31 13 0.07
32 36 0.19
33 136 0.74
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (33 bp):
TAAGCCCAAATTAGCTAGCACCTAATGAAAATT
Found at i:17839833 original size:66 final size:65
Alignment explanation
Indices: 17839738--17839998 Score: 289
Period size: 66 Copynumber: 4.0 Consensus size: 65
17839728 AAGCCCAAAC
* *
17839738 TAGCTAGCACATAATGAAAATTTAAGCCTAGTTTAGCTAGCACACAATGAAAATTTAAGCTCAGA
1 TAGCTAGCACCTAATGAAAATTTAAGCCTAGATTAGCTAGCAC-CAATGAAAATTTAAGCTCA-A
17839803 -T
64 TT
* * * *
17839804 TAGCTAGCACCTAATGAAAATTTATGCCTA-ATTAGCTGGCACTC-ATGAAAATCTAAGCTTAAT
1 TAGCTAGCACCTAATGAAAATTTAAGCCTAGATTAGCTAGCAC-CAATGAAAATTTAAGCTCAAT
17839867 T
65 T
* * * * * *
17839868 TAGCTGGTACCCAATGAAAATTTAAGCCCAAATTAGTTAGCACCTAATGAAAATTTAAGC-CTAA
1 TAGCTAGCACCTAATGAAAATTTAAGCCTAGATTAGCTAGCACC-AATGAAAATTTAAGCTC-AA
17839932 TT
64 TT
** * **
17839934 TAAATGGCACCTAATGAAAATTTAATTCTAGATTAGCTAGCACCAATGAAAATTTAAGC-CAATT
1 TAGCTAGCACCTAATGAAAATTTAAGCCTAGATTAGCTAGCACCAATGAAAATTTAAGCTCAATT
17839998 T
1 T
17839999 TAGTTGGTAA
Statistics
Matches: 165, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
63 1 0.01
64 47 0.28
65 37 0.22
66 80 0.48
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (65 bp):
TAGCTAGCACCTAATGAAAATTTAAGCCTAGATTAGCTAGCACCAATGAAAATTTAAGCTCAATT
Found at i:17839861 original size:97 final size:98
Alignment explanation
Indices: 17839744--17839993 Score: 324
Period size: 97 Copynumber: 2.6 Consensus size: 98
17839734 AAACTAGCTA
* * *
17839744 GCACATAATGAAAATTTAAGCCTAGTTTAGCTAGCACACAATGAAAATTTAAGCTCAGATTAGCT
1 GCACCTAATGAAAATTTAAGCCTAGTTTAGCTAGCAC-CAATGAAAATTTAAGCCCAAATTAGCT
* **
17839809 AGCACCTAATGAAAATTTATGCCTAA-TTAGCTG
65 AGCACCTAATGAAAATTTAAGCCTAATTTAAATG
* * * * * * *
17839842 GCA-CTCATGAAAATCTAAGCTTAATTTAGCTGGTACCCAATGAAAATTTAAGCCCAAATTAGTT
1 GCACCTAATGAAAATTTAAGCCTAGTTTAGCTAGCA-CCAATGAAAATTTAAGCCCAAATTAGCT
17839906 AGCACCTAATGAAAATTTAAGCCTAATTTAAATG
65 AGCACCTAATGAAAATTTAAGCCTAATTTAAATG
** *
17839940 GCACCTAATGAAAATTTAATTCTAGATTAGCTAGCACCAATGAAAATTTAAGCC
1 GCACCTAATGAAAATTTAAGCCTAGTTTAGCTAGCACCAATGAAAATTTAAGCC
17839994 AATTTTAGTT
Statistics
Matches: 127, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
97 74 0.58
98 30 0.24
99 23 0.18
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.29
Consensus pattern (98 bp):
GCACCTAATGAAAATTTAAGCCTAGTTTAGCTAGCACCAATGAAAATTTAAGCCCAAATTAGCTA
GCACCTAATGAAAATTTAAGCCTAATTTAAATG
Found at i:17839998 original size:130 final size:131
Alignment explanation
Indices: 17839750--17840007 Score: 305
Period size: 130 Copynumber: 2.0 Consensus size: 131
17839740 GCTAGCACAT
* ** **
17839750 AATGAAAATTTAAGCCTAGTTTAGCTAGCACACAATGAAAATTTAAGCTCAGATTAGCTAGCACC
1 AATGAAAATTTAAGCCCAAATTAGCTAGCACACAATGAAAATTTAAGCTCAGATTAAATAGCACC
* *
17839815 TAATGAAAATTTATGCCTAATTAGCTGGCACTCATGAAAATCTAAGCTTAA-TTTAGCTGGTACC
66 TAATGAAAATTTATGCCTAATTAGCTAGCACTCATGAAAATCTAAGCTCAATTTTAGCTGGTACC
17839879 C
131 C
* *
17839880 AATGAAAATTTAAGCCCAAATTAGTTAGCAC-CTAATGAAAATTTAAGC-CTA-ATTTAAATGGC
1 AATGAAAATTTAAGCCCAAATTAGCTAGCACAC-AATGAAAATTTAAGCTC-AGA-TTAAATAGC
* * *
17839942 ACCTAATGAAAATTTAAT-TCTAGATTAGCTAGCAC-CAATGAAAATTTAAGC-CAATTTTAGTT
63 ACCTAATGAAAATTT-ATGCCTA-ATTAGCTAGCACTC-ATGAAAATCTAAGCTCAATTTTAGCT
17840004 GGTA
125 GGTA
17840008 ATTAATGAAA
Statistics
Matches: 109, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
129 3 0.03
130 70 0.64
131 36 0.33
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.30
Consensus pattern (131 bp):
AATGAAAATTTAAGCCCAAATTAGCTAGCACACAATGAAAATTTAAGCTCAGATTAAATAGCACC
TAATGAAAATTTATGCCTAATTAGCTAGCACTCATGAAAATCTAAGCTCAATTTTAGCTGGTACC
C
Found at i:17840023 original size:33 final size:33
Alignment explanation
Indices: 17839978--17840071 Score: 111
Period size: 33 Copynumber: 2.9 Consensus size: 33
17839968 AGCTAGCACC
17839978 AATGAAAATTTAAGC-CAATTTTAGTTGGTAATT
1 AATGAAAATTTAAGCTCAATTTTAGTTGG-AATT
* * * *
17840011 AATGAAATTTTAAACTC-ACTTTAGTTGGCATT
1 AATGAAAATTTAAGCTCAATTTTAGTTGGAATT
* *
17840043 AATAAAAATTTAAGCTCAATCTTAGTTGG
1 AATGAAAATTTAAGCTCAATTTTAGTTGG
17840072 CACCTTTAAG
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
32 17 0.34
33 32 0.64
34 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (33 bp):
AATGAAAATTTAAGCTCAATTTTAGTTGGAATT
Found at i:17840053 original size:163 final size:163
Alignment explanation
Indices: 17839727--17840076 Score: 377
Period size: 163 Copynumber: 2.1 Consensus size: 163
17839717 GCATGCAACA
* * * * **
17839727 TAAGCCCAAACTAGCTAGCACATAATGAAAATTTAAGCCTAGTTTAGCTAGCACACAATGAAAAT
1 TAAGCCCAAATTAGTTAGCACCTAATGAAAATTTAAGCCTAATTTAAATAGCACACAATGAAAAT
* * *
17839792 TTAAGCTCAGATTAGCTAGCACCTAATGAAAATTTATGCCTAATTAGCTGGCACTCATGAAAATC
66 TTAAGCTCAGATTAGCTAGCACCTAATGAAAATTTAAGCCTAATTAGCTGGAACTAATGAAAATC
* * * *
17839857 TAAGCTTAATTTAGCTGGTACCCAATGAAAATT
131 TAAACTCAATTTAGCTGGCACCCAATAAAAATT
*
17839890 TAAGCCCAAATTAGTTAGCACCTAATGAAAATTTAAGCCTAATTTAAATGGCAC-CTAATGAAAA
1 TAAGCCCAAATTAGTTAGCACCTAATGAAAATTTAAGCCTAATTTAAATAGCACAC-AATGAAAA
* * *
17839954 TTTAA-TTCTAGATTAGCTAGCACC-AATGAAAATTTAAGCC-AATTTTAGTTGGTAATTAATGA
65 TTTAAGCTC-AGATTAGCTAGCACCTAATGAAAATTTAAGCCTAA--TTAGCTGG-AACTAATGA
* * * * **
17840016 AATTTTAAACTCACTTTAGTTGGCA-TTAATAAAAATT
126 AAATCTAAACTCAATTTAGCTGGCACCCAATAAAAATT
* * *
17840053 TAAGCTCAATCTTAGTTGGCACCT
1 TAAGCCCAA-ATTAGTTAGCACCT
17840077 TTAAGTCTTA
Statistics
Matches: 155, Mismatches: 26, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
161 2 0.01
162 18 0.12
163 99 0.64
164 36 0.23
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.31
Consensus pattern (163 bp):
TAAGCCCAAATTAGTTAGCACCTAATGAAAATTTAAGCCTAATTTAAATAGCACACAATGAAAAT
TTAAGCTCAGATTAGCTAGCACCTAATGAAAATTTAAGCCTAATTAGCTGGAACTAATGAAAATC
TAAACTCAATTTAGCTGGCACCCAATAAAAATT
Found at i:17840073 original size:131 final size:130
Alignment explanation
Indices: 17839750--17840076 Score: 299
Period size: 130 Copynumber: 2.5 Consensus size: 130
17839740 GCTAGCACAT
* * ** * * * *
17839750 AATGAAAATTTAAGCCTAGTTTAGCTAGCACAC-AATGAAAATTTAAGCTCAGA-TTAGCTAGCA
1 AATGAAAATTTAAACCCAAATTAGTTAGCAC-CTAATAAAAATTTAAGCTCA-ATTTAGATGGCA
* * *
17839813 CCTAATGAAAATTTATGCCTAATTAGCTGGCACTCATGAAAATCTAAGCTTAATTTAGCTGGTAC
64 CCTAATGAAAATTTATGCCTAATTAGCTAGCACTCATGAAAATCTAAGCTCAATTTAGCTGGTAA
17839878 CC
129 CC
* * *
17839880 AATGAAAATTTAAGCCCAAATTAGTTAGCACCTAATGAAAATTTAAGC-CTAATTTAAATGGCAC
1 AATGAAAATTTAAACCCAAATTAGTTAGCACCTAATAAAAATTTAAGCTC-AATTTAGATGGCAC
* * *
17839944 CTAATGAAAATTTAAT-TCTAGATTAGCTAGCAC-CAATGAAAATTTAAGC-CAATTTTAGTTGG
65 CTAATGAAAATTT-ATGCCTA-ATTAGCTAGCACTC-ATGAAAATCTAAGCTCAA-TTTAGCTGG
**
17840006 TAATT
126 TAACC
* * ** * * *
17840011 AATGAAATTTTAAACTCACTTTAGTTGGCA-TTAATAAAAATTTAAGCTCAATCTTAGTTGGCAC
1 AATGAAAATTTAAACCCAAATTAGTTAGCACCTAATAAAAATTTAAGCTCAAT-TTAGATGGCAC
17840075 CT
65 CT
17840077 TTAAGTCTTA
Statistics
Matches: 163, Mismatches: 25, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
129 3 0.02
130 88 0.54
131 72 0.44
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (130 bp):
AATGAAAATTTAAACCCAAATTAGTTAGCACCTAATAAAAATTTAAGCTCAATTTAGATGGCACC
TAATGAAAATTTATGCCTAATTAGCTAGCACTCATGAAAATCTAAGCTCAATTTAGCTGGTAACC
Found at i:17842725 original size:3 final size:3
Alignment explanation
Indices: 17842717--17842768 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
17842707 TTAGAAAGCT
17842717 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17842765 TAA T
1 TAA T
17842769 GTTAAAAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17842901 original size:33 final size:34
Alignment explanation
Indices: 17842858--17842923 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
17842848 ATGTTGAGAA
*
17842858 ATTATAAAATAATAA-AAATAATAATAATAAAAG
1 ATTATAAAATAATAATAAAAAATAATAATAAAAG
* **
17842891 ATTATTAAATAATAATAAAAAATTTTAATAAAA
1 ATTATAAAATAATAATAAAAAATAATAATAAAA
17842924 AGAAAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 14 0.50
34 14 0.50
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (34 bp):
ATTATAAAATAATAATAAAAAATAATAATAAAAG
Found at i:17842903 original size:21 final size:20
Alignment explanation
Indices: 17842877--17842918 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
17842867 TAATAAAAAT
*
17842877 AATAATAATAAAAGATTATTA
1 AATAATAATAAAAAATT-TTA
17842898 AATAATAATAAAAAATTTTA
1 AATAATAATAAAAAATTTTA
17842918 A
1 A
17842919 TAAAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AATAATAATAAAAAATTTTA
Found at i:17843061 original size:13 final size:13
Alignment explanation
Indices: 17843043--17843105 Score: 74
Period size: 13 Copynumber: 4.9 Consensus size: 13
17843033 TTTAAAATCC
17843043 TGAAACCCTAAAG
1 TGAAACCCTAAAG
* *
17843056 TGAAACCTTAATG
1 TGAAACCCTAAAG
* *
17843069 TGAAGCCCTAAAA
1 TGAAACCCTAAAG
*
17843082 TGAAACCCT-AGG
1 TGAAACCCTAAAG
17843094 TGAAACCCTAAA
1 TGAAACCCTAAA
17843106 CATTAGGTGA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
12 10 0.26
13 29 0.74
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (13 bp):
TGAAACCCTAAAG
Found at i:17843299 original size:20 final size:20
Alignment explanation
Indices: 17843271--17843308 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17843261 TTAATTCTTT
17843271 AATCTAATAATAATAAAATTA
1 AATCTAATAATAA-AAAATTA
17843292 AATC-AATAATAAAAAAT
1 AATCTAATAATAAAAAAT
17843309 AAAAATGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
AATCTAATAATAAAAAATTA
Found at i:17843314 original size:20 final size:21
Alignment explanation
Indices: 17843271--17843312 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
17843261 TTAATTCTTT
*
17843271 AATCTAATAATAATAAAATTA
1 AATCTAATAATAATAAAATAA
17843292 AATC-AATAATAA-AAAATAA
1 AATCTAATAATAATAAAATAA
17843311 AA
1 AA
17843313 ATGGGATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 8 0.40
21 4 0.20
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (21 bp):
AATCTAATAATAATAAAATAA
Found at i:17847003 original size:36 final size:37
Alignment explanation
Indices: 17846931--17847032 Score: 109
Period size: 36 Copynumber: 2.8 Consensus size: 37
17846921 GATATTAAAG
* * * * *
17846931 GTTACTACCTT-AGCCTAGAAAGGTAGGGAATTAGAA
1 GTTACTATCTTAATCCTATAAAGATAGGGAATGAGAA
* *
17846967 GTTCCTATCTTAAT-CTATATAGATAGGGAATGAGAA
1 GTTACTATCTTAATCCTATAAAGATAGGGAATGAGAA
* *
17847003 GTTACTATCTTAGTCCTTTAAAGATAGGGA
1 GTTACTATCTTAATCCTATAAAGATAGGGA
17847033 TTGTTTTTTG
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
36 39 0.74
37 14 0.26
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (37 bp):
GTTACTATCTTAATCCTATAAAGATAGGGAATGAGAA
Found at i:17852001 original size:36 final size:35
Alignment explanation
Indices: 17851961--17852054 Score: 116
Period size: 36 Copynumber: 2.6 Consensus size: 35
17851951 AGATTACTAA
* *
17851961 CTTAGCCTAGAAAGATAGGGAATTAGATGTTGCTAT
1 CTTAGCCTA-AAAGATAGGGAATGAGAGGTTGCTAT
*
17851997 CTTAGCCTATAAAGATAGGGAATGAGAGGTTGTTAT
1 CTTAGCCTA-AAAGATAGGGAATGAGAGGTTGCTAT
*
17852033 CTTAGTCCTTAAAATATAGGGA
1 CTTAG-CC-TAAAAGATAGGGA
17852055 TTGTATTTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
36 37 0.73
37 12 0.24
38 2 0.04
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (35 bp):
CTTAGCCTAAAAGATAGGGAATGAGAGGTTGCTAT
Found at i:17852234 original size:104 final size:104
Alignment explanation
Indices: 17852054--17852260 Score: 310
Period size: 104 Copynumber: 2.0 Consensus size: 104
17852044 AAATATAGGG
*
17852054 ATTGTATTTTGATTCAACTAATGGATTGATCTTAACTTGAAGAGAGAAAGAAAGGACATAGGTGC
1 ATTGTATTTTGATTCAACTAATGGATTAATCTTAACTTGAAGAGAGAAAGAAAGGACATAGGTGC
* *
17852119 ATTTAGAGAATGACCGAACCTTTATAAATTATTGTGTTA
66 AATTAGAGAATGACCGAACCTCTATAAATTATTGTGTTA
* **
17852158 ATTGTATTTTGATTCAACTAATGGATTAATCTTAGCTTGAAGAGCA-AGGGAAAAGGACATA-GT
1 ATTGTATTTTGATTCAACTAATGGATTAATCTTAACTTGAAGAG-AGAAAG-AAAGGACATAGGT
* *
17852221 GCAATTGGAGAATGATCGAACCTCTATAAATTATTGTGTT
64 GCAATTAGAGAATGACCGAACCTCTATAAATTATTGTGTT
17852261 TGATCTTTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
104 82 0.88
105 11 0.12
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (104 bp):
ATTGTATTTTGATTCAACTAATGGATTAATCTTAACTTGAAGAGAGAAAGAAAGGACATAGGTGC
AATTAGAGAATGACCGAACCTCTATAAATTATTGTGTTA
Found at i:17855712 original size:2 final size:2
Alignment explanation
Indices: 17855705--17855731 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17855695 ATTTAGCCAA
17855705 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 A
17855732 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17857782 original size:13 final size:13
Alignment explanation
Indices: 17857764--17857788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17857754 TTTTTCTAGT
17857764 TAATATAAATTTA
1 TAATATAAATTTA
17857777 TAATATAAATTT
1 TAATATAAATTT
17857789 TTTTTTAGAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATATAAATTTA
Found at i:17860021 original size:3 final size:3
Alignment explanation
Indices: 17860015--17860040 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17860005 TATTATTATT
17860015 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
17860041 TATCTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:17860069 original size:16 final size:16
Alignment explanation
Indices: 17860045--17860078 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17860035 CATCATTATC
* *
17860045 TTTCTTTTCCTTTCTT
1 TTTCATTTCATTTCTT
17860061 TTTCATTTCATTTCTT
1 TTTCATTTCATTTCTT
17860077 TT
1 TT
17860079 CCCATTCCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCATTTCATTTCTT
Found at i:17860365 original size:14 final size:14
Alignment explanation
Indices: 17860348--17860374 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17860338 CCTATAAAAG
17860348 AAAAAAAAAACCCA
1 AAAAAAAAAACCCA
17860362 AAAAAAAAAACCC
1 AAAAAAAAAACCC
17860375 CTCCAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACCCA
Found at i:17861442 original size:16 final size:15
Alignment explanation
Indices: 17861404--17861436 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17861394 TTTAACATTA
*
17861404 AAATA-AAATAAGAT
1 AAATATAAATAAAAT
17861418 AAATATAAATAAAAT
1 AAATATAAATAAAAT
17861433 AAAT
1 AAAT
17861437 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
AAATATAAATAAAAT
Found at i:17863490 original size:11 final size:11
Alignment explanation
Indices: 17863474--17863508 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
17863464 GCCAATAACT
17863474 AAACTAAAGAA
1 AAACTAAAGAA
17863485 AAACTAAAGAA
1 AAACTAAAGAA
*
17863496 GAACTAAA-AA
1 AAACTAAAGAA
17863506 AAA
1 AAA
17863509 AAAAAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.74, C:0.09, G:0.09, T:0.09
Consensus pattern (11 bp):
AAACTAAAGAA
Found at i:17863519 original size:22 final size:22
Alignment explanation
Indices: 17863475--17863519 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
17863465 CCAATAACTA
* ** *
17863475 AACTAAAGAAAAACTAAAGAAG
1 AACTAAAAAAAAAAAAAAAAAG
17863497 AACTAAAAAAAAAAAAAAAAAG
1 AACTAAAAAAAAAAAAAAAAAG
17863519 A
1 A
17863520 GAAGAAAAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.78, C:0.07, G:0.09, T:0.07
Consensus pattern (22 bp):
AACTAAAAAAAAAAAAAAAAAG
Found at i:17870391 original size:23 final size:23
Alignment explanation
Indices: 17870374--17870417 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
17870364 CAAATATTAA
*
17870374 AAAAAAAGAAAGAA-AAATAAAT
1 AAAAAAAGAAAAAATAAATAAAT
17870396 AAAAAAAGAAAAAATAAATAAA
1 AAAAAAAGAAAAAATAAATAAA
17870418 GAAAGCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (23 bp):
AAAAAAAGAAAAAATAAATAAAT
Found at i:17870408 original size:19 final size:18
Alignment explanation
Indices: 17870377--17870422 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
17870367 ATATTAAAAA
17870377 AAAAGAAAGAAAAATAAAT
1 AAAA-AAAGAAAAATAAAT
17870396 AAAAAAAGAAAAAATAAAT
1 AAAAAAAG-AAAAATAAAT
*
17870415 AAAGAAAG
1 AAAAAAAG
17870423 CAAATGCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (18 bp):
AAAAAAAGAAAAATAAAT
Found at i:17870412 original size:15 final size:15
Alignment explanation
Indices: 17870392--17870421 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17870382 AAAGAAAAAT
17870392 AAATAAAAAAAGAAA
1 AAATAAAAAAAGAAA
*
17870407 AAATAAATAAAGAAA
1 AAATAAAAAAAGAAA
17870422 GCAAATGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (15 bp):
AAATAAAAAAAGAAA
Found at i:17871367 original size:21 final size:23
Alignment explanation
Indices: 17871326--17871378 Score: 74
Period size: 21 Copynumber: 2.4 Consensus size: 23
17871316 TATTCATTAA
*
17871326 ATAAAAAAATGAAAATTGTAAAC
1 ATAAAAAAATGAAAATAGTAAAC
17871349 ATAAAAAAAT-AAAA-AGTAAAC
1 ATAAAAAAATGAAAATAGTAAAC
*
17871370 ATGAAAAAA
1 ATAAAAAAA
17871379 GAATCAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 14 0.50
22 4 0.14
23 10 0.36
ACGTcount: A:0.72, C:0.04, G:0.08, T:0.17
Consensus pattern (23 bp):
ATAAAAAAATGAAAATAGTAAAC
Found at i:17871828 original size:8 final size:8
Alignment explanation
Indices: 17871815--17871866 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
17871805 TTTAAAAATT
17871815 AATAATAA
1 AATAATAA
17871823 AATAATAA
1 AATAATAA
17871831 AA-ATATAA
1 AATA-ATAA
17871839 AATAATAA
1 AATAATAA
*
17871847 AA-AGCTTAA
1 AATA--ATAA
17871856 AATAATAA
1 AATAATAA
17871864 AAT
1 AAT
17871867 GATCCTACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 2 0.05
8 28 0.76
9 6 0.16
10 1 0.03
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (8 bp):
AATAATAA
Found at i:17871840 original size:16 final size:17
Alignment explanation
Indices: 17871819--17871865 Score: 71
Period size: 16 Copynumber: 2.8 Consensus size: 17
17871809 AAAATTAATA
17871819 ATAAAATAATAAAAA-T
1 ATAAAATAATAAAAACT
17871835 ATAAAATAATAAAAAGCT
1 ATAAAATAATAAAAA-CT
17871853 -TAAAATAATAAAA
1 ATAAAATAATAAAA
17871866 TGATCCTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 15 0.52
17 13 0.45
18 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (17 bp):
ATAAAATAATAAAAACT
Found at i:17871849 original size:17 final size:18
Alignment explanation
Indices: 17871819--17871865 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
17871809 AAAATTAATA
17871819 ATAAAATAAT-AAAA-AT
1 ATAAAATAATAAAAAGAT
*
17871835 ATAAAATAATAAAAAGCT
1 ATAAAATAATAAAAAGAT
17871853 -TAAAATAATAAAA
1 ATAAAATAATAAAA
17871866 TGATCCTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 10 0.36
17 17 0.61
18 1 0.04
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (18 bp):
ATAAAATAATAAAAAGAT
Found at i:17877244 original size:39 final size:39
Alignment explanation
Indices: 17877190--17877268 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
17877180 GTAGGCAAGG
*
17877190 AAGGAATTCTATGACACCAAGTGTATCTTTATCATCATT
1 AAGGAATTCTATGACACCAAGTGTATCTTCATCATCATT
* *
17877229 AAGGAATTCTATGACACTAAGTGTATCTTCATCATTATT
1 AAGGAATTCTATGACACCAAGTGTATCTTCATCATCATT
17877268 A
1 A
17877269 TCTTCCAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (39 bp):
AAGGAATTCTATGACACCAAGTGTATCTTCATCATCATT
Found at i:17880782 original size:2 final size:2
Alignment explanation
Indices: 17880775--17880800 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17880765 GAAAGGATAG
17880775 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
17880801 TTTCTTTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:17885326 original size:163 final size:161
Alignment explanation
Indices: 17885015--17885339 Score: 560
Period size: 163 Copynumber: 2.0 Consensus size: 161
17885005 CAATACTCCA
* * *
17885015 CAACAAAATGCATTGGTAGAAAGGAAAAACAGCCATTTACTAGCCACAACCCAAGCCTTACTTTT
1 CAACAAAATGCATTGGCAGAAAGGAAAAACAACCATTTACTAGACACAACCCAAGCCTTACTTTT
* *
17885080 TCAAGCAAATGTACCCAAATCTTACTGGGGAAGCTGTTTTCACTGTCACACATATTATAAATAGG
66 TCAAGCAAATGTACCCAAATCTTACTGGGGAAGCTGTTCTCACTGCCACACATATTATAAATAGG
17885145 TTACCTTCAAGGGTTTTGGGATTTAAAACTC
131 TTACCTTCAAGGGTTTTGGGATTTAAAACTC
* * *
17885176 CAACAAAATGTATTGGCAGAAAGGAAAAACAACCATTTTACTAGACACAATCCGAGCCTTACTTT
1 CAACAAAATGCATTGGCAGAAAGGAAAAACAACCA-TTTACTAGACACAACCCAAGCCTTACTTT
17885241 TTCAAGCAAATGTACCCAAATCTTACTGGGGGAAGCTGTTCTCACTGCCACACATATTATAAATA
65 TTCAAGCAAATGTACCCAAATCTTACT-GGGGAAGCTGTTCTCACTGCCACACATATTATAAATA
17885306 GGTTACCTTCAAGGGTTTTGGGATTTAAAACTC
129 GGTTACCTTCAAGGGTTTTGGGATTTAAAACTC
17885339 C
1 C
17885340 TATGGAACTA
Statistics
Matches: 154, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
161 32 0.21
162 53 0.34
163 69 0.45
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (161 bp):
CAACAAAATGCATTGGCAGAAAGGAAAAACAACCATTTACTAGACACAACCCAAGCCTTACTTTT
TCAAGCAAATGTACCCAAATCTTACTGGGGAAGCTGTTCTCACTGCCACACATATTATAAATAGG
TTACCTTCAAGGGTTTTGGGATTTAAAACTC
Found at i:17889382 original size:30 final size:30
Alignment explanation
Indices: 17889346--17889422 Score: 120
Period size: 30 Copynumber: 2.6 Consensus size: 30
17889336 ACACGATTTG
* *
17889346 GATGACTCAATAAATGGTACAAACTCAATA
1 GATGACTCAACAAATGGTACAAACTCAACA
17889376 GATGACTCAACAAATGGTACAAACTCAACA
1 GATGACTCAACAAATGGTACAAACTCAACA
17889406 GATGAGC-CAACAAATGG
1 GATGA-CTCAACAAATGG
17889423 AGTAGTAGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 43 0.98
31 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.18
Consensus pattern (30 bp):
GATGACTCAACAAATGGTACAAACTCAACA
Found at i:17894753 original size:15 final size:15
Alignment explanation
Indices: 17894733--17894764 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
17894723 GAAAAAGGTG
17894733 TTTTTTTACATTCGA
1 TTTTTTTACATTCGA
17894748 TTTTTTTACATTCGA
1 TTTTTTTACATTCGA
17894763 TT
1 TT
17894765 ATAAAATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.12, G:0.06, T:0.62
Consensus pattern (15 bp):
TTTTTTTACATTCGA
Found at i:17902120 original size:15 final size:16
Alignment explanation
Indices: 17902100--17902133 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17902090 ATTAAAAAAA
17902100 AAGTTTAG-ATTTTAT
1 AAGTTTAGAATTTTAT
*
17902115 AAGTTTAGAATTTTTT
1 AAGTTTAGAATTTTAT
17902131 AAG
1 AAG
17902134 AATTTTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (16 bp):
AAGTTTAGAATTTTAT
Found at i:17902139 original size:10 final size:10
Alignment explanation
Indices: 17902121--17902218 Score: 69
Period size: 10 Copynumber: 9.9 Consensus size: 10
17902111 TTATAAGTTT
17902121 AGAATTTTTTA
1 AGAA-TTTTTA
17902132 AGAATTTTTA
1 AGAATTTTTA
*
17902142 AGAATATTTA
1 AGAATTTTTA
*
17902152 GAAAATTTTTTA
1 -AGAA-TTTTTA
*
17902164 A-AATTTTCA
1 AGAATTTTTA
*
17902173 AAAATTTTTA
1 AGAATTTTTA
*
17902183 A-AATTTTCA
1 AGAATTTTTA
* *
17902192 AAAAATTTTA
1 AGAATTTTTA
*
17902202 A-AATTTTTT
1 AGAATTTTTA
17902211 AG-ATTTTT
1 AGAATTTTT
17902219 TTTTTGAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
9 27 0.38
10 32 0.44
11 8 0.11
12 5 0.07
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (10 bp):
AGAATTTTTA
Found at i:17902219 original size:19 final size:19
Alignment explanation
Indices: 17902134--17902208 Score: 98
Period size: 19 Copynumber: 3.8 Consensus size: 19
17902124 ATTTTTTAAG
17902134 AATTTTTAAGAATATTT-AGAA
1 AATTTTTAA-AAT-TTTCA-AA
17902155 AATTTTTTAAAATTTTCAAA
1 AA-TTTTTAAAATTTTCAAA
17902175 AATTTTTAAAATTTTCAAA
1 AATTTTTAAAATTTTCAAA
*
17902194 AAATTTTAAAATTTT
1 AATTTTTAAAATTTT
17902209 TTAGATTTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
19 31 0.61
20 7 0.14
21 6 0.12
22 7 0.14
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (19 bp):
AATTTTTAAAATTTTCAAA
Found at i:17906595 original size:20 final size:19
Alignment explanation
Indices: 17906549--17906598 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
17906539 GAAAATGAAA
*
17906549 AAGAAAAAAAGAAAAAGAG
1 AAGAAAAAAAGAAAAAAAG
* *
17906568 AGATAAAAAAAGAAAAAAACT
1 A-AGAAAAAAAGAAAAAAA-G
17906589 AAGAAAAAAA
1 AAGAAAAAAA
17906599 TATTTTAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 23 0.92
21 1 0.04
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (19 bp):
AAGAAAAAAAGAAAAAAAG
Found at i:17908348 original size:21 final size:22
Alignment explanation
Indices: 17908305--17908372 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 22
17908295 ATAAAAGACA
*
17908305 TTTAATATTAATATTTAAAATT
1 TTTAATATTAATAATTAAAATT
17908327 TTTAA-ATTAA-AATTAAATATT
1 TTTAATATTAATAATTAAA-ATT
* *
17908348 TTT--TATTAATACAATAATATT
1 TTTAATATTAATA-ATTAAAATT
17908369 TTTA
1 TTTA
17908373 TTAATATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
20 11 0.29
21 18 0.47
22 9 0.24
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAATATTAATAATTAAAATT
Found at i:17908370 original size:20 final size:20
Alignment explanation
Indices: 17908342--17908390 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
17908332 ATTAAAATTA
17908342 AATATTTTTTATTAATACAAT
1 AATA-TTTTTATTAATACAAT
*
17908363 AATATTTTTATTAATATAAT
1 AATATTTTTATTAATACAAT
17908383 AATATTTT
1 AATATTTT
17908391 GGGTTAGATC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
AATATTTTTATTAATACAAT
Found at i:17918175 original size:43 final size:43
Alignment explanation
Indices: 17918117--17918247 Score: 113
Period size: 44 Copynumber: 3.0 Consensus size: 43
17918107 ATTTACAACC
* *
17918117 CTAAAGGCTCATTTAAACAGAGGCTCATGACTTTTGATAAATGAA
1 CTAAA-GCTCCTTTAAACAGAGGCTCATGACTTTTGAAAAAT-AA
* * * *
17918162 -TAAAGCTCCTTTAAATAAAGACTCAATGACTTTTTAAAAATAA
1 CTAAAGCTCCTTTAAACAGAGGCTC-ATGACTTTTGAAAAATAA
* * * * *
17918205 CTAAGGCTCCTCTAAGCAGAGGTTCAGTGAC-TTTAAAAAATAA
1 CTAAAGCTCCTTTAAACAGAGGCTCA-TGACTTTTGAAAAATAA
17918248 ACACTTAATT
Statistics
Matches: 69, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
43 30 0.43
44 39 0.57
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (43 bp):
CTAAAGCTCCTTTAAACAGAGGCTCATGACTTTTGAAAAATAA
Found at i:17918749 original size:7 final size:7
Alignment explanation
Indices: 17918722--17918811 Score: 108
Period size: 7 Copynumber: 12.4 Consensus size: 7
17918712 TGATATTAAA
17918722 GTTTAGG
1 GTTTAGG
17918729 GTTTTAGG
1 G-TTTAGG
17918737 GTTTTAGG
1 G-TTTAGG
17918745 GTTTAGG
1 GTTTAGG
17918752 GTTTAGG
1 GTTTAGG
17918759 GTTTAGG
1 GTTTAGG
*
17918766 ATTTTAGG
1 -GTTTAGG
17918774 GTTTAGG
1 GTTTAGG
*
17918781 GCTTAGG
1 GTTTAGG
*
17918788 GCTTAGG
1 GTTTAGG
*
17918795 GCTTAGG
1 GTTTAGG
*
17918802 GCTTAGG
1 GTTTAGG
17918809 GTT
1 GTT
17918812 AGAAGTGGAA
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
7 56 0.73
8 21 0.27
ACGTcount: A:0.14, C:0.04, G:0.40, T:0.41
Consensus pattern (7 bp):
GTTTAGG
Found at i:17918771 original size:29 final size:28
Alignment explanation
Indices: 17918722--17918811 Score: 108
Period size: 29 Copynumber: 3.1 Consensus size: 28
17918712 TGATATTAAA
17918722 GTTTAGGGTTTTAGGGTTTTAGGGTTTAGG
1 GTTTAGGG-TTTA-GGTTTTAGGGTTTAGG
17918752 GTTTAGGGTTTAGGATTTTAGGGTTTAGG
1 GTTTAGGGTTTAGG-TTTTAGGGTTTAGG
* * ** *
17918781 GCTTAGGGCTTAGGGCTTAGGGCTTAGG
1 GTTTAGGGTTTAGGTTTTAGGGTTTAGG
17918809 GTT
1 GTT
17918812 AGAAGTGGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
28 15 0.28
29 30 0.57
30 8 0.15
ACGTcount: A:0.14, C:0.04, G:0.40, T:0.41
Consensus pattern (28 bp):
GTTTAGGGTTTAGGTTTTAGGGTTTAGG
Found at i:17922164 original size:41 final size:41
Alignment explanation
Indices: 17922090--17922169 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
17922080 TTTTCTTTTT
** * * **
17922090 TCTCGATGTGAATGTGTTTTTTTATGTGTGCTTGAGACTGA
1 TCTCGATACGAATGTATCTTTTTATGTACGCTTGAGACTGA
*
17922131 TCTCGATACGAATGTATCTTTTTATGTACGCTTGGGACT
1 TCTCGATACGAATGTATCTTTTTATGTACGCTTGAGACT
17922170 AACTGTAGCT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.44
Consensus pattern (41 bp):
TCTCGATACGAATGTATCTTTTTATGTACGCTTGAGACTGA
Found at i:17922708 original size:3 final size:3
Alignment explanation
Indices: 17922702--17922735 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
17922692 TGCTTAATTG
17922702 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
17922736 TTTATTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17923632 original size:19 final size:19
Alignment explanation
Indices: 17923595--17923634 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17923585 TTTTAAGTCC
*
17923595 AACTCAAACTCTCCTATCT
1 AACTCAAACTCTCCAATCT
* *
17923614 AACTCAAACTTTTCAATCT
1 AACTCAAACTCTCCAATCT
17923633 AA
1 AA
17923635 ACAGATAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.30, G:0.00, T:0.33
Consensus pattern (19 bp):
AACTCAAACTCTCCAATCT
Found at i:17924038 original size:26 final size:28
Alignment explanation
Indices: 17923972--17924038 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
17923962 AAGGTTTCTC
*
17923972 TAAACAAAGGCTCACAACTTTTGAAAAA
1 TAAATAAAGGCTCACAACTTTTGAAAAA
* *
17924000 TAAATAAAAGCTCAACGAC-TTT-AAAAA
1 TAAATAAAGGCTC-ACAACTTTTGAAAAA
17924027 TAAAT-AAGGCTC
1 TAAATAAAGGCTC
17924039 TTAAGGATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 6 0.18
27 10 0.29
28 14 0.41
29 4 0.12
ACGTcount: A:0.51, C:0.16, G:0.10, T:0.22
Consensus pattern (28 bp):
TAAATAAAGGCTCACAACTTTTGAAAAA
Found at i:17930502 original size:48 final size:48
Alignment explanation
Indices: 17930418--17930518 Score: 139
Period size: 48 Copynumber: 2.1 Consensus size: 48
17930408 ATCAAGGCAC
* *
17930418 CATTATGCCTCACATCATTACATCTATGCCTGCACCATAACAAGACAA
1 CATTATGCCTCACATCATTACACCTATGCCTCCACCATAACAAGACAA
* * * * *
17930466 CATTGTGCCTTACATCATTACACCTGTGGCTCCACCATAACAAGGCAA
1 CATTATGCCTCACATCATTACACCTATGCCTCCACCATAACAAGACAA
17930514 CATTA
1 CATTA
17930519 GTAAGGTACA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.33, C:0.31, G:0.11, T:0.26
Consensus pattern (48 bp):
CATTATGCCTCACATCATTACACCTATGCCTCCACCATAACAAGACAA
Found at i:17930722 original size:12 final size:12
Alignment explanation
Indices: 17930705--17930730 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17930695 ATTCCTAATG
17930705 GCTATTTTGCAA
1 GCTATTTTGCAA
17930717 GCTATTTTGCAA
1 GCTATTTTGCAA
17930729 GC
1 GC
17930731 AATGAGCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (12 bp):
GCTATTTTGCAA
Found at i:17931803 original size:45 final size:45
Alignment explanation
Indices: 17931749--17931836 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
17931739 CTAGCATCGA
* * * * *
17931749 CATATGTTGGCCCTTGGTATGGGTACTTACCTTGACCACCATTAG
1 CATAAGTTGGCCCTTGGTACGAGCACTTACCTCGACCACCATTAG
*
17931794 CATAAGTTGGCCTTTGGTACGAGCACTTACCTCGACCACCATT
1 CATAAGTTGGCCCTTGGTACGAGCACTTACCTCGACCACCATT
17931837 GGCGTAAGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (45 bp):
CATAAGTTGGCCCTTGGTACGAGCACTTACCTCGACCACCATTAG
Found at i:17938496 original size:20 final size:20
Alignment explanation
Indices: 17938471--17938521 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
17938461 TTTTGTCAAC
17938471 CCTGAGAATTATAAGGGGAT
1 CCTGAGAATTATAAGGGGAT
17938491 CCTGAGAATTATAAGGGGAT
1 CCTGAGAATTATAAGGGGAT
*
17938511 CCTTAGAATTA
1 CCTGAGAATTA
17938522 GGATGTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.27
Consensus pattern (20 bp):
CCTGAGAATTATAAGGGGAT
Found at i:17938926 original size:45 final size:44
Alignment explanation
Indices: 17938868--17938973 Score: 113
Period size: 45 Copynumber: 2.4 Consensus size: 44
17938858 CACATGTTGG
* * *
17938868 GCCTTGGTGTAGGCACAAGCCTCTATCACCATCGACACAAACTA
1 GCCTTGGTATAGGCACAAGCCTCAACCACCATCGACACAAACTA
** * * *
17938912 GCCCTTGGTATAGGCACTTGTCTCAACCACCATCGACATAAGCTA
1 G-CCTTGGTATAGGCACAAGCCTCAACCACCATCGACACAAACTA
*
17938957 GCCTATGGTATGGGCAC
1 GCCT-TGGTATAGGCAC
17938974 TTACCTTAAC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
44 4 0.08
45 47 0.92
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (44 bp):
GCCTTGGTATAGGCACAAGCCTCAACCACCATCGACACAAACTA
Found at i:17938974 original size:45 final size:45
Alignment explanation
Indices: 17938894--17938989 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 45
17938884 AAGCCTCTAT
**
17938894 CACCATCGACACAAACTAGCCCTTGGTATAGGCACTTGTCTCAAC
1 CACCATCGACACAAACTAGCCCTTGGTATAGGCACTTACCTCAAC
* * * *
17938939 CACCATCGACATAAGCTAG-CCTATGGTATGGGCACTTACCTTAAC
1 CACCATCGACACAAACTAGCCCT-TGGTATAGGCACTTACCTCAAC
17938984 CACCAT
1 CACCAT
17938990 TGGCATATGC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
44 3 0.07
45 41 0.93
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.23
Consensus pattern (45 bp):
CACCATCGACACAAACTAGCCCTTGGTATAGGCACTTACCTCAAC
Done.